Multiple sequence alignment - TraesCS2D01G104700

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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 TraesCS2D01G104700 chr2D 100.000 3905 0 0 1 3905 56444770 56448674 0.000000e+00 7212.0
1 TraesCS2D01G104700 chr2D 92.158 1849 75 27 1 1802 56296919 56298744 0.000000e+00 2547.0
2 TraesCS2D01G104700 chr2D 98.165 763 14 0 2907 3669 606599744 606600506 0.000000e+00 1332.0
3 TraesCS2D01G104700 chr2D 97.826 690 14 1 2901 3590 629996777 629997465 0.000000e+00 1190.0
4 TraesCS2D01G104700 chr2D 96.221 688 26 0 2903 3590 600425700 600426387 0.000000e+00 1127.0
5 TraesCS2D01G104700 chr2D 87.577 974 50 14 1950 2890 56298768 56299703 0.000000e+00 1062.0
6 TraesCS2D01G104700 chr2D 83.511 655 84 7 2251 2881 56255256 56255910 1.210000e-164 590.0
7 TraesCS2D01G104700 chr2D 99.163 239 2 0 3667 3905 606600708 606600946 7.750000e-117 431.0
8 TraesCS2D01G104700 chr2D 99.163 239 2 0 3667 3905 629998053 629998291 7.750000e-117 431.0
9 TraesCS2D01G104700 chr2D 98.745 239 3 0 3667 3905 15957280 15957518 3.610000e-115 425.0
10 TraesCS2D01G104700 chr2D 97.647 85 2 0 3585 3669 629997767 629997851 3.140000e-31 147.0
11 TraesCS2D01G104700 chr2D 96.471 85 3 0 3585 3669 15956994 15957078 1.460000e-29 141.0
12 TraesCS2D01G104700 chr2D 96.471 85 3 0 3585 3669 600426689 600426773 1.460000e-29 141.0
13 TraesCS2D01G104700 chr2B 88.973 1451 88 29 1 1402 89430118 89431545 0.000000e+00 1727.0
14 TraesCS2D01G104700 chr2B 92.602 757 44 7 2155 2901 89432455 89433209 0.000000e+00 1077.0
15 TraesCS2D01G104700 chr2B 97.490 239 6 0 3667 3905 186373636 186373398 3.630000e-110 409.0
16 TraesCS2D01G104700 chr2B 90.995 211 16 2 1447 1655 89431658 89431867 8.260000e-72 281.0
17 TraesCS2D01G104700 chr2B 89.231 195 11 3 1958 2144 89432212 89432404 6.520000e-58 235.0
18 TraesCS2D01G104700 chr2B 93.210 162 1 2 1651 1802 89432028 89432189 3.030000e-56 230.0
19 TraesCS2D01G104700 chr1B 97.242 689 19 0 2902 3590 560244998 560245686 0.000000e+00 1168.0
20 TraesCS2D01G104700 chr1B 99.163 239 2 0 3667 3905 560246274 560246512 7.750000e-117 431.0
21 TraesCS2D01G104700 chr1B 96.471 85 3 0 3585 3669 560245988 560246072 1.460000e-29 141.0
22 TraesCS2D01G104700 chr1B 83.962 106 11 5 60 162 662152570 662152672 3.210000e-16 97.1
23 TraesCS2D01G104700 chr1B 100.000 32 0 0 604 635 635155758 635155789 4.210000e-05 60.2
24 TraesCS2D01G104700 chrUn 96.702 667 21 1 2924 3590 347185721 347185056 0.000000e+00 1109.0
25 TraesCS2D01G104700 chrUn 96.471 85 3 0 3585 3669 347184754 347184670 1.460000e-29 141.0
26 TraesCS2D01G104700 chr7B 95.065 689 31 2 2903 3590 66976141 66975455 0.000000e+00 1081.0
27 TraesCS2D01G104700 chr7B 97.908 239 5 0 3667 3905 66974867 66974629 7.810000e-112 414.0
28 TraesCS2D01G104700 chr7B 96.471 85 3 0 3585 3669 66975153 66975069 1.460000e-29 141.0
29 TraesCS2D01G104700 chr4A 94.913 688 35 0 2903 3590 586857152 586856465 0.000000e+00 1077.0
30 TraesCS2D01G104700 chr4A 94.622 688 37 0 2903 3590 586920717 586921404 0.000000e+00 1066.0
