Multiple sequence alignment - TraesCS2A01G248900

Loading Multiple Alignment...

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 TraesCS2A01G248900 chr2A 100.000 2468 0 0 1 2468 372742763 372745230 0.000000e+00 4558.0
1 TraesCS2A01G248900 chr2A 86.189 572 61 7 1755 2319 778405981 778406541 9.760000e-169 603.0
2 TraesCS2A01G248900 chr2A 94.792 192 10 0 1755 1946 677897757 677897566 1.430000e-77 300.0
3 TraesCS2A01G248900 chr2A 85.507 69 10 0 2249 2317 677897239 677897171 3.400000e-09 73.1
4 TraesCS2A01G248900 chr7B 95.125 1805 84 3 1 1803 34282307 34280505 0.000000e+00 2843.0
5 TraesCS2A01G248900 chr7B 85.897 156 19 3 2315 2468 34256322 34256168 1.960000e-36 163.0
6 TraesCS2A01G248900 chr7B 85.621 153 19 3 2318 2468 34280218 34280067 9.140000e-35 158.0
7 TraesCS2A01G248900 chr3A 94.521 1807 93 3 1 1803 44774225 44772421 0.000000e+00 2784.0
8 TraesCS2A01G248900 chr3A 94.230 1785 83 15 1 1779 635312064 635313834 0.000000e+00 2708.0
9 TraesCS2A01G248900 chr3A 86.066 122 7 6 1695 1813 145557263 145557149 3.330000e-24 122.0
10 TraesCS2A01G248900 chr3A 86.364 66 9 0 2249 2314 635314301 635314366 3.400000e-09 73.1
11 TraesCS2A01G248900 chr5D 94.599 1796 76 12 1 1785 387840682 387838897 0.000000e+00 2760.0
12 TraesCS2A01G248900 chr4A 93.654 1828 93 13 1 1813 737660730 737662549 0.000000e+00 2712.0
13 TraesCS2A01G248900 chr4A 88.800 375 24 1 1755 2111 514405933 514405559 6.260000e-121 444.0
14 TraesCS2A01G248900 chr4A 90.640 203 18 1 2037 2238 514389456 514389254 4.050000e-68 268.0
15 TraesCS2A01G248900 chr4A 86.975 238 19 4 2242 2468 514389123 514388887 8.760000e-65 257.0
16 TraesCS2A01G248900 chr4A 80.782 307 37 19 1971 2257 514389451 514389147 1.150000e-53 220.0
17 TraesCS2A01G248900 chr4A 95.918 49 2 0 2266 2314 637835366 637835318 2.030000e-11 80.5
18 TraesCS2A01G248900 chr1A 93.774 1815 86 19 1 1803 480958135 480959934 0.000000e+00 2700.0
19 TraesCS2A01G248900 chr1A 94.271 192 11 0 1755 1946 480959823 480960014 6.670000e-76 294.0
20 TraesCS2A01G248900 chr3B 93.736 1788 100 7 1 1777 112909779 112911565 0.000000e+00 2671.0
21 TraesCS2A01G248900 chr3B 88.820 1136 91 15 645 1777 16202832 16201730 0.000000e+00 1362.0
22 TraesCS2A01G248900 chr3B 85.987 157 18 4 2035 2188 16201555 16201400 5.460000e-37 165.0
23 TraesCS2A01G248900 chr7A 93.044 1797 93 20 1 1782 38737234 38739013 0.000000e+00 2597.0
24 TraesCS2A01G248900 chr7A 86.978 407 34 2 1755 2142 595031333 595030927 8.100000e-120 440.0
25 TraesCS2A01G248900 chr7A 89.535 172 18 0 1971 2142 595030388 595030217 4.130000e-53 219.0
26 TraesCS2A01G248900 chr7A 88.953 172 19 0 1971 2142 595030956 595030785 1.920000e-51 213.0
27 TraesCS2A01G248900 chr7A 88.372 172 20 0 1971 2142 595030317 595030146 8.950000e-50 207.0
28 TraesCS2A01G248900 chr7A 87.791 172 21 0 1971 2142 595030601 595030430 4.160000e-48 202.0
29 TraesCS2A01G248900 chr7A 85.621 153 19 3 2318 2468 595029940 595029789 9.140000e-35 158.0
30 TraesCS2A01G248900 chr7A 75.862 203 28 9 2113 2314 38739361 38739543 1.570000e-12 84.2
31 TraesCS2A01G248900 chr7A 88.060 67 6 2 2249 2314 699320969 699320904 7.320000e-11 78.7
32 TraesCS2A01G248900 chr5B 92.933 1783 116 7 1 1777 578837551 578835773 0.000000e+00 2586.0
