Multiple sequence alignment - TraesCS1D01G187200

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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 TraesCS1D01G187200 chr1D 100.000 3535 0 0 1 3535 258574676 258578210 0.000000e+00 6529.0
1 TraesCS1D01G187200 chr1D 77.612 402 78 7 1647 2039 258553659 258554057 2.120000e-57 233.0
2 TraesCS1D01G187200 chr1A 94.188 3097 104 37 485 3535 342394003 342390937 0.000000e+00 4652.0
3 TraesCS1D01G187200 chr1A 92.877 716 21 13 6 710 342395011 342394315 0.000000e+00 1013.0
4 TraesCS1D01G187200 chr1A 79.052 401 74 5 1647 2039 342434643 342434245 2.090000e-67 267.0
5 TraesCS1D01G187200 chr1B 92.678 1038 53 13 829 1850 354235426 354234396 0.000000e+00 1474.0
6 TraesCS1D01G187200 chr1B 96.879 833 22 3 2706 3535 354233251 354232420 0.000000e+00 1391.0
7 TraesCS1D01G187200 chr1B 95.017 883 26 8 1847 2712 354234288 354233407 0.000000e+00 1371.0
8 TraesCS1D01G187200 chr1B 95.718 724 23 5 4 720 354236174 354235452 0.000000e+00 1158.0
9 TraesCS1D01G187200 chr1B 78.358 402 75 7 1647 2039 354240235 354239837 2.110000e-62 250.0
10 TraesCS1D01G187200 chr2A 100.000 28 0 0 2703 2730 318377880 318377907 6.000000e-03 52.8


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 TraesCS1D01G187200 chr1D 258574676 258578210 3534 False 6529.0 6529 100.0000 1 3535 1 chr1D.!!$F2 3534
1 TraesCS1D01G187200 chr1A 342390937 342395011 4074 True 2832.5 4652 93.5325 6 3535 2 chr1A.!!$R2 3529
2 TraesCS1D01G187200 chr1B 354232420 354240235 7815 True 1128.8 1474 91.7300 4 3535 5 chr1B.!!$R1 3531

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
181 4243 0.539438 TAGCAAAGCAACCAGGTGGG 60.539 55.000 0.00 0.0 44.81 4.61 F
1080 5710 1.001974 TCAGCAAAGTGTCACCGCTAT 59.998 47.619 10.77 0.0 0.00 2.97 F
1126 5756 0.525761 CCCACCCAACACATTAAGCG 59.474 55.000 0.00 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1126 5756 0.035915 GTTGGAGCAGGAAGAGGACC 60.036 60.000 0.00 0.00 0.0 4.46 R
2151 6899 1.067212 GCATCAGGGTCGTACGAGATT 59.933 52.381 20.18 3.73 0.0 2.40 R
3101 8033 2.618709 CGGCTGTGTTTCTTTTTCTCCT 59.381 45.455 0.00 0.00 0.0 3.69 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
104 4163 5.000591 TGATTTTAGCACATGTTTCTCCGA 58.999 37.500 0.00 0.00 0.00 4.55
181 4243 0.539438 TAGCAAAGCAACCAGGTGGG 60.539 55.000 0.00 0.00 44.81 4.61
287 4349 1.278127 CCAAGAACACTACCGACCCAT 59.722 52.381 0.00 0.00 0.00 4.00
319 4381 2.989173 ATCCCCTCATTGGCCATGCG 62.989 60.000 6.09 2.02 32.13 4.73
