Multiple sequence alignment - TraesCS4B01G213100

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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 TraesCS4B01G213100 chr4B 100.000 2540 0 0 1 2540 451492032 451489493 0.000000e+00 4691
1 TraesCS4B01G213100 chr4B 100.000 74 0 0 802 875 451491161 451491088 1.230000e-28 137
2 TraesCS4B01G213100 chr4B 100.000 74 0 0 872 945 451491231 451491158 1.230000e-28 137
3 TraesCS4B01G213100 chr4D 88.795 1660 90 37 872 2493 366692454 366690853 0.000000e+00 1947
4 TraesCS4B01G213100 chr4D 89.019 856 59 15 1 854 366693225 366692403 0.000000e+00 1027
5 TraesCS4B01G213100 chr4A 91.100 809 28 11 1711 2494 98559376 98560165 0.000000e+00 1055
6 TraesCS4B01G213100 chr4A 89.202 815 55 16 2 806 98557736 98558527 0.000000e+00 987
7 TraesCS4B01G213100 chr4A 90.162 742 32 18 983 1707 98558577 98559294 0.000000e+00 928


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 TraesCS4B01G213100 chr4B 451489493 451492032 2539 True 1655 4691 100.000000 1 2540 3 chr4B.!!$R1 2539
1 TraesCS4B01G213100 chr4D 366690853 366693225 2372 True 1487 1947 88.907000 1 2493 2 chr4D.!!$R1 2492
2 TraesCS4B01G213100 chr4A 98557736 98560165 2429 False 990 1055 90.154667 2 2494 3 chr4A.!!$F1 2492

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
825 836 0.035317 ACCAGCGTGCAAAGAGATCA 59.965 50.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1965 0.109723 TGTGTTAGAACTGCCCCCAC 59.89 55.0 0.0 0.0 0.0 4.61 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
28 29 3.552604 AACAATTTCGTATGCGCAACT 57.447 38.095 17.11 0.00 38.14 3.16
62 63 3.728845 TCAGGTGAAGAAAAAGAGACCG 58.271 45.455 0.00 0.00 0.00 4.79
126 127 2.793790 GTGAGCTCGTGATAGCAATGAG 59.206 50.000 9.64 7.04 45.30 2.90
146 147 4.399618 TGAGCCTTGTGACATACTACTCTC 59.600 45.833 0.00 0.00 0.00 3.20
161 162 0.979665 CTCTCAAGAGCTGGGTGGAA 59.020 55.000 0.00 0.00 35.13 3.53
162 163 1.558756 CTCTCAAGAGCTGGGTGGAAT 59.441 52.381 0.00 0.00 35.13 3.01
164 165 2.501723 TCTCAAGAGCTGGGTGGAATAC 59.498 50.000 0.00 0.00 0.00 1.89
165 166 2.237143 CTCAAGAGCTGGGTGGAATACA 59.763 50.000 0.00 0.00 0.00 2.29
166 167 2.846206 TCAAGAGCTGGGTGGAATACAT 59.154 45.455 0.00 0.00 0.00 2.29
167 168 2.947652 CAAGAGCTGGGTGGAATACATG 59.052 50.000 0.00 0.00 0.00 3.21
168 169 1.492176 AGAGCTGGGTGGAATACATGG 59.508 52.381 0.00 0.00 0.00 3.66
169 170 0.552848 AGCTGGGTGGAATACATGGG 59.447 55.000 0.00 0.00 0.00 4.00
170 171 0.258774 GCTGGGTGGAATACATGGGT 59.741 55.000 0.00 0.00 0.00 4.51
171 172 2.023788 GCTGGGTGGAATACATGGGTG 61.024 57.143 0.00 0.00 0.00 4.61
193 194 1.271652 TGGGCCTAAGAATGAAACGCA 60.272 47.619 4.53 0.00 0.00 5.24
194 195 1.816224 GGGCCTAAGAATGAAACGCAA 59.184 47.619 0.84 0.00 0.00 4.85
195 196 2.230266 GGGCCTAAGAATGAAACGCAAA 59.770 45.455 0.84 0.00 0.00 3.68
196 197 3.501950 GGCCTAAGAATGAAACGCAAAG 58.498 45.455 0.00 0.00 0.00 2.77
197 198 3.190535 GGCCTAAGAATGAAACGCAAAGA 59.809 43.478 0.00 0.00 0.00 2.52
213 214 4.614946 GCAAAGAAGTTTTGATGCTGTCT 58.385 39.130 3.97 0.00 0.00 3.41
218 219 4.641989 AGAAGTTTTGATGCTGTCTTGTGT 59.358 37.500 0.00 0.00 0.00 3.72
222 223 5.009010 AGTTTTGATGCTGTCTTGTGTAAGG 59.991 40.000 0.00 0.00 34.59 2.69
320 323 5.777850 TGTTTGCTATACATACGGCTAGA 57.222 39.130 0.00 0.00 33.34 2.43
564 571 9.826574 GATTCTTTTGGTACTGTGTATGGTATA 57.173 33.333 0.00 0.00 0.00 1.47
590 597 5.050490 GTGTGAACTGTGTGATTCAGTAGT 58.950 41.667 0.00 0.00 44.03 2.73
593 600 7.385205 GTGTGAACTGTGTGATTCAGTAGTAAT 59.615 37.037 0.00 0.00 44.03 1.89
