Multiple sequence alignment - TraesCS3D01G410500

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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 TraesCS3D01G410500 chr3D 100.000 2471 0 0 1 2471 523715702 523713232 0.000000e+00 4564
1 TraesCS3D01G410500 chr3D 91.339 381 30 1 1821 2201 399719030 399719407 3.640000e-143 518
2 TraesCS3D01G410500 chr2D 96.599 2205 64 5 1 2201 604414189 604411992 0.000000e+00 3646
3 TraesCS3D01G410500 chr2D 98.391 373 6 0 1983 2355 200930746 200930374 0.000000e+00 656
4 TraesCS3D01G410500 chr2D 94.587 351 15 2 1851 2201 382488462 382488808 7.770000e-150 540
5 TraesCS3D01G410500 chr2D 91.489 94 7 1 1781 1874 382488443 382488535 7.170000e-26 128
6 TraesCS3D01G410500 chr2D 96.000 75 3 0 1800 1874 604412339 604412265 3.340000e-24 122
7 TraesCS3D01G410500 chr7D 96.419 2206 64 10 1 2201 307120964 307123159 0.000000e+00 3622
8 TraesCS3D01G410500 chr6A 95.255 2234 73 21 1 2201 64687538 64685305 0.000000e+00 3507
9 TraesCS3D01G410500 chr7A 94.539 2234 86 22 1 2201 60253093 60255323 0.000000e+00 3417
10 TraesCS3D01G410500 chr4B 94.402 2233 91 21 1 2201 209133140 209135370 0.000000e+00 3400
11 TraesCS3D01G410500 chrUn 95.439 2061 60 21 1 2027 86467997 86465937 0.000000e+00 3254
12 TraesCS3D01G410500 chrUn 89.107 661 44 13 1569 2201 449376047 449375387 0.000000e+00 797
13 TraesCS3D01G410500 chrUn 99.196 373 3 0 1983 2355 189418355 189417983 0.000000e+00 673
14 TraesCS3D01G410500 chr6D 96.803 1877 43 6 1 1874 102373366 102375228 0.000000e+00 3118
15 TraesCS3D01G410500 chr6D 94.017 351 18 1 1851 2201 102375154 102375501 1.680000e-146 529
16 TraesCS3D01G410500 chr3A 95.119 1967 59 24 1 1932 633121759 633123723 0.000000e+00 3066
17 TraesCS3D01G410500 chr1B 94.534 1976 76 21 1 1944 672580357 672578382 0.000000e+00 3022
18 TraesCS3D01G410500 chr5D 98.928 373 4 0 1983 2355 562921004 562920632 0.000000e+00 667
19 TraesCS3D01G410500 chr5D 90.931 419 34 3 1784 2201 324471383 324470968 5.970000e-156 560
20 TraesCS3D01G410500 chr5A 98.928 373 4 0 1983 2355 614339669 614339297 0.000000e+00 667
21 TraesCS3D01G410500 chr4D 98.928 373 4 0 1983 2355 123746728 123746356 0.000000e+00 667
22 TraesCS3D01G410500 chr4D 98.660 373 5 0 1983 2355 123517262 123516890 0.000000e+00 662
23 TraesCS3D01G410500 chr2A 98.660 373 5 0 1983 2355 755510177 755509805 0.000000e+00 662
24 TraesCS3D01G410500 chr6B 84.742 426 39 15 1800 2201 215778855 215779278 1.060000e-108 403
25 TraesCS3D01G410500 chr4A 92.593 81 6 0 2384 2464 571063220 571063140 1.550000e-22 117


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 TraesCS3D01G410500 chr3D 523713232 523715702 2470 True 4564.0 4564 100.0000 1 2471 1 chr3D.!!$R1 2470
1 TraesCS3D01G410500 chr2D 604411992 604414189 2197 True 1884.0 3646 96.2995 1 2201 2 chr2D.!!$R2 2200
2 TraesCS3D01G410500 chr7D 307120964 307123159 2195 False 3622.0 3622 96.4190 1 2201 1 chr7D.!!$F1 2200
3 TraesCS3D01G410500 chr6A 64685305 64687538 2233 True 3507.0 3507 95.2550 1 2201 1 chr6A.!!$R1 2200
4 TraesCS3D01G410500 chr7A 60253093 60255323 2230 False 3417.0 3417 94.5390 1 2201 1 chr7A.!!$F1 2200
5 TraesCS3D01G410500 chr4B 209133140 209135370 2230 False 3400.0 3400 94.4020 1 2201 1 chr4B.!!$F1 2200
6 TraesCS3D01G410500 chrUn 86465937 86467997 2060 True 3254.0 3254 95.4390 1 2027 1 chrUn.!!$R1 2026
7 TraesCS3D01G410500 chrUn 449375387 449376047 660 True 797.0 797 89.1070 1569 2201 1 chrUn.!!$R3 632
8 TraesCS3D01G410500 chr6D 102373366 102375501 2135 False 1823.5 3118 95.4100 1 2201 2 chr6D.!!$F1 2200
9 TraesCS3D01G410500 chr3A 633121759 633123723 1964 False 3066.0 3066 95.1190 1 1932 1 chr3A.!!$F1 1931
10 TraesCS3D01G410500 chr1B 672578382 672580357 1975 True 3022.0 3022 94.5340 1 1944 1 chr1B.!!$R1 1943

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
624 625 3.327464 TGTGTTGGATCTGATGGTTGAGA 59.673 43.478 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2393 0.036671 TGCAGCACATCTCTCAGTGG 60.037 55.0 0.0 0.0 36.29 4.0 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
205 206 9.095065 GTTAGTATCTTTCGGTGTATCAACAAT 57.905 33.333 0.00 0.00 37.36 2.71
247 248 4.098807 TGAACTTTAAACCACAAGGGAAGC 59.901 41.667 0.00 0.00 41.15 3.86
259 260 4.520492 CACAAGGGAAGCTTTCACATAAGT 59.480 41.667 7.16 0.00 34.83 2.24
428 429 8.462016 GCCAGATGAAAACAAGTTCATAGTAAT 58.538 33.333 0.61 0.00 45.98 1.89
624 625 3.327464 TGTGTTGGATCTGATGGTTGAGA 59.673 43.478 0.00 0.00 0.00 3.27
897 898 3.784763 ACCTCCCTCATTCACATCAGAAT 59.215 43.478 0.00 0.00 38.72 2.40
1192 1203 4.385754 GCAAGGACCCTAAGAATCTGGAAT 60.386 45.833 0.00 0.00 0.00 3.01
1233 1244 6.665992 TTTAGCACCGGTCTCTCATATATT 57.334 37.500 2.59 0.00 0.00 1.28
1435 1446 6.757237 TGTTGGAAAAACATAATGCTCACAT 58.243 32.000 0.00 0.00 38.49 3.21
1791 1807 5.163055 CCCCCTTTTCCAGATCATGATTCTA 60.163 44.000 10.14 0.00 0.00 2.10
1793 1812 6.183361 CCCCTTTTCCAGATCATGATTCTAGA 60.183 42.308 10.14 4.68 0.00 2.43
2155 2248 2.417516 CGAGGCCACTGATACCCG 59.582 66.667 5.01 0.00 0.00 5.28
2157 2250 1.672854 CGAGGCCACTGATACCCGAA 61.673 60.000 5.01 0.00 0.00 4.30
2180 2273 4.016479 AGTGGTTAGGTGGGATAGAAGAGA 60.016 45.833 0.00 0.00 0.00 3.10
2184 2277 2.227703 AGGTGGGATAGAAGAGAGGGA 58.772 52.381 0.00 0.00 0.00 4.20
2186 2279 3.014110 AGGTGGGATAGAAGAGAGGGAAA 59.986 47.826 0.00 0.00 0.00 3.13
