Multiple sequence alignment - TraesCS7A01G376400

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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 TraesCS7A01G376400 chr7A 100.000 4727 0 0 1 4727 549397468 549402194 0 8730
1 TraesCS7A01G376400 chr3A 98.499 4730 64 6 1 4727 212717363 212712638 0 8335
2 TraesCS7A01G376400 chr2A 98.456 4729 69 3 1 4727 306631054 306626328 0 8325
3 TraesCS7A01G376400 chr2A 98.245 4729 78 5 1 4727 740477618 740472893 0 8268
4 TraesCS7A01G376400 chr7B 98.435 4729 69 5 1 4727 147718767 147714042 0 8318
5 TraesCS7A01G376400 chr3B 98.435 4728 70 4 1 4727 193965016 193969740 0 8318
6 TraesCS7A01G376400 chr3B 98.414 4728 72 3 1 4727 542902185 542906910 0 8312
7 TraesCS7A01G376400 chr3B 98.371 4728 73 4 1 4727 798434502 798429778 0 8301
8 TraesCS7A01G376400 chr4B 98.393 4729 70 5 1 4727 189137280 189142004 0 8307


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 TraesCS7A01G376400 chr7A 549397468 549402194 4726 False 8730 8730 100.000 1 4727 1 chr7A.!!$F1 4726
1 TraesCS7A01G376400 chr3A 212712638 212717363 4725 True 8335 8335 98.499 1 4727 1 chr3A.!!$R1 4726
2 TraesCS7A01G376400 chr2A 306626328 306631054 4726 True 8325 8325 98.456 1 4727 1 chr2A.!!$R1 4726
3 TraesCS7A01G376400 chr2A 740472893 740477618 4725 True 8268 8268 98.245 1 4727 1 chr2A.!!$R2 4726
4 TraesCS7A01G376400 chr7B 147714042 147718767 4725 True 8318 8318 98.435 1 4727 1 chr7B.!!$R1 4726
5 TraesCS7A01G376400 chr3B 193965016 193969740 4724 False 8318 8318 98.435 1 4727 1 chr3B.!!$F1 4726
6 TraesCS7A01G376400 chr3B 542902185 542906910 4725 False 8312 8312 98.414 1 4727 1 chr3B.!!$F2 4726
7 TraesCS7A01G376400 chr3B 798429778 798434502 4724 True 8301 8301 98.371 1 4727 1 chr3B.!!$R1 4726
8 TraesCS7A01G376400 chr4B 189137280 189142004 4724 False 8307 8307 98.393 1 4727 1 chr4B.!!$F1 4726

