Multiple sequence alignment - TraesCS2A01G539900

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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 TraesCS2A01G539900 chr2A 100.000 3901 0 0 1 3901 752099670 752103570 0.000000e+00 7204
1 TraesCS2A01G539900 chr2A 92.778 900 51 7 1 892 59004195 59003302 0.000000e+00 1290
2 TraesCS2A01G539900 chr2A 92.746 896 51 9 1 889 160012743 160011855 0.000000e+00 1282
3 TraesCS2A01G539900 chr2A 92.556 900 50 12 3 892 65198129 65199021 0.000000e+00 1275
4 TraesCS2A01G539900 chr2D 93.715 1241 51 5 1987 3209 620527150 620528381 0.000000e+00 1834
5 TraesCS2A01G539900 chr2D 92.667 900 53 8 1 893 647410736 647411629 0.000000e+00 1284
6 TraesCS2A01G539900 chr2D 90.929 926 45 17 888 1809 620526163 620527053 0.000000e+00 1208
7 TraesCS2A01G539900 chr2D 93.429 624 30 8 3275 3895 620528492 620529107 0.000000e+00 915
8 TraesCS2A01G539900 chr2D 93.617 94 6 0 1885 1978 589522339 589522246 1.460000e-29 141
9 TraesCS2A01G539900 chr7A 92.786 901 48 10 1 892 494626791 494625899 0.000000e+00 1288
10 TraesCS2A01G539900 chr7A 92.857 896 46 10 1 889 217947160 217948044 0.000000e+00 1284
11 TraesCS2A01G539900 chr7A 92.522 896 52 9 1 889 55367868 55368755 0.000000e+00 1269
12 TraesCS2A01G539900 chr1A 92.522 896 54 8 1 889 117931257 117932146 0.000000e+00 1271
13 TraesCS2A01G539900 chr5A 92.299 896 55 9 1 889 411879904 411880792 0.000000e+00 1260
14 TraesCS2A01G539900 chr5A 96.552 87 3 0 1885 1971 526875314 526875400 1.130000e-30 145
15 TraesCS2A01G539900 chr2B 89.849 926 63 16 2524 3432 760930760 760931671 0.000000e+00 1160
16 TraesCS2A01G539900 chr2B 90.867 646 42 7 890 1519 760928080 760928724 0.000000e+00 850
17 TraesCS2A01G539900 chr2B 89.144 479 22 8 3429 3900 760931727 760932182 1.570000e-158 569
18 TraesCS2A01G539900 chr2B 89.610 308 28 1 1586 1889 760928753 760929060 4.730000e-104 388
19 TraesCS2A01G539900 chr2B 91.791 268 21 1 1967 2234 760929055 760929321 4.760000e-99 372
20 TraesCS2A01G539900 chr2B 89.222 167 16 2 2316 2482 760929501 760929665 1.420000e-49 207
21 TraesCS2A01G539900 chr2B 87.261 157 12 2 888 1037 760896937 760897092 5.180000e-39 172
22 TraesCS2A01G539900 chr2B 97.647 85 2 0 1887 1971 494265169 494265085 3.140000e-31 147
23 TraesCS2A01G539900 chr6B 95.745 94 4 0 1879 1972 551951862 551951955 6.750000e-33 152
24 TraesCS2A01G539900 chr5D 96.552 87 3 0 1885 1971 128577586 128577672 1.130000e-30 145
25 TraesCS2A01G539900 chr3A 94.624 93 4 1 1880 1972 57262242 57262151 4.060000e-30 143
26 TraesCS2A01G539900 chr3B 93.617 94 6 0 1879 1972 635348212 635348119 1.460000e-29 141
27 TraesCS2A01G539900 chr7D 92.708 96 7 0 1877 1972 167548410 167548505 5.260000e-29 139
28 TraesCS2A01G539900 chrUn 91.176 102 7 2 1870 1971 104889222 104889321 1.890000e-28 137


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 TraesCS2A01G539900 chr2A 752099670 752103570 3900 False 7204 7204 100.0000 1 3901 1 chr2A.!!$F2 3900
1 TraesCS2A01G539900 chr2A 59003302 59004195 893 True 1290 1290 92.7780 1 892 1 chr2A.!!$R1 891
2 TraesCS2A01G539900 chr2A 160011855 160012743 888 True 1282 1282 92.7460 1 889 1 chr2A.!!$R2 888
3 TraesCS2A01G539900 chr2A 65198129 65199021 892 False 1275 1275 92.5560 3 892 1 chr2A.!!$F1 889
