Multiple sequence alignment - TraesCS4B01G184200

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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 TraesCS4B01G184200 chr4B 100.000 2408 0 0 1 2408 403448178 403445771 0 4447
1 TraesCS4B01G184200 chr4B 93.292 2400 149 8 16 2408 46248715 46251109 0 3530
2 TraesCS4B01G184200 chr4B 92.571 2396 163 11 18 2408 48169357 48171742 0 3424
3 TraesCS4B01G184200 chr5B 93.292 2400 149 4 20 2408 374919235 374921633 0 3530
4 TraesCS4B01G184200 chr3B 92.955 2399 159 7 18 2408 474428107 474430503 0 3485
5 TraesCS4B01G184200 chr2B 92.991 2397 157 8 19 2408 715273292 715270900 0 3485
6 TraesCS4B01G184200 chr2B 92.157 2397 178 7 20 2408 710251279 710253673 0 3376
7 TraesCS4B01G184200 chr2B 91.952 2398 185 7 16 2408 642425159 642427553 0 3352
8 TraesCS4B01G184200 chr6B 92.625 2400 164 10 18 2408 479066946 479064551 0 3439
9 TraesCS4B01G184200 chr1B 92.276 2395 177 7 20 2408 456117120 456114728 0 3391


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 TraesCS4B01G184200 chr4B 403445771 403448178 2407 True 4447 4447 100.000 1 2408 1 chr4B.!!$R1 2407
1 TraesCS4B01G184200 chr4B 46248715 46251109 2394 False 3530 3530 93.292 16 2408 1 chr4B.!!$F1 2392
2 TraesCS4B01G184200 chr4B 48169357 48171742 2385 False 3424 3424 92.571 18 2408 1 chr4B.!!$F2 2390
3 TraesCS4B01G184200 chr5B 374919235 374921633 2398 False 3530 3530 93.292 20 2408 1 chr5B.!!$F1 2388
4 TraesCS4B01G184200 chr3B 474428107 474430503 2396 False 3485 3485 92.955 18 2408 1 chr3B.!!$F1 2390
5 TraesCS4B01G184200 chr2B 715270900 715273292 2392 True 3485 3485 92.991 19 2408 1 chr2B.!!$R1 2389
6 TraesCS4B01G184200 chr2B 710251279 710253673 2394 False 3376 3376 92.157 20 2408 1 chr2B.!!$F2 2388
7 TraesCS4B01G184200 chr2B 642425159 642427553 2394 False 3352 3352 91.952 16 2408 1 chr2B.!!$F1 2392
8 TraesCS4B01G184200 chr6B 479064551 479066946 2395 True 3439 3439 92.625 18 2408 1 chr6B.!!$R1 2390
9 TraesCS4B01G184200 chr1B 456114728 456117120 2392 True 3391 3391 92.276 20 2408 1 chr1B.!!$R1 2388

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
162 163 0.03467 GCAGCCAGATTCCTGAACCT 60.035 55.0 0.0 0.0 43.02 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 1440 0.830648 TTCAATCCGGCTAGGGACTG 59.169 55.0 0.0 0.0 41.52 3.51 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
162 163 0.034670 GCAGCCAGATTCCTGAACCT 60.035 55.000 0.00 0.00 43.02 3.50
532 536 6.694445 AGAATACCCATTTATCTCAGGAGG 57.306 41.667 0.00 0.00 0.00 4.30
595 600 1.084018 AGAGGAATCCCAAAAGGCCA 58.916 50.000 5.01 0.00 34.51 5.36
