Multiple sequence alignment - TraesCS2A01G165000

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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 TraesCS2A01G165000 chr2A 100.000 2111 0 0 1 2111 117389061 117386951 0.000000e+00 3899
1 TraesCS2A01G165000 chr2A 84.334 383 37 11 844 1222 117363377 117363014 9.270000e-94 353
2 TraesCS2A01G165000 chr2B 94.224 1714 69 10 402 2111 166467069 166465382 0.000000e+00 2590
3 TraesCS2A01G165000 chr2B 95.395 304 12 1 1 304 166467477 166467176 1.130000e-132 483
4 TraesCS2A01G165000 chr2B 87.817 394 42 6 801 1191 166407087 166406697 6.870000e-125 457
5 TraesCS2A01G165000 chr2B 100.000 74 0 0 300 373 166467143 166467070 1.020000e-28 137
6 TraesCS2A01G165000 chr2D 92.671 1228 65 13 513 1736 115942968 115941762 0.000000e+00 1746
7 TraesCS2A01G165000 chr2D 94.792 192 9 1 1825 2015 115941606 115941415 4.400000e-77 298
8 TraesCS2A01G165000 chr2D 90.116 172 13 4 815 983 115929532 115929362 9.810000e-54 220
9 TraesCS2A01G165000 chr2D 94.681 94 4 1 2016 2108 115941210 115941117 6.070000e-31 145
10 TraesCS2A01G165000 chr2D 91.000 100 5 1 1728 1823 115941742 115941643 4.730000e-27 132
11 TraesCS2A01G165000 chr6D 93.333 150 10 0 513 662 353733072 353732923 2.730000e-54 222


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 TraesCS2A01G165000 chr2A 117386951 117389061 2110 True 3899.00 3899 100.000000 1 2111 1 chr2A.!!$R2 2110
1 TraesCS2A01G165000 chr2B 166465382 166467477 2095 True 1070.00 2590 96.539667 1 2111 3 chr2B.!!$R2 2110
2 TraesCS2A01G165000 chr2D 115941117 115942968 1851 True 580.25 1746 93.286000 513 2108 4 chr2D.!!$R2 1595

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
487 525 0.543749 CAGAGGACACCCTTCCCATC 59.456 60.0 0.0 0.0 44.53 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2082 0.109781 GGCCAAACACATGTACTGCG 60.11 55.0 0.0 0.0 0.0 5.18 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
52 53 2.437413 CAGTAGAAACTTGGGAAGGGC 58.563 52.381 0.00 0.00 31.97 5.19
71 72 4.166725 AGGGCAATGAAGATATGAAGACCA 59.833 41.667 0.00 0.00 0.00 4.02
138 139 6.280643 TGTATAGCTATCATTGCACGTTTCT 58.719 36.000 10.16 0.00 0.00 2.52
140 141 4.346734 AGCTATCATTGCACGTTTCTTG 57.653 40.909 0.00 0.00 0.00 3.02
164 165 5.233902 GCATGTTCTATTACACTGCAGAGAG 59.766 44.000 23.35 12.22 35.03 3.20
198 199 8.439993 TGTACAGCAGTTAACTAAATTTCACA 57.560 30.769 8.04 4.47 0.00 3.58
199 200 8.339714 TGTACAGCAGTTAACTAAATTTCACAC 58.660 33.333 8.04 0.00 0.00 3.82
200 201 6.735130 ACAGCAGTTAACTAAATTTCACACC 58.265 36.000 8.04 0.00 0.00 4.16
