Multiple sequence alignment - TraesCS6A01G187100

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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 TraesCS6A01G187100 chr6A 100.000 5653 0 0 1 5653 223407692 223413344 0.000000e+00 10440
1 TraesCS6A01G187100 chr6A 95.000 80 2 2 3000 3079 533168032 533167955 2.140000e-24 124
2 TraesCS6A01G187100 chr6A 89.796 98 7 3 1746 1840 511530190 511530093 7.690000e-24 122
3 TraesCS6A01G187100 chr6D 96.430 2577 67 17 3085 5653 163130197 163132756 0.000000e+00 4226
4 TraesCS6A01G187100 chr6D 93.220 1180 32 13 1865 2998 163129019 163130196 0.000000e+00 1692
5 TraesCS6A01G187100 chr6D 96.387 858 28 3 850 1707 163128101 163128955 0.000000e+00 1410
6 TraesCS6A01G187100 chr6D 94.186 86 3 2 3137 3221 145788462 145788546 4.600000e-26 130
7 TraesCS6A01G187100 chr6B 95.176 2446 64 18 3219 5653 299051416 299049014 0.000000e+00 3814
8 TraesCS6A01G187100 chr6B 91.430 1867 99 28 898 2727 299054933 299053091 0.000000e+00 2505
9 TraesCS6A01G187100 chr6B 90.994 322 20 7 2749 3070 299051798 299051486 5.230000e-115 425
10 TraesCS6A01G187100 chr7D 86.279 860 102 12 1 850 385704831 385705684 0.000000e+00 920
11 TraesCS6A01G187100 chr7D 85.909 809 103 8 2 803 469191163 469190359 0.000000e+00 852
12 TraesCS6A01G187100 chr7D 84.633 859 109 15 2 846 156785058 156784209 0.000000e+00 833
13 TraesCS6A01G187100 chr7D 84.307 873 116 18 1 859 251031972 251031107 0.000000e+00 833
14 TraesCS6A01G187100 chr7D 100.000 71 0 0 3000 3070 501098090 501098020 1.280000e-26 132
15 TraesCS6A01G187100 chr7D 92.473 93 3 4 1752 1841 626199971 626199880 4.600000e-26 130
16 TraesCS6A01G187100 chr7D 88.571 105 7 5 1754 1853 506141369 506141473 7.690000e-24 122
17 TraesCS6A01G187100 chr2B 85.698 853 104 16 1 846 173438885 173438044 0.000000e+00 883
18 TraesCS6A01G187100 chr2B 90.526 95 7 2 1752 1845 103270301 103270394 2.140000e-24 124
19 TraesCS6A01G187100 chr1D 84.813 856 119 9 1 850 26698405 26699255 0.000000e+00 850
20 TraesCS6A01G187100 chr1D 84.633 859 110 16 1 846 140108802 140109651 0.000000e+00 835
21 TraesCS6A01G187100 chr1D 95.402 87 3 1 3137 3222 337216806 337216892 2.750000e-28 137
22 TraesCS6A01G187100 chr4D 84.795 855 118 11 1 846 69193131 69192280 0.000000e+00 848
23 TraesCS6A01G187100 chr4D 92.553 94 3 4 1751 1840 449455704 449455611 1.280000e-26 132
24 TraesCS6A01G187100 chr5D 85.158 822 107 8 1 815 456165943 456166756 0.000000e+00 828
25 TraesCS6A01G187100 chr5D 95.506 89 3 1 3134 3221 240428130 240428042 2.120000e-29 141
26 TraesCS6A01G187100 chr5D 94.118 85 5 0 3138 3222 240371755 240371839 4.600000e-26 130
27 TraesCS6A01G187100 chr5D 90.816 98 6 3 3126 3221 503136552 503136648 1.650000e-25 128
28 TraesCS6A01G187100 chr5D 90.625 96 6 3 1743 1835 297738437 297738342 2.140000e-24 124
29 TraesCS6A01G187100 chr1A 100.000 71 0 0 3000 3070 425722411 425722481 1.280000e-26 132
30 TraesCS6A01G187100 chr5B 94.118 85 5 0 3138 3222 103464778 103464862 4.600000e-26 130
31 TraesCS6A01G187100 chr5B 94.118 85 5 0 3138 3222 105695946 105696030 4.600000e-26 130
32 TraesCS6A01G187100 chr5B 91.209 91 5 3 3000 3090 97912319 97912232 2.770000e-23 121
33 TraesCS6A01G187100 chr2A 94.118 85 5 0 3137 3221 562095142 562095058 4.600000e-26 130
34 TraesCS6A01G187100 chr2A 93.902 82 3 2 3000 3081 472098070 472097991 7.690000e-24 122
35 TraesCS6A01G187100 chr3D 91.579 95 5 3 1749 1840 362238378 362238284 1.650000e-25 128
