Multiple sequence alignment - TraesCS5D01G356900

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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 TraesCS5D01G356900 chr5D 100.000 2593 0 0 1 2593 437832569 437829977 0.000000e+00 4789
1 TraesCS5D01G356900 chr5B 93.642 2265 40 22 362 2593 531737339 531735146 0.000000e+00 3290
2 TraesCS5D01G356900 chr5B 92.643 367 8 8 1 365 531737826 531737477 6.400000e-141 510
3 TraesCS5D01G356900 chr5A 97.479 833 10 7 1766 2593 552776458 552775632 0.000000e+00 1411
4 TraesCS5D01G356900 chr5A 96.879 801 22 1 968 1768 552777415 552776618 0.000000e+00 1338
5 TraesCS5D01G356900 chr5A 90.519 1002 25 19 1 977 552783656 552782700 0.000000e+00 1260


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 TraesCS5D01G356900 chr5D 437829977 437832569 2592 True 4789.0 4789 100.0000 1 2593 1 chr5D.!!$R1 2592
1 TraesCS5D01G356900 chr5B 531735146 531737826 2680 True 1900.0 3290 93.1425 1 2593 2 chr5B.!!$R1 2592
2 TraesCS5D01G356900 chr5A 552775632 552777415 1783 True 1374.5 1411 97.1790 968 2593 2 chr5A.!!$R2 1625
3 TraesCS5D01G356900 chr5A 552782700 552783656 956 True 1260.0 1260 90.5190 1 977 1 chr5A.!!$R1 976

