Multiple sequence alignment - TraesCS1B01G405500

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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 TraesCS1B01G405500 chr1B 100.000 2405 0 0 1 2405 633728865 633726461 0.000000e+00 4442
1 TraesCS1B01G405500 chr2D 97.951 2050 32 4 1 2047 33933815 33935857 0.000000e+00 3544
2 TraesCS1B01G405500 chr2D 97.901 2049 34 3 1 2047 630270292 630272333 0.000000e+00 3537
3 TraesCS1B01G405500 chr2D 98.352 364 6 0 2042 2405 28724875 28724512 7.250000e-180 640
4 TraesCS1B01G405500 chr2D 97.790 362 8 0 2042 2403 628283433 628283072 2.030000e-175 625
5 TraesCS1B01G405500 chr3B 97.755 2049 43 3 1 2047 201560775 201558728 0.000000e+00 3526
6 TraesCS1B01G405500 chr3B 97.802 364 7 1 2042 2405 201504330 201503968 5.640000e-176 627
7 TraesCS1B01G405500 chr3B 98.814 253 3 0 1 253 810472419 810472167 3.650000e-123 451
8 TraesCS1B01G405500 chr3B 98.814 253 3 0 1 253 810482468 810482216 3.650000e-123 451
9 TraesCS1B01G405500 chr3B 95.812 191 8 0 346 536 550898760 550898570 2.320000e-80 309
10 TraesCS1B01G405500 chr3A 97.510 2048 48 3 1 2047 672878433 672876388 0.000000e+00 3496
11 TraesCS1B01G405500 chr5D 96.392 2051 65 9 1 2047 432292719 432290674 0.000000e+00 3369
12 TraesCS1B01G405500 chr5B 95.994 2047 66 5 1 2045 432876723 432878755 0.000000e+00 3312
13 TraesCS1B01G405500 chr5B 97.881 1463 27 3 589 2047 413608022 413609484 0.000000e+00 2527
14 TraesCS1B01G405500 chr4A 95.705 2049 83 4 1 2047 310762405 310764450 0.000000e+00 3291
15 TraesCS1B01G405500 chr4D 96.036 1867 71 3 182 2047 245648863 245650727 0.000000e+00 3035
16 TraesCS1B01G405500 chr1A 97.802 364 8 0 2042 2405 554467271 554467634 1.570000e-176 628
17 TraesCS1B01G405500 chrUn 98.584 353 5 0 2042 2394 390489321 390489673 2.030000e-175 625
18 TraesCS1B01G405500 chr2A 97.527 364 9 0 2042 2405 276443322 276443685 7.300000e-175 623
19 TraesCS1B01G405500 chr1D 97.527 364 9 0 2042 2405 254487459 254487096 7.300000e-175 623
20 TraesCS1B01G405500 chr5A 97.238 362 10 0 2042 2403 684323365 684323004 4.390000e-172 614
21 TraesCS1B01G405500 chr3D 97.245 363 9 1 2042 2403 21895320 21894958 4.390000e-172 614


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 TraesCS1B01G405500 chr1B 633726461 633728865 2404 True 4442 4442 100.000 1 2405 1 chr1B.!!$R1 2404
1 TraesCS1B01G405500 chr2D 33933815 33935857 2042 False 3544 3544 97.951 1 2047 1 chr2D.!!$F1 2046
2 TraesCS1B01G405500 chr2D 630270292 630272333 2041 False 3537 3537 97.901 1 2047 1 chr2D.!!$F2 2046
3 TraesCS1B01G405500 chr3B 201558728 201560775 2047 True 3526 3526 97.755 1 2047 1 chr3B.!!$R2 2046
4 TraesCS1B01G405500 chr3A 672876388 672878433 2045 True 3496 3496 97.510 1 2047 1 chr3A.!!$R1 2046
5 TraesCS1B01G405500 chr5D 432290674 432292719 2045 True 3369 3369 96.392 1 2047 1 chr5D.!!$R1 2046
6 TraesCS1B01G405500 chr5B 432876723 432878755 2032 False 3312 3312 95.994 1 2045 1 chr5B.!!$F2 2044
7 TraesCS1B01G405500 chr5B 413608022 413609484 1462 False 2527 2527 97.881 589 2047 1 chr5B.!!$F1 1458
8 TraesCS1B01G405500 chr4A 310762405 310764450 2045 False 3291 3291 95.705 1 2047 1 chr4A.!!$F1 2046
9 TraesCS1B01G405500 chr4D 245648863 245650727 1864 False 3035 3035 96.036 182 2047 1 chr4D.!!$F1 1865

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
443 444 5.509163 CGATAGATCTACCCGTTGTGGATTT 60.509 44.0 4.1 1.26 44.37 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2209 0.034896 CACTACGTGTCCAAGGCCTT 59.965 55.0 13.78 13.78 0.0 4.35 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
278 279 9.802039 AAGGTACATAGGTCAAAGTTTCATAAA 57.198 29.630 0.00 0.00 0.00 1.40
443 444 5.509163 CGATAGATCTACCCGTTGTGGATTT 60.509 44.000 4.10 1.26 44.37 2.17
680 681 8.977505 CACAATTCAAACAATTAGGAATTCGTT 58.022 29.630 5.89 0.00 37.75 3.85
1183 1189 4.569761 TCCTACTTTGTAGCTATCGCAG 57.430 45.455 0.00 0.00 39.10 5.18
1308 1314 3.162666 AGATGGGTTCACTTCACTCGTA 58.837 45.455 0.00 0.00 0.00 3.43
1524 1530 2.434336 AGGTGCAATTACTATGGCTCGA 59.566 45.455 0.00 0.00 31.51 4.04
1711 1717 5.506317 CGGTTCAATTCTTGCCCTCATATTC 60.506 44.000 0.00 0.00 0.00 1.75
2067 2074 7.935338 AATTCTAGCAATTGCCAATAAATCG 57.065 32.000 26.45 2.94 43.38 3.34
2068 2075 6.691754 TTCTAGCAATTGCCAATAAATCGA 57.308 33.333 26.45 5.34 43.38 3.59
2069 2076 6.304356 TCTAGCAATTGCCAATAAATCGAG 57.696 37.500 26.45 8.53 43.38 4.04
2070 2077 4.311816 AGCAATTGCCAATAAATCGAGG 57.688 40.909 26.45 0.00 43.38 4.63
2079 2086 5.041287 GCCAATAAATCGAGGCTTTTTACC 58.959 41.667 3.98 0.00 43.70 2.85
2080 2087 5.393678 GCCAATAAATCGAGGCTTTTTACCA 60.394 40.000 3.98 0.00 43.70 3.25
2081 2088 6.626302 CCAATAAATCGAGGCTTTTTACCAA 58.374 36.000 0.00 0.00 0.00 3.67
2082 2089 6.530181 CCAATAAATCGAGGCTTTTTACCAAC 59.470 38.462 0.00 0.00 0.00 3.77
2083 2090 7.312899 CAATAAATCGAGGCTTTTTACCAACT 58.687 34.615 0.00 0.00 0.00 3.16
2084 2091 5.784578 AAATCGAGGCTTTTTACCAACTT 57.215 34.783 0.00 0.00 0.00 2.66
2085 2092 4.766404 ATCGAGGCTTTTTACCAACTTG 57.234 40.909 0.00 0.00 0.00 3.16