4 TraesCS2A01G539900 chr2D 620526163 620529107 2944 False 1319 1834 92.6910 888 3895 3 chr2D.!!$F2 3007
5 TraesCS2A01G539900 chr2D 647410736 647411629 893 False 1284 1284 92.6670 1 893 1 chr2D.!!$F1 892
6 TraesCS2A01G539900 chr7A 494625899 494626791 892 True 1288 1288 92.7860 1 892 1 chr7A.!!$R1 891
7 TraesCS2A01G539900 chr7A 217947160 217948044 884 False 1284 1284 92.8570 1 889 1 chr7A.!!$F2 888
8 TraesCS2A01G539900 chr7A 55367868 55368755 887 False 1269 1269 92.5220 1 889 1 chr7A.!!$F1 888
9 TraesCS2A01G539900 chr1A 117931257 117932146 889 False 1271 1271 92.5220 1 889 1 chr1A.!!$F1 888
10 TraesCS2A01G539900 chr5A 411879904 411880792 888 False 1260 1260 92.2990 1 889 1 chr5A.!!$F1 888
11 TraesCS2A01G539900 chr2B 760928080 760932182 4102 False 591 1160 90.0805 890 3900 6 chr2B.!!$F2 3010

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
960 986 0.035056 CCAAGGTTGAATCCTCCGCT 60.035 55.0 0.0 0.0 36.74 5.52 F
1143 1175 0.177141 TCCCCTTCCGATTTAGCGTG 59.823 55.0 0.0 0.0 0.00 5.34 F
1361 1397 0.601046 TGCCTGACAGCGAAGAACAG 60.601 55.0 0.0 0.0 34.65 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1853 0.391661 ATCTTGCGGTACTGTGGCTG 60.392 55.000 3.1 0.0 0.00 4.85 R
1959 2011 1.147191 TCTGTGTGGTACTCCCTCTGT 59.853 52.381 0.0 0.0 0.00 3.41 R
3314 4583 0.175760 GGCCTGAGCTTGTCGTGATA 59.824 55.000 0.0 0.0 39.73 2.15 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
51 52 5.163550 CGGTCACCACTGATGAGTAAGATTA 60.164 44.000 0.00 0.00 0.00 1.75
65 66 8.153221 TGAGTAAGATTACAAATGGGGAGTTA 57.847 34.615 5.59 0.00 36.12 2.24
81 82 1.026584 GTTACCACCGGTGCAGTTTT 58.973 50.000 29.75 10.27 36.19 2.43
83 84 1.025812 TACCACCGGTGCAGTTTTTG 58.974 50.000 29.75 14.99 36.19 2.44
84 85 0.968393 ACCACCGGTGCAGTTTTTGT 60.968 50.000 29.75 15.68 32.98 2.83
108 110 4.948341 ATGGCCGTACATACAACTATGA 57.052 40.909 0.00 0.00 34.77 2.15
127 129 7.120051 ACTATGACTATTATCTAGCGGATGGT 58.880 38.462 5.66 0.00 35.98 3.55
184 186 6.209361 GTTGAAAAAGCCAGAAGGTAAGAAG 58.791 40.000 0.00 0.00 37.19 2.85
245 247 2.909006 AGATGTGGAGAGAGCTTTTGGA 59.091 45.455 0.00 0.00 0.00 3.53
255 257 5.673514 AGAGAGCTTTTGGAATTTTGCAAA 58.326 33.333 8.05 8.05 44.88 3.68
300 303 1.664873 GACCGGCTAGATTTTGGGAC 58.335 55.000 0.00 0.00 0.00 4.46
330 333 3.504134 TGTTTTGGTACATAATGCACGCT 59.496 39.130 0.00 0.00 39.30 5.07
393 396 3.003897 GGCCAAGATGTAGACTACTCTCG 59.996 52.174 13.67 4.20 0.00 4.04
437 440 2.104859 CGAGTGCGACGGAGGACTA 61.105 63.158 6.55 0.00 42.89 2.59
480 483 2.037641 CCTCCTATCATGCCATTCGACA 59.962 50.000 0.00 0.00 0.00 4.35
760 771 1.730192 CATTTTTGCGCGCTGCTGA 60.730 52.632 33.29 14.58 46.63 4.26
796 812 0.536233 TTTTAGTGCGGCTGCTGGAA 60.536 50.000 20.27 6.76 43.34 3.53
797 813 0.322456 TTTAGTGCGGCTGCTGGAAT 60.322 50.000 20.27 9.57 43.34 3.01
833 849 1.228094 TCAAACCAGGTGATGCGCA 60.228 52.632 14.96 14.96 0.00 6.09
885 901 2.825836 GGCGCCTGTTGGAGATGG 60.826 66.667 22.15 0.00 34.95 3.51
957 983 0.684479 GCCCCAAGGTTGAATCCTCC 60.684 60.000 0.00 0.00 36.74 4.30
958 984 0.394352 CCCCAAGGTTGAATCCTCCG 60.394 60.000 0.00 0.00 36.74 4.63
960 986 0.035056 CCAAGGTTGAATCCTCCGCT 60.035 55.000 0.00 0.00 36.74 5.52
961 987 1.209504 CCAAGGTTGAATCCTCCGCTA 59.790 52.381 0.00 0.00 36.74 4.26
975 1001 2.508439 GCTAACACAGCGCCGCTA 60.508 61.111 13.03 0.00 41.37 4.26
