Multiple sequence alignment - TraesCS5A01G212400

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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 TraesCS5A01G212400 chr5A 100.000 3017 0 0 1 3017 427821907 427818891 0.000000e+00 5572.0
1 TraesCS5A01G212400 chr5A 93.583 187 10 2 2302 2487 305851051 305851236 8.240000e-71 278.0
2 TraesCS5A01G212400 chr5A 91.000 200 17 1 2292 2491 552964561 552964759 4.960000e-68 268.0
3 TraesCS5A01G212400 chr5A 76.431 297 31 14 2223 2489 1757924 1758211 1.140000e-24 124.0
4 TraesCS5A01G212400 chr5B 88.943 2279 148 46 1 2219 382080372 382082606 0.000000e+00 2717.0
5 TraesCS5A01G212400 chr5B 88.172 558 39 9 2487 3017 382082611 382083168 9.120000e-180 640.0
6 TraesCS5A01G212400 chr5D 91.279 1376 60 21 691 2035 328724837 328726183 0.000000e+00 1821.0
7 TraesCS5A01G212400 chr5D 92.161 472 18 10 1 455 328724265 328724734 0.000000e+00 649.0
8 TraesCS5A01G212400 chr5D 91.061 358 31 1 2660 3017 328727139 328727495 1.630000e-132 483.0
9 TraesCS5A01G212400 chr5D 92.857 196 14 0 2292 2487 419976232 419976037 4.920000e-73 285.0
10 TraesCS5A01G212400 chr5D 96.774 62 2 0 2581 2642 328726193 328726254 1.480000e-18 104.0
11 TraesCS5A01G212400 chr7A 93.401 197 11 2 2292 2487 283880758 283880563 1.060000e-74 291.0
12 TraesCS5A01G212400 chr7A 92.347 196 14 1 2292 2487 618444916 618445110 8.240000e-71 278.0
13 TraesCS5A01G212400 chr7A 90.419 167 15 1 2736 2902 140112012 140112177 5.060000e-53 219.0
14 TraesCS5A01G212400 chr7A 80.132 302 22 14 2224 2489 211737367 211737666 1.100000e-44 191.0
15 TraesCS5A01G212400 chr6A 92.386 197 14 1 2292 2487 392126716 392126520 2.290000e-71 279.0
16 TraesCS5A01G212400 chr6A 92.308 195 15 0 2293 2487 572453736 572453930 8.240000e-71 278.0
17 TraesCS5A01G212400 chr6A 88.554 166 19 0 2737 2902 100424059 100424224 5.100000e-48 202.0
18 TraesCS5A01G212400 chr6A 81.786 280 15 12 2244 2487 351141735 351142014 5.100000e-48 202.0
19 TraesCS5A01G212400 chr6A 87.952 166 20 0 2737 2902 601875412 601875577 2.370000e-46 196.0
20 TraesCS5A01G212400 chr6A 90.000 60 3 2 2244 2300 39142394 39142453 1.160000e-09 75.0
21 TraesCS5A01G212400 chr1A 92.347 196 15 0 2292 2487 256599256 256599061 2.290000e-71 279.0
22 TraesCS5A01G212400 chr1A 91.837 196 16 0 2292 2487 297482778 297482973 1.070000e-69 274.0
23 TraesCS5A01G212400 chr1D 92.208 154 12 0 2737 2890 270211229 270211382 5.060000e-53 219.0
24 TraesCS5A01G212400 chr3D 91.667 156 13 0 2737 2892 601955703 601955858 1.820000e-52 217.0
25 TraesCS5A01G212400 chr2B 89.375 160 17 0 2743 2902 201248034 201247875 5.100000e-48 202.0
26 TraesCS5A01G212400 chr4A 88.750 160 18 0 2743 2902 734945672 734945831 2.370000e-46 196.0
27 TraesCS5A01G212400 chr2A 87.647 170 17 3 2244 2410 434979359 434979527 8.530000e-46 195.0
28 TraesCS5A01G212400 chr3A 81.008 258 24 12 2235 2482 716402180 716401938 6.640000e-42 182.0
29 TraesCS5A01G212400 chrUn 78.929 280 22 15 2244 2487 191788974 191788696 4.030000e-34 156.0
30 TraesCS5A01G212400 chrUn 78.929 280 22 12 2244 2487 343192741 343192463 4.030000e-34 156.0
31 TraesCS5A01G212400 chrUn 97.872 47 1 0 2920 2966 87311576 87311530 6.930000e-12 82.4
32 TraesCS5A01G212400 chr6B 83.721 172 9 6 2332 2486 585903988 585903819 8.720000e-31 145.0
33 TraesCS5A01G212400 chr7B 86.420 81 10 1 2332 2411 632164361 632164281 1.490000e-13 87.9


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 TraesCS5A01G212400 chr5A 427818891 427821907 3016 True 5572.00 5572 100.00000 1 3017 1 chr5A.!!$R1 3016
1 TraesCS5A01G212400 chr5B 382080372 382083168 2796 False 1678.50 2717 88.55750 1 3017 2 chr5B.!!$F1 3016
2 TraesCS5A01G212400 chr5D 328724265 328727495 3230 False 764.25 1821 92.81875 1 3017 4 chr5D.!!$F1 3016

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
506 539 0.170116 GTCAGCGAGACAGAGACTGG 59.83 60.0 7.37 0.0 46.77 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2377 0.106708 GAAGGTGTGCTCAGGTGACA 59.893 55.0 0.0 0.0 0.0 3.58 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
29 30 2.223433 GGTGCTGTCATCATAAGCTTGC 60.223 50.000 9.86 0.49 37.82 4.01
38 39 0.183492 CATAAGCTTGCCCTGCCCTA 59.817 55.000 9.86 0.00 0.00 3.53
110 120 4.293415 CTCTTTGCTTGTGATTGGTGAAC 58.707 43.478 0.00 0.00 0.00 3.18
111 121 3.953612 TCTTTGCTTGTGATTGGTGAACT 59.046 39.130 0.00 0.00 0.00 3.01
195 208 0.871057 GACTTCAGAAGTGGCTGTGC 59.129 55.000 21.00 0.34 43.03 4.57
197 210 1.155042 CTTCAGAAGTGGCTGTGCTC 58.845 55.000 1.48 0.00 37.20 4.26
291 313 1.828979 TGGCCGACTGAAAATAACCC 58.171 50.000 0.00 0.00 0.00 4.11
315 338 1.508632 TGTGAAGAACGCTTGGTAGC 58.491 50.000 0.00 0.00 44.21 3.58
433 466 5.584913 ACAGAAGATTTGTCTCTAGGAGGA 58.415 41.667 0.00 0.00 0.00 3.71
435 468 7.358263 ACAGAAGATTTGTCTCTAGGAGGATA 58.642 38.462 0.00 0.00 0.00 2.59