33 TraesCS2A01G248900 chr5B 94.416 197 11 0 1755 1951 35439756 35439952 1.110000e-78 303.0
34 TraesCS2A01G248900 chr5B 86.538 156 18 3 2315 2468 35440171 35440325 4.220000e-38 169.0
35 TraesCS2A01G248900 chr5B 76.077 209 29 12 2108 2315 428833481 428833669 3.380000e-14 89.8
36 TraesCS2A01G248900 chr7D 87.042 409 31 5 1755 2142 16798006 16797599 2.250000e-120 442.0
37 TraesCS2A01G248900 chr7D 88.950 181 15 5 2059 2236 21072539 21072361 4.130000e-53 219.0
38 TraesCS2A01G248900 chr7D 88.372 172 20 0 1971 2142 16797485 16797314 8.950000e-50 207.0
39 TraesCS2A01G248900 chr7D 86.093 151 18 3 2318 2466 16797392 16797243 2.540000e-35 159.0
40 TraesCS2A01G248900 chr7D 86.093 151 18 3 2318 2466 16797463 16797314 2.540000e-35 159.0
41 TraesCS2A01G248900 chr6B 86.861 411 34 9 1755 2146 425597683 425598092 2.250000e-120 442.0
42 TraesCS2A01G248900 chr2B 85.714 406 40 6 1755 2142 47386092 47385687 1.770000e-111 412.0
43 TraesCS2A01G248900 chr2B 85.621 153 19 3 2318 2468 47385765 47385614 9.140000e-35 158.0
44 TraesCS2A01G248900 chr2B 85.333 150 18 4 2042 2188 102804238 102804386 4.250000e-33 152.0
45 TraesCS2A01G248900 chr2B 83.117 154 24 2 2035 2186 102804078 102804231 3.310000e-29 139.0
46 TraesCS2A01G248900 chr1D 85.432 405 39 5 1755 2140 490890336 490890739 1.060000e-108 403.0
47 TraesCS2A01G248900 chr1D 87.283 173 20 2 1971 2142 490890783 490890954 1.940000e-46 196.0
48 TraesCS2A01G248900 chr1D 86.538 156 18 3 2315 2468 490890660 490890814 4.220000e-38 169.0
49 TraesCS2A01G248900 chr1D 85.567 97 12 2 2315 2410 490890873 490890968 1.560000e-17 100.0
50 TraesCS2A01G248900 chr6A 86.620 142 18 1 2328 2468 79830204 79830063 3.290000e-34 156.0
51 TraesCS2A01G248900 chr5A 75.122 205 40 10 2113 2314 606689795 606689991 4.370000e-13 86.1
52 TraesCS2A01G248900 chr5A 89.394 66 7 0 2249 2314 288266686 288266621 1.570000e-12 84.2
53 TraesCS2A01G248900 chr4B 84.000 75 12 0 2247 2321 469021061 469020987 3.400000e-09 73.1
54 TraesCS2A01G248900 chrUn 96.970 33 1 0 2433 2465 416566866 416566834 3.430000e-04 56.5
55 TraesCS2A01G248900 chrUn 94.444 36 1 1 2433 2467 361055521 361055486 1.000000e-03 54.7


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 TraesCS2A01G248900 chr2A 372742763 372745230 2467 False 4558.000000 4558 100.000000 1 2468 1 chr2A.!!$F1 2467
1 TraesCS2A01G248900 chr2A 778405981 778406541 560 False 603.000000 603 86.189000 1755 2319 1 chr2A.!!$F2 564
2 TraesCS2A01G248900 chr7B 34280067 34282307 2240 True 1500.500000 2843 90.373000 1 2468 2 chr7B.!!$R2 2467
3 TraesCS2A01G248900 chr3A 44772421 44774225 1804 True 2784.000000 2784 94.521000 1 1803 1 chr3A.!!$R1 1802
4 TraesCS2A01G248900 chr3A 635312064 635314366 2302 False 1390.550000 2708 90.297000 1 2314 2 chr3A.!!$F1 2313
5 TraesCS2A01G248900 chr5D 387838897 387840682 1785 True 2760.000000 2760 94.599000 1 1785 1 chr5D.!!$R1 1784
6 TraesCS2A01G248900 chr4A 737660730 737662549 1819 False 2712.000000 2712 93.654000 1 1813 1 chr4A.!!$F1 1812
7 TraesCS2A01G248900 chr4A 514388887 514389456 569 True 248.333333 268 86.132333 1971 2468 3 chr4A.!!$R3 497
8 TraesCS2A01G248900 chr1A 480958135 480960014 1879 False 1497.000000 2700 94.022500 1 1946 2 chr1A.!!$F1 1945