1131 1163 2.368011 CGAACCTCCCCTCCCCTTC 61.368 68.421 0.00 0.00 0.00 3.46
1143 1175 0.177141 TCCCCTTCCGATTTAGCGTG 59.823 55.000 0.00 0.00 0.00 5.34
1289 1321 2.157738 GCAGCAGATTCCAAGTCTTGT 58.842 47.619 11.61 0.00 0.00 3.16
1312 1348 5.794687 TCGTCAGGCTGTGTATTAAAATG 57.205 39.130 15.27 0.00 0.00 2.32
1361 1397 0.601046 TGCCTGACAGCGAAGAACAG 60.601 55.000 0.00 0.00 34.65 3.16
1473 1509 1.078709 CGAAGAAGAGCGCCATTGAA 58.921 50.000 2.29 0.00 0.00 2.69
1524 1560 7.393515 ACAGATCATACACTGTGTTCTACTGTA 59.606 37.037 19.73 0.00 44.18 2.74
1525 1561 8.409371 CAGATCATACACTGTGTTCTACTGTAT 58.591 37.037 19.73 0.58 39.15 2.29
1526 1562 8.972127 AGATCATACACTGTGTTCTACTGTATT 58.028 33.333 19.73 0.00 39.15 1.89
1529 1565 9.239551 TCATACACTGTGTTCTACTGTATTACT 57.760 33.333 19.73 0.00 39.15 2.24
1530 1566 9.290483 CATACACTGTGTTCTACTGTATTACTG 57.710 37.037 19.73 0.00 39.15 2.74
1531 1567 7.520451 ACACTGTGTTCTACTGTATTACTGA 57.480 36.000 7.80 0.00 39.15 3.41
1559 1595 1.788229 TCCACCTCTGGCGATATCAA 58.212 50.000 3.12 0.00 37.49 2.57
1604 1640 5.471116 TCATATCATAGAAGCAATGTGCCAC 59.529 40.000 0.00 0.00 46.52 5.01
1629 1665 4.440880 GCTGCATCTCTAGTGAATGTTCT 58.559 43.478 0.00 0.00 0.00 3.01
1681 1717 3.707793 GATAGGTCTCGGTGTGAACATC 58.292 50.000 0.00 0.00 0.00 3.06
1699 1735 0.934496 TCGTGAAGTTTGCCTGTTCG 59.066 50.000 0.00 0.00 0.00 3.95
1703 1739 2.354821 GTGAAGTTTGCCTGTTCGTCTT 59.645 45.455 0.00 0.00 0.00 3.01
1710 1746 1.411246 TGCCTGTTCGTCTTACACACT 59.589 47.619 0.00 0.00 0.00 3.55
1790 1830 5.337578 TGCTTAGAAGTGCAAAACCTTTT 57.662 34.783 0.00 0.00 36.15 2.27
1796 1836 9.581099 CTTAGAAGTGCAAAACCTTTTCTTTTA 57.419 29.630 0.00 0.00 0.00 1.52
1813 1853 4.522789 TCTTTTAGGAAAACATGGTCTGGC 59.477 41.667 0.00 0.00 0.00 4.85
1841 1893 4.277672 ACAGTACCGCAAGATATCGTATGT 59.722 41.667 0.00 0.00 43.02 2.29
1866 1918 6.755542 AATAGTAGGCTGCCTAATCTCTTT 57.244 37.500 29.64 16.80 37.91 2.52
1869 1921 6.755542 AGTAGGCTGCCTAATCTCTTTAAT 57.244 37.500 28.89 3.07 37.91 1.40
1884 1936 9.558396 AATCTCTTTAATTTGCCAATTTGTTGA 57.442 25.926 0.53 0.00 34.29 3.18
1885 1937 8.592105 TCTCTTTAATTTGCCAATTTGTTGAG 57.408 30.769 0.53 5.37 34.29 3.02
1886 1938 8.203485 TCTCTTTAATTTGCCAATTTGTTGAGT 58.797 29.630 0.53 0.00 34.29 3.41
1887 1939 9.474920 CTCTTTAATTTGCCAATTTGTTGAGTA 57.525 29.630 0.53 0.00 34.29 2.59
1888 1940 9.255304 TCTTTAATTTGCCAATTTGTTGAGTAC 57.745 29.630 0.53 0.00 34.29 2.73
1889 1941 9.260002 CTTTAATTTGCCAATTTGTTGAGTACT 57.740 29.630 0.53 0.00 34.29 2.73
1890 1942 8.810652 TTAATTTGCCAATTTGTTGAGTACTC 57.189 30.769 16.32 16.32 34.29 2.59
1891 1943 4.846779 TTGCCAATTTGTTGAGTACTCC 57.153 40.909 20.11 6.32 0.00 3.85
1892 1944 3.153919 TGCCAATTTGTTGAGTACTCCC 58.846 45.455 20.11 11.07 0.00 4.30
1893 1945 3.181434 TGCCAATTTGTTGAGTACTCCCT 60.181 43.478 20.11 0.00 0.00 4.20
1894 1946 3.440522 GCCAATTTGTTGAGTACTCCCTC 59.559 47.826 20.11 10.56 0.00 4.30
1895 1947 4.010349 CCAATTTGTTGAGTACTCCCTCC 58.990 47.826 20.11 5.92 0.00 4.30
1896 1948 3.611766 ATTTGTTGAGTACTCCCTCCG 57.388 47.619 20.11 0.00 0.00 4.63
1897 1949 2.005370 TTGTTGAGTACTCCCTCCGT 57.995 50.000 20.11 0.00 0.00 4.69
1898 1950 2.885135 TGTTGAGTACTCCCTCCGTA 57.115 50.000 20.11 0.00 0.00 4.02
