Multiple sequence alignment - TraesCS2A01G073900

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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 TraesCS2A01G073900 chr2A 100.000 2237 0 0 1 2237 32525778 32528014 0.000000e+00 4132.0
1 TraesCS2A01G073900 chr2A 100.000 177 0 0 46 222 24354476 24354300 5.960000e-86 327.0
2 TraesCS2A01G073900 chr2A 94.737 133 6 1 446 577 753226956 753227088 2.910000e-49 206.0
3 TraesCS2A01G073900 chr2A 100.000 60 0 0 124 183 639610255 639610314 6.530000e-21 111.0
4 TraesCS2A01G073900 chr2A 90.141 71 7 0 169 239 418815629 418815699 2.370000e-15 93.5
5 TraesCS2A01G073900 chr2A 90.323 62 5 1 2173 2233 24165721 24165660 1.840000e-11 80.5
6 TraesCS2A01G073900 chr5D 97.352 2039 43 10 43 2079 6177656 6175627 0.000000e+00 3456.0
7 TraesCS2A01G073900 chr1D 97.206 2040 46 9 43 2079 254434292 254436323 0.000000e+00 3441.0
8 TraesCS2A01G073900 chr1D 95.683 1552 51 9 530 2079 51872191 51870654 0.000000e+00 2481.0
9 TraesCS2A01G073900 chr2D 97.206 2040 44 9 43 2079 638423767 638425796 0.000000e+00 3439.0
10 TraesCS2A01G073900 chr4B 96.225 2040 67 9 43 2079 308680508 308678476 0.000000e+00 3332.0
11 TraesCS2A01G073900 chr4A 95.049 2040 87 11 43 2079 309490539 309488511 0.000000e+00 3195.0
12 TraesCS2A01G073900 chr4D 93.451 2046 107 18 43 2079 207068970 207066943 0.000000e+00 3011.0
13 TraesCS2A01G073900 chr3D 92.745 2040 113 12 43 2079 235618164 235620171 0.000000e+00 2915.0
14 TraesCS2A01G073900 chr5A 95.838 1802 62 10 286 2079 657451090 657452886 0.000000e+00 2900.0


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 TraesCS2A01G073900 chr2A 32525778 32528014 2236 False 4132 4132 100.000 1 2237 1 chr2A.!!$F1 2236
1 TraesCS2A01G073900 chr5D 6175627 6177656 2029 True 3456 3456 97.352 43 2079 1 chr5D.!!$R1 2036
2 TraesCS2A01G073900 chr1D 254434292 254436323 2031 False 3441 3441 97.206 43 2079 1 chr1D.!!$F1 2036
3 TraesCS2A01G073900 chr1D 51870654 51872191 1537 True 2481 2481 95.683 530 2079 1 chr1D.!!$R1 1549
4 TraesCS2A01G073900 chr2D 638423767 638425796 2029 False 3439 3439 97.206 43 2079 1 chr2D.!!$F1 2036
5 TraesCS2A01G073900 chr4B 308678476 308680508 2032 True 3332 3332 96.225 43 2079 1 chr4B.!!$R1 2036
6 TraesCS2A01G073900 chr4A 309488511 309490539 2028 True 3195 3195 95.049 43 2079 1 chr4A.!!$R1 2036
7 TraesCS2A01G073900 chr4D 207066943 207068970 2027 True 3011 3011 93.451 43 2079 1 chr4D.!!$R1 2036
8 TraesCS2A01G073900 chr3D 235618164 235620171 2007 False 2915 2915 92.745 43 2079 1 chr3D.!!$F1 2036
9 TraesCS2A01G073900 chr5A 657451090 657452886 1796 False 2900 2900 95.838 286 2079 1 chr5A.!!$F1 1793

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
794 804 0.037232 ACCAGCGTCTTGGAGCTAAC 60.037 55.0 9.28 0.0 42.52 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2146 0.035056 CCCTCGGTTCCTGCAGAATT 60.035 55.0 17.39 0.0 36.69 2.17 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
21 22 4.622701 GATGCAACCAAATAGAGTCACC 57.377 45.455 0.00 0.00 0.00 4.02
22 23 3.500448 TGCAACCAAATAGAGTCACCA 57.500 42.857 0.00 0.00 0.00 4.17
23 24 3.146066 TGCAACCAAATAGAGTCACCAC 58.854 45.455 0.00 0.00 0.00 4.16
24 25 2.488153 GCAACCAAATAGAGTCACCACC 59.512 50.000 0.00 0.00 0.00 4.61
