Multiple sequence alignment - TraesCS5B01G452100

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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 TraesCS5B01G452100 chr5B 100.000 2624 0 0 1 2624 625038537 625035914 0.000000e+00 4846
1 TraesCS5B01G452100 chr5B 99.508 2234 10 1 1 2234 628609607 628607375 0.000000e+00 4063
2 TraesCS5B01G452100 chr5B 99.681 313 0 1 2312 2624 628607119 628606808 2.930000e-159 571
3 TraesCS5B01G452100 chr3B 99.259 1620 12 0 502 2121 134226063 134224444 0.000000e+00 2926
4 TraesCS5B01G452100 chr3B 99.115 339 3 0 2286 2624 134224447 134224109 6.210000e-171 610
5 TraesCS5B01G452100 chr3B 98.039 153 3 0 174 326 134238043 134237891 1.550000e-67 267
6 TraesCS5B01G452100 chr4B 79.559 499 79 14 434 925 72886020 72886502 4.180000e-88 335
7 TraesCS5B01G452100 chr3A 96.850 127 4 0 1 127 688116862 688116988 2.050000e-51 213
8 TraesCS5B01G452100 chr6B 96.063 127 5 0 1 127 432491382 432491508 9.520000e-50 207
9 TraesCS5B01G452100 chr1A 96.063 127 5 0 1 127 293742661 293742787 9.520000e-50 207
10 TraesCS5B01G452100 chr1A 94.488 127 7 0 1 127 494436310 494436436 2.060000e-46 196
11 TraesCS5B01G452100 chr7A 95.276 127 6 0 1 127 21105590 21105464 4.430000e-48 202
12 TraesCS5B01G452100 chr7A 92.913 127 9 0 1 127 602095198 602095324 4.460000e-43 185
13 TraesCS5B01G452100 chrUn 95.161 124 6 0 1 124 117156272 117156149 2.060000e-46 196


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 TraesCS5B01G452100 chr5B 625035914 625038537 2623 True 4846 4846 100.0000 1 2624 1 chr5B.!!$R1 2623
1 TraesCS5B01G452100 chr5B 628606808 628609607 2799 True 2317 4063 99.5945 1 2624 2 chr5B.!!$R2 2623
2 TraesCS5B01G452100 chr3B 134224109 134226063 1954 True 1768 2926 99.1870 502 2624 2 chr3B.!!$R2 2122

