Multiple sequence alignment - TraesCS3A01G264300

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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 TraesCS3A01G264300 chr3A 100.000 2844 0 0 1 2844 488262391 488259548 0.000000e+00 5252.0
1 TraesCS3A01G264300 chr3A 84.431 957 95 23 1018 1927 488303983 488303034 0.000000e+00 893.0
2 TraesCS3A01G264300 chr1A 98.502 868 10 2 1 868 288490482 288489618 0.000000e+00 1528.0
3 TraesCS3A01G264300 chr5B 98.488 860 13 0 1 860 80213078 80212219 0.000000e+00 1517.0
4 TraesCS3A01G264300 chr5B 98.372 860 13 1 1 860 80617593 80616735 0.000000e+00 1509.0
5 TraesCS3A01G264300 chr6A 98.481 856 13 0 1 856 112047913 112048768 0.000000e+00 1509.0
6 TraesCS3A01G264300 chr3B 98.366 857 14 0 1 857 533589669 533590525 0.000000e+00 1506.0
7 TraesCS3A01G264300 chr3B 92.626 773 52 4 950 1721 477370084 477369316 0.000000e+00 1107.0
8 TraesCS3A01G264300 chr3B 85.507 759 76 19 1018 1753 477626077 477625330 0.000000e+00 761.0
9 TraesCS3A01G264300 chr3B 87.064 487 43 16 1768 2243 477369313 477368836 1.500000e-147 532.0
10 TraesCS3A01G264300 chr3B 90.943 265 16 5 957 1219 477371250 477370992 1.620000e-92 350.0
11 TraesCS3A01G264300 chr2A 98.368 858 13 1 1 857 380235047 380234190 0.000000e+00 1506.0
12 TraesCS3A01G264300 chr2A 98.248 856 15 0 1 856 455278592 455279447 0.000000e+00 1498.0
13 TraesCS3A01G264300 chr6B 98.133 857 15 1 1 857 443298338 443299193 0.000000e+00 1493.0
14 TraesCS3A01G264300 chr4A 98.131 856 15 1 1 856 141288681 141287827 0.000000e+00 1491.0
15 TraesCS3A01G264300 chr3D 94.360 727 36 2 950 1675 366015397 366014675 0.000000e+00 1110.0
16 TraesCS3A01G264300 chr3D 88.496 791 64 4 961 1728 366208971 366208185 0.000000e+00 931.0
17 TraesCS3A01G264300 chr3D 92.784 582 39 1 2247 2825 79595105 79594524 0.000000e+00 839.0
18 TraesCS3A01G264300 chr3D 85.248 766 63 12 1018 1754 366224544 366223800 0.000000e+00 743.0
19 TraesCS3A01G264300 chr3D 93.028 459 29 3 1802 2258 366013109 366012652 0.000000e+00 667.0
20 TraesCS3A01G264300 chr3D 82.775 209 23 9 1723 1921 366207715 366207510 1.050000e-39 174.0
21 TraesCS3A01G264300 chr3D 93.902 82 5 0 1731 1812 366014679 366014598 1.070000e-24 124.0
22 TraesCS3A01G264300 chr6D 93.814 582 33 1 2247 2825 32009538 32008957 0.000000e+00 872.0
23 TraesCS3A01G264300 chr6D 92.771 581 39 1 2245 2822 98088488 98089068 0.000000e+00 837.0
24 TraesCS3A01G264300 chr6D 92.241 580 42 1 2247 2823 17961054 17960475 0.000000e+00 819.0
25 TraesCS3A01G264300 chr5D 93.186 587 37 1 2242 2825 429303508 429302922 0.000000e+00 859.0
26 TraesCS3A01G264300 chr5D 90.783 575 49 2 2247 2818 81819445 81820018 0.000000e+00 765.0
27 TraesCS3A01G264300 chr4D 90.940 585 46 4 2247 2825 62312092 62312675 0.000000e+00 780.0
28 TraesCS3A01G264300 chr4D 90.476 588 47 4 2247 2825 103458747 103459334 0.000000e+00 767.0
29 TraesCS3A01G264300 chr4D 90.395 583 51 3 2247 2825 103464364 103464945 0.000000e+00 761.0