2188 2281 3.041946 TGGGATAGAAGAGAGGGAAAGC 58.958 50.000 0.00 0.00 0.00 3.51
2201 2294 1.300481 GGAAAGCGGGCTTCTATCAC 58.700 55.000 6.35 0.00 34.84 3.06
2202 2295 1.406887 GGAAAGCGGGCTTCTATCACA 60.407 52.381 6.35 0.00 34.84 3.58
2203 2296 2.565841 GAAAGCGGGCTTCTATCACAT 58.434 47.619 6.35 0.00 34.84 3.21
2204 2297 3.494398 GGAAAGCGGGCTTCTATCACATA 60.494 47.826 6.35 0.00 34.84 2.29
2205 2298 3.393089 AAGCGGGCTTCTATCACATAG 57.607 47.619 0.00 0.00 0.00 2.23
2206 2299 2.320781 AGCGGGCTTCTATCACATAGT 58.679 47.619 0.00 0.00 34.47 2.12
2207 2300 2.700897 AGCGGGCTTCTATCACATAGTT 59.299 45.455 0.00 0.00 34.47 2.24
2208 2301 3.134804 AGCGGGCTTCTATCACATAGTTT 59.865 43.478 0.00 0.00 34.47 2.66
2209 2302 3.495001 GCGGGCTTCTATCACATAGTTTC 59.505 47.826 0.00 0.00 34.47 2.78
2210 2303 4.740934 GCGGGCTTCTATCACATAGTTTCT 60.741 45.833 0.00 0.00 34.47 2.52
2211 2304 4.985409 CGGGCTTCTATCACATAGTTTCTC 59.015 45.833 0.00 0.00 34.47 2.87
2212 2305 5.221342 CGGGCTTCTATCACATAGTTTCTCT 60.221 44.000 0.00 0.00 34.47 3.10
2213 2306 6.587273 GGGCTTCTATCACATAGTTTCTCTT 58.413 40.000 0.00 0.00 34.47 2.85
2214 2307 7.051000 GGGCTTCTATCACATAGTTTCTCTTT 58.949 38.462 0.00 0.00 34.47 2.52
2215 2308 7.225734 GGGCTTCTATCACATAGTTTCTCTTTC 59.774 40.741 0.00 0.00 34.47 2.62
2216 2309 7.766278 GGCTTCTATCACATAGTTTCTCTTTCA 59.234 37.037 0.00 0.00 34.47 2.69
2217 2310 8.816144 GCTTCTATCACATAGTTTCTCTTTCAG 58.184 37.037 0.00 0.00 34.47 3.02
2218 2311 9.311916 CTTCTATCACATAGTTTCTCTTTCAGG 57.688 37.037 0.00 0.00 34.47 3.86
2219 2312 7.786030 TCTATCACATAGTTTCTCTTTCAGGG 58.214 38.462 0.00 0.00 34.47 4.45
2220 2313 5.825593 TCACATAGTTTCTCTTTCAGGGT 57.174 39.130 0.00 0.00 0.00 4.34
2221 2314 6.928348 TCACATAGTTTCTCTTTCAGGGTA 57.072 37.500 0.00 0.00 0.00 3.69
2222 2315 6.698380 TCACATAGTTTCTCTTTCAGGGTAC 58.302 40.000 0.00 0.00 0.00 3.34
2223 2316 6.269077 TCACATAGTTTCTCTTTCAGGGTACA 59.731 38.462 0.00 0.00 0.00 2.90
2224 2317 7.038302 TCACATAGTTTCTCTTTCAGGGTACAT 60.038 37.037 0.00 0.00 0.00 2.29
2225 2318 8.258007 CACATAGTTTCTCTTTCAGGGTACATA 58.742 37.037 0.00 0.00 0.00 2.29
2226 2319 8.478877 ACATAGTTTCTCTTTCAGGGTACATAG 58.521 37.037 0.00 0.00 0.00 2.23
2227 2320 6.301169 AGTTTCTCTTTCAGGGTACATAGG 57.699 41.667 0.00 0.00 0.00 2.57
2228 2321 6.023603 AGTTTCTCTTTCAGGGTACATAGGA 58.976 40.000 0.00 0.00 0.00 2.94
2229 2322 5.934402 TTCTCTTTCAGGGTACATAGGAC 57.066 43.478 0.00 0.00 0.00 3.85
2230 2323 3.952323 TCTCTTTCAGGGTACATAGGACG 59.048 47.826 0.00 0.00 0.00 4.79
2231 2324 3.028850 TCTTTCAGGGTACATAGGACGG 58.971 50.000 0.00 0.00 0.00 4.79
2232 2325 1.117150 TTCAGGGTACATAGGACGGC 58.883 55.000 0.00 0.00 0.00 5.68
2233 2326 0.757935 TCAGGGTACATAGGACGGCC 60.758 60.000 0.00 0.00 0.00 6.13
2234 2327 1.458967 AGGGTACATAGGACGGCCC 60.459 63.158 1.76 0.00 36.46 5.80
2236 2329 1.470165 GGGTACATAGGACGGCCCTC 61.470 65.000 1.76 0.00 43.31 4.30
2237 2330 0.469518 GGTACATAGGACGGCCCTCT 60.470 60.000 1.76 0.00 43.31 3.69
2238 2331 0.960286 GTACATAGGACGGCCCTCTC 59.040 60.000 1.76 0.00 43.31 3.20
2239 2332 0.536687 TACATAGGACGGCCCTCTCG 60.537 60.000 1.76 0.00 43.31 4.04
2240 2333 1.828660 CATAGGACGGCCCTCTCGT 60.829 63.158 1.76 0.00 43.31 4.18
2245 2338 4.349682 ACGGCCCTCTCGTCATTA 57.650 55.556 0.00 0.00 35.87 1.90
2246 2339 1.814527 ACGGCCCTCTCGTCATTAC 59.185 57.895 0.00 0.00 35.87 1.89
2247 2340 1.067582 CGGCCCTCTCGTCATTACC 59.932 63.158 0.00 0.00 0.00 2.85
2248 2341 1.392710 CGGCCCTCTCGTCATTACCT 61.393 60.000 0.00 0.00 0.00 3.08
2249 2342 0.831307 GGCCCTCTCGTCATTACCTT 59.169 55.000 0.00 0.00 0.00 3.50
2250 2343 1.209747 GGCCCTCTCGTCATTACCTTT 59.790 52.381 0.00 0.00 0.00 3.11
2251 2344 2.355818 GGCCCTCTCGTCATTACCTTTT 60.356 50.000 0.00 0.00 0.00 2.27
2252 2345 2.678336 GCCCTCTCGTCATTACCTTTTG 59.322 50.000 0.00 0.00 0.00 2.44
2253 2346 3.868754 GCCCTCTCGTCATTACCTTTTGT 60.869 47.826 0.00 0.00 0.00 2.83
2254 2347 3.684788 CCCTCTCGTCATTACCTTTTGTG 59.315 47.826 0.00 0.00 0.00 3.33
2255 2348 3.125316 CCTCTCGTCATTACCTTTTGTGC 59.875 47.826 0.00 0.00 0.00 4.57
2256 2349 3.997021 CTCTCGTCATTACCTTTTGTGCT 59.003 43.478 0.00 0.00 0.00 4.40
2257 2350 4.385825 TCTCGTCATTACCTTTTGTGCTT 58.614 39.130 0.00 0.00 0.00 3.91
2258 2351 5.543714 TCTCGTCATTACCTTTTGTGCTTA 58.456 37.500 0.00 0.00 0.00 3.09
2259 2352 5.407387 TCTCGTCATTACCTTTTGTGCTTAC 59.593 40.000 0.00 0.00 0.00 2.34
2260 2353 4.453136 TCGTCATTACCTTTTGTGCTTACC 59.547 41.667 0.00 0.00 0.00 2.85
2261 2354 4.379082 CGTCATTACCTTTTGTGCTTACCC 60.379 45.833 0.00 0.00 0.00 3.69
2262 2355 4.521256 GTCATTACCTTTTGTGCTTACCCA 59.479 41.667 0.00 0.00 0.00 4.51
2263 2356 5.185056 GTCATTACCTTTTGTGCTTACCCAT 59.815 40.000 0.00 0.00 0.00 4.00
2264 2357 6.376018 GTCATTACCTTTTGTGCTTACCCATA 59.624 38.462 0.00 0.00 0.00 2.74
2265 2358 6.601613 TCATTACCTTTTGTGCTTACCCATAG 59.398 38.462 0.00 0.00 0.00 2.23
2266 2359 3.089284 ACCTTTTGTGCTTACCCATAGC 58.911 45.455 0.00 0.00 39.10 2.97
2267 2360 3.245264 ACCTTTTGTGCTTACCCATAGCT 60.245 43.478 0.00 0.00 39.38 3.32
2268 2361 4.018779 ACCTTTTGTGCTTACCCATAGCTA 60.019 41.667 0.00 0.00 39.38 3.32
2269 2362 4.576463 CCTTTTGTGCTTACCCATAGCTAG 59.424 45.833 0.00 0.00 39.38 3.42
2270 2363 2.910688 TGTGCTTACCCATAGCTAGC 57.089 50.000 6.62 6.62 39.38 3.42
2271 2364 2.398588 TGTGCTTACCCATAGCTAGCT 58.601 47.619 23.12 23.12 39.38 3.32
