Multiple sequence alignment - TraesCS6D01G027200

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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 TraesCS6D01G027200 chr6D 100.000 4234 0 0 1 4234 10346657 10342424 0.000000e+00 7819.0
1 TraesCS6D01G027200 chr6D 93.319 3697 160 35 62 3726 10374042 10370401 0.000000e+00 5378.0
2 TraesCS6D01G027200 chr6D 94.274 3388 127 23 700 4061 10337944 10334598 0.000000e+00 5120.0
3 TraesCS6D01G027200 chr6D 97.418 426 9 2 3809 4234 10351551 10351128 0.000000e+00 725.0
4 TraesCS6D01G027200 chr6A 93.634 3566 164 32 62 3595 11887135 11883601 0.000000e+00 5269.0
5 TraesCS6D01G027200 chr6A 93.851 2911 146 18 701 3583 11841890 11838985 0.000000e+00 4353.0
6 TraesCS6D01G027200 chr6A 94.996 2438 83 20 1 2429 11855233 11852826 0.000000e+00 3790.0
7 TraesCS6D01G027200 chr6A 95.577 1899 64 9 2342 4227 11852819 11850928 0.000000e+00 3024.0
8 TraesCS6D01G027200 chr6A 91.585 511 37 4 3555 4061 11838971 11838463 0.000000e+00 701.0
9 TraesCS6D01G027200 chr6A 88.462 104 12 0 3743 3846 11883358 11883255 4.440000e-25 126.0
10 TraesCS6D01G027200 chr6B 92.629 3419 198 26 199 3578 18945105 18941702 0.000000e+00 4868.0
11 TraesCS6D01G027200 chr6B 92.868 3155 183 21 457 3579 19118838 19121982 0.000000e+00 4542.0
12 TraesCS6D01G027200 chr6B 92.160 676 40 11 3554 4224 19121996 19122663 0.000000e+00 942.0
13 TraesCS6D01G027200 chr6B 91.753 679 45 10 3554 4227 18941693 18941021 0.000000e+00 933.0
14 TraesCS6D01G027200 chr5B 74.004 527 104 25 1664 2166 537535701 537535184 2.600000e-42 183.0
15 TraesCS6D01G027200 chr5B 100.000 28 0 0 4157 4184 677737216 677737243 8.000000e-03 52.8
16 TraesCS6D01G027200 chr7A 83.761 117 17 2 2078 2192 728088775 728088659 4.480000e-20 110.0
17 TraesCS6D01G027200 chr7A 74.427 262 55 9 1938 2192 728055869 728055613 7.490000e-18 102.0
18 TraesCS6D01G027200 chr7A 84.615 104 12 4 3977 4077 20205555 20205453 2.690000e-17 100.0
19 TraesCS6D01G027200 chr1D 100.000 45 0 0 1 45 185998367 185998323 2.710000e-12 84.2
20 TraesCS6D01G027200 chr1B 100.000 45 0 0 1 45 483878705 483878749 2.710000e-12 84.2
21 TraesCS6D01G027200 chr3D 95.556 45 2 0 1 45 550718152 550718196 5.870000e-09 73.1
22 TraesCS6D01G027200 chr2D 77.228 101 19 3 4083 4182 61814858 61814955 5.910000e-04 56.5


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 TraesCS6D01G027200 chr6D 10342424 10346657 4233 True 7819.0 7819 100.0000 1 4234 1 chr6D.!!$R2 4233
