Multiple sequence alignment - TraesCS2B01G247600

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 TraesCS2B01G247600 chr2B 100.000 2788 0 0 1 2788 254239334 254236547 0 5149
1 TraesCS2B01G247600 chr2B 84.490 735 102 8 1 723 481136655 481137389 0 715
2 TraesCS2B01G247600 chr2A 94.089 1861 82 15 786 2633 213097981 213096136 0 2802
3 TraesCS2B01G247600 chr2D 92.105 1976 84 22 830 2788 196791231 196789311 0 2719
4 TraesCS2B01G247600 chr2D 86.667 870 76 17 1 834 196807052 196806187 0 928
5 TraesCS2B01G247600 chr2D 85.185 729 93 9 6 722 380063393 380062668 0 734
6 TraesCS2B01G247600 chr7B 85.616 730 93 8 1 718 595711821 595711092 0 756
7 TraesCS2B01G247600 chr5D 84.939 737 94 12 1 723 156630107 156629374 0 730
8 TraesCS2B01G247600 chr5A 84.803 737 96 12 1 722 544640523 544639788 0 726
9 TraesCS2B01G247600 chr1A 84.658 730 100 7 1 718 403132895 403133624 0 717
10 TraesCS2B01G247600 chr1A 84.447 733 98 8 1 718 403141821 403142552 0 708
11 TraesCS2B01G247600 chr1B 84.247 730 103 8 1 718 637532879 637533608 0 701


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 TraesCS2B01G247600 chr2B 254236547 254239334 2787 True 5149 5149 100.000 1 2788 1 chr2B.!!$R1 2787
1 TraesCS2B01G247600 chr2B 481136655 481137389 734 False 715 715 84.490 1 723 1 chr2B.!!$F1 722
2 TraesCS2B01G247600 chr2A 213096136 213097981 1845 True 2802 2802 94.089 786 2633 1 chr2A.!!$R1 1847
3 TraesCS2B01G247600 chr2D 196789311 196791231 1920 True 2719 2719 92.105 830 2788 1 chr2D.!!$R1 1958
4 TraesCS2B01G247600 chr2D 196806187 196807052 865 True 928 928 86.667 1 834 1 chr2D.!!$R2 833
5 TraesCS2B01G247600 chr2D 380062668 380063393 725 True 734 734 85.185 6 722 1 chr2D.!!$R3 716
6 TraesCS2B01G247600 chr7B 595711092 595711821 729 True 756 756 85.616 1 718 1 chr7B.!!$R1 717
7 TraesCS2B01G247600 chr5D 156629374 156630107 733 True 730 730 84.939 1 723 1 chr5D.!!$R1 722
8 TraesCS2B01G247600 chr5A 544639788 544640523 735 True 726 726 84.803 1 722 1 chr5A.!!$R1 721
9 TraesCS2B01G247600 chr1A 403132895 403133624 729 False 717 717 84.658 1 718 1 chr1A.!!$F1 717
10 TraesCS2B01G247600 chr1A 403141821 403142552 731 False 708 708 84.447 1 718 1 chr1A.!!$F2 717
11 TraesCS2B01G247600 chr1B 637532879 637533608 729 False 701 701 84.247 1 718 1 chr1B.!!$F1 717

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
