Multiple sequence alignment - TraesCS5D01G032600

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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 TraesCS5D01G032600 chr5D 100.000 3530 0 0 1 3530 30067784 30064255 0.000000e+00 6519.0
1 TraesCS5D01G032600 chr5D 87.082 1347 79 38 967 2272 507881429 507882721 0.000000e+00 1435.0
2 TraesCS5D01G032600 chr5D 93.271 862 50 7 3 861 303054427 303053571 0.000000e+00 1264.0
3 TraesCS5D01G032600 chr5D 90.217 828 68 12 42 861 136408660 136407838 0.000000e+00 1068.0
4 TraesCS5D01G032600 chr5D 84.949 990 66 38 967 1949 419085279 419084366 0.000000e+00 926.0
5 TraesCS5D01G032600 chr5A 86.459 1477 77 41 869 2272 635496357 635497783 0.000000e+00 1506.0
6 TraesCS5D01G032600 chr5A 98.039 51 1 0 2815 2865 139788088 139788038 4.850000e-14 89.8
7 TraesCS5D01G032600 chr4D 92.923 862 55 6 3 861 280170835 280169977 0.000000e+00 1249.0
8 TraesCS5D01G032600 chr4D 97.751 667 15 0 2864 3530 116066701 116066035 0.000000e+00 1149.0
9 TraesCS5D01G032600 chr4D 89.379 838 73 16 29 861 182730378 182731204 0.000000e+00 1040.0
10 TraesCS5D01G032600 chr4D 96.078 51 2 0 2815 2865 116066918 116066868 2.260000e-12 84.2
11 TraesCS5D01G032600 chr3D 92.477 864 56 8 3 861 208775375 208776234 0.000000e+00 1227.0
12 TraesCS5D01G032600 chr3D 92.245 864 58 8 3 861 208767584 208768443 0.000000e+00 1216.0
13 TraesCS5D01G032600 chr3D 92.125 546 33 4 2272 2816 213294041 213294577 0.000000e+00 761.0
14 TraesCS5D01G032600 chr7D 91.580 867 62 9 1 861 182360224 182359363 0.000000e+00 1186.0
15 TraesCS5D01G032600 chr5B 84.175 1327 92 48 967 2272 639154951 639153722 0.000000e+00 1179.0
16 TraesCS5D01G032600 chr5B 90.958 553 40 5 2272 2816 342899472 342898922 0.000000e+00 736.0
17 TraesCS5D01G032600 chr5B 90.842 546 46 3 2272 2816 661001396 661000854 0.000000e+00 728.0
18 TraesCS5D01G032600 chr6D 98.351 667 11 0 2864 3530 366985638 366984972 0.000000e+00 1171.0
19 TraesCS5D01G032600 chr6D 88.479 868 83 17 1 861 38258812 38257955 0.000000e+00 1033.0
20 TraesCS5D01G032600 chr6D 98.039 51 1 0 2815 2865 366985855 366985805 4.850000e-14 89.8
21 TraesCS5D01G032600 chr4A 97.447 666 17 0 2865 3530 346676818 346676153 0.000000e+00 1136.0
22 TraesCS5D01G032600 chr4A 94.000 50 3 0 2816 2865 346677035 346676986 3.780000e-10 76.8
23 TraesCS5D01G032600 chrUn 96.341 656 24 0 2875 3530 318575750 318575095 0.000000e+00 1079.0
24 TraesCS5D01G032600 chrUn 96.189 656 25 0 2875 3530 250121664 250122319 0.000000e+00 1074.0
25 TraesCS5D01G032600 chrUn 96.037 656 26 0 2875 3530 333585173 333584518 0.000000e+00 1068.0
26 TraesCS5D01G032600 chrUn 95.579 656 29 0 2875 3530 366319857 366319202 0.000000e+00 1051.0
27 TraesCS5D01G032600 chr1D 96.341 656 24 0 2875 3530 17295509 17294854 0.000000e+00 1079.0