201 202 6.546034 ACAGCAGTTAACTAAATTTCACACCT 59.454 34.615 8.04 0.00 0.00 4.00
202 203 7.078228 CAGCAGTTAACTAAATTTCACACCTC 58.922 38.462 8.04 0.00 0.00 3.85
290 291 8.465999 TGTCTTGCTTTCATTTGAAACTTTCTA 58.534 29.630 1.66 0.00 38.94 2.10
380 418 9.703892 CAGTATGCTCTTCATAGCTTAAAGTAT 57.296 33.333 0.00 0.00 43.19 2.12
381 419 9.703892 AGTATGCTCTTCATAGCTTAAAGTATG 57.296 33.333 0.00 0.00 43.19 2.39
382 420 7.976135 ATGCTCTTCATAGCTTAAAGTATGG 57.024 36.000 0.00 0.00 43.19 2.74
383 421 6.889198 TGCTCTTCATAGCTTAAAGTATGGT 58.111 36.000 0.00 0.00 43.19 3.55
384 422 6.986817 TGCTCTTCATAGCTTAAAGTATGGTC 59.013 38.462 0.00 0.00 43.19 4.02
385 423 6.986817 GCTCTTCATAGCTTAAAGTATGGTCA 59.013 38.462 0.00 0.00 39.50 4.02
386 424 7.659390 GCTCTTCATAGCTTAAAGTATGGTCAT 59.341 37.037 0.00 0.00 39.50 3.06
387 425 9.553064 CTCTTCATAGCTTAAAGTATGGTCATT 57.447 33.333 0.00 0.00 0.00 2.57
388 426 9.547753 TCTTCATAGCTTAAAGTATGGTCATTC 57.452 33.333 0.00 0.00 0.00 2.67
389 427 9.553064 CTTCATAGCTTAAAGTATGGTCATTCT 57.447 33.333 0.00 0.00 0.00 2.40
390 428 9.905713 TTCATAGCTTAAAGTATGGTCATTCTT 57.094 29.630 0.00 0.00 31.09 2.52
391 429 9.905713 TCATAGCTTAAAGTATGGTCATTCTTT 57.094 29.630 15.99 15.99 40.15 2.52
394 432 8.273780 AGCTTAAAGTATGGTCATTCTTTCTG 57.726 34.615 15.43 11.75 38.66 3.02
395 433 8.103305 AGCTTAAAGTATGGTCATTCTTTCTGA 58.897 33.333 15.43 6.33 38.66 3.27
396 434 8.897752 GCTTAAAGTATGGTCATTCTTTCTGAT 58.102 33.333 15.43 0.02 38.66 2.90
398 436 9.958180 TTAAAGTATGGTCATTCTTTCTGATCA 57.042 29.630 15.43 0.00 38.66 2.92
400 438 8.447924 AAGTATGGTCATTCTTTCTGATCATG 57.552 34.615 8.85 0.00 42.82 3.07
439 477 6.946009 AGTTTATCTAGCTAGTCTCCCATCTC 59.054 42.308 20.10 3.13 0.00 2.75
470 508 2.457598 TCCCTGAACTACAGTAGGCAG 58.542 52.381 18.87 18.87 44.40 4.85
487 525 0.543749 CAGAGGACACCCTTCCCATC 59.456 60.000 0.00 0.00 44.53 3.51
490 528 0.978146 AGGACACCCTTCCCATCTCG 60.978 60.000 0.00 0.00 40.78 4.04
520 558 6.865834 TGGATGGCCTAATTTGTATTTTGT 57.134 33.333 3.32 0.00 34.31 2.83
565 603 9.304335 TCAATGCATATCATGATAAAAGTGGAT 57.696 29.630 19.03 15.34 35.13 3.41
688 726 2.582636 AGATTTGTAGGAACATGCCCCT 59.417 45.455 10.82 10.82 34.97 4.79
747 785 7.196532 CCATATGATGGTTAAGCAGGGCTTTA 61.197 42.308 13.51 0.00 45.03 1.85
767 805 2.378038 ACCACATGTTTGACTTGCTGT 58.622 42.857 0.00 0.00 0.00 4.40
825 864 1.818642 CTTAGTGCTGCTTCTTGCCT 58.181 50.000 0.00 0.00 42.00 4.75
839 878 1.882623 CTTGCCTTCCTTTCTGACACC 59.117 52.381 0.00 0.00 0.00 4.16
856 895 2.546321 CACACGCACAGCTCGTTC 59.454 61.111 0.00 0.00 38.19 3.95
878 918 7.298122 GTTCATACCTCTGTTTGTATGTTGTG 58.702 38.462 8.89 0.00 43.02 3.33