31 TraesCS2D01G104700 chr4A 98.745 239 3 0 3667 3905 586855877 586855639 3.610000e-115 425.0
32 TraesCS2D01G104700 chr4A 98.326 239 4 0 3667 3905 586921992 586922230 1.680000e-113 420.0
33 TraesCS2D01G104700 chr4A 97.647 85 2 0 3585 3669 586921706 586921790 3.140000e-31 147.0
34 TraesCS2D01G104700 chr6D 94.501 691 32 5 2903 3590 446723334 446724021 0.000000e+00 1061.0
35 TraesCS2D01G104700 chr2A 87.980 782 58 15 1 772 57888002 57888757 0.000000e+00 891.0
36 TraesCS2D01G104700 chr2A 90.393 687 36 7 2227 2901 57890163 57890831 0.000000e+00 876.0
37 TraesCS2D01G104700 chr2A 87.954 689 42 11 767 1447 57888783 57889438 0.000000e+00 774.0
38 TraesCS2D01G104700 chr2A 83.051 649 92 4 2251 2881 57865528 57866176 1.220000e-159 573.0
39 TraesCS2D01G104700 chr2A 96.073 331 11 2 1472 1802 57889579 57889907 4.440000e-149 538.0
40 TraesCS2D01G104700 chr2A 90.000 50 5 0 2103 2152 57889981 57890030 9.060000e-07 65.8
41 TraesCS2D01G104700 chr7A 93.724 239 15 0 3667 3905 118196158 118196396 3.710000e-95 359.0
42 TraesCS2D01G104700 chr7A 90.196 51 3 2 1893 1942 96561760 96561711 9.060000e-07 65.8
43 TraesCS2D01G104700 chr5D 96.471 85 3 0 3585 3669 398486501 398486585 1.460000e-29 141.0
44 TraesCS2D01G104700 chr5D 82.069 145 19 6 12 154 310494913 310494774 2.470000e-22 117.0
45 TraesCS2D01G104700 chr3A 83.448 145 20 3 12 155 206622153 206622012 8.800000e-27 132.0
46 TraesCS2D01G104700 chr5B 85.849 106 9 6 51 155 395739469 395739569 1.480000e-19 108.0


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 TraesCS2D01G104700 chr2D 56444770 56448674 3904 False 7212.000000 7212 100.000000 1 3905 1 chr2D.!!$F2 3904
1 TraesCS2D01G104700 chr2D 56296919 56299703 2784 False 1804.500000 2547 89.867500 1 2890 2 chr2D.!!$F4 2889
2 TraesCS2D01G104700 chr2D 606599744 606600946 1202 False 881.500000 1332 98.664000 2907 3905 2 chr2D.!!$F6 998
3 TraesCS2D01G104700 chr2D 600425700 600426773 1073 False 634.000000 1127 96.346000 2903 3669 2 chr2D.!!$F5 766
4 TraesCS2D01G104700 chr2D 56255256 56255910 654 False 590.000000 590 83.511000 2251 2881 1 chr2D.!!$F1 630
5 TraesCS2D01G104700 chr2D 629996777 629998291 1514 False 589.333333 1190 98.212000 2901 3905 3 chr2D.!!$F7 1004
6 TraesCS2D01G104700 chr2D 15956994 15957518 524 False 283.000000 425 97.608000 3585 3905 2 chr2D.!!$F3 320
7 TraesCS2D01G104700 chr2B 89430118 89433209 3091 False 710.000000 1727 91.002200 1 2901 5 chr2B.!!$F1 2900
8 TraesCS2D01G104700 chr1B 560244998 560246512 1514 False 580.000000 1168 97.625333 2902 3905 3 chr1B.!!$F3 1003
9 TraesCS2D01G104700 chrUn 347184670 347185721 1051 True 625.000000 1109 96.586500 2924 3669 2 chrUn.!!$R1 745
10 TraesCS2D01G104700 chr7B 66974629 66976141 1512 True 545.333333 1081 96.481333 2903 3905 3 chr7B.!!$R1 1002
11 TraesCS2D01G104700 chr4A 586855639 586857152 1513 True 751.000000 1077 96.829000 2903 3905 2 chr4A.!!$R1 1002
12 TraesCS2D01G104700 chr4A 586920717 586922230 1513 False 544.333333 1066 96.865000 2903 3905 3 chr4A.!!$F1 1002
13 TraesCS2D01G104700 chr6D 446723334 446724021 687 False 1061.000000 1061 94.501000 2903 3590 1 chr6D.!!$F1 687