30 TraesCS3A01G264300 chr2B 91.837 49 1 2 2008 2053 689162345 689162297 6.580000e-07 65.8
31 TraesCS3A01G264300 chr7B 94.737 38 0 2 1997 2034 676035054 676035089 1.100000e-04 58.4


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 TraesCS3A01G264300 chr3A 488259548 488262391 2843 True 5252.000000 5252 100.000000 1 2844 1 chr3A.!!$R1 2843
1 TraesCS3A01G264300 chr3A 488303034 488303983 949 True 893.000000 893 84.431000 1018 1927 1 chr3A.!!$R2 909
2 TraesCS3A01G264300 chr1A 288489618 288490482 864 True 1528.000000 1528 98.502000 1 868 1 chr1A.!!$R1 867
3 TraesCS3A01G264300 chr5B 80212219 80213078 859 True 1517.000000 1517 98.488000 1 860 1 chr5B.!!$R1 859
4 TraesCS3A01G264300 chr5B 80616735 80617593 858 True 1509.000000 1509 98.372000 1 860 1 chr5B.!!$R2 859
5 TraesCS3A01G264300 chr6A 112047913 112048768 855 False 1509.000000 1509 98.481000 1 856 1 chr6A.!!$F1 855
6 TraesCS3A01G264300 chr3B 533589669 533590525 856 False 1506.000000 1506 98.366000 1 857 1 chr3B.!!$F1 856
7 TraesCS3A01G264300 chr3B 477625330 477626077 747 True 761.000000 761 85.507000 1018 1753 1 chr3B.!!$R1 735
8 TraesCS3A01G264300 chr3B 477368836 477371250 2414 True 663.000000 1107 90.211000 950 2243 3 chr3B.!!$R2 1293
9 TraesCS3A01G264300 chr2A 380234190 380235047 857 True 1506.000000 1506 98.368000 1 857 1 chr2A.!!$R1 856
10 TraesCS3A01G264300 chr2A 455278592 455279447 855 False 1498.000000 1498 98.248000 1 856 1 chr2A.!!$F1 855
11 TraesCS3A01G264300 chr6B 443298338 443299193 855 False 1493.000000 1493 98.133000 1 857 1 chr6B.!!$F1 856
12 TraesCS3A01G264300 chr4A 141287827 141288681 854 True 1491.000000 1491 98.131000 1 856 1 chr4A.!!$R1 855
13 TraesCS3A01G264300 chr3D 79594524 79595105 581 True 839.000000 839 92.784000 2247 2825 1 chr3D.!!$R1 578
14 TraesCS3A01G264300 chr3D 366223800 366224544 744 True 743.000000 743 85.248000 1018 1754 1 chr3D.!!$R2 736
15 TraesCS3A01G264300 chr3D 366012652 366015397 2745 True 633.666667 1110 93.763333 950 2258 3 chr3D.!!$R3 1308
16 TraesCS3A01G264300 chr3D 366207510 366208971 1461 True 552.500000 931 85.635500 961 1921 2 chr3D.!!$R4 960
17 TraesCS3A01G264300 chr6D 32008957 32009538 581 True 872.000000 872 93.814000 2247 2825 1 chr6D.!!$R2 578
18 TraesCS3A01G264300 chr6D 98088488 98089068 580 False 837.000000 837 92.771000 2245 2822 1 chr6D.!!$F1 577
19 TraesCS3A01G264300 chr6D 17960475 17961054 579 True 819.000000 819 92.241000 2247 2823 1 chr6D.!!$R1 576
20 TraesCS3A01G264300 chr5D 429302922 429303508 586 True 859.000000 859 93.186000 2242 2825 1 chr5D.!!$R1 583
21 TraesCS3A01G264300 chr5D 81819445 81820018 573 False 765.000000 765 90.783000 2247 2818 1 chr5D.!!$F1 571
22 TraesCS3A01G264300 chr4D 62312092 62312675 583 False 780.000000 780 90.940000 2247 2825 1 chr4D.!!$F1 578
23 TraesCS3A01G264300 chr4D 103458747 103459334 587 False 767.000000 767 90.476000 2247 2825 1 chr4D.!!$F2 578
