Multiple sequence alignment - TraesCS3A01G328500

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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 TraesCS3A01G328500 chr3A 100.000 1667 0 0 1 1667 574011054 574009388 0.000000e+00 3079.0
1 TraesCS3A01G328500 chr3A 100.000 446 0 0 2134 2579 574008921 574008476 0.000000e+00 824.0
2 TraesCS3A01G328500 chr3B 89.443 1743 89 39 1 1667 571297897 571296174 0.000000e+00 2111.0
3 TraesCS3A01G328500 chr3D 92.201 1013 37 19 694 1667 435292068 435291059 0.000000e+00 1395.0
4 TraesCS3A01G328500 chr3D 84.965 705 31 18 1 655 435292746 435292067 0.000000e+00 645.0
5 TraesCS3A01G328500 chr3D 81.481 270 42 3 2135 2396 488391166 488391435 5.590000e-52 215.0
6 TraesCS3A01G328500 chr3D 84.409 186 18 8 2401 2578 435288421 435288239 3.410000e-39 172.0
7 TraesCS3A01G328500 chr4B 82.609 276 38 7 2135 2402 599914862 599915135 4.290000e-58 235.0
8 TraesCS3A01G328500 chr4B 80.669 269 44 5 2135 2395 66540514 66540782 4.350000e-48 202.0
9 TraesCS3A01G328500 chr2A 80.727 275 43 7 2135 2399 459222111 459221837 3.360000e-49 206.0
10 TraesCS3A01G328500 chr2A 80.370 270 43 6 2135 2396 65240263 65239996 2.020000e-46 196.0
11 TraesCS3A01G328500 chr2A 91.667 48 3 1 48 94 764149055 764149008 5.960000e-07 65.8
12 TraesCS3A01G328500 chr5D 81.423 253 39 5 2152 2396 482898289 482898541 1.570000e-47 200.0
13 TraesCS3A01G328500 chr7A 80.220 273 42 8 2135 2398 20505342 20505073 7.280000e-46 195.0
14 TraesCS3A01G328500 chr6D 79.927 274 42 9 2135 2398 89707065 89707335 3.390000e-44 189.0
15 TraesCS3A01G328500 chr7B 80.147 272 35 12 2135 2397 175990482 175990221 4.380000e-43 185.0
16 TraesCS3A01G328500 chr2B 95.349 43 1 1 55 97 794623420 794623461 1.660000e-07 67.6
17 TraesCS3A01G328500 chr2B 91.667 48 3 1 48 94 796837388 796837341 5.960000e-07 65.8


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 TraesCS3A01G328500 chr3A 574008476 574011054 2578 True 1951.500000 3079 100.000000 1 2579 2 chr3A.!!$R1 2578
1 TraesCS3A01G328500 chr3B 571296174 571297897 1723 True 2111.000000 2111 89.443000 1 1667 1 chr3B.!!$R1 1666
2 TraesCS3A01G328500 chr3D 435288239 435292746 4507 True 737.333333 1395 87.191667 1 2578 3 chr3D.!!$R1 2577

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
982 1055 0.461339 AGGCGTTCGAACTTGTGTGT 60.461 50.0 24.8 1.1 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2337 0.026027 CTACGAGACGTCTACGGTGC 59.974 60.0 28.32 13.67 44.95 5.01 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
36 37 2.101575 CTACGCCGCGAGCAAGTA 59.898 61.111 21.79 7.35 44.04 2.24
182 183 9.863845 GAGCTAAACTAATTGTAGAGAAGAACT 57.136 33.333 0.00 0.00 0.00 3.01
183 184 9.646427 AGCTAAACTAATTGTAGAGAAGAACTG 57.354 33.333 0.00 0.00 0.00 3.16
184 185 9.640963 GCTAAACTAATTGTAGAGAAGAACTGA 57.359 33.333 0.00 0.00 0.00 3.41
204 211 6.171921 ACTGAGATTGAGAAGATCACCAAAG 58.828 40.000 0.00 0.00 37.77 2.77
222 229 3.537795 AAGGGTGGTGTACTCTGTAGA 57.462 47.619 0.00 0.00 39.94 2.59
223 230 2.805194 AGGGTGGTGTACTCTGTAGAC 58.195 52.381 0.00 0.00 39.16 2.59
224 231 2.379226 AGGGTGGTGTACTCTGTAGACT 59.621 50.000 0.00 0.00 39.16 3.24
225 232 2.492484 GGGTGGTGTACTCTGTAGACTG 59.508 54.545 0.00 0.00 0.00 3.51
226 233 3.155501 GGTGGTGTACTCTGTAGACTGT 58.844 50.000 0.00 0.00 0.00 3.55
227 234 4.330250 GGTGGTGTACTCTGTAGACTGTA 58.670 47.826 0.00 0.00 0.00 2.74
228 235 4.395542 GGTGGTGTACTCTGTAGACTGTAG 59.604 50.000 0.00 0.00 0.00 2.74
257 264 8.514594 TGTGCTATCTTCAAAAATTCTTAGGTG 58.485 33.333 0.00 0.00 0.00 4.00
274 281 3.081061 AGGTGATATGTGCGCTTTCAAA 58.919 40.909 9.73 0.00 0.00 2.69
359 366 2.635915 TCGGTTCCACTGAAACCAGTAT 59.364 45.455 0.00 0.00 42.60 2.12
372 379 2.941480 ACCAGTATAGTACGAGGTGGG 58.059 52.381 0.00 1.90 39.40 4.61
380 387 5.979288 ATAGTACGAGGTGGGAATATCAC 57.021 43.478 0.00 0.00 34.61 3.06
453 460 5.596836 TTTGCAAGTCTCCACAAAATTCT 57.403 34.783 0.00 0.00 0.00 2.40
522 553 7.660030 AATATACAATGAGAAACAAAGGGGG 57.340 36.000 0.00 0.00 0.00 5.40
541 595 2.099756 GGGCAAATCTAGCATGAACACC 59.900 50.000 0.00 0.00 0.00 4.16
574 628 8.877808 ATTGAATTTGTCTTCTTTGTTTCTCC 57.122 30.769 0.00 0.00 0.00 3.71
599 653 4.244862 GTGCATTTCGAATTTGGGATTGT 58.755 39.130 0.00 0.00 0.00 2.71
708 764 3.026630 AGCGGTTGTATCATGGTATCG 57.973 47.619 0.00 0.00 0.00 2.92
