Multiple sequence alignment - TraesCS1B01G183900

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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 TraesCS1B01G183900 chr1B 100.000 2565 0 0 1 2565 330511345 330508781 0.000000e+00 4737.0
1 TraesCS1B01G183900 chr1D 95.329 942 21 4 1645 2565 247298919 247299858 0.000000e+00 1474.0
2 TraesCS1B01G183900 chr1D 94.751 762 39 1 1 761 478398057 478398818 0.000000e+00 1184.0
3 TraesCS1B01G183900 chr1D 88.000 750 71 11 922 1653 247294006 247294754 0.000000e+00 869.0
4 TraesCS1B01G183900 chr1D 96.528 144 4 1 759 902 320973634 320973492 1.190000e-58 237.0
5 TraesCS1B01G183900 chr5B 94.868 760 38 1 1 759 243413889 243414648 0.000000e+00 1186.0
6 TraesCS1B01G183900 chr5B 93.832 762 45 2 1 761 137838686 137837926 0.000000e+00 1146.0
7 TraesCS1B01G183900 chr5B 95.172 145 6 1 759 903 82463913 82464056 7.140000e-56 228.0
8 TraesCS1B01G183900 chr3D 94.730 759 39 1 1 758 41421712 41422470 0.000000e+00 1179.0
9 TraesCS1B01G183900 chr2B 93.848 764 45 2 1 762 36788454 36789217 0.000000e+00 1149.0
10 TraesCS1B01G183900 chr2B 93.824 761 45 2 1 759 89463387 89464147 0.000000e+00 1144.0
11 TraesCS1B01G183900 chr2B 93.816 760 46 1 1 759 754884439 754885198 0.000000e+00 1142.0
12 TraesCS1B01G183900 chr2B 93.586 764 47 2 1 763 7472775 7472013 0.000000e+00 1138.0
13 TraesCS1B01G183900 chr7B 93.808 759 46 1 1 758 531806648 531805890 0.000000e+00 1140.0
14 TraesCS1B01G183900 chr1A 98.200 500 7 2 2066 2565 300111504 300111007 0.000000e+00 872.0
15 TraesCS1B01G183900 chr1A 88.007 567 62 3 997 1558 300116712 300116147 0.000000e+00 665.0
16 TraesCS1B01G183900 chr1A 84.815 270 25 6 1554 1808 300111960 300111692 9.110000e-65 257.0
17 TraesCS1B01G183900 chr1A 88.718 195 3 4 1860 2035 300111699 300111505 1.190000e-53 220.0
18 TraesCS1B01G183900 chr1A 82.787 244 37 2 996 1234 300117013 300116770 2.000000e-51 213.0
19 TraesCS1B01G183900 chr4B 88.889 702 68 7 973 1666 603166197 603166896 0.000000e+00 856.0
20 TraesCS1B01G183900 chr4D 90.344 611 54 3 973 1578 477577467 477578077 0.000000e+00 797.0
21 TraesCS1B01G183900 chr4D 86.022 93 10 2 1659 1751 477578156 477578245 2.100000e-16 97.1
22 TraesCS1B01G183900 chr4A 87.607 702 67 9 968 1663 684503120 684503807 0.000000e+00 797.0
23 TraesCS1B01G183900 chr4A 87.234 94 9 1 1658 1751 684503842 684503932 1.260000e-18 104.0
24 TraesCS1B01G183900 chr6B 88.982 599 61 3 973 1566 15928413 15927815 0.000000e+00 736.0
25 TraesCS1B01G183900 chr6B 95.862 145 6 0 759 903 183044569 183044713 4.270000e-58 235.0
26 TraesCS1B01G183900 chr6D 87.722 619 63 6 988 1601 8743573 8742963 0.000000e+00 710.0
27 TraesCS1B01G183900 chr6D 77.990 209 31 7 1658 1865 8757844 8757650 1.610000e-22 117.0
28 TraesCS1B01G183900 chrUn 87.954 606 60 6 1001 1601 357590841 357590244 0.000000e+00 702.0
29 TraesCS1B01G183900 chrUn 87.789 606 61 6 1001 1601 461056157 461056754 0.000000e+00 697.0
30 TraesCS1B01G183900 chr3B 95.862 145 5 1 759 902 690108752 690108608 1.530000e-57 233.0
31 TraesCS1B01G183900 chr2D 95.172 145 7 0 759 903 599938709 599938853 1.990000e-56 230.0
32 TraesCS1B01G183900 chr2D 95.139 144 6 1 759 902 53781185 53781327 2.570000e-55 226.0
33 TraesCS1B01G183900 chr5A 95.172 145 6 1 759 903 110380289 110380432 7.140000e-56 228.0