2272 2365 2.103094 TGTGCTTACCCATAGCTAGCTG 59.897 50.000 27.68 12.81 39.38 4.24
2273 2366 2.103263 GTGCTTACCCATAGCTAGCTGT 59.897 50.000 27.68 18.59 39.38 4.40
2274 2367 2.103094 TGCTTACCCATAGCTAGCTGTG 59.897 50.000 29.01 29.01 39.38 3.66
2275 2368 2.760374 CTTACCCATAGCTAGCTGTGC 58.240 52.381 30.16 0.00 34.46 4.57
2276 2369 1.048601 TACCCATAGCTAGCTGTGCC 58.951 55.000 30.16 0.00 34.46 5.01
2277 2370 0.692419 ACCCATAGCTAGCTGTGCCT 60.692 55.000 30.16 16.93 34.46 4.75
2278 2371 0.250209 CCCATAGCTAGCTGTGCCTG 60.250 60.000 30.16 19.00 34.46 4.85
2279 2372 0.755079 CCATAGCTAGCTGTGCCTGA 59.245 55.000 30.16 9.63 34.46 3.86
2280 2373 1.139654 CCATAGCTAGCTGTGCCTGAA 59.860 52.381 30.16 8.88 34.46 3.02
2281 2374 2.481854 CATAGCTAGCTGTGCCTGAAG 58.518 52.381 25.86 3.63 0.00 3.02
2282 2375 1.561643 TAGCTAGCTGTGCCTGAAGT 58.438 50.000 27.68 0.00 0.00 3.01
2283 2376 0.248843 AGCTAGCTGTGCCTGAAGTC 59.751 55.000 18.57 0.00 0.00 3.01
2284 2377 0.036952 GCTAGCTGTGCCTGAAGTCA 60.037 55.000 7.70 0.00 0.00 3.41
2285 2378 1.406614 GCTAGCTGTGCCTGAAGTCAT 60.407 52.381 7.70 0.00 0.00 3.06
2286 2379 2.277969 CTAGCTGTGCCTGAAGTCATG 58.722 52.381 0.00 0.00 0.00 3.07
2287 2380 0.322277 AGCTGTGCCTGAAGTCATGG 60.322 55.000 0.00 0.00 0.00 3.66
2288 2381 0.321919 GCTGTGCCTGAAGTCATGGA 60.322 55.000 0.00 0.00 0.00 3.41
2289 2382 1.681166 GCTGTGCCTGAAGTCATGGAT 60.681 52.381 0.00 0.00 0.00 3.41
2290 2383 2.014857 CTGTGCCTGAAGTCATGGATG 58.985 52.381 0.00 0.00 0.00 3.51
2291 2384 1.629861 TGTGCCTGAAGTCATGGATGA 59.370 47.619 0.00 0.00 0.00 2.92
2292 2385 2.240414 TGTGCCTGAAGTCATGGATGAT 59.760 45.455 0.00 0.00 39.30 2.45
2293 2386 2.617308 GTGCCTGAAGTCATGGATGATG 59.383 50.000 0.00 0.00 39.30 3.07
2294 2387 1.607628 GCCTGAAGTCATGGATGATGC 59.392 52.381 0.00 0.00 39.30 3.91
2295 2388 2.748798 GCCTGAAGTCATGGATGATGCT 60.749 50.000 0.00 0.00 39.30 3.79
2296 2389 3.495629 GCCTGAAGTCATGGATGATGCTA 60.496 47.826 0.00 0.00 39.30 3.49
2297 2390 4.806625 GCCTGAAGTCATGGATGATGCTAT 60.807 45.833 0.00 0.00 39.30 2.97
2298 2391 5.314529 CCTGAAGTCATGGATGATGCTATT 58.685 41.667 0.00 0.00 39.30 1.73
2299 2392 5.411977 CCTGAAGTCATGGATGATGCTATTC 59.588 44.000 0.00 0.00 39.30 1.75
2300 2393 5.311265 TGAAGTCATGGATGATGCTATTCC 58.689 41.667 0.00 0.00 39.30 3.01
2301 2394 4.298103 AGTCATGGATGATGCTATTCCC 57.702 45.455 0.00 0.00 39.30 3.97
2302 2395 3.654321 AGTCATGGATGATGCTATTCCCA 59.346 43.478 0.00 0.00 39.30 4.37
2303 2396 3.755378 GTCATGGATGATGCTATTCCCAC 59.245 47.826 0.00 0.00 39.30 4.61
2304 2397 3.654321 TCATGGATGATGCTATTCCCACT 59.346 43.478 0.00 0.00 31.32 4.00
2305 2398 3.497103 TGGATGATGCTATTCCCACTG 57.503 47.619 0.00 0.00 0.00 3.66
2306 2399 3.047857 TGGATGATGCTATTCCCACTGA 58.952 45.455 0.00 0.00 0.00 3.41
2307 2400 3.072038 TGGATGATGCTATTCCCACTGAG 59.928 47.826 0.00 0.00 0.00 3.35
2308 2401 3.326006 GGATGATGCTATTCCCACTGAGA 59.674 47.826 0.00 0.00 0.00 3.27
2309 2402 4.563168 GGATGATGCTATTCCCACTGAGAG 60.563 50.000 0.00 0.00 0.00 3.20
2310 2403 3.646534 TGATGCTATTCCCACTGAGAGA 58.353 45.455 0.00 0.00 0.00 3.10
2311 2404 4.229639 TGATGCTATTCCCACTGAGAGAT 58.770 43.478 0.00 0.00 0.00 2.75
2312 2405 4.040095 TGATGCTATTCCCACTGAGAGATG 59.960 45.833 0.00 0.00 0.00 2.90
2313 2406 3.378512 TGCTATTCCCACTGAGAGATGT 58.621 45.455 0.00 0.00 0.00 3.06
2314 2407 3.133542 TGCTATTCCCACTGAGAGATGTG 59.866 47.826 0.00 0.00 0.00 3.21
2315 2408 2.706339 ATTCCCACTGAGAGATGTGC 57.294 50.000 0.00 0.00 33.26 4.57
2316 2409 1.649321 TTCCCACTGAGAGATGTGCT 58.351 50.000 0.00 0.00 33.26 4.40
2317 2410 0.900421 TCCCACTGAGAGATGTGCTG 59.100 55.000 0.00 0.00 33.26 4.41
2318 2411 0.743701 CCCACTGAGAGATGTGCTGC 60.744 60.000 0.00 0.00 33.26 5.25
2319 2412 0.036671 CCACTGAGAGATGTGCTGCA 60.037 55.000 0.00 0.00 33.26 4.41
2320 2413 1.609841 CCACTGAGAGATGTGCTGCAA 60.610 52.381 2.77 0.00 33.26 4.08
2321 2414 2.148768 CACTGAGAGATGTGCTGCAAA 58.851 47.619 2.77 0.00 0.00 3.68
2322 2415 2.551032 CACTGAGAGATGTGCTGCAAAA 59.449 45.455 2.77 0.00 0.00 2.44
2323 2416 3.190744 CACTGAGAGATGTGCTGCAAAAT 59.809 43.478 2.77 0.59 0.00 1.82
2324 2417 3.190744 ACTGAGAGATGTGCTGCAAAATG 59.809 43.478 2.77 0.00 0.00 2.32
2325 2418 2.490509 TGAGAGATGTGCTGCAAAATGG 59.509 45.455 2.77 0.00 0.00 3.16
2326 2419 2.751259 GAGAGATGTGCTGCAAAATGGA 59.249 45.455 2.77 0.00 0.00 3.41
2327 2420 3.362706 AGAGATGTGCTGCAAAATGGAT 58.637 40.909 2.77 0.00 0.00 3.41
2328 2421 3.130516 AGAGATGTGCTGCAAAATGGATG 59.869 43.478 2.77 0.00 0.00 3.51
2329 2422 2.829720 AGATGTGCTGCAAAATGGATGT 59.170 40.909 2.77 0.00 0.00 3.06
2330 2423 3.259876 AGATGTGCTGCAAAATGGATGTT 59.740 39.130 2.77 0.00 0.00 2.71
2331 2424 2.756829 TGTGCTGCAAAATGGATGTTG 58.243 42.857 2.77 0.00 0.00 3.33
2332 2425 2.102757 TGTGCTGCAAAATGGATGTTGT 59.897 40.909 2.77 0.00 0.00 3.32
2333 2426 2.477375 GTGCTGCAAAATGGATGTTGTG 59.523 45.455 2.77 0.00 0.00 3.33
2334 2427 2.102757 TGCTGCAAAATGGATGTTGTGT 59.897 40.909 0.00 0.00 0.00 3.72
2335 2428 3.132925 GCTGCAAAATGGATGTTGTGTT 58.867 40.909 0.00 0.00 0.00 3.32
2336 2429 4.202192 TGCTGCAAAATGGATGTTGTGTTA 60.202 37.500 0.00 0.00 0.00 2.41
2337 2430 4.386652 GCTGCAAAATGGATGTTGTGTTAG 59.613 41.667 0.00 0.00 0.00 2.34
2338 2431 5.528043 TGCAAAATGGATGTTGTGTTAGT 57.472 34.783 0.00 0.00 0.00 2.24
2339 2432 5.527951 TGCAAAATGGATGTTGTGTTAGTC 58.472 37.500 0.00 0.00 0.00 2.59