1899 1951 3.159213 TGTTGAGTACTCCCTCCGTAA 57.841 47.619 20.11 3.03 0.00 3.18
1900 1952 3.499338 TGTTGAGTACTCCCTCCGTAAA 58.501 45.455 20.11 2.29 0.00 2.01
1901 1953 3.508793 TGTTGAGTACTCCCTCCGTAAAG 59.491 47.826 20.11 0.00 0.00 1.85
1902 1954 3.726557 TGAGTACTCCCTCCGTAAAGA 57.273 47.619 20.11 0.00 0.00 2.52
1903 1955 4.038271 TGAGTACTCCCTCCGTAAAGAA 57.962 45.455 20.11 0.00 0.00 2.52
1904 1956 4.410099 TGAGTACTCCCTCCGTAAAGAAA 58.590 43.478 20.11 0.00 0.00 2.52
1905 1957 5.021458 TGAGTACTCCCTCCGTAAAGAAAT 58.979 41.667 20.11 0.00 0.00 2.17
1906 1958 6.189859 TGAGTACTCCCTCCGTAAAGAAATA 58.810 40.000 20.11 0.00 0.00 1.40
1907 1959 6.837568 TGAGTACTCCCTCCGTAAAGAAATAT 59.162 38.462 20.11 0.00 0.00 1.28
1908 1960 8.000709 TGAGTACTCCCTCCGTAAAGAAATATA 58.999 37.037 20.11 0.00 0.00 0.86
1909 1961 8.773033 AGTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
1910 1962 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
1911 1963 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
1912 1964 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
1913 1965 7.564292 ACTCCCTCCGTAAAGAAATATAAGAGT 59.436 37.037 0.00 0.00 0.00 3.24
1914 1966 7.723324 TCCCTCCGTAAAGAAATATAAGAGTG 58.277 38.462 0.00 0.00 0.00 3.51
1915 1967 7.343833 TCCCTCCGTAAAGAAATATAAGAGTGT 59.656 37.037 0.00 0.00 0.00 3.55
1916 1968 7.985752 CCCTCCGTAAAGAAATATAAGAGTGTT 59.014 37.037 0.00 0.00 0.00 3.32
1917 1969 9.379791 CCTCCGTAAAGAAATATAAGAGTGTTT 57.620 33.333 0.00 0.00 0.00 2.83
1944 1996 8.870879 AGATCATTACTTTAGTGTTCTAAACGC 58.129 33.333 0.00 0.00 40.05 4.84
1965 2017 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
1994 2046 5.765182 ACCACACAGAGTCTAAAGGAAATTG 59.235 40.000 0.00 0.00 0.00 2.32
2033 2085 6.032094 CGGTCACTATTATTCACTTGTACGT 58.968 40.000 0.00 0.00 0.00 3.57
2087 2139 4.295051 TGCTGAAATACGCCTTTTTGTTC 58.705 39.130 0.00 0.00 0.00 3.18
2094 2146 3.369546 ACGCCTTTTTGTTCATCTTGG 57.630 42.857 0.00 0.00 0.00 3.61
2104 2156 2.239402 TGTTCATCTTGGGCAGAGCATA 59.761 45.455 0.00 0.00 33.87 3.14
2144 2196 7.159372 TCAGGAAGAAACTATGTGGTAAGAAC 58.841 38.462 0.00 0.00 0.00 3.01
2152 2204 8.494016 AAACTATGTGGTAAGAACTATTCTGC 57.506 34.615 0.00 0.00 40.59 4.26
2239 2291 9.642312 CTGACATGAAAATGTGAATAATAGTCG 57.358 33.333 0.00 0.00 34.45 4.18
2251 2321 5.405269 TGAATAATAGTCGTGCATTGGATCG 59.595 40.000 0.00 0.00 0.00 3.69
2296 2384 4.984785 TCACTAGCTTCACGATCATTATGC 59.015 41.667 0.00 0.00 0.00 3.14
2534 3745 4.388773 TCATGCATAGTTGTCGAAACACTC 59.611 41.667 0.00 0.00 34.35 3.51
2580 3791 2.086869 ACTTTCATGGAGATGTTGCGG 58.913 47.619 0.00 0.00 0.00 5.69
2669 3880 4.373116 GAAGCGGACCAGGCGACA 62.373 66.667 0.00 0.00 35.00 4.35
2720 3931 1.856539 AAGACCAGGCCTCACATGGG 61.857 60.000 0.00 1.65 38.48 4.00
2721 3932 2.532715 ACCAGGCCTCACATGGGT 60.533 61.111 0.00 2.48 38.48 4.51
2762 3973 0.545646 ATCTCTTTGCTCAGGCCTCC 59.454 55.000 0.00 0.00 37.74 4.30
2793 4004 4.039092 GAGGGAGCAGCTTGCCCA 62.039 66.667 19.28 0.00 46.52 5.36
2905 4119 2.227036 AGCACCCTCCCTGACCTTG 61.227 63.158 0.00 0.00 0.00 3.61
2943 4157 7.754625 ACATTGTTTTCGTTGTAAGTTAGTGT 58.245 30.769 0.00 0.00 0.00 3.55
2950 4164 4.114073 CGTTGTAAGTTAGTGTGGTGTGA 58.886 43.478 0.00 0.00 0.00 3.58
2955 4169 2.561569 AGTTAGTGTGGTGTGACAAGC 58.438 47.619 0.00 0.00 0.00 4.01
