Multiple sequence alignment - TraesCS1A01G226100

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 TraesCS1A01G226100 chr1A 100.000 4789 0 0 1 4789 396420637 396425425 0.000000e+00 8844.0
1 TraesCS1A01G226100 chr1D 95.473 3026 109 15 907 3914 315972031 315975046 0.000000e+00 4804.0
2 TraesCS1A01G226100 chr1D 87.322 773 54 16 3913 4668 315975127 315975872 0.000000e+00 845.0
3 TraesCS1A01G226100 chr1B 94.014 2606 109 17 2213 4789 428064192 428066779 0.000000e+00 3904.0
4 TraesCS1A01G226100 chr1B 92.273 1333 58 23 907 2210 428062637 428063953 0.000000e+00 1849.0
5 TraesCS1A01G226100 chr1B 84.809 836 100 17 37 848 32772884 32773716 0.000000e+00 815.0
6 TraesCS1A01G226100 chr1B 87.396 603 54 4 268 848 73132308 73132910 0.000000e+00 673.0
7 TraesCS1A01G226100 chr3A 90.632 886 46 10 4 854 716626496 716625613 0.000000e+00 1142.0
8 TraesCS1A01G226100 chr3A 93.679 617 39 0 4 620 523155557 523154941 0.000000e+00 924.0
9 TraesCS1A01G226100 chr2A 90.515 854 56 10 1 834 72749863 72750711 0.000000e+00 1105.0
10 TraesCS1A01G226100 chr2A 100.000 28 0 0 856 883 36470021 36469994 9.000000e-03 52.8
11 TraesCS1A01G226100 chr4D 89.631 868 58 13 1 848 64724001 64724856 0.000000e+00 1075.0
12 TraesCS1A01G226100 chr4A 85.988 835 90 14 37 847 466569248 466570079 0.000000e+00 869.0
13 TraesCS1A01G226100 chr4A 85.132 834 99 15 37 848 625260470 625261300 0.000000e+00 830.0
14 TraesCS1A01G226100 chr7B 84.809 836 97 19 37 848 679615500 679616329 0.000000e+00 813.0
15 TraesCS1A01G226100 chr7B 88.391 603 48 4 268 848 671022417 671021815 0.000000e+00 706.0
16 TraesCS1A01G226100 chr7B 88.245 604 48 4 268 848 671100333 671099730 0.000000e+00 701.0
17 TraesCS1A01G226100 chr7B 97.959 49 1 0 1986 2034 543192835 543192883 8.540000e-13 86.1
18 TraesCS1A01G226100 chr2B 85.405 740 82 7 132 848 723385471 723386207 0.000000e+00 745.0
19 TraesCS1A01G226100 chrUn 88.391 603 48 4 268 848 147258966 147258364 0.000000e+00 706.0
20 TraesCS1A01G226100 chrUn 88.079 604 49 4 268 848 147112008 147111405 0.000000e+00 695.0
21 TraesCS1A01G226100 chrUn 88.147 599 49 3 272 848 401084696 401085294 0.000000e+00 693.0
22 TraesCS1A01G226100 chrUn 87.748 604 51 4 268 848 147188616 147188013 0.000000e+00 684.0
23 TraesCS1A01G226100 chrUn 87.748 604 51 4 268 848 410619607 410619004 0.000000e+00 684.0
24 TraesCS1A01G226100 chr5D 96.154 52 1 1 856 906 469466570 469466621 3.070000e-12 84.2
25 TraesCS1A01G226100 chr6A 100.000 29 0 0 856 884 412367431 412367459 2.000000e-03 54.7
26 TraesCS1A01G226100 chr6B 100.000 28 0 0 856 883 693080487 693080514 9.000000e-03 52.8
27 TraesCS1A01G226100 chr2D 100.000 28 0 0 856 883 178280757 178280784 9.000000e-03 52.8


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 TraesCS1A01G226100 chr1A 396420637 396425425 4788 False 8844.0 8844 100.0000 1 4789 1 chr1A.!!$F1 4788
1 TraesCS1A01G226100 chr1D 315972031 315975872 3841 False 2824.5 4804 91.3975 907 4668 2 chr1D.!!$F1 3761
2 TraesCS1A01G226100 chr1B 428062637 428066779 4142 False 2876.5 3904 93.1435 907 4789 2 chr1B.!!$F3 3882
