Multiple sequence alignment - TraesCS3A01G329800

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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 TraesCS3A01G329800 chr3A 100.000 2551 0 0 1 2551 574863267 574865817 0.000000e+00 4711
1 TraesCS3A01G329800 chr3A 82.329 249 38 6 2182 2428 439278499 439278743 7.150000e-51 211
2 TraesCS3A01G329800 chr3A 83.190 232 33 5 2193 2423 501028793 501028567 9.250000e-50 207
3 TraesCS3A01G329800 chr3D 92.567 2018 105 12 569 2549 436042062 436044071 0.000000e+00 2854
4 TraesCS3A01G329800 chr3D 92.994 628 41 2 1926 2551 436162662 436163288 0.000000e+00 913
5 TraesCS3A01G329800 chr3D 92.845 573 36 3 1 570 436039605 436040175 0.000000e+00 826
6 TraesCS3A01G329800 chr3B 92.767 1507 89 10 1050 2549 571809749 571811242 0.000000e+00 2161
7 TraesCS3A01G329800 chr3B 89.248 1144 76 15 1 1125 571808677 571809792 0.000000e+00 1387
8 TraesCS3A01G329800 chr6D 83.648 318 45 6 1807 2121 461867050 461867363 2.480000e-75 292
9 TraesCS3A01G329800 chr6D 80.757 317 58 3 1806 2121 429711566 429711880 7.050000e-61 244
10 TraesCS3A01G329800 chr5D 87.854 247 27 3 2192 2437 542699524 542699280 1.150000e-73 287
11 TraesCS3A01G329800 chr7D 80.363 331 56 8 1805 2130 575010861 575011187 2.540000e-60 243
12 TraesCS3A01G329800 chr7D 81.600 250 40 5 2183 2430 628130391 628130636 4.300000e-48 202
13 TraesCS3A01G329800 chr2D 80.495 323 55 7 1824 2142 625355779 625356097 9.120000e-60 241
14 TraesCS3A01G329800 chr2D 83.913 230 26 7 2208 2436 509751350 509751569 2.570000e-50 209
15 TraesCS3A01G329800 chr5B 79.472 341 64 5 1806 2142 547273947 547274285 1.180000e-58 237
16 TraesCS3A01G329800 chr2A 80.189 318 60 3 1806 2121 724512397 724512081 4.240000e-58 235
17 TraesCS3A01G329800 chr6A 80.455 220 35 6 2212 2430 6585422 6585210 7.300000e-36 161


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 TraesCS3A01G329800 chr3A 574863267 574865817 2550 False 4711 4711 100.0000 1 2551 1 chr3A.!!$F2 2550
1 TraesCS3A01G329800 chr3D 436039605 436044071 4466 False 1840 2854 92.7060 1 2549 2 chr3D.!!$F2 2548
2 TraesCS3A01G329800 chr3D 436162662 436163288 626 False 913 913 92.9940 1926 2551 1 chr3D.!!$F1 625
3 TraesCS3A01G329800 chr3B 571808677 571811242 2565 False 1774 2161 91.0075 1 2549 2 chr3B.!!$F1 2548

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