2340 2433 4.923281 GCAAAATGGATGTTGTGTTAGTCC 59.077 41.667 0.00 0.00 0.00 3.85
2341 2434 5.278957 GCAAAATGGATGTTGTGTTAGTCCT 60.279 40.000 0.00 0.00 0.00 3.85
2342 2435 6.381801 CAAAATGGATGTTGTGTTAGTCCTC 58.618 40.000 0.00 0.00 0.00 3.71
2343 2436 3.313012 TGGATGTTGTGTTAGTCCTCG 57.687 47.619 0.00 0.00 0.00 4.63
2344 2437 2.028476 TGGATGTTGTGTTAGTCCTCGG 60.028 50.000 0.00 0.00 0.00 4.63
2345 2438 2.000447 GATGTTGTGTTAGTCCTCGGC 59.000 52.381 0.00 0.00 0.00 5.54
2346 2439 1.045407 TGTTGTGTTAGTCCTCGGCT 58.955 50.000 0.00 0.00 0.00 5.52
2347 2440 2.241160 TGTTGTGTTAGTCCTCGGCTA 58.759 47.619 0.00 0.00 0.00 3.93
2348 2441 2.629137 TGTTGTGTTAGTCCTCGGCTAA 59.371 45.455 0.00 0.00 0.00 3.09
2349 2442 3.069872 TGTTGTGTTAGTCCTCGGCTAAA 59.930 43.478 0.00 0.00 31.22 1.85
2350 2443 4.060205 GTTGTGTTAGTCCTCGGCTAAAA 58.940 43.478 0.00 0.00 31.22 1.52
2351 2444 4.546829 TGTGTTAGTCCTCGGCTAAAAT 57.453 40.909 0.00 0.00 31.22 1.82
2352 2445 4.501071 TGTGTTAGTCCTCGGCTAAAATC 58.499 43.478 0.00 0.00 31.22 2.17
2353 2446 4.020928 TGTGTTAGTCCTCGGCTAAAATCA 60.021 41.667 0.00 0.00 31.22 2.57
2354 2447 5.116882 GTGTTAGTCCTCGGCTAAAATCAT 58.883 41.667 0.00 0.00 31.22 2.45
2355 2448 5.006746 GTGTTAGTCCTCGGCTAAAATCATG 59.993 44.000 0.00 0.00 31.22 3.07
2356 2449 3.914426 AGTCCTCGGCTAAAATCATGT 57.086 42.857 0.00 0.00 0.00 3.21
2357 2450 3.535561 AGTCCTCGGCTAAAATCATGTG 58.464 45.455 0.00 0.00 0.00 3.21
2358 2451 3.055094 AGTCCTCGGCTAAAATCATGTGT 60.055 43.478 0.00 0.00 0.00 3.72
2359 2452 3.689649 GTCCTCGGCTAAAATCATGTGTT 59.310 43.478 0.00 0.00 0.00 3.32
2360 2453 3.689161 TCCTCGGCTAAAATCATGTGTTG 59.311 43.478 0.00 0.00 0.00 3.33
2361 2454 3.440173 CCTCGGCTAAAATCATGTGTTGT 59.560 43.478 0.00 0.00 0.00 3.32
2362 2455 4.082787 CCTCGGCTAAAATCATGTGTTGTT 60.083 41.667 0.00 0.00 0.00 2.83
2363 2456 5.123186 CCTCGGCTAAAATCATGTGTTGTTA 59.877 40.000 0.00 0.00 0.00 2.41
2364 2457 6.348950 CCTCGGCTAAAATCATGTGTTGTTAA 60.349 38.462 0.00 0.00 0.00 2.01
2365 2458 6.607689 TCGGCTAAAATCATGTGTTGTTAAG 58.392 36.000 0.00 0.00 0.00 1.85
2366 2459 5.799936 CGGCTAAAATCATGTGTTGTTAAGG 59.200 40.000 0.00 0.00 0.00 2.69
2367 2460 6.569610 CGGCTAAAATCATGTGTTGTTAAGGT 60.570 38.462 0.00 0.00 0.00 3.50
2368 2461 6.586082 GGCTAAAATCATGTGTTGTTAAGGTG 59.414 38.462 0.00 0.00 0.00 4.00
2369 2462 7.367285 GCTAAAATCATGTGTTGTTAAGGTGA 58.633 34.615 0.00 0.00 0.00 4.02
2370 2463 7.326063 GCTAAAATCATGTGTTGTTAAGGTGAC 59.674 37.037 0.00 0.00 0.00 3.67
2372 2465 5.947228 ATCATGTGTTGTTAAGGTGACTG 57.053 39.130 0.00 0.00 42.68 3.51
2373 2466 5.029807 TCATGTGTTGTTAAGGTGACTGA 57.970 39.130 0.00 0.00 42.68 3.41
2374 2467 5.432645 TCATGTGTTGTTAAGGTGACTGAA 58.567 37.500 0.00 0.00 42.68 3.02
2375 2468 5.527214 TCATGTGTTGTTAAGGTGACTGAAG 59.473 40.000 0.00 0.00 42.68 3.02
2376 2469 5.092554 TGTGTTGTTAAGGTGACTGAAGA 57.907 39.130 0.00 0.00 42.68 2.87
2377 2470 4.873827 TGTGTTGTTAAGGTGACTGAAGAC 59.126 41.667 0.00 0.00 42.68 3.01
2378 2471 4.873827 GTGTTGTTAAGGTGACTGAAGACA 59.126 41.667 0.00 0.00 42.68 3.41
2379 2472 5.353123 GTGTTGTTAAGGTGACTGAAGACAA 59.647 40.000 0.00 0.00 42.68 3.18
2380 2473 5.584649 TGTTGTTAAGGTGACTGAAGACAAG 59.415 40.000 0.00 0.00 42.68 3.16
2381 2474 4.127171 TGTTAAGGTGACTGAAGACAAGC 58.873 43.478 0.00 0.00 42.68 4.01
2382 2475 2.262423 AAGGTGACTGAAGACAAGCC 57.738 50.000 0.00 0.00 42.68 4.35
2383 2476 1.428869 AGGTGACTGAAGACAAGCCT 58.571 50.000 0.00 0.00 41.13 4.58
2384 2477 2.609747 AGGTGACTGAAGACAAGCCTA 58.390 47.619 0.00 0.00 41.13 3.93
2385 2478 3.177228 AGGTGACTGAAGACAAGCCTAT 58.823 45.455 0.00 0.00 41.13 2.57
2386 2479 4.353777 AGGTGACTGAAGACAAGCCTATA 58.646 43.478 0.00 0.00 41.13 1.31
2387 2480 4.965532 AGGTGACTGAAGACAAGCCTATAT 59.034 41.667 0.00 0.00 41.13 0.86
2388 2481 6.136857 AGGTGACTGAAGACAAGCCTATATA 58.863 40.000 0.00 0.00 41.13 0.86
2389 2482 6.784969 AGGTGACTGAAGACAAGCCTATATAT 59.215 38.462 0.00 0.00 41.13 0.86
2390 2483 7.291182 AGGTGACTGAAGACAAGCCTATATATT 59.709 37.037 0.00 0.00 41.13 1.28
2391 2484 7.934120 GGTGACTGAAGACAAGCCTATATATTT 59.066 37.037 0.00 0.00 0.00 1.40
2392 2485 8.983724 GTGACTGAAGACAAGCCTATATATTTC 58.016 37.037 0.00 0.00 0.00 2.17
2393 2486 8.704668 TGACTGAAGACAAGCCTATATATTTCA 58.295 33.333 0.00 0.00 0.00 2.69
2394 2487 9.717942 GACTGAAGACAAGCCTATATATTTCAT 57.282 33.333 0.00 0.00 0.00 2.57
2395 2488 9.717942 ACTGAAGACAAGCCTATATATTTCATC 57.282 33.333 0.00 0.00 0.00 2.92
2396 2489 9.941325 CTGAAGACAAGCCTATATATTTCATCT 57.059 33.333 0.00 0.00 0.00 2.90
2397 2490 9.935241 TGAAGACAAGCCTATATATTTCATCTC 57.065 33.333 0.00 0.00 0.00 2.75
2416 2509 8.327941 TCATCTCTAAAAGTTCATGTTTCTGG 57.672 34.615 0.00 0.00 0.00 3.86
2417 2510 6.560253 TCTCTAAAAGTTCATGTTTCTGGC 57.440 37.500 0.00 0.00 0.00 4.85
2418 2511 6.299141 TCTCTAAAAGTTCATGTTTCTGGCT 58.701 36.000 0.00 0.00 0.00 4.75
2419 2512 6.772716 TCTCTAAAAGTTCATGTTTCTGGCTT 59.227 34.615 0.00 0.00 0.00 4.35
2420 2513 7.285401 TCTCTAAAAGTTCATGTTTCTGGCTTT 59.715 33.333 0.00 0.00 0.00 3.51
2421 2514 7.781056 TCTAAAAGTTCATGTTTCTGGCTTTT 58.219 30.769 0.00 0.00 36.58 2.27
2422 2515 8.908903 TCTAAAAGTTCATGTTTCTGGCTTTTA 58.091 29.630 0.00 0.00 35.50 1.52
2423 2516 9.185192 CTAAAAGTTCATGTTTCTGGCTTTTAG 57.815 33.333 14.99 14.99 40.42 1.85
2424 2517 5.712152 AGTTCATGTTTCTGGCTTTTAGG 57.288 39.130 0.00 0.00 0.00 2.69
2425 2518 4.021981 AGTTCATGTTTCTGGCTTTTAGGC 60.022 41.667 0.00 0.00 41.77 3.93
