Multiple sequence alignment - TraesCS6D01G264600

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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 TraesCS6D01G264600 chr6D 100.000 2741 0 0 1 2741 373393392 373390652 0.000000e+00 5062.0
1 TraesCS6D01G264600 chr6D 86.486 370 44 4 1370 1733 372950680 372950311 4.250000e-108 401.0
2 TraesCS6D01G264600 chr6D 83.081 396 54 12 879 1270 372951122 372950736 5.620000e-92 348.0
3 TraesCS6D01G264600 chr6D 86.577 298 40 0 969 1266 373418568 373418271 2.030000e-86 329.0
4 TraesCS6D01G264600 chr6D 83.965 343 45 5 317 654 283554031 283554368 1.220000e-83 320.0
5 TraesCS6D01G264600 chr6D 87.826 230 13 5 691 919 373409405 373409190 3.500000e-64 255.0
6 TraesCS6D01G264600 chr6D 87.558 217 10 5 1 200 114949459 114949243 4.560000e-58 235.0
7 TraesCS6D01G264600 chr6D 78.616 318 44 12 321 626 373392767 373393072 3.600000e-44 189.0
8 TraesCS6D01G264600 chr6D 82.609 161 16 6 796 948 373245178 373245022 6.160000e-27 132.0
9 TraesCS6D01G264600 chr6A 91.132 1838 95 26 1 1804 515645111 515643308 0.000000e+00 2429.0
10 TraesCS6D01G264600 chr6A 79.955 893 145 27 876 1742 515035063 515034179 6.440000e-176 627.0
11 TraesCS6D01G264600 chr6A 85.519 366 45 8 1366 1730 515658079 515657721 2.580000e-100 375.0
12 TraesCS6D01G264600 chr6A 94.149 188 9 1 1950 2137 515643285 515643100 4.470000e-73 285.0
13 TraesCS6D01G264600 chr6A 86.667 225 15 5 691 914 515650376 515650166 4.560000e-58 235.0
14 TraesCS6D01G264600 chr6B 89.238 1877 100 36 1 1830 561042235 561044056 0.000000e+00 2254.0
15 TraesCS6D01G264600 chr6B 88.955 670 26 16 2120 2741 561044806 561045475 0.000000e+00 784.0
16 TraesCS6D01G264600 chr6B 87.017 362 41 3 1366 1721 558734123 558734484 1.180000e-108 403.0
17 TraesCS6D01G264600 chr6B 87.017 362 41 3 1366 1721 558816718 558817079 1.180000e-108 403.0
18 TraesCS6D01G264600 chr6B 85.533 394 34 10 290 666 75963621 75963234 9.200000e-105 390.0
19 TraesCS6D01G264600 chr6B 84.694 392 52 8 876 1266 558733614 558733998 4.280000e-103 385.0
20 TraesCS6D01G264600 chr6B 84.184 392 54 8 876 1266 558816209 558816593 9.270000e-100 374.0
21 TraesCS6D01G264600 chr6B 83.284 341 46 11 1397 1730 561145992 561145656 1.230000e-78 303.0
22 TraesCS6D01G264600 chr6B 82.081 346 50 5 317 654 444540803 444541144 4.470000e-73 285.0
23 TraesCS6D01G264600 chr6B 83.934 305 40 5 971 1266 561146457 561146153 1.610000e-72 283.0
24 TraesCS6D01G264600 chr6B 94.413 179 8 1 1950 2128 561044039 561044215 9.670000e-70 274.0
25 TraesCS6D01G264600 chr6B 79.006 362 47 15 304 648 561042901 561042552 1.280000e-53 220.0
26 TraesCS6D01G264600 chr6B 90.173 173 9 4 747 919 561012824 561012988 4.600000e-53 219.0
27 TraesCS6D01G264600 chrUn 87.293 362 40 3 1366 1721 410293180 410293541 2.540000e-110 409.0
28 TraesCS6D01G264600 chrUn 83.163 392 45 14 876 1266 459912210 459912581 3.380000e-89 339.0
29 TraesCS6D01G264600 chrUn 83.945 218 17 9 1 200 126958429 126958646 2.790000e-45 193.0
30 TraesCS6D01G264600 chrUn 97.273 110 1 2 1830 1939 178519963 178519856 4.660000e-43 185.0
31 TraesCS6D01G264600 chrUn 97.248 109 1 2 1831 1939 178502905 178502799 1.680000e-42 183.0
32 TraesCS6D01G264600 chr7A 87.654 324 35 4 304 626 97911741 97912060 3.330000e-99 372.0
33 TraesCS6D01G264600 chr7A 88.372 215 8 5 3 200 578444713 578444499 2.730000e-60 243.0
34 TraesCS6D01G264600 chr7A 93.590 156 9 1 3 157 449650352 449650507 5.900000e-57 231.0
