Multiple sequence alignment - TraesCS4D01G217700

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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 TraesCS4D01G217700 chr4D 100.000 4635 0 0 1 4635 373211370 373206736 0.000000e+00 8560.0
1 TraesCS4D01G217700 chr4D 97.633 169 4 0 4012 4180 3846927 3846759 1.630000e-74 291.0
2 TraesCS4D01G217700 chr4D 98.039 51 1 0 2190 2240 373209104 373209054 6.390000e-14 89.8
3 TraesCS4D01G217700 chr4D 98.039 51 1 0 2267 2317 373209181 373209131 6.390000e-14 89.8
4 TraesCS4D01G217700 chr4A 93.571 4091 114 71 3 4012 91468829 91472851 0.000000e+00 5960.0
5 TraesCS4D01G217700 chr4A 89.149 470 30 7 4180 4635 91472853 91473315 2.420000e-157 566.0
6 TraesCS4D01G217700 chr4A 82.727 110 13 6 4246 4350 605425258 605425150 4.940000e-15 93.5
7 TraesCS4D01G217700 chr4B 93.292 3354 104 54 701 4012 458460306 458457032 0.000000e+00 4835.0
8 TraesCS4D01G217700 chr4B 94.640 709 21 6 1 701 458461047 458460348 0.000000e+00 1083.0
9 TraesCS4D01G217700 chr4B 95.031 161 7 1 4476 4635 458456461 458456301 7.700000e-63 252.0
10 TraesCS4D01G217700 chr4B 85.854 205 19 5 4180 4380 458457030 458456832 4.700000e-50 209.0
11 TraesCS4D01G217700 chr4B 93.966 116 6 1 4366 4480 458456808 458456693 1.710000e-39 174.0
12 TraesCS4D01G217700 chrUn 98.235 170 3 0 4009 4178 102836926 102837095 9.750000e-77 298.0
13 TraesCS4D01G217700 chr5D 96.648 179 6 0 4002 4180 218937483 218937305 9.750000e-77 298.0
14 TraesCS4D01G217700 chr5D 97.674 172 4 0 4009 4180 539072645 539072816 3.510000e-76 296.0
15 TraesCS4D01G217700 chr5D 96.045 177 7 0 4004 4180 15538019 15537843 5.870000e-74 289.0
16 TraesCS4D01G217700 chr5D 87.075 147 17 2 1554 1699 345848407 345848262 1.030000e-36 165.0
17 TraesCS4D01G217700 chr1D 97.688 173 4 0 4008 4180 110906841 110906669 9.750000e-77 298.0
18 TraesCS4D01G217700 chr1D 97.633 169 4 0 4012 4180 427704709 427704541 1.630000e-74 291.0
19 TraesCS4D01G217700 chr1D 96.532 173 6 0 4008 4180 298577771 298577599 2.110000e-73 287.0
20 TraesCS4D01G217700 chr2D 95.628 183 7 1 3999 4180 62026098 62026280 4.540000e-75 292.0
21 TraesCS4D01G217700 chr5A 87.500 144 18 0 1556 1699 445392218 445392361 2.870000e-37 167.0
22 TraesCS4D01G217700 chr5B 86.806 144 19 0 1556 1699 405768065 405768208 1.330000e-35 161.0
23 TraesCS4D01G217700 chr2B 80.808 99 15 4 4245 4339 801055124 801055222 1.790000e-09 75.0
24 TraesCS4D01G217700 chr7D 100.000 37 0 0 832 868 185418984 185419020 8.320000e-08 69.4
25 TraesCS4D01G217700 chr6B 97.500 40 1 0 832 871 353088544 353088505 8.320000e-08 69.4
26 TraesCS4D01G217700 chr6B 100.000 29 0 0 4323 4351 519806557 519806585 2.000000e-03 54.7
27 TraesCS4D01G217700 chr6B 96.774 31 1 0 4317 4347 646227500 646227470 8.000000e-03 52.8
28 TraesCS4D01G217700 chr6D 100.000 29 0 0 4323 4351 344252892 344252920 2.000000e-03 54.7


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 TraesCS4D01G217700 chr4D 373206736 373211370 4634 True 2913.2 8560 98.692667 1 4635 3 chr4D.!!$R2 4634
1 TraesCS4D01G217700 chr4A 91468829 91473315 4486 False 3263.0 5960 91.360000 3 4635 2 chr4A.!!$F1 4632
2 TraesCS4D01G217700 chr4B 458456301 458461047 4746 True 1310.6 4835 92.556600 1 4635 5 chr4B.!!$R1 4634

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
247 255 1.064758 GCACCAGAGAGAGAGAGAGGA 60.065 57.143 0.00 0.0 0.00 3.71 F
248 256 2.620367 GCACCAGAGAGAGAGAGAGGAA 60.620 54.545 0.00 0.0 0.00 3.36 F
1865 1957 0.242825 CAACACTCCATTGCTGGCTG 59.757 55.000 0.00 0.0 42.80 4.85 F
2541 2692 0.040958 GCATGCTGCACGTATAAGCC 60.041 55.000 11.37 0.0 44.26 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 1143 0.033991 TCCTCCTCCTCTTCGTCCAG 60.034 60.0 0.00 0.0 0.00 3.86 R