2426 2519 3.766545 TCATGTTTCTGGCTTTTAGGCT 58.233 40.909 0.00 0.00 41.96 4.58
2427 2520 3.507233 TCATGTTTCTGGCTTTTAGGCTG 59.493 43.478 0.00 1.68 41.96 4.85
2428 2521 2.944129 TGTTTCTGGCTTTTAGGCTGT 58.056 42.857 0.00 0.00 41.96 4.40
2429 2522 4.093472 TGTTTCTGGCTTTTAGGCTGTA 57.907 40.909 0.00 0.00 41.96 2.74
2430 2523 3.818773 TGTTTCTGGCTTTTAGGCTGTAC 59.181 43.478 0.00 0.00 41.96 2.90
2431 2524 4.072839 GTTTCTGGCTTTTAGGCTGTACT 58.927 43.478 0.00 0.00 41.96 2.73
2432 2525 4.367039 TTCTGGCTTTTAGGCTGTACTT 57.633 40.909 0.00 0.00 41.96 2.24
2433 2526 5.492855 TTCTGGCTTTTAGGCTGTACTTA 57.507 39.130 0.00 0.00 41.96 2.24
2434 2527 5.693769 TCTGGCTTTTAGGCTGTACTTAT 57.306 39.130 0.00 0.00 41.96 1.73
2435 2528 6.062258 TCTGGCTTTTAGGCTGTACTTATT 57.938 37.500 0.00 0.00 41.96 1.40
2436 2529 5.880332 TCTGGCTTTTAGGCTGTACTTATTG 59.120 40.000 0.00 0.00 41.96 1.90
2437 2530 5.811190 TGGCTTTTAGGCTGTACTTATTGA 58.189 37.500 0.00 0.00 41.96 2.57
2438 2531 6.242396 TGGCTTTTAGGCTGTACTTATTGAA 58.758 36.000 0.00 0.00 41.96 2.69
2439 2532 6.374333 TGGCTTTTAGGCTGTACTTATTGAAG 59.626 38.462 0.00 0.00 41.96 3.02
2440 2533 6.183360 GGCTTTTAGGCTGTACTTATTGAAGG 60.183 42.308 0.00 0.00 37.85 3.46
2441 2534 6.183360 GCTTTTAGGCTGTACTTATTGAAGGG 60.183 42.308 0.00 0.00 36.95 3.95
2442 2535 6.382919 TTTAGGCTGTACTTATTGAAGGGT 57.617 37.500 0.00 0.00 36.95 4.34
2443 2536 4.929146 AGGCTGTACTTATTGAAGGGTT 57.071 40.909 0.00 0.00 36.95 4.11
2444 2537 5.256806 AGGCTGTACTTATTGAAGGGTTT 57.743 39.130 0.00 0.00 36.95 3.27
2445 2538 6.382919 AGGCTGTACTTATTGAAGGGTTTA 57.617 37.500 0.00 0.00 36.95 2.01
2446 2539 6.415573 AGGCTGTACTTATTGAAGGGTTTAG 58.584 40.000 0.00 0.00 36.95 1.85
2447 2540 6.012771 AGGCTGTACTTATTGAAGGGTTTAGT 60.013 38.462 0.00 0.00 36.95 2.24
2448 2541 6.657966 GGCTGTACTTATTGAAGGGTTTAGTT 59.342 38.462 0.00 0.00 36.95 2.24
2449 2542 7.361799 GGCTGTACTTATTGAAGGGTTTAGTTG 60.362 40.741 0.00 0.00 36.95 3.16
2450 2543 7.174426 GCTGTACTTATTGAAGGGTTTAGTTGT 59.826 37.037 0.00 0.00 36.95 3.32
2451 2544 9.715121 CTGTACTTATTGAAGGGTTTAGTTGTA 57.285 33.333 0.00 0.00 36.95 2.41
2455 2548 9.020731 ACTTATTGAAGGGTTTAGTTGTATTGG 57.979 33.333 0.00 0.00 36.95 3.16
2456 2549 9.238368 CTTATTGAAGGGTTTAGTTGTATTGGA 57.762 33.333 0.00 0.00 0.00 3.53
2457 2550 6.887626 TTGAAGGGTTTAGTTGTATTGGAC 57.112 37.500 0.00 0.00 0.00 4.02
2458 2551 5.318630 TGAAGGGTTTAGTTGTATTGGACC 58.681 41.667 0.00 0.00 0.00 4.46
2459 2552 5.163077 TGAAGGGTTTAGTTGTATTGGACCA 60.163 40.000 0.00 0.00 0.00 4.02
2460 2553 4.918588 AGGGTTTAGTTGTATTGGACCAG 58.081 43.478 0.00 0.00 0.00 4.00
2461 2554 4.352893 AGGGTTTAGTTGTATTGGACCAGT 59.647 41.667 0.00 0.00 0.00 4.00
2462 2555 4.698780 GGGTTTAGTTGTATTGGACCAGTC 59.301 45.833 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.431486 CCAGGCCTGATAGTCTTCAACTC 60.431 52.174 34.91 0.00 39.55 3.01
205 206 7.618019 AGTTCAAATAGATCAGGTGCCTATA 57.382 36.000 0.00 0.00 0.00 1.31
259 260 2.888414 CCTTTTAACGGGAGAAAGGCAA 59.112 45.455 8.31 0.00 41.90 4.52
300 301 0.833287 ATAGCATGCACGGGAGAAGT 59.167 50.000 21.98 0.00 0.00 3.01
345 346 0.450184 CTTTCGGGTTGCCGTATTGG 59.550 55.000 0.00 0.00 42.50 3.16
428 429 2.656069 GGAGCTCAACGGCCACCTA 61.656 63.158 17.19 0.00 0.00 3.08
624 625 1.680338 AGGCTCGCAAAGAACAAAGT 58.320 45.000 0.00 0.00 0.00 2.66
874 875 2.768527 TCTGATGTGAATGAGGGAGGTC 59.231 50.000 0.00 0.00 0.00 3.85
1158 1163 1.407989 GGGTCCTTGCTCTGGATCTTG 60.408 57.143 0.00 0.00 35.18 3.02
1159 1164 0.915364 GGGTCCTTGCTCTGGATCTT 59.085 55.000 0.00 0.00 35.18 2.40
1192 1203 7.709613 GGTGCTAAAACCTTTTCTCGAGATATA 59.290 37.037 17.44 0.00 37.24 0.86
1233 1244 6.041296 GGGATACTTCGGATAAACTGGAGTAA 59.959 42.308 0.00 0.00 45.70 2.24
1791 1807 6.436847 TCAGTTTCTGAATCATCACTCTCTCT 59.563 38.462 0.00 0.00 37.57 3.10
1793 1812 6.602410 TCAGTTTCTGAATCATCACTCTCT 57.398 37.500 0.00 0.00 37.57 3.10
1834 1925 9.551734 CTGAATCATCAGTTAAGTCATAATCCA 57.448 33.333 0.00 0.00 46.60 3.41
1981 2074 7.500992 AGAAAGATTATCAGACGGCTTTCATA 58.499 34.615 1.03 0.00 42.03 2.15
2155 2248 4.715297 TCTTCTATCCCACCTAACCACTTC 59.285 45.833 0.00 0.00 0.00 3.01
2157 2250 4.016479 TCTCTTCTATCCCACCTAACCACT 60.016 45.833 0.00 0.00 0.00 4.00
2162 2255 3.797845 TCCCTCTCTTCTATCCCACCTAA 59.202 47.826 0.00 0.00 0.00 2.69
2180 2273 0.470341 GATAGAAGCCCGCTTTCCCT 59.530 55.000 2.98 0.00 36.26 4.20
2184 2277 2.717639 ATGTGATAGAAGCCCGCTTT 57.282 45.000 2.98 0.00 36.26 3.51
2186 2279 2.320781 ACTATGTGATAGAAGCCCGCT 58.679 47.619 0.00 0.00 36.68 5.52
2188 2281 4.950050 AGAAACTATGTGATAGAAGCCCG 58.050 43.478 0.00 0.00 36.68 6.13
2201 2294 7.928706 CCTATGTACCCTGAAAGAGAAACTATG 59.071 40.741 0.00 0.00 34.07 2.23
2202 2295 7.844779 TCCTATGTACCCTGAAAGAGAAACTAT 59.155 37.037 0.00 0.00 34.07 2.12
2203 2296 7.123847 GTCCTATGTACCCTGAAAGAGAAACTA 59.876 40.741 0.00 0.00 34.07 2.24
2204 2297 6.023603 TCCTATGTACCCTGAAAGAGAAACT 58.976 40.000 0.00 0.00 34.07 2.66
2205 2298 6.107343 GTCCTATGTACCCTGAAAGAGAAAC 58.893 44.000 0.00 0.00 34.07 2.78
2206 2299 5.105473 CGTCCTATGTACCCTGAAAGAGAAA 60.105 44.000 0.00 0.00 34.07 2.52
2207 2300 4.401519 CGTCCTATGTACCCTGAAAGAGAA 59.598 45.833 0.00 0.00 34.07 2.87
2208 2301 3.952323 CGTCCTATGTACCCTGAAAGAGA 59.048 47.826 0.00 0.00 34.07 3.10
2209 2302 3.068307 CCGTCCTATGTACCCTGAAAGAG 59.932 52.174 0.00 0.00 34.07 2.85
