Multiple sequence alignment - TraesCS2B01G500000

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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 TraesCS2B01G500000 chr2B 100.000 2648 0 0 1 2648 695593529 695596176 0.000000e+00 4891
1 TraesCS2B01G500000 chr2B 82.258 496 79 7 2157 2648 695735475 695735965 1.130000e-113 420
2 TraesCS2B01G500000 chr2D 89.182 2200 118 64 1 2142 578702624 578704761 0.000000e+00 2634
3 TraesCS2B01G500000 chr2D 93.933 511 23 6 2142 2648 578705199 578705705 0.000000e+00 765
4 TraesCS2B01G500000 chr2D 78.068 497 83 12 2156 2640 578927577 578928059 9.270000e-75 291
5 TraesCS2B01G500000 chr2A 89.340 1454 77 31 309 1734 716233828 716235231 0.000000e+00 1755
6 TraesCS2B01G500000 chr2A 92.254 568 34 6 2087 2648 716235655 716236218 0.000000e+00 797
7 TraesCS2B01G500000 chr2A 95.484 310 14 0 1780 2089 716235247 716235556 1.830000e-136 496
8 TraesCS2B01G500000 chr2A 76.992 891 132 40 1785 2640 716454777 716455629 2.420000e-120 442
9 TraesCS2B01G500000 chr2A 88.889 252 17 5 1 251 716233589 716233830 1.540000e-77 300


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 TraesCS2B01G500000 chr2B 695593529 695596176 2647 False 4891.0 4891 100.00000 1 2648 1 chr2B.!!$F1 2647
1 TraesCS2B01G500000 chr2D 578702624 578705705 3081 False 1699.5 2634 91.55750 1 2648 2 chr2D.!!$F2 2647
2 TraesCS2B01G500000 chr2A 716233589 716236218 2629 False 837.0 1755 91.49175 1 2648 4 chr2A.!!$F2 2647
3 TraesCS2B01G500000 chr2A 716454777 716455629 852 False 442.0 442 76.99200 1785 2640 1 chr2A.!!$F1 855

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
447 465 0.25064 GCTAGCTCCACATGGATGGG 60.251 60.0 7.7 0.0 44.46 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 3091 0.745486 CACGGATGCTGAGATTGCCA 60.745 55.0 0.0 0.0 0.0 4.92 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
23 24 4.166011 GCGCCGTGAACCAGATGC 62.166 66.667 0.00 0.00 0.00 3.91
73 74 3.048337 TCATCGGCCCGTAAATTATCC 57.952 47.619 1.63 0.00 0.00 2.59
149 158 5.063060 GCATCATTGTCTTTCTTCATTTGCC 59.937 40.000 0.00 0.00 0.00 4.52
168 177 3.110358 GCCTTGTTTGTTCGTTTGTACC 58.890 45.455 0.00 0.00 0.00 3.34
218 227 7.170151 TGTTTGCTTGATTGATTCAGTGAAATG 59.830 33.333 10.14 0.00 35.27 2.32
222 231 7.033791 GCTTGATTGATTCAGTGAAATGATGT 58.966 34.615 10.14 0.00 35.27 3.06
306 316 1.512734 CGGCTCGTACACGGTACAC 60.513 63.158 12.62 3.86 40.29 2.90
447 465 0.250640 GCTAGCTCCACATGGATGGG 60.251 60.000 7.70 0.00 44.46 4.00