28 TraesCS5D01G032600 chr1D 96.037 656 26 0 2875 3530 17283816 17283161 0.000000e+00 1068.0
29 TraesCS5D01G032600 chr2D 89.651 831 68 16 42 861 557516156 557516979 0.000000e+00 1042.0
30 TraesCS5D01G032600 chr3B 84.730 871 70 27 967 1827 767724910 767725727 0.000000e+00 813.0
31 TraesCS5D01G032600 chr3B 84.386 871 73 27 967 1827 767738017 767738834 0.000000e+00 797.0
32 TraesCS5D01G032600 chr3B 91.408 547 41 4 2272 2816 451157947 451157405 0.000000e+00 745.0
33 TraesCS5D01G032600 chr1B 91.606 548 40 5 2272 2816 468211995 468212539 0.000000e+00 752.0
34 TraesCS5D01G032600 chr7A 91.408 547 39 6 2272 2816 408604644 408604104 0.000000e+00 743.0
35 TraesCS5D01G032600 chr7A 90.597 553 41 5 2272 2816 705110769 705111318 0.000000e+00 723.0
36 TraesCS5D01G032600 chr7A 90.476 546 47 3 2272 2816 164159385 164158844 0.000000e+00 715.0
37 TraesCS5D01G032600 chr7A 98.039 51 1 0 2815 2865 408602956 408602906 4.850000e-14 89.8
38 TraesCS5D01G032600 chr7A 98.039 51 1 0 2815 2865 705114123 705114173 4.850000e-14 89.8
39 TraesCS5D01G032600 chr6B 91.408 547 39 6 2272 2816 233929094 233929634 0.000000e+00 743.0
40 TraesCS5D01G032600 chr2A 92.157 51 4 0 2815 2865 345852581 345852531 4.890000e-09 73.1


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 TraesCS5D01G032600 chr5D 30064255 30067784 3529 True 6519.0 6519 100.0000 1 3530 1 chr5D.!!$R1 3529
1 TraesCS5D01G032600 chr5D 507881429 507882721 1292 False 1435.0 1435 87.0820 967 2272 1 chr5D.!!$F1 1305
2 TraesCS5D01G032600 chr5D 303053571 303054427 856 True 1264.0 1264 93.2710 3 861 1 chr5D.!!$R3 858
3 TraesCS5D01G032600 chr5D 136407838 136408660 822 True 1068.0 1068 90.2170 42 861 1 chr5D.!!$R2 819
4 TraesCS5D01G032600 chr5D 419084366 419085279 913 True 926.0 926 84.9490 967 1949 1 chr5D.!!$R4 982
5 TraesCS5D01G032600 chr5A 635496357 635497783 1426 False 1506.0 1506 86.4590 869 2272 1 chr5A.!!$F1 1403
6 TraesCS5D01G032600 chr4D 280169977 280170835 858 True 1249.0 1249 92.9230 3 861 1 chr4D.!!$R1 858
7 TraesCS5D01G032600 chr4D 182730378 182731204 826 False 1040.0 1040 89.3790 29 861 1 chr4D.!!$F1 832
8 TraesCS5D01G032600 chr4D 116066035 116066918 883 True 616.6 1149 96.9145 2815 3530 2 chr4D.!!$R2 715
9 TraesCS5D01G032600 chr3D 208775375 208776234 859 False 1227.0 1227 92.4770 3 861 1 chr3D.!!$F2 858
10 TraesCS5D01G032600 chr3D 208767584 208768443 859 False 1216.0 1216 92.2450 3 861 1 chr3D.!!$F1 858
11 TraesCS5D01G032600 chr3D 213294041 213294577 536 False 761.0 761 92.1250 2272 2816 1 chr3D.!!$F3 544
12 TraesCS5D01G032600 chr7D 182359363 182360224 861 True 1186.0 1186 91.5800 1 861 1 chr7D.!!$R1 860
13 TraesCS5D01G032600 chr5B 639153722 639154951 1229 True 1179.0 1179 84.1750 967 2272 1 chr5B.!!$R2 1305