1872 1964 0.748450 ATGCTGAAATGGAATGGCCG 59.252 50.0 0.00 0.0 40.66 6.13 R
2862 3026 0.107508 CCGTGGAATGCATGTCTCCT 60.108 55.0 15.32 0.0 0.00 3.69 R
4099 4294 0.320160 GGTACAACCCACGTCAGGAC 60.320 60.0 8.14 0.0 30.04 3.85 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
69 70 1.403814 TAGTTGCTAGCTGCGGAGAT 58.596 50.000 17.23 3.10 46.63 2.75
94 95 1.709147 GAGTGGTGCATTAGCCTGCG 61.709 60.000 0.00 0.00 45.30 5.18
164 169 1.751924 CCCTGGTCTGAGTACAGTAGC 59.248 57.143 0.00 0.00 43.81 3.58
187 192 6.024049 GCACTAACAAGATTGATTACTGCAC 58.976 40.000 0.00 0.00 0.00 4.57
242 250 2.049185 GCGGCACCAGAGAGAGAGA 61.049 63.158 0.00 0.00 0.00 3.10
247 255 1.064758 GCACCAGAGAGAGAGAGAGGA 60.065 57.143 0.00 0.00 0.00 3.71
248 256 2.620367 GCACCAGAGAGAGAGAGAGGAA 60.620 54.545 0.00 0.00 0.00 3.36
972 1061 3.567797 GGCTTCGATCGTGCTGCC 61.568 66.667 25.42 22.82 0.00 4.85
1054 1143 1.602771 GAAGAGGTGGGGGTGCTAC 59.397 63.158 0.00 0.00 0.00 3.58
1865 1957 0.242825 CAACACTCCATTGCTGGCTG 59.757 55.000 0.00 0.00 42.80 4.85
1866 1958 0.896940 AACACTCCATTGCTGGCTGG 60.897 55.000 0.00 0.00 42.80 4.85
1867 1959 2.362120 ACTCCATTGCTGGCTGGC 60.362 61.111 0.00 0.00 42.80 4.85
1868 1960 2.044252 CTCCATTGCTGGCTGGCT 60.044 61.111 2.00 0.00 42.80 4.75
1869 1961 2.044650 TCCATTGCTGGCTGGCTC 60.045 61.111 2.00 0.00 42.80 4.70
1870 1962 3.145551 CCATTGCTGGCTGGCTCC 61.146 66.667 2.00 0.00 35.23 4.70
1871 1963 3.145551 CATTGCTGGCTGGCTCCC 61.146 66.667 2.00 0.00 0.00 4.30
1872 1964 4.453892 ATTGCTGGCTGGCTCCCC 62.454 66.667 2.00 0.00 0.00 4.81
1903 1995 9.812347 ATTCCATTTCAGCATATTCTATGGTAA 57.188 29.630 0.00 0.00 34.21 2.85
2043 2135 2.878429 GAGGAGAGACAAGCGCGA 59.122 61.111 12.10 0.00 0.00 5.87
2168 2266 3.637821 AGCCCCAGATCCTTCTACATA 57.362 47.619 0.00 0.00 0.00 2.29
2173 2271 4.660771 CCCCAGATCCTTCTACATACCTTT 59.339 45.833 0.00 0.00 0.00 3.11
2174 2272 5.132816 CCCCAGATCCTTCTACATACCTTTT 59.867 44.000 0.00 0.00 0.00 2.27
2175 2273 6.329197 CCCCAGATCCTTCTACATACCTTTTA 59.671 42.308 0.00 0.00 0.00 1.52
2176 2274 7.445945 CCCAGATCCTTCTACATACCTTTTAG 58.554 42.308 0.00 0.00 0.00 1.85
2177 2275 6.931840 CCAGATCCTTCTACATACCTTTTAGC 59.068 42.308 0.00 0.00 0.00 3.09
2203 2301 4.202264 GCTAGCTAGCTCTTCCAAACCATA 60.202 45.833 33.71 0.00 45.62 2.74
2214 2312 5.424252 TCTTCCAAACCATACGAGTTATCCT 59.576 40.000 0.00 0.00 0.00 3.24
2227 2325 5.593095 ACGAGTTATCCTATGCAACTGAGTA 59.407 40.000 0.00 0.00 32.79 2.59
2228 2326 6.265649 ACGAGTTATCCTATGCAACTGAGTAT 59.734 38.462 0.00 0.00 32.79 2.12
2229 2327 6.584184 CGAGTTATCCTATGCAACTGAGTATG 59.416 42.308 0.00 0.00 32.79 2.39
2230 2328 7.522236 CGAGTTATCCTATGCAACTGAGTATGA 60.522 40.741 0.00 0.00 32.79 2.15
2231 2329 8.200024 AGTTATCCTATGCAACTGAGTATGAT 57.800 34.615 0.00 0.00 31.47 2.45
2232 2330 8.654997 AGTTATCCTATGCAACTGAGTATGATT 58.345 33.333 0.00 0.00 31.47 2.57
2233 2331 9.929180 GTTATCCTATGCAACTGAGTATGATTA 57.071 33.333 0.00 0.00 0.00 1.75
2260 2392 3.863041 ACTCTTTCATCTTTACCGGAGC 58.137 45.455 9.46 0.00 0.00 4.70
2261 2393 2.860735 CTCTTTCATCTTTACCGGAGCG 59.139 50.000 9.46 0.00 0.00 5.03
2262 2394 2.494471 TCTTTCATCTTTACCGGAGCGA 59.506 45.455 9.46 0.00 0.00 4.93
2263 2395 2.579207 TTCATCTTTACCGGAGCGAG 57.421 50.000 9.46 0.00 0.00 5.03
2264 2396 1.471119 TCATCTTTACCGGAGCGAGT 58.529 50.000 9.46 0.00 0.00 4.18
2265 2397 2.646930 TCATCTTTACCGGAGCGAGTA 58.353 47.619 9.46 0.00 0.00 2.59
2266 2398 2.357009 TCATCTTTACCGGAGCGAGTAC 59.643 50.000 9.46 0.00 0.00 2.73
2267 2399 2.119801 TCTTTACCGGAGCGAGTACT 57.880 50.000 9.46 0.00 0.00 2.73
2268 2400 2.012673 TCTTTACCGGAGCGAGTACTC 58.987 52.381 9.46 13.18 35.86 2.59
