Multiple sequence alignment - TraesCS2B01G334300

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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 TraesCS2B01G334300 chr2B 100.000 2960 0 0 1 2960 477609586 477606627 0.000000e+00 5467
1 TraesCS2B01G334300 chr2A 95.262 2596 92 15 1 2593 541845520 541842953 0.000000e+00 4084
2 TraesCS2B01G334300 chr2A 94.294 333 11 2 2628 2960 541842951 541842627 1.220000e-138 503
3 TraesCS2B01G334300 chr2D 95.622 2490 81 14 1 2488 403506961 403504498 0.000000e+00 3969
4 TraesCS2B01G334300 chr2D 93.096 478 23 3 2485 2960 403502920 403502451 0.000000e+00 691


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 TraesCS2B01G334300 chr2B 477606627 477609586 2959 True 5467.0 5467 100.000 1 2960 1 chr2B.!!$R1 2959
1 TraesCS2B01G334300 chr2A 541842627 541845520 2893 True 2293.5 4084 94.778 1 2960 2 chr2A.!!$R1 2959
2 TraesCS2B01G334300 chr2D 403502451 403506961 4510 True 2330.0 3969 94.359 1 2960 2 chr2D.!!$R1 2959

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
149 150 3.863424 GCATTTTGAGATCCATGCTTGTG 59.137 43.478 0.0 0.0 39.2 3.33 F
1508 1510 1.202855 ACTCTGCAAGCATGTGAAGGT 60.203 47.619 0.0 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1547 0.322366 TCCATTCAGCCAATCGTGCA 60.322 50.0 0.0 0.0 0.00 4.57 R
2349 2353 0.923358 AACACCCAACAGGAACCTCA 59.077 50.0 0.0 0.0 39.89 3.86 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
149 150 3.863424 GCATTTTGAGATCCATGCTTGTG 59.137 43.478 0.00 0.00 39.20 3.33
164 165 6.406177 CCATGCTTGTGGTTTCTAGCAATTAT 60.406 38.462 0.00 0.00 45.41 1.28
505 506 4.363991 TGCTTTTGCCCCAATTGTTTAT 57.636 36.364 4.43 0.00 46.87 1.40
565 566 5.725110 ATTGCAGCTGTTAGATAAGTTCG 57.275 39.130 16.64 0.00 0.00 3.95
814 815 9.582648 TTCTGTATACAGTATAGCTCATGGTAA 57.417 33.333 27.83 10.39 44.12 2.85
815 816 9.232473 TCTGTATACAGTATAGCTCATGGTAAG 57.768 37.037 27.83 1.86 44.12 2.34
1017 1019 2.019984 GCTATGGCAAGAACTCCAAGG 58.980 52.381 0.00 0.00 35.75 3.61
1091 1093 2.955660 CCCACTACCAGAAAGCAACAAA 59.044 45.455 0.00 0.00 0.00 2.83
1251 1253 4.922206 ACATGTGTGGAACCAACTATCAT 58.078 39.130 0.00 0.00 34.36 2.45
1299 1301 9.912634 TTTAAAAATGCTTATGTGAAGGAGAAG 57.087 29.630 0.00 0.00 0.00 2.85
1467 1469 2.733820 GCATTCATGAAGACTGCTCG 57.266 50.000 20.30 2.27 46.18 5.03
1473 1475 3.653256 CATGAAGACTGCTCGTTCATG 57.347 47.619 9.26 9.26 46.63 3.07
1508 1510 1.202855 ACTCTGCAAGCATGTGAAGGT 60.203 47.619 0.00 0.00 0.00 3.50
1545 1547 1.129058 AACCTCGTGAAGTTGACCCT 58.871 50.000 0.00 0.00 0.00 4.34
1551 1553 0.531974 GTGAAGTTGACCCTGCACGA 60.532 55.000 0.00 0.00 31.48 4.35
1686 1688 1.227943 TGGCAGCAGCGACTCTTTT 60.228 52.632 0.00 0.00 43.41 2.27
1882 1884 1.302033 AGAAGCAGTGGAAGGCGTG 60.302 57.895 0.00 0.00 34.54 5.34
1923 1925 1.953231 CTCTGTCAGCTCGGATGCCA 61.953 60.000 0.00 0.00 0.00 4.92
