Multiple sequence alignment - TraesCS1B01G285500

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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 TraesCS1B01G285500 chr1B 100.000 1630 0 0 827 2456 496561459 496559830 0.000000e+00 3011
1 TraesCS1B01G285500 chr1B 100.000 536 0 0 1 536 496562285 496561750 0.000000e+00 990
2 TraesCS1B01G285500 chr1B 90.252 318 28 3 2140 2456 496559809 496560124 1.760000e-111 412
3 TraesCS1B01G285500 chr1D 92.024 1354 64 24 827 2143 371750259 371748913 0.000000e+00 1862
4 TraesCS1B01G285500 chr1D 90.364 550 31 4 1 536 371750790 371750249 0.000000e+00 702
5 TraesCS1B01G285500 chr1A 89.579 1353 89 27 827 2143 471488829 471487493 0.000000e+00 1670
6 TraesCS1B01G285500 chr1A 88.267 554 42 11 1 535 471489369 471488820 2.060000e-180 641
7 TraesCS1B01G285500 chr1A 87.988 333 33 5 2130 2456 27247559 27247890 1.070000e-103 387
8 TraesCS1B01G285500 chr7A 89.506 324 29 5 2133 2454 41424868 41424548 2.940000e-109 405
9 TraesCS1B01G285500 chr7A 89.655 319 28 3 2138 2456 12118927 12118614 3.800000e-108 401
10 TraesCS1B01G285500 chr7A 88.889 315 30 2 2139 2453 12118591 12118900 1.380000e-102 383
11 TraesCS1B01G285500 chr5B 84.923 325 36 9 2135 2456 677663549 677663863 1.420000e-82 316
12 TraesCS1B01G285500 chr5B 85.174 317 35 9 2140 2454 677663885 677663579 5.100000e-82 315
13 TraesCS1B01G285500 chr2A 84.326 319 46 4 2140 2456 382320757 382321073 2.370000e-80 309
14 TraesCS1B01G285500 chr2A 84.539 304 41 6 2151 2452 382321083 382320784 1.850000e-76 296


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 TraesCS1B01G285500 chr1B 496559830 496562285 2455 True 2000.5 3011 100.000 1 2456 2 chr1B.!!$R1 2455
1 TraesCS1B01G285500 chr1D 371748913 371750790 1877 True 1282.0 1862 91.194 1 2143 2 chr1D.!!$R1 2142
2 TraesCS1B01G285500 chr1A 471487493 471489369 1876 True 1155.5 1670 88.923 1 2143 2 chr1A.!!$R1 2142


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
128 134 0.178992 CCACCACCTTCTTGGCTTCA 60.179 55.0 0.0 0.0 40.77 3.02 F
1108 1141 0.179200 CATCGGTTACGCCAAGCAAC 60.179 55.0 0.0 0.0 40.69 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1389 0.178767 CGCCCATCTGGTTCTCATCA 59.821 55.000 0.0 0.0 36.04 3.07 R
2288 2360 1.064091 GGTAGTACTCCCTCCGTTCCT 60.064 57.143 0.0 0.0 0.00 3.36 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
85 91 1.577922 CCGTCTGTTTCGTCGGAGA 59.422 57.895 0.00 0.00 44.86 3.71
117 123 3.075005 CCCGTCGATCCACCACCT 61.075 66.667 0.00 0.00 0.00 4.00
122 128 1.726853 GTCGATCCACCACCTTCTTG 58.273 55.000 0.00 0.00 0.00 3.02
128 134 0.178992 CCACCACCTTCTTGGCTTCA 60.179 55.000 0.00 0.00 40.77 3.02
137 143 3.626670 CCTTCTTGGCTTCACTGATGATC 59.373 47.826 0.00 0.00 33.85 2.92
195 208 2.488952 TGTTTGTTGCTGTAGATCGCA 58.511 42.857 0.00 0.00 0.00 5.10
302 325 1.614850 GGTCGATAGGTTTTTGGCCCA 60.615 52.381 0.00 0.00 0.00 5.36
328 351 7.695480 AGCACTATACTACTGTCCATATCAG 57.305 40.000 0.00 0.00 38.68 2.90
334 357 4.219115 ACTACTGTCCATATCAGGGTGAG 58.781 47.826 0.00 0.00 37.25 3.51
360 383 1.128188 GGAGTGGGGACAGAACTGGT 61.128 60.000 6.76 0.00 44.46 4.00
368 391 3.568430 GGGGACAGAACTGGTTTTTGTAG 59.432 47.826 6.76 0.00 34.19 2.74
413 436 8.622157 GTTATTAGGGGCTTCTAATTTGAACTC 58.378 37.037 15.00 0.00 39.71 3.01
438 461 3.164268 TCAATTGGGACAGTGATTTGGG 58.836 45.455 5.42 0.00 42.39 4.12
455 478 0.604511 GGGGTTGGTGTTGGTCTACG 60.605 60.000 0.00 0.00 0.00 3.51
480 511 4.424626 ACAATCACATACTCTGCTGTACG 58.575 43.478 0.00 0.00 0.00 3.67
530 561 4.574013 CCACTCTTAAGCTTTGCAGATAGG 59.426 45.833 3.20 5.56 0.00 2.57
531 562 5.423015 CACTCTTAAGCTTTGCAGATAGGA 58.577 41.667 3.20 0.00 0.00 2.94
532 563 5.293079 CACTCTTAAGCTTTGCAGATAGGAC 59.707 44.000 3.20 0.00 0.00 3.85
533 564 5.188751 ACTCTTAAGCTTTGCAGATAGGACT 59.811 40.000 3.20 0.00 0.00 3.85
534 565 6.381420 ACTCTTAAGCTTTGCAGATAGGACTA 59.619 38.462 3.20 0.00 0.00 2.59
535 566 7.093289 ACTCTTAAGCTTTGCAGATAGGACTAA 60.093 37.037 3.20 0.00 0.00 2.24
987 1020 8.989653 TTTCGACCTAATTTTGTGTTTTCTTT 57.010 26.923 0.00 0.00 0.00 2.52
988 1021 7.979115 TCGACCTAATTTTGTGTTTTCTTTG 57.021 32.000 0.00 0.00 0.00 2.77
1108 1141 0.179200 CATCGGTTACGCCAAGCAAC 60.179 55.000 0.00 0.00 40.69 4.17
1123 1156 2.456577 AGCAACCACCAAACTTGTCTT 58.543 42.857 0.00 0.00 0.00 3.01