3000 4214 1.980765 TCTGCTCAATCTGGTTCCTGT 59.019 47.619 0.00 0.00 0.00 4.00
3061 4281 6.872020 CCCTTTCTTCTTCGTATTACTGTGAA 59.128 38.462 0.00 0.00 0.00 3.18
3066 4286 7.039882 TCTTCTTCGTATTACTGTGAAATCCC 58.960 38.462 0.00 0.00 0.00 3.85
3109 4329 1.676916 CCTGATGCACGTGGAATCAGT 60.677 52.381 29.04 12.49 37.60 3.41
3129 4353 1.736681 TGAATCGCGCATGATGAACAA 59.263 42.857 8.75 0.00 0.00 2.83
3152 4376 7.284489 ACAACGTAAATGCAAGGTGGAATATAT 59.716 33.333 0.00 0.00 0.00 0.86
3159 4383 8.938801 AATGCAAGGTGGAATATATGAATGTA 57.061 30.769 0.00 0.00 0.00 2.29
3302 4571 4.597507 ACCAACACAGATATACTATGGGGG 59.402 45.833 0.00 0.00 29.79 5.40
3314 4583 0.540830 TATGGGGGCGCAAAAACAGT 60.541 50.000 10.83 0.00 0.00 3.55
3318 4587 0.885196 GGGGCGCAAAAACAGTATCA 59.115 50.000 10.83 0.00 0.00 2.15
3326 4595 3.664025 GCAAAAACAGTATCACGACAAGC 59.336 43.478 0.00 0.00 0.00 4.01
3337 4606 2.320587 CGACAAGCTCAGGCCACAC 61.321 63.158 5.01 0.00 39.73 3.82
3411 4680 2.366916 ACTGTAGCCATCCATCTAGCAC 59.633 50.000 0.00 0.00 0.00 4.40
3460 4788 6.644592 GGTTACGGTACATTTACAACACTACA 59.355 38.462 0.00 0.00 0.00 2.74
3461 4789 7.170658 GGTTACGGTACATTTACAACACTACAA 59.829 37.037 0.00 0.00 0.00 2.41
3462 4790 6.529463 ACGGTACATTTACAACACTACAAC 57.471 37.500 0.00 0.00 0.00 3.32
3503 4838 3.071837 TCGCTGCCCGGATACACA 61.072 61.111 0.73 0.00 37.59 3.72
3516 4852 3.679917 CGGATACACACTTGATGCTCCTT 60.680 47.826 0.00 0.00 0.00 3.36
3520 4856 1.808945 CACACTTGATGCTCCTTGGTC 59.191 52.381 0.00 0.00 0.00 4.02
3538 4874 1.338973 GTCCGTCGGTTATGATAGGCA 59.661 52.381 11.88 0.00 0.00 4.75
3593 4929 5.338365 CATCCAAGCATCTTCTTTAGCAAC 58.662 41.667 0.00 0.00 0.00 4.17
3607 4943 0.957395 AGCAACGACCAAGGCTGATG 60.957 55.000 0.00 0.00 34.83 3.07
3608 4944 1.926511 GCAACGACCAAGGCTGATGG 61.927 60.000 3.63 3.63 43.84 3.51
3611 4947 1.153289 CGACCAAGGCTGATGGAGG 60.153 63.158 12.14 0.00 40.56 4.30
3612 4948 1.617018 CGACCAAGGCTGATGGAGGA 61.617 60.000 12.14 0.00 40.56 3.71
3613 4949 0.620556 GACCAAGGCTGATGGAGGAA 59.379 55.000 12.14 0.00 40.56 3.36
3614 4950 1.213926 GACCAAGGCTGATGGAGGAAT 59.786 52.381 12.14 0.00 40.56 3.01
3852 5188 5.474532 TCCAGACAAGATGAAAAACCATCAG 59.525 40.000 0.00 0.00 43.99 2.90
3895 5231 8.024285 GGATACTACAATCGGATAGTTTCTCAG 58.976 40.741 8.66 0.00 32.85 3.35
3900 5236 6.051717 ACAATCGGATAGTTTCTCAGATTGG 58.948 40.000 21.54 10.24 40.59 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.597578 GGTGGTAACTCCCCATTTGT 57.402 50.000 0.00 0.00 44.68 2.83
65 66 0.968393 ACAAAAACTGCACCGGTGGT 60.968 50.000 34.58 22.42 35.62 4.16
81 82 5.247084 AGTTGTATGTACGGCCATTTACAA 58.753 37.500 11.73 10.12 32.07 2.41
83 84 6.702723 TCATAGTTGTATGTACGGCCATTTAC 59.297 38.462 2.24 0.93 37.81 2.01
84 85 6.702723 GTCATAGTTGTATGTACGGCCATTTA 59.297 38.462 2.24 0.00 37.81 1.40
108 110 9.509956 GATAGATACCATCCGCTAGATAATAGT 57.490 37.037 0.00 0.00 32.37 2.12
127 129 5.450818 AGGTTTGCCACTTTGGATAGATA 57.549 39.130 0.00 0.00 40.96 1.98
255 257 4.406456 TCACTCACAATAGCAAATTGGGT 58.594 39.130 12.25 7.38 34.26 4.51
270 272 0.680280 TAGCCGGTCCTCTCACTCAC 60.680 60.000 1.90 0.00 0.00 3.51
271 273 0.394488 CTAGCCGGTCCTCTCACTCA 60.394 60.000 1.90 0.00 0.00 3.41
272 274 0.107116 TCTAGCCGGTCCTCTCACTC 60.107 60.000 1.90 0.00 0.00 3.51