35 TraesCS6D01G264600 chr7A 89.231 130 14 0 315 444 61431484 61431613 2.180000e-36 163.0
36 TraesCS6D01G264600 chr3A 78.926 484 79 10 2275 2737 657329385 657329866 9.530000e-80 307.0
37 TraesCS6D01G264600 chr3A 86.603 209 18 8 1 200 595949756 595949549 3.550000e-54 222.0
38 TraesCS6D01G264600 chr3A 84.862 218 15 10 1 200 618434084 618433867 1.290000e-48 204.0
39 TraesCS6D01G264600 chr3B 83.003 353 27 13 317 663 612365078 612365403 3.450000e-74 289.0
40 TraesCS6D01G264600 chr3B 97.297 111 2 1 1829 1939 780741335 780741226 1.300000e-43 187.0
41 TraesCS6D01G264600 chr7D 80.990 384 44 16 286 655 64516115 64515747 7.480000e-71 278.0
42 TraesCS6D01G264600 chr7D 86.175 217 13 7 1 200 557415919 557416135 4.600000e-53 219.0
43 TraesCS6D01G264600 chr3D 81.988 322 50 6 2424 2741 522750910 522751227 1.620000e-67 267.0
44 TraesCS6D01G264600 chr3D 93.038 158 8 3 1 156 91831666 91831822 7.640000e-56 228.0
45 TraesCS6D01G264600 chr3D 84.332 217 17 9 1 200 455444510 455444294 2.150000e-46 196.0
46 TraesCS6D01G264600 chr5A 87.665 227 10 7 1 209 85269543 85269769 5.860000e-62 248.0
47 TraesCS6D01G264600 chr1D 79.944 354 54 10 317 663 31413623 31413966 7.580000e-61 244.0
48 TraesCS6D01G264600 chr1D 97.248 109 1 2 1831 1939 444483566 444483672 1.680000e-42 183.0
49 TraesCS6D01G264600 chr1A 87.558 217 10 6 1 200 147365734 147365950 4.560000e-58 235.0
50 TraesCS6D01G264600 chr2A 86.979 192 14 8 478 666 753474962 753474779 3.580000e-49 206.0
51 TraesCS6D01G264600 chr2A 85.926 135 16 3 304 435 753474796 753474930 1.020000e-29 141.0
52 TraesCS6D01G264600 chr5D 97.297 111 1 2 1829 1939 542541868 542541760 1.300000e-43 187.0
53 TraesCS6D01G264600 chr5D 84.153 183 23 4 2563 2741 482151834 482152014 3.630000e-39 172.0
54 TraesCS6D01G264600 chr4D 96.429 112 2 2 1828 1939 449394934 449395043 1.680000e-42 183.0
55 TraesCS6D01G264600 chr2D 96.429 112 3 1 1828 1939 643240382 643240272 1.680000e-42 183.0
56 TraesCS6D01G264600 chr2D 97.368 38 1 0 2224 2261 6842142 6842179 6.340000e-07 65.8
57 TraesCS6D01G264600 chr2B 97.222 108 1 2 1832 1939 30178875 30178980 6.030000e-42 182.0
58 TraesCS6D01G264600 chr2B 96.364 110 2 2 1830 1939 30165480 30165587 2.170000e-41 180.0
59 TraesCS6D01G264600 chr4A 90.164 61 5 1 2681 2741 170728196 170728255 8.140000e-11 78.7


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 TraesCS6D01G264600 chr6D 373390652 373393392 2740 True 5062.0 5062 100.000000 1 2741 1 chr6D.!!$R3 2740
1 TraesCS6D01G264600 chr6D 372950311 372951122 811 True 374.5 401 84.783500 879 1733 2 chr6D.!!$R6 854
2 TraesCS6D01G264600 chr6A 515643100 515645111 2011 True 1357.0 2429 92.640500 1 2137 2 chr6A.!!$R4 2136
3 TraesCS6D01G264600 chr6A 515034179 515035063 884 True 627.0 627 79.955000 876 1742 1 chr6A.!!$R1 866
4 TraesCS6D01G264600 chr6B 561042235 561045475 3240 False 1104.0 2254 90.868667 1 2741 3 chr6B.!!$F5 2740
5 TraesCS6D01G264600 chr6B 558733614 558734484 870 False 394.0 403 85.855500 876 1721 2 chr6B.!!$F3 845
6 TraesCS6D01G264600 chr6B 558816209 558817079 870 False 388.5 403 85.600500 876 1721 2 chr6B.!!$F4 845
7 TraesCS6D01G264600 chr6B 561145656 561146457 801 True 293.0 303 83.609000 971 1730 2 chr6B.!!$R3 759

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
961 1006 0.650512 CATTACCCAACGTAGCTGCG 59.349 55.0 23.12 23.12 37.94 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2043 0.036294 GCCCGGACAATATCCCTAGC 60.036 60.0 0.73 0.0 46.04 3.42 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
