Multiple sequence alignment - TraesCS1A01G097100

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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 TraesCS1A01G097100 chr1A 100.000 5094 0 0 1 5094 93398347 93393254 0.000000e+00 9407
1 TraesCS1A01G097100 chr1D 96.791 2337 54 8 947 3280 97917494 97915176 0.000000e+00 3880
2 TraesCS1A01G097100 chr1D 93.842 1624 63 14 3280 4895 97915055 97913461 0.000000e+00 2410
3 TraesCS1A01G097100 chr1D 90.899 934 32 19 1 912 97918592 97917690 0.000000e+00 1205
4 TraesCS1A01G097100 chr1D 85.217 230 15 9 4878 5094 97913450 97913227 8.590000e-53 219
5 TraesCS1A01G097100 chr1B 95.686 1808 55 6 944 2740 155411715 155413510 0.000000e+00 2885
6 TraesCS1A01G097100 chr1B 94.811 1137 39 10 3275 4406 155425088 155426209 0.000000e+00 1755
7 TraesCS1A01G097100 chr1B 94.805 924 34 5 1 919 155410443 155411357 0.000000e+00 1428
8 TraesCS1A01G097100 chr1B 94.134 699 14 11 4399 5094 155429437 155430111 0.000000e+00 1038
9 TraesCS1A01G097100 chr1B 97.619 546 13 0 2735 3280 155424426 155424971 0.000000e+00 937


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 TraesCS1A01G097100 chr1A 93393254 93398347 5093 True 9407.000000 9407 100.000000 1 5094 1 chr1A.!!$R1 5093
1 TraesCS1A01G097100 chr1D 97913227 97918592 5365 True 1928.500000 3880 91.687250 1 5094 4 chr1D.!!$R1 5093
2 TraesCS1A01G097100 chr1B 155410443 155413510 3067 False 2156.500000 2885 95.245500 1 2740 2 chr1B.!!$F1 2739
3 TraesCS1A01G097100 chr1B 155424426 155430111 5685 False 1243.333333 1755 95.521333 2735 5094 3 chr1B.!!$F2 2359

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
919 945 0.252558 TGAACCAGGTACCTCCTCCC 60.253 60.000 12.84 1.15 46.24 4.30 F
1000 1359 0.458197 CTGCTCCGCTCTTGTCTGAG 60.458 60.000 0.00 0.00 37.16 3.35 F
1945 2307 0.909623 ATACACCGGTCCTGGAAAGG 59.090 55.000 2.59 14.89 0.00 3.11 F
1956 2318 2.512056 TCCTGGAAAGGAAACTGTGGAA 59.488 45.455 0.00 0.00 42.68 3.53 F
2858 3228 2.851263 TGGAGTTACCAAGTGCGAAT 57.149 45.000 0.00 0.00 46.75 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2318 1.542492 CTTGGCCAGCTCTGAAACAT 58.458 50.000 5.11 0.00 0.00 2.71 R
2638 3008 2.843701 ACAAGAGTGCAAGGTCTTCAG 58.156 47.619 4.61 0.00 30.31 3.02 R
3099 3469 3.079478 TGAGCTCTGCTGGCCGAT 61.079 61.111 16.19 0.00 39.88 4.18 R
3933 4427 4.595350 GGGATAGAGGAAAAGCTGATACCT 59.405 45.833 0.00 0.00 0.00 3.08 R
4449 8182 0.323451 GCTGGGAGGGGTTAACCAAG 60.323 60.000 25.71 13.03 42.91 3.61 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
218 220 5.348724 GTCGTCTAATGCAAGAACAAGATCA 59.651 40.000 0.00 0.00 0.00 2.92
273 294 6.327154 CAATGCAAGCAATCAGAGAACATTA 58.673 36.000 0.00 0.00 0.00 1.90