25 26 3.810743 GCAACCAAATAGAGTCACCACCT 60.811 47.826 0.00 0.00 0.00 4.00
26 27 3.983044 ACCAAATAGAGTCACCACCTC 57.017 47.619 0.00 0.00 0.00 3.85
27 28 3.248024 ACCAAATAGAGTCACCACCTCA 58.752 45.455 0.00 0.00 0.00 3.86
28 29 3.008049 ACCAAATAGAGTCACCACCTCAC 59.992 47.826 0.00 0.00 0.00 3.51
29 30 3.600388 CAAATAGAGTCACCACCTCACC 58.400 50.000 0.00 0.00 0.00 4.02
30 31 1.867363 ATAGAGTCACCACCTCACCC 58.133 55.000 0.00 0.00 0.00 4.61
31 32 0.252103 TAGAGTCACCACCTCACCCC 60.252 60.000 0.00 0.00 0.00 4.95
32 33 2.529389 AGTCACCACCTCACCCCC 60.529 66.667 0.00 0.00 0.00 5.40
234 235 1.190643 CTTCTGGGACCTGAGACTCC 58.809 60.000 0.00 0.00 0.00 3.85
378 379 9.733556 TCTTTATTTTGGCGGTGTATATGATAT 57.266 29.630 0.00 0.00 0.00 1.63
536 546 1.256812 GTGGGCATATATGGTTGGGC 58.743 55.000 14.51 0.18 0.00 5.36
625 635 3.616956 TGTATGGTCTGGAGAAGCTTG 57.383 47.619 2.10 0.00 0.00 4.01
677 687 4.148174 GTCTTTGGTTTTATCGCTTGTTGC 59.852 41.667 0.00 0.00 38.57 4.17
794 804 0.037232 ACCAGCGTCTTGGAGCTAAC 60.037 55.000 9.28 0.00 42.52 2.34
851 861 2.052782 ATCTAATGCGTTCCCCAACC 57.947 50.000 0.00 0.00 0.00 3.77
853 863 0.391927 CTAATGCGTTCCCCAACCGA 60.392 55.000 0.00 0.00 0.00 4.69
878 888 3.660669 AGGTTATCTTTGGAGGGGAAACA 59.339 43.478 0.00 0.00 0.00 2.83
1062 1072 2.843063 CGTAGCTATCGAGATCAATGCG 59.157 50.000 0.00 0.00 0.00 4.73
1072 1082 6.706055 TCGAGATCAATGCGGTTAATTATC 57.294 37.500 0.00 0.00 0.00 1.75
1388 1404 7.254590 CGTATTCAATAAGCAAAAGGAGAGAGG 60.255 40.741 0.00 0.00 0.00 3.69
1436 1452 7.343833 TCCTAGAACTATACCGGTTTTCAAGAT 59.656 37.037 15.04 0.00 0.00 2.40
1466 1482 1.554160 CAACCACTCAGCCATCTCTCT 59.446 52.381 0.00 0.00 0.00 3.10
1548 1570 8.729805 AAGATTTGTTAGCCTCTAGAAAGATG 57.270 34.615 0.00 0.00 0.00 2.90
1679 1703 9.541143 CCATATCCAAATAAAAAGCGGTTTAAT 57.459 29.630 13.75 7.47 0.00 1.40
1745 1769 7.578458 TTAAACCCCTCCTACTTCTTGTATT 57.422 36.000 0.00 0.00 0.00 1.89
1786 1814 9.574516 GGTTTAAGTGAGGGATCAAATATGTAT 57.425 33.333 0.00 0.00 0.00 2.29
1877 1905 4.355543 GCATTAATTGCGACTTCCTCAA 57.644 40.909 0.00 0.00 42.54 3.02
1883 1911 7.915293 TTAATTGCGACTTCCTCAATCTTAA 57.085 32.000 0.00 0.00 30.84 1.85
1966 1994 8.832521 GTTGTATTTTCCGGTACATCATTATGA 58.167 33.333 0.00 0.00 36.54 2.15
1979 2007 9.988815 GTACATCATTATGAATTGGACTAGTCT 57.011 33.333 21.88 2.22 36.54 3.24
2082 2110 9.920946 ATAATAAAGGCCATTTCTTCTAAGACA 57.079 29.630 5.01 0.00 34.13 3.41
2083 2111 8.829373 AATAAAGGCCATTTCTTCTAAGACAT 57.171 30.769 5.01 0.00 34.13 3.06
2084 2112 6.765915 AAAGGCCATTTCTTCTAAGACATC 57.234 37.500 5.01 0.00 34.13 3.06
2085 2113 5.707066 AGGCCATTTCTTCTAAGACATCT 57.293 39.130 5.01 0.00 34.13 2.90
2086 2114 6.814954 AGGCCATTTCTTCTAAGACATCTA 57.185 37.500 5.01 0.00 34.13 1.98
2087 2115 6.587273 AGGCCATTTCTTCTAAGACATCTAC 58.413 40.000 5.01 0.00 34.13 2.59
2088 2116 5.760743 GGCCATTTCTTCTAAGACATCTACC 59.239 44.000 0.00 0.00 34.13 3.18
2089 2117 6.349300 GCCATTTCTTCTAAGACATCTACCA 58.651 40.000 0.00 0.00 34.13 3.25
2090 2118 6.258947 GCCATTTCTTCTAAGACATCTACCAC 59.741 42.308 0.00 0.00 34.13 4.16
2091 2119 7.560368 CCATTTCTTCTAAGACATCTACCACT 58.440 38.462 0.00 0.00 34.13 4.00
2092 2120 8.043710 CCATTTCTTCTAAGACATCTACCACTT 58.956 37.037 0.00 0.00 34.13 3.16
