Multiple sequence alignment - TraesCS6B01G304000

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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 TraesCS6B01G304000 chr6B 100.000 3351 0 0 1 3351 544923244 544926594 0.000000e+00 6189
1 TraesCS6B01G304000 chr6B 96.601 1118 26 1 1231 2336 544797767 544798884 0.000000e+00 1844
2 TraesCS6B01G304000 chr6B 97.350 1019 24 2 2335 3351 544801608 544802625 0.000000e+00 1729
3 TraesCS6B01G304000 chr6B 96.983 928 17 4 1 927 651017914 651018831 0.000000e+00 1548
4 TraesCS6B01G304000 chr6B 92.547 738 42 10 2617 3351 163547259 163546532 0.000000e+00 1046
5 TraesCS6B01G304000 chr6B 97.078 308 8 1 928 1234 544797117 544797424 4.960000e-143 518
6 TraesCS6B01G304000 chr2B 97.303 927 15 2 1 927 245115135 245114219 0.000000e+00 1565
7 TraesCS6B01G304000 chr1B 97.091 928 25 2 1 927 296752769 296753695 0.000000e+00 1563
8 TraesCS6B01G304000 chr1B 92.318 742 43 12 2614 3351 655840367 655841098 0.000000e+00 1042
9 TraesCS6B01G304000 chr3B 96.872 927 19 3 1 927 75728109 75727193 0.000000e+00 1543
10 TraesCS6B01G304000 chr4B 96.659 928 20 4 1 928 567596209 567597125 0.000000e+00 1531
11 TraesCS6B01G304000 chr7B 96.121 928 25 3 1 927 667167274 667166357 0.000000e+00 1504
12 TraesCS6B01G304000 chr7B 92.038 741 47 9 2614 3351 115234266 115233535 0.000000e+00 1031
13 TraesCS6B01G304000 chr5D 93.096 927 57 2 1 927 405529492 405528573 0.000000e+00 1351
14 TraesCS6B01G304000 chr7D 92.719 934 59 4 1 933 629544905 629545830 0.000000e+00 1339
15 TraesCS6B01G304000 chr7D 91.322 726 51 7 204 928 555826031 555826745 0.000000e+00 981
16 TraesCS6B01G304000 chr2A 92.713 741 41 10 2614 3351 113932690 113931960 0.000000e+00 1057
17 TraesCS6B01G304000 chr1D 92.391 736 44 9 2620 3351 436094142 436093415 0.000000e+00 1038
18 TraesCS6B01G304000 chr1D 92.173 741 48 7 2614 3351 457085875 457085142 0.000000e+00 1038
19 TraesCS6B01G304000 chr1D 90.923 672 50 5 261 928 9480791 9481455 0.000000e+00 893
20 TraesCS6B01G304000 chr3D 92.183 742 43 10 2613 3351 606795843 606795114 0.000000e+00 1035
21 TraesCS6B01G304000 chr6D 91.925 743 45 13 2613 3351 71517866 71518597 0.000000e+00 1026


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 TraesCS6B01G304000 chr6B 544923244 544926594 3350 False 6189.000000 6189 100.000000 1 3351 1 chr6B.!!$F1 3350
1 TraesCS6B01G304000 chr6B 651017914 651018831 917 False 1548.000000 1548 96.983000 1 927 1 chr6B.!!$F2 926
2 TraesCS6B01G304000 chr6B 544797117 544802625 5508 False 1363.666667 1844 97.009667 928 3351 3 chr6B.!!$F3 2423