9 TraesCS2A01G248900 chr3B 112909779 112911565 1786 False 2671.000000 2671 93.736000 1 1777 1 chr3B.!!$F1 1776
10 TraesCS2A01G248900 chr3B 16201400 16202832 1432 True 763.500000 1362 87.403500 645 2188 2 chr3B.!!$R1 1543
11 TraesCS2A01G248900 chr7A 38737234 38739543 2309 False 1340.600000 2597 84.453000 1 2314 2 chr7A.!!$F1 2313
12 TraesCS2A01G248900 chr7A 595029789 595031333 1544 True 239.833333 440 87.875000 1755 2468 6 chr7A.!!$R2 713
13 TraesCS2A01G248900 chr5B 578835773 578837551 1778 True 2586.000000 2586 92.933000 1 1777 1 chr5B.!!$R1 1776
14 TraesCS2A01G248900 chr5B 35439756 35440325 569 False 236.000000 303 90.477000 1755 2468 2 chr5B.!!$F2 713
15 TraesCS2A01G248900 chr7D 16797243 16798006 763 True 241.750000 442 86.900000 1755 2466 4 chr7D.!!$R2 711
16 TraesCS2A01G248900 chr1D 490890336 490890968 632 False 217.000000 403 86.205000 1755 2468 4 chr1D.!!$F1 713

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
584 585 0.037303 CAAGTCATGGAGGTGGCACT 59.963 55.0 18.45 3.24 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 3479 0.165944 CAAAACGATCCAGACGCCAC 59.834 55.0 0.0 0.0 0.0 5.01 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
23 24 1.599071 CAAGCAAGCAAGTCTTCACGA 59.401 47.619 0.00 0.00 31.27 4.35
202 203 1.732941 TGCTCGCATTTGATAACGGT 58.267 45.000 0.00 0.00 0.00 4.83
209 210 2.414824 GCATTTGATAACGGTGGCGAAA 60.415 45.455 0.00 0.00 0.00 3.46
426 427 3.350992 TCAGGGGTGATATGGATGACT 57.649 47.619 0.00 0.00 0.00 3.41
457 458 4.669206 ACACTGGCATGAAACAATTTGA 57.331 36.364 2.79 0.00 0.00 2.69
584 585 0.037303 CAAGTCATGGAGGTGGCACT 59.963 55.000 18.45 3.24 0.00 4.40
716 725 3.693085 CGTAGAGGGAGTACAAGTGCTAA 59.307 47.826 0.00 0.00 0.00 3.09
732 747 0.736325 CTAAAGGTGGTGGTCGAGCG 60.736 60.000 10.46 0.00 0.00 5.03
788 809 2.223803 AGTGCTAGAGGTGCTAGTGT 57.776 50.000 0.00 0.00 46.81 3.55
874 931 4.273969 CGGCCTTCGGTTATTTGCTTAATA 59.726 41.667 0.00 0.00 34.75 0.98
1080 1140 1.622607 CGTGGATGGAGGCCAGGTTA 61.623 60.000 5.01 0.00 36.75 2.85
1083 1143 0.761802 GGATGGAGGCCAGGTTAGAG 59.238 60.000 5.01 0.00 36.75 2.43
1220 1280 3.054508 TGTCCCAACTATGCACATGATCA 60.055 43.478 0.00 0.00 0.00 2.92
1226 1286 5.180680 CCAACTATGCACATGATCATCGAAT 59.819 40.000 4.86 2.85 0.00 3.34
1469 1530 1.133575 CATGGGGATTGGAGCATGAGT 60.134 52.381 0.00 0.00 0.00 3.41
1497 1558 0.667792 AAGGAGAAGAACGAGCGCAC 60.668 55.000 11.47 0.96 0.00 5.34
1522 1583 1.908299 TGAGCAAGAGAGGGCACGA 60.908 57.895 0.00 0.00 0.00 4.35
1531 1592 2.368875 AGAGAGGGCACGAAAAGAGAAA 59.631 45.455 0.00 0.00 0.00 2.52
1676 1739 1.335964 CGGCGTCGATGATGGACTATT 60.336 52.381 1.44 0.00 39.00 1.73
1776 1842 5.609696 CGTGTGTGAACTTGTTATTCGAGAC 60.610 44.000 0.00 0.00 0.00 3.36
1777 1843 4.748102 TGTGTGAACTTGTTATTCGAGACC 59.252 41.667 0.00 0.00 0.00 3.85
1778 1844 4.989168 GTGTGAACTTGTTATTCGAGACCT 59.011 41.667 0.00 0.00 0.00 3.85
1779 1845 5.465724 GTGTGAACTTGTTATTCGAGACCTT 59.534 40.000 0.00 0.00 0.00 3.50
1780 1846 6.643770 GTGTGAACTTGTTATTCGAGACCTTA 59.356 38.462 0.00 0.00 0.00 2.69
1781 1847 7.331193 GTGTGAACTTGTTATTCGAGACCTTAT 59.669 37.037 0.00 0.00 0.00 1.73
1782 1848 7.330946 TGTGAACTTGTTATTCGAGACCTTATG 59.669 37.037 0.00 0.00 0.00 1.90
1783 1849 7.331193 GTGAACTTGTTATTCGAGACCTTATGT 59.669 37.037 0.00 0.00 0.00 2.29