1947 1949 1.003580 GGGAGACAAGCAAGATCCACA 59.996 52.381 0.00 0.00 0.00 4.17
1996 1998 3.239464 TGCCAGGAAGCAGACACA 58.761 55.556 0.00 0.00 38.00 3.72
2018 2020 1.208052 GCACCTTACCATGAGAGCTGA 59.792 52.381 0.00 0.00 0.00 4.26
2021 2023 2.703007 ACCTTACCATGAGAGCTGATCC 59.297 50.000 0.00 0.00 0.00 3.36
2029 2031 2.186903 GAGCTGATCCGGCGGAAA 59.813 61.111 34.58 22.66 41.21 3.13
2032 2034 2.464459 GCTGATCCGGCGGAAACAG 61.464 63.158 37.87 37.87 40.40 3.16
2055 2057 7.776969 ACAGTATTCATGAATCCTTTAGCATGT 59.223 33.333 23.95 8.76 39.22 3.21
2067 2069 5.833131 TCCTTTAGCATGTTTCTTTCTGGTT 59.167 36.000 0.00 0.00 0.00 3.67
2079 2081 5.165961 TCTTTCTGGTTTGGTCATAGAGG 57.834 43.478 0.00 0.00 0.00 3.69
2085 2087 1.633945 GTTTGGTCATAGAGGGTGGGT 59.366 52.381 0.00 0.00 0.00 4.51
2089 2091 2.719705 TGGTCATAGAGGGTGGGTTTTT 59.280 45.455 0.00 0.00 0.00 1.94
2138 2141 5.471456 ACTTCTTTTTCTCTGATGAATGCGT 59.529 36.000 0.00 0.00 0.00 5.24
2146 2149 4.056740 CTCTGATGAATGCGTTGCTAGAT 58.943 43.478 0.00 0.00 0.00 1.98
2203 2206 6.144724 CCAAAGTAGAATAGAAGCAGCGTATC 59.855 42.308 0.00 0.00 0.00 2.24
2204 2207 6.642707 AAGTAGAATAGAAGCAGCGTATCT 57.357 37.500 4.21 4.21 0.00 1.98
2246 2249 3.778265 AGCCATTGGTGTTATTGTCCTT 58.222 40.909 4.26 0.00 0.00 3.36
2315 2319 8.739972 GTCAGACCATTTTGTTATATGTTTCCT 58.260 33.333 0.00 0.00 0.00 3.36
2316 2320 8.739039 TCAGACCATTTTGTTATATGTTTCCTG 58.261 33.333 0.00 0.00 0.00 3.86
2319 2323 9.520204 GACCATTTTGTTATATGTTTCCTGATG 57.480 33.333 0.00 0.00 0.00 3.07
2349 2353 7.609760 TGACATATTGCTCGACTTGTATTTT 57.390 32.000 0.00 0.00 0.00 1.82
2361 2365 5.238650 CGACTTGTATTTTGAGGTTCCTGTT 59.761 40.000 0.00 0.00 0.00 3.16
2369 2373 2.128535 TGAGGTTCCTGTTGGGTGTTA 58.871 47.619 0.00 0.00 36.25 2.41
2380 2384 3.454447 TGTTGGGTGTTATCCGATCTCAT 59.546 43.478 0.00 0.00 0.00 2.90
2389 2393 2.299993 TCCGATCTCATTGTGCTGAC 57.700 50.000 0.00 0.00 0.00 3.51
2400 2404 2.664851 TGCTGACTTGCGGTTCCG 60.665 61.111 6.90 6.90 35.36 4.30
2429 2433 2.218603 ACTTGTTAGGAGTTGGTTGCG 58.781 47.619 0.00 0.00 0.00 4.85
2456 2460 5.811190 TGCAAGCTAGTTTTCCCAGTAATA 58.189 37.500 0.00 0.00 0.00 0.98
2457 2461 6.242396 TGCAAGCTAGTTTTCCCAGTAATAA 58.758 36.000 0.00 0.00 0.00 1.40
2458 2462 6.717540 TGCAAGCTAGTTTTCCCAGTAATAAA 59.282 34.615 0.00 0.00 0.00 1.40
2459 2463 7.027760 GCAAGCTAGTTTTCCCAGTAATAAAC 58.972 38.462 0.00 0.00 0.00 2.01
2464 2468 8.880750 GCTAGTTTTCCCAGTAATAAACAGTAG 58.119 37.037 0.00 0.00 33.94 2.57
2524 4109 5.464057 CGGCAATGAACACGGTTTATATCTA 59.536 40.000 0.00 0.00 0.00 1.98
2565 4150 0.391228 TCTGCGCTCAGTTTACACCA 59.609 50.000 9.73 0.00 41.10 4.17
2589 4174 2.952978 GAGAGGGTGACGATCTACATGT 59.047 50.000 2.69 2.69 0.00 3.21
2616 4201 3.549471 CGACAGTACATGAATGACAGAGC 59.451 47.826 0.00 0.00 0.00 4.09