2093 2121 9.092876 CATTTCTTCTAAGACATCTACCACTTC 57.907 37.037 0.00 0.00 34.13 3.01
2094 2122 6.438259 TCTTCTAAGACATCTACCACTTCG 57.562 41.667 0.00 0.00 0.00 3.79
2095 2123 5.944599 TCTTCTAAGACATCTACCACTTCGT 59.055 40.000 0.00 0.00 0.00 3.85
2096 2124 5.814764 TCTAAGACATCTACCACTTCGTC 57.185 43.478 0.00 0.00 0.00 4.20
2097 2125 3.870633 AAGACATCTACCACTTCGTCC 57.129 47.619 0.00 0.00 0.00 4.79
2098 2126 2.100989 AGACATCTACCACTTCGTCCC 58.899 52.381 0.00 0.00 0.00 4.46
2099 2127 2.100989 GACATCTACCACTTCGTCCCT 58.899 52.381 0.00 0.00 0.00 4.20
2100 2128 1.825474 ACATCTACCACTTCGTCCCTG 59.175 52.381 0.00 0.00 0.00 4.45
2101 2129 1.137086 CATCTACCACTTCGTCCCTGG 59.863 57.143 0.00 0.00 0.00 4.45
2102 2130 1.218316 CTACCACTTCGTCCCTGGC 59.782 63.158 0.00 0.00 0.00 4.85
2103 2131 1.534476 TACCACTTCGTCCCTGGCA 60.534 57.895 0.00 0.00 0.00 4.92
2104 2132 1.122632 TACCACTTCGTCCCTGGCAA 61.123 55.000 0.00 0.00 0.00 4.52
2105 2133 1.228124 CCACTTCGTCCCTGGCAAA 60.228 57.895 0.00 0.00 0.00 3.68
2106 2134 0.821711 CCACTTCGTCCCTGGCAAAA 60.822 55.000 0.00 0.00 0.00 2.44
2107 2135 0.593128 CACTTCGTCCCTGGCAAAAG 59.407 55.000 0.00 0.00 0.00 2.27
2108 2136 0.537371 ACTTCGTCCCTGGCAAAAGG 60.537 55.000 0.00 0.00 37.05 3.11
2109 2137 1.866853 CTTCGTCCCTGGCAAAAGGC 61.867 60.000 0.00 0.00 43.74 4.35
2118 2146 2.744709 GCAAAAGGCCGCTACCGA 60.745 61.111 0.00 0.00 36.29 4.69
2119 2147 2.329614 GCAAAAGGCCGCTACCGAA 61.330 57.895 0.00 0.00 36.29 4.30
2120 2148 1.654023 GCAAAAGGCCGCTACCGAAT 61.654 55.000 0.00 0.00 36.29 3.34
2121 2149 0.808755 CAAAAGGCCGCTACCGAATT 59.191 50.000 0.00 0.00 36.29 2.17
2122 2150 1.092348 AAAAGGCCGCTACCGAATTC 58.908 50.000 0.00 0.00 36.29 2.17
2123 2151 0.252197 AAAGGCCGCTACCGAATTCT 59.748 50.000 3.52 0.00 36.29 2.40
2124 2152 0.462047 AAGGCCGCTACCGAATTCTG 60.462 55.000 3.52 0.00 36.29 3.02
2125 2153 2.534903 GGCCGCTACCGAATTCTGC 61.535 63.158 3.52 2.20 36.29 4.26
2126 2154 1.813753 GCCGCTACCGAATTCTGCA 60.814 57.895 3.52 0.00 36.29 4.41
2127 2155 1.766143 GCCGCTACCGAATTCTGCAG 61.766 60.000 7.63 7.63 36.29 4.41
2128 2156 1.154205 CCGCTACCGAATTCTGCAGG 61.154 60.000 15.13 0.00 36.29 4.85
2129 2157 0.179111 CGCTACCGAATTCTGCAGGA 60.179 55.000 15.13 5.14 36.29 3.86
2130 2158 1.739035 CGCTACCGAATTCTGCAGGAA 60.739 52.381 15.13 7.46 35.93 3.36
2131 2159 1.666189 GCTACCGAATTCTGCAGGAAC 59.334 52.381 15.13 3.07 36.70 3.62
2132 2160 2.280628 CTACCGAATTCTGCAGGAACC 58.719 52.381 15.13 0.00 36.70 3.62
2133 2161 0.673644 ACCGAATTCTGCAGGAACCG 60.674 55.000 15.13 12.81 36.70 4.44
2134 2162 0.391130 CCGAATTCTGCAGGAACCGA 60.391 55.000 15.13 0.00 36.70 4.69
2135 2163 1.002366 CGAATTCTGCAGGAACCGAG 58.998 55.000 15.13 0.00 36.70 4.63
2136 2164 1.373570 GAATTCTGCAGGAACCGAGG 58.626 55.000 15.13 0.00 36.70 4.63
2137 2165 0.035056 AATTCTGCAGGAACCGAGGG 60.035 55.000 15.13 0.00 36.70 4.30
2138 2166 1.915078 ATTCTGCAGGAACCGAGGGG 61.915 60.000 15.13 0.00 36.70 4.79
2139 2167 4.785453 CTGCAGGAACCGAGGGGC 62.785 72.222 5.57 0.00 36.48 5.80
2142 2170 4.148825 CAGGAACCGAGGGGCGAG 62.149 72.222 0.00 0.00 44.57 5.03
2154 2182 4.840005 GGCGAGGCCGGAAGAAGG 62.840 72.222 5.05 0.00 39.62 3.46
2161 2189 4.800554 CCGGAAGAAGGCAGTGTT 57.199 55.556 0.00 0.00 0.00 3.32
2162 2190 3.021451 CCGGAAGAAGGCAGTGTTT 57.979 52.632 0.00 0.00 0.00 2.83