14 TraesCS2D01G104700 chr2A 57888002 57890831 2829 False 628.960000 891 90.480000 1 2901 5 chr2A.!!$F2 2900
15 TraesCS2D01G104700 chr2A 57865528 57866176 648 False 573.000000 573 83.051000 2251 2881 1 chr2A.!!$F1 630

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
82 83 1.605992 CTCCAGCCAGCAAGGATCA 59.394 57.895 4.58 0.00 41.22 2.92 F
1458 1633 1.068281 ACAGCATGCTCCGACTATCTG 59.932 52.381 19.68 5.93 42.53 2.90 F
1848 2295 0.307453 TCGTGCATGTTTGTGTCTGC 59.693 50.000 5.68 0.00 35.21 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 2288 0.169672 TAAGTACCTCGCGCAGACAC 59.830 55.0 8.75 5.6 0.0 3.67 R
2549 3113 0.037232 GCTGTAGTTGGAGAAGCGGT 60.037 55.0 0.00 0.0 0.0 5.68 R
3723 5137 0.555769 TGGTGTCAAAGGAAAGGGCT 59.444 50.0 0.00 0.0 0.0 5.19 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
72 73 1.719063 AAAACAGAGCCCTCCAGCCA 61.719 55.000 0.00 0.00 0.00 4.75
82 83 1.605992 CTCCAGCCAGCAAGGATCA 59.394 57.895 4.58 0.00 41.22 2.92
449 462 8.484575 TGTATGTTTACGGGATTGGTAAATCTA 58.515 33.333 1.09 0.00 40.69 1.98
462 475 4.880120 TGGTAAATCTACGTCGACTGAGAT 59.120 41.667 18.37 18.37 0.00 2.75
485 498 2.820059 ACGAAGTCTCTGTTGATGCA 57.180 45.000 0.00 0.00 29.74 3.96
523 544 8.786826 TCTTACATGAAGATCCGTACAATTTT 57.213 30.769 0.00 0.00 39.36 1.82
596 617 2.844946 TCTCAGTCGAGATCTAGCCAG 58.155 52.381 0.00 0.00 43.55 4.85
1349 1452 2.705127 GGAGGAAGAAGAGATCAGGCAT 59.295 50.000 0.00 0.00 0.00 4.40
1353 1456 1.210538 AGAAGAGATCAGGCATGGCA 58.789 50.000 22.64 1.17 0.00 4.92
1359 1465 4.881440 TCAGGCATGGCATCCGGC 62.881 66.667 22.64 0.00 43.74 6.13
1397 1503 2.170187 CCTCCAGGAGAAGGTGATCAAG 59.830 54.545 19.21 0.00 37.39 3.02
1413 1519 6.162777 GTGATCAAGGAAAGCCTAGCTATAG 58.837 44.000 0.00 0.00 46.28 1.31
1450 1625 1.518056 AAACACCACAGCATGCTCCG 61.518 55.000 19.68 10.68 42.53 4.63
1458 1633 1.068281 ACAGCATGCTCCGACTATCTG 59.932 52.381 19.68 5.93 42.53 2.90
1605 1873 7.651027 AAGTAGATGCTGCCAATTAAGATTT 57.349 32.000 0.00 0.00 0.00 2.17
1797 2244 2.948315 CCTCTACTAACCCGAGGTACAC 59.052 54.545 0.00 0.00 39.54 2.90
1802 2249 6.000219 TCTACTAACCCGAGGTACACATATC 59.000 44.000 0.00 0.00 33.12 1.63
1803 2250 4.539726 ACTAACCCGAGGTACACATATCA 58.460 43.478 0.00 0.00 33.12 2.15
1805 2252 2.742348 ACCCGAGGTACACATATCACA 58.258 47.619 0.00 0.00 32.11 3.58
1806 2253 3.305720 ACCCGAGGTACACATATCACAT 58.694 45.455 0.00 0.00 32.11 3.21
1807 2254 4.476297 ACCCGAGGTACACATATCACATA 58.524 43.478 0.00 0.00 32.11 2.29
1808 2255 5.084519 ACCCGAGGTACACATATCACATAT 58.915 41.667 0.00 0.00 32.11 1.78
1809 2256 5.047306 ACCCGAGGTACACATATCACATATG 60.047 44.000 0.00 0.00 40.49 1.78
1810 2257 7.425667 ACCCGAGGTACACATATCACATATGT 61.426 42.308 1.41 1.41 44.61 2.29
1829 2276 9.404848 ACATATGTGTGTATGTAGTGTAGTACT 57.595 33.333 7.78 0.00 42.03 2.73
1830 2277 9.880064 CATATGTGTGTATGTAGTGTAGTACTC 57.120 37.037 0.00 0.00 40.89 2.59
1831 2278 6.413018 TGTGTGTATGTAGTGTAGTACTCG 57.587 41.667 0.00 0.00 40.89 4.18
1832 2279 5.934043 TGTGTGTATGTAGTGTAGTACTCGT 59.066 40.000 0.00 0.00 40.89 4.18