472 505 3.058570 TGCTATTTGTGCGTTGTTACCTG 60.059 43.478 0.00 0.00 0.00 4.00
481 514 1.000955 CGTTGTTACCTGACCAGCTCT 59.999 52.381 0.00 0.00 0.00 4.09
482 515 2.548067 CGTTGTTACCTGACCAGCTCTT 60.548 50.000 0.00 0.00 0.00 2.85
494 527 1.606480 CCAGCTCTTTCTTGTCAGCGA 60.606 52.381 0.00 0.00 36.95 4.93
505 538 3.692998 GTCAGCGAGACAGAGACTG 57.307 57.895 7.37 0.00 46.77 3.51
506 539 0.170116 GTCAGCGAGACAGAGACTGG 59.830 60.000 7.37 0.00 46.77 4.00
515 548 2.037772 AGACAGAGACTGGCAAATCGTT 59.962 45.455 7.36 0.00 42.99 3.85
516 549 3.258372 AGACAGAGACTGGCAAATCGTTA 59.742 43.478 7.36 0.00 42.99 3.18
517 550 3.994392 GACAGAGACTGGCAAATCGTTAA 59.006 43.478 0.00 0.00 39.71 2.01
521 554 2.095853 AGACTGGCAAATCGTTAATGCG 59.904 45.455 0.00 0.00 40.94 4.73
547 580 4.136796 TCTGAAAGACAATGTCCAACTGG 58.863 43.478 10.12 0.00 38.67 4.00
591 642 4.093556 CGAAAGGCAGATCTTAACAAGGAC 59.906 45.833 0.00 0.00 0.00 3.85
598 651 6.317857 GCAGATCTTAACAAGGACACAAATC 58.682 40.000 0.00 0.00 0.00 2.17
639 692 1.424493 CTAGCTTTTCCGAGCCTGCG 61.424 60.000 0.00 0.00 43.74 5.18
660 714 3.496884 CGGTTCGTGAAGGAAAAATCAGA 59.503 43.478 0.00 0.00 0.00 3.27
708 762 2.811317 GACGTGAGAAGCTGGCCG 60.811 66.667 0.00 0.00 0.00 6.13
801 863 2.664424 CGCGACCGAATCAAAACACAAT 60.664 45.455 0.00 0.00 36.29 2.71
809 871 5.390613 CGAATCAAAACACAATACACTCCC 58.609 41.667 0.00 0.00 0.00 4.30
856 918 0.396417 ACGAGATCCTCTGGACTGGG 60.396 60.000 0.00 0.00 32.98 4.45
887 949 1.745489 GGTCACATTCGCACCTCCC 60.745 63.158 0.00 0.00 0.00 4.30
1233 1310 2.281761 CACAGGAGCCACCACCAC 60.282 66.667 0.47 0.00 42.04 4.16
1355 1438 3.771160 GCCGTCGGGAGTGTCCAT 61.771 66.667 14.38 0.00 38.64 3.41
1356 1439 2.494918 CCGTCGGGAGTGTCCATC 59.505 66.667 2.34 0.00 38.64 3.51
1357 1440 2.494918 CGTCGGGAGTGTCCATCC 59.505 66.667 0.00 0.00 38.64 3.51
1692 1775 4.337060 CACGCGACGGTGGAGTCA 62.337 66.667 15.93 0.00 40.98 3.41
1742 1825 4.373116 GTCACGGGCGAGGAAGCA 62.373 66.667 0.00 0.00 39.27 3.91
1785 1868 3.211288 CCGGTGATCTTCTCGGCT 58.789 61.111 0.00 0.00 35.95 5.52
1992 2075 2.045340 CACCGGTTCCCCATGACC 60.045 66.667 2.97 0.00 0.00 4.02
2058 2141 3.266376 GCACGCGGCGCCTAATAA 61.266 61.111 27.87 0.00 0.00 1.40
2059 2142 2.815298 GCACGCGGCGCCTAATAAA 61.815 57.895 27.87 0.00 0.00 1.40
2060 2143 1.275657 CACGCGGCGCCTAATAAAG 59.724 57.895 27.87 12.10 0.00 1.85
2061 2144 1.142314 ACGCGGCGCCTAATAAAGA 59.858 52.632 27.87 0.00 0.00 2.52
2062 2145 0.874607 ACGCGGCGCCTAATAAAGAG 60.875 55.000 27.87 11.22 0.00 2.85
2094 2177 1.475751 CCATTAGATGCCCTCTGCGTT 60.476 52.381 0.00 0.00 45.60 4.84
2095 2178 1.600957 CATTAGATGCCCTCTGCGTTG 59.399 52.381 0.00 0.00 45.60 4.10
2105 2188 4.988598 CTGCGTTGCTCGTGGGGT 62.989 66.667 4.16 0.00 42.13 4.95
2112 2195 3.423154 GCTCGTGGGGTTGCTTCG 61.423 66.667 0.00 0.00 0.00 3.79
2118 2201 2.741211 GGGGTTGCTTCGTCGACC 60.741 66.667 10.58 0.00 39.35 4.79
2156 2243 4.802039 GCTTTGTATTGTGCTCCATGAATG 59.198 41.667 0.00 0.00 0.00 2.67
2160 2247 5.255687 TGTATTGTGCTCCATGAATGAACT 58.744 37.500 0.00 0.00 0.00 3.01
2186 2273 2.845752 TATCCGCTTGTGTGGTCCGC 62.846 60.000 0.00 0.00 43.94 5.54
2215 2302 0.176680 AGATGTGGCGCGAGAGAAAT 59.823 50.000 12.10 0.00 0.00 2.17
2223 2310 2.998668 CGCGAGAGAAATGCGTATTT 57.001 45.000 11.47 11.47 46.29 1.40
2225 2312 4.431894 CGCGAGAGAAATGCGTATTTAA 57.568 40.909 11.62 0.00 46.29 1.52
2226 2313 4.437440 CGCGAGAGAAATGCGTATTTAAG 58.563 43.478 11.62 3.48 46.29 1.85
2227 2314 4.606232 CGCGAGAGAAATGCGTATTTAAGG 60.606 45.833 11.62 1.85 46.29 2.69
2228 2315 4.762809 CGAGAGAAATGCGTATTTAAGGC 58.237 43.478 11.62 0.00 36.66 4.35
2229 2316 4.318831 CGAGAGAAATGCGTATTTAAGGCC 60.319 45.833 11.62 0.00 36.66 5.19
2230 2317 3.883489 AGAGAAATGCGTATTTAAGGCCC 59.117 43.478 11.62 0.00 36.66 5.80
2231 2318 3.883489 GAGAAATGCGTATTTAAGGCCCT 59.117 43.478 11.62 3.59 36.66 5.19
2232 2319 3.632145 AGAAATGCGTATTTAAGGCCCTG 59.368 43.478 11.62 0.00 36.66 4.45
2233 2320 2.729028 ATGCGTATTTAAGGCCCTGT 57.271 45.000 0.00 0.00 38.23 4.00
2234 2321 2.500392 TGCGTATTTAAGGCCCTGTT 57.500 45.000 0.00 0.00 38.23 3.16
2235 2322 2.797786 TGCGTATTTAAGGCCCTGTTT 58.202 42.857 0.00 0.00 38.23 2.83
2236 2323 2.490115 TGCGTATTTAAGGCCCTGTTTG 59.510 45.455 0.00 0.00 38.23 2.93
2237 2324 2.750712 GCGTATTTAAGGCCCTGTTTGA 59.249 45.455 0.00 0.00 32.71 2.69
2238 2325 3.380320 GCGTATTTAAGGCCCTGTTTGAT 59.620 43.478 0.00 0.00 32.71 2.57
2239 2326 4.142249 GCGTATTTAAGGCCCTGTTTGATT 60.142 41.667 0.00 0.00 32.71 2.57
2240 2327 5.623596 GCGTATTTAAGGCCCTGTTTGATTT 60.624 40.000 0.00 0.00 32.71 2.17
2241 2328 6.033966 CGTATTTAAGGCCCTGTTTGATTTC 58.966 40.000 0.00 0.00 0.00 2.17
2242 2329 6.349777 CGTATTTAAGGCCCTGTTTGATTTCA 60.350 38.462 0.00 0.00 0.00 2.69
2243 2330 5.878406 TTTAAGGCCCTGTTTGATTTCAA 57.122 34.783 0.00 0.00 0.00 2.69