3 TraesCS1A01G226100 chr1B 32772884 32773716 832 False 815.0 815 84.8090 37 848 1 chr1B.!!$F1 811
4 TraesCS1A01G226100 chr1B 73132308 73132910 602 False 673.0 673 87.3960 268 848 1 chr1B.!!$F2 580
5 TraesCS1A01G226100 chr3A 716625613 716626496 883 True 1142.0 1142 90.6320 4 854 1 chr3A.!!$R2 850
6 TraesCS1A01G226100 chr3A 523154941 523155557 616 True 924.0 924 93.6790 4 620 1 chr3A.!!$R1 616
7 TraesCS1A01G226100 chr2A 72749863 72750711 848 False 1105.0 1105 90.5150 1 834 1 chr2A.!!$F1 833
8 TraesCS1A01G226100 chr4D 64724001 64724856 855 False 1075.0 1075 89.6310 1 848 1 chr4D.!!$F1 847
9 TraesCS1A01G226100 chr4A 466569248 466570079 831 False 869.0 869 85.9880 37 847 1 chr4A.!!$F1 810
10 TraesCS1A01G226100 chr4A 625260470 625261300 830 False 830.0 830 85.1320 37 848 1 chr4A.!!$F2 811
11 TraesCS1A01G226100 chr7B 679615500 679616329 829 False 813.0 813 84.8090 37 848 1 chr7B.!!$F2 811
12 TraesCS1A01G226100 chr7B 671021815 671022417 602 True 706.0 706 88.3910 268 848 1 chr7B.!!$R1 580
13 TraesCS1A01G226100 chr7B 671099730 671100333 603 True 701.0 701 88.2450 268 848 1 chr7B.!!$R2 580
14 TraesCS1A01G226100 chr2B 723385471 723386207 736 False 745.0 745 85.4050 132 848 1 chr2B.!!$F1 716
15 TraesCS1A01G226100 chrUn 147258364 147258966 602 True 706.0 706 88.3910 268 848 1 chrUn.!!$R3 580
16 TraesCS1A01G226100 chrUn 147111405 147112008 603 True 695.0 695 88.0790 268 848 1 chrUn.!!$R1 580
17 TraesCS1A01G226100 chrUn 401084696 401085294 598 False 693.0 693 88.1470 272 848 1 chrUn.!!$F1 576
18 TraesCS1A01G226100 chrUn 147188013 147188616 603 True 684.0 684 87.7480 268 848 1 chrUn.!!$R2 580
19 TraesCS1A01G226100 chrUn 410619004 410619607 603 True 684.0 684 87.7480 268 848 1 chrUn.!!$R4 580

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
29 30 0.176680 ATGTTTTGTTGCAACCGCCA 59.823 45.0 26.14 16.90 37.32 5.69 F
1541 1622 0.175760 GAGAGGTAAGGTCGCATGCA 59.824 55.0 19.57 1.73 0.00 3.96 F
1988 2087 0.168128 GCACCGATACAAACACTGGC 59.832 55.0 0.00 0.00 0.00 4.85 F
2401 2738 0.956633 ATTGTGTGAGTGCTTGGCTG 59.043 50.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1814 1.383799 CATTTGGCCTGGACCCAGA 59.616 57.895 17.19 0.0 46.30 3.86 R
3506 3843 1.067295 TCCACACCCTCAGAGCATTT 58.933 50.000 0.00 0.0 0.00 2.32 R
3696 4033 0.604780 CAGTGGTCTCTGTTGGCCAG 60.605 60.000 5.11 0.0 42.97 4.85 R
3934 4360 0.741221 GAAGCAACTCGGGCGAGAAT 60.741 55.000 0.00 0.0 44.53 2.40 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
29 30 0.176680 ATGTTTTGTTGCAACCGCCA 59.823 45.000 26.14 16.90 37.32 5.69
128 129 1.003112 GGTGGCGACCATGGTGTTA 60.003 57.895 25.52 2.56 42.59 2.41
253 256 1.600013 CCACGACGAAATTTGTGGTGA 59.400 47.619 24.09 0.00 45.40 4.02
262 265 2.702751 ATTTGTGGTGACGACGGCGA 62.703 55.000 22.49 0.00 41.64 5.54
369 374 3.419759 GCAAATCGTGGTCGCCGT 61.420 61.111 0.00 0.00 36.96 5.68
375 380 4.771356 CGTGGTCGCCGTCGTGAT 62.771 66.667 0.00 0.00 36.96 3.06
434 439 5.457140 GGTCGTAGCAAAAATGAACAATGA 58.543 37.500 0.00 0.00 0.00 2.57