2269 2401 2.015587 CTTTACCGGAGCGAGTACTCT 58.984 52.381 20.34 2.62 36.87 3.24
2270 2402 2.119801 TTACCGGAGCGAGTACTCTT 57.880 50.000 20.34 8.75 36.87 2.85
2271 2403 1.661341 TACCGGAGCGAGTACTCTTC 58.339 55.000 20.34 16.27 36.87 2.87
2272 2404 1.031029 ACCGGAGCGAGTACTCTTCC 61.031 60.000 23.49 23.49 36.87 3.46
2273 2405 1.030488 CCGGAGCGAGTACTCTTCCA 61.030 60.000 28.45 0.00 36.87 3.53
2274 2406 0.809385 CGGAGCGAGTACTCTTCCAA 59.191 55.000 28.45 0.00 36.87 3.53
2275 2407 1.201647 CGGAGCGAGTACTCTTCCAAA 59.798 52.381 28.45 0.00 36.87 3.28
2276 2408 2.608268 GGAGCGAGTACTCTTCCAAAC 58.392 52.381 26.30 11.18 36.87 2.93
2277 2409 2.608268 GAGCGAGTACTCTTCCAAACC 58.392 52.381 20.34 0.00 33.69 3.27
2278 2410 1.968493 AGCGAGTACTCTTCCAAACCA 59.032 47.619 20.34 0.00 0.00 3.67
2279 2411 2.567615 AGCGAGTACTCTTCCAAACCAT 59.432 45.455 20.34 0.00 0.00 3.55
2280 2412 3.767673 AGCGAGTACTCTTCCAAACCATA 59.232 43.478 20.34 0.00 0.00 2.74
2281 2413 3.864003 GCGAGTACTCTTCCAAACCATAC 59.136 47.826 20.34 0.00 0.00 2.39
2282 2414 4.103357 CGAGTACTCTTCCAAACCATACG 58.897 47.826 20.34 0.00 0.00 3.06
2283 2415 4.142534 CGAGTACTCTTCCAAACCATACGA 60.143 45.833 20.34 0.00 0.00 3.43
2284 2416 5.326200 AGTACTCTTCCAAACCATACGAG 57.674 43.478 0.00 0.00 0.00 4.18
2285 2417 4.771054 AGTACTCTTCCAAACCATACGAGT 59.229 41.667 0.00 0.00 34.88 4.18
2286 2418 4.618920 ACTCTTCCAAACCATACGAGTT 57.381 40.909 0.00 0.00 0.00 3.01
2287 2419 5.733620 ACTCTTCCAAACCATACGAGTTA 57.266 39.130 0.00 0.00 0.00 2.24
2288 2420 6.295719 ACTCTTCCAAACCATACGAGTTAT 57.704 37.500 0.00 0.00 0.00 1.89
2289 2421 6.338937 ACTCTTCCAAACCATACGAGTTATC 58.661 40.000 0.00 0.00 0.00 1.75
2290 2422 5.667466 TCTTCCAAACCATACGAGTTATCC 58.333 41.667 0.00 0.00 0.00 2.59
2291 2423 5.424252 TCTTCCAAACCATACGAGTTATCCT 59.576 40.000 0.00 0.00 0.00 3.24
2292 2424 6.608405 TCTTCCAAACCATACGAGTTATCCTA 59.392 38.462 0.00 0.00 0.00 2.94
2293 2425 6.989155 TCCAAACCATACGAGTTATCCTAT 57.011 37.500 0.00 0.00 0.00 2.57
2294 2426 6.755206 TCCAAACCATACGAGTTATCCTATG 58.245 40.000 0.00 0.00 0.00 2.23
2295 2427 5.408604 CCAAACCATACGAGTTATCCTATGC 59.591 44.000 0.00 0.00 0.00 3.14
2296 2428 5.801531 AACCATACGAGTTATCCTATGCA 57.198 39.130 0.00 0.00 0.00 3.96
2297 2429 5.801531 ACCATACGAGTTATCCTATGCAA 57.198 39.130 0.00 0.00 0.00 4.08
2298 2430 5.539048 ACCATACGAGTTATCCTATGCAAC 58.461 41.667 0.00 0.00 0.00 4.17
2299 2431 5.304614 ACCATACGAGTTATCCTATGCAACT 59.695 40.000 0.00 0.00 35.27 3.16
2300 2432 5.635280 CCATACGAGTTATCCTATGCAACTG 59.365 44.000 0.00 0.00 32.79 3.16
2301 2433 6.447162 CATACGAGTTATCCTATGCAACTGA 58.553 40.000 0.00 0.00 32.79 3.41
2302 2434 4.938080 ACGAGTTATCCTATGCAACTGAG 58.062 43.478 0.00 0.00 32.79 3.35
2303 2435 4.402793 ACGAGTTATCCTATGCAACTGAGT 59.597 41.667 0.00 0.00 32.79 3.41
2304 2436 5.593095 ACGAGTTATCCTATGCAACTGAGTA 59.407 40.000 0.00 0.00 32.79 2.59
2305 2437 6.265649 ACGAGTTATCCTATGCAACTGAGTAT 59.734 38.462 0.00 0.00 32.79 2.12
2306 2438 6.584184 CGAGTTATCCTATGCAACTGAGTATG 59.416 42.308 0.00 0.00 32.79 2.39
2307 2439 7.522236 CGAGTTATCCTATGCAACTGAGTATGA 60.522 40.741 0.00 0.00 32.79 2.15
2308 2440 8.200024 AGTTATCCTATGCAACTGAGTATGAT 57.800 34.615 0.00 0.00 31.47 2.45
2309 2441 8.654997 AGTTATCCTATGCAACTGAGTATGATT 58.345 33.333 0.00 0.00 31.47 2.57
2310 2442 9.929180 GTTATCCTATGCAACTGAGTATGATTA 57.071 33.333 0.00 0.00 0.00 1.75
2381 2522 1.540797 GGTCAAAAGGCAGCAATGCAA 60.541 47.619 8.35 0.00 36.33 4.08
2400 2541 3.125146 GCAATGCGTTGTTACTGATCTGA 59.875 43.478 19.49 0.00 37.65 3.27
2420 2561 7.526142 TCTGATGACTGTTCTAGTAGTGTTT 57.474 36.000 0.00 0.00 40.53 2.83
2462 2606 7.013559 TGGTTTCTGGATGCTTATAATGACATG 59.986 37.037 0.00 0.00 0.00 3.21