2244 2331 6.432403 TTTAAGGCCCTGTTTGATTTCAAT 57.568 33.333 0.00 0.00 35.55 2.57
2245 2332 7.546250 TTTAAGGCCCTGTTTGATTTCAATA 57.454 32.000 0.00 0.00 35.55 1.90
2246 2333 7.546250 TTAAGGCCCTGTTTGATTTCAATAA 57.454 32.000 0.00 0.00 35.55 1.40
2247 2334 5.665916 AGGCCCTGTTTGATTTCAATAAG 57.334 39.130 0.00 0.00 35.55 1.73
2248 2335 5.086621 AGGCCCTGTTTGATTTCAATAAGT 58.913 37.500 0.00 0.00 35.55 2.24
2249 2336 5.185828 AGGCCCTGTTTGATTTCAATAAGTC 59.814 40.000 0.00 0.00 35.55 3.01
2250 2337 5.047377 GGCCCTGTTTGATTTCAATAAGTCA 60.047 40.000 0.00 0.00 35.55 3.41
2251 2338 5.863935 GCCCTGTTTGATTTCAATAAGTCAC 59.136 40.000 0.00 0.00 35.55 3.67
2252 2339 6.389906 CCCTGTTTGATTTCAATAAGTCACC 58.610 40.000 0.00 0.00 35.55 4.02
2253 2340 6.209391 CCCTGTTTGATTTCAATAAGTCACCT 59.791 38.462 0.00 0.00 35.55 4.00
2254 2341 7.086376 CCTGTTTGATTTCAATAAGTCACCTG 58.914 38.462 0.00 0.00 35.55 4.00
2255 2342 7.040478 CCTGTTTGATTTCAATAAGTCACCTGA 60.040 37.037 0.00 0.00 35.55 3.86
2256 2343 7.648142 TGTTTGATTTCAATAAGTCACCTGAC 58.352 34.615 0.00 0.00 39.26 3.51
2257 2344 7.502226 TGTTTGATTTCAATAAGTCACCTGACT 59.498 33.333 1.87 1.87 45.11 3.41
2291 2378 8.099364 ACTTATAAGTCATGTCTGTTTGGTTG 57.901 34.615 12.50 0.00 32.86 3.77
2292 2379 7.719633 ACTTATAAGTCATGTCTGTTTGGTTGT 59.280 33.333 12.50 0.00 32.86 3.32
2293 2380 4.900635 AAGTCATGTCTGTTTGGTTGTC 57.099 40.909 0.00 0.00 0.00 3.18
2294 2381 3.884895 AGTCATGTCTGTTTGGTTGTCA 58.115 40.909 0.00 0.00 0.00 3.58
2295 2382 3.627577 AGTCATGTCTGTTTGGTTGTCAC 59.372 43.478 0.00 0.00 0.00 3.67
2296 2383 2.948979 TCATGTCTGTTTGGTTGTCACC 59.051 45.455 0.00 0.00 44.56 4.02
2297 2384 2.799126 TGTCTGTTTGGTTGTCACCT 57.201 45.000 0.00 0.00 44.61 4.00
2298 2385 2.364632 TGTCTGTTTGGTTGTCACCTG 58.635 47.619 0.00 0.00 44.61 4.00
2299 2386 2.026729 TGTCTGTTTGGTTGTCACCTGA 60.027 45.455 0.00 0.00 44.61 3.86
2300 2387 2.614057 GTCTGTTTGGTTGTCACCTGAG 59.386 50.000 0.00 0.00 44.61 3.35
2301 2388 1.334869 CTGTTTGGTTGTCACCTGAGC 59.665 52.381 0.00 0.00 44.61 4.26
2302 2389 1.340502 TGTTTGGTTGTCACCTGAGCA 60.341 47.619 0.00 0.00 44.61 4.26
2303 2390 1.065551 GTTTGGTTGTCACCTGAGCAC 59.934 52.381 0.00 0.00 44.61 4.40
2304 2391 0.254462 TTGGTTGTCACCTGAGCACA 59.746 50.000 0.00 0.00 44.61 4.57
2305 2392 0.463654 TGGTTGTCACCTGAGCACAC 60.464 55.000 0.00 0.00 44.61 3.82
2306 2393 1.166531 GGTTGTCACCTGAGCACACC 61.167 60.000 0.00 0.00 40.44 4.16
2307 2394 0.179045 GTTGTCACCTGAGCACACCT 60.179 55.000 0.00 0.00 0.00 4.00
2308 2395 0.546122 TTGTCACCTGAGCACACCTT 59.454 50.000 0.00 0.00 0.00 3.50
2309 2396 0.106708 TGTCACCTGAGCACACCTTC 59.893 55.000 0.00 0.00 0.00 3.46
2310 2397 0.603975 GTCACCTGAGCACACCTTCC 60.604 60.000 0.00 0.00 0.00 3.46
2311 2398 1.302832 CACCTGAGCACACCTTCCC 60.303 63.158 0.00 0.00 0.00 3.97
2312 2399 1.770110 ACCTGAGCACACCTTCCCA 60.770 57.895 0.00 0.00 0.00 4.37
2313 2400 1.302832 CCTGAGCACACCTTCCCAC 60.303 63.158 0.00 0.00 0.00 4.61
2314 2401 1.302832 CTGAGCACACCTTCCCACC 60.303 63.158 0.00 0.00 0.00 4.61
2315 2402 1.770110 TGAGCACACCTTCCCACCT 60.770 57.895 0.00 0.00 0.00 4.00
2316 2403 1.352622 TGAGCACACCTTCCCACCTT 61.353 55.000 0.00 0.00 0.00 3.50
2317 2404 0.890996 GAGCACACCTTCCCACCTTG 60.891 60.000 0.00 0.00 0.00 3.61
2318 2405 1.152756 GCACACCTTCCCACCTTGT 60.153 57.895 0.00 0.00 0.00 3.16
2319 2406 0.755327 GCACACCTTCCCACCTTGTT 60.755 55.000 0.00 0.00 0.00 2.83
2320 2407 1.775385 CACACCTTCCCACCTTGTTT 58.225 50.000 0.00 0.00 0.00 2.83
2321 2408 2.107366 CACACCTTCCCACCTTGTTTT 58.893 47.619 0.00 0.00 0.00 2.43
2322 2409 2.499693 CACACCTTCCCACCTTGTTTTT 59.500 45.455 0.00 0.00 0.00 1.94
2323 2410 3.702045 CACACCTTCCCACCTTGTTTTTA 59.298 43.478 0.00 0.00 0.00 1.52
2324 2411 4.160626 CACACCTTCCCACCTTGTTTTTAA 59.839 41.667 0.00 0.00 0.00 1.52
2325 2412 4.966168 ACACCTTCCCACCTTGTTTTTAAT 59.034 37.500 0.00 0.00 0.00 1.40
2326 2413 5.427157 ACACCTTCCCACCTTGTTTTTAATT 59.573 36.000 0.00 0.00 0.00 1.40
2327 2414 5.757808 CACCTTCCCACCTTGTTTTTAATTG 59.242 40.000 0.00 0.00 0.00 2.32
2328 2415 5.427157 ACCTTCCCACCTTGTTTTTAATTGT 59.573 36.000 0.00 0.00 0.00 2.71
2329 2416 6.612049 ACCTTCCCACCTTGTTTTTAATTGTA 59.388 34.615 0.00 0.00 0.00 2.41
2330 2417 7.125963 ACCTTCCCACCTTGTTTTTAATTGTAA 59.874 33.333 0.00 0.00 0.00 2.41
2331 2418 7.988028 CCTTCCCACCTTGTTTTTAATTGTAAA 59.012 33.333 0.00 0.00 0.00 2.01
2332 2419 8.950208 TTCCCACCTTGTTTTTAATTGTAAAG 57.050 30.769 0.00 0.00 30.92 1.85
2333 2420 7.501844 TCCCACCTTGTTTTTAATTGTAAAGG 58.498 34.615 0.00 0.00 38.89 3.11
2334 2421 7.125963 TCCCACCTTGTTTTTAATTGTAAAGGT 59.874 33.333 0.00 0.00 45.13 3.50
2338 2425 9.541143 ACCTTGTTTTTAATTGTAAAGGTGATG 57.459 29.630 3.50 0.00 43.19 3.07
2339 2426 8.987890 CCTTGTTTTTAATTGTAAAGGTGATGG 58.012 33.333 0.00 0.00 30.92 3.51