36 TraesCS6A01G187100 chr3D 95.000 80 2 2 3000 3079 52921487 52921410 2.140000e-24 124
37 TraesCS6A01G187100 chr7B 92.222 90 4 2 1753 1839 611720254 611720343 2.140000e-24 124
38 TraesCS6A01G187100 chr2D 95.000 80 2 2 3000 3079 350306022 350306099 2.140000e-24 124
39 TraesCS6A01G187100 chr4A 93.902 82 3 2 3000 3081 558788369 558788290 7.690000e-24 122
40 TraesCS6A01G187100 chr3B 87.850 107 9 3 1745 1848 424785307 424785202 7.690000e-24 122


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 TraesCS6A01G187100 chr6A 223407692 223413344 5652 False 10440.000000 10440 100.000000 1 5653 1 chr6A.!!$F1 5652
1 TraesCS6A01G187100 chr6D 163128101 163132756 4655 False 2442.666667 4226 95.345667 850 5653 3 chr6D.!!$F2 4803
2 TraesCS6A01G187100 chr6B 299049014 299054933 5919 True 2248.000000 3814 92.533333 898 5653 3 chr6B.!!$R1 4755
3 TraesCS6A01G187100 chr7D 385704831 385705684 853 False 920.000000 920 86.279000 1 850 1 chr7D.!!$F1 849
4 TraesCS6A01G187100 chr7D 469190359 469191163 804 True 852.000000 852 85.909000 2 803 1 chr7D.!!$R3 801
5 TraesCS6A01G187100 chr7D 156784209 156785058 849 True 833.000000 833 84.633000 2 846 1 chr7D.!!$R1 844
6 TraesCS6A01G187100 chr7D 251031107 251031972 865 True 833.000000 833 84.307000 1 859 1 chr7D.!!$R2 858
7 TraesCS6A01G187100 chr2B 173438044 173438885 841 True 883.000000 883 85.698000 1 846 1 chr2B.!!$R1 845
8 TraesCS6A01G187100 chr1D 26698405 26699255 850 False 850.000000 850 84.813000 1 850 1 chr1D.!!$F1 849
9 TraesCS6A01G187100 chr1D 140108802 140109651 849 False 835.000000 835 84.633000 1 846 1 chr1D.!!$F2 845
10 TraesCS6A01G187100 chr4D 69192280 69193131 851 True 848.000000 848 84.795000 1 846 1 chr4D.!!$R1 845
11 TraesCS6A01G187100 chr5D 456165943 456166756 813 False 828.000000 828 85.158000 1 815 1 chr5D.!!$F2 814

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
225 233 0.103755 CGATGCCTCTGCTTGCTCTA 59.896 55.000 0.00 0.0 38.71 2.43 F
1630 1669 0.036010 CGAGCTGTTGAAGTCCCCAT 60.036 55.000 0.00 0.0 0.00 4.00 F
1774 1813 0.035458 CTCCCTCCGTCCCATAATGC 59.965 60.000 0.00 0.0 0.00 3.56 F
1775 1814 0.692756 TCCCTCCGTCCCATAATGCA 60.693 55.000 0.00 0.0 0.00 3.96 F
1937 1988 1.202698 GCCCGTTCTGCTGGATATTCT 60.203 52.381 0.00 0.0 0.00 2.40 F
3025 4401 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.0 42.05 4.02 F
3026 4402 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.0 37.50 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 1794 0.035458 GCATTATGGGACGGAGGGAG 59.965 60.000 0.00 0.0 0.00 4.30 R
2999 4375 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.0 46.06 3.85 R
3394 4798 1.400494 CCAGCCAATTAGCCAACGTAC 59.600 52.381 0.00 0.0 0.00 3.67 R
3724 5128 3.389221 AGCTGGTTTTAATTGGTTTGCG 58.611 40.909 0.00 0.0 0.00 4.85 R
3872 5277 4.892934 ACTCCTATAAGAGAAGCTCACAGG 59.107 45.833 5.33 0.0 37.33 4.00 R
4195 5601 2.229062 GACAAAAGCCTACAGAAAGGGC 59.771 50.000 0.00 0.0 45.57 5.19 R
4765 6171 2.979813 GCAAATGTCTAACCAAGCGTTG 59.020 45.455 0.00 0.0 35.79 4.10 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
33 35 2.978978 TCTGGAGTGAGGTGAATCCAAA 59.021 45.455 0.00 0.00 41.17 3.28
79 81 5.053145 CACTTGAAGTAGCTGTCAAACTCT 58.947 41.667 0.00 0.00 33.52 3.24
93 95 4.878397 GTCAAACTCTCGGATGGAATTCAT 59.122 41.667 7.93 0.00 39.13 2.57
104 106 4.633565 GGATGGAATTCATAATCTCGAGGC 59.366 45.833 13.56 0.00 35.97 4.70
107 109 4.101585 TGGAATTCATAATCTCGAGGCAGT 59.898 41.667 13.56 0.00 0.00 4.40
204 212 0.554792 AGCAAGCAATAGCCCTCCAT 59.445 50.000 0.00 0.00 43.56 3.41