594 601 7.598869 TGTGAACTGTGTGATTCAGTAGTAATC 59.401 37.037 0.00 0.00 44.03 1.75
642 649 7.172703 TGGTTTGTGTAAATTTTTGTTTTCCGT 59.827 29.630 0.00 0.00 0.00 4.69
704 712 3.254657 CAGGCACCCGTTCTTTTCATTTA 59.745 43.478 0.00 0.00 0.00 1.40
709 717 6.203915 GGCACCCGTTCTTTTCATTTATTTTT 59.796 34.615 0.00 0.00 0.00 1.94
710 718 7.068955 GCACCCGTTCTTTTCATTTATTTTTG 58.931 34.615 0.00 0.00 0.00 2.44
712 720 8.821894 CACCCGTTCTTTTCATTTATTTTTGAA 58.178 29.630 0.00 0.00 0.00 2.69
713 721 8.822855 ACCCGTTCTTTTCATTTATTTTTGAAC 58.177 29.630 0.00 0.00 31.87 3.18
714 722 8.821894 CCCGTTCTTTTCATTTATTTTTGAACA 58.178 29.630 0.00 0.00 31.87 3.18
755 763 7.800155 TGTGTTCTGATCAGTTATTTGTTGA 57.200 32.000 21.92 0.00 0.00 3.18
756 764 8.394971 TGTGTTCTGATCAGTTATTTGTTGAT 57.605 30.769 21.92 0.00 0.00 2.57
777 788 5.465390 TGATAATAGTTTGGCTGATACGTGC 59.535 40.000 0.00 0.00 0.00 5.34
795 806 3.853712 GTGCTCACGTCTGCAGAG 58.146 61.111 18.89 13.73 40.06 3.35
813 824 1.204941 GAGATGTTGAGGTACCAGCGT 59.795 52.381 15.94 0.00 0.00 5.07
817 828 0.882927 GTTGAGGTACCAGCGTGCAA 60.883 55.000 15.94 5.56 0.00 4.08
818 829 0.179043 TTGAGGTACCAGCGTGCAAA 60.179 50.000 15.94 0.00 0.00 3.68
825 836 0.035317 ACCAGCGTGCAAAGAGATCA 59.965 50.000 0.00 0.00 0.00 2.92
835 846 3.890756 TGCAAAGAGATCACCATGTTTGT 59.109 39.130 0.00 0.00 0.00 2.83
854 865 8.642935 TGTTTGTTTAATCCACTCATCCATAA 57.357 30.769 0.00 0.00 0.00 1.90
855 866 9.253832 TGTTTGTTTAATCCACTCATCCATAAT 57.746 29.630 0.00 0.00 0.00 1.28
858 869 8.463930 TGTTTAATCCACTCATCCATAATTCC 57.536 34.615 0.00 0.00 0.00 3.01
859 870 8.058235 TGTTTAATCCACTCATCCATAATTCCA 58.942 33.333 0.00 0.00 0.00 3.53
860 871 9.082313 GTTTAATCCACTCATCCATAATTCCAT 57.918 33.333 0.00 0.00 0.00 3.41
864 875 6.962182 TCCACTCATCCATAATTCCATATCC 58.038 40.000 0.00 0.00 0.00 2.59
865 876 6.069440 TCCACTCATCCATAATTCCATATCCC 60.069 42.308 0.00 0.00 0.00 3.85
866 877 6.069206 CCACTCATCCATAATTCCATATCCCT 60.069 42.308 0.00 0.00 0.00 4.20
867 878 7.052873 CACTCATCCATAATTCCATATCCCTC 58.947 42.308 0.00 0.00 0.00 4.30
868 879 6.970640 ACTCATCCATAATTCCATATCCCTCT 59.029 38.462 0.00 0.00 0.00 3.69
869 880 7.463618 ACTCATCCATAATTCCATATCCCTCTT 59.536 37.037 0.00 0.00 0.00 2.85
870 881 7.636579 TCATCCATAATTCCATATCCCTCTTG 58.363 38.462 0.00 0.00 0.00 3.02
871 882 6.392911 TCCATAATTCCATATCCCTCTTGG 57.607 41.667 0.00 0.00 0.00 3.61
886 897 2.920384 TGGAGGTACCAGCGTGCA 60.920 61.111 15.94 1.26 44.64 4.57
887 898 2.345991 GGAGGTACCAGCGTGCAA 59.654 61.111 15.94 0.00 38.79 4.08
888 899 1.302192 GGAGGTACCAGCGTGCAAA 60.302 57.895 15.94 0.00 38.79 3.68
889 900 1.298859 GGAGGTACCAGCGTGCAAAG 61.299 60.000 15.94 0.00 38.79 2.77
890 901 0.320421 GAGGTACCAGCGTGCAAAGA 60.320 55.000 15.94 0.00 0.00 2.52
891 902 0.320771 AGGTACCAGCGTGCAAAGAG 60.321 55.000 15.94 0.00 0.00 2.85
892 903 0.320421 GGTACCAGCGTGCAAAGAGA 60.320 55.000 7.15 0.00 0.00 3.10
893 904 1.676014 GGTACCAGCGTGCAAAGAGAT 60.676 52.381 7.15 0.00 0.00 2.75
894 905 1.661112 GTACCAGCGTGCAAAGAGATC 59.339 52.381 0.00 0.00 0.00 2.75
895 906 0.035317 ACCAGCGTGCAAAGAGATCA 59.965 50.000 0.00 0.00 0.00 2.92
896 907 0.445436 CCAGCGTGCAAAGAGATCAC 59.555 55.000 0.00 0.00 0.00 3.06
897 908 0.445436 CAGCGTGCAAAGAGATCACC 59.555 55.000 0.00 0.00 0.00 4.02
898 909 0.035317 AGCGTGCAAAGAGATCACCA 59.965 50.000 0.00 0.00 0.00 4.17
899 910 1.089920 GCGTGCAAAGAGATCACCAT 58.910 50.000 0.00 0.00 0.00 3.55
900 911 1.202110 GCGTGCAAAGAGATCACCATG 60.202 52.381 0.00 0.00 0.00 3.66
901 912 2.079158 CGTGCAAAGAGATCACCATGT 58.921 47.619 0.00 0.00 0.00 3.21