788 834 0.253894 TGTCATGCCATCCTCACAGG 59.746 55.0 0.0 0.0 36.46 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2753 2817 0.39034 AGCATGGACACAGTAGCGTG 60.39 55.0 0.0 0.0 42.81 5.34 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
25 26 2.232452 TGTTCTAGAGAGCTTGGCACTC 59.768 50.000 8.49 8.49 44.36 3.51
120 123 4.433615 GGCATCTTTCTCGTCTTGTCATA 58.566 43.478 0.00 0.00 0.00 2.15
201 204 5.366768 CCAACCACTAATATGGAGAGGAAGA 59.633 44.000 7.96 0.00 43.02 2.87
218 221 3.560105 GAAGATTATTCCTTGGCAGCCT 58.440 45.455 14.15 0.00 0.00 4.58
228 233 3.415087 GGCAGCCTCCCACCTCAT 61.415 66.667 3.29 0.00 0.00 2.90
256 261 7.376435 TCTTCAAGATTAATGTCGATGCAAA 57.624 32.000 0.00 0.00 0.00 3.68
266 271 4.313277 TGTCGATGCAAATTTTGTGGAA 57.687 36.364 10.65 0.00 0.00 3.53
306 313 1.569548 TGGGGGTGGTTGTAAGAAACA 59.430 47.619 0.00 0.00 35.88 2.83
375 389 4.571369 TCGAGGAAGAGGAACTTAGAGA 57.429 45.455 0.00 0.00 41.55 3.10
381 395 3.391799 AGAGGAACTTAGAGAGACCCC 57.608 52.381 0.00 0.00 41.55 4.95
385 399 1.401199 GAACTTAGAGAGACCCCGTCG 59.599 57.143 0.00 0.00 37.67 5.12
405 419 4.081087 GTCGGGCCTGTATATTGGTATGAT 60.081 45.833 12.43 0.00 0.00 2.45
411 425 7.275920 GGCCTGTATATTGGTATGATTCTAGG 58.724 42.308 0.00 0.00 0.00 3.02
416 430 8.825774 TGTATATTGGTATGATTCTAGGCATGT 58.174 33.333 0.00 0.00 0.00 3.21
424 438 3.895041 TGATTCTAGGCATGTCCGTCATA 59.105 43.478 0.00 0.00 40.77 2.15
438 452 5.186215 TGTCCGTCATATTGGAAACTGACTA 59.814 40.000 0.00 0.00 38.80 2.59
485 499 5.582665 GGAAGAGATTGTATGAACAGGTCAC 59.417 44.000 0.00 0.00 39.72 3.67
505 519 5.768164 GTCACCCCTTGTTGATCTAAAGAAA 59.232 40.000 0.00 0.00 0.00 2.52
575 589 4.166725 AGATCAACAGGAGGGCAAATATGA 59.833 41.667 0.00 0.00 0.00 2.15
668 682 3.891324 TGCGTGGTAAAGTTTGTAATGC 58.109 40.909 0.00 1.46 0.00 3.56
682 696 9.524106 AAGTTTGTAATGCATGATTGTATGATG 57.476 29.630 0.00 0.00 0.00 3.07
760 806 1.556373 GCCCTACCCCGGTGTAACTT 61.556 60.000 0.00 0.00 36.74 2.66
778 824 3.623703 ACTTAGCAATGATGTCATGCCA 58.376 40.909 11.26 0.00 36.56 4.92
784 830 3.219281 CAATGATGTCATGCCATCCTCA 58.781 45.455 13.84 0.00 40.43 3.86
788 834 0.253894 TGTCATGCCATCCTCACAGG 59.746 55.000 0.00 0.00 36.46 4.00
826 873 5.221303 TGGTTCTTTCTTGAGCTTGGAAATG 60.221 40.000 9.13 5.69 0.00 2.32
940 988 2.889606 TAGAACCGGCCTGCTTGCA 61.890 57.895 0.00 0.00 0.00 4.08
1366 1417 1.739562 GCGTCCTCAAGCACCTCAG 60.740 63.158 0.00 0.00 0.00 3.35
