Multiple sequence alignment - TraesCS5B01G273100

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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 TraesCS5B01G273100 chr5B 100.000 2312 0 0 1 2312 458662622 458660311 0.000000e+00 4270
1 TraesCS5B01G273100 chr5B 95.252 1685 55 9 1 1671 158924381 158926054 0.000000e+00 2645
2 TraesCS5B01G273100 chr5B 95.228 901 35 4 1192 2092 655385593 655386485 0.000000e+00 1419
3 TraesCS5B01G273100 chr5B 94.657 861 41 3 338 1194 655376063 655376922 0.000000e+00 1330
4 TraesCS5B01G273100 chr5B 95.518 647 23 2 1659 2305 158926606 158927246 0.000000e+00 1029
5 TraesCS5B01G273100 chr5B 95.677 347 8 2 1 345 655375228 655375569 3.360000e-153 551
6 TraesCS5B01G273100 chr5B 96.279 215 6 1 2087 2301 655390552 655390764 3.650000e-93 351
7 TraesCS5B01G273100 chr5B 89.850 266 23 3 2009 2272 656711079 656711342 2.850000e-89 339
8 TraesCS5B01G273100 chr7A 87.978 183 12 3 28 210 647142929 647142757 8.370000e-50 207
9 TraesCS5B01G273100 chr7D 91.071 112 8 2 141 251 562066935 562066825 1.430000e-32 150


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 TraesCS5B01G273100 chr5B 458660311 458662622 2311 True 4270.0 4270 100.000 1 2312 1 chr5B.!!$R1 2311
1 TraesCS5B01G273100 chr5B 158924381 158927246 2865 False 1837.0 2645 95.385 1 2305 2 chr5B.!!$F4 2304
2 TraesCS5B01G273100 chr5B 655385593 655386485 892 False 1419.0 1419 95.228 1192 2092 1 chr5B.!!$F1 900
3 TraesCS5B01G273100 chr5B 655375228 655376922 1694 False 940.5 1330 95.167 1 1194 2 chr5B.!!$F5 1193

