Multiple sequence alignment - TraesCS1B01G324800

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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 TraesCS1B01G324800 chr1B 100.000 2264 0 0 1 2264 550440098 550437835 0 4181
1 TraesCS1B01G324800 chr1B 96.513 803 22 3 1 797 38183421 38184223 0 1323
2 TraesCS1B01G324800 chr2B 97.968 2264 46 0 1 2264 717652052 717654315 0 3927
3 TraesCS1B01G324800 chr2B 95.179 1701 65 4 571 2264 45596552 45598242 0 2671
4 TraesCS1B01G324800 chr2B 96.526 806 21 4 1 800 42193433 42194237 0 1327
5 TraesCS1B01G324800 chr2B 94.264 523 28 2 1742 2264 138733566 138734086 0 798
6 TraesCS1B01G324800 chr7B 95.803 1763 64 5 512 2264 235457593 235455831 0 2837
7 TraesCS1B01G324800 chr7B 97.378 1602 41 1 663 2264 130334623 130336223 0 2724
8 TraesCS1B01G324800 chr7B 92.543 1703 79 12 591 2264 577211915 577213598 0 2398
9 TraesCS1B01G324800 chr7B 97.146 806 17 3 1 800 235458064 235457259 0 1356
10 TraesCS1B01G324800 chr7B 97.146 806 17 3 1 800 687040652 687041457 0 1356
11 TraesCS1B01G324800 chr5B 95.208 1753 74 5 521 2264 530940320 530938569 0 2763
12 TraesCS1B01G324800 chr5B 97.519 806 14 3 1 800 464634136 464634941 0 1373
13 TraesCS1B01G324800 chr4B 94.689 1770 73 7 496 2264 49106178 49107927 0 2728
14 TraesCS1B01G324800 chr4B 96.774 806 20 3 1 800 402787173 402786368 0 1339
15 TraesCS1B01G324800 chr6B 95.893 1680 57 4 591 2264 114144244 114142571 0 2710
16 TraesCS1B01G324800 chr6B 93.236 1715 72 15 591 2264 650646111 650644400 0 2484
17 TraesCS1B01G324800 chr6B 94.057 1649 64 15 591 2233 661052199 661053819 0 2471
18 TraesCS1B01G324800 chr3B 93.271 1486 60 15 814 2264 393329884 393331364 0 2154
19 TraesCS1B01G324800 chr3B 96.402 806 22 4 1 800 16124406 16123602 0 1321
20 TraesCS1B01G324800 chr4A 96.774 806 20 3 1 800 712877508 712878313 0 1339
21 TraesCS1B01G324800 chr4A 95.938 517 21 0 1748 2264 712879259 712879775 0 839


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 TraesCS1B01G324800 chr1B 550437835 550440098 2263 True 4181.0 4181 100.0000 1 2264 1 chr1B.!!$R1 2263
1 TraesCS1B01G324800 chr1B 38183421 38184223 802 False 1323.0 1323 96.5130 1 797 1 chr1B.!!$F1 796
2 TraesCS1B01G324800 chr2B 717652052 717654315 2263 False 3927.0 3927 97.9680 1 2264 1 chr2B.!!$F4 2263
3 TraesCS1B01G324800 chr2B 45596552 45598242 1690 False 2671.0 2671 95.1790 571 2264 1 chr2B.!!$F2 1693
4 TraesCS1B01G324800 chr2B 42193433 42194237 804 False 1327.0 1327 96.5260 1 800 1 chr2B.!!$F1 799
5 TraesCS1B01G324800 chr2B 138733566 138734086 520 False 798.0 798 94.2640 1742 2264 1 chr2B.!!$F3 522
6 TraesCS1B01G324800 chr7B 130334623 130336223 1600 False 2724.0 2724 97.3780 663 2264 1 chr7B.!!$F1 1601