751 812 2.661594 CACATGAACGAAGTCGAGTCA 58.338 47.619 7.87 10.44 45.00 3.41
828 889 1.918609 CGACGACTAAGTTAAGCCAGC 59.081 52.381 0.00 0.00 0.00 4.85
937 1002 2.486982 ACTATATACCGGTACTGCGCTG 59.513 50.000 18.55 13.23 0.00 5.18
939 1004 1.457823 TATACCGGTACTGCGCTGGG 61.458 60.000 18.55 11.93 36.71 4.45
945 1010 3.310307 TACTGCGCTGGGCTGACA 61.310 61.111 25.84 12.74 42.69 3.58
952 1025 2.373707 GCTGGGCTGACATCTCCCT 61.374 63.158 9.98 0.00 40.69 4.20
955 1028 1.622811 CTGGGCTGACATCTCCCTATC 59.377 57.143 9.98 0.00 40.69 2.08
974 1047 2.033194 CCCTCCAAGGCGTTCGAAC 61.033 63.158 18.47 18.47 32.73 3.95
982 1055 0.461339 AGGCGTTCGAACTTGTGTGT 60.461 50.000 24.80 1.10 0.00 3.72
986 1059 2.466846 CGTTCGAACTTGTGTGTACCT 58.533 47.619 24.80 0.00 0.00 3.08
1010 1083 2.045926 GAGCGCCATGTCCCAAGT 60.046 61.111 2.29 0.00 0.00 3.16
1110 1201 2.647158 GGAGGAAACCGGCGAGAGT 61.647 63.158 9.30 0.00 0.00 3.24
1333 1436 1.068753 CTGCCGGTGGAGCTGATAG 59.931 63.158 1.90 0.00 0.00 2.08
1631 1734 0.457853 CCGAAAACGATGCGAGAGGA 60.458 55.000 0.00 0.00 0.00 3.71
1641 1744 1.372623 GCGAGAGGAAAACCGTCGT 60.373 57.895 0.00 0.00 34.99 4.34
2157 2260 2.065993 ATACGCGCATACACTCATCC 57.934 50.000 5.73 0.00 0.00 3.51
2158 2261 1.029681 TACGCGCATACACTCATCCT 58.970 50.000 5.73 0.00 0.00 3.24
2159 2262 1.029681 ACGCGCATACACTCATCCTA 58.970 50.000 5.73 0.00 0.00 2.94
2162 2265 2.351738 CGCGCATACACTCATCCTATGA 60.352 50.000 8.75 0.00 37.76 2.15
2164 2267 3.237628 CGCATACACTCATCCTATGACG 58.762 50.000 0.00 0.00 35.06 4.35
2165 2268 2.989840 GCATACACTCATCCTATGACGC 59.010 50.000 0.00 0.00 35.06 5.19
2166 2269 3.552890 GCATACACTCATCCTATGACGCA 60.553 47.826 0.00 0.00 35.06 5.24
2167 2270 2.586258 ACACTCATCCTATGACGCAC 57.414 50.000 0.00 0.00 35.06 5.34
2168 2271 1.824852 ACACTCATCCTATGACGCACA 59.175 47.619 0.00 0.00 35.06 4.57
2169 2272 2.196749 CACTCATCCTATGACGCACAC 58.803 52.381 0.00 0.00 35.06 3.82
2170 2273 1.824852 ACTCATCCTATGACGCACACA 59.175 47.619 0.00 0.00 35.06 3.72
2171 2274 2.432146 ACTCATCCTATGACGCACACAT 59.568 45.455 0.00 0.00 35.06 3.21
2172 2275 3.636764 ACTCATCCTATGACGCACACATA 59.363 43.478 0.00 0.00 35.06 2.29
2173 2276 3.977427 TCATCCTATGACGCACACATAC 58.023 45.455 0.00 0.00 33.59 2.39
2174 2277 3.383185 TCATCCTATGACGCACACATACA 59.617 43.478 0.00 0.00 33.59 2.29
2175 2278 3.159353 TCCTATGACGCACACATACAC 57.841 47.619 0.00 0.00 0.00 2.90
2176 2279 1.852280 CCTATGACGCACACATACACG 59.148 52.381 0.00 0.00 0.00 4.49
2177 2280 2.526077 CTATGACGCACACATACACGT 58.474 47.619 0.00 0.00 42.27 4.49
2178 2281 1.790755 ATGACGCACACATACACGTT 58.209 45.000 0.00 0.00 39.16 3.99
2179 2282 1.133407 TGACGCACACATACACGTTC 58.867 50.000 0.00 0.00 39.16 3.95
2180 2283 1.269361 TGACGCACACATACACGTTCT 60.269 47.619 0.00 0.00 39.16 3.01
2181 2284 2.030981 TGACGCACACATACACGTTCTA 60.031 45.455 0.00 0.00 39.16 2.10
2182 2285 3.176708 GACGCACACATACACGTTCTAT 58.823 45.455 0.00 0.00 39.16 1.98
2183 2286 3.176708 ACGCACACATACACGTTCTATC 58.823 45.455 0.00 0.00 34.62 2.08
2184 2287 3.119602 ACGCACACATACACGTTCTATCT 60.120 43.478 0.00 0.00 34.62 1.98
2185 2288 3.482472 CGCACACATACACGTTCTATCTC 59.518 47.826 0.00 0.00 0.00 2.75
2186 2289 4.673441 GCACACATACACGTTCTATCTCT 58.327 43.478 0.00 0.00 0.00 3.10
2187 2290 5.503520 CGCACACATACACGTTCTATCTCTA 60.504 44.000 0.00 0.00 0.00 2.43
2188 2291 6.439599 GCACACATACACGTTCTATCTCTAT 58.560 40.000 0.00 0.00 0.00 1.98
2189 2292 6.360947 GCACACATACACGTTCTATCTCTATG 59.639 42.308 0.00 0.00 0.00 2.23
2190 2293 7.639945 CACACATACACGTTCTATCTCTATGA 58.360 38.462 0.00 0.00 0.00 2.15
2191 2294 7.800847 CACACATACACGTTCTATCTCTATGAG 59.199 40.741 0.00 0.00 0.00 2.90
2192 2295 6.799441 CACATACACGTTCTATCTCTATGAGC 59.201 42.308 0.00 0.00 0.00 4.26
2193 2296 4.839668 ACACGTTCTATCTCTATGAGCC 57.160 45.455 0.00 0.00 0.00 4.70
2194 2297 3.251245 ACACGTTCTATCTCTATGAGCCG 59.749 47.826 0.00 0.00 0.00 5.52
2195 2298 3.498777 CACGTTCTATCTCTATGAGCCGA 59.501 47.826 0.00 0.00 0.00 5.54
2196 2299 3.749088 ACGTTCTATCTCTATGAGCCGAG 59.251 47.826 0.00 0.00 0.00 4.63
2197 2300 3.997681 CGTTCTATCTCTATGAGCCGAGA 59.002 47.826 0.00 0.00 40.26 4.04
2198 2301 4.092821 CGTTCTATCTCTATGAGCCGAGAG 59.907 50.000 0.00 0.00 39.43 3.20