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
454 605 0.387929 CATAAACCCTCTCCGCGCTA 59.612 55.0 5.56 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2462 5.418676 ACCTGAGTTGTCCAACAATTTTTG 58.581 37.5 12.32 0.0 40.59 2.44 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
68 70 0.485543 TCCCTAGGTGTGGAGTGTGA 59.514 55.000 8.29 0.00 0.00 3.58
253 260 8.500753 TGTACGTTTTTGAAAGATAGGCATAT 57.499 30.769 0.00 0.00 0.00 1.78
254 261 9.602568 TGTACGTTTTTGAAAGATAGGCATATA 57.397 29.630 0.00 0.00 0.00 0.86
297 304 7.667557 AGTAATTTTCTGGTCGCTAGCATATA 58.332 34.615 16.45 0.00 31.47 0.86
298 305 6.787085 AATTTTCTGGTCGCTAGCATATAC 57.213 37.500 16.45 6.74 31.47 1.47
299 306 3.554259 TTCTGGTCGCTAGCATATACG 57.446 47.619 16.45 0.00 31.47 3.06
300 307 2.501261 TCTGGTCGCTAGCATATACGT 58.499 47.619 16.45 0.00 31.47 3.57
301 308 3.667360 TCTGGTCGCTAGCATATACGTA 58.333 45.455 16.45 0.00 31.47 3.57
302 309 4.259356 TCTGGTCGCTAGCATATACGTAT 58.741 43.478 16.45 13.54 31.47 3.06
348 355 1.138266 GCCGCCTCTGGATTTACTGTA 59.862 52.381 0.00 0.00 0.00 2.74
349 356 2.224305 GCCGCCTCTGGATTTACTGTAT 60.224 50.000 0.00 0.00 0.00 2.29
350 357 3.744530 GCCGCCTCTGGATTTACTGTATT 60.745 47.826 0.00 0.00 0.00 1.89
351 358 4.502604 GCCGCCTCTGGATTTACTGTATTA 60.503 45.833 0.00 0.00 0.00 0.98
378 526 1.202486 TCTCTTAATTAGCACGCGGGG 60.202 52.381 11.92 2.33 0.00 5.73
407 555 4.843220 CGGGTACGGTATTCTCATTACT 57.157 45.455 0.00 0.00 36.18 2.24
408 556 5.947228 CGGGTACGGTATTCTCATTACTA 57.053 43.478 0.00 0.00 36.18 1.82
409 557 6.506500 CGGGTACGGTATTCTCATTACTAT 57.493 41.667 0.00 0.00 36.18 2.12
410 558 7.615582 CGGGTACGGTATTCTCATTACTATA 57.384 40.000 0.00 0.00 36.18 1.31
411 559 7.467623 CGGGTACGGTATTCTCATTACTATAC 58.532 42.308 0.00 0.00 36.18 1.47
412 560 7.335422 CGGGTACGGTATTCTCATTACTATACT 59.665 40.741 0.00 0.00 36.18 2.12
413 561 9.672673 GGGTACGGTATTCTCATTACTATACTA 57.327 37.037 0.00 0.00 0.00 1.82
454 605 0.387929 CATAAACCCTCTCCGCGCTA 59.612 55.000 5.56 0.00 0.00 4.26
455 606 0.674534 ATAAACCCTCTCCGCGCTAG 59.325 55.000 5.56 2.59 0.00 3.42
456 607 2.012902 TAAACCCTCTCCGCGCTAGC 62.013 60.000 5.56 4.06 40.74 3.42
457 608 4.824515 ACCCTCTCCGCGCTAGCT 62.825 66.667 13.93 0.00 42.32 3.32
614 765 4.924305 TCTTGCAGCTCTTTCATGTTTT 57.076 36.364 0.00 0.00 0.00 2.43
789 953 4.686972 GTCGTTACCAGTATTAACCCTCC 58.313 47.826 0.00 0.00 0.00 4.30
790 954 4.160252 GTCGTTACCAGTATTAACCCTCCA 59.840 45.833 0.00 0.00 0.00 3.86
791 955 4.964262 TCGTTACCAGTATTAACCCTCCAT 59.036 41.667 0.00 0.00 0.00 3.41
792 956 5.054477 CGTTACCAGTATTAACCCTCCATG 58.946 45.833 0.00 0.00 0.00 3.66
868 1032 8.571336 AGTCCTAATAATAACAAATGAGCATGC 58.429 33.333 10.51 10.51 0.00 4.06
869 1033 8.352201 GTCCTAATAATAACAAATGAGCATGCA 58.648 33.333 21.98 0.00 0.00 3.96
870 1034 9.081204 TCCTAATAATAACAAATGAGCATGCAT 57.919 29.630 21.98 1.94 0.00 3.96
871 1035 9.135843 CCTAATAATAACAAATGAGCATGCATG 57.864 33.333 22.70 22.70 0.00 4.06
888 1052 2.422803 GCATGTTGTCCAAGGGGCTATA 60.423 50.000 0.00 0.00 0.00 1.31
890 1054 4.506625 GCATGTTGTCCAAGGGGCTATATA 60.507 45.833 0.00 0.00 0.00 0.86
893 1057 4.010349 GTTGTCCAAGGGGCTATATATGC 58.990 47.826 0.00 0.00 0.00 3.14
894 1058 3.531059 TGTCCAAGGGGCTATATATGCT 58.469 45.455 0.00 0.00 0.00 3.79
895 1059 3.916349 TGTCCAAGGGGCTATATATGCTT 59.084 43.478 0.00 0.00 0.00 3.91
896 1060 4.263462 TGTCCAAGGGGCTATATATGCTTG 60.263 45.833 0.00 0.00 0.00 4.01
1004 1182 1.092348 GGACCGTTTCAACCTATGGC 58.908 55.000 0.00 0.00 0.00 4.40
1166 1344 3.064207 GACTTGCATTGGACGACTTACA 58.936 45.455 0.00 0.00 0.00 2.41
1167 1345 2.806244 ACTTGCATTGGACGACTTACAC 59.194 45.455 0.00 0.00 0.00 2.90
1168 1346 2.831685 TGCATTGGACGACTTACACT 57.168 45.000 0.00 0.00 0.00 3.55
1204 1382 9.139174 GTAGTACTAGCTAGCACTATACAGTAC 57.861 40.741 28.51 18.37 35.34 2.73
1211 1389 7.887381 AGCTAGCACTATACAGTACCATTTAG 58.113 38.462 18.83 0.00 32.21 1.85
1252 1430 3.491652 GTTTCTCTCAGCGGCGCC 61.492 66.667 30.40 19.07 0.00 6.53