2210 2303 3.028850 CCGTCCTATGTACCCTGAAAGA 58.971 50.000 0.00 0.00 34.07 2.52
2211 2304 2.483188 GCCGTCCTATGTACCCTGAAAG 60.483 54.545 0.00 0.00 0.00 2.62
2212 2305 1.483415 GCCGTCCTATGTACCCTGAAA 59.517 52.381 0.00 0.00 0.00 2.69
2213 2306 1.117150 GCCGTCCTATGTACCCTGAA 58.883 55.000 0.00 0.00 0.00 3.02
2214 2307 0.757935 GGCCGTCCTATGTACCCTGA 60.758 60.000 0.00 0.00 0.00 3.86
2215 2308 1.746517 GGCCGTCCTATGTACCCTG 59.253 63.158 0.00 0.00 0.00 4.45
2216 2309 1.458967 GGGCCGTCCTATGTACCCT 60.459 63.158 0.00 0.00 34.34 4.34
2217 2310 1.458967 AGGGCCGTCCTATGTACCC 60.459 63.158 0.00 0.00 45.98 3.69
2218 2311 4.290023 AGGGCCGTCCTATGTACC 57.710 61.111 0.00 0.00 45.98 3.34
2228 2321 1.673808 GGTAATGACGAGAGGGCCGT 61.674 60.000 0.00 0.00 43.56 5.68
2229 2322 1.067582 GGTAATGACGAGAGGGCCG 59.932 63.158 0.00 0.00 0.00 6.13
2230 2323 0.831307 AAGGTAATGACGAGAGGGCC 59.169 55.000 0.00 0.00 0.00 5.80
2231 2324 2.678336 CAAAAGGTAATGACGAGAGGGC 59.322 50.000 0.00 0.00 0.00 5.19
2232 2325 3.684788 CACAAAAGGTAATGACGAGAGGG 59.315 47.826 0.00 0.00 0.00 4.30
2233 2326 3.125316 GCACAAAAGGTAATGACGAGAGG 59.875 47.826 0.00 0.00 0.00 3.69
2234 2327 3.997021 AGCACAAAAGGTAATGACGAGAG 59.003 43.478 0.00 0.00 0.00 3.20
2235 2328 4.002906 AGCACAAAAGGTAATGACGAGA 57.997 40.909 0.00 0.00 0.00 4.04
2236 2329 4.749245 AAGCACAAAAGGTAATGACGAG 57.251 40.909 0.00 0.00 0.00 4.18
2237 2330 4.453136 GGTAAGCACAAAAGGTAATGACGA 59.547 41.667 0.00 0.00 0.00 4.20
2238 2331 4.379082 GGGTAAGCACAAAAGGTAATGACG 60.379 45.833 0.00 0.00 0.00 4.35
2239 2332 4.521256 TGGGTAAGCACAAAAGGTAATGAC 59.479 41.667 0.00 0.00 0.00 3.06
2240 2333 4.730966 TGGGTAAGCACAAAAGGTAATGA 58.269 39.130 0.00 0.00 0.00 2.57
2241 2334 5.659440 ATGGGTAAGCACAAAAGGTAATG 57.341 39.130 0.00 0.00 0.00 1.90
2242 2335 5.359860 GCTATGGGTAAGCACAAAAGGTAAT 59.640 40.000 0.00 0.00 39.83 1.89
2243 2336 4.703093 GCTATGGGTAAGCACAAAAGGTAA 59.297 41.667 0.00 0.00 39.83 2.85
2244 2337 4.018779 AGCTATGGGTAAGCACAAAAGGTA 60.019 41.667 0.00 0.00 42.62 3.08
2245 2338 3.089284 GCTATGGGTAAGCACAAAAGGT 58.911 45.455 0.00 0.00 39.83 3.50
2246 2339 3.356290 AGCTATGGGTAAGCACAAAAGG 58.644 45.455 0.00 0.00 42.62 3.11
2247 2340 4.035675 GCTAGCTATGGGTAAGCACAAAAG 59.964 45.833 7.70 0.00 42.62 2.27
2248 2341 3.945285 GCTAGCTATGGGTAAGCACAAAA 59.055 43.478 7.70 0.00 42.62 2.44
2249 2342 3.199946 AGCTAGCTATGGGTAAGCACAAA 59.800 43.478 17.69 0.00 42.62 2.83
2250 2343 2.771943 AGCTAGCTATGGGTAAGCACAA 59.228 45.455 17.69 0.00 42.62 3.33
2251 2344 2.103094 CAGCTAGCTATGGGTAAGCACA 59.897 50.000 18.86 0.00 42.62 4.57
2252 2345 2.103263 ACAGCTAGCTATGGGTAAGCAC 59.897 50.000 18.86 0.00 42.62 4.40
2253 2346 2.103094 CACAGCTAGCTATGGGTAAGCA 59.897 50.000 18.86 0.00 42.62 3.91
2254 2347 2.760374 CACAGCTAGCTATGGGTAAGC 58.240 52.381 18.86 0.00 40.40 3.09
2255 2348 2.548920 GGCACAGCTAGCTATGGGTAAG 60.549 54.545 23.84 8.87 0.00 2.34
2256 2349 1.416401 GGCACAGCTAGCTATGGGTAA 59.584 52.381 23.84 0.00 0.00 2.85
2257 2350 1.048601 GGCACAGCTAGCTATGGGTA 58.951 55.000 23.84 0.00 0.00 3.69
2258 2351 0.692419 AGGCACAGCTAGCTATGGGT 60.692 55.000 23.84 12.11 0.00 4.51
2259 2352 0.250209 CAGGCACAGCTAGCTATGGG 60.250 60.000 23.84 13.22 0.00 4.00
2260 2353 0.755079 TCAGGCACAGCTAGCTATGG 59.245 55.000 23.84 14.01 0.00 2.74
2261 2354 2.158986 ACTTCAGGCACAGCTAGCTATG 60.159 50.000 18.88 18.88 0.00 2.23
2262 2355 2.102252 GACTTCAGGCACAGCTAGCTAT 59.898 50.000 18.86 2.05 0.00 2.97
2263 2356 1.478510 GACTTCAGGCACAGCTAGCTA 59.521 52.381 18.86 0.00 0.00 3.32
2264 2357 0.248843 GACTTCAGGCACAGCTAGCT 59.751 55.000 12.68 12.68 0.00 3.32
2265 2358 0.036952 TGACTTCAGGCACAGCTAGC 60.037 55.000 6.62 6.62 0.00 3.42
2266 2359 2.277969 CATGACTTCAGGCACAGCTAG 58.722 52.381 0.00 0.00 0.00 3.42
2267 2360 1.065926 CCATGACTTCAGGCACAGCTA 60.066 52.381 0.00 0.00 0.00 3.32
2268 2361 0.322277 CCATGACTTCAGGCACAGCT 60.322 55.000 0.00 0.00 0.00 4.24
2269 2362 0.321919 TCCATGACTTCAGGCACAGC 60.322 55.000 0.00 0.00 0.00 4.40
2270 2363 2.014857 CATCCATGACTTCAGGCACAG 58.985 52.381 0.00 0.00 0.00 3.66
2271 2364 1.629861 TCATCCATGACTTCAGGCACA 59.370 47.619 0.00 0.00 0.00 4.57
2272 2365 2.408271 TCATCCATGACTTCAGGCAC 57.592 50.000 0.00 0.00 0.00 5.01
2273 2366 2.927028 CATCATCCATGACTTCAGGCA 58.073 47.619 0.00 0.00 40.03 4.75
2274 2367 1.607628 GCATCATCCATGACTTCAGGC 59.392 52.381 0.00 0.00 40.03 4.85
2275 2368 3.210232 AGCATCATCCATGACTTCAGG 57.790 47.619 0.00 0.00 40.03 3.86
2276 2369 5.411977 GGAATAGCATCATCCATGACTTCAG 59.588 44.000 0.00 0.00 40.03 3.02
2277 2370 5.311265 GGAATAGCATCATCCATGACTTCA 58.689 41.667 0.00 0.00 40.03 3.02
2278 2371 4.699257 GGGAATAGCATCATCCATGACTTC 59.301 45.833 0.00 0.00 40.03 3.01
2279 2372 4.105217 TGGGAATAGCATCATCCATGACTT 59.895 41.667 0.00 0.00 40.03 3.01
2280 2373 3.654321 TGGGAATAGCATCATCCATGACT 59.346 43.478 0.00 0.00 40.03 3.41
2281 2374 3.755378 GTGGGAATAGCATCATCCATGAC 59.245 47.826 0.00 0.00 40.03 3.06
2282 2375 3.654321 AGTGGGAATAGCATCATCCATGA 59.346 43.478 0.00 0.00 41.70 3.07
2283 2376 3.756963 CAGTGGGAATAGCATCATCCATG 59.243 47.826 0.00 0.00 34.82 3.66
2284 2377 3.654321 TCAGTGGGAATAGCATCATCCAT 59.346 43.478 0.00 0.00 34.82 3.41
2285 2378 3.047857 TCAGTGGGAATAGCATCATCCA 58.952 45.455 0.00 0.00 34.82 3.41
2286 2379 3.326006 TCTCAGTGGGAATAGCATCATCC 59.674 47.826 0.00 0.00 0.00 3.51