2163 2191 0.875059 CCGGAAGAAGGCAGTGTTTC 59.125 55.000 0.00 0.00 0.00 2.78
2164 2192 1.543429 CCGGAAGAAGGCAGTGTTTCT 60.543 52.381 0.00 6.30 35.25 2.52
2165 2193 1.801178 CGGAAGAAGGCAGTGTTTCTC 59.199 52.381 11.00 6.51 32.71 2.87
2166 2194 1.801178 GGAAGAAGGCAGTGTTTCTCG 59.199 52.381 11.00 0.00 32.71 4.04
2167 2195 1.801178 GAAGAAGGCAGTGTTTCTCGG 59.199 52.381 11.00 0.00 32.71 4.63
2168 2196 0.603975 AGAAGGCAGTGTTTCTCGGC 60.604 55.000 6.30 0.00 0.00 5.54
2169 2197 1.901650 GAAGGCAGTGTTTCTCGGCG 61.902 60.000 0.00 0.00 0.00 6.46
2170 2198 3.423154 GGCAGTGTTTCTCGGCGG 61.423 66.667 7.21 0.00 0.00 6.13
2171 2199 3.423154 GCAGTGTTTCTCGGCGGG 61.423 66.667 7.21 2.41 0.00 6.13
2172 2200 2.742372 CAGTGTTTCTCGGCGGGG 60.742 66.667 7.05 0.00 0.00 5.73
2173 2201 4.699522 AGTGTTTCTCGGCGGGGC 62.700 66.667 7.05 0.00 0.00 5.80
2175 2203 4.697756 TGTTTCTCGGCGGGGCAG 62.698 66.667 7.05 0.00 0.00 4.85
2176 2204 4.388499 GTTTCTCGGCGGGGCAGA 62.388 66.667 7.05 0.00 0.00 4.26
2177 2205 3.632080 TTTCTCGGCGGGGCAGAA 61.632 61.111 7.05 5.72 31.77 3.02
2178 2206 3.185299 TTTCTCGGCGGGGCAGAAA 62.185 57.895 14.97 14.97 34.47 2.52
2179 2207 2.684192 TTTCTCGGCGGGGCAGAAAA 62.684 55.000 16.16 3.11 34.04 2.29
2180 2208 3.127533 CTCGGCGGGGCAGAAAAG 61.128 66.667 7.21 0.00 31.77 2.27
2181 2209 4.715523 TCGGCGGGGCAGAAAAGG 62.716 66.667 7.21 0.00 28.67 3.11
2182 2210 4.715523 CGGCGGGGCAGAAAAGGA 62.716 66.667 0.00 0.00 0.00 3.36
2183 2211 2.282887 GGCGGGGCAGAAAAGGAA 60.283 61.111 0.00 0.00 0.00 3.36
2184 2212 1.682344 GGCGGGGCAGAAAAGGAAT 60.682 57.895 0.00 0.00 0.00 3.01
2185 2213 1.667154 GGCGGGGCAGAAAAGGAATC 61.667 60.000 0.00 0.00 0.00 2.52
2186 2214 0.681243 GCGGGGCAGAAAAGGAATCT 60.681 55.000 0.00 0.00 0.00 2.40
2187 2215 1.383523 CGGGGCAGAAAAGGAATCTC 58.616 55.000 0.00 0.00 0.00 2.75
2188 2216 1.769026 GGGGCAGAAAAGGAATCTCC 58.231 55.000 0.00 0.00 36.58 3.71
2189 2217 1.686428 GGGGCAGAAAAGGAATCTCCC 60.686 57.143 0.00 0.00 37.19 4.30
2190 2218 1.383523 GGCAGAAAAGGAATCTCCCG 58.616 55.000 0.00 0.00 37.19 5.14
2191 2219 1.383523 GCAGAAAAGGAATCTCCCGG 58.616 55.000 0.00 0.00 37.19 5.73
2192 2220 1.065418 GCAGAAAAGGAATCTCCCGGA 60.065 52.381 0.73 0.00 37.19 5.14
2193 2221 2.911484 CAGAAAAGGAATCTCCCGGAG 58.089 52.381 8.30 8.30 37.19 4.63
2194 2222 1.210722 AGAAAAGGAATCTCCCGGAGC 59.789 52.381 9.87 0.00 37.19 4.70
2195 2223 0.107654 AAAAGGAATCTCCCGGAGCG 60.108 55.000 9.87 0.00 37.19 5.03
2196 2224 0.976073 AAAGGAATCTCCCGGAGCGA 60.976 55.000 9.87 0.00 37.19 4.93
2197 2225 0.976073 AAGGAATCTCCCGGAGCGAA 60.976 55.000 9.87 0.00 37.19 4.70
2198 2226 0.976073 AGGAATCTCCCGGAGCGAAA 60.976 55.000 9.87 0.00 37.19 3.46
2199 2227 0.530870 GGAATCTCCCGGAGCGAAAG 60.531 60.000 9.87 0.00 0.00 2.62
2200 2228 0.460311 GAATCTCCCGGAGCGAAAGA 59.540 55.000 9.87 0.00 0.00 2.52
2201 2229 0.902531 AATCTCCCGGAGCGAAAGAA 59.097 50.000 9.87 0.00 0.00 2.52
2202 2230 0.902531 ATCTCCCGGAGCGAAAGAAA 59.097 50.000 9.87 0.00 0.00 2.52
2203 2231 0.902531 TCTCCCGGAGCGAAAGAAAT 59.097 50.000 9.87 0.00 0.00 2.17
2204 2232 1.009829 CTCCCGGAGCGAAAGAAATG 58.990 55.000 0.73 0.00 0.00 2.32
2205 2233 0.392461 TCCCGGAGCGAAAGAAATGG 60.392 55.000 0.73 0.00 0.00 3.16