14 TraesCS5D01G032600 chr5B 342898922 342899472 550 True 736.0 736 90.9580 2272 2816 1 chr5B.!!$R1 544
15 TraesCS5D01G032600 chr5B 661000854 661001396 542 True 728.0 728 90.8420 2272 2816 1 chr5B.!!$R3 544
16 TraesCS5D01G032600 chr6D 38257955 38258812 857 True 1033.0 1033 88.4790 1 861 1 chr6D.!!$R1 860
17 TraesCS5D01G032600 chr6D 366984972 366985855 883 True 630.4 1171 98.1950 2815 3530 2 chr6D.!!$R2 715
18 TraesCS5D01G032600 chr4A 346676153 346677035 882 True 606.4 1136 95.7235 2816 3530 2 chr4A.!!$R1 714
19 TraesCS5D01G032600 chrUn 318575095 318575750 655 True 1079.0 1079 96.3410 2875 3530 1 chrUn.!!$R1 655
20 TraesCS5D01G032600 chrUn 250121664 250122319 655 False 1074.0 1074 96.1890 2875 3530 1 chrUn.!!$F1 655
21 TraesCS5D01G032600 chrUn 333584518 333585173 655 True 1068.0 1068 96.0370 2875 3530 1 chrUn.!!$R2 655
22 TraesCS5D01G032600 chrUn 366319202 366319857 655 True 1051.0 1051 95.5790 2875 3530 1 chrUn.!!$R3 655
23 TraesCS5D01G032600 chr1D 17294854 17295509 655 True 1079.0 1079 96.3410 2875 3530 1 chr1D.!!$R2 655
24 TraesCS5D01G032600 chr1D 17283161 17283816 655 True 1068.0 1068 96.0370 2875 3530 1 chr1D.!!$R1 655
25 TraesCS5D01G032600 chr2D 557516156 557516979 823 False 1042.0 1042 89.6510 42 861 1 chr2D.!!$F1 819
26 TraesCS5D01G032600 chr3B 767724910 767725727 817 False 813.0 813 84.7300 967 1827 1 chr3B.!!$F1 860
27 TraesCS5D01G032600 chr3B 767738017 767738834 817 False 797.0 797 84.3860 967 1827 1 chr3B.!!$F2 860
28 TraesCS5D01G032600 chr3B 451157405 451157947 542 True 745.0 745 91.4080 2272 2816 1 chr3B.!!$R1 544
29 TraesCS5D01G032600 chr1B 468211995 468212539 544 False 752.0 752 91.6060 2272 2816 1 chr1B.!!$F1 544
30 TraesCS5D01G032600 chr7A 164158844 164159385 541 True 715.0 715 90.4760 2272 2816 1 chr7A.!!$R1 544
31 TraesCS5D01G032600 chr7A 408602906 408604644 1738 True 416.4 743 94.7235 2272 2865 2 chr7A.!!$R2 593
32 TraesCS5D01G032600 chr7A 705110769 705114173 3404 False 406.4 723 94.3180 2272 2865 2 chr7A.!!$F1 593
33 TraesCS5D01G032600 chr6B 233929094 233929634 540 False 743.0 743 91.4080 2272 2816 1 chr6B.!!$F1 544

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
878 889 0.892755 TTGAACATACCCTCTCGCGT 59.107 50.0 5.77 0.0 0.0 6.01 F
1394 1421 0.250209 CTCCTGCTGCTCACTGTGTT 60.250 55.0 7.79 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1911 0.244994 GAAGCGGTCTGAAGCTGAGA 59.755 55.0 9.23 0.0 43.78 3.27 R
2656 2798 0.306533 TTCGCGACCAGAAAAAGTGC 59.693 50.0 9.15 0.0 0.00 4.40 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
461 466 6.698008 AATATGCACATGAGGATTTTTCGA 57.302 33.333 1.99 0.00 0.00 3.71
477 482 7.960195 GGATTTTTCGAAATTGTTGTTTGTTGT 59.040 29.630 12.12 0.00 0.00 3.32
500 505 1.543802 CCGGCCTCATTTAAACTTGCA 59.456 47.619 0.00 0.00 0.00 4.08