195 211 7.459394 TCTTATATGCGAACTAAAAAGACCG 57.541 36.000 0.00 0.00 0.00 4.79
198 214 2.409975 TGCGAACTAAAAAGACCGGAG 58.590 47.619 9.46 0.00 0.00 4.63
250 273 7.418337 TCTTCTTCTTATACACTATGCCACA 57.582 36.000 0.00 0.00 0.00 4.17
335 369 1.537990 GCACCCACGCAAGAAAACATT 60.538 47.619 0.00 0.00 43.62 2.71
443 479 2.236146 ACATCCGAGGAGCATTGTACAA 59.764 45.455 11.41 11.41 0.00 2.41
489 525 7.537715 TCAAACAGTGCACATATATTTTGAGG 58.462 34.615 21.04 1.79 30.37 3.86
594 632 8.122330 GTCATTCCCACAAAATTTCAGTTTTTC 58.878 33.333 0.00 0.00 0.00 2.29
626 664 9.541884 AATGGTTTACTATATTTTCTTGGGTGT 57.458 29.630 0.00 0.00 0.00 4.16
628 666 9.675464 TGGTTTACTATATTTTCTTGGGTGTAG 57.325 33.333 0.00 0.00 0.00 2.74
629 667 8.618677 GGTTTACTATATTTTCTTGGGTGTAGC 58.381 37.037 0.00 0.00 0.00 3.58
663 706 1.880027 GCTGGGTGTAGAAAACCACTG 59.120 52.381 0.00 0.00 39.65 3.66
671 714 4.748102 GTGTAGAAAACCACTGTCATCGAA 59.252 41.667 0.00 0.00 0.00 3.71
681 724 4.498850 CCACTGTCATCGAATGAGACCTAG 60.499 50.000 0.00 0.00 40.53 3.02
708 751 5.045578 ACACCCAATTATTAGAGCACAGTCT 60.046 40.000 0.00 0.00 0.00 3.24
792 836 6.366332 CGTAAACTGATCTTACCCTATCATGC 59.634 42.308 0.00 0.00 31.95 4.06
821 865 5.298276 TGCGGTCTATTTTCTGAAAAGTGTT 59.702 36.000 19.14 6.79 33.22 3.32
943 988 4.956700 ACCTAGCTAGTACTGCAGATTTCA 59.043 41.667 23.35 0.00 0.00 2.69
948 993 6.284459 AGCTAGTACTGCAGATTTCATTACC 58.716 40.000 23.35 0.00 0.00 2.85
950 995 5.435686 AGTACTGCAGATTTCATTACCCA 57.564 39.130 23.35 0.00 0.00 4.51
953 998 3.440173 ACTGCAGATTTCATTACCCAACG 59.560 43.478 23.35 0.00 0.00 4.10
954 999 3.417101 TGCAGATTTCATTACCCAACGT 58.583 40.909 0.00 0.00 0.00 3.99
960 1005 2.018542 TCATTACCCAACGTAGCTGC 57.981 50.000 0.00 0.00 0.00 5.25
961 1006 0.650512 CATTACCCAACGTAGCTGCG 59.349 55.000 23.12 23.12 37.94 5.18
1240 1296 0.106669 GAAGTACCCCATGAAGCCCC 60.107 60.000 0.00 0.00 0.00 5.80
1246 1302 1.574526 CCCCATGAAGCCCCTCAAGA 61.575 60.000 0.00 0.00 0.00 3.02
1664 1795 3.902086 GGAGGAGGCGGCGACTAC 61.902 72.222 19.79 19.79 0.00 2.73
1697 1828 0.925466 CGTCGTCGTTTTTGTGGAGT 59.075 50.000 0.00 0.00 0.00 3.85
1747 1881 1.839354 TCCTTGCCATCTAGTGCATGA 59.161 47.619 0.00 8.55 37.33 3.07
1755 1889 0.175760 TCTAGTGCATGAGTTCGGCC 59.824 55.000 0.00 0.00 0.00 6.13
1756 1890 1.148157 CTAGTGCATGAGTTCGGCCG 61.148 60.000 22.12 22.12 0.00 6.13
1757 1891 1.884075 TAGTGCATGAGTTCGGCCGT 61.884 55.000 27.15 5.51 0.00 5.68
1758 1892 1.447140 GTGCATGAGTTCGGCCGTA 60.447 57.895 27.15 14.12 0.00 4.02
1779 1913 0.093026 GTTCACCGCGATGAAGTTCG 59.907 55.000 18.16 0.00 39.25 3.95
1812 1961 8.027771 ACAAGAACTACTGGTCTAGTAATTTCG 58.972 37.037 0.00 0.00 41.20 3.46
1813 1962 7.934855 AGAACTACTGGTCTAGTAATTTCGA 57.065 36.000 0.00 0.00 41.20 3.71
1814 1963 8.522542 AGAACTACTGGTCTAGTAATTTCGAT 57.477 34.615 0.00 0.00 41.20 3.59
1815 1964 9.624373 AGAACTACTGGTCTAGTAATTTCGATA 57.376 33.333 0.00 0.00 41.20 2.92
1816 1965 9.881529 GAACTACTGGTCTAGTAATTTCGATAG 57.118 37.037 0.00 0.00 41.20 2.08
1817 1966 9.624373 AACTACTGGTCTAGTAATTTCGATAGA 57.376 33.333 0.00 0.00 41.20 1.98
1818 1967 9.275398 ACTACTGGTCTAGTAATTTCGATAGAG 57.725 37.037 0.00 0.00 43.53 2.43
1819 1968 9.275398 CTACTGGTCTAGTAATTTCGATAGAGT 57.725 37.037 0.00 0.00 43.53 3.24
1820 1969 7.932335 ACTGGTCTAGTAATTTCGATAGAGTG 58.068 38.462 0.00 0.00 42.36 3.51
1821 1970 7.013464 ACTGGTCTAGTAATTTCGATAGAGTGG 59.987 40.741 0.00 0.00 42.36 4.00