562 567 2.842394 CTTCACCCGTCGCTGCTGAT 62.842 60.000 0.00 0.00 0.00 2.90
800 864 0.971959 GCAAGATCCAATGGCCCACA 60.972 55.000 0.00 0.00 0.00 4.17
850 914 2.125269 CCGAACGGTTGGGCCTAG 60.125 66.667 9.04 0.00 34.25 3.02
851 915 2.660802 CGAACGGTTGGGCCTAGT 59.339 61.111 4.53 0.00 34.25 2.57
852 916 1.740296 CGAACGGTTGGGCCTAGTG 60.740 63.158 4.53 0.00 34.25 2.74
853 917 2.033602 AACGGTTGGGCCTAGTGC 59.966 61.111 4.53 0.00 40.16 4.40
863 927 3.145228 GCCTAGTGCCTGACTCAAC 57.855 57.895 0.00 0.00 35.96 3.18
864 928 0.610687 GCCTAGTGCCTGACTCAACT 59.389 55.000 0.00 0.00 35.96 3.16
865 929 1.002544 GCCTAGTGCCTGACTCAACTT 59.997 52.381 0.00 0.00 35.96 2.66
866 930 2.551071 GCCTAGTGCCTGACTCAACTTT 60.551 50.000 0.00 0.00 35.96 2.66
867 931 3.070018 CCTAGTGCCTGACTCAACTTTG 58.930 50.000 0.00 0.00 35.96 2.77
868 932 2.717639 AGTGCCTGACTCAACTTTGT 57.282 45.000 0.00 0.00 0.00 2.83
869 933 3.838244 AGTGCCTGACTCAACTTTGTA 57.162 42.857 0.00 0.00 0.00 2.41
870 934 3.467803 AGTGCCTGACTCAACTTTGTAC 58.532 45.455 0.00 0.00 0.00 2.90
871 935 3.134804 AGTGCCTGACTCAACTTTGTACT 59.865 43.478 0.00 0.00 0.00 2.73
872 936 4.344102 AGTGCCTGACTCAACTTTGTACTA 59.656 41.667 0.00 0.00 0.00 1.82
873 937 5.054477 GTGCCTGACTCAACTTTGTACTAA 58.946 41.667 0.00 0.00 0.00 2.24
874 938 5.050295 GTGCCTGACTCAACTTTGTACTAAC 60.050 44.000 0.00 0.00 0.00 2.34
875 939 5.163343 TGCCTGACTCAACTTTGTACTAACT 60.163 40.000 0.00 0.00 0.00 2.24
876 940 5.758784 GCCTGACTCAACTTTGTACTAACTT 59.241 40.000 0.00 0.00 0.00 2.66
877 941 6.260271 GCCTGACTCAACTTTGTACTAACTTT 59.740 38.462 0.00 0.00 0.00 2.66
878 942 7.630924 CCTGACTCAACTTTGTACTAACTTTG 58.369 38.462 0.00 0.00 0.00 2.77
879 943 7.280205 CCTGACTCAACTTTGTACTAACTTTGT 59.720 37.037 0.00 0.00 0.00 2.83
880 944 9.309516 CTGACTCAACTTTGTACTAACTTTGTA 57.690 33.333 0.00 0.00 0.00 2.41
881 945 9.090692 TGACTCAACTTTGTACTAACTTTGTAC 57.909 33.333 6.58 6.58 40.27 2.90
882 946 8.429493 ACTCAACTTTGTACTAACTTTGTACC 57.571 34.615 9.98 0.00 39.42 3.34
883 947 8.262933 ACTCAACTTTGTACTAACTTTGTACCT 58.737 33.333 9.98 0.00 39.42 3.08
884 948 9.754382 CTCAACTTTGTACTAACTTTGTACCTA 57.246 33.333 9.98 0.00 39.42 3.08
894 958 8.091385 ACTAACTTTGTACCTATTTTGGAACG 57.909 34.615 0.00 0.00 0.00 3.95
895 959 5.952526 ACTTTGTACCTATTTTGGAACGG 57.047 39.130 0.00 0.00 0.00 4.44
896 960 4.763279 ACTTTGTACCTATTTTGGAACGGG 59.237 41.667 0.00 0.00 0.00 5.28
897 961 3.353370 TGTACCTATTTTGGAACGGGG 57.647 47.619 0.00 0.00 0.00 5.73
898 962 2.026075 TGTACCTATTTTGGAACGGGGG 60.026 50.000 0.00 0.00 0.00 5.40
899 963 1.374572 ACCTATTTTGGAACGGGGGA 58.625 50.000 0.00 0.00 0.00 4.81
900 964 1.283905 ACCTATTTTGGAACGGGGGAG 59.716 52.381 0.00 0.00 0.00 4.30
901 965 1.283905 CCTATTTTGGAACGGGGGAGT 59.716 52.381 0.00 0.00 0.00 3.85
902 966 2.506644 CCTATTTTGGAACGGGGGAGTA 59.493 50.000 0.00 0.00 0.00 2.59
903 967 2.801077 ATTTTGGAACGGGGGAGTAG 57.199 50.000 0.00 0.00 0.00 2.57
904 968 1.437397 TTTTGGAACGGGGGAGTAGT 58.563 50.000 0.00 0.00 0.00 2.73
905 969 2.323999 TTTGGAACGGGGGAGTAGTA 57.676 50.000 0.00 0.00 0.00 1.82