2086 2093 3.811083 TCGAGGCTTTTTACCAACTTGA 58.189 40.909 0.00 0.00 0.00 3.02
2087 2094 4.394729 TCGAGGCTTTTTACCAACTTGAT 58.605 39.130 0.00 0.00 0.00 2.57
2088 2095 4.215399 TCGAGGCTTTTTACCAACTTGATG 59.785 41.667 0.00 0.00 0.00 3.07
2089 2096 4.615912 CGAGGCTTTTTACCAACTTGATGG 60.616 45.833 0.00 0.00 46.38 3.51
2100 2107 4.662145 CCAACTTGATGGTAAGAAATCGC 58.338 43.478 0.00 0.00 35.65 4.58
2101 2108 4.334443 CAACTTGATGGTAAGAAATCGCG 58.666 43.478 0.00 0.00 0.00 5.87
2102 2109 3.857052 ACTTGATGGTAAGAAATCGCGA 58.143 40.909 13.09 13.09 0.00 5.87
2103 2110 3.865745 ACTTGATGGTAAGAAATCGCGAG 59.134 43.478 16.66 0.00 0.00 5.03
2105 2112 3.444916 TGATGGTAAGAAATCGCGAGAC 58.555 45.455 16.66 8.42 46.97 3.36
2106 2113 2.288961 TGGTAAGAAATCGCGAGACC 57.711 50.000 16.66 14.41 46.97 3.85
2107 2114 1.822990 TGGTAAGAAATCGCGAGACCT 59.177 47.619 16.66 8.06 46.97 3.85
2108 2115 3.018856 TGGTAAGAAATCGCGAGACCTA 58.981 45.455 16.66 0.00 46.97 3.08
2109 2116 3.066342 TGGTAAGAAATCGCGAGACCTAG 59.934 47.826 16.66 0.00 46.97 3.02
2110 2117 3.314635 GGTAAGAAATCGCGAGACCTAGA 59.685 47.826 16.66 0.39 46.97 2.43
2111 2118 4.201990 GGTAAGAAATCGCGAGACCTAGAA 60.202 45.833 16.66 0.00 46.97 2.10
2112 2119 4.451629 AAGAAATCGCGAGACCTAGAAA 57.548 40.909 16.66 0.00 46.97 2.52
2113 2120 4.657436 AGAAATCGCGAGACCTAGAAAT 57.343 40.909 16.66 0.00 46.97 2.17
2114 2121 5.012328 AGAAATCGCGAGACCTAGAAATT 57.988 39.130 16.66 0.00 46.97 1.82
2115 2122 5.044558 AGAAATCGCGAGACCTAGAAATTC 58.955 41.667 16.66 6.02 46.97 2.17
2116 2123 4.386867 AATCGCGAGACCTAGAAATTCA 57.613 40.909 16.66 0.00 46.97 2.57
2117 2124 4.592485 ATCGCGAGACCTAGAAATTCAT 57.408 40.909 16.66 0.00 46.97 2.57
2118 2125 4.386867 TCGCGAGACCTAGAAATTCATT 57.613 40.909 3.71 0.00 33.31 2.57
2119 2126 4.755411 TCGCGAGACCTAGAAATTCATTT 58.245 39.130 3.71 0.00 33.31 2.32
2120 2127 4.804139 TCGCGAGACCTAGAAATTCATTTC 59.196 41.667 3.71 4.35 40.07 2.17
2121 2128 6.460937 TCGCGAGACCTAGAAATTCATTTCG 61.461 44.000 3.71 0.00 42.49 3.46
2122 2129 8.763084 TCGCGAGACCTAGAAATTCATTTCGT 62.763 42.308 3.71 0.14 42.49 3.85
2123 2130 9.479338 TCGCGAGACCTAGAAATTCATTTCGTA 62.479 40.741 3.71 0.94 42.49 3.43
2134 2141 8.742554 GAAATTCATTTCGTACAATTGAACCT 57.257 30.769 13.59 0.00 37.09 3.50
2135 2142 9.191995 GAAATTCATTTCGTACAATTGAACCTT 57.808 29.630 13.59 10.81 37.09 3.50
2136 2143 9.541143 AAATTCATTTCGTACAATTGAACCTTT 57.459 25.926 13.59 10.00 0.00 3.11
2137 2144 9.541143 AATTCATTTCGTACAATTGAACCTTTT 57.459 25.926 13.59 0.00 0.00 2.27
2138 2145 8.568732 TTCATTTCGTACAATTGAACCTTTTC 57.431 30.769 13.59 0.00 0.00 2.29
2139 2146 7.708051 TCATTTCGTACAATTGAACCTTTTCA 58.292 30.769 13.59 0.00 40.14 2.69
2152 2159 8.669946 TTGAACCTTTTCAAACTGTTTCTTTT 57.330 26.923 2.13 0.00 46.59 2.27
2153 2160 8.669946 TGAACCTTTTCAAACTGTTTCTTTTT 57.330 26.923 2.13 0.00 38.87 1.94
2154 2161 8.555361 TGAACCTTTTCAAACTGTTTCTTTTTG 58.445 29.630 2.13 0.00 38.87 2.44
2155 2162 8.669946 AACCTTTTCAAACTGTTTCTTTTTGA 57.330 26.923 2.13 0.00 37.44 2.69
2156 2163 8.310406 ACCTTTTCAAACTGTTTCTTTTTGAG 57.690 30.769 2.13 0.00 39.68 3.02
2157 2164 8.147704 ACCTTTTCAAACTGTTTCTTTTTGAGA 58.852 29.630 2.13 0.00 39.68 3.27
2158 2165 8.987890 CCTTTTCAAACTGTTTCTTTTTGAGAA 58.012 29.630 2.13 0.00 42.56 2.87
2159 2166 9.797473 CTTTTCAAACTGTTTCTTTTTGAGAAC 57.203 29.630 2.13 0.00 43.90 3.01
2160 2167 7.883229 TTCAAACTGTTTCTTTTTGAGAACC 57.117 32.000 2.13 0.00 43.90 3.62
2161 2168 6.987386 TCAAACTGTTTCTTTTTGAGAACCA 58.013 32.000 2.13 0.00 43.90 3.67
2162 2169 7.437748 TCAAACTGTTTCTTTTTGAGAACCAA 58.562 30.769 2.13 0.00 43.90 3.67
2163 2170 7.928706 TCAAACTGTTTCTTTTTGAGAACCAAA 59.071 29.630 2.13 0.00 43.90 3.28
2188 2195 7.481275 AAAACTTGTGCCAAAATAACTGATG 57.519 32.000 0.00 0.00 0.00 3.07
2189 2196 4.559153 ACTTGTGCCAAAATAACTGATGC 58.441 39.130 0.00 0.00 0.00 3.91
2190 2197 4.039004 ACTTGTGCCAAAATAACTGATGCA 59.961 37.500 0.00 0.00 0.00 3.96
2191 2198 4.597404 TGTGCCAAAATAACTGATGCAA 57.403 36.364 0.00 0.00 0.00 4.08
2192 2199 4.953667 TGTGCCAAAATAACTGATGCAAA 58.046 34.783 0.00 0.00 0.00 3.68
2193 2200 4.989797 TGTGCCAAAATAACTGATGCAAAG 59.010 37.500 0.00 0.00 0.00 2.77
2194 2201 5.221402 TGTGCCAAAATAACTGATGCAAAGA 60.221 36.000 6.76 0.00 0.00 2.52
2195 2202 5.695816 GTGCCAAAATAACTGATGCAAAGAA 59.304 36.000 6.76 0.00 0.00 2.52
2196 2203 5.927689 TGCCAAAATAACTGATGCAAAGAAG 59.072 36.000 6.76 0.00 0.00 2.85
2197 2204 6.158598 GCCAAAATAACTGATGCAAAGAAGA 58.841 36.000 6.76 0.00 0.00 2.87
2198 2205 6.646240 GCCAAAATAACTGATGCAAAGAAGAA 59.354 34.615 6.76 0.00 0.00 2.52
2199 2206 7.359514 GCCAAAATAACTGATGCAAAGAAGAAC 60.360 37.037 6.76 0.00 0.00 3.01
2200 2207 7.652909 CCAAAATAACTGATGCAAAGAAGAACA 59.347 33.333 6.76 0.00 0.00 3.18
2201 2208 9.033481 CAAAATAACTGATGCAAAGAAGAACAA 57.967 29.630 6.76 0.00 0.00 2.83
2202 2209 9.598517 AAAATAACTGATGCAAAGAAGAACAAA 57.401 25.926 6.76 0.00 0.00 2.83
2203 2210 9.598517 AAATAACTGATGCAAAGAAGAACAAAA 57.401 25.926 6.76 0.00 0.00 2.44
