Multiple sequence alignment - TraesCS7D01G337400

Loading Multiple Alignment...

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 TraesCS7D01G337400 chr7D 100.000 3482 0 0 1 3482 430229418 430232899 0.000000e+00 6431
1 TraesCS7D01G337400 chr7B 97.705 2701 51 7 784 3482 447974603 447977294 0.000000e+00 4634
2 TraesCS7D01G337400 chr7B 88.317 796 55 25 1 787 447972932 447973698 0.000000e+00 920
3 TraesCS7D01G337400 chr7A 97.536 1583 39 0 1075 2657 502254998 502253416 0.000000e+00 2708
4 TraesCS7D01G337400 chr7A 95.401 848 28 4 2640 3482 502253401 502252560 0.000000e+00 1339
5 TraesCS7D01G337400 chr7A 89.216 612 48 12 473 1074 502255781 502255178 0.000000e+00 749
6 TraesCS7D01G337400 chr7A 88.050 477 52 3 1 475 502256377 502255904 8.440000e-156 560
7 TraesCS7D01G337400 chr2D 95.714 280 9 1 3203 3482 104969966 104969690 6.860000e-122 448
8 TraesCS7D01G337400 chr2D 95.000 280 11 1 3203 3482 89148469 89148745 1.480000e-118 436
9 TraesCS7D01G337400 chr4B 94.271 192 11 0 3291 3482 41368820 41369011 9.450000e-76 294
10 TraesCS7D01G337400 chr4B 91.489 94 6 2 3203 3296 41339201 41339292 1.010000e-25 128
11 TraesCS7D01G337400 chr5D 92.647 68 5 0 1214 1281 473516305 473516372 7.950000e-17 99


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 TraesCS7D01G337400 chr7D 430229418 430232899 3481 False 6431 6431 100.00000 1 3482 1 chr7D.!!$F1 3481
1 TraesCS7D01G337400 chr7B 447972932 447977294 4362 False 2777 4634 93.01100 1 3482 2 chr7B.!!$F1 3481
2 TraesCS7D01G337400 chr7A 502252560 502256377 3817 True 1339 2708 92.55075 1 3482 4 chr7A.!!$R1 3481