918 982 3.995048 GGGAGTAGTACACAAAACTCAGC 59.005 47.826 2.52 0.00 40.09 4.26
924 988 7.996385 AGTAGTACACAAAACTCAGCAAAAAT 58.004 30.769 2.52 0.00 0.00 1.82
950 1014 4.753662 TCGTCCTACTGGGCCGCT 62.754 66.667 0.00 0.00 33.53 5.52
991 1072 4.567385 CGCTCGCTGGCCTCTCTC 62.567 72.222 3.32 0.00 0.00 3.20
992 1073 3.146913 GCTCGCTGGCCTCTCTCT 61.147 66.667 3.32 0.00 0.00 3.10
993 1074 3.119193 CTCGCTGGCCTCTCTCTC 58.881 66.667 3.32 0.00 0.00 3.20
994 1075 1.453745 CTCGCTGGCCTCTCTCTCT 60.454 63.158 3.32 0.00 0.00 3.10
995 1076 1.447317 CTCGCTGGCCTCTCTCTCTC 61.447 65.000 3.32 0.00 0.00 3.20
996 1077 1.453745 CGCTGGCCTCTCTCTCTCT 60.454 63.158 3.32 0.00 0.00 3.10
997 1078 1.447317 CGCTGGCCTCTCTCTCTCTC 61.447 65.000 3.32 0.00 0.00 3.20
1055 1136 3.400054 CCTCCTCCCCCACCGTTC 61.400 72.222 0.00 0.00 0.00 3.95
1090 1171 2.202756 GCCACGTTAGCCTCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
1091 1172 3.003113 GCCACGTTAGCCTCTCCGT 62.003 63.158 0.00 0.00 0.00 4.69
1130 1211 0.294887 CAAAGCGACATCGAGTACGC 59.705 55.000 19.70 19.70 42.80 4.42
1259 1340 3.837731 CTCCTTCTTTCCTCCTCTTCTGT 59.162 47.826 0.00 0.00 0.00 3.41
1425 1506 1.893808 GCACCTGGCCATATGGTCG 60.894 63.158 21.17 15.09 44.44 4.79
1536 1617 1.112113 TGATGGAGAGGTAAGGTCGC 58.888 55.000 0.00 0.00 0.00 5.19
1541 1622 0.175760 GAGAGGTAAGGTCGCATGCA 59.824 55.000 19.57 1.73 0.00 3.96
1646 1727 6.092955 TCTTGTAGAACTATGTTCCGTTGT 57.907 37.500 6.80 0.00 0.00 3.32
1714 1796 2.175202 TGCGGTTTAAGGATTTGCCAT 58.825 42.857 0.00 0.00 40.02 4.40
1728 1810 0.460109 TGCCATTCGGTGTCTGATCG 60.460 55.000 0.00 0.00 33.28 3.69
1732 1814 0.809385 ATTCGGTGTCTGATCGACGT 59.191 50.000 11.33 0.00 45.87 4.34
1735 1817 0.521450 CGGTGTCTGATCGACGTCTG 60.521 60.000 14.70 7.51 45.87 3.51
1755 1837 0.817654 GGTCCAGGCCAAATGTAAGC 59.182 55.000 5.01 0.00 0.00 3.09
1756 1838 1.544724 GTCCAGGCCAAATGTAAGCA 58.455 50.000 5.01 0.00 0.00 3.91
1890 1983 9.092270 AAGGGACTAGGTATATAACCAGCAACG 62.092 44.444 0.00 0.00 46.66 4.10
1988 2087 0.168128 GCACCGATACAAACACTGGC 59.832 55.000 0.00 0.00 0.00 4.85
2157 2258 6.017400 ACATTCTGCTGATAACTTTTGTGG 57.983 37.500 0.00 0.00 0.00 4.17
2278 2614 2.159327 AAAAGTGATTGCCTGCTTGC 57.841 45.000 0.00 0.00 0.00 4.01
2399 2736 1.879380 TGTATTGTGTGAGTGCTTGGC 59.121 47.619 0.00 0.00 0.00 4.52
2401 2738 0.956633 ATTGTGTGAGTGCTTGGCTG 59.043 50.000 0.00 0.00 0.00 4.85
2514 2851 8.310406 TGTTGCTGTCATAAATCCTATATTCG 57.690 34.615 0.00 0.00 0.00 3.34
2528 2865 5.916883 TCCTATATTCGCGCTTTTAGTGTAC 59.083 40.000 5.56 0.00 0.00 2.90
2582 2919 7.971168 CCCTACATCTGAATCTATTTACTAGCG 59.029 40.741 0.00 0.00 0.00 4.26
2610 2947 2.632996 TGGGGCTCCTCTTACATTATCG 59.367 50.000 3.07 0.00 0.00 2.92
2676 3013 1.408702 GACCAAAGTGAAAAGCAGCCA 59.591 47.619 0.00 0.00 0.00 4.75
2736 3073 4.701651 TGTCCCATGCTTCTTTCATTGTAG 59.298 41.667 0.00 0.00 0.00 2.74
2894 3231 6.969473 GCAGAAGTAAAAACATAGAAGATGCC 59.031 38.462 0.00 0.00 0.00 4.40
3005 3342 2.416836 CGATGTGGCCGAAGTAAAGAGA 60.417 50.000 0.00 0.00 0.00 3.10