34 TraesCS1B01G183900 chr3A 95.172 145 5 2 759 902 221916005 221916148 7.140000e-56 228.0
35 TraesCS1B01G183900 chr3A 95.172 145 6 1 759 903 725496024 725496167 7.140000e-56 228.0
36 TraesCS1B01G183900 chr6A 82.464 211 23 6 1656 1865 9181998 9182195 3.390000e-39 172.0


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 TraesCS1B01G183900 chr1B 330508781 330511345 2564 True 4737.000000 4737 100.000000 1 2565 1 chr1B.!!$R1 2564
1 TraesCS1B01G183900 chr1D 247298919 247299858 939 False 1474.000000 1474 95.329000 1645 2565 1 chr1D.!!$F2 920
2 TraesCS1B01G183900 chr1D 478398057 478398818 761 False 1184.000000 1184 94.751000 1 761 1 chr1D.!!$F3 760
3 TraesCS1B01G183900 chr1D 247294006 247294754 748 False 869.000000 869 88.000000 922 1653 1 chr1D.!!$F1 731
4 TraesCS1B01G183900 chr5B 243413889 243414648 759 False 1186.000000 1186 94.868000 1 759 1 chr5B.!!$F2 758
5 TraesCS1B01G183900 chr5B 137837926 137838686 760 True 1146.000000 1146 93.832000 1 761 1 chr5B.!!$R1 760
6 TraesCS1B01G183900 chr3D 41421712 41422470 758 False 1179.000000 1179 94.730000 1 758 1 chr3D.!!$F1 757
7 TraesCS1B01G183900 chr2B 36788454 36789217 763 False 1149.000000 1149 93.848000 1 762 1 chr2B.!!$F1 761
8 TraesCS1B01G183900 chr2B 89463387 89464147 760 False 1144.000000 1144 93.824000 1 759 1 chr2B.!!$F2 758
9 TraesCS1B01G183900 chr2B 754884439 754885198 759 False 1142.000000 1142 93.816000 1 759 1 chr2B.!!$F3 758
10 TraesCS1B01G183900 chr2B 7472013 7472775 762 True 1138.000000 1138 93.586000 1 763 1 chr2B.!!$R1 762
11 TraesCS1B01G183900 chr7B 531805890 531806648 758 True 1140.000000 1140 93.808000 1 758 1 chr7B.!!$R1 757
12 TraesCS1B01G183900 chr1A 300111007 300111960 953 True 449.666667 872 90.577667 1554 2565 3 chr1A.!!$R1 1011
13 TraesCS1B01G183900 chr1A 300116147 300117013 866 True 439.000000 665 85.397000 996 1558 2 chr1A.!!$R2 562
14 TraesCS1B01G183900 chr4B 603166197 603166896 699 False 856.000000 856 88.889000 973 1666 1 chr4B.!!$F1 693
15 TraesCS1B01G183900 chr4D 477577467 477578245 778 False 447.050000 797 88.183000 973 1751 2 chr4D.!!$F1 778
16 TraesCS1B01G183900 chr4A 684503120 684503932 812 False 450.500000 797 87.420500 968 1751 2 chr4A.!!$F1 783
17 TraesCS1B01G183900 chr6B 15927815 15928413 598 True 736.000000 736 88.982000 973 1566 1 chr6B.!!$R1 593
18 TraesCS1B01G183900 chr6D 8742963 8743573 610 True 710.000000 710 87.722000 988 1601 1 chr6D.!!$R1 613
19 TraesCS1B01G183900 chrUn 357590244 357590841 597 True 702.000000 702 87.954000 1001 1601 1 chrUn.!!$R1 600
20 TraesCS1B01G183900 chrUn 461056157 461056754 597 False 697.000000 697 87.789000 1001 1601 1 chrUn.!!$F1 600

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
166 167 0.392706 ATCAGATGACGGCGGCATTA 59.607 50.0 31.2 18.57 0.00 1.90 F
1122 1138 0.036875 GTGCAAGTGGCTACCTTCCT 59.963 55.0 0.0 0.00 45.15 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1141 0.250467 GCTCTTCTCACAGTTGCCCA 60.250 55.000 0.0 0.0 0.0 5.36 R
2503 2645 2.703536 TGCTCCAACCTTTCTGTACTCA 59.296 45.455 0.0 0.0 0.0 3.41 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
38 39 2.035237 TTGGTCTTCGGTCGTTGGCT 62.035 55.000 0.00 0.00 0.00 4.75
54 55 2.981302 CTGGAGCCGGTGATGACA 59.019 61.111 1.90 0.00 0.00 3.58
55 56 1.524002 CTGGAGCCGGTGATGACAT 59.476 57.895 1.90 0.00 0.00 3.06
60 61 2.045708 GCCGGTGATGACATTGCCA 61.046 57.895 1.90 0.00 0.00 4.92
