Multiple sequence alignment - TraesCS5A01G300900

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 TraesCS5A01G300900 chr5A 100.000 2211 0 0 1 2211 510135610 510137820 0.000000e+00 4084
1 TraesCS5A01G300900 chr3B 99.685 1906 5 1 1 1905 101916062 101914157 0.000000e+00 3485
2 TraesCS5A01G300900 chr3B 99.003 1905 19 0 1 1905 201531910 201530006 0.000000e+00 3413
3 TraesCS5A01G300900 chr3B 89.711 311 26 4 1906 2211 657493854 657493545 2.060000e-105 392
4 TraesCS5A01G300900 chr6D 99.003 1906 13 3 1 1905 168262552 168260652 0.000000e+00 3410
5 TraesCS5A01G300900 chrUn 98.951 1906 12 3 1 1905 216513723 216515621 0.000000e+00 3402
6 TraesCS5A01G300900 chrUn 98.951 1906 12 3 1 1905 286269660 286267762 0.000000e+00 3402
7 TraesCS5A01G300900 chr5D 98.950 1904 14 2 1 1903 503223102 503221204 0.000000e+00 3400
8 TraesCS5A01G300900 chr5D 92.926 311 16 4 1906 2211 394277354 394277663 4.330000e-122 448
9 TraesCS5A01G300900 chr2B 98.898 1905 20 1 1 1905 474913326 474911423 0.000000e+00 3400
10 TraesCS5A01G300900 chr3D 98.846 1906 15 3 1 1905 589272074 589273973 0.000000e+00 3391
11 TraesCS5A01G300900 chr1D 98.531 1906 22 2 1 1905 254393230 254395130 0.000000e+00 3360
12 TraesCS5A01G300900 chr7A 94.805 308 14 2 1906 2211 645933451 645933758 1.540000e-131 479
13 TraesCS5A01G300900 chr7A 88.673 309 29 4 1906 2209 126467586 126467893 2.680000e-99 372
14 TraesCS5A01G300900 chr7D 91.640 311 20 4 1906 2211 16355202 16354893 2.030000e-115 425
15 TraesCS5A01G300900 chr4B 91.667 312 18 6 1906 2211 412122837 412123146 2.030000e-115 425
16 TraesCS5A01G300900 chr4B 89.068 311 28 4 1906 2211 213140248 213140557 4.450000e-102 381
17 TraesCS5A01G300900 chr6B 90.354 311 23 5 1906 2211 191376079 191376387 3.420000e-108 401
18 TraesCS5A01G300900 chr6B 88.462 312 28 6 1906 2211 697939647 697939956 9.640000e-99 370


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 TraesCS5A01G300900 chr5A 510135610 510137820 2210 False 4084 4084 100.000 1 2211 1 chr5A.!!$F1 2210
1 TraesCS5A01G300900 chr3B 101914157 101916062 1905 True 3485 3485 99.685 1 1905 1 chr3B.!!$R1 1904
2 TraesCS5A01G300900 chr3B 201530006 201531910 1904 True 3413 3413 99.003 1 1905 1 chr3B.!!$R2 1904
3 TraesCS5A01G300900 chr6D 168260652 168262552 1900 True 3410 3410 99.003 1 1905 1 chr6D.!!$R1 1904
4 TraesCS5A01G300900 chrUn 216513723 216515621 1898 False 3402 3402 98.951 1 1905 1 chrUn.!!$F1 1904
5 TraesCS5A01G300900 chrUn 286267762 286269660 1898 True 3402 3402 98.951 1 1905 1 chrUn.!!$R1 1904
6 TraesCS5A01G300900 chr5D 503221204 503223102 1898 True 3400 3400 98.950 1 1903 1 chr5D.!!$R1 1902
7 TraesCS5A01G300900 chr2B 474911423 474913326 1903 True 3400 3400 98.898 1 1905 1 chr2B.!!$R1 1904
8 TraesCS5A01G300900 chr3D 589272074 589273973 1899 False 3391 3391 98.846 1 1905 1 chr3D.!!$F1 1904
9 TraesCS5A01G300900 chr1D 254393230 254395130 1900 False 3360 3360 98.531 1 1905 1 chr1D.!!$F1 1904

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
654 655 3.959535 TGAACCCCATTCTTGCAATTC 57.04 42.857 0.0 0.0 38.25 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2057 0.391966 GGGGCCGAGTTACATCTACC 59.608 60.0 0.0 0.0 0.0 3.18 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
264 265 8.236585 TGCTTGCATTGTATTATTTGGTCTAT 57.763 30.769 0.00 0.00 0.00 1.98