3021 3358 2.704572 AGAGAGTTTGGCGAGAAATGG 58.295 47.619 0.00 0.00 0.00 3.16
3381 3718 4.562394 CCATTTTGACGTACCATGCATTTC 59.438 41.667 0.00 0.00 0.00 2.17
3506 3843 7.405292 AGTTTATCCAATTGAATGAGTCTGGA 58.595 34.615 7.12 0.00 33.78 3.86
3539 3876 1.197721 GTGTGGACTGAAATGCGAAGG 59.802 52.381 0.00 0.00 0.00 3.46
3577 3914 1.667236 TATGCACACTACATGGCAGC 58.333 50.000 0.00 0.00 37.74 5.25
3737 4074 2.680339 GAGAGGAGCAGGCAAATACAAC 59.320 50.000 0.00 0.00 0.00 3.32
3776 4113 3.985279 TCAAACATTCTACAAGACGGACG 59.015 43.478 0.00 0.00 0.00 4.79
3782 4119 4.352600 TTCTACAAGACGGACGAGAATC 57.647 45.455 0.00 0.00 0.00 2.52
3904 4248 5.471456 CAGTTAACAAGTTGCTCCTGAATCT 59.529 40.000 8.61 0.00 0.00 2.40
3907 4251 4.090761 ACAAGTTGCTCCTGAATCTTCA 57.909 40.909 1.81 0.00 35.57 3.02
3934 4360 6.797454 ACTAACAAACATGAAACCGCTAAAA 58.203 32.000 0.00 0.00 0.00 1.52
3994 4420 0.553612 AGGGATTTTCCTCAGGGGCT 60.554 55.000 0.00 0.00 36.57 5.19
4023 4449 4.998033 TCGAAAAATGTACATGGTGTAGCA 59.002 37.500 9.63 0.00 32.84 3.49
4093 4531 9.213819 CTGTGTTTATAATGTGTGATCATTTCG 57.786 33.333 0.00 0.00 38.68 3.46
4306 4748 6.853872 GTCACATGAAAAGCATACGTTTTACA 59.146 34.615 0.00 0.00 34.82 2.41
4325 4767 3.604582 ACAAGATGAGCAAGTAGGCTTC 58.395 45.455 0.00 0.00 45.99 3.86
4375 4817 1.064803 CGGCAAAAGTTACACAGCACA 59.935 47.619 0.00 0.00 0.00 4.57
4406 4848 4.217754 TGGCGTAACAAGTGACAAAATC 57.782 40.909 0.00 0.00 0.00 2.17
4595 5043 5.064558 TGAAACTTTAGTGCCGGTGAAATA 58.935 37.500 1.90 0.00 0.00 1.40
4626 5077 9.847224 ACTAATATAATAGAAACTGTTGGTGGG 57.153 33.333 1.72 0.00 0.00 4.61
4651 5102 3.188048 CACACCTTGAGAAAGTGCATCTC 59.812 47.826 8.58 8.58 42.94 2.75
4659 5110 3.357203 AGAAAGTGCATCTCGAGGAGTA 58.643 45.455 13.56 1.99 0.00 2.59
4660 5111 3.129638 AGAAAGTGCATCTCGAGGAGTAC 59.870 47.826 13.56 14.34 0.00 2.73
4668 5119 6.480320 GTGCATCTCGAGGAGTACAAATATTT 59.520 38.462 13.56 0.00 0.00 1.40
4705 5156 1.448985 TCCTTTTCAAATCTCCGCCG 58.551 50.000 0.00 0.00 0.00 6.46
4712 5163 2.222886 TCAAATCTCCGCCGAAAACAA 58.777 42.857 0.00 0.00 0.00 2.83
4718 5169 1.849829 CTCCGCCGAAAACAAAAACAC 59.150 47.619 0.00 0.00 0.00 3.32
4730 5181 5.844301 AACAAAAACACTGCAGAAAGTTG 57.156 34.783 23.35 18.12 0.00 3.16
4732 5183 3.525268 AAAACACTGCAGAAAGTTGGG 57.475 42.857 23.35 0.00 0.00 4.12
4735 5186 1.108727 CACTGCAGAAAGTTGGGCCA 61.109 55.000 23.35 0.00 0.00 5.36
4772 5223 2.096218 GGCAAACGTAGCAAAGAGTGAG 60.096 50.000 13.92 0.00 0.00 3.51
4782 5233 2.294233 GCAAAGAGTGAGCAATTGACCA 59.706 45.455 10.34 2.72 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.249238 GCAACAAAACATGGTCGCCA 60.249 50.000 0.00 1.01 38.19 5.69
12 13 1.004079 CAATGGCGGTTGCAACAAAAC 60.004 47.619 29.55 16.80 45.35 2.43
73 74 1.936203 GCCATTGCAGCAAATCACGTT 60.936 47.619 12.97 0.00 37.47 3.99
121 122 1.472878 TGCAGCAAAAACGTAACACCA 59.527 42.857 0.00 0.00 0.00 4.17
128 129 1.226831 CCGGTTGCAGCAAAAACGT 60.227 52.632 10.11 0.00 0.00 3.99
262 265 1.730547 GCAGCAAAAATCGCAGCGT 60.731 52.632 15.93 0.00 32.05 5.07
