Multiple sequence alignment - TraesCS2D01G047800

Loading Multiple Alignment...

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 TraesCS2D01G047800 chr2D 100.000 2386 0 0 1 2386 17500899 17498514 0.000000e+00 4407
1 TraesCS2D01G047800 chr2A 96.554 1654 34 13 570 2214 18912860 18911221 0.000000e+00 2717
2 TraesCS2D01G047800 chr2A 95.096 571 10 5 1 571 18913472 18912920 0.000000e+00 883
3 TraesCS2D01G047800 chr2A 95.868 242 9 1 2146 2386 18911219 18910978 8.000000e-105 390
4 TraesCS2D01G047800 chr2B 91.960 1306 73 16 472 1758 29706236 29707528 0.000000e+00 1801
5 TraesCS2D01G047800 chr2B 92.534 442 28 4 1 439 29705283 29705722 1.560000e-176 628


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 TraesCS2D01G047800 chr2D 17498514 17500899 2385 True 4407.0 4407 100.000000 1 2386 1 chr2D.!!$R1 2385
1 TraesCS2D01G047800 chr2A 18910978 18913472 2494 True 1330.0 2717 95.839333 1 2386 3 chr2A.!!$R1 2385
2 TraesCS2D01G047800 chr2B 29705283 29707528 2245 False 1214.5 1801 92.247000 1 1758 2 chr2B.!!$F1 1757

