Multiple sequence alignment - TraesCS1B01G405200

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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 TraesCS1B01G405200 chr1B 100.000 2576 0 0 1 2576 633718755 633721330 0 4758
1 TraesCS1B01G405200 chr3A 97.428 1866 36 5 722 2576 105554486 105552622 0 3169
2 TraesCS1B01G405200 chr5D 97.373 1865 37 5 722 2576 6250802 6248940 0 3162
3 TraesCS1B01G405200 chr5D 97.265 1865 38 7 722 2576 503315976 503317837 0 3149
4 TraesCS1B01G405200 chr5D 96.183 1860 57 7 727 2576 432267807 432265952 0 3029
5 TraesCS1B01G405200 chr5D 97.271 733 15 1 1 728 299970204 299969472 0 1238
6 TraesCS1B01G405200 chr5D 96.999 733 17 1 1 728 6251490 6250758 0 1227
7 TraesCS1B01G405200 chr5D 96.589 733 19 2 1 728 503341228 503341959 0 1210
8 TraesCS1B01G405200 chr1D 97.056 1868 42 7 722 2576 254461875 254463742 0 3133
9 TraesCS1B01G405200 chr1D 96.088 1866 54 9 722 2576 51829492 51827635 0 3024
10 TraesCS1B01G405200 chr1D 96.862 733 18 1 1 728 254461187 254461919 0 1221
11 TraesCS1B01G405200 chr4A 96.117 1854 57 8 734 2576 309408124 309406275 0 3011
12 TraesCS1B01G405200 chr4D 95.815 1864 63 10 722 2576 19903194 19905051 0 2996
13 TraesCS1B01G405200 chr7A 95.550 1865 62 9 722 2576 537838939 537837086 0 2964
14 TraesCS1B01G405200 chr5B 97.408 733 14 1 1 728 57513339 57512607 0 1243
15 TraesCS1B01G405200 chr5A 97.408 733 14 1 1 728 559030164 559029432 0 1243
16 TraesCS1B01G405200 chr1A 97.135 733 16 1 1 728 554483807 554484539 0 1232
17 TraesCS1B01G405200 chr2B 96.862 733 18 1 1 728 683729227 683729959 0 1221
18 TraesCS1B01G405200 chrUn 96.726 733 19 1 1 728 261566907 261566175 0 1216


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 TraesCS1B01G405200 chr1B 633718755 633721330 2575 False 4758.0 4758 100.000 1 2576 1 chr1B.!!$F1 2575
1 TraesCS1B01G405200 chr3A 105552622 105554486 1864 True 3169.0 3169 97.428 722 2576 1 chr3A.!!$R1 1854
2 TraesCS1B01G405200 chr5D 503315976 503317837 1861 False 3149.0 3149 97.265 722 2576 1 chr5D.!!$F1 1854
3 TraesCS1B01G405200 chr5D 432265952 432267807 1855 True 3029.0 3029 96.183 727 2576 1 chr5D.!!$R2 1849
4 TraesCS1B01G405200 chr5D 6248940 6251490 2550 True 2194.5 3162 97.186 1 2576 2 chr5D.!!$R3 2575
5 TraesCS1B01G405200 chr5D 299969472 299970204 732 True 1238.0 1238 97.271 1 728 1 chr5D.!!$R1 727
6 TraesCS1B01G405200 chr5D 503341228 503341959 731 False 1210.0 1210 96.589 1 728 1 chr5D.!!$F2 727
7 TraesCS1B01G405200 chr1D 51827635 51829492 1857 True 3024.0 3024 96.088 722 2576 1 chr1D.!!$R1 1854
8 TraesCS1B01G405200 chr1D 254461187 254463742 2555 False 2177.0 3133 96.959 1 2576 2 chr1D.!!$F1 2575