1367 1418 1.967535 CGTCCTCAAGCACCTCAGA 59.032 57.895 0.00 0.00 0.00 3.27
1404 1455 1.196012 GTCTCCCCGTTCTTGATCCT 58.804 55.000 0.00 0.00 0.00 3.24
1469 1520 5.586643 GGGAAACTAATCTGCCTTCTACTTG 59.413 44.000 0.00 0.00 0.00 3.16
1666 1725 3.432592 CACTGACAGCTGATGAAACTCTG 59.567 47.826 23.35 11.72 0.00 3.35
1757 1816 3.055458 TGCACCGATGAGTTTTGGATCTA 60.055 43.478 0.00 0.00 0.00 1.98
1770 1829 8.567285 AGTTTTGGATCTAATGTTTCGAGAAT 57.433 30.769 0.00 0.00 0.00 2.40
1777 1836 9.314321 GGATCTAATGTTTCGAGAATTAAGTCA 57.686 33.333 5.62 0.00 0.00 3.41
2000 2064 2.680312 TCTAACTCATGCTGCCAGTC 57.320 50.000 0.00 0.00 0.00 3.51
2008 2072 0.403271 ATGCTGCCAGTCTGTCCTTT 59.597 50.000 0.00 0.00 0.00 3.11
2009 2073 0.535780 TGCTGCCAGTCTGTCCTTTG 60.536 55.000 0.00 0.00 0.00 2.77
2013 2077 0.606673 GCCAGTCTGTCCTTTGGTCC 60.607 60.000 0.00 0.00 33.21 4.46
2129 2193 6.983474 AAAATCTGGTTTGGAAAACAACAG 57.017 33.333 5.33 4.55 39.19 3.16
2219 2283 6.212955 CAAAGTCGGCCAAGATTTTTCTTTA 58.787 36.000 2.24 0.00 29.42 1.85
2226 2290 6.308766 CGGCCAAGATTTTTCTTTAATCTGTG 59.691 38.462 2.24 0.00 40.51 3.66
2280 2344 6.389830 AACACTGCATGAAAAACTGTCATA 57.610 33.333 0.00 0.00 33.91 2.15
2294 2358 4.391155 ACTGTCATAGATACTCGGAGGTC 58.609 47.826 10.23 7.21 0.00 3.85
2318 2382 3.988379 AGAAACGCTTGAAAATGAGCA 57.012 38.095 0.00 0.00 38.81 4.26
2421 2485 7.364522 TGCTAATTTTACTCACAGACATGTC 57.635 36.000 18.47 18.47 37.65 3.06
2422 2486 6.371548 TGCTAATTTTACTCACAGACATGTCC 59.628 38.462 22.21 4.75 37.65 4.02
2423 2487 6.371548 GCTAATTTTACTCACAGACATGTCCA 59.628 38.462 22.21 3.40 37.65 4.02
2424 2488 7.066284 GCTAATTTTACTCACAGACATGTCCAT 59.934 37.037 22.21 7.94 37.65 3.41
2425 2489 6.992063 ATTTTACTCACAGACATGTCCATC 57.008 37.500 22.21 0.00 37.65 3.51
2434 2498 3.072622 CAGACATGTCCATCCATCCTCAT 59.927 47.826 22.21 0.00 0.00 2.90
2532 2596 1.412343 GCCACCAAAGGTCAACATTGT 59.588 47.619 0.00 0.00 31.02 2.71
2565 2629 9.730705 TGAATAGATTAGAAATCCTTGCATAGG 57.269 33.333 8.22 8.22 46.27 2.57
2638 2702 8.070171 CGTTCATTATTGCTATTCTTTAGGTGG 58.930 37.037 0.00 0.00 0.00 4.61
2645 2709 3.371595 GCTATTCTTTAGGTGGGGAAGCA 60.372 47.826 0.00 0.00 0.00 3.91
2692 2756 2.680841 CCAAATTTGGGCTGCATGATTG 59.319 45.455 26.87 0.00 44.70 2.67
2753 2817 4.035208 CGTGGATATTGTAAAGTGGAAGCC 59.965 45.833 0.00 0.00 0.00 4.35