1784 1850 7.330946 TGAACTTGTTATTCGAGACCTTATGTG 59.669 37.037 0.00 0.00 0.00 3.21
1785 1851 6.106673 ACTTGTTATTCGAGACCTTATGTGG 58.893 40.000 0.00 0.00 0.00 4.17
1786 1852 5.670792 TGTTATTCGAGACCTTATGTGGT 57.329 39.130 0.00 0.00 44.10 4.16
1798 1864 6.374417 ACCTTATGTGGTCATGAACTACTT 57.626 37.500 12.94 9.13 39.91 2.24
1799 1865 7.490657 ACCTTATGTGGTCATGAACTACTTA 57.509 36.000 12.94 8.23 39.91 2.24
1800 1866 8.090788 ACCTTATGTGGTCATGAACTACTTAT 57.909 34.615 12.94 2.18 39.91 1.73
1801 1867 7.987458 ACCTTATGTGGTCATGAACTACTTATG 59.013 37.037 12.94 11.67 39.91 1.90
1802 1868 7.987458 CCTTATGTGGTCATGAACTACTTATGT 59.013 37.037 12.94 0.00 39.91 2.29
1803 1869 8.942338 TTATGTGGTCATGAACTACTTATGTC 57.058 34.615 12.94 0.00 39.91 3.06
1804 1870 6.353404 TGTGGTCATGAACTACTTATGTCA 57.647 37.500 12.94 0.00 39.91 3.58
1805 1871 6.946340 TGTGGTCATGAACTACTTATGTCAT 58.054 36.000 12.94 0.00 39.91 3.06
1806 1872 7.394016 TGTGGTCATGAACTACTTATGTCATT 58.606 34.615 12.94 0.00 39.91 2.57
1807 1873 7.882791 TGTGGTCATGAACTACTTATGTCATTT 59.117 33.333 12.94 0.00 39.91 2.32
1808 1874 8.177663 GTGGTCATGAACTACTTATGTCATTTG 58.822 37.037 12.94 0.00 36.49 2.32
1809 1875 8.100164 TGGTCATGAACTACTTATGTCATTTGA 58.900 33.333 12.94 0.00 0.00 2.69
1810 1876 8.607459 GGTCATGAACTACTTATGTCATTTGAG 58.393 37.037 2.64 0.00 0.00 3.02
1811 1877 9.371136 GTCATGAACTACTTATGTCATTTGAGA 57.629 33.333 0.00 0.00 0.00 3.27
1812 1878 9.371136 TCATGAACTACTTATGTCATTTGAGAC 57.629 33.333 0.00 0.00 38.99 3.36
1821 1887 4.690184 TGTCATTTGAGACATCATGTGC 57.310 40.909 0.00 0.00 43.18 4.57
1822 1888 3.125658 TGTCATTTGAGACATCATGTGCG 59.874 43.478 0.00 0.00 43.18 5.34
1823 1889 3.371898 GTCATTTGAGACATCATGTGCGA 59.628 43.478 0.00 0.00 38.40 5.10
1824 1890 4.002316 TCATTTGAGACATCATGTGCGAA 58.998 39.130 0.00 0.00 34.73 4.70
1825 1891 3.811722 TTTGAGACATCATGTGCGAAC 57.188 42.857 0.00 0.00 34.73 3.95
1826 1892 2.749280 TGAGACATCATGTGCGAACT 57.251 45.000 0.00 0.00 0.00 3.01
1827 1893 3.044235 TGAGACATCATGTGCGAACTT 57.956 42.857 0.00 0.00 0.00 2.66
1828 1894 2.738314 TGAGACATCATGTGCGAACTTG 59.262 45.455 0.00 2.95 0.00 3.16
1829 1895 2.738846 GAGACATCATGTGCGAACTTGT 59.261 45.455 9.13 1.07 0.00 3.16
1830 1896 3.141398 AGACATCATGTGCGAACTTGTT 58.859 40.909 9.13 0.00 0.00 2.83
1831 1897 4.314961 AGACATCATGTGCGAACTTGTTA 58.685 39.130 9.13 0.00 0.00 2.41
1832 1898 4.937620 AGACATCATGTGCGAACTTGTTAT 59.062 37.500 9.13 0.00 0.00 1.89
1833 1899 5.412594 AGACATCATGTGCGAACTTGTTATT 59.587 36.000 9.13 0.00 0.00 1.40
1834 1900 5.631026 ACATCATGTGCGAACTTGTTATTC 58.369 37.500 9.13 0.00 0.00 1.75
1859 1925 3.740115 ACCTTGTGTGGTCATGAACTAC 58.260 45.455 12.94 11.54 39.67 2.73
1860 1926 3.391296 ACCTTGTGTGGTCATGAACTACT 59.609 43.478 12.94 0.00 39.91 2.57
1879 1976 9.983804 GAACTACTTATGTGCAACCTATTTAAC 57.016 33.333 0.00 0.00 34.36 2.01
1989 2195 1.043116 CCAGACGCCATAGACCCTGA 61.043 60.000 0.00 0.00 0.00 3.86
2016 2222 1.691434 GGTCCCTATCCAGAGAGCAAG 59.309 57.143 0.00 0.00 0.00 4.01
2086 3279 1.692762 GGGTCCCTATCCAGAGAGCAA 60.693 57.143 0.00 0.00 0.00 3.91
2099 3292 4.038402 CCAGAGAGCAAAATTCCAGTTTGT 59.962 41.667 0.00 0.00 38.09 2.83
2122 3385 4.927782 TGCACACCCAGACGCCAC 62.928 66.667 0.00 0.00 0.00 5.01