672 683 2.222007 TGTTTGTGCACTTTGCCATC 57.778 45.000 19.41 1.01 44.23 3.51
673 684 1.479730 TGTTTGTGCACTTTGCCATCA 59.520 42.857 19.41 3.54 44.23 3.07
696 707 7.281841 TCACATGCCTCATTAAATCAGACATA 58.718 34.615 0.00 0.00 0.00 2.29
768 779 4.993029 ATGTTGTTTGTTTCTTTCCGGA 57.007 36.364 0.00 0.00 0.00 5.14
807 818 1.572941 GGTTTCGTTCCGGAGTTGC 59.427 57.895 3.34 0.00 0.00 4.17
839 850 6.534793 TCGTTTAACTAAGTCCGTTTGTCTTT 59.465 34.615 0.00 0.00 0.00 2.52
843 854 5.746307 ACTAAGTCCGTTTGTCTTTTTCC 57.254 39.130 0.00 0.00 0.00 3.13
851 862 3.877508 CGTTTGTCTTTTTCCTGGACTCT 59.122 43.478 0.00 0.00 0.00 3.24
852 863 4.260784 CGTTTGTCTTTTTCCTGGACTCTG 60.261 45.833 0.00 0.00 0.00 3.35
853 864 4.503714 TTGTCTTTTTCCTGGACTCTGT 57.496 40.909 0.00 0.00 0.00 3.41
854 865 4.503714 TGTCTTTTTCCTGGACTCTGTT 57.496 40.909 0.00 0.00 0.00 3.16
855 866 4.451900 TGTCTTTTTCCTGGACTCTGTTC 58.548 43.478 0.00 0.00 0.00 3.18
856 867 4.164221 TGTCTTTTTCCTGGACTCTGTTCT 59.836 41.667 0.00 0.00 0.00 3.01
857 868 5.126779 GTCTTTTTCCTGGACTCTGTTCTT 58.873 41.667 0.00 0.00 0.00 2.52
858 869 5.237561 GTCTTTTTCCTGGACTCTGTTCTTC 59.762 44.000 0.00 0.00 0.00 2.87
859 870 5.131142 TCTTTTTCCTGGACTCTGTTCTTCT 59.869 40.000 0.00 0.00 0.00 2.85
860 871 5.373812 TTTTCCTGGACTCTGTTCTTCTT 57.626 39.130 0.00 0.00 0.00 2.52
861 872 4.342862 TTCCTGGACTCTGTTCTTCTTG 57.657 45.455 0.00 0.00 0.00 3.02
862 873 3.576861 TCCTGGACTCTGTTCTTCTTGA 58.423 45.455 0.00 0.00 0.00 3.02
863 874 3.967326 TCCTGGACTCTGTTCTTCTTGAA 59.033 43.478 0.00 0.00 0.00 2.69
878 889 0.892755 TTGAACATACCCTCTCGCGT 59.107 50.000 5.77 0.00 0.00 6.01
916 927 2.874751 GGATCAACCCGTTTGCCG 59.125 61.111 0.00 0.00 34.88 5.69
946 957 1.520342 GGAGATCGCTGCTGGTGAC 60.520 63.158 0.00 0.00 37.27 3.67
960 971 2.119611 TGACGGCCTGAAGAGGGA 59.880 61.111 0.00 0.00 40.19 4.20
965 976 3.077556 GCCTGAAGAGGGAGCGGA 61.078 66.667 0.00 0.00 40.19 5.54
988 999 6.029346 AGATTTGATTTGTGATTTCGGCTT 57.971 33.333 0.00 0.00 0.00 4.35
1233 1254 1.356124 CCTCCAGATCCCATCCGATT 58.644 55.000 0.00 0.00 0.00 3.34
1310 1331 1.941734 GACGCCGCTCTGATTCTCG 60.942 63.158 0.00 0.00 0.00 4.04
1394 1421 0.250209 CTCCTGCTGCTCACTGTGTT 60.250 55.000 7.79 0.00 0.00 3.32
1395 1422 0.533531 TCCTGCTGCTCACTGTGTTG 60.534 55.000 7.79 3.68 0.00 3.33
1493 1550 1.102154 CCAACCACTGTTTGCTCACA 58.898 50.000 0.00 0.00 30.42 3.58
1712 1803 7.010923 GCTCTTCTTGTTCATCTAACCATGTAG 59.989 40.741 0.00 0.00 37.27 2.74
1713 1804 7.907389 TCTTCTTGTTCATCTAACCATGTAGT 58.093 34.615 0.00 0.00 37.27 2.73
1758 1852 3.181482 CGACTACAGAGTGCTCATGGATT 60.181 47.826 1.82 0.00 35.45 3.01
1778 1872 7.918076 TGGATTATTTTAGACAAGTCTCCACT 58.082 34.615 5.91 0.00 40.93 4.00
1811 1905 5.306114 AGCTAGGCGAAGGGTAATAATTT 57.694 39.130 0.00 0.00 0.00 1.82