902 913 2.485426 CGTGCAAAGAGATCACCATGTT 59.515 45.455 0.00 0.00 0.00 2.71
903 914 3.058016 CGTGCAAAGAGATCACCATGTTT 60.058 43.478 0.00 0.00 0.00 2.83
904 915 4.232221 GTGCAAAGAGATCACCATGTTTG 58.768 43.478 0.00 0.00 0.00 2.93
905 916 3.890756 TGCAAAGAGATCACCATGTTTGT 59.109 39.130 0.00 0.00 0.00 2.83
906 917 4.341806 TGCAAAGAGATCACCATGTTTGTT 59.658 37.500 0.00 0.00 0.00 2.83
907 918 5.163426 TGCAAAGAGATCACCATGTTTGTTT 60.163 36.000 0.00 0.00 0.00 2.83
908 919 6.040278 TGCAAAGAGATCACCATGTTTGTTTA 59.960 34.615 0.00 0.00 0.00 2.01
909 920 6.922957 GCAAAGAGATCACCATGTTTGTTTAA 59.077 34.615 0.00 0.00 0.00 1.52
910 921 7.599998 GCAAAGAGATCACCATGTTTGTTTAAT 59.400 33.333 0.00 0.00 0.00 1.40
911 922 9.132521 CAAAGAGATCACCATGTTTGTTTAATC 57.867 33.333 0.00 0.00 0.00 1.75
912 923 7.396540 AGAGATCACCATGTTTGTTTAATCC 57.603 36.000 0.00 0.00 0.00 3.01
913 924 6.947733 AGAGATCACCATGTTTGTTTAATCCA 59.052 34.615 0.00 0.00 0.00 3.41
914 925 6.924111 AGATCACCATGTTTGTTTAATCCAC 58.076 36.000 0.00 0.00 0.00 4.02
915 926 6.721208 AGATCACCATGTTTGTTTAATCCACT 59.279 34.615 0.00 0.00 0.00 4.00
916 927 6.325919 TCACCATGTTTGTTTAATCCACTC 57.674 37.500 0.00 0.00 0.00 3.51
917 928 5.830457 TCACCATGTTTGTTTAATCCACTCA 59.170 36.000 0.00 0.00 0.00 3.41
918 929 6.493115 TCACCATGTTTGTTTAATCCACTCAT 59.507 34.615 0.00 0.00 0.00 2.90
919 930 6.808212 CACCATGTTTGTTTAATCCACTCATC 59.192 38.462 0.00 0.00 0.00 2.92
920 931 6.071391 ACCATGTTTGTTTAATCCACTCATCC 60.071 38.462 0.00 0.00 0.00 3.51
921 932 6.071447 CCATGTTTGTTTAATCCACTCATCCA 60.071 38.462 0.00 0.00 0.00 3.41
922 933 7.364056 CCATGTTTGTTTAATCCACTCATCCAT 60.364 37.037 0.00 0.00 0.00 3.41
923 934 8.685427 CATGTTTGTTTAATCCACTCATCCATA 58.315 33.333 0.00 0.00 0.00 2.74
924 935 8.642935 TGTTTGTTTAATCCACTCATCCATAA 57.357 30.769 0.00 0.00 0.00 1.90
925 936 9.253832 TGTTTGTTTAATCCACTCATCCATAAT 57.746 29.630 0.00 0.00 0.00 1.28
928 939 8.463930 TGTTTAATCCACTCATCCATAATTCC 57.536 34.615 0.00 0.00 0.00 3.01
929 940 8.058235 TGTTTAATCCACTCATCCATAATTCCA 58.942 33.333 0.00 0.00 0.00 3.53
930 941 9.082313 GTTTAATCCACTCATCCATAATTCCAT 57.918 33.333 0.00 0.00 0.00 3.41
1025 1047 0.037697 CAGATTCACCGGACCGTCAA 60.038 55.000 9.46 2.42 0.00 3.18
1060 1082 6.991938 ACTTGTTCAATAAAAATAGGCAGCA 58.008 32.000 0.00 0.00 0.00 4.41
1111 1140 0.321671 TCTTGAACCCCGCAGAGAAG 59.678 55.000 0.00 0.00 0.00 2.85
1119 1152 0.745468 CCCGCAGAGAAGGTAGGTAC 59.255 60.000 0.00 0.00 0.00 3.34
1132 1165 2.098770 GGTAGGTACACGGACACATCTC 59.901 54.545 0.00 0.00 0.00 2.75
1142 1175 1.442769 GACACATCTCGCCAACACAT 58.557 50.000 0.00 0.00 0.00 3.21
1149 1182 0.168788 CTCGCCAACACATCGCAATT 59.831 50.000 0.00 0.00 0.00 2.32
1155 1195 0.168788 AACACATCGCAATTCGGCAG 59.831 50.000 0.00 0.00 39.05 4.85
1176 1217 4.705519 CCGCAGCCCAAGCAAACG 62.706 66.667 0.00 0.00 43.56 3.60
1599 1669 9.925268 GCCAACATCAATCAATCAATAAAAATC 57.075 29.630 0.00 0.00 0.00 2.17
1620 1714 2.250939 GCGCACTTGCAGGTGTGTA 61.251 57.895 33.99 0.00 45.91 2.90
1625 1719 1.128200 ACTTGCAGGTGTGTAGGACA 58.872 50.000 0.00 0.00 0.00 4.02
1626 1720 1.070758 ACTTGCAGGTGTGTAGGACAG 59.929 52.381 0.00 0.00 34.28 3.51
1628 1722 2.003937 TGCAGGTGTGTAGGACAGTA 57.996 50.000 0.00 0.00 34.28 2.74
1629 1723 1.893137 TGCAGGTGTGTAGGACAGTAG 59.107 52.381 0.00 0.00 34.28 2.57
1630 1724 1.204941 GCAGGTGTGTAGGACAGTAGG 59.795 57.143 0.00 0.00 34.28 3.18
1631 1725 2.803956 CAGGTGTGTAGGACAGTAGGA 58.196 52.381 0.00 0.00 34.28 2.94