654 655 3.959535 TGAACCCCATTCTTGCAATTC 57.040 42.857 0.00 0.00 38.25 2.17
1028 1029 5.195940 CCTCTTTGGGCTTCTATTGAATCA 58.804 41.667 0.00 0.00 0.00 2.57
1132 1133 6.841443 AATCGAAGCTATTTGATGTCTGAG 57.159 37.500 0.00 0.00 39.16 3.35
1611 1614 4.721776 TGTATCCCAACCTCTATTGCTCTT 59.278 41.667 0.00 0.00 0.00 2.85
1907 1916 7.624360 ACAAGAGTGAAGACTAGTAGAGATG 57.376 40.000 3.59 0.00 30.16 2.90
1908 1917 6.094881 ACAAGAGTGAAGACTAGTAGAGATGC 59.905 42.308 3.59 0.00 30.16 3.91
1909 1918 6.001449 AGAGTGAAGACTAGTAGAGATGCT 57.999 41.667 3.59 0.00 30.16 3.79
1910 1919 6.055588 AGAGTGAAGACTAGTAGAGATGCTC 58.944 44.000 3.59 4.61 30.16 4.26
1911 1920 6.001449 AGTGAAGACTAGTAGAGATGCTCT 57.999 41.667 3.59 2.22 43.83 4.09
1912 1921 6.055588 AGTGAAGACTAGTAGAGATGCTCTC 58.944 44.000 3.59 5.36 43.70 3.20
1913 1922 5.820423 GTGAAGACTAGTAGAGATGCTCTCA 59.180 44.000 3.59 0.00 45.73 3.27
1914 1923 6.486657 GTGAAGACTAGTAGAGATGCTCTCAT 59.513 42.308 3.59 0.00 45.73 2.90
1915 1924 6.486320 TGAAGACTAGTAGAGATGCTCTCATG 59.514 42.308 3.59 0.00 45.73 3.07
1916 1925 6.186420 AGACTAGTAGAGATGCTCTCATGA 57.814 41.667 3.59 0.00 45.73 3.07
1917 1926 6.782986 AGACTAGTAGAGATGCTCTCATGAT 58.217 40.000 3.59 0.00 45.73 2.45
1918 1927 6.656270 AGACTAGTAGAGATGCTCTCATGATG 59.344 42.308 3.59 0.00 45.73 3.07
1919 1928 5.711506 ACTAGTAGAGATGCTCTCATGATGG 59.288 44.000 3.59 0.00 45.73 3.51
1920 1929 4.738685 AGTAGAGATGCTCTCATGATGGA 58.261 43.478 13.42 0.00 45.73 3.41
1921 1930 5.335261 AGTAGAGATGCTCTCATGATGGAT 58.665 41.667 13.42 0.00 45.73 3.41
1922 1931 5.781306 AGTAGAGATGCTCTCATGATGGATT 59.219 40.000 13.42 0.00 45.73 3.01
1923 1932 5.570205 AGAGATGCTCTCATGATGGATTT 57.430 39.130 13.42 0.00 45.73 2.17
1924 1933 5.309638 AGAGATGCTCTCATGATGGATTTG 58.690 41.667 13.42 0.00 45.73 2.32
1925 1934 5.071923 AGAGATGCTCTCATGATGGATTTGA 59.928 40.000 13.42 0.00 45.73 2.69
1926 1935 5.691896 AGATGCTCTCATGATGGATTTGAA 58.308 37.500 0.00 0.00 31.96 2.69
1927 1936 6.127101 AGATGCTCTCATGATGGATTTGAAA 58.873 36.000 0.00 0.00 31.96 2.69
1928 1937 6.605995 AGATGCTCTCATGATGGATTTGAAAA 59.394 34.615 0.00 0.00 31.96 2.29
1929 1938 6.203808 TGCTCTCATGATGGATTTGAAAAG 57.796 37.500 0.00 0.00 0.00 2.27
1930 1939 5.713389 TGCTCTCATGATGGATTTGAAAAGT 59.287 36.000 0.00 0.00 0.00 2.66
1931 1940 6.209986 TGCTCTCATGATGGATTTGAAAAGTT 59.790 34.615 0.00 0.00 0.00 2.66
1932 1941 7.394077 TGCTCTCATGATGGATTTGAAAAGTTA 59.606 33.333 0.00 0.00 0.00 2.24
1933 1942 8.246180 GCTCTCATGATGGATTTGAAAAGTTAA 58.754 33.333 0.00 0.00 0.00 2.01
1990 1999 9.170734 TGATTTTCAGAGATGGAGAACATAAAG 57.829 33.333 0.00 0.00 40.72 1.85
1991 2000 9.171877 GATTTTCAGAGATGGAGAACATAAAGT 57.828 33.333 0.00 0.00 40.72 2.66
1993 2002 9.658799 TTTTCAGAGATGGAGAACATAAAGTAG 57.341 33.333 0.00 0.00 40.72 2.57
1994 2003 6.810911 TCAGAGATGGAGAACATAAAGTAGC 58.189 40.000 0.00 0.00 40.72 3.58
1995 2004 6.381133 TCAGAGATGGAGAACATAAAGTAGCA 59.619 38.462 0.00 0.00 40.72 3.49
1996 2005 6.478344 CAGAGATGGAGAACATAAAGTAGCAC 59.522 42.308 0.00 0.00 40.72 4.40
1997 2006 6.382570 AGAGATGGAGAACATAAAGTAGCACT 59.617 38.462 0.00 0.00 40.72 4.40
1998 2007 6.951971 AGATGGAGAACATAAAGTAGCACTT 58.048 36.000 0.00 0.00 40.72 3.16
1999 2008 7.044798 AGATGGAGAACATAAAGTAGCACTTC 58.955 38.462 2.65 0.00 40.72 3.01