1833 2280 6.128472 TGTGTGTATGTAGTGTAGTACTCGTG 60.128 42.308 0.00 0.00 40.89 4.35
1834 2281 5.163824 TGTGTATGTAGTGTAGTACTCGTGC 60.164 44.000 0.00 0.00 40.89 5.34
1835 2282 4.937015 TGTATGTAGTGTAGTACTCGTGCA 59.063 41.667 0.00 0.00 40.89 4.57
1836 2283 5.587443 TGTATGTAGTGTAGTACTCGTGCAT 59.413 40.000 0.00 0.89 40.89 3.96
1837 2284 4.351131 TGTAGTGTAGTACTCGTGCATG 57.649 45.455 0.00 0.00 40.89 4.06
1838 2285 3.754850 TGTAGTGTAGTACTCGTGCATGT 59.245 43.478 5.68 0.48 40.89 3.21
1839 2286 3.936372 AGTGTAGTACTCGTGCATGTT 57.064 42.857 5.68 0.00 33.17 2.71
1840 2287 4.252971 AGTGTAGTACTCGTGCATGTTT 57.747 40.909 5.68 0.00 33.17 2.83
1841 2288 3.987868 AGTGTAGTACTCGTGCATGTTTG 59.012 43.478 5.68 0.61 33.17 2.93
1842 2289 3.739300 GTGTAGTACTCGTGCATGTTTGT 59.261 43.478 5.68 6.52 0.00 2.83
1843 2290 3.738791 TGTAGTACTCGTGCATGTTTGTG 59.261 43.478 5.68 0.00 0.00 3.33
1844 2291 2.833794 AGTACTCGTGCATGTTTGTGT 58.166 42.857 5.68 1.88 0.00 3.72
1845 2292 2.800544 AGTACTCGTGCATGTTTGTGTC 59.199 45.455 5.68 3.15 0.00 3.67
1846 2293 1.953559 ACTCGTGCATGTTTGTGTCT 58.046 45.000 5.68 0.00 0.00 3.41
1847 2294 1.599071 ACTCGTGCATGTTTGTGTCTG 59.401 47.619 5.68 0.00 0.00 3.51
1848 2295 0.307453 TCGTGCATGTTTGTGTCTGC 59.693 50.000 5.68 0.00 35.21 4.26
1849 2296 0.993251 CGTGCATGTTTGTGTCTGCG 60.993 55.000 0.00 0.00 37.44 5.18
1850 2297 1.008652 TGCATGTTTGTGTCTGCGC 60.009 52.632 0.00 0.00 37.44 6.09
1851 2298 2.076628 GCATGTTTGTGTCTGCGCG 61.077 57.895 0.00 0.00 0.00 6.86
1852 2299 1.569003 CATGTTTGTGTCTGCGCGA 59.431 52.632 12.10 0.00 0.00 5.87
1853 2300 0.451628 CATGTTTGTGTCTGCGCGAG 60.452 55.000 12.10 4.52 0.00 5.03
1854 2301 1.568612 ATGTTTGTGTCTGCGCGAGG 61.569 55.000 12.10 0.20 0.00 4.63
1855 2302 2.108157 TTTGTGTCTGCGCGAGGT 59.892 55.556 12.10 0.00 0.00 3.85
1856 2303 0.942410 GTTTGTGTCTGCGCGAGGTA 60.942 55.000 12.10 0.00 0.00 3.08
1857 2304 0.942410 TTTGTGTCTGCGCGAGGTAC 60.942 55.000 12.10 1.83 0.00 3.34
1868 2315 5.182570 TCTGCGCGAGGTACTTACATATATT 59.817 40.000 12.10 0.00 41.55 1.28
1894 2341 8.850454 TCTTTTTCTGTTGTGCTACAAATTAC 57.150 30.769 3.74 0.00 40.15 1.89
1895 2342 7.918562 TCTTTTTCTGTTGTGCTACAAATTACC 59.081 33.333 3.74 0.00 40.15 2.85
1896 2343 5.699097 TTCTGTTGTGCTACAAATTACCC 57.301 39.130 3.74 0.00 40.15 3.69
1897 2344 4.076394 TCTGTTGTGCTACAAATTACCCC 58.924 43.478 3.74 0.00 40.15 4.95
1898 2345 3.158676 TGTTGTGCTACAAATTACCCCC 58.841 45.455 3.74 0.00 40.15 5.40
1899 2346 3.181427 TGTTGTGCTACAAATTACCCCCT 60.181 43.478 3.74 0.00 40.15 4.79
1900 2347 3.359695 TGTGCTACAAATTACCCCCTC 57.640 47.619 0.00 0.00 0.00 4.30
1901 2348 2.025699 TGTGCTACAAATTACCCCCTCC 60.026 50.000 0.00 0.00 0.00 4.30
1902 2349 1.210967 TGCTACAAATTACCCCCTCCG 59.789 52.381 0.00 0.00 0.00 4.63
1903 2350 1.211212 GCTACAAATTACCCCCTCCGT 59.789 52.381 0.00 0.00 0.00 4.69
1904 2351 2.356432 GCTACAAATTACCCCCTCCGTT 60.356 50.000 0.00 0.00 0.00 4.44
1905 2352 2.502142 ACAAATTACCCCCTCCGTTC 57.498 50.000 0.00 0.00 0.00 3.95
1906 2353 1.990327 ACAAATTACCCCCTCCGTTCT 59.010 47.619 0.00 0.00 0.00 3.01