225 233 0.103755 CGATGCCTCTGCTTGCTCTA 59.896 55.000 0.00 0.00 38.71 2.43
226 234 1.472201 CGATGCCTCTGCTTGCTCTAA 60.472 52.381 0.00 0.00 38.71 2.10
322 331 0.827925 TGAGGTGCTCTTCGTCCTGT 60.828 55.000 0.00 0.00 0.00 4.00
333 342 3.755628 GTCCTGTGCGTCGGCCTA 61.756 66.667 0.00 0.00 38.85 3.93
387 396 2.881074 CTCATCGTTTGAGTCCATCGT 58.119 47.619 9.16 0.00 45.79 3.73
414 423 2.184167 CAAACCGCCGAACACCTGT 61.184 57.895 0.00 0.00 0.00 4.00
500 511 1.133167 TCAGGAGCGGGATGAAGGATA 60.133 52.381 0.00 0.00 0.00 2.59
522 537 1.605753 GCGGTGAACCCTCTCTTTTT 58.394 50.000 0.00 0.00 0.00 1.94
554 570 3.771160 CTTCCTAGCGGCGGTGGT 61.771 66.667 23.33 0.00 0.00 4.16
568 584 2.927856 TGGTCAGGTGGGCATCGT 60.928 61.111 0.00 0.00 0.00 3.73
601 617 4.400961 GGCGGAAGAGGCAGTGCT 62.401 66.667 16.11 0.33 36.61 4.40
703 731 3.850098 CTTCAAGCGCCCCCAGTGT 62.850 63.158 2.29 0.00 0.00 3.55
719 748 4.643387 GTGCTGGGTTCGGCCTGT 62.643 66.667 0.00 0.00 44.42 4.00
730 759 4.740822 GGCCTGTGATTGCCGGGT 62.741 66.667 2.18 0.00 38.00 5.28
766 797 1.260206 CTGACAGAATTCGACGTCCG 58.740 55.000 10.58 5.50 40.25 4.79
769 800 2.165301 CAGAATTCGACGTCCGGGC 61.165 63.158 10.58 0.00 39.14 6.13
770 801 2.889018 GAATTCGACGTCCGGGCC 60.889 66.667 10.58 0.00 39.14 5.80
828 867 4.748144 CTGGAGGGCTGTTGGGGC 62.748 72.222 0.00 0.00 0.00 5.80
846 885 1.427592 GCGCTGAGTGAAGATGCTCC 61.428 60.000 0.00 0.00 0.00 4.70
854 893 3.070018 AGTGAAGATGCTCCAAGAAACG 58.930 45.455 0.00 0.00 0.00 3.60
904 943 3.374402 CACGACTCCACGAGGCCT 61.374 66.667 3.86 3.86 33.37 5.19
1110 1149 2.383855 CTCTTCCTCCTAGTCCACCTG 58.616 57.143 0.00 0.00 0.00 4.00
1227 1266 4.137872 TTCGACCCCGTCATCGCC 62.138 66.667 0.00 0.00 38.24 5.54
1238 1277 4.193334 CATCGCCGACCTCGAGCA 62.193 66.667 6.99 0.00 43.02 4.26
1335 1374 1.686355 CAGAGGACCTCGCAGACTAT 58.314 55.000 15.97 0.00 35.36 2.12
1617 1656 3.237628 CGTATGTGTATGATCCGAGCTG 58.762 50.000 0.00 0.00 0.00 4.24
1618 1657 3.304726 CGTATGTGTATGATCCGAGCTGT 60.305 47.826 0.00 0.00 0.00 4.40
1622 1661 3.056179 TGTGTATGATCCGAGCTGTTGAA 60.056 43.478 0.00 0.00 0.00 2.69
1630 1669 0.036010 CGAGCTGTTGAAGTCCCCAT 60.036 55.000 0.00 0.00 0.00 4.00
1687 1726 3.813724 GCCTAGTCAGGAAAAAGTTCGTT 59.186 43.478 0.00 0.00 45.91 3.85
1722 1761 4.699925 TTATACCAATGTCAGGGTAGCC 57.300 45.455 1.60 1.60 42.55 3.93
1746 1785 2.299326 AAGCTCTGGATTTTGGTGCT 57.701 45.000 0.00 0.00 0.00 4.40
1747 1786 1.542492 AGCTCTGGATTTTGGTGCTG 58.458 50.000 0.00 0.00 0.00 4.41
1749 1788 1.068055 GCTCTGGATTTTGGTGCTGTG 60.068 52.381 0.00 0.00 0.00 3.66
1750 1789 2.507484 CTCTGGATTTTGGTGCTGTGA 58.493 47.619 0.00 0.00 0.00 3.58
1751 1790 3.087031 CTCTGGATTTTGGTGCTGTGAT 58.913 45.455 0.00 0.00 0.00 3.06
1752 1791 2.821378 TCTGGATTTTGGTGCTGTGATG 59.179 45.455 0.00 0.00 0.00 3.07
1754 1793 3.758023 CTGGATTTTGGTGCTGTGATGTA 59.242 43.478 0.00 0.00 0.00 2.29
1755 1794 3.505680 TGGATTTTGGTGCTGTGATGTAC 59.494 43.478 0.00 0.00 0.00 2.90
1756 1795 3.758554 GGATTTTGGTGCTGTGATGTACT 59.241 43.478 0.00 0.00 0.00 2.73
1758 1797 2.472695 TTGGTGCTGTGATGTACTCC 57.527 50.000 0.00 0.00 0.00 3.85
1760 1799 0.905357 GGTGCTGTGATGTACTCCCT 59.095 55.000 0.00 0.00 0.00 4.20
1761 1800 1.134670 GGTGCTGTGATGTACTCCCTC 60.135 57.143 0.00 0.00 0.00 4.30
1765 1804 1.405821 CTGTGATGTACTCCCTCCGTC 59.594 57.143 0.00 0.00 0.00 4.79
1766 1805 0.745468 GTGATGTACTCCCTCCGTCC 59.255 60.000 0.00 0.00 0.00 4.79
1767 1806 0.396695 TGATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