688 711 2.430694 GCTCTTCTCTTCCTCTTCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
735 758 1.228429 CTTCCTTTTGGGCCGGTGA 60.228 57.895 1.90 0.00 40.87 4.02
919 945 0.252558 TGAACCAGGTACCTCCTCCC 60.253 60.000 12.84 1.15 46.24 4.30
974 1333 1.804326 CAGTCTACGAAACCCGCCG 60.804 63.158 0.00 0.00 43.32 6.46
1000 1359 0.458197 CTGCTCCGCTCTTGTCTGAG 60.458 60.000 0.00 0.00 37.16 3.35
1297 1656 2.093235 CCTGCAAAGGTTGTCCCAAAAA 60.093 45.455 0.00 0.00 34.66 1.94
1392 1751 8.383175 ACGGTATCATGGGATTTAGTTGATTAT 58.617 33.333 0.00 0.00 34.89 1.28
1393 1752 9.884636 CGGTATCATGGGATTTAGTTGATTATA 57.115 33.333 0.00 0.00 34.89 0.98
1538 1897 4.992951 AGCTTTTTGTTTGATGGCTGATTC 59.007 37.500 0.00 0.00 0.00 2.52
1945 2307 0.909623 ATACACCGGTCCTGGAAAGG 59.090 55.000 2.59 14.89 0.00 3.11
1956 2318 2.512056 TCCTGGAAAGGAAACTGTGGAA 59.488 45.455 0.00 0.00 42.68 3.53
2045 2407 6.112734 ACATATTGCGAATAACTTGTGAGGA 58.887 36.000 0.00 0.00 0.00 3.71
2207 2569 8.368668 TGTTAAAGAAACTCTCTTAGCTTAGCT 58.631 33.333 12.67 12.67 44.00 3.32
2319 2681 7.098477 TGGCATTTTCTCTGTAAATTTGGATG 58.902 34.615 0.00 0.00 0.00 3.51
2638 3008 7.490962 TGCTGTACATATTAGTGTATTTGGC 57.509 36.000 0.00 0.00 36.98 4.52
2670 3040 4.295870 TGCACTCTTGTAGTTGTTAGTCG 58.704 43.478 0.00 0.00 35.76 4.18
2723 3093 4.002982 GGAACACAGATCATGCAACACTA 58.997 43.478 0.00 0.00 0.00 2.74
2858 3228 2.851263 TGGAGTTACCAAGTGCGAAT 57.149 45.000 0.00 0.00 46.75 3.34
2891 3261 5.192176 TGTCTTCCTGTGCATGCATTATTA 58.808 37.500 25.64 8.99 0.00 0.98
3099 3469 5.307976 TGATGAAGAGGAGTTTGGAGAGAAA 59.692 40.000 0.00 0.00 0.00 2.52
3933 4427 3.631087 CCTGGACTTCATTCTAGGAGGGA 60.631 52.174 0.00 0.00 45.10 4.20
3946 4440 2.852130 AGGAGGGAGGTATCAGCTTTT 58.148 47.619 0.00 0.00 0.00 2.27
3947 4441 2.774809 AGGAGGGAGGTATCAGCTTTTC 59.225 50.000 0.00 0.00 0.00 2.29
3948 4442 2.158740 GGAGGGAGGTATCAGCTTTTCC 60.159 54.545 0.00 0.00 0.00 3.13
3949 4443 2.774809 GAGGGAGGTATCAGCTTTTCCT 59.225 50.000 0.00 0.00 0.00 3.36
3950 4444 2.774809 AGGGAGGTATCAGCTTTTCCTC 59.225 50.000 12.75 12.75 42.53 3.71
3951 4445 2.774809 GGGAGGTATCAGCTTTTCCTCT 59.225 50.000 17.68 0.00 42.76 3.69
3952 4446 3.967987 GGGAGGTATCAGCTTTTCCTCTA 59.032 47.826 17.68 0.00 42.76 2.43
3978 4472 8.893563 TCCCAATATGATAGTCTTTGGTTTTT 57.106 30.769 2.84 0.00 36.02 1.94
3996 4490 5.465056 GGTTTTTCGAGGAAATGCATTGAAA 59.535 36.000 13.82 14.25 38.52 2.69
3997 4491 6.346838 GGTTTTTCGAGGAAATGCATTGAAAG 60.347 38.462 13.82 4.40 40.58 2.62
3998 4492 4.439305 TTCGAGGAAATGCATTGAAAGG 57.561 40.909 13.82 3.31 28.26 3.11
4046 4540 5.929058 AATAGATCAGTGCTGAAGTGAGA 57.071 39.130 5.95 0.00 41.59 3.27