2202 2305 2.844946 TCTCTATGAGCCGAGAGACTG 58.155 52.381 0.00 0.00 42.57 3.51
2203 2306 2.436173 TCTCTATGAGCCGAGAGACTGA 59.564 50.000 0.00 0.00 42.57 3.41
2204 2307 2.548057 CTCTATGAGCCGAGAGACTGAC 59.452 54.545 0.00 0.00 41.55 3.51
2205 2308 1.606668 CTATGAGCCGAGAGACTGACC 59.393 57.143 0.00 0.00 0.00 4.02
2206 2309 1.040339 ATGAGCCGAGAGACTGACCC 61.040 60.000 0.00 0.00 0.00 4.46
2207 2310 2.752238 AGCCGAGAGACTGACCCG 60.752 66.667 0.00 0.00 0.00 5.28
2208 2311 3.827898 GCCGAGAGACTGACCCGG 61.828 72.222 0.00 0.00 42.74 5.73
2209 2312 3.827898 CCGAGAGACTGACCCGGC 61.828 72.222 0.00 0.00 33.47 6.13
2210 2313 3.062466 CGAGAGACTGACCCGGCA 61.062 66.667 0.00 0.00 0.00 5.69
2211 2314 2.418910 CGAGAGACTGACCCGGCAT 61.419 63.158 0.00 0.00 0.00 4.40
2212 2315 1.101635 CGAGAGACTGACCCGGCATA 61.102 60.000 0.00 0.00 0.00 3.14
2213 2316 1.333177 GAGAGACTGACCCGGCATAT 58.667 55.000 0.00 0.00 0.00 1.78
2214 2317 1.271102 GAGAGACTGACCCGGCATATC 59.729 57.143 0.00 0.00 0.00 1.63
2215 2318 1.040646 GAGACTGACCCGGCATATCA 58.959 55.000 0.00 0.00 0.00 2.15
2216 2319 1.620819 GAGACTGACCCGGCATATCAT 59.379 52.381 0.00 0.00 0.00 2.45
2217 2320 1.345741 AGACTGACCCGGCATATCATG 59.654 52.381 0.00 0.00 0.00 3.07
2218 2321 1.070758 GACTGACCCGGCATATCATGT 59.929 52.381 0.00 0.00 0.00 3.21
2219 2322 1.490490 ACTGACCCGGCATATCATGTT 59.510 47.619 0.00 0.00 0.00 2.71
2220 2323 2.703536 ACTGACCCGGCATATCATGTTA 59.296 45.455 0.00 0.00 0.00 2.41
2221 2324 3.135712 ACTGACCCGGCATATCATGTTAA 59.864 43.478 0.00 0.00 0.00 2.01
2222 2325 4.202461 ACTGACCCGGCATATCATGTTAAT 60.202 41.667 0.00 0.00 0.00 1.40
2223 2326 5.012664 ACTGACCCGGCATATCATGTTAATA 59.987 40.000 0.00 0.00 0.00 0.98
2224 2327 6.061022 TGACCCGGCATATCATGTTAATAT 57.939 37.500 0.00 0.00 0.00 1.28
2225 2328 6.480763 TGACCCGGCATATCATGTTAATATT 58.519 36.000 0.00 0.00 0.00 1.28
2226 2329 6.945435 TGACCCGGCATATCATGTTAATATTT 59.055 34.615 0.00 0.00 0.00 1.40
2227 2330 7.450014 TGACCCGGCATATCATGTTAATATTTT 59.550 33.333 0.00 0.00 0.00 1.82
2228 2331 8.871629 ACCCGGCATATCATGTTAATATTTTA 57.128 30.769 0.00 0.00 0.00 1.52
2229 2332 9.474313 ACCCGGCATATCATGTTAATATTTTAT 57.526 29.630 0.00 0.00 0.00 1.40
2230 2333 9.734620 CCCGGCATATCATGTTAATATTTTATG 57.265 33.333 0.00 0.00 0.00 1.90
2239 2342 8.349245 TCATGTTAATATTTTATGAAGGCACCG 58.651 33.333 0.00 0.00 0.00 4.94
2240 2343 7.633193 TGTTAATATTTTATGAAGGCACCGT 57.367 32.000 0.00 0.00 0.00 4.83
2241 2344 8.734218 TGTTAATATTTTATGAAGGCACCGTA 57.266 30.769 0.00 0.00 0.00 4.02
2242 2345 8.832521 TGTTAATATTTTATGAAGGCACCGTAG 58.167 33.333 0.00 0.00 0.00 3.51
2243 2346 9.048446 GTTAATATTTTATGAAGGCACCGTAGA 57.952 33.333 0.00 0.00 0.00 2.59
2244 2347 7.492352 AATATTTTATGAAGGCACCGTAGAC 57.508 36.000 0.00 0.00 0.00 2.59
2245 2348 2.572191 TTATGAAGGCACCGTAGACG 57.428 50.000 0.00 0.00 39.44 4.18
2246 2349 1.466856 TATGAAGGCACCGTAGACGT 58.533 50.000 0.85 0.00 37.74 4.34
2247 2350 0.172803 ATGAAGGCACCGTAGACGTC 59.827 55.000 7.70 7.70 37.74 4.34
2248 2351 0.892358 TGAAGGCACCGTAGACGTCT 60.892 55.000 23.66 23.66 37.74 4.18
2249 2352 0.179169 GAAGGCACCGTAGACGTCTC 60.179 60.000 23.89 12.76 37.74 3.36
2250 2353 1.919956 AAGGCACCGTAGACGTCTCG 61.920 60.000 23.89 22.90 37.74 4.04
2251 2354 2.684843 GGCACCGTAGACGTCTCGT 61.685 63.158 23.89 13.92 45.10 4.18
2252 2355 1.361668 GGCACCGTAGACGTCTCGTA 61.362 60.000 23.89 0.83 41.37 3.43
2253 2356 0.026027 GCACCGTAGACGTCTCGTAG 59.974 60.000 23.89 18.01 41.37 3.51
2254 2357 1.354040 CACCGTAGACGTCTCGTAGT 58.646 55.000 23.89 15.32 41.37 2.73
2255 2358 1.322936 CACCGTAGACGTCTCGTAGTC 59.677 57.143 23.89 6.09 41.37 2.59
2256 2359 0.569810 CCGTAGACGTCTCGTAGTCG 59.430 60.000 23.89 16.47 41.37 4.18
2257 2360 1.539341 CGTAGACGTCTCGTAGTCGA 58.461 55.000 23.89 0.00 41.37 4.20
2258 2361 1.251508 CGTAGACGTCTCGTAGTCGAC 59.748 57.143 23.89 7.70 41.37 4.20
2269 2372 2.541055 GTAGTCGACGGGAACTTCTC 57.459 55.000 10.46 0.00 0.00 2.87
2270 2373 1.132073 GTAGTCGACGGGAACTTCTCC 59.868 57.143 10.46 0.00 44.54 3.71
2271 2374 0.251253 AGTCGACGGGAACTTCTCCT 60.251 55.000 10.46 0.00 44.68 3.69
2272 2375 0.170784 GTCGACGGGAACTTCTCCTC 59.829 60.000 0.00 0.00 44.68 3.71
2273 2376 1.136984 CGACGGGAACTTCTCCTCG 59.863 63.158 0.00 0.00 44.68 4.63
2274 2377 1.153804 GACGGGAACTTCTCCTCGC 60.154 63.158 0.00 0.00 44.68 5.03