852 2755 0.322546 ATCCAAAGCACCCGTCCTTC 60.323 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 3743 0.243636 ACGCCCACAAAATAAGCTGC 59.756 50.0 0.0 0.0 0.0 5.25 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
128 129 2.822399 GCCGTATCCAGGGGTCAG 59.178 66.667 0.00 0.00 0.00 3.51
149 150 7.970614 GGTCAGAGATTCACAAATCATTAAACC 59.029 37.037 1.41 0.00 43.21 3.27
218 219 7.440523 AGTTTGTCACTTTGTTCAGATATCC 57.559 36.000 0.00 0.00 27.32 2.59
225 226 5.702670 CACTTTGTTCAGATATCCAGTGTGT 59.297 40.000 0.00 0.00 0.00 3.72
233 234 3.133003 AGATATCCAGTGTGTAGTGTGCC 59.867 47.826 0.00 0.00 0.00 5.01
244 245 2.224646 TGTAGTGTGCCAAGCCAATGTA 60.225 45.455 0.00 0.00 0.00 2.29
254 255 4.627467 GCCAAGCCAATGTACGATATCTAG 59.373 45.833 0.34 0.00 0.00 2.43
260 261 5.164233 CCAATGTACGATATCTAGGCACAG 58.836 45.833 0.34 0.00 0.00 3.66
263 264 3.634910 TGTACGATATCTAGGCACAGCAA 59.365 43.478 0.34 0.00 0.00 3.91
294 298 4.908156 GCGAGAATAAGCACAGCATATTTG 59.092 41.667 1.68 0.00 33.52 2.32
297 301 6.795593 CGAGAATAAGCACAGCATATTTGATG 59.204 38.462 0.00 0.00 44.83 3.07
318 322 8.589335 TGATGTAGTACAAGTGAAGTTTTCTC 57.411 34.615 7.16 0.00 0.00 2.87
327 331 3.309954 AGTGAAGTTTTCTCGTTCTGTGC 59.690 43.478 0.00 0.00 0.00 4.57
340 344 3.057315 CGTTCTGTGCTGGGAAAATTGAT 60.057 43.478 0.00 0.00 0.00 2.57
366 370 6.486993 AGGAAAGCTACACCTGAAAACTTTAG 59.513 38.462 5.63 0.00 32.39 1.85
367 371 5.690997 AAGCTACACCTGAAAACTTTAGC 57.309 39.130 0.00 0.00 0.00 3.09
382 386 5.972107 ACTTTAGCGAAGGTGTTACTAGA 57.028 39.130 0.00 0.00 40.22 2.43
481 490 5.003692 TGCACAGAAAACACAATAGCAAA 57.996 34.783 0.00 0.00 0.00 3.68
538 547 2.372264 AGATGCTTACTTGCACATGGG 58.628 47.619 0.00 0.00 46.33 4.00
539 548 2.025981 AGATGCTTACTTGCACATGGGA 60.026 45.455 0.00 0.00 46.33 4.37
540 549 1.533625 TGCTTACTTGCACATGGGAC 58.466 50.000 0.00 0.00 38.12 4.46
570 579 8.557592 TTCATCTACGAAGAAACAGAGTACTA 57.442 34.615 0.00 0.00 34.73 1.82
571 580 8.557592 TCATCTACGAAGAAACAGAGTACTAA 57.442 34.615 0.00 0.00 34.73 2.24
572 581 9.006839 TCATCTACGAAGAAACAGAGTACTAAA 57.993 33.333 0.00 0.00 34.73 1.85
573 582 9.279904 CATCTACGAAGAAACAGAGTACTAAAG 57.720 37.037 0.00 0.00 34.73 1.85
574 583 8.388484 TCTACGAAGAAACAGAGTACTAAAGT 57.612 34.615 0.00 0.00 0.00 2.66
576 585 9.460906 CTACGAAGAAACAGAGTACTAAAGTTT 57.539 33.333 15.56 15.56 35.33 2.66