1831 1980 4.884668 TCGATAGAGTGGGTTGTCTTTT 57.115 40.909 0.00 0.00 42.67 2.27
1832 1981 5.223449 TCGATAGAGTGGGTTGTCTTTTT 57.777 39.130 0.00 0.00 42.67 1.94
1852 2001 5.803237 TTTTATTTTGCGGGGTAAAAGGA 57.197 34.783 0.00 0.00 31.52 3.36
1853 2002 5.803237 TTTATTTTGCGGGGTAAAAGGAA 57.197 34.783 0.00 0.00 31.52 3.36
1854 2003 6.361768 TTTATTTTGCGGGGTAAAAGGAAT 57.638 33.333 0.00 0.00 31.52 3.01
1855 2004 4.901197 ATTTTGCGGGGTAAAAGGAATT 57.099 36.364 0.00 0.00 31.52 2.17
1856 2005 4.691326 TTTTGCGGGGTAAAAGGAATTT 57.309 36.364 0.00 0.00 34.92 1.82
1857 2006 3.669251 TTGCGGGGTAAAAGGAATTTG 57.331 42.857 0.00 0.00 32.27 2.32
1858 2007 2.599677 TGCGGGGTAAAAGGAATTTGT 58.400 42.857 0.00 0.00 32.27 2.83
1859 2008 3.764218 TGCGGGGTAAAAGGAATTTGTA 58.236 40.909 0.00 0.00 32.27 2.41
1860 2009 4.345854 TGCGGGGTAAAAGGAATTTGTAT 58.654 39.130 0.00 0.00 32.27 2.29
1861 2010 4.773149 TGCGGGGTAAAAGGAATTTGTATT 59.227 37.500 0.00 0.00 32.27 1.89
1862 2011 5.950549 TGCGGGGTAAAAGGAATTTGTATTA 59.049 36.000 0.00 0.00 32.27 0.98
1863 2012 6.127675 TGCGGGGTAAAAGGAATTTGTATTAC 60.128 38.462 0.00 0.00 32.27 1.89
1864 2013 6.095860 GCGGGGTAAAAGGAATTTGTATTACT 59.904 38.462 0.00 0.00 36.44 2.24
1865 2014 7.680350 GCGGGGTAAAAGGAATTTGTATTACTC 60.680 40.741 0.00 0.00 33.63 2.59
1866 2015 7.337436 CGGGGTAAAAGGAATTTGTATTACTCA 59.663 37.037 0.00 0.00 33.63 3.41
1867 2016 9.027202 GGGGTAAAAGGAATTTGTATTACTCAA 57.973 33.333 0.00 0.00 33.63 3.02
1872 2021 7.631717 AAGGAATTTGTATTACTCAAGAGCC 57.368 36.000 0.00 0.00 33.63 4.70
1873 2022 6.721318 AGGAATTTGTATTACTCAAGAGCCA 58.279 36.000 0.00 0.00 28.12 4.75
1874 2023 7.175104 AGGAATTTGTATTACTCAAGAGCCAA 58.825 34.615 0.00 0.00 28.12 4.52
1875 2024 7.337942 AGGAATTTGTATTACTCAAGAGCCAAG 59.662 37.037 0.00 0.00 28.12 3.61
1876 2025 7.336931 GGAATTTGTATTACTCAAGAGCCAAGA 59.663 37.037 0.00 0.00 0.00 3.02
1877 2026 8.635765 AATTTGTATTACTCAAGAGCCAAGAA 57.364 30.769 0.00 0.00 0.00 2.52
1878 2027 7.672983 TTTGTATTACTCAAGAGCCAAGAAG 57.327 36.000 0.00 0.00 0.00 2.85
1879 2028 5.734720 TGTATTACTCAAGAGCCAAGAAGG 58.265 41.667 0.00 0.00 41.84 3.46
1880 2029 4.917906 ATTACTCAAGAGCCAAGAAGGT 57.082 40.909 0.00 0.00 40.61 3.50
1881 2030 2.849294 ACTCAAGAGCCAAGAAGGTC 57.151 50.000 0.00 0.00 40.61 3.85
1882 2031 1.349357 ACTCAAGAGCCAAGAAGGTCC 59.651 52.381 0.00 0.00 40.61 4.46
1883 2032 1.627834 CTCAAGAGCCAAGAAGGTCCT 59.372 52.381 0.00 0.00 40.61 3.85
1884 2033 1.625818 TCAAGAGCCAAGAAGGTCCTC 59.374 52.381 0.00 0.00 40.61 3.71
1885 2034 0.988063 AAGAGCCAAGAAGGTCCTCC 59.012 55.000 0.00 0.00 40.61 4.30
1886 2035 0.912006 AGAGCCAAGAAGGTCCTCCC 60.912 60.000 0.00 0.00 40.61 4.30
1888 2037 0.417841 AGCCAAGAAGGTCCTCCCTA 59.582 55.000 0.00 0.00 45.47 3.53
1889 2038 0.542333 GCCAAGAAGGTCCTCCCTAC 59.458 60.000 0.00 0.00 45.47 3.18
1890 2039 1.952621 CCAAGAAGGTCCTCCCTACA 58.047 55.000 0.00 0.00 45.47 2.74
1891 2040 1.555533 CCAAGAAGGTCCTCCCTACAC 59.444 57.143 0.00 0.00 45.47 2.90
1892 2041 2.257207 CAAGAAGGTCCTCCCTACACA 58.743 52.381 0.00 0.00 45.47 3.72
1893 2042 2.637872 CAAGAAGGTCCTCCCTACACAA 59.362 50.000 0.00 0.00 45.47 3.33
1894 2043 2.541466 AGAAGGTCCTCCCTACACAAG 58.459 52.381 0.00 0.00 45.47 3.16
1895 2044 0.984995 AAGGTCCTCCCTACACAAGC 59.015 55.000 0.00 0.00 45.47 4.01
1896 2045 0.117340 AGGTCCTCCCTACACAAGCT 59.883 55.000 0.00 0.00 43.87 3.74
1897 2046 1.361543 AGGTCCTCCCTACACAAGCTA 59.638 52.381 0.00 0.00 43.87 3.32
