Multiple sequence alignment - TraesCS2B01G546200

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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 TraesCS2B01G546200 chr2B 100.000 2198 0 0 1 2198 742892185 742894382 0.000000e+00 4060
1 TraesCS2B01G546200 chr2A 94.055 1884 92 10 326 2196 740873367 740875243 0.000000e+00 2841
2 TraesCS2B01G546200 chr2A 96.215 317 10 1 1 315 740872996 740873312 3.230000e-143 518
3 TraesCS2B01G546200 chr2D 94.172 1287 54 11 330 1605 608978956 608980232 0.000000e+00 1941
4 TraesCS2B01G546200 chr2D 89.701 602 51 8 1601 2196 608980333 608980929 0.000000e+00 758
5 TraesCS2B01G546200 chr2D 96.677 331 11 0 1 331 608978572 608978902 3.190000e-153 551


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 TraesCS2B01G546200 chr2B 742892185 742894382 2197 False 4060.000000 4060 100.000000 1 2198 1 chr2B.!!$F1 2197
1 TraesCS2B01G546200 chr2A 740872996 740875243 2247 False 1679.500000 2841 95.135000 1 2196 2 chr2A.!!$F1 2195
2 TraesCS2B01G546200 chr2D 608978572 608980929 2357 False 1083.333333 1941 93.516667 1 2196 3 chr2D.!!$F1 2195

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
423 486 0.041312 GCGCACGAAACAGTGAACAT 60.041 50.0 0.3 0.0 44.43 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1581 1.000274 GCCACCAGTGCTACAAAAAGG 60.0 52.381 0.0 0.0 0.0 3.11 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
27 28 3.126831 GAGTCGAGGATGTAGGCATTTG 58.873 50.000 0.00 0.00 35.07 2.32
64 65 8.771920 ATTAACAAATCTGAGTGTCGTATTGA 57.228 30.769 0.00 0.00 0.00 2.57
343 401 4.126437 TGGCGATGATACACGAATCATTT 58.874 39.130 11.84 0.00 44.69 2.32
356 419 8.044060 ACACGAATCATTTGTAATCAAGACAT 57.956 30.769 0.00 0.00 34.88 3.06
363 426 8.883954 TCATTTGTAATCAAGACATGCAAAAA 57.116 26.923 0.00 0.00 34.88 1.94
364 427 8.980610 TCATTTGTAATCAAGACATGCAAAAAG 58.019 29.630 0.00 0.00 34.88 2.27
365 428 8.980610 CATTTGTAATCAAGACATGCAAAAAGA 58.019 29.630 0.00 0.00 34.88 2.52
366 429 9.715121 ATTTGTAATCAAGACATGCAAAAAGAT 57.285 25.926 0.00 0.00 34.88 2.40
367 430 8.523523 TTGTAATCAAGACATGCAAAAAGATG 57.476 30.769 0.00 0.00 0.00 2.90
368 431 6.587226 TGTAATCAAGACATGCAAAAAGATGC 59.413 34.615 0.00 0.00 46.58 3.91
376 439 2.955607 GCAAAAAGATGCAACTTGCC 57.044 45.000 10.27 0.00 44.23 4.52
377 440 2.486918 GCAAAAAGATGCAACTTGCCT 58.513 42.857 10.27 0.92 44.23 4.75
378 441 3.652274 GCAAAAAGATGCAACTTGCCTA 58.348 40.909 10.27 0.00 44.23 3.93
380 443 4.092383 GCAAAAAGATGCAACTTGCCTATG 59.908 41.667 10.27 6.56 44.23 2.23