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
237 239 0.618458 TTCCCCGCAAAGAGCACTAT 59.382 50.0 0.00 0.0 46.13 2.12 F
495 623 1.189752 TGCCAACTTTGCCTTGTTGA 58.810 45.0 12.37 0.0 44.29 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 3064 0.620556 GGTCTCCCATCTTCAGCCAA 59.379 55.000 0.00 0.00 0.00 4.52 R
2585 3824 1.225704 CCTGGCAAGCCCTCTAAGG 59.774 63.158 8.89 4.31 34.56 2.69 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
119 121 9.965902 AAGATTTCAGTGAGTTAGTCCATAAAT 57.034 29.630 0.00 0.00 0.00 1.40
126 128 8.251026 CAGTGAGTTAGTCCATAAATGTAGTGA 58.749 37.037 0.00 0.00 0.00 3.41
127 129 8.812972 AGTGAGTTAGTCCATAAATGTAGTGAA 58.187 33.333 0.00 0.00 0.00 3.18
176 178 1.145738 AGAGTTGAAGCCCACCAACAT 59.854 47.619 0.00 0.00 43.60 2.71
210 212 6.599244 GTCACTTTGATGTTCAATCTCCCATA 59.401 38.462 0.00 0.00 36.11 2.74
237 239 0.618458 TTCCCCGCAAAGAGCACTAT 59.382 50.000 0.00 0.00 46.13 2.12
264 266 6.385443 TGTAGAAAGATGATCTGGATACCCT 58.615 40.000 0.00 0.00 0.00 4.34
273 275 4.101585 TGATCTGGATACCCTCAACATGTC 59.898 45.833 0.00 0.00 0.00 3.06
277 279 3.452264 TGGATACCCTCAACATGTCTCAG 59.548 47.826 0.00 0.00 0.00 3.35
370 373 6.885735 AATAATTATCAAAGGTGCGCAAAC 57.114 33.333 14.00 8.77 0.00 2.93
421 424 1.654954 CCTCAGATGCTGCTGCCAAC 61.655 60.000 13.47 4.57 38.71 3.77
424 427 3.058160 GATGCTGCTGCCAACCGT 61.058 61.111 13.47 0.00 38.71 4.83
495 623 1.189752 TGCCAACTTTGCCTTGTTGA 58.810 45.000 12.37 0.00 44.29 3.18
499 627 3.248363 GCCAACTTTGCCTTGTTGATTTC 59.752 43.478 12.37 0.00 44.29 2.17
501 629 3.369546 ACTTTGCCTTGTTGATTTCCG 57.630 42.857 0.00 0.00 0.00 4.30
513 641 6.836577 TGTTGATTTCCGGAATTTTCAAAC 57.163 33.333 26.40 21.76 0.00 2.93
514 642 6.341316 TGTTGATTTCCGGAATTTTCAAACA 58.659 32.000 26.40 23.14 0.00 2.83
515 643 6.256757 TGTTGATTTCCGGAATTTTCAAACAC 59.743 34.615 26.40 19.70 0.00 3.32
518 646 6.478344 TGATTTCCGGAATTTTCAAACACAAG 59.522 34.615 19.62 0.00 0.00 3.16
558 687 6.209589 CAGGAATAGAGTCCGAATGAATCCTA 59.790 42.308 0.00 0.00 43.03 2.94
559 688 6.435904 AGGAATAGAGTCCGAATGAATCCTAG 59.564 42.308 0.00 0.00 43.03 3.02
560 689 6.350612 GGAATAGAGTCCGAATGAATCCTAGG 60.351 46.154 0.82 0.82 38.87 3.02
562 691 4.148838 AGAGTCCGAATGAATCCTAGGAG 58.851 47.826 18.34 1.06 38.87 3.69
563 692 4.141135 AGAGTCCGAATGAATCCTAGGAGA 60.141 45.833 18.34 3.22 38.87 3.71
566 695 5.425539 AGTCCGAATGAATCCTAGGAGAAAA 59.574 40.000 18.34 3.17 0.00 2.29
567 696 6.100424 AGTCCGAATGAATCCTAGGAGAAAAT 59.900 38.462 18.34 5.48 0.00 1.82
568 697 6.425417 GTCCGAATGAATCCTAGGAGAAAATC 59.575 42.308 18.34 11.37 0.00 2.17
592 731 9.751542 ATCCTAAAGATTTCAATCTACGTACTG 57.248 33.333 2.41 0.00 44.67 2.74
695 838 6.033196 GCACATTCTTGATCGACAAAATTCAG 59.967 38.462 0.00 0.00 38.08 3.02
722 865 7.576861 AATAACGGGTTCAATTATACCAAGG 57.423 36.000 9.61 0.00 36.10 3.61
728 873 6.071278 CGGGTTCAATTATACCAAGGGAAAAA 60.071 38.462 9.61 0.00 36.10 1.94
794 1847 4.650754 ATATAAGACGTCTCGGCACTTT 57.349 40.909 20.33 2.64 37.34 2.66
806 1859 6.183360 CGTCTCGGCACTTTAATTTAATCTGT 60.183 38.462 0.00 0.00 0.00 3.41
854 1911 1.515081 TTCGGTCGGTTTGATGGTTC 58.485 50.000 0.00 0.00 0.00 3.62
1761 3000 1.273759 TCACTGATGAGGAGCTTGCT 58.726 50.000 0.00 0.00 0.00 3.91
1776 3015 2.046314 GCTGTGCGGCTAAAGGGA 60.046 61.111 0.00 0.00 0.00 4.20
1818 3057 2.030274 GTCAAACACCAGGTTACATGGC 60.030 50.000 16.44 0.00 41.87 4.40
1825 3064 1.549203 CAGGTTACATGGCAAGGCTT 58.451 50.000 0.00 0.00 0.00 4.35
1836 3075 0.893447 GCAAGGCTTTGGCTGAAGAT 59.107 50.000 10.89 0.00 38.81 2.40
2453 3692 1.321074 GGATCACGGTCTCCTTCGGT 61.321 60.000 0.00 0.00 0.00 4.69
2614 3853 2.094545 GGCTTGCCAGGTCATTAAACTG 60.095 50.000 6.79 0.00 0.00 3.16
2638 3877 2.574929 CATTTGCATGGCAGGCGT 59.425 55.556 19.99 5.13 40.61 5.68
2659 3930 5.523916 GCGTCCTCAGTGTATTGTGATTTAT 59.476 40.000 0.00 0.00 0.00 1.40