1898 2047 1.757699 GGTCCTCCCTACACAAGCTAG 59.242 57.143 0.00 0.00 0.00 3.42
1899 2048 1.757699 GTCCTCCCTACACAAGCTAGG 59.242 57.143 0.00 0.00 0.00 3.02
1907 2056 5.552870 CCTACACAAGCTAGGGATATTGT 57.447 43.478 0.00 0.00 36.34 2.71
1908 2057 5.542779 CCTACACAAGCTAGGGATATTGTC 58.457 45.833 0.00 0.00 33.76 3.18
1916 2065 4.675404 GGATATTGTCCGGGCTCG 57.325 61.111 7.97 0.00 37.23 5.03
1937 2086 3.694746 CGGAGCCAGACCACAGTA 58.305 61.111 0.00 0.00 0.00 2.74
1938 2087 1.215647 CGGAGCCAGACCACAGTAC 59.784 63.158 0.00 0.00 0.00 2.73
1939 2088 1.532604 CGGAGCCAGACCACAGTACA 61.533 60.000 0.00 0.00 0.00 2.90
1940 2089 0.037232 GGAGCCAGACCACAGTACAC 60.037 60.000 0.00 0.00 0.00 2.90
1941 2090 0.679505 GAGCCAGACCACAGTACACA 59.320 55.000 0.00 0.00 0.00 3.72
1942 2091 1.070134 GAGCCAGACCACAGTACACAA 59.930 52.381 0.00 0.00 0.00 3.33
1943 2092 1.070758 AGCCAGACCACAGTACACAAG 59.929 52.381 0.00 0.00 0.00 3.16
1944 2093 1.512926 CCAGACCACAGTACACAAGC 58.487 55.000 0.00 0.00 0.00 4.01
1945 2094 1.070758 CCAGACCACAGTACACAAGCT 59.929 52.381 0.00 0.00 0.00 3.74
1946 2095 2.299013 CCAGACCACAGTACACAAGCTA 59.701 50.000 0.00 0.00 0.00 3.32
1947 2096 3.579709 CAGACCACAGTACACAAGCTAG 58.420 50.000 0.00 0.00 0.00 3.42
1948 2097 2.563179 AGACCACAGTACACAAGCTAGG 59.437 50.000 0.00 0.00 0.00 3.02
1990 2139 6.604735 AATTAGTCATGTTCGGATGCTTAC 57.395 37.500 0.00 0.00 0.00 2.34
2014 2163 0.814010 GTTGGTGTGAGCCTCGTTGT 60.814 55.000 0.00 0.00 0.00 3.32
2069 2218 0.966179 TGCTCCTACGCAACTTCTGA 59.034 50.000 0.00 0.00 36.89 3.27
2079 2228 5.248870 ACGCAACTTCTGAAAACAGAAAT 57.751 34.783 12.54 1.74 40.26 2.17
2142 2890 2.242047 TGTGTGCTGCCGTTAAGTTA 57.758 45.000 0.00 0.00 0.00 2.24
2193 2945 3.071479 TCTAGTTGGCGGTGACAATTTC 58.929 45.455 0.00 0.00 31.24 2.17
2214 2966 5.248870 TCTGAGGCTTTTGTTCACTTTTC 57.751 39.130 0.00 0.00 0.00 2.29
2222 2974 6.371548 GGCTTTTGTTCACTTTTCCTTTCTTT 59.628 34.615 0.00 0.00 0.00 2.52
2282 3060 2.040178 GAACTCGGGACCTCATACCAT 58.960 52.381 0.00 0.00 0.00 3.55
2290 3069 2.483188 GGACCTCATACCATGGAACGAC 60.483 54.545 21.47 1.80 0.00 4.34
2338 3117 4.811908 TGATGTTGACGATTAGGAAACGA 58.188 39.130 0.00 0.00 0.00 3.85
2355 3134 7.112779 AGGAAACGAGGATCATTTAAGAACAT 58.887 34.615 0.00 0.00 33.17 2.71
2366 3145 7.892778 TCATTTAAGAACATAGCACAACGTA 57.107 32.000 0.00 0.00 0.00 3.57
2566 3362 9.393512 TCTTGAACAATTTTTCAAAACATGGAT 57.606 25.926 17.86 0.00 43.29 3.41
2589 3385 7.486870 GGATAATTTTTAAAACTCGCCGAACAT 59.513 33.333 0.00 0.00 0.00 2.71
2599 3395 2.993899 CTCGCCGAACATGTTTTAGAGT 59.006 45.455 13.36 0.00 0.00 3.24
2607 3403 5.179368 CGAACATGTTTTAGAGTGTGGACAT 59.821 40.000 13.36 0.00 0.00 3.06
2713 3509 7.475771 TTTGCACCATTTAGAAAATGTTGAC 57.524 32.000 12.38 6.01 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 7.854534 CATCATTAGATGCGTCATGACTTTAA 58.145 34.615 22.95 10.82 44.61 1.52
192 208 2.091541 CATAATTTGTGCACCTCCGGT 58.908 47.619 15.69 0.00 35.62 5.28
193 209 2.091541 ACATAATTTGTGCACCTCCGG 58.908 47.619 15.69 0.00 37.11 5.14
195 211 5.634859 CAGAAAACATAATTTGTGCACCTCC 59.365 40.000 15.69 0.00 38.99 4.30
198 214 6.843069 AACAGAAAACATAATTTGTGCACC 57.157 33.333 15.69 0.00 38.99 5.01
239 262 6.753279 CCAAATTTTAGTCATGTGGCATAGTG 59.247 38.462 0.00 0.00 0.00 2.74
246 269 9.927668 AGATTTAACCAAATTTTAGTCATGTGG 57.072 29.630 0.00 0.00 34.44 4.17
280 303 1.133809 AGCCACTACTTGCCCCTCAA 61.134 55.000 0.00 0.00 0.00 3.02
356 391 7.405292 TCATAGTCATTCCCAGAAAGTTTCAT 58.595 34.615 17.65 0.00 0.00 2.57
