Multiple sequence alignment - TraesCS5D01G415300

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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 TraesCS5D01G415300 chr5D 100.000 2564 0 0 1 2564 477395094 477392531 0.000000e+00 4735
1 TraesCS5D01G415300 chr5D 89.355 310 14 4 1235 1544 7043680 7043390 3.120000e-99 372
2 TraesCS5D01G415300 chr5B 92.083 2602 107 42 16 2564 585025471 585022916 0.000000e+00 3572
3 TraesCS5D01G415300 chr5A 93.075 2094 89 21 495 2564 596581710 596579649 0.000000e+00 3013
4 TraesCS5D01G415300 chr5A 87.090 488 27 10 1 470 596582523 596582054 1.050000e-143 520
5 TraesCS5D01G415300 chr1A 95.000 120 5 1 1425 1544 31028717 31028599 1.210000e-43 187
6 TraesCS5D01G415300 chr6A 91.603 131 9 2 1414 1544 583369047 583368919 2.030000e-41 180


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 TraesCS5D01G415300 chr5D 477392531 477395094 2563 True 4735.0 4735 100.0000 1 2564 1 chr5D.!!$R2 2563
1 TraesCS5D01G415300 chr5B 585022916 585025471 2555 True 3572.0 3572 92.0830 16 2564 1 chr5B.!!$R1 2548
2 TraesCS5D01G415300 chr5A 596579649 596582523 2874 True 1766.5 3013 90.0825 1 2564 2 chr5A.!!$R1 2563

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
204 216 0.179176 CACAACACAACACCCACACG 60.179 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2506 0.03779 AGCAGCGGAGAAACAGAGAC 60.038 55.0 0.0 0.0 0.0 3.36 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
24 25 1.881252 CGCCACACACGTATAGCCC 60.881 63.158 0.00 0.00 0.00 5.19
27 28 1.618876 CCACACACGTATAGCCCCCA 61.619 60.000 0.00 0.00 0.00 4.96
98 105 3.117491 AGATTCATCCATGCCTACGTG 57.883 47.619 0.00 0.00 0.00 4.49
191 203 3.644774 CAGCATGCACAACACAACA 57.355 47.368 21.98 0.00 0.00 3.33
201 213 1.271102 ACAACACAACACAACACCCAC 59.729 47.619 0.00 0.00 0.00 4.61
202 214 1.270826 CAACACAACACAACACCCACA 59.729 47.619 0.00 0.00 0.00 4.17
204 216 0.179176 CACAACACAACACCCACACG 60.179 55.000 0.00 0.00 0.00 4.49
205 217 0.606944 ACAACACAACACCCACACGT 60.607 50.000 0.00 0.00 0.00 4.49
206 218 1.338864 ACAACACAACACCCACACGTA 60.339 47.619 0.00 0.00 0.00 3.57
315 347 2.561467 TACGAGATCCTGGGTCGCCA 62.561 60.000 5.05 0.00 37.20 5.69
316 348 2.502492 CGAGATCCTGGGTCGCCAT 61.502 63.158 5.05 0.00 0.00 4.40
317 349 1.070445 GAGATCCTGGGTCGCCATG 59.930 63.158 0.32 0.00 0.00 3.66
318 350 2.111878 GATCCTGGGTCGCCATGG 59.888 66.667 7.63 7.63 0.00 3.66