1817 1911 5.949952 AGGCGAAGGGTAATAATTTCTGTTT 59.050 36.000 0.00 0.00 0.00 2.83
1830 1924 5.938438 ATTTCTGTTTCTCAGCTTCAGAC 57.062 39.130 0.00 0.00 43.32 3.51
1851 1948 4.642429 ACCGCTTCTCATTTTCTGTACTT 58.358 39.130 0.00 0.00 0.00 2.24
1852 1949 5.063880 ACCGCTTCTCATTTTCTGTACTTT 58.936 37.500 0.00 0.00 0.00 2.66
1853 1950 5.179555 ACCGCTTCTCATTTTCTGTACTTTC 59.820 40.000 0.00 0.00 0.00 2.62
1867 1973 5.713861 TCTGTACTTTCCTAGTTCCCAGTAC 59.286 44.000 0.00 0.00 38.33 2.73
1870 1976 2.226962 TTCCTAGTTCCCAGTACGCT 57.773 50.000 0.00 0.00 0.00 5.07
1910 2016 5.721876 TCGTACGAATTGTTGTTTTGTCT 57.278 34.783 17.11 0.00 0.00 3.41
1923 2029 3.460340 TGTTTTGTCTAAGTCCTTGGGGA 59.540 43.478 0.00 0.00 39.70 4.81
1959 2068 7.708322 TCATTTAGTCAGCACTGATATCACTTC 59.292 37.037 0.00 0.00 42.18 3.01
1961 2070 5.008619 AGTCAGCACTGATATCACTTCTG 57.991 43.478 0.00 8.79 42.18 3.02
1979 2095 7.225931 TCACTTCTGTAAAAGTAAACGCAAGAT 59.774 33.333 0.00 0.00 37.38 2.40
1982 2098 8.555166 TTCTGTAAAAGTAAACGCAAGATTTG 57.445 30.769 0.00 0.00 43.62 2.32
2018 2144 6.974965 AGCTTTTATTGGCTATCATTAGTGC 58.025 36.000 0.00 0.00 37.00 4.40
2023 2149 9.748708 TTTTATTGGCTATCATTAGTGCAATTC 57.251 29.630 0.00 0.00 0.00 2.17
2032 2158 6.426980 TCATTAGTGCAATTCTCATGTCAC 57.573 37.500 0.00 0.00 0.00 3.67
2034 2162 7.330262 TCATTAGTGCAATTCTCATGTCACTA 58.670 34.615 0.00 0.00 36.87 2.74
2092 2225 6.791867 TGCTCATAGTTACACTTACAGGAT 57.208 37.500 0.00 0.00 0.00 3.24
2093 2226 7.182817 TGCTCATAGTTACACTTACAGGATT 57.817 36.000 0.00 0.00 0.00 3.01
2094 2227 8.301252 TGCTCATAGTTACACTTACAGGATTA 57.699 34.615 0.00 0.00 0.00 1.75
2095 2228 8.195436 TGCTCATAGTTACACTTACAGGATTAC 58.805 37.037 0.00 0.00 0.00 1.89
2096 2229 8.195436 GCTCATAGTTACACTTACAGGATTACA 58.805 37.037 0.00 0.00 0.00 2.41
2097 2230 9.737427 CTCATAGTTACACTTACAGGATTACAG 57.263 37.037 0.00 0.00 0.00 2.74
2098 2231 8.692710 TCATAGTTACACTTACAGGATTACAGG 58.307 37.037 0.00 0.00 0.00 4.00
2099 2232 8.692710 CATAGTTACACTTACAGGATTACAGGA 58.307 37.037 0.00 0.00 0.00 3.86
2100 2233 7.171630 AGTTACACTTACAGGATTACAGGAG 57.828 40.000 0.00 0.00 0.00 3.69
2152 2285 9.429359 AGAATTGAATAGTCAGTTGTACTTCTG 57.571 33.333 5.61 10.21 34.13 3.02
2153 2286 9.424319 GAATTGAATAGTCAGTTGTACTTCTGA 57.576 33.333 5.61 13.61 34.13 3.27
2154 2287 9.950496 AATTGAATAGTCAGTTGTACTTCTGAT 57.050 29.630 18.19 12.17 41.67 2.90
2173 2306 9.670719 CTTCTGATTTCTGAAGGTTTTCTTTAC 57.329 33.333 15.57 0.00 43.68 2.01
2177 2310 8.405531 TGATTTCTGAAGGTTTTCTTTACTGTG 58.594 33.333 0.00 0.00 35.50 3.66
2184 2317 5.625150 AGGTTTTCTTTACTGTGCTCAGAT 58.375 37.500 21.96 9.03 43.76 2.90
2229 2363 5.756849 CCAACTTTTGCTTGTTTTGTGTTT 58.243 33.333 0.00 0.00 0.00 2.83
2321 2455 9.787435 TCACCTTCAATAACTTTGTAAGTACAT 57.213 29.630 0.00 0.00 41.91 2.29