2206 2234 1.376609 CCCGGAGCGAAAGAAATGGG 61.377 60.000 0.73 0.00 0.00 4.00
2207 2235 1.376609 CCGGAGCGAAAGAAATGGGG 61.377 60.000 0.00 0.00 0.00 4.96
2208 2236 0.392461 CGGAGCGAAAGAAATGGGGA 60.392 55.000 0.00 0.00 0.00 4.81
2209 2237 1.747206 CGGAGCGAAAGAAATGGGGAT 60.747 52.381 0.00 0.00 0.00 3.85
2210 2238 2.484770 CGGAGCGAAAGAAATGGGGATA 60.485 50.000 0.00 0.00 0.00 2.59
2211 2239 3.551846 GGAGCGAAAGAAATGGGGATAA 58.448 45.455 0.00 0.00 0.00 1.75
2212 2240 3.951680 GGAGCGAAAGAAATGGGGATAAA 59.048 43.478 0.00 0.00 0.00 1.40
2213 2241 4.401202 GGAGCGAAAGAAATGGGGATAAAA 59.599 41.667 0.00 0.00 0.00 1.52
2214 2242 5.069119 GGAGCGAAAGAAATGGGGATAAAAT 59.931 40.000 0.00 0.00 0.00 1.82
2215 2243 6.406961 GGAGCGAAAGAAATGGGGATAAAATT 60.407 38.462 0.00 0.00 0.00 1.82
2216 2244 6.573434 AGCGAAAGAAATGGGGATAAAATTC 58.427 36.000 0.00 0.00 0.00 2.17
2217 2245 6.154363 AGCGAAAGAAATGGGGATAAAATTCA 59.846 34.615 0.00 0.00 0.00 2.57
2218 2246 6.816140 GCGAAAGAAATGGGGATAAAATTCAA 59.184 34.615 0.00 0.00 0.00 2.69
2219 2247 7.010460 GCGAAAGAAATGGGGATAAAATTCAAG 59.990 37.037 0.00 0.00 0.00 3.02
2220 2248 7.492344 CGAAAGAAATGGGGATAAAATTCAAGG 59.508 37.037 0.00 0.00 0.00 3.61
2221 2249 7.813087 AAGAAATGGGGATAAAATTCAAGGT 57.187 32.000 0.00 0.00 0.00 3.50
2222 2250 7.423844 AGAAATGGGGATAAAATTCAAGGTC 57.576 36.000 0.00 0.00 0.00 3.85
2223 2251 6.959366 AGAAATGGGGATAAAATTCAAGGTCA 59.041 34.615 0.00 0.00 0.00 4.02
2224 2252 7.457535 AGAAATGGGGATAAAATTCAAGGTCAA 59.542 33.333 0.00 0.00 0.00 3.18
2225 2253 6.796785 ATGGGGATAAAATTCAAGGTCAAG 57.203 37.500 0.00 0.00 0.00 3.02
2226 2254 4.466015 TGGGGATAAAATTCAAGGTCAAGC 59.534 41.667 0.00 0.00 0.00 4.01
2227 2255 4.711846 GGGGATAAAATTCAAGGTCAAGCT 59.288 41.667 0.00 0.00 0.00 3.74
2228 2256 5.891551 GGGGATAAAATTCAAGGTCAAGCTA 59.108 40.000 0.00 0.00 0.00 3.32
2229 2257 6.551227 GGGGATAAAATTCAAGGTCAAGCTAT 59.449 38.462 0.00 0.00 0.00 2.97
2230 2258 7.724061 GGGGATAAAATTCAAGGTCAAGCTATA 59.276 37.037 0.00 0.00 0.00 1.31
2231 2259 8.568794 GGGATAAAATTCAAGGTCAAGCTATAC 58.431 37.037 0.00 0.00 0.00 1.47
2232 2260 9.120538 GGATAAAATTCAAGGTCAAGCTATACA 57.879 33.333 0.00 0.00 0.00 2.29
2235 2263 7.396540 AAATTCAAGGTCAAGCTATACAAGG 57.603 36.000 0.00 0.00 0.00 3.61
2236 2264 5.755409 TTCAAGGTCAAGCTATACAAGGA 57.245 39.130 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.009675 TGGTGACTCTATTTGGTTGCATC 58.990 43.478 0.00 0.00 0.00 3.91
1 2 3.758554 GTGGTGACTCTATTTGGTTGCAT 59.241 43.478 0.00 0.00 0.00 3.96
2 3 3.146066 GTGGTGACTCTATTTGGTTGCA 58.854 45.455 0.00 0.00 0.00 4.08
3 4 2.488153 GGTGGTGACTCTATTTGGTTGC 59.512 50.000 0.00 0.00 0.00 4.17
4 5 4.003648 GAGGTGGTGACTCTATTTGGTTG 58.996 47.826 0.00 0.00 32.28 3.77
5 6 3.650942 TGAGGTGGTGACTCTATTTGGTT 59.349 43.478 0.00 0.00 35.98 3.67
6 7 3.008049 GTGAGGTGGTGACTCTATTTGGT 59.992 47.826 0.00 0.00 35.98 3.67
7 8 3.600388 GTGAGGTGGTGACTCTATTTGG 58.400 50.000 0.00 0.00 35.98 3.28
8 9 3.600388 GGTGAGGTGGTGACTCTATTTG 58.400 50.000 0.00 0.00 35.98 2.32
9 10 2.572104 GGGTGAGGTGGTGACTCTATTT 59.428 50.000 0.00 0.00 35.98 1.40
10 11 2.188817 GGGTGAGGTGGTGACTCTATT 58.811 52.381 0.00 0.00 35.98 1.73
11 12 1.622725 GGGGTGAGGTGGTGACTCTAT 60.623 57.143 0.00 0.00 35.98 1.98
12 13 0.252103 GGGGTGAGGTGGTGACTCTA 60.252 60.000 0.00 0.00 35.98 2.43