7 TraesCS1B01G324800 chr7B 577211915 577213598 1683 False 2398.0 2398 92.5430 591 2264 1 chr7B.!!$F2 1673
8 TraesCS1B01G324800 chr7B 235455831 235458064 2233 True 2096.5 2837 96.4745 1 2264 2 chr7B.!!$R1 2263
9 TraesCS1B01G324800 chr7B 687040652 687041457 805 False 1356.0 1356 97.1460 1 800 1 chr7B.!!$F3 799
10 TraesCS1B01G324800 chr5B 530938569 530940320 1751 True 2763.0 2763 95.2080 521 2264 1 chr5B.!!$R1 1743
11 TraesCS1B01G324800 chr5B 464634136 464634941 805 False 1373.0 1373 97.5190 1 800 1 chr5B.!!$F1 799
12 TraesCS1B01G324800 chr4B 49106178 49107927 1749 False 2728.0 2728 94.6890 496 2264 1 chr4B.!!$F1 1768
13 TraesCS1B01G324800 chr4B 402786368 402787173 805 True 1339.0 1339 96.7740 1 800 1 chr4B.!!$R1 799
14 TraesCS1B01G324800 chr6B 114142571 114144244 1673 True 2710.0 2710 95.8930 591 2264 1 chr6B.!!$R1 1673
15 TraesCS1B01G324800 chr6B 650644400 650646111 1711 True 2484.0 2484 93.2360 591 2264 1 chr6B.!!$R2 1673
16 TraesCS1B01G324800 chr6B 661052199 661053819 1620 False 2471.0 2471 94.0570 591 2233 1 chr6B.!!$F1 1642
17 TraesCS1B01G324800 chr3B 393329884 393331364 1480 False 2154.0 2154 93.2710 814 2264 1 chr3B.!!$F1 1450
18 TraesCS1B01G324800 chr3B 16123602 16124406 804 True 1321.0 1321 96.4020 1 800 1 chr3B.!!$R1 799
19 TraesCS1B01G324800 chr4A 712877508 712879775 2267 False 1089.0 1339 96.3560 1 2264 2 chr4A.!!$F1 2263

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
725 886 0.687354 ACAAGTGCTAGAGGTGGTGG 59.313 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 2317 1.812922 CGAGCAAAGCGAGCCAGAT 60.813 57.895 0.0 0.0 0.0 2.9 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
103 104 2.351726 GCGAAGGCGAGAAACATACATT 59.648 45.455 0.00 0.00 40.82 2.71
120 121 9.612066 AACATACATTTTTGTGATGGAAAAACT 57.388 25.926 0.00 0.00 35.64 2.66
189 190 2.752903 GCCAAGATTTCGCCCTTTCTTA 59.247 45.455 0.00 0.00 0.00 2.10
417 419 1.133598 CACAATGAGCGGACATGCAAT 59.866 47.619 0.00 0.00 37.31 3.56
590 592 3.757493 AGTGTTCGTAGAGGGAGTACAAG 59.243 47.826 0.00 0.00 38.43 3.16
705 866 1.534235 AGGTGGTGGTCGAGCTTCT 60.534 57.895 16.64 3.41 0.00 2.85
713 874 1.336887 TGGTCGAGCTTCTACAAGTGC 60.337 52.381 16.64 0.00 31.45 4.40
714 875 1.067495 GGTCGAGCTTCTACAAGTGCT 60.067 52.381 7.51 0.00 38.59 4.40
715 876 2.163815 GGTCGAGCTTCTACAAGTGCTA 59.836 50.000 7.51 0.00 35.76 3.49
716 877 3.430931 GTCGAGCTTCTACAAGTGCTAG 58.569 50.000 0.00 0.00 35.76 3.42
717 878 3.127203 GTCGAGCTTCTACAAGTGCTAGA 59.873 47.826 0.00 0.00 35.76 2.43
718 879 3.375610 TCGAGCTTCTACAAGTGCTAGAG 59.624 47.826 0.00 0.00 35.76 2.43
719 880 3.488384 CGAGCTTCTACAAGTGCTAGAGG 60.488 52.174 0.00 0.00 35.76 3.69