2276 2379 1.446272 CGGGAACTTCTCCTCGCAC 60.446 63.158 0.00 0.00 44.68 5.34
2279 2382 0.603569 GGAACTTCTCCTCGCACTGA 59.396 55.000 0.00 0.00 41.61 3.41
2285 2388 0.390340 TCTCCTCGCACTGAACATGC 60.390 55.000 0.00 0.00 39.81 4.06
2288 2391 0.376152 CCTCGCACTGAACATGCATC 59.624 55.000 0.00 0.00 43.57 3.91
2290 2393 1.669265 CTCGCACTGAACATGCATCAT 59.331 47.619 0.00 0.00 43.57 2.45
2293 2396 1.667212 GCACTGAACATGCATCATCGA 59.333 47.619 0.00 0.00 42.88 3.59
2294 2397 2.096335 GCACTGAACATGCATCATCGAA 59.904 45.455 0.00 0.00 42.88 3.71
2296 2399 4.725359 CACTGAACATGCATCATCGAAAA 58.275 39.130 0.00 0.00 0.00 2.29
2297 2400 5.337554 CACTGAACATGCATCATCGAAAAT 58.662 37.500 0.00 0.00 0.00 1.82
2302 2405 8.754230 TGAACATGCATCATCGAAAATTTTAA 57.246 26.923 2.75 0.00 0.00 1.52
2335 4335 6.155221 TCAGAATAAATGTGAGTAGCAGGACT 59.845 38.462 0.00 0.00 0.00 3.85
2336 4336 6.820656 CAGAATAAATGTGAGTAGCAGGACTT 59.179 38.462 0.00 0.00 0.00 3.01
2337 4337 6.820656 AGAATAAATGTGAGTAGCAGGACTTG 59.179 38.462 0.00 0.00 0.00 3.16
2345 4345 3.100671 AGTAGCAGGACTTGAACCCTAG 58.899 50.000 0.00 0.00 0.00 3.02
2346 4346 2.031495 AGCAGGACTTGAACCCTAGT 57.969 50.000 0.00 0.00 0.00 2.57
2347 4347 1.625818 AGCAGGACTTGAACCCTAGTG 59.374 52.381 0.00 0.00 0.00 2.74
2348 4348 1.339151 GCAGGACTTGAACCCTAGTGG 60.339 57.143 0.00 0.00 41.37 4.00
2361 4361 2.894731 CCTAGTGGGCTGAGGATATCA 58.105 52.381 4.83 0.00 36.21 2.15
2375 4375 4.484912 AGGATATCAGTGTCCTCCTAACC 58.515 47.826 4.83 0.00 41.68 2.85
2376 4376 4.078571 AGGATATCAGTGTCCTCCTAACCA 60.079 45.833 4.83 0.00 41.68 3.67
2377 4377 4.841246 GGATATCAGTGTCCTCCTAACCAT 59.159 45.833 4.83 0.00 33.16 3.55
2379 4379 2.467880 TCAGTGTCCTCCTAACCATCC 58.532 52.381 0.00 0.00 0.00 3.51
2380 4380 2.187958 CAGTGTCCTCCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
2381 4381 2.571653 CAGTGTCCTCCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
2383 4383 1.913419 TGTCCTCCTAACCATCCAACC 59.087 52.381 0.00 0.00 0.00 3.77
2384 4384 1.913419 GTCCTCCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
2386 4386 1.633432 CCTCCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
2388 4388 2.571653 CTCCTAACCATCCAACCACAGA 59.428 50.000 0.00 0.00 0.00 3.41
2389 4389 3.189606 TCCTAACCATCCAACCACAGAT 58.810 45.455 0.00 0.00 0.00 2.90
2390 4390 3.591527 TCCTAACCATCCAACCACAGATT 59.408 43.478 0.00 0.00 0.00 2.40
2391 4391 3.696051 CCTAACCATCCAACCACAGATTG 59.304 47.826 0.00 0.00 0.00 2.67
2417 4529 2.418669 CCCCTAGGGCATCTTTAAGGA 58.581 52.381 23.84 0.00 35.35 3.36
2420 4532 3.395941 CCCTAGGGCATCTTTAAGGACAT 59.604 47.826 16.90 0.00 0.00 3.06
2433 4545 1.825090 AGGACATTGCTCAAATCGCA 58.175 45.000 0.00 0.00 35.22 5.10
2438 4550 1.679680 CATTGCTCAAATCGCATCCCT 59.320 47.619 0.00 0.00 37.22 4.20
2439 4551 2.708216 TTGCTCAAATCGCATCCCTA 57.292 45.000 0.00 0.00 37.22 3.53
2440 4552 2.936919 TGCTCAAATCGCATCCCTAT 57.063 45.000 0.00 0.00 31.40 2.57
2442 4554 3.141398 TGCTCAAATCGCATCCCTATTC 58.859 45.455 0.00 0.00 31.40 1.75
2443 4555 3.141398 GCTCAAATCGCATCCCTATTCA 58.859 45.455 0.00 0.00 0.00 2.57
2444 4556 3.755378 GCTCAAATCGCATCCCTATTCAT 59.245 43.478 0.00 0.00 0.00 2.57
2445 4557 4.142730 GCTCAAATCGCATCCCTATTCATC 60.143 45.833 0.00 0.00 0.00 2.92
2446 4558 5.233083 TCAAATCGCATCCCTATTCATCT 57.767 39.130 0.00 0.00 0.00 2.90
2447 4559 6.358974 TCAAATCGCATCCCTATTCATCTA 57.641 37.500 0.00 0.00 0.00 1.98
2448 4560 6.401394 TCAAATCGCATCCCTATTCATCTAG 58.599 40.000 0.00 0.00 0.00 2.43
2473 4593 8.726988 AGTATAAATGTTGTTCTGCGTATTGTT 58.273 29.630 0.00 0.00 0.00 2.83
2478 4598 4.334203 TGTTGTTCTGCGTATTGTTGAAGT 59.666 37.500 0.00 0.00 0.00 3.01
2481 4601 4.151689 TGTTCTGCGTATTGTTGAAGTAGC 59.848 41.667 0.00 0.00 0.00 3.58
2487 4607 6.827641 TGCGTATTGTTGAAGTAGCTAAAAG 58.172 36.000 0.00 0.00 0.00 2.27
2491 4611 5.432885 TTGTTGAAGTAGCTAAAAGTGCC 57.567 39.130 0.00 0.00 0.00 5.01
2492 4612 4.456535 TGTTGAAGTAGCTAAAAGTGCCA 58.543 39.130 0.00 0.00 0.00 4.92
2496 4616 6.648879 TGAAGTAGCTAAAAGTGCCAAATT 57.351 33.333 0.00 0.00 0.00 1.82
2501 4621 4.737054 AGCTAAAAGTGCCAAATTGATCG 58.263 39.130 0.00 0.00 0.00 3.69
2509 4629 3.080319 TGCCAAATTGATCGATGACACA 58.920 40.909 0.54 0.00 0.00 3.72
2516 4636 4.470334 TTGATCGATGACACAATCCTGA 57.530 40.909 0.54 0.00 0.00 3.86