13 14 1.536662 GGGGTGAGGTGGTGACTCT 60.537 63.158 0.00 0.00 35.98 3.24
14 15 2.593956 GGGGGTGAGGTGGTGACTC 61.594 68.421 0.00 0.00 35.55 3.36
15 16 2.529389 GGGGGTGAGGTGGTGACT 60.529 66.667 0.00 0.00 0.00 3.41
36 37 1.378119 GCTTTTCTGGTACCGGGGG 60.378 63.158 20.89 9.34 0.00 5.40
37 38 1.378119 GGCTTTTCTGGTACCGGGG 60.378 63.158 20.89 6.93 0.00 5.73
38 39 1.378119 GGGCTTTTCTGGTACCGGG 60.378 63.158 20.89 9.52 0.00 5.73
39 40 0.034477 ATGGGCTTTTCTGGTACCGG 60.034 55.000 15.21 15.21 0.00 5.28
40 41 1.094785 CATGGGCTTTTCTGGTACCG 58.905 55.000 7.57 2.25 0.00 4.02
41 42 2.215942 ACATGGGCTTTTCTGGTACC 57.784 50.000 4.43 4.43 0.00 3.34
408 417 3.699538 GGGCTAAGGGTCAAATTGGTAAG 59.300 47.826 0.00 0.00 0.00 2.34
525 535 7.912778 ATACACAAATAAAGCCCAACCATAT 57.087 32.000 0.00 0.00 0.00 1.78
536 546 7.826260 AATTCCGCCAAATACACAAATAAAG 57.174 32.000 0.00 0.00 0.00 1.85
851 861 2.103263 CCCTCCAAAGATAACCTCCTCG 59.897 54.545 0.00 0.00 0.00 4.63
853 863 2.047296 TCCCCTCCAAAGATAACCTCCT 59.953 50.000 0.00 0.00 0.00 3.69
878 888 1.000717 CGAAGGTCCCAAAAACGCATT 60.001 47.619 0.00 0.00 0.00 3.56
959 969 3.754965 TCTTGCCAAGCTTGTATGTCTT 58.245 40.909 24.35 0.00 0.00 3.01
970 980 2.127232 GCGTCGTTCTTGCCAAGC 60.127 61.111 0.00 0.00 0.00 4.01
1062 1072 9.974980 CAACTTCTAGGAGAGAGATAATTAACC 57.025 37.037 4.59 0.00 34.93 2.85
1072 1082 7.411486 TTGATAACCAACTTCTAGGAGAGAG 57.589 40.000 4.59 0.00 34.93 3.20
1167 1177 2.882137 TCCCTTTTCAAAACCTGCTACG 59.118 45.455 0.00 0.00 0.00 3.51
1436 1452 1.751351 CTGAGTGGTTGATAGCTCCGA 59.249 52.381 0.00 0.00 0.00 4.55
1466 1482 8.562949 AGGAGTAAAATAAGGATTAGGCTGTA 57.437 34.615 0.00 0.00 31.76 2.74
1530 1552 6.458232 TCTGACATCTTTCTAGAGGCTAAC 57.542 41.667 0.00 0.00 35.63 2.34
1608 1630 6.646267 TCTTTATTTCACAAGCGGGTATAGT 58.354 36.000 0.00 0.00 0.00 2.12
1786 1814 8.946085 CAAGCTACCATCAAATAAAGTTGACTA 58.054 33.333 0.00 0.00 40.22 2.59
1787 1815 7.094205 CCAAGCTACCATCAAATAAAGTTGACT 60.094 37.037 0.00 0.00 40.22 3.41
1883 1911 9.695155 AGCAAATACAAAGGGTACACTAATTAT 57.305 29.630 0.00 0.00 34.07 1.28
1898 1926 5.324409 ACCATCAGGAGAAGCAAATACAAA 58.676 37.500 0.00 0.00 38.69 2.83
1966 1994 6.071278 AGCTACGAGAAAAGACTAGTCCAATT 60.071 38.462 19.38 11.63 0.00 2.32
1979 2007 8.470805 AGAGAATTCAGAATAGCTACGAGAAAA 58.529 33.333 8.44 0.00 0.00 2.29
2090 2118 1.866853 GCCTTTTGCCAGGGACGAAG 61.867 60.000 0.00 0.00 34.01 3.79
2091 2119 1.901464 GCCTTTTGCCAGGGACGAA 60.901 57.895 0.00 0.00 34.01 3.85
2092 2120 2.282180 GCCTTTTGCCAGGGACGA 60.282 61.111 0.00 0.00 34.01 4.20
2101 2129 1.654023 ATTCGGTAGCGGCCTTTTGC 61.654 55.000 15.23 0.00 40.16 3.68
2102 2130 0.808755 AATTCGGTAGCGGCCTTTTG 59.191 50.000 15.23 0.00 0.00 2.44
2103 2131 1.092348 GAATTCGGTAGCGGCCTTTT 58.908 50.000 15.23 1.50 0.00 2.27
2104 2132 0.252197 AGAATTCGGTAGCGGCCTTT 59.748 50.000 15.23 3.28 0.00 3.11
2105 2133 0.462047 CAGAATTCGGTAGCGGCCTT 60.462 55.000 15.23 5.62 0.00 4.35
2106 2134 1.144057 CAGAATTCGGTAGCGGCCT 59.856 57.895 15.23 3.89 0.00 5.19
2107 2135 2.534903 GCAGAATTCGGTAGCGGCC 61.535 63.158 15.23 0.00 0.00 6.13
2108 2136 1.766143 CTGCAGAATTCGGTAGCGGC 61.766 60.000 15.23 9.17 0.00 6.53
2109 2137 1.154205 CCTGCAGAATTCGGTAGCGG 61.154 60.000 17.39 14.73 0.00 5.52