1 TraesCS6D01G027200 chr6D 10370401 10374042 3641 True 5378.0 5378 93.3190 62 3726 1 chr6D.!!$R4 3664
2 TraesCS6D01G027200 chr6D 10334598 10337944 3346 True 5120.0 5120 94.2740 700 4061 1 chr6D.!!$R1 3361
3 TraesCS6D01G027200 chr6A 11850928 11855233 4305 True 3407.0 3790 95.2865 1 4227 2 chr6A.!!$R2 4226
4 TraesCS6D01G027200 chr6A 11883255 11887135 3880 True 2697.5 5269 91.0480 62 3846 2 chr6A.!!$R3 3784
5 TraesCS6D01G027200 chr6A 11838463 11841890 3427 True 2527.0 4353 92.7180 701 4061 2 chr6A.!!$R1 3360
6 TraesCS6D01G027200 chr6B 18941021 18945105 4084 True 2900.5 4868 92.1910 199 4227 2 chr6B.!!$R1 4028
7 TraesCS6D01G027200 chr6B 19118838 19122663 3825 False 2742.0 4542 92.5140 457 4224 2 chr6B.!!$F1 3767

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
602 622 0.544223 TGTACATGGCCACCGCTAAT 59.456 50.0 8.16 0.0 34.44 1.73 F
1063 1095 0.687427 TGAGATCCTCATCCGCACCA 60.687 55.0 0.00 0.0 35.39 4.17 F
1994 2026 0.472471 GTGTTCTTGGACAGGGGTCA 59.528 55.0 0.00 0.0 46.17 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2020 1.106285 GAGGAATGTGCATTGACCCC 58.894 55.000 1.77 0.0 0.00 4.95 R
2728 2845 5.163754 CCGTATCCTTTCTCGCAAAAAGAAT 60.164 40.000 4.51 0.0 36.09 2.40 R
3777 4115 1.339610 CGGCTTGGATCCTGAGTAGAG 59.660 57.143 14.23 1.1 0.00 2.43 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
602 622 0.544223 TGTACATGGCCACCGCTAAT 59.456 50.000 8.16 0.0 34.44 1.73
695 715 0.994247 ATGGGTCAGCACCTGAATGA 59.006 50.000 0.00 0.0 42.46 2.57
896 927 5.239744 TGCCTGAAACGTAAGCAATTAAAGA 59.760 36.000 0.00 0.0 45.62 2.52
917 948 5.056480 AGAATGAGTGTCACAATTTCGTCA 58.944 37.500 5.62 0.0 0.00 4.35
1054 1086 1.643286 ACCTCCTCAGTGAGATCCTCA 59.357 52.381 22.09 0.0 38.25 3.86
1063 1095 0.687427 TGAGATCCTCATCCGCACCA 60.687 55.000 0.00 0.0 35.39 4.17
1264 1296 2.182791 CTGCTGTCATCCGTCGCT 59.817 61.111 0.00 0.0 0.00 4.93
1333 1365 1.283613 ACATCCTTGGTTGCCGGAATA 59.716 47.619 5.05 0.0 0.00 1.75
1501 1533 1.704628 TCATGTCCAAAGAAGAGGGCA 59.295 47.619 0.00 0.0 44.75 5.36
1722 1754 2.749839 TTGGATTTGGCGGCCTCG 60.750 61.111 21.46 0.0 39.81 4.63
1791 1823 3.439857 AACACCATATTGTCACAGGCT 57.560 42.857 0.00 0.0 0.00 4.58
1928 1960 4.132336 GCTGATTTGAGTATGGCAGATGA 58.868 43.478 0.00 0.0 0.00 2.92
1988 2020 2.287915 CCGAGTTTGTGTTCTTGGACAG 59.712 50.000 0.00 0.0 37.40 3.51