2533 4653 8.772250 ACAATCCTGATTCTCATTCCTAAAGTA 58.228 33.333 0.00 0.00 0.00 2.24
2536 4656 9.790344 ATCCTGATTCTCATTCCTAAAGTATTG 57.210 33.333 0.00 0.00 0.00 1.90
2575 4695 1.757118 CAATTCCGTCCTCTCAGCCTA 59.243 52.381 0.00 0.00 0.00 3.93
2578 4698 1.109920 TCCGTCCTCTCAGCCTATGC 61.110 60.000 0.00 0.00 37.95 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.030562 CGTGGAAGTTGCTCCGGT 59.969 61.111 0.00 0.00 38.44 5.28
124 125 1.982660 CCTCTATCCGGTACTGCTCA 58.017 55.000 0.00 0.00 0.00 4.26
182 183 5.494724 CCTTTGGTGATCTTCTCAATCTCA 58.505 41.667 0.00 0.00 35.07 3.27
183 184 4.880696 CCCTTTGGTGATCTTCTCAATCTC 59.119 45.833 0.00 0.00 35.07 2.75
184 185 4.290722 ACCCTTTGGTGATCTTCTCAATCT 59.709 41.667 0.00 0.00 45.58 2.40
185 186 4.593956 ACCCTTTGGTGATCTTCTCAATC 58.406 43.478 0.00 0.00 45.58 2.67
186 187 4.664688 ACCCTTTGGTGATCTTCTCAAT 57.335 40.909 0.00 0.00 45.58 2.57
204 211 2.492484 CAGTCTACAGAGTACACCACCC 59.508 54.545 0.00 0.00 0.00 4.61
222 229 5.984695 TTGAAGATAGCACAGACTACAGT 57.015 39.130 0.00 0.00 0.00 3.55
223 230 7.658179 TTTTTGAAGATAGCACAGACTACAG 57.342 36.000 0.00 0.00 0.00 2.74
224 231 8.621532 AATTTTTGAAGATAGCACAGACTACA 57.378 30.769 0.00 0.00 0.00 2.74
225 232 8.940952 AGAATTTTTGAAGATAGCACAGACTAC 58.059 33.333 0.00 0.00 0.00 2.73
226 233 9.507329 AAGAATTTTTGAAGATAGCACAGACTA 57.493 29.630 0.00 0.00 0.00 2.59
227 234 7.992754 AGAATTTTTGAAGATAGCACAGACT 57.007 32.000 0.00 0.00 0.00 3.24
228 235 9.766277 CTAAGAATTTTTGAAGATAGCACAGAC 57.234 33.333 0.00 0.00 0.00 3.51
257 264 6.966632 TCAAGTTATTTGAAAGCGCACATATC 59.033 34.615 11.47 0.13 42.69 1.63
274 281 9.903682 CAAACTGACAAGATCAATTCAAGTTAT 57.096 29.630 0.00 0.00 36.69 1.89
284 291 6.461370 CCAATTCACCAAACTGACAAGATCAA 60.461 38.462 0.00 0.00 36.69 2.57
359 366 4.795469 TGTGATATTCCCACCTCGTACTA 58.205 43.478 0.00 0.00 33.80 1.82
372 379 7.495606 TGTGAAGTGTGGTATCATGTGATATTC 59.504 37.037 6.04 5.71 39.03 1.75
380 387 4.937015 TGTCATGTGAAGTGTGGTATCATG 59.063 41.667 0.00 0.00 34.46 3.07
410 417 5.520376 AATTTGAAGTTTGAGGAGTGGTG 57.480 39.130 0.00 0.00 0.00 4.17
471 502 7.014808 TCGAATTTGGGTCTGAAAATTTAAGGT 59.985 33.333 0.00 0.00 36.40 3.50
518 549 1.683385 GTTCATGCTAGATTTGCCCCC 59.317 52.381 0.00 0.00 0.00 5.40
522 553 4.644103 ATGGTGTTCATGCTAGATTTGC 57.356 40.909 0.00 0.00 34.22 3.68
574 628 1.984990 CCCAAATTCGAAATGCACACG 59.015 47.619 0.00 0.00 0.00 4.49
686 742 4.552355 CGATACCATGATACAACCGCTAA 58.448 43.478 0.00 0.00 0.00 3.09
687 743 3.613193 GCGATACCATGATACAACCGCTA 60.613 47.826 0.00 0.00 37.51 4.26
688 744 2.866460 GCGATACCATGATACAACCGCT 60.866 50.000 0.00 0.00 37.51 5.52
690 746 1.719246 CGCGATACCATGATACAACCG 59.281 52.381 0.00 0.00 0.00 4.44
691 747 3.021269 TCGCGATACCATGATACAACC 57.979 47.619 3.71 0.00 0.00 3.77
730 786 1.387084 GACTCGACTTCGTTCATGTGC 59.613 52.381 0.00 0.00 40.80 4.57
733 789 3.420544 CGTTTGACTCGACTTCGTTCATG 60.421 47.826 0.00 0.00 40.80 3.07
735 791 2.114056 CGTTTGACTCGACTTCGTTCA 58.886 47.619 0.00 0.60 40.80 3.18
751 812 0.519961 GTATGGCGCTTGGTTCGTTT 59.480 50.000 7.64 0.00 0.00 3.60
900 961 0.538746 TAGTGAGGTGCGTCAGGTCA 60.539 55.000 0.00 0.00 0.00 4.02
906 967 2.095364 CCGGTATATAGTGAGGTGCGTC 60.095 54.545 0.00 0.00 0.00 5.19
909 970 4.077822 AGTACCGGTATATAGTGAGGTGC 58.922 47.826 19.19 0.00 35.16 5.01
937 1002 0.980423 GGATAGGGAGATGTCAGCCC 59.020 60.000 0.00 0.00 42.37 5.19
939 1004 0.980423 GGGGATAGGGAGATGTCAGC 59.020 60.000 0.00 0.00 0.00 4.26
940 1005 2.534990 GAGGGGATAGGGAGATGTCAG 58.465 57.143 0.00 0.00 0.00 3.51
941 1006 1.150135 GGAGGGGATAGGGAGATGTCA 59.850 57.143 0.00 0.00 0.00 3.58
945 1010 1.153132 CCTTGGAGGGGATAGGGAGAT 59.847 57.143 0.00 0.00 0.00 2.75
974 1047 2.325082 GCCGGCAGGTACACACAAG 61.325 63.158 24.80 0.00 40.50 3.16
1631 1734 2.098443 ACTTCATGCAAACGACGGTTTT 59.902 40.909 0.00 0.00 43.69 2.43
1641 1744 1.268999 GCGACACCAACTTCATGCAAA 60.269 47.619 0.00 0.00 0.00 3.68
2134 2237 5.299531 AGGATGAGTGTATGCGCGTATATAT 59.700 40.000 19.79 9.03 0.00 0.86
2135 2238 4.638865 AGGATGAGTGTATGCGCGTATATA 59.361 41.667 19.79 14.59 0.00 0.86
2136 2239 3.444034 AGGATGAGTGTATGCGCGTATAT 59.556 43.478 19.79 4.31 0.00 0.86
2137 2240 2.817844 AGGATGAGTGTATGCGCGTATA 59.182 45.455 13.13 13.13 0.00 1.47
2138 2241 1.613925 AGGATGAGTGTATGCGCGTAT 59.386 47.619 15.52 15.52 0.00 3.06