448 4511 2.614057 CACACTTCTTCACCAACTCCAC 59.386 50.000 0.00 0.00 0.00 4.02
449 4512 2.505819 ACACTTCTTCACCAACTCCACT 59.494 45.455 0.00 0.00 0.00 4.00
511 4575 6.652900 GCAGGAGAGACAAGAATAGAGTTTTT 59.347 38.462 0.00 0.00 0.00 1.94
532 4596 5.900339 TTGTGAAGTACTAGAAAGCAACG 57.100 39.130 0.00 0.00 0.00 4.10
536 4600 4.202182 TGAAGTACTAGAAAGCAACGGTGT 60.202 41.667 0.66 0.00 0.00 4.16
658 4724 6.149973 CCACTTGCATCCACAGGTTATATATG 59.850 42.308 0.00 0.00 0.00 1.78
722 5056 9.700831 AAAATGGTTATAGCTCAAACCTAATCT 57.299 29.630 23.50 8.27 44.55 2.40
724 5058 9.780186 AATGGTTATAGCTCAAACCTAATCTAC 57.220 33.333 23.50 3.46 44.55 2.59
725 5059 8.313944 TGGTTATAGCTCAAACCTAATCTACA 57.686 34.615 23.50 5.48 44.55 2.74
726 5060 8.421784 TGGTTATAGCTCAAACCTAATCTACAG 58.578 37.037 23.50 0.00 44.55 2.74
727 5061 8.639761 GGTTATAGCTCAAACCTAATCTACAGA 58.360 37.037 18.50 0.00 41.63 3.41
728 5062 9.465985 GTTATAGCTCAAACCTAATCTACAGAC 57.534 37.037 0.00 0.00 0.00 3.51
729 5063 5.346181 AGCTCAAACCTAATCTACAGACC 57.654 43.478 0.00 0.00 0.00 3.85
730 5064 5.026790 AGCTCAAACCTAATCTACAGACCT 58.973 41.667 0.00 0.00 0.00 3.85
732 5066 6.841755 AGCTCAAACCTAATCTACAGACCTAT 59.158 38.462 0.00 0.00 0.00 2.57
733 5067 8.005388 AGCTCAAACCTAATCTACAGACCTATA 58.995 37.037 0.00 0.00 0.00 1.31
734 5068 8.808092 GCTCAAACCTAATCTACAGACCTATAT 58.192 37.037 0.00 0.00 0.00 0.86
793 5411 3.429085 GAACGCGAGATTCATTTTGCAT 58.571 40.909 15.93 0.00 0.00 3.96
795 5413 2.419673 ACGCGAGATTCATTTTGCATGA 59.580 40.909 15.93 0.00 0.00 3.07
796 5414 3.065786 ACGCGAGATTCATTTTGCATGAT 59.934 39.130 15.93 0.00 0.00 2.45
917 5540 8.722394 AGGAAAAGCTTAAGAGAAAATTACTCG 58.278 33.333 6.67 0.00 39.12 4.18
975 5598 4.724279 AAATTGGTGGTAGGTGAAGAGT 57.276 40.909 0.00 0.00 0.00 3.24
1080 5710 1.001974 TCAGCAAAGTGTCACCGCTAT 59.998 47.619 10.77 0.00 0.00 2.97
1087 5717 2.100197 AGTGTCACCGCTATTCAGCTA 58.900 47.619 0.00 0.00 46.26 3.32
1088 5718 2.099921 AGTGTCACCGCTATTCAGCTAG 59.900 50.000 0.00 0.00 46.26 3.42
1126 5756 0.525761 CCCACCCAACACATTAAGCG 59.474 55.000 0.00 0.00 0.00 4.68
1133 5763 2.615493 CCAACACATTAAGCGGTCCTCT 60.615 50.000 0.00 0.00 0.00 3.69
1162 5793 3.430862 CAACGCCACACATCCCCG 61.431 66.667 0.00 0.00 0.00 5.73
1292 5929 3.591835 CGGCAGCGGTTTTGGTGT 61.592 61.111 0.00 0.00 39.49 4.16
1293 5930 2.335011 GGCAGCGGTTTTGGTGTC 59.665 61.111 0.00 0.00 39.49 3.67
1294 5931 2.051345 GCAGCGGTTTTGGTGTCG 60.051 61.111 0.00 0.00 39.49 4.35