3 TraesCS6B01G304000 chr6B 163546532 163547259 727 True 1046.000000 1046 92.547000 2617 3351 1 chr6B.!!$R1 734
4 TraesCS6B01G304000 chr2B 245114219 245115135 916 True 1565.000000 1565 97.303000 1 927 1 chr2B.!!$R1 926
5 TraesCS6B01G304000 chr1B 296752769 296753695 926 False 1563.000000 1563 97.091000 1 927 1 chr1B.!!$F1 926
6 TraesCS6B01G304000 chr1B 655840367 655841098 731 False 1042.000000 1042 92.318000 2614 3351 1 chr1B.!!$F2 737
7 TraesCS6B01G304000 chr3B 75727193 75728109 916 True 1543.000000 1543 96.872000 1 927 1 chr3B.!!$R1 926
8 TraesCS6B01G304000 chr4B 567596209 567597125 916 False 1531.000000 1531 96.659000 1 928 1 chr4B.!!$F1 927
9 TraesCS6B01G304000 chr7B 667166357 667167274 917 True 1504.000000 1504 96.121000 1 927 1 chr7B.!!$R2 926
10 TraesCS6B01G304000 chr7B 115233535 115234266 731 True 1031.000000 1031 92.038000 2614 3351 1 chr7B.!!$R1 737
11 TraesCS6B01G304000 chr5D 405528573 405529492 919 True 1351.000000 1351 93.096000 1 927 1 chr5D.!!$R1 926
12 TraesCS6B01G304000 chr7D 629544905 629545830 925 False 1339.000000 1339 92.719000 1 933 1 chr7D.!!$F2 932
13 TraesCS6B01G304000 chr7D 555826031 555826745 714 False 981.000000 981 91.322000 204 928 1 chr7D.!!$F1 724
14 TraesCS6B01G304000 chr2A 113931960 113932690 730 True 1057.000000 1057 92.713000 2614 3351 1 chr2A.!!$R1 737
15 TraesCS6B01G304000 chr1D 436093415 436094142 727 True 1038.000000 1038 92.391000 2620 3351 1 chr1D.!!$R1 731
16 TraesCS6B01G304000 chr1D 457085142 457085875 733 True 1038.000000 1038 92.173000 2614 3351 1 chr1D.!!$R2 737
17 TraesCS6B01G304000 chr1D 9480791 9481455 664 False 893.000000 893 90.923000 261 928 1 chr1D.!!$F1 667
18 TraesCS6B01G304000 chr3D 606795114 606795843 729 True 1035.000000 1035 92.183000 2613 3351 1 chr3D.!!$R1 738
19 TraesCS6B01G304000 chr6D 71517866 71518597 731 False 1026.000000 1026 91.925000 2613 3351 1 chr6D.!!$F1 738

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
705 722 2.121963 AGAGGGGTGGTGGCTTCA 60.122 61.111 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 5511 0.381801 CACCAACCAACACAGCTGAC 59.618 55.0 23.35 0.0 0.0 3.51 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
705 722 2.121963 AGAGGGGTGGTGGCTTCA 60.122 61.111 0.00 0.00 0.00 3.02
715 732 3.555324 TGGCTTCAGTGGCACCGA 61.555 61.111 15.27 6.76 37.59 4.69
869 889 7.607607 TCGTACAATATACGGACACCTATACAT 59.392 37.037 6.63 0.00 40.90 2.29
878 898 6.540995 ACGGACACCTATACATAGACTACAT 58.459 40.000 0.00 0.00 32.05 2.29
879 899 6.430308 ACGGACACCTATACATAGACTACATG 59.570 42.308 0.00 0.00 32.05 3.21