24 TraesCS3A01G264300 chr4D 103464364 103464945 581 False 761.000000 761 90.395000 2247 2825 1 chr4D.!!$F3 578

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
944 946 0.229753 GCTACACGATGCACATACGC 59.77 55.0 0.0 0.0 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 5698 0.320374 TCGAGGTCCTGCGACAATTT 59.68 50.0 0.0 0.0 41.13 1.82 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
605 606 2.907042 ACTCACCTTAAACCCTCTCCTG 59.093 50.000 0.00 0.00 0.00 3.86
649 650 2.563179 CGCACTCTATATAAGCCACCCT 59.437 50.000 0.00 0.00 0.00 4.34
682 683 1.073548 GGGGTTCGGCACCTTGTAA 59.926 57.895 0.00 0.00 46.38 2.41
691 692 4.776349 TCGGCACCTTGTAATTCATACAT 58.224 39.130 0.00 0.00 43.84 2.29
860 862 1.676014 GCTTAGAACCACGACAGCCAT 60.676 52.381 0.00 0.00 0.00 4.40
861 863 2.271800 CTTAGAACCACGACAGCCATC 58.728 52.381 0.00 0.00 0.00 3.51
863 865 2.740714 GAACCACGACAGCCATCGC 61.741 63.158 7.10 0.00 46.22 4.58
864 866 4.760047 ACCACGACAGCCATCGCC 62.760 66.667 7.10 0.00 46.22 5.54
873 875 4.838152 GCCATCGCCGCCTCTGAA 62.838 66.667 0.00 0.00 0.00 3.02
874 876 2.587194 CCATCGCCGCCTCTGAAG 60.587 66.667 0.00 0.00 0.00 3.02
875 877 2.185350 CATCGCCGCCTCTGAAGT 59.815 61.111 0.00 0.00 0.00 3.01
876 878 2.169789 CATCGCCGCCTCTGAAGTG 61.170 63.158 0.00 0.00 0.00 3.16
877 879 2.351244 ATCGCCGCCTCTGAAGTGA 61.351 57.895 0.00 0.00 0.00 3.41
878 880 1.888436 ATCGCCGCCTCTGAAGTGAA 61.888 55.000 0.00 0.00 0.00 3.18
879 881 2.097038 CGCCGCCTCTGAAGTGAAG 61.097 63.158 0.00 0.00 0.00 3.02
880 882 1.293498 GCCGCCTCTGAAGTGAAGA 59.707 57.895 0.00 0.00 0.00 2.87
881 883 1.016653 GCCGCCTCTGAAGTGAAGAC 61.017 60.000 0.00 0.00 0.00 3.01
882 884 0.734253 CCGCCTCTGAAGTGAAGACG 60.734 60.000 0.00 0.00 0.00 4.18
883 885 0.241213 CGCCTCTGAAGTGAAGACGA 59.759 55.000 0.00 0.00 0.00 4.20
884 886 1.135257 CGCCTCTGAAGTGAAGACGAT 60.135 52.381 0.00 0.00 0.00 3.73
885 887 2.266554 GCCTCTGAAGTGAAGACGATG 58.733 52.381 0.00 0.00 0.00 3.84
886 888 2.094494 GCCTCTGAAGTGAAGACGATGA 60.094 50.000 0.00 0.00 0.00 2.92
887 889 3.615110 GCCTCTGAAGTGAAGACGATGAA 60.615 47.826 0.00 0.00 0.00 2.57
888 890 3.923461 CCTCTGAAGTGAAGACGATGAAC 59.077 47.826 0.00 0.00 0.00 3.18
896 898 3.864944 GACGATGAACGGCCGAAA 58.135 55.556 35.90 17.24 45.37 3.46
897 899 2.155665 GACGATGAACGGCCGAAAA 58.844 52.632 35.90 16.83 45.37 2.29
898 900 0.513820 GACGATGAACGGCCGAAAAA 59.486 50.000 35.90 14.79 45.37 1.94
899 901 1.129811 GACGATGAACGGCCGAAAAAT 59.870 47.619 35.90 19.12 45.37 1.82
900 902 1.810197 CGATGAACGGCCGAAAAATC 58.190 50.000 35.90 24.69 38.46 2.17
901 903 1.129624 CGATGAACGGCCGAAAAATCA 59.870 47.619 35.90 24.99 38.46 2.57
902 904 2.413502 CGATGAACGGCCGAAAAATCAA 60.414 45.455 35.90 8.32 38.46 2.57
903 905 3.570559 GATGAACGGCCGAAAAATCAAA 58.429 40.909 35.90 6.57 0.00 2.69
904 906 3.006659 TGAACGGCCGAAAAATCAAAG 57.993 42.857 35.90 0.00 0.00 2.77