1158 1191 0.839946 ACAAGTTCAGGGTGTCTGCT 59.160 50.000 0.00 0.00 43.06 4.24
1206 1239 2.579201 CCGGACGGTGAAGAGCAT 59.421 61.111 0.00 0.00 0.00 3.79
1239 1272 3.264450 CCCCTGAAGACACCTACATTCTT 59.736 47.826 0.00 0.00 32.14 2.52
1374 1407 2.295885 CTTGATGAGAACCAGATGGGC 58.704 52.381 3.48 0.00 42.05 5.36
1398 1431 3.118905 GGATACCTTCTGACCTGCATC 57.881 52.381 0.00 0.00 0.00 3.91
1413 1446 0.183492 GCATCTCATACCCCAAGGCA 59.817 55.000 0.00 0.00 36.11 4.75
1469 1530 8.221766 GGAACTCTACTAATTGTTGAAGTTTCG 58.778 37.037 0.00 0.00 30.68 3.46
1480 1541 3.201353 TGAAGTTTCGTGGTGGATTCA 57.799 42.857 0.00 0.00 0.00 2.57
1510 1574 5.221342 CGGTTGCCTTCTGTTATCTAGAGAT 60.221 44.000 0.00 0.00 38.51 2.75
1524 1588 1.650528 AGAGATATGGCTAGGTGGGC 58.349 55.000 0.00 0.00 0.00 5.36
1535 1599 2.872732 CTAGGTGGGCGTATCTTCCTA 58.127 52.381 0.00 0.00 0.00 2.94
1537 1601 1.217183 AGGTGGGCGTATCTTCCTAGA 59.783 52.381 0.00 0.00 34.21 2.43
1543 1607 4.202223 TGGGCGTATCTTCCTAGAAATCAC 60.202 45.833 0.00 0.00 33.20 3.06
1545 1609 5.453480 GGGCGTATCTTCCTAGAAATCACTT 60.453 44.000 0.00 0.00 33.20 3.16
1547 1611 6.273825 GCGTATCTTCCTAGAAATCACTTCA 58.726 40.000 0.00 0.00 36.40 3.02
1559 1623 7.211966 AGAAATCACTTCAGTCTTTTGATGG 57.788 36.000 0.00 0.00 36.40 3.51
1566 1630 3.599343 TCAGTCTTTTGATGGGATCGTG 58.401 45.455 0.00 0.00 0.00 4.35
1567 1631 3.260632 TCAGTCTTTTGATGGGATCGTGA 59.739 43.478 0.00 0.00 0.00 4.35
1730 1799 0.459489 TTTGGCCACTCTGTTTGCAC 59.541 50.000 3.88 0.00 0.00 4.57
1732 1801 0.819259 TGGCCACTCTGTTTGCACTC 60.819 55.000 0.00 0.00 0.00 3.51
1774 1843 4.381505 GGATGTCAGGAGTTCAGAAGTCTC 60.382 50.000 16.19 5.28 0.00 3.36
1791 1860 8.669243 CAGAAGTCTCAACTTTTTAGTCTTTGT 58.331 33.333 0.00 0.00 45.80 2.83
2001 2072 3.857010 GCCAATTCCAACTTTCCAAGTCG 60.857 47.826 0.00 0.00 41.91 4.18
2006 2077 1.333791 CCAACTTTCCAAGTCGCGTTC 60.334 52.381 5.77 0.31 41.91 3.95
2072 2144 9.453572 TGTTCATGCTCTATCTTTCAGTTAAAT 57.546 29.630 0.00 0.00 0.00 1.40
2100 2172 3.547054 ACTACCAACTGAAACGGTTCA 57.453 42.857 16.40 16.40 41.57 3.18
2127 2199 3.264450 AGGTTCCTTCCAGTAATCCAGTG 59.736 47.826 0.00 0.00 0.00 3.66
2144 2216 7.986085 ATCCAGTGCACATAATTTATACTCC 57.014 36.000 21.04 0.00 0.00 3.85
2145 2217 6.296026 TCCAGTGCACATAATTTATACTCCC 58.704 40.000 21.04 0.00 0.00 4.30
2146 2218 6.101150 TCCAGTGCACATAATTTATACTCCCT 59.899 38.462 21.04 0.00 0.00 4.20
2147 2219 6.428159 CCAGTGCACATAATTTATACTCCCTC 59.572 42.308 21.04 0.00 0.00 4.30
2148 2220 6.428159 CAGTGCACATAATTTATACTCCCTCC 59.572 42.308 21.04 0.00 0.00 4.30
2149 2221 5.408604 GTGCACATAATTTATACTCCCTCCG 59.591 44.000 13.17 0.00 0.00 4.63
2150 2222 5.071250 TGCACATAATTTATACTCCCTCCGT 59.929 40.000 0.00 0.00 0.00 4.69
2151 2223 5.995897 GCACATAATTTATACTCCCTCCGTT 59.004 40.000 0.00 0.00 0.00 4.44
2152 2224 6.147328 GCACATAATTTATACTCCCTCCGTTC 59.853 42.308 0.00 0.00 0.00 3.95
2153 2225 6.365247 CACATAATTTATACTCCCTCCGTTCG 59.635 42.308 0.00 0.00 0.00 3.95
2154 2226 6.041296 ACATAATTTATACTCCCTCCGTTCGT 59.959 38.462 0.00 0.00 0.00 3.85
2155 2227 7.231317 ACATAATTTATACTCCCTCCGTTCGTA 59.769 37.037 0.00 0.00 0.00 3.43
2156 2228 6.469782 AATTTATACTCCCTCCGTTCGTAA 57.530 37.500 0.00 0.00 0.00 3.18
2157 2229 5.913137 TTTATACTCCCTCCGTTCGTAAA 57.087 39.130 0.00 0.00 0.00 2.01
2158 2230 6.469782 TTTATACTCCCTCCGTTCGTAAAT 57.530 37.500 0.00 0.00 0.00 1.40
2159 2231 7.581213 TTTATACTCCCTCCGTTCGTAAATA 57.419 36.000 0.00 0.00 0.00 1.40
2160 2232 7.765695 TTATACTCCCTCCGTTCGTAAATAT 57.234 36.000 0.00 0.00 0.00 1.28
2161 2233 6.661304 ATACTCCCTCCGTTCGTAAATATT 57.339 37.500 0.00 0.00 0.00 1.28
2162 2234 5.349061 ACTCCCTCCGTTCGTAAATATTT 57.651 39.130 5.89 5.89 0.00 1.40
2163 2235 5.114081 ACTCCCTCCGTTCGTAAATATTTG 58.886 41.667 11.05 0.00 0.00 2.32
2164 2236 5.088680 TCCCTCCGTTCGTAAATATTTGT 57.911 39.130 11.05 0.00 0.00 2.83
2165 2237 5.111293 TCCCTCCGTTCGTAAATATTTGTC 58.889 41.667 11.05 3.49 0.00 3.18
2166 2238 5.105228 TCCCTCCGTTCGTAAATATTTGTCT 60.105 40.000 11.05 0.00 0.00 3.41
2167 2239 5.583457 CCCTCCGTTCGTAAATATTTGTCTT 59.417 40.000 11.05 0.00 0.00 3.01
2168 2240 6.093082 CCCTCCGTTCGTAAATATTTGTCTTT 59.907 38.462 11.05 0.00 0.00 2.52
2169 2241 7.178074 CCTCCGTTCGTAAATATTTGTCTTTC 58.822 38.462 11.05 0.00 0.00 2.62
2170 2242 7.064253 CCTCCGTTCGTAAATATTTGTCTTTCT 59.936 37.037 11.05 0.00 0.00 2.52