273 275 0.553819 ATCTAGCCGGTCCTCTCACT 59.446 55.000 1.90 0.00 0.00 3.41
310 313 4.775058 AAGCGTGCATTATGTACCAAAA 57.225 36.364 7.79 0.00 28.65 2.44
393 396 4.479786 GGATATCCCAAGAGCTCATACC 57.520 50.000 17.77 5.43 34.14 2.73
434 437 0.186630 AAACGGGCCACCCTTTTAGT 59.813 50.000 4.39 0.00 42.24 2.24
437 440 0.978667 ACAAAACGGGCCACCCTTTT 60.979 50.000 4.39 1.48 45.27 2.27
480 483 3.748083 AGATCATTATGCGTTGCAGGAT 58.252 40.909 0.00 0.00 43.65 3.24
540 543 5.048504 ACAAATCATGATGCTCTTTGTCGTT 60.049 36.000 15.39 0.00 35.70 3.85
632 637 8.603983 TCGTTTATTACAACTCAAACAAACAC 57.396 30.769 0.00 0.00 31.80 3.32
730 739 0.861034 CAAAAATGCAGCGCGCGATA 60.861 50.000 37.18 14.96 46.97 2.92
731 740 2.153945 CAAAAATGCAGCGCGCGAT 61.154 52.632 37.18 28.60 46.97 4.58
815 831 1.228094 TGCGCATCACCTGGTTTGA 60.228 52.632 5.66 0.44 0.00 2.69
825 841 3.801971 CATGCCACGTGCGCATCA 61.802 61.111 29.68 15.08 45.06 3.07
960 986 2.505337 CGTAGCGGCGCTGTGTTA 60.505 61.111 41.59 21.26 40.10 2.41
961 987 4.657824 ACGTAGCGGCGCTGTGTT 62.658 61.111 41.59 21.37 40.10 3.32
971 997 3.989698 CTGGTGCCCTGACGTAGCG 62.990 68.421 0.00 0.00 0.00 4.26
1104 1136 1.306970 GGGAGGTTCGAGGGAGAGA 59.693 63.158 0.00 0.00 0.00 3.10
1131 1163 1.881252 CCGGGTCACGCTAAATCGG 60.881 63.158 0.00 0.00 42.52 4.18
1154 1186 0.890683 CTGGGAGCAAACAACCATCC 59.109 55.000 0.00 0.00 31.62 3.51
1157 1189 1.152567 CCCTGGGAGCAAACAACCA 60.153 57.895 7.01 0.00 0.00 3.67
1225 1257 0.029567 CCTCGTCGGAGAAATCTCGG 59.970 60.000 10.73 10.73 43.27 4.63
1230 1262 4.779113 TCCCCTCGTCGGAGAAAT 57.221 55.556 0.00 0.00 43.27 2.17
1289 1321 5.391523 GCATTTTAATACACAGCCTGACGAA 60.392 40.000 0.00 0.00 0.00 3.85
1312 1348 0.588252 AAGCAATGTCACACGTCTGC 59.412 50.000 0.00 0.00 0.00 4.26
1443 1479 1.923204 CTCTTCTTCGCATCCTTCACG 59.077 52.381 0.00 0.00 0.00 4.35
1473 1509 0.250209 CTGACCTGACAGCAAGCAGT 60.250 55.000 0.00 0.00 0.00 4.40
1508 1544 8.812147 TTTCAGTAATACAGTAGAACACAGTG 57.188 34.615 0.00 0.00 0.00 3.66
1559 1595 6.192970 TGAAGGTTTTCAGAGAGATTCCTT 57.807 37.500 0.00 0.00 38.37 3.36
1604 1640 2.975732 TTCACTAGAGATGCAGCCAG 57.024 50.000 0.00 0.00 0.00 4.85
1614 1650 4.096532 TCGCCTACAGAACATTCACTAGAG 59.903 45.833 0.00 0.00 0.00 2.43
1650 1686 1.722119 CGAGACCTATCGCGTCGAATC 60.722 57.143 5.77 0.00 42.49 2.52
1681 1717 0.655733 ACGAACAGGCAAACTTCACG 59.344 50.000 0.00 0.00 0.00 4.35
1699 1735 6.268825 TCCAACTATCTCAGTGTGTAAGAC 57.731 41.667 0.00 0.00 37.63 3.01
1703 1739 5.542635 AGGTTTCCAACTATCTCAGTGTGTA 59.457 40.000 0.00 0.00 37.63 2.90
1710 1746 4.425772 TCCTCAGGTTTCCAACTATCTCA 58.574 43.478 0.00 0.00 0.00 3.27
1734 1770 9.346725 CCTGCTTTTATTTTTCTACAACTGATC 57.653 33.333 0.00 0.00 0.00 2.92
1790 1830 4.522789 GCCAGACCATGTTTTCCTAAAAGA 59.477 41.667 0.00 0.00 0.00 2.52
1796 1836 1.915141 CTGCCAGACCATGTTTTCCT 58.085 50.000 0.00 0.00 0.00 3.36
1813 1853 0.391661 ATCTTGCGGTACTGTGGCTG 60.392 55.000 3.10 0.00 0.00 4.85
1841 1893 7.857404 AAGAGATTAGGCAGCCTACTATTAA 57.143 36.000 21.76 7.66 35.63 1.40
1866 1918 7.375053 GGAGTACTCAACAAATTGGCAAATTA 58.625 34.615 23.91 0.00 34.84 1.40
1869 1921 4.038642 GGGAGTACTCAACAAATTGGCAAA 59.961 41.667 23.91 0.00 36.39 3.68
1883 1935 5.595257 ATTTCTTTACGGAGGGAGTACTC 57.405 43.478 14.87 14.87 36.76 2.59