478 496 2.001812 CCATCCACTCGTCAACTCTG 57.998 55.000 0.00 0.00 0.00 3.35
514 532 4.409247 ACACTCCTTGTACACTTCCTTTCT 59.591 41.667 0.00 0.00 36.32 2.52
672 706 9.846248 AGACAACTAATAATCAGCAACATTTTC 57.154 29.630 0.00 0.00 0.00 2.29
673 707 9.846248 GACAACTAATAATCAGCAACATTTTCT 57.154 29.630 0.00 0.00 0.00 2.52
709 767 7.462571 AAATCCTTTTGTATACACCACCTTC 57.537 36.000 4.68 0.00 0.00 3.46
710 768 5.836024 TCCTTTTGTATACACCACCTTCT 57.164 39.130 4.68 0.00 0.00 2.85
714 772 7.562088 TCCTTTTGTATACACCACCTTCTTTTT 59.438 33.333 4.68 0.00 0.00 1.94
715 773 7.651704 CCTTTTGTATACACCACCTTCTTTTTG 59.348 37.037 4.68 0.00 0.00 2.44
716 774 5.699097 TGTATACACCACCTTCTTTTTGC 57.301 39.130 0.08 0.00 0.00 3.68
717 775 5.381757 TGTATACACCACCTTCTTTTTGCT 58.618 37.500 0.08 0.00 0.00 3.91
718 776 5.472137 TGTATACACCACCTTCTTTTTGCTC 59.528 40.000 0.08 0.00 0.00 4.26
719 777 1.676006 ACACCACCTTCTTTTTGCTCG 59.324 47.619 0.00 0.00 0.00 5.03
720 778 1.676006 CACCACCTTCTTTTTGCTCGT 59.324 47.619 0.00 0.00 0.00 4.18
721 779 1.947456 ACCACCTTCTTTTTGCTCGTC 59.053 47.619 0.00 0.00 0.00 4.20
722 780 1.266989 CCACCTTCTTTTTGCTCGTCC 59.733 52.381 0.00 0.00 0.00 4.79
723 781 1.946768 CACCTTCTTTTTGCTCGTCCA 59.053 47.619 0.00 0.00 0.00 4.02
724 782 2.357637 CACCTTCTTTTTGCTCGTCCAA 59.642 45.455 0.00 0.00 0.00 3.53
725 783 3.004734 CACCTTCTTTTTGCTCGTCCAAT 59.995 43.478 0.00 0.00 0.00 3.16
726 784 3.004734 ACCTTCTTTTTGCTCGTCCAATG 59.995 43.478 0.00 0.00 0.00 2.82
727 785 3.253188 CCTTCTTTTTGCTCGTCCAATGA 59.747 43.478 0.00 0.00 0.00 2.57
728 786 4.082571 CCTTCTTTTTGCTCGTCCAATGAT 60.083 41.667 0.00 0.00 0.00 2.45
729 787 5.452078 TTCTTTTTGCTCGTCCAATGATT 57.548 34.783 0.00 0.00 0.00 2.57
730 788 6.349280 CCTTCTTTTTGCTCGTCCAATGATTA 60.349 38.462 0.00 0.00 0.00 1.75
731 789 6.757897 TCTTTTTGCTCGTCCAATGATTAT 57.242 33.333 0.00 0.00 0.00 1.28
732 790 6.785191 TCTTTTTGCTCGTCCAATGATTATC 58.215 36.000 0.00 0.00 0.00 1.75
733 791 6.374053 TCTTTTTGCTCGTCCAATGATTATCA 59.626 34.615 0.00 0.00 0.00 2.15
734 792 6.698008 TTTTGCTCGTCCAATGATTATCAT 57.302 33.333 1.25 1.25 39.09 2.45
735 793 5.929697 TTGCTCGTCCAATGATTATCATC 57.070 39.130 8.26 0.00 35.76 2.92
745 817 5.048504 CCAATGATTATCATCCCAAGTTCCG 60.049 44.000 8.26 0.00 35.76 4.30
763 835 1.403780 CCGAACCGAAAGACGAGGAAT 60.404 52.381 0.00 0.00 45.77 3.01
766 838 2.959275 CCGAAAGACGAGGAATCGG 58.041 57.895 2.46 0.00 45.88 4.18
768 840 2.273370 CGAAAGACGAGGAATCGGAA 57.727 50.000 2.46 0.00 45.77 4.30
769 841 2.810650 CGAAAGACGAGGAATCGGAAT 58.189 47.619 2.46 0.00 45.77 3.01