2463 2607 7.229306 GGTTTCTGGATGCTTATAATGACATGA 59.771 37.037 0.00 0.00 0.00 3.07
2464 2608 7.734924 TTCTGGATGCTTATAATGACATGAC 57.265 36.000 0.00 0.00 0.00 3.06
2470 2614 8.877779 GGATGCTTATAATGACATGACATACTC 58.122 37.037 11.06 0.00 0.00 2.59
2502 2653 3.064207 CCCGTAATCCATGGATAACACG 58.936 50.000 30.78 30.78 34.93 4.49
2505 2656 3.059868 CGTAATCCATGGATAACACGCAC 60.060 47.826 28.74 17.62 33.97 5.34
2506 2657 1.581934 ATCCATGGATAACACGCACG 58.418 50.000 26.25 0.00 32.36 5.34
2512 2663 0.810031 GGATAACACGCACGCATCCT 60.810 55.000 0.00 0.00 33.74 3.24
2524 2675 3.094062 GCATCCTCCGGCTAGTGCA 62.094 63.158 14.18 0.00 41.91 4.57
2525 2676 1.750930 CATCCTCCGGCTAGTGCAT 59.249 57.895 0.00 0.00 41.91 3.96
2526 2677 0.602106 CATCCTCCGGCTAGTGCATG 60.602 60.000 0.00 0.00 41.91 4.06
2527 2678 2.388890 ATCCTCCGGCTAGTGCATGC 62.389 60.000 11.82 11.82 41.91 4.06
2528 2679 2.503061 CTCCGGCTAGTGCATGCT 59.497 61.111 20.33 1.26 41.91 3.79
2530 2681 3.580193 CCGGCTAGTGCATGCTGC 61.580 66.667 20.33 16.50 45.29 5.25
2540 2691 3.444657 GCATGCTGCACGTATAAGC 57.555 52.632 11.37 8.84 44.26 3.09
2541 2692 0.040958 GCATGCTGCACGTATAAGCC 60.041 55.000 11.37 0.00 44.26 4.35
2542 2693 0.588252 CATGCTGCACGTATAAGCCC 59.412 55.000 3.57 0.00 36.05 5.19
2543 2694 0.535102 ATGCTGCACGTATAAGCCCC 60.535 55.000 3.57 0.00 36.05 5.80
2721 2875 2.670934 GAGCACCACCACCAGCAG 60.671 66.667 0.00 0.00 0.00 4.24
2722 2876 4.275508 AGCACCACCACCAGCAGG 62.276 66.667 0.00 0.00 42.21 4.85
2724 2878 4.584518 CACCACCACCAGCAGGCA 62.585 66.667 0.00 0.00 39.06 4.75
2725 2879 4.275508 ACCACCACCAGCAGGCAG 62.276 66.667 0.00 0.00 39.06 4.85
2867 3031 2.895865 CGCTCGTCGGCTAGGAGA 60.896 66.667 12.29 0.00 41.70 3.71
3124 3317 1.375908 GCAGACGGACAAGGCATCA 60.376 57.895 0.00 0.00 0.00 3.07
3182 3375 2.413765 GGCAGACGTCGGAGATCC 59.586 66.667 20.25 7.09 40.67 3.36
3226 3419 3.444805 GAGGCCGACGAGCTCACT 61.445 66.667 15.40 0.00 0.00 3.41
3472 3665 4.429522 ATGCAGGCGCCCATGTCA 62.430 61.111 26.15 17.60 37.32 3.58
3695 3888 4.952262 TCTATCAGCTGATGTGCAAAAC 57.048 40.909 34.48 0.00 36.05 2.43
3696 3889 2.624316 ATCAGCTGATGTGCAAAACG 57.376 45.000 28.21 0.00 32.68 3.60
3697 3890 0.592637 TCAGCTGATGTGCAAAACGG 59.407 50.000 13.74 0.00 34.99 4.44
3698 3891 0.592637 CAGCTGATGTGCAAAACGGA 59.407 50.000 8.42 0.00 34.99 4.69
3699 3892 1.001487 CAGCTGATGTGCAAAACGGAA 60.001 47.619 8.42 0.00 34.99 4.30
3846 4039 7.655328 GGTCATAATATCTTCTCCAGAGTGTTG 59.345 40.741 0.00 0.00 33.87 3.33
3901 4094 9.615660 TCTCCCCATTGATTTATATACTAGTGT 57.384 33.333 5.39 0.39 0.00 3.55
3939 4134 5.215903 GTGGTGTGTGTATCGATATCTCTG 58.784 45.833 8.66 0.00 0.00 3.35
3944 4139 5.010012 TGTGTGTATCGATATCTCTGCATGT 59.990 40.000 8.66 0.00 0.00 3.21
3955 4150 2.031333 TCTCTGCATGTGATCGATCTCG 60.031 50.000 25.02 11.54 41.45 4.04
4012 4207 9.092876 CTTGCTGGAGTTTAACATTTTAAAACA 57.907 29.630 1.97 0.00 38.60 2.83
4013 4208 8.641499 TGCTGGAGTTTAACATTTTAAAACAG 57.359 30.769 1.97 14.29 38.60 3.16
4014 4209 8.254508 TGCTGGAGTTTAACATTTTAAAACAGT 58.745 29.630 1.97 2.49 38.60 3.55
4015 4210 9.093970 GCTGGAGTTTAACATTTTAAAACAGTT 57.906 29.630 18.81 18.81 38.60 3.16
4026 4221 9.869757 ACATTTTAAAACAGTTTTGCTAGAACT 57.130 25.926 19.77 0.00 37.82 3.01
4030 4225 9.730420 TTTAAAACAGTTTTGCTAGAACTCATC 57.270 29.630 19.77 0.00 35.26 2.92
4031 4226 7.573968 AAAACAGTTTTGCTAGAACTCATCT 57.426 32.000 10.62 0.00 42.48 2.90
4032 4227 8.677148 AAAACAGTTTTGCTAGAACTCATCTA 57.323 30.769 10.62 0.00 39.71 1.98
4060 4255 7.500992 TGAGATATAGTTTGGTCTCATTCACC 58.499 38.462 0.16 0.00 41.40 4.02
4061 4256 7.345653 TGAGATATAGTTTGGTCTCATTCACCT 59.654 37.037 0.16 0.00 41.40 4.00