2171 2243 8.984891 TCCGTTCGTAAATATTTGTCTTTCTA 57.015 30.769 11.05 0.00 0.00 2.10
2172 2244 9.079833 TCCGTTCGTAAATATTTGTCTTTCTAG 57.920 33.333 11.05 0.00 0.00 2.43
2173 2245 7.844653 CCGTTCGTAAATATTTGTCTTTCTAGC 59.155 37.037 11.05 0.00 0.00 3.42
2174 2246 7.574481 CGTTCGTAAATATTTGTCTTTCTAGCG 59.426 37.037 11.05 0.00 0.00 4.26
2175 2247 8.589629 GTTCGTAAATATTTGTCTTTCTAGCGA 58.410 33.333 11.05 3.14 0.00 4.93
2176 2248 8.867112 TCGTAAATATTTGTCTTTCTAGCGAT 57.133 30.769 11.05 0.00 0.00 4.58
2177 2249 9.309516 TCGTAAATATTTGTCTTTCTAGCGATT 57.690 29.630 11.05 0.00 0.00 3.34
2178 2250 9.916397 CGTAAATATTTGTCTTTCTAGCGATTT 57.084 29.630 11.05 0.00 0.00 2.17
2182 2254 9.774742 AATATTTGTCTTTCTAGCGATTTCAAC 57.225 29.630 0.00 0.00 0.00 3.18
2183 2255 6.612247 TTTGTCTTTCTAGCGATTTCAACA 57.388 33.333 0.00 0.00 0.00 3.33
2184 2256 6.612247 TTGTCTTTCTAGCGATTTCAACAA 57.388 33.333 0.00 0.00 0.00 2.83
2185 2257 6.228273 TGTCTTTCTAGCGATTTCAACAAG 57.772 37.500 0.00 0.00 0.00 3.16
2186 2258 5.758296 TGTCTTTCTAGCGATTTCAACAAGT 59.242 36.000 0.00 0.00 0.00 3.16
2187 2259 6.074005 GTCTTTCTAGCGATTTCAACAAGTG 58.926 40.000 0.00 0.00 0.00 3.16
2188 2260 5.989168 TCTTTCTAGCGATTTCAACAAGTGA 59.011 36.000 0.00 0.00 0.00 3.41
2189 2261 5.591643 TTCTAGCGATTTCAACAAGTGAC 57.408 39.130 0.00 0.00 35.39 3.67
2190 2262 4.883083 TCTAGCGATTTCAACAAGTGACT 58.117 39.130 0.00 0.00 35.39 3.41
2191 2263 6.020971 TCTAGCGATTTCAACAAGTGACTA 57.979 37.500 0.00 0.00 35.39 2.59
2192 2264 4.992381 AGCGATTTCAACAAGTGACTAC 57.008 40.909 0.00 0.00 35.39 2.73
2193 2265 4.377021 AGCGATTTCAACAAGTGACTACA 58.623 39.130 0.00 0.00 35.39 2.74
2194 2266 4.997395 AGCGATTTCAACAAGTGACTACAT 59.003 37.500 0.00 0.00 35.39 2.29
2195 2267 6.163476 AGCGATTTCAACAAGTGACTACATA 58.837 36.000 0.00 0.00 35.39 2.29
2196 2268 6.090898 AGCGATTTCAACAAGTGACTACATAC 59.909 38.462 0.00 0.00 35.39 2.39
2197 2269 6.458503 CGATTTCAACAAGTGACTACATACG 58.541 40.000 0.00 0.00 35.39 3.06
2198 2270 6.307077 CGATTTCAACAAGTGACTACATACGA 59.693 38.462 0.00 0.00 35.39 3.43
2199 2271 7.148869 CGATTTCAACAAGTGACTACATACGAA 60.149 37.037 0.00 0.00 35.39 3.85
2200 2272 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
2201 2273 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
2202 2274 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
2203 2275 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
2204 2276 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
2205 2277 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
2206 2278 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
2207 2279 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
2208 2280 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
2209 2281 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
2210 2282 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
2211 2283 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
2212 2284 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2213 2285 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
2214 2286 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
2215 2287 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
2216 2288 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
2217 2289 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
2218 2290 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2219 2291 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
2220 2292 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
2253 2325 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2255 2327 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
2256 2328 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
2257 2329 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
2258 2330 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2259 2331 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2260 2332 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2261 2333 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2262 2334 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2263 2335 5.364446 ACATCCGTATGTGGTAGTCCATTTA 59.636 40.000 0.00 0.00 44.79 1.40
2264 2336 5.936187 TCCGTATGTGGTAGTCCATTTAA 57.064 39.130 0.00 0.00 46.20 1.52
2265 2337 6.297080 TCCGTATGTGGTAGTCCATTTAAA 57.703 37.500 0.00 0.00 46.20 1.52