2126 3389 3.687102 CACCCAGACGCCACGGTA 61.687 66.667 0.00 0.00 0.00 4.02
2142 3405 2.118732 TACCTGGCGTCTGGGTCA 59.881 61.111 17.84 0.00 36.44 4.02
2154 3418 1.144708 TCTGGGTCATTTTGGTCAGCA 59.855 47.619 0.00 0.00 0.00 4.41
2170 3434 1.190833 AGCAGGAGACCAGACACCTG 61.191 60.000 0.00 0.00 46.26 4.00
2181 3445 2.321213 GACACCTGTCTGTTGTGGC 58.679 57.895 0.00 0.00 41.65 5.01
2182 3446 0.179045 GACACCTGTCTGTTGTGGCT 60.179 55.000 0.00 0.00 41.65 4.75
2183 3447 0.464373 ACACCTGTCTGTTGTGGCTG 60.464 55.000 0.00 0.00 34.33 4.85
2184 3448 0.179048 CACCTGTCTGTTGTGGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
2185 3449 0.767375 ACCTGTCTGTTGTGGCTGAT 59.233 50.000 0.00 0.00 0.00 2.90
2186 3450 1.162698 CCTGTCTGTTGTGGCTGATG 58.837 55.000 0.00 0.00 0.00 3.07
2187 3451 0.520404 CTGTCTGTTGTGGCTGATGC 59.480 55.000 0.00 0.00 38.76 3.91
2210 3474 3.936203 GGCGACCCAGACACCACA 61.936 66.667 0.00 0.00 0.00 4.17
2211 3475 2.357517 GCGACCCAGACACCACAG 60.358 66.667 0.00 0.00 0.00 3.66
2212 3476 2.867855 GCGACCCAGACACCACAGA 61.868 63.158 0.00 0.00 0.00 3.41
2213 3477 1.006102 CGACCCAGACACCACAGAC 60.006 63.158 0.00 0.00 0.00 3.51
2214 3478 1.371558 GACCCAGACACCACAGACC 59.628 63.158 0.00 0.00 0.00 3.85
2215 3479 2.343758 CCCAGACACCACAGACCG 59.656 66.667 0.00 0.00 0.00 4.79
2216 3480 2.507854 CCCAGACACCACAGACCGT 61.508 63.158 0.00 0.00 0.00 4.83
2217 3481 1.300931 CCAGACACCACAGACCGTG 60.301 63.158 0.00 0.00 45.92 4.94
2227 3491 2.680352 AGACCGTGGCGTCTGGAT 60.680 61.111 5.87 0.00 41.60 3.41
2228 3492 2.202756 GACCGTGGCGTCTGGATC 60.203 66.667 5.87 0.00 0.00 3.36
2229 3493 4.129737 ACCGTGGCGTCTGGATCG 62.130 66.667 5.87 0.00 0.00 3.69
2230 3494 4.129737 CCGTGGCGTCTGGATCGT 62.130 66.667 0.00 0.00 0.00 3.73
2231 3495 2.126071 CGTGGCGTCTGGATCGTT 60.126 61.111 0.00 0.00 0.00 3.85
2232 3496 1.736645 CGTGGCGTCTGGATCGTTT 60.737 57.895 0.00 0.00 0.00 3.60
2233 3497 1.289109 CGTGGCGTCTGGATCGTTTT 61.289 55.000 0.00 0.00 0.00 2.43
2234 3498 0.165944 GTGGCGTCTGGATCGTTTTG 59.834 55.000 0.00 0.00 0.00 2.44
2235 3499 0.953471 TGGCGTCTGGATCGTTTTGG 60.953 55.000 0.00 0.00 0.00 3.28
2236 3500 0.953960 GGCGTCTGGATCGTTTTGGT 60.954 55.000 0.00 0.00 0.00 3.67
2237 3501 0.442699 GCGTCTGGATCGTTTTGGTC 59.557 55.000 0.00 0.00 0.00 4.02
2238 3502 1.939838 GCGTCTGGATCGTTTTGGTCT 60.940 52.381 0.00 0.00 0.00 3.85
2239 3503 2.413837 CGTCTGGATCGTTTTGGTCTT 58.586 47.619 0.00 0.00 0.00 3.01
2240 3504 2.806244 CGTCTGGATCGTTTTGGTCTTT 59.194 45.455 0.00 0.00 0.00 2.52
2241 3505 3.120649 CGTCTGGATCGTTTTGGTCTTTC 60.121 47.826 0.00 0.00 0.00 2.62
2242 3506 3.064207 TCTGGATCGTTTTGGTCTTTCG 58.936 45.455 0.00 0.00 0.00 3.46
2243 3507 2.147958 TGGATCGTTTTGGTCTTTCGG 58.852 47.619 0.00 0.00 0.00 4.30
2244 3508 2.148768 GGATCGTTTTGGTCTTTCGGT 58.851 47.619 0.00 0.00 0.00 4.69
2245 3509 2.095919 GGATCGTTTTGGTCTTTCGGTG 60.096 50.000 0.00 0.00 0.00 4.94
2259 3523 3.936203 GGTGACCCAGACGCCACA 61.936 66.667 0.00 0.00 37.78 4.17
2260 3524 2.110213 GTGACCCAGACGCCACAA 59.890 61.111 0.00 0.00 0.00 3.33
2264 3528 2.203280 CCCAGACGCCACAAACCA 60.203 61.111 0.00 0.00 0.00 3.67
2278 3542 2.063015 AAACCATGGCGTCTGGGTCA 62.063 55.000 13.04 0.00 38.14 4.02