1768 1807 0.396695 GATGTACTCCCTCCGTCCCA 60.397 60.000 0.00 0.00 0.00 4.37
1770 1809 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
1772 1811 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
1773 1812 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1774 1813 0.035458 CTCCCTCCGTCCCATAATGC 59.965 60.000 0.00 0.00 0.00 3.56
1775 1814 0.692756 TCCCTCCGTCCCATAATGCA 60.693 55.000 0.00 0.00 0.00 3.96
1777 1816 1.597742 CCTCCGTCCCATAATGCAAG 58.402 55.000 0.00 0.00 0.00 4.01
1780 1819 2.810274 CTCCGTCCCATAATGCAAGATG 59.190 50.000 0.00 0.00 0.00 2.90
1781 1820 2.437651 TCCGTCCCATAATGCAAGATGA 59.562 45.455 11.71 0.00 0.00 2.92
1782 1821 3.072915 TCCGTCCCATAATGCAAGATGAT 59.927 43.478 11.71 0.00 0.00 2.45
1783 1822 3.822735 CCGTCCCATAATGCAAGATGATT 59.177 43.478 11.71 0.00 0.00 2.57
1784 1823 4.279169 CCGTCCCATAATGCAAGATGATTT 59.721 41.667 11.71 0.00 0.00 2.17
1785 1824 5.221303 CCGTCCCATAATGCAAGATGATTTT 60.221 40.000 11.71 0.00 0.00 1.82
1787 1826 6.199531 CGTCCCATAATGCAAGATGATTTTTG 59.800 38.462 11.71 0.00 0.00 2.44
1789 1828 7.223387 GTCCCATAATGCAAGATGATTTTTGAC 59.777 37.037 11.71 5.86 0.00 3.18
1792 1831 7.762615 CCATAATGCAAGATGATTTTTGACACT 59.237 33.333 11.71 0.00 0.00 3.55
1795 1834 6.631971 TGCAAGATGATTTTTGACACTACA 57.368 33.333 0.00 0.00 0.00 2.74
1796 1835 6.437928 TGCAAGATGATTTTTGACACTACAC 58.562 36.000 0.00 0.00 0.00 2.90
1797 1836 6.262944 TGCAAGATGATTTTTGACACTACACT 59.737 34.615 0.00 0.00 0.00 3.55
1798 1837 7.443879 TGCAAGATGATTTTTGACACTACACTA 59.556 33.333 0.00 0.00 0.00 2.74
1802 1841 9.209175 AGATGATTTTTGACACTACACTAAGTC 57.791 33.333 0.00 0.00 0.00 3.01
1829 1868 2.750948 CGTCTTACATTATGGGACGGG 58.249 52.381 20.50 4.10 43.69 5.28
1830 1869 2.547218 CGTCTTACATTATGGGACGGGG 60.547 54.545 20.50 3.61 43.69 5.73
1831 1870 2.701951 GTCTTACATTATGGGACGGGGA 59.298 50.000 0.00 0.00 0.00 4.81
1832 1871 2.969950 TCTTACATTATGGGACGGGGAG 59.030 50.000 0.00 0.00 0.00 4.30
1833 1872 2.482414 TACATTATGGGACGGGGAGT 57.518 50.000 0.00 0.00 0.00 3.85
1936 1987 1.230324 GCCCGTTCTGCTGGATATTC 58.770 55.000 0.00 0.00 0.00 1.75
1937 1988 1.202698 GCCCGTTCTGCTGGATATTCT 60.203 52.381 0.00 0.00 0.00 2.40
1960 2011 4.592485 AGTCATTTACATAGGCTCTCCG 57.408 45.455 0.00 0.00 37.47 4.63
2075 2162 4.366586 GGTAGGTACCATTCTAAGTTCGC 58.633 47.826 15.94 0.00 45.73 4.70
2078 2165 2.856557 GGTACCATTCTAAGTTCGCGTC 59.143 50.000 7.15 0.31 0.00 5.19
2113 2209 6.001449 TCTAAGCATACCAAGCACCTATTT 57.999 37.500 0.00 0.00 0.00 1.40
2114 2210 6.423182 TCTAAGCATACCAAGCACCTATTTT 58.577 36.000 0.00 0.00 0.00 1.82
2252 2348 2.099756 GCTTGAATAGTTCCCATGTGGC 59.900 50.000 0.00 0.00 0.00 5.01
2353 2456 2.423538 AGCATCCTTTGATAAACCGTGC 59.576 45.455 0.00 0.00 0.00 5.34
2734 2838 5.850557 TTTCCTTTCAGATTTCAACAGCA 57.149 34.783 0.00 0.00 0.00 4.41
2773 4149 7.078228 CCTTATTAGTGTTCAGTTCTGCAAAC 58.922 38.462 0.00 0.00 0.00 2.93
2870 4246 6.231951 AGTGATATCAGAGGCAGATCATTTG 58.768 40.000 5.42 0.00 0.00 2.32
2998 4374 6.162079 ACTATGATGCTGCATGATACTACAC 58.838 40.000 21.53 2.48 0.00 2.90
2999 4375 4.405116 TGATGCTGCATGATACTACACA 57.595 40.909 21.53 5.31 0.00 3.72
3010 4386 2.119801 TACTACACACTCCCTCCGTC 57.880 55.000 0.00 0.00 0.00 4.79
3016 4392 2.118951 ACTCCCTCCGTCCGGAAA 59.881 61.111 5.23 0.00 44.66 3.13
3025 4401 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
3026 4402 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
3035 4411 6.113411 CGGAAATACTTGTCCTAGAAATGGT 58.887 40.000 0.00 0.00 0.00 3.55