2000 2009 6.360370 TGGAGAACATAAAGTAGCACTTCT 57.640 37.500 2.65 0.00 37.47 2.85
2001 2010 6.166279 TGGAGAACATAAAGTAGCACTTCTG 58.834 40.000 2.65 6.19 37.47 3.02
2002 2011 6.014584 TGGAGAACATAAAGTAGCACTTCTGA 60.015 38.462 13.43 2.17 37.47 3.27
2003 2012 6.874134 GGAGAACATAAAGTAGCACTTCTGAA 59.126 38.462 13.43 0.00 37.47 3.02
2004 2013 7.550906 GGAGAACATAAAGTAGCACTTCTGAAT 59.449 37.037 13.43 6.52 37.47 2.57
2005 2014 8.854614 AGAACATAAAGTAGCACTTCTGAATT 57.145 30.769 13.43 0.00 37.47 2.17
2006 2015 9.944376 AGAACATAAAGTAGCACTTCTGAATTA 57.056 29.630 13.43 0.00 37.47 1.40
2031 2040 4.561735 AAACCCAAACTGTTCACATACG 57.438 40.909 0.00 0.00 0.00 3.06
2032 2041 3.202829 ACCCAAACTGTTCACATACGT 57.797 42.857 0.00 0.00 0.00 3.57
2033 2042 3.547746 ACCCAAACTGTTCACATACGTT 58.452 40.909 0.00 0.00 0.00 3.99
2034 2043 4.706035 ACCCAAACTGTTCACATACGTTA 58.294 39.130 0.00 0.00 0.00 3.18
2035 2044 5.310451 ACCCAAACTGTTCACATACGTTAT 58.690 37.500 0.00 0.00 0.00 1.89
2036 2045 5.180492 ACCCAAACTGTTCACATACGTTATG 59.820 40.000 0.00 0.00 41.88 1.90
2038 2047 6.304126 CCAAACTGTTCACATACGTTATGTC 58.696 40.000 0.00 0.00 45.83 3.06
2039 2048 6.073494 CCAAACTGTTCACATACGTTATGTCA 60.073 38.462 0.00 0.00 45.83 3.58
2040 2049 6.706055 AACTGTTCACATACGTTATGTCAG 57.294 37.500 15.57 15.57 45.83 3.51
2041 2050 5.779922 ACTGTTCACATACGTTATGTCAGT 58.220 37.500 16.33 16.33 45.83 3.41
2042 2051 6.220930 ACTGTTCACATACGTTATGTCAGTT 58.779 36.000 16.33 8.27 45.83 3.16
2043 2052 6.704493 ACTGTTCACATACGTTATGTCAGTTT 59.296 34.615 16.33 5.12 45.83 2.66
2044 2053 6.883129 TGTTCACATACGTTATGTCAGTTTG 58.117 36.000 0.00 0.00 45.83 2.93
2045 2054 6.480651 TGTTCACATACGTTATGTCAGTTTGT 59.519 34.615 0.00 0.00 45.83 2.83
2046 2055 7.011576 TGTTCACATACGTTATGTCAGTTTGTT 59.988 33.333 0.00 0.00 45.83 2.83
2047 2056 8.489559 GTTCACATACGTTATGTCAGTTTGTTA 58.510 33.333 0.00 0.00 45.83 2.41
2048 2057 8.234887 TCACATACGTTATGTCAGTTTGTTAG 57.765 34.615 0.00 0.00 45.83 2.34
2049 2058 7.329962 TCACATACGTTATGTCAGTTTGTTAGG 59.670 37.037 0.00 0.00 45.83 2.69
2050 2059 7.117236 CACATACGTTATGTCAGTTTGTTAGGT 59.883 37.037 0.00 0.00 45.83 3.08
2051 2060 8.306038 ACATACGTTATGTCAGTTTGTTAGGTA 58.694 33.333 0.00 0.00 45.83 3.08
2052 2061 8.804743 CATACGTTATGTCAGTTTGTTAGGTAG 58.195 37.037 0.00 0.00 0.00 3.18
2053 2062 6.985117 ACGTTATGTCAGTTTGTTAGGTAGA 58.015 36.000 0.00 0.00 0.00 2.59
2054 2063 7.609056 ACGTTATGTCAGTTTGTTAGGTAGAT 58.391 34.615 0.00 0.00 0.00 1.98
2055 2064 7.544566 ACGTTATGTCAGTTTGTTAGGTAGATG 59.455 37.037 0.00 0.00 0.00 2.90
2056 2065 7.544566 CGTTATGTCAGTTTGTTAGGTAGATGT 59.455 37.037 0.00 0.00 0.00 3.06
2057 2066 9.865321 GTTATGTCAGTTTGTTAGGTAGATGTA 57.135 33.333 0.00 0.00 0.00 2.29
2059 2068 8.773404 ATGTCAGTTTGTTAGGTAGATGTAAC 57.227 34.615 0.00 0.00 0.00 2.50
2060 2069 7.959175 TGTCAGTTTGTTAGGTAGATGTAACT 58.041 34.615 0.00 0.00 31.54 2.24
2061 2070 8.086522 TGTCAGTTTGTTAGGTAGATGTAACTC 58.913 37.037 0.00 0.00 31.54 3.01
2062 2071 7.272948 GTCAGTTTGTTAGGTAGATGTAACTCG 59.727 40.741 0.00 0.00 31.54 4.18
2063 2072 6.530534 CAGTTTGTTAGGTAGATGTAACTCGG 59.469 42.308 0.00 0.00 31.54 4.63
2064 2073 4.644103 TGTTAGGTAGATGTAACTCGGC 57.356 45.455 0.00 0.00 31.54 5.54
2065 2074 3.382546 TGTTAGGTAGATGTAACTCGGCC 59.617 47.826 0.00 0.00 31.54 6.13