1632 1726 2.755655 CAGGTGTGTAGGACAGTAGGAG 59.244 54.545 0.00 0.00 34.28 3.69
1633 1727 2.379226 AGGTGTGTAGGACAGTAGGAGT 59.621 50.000 0.00 0.00 34.28 3.85
1634 1728 3.590630 AGGTGTGTAGGACAGTAGGAGTA 59.409 47.826 0.00 0.00 34.28 2.59
1635 1729 4.230041 AGGTGTGTAGGACAGTAGGAGTAT 59.770 45.833 0.00 0.00 34.28 2.12
1636 1730 4.579753 GGTGTGTAGGACAGTAGGAGTATC 59.420 50.000 0.00 0.00 34.28 2.24
1657 1751 2.494073 CTGTCTACTGAGGTTCCTGGTC 59.506 54.545 0.00 0.00 0.00 4.02
1669 1763 4.466726 AGGTTCCTGGTCTATGTGTACTTC 59.533 45.833 0.00 0.00 0.00 3.01
1677 1771 2.430694 TCTATGTGTACTTCCTGCGCAT 59.569 45.455 12.24 0.00 38.95 4.73
1678 1772 2.113860 ATGTGTACTTCCTGCGCATT 57.886 45.000 12.24 0.00 32.25 3.56
1679 1773 1.890876 TGTGTACTTCCTGCGCATTT 58.109 45.000 12.24 0.00 0.00 2.32
1680 1774 1.804151 TGTGTACTTCCTGCGCATTTC 59.196 47.619 12.24 0.00 0.00 2.17
1681 1775 1.804151 GTGTACTTCCTGCGCATTTCA 59.196 47.619 12.24 0.86 0.00 2.69
1695 1789 3.345714 GCATTTCATTTCTCTACGCACG 58.654 45.455 0.00 0.00 0.00 5.34
1707 1801 6.140303 TCTCTACGCACGGAAAAATACTAT 57.860 37.500 0.00 0.00 0.00 2.12
1709 1803 7.706159 TCTCTACGCACGGAAAAATACTATTA 58.294 34.615 0.00 0.00 0.00 0.98
1773 1965 2.431454 GCCTTTCTCTTCTCCTTGGTG 58.569 52.381 0.00 0.00 0.00 4.17
1878 2071 2.544277 CGACCCACGAGTTTGACAAGTA 60.544 50.000 0.00 0.00 45.77 2.24
1879 2072 3.057734 GACCCACGAGTTTGACAAGTAG 58.942 50.000 0.00 0.00 0.00 2.57
1981 2184 3.808466 AGACACACGCATCTGATGTAT 57.192 42.857 18.19 4.92 0.00 2.29
1982 2185 3.451526 AGACACACGCATCTGATGTATG 58.548 45.455 18.19 17.33 0.00 2.39
1986 2189 3.805971 CACACGCATCTGATGTATGATGT 59.194 43.478 22.05 14.94 41.33 3.06
1997 2200 5.744171 TGATGTATGATGTTTGGCTGTAGT 58.256 37.500 0.00 0.00 0.00 2.73
2104 2307 0.732880 AACCGTCGATGAGAACTGCG 60.733 55.000 6.11 0.00 0.00 5.18
2160 2372 2.669229 TACCGTGTCCGCTGACGA 60.669 61.111 3.71 0.00 44.86 4.20
2185 2397 2.592287 TCGTTTGTGGCGGGGTTC 60.592 61.111 0.00 0.00 0.00 3.62
2227 2439 2.202892 GTCGCATCCGGGTCTTCC 60.203 66.667 0.00 0.00 34.56 3.46
2278 2490 1.026718 CCACCTTGATGAAGCCCGTC 61.027 60.000 0.00 0.00 0.00 4.79
2300 2512 1.741770 GTCTGCACCACGTCCATCC 60.742 63.158 0.00 0.00 0.00 3.51
2330 2542 3.717707 TCAGTTCAGCGGCTCATATAAC 58.282 45.455 0.00 0.25 0.00 1.89
2477 2689 1.564622 CACACCAGTTTCTGCGACG 59.435 57.895 0.00 0.00 0.00 5.12
2479 2691 0.874607 ACACCAGTTTCTGCGACGAC 60.875 55.000 0.00 0.00 0.00 4.34
2485 2697 0.382636 GTTTCTGCGACGACAAACCG 60.383 55.000 0.00 0.00 0.00 4.44
2494 2706 3.578272 GACAAACCGCACGCACCA 61.578 61.111 0.00 0.00 0.00 4.17
2495 2707 3.800323 GACAAACCGCACGCACCAC 62.800 63.158 0.00 0.00 0.00 4.16
2496 2708 4.622456 CAAACCGCACGCACCACC 62.622 66.667 0.00 0.00 0.00 4.61
2515 2727 2.432456 CCGCGTCAGCTGCTTGTA 60.432 61.111 9.47 0.00 42.32 2.41
2516 2728 2.027073 CCGCGTCAGCTGCTTGTAA 61.027 57.895 9.47 0.00 42.32 2.41
2517 2729 1.417592 CGCGTCAGCTGCTTGTAAG 59.582 57.895 9.47 0.00 42.32 2.34
2518 2730 1.008875 CGCGTCAGCTGCTTGTAAGA 61.009 55.000 9.47 0.00 42.32 2.10
2519 2731 1.363744 GCGTCAGCTGCTTGTAAGAT 58.636 50.000 9.47 0.00 41.01 2.40
2520 2732 1.734465 GCGTCAGCTGCTTGTAAGATT 59.266 47.619 9.47 0.00 41.01 2.40
2521 2733 2.222908 GCGTCAGCTGCTTGTAAGATTC 60.223 50.000 9.47 0.00 41.01 2.52
2522 2734 2.995939 CGTCAGCTGCTTGTAAGATTCA 59.004 45.455 9.47 0.00 0.00 2.57
2523 2735 3.433274 CGTCAGCTGCTTGTAAGATTCAA 59.567 43.478 9.47 0.00 0.00 2.69
2524 2736 4.667668 CGTCAGCTGCTTGTAAGATTCAAC 60.668 45.833 9.47 0.00 0.00 3.18
2525 2737 4.453819 GTCAGCTGCTTGTAAGATTCAACT 59.546 41.667 9.47 0.00 0.00 3.16