892 969 1.147600 GGGCCAGTATAACACCCGG 59.852 63.158 4.39 0.00 0.00 5.73
900 977 2.299867 AGTATAACACCCGGAACAACGT 59.700 45.455 0.73 0.00 0.00 3.99
916 993 3.246699 ACAACGTCGTAATCAAACCTGTG 59.753 43.478 0.00 0.00 0.00 3.66
983 1072 3.590574 GAACAAGGGGGCAGGGGT 61.591 66.667 0.00 0.00 0.00 4.95
1087 1176 4.641645 TGACCCGCTGCACCAAGG 62.642 66.667 0.00 0.00 0.00 3.61
1120 1209 1.613630 TTCCTCACCCTGCTCCTCC 60.614 63.158 0.00 0.00 0.00 4.30
1277 1366 2.359354 CATCCGCAACCCGAACCA 60.359 61.111 0.00 0.00 40.02 3.67
1284 1373 1.667151 CAACCCGAACCAGGACGTA 59.333 57.895 0.00 0.00 0.00 3.57
1320 1409 0.807667 GGCTCTACATGTCCGTGCTG 60.808 60.000 0.00 0.00 0.00 4.41
1521 1613 4.267503 GTCCGGTCGAGGATCCGC 62.268 72.222 5.98 5.59 44.63 5.54
1575 1667 2.338620 CTCCACGTGGACTGCGAA 59.661 61.111 33.23 11.55 39.78 4.70
1672 1764 2.369257 ATCCGCCTGCATGAGTACGG 62.369 60.000 10.36 10.36 39.68 4.02
1676 1768 1.084370 GCCTGCATGAGTACGGACAC 61.084 60.000 0.00 0.00 0.00 3.67
1683 1775 2.519377 TGAGTACGGACACAACAAGG 57.481 50.000 0.00 0.00 0.00 3.61
1734 1854 7.094975 TGCCGGCAAGTAATTAACATCATATAC 60.095 37.037 30.74 0.00 0.00 1.47
1736 1856 8.443160 CCGGCAAGTAATTAACATCATATACTG 58.557 37.037 0.00 0.00 0.00 2.74
1737 1857 8.988934 CGGCAAGTAATTAACATCATATACTGT 58.011 33.333 0.00 0.00 0.00 3.55
1829 1952 5.939764 TCACCTGTTGCTTCTCTGTATAT 57.060 39.130 0.00 0.00 0.00 0.86
1857 1980 0.257039 CCTCCTCCATGACTTTGGGG 59.743 60.000 0.00 0.00 36.96 4.96
1941 2064 0.732880 AATCTGTCAACGCCGACTCG 60.733 55.000 0.00 0.00 36.82 4.18
2127 2351 9.744468 ACAAAACAACATCTTCTAATTAACACC 57.256 29.630 0.00 0.00 0.00 4.16
2203 2867 7.384932 GTGGGGTTAAAAGAAGTGATGAAATTG 59.615 37.037 0.00 0.00 0.00 2.32
2224 2888 5.602458 TGATATACGTACCTTCGTAGCAG 57.398 43.478 0.00 0.00 46.70 4.24
2424 3091 2.583319 CTCATGCGCGATGACGGT 60.583 61.111 12.10 0.00 36.06 4.83
2491 3158 6.099269 TGAAGACTATAATCTTACCACCACCC 59.901 42.308 0.00 0.00 39.08 4.61
2519 3189 3.069289 CAATGTGCTCTCTTGCTGTGTA 58.931 45.455 0.00 0.00 0.00 2.90
2589 3259 1.606313 CCATGTGTGGTGGTTCCCC 60.606 63.158 0.00 0.00 40.83 4.81
2594 3264 1.846124 TGTGGTGGTTCCCCTCCTC 60.846 63.158 1.93 0.00 43.59 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.280389 CGGCCTACATGCGCATCT 60.280 61.111 22.51 12.42 0.00 2.90
73 74 9.173021 TCAATTATACAATACCCACAGACTTTG 57.827 33.333 0.00 0.00 0.00 2.77
187 196 8.339714 CACTGAATCAATCAAGCAAACATTTTT 58.660 29.630 0.00 0.00 37.67 1.94