1994 2026 0.472471 GTGTTCTTGGACAGGGGTCA 59.528 55.000 0.00 0.0 46.17 4.02
2307 2343 6.538742 CACCAACATATCCAGTGTAGTTAAGG 59.461 42.308 0.00 0.0 0.00 2.69
2492 2607 3.338249 AGCATGATTTCGCTACAGTTGT 58.662 40.909 0.00 0.0 36.50 3.32
3221 3355 6.498303 TGCTCAGGCTAAAGATCAAGGATATA 59.502 38.462 0.00 0.0 39.59 0.86
3241 3375 8.217799 GGATATAGATGGACACTAGCTATCTCT 58.782 40.741 0.00 0.0 31.19 3.10
3336 3472 0.537143 GGGTGACATGTGCAACCTGA 60.537 55.000 19.28 0.0 40.04 3.86
3617 3812 3.690460 TGTTTGCCCCAAATTGTTGTTT 58.310 36.364 0.00 0.0 35.74 2.83
3652 3858 2.292267 CATGCTGCCACTTTAGGTAGG 58.708 52.381 0.00 0.0 41.18 3.18
3655 3861 1.739067 CTGCCACTTTAGGTAGGTGC 58.261 55.000 0.00 0.0 37.69 5.01
3656 3862 1.279271 CTGCCACTTTAGGTAGGTGCT 59.721 52.381 0.00 0.0 37.69 4.40
3657 3863 2.500098 CTGCCACTTTAGGTAGGTGCTA 59.500 50.000 0.00 0.0 37.69 3.49
3658 3864 3.112263 TGCCACTTTAGGTAGGTGCTAT 58.888 45.455 0.00 0.0 0.00 2.97
3659 3865 3.118408 TGCCACTTTAGGTAGGTGCTATG 60.118 47.826 0.00 0.0 0.00 2.23
3660 3866 3.467803 CCACTTTAGGTAGGTGCTATGC 58.532 50.000 0.00 0.0 0.00 3.14
3661 3867 3.118408 CCACTTTAGGTAGGTGCTATGCA 60.118 47.826 0.00 0.0 35.60 3.96
3662 3868 4.122776 CACTTTAGGTAGGTGCTATGCAG 58.877 47.826 0.00 0.0 40.08 4.41
3663 3869 4.030913 ACTTTAGGTAGGTGCTATGCAGA 58.969 43.478 0.00 0.0 40.08 4.26
3664 3870 4.656112 ACTTTAGGTAGGTGCTATGCAGAT 59.344 41.667 0.00 0.0 40.08 2.90
3665 3871 4.607293 TTAGGTAGGTGCTATGCAGATG 57.393 45.455 0.00 0.0 40.08 2.90
3666 3872 2.402564 AGGTAGGTGCTATGCAGATGT 58.597 47.619 0.00 0.0 40.08 3.06
3754 4092 1.550524 TCACTCTCAACCTTCATCGGG 59.449 52.381 0.00 0.0 0.00 5.14
3777 4115 2.038295 CCTGCTCCCTATCCTTCACATC 59.962 54.545 0.00 0.0 0.00 3.06
3928 4269 2.236146 TGGCATTCCATACGAAGTCTGT 59.764 45.455 0.00 0.0 38.89 3.41
4134 4477 5.534654 TCACGAATTTGGGAAAAGAATCACT 59.465 36.000 0.00 0.0 0.00 3.41
4172 4516 8.180317 AGTTTGTGGATTTTTAAAAGTTCACG 57.820 30.769 22.66 0.0 0.00 4.35
4174 4518 7.979115 TTGTGGATTTTTAAAAGTTCACGAG 57.021 32.000 22.66 0.0 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
494 505 9.050601 TGCAAAATTTTATTGTTTCTTACTGGG 57.949 29.630 2.44 0.00 0.00 4.45
695 715 0.744874 CATCGGTCCACTACGGTCAT 59.255 55.000 0.00 0.00 35.57 3.06
896 927 4.319766 GCTGACGAAATTGTGACACTCATT 60.320 41.667 7.20 2.70 0.00 2.57
1054 1086 0.392998 GTGGTGAAGATGGTGCGGAT 60.393 55.000 0.00 0.00 0.00 4.18