2066 2075 1.411041 AGGTAGATGTAACTCGGCCC 58.589 55.000 0.00 0.00 0.00 5.80
2067 2076 0.391966 GGTAGATGTAACTCGGCCCC 59.608 60.000 0.00 0.00 0.00 5.80
2068 2077 1.117150 GTAGATGTAACTCGGCCCCA 58.883 55.000 0.00 0.00 0.00 4.96
2069 2078 1.483415 GTAGATGTAACTCGGCCCCAA 59.517 52.381 0.00 0.00 0.00 4.12
2070 2079 0.988832 AGATGTAACTCGGCCCCAAA 59.011 50.000 0.00 0.00 0.00 3.28
2071 2080 1.065418 AGATGTAACTCGGCCCCAAAG 60.065 52.381 0.00 0.00 0.00 2.77
2072 2081 0.696501 ATGTAACTCGGCCCCAAAGT 59.303 50.000 0.00 0.00 0.00 2.66
2073 2082 0.475044 TGTAACTCGGCCCCAAAGTT 59.525 50.000 0.00 4.94 37.10 2.66
2074 2083 1.133730 TGTAACTCGGCCCCAAAGTTT 60.134 47.619 11.38 0.00 35.08 2.66
2075 2084 1.268625 GTAACTCGGCCCCAAAGTTTG 59.731 52.381 8.73 8.73 35.08 2.93
2076 2085 0.396556 AACTCGGCCCCAAAGTTTGT 60.397 50.000 14.36 0.00 29.09 2.83
2077 2086 0.475044 ACTCGGCCCCAAAGTTTGTA 59.525 50.000 14.36 0.00 0.00 2.41
2078 2087 1.165270 CTCGGCCCCAAAGTTTGTAG 58.835 55.000 14.36 6.34 0.00 2.74
2079 2088 0.766131 TCGGCCCCAAAGTTTGTAGA 59.234 50.000 14.36 3.80 0.00 2.59
2080 2089 1.143277 TCGGCCCCAAAGTTTGTAGAA 59.857 47.619 14.36 0.00 0.00 2.10
2081 2090 1.957877 CGGCCCCAAAGTTTGTAGAAA 59.042 47.619 14.36 0.00 0.00 2.52
2082 2091 2.030274 CGGCCCCAAAGTTTGTAGAAAG 60.030 50.000 14.36 0.00 0.00 2.62
2083 2092 2.288825 GGCCCCAAAGTTTGTAGAAAGC 60.289 50.000 14.36 7.35 0.00 3.51
2084 2093 2.288825 GCCCCAAAGTTTGTAGAAAGCC 60.289 50.000 14.36 0.00 0.00 4.35
2085 2094 2.962421 CCCCAAAGTTTGTAGAAAGCCA 59.038 45.455 14.36 0.00 0.00 4.75
2086 2095 3.386402 CCCCAAAGTTTGTAGAAAGCCAA 59.614 43.478 14.36 0.00 0.00 4.52
2087 2096 4.501400 CCCCAAAGTTTGTAGAAAGCCAAG 60.501 45.833 14.36 0.00 0.00 3.61
2088 2097 4.051237 CCAAAGTTTGTAGAAAGCCAAGC 58.949 43.478 14.36 0.00 0.00 4.01
2089 2098 3.626028 AAGTTTGTAGAAAGCCAAGCG 57.374 42.857 0.00 0.00 0.00 4.68
2090 2099 1.266989 AGTTTGTAGAAAGCCAAGCGC 59.733 47.619 0.00 0.00 37.98 5.92
2091 2100 1.001815 GTTTGTAGAAAGCCAAGCGCA 60.002 47.619 11.47 0.00 41.38 6.09
2092 2101 1.313772 TTGTAGAAAGCCAAGCGCAA 58.686 45.000 11.47 0.00 41.38 4.85
2093 2102 0.591170 TGTAGAAAGCCAAGCGCAAC 59.409 50.000 11.47 0.00 41.38 4.17
2094 2103 0.591170 GTAGAAAGCCAAGCGCAACA 59.409 50.000 11.47 0.00 41.38 3.33
2095 2104 0.591170 TAGAAAGCCAAGCGCAACAC 59.409 50.000 11.47 0.00 41.38 3.32
2096 2105 1.065600 GAAAGCCAAGCGCAACACA 59.934 52.632 11.47 0.00 41.38 3.72
2097 2106 1.208642 GAAAGCCAAGCGCAACACAC 61.209 55.000 11.47 0.00 41.38 3.82
2098 2107 1.666209 AAAGCCAAGCGCAACACACT 61.666 50.000 11.47 0.00 41.38 3.55
2099 2108 0.817634 AAGCCAAGCGCAACACACTA 60.818 50.000 11.47 0.00 41.38 2.74
2100 2109 1.082104 GCCAAGCGCAACACACTAC 60.082 57.895 11.47 0.00 37.47 2.73
2101 2110 1.507141 GCCAAGCGCAACACACTACT 61.507 55.000 11.47 0.00 37.47 2.57
2102 2111 1.790755 CCAAGCGCAACACACTACTA 58.209 50.000 11.47 0.00 0.00 1.82
2103 2112 1.459592 CCAAGCGCAACACACTACTAC 59.540 52.381 11.47 0.00 0.00 2.73
2104 2113 1.459592 CAAGCGCAACACACTACTACC 59.540 52.381 11.47 0.00 0.00 3.18
2105 2114 0.966920 AGCGCAACACACTACTACCT 59.033 50.000 11.47 0.00 0.00 3.08
2106 2115 1.343465 AGCGCAACACACTACTACCTT 59.657 47.619 11.47 0.00 0.00 3.50
2107 2116 2.140717 GCGCAACACACTACTACCTTT 58.859 47.619 0.30 0.00 0.00 3.11
2108 2117 2.546789 GCGCAACACACTACTACCTTTT 59.453 45.455 0.30 0.00 0.00 2.27