4062 4257 8.095452 AGATATAGTTTGGTCTCATTCACCTT 57.905 34.615 0.00 0.00 34.66 3.50
4063 4258 8.552296 AGATATAGTTTGGTCTCATTCACCTTT 58.448 33.333 0.00 0.00 34.66 3.11
4064 4259 9.178758 GATATAGTTTGGTCTCATTCACCTTTT 57.821 33.333 0.00 0.00 34.66 2.27
4068 4263 8.567285 AGTTTGGTCTCATTCACCTTTTATAG 57.433 34.615 0.00 0.00 34.66 1.31
4069 4264 7.121315 AGTTTGGTCTCATTCACCTTTTATAGC 59.879 37.037 0.00 0.00 34.66 2.97
4070 4265 5.437060 TGGTCTCATTCACCTTTTATAGCC 58.563 41.667 0.00 0.00 34.66 3.93
4071 4266 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
4072 4267 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
4073 4268 6.547510 GGTCTCATTCACCTTTTATAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
4074 4269 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
4075 4270 6.547141 TCTCATTCACCTTTTATAGCCATTGG 59.453 38.462 0.00 0.00 0.00 3.16
4076 4271 6.430864 TCATTCACCTTTTATAGCCATTGGA 58.569 36.000 6.95 0.00 0.00 3.53
4077 4272 7.068702 TCATTCACCTTTTATAGCCATTGGAT 58.931 34.615 6.95 1.78 0.00 3.41
4078 4273 6.713762 TTCACCTTTTATAGCCATTGGATG 57.286 37.500 6.95 0.00 0.00 3.51
4079 4274 5.765510 TCACCTTTTATAGCCATTGGATGT 58.234 37.500 6.95 0.10 0.00 3.06
4080 4275 5.593909 TCACCTTTTATAGCCATTGGATGTG 59.406 40.000 6.95 2.95 0.00 3.21
4081 4276 5.593909 CACCTTTTATAGCCATTGGATGTGA 59.406 40.000 6.95 0.00 0.00 3.58
4082 4277 6.266103 CACCTTTTATAGCCATTGGATGTGAT 59.734 38.462 6.95 0.00 0.00 3.06
4083 4278 6.266103 ACCTTTTATAGCCATTGGATGTGATG 59.734 38.462 6.95 0.00 0.00 3.07
4084 4279 6.266103 CCTTTTATAGCCATTGGATGTGATGT 59.734 38.462 6.95 0.00 0.00 3.06
4085 4280 7.201938 CCTTTTATAGCCATTGGATGTGATGTT 60.202 37.037 6.95 0.00 0.00 2.71
4086 4281 8.759481 TTTTATAGCCATTGGATGTGATGTTA 57.241 30.769 6.95 0.00 0.00 2.41
4087 4282 8.938801 TTTATAGCCATTGGATGTGATGTTAT 57.061 30.769 6.95 0.00 0.00 1.89
4090 4285 6.889301 AGCCATTGGATGTGATGTTATAAG 57.111 37.500 6.95 0.00 0.00 1.73
4091 4286 6.604171 AGCCATTGGATGTGATGTTATAAGA 58.396 36.000 6.95 0.00 0.00 2.10
4092 4287 7.236529 AGCCATTGGATGTGATGTTATAAGAT 58.763 34.615 6.95 0.00 0.00 2.40
4093 4288 7.176165 AGCCATTGGATGTGATGTTATAAGATG 59.824 37.037 6.95 0.00 0.00 2.90
4094 4289 7.310664 CCATTGGATGTGATGTTATAAGATGC 58.689 38.462 0.00 0.00 0.00 3.91
4095 4290 6.544038 TTGGATGTGATGTTATAAGATGCG 57.456 37.500 0.00 0.00 0.00 4.73
4096 4291 5.610398 TGGATGTGATGTTATAAGATGCGT 58.390 37.500 0.00 0.00 0.00 5.24
4097 4292 5.466393 TGGATGTGATGTTATAAGATGCGTG 59.534 40.000 0.00 0.00 0.00 5.34
4098 4293 5.466728 GGATGTGATGTTATAAGATGCGTGT 59.533 40.000 0.00 0.00 0.00 4.49
4099 4294 5.717038 TGTGATGTTATAAGATGCGTGTG 57.283 39.130 0.00 0.00 0.00 3.82
4100 4295 5.175127 TGTGATGTTATAAGATGCGTGTGT 58.825 37.500 0.00 0.00 0.00 3.72
4101 4296 5.290885 TGTGATGTTATAAGATGCGTGTGTC 59.709 40.000 0.00 0.00 0.00 3.67
4102 4297 4.808895 TGATGTTATAAGATGCGTGTGTCC 59.191 41.667 0.00 0.00 0.00 4.02
4103 4298 4.465632 TGTTATAAGATGCGTGTGTCCT 57.534 40.909 0.00 0.00 0.00 3.85
4104 4299 4.180817 TGTTATAAGATGCGTGTGTCCTG 58.819 43.478 0.00 0.00 0.00 3.86
4105 4300 4.081917 TGTTATAAGATGCGTGTGTCCTGA 60.082 41.667 0.00 0.00 0.00 3.86
4106 4301 2.363788 TAAGATGCGTGTGTCCTGAC 57.636 50.000 0.00 0.00 0.00 3.51
4107 4302 0.667487 AAGATGCGTGTGTCCTGACG 60.667 55.000 0.00 0.00 38.63 4.35
4108 4303 1.372997 GATGCGTGTGTCCTGACGT 60.373 57.895 0.00 0.00 37.89 4.34
4109 4304 1.617755 GATGCGTGTGTCCTGACGTG 61.618 60.000 0.00 0.00 37.89 4.49
4110 4305 3.036084 GCGTGTGTCCTGACGTGG 61.036 66.667 0.00 0.00 37.89 4.94
4111 4306 2.355837 CGTGTGTCCTGACGTGGG 60.356 66.667 0.00 0.00 0.00 4.61
4112 4307 2.819550 GTGTGTCCTGACGTGGGT 59.180 61.111 0.00 0.00 0.00 4.51
