Multiple sequence alignment - TraesCS6A01G297700

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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 TraesCS6A01G297700 chr6A 100.000 2997 0 0 1 2997 531061000 531058004 0.000000e+00 5535
1 TraesCS6A01G297700 chr7A 95.918 2915 91 11 1 2907 675349863 675352757 0.000000e+00 4698
2 TraesCS6A01G297700 chr5A 95.712 2915 107 13 1 2907 169176618 169179522 0.000000e+00 4674
3 TraesCS6A01G297700 chr5A 95.643 2915 112 12 1 2906 524683173 524680265 0.000000e+00 4665
4 TraesCS6A01G297700 chr5A 95.261 2912 121 13 4 2906 33912475 33909572 0.000000e+00 4597
5 TraesCS6A01G297700 chr5A 96.262 107 2 1 2891 2997 577982525 577982629 1.100000e-39 174
6 TraesCS6A01G297700 chr2A 95.604 2912 115 10 4 2906 614225526 614222619 0.000000e+00 4656
7 TraesCS6A01G297700 chr2A 95.341 2919 113 15 4 2906 733077883 733074972 0.000000e+00 4615
8 TraesCS6A01G297700 chr2A 96.396 111 2 2 2889 2997 603307424 603307534 6.600000e-42 182
9 TraesCS6A01G297700 chr1A 95.506 2915 111 16 3 2906 365638851 365635946 0.000000e+00 4639
10 TraesCS6A01G297700 chr4A 95.305 2918 115 17 4 2906 37336188 37333278 0.000000e+00 4610
11 TraesCS6A01G297700 chr3A 94.892 2917 130 14 1 2906 711570740 711573648 0.000000e+00 4543
12 TraesCS6A01G297700 chr3A 92.373 118 7 2 2881 2997 680255103 680255219 1.850000e-37 167
13 TraesCS6A01G297700 chr7D 97.143 105 2 1 2893 2997 556942016 556941913 3.070000e-40 176
14 TraesCS6A01G297700 chr5B 96.262 107 3 1 2891 2997 58347194 58347089 1.100000e-39 174
15 TraesCS6A01G297700 chr5B 91.803 122 6 4 2880 2997 694130934 694131055 1.850000e-37 167
16 TraesCS6A01G297700 chr2D 93.333 120 5 3 2880 2997 139972908 139973026 1.100000e-39 174
17 TraesCS6A01G297700 chr2D 92.437 119 5 4 2879 2997 429664609 429664723 1.850000e-37 167
18 TraesCS6A01G297700 chr3D 93.103 116 6 2 2882 2997 532329105 532329218 5.140000e-38 169


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 TraesCS6A01G297700 chr6A 531058004 531061000 2996 True 5535 5535 100.000 1 2997 1 chr6A.!!$R1 2996
1 TraesCS6A01G297700 chr7A 675349863 675352757 2894 False 4698 4698 95.918 1 2907 1 chr7A.!!$F1 2906
2 TraesCS6A01G297700 chr5A 169176618 169179522 2904 False 4674 4674 95.712 1 2907 1 chr5A.!!$F1 2906
3 TraesCS6A01G297700 chr5A 524680265 524683173 2908 True 4665 4665 95.643 1 2906 1 chr5A.!!$R2 2905
4 TraesCS6A01G297700 chr5A 33909572 33912475 2903 True 4597 4597 95.261 4 2906 1 chr5A.!!$R1 2902
5 TraesCS6A01G297700 chr2A 614222619 614225526 2907 True 4656 4656 95.604 4 2906 1 chr2A.!!$R1 2902
6 TraesCS6A01G297700 chr2A 733074972 733077883 2911 True 4615 4615 95.341 4 2906 1 chr2A.!!$R2 2902
7 TraesCS6A01G297700 chr1A 365635946 365638851 2905 True 4639 4639 95.506 3 2906 1 chr1A.!!$R1 2903
8 TraesCS6A01G297700 chr4A 37333278 37336188 2910 True 4610 4610 95.305 4 2906 1 chr4A.!!$R1 2902
9 TraesCS6A01G297700 chr3A 711570740 711573648 2908 False 4543 4543 94.892 1 2906 1 chr3A.!!$F2 2905