2856 4443 1.590932 CCATGATCAGCTACAGTGCC 58.409 55.000 0.09 0.00 0.00 5.01
2885 4472 2.025544 CGAAATCAAACCGCAAACGA 57.974 45.000 0.00 0.00 43.93 3.85
2892 4479 3.509740 TCAAACCGCAAACGATACGATA 58.490 40.909 0.00 0.00 43.93 2.92
2893 4480 3.548668 TCAAACCGCAAACGATACGATAG 59.451 43.478 0.00 0.00 43.93 2.08
2894 4481 3.425577 AACCGCAAACGATACGATAGA 57.574 42.857 0.00 0.00 43.93 1.98
2895 4482 3.425577 ACCGCAAACGATACGATAGAA 57.574 42.857 0.00 0.00 43.93 2.10
2896 4483 3.973657 ACCGCAAACGATACGATAGAAT 58.026 40.909 0.00 0.00 43.93 2.40
2897 4484 5.112220 ACCGCAAACGATACGATAGAATA 57.888 39.130 0.00 0.00 43.93 1.75
2898 4485 4.913924 ACCGCAAACGATACGATAGAATAC 59.086 41.667 0.00 0.00 43.93 1.89
2899 4486 4.913345 CCGCAAACGATACGATAGAATACA 59.087 41.667 0.00 0.00 43.93 2.29
2900 4487 5.571741 CCGCAAACGATACGATAGAATACAT 59.428 40.000 0.00 0.00 43.93 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.185635 CCTTCTTTTCCATGGAGTTGCATAA 59.814 40.000 15.53 1.20 0.00 1.90
390 391 8.573885 CAGAAACTCGGTACATGGTATATCTAA 58.426 37.037 0.00 0.00 0.00 2.10
565 566 2.421424 GTGAGGAAGCATGGACATGTTC 59.579 50.000 13.29 13.72 40.80 3.18
679 680 7.868415 ACCATATCTCACGTAGAAGCTAATTTC 59.132 37.037 0.00 0.00 37.89 2.17
814 815 7.935338 CAACAAATGAAGTTGCACTATTTCT 57.065 32.000 0.00 0.00 39.76 2.52
953 954 6.037610 GGATCTAGAATAGTGGCACAAAAGTG 59.962 42.308 21.41 4.39 44.16 3.16
1017 1019 1.348594 GCTTGATAAGTCGCGGTGC 59.651 57.895 6.13 0.00 0.00 5.01
1091 1093 4.531732 TCAATTTATTTTCCTTGGCTGCCT 59.468 37.500 21.03 0.00 0.00 4.75
1251 1253 5.707242 ACTGTTCGAGACAATTAGACTGA 57.293 39.130 2.82 0.00 37.93 3.41
1299 1301 3.715628 ATTGATACTTCATTTGCCGGC 57.284 42.857 22.73 22.73 0.00 6.13
1421 1423 6.091986 AGTTCTCTTCTTGCGATTGAGAAATC 59.908 38.462 12.22 5.01 39.03 2.17
1467 1469 8.997323 CAGAGTTTCTTATATGATCCCATGAAC 58.003 37.037 0.00 0.00 34.31 3.18
1473 1475 6.072783 GCTTGCAGAGTTTCTTATATGATCCC 60.073 42.308 0.00 0.00 0.00 3.85
1508 1510 5.246981 AGGTTTTGATGAAGGATGTCTGA 57.753 39.130 0.00 0.00 0.00 3.27
1545 1547 0.322366 TCCATTCAGCCAATCGTGCA 60.322 50.000 0.00 0.00 0.00 4.57
1551 1553 1.287146 AGCTCCTTCCATTCAGCCAAT 59.713 47.619 0.00 0.00 31.81 3.16
1680 1682 9.270640 CTCCAATCAGAGTTATCCATAAAAGAG 57.729 37.037 0.00 0.00 0.00 2.85
1686 1688 7.510343 TCATCACTCCAATCAGAGTTATCCATA 59.490 37.037 0.00 0.00 44.83 2.74
1882 1884 4.740822 ACCAACCTGCGGCCATCC 62.741 66.667 2.24 0.00 0.00 3.51
1923 1925 1.283321 GATCTTGCTTGTCTCCCCCTT 59.717 52.381 0.00 0.00 0.00 3.95
1947 1949 4.015084 CTCCCATTTCTCAGCTGTCATTT 58.985 43.478 14.67 0.00 0.00 2.32
1995 1997 2.012673 GCTCTCATGGTAAGGTGCTTG 58.987 52.381 0.00 0.00 0.00 4.01
1996 1998 1.912043 AGCTCTCATGGTAAGGTGCTT 59.088 47.619 0.00 0.00 0.00 3.91
2018 2020 1.208535 TGAATACTGTTTCCGCCGGAT 59.791 47.619 6.69 0.00 0.00 4.18