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
868 869 0.104304 GGTACCTCAGCCACCATACG 59.896 60.000 4.06 0.00 32.32 3.06 F
1367 1368 0.782384 GCTGACGTCACAAACCTACG 59.218 55.000 15.76 2.48 42.17 3.51 F
1692 1693 1.903860 ACAGATGGGTACGTTTGGCTA 59.096 47.619 0.00 0.00 0.00 3.93 F
3052 3058 1.376812 GCTTTCCGGGTGGACGAAT 60.377 57.895 0.00 0.00 46.45 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 2512 0.111061 TGCTCCAATGGAAGCACAGT 59.889 50.000 18.02 0.00 33.43 3.55 R
3003 3009 2.162408 GCTGGCACGCTTTATTTCTTCT 59.838 45.455 2.30 0.00 0.00 2.85 R
3371 3377 1.064060 AGTTCTTTGTCAGCACAACGC 59.936 47.619 0.00 0.00 42.46 4.84 R
4526 4538 3.878160 TCTGTAATACATGTGCGGACA 57.122 42.857 13.59 13.59 36.22 4.02 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
27 28 3.872696 ACTACAATTGCCATGTCATCGA 58.127 40.909 5.05 0.00 32.27 3.59
199 200 5.179045 ACTATGCTTACAGCGTATTACGT 57.821 39.130 16.87 0.00 46.26 3.57
283 284 1.003696 TGGTGTCACAGACCACACAAA 59.996 47.619 5.12 0.00 44.07 2.83
602 603 4.235762 AGTGAACAGCGGTGCGGT 62.236 61.111 15.82 0.00 38.82 5.68
804 805 4.940046 ACTGAAGCGAATGATGAAACTGAT 59.060 37.500 0.00 0.00 0.00 2.90
868 869 0.104304 GGTACCTCAGCCACCATACG 59.896 60.000 4.06 0.00 32.32 3.06
895 896 2.868583 CAGAGATTTGGATCGTTCGCAT 59.131 45.455 0.00 0.00 37.37 4.73
959 960 4.565531 GGTCAACACCGAGTACCG 57.434 61.111 0.00 0.00 31.06 4.02
1051 1052 1.302993 GGGAAAGGTGTTGCGCCTA 60.303 57.895 4.18 0.00 44.35 3.93
1135 1136 1.831106 ACGTAGATGGAGCAACATGGA 59.169 47.619 0.00 0.00 0.00 3.41
1367 1368 0.782384 GCTGACGTCACAAACCTACG 59.218 55.000 15.76 2.48 42.17 3.51
1692 1693 1.903860 ACAGATGGGTACGTTTGGCTA 59.096 47.619 0.00 0.00 0.00 3.93
2098 2099 4.040339 AGGGGTTCAATGCTGTTTTAAAGG 59.960 41.667 0.00 0.00 0.00 3.11
2250 2251 6.238374 CGTATTTACCGATGAAGAGGCAAATT 60.238 38.462 0.00 0.00 35.67 1.82
2347 2348 4.554553 AGTCAGTAGGGGCCTTATAGAA 57.445 45.455 0.84 0.00 0.00 2.10
2440 2442 5.996513 TGCAGTTGCCATGTTAAAATGAAAT 59.003 32.000 7.23 0.00 41.18 2.17
2510 2512 2.036862 TGCAGTTGCCATGTTTTATGCA 59.963 40.909 7.74 7.74 39.89 3.96
2834 2839 2.619147 TGTAATGCATTTGCCATGTGC 58.381 42.857 18.75 0.00 41.18 4.57
3003 3009 4.081752 ACACACAAAACTTGCAGATTCCAA 60.082 37.500 0.00 0.00 0.00 3.53
3052 3058 1.376812 GCTTTCCGGGTGGACGAAT 60.377 57.895 0.00 0.00 46.45 3.34
3132 3138 5.279156 GGACAAAGGAAGGAACTACTTCGTA 60.279 44.000 0.00 0.00 46.06 3.43
3258 3264 4.146075 CGCATGCCCCGCCATTTT 62.146 61.111 13.15 0.00 0.00 1.82
3465 3471 4.202010 GCAGAAAAACACAGAAAGGCACTA 60.202 41.667 0.00 0.00 38.49 2.74
3563 3569 2.445085 ATCCACGGGGCCATCGTA 60.445 61.111 20.34 8.98 38.94 3.43
3728 3734 2.492773 GGGCGGGCAATCAATGAGG 61.493 63.158 3.27 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.159338 GCAGTTTCGATGACATGGCAAT 60.159 45.455 4.70 0.00 0.00 3.56
27 28 0.963962 CTCCATGGCAACTGCAGTTT 59.036 50.000 29.23 12.59 44.36 2.66
199 200 1.152860 ATTGCCGTGTCACCACCAA 60.153 52.632 0.00 0.00 38.41 3.67
283 284 0.397187 TTGTGCTGCATTTGGCCATT 59.603 45.000 6.09 0.00 43.89 3.16
602 603 1.676678 GCTCCCCGCAGTAGATGTCA 61.677 60.000 0.00 0.00 38.92 3.58
804 805 1.550072 TCATCCTCTTGTGCGTCATCA 59.450 47.619 0.00 0.00 0.00 3.07
868 869 1.672881 CGATCCAAATCTCTGCCCAAC 59.327 52.381 0.00 0.00 0.00 3.77
895 896 4.226394 TGCCTGGTAGTATTCCTTTGCTTA 59.774 41.667 0.00 0.00 0.00 3.09
1367 1368 0.745468 CTCTCTACGGTACTTGGCCC 59.255 60.000 0.00 0.00 0.00 5.80
1448 1449 8.705594 CCAACCTTATCCTGTAGAAGAAATCTA 58.294 37.037 0.00 0.00 39.71 1.98
2182 2183 0.670546 GCTGTGGTCGCTTCTTGCTA 60.671 55.000 0.00 0.00 40.11 3.49
2250 2251 8.023021 AGATCTTGTTGGTGTATATCTTGCTA 57.977 34.615 0.00 0.00 0.00 3.49
2510 2512 0.111061 TGCTCCAATGGAAGCACAGT 59.889 50.000 18.02 0.00 33.43 3.55
2571 2575 5.762711 AGCATATGTGTCGCCAATATAACAA 59.237 36.000 4.29 0.00 0.00 2.83
2834 2839 2.229543 ACATGGCAAATGCAGTACACTG 59.770 45.455 7.80 4.96 46.40 3.66
3003 3009 2.162408 GCTGGCACGCTTTATTTCTTCT 59.838 45.455 2.30 0.00 0.00 2.85
3052 3058 8.714179 CAAAATAGAACACACCTTGAACGTATA 58.286 33.333 0.00 0.00 0.00 1.47
3258 3264 2.632996 CCAAGTCCATCGCCTCCTTATA 59.367 50.000 0.00 0.00 0.00 0.98
3371 3377 1.064060 AGTTCTTTGTCAGCACAACGC 59.936 47.619 0.00 0.00 42.46 4.84
3563 3569 6.843333 TCCAGATCCTATCTCTGAGTTTTCAT 59.157 38.462 4.32 0.00 42.22 2.57
3728 3734 2.094066 CGCAGCGCCCCAATTTTTC 61.094 57.895 2.29 0.00 0.00 2.29
3827 3835 9.003658 TCAATGAATTTTCCTTCTACTTCTGTC 57.996 33.333 0.00 0.00 0.00 3.51
3891 3899 7.415095 GCAGATTAACTACACATAACATGGCAA 60.415 37.037 0.00 0.00 33.60 4.52
4526 4538 3.878160 TCTGTAATACATGTGCGGACA 57.122 42.857 13.59 13.59 36.22 4.02
4531 4543 9.672086 TTTTAGTGTTTTCTGTAATACATGTGC 57.328 29.630 9.11 0.00 30.73 4.57


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

AutoCloner maintained by Alex Coulton.