905 907 1.719246 GAACGGCCGAAAAATCAAAGC 59.281 47.619 35.90 2.46 0.00 3.51
906 908 0.958822 ACGGCCGAAAAATCAAAGCT 59.041 45.000 35.90 0.00 0.00 3.74
907 909 2.156098 ACGGCCGAAAAATCAAAGCTA 58.844 42.857 35.90 0.00 0.00 3.32
908 910 2.095415 ACGGCCGAAAAATCAAAGCTAC 60.095 45.455 35.90 0.00 0.00 3.58
909 911 2.161609 CGGCCGAAAAATCAAAGCTACT 59.838 45.455 24.07 0.00 0.00 2.57
910 912 3.372822 CGGCCGAAAAATCAAAGCTACTA 59.627 43.478 24.07 0.00 0.00 1.82
911 913 4.494199 CGGCCGAAAAATCAAAGCTACTAG 60.494 45.833 24.07 0.00 0.00 2.57
912 914 4.634443 GGCCGAAAAATCAAAGCTACTAGA 59.366 41.667 0.00 0.00 0.00 2.43
913 915 5.220681 GGCCGAAAAATCAAAGCTACTAGAG 60.221 44.000 0.00 0.00 0.00 2.43
926 928 4.873817 GCTACTAGAGCCTAACCTAAAGC 58.126 47.826 0.00 0.00 46.41 3.51
927 929 4.585581 GCTACTAGAGCCTAACCTAAAGCT 59.414 45.833 0.00 0.00 46.41 3.74
928 930 5.769162 GCTACTAGAGCCTAACCTAAAGCTA 59.231 44.000 0.00 0.00 46.41 3.32
929 931 6.294120 GCTACTAGAGCCTAACCTAAAGCTAC 60.294 46.154 0.00 0.00 46.41 3.58
930 932 5.516984 ACTAGAGCCTAACCTAAAGCTACA 58.483 41.667 0.00 0.00 35.23 2.74
931 933 4.739587 AGAGCCTAACCTAAAGCTACAC 57.260 45.455 0.00 0.00 35.23 2.90
932 934 3.130693 AGAGCCTAACCTAAAGCTACACG 59.869 47.826 0.00 0.00 35.23 4.49
933 935 3.094572 AGCCTAACCTAAAGCTACACGA 58.905 45.455 0.00 0.00 32.73 4.35
934 936 3.705072 AGCCTAACCTAAAGCTACACGAT 59.295 43.478 0.00 0.00 32.73 3.73
935 937 3.802685 GCCTAACCTAAAGCTACACGATG 59.197 47.826 0.00 0.00 0.00 3.84
936 938 3.802685 CCTAACCTAAAGCTACACGATGC 59.197 47.826 0.00 0.00 0.00 3.91
937 939 3.328382 AACCTAAAGCTACACGATGCA 57.672 42.857 0.00 0.00 0.00 3.96
938 940 2.618053 ACCTAAAGCTACACGATGCAC 58.382 47.619 0.00 0.00 0.00 4.57
939 941 2.028476 ACCTAAAGCTACACGATGCACA 60.028 45.455 0.00 0.00 0.00 4.57
940 942 3.198068 CCTAAAGCTACACGATGCACAT 58.802 45.455 0.00 0.00 0.00 3.21
941 943 4.142026 ACCTAAAGCTACACGATGCACATA 60.142 41.667 0.00 0.00 0.00 2.29
942 944 4.209288 CCTAAAGCTACACGATGCACATAC 59.791 45.833 0.00 0.00 0.00 2.39
943 945 1.840181 AGCTACACGATGCACATACG 58.160 50.000 0.00 0.00 0.00 3.06
944 946 0.229753 GCTACACGATGCACATACGC 59.770 55.000 0.00 0.00 0.00 4.42
945 947 1.840181 CTACACGATGCACATACGCT 58.160 50.000 0.00 0.00 0.00 5.07
946 948 2.857104 GCTACACGATGCACATACGCTA 60.857 50.000 0.00 0.00 0.00 4.26
947 949 2.509052 ACACGATGCACATACGCTAT 57.491 45.000 0.00 0.00 0.00 2.97
948 950 2.821546 ACACGATGCACATACGCTATT 58.178 42.857 0.00 0.00 0.00 1.73
1031 1034 1.352114 TTAATCACGCGTTTCCTCCG 58.648 50.000 10.22 0.00 0.00 4.63
1037 1043 2.890961 GCGTTTCCTCCGGCTAGC 60.891 66.667 6.04 6.04 0.00 3.42
1096 1107 1.667830 ACACGCCGAACCATCACAG 60.668 57.895 0.00 0.00 0.00 3.66
1129 1153 1.727335 GCACTCTGTCTTCGCCTTTAC 59.273 52.381 0.00 0.00 0.00 2.01
1225 2429 4.227134 CAGGATCGTGCTCCCCGG 62.227 72.222 1.88 0.00 35.79 5.73
1371 2575 3.700831 GAGGACCTCGAGCTCGGGA 62.701 68.421 36.90 17.47 43.86 5.14