577 586 8.350238 ACGAAGAAACAGAGTACTAAAGTTTC 57.650 34.615 25.08 25.08 44.99 2.78
595 2492 2.478547 TCGACAAATGTATAGCGCGA 57.521 45.000 12.10 0.00 0.00 5.87
604 2501 1.135603 TGTATAGCGCGAACGTTCACT 60.136 47.619 26.71 21.12 42.83 3.41
645 2542 1.076850 TACCCTGCACCGTCCGATA 60.077 57.895 0.00 0.00 0.00 2.92
699 2600 2.813908 GTCAGGGCTAACGTGCGG 60.814 66.667 0.00 0.00 35.01 5.69
784 2687 2.106566 TGAGCTTGGCAAAAACAAGGA 58.893 42.857 0.00 0.00 44.16 3.36
812 2715 1.767759 ACATGAGCTGGGCCATTAAC 58.232 50.000 6.72 0.00 0.00 2.01
815 2718 1.838112 TGAGCTGGGCCATTAACAAG 58.162 50.000 6.72 0.00 0.00 3.16
816 2719 1.075374 TGAGCTGGGCCATTAACAAGT 59.925 47.619 6.72 0.00 0.00 3.16
819 2722 2.041081 AGCTGGGCCATTAACAAGTACA 59.959 45.455 6.72 0.00 0.00 2.90
826 2729 5.453480 GGGCCATTAACAAGTACAAAACCAA 60.453 40.000 4.39 0.00 0.00 3.67
828 2731 5.694458 GCCATTAACAAGTACAAAACCAAGG 59.306 40.000 0.00 0.00 0.00 3.61
852 2755 0.322546 ATCCAAAGCACCCGTCCTTC 60.323 55.000 0.00 0.00 0.00 3.46
869 2772 1.812571 CTTCACCAAACCAAGATCCCG 59.187 52.381 0.00 0.00 0.00 5.14
882 2785 7.311092 ACCAAGATCCCGACATATATAAACA 57.689 36.000 0.00 0.00 0.00 2.83
940 2851 2.933287 CCAGCCACCCACCCACTA 60.933 66.667 0.00 0.00 0.00 2.74
975 2886 3.326889 TACCGCACTCCGCACGTAC 62.327 63.158 0.00 0.00 42.60 3.67
979 2890 3.467119 CACTCCGCACGTACACGC 61.467 66.667 0.85 0.00 44.43 5.34
994 2905 3.405170 ACACGCAAGAACTGAAACTTG 57.595 42.857 0.00 0.00 44.05 3.16
1042 2953 0.603707 CTTGGTTCTGCTCGCCTTCA 60.604 55.000 0.00 0.00 0.00 3.02
1399 3355 6.583562 GGAAGTAAGTGTTAGACCATATGCT 58.416 40.000 0.00 0.00 0.00 3.79
1472 3428 6.790232 ATTTTCTGAAAGTTGGACAAAGGA 57.210 33.333 2.75 0.00 33.76 3.36
1482 3438 4.837860 AGTTGGACAAAGGAAATGCCAATA 59.162 37.500 0.00 0.00 40.02 1.90
1540 3496 2.267961 CTACCCCGTTCCTGGTGC 59.732 66.667 0.00 0.00 36.04 5.01
1584 3540 7.201947 TATCTTCTGATTGGATGATCACGAAGT 60.202 37.037 0.00 0.00 39.32 3.01
1586 3542 4.403752 TCTGATTGGATGATCACGAAGTCT 59.596 41.667 0.00 0.00 41.61 3.24
1604 3560 4.841422 AGTCTGCAGATGCTATTTTCAGT 58.159 39.130 21.47 0.00 42.66 3.41
1615 3571 9.023962 AGATGCTATTTTCAGTTTTCACCATTA 57.976 29.630 0.00 0.00 0.00 1.90
1618 3574 9.421806 TGCTATTTTCAGTTTTCACCATTATTG 57.578 29.630 0.00 0.00 0.00 1.90
1623 3579 9.743057 TTTTCAGTTTTCACCATTATTGTACTG 57.257 29.630 0.00 0.00 0.00 2.74