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
987 1507 3.432051 CTTGCGGTAGAGCTCCCGG 62.432 68.421 26.28 15.93 44.36 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 3205 2.678471 ACGGGGAAGTGGTATAAACG 57.322 50.0 0.0 0.0 0.0 3.6 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
139 142 5.422012 TCTCCTGAGCATATACTGAACAACA 59.578 40.000 0.00 0.00 0.00 3.33
140 143 6.048732 TCCTGAGCATATACTGAACAACAA 57.951 37.500 0.00 0.00 0.00 2.83
141 144 5.874810 TCCTGAGCATATACTGAACAACAAC 59.125 40.000 0.00 0.00 0.00 3.32
142 145 5.643348 CCTGAGCATATACTGAACAACAACA 59.357 40.000 0.00 0.00 0.00 3.33
257 272 6.707440 GAGAACTCTCTATGGAAGTGATGA 57.293 41.667 0.00 0.00 39.81 2.92
260 275 8.088463 AGAACTCTCTATGGAAGTGATGAATT 57.912 34.615 0.00 0.00 0.00 2.17
362 878 6.112927 TGCATGTATATCTGCTGGTCATTA 57.887 37.500 9.90 0.00 39.16 1.90
457 973 8.947115 GTGTTGCTCCTATGAATTACTTAAACT 58.053 33.333 0.00 0.00 0.00 2.66
803 1322 9.421806 CATCATTCTAAAAGTGTTTTTATGGCA 57.578 29.630 0.00 0.00 37.92 4.92
987 1507 3.432051 CTTGCGGTAGAGCTCCCGG 62.432 68.421 26.28 15.93 44.36 5.73
1065 1585 0.390866 CTGCTGATGAGAACGCTGGT 60.391 55.000 0.00 0.00 0.00 4.00
1115 1635 1.069090 GTGTTCACGGTGGAGCAGA 59.931 57.895 8.50 0.00 0.00 4.26
1198 1718 0.813184 CATGAGCATGGCCTTTTCGT 59.187 50.000 3.32 0.00 35.24 3.85
1234 1754 1.002746 TTAATCGCAGCCTGCCACA 60.003 52.632 11.83 0.00 41.12 4.17
1239 1759 2.993264 GCAGCCTGCCACATGGTT 60.993 61.111 5.06 0.00 37.42 3.67
1410 1930 5.600696 TGCACGATGCTTTCTATCTTGATA 58.399 37.500 10.54 0.00 45.31 2.15
1616 2137 1.705337 CTAATGTTCGGCCCGTGCTG 61.705 60.000 1.63 0.00 45.75 4.41
1876 2961 4.077822 TGCATGTATGGTGTCATTGTTCA 58.922 39.130 0.00 0.00 34.96 3.18
2021 3106 1.406539 GGTTGCCTTGATGTGCTATGG 59.593 52.381 0.00 0.00 0.00 2.74
2079 3164 7.095691 GCTTCTACTCTCATCTGTCATTTATGC 60.096 40.741 0.00 0.00 0.00 3.14
2103 3188 8.253113 TGCATATGTACATGTAAGATCGATCAT 58.747 33.333 26.47 17.80 0.00 2.45
2120 3205 7.026631 TCGATCATGATTATTTTGGACCAAC 57.973 36.000 10.14 0.00 0.00 3.77
2165 3250 5.636121 TGTTAATATACGGGACATCGATTGC 59.364 40.000 0.00 0.00 0.00 3.56
2230 3315 9.865321 AAGAATTTTGTTCCATCTATGTGATTG 57.135 29.630 0.00 0.00 32.05 2.67
2253 3338 4.451096 GTGTGATGTTCCTGAAACGTATGT 59.549 41.667 0.00 0.00 41.02 2.29
2271 3356 6.100004 CGTATGTTCACTTGTCTATTGTCCT 58.900 40.000 0.00 0.00 0.00 3.85
2279 3364 4.020128 ACTTGTCTATTGTCCTCTTGGGTC 60.020 45.833 0.00 0.00 36.25 4.46
2281 3366 3.515502 TGTCTATTGTCCTCTTGGGTCTG 59.484 47.826 0.00 0.00 36.25 3.51
2305 3390 7.765307 TGAAATATTGTTGCTCATCCTTTCTC 58.235 34.615 0.00 0.00 0.00 2.87
2306 3391 7.394077 TGAAATATTGTTGCTCATCCTTTCTCA 59.606 33.333 0.00 0.00 0.00 3.27
2307 3392 7.893124 AATATTGTTGCTCATCCTTTCTCAT 57.107 32.000 0.00 0.00 0.00 2.90
2308 3393 5.831702 ATTGTTGCTCATCCTTTCTCATC 57.168 39.130 0.00 0.00 0.00 2.92
2309 3394 4.290711 TGTTGCTCATCCTTTCTCATCA 57.709 40.909 0.00 0.00 0.00 3.07
2310 3395 4.851843 TGTTGCTCATCCTTTCTCATCAT 58.148 39.130 0.00 0.00 0.00 2.45