1907 2354 2.026542 ACAAATTACCCCCTCCGTTCTC 60.027 50.000 0.00 0.00 0.00 2.87
1908 2355 1.961133 AATTACCCCCTCCGTTCTCA 58.039 50.000 0.00 0.00 0.00 3.27
1909 2356 2.191981 ATTACCCCCTCCGTTCTCAT 57.808 50.000 0.00 0.00 0.00 2.90
1910 2357 2.852714 TTACCCCCTCCGTTCTCATA 57.147 50.000 0.00 0.00 0.00 2.15
1911 2358 2.852714 TACCCCCTCCGTTCTCATAA 57.147 50.000 0.00 0.00 0.00 1.90
1912 2359 2.191981 ACCCCCTCCGTTCTCATAAT 57.808 50.000 0.00 0.00 0.00 1.28
1913 2360 3.339713 ACCCCCTCCGTTCTCATAATA 57.660 47.619 0.00 0.00 0.00 0.98
1914 2361 3.870559 ACCCCCTCCGTTCTCATAATAT 58.129 45.455 0.00 0.00 0.00 1.28
1915 2362 5.019657 ACCCCCTCCGTTCTCATAATATA 57.980 43.478 0.00 0.00 0.00 0.86
1916 2363 5.408824 ACCCCCTCCGTTCTCATAATATAA 58.591 41.667 0.00 0.00 0.00 0.98
1917 2364 5.847817 ACCCCCTCCGTTCTCATAATATAAA 59.152 40.000 0.00 0.00 0.00 1.40
1918 2365 6.330778 ACCCCCTCCGTTCTCATAATATAAAA 59.669 38.462 0.00 0.00 0.00 1.52
1919 2366 6.879458 CCCCCTCCGTTCTCATAATATAAAAG 59.121 42.308 0.00 0.00 0.00 2.27
1920 2367 6.371825 CCCCTCCGTTCTCATAATATAAAAGC 59.628 42.308 0.00 0.00 0.00 3.51
1921 2368 7.162082 CCCTCCGTTCTCATAATATAAAAGCT 58.838 38.462 0.00 0.00 0.00 3.74
1922 2369 7.661847 CCCTCCGTTCTCATAATATAAAAGCTT 59.338 37.037 0.00 0.00 0.00 3.74
1923 2370 9.057089 CCTCCGTTCTCATAATATAAAAGCTTT 57.943 33.333 5.69 5.69 0.00 3.51
1948 2395 2.732412 CACTACACTGTGTGAGGGAG 57.268 55.000 22.97 13.97 36.96 4.30
1949 2396 1.964223 CACTACACTGTGTGAGGGAGT 59.036 52.381 22.97 14.60 36.96 3.85
1950 2397 3.154710 CACTACACTGTGTGAGGGAGTA 58.845 50.000 22.97 0.00 36.96 2.59
1956 2403 4.102524 ACACTGTGTGAGGGAGTAATTTGA 59.897 41.667 13.50 0.00 36.96 2.69
2000 2454 4.707448 ACTGAGGTAGTATGAAGTGAGGTG 59.293 45.833 0.00 0.00 38.04 4.00
2035 2492 5.631929 AGAACCGAAAAAGAAACAACACAAC 59.368 36.000 0.00 0.00 0.00 3.32
2077 2534 7.547019 TGTCAAAGTATAGCTGAAGAGTGATTG 59.453 37.037 0.00 0.00 0.00 2.67
2112 2569 4.617253 TGAAGCTAGCCAAAGACACTTA 57.383 40.909 12.13 0.00 0.00 2.24
2120 2579 2.949644 GCCAAAGACACTTACCAACTGT 59.050 45.455 0.00 0.00 0.00 3.55
2121 2580 3.003378 GCCAAAGACACTTACCAACTGTC 59.997 47.826 0.00 0.00 35.51 3.51
2208 2720 5.302059 TGTGGTATTAACTAGGCTCTAGCTG 59.698 44.000 0.00 0.00 41.70 4.24
2289 2835 1.483827 TGCTCTCATAAGCCAGACCAG 59.516 52.381 0.00 0.00 41.77 4.00
2334 2880 1.003118 CAAGAATCCGACTCCAACCCA 59.997 52.381 0.00 0.00 0.00 4.51
2464 3010 3.817084 CTCAAACCTCATCAGCTTCACAA 59.183 43.478 0.00 0.00 0.00 3.33
2549 3113 4.344968 TGATCTTCATCCGATGCTTTCCTA 59.655 41.667 3.25 0.00 0.00 2.94
2577 3141 1.591703 CAACTACAGCTCCTCGCCA 59.408 57.895 0.00 0.00 40.39 5.69
2595 3159 2.214920 ACCGGTTCAGGAGGGTGTC 61.215 63.158 0.00 0.00 34.73 3.67
2606 3170 4.021925 GGGTGTCTCCAGCGGCTT 62.022 66.667 0.00 0.00 40.03 4.35
2706 3270 1.296715 GTTGACCGTGGGATCAGCT 59.703 57.895 0.00 0.00 0.00 4.24
2845 3433 5.550290 GGGGGTCATTTGGCAATAATATTG 58.450 41.667 8.55 8.55 0.00 1.90
2859 3447 2.752144 ATATTGACGACGACGACCTC 57.248 50.000 15.32 1.68 42.66 3.85
3112 3708 2.808919 ACTCATCTCCGTCTCTTCCAA 58.191 47.619 0.00 0.00 0.00 3.53