9 TraesCS1B01G405200 chr4A 309406275 309408124 1849 True 3011.0 3011 96.117 734 2576 1 chr4A.!!$R1 1842
10 TraesCS1B01G405200 chr4D 19903194 19905051 1857 False 2996.0 2996 95.815 722 2576 1 chr4D.!!$F1 1854
11 TraesCS1B01G405200 chr7A 537837086 537838939 1853 True 2964.0 2964 95.550 722 2576 1 chr7A.!!$R1 1854
12 TraesCS1B01G405200 chr5B 57512607 57513339 732 True 1243.0 1243 97.408 1 728 1 chr5B.!!$R1 727
13 TraesCS1B01G405200 chr5A 559029432 559030164 732 True 1243.0 1243 97.408 1 728 1 chr5A.!!$R1 727
14 TraesCS1B01G405200 chr1A 554483807 554484539 732 False 1232.0 1232 97.135 1 728 1 chr1A.!!$F1 727
15 TraesCS1B01G405200 chr2B 683729227 683729959 732 False 1221.0 1221 96.862 1 728 1 chr2B.!!$F1 727
16 TraesCS1B01G405200 chrUn 261566175 261566907 732 True 1216.0 1216 96.726 1 728 1 chrUn.!!$R1 727

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
717 718 0.101219 GCTGAAATGGCGGATTCACC 59.899 55.0 0.0 0.0 32.46 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2431 2449 1.924731 TTCAGAGGGAGAAGAAGCGA 58.075 50.0 0.0 0.0 0.0 4.93 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
154 155 2.154462 GGGATGGGATTGCTCGTATTG 58.846 52.381 0.00 0.00 0.00 1.90
176 177 8.650143 ATTGTAGGTCTTGGTGAAATAATGTT 57.350 30.769 0.00 0.00 0.00 2.71
449 450 4.207165 GCTCCAAGTATAATTTCCAGGCA 58.793 43.478 0.00 0.00 0.00 4.75
461 462 3.417069 TTCCAGGCATTCCATATACGG 57.583 47.619 0.00 0.00 33.74 4.02
574 575 4.497006 GCAAAATAGCAGTAGCCACAGATG 60.497 45.833 0.00 0.00 43.56 2.90
635 636 8.630037 TGTTTATGTAGCTATCGATCAAAGAGA 58.370 33.333 0.00 0.00 0.00 3.10
654 655 2.428890 AGAATCCTCCGTAGCTCAAGTG 59.571 50.000 0.00 0.00 0.00 3.16
688 689 2.046855 AGGAGGGGGCCATGGAAT 59.953 61.111 18.40 0.00 0.00 3.01
689 690 0.772124 GAGGAGGGGGCCATGGAATA 60.772 60.000 18.40 0.00 0.00 1.75
690 691 0.103173 AGGAGGGGGCCATGGAATAT 60.103 55.000 18.40 0.00 0.00 1.28
691 692 0.786435 GGAGGGGGCCATGGAATATT 59.214 55.000 18.40 0.00 0.00 1.28
692 693 1.550869 GGAGGGGGCCATGGAATATTG 60.551 57.143 18.40 0.00 0.00 1.90
693 694 1.147817 GAGGGGGCCATGGAATATTGT 59.852 52.381 18.40 0.00 0.00 2.71
694 695 2.378547 GAGGGGGCCATGGAATATTGTA 59.621 50.000 18.40 0.00 0.00 2.41
695 696 2.379907 AGGGGGCCATGGAATATTGTAG 59.620 50.000 18.40 0.00 0.00 2.74
696 697 2.110011 GGGGGCCATGGAATATTGTAGT 59.890 50.000 18.40 0.00 0.00 2.73
697 698 3.332485 GGGGGCCATGGAATATTGTAGTA 59.668 47.826 18.40 0.00 0.00 1.82
698 699 4.567747 GGGGGCCATGGAATATTGTAGTAG 60.568 50.000 18.40 0.00 0.00 2.57
699 700 4.010349 GGGCCATGGAATATTGTAGTAGC 58.990 47.826 18.40 0.00 0.00 3.58
700 701 4.263506 GGGCCATGGAATATTGTAGTAGCT 60.264 45.833 18.40 0.00 0.00 3.32