891 931 4.582656 TGTATGTTGTGCTTTAGCCTTTGT 59.417 37.500 0.00 0.00 41.18 2.83
913 953 9.685276 TTTGTTTCCATGTCATATACTTCTGAT 57.315 29.630 0.00 0.00 0.00 2.90
936 976 2.884639 AGTGGCAACCAGTACATTTGAC 59.115 45.455 0.00 0.00 35.09 3.18
946 986 8.554528 CAACCAGTACATTTGACTATCATCATC 58.445 37.037 0.00 0.00 0.00 2.92
1136 1176 4.261994 GCCTTTTGTTTAGCAATGAGACCA 60.262 41.667 0.00 0.00 36.89 4.02
1169 1209 4.263905 TGGAGCAAATAGGGAAATGTGTCT 60.264 41.667 0.00 0.00 0.00 3.41
1274 1314 3.809832 ACAAGTGAACTGTGGAGATTTCG 59.190 43.478 0.00 0.00 0.00 3.46
1331 1371 5.697633 CCTGCTTGTTATTTGCTGTTTGATT 59.302 36.000 0.00 0.00 0.00 2.57
1352 1392 7.933396 TGATTATGTGATCTGTATTGCCTTTG 58.067 34.615 0.00 0.00 0.00 2.77
1369 1409 3.181456 CCTTTGGGGTTGCAAAATTCTCA 60.181 43.478 0.00 0.00 0.00 3.27
1525 1565 3.320626 TGTCGATGAAGCAGAGTTTCTG 58.679 45.455 1.75 1.75 46.90 3.02
1661 1701 4.034510 CCGTATTCAGAGAATGGAAGTTGC 59.965 45.833 2.65 0.00 0.00 4.17
1719 1759 6.058833 TCTACAGTGGTAGCAAAAATGAACA 58.941 36.000 0.00 0.00 45.42 3.18
1730 1798 9.463443 GTAGCAAAAATGAACAGTTCAATAGTT 57.537 29.630 19.92 7.03 43.95 2.24
1736 1804 5.560722 TGAACAGTTCAATAGTTCTGGGA 57.439 39.130 13.90 0.00 41.56 4.37
1823 1904 5.697067 ACCACTGTGGGTTATTTTAGTTCA 58.303 37.500 29.05 0.00 43.37 3.18
1854 1963 4.264460 ACAAACACCAGCAAGACAAAAA 57.736 36.364 0.00 0.00 0.00 1.94
1868 1977 5.754543 AGACAAAAATGGCAAAATGTTGG 57.245 34.783 0.00 0.00 35.10 3.77
1903 2012 6.704937 TGCATGAAATATACTCTGAGAAGCAG 59.295 38.462 12.44 0.00 46.31 4.24
1972 2082 6.073003 CCACAGAAAATCTAACACTCTTGACC 60.073 42.308 0.00 0.00 0.00 4.02
2021 2335 3.982058 GCATTATTCTACTCCCGTCTTCG 59.018 47.826 0.00 0.00 0.00 3.79
2102 2416 9.906660 TTAGTCGCAAAGATAAAAATGAAATGT 57.093 25.926 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.307496 TCCTGGTGCACCAATTCATT 57.693 45.000 36.71 0.00 46.97 2.57
87 88 4.537135 ACACACATAACACGATCTTCCT 57.463 40.909 0.00 0.00 0.00 3.36
94 95 4.689071 ACAGAGAAACACACATAACACGA 58.311 39.130 0.00 0.00 0.00 4.35
138 139 5.244755 TCTGCAGTGTAATAGAACATGCAA 58.755 37.500 14.67 0.00 40.25 4.08
140 141 5.111989 TCTCTGCAGTGTAATAGAACATGC 58.888 41.667 14.67 0.00 35.89 4.06
164 165 2.447244 ACTGCTGTACAAGAGCACTC 57.553 50.000 4.29 0.00 41.56 3.51
198 199 1.888512 GTGCAACACATGAATGGAGGT 59.111 47.619 0.00 0.00 36.32 3.85
199 200 2.094906 CAGTGCAACACATGAATGGAGG 60.095 50.000 0.00 0.00 41.43 4.30
200 201 2.094906 CCAGTGCAACACATGAATGGAG 60.095 50.000 0.00 0.00 41.43 3.86
201 202 1.887854 CCAGTGCAACACATGAATGGA 59.112 47.619 0.00 0.00 41.43 3.41