3115 3711 3.165875 TCATCTCCGTCTCTTCCAACTT 58.834 45.455 0.00 0.00 0.00 2.66
3243 3839 1.055849 TCAGTACACATGCCACACCT 58.944 50.000 0.00 0.00 0.00 4.00
3260 3856 4.160439 CACACCTAGCACAATCCTCTCTTA 59.840 45.833 0.00 0.00 0.00 2.10
3297 3893 7.465353 TTGATTGATTCAATTACCTTGCAGA 57.535 32.000 12.96 0.00 39.44 4.26
3370 3966 0.545646 GCCTCTGCTCCAGAATCCTT 59.454 55.000 0.00 0.00 40.18 3.36
3616 4826 1.550524 AGCGTCAACTCTTAGATGCCA 59.449 47.619 0.00 0.00 45.54 4.92
3723 5137 6.213397 TCATGGACTATTCTGTCTTTGGAGAA 59.787 38.462 0.00 0.00 37.16 2.87
3743 5157 1.063266 AGCCCTTTCCTTTGACACCAA 60.063 47.619 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 0.765903 ATGGAGATGCGGTGGATCCT 60.766 55.000 14.23 0.00 0.00 3.24
247 251 1.393603 GGAGAAGGGCCAGTTAATGC 58.606 55.000 6.18 0.00 0.00 3.56
449 462 3.818961 TCGTTAAATCTCAGTCGACGT 57.181 42.857 10.46 0.00 0.00 4.34
462 475 5.053811 TGCATCAACAGAGACTTCGTTAAA 58.946 37.500 0.00 0.00 0.00 1.52
479 492 7.209475 TGTAAGATCTCACGATTATTGCATCA 58.791 34.615 0.00 0.00 0.00 3.07
596 617 7.063898 CCATCTCATCATGTAAACATACGGATC 59.936 40.741 0.00 0.00 34.26 3.36
688 742 3.758554 ACTCCTACCATTTGTTGATGCAC 59.241 43.478 0.00 0.00 0.00 4.57
1127 1221 1.677820 CCACCAGGTCGTCATAAACCC 60.678 57.143 0.00 0.00 36.11 4.11
1131 1225 1.191535 CCTCCACCAGGTCGTCATAA 58.808 55.000 0.00 0.00 37.53 1.90
1290 1387 4.796231 CCGGAAGACGCCTCCACG 62.796 72.222 0.00 0.00 42.52 4.94
1323 1420 1.765904 GATCTCTTCTTCCTCCCACCC 59.234 57.143 0.00 0.00 0.00 4.61
1442 1588 3.242543 GCAAAACAGATAGTCGGAGCATG 60.243 47.826 0.00 0.00 0.00 4.06
1458 1633 9.810231 CCAAATGAATAGTACAATTTGCAAAAC 57.190 29.630 17.19 9.78 0.00 2.43
1478 1743 2.120909 CCCACTAGGCCGCCAAATG 61.121 63.158 13.15 6.01 0.00 2.32
1498 1763 4.941263 ACTGATCATTGGCGCTTAAAGTTA 59.059 37.500 7.64 0.00 0.00 2.24
1530 1795 3.556004 GGTCATCAGAAGCAGCCTATACC 60.556 52.174 0.00 0.00 0.00 2.73
1605 1873 2.361483 ATGCGTGCATGCCCAAGA 60.361 55.556 27.43 9.44 35.03 3.02
1803 2250 9.404848 AGTACTACACTACATACACACATATGT 57.595 33.333 1.41 1.41 45.60 2.29
1805 2252 8.771766 CGAGTACTACACTACATACACACATAT 58.228 37.037 0.00 0.00 37.72 1.78
1806 2253 7.765819 ACGAGTACTACACTACATACACACATA 59.234 37.037 0.00 0.00 37.72 2.29
1807 2254 6.596888 ACGAGTACTACACTACATACACACAT 59.403 38.462 0.00 0.00 37.72 3.21
1808 2255 5.934043 ACGAGTACTACACTACATACACACA 59.066 40.000 0.00 0.00 37.72 3.72
1809 2256 6.246449 CACGAGTACTACACTACATACACAC 58.754 44.000 0.00 0.00 37.72 3.82
1810 2257 5.163824 GCACGAGTACTACACTACATACACA 60.164 44.000 0.00 0.00 37.72 3.72
1811 2258 5.163824 TGCACGAGTACTACACTACATACAC 60.164 44.000 0.00 0.00 37.72 2.90
1812 2259 4.937015 TGCACGAGTACTACACTACATACA 59.063 41.667 0.00 0.00 37.72 2.29
1813 2260 5.475273 TGCACGAGTACTACACTACATAC 57.525 43.478 0.00 0.00 37.72 2.39
1814 2261 5.587443 ACATGCACGAGTACTACACTACATA 59.413 40.000 0.00 0.00 37.72 2.29
1815 2262 4.398358 ACATGCACGAGTACTACACTACAT 59.602 41.667 0.00 0.00 37.72 2.29
1816 2263 3.754850 ACATGCACGAGTACTACACTACA 59.245 43.478 0.00 0.00 37.72 2.74