2407 2541 3.020274 AGTCTCTACATGCACAGTCGAT 58.980 45.455 0.00 0.00 0.00 3.59
2449 2583 0.250513 GCATCAGGGAGGTCGAGTTT 59.749 55.000 0.00 0.00 0.00 2.66
2482 2616 1.084289 GTACATGGTTGTCGGCTTCC 58.916 55.000 0.00 0.00 37.28 3.46
2496 2630 1.202940 GGCTTCCACTTTCTTCCACCT 60.203 52.381 0.00 0.00 0.00 4.00
2507 2641 1.275291 TCTTCCACCTAGGTGCTTTCG 59.725 52.381 32.98 20.27 44.16 3.46
2517 2651 0.459585 GGTGCTTTCGCTCGGTGATA 60.460 55.000 0.00 0.00 36.97 2.15
2523 2657 0.459585 TTCGCTCGGTGATACAAGGC 60.460 55.000 0.00 0.00 0.00 4.35
2560 2694 3.719268 TGTGAGCTCTCTCTCTCTCTT 57.281 47.619 16.19 0.00 40.03 2.85
2583 2723 4.055360 TCACTGTCCGTGTTCATGTTTAG 58.945 43.478 0.00 0.00 44.16 1.85
2640 2780 4.827692 TGGCGAACATACTTTGTGTAGAT 58.172 39.130 0.00 0.00 38.99 1.98
2645 2785 7.691050 GGCGAACATACTTTGTGTAGATAAAAC 59.309 37.037 0.00 0.00 38.99 2.43
2672 2814 2.492019 AAAGCACTTTTTCTGGTCGC 57.508 45.000 0.00 0.00 0.00 5.19
2683 2825 0.793861 TCTGGTCGCGAAATTTTCCG 59.206 50.000 12.06 3.63 0.00 4.30
2694 2836 5.275418 CGCGAAATTTTCCGAATTTGATCTG 60.275 40.000 0.00 0.00 30.68 2.90
2855 5833 0.250858 TGCATATGGAAGCATCCCCG 60.251 55.000 5.34 0.00 45.95 5.73
3027 6173 5.380900 TCAGTTCAGATCTCGATAGACCAT 58.619 41.667 0.00 0.00 42.67 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 5.237344 ACACTGGATAATGCTAAAATCGCTC 59.763 40.000 0.00 0.00 0.00 5.03
340 345 6.523035 TCTATGCATTTTCCTACCCCATTA 57.477 37.500 3.54 0.00 0.00 1.90
461 466 4.142795 GCCGGAAACAACAAACAACAATTT 60.143 37.500 5.05 0.00 0.00 1.82
477 482 3.305744 GCAAGTTTAAATGAGGCCGGAAA 60.306 43.478 5.05 0.00 0.00 3.13
672 683 5.823209 TGTCTGATTTAATGAGGCATGTG 57.177 39.130 0.00 0.00 0.00 3.21
673 684 7.056006 TGTATGTCTGATTTAATGAGGCATGT 58.944 34.615 18.90 0.27 39.18 3.21
717 728 5.046448 ACAACCATCACATAAACATGGCATT 60.046 36.000 0.00 0.00 40.85 3.56
768 779 3.182967 CGAAGCTAACGAGAGAAGCAAT 58.817 45.455 7.33 0.00 42.97 3.56
819 830 7.011669 CAGGAAAAAGACAAACGGACTTAGTTA 59.988 37.037 0.00 0.00 31.22 2.24
820 831 5.884232 AGGAAAAAGACAAACGGACTTAGTT 59.116 36.000 0.00 0.00 31.22 2.24
825 836 2.949644 CCAGGAAAAAGACAAACGGACT 59.050 45.455 0.00 0.00 0.00 3.85
839 850 4.408921 TCAAGAAGAACAGAGTCCAGGAAA 59.591 41.667 0.00 0.00 0.00 3.13
853 864 4.620803 GCGAGAGGGTATGTTCAAGAAGAA 60.621 45.833 0.00 0.00 0.00 2.52
854 865 3.119101 GCGAGAGGGTATGTTCAAGAAGA 60.119 47.826 0.00 0.00 0.00 2.87
855 866 3.190874 GCGAGAGGGTATGTTCAAGAAG 58.809 50.000 0.00 0.00 0.00 2.85
856 867 2.416836 CGCGAGAGGGTATGTTCAAGAA 60.417 50.000 0.00 0.00 39.50 2.52
857 868 1.134367 CGCGAGAGGGTATGTTCAAGA 59.866 52.381 0.00 0.00 39.50 3.02
858 869 1.560923 CGCGAGAGGGTATGTTCAAG 58.439 55.000 0.00 0.00 39.50 3.02
859 870 3.733236 CGCGAGAGGGTATGTTCAA 57.267 52.632 0.00 0.00 39.50 2.69