827 834 4.129380 CAAGATGCCAATATCCGACTGAA 58.871 43.478 0.00 0.00 0.00 3.02
937 946 3.944055 ACGAGCTACAGAACAGTTCAT 57.056 42.857 15.85 5.76 0.00 2.57
952 961 2.932614 AGTTCATCGAGGAAGCGAATTG 59.067 45.455 13.59 0.00 44.22 2.32
953 962 1.939974 TCATCGAGGAAGCGAATTGG 58.060 50.000 0.00 0.00 44.22 3.16
1034 1043 1.741706 AGGTGATTTGCTGCAAGATCG 59.258 47.619 15.39 0.00 34.07 3.69
1109 1118 2.381941 GGCCATCCTCTTCCCTGCT 61.382 63.158 0.00 0.00 0.00 4.24
1138 1147 0.601311 GAGCGAGCTTGTGGAGTTGT 60.601 55.000 2.14 0.00 0.00 3.32
1204 1213 0.541863 CCGACAAGGTGCTAGGGAAT 59.458 55.000 0.00 0.00 34.51 3.01
1274 1283 3.367743 CGAAGTCGGACCGGTGGA 61.368 66.667 14.63 6.28 35.37 4.02
1431 1440 7.661437 TGACTATGTAATTCAATGGACCTATGC 59.339 37.037 0.00 0.00 0.00 3.14
1642 1652 6.889198 TGGATAGTAAGAAACATCTTCCAGG 58.111 40.000 0.00 0.00 0.00 4.45
1653 1663 6.394345 AACATCTTCCAGGGAGAATAGTTT 57.606 37.500 0.00 0.00 0.00 2.66
1714 1724 0.865111 CATGTCCGAACTGCGAACAA 59.135 50.000 0.00 0.00 44.57 2.83
1733 1743 1.555477 AAAGCGCAGGAAACAAAACG 58.445 45.000 11.47 0.00 0.00 3.60
1743 1753 2.228103 GGAAACAAAACGTCTGGGGATC 59.772 50.000 0.00 0.00 0.00 3.36
1889 1900 1.722034 CTCTCCTTATGCCCTAGCCA 58.278 55.000 0.00 0.00 38.69 4.75
1899 1910 1.282447 TGCCCTAGCCAAATTAACGGA 59.718 47.619 0.00 0.00 38.69 4.69
2022 2033 0.457035 GCATATGTGGTTGGCAGTGG 59.543 55.000 4.29 0.00 0.00 4.00
2158 2169 2.764439 AAGGTAAAGAGGGCGAGAAC 57.236 50.000 0.00 0.00 0.00 3.01
2258 2272 2.359354 CCGCGTTCCATGGGTTCA 60.359 61.111 13.02 0.00 0.00 3.18
2265 2279 2.238521 GTTCCATGGGTTCAGCTTGAA 58.761 47.619 13.02 0.00 33.32 2.69
2267 2281 4.016444 GTTCCATGGGTTCAGCTTGAATA 58.984 43.478 13.02 0.00 38.79 1.75
2296 2310 3.999001 CAGATGTATTGCGCAGATGGTAT 59.001 43.478 11.31 2.14 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.876342 CGCTGATCCTAACCGCCTTC 60.876 60.000 0.00 0.00 0.00 3.46
1 2 1.144057 CGCTGATCCTAACCGCCTT 59.856 57.895 0.00 0.00 0.00 4.35
2 3 2.815308 CGCTGATCCTAACCGCCT 59.185 61.111 0.00 0.00 0.00 5.52
3 4 2.967615 GCGCTGATCCTAACCGCC 60.968 66.667 0.00 0.00 38.84 6.13
4 5 2.202878 TGCGCTGATCCTAACCGC 60.203 61.111 9.73 0.00 44.39 5.68
5 6 0.596083 CTCTGCGCTGATCCTAACCG 60.596 60.000 17.78 0.00 0.00 4.44
6 7 0.249657 CCTCTGCGCTGATCCTAACC 60.250 60.000 17.78 0.00 0.00 2.85
7 8 0.461961 ACCTCTGCGCTGATCCTAAC 59.538 55.000 17.78 0.00 0.00 2.34
8 9 1.681793 GTACCTCTGCGCTGATCCTAA 59.318 52.381 17.78 0.00 0.00 2.69
9 10 1.319541 GTACCTCTGCGCTGATCCTA 58.680 55.000 17.78 4.76 0.00 2.94
10 11 0.684479 TGTACCTCTGCGCTGATCCT 60.684 55.000 17.78 5.70 0.00 3.24