369 374 2.929398 CCATTCATGTCGACAATCACGA 59.071 45.455 24.13 11.18 37.43 4.35
375 380 3.435327 GCTACAACCATTCATGTCGACAA 59.565 43.478 24.13 6.61 0.00 3.18
434 439 5.097529 CGTGCAGATGTATTTTGCTTCAAT 58.902 37.500 0.00 0.00 38.60 2.57
448 453 1.944032 TCATCATCCACGTGCAGATG 58.056 50.000 24.83 24.83 41.05 2.90
498 503 2.758327 TCACCGCAGCCCTATCGT 60.758 61.111 0.00 0.00 0.00 3.73
523 528 2.265739 CAGGTTGCAGCTCCGCTA 59.734 61.111 0.00 0.00 36.40 4.26
562 567 1.548081 TGCACCTACGGTTGTAGCTA 58.452 50.000 0.00 0.00 45.57 3.32
698 720 2.627737 GGTGACTGACCTCGTCGCT 61.628 63.158 0.00 0.00 42.25 4.93
783 847 0.680921 CGTGTGGGCCATTGGATCTT 60.681 55.000 10.70 0.00 0.00 2.40
800 864 1.463674 GACCATTGGATTTGAGCCGT 58.536 50.000 10.37 0.00 0.00 5.68
848 912 3.838244 ACAAAGTTGAGTCAGGCACTA 57.162 42.857 0.00 0.00 36.02 2.74
849 913 2.717639 ACAAAGTTGAGTCAGGCACT 57.282 45.000 0.00 0.00 43.88 4.40
850 914 3.467803 AGTACAAAGTTGAGTCAGGCAC 58.532 45.455 0.00 0.00 0.00 5.01
851 915 3.838244 AGTACAAAGTTGAGTCAGGCA 57.162 42.857 0.00 0.00 0.00 4.75
852 916 5.298347 AGTTAGTACAAAGTTGAGTCAGGC 58.702 41.667 0.00 0.00 0.00 4.85
853 917 7.280205 ACAAAGTTAGTACAAAGTTGAGTCAGG 59.720 37.037 0.00 0.00 0.00 3.86
854 918 8.197988 ACAAAGTTAGTACAAAGTTGAGTCAG 57.802 34.615 0.00 0.00 0.00 3.51
855 919 9.090692 GTACAAAGTTAGTACAAAGTTGAGTCA 57.909 33.333 0.00 0.00 41.08 3.41
856 920 8.546244 GGTACAAAGTTAGTACAAAGTTGAGTC 58.454 37.037 0.00 0.00 42.73 3.36
857 921 8.262933 AGGTACAAAGTTAGTACAAAGTTGAGT 58.737 33.333 0.00 0.00 42.73 3.41
858 922 8.658499 AGGTACAAAGTTAGTACAAAGTTGAG 57.342 34.615 0.00 0.00 42.73 3.02
868 932 9.206870 CGTTCCAAAATAGGTACAAAGTTAGTA 57.793 33.333 0.00 0.00 0.00 1.82
869 933 7.173735 CCGTTCCAAAATAGGTACAAAGTTAGT 59.826 37.037 0.00 0.00 0.00 2.24
870 934 7.361457 CCCGTTCCAAAATAGGTACAAAGTTAG 60.361 40.741 0.00 0.00 0.00 2.34
871 935 6.430616 CCCGTTCCAAAATAGGTACAAAGTTA 59.569 38.462 0.00 0.00 0.00 2.24
872 936 5.242171 CCCGTTCCAAAATAGGTACAAAGTT 59.758 40.000 0.00 0.00 0.00 2.66
873 937 4.763279 CCCGTTCCAAAATAGGTACAAAGT 59.237 41.667 0.00 0.00 0.00 2.66
874 938 4.157105 CCCCGTTCCAAAATAGGTACAAAG 59.843 45.833 0.00 0.00 0.00 2.77
875 939 4.080687 CCCCGTTCCAAAATAGGTACAAA 58.919 43.478 0.00 0.00 0.00 2.83
876 940 3.561744 CCCCCGTTCCAAAATAGGTACAA 60.562 47.826 0.00 0.00 0.00 2.41
877 941 2.026075 CCCCCGTTCCAAAATAGGTACA 60.026 50.000 0.00 0.00 0.00 2.90
878 942 2.239402 TCCCCCGTTCCAAAATAGGTAC 59.761 50.000 0.00 0.00 0.00 3.34
879 943 2.506644 CTCCCCCGTTCCAAAATAGGTA 59.493 50.000 0.00 0.00 0.00 3.08
880 944 1.283905 CTCCCCCGTTCCAAAATAGGT 59.716 52.381 0.00 0.00 0.00 3.08
881 945 1.283905 ACTCCCCCGTTCCAAAATAGG 59.716 52.381 0.00 0.00 0.00 2.57
882 946 2.801077 ACTCCCCCGTTCCAAAATAG 57.199 50.000 0.00 0.00 0.00 1.73
883 947 3.183801 ACTACTCCCCCGTTCCAAAATA 58.816 45.455 0.00 0.00 0.00 1.40
884 948 1.990327 ACTACTCCCCCGTTCCAAAAT 59.010 47.619 0.00 0.00 0.00 1.82
885 949 1.437397 ACTACTCCCCCGTTCCAAAA 58.563 50.000 0.00 0.00 0.00 2.44
886 950 1.901833 GTACTACTCCCCCGTTCCAAA 59.098 52.381 0.00 0.00 0.00 3.28