943 954 1.984570 CTCCCTCTTCAGGCCGTCA 60.985 63.158 0.00 0.00 38.72 4.35
946 957 4.521062 CGCTCCCTCTTCAGGCCG 62.521 72.222 0.00 0.00 38.72 6.13
960 971 5.644644 GAAATCACAAATCAAATCTCCGCT 58.355 37.500 0.00 0.00 0.00 5.52
965 976 5.649782 AGCCGAAATCACAAATCAAATCT 57.350 34.783 0.00 0.00 0.00 2.40
1039 1053 3.123620 CGCCAGCTTGAGCCTGAC 61.124 66.667 0.00 0.00 43.38 3.51
1075 1089 3.237741 CTCCTGGGGCGGGATCTC 61.238 72.222 0.00 0.00 38.36 2.75
1219 1240 2.613977 GCATTCGAATCGGATGGGATCT 60.614 50.000 23.55 0.00 42.49 2.75
1261 1282 0.884704 GCGTTTCAGAGAGTTGCCCA 60.885 55.000 0.00 0.00 0.00 5.36
1297 1318 1.208009 GCAGAGCGAGAATCAGAGCG 61.208 60.000 0.00 0.00 33.17 5.03
1304 1325 0.390866 CACACCTGCAGAGCGAGAAT 60.391 55.000 17.39 0.00 0.00 2.40
1310 1331 3.418068 GACGCACACCTGCAGAGC 61.418 66.667 17.39 12.44 44.50 4.09
1368 1389 3.678951 GAGCAGCAGGAGTGAGGGC 62.679 68.421 0.00 0.00 0.00 5.19
1394 1421 5.123027 GGCAAAAGGAATTCAAACAAACACA 59.877 36.000 7.93 0.00 0.00 3.72
1395 1422 5.568482 GGCAAAAGGAATTCAAACAAACAC 58.432 37.500 7.93 0.00 0.00 3.32
1562 1623 3.592059 GTTGTAGATGTGGCGGTAGAAA 58.408 45.455 0.00 0.00 0.00 2.52
1686 1765 5.645497 ACATGGTTAGATGAACAAGAAGAGC 59.355 40.000 0.00 0.00 40.09 4.09
1687 1766 8.037758 ACTACATGGTTAGATGAACAAGAAGAG 58.962 37.037 0.00 0.00 40.09 2.85
1712 1803 0.961753 CTCCACCTGAAGGCCAAAAC 59.038 55.000 5.01 0.00 39.32 2.43
1713 1804 0.827507 GCTCCACCTGAAGGCCAAAA 60.828 55.000 5.01 0.00 39.32 2.44
1758 1852 6.360370 AGCAGTGGAGACTTGTCTAAAATA 57.640 37.500 3.00 0.00 0.00 1.40
1778 1872 0.391661 CGCCTAGCTCCAAGAAAGCA 60.392 55.000 0.00 0.00 42.35 3.91
1817 1911 0.244994 GAAGCGGTCTGAAGCTGAGA 59.755 55.000 9.23 0.00 43.78 3.27
1830 1924 5.390991 GGAAAGTACAGAAAATGAGAAGCGG 60.391 44.000 0.00 0.00 0.00 5.52
1851 1948 1.822990 CAGCGTACTGGGAACTAGGAA 59.177 52.381 0.00 0.00 40.48 3.36
1852 1949 1.471119 CAGCGTACTGGGAACTAGGA 58.529 55.000 0.00 0.00 40.48 2.94
1867 1973 1.008538 GCACAAGTTCCCAACAGCG 60.009 57.895 0.00 0.00 0.00 5.18
1870 1976 1.398692 GAAGGCACAAGTTCCCAACA 58.601 50.000 0.00 0.00 0.00 3.33
1910 2016 2.983192 TGATGTGTTCCCCAAGGACTTA 59.017 45.455 0.00 0.00 43.90 2.24
1923 2029 6.432162 AGTGCTGACTAAATGATTGATGTGTT 59.568 34.615 0.00 0.00 0.00 3.32
1959 2068 7.908193 ACAAATCTTGCGTTTACTTTTACAG 57.092 32.000 0.00 0.00 0.00 2.74
2018 2144 7.206981 ACAAACCTTAGTGACATGAGAATTG 57.793 36.000 0.00 0.00 0.00 2.32
2023 2149 5.643777 CCCTTACAAACCTTAGTGACATGAG 59.356 44.000 0.00 0.00 0.00 2.90
2032 2158 8.454570 TTTTACTTCACCCTTACAAACCTTAG 57.545 34.615 0.00 0.00 0.00 2.18
2034 2162 7.721409 TTTTTACTTCACCCTTACAAACCTT 57.279 32.000 0.00 0.00 0.00 3.50
2096 2229 4.656112 TCTCTTTCTTTGTCAGGTTCTCCT 59.344 41.667 0.00 0.00 46.37 3.69
2097 2230 4.962155 TCTCTTTCTTTGTCAGGTTCTCC 58.038 43.478 0.00 0.00 0.00 3.71