382 445 5.927281 AAAAGATGCAACTTGCCTATGAT 57.073 34.783 10.27 0.00 44.23 2.45
383 446 5.511234 AAAGATGCAACTTGCCTATGATC 57.489 39.130 10.27 7.04 44.23 2.92
384 447 4.160642 AGATGCAACTTGCCTATGATCA 57.839 40.909 11.29 0.00 44.23 2.92
385 448 4.529897 AGATGCAACTTGCCTATGATCAA 58.470 39.130 11.29 0.00 44.23 2.57
386 449 4.337555 AGATGCAACTTGCCTATGATCAAC 59.662 41.667 11.29 0.00 44.23 3.18
403 466 1.001924 CAACGCAGCACAATGGTTGTA 60.002 47.619 0.00 0.00 43.23 2.41
406 469 0.454957 GCAGCACAATGGTTGTAGCG 60.455 55.000 0.00 0.00 43.23 4.26
423 486 0.041312 GCGCACGAAACAGTGAACAT 60.041 50.000 0.30 0.00 44.43 2.71
718 781 0.832135 GGCATCTCTCCCATCGGGTA 60.832 60.000 0.00 0.00 44.74 3.69
751 814 2.617274 GGTTCTTGTGGCACTCCGC 61.617 63.158 19.83 5.33 43.16 5.54
809 872 4.760047 TTCTCAAGCTCGGCCGGC 62.760 66.667 27.83 26.36 0.00 6.13
830 893 2.038007 TCTTGCGGCCTCTCCTCT 59.962 61.111 0.00 0.00 0.00 3.69
838 901 0.399806 GGCCTCTCCTCTTCCCTGAT 60.400 60.000 0.00 0.00 0.00 2.90
839 902 1.506025 GCCTCTCCTCTTCCCTGATT 58.494 55.000 0.00 0.00 0.00 2.57
843 906 0.179062 CTCCTCTTCCCTGATTGCCG 60.179 60.000 0.00 0.00 0.00 5.69
859 922 1.956170 CCGGCATGGTCGCTGATAC 60.956 63.158 0.00 0.00 41.00 2.24
929 995 4.162690 GGCGGCTGAGGGTGGTAG 62.163 72.222 0.00 0.00 0.00 3.18
1301 1370 2.546368 GACTGCGTTATTGTTGGTGTCA 59.454 45.455 0.00 0.00 0.00 3.58
1432 1501 5.104941 TGGAGAGTTTCTTTGTGACTGAGAA 60.105 40.000 0.00 0.00 0.00 2.87
1446 1515 3.062763 ACTGAGAAGCATGAACGAACAG 58.937 45.455 0.00 0.92 0.00 3.16
1450 1519 5.478407 TGAGAAGCATGAACGAACAGATAA 58.522 37.500 0.00 0.00 0.00 1.75
1588 1658 3.544684 TGTGTTGACAGAAGCATCAGTT 58.455 40.909 0.00 0.00 0.00 3.16
1723 1898 4.051237 GGACACAAAAACTGCAATTCCTC 58.949 43.478 0.00 0.00 0.00 3.71
1724 1899 3.705604 ACACAAAAACTGCAATTCCTCG 58.294 40.909 0.00 0.00 0.00 4.63
1734 1909 4.245660 CTGCAATTCCTCGACTACTTGAA 58.754 43.478 0.00 0.00 0.00 2.69
1741 1916 7.829378 ATTCCTCGACTACTTGAACAATAAC 57.171 36.000 0.00 0.00 0.00 1.89
1773 1948 7.568199 TCTTTGGAACTCAGGTTTCTAAAAG 57.432 36.000 0.00 0.00 35.58 2.27
1781 1956 8.870075 AACTCAGGTTTCTAAAAGCTTATGAT 57.130 30.769 0.00 0.00 30.55 2.45
1834 2010 2.490718 CCTCTTTGGTCCATGGGAAACA 60.491 50.000 13.02 0.00 31.38 2.83
1843 2019 5.782331 TGGTCCATGGGAAACAAAAATATGA 59.218 36.000 13.02 0.00 31.38 2.15
1910 2088 7.429374 AATATGAAGTGAGAAGATGTCTGGA 57.571 36.000 0.00 0.00 36.41 3.86
1924 2102 3.146066 TGTCTGGAAGGCACAAATACAC 58.854 45.455 0.00 0.00 44.24 2.90
1934 2112 4.527816 AGGCACAAATACACATTTCCATGT 59.472 37.500 0.00 0.00 45.18 3.21