1884 1936 8.773033 TTATATTTCTTTACGGAGGGAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
1885 1937 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
1886 1938 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
1887 1939 7.564292 ACTCTTATATTTCTTTACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
1888 1940 7.868415 CACTCTTATATTTCTTTACGGAGGGAG 59.132 40.741 0.00 0.00 0.00 4.30
1889 1941 7.343833 ACACTCTTATATTTCTTTACGGAGGGA 59.656 37.037 0.00 0.00 0.00 4.20
1890 1942 7.498443 ACACTCTTATATTTCTTTACGGAGGG 58.502 38.462 0.00 0.00 0.00 4.30
1891 1943 8.943909 AACACTCTTATATTTCTTTACGGAGG 57.056 34.615 0.00 0.00 0.00 4.30
1918 1970 8.870879 GCGTTTAGAACACTAAAGTAATGATCT 58.129 33.333 0.00 0.00 36.97 2.75
1919 1971 8.870879 AGCGTTTAGAACACTAAAGTAATGATC 58.129 33.333 0.00 0.00 36.97 2.92
1920 1972 8.773404 AGCGTTTAGAACACTAAAGTAATGAT 57.227 30.769 0.00 0.00 36.97 2.45
1921 1973 8.086522 AGAGCGTTTAGAACACTAAAGTAATGA 58.913 33.333 0.00 0.00 36.97 2.57
1922 1974 8.240883 AGAGCGTTTAGAACACTAAAGTAATG 57.759 34.615 0.00 0.00 36.97 1.90
1923 1975 8.828688 AAGAGCGTTTAGAACACTAAAGTAAT 57.171 30.769 0.00 0.00 36.97 1.89
1924 1976 9.918630 ATAAGAGCGTTTAGAACACTAAAGTAA 57.081 29.630 0.00 0.00 36.97 2.24
1931 1983 9.654663 AAGAAATATAAGAGCGTTTAGAACACT 57.345 29.630 0.00 0.00 0.00 3.55
1939 1991 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
1940 1992 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
1941 1993 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
1942 1994 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
1943 1995 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
1946 1998 9.984190 GGTACTCCCTCTGTAAAGAAATATAAG 57.016 37.037 0.00 0.00 0.00 1.73
1947 1999 9.496710 TGGTACTCCCTCTGTAAAGAAATATAA 57.503 33.333 0.00 0.00 0.00 0.98
1948 2000 8.921205 GTGGTACTCCCTCTGTAAAGAAATATA 58.079 37.037 0.00 0.00 0.00 0.86
1949 2001 7.402071 TGTGGTACTCCCTCTGTAAAGAAATAT 59.598 37.037 0.00 0.00 0.00 1.28
1950 2002 6.727231 TGTGGTACTCCCTCTGTAAAGAAATA 59.273 38.462 0.00 0.00 0.00 1.40
1951 2003 5.546499 TGTGGTACTCCCTCTGTAAAGAAAT 59.454 40.000 0.00 0.00 0.00 2.17
1952 2004 4.903049 TGTGGTACTCCCTCTGTAAAGAAA 59.097 41.667 0.00 0.00 0.00 2.52
1953 2005 4.282703 GTGTGGTACTCCCTCTGTAAAGAA 59.717 45.833 0.00 0.00 0.00 2.52
1954 2006 3.830755 GTGTGGTACTCCCTCTGTAAAGA 59.169 47.826 0.00 0.00 0.00 2.52
1955 2007 3.576982 TGTGTGGTACTCCCTCTGTAAAG 59.423 47.826 0.00 0.00 0.00 1.85
1956 2008 3.576982 CTGTGTGGTACTCCCTCTGTAAA 59.423 47.826 0.00 0.00 0.00 2.01
1957 2009 3.162666 CTGTGTGGTACTCCCTCTGTAA 58.837 50.000 0.00 0.00 0.00 2.41
1958 2010 2.377531 TCTGTGTGGTACTCCCTCTGTA 59.622 50.000 0.00 0.00 0.00 2.74
1959 2011 1.147191 TCTGTGTGGTACTCCCTCTGT 59.853 52.381 0.00 0.00 0.00 3.41
1960 2012 1.821753 CTCTGTGTGGTACTCCCTCTG 59.178 57.143 0.00 0.00 0.00 3.35
1961 2013 1.429687 ACTCTGTGTGGTACTCCCTCT 59.570 52.381 0.00 0.00 0.00 3.69
1962 2014 1.819903 GACTCTGTGTGGTACTCCCTC 59.180 57.143 0.00 0.00 0.00 4.30
1963 2015 1.429687 AGACTCTGTGTGGTACTCCCT 59.570 52.381 0.00 0.00 0.00 4.20
1964 2016 1.926108 AGACTCTGTGTGGTACTCCC 58.074 55.000 0.00 0.00 0.00 4.30
1965 2017 4.082136 CCTTTAGACTCTGTGTGGTACTCC 60.082 50.000 0.00 0.00 0.00 3.85
1994 2046 1.268999 TGACCGCAATTCAAAGCACAC 60.269 47.619 0.00 0.00 0.00 3.82