357 392 6.778821 TCATAGTCATTCCCAGAAAGTTTCA 58.221 36.000 17.65 0.00 0.00 2.69
366 402 6.764308 ACATTTGTTCATAGTCATTCCCAG 57.236 37.500 0.00 0.00 0.00 4.45
411 447 2.505407 TCCTCGGATGTCATTTGACCAT 59.495 45.455 8.16 2.53 44.15 3.55
452 488 5.290643 GTGCACTGTTTGAGCAAAATTTGTA 59.709 36.000 10.32 0.00 43.40 2.41
622 660 3.047877 GTGCACCCACGCTACACC 61.048 66.667 5.22 0.00 31.34 4.16
626 664 4.063967 CTCGGTGCACCCACGCTA 62.064 66.667 29.95 7.80 43.00 4.26
663 706 4.096532 TGTGTCTAGGTCTCATTCGATGAC 59.903 45.833 0.00 0.00 35.06 3.06
671 714 2.623418 TGGGTGTGTCTAGGTCTCAT 57.377 50.000 0.00 0.00 0.00 2.90
681 724 4.941263 TGTGCTCTAATAATTGGGTGTGTC 59.059 41.667 0.00 0.00 0.00 3.67
708 751 3.645687 AGGGCAGCCTCAAAAATTGTTTA 59.354 39.130 12.43 0.00 0.00 2.01
792 836 3.849911 TCAGAAAATAGACCGCACTCTG 58.150 45.455 0.00 0.00 0.00 3.35
821 865 1.269723 CTGCGTCAGACCACACTCTAA 59.730 52.381 0.00 0.00 32.44 2.10
849 894 1.277557 CTGGAGACCTTGACTTGGAGG 59.722 57.143 0.00 0.00 39.02 4.30
943 988 0.461339 CCGCAGCTACGTTGGGTAAT 60.461 55.000 5.47 0.00 0.00 1.89
1077 1133 2.347490 GGGTCGAGCCAGAGCAAA 59.653 61.111 28.27 0.00 43.56 3.68
1078 1134 3.706373 GGGGTCGAGCCAGAGCAA 61.706 66.667 32.94 0.00 43.56 3.91
1240 1296 7.138692 CCTTAGTTTTGAAGGTGATCTTGAG 57.861 40.000 0.00 0.00 38.97 3.02
1633 1758 1.994507 CCTCCAGCAGCTCCTTCCT 60.995 63.158 0.00 0.00 0.00 3.36
1688 1819 2.008242 CCATTTCCCCACTCCACAAA 57.992 50.000 0.00 0.00 0.00 2.83
1697 1828 1.253100 GAAGAAACGCCATTTCCCCA 58.747 50.000 4.82 0.00 46.94 4.96
1747 1881 1.372128 GTGAACGTACGGCCGAACT 60.372 57.895 35.90 12.99 0.00 3.01
1755 1889 1.066656 TTCATCGCGGTGAACGTACG 61.067 55.000 29.90 15.01 46.52 3.67
1756 1890 0.638746 CTTCATCGCGGTGAACGTAC 59.361 55.000 29.90 0.00 46.52 3.67
1757 1891 0.241749 ACTTCATCGCGGTGAACGTA 59.758 50.000 29.90 11.09 46.52 3.57
1758 1892 0.599204 AACTTCATCGCGGTGAACGT 60.599 50.000 29.90 25.72 46.52 3.99
1779 1913 3.805207 ACCAGTAGTTCTTGTGGTGAAC 58.195 45.455 0.00 0.00 41.88 3.18
1829 1978 6.170846 TCCTTTTACCCCGCAAAATAAAAA 57.829 33.333 0.00 0.00 0.00 1.94
1830 1979 5.803237 TCCTTTTACCCCGCAAAATAAAA 57.197 34.783 0.00 0.00 0.00 1.52
1831 1980 5.803237 TTCCTTTTACCCCGCAAAATAAA 57.197 34.783 0.00 0.00 0.00 1.40
1832 1981 6.361768 AATTCCTTTTACCCCGCAAAATAA 57.638 33.333 0.00 0.00 0.00 1.40
1833 1982 6.166982 CAAATTCCTTTTACCCCGCAAAATA 58.833 36.000 0.00 0.00 0.00 1.40
1834 1983 4.901197 AATTCCTTTTACCCCGCAAAAT 57.099 36.364 0.00 0.00 0.00 1.82
1835 1984 4.141688 ACAAATTCCTTTTACCCCGCAAAA 60.142 37.500 0.00 0.00 0.00 2.44
1836 1985 3.388350 ACAAATTCCTTTTACCCCGCAAA 59.612 39.130 0.00 0.00 0.00 3.68
1837 1986 2.966516 ACAAATTCCTTTTACCCCGCAA 59.033 40.909 0.00 0.00 0.00 4.85
1838 1987 2.599677 ACAAATTCCTTTTACCCCGCA 58.400 42.857 0.00 0.00 0.00 5.69
1839 1988 4.994907 ATACAAATTCCTTTTACCCCGC 57.005 40.909 0.00 0.00 0.00 6.13
1840 1989 7.337436 TGAGTAATACAAATTCCTTTTACCCCG 59.663 37.037 0.00 0.00 0.00 5.73
1841 1990 8.584063 TGAGTAATACAAATTCCTTTTACCCC 57.416 34.615 0.00 0.00 0.00 4.95
1846 1995 8.523658 GGCTCTTGAGTAATACAAATTCCTTTT 58.476 33.333 0.00 0.00 0.00 2.27
1847 1996 7.669722 TGGCTCTTGAGTAATACAAATTCCTTT 59.330 33.333 0.00 0.00 0.00 3.11
1848 1997 7.175104 TGGCTCTTGAGTAATACAAATTCCTT 58.825 34.615 0.00 0.00 0.00 3.36
1849 1998 6.721318 TGGCTCTTGAGTAATACAAATTCCT 58.279 36.000 0.00 0.00 0.00 3.36
1850 1999 7.336931 TCTTGGCTCTTGAGTAATACAAATTCC 59.663 37.037 0.00 0.00 0.00 3.01
