Multiple sequence alignment - TraesCS5D01G149400

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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 TraesCS5D01G149400 chr5D 100.000 2285 0 0 1 2285 238382001 238384285 0.000000e+00 4220.0
1 TraesCS5D01G149400 chr5B 92.854 2309 127 19 1 2285 267114736 267112442 0.000000e+00 3315.0
2 TraesCS5D01G149400 chr5A 92.886 1715 52 22 623 2285 316351776 316350080 0.000000e+00 2427.0
3 TraesCS5D01G149400 chr5A 89.802 657 63 3 4 656 316352551 316351895 0.000000e+00 839.0
4 TraesCS5D01G149400 chr3D 87.209 86 10 1 144 228 413646100 413646185 1.870000e-16 97.1


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 TraesCS5D01G149400 chr5D 238382001 238384285 2284 False 4220 4220 100.000 1 2285 1 chr5D.!!$F1 2284
1 TraesCS5D01G149400 chr5B 267112442 267114736 2294 True 3315 3315 92.854 1 2285 1 chr5B.!!$R1 2284
2 TraesCS5D01G149400 chr5A 316350080 316352551 2471 True 1633 2427 91.344 4 2285 2 chr5A.!!$R1 2281

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
468 470 0.178068 CCATCTTCCGTCGTCCCAAT 59.822 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 1481 0.60478 GAGCCAGCAAGAGAACAGCA 60.605 55.0 0.0 0.0 0.0 4.41 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
71 72 1.067974 TGTCCCACACGTCAGTAACAG 59.932 52.381 0.00 0.00 0.00 3.16
76 77 0.382873 ACACGTCAGTAACAGCGACA 59.617 50.000 0.00 0.00 0.00 4.35
92 93 2.886081 CGACAGCTAGCAATCAACTCT 58.114 47.619 18.83 0.00 0.00 3.24
293 295 3.157087 TCAACCCAAAGCCATCTTTCTC 58.843 45.455 0.00 0.00 40.35 2.87
302 304 1.777101 CCATCTTTCTCGCGATCTCC 58.223 55.000 10.36 0.00 0.00 3.71
310 312 2.180769 CGCGATCTCCGTCACCAA 59.819 61.111 0.00 0.00 41.15 3.67
354 356 1.296715 GACCTCGCATCAACCCACT 59.703 57.895 0.00 0.00 0.00 4.00
357 359 1.361668 CCTCGCATCAACCCACTTCG 61.362 60.000 0.00 0.00 0.00 3.79
365 367 3.226346 TCAACCCACTTCGTCTAATCG 57.774 47.619 0.00 0.00 0.00 3.34
397 399 4.643387 GCCGCCCCACAGTGAGTT 62.643 66.667 0.62 0.00 0.00 3.01
405 407 1.002888 CCCACAGTGAGTTGAGAGCAT 59.997 52.381 0.62 0.00 0.00 3.79
408 410 3.597255 CACAGTGAGTTGAGAGCATCAT 58.403 45.455 0.00 0.00 37.89 2.45
422 424 3.102972 AGCATCATCCGGTCTAGCATAT 58.897 45.455 0.00 0.00 0.00 1.78
442 444 1.063942 TCCTCACCGCTCTAGAATCCA 60.064 52.381 0.00 0.00 0.00 3.41
446 448 0.315568 ACCGCTCTAGAATCCATCGC 59.684 55.000 0.00 0.00 0.00 4.58
468 470 0.178068 CCATCTTCCGTCGTCCCAAT 59.822 55.000 0.00 0.00 0.00 3.16
484 486 6.264292 TCGTCCCAATTTCAAAAGAGATCAAA 59.736 34.615 0.00 0.00 0.00 2.69
488 490 6.707161 CCCAATTTCAAAAGAGATCAAAGCAA 59.293 34.615 0.00 0.00 0.00 3.91
492 494 4.813027 TCAAAAGAGATCAAAGCAATGGC 58.187 39.130 0.00 0.00 41.61 4.40
500 502 1.614903 TCAAAGCAATGGCCTTGACAG 59.385 47.619 16.28 5.44 43.62 3.51
523 525 3.061322 CCCAATTTTAGTCGACGTCACA 58.939 45.455 17.16 0.00 0.00 3.58
525 527 4.153475 CCCAATTTTAGTCGACGTCACAAT 59.847 41.667 17.16 2.90 0.00 2.71
542 544 1.227999 AATGACACCAGACAACGCCG 61.228 55.000 0.00 0.00 0.00 6.46
578 580 7.468631 GCACGTCCATCATAGAATTTACCAATT 60.469 37.037 0.00 0.00 35.12 2.32
579 581 9.051679 CACGTCCATCATAGAATTTACCAATTA 57.948 33.333 0.00 0.00 32.35 1.40
580 582 9.052759 ACGTCCATCATAGAATTTACCAATTAC 57.947 33.333 0.00 0.00 32.35 1.89
657 814 5.347012 ACCGGTTACGTAAACAAGAAATG 57.653 39.130 22.44 4.84 40.08 2.32
947 1112 2.190578 CTTCCATCCCAGACGCCC 59.809 66.667 0.00 0.00 0.00 6.13
948 1113 2.609299 TTCCATCCCAGACGCCCA 60.609 61.111 0.00 0.00 0.00 5.36