319 351 3.482232 GATCCTGGGTCGCCATGGG 62.482 68.421 15.13 3.69 0.00 4.00
321 353 4.047125 CCTGGGTCGCCATGGGTT 62.047 66.667 15.13 0.00 0.00 4.11
322 354 2.751436 CTGGGTCGCCATGGGTTG 60.751 66.667 15.13 0.00 0.00 3.77
474 517 6.627671 CCATTACTTCGCGATTAAGCTAAAAC 59.372 38.462 10.88 0.00 34.40 2.43
556 918 2.115266 ACCCACGCAAAAGGAGGG 59.885 61.111 0.00 0.00 45.20 4.30
559 921 3.373565 CACGCAAAAGGAGGGGGC 61.374 66.667 0.00 0.00 0.00 5.80
745 1111 1.663161 CGAGAAGAAAAAGGCGGCAAC 60.663 52.381 13.08 0.00 0.00 4.17
759 1125 2.281208 CAACGAAAGCCACCGGGA 60.281 61.111 6.32 0.00 35.59 5.14
786 1152 3.432592 GGAAGAAGAAGCCTCACGTAAAC 59.567 47.826 0.00 0.00 0.00 2.01
1332 1703 4.473520 GAGCTGGCCGCCAAGCTA 62.474 66.667 26.49 1.79 37.83 3.32
1566 1937 4.746466 CTTCCCTCATGACCTACTAGGAT 58.254 47.826 9.28 0.00 37.67 3.24
1648 2019 3.948473 TGTGAAAGTTTTGGAACGGATGA 59.052 39.130 0.00 0.00 40.75 2.92
1749 2136 2.222953 CCCGTGCTTATTTAGTTGACGC 60.223 50.000 0.00 0.00 0.00 5.19
1843 2233 4.648651 ACTAAATGGAAAACTACTGCCGT 58.351 39.130 0.00 0.00 0.00 5.68
1945 2336 2.547218 GCACCGGTCTCTCTGTTTTACA 60.547 50.000 2.59 0.00 0.00 2.41
1946 2337 3.724374 CACCGGTCTCTCTGTTTTACAA 58.276 45.455 2.59 0.00 0.00 2.41
2008 2406 1.148310 ACGGAAAAGATGCACGTCTG 58.852 50.000 0.00 0.00 31.39 3.51
2033 2431 2.341846 TTTATCCCCTGATTCACCGC 57.658 50.000 0.00 0.00 32.18 5.68
2034 2432 1.507140 TTATCCCCTGATTCACCGCT 58.493 50.000 0.00 0.00 32.18 5.52
2035 2433 1.048601 TATCCCCTGATTCACCGCTC 58.951 55.000 0.00 0.00 32.18 5.03
2036 2434 0.982852 ATCCCCTGATTCACCGCTCA 60.983 55.000 0.00 0.00 0.00 4.26
2037 2435 1.153289 CCCCTGATTCACCGCTCAG 60.153 63.158 0.00 0.00 38.88 3.35
2038 2436 1.817099 CCCTGATTCACCGCTCAGC 60.817 63.158 0.00 0.00 38.03 4.26
2067 2465 3.614176 CAGATTCACTGTGTGACCATACG 59.386 47.826 7.79 0.00 42.60 3.06
2108 2506 1.373748 CAGGTTGACGTACCCGGTG 60.374 63.158 0.00 0.00 39.08 4.94
2118 2516 1.668047 CGTACCCGGTGTCTCTGTTTC 60.668 57.143 0.00 0.00 0.00 2.78
2122 2520 0.388649 CCGGTGTCTCTGTTTCTCCG 60.389 60.000 0.00 0.00 37.77 4.63
2167 2565 1.596260 CTACGCCGTCTCTTGTCGATA 59.404 52.381 0.00 0.00 0.00 2.92
2284 2682 5.310451 AGTGAAAACAAAGAATAGGCCGTA 58.690 37.500 0.00 0.00 0.00 4.02
2361 2759 0.449388 CCAGCAGCCTTGAATCGAAC 59.551 55.000 0.00 0.00 0.00 3.95
2444 2846 3.620615 TTGCAGTTCAACAGTTGCG 57.379 47.368 8.58 0.00 39.34 4.85
2450 2852 0.307760 GTTCAACAGTTGCGTCCAGG 59.692 55.000 8.58 0.00 0.00 4.45