2847 4118 5.049267 GGTGTTACCAAAATAACTTCTCGCA 60.049 40.000 0.00 0.00 38.42 5.10
2852 4123 3.853671 CCAAAATAACTTCTCGCACATGC 59.146 43.478 0.00 0.00 37.78 4.06
2916 4187 6.183360 GCTTGGCGTGTATTATAGCGATTATT 60.183 38.462 0.00 0.00 0.00 1.40
2917 4188 7.009815 GCTTGGCGTGTATTATAGCGATTATTA 59.990 37.037 0.00 0.00 0.00 0.98
2918 4189 8.936070 TTGGCGTGTATTATAGCGATTATTAT 57.064 30.769 0.00 0.00 0.00 1.28
3060 4331 3.559655 TGGATTCATGTAGCACATAACGC 59.440 43.478 0.00 0.00 36.53 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.121382 TCAAAGATAAGAGAAAGGGATTGCAT 58.879 34.615 0.00 0.00 0.00 3.96
80 82 7.542890 TCACTGAAATCTTCTAGAAGTAGCAG 58.457 38.462 27.59 26.97 39.38 4.24
176 178 5.417266 TGAACATCAAAGTGACAACCTCAAA 59.583 36.000 0.00 0.00 0.00 2.69
210 212 1.153127 TTTGCGGGGAACTTCACGT 60.153 52.632 6.88 0.00 0.00 4.49
237 239 7.038729 GGGTATCCAGATCATCTTTCTACATGA 60.039 40.741 0.00 0.00 33.55 3.07
264 266 2.618442 TGCACACTGAGACATGTTGA 57.382 45.000 0.00 0.00 0.00 3.18
273 275 7.997107 AAATTATTATGCATTGCACACTGAG 57.003 32.000 14.66 0.00 43.04 3.35
277 279 9.179552 TCGAATAAATTATTATGCATTGCACAC 57.820 29.630 14.66 0.00 43.04 3.82
354 357 2.472816 CAAAGTTTGCGCACCTTTGAT 58.527 42.857 35.78 16.55 44.90 2.57
370 373 5.776744 ACTTGGCATAAAGAGAAAGCAAAG 58.223 37.500 0.00 0.00 41.01 2.77
375 378 5.964958 TCCAACTTGGCATAAAGAGAAAG 57.035 39.130 2.52 0.00 37.47 2.62
414 417 0.888736 TCAACATGGACGGTTGGCAG 60.889 55.000 0.00 0.00 44.38 4.85
424 427 0.885879 AGTAGACGCGTCAACATGGA 59.114 50.000 37.85 13.08 0.00 3.41
439 442 3.739519 GCTTGACAGCCCACTATGAGTAG 60.740 52.174 0.00 0.00 40.61 2.57
462 465 6.038161 GCAAAGTTGGCATGTATGTGATAGTA 59.962 38.462 0.00 0.00 0.00 1.82
495 623 6.578023 TCTTGTGTTTGAAAATTCCGGAAAT 58.422 32.000 23.08 10.67 0.00 2.17
499 627 7.367285 TCTATTCTTGTGTTTGAAAATTCCGG 58.633 34.615 0.00 0.00 0.00 5.14
566 695 9.751542 CAGTACGTAGATTGAAATCTTTAGGAT 57.248 33.333 10.66 0.00 42.96 3.24
567 696 8.963725 TCAGTACGTAGATTGAAATCTTTAGGA 58.036 33.333 10.66 0.00 42.96 2.94
568 697 9.751542 ATCAGTACGTAGATTGAAATCTTTAGG 57.248 33.333 10.66 3.13 42.96 2.69
648 790 3.118992 CCCTAAGCATTTTTGGCCTCTTC 60.119 47.826 3.32 0.00 0.00 2.87
728 873 9.211485 GAATGAAATGAATGATGAAACCAGTTT 57.789 29.630 0.00 0.00 35.14 2.66
806 1859 8.966868 GGAATCCTATGAGGTAAAACAATTTGA 58.033 33.333 2.79 0.00 36.53 2.69
854 1911 0.650512 AGGCAAATATTGACGCGTCG 59.349 50.000 31.88 17.83 45.70 5.12
1155 2391 1.082679 CGTAGCTGTCCTCGTCGAGA 61.083 60.000 23.74 7.04 0.00 4.04
1436 2675 2.272797 CGTCCTCGTCCTCCTCCT 59.727 66.667 0.00 0.00 0.00 3.69
1695 2934 3.412386 GTGGTACATGAGCAGGTTCTTT 58.588 45.455 0.00 0.00 44.52 2.52
1761 3000 1.295423 GAGTCCCTTTAGCCGCACA 59.705 57.895 0.00 0.00 0.00 4.57
1776 3015 1.924731 TGTCGATCTCCTTGGTGAGT 58.075 50.000 0.00 0.00 33.93 3.41
1818 3057 1.203994 CCATCTTCAGCCAAAGCCTTG 59.796 52.381 0.00 0.00 41.25 3.61
1825 3064 0.620556 GGTCTCCCATCTTCAGCCAA 59.379 55.000 0.00 0.00 0.00 4.52
2585 3824 1.225704 CCTGGCAAGCCCTCTAAGG 59.774 63.158 8.89 4.31 34.56 2.69
2638 3877 9.685276 AATCAATAAATCACAATACACTGAGGA 57.315 29.630 0.00 0.00 0.00 3.71
2916 4187 9.877222 TCCTTAACTCTGATATGACCTGTTATA 57.123 33.333 0.00 0.00 0.00 0.98
2917 4188 8.783660 TCCTTAACTCTGATATGACCTGTTAT 57.216 34.615 0.00 0.00 0.00 1.89
2918 4189 8.603898 TTCCTTAACTCTGATATGACCTGTTA 57.396 34.615 0.00 0.00 0.00 2.41
3060 4331 3.213506 TGATGGGAAGAAAGTGTGTGTG 58.786 45.455 0.00 0.00 0.00 3.82
3190 4461 1.890876 AACTTGACCGCAGCATAACA 58.109 45.000 0.00 0.00 0.00 2.41
3272 4543 9.822185 GAGGGCATTCACAAAGAAATTTATAAT 57.178 29.630 0.00 0.00 40.22 1.28
3273 4544 7.973388 CGAGGGCATTCACAAAGAAATTTATAA 59.027 33.333 0.00 0.00 40.22 0.98
3366 4644 2.309528 TCAACACATAGCTTAGGCCG 57.690 50.000 0.00 0.00 39.73 6.13


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

AutoCloner maintained by Alex Coulton.