2204 2211 8.807667 ATAACTGATGCAAAGAAGAACAAAAG 57.192 30.769 6.76 0.00 0.00 2.27
2205 2212 5.594926 ACTGATGCAAAGAAGAACAAAAGG 58.405 37.500 6.76 0.00 0.00 3.11
2206 2213 4.370917 TGATGCAAAGAAGAACAAAAGGC 58.629 39.130 0.00 0.00 0.00 4.35
2207 2214 3.177997 TGCAAAGAAGAACAAAAGGCC 57.822 42.857 0.00 0.00 0.00 5.19
2208 2215 2.765699 TGCAAAGAAGAACAAAAGGCCT 59.234 40.909 0.00 0.00 0.00 5.19
2209 2216 3.197549 TGCAAAGAAGAACAAAAGGCCTT 59.802 39.130 13.78 13.78 0.00 4.35
2210 2217 3.557185 GCAAAGAAGAACAAAAGGCCTTG 59.443 43.478 21.33 11.36 0.00 3.61
2211 2218 4.122046 CAAAGAAGAACAAAAGGCCTTGG 58.878 43.478 21.33 17.12 0.00 3.61
2212 2219 3.312736 AGAAGAACAAAAGGCCTTGGA 57.687 42.857 21.33 0.00 0.00 3.53
2213 2220 2.959030 AGAAGAACAAAAGGCCTTGGAC 59.041 45.455 21.33 13.44 0.00 4.02
2214 2221 2.452600 AGAACAAAAGGCCTTGGACA 57.547 45.000 21.33 0.00 0.00 4.02
2215 2222 2.031870 AGAACAAAAGGCCTTGGACAC 58.968 47.619 21.33 11.17 0.00 3.67
2216 2223 0.744281 AACAAAAGGCCTTGGACACG 59.256 50.000 21.33 6.64 0.00 4.49
2217 2224 0.395173 ACAAAAGGCCTTGGACACGT 60.395 50.000 21.33 7.30 0.00 4.49
2218 2225 1.134037 ACAAAAGGCCTTGGACACGTA 60.134 47.619 21.33 0.00 0.00 3.57
2219 2226 1.535462 CAAAAGGCCTTGGACACGTAG 59.465 52.381 21.33 0.00 0.00 3.51
2233 2240 1.557099 ACGTAGTGGATCCTGAAGCA 58.443 50.000 14.23 0.00 42.51 3.91
2234 2241 1.204941 ACGTAGTGGATCCTGAAGCAC 59.795 52.381 14.23 0.96 42.51 4.40
2235 2242 1.799181 CGTAGTGGATCCTGAAGCACG 60.799 57.143 14.23 9.90 0.00 5.34
2236 2243 1.476891 GTAGTGGATCCTGAAGCACGA 59.523 52.381 14.23 0.00 0.00 4.35
2237 2244 1.198713 AGTGGATCCTGAAGCACGAT 58.801 50.000 14.23 0.00 0.00 3.73
2238 2245 1.556911 AGTGGATCCTGAAGCACGATT 59.443 47.619 14.23 0.00 0.00 3.34
2239 2246 2.026822 AGTGGATCCTGAAGCACGATTT 60.027 45.455 14.23 0.00 0.00 2.17
2240 2247 2.352960 GTGGATCCTGAAGCACGATTTC 59.647 50.000 14.23 0.00 0.00 2.17
2241 2248 1.943340 GGATCCTGAAGCACGATTTCC 59.057 52.381 3.84 0.00 0.00 3.13
2242 2249 1.594862 GATCCTGAAGCACGATTTCCG 59.405 52.381 0.00 0.00 45.44 4.30
2243 2250 1.019278 TCCTGAAGCACGATTTCCGC 61.019 55.000 0.00 0.00 43.32 5.54
2244 2251 1.059369 CTGAAGCACGATTTCCGCG 59.941 57.895 0.00 0.00 43.32 6.46
2245 2252 2.276680 GAAGCACGATTTCCGCGC 60.277 61.111 0.00 0.00 45.81 6.86
2246 2253 3.718480 GAAGCACGATTTCCGCGCC 62.718 63.158 0.00 0.00 46.57 6.53
2263 2270 4.843624 CCCCCTGACCAAAACCTC 57.156 61.111 0.00 0.00 0.00 3.85
2264 2271 1.076727 CCCCCTGACCAAAACCTCC 59.923 63.158 0.00 0.00 0.00 4.30
2265 2272 1.076727 CCCCTGACCAAAACCTCCC 59.923 63.158 0.00 0.00 0.00 4.30
2266 2273 1.725169 CCCCTGACCAAAACCTCCCA 61.725 60.000 0.00 0.00 0.00 4.37
2267 2274 0.539669 CCCTGACCAAAACCTCCCAC 60.540 60.000 0.00 0.00 0.00 4.61
2268 2275 0.184933 CCTGACCAAAACCTCCCACA 59.815 55.000 0.00 0.00 0.00 4.17
2269 2276 1.203050 CCTGACCAAAACCTCCCACAT 60.203 52.381 0.00 0.00 0.00 3.21
2270 2277 2.597455 CTGACCAAAACCTCCCACATT 58.403 47.619 0.00 0.00 0.00 2.71
2271 2278 3.499563 CCTGACCAAAACCTCCCACATTA 60.500 47.826 0.00 0.00 0.00 1.90
2272 2279 3.758554 CTGACCAAAACCTCCCACATTAG 59.241 47.826 0.00 0.00 0.00 1.73
2273 2280 3.089284 GACCAAAACCTCCCACATTAGG 58.911 50.000 0.00 0.00 38.93 2.69
2274 2281 2.719705 ACCAAAACCTCCCACATTAGGA 59.280 45.455 0.00 0.00 36.66 2.94
2275 2282 3.336694 ACCAAAACCTCCCACATTAGGAT 59.663 43.478 0.00 0.00 36.66 3.24
2276 2283 4.202781 ACCAAAACCTCCCACATTAGGATT 60.203 41.667 0.00 0.00 36.66 3.01
2277 2284 4.160252 CCAAAACCTCCCACATTAGGATTG 59.840 45.833 0.00 0.00 36.66 2.67
2278 2285 2.736670 ACCTCCCACATTAGGATTGC 57.263 50.000 0.00 0.00 36.66 3.56
2279 2286 2.208872 ACCTCCCACATTAGGATTGCT 58.791 47.619 0.00 0.00 36.66 3.91
2280 2287 2.582636 ACCTCCCACATTAGGATTGCTT 59.417 45.455 0.00 0.00 36.66 3.91
2281 2288 2.954318 CCTCCCACATTAGGATTGCTTG 59.046 50.000 0.00 0.00 34.58 4.01
2282 2289 3.624777 CTCCCACATTAGGATTGCTTGT 58.375 45.455 0.00 0.00 31.48 3.16
2283 2290 4.019174 CTCCCACATTAGGATTGCTTGTT 58.981 43.478 0.00 0.00 31.48 2.83
2284 2291 5.186256 TCCCACATTAGGATTGCTTGTTA 57.814 39.130 0.00 0.00 0.00 2.41
2285 2292 5.575157 TCCCACATTAGGATTGCTTGTTAA 58.425 37.500 0.00 0.00 0.00 2.01
2286 2293 6.194235 TCCCACATTAGGATTGCTTGTTAAT 58.806 36.000 0.00 0.00 0.00 1.40
2287 2294 6.096705 TCCCACATTAGGATTGCTTGTTAATG 59.903 38.462 0.00 0.00 37.60 1.90
2288 2295 6.275335 CCACATTAGGATTGCTTGTTAATGG 58.725 40.000 7.27 0.00 36.51 3.16
2289 2296 6.127366 CCACATTAGGATTGCTTGTTAATGGT 60.127 38.462 7.27 0.00 36.51 3.55
2290 2297 7.322664 CACATTAGGATTGCTTGTTAATGGTT 58.677 34.615 7.27 0.00 36.51 3.67
2291 2298 7.276218 CACATTAGGATTGCTTGTTAATGGTTG 59.724 37.037 7.27 0.00 36.51 3.77
2292 2299 7.178274 ACATTAGGATTGCTTGTTAATGGTTGA 59.822 33.333 7.27 0.00 36.51 3.18
2293 2300 7.716799 TTAGGATTGCTTGTTAATGGTTGAT 57.283 32.000 0.00 0.00 0.00 2.57
2294 2301 6.212888 AGGATTGCTTGTTAATGGTTGATC 57.787 37.500 0.00 0.00 0.00 2.92
2295 2302 5.716228 AGGATTGCTTGTTAATGGTTGATCA 59.284 36.000 0.00 0.00 0.00 2.92
2296 2303 6.211184 AGGATTGCTTGTTAATGGTTGATCAA 59.789 34.615 3.38 3.38 0.00 2.57