166 167 0.392706 ATCAGATGACGGCGGCATTA 59.607 50.000 31.20 18.57 0.00 1.90
271 272 5.291128 AGCGGTGTTTCTTTCTACATATTCG 59.709 40.000 0.00 0.00 0.00 3.34
273 274 6.401796 GCGGTGTTTCTTTCTACATATTCGTT 60.402 38.462 0.00 0.00 0.00 3.85
360 361 2.282251 AGGTCGACGCTGTCTGGA 60.282 61.111 9.92 0.00 0.00 3.86
488 489 2.031012 CTGGTTGAGGAGCACGCA 59.969 61.111 0.00 0.00 0.00 5.24
583 584 2.093128 AGGTCTGTTTGGTATTAGGCCG 60.093 50.000 0.00 0.00 39.84 6.13
680 682 8.185506 TCTGTTGTATGACTTTGTAAGGTCTA 57.814 34.615 8.11 0.00 34.01 2.59
739 742 2.525877 GCAGAGGCCGGGGGTATA 60.526 66.667 2.18 0.00 0.00 1.47
779 782 7.769272 AAAATCACCAAACTTTACACATGTG 57.231 32.000 24.25 24.25 0.00 3.21
780 783 6.463995 AATCACCAAACTTTACACATGTGT 57.536 33.333 32.47 32.47 46.87 3.72
781 784 7.575414 AATCACCAAACTTTACACATGTGTA 57.425 32.000 30.31 30.31 44.42 2.90
802 805 9.801873 TGTGTAATATACATCCATATGATCACG 57.198 33.333 3.65 0.00 41.34 4.35
803 806 9.803315 GTGTAATATACATCCATATGATCACGT 57.197 33.333 3.65 0.00 41.34 4.49
811 814 8.908786 ACATCCATATGATCACGTAGAATTTT 57.091 30.769 3.65 0.00 36.54 1.82
812 815 9.342308 ACATCCATATGATCACGTAGAATTTTT 57.658 29.630 3.65 0.00 36.54 1.94
852 855 9.883142 TGAAACCTTAAATGTGATTTTCAAAGT 57.117 25.926 0.00 0.00 33.82 2.66
881 884 6.753107 AAATAAAGTCCTTCAATACACCCG 57.247 37.500 0.00 0.00 0.00 5.28
882 885 3.782656 AAAGTCCTTCAATACACCCGT 57.217 42.857 0.00 0.00 0.00 5.28
883 886 2.762535 AGTCCTTCAATACACCCGTG 57.237 50.000 0.00 0.00 0.00 4.94
884 887 1.975680 AGTCCTTCAATACACCCGTGT 59.024 47.619 5.69 5.69 46.87 4.49
885 888 2.370849 AGTCCTTCAATACACCCGTGTT 59.629 45.455 5.69 0.00 41.83 3.32
886 889 2.740447 GTCCTTCAATACACCCGTGTTC 59.260 50.000 5.69 0.00 41.83 3.18
887 890 2.081462 CCTTCAATACACCCGTGTTCC 58.919 52.381 5.69 0.00 41.83 3.62
888 891 2.551287 CCTTCAATACACCCGTGTTCCA 60.551 50.000 5.69 0.00 41.83 3.53
889 892 2.932855 TCAATACACCCGTGTTCCAA 57.067 45.000 5.69 0.00 41.83 3.53
890 893 3.210232 TCAATACACCCGTGTTCCAAA 57.790 42.857 5.69 0.00 41.83 3.28
891 894 3.552875 TCAATACACCCGTGTTCCAAAA 58.447 40.909 5.69 0.00 41.83 2.44
892 895 3.952323 TCAATACACCCGTGTTCCAAAAA 59.048 39.130 5.69 0.00 41.83 1.94
893 896 4.585162 TCAATACACCCGTGTTCCAAAAAT 59.415 37.500 5.69 0.00 41.83 1.82
894 897 4.776795 ATACACCCGTGTTCCAAAAATC 57.223 40.909 5.69 0.00 41.83 2.17
895 898 1.684450 ACACCCGTGTTCCAAAAATCC 59.316 47.619 0.00 0.00 41.83 3.01
896 899 1.683917 CACCCGTGTTCCAAAAATCCA 59.316 47.619 0.00 0.00 0.00 3.41
897 900 1.684450 ACCCGTGTTCCAAAAATCCAC 59.316 47.619 0.00 0.00 0.00 4.02
898 901 1.960689 CCCGTGTTCCAAAAATCCACT 59.039 47.619 0.00 0.00 0.00 4.00
899 902 2.030274 CCCGTGTTCCAAAAATCCACTC 60.030 50.000 0.00 0.00 0.00 3.51
900 903 2.884639 CCGTGTTCCAAAAATCCACTCT 59.115 45.455 0.00 0.00 0.00 3.24
901 904 3.058224 CCGTGTTCCAAAAATCCACTCTC 60.058 47.826 0.00 0.00 0.00 3.20
902 905 3.363970 CGTGTTCCAAAAATCCACTCTCG 60.364 47.826 0.00 0.00 0.00 4.04
903 906 2.552315 TGTTCCAAAAATCCACTCTCGC 59.448 45.455 0.00 0.00 0.00 5.03
904 907 1.821216 TCCAAAAATCCACTCTCGCC 58.179 50.000 0.00 0.00 0.00 5.54
905 908 0.811281 CCAAAAATCCACTCTCGCCC 59.189 55.000 0.00 0.00 0.00 6.13
906 909 1.614317 CCAAAAATCCACTCTCGCCCT 60.614 52.381 0.00 0.00 0.00 5.19
907 910 1.470098 CAAAAATCCACTCTCGCCCTG 59.530 52.381 0.00 0.00 0.00 4.45