2487 2889 2.226674 GGGTTAGAGCAACTTCAACAGC 59.773 50.000 0.00 0.00 37.30 4.40
2491 2893 0.538287 GAGCAACTTCAACAGCCCCT 60.538 55.000 0.00 0.00 0.00 4.79
2492 2894 0.771127 AGCAACTTCAACAGCCCCTA 59.229 50.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.523032 GGGGCTATACGTGTGTGGC 60.523 63.158 0.00 1.51 0.00 5.01
24 25 4.173971 GTACGCGTGGTACTTGGG 57.826 61.111 24.59 0.00 46.50 4.12
42 43 4.089493 CACTGCACAAGTATGTACACGTAC 59.911 45.833 0.00 0.00 37.82 3.67
98 105 5.228012 GTCACGTGGTAAATAAGTAGTACGC 59.772 44.000 17.00 0.00 34.01 4.42
191 203 2.034124 ACTACTACGTGTGGGTGTTGT 58.966 47.619 0.00 0.00 0.00 3.32
201 213 3.059461 GCTAGCTAGCTGACTACTACGTG 60.059 52.174 33.71 0.00 45.62 4.49
202 214 3.132925 GCTAGCTAGCTGACTACTACGT 58.867 50.000 33.71 0.00 45.62 3.57
204 216 2.096119 GCGCTAGCTAGCTGACTACTAC 60.096 54.545 36.02 15.36 46.85 2.73
205 217 2.144730 GCGCTAGCTAGCTGACTACTA 58.855 52.381 36.02 4.07 46.85 1.82
206 218 0.948678 GCGCTAGCTAGCTGACTACT 59.051 55.000 36.02 1.05 46.85 2.57
226 240 1.079503 GGCTTTGTCTCAACCGCTAG 58.920 55.000 0.00 0.00 0.00 3.42
227 241 0.321298 GGGCTTTGTCTCAACCGCTA 60.321 55.000 0.00 0.00 0.00 4.26
229 243 2.954611 GGGCTTTGTCTCAACCGC 59.045 61.111 0.00 0.00 0.00 5.68
230 244 1.597027 ACGGGCTTTGTCTCAACCG 60.597 57.895 0.00 0.00 46.16 4.44
231 245 0.818040 ACACGGGCTTTGTCTCAACC 60.818 55.000 0.00 0.00 0.00 3.77
232 246 0.586802 GACACGGGCTTTGTCTCAAC 59.413 55.000 10.57 0.00 40.30 3.18
233 247 0.534203 GGACACGGGCTTTGTCTCAA 60.534 55.000 15.46 0.00 42.63 3.02
234 248 1.070786 GGACACGGGCTTTGTCTCA 59.929 57.895 15.46 0.00 42.63 3.27
235 249 1.671379 GGGACACGGGCTTTGTCTC 60.671 63.158 15.46 10.09 42.63 3.36
236 250 2.113243 GAGGGACACGGGCTTTGTCT 62.113 60.000 15.46 1.23 42.63 3.41
239 253 2.359975 GGAGGGACACGGGCTTTG 60.360 66.667 0.00 0.00 0.00 2.77
296 328 1.826921 GGCGACCCAGGATCTCGTA 60.827 63.158 3.64 0.00 0.00 3.43
493 855 4.143333 CCCGCGTAGGTCCAGGTG 62.143 72.222 4.92 0.00 38.74 4.00
591 953 2.967076 CAATGGACGGCGGATCGG 60.967 66.667 13.24 0.00 0.00 4.18
662 1024 1.070275 CCGGGCCCGTATAAACCTC 59.930 63.158 40.52 0.00 37.81 3.85
745 1111 3.869473 TTCGTCCCGGTGGCTTTCG 62.869 63.158 0.00 0.00 0.00 3.46
759 1125 1.971357 TGAGGCTTCTTCTTCCTTCGT 59.029 47.619 0.00 0.00 0.00 3.85
1026 1397 0.460109 TCATCGCGTCCATGTCAAGG 60.460 55.000 5.77 0.00 0.00 3.61
1304 1675 4.482684 CCAGCTCGCGCTTCTCGA 62.483 66.667 5.56 0.00 46.47 4.04