1063 1095 1.630878 GAGAAGGGTGGTGGTGAAGAT 59.369 52.381 0.00 0.00 0.00 2.40
1282 1314 2.224233 CCGACGGTACTCTCTGATAGGA 60.224 54.545 5.48 0.00 0.00 2.94
1386 1418 0.828022 TCTCAGGACACACCACGTTT 59.172 50.000 0.00 0.00 42.04 3.60
1501 1533 6.003950 ACACATACAAGTAAGACAAGGCATT 58.996 36.000 0.00 0.00 0.00 3.56
1722 1754 4.819088 GGGAGCTCAATTATGGAGAAACTC 59.181 45.833 17.19 0.00 34.24 3.01
1791 1823 6.178607 AGATATACACCAGCAACATCATCA 57.821 37.500 0.00 0.00 0.00 3.07
1928 1960 5.189180 GGTTTATCAGGAGAGAAGCATTGT 58.811 41.667 0.00 0.00 29.11 2.71
1988 2020 1.106285 GAGGAATGTGCATTGACCCC 58.894 55.000 1.77 0.00 0.00 4.95
2720 2837 5.856126 TCTCGCAAAAAGAATAACGACAT 57.144 34.783 0.00 0.00 0.00 3.06
2724 2841 5.685841 TCCTTTCTCGCAAAAAGAATAACG 58.314 37.500 4.51 0.00 36.09 3.18
2728 2845 5.163754 CCGTATCCTTTCTCGCAAAAAGAAT 60.164 40.000 4.51 0.00 36.09 2.40
3206 3340 8.503428 AGTGTCCATCTATATCCTTGATCTTT 57.497 34.615 0.00 0.00 0.00 2.52
3221 3355 6.448369 AGTAGAGATAGCTAGTGTCCATCT 57.552 41.667 0.00 0.00 0.00 2.90
3241 3375 5.027460 TGGAGCTCCAGTTTATTGGTAGTA 58.973 41.667 32.00 2.41 42.01 1.82
3617 3812 2.894765 CAGCATGCATATGATTTGGGGA 59.105 45.455 21.98 0.00 36.36 4.81
3660 3866 3.754850 TCAATCAGGTTTGCAGACATCTG 59.245 43.478 9.87 8.31 46.40 2.90
3661 3867 4.008330 CTCAATCAGGTTTGCAGACATCT 58.992 43.478 9.87 0.00 0.00 2.90
3662 3868 3.755378 ACTCAATCAGGTTTGCAGACATC 59.245 43.478 9.87 0.00 0.00 3.06
3663 3869 3.759581 ACTCAATCAGGTTTGCAGACAT 58.240 40.909 9.87 0.00 0.00 3.06
3664 3870 3.213206 ACTCAATCAGGTTTGCAGACA 57.787 42.857 9.87 0.00 0.00 3.41
3665 3871 5.452777 GTTAACTCAATCAGGTTTGCAGAC 58.547 41.667 0.00 0.00 0.00 3.51
3666 3872 4.518970 GGTTAACTCAATCAGGTTTGCAGA 59.481 41.667 5.42 0.00 0.00 4.26
3754 4092 1.414550 GTGAAGGATAGGGAGCAGGTC 59.585 57.143 0.00 0.00 0.00 3.85
3777 4115 1.339610 CGGCTTGGATCCTGAGTAGAG 59.660 57.143 14.23 1.10 0.00 2.43
3928 4269 5.065602 GCAACTGTTGATTCAGCATCATCTA 59.934 40.000 23.81 0.00 41.82 1.98
3945 4286 1.928706 AAAACCACGCACGCAACTGT 61.929 50.000 0.00 0.00 0.00 3.55
4113 4456 6.012658 TCAGTGATTCTTTTCCCAAATTCG 57.987 37.500 0.00 0.00 0.00 3.34
4151 4494 7.090953 ACTCGTGAACTTTTAAAAATCCACA 57.909 32.000 18.21 7.47 0.00 4.17
4172 4516 3.375922 TGTCCGTGACCTTTTTCAAACTC 59.624 43.478 2.23 0.00 0.00 3.01
4174 4518 3.768468 TGTCCGTGACCTTTTTCAAAC 57.232 42.857 2.23 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.