2109 2118 3.002965 GCGCAACACACTACTACCTTTTT 59.997 43.478 0.30 0.00 0.00 1.94
2110 2119 4.211794 GCGCAACACACTACTACCTTTTTA 59.788 41.667 0.30 0.00 0.00 1.52
2111 2120 5.277442 GCGCAACACACTACTACCTTTTTAA 60.277 40.000 0.30 0.00 0.00 1.52
2112 2121 6.567132 GCGCAACACACTACTACCTTTTTAAT 60.567 38.462 0.30 0.00 0.00 1.40
2113 2122 7.357303 CGCAACACACTACTACCTTTTTAATT 58.643 34.615 0.00 0.00 0.00 1.40
2114 2123 8.497554 CGCAACACACTACTACCTTTTTAATTA 58.502 33.333 0.00 0.00 0.00 1.40
2146 2155 8.263940 TCAAACTGTTATTAGTAATCACCTGC 57.736 34.615 0.00 0.00 0.00 4.85
2147 2156 8.100791 TCAAACTGTTATTAGTAATCACCTGCT 58.899 33.333 0.00 0.00 0.00 4.24
2148 2157 8.730680 CAAACTGTTATTAGTAATCACCTGCTT 58.269 33.333 0.00 0.00 0.00 3.91
2149 2158 8.494016 AACTGTTATTAGTAATCACCTGCTTC 57.506 34.615 0.00 0.00 0.00 3.86
2150 2159 7.852263 ACTGTTATTAGTAATCACCTGCTTCT 58.148 34.615 0.00 0.00 0.00 2.85
2151 2160 8.978472 ACTGTTATTAGTAATCACCTGCTTCTA 58.022 33.333 0.00 0.00 0.00 2.10
2152 2161 9.469807 CTGTTATTAGTAATCACCTGCTTCTAG 57.530 37.037 0.00 0.00 0.00 2.43
2153 2162 8.978472 TGTTATTAGTAATCACCTGCTTCTAGT 58.022 33.333 0.00 0.00 0.00 2.57
2154 2163 9.819267 GTTATTAGTAATCACCTGCTTCTAGTT 57.181 33.333 0.00 0.00 0.00 2.24
2157 2166 5.908341 AGTAATCACCTGCTTCTAGTTAGC 58.092 41.667 11.19 11.19 39.10 3.09
2158 2167 4.826274 AATCACCTGCTTCTAGTTAGCA 57.174 40.909 17.27 17.27 45.78 3.49
2159 2168 3.594603 TCACCTGCTTCTAGTTAGCAC 57.405 47.619 15.23 0.00 43.30 4.40
2160 2169 2.897326 TCACCTGCTTCTAGTTAGCACA 59.103 45.455 15.23 0.70 43.30 4.57
2161 2170 2.996621 CACCTGCTTCTAGTTAGCACAC 59.003 50.000 15.23 0.00 43.30 3.82
2162 2171 2.900546 ACCTGCTTCTAGTTAGCACACT 59.099 45.455 15.23 0.00 43.30 3.55
2163 2172 3.056465 ACCTGCTTCTAGTTAGCACACTC 60.056 47.826 15.23 0.00 43.30 3.51
2164 2173 3.516615 CTGCTTCTAGTTAGCACACTCC 58.483 50.000 15.23 0.00 43.30 3.85
2165 2174 2.897326 TGCTTCTAGTTAGCACACTCCA 59.103 45.455 15.23 0.00 43.30 3.86
2166 2175 3.323691 TGCTTCTAGTTAGCACACTCCAA 59.676 43.478 15.23 0.00 43.30 3.53
2167 2176 4.202315 TGCTTCTAGTTAGCACACTCCAAA 60.202 41.667 15.23 0.00 43.30 3.28
2168 2177 4.755123 GCTTCTAGTTAGCACACTCCAAAA 59.245 41.667 12.65 0.00 38.51 2.44
2169 2178 5.334182 GCTTCTAGTTAGCACACTCCAAAAC 60.334 44.000 12.65 0.00 38.51 2.43
2170 2179 4.638304 TCTAGTTAGCACACTCCAAAACC 58.362 43.478 0.00 0.00 0.00 3.27
2171 2180 3.577805 AGTTAGCACACTCCAAAACCT 57.422 42.857 0.00 0.00 0.00 3.50
2172 2181 3.898482 AGTTAGCACACTCCAAAACCTT 58.102 40.909 0.00 0.00 0.00 3.50
2173 2182 4.278310 AGTTAGCACACTCCAAAACCTTT 58.722 39.130 0.00 0.00 0.00 3.11
2174 2183 5.442391 AGTTAGCACACTCCAAAACCTTTA 58.558 37.500 0.00 0.00 0.00 1.85
2175 2184 5.889289 AGTTAGCACACTCCAAAACCTTTAA 59.111 36.000 0.00 0.00 0.00 1.52
2176 2185 6.549736 AGTTAGCACACTCCAAAACCTTTAAT 59.450 34.615 0.00 0.00 0.00 1.40
2177 2186 7.722285 AGTTAGCACACTCCAAAACCTTTAATA 59.278 33.333 0.00 0.00 0.00 0.98
2178 2187 6.969993 AGCACACTCCAAAACCTTTAATAA 57.030 33.333 0.00 0.00 0.00 1.40
2179 2188 7.539034 AGCACACTCCAAAACCTTTAATAAT 57.461 32.000 0.00 0.00 0.00 1.28
2180 2189 7.962441 AGCACACTCCAAAACCTTTAATAATT 58.038 30.769 0.00 0.00 0.00 1.40
2181 2190 9.084533 AGCACACTCCAAAACCTTTAATAATTA 57.915 29.630 0.00 0.00 0.00 1.40
2182 2191 9.353999 GCACACTCCAAAACCTTTAATAATTAG 57.646 33.333 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