2297 2304 6.532657 GGATTGCTTGTTAATGGTTGATCAAG 59.467 38.462 8.80 0.00 36.42 3.02
2301 2308 6.939551 CTTGTTAATGGTTGATCAAGCTTG 57.060 37.500 31.37 20.81 39.38 4.01
2302 2309 6.647334 TTGTTAATGGTTGATCAAGCTTGA 57.353 33.333 30.23 30.23 42.14 3.02
2312 2319 2.442236 TCAAGCTTGATGGATTCCCC 57.558 50.000 25.16 0.00 31.01 4.81
2313 2320 1.063717 TCAAGCTTGATGGATTCCCCC 60.064 52.381 25.16 0.00 31.01 5.40
2314 2321 1.063417 CAAGCTTGATGGATTCCCCCT 60.063 52.381 22.31 0.00 0.00 4.79
2315 2322 0.849417 AGCTTGATGGATTCCCCCTC 59.151 55.000 0.00 0.00 0.00 4.30
2316 2323 0.849417 GCTTGATGGATTCCCCCTCT 59.151 55.000 0.00 0.00 31.62 3.69
2317 2324 1.478288 GCTTGATGGATTCCCCCTCTG 60.478 57.143 0.00 0.00 31.62 3.35
2318 2325 2.130193 CTTGATGGATTCCCCCTCTGA 58.870 52.381 0.00 0.00 31.62 3.27
2319 2326 2.285275 TGATGGATTCCCCCTCTGAA 57.715 50.000 0.00 0.00 31.62 3.02
2320 2327 2.572340 TGATGGATTCCCCCTCTGAAA 58.428 47.619 0.00 0.00 31.62 2.69
2321 2328 2.242196 TGATGGATTCCCCCTCTGAAAC 59.758 50.000 0.00 0.00 31.62 2.78
2322 2329 1.753903 TGGATTCCCCCTCTGAAACA 58.246 50.000 0.00 0.00 0.00 2.83
2323 2330 2.069775 TGGATTCCCCCTCTGAAACAA 58.930 47.619 0.00 0.00 0.00 2.83
2324 2331 2.041620 TGGATTCCCCCTCTGAAACAAG 59.958 50.000 0.00 0.00 0.00 3.16
2325 2332 2.308866 GGATTCCCCCTCTGAAACAAGA 59.691 50.000 0.00 0.00 0.00 3.02
2326 2333 3.245264 GGATTCCCCCTCTGAAACAAGAA 60.245 47.826 0.00 0.00 0.00 2.52
2327 2334 3.508845 TTCCCCCTCTGAAACAAGAAG 57.491 47.619 0.00 0.00 0.00 2.85
2328 2335 2.418669 TCCCCCTCTGAAACAAGAAGT 58.581 47.619 0.00 0.00 0.00 3.01
2329 2336 2.783510 TCCCCCTCTGAAACAAGAAGTT 59.216 45.455 0.00 0.00 43.89 2.66
2330 2337 3.149981 CCCCCTCTGAAACAAGAAGTTC 58.850 50.000 0.00 0.00 40.26 3.01
2331 2338 3.181439 CCCCCTCTGAAACAAGAAGTTCT 60.181 47.826 0.00 0.00 40.26 3.01
2332 2339 3.817647 CCCCTCTGAAACAAGAAGTTCTG 59.182 47.826 6.06 3.62 40.26 3.02
2333 2340 3.817647 CCCTCTGAAACAAGAAGTTCTGG 59.182 47.826 6.06 5.85 40.26 3.86
2334 2341 4.455606 CCTCTGAAACAAGAAGTTCTGGT 58.544 43.478 7.12 7.12 40.26 4.00
2335 2342 4.513318 CCTCTGAAACAAGAAGTTCTGGTC 59.487 45.833 13.44 2.99 40.26 4.02
2336 2343 4.451900 TCTGAAACAAGAAGTTCTGGTCC 58.548 43.478 13.44 9.12 40.26 4.46
2337 2344 3.202906 TGAAACAAGAAGTTCTGGTCCG 58.797 45.455 13.44 0.00 40.26 4.79
2338 2345 2.256117 AACAAGAAGTTCTGGTCCGG 57.744 50.000 13.44 0.00 34.74 5.14
2339 2346 0.396811 ACAAGAAGTTCTGGTCCGGG 59.603 55.000 7.12 0.00 0.00 5.73
2340 2347 0.685097 CAAGAAGTTCTGGTCCGGGA 59.315 55.000 6.06 0.00 0.00 5.14
2341 2348 0.977395 AAGAAGTTCTGGTCCGGGAG 59.023 55.000 6.06 0.00 0.00 4.30
2360 2367 7.834068 CGGGAGGTATAATATCAATCACTTG 57.166 40.000 0.00 0.00 0.00 3.16
2361 2368 6.818644 CGGGAGGTATAATATCAATCACTTGG 59.181 42.308 0.00 0.00 32.95 3.61
2362 2369 6.599638 GGGAGGTATAATATCAATCACTTGGC 59.400 42.308 0.00 0.00 32.95 4.52
2363 2370 6.313905 GGAGGTATAATATCAATCACTTGGCG 59.686 42.308 0.00 0.00 32.95 5.69
2364 2371 6.769512 AGGTATAATATCAATCACTTGGCGT 58.230 36.000 0.00 0.00 32.95 5.68
2365 2372 6.874134 AGGTATAATATCAATCACTTGGCGTC 59.126 38.462 0.00 0.00 32.95 5.19
2366 2373 6.092259 GGTATAATATCAATCACTTGGCGTCC 59.908 42.308 0.00 0.00 32.95 4.79
2367 2374 3.558931 ATATCAATCACTTGGCGTCCA 57.441 42.857 0.00 0.00 32.95 4.02
2368 2375 2.425143 ATCAATCACTTGGCGTCCAT 57.575 45.000 0.00 0.00 31.53 3.41
2369 2376 1.737838 TCAATCACTTGGCGTCCATC 58.262 50.000 0.00 0.00 31.53 3.51
2370 2377 1.278985 TCAATCACTTGGCGTCCATCT 59.721 47.619 0.00 0.00 31.53 2.90
2371 2378 1.399440 CAATCACTTGGCGTCCATCTG 59.601 52.381 0.00 0.00 31.53 2.90
2372 2379 0.904649 ATCACTTGGCGTCCATCTGA 59.095 50.000 0.00 4.50 31.53 3.27
2373 2380 0.904649 TCACTTGGCGTCCATCTGAT 59.095 50.000 0.00 0.00 31.53 2.90
2374 2381 1.012086 CACTTGGCGTCCATCTGATG 58.988 55.000 10.71 10.71 31.53 3.07
2382 2389 2.558378 CGTCCATCTGATGCATCAACT 58.442 47.619 28.39 16.39 36.18 3.16
2383 2390 3.721035 CGTCCATCTGATGCATCAACTA 58.279 45.455 28.39 17.60 36.18 2.24
2384 2391 4.313282 CGTCCATCTGATGCATCAACTAT 58.687 43.478 28.39 18.91 36.18 2.12
2385 2392 4.151867 CGTCCATCTGATGCATCAACTATG 59.848 45.833 28.39 26.57 36.18 2.23
2386 2393 4.454847 GTCCATCTGATGCATCAACTATGG 59.545 45.833 34.17 34.17 40.00 2.74
2387 2394 4.348754 TCCATCTGATGCATCAACTATGGA 59.651 41.667 36.10 36.10 42.35 3.41
2389 2396 6.214005 TCCATCTGATGCATCAACTATGGATA 59.786 38.462 36.10 26.33 45.73 2.59
2390 2397 7.054751 CCATCTGATGCATCAACTATGGATAT 58.945 38.462 35.32 15.81 45.73 1.63
2391 2398 7.556635 CCATCTGATGCATCAACTATGGATATT 59.443 37.037 35.32 15.29 45.73 1.28
2392 2399 8.957466 CATCTGATGCATCAACTATGGATATTT 58.043 33.333 28.39 5.32 45.73 1.40
2393 2400 8.557592 TCTGATGCATCAACTATGGATATTTC 57.442 34.615 28.39 0.00 45.73 2.17
2394 2401 8.158789 TCTGATGCATCAACTATGGATATTTCA 58.841 33.333 28.39 2.80 45.73 2.69
2395 2402 8.873186 TGATGCATCAACTATGGATATTTCAT 57.127 30.769 26.87 0.00 45.73 2.57
2396 2403 9.962809 TGATGCATCAACTATGGATATTTCATA 57.037 29.630 26.87 0.00 45.73 2.15
2398 2405 8.565896 TGCATCAACTATGGATATTTCATACC 57.434 34.615 0.00 0.00 35.99 2.73