2340 2427 8.894768 TTGTTTTTAATTGTAAAGGTGATGGG 57.105 30.769 0.00 0.00 30.92 4.00
2341 2428 8.251383 TGTTTTTAATTGTAAAGGTGATGGGA 57.749 30.769 0.00 0.00 30.92 4.37
2342 2429 8.145122 TGTTTTTAATTGTAAAGGTGATGGGAC 58.855 33.333 0.00 0.00 30.92 4.46
2343 2430 6.844097 TTTAATTGTAAAGGTGATGGGACC 57.156 37.500 0.00 0.00 36.09 4.46
2344 2431 2.891191 TTGTAAAGGTGATGGGACCC 57.109 50.000 2.45 2.45 36.56 4.46
2345 2432 1.748732 TGTAAAGGTGATGGGACCCA 58.251 50.000 17.73 17.73 36.56 4.51
2347 2434 2.025416 TGTAAAGGTGATGGGACCCATG 60.025 50.000 31.39 0.00 45.26 3.66
2348 2435 0.324645 AAAGGTGATGGGACCCATGC 60.325 55.000 31.39 21.14 45.26 4.06
2349 2436 1.508667 AAGGTGATGGGACCCATGCA 61.509 55.000 31.39 22.86 45.26 3.96
2350 2437 1.000233 GGTGATGGGACCCATGCAA 60.000 57.895 31.39 13.08 45.26 4.08
2351 2438 0.614415 GGTGATGGGACCCATGCAAA 60.614 55.000 31.39 10.49 45.26 3.68
2352 2439 1.265236 GTGATGGGACCCATGCAAAA 58.735 50.000 31.39 7.95 45.26 2.44
2353 2440 1.622811 GTGATGGGACCCATGCAAAAA 59.377 47.619 31.39 6.16 45.26 1.94
2384 2471 9.729281 TGACTTATAAGTTTTAAGTTAGGGTGG 57.271 33.333 18.96 0.00 39.40 4.61
2385 2472 9.948964 GACTTATAAGTTTTAAGTTAGGGTGGA 57.051 33.333 18.96 0.00 39.40 4.02
2389 2476 8.999905 ATAAGTTTTAAGTTAGGGTGGAACAA 57.000 30.769 0.00 0.00 44.16 2.83
2414 2501 6.549433 TTATGACTTATAAGTTGGGTCCGT 57.451 37.500 18.96 9.13 39.88 4.69
2415 2502 4.895668 TGACTTATAAGTTGGGTCCGTT 57.104 40.909 18.96 0.00 39.88 4.44
2416 2503 5.231702 TGACTTATAAGTTGGGTCCGTTT 57.768 39.130 18.96 0.00 39.88 3.60
2417 2504 4.998672 TGACTTATAAGTTGGGTCCGTTTG 59.001 41.667 18.96 0.00 39.88 2.93
2418 2505 4.329392 ACTTATAAGTTGGGTCCGTTTGG 58.671 43.478 12.50 0.00 35.21 3.28
2419 2506 1.541379 ATAAGTTGGGTCCGTTTGGC 58.459 50.000 0.00 0.00 34.14 4.52
2420 2507 0.183014 TAAGTTGGGTCCGTTTGGCA 59.817 50.000 0.00 0.00 34.14 4.92
2421 2508 0.684805 AAGTTGGGTCCGTTTGGCAA 60.685 50.000 0.00 0.00 34.14 4.52
2422 2509 0.684805 AGTTGGGTCCGTTTGGCAAA 60.685 50.000 8.93 8.93 34.14 3.68
2423 2510 0.175989 GTTGGGTCCGTTTGGCAAAA 59.824 50.000 15.29 0.00 34.14 2.44
2424 2511 1.123928 TTGGGTCCGTTTGGCAAAAT 58.876 45.000 15.29 0.00 34.14 1.82
2425 2512 1.996798 TGGGTCCGTTTGGCAAAATA 58.003 45.000 15.29 0.00 34.14 1.40
2426 2513 2.317040 TGGGTCCGTTTGGCAAAATAA 58.683 42.857 15.29 0.00 34.14 1.40
2427 2514 2.297597 TGGGTCCGTTTGGCAAAATAAG 59.702 45.455 15.29 6.63 34.14 1.73
2428 2515 2.297880 GGGTCCGTTTGGCAAAATAAGT 59.702 45.455 15.29 0.00 34.14 2.24
2429 2516 3.571571 GGTCCGTTTGGCAAAATAAGTC 58.428 45.455 15.29 0.00 34.14 3.01
2430 2517 3.004944 GGTCCGTTTGGCAAAATAAGTCA 59.995 43.478 15.29 0.00 34.14 3.41
2431 2518 3.978855 GTCCGTTTGGCAAAATAAGTCAC 59.021 43.478 15.29 0.00 34.14 3.67
2432 2519 3.886505 TCCGTTTGGCAAAATAAGTCACT 59.113 39.130 15.29 0.00 34.14 3.41
2433 2520 4.339814 TCCGTTTGGCAAAATAAGTCACTT 59.660 37.500 15.29 0.00 34.14 3.16
2434 2521 5.047188 CCGTTTGGCAAAATAAGTCACTTT 58.953 37.500 15.29 0.00 0.00 2.66
2435 2522 5.522097 CCGTTTGGCAAAATAAGTCACTTTT 59.478 36.000 15.29 0.00 0.00 2.27
2436 2523 6.036626 CCGTTTGGCAAAATAAGTCACTTTTT 59.963 34.615 15.29 0.00 0.00 1.94
2437 2524 7.222999 CCGTTTGGCAAAATAAGTCACTTTTTA 59.777 33.333 15.29 0.00 0.00 1.52
2438 2525 8.053653 CGTTTGGCAAAATAAGTCACTTTTTAC 58.946 33.333 15.29 0.00 0.00 2.01
2439 2526 8.874816 GTTTGGCAAAATAAGTCACTTTTTACA 58.125 29.630 15.29 0.00 0.00 2.41
2440 2527 7.995463 TGGCAAAATAAGTCACTTTTTACAC 57.005 32.000 0.00 0.00 0.00 2.90
2441 2528 7.777095 TGGCAAAATAAGTCACTTTTTACACT 58.223 30.769 0.00 0.00 0.00 3.55
2442 2529 8.254508 TGGCAAAATAAGTCACTTTTTACACTT 58.745 29.630 0.00 0.00 33.63 3.16
2443 2530 9.093970 GGCAAAATAAGTCACTTTTTACACTTT 57.906 29.630 0.00 0.00 31.52 2.66
2478 2565 8.528044 AAGTTAGTGACTTATTTGGAACCAAA 57.472 30.769 19.15 19.15 46.61 3.28
2479 2566 7.937649 AGTTAGTGACTTATTTGGAACCAAAC 58.062 34.615 19.23 8.57 41.09 2.93
2480 2567 7.558444 AGTTAGTGACTTATTTGGAACCAAACA 59.442 33.333 19.23 7.15 41.09 2.83
2481 2568 6.391227 AGTGACTTATTTGGAACCAAACAG 57.609 37.500 19.23 18.64 46.80 3.16
2482 2569 6.126409 AGTGACTTATTTGGAACCAAACAGA 58.874 36.000 23.08 11.42 46.80 3.41
2483 2570 6.263168 AGTGACTTATTTGGAACCAAACAGAG 59.737 38.462 23.08 19.73 46.80 3.35
2484 2571 5.009610 TGACTTATTTGGAACCAAACAGAGC 59.990 40.000 23.08 17.21 46.80 4.09
2485 2572 4.280929 ACTTATTTGGAACCAAACAGAGCC 59.719 41.667 23.08 0.00 46.80 4.70
2527 2614 2.320745 TGCAGCGAGTCATCAATCAT 57.679 45.000 0.00 0.00 0.00 2.45
2565 2652 5.995446 AGGGTTTCTAGTTGAAGATGGATC 58.005 41.667 0.00 0.00 35.89 3.36
2572 2659 4.425577 AGTTGAAGATGGATCGCAAAAC 57.574 40.909 0.00 0.00 31.42 2.43
2625 2722 3.430236 CGGGTTTGGAGCAAGTTCTTTTT 60.430 43.478 0.00 0.00 0.00 1.94
2645 2742 1.892209 TCCTCCCTTTCGCTTTTCAC 58.108 50.000 0.00 0.00 0.00 3.18