3047 4423 7.839705 TGTCCTAGAAATGGTTGTATCTAGACT 59.160 37.037 9.60 0.00 42.48 3.24
3161 4563 5.600749 ACTCCCTCCGTCCCATAATATAAT 58.399 41.667 0.00 0.00 0.00 1.28
3171 4573 7.960738 CCGTCCCATAATATAATAGCGTTTTTG 59.039 37.037 0.00 0.00 0.00 2.44
3208 4611 9.609346 AGTGTAAAAACGCTCTTATATTATGGT 57.391 29.630 0.00 0.00 0.00 3.55
3565 4969 3.559171 GCACTTTGGGTATCAAGGAGTCA 60.559 47.826 0.00 0.00 36.16 3.41
3578 4982 8.946085 GTATCAAGGAGTCATATGAAAACAACA 58.054 33.333 7.07 0.00 0.00 3.33
3596 5000 7.823745 AACAACAAGTCCATACTCTGAATTT 57.176 32.000 0.00 0.00 33.75 1.82
3660 5064 3.561143 ACCATTTGTGCAGGTAAACAGA 58.439 40.909 0.00 0.00 32.92 3.41
3669 5073 8.942338 TTGTGCAGGTAAACAGAATAGTATAG 57.058 34.615 0.00 0.00 0.00 1.31
3724 5128 2.134789 AAATCTCTGCCCATCACACC 57.865 50.000 0.00 0.00 0.00 4.16
3872 5277 1.538047 ACCCTGACACAATCACATGC 58.462 50.000 0.00 0.00 32.37 4.06
4195 5601 1.001406 AGTCTGAGTTTGGAGGCTTCG 59.999 52.381 0.00 0.00 0.00 3.79
4525 5931 8.049117 TGCTGATTTGTTATCTGATAGACCTTT 58.951 33.333 0.00 0.00 0.00 3.11
4529 5935 9.606631 GATTTGTTATCTGATAGACCTTTCTGT 57.393 33.333 0.00 0.00 32.75 3.41
4682 6088 0.452987 GTACGTGGTGCTCGGTATCA 59.547 55.000 0.00 0.00 0.00 2.15
4765 6171 4.470304 AGTAGGTGGTATTCAGGACCTTTC 59.530 45.833 0.00 0.00 39.59 2.62
4784 6190 5.507315 CCTTTCAACGCTTGGTTAGACATTT 60.507 40.000 0.00 0.00 36.49 2.32
4790 6196 2.030007 GCTTGGTTAGACATTTGCTGCA 60.030 45.455 0.00 0.00 0.00 4.41
4890 6297 5.107065 CCTTATCGGTTCTTATTCATTCGCC 60.107 44.000 0.00 0.00 0.00 5.54
4899 6306 1.255882 ATTCATTCGCCTTTGCACCA 58.744 45.000 0.00 0.00 37.32 4.17
4916 6323 3.682858 GCACCAAAGTATTCGAGTGCTTA 59.317 43.478 11.43 0.00 41.86 3.09
5256 6671 7.560368 TGAAAGTGATTCTATTCTCTTCCTCC 58.440 38.462 0.00 0.00 38.92 4.30
5263 6678 1.561643 ATTCTCTTCCTCCTCGTGCA 58.438 50.000 0.00 0.00 0.00 4.57
5314 6729 1.229428 TTTGCCAGAAAGAGCACTCG 58.771 50.000 0.00 0.00 39.10 4.18
5325 6740 4.802876 AAGAGCACTCGTTCTTTCTTTG 57.197 40.909 0.00 0.00 39.42 2.77
5530 6945 7.759433 AGTTTTGTCACTTTGACCAAGTTTATG 59.241 33.333 3.91 0.00 43.89 1.90
5533 6948 4.825085 GTCACTTTGACCAAGTTTATGGGA 59.175 41.667 0.00 0.00 43.89 4.37
5599 7020 5.359194 TCAAACTGAGAAGAAGTTGGACT 57.641 39.130 0.00 0.00 37.90 3.85
5600 7021 5.745227 TCAAACTGAGAAGAAGTTGGACTT 58.255 37.500 0.00 0.00 41.95 3.01
5614 7035 3.396260 TGGACTTCGGGACAAAACTAG 57.604 47.619 0.00 0.00 0.00 2.57
5636 7057 5.634896 AGTAGAATTGCTTGCATTTTCGAG 58.365 37.500 0.00 0.00 0.00 4.04
5640 7061 0.241749 TGCTTGCATTTTCGAGCAGG 59.758 50.000 4.41 2.60 45.72 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 5.336770 CCTCGAGATTATGAATTCCATCCGA 60.337 44.000 15.71 11.06 36.71 4.55
93 95 2.735444 CGAAAGCACTGCCTCGAGATTA 60.735 50.000 15.71 0.00 36.80 1.75
204 212 0.179100 GAGCAAGCAGAGGCATCGTA 60.179 55.000 0.00 0.00 44.61 3.43
256 264 2.259204 GCGAGCAATGCAAAGCCA 59.741 55.556 8.35 0.00 0.00 4.75
322 331 4.143333 GAAGCCTAGGCCGACGCA 62.143 66.667 30.42 0.00 43.17 5.24
333 342 1.994507 CTGCTGGAGGAGGAAGCCT 60.995 63.158 0.00 0.00 42.17 4.58
387 396 2.357034 GGCGGTTTGTCTGCTCGA 60.357 61.111 0.00 0.00 46.74 4.04
480 491 0.399091 ATCCTTCATCCCGCTCCTGA 60.399 55.000 0.00 0.00 0.00 3.86
494 505 1.219935 GGTTCACCGCCGTATCCTT 59.780 57.895 0.00 0.00 0.00 3.36
500 511 3.692406 GAGAGGGTTCACCGCCGT 61.692 66.667 0.00 0.00 46.96 5.68
522 537 1.356398 AGGAAGGCCATTTTCCCGTAA 59.644 47.619 16.64 0.00 44.19 3.18
554 570 3.770040 CCGACGATGCCCACCTGA 61.770 66.667 0.00 0.00 0.00 3.86