1851 2000 8.268850 TCTTGGCTCTTGAGTAATACAAATTC 57.731 34.615 0.00 0.00 0.00 2.17
1852 2001 8.635765 TTCTTGGCTCTTGAGTAATACAAATT 57.364 30.769 0.00 0.00 0.00 1.82
1853 2002 7.337942 CCTTCTTGGCTCTTGAGTAATACAAAT 59.662 37.037 0.00 0.00 0.00 2.32
1854 2003 6.655003 CCTTCTTGGCTCTTGAGTAATACAAA 59.345 38.462 0.00 0.00 0.00 2.83
1855 2004 6.173339 CCTTCTTGGCTCTTGAGTAATACAA 58.827 40.000 0.00 0.00 0.00 2.41
1856 2005 5.248477 ACCTTCTTGGCTCTTGAGTAATACA 59.752 40.000 0.00 0.00 40.22 2.29
1857 2006 5.735766 ACCTTCTTGGCTCTTGAGTAATAC 58.264 41.667 0.00 0.00 40.22 1.89
1858 2007 5.104900 GGACCTTCTTGGCTCTTGAGTAATA 60.105 44.000 0.00 0.00 40.22 0.98
1859 2008 4.323868 GGACCTTCTTGGCTCTTGAGTAAT 60.324 45.833 0.00 0.00 40.22 1.89
1860 2009 3.008049 GGACCTTCTTGGCTCTTGAGTAA 59.992 47.826 0.00 0.00 40.22 2.24
1861 2010 2.567615 GGACCTTCTTGGCTCTTGAGTA 59.432 50.000 0.00 0.00 40.22 2.59
1862 2011 1.349357 GGACCTTCTTGGCTCTTGAGT 59.651 52.381 0.00 0.00 40.22 3.41
1863 2012 1.627834 AGGACCTTCTTGGCTCTTGAG 59.372 52.381 0.00 0.00 40.22 3.02
1864 2013 1.625818 GAGGACCTTCTTGGCTCTTGA 59.374 52.381 0.00 0.00 40.22 3.02
1865 2014 1.339535 GGAGGACCTTCTTGGCTCTTG 60.340 57.143 0.00 0.00 40.22 3.02
1866 2015 0.988063 GGAGGACCTTCTTGGCTCTT 59.012 55.000 0.00 0.00 40.22 2.85
1867 2016 0.912006 GGGAGGACCTTCTTGGCTCT 60.912 60.000 0.00 0.00 40.22 4.09
1868 2017 1.604915 GGGAGGACCTTCTTGGCTC 59.395 63.158 0.00 0.00 40.22 4.70
1869 2018 3.827752 GGGAGGACCTTCTTGGCT 58.172 61.111 0.00 0.00 40.22 4.75
1878 2027 1.757699 CTAGCTTGTGTAGGGAGGACC 59.242 57.143 0.00 0.00 40.67 4.46
1879 2028 1.757699 CCTAGCTTGTGTAGGGAGGAC 59.242 57.143 0.00 0.00 34.42 3.85
1880 2029 2.160721 CCTAGCTTGTGTAGGGAGGA 57.839 55.000 0.00 0.00 34.42 3.71
1885 2034 5.511545 GGACAATATCCCTAGCTTGTGTAGG 60.512 48.000 0.00 0.00 42.46 3.18
1886 2035 5.542779 GGACAATATCCCTAGCTTGTGTAG 58.457 45.833 0.00 0.00 42.46 2.74
1887 2036 4.038763 CGGACAATATCCCTAGCTTGTGTA 59.961 45.833 0.00 0.00 46.04 2.90
1888 2037 3.181465 CGGACAATATCCCTAGCTTGTGT 60.181 47.826 0.00 0.00 46.04 3.72
1889 2038 3.393800 CGGACAATATCCCTAGCTTGTG 58.606 50.000 0.00 0.00 46.04 3.33
1890 2039 2.368875 CCGGACAATATCCCTAGCTTGT 59.631 50.000 0.00 0.00 46.04 3.16
1891 2040 2.289694 CCCGGACAATATCCCTAGCTTG 60.290 54.545 0.73 0.00 46.04 4.01
1892 2041 1.978580 CCCGGACAATATCCCTAGCTT 59.021 52.381 0.73 0.00 46.04 3.74
1893 2042 1.645710 CCCGGACAATATCCCTAGCT 58.354 55.000 0.73 0.00 46.04 3.32
1894 2043 0.036294 GCCCGGACAATATCCCTAGC 60.036 60.000 0.73 0.00 46.04 3.42
1895 2044 1.550976 GAGCCCGGACAATATCCCTAG 59.449 57.143 0.73 0.00 46.04 3.02
1896 2045 1.640917 GAGCCCGGACAATATCCCTA 58.359 55.000 0.73 0.00 46.04 3.53
1897 2046 1.472662 CGAGCCCGGACAATATCCCT 61.473 60.000 0.73 0.00 46.04 4.20
1898 2047 1.004918 CGAGCCCGGACAATATCCC 60.005 63.158 0.73 0.00 46.04 3.85
1899 2048 4.675404 CGAGCCCGGACAATATCC 57.325 61.111 0.73 0.00 45.20 2.59
1913 2062 4.200283 GTCTGGCTCCGCTCCGAG 62.200 72.222 0.00 0.00 0.00 4.63
1916 2065 4.459089 GTGGTCTGGCTCCGCTCC 62.459 72.222 0.00 0.00 33.26 4.70
1917 2066 3.655810 CTGTGGTCTGGCTCCGCTC 62.656 68.421 8.38 0.00 36.54 5.03
1918 2067 3.699894 CTGTGGTCTGGCTCCGCT 61.700 66.667 8.38 0.00 36.54 5.52
1919 2068 2.646175 TACTGTGGTCTGGCTCCGC 61.646 63.158 0.00 0.00 36.18 5.54
1920 2069 1.215647 GTACTGTGGTCTGGCTCCG 59.784 63.158 0.00 0.00 0.00 4.63
1921 2070 0.037232 GTGTACTGTGGTCTGGCTCC 60.037 60.000 0.00 0.00 0.00 4.70