2311 3396 5.258841 TGTTGCTCATCCTTTCTCATCATT 58.741 37.500 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 54 5.698104 TCAGATATCTTGGCATCCACAATT 58.302 37.500 1.33 0.00 30.78 2.32
257 272 8.421002 AGTTTTGTACCTGTAAGCATTCAAATT 58.579 29.630 0.00 0.00 0.00 1.82
260 275 6.320164 ACAGTTTTGTACCTGTAAGCATTCAA 59.680 34.615 1.17 0.00 35.25 2.69
362 878 8.561738 AAAACACCAGTTCGACTATATTCATT 57.438 30.769 0.00 0.00 36.84 2.57
457 973 8.727149 ACTATTAATGAAATCCCTGGATTCTGA 58.273 33.333 11.69 0.31 43.26 3.27
574 1093 5.049474 CACTCAGTCGTTTCCAAATCATTGA 60.049 40.000 0.00 0.00 38.94 2.57
644 1163 7.827819 TGATTTGTCTTTGAACTATACTCCG 57.172 36.000 0.00 0.00 0.00 4.63
707 1226 5.170748 GTGGCCCAACTAATTCTTGAATTG 58.829 41.667 16.22 9.97 0.00 2.32
803 1322 5.760253 CCTGTACCTGAAATTAGCATCGAAT 59.240 40.000 0.00 0.00 0.00 3.34
929 1449 1.811266 CGGGAGAGTGACATTGGCG 60.811 63.158 0.00 0.00 0.00 5.69
1005 1525 1.692749 GTCCATCCTGCCTACCCCA 60.693 63.158 0.00 0.00 0.00 4.96
1039 1559 0.107800 TTCTCATCAGCAGCCTCAGC 60.108 55.000 0.00 0.00 40.32 4.26
1163 1683 1.170442 CATGGAGCTGCACACATTCA 58.830 50.000 11.23 0.00 0.00 2.57
1234 1754 2.350522 GAAGAGTGCATCGTCAACCAT 58.649 47.619 0.00 0.00 36.53 3.55
1239 1759 1.847328 TAGGGAAGAGTGCATCGTCA 58.153 50.000 11.72 0.00 38.08 4.35
1410 1930 5.733620 ATCAGCTCATCCAACACAAAAAT 57.266 34.783 0.00 0.00 0.00 1.82
1637 2158 9.950496 AATTTGATAGGACTGGTATCATCATAC 57.050 33.333 0.00 0.00 36.89 2.39
1638 2159 9.948964 CAATTTGATAGGACTGGTATCATCATA 57.051 33.333 0.00 0.00 36.89 2.15
1639 2160 8.443176 ACAATTTGATAGGACTGGTATCATCAT 58.557 33.333 2.79 0.00 36.89 2.45
1640 2161 7.805163 ACAATTTGATAGGACTGGTATCATCA 58.195 34.615 2.79 0.00 36.89 3.07
1641 2162 8.682936 AACAATTTGATAGGACTGGTATCATC 57.317 34.615 2.79 0.00 36.89 2.92
1786 2871 9.937175 GTTTAACATCCAGCAGAATTTAGATAC 57.063 33.333 0.00 0.00 0.00 2.24
1876 2961 9.661563 AACAATGAAAAATCATACATGCAATCT 57.338 25.926 0.00 0.00 0.00 2.40
2021 3106 6.343226 GAGATGTCTCTGCTAATTGTTCAC 57.657 41.667 2.80 0.00 39.81 3.18
2079 3164 9.793252 TCATGATCGATCTTACATGTACATATG 57.207 33.333 25.02 14.96 40.32 1.78
2103 3188 8.460428 GGTATAAACGTTGGTCCAAAATAATCA 58.540 33.333 5.69 0.00 0.00 2.57
2111 3196 4.354893 AGTGGTATAAACGTTGGTCCAA 57.645 40.909 0.00 0.00 0.00 3.53
2116 3201 3.011818 GGGGAAGTGGTATAAACGTTGG 58.988 50.000 0.00 0.00 0.00 3.77
2120 3205 2.678471 ACGGGGAAGTGGTATAAACG 57.322 50.000 0.00 0.00 0.00 3.60
2153 3238 3.829886 TTTCACAAGCAATCGATGTCC 57.170 42.857 0.00 0.00 0.00 4.02
2229 3314 2.912771 ACGTTTCAGGAACATCACACA 58.087 42.857 0.00 0.00 38.18 3.72
2230 3315 4.451096 ACATACGTTTCAGGAACATCACAC 59.549 41.667 0.00 0.00 38.18 3.82
2253 3338 5.513094 CCCAAGAGGACAATAGACAAGTGAA 60.513 44.000 0.00 0.00 38.24 3.18
2271 3356 5.324409 AGCAACAATATTTCAGACCCAAGA 58.676 37.500 0.00 0.00 0.00 3.02
2279 3364 7.769220 AGAAAGGATGAGCAACAATATTTCAG 58.231 34.615 14.06 0.00 33.52 3.02
2281 3366 7.765307 TGAGAAAGGATGAGCAACAATATTTC 58.235 34.615 0.00 0.00 32.40 2.17


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

AutoCloner maintained by Alex Coulton.