264 265 4.158209 TCGAATGTTATCAGTTCCGGTACA 59.842 41.667 14.14 0.00 0.00 2.90
654 655 3.970640 AGCTAAAAGAGGGTATCCTGAGG 59.029 47.826 0.00 0.00 45.05 3.86
1132 1133 2.159366 CGATCGGTCATATAGGCCTGAC 60.159 54.545 17.99 15.11 40.99 3.51
1905 1914 6.380274 ACTTTTCAAATCCATCATGAGAGCAT 59.620 34.615 0.09 0.00 34.29 3.79
1906 1915 5.713389 ACTTTTCAAATCCATCATGAGAGCA 59.287 36.000 0.09 0.00 0.00 4.26
1907 1916 6.205101 ACTTTTCAAATCCATCATGAGAGC 57.795 37.500 0.09 0.00 0.00 4.09
1960 1969 6.169094 GTTCTCCATCTCTGAAAATCAGTGA 58.831 40.000 12.79 12.79 46.74 3.41
1961 1970 5.936372 TGTTCTCCATCTCTGAAAATCAGTG 59.064 40.000 7.21 5.35 44.58 3.66
1962 1971 6.119240 TGTTCTCCATCTCTGAAAATCAGT 57.881 37.500 7.21 0.00 44.58 3.41
1963 1972 8.728337 TTATGTTCTCCATCTCTGAAAATCAG 57.272 34.615 0.88 0.88 39.14 2.90
1964 1973 9.170734 CTTTATGTTCTCCATCTCTGAAAATCA 57.829 33.333 0.00 0.00 34.86 2.57
1965 1974 9.171877 ACTTTATGTTCTCCATCTCTGAAAATC 57.828 33.333 0.00 0.00 34.86 2.17
1967 1976 9.658799 CTACTTTATGTTCTCCATCTCTGAAAA 57.341 33.333 0.00 0.00 34.86 2.29
1968 1977 7.766278 GCTACTTTATGTTCTCCATCTCTGAAA 59.234 37.037 0.00 0.00 34.86 2.69
1969 1978 7.093333 TGCTACTTTATGTTCTCCATCTCTGAA 60.093 37.037 0.00 0.00 34.86 3.02
1970 1979 6.381133 TGCTACTTTATGTTCTCCATCTCTGA 59.619 38.462 0.00 0.00 34.86 3.27
1971 1980 6.478344 GTGCTACTTTATGTTCTCCATCTCTG 59.522 42.308 0.00 0.00 34.86 3.35
1972 1981 6.382570 AGTGCTACTTTATGTTCTCCATCTCT 59.617 38.462 0.00 0.00 34.86 3.10
1973 1982 6.578023 AGTGCTACTTTATGTTCTCCATCTC 58.422 40.000 0.00 0.00 34.86 2.75
1974 1983 6.552445 AGTGCTACTTTATGTTCTCCATCT 57.448 37.500 0.00 0.00 34.86 2.90
1975 1984 7.010923 CAGAAGTGCTACTTTATGTTCTCCATC 59.989 40.741 3.56 0.00 38.80 3.51
1976 1985 6.820656 CAGAAGTGCTACTTTATGTTCTCCAT 59.179 38.462 3.56 0.00 38.80 3.41
1977 1986 6.014584 TCAGAAGTGCTACTTTATGTTCTCCA 60.015 38.462 3.56 0.00 38.80 3.86
1978 1987 6.398918 TCAGAAGTGCTACTTTATGTTCTCC 58.601 40.000 3.56 0.00 38.80 3.71
1979 1988 7.891183 TTCAGAAGTGCTACTTTATGTTCTC 57.109 36.000 3.56 0.00 38.80 2.87
1980 1989 8.854614 AATTCAGAAGTGCTACTTTATGTTCT 57.145 30.769 3.56 0.00 38.80 3.01
2008 2017 5.105675 ACGTATGTGAACAGTTTGGGTTTTT 60.106 36.000 0.00 0.00 0.00 1.94
2009 2018 4.399934 ACGTATGTGAACAGTTTGGGTTTT 59.600 37.500 0.00 0.00 0.00 2.43
2010 2019 3.949113 ACGTATGTGAACAGTTTGGGTTT 59.051 39.130 0.00 0.00 0.00 3.27
2011 2020 3.547746 ACGTATGTGAACAGTTTGGGTT 58.452 40.909 0.00 0.00 0.00 4.11
2012 2021 3.202829 ACGTATGTGAACAGTTTGGGT 57.797 42.857 0.00 0.00 0.00 4.51
2013 2022 5.180492 ACATAACGTATGTGAACAGTTTGGG 59.820 40.000 9.05 0.00 46.94 4.12
2014 2023 6.236017 ACATAACGTATGTGAACAGTTTGG 57.764 37.500 9.05 0.00 46.94 3.28
2026 2035 7.591006 ACCTAACAAACTGACATAACGTATG 57.409 36.000 0.00 0.00 41.88 2.39
2027 2036 8.742777 TCTACCTAACAAACTGACATAACGTAT 58.257 33.333 0.00 0.00 0.00 3.06
2028 2037 8.109705 TCTACCTAACAAACTGACATAACGTA 57.890 34.615 0.00 0.00 0.00 3.57
2029 2038 6.985117 TCTACCTAACAAACTGACATAACGT 58.015 36.000 0.00 0.00 0.00 3.99
2030 2039 7.544566 ACATCTACCTAACAAACTGACATAACG 59.455 37.037 0.00 0.00 0.00 3.18
2031 2040 8.773404 ACATCTACCTAACAAACTGACATAAC 57.227 34.615 0.00 0.00 0.00 1.89
2033 2042 9.865321 GTTACATCTACCTAACAAACTGACATA 57.135 33.333 0.00 0.00 0.00 2.29