686 711 3.884774 ACACTGGGGGCGCTTGAA 61.885 61.111 7.64 0.00 0.00 2.69
687 712 4.641645 CACACTGGGGGCGCTTGA 62.642 66.667 7.64 0.00 0.00 3.02
703 731 4.641645 CACAGGCCGAACCCAGCA 62.642 66.667 0.00 0.00 40.58 4.41
748 779 0.109458 CCGGACGTCGAATTCTGTCA 60.109 55.000 9.92 0.00 42.43 3.58
828 867 0.108472 TGGAGCATCTTCACTCAGCG 60.108 55.000 0.00 0.00 34.48 5.18
829 868 2.008329 CTTGGAGCATCTTCACTCAGC 58.992 52.381 0.00 0.00 34.48 4.26
830 869 3.606595 TCTTGGAGCATCTTCACTCAG 57.393 47.619 0.00 0.00 34.48 3.35
863 902 5.589050 GGGTGAACTCACTGTACTTCTTTTT 59.411 40.000 9.60 0.00 45.73 1.94
868 907 3.391049 GTGGGTGAACTCACTGTACTTC 58.609 50.000 6.20 0.00 45.73 3.01
874 913 0.389391 AGTCGTGGGTGAACTCACTG 59.611 55.000 11.50 5.61 45.73 3.66
904 943 2.727777 CGACTGTCAAACTTGTCTCGA 58.272 47.619 8.73 0.00 0.00 4.04
1084 1123 1.216930 GACTAGGAGGAAGAGGAGGCT 59.783 57.143 0.00 0.00 0.00 4.58
1110 1149 2.202892 GATGGCGACGAAGGGGAC 60.203 66.667 0.00 0.00 0.00 4.46
1329 1368 5.037383 TGATGTACTCGTCCTCATAGTCT 57.963 43.478 0.00 0.00 0.00 3.24
1335 1374 3.181500 CGTCATTGATGTACTCGTCCTCA 60.181 47.826 0.00 0.00 0.00 3.86
1617 1656 4.528206 AGATCCAAAAATGGGGACTTCAAC 59.472 41.667 0.00 0.00 35.67 3.18
1618 1657 4.527816 CAGATCCAAAAATGGGGACTTCAA 59.472 41.667 0.00 0.00 35.67 2.69
1622 1661 3.181418 ACACAGATCCAAAAATGGGGACT 60.181 43.478 0.00 0.00 35.67 3.85
1630 1669 5.483811 TGTATCGCTACACAGATCCAAAAA 58.516 37.500 0.00 0.00 32.88 1.94
1708 1747 2.154567 TACTCGGCTACCCTGACATT 57.845 50.000 0.00 0.00 0.00 2.71
1746 1785 1.471119 GACGGAGGGAGTACATCACA 58.529 55.000 0.00 0.00 31.63 3.58
1747 1786 0.745468 GGACGGAGGGAGTACATCAC 59.255 60.000 0.00 0.00 0.00 3.06
1749 1788 0.396695 TGGGACGGAGGGAGTACATC 60.397 60.000 0.00 0.00 0.00 3.06
1750 1789 0.264955 ATGGGACGGAGGGAGTACAT 59.735 55.000 0.00 0.00 0.00 2.29
1751 1790 0.928505 TATGGGACGGAGGGAGTACA 59.071 55.000 0.00 0.00 0.00 2.90
1752 1791 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
1754 1793 1.424638 CATTATGGGACGGAGGGAGT 58.575 55.000 0.00 0.00 0.00 3.85
1755 1794 0.035458 GCATTATGGGACGGAGGGAG 59.965 60.000 0.00 0.00 0.00 4.30
1756 1795 0.692756 TGCATTATGGGACGGAGGGA 60.693 55.000 0.00 0.00 0.00 4.20
1758 1797 1.140852 TCTTGCATTATGGGACGGAGG 59.859 52.381 0.00 0.00 0.00 4.30
1760 1799 2.437651 TCATCTTGCATTATGGGACGGA 59.562 45.455 8.47 0.00 0.00 4.69
1761 1800 2.849942 TCATCTTGCATTATGGGACGG 58.150 47.619 8.47 0.00 0.00 4.79
1765 1804 7.010738 GTGTCAAAAATCATCTTGCATTATGGG 59.989 37.037 8.47 0.00 0.00 4.00
1766 1805 7.762615 AGTGTCAAAAATCATCTTGCATTATGG 59.237 33.333 8.47 0.00 0.00 2.74
1767 1806 8.697846 AGTGTCAAAAATCATCTTGCATTATG 57.302 30.769 0.00 0.00 0.00 1.90
1768 1807 9.793252 GTAGTGTCAAAAATCATCTTGCATTAT 57.207 29.630 0.00 0.00 0.00 1.28
1770 1809 7.596248 GTGTAGTGTCAAAAATCATCTTGCATT 59.404 33.333 0.00 0.00 0.00 3.56
1772 1811 6.262944 AGTGTAGTGTCAAAAATCATCTTGCA 59.737 34.615 0.00 0.00 0.00 4.08
1773 1812 6.672147 AGTGTAGTGTCAAAAATCATCTTGC 58.328 36.000 0.00 0.00 0.00 4.01
1774 1813 9.817365 CTTAGTGTAGTGTCAAAAATCATCTTG 57.183 33.333 0.00 0.00 0.00 3.02
1775 1814 9.561069 ACTTAGTGTAGTGTCAAAAATCATCTT 57.439 29.630 0.00 0.00 0.00 2.40
1777 1816 8.988934 TGACTTAGTGTAGTGTCAAAAATCATC 58.011 33.333 0.00 0.00 36.64 2.92
1805 1844 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
1806 1845 4.186159 CCGTCCCATAATGTAAGACGTTT 58.814 43.478 9.63 0.00 46.62 3.60
1807 1846 3.431207 CCCGTCCCATAATGTAAGACGTT 60.431 47.826 9.63 0.00 46.62 3.99