1296 5933 1.890041 CAGCGGTTTTGGTGTCGGA 60.890 57.895 0.00 0.00 32.82 4.55
1297 5934 1.890510 AGCGGTTTTGGTGTCGGAC 60.891 57.895 0.00 0.00 0.00 4.79
1298 5935 2.932905 CGGTTTTGGTGTCGGACG 59.067 61.111 3.34 0.00 0.00 4.79
1978 6726 1.067582 GCTCCGCGTTGCCTACTAT 59.932 57.895 4.92 0.00 0.00 2.12
2101 6849 1.692042 CCTCATGGCCCTCTCCACT 60.692 63.158 0.00 0.00 39.25 4.00
2151 6899 1.565390 CCTCAGCTCCCCCATTGTCA 61.565 60.000 0.00 0.00 0.00 3.58
2418 7182 4.129737 GCTACCACGAGCTCGCCA 62.130 66.667 34.83 16.50 44.43 5.69
2475 7239 0.689080 AGACAGGATCATCGGCACCT 60.689 55.000 0.00 0.00 0.00 4.00
2601 7365 4.516365 AGGAAGCAATGCTGAAGAAAAG 57.484 40.909 9.14 0.00 39.62 2.27
2608 7372 7.458409 AGCAATGCTGAAGAAAAGAAGATTA 57.542 32.000 7.07 0.00 37.57 1.75
2692 7457 4.670621 GCATTTAGTGTGTTTGTTCACTCG 59.329 41.667 1.08 0.00 42.77 4.18
2814 7744 6.663944 ACTGTACAAACAAACTGAAGAGAC 57.336 37.500 0.00 0.00 34.49 3.36
2817 7747 4.622701 ACAAACAAACTGAAGAGACTGC 57.377 40.909 0.00 0.00 0.00 4.40
2989 7919 5.048782 GCTATGATCTAGACTCACTCACAGG 60.049 48.000 0.00 0.00 0.00 4.00
3006 7938 1.948834 CAGGCTCATGACACAACACAA 59.051 47.619 0.00 0.00 0.00 3.33
3445 8377 2.114670 CGACGGAAATGGGCTGCAT 61.115 57.895 0.50 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 4163 8.562949 TGCTTATCCTTCCTAGGTTATTTACT 57.437 34.615 9.08 0.00 42.60 2.24
181 4243 1.600916 GTCAAGGTGCACCACTCCC 60.601 63.158 36.39 16.58 38.89 4.30
287 4349 0.399949 AGGGGATGACGATGGCCTTA 60.400 55.000 3.32 0.00 0.00 2.69
319 4381 0.664166 CAACAATGGCGACCTGTTGC 60.664 55.000 17.45 0.65 42.52 4.17
448 4511 3.103793 CGTAGTCCGTCAAATTTGCAG 57.896 47.619 13.54 9.17 0.00 4.41
482 4546 1.270907 TTCTTGTCTCTCCTGCCTCC 58.729 55.000 0.00 0.00 0.00 4.30
511 4575 4.202182 ACCGTTGCTTTCTAGTACTTCACA 60.202 41.667 0.00 0.00 0.00 3.58
532 4596 6.183360 TGTCTTACAAATGGTTTACACACACC 60.183 38.462 0.00 0.00 0.00 4.16
536 4600 7.809546 TGATGTCTTACAAATGGTTTACACA 57.190 32.000 0.00 0.00 0.00 3.72
666 4734 9.739276 TTAATGATAATCAAAACACTCAGGTCT 57.261 29.630 0.00 0.00 0.00 3.85
727 5061 9.498176 GGGAAATGTAAAACGACATATATAGGT 57.502 33.333 0.00 0.00 39.16 3.08
728 5062 9.496873 TGGGAAATGTAAAACGACATATATAGG 57.503 33.333 0.00 0.00 39.16 2.57
730 5064 9.833917 TGTGGGAAATGTAAAACGACATATATA 57.166 29.630 0.00 0.00 39.16 0.86
732 5066 7.606839 TGTGTGGGAAATGTAAAACGACATATA 59.393 33.333 0.00 0.00 39.16 0.86
733 5067 6.431543 TGTGTGGGAAATGTAAAACGACATAT 59.568 34.615 0.00 0.00 39.16 1.78