2098 2231 7.657761 TGTAATCTCTTTCTTTGTCAGGTTCTC 59.342 37.037 0.00 0.00 0.00 2.87
2099 2232 7.509546 TGTAATCTCTTTCTTTGTCAGGTTCT 58.490 34.615 0.00 0.00 0.00 3.01
2100 2233 7.730364 TGTAATCTCTTTCTTTGTCAGGTTC 57.270 36.000 0.00 0.00 0.00 3.62
2130 2263 9.778741 AAATCAGAAGTACAACTGACTATTCAA 57.221 29.630 19.15 1.59 44.18 2.69
2140 2273 6.831976 ACCTTCAGAAATCAGAAGTACAACT 58.168 36.000 12.67 0.00 37.66 3.16
2142 2275 8.519799 AAAACCTTCAGAAATCAGAAGTACAA 57.480 30.769 12.67 0.00 37.66 2.41
2150 2283 8.624776 ACAGTAAAGAAAACCTTCAGAAATCAG 58.375 33.333 0.00 0.00 33.02 2.90
2152 2285 7.379797 GCACAGTAAAGAAAACCTTCAGAAATC 59.620 37.037 0.00 0.00 33.02 2.17
2153 2286 7.068716 AGCACAGTAAAGAAAACCTTCAGAAAT 59.931 33.333 0.00 0.00 33.02 2.17
2154 2287 6.377146 AGCACAGTAAAGAAAACCTTCAGAAA 59.623 34.615 0.00 0.00 33.02 2.52
2177 2310 4.685628 GCTCTAGTGCTTATGAATCTGAGC 59.314 45.833 9.52 0.00 36.83 4.26
2294 2428 9.787435 TGTACTTACAAAGTTATTGAAGGTGAT 57.213 29.630 0.00 0.00 42.81 3.06
2352 2486 4.646040 CACCCATTCCTCAGATTGCAATAA 59.354 41.667 12.97 1.92 0.00 1.40
2367 2501 7.727181 AGAGACTACAATATACACACCCATTC 58.273 38.462 0.00 0.00 0.00 2.67
2407 2541 2.058705 TGGGGTTGGACTGAACACATA 58.941 47.619 0.00 0.00 30.15 2.29
2449 2583 2.126463 GTACTGCTGCTCGCGACA 60.126 61.111 3.71 8.02 43.27 4.35
2482 2616 2.039084 AGCACCTAGGTGGAAGAAAGTG 59.961 50.000 36.91 13.36 45.49 3.16
2507 2641 1.009829 CAAGCCTTGTATCACCGAGC 58.990 55.000 0.00 0.00 0.00 5.03
2523 2657 4.154918 GCTCACAAGGGAGAACATTACAAG 59.845 45.833 2.96 0.00 37.05 3.16
2531 2665 1.899142 AGAGAGCTCACAAGGGAGAAC 59.101 52.381 17.77 0.00 37.05 3.01
2583 2723 6.088616 GCATCACAAAGAAATTGAAGCAGTAC 59.911 38.462 0.00 0.00 41.85 2.73
2618 2758 4.260139 TCTACACAAAGTATGTTCGCCA 57.740 40.909 0.00 0.00 41.46 5.69
2656 2798 0.306533 TTCGCGACCAGAAAAAGTGC 59.693 50.000 9.15 0.00 0.00 4.40
2670 2812 4.793216 AGATCAAATTCGGAAAATTTCGCG 59.207 37.500 0.00 0.00 0.00 5.87
2672 2814 6.092748 ACCAGATCAAATTCGGAAAATTTCG 58.907 36.000 0.00 0.00 0.00 3.46
2683 2825 5.877012 TGAACTGCTAGACCAGATCAAATTC 59.123 40.000 7.54 0.85 40.31 2.17
2694 2836 5.643777 ACAATACATGTTGAACTGCTAGACC 59.356 40.000 2.30 0.00 40.06 3.85
2801 2945 4.129380 CACCAAGACACTGATCTGTTCAA 58.871 43.478 1.95 0.00 32.78 2.69
2806 2950 2.174363 TGCACCAAGACACTGATCTG 57.826 50.000 0.00 0.00 0.00 2.90
2808 2952 2.703416 TCATGCACCAAGACACTGATC 58.297 47.619 0.00 0.00 0.00 2.92
2809 2953 2.865119 TCATGCACCAAGACACTGAT 57.135 45.000 0.00 0.00 0.00 2.90
2810 2954 2.703416 GATCATGCACCAAGACACTGA 58.297 47.619 0.00 0.00 0.00 3.41
2811 2955 1.395954 CGATCATGCACCAAGACACTG 59.604 52.381 0.00 0.00 0.00 3.66
2812 2956 1.276138 TCGATCATGCACCAAGACACT 59.724 47.619 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.