2526 2738 5.639506 GTCAGCTGCTTGTAAGATTCAACTA 59.360 40.000 9.47 0.00 0.00 2.24
2527 2739 5.639506 TCAGCTGCTTGTAAGATTCAACTAC 59.360 40.000 9.47 0.00 0.00 2.73
2528 2740 4.627467 AGCTGCTTGTAAGATTCAACTACG 59.373 41.667 0.00 0.00 0.00 3.51
2529 2741 4.625742 GCTGCTTGTAAGATTCAACTACGA 59.374 41.667 0.00 0.00 0.00 3.43
2530 2742 5.220303 GCTGCTTGTAAGATTCAACTACGAG 60.220 44.000 0.00 0.00 0.00 4.18
2531 2743 5.779922 TGCTTGTAAGATTCAACTACGAGT 58.220 37.500 0.00 0.00 0.00 4.18
2532 2744 6.220930 TGCTTGTAAGATTCAACTACGAGTT 58.779 36.000 0.00 0.00 39.39 3.01
2533 2745 6.704493 TGCTTGTAAGATTCAACTACGAGTTT 59.296 34.615 0.00 0.00 36.03 2.66
2534 2746 7.010023 GCTTGTAAGATTCAACTACGAGTTTG 58.990 38.462 0.00 0.00 36.03 2.93
2535 2747 7.095774 GCTTGTAAGATTCAACTACGAGTTTGA 60.096 37.037 0.00 0.00 36.03 2.69
2536 2748 8.827177 TTGTAAGATTCAACTACGAGTTTGAT 57.173 30.769 0.00 0.00 36.03 2.57
2537 2749 8.239681 TGTAAGATTCAACTACGAGTTTGATG 57.760 34.615 0.00 0.00 36.03 3.07
2538 2750 8.085909 TGTAAGATTCAACTACGAGTTTGATGA 58.914 33.333 0.00 0.00 36.03 2.92
2539 2751 7.962964 AAGATTCAACTACGAGTTTGATGAA 57.037 32.000 0.00 0.00 36.03 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.316308 TCTTTTTCTTCACCTGAGCAAGC 59.684 43.478 0.00 0.00 0.00 4.01
36 37 4.818546 TCTCTTTTTCTTCACCTGAGCAAG 59.181 41.667 0.00 0.00 0.00 4.01
62 63 0.480252 CCATCTTCCCATCCCTTCCC 59.520 60.000 0.00 0.00 0.00 3.97
126 127 4.720649 TGAGAGTAGTATGTCACAAGGC 57.279 45.455 0.00 0.00 0.00 4.35
146 147 2.787473 TGTATTCCACCCAGCTCTTG 57.213 50.000 0.00 0.00 0.00 3.02
161 162 2.132303 TAGGCCCATCACCCATGTAT 57.868 50.000 0.00 0.00 0.00 2.29
162 163 1.774254 CTTAGGCCCATCACCCATGTA 59.226 52.381 0.00 0.00 0.00 2.29
164 165 0.846015 TCTTAGGCCCATCACCCATG 59.154 55.000 0.00 0.00 0.00 3.66
165 166 1.607225 TTCTTAGGCCCATCACCCAT 58.393 50.000 0.00 0.00 0.00 4.00
166 167 1.215173 CATTCTTAGGCCCATCACCCA 59.785 52.381 0.00 0.00 0.00 4.51
167 168 1.494721 TCATTCTTAGGCCCATCACCC 59.505 52.381 0.00 0.00 0.00 4.61
168 169 3.297134 TTCATTCTTAGGCCCATCACC 57.703 47.619 0.00 0.00 0.00 4.02
169 170 3.065371 CGTTTCATTCTTAGGCCCATCAC 59.935 47.826 0.00 0.00 0.00 3.06
170 171 3.278574 CGTTTCATTCTTAGGCCCATCA 58.721 45.455 0.00 0.00 0.00 3.07
171 172 2.033424 GCGTTTCATTCTTAGGCCCATC 59.967 50.000 0.00 0.00 0.00 3.51
193 194 6.038356 CACAAGACAGCATCAAAACTTCTTT 58.962 36.000 0.00 0.00 0.00 2.52
194 195 5.126061 ACACAAGACAGCATCAAAACTTCTT 59.874 36.000 0.00 0.00 0.00 2.52
195 196 4.641989 ACACAAGACAGCATCAAAACTTCT 59.358 37.500 0.00 0.00 0.00 2.85
196 197 4.925068 ACACAAGACAGCATCAAAACTTC 58.075 39.130 0.00 0.00 0.00 3.01
197 198 4.989279 ACACAAGACAGCATCAAAACTT 57.011 36.364 0.00 0.00 0.00 2.66
213 214 6.177610 GTTGGATATGTCCTTCCTTACACAA 58.822 40.000 10.16 0.00 45.32 3.33
218 219 4.641868 AGGGTTGGATATGTCCTTCCTTA 58.358 43.478 10.16 0.00 45.32 2.69
222 223 4.455606 CAAGAGGGTTGGATATGTCCTTC 58.544 47.826 10.16 2.90 45.32 3.46
243 244 0.462225 CACCGTACAACCACACACCA 60.462 55.000 0.00 0.00 0.00 4.17
244 245 1.778027 GCACCGTACAACCACACACC 61.778 60.000 0.00 0.00 0.00 4.16
252 255 0.872881 ATATCGCCGCACCGTACAAC 60.873 55.000 0.00 0.00 0.00 3.32
320 323 7.104939 CCCATGTAAACAATGAATTGAATGGT 58.895 34.615 9.94 0.00 40.14 3.55
495 498 5.790593 CCTACAGTTTACAACAGCCTCTTA 58.209 41.667 0.00 0.00 0.00 2.10
535 542 8.325787 ACCATACACAGTACCAAAAGAATCATA 58.674 33.333 0.00 0.00 0.00 2.15
537 544 6.539173 ACCATACACAGTACCAAAAGAATCA 58.461 36.000 0.00 0.00 0.00 2.57