4092 4586 6.519679 TTGGTAGTAAAGATAAGCTCGTGA 57.480 37.500 0.00 0.00 0.00 4.35
4094 4588 7.108841 TGGTAGTAAAGATAAGCTCGTGAAT 57.891 36.000 0.00 0.00 0.00 2.57
4123 4617 2.032528 CCTTGTTCAGGCCGCTCA 59.967 61.111 0.00 0.00 35.13 4.26
4137 4631 2.226437 GCCGCTCAATCAAGTTTTCTCA 59.774 45.455 0.00 0.00 0.00 3.27
4264 4763 4.189231 TCTTAGATTGCGCCCTTACTTTC 58.811 43.478 4.18 0.00 0.00 2.62
4289 4788 3.693807 ACAGATGTGCATCTCCATTTGT 58.306 40.909 11.38 5.64 45.78 2.83
4300 4799 3.221771 TCTCCATTTGTGTCACCAAAGG 58.778 45.455 4.99 4.99 37.71 3.11
4362 4861 2.616842 CTCACCACGTTAGGCTTTGTTT 59.383 45.455 0.00 0.00 0.00 2.83
4376 4875 0.818296 TTGTTTGGTTTGTCGGGTGG 59.182 50.000 0.00 0.00 0.00 4.61
4379 4878 1.096386 TTTGGTTTGTCGGGTGGTCG 61.096 55.000 0.00 0.00 0.00 4.79
4449 8182 3.515104 TCAATCCCTCCCTGAATTTTTGC 59.485 43.478 0.00 0.00 0.00 3.68
4591 8324 7.907389 AGATAACCAGTCAGAATCAAGTACAA 58.093 34.615 0.00 0.00 0.00 2.41
4754 8489 6.813152 TGGCAAAGAATTTTGAATAGCTAAGC 59.187 34.615 0.00 0.00 45.21 3.09
5073 8853 2.550978 CAGTTGGAACATACCCTAGCG 58.449 52.381 0.00 0.00 39.30 4.26
5079 8859 3.262405 TGGAACATACCCTAGCGAAACTT 59.738 43.478 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 220 1.992557 TGAAATGGGCTCCACTTAGGT 59.007 47.619 0.00 0.00 35.80 3.08
273 294 1.494824 GCGTTCGTTTGTAGGTCAGT 58.505 50.000 0.00 0.00 0.00 3.41
487 508 4.489771 CGCCCAGGAATCCCGCTT 62.490 66.667 0.00 0.00 37.58 4.68
688 711 1.464734 TGTGAGCCGACCTAGAAGAG 58.535 55.000 0.00 0.00 0.00 2.85
735 758 7.500892 AGATCATATACGAGCCGAGAATCTTAT 59.499 37.037 0.00 0.00 0.00 1.73
793 816 3.119919 ACGTCGACTATTTCTTTCGAGCT 60.120 43.478 14.70 0.00 42.16 4.09
893 919 2.099427 GAGGTACCTGGTTCAGACGATC 59.901 54.545 22.10 0.00 32.44 3.69
1239 1598 1.828979 TGGGTGCGAATTTAAGTCCC 58.171 50.000 0.00 0.00 0.00 4.46
1297 1656 9.141400 GAAAATCTAGACAGAAGAAACATACGT 57.859 33.333 0.00 0.00 33.50 3.57
1343 1702 3.019564 CCTGCCCATCTAGAAAACCTTG 58.980 50.000 0.00 0.00 0.00 3.61
1392 1751 2.832129 CAGGCTCCCTGTAGACAGTTTA 59.168 50.000 8.78 0.00 45.82 2.01
1393 1752 1.625818 CAGGCTCCCTGTAGACAGTTT 59.374 52.381 8.78 0.00 45.82 2.66
1719 2078 8.926092 AAGATTTAGAACTTAAGAGGTGCTTT 57.074 30.769 10.09 0.00 38.05 3.51
1956 2318 1.542492 CTTGGCCAGCTCTGAAACAT 58.458 50.000 5.11 0.00 0.00 2.71
2045 2407 6.546034 ACATGAAGCCTTGTAAGTTACAGTTT 59.454 34.615 15.06 9.39 40.24 2.66
2191 2553 6.663523 AGAAGAAAGAGCTAAGCTAAGAGAGT 59.336 38.462 0.00 0.00 39.88 3.24
2461 2823 7.737311 GTGGAACGTTTAACTAAACATAGAACG 59.263 37.037 0.46 0.00 44.29 3.95
2628 2998 3.366374 GCAAGGTCTTCAGCCAAATACAC 60.366 47.826 0.00 0.00 0.00 2.90
2638 3008 2.843701 ACAAGAGTGCAAGGTCTTCAG 58.156 47.619 4.61 0.00 30.31 3.02