1963 2141 5.578157 ACCACTATTTTTCACTAGGTGGT 57.422 39.130 8.76 8.76 37.79 4.16
2030 2208 9.374838 AGAAAACAATCCATAGAAATTGATTGC 57.625 29.630 11.73 0.00 43.86 3.56
2033 2211 7.427989 ACAATCCATAGAAATTGATTGCCTT 57.572 32.000 11.73 0.00 43.86 4.35
2049 2227 4.519540 TGCCTTGCTTCTTTTATCCAAC 57.480 40.909 0.00 0.00 0.00 3.77
2071 2249 6.800072 ACTGACCCTAAAAACAAATTTCCA 57.200 33.333 0.00 0.00 0.00 3.53
2102 2280 9.042008 GCAGAAATCATGCAAAAATCTTATGAT 57.958 29.630 0.00 0.00 43.31 2.45
2181 2361 3.023119 TGCATATGGACACATGGGTTTC 58.977 45.455 0.00 0.00 37.97 2.78
2189 2369 3.754323 GGACACATGGGTTTCGAATTACA 59.246 43.478 0.00 0.00 0.00 2.41
2196 2376 5.682943 TGGGTTTCGAATTACAAGAAGTG 57.317 39.130 0.00 0.00 0.00 3.16
2197 2377 5.369833 TGGGTTTCGAATTACAAGAAGTGA 58.630 37.500 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.681538 TGCCTACATCCTCGACTCTC 58.318 55.000 0.00 0.00 0.00 3.20
10 11 2.632377 ACACAAATGCCTACATCCTCG 58.368 47.619 0.00 0.00 34.62 4.63
27 28 9.612620 CTCAGATTTGTTAATAAGGTTCAACAC 57.387 33.333 0.00 0.00 31.00 3.32
64 65 9.944663 AAATTCGTACGATTAAATGCAATACAT 57.055 25.926 20.27 0.93 42.30 2.29
343 401 6.587226 GCATCTTTTTGCATGTCTTGATTACA 59.413 34.615 0.00 0.00 42.31 2.41
367 430 2.792542 GCGTTGATCATAGGCAAGTTGC 60.793 50.000 19.87 19.87 44.08 4.17
368 431 2.419673 TGCGTTGATCATAGGCAAGTTG 59.580 45.455 17.13 0.00 33.91 3.16
369 432 2.679837 CTGCGTTGATCATAGGCAAGTT 59.320 45.455 18.81 0.00 36.15 2.66
371 434 1.003116 GCTGCGTTGATCATAGGCAAG 60.003 52.381 18.81 15.15 36.15 4.01
372 435 1.016627 GCTGCGTTGATCATAGGCAA 58.983 50.000 18.81 8.98 36.15 4.52
374 437 0.305922 GTGCTGCGTTGATCATAGGC 59.694 55.000 0.00 5.98 0.00 3.93
375 438 1.655484 TGTGCTGCGTTGATCATAGG 58.345 50.000 0.00 0.00 0.00 2.57
376 439 3.547413 CCATTGTGCTGCGTTGATCATAG 60.547 47.826 0.00 0.00 0.00 2.23
377 440 2.355444 CCATTGTGCTGCGTTGATCATA 59.645 45.455 0.00 0.00 0.00 2.15
378 441 1.133598 CCATTGTGCTGCGTTGATCAT 59.866 47.619 0.00 0.00 0.00 2.45
380 443 0.523072 ACCATTGTGCTGCGTTGATC 59.477 50.000 0.00 0.00 0.00 2.92
382 445 0.030504 CAACCATTGTGCTGCGTTGA 59.969 50.000 9.32 0.00 36.72 3.18
383 446 0.248990 ACAACCATTGTGCTGCGTTG 60.249 50.000 12.26 12.26 43.48 4.10
384 447 1.266718 CTACAACCATTGTGCTGCGTT 59.733 47.619 4.46 0.00 45.03 4.84
385 448 0.874390 CTACAACCATTGTGCTGCGT 59.126 50.000 4.46 0.00 45.03 5.24
386 449 0.454957 GCTACAACCATTGTGCTGCG 60.455 55.000 4.46 0.00 45.03 5.18
403 466 1.087202 TGTTCACTGTTTCGTGCGCT 61.087 50.000 9.73 0.00 34.92 5.92
406 469 4.661993 TGATATGTTCACTGTTTCGTGC 57.338 40.909 0.00 0.00 34.92 5.34