1566 1937 2.272146 GCGCCCTCCTTCATTCCA 59.728 61.111 0.00 0.00 0.00 3.53
1648 2019 0.718343 GCACGTAGTACTCTCGTCGT 59.282 55.000 18.64 11.64 41.61 4.34
1717 2093 1.562672 AAGCACGGGTCCCTAGCATT 61.563 55.000 19.94 10.59 0.00 3.56
1724 2100 2.681344 CAACTAAATAAGCACGGGTCCC 59.319 50.000 0.00 0.00 0.00 4.46
1778 2165 6.166984 ACGATCCATTCATTCATGTAGAGT 57.833 37.500 0.00 0.00 0.00 3.24
1779 2166 5.636965 GGACGATCCATTCATTCATGTAGAG 59.363 44.000 0.00 0.00 36.28 2.43
1780 2167 5.541845 GGACGATCCATTCATTCATGTAGA 58.458 41.667 0.00 0.00 36.28 2.59
1843 2233 0.938713 CTTCACGTACGGTGCCAAAA 59.061 50.000 21.06 5.18 46.56 2.44
1945 2336 4.982916 GCTGTCGACGTTAGATAATCCATT 59.017 41.667 11.62 0.00 0.00 3.16
1946 2337 4.547532 GCTGTCGACGTTAGATAATCCAT 58.452 43.478 11.62 0.00 0.00 3.41
2021 2419 3.805267 GCTGAGCGGTGAATCAGG 58.195 61.111 0.00 0.00 42.62 3.86
2035 2433 1.657594 CAGTGAATCTGCAGTACGCTG 59.342 52.381 23.82 23.82 45.23 5.18
2036 2434 2.001812 CAGTGAATCTGCAGTACGCT 57.998 50.000 14.67 14.31 43.06 5.07
2038 2436 5.889295 GTCACACAGTGAATCTGCAGTACG 61.889 50.000 14.67 8.08 44.49 3.67
2039 2437 3.430218 GTCACACAGTGAATCTGCAGTAC 59.570 47.826 14.67 9.06 44.49 2.73
2040 2438 3.554960 GGTCACACAGTGAATCTGCAGTA 60.555 47.826 14.67 0.48 44.49 2.74
2041 2439 2.487934 GTCACACAGTGAATCTGCAGT 58.512 47.619 14.67 0.00 44.49 4.40
2042 2440 1.802960 GGTCACACAGTGAATCTGCAG 59.197 52.381 7.63 7.63 44.49 4.41
2066 2464 0.247655 CATGCCGACGACCATTTTCG 60.248 55.000 0.00 0.00 44.87 3.46
2067 2465 0.802494 ACATGCCGACGACCATTTTC 59.198 50.000 0.00 0.00 0.00 2.29
2108 2506 0.037790 AGCAGCGGAGAAACAGAGAC 60.038 55.000 0.00 0.00 0.00 3.36
2118 2516 2.030457 CACCGTTAAATAAGCAGCGGAG 59.970 50.000 7.80 0.00 41.45 4.63
2122 2520 2.911819 TGCACCGTTAAATAAGCAGC 57.088 45.000 0.00 0.00 0.00 5.25
2284 2682 7.473735 TCTGTCTCTGTCAAATTCTATCACT 57.526 36.000 0.00 0.00 0.00 3.41
2361 2759 1.815003 CTCTTGCCTTTGCCCTACTTG 59.185 52.381 0.00 0.00 36.33 3.16
2444 2846 4.884164 CCTTTAGATCAATGGAACCTGGAC 59.116 45.833 0.00 0.00 34.08 4.02
2450 2852 6.261158 GCTCTAACCCTTTAGATCAATGGAAC 59.739 42.308 0.00 0.00 42.35 3.62
2487 2889 2.438392 GACTGGGGACTATGTTTAGGGG 59.562 54.545 0.00 0.00 0.00 4.79
2491 2893 2.046729 AGGGGACTGGGGACTATGTTTA 59.953 50.000 0.00 0.00 41.13 2.01
2492 2894 1.203570 AGGGGACTGGGGACTATGTTT 60.204 52.381 0.00 0.00 41.13 2.83


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

AutoCloner maintained by Alex Coulton.