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
459 462 0.533755 GCTTATCACAGGCTCGCCAT 60.534 55.0 11.02 0.0 38.92 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2942 0.107017 CATCCTCATCCCCGCTGTTT 60.107 55.0 0.0 0.0 0.0 2.83 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 2.888464 TAGTCCTCTCGAGTGCCCGG 62.888 65.000 13.13 0.00 0.00 5.73
391 393 1.712977 CTCTCAGGCTCGCCATTTGC 61.713 60.000 11.02 0.00 38.92 3.68
412 415 5.540911 TGCGATCTAATGCTATCATTCACA 58.459 37.500 0.00 0.00 41.68 3.58
440 443 2.883386 AGAAGCTGAAGAAAAGCAGGTG 59.117 45.455 0.00 0.00 43.37 4.00
441 444 0.957362 AGCTGAAGAAAAGCAGGTGC 59.043 50.000 0.00 0.00 43.37 5.01
456 459 2.009888 GTGCTTATCACAGGCTCGC 58.990 57.895 0.00 0.00 44.98 5.03
457 460 1.153369 TGCTTATCACAGGCTCGCC 60.153 57.895 0.00 0.00 0.00 5.54
458 461 1.153369 GCTTATCACAGGCTCGCCA 60.153 57.895 11.02 0.00 38.92 5.69
459 462 0.533755 GCTTATCACAGGCTCGCCAT 60.534 55.000 11.02 0.00 38.92 4.40
460 463 1.959042 CTTATCACAGGCTCGCCATT 58.041 50.000 11.02 0.00 38.92 3.16
496 997 7.921214 CGTTCATACCTCTTATCACACTTACAT 59.079 37.037 0.00 0.00 0.00 2.29
687 1250 6.061022 TCAGGTTTCAGCACTATGGATTTA 57.939 37.500 0.00 0.00 0.00 1.40
987 1551 5.088026 CACATCCCCCTTTAACCCTTTTAA 58.912 41.667 0.00 0.00 0.00 1.52
1346 1915 3.946201 ACCAGCGGCAAGTGCTCT 61.946 61.111 1.45 0.00 41.72 4.09
1405 1978 4.803098 AGCTAGACTGATAAAACGTGGT 57.197 40.909 0.00 0.00 0.00 4.16
1497 2071 1.943968 GCATACTTCAGGTTCACGGCA 60.944 52.381 0.00 0.00 0.00 5.69
1601 2181 7.377928 GCATGCAAGTGTTCATTGTATTCTATC 59.622 37.037 14.21 0.00 31.67 2.08
1806 2386 4.783959 GTTTACGAAAACCTGTCTCGTT 57.216 40.909 11.17 0.00 42.86 3.85
1837 2417 2.094078 CACATCCAACCATCCGCATTTT 60.094 45.455 0.00 0.00 0.00 1.82
1918 2498 4.957327 ACTAGGATCTACAGTGACTTTCCC 59.043 45.833 0.00 0.00 0.00 3.97
1941 2521 5.229921 TGAACAAAGAACGAGTCCTTTTG 57.770 39.130 0.00 0.00 30.89 2.44
1942 2522 3.692791 ACAAAGAACGAGTCCTTTTGC 57.307 42.857 0.00 0.00 30.89 3.68
1943 2523 3.279434 ACAAAGAACGAGTCCTTTTGCT 58.721 40.909 0.00 0.00 30.89 3.91
1944 2524 4.448210 ACAAAGAACGAGTCCTTTTGCTA 58.552 39.130 0.00 0.00 30.89 3.49
1945 2525 4.879545 ACAAAGAACGAGTCCTTTTGCTAA 59.120 37.500 0.00 0.00 30.89 3.09
1946 2526 5.205565 CAAAGAACGAGTCCTTTTGCTAAC 58.794 41.667 0.00 0.00 30.89 2.34
1947 2527 4.067972 AGAACGAGTCCTTTTGCTAACA 57.932 40.909 0.00 0.00 0.00 2.41
1948 2528 4.642429 AGAACGAGTCCTTTTGCTAACAT 58.358 39.130 0.00 0.00 0.00 2.71
1949 2529 5.063880 AGAACGAGTCCTTTTGCTAACATT 58.936 37.500 0.00 0.00 0.00 2.71
1950 2530 5.531287 AGAACGAGTCCTTTTGCTAACATTT 59.469 36.000 0.00 0.00 0.00 2.32
1951 2531 5.767816 ACGAGTCCTTTTGCTAACATTTT 57.232 34.783 0.00 0.00 0.00 1.82
1952 2532 6.870971 ACGAGTCCTTTTGCTAACATTTTA 57.129 33.333 0.00 0.00 0.00 1.52
2224 2876 2.734673 GAACTCCAAGCGAGCGCAG 61.735 63.158 17.68 3.93 43.01 5.18
2290 2942 0.034960 AGGCGAGAGAGACTGCTGTA 60.035 55.000 0.00 0.00 0.00 2.74
2339 2991 2.449345 TCTTGGGGCTAGGGTTTTTCTT 59.551 45.455 0.00 0.00 0.00 2.52
2375 3028 6.716628 GGGAATGAGAGCATTGGTGAATATTA 59.283 38.462 0.00 0.00 44.47 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.613691 CATGCAAATTCTTCACCCTGC 58.386 47.619 0.00 0.00 0.00 4.85