218 227 0.460987 CGAGGTTGGCAGAGGACATC 60.461 60.000 0.00 0.00 0.00 3.06
222 231 0.614697 TCATCGAGGTTGGCAGAGGA 60.615 55.000 0.00 0.00 0.00 3.71
286 295 1.061570 GTACCGTGTACGAGCCGAG 59.938 63.158 5.91 0.00 43.02 4.63
306 316 2.069273 CAGCCTCAAGTTTCCTGTACG 58.931 52.381 0.00 0.00 0.00 3.67
478 496 0.871057 GGAGTGTGAGACAAGCTTGC 59.129 55.000 26.27 18.03 0.00 4.01
690 724 7.169140 GCAAAAAGAAGGTGGTGTATACAAAAG 59.831 37.037 7.25 0.00 0.00 2.27
709 767 6.554419 TGATAATCATTGGACGAGCAAAAAG 58.446 36.000 0.00 0.00 0.00 2.27
710 768 6.507958 TGATAATCATTGGACGAGCAAAAA 57.492 33.333 0.00 0.00 0.00 1.94
714 772 4.318332 GGATGATAATCATTGGACGAGCA 58.682 43.478 0.00 0.00 37.20 4.26
715 773 3.686726 GGGATGATAATCATTGGACGAGC 59.313 47.826 0.00 0.00 37.20 5.03
716 774 4.898320 TGGGATGATAATCATTGGACGAG 58.102 43.478 0.00 0.00 37.20 4.18
717 775 4.972751 TGGGATGATAATCATTGGACGA 57.027 40.909 0.00 0.00 37.20 4.20
718 776 5.065914 ACTTGGGATGATAATCATTGGACG 58.934 41.667 0.00 0.00 37.20 4.79
719 777 6.015940 GGAACTTGGGATGATAATCATTGGAC 60.016 42.308 0.00 0.00 37.20 4.02
720 778 6.070656 GGAACTTGGGATGATAATCATTGGA 58.929 40.000 0.00 0.00 37.20 3.53
721 779 5.048504 CGGAACTTGGGATGATAATCATTGG 60.049 44.000 0.00 0.00 37.20 3.16
722 780 5.764686 TCGGAACTTGGGATGATAATCATTG 59.235 40.000 0.00 0.00 37.20 2.82
723 781 5.940617 TCGGAACTTGGGATGATAATCATT 58.059 37.500 0.00 0.00 37.20 2.57
724 782 5.567037 TCGGAACTTGGGATGATAATCAT 57.433 39.130 0.00 0.00 40.34 2.45
725 783 5.123227 GTTCGGAACTTGGGATGATAATCA 58.877 41.667 13.49 0.00 0.00 2.57
726 784 4.515567 GGTTCGGAACTTGGGATGATAATC 59.484 45.833 19.40 0.00 0.00 1.75
727 785 4.461198 GGTTCGGAACTTGGGATGATAAT 58.539 43.478 19.40 0.00 0.00 1.28
728 786 3.680475 CGGTTCGGAACTTGGGATGATAA 60.680 47.826 19.40 0.00 0.00 1.75
729 787 2.159014 CGGTTCGGAACTTGGGATGATA 60.159 50.000 19.40 0.00 0.00 2.15
730 788 1.406887 CGGTTCGGAACTTGGGATGAT 60.407 52.381 19.40 0.00 0.00 2.45
731 789 0.036765 CGGTTCGGAACTTGGGATGA 60.037 55.000 19.40 0.00 0.00 2.92
732 790 0.036765 TCGGTTCGGAACTTGGGATG 60.037 55.000 19.40 3.13 0.00 3.51
733 791 0.688487 TTCGGTTCGGAACTTGGGAT 59.312 50.000 19.40 0.00 0.00 3.85
734 792 0.469070 TTTCGGTTCGGAACTTGGGA 59.531 50.000 19.40 9.78 0.00 4.37
735 793 0.872388 CTTTCGGTTCGGAACTTGGG 59.128 55.000 19.40 7.84 0.00 4.12
745 817 1.918609 CGATTCCTCGTCTTTCGGTTC 59.081 52.381 0.00 0.00 40.07 3.62
766 838 6.307318 CGAGCTTTGGTGTACGGTATATATTC 59.693 42.308 0.00 0.00 0.00 1.75
767 839 6.016024 TCGAGCTTTGGTGTACGGTATATATT 60.016 38.462 0.00 0.00 0.00 1.28