1922 2071 0.679505 TGTGTACTGTGGTCTGGCTC 59.320 55.000 0.00 0.00 0.00 4.70
1923 2072 1.070758 CTTGTGTACTGTGGTCTGGCT 59.929 52.381 0.00 0.00 0.00 4.75
1924 2073 1.512926 CTTGTGTACTGTGGTCTGGC 58.487 55.000 0.00 0.00 0.00 4.85
1925 2074 1.070758 AGCTTGTGTACTGTGGTCTGG 59.929 52.381 0.00 0.00 0.00 3.86
1926 2075 2.533266 AGCTTGTGTACTGTGGTCTG 57.467 50.000 0.00 0.00 0.00 3.51
1927 2076 2.563179 CCTAGCTTGTGTACTGTGGTCT 59.437 50.000 0.00 0.00 0.00 3.85
1928 2077 2.353803 CCCTAGCTTGTGTACTGTGGTC 60.354 54.545 0.00 0.00 0.00 4.02
1929 2078 1.623811 CCCTAGCTTGTGTACTGTGGT 59.376 52.381 0.00 0.00 0.00 4.16
1930 2079 1.899814 TCCCTAGCTTGTGTACTGTGG 59.100 52.381 0.00 0.00 0.00 4.17
1931 2080 3.895232 ATCCCTAGCTTGTGTACTGTG 57.105 47.619 0.00 0.00 0.00 3.66
1932 2081 4.868268 TCTATCCCTAGCTTGTGTACTGT 58.132 43.478 0.00 0.00 0.00 3.55
1933 2082 4.890581 ACTCTATCCCTAGCTTGTGTACTG 59.109 45.833 0.00 0.00 0.00 2.74
1934 2083 4.890581 CACTCTATCCCTAGCTTGTGTACT 59.109 45.833 0.00 0.00 0.00 2.73
1935 2084 4.038162 CCACTCTATCCCTAGCTTGTGTAC 59.962 50.000 0.00 0.00 0.00 2.90
1936 2085 4.215908 CCACTCTATCCCTAGCTTGTGTA 58.784 47.826 0.00 0.00 0.00 2.90
1937 2086 3.034635 CCACTCTATCCCTAGCTTGTGT 58.965 50.000 0.00 0.00 0.00 3.72
1938 2087 2.366916 CCCACTCTATCCCTAGCTTGTG 59.633 54.545 0.00 0.00 0.00 3.33
1939 2088 2.022918 ACCCACTCTATCCCTAGCTTGT 60.023 50.000 0.00 0.00 0.00 3.16
1940 2089 2.683768 ACCCACTCTATCCCTAGCTTG 58.316 52.381 0.00 0.00 0.00 4.01
1941 2090 3.041946 CAACCCACTCTATCCCTAGCTT 58.958 50.000 0.00 0.00 0.00 3.74
1942 2091 2.022918 ACAACCCACTCTATCCCTAGCT 60.023 50.000 0.00 0.00 0.00 3.32
1943 2092 2.365941 GACAACCCACTCTATCCCTAGC 59.634 54.545 0.00 0.00 0.00 3.42
1944 2093 3.917300 AGACAACCCACTCTATCCCTAG 58.083 50.000 0.00 0.00 0.00 3.02
1945 2094 4.348020 AAGACAACCCACTCTATCCCTA 57.652 45.455 0.00 0.00 0.00 3.53
1946 2095 2.950990 AGACAACCCACTCTATCCCT 57.049 50.000 0.00 0.00 0.00 4.20
1947 2096 5.632034 ATTAAGACAACCCACTCTATCCC 57.368 43.478 0.00 0.00 0.00 3.85
1948 2097 7.793036 ACTAATTAAGACAACCCACTCTATCC 58.207 38.462 0.00 0.00 0.00 2.59
1990 2139 3.357079 GGCTCACACCAACGCCAG 61.357 66.667 0.00 0.00 42.06 4.85
2031 2180 1.660607 CATGCATCGACCACTACACAC 59.339 52.381 0.00 0.00 0.00 3.82
2032 2181 2.006552 GCATGCATCGACCACTACACA 61.007 52.381 14.21 0.00 0.00 3.72
2069 2218 7.397192 AGGCACAGATACCATAATTTCTGTTTT 59.603 33.333 5.64 0.00 44.77 2.43
2079 2228 4.947388 GGAACAAAGGCACAGATACCATAA 59.053 41.667 0.00 0.00 0.00 1.90
2150 2898 0.661020 GTACAAACGGCAGCACACTT 59.339 50.000 0.00 0.00 0.00 3.16
2193 2945 4.098501 AGGAAAAGTGAACAAAAGCCTCAG 59.901 41.667 0.00 0.00 0.00 3.35
2282 3060 2.696707 AGTGGTAGAAACTGTCGTTCCA 59.303 45.455 0.00 0.00 31.66 3.53
2290 3069 2.557056 TCTGTCGGAGTGGTAGAAACTG 59.443 50.000 0.00 0.00 0.00 3.16
2338 3117 7.201644 CGTTGTGCTATGTTCTTAAATGATCCT 60.202 37.037 0.00 0.00 0.00 3.24
2355 3134 6.072342 TGTCTTCTAATCTGTACGTTGTGCTA 60.072 38.462 0.00 0.00 0.00 3.49
2566 3362 7.140048 ACATGTTCGGCGAGTTTTAAAAATTA 58.860 30.769 10.46 0.00 0.00 1.40
2578 3374 2.993899 ACTCTAAAACATGTTCGGCGAG 59.006 45.455 12.39 16.10 0.00 5.03
2589 3385 7.397892 TCAAAAATGTCCACACTCTAAAACA 57.602 32.000 0.00 0.00 0.00 2.83
2599 3395 7.391554 TGTTTGGAATTTTCAAAAATGTCCACA 59.608 29.630 19.96 15.34 40.72 4.17
2708 3504 9.881529 ATGCATGAACATTTTTAAAATGTCAAC 57.118 25.926 28.82 22.87 39.73 3.18


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

AutoCloner maintained by Alex Coulton.