2266 2338 6.709281 TCCGTATGTGGTAGTCCATTTAAAA 58.291 36.000 0.00 0.00 46.20 1.52
2267 2339 7.340256 TCCGTATGTGGTAGTCCATTTAAAAT 58.660 34.615 0.00 0.00 46.20 1.82
2268 2340 8.484575 TCCGTATGTGGTAGTCCATTTAAAATA 58.515 33.333 0.00 0.00 46.20 1.40
2269 2341 9.280174 CCGTATGTGGTAGTCCATTTAAAATAT 57.720 33.333 0.00 0.00 46.20 1.28
2295 2367 9.595823 TCTAAGAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2296 2368 9.595823 CTAAGAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2297 2369 8.494016 AAGAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2298 2370 7.048512 AGAAGACAAATATTTAGGAACGGAGG 58.951 38.462 0.00 0.00 0.00 4.30
2299 2371 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2300 2372 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2301 2373 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2302 2374 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2303 2375 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2304 2376 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
2305 2377 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
2306 2378 4.591321 TTTAGGAACGGAGGGAGTACTA 57.409 45.455 0.00 0.00 0.00 1.82
2307 2379 2.433662 AGGAACGGAGGGAGTACTAC 57.566 55.000 0.00 0.00 0.00 2.73
2308 2380 1.064091 AGGAACGGAGGGAGTACTACC 60.064 57.143 17.30 17.30 0.00 3.18
2310 2382 2.173569 GGAACGGAGGGAGTACTACCTA 59.826 54.545 27.44 0.00 46.12 3.08
2311 2383 3.372025 GGAACGGAGGGAGTACTACCTAA 60.372 52.174 27.44 0.00 46.12 2.69
2312 2384 4.273318 GAACGGAGGGAGTACTACCTAAA 58.727 47.826 27.44 0.00 46.12 1.85
2313 2385 4.533001 ACGGAGGGAGTACTACCTAAAT 57.467 45.455 27.44 11.95 46.12 1.40
2314 2386 5.653255 ACGGAGGGAGTACTACCTAAATA 57.347 43.478 27.44 0.00 46.12 1.40
2315 2387 5.380900 ACGGAGGGAGTACTACCTAAATAC 58.619 45.833 27.44 13.69 46.12 1.89
2316 2388 5.133491 ACGGAGGGAGTACTACCTAAATACT 59.867 44.000 27.44 2.59 46.12 2.12
2317 2389 5.704978 CGGAGGGAGTACTACCTAAATACTC 59.295 48.000 27.44 12.43 46.12 2.59
2323 2395 5.629125 AGTACTACCTAAATACTCCCTCCG 58.371 45.833 0.00 0.00 0.00 4.63
2324 2396 4.533001 ACTACCTAAATACTCCCTCCGT 57.467 45.455 0.00 0.00 0.00 4.69
2325 2397 4.876580 ACTACCTAAATACTCCCTCCGTT 58.123 43.478 0.00 0.00 0.00 4.44
2326 2398 4.892345 ACTACCTAAATACTCCCTCCGTTC 59.108 45.833 0.00 0.00 0.00 3.95
2327 2399 3.036819 ACCTAAATACTCCCTCCGTTCC 58.963 50.000 0.00 0.00 0.00 3.62
2328 2400 3.306613 CCTAAATACTCCCTCCGTTCCT 58.693 50.000 0.00 0.00 0.00 3.36
2329 2401 4.078980 ACCTAAATACTCCCTCCGTTCCTA 60.079 45.833 0.00 0.00 0.00 2.94
2330 2402 4.897670 CCTAAATACTCCCTCCGTTCCTAA 59.102 45.833 0.00 0.00 0.00 2.69
2331 2403 5.364735 CCTAAATACTCCCTCCGTTCCTAAA 59.635 44.000 0.00 0.00 0.00 1.85
2332 2404 5.970501 AAATACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
2333 2405 7.234166 CCTAAATACTCCCTCCGTTCCTAAATA 59.766 40.741 0.00 0.00 0.00 1.40
2334 2406 7.628501 AAATACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
2335 2407 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
2336 2408 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2337 2409 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2338 2410 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2339 2411 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2340 2412 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2341 2413 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2342 2414 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2343 2415 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2344 2416 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2345 2417 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2346 2418 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2347 2419 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2418 2490 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2419 2491 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2420 2492 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2421 2493 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2422 2494 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2423 2495 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2424 2496 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2425 2497 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2426 2498 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2427 2499 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2428 2500 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2429 2501 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2430 2502 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2431 2503 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2432 2504 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2433 2505 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2434 2506 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2435 2507 2.165641 TGCTCCGTATGTAGTCACTTGG 59.834 50.000 0.00 0.00 0.00 3.61