701 702 4.697352 GGCCATGGAATATTGTAGTAGCTG 59.303 45.833 18.40 0.00 0.00 4.24
702 703 5.513094 GGCCATGGAATATTGTAGTAGCTGA 60.513 44.000 18.40 0.00 0.00 4.26
703 704 5.997746 GCCATGGAATATTGTAGTAGCTGAA 59.002 40.000 18.40 0.00 0.00 3.02
704 705 6.486657 GCCATGGAATATTGTAGTAGCTGAAA 59.513 38.462 18.40 0.00 0.00 2.69
705 706 7.175641 GCCATGGAATATTGTAGTAGCTGAAAT 59.824 37.037 18.40 0.00 0.00 2.17
706 707 8.509690 CCATGGAATATTGTAGTAGCTGAAATG 58.490 37.037 5.56 0.00 0.00 2.32
707 708 8.509690 CATGGAATATTGTAGTAGCTGAAATGG 58.490 37.037 0.00 0.00 0.00 3.16
708 709 6.486657 TGGAATATTGTAGTAGCTGAAATGGC 59.513 38.462 0.00 0.00 0.00 4.40
709 710 6.347725 GGAATATTGTAGTAGCTGAAATGGCG 60.348 42.308 0.00 0.00 34.52 5.69
710 711 2.309528 TGTAGTAGCTGAAATGGCGG 57.690 50.000 0.00 0.00 34.52 6.13
711 712 1.828595 TGTAGTAGCTGAAATGGCGGA 59.171 47.619 0.00 0.00 34.52 5.54
712 713 2.434336 TGTAGTAGCTGAAATGGCGGAT 59.566 45.455 0.00 0.00 34.52 4.18
713 714 2.717639 AGTAGCTGAAATGGCGGATT 57.282 45.000 0.00 0.00 34.52 3.01
714 715 2.565841 AGTAGCTGAAATGGCGGATTC 58.434 47.619 0.00 0.00 34.52 2.52
715 716 2.092968 AGTAGCTGAAATGGCGGATTCA 60.093 45.455 0.00 0.56 34.57 2.57
716 717 1.098050 AGCTGAAATGGCGGATTCAC 58.902 50.000 0.00 0.00 32.46 3.18
717 718 0.101219 GCTGAAATGGCGGATTCACC 59.899 55.000 0.00 0.00 32.46 4.02
718 719 1.755179 CTGAAATGGCGGATTCACCT 58.245 50.000 0.00 0.00 36.31 4.00
719 720 1.402968 CTGAAATGGCGGATTCACCTG 59.597 52.381 0.00 0.00 36.31 4.00
720 721 0.101219 GAAATGGCGGATTCACCTGC 59.899 55.000 0.00 0.00 37.42 4.85
725 726 0.179045 GGCGGATTCACCTGCTACAT 60.179 55.000 0.00 0.00 37.93 2.29
961 963 5.356882 TGTTCATTCACGCCTTTTAGAAG 57.643 39.130 0.00 0.00 0.00 2.85
1245 1247 3.664107 TCAATTCGCAGAGTTACAAGCT 58.336 40.909 0.00 0.00 32.99 3.74
1335 1337 4.843516 AGGGAATTGCTTAAACAATCCCAA 59.156 37.500 25.08 5.19 43.08 4.12
2107 2124 3.054065 CAGAATGGTAAAGAGGGCTCCTT 60.054 47.826 0.00 0.00 31.76 3.36
2142 2159 9.473007 TCAATTCCAGAAATCCATACAAATACA 57.527 29.630 0.00 0.00 0.00 2.29
2226 2243 1.511850 TTCTCGAAGTACGTGTCCGA 58.488 50.000 0.00 1.02 43.13 4.55
2515 2533 9.592196 TTACCAAGTATACGGTTCTAATCCTAT 57.408 33.333 7.63 0.00 36.69 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.472137 GGTTGCCATTAGTGTTTCTTGACTA 59.528 40.000 0.00 0.00 0.00 2.59
154 155 7.827729 ACCTAACATTATTTCACCAAGACCTAC 59.172 37.037 0.00 0.00 0.00 3.18
176 177 7.994425 TCTGCAAATTTGACTAATTCACCTA 57.006 32.000 22.31 0.00 35.39 3.08
449 450 6.126883 TGTTTGAAGAGGTCCGTATATGGAAT 60.127 38.462 15.48 7.42 40.44 3.01
461 462 2.278332 AAGCCCTGTTTGAAGAGGTC 57.722 50.000 6.23 0.00 37.75 3.85