2021 2023 2.276201 TCATGAATACTGTTTCCGCCG 58.724 47.619 0.00 0.00 0.00 6.46
2029 2031 7.776969 ACATGCTAAAGGATTCATGAATACTGT 59.223 33.333 29.82 26.83 40.97 3.55
2032 2034 9.455847 GAAACATGCTAAAGGATTCATGAATAC 57.544 33.333 21.26 21.26 31.71 1.89
2055 2057 6.003950 CCTCTATGACCAAACCAGAAAGAAA 58.996 40.000 0.00 0.00 0.00 2.52
2067 2069 2.053747 AACCCACCCTCTATGACCAA 57.946 50.000 0.00 0.00 0.00 3.67
2138 2141 4.456280 ACGTCATTCACAGATCTAGCAA 57.544 40.909 0.00 0.00 0.00 3.91
2146 2149 8.073768 GGAAATAAAAGAAACGTCATTCACAGA 58.926 33.333 3.01 0.00 0.00 3.41
2178 2181 4.184629 ACGCTGCTTCTATTCTACTTTGG 58.815 43.478 0.00 0.00 0.00 3.28
2246 2249 2.733956 AGAGTTGGGTTGTGCTTTTCA 58.266 42.857 0.00 0.00 0.00 2.69
2315 2319 5.874261 TCGAGCAATATGTCAAAAGACATCA 59.126 36.000 13.76 3.15 43.89 3.07
2316 2320 6.036517 AGTCGAGCAATATGTCAAAAGACATC 59.963 38.462 13.76 1.45 43.89 3.06
2319 2323 5.786401 AGTCGAGCAATATGTCAAAAGAC 57.214 39.130 0.00 0.00 0.00 3.01
2349 2353 0.923358 AACACCCAACAGGAACCTCA 59.077 50.000 0.00 0.00 39.89 3.86
2361 2365 3.454447 ACAATGAGATCGGATAACACCCA 59.546 43.478 0.00 0.00 0.00 4.51
2369 2373 2.433604 AGTCAGCACAATGAGATCGGAT 59.566 45.455 0.00 0.00 0.00 4.18
2380 2384 1.444119 GGAACCGCAAGTCAGCACAA 61.444 55.000 0.00 0.00 0.00 3.33
2389 2393 2.165301 GGATCGACGGAACCGCAAG 61.165 63.158 13.32 5.17 44.19 4.01
2400 2404 4.189639 ACTCCTAACAAGTTGGATCGAC 57.810 45.455 7.96 0.00 0.00 4.20
2429 2433 2.884639 TGGGAAAACTAGCTTGCAAGTC 59.115 45.455 26.55 18.45 0.00 3.01
2457 2461 6.119536 TGATGACAAACTGAAACCTACTGTT 58.880 36.000 0.00 0.00 39.43 3.16
2458 2462 5.680619 TGATGACAAACTGAAACCTACTGT 58.319 37.500 0.00 0.00 0.00 3.55
2459 2463 5.180117 CCTGATGACAAACTGAAACCTACTG 59.820 44.000 0.00 0.00 0.00 2.74
2464 2468 5.562890 GCTTACCTGATGACAAACTGAAACC 60.563 44.000 0.00 0.00 0.00 3.27
2468 2472 4.040339 TCTGCTTACCTGATGACAAACTGA 59.960 41.667 0.00 0.00 0.00 3.41
2500 4085 2.911819 ATAAACCGTGTTCATTGCCG 57.088 45.000 0.00 0.00 0.00 5.69
2524 4109 7.708752 GCAGATAGCTAAGTAAACTCATGTTCT 59.291 37.037 0.00 0.00 41.15 3.01
2565 4150 2.026169 TGTAGATCGTCACCCTCTCAGT 60.026 50.000 0.00 0.00 0.00 3.41
2577 4162 4.156190 ACTGTCGAGAAACATGTAGATCGT 59.844 41.667 19.61 4.73 0.00 3.73
2589 4174 5.778862 TGTCATTCATGTACTGTCGAGAAA 58.221 37.500 0.00 0.00 0.00 2.52
2616 4201 2.560542 CCAGCTCCTATACCTGCTACAG 59.439 54.545 0.00 0.00 34.10 2.74
2619 4204 3.435275 CATCCAGCTCCTATACCTGCTA 58.565 50.000 0.00 0.00 34.10 3.49
2775 4362 2.654912 GGTGTTCGGCTTCGTCGTG 61.655 63.158 0.00 0.00 35.06 4.35
2778 4365 2.355481 ACGGTGTTCGGCTTCGTC 60.355 61.111 0.00 0.00 44.45 4.20
2856 4443 2.412770 GGTTTGATTTCGCCATTGCAAG 59.587 45.455 4.94 0.00 37.32 4.01
2885 4472 8.972127 AGGTAAGCATGATGTATTCTATCGTAT 58.028 33.333 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.