2653 2750 1.503818 TTCGCTTTTCACGTGCTCCC 61.504 55.000 11.67 0.00 0.00 4.30
2663 3627 2.671177 CGTGCTCCCGCTGTTTCTG 61.671 63.158 0.00 0.00 36.97 3.02
2668 3632 2.084546 GCTCCCGCTGTTTCTGTTTAT 58.915 47.619 0.00 0.00 0.00 1.40
2676 3640 4.556135 CGCTGTTTCTGTTTATTCTGCATG 59.444 41.667 0.00 0.00 0.00 4.06
2689 3653 8.699749 GTTTATTCTGCATGTTAGTTTTGAACC 58.300 33.333 0.00 0.00 0.00 3.62
2762 3733 6.928979 TCAAACTATTTCGAAGGTGTCAAA 57.071 33.333 0.00 0.00 0.00 2.69
2763 3734 7.504924 TCAAACTATTTCGAAGGTGTCAAAT 57.495 32.000 0.00 0.00 0.00 2.32
2766 3737 8.717821 CAAACTATTTCGAAGGTGTCAAATAGA 58.282 33.333 13.46 0.00 38.27 1.98
2779 3750 9.213777 AGGTGTCAAATAGATCCTCAAACTATA 57.786 33.333 0.00 0.00 31.01 1.31
2808 3779 5.940470 GTGTCATGTAGGTCCTTGAAAATCT 59.060 40.000 0.00 0.00 0.00 2.40
2856 3827 4.556233 TGTGACACCTCTGAAATAGTTCG 58.444 43.478 2.45 0.00 36.46 3.95
2914 3885 7.289317 AGGATCTGGGTGACGATTTTTATAGTA 59.711 37.037 0.00 0.00 0.00 1.82
2941 3921 4.158025 GGACACCTCTGAAATAGTTCGAGA 59.842 45.833 19.22 12.61 36.95 4.04
2957 3937 4.471904 TCGAGAACCTATGATGCACTTT 57.528 40.909 0.00 0.00 0.00 2.66
2966 3946 9.331282 GAACCTATGATGCACTTTACTCTTTAT 57.669 33.333 0.00 0.00 0.00 1.40
2968 3948 9.686683 ACCTATGATGCACTTTACTCTTTATTT 57.313 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.223433 GCAAGCTTATGATGACAGCACC 60.223 50.000 0.00 0.00 0.00 5.01
29 30 0.460311 CTAGTTCACGTAGGGCAGGG 59.540 60.000 0.00 0.00 0.00 4.45
110 120 2.740981 AGAGCGAAGAAGCAATTCACAG 59.259 45.455 0.00 0.00 40.15 3.66
111 121 2.771089 AGAGCGAAGAAGCAATTCACA 58.229 42.857 0.00 0.00 40.15 3.58
291 313 0.453282 CAAGCGTTCTTCACATGGCG 60.453 55.000 0.00 0.00 0.00 5.69
334 357 1.236616 CCGAGCCAAGTGCAATGTCA 61.237 55.000 0.00 0.00 44.83 3.58
363 386 7.119992 AGACGAGTAGTATTATCCAGCATAGTG 59.880 40.741 0.00 0.00 0.00 2.74
369 392 4.477780 GCAGACGAGTAGTATTATCCAGC 58.522 47.826 0.00 0.00 0.00 4.85
435 468 9.520204 GCACAAATAGCATTTTTGTATGACTAT 57.480 29.630 10.19 0.00 43.51 2.12
449 482 3.756434 AGGTAACAACGCACAAATAGCAT 59.244 39.130 0.00 0.00 41.41 3.79
472 505 1.803555 GCTGACAAGAAAGAGCTGGTC 59.196 52.381 0.00 0.00 38.95 4.02
494 527 1.620819 ACGATTTGCCAGTCTCTGTCT 59.379 47.619 0.00 0.00 0.00 3.41
497 530 4.728882 GCATTAACGATTTGCCAGTCTCTG 60.729 45.833 0.00 0.00 0.00 3.35
501 534 2.440501 CGCATTAACGATTTGCCAGTC 58.559 47.619 0.00 0.00 32.76 3.51
502 535 1.132262 CCGCATTAACGATTTGCCAGT 59.868 47.619 0.00 0.00 32.76 4.00
503 536 1.826327 CCGCATTAACGATTTGCCAG 58.174 50.000 0.00 0.00 32.76 4.85
504 537 0.179150 GCCGCATTAACGATTTGCCA 60.179 50.000 0.00 0.00 32.76 4.92
505 538 0.179150 TGCCGCATTAACGATTTGCC 60.179 50.000 0.00 0.00 32.76 4.52
506 539 1.780860 GATGCCGCATTAACGATTTGC 59.219 47.619 7.43 0.00 34.06 3.68
515 548 2.984562 TGTCTTTCAGATGCCGCATTA 58.015 42.857 7.43 0.00 0.00 1.90
516 549 1.825090 TGTCTTTCAGATGCCGCATT 58.175 45.000 7.43 0.00 0.00 3.56
517 550 1.825090 TTGTCTTTCAGATGCCGCAT 58.175 45.000 5.28 5.28 0.00 4.73
521 554 3.084039 TGGACATTGTCTTTCAGATGCC 58.916 45.455 16.02 0.00 32.47 4.40
545 578 2.350895 CGGGTGGCATCAGTTCCA 59.649 61.111 0.00 0.00 0.00 3.53
547 580 1.450312 CTCCGGGTGGCATCAGTTC 60.450 63.158 0.00 0.00 34.14 3.01
591 642 4.157289 CAGAATTGACTGGGGAGATTTGTG 59.843 45.833 0.00 0.00 34.64 3.33
639 692 4.613850 GCTCTGATTTTTCCTTCACGAACC 60.614 45.833 0.00 0.00 0.00 3.62
644 697 3.192212 CAGGGCTCTGATTTTTCCTTCAC 59.808 47.826 8.28 0.00 43.49 3.18
660 714 1.006102 CGAAAGTCGTGACAGGGCT 60.006 57.895 0.00 0.00 34.72 5.19
695 749 3.706373 GACCCGGCCAGCTTCTCA 61.706 66.667 2.24 0.00 0.00 3.27
801 863 1.156803 ACGGGGTCTTGGGAGTGTA 59.843 57.895 0.00 0.00 0.00 2.90
887 949 1.060308 CCGCGGCGTGATTAAGTTG 59.940 57.895 23.75 0.00 0.00 3.16
961 1023 2.125912 AGACGATCCTGTGCGTGC 60.126 61.111 0.00 0.00 41.34 5.34
962 1024 0.799917 CAGAGACGATCCTGTGCGTG 60.800 60.000 0.00 0.00 41.34 5.34
963 1025 1.244697 ACAGAGACGATCCTGTGCGT 61.245 55.000 2.02 0.00 41.59 5.24
964 1026 0.524392 GACAGAGACGATCCTGTGCG 60.524 60.000 7.03 0.00 43.02 5.34
965 1027 0.814457 AGACAGAGACGATCCTGTGC 59.186 55.000 7.03 0.93 43.02 4.57
974 1036 0.167033 CGTGGAGACAGACAGAGACG 59.833 60.000 0.00 0.00 44.46 4.18
1224 1301 4.584518 TGCTGCTGGTGGTGGTGG 62.585 66.667 0.00 0.00 0.00 4.61
1225 1302 2.981909 CTGCTGCTGGTGGTGGTG 60.982 66.667 0.00 0.00 0.00 4.17
1226 1303 4.962836 GCTGCTGCTGGTGGTGGT 62.963 66.667 8.53 0.00 36.03 4.16
1230 1307 2.746671 CTCTGCTGCTGCTGGTGG 60.747 66.667 19.63 8.85 40.48 4.61
1323 1406 2.997897 GGCACCGTCCTCCTCACT 60.998 66.667 0.00 0.00 0.00 3.41
1473 1556 2.617274 GCAGTCGCCCAACAAGTCC 61.617 63.158 0.00 0.00 0.00 3.85
1692 1775 3.637273 GTCTCCGCCCACCTTGGT 61.637 66.667 0.00 0.00 35.17 3.67
1734 1817 2.045536 CTGCCCCACTGCTTCCTC 60.046 66.667 0.00 0.00 0.00 3.71