2139 2242 1.029681 AGGATGAGTGTATGCGCGTA 58.970 50.000 8.43 4.92 0.00 4.42
2141 2244 1.988467 CATAGGATGAGTGTATGCGCG 59.012 52.381 0.00 0.00 0.00 6.86
2142 2245 2.989840 GTCATAGGATGAGTGTATGCGC 59.010 50.000 0.00 0.00 40.53 6.09
2143 2246 3.237628 CGTCATAGGATGAGTGTATGCG 58.762 50.000 0.00 0.00 40.53 4.73
2144 2247 2.989840 GCGTCATAGGATGAGTGTATGC 59.010 50.000 0.00 0.00 40.53 3.14
2145 2248 3.983988 GTGCGTCATAGGATGAGTGTATG 59.016 47.826 0.00 0.00 40.53 2.39
2146 2249 3.636764 TGTGCGTCATAGGATGAGTGTAT 59.363 43.478 0.00 0.00 40.53 2.29
2148 2251 1.824852 TGTGCGTCATAGGATGAGTGT 59.175 47.619 0.00 0.00 40.53 3.55
2149 2252 2.196749 GTGTGCGTCATAGGATGAGTG 58.803 52.381 0.00 0.00 40.53 3.51
2150 2253 1.824852 TGTGTGCGTCATAGGATGAGT 59.175 47.619 0.00 0.00 40.53 3.41
2151 2254 2.584492 TGTGTGCGTCATAGGATGAG 57.416 50.000 0.00 0.00 40.53 2.90
2153 2256 3.490896 GTGTATGTGTGCGTCATAGGATG 59.509 47.826 0.00 0.00 0.00 3.51
2155 2258 2.478879 CGTGTATGTGTGCGTCATAGGA 60.479 50.000 0.00 0.00 0.00 2.94
2156 2259 1.852280 CGTGTATGTGTGCGTCATAGG 59.148 52.381 0.00 0.00 0.00 2.57
2157 2260 2.526077 ACGTGTATGTGTGCGTCATAG 58.474 47.619 0.00 0.00 31.54 2.23
2158 2261 2.640346 ACGTGTATGTGTGCGTCATA 57.360 45.000 0.00 0.00 31.54 2.15
2159 2262 1.724623 GAACGTGTATGTGTGCGTCAT 59.275 47.619 0.00 0.00 36.51 3.06
2162 2265 2.710220 TAGAACGTGTATGTGTGCGT 57.290 45.000 0.00 0.00 39.37 5.24
2164 2267 4.673441 AGAGATAGAACGTGTATGTGTGC 58.327 43.478 0.00 0.00 0.00 4.57
2165 2268 7.639945 TCATAGAGATAGAACGTGTATGTGTG 58.360 38.462 0.00 0.00 0.00 3.82
2166 2269 7.520776 GCTCATAGAGATAGAACGTGTATGTGT 60.521 40.741 0.00 0.00 0.00 3.72
2167 2270 6.799441 GCTCATAGAGATAGAACGTGTATGTG 59.201 42.308 0.00 0.00 0.00 3.21
2168 2271 6.072397 GGCTCATAGAGATAGAACGTGTATGT 60.072 42.308 0.00 0.00 0.00 2.29
2169 2272 6.318628 GGCTCATAGAGATAGAACGTGTATG 58.681 44.000 0.00 0.00 0.00 2.39
2170 2273 5.122554 CGGCTCATAGAGATAGAACGTGTAT 59.877 44.000 0.00 0.00 0.00 2.29
2171 2274 4.451435 CGGCTCATAGAGATAGAACGTGTA 59.549 45.833 0.00 0.00 0.00 2.90
2172 2275 3.251245 CGGCTCATAGAGATAGAACGTGT 59.749 47.826 0.00 0.00 0.00 4.49
2173 2276 3.498777 TCGGCTCATAGAGATAGAACGTG 59.501 47.826 0.00 0.00 0.00 4.49
2174 2277 3.741249 TCGGCTCATAGAGATAGAACGT 58.259 45.455 0.00 0.00 0.00 3.99
2175 2278 3.997681 TCTCGGCTCATAGAGATAGAACG 59.002 47.826 0.00 0.00 38.46 3.95
2176 2279 5.242434 TCTCTCGGCTCATAGAGATAGAAC 58.758 45.833 0.00 0.00 42.52 3.01
2177 2280 5.491323 TCTCTCGGCTCATAGAGATAGAA 57.509 43.478 0.00 0.00 42.52 2.10
2182 2285 2.436173 TCAGTCTCTCGGCTCATAGAGA 59.564 50.000 0.00 0.00 44.59 3.10
2183 2286 2.548057 GTCAGTCTCTCGGCTCATAGAG 59.452 54.545 0.00 0.00 40.54 2.43
2184 2287 2.566913 GTCAGTCTCTCGGCTCATAGA 58.433 52.381 0.00 0.00 0.00 1.98
2185 2288 1.606668 GGTCAGTCTCTCGGCTCATAG 59.393 57.143 0.00 0.00 0.00 2.23
2186 2289 1.681538 GGTCAGTCTCTCGGCTCATA 58.318 55.000 0.00 0.00 0.00 2.15
2187 2290 1.040339 GGGTCAGTCTCTCGGCTCAT 61.040 60.000 0.00 0.00 0.00 2.90
2188 2291 1.679305 GGGTCAGTCTCTCGGCTCA 60.679 63.158 0.00 0.00 0.00 4.26
2189 2292 2.766400 CGGGTCAGTCTCTCGGCTC 61.766 68.421 0.00 0.00 0.00 4.70
2190 2293 2.752238 CGGGTCAGTCTCTCGGCT 60.752 66.667 0.00 0.00 0.00 5.52
2191 2294 3.827898 CCGGGTCAGTCTCTCGGC 61.828 72.222 0.00 0.00 34.17 5.54
2192 2295 3.827898 GCCGGGTCAGTCTCTCGG 61.828 72.222 2.18 0.00 43.13 4.63
2193 2296 1.101635 TATGCCGGGTCAGTCTCTCG 61.102 60.000 2.18 0.00 0.00 4.04
2194 2297 1.271102 GATATGCCGGGTCAGTCTCTC 59.729 57.143 2.18 0.00 0.00 3.20
2195 2298 1.333177 GATATGCCGGGTCAGTCTCT 58.667 55.000 2.18 0.00 0.00 3.10
2196 2299 1.040646 TGATATGCCGGGTCAGTCTC 58.959 55.000 2.18 0.00 0.00 3.36
2197 2300 1.345741 CATGATATGCCGGGTCAGTCT 59.654 52.381 2.18 0.00 0.00 3.24
2198 2301 1.070758 ACATGATATGCCGGGTCAGTC 59.929 52.381 2.18 0.00 0.00 3.51
2199 2302 1.131638 ACATGATATGCCGGGTCAGT 58.868 50.000 2.18 0.00 0.00 3.41
2200 2303 2.260844 AACATGATATGCCGGGTCAG 57.739 50.000 2.18 0.00 0.00 3.51
2201 2304 3.847671 TTAACATGATATGCCGGGTCA 57.152 42.857 2.18 0.00 0.00 4.02
2202 2305 7.391148 AAATATTAACATGATATGCCGGGTC 57.609 36.000 2.18 0.00 0.00 4.46
2203 2306 7.775053 AAAATATTAACATGATATGCCGGGT 57.225 32.000 2.18 0.00 0.00 5.28