202 203 1.887854 TCCAGTGCAACACATGAATGG 59.112 47.619 0.00 0.00 41.43 3.16
256 257 8.394971 TCAAATGAAAGCAAGACAGAAAGATA 57.605 30.769 0.00 0.00 0.00 1.98
290 291 8.713708 ACTGAACCTGCACTACTAATATCTAT 57.286 34.615 0.00 0.00 0.00 1.98
374 412 8.900781 CATGATCAGAAAGAATGACCATACTTT 58.099 33.333 0.09 0.00 35.68 2.66
375 413 7.013083 GCATGATCAGAAAGAATGACCATACTT 59.987 37.037 0.09 0.00 0.00 2.24
376 414 6.485984 GCATGATCAGAAAGAATGACCATACT 59.514 38.462 0.09 0.00 0.00 2.12
377 415 6.485984 AGCATGATCAGAAAGAATGACCATAC 59.514 38.462 0.09 0.00 0.00 2.39
378 416 6.598503 AGCATGATCAGAAAGAATGACCATA 58.401 36.000 0.09 0.00 0.00 2.74
379 417 5.446860 AGCATGATCAGAAAGAATGACCAT 58.553 37.500 0.09 0.00 0.00 3.55
380 418 4.851843 AGCATGATCAGAAAGAATGACCA 58.148 39.130 0.09 0.00 0.00 4.02
381 419 5.819379 TGTAGCATGATCAGAAAGAATGACC 59.181 40.000 0.09 0.00 0.00 4.02
382 420 6.238320 GGTGTAGCATGATCAGAAAGAATGAC 60.238 42.308 0.09 0.00 0.00 3.06
383 421 5.819379 GGTGTAGCATGATCAGAAAGAATGA 59.181 40.000 0.09 0.00 0.00 2.57
384 422 5.587443 TGGTGTAGCATGATCAGAAAGAATG 59.413 40.000 0.09 0.00 0.00 2.67
385 423 5.587844 GTGGTGTAGCATGATCAGAAAGAAT 59.412 40.000 0.09 0.00 0.00 2.40
386 424 4.937620 GTGGTGTAGCATGATCAGAAAGAA 59.062 41.667 0.09 0.00 0.00 2.52
387 425 4.223700 AGTGGTGTAGCATGATCAGAAAGA 59.776 41.667 0.09 0.00 0.00 2.52
388 426 4.511527 AGTGGTGTAGCATGATCAGAAAG 58.488 43.478 0.09 0.00 0.00 2.62
389 427 4.558226 AGTGGTGTAGCATGATCAGAAA 57.442 40.909 0.09 0.00 0.00 2.52
390 428 5.675684 TTAGTGGTGTAGCATGATCAGAA 57.324 39.130 0.09 0.00 0.00 3.02
391 429 5.675684 TTTAGTGGTGTAGCATGATCAGA 57.324 39.130 0.09 0.00 0.00 3.27
392 430 5.877012 ACTTTTAGTGGTGTAGCATGATCAG 59.123 40.000 0.09 0.00 0.00 2.90
393 431 5.804639 ACTTTTAGTGGTGTAGCATGATCA 58.195 37.500 0.00 0.00 0.00 2.92
394 432 6.743575 AACTTTTAGTGGTGTAGCATGATC 57.256 37.500 0.00 0.00 0.00 2.92
395 433 8.807948 ATAAACTTTTAGTGGTGTAGCATGAT 57.192 30.769 0.00 0.00 0.00 2.45
396 434 8.100791 AGATAAACTTTTAGTGGTGTAGCATGA 58.899 33.333 0.00 0.00 0.00 3.07
397 435 8.268850 AGATAAACTTTTAGTGGTGTAGCATG 57.731 34.615 0.00 0.00 0.00 4.06
398 436 9.601217 CTAGATAAACTTTTAGTGGTGTAGCAT 57.399 33.333 0.00 0.00 0.00 3.79
399 437 7.548075 GCTAGATAAACTTTTAGTGGTGTAGCA 59.452 37.037 0.00 0.00 32.25 3.49
400 438 7.764901 AGCTAGATAAACTTTTAGTGGTGTAGC 59.235 37.037 0.00 0.00 32.18 3.58
439 477 0.108138 GTTCAGGGATGAGTCGTGGG 60.108 60.000 0.00 0.00 0.00 4.61
470 508 0.833949 GAGATGGGAAGGGTGTCCTC 59.166 60.000 0.00 0.00 44.07 3.71
487 525 1.071471 GGCCATCCATGTACCCGAG 59.929 63.158 0.00 0.00 0.00 4.63