551 558 6.479990 CAGTTCACACCATATACCATACACAG 59.520 42.308 0.00 0.00 0.00 3.66
564 571 3.817084 CTGAATCACACAGTTCACACCAT 59.183 43.478 0.00 0.00 31.55 3.55
565 572 3.205338 CTGAATCACACAGTTCACACCA 58.795 45.455 0.00 0.00 31.55 4.17
614 621 9.847706 GGAAAACAAAAATTTACACAAACCATT 57.152 25.926 0.00 0.00 0.00 3.16
716 724 6.094719 TCAGAACACATTGAATGCAAATAGC 58.905 36.000 4.84 0.00 45.96 2.97
717 725 7.971722 TGATCAGAACACATTGAATGCAAATAG 59.028 33.333 4.84 0.00 37.59 1.73
718 726 7.828712 TGATCAGAACACATTGAATGCAAATA 58.171 30.769 4.84 0.00 37.59 1.40
719 727 6.693466 TGATCAGAACACATTGAATGCAAAT 58.307 32.000 4.84 0.00 37.59 2.32
720 728 6.086785 TGATCAGAACACATTGAATGCAAA 57.913 33.333 4.84 0.00 37.59 3.68
721 729 5.242171 ACTGATCAGAACACATTGAATGCAA 59.758 36.000 29.27 0.00 38.60 4.08
722 730 4.763279 ACTGATCAGAACACATTGAATGCA 59.237 37.500 29.27 0.00 0.00 3.96
729 737 8.849168 TCAACAAATAACTGATCAGAACACATT 58.151 29.630 29.27 13.73 0.00 2.71
755 763 4.447724 CGCACGTATCAGCCAAACTATTAT 59.552 41.667 0.00 0.00 0.00 1.28
756 764 3.799963 CGCACGTATCAGCCAAACTATTA 59.200 43.478 0.00 0.00 0.00 0.98
794 805 1.066858 CACGCTGGTACCTCAACATCT 60.067 52.381 14.36 0.00 0.00 2.90
795 806 1.359848 CACGCTGGTACCTCAACATC 58.640 55.000 14.36 0.00 0.00 3.06
813 824 3.890756 ACAAACATGGTGATCTCTTTGCA 59.109 39.130 5.73 0.00 0.00 4.08
817 828 7.451255 TGGATTAAACAAACATGGTGATCTCTT 59.549 33.333 5.73 0.00 0.00 2.85
818 829 6.947733 TGGATTAAACAAACATGGTGATCTCT 59.052 34.615 5.73 0.00 0.00 3.10
825 836 6.071391 GGATGAGTGGATTAAACAAACATGGT 60.071 38.462 0.00 0.00 0.00 3.55
865 876 0.108615 CACGCTGGTACCTCCAAGAG 60.109 60.000 14.36 6.31 46.59 2.85
866 877 1.972198 CACGCTGGTACCTCCAAGA 59.028 57.895 14.36 0.00 46.59 3.02
867 878 1.741770 GCACGCTGGTACCTCCAAG 60.742 63.158 14.36 2.77 46.59 3.61
868 879 2.046009 TTGCACGCTGGTACCTCCAA 62.046 55.000 14.36 4.66 46.59 3.53
869 880 2.046009 TTTGCACGCTGGTACCTCCA 62.046 55.000 14.36 0.00 45.01 3.86
870 881 1.298859 CTTTGCACGCTGGTACCTCC 61.299 60.000 14.36 2.81 0.00 4.30
871 882 0.320421 TCTTTGCACGCTGGTACCTC 60.320 55.000 14.36 4.04 0.00 3.85
872 883 0.320771 CTCTTTGCACGCTGGTACCT 60.321 55.000 14.36 0.00 0.00 3.08
873 884 0.320421 TCTCTTTGCACGCTGGTACC 60.320 55.000 4.43 4.43 0.00 3.34
874 885 1.661112 GATCTCTTTGCACGCTGGTAC 59.339 52.381 0.00 0.00 0.00 3.34
875 886 1.275010 TGATCTCTTTGCACGCTGGTA 59.725 47.619 0.00 0.00 0.00 3.25
876 887 0.035317 TGATCTCTTTGCACGCTGGT 59.965 50.000 0.00 0.00 0.00 4.00
877 888 0.445436 GTGATCTCTTTGCACGCTGG 59.555 55.000 0.00 0.00 0.00 4.85
878 889 0.445436 GGTGATCTCTTTGCACGCTG 59.555 55.000 0.00 0.00 33.48 5.18
879 890 0.035317 TGGTGATCTCTTTGCACGCT 59.965 50.000 0.00 0.00 33.48 5.07
880 891 1.089920 ATGGTGATCTCTTTGCACGC 58.910 50.000 0.00 0.00 33.48 5.34
881 892 2.079158 ACATGGTGATCTCTTTGCACG 58.921 47.619 0.00 0.00 33.48 5.34
882 893 4.232221 CAAACATGGTGATCTCTTTGCAC 58.768 43.478 0.00 0.00 0.00 4.57
883 894 3.890756 ACAAACATGGTGATCTCTTTGCA 59.109 39.130 5.73 0.00 0.00 4.08
884 895 4.510038 ACAAACATGGTGATCTCTTTGC 57.490 40.909 5.73 0.00 0.00 3.68
885 896 9.132521 GATTAAACAAACATGGTGATCTCTTTG 57.867 33.333 5.73 3.19 0.00 2.77
886 897 8.306761 GGATTAAACAAACATGGTGATCTCTTT 58.693 33.333 5.73 0.00 0.00 2.52
887 898 7.451255 TGGATTAAACAAACATGGTGATCTCTT 59.549 33.333 5.73 0.00 0.00 2.85
888 899 6.947733 TGGATTAAACAAACATGGTGATCTCT 59.052 34.615 5.73 0.00 0.00 3.10
889 900 7.029563 GTGGATTAAACAAACATGGTGATCTC 58.970 38.462 5.73 0.00 0.00 2.75
890 901 6.721208 AGTGGATTAAACAAACATGGTGATCT 59.279 34.615 5.73 0.00 0.00 2.75