2436 2508 2.165845 GCTCCGTATGTAGTCACTTGGT 59.834 50.000 0.00 0.00 0.00 3.67
2437 2509 3.770666 CTCCGTATGTAGTCACTTGGTG 58.229 50.000 0.00 0.00 34.45 4.17
2438 2510 3.423749 TCCGTATGTAGTCACTTGGTGA 58.576 45.455 0.00 0.00 40.50 4.02
2439 2511 3.827876 TCCGTATGTAGTCACTTGGTGAA 59.172 43.478 1.77 0.00 44.49 3.18
2440 2512 4.281435 TCCGTATGTAGTCACTTGGTGAAA 59.719 41.667 1.77 0.00 44.49 2.69
2441 2513 5.046878 TCCGTATGTAGTCACTTGGTGAAAT 60.047 40.000 1.77 0.00 44.49 2.17
2442 2514 5.063438 CCGTATGTAGTCACTTGGTGAAATG 59.937 44.000 1.77 0.00 44.49 2.32
2443 2515 5.637810 CGTATGTAGTCACTTGGTGAAATGT 59.362 40.000 1.77 0.00 44.49 2.71
2444 2516 6.183360 CGTATGTAGTCACTTGGTGAAATGTC 60.183 42.308 1.77 0.00 44.49 3.06
2445 2517 5.290493 TGTAGTCACTTGGTGAAATGTCT 57.710 39.130 1.77 0.00 44.49 3.41
2446 2518 6.413783 TGTAGTCACTTGGTGAAATGTCTA 57.586 37.500 1.77 0.00 44.49 2.59
2447 2519 6.455647 TGTAGTCACTTGGTGAAATGTCTAG 58.544 40.000 1.77 0.00 44.49 2.43
2448 2520 5.808366 AGTCACTTGGTGAAATGTCTAGA 57.192 39.130 1.77 0.00 44.49 2.43
2449 2521 6.174720 AGTCACTTGGTGAAATGTCTAGAA 57.825 37.500 0.00 0.00 44.49 2.10
2450 2522 6.591935 AGTCACTTGGTGAAATGTCTAGAAA 58.408 36.000 0.00 0.00 44.49 2.52
2451 2523 6.708054 AGTCACTTGGTGAAATGTCTAGAAAG 59.292 38.462 0.00 0.00 44.49 2.62
2452 2524 6.706270 GTCACTTGGTGAAATGTCTAGAAAGA 59.294 38.462 0.00 0.00 44.49 2.52
2453 2525 6.706270 TCACTTGGTGAAATGTCTAGAAAGAC 59.294 38.462 0.00 0.00 44.54 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 117 0.846693 AGTGAAGCCAAGAAGGTGGT 59.153 50.000 0.00 0.00 41.12 4.16
117 123 3.055891 TCGATCATCAGTGAAGCCAAGAA 60.056 43.478 0.00 0.00 38.01 2.52
122 128 2.057316 CGATCGATCATCAGTGAAGCC 58.943 52.381 24.40 0.00 38.01 4.35
195 208 2.629656 GCGCATCACAACCAAGGCT 61.630 57.895 0.30 0.00 0.00 4.58
302 325 9.402320 CTGATATGGACAGTAGTATAGTGCTAT 57.598 37.037 0.00 0.00 45.90 2.97
328 351 2.284995 ACTCCCCAGAGCTCACCC 60.285 66.667 17.77 0.00 44.65 4.61
334 357 3.403558 GTCCCCACTCCCCAGAGC 61.404 72.222 0.00 0.00 44.65 4.09
360 383 7.346751 AGCAAGTGGATTTCTTCTACAAAAA 57.653 32.000 0.00 0.00 38.25 1.94
413 436 4.503741 AATCACTGTCCCAATTGAAACG 57.496 40.909 7.12 4.24 0.00 3.60
438 461 1.342174 TCTCGTAGACCAACACCAACC 59.658 52.381 0.00 0.00 0.00 3.77
455 478 4.753233 ACAGCAGAGTATGTGATTGTCTC 58.247 43.478 0.00 0.00 25.68 3.36
826 857 9.610705 ATGCATATGATCAACATTAGTCCTATC 57.389 33.333 6.97 0.00 40.07 2.08
827 858 9.392259 CATGCATATGATCAACATTAGTCCTAT 57.608 33.333 6.97 0.00 40.07 2.57
828 859 8.596293 TCATGCATATGATCAACATTAGTCCTA 58.404 33.333 6.97 0.00 38.37 2.94
829 860 7.455891 TCATGCATATGATCAACATTAGTCCT 58.544 34.615 6.97 0.00 38.37 3.85
830 861 7.677454 TCATGCATATGATCAACATTAGTCC 57.323 36.000 6.97 0.00 38.37 3.85
945 976 8.732746 AGGTCGAAATAAAAGTATAACAGCAT 57.267 30.769 0.00 0.00 0.00 3.79
987 1020 5.048083 GGCAGTTGACATTTTTCTGATACCA 60.048 40.000 0.00 0.00 0.00 3.25
988 1021 5.048083 TGGCAGTTGACATTTTTCTGATACC 60.048 40.000 0.00 0.00 0.00 2.73
996 1029 2.431782 AGCAGTGGCAGTTGACATTTTT 59.568 40.909 0.00 0.00 44.61 1.94
1108 1141 1.402787 AGGCAAGACAAGTTTGGTGG 58.597 50.000 0.00 0.00 0.00 4.61
1123 1156 4.098914 ACTTGTTTGACATCCTTAGGCA 57.901 40.909 0.00 0.00 0.00 4.75
1206 1239 0.401738 CTTCAGGGGCCTCAAACTCA 59.598 55.000 4.79 0.00 0.00 3.41
1356 1389 0.178767 CGCCCATCTGGTTCTCATCA 59.821 55.000 0.00 0.00 36.04 3.07
1374 1407 1.683917 CAGGTCAGAAGGTATCCCTCG 59.316 57.143 0.00 0.00 41.56 4.63
1398 1431 2.579873 CAATCTGCCTTGGGGTATGAG 58.420 52.381 0.00 0.00 34.45 2.90
1413 1446 2.228822 GTGGGTTTGAATGACGCAATCT 59.771 45.455 0.00 0.00 40.87 2.40
1460 1493 3.201353 TGAATCCACCACGAAACTTCA 57.799 42.857 0.00 0.00 0.00 3.02