908 911 0.678048 AAAATCCACTCTCGCCCTGC 60.678 55.000 0.00 0.00 0.00 4.85
909 912 1.841302 AAATCCACTCTCGCCCTGCA 61.841 55.000 0.00 0.00 0.00 4.41
910 913 2.249413 AATCCACTCTCGCCCTGCAG 62.249 60.000 6.78 6.78 0.00 4.41
912 915 4.079850 CACTCTCGCCCTGCAGCT 62.080 66.667 8.66 0.00 0.00 4.24
913 916 3.768922 ACTCTCGCCCTGCAGCTC 61.769 66.667 8.66 0.30 0.00 4.09
914 917 3.459965 CTCTCGCCCTGCAGCTCT 61.460 66.667 8.66 0.00 0.00 4.09
915 918 3.429080 CTCTCGCCCTGCAGCTCTC 62.429 68.421 8.66 0.00 0.00 3.20
916 919 3.459965 CTCGCCCTGCAGCTCTCT 61.460 66.667 8.66 0.00 0.00 3.10
917 920 3.429080 CTCGCCCTGCAGCTCTCTC 62.429 68.421 8.66 0.00 0.00 3.20
918 921 3.767806 CGCCCTGCAGCTCTCTCA 61.768 66.667 8.66 0.00 0.00 3.27
919 922 2.187424 GCCCTGCAGCTCTCTCAG 59.813 66.667 8.66 0.00 0.00 3.35
920 923 2.901813 CCCTGCAGCTCTCTCAGG 59.098 66.667 8.66 11.81 45.24 3.86
957 961 2.456577 ACAAGAGGCAAACAAACCAGT 58.543 42.857 0.00 0.00 0.00 4.00
962 966 1.681264 AGGCAAACAAACCAGTGTAGC 59.319 47.619 0.00 0.00 33.97 3.58
968 972 1.949525 ACAAACCAGTGTAGCAGCAAG 59.050 47.619 0.00 0.00 0.00 4.01
969 973 2.221169 CAAACCAGTGTAGCAGCAAGA 58.779 47.619 0.00 0.00 0.00 3.02
992 1008 4.513318 AGCTACAGTTCAAGAGTTTTCAGC 59.487 41.667 0.00 0.00 0.00 4.26
994 1010 5.220854 GCTACAGTTCAAGAGTTTTCAGCAA 60.221 40.000 0.00 0.00 0.00 3.91
1011 1027 1.209128 CAACTAAGATGGCTACCGCG 58.791 55.000 0.00 0.00 36.88 6.46
1063 1079 4.704103 TGGCGCTCTCCACCTCCT 62.704 66.667 7.64 0.00 0.00 3.69
1080 1096 2.363680 CTCCTACATCGCATCCTCACTT 59.636 50.000 0.00 0.00 0.00 3.16
1122 1138 0.036875 GTGCAAGTGGCTACCTTCCT 59.963 55.000 0.00 0.00 45.15 3.36
1124 1140 1.308783 GCAAGTGGCTACCTTCCTGC 61.309 60.000 0.00 0.00 40.25 4.85
1125 1141 0.326264 CAAGTGGCTACCTTCCTGCT 59.674 55.000 0.00 0.00 0.00 4.24
1158 1179 0.250513 AAGAGCAATGACCCGGACTC 59.749 55.000 0.73 0.00 0.00 3.36
1201 1222 3.805928 CAGTACCACTGCTCCCCA 58.194 61.111 0.00 0.00 39.62 4.96
1358 1379 1.530419 AAGAACATGGCCCGTTGCA 60.530 52.632 12.10 0.00 43.89 4.08
1380 1401 3.517100 AGGCACTGTATCAAGATCACTGT 59.483 43.478 0.00 0.00 37.18 3.55
1427 1448 2.596338 TGGACGAGTGCGACTCCA 60.596 61.111 9.71 0.00 42.12 3.86
1469 1490 1.273048 ACAACTACGAACCGCCATGTA 59.727 47.619 0.00 0.00 0.00 2.29
1632 1657 2.030958 GTACCACTTTGCCGGTCGG 61.031 63.158 1.90 4.85 36.69 4.79
1736 1798 1.629013 TAGCACGCATGAGAAGTTCG 58.371 50.000 2.50 0.00 0.00 3.95
1765 1827 7.339732 CGTGACCTTCAAGCATATAATAGTC 57.660 40.000 0.00 0.00 0.00 2.59
1807 1927 9.442047 AAAGAATTTGGAAACACAAAACATACA 57.558 25.926 0.00 0.00 42.91 2.29
1808 1928 9.442047 AAGAATTTGGAAACACAAAACATACAA 57.558 25.926 0.00 0.00 42.91 2.41
1809 1929 9.097257 AGAATTTGGAAACACAAAACATACAAG 57.903 29.630 0.00 0.00 42.91 3.16
1810 1930 9.092876 GAATTTGGAAACACAAAACATACAAGA 57.907 29.630 0.00 0.00 42.91 3.02
1811 1931 9.442047 AATTTGGAAACACAAAACATACAAGAA 57.558 25.926 0.00 0.00 42.91 2.52
1812 1932 8.472683 TTTGGAAACACAAAACATACAAGAAG 57.527 30.769 0.00 0.00 42.67 2.85
1813 1933 6.039616 TGGAAACACAAAACATACAAGAAGC 58.960 36.000 0.00 0.00 33.40 3.86
1814 1934 6.127479 TGGAAACACAAAACATACAAGAAGCT 60.127 34.615 0.00 0.00 33.40 3.74
1815 1935 6.756542 GGAAACACAAAACATACAAGAAGCTT 59.243 34.615 0.00 0.00 0.00 3.74
1816 1936 7.254084 GGAAACACAAAACATACAAGAAGCTTG 60.254 37.037 2.10 5.67 0.00 4.01
1817 1937 6.449635 ACACAAAACATACAAGAAGCTTGA 57.550 33.333 2.10 0.00 0.00 3.02