720 881 3.436243 AGCTTCTACAAGTGCTAGAGGT 58.564 45.455 0.00 0.00 33.64 3.85
721 882 3.194542 AGCTTCTACAAGTGCTAGAGGTG 59.805 47.826 0.00 0.00 33.64 4.00
722 883 3.677424 GCTTCTACAAGTGCTAGAGGTGG 60.677 52.174 0.00 0.00 31.45 4.61
723 884 3.170991 TCTACAAGTGCTAGAGGTGGT 57.829 47.619 0.00 0.00 0.00 4.16
724 885 2.826128 TCTACAAGTGCTAGAGGTGGTG 59.174 50.000 0.00 0.00 0.00 4.17
725 886 0.687354 ACAAGTGCTAGAGGTGGTGG 59.313 55.000 0.00 0.00 0.00 4.61
726 887 0.687354 CAAGTGCTAGAGGTGGTGGT 59.313 55.000 0.00 0.00 0.00 4.16
727 888 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
728 889 1.215647 GTGCTAGAGGTGGTGGTCG 59.784 63.158 0.00 0.00 0.00 4.79
729 890 1.076014 TGCTAGAGGTGGTGGTCGA 59.924 57.895 0.00 0.00 0.00 4.20
730 891 0.965866 TGCTAGAGGTGGTGGTCGAG 60.966 60.000 0.00 0.00 0.00 4.04
731 892 1.810532 CTAGAGGTGGTGGTCGAGC 59.189 63.158 7.89 7.89 0.00 5.03
732 893 0.965866 CTAGAGGTGGTGGTCGAGCA 60.966 60.000 14.39 14.39 0.00 4.26
733 894 0.965866 TAGAGGTGGTGGTCGAGCAG 60.966 60.000 19.24 0.00 30.97 4.24
734 895 3.302347 GAGGTGGTGGTCGAGCAGG 62.302 68.421 19.24 0.00 30.97 4.85
736 897 4.314440 GTGGTGGTCGAGCAGGCA 62.314 66.667 19.24 0.00 30.97 4.75
737 898 4.314440 TGGTGGTCGAGCAGGCAC 62.314 66.667 19.24 5.94 0.00 5.01
738 899 4.314440 GGTGGTCGAGCAGGCACA 62.314 66.667 19.24 0.00 0.00 4.57
739 900 2.280797 GTGGTCGAGCAGGCACAA 60.281 61.111 19.24 0.00 0.00 3.33
740 901 2.031012 TGGTCGAGCAGGCACAAG 59.969 61.111 14.39 0.00 0.00 3.16
741 902 2.031163 GGTCGAGCAGGCACAAGT 59.969 61.111 10.30 0.00 0.00 3.16
742 903 1.598130 GGTCGAGCAGGCACAAGTT 60.598 57.895 10.30 0.00 0.00 2.66
1111 1272 0.038166 GGAGAAGGATGTGCCCACAA 59.962 55.000 5.08 0.00 45.41 3.33
1236 1397 2.167693 TGATCGTCGAAGGCCAACTAAT 59.832 45.455 5.01 0.00 0.00 1.73
1255 1416 4.350368 AATGCATATGACATACCACCGA 57.650 40.909 6.97 0.00 0.00 4.69
1488 1649 0.099082 CGTCGTGAGAAGGAGGCTAC 59.901 60.000 0.00 0.00 45.01 3.58
1673 1890 2.237751 CCGGCGTCGATGATGAACC 61.238 63.158 12.93 0.00 39.00 3.62
2032 2285 1.987855 CCAAGGTCCCTGGCGTCTA 60.988 63.158 0.00 0.00 0.00 2.59
2054 2307 3.625897 CCACACCCAGACGCCAGA 61.626 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 5.047021 TCCACACAGTTTTTCCATCACAAAA 60.047 36.000 0.00 0.00 0.00 2.44
120 121 1.142667 TGGAACTCTTGCATCCACACA 59.857 47.619 1.73 0.00 38.30 3.72
189 190 2.468015 AGGCCACTGTGATTGGTCT 58.532 52.632 9.86 0.00 44.64 3.85
590 592 1.215647 CGACCACCACCTCTAGCAC 59.784 63.158 0.00 0.00 0.00 4.40
705 866 1.899814 CCACCACCTCTAGCACTTGTA 59.100 52.381 0.00 0.00 0.00 2.41
713 874 0.965866 TGCTCGACCACCACCTCTAG 60.966 60.000 0.00 0.00 0.00 2.43
714 875 0.965866 CTGCTCGACCACCACCTCTA 60.966 60.000 0.00 0.00 0.00 2.43