2034 2043 8.594550 AGTTACATCTACCTAACAAACTGACAT 58.405 33.333 0.00 0.00 0.00 3.06
2035 2044 7.959175 AGTTACATCTACCTAACAAACTGACA 58.041 34.615 0.00 0.00 0.00 3.58
2036 2045 7.272948 CGAGTTACATCTACCTAACAAACTGAC 59.727 40.741 0.00 0.00 0.00 3.51
2037 2046 7.310664 CGAGTTACATCTACCTAACAAACTGA 58.689 38.462 0.00 0.00 0.00 3.41
2038 2047 6.530534 CCGAGTTACATCTACCTAACAAACTG 59.469 42.308 0.00 0.00 0.00 3.16
2039 2048 6.628185 CCGAGTTACATCTACCTAACAAACT 58.372 40.000 0.00 0.00 0.00 2.66
2040 2049 5.290400 GCCGAGTTACATCTACCTAACAAAC 59.710 44.000 0.00 0.00 0.00 2.93
2041 2050 5.413499 GCCGAGTTACATCTACCTAACAAA 58.587 41.667 0.00 0.00 0.00 2.83
2042 2051 4.142093 GGCCGAGTTACATCTACCTAACAA 60.142 45.833 0.00 0.00 0.00 2.83
2043 2052 3.382546 GGCCGAGTTACATCTACCTAACA 59.617 47.826 0.00 0.00 0.00 2.41
2044 2053 3.243670 GGGCCGAGTTACATCTACCTAAC 60.244 52.174 0.00 0.00 0.00 2.34
2045 2054 2.961062 GGGCCGAGTTACATCTACCTAA 59.039 50.000 0.00 0.00 0.00 2.69
2046 2055 2.590821 GGGCCGAGTTACATCTACCTA 58.409 52.381 0.00 0.00 0.00 3.08
2047 2056 1.411041 GGGCCGAGTTACATCTACCT 58.589 55.000 0.00 0.00 0.00 3.08
2048 2057 0.391966 GGGGCCGAGTTACATCTACC 59.608 60.000 0.00 0.00 0.00 3.18
2049 2058 1.117150 TGGGGCCGAGTTACATCTAC 58.883 55.000 0.00 0.00 0.00 2.59
2050 2059 1.868713 TTGGGGCCGAGTTACATCTA 58.131 50.000 0.00 0.00 0.00 1.98
2051 2060 0.988832 TTTGGGGCCGAGTTACATCT 59.011 50.000 0.00 0.00 0.00 2.90
2052 2061 1.339727 ACTTTGGGGCCGAGTTACATC 60.340 52.381 0.00 0.00 0.00 3.06
2053 2062 0.696501 ACTTTGGGGCCGAGTTACAT 59.303 50.000 0.00 0.00 0.00 2.29
2054 2063 0.475044 AACTTTGGGGCCGAGTTACA 59.525 50.000 14.48 0.00 32.22 2.41
2055 2064 1.268625 CAAACTTTGGGGCCGAGTTAC 59.731 52.381 15.86 0.00 33.54 2.50
2056 2065 1.133730 ACAAACTTTGGGGCCGAGTTA 60.134 47.619 15.86 0.00 33.54 2.24
2057 2066 0.396556 ACAAACTTTGGGGCCGAGTT 60.397 50.000 11.38 11.38 35.27 3.01
2058 2067 0.475044 TACAAACTTTGGGGCCGAGT 59.525 50.000 6.47 0.00 34.12 4.18
2059 2068 1.165270 CTACAAACTTTGGGGCCGAG 58.835 55.000 6.47 0.00 34.12 4.63
2060 2069 0.766131 TCTACAAACTTTGGGGCCGA 59.234 50.000 6.47 0.00 34.12 5.54
2061 2070 1.611519 TTCTACAAACTTTGGGGCCG 58.388 50.000 6.47 0.00 34.12 6.13
2062 2071 2.288825 GCTTTCTACAAACTTTGGGGCC 60.289 50.000 6.47 0.00 34.12 5.80
2063 2072 2.288825 GGCTTTCTACAAACTTTGGGGC 60.289 50.000 6.47 1.68 34.12 5.80
2064 2073 2.962421 TGGCTTTCTACAAACTTTGGGG 59.038 45.455 6.47 0.00 34.12 4.96
2065 2074 4.620982 CTTGGCTTTCTACAAACTTTGGG 58.379 43.478 6.47 0.00 34.12 4.12
2066 2075 4.051237 GCTTGGCTTTCTACAAACTTTGG 58.949 43.478 6.47 0.00 34.12 3.28
2067 2076 3.730715 CGCTTGGCTTTCTACAAACTTTG 59.269 43.478 0.00 0.00 0.00 2.77
2068 2077 3.795488 GCGCTTGGCTTTCTACAAACTTT 60.795 43.478 0.00 0.00 39.11 2.66
2069 2078 2.287608 GCGCTTGGCTTTCTACAAACTT 60.288 45.455 0.00 0.00 39.11 2.66
2070 2079 1.266989 GCGCTTGGCTTTCTACAAACT 59.733 47.619 0.00 0.00 39.11 2.66
2071 2080 1.001815 TGCGCTTGGCTTTCTACAAAC 60.002 47.619 9.73 0.00 44.05 2.93
2072 2081 1.313772 TGCGCTTGGCTTTCTACAAA 58.686 45.000 9.73 0.00 44.05 2.83
2073 2082 1.001815 GTTGCGCTTGGCTTTCTACAA 60.002 47.619 9.73 0.00 44.05 2.41
2074 2083 0.591170 GTTGCGCTTGGCTTTCTACA 59.409 50.000 9.73 0.00 44.05 2.74
2075 2084 0.591170 TGTTGCGCTTGGCTTTCTAC 59.409 50.000 9.73 0.00 44.05 2.59