2065 2117 4.202060 TGAACAAAAAGGCGTATTTCAGCA 60.202 37.500 0.00 0.00 34.54 4.41
2087 2139 2.219458 CTGTATGCTCTGCCCAAGATG 58.781 52.381 0.00 0.00 33.29 2.90
2094 2146 2.417933 CAGAAACACTGTATGCTCTGCC 59.582 50.000 0.00 0.00 41.30 4.85
2104 2156 2.042464 TCCTGAGCTCAGAAACACTGT 58.958 47.619 39.34 0.00 46.59 3.55
2239 2291 1.290203 ATGACGACGATCCAATGCAC 58.710 50.000 0.00 0.00 0.00 4.57
2251 2321 7.987268 TGAATAGTGATTCAACTATGACGAC 57.013 36.000 0.00 0.00 46.75 4.34
2296 2384 7.331687 ACAAAGAAGGCATGAAAATTTATTCCG 59.668 33.333 0.00 0.00 0.00 4.30
2516 3724 3.000727 GGGGAGTGTTTCGACAACTATG 58.999 50.000 10.41 0.00 0.00 2.23
2534 3745 8.735692 AAGCATAAAAATTAATGTCAATGGGG 57.264 30.769 0.00 0.00 0.00 4.96
2580 3791 5.752892 ACATGAGATGCTTGATGAATGAC 57.247 39.130 0.00 0.00 0.00 3.06
2656 3867 3.649277 CTCCTTGTCGCCTGGTCCG 62.649 68.421 0.00 0.00 0.00 4.79
2669 3880 1.371558 GTCCTGGAACACGCTCCTT 59.628 57.895 0.00 0.00 36.35 3.36
2720 3931 3.340814 TCCATGGAAGCTTCTGAGAAC 57.659 47.619 25.05 8.65 0.00 3.01
2721 3932 3.520721 TGATCCATGGAAGCTTCTGAGAA 59.479 43.478 25.05 9.68 0.00 2.87
2905 4119 2.409948 ACAATGTAGAGCAGAAGGCC 57.590 50.000 0.00 0.00 46.50 5.19
2943 4157 2.632643 GCAGATGCTTGTCACACCA 58.367 52.632 0.00 0.00 38.21 4.17
3066 4286 3.089284 GTTCCCACCTAACCTCCAATTG 58.911 50.000 0.00 0.00 0.00 2.32
3080 4300 1.577328 CGTGCATCAGGTGTTCCCAC 61.577 60.000 0.00 0.00 41.06 4.61
3109 4329 1.367659 TGTTCATCATGCGCGATTCA 58.632 45.000 12.10 0.00 0.00 2.57
3129 4353 6.995686 TCATATATTCCACCTTGCATTTACGT 59.004 34.615 0.00 0.00 0.00 3.57
3180 4404 5.483685 TCAGCCACTGTTATCAAAGTACT 57.516 39.130 0.00 0.00 32.61 2.73
3214 4469 6.243811 TCAAAATTCCATGCAAAAATCAGC 57.756 33.333 0.00 0.00 0.00 4.26
3256 4511 3.178865 TGGTCTAAGTTTGGGACTAGGG 58.821 50.000 0.00 0.00 37.72 3.53
3302 4571 2.230864 GTCGTGATACTGTTTTTGCGC 58.769 47.619 0.00 0.00 0.00 6.09
3314 4583 0.175760 GGCCTGAGCTTGTCGTGATA 59.824 55.000 0.00 0.00 39.73 2.15
3318 4587 2.031163 GTGGCCTGAGCTTGTCGT 59.969 61.111 3.32 0.00 39.73 4.34
3359 4628 5.221722 ACAGTTAGAACTTTCTCATGCTCCA 60.222 40.000 0.00 0.00 37.08 3.86
3460 4788 5.278957 GCACCAATACAGTTCTTCCAATGTT 60.279 40.000 0.00 0.00 0.00 2.71
3461 4789 4.218417 GCACCAATACAGTTCTTCCAATGT 59.782 41.667 0.00 0.00 0.00 2.71
3462 4790 4.380867 GGCACCAATACAGTTCTTCCAATG 60.381 45.833 0.00 0.00 0.00 2.82
3498 4833 2.371841 ACCAAGGAGCATCAAGTGTGTA 59.628 45.455 0.00 0.00 36.25 2.90
3503 4838 0.036010 CGGACCAAGGAGCATCAAGT 60.036 55.000 0.00 0.00 36.25 3.16
3516 4852 1.958579 CCTATCATAACCGACGGACCA 59.041 52.381 23.38 5.01 0.00 4.02
3520 4856 1.340248 ACTGCCTATCATAACCGACGG 59.660 52.381 13.61 13.61 0.00 4.79
3538 4874 1.507141 CGTTTGCGCTTTCCAGGACT 61.507 55.000 9.73 0.00 0.00 3.85
3593 4929 1.153289 CCTCCATCAGCCTTGGTCG 60.153 63.158 0.00 0.00 35.64 4.79
3611 4947 9.668497 CCCCTAACTTTAACCTGCTATATATTC 57.332 37.037 0.00 0.00 0.00 1.75
3612 4948 9.401496 TCCCCTAACTTTAACCTGCTATATATT 57.599 33.333 0.00 0.00 0.00 1.28
3613 4949 8.984112 TCCCCTAACTTTAACCTGCTATATAT 57.016 34.615 0.00 0.00 0.00 0.86
3614 4950 8.984112 ATCCCCTAACTTTAACCTGCTATATA 57.016 34.615 0.00 0.00 0.00 0.86
3852 5188 4.770010 AGTATCCTAACATCCTAGAGCTGC 59.230 45.833 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.