2204 2307 9.734620 CATAAAATATTAACATGATATGCCGGG 57.265 33.333 2.18 0.00 0.00 5.73
2213 2316 8.349245 CGGTGCCTTCATAAAATATTAACATGA 58.651 33.333 0.00 0.00 0.00 3.07
2214 2317 8.134895 ACGGTGCCTTCATAAAATATTAACATG 58.865 33.333 0.00 0.00 0.00 3.21
2215 2318 8.232913 ACGGTGCCTTCATAAAATATTAACAT 57.767 30.769 0.00 0.00 0.00 2.71
2216 2319 7.633193 ACGGTGCCTTCATAAAATATTAACA 57.367 32.000 0.00 0.00 0.00 2.41
2217 2320 9.048446 TCTACGGTGCCTTCATAAAATATTAAC 57.952 33.333 0.00 0.00 0.00 2.01
2218 2321 9.048446 GTCTACGGTGCCTTCATAAAATATTAA 57.952 33.333 0.00 0.00 0.00 1.40
2219 2322 7.383029 CGTCTACGGTGCCTTCATAAAATATTA 59.617 37.037 0.00 0.00 35.37 0.98
2220 2323 6.202188 CGTCTACGGTGCCTTCATAAAATATT 59.798 38.462 0.00 0.00 35.37 1.28
2221 2324 5.694910 CGTCTACGGTGCCTTCATAAAATAT 59.305 40.000 0.00 0.00 35.37 1.28
2222 2325 5.045215 CGTCTACGGTGCCTTCATAAAATA 58.955 41.667 0.00 0.00 35.37 1.40
2223 2326 3.869246 CGTCTACGGTGCCTTCATAAAAT 59.131 43.478 0.00 0.00 35.37 1.82
2224 2327 3.255725 CGTCTACGGTGCCTTCATAAAA 58.744 45.455 0.00 0.00 35.37 1.52
2225 2328 2.231964 ACGTCTACGGTGCCTTCATAAA 59.768 45.455 7.50 0.00 44.95 1.40
2226 2329 1.820519 ACGTCTACGGTGCCTTCATAA 59.179 47.619 7.50 0.00 44.95 1.90
2227 2330 1.402968 GACGTCTACGGTGCCTTCATA 59.597 52.381 8.70 0.00 44.95 2.15
2228 2331 0.172803 GACGTCTACGGTGCCTTCAT 59.827 55.000 8.70 0.00 44.95 2.57
2229 2332 0.892358 AGACGTCTACGGTGCCTTCA 60.892 55.000 18.46 0.00 44.95 3.02
2230 2333 0.179169 GAGACGTCTACGGTGCCTTC 60.179 60.000 20.09 0.00 44.95 3.46
2231 2334 1.881602 GAGACGTCTACGGTGCCTT 59.118 57.895 20.09 0.00 44.95 4.35
2232 2335 2.396955 CGAGACGTCTACGGTGCCT 61.397 63.158 20.09 0.00 44.95 4.75
2233 2336 1.361668 TACGAGACGTCTACGGTGCC 61.362 60.000 28.32 13.08 44.95 5.01
2234 2337 0.026027 CTACGAGACGTCTACGGTGC 59.974 60.000 28.32 13.67 44.95 5.01
2235 2338 1.322936 GACTACGAGACGTCTACGGTG 59.677 57.143 28.32 23.41 44.95 4.94
2236 2339 1.634702 GACTACGAGACGTCTACGGT 58.365 55.000 28.32 23.19 44.95 4.83
2237 2340 0.569810 CGACTACGAGACGTCTACGG 59.430 60.000 28.32 19.83 41.54 4.02
2238 2341 1.539341 TCGACTACGAGACGTCTACG 58.461 55.000 20.09 23.56 43.81 3.51
2250 2353 1.132073 GGAGAAGTTCCCGTCGACTAC 59.868 57.143 14.70 6.45 40.37 2.73
2251 2354 1.457346 GGAGAAGTTCCCGTCGACTA 58.543 55.000 14.70 0.00 40.37 2.59
2252 2355 2.265096 GGAGAAGTTCCCGTCGACT 58.735 57.895 14.70 0.00 40.37 4.18
2253 2356 4.885157 GGAGAAGTTCCCGTCGAC 57.115 61.111 5.18 5.18 40.37 4.20
2261 2364 2.062519 GTTCAGTGCGAGGAGAAGTTC 58.937 52.381 0.00 0.00 0.00 3.01
2262 2365 1.412710 TGTTCAGTGCGAGGAGAAGTT 59.587 47.619 0.00 0.00 0.00 2.66
2263 2366 1.040646 TGTTCAGTGCGAGGAGAAGT 58.959 50.000 0.00 0.00 0.00 3.01
2264 2367 1.998315 CATGTTCAGTGCGAGGAGAAG 59.002 52.381 0.00 0.00 0.00 2.85
2265 2368 1.941209 GCATGTTCAGTGCGAGGAGAA 60.941 52.381 0.00 0.00 32.29 2.87
2266 2369 0.390340 GCATGTTCAGTGCGAGGAGA 60.390 55.000 0.00 0.00 32.29 3.71
2267 2370 0.671472 TGCATGTTCAGTGCGAGGAG 60.671 55.000 0.00 0.00 45.37 3.69
2268 2371 0.036105 ATGCATGTTCAGTGCGAGGA 60.036 50.000 0.00 0.00 45.37 3.71
2269 2372 0.376152 GATGCATGTTCAGTGCGAGG 59.624 55.000 2.46 0.00 45.37 4.63
2270 2373 1.081094 TGATGCATGTTCAGTGCGAG 58.919 50.000 2.46 0.00 45.37 5.03
2271 2374 1.667212 GATGATGCATGTTCAGTGCGA 59.333 47.619 2.46 0.00 45.37 5.10
2272 2375 1.593793 CGATGATGCATGTTCAGTGCG 60.594 52.381 2.46 0.00 45.37 5.34
2273 2376 1.667212 TCGATGATGCATGTTCAGTGC 59.333 47.619 2.46 0.00 42.81 4.40
2274 2377 4.345271 TTTCGATGATGCATGTTCAGTG 57.655 40.909 2.46 0.00 0.00 3.66
2276 2379 6.880822 AAATTTTCGATGATGCATGTTCAG 57.119 33.333 2.46 0.00 0.00 3.02
2306 2409 8.680903 CCTGCTACTCACATTTATTCTGAATTT 58.319 33.333 8.38 0.00 0.00 1.82
2309 2412 6.818644 GTCCTGCTACTCACATTTATTCTGAA 59.181 38.462 0.00 0.00 0.00 3.02
2311 2414 6.344500 AGTCCTGCTACTCACATTTATTCTG 58.656 40.000 0.00 0.00 0.00 3.02
2312 2415 6.552445 AGTCCTGCTACTCACATTTATTCT 57.448 37.500 0.00 0.00 0.00 2.40
2313 2416 6.818644 TCAAGTCCTGCTACTCACATTTATTC 59.181 38.462 0.00 0.00 0.00 1.75
2314 2417 6.711277 TCAAGTCCTGCTACTCACATTTATT 58.289 36.000 0.00 0.00 0.00 1.40
2317 2420 4.623932 TCAAGTCCTGCTACTCACATTT 57.376 40.909 0.00 0.00 0.00 2.32
2319 2422 3.307059 GGTTCAAGTCCTGCTACTCACAT 60.307 47.826 0.00 0.00 0.00 3.21
