Multiple sequence alignment - TraesCS6A01G206100

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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 TraesCS6A01G206100 chr6A 100.000 4002 0 0 1 4002 362227353 362223352 0.000000e+00 7391.0
1 TraesCS6A01G206100 chr6A 98.683 835 11 0 1 835 221349702 221350536 0.000000e+00 1482.0
2 TraesCS6A01G206100 chr6A 97.488 836 21 0 1 836 324267865 324267030 0.000000e+00 1428.0
3 TraesCS6A01G206100 chr6A 97.488 836 21 0 1 836 324279916 324279081 0.000000e+00 1428.0
4 TraesCS6A01G206100 chr6A 97.665 771 17 1 66 836 223558513 223557744 0.000000e+00 1323.0
5 TraesCS6A01G206100 chr6A 93.415 820 48 4 1 819 576232522 576233336 0.000000e+00 1210.0
6 TraesCS6A01G206100 chr6D 97.302 3187 63 9 836 4002 246436068 246439251 0.000000e+00 5387.0
7 TraesCS6A01G206100 chr6B 94.507 3186 141 10 836 4002 402213273 402210103 0.000000e+00 4883.0
8 TraesCS6A01G206100 chr3A 97.485 835 18 1 1 835 83737107 83737938 0.000000e+00 1423.0
9 TraesCS6A01G206100 chr5A 95.352 839 21 8 1 838 672038024 672037203 0.000000e+00 1317.0
10 TraesCS6A01G206100 chr7D 89.206 806 72 11 1 803 110570508 110571301 0.000000e+00 992.0
11 TraesCS6A01G206100 chr2A 87.194 859 89 17 1 850 84148069 84147223 0.000000e+00 957.0
12 TraesCS6A01G206100 chr7A 90.000 60 6 0 3088 3147 611559705 611559764 1.190000e-10 78.7


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 TraesCS6A01G206100 chr6A 362223352 362227353 4001 True 7391 7391 100.000 1 4002 1 chr6A.!!$R4 4001
1 TraesCS6A01G206100 chr6A 221349702 221350536 834 False 1482 1482 98.683 1 835 1 chr6A.!!$F1 834
2 TraesCS6A01G206100 chr6A 324267030 324267865 835 True 1428 1428 97.488 1 836 1 chr6A.!!$R2 835
3 TraesCS6A01G206100 chr6A 324279081 324279916 835 True 1428 1428 97.488 1 836 1 chr6A.!!$R3 835
4 TraesCS6A01G206100 chr6A 223557744 223558513 769 True 1323 1323 97.665 66 836 1 chr6A.!!$R1 770
5 TraesCS6A01G206100 chr6A 576232522 576233336 814 False 1210 1210 93.415 1 819 1 chr6A.!!$F2 818
6 TraesCS6A01G206100 chr6D 246436068 246439251 3183 False 5387 5387 97.302 836 4002 1 chr6D.!!$F1 3166
7 TraesCS6A01G206100 chr6B 402210103 402213273 3170 True 4883 4883 94.507 836 4002 1 chr6B.!!$R1 3166
8 TraesCS6A01G206100 chr3A 83737107 83737938 831 False 1423 1423 97.485 1 835 1 chr3A.!!$F1 834
9 TraesCS6A01G206100 chr5A 672037203 672038024 821 True 1317 1317 95.352 1 838 1 chr5A.!!$R1 837
10 TraesCS6A01G206100 chr7D 110570508 110571301 793 False 992 992 89.206 1 803 1 chr7D.!!$F1 802
11 TraesCS6A01G206100 chr2A 84147223 84148069 846 True 957 957 87.194 1 850 1 chr2A.!!$R1 849

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
101 102 0.812412 GCCATGTATTACGCCCGTGT 60.812 55.000 3.22 0.0 0.00 4.49 F