768 840 5.474532 TCGAGCTTTGGTGTACGGTATATAT 59.525 40.000 0.00 0.00 0.00 0.86
769 841 4.821260 TCGAGCTTTGGTGTACGGTATATA 59.179 41.667 0.00 0.00 0.00 0.86
892 969 4.025480 ACAGGTTTGATTACGACGTTGTTC 60.025 41.667 14.93 7.22 0.00 3.18
900 977 2.161410 GCATGCACAGGTTTGATTACGA 59.839 45.455 14.21 0.00 0.00 3.43
936 1025 2.877582 CCCTACGTGCGTGCGTAC 60.878 66.667 7.55 2.83 45.06 3.67
937 1026 4.781959 GCCCTACGTGCGTGCGTA 62.782 66.667 7.55 11.70 45.06 4.42
944 1033 3.701604 CTCTGGTCGCCCTACGTGC 62.702 68.421 0.00 0.00 44.19 5.34
1087 1176 3.173240 GAACGCCGAGCAGACGAC 61.173 66.667 0.00 0.00 35.09 4.34
1235 1324 3.053896 GCCCGGAAAAGACCACGG 61.054 66.667 0.73 0.00 45.57 4.94
1284 1373 1.946475 GCCGGTCGTAGAAGAAGGCT 61.946 60.000 1.90 0.00 40.63 4.58
1626 1718 4.219944 ACCTACAAGAAGTCTATGTCGCAA 59.780 41.667 0.00 0.00 0.00 4.85
1672 1764 6.628919 ATGTTACTAAACCCTTGTTGTGTC 57.371 37.500 0.00 0.00 34.13 3.67
1676 1768 6.642707 TGGAATGTTACTAAACCCTTGTTG 57.357 37.500 0.00 0.00 34.13 3.33
1768 1888 8.576442 TCAAGGATTTGGTTTGTCTTAATCTTC 58.424 33.333 0.00 0.00 34.97 2.87
1769 1889 8.477419 TCAAGGATTTGGTTTGTCTTAATCTT 57.523 30.769 0.00 0.00 34.97 2.40
1770 1890 8.655935 ATCAAGGATTTGGTTTGTCTTAATCT 57.344 30.769 0.00 0.00 34.97 2.40
1771 1891 9.143631 CAATCAAGGATTTGGTTTGTCTTAATC 57.856 33.333 0.00 0.00 35.47 1.75
1772 1892 8.650490 ACAATCAAGGATTTGGTTTGTCTTAAT 58.350 29.630 0.00 0.00 35.47 1.40
1773 1893 7.925483 CACAATCAAGGATTTGGTTTGTCTTAA 59.075 33.333 6.57 0.00 35.47 1.85
1829 1952 1.640149 TCATGGAGGAGGCAATGGAAA 59.360 47.619 0.00 0.00 0.00 3.13
1857 1980 4.397417 AGAAGAGCATGGCTTTTATCACAC 59.603 41.667 0.00 0.00 39.88 3.82
1941 2064 2.514824 GCAGGAAGGATGGACGGC 60.515 66.667 0.00 0.00 0.00 5.68
2203 2867 5.380651 CACTGCTACGAAGGTACGTATATC 58.619 45.833 0.00 0.00 45.37 1.63
2207 2871 1.739466 CCACTGCTACGAAGGTACGTA 59.261 52.381 0.00 0.00 44.72 3.57
2209 2873 0.801067 GCCACTGCTACGAAGGTACG 60.801 60.000 0.00 0.00 35.37 3.67
2210 2874 0.801067 CGCCACTGCTACGAAGGTAC 60.801 60.000 0.00 0.00 34.43 3.34
2331 2998 8.911247 AATTTTCAAAGCCGATAGTATTGTTC 57.089 30.769 0.00 0.00 0.00 3.18
2424 3091 0.745486 CACGGATGCTGAGATTGCCA 60.745 55.000 0.00 0.00 0.00 4.92
2519 3189 0.907704 TGGGAGGTGATAGTTGCCGT 60.908 55.000 0.00 0.00 0.00 5.68
2589 3259 4.109050 GAGCAAGATAGAACAACGAGGAG 58.891 47.826 0.00 0.00 0.00 3.69
2594 3264 5.220548 CCATCAAGAGCAAGATAGAACAACG 60.221 44.000 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.