1817 2264 4.352600 ACATGCACGAGTACTACACTAC 57.647 45.455 0.00 0.00 37.72 2.73
1818 2265 5.158494 CAAACATGCACGAGTACTACACTA 58.842 41.667 0.00 0.00 37.72 2.74
1819 2266 3.936372 AACATGCACGAGTACTACACT 57.064 42.857 0.00 0.00 41.47 3.55
1820 2267 3.739300 ACAAACATGCACGAGTACTACAC 59.261 43.478 0.00 0.00 0.00 2.90
1821 2268 3.738791 CACAAACATGCACGAGTACTACA 59.261 43.478 0.00 0.00 0.00 2.74
1822 2269 3.739300 ACACAAACATGCACGAGTACTAC 59.261 43.478 0.00 0.00 0.00 2.73
1823 2270 3.985008 ACACAAACATGCACGAGTACTA 58.015 40.909 0.00 0.00 0.00 1.82
1824 2271 2.800544 GACACAAACATGCACGAGTACT 59.199 45.455 0.00 0.00 0.00 2.73
1825 2272 2.800544 AGACACAAACATGCACGAGTAC 59.199 45.455 0.00 0.00 0.00 2.73
1826 2273 2.799978 CAGACACAAACATGCACGAGTA 59.200 45.455 0.00 0.00 0.00 2.59
1827 2274 1.599071 CAGACACAAACATGCACGAGT 59.401 47.619 0.00 0.00 0.00 4.18
1828 2275 1.661178 GCAGACACAAACATGCACGAG 60.661 52.381 0.00 0.00 38.54 4.18
1829 2276 0.307453 GCAGACACAAACATGCACGA 59.693 50.000 0.00 0.00 38.54 4.35
1830 2277 0.993251 CGCAGACACAAACATGCACG 60.993 55.000 0.00 0.00 38.60 5.34
1831 2278 1.270777 GCGCAGACACAAACATGCAC 61.271 55.000 0.30 0.00 38.60 4.57
1832 2279 1.008652 GCGCAGACACAAACATGCA 60.009 52.632 0.30 0.00 38.60 3.96
1833 2280 2.076628 CGCGCAGACACAAACATGC 61.077 57.895 8.75 0.00 35.32 4.06
1834 2281 0.451628 CTCGCGCAGACACAAACATG 60.452 55.000 8.75 0.00 0.00 3.21
1835 2282 1.568612 CCTCGCGCAGACACAAACAT 61.569 55.000 8.75 0.00 0.00 2.71
1836 2283 2.243957 CCTCGCGCAGACACAAACA 61.244 57.895 8.75 0.00 0.00 2.83
1837 2284 0.942410 TACCTCGCGCAGACACAAAC 60.942 55.000 8.75 0.00 0.00 2.93
1838 2285 0.942410 GTACCTCGCGCAGACACAAA 60.942 55.000 8.75 0.00 0.00 2.83
1839 2286 1.372499 GTACCTCGCGCAGACACAA 60.372 57.895 8.75 0.00 0.00 3.33
1840 2287 1.802337 AAGTACCTCGCGCAGACACA 61.802 55.000 8.75 0.00 0.00 3.72
1841 2288 0.169672 TAAGTACCTCGCGCAGACAC 59.830 55.000 8.75 5.60 0.00 3.67
1842 2289 0.169672 GTAAGTACCTCGCGCAGACA 59.830 55.000 8.75 0.00 0.00 3.41
1843 2290 0.169672 TGTAAGTACCTCGCGCAGAC 59.830 55.000 8.75 0.00 0.00 3.51
1844 2291 1.100510 ATGTAAGTACCTCGCGCAGA 58.899 50.000 8.75 4.86 0.00 4.26
1845 2292 2.768833 TATGTAAGTACCTCGCGCAG 57.231 50.000 8.75 3.84 0.00 5.18
1846 2293 5.381174 AATATATGTAAGTACCTCGCGCA 57.619 39.130 8.75 0.00 0.00 6.09
1847 2294 6.091437 AGAAATATATGTAAGTACCTCGCGC 58.909 40.000 0.00 0.00 0.00 6.86
1848 2295 8.516811 AAAGAAATATATGTAAGTACCTCGCG 57.483 34.615 0.00 0.00 0.00 5.87
1868 2315 9.296400 GTAATTTGTAGCACAACAGAAAAAGAA 57.704 29.630 1.85 0.00 37.90 2.52
1886 2333 1.990327 AGAACGGAGGGGGTAATTTGT 59.010 47.619 0.00 0.00 0.00 2.83
1894 2341 6.368779 TTTATATTATGAGAACGGAGGGGG 57.631 41.667 0.00 0.00 0.00 5.40
1895 2342 6.371825 GCTTTTATATTATGAGAACGGAGGGG 59.628 42.308 0.00 0.00 0.00 4.79
1896 2343 7.162082 AGCTTTTATATTATGAGAACGGAGGG 58.838 38.462 0.00 0.00 0.00 4.30
1897 2344 8.608844 AAGCTTTTATATTATGAGAACGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
1929 2376 1.964223 ACTCCCTCACACAGTGTAGTG 59.036 52.381 5.69 15.52 44.93 2.74
1930 2377 2.383442 ACTCCCTCACACAGTGTAGT 57.617 50.000 5.69 2.87 34.79 2.73