1742 1825 4.664267 TCTCCAGGCTGCCCCACT 62.664 66.667 16.57 0.00 35.39 4.00
1880 1963 3.186047 CGGATTCACGTCCACCGC 61.186 66.667 6.97 0.00 41.42 5.68
1884 1967 3.375239 TCGCCGGATTCACGTCCA 61.375 61.111 5.05 0.00 38.21 4.02
2057 2140 2.270352 TGGCATCACGGTTTCTCTTT 57.730 45.000 0.00 0.00 0.00 2.52
2058 2141 2.496899 ATGGCATCACGGTTTCTCTT 57.503 45.000 0.00 0.00 0.00 2.85
2059 2142 2.496899 AATGGCATCACGGTTTCTCT 57.503 45.000 0.00 0.00 0.00 3.10
2060 2143 3.531538 TCTAATGGCATCACGGTTTCTC 58.468 45.455 0.00 0.00 0.00 2.87
2061 2144 3.627395 TCTAATGGCATCACGGTTTCT 57.373 42.857 0.00 0.00 0.00 2.52
2062 2145 3.548818 GCATCTAATGGCATCACGGTTTC 60.549 47.826 0.00 0.00 0.00 2.78
2094 2177 2.281484 GAAGCAACCCCACGAGCA 60.281 61.111 0.00 0.00 0.00 4.26
2095 2178 3.423154 CGAAGCAACCCCACGAGC 61.423 66.667 0.00 0.00 0.00 5.03
2112 2195 1.154225 CAAAAGCATGGCGGTCGAC 60.154 57.895 7.13 7.13 0.00 4.20
2139 2226 5.711506 ACAAGTTCATTCATGGAGCACAATA 59.288 36.000 0.00 0.00 0.00 1.90
2144 2231 5.164620 TCTACAAGTTCATTCATGGAGCA 57.835 39.130 0.00 0.00 0.00 4.26
2156 2243 5.005779 CACACAAGCGGATATCTACAAGTTC 59.994 44.000 2.05 0.00 0.00 3.01
2160 2247 3.196901 ACCACACAAGCGGATATCTACAA 59.803 43.478 2.05 0.00 0.00 2.41
2186 2273 1.135859 GCGCCACATCTCTCAAACAAG 60.136 52.381 0.00 0.00 0.00 3.16
2215 2302 2.490115 CAAACAGGGCCTTAAATACGCA 59.510 45.455 1.32 0.00 0.00 5.24
2219 2306 7.546250 TTGAAATCAAACAGGGCCTTAAATA 57.454 32.000 1.32 0.00 32.11 1.40
2220 2307 6.432403 TTGAAATCAAACAGGGCCTTAAAT 57.568 33.333 1.32 0.00 32.11 1.40
2221 2308 5.878406 TTGAAATCAAACAGGGCCTTAAA 57.122 34.783 1.32 0.00 32.11 1.52
2223 2310 6.723977 ACTTATTGAAATCAAACAGGGCCTTA 59.276 34.615 1.32 0.00 39.55 2.69
2224 2311 5.543790 ACTTATTGAAATCAAACAGGGCCTT 59.456 36.000 1.32 0.00 39.55 4.35
2225 2312 5.086621 ACTTATTGAAATCAAACAGGGCCT 58.913 37.500 0.00 0.00 39.55 5.19
2226 2313 5.047377 TGACTTATTGAAATCAAACAGGGCC 60.047 40.000 0.00 0.00 39.55 5.80
2227 2314 5.863935 GTGACTTATTGAAATCAAACAGGGC 59.136 40.000 0.00 0.00 39.55 5.19
2228 2315 6.209391 AGGTGACTTATTGAAATCAAACAGGG 59.791 38.462 0.00 0.00 37.44 4.45
2229 2316 7.040478 TCAGGTGACTTATTGAAATCAAACAGG 60.040 37.037 0.00 0.00 40.21 4.00
2230 2317 7.805071 GTCAGGTGACTTATTGAAATCAAACAG 59.195 37.037 2.72 2.29 41.65 3.16
2231 2318 7.648142 GTCAGGTGACTTATTGAAATCAAACA 58.352 34.615 2.72 0.00 41.65 2.83
2266 2353 7.719633 ACAACCAAACAGACATGACTTATAAGT 59.280 33.333 18.05 18.05 43.16 2.24
2267 2354 8.099364 ACAACCAAACAGACATGACTTATAAG 57.901 34.615 11.05 11.05 0.00 1.73
2268 2355 7.717436 TGACAACCAAACAGACATGACTTATAA 59.283 33.333 0.00 0.00 0.00 0.98
2269 2356 7.172532 GTGACAACCAAACAGACATGACTTATA 59.827 37.037 0.00 0.00 0.00 0.98
2270 2357 6.017109 GTGACAACCAAACAGACATGACTTAT 60.017 38.462 0.00 0.00 0.00 1.73
2271 2358 5.295787 GTGACAACCAAACAGACATGACTTA 59.704 40.000 0.00 0.00 0.00 2.24
2272 2359 4.096382 GTGACAACCAAACAGACATGACTT 59.904 41.667 0.00 0.00 0.00 3.01
2273 2360 3.627577 GTGACAACCAAACAGACATGACT 59.372 43.478 0.00 0.00 0.00 3.41
2274 2361 3.243068 GGTGACAACCAAACAGACATGAC 60.243 47.826 0.00 0.00 46.75 3.06
2275 2362 2.948979 GGTGACAACCAAACAGACATGA 59.051 45.455 0.00 0.00 46.75 3.07
2276 2363 3.354089 GGTGACAACCAAACAGACATG 57.646 47.619 0.00 0.00 46.75 3.21
2288 2375 0.179045 AGGTGTGCTCAGGTGACAAC 60.179 55.000 0.00 0.00 0.00 3.32
2289 2376 0.546122 AAGGTGTGCTCAGGTGACAA 59.454 50.000 0.00 0.00 0.00 3.18
2290 2377 0.106708 GAAGGTGTGCTCAGGTGACA 59.893 55.000 0.00 0.00 0.00 3.58
2291 2378 0.603975 GGAAGGTGTGCTCAGGTGAC 60.604 60.000 0.00 0.00 0.00 3.67
2292 2379 1.754745 GGAAGGTGTGCTCAGGTGA 59.245 57.895 0.00 0.00 0.00 4.02
2293 2380 1.302832 GGGAAGGTGTGCTCAGGTG 60.303 63.158 0.00 0.00 0.00 4.00
2294 2381 1.770110 TGGGAAGGTGTGCTCAGGT 60.770 57.895 0.00 0.00 0.00 4.00
2295 2382 1.302832 GTGGGAAGGTGTGCTCAGG 60.303 63.158 0.00 0.00 0.00 3.86
2296 2383 1.302832 GGTGGGAAGGTGTGCTCAG 60.303 63.158 0.00 0.00 0.00 3.35
2297 2384 1.352622 AAGGTGGGAAGGTGTGCTCA 61.353 55.000 0.00 0.00 0.00 4.26
2298 2385 0.890996 CAAGGTGGGAAGGTGTGCTC 60.891 60.000 0.00 0.00 0.00 4.26
2299 2386 1.151450 CAAGGTGGGAAGGTGTGCT 59.849 57.895 0.00 0.00 0.00 4.40
2300 2387 0.755327 AACAAGGTGGGAAGGTGTGC 60.755 55.000 0.00 0.00 0.00 4.57
2301 2388 1.775385 AAACAAGGTGGGAAGGTGTG 58.225 50.000 0.00 0.00 0.00 3.82
2302 2389 2.543037 AAAACAAGGTGGGAAGGTGT 57.457 45.000 0.00 0.00 0.00 4.16
2303 2390 5.545063 ATTAAAAACAAGGTGGGAAGGTG 57.455 39.130 0.00 0.00 0.00 4.00
2304 2391 5.427157 ACAATTAAAAACAAGGTGGGAAGGT 59.573 36.000 0.00 0.00 0.00 3.50
2305 2392 5.924356 ACAATTAAAAACAAGGTGGGAAGG 58.076 37.500 0.00 0.00 0.00 3.46
2306 2393 8.950208 TTTACAATTAAAAACAAGGTGGGAAG 57.050 30.769 0.00 0.00 0.00 3.46
2307 2394 7.988028 CCTTTACAATTAAAAACAAGGTGGGAA 59.012 33.333 0.00 0.00 0.00 3.97