1810 1849 2.701951 TCCCCGTCCCATAATGTAAGAC 59.298 50.000 0.00 0.00 0.00 3.01
1811 1850 2.969950 CTCCCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
1812 1851 2.704065 ACTCCCCGTCCCATAATGTAAG 59.296 50.000 0.00 0.00 0.00 2.34
1813 1852 2.766736 ACTCCCCGTCCCATAATGTAA 58.233 47.619 0.00 0.00 0.00 2.41
1814 1853 2.482414 ACTCCCCGTCCCATAATGTA 57.518 50.000 0.00 0.00 0.00 2.29
1815 1854 2.326428 CTACTCCCCGTCCCATAATGT 58.674 52.381 0.00 0.00 0.00 2.71
1816 1855 2.326428 ACTACTCCCCGTCCCATAATG 58.674 52.381 0.00 0.00 0.00 1.90
1817 1856 2.789323 ACTACTCCCCGTCCCATAAT 57.211 50.000 0.00 0.00 0.00 1.28
1818 1857 3.909427 ATACTACTCCCCGTCCCATAA 57.091 47.619 0.00 0.00 0.00 1.90
1819 1858 3.899360 CAAATACTACTCCCCGTCCCATA 59.101 47.826 0.00 0.00 0.00 2.74
1820 1859 2.704065 CAAATACTACTCCCCGTCCCAT 59.296 50.000 0.00 0.00 0.00 4.00
1821 1860 2.112998 CAAATACTACTCCCCGTCCCA 58.887 52.381 0.00 0.00 0.00 4.37
1822 1861 2.391678 TCAAATACTACTCCCCGTCCC 58.608 52.381 0.00 0.00 0.00 4.46
1823 1862 4.100498 TGAATCAAATACTACTCCCCGTCC 59.900 45.833 0.00 0.00 0.00 4.79
1824 1863 5.068723 TCTGAATCAAATACTACTCCCCGTC 59.931 44.000 0.00 0.00 0.00 4.79
1825 1864 4.960469 TCTGAATCAAATACTACTCCCCGT 59.040 41.667 0.00 0.00 0.00 5.28
1826 1865 5.531122 TCTGAATCAAATACTACTCCCCG 57.469 43.478 0.00 0.00 0.00 5.73
1827 1866 5.071115 AGCTCTGAATCAAATACTACTCCCC 59.929 44.000 0.00 0.00 0.00 4.81
1828 1867 5.988561 CAGCTCTGAATCAAATACTACTCCC 59.011 44.000 0.00 0.00 0.00 4.30
1829 1868 6.578023 ACAGCTCTGAATCAAATACTACTCC 58.422 40.000 3.60 0.00 0.00 3.85
1830 1869 8.410141 ACTACAGCTCTGAATCAAATACTACTC 58.590 37.037 3.60 0.00 0.00 2.59
1831 1870 8.299990 ACTACAGCTCTGAATCAAATACTACT 57.700 34.615 3.60 0.00 0.00 2.57
1832 1871 7.650104 GGACTACAGCTCTGAATCAAATACTAC 59.350 40.741 3.60 0.00 0.00 2.73
1833 1872 7.342026 TGGACTACAGCTCTGAATCAAATACTA 59.658 37.037 3.60 0.00 0.00 1.82
1920 1969 5.592054 TGACTTAGAATATCCAGCAGAACG 58.408 41.667 0.00 0.00 0.00 3.95
1936 1987 6.153067 CGGAGAGCCTATGTAAATGACTTAG 58.847 44.000 0.00 0.00 36.16 2.18
1937 1988 5.010719 CCGGAGAGCCTATGTAAATGACTTA 59.989 44.000 0.00 0.00 0.00 2.24
1960 2011 2.217510 TGTAGTCAGGACTGAGGACC 57.782 55.000 12.07 0.00 42.52 4.46
2075 2162 5.356882 TGCTTAGAAAATTGTTCAGGACG 57.643 39.130 0.00 0.00 0.00 4.79
2078 2165 7.156876 TGGTATGCTTAGAAAATTGTTCAGG 57.843 36.000 0.00 0.00 0.00 3.86
2206 2302 7.201767 GCTGGATCTATATGCAAAACTCTGTTT 60.202 37.037 0.00 0.00 32.50 2.83
2252 2348 8.365399 TCAGTGTGAGATACAACTTTGTTAAG 57.635 34.615 0.00 0.00 41.89 1.85
2287 2389 7.503521 TGATAGGCGCACATGAATTTATTTA 57.496 32.000 10.83 0.00 0.00 1.40
2291 2393 4.261155 GCTTGATAGGCGCACATGAATTTA 60.261 41.667 10.83 0.00 0.00 1.40
2292 2394 3.489738 GCTTGATAGGCGCACATGAATTT 60.490 43.478 10.83 0.00 0.00 1.82
2293 2395 2.033801 GCTTGATAGGCGCACATGAATT 59.966 45.455 10.83 0.00 0.00 2.17
2353 2456 7.120285 ACATGTGATCATTTGGTAGTTGAAGAG 59.880 37.037 0.00 0.00 31.15 2.85
2527 2630 9.495382 AAGGAGGTCAGATAGAAAGTTATACTT 57.505 33.333 0.00 0.00 40.80 2.24
2704 2808 6.761312 TGAAATCTGAAAGGAAAATGTGCAT 58.239 32.000 0.00 0.00 0.00 3.96
2734 2838 6.607198 ACACTAATAAGGCCATGCAAAAGTAT 59.393 34.615 5.01 0.00 0.00 2.12
2998 4374 1.614241 ATTTCCGGACGGAGGGAGTG 61.614 60.000 13.64 0.00 46.06 3.51
2999 4375 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3010 4386 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
3016 4392 8.993424 AGATACAACCATTTCTAGGACAAGTAT 58.007 33.333 0.00 0.00 0.00 2.12