11 12 0.175760 TTGTACCTCTGCGCTGATCC 59.824 55.000 17.78 6.57 0.00 3.36
12 13 2.010145 TTTGTACCTCTGCGCTGATC 57.990 50.000 17.78 9.15 0.00 2.92
13 14 2.698855 ATTTGTACCTCTGCGCTGAT 57.301 45.000 17.78 6.54 0.00 2.90
14 15 2.472695 AATTTGTACCTCTGCGCTGA 57.527 45.000 16.55 16.55 0.00 4.26
149 150 2.232452 CGTGAGTCAGGTTCAGGAATCT 59.768 50.000 4.63 0.00 33.48 2.40
162 163 3.311110 GCCTCCACCCGTGAGTCA 61.311 66.667 0.00 0.00 0.00 3.41
532 536 2.440980 GGCCTGGCATTCCTCCAC 60.441 66.667 22.05 0.00 0.00 4.02
827 834 1.732259 GAACATCTGCCAATTCGACGT 59.268 47.619 0.00 0.00 0.00 4.34
937 946 2.097036 TCTACCAATTCGCTTCCTCGA 58.903 47.619 0.00 0.00 36.60 4.04
952 961 6.490721 AGCATACCTACAGACATAACTCTACC 59.509 42.308 0.00 0.00 0.00 3.18
953 962 7.228906 TCAGCATACCTACAGACATAACTCTAC 59.771 40.741 0.00 0.00 0.00 2.59
1034 1043 1.083401 CGCTCGTGCAGTTGTGAAC 60.083 57.895 10.43 0.00 39.64 3.18
1109 1118 1.045350 AAGCTCGCTCATGCCTCCTA 61.045 55.000 0.00 0.00 35.36 2.94
1138 1147 2.260869 GCTGCCGTGCTCCTTTGAA 61.261 57.895 0.00 0.00 0.00 2.69
1197 1206 1.067762 CCATGGCCCAGGATTCCCTA 61.068 60.000 0.00 0.00 42.02 3.53
1204 1213 1.541118 TCTTCACCATGGCCCAGGA 60.541 57.895 13.04 1.08 0.00 3.86
1274 1283 2.703007 GGTATCTCTTGCCCATCTGACT 59.297 50.000 0.00 0.00 0.00 3.41
1431 1440 0.830648 TTCAATCCGGCTAGGGACTG 59.169 55.000 0.00 0.00 41.52 3.51
1642 1652 5.651139 GGAACCCCTAACAAAACTATTCTCC 59.349 44.000 0.00 0.00 0.00 3.71
1653 1663 2.984435 GGGAAAGGAACCCCTAACAA 57.016 50.000 0.00 0.00 43.48 2.83
1714 1724 1.135228 ACGTTTTGTTTCCTGCGCTTT 60.135 42.857 9.73 0.00 0.00 3.51
1733 1743 0.899720 TACAACGTGGATCCCCAGAC 59.100 55.000 9.90 0.00 44.55 3.51
1873 1884 3.971468 AATTTGGCTAGGGCATAAGGA 57.029 42.857 0.00 0.00 38.08 3.36
1899 1910 5.296035 GCTCTTGTATTTATGCCCTACGTTT 59.704 40.000 0.00 0.00 0.00 3.60
1915 1926 1.378762 GGGTTGCCTGGCTCTTGTA 59.621 57.895 21.03 0.00 0.00 2.41
1937 1948 5.584649 TCGATATGACTTAAGTTTTGGCCAG 59.415 40.000 10.02 0.00 0.00 4.85
2051 2062 3.666975 ATACCTGGGGGCTTCCTATAA 57.333 47.619 0.00 0.00 35.63 0.98
2158 2169 5.428253 TCTTTCAATTATGTCCTCCTTCCG 58.572 41.667 0.00 0.00 0.00 4.30
2188 2202 4.477780 GAACTCAGTGTTCGTCTCCTTAG 58.522 47.826 0.00 0.00 44.49 2.18
2211 2225 2.033550 CGAAGATTCTACGCCTAGTGCT 59.966 50.000 2.39 0.00 38.05 4.40
2258 2272 8.618677 CAATACATCTGACAACATATTCAAGCT 58.381 33.333 0.00 0.00 0.00 3.74
2265 2279 4.815846 TGCGCAATACATCTGACAACATAT 59.184 37.500 8.16 0.00 0.00 1.78
2267 2281 3.009026 TGCGCAATACATCTGACAACAT 58.991 40.909 8.16 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.