1400 1578 4.083802 GCGTCATTATTTCCCTGCATACTC 60.084 45.833 0.00 0.00 0.00 2.59
1892 2237 3.507233 TCAGCACACATTTGAAAGGGATC 59.493 43.478 0.00 0.00 0.00 3.36
1893 2238 2.489329 AGCACACATTTGAAAGGGATCG 59.511 45.455 0.00 0.00 0.00 3.69
1894 2239 2.487762 GCACACATTTGAAAGGGATCGA 59.512 45.455 0.00 0.00 0.00 3.59
1895 2240 3.129287 GCACACATTTGAAAGGGATCGAT 59.871 43.478 0.00 0.00 0.00 3.59
2112 2462 5.356882 TTGGATTTCATTCGTGAGACAAC 57.643 39.130 0.00 0.00 41.84 3.32
2518 2868 1.268066 TAGGAACATGCACCGTACCA 58.732 50.000 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 2.665603 GAAGGCCAGGAGCTCGTT 59.334 61.111 5.01 0.00 43.05 3.85
87 89 0.038159 GTGGGACTTGACGACAGAGG 60.038 60.000 0.00 0.00 0.00 3.69
91 93 1.829096 TCGGTGGGACTTGACGACA 60.829 57.895 0.00 0.00 0.00 4.35
134 136 1.929038 GCTGACGTACGTGCAAGAAGA 60.929 52.381 28.16 0.00 0.00 2.87
170 173 4.031611 ACCTTCCACTTCCAGTACTATCC 58.968 47.826 0.00 0.00 0.00 2.59
256 263 9.460019 AGAAAATTACTACGTACTACTTCTCCT 57.540 33.333 0.00 0.00 0.00 3.69
297 304 5.932303 GTCCAAACATCCATGCTATATACGT 59.068 40.000 0.00 0.00 0.00 3.57
298 305 5.062183 CGTCCAAACATCCATGCTATATACG 59.938 44.000 0.00 0.00 0.00 3.06
299 306 6.163476 TCGTCCAAACATCCATGCTATATAC 58.837 40.000 0.00 0.00 0.00 1.47
300 307 6.353404 TCGTCCAAACATCCATGCTATATA 57.647 37.500 0.00 0.00 0.00 0.86
301 308 5.227569 TCGTCCAAACATCCATGCTATAT 57.772 39.130 0.00 0.00 0.00 0.86
302 309 4.681074 TCGTCCAAACATCCATGCTATA 57.319 40.909 0.00 0.00 0.00 1.31
348 355 7.857885 GCGTGCTAATTAAGAGAAGCAATTAAT 59.142 33.333 0.02 0.00 45.81 1.40
349 356 7.186804 GCGTGCTAATTAAGAGAAGCAATTAA 58.813 34.615 0.02 0.00 45.81 1.40
350 357 6.509517 CGCGTGCTAATTAAGAGAAGCAATTA 60.510 38.462 0.00 0.00 45.81 1.40
351 358 5.573146 GCGTGCTAATTAAGAGAAGCAATT 58.427 37.500 0.02 0.00 45.81 2.32
614 765 5.726980 AAAGATGCATGCCAAGAGTAAAA 57.273 34.783 16.68 0.00 0.00 1.52
633 784 2.739932 CGTGCAGATGGGAGGACTAAAG 60.740 54.545 0.00 0.00 0.00 1.85
724 879 9.429359 GACATCTTCTTGGGTTGATGTATATAG 57.571 37.037 7.33 0.00 46.22 1.31
725 880 8.088365 CGACATCTTCTTGGGTTGATGTATATA 58.912 37.037 7.33 0.00 46.22 0.86
726 881 6.931281 CGACATCTTCTTGGGTTGATGTATAT 59.069 38.462 7.33 0.00 46.22 0.86
727 882 6.280643 CGACATCTTCTTGGGTTGATGTATA 58.719 40.000 7.33 0.00 46.22 1.47
792 956 2.188829 TGCCCAGATGCGCTAATGC 61.189 57.895 9.73 4.56 0.00 3.56
868 1032 2.442236 ATAGCCCCTTGGACAACATG 57.558 50.000 0.00 0.00 0.00 3.21
869 1033 5.807721 GCATATATAGCCCCTTGGACAACAT 60.808 44.000 0.00 0.00 0.00 2.71
870 1034 4.506625 GCATATATAGCCCCTTGGACAACA 60.507 45.833 0.00 0.00 0.00 3.33
871 1035 4.010349 GCATATATAGCCCCTTGGACAAC 58.990 47.826 0.00 0.00 0.00 3.32
888 1052 4.202472 GGAGCCTAACCCTAACAAGCATAT 60.202 45.833 0.00 0.00 0.00 1.78
890 1054 2.092375 GGAGCCTAACCCTAACAAGCAT 60.092 50.000 0.00 0.00 0.00 3.79
893 1057 1.134491 CGGGAGCCTAACCCTAACAAG 60.134 57.143 0.00 0.00 44.72 3.16
894 1058 0.906775 CGGGAGCCTAACCCTAACAA 59.093 55.000 0.00 0.00 44.72 2.83
895 1059 0.979187 CCGGGAGCCTAACCCTAACA 60.979 60.000 0.00 0.00 44.72 2.41
896 1060 1.693152 CCCGGGAGCCTAACCCTAAC 61.693 65.000 18.48 0.00 44.72 2.34
921 1086 2.103263 GTCTCTCCAGTGAACTGTTGGT 59.897 50.000 9.49 0.00 42.27 3.67
1004 1182 3.561503 TCAATAGATACATCCGCGAACG 58.438 45.455 8.23 0.00 39.67 3.95
1204 1382 4.142381 GCCCAGCTTCAGTAAACTAAATGG 60.142 45.833 0.00 0.00 0.00 3.16
1211 1389 1.911057 AAGGCCCAGCTTCAGTAAAC 58.089 50.000 0.00 0.00 0.00 2.01
1400 1578 7.077605 CACCAAAACATAAGTGTCATGTGTAG 58.922 38.462 0.00 0.00 37.67 2.74
1502 1680 6.053005 TGGGATTAGAAACAGCCTATAAACG 58.947 40.000 0.00 0.00 0.00 3.60
1892 2237 5.779806 AGTTTCATCTTTCCGTGTAATCG 57.220 39.130 0.00 0.00 0.00 3.34
1895 2240 9.932207 TTCTTATAGTTTCATCTTTCCGTGTAA 57.068 29.630 0.00 0.00 0.00 2.41
2112 2462 5.418676 ACCTGAGTTGTCCAACAATTTTTG 58.581 37.500 12.32 0.00 40.59 2.44


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

AutoCloner maintained by Alex Coulton.