1588 2810 3.423154 GGACAACGAAGCGGCTGG 61.423 66.667 1.81 0.88 0.00 4.85
1620 2842 3.487574 CGAAGAGCTCAATCAACGGATAC 59.512 47.826 17.77 0.00 32.09 2.24
1689 2911 1.298488 GAGAGCTACGCCGCACTAC 60.298 63.158 0.00 0.00 30.92 2.73
1706 2928 4.260784 GCACTACCATGCTAATGCTACAAC 60.261 45.833 0.00 0.00 42.62 3.32
1711 2933 4.396166 ACCATGCTAATGCTACAACTCAAC 59.604 41.667 0.00 0.00 40.48 3.18
1721 2943 1.392589 ACAACTCAACTGGCCACTTG 58.607 50.000 16.59 16.59 0.00 3.16
1728 3425 1.750778 CAACTGGCCACTTGACAAACT 59.249 47.619 17.52 0.00 0.00 2.66
1762 3464 3.108376 AGGCCTTCTCTCGTATTTTCCT 58.892 45.455 0.00 0.00 0.00 3.36
1799 3501 3.428534 GTGTAAAATTTGCCGCCTCTTTG 59.571 43.478 0.00 0.00 0.00 2.77
1816 5017 6.587608 GCCTCTTTGTTCATGTATTTTTGAGG 59.412 38.462 0.00 0.00 39.15 3.86
1885 5091 5.882557 TGAATCAAGGAGAGCCTACAATTTC 59.117 40.000 0.00 0.00 46.28 2.17
1922 5128 2.102252 AGGAGATCGAGCAATTCTCACC 59.898 50.000 13.46 2.48 41.98 4.02
1975 5200 0.326264 CATCCGATCTTCCCCCATCC 59.674 60.000 0.00 0.00 0.00 3.51
1979 5204 1.131638 CGATCTTCCCCCATCCTTCA 58.868 55.000 0.00 0.00 0.00 3.02
2109 5334 3.733727 GTCTATGTTGCAACCGTTTTTGG 59.266 43.478 26.14 8.24 0.00 3.28
2128 5353 1.596752 TGCTGTCGCCGTCATTTGT 60.597 52.632 0.00 0.00 34.43 2.83
2135 5360 2.413796 GTCGCCGTCATTTGTAACATGA 59.586 45.455 0.00 0.00 0.00 3.07
2138 5363 3.607439 GCCGTCATTTGTAACATGATCG 58.393 45.455 0.00 0.00 33.22 3.69
2139 5364 3.308595 GCCGTCATTTGTAACATGATCGA 59.691 43.478 0.00 0.00 33.22 3.59
2144 5369 4.821260 TCATTTGTAACATGATCGATGGGG 59.179 41.667 0.54 0.00 36.23 4.96
2191 5416 1.299089 GGCGCGCCAAAATATCACC 60.299 57.895 43.55 12.83 35.81 4.02
2405 5634 5.753721 AACCAAGTTTCTCTAGAGCAGAT 57.246 39.130 15.35 0.00 31.13 2.90
2468 5698 2.733956 AGGGCAAACAACAGAACAAGA 58.266 42.857 0.00 0.00 0.00 3.02
2475 5705 6.455513 GGCAAACAACAGAACAAGAAATTGTC 60.456 38.462 0.00 0.00 33.35 3.18
2489 5719 0.537188 ATTGTCGCAGGACCTCGAAT 59.463 50.000 14.87 6.29 42.73 3.34
2529 5762 3.432588 GGACAGCAGCAGCAGCAG 61.433 66.667 12.92 6.60 45.49 4.24
2594 5827 1.286880 GTCGACGTCGGGGAAGAAA 59.713 57.895 35.05 12.79 40.29 2.52
2609 5842 2.554370 AGAAATCGTCGTTGGGGAAA 57.446 45.000 0.00 0.00 0.00 3.13
2618 5851 1.894466 TCGTTGGGGAAATAGTCGTCA 59.106 47.619 0.00 0.00 0.00 4.35
2623 5856 3.170717 TGGGGAAATAGTCGTCAGAGTT 58.829 45.455 0.00 0.00 0.00 3.01
2708 5941 4.383118 CCTTCTCCCGTACATGACTCAAAT 60.383 45.833 0.00 0.00 0.00 2.32
2725 5958 0.611714 AATAGGTGCGGTTTCGGAGT 59.388 50.000 0.00 0.00 37.41 3.85
2780 6013 0.908198 GGGATGAGGAAGACAGCAGT 59.092 55.000 0.00 0.00 0.00 4.40
2799 6032 4.766891 GCAGTAGCTCAGAGATTAGATCCT 59.233 45.833 0.00 0.00 37.91 3.24
2825 6061 2.558795 CGAGAGGAAGAAGTTCTGGTGA 59.441 50.000 6.06 0.00 32.72 4.02
2826 6062 3.366883 CGAGAGGAAGAAGTTCTGGTGAG 60.367 52.174 6.06 0.00 32.72 3.51
2827 6063 3.829601 GAGAGGAAGAAGTTCTGGTGAGA 59.170 47.826 6.06 0.00 32.72 3.27