4113 4308 1.145377 GTGTGTCCTGACGTGGGTT 59.855 57.895 0.00 0.00 0.00 4.11
4114 4309 1.145156 TGTGTCCTGACGTGGGTTG 59.855 57.895 0.00 0.00 0.00 3.77
4115 4310 1.145377 GTGTCCTGACGTGGGTTGT 59.855 57.895 0.00 0.00 0.00 3.32
4116 4311 0.390124 GTGTCCTGACGTGGGTTGTA 59.610 55.000 0.00 0.00 0.00 2.41
4117 4312 0.390124 TGTCCTGACGTGGGTTGTAC 59.610 55.000 0.00 0.00 0.00 2.90
4118 4313 0.320160 GTCCTGACGTGGGTTGTACC 60.320 60.000 0.00 0.00 37.60 3.34
4119 4314 0.470456 TCCTGACGTGGGTTGTACCT 60.470 55.000 0.00 0.00 38.64 3.08
4120 4315 1.203038 TCCTGACGTGGGTTGTACCTA 60.203 52.381 0.00 0.00 38.64 3.08
4121 4316 1.829222 CCTGACGTGGGTTGTACCTAT 59.171 52.381 0.00 0.00 38.64 2.57
4122 4317 2.235402 CCTGACGTGGGTTGTACCTATT 59.765 50.000 0.00 0.00 38.64 1.73
4123 4318 3.307199 CCTGACGTGGGTTGTACCTATTT 60.307 47.826 0.00 0.00 38.64 1.40
4124 4319 4.320870 CTGACGTGGGTTGTACCTATTTT 58.679 43.478 0.00 0.00 38.64 1.82
4125 4320 4.716794 TGACGTGGGTTGTACCTATTTTT 58.283 39.130 0.00 0.00 38.64 1.94
4126 4321 4.515944 TGACGTGGGTTGTACCTATTTTTG 59.484 41.667 0.00 0.00 38.64 2.44
4127 4322 4.463070 ACGTGGGTTGTACCTATTTTTGT 58.537 39.130 0.00 0.00 38.64 2.83
4128 4323 4.888823 ACGTGGGTTGTACCTATTTTTGTT 59.111 37.500 0.00 0.00 38.64 2.83
4129 4324 5.360429 ACGTGGGTTGTACCTATTTTTGTTT 59.640 36.000 0.00 0.00 38.64 2.83
4130 4325 6.127394 ACGTGGGTTGTACCTATTTTTGTTTT 60.127 34.615 0.00 0.00 38.64 2.43
4131 4326 6.418523 CGTGGGTTGTACCTATTTTTGTTTTC 59.581 38.462 0.00 0.00 38.64 2.29
4132 4327 7.266400 GTGGGTTGTACCTATTTTTGTTTTCA 58.734 34.615 0.00 0.00 38.64 2.69
4133 4328 7.764901 GTGGGTTGTACCTATTTTTGTTTTCAA 59.235 33.333 0.00 0.00 38.64 2.69
4134 4329 7.982354 TGGGTTGTACCTATTTTTGTTTTCAAG 59.018 33.333 0.00 0.00 38.57 3.02
4135 4330 7.439955 GGGTTGTACCTATTTTTGTTTTCAAGG 59.560 37.037 0.00 0.00 38.57 3.61
4136 4331 7.982919 GGTTGTACCTATTTTTGTTTTCAAGGT 59.017 33.333 0.00 0.00 36.86 3.50
4137 4332 8.813282 GTTGTACCTATTTTTGTTTTCAAGGTG 58.187 33.333 0.00 0.00 41.09 4.00
4138 4333 8.294954 TGTACCTATTTTTGTTTTCAAGGTGA 57.705 30.769 0.00 0.00 41.09 4.02
4139 4334 8.750298 TGTACCTATTTTTGTTTTCAAGGTGAA 58.250 29.630 0.00 0.00 41.09 3.18
4140 4335 9.758651 GTACCTATTTTTGTTTTCAAGGTGAAT 57.241 29.630 0.00 0.00 41.09 2.57
4141 4336 8.661352 ACCTATTTTTGTTTTCAAGGTGAATG 57.339 30.769 0.00 0.00 41.09 2.67
4142 4337 8.482128 ACCTATTTTTGTTTTCAAGGTGAATGA 58.518 29.630 0.00 0.00 41.09 2.57
4143 4338 8.981647 CCTATTTTTGTTTTCAAGGTGAATGAG 58.018 33.333 0.00 0.00 41.09 2.90
4144 4339 9.748708 CTATTTTTGTTTTCAAGGTGAATGAGA 57.251 29.630 0.00 0.00 41.09 3.27
4145 4340 7.826260 TTTTTGTTTTCAAGGTGAATGAGAC 57.174 32.000 0.00 0.00 41.09 3.36
4146 4341 5.514274 TTGTTTTCAAGGTGAATGAGACC 57.486 39.130 0.00 0.00 36.11 3.85
4147 4342 4.531854 TGTTTTCAAGGTGAATGAGACCA 58.468 39.130 0.00 0.00 36.11 4.02
4148 4343 4.952957 TGTTTTCAAGGTGAATGAGACCAA 59.047 37.500 0.00 0.00 36.11 3.67
4149 4344 5.420421 TGTTTTCAAGGTGAATGAGACCAAA 59.580 36.000 0.00 0.00 36.11 3.28
4150 4345 6.098124 TGTTTTCAAGGTGAATGAGACCAAAT 59.902 34.615 0.00 0.00 36.11 2.32
4151 4346 6.729690 TTTCAAGGTGAATGAGACCAAATT 57.270 33.333 0.00 0.00 36.11 1.82
4152 4347 7.831691 TTTCAAGGTGAATGAGACCAAATTA 57.168 32.000 0.00 0.00 36.11 1.40
4153 4348 8.421249 TTTCAAGGTGAATGAGACCAAATTAT 57.579 30.769 0.00 0.00 36.11 1.28
4154 4349 9.527157 TTTCAAGGTGAATGAGACCAAATTATA 57.473 29.630 0.00 0.00 36.11 0.98
4155 4350 9.699410 TTCAAGGTGAATGAGACCAAATTATAT 57.301 29.630 0.00 0.00 35.76 0.86
4156 4351 9.342308 TCAAGGTGAATGAGACCAAATTATATC 57.658 33.333 0.00 0.00 35.76 1.63
4157 4352 9.347240 CAAGGTGAATGAGACCAAATTATATCT 57.653 33.333 0.00 0.00 35.76 1.98