734 5068 5.763698 TGTGTGGGAAATGTAAAACGACATA 59.236 36.000 0.00 0.00 39.16 2.29
735 5069 4.580995 TGTGTGGGAAATGTAAAACGACAT 59.419 37.500 0.00 0.00 41.92 3.06
746 5364 1.608055 TGCTCTGTGTGTGGGAAATG 58.392 50.000 0.00 0.00 0.00 2.32
825 5443 6.166984 AGAATTTCTATCATGCTCCGAGAA 57.833 37.500 0.00 0.00 0.00 2.87
861 5482 7.671398 ACAAAATAATGTTGGAGGAGAACAGAT 59.329 33.333 0.00 0.00 36.77 2.90
917 5540 1.004918 AAGCACGCCTGACAGGTAC 60.005 57.895 22.58 9.76 37.80 3.34
1088 5718 1.202545 GGTACTGGGCTAAGCTAGTGC 60.203 57.143 0.00 0.00 40.05 4.40
1126 5756 0.035915 GTTGGAGCAGGAAGAGGACC 60.036 60.000 0.00 0.00 0.00 4.46
1133 5763 1.896660 GGCGTTGTTGGAGCAGGAA 60.897 57.895 0.00 0.00 0.00 3.36
1162 5793 4.040461 TCTGGGATCCTTATCGAAATGGAC 59.960 45.833 12.58 0.00 32.44 4.02
1292 5929 2.016171 CATGCATGCATTCGTCCGA 58.984 52.632 30.32 0.00 33.90 4.55
1293 5930 4.601315 CATGCATGCATTCGTCCG 57.399 55.556 30.32 14.35 33.90 4.79
1737 6374 2.060980 GCGAGGTCCTGGATGTCCT 61.061 63.158 4.84 1.12 36.82 3.85
1969 6717 2.106131 CACGGCGCATAGTAGGCA 59.894 61.111 10.83 0.00 0.00 4.75
2012 6760 4.052518 GGAGGTGGGCAGCCATGT 62.053 66.667 15.19 0.00 0.00 3.21
2050 6798 2.856988 AGGGCGTTGGGGAAGGAA 60.857 61.111 0.00 0.00 0.00 3.36
2151 6899 1.067212 GCATCAGGGTCGTACGAGATT 59.933 52.381 20.18 3.73 0.00 2.40
2418 7182 3.260100 CAGGAAGTGCCCCACCCT 61.260 66.667 0.00 0.00 37.37 4.34
2601 7365 4.417426 TGGAACGGAGGGAATAATCTTC 57.583 45.455 0.00 0.00 0.00 2.87
2608 7372 7.351166 TCTTATAATTTTGGAACGGAGGGAAT 58.649 34.615 0.00 0.00 0.00 3.01
2667 7431 3.728718 GTGAACAAACACACTAAATGCGG 59.271 43.478 0.00 0.00 40.11 5.69
2692 7457 3.782046 ACGGACTACATACATGCTGAAC 58.218 45.455 3.07 0.00 0.00 3.18
2732 7661 6.500589 TTTCCTCCCTTCACTATCATAAGG 57.499 41.667 0.00 0.00 39.63 2.69
2738 7668 4.156455 TGCATTTCCTCCCTTCACTATC 57.844 45.455 0.00 0.00 0.00 2.08
2814 7744 7.544915 CCTGATGATATATAGATTATGCCGCAG 59.455 40.741 0.00 0.00 0.00 5.18
2817 7747 7.326454 CCCCTGATGATATATAGATTATGCCG 58.674 42.308 0.00 0.00 0.00 5.69
2989 7919 5.808042 ATCTATTGTGTTGTGTCATGAGC 57.192 39.130 0.00 0.00 0.00 4.26
3006 7938 9.587772 GTATTGTAACATTCGGCTCATATCTAT 57.412 33.333 0.00 0.00 0.00 1.98
3101 8033 2.618709 CGGCTGTGTTTCTTTTTCTCCT 59.381 45.455 0.00 0.00 0.00 3.69
3343 8275 1.900351 CTCCGAGGTGCAATCTCCA 59.100 57.895 11.34 0.53 0.00 3.86


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

AutoCloner maintained by Alex Coulton.