887 951 1.203162 TGTACTACTCCCCCGTTCCAA 60.203 52.381 0.00 0.00 0.00 3.53
888 952 0.409092 TGTACTACTCCCCCGTTCCA 59.591 55.000 0.00 0.00 0.00 3.53
889 953 0.820226 GTGTACTACTCCCCCGTTCC 59.180 60.000 0.00 0.00 0.00 3.62
890 954 1.549203 TGTGTACTACTCCCCCGTTC 58.451 55.000 0.00 0.00 0.00 3.95
891 955 2.014010 TTGTGTACTACTCCCCCGTT 57.986 50.000 0.00 0.00 0.00 4.44
892 956 2.014010 TTTGTGTACTACTCCCCCGT 57.986 50.000 0.00 0.00 0.00 5.28
893 957 2.301009 AGTTTTGTGTACTACTCCCCCG 59.699 50.000 0.00 0.00 0.00 5.73
894 958 3.325716 TGAGTTTTGTGTACTACTCCCCC 59.674 47.826 0.00 0.00 36.94 5.40
895 959 4.566987 CTGAGTTTTGTGTACTACTCCCC 58.433 47.826 0.00 0.00 36.94 4.81
896 960 3.995048 GCTGAGTTTTGTGTACTACTCCC 59.005 47.826 0.00 0.00 36.94 4.30
897 961 4.628074 TGCTGAGTTTTGTGTACTACTCC 58.372 43.478 0.00 0.00 36.94 3.85
898 962 6.598753 TTTGCTGAGTTTTGTGTACTACTC 57.401 37.500 0.00 0.00 37.97 2.59
899 963 6.995511 TTTTGCTGAGTTTTGTGTACTACT 57.004 33.333 0.00 0.00 0.00 2.57
900 964 7.111593 CGATTTTTGCTGAGTTTTGTGTACTAC 59.888 37.037 0.00 0.00 0.00 2.73
901 965 7.129622 CGATTTTTGCTGAGTTTTGTGTACTA 58.870 34.615 0.00 0.00 0.00 1.82
902 966 5.971202 CGATTTTTGCTGAGTTTTGTGTACT 59.029 36.000 0.00 0.00 0.00 2.73
903 967 5.173131 CCGATTTTTGCTGAGTTTTGTGTAC 59.827 40.000 0.00 0.00 0.00 2.90
904 968 5.277825 CCGATTTTTGCTGAGTTTTGTGTA 58.722 37.500 0.00 0.00 0.00 2.90
905 969 4.111916 CCGATTTTTGCTGAGTTTTGTGT 58.888 39.130 0.00 0.00 0.00 3.72
918 982 0.027586 GACGATCGGCCCGATTTTTG 59.972 55.000 21.39 12.82 47.00 2.44
924 988 2.903855 GTAGGACGATCGGCCCGA 60.904 66.667 36.22 22.27 46.93 5.14
990 1071 3.157252 GGCGCCATGGGAGAGAGA 61.157 66.667 24.80 0.00 0.00 3.10
991 1072 4.598894 CGGCGCCATGGGAGAGAG 62.599 72.222 28.98 0.98 0.00 3.20
1090 1171 2.716017 CGGAGGAGGAGTGGCTGAC 61.716 68.421 0.00 0.00 0.00 3.51
1091 1172 2.363018 CGGAGGAGGAGTGGCTGA 60.363 66.667 0.00 0.00 0.00 4.26
1536 1617 7.036829 TGAAATGGTGAAAGATTATGTGCATG 58.963 34.615 0.00 0.00 0.00 4.06
1635 1716 2.501723 AGAGCCATAGACAACGGAACAT 59.498 45.455 0.00 0.00 0.00 2.71
1646 1727 7.553504 TTTGCCTACATTATAGAGCCATAGA 57.446 36.000 0.00 0.00 0.00 1.98
1678 1760 1.801771 CCGCAATACACCGAGACAAAA 59.198 47.619 0.00 0.00 0.00 2.44
1687 1769 4.976224 AATCCTTAAACCGCAATACACC 57.024 40.909 0.00 0.00 0.00 4.16
1728 1810 4.083862 GGCCTGGACCCAGACGTC 62.084 72.222 17.19 7.70 46.30 4.34
1732 1814 1.383799 CATTTGGCCTGGACCCAGA 59.616 57.895 17.19 0.00 46.30 3.86
1735 1817 1.474330 CTTACATTTGGCCTGGACCC 58.526 55.000 3.32 0.00 0.00 4.46
1794 1877 7.281999 CCACTCAAAATGGGTTTACAAACATTT 59.718 33.333 7.12 0.00 43.20 2.32
1890 1983 4.554960 AAGTAAGCACCTCCTTTACTCC 57.445 45.455 0.00 0.00 0.00 3.85
1988 2087 8.462143 AATTATGTGTCTACTTCACTAACACG 57.538 34.615 0.00 0.00 42.37 4.49
2077 2176 2.626266 CCCTGTTTACCTGAAACCCAAC 59.374 50.000 0.00 0.00 45.94 3.77
2157 2258 7.448588 TTGCATAACAAAATATGTCGAATGC 57.551 32.000 12.66 12.66 42.99 3.56
2329 2666 7.738847 TCATCATCACATGGCTAGAAGATTAA 58.261 34.615 0.00 0.00 0.00 1.40