2110 2138 0.179111 TCCTGCAGAATTCGGTAGCG 60.179 55.000 17.39 8.29 0.00 4.26
2111 2139 1.666189 GTTCCTGCAGAATTCGGTAGC 59.334 52.381 17.39 11.80 36.69 3.58
2112 2140 2.280628 GGTTCCTGCAGAATTCGGTAG 58.719 52.381 17.39 14.99 36.69 3.18
2113 2141 1.404986 CGGTTCCTGCAGAATTCGGTA 60.405 52.381 17.39 1.80 36.69 4.02
2114 2142 0.673644 CGGTTCCTGCAGAATTCGGT 60.674 55.000 17.39 0.00 36.69 4.69
2115 2143 0.391130 TCGGTTCCTGCAGAATTCGG 60.391 55.000 17.39 0.69 36.69 4.30
2116 2144 1.002366 CTCGGTTCCTGCAGAATTCG 58.998 55.000 17.39 13.57 36.69 3.34
2117 2145 1.373570 CCTCGGTTCCTGCAGAATTC 58.626 55.000 17.39 0.00 36.69 2.17
2118 2146 0.035056 CCCTCGGTTCCTGCAGAATT 60.035 55.000 17.39 0.00 36.69 2.17
2119 2147 1.604378 CCCTCGGTTCCTGCAGAAT 59.396 57.895 17.39 0.00 36.69 2.40
2120 2148 2.592993 CCCCTCGGTTCCTGCAGAA 61.593 63.158 17.39 4.81 0.00 3.02
2121 2149 3.003173 CCCCTCGGTTCCTGCAGA 61.003 66.667 17.39 0.00 0.00 4.26
2122 2150 4.785453 GCCCCTCGGTTCCTGCAG 62.785 72.222 6.78 6.78 0.00 4.41
2125 2153 4.148825 CTCGCCCCTCGGTTCCTG 62.149 72.222 0.00 0.00 39.05 3.86
2137 2165 4.840005 CCTTCTTCCGGCCTCGCC 62.840 72.222 0.00 0.00 46.75 5.54
2144 2172 0.875059 GAAACACTGCCTTCTTCCGG 59.125 55.000 0.00 0.00 0.00 5.14
2145 2173 1.801178 GAGAAACACTGCCTTCTTCCG 59.199 52.381 0.00 0.00 32.01 4.30
2146 2174 1.801178 CGAGAAACACTGCCTTCTTCC 59.199 52.381 0.00 0.00 32.01 3.46
2147 2175 1.801178 CCGAGAAACACTGCCTTCTTC 59.199 52.381 0.00 0.00 32.01 2.87
2148 2176 1.884235 CCGAGAAACACTGCCTTCTT 58.116 50.000 0.00 0.00 32.01 2.52
2149 2177 0.603975 GCCGAGAAACACTGCCTTCT 60.604 55.000 0.00 0.00 34.58 2.85
2150 2178 1.869690 GCCGAGAAACACTGCCTTC 59.130 57.895 0.00 0.00 0.00 3.46
2151 2179 1.961277 CGCCGAGAAACACTGCCTT 60.961 57.895 0.00 0.00 0.00 4.35
2152 2180 2.357517 CGCCGAGAAACACTGCCT 60.358 61.111 0.00 0.00 0.00 4.75
2153 2181 3.423154 CCGCCGAGAAACACTGCC 61.423 66.667 0.00 0.00 0.00 4.85
2154 2182 3.423154 CCCGCCGAGAAACACTGC 61.423 66.667 0.00 0.00 0.00 4.40
2155 2183 2.742372 CCCCGCCGAGAAACACTG 60.742 66.667 0.00 0.00 0.00 3.66
2156 2184 4.699522 GCCCCGCCGAGAAACACT 62.700 66.667 0.00 0.00 0.00 3.55
2158 2186 4.697756 CTGCCCCGCCGAGAAACA 62.698 66.667 0.00 0.00 0.00 2.83
2159 2187 3.894547 TTCTGCCCCGCCGAGAAAC 62.895 63.158 0.00 0.00 0.00 2.78
2160 2188 2.684192 TTTTCTGCCCCGCCGAGAAA 62.684 55.000 0.00 0.00 34.63 2.52
2161 2189 3.185299 TTTTCTGCCCCGCCGAGAA 62.185 57.895 0.00 0.00 0.00 2.87
2162 2190 3.605749 CTTTTCTGCCCCGCCGAGA 62.606 63.158 0.00 0.00 0.00 4.04
2163 2191 3.127533 CTTTTCTGCCCCGCCGAG 61.128 66.667 0.00 0.00 0.00 4.63
2164 2192 4.715523 CCTTTTCTGCCCCGCCGA 62.716 66.667 0.00 0.00 0.00 5.54
2165 2193 4.715523 TCCTTTTCTGCCCCGCCG 62.716 66.667 0.00 0.00 0.00 6.46
2166 2194 1.667154 GATTCCTTTTCTGCCCCGCC 61.667 60.000 0.00 0.00 0.00 6.13
2167 2195 0.681243 AGATTCCTTTTCTGCCCCGC 60.681 55.000 0.00 0.00 0.00 6.13
2168 2196 1.383523 GAGATTCCTTTTCTGCCCCG 58.616 55.000 0.00 0.00 0.00 5.73
2169 2197 1.686428 GGGAGATTCCTTTTCTGCCCC 60.686 57.143 0.18 0.00 43.73 5.80
2170 2198 1.769026 GGGAGATTCCTTTTCTGCCC 58.231 55.000 0.18 0.00 43.73 5.36
2171 2199 1.383523 CGGGAGATTCCTTTTCTGCC 58.616 55.000 1.52 1.52 45.42 4.85
2172 2200 1.065418 TCCGGGAGATTCCTTTTCTGC 60.065 52.381 0.00 0.00 36.57 4.26
