Multiple sequence alignment - TraesCS5D01G069600

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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 TraesCS5D01G069600 chr5D 100.000 2584 0 0 1 2584 67323399 67325982 0 4772
1 TraesCS5D01G069600 chr5B 93.514 2621 74 23 1 2580 73346890 73349455 0 3810
2 TraesCS5D01G069600 chr5A 93.148 2627 78 35 2 2584 56839881 56837313 0 3760


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 TraesCS5D01G069600 chr5D 67323399 67325982 2583 False 4772 4772 100.000 1 2584 1 chr5D.!!$F1 2583
1 TraesCS5D01G069600 chr5B 73346890 73349455 2565 False 3810 3810 93.514 1 2580 1 chr5B.!!$F1 2579
2 TraesCS5D01G069600 chr5A 56837313 56839881 2568 True 3760 3760 93.148 2 2584 1 chr5A.!!$R1 2582

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
345 353 0.251165 CCGTGTGGTTCCCCATTTCT 60.251 55.0 0.0 0.0 44.35 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 2145 0.033796 ACACATCTCCATGGCCTTGG 60.034 55.0 28.04 28.04 38.18 3.61 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
345 353 0.251165 CCGTGTGGTTCCCCATTTCT 60.251 55.000 0.00 0.00 44.35 2.52
563 571 2.350863 AACATCAACCTCCTCTCCCT 57.649 50.000 0.00 0.00 0.00 4.20
600 608 9.607333 TTTATCTCTCTCTATCTCTCTCTCTCT 57.393 37.037 0.00 0.00 0.00 3.10
601 609 7.716799 ATCTCTCTCTATCTCTCTCTCTCTC 57.283 44.000 0.00 0.00 0.00 3.20
602 610 6.857848 TCTCTCTCTATCTCTCTCTCTCTCT 58.142 44.000 0.00 0.00 0.00 3.10
603 611 6.945435 TCTCTCTCTATCTCTCTCTCTCTCTC 59.055 46.154 0.00 0.00 0.00 3.20
604 612 6.857848 TCTCTCTATCTCTCTCTCTCTCTCT 58.142 44.000 0.00 0.00 0.00 3.10
644 652 2.439880 TGTTGGGGATCTGTGTTGTGTA 59.560 45.455 0.00 0.00 0.00 2.90
663 671 0.324830 AGTCTGGGGTAGAGGTGAGC 60.325 60.000 0.00 0.00 35.70 4.26
743 751 5.418676 TGTTCTTGCAAAAAGAGGGAAAAG 58.581 37.500 0.00 0.00 0.00 2.27
744 752 4.670896 TCTTGCAAAAAGAGGGAAAAGG 57.329 40.909 0.00 0.00 0.00 3.11
746 754 4.901250 TCTTGCAAAAAGAGGGAAAAGGAT 59.099 37.500 0.00 0.00 0.00 3.24
750 759 4.322273 GCAAAAAGAGGGAAAAGGATGAGG 60.322 45.833 0.00 0.00 0.00 3.86
755 764 2.107378 GAGGGAAAAGGATGAGGGGATC 59.893 54.545 0.00 0.00 0.00 3.36
768 777 2.569404 GAGGGGATCTGTTCTTCTGTGT 59.431 50.000 0.00 0.00 0.00 3.72
862 871 3.380142 CAAATGGTTTTTGGTGTCTCGG 58.620 45.455 0.00 0.00 0.00 4.63
863 872 0.958822 ATGGTTTTTGGTGTCTCGGC 59.041 50.000 0.00 0.00 0.00 5.54
867 876 1.880027 GTTTTTGGTGTCTCGGCTCAT 59.120 47.619 0.00 0.00 0.00 2.90
1199 1214 1.270893 GGTGAGTTCTTTCTCCGCCTT 60.271 52.381 0.00 0.00 33.93 4.35
1252 1267 0.681887 TCTCCAACGGGTCGCTGATA 60.682 55.000 0.00 0.00 34.93 2.15
1270 1285 4.843728 TGATATTTCTGCTCCGGTTCTTT 58.156 39.130 0.00 0.00 0.00 2.52
1640 1676 1.271597 CCCCTCAGTAGTGCAAAAGCT 60.272 52.381 0.00 0.00 0.00 3.74
1669 1707 3.480470 GAGAGAGATGAGAGTGAGGAGG 58.520 54.545 0.00 0.00 0.00 4.30