891 902 6.924111 AGTGGATTAAACAAACATGGTGATC 58.076 36.000 5.73 0.00 0.00 2.92
892 903 6.493115 TGAGTGGATTAAACAAACATGGTGAT 59.507 34.615 5.73 0.00 0.00 3.06
893 904 5.830457 TGAGTGGATTAAACAAACATGGTGA 59.170 36.000 5.73 0.00 0.00 4.02
894 905 6.083098 TGAGTGGATTAAACAAACATGGTG 57.917 37.500 0.00 0.00 0.00 4.17
895 906 6.071391 GGATGAGTGGATTAAACAAACATGGT 60.071 38.462 0.00 0.00 0.00 3.55
896 907 6.071447 TGGATGAGTGGATTAAACAAACATGG 60.071 38.462 0.00 0.00 0.00 3.66
897 908 6.923012 TGGATGAGTGGATTAAACAAACATG 58.077 36.000 0.00 0.00 0.00 3.21
898 909 7.722949 ATGGATGAGTGGATTAAACAAACAT 57.277 32.000 0.00 0.00 0.00 2.71
899 910 8.642935 TTATGGATGAGTGGATTAAACAAACA 57.357 30.769 0.00 0.00 0.00 2.83
902 913 8.912988 GGAATTATGGATGAGTGGATTAAACAA 58.087 33.333 0.00 0.00 0.00 2.83
903 914 8.058235 TGGAATTATGGATGAGTGGATTAAACA 58.942 33.333 0.00 0.00 0.00 2.83
904 915 8.463930 TGGAATTATGGATGAGTGGATTAAAC 57.536 34.615 0.00 0.00 0.00 2.01
908 919 8.057623 GGATATGGAATTATGGATGAGTGGATT 58.942 37.037 0.00 0.00 0.00 3.01
909 920 7.367186 GGGATATGGAATTATGGATGAGTGGAT 60.367 40.741 0.00 0.00 0.00 3.41
910 921 6.069440 GGGATATGGAATTATGGATGAGTGGA 60.069 42.308 0.00 0.00 0.00 4.02
911 922 6.069206 AGGGATATGGAATTATGGATGAGTGG 60.069 42.308 0.00 0.00 0.00 4.00
912 923 6.966751 AGGGATATGGAATTATGGATGAGTG 58.033 40.000 0.00 0.00 0.00 3.51
913 924 6.970640 AGAGGGATATGGAATTATGGATGAGT 59.029 38.462 0.00 0.00 0.00 3.41
914 925 7.448915 AGAGGGATATGGAATTATGGATGAG 57.551 40.000 0.00 0.00 0.00 2.90
915 926 7.312120 CCAAGAGGGATATGGAATTATGGATGA 60.312 40.741 0.00 0.00 40.01 2.92
916 927 6.832384 CCAAGAGGGATATGGAATTATGGATG 59.168 42.308 0.00 0.00 40.01 3.51
917 928 6.741922 TCCAAGAGGGATATGGAATTATGGAT 59.258 38.462 0.00 0.00 42.15 3.41
918 929 6.097753 TCCAAGAGGGATATGGAATTATGGA 58.902 40.000 0.00 0.00 42.15 3.41
919 930 6.392911 TCCAAGAGGGATATGGAATTATGG 57.607 41.667 0.00 0.00 42.15 2.74
964 975 1.070471 CAACACAATTTAGGCGGCGC 61.070 55.000 26.17 26.17 0.00 6.53
1060 1082 1.605712 GCTAGCGACCAACTGACTTGT 60.606 52.381 0.00 0.00 0.00 3.16
1111 1140 2.097825 AGATGTGTCCGTGTACCTACC 58.902 52.381 0.00 0.00 0.00 3.18
1119 1152 1.374125 TTGGCGAGATGTGTCCGTG 60.374 57.895 0.00 0.00 0.00 4.94
1132 1165 1.127571 CGAATTGCGATGTGTTGGCG 61.128 55.000 0.00 0.00 44.57 5.69
1142 1175 2.560861 GTTGCTGCCGAATTGCGA 59.439 55.556 0.00 0.00 44.57 5.10
1176 1217 2.768344 TCCTTCCCCATCGCCTCC 60.768 66.667 0.00 0.00 0.00 4.30
1525 1590 3.034878 CGATCAGTCGGAGGCGAT 58.965 61.111 0.00 0.00 44.00 4.58
1540 1605 3.411418 GAAGAGACGGGCGCATCGA 62.411 63.158 24.99 0.00 0.00 3.59
1625 1719 5.668535 ACCTCAGTAGACAGATACTCCTACT 59.331 44.000 0.00 0.00 41.57 2.57
1626 1720 5.932455 ACCTCAGTAGACAGATACTCCTAC 58.068 45.833 0.00 0.00 33.68 3.18
1628 1722 5.442391 GAACCTCAGTAGACAGATACTCCT 58.558 45.833 0.00 0.00 33.68 3.69
1629 1723 4.581409 GGAACCTCAGTAGACAGATACTCC 59.419 50.000 0.00 0.00 33.68 3.85
1630 1724 5.298276 CAGGAACCTCAGTAGACAGATACTC 59.702 48.000 0.00 0.00 33.68 2.59
1631 1725 5.197451 CAGGAACCTCAGTAGACAGATACT 58.803 45.833 0.00 0.00 36.41 2.12
1632 1726 4.339814 CCAGGAACCTCAGTAGACAGATAC 59.660 50.000 0.00 0.00 0.00 2.24
1633 1727 4.017407 ACCAGGAACCTCAGTAGACAGATA 60.017 45.833 0.00 0.00 0.00 1.98
1634 1728 3.245803 ACCAGGAACCTCAGTAGACAGAT 60.246 47.826 0.00 0.00 0.00 2.90
1635 1729 2.110188 ACCAGGAACCTCAGTAGACAGA 59.890 50.000 0.00 0.00 0.00 3.41
1636 1730 2.494073 GACCAGGAACCTCAGTAGACAG 59.506 54.545 0.00 0.00 0.00 3.51
1657 1751 2.293677 TGCGCAGGAAGTACACATAG 57.706 50.000 5.66 0.00 0.00 2.23
