Multiple sequence alignment - TraesCS1B01G189000

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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 TraesCS1B01G189000 chr1B 100.000 4014 0 0 1 4014 338928441 338932454 0 7413
1 TraesCS1B01G189000 chr7B 97.867 4031 66 9 1 4014 743066305 743070332 0 6950
2 TraesCS1B01G189000 chr5A 97.818 4033 68 12 1 4014 16623275 16619244 0 6942
3 TraesCS1B01G189000 chr5A 97.519 4031 81 7 1 4014 300048565 300052593 0 6872
4 TraesCS1B01G189000 chr3D 97.791 4029 73 6 1 4014 202611946 202615973 0 6933
5 TraesCS1B01G189000 chr7A 97.717 4030 74 8 1 4014 671960568 671956541 0 6916
6 TraesCS1B01G189000 chr7A 97.666 4027 78 6 1 4014 120828848 120824825 0 6902
7 TraesCS1B01G189000 chr7A 97.326 2431 46 5 1 2414 672005153 672007581 0 4111
8 TraesCS1B01G189000 chr2D 97.717 4029 75 6 1 4014 635037260 635041286 0 6914
9 TraesCS1B01G189000 chr2A 97.569 4031 79 10 1 4014 735172799 735176827 0 6883
10 TraesCS1B01G189000 chr3B 97.566 4027 83 5 1 4014 201635803 201631779 0 6879
11 TraesCS1B01G189000 chr5B 97.566 4026 81 6 4 4014 713046208 713042185 0 6876
12 TraesCS1B01G189000 chr6B 97.392 2761 57 5 1269 4014 525679433 525682193 0 4686
13 TraesCS1B01G189000 chr7D 97.952 2344 32 5 1686 4014 382012479 382010137 0 4048


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 TraesCS1B01G189000 chr1B 338928441 338932454 4013 False 7413 7413 100.000 1 4014 1 chr1B.!!$F1 4013
1 TraesCS1B01G189000 chr7B 743066305 743070332 4027 False 6950 6950 97.867 1 4014 1 chr7B.!!$F1 4013
2 TraesCS1B01G189000 chr5A 16619244 16623275 4031 True 6942 6942 97.818 1 4014 1 chr5A.!!$R1 4013
3 TraesCS1B01G189000 chr5A 300048565 300052593 4028 False 6872 6872 97.519 1 4014 1 chr5A.!!$F1 4013
4 TraesCS1B01G189000 chr3D 202611946 202615973 4027 False 6933 6933 97.791 1 4014 1 chr3D.!!$F1 4013
5 TraesCS1B01G189000 chr7A 671956541 671960568 4027 True 6916 6916 97.717 1 4014 1 chr7A.!!$R2 4013
6 TraesCS1B01G189000 chr7A 120824825 120828848 4023 True 6902 6902 97.666 1 4014 1 chr7A.!!$R1 4013
7 TraesCS1B01G189000 chr7A 672005153 672007581 2428 False 4111 4111 97.326 1 2414 1 chr7A.!!$F1 2413
8 TraesCS1B01G189000 chr2D 635037260 635041286 4026 False 6914 6914 97.717 1 4014 1 chr2D.!!$F1 4013
9 TraesCS1B01G189000 chr2A 735172799 735176827 4028 False 6883 6883 97.569 1 4014 1 chr2A.!!$F1 4013
10 TraesCS1B01G189000 chr3B 201631779 201635803 4024 True 6879 6879 97.566 1 4014 1 chr3B.!!$R1 4013
11 TraesCS1B01G189000 chr5B 713042185 713046208 4023 True 6876 6876 97.566 4 4014 1 chr5B.!!$R1 4010
12 TraesCS1B01G189000 chr6B 525679433 525682193 2760 False 4686 4686 97.392 1269 4014 1 chr6B.!!$F1 2745
13 TraesCS1B01G189000 chr7D 382010137 382012479 2342 True 4048 4048 97.952 1686 4014 1 chr7D.!!$R1 2328