1818 1938 6.498304 ACACAAAACATACAAGAAGCTTGAG 58.502 36.000 2.10 0.00 0.00 3.02
1819 1939 6.318648 ACACAAAACATACAAGAAGCTTGAGA 59.681 34.615 2.10 2.30 0.00 3.27
1820 1940 7.148086 ACACAAAACATACAAGAAGCTTGAGAA 60.148 33.333 2.10 0.29 0.00 2.87
1821 1941 7.701924 CACAAAACATACAAGAAGCTTGAGAAA 59.298 33.333 2.10 0.00 0.00 2.52
1822 1942 7.917505 ACAAAACATACAAGAAGCTTGAGAAAG 59.082 33.333 2.10 0.00 0.00 2.62
1823 1943 5.619625 ACATACAAGAAGCTTGAGAAAGC 57.380 39.130 2.10 2.21 45.81 3.51
1833 1953 3.866651 GCTTGAGAAAGCTGTAGGATCA 58.133 45.455 3.24 0.00 42.32 2.92
1834 1954 4.450053 GCTTGAGAAAGCTGTAGGATCAT 58.550 43.478 3.24 0.00 42.32 2.45
1835 1955 4.880696 GCTTGAGAAAGCTGTAGGATCATT 59.119 41.667 3.24 0.00 42.32 2.57
1836 1956 5.356470 GCTTGAGAAAGCTGTAGGATCATTT 59.644 40.000 3.24 0.00 42.32 2.32
1837 1957 6.458070 GCTTGAGAAAGCTGTAGGATCATTTC 60.458 42.308 3.24 0.00 42.32 2.17
1838 1958 5.431765 TGAGAAAGCTGTAGGATCATTTCC 58.568 41.667 0.00 0.00 45.85 3.13
1848 1968 2.954792 GGATCATTTCCAAGGGATGCT 58.045 47.619 0.00 0.00 44.74 3.79
1849 1969 2.626743 GGATCATTTCCAAGGGATGCTG 59.373 50.000 0.00 0.00 44.74 4.41
1850 1970 3.559069 GATCATTTCCAAGGGATGCTGA 58.441 45.455 0.00 0.00 0.00 4.26
1851 1971 3.454719 TCATTTCCAAGGGATGCTGAA 57.545 42.857 0.00 0.00 0.00 3.02
1852 1972 3.091545 TCATTTCCAAGGGATGCTGAAC 58.908 45.455 0.00 0.00 0.00 3.18
1853 1973 2.673775 TTTCCAAGGGATGCTGAACA 57.326 45.000 0.00 0.00 0.00 3.18
1854 1974 2.673775 TTCCAAGGGATGCTGAACAA 57.326 45.000 0.00 0.00 0.00 2.83
1855 1975 2.205022 TCCAAGGGATGCTGAACAAG 57.795 50.000 0.00 0.00 0.00 3.16
1856 1976 1.425066 TCCAAGGGATGCTGAACAAGT 59.575 47.619 0.00 0.00 0.00 3.16
1857 1977 2.642311 TCCAAGGGATGCTGAACAAGTA 59.358 45.455 0.00 0.00 0.00 2.24
1858 1978 3.266772 TCCAAGGGATGCTGAACAAGTAT 59.733 43.478 0.00 0.00 33.31 2.12
1859 1979 4.473196 TCCAAGGGATGCTGAACAAGTATA 59.527 41.667 0.00 0.00 30.34 1.47
1860 1980 5.045213 TCCAAGGGATGCTGAACAAGTATAA 60.045 40.000 0.00 0.00 30.34 0.98
1861 1981 5.066505 CCAAGGGATGCTGAACAAGTATAAC 59.933 44.000 0.00 0.00 30.34 1.89
1862 1982 5.435686 AGGGATGCTGAACAAGTATAACA 57.564 39.130 0.00 0.00 30.34 2.41
1863 1983 5.815581 AGGGATGCTGAACAAGTATAACAA 58.184 37.500 0.00 0.00 30.34 2.83
1864 1984 6.245408 AGGGATGCTGAACAAGTATAACAAA 58.755 36.000 0.00 0.00 30.34 2.83
1906 2026 4.900054 AGGAGTAACTTAAGTGGTCACAGT 59.100 41.667 9.34 0.00 0.00 3.55
2051 2190 5.807011 GCAAAAGCATGAAGAAATTATCCGT 59.193 36.000 0.00 0.00 0.00 4.69
2146 2285 3.193263 CGAGAAATCAGCACATACAGCT 58.807 45.455 0.00 0.00 44.62 4.24
2422 2564 8.752187 GGAGAGAGATCTTCTAAGATATGCAAT 58.248 37.037 4.65 0.00 45.39 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.392863 CAATGTCATCACCGGCTCCA 60.393 55.000 0.00 0.00 0.00 3.86
54 55 5.593909 TGAAGGAAACGATGATAATGGCAAT 59.406 36.000 0.00 0.00 0.00 3.56
55 56 4.946772 TGAAGGAAACGATGATAATGGCAA 59.053 37.500 0.00 0.00 0.00 4.52
166 167 1.271707 CCAAGGGGGTAACGACACATT 60.272 52.381 0.00 0.00 37.60 2.71
310 311 0.737367 ATCACCACACATCTGACGCG 60.737 55.000 3.53 3.53 0.00 6.01
360 361 4.760047 GCCGACGCCACCATGACT 62.760 66.667 0.00 0.00 0.00 3.41
391 392 1.744368 CTGCTGCATCGACCTTGCT 60.744 57.895 1.31 0.00 40.77 3.91
583 584 0.032815 GAAGGGGCGCTGATAGTCTC 59.967 60.000 7.64 0.00 0.00 3.36