2076 2085 0.591170 GTGTTGCGCTTGGCTTTCTA 59.409 50.000 9.73 0.00 44.05 2.10
2077 2086 1.360192 GTGTTGCGCTTGGCTTTCT 59.640 52.632 9.73 0.00 44.05 2.52
2078 2087 1.065600 TGTGTTGCGCTTGGCTTTC 59.934 52.632 9.73 0.00 44.05 2.62
2079 2088 1.226945 GTGTGTTGCGCTTGGCTTT 60.227 52.632 9.73 0.00 44.05 3.51
2080 2089 0.817634 TAGTGTGTTGCGCTTGGCTT 60.818 50.000 9.73 0.00 44.05 4.35
2081 2090 1.227823 TAGTGTGTTGCGCTTGGCT 60.228 52.632 9.73 1.96 44.05 4.75
2082 2091 1.082104 GTAGTGTGTTGCGCTTGGC 60.082 57.895 9.73 0.00 43.96 4.52
2083 2092 1.459592 GTAGTAGTGTGTTGCGCTTGG 59.540 52.381 9.73 0.00 39.02 3.61
2084 2093 1.459592 GGTAGTAGTGTGTTGCGCTTG 59.540 52.381 9.73 0.00 39.02 4.01
2085 2094 1.343465 AGGTAGTAGTGTGTTGCGCTT 59.657 47.619 9.73 0.00 39.02 4.68
2086 2095 0.966920 AGGTAGTAGTGTGTTGCGCT 59.033 50.000 9.73 0.00 41.45 5.92
2087 2096 1.792006 AAGGTAGTAGTGTGTTGCGC 58.208 50.000 0.00 0.00 0.00 6.09
2088 2097 4.806342 AAAAAGGTAGTAGTGTGTTGCG 57.194 40.909 0.00 0.00 0.00 4.85
2120 2129 8.726988 GCAGGTGATTACTAATAACAGTTTGAA 58.273 33.333 0.00 0.00 0.00 2.69
2121 2130 8.100791 AGCAGGTGATTACTAATAACAGTTTGA 58.899 33.333 0.00 0.00 0.00 2.69
2122 2131 8.268850 AGCAGGTGATTACTAATAACAGTTTG 57.731 34.615 0.00 0.00 0.00 2.93
2123 2132 8.863872 AAGCAGGTGATTACTAATAACAGTTT 57.136 30.769 0.00 0.00 0.00 2.66
2124 2133 8.322091 AGAAGCAGGTGATTACTAATAACAGTT 58.678 33.333 0.00 0.00 0.00 3.16
2125 2134 7.852263 AGAAGCAGGTGATTACTAATAACAGT 58.148 34.615 0.00 0.00 0.00 3.55
2126 2135 9.469807 CTAGAAGCAGGTGATTACTAATAACAG 57.530 37.037 0.00 0.00 0.00 3.16
2127 2136 8.978472 ACTAGAAGCAGGTGATTACTAATAACA 58.022 33.333 0.00 0.00 0.00 2.41
2128 2137 9.819267 AACTAGAAGCAGGTGATTACTAATAAC 57.181 33.333 0.00 0.00 0.00 1.89
2131 2140 8.145122 GCTAACTAGAAGCAGGTGATTACTAAT 58.855 37.037 14.37 0.00 39.83 1.73
2132 2141 7.123697 TGCTAACTAGAAGCAGGTGATTACTAA 59.876 37.037 16.97 0.00 44.78 2.24
2133 2142 6.605995 TGCTAACTAGAAGCAGGTGATTACTA 59.394 38.462 16.97 0.00 44.78 1.82
2134 2143 5.422331 TGCTAACTAGAAGCAGGTGATTACT 59.578 40.000 16.97 0.00 44.78 2.24
2135 2144 5.661458 TGCTAACTAGAAGCAGGTGATTAC 58.339 41.667 16.97 0.00 44.78 1.89
2136 2145 5.932619 TGCTAACTAGAAGCAGGTGATTA 57.067 39.130 16.97 0.00 44.78 1.75
2137 2146 4.826274 TGCTAACTAGAAGCAGGTGATT 57.174 40.909 16.97 0.00 44.78 2.57
2145 2154 3.594603 TGGAGTGTGCTAACTAGAAGC 57.405 47.619 12.93 12.93 40.50 3.86
2146 2155 5.179555 GGTTTTGGAGTGTGCTAACTAGAAG 59.820 44.000 0.00 0.00 0.00 2.85
2147 2156 5.061179 GGTTTTGGAGTGTGCTAACTAGAA 58.939 41.667 0.00 0.00 0.00 2.10
2148 2157 4.347000 AGGTTTTGGAGTGTGCTAACTAGA 59.653 41.667 0.00 0.00 0.00 2.43
2149 2158 4.642429 AGGTTTTGGAGTGTGCTAACTAG 58.358 43.478 0.00 0.00 0.00 2.57
2150 2159 4.699925 AGGTTTTGGAGTGTGCTAACTA 57.300 40.909 0.00 0.00 0.00 2.24
2151 2160 3.577805 AGGTTTTGGAGTGTGCTAACT 57.422 42.857 0.00 0.00 0.00 2.24
2152 2161 4.649088 AAAGGTTTTGGAGTGTGCTAAC 57.351 40.909 0.00 0.00 0.00 2.34
2153 2162 6.969993 ATTAAAGGTTTTGGAGTGTGCTAA 57.030 33.333 0.00 0.00 0.00 3.09
2154 2163 8.644374 ATTATTAAAGGTTTTGGAGTGTGCTA 57.356 30.769 0.00 0.00 0.00 3.49
2155 2164 6.969993 TTATTAAAGGTTTTGGAGTGTGCT 57.030 33.333 0.00 0.00 0.00 4.40
2156 2165 9.353999 CTAATTATTAAAGGTTTTGGAGTGTGC 57.646 33.333 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.