2399 2406 7.611467 TGCATCAACTATGGATATTTCATACCC 59.389 37.037 0.00 0.00 35.99 3.69
2400 2407 7.067494 GCATCAACTATGGATATTTCATACCCC 59.933 40.741 0.00 0.00 35.99 4.95
2401 2408 7.027874 TCAACTATGGATATTTCATACCCCC 57.972 40.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 6.866480 TGAGAGAGCTTTTGTGTTGAAAATT 58.134 32.000 0.00 0.00 0.00 1.82
278 279 5.367945 ACGATTTGTGTGGGATAAGGTAT 57.632 39.130 0.00 0.00 0.00 2.73
341 342 0.035056 CCCTCGGAAATGCTCTGGTT 60.035 55.000 0.00 0.00 0.00 3.67
350 351 1.005924 AGTGGATTTGCCCTCGGAAAT 59.994 47.619 0.00 0.00 34.97 2.17
514 515 2.548057 AGTACTCAACACAATTGCCACG 59.452 45.455 5.05 0.00 0.00 4.94
1183 1189 5.885912 TGGCTCCCACATAAATAAGAAGTTC 59.114 40.000 0.00 0.00 0.00 3.01
1337 1343 4.765856 ACCACGATGTATCTGGGATAGTAC 59.234 45.833 12.06 0.00 32.74 2.73
1402 1408 9.967451 TTGTTGAACATTATTTATGAGACCCTA 57.033 29.630 0.00 0.00 37.69 3.53
1711 1717 8.375608 ACTCCTTATCAATCTCGATTCATTTG 57.624 34.615 0.00 0.00 0.00 2.32
1792 1798 5.934043 CGGCTTGTGATCAATCCATAGATAA 59.066 40.000 0.00 0.00 39.11 1.75
2047 2054 5.455392 CCTCGATTTATTGGCAATTGCTAG 58.545 41.667 28.42 10.16 41.70 3.42
2048 2055 4.261572 GCCTCGATTTATTGGCAATTGCTA 60.262 41.667 28.42 21.46 44.34 3.49
2049 2056 3.491447 GCCTCGATTTATTGGCAATTGCT 60.491 43.478 28.42 12.82 44.34 3.91
2050 2057 2.796593 GCCTCGATTTATTGGCAATTGC 59.203 45.455 22.47 22.47 44.34 3.56
2056 2063 5.041287 GGTAAAAAGCCTCGATTTATTGGC 58.959 41.667 3.02 3.02 45.21 4.52
2057 2064 6.202516 TGGTAAAAAGCCTCGATTTATTGG 57.797 37.500 0.00 0.00 0.00 3.16
2058 2065 7.312899 AGTTGGTAAAAAGCCTCGATTTATTG 58.687 34.615 0.00 0.00 0.00 1.90
2059 2066 7.462571 AGTTGGTAAAAAGCCTCGATTTATT 57.537 32.000 0.00 0.00 0.00 1.40
2060 2067 7.175990 TCAAGTTGGTAAAAAGCCTCGATTTAT 59.824 33.333 2.34 0.00 0.00 1.40
2061 2068 6.487331 TCAAGTTGGTAAAAAGCCTCGATTTA 59.513 34.615 2.34 0.00 0.00 1.40
2062 2069 5.300792 TCAAGTTGGTAAAAAGCCTCGATTT 59.699 36.000 2.34 0.00 0.00 2.17
2063 2070 4.825085 TCAAGTTGGTAAAAAGCCTCGATT 59.175 37.500 2.34 0.00 0.00 3.34
2064 2071 4.394729 TCAAGTTGGTAAAAAGCCTCGAT 58.605 39.130 2.34 0.00 0.00 3.59
2065 2072 3.811083 TCAAGTTGGTAAAAAGCCTCGA 58.189 40.909 2.34 0.00 0.00 4.04
2066 2073 4.475944 CATCAAGTTGGTAAAAAGCCTCG 58.524 43.478 2.34 0.00 0.00 4.63
2067 2074 4.809673 CCATCAAGTTGGTAAAAAGCCTC 58.190 43.478 2.34 0.00 31.74 4.70
2068 2075 4.871933 CCATCAAGTTGGTAAAAAGCCT 57.128 40.909 2.34 0.00 31.74 4.58
2078 2085 4.662145 GCGATTTCTTACCATCAAGTTGG 58.338 43.478 2.34 0.00 42.82 3.77
2079 2086 4.092821 TCGCGATTTCTTACCATCAAGTTG 59.907 41.667 3.71 0.00 0.00 3.16
2080 2087 4.250464 TCGCGATTTCTTACCATCAAGTT 58.750 39.130 3.71 0.00 0.00 2.66
2081 2088 3.857052 TCGCGATTTCTTACCATCAAGT 58.143 40.909 3.71 0.00 0.00 3.16
2082 2089 4.026475 GTCTCGCGATTTCTTACCATCAAG 60.026 45.833 10.36 0.00 0.00 3.02
2083 2090 3.863424 GTCTCGCGATTTCTTACCATCAA 59.137 43.478 10.36 0.00 0.00 2.57
2084 2091 3.444916 GTCTCGCGATTTCTTACCATCA 58.555 45.455 10.36 0.00 0.00 3.07
2085 2092 2.795470 GGTCTCGCGATTTCTTACCATC 59.205 50.000 10.36 0.00 0.00 3.51
2086 2093 2.431057 AGGTCTCGCGATTTCTTACCAT 59.569 45.455 10.36 0.00 0.00 3.55
2087 2094 1.822990 AGGTCTCGCGATTTCTTACCA 59.177 47.619 10.36 0.00 0.00 3.25
2088 2095 2.580966 AGGTCTCGCGATTTCTTACC 57.419 50.000 10.36 10.71 0.00 2.85
2089 2096 4.548991 TCTAGGTCTCGCGATTTCTTAC 57.451 45.455 10.36 1.26 0.00 2.34
2090 2097 5.571784 TTTCTAGGTCTCGCGATTTCTTA 57.428 39.130 10.36 3.27 0.00 2.10
2091 2098 4.451629 TTTCTAGGTCTCGCGATTTCTT 57.548 40.909 10.36 2.12 0.00 2.52
2092 2099 4.657436 ATTTCTAGGTCTCGCGATTTCT 57.343 40.909 10.36 9.82 0.00 2.52
2093 2100 4.804139 TGAATTTCTAGGTCTCGCGATTTC 59.196 41.667 10.36 2.77 0.00 2.17
2094 2101 4.755411 TGAATTTCTAGGTCTCGCGATTT 58.245 39.130 10.36 0.00 0.00 2.17
2095 2102 4.386867 TGAATTTCTAGGTCTCGCGATT 57.613 40.909 10.36 0.00 0.00 3.34
2096 2103 4.592485 ATGAATTTCTAGGTCTCGCGAT 57.408 40.909 10.36 0.00 0.00 4.58
2097 2104 4.386867 AATGAATTTCTAGGTCTCGCGA 57.613 40.909 9.26 9.26 0.00 5.87
2098 2105 4.317418 CGAAATGAATTTCTAGGTCTCGCG 60.317 45.833 0.00 0.00 42.96 5.87
2099 2106 4.567159 ACGAAATGAATTTCTAGGTCTCGC 59.433 41.667 12.61 0.00 42.96 5.03
2100 2107 6.750501 TGTACGAAATGAATTTCTAGGTCTCG 59.249 38.462 12.61 2.16 42.96 4.04
2101 2108 8.475331 TTGTACGAAATGAATTTCTAGGTCTC 57.525 34.615 12.61 3.79 42.96 3.36
2102 2109 9.449719 AATTGTACGAAATGAATTTCTAGGTCT 57.550 29.630 12.61 0.00 42.96 3.85
2103 2110 9.490663 CAATTGTACGAAATGAATTTCTAGGTC 57.509 33.333 12.61 2.16 42.96 3.85
2104 2111 9.226606 TCAATTGTACGAAATGAATTTCTAGGT 57.773 29.630 12.61 6.99 42.96 3.08
2107 2114 9.834628 GGTTCAATTGTACGAAATGAATTTCTA 57.165 29.630 14.42 3.61 42.96 2.10
2108 2115 8.576442 AGGTTCAATTGTACGAAATGAATTTCT 58.424 29.630 14.42 10.91 42.96 2.52
2109 2116 8.742554 AGGTTCAATTGTACGAAATGAATTTC 57.257 30.769 14.42 5.81 42.00 2.17
2110 2117 9.541143 AAAGGTTCAATTGTACGAAATGAATTT 57.459 25.926 14.42 10.54 0.00 1.82