2401 2738 9.797556 AACAAGTAACTGAACCAAAGTAAATTC 57.202 29.630 0.00 0.00 0.00 2.17
2514 2851 4.084013 ACACATCAAGTACACTAAAAGCGC 60.084 41.667 0.00 0.00 0.00 5.92
2528 2865 6.704289 ATATGTTCCATCCAACACATCAAG 57.296 37.500 0.00 0.00 39.09 3.02
2582 2919 1.704007 AAGAGGAGCCCCATAGCAGC 61.704 60.000 0.00 0.00 34.23 5.25
2610 2947 7.383102 ACAGTTATGATGTCAAAAGTGATCC 57.617 36.000 0.00 0.00 35.80 3.36
2691 3028 8.033626 GGACACAAATAGTAGCAGTAACTAGTT 58.966 37.037 13.68 13.68 38.02 2.24
3005 3342 1.327303 TTGCCATTTCTCGCCAAACT 58.673 45.000 0.00 0.00 0.00 2.66
3021 3358 3.119388 TCAGGAGTAATGCAGCAATTTGC 60.119 43.478 13.55 13.55 45.46 3.68
3323 3660 4.337555 CCCTTCATTGTCATGTCTTCCATC 59.662 45.833 0.00 0.00 0.00 3.51
3381 3718 2.095567 CGTCAATGCCTTCCTGTTTCAG 60.096 50.000 0.00 0.00 0.00 3.02
3506 3843 1.067295 TCCACACCCTCAGAGCATTT 58.933 50.000 0.00 0.00 0.00 2.32
3539 3876 2.685850 AACCAGGCCTAATGTCGTAC 57.314 50.000 3.98 0.00 0.00 3.67
3577 3914 4.839668 TGTTTAATCAAACCTTGGACCG 57.160 40.909 0.00 0.00 42.88 4.79
3696 4033 0.604780 CAGTGGTCTCTGTTGGCCAG 60.605 60.000 5.11 0.00 42.97 4.85
3737 4074 4.634004 TGTTTGATACGCTGTGGAATAAGG 59.366 41.667 0.00 0.00 0.00 2.69
3776 4113 5.462398 GTGACACATGTATTACGGGATTCTC 59.538 44.000 0.00 0.00 0.00 2.87
3782 4119 3.857052 ACAGTGACACATGTATTACGGG 58.143 45.455 8.59 0.00 0.00 5.28
3904 4248 6.858993 GCGGTTTCATGTTTGTTAGTTATGAA 59.141 34.615 0.00 0.00 36.35 2.57
3907 4251 6.569179 AGCGGTTTCATGTTTGTTAGTTAT 57.431 33.333 0.00 0.00 0.00 1.89
3934 4360 0.741221 GAAGCAACTCGGGCGAGAAT 60.741 55.000 0.00 0.00 44.53 2.40
3994 4420 6.038825 ACACCATGTACATTTTTCGAAACTCA 59.961 34.615 10.79 4.49 0.00 3.41
4023 4449 4.870636 TGGCAATCATAGGACCTTTTGAT 58.129 39.130 0.00 6.56 0.00 2.57
4093 4531 6.769512 TGTAATTCTGGGAAGGCATAGATAC 58.230 40.000 0.00 0.00 0.00 2.24
4267 4706 7.815840 TTTCATGTGACCAACTTAATCTTCA 57.184 32.000 0.00 0.00 0.00 3.02
4306 4748 3.370315 CCAGAAGCCTACTTGCTCATCTT 60.370 47.826 0.00 0.00 41.80 2.40
4325 4767 2.026641 CCAACCACTGCCAATATCCAG 58.973 52.381 0.00 0.00 35.26 3.86
4375 4817 3.195825 ACTTGTTACGCCAGCTTCTCTAT 59.804 43.478 0.00 0.00 0.00 1.98
4473 4916 1.066286 CCTCCTCTCTTTGCAGGACTG 60.066 57.143 0.00 0.00 34.87 3.51
4626 5077 2.763249 CACTTTCTCAAGGTGTGCAC 57.237 50.000 10.75 10.75 33.82 4.57
4685 5136 1.810151 CGGCGGAGATTTGAAAAGGAA 59.190 47.619 0.00 0.00 0.00 3.36
4687 5138 1.448985 TCGGCGGAGATTTGAAAAGG 58.551 50.000 7.21 0.00 0.00 3.11
4700 5151 1.586123 CAGTGTTTTTGTTTTCGGCGG 59.414 47.619 7.21 0.00 0.00 6.13
4705 5156 6.466308 ACTTTCTGCAGTGTTTTTGTTTTC 57.534 33.333 14.67 0.00 0.00 2.29
4712 5163 2.418609 GCCCAACTTTCTGCAGTGTTTT 60.419 45.455 14.67 0.59 0.00 2.43
4718 5169 0.245539 CATGGCCCAACTTTCTGCAG 59.754 55.000 7.63 7.63 0.00 4.41
4730 5181 1.134907 CACAAGAAATGCTCATGGCCC 60.135 52.381 0.00 0.00 40.92 5.80
4732 5183 1.134907 CCCACAAGAAATGCTCATGGC 60.135 52.381 0.00 0.00 42.22 4.40
4735 5186 1.927487 TGCCCACAAGAAATGCTCAT 58.073 45.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.