1670 1708 3.122480 AGAGAGATGAGAGTGAGGAGGA 58.878 50.000 0.00 0.00 0.00 3.71
1671 1709 3.137176 AGAGAGATGAGAGTGAGGAGGAG 59.863 52.174 0.00 0.00 0.00 3.69
1876 1914 3.325425 GGGGTAGAAGAAATCTAGAGGGC 59.675 52.174 0.00 0.00 41.31 5.19
1934 1973 6.904626 AGTTTAGCCCTCTTGTATGAATCAT 58.095 36.000 0.00 0.00 0.00 2.45
2099 2139 3.006752 GTCCATGCAACCAAGAAATCCAA 59.993 43.478 0.00 0.00 0.00 3.53
2105 2145 1.632589 ACCAAGAAATCCAAGGCCAC 58.367 50.000 5.01 0.00 0.00 5.01
2197 2238 4.769688 AGTCAATGAGTGAGTTGTGTGAA 58.230 39.130 0.00 0.00 36.42 3.18
2322 2363 9.090692 CAGCCCTTGTGATATCTTTTATTTTTG 57.909 33.333 3.98 0.00 0.00 2.44
2324 2365 8.257306 GCCCTTGTGATATCTTTTATTTTTGGA 58.743 33.333 3.98 0.00 0.00 3.53
2362 2405 5.389520 TCAATATCTTGGTGGTTGGTTGAA 58.610 37.500 0.00 0.00 32.95 2.69
2366 2417 3.370104 TCTTGGTGGTTGGTTGAATTGT 58.630 40.909 0.00 0.00 0.00 2.71
2388 2439 1.615651 GCCCCATCACAACACATGGTA 60.616 52.381 0.00 0.00 38.37 3.25
2456 2507 4.427312 CAATGACTAATGCAAAAGAGCCC 58.573 43.478 5.73 0.00 0.00 5.19
2458 2509 1.401905 GACTAATGCAAAAGAGCCCGG 59.598 52.381 0.00 0.00 0.00 5.73
2512 2563 2.443255 GGGATCTGAAGGGCCAAAGATA 59.557 50.000 6.18 0.00 29.59 1.98
2528 2582 8.664798 GGCCAAAGATAAAATACCATGTTTTTC 58.335 33.333 0.00 0.00 31.71 2.29
2580 2639 5.891451 TCTTTGAGATGTAGATGTGGTACG 58.109 41.667 0.00 0.00 0.00 3.67
2581 2640 5.417894 TCTTTGAGATGTAGATGTGGTACGT 59.582 40.000 0.00 0.00 0.00 3.57
2582 2641 6.600427 TCTTTGAGATGTAGATGTGGTACGTA 59.400 38.462 0.00 0.00 0.00 3.57
2583 2642 5.746307 TGAGATGTAGATGTGGTACGTAC 57.254 43.478 17.56 17.56 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.001706 GAGGCTGGTTTTCGTGTTTCC 60.002 52.381 0.00 0.00 0.00 3.13
62 63 3.005897 GGAGGCCACCTTTTCTTTCTTTC 59.994 47.826 12.67 0.00 31.76 2.62
63 64 2.965831 GGAGGCCACCTTTTCTTTCTTT 59.034 45.455 12.67 0.00 31.76 2.52
64 65 2.091333 TGGAGGCCACCTTTTCTTTCTT 60.091 45.455 20.77 0.00 31.76 2.52
65 66 1.499007 TGGAGGCCACCTTTTCTTTCT 59.501 47.619 20.77 0.00 31.76 2.52
587 595 6.619464 ACTAGAGAGAGAGAGAGAGAGAGAT 58.381 44.000 0.00 0.00 0.00 2.75
588 596 6.019656 ACTAGAGAGAGAGAGAGAGAGAGA 57.980 45.833 0.00 0.00 0.00 3.10
589 597 6.723298 AACTAGAGAGAGAGAGAGAGAGAG 57.277 45.833 0.00 0.00 0.00 3.20
590 598 6.897966 AGAAACTAGAGAGAGAGAGAGAGAGA 59.102 42.308 0.00 0.00 0.00 3.10
591 599 7.118496 AGAAACTAGAGAGAGAGAGAGAGAG 57.882 44.000 0.00 0.00 0.00 3.20
592 600 6.667848 TGAGAAACTAGAGAGAGAGAGAGAGA 59.332 42.308 0.00 0.00 0.00 3.10
593 601 6.878317 TGAGAAACTAGAGAGAGAGAGAGAG 58.122 44.000 0.00 0.00 0.00 3.20
594 602 6.867519 TGAGAAACTAGAGAGAGAGAGAGA 57.132 41.667 0.00 0.00 0.00 3.10
595 603 7.504403 AGATGAGAAACTAGAGAGAGAGAGAG 58.496 42.308 0.00 0.00 0.00 3.20
596 604 7.437713 AGATGAGAAACTAGAGAGAGAGAGA 57.562 40.000 0.00 0.00 0.00 3.10