701 703 1.068083 CTGGACGATGCATACGGCT 59.932 57.895 19.23 3.70 45.15 5.52
776 779 9.801873 CGTGATCATATGGATGTATATTACACA 57.198 33.333 0.00 0.00 42.23 3.72
777 780 9.803315 ACGTGATCATATGGATGTATATTACAC 57.197 33.333 0.00 0.00 42.23 2.90
785 788 9.996554 AAAATTCTACGTGATCATATGGATGTA 57.003 29.630 0.00 3.17 36.00 2.29
786 789 8.908786 AAAATTCTACGTGATCATATGGATGT 57.091 30.769 0.00 2.17 36.00 3.06
826 829 9.883142 ACTTTGAAAATCACATTTAAGGTTTCA 57.117 25.926 0.00 0.00 33.10 2.69
855 858 8.732531 CGGGTGTATTGAAGGACTTTATTTTAA 58.267 33.333 0.00 0.00 0.00 1.52
856 859 7.884354 ACGGGTGTATTGAAGGACTTTATTTTA 59.116 33.333 0.00 0.00 0.00 1.52
857 860 6.717997 ACGGGTGTATTGAAGGACTTTATTTT 59.282 34.615 0.00 0.00 0.00 1.82
858 861 6.150474 CACGGGTGTATTGAAGGACTTTATTT 59.850 38.462 0.00 0.00 0.00 1.40
859 862 5.646360 CACGGGTGTATTGAAGGACTTTATT 59.354 40.000 0.00 0.00 0.00 1.40
860 863 5.183228 CACGGGTGTATTGAAGGACTTTAT 58.817 41.667 0.00 0.00 0.00 1.40
861 864 4.040706 ACACGGGTGTATTGAAGGACTTTA 59.959 41.667 1.96 0.00 42.90 1.85
862 865 3.181448 ACACGGGTGTATTGAAGGACTTT 60.181 43.478 1.96 0.00 42.90 2.66
863 866 2.370849 ACACGGGTGTATTGAAGGACTT 59.629 45.455 1.96 0.00 42.90 3.01
864 867 1.975680 ACACGGGTGTATTGAAGGACT 59.024 47.619 1.96 0.00 42.90 3.85
865 868 2.467566 ACACGGGTGTATTGAAGGAC 57.532 50.000 1.96 0.00 42.90 3.85
866 869 2.289819 GGAACACGGGTGTATTGAAGGA 60.290 50.000 4.68 0.00 44.13 3.36
867 870 2.081462 GGAACACGGGTGTATTGAAGG 58.919 52.381 4.68 0.00 44.13 3.46
868 871 2.773487 TGGAACACGGGTGTATTGAAG 58.227 47.619 4.68 0.00 44.13 3.02
869 872 2.932855 TGGAACACGGGTGTATTGAA 57.067 45.000 4.68 0.00 44.13 2.69
870 873 2.932855 TTGGAACACGGGTGTATTGA 57.067 45.000 4.68 0.00 44.13 2.57
871 874 3.992260 TTTTGGAACACGGGTGTATTG 57.008 42.857 4.68 0.00 44.13 1.90
872 875 4.021807 GGATTTTTGGAACACGGGTGTATT 60.022 41.667 4.68 0.00 44.13 1.89
873 876 3.508402 GGATTTTTGGAACACGGGTGTAT 59.492 43.478 4.68 0.00 44.13 2.29
874 877 2.885894 GGATTTTTGGAACACGGGTGTA 59.114 45.455 4.68 0.00 44.13 2.90
876 879 1.683917 TGGATTTTTGGAACACGGGTG 59.316 47.619 0.00 0.00 39.29 4.61
877 880 1.684450 GTGGATTTTTGGAACACGGGT 59.316 47.619 0.00 0.00 39.29 5.28
878 881 1.960689 AGTGGATTTTTGGAACACGGG 59.039 47.619 0.00 0.00 39.29 5.28
879 882 2.884639 AGAGTGGATTTTTGGAACACGG 59.115 45.455 0.00 0.00 39.29 4.94
880 883 3.363970 CGAGAGTGGATTTTTGGAACACG 60.364 47.826 0.00 0.00 39.29 4.49
881 884 3.609409 GCGAGAGTGGATTTTTGGAACAC 60.609 47.826 0.00 0.00 39.29 3.32
882 885 2.552315 GCGAGAGTGGATTTTTGGAACA 59.448 45.455 0.00 0.00 0.00 3.18
883 886 2.095212 GGCGAGAGTGGATTTTTGGAAC 60.095 50.000 0.00 0.00 0.00 3.62
884 887 2.159382 GGCGAGAGTGGATTTTTGGAA 58.841 47.619 0.00 0.00 0.00 3.53
885 888 1.613255 GGGCGAGAGTGGATTTTTGGA 60.613 52.381 0.00 0.00 0.00 3.53
886 889 0.811281 GGGCGAGAGTGGATTTTTGG 59.189 55.000 0.00 0.00 0.00 3.28
887 890 1.470098 CAGGGCGAGAGTGGATTTTTG 59.530 52.381 0.00 0.00 0.00 2.44
888 891 1.826385 CAGGGCGAGAGTGGATTTTT 58.174 50.000 0.00 0.00 0.00 1.94
889 892 0.678048 GCAGGGCGAGAGTGGATTTT 60.678 55.000 0.00 0.00 0.00 1.82
890 893 1.078143 GCAGGGCGAGAGTGGATTT 60.078 57.895 0.00 0.00 0.00 2.17
891 894 2.249413 CTGCAGGGCGAGAGTGGATT 62.249 60.000 5.57 0.00 0.00 3.01
892 895 2.685017 TGCAGGGCGAGAGTGGAT 60.685 61.111 0.00 0.00 0.00 3.41
893 896 3.385384 CTGCAGGGCGAGAGTGGA 61.385 66.667 5.57 0.00 0.00 4.02