490 528 3.525800 AATTAGGCCATCCATGTACCC 57.474 47.619 5.01 0.00 33.74 3.69
520 558 6.405731 GCATTGATTAAGGAACCTTGCATGTA 60.406 38.462 15.37 0.00 37.47 2.29
565 603 5.740513 GCAAATAAACTGGGGTTAAGTGCAA 60.741 40.000 0.00 0.00 34.90 4.08
675 713 1.919600 GAGCTCAGGGGCATGTTCCT 61.920 60.000 9.40 3.58 34.17 3.36
688 726 4.040829 TCCAAACAAAGATCTCTGAGCTCA 59.959 41.667 17.19 17.19 0.00 4.26
747 785 2.099592 CACAGCAAGTCAAACATGTGGT 59.900 45.455 0.00 0.00 35.54 4.16
767 805 4.947388 GGGATAGGCTGTCAATACAAAACA 59.053 41.667 13.49 0.00 34.49 2.83
825 864 1.948104 CGTGTGGTGTCAGAAAGGAA 58.052 50.000 0.00 0.00 0.00 3.36
839 878 1.560004 ATGAACGAGCTGTGCGTGTG 61.560 55.000 0.00 0.00 41.75 3.82
913 953 4.517453 GTCAAATGTACTGGTTGCCACTTA 59.483 41.667 0.00 0.00 0.00 2.24
936 976 5.936686 AAACAGGCAATCGATGATGATAG 57.063 39.130 0.00 0.00 0.00 2.08
946 986 3.837213 AGATGTGAAAACAGGCAATCG 57.163 42.857 0.00 0.00 0.00 3.34
1146 1186 4.016444 GACACATTTCCCTATTTGCTCCA 58.984 43.478 0.00 0.00 0.00 3.86
1169 1209 3.328382 AGCGCTCTGTTACCATTAACA 57.672 42.857 2.64 0.00 44.40 2.41
1331 1371 5.132502 CCCAAAGGCAATACAGATCACATA 58.867 41.667 0.00 0.00 0.00 2.29
1352 1392 5.452356 CCAGATATGAGAATTTTGCAACCCC 60.452 44.000 0.00 0.00 0.00 4.95
1369 1409 2.136026 GGGGGTTCAAGTCCCAGATAT 58.864 52.381 3.37 0.00 46.26 1.63
1434 1474 5.376625 TCCGGCAAGCTTTATTGATTAGAT 58.623 37.500 0.00 0.00 31.55 1.98
1525 1565 1.538512 GGGTAAAACAAGGCGGAGAAC 59.461 52.381 0.00 0.00 0.00 3.01
1582 1622 1.167851 AATTGTGATCTGTGCACCGG 58.832 50.000 15.69 0.00 35.43 5.28
1592 1632 8.915871 AATACAAAGCACATGTAATTGTGATC 57.084 30.769 23.03 0.00 44.89 2.92
1661 1701 7.746526 GCTTAAGCACAATCCAAAATCTTAG 57.253 36.000 22.59 0.00 41.59 2.18
1719 1759 6.380079 AACAGATCCCAGAACTATTGAACT 57.620 37.500 0.00 0.00 0.00 3.01
1730 1798 2.239654 GTCCATCCAAACAGATCCCAGA 59.760 50.000 0.00 0.00 0.00 3.86
1736 1804 3.370527 CCCTTACGTCCATCCAAACAGAT 60.371 47.826 0.00 0.00 0.00 2.90
1854 1963 4.223477 AGAGTTATGCCAACATTTTGCCAT 59.777 37.500 0.00 0.00 35.11 4.40
1868 1977 8.997323 AGAGTATATTTCATGCAAGAGTTATGC 58.003 33.333 0.00 0.00 44.08 3.14
1903 2012 8.725148 TCTTCTTGCAAGAACTGAGATAAATTC 58.275 33.333 32.86 0.00 39.95 2.17
1915 2024 6.615088 TCAGCATATTTCTTCTTGCAAGAAC 58.385 36.000 32.86 21.63 39.95 3.01
1972 2082 0.109781 GGCCAAACACATGTACTGCG 60.110 55.000 0.00 0.00 0.00 5.18
2021 2335 9.503427 GGTTTGCAGAACAATTCATTACTATAC 57.497 33.333 11.93 0.00 38.31 1.47


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

AutoCloner maintained by Alex Coulton.