2828 6064 4.227197 AGAGGAAGAAGTTCTGGTGAGAA 58.773 43.478 6.06 0.00 35.75 2.87
2829 6065 4.283212 AGAGGAAGAAGTTCTGGTGAGAAG 59.717 45.833 6.06 0.00 38.95 2.85
2830 6066 3.326297 AGGAAGAAGTTCTGGTGAGAAGG 59.674 47.826 6.06 0.00 38.95 3.46
2831 6067 3.325135 GGAAGAAGTTCTGGTGAGAAGGA 59.675 47.826 6.06 0.00 38.95 3.36
2832 6068 4.562552 GGAAGAAGTTCTGGTGAGAAGGAG 60.563 50.000 6.06 0.00 38.95 3.69
2833 6069 2.903135 AGAAGTTCTGGTGAGAAGGAGG 59.097 50.000 4.10 0.00 38.95 4.30
2834 6070 0.980423 AGTTCTGGTGAGAAGGAGGC 59.020 55.000 0.00 0.00 38.95 4.70
2835 6071 0.390472 GTTCTGGTGAGAAGGAGGCG 60.390 60.000 0.00 0.00 38.95 5.52
2836 6072 1.544825 TTCTGGTGAGAAGGAGGCGG 61.545 60.000 0.00 0.00 32.98 6.13
2837 6073 3.003173 TGGTGAGAAGGAGGCGGG 61.003 66.667 0.00 0.00 0.00 6.13
2838 6074 2.683933 GGTGAGAAGGAGGCGGGA 60.684 66.667 0.00 0.00 0.00 5.14
2839 6075 2.726351 GGTGAGAAGGAGGCGGGAG 61.726 68.421 0.00 0.00 0.00 4.30
2840 6076 2.364317 TGAGAAGGAGGCGGGAGG 60.364 66.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
441 442 1.228894 TGGTCGAGTCCTTCAGGCT 60.229 57.895 0.00 0.00 34.44 4.58
618 619 2.880629 ATAGAGTGCGCCAGGACCCT 62.881 60.000 4.18 0.00 39.75 4.34
682 683 7.604164 GGTCGAGTGGATTATGAATGTATGAAT 59.396 37.037 0.00 0.00 0.00 2.57
691 692 1.202486 GGCGGTCGAGTGGATTATGAA 60.202 52.381 0.00 0.00 0.00 2.57
860 862 2.492449 CTTCACTTCAGAGGCGGCGA 62.492 60.000 12.98 0.00 0.00 5.54
861 863 2.048222 TTCACTTCAGAGGCGGCG 60.048 61.111 0.51 0.51 0.00 6.46
862 864 1.016653 GTCTTCACTTCAGAGGCGGC 61.017 60.000 0.00 0.00 0.00 6.53
863 865 0.734253 CGTCTTCACTTCAGAGGCGG 60.734 60.000 0.00 0.00 0.00 6.13
864 866 0.241213 TCGTCTTCACTTCAGAGGCG 59.759 55.000 0.00 0.00 0.00 5.52
865 867 2.094494 TCATCGTCTTCACTTCAGAGGC 60.094 50.000 0.00 0.00 0.00 4.70
866 868 3.857549 TCATCGTCTTCACTTCAGAGG 57.142 47.619 0.00 0.00 0.00 3.69
867 869 3.605916 CGTTCATCGTCTTCACTTCAGAG 59.394 47.826 0.00 0.00 34.52 3.35
868 870 3.565516 CGTTCATCGTCTTCACTTCAGA 58.434 45.455 0.00 0.00 34.52 3.27
869 871 2.663602 CCGTTCATCGTCTTCACTTCAG 59.336 50.000 0.00 0.00 37.94 3.02
870 872 2.672714 CCGTTCATCGTCTTCACTTCA 58.327 47.619 0.00 0.00 37.94 3.02
871 873 1.390463 GCCGTTCATCGTCTTCACTTC 59.610 52.381 0.00 0.00 37.94 3.01
872 874 1.429463 GCCGTTCATCGTCTTCACTT 58.571 50.000 0.00 0.00 37.94 3.16
873 875 0.389948 GGCCGTTCATCGTCTTCACT 60.390 55.000 0.00 0.00 37.94 3.41
874 876 1.683790 CGGCCGTTCATCGTCTTCAC 61.684 60.000 19.50 0.00 37.94 3.18
875 877 1.445410 CGGCCGTTCATCGTCTTCA 60.445 57.895 19.50 0.00 37.94 3.02
876 878 0.734942 TTCGGCCGTTCATCGTCTTC 60.735 55.000 27.15 0.00 37.94 2.87
877 879 0.320073 TTTCGGCCGTTCATCGTCTT 60.320 50.000 27.15 0.00 37.94 3.01
878 880 0.320073 TTTTCGGCCGTTCATCGTCT 60.320 50.000 27.15 0.00 37.94 4.18
879 881 0.513820 TTTTTCGGCCGTTCATCGTC 59.486 50.000 27.15 0.00 37.94 4.20
880 882 1.129811 GATTTTTCGGCCGTTCATCGT 59.870 47.619 27.15 6.48 37.94 3.73