2320 2423 2.037251 GGTTCAAGTCCTGCTACTCACA 59.963 50.000 0.00 0.00 0.00 3.58
2321 2424 2.613223 GGGTTCAAGTCCTGCTACTCAC 60.613 54.545 0.00 0.00 0.00 3.51
2322 2425 1.623811 GGGTTCAAGTCCTGCTACTCA 59.376 52.381 0.00 0.00 0.00 3.41
2323 2426 1.903183 AGGGTTCAAGTCCTGCTACTC 59.097 52.381 0.00 0.00 31.11 2.59
2324 2427 2.031495 AGGGTTCAAGTCCTGCTACT 57.969 50.000 0.00 0.00 31.11 2.57
2325 2428 2.832733 ACTAGGGTTCAAGTCCTGCTAC 59.167 50.000 0.00 0.00 34.75 3.58
2326 2429 2.832129 CACTAGGGTTCAAGTCCTGCTA 59.168 50.000 0.00 0.00 34.75 3.49
2355 4355 5.046950 GGATGGTTAGGAGGACACTGATATC 60.047 48.000 0.00 0.00 0.00 1.63
2357 4357 4.223953 GGATGGTTAGGAGGACACTGATA 58.776 47.826 0.00 0.00 0.00 2.15
2358 4358 3.041946 GGATGGTTAGGAGGACACTGAT 58.958 50.000 0.00 0.00 0.00 2.90
2359 4359 2.225522 TGGATGGTTAGGAGGACACTGA 60.226 50.000 0.00 0.00 0.00 3.41
2360 4360 2.187958 TGGATGGTTAGGAGGACACTG 58.812 52.381 0.00 0.00 0.00 3.66
2361 4361 2.572104 GTTGGATGGTTAGGAGGACACT 59.428 50.000 0.00 0.00 0.00 3.55
2362 4362 2.355818 GGTTGGATGGTTAGGAGGACAC 60.356 54.545 0.00 0.00 0.00 3.67
2364 4364 1.913419 TGGTTGGATGGTTAGGAGGAC 59.087 52.381 0.00 0.00 0.00 3.85
2366 4366 1.633432 TGTGGTTGGATGGTTAGGAGG 59.367 52.381 0.00 0.00 0.00 4.30
2367 4367 2.571653 TCTGTGGTTGGATGGTTAGGAG 59.428 50.000 0.00 0.00 0.00 3.69
2368 4368 2.626785 TCTGTGGTTGGATGGTTAGGA 58.373 47.619 0.00 0.00 0.00 2.94
2369 4369 3.652057 ATCTGTGGTTGGATGGTTAGG 57.348 47.619 0.00 0.00 0.00 2.69
2370 4370 4.970662 CAATCTGTGGTTGGATGGTTAG 57.029 45.455 0.00 0.00 0.00 2.34
2383 4383 2.356125 CCTAGGGGTGAACCAATCTGTG 60.356 54.545 0.00 0.00 42.91 3.66
2384 4384 1.916181 CCTAGGGGTGAACCAATCTGT 59.084 52.381 0.00 0.00 42.91 3.41
2386 4386 1.596496 CCCTAGGGGTGAACCAATCT 58.404 55.000 21.44 0.00 42.91 2.40
2388 4388 0.849094 TGCCCTAGGGGTGAACCAAT 60.849 55.000 29.57 0.00 46.51 3.16
2389 4389 0.849094 ATGCCCTAGGGGTGAACCAA 60.849 55.000 29.57 3.11 46.51 3.67
2390 4390 1.230149 ATGCCCTAGGGGTGAACCA 60.230 57.895 29.57 17.31 46.51 3.67
2391 4391 0.988678 AGATGCCCTAGGGGTGAACC 60.989 60.000 29.57 11.83 46.51 3.62
2393 4393 1.681229 AAAGATGCCCTAGGGGTGAA 58.319 50.000 29.57 0.00 46.51 3.18
2394 4394 2.579624 TAAAGATGCCCTAGGGGTGA 57.420 50.000 29.57 2.19 46.51 4.02
2396 4396 2.136026 CCTTAAAGATGCCCTAGGGGT 58.864 52.381 29.57 0.00 46.51 4.95
2398 4398 2.777692 TGTCCTTAAAGATGCCCTAGGG 59.222 50.000 24.89 24.89 38.57 3.53
2399 4399 4.713792 ATGTCCTTAAAGATGCCCTAGG 57.286 45.455 0.06 0.06 0.00 3.02
2407 4519 6.678900 GCGATTTGAGCAATGTCCTTAAAGAT 60.679 38.462 0.00 0.00 34.19 2.40
2440 4552 8.817100 CGCAGAACAACATTTATACTAGATGAA 58.183 33.333 0.00 0.00 0.00 2.57
2442 4554 8.131455 ACGCAGAACAACATTTATACTAGATG 57.869 34.615 0.00 0.00 0.00 2.90
2443 4555 9.982651 ATACGCAGAACAACATTTATACTAGAT 57.017 29.630 0.00 0.00 0.00 1.98
2444 4556 9.811995 AATACGCAGAACAACATTTATACTAGA 57.188 29.630 0.00 0.00 0.00 2.43
2445 4557 9.849607 CAATACGCAGAACAACATTTATACTAG 57.150 33.333 0.00 0.00 0.00 2.57
2446 4558 9.373603 ACAATACGCAGAACAACATTTATACTA 57.626 29.630 0.00 0.00 0.00 1.82
2447 4559 8.263940 ACAATACGCAGAACAACATTTATACT 57.736 30.769 0.00 0.00 0.00 2.12
2448 4560 8.785101 CAACAATACGCAGAACAACATTTATAC 58.215 33.333 0.00 0.00 0.00 1.47
2462 4582 6.403333 TTTAGCTACTTCAACAATACGCAG 57.597 37.500 0.00 0.00 0.00 5.18
2473 4593 6.264292 TCAATTTGGCACTTTTAGCTACTTCA 59.736 34.615 0.00 0.00 0.00 3.02
2478 4598 5.645929 TCGATCAATTTGGCACTTTTAGCTA 59.354 36.000 0.00 0.00 0.00 3.32
2481 4601 6.470235 GTCATCGATCAATTTGGCACTTTTAG 59.530 38.462 0.00 0.00 0.00 1.85
2487 4607 3.119884 TGTGTCATCGATCAATTTGGCAC 60.120 43.478 11.28 11.28 43.25 5.01
2491 4611 5.969435 CAGGATTGTGTCATCGATCAATTTG 59.031 40.000 10.38 8.89 31.87 2.32
2492 4612 5.882000 TCAGGATTGTGTCATCGATCAATTT 59.118 36.000 10.38 2.27 31.87 1.82
2496 4616 4.677673 ATCAGGATTGTGTCATCGATCA 57.322 40.909 0.00 0.00 31.73 2.92
2516 4636 8.560903 AGGGTTCAATACTTTAGGAATGAGAAT 58.439 33.333 0.00 0.00 0.00 2.40
2533 4653 5.819991 TGAGATAAAGCTGAAGGGTTCAAT 58.180 37.500 0.00 0.00 39.58 2.57
2535 4655 4.908601 TGAGATAAAGCTGAAGGGTTCA 57.091 40.909 0.00 0.00 38.17 3.18
2536 4656 6.183360 GGAATTGAGATAAAGCTGAAGGGTTC 60.183 42.308 0.00 0.00 34.22 3.62


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

AutoCloner maintained by Alex Coulton.