144 145 0.904865 TCCAGCAGGAATCACCGTCT 60.905 55.000 0.00 0.0 42.23 4.18 F
1346 1356 3.735746 GCAAAATCTTTCCACAAACCGAG 59.264 43.478 0.00 0.0 0.00 4.63 F
1853 1863 0.037447 TCCGCAAATGTGGGTCATGA 59.963 50.000 12.77 0.0 45.45 3.07 F
2876 2910 1.747709 ATCTCATGCCTCTGTTGTGC 58.252 50.000 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1346 1356 1.876156 CAGGTTGAACTGCTTCTGGTC 59.124 52.381 0.00 0.0 0.00 4.02 R
1853 1863 3.266510 TGGATGCAATAGCTTCGACTT 57.733 42.857 0.00 0.0 43.69 3.01 R
2439 2473 0.167470 CAGGTGCATTCTGTTCGCAG 59.833 55.000 10.68 0.0 46.29 5.18 R
2923 2957 0.753262 GCTCTCCTTTCGCCATCCTA 59.247 55.000 0.00 0.0 0.00 2.94 R
3835 3881 7.099120 AGCTTTGAAGATCTTTGTGTGTTTTT 58.901 30.769 9.87 0.0 0.00 1.94 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
101 102 0.812412 GCCATGTATTACGCCCGTGT 60.812 55.000 3.22 0.00 0.00 4.49
144 145 0.904865 TCCAGCAGGAATCACCGTCT 60.905 55.000 0.00 0.00 42.23 4.18
871 881 7.110155 TGATAACTTGGTTAAAGATGGAGACC 58.890 38.462 0.00 0.00 39.38 3.85
1346 1356 3.735746 GCAAAATCTTTCCACAAACCGAG 59.264 43.478 0.00 0.00 0.00 4.63
1483 1493 8.868916 GTGATCTCAGTGAGAAGAAAATAAGTC 58.131 37.037 26.06 14.90 42.27 3.01
1766 1776 4.359434 TGCATCAACACACTTTAGGGTA 57.641 40.909 0.00 0.00 0.00 3.69
1853 1863 0.037447 TCCGCAAATGTGGGTCATGA 59.963 50.000 12.77 0.00 45.45 3.07
1874 1884 3.482156 AGTCGAAGCTATTGCATCCAT 57.518 42.857 1.12 0.00 42.74 3.41
1879 1889 4.067896 CGAAGCTATTGCATCCATAACCT 58.932 43.478 1.12 0.00 42.74 3.50
1885 1895 6.270000 AGCTATTGCATCCATAACCTGTAGTA 59.730 38.462 1.12 0.00 42.74 1.82
2105 2115 2.480416 CGACTGGACCTATCTGCACTTC 60.480 54.545 0.00 0.00 0.00 3.01
2195 2229 2.379972 AGGTTCAGAGATCCGATCGTT 58.620 47.619 15.09 0.27 0.00 3.85
2261 2295 7.215789 ACAATAACCAACAAGATGCATGAAAA 58.784 30.769 2.46 0.00 0.00 2.29
2439 2473 3.129113 TGCTGGCACAACATGATAATGTC 59.871 43.478 0.00 0.00 38.70 3.06
2501 2535 2.072366 CTGGAAACGGTTACCCCCT 58.928 57.895 0.00 0.00 0.00 4.79
2518 2552 2.489437 CCCCTCTTTGAACCGGGTTTTA 60.489 50.000 14.69 3.77 34.81 1.52
2876 2910 1.747709 ATCTCATGCCTCTGTTGTGC 58.252 50.000 0.00 0.00 0.00 4.57
2923 2957 3.329889 TGGATCAGCAGCCCGGTT 61.330 61.111 0.00 0.00 0.00 4.44
3015 3049 0.949105 TTCTGAGCGCGTTTTCCCTC 60.949 55.000 8.43 4.99 0.00 4.30
3075 3110 0.250467 GCTTGTGCTCCCTCTGTTCA 60.250 55.000 0.00 0.00 36.03 3.18
3159 3194 1.927174 CAGCGACAGGTAATTCCGAAG 59.073 52.381 0.00 0.00 41.99 3.79
3264 3299 3.245052 GCCCTAGGTCCTGCATGAATTAT 60.245 47.826 8.29 0.00 0.00 1.28
3366 3405 0.232303 GTGCTTTGAACGGTGTCTCG 59.768 55.000 0.00 0.00 0.00 4.04
3392 3431 5.007724 GGGTGTTTTGTTACTTCTGTCTGAG 59.992 44.000 0.00 0.00 0.00 3.35