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
378 383 0.523519 GCTTTACACTGCCCTCTTGC 59.476 55.0 0.00 0.0 0.00 4.01 F
879 892 0.833949 GAGGGAGGCCTTTCACCTAG 59.166 60.0 6.77 0.0 37.77 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1650 1.308047 CCACTGTGCAACTGCTTACA 58.692 50.000 1.29 0.0 39.67 2.41 R
2716 2751 1.078426 AAGTACCATGACAGGCCGC 60.078 57.895 0.00 0.0 0.00 6.53 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
104 105 5.184287 TGTGATTTGCATTGATGAGTGTGAT 59.816 36.000 0.00 0.00 0.00 3.06
200 202 2.225091 TGGTTCACCAGAGAATTGCCAT 60.225 45.455 0.00 0.00 42.01 4.40
378 383 0.523519 GCTTTACACTGCCCTCTTGC 59.476 55.000 0.00 0.00 0.00 4.01
411 416 4.110482 GCATCACAAAGGAGCAAATGATC 58.890 43.478 0.00 0.00 0.00 2.92
428 433 4.216411 TGATCAAGCTACCAGGTAAACC 57.784 45.455 0.00 0.00 0.00 3.27
557 562 9.467258 CACACTGTTCTGTTTTCAATTTCATAT 57.533 29.630 0.00 0.00 0.00 1.78
685 695 6.969828 AAAGGAGTTAGTTGATTCGATGAC 57.030 37.500 0.00 0.00 0.00 3.06
803 813 6.687105 CACTGAGGTTTTCTGTAAGTTTTTCG 59.313 38.462 0.00 0.00 36.35 3.46
814 825 8.047413 TCTGTAAGTTTTTCGAAAACCTTCTT 57.953 30.769 29.37 24.74 33.52 2.52
879 892 0.833949 GAGGGAGGCCTTTCACCTAG 59.166 60.000 6.77 0.00 37.77 3.02
1181 1195 2.542595 GTCTGAAATCGTTCACGGTTGT 59.457 45.455 0.00 0.00 42.51 3.32
1269 1283 4.082026 GGTCTTCAATGTCAATTTGAGGGG 60.082 45.833 0.00 0.00 34.76 4.79
1274 1288 2.214376 TGTCAATTTGAGGGGCGAAT 57.786 45.000 0.00 0.00 31.73 3.34
1278 1292 1.106285 AATTTGAGGGGCGAATGCTC 58.894 50.000 0.00 0.00 42.57 4.26
1634 1650 2.276732 AAGTAGTTGCACACTGGCAT 57.723 45.000 10.59 0.00 44.48 4.40
1681 1699 7.228507 ACATAATGAGTTGCAGTAGAACACAAA 59.771 33.333 0.00 0.00 29.64 2.83
1683 1701 4.513442 TGAGTTGCAGTAGAACACAAACT 58.487 39.130 0.00 0.00 33.06 2.66
1758 1776 3.077484 AGGACATAAGCAGTTGCACAT 57.923 42.857 6.90 0.00 45.16 3.21
1896 1917 2.267961 GCCCAACTACGACCCCAG 59.732 66.667 0.00 0.00 0.00 4.45
1956 1977 2.179547 TCACCAGCGTGCACAACAG 61.180 57.895 18.64 4.96 40.04 3.16
2404 2437 2.613977 GCAGTGTGCTCTGTAGATTGGT 60.614 50.000 0.00 0.00 40.96 3.67
2489 2523 4.003584 TGCCCTACCCTTTGTAGTAGAT 57.996 45.455 0.00 0.00 44.66 1.98
2736 2771 0.249120 CGGCCTGTCATGGTACTTGA 59.751 55.000 0.00 0.00 0.00 3.02
2921 2958 4.793201 AGGTACTTGAAGGAAATATGCCC 58.207 43.478 0.00 0.00 27.25 5.36
2922 2959 4.478686 AGGTACTTGAAGGAAATATGCCCT 59.521 41.667 0.00 0.00 27.25 5.19
2923 2960 5.670361 AGGTACTTGAAGGAAATATGCCCTA 59.330 40.000 0.00 0.00 27.25 3.53