2111 2118 9.541143 AAAAGGTTCAATTGTACGAAATGAATT 57.459 25.926 14.42 6.54 0.00 2.17
2112 2119 9.191995 GAAAAGGTTCAATTGTACGAAATGAAT 57.808 29.630 14.42 2.90 33.61 2.57
2113 2120 8.191446 TGAAAAGGTTCAATTGTACGAAATGAA 58.809 29.630 5.13 9.51 40.87 2.57
2114 2121 7.708051 TGAAAAGGTTCAATTGTACGAAATGA 58.292 30.769 5.13 0.00 40.87 2.57
2115 2122 7.922505 TGAAAAGGTTCAATTGTACGAAATG 57.077 32.000 5.13 0.00 40.87 2.32
2128 2135 8.555361 CAAAAAGAAACAGTTTGAAAAGGTTCA 58.445 29.630 2.34 0.00 42.12 3.18
2129 2136 8.769891 TCAAAAAGAAACAGTTTGAAAAGGTTC 58.230 29.630 2.34 2.31 38.09 3.62
2130 2137 8.669946 TCAAAAAGAAACAGTTTGAAAAGGTT 57.330 26.923 2.34 0.00 38.09 3.50
2131 2138 8.147704 TCTCAAAAAGAAACAGTTTGAAAAGGT 58.852 29.630 2.34 0.00 39.92 3.50
2132 2139 8.532977 TCTCAAAAAGAAACAGTTTGAAAAGG 57.467 30.769 2.34 0.00 39.92 3.11
2133 2140 9.797473 GTTCTCAAAAAGAAACAGTTTGAAAAG 57.203 29.630 2.34 0.00 45.50 2.27
2170 2177 4.597404 TTGCATCAGTTATTTTGGCACA 57.403 36.364 0.00 0.00 0.00 4.57
2171 2178 5.229423 TCTTTGCATCAGTTATTTTGGCAC 58.771 37.500 0.00 0.00 0.00 5.01
2172 2179 5.465532 TCTTTGCATCAGTTATTTTGGCA 57.534 34.783 0.00 0.00 0.00 4.92
2173 2180 6.158598 TCTTCTTTGCATCAGTTATTTTGGC 58.841 36.000 0.00 0.00 0.00 4.52
2174 2181 7.652909 TGTTCTTCTTTGCATCAGTTATTTTGG 59.347 33.333 0.00 0.00 0.00 3.28
2175 2182 8.578308 TGTTCTTCTTTGCATCAGTTATTTTG 57.422 30.769 0.00 0.00 0.00 2.44
2176 2183 9.598517 TTTGTTCTTCTTTGCATCAGTTATTTT 57.401 25.926 0.00 0.00 0.00 1.82
2177 2184 9.598517 TTTTGTTCTTCTTTGCATCAGTTATTT 57.401 25.926 0.00 0.00 0.00 1.40
2178 2185 9.252962 CTTTTGTTCTTCTTTGCATCAGTTATT 57.747 29.630 0.00 0.00 0.00 1.40
2179 2186 7.869429 CCTTTTGTTCTTCTTTGCATCAGTTAT 59.131 33.333 0.00 0.00 0.00 1.89
2180 2187 7.202526 CCTTTTGTTCTTCTTTGCATCAGTTA 58.797 34.615 0.00 0.00 0.00 2.24
2181 2188 6.044682 CCTTTTGTTCTTCTTTGCATCAGTT 58.955 36.000 0.00 0.00 0.00 3.16
2182 2189 5.594926 CCTTTTGTTCTTCTTTGCATCAGT 58.405 37.500 0.00 0.00 0.00 3.41
2183 2190 4.446719 GCCTTTTGTTCTTCTTTGCATCAG 59.553 41.667 0.00 0.00 0.00 2.90
2184 2191 4.370917 GCCTTTTGTTCTTCTTTGCATCA 58.629 39.130 0.00 0.00 0.00 3.07
2185 2192 3.742882 GGCCTTTTGTTCTTCTTTGCATC 59.257 43.478 0.00 0.00 0.00 3.91
2186 2193 3.389002 AGGCCTTTTGTTCTTCTTTGCAT 59.611 39.130 0.00 0.00 0.00 3.96
2187 2194 2.765699 AGGCCTTTTGTTCTTCTTTGCA 59.234 40.909 0.00 0.00 0.00 4.08
2188 2195 3.459232 AGGCCTTTTGTTCTTCTTTGC 57.541 42.857 0.00 0.00 0.00 3.68
2189 2196 4.122046 CCAAGGCCTTTTGTTCTTCTTTG 58.878 43.478 17.61 0.00 0.00 2.77
2190 2197 4.030216 TCCAAGGCCTTTTGTTCTTCTTT 58.970 39.130 17.61 0.00 0.00 2.52
2191 2198 3.384789 GTCCAAGGCCTTTTGTTCTTCTT 59.615 43.478 17.61 0.00 0.00 2.52
2192 2199 2.959030 GTCCAAGGCCTTTTGTTCTTCT 59.041 45.455 17.61 0.00 0.00 2.85
2193 2200 2.693074 TGTCCAAGGCCTTTTGTTCTTC 59.307 45.455 17.61 1.53 0.00 2.87
2194 2201 2.430694 GTGTCCAAGGCCTTTTGTTCTT 59.569 45.455 17.61 0.00 0.00 2.52
2195 2202 2.031870 GTGTCCAAGGCCTTTTGTTCT 58.968 47.619 17.61 0.00 0.00 3.01
2196 2203 1.269051 CGTGTCCAAGGCCTTTTGTTC 60.269 52.381 17.61 5.98 0.00 3.18
2197 2204 0.744281 CGTGTCCAAGGCCTTTTGTT 59.256 50.000 17.61 0.00 0.00 2.83
2198 2205 0.395173 ACGTGTCCAAGGCCTTTTGT 60.395 50.000 17.61 5.24 0.00 2.83
2199 2206 1.535462 CTACGTGTCCAAGGCCTTTTG 59.465 52.381 17.61 10.56 0.00 2.44
2200 2207 1.142262 ACTACGTGTCCAAGGCCTTTT 59.858 47.619 17.61 0.00 0.00 2.27
2201 2208 0.763035 ACTACGTGTCCAAGGCCTTT 59.237 50.000 17.61 1.31 0.00 3.11
2202 2209 0.034896 CACTACGTGTCCAAGGCCTT 59.965 55.000 13.78 13.78 0.00 4.35
2203 2210 1.671742 CACTACGTGTCCAAGGCCT 59.328 57.895 0.00 0.00 0.00 5.19
2204 2211 1.375523 CCACTACGTGTCCAAGGCC 60.376 63.158 0.00 0.00 0.00 5.19
2205 2212 0.249398 ATCCACTACGTGTCCAAGGC 59.751 55.000 0.00 0.00 0.00 4.35
2206 2213 1.134788 GGATCCACTACGTGTCCAAGG 60.135 57.143 6.95 0.00 31.59 3.61
2207 2214 1.825474 AGGATCCACTACGTGTCCAAG 59.175 52.381 15.82 0.00 33.05 3.61
2208 2215 1.548719 CAGGATCCACTACGTGTCCAA 59.451 52.381 15.82 0.00 33.05 3.53
2209 2216 1.182667 CAGGATCCACTACGTGTCCA 58.817 55.000 15.82 0.00 33.05 4.02
2210 2217 1.471119 TCAGGATCCACTACGTGTCC 58.529 55.000 15.82 0.00 31.45 4.02
2211 2218 2.735762 GCTTCAGGATCCACTACGTGTC 60.736 54.545 15.82 0.00 0.00 3.67
2212 2219 1.204941 GCTTCAGGATCCACTACGTGT 59.795 52.381 15.82 0.00 0.00 4.49
2213 2220 1.204704 TGCTTCAGGATCCACTACGTG 59.795 52.381 15.82 1.89 0.00 4.49
2214 2221 1.204941 GTGCTTCAGGATCCACTACGT 59.795 52.381 15.82 0.00 0.00 3.57
2215 2222 1.799181 CGTGCTTCAGGATCCACTACG 60.799 57.143 15.82 11.41 0.00 3.51
2216 2223 1.476891 TCGTGCTTCAGGATCCACTAC 59.523 52.381 15.82 3.24 0.00 2.73
2217 2224 1.847328 TCGTGCTTCAGGATCCACTA 58.153 50.000 15.82 0.00 0.00 2.74
2218 2225 1.198713 ATCGTGCTTCAGGATCCACT 58.801 50.000 15.82 0.00 34.48 4.00
2219 2226 2.029838 AATCGTGCTTCAGGATCCAC 57.970 50.000 15.82 0.54 37.89 4.02
2220 2227 2.632377 GAAATCGTGCTTCAGGATCCA 58.368 47.619 15.82 0.00 37.89 3.41
2221 2228 1.943340 GGAAATCGTGCTTCAGGATCC 59.057 52.381 2.48 2.48 37.89 3.36