881 883 1.129624 TGATTTTTCGGCCGTTCATCG 59.870 47.619 27.15 0.00 39.52 3.84
882 884 2.911819 TGATTTTTCGGCCGTTCATC 57.088 45.000 27.15 20.82 0.00 2.92
883 885 3.574614 CTTTGATTTTTCGGCCGTTCAT 58.425 40.909 27.15 13.13 0.00 2.57
884 886 2.860582 GCTTTGATTTTTCGGCCGTTCA 60.861 45.455 27.15 17.49 0.00 3.18
885 887 1.719246 GCTTTGATTTTTCGGCCGTTC 59.281 47.619 27.15 15.18 0.00 3.95
886 888 1.339929 AGCTTTGATTTTTCGGCCGTT 59.660 42.857 27.15 6.00 0.00 4.44
887 889 0.958822 AGCTTTGATTTTTCGGCCGT 59.041 45.000 27.15 4.54 0.00 5.68
888 890 2.161609 AGTAGCTTTGATTTTTCGGCCG 59.838 45.455 22.12 22.12 0.00 6.13
889 891 3.850122 AGTAGCTTTGATTTTTCGGCC 57.150 42.857 0.00 0.00 0.00 6.13
890 892 5.796350 TCTAGTAGCTTTGATTTTTCGGC 57.204 39.130 0.00 0.00 0.00 5.54
905 907 6.771749 TGTAGCTTTAGGTTAGGCTCTAGTAG 59.228 42.308 0.00 0.00 36.40 2.57
906 908 6.545298 GTGTAGCTTTAGGTTAGGCTCTAGTA 59.455 42.308 0.00 0.00 36.40 1.82
907 909 5.360429 GTGTAGCTTTAGGTTAGGCTCTAGT 59.640 44.000 0.00 0.00 36.40 2.57
908 910 5.505985 CGTGTAGCTTTAGGTTAGGCTCTAG 60.506 48.000 0.00 0.00 36.40 2.43
909 911 4.337555 CGTGTAGCTTTAGGTTAGGCTCTA 59.662 45.833 0.00 0.00 36.40 2.43
910 912 3.130693 CGTGTAGCTTTAGGTTAGGCTCT 59.869 47.826 0.00 0.00 36.40 4.09
911 913 3.129988 TCGTGTAGCTTTAGGTTAGGCTC 59.870 47.826 0.00 0.00 36.40 4.70
912 914 3.094572 TCGTGTAGCTTTAGGTTAGGCT 58.905 45.455 0.00 0.00 38.62 4.58
913 915 3.515330 TCGTGTAGCTTTAGGTTAGGC 57.485 47.619 0.00 0.00 0.00 3.93
914 916 3.802685 GCATCGTGTAGCTTTAGGTTAGG 59.197 47.826 0.00 0.00 0.00 2.69
915 917 4.267928 GTGCATCGTGTAGCTTTAGGTTAG 59.732 45.833 0.00 0.00 0.00 2.34
916 918 4.178540 GTGCATCGTGTAGCTTTAGGTTA 58.821 43.478 0.00 0.00 0.00 2.85
917 919 3.000727 GTGCATCGTGTAGCTTTAGGTT 58.999 45.455 0.00 0.00 0.00 3.50
918 920 2.028476 TGTGCATCGTGTAGCTTTAGGT 60.028 45.455 0.00 0.00 0.00 3.08
919 921 2.616960 TGTGCATCGTGTAGCTTTAGG 58.383 47.619 0.00 0.00 0.00 2.69
920 922 4.085568 CGTATGTGCATCGTGTAGCTTTAG 60.086 45.833 0.00 0.00 0.00 1.85
921 923 3.794564 CGTATGTGCATCGTGTAGCTTTA 59.205 43.478 0.00 0.00 0.00 1.85
922 924 2.603110 CGTATGTGCATCGTGTAGCTTT 59.397 45.455 0.00 0.00 0.00 3.51
923 925 2.193447 CGTATGTGCATCGTGTAGCTT 58.807 47.619 0.00 0.00 0.00 3.74
924 926 1.840181 CGTATGTGCATCGTGTAGCT 58.160 50.000 0.00 0.00 0.00 3.32
925 927 0.229753 GCGTATGTGCATCGTGTAGC 59.770 55.000 0.00 0.00 34.15 3.58
926 928 1.840181 AGCGTATGTGCATCGTGTAG 58.160 50.000 0.00 0.00 37.31 2.74
927 929 3.636282 ATAGCGTATGTGCATCGTGTA 57.364 42.857 0.00 0.00 37.31 2.90
928 930 2.509052 ATAGCGTATGTGCATCGTGT 57.491 45.000 0.00 0.00 37.31 4.49
929 931 3.859745 AAATAGCGTATGTGCATCGTG 57.140 42.857 0.00 0.00 37.31 4.35
930 932 4.875544 AAAAATAGCGTATGTGCATCGT 57.124 36.364 0.00 0.00 37.31 3.73
1031 1034 0.106894 GCGGGGGATATATGCTAGCC 59.893 60.000 13.29 0.00 0.00 3.93
1034 1037 0.973496 TGCGCGGGGGATATATGCTA 60.973 55.000 8.83 0.00 0.00 3.49
1037 1043 1.024579 GGTTGCGCGGGGGATATATG 61.025 60.000 8.83 0.00 0.00 1.78