1671 3627 7.365497 TGAGAGATAAGTTGCTGGATTATCA 57.635 36.000 6.87 0.00 38.04 2.15
1786 3743 5.209977 GTGTACTTGCGTTTCTTTAAAGGG 58.790 41.667 15.13 4.17 32.37 3.95
1790 3747 1.000717 TGCGTTTCTTTAAAGGGCAGC 60.001 47.619 15.13 15.01 32.96 5.25
1792 3749 2.288213 GCGTTTCTTTAAAGGGCAGCTT 60.288 45.455 15.13 0.00 32.37 3.74
1865 3822 6.106673 ACTCATGAGAAGTACAAAATACCGG 58.893 40.000 29.27 0.00 0.00 5.28
1869 3826 7.827236 TCATGAGAAGTACAAAATACCGGAAAT 59.173 33.333 9.46 0.00 0.00 2.17
1903 3860 1.613317 ATCGAAGTCCATGGACCGCA 61.613 55.000 36.09 22.91 45.59 5.69
1945 3905 4.492160 GAGTCACCGATGCGCCGA 62.492 66.667 4.18 0.00 0.00 5.54
2004 3964 1.552337 GATGACAGCTGGGAAGTCTGA 59.448 52.381 19.93 0.00 33.56 3.27
2051 4011 2.049063 GAAGCCACAGTCGTCGCT 60.049 61.111 0.00 0.00 41.82 4.93
2079 4039 7.865820 TGAATCCTTGAATAGACCTGAAGAAT 58.134 34.615 0.00 0.00 0.00 2.40
2084 4044 7.346698 TCCTTGAATAGACCTGAAGAATCTGAT 59.653 37.037 0.00 0.00 0.00 2.90
2098 4058 6.808008 AGAATCTGATACCAAATATTGCCG 57.192 37.500 0.00 0.00 0.00 5.69
2131 4093 4.915667 CACGACAAGAAACGAATCTCACTA 59.084 41.667 0.00 0.00 0.00 2.74
2145 4107 0.406750 TCACTACCCCGAGGAGTCAA 59.593 55.000 0.00 0.00 36.73 3.18
2204 4166 2.561419 GGACTCTAGTAAGTGCCACACA 59.439 50.000 0.00 0.00 36.74 3.72
2229 4191 2.753055 TACGAGCACATGCCAACTTA 57.247 45.000 0.00 0.00 43.38 2.24
2341 4303 1.651987 AACTTGTCGTGTGTCACTGG 58.348 50.000 4.27 0.00 31.34 4.00
2388 4350 5.009010 GGAATTGCCATCGAATAATGTCAGT 59.991 40.000 0.00 0.00 36.34 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 9.859427 TTCATGGTTTAATGATTTGTGAATCTC 57.141 29.630 0.00 0.00 41.80 2.75
218 219 0.588252 GCTTGGCACACTACACACTG 59.412 55.000 0.00 0.00 39.29 3.66
225 226 2.432444 GTACATTGGCTTGGCACACTA 58.568 47.619 0.00 0.00 39.29 2.74
233 234 4.627467 GCCTAGATATCGTACATTGGCTTG 59.373 45.833 6.99 0.00 35.44 4.01
244 245 4.342862 AATTGCTGTGCCTAGATATCGT 57.657 40.909 0.00 0.00 0.00 3.73
294 298 7.381678 ACGAGAAAACTTCACTTGTACTACATC 59.618 37.037 0.00 0.00 0.00 3.06
297 301 7.434602 AGAACGAGAAAACTTCACTTGTACTAC 59.565 37.037 0.00 0.00 0.00 2.73
304 308 4.201822 GCACAGAACGAGAAAACTTCACTT 60.202 41.667 0.00 0.00 0.00 3.16
318 322 2.293122 TCAATTTTCCCAGCACAGAACG 59.707 45.455 0.00 0.00 0.00 3.95
327 331 6.603201 TGTAGCTTTCCTATCAATTTTCCCAG 59.397 38.462 0.00 0.00 0.00 4.45