1034 1054 0.321034 CAGCCAGAACTGCTAGCACA 60.321 55.000 14.93 0.00 36.81 4.57
1062 1082 0.034198 TCGTCTTGTTCATTCCCGCA 59.966 50.000 0.00 0.00 0.00 5.69
1102 1123 2.719739 CCTCCATATGATGCCCATGAC 58.280 52.381 3.65 0.00 36.71 3.06
1128 1149 0.110486 ATTTTGCAGGTCACGGGTCT 59.890 50.000 0.00 0.00 0.00 3.85
1198 1219 0.107456 CTCACACCACTGAGCAAGGT 59.893 55.000 0.00 0.00 35.65 3.50
1248 1615 4.072088 GCGCTTCGGTGTTGGACG 62.072 66.667 0.00 0.00 0.00 4.79
1258 1625 2.357034 GTTGGACGAAGCCGCTCA 60.357 61.111 0.00 0.00 39.95 4.26
1266 1633 2.009888 GAAGCCGCTCATTCTTCGG 58.990 57.895 0.00 0.00 45.46 4.30
1269 1636 2.464459 GCCGCTCATTCTTCGGTGG 61.464 63.158 1.83 0.00 44.58 4.61
1277 1644 4.065088 CTCATTCTTCGGTGGACAAGAAA 58.935 43.478 0.00 0.00 40.99 2.52
1284 1651 2.552315 TCGGTGGACAAGAAATTGAAGC 59.448 45.455 0.00 0.00 0.00 3.86
1313 1680 2.029666 GGGATCGAGCACGGGATG 59.970 66.667 1.84 0.00 40.21 3.51
1320 1687 0.673644 CGAGCACGGGATGGAAGTTT 60.674 55.000 0.00 0.00 35.72 2.66
1321 1688 1.534729 GAGCACGGGATGGAAGTTTT 58.465 50.000 0.00 0.00 0.00 2.43
1338 1705 4.010349 AGTTTTCCGTTTCTGGGATGATC 58.990 43.478 0.00 0.00 32.58 2.92
1349 1716 2.103771 CTGGGATGATCACAAGGACGAT 59.896 50.000 0.00 0.00 0.00 3.73
1406 1773 2.679287 GGGAGTTCTCCGTCGGGT 60.679 66.667 12.29 0.00 33.83 5.28
1472 1839 1.302431 CATCAACAGCCCGGTCACA 60.302 57.895 0.00 0.00 0.00 3.58
1548 1915 2.970868 GGCAACTATACGGCGGGC 60.971 66.667 13.24 0.00 0.00 6.13
1566 1933 4.988598 AGCCGTGGCCGAACTGTG 62.989 66.667 7.39 0.00 43.17 3.66
1618 1985 1.603172 CCCTTACGCCGATCATCACTC 60.603 57.143 0.00 0.00 0.00 3.51
1649 2016 0.459489 GCAAAGCCACCTTGTTCACA 59.541 50.000 0.00 0.00 0.00 3.58
1738 2117 3.854669 CCTCGGCCTCGGCAGATT 61.855 66.667 11.09 0.00 43.61 2.40
2407 5511 4.388165 TGTTGTCATGTTTGTGTGCAAAAG 59.612 37.500 0.00 0.00 45.01 2.27
2421 5525 1.134946 GCAAAAGTCAGCTGTGTTGGT 59.865 47.619 14.67 0.00 0.00 3.67
2638 5742 1.444836 TTCGAGGGTACGCAAATTGG 58.555 50.000 12.95 0.00 0.00 3.16
2948 6057 1.202818 GGAGTGCCAACAGGAAACTCT 60.203 52.381 13.81 0.00 40.21 3.24
3240 6352 2.324330 CGTCACCGCAGCAAATCCA 61.324 57.895 0.00 0.00 0.00 3.41
3342 6454 4.631377 CGAGAAGCAACTACATCATCCAAA 59.369 41.667 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.276857 GTTGATGATGCTGAGATGGTGT 58.723 45.455 0.00 0.00 0.00 4.16
485 486 2.125753 GACCTCTCTGCACGCCTG 60.126 66.667 0.00 0.00 0.00 4.85
496 497 2.108425 GGGGTCTTTTTCCTTGACCTCT 59.892 50.000 10.60 0.00 45.30 3.69
705 722 0.035458 CTCCTCTTTTCGGTGCCACT 59.965 55.000 0.00 0.00 0.00 4.00