2924 2961 5.998363 GGTACTTGAAGGAAATATGCCCTAG 59.002 44.000 0.00 0.00 31.36 3.02
2925 2962 5.975988 ACTTGAAGGAAATATGCCCTAGA 57.024 39.130 0.00 0.00 31.36 2.43
2926 2963 5.934781 ACTTGAAGGAAATATGCCCTAGAG 58.065 41.667 0.00 0.00 31.36 2.43
2927 2964 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 1.895020 AATCACACCGGCTTCCGCTA 61.895 55.000 0.00 0.00 46.86 4.26
104 105 1.529010 CACAGCTGCTGGGTCCAAA 60.529 57.895 31.00 0.00 35.51 3.28
200 202 0.032952 GTTCTGCGCATATCGGGGTA 59.967 55.000 12.24 0.00 38.94 3.69
378 383 1.548081 TTGTGATGCCTGACCCAATG 58.452 50.000 0.00 0.00 0.00 2.82
411 416 3.751518 AGTTGGTTTACCTGGTAGCTTG 58.248 45.455 6.66 0.00 36.82 4.01
428 433 0.620556 ATGTAGGCTGTGGGGAGTTG 59.379 55.000 0.00 0.00 0.00 3.16
685 695 0.950836 TGACAACCATTGAACCAGCG 59.049 50.000 0.00 0.00 0.00 5.18
803 813 7.526142 AGATGAGGGTAAAAAGAAGGTTTTC 57.474 36.000 0.00 0.00 32.95 2.29
814 825 6.430000 GCTACAGAACAAAGATGAGGGTAAAA 59.570 38.462 0.00 0.00 0.00 1.52
879 892 5.453567 AAACATGGCTCAAAACTCCTTAC 57.546 39.130 0.00 0.00 0.00 2.34
1000 1014 1.202915 TCATGTGGGCACAACACTCAT 60.203 47.619 0.00 0.00 45.41 2.90
1054 1068 2.551032 CAGATGTGTCATGTGCAACTGT 59.449 45.455 12.25 0.00 38.04 3.55
1269 1283 2.738846 TCAAGAACTTCAGAGCATTCGC 59.261 45.455 0.00 0.00 38.99 4.70
1274 1288 4.375272 CTTGAGTCAAGAACTTCAGAGCA 58.625 43.478 25.83 0.00 43.42 4.26
1278 1292 3.497640 CCTGCTTGAGTCAAGAACTTCAG 59.502 47.826 32.39 26.04 43.42 3.02
1405 1420 7.066887 TGCTTCGGTACATCAATGTCAATAATT 59.933 33.333 0.00 0.00 41.97 1.40
1634 1650 1.308047 CCACTGTGCAACTGCTTACA 58.692 50.000 1.29 0.00 39.67 2.41
1806 1825 5.182950 CACTCATTACTGTAAAATGGGCACA 59.817 40.000 4.11 0.00 38.19 4.57
1807 1826 5.183140 ACACTCATTACTGTAAAATGGGCAC 59.817 40.000 4.11 0.00 38.19 5.01
1818 1839 3.857157 ACAACCCACACTCATTACTGT 57.143 42.857 0.00 0.00 0.00 3.55
1896 1917 4.223032 TCTTCCTGATGTTGAGTACTTCCC 59.777 45.833 0.00 0.00 31.60 3.97
1956 1977 3.645268 AACTTCCTCCATGGGGCGC 62.645 63.158 13.02 0.00 36.20 6.53
2404 2437 4.935352 AGAAAAACAAATGCAGCCAGTA 57.065 36.364 0.00 0.00 0.00 2.74
2489 2523 1.694169 GCCCAGGGATCCTCCAAGA 60.694 63.158 10.89 0.00 38.64 3.02
2541 2575 1.201429 CCTACTGCCCTGTTGGAGGT 61.201 60.000 0.80 0.00 40.87 3.85
2716 2751 1.078426 AAGTACCATGACAGGCCGC 60.078 57.895 0.00 0.00 0.00 6.53
2884 2920 2.701951 AGTACCTTCACCGACTCCAAAA 59.298 45.455 0.00 0.00 0.00 2.44
2918 2955 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19


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

AutoCloner maintained by Alex Coulton.