4158 4353 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
4200 4395 6.763135 GGCACATATACATTCAACTTCTCAGA 59.237 38.462 0.00 0.00 0.00 3.27
4229 4424 2.811431 CGTTTTCAACCTGCAGATACCA 59.189 45.455 17.39 0.00 0.00 3.25
4253 4448 7.716998 CCACTAGAATGCATGTTTATTACTCCT 59.283 37.037 0.00 0.00 0.00 3.69
4254 4449 9.764363 CACTAGAATGCATGTTTATTACTCCTA 57.236 33.333 0.00 0.00 0.00 2.94
4262 4457 9.020731 TGCATGTTTATTACTCCTATCGATCTA 57.979 33.333 0.00 0.00 0.00 1.98
4314 4513 8.678593 TCTAGACGTATTTCAGTGATACATCT 57.321 34.615 7.44 7.44 36.71 2.90
4321 4520 8.820933 CGTATTTCAGTGATACATCTGTTTGAT 58.179 33.333 0.00 0.00 35.40 2.57
4346 4545 5.316987 GACAAGTAATATGGATTGGAGGGG 58.683 45.833 0.00 0.00 0.00 4.79
4398 4635 8.221965 ACTCATTATGTCTTACATCGTCTGTA 57.778 34.615 0.00 0.00 39.88 2.74
4515 4990 7.497579 TGTTTGCACCTATATACGATCAATGTT 59.502 33.333 0.00 0.00 0.00 2.71
4631 5106 9.554395 TGTTGTGAATACTTAGATTGAACTTGA 57.446 29.630 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.420547 GGCTAATGCACCACTCATCTCA 60.421 50.000 0.00 0.00 41.91 3.27
155 156 8.480643 AATCAATCTTGTTAGTGCTACTGTAC 57.519 34.615 0.00 0.00 0.00 2.90
156 157 9.582431 GTAATCAATCTTGTTAGTGCTACTGTA 57.418 33.333 0.00 0.00 0.00 2.74
164 169 7.369803 AGTGCAGTAATCAATCTTGTTAGTG 57.630 36.000 0.00 11.56 33.38 2.74
242 250 1.394532 TACACTCCTCCCCTTCCTCT 58.605 55.000 0.00 0.00 0.00 3.69
247 255 2.661176 TGGAATACACTCCTCCCCTT 57.339 50.000 0.00 0.00 36.35 3.95
248 256 2.045885 TCTTGGAATACACTCCTCCCCT 59.954 50.000 0.00 0.00 36.35 4.79
456 480 0.829990 GAGAGCAGGGAAAGAGGAGG 59.170 60.000 0.00 0.00 0.00 4.30
1054 1143 0.033991 TCCTCCTCCTCTTCGTCCAG 60.034 60.000 0.00 0.00 0.00 3.86
1365 1454 4.157120 GCTAAGAAGGGCGGCGGA 62.157 66.667 9.78 0.00 0.00 5.54
1811 1903 2.200899 GCACACACATGTTTTGGGTTC 58.799 47.619 0.00 0.00 39.64 3.62
1866 1958 3.738745 AATGGAATGGCCGGGGAGC 62.739 63.158 2.18 0.00 40.66 4.70
1867 1959 1.076044 AAATGGAATGGCCGGGGAG 60.076 57.895 2.18 0.00 40.66 4.30
1868 1960 1.076339 GAAATGGAATGGCCGGGGA 60.076 57.895 2.18 0.00 40.66 4.81
1869 1961 1.381056 TGAAATGGAATGGCCGGGG 60.381 57.895 2.18 0.00 40.66 5.73
1870 1962 2.019897 GCTGAAATGGAATGGCCGGG 62.020 60.000 2.18 0.00 40.66 5.73
1871 1963 1.321805 TGCTGAAATGGAATGGCCGG 61.322 55.000 0.00 0.00 40.66 6.13
1872 1964 0.748450 ATGCTGAAATGGAATGGCCG 59.252 50.000 0.00 0.00 40.66 6.13
1873 1965 4.282703 AGAATATGCTGAAATGGAATGGCC 59.717 41.667 0.00 0.00 37.10 5.36
1874 1966 5.464030 AGAATATGCTGAAATGGAATGGC 57.536 39.130 0.00 0.00 0.00 4.40
1903 1995 2.847449 TGTCTCCTAGTAGCTCACTCCT 59.153 50.000 0.00 0.00 38.80 3.69
2043 2135 3.341263 TGTACCTGACACGAGCTCT 57.659 52.632 12.85 0.00 31.20 4.09
2203 2301 4.402793 ACTCAGTTGCATAGGATAACTCGT 59.597 41.667 0.00 0.00 32.69 4.18
2214 2312 9.529325 GTACTGTTAATCATACTCAGTTGCATA 57.471 33.333 0.00 0.00 39.54 3.14
2230 2328 9.367444 CGGTAAAGATGAAAGAGTACTGTTAAT 57.633 33.333 5.58 3.34 0.00 1.40
2231 2329 7.816031 CCGGTAAAGATGAAAGAGTACTGTTAA 59.184 37.037 5.58 0.00 0.00 2.01
2232 2330 7.177216 TCCGGTAAAGATGAAAGAGTACTGTTA 59.823 37.037 5.58 0.00 0.00 2.41
2233 2331 6.014840 TCCGGTAAAGATGAAAGAGTACTGTT 60.015 38.462 0.00 0.00 0.00 3.16
2234 2332 5.479375 TCCGGTAAAGATGAAAGAGTACTGT 59.521 40.000 0.00 0.00 0.00 3.55
2260 2392 4.103357 CGTATGGTTTGGAAGAGTACTCG 58.897 47.826 17.07 0.00 34.09 4.18
2261 2393 5.105837 ACTCGTATGGTTTGGAAGAGTACTC 60.106 44.000 15.41 15.41 35.95 2.59
2262 2394 4.771054 ACTCGTATGGTTTGGAAGAGTACT 59.229 41.667 0.00 0.00 35.95 2.73
2263 2395 5.069501 ACTCGTATGGTTTGGAAGAGTAC 57.930 43.478 0.00 0.00 35.95 2.73
2264 2396 5.733620 AACTCGTATGGTTTGGAAGAGTA 57.266 39.130 0.00 0.00 36.59 2.59