2289 3553 0.953471 TCTGGGTCATTTTGGTCGCG 60.953 55.000 0.00 0.00 0.00 5.87
2319 3583 0.901124 GACACCTGTCTGATGCCTCT 59.099 55.000 0.00 0.00 41.65 3.69
2325 3646 0.842030 TGTCTGATGCCTCTGGGGTT 60.842 55.000 0.00 0.00 37.43 4.11
2331 3652 2.090210 TGATGCCTCTGGGGTTCCTATA 60.090 50.000 0.00 0.00 37.43 1.31
2332 3653 1.802553 TGCCTCTGGGGTTCCTATAC 58.197 55.000 0.00 0.00 37.43 1.47
2334 3655 2.339769 GCCTCTGGGGTTCCTATACAT 58.660 52.381 0.00 0.00 37.43 2.29
2346 3668 8.161425 GGGGTTCCTATACATAGAGCATTTTTA 58.839 37.037 0.00 0.00 32.05 1.52
2382 3929 3.322466 CCCAGACGCCAAGGTCCT 61.322 66.667 0.00 0.00 37.66 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 1.730064 GTATGTTTCTCGCTTTCGCCA 59.270 47.619 0.00 0.00 35.26 5.69
426 427 0.625316 ATGCCAGTGTATCCAGCCAA 59.375 50.000 0.00 0.00 0.00 4.52
584 585 1.001974 CTTCCACCTCGTTCACCATCA 59.998 52.381 0.00 0.00 0.00 3.07
716 725 4.003788 CCGCTCGACCACCACCTT 62.004 66.667 0.00 0.00 0.00 3.50
732 747 0.674895 CACCTCTAGCACTTGTGCCC 60.675 60.000 20.39 0.00 34.90 5.36
782 803 3.190744 TGTGCTTCCTCTACGAACACTAG 59.809 47.826 0.00 0.00 31.13 2.57
788 809 2.866460 GCACTTGTGCTTCCTCTACGAA 60.866 50.000 17.36 0.00 0.00 3.85
942 1000 8.799091 CACAAAGAGAGTACATGAGTAAATACG 58.201 37.037 0.00 0.00 30.67 3.06
951 1009 5.985530 CACAAGACACAAAGAGAGTACATGA 59.014 40.000 0.00 0.00 0.00 3.07
1080 1140 4.264804 ACATCCTTCTCCTTCTCCTTCTCT 60.265 45.833 0.00 0.00 0.00 3.10
1083 1143 3.681313 GCACATCCTTCTCCTTCTCCTTC 60.681 52.174 0.00 0.00 0.00 3.46
1220 1280 1.732941 TGCGTTAGTTGGCATTCGAT 58.267 45.000 0.00 0.00 33.52 3.59
1226 1286 2.979240 TGTCATATGCGTTAGTTGGCA 58.021 42.857 0.00 0.00 44.29 4.92
1469 1530 2.031069 CGTTCTTCTCCTTCTCACGACA 60.031 50.000 0.00 0.00 0.00 4.35
1497 1558 1.075425 CCTCTCTTGCTCACGCTTCG 61.075 60.000 0.00 0.00 36.97 3.79
1522 1583 3.753294 TGACGAGCCTCTTTCTCTTTT 57.247 42.857 0.00 0.00 0.00 2.27
1531 1592 2.091541 CTCTCTTCTTGACGAGCCTCT 58.908 52.381 0.00 0.00 0.00 3.69
1776 1842 7.987458 ACATAAGTAGTTCATGACCACATAAGG 59.013 37.037 0.00 0.00 35.09 2.69
1777 1843 8.948631 ACATAAGTAGTTCATGACCACATAAG 57.051 34.615 0.00 0.00 35.09 1.73
1778 1844 8.536175 TGACATAAGTAGTTCATGACCACATAA 58.464 33.333 0.00 0.00 35.09 1.90
1779 1845 8.073467 TGACATAAGTAGTTCATGACCACATA 57.927 34.615 0.00 0.00 35.09 2.29
1780 1846 6.946340 TGACATAAGTAGTTCATGACCACAT 58.054 36.000 0.00 0.00 37.19 3.21
1781 1847 6.353404 TGACATAAGTAGTTCATGACCACA 57.647 37.500 0.00 0.00 0.00 4.17
1782 1848 7.849804 AATGACATAAGTAGTTCATGACCAC 57.150 36.000 0.00 0.00 0.00 4.16
1783 1849 8.100164 TCAAATGACATAAGTAGTTCATGACCA 58.900 33.333 0.00 0.00 0.00 4.02
1784 1850 8.492673 TCAAATGACATAAGTAGTTCATGACC 57.507 34.615 0.00 0.00 0.00 4.02
1785 1851 9.371136 TCTCAAATGACATAAGTAGTTCATGAC 57.629 33.333 0.00 0.00 0.00 3.06
1786 1852 9.371136 GTCTCAAATGACATAAGTAGTTCATGA 57.629 33.333 0.00 0.00 36.97 3.07
1787 1853 9.154847 TGTCTCAAATGACATAAGTAGTTCATG 57.845 33.333 0.00 0.00 41.43 3.07
1801 1867 3.371898 TCGCACATGATGTCTCAAATGAC 59.628 43.478 0.00 0.00 34.37 3.06
1802 1868 3.598299 TCGCACATGATGTCTCAAATGA 58.402 40.909 0.00 0.00 34.37 2.57
1803 1869 4.093514 GTTCGCACATGATGTCTCAAATG 58.906 43.478 0.00 0.00 34.37 2.32
1804 1870 4.005650 AGTTCGCACATGATGTCTCAAAT 58.994 39.130 0.00 0.00 34.37 2.32