2308 2395 7.125963 ACCTTTACAATTAAAAACAAGGTGGGA 59.874 33.333 0.00 0.00 0.00 4.37
2309 2396 7.225734 CACCTTTACAATTAAAAACAAGGTGGG 59.774 37.037 16.99 0.00 36.14 4.61
2310 2397 7.982354 TCACCTTTACAATTAAAAACAAGGTGG 59.018 33.333 22.02 8.87 38.20 4.61
2311 2398 8.934507 TCACCTTTACAATTAAAAACAAGGTG 57.065 30.769 18.20 18.20 38.59 4.00
2312 2399 9.541143 CATCACCTTTACAATTAAAAACAAGGT 57.459 29.630 0.00 0.00 0.00 3.50
2313 2400 8.987890 CCATCACCTTTACAATTAAAAACAAGG 58.012 33.333 0.00 0.00 0.00 3.61
2314 2401 8.987890 CCCATCACCTTTACAATTAAAAACAAG 58.012 33.333 0.00 0.00 0.00 3.16
2315 2402 8.705594 TCCCATCACCTTTACAATTAAAAACAA 58.294 29.630 0.00 0.00 0.00 2.83
2316 2403 8.145122 GTCCCATCACCTTTACAATTAAAAACA 58.855 33.333 0.00 0.00 0.00 2.83
2317 2404 7.601130 GGTCCCATCACCTTTACAATTAAAAAC 59.399 37.037 0.00 0.00 33.08 2.43
2318 2405 7.256368 GGGTCCCATCACCTTTACAATTAAAAA 60.256 37.037 1.78 0.00 36.57 1.94
2319 2406 6.211785 GGGTCCCATCACCTTTACAATTAAAA 59.788 38.462 1.78 0.00 36.57 1.52
2320 2407 5.717654 GGGTCCCATCACCTTTACAATTAAA 59.282 40.000 1.78 0.00 36.57 1.52
2321 2408 5.222358 TGGGTCCCATCACCTTTACAATTAA 60.222 40.000 6.47 0.00 36.57 1.40
2322 2409 4.292571 TGGGTCCCATCACCTTTACAATTA 59.707 41.667 6.47 0.00 36.57 1.40
2323 2410 3.076785 TGGGTCCCATCACCTTTACAATT 59.923 43.478 6.47 0.00 36.57 2.32
2324 2411 2.652348 TGGGTCCCATCACCTTTACAAT 59.348 45.455 6.47 0.00 36.57 2.71
2325 2412 2.066592 TGGGTCCCATCACCTTTACAA 58.933 47.619 6.47 0.00 36.57 2.41
2326 2413 1.748732 TGGGTCCCATCACCTTTACA 58.251 50.000 6.47 0.00 36.57 2.41
2327 2414 2.654863 CATGGGTCCCATCACCTTTAC 58.345 52.381 21.49 0.00 43.15 2.01
2328 2415 1.064017 GCATGGGTCCCATCACCTTTA 60.064 52.381 21.49 0.00 43.15 1.85
2329 2416 0.324645 GCATGGGTCCCATCACCTTT 60.325 55.000 21.49 0.00 43.15 3.11
2330 2417 1.307647 GCATGGGTCCCATCACCTT 59.692 57.895 21.49 0.00 43.15 3.50
2331 2418 1.508667 TTGCATGGGTCCCATCACCT 61.509 55.000 21.49 0.00 43.15 4.00
2332 2419 0.614415 TTTGCATGGGTCCCATCACC 60.614 55.000 21.49 12.40 43.15 4.02
2333 2420 1.265236 TTTTGCATGGGTCCCATCAC 58.735 50.000 21.49 16.04 43.15 3.06
2334 2421 2.021262 TTTTTGCATGGGTCCCATCA 57.979 45.000 21.49 17.75 43.15 3.07
2358 2445 9.729281 CCACCCTAACTTAAAACTTATAAGTCA 57.271 33.333 18.28 4.72 41.49 3.41
2359 2446 9.948964 TCCACCCTAACTTAAAACTTATAAGTC 57.051 33.333 18.28 0.00 41.49 3.01
2364 2451 8.853126 GTTGTTCCACCCTAACTTAAAACTTAT 58.147 33.333 0.00 0.00 0.00 1.73
2365 2452 8.054572 AGTTGTTCCACCCTAACTTAAAACTTA 58.945 33.333 0.00 0.00 29.65 2.24
2366 2453 6.893554 AGTTGTTCCACCCTAACTTAAAACTT 59.106 34.615 0.00 0.00 29.65 2.66
2367 2454 6.429151 AGTTGTTCCACCCTAACTTAAAACT 58.571 36.000 0.00 0.00 29.65 2.66
2368 2455 6.704289 AGTTGTTCCACCCTAACTTAAAAC 57.296 37.500 0.00 0.00 29.65 2.43
2369 2456 8.852135 CATAAGTTGTTCCACCCTAACTTAAAA 58.148 33.333 11.09 0.00 44.18 1.52
2370 2457 8.219178 TCATAAGTTGTTCCACCCTAACTTAAA 58.781 33.333 11.09 2.80 44.18 1.52
2371 2458 7.662669 GTCATAAGTTGTTCCACCCTAACTTAA 59.337 37.037 11.09 0.00 44.18 1.85
2372 2459 7.016858 AGTCATAAGTTGTTCCACCCTAACTTA 59.983 37.037 9.88 9.88 44.72 2.24
2373 2460 6.002082 GTCATAAGTTGTTCCACCCTAACTT 58.998 40.000 0.00 0.00 43.48 2.66
2374 2461 5.309806 AGTCATAAGTTGTTCCACCCTAACT 59.690 40.000 0.00 0.00 35.06 2.24
2375 2462 5.557866 AGTCATAAGTTGTTCCACCCTAAC 58.442 41.667 0.00 0.00 0.00 2.34
2376 2463 5.836024 AGTCATAAGTTGTTCCACCCTAA 57.164 39.130 0.00 0.00 0.00 2.69
2377 2464 5.836024 AAGTCATAAGTTGTTCCACCCTA 57.164 39.130 0.00 0.00 0.00 3.53
2378 2465 4.724279 AAGTCATAAGTTGTTCCACCCT 57.276 40.909 0.00 0.00 0.00 4.34
2379 2466 8.209917 CTTATAAGTCATAAGTTGTTCCACCC 57.790 38.462 4.18 0.00 40.84 4.61
2391 2478 6.549433 ACGGACCCAACTTATAAGTCATAA 57.451 37.500 18.28 0.00 38.57 1.90
2392 2479 6.549433 AACGGACCCAACTTATAAGTCATA 57.451 37.500 18.28 0.00 38.57 2.15
2393 2480 5.431179 AACGGACCCAACTTATAAGTCAT 57.569 39.130 18.28 1.19 38.57 3.06
2394 2481 4.895668 AACGGACCCAACTTATAAGTCA 57.104 40.909 18.28 0.00 38.57 3.41
2395 2482 4.393990 CCAAACGGACCCAACTTATAAGTC 59.606 45.833 18.28 5.98 38.57 3.01
2396 2483 4.329392 CCAAACGGACCCAACTTATAAGT 58.671 43.478 12.50 12.50 42.04 2.24
2397 2484 3.128068 GCCAAACGGACCCAACTTATAAG 59.872 47.826 11.05 11.05 0.00 1.73
2398 2485 3.083293 GCCAAACGGACCCAACTTATAA 58.917 45.455 0.00 0.00 0.00 0.98
2399 2486 2.040012 TGCCAAACGGACCCAACTTATA 59.960 45.455 0.00 0.00 0.00 0.98
2400 2487 1.202952 TGCCAAACGGACCCAACTTAT 60.203 47.619 0.00 0.00 0.00 1.73
2401 2488 0.183014 TGCCAAACGGACCCAACTTA 59.817 50.000 0.00 0.00 0.00 2.24
2402 2489 0.684805 TTGCCAAACGGACCCAACTT 60.685 50.000 0.00 0.00 0.00 2.66
2403 2490 0.684805 TTTGCCAAACGGACCCAACT 60.685 50.000 0.00 0.00 0.00 3.16
2404 2491 0.175989 TTTTGCCAAACGGACCCAAC 59.824 50.000 0.00 0.00 0.00 3.77