3581 3622 6.373779 AGATTTATGAAAAGTGCGTGAACAG 58.626 36.000 0.00 0.00 0.00 3.16
3960 4006 0.977395 GGTTCCTCCACTAGTGCACT 59.023 55.000 25.12 25.12 35.97 4.40
3976 4022 3.947834 GTGCACTCAAGCCCTATGTAAAT 59.052 43.478 10.32 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 1.304134 TAGCGACCCAGCAGTCTGA 60.304 57.895 3.32 0.00 42.95 3.27
244 245 3.324930 CTCTGCTGGGGTGAGCCA 61.325 66.667 1.97 0.00 38.28 4.75
258 259 1.500512 GGCGACGCTCGAGTATCTCT 61.501 60.000 20.77 0.00 43.74 3.10
333 334 2.131776 CCTCCAGGTAGAAGAGTCGT 57.868 55.000 0.00 0.00 0.00 4.34
871 881 4.979815 TGTTGTAGTATTATCATGACGCCG 59.020 41.667 0.00 0.00 0.00 6.46
1346 1356 1.876156 CAGGTTGAACTGCTTCTGGTC 59.124 52.381 0.00 0.00 0.00 4.02
1483 1493 8.030106 ACTTTCGAGTCTAAGTAATTCTTCCAG 58.970 37.037 0.00 0.00 37.56 3.86
1693 1703 9.905713 AGAACACCACTATATTTTGTATGATGT 57.094 29.630 0.00 0.00 0.00 3.06
1778 1788 4.839668 TTAACATCGTGAAGTTTTGGGG 57.160 40.909 0.00 0.00 0.00 4.96
1853 1863 3.266510 TGGATGCAATAGCTTCGACTT 57.733 42.857 0.00 0.00 43.69 3.01
2105 2115 6.205853 AGCACTAATAGTATCAGTCTTCTCGG 59.794 42.308 0.00 0.00 0.00 4.63
2195 2229 5.008316 CCATTCTGATCATTGATCTTCGCAA 59.992 40.000 23.49 11.48 39.56 4.85
2204 2238 7.657354 CCGTAATACTTCCATTCTGATCATTGA 59.343 37.037 0.00 0.00 0.00 2.57
2261 2295 4.645535 TGATGAAGTTGTAGCTGCTTCTT 58.354 39.130 7.79 8.01 39.30 2.52
2439 2473 0.167470 CAGGTGCATTCTGTTCGCAG 59.833 55.000 10.68 0.00 46.29 5.18
2501 2535 3.136992 AGGACTAAAACCCGGTTCAAAGA 59.863 43.478 2.46 0.00 0.00 2.52
2518 2552 5.706447 TGGAGCAGACATAATACTAGGACT 58.294 41.667 0.00 0.00 0.00 3.85
2678 2712 4.837093 TTCTCCCAGATAAAATGACCGT 57.163 40.909 0.00 0.00 0.00 4.83
2876 2910 1.600957 CAGTCTGTTCCACAAGTGCAG 59.399 52.381 0.00 0.00 0.00 4.41
2923 2957 0.753262 GCTCTCCTTTCGCCATCCTA 59.247 55.000 0.00 0.00 0.00 2.94
3015 3049 9.875675 GCAATAGAACAGATATAAAAGCTCTTG 57.124 33.333 0.00 0.00 0.00 3.02
3075 3110 4.883083 TCACTTCAGCGACAGTTAATTCT 58.117 39.130 0.00 0.00 0.00 2.40
3159 3194 8.867097 TCATGATACAAATTACTACTACCTCCC 58.133 37.037 0.00 0.00 0.00 4.30
3170 3205 7.981789 TCACCTCACTCTCATGATACAAATTAC 59.018 37.037 0.00 0.00 0.00 1.89
3231 3266 1.224592 CCTAGGGCCAAGCACGATT 59.775 57.895 6.18 0.00 36.86 3.34
3244 3279 6.966534 AAAATAATTCATGCAGGACCTAGG 57.033 37.500 7.41 7.41 0.00 3.02
3366 3405 3.293337 ACAGAAGTAACAAAACACCCCC 58.707 45.455 0.00 0.00 0.00 5.40
3392 3431 2.440247 CCGGCCCAGTTGGATTCC 60.440 66.667 0.00 0.00 37.39 3.01
3581 3622 4.802876 AGCGCTCAAGCATCTAAATAAC 57.197 40.909 2.64 0.00 42.21 1.89
3835 3881 7.099120 AGCTTTGAAGATCTTTGTGTGTTTTT 58.901 30.769 9.87 0.00 0.00 1.94
3960 4006 7.832769 GTTTAAACCATTTACATAGGGCTTGA 58.167 34.615 7.12 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.