1096 1107 2.008329 CAGAGTGCAAGGAATGAGAGC 58.992 52.381 0.00 0.00 0.00 4.09
1129 1153 3.146066 CCGAAGAGAGTCAGAGATAGGG 58.854 54.545 0.00 0.00 0.00 3.53
1174 1204 4.193893 CGGGGATCATGGCCAGCA 62.194 66.667 13.05 0.00 0.00 4.41
1352 2556 2.438614 CCGAGCTCGAGGTCCTCA 60.439 66.667 36.59 5.40 43.02 3.86
1371 2575 2.416432 GGAAGGCGGCGTAGACTCT 61.416 63.158 9.37 0.00 0.00 3.24
1588 2810 2.185608 GCTCTTCGGTCTCTGCCC 59.814 66.667 0.00 0.00 0.00 5.36
1597 2819 1.002366 CCGTTGATTGAGCTCTTCGG 58.998 55.000 16.19 14.50 0.00 4.30
1622 2844 4.717629 CTCGACAAGCGACCGCCA 62.718 66.667 11.03 0.00 45.59 5.69
1689 2911 4.637534 AGTTGAGTTGTAGCATTAGCATGG 59.362 41.667 0.00 0.00 45.49 3.66
1711 2933 1.605710 CTCAGTTTGTCAAGTGGCCAG 59.394 52.381 5.11 0.00 34.45 4.85
1721 2943 3.190118 CCTTTGCCATCTCTCAGTTTGTC 59.810 47.826 0.00 0.00 0.00 3.18
1762 3464 9.784824 CAAATTTTACACGCGATCAAAAATAAA 57.215 25.926 15.93 2.72 31.41 1.40
1799 3501 7.761249 CCTTTCATCCCTCAAAAATACATGAAC 59.239 37.037 0.00 0.00 30.46 3.18
1816 5017 1.826720 TGCTCAATTGCCCTTTCATCC 59.173 47.619 0.00 0.00 0.00 3.51
1874 5078 7.073342 ACTCGTTGATTAAGAAATTGTAGGC 57.927 36.000 0.00 0.00 0.00 3.93
1885 5091 5.457148 CGATCTCCTTGACTCGTTGATTAAG 59.543 44.000 0.00 0.00 0.00 1.85
2128 5353 1.540146 CGTGCCCCATCGATCATGTTA 60.540 52.381 0.00 0.00 0.00 2.41
2135 5360 4.891727 GACGCGTGCCCCATCGAT 62.892 66.667 20.70 0.00 0.00 3.59
2138 5363 2.108157 TATGACGCGTGCCCCATC 59.892 61.111 20.70 0.00 0.00 3.51
2139 5364 2.203015 GTATGACGCGTGCCCCAT 60.203 61.111 20.70 16.75 0.00 4.00
2191 5416 3.665675 AAGGCTAGCGCTCAACCGG 62.666 63.158 16.34 0.00 36.09 5.28
2405 5634 8.934697 ACTTCATATATGAAACTTGCCCTACTA 58.065 33.333 24.61 2.47 45.26 1.82
2468 5698 0.320374 TCGAGGTCCTGCGACAATTT 59.680 50.000 0.00 0.00 41.13 1.82
2475 5705 2.464865 CTTTCTATTCGAGGTCCTGCG 58.535 52.381 0.00 0.00 0.00 5.18
2489 5719 5.105473 CCCGTATGTGTTCTTCTCCTTTCTA 60.105 44.000 0.00 0.00 0.00 2.10
2529 5762 2.032071 CACCGACCCCAAGTCCAC 59.968 66.667 0.00 0.00 43.08 4.02
2594 5827 2.480759 CGACTATTTCCCCAACGACGAT 60.481 50.000 0.00 0.00 0.00 3.73
2609 5842 1.390565 CCCCGAACTCTGACGACTAT 58.609 55.000 0.00 0.00 0.00 2.12
2676 5909 2.249309 ACGGGAGAAGGGTGATAAGT 57.751 50.000 0.00 0.00 0.00 2.24
2708 5941 1.588082 GACTCCGAAACCGCACCTA 59.412 57.895 0.00 0.00 0.00 3.08
2725 5958 1.748122 GCGAGTCGGGACAGTAGGA 60.748 63.158 15.52 0.00 0.00 2.94
2780 6013 5.076182 CCACAGGATCTAATCTCTGAGCTA 58.924 45.833 0.00 0.00 34.09 3.32
2796 6029 0.541998 TTCTTCCTCTCGCCACAGGA 60.542 55.000 0.00 0.00 37.00 3.86
2799 6032 1.000955 GAACTTCTTCCTCTCGCCACA 59.999 52.381 0.00 0.00 0.00 4.17
2825 6061 3.010226 TAGCCTCCCGCCTCCTTCT 62.010 63.158 0.00 0.00 38.78 2.85
2826 6062 2.444140 TAGCCTCCCGCCTCCTTC 60.444 66.667 0.00 0.00 38.78 3.46


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

AutoCloner maintained by Alex Coulton.