511 512 0.530744 ATTAACTCTCGCTGACCGCA 59.469 50.000 0.00 0.00 39.08 5.69
574 575 4.317488 TGCCCTTTTTGATTGAGAATTGC 58.683 39.130 0.00 0.00 0.00 3.56
626 627 3.964031 AGCTACGGAGGATTCTCTTTGAT 59.036 43.478 0.00 0.00 39.86 2.57
635 636 1.482593 CCACTTGAGCTACGGAGGATT 59.517 52.381 0.00 0.00 0.00 3.01
654 655 4.141688 CCCTCCTCATGGAAAGTAGTTACC 60.142 50.000 0.00 0.00 42.66 2.85
688 689 4.100344 TCCGCCATTTCAGCTACTACAATA 59.900 41.667 0.00 0.00 0.00 1.90
689 690 3.118408 TCCGCCATTTCAGCTACTACAAT 60.118 43.478 0.00 0.00 0.00 2.71
690 691 2.235155 TCCGCCATTTCAGCTACTACAA 59.765 45.455 0.00 0.00 0.00 2.41
691 692 1.828595 TCCGCCATTTCAGCTACTACA 59.171 47.619 0.00 0.00 0.00 2.74
692 693 2.596904 TCCGCCATTTCAGCTACTAC 57.403 50.000 0.00 0.00 0.00 2.73
693 694 3.133901 TGAATCCGCCATTTCAGCTACTA 59.866 43.478 0.00 0.00 0.00 1.82
694 695 2.092968 TGAATCCGCCATTTCAGCTACT 60.093 45.455 0.00 0.00 0.00 2.57
695 696 2.032178 GTGAATCCGCCATTTCAGCTAC 59.968 50.000 0.00 0.00 32.79 3.58
696 697 2.288666 GTGAATCCGCCATTTCAGCTA 58.711 47.619 0.00 0.00 32.79 3.32
697 698 1.098050 GTGAATCCGCCATTTCAGCT 58.902 50.000 0.00 0.00 32.79 4.24
698 699 0.101219 GGTGAATCCGCCATTTCAGC 59.899 55.000 0.00 0.00 42.48 4.26
699 700 1.402968 CAGGTGAATCCGCCATTTCAG 59.597 52.381 0.00 0.00 45.32 3.02
700 701 1.462616 CAGGTGAATCCGCCATTTCA 58.537 50.000 0.00 0.00 45.32 2.69
701 702 0.101219 GCAGGTGAATCCGCCATTTC 59.899 55.000 0.00 0.00 45.32 2.17
702 703 0.323725 AGCAGGTGAATCCGCCATTT 60.324 50.000 0.00 0.00 45.32 2.32
703 704 0.546122 TAGCAGGTGAATCCGCCATT 59.454 50.000 0.00 0.00 45.32 3.16
704 705 0.179045 GTAGCAGGTGAATCCGCCAT 60.179 55.000 0.00 0.00 45.32 4.40
705 706 1.220749 GTAGCAGGTGAATCCGCCA 59.779 57.895 0.00 0.00 45.32 5.69
706 707 0.179045 ATGTAGCAGGTGAATCCGCC 60.179 55.000 0.00 0.00 43.25 6.13
707 708 1.668419 AATGTAGCAGGTGAATCCGC 58.332 50.000 0.00 0.00 41.99 5.54
708 709 4.816385 ACAATAATGTAGCAGGTGAATCCG 59.184 41.667 0.00 0.00 38.24 4.18
725 726 4.814234 CCGCCATTTCAGCTACTACAATAA 59.186 41.667 0.00 0.00 0.00 1.40
940 942 4.723248 CCTTCTAAAAGGCGTGAATGAAC 58.277 43.478 0.00 0.00 45.50 3.18
1245 1247 1.602668 GCAGAGGCGAATTGTGCAAAA 60.603 47.619 0.00 0.00 34.18 2.44
1335 1337 0.622665 CCACTGGGAGAGGATTTGCT 59.377 55.000 0.00 0.00 35.59 3.91
1499 1501 1.796796 GCTTGCTCGGTGAATGTCC 59.203 57.895 0.00 0.00 0.00 4.02
2142 2159 9.031537 CAGTTGGTAAGGATAAAATACCCTTTT 57.968 33.333 0.00 0.00 40.47 2.27
2226 2243 6.204882 GCTAACTATCGACATTTTGGGCTATT 59.795 38.462 0.00 0.00 0.00 1.73
2431 2449 1.924731 TTCAGAGGGAGAAGAAGCGA 58.075 50.000 0.00 0.00 0.00 4.93


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

AutoCloner maintained by Alex Coulton.