2769 2833 1.079127 GCCACGCTACTGTGTCCAT 60.079 57.895 0.00 0.00 38.20 3.41
2774 2838 1.135083 ACGCTACTGTGTCCATGCTAC 60.135 52.381 0.00 0.00 29.93 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.603236 CCTCGAGTGCCAAGCTCTCT 61.603 60.000 12.31 0.00 44.02 3.10
25 26 5.824904 ACCAAAGATCAAATCATTCCTCG 57.175 39.130 0.00 0.00 0.00 4.63
120 123 4.082571 GCACATCTTCACCTGCATTTTAGT 60.083 41.667 0.00 0.00 0.00 2.24
201 204 1.133356 GGGAGGCTGCCAAGGAATAAT 60.133 52.381 21.34 0.00 0.00 1.28
218 221 6.581388 ATCTTGAAGAATTATGAGGTGGGA 57.419 37.500 0.00 0.00 0.00 4.37
228 233 9.108284 TGCATCGACATTAATCTTGAAGAATTA 57.892 29.630 0.00 0.00 0.00 1.40
256 261 5.240121 CAGCTTTAATGGCTTCCACAAAAT 58.760 37.500 1.38 0.00 38.03 1.82
266 271 0.171903 CGCTTGCAGCTTTAATGGCT 59.828 50.000 0.00 0.00 39.60 4.75
306 313 7.525158 TCCCAGGAGGAAGAATAACTTAATT 57.475 36.000 0.00 0.00 43.78 1.40
381 395 0.391597 ACCAATATACAGGCCCGACG 59.608 55.000 0.00 0.00 0.00 5.12
385 399 6.067217 AGAATCATACCAATATACAGGCCC 57.933 41.667 0.00 0.00 0.00 5.80
405 419 4.503123 CCAATATGACGGACATGCCTAGAA 60.503 45.833 3.21 0.00 39.77 2.10
411 425 3.627577 AGTTTCCAATATGACGGACATGC 59.372 43.478 3.21 0.00 39.77 4.06
416 430 4.819105 AGTCAGTTTCCAATATGACGGA 57.181 40.909 0.00 0.00 45.25 4.69
424 438 6.209391 CCACAAAGGAATAGTCAGTTTCCAAT 59.791 38.462 4.66 0.00 43.21 3.16
438 452 3.308401 AGAACAAAGGCCACAAAGGAAT 58.692 40.909 5.01 0.00 41.22 3.01
485 499 5.649831 CCTCTTTCTTTAGATCAACAAGGGG 59.350 44.000 0.00 0.00 0.00 4.79
505 519 3.008049 ACTTTGAGACATTTACCGCCTCT 59.992 43.478 0.00 0.00 0.00 3.69
575 589 1.754803 CATTGCAATCTGGTGAGCCAT 59.245 47.619 9.53 0.00 45.05 4.40
718 739 1.001378 AGCAACAGCGTGGTCAATTTC 60.001 47.619 0.00 0.00 0.00 2.17
778 824 0.333993 AAATGCAGGCCTGTGAGGAT 59.666 50.000 32.81 11.87 37.67 3.24
784 830 2.905736 ACCAAATAAAATGCAGGCCTGT 59.094 40.909 32.81 16.06 0.00 4.00
788 834 5.934043 AGAAAGAACCAAATAAAATGCAGGC 59.066 36.000 0.00 0.00 0.00 4.85
1166 1217 1.598130 GAACTGCGCCTTCCAGTGT 60.598 57.895 4.18 0.00 42.37 3.55
1233 1284 4.834892 CTTCGCAAATGCCGCCGG 62.835 66.667 0.00 0.00 37.91 6.13
1366 1417 0.105778 CCCGAGCCTCCTGAGATTTC 59.894 60.000 0.00 0.00 0.00 2.17
1367 1418 0.618968 ACCCGAGCCTCCTGAGATTT 60.619 55.000 0.00 0.00 0.00 2.17
1404 1455 3.653835 TTCAGAAGGAGGAGATCGAGA 57.346 47.619 0.00 0.00 0.00 4.04