1669 1763 3.544834 CGTAGAGAAATGAAATGCGCAGG 60.545 47.826 18.32 0.00 0.00 4.85
1677 1771 3.306917 TCCGTGCGTAGAGAAATGAAA 57.693 42.857 0.00 0.00 0.00 2.69
1678 1772 3.306917 TTCCGTGCGTAGAGAAATGAA 57.693 42.857 0.00 0.00 0.00 2.57
1679 1773 3.306917 TTTCCGTGCGTAGAGAAATGA 57.693 42.857 0.00 0.00 0.00 2.57
1680 1774 4.398549 TTTTTCCGTGCGTAGAGAAATG 57.601 40.909 0.00 0.00 0.00 2.32
1681 1775 5.873164 AGTATTTTTCCGTGCGTAGAGAAAT 59.127 36.000 0.00 4.40 33.09 2.17
1707 1801 4.286032 AGAGGCAAAGACACATGGTAGTAA 59.714 41.667 0.00 0.00 0.00 2.24
1709 1803 2.639839 AGAGGCAAAGACACATGGTAGT 59.360 45.455 0.00 0.00 0.00 2.73
1773 1965 0.109723 TGTGTTAGAACTGCCCCCAC 59.890 55.000 0.00 0.00 0.00 4.61
1878 2071 7.286775 GGATTCTTGTGAGGTTCTATCTACTCT 59.713 40.741 0.00 0.00 0.00 3.24
1879 2072 7.430441 GGATTCTTGTGAGGTTCTATCTACTC 58.570 42.308 0.00 0.00 0.00 2.59
1963 2166 3.525268 TCATACATCAGATGCGTGTGT 57.475 42.857 10.59 0.00 0.00 3.72
1981 2184 3.769739 ACAGACTACAGCCAAACATCA 57.230 42.857 0.00 0.00 0.00 3.07
1982 2185 4.865365 GTCTACAGACTACAGCCAAACATC 59.135 45.833 2.03 0.00 41.65 3.06
1986 2189 3.236047 TGGTCTACAGACTACAGCCAAA 58.764 45.455 9.15 0.00 44.20 3.28
1997 2200 1.904771 CCGGGCAATGGTCTACAGA 59.095 57.895 0.00 0.00 0.00 3.41
2087 2290 1.874019 CCGCAGTTCTCATCGACGG 60.874 63.158 0.00 0.00 0.00 4.79
2104 2307 3.901222 CCCTCTCTCCCTCTTCTATTTCC 59.099 52.174 0.00 0.00 0.00 3.13
2185 2397 1.076485 CCATGCTTCCTCCAAGGGG 60.076 63.158 0.00 0.00 35.59 4.79
2278 2490 2.357517 GACGTGGTGCAGACTGGG 60.358 66.667 4.26 0.00 0.00 4.45
2300 2512 0.439985 CGCTGAACTGAATCGTGGTG 59.560 55.000 0.00 0.00 0.00 4.17
2349 2561 3.200605 TGCCTTCTTCCTCTGCATTGATA 59.799 43.478 0.00 0.00 0.00 2.15
2350 2562 2.025605 TGCCTTCTTCCTCTGCATTGAT 60.026 45.455 0.00 0.00 0.00 2.57
2351 2563 1.352017 TGCCTTCTTCCTCTGCATTGA 59.648 47.619 0.00 0.00 0.00 2.57
2477 2689 3.578272 TGGTGCGTGCGGTTTGTC 61.578 61.111 0.00 0.00 0.00 3.18
2479 2691 4.622456 GGTGGTGCGTGCGGTTTG 62.622 66.667 0.00 0.00 0.00 2.93
2498 2710 1.959899 CTTACAAGCAGCTGACGCGG 61.960 60.000 20.43 3.76 42.32 6.46
2499 2711 1.008875 TCTTACAAGCAGCTGACGCG 61.009 55.000 20.43 3.53 42.32 6.01
2500 2712 1.363744 ATCTTACAAGCAGCTGACGC 58.636 50.000 20.43 1.09 0.00 5.19
2501 2713 2.995939 TGAATCTTACAAGCAGCTGACG 59.004 45.455 20.43 6.92 0.00 4.35
2502 2714 4.453819 AGTTGAATCTTACAAGCAGCTGAC 59.546 41.667 20.43 9.11 0.00 3.51
2503 2715 4.645535 AGTTGAATCTTACAAGCAGCTGA 58.354 39.130 20.43 0.00 0.00 4.26
2504 2716 5.445142 CGTAGTTGAATCTTACAAGCAGCTG 60.445 44.000 10.11 10.11 0.00 4.24
2505 2717 4.627467 CGTAGTTGAATCTTACAAGCAGCT 59.373 41.667 0.00 0.00 0.00 4.24
2506 2718 4.625742 TCGTAGTTGAATCTTACAAGCAGC 59.374 41.667 0.00 0.00 0.00 5.25
2507 2719 5.864474 ACTCGTAGTTGAATCTTACAAGCAG 59.136 40.000 0.00 0.00 0.00 4.24
2508 2720 5.779922 ACTCGTAGTTGAATCTTACAAGCA 58.220 37.500 0.00 0.00 0.00 3.91
2509 2721 6.707599 AACTCGTAGTTGAATCTTACAAGC 57.292 37.500 0.35 0.00 37.00 4.01
2510 2722 8.294341 TCAAACTCGTAGTTGAATCTTACAAG 57.706 34.615 1.80 0.00 38.66 3.16
2511 2723 8.708742 CATCAAACTCGTAGTTGAATCTTACAA 58.291 33.333 1.80 0.00 38.66 2.41
2512 2724 8.085909 TCATCAAACTCGTAGTTGAATCTTACA 58.914 33.333 1.80 0.00 38.66 2.41
2513 2725 8.462143 TCATCAAACTCGTAGTTGAATCTTAC 57.538 34.615 1.80 0.00 38.66 2.34
2515 2727 7.962964 TTCATCAAACTCGTAGTTGAATCTT 57.037 32.000 1.80 0.00 38.66 2.40


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

AutoCloner maintained by Alex Coulton.