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
189 190 1.420641 GGCCGAAAATTCAATGGCGC 61.421 55.000 0.0 0.0 46.66 6.53 F
440 441 9.268268 GTGGTCGATCAATATTAACAAATCCTA 57.732 33.333 0.0 0.0 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 1164 3.705043 AGACTGCAGCAAACAAAGAAG 57.295 42.857 15.27 0.0 0.0 2.85 R
2275 2276 0.377203 CACCTAAAAATCTCGCCGCC 59.623 55.000 0.00 0.0 0.0 6.13 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
189 190 1.420641 GGCCGAAAATTCAATGGCGC 61.421 55.000 0.00 0.00 46.66 6.53
440 441 9.268268 GTGGTCGATCAATATTAACAAATCCTA 57.732 33.333 0.00 0.00 0.00 2.94
1163 1164 6.372659 TGTTCATGAGAGATTTGTTAGAAGGC 59.627 38.462 0.00 0.00 0.00 4.35
2234 2235 2.505650 TCCAGAAAATTCATGCCGGA 57.494 45.000 5.05 0.00 0.00 5.14
2235 2236 2.801483 TCCAGAAAATTCATGCCGGAA 58.199 42.857 5.05 0.00 0.00 4.30
2236 2237 3.364549 TCCAGAAAATTCATGCCGGAAT 58.635 40.909 5.05 0.00 39.11 3.01
2237 2238 3.130869 TCCAGAAAATTCATGCCGGAATG 59.869 43.478 17.25 17.25 37.55 2.67
2238 2239 3.130869 CCAGAAAATTCATGCCGGAATGA 59.869 43.478 22.06 22.06 37.55 2.57
2239 2240 4.202182 CCAGAAAATTCATGCCGGAATGAT 60.202 41.667 26.18 11.16 37.55 2.45
2240 2241 4.743151 CAGAAAATTCATGCCGGAATGATG 59.257 41.667 26.18 15.76 37.55 3.07
2241 2242 4.403432 AGAAAATTCATGCCGGAATGATGT 59.597 37.500 26.18 14.83 37.55 3.06
2242 2243 3.720949 AATTCATGCCGGAATGATGTG 57.279 42.857 26.18 0.00 37.55 3.21
2243 2244 2.127271 TTCATGCCGGAATGATGTGT 57.873 45.000 26.18 0.00 36.48 3.72
2244 2245 1.381522 TCATGCCGGAATGATGTGTG 58.618 50.000 22.06 0.00 31.58 3.82
2245 2246 1.097232 CATGCCGGAATGATGTGTGT 58.903 50.000 18.61 0.00 0.00 3.72
2246 2247 1.097232 ATGCCGGAATGATGTGTGTG 58.903 50.000 5.05 0.00 0.00 3.82
2247 2248 0.250684 TGCCGGAATGATGTGTGTGT 60.251 50.000 5.05 0.00 0.00 3.72
2248 2249 0.168788 GCCGGAATGATGTGTGTGTG 59.831 55.000 5.05 0.00 0.00 3.82
2249 2250 1.522668 CCGGAATGATGTGTGTGTGT 58.477 50.000 0.00 0.00 0.00 3.72
2250 2251 1.197492 CCGGAATGATGTGTGTGTGTG 59.803 52.381 0.00 0.00 0.00 3.82
2251 2252 1.872952 CGGAATGATGTGTGTGTGTGT 59.127 47.619 0.00 0.00 0.00 3.72
2252 2253 2.349722 CGGAATGATGTGTGTGTGTGTG 60.350 50.000 0.00 0.00 0.00 3.82
2253 2254 2.618241 GGAATGATGTGTGTGTGTGTGT 59.382 45.455 0.00 0.00 0.00 3.72
2254 2255 3.066621 GGAATGATGTGTGTGTGTGTGTT 59.933 43.478 0.00 0.00 0.00 3.32
2255 2256 3.696281 ATGATGTGTGTGTGTGTGTTG 57.304 42.857 0.00 0.00 0.00 3.33
2256 2257 1.742268 TGATGTGTGTGTGTGTGTTGG 59.258 47.619 0.00 0.00 0.00 3.77
2257 2258 1.065401 GATGTGTGTGTGTGTGTTGGG 59.935 52.381 0.00 0.00 0.00 4.12
2258 2259 0.962855 TGTGTGTGTGTGTGTTGGGG 60.963 55.000 0.00 0.00 0.00 4.96
2259 2260 1.379176 TGTGTGTGTGTGTTGGGGG 60.379 57.895 0.00 0.00 0.00 5.40
2287 2288 4.796495 GGTGGGGCGGCGAGATTT 62.796 66.667 12.98 0.00 0.00 2.17
2288 2289 2.750237 GTGGGGCGGCGAGATTTT 60.750 61.111 12.98 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1163 1164 3.705043 AGACTGCAGCAAACAAAGAAG 57.295 42.857 15.27 0.0 0.00 2.85
2234 2235 3.181488 CCAACACACACACACACATCATT 60.181 43.478 0.00 0.0 0.00 2.57
2235 2236 2.358582 CCAACACACACACACACATCAT 59.641 45.455 0.00 0.0 0.00 2.45
2236 2237 1.742268 CCAACACACACACACACATCA 59.258 47.619 0.00 0.0 0.00 3.07
2237 2238 1.065401 CCCAACACACACACACACATC 59.935 52.381 0.00 0.0 0.00 3.06
2238 2239 1.102154 CCCAACACACACACACACAT 58.898 50.000 0.00 0.0 0.00 3.21
2239 2240 0.962855 CCCCAACACACACACACACA 60.963 55.000 0.00 0.0 0.00 3.72
2240 2241 1.662438 CCCCCAACACACACACACAC 61.662 60.000 0.00 0.0 0.00 3.82
2241 2242 1.379176 CCCCCAACACACACACACA 60.379 57.895 0.00 0.0 0.00 3.72
2242 2243 3.520402 CCCCCAACACACACACAC 58.480 61.111 0.00 0.0 0.00 3.82
2270 2271 4.796495 AAATCTCGCCGCCCCACC 62.796 66.667 0.00 0.0 0.00 4.61
2271 2272 1.027792 TAAAAATCTCGCCGCCCCAC 61.028 55.000 0.00 0.0 0.00 4.61
2272 2273 0.746563 CTAAAAATCTCGCCGCCCCA 60.747 55.000 0.00 0.0 0.00 4.96
2273 2274 1.444917 CCTAAAAATCTCGCCGCCCC 61.445 60.000 0.00 0.0 0.00 5.80
2274 2275 0.746923 ACCTAAAAATCTCGCCGCCC 60.747 55.000 0.00 0.0 0.00 6.13
2275 2276 0.377203 CACCTAAAAATCTCGCCGCC 59.623 55.000 0.00 0.0 0.00 6.13
2276 2277 1.365699 TCACCTAAAAATCTCGCCGC 58.634 50.000 0.00 0.0 0.00 6.53
2277 2278 4.616181 AAATCACCTAAAAATCTCGCCG 57.384 40.909 0.00 0.0 0.00 6.46
2278 2279 6.308041 GTGAAAAATCACCTAAAAATCTCGCC 59.692 38.462 0.00 0.0 34.74 5.54
2279 2280 7.061094 CAGTGAAAAATCACCTAAAAATCTCGC 59.939 37.037 5.40 0.0 41.26 5.03
2280 2281 7.538678 CCAGTGAAAAATCACCTAAAAATCTCG 59.461 37.037 5.40 0.0 41.26 4.04
2281 2282 8.576442 TCCAGTGAAAAATCACCTAAAAATCTC 58.424 33.333 5.40 0.0 41.26 2.75
2282 2283 8.477419 TCCAGTGAAAAATCACCTAAAAATCT 57.523 30.769 5.40 0.0 41.26 2.40
2285 2286 9.581289 TCTATCCAGTGAAAAATCACCTAAAAA 57.419 29.630 5.40 0.0 41.26 1.94
2286 2287 9.231297 CTCTATCCAGTGAAAAATCACCTAAAA 57.769 33.333 5.40 0.0 41.26 1.52
2287 2288 8.383175 ACTCTATCCAGTGAAAAATCACCTAAA 58.617 33.333 5.40 0.0 41.26 1.85
2288 2289 7.824289 CACTCTATCCAGTGAAAAATCACCTAA 59.176 37.037 5.40 0.0 45.92 2.69


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

AutoCloner maintained by Alex Coulton.