1435 1486 6.278363 GCAGATTAGTTTCCCTGATACGTAA 58.722 40.000 0.00 0.00 0.00 3.18
1437 1488 4.443034 GGCAGATTAGTTTCCCTGATACGT 60.443 45.833 0.00 0.00 0.00 3.57
1438 1489 4.058817 GGCAGATTAGTTTCCCTGATACG 58.941 47.826 0.00 0.00 0.00 3.06
1441 1492 4.476479 AGAAGGCAGATTAGTTTCCCTGAT 59.524 41.667 0.00 0.00 0.00 2.90
1455 1506 4.499865 GCGATGATACAAGTAGAAGGCAGA 60.500 45.833 0.00 0.00 0.00 4.26
1469 1520 6.525121 TGTTGTTAGCTATTGCGATGATAC 57.475 37.500 0.00 0.00 45.42 2.24
1642 1701 3.661944 AGTTTCATCAGCTGTCAGTGAG 58.338 45.455 14.67 0.00 0.00 3.51
1666 1725 6.765036 AGGATATGCTGCATATACATAACTGC 59.235 38.462 34.62 19.80 39.44 4.40
1817 1876 4.707448 AGCCGTTTTCTCTAGAGATCTTGA 59.293 41.667 22.93 5.11 37.29 3.02
2000 2064 3.981071 TCATACTGGACCAAAGGACAG 57.019 47.619 0.00 9.68 37.30 3.51
2008 2072 4.641396 CAGTTCAACTTCATACTGGACCA 58.359 43.478 0.00 0.00 35.51 4.02
2009 2073 3.437049 GCAGTTCAACTTCATACTGGACC 59.563 47.826 0.00 0.00 38.68 4.46
2013 2077 5.388111 CACATGCAGTTCAACTTCATACTG 58.612 41.667 2.07 0.00 40.65 2.74
2051 2115 2.572290 AGGAATTTTCGCGAATAGGGG 58.428 47.619 24.05 0.00 0.00 4.79
2129 2193 1.197949 GAAAGGAAACGAAGCTCCAGC 59.802 52.381 0.00 0.00 35.48 4.85
2203 2267 8.816640 TTCACAGATTAAAGAAAAATCTTGGC 57.183 30.769 0.00 0.00 40.81 4.52
2219 2283 0.462047 GCCCCGTCGATTCACAGATT 60.462 55.000 0.00 0.00 0.00 2.40
2226 2290 1.582610 TTTGCTTGCCCCGTCGATTC 61.583 55.000 0.00 0.00 0.00 2.52
2294 2358 4.143742 GCTCATTTTCAAGCGTTTCTTTCG 60.144 41.667 0.00 0.00 31.27 3.46
2318 2382 3.340928 GCCCGTTTACTTGGTATGTTCT 58.659 45.455 0.00 0.00 0.00 3.01
2421 2485 2.651382 TTCTGCATGAGGATGGATGG 57.349 50.000 0.00 0.00 0.00 3.51
2422 2486 4.142038 TCAATTCTGCATGAGGATGGATG 58.858 43.478 0.00 0.00 0.00 3.51
2423 2487 4.448720 TCAATTCTGCATGAGGATGGAT 57.551 40.909 0.00 0.00 0.00 3.41
2424 2488 3.937778 TCAATTCTGCATGAGGATGGA 57.062 42.857 0.00 0.00 0.00 3.41
2425 2489 4.142038 TGATCAATTCTGCATGAGGATGG 58.858 43.478 0.00 0.00 0.00 3.51
2434 2498 4.768448 ACCTGACATTTGATCAATTCTGCA 59.232 37.500 9.40 8.79 0.00 4.41
2565 2629 3.686241 GCAGGCAATTTCAAATCCTTTCC 59.314 43.478 0.00 0.00 0.00 3.13
2692 2756 2.223923 ACAATATCTCTCTGTGCCTCGC 60.224 50.000 0.00 0.00 0.00 5.03
2753 2817 0.390340 AGCATGGACACAGTAGCGTG 60.390 55.000 0.00 0.00 42.81 5.34
2769 2833 2.199117 CGGCCAGTAGAAGGTAGCA 58.801 57.895 2.24 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.