597 605 7.989741 AGAAGATGAGAAACTAGAGAGAGAGAG 59.010 40.741 0.00 0.00 0.00 3.20
598 606 7.770433 CAGAAGATGAGAAACTAGAGAGAGAGA 59.230 40.741 0.00 0.00 0.00 3.10
599 607 7.554118 ACAGAAGATGAGAAACTAGAGAGAGAG 59.446 40.741 0.00 0.00 0.00 3.20
600 608 7.402054 ACAGAAGATGAGAAACTAGAGAGAGA 58.598 38.462 0.00 0.00 0.00 3.10
601 609 7.630242 ACAGAAGATGAGAAACTAGAGAGAG 57.370 40.000 0.00 0.00 0.00 3.20
602 610 7.093988 CCAACAGAAGATGAGAAACTAGAGAGA 60.094 40.741 0.00 0.00 0.00 3.10
603 611 7.035004 CCAACAGAAGATGAGAAACTAGAGAG 58.965 42.308 0.00 0.00 0.00 3.20
604 612 6.071108 CCCAACAGAAGATGAGAAACTAGAGA 60.071 42.308 0.00 0.00 0.00 3.10
644 652 0.324830 GCTCACCTCTACCCCAGACT 60.325 60.000 0.00 0.00 0.00 3.24
663 671 5.734855 TCAAGAAAACAGAAAGAACGAGG 57.265 39.130 0.00 0.00 0.00 4.63
743 751 3.044894 AGAAGAACAGATCCCCTCATCC 58.955 50.000 0.00 0.00 0.00 3.51
744 752 3.454082 ACAGAAGAACAGATCCCCTCATC 59.546 47.826 0.00 0.00 0.00 2.92
746 754 2.568956 CACAGAAGAACAGATCCCCTCA 59.431 50.000 0.00 0.00 0.00 3.86
750 759 3.685139 TGACACAGAAGAACAGATCCC 57.315 47.619 0.00 0.00 0.00 3.85
755 764 6.293298 CCAGAAGATTTGACACAGAAGAACAG 60.293 42.308 0.00 0.00 0.00 3.16
862 871 3.307674 TCACACGAAATTTTGCATGAGC 58.692 40.909 5.27 0.00 42.57 4.26
863 872 5.214417 TCTTCACACGAAATTTTGCATGAG 58.786 37.500 5.27 4.68 0.00 2.90
867 876 5.586339 TCAATCTTCACACGAAATTTTGCA 58.414 33.333 5.27 0.00 0.00 4.08
1199 1214 1.002069 AACTCATGGATCTTGGGCCA 58.998 50.000 0.00 0.00 38.78 5.36
1252 1267 1.541588 GCAAAGAACCGGAGCAGAAAT 59.458 47.619 9.46 0.00 0.00 2.17
1640 1676 3.012274 ACTCTCATCTCTCTCCCTCCAAA 59.988 47.826 0.00 0.00 0.00 3.28
1669 1707 4.644685 ACTTAAGCTCCTCTCACTCATCTC 59.355 45.833 1.29 0.00 0.00 2.75
1670 1708 4.609301 ACTTAAGCTCCTCTCACTCATCT 58.391 43.478 1.29 0.00 0.00 2.90
1671 1709 4.202111 GGACTTAAGCTCCTCTCACTCATC 60.202 50.000 1.29 0.00 0.00 2.92
1876 1914 2.136878 CCTCTGTCCCTGATCCCCG 61.137 68.421 0.00 0.00 0.00 5.73
2105 2145 0.033796 ACACATCTCCATGGCCTTGG 60.034 55.000 28.04 28.04 38.18 3.61
2197 2238 4.276678 CCACGAATACATCATTCATGCCTT 59.723 41.667 0.00 0.00 42.86 4.35
2324 2365 7.559170 CCAAGATATTGAGAGGTGAGGAAAATT 59.441 37.037 0.54 0.00 0.00 1.82
2344 2387 3.966665 ACAATTCAACCAACCACCAAGAT 59.033 39.130 0.00 0.00 0.00 2.40
2362 2405 2.224992 TGTGTTGTGATGGGGCTACAAT 60.225 45.455 0.00 0.00 36.78 2.71
2366 2417 1.340893 CCATGTGTTGTGATGGGGCTA 60.341 52.381 0.00 0.00 36.26 3.93
2456 2507 3.243873 TGAGATTATTAGCCACTCAGCCG 60.244 47.826 0.00 0.00 33.57 5.52
2458 2509 4.213059 GCTTGAGATTATTAGCCACTCAGC 59.787 45.833 0.00 0.00 38.52 4.26
2512 2563 5.762711 GCCACAAGGAAAAACATGGTATTTT 59.237 36.000 0.00 1.72 36.89 1.82
2528 2582 2.445492 ATGGGGTGAAGGCCACAAGG 62.445 60.000 5.01 0.00 46.20 3.61


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

AutoCloner maintained by Alex Coulton.