715 876 2.203640 TGCTCGACCACCACCTCT 60.204 61.111 0.00 0.00 0.00 3.69
716 877 2.262915 CTGCTCGACCACCACCTC 59.737 66.667 0.00 0.00 0.00 3.85
717 878 3.314331 CCTGCTCGACCACCACCT 61.314 66.667 0.00 0.00 0.00 4.00
719 880 4.314440 TGCCTGCTCGACCACCAC 62.314 66.667 0.00 0.00 0.00 4.16
720 881 4.314440 GTGCCTGCTCGACCACCA 62.314 66.667 0.00 0.00 0.00 4.17
721 882 3.825160 TTGTGCCTGCTCGACCACC 62.825 63.158 0.00 0.00 0.00 4.61
722 883 2.280797 TTGTGCCTGCTCGACCAC 60.281 61.111 0.00 0.00 0.00 4.16
723 884 2.031012 CTTGTGCCTGCTCGACCA 59.969 61.111 0.00 0.00 0.00 4.02
724 885 1.569479 GAACTTGTGCCTGCTCGACC 61.569 60.000 0.00 0.00 0.00 4.79
725 886 0.601311 AGAACTTGTGCCTGCTCGAC 60.601 55.000 0.00 0.00 0.00 4.20
726 887 0.966179 TAGAACTTGTGCCTGCTCGA 59.034 50.000 0.00 0.00 0.00 4.04
727 888 1.067565 TCTAGAACTTGTGCCTGCTCG 60.068 52.381 0.00 0.00 0.00 5.03
728 889 2.615869 CTCTAGAACTTGTGCCTGCTC 58.384 52.381 0.00 0.00 0.00 4.26
729 890 1.277557 CCTCTAGAACTTGTGCCTGCT 59.722 52.381 0.00 0.00 0.00 4.24
730 891 1.002544 ACCTCTAGAACTTGTGCCTGC 59.997 52.381 0.00 0.00 0.00 4.85
731 892 2.613977 CCACCTCTAGAACTTGTGCCTG 60.614 54.545 0.00 0.00 0.00 4.85
732 893 1.625818 CCACCTCTAGAACTTGTGCCT 59.374 52.381 0.00 0.00 0.00 4.75
733 894 1.348036 ACCACCTCTAGAACTTGTGCC 59.652 52.381 0.00 0.00 0.00 5.01
734 895 2.417719 CACCACCTCTAGAACTTGTGC 58.582 52.381 0.00 0.00 0.00 4.57
735 896 2.368875 ACCACCACCTCTAGAACTTGTG 59.631 50.000 0.00 0.00 0.00 3.33
736 897 2.633481 GACCACCACCTCTAGAACTTGT 59.367 50.000 0.00 0.00 0.00 3.16
737 898 2.352814 CGACCACCACCTCTAGAACTTG 60.353 54.545 0.00 0.00 0.00 3.16
738 899 1.893801 CGACCACCACCTCTAGAACTT 59.106 52.381 0.00 0.00 0.00 2.66
739 900 1.075050 TCGACCACCACCTCTAGAACT 59.925 52.381 0.00 0.00 0.00 3.01
740 901 1.473278 CTCGACCACCACCTCTAGAAC 59.527 57.143 0.00 0.00 0.00 3.01
741 902 1.835494 CTCGACCACCACCTCTAGAA 58.165 55.000 0.00 0.00 0.00 2.10
742 903 0.680280 GCTCGACCACCACCTCTAGA 60.680 60.000 0.00 0.00 0.00 2.43
951 1112 7.880195 AGCACAAGACATAAAGAGAGTAAATGT 59.120 33.333 0.00 0.00 33.63 2.71
1111 1272 1.761449 TCAGCACACCAACATGTTGT 58.239 45.000 31.20 19.25 38.85 3.32
1194 1355 1.141858 TGTGCATAGTTGGGACACACA 59.858 47.619 0.00 0.00 39.29 3.72
1236 1397 5.046663 ACATATCGGTGGTATGTCATATGCA 60.047 40.000 0.00 0.00 38.10 3.96
1673 1890 9.953825 GTTCATACATTAAACAAAGTCTAGACG 57.046 33.333 17.07 6.00 36.20 4.18
2032 2285 2.923035 CGTCTGGGTGTGGGAGGT 60.923 66.667 0.00 0.00 0.00 3.85
2054 2307 2.285969 AGCCAGATGCCAGGGTCT 60.286 61.111 0.00 0.00 42.71 3.85
2064 2317 1.812922 CGAGCAAAGCGAGCCAGAT 60.813 57.895 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.