1461 1494 4.023193 ACAATGAATCCACCACGAAACTTC 60.023 41.667 0.00 0.00 0.00 3.01
1462 1495 3.888930 ACAATGAATCCACCACGAAACTT 59.111 39.130 0.00 0.00 0.00 2.66
1464 1497 3.915437 ACAATGAATCCACCACGAAAC 57.085 42.857 0.00 0.00 0.00 2.78
1465 1498 3.058570 CGAACAATGAATCCACCACGAAA 60.059 43.478 0.00 0.00 0.00 3.46
1469 1530 2.159382 ACCGAACAATGAATCCACCAC 58.841 47.619 0.00 0.00 0.00 4.16
1480 1541 1.981256 ACAGAAGGCAACCGAACAAT 58.019 45.000 0.00 0.00 37.17 2.71
1510 1574 1.203137 AGATACGCCCACCTAGCCATA 60.203 52.381 0.00 0.00 0.00 2.74
1524 1588 7.484975 ACTGAAGTGATTTCTAGGAAGATACG 58.515 38.462 0.00 0.00 36.71 3.06
1535 1599 6.208204 CCCATCAAAAGACTGAAGTGATTTCT 59.792 38.462 0.00 0.00 36.71 2.52
1537 1601 6.070656 TCCCATCAAAAGACTGAAGTGATTT 58.929 36.000 0.00 0.00 0.00 2.17
1543 1607 4.093998 CACGATCCCATCAAAAGACTGAAG 59.906 45.833 0.00 0.00 0.00 3.02
1545 1609 3.260632 TCACGATCCCATCAAAAGACTGA 59.739 43.478 0.00 0.00 0.00 3.41
1547 1611 3.981071 TCACGATCCCATCAAAAGACT 57.019 42.857 0.00 0.00 0.00 3.24
1559 1623 6.447162 TGTCACAACTCATATATCACGATCC 58.553 40.000 0.00 0.00 0.00 3.36
1622 1686 2.095110 CGAATTGCTGCAATCTGGACAA 60.095 45.455 26.40 0.00 32.43 3.18
1626 1690 2.163010 AGTTCGAATTGCTGCAATCTGG 59.837 45.455 26.40 18.00 32.43 3.86
1730 1799 6.633500 TCCATTCAAGTAACCAAAACAGAG 57.367 37.500 0.00 0.00 0.00 3.35
1732 1801 6.748132 ACATCCATTCAAGTAACCAAAACAG 58.252 36.000 0.00 0.00 0.00 3.16
1802 1871 5.051153 GCTAGGACCAAGCTATTCAGTTAC 58.949 45.833 0.00 0.00 37.01 2.50
1803 1872 4.202121 CGCTAGGACCAAGCTATTCAGTTA 60.202 45.833 0.00 0.00 37.85 2.24
1804 1873 3.430929 CGCTAGGACCAAGCTATTCAGTT 60.431 47.826 0.00 0.00 37.85 3.16
1808 1877 1.503294 GCGCTAGGACCAAGCTATTC 58.497 55.000 0.00 0.00 37.85 1.75
2001 2072 2.536803 TGTTAACTGAACTGACGAACGC 59.463 45.455 7.22 0.00 38.98 4.84
2006 2077 4.109766 TCACTGTGTTAACTGAACTGACG 58.890 43.478 7.79 0.00 38.98 4.35
2072 2144 7.895759 ACCGTTTCAGTTGGTAGTAGTTTATA 58.104 34.615 0.00 0.00 33.25 0.98
2073 2145 6.762333 ACCGTTTCAGTTGGTAGTAGTTTAT 58.238 36.000 0.00 0.00 33.25 1.40
2085 2157 3.304659 CCTCCATTGAACCGTTTCAGTTG 60.305 47.826 0.00 0.00 42.79 3.16
2100 2172 4.079730 GGATTACTGGAAGGAACCTCCATT 60.080 45.833 10.67 8.79 41.57 3.16
2127 2199 5.548406 ACGGAGGGAGTATAAATTATGTGC 58.452 41.667 0.00 0.00 0.00 4.57
2143 2215 5.114081 AGACAAATATTTACGAACGGAGGG 58.886 41.667 0.00 0.00 0.00 4.30
2144 2216 6.657836 AAGACAAATATTTACGAACGGAGG 57.342 37.500 0.00 0.00 0.00 4.30
2145 2217 7.960793 AGAAAGACAAATATTTACGAACGGAG 58.039 34.615 0.00 0.00 0.00 4.63
2146 2218 7.894376 AGAAAGACAAATATTTACGAACGGA 57.106 32.000 0.00 0.00 0.00 4.69
2147 2219 7.844653 GCTAGAAAGACAAATATTTACGAACGG 59.155 37.037 0.00 0.00 0.00 4.44
2148 2220 7.574481 CGCTAGAAAGACAAATATTTACGAACG 59.426 37.037 0.00 0.00 0.00 3.95
2149 2221 8.589629 TCGCTAGAAAGACAAATATTTACGAAC 58.410 33.333 0.00 0.00 0.00 3.95
2150 2222 8.692110 TCGCTAGAAAGACAAATATTTACGAA 57.308 30.769 0.00 0.00 0.00 3.85
2151 2223 8.867112 ATCGCTAGAAAGACAAATATTTACGA 57.133 30.769 0.00 0.00 0.00 3.43
2152 2224 9.916397 AAATCGCTAGAAAGACAAATATTTACG 57.084 29.630 0.00 0.00 0.00 3.18
2156 2228 9.774742 GTTGAAATCGCTAGAAAGACAAATATT 57.225 29.630 0.00 0.00 0.00 1.28
2157 2229 8.946085 TGTTGAAATCGCTAGAAAGACAAATAT 58.054 29.630 0.00 0.00 0.00 1.28
2158 2230 8.317891 TGTTGAAATCGCTAGAAAGACAAATA 57.682 30.769 0.00 0.00 0.00 1.40
2159 2231 7.202016 TGTTGAAATCGCTAGAAAGACAAAT 57.798 32.000 0.00 0.00 0.00 2.32
2160 2232 6.612247 TGTTGAAATCGCTAGAAAGACAAA 57.388 33.333 0.00 0.00 0.00 2.83
2161 2233 6.260050 ACTTGTTGAAATCGCTAGAAAGACAA 59.740 34.615 0.00 0.00 0.00 3.18
2162 2234 5.758296 ACTTGTTGAAATCGCTAGAAAGACA 59.242 36.000 0.00 0.00 0.00 3.41
2163 2235 6.073765 TCACTTGTTGAAATCGCTAGAAAGAC 60.074 38.462 0.00 0.00 0.00 3.01
2164 2236 5.989168 TCACTTGTTGAAATCGCTAGAAAGA 59.011 36.000 0.00 0.00 0.00 2.52
2165 2237 6.073548 AGTCACTTGTTGAAATCGCTAGAAAG 60.074 38.462 0.00 0.00 35.39 2.62
2166 2238 5.758296 AGTCACTTGTTGAAATCGCTAGAAA 59.242 36.000 0.00 0.00 35.39 2.52
2167 2239 5.297547 AGTCACTTGTTGAAATCGCTAGAA 58.702 37.500 0.00 0.00 35.39 2.10
2168 2240 4.883083 AGTCACTTGTTGAAATCGCTAGA 58.117 39.130 0.00 0.00 35.39 2.43
2169 2241 5.633601 TGTAGTCACTTGTTGAAATCGCTAG 59.366 40.000 0.00 0.00 35.39 3.42
2170 2242 5.534407 TGTAGTCACTTGTTGAAATCGCTA 58.466 37.500 0.00 0.00 35.39 4.26