423 486 3.631686 GGTGCTTGCACCATAATGTGATA 59.368 43.478 32.37 0.00 44.39 2.15
718 781 0.637743 GAACCCTAGGGAGAGGAGGT 59.362 60.000 35.38 6.09 39.15 3.85
751 814 0.322456 TTTCGTGCCAGAATCAGGGG 60.322 55.000 0.00 0.00 0.00 4.79
757 820 1.004745 AGGTCCATTTCGTGCCAGAAT 59.995 47.619 0.00 0.00 0.00 2.40
809 872 2.498726 GAGAGGCCGCAAGAGAGG 59.501 66.667 9.88 0.00 43.02 3.69
830 893 1.753848 CATGCCGGCAATCAGGGAA 60.754 57.895 36.33 6.47 0.00 3.97
843 906 0.601311 GAGGTATCAGCGACCATGCC 60.601 60.000 0.00 0.00 39.65 4.40
1016 1082 3.324108 TACCCTCAACCGCCCACC 61.324 66.667 0.00 0.00 0.00 4.61
1025 1091 1.837439 CCACAGGCATACTACCCTCAA 59.163 52.381 0.00 0.00 0.00 3.02
1058 1127 2.440627 ACAAGCATATCATCCTCAGCCA 59.559 45.455 0.00 0.00 0.00 4.75
1097 1166 4.097361 GGGAAGGAGTCACCGCCC 62.097 72.222 4.92 4.92 45.58 6.13
1204 1273 1.304381 GGCAAGGTGATCAAGGGCA 60.304 57.895 0.00 0.00 0.00 5.36
1432 1501 6.818644 ACTAATGTTATCTGTTCGTTCATGCT 59.181 34.615 0.00 0.00 0.00 3.79
1446 1515 7.258441 TCTGACTGTACTGCACTAATGTTATC 58.742 38.462 0.00 0.00 0.00 1.75
1450 1519 5.047021 ACATCTGACTGTACTGCACTAATGT 60.047 40.000 0.00 2.03 0.00 2.71
1511 1581 1.000274 GCCACCAGTGCTACAAAAAGG 60.000 52.381 0.00 0.00 0.00 3.11
1723 1898 5.390567 GCCCTTGTTATTGTTCAAGTAGTCG 60.391 44.000 0.00 0.00 39.25 4.18
1724 1899 5.472137 TGCCCTTGTTATTGTTCAAGTAGTC 59.528 40.000 0.00 0.00 39.25 2.59
1734 1909 4.415596 TCCAAAGATGCCCTTGTTATTGT 58.584 39.130 0.00 0.00 34.79 2.71
1741 1916 2.490903 CTGAGTTCCAAAGATGCCCTTG 59.509 50.000 0.00 0.00 34.79 3.61
1773 1948 8.143835 ACCATACATTTTTGCCTAATCATAAGC 58.856 33.333 0.00 0.00 0.00 3.09
1781 1956 9.030452 ACATCTTAACCATACATTTTTGCCTAA 57.970 29.630 0.00 0.00 0.00 2.69
1843 2019 8.345724 AGCATCAAATGAGTCAAGTAAATTCT 57.654 30.769 0.00 0.00 0.00 2.40
1910 2088 5.011943 ACATGGAAATGTGTATTTGTGCCTT 59.988 36.000 0.00 0.00 36.66 4.35
1963 2141 6.536447 AGGATTTCTAAGAACGGGTTAAACA 58.464 36.000 0.00 0.00 0.00 2.83
1972 2150 9.708222 CACAATTTCATAGGATTTCTAAGAACG 57.292 33.333 0.00 0.00 35.98 3.95
2028 2206 4.022068 CAGTTGGATAAAAGAAGCAAGGCA 60.022 41.667 0.00 0.00 0.00 4.75
2030 2208 5.335976 GGTCAGTTGGATAAAAGAAGCAAGG 60.336 44.000 0.00 0.00 0.00 3.61
2033 2211 4.079253 GGGTCAGTTGGATAAAAGAAGCA 58.921 43.478 0.00 0.00 0.00 3.91
2049 2227 6.200097 CGTTGGAAATTTGTTTTTAGGGTCAG 59.800 38.462 0.00 0.00 0.00 3.51
2071 2249 3.921119 TTTGCATGATTTCTGCTCGTT 57.079 38.095 0.00 0.00 40.34 3.85
2165 2345 2.577606 TTCGAAACCCATGTGTCCAT 57.422 45.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.