340 344 5.562298 AGTTTTCAGGTGTAGCTTTCCTA 57.438 39.130 0.00 0.00 0.00 2.94
366 370 1.266466 GCGTCTAGTAACACCTTCGC 58.734 55.000 0.00 0.00 36.06 4.70
367 371 1.468736 GGGCGTCTAGTAACACCTTCG 60.469 57.143 0.00 0.00 0.00 3.79
382 386 0.675522 CCTGAACATTTACGGGGCGT 60.676 55.000 0.00 0.00 44.35 5.68
481 490 7.448777 TCTGTACTTCTCTGAACTGACACTAAT 59.551 37.037 0.00 0.00 0.00 1.73
565 574 9.897349 GCTATACATTTGTCGAAACTTTAGTAC 57.103 33.333 0.00 0.00 0.00 2.73
570 579 5.321516 GCGCTATACATTTGTCGAAACTTT 58.678 37.500 0.00 0.00 0.00 2.66
571 580 4.491924 CGCGCTATACATTTGTCGAAACTT 60.492 41.667 5.56 0.00 0.00 2.66
572 581 3.000078 CGCGCTATACATTTGTCGAAACT 60.000 43.478 5.56 0.00 0.00 2.66
573 582 3.000476 TCGCGCTATACATTTGTCGAAAC 60.000 43.478 5.56 0.00 0.00 2.78
574 583 3.180613 TCGCGCTATACATTTGTCGAAA 58.819 40.909 5.56 0.00 0.00 3.46
576 585 2.478547 TCGCGCTATACATTTGTCGA 57.521 45.000 5.56 0.00 0.00 4.20
577 586 2.652960 CGTTCGCGCTATACATTTGTCG 60.653 50.000 5.56 0.00 0.00 4.35
578 587 2.280708 ACGTTCGCGCTATACATTTGTC 59.719 45.455 5.56 0.00 46.04 3.18
595 2492 3.549997 GCATGTTGCAGTGAACGTT 57.450 47.368 0.00 0.00 44.26 3.99
624 2521 3.391382 GGACGGTGCAGGGTAGCT 61.391 66.667 0.00 0.00 34.99 3.32
645 2542 1.030488 GCATGCTGCATCACCACTCT 61.030 55.000 13.10 0.00 44.26 3.24
784 2687 2.165167 CCCAGCTCATGTTCACACATT 58.835 47.619 0.00 0.00 41.16 2.71
812 2715 6.041069 TGGATTTACCCTTGGTTTTGTACTTG 59.959 38.462 0.00 0.00 37.09 3.16
815 2718 6.408107 TTGGATTTACCCTTGGTTTTGTAC 57.592 37.500 0.00 0.00 37.09 2.90
816 2719 6.463190 GCTTTGGATTTACCCTTGGTTTTGTA 60.463 38.462 0.00 0.00 37.09 2.41
819 2722 4.410555 TGCTTTGGATTTACCCTTGGTTTT 59.589 37.500 0.00 0.00 37.09 2.43
826 2729 1.615919 CGGGTGCTTTGGATTTACCCT 60.616 52.381 8.90 0.00 46.97 4.34
828 2731 1.471287 GACGGGTGCTTTGGATTTACC 59.529 52.381 0.00 0.00 39.54 2.85
852 2755 1.165270 GTCGGGATCTTGGTTTGGTG 58.835 55.000 0.00 0.00 0.00 4.17
869 2772 6.237901 TGGGATGGCTGTGTTTATATATGTC 58.762 40.000 0.00 0.00 0.00 3.06
882 2785 1.549203 GTTTGACATGGGATGGCTGT 58.451 50.000 0.00 0.00 39.69 4.40
975 2886 2.097466 ACCAAGTTTCAGTTCTTGCGTG 59.903 45.455 0.00 0.00 39.47 5.34
979 2890 2.426738 TGGCACCAAGTTTCAGTTCTTG 59.573 45.455 0.00 0.00 40.19 3.02
1142 3098 3.414700 GGTCGCTGTTGCAGTCGG 61.415 66.667 10.94 0.00 39.64 4.79