1805 1871 3.402110 AGTTCGCACATGATGTCTCAAA 58.598 40.909 0.00 0.00 34.37 2.69
1806 1872 3.044235 AGTTCGCACATGATGTCTCAA 57.956 42.857 0.00 0.00 34.37 3.02
1807 1873 2.738314 CAAGTTCGCACATGATGTCTCA 59.262 45.455 0.00 0.00 35.41 3.27
1808 1874 2.738846 ACAAGTTCGCACATGATGTCTC 59.261 45.455 0.00 0.00 0.00 3.36
1809 1875 2.771089 ACAAGTTCGCACATGATGTCT 58.229 42.857 0.00 0.00 0.00 3.41
1810 1876 3.542712 AACAAGTTCGCACATGATGTC 57.457 42.857 0.00 0.00 0.00 3.06
1811 1877 5.627499 AATAACAAGTTCGCACATGATGT 57.373 34.783 0.00 0.00 0.00 3.06
1812 1878 4.725280 CGAATAACAAGTTCGCACATGATG 59.275 41.667 0.00 0.00 41.43 3.07
1813 1879 4.629634 TCGAATAACAAGTTCGCACATGAT 59.370 37.500 0.00 0.00 45.83 2.45
1814 1880 3.991121 TCGAATAACAAGTTCGCACATGA 59.009 39.130 0.00 0.00 45.83 3.07
1815 1881 4.091365 TCTCGAATAACAAGTTCGCACATG 59.909 41.667 3.60 0.00 45.83 3.21
1816 1882 4.091509 GTCTCGAATAACAAGTTCGCACAT 59.908 41.667 3.60 0.00 45.83 3.21
1817 1883 3.427528 GTCTCGAATAACAAGTTCGCACA 59.572 43.478 3.60 0.00 45.83 4.57
1818 1884 3.181533 GGTCTCGAATAACAAGTTCGCAC 60.182 47.826 3.60 3.39 45.83 5.34
1819 1885 2.991190 GGTCTCGAATAACAAGTTCGCA 59.009 45.455 3.60 0.00 45.83 5.10
1820 1886 3.251571 AGGTCTCGAATAACAAGTTCGC 58.748 45.455 3.60 0.00 45.83 4.70
1822 1888 5.465724 ACACAAGGTCTCGAATAACAAGTTC 59.534 40.000 0.00 0.00 0.00 3.01
1823 1889 5.236478 CACACAAGGTCTCGAATAACAAGTT 59.764 40.000 0.00 0.00 0.00 2.66
1824 1890 4.750098 CACACAAGGTCTCGAATAACAAGT 59.250 41.667 0.00 0.00 0.00 3.16
1825 1891 4.152402 CCACACAAGGTCTCGAATAACAAG 59.848 45.833 0.00 0.00 0.00 3.16
1826 1892 4.062293 CCACACAAGGTCTCGAATAACAA 58.938 43.478 0.00 0.00 0.00 2.83
1827 1893 3.070446 ACCACACAAGGTCTCGAATAACA 59.930 43.478 0.00 0.00 37.28 2.41
1828 1894 3.660865 ACCACACAAGGTCTCGAATAAC 58.339 45.455 0.00 0.00 37.28 1.89
1838 1904 3.391296 AGTAGTTCATGACCACACAAGGT 59.609 43.478 0.00 0.00 46.82 3.50
1839 1905 4.008074 AGTAGTTCATGACCACACAAGG 57.992 45.455 0.00 0.00 0.00 3.61
1989 2195 1.701603 TGGATAGGGACCCAGACGT 59.298 57.895 14.60 0.00 0.00 4.34
2086 3279 6.257630 GTGTGCACATTTACAAACTGGAATTT 59.742 34.615 24.69 0.00 0.00 1.82
2099 3292 1.518325 CGTCTGGGTGTGCACATTTA 58.482 50.000 24.69 11.00 0.00 1.40
2122 3385 4.143333 CCCAGACGCCAGGTACCG 62.143 72.222 6.18 1.26 0.00 4.02
2126 3389 1.779061 AAATGACCCAGACGCCAGGT 61.779 55.000 0.00 0.00 36.31 4.00
2154 3418 3.059287 GACAGGTGTCTGGTCTCCT 57.941 57.895 2.72 0.00 44.99 3.69
2193 3457 3.883744 CTGTGGTGTCTGGGTCGCC 62.884 68.421 0.00 0.00 36.18 5.54
2194 3458 2.357517 CTGTGGTGTCTGGGTCGC 60.358 66.667 0.00 0.00 0.00 5.19
2195 3459 1.006102 GTCTGTGGTGTCTGGGTCG 60.006 63.158 0.00 0.00 0.00 4.79
2196 3460 1.371558 GGTCTGTGGTGTCTGGGTC 59.628 63.158 0.00 0.00 0.00 4.46
2197 3461 2.507854 CGGTCTGTGGTGTCTGGGT 61.508 63.158 0.00 0.00 0.00 4.51
2198 3462 2.343758 CGGTCTGTGGTGTCTGGG 59.656 66.667 0.00 0.00 0.00 4.45
2199 3463 1.300931 CACGGTCTGTGGTGTCTGG 60.301 63.158 3.65 0.00 45.21 3.86
2200 3464 4.343581 CACGGTCTGTGGTGTCTG 57.656 61.111 3.65 0.00 45.21 3.51
2211 3475 2.202756 GATCCAGACGCCACGGTC 60.203 66.667 0.00 0.00 37.19 4.79
2212 3476 4.129737 CGATCCAGACGCCACGGT 62.130 66.667 0.00 0.00 0.00 4.83
2213 3477 3.642778 AACGATCCAGACGCCACGG 62.643 63.158 0.00 0.00 0.00 4.94