2173 2201 2.911484 CTCCGGGAGATTCCTTTTCTG 58.089 52.381 19.57 0.00 36.57 3.02
2174 2202 1.210722 GCTCCGGGAGATTCCTTTTCT 59.789 52.381 27.95 0.00 36.57 2.52
2175 2203 1.669604 GCTCCGGGAGATTCCTTTTC 58.330 55.000 27.95 2.48 36.57 2.29
2176 2204 0.107654 CGCTCCGGGAGATTCCTTTT 60.108 55.000 27.95 0.00 36.57 2.27
2177 2205 0.976073 TCGCTCCGGGAGATTCCTTT 60.976 55.000 27.95 0.00 36.57 3.11
2178 2206 0.976073 TTCGCTCCGGGAGATTCCTT 60.976 55.000 27.95 0.00 36.57 3.36
2179 2207 0.976073 TTTCGCTCCGGGAGATTCCT 60.976 55.000 27.95 0.00 36.57 3.36
2180 2208 0.530870 CTTTCGCTCCGGGAGATTCC 60.531 60.000 27.95 8.70 35.23 3.01
2181 2209 0.460311 TCTTTCGCTCCGGGAGATTC 59.540 55.000 27.95 9.07 0.00 2.52
2182 2210 0.902531 TTCTTTCGCTCCGGGAGATT 59.097 50.000 27.95 0.00 0.00 2.40
2183 2211 0.902531 TTTCTTTCGCTCCGGGAGAT 59.097 50.000 27.95 0.00 0.00 2.75
2184 2212 0.902531 ATTTCTTTCGCTCCGGGAGA 59.097 50.000 27.95 4.94 0.00 3.71
2185 2213 1.009829 CATTTCTTTCGCTCCGGGAG 58.990 55.000 19.95 19.95 0.00 4.30
2186 2214 0.392461 CCATTTCTTTCGCTCCGGGA 60.392 55.000 0.00 0.00 0.00 5.14
2187 2215 1.376609 CCCATTTCTTTCGCTCCGGG 61.377 60.000 0.00 0.00 0.00 5.73
2188 2216 1.376609 CCCCATTTCTTTCGCTCCGG 61.377 60.000 0.00 0.00 0.00 5.14
2189 2217 0.392461 TCCCCATTTCTTTCGCTCCG 60.392 55.000 0.00 0.00 0.00 4.63
2190 2218 2.058593 ATCCCCATTTCTTTCGCTCC 57.941 50.000 0.00 0.00 0.00 4.70
2191 2219 5.576447 TTTTATCCCCATTTCTTTCGCTC 57.424 39.130 0.00 0.00 0.00 5.03
2192 2220 6.154363 TGAATTTTATCCCCATTTCTTTCGCT 59.846 34.615 0.00 0.00 0.00 4.93
2193 2221 6.337356 TGAATTTTATCCCCATTTCTTTCGC 58.663 36.000 0.00 0.00 0.00 4.70
2194 2222 7.492344 CCTTGAATTTTATCCCCATTTCTTTCG 59.508 37.037 0.00 0.00 0.00 3.46
2195 2223 8.321353 ACCTTGAATTTTATCCCCATTTCTTTC 58.679 33.333 0.00 0.00 0.00 2.62
2196 2224 8.218423 ACCTTGAATTTTATCCCCATTTCTTT 57.782 30.769 0.00 0.00 0.00 2.52
2197 2225 7.457535 TGACCTTGAATTTTATCCCCATTTCTT 59.542 33.333 0.00 0.00 0.00 2.52
2198 2226 6.959366 TGACCTTGAATTTTATCCCCATTTCT 59.041 34.615 0.00 0.00 0.00 2.52
2199 2227 7.181569 TGACCTTGAATTTTATCCCCATTTC 57.818 36.000 0.00 0.00 0.00 2.17
2200 2228 7.566658 TTGACCTTGAATTTTATCCCCATTT 57.433 32.000 0.00 0.00 0.00 2.32
2201 2229 6.352137 GCTTGACCTTGAATTTTATCCCCATT 60.352 38.462 0.00 0.00 0.00 3.16
2202 2230 5.129320 GCTTGACCTTGAATTTTATCCCCAT 59.871 40.000 0.00 0.00 0.00 4.00
2203 2231 4.466015 GCTTGACCTTGAATTTTATCCCCA 59.534 41.667 0.00 0.00 0.00 4.96
2204 2232 4.711846 AGCTTGACCTTGAATTTTATCCCC 59.288 41.667 0.00 0.00 0.00 4.81
2205 2233 5.921962 AGCTTGACCTTGAATTTTATCCC 57.078 39.130 0.00 0.00 0.00 3.85
2206 2234 9.120538 TGTATAGCTTGACCTTGAATTTTATCC 57.879 33.333 0.00 0.00 0.00 2.59
2209 2237 8.956426 CCTTGTATAGCTTGACCTTGAATTTTA 58.044 33.333 0.00 0.00 0.00 1.52
2210 2238 7.669722 TCCTTGTATAGCTTGACCTTGAATTTT 59.330 33.333 0.00 0.00 0.00 1.82
2211 2239 7.175104 TCCTTGTATAGCTTGACCTTGAATTT 58.825 34.615 0.00 0.00 0.00 1.82
2212 2240 6.721318 TCCTTGTATAGCTTGACCTTGAATT 58.279 36.000 0.00 0.00 0.00 2.17
2213 2241 6.313519 TCCTTGTATAGCTTGACCTTGAAT 57.686 37.500 0.00 0.00 0.00 2.57
2214 2242 5.755409 TCCTTGTATAGCTTGACCTTGAA 57.245 39.130 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.