1294 3250 1.107114 ATGCAGACGACCTTCTCGAT 58.893 50.000 0.00 0.00 46.14 3.59
1540 3496 1.624487 TATGCTGCACTACACGAACG 58.376 50.000 3.57 0.00 0.00 3.95
1542 3498 3.801114 AGATATGCTGCACTACACGAA 57.199 42.857 3.57 0.00 0.00 3.85
1584 3540 6.207221 TGAAAACTGAAAATAGCATCTGCAGA 59.793 34.615 20.79 20.79 45.16 4.26
1586 3542 6.151691 GTGAAAACTGAAAATAGCATCTGCA 58.848 36.000 4.79 0.00 45.16 4.41
1615 3571 3.492102 AGTCACAAGCACCAGTACAAT 57.508 42.857 0.00 0.00 0.00 2.71
1617 3573 2.560504 CAAGTCACAAGCACCAGTACA 58.439 47.619 0.00 0.00 0.00 2.90
1618 3574 1.264288 GCAAGTCACAAGCACCAGTAC 59.736 52.381 0.00 0.00 0.00 2.73
1622 3578 2.268762 TATGCAAGTCACAAGCACCA 57.731 45.000 0.00 0.00 41.60 4.17
1623 3579 3.855689 AATATGCAAGTCACAAGCACC 57.144 42.857 0.00 0.00 41.60 5.01
1786 3743 0.243636 ACGCCCACAAAATAAGCTGC 59.756 50.000 0.00 0.00 0.00 5.25
1790 3747 5.726729 AAAACAAACGCCCACAAAATAAG 57.273 34.783 0.00 0.00 0.00 1.73
1842 3799 6.338146 TCCGGTATTTTGTACTTCTCATGAG 58.662 40.000 17.07 17.07 0.00 2.90
1875 3832 6.458342 GGTCCATGGACTTCGATGTAATTTTC 60.458 42.308 37.26 15.94 44.04 2.29
1889 3846 1.296715 GTTCTGCGGTCCATGGACT 59.703 57.895 37.26 0.00 44.04 3.85
1903 3860 3.118454 CGGCGCAATGGTCGTTCT 61.118 61.111 10.83 0.00 0.00 3.01
1931 3891 4.141965 ACATCGGCGCATCGGTGA 62.142 61.111 23.14 5.38 43.26 4.02
1945 3905 1.740285 GGTATGGGAGCGACGACAT 59.260 57.895 0.00 0.00 0.00 3.06
2004 3964 2.238898 GGTCTTTAGGGGTACATGCACT 59.761 50.000 0.00 0.00 0.00 4.40
2051 4011 6.874278 TCAGGTCTATTCAAGGATTCAAGA 57.126 37.500 0.00 0.00 0.00 3.02
2079 4039 4.036262 GCAACGGCAATATTTGGTATCAGA 59.964 41.667 0.00 0.00 40.72 3.27
2084 4044 2.085320 ACGCAACGGCAATATTTGGTA 58.915 42.857 0.00 0.00 41.24 3.25
2114 4074 3.368116 CGGGGTAGTGAGATTCGTTTCTT 60.368 47.826 0.00 0.00 0.00 2.52
2131 4093 2.640826 TGTATTTTTGACTCCTCGGGGT 59.359 45.455 0.00 0.00 0.00 4.95
2180 4142 3.006537 TGTGGCACTTACTAGAGTCCAAC 59.993 47.826 19.83 0.00 32.50 3.77
2204 4166 3.751479 TGGCATGTGCTCGTATCTTAT 57.249 42.857 4.84 0.00 41.70 1.73
2257 4219 2.722094 ACTAAAATTGCCATCCTCGCA 58.278 42.857 0.00 0.00 0.00 5.10
2292 4254 7.476667 TCGAAAAATAAACTGAAGCACAAAGA 58.523 30.769 0.00 0.00 0.00 2.52
2341 4303 4.614284 CAGTCACGCAAAGATGACAAATTC 59.386 41.667 7.10 0.00 46.34 2.17


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

AutoCloner maintained by Alex Coulton.