2171 2243 4.377021 TGTAGTCACTTGTTGAAATCGCT 58.623 39.130 0.00 0.00 35.39 4.93
2172 2244 4.725556 TGTAGTCACTTGTTGAAATCGC 57.274 40.909 0.00 0.00 35.39 4.58
2173 2245 6.307077 TCGTATGTAGTCACTTGTTGAAATCG 59.693 38.462 0.00 0.00 35.39 3.34
2174 2246 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
2175 2247 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
2176 2248 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
2177 2249 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
2178 2250 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
2179 2251 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
2180 2252 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
2181 2253 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
2182 2254 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
2183 2255 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
2184 2256 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
2185 2257 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
2186 2258 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
2187 2259 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
2188 2260 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2189 2261 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2190 2262 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
2191 2263 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
2192 2264 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
2193 2265 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2194 2266 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
2195 2267 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
2196 2268 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
2197 2269 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
2227 2299 9.470399 ACCACATACGGATGTATATAGACATAA 57.530 33.333 14.23 0.77 44.82 1.90
2229 2301 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2230 2302 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
2231 2303 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
2232 2304 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
2233 2305 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
2234 2306 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2235 2307 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
2236 2308 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2237 2309 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2238 2310 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2269 2341 9.595823 CCGTTCCTAAATATTTGTCTTCTTAGA 57.404 33.333 11.05 0.00 0.00 2.10
2270 2342 9.595823 TCCGTTCCTAAATATTTGTCTTCTTAG 57.404 33.333 11.05 0.00 0.00 2.18
2271 2343 9.595823 CTCCGTTCCTAAATATTTGTCTTCTTA 57.404 33.333 11.05 0.00 0.00 2.10
2272 2344 7.553044 CCTCCGTTCCTAAATATTTGTCTTCTT 59.447 37.037 11.05 0.00 0.00 2.52
2273 2345 7.048512 CCTCCGTTCCTAAATATTTGTCTTCT 58.951 38.462 11.05 0.00 0.00 2.85
2274 2346 6.260271 CCCTCCGTTCCTAAATATTTGTCTTC 59.740 42.308 11.05 0.00 0.00 2.87
2275 2347 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2276 2348 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2277 2349 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2278 2350 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2279 2351 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2280 2352 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2281 2353 6.141790 AGTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2282 2354 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2283 2355 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2284 2356 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2285 2357 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2286 2358 3.372025 GGTAGTACTCCCTCCGTTCCTAA 60.372 52.174 0.00 0.00 0.00 2.69
2287 2359 2.173569 GGTAGTACTCCCTCCGTTCCTA 59.826 54.545 0.00 0.00 0.00 2.94
2288 2360 1.064091 GGTAGTACTCCCTCCGTTCCT 60.064 57.143 0.00 0.00 0.00 3.36
2289 2361 1.064091 AGGTAGTACTCCCTCCGTTCC 60.064 57.143 0.11 0.00 0.00 3.62
2290 2362 2.433662 AGGTAGTACTCCCTCCGTTC 57.566 55.000 0.11 0.00 0.00 3.95
2291 2363 4.322057 TTTAGGTAGTACTCCCTCCGTT 57.678 45.455 10.79 0.00 32.08 4.44
2292 2364 4.533001 ATTTAGGTAGTACTCCCTCCGT 57.467 45.455 10.79 0.00 32.08 4.69