895 898 4.079850 AGCTGCAGGGCGAGAGTG 62.080 66.667 17.12 0.00 37.29 3.51
896 899 3.768922 GAGCTGCAGGGCGAGAGT 61.769 66.667 17.12 0.00 37.29 3.24
897 900 3.429080 GAGAGCTGCAGGGCGAGAG 62.429 68.421 17.12 0.00 37.29 3.20
898 901 3.456365 GAGAGCTGCAGGGCGAGA 61.456 66.667 17.12 0.00 37.29 4.04
899 902 3.429080 GAGAGAGCTGCAGGGCGAG 62.429 68.421 17.12 0.00 37.29 5.03
900 903 3.456365 GAGAGAGCTGCAGGGCGA 61.456 66.667 17.12 0.00 37.29 5.54
901 904 3.719883 CTGAGAGAGCTGCAGGGCG 62.720 68.421 17.12 0.00 37.29 6.13
902 905 2.187424 CTGAGAGAGCTGCAGGGC 59.813 66.667 17.12 2.13 0.00 5.19
903 906 2.901813 CCTGAGAGAGCTGCAGGG 59.098 66.667 17.12 0.93 44.24 4.45
905 908 1.761449 TAGACCTGAGAGAGCTGCAG 58.239 55.000 10.11 10.11 0.00 4.41
906 909 1.821753 GTTAGACCTGAGAGAGCTGCA 59.178 52.381 1.02 0.00 0.00 4.41
907 910 1.136110 GGTTAGACCTGAGAGAGCTGC 59.864 57.143 0.00 0.00 34.73 5.25
908 911 2.165437 GTGGTTAGACCTGAGAGAGCTG 59.835 54.545 0.00 0.00 39.58 4.24
909 912 2.452505 GTGGTTAGACCTGAGAGAGCT 58.547 52.381 0.00 0.00 39.58 4.09
910 913 1.133407 CGTGGTTAGACCTGAGAGAGC 59.867 57.143 0.00 0.00 39.58 4.09
911 914 1.133407 GCGTGGTTAGACCTGAGAGAG 59.867 57.143 0.00 0.00 39.58 3.20
912 915 1.174783 GCGTGGTTAGACCTGAGAGA 58.825 55.000 0.00 0.00 39.58 3.10
913 916 0.888619 TGCGTGGTTAGACCTGAGAG 59.111 55.000 0.00 0.00 39.58 3.20
914 917 1.334160 TTGCGTGGTTAGACCTGAGA 58.666 50.000 0.00 0.00 39.58 3.27
915 918 2.271800 GATTGCGTGGTTAGACCTGAG 58.728 52.381 0.00 0.00 39.58 3.35
916 919 1.621317 TGATTGCGTGGTTAGACCTGA 59.379 47.619 0.00 0.00 39.58 3.86
917 920 2.093306 TGATTGCGTGGTTAGACCTG 57.907 50.000 0.00 0.00 39.58 4.00
918 921 2.224426 TGTTGATTGCGTGGTTAGACCT 60.224 45.455 0.00 0.00 39.58 3.85
919 922 2.147958 TGTTGATTGCGTGGTTAGACC 58.852 47.619 0.00 0.00 39.22 3.85
920 923 3.496884 TCTTGTTGATTGCGTGGTTAGAC 59.503 43.478 0.00 0.00 0.00 2.59
968 972 5.333721 GCTGAAAACTCTTGAACTGTAGCTC 60.334 44.000 0.00 0.00 0.00 4.09
969 973 4.513318 GCTGAAAACTCTTGAACTGTAGCT 59.487 41.667 0.00 0.00 0.00 3.32
992 1008 1.202371 TCGCGGTAGCCATCTTAGTTG 60.202 52.381 6.13 0.00 41.18 3.16
994 1010 1.108776 TTCGCGGTAGCCATCTTAGT 58.891 50.000 6.13 0.00 41.18 2.24
1011 1027 1.673168 CCATGGTGGCTAGAGCTTTC 58.327 55.000 2.57 0.00 41.70 2.62
1063 1079 1.536072 GCGAAGTGAGGATGCGATGTA 60.536 52.381 0.00 0.00 0.00 2.29
1101 1117 0.320421 GAAGGTAGCCACTTGCACGA 60.320 55.000 0.00 0.00 44.83 4.35
1122 1138 0.535780 CTTCTCACAGTTGCCCAGCA 60.536 55.000 0.00 0.00 36.47 4.41
1124 1140 1.805869 CTCTTCTCACAGTTGCCCAG 58.194 55.000 0.00 0.00 0.00 4.45
1125 1141 0.250467 GCTCTTCTCACAGTTGCCCA 60.250 55.000 0.00 0.00 0.00 5.36
1158 1179 0.318441 TCTCTTGCCGTCCTCACAAG 59.682 55.000 0.00 0.00 41.70 3.16
1213 1234 0.817634 TCAAGACGGCCTTTGTGGTG 60.818 55.000 0.00 0.00 38.35 4.17
1241 1262 0.251341 TCCTTGCCCTTCTCAAAGCC 60.251 55.000 0.00 0.00 0.00 4.35
1358 1379 3.517100 ACAGTGATCTTGATACAGTGCCT 59.483 43.478 0.00 0.00 38.17 4.75
1380 1401 1.803334 GTACACGGAGTTGCCATTGA 58.197 50.000 0.00 0.00 41.61 2.57
1427 1448 0.815095 TCGTCGTCACAGCCATACAT 59.185 50.000 0.00 0.00 0.00 2.29
1469 1490 1.425412 GCGTCGACTATGTTGTTGGT 58.575 50.000 14.70 0.00 0.00 3.67
1694 1756 3.282021 ACCATAGGCTGCACTGTTTATG 58.718 45.455 0.50 0.16 0.00 1.90
1736 1798 1.279840 GCTTGAAGGTCACGCACAC 59.720 57.895 2.19 0.00 40.80 3.82