949 1114 1.987807 CTTCCATCCCAGACGCCCAT 61.988 60.000 0.00 0.00 0.00 4.00
1587 1771 3.084070 TCGATCGGTGAGATGAACATG 57.916 47.619 16.41 0.00 40.26 3.21
1629 1813 1.600413 GCTTCTTGTTTGGAACCAGCG 60.600 52.381 0.00 0.00 0.00 5.18
1799 2002 5.412904 GCTAGCATGGGTCATTTAGGTATTC 59.587 44.000 10.63 0.00 0.00 1.75
1841 2044 7.763071 GCCGGAATATAGTAACCTAAATTCGAT 59.237 37.037 5.05 0.00 0.00 3.59
1970 2184 2.093553 ACCCATTTGTTGGTATGCATGC 60.094 45.455 11.82 11.82 44.83 4.06
2029 2243 6.536224 TGATGCTGTCAGTGACTGTAATAATG 59.464 38.462 25.42 7.41 34.68 1.90
2146 2361 2.556534 ACCAGATCAAGCGTACGTAC 57.443 50.000 17.90 15.90 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 1.325943 GAGTTGATTGCTAGCTGTCGC 59.674 52.381 17.23 10.32 0.00 5.19
76 77 4.815533 TCAAGAGAGTTGATTGCTAGCT 57.184 40.909 17.23 0.00 0.00 3.32
92 93 3.559655 CAGGTGTTTGTCGTTGATCAAGA 59.440 43.478 8.80 5.97 0.00 3.02
246 248 8.277490 TCTATGTATTTGTGTTCTCGTACTCT 57.723 34.615 0.00 0.00 0.00 3.24
293 295 2.158959 GTTGGTGACGGAGATCGCG 61.159 63.158 0.00 0.00 43.89 5.87
302 304 0.395312 ACCTTACAGGGTTGGTGACG 59.605 55.000 0.00 0.00 40.58 4.35
310 312 3.330701 ACACATCATCAACCTTACAGGGT 59.669 43.478 0.00 0.00 40.58 4.34
320 322 2.668457 GAGGTCACGACACATCATCAAC 59.332 50.000 0.00 0.00 0.00 3.18
365 367 4.943822 GGCTTGGTGAGGCTACTC 57.056 61.111 0.00 0.00 46.86 2.59
397 399 2.234143 CTAGACCGGATGATGCTCTCA 58.766 52.381 9.46 0.00 38.53 3.27
405 407 3.245264 TGAGGATATGCTAGACCGGATGA 60.245 47.826 9.46 0.00 0.00 2.92
408 410 2.515854 GTGAGGATATGCTAGACCGGA 58.484 52.381 9.46 0.00 0.00 5.14
422 424 1.063942 TGGATTCTAGAGCGGTGAGGA 60.064 52.381 0.00 0.00 0.00 3.71
442 444 1.742768 GACGGAAGATGGAGGCGAT 59.257 57.895 0.00 0.00 0.00 4.58
446 448 1.437986 GGACGACGGAAGATGGAGG 59.562 63.158 0.00 0.00 0.00 4.30
468 470 5.697633 GCCATTGCTTTGATCTCTTTTGAAA 59.302 36.000 0.00 0.00 33.53 2.69
484 486 4.428845 CCTGTCAAGGCCATTGCT 57.571 55.556 5.01 0.00 38.89 3.91
497 499 2.433436 GTCGACTAAAATTGGGCCTGT 58.567 47.619 8.70 0.00 0.00 4.00
500 502 1.395954 GACGTCGACTAAAATTGGGCC 59.604 52.381 14.70 0.00 0.00 5.80
507 509 4.959631 GTCATTGTGACGTCGACTAAAA 57.040 40.909 14.70 1.84 37.67 1.52
523 525 1.227999 CGGCGTTGTCTGGTGTCATT 61.228 55.000 0.00 0.00 0.00 2.57
525 527 2.279851 CGGCGTTGTCTGGTGTCA 60.280 61.111 0.00 0.00 0.00 3.58
550 552 2.890808 ATTCTATGATGGACGTGCGT 57.109 45.000 0.00 0.00 0.00 5.24
554 556 9.052759 GTAATTGGTAAATTCTATGATGGACGT 57.947 33.333 0.00 0.00 37.23 4.34
657 814 2.386661 ATCGTGTGTGGTCTGGATTC 57.613 50.000 0.00 0.00 0.00 2.52
1312 1481 0.604780 GAGCCAGCAAGAGAACAGCA 60.605 55.000 0.00 0.00 0.00 4.41
1405 1579 9.288576 CGGGCCATATATATGTATTTGATTGAT 57.711 33.333 19.11 0.00 31.82 2.57
1406 1580 7.719193 CCGGGCCATATATATGTATTTGATTGA 59.281 37.037 19.11 0.00 31.82 2.57
1407 1581 7.502226 ACCGGGCCATATATATGTATTTGATTG 59.498 37.037 19.11 4.28 31.82 2.67
1408 1582 7.582719 ACCGGGCCATATATATGTATTTGATT 58.417 34.615 19.11 0.00 31.82 2.57
1587 1771 8.574196 AAGCACAAATCTGTACAAATTACAAC 57.426 30.769 0.00 0.00 33.22 3.32
1799 2002 1.467374 CCGGCCGTGCTAATTGAAAAG 60.467 52.381 26.12 0.00 0.00 2.27
1970 2184 6.586868 TTTGAGCATTGTTTTAAACTGCAG 57.413 33.333 19.29 13.48 35.32 4.41
1985 2199 7.924412 CAGCATCATTAACCTTAATTTGAGCAT 59.076 33.333 0.00 0.00 31.28 3.79
2029 2243 4.515191 TGACTTTGATGCACAGGTTAAGTC 59.485 41.667 16.39 16.39 40.31 3.01
2146 2361 5.062308 GTGAGGTTTAATTCTACAGCGACAG 59.938 44.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.