2222 2229 1.594862 CGGAAATCGTGCTTCAGGATC 59.405 52.381 2.99 0.00 37.89 3.36
2223 2230 1.656652 CGGAAATCGTGCTTCAGGAT 58.343 50.000 0.00 0.00 40.09 3.24
2224 2231 1.019278 GCGGAAATCGTGCTTCAGGA 61.019 55.000 0.00 0.00 41.72 3.86
2225 2232 1.425428 GCGGAAATCGTGCTTCAGG 59.575 57.895 0.00 0.00 41.72 3.86
2226 2233 1.059369 CGCGGAAATCGTGCTTCAG 59.941 57.895 0.00 0.00 42.62 3.02
2227 2234 3.164576 CGCGGAAATCGTGCTTCA 58.835 55.556 0.00 0.00 42.62 3.02
2246 2253 1.076727 GGAGGTTTTGGTCAGGGGG 59.923 63.158 0.00 0.00 0.00 5.40
2247 2254 1.076727 GGGAGGTTTTGGTCAGGGG 59.923 63.158 0.00 0.00 0.00 4.79
2248 2255 0.539669 GTGGGAGGTTTTGGTCAGGG 60.540 60.000 0.00 0.00 0.00 4.45
2249 2256 0.184933 TGTGGGAGGTTTTGGTCAGG 59.815 55.000 0.00 0.00 0.00 3.86
2250 2257 2.292828 ATGTGGGAGGTTTTGGTCAG 57.707 50.000 0.00 0.00 0.00 3.51
2251 2258 2.765689 AATGTGGGAGGTTTTGGTCA 57.234 45.000 0.00 0.00 0.00 4.02
2252 2259 3.089284 CCTAATGTGGGAGGTTTTGGTC 58.911 50.000 0.00 0.00 0.00 4.02
2253 2260 2.719705 TCCTAATGTGGGAGGTTTTGGT 59.280 45.455 0.00 0.00 34.20 3.67
2254 2261 3.449746 TCCTAATGTGGGAGGTTTTGG 57.550 47.619 0.00 0.00 34.20 3.28
2255 2262 4.381932 GCAATCCTAATGTGGGAGGTTTTG 60.382 45.833 0.00 0.00 36.21 2.44
2256 2263 3.769300 GCAATCCTAATGTGGGAGGTTTT 59.231 43.478 0.00 0.00 36.21 2.43
2257 2264 3.011708 AGCAATCCTAATGTGGGAGGTTT 59.988 43.478 0.00 0.00 36.21 3.27
2258 2265 2.582636 AGCAATCCTAATGTGGGAGGTT 59.417 45.455 0.00 0.00 36.21 3.50
2259 2266 2.208872 AGCAATCCTAATGTGGGAGGT 58.791 47.619 0.00 0.00 36.21 3.85
2260 2267 2.954318 CAAGCAATCCTAATGTGGGAGG 59.046 50.000 0.00 0.00 36.21 4.30
2261 2268 3.624777 ACAAGCAATCCTAATGTGGGAG 58.375 45.455 0.00 0.00 36.21 4.30
2262 2269 3.737559 ACAAGCAATCCTAATGTGGGA 57.262 42.857 0.00 0.00 37.26 4.37
2263 2270 5.913137 TTAACAAGCAATCCTAATGTGGG 57.087 39.130 0.00 0.00 0.00 4.61
2264 2271 6.127366 ACCATTAACAAGCAATCCTAATGTGG 60.127 38.462 0.00 0.00 31.10 4.17
2265 2272 6.866480 ACCATTAACAAGCAATCCTAATGTG 58.134 36.000 0.00 0.00 31.10 3.21
2266 2273 7.178274 TCAACCATTAACAAGCAATCCTAATGT 59.822 33.333 0.00 0.00 31.10 2.71
2267 2274 7.546358 TCAACCATTAACAAGCAATCCTAATG 58.454 34.615 0.00 0.00 32.28 1.90
2268 2275 7.716799 TCAACCATTAACAAGCAATCCTAAT 57.283 32.000 0.00 0.00 0.00 1.73
2269 2276 7.395772 TGATCAACCATTAACAAGCAATCCTAA 59.604 33.333 0.00 0.00 0.00 2.69
2270 2277 6.889177 TGATCAACCATTAACAAGCAATCCTA 59.111 34.615 0.00 0.00 0.00 2.94
2271 2278 5.716228 TGATCAACCATTAACAAGCAATCCT 59.284 36.000 0.00 0.00 0.00 3.24
2272 2279 5.964758 TGATCAACCATTAACAAGCAATCC 58.035 37.500 0.00 0.00 0.00 3.01
2273 2280 7.515957 CTTGATCAACCATTAACAAGCAATC 57.484 36.000 3.38 0.00 0.00 2.67
2278 2285 6.680810 TCAAGCTTGATCAACCATTAACAAG 58.319 36.000 25.16 0.00 38.07 3.16
2279 2286 6.647334 TCAAGCTTGATCAACCATTAACAA 57.353 33.333 25.16 0.00 31.01 2.83
2280 2287 6.350361 CCATCAAGCTTGATCAACCATTAACA 60.350 38.462 33.95 7.99 45.62 2.41
2281 2288 6.038356 CCATCAAGCTTGATCAACCATTAAC 58.962 40.000 33.95 0.00 45.62 2.01
2282 2289 5.951148 TCCATCAAGCTTGATCAACCATTAA 59.049 36.000 33.95 8.63 45.62 1.40
2283 2290 5.508567 TCCATCAAGCTTGATCAACCATTA 58.491 37.500 33.95 13.59 45.62 1.90
2284 2291 4.346730 TCCATCAAGCTTGATCAACCATT 58.653 39.130 33.95 13.45 45.62 3.16
2285 2292 3.972133 TCCATCAAGCTTGATCAACCAT 58.028 40.909 33.95 14.18 45.62 3.55
2286 2293 3.438216 TCCATCAAGCTTGATCAACCA 57.562 42.857 33.95 16.07 45.62 3.67
2287 2294 4.202090 GGAATCCATCAAGCTTGATCAACC 60.202 45.833 33.95 26.20 45.62 3.77
2288 2295 4.202090 GGGAATCCATCAAGCTTGATCAAC 60.202 45.833 33.95 22.63 45.62 3.18
2289 2296 3.956199 GGGAATCCATCAAGCTTGATCAA 59.044 43.478 33.95 25.30 45.62 2.57
2290 2297 3.559069 GGGAATCCATCAAGCTTGATCA 58.441 45.455 33.95 24.62 45.62 2.92
2291 2298 2.889678 GGGGAATCCATCAAGCTTGATC 59.110 50.000 33.95 24.29 45.62 2.92
2293 2300 1.063717 GGGGGAATCCATCAAGCTTGA 60.064 52.381 30.23 30.23 42.14 3.02
2294 2301 1.063417 AGGGGGAATCCATCAAGCTTG 60.063 52.381 20.81 20.81 37.22 4.01
2295 2302 1.216427 GAGGGGGAATCCATCAAGCTT 59.784 52.381 0.09 0.00 45.15 3.74
2296 2303 0.849417 GAGGGGGAATCCATCAAGCT 59.151 55.000 0.09 0.00 45.15 3.74
2297 2304 3.428687 GAGGGGGAATCCATCAAGC 57.571 57.895 0.09 0.00 45.15 4.01
2301 2308 2.242196 TGTTTCAGAGGGGGAATCCATC 59.758 50.000 0.09 0.00 46.11 3.51
2302 2309 2.287584 TGTTTCAGAGGGGGAATCCAT 58.712 47.619 0.09 0.00 37.22 3.41
2303 2310 1.753903 TGTTTCAGAGGGGGAATCCA 58.246 50.000 0.09 0.00 37.22 3.41
2304 2311 2.308866 TCTTGTTTCAGAGGGGGAATCC 59.691 50.000 0.00 0.00 0.00 3.01
2305 2312 3.721087 TCTTGTTTCAGAGGGGGAATC 57.279 47.619 0.00 0.00 0.00 2.52
2306 2313 3.399305 ACTTCTTGTTTCAGAGGGGGAAT 59.601 43.478 0.00 0.00 0.00 3.01
2307 2314 2.783510 ACTTCTTGTTTCAGAGGGGGAA 59.216 45.455 0.00 0.00 0.00 3.97
2308 2315 2.418669 ACTTCTTGTTTCAGAGGGGGA 58.581 47.619 0.00 0.00 0.00 4.81
2309 2316 2.959465 ACTTCTTGTTTCAGAGGGGG 57.041 50.000 0.00 0.00 0.00 5.40
2310 2317 3.817647 CAGAACTTCTTGTTTCAGAGGGG 59.182 47.826 0.00 0.00 39.30 4.79