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
619 621 1.136305 CCCTTCGACTTCGGCTATGAA 59.864 52.381 0.0 0.0 40.29 2.57 F
2259 2285 1.081892 CTACGCAAGCAGCATTGTCT 58.918 50.000 0.0 0.0 46.13 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 2309 0.243907 TTTCCGCCTTGACTCTCGAG 59.756 55.0 5.93 5.93 0.0 4.04 R
3334 3363 0.534877 CAGCCACGCCATAATAGCCA 60.535 55.0 0.00 0.00 0.0 4.75 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
57 58 2.187946 CCGACTGATGGCTCACCC 59.812 66.667 0.00 0.00 33.59 4.61
194 196 2.574450 TCACTTTGCAGCAGTTCATCA 58.426 42.857 0.00 0.00 0.00 3.07
232 234 1.826096 GAGGTACCTTTTCTCGAGCCT 59.174 52.381 17.53 5.56 0.00 4.58
338 340 7.240616 ACAGGCTTATCTATTTTATGGGGAGAT 59.759 37.037 0.00 0.00 0.00 2.75
394 396 3.551496 TTGCTCCTTCCACTGCCGG 62.551 63.158 0.00 0.00 0.00 6.13
619 621 1.136305 CCCTTCGACTTCGGCTATGAA 59.864 52.381 0.00 0.00 40.29 2.57
660 662 5.127519 TGAATAGGCGTAACAAAGCTACCTA 59.872 40.000 0.00 0.00 33.12 3.08
661 663 3.967332 AGGCGTAACAAAGCTACCTAA 57.033 42.857 0.00 0.00 0.00 2.69
703 705 7.028962 CCTTAGATTGAAATCGACAAATTGCA 58.971 34.615 0.00 0.00 40.35 4.08
706 708 7.515957 AGATTGAAATCGACAAATTGCATTC 57.484 32.000 0.00 0.00 40.35 2.67
876 883 1.458927 GGTGCACCTAACCCACCTT 59.541 57.895 29.12 0.00 44.32 3.50
1032 1039 6.779117 ACATTTCTGTGAATGCTATTTCGAG 58.221 36.000 0.00 0.00 39.97 4.04
1196 1203 2.960384 TCGATCCTTCTACGGCCAAATA 59.040 45.455 2.24 0.00 0.00 1.40
1965 1990 1.623811 GGCAGGTTAGTTCCTCTGTCA 59.376 52.381 0.00 0.00 35.37 3.58
2258 2284 3.593247 CTACGCAAGCAGCATTGTC 57.407 52.632 0.00 0.00 46.13 3.18
2259 2285 1.081892 CTACGCAAGCAGCATTGTCT 58.918 50.000 0.00 0.00 46.13 3.41
2283 2309 0.875059 CCACCCGAGAAGCAAAAGAC 59.125 55.000 0.00 0.00 0.00 3.01
2331 2357 3.561725 GCATAGTGGTCTAATGACAAGGC 59.438 47.826 0.00 0.00 44.61 4.35
2434 2460 1.272769 GAGCTTCGACCAACTACCACT 59.727 52.381 0.00 0.00 0.00 4.00
2445 2471 3.497763 CCAACTACCACTGGTCAATTCCA 60.498 47.826 3.21 0.00 37.09 3.53
3050 3079 1.122227 AAGGCCAAAACATGTGTGCT 58.878 45.000 5.01 0.00 0.00 4.40
3087 3116 4.627015 TCAACCTACTAGCAATAGGGGAA 58.373 43.478 9.17 0.00 43.19 3.97
3113 3142 3.315191 ACTTAGCATGTCGCAACAAAAGT 59.685 39.130 0.00 0.00 46.13 2.66
3334 3363 4.320494 CGCTTGCTTCTTTCTTATTGTGGT 60.320 41.667 0.00 0.00 0.00 4.16
3951 3980 2.426023 GGGACAGGTGCACGAACT 59.574 61.111 11.45 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.783828 ACTGCGTCGGATCAGATAAG 57.216 50.000 14.43 0.41 34.57 1.73
80 81 2.172717 ACCAAACTGCTGACCTACTGTT 59.827 45.455 0.00 0.00 0.00 3.16
338 340 8.539117 TTTATCTCATCCAAGATAGTGTCTCA 57.461 34.615 0.00 0.00 38.97 3.27
619 621 1.207488 TCAGCTAGGTGGGGCATTGT 61.207 55.000 21.22 0.00 0.00 2.71
703 705 6.257994 TCTAAAGAATCCATCTGGCAGAAT 57.742 37.500 22.84 7.89 38.79 2.40
706 708 6.118170 TCTTTCTAAAGAATCCATCTGGCAG 58.882 40.000 8.58 8.58 41.75 4.85
876 883 4.801330 ACACCGTAATTGATGAGTGAGA 57.199 40.909 0.00 0.00 0.00 3.27
1032 1039 4.202172 GGACAGAGAATAGGACCACTTAGC 60.202 50.000 0.00 0.00 0.00 3.09
1159 1166 4.528596 AGGATCGAATTGTATCCGAGGAAT 59.471 41.667 9.11 0.00 45.35 3.01
1196 1203 3.826157 TCGAAGGCTTTCCACAAATTGAT 59.174 39.130 0.00 0.00 33.74 2.57
1586 1593 2.541466 CACAAGACTACCCCTCTTCCT 58.459 52.381 0.00 0.00 0.00 3.36
1669 1677 0.615331 ACGAGGTACCCACTACTCGA 59.385 55.000 21.62 0.00 37.69 4.04
1965 1990 0.678048 GCCAAGAACTCTCCGGCAAT 60.678 55.000 12.88 0.00 41.51 3.56
2212 2238 3.352338 CTCGCCCGTCGTTTAGGCT 62.352 63.158 8.34 0.00 44.84 4.58
2258 2284 2.046892 CTTCTCGGGTGGTGGCAG 60.047 66.667 0.00 0.00 0.00 4.85
2259 2285 4.329545 GCTTCTCGGGTGGTGGCA 62.330 66.667 0.00 0.00 0.00 4.92
2283 2309 0.243907 TTTCCGCCTTGACTCTCGAG 59.756 55.000 5.93 5.93 0.00 4.04
2434 2460 2.008242 CCCCAAAGTGGAATTGACCA 57.992 50.000 0.00 0.00 40.96 4.02
2627 2653 1.904287 TGGCACCGCTCACTAAATTT 58.096 45.000 0.00 0.00 0.00 1.82
2811 2838 1.488812 CCTCGGGAAACATGGGTATGA 59.511 52.381 0.00 0.00 37.73 2.15
3087 3116 4.300189 TGTTGCGACATGCTAAGTTTTT 57.700 36.364 1.50 0.00 46.63 1.94
3113 3142 1.136774 CTGACGCCTCGAATCGACA 59.863 57.895 0.00 10.81 0.00 4.35
3334 3363 0.534877 CAGCCACGCCATAATAGCCA 60.535 55.000 0.00 0.00 0.00 4.75
3489 3518 4.371786 TCGATTTCTTTCTGATGGATCCG 58.628 43.478 7.39 0.00 0.00 4.18
3951 3980 3.804786 TGTCTGACGTTTGGAGTTGTA 57.195 42.857 2.98 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.