2265 2397 4.618920 AACTCGTATGGTTTGGAAGAGT 57.381 40.909 0.00 0.00 38.89 3.24
2266 2398 5.753921 GGATAACTCGTATGGTTTGGAAGAG 59.246 44.000 0.00 0.00 0.00 2.85
2267 2399 5.424252 AGGATAACTCGTATGGTTTGGAAGA 59.576 40.000 0.00 0.00 0.00 2.87
2268 2400 5.671493 AGGATAACTCGTATGGTTTGGAAG 58.329 41.667 0.00 0.00 0.00 3.46
2269 2401 5.687166 AGGATAACTCGTATGGTTTGGAA 57.313 39.130 0.00 0.00 0.00 3.53
2270 2402 6.740401 GCATAGGATAACTCGTATGGTTTGGA 60.740 42.308 13.91 0.00 44.67 3.53
2271 2403 5.408604 GCATAGGATAACTCGTATGGTTTGG 59.591 44.000 13.91 0.00 44.67 3.28
2272 2404 5.989168 TGCATAGGATAACTCGTATGGTTTG 59.011 40.000 13.91 0.00 44.67 2.93
2273 2405 6.169557 TGCATAGGATAACTCGTATGGTTT 57.830 37.500 13.91 0.00 44.67 3.27
2274 2406 5.801531 TGCATAGGATAACTCGTATGGTT 57.198 39.130 13.91 0.00 44.67 3.67
2275 2407 5.304614 AGTTGCATAGGATAACTCGTATGGT 59.695 40.000 13.91 0.00 44.67 3.55
2276 2408 5.635280 CAGTTGCATAGGATAACTCGTATGG 59.365 44.000 13.91 1.45 44.67 2.74
2277 2409 6.447162 TCAGTTGCATAGGATAACTCGTATG 58.553 40.000 9.73 9.73 46.12 2.39
2278 2410 6.265649 ACTCAGTTGCATAGGATAACTCGTAT 59.734 38.462 0.00 0.00 32.69 3.06
2279 2411 5.593095 ACTCAGTTGCATAGGATAACTCGTA 59.407 40.000 0.00 0.00 32.69 3.43
2280 2412 4.402793 ACTCAGTTGCATAGGATAACTCGT 59.597 41.667 0.00 0.00 32.69 4.18
2281 2413 4.938080 ACTCAGTTGCATAGGATAACTCG 58.062 43.478 0.00 0.00 32.69 4.18
2282 2414 7.661968 TCATACTCAGTTGCATAGGATAACTC 58.338 38.462 0.00 0.00 32.69 3.01
2283 2415 7.603180 TCATACTCAGTTGCATAGGATAACT 57.397 36.000 0.00 0.00 35.18 2.24
2284 2416 8.839310 AATCATACTCAGTTGCATAGGATAAC 57.161 34.615 0.00 0.00 0.00 1.89
2289 2421 9.935241 ACTATTAATCATACTCAGTTGCATAGG 57.065 33.333 0.00 0.00 0.00 2.57
2292 2424 9.429359 GCTACTATTAATCATACTCAGTTGCAT 57.571 33.333 11.38 0.00 34.75 3.96
2293 2425 8.421002 TGCTACTATTAATCATACTCAGTTGCA 58.579 33.333 13.67 13.67 39.64 4.08
2294 2426 8.818141 TGCTACTATTAATCATACTCAGTTGC 57.182 34.615 10.06 10.06 35.05 4.17
2296 2428 9.935241 CCATGCTACTATTAATCATACTCAGTT 57.065 33.333 0.00 0.00 0.00 3.16
2297 2429 9.314133 TCCATGCTACTATTAATCATACTCAGT 57.686 33.333 0.00 0.00 0.00 3.41
2298 2430 9.800433 CTCCATGCTACTATTAATCATACTCAG 57.200 37.037 0.00 0.00 0.00 3.35
2299 2431 8.253810 GCTCCATGCTACTATTAATCATACTCA 58.746 37.037 0.00 0.00 38.95 3.41
2300 2432 7.433719 CGCTCCATGCTACTATTAATCATACTC 59.566 40.741 0.00 0.00 40.11 2.59
2301 2433 7.122799 TCGCTCCATGCTACTATTAATCATACT 59.877 37.037 0.00 0.00 40.11 2.12
2302 2434 7.258441 TCGCTCCATGCTACTATTAATCATAC 58.742 38.462 0.00 0.00 40.11 2.39
2303 2435 7.122799 ACTCGCTCCATGCTACTATTAATCATA 59.877 37.037 0.00 0.00 40.11 2.15
2304 2436 6.071108 ACTCGCTCCATGCTACTATTAATCAT 60.071 38.462 0.00 0.00 40.11 2.45
2305 2437 5.243954 ACTCGCTCCATGCTACTATTAATCA 59.756 40.000 0.00 0.00 40.11 2.57
2306 2438 5.715070 ACTCGCTCCATGCTACTATTAATC 58.285 41.667 0.00 0.00 40.11 1.75
2307 2439 5.620205 CGACTCGCTCCATGCTACTATTAAT 60.620 44.000 0.00 0.00 40.11 1.40
2308 2440 4.320275 CGACTCGCTCCATGCTACTATTAA 60.320 45.833 0.00 0.00 40.11 1.40
2309 2441 3.188667 CGACTCGCTCCATGCTACTATTA 59.811 47.826 0.00 0.00 40.11 0.98
2310 2442 2.030717 CGACTCGCTCCATGCTACTATT 60.031 50.000 0.00 0.00 40.11 1.73
2311 2443 1.537638 CGACTCGCTCCATGCTACTAT 59.462 52.381 0.00 0.00 40.11 2.12
2381 2522 4.568359 GTCATCAGATCAGTAACAACGCAT 59.432 41.667 0.00 0.00 0.00 4.73
2385 2526 6.870965 AGAACAGTCATCAGATCAGTAACAAC 59.129 38.462 0.00 0.00 0.00 3.32
2400 2541 6.420913 ACCAAACACTACTAGAACAGTCAT 57.579 37.500 0.00 0.00 38.80 3.06
2455 2599 7.392113 GCTAGTAGTAGGAGTATGTCATGTCAT 59.608 40.741 10.31 10.31 0.00 3.06
2462 2606 4.002316 CGGGCTAGTAGTAGGAGTATGTC 58.998 52.174 6.73 0.00 0.00 3.06
2463