2311 2318 3.817647 CCAGAACTTCTTGTTTCAGAGGG 59.182 47.826 0.00 0.00 39.30 4.30
2312 2319 4.455606 ACCAGAACTTCTTGTTTCAGAGG 58.544 43.478 0.00 0.00 39.30 3.69
2313 2320 4.513318 GGACCAGAACTTCTTGTTTCAGAG 59.487 45.833 0.00 0.00 39.30 3.35
2314 2321 4.451900 GGACCAGAACTTCTTGTTTCAGA 58.548 43.478 0.00 0.00 39.30 3.27
2315 2322 3.248602 CGGACCAGAACTTCTTGTTTCAG 59.751 47.826 0.00 0.00 39.30 3.02
2316 2323 3.202906 CGGACCAGAACTTCTTGTTTCA 58.797 45.455 0.00 0.00 39.30 2.69
2317 2324 2.548480 CCGGACCAGAACTTCTTGTTTC 59.452 50.000 0.00 0.00 39.30 2.78
2318 2325 2.572290 CCGGACCAGAACTTCTTGTTT 58.428 47.619 0.00 0.00 39.30 2.83
2319 2326 1.202770 CCCGGACCAGAACTTCTTGTT 60.203 52.381 0.73 0.00 42.38 2.83
2320 2327 0.396811 CCCGGACCAGAACTTCTTGT 59.603 55.000 0.73 0.00 0.00 3.16
2321 2328 0.685097 TCCCGGACCAGAACTTCTTG 59.315 55.000 0.73 0.00 0.00 3.02
2322 2329 0.977395 CTCCCGGACCAGAACTTCTT 59.023 55.000 0.73 0.00 0.00 2.52
2323 2330 0.905337 CCTCCCGGACCAGAACTTCT 60.905 60.000 0.73 0.00 0.00 2.85
2324 2331 1.192803 ACCTCCCGGACCAGAACTTC 61.193 60.000 0.73 0.00 0.00 3.01
2325 2332 0.115745 TACCTCCCGGACCAGAACTT 59.884 55.000 0.73 0.00 0.00 2.66
2326 2333 0.338814 ATACCTCCCGGACCAGAACT 59.661 55.000 0.73 0.00 0.00 3.01
2327 2334 2.077687 TATACCTCCCGGACCAGAAC 57.922 55.000 0.73 0.00 0.00 3.01
2328 2335 2.852714 TTATACCTCCCGGACCAGAA 57.147 50.000 0.73 0.00 0.00 3.02
2329 2336 4.044952 TGATATTATACCTCCCGGACCAGA 59.955 45.833 0.73 0.00 0.00 3.86
2330 2337 4.350245 TGATATTATACCTCCCGGACCAG 58.650 47.826 0.73 0.00 0.00 4.00
2331 2338 4.407329 TGATATTATACCTCCCGGACCA 57.593 45.455 0.73 0.00 0.00 4.02
2332 2339 5.424252 TGATTGATATTATACCTCCCGGACC 59.576 44.000 0.73 0.00 0.00 4.46
2333 2340 6.154706 AGTGATTGATATTATACCTCCCGGAC 59.845 42.308 0.73 0.00 0.00 4.79
2334 2341 6.261435 AGTGATTGATATTATACCTCCCGGA 58.739 40.000 0.73 0.00 0.00 5.14
2335 2342 6.546428 AGTGATTGATATTATACCTCCCGG 57.454 41.667 0.00 0.00 0.00 5.73
2336 2343 6.818644 CCAAGTGATTGATATTATACCTCCCG 59.181 42.308 0.00 0.00 0.00 5.14
2337 2344 6.599638 GCCAAGTGATTGATATTATACCTCCC 59.400 42.308 0.00 0.00 0.00 4.30
2338 2345 6.313905 CGCCAAGTGATTGATATTATACCTCC 59.686 42.308 0.00 0.00 0.00 4.30
2339 2346 6.874134 ACGCCAAGTGATTGATATTATACCTC 59.126 38.462 0.00 0.00 0.00 3.85
2340 2347 6.769512 ACGCCAAGTGATTGATATTATACCT 58.230 36.000 0.00 0.00 0.00 3.08
2341 2348 6.092259 GGACGCCAAGTGATTGATATTATACC 59.908 42.308 0.00 0.00 0.00 2.73
2342 2349 6.649141 TGGACGCCAAGTGATTGATATTATAC 59.351 38.462 0.00 0.00 0.00 1.47
2343 2350 6.764379 TGGACGCCAAGTGATTGATATTATA 58.236 36.000 0.00 0.00 0.00 0.98
2344 2351 5.620206 TGGACGCCAAGTGATTGATATTAT 58.380 37.500 0.00 0.00 0.00 1.28
2345 2352 5.029807 TGGACGCCAAGTGATTGATATTA 57.970 39.130 0.00 0.00 0.00 0.98
2346 2353 3.884895 TGGACGCCAAGTGATTGATATT 58.115 40.909 0.00 0.00 0.00 1.28
2347 2354 3.558931 TGGACGCCAAGTGATTGATAT 57.441 42.857 0.00 0.00 0.00 1.63
2348 2355 3.134623 AGATGGACGCCAAGTGATTGATA 59.865 43.478 2.68 0.00 36.95 2.15
2349 2356 2.092753 AGATGGACGCCAAGTGATTGAT 60.093 45.455 2.68 0.00 36.95 2.57
2350 2357 1.278985 AGATGGACGCCAAGTGATTGA 59.721 47.619 2.68 0.00 36.95 2.57
2351 2358 1.399440 CAGATGGACGCCAAGTGATTG 59.601 52.381 2.68 0.00 36.95 2.67
2352 2359 1.278985 TCAGATGGACGCCAAGTGATT 59.721 47.619 2.68 0.00 36.95 2.57
2353 2360 0.904649 TCAGATGGACGCCAAGTGAT 59.095 50.000 2.68 0.00 36.95 3.06
2354 2361 0.904649 ATCAGATGGACGCCAAGTGA 59.095 50.000 12.57 12.57 36.95 3.41
2355 2362 1.012086 CATCAGATGGACGCCAAGTG 58.988 55.000 1.95 4.16 36.95 3.16
2356 2363 0.745845 GCATCAGATGGACGCCAAGT 60.746 55.000 12.54 0.00 36.95 3.16
2357 2364 0.745486 TGCATCAGATGGACGCCAAG 60.745 55.000 12.54 0.00 36.95 3.61
2358 2365 0.107066 ATGCATCAGATGGACGCCAA 60.107 50.000 12.54 0.00 36.95 4.52
2359 2366 0.533531 GATGCATCAGATGGACGCCA 60.534 55.000 21.92 1.54 38.19 5.69
2360 2367 0.533531 TGATGCATCAGATGGACGCC 60.534 55.000 25.42 3.61 31.88 5.68
2361 2368 1.003116 GTTGATGCATCAGATGGACGC 60.003 52.381 27.25 6.15 38.19 5.19
2362 2369 2.558378 AGTTGATGCATCAGATGGACG 58.442 47.619 27.25 0.00 38.19 4.79
2363 2370 4.454847 CCATAGTTGATGCATCAGATGGAC 59.545 45.833 35.97 28.19 41.27 4.02
2364 2371 4.348754 TCCATAGTTGATGCATCAGATGGA 59.651 41.667 36.71 36.71 43.04 3.41
2365 2372 4.648651 TCCATAGTTGATGCATCAGATGG 58.351 43.478 34.81 34.81 40.75 3.51
2366 2373 8.507524 AATATCCATAGTTGATGCATCAGATG 57.492 34.615 27.25 26.63 38.19 2.90
2367 2374 9.175312 GAAATATCCATAGTTGATGCATCAGAT 57.825 33.333 27.25 24.61 38.19 2.90
2368 2375 8.158789 TGAAATATCCATAGTTGATGCATCAGA 58.841 33.333 27.25 20.26 38.19 3.27
2369 2376 8.331730 TGAAATATCCATAGTTGATGCATCAG 57.668 34.615 27.25 16.23 38.19 2.90
2370 2377 8.873186 ATGAAATATCCATAGTTGATGCATCA 57.127 30.769 25.42 25.42 33.79 3.07
2372 2379 9.182214 GGTATGAAATATCCATAGTTGATGCAT 57.818 33.333 0.00 0.00 33.79 3.96
2373 2380 8.565896 GGTATGAAATATCCATAGTTGATGCA 57.434 34.615 0.00 0.00 33.79 3.96


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

AutoCloner maintained by Alex Coulton.