1765 1827 2.153645 TCTTTATGCACCACACTGCTG 58.846 47.619 0.00 0.00 38.07 4.41
1813 1933 6.038050 GGAAATGATCCTACAGCTTTCTCAAG 59.962 42.308 0.00 0.00 45.56 3.02
1814 1934 5.882557 GGAAATGATCCTACAGCTTTCTCAA 59.117 40.000 0.00 0.00 45.56 3.02
1815 1935 5.431765 GGAAATGATCCTACAGCTTTCTCA 58.568 41.667 0.00 0.00 45.56 3.27
1829 1949 3.559069 TCAGCATCCCTTGGAAATGATC 58.441 45.455 6.29 0.00 34.34 2.92
1830 1950 3.675348 TCAGCATCCCTTGGAAATGAT 57.325 42.857 6.29 0.00 34.34 2.45
1831 1951 3.091545 GTTCAGCATCCCTTGGAAATGA 58.908 45.455 6.29 0.00 34.34 2.57
1832 1952 2.827322 TGTTCAGCATCCCTTGGAAATG 59.173 45.455 0.00 0.00 34.34 2.32
1833 1953 3.173953 TGTTCAGCATCCCTTGGAAAT 57.826 42.857 0.00 0.00 34.34 2.17
1834 1954 2.673775 TGTTCAGCATCCCTTGGAAA 57.326 45.000 0.00 0.00 34.34 3.13
1835 1955 2.158475 ACTTGTTCAGCATCCCTTGGAA 60.158 45.455 0.00 0.00 34.34 3.53
1836 1956 1.425066 ACTTGTTCAGCATCCCTTGGA 59.575 47.619 0.00 0.00 35.55 3.53
1837 1957 1.915141 ACTTGTTCAGCATCCCTTGG 58.085 50.000 0.00 0.00 0.00 3.61
1838 1958 5.647658 TGTTATACTTGTTCAGCATCCCTTG 59.352 40.000 0.00 0.00 0.00 3.61
1839 1959 5.815581 TGTTATACTTGTTCAGCATCCCTT 58.184 37.500 0.00 0.00 0.00 3.95
1840 1960 5.435686 TGTTATACTTGTTCAGCATCCCT 57.564 39.130 0.00 0.00 0.00 4.20
1841 1961 6.072175 TGTTTGTTATACTTGTTCAGCATCCC 60.072 38.462 0.00 0.00 0.00 3.85
1842 1962 6.801862 GTGTTTGTTATACTTGTTCAGCATCC 59.198 38.462 0.00 0.00 0.00 3.51
1843 1963 7.359595 TGTGTTTGTTATACTTGTTCAGCATC 58.640 34.615 0.00 0.00 0.00 3.91
1844 1964 7.270757 TGTGTTTGTTATACTTGTTCAGCAT 57.729 32.000 0.00 0.00 0.00 3.79
1845 1965 6.685527 TGTGTTTGTTATACTTGTTCAGCA 57.314 33.333 0.00 0.00 0.00 4.41
1846 1966 7.359595 TGATGTGTTTGTTATACTTGTTCAGC 58.640 34.615 0.00 0.00 0.00 4.26
1847 1967 9.897744 AATGATGTGTTTGTTATACTTGTTCAG 57.102 29.630 0.00 0.00 0.00 3.02
1848 1968 9.891828 GAATGATGTGTTTGTTATACTTGTTCA 57.108 29.630 0.00 0.00 0.00 3.18
1849 1969 9.891828 TGAATGATGTGTTTGTTATACTTGTTC 57.108 29.630 0.00 0.00 0.00 3.18
1850 1970 9.677567 GTGAATGATGTGTTTGTTATACTTGTT 57.322 29.630 0.00 0.00 0.00 2.83
1851 1971 8.845227 TGTGAATGATGTGTTTGTTATACTTGT 58.155 29.630 0.00 0.00 0.00 3.16
1852 1972 9.844790 ATGTGAATGATGTGTTTGTTATACTTG 57.155 29.630 0.00 0.00 0.00 3.16
1856 1976 9.138062 GCAAATGTGAATGATGTGTTTGTTATA 57.862 29.630 0.00 0.00 0.00 0.98
1857 1977 7.656542 TGCAAATGTGAATGATGTGTTTGTTAT 59.343 29.630 0.00 0.00 0.00 1.89
1858 1978 6.982724 TGCAAATGTGAATGATGTGTTTGTTA 59.017 30.769 0.00 0.00 0.00 2.41
1859 1979 5.816258 TGCAAATGTGAATGATGTGTTTGTT 59.184 32.000 0.00 0.00 0.00 2.83
1860 1980 5.358090 TGCAAATGTGAATGATGTGTTTGT 58.642 33.333 0.00 0.00 0.00 2.83
1861 1981 5.107259 CCTGCAAATGTGAATGATGTGTTTG 60.107 40.000 0.00 0.00 0.00 2.93
1862 1982 4.992319 CCTGCAAATGTGAATGATGTGTTT 59.008 37.500 0.00 0.00 0.00 2.83
1863 1983 4.281435 TCCTGCAAATGTGAATGATGTGTT 59.719 37.500 0.00 0.00 0.00 3.32
1864 1984 3.827876 TCCTGCAAATGTGAATGATGTGT 59.172 39.130 0.00 0.00 0.00 3.72
1906 2026 5.468746 GTGTTAACTGTCTTTGGTATCTGCA 59.531 40.000 7.22 0.00 0.00 4.41
2051 2190 6.430925 ACTGAAATACTAAGCATCAACAAGCA 59.569 34.615 0.00 0.00 0.00 3.91
2422 2564 8.307483 CACTTAACAGGAGAGATAGAAGAACAA 58.693 37.037 0.00 0.00 0.00 2.83
2503 2645 2.703536 TGCTCCAACCTTTCTGTACTCA 59.296 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.