2293 2365 5.629125 AGTATTTAGGTAGTACTCCCTCCG 58.371 45.833 10.79 0.00 32.08 4.63
2299 2371 5.704978 CGGAGGGAGTATTTAGGTAGTACTC 59.295 48.000 0.00 3.76 42.14 2.59
2300 2372 5.133491 ACGGAGGGAGTATTTAGGTAGTACT 59.867 44.000 0.00 0.00 0.00 2.73
2301 2373 5.380900 ACGGAGGGAGTATTTAGGTAGTAC 58.619 45.833 0.00 0.00 0.00 2.73
2302 2374 5.653255 ACGGAGGGAGTATTTAGGTAGTA 57.347 43.478 0.00 0.00 0.00 1.82
2303 2375 4.533001 ACGGAGGGAGTATTTAGGTAGT 57.467 45.455 0.00 0.00 0.00 2.73
2304 2376 4.280425 GGAACGGAGGGAGTATTTAGGTAG 59.720 50.000 0.00 0.00 0.00 3.18
2305 2377 4.078980 AGGAACGGAGGGAGTATTTAGGTA 60.079 45.833 0.00 0.00 0.00 3.08
2306 2378 3.036819 GGAACGGAGGGAGTATTTAGGT 58.963 50.000 0.00 0.00 0.00 3.08
2307 2379 3.306613 AGGAACGGAGGGAGTATTTAGG 58.693 50.000 0.00 0.00 0.00 2.69
2308 2380 6.475596 TTTAGGAACGGAGGGAGTATTTAG 57.524 41.667 0.00 0.00 0.00 1.85
2309 2381 8.731591 ATATTTAGGAACGGAGGGAGTATTTA 57.268 34.615 0.00 0.00 0.00 1.40
2310 2382 5.970501 ATTTAGGAACGGAGGGAGTATTT 57.029 39.130 0.00 0.00 0.00 1.40
2311 2383 7.628501 AATATTTAGGAACGGAGGGAGTATT 57.371 36.000 0.00 0.00 0.00 1.89
2312 2384 7.072076 ACAAATATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
2313 2385 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2314 2386 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2315 2387 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2316 2388 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2317 2389 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2318 2390 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2319 2391 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2320 2392 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2321 2393 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2340 2412 9.527157 TGGTAATCCATTTGAAATGTCTAGAAA 57.473 29.630 15.93 0.00 39.03 2.52
2396 2468 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2397 2469 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2398 2470 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2399 2471 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2400 2472 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2401 2473 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2402 2474 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2403 2475 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2404 2476 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2405 2477 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2406 2478 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2407 2479 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2408 2480 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2409 2481 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2410 2482 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2411 2483 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2412 2484 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2413 2485 3.368013 CCAAGTGACTACATACGGAGCAA 60.368 47.826 0.00 0.00 0.00 3.91
2414 2486 2.165641 CCAAGTGACTACATACGGAGCA 59.834 50.000 0.00 0.00 0.00 4.26
2415 2487 2.165845 ACCAAGTGACTACATACGGAGC 59.834 50.000 0.00 0.00 0.00 4.70
2416 2488 3.442625 TCACCAAGTGACTACATACGGAG 59.557 47.826 0.00 0.00 37.67 4.63
2417 2489 3.423749 TCACCAAGTGACTACATACGGA 58.576 45.455 0.00 0.00 37.67 4.69
2418 2490 3.861276 TCACCAAGTGACTACATACGG 57.139 47.619 0.00 0.00 37.67 4.02
2419 2491 5.637810 ACATTTCACCAAGTGACTACATACG 59.362 40.000 0.00 0.00 42.60 3.06
2420 2492 6.874134 AGACATTTCACCAAGTGACTACATAC 59.126 38.462 0.00 0.00 42.60 2.39
2421 2493 7.004555 AGACATTTCACCAAGTGACTACATA 57.995 36.000 0.00 0.00 42.60 2.29
2422 2494 5.869579 AGACATTTCACCAAGTGACTACAT 58.130 37.500 0.00 0.00 42.60 2.29
2423 2495 5.290493 AGACATTTCACCAAGTGACTACA 57.710 39.130 0.00 0.00 42.60 2.74
2424 2496 6.688578 TCTAGACATTTCACCAAGTGACTAC 58.311 40.000 0.00 0.00 42.60 2.73
2425 2497 6.911250 TCTAGACATTTCACCAAGTGACTA 57.089 37.500 0.00 0.00 42.60 2.59
2426 2498 5.808366 TCTAGACATTTCACCAAGTGACT 57.192 39.130 0.00 0.00 42.60 3.41
2427 2499 6.706270 TCTTTCTAGACATTTCACCAAGTGAC 59.294 38.462 0.00 0.00 42.60 3.67
2428 2500 6.826668 TCTTTCTAGACATTTCACCAAGTGA 58.173 36.000 0.00 0.00 41.09 3.41



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

AutoCloner maintained by Alex Coulton.