2405 2492 1.123928 ATTTTGCCAAACGGACCCAA 58.876 45.000 0.00 0.00 0.00 4.12
2406 2493 1.996798 TATTTTGCCAAACGGACCCA 58.003 45.000 0.00 0.00 0.00 4.51
2407 2494 2.297880 ACTTATTTTGCCAAACGGACCC 59.702 45.455 0.00 0.00 0.00 4.46
2408 2495 3.004944 TGACTTATTTTGCCAAACGGACC 59.995 43.478 0.00 0.00 0.00 4.46
2409 2496 3.978855 GTGACTTATTTTGCCAAACGGAC 59.021 43.478 0.00 0.00 0.00 4.79
2410 2497 3.886505 AGTGACTTATTTTGCCAAACGGA 59.113 39.130 0.00 0.00 0.00 4.69
2411 2498 4.237349 AGTGACTTATTTTGCCAAACGG 57.763 40.909 0.00 0.00 0.00 4.44
2412 2499 6.582437 AAAAGTGACTTATTTTGCCAAACG 57.418 33.333 0.00 0.00 0.00 3.60
2413 2500 8.874816 TGTAAAAAGTGACTTATTTTGCCAAAC 58.125 29.630 0.00 0.00 30.65 2.93
2414 2501 8.874816 GTGTAAAAAGTGACTTATTTTGCCAAA 58.125 29.630 0.00 0.00 30.65 3.28
2415 2502 8.254508 AGTGTAAAAAGTGACTTATTTTGCCAA 58.745 29.630 0.00 0.00 30.65 4.52
2416 2503 7.777095 AGTGTAAAAAGTGACTTATTTTGCCA 58.223 30.769 0.00 0.00 30.65 4.92
2417 2504 8.642908 AAGTGTAAAAAGTGACTTATTTTGCC 57.357 30.769 0.00 0.00 30.65 4.52
2453 2540 8.410912 GTTTGGTTCCAAATAAGTCACTAACTT 58.589 33.333 18.11 0.00 39.75 2.66
2454 2541 7.558444 TGTTTGGTTCCAAATAAGTCACTAACT 59.442 33.333 18.11 0.00 37.76 2.24
2455 2542 7.708998 TGTTTGGTTCCAAATAAGTCACTAAC 58.291 34.615 18.11 4.50 38.07 2.34
2456 2543 7.776030 TCTGTTTGGTTCCAAATAAGTCACTAA 59.224 33.333 18.11 2.90 38.07 2.24
2457 2544 7.284074 TCTGTTTGGTTCCAAATAAGTCACTA 58.716 34.615 18.11 3.44 38.07 2.74
2458 2545 6.126409 TCTGTTTGGTTCCAAATAAGTCACT 58.874 36.000 18.11 0.00 38.07 3.41
2459 2546 6.385649 TCTGTTTGGTTCCAAATAAGTCAC 57.614 37.500 18.11 6.79 38.07 3.67
2460 2547 5.009610 GCTCTGTTTGGTTCCAAATAAGTCA 59.990 40.000 18.11 10.94 38.07 3.41
2461 2548 5.461526 GCTCTGTTTGGTTCCAAATAAGTC 58.538 41.667 18.11 7.40 38.07 3.01
2462 2549 4.280929 GGCTCTGTTTGGTTCCAAATAAGT 59.719 41.667 18.11 0.00 38.07 2.24
2463 2550 4.524328 AGGCTCTGTTTGGTTCCAAATAAG 59.476 41.667 18.11 17.33 38.07 1.73
2464 2551 4.479158 AGGCTCTGTTTGGTTCCAAATAA 58.521 39.130 18.11 10.23 38.07 1.40
2465 2552 4.112634 AGGCTCTGTTTGGTTCCAAATA 57.887 40.909 18.11 14.87 38.07 1.40
2466 2553 2.962859 AGGCTCTGTTTGGTTCCAAAT 58.037 42.857 18.11 0.31 38.07 2.32
2467 2554 2.452600 AGGCTCTGTTTGGTTCCAAA 57.547 45.000 12.29 12.29 34.09 3.28
2468 2555 3.586470 TTAGGCTCTGTTTGGTTCCAA 57.414 42.857 0.00 0.00 0.00 3.53
2469 2556 3.586470 TTTAGGCTCTGTTTGGTTCCA 57.414 42.857 0.00 0.00 0.00 3.53
2470 2557 4.079253 TGATTTAGGCTCTGTTTGGTTCC 58.921 43.478 0.00 0.00 0.00 3.62
2471 2558 4.518970 TGTGATTTAGGCTCTGTTTGGTTC 59.481 41.667 0.00 0.00 0.00 3.62
2472 2559 4.469657 TGTGATTTAGGCTCTGTTTGGTT 58.530 39.130 0.00 0.00 0.00 3.67
2473 2560 4.098914 TGTGATTTAGGCTCTGTTTGGT 57.901 40.909 0.00 0.00 0.00 3.67
2474 2561 5.452078 TTTGTGATTTAGGCTCTGTTTGG 57.548 39.130 0.00 0.00 0.00 3.28
2475 2562 7.869429 AGAAATTTGTGATTTAGGCTCTGTTTG 59.131 33.333 0.00 0.00 0.00 2.93
2476 2563 7.955918 AGAAATTTGTGATTTAGGCTCTGTTT 58.044 30.769 0.00 0.00 0.00 2.83
2477 2564 7.530426 AGAAATTTGTGATTTAGGCTCTGTT 57.470 32.000 0.00 0.00 0.00 3.16
2478 2565 6.128172 CGAGAAATTTGTGATTTAGGCTCTGT 60.128 38.462 0.00 0.00 0.00 3.41
2479 2566 6.253746 CGAGAAATTTGTGATTTAGGCTCTG 58.746 40.000 0.00 0.00 0.00 3.35
2480 2567 5.163713 GCGAGAAATTTGTGATTTAGGCTCT 60.164 40.000 0.00 0.00 0.00 4.09
2481 2568 5.030936 GCGAGAAATTTGTGATTTAGGCTC 58.969 41.667 0.00 0.00 0.00 4.70
2482 2569 4.142381 GGCGAGAAATTTGTGATTTAGGCT 60.142 41.667 0.00 0.00 0.00 4.58
2483 2570 4.105486 GGCGAGAAATTTGTGATTTAGGC 58.895 43.478 0.00 0.00 0.00 3.93
2484 2571 5.567138 AGGCGAGAAATTTGTGATTTAGG 57.433 39.130 0.00 0.00 0.00 2.69
2485 2572 6.634436 GCATAGGCGAGAAATTTGTGATTTAG 59.366 38.462 0.00 0.00 0.00 1.85
2565 2652 0.096976 CGCTACATCCAGGTTTTGCG 59.903 55.000 0.00 0.00 36.41 4.85
2572 2659 1.732259 GTCACAAACGCTACATCCAGG 59.268 52.381 0.00 0.00 0.00 4.45
2625 2722 2.227194 GTGAAAAGCGAAAGGGAGGAA 58.773 47.619 0.00 0.00 0.00 3.36
2653 2750 4.145876 TGCAGAATAAACAGAAACAGCG 57.854 40.909 0.00 0.00 0.00 5.18
2663 3627 8.699749 GGTTCAAAACTAACATGCAGAATAAAC 58.300 33.333 0.00 0.00 0.00 2.01
2668 3632 5.843673 TGGTTCAAAACTAACATGCAGAA 57.156 34.783 0.00 0.00 0.00 3.02
2676 3640 9.967245 GAAAGTTTGATTTGGTTCAAAACTAAC 57.033 29.630 14.59 14.59 44.71 2.34
2734 3698 8.038351 TGACACCTTCGAAATAGTTTGATGATA 58.962 33.333 0.00 0.00 0.00 2.15
2738 3702 7.504924 TTTGACACCTTCGAAATAGTTTGAT 57.495 32.000 0.00 0.00 0.00 2.57
2766 3737 9.520515 ACATGACACTTTTTATAGTTTGAGGAT 57.479 29.630 0.00 0.00 0.00 3.24
2779 3750 5.690865 TCAAGGACCTACATGACACTTTTT 58.309 37.500 0.00 0.00 0.00 1.94
2856 3827 2.993899 CAAAGGTGTCACGTAGGTCATC 59.006 50.000 0.00 0.00 0.00 2.92
2941 3921 9.686683 AATAAAGAGTAAAGTGCATCATAGGTT 57.313 29.630 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.