2287 2380 4.282957 TCTCTCAGTGGGAATAGCATCATC 59.717 45.833 0.00 0.00 0.00 2.92
2288 2381 4.229639 TCTCTCAGTGGGAATAGCATCAT 58.770 43.478 0.00 0.00 0.00 2.45
2289 2382 3.646534 TCTCTCAGTGGGAATAGCATCA 58.353 45.455 0.00 0.00 0.00 3.07
2290 2383 4.040217 ACATCTCTCAGTGGGAATAGCATC 59.960 45.833 0.00 0.00 0.00 3.91
2291 2384 3.972638 ACATCTCTCAGTGGGAATAGCAT 59.027 43.478 0.00 0.00 0.00 3.79
2292 2385 3.133542 CACATCTCTCAGTGGGAATAGCA 59.866 47.826 0.00 0.00 32.24 3.49
2293 2386 3.726607 CACATCTCTCAGTGGGAATAGC 58.273 50.000 0.00 0.00 32.24 2.97
2294 2387 3.387374 AGCACATCTCTCAGTGGGAATAG 59.613 47.826 0.00 0.00 36.29 1.73
2295 2388 3.133542 CAGCACATCTCTCAGTGGGAATA 59.866 47.826 0.00 0.00 36.29 1.75
2296 2389 2.093075 CAGCACATCTCTCAGTGGGAAT 60.093 50.000 0.00 0.00 36.29 3.01
2297 2390 1.277273 CAGCACATCTCTCAGTGGGAA 59.723 52.381 0.00 0.00 36.29 3.97
2298 2391 0.900421 CAGCACATCTCTCAGTGGGA 59.100 55.000 0.00 0.00 36.29 4.37
2299 2392 0.743701 GCAGCACATCTCTCAGTGGG 60.744 60.000 0.00 0.00 36.29 4.61
2300 2393 0.036671 TGCAGCACATCTCTCAGTGG 60.037 55.000 0.00 0.00 36.29 4.00
2301 2394 1.804601 TTGCAGCACATCTCTCAGTG 58.195 50.000 0.00 0.00 38.74 3.66
2302 2395 2.556144 TTTGCAGCACATCTCTCAGT 57.444 45.000 0.00 0.00 0.00 3.41
2303 2396 3.427638 CCATTTTGCAGCACATCTCTCAG 60.428 47.826 0.00 0.00 0.00 3.35
2304 2397 2.490509 CCATTTTGCAGCACATCTCTCA 59.509 45.455 0.00 0.00 0.00 3.27
2305 2398 2.751259 TCCATTTTGCAGCACATCTCTC 59.249 45.455 0.00 0.00 0.00 3.20
2306 2399 2.799017 TCCATTTTGCAGCACATCTCT 58.201 42.857 0.00 0.00 0.00 3.10
2307 2400 3.119245 ACATCCATTTTGCAGCACATCTC 60.119 43.478 0.00 0.00 0.00 2.75
2308 2401 2.829720 ACATCCATTTTGCAGCACATCT 59.170 40.909 0.00 0.00 0.00 2.90
2309 2402 3.241067 ACATCCATTTTGCAGCACATC 57.759 42.857 0.00 0.00 0.00 3.06
2310 2403 3.244284 ACAACATCCATTTTGCAGCACAT 60.244 39.130 0.00 0.00 0.00 3.21
2311 2404 2.102757 ACAACATCCATTTTGCAGCACA 59.897 40.909 0.00 0.00 0.00 4.57
2312 2405 2.477375 CACAACATCCATTTTGCAGCAC 59.523 45.455 0.00 0.00 0.00 4.40
2313 2406 2.102757 ACACAACATCCATTTTGCAGCA 59.897 40.909 0.00 0.00 0.00 4.41
2314 2407 2.758009 ACACAACATCCATTTTGCAGC 58.242 42.857 0.00 0.00 0.00 5.25
2315 2408 5.531634 ACTAACACAACATCCATTTTGCAG 58.468 37.500 0.00 0.00 0.00 4.41
2316 2409 5.508825 GGACTAACACAACATCCATTTTGCA 60.509 40.000 0.00 0.00 0.00 4.08
2317 2410 4.923281 GGACTAACACAACATCCATTTTGC 59.077 41.667 0.00 0.00 0.00 3.68
2318 2411 6.331369 AGGACTAACACAACATCCATTTTG 57.669 37.500 0.00 0.00 31.41 2.44
2319 2412 5.181245 CGAGGACTAACACAACATCCATTTT 59.819 40.000 0.00 0.00 31.41 1.82
2320 2413 4.695455 CGAGGACTAACACAACATCCATTT 59.305 41.667 0.00 0.00 31.41 2.32
2321 2414 4.253685 CGAGGACTAACACAACATCCATT 58.746 43.478 0.00 0.00 31.41 3.16
2322 2415 3.369471 CCGAGGACTAACACAACATCCAT 60.369 47.826 0.00 0.00 31.41 3.41
2323 2416 2.028476 CCGAGGACTAACACAACATCCA 60.028 50.000 0.00 0.00 31.41 3.41
2324 2417 2.618053 CCGAGGACTAACACAACATCC 58.382 52.381 0.00 0.00 0.00 3.51
2325 2418 2.000447 GCCGAGGACTAACACAACATC 59.000 52.381 0.00 0.00 0.00 3.06
2326 2419 1.623811 AGCCGAGGACTAACACAACAT 59.376 47.619 0.00 0.00 0.00 2.71
2327 2420 1.045407 AGCCGAGGACTAACACAACA 58.955 50.000 0.00 0.00 0.00 3.33
2328 2421 3.308438 TTAGCCGAGGACTAACACAAC 57.692 47.619 0.00 0.00 0.00 3.32
2329 2422 4.339872 TTTTAGCCGAGGACTAACACAA 57.660 40.909 0.00 0.00 29.52 3.33
2330 2423 4.020928 TGATTTTAGCCGAGGACTAACACA 60.021 41.667 0.00 0.00 29.52 3.72
2331 2424 4.501071 TGATTTTAGCCGAGGACTAACAC 58.499 43.478 0.00 0.00 29.52 3.32
2332 2425 4.811969 TGATTTTAGCCGAGGACTAACA 57.188 40.909 0.00 0.00 29.52 2.41
2333 2426 5.006746 CACATGATTTTAGCCGAGGACTAAC 59.993 44.000 0.00 0.00 29.52 2.34
2334 2427 5.116180 CACATGATTTTAGCCGAGGACTAA 58.884 41.667 0.00 0.00 0.00 2.24
2335 2428 4.161565 ACACATGATTTTAGCCGAGGACTA 59.838 41.667 0.00 0.00 0.00 2.59
2336 2429 3.055094 ACACATGATTTTAGCCGAGGACT 60.055 43.478 0.00 0.00 0.00 3.85
2337 2430 3.270877 ACACATGATTTTAGCCGAGGAC 58.729 45.455 0.00 0.00 0.00 3.85
2338 2431 3.627395 ACACATGATTTTAGCCGAGGA 57.373 42.857 0.00 0.00 0.00 3.71
2339 2432 3.440173 ACAACACATGATTTTAGCCGAGG 59.560 43.478 0.00 0.00 0.00 4.63
2340 2433 4.685169 ACAACACATGATTTTAGCCGAG 57.315 40.909 0.00 0.00 0.00 4.63
2341 2434 6.348950 CCTTAACAACACATGATTTTAGCCGA 60.349 38.462 0.00 0.00 0.00 5.54
2342 2435 5.799936 CCTTAACAACACATGATTTTAGCCG 59.200 40.000 0.00 0.00 0.00 5.52
2343 2436 6.586082 CACCTTAACAACACATGATTTTAGCC 59.414 38.462 0.00 0.00 0.00 3.93
2344 2437 7.326063 GTCACCTTAACAACACATGATTTTAGC 59.674 37.037 0.00 0.00 0.00 3.09
2345 2438 8.567948 AGTCACCTTAACAACACATGATTTTAG 58.432 33.333 0.00 0.00 0.00 1.85
2346 2439 8.349245 CAGTCACCTTAACAACACATGATTTTA 58.651 33.333 0.00 0.00 0.00 1.52
2347 2440 7.068103 TCAGTCACCTTAACAACACATGATTTT 59.932 33.333 0.00 0.00 0.00 1.82
2348 2441 6.545666 TCAGTCACCTTAACAACACATGATTT 59.454 34.615 0.00 0.00 0.00 2.17
2349 2442 6.061441 TCAGTCACCTTAACAACACATGATT 58.939 36.000 0.00 0.00 0.00 2.57
2350 2443 5.620206 TCAGTCACCTTAACAACACATGAT 58.380 37.500 0.00 0.00 0.00 2.45
2351 2444 5.029807 TCAGTCACCTTAACAACACATGA 57.970 39.130 0.00 0.00 0.00 3.07
2352 2445 5.527214 TCTTCAGTCACCTTAACAACACATG 59.473 40.000 0.00 0.00 0.00 3.21
2353 2446 5.527582 GTCTTCAGTCACCTTAACAACACAT 59.472 40.000 0.00 0.00 0.00 3.21