712 729 1.222113 GCCCTCCTCCTCTTTTCGG 59.778 63.158 0.00 0.00 0.00 4.30
715 732 2.972819 GCCGCCCTCCTCCTCTTTT 61.973 63.158 0.00 0.00 0.00 2.27
980 1000 1.810030 GCGTAGGAGCAAGGAACGG 60.810 63.158 0.00 0.00 37.05 4.44
1034 1054 3.417069 TGAACAAGACGAATGGGATGT 57.583 42.857 0.00 0.00 0.00 3.06
1062 1082 1.404315 GCGAGAAAACGAGGATGGTCT 60.404 52.381 0.00 0.00 35.09 3.85
1102 1123 3.773117 GACCTGCAAAATGTGGTCG 57.227 52.632 4.95 0.00 39.39 4.79
1128 1149 4.779733 GACGAGGGGGAGGAGGCA 62.780 72.222 0.00 0.00 0.00 4.75
1198 1219 1.136891 CACTGACGTCTATGGCCATGA 59.863 52.381 29.04 19.50 0.00 3.07
1248 1615 2.009888 CCGAAGAATGAGCGGCTTC 58.990 57.895 2.97 0.00 38.46 3.86
1258 1625 5.070001 TCAATTTCTTGTCCACCGAAGAAT 58.930 37.500 0.00 0.00 37.87 2.40
1266 1633 4.874970 ACATGCTTCAATTTCTTGTCCAC 58.125 39.130 0.00 0.00 33.87 4.02
1269 1636 6.919662 TCTTTGACATGCTTCAATTTCTTGTC 59.080 34.615 0.00 0.00 35.42 3.18
1277 1644 4.410099 TCCCTTCTTTGACATGCTTCAAT 58.590 39.130 0.00 0.00 35.42 2.57
1284 1651 2.611292 GCTCGATCCCTTCTTTGACATG 59.389 50.000 0.00 0.00 0.00 3.21
1313 1680 2.578786 TCCCAGAAACGGAAAACTTCC 58.421 47.619 0.00 0.00 46.62 3.46
1320 1687 2.304470 TGTGATCATCCCAGAAACGGAA 59.696 45.455 0.00 0.00 31.75 4.30
1321 1688 1.905894 TGTGATCATCCCAGAAACGGA 59.094 47.619 0.00 0.00 0.00 4.69
1338 1705 5.295431 TGCTTTTTGATATCGTCCTTGTG 57.705 39.130 0.00 0.00 0.00 3.33
1349 1716 2.642139 GCTGCAGCTGCTTTTTGATA 57.358 45.000 36.61 15.14 42.66 2.15
1369 1736 1.485294 TTGGGCTCCAGGCGTAAGAA 61.485 55.000 0.00 0.00 42.94 2.52
1406 1773 2.555782 CCGGTGTCGACGACGTAA 59.444 61.111 22.06 2.87 40.69 3.18
1570 1937 3.703127 GAAGTTCTCCCGGGCCGT 61.703 66.667 26.32 2.48 0.00 5.68
1582 1949 2.435203 AGGGTAAGGACAGGGAAGTT 57.565 50.000 0.00 0.00 0.00 2.66
1585 1952 2.181975 CGTAAGGGTAAGGACAGGGAA 58.818 52.381 0.00 0.00 0.00 3.97
1594 1961 2.035449 TGATGATCGGCGTAAGGGTAAG 59.965 50.000 6.85 0.00 38.28 2.34
2407 5511 0.381801 CACCAACCAACACAGCTGAC 59.618 55.000 23.35 0.00 0.00 3.51
2421 5525 1.542030 ACAAAACGCTCAACACACCAA 59.458 42.857 0.00 0.00 0.00 3.67
2638 5742 7.742767 TCCTCCTTTTATAAAGCTATGGTACC 58.257 38.462 4.43 4.43 0.00 3.34
2932 6041 1.490490 AGACAGAGTTTCCTGTTGGCA 59.510 47.619 0.00 0.00 46.45 4.92
2948 6057 2.181777 GCATCGTGCGAGGAGACA 59.818 61.111 10.46 0.00 31.71 3.41
3034 6143 1.750778 CTTGGTGTTGGCAGTTGTCTT 59.249 47.619 0.00 0.00 0.00 3.01
3193 6305 0.877743 GGCTTCAGGAACAGTTCTGC 59.122 55.000 13.13 9.42 0.00 4.26
3197 6309 1.322442 GCTTGGCTTCAGGAACAGTT 58.678 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.