2670 3040 3.565063 AGTGAAACAAAATTGCAATGCCC 59.435 39.130 13.82 0.00 41.43 5.36
2744 3114 5.887214 AAGGGTGTTAAAGCTCCAAAAAT 57.113 34.783 0.00 0.00 0.00 1.82
2746 3116 4.959839 AGAAAGGGTGTTAAAGCTCCAAAA 59.040 37.500 0.00 0.00 0.00 2.44
2858 3228 5.499313 TGCACAGGAAGACATTCATATTGA 58.501 37.500 0.00 0.00 37.15 2.57
3099 3469 3.079478 TGAGCTCTGCTGGCCGAT 61.079 61.111 16.19 0.00 39.88 4.18
3256 3626 7.633193 TTTAAAAGGTTCAAGCAGTTAGACA 57.367 32.000 0.00 0.00 0.00 3.41
3933 4427 4.595350 GGGATAGAGGAAAAGCTGATACCT 59.405 45.833 0.00 0.00 0.00 3.08
3946 4440 9.040259 CAAAGACTATCATATTGGGATAGAGGA 57.960 37.037 14.43 0.00 44.47 3.71
3947 4441 8.263640 CCAAAGACTATCATATTGGGATAGAGG 58.736 40.741 14.43 6.08 44.47 3.69
3948 4442 8.820831 ACCAAAGACTATCATATTGGGATAGAG 58.179 37.037 14.43 0.00 44.47 2.43
3949 4443 8.742125 ACCAAAGACTATCATATTGGGATAGA 57.258 34.615 14.43 0.00 44.47 1.98
3950 4444 9.799106 AAACCAAAGACTATCATATTGGGATAG 57.201 33.333 7.65 7.65 46.19 2.08
3952 4446 9.492730 AAAAACCAAAGACTATCATATTGGGAT 57.507 29.630 7.65 0.00 43.77 3.85
3978 4472 3.420893 ACCTTTCAATGCATTTCCTCGA 58.579 40.909 9.83 0.22 0.00 4.04
3996 4490 6.014242 TCACTGACTGATCAATTCAACTACCT 60.014 38.462 7.82 0.00 33.30 3.08
3997 4491 6.091441 GTCACTGACTGATCAATTCAACTACC 59.909 42.308 1.58 0.00 33.30 3.18
3998 4492 6.646653 TGTCACTGACTGATCAATTCAACTAC 59.353 38.462 10.54 6.69 33.30 2.73
4046 4540 2.418368 TGCGACTTTATGCCATTCCT 57.582 45.000 0.00 0.00 0.00 3.36
4092 4586 5.528320 CCTGAACAAGGCACAAAAATCAATT 59.472 36.000 0.00 0.00 39.93 2.32
4094 4588 4.440880 CCTGAACAAGGCACAAAAATCAA 58.559 39.130 0.00 0.00 39.93 2.57
4123 4617 8.624776 CCTTCACTTTACTGAGAAAACTTGATT 58.375 33.333 0.00 0.00 0.00 2.57
4137 4631 7.393234 TGCAAATATAAGCACCTTCACTTTACT 59.607 33.333 0.00 0.00 35.51 2.24
4244 4743 3.054655 AGGAAAGTAAGGGCGCAATCTAA 60.055 43.478 10.83 0.00 0.00 2.10
4251 4750 2.007608 CTGTTAGGAAAGTAAGGGCGC 58.992 52.381 0.00 0.00 0.00 6.53
4289 4788 1.827789 GGCTGTGCCTTTGGTGACA 60.828 57.895 0.73 0.00 46.69 3.58
4300 4799 5.688621 CACATCACATTATAATTGGCTGTGC 59.311 40.000 13.10 0.00 37.66 4.57
4362 4861 2.109387 CGACCACCCGACAAACCA 59.891 61.111 0.00 0.00 0.00 3.67
4376 4875 2.047179 GGGTGAGGAAGTGGCGAC 60.047 66.667 0.00 0.00 0.00 5.19
4379 4878 0.681243 GGAATGGGTGAGGAAGTGGC 60.681 60.000 0.00 0.00 0.00 5.01
4415 8148 4.413851 GGGAGGGATTGAGGAGAATTTAGT 59.586 45.833 0.00 0.00 0.00 2.24
4449 8182 0.323451 GCTGGGAGGGGTTAACCAAG 60.323 60.000 25.71 13.03 42.91 3.61
4572 8305 5.997746 TCCTTTTGTACTTGATTCTGACTGG 59.002 40.000 0.00 0.00 0.00 4.00
4754 8489 1.349234 TTGTGCAGATGATGACGACG 58.651 50.000 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.