2214 3478 1.289109 AAAACGATCCAGACGCCACG 61.289 55.000 0.00 0.00 0.00 4.94
2215 3479 0.165944 CAAAACGATCCAGACGCCAC 59.834 55.000 0.00 0.00 0.00 5.01
2216 3480 0.953471 CCAAAACGATCCAGACGCCA 60.953 55.000 0.00 0.00 0.00 5.69
2217 3481 0.953960 ACCAAAACGATCCAGACGCC 60.954 55.000 0.00 0.00 0.00 5.68
2218 3482 0.442699 GACCAAAACGATCCAGACGC 59.557 55.000 0.00 0.00 0.00 5.19
2219 3483 2.080286 AGACCAAAACGATCCAGACG 57.920 50.000 0.00 0.00 0.00 4.18
2220 3484 3.120649 CGAAAGACCAAAACGATCCAGAC 60.121 47.826 0.00 0.00 0.00 3.51
2221 3485 3.064207 CGAAAGACCAAAACGATCCAGA 58.936 45.455 0.00 0.00 0.00 3.86
2222 3486 2.159627 CCGAAAGACCAAAACGATCCAG 59.840 50.000 0.00 0.00 0.00 3.86
2223 3487 2.147958 CCGAAAGACCAAAACGATCCA 58.852 47.619 0.00 0.00 0.00 3.41
2224 3488 2.095919 CACCGAAAGACCAAAACGATCC 60.096 50.000 0.00 0.00 0.00 3.36
2225 3489 2.803956 TCACCGAAAGACCAAAACGATC 59.196 45.455 0.00 0.00 0.00 3.69
2226 3490 2.546789 GTCACCGAAAGACCAAAACGAT 59.453 45.455 0.00 0.00 0.00 3.73
2227 3491 1.935199 GTCACCGAAAGACCAAAACGA 59.065 47.619 0.00 0.00 0.00 3.85
2228 3492 2.378507 GTCACCGAAAGACCAAAACG 57.621 50.000 0.00 0.00 0.00 3.60
2235 3499 0.666577 CGTCTGGGTCACCGAAAGAC 60.667 60.000 11.31 11.31 40.75 3.01
2236 3500 1.663739 CGTCTGGGTCACCGAAAGA 59.336 57.895 0.00 0.00 40.75 2.52
2237 3501 2.027625 GCGTCTGGGTCACCGAAAG 61.028 63.158 0.00 0.00 40.75 2.62
2238 3502 2.029964 GCGTCTGGGTCACCGAAA 59.970 61.111 0.00 0.00 40.75 3.46
2239 3503 3.998672 GGCGTCTGGGTCACCGAA 61.999 66.667 0.00 0.00 40.75 4.30
2242 3506 2.951475 TTTGTGGCGTCTGGGTCACC 62.951 60.000 0.00 0.00 37.24 4.02
2243 3507 1.525077 TTTGTGGCGTCTGGGTCAC 60.525 57.895 0.00 0.00 0.00 3.67
2244 3508 1.525077 GTTTGTGGCGTCTGGGTCA 60.525 57.895 0.00 0.00 0.00 4.02
2245 3509 2.258726 GGTTTGTGGCGTCTGGGTC 61.259 63.158 0.00 0.00 0.00 4.46
2258 3522 1.586154 GACCCAGACGCCATGGTTTG 61.586 60.000 14.67 6.42 35.96 2.93
2259 3523 1.303317 GACCCAGACGCCATGGTTT 60.303 57.895 14.67 0.00 35.96 3.27
2260 3524 1.852157 ATGACCCAGACGCCATGGTT 61.852 55.000 14.67 0.00 35.96 3.67
2264 3528 1.176527 CAAAATGACCCAGACGCCAT 58.823 50.000 0.00 0.00 0.00 4.40
2278 3542 1.003839 TCTCCTGCGCGACCAAAAT 60.004 52.632 12.10 0.00 0.00 1.82
2289 3553 1.294780 CAGGTGTCTGGTCTCCTGC 59.705 63.158 0.00 0.00 40.52 4.85
2314 3578 1.802553 TGTATAGGAACCCCAGAGGC 58.197 55.000 0.00 0.00 40.58 4.70
2315 3579 5.011982 TCTATGTATAGGAACCCCAGAGG 57.988 47.826 0.00 0.00 43.78 3.69
2316 3580 4.464597 GCTCTATGTATAGGAACCCCAGAG 59.535 50.000 0.00 0.00 33.88 3.35
2317 3581 4.140782 TGCTCTATGTATAGGAACCCCAGA 60.141 45.833 0.00 0.00 33.88 3.86
2319 3583 4.207698 TGCTCTATGTATAGGAACCCCA 57.792 45.455 0.00 0.00 33.88 4.96
2331 3652 9.439500 AAATGCAAACATAAAAATGCTCTATGT 57.561 25.926 0.00 0.00 39.49 2.29
2332 3653 9.697250 CAAATGCAAACATAAAAATGCTCTATG 57.303 29.630 0.00 0.00 39.49 2.23
2334 3655 8.710551 CACAAATGCAAACATAAAAATGCTCTA 58.289 29.630 0.00 0.00 39.49 2.43
2355 3819 2.477176 GCGTCTGGGTGTGCACAAA 61.477 57.895 23.59 9.55 0.00 2.83
2356 3820 2.899838 GCGTCTGGGTGTGCACAA 60.900 61.111 23.59 5.14 0.00 3.33
2382 3929 3.636231 CAGGGACCCAGACGCCAA 61.636 66.667 14.60 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.