1931 2378 5.407407 AATTACTCCCTCACACAGTGTAG 57.593 43.478 5.69 2.17 34.79 2.74
1932 2379 5.305902 TCAAATTACTCCCTCACACAGTGTA 59.694 40.000 5.69 0.00 34.79 2.90
1933 2380 4.102524 TCAAATTACTCCCTCACACAGTGT 59.897 41.667 0.00 0.00 34.79 3.55
1934 2381 4.641396 TCAAATTACTCCCTCACACAGTG 58.359 43.478 0.00 0.00 34.45 3.66
1935 2382 4.974645 TCAAATTACTCCCTCACACAGT 57.025 40.909 0.00 0.00 0.00 3.55
1936 2383 5.997746 TCTTTCAAATTACTCCCTCACACAG 59.002 40.000 0.00 0.00 0.00 3.66
1937 2384 5.935945 TCTTTCAAATTACTCCCTCACACA 58.064 37.500 0.00 0.00 0.00 3.72
1938 2385 6.877611 TTCTTTCAAATTACTCCCTCACAC 57.122 37.500 0.00 0.00 0.00 3.82
1939 2386 7.014230 CCTTTTCTTTCAAATTACTCCCTCACA 59.986 37.037 0.00 0.00 0.00 3.58
1940 2387 7.371159 CCTTTTCTTTCAAATTACTCCCTCAC 58.629 38.462 0.00 0.00 0.00 3.51
1941 2388 6.493458 CCCTTTTCTTTCAAATTACTCCCTCA 59.507 38.462 0.00 0.00 0.00 3.86
1942 2389 6.719829 TCCCTTTTCTTTCAAATTACTCCCTC 59.280 38.462 0.00 0.00 0.00 4.30
1943 2390 6.620429 TCCCTTTTCTTTCAAATTACTCCCT 58.380 36.000 0.00 0.00 0.00 4.20
1944 2391 6.911250 TCCCTTTTCTTTCAAATTACTCCC 57.089 37.500 0.00 0.00 0.00 4.30
1945 2392 9.607988 TTTTTCCCTTTTCTTTCAAATTACTCC 57.392 29.630 0.00 0.00 0.00 3.85
1974 2421 7.068839 CACCTCACTTCATACTACCTCAGTTAT 59.931 40.741 0.00 0.00 38.80 1.89
1975 2422 6.377429 CACCTCACTTCATACTACCTCAGTTA 59.623 42.308 0.00 0.00 38.80 2.24
1976 2423 5.186021 CACCTCACTTCATACTACCTCAGTT 59.814 44.000 0.00 0.00 38.80 3.16
1977 2424 4.707448 CACCTCACTTCATACTACCTCAGT 59.293 45.833 0.00 0.00 41.62 3.41
2000 2454 0.804364 TTCGGTTCTGCATGCATGAC 59.196 50.000 30.64 20.98 0.00 3.06
2077 2534 6.094048 TGGCTAGCTTCAACTAATGATTCAAC 59.906 38.462 15.72 0.00 38.03 3.18
2112 2569 4.357918 ACTAGCAAATCAGACAGTTGGT 57.642 40.909 0.00 0.00 43.04 3.67
2194 2697 1.497286 ACTAGCCAGCTAGAGCCTAGT 59.503 52.381 28.73 8.25 46.56 2.57
2316 2862 1.486726 GATGGGTTGGAGTCGGATTCT 59.513 52.381 0.37 0.00 0.00 2.40
2334 2880 4.402829 AGTAGCTGATGATGTACTCCGAT 58.597 43.478 0.00 0.00 0.00 4.18
2464 3010 4.838152 AGCCGCGCCATTGATCGT 62.838 61.111 0.00 0.00 0.00 3.73
2494 3058 2.061773 CACGAGACGATGAGCAAAAGT 58.938 47.619 0.00 0.00 0.00 2.66
2549 3113 0.037232 GCTGTAGTTGGAGAAGCGGT 60.037 55.000 0.00 0.00 0.00 5.68
2577 3141 2.122547 ACACCCTCCTGAACCGGT 60.123 61.111 0.00 0.00 0.00 5.28
2743 3310 3.764049 GCCAGCGTTCGTGTCGAC 61.764 66.667 9.11 9.11 34.89 4.20
2845 3433 4.741570 GAAGAGGTCGTCGTCGTC 57.258 61.111 1.33 4.36 38.33 4.20
3243 3839 5.394663 GCTTCAGTAAGAGAGGATTGTGCTA 60.395 44.000 0.00 0.00 34.37 3.49
3260 3856 5.771666 TGAATCAATCAAAAGAGGCTTCAGT 59.228 36.000 0.00 0.00 34.30 3.41
3297 3893 1.002087 AGTCTCAGTCGCCGGAAATTT 59.998 47.619 5.05 0.00 0.00 1.82
3370 3966 0.835971 TGGAGTAGCTGTGGGCAGAA 60.836 55.000 0.00 0.00 45.28 3.02
3433 4029 2.825223 TGCTTCAGGAAGAGAGGATCA 58.175 47.619 13.01 0.00 40.79 2.92
3616 4826 4.717233 TTTGCTTAATCATGTGGCGATT 57.283 36.364 0.00 0.00 36.97 3.34
3723 5137 0.555769 TGGTGTCAAAGGAAAGGGCT 59.444 50.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.