3073 4449 9.017669 CGCACGAAAACTAATACTAGAATAAGT 57.982 33.333 0.00 0.00 0.00 2.24
3075 4451 7.975616 ACCGCACGAAAACTAATACTAGAATAA 59.024 33.333 0.00 0.00 0.00 1.40
3076 4452 7.483307 ACCGCACGAAAACTAATACTAGAATA 58.517 34.615 0.00 0.00 0.00 1.75
3078 4454 5.713025 ACCGCACGAAAACTAATACTAGAA 58.287 37.500 0.00 0.00 0.00 2.10
3079 4455 5.314923 ACCGCACGAAAACTAATACTAGA 57.685 39.130 0.00 0.00 0.00 2.43
3081 4457 7.090173 ACTAAACCGCACGAAAACTAATACTA 58.910 34.615 0.00 0.00 0.00 1.82
3087 4489 7.148656 GGTTATAACTAAACCGCACGAAAACTA 60.149 37.037 15.05 0.00 37.26 2.24
3161 4563 2.634600 AGTGTGGTGTCAAAAACGCTA 58.365 42.857 0.00 0.00 38.49 4.26
3208 4611 3.461085 AGTACCAAGATACTCCCTCCGTA 59.539 47.826 0.00 0.00 28.86 4.02
3390 4794 3.055675 AGCCAATTAGCCAACGTACTACA 60.056 43.478 0.00 0.00 0.00 2.74
3394 4798 1.400494 CCAGCCAATTAGCCAACGTAC 59.600 52.381 0.00 0.00 0.00 3.67
3565 4969 8.950210 CAGAGTATGGACTTGTTGTTTTCATAT 58.050 33.333 0.00 0.00 35.45 1.78
3578 4982 9.533831 AATAAACCAAATTCAGAGTATGGACTT 57.466 29.630 0.00 0.00 35.45 3.01
3724 5128 3.389221 AGCTGGTTTTAATTGGTTTGCG 58.611 40.909 0.00 0.00 0.00 4.85
3872 5277 4.892934 ACTCCTATAAGAGAAGCTCACAGG 59.107 45.833 5.33 0.00 37.33 4.00
4158 5564 9.725019 AACTCAGACTCACAATTACATTATTCA 57.275 29.630 0.00 0.00 0.00 2.57
4195 5601 2.229062 GACAAAAGCCTACAGAAAGGGC 59.771 50.000 0.00 0.00 45.57 5.19
4525 5931 4.039852 TGTTTGTGTCAGCCTACATACAGA 59.960 41.667 0.00 0.00 35.07 3.41
4529 5935 5.616270 TCTTTGTTTGTGTCAGCCTACATA 58.384 37.500 0.00 0.00 0.00 2.29
4682 6088 8.798859 ACAGTGAAATAAAGCATATGAAGTCT 57.201 30.769 6.97 0.00 0.00 3.24
4765 6171 2.979813 GCAAATGTCTAACCAAGCGTTG 59.020 45.455 0.00 0.00 35.79 4.10
4784 6190 9.543783 GATCATTGAAGATATATATCTGCAGCA 57.456 33.333 25.87 16.88 46.28 4.41
4899 6306 9.654663 AGAAAATAGTAAGCACTCGAATACTTT 57.345 29.630 0.00 0.00 36.14 2.66
5253 6668 1.666888 GCCAAAATGTTGCACGAGGAG 60.667 52.381 0.00 0.00 33.01 3.69
5254 6669 0.313672 GCCAAAATGTTGCACGAGGA 59.686 50.000 0.00 0.00 33.01 3.71
5255 6670 0.031857 TGCCAAAATGTTGCACGAGG 59.968 50.000 0.00 0.00 33.01 4.63
5256 6671 1.987770 GATGCCAAAATGTTGCACGAG 59.012 47.619 0.00 0.00 33.01 4.18
5263 6678 4.792704 GCGGATTATCGATGCCAAAATGTT 60.793 41.667 8.54 0.00 0.00 2.71
5314 6729 0.039165 CGCCTGCCCAAAGAAAGAAC 60.039 55.000 0.00 0.00 0.00 3.01
5325 6740 2.639327 ATTTTGACTGCGCCTGCCC 61.639 57.895 4.18 0.00 41.78 5.36
5393 6808 5.939447 ACGAGTAGGCTTAGGTACTTAGAT 58.061 41.667 0.00 0.00 37.25 1.98
5394 6809 5.365021 ACGAGTAGGCTTAGGTACTTAGA 57.635 43.478 0.00 0.00 37.25 2.10
5404 6819 8.405418 ACAGATGATATTTACGAGTAGGCTTA 57.595 34.615 0.00 0.00 0.00 3.09
5599 7020 5.410439 GCAATTCTACTAGTTTTGTCCCGAA 59.590 40.000 0.00 0.00 0.00 4.30
5600 7021 4.933400 GCAATTCTACTAGTTTTGTCCCGA 59.067 41.667 0.00 0.00 0.00 5.14
5601 7022 4.935808 AGCAATTCTACTAGTTTTGTCCCG 59.064 41.667 0.00 0.00 0.00 5.14
5602 7023 6.612306 CAAGCAATTCTACTAGTTTTGTCCC 58.388 40.000 0.00 0.00 0.00 4.46
5603 7024 6.086871 GCAAGCAATTCTACTAGTTTTGTCC 58.913 40.000 0.00 0.00 0.00 4.02
5604 7025 6.668323 TGCAAGCAATTCTACTAGTTTTGTC 58.332 36.000 0.00 0.00 0.00 3.18
5605 7026 6.633500 TGCAAGCAATTCTACTAGTTTTGT 57.367 33.333 0.00 0.00 0.00 2.83
5606 7027 8.524870 AAATGCAAGCAATTCTACTAGTTTTG 57.475 30.769 0.00 2.17 0.00 2.44
5614 7035 4.263911 GCTCGAAAATGCAAGCAATTCTAC 59.736 41.667 16.60 6.96 34.86 2.59


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

AutoCloner maintained by Alex Coulton.