2354 2447 4.873827 GTCTTCAGTCACCTTAACAACACA 59.126 41.667 0.00 0.00 0.00 3.72
2355 2448 4.873827 TGTCTTCAGTCACCTTAACAACAC 59.126 41.667 0.00 0.00 0.00 3.32
2356 2449 5.092554 TGTCTTCAGTCACCTTAACAACA 57.907 39.130 0.00 0.00 0.00 3.33
2357 2450 5.504173 GCTTGTCTTCAGTCACCTTAACAAC 60.504 44.000 0.00 0.00 0.00 3.32
2358 2451 4.574828 GCTTGTCTTCAGTCACCTTAACAA 59.425 41.667 0.00 0.00 0.00 2.83
2359 2452 4.127171 GCTTGTCTTCAGTCACCTTAACA 58.873 43.478 0.00 0.00 0.00 2.41
2360 2453 3.498777 GGCTTGTCTTCAGTCACCTTAAC 59.501 47.826 0.00 0.00 0.00 2.01
2361 2454 3.391296 AGGCTTGTCTTCAGTCACCTTAA 59.609 43.478 0.00 0.00 0.00 1.85
2362 2455 2.972713 AGGCTTGTCTTCAGTCACCTTA 59.027 45.455 0.00 0.00 0.00 2.69
2363 2456 1.771255 AGGCTTGTCTTCAGTCACCTT 59.229 47.619 0.00 0.00 0.00 3.50
2364 2457 1.428869 AGGCTTGTCTTCAGTCACCT 58.571 50.000 0.00 0.00 0.00 4.00
2365 2458 3.618690 ATAGGCTTGTCTTCAGTCACC 57.381 47.619 0.00 0.00 0.00 4.02
2366 2459 8.894768 AAATATATAGGCTTGTCTTCAGTCAC 57.105 34.615 0.00 0.00 0.00 3.67
2367 2460 8.704668 TGAAATATATAGGCTTGTCTTCAGTCA 58.295 33.333 0.00 0.00 0.00 3.41
2368 2461 9.717942 ATGAAATATATAGGCTTGTCTTCAGTC 57.282 33.333 0.00 0.00 0.00 3.51
2369 2462 9.717942 GATGAAATATATAGGCTTGTCTTCAGT 57.282 33.333 0.00 0.00 0.00 3.41
2370 2463 9.941325 AGATGAAATATATAGGCTTGTCTTCAG 57.059 33.333 0.00 0.00 0.00 3.02
2371 2464 9.935241 GAGATGAAATATATAGGCTTGTCTTCA 57.065 33.333 0.00 0.00 0.00 3.02
2390 2483 8.786898 CCAGAAACATGAACTTTTAGAGATGAA 58.213 33.333 0.00 0.00 0.00 2.57
2391 2484 7.094634 GCCAGAAACATGAACTTTTAGAGATGA 60.095 37.037 0.00 0.00 0.00 2.92
2392 2485 7.025963 GCCAGAAACATGAACTTTTAGAGATG 58.974 38.462 0.00 0.00 0.00 2.90
2393 2486 6.944862 AGCCAGAAACATGAACTTTTAGAGAT 59.055 34.615 0.00 0.00 0.00 2.75
2394 2487 6.299141 AGCCAGAAACATGAACTTTTAGAGA 58.701 36.000 0.00 0.00 0.00 3.10
2395 2488 6.566197 AGCCAGAAACATGAACTTTTAGAG 57.434 37.500 0.00 0.00 0.00 2.43
2396 2489 6.959639 AAGCCAGAAACATGAACTTTTAGA 57.040 33.333 0.00 0.00 0.00 2.10
2397 2490 9.185192 CTAAAAGCCAGAAACATGAACTTTTAG 57.815 33.333 14.37 14.37 42.37 1.85
2398 2491 8.141268 CCTAAAAGCCAGAAACATGAACTTTTA 58.859 33.333 0.00 7.63 37.46 1.52
2399 2492 6.986231 CCTAAAAGCCAGAAACATGAACTTTT 59.014 34.615 0.00 6.93 38.62 2.27
2400 2493 6.515832 CCTAAAAGCCAGAAACATGAACTTT 58.484 36.000 0.00 0.00 31.69 2.66
2401 2494 5.509670 GCCTAAAAGCCAGAAACATGAACTT 60.510 40.000 0.00 0.00 0.00 2.66
2402 2495 4.021981 GCCTAAAAGCCAGAAACATGAACT 60.022 41.667 0.00 0.00 0.00 3.01
2403 2496 4.021981 AGCCTAAAAGCCAGAAACATGAAC 60.022 41.667 0.00 0.00 0.00 3.18
2404 2497 4.022068 CAGCCTAAAAGCCAGAAACATGAA 60.022 41.667 0.00 0.00 0.00 2.57
2405 2498 3.507233 CAGCCTAAAAGCCAGAAACATGA 59.493 43.478 0.00 0.00 0.00 3.07
2406 2499 3.256631 ACAGCCTAAAAGCCAGAAACATG 59.743 43.478 0.00 0.00 0.00 3.21
2407 2500 3.500343 ACAGCCTAAAAGCCAGAAACAT 58.500 40.909 0.00 0.00 0.00 2.71
2408 2501 2.944129 ACAGCCTAAAAGCCAGAAACA 58.056 42.857 0.00 0.00 0.00 2.83
2409 2502 4.072839 AGTACAGCCTAAAAGCCAGAAAC 58.927 43.478 0.00 0.00 0.00 2.78
2410 2503 4.367039 AGTACAGCCTAAAAGCCAGAAA 57.633 40.909 0.00 0.00 0.00 2.52
2411 2504 4.367039 AAGTACAGCCTAAAAGCCAGAA 57.633 40.909 0.00 0.00 0.00 3.02
2412 2505 5.693769 ATAAGTACAGCCTAAAAGCCAGA 57.306 39.130 0.00 0.00 0.00 3.86
2413 2506 5.880332 TCAATAAGTACAGCCTAAAAGCCAG 59.120 40.000 0.00 0.00 0.00 4.85
2414 2507 5.811190 TCAATAAGTACAGCCTAAAAGCCA 58.189 37.500 0.00 0.00 0.00 4.75
2415 2508 6.183360 CCTTCAATAAGTACAGCCTAAAAGCC 60.183 42.308 0.00 0.00 0.00 4.35
2416 2509 6.183360 CCCTTCAATAAGTACAGCCTAAAAGC 60.183 42.308 0.00 0.00 0.00 3.51
2417 2510 6.884836 ACCCTTCAATAAGTACAGCCTAAAAG 59.115 38.462 0.00 0.00 0.00 2.27
2418 2511 6.786122 ACCCTTCAATAAGTACAGCCTAAAA 58.214 36.000 0.00 0.00 0.00 1.52
2419 2512 6.382919 ACCCTTCAATAAGTACAGCCTAAA 57.617 37.500 0.00 0.00 0.00 1.85
2420 2513 6.382919 AACCCTTCAATAAGTACAGCCTAA 57.617 37.500 0.00 0.00 0.00 2.69
2421 2514 6.382919 AAACCCTTCAATAAGTACAGCCTA 57.617 37.500 0.00 0.00 0.00 3.93
2422 2515 4.929146 AACCCTTCAATAAGTACAGCCT 57.071 40.909 0.00 0.00 0.00 4.58
2423 2516 6.178324 ACTAAACCCTTCAATAAGTACAGCC 58.822 40.000 0.00 0.00 0.00 4.85
2424 2517 7.174426 ACAACTAAACCCTTCAATAAGTACAGC 59.826 37.037 0.00 0.00 0.00 4.40
2425 2518 8.617290 ACAACTAAACCCTTCAATAAGTACAG 57.383 34.615 0.00 0.00 0.00 2.74
2429 2522 9.020731 CCAATACAACTAAACCCTTCAATAAGT 57.979 33.333 0.00 0.00 0.00 2.24
2430 2523 9.238368 TCCAATACAACTAAACCCTTCAATAAG 57.762 33.333 0.00 0.00 0.00 1.73
2431 2524 9.016438 GTCCAATACAACTAAACCCTTCAATAA 57.984 33.333 0.00 0.00 0.00 1.40
2432 2525 7.612633 GGTCCAATACAACTAAACCCTTCAATA 59.387 37.037 0.00 0.00 0.00 1.90
2433 2526 6.436218 GGTCCAATACAACTAAACCCTTCAAT 59.564 38.462 0.00 0.00 0.00 2.57
2434 2527 5.771165 GGTCCAATACAACTAAACCCTTCAA 59.229 40.000 0.00 0.00 0.00 2.69
2435 2528 5.163077 TGGTCCAATACAACTAAACCCTTCA 60.163 40.000 0.00 0.00 0.00 3.02
2436 2529 5.318630 TGGTCCAATACAACTAAACCCTTC 58.681 41.667 0.00 0.00 0.00 3.46
2437 2530 5.163023 ACTGGTCCAATACAACTAAACCCTT 60.163 40.000 0.00 0.00 0.00 3.95
2438 2531 4.352893 ACTGGTCCAATACAACTAAACCCT 59.647 41.667 0.00 0.00 0.00 4.34
2439 2532 4.659115 ACTGGTCCAATACAACTAAACCC 58.341 43.478 0.00 0.00 0.00 4.11
2440 2533 5.874895 GACTGGTCCAATACAACTAAACC 57.125 43.478 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.