391 393 5.858581 TCGTGTGAATGATAGCATTAGATCG 59.141 40.000 6.12 9.70 44.47 3.69
412 415 4.083590 GCTTTTCTTCAGCTTCTTCATCGT 60.084 41.667 0.00 0.00 34.15 3.73
440 443 0.533755 ATGGCGAGCCTGTGATAAGC 60.534 55.000 15.75 0.00 36.94 3.09
441 444 1.959042 AATGGCGAGCCTGTGATAAG 58.041 50.000 15.75 0.00 36.94 1.73
442 445 2.288666 GAAATGGCGAGCCTGTGATAA 58.711 47.619 15.75 0.00 36.94 1.75
443 446 1.475034 GGAAATGGCGAGCCTGTGATA 60.475 52.381 15.75 0.00 36.94 2.15
444 447 0.749454 GGAAATGGCGAGCCTGTGAT 60.749 55.000 15.75 0.00 36.94 3.06
445 448 1.377202 GGAAATGGCGAGCCTGTGA 60.377 57.895 15.75 0.00 36.94 3.58
446 449 0.962356 AAGGAAATGGCGAGCCTGTG 60.962 55.000 15.75 0.00 36.94 3.66
447 450 0.962356 CAAGGAAATGGCGAGCCTGT 60.962 55.000 15.75 1.23 36.94 4.00
448 451 0.962356 ACAAGGAAATGGCGAGCCTG 60.962 55.000 15.75 5.75 36.94 4.85
449 452 0.962356 CACAAGGAAATGGCGAGCCT 60.962 55.000 15.75 0.00 36.94 4.58
450 453 1.508088 CACAAGGAAATGGCGAGCC 59.492 57.895 7.26 7.26 0.00 4.70
451 454 1.508088 CCACAAGGAAATGGCGAGC 59.492 57.895 0.00 0.00 36.89 5.03
456 459 0.958091 TGAACGCCACAAGGAAATGG 59.042 50.000 0.00 0.00 39.16 3.16
457 460 3.427503 GGTATGAACGCCACAAGGAAATG 60.428 47.826 0.00 0.00 36.89 2.32
458 461 2.752903 GGTATGAACGCCACAAGGAAAT 59.247 45.455 0.00 0.00 36.89 2.17
459 462 2.156098 GGTATGAACGCCACAAGGAAA 58.844 47.619 0.00 0.00 36.89 3.13
460 463 1.349688 AGGTATGAACGCCACAAGGAA 59.650 47.619 0.00 0.00 36.89 3.36
687 1250 7.499321 TCACAAACGTACCACTTTTTCATAT 57.501 32.000 0.00 0.00 0.00 1.78
708 1271 5.126061 ACAATTGCCAAATGTCCTCTATCAC 59.874 40.000 5.05 0.00 0.00 3.06
844 1407 2.440501 GAATTGCGTTATTGAGCACCG 58.559 47.619 0.00 0.00 43.69 4.94
987 1551 1.883926 GACGCCATTTTTGGTAGGTGT 59.116 47.619 0.00 0.00 46.67 4.16
1128 1693 7.490402 TGCATATTGATTCGTATGAGCATAGAG 59.510 37.037 11.10 0.00 31.48 2.43
1239 1808 4.778415 CGTCTCGCACACCCTCGG 62.778 72.222 0.00 0.00 0.00 4.63
1346 1915 0.473755 TGCACTTCCTCTTCAAGCCA 59.526 50.000 0.00 0.00 0.00 4.75
1422 1995 8.001292 TCAGACCATCTTGAGAACAGATCTATA 58.999 37.037 0.00 0.00 38.96 1.31
1438 2011 2.728007 TCGATGTGACTCAGACCATCT 58.272 47.619 6.57 0.00 33.24 2.90
1497 2071 3.589988 ACTGAAGAAAGAACATCGCGAT 58.410 40.909 17.62 17.62 0.00 4.58
1618 2198 9.668497 AACTGTAATAACATAGAGAAAAGGGTC 57.332 33.333 0.00 0.00 34.37 4.46
1806 2386 1.139853 GGTTGGATGTGCACCCAAAAA 59.860 47.619 23.85 5.26 43.30 1.94
1818 2398 2.428171 AGAAAATGCGGATGGTTGGATG 59.572 45.455 0.00 0.00 0.00 3.51
1837 2417 6.353323 TGATTTTATACATGGAGCGGAAAGA 58.647 36.000 0.00 0.00 0.00 2.52
1887 2467 6.717540 GTCACTGTAGATCCTAGTGTCCATAT 59.282 42.308 16.51 0.00 41.82 1.78
1918 2498 5.266242 CAAAAGGACTCGTTCTTTGTTCAG 58.734 41.667 4.19 0.00 33.96 3.02
2130 2712 3.318275 AGAGACGTACGGCATCACAATAT 59.682 43.478 25.52 0.00 0.00 1.28
2205 2787 3.491652 GCGCTCGCTTGGAGTTCC 61.492 66.667 0.00 0.00 45.03 3.62
2214 2866 2.497173 ATGGATCTCTGCGCTCGCT 61.497 57.895 9.73 0.00 42.51 4.93
2290 2942 0.107017 CATCCTCATCCCCGCTGTTT 60.107 55.000 0.00 0.00 0.00 2.83
2302 2954 2.568956 CCAAGACAACCTCTCATCCTCA 59.431 50.000 0.00 0.00 0.00 3.86
2348 3001 0.259938 ACCAATGCTCTCATTCCCCC 59.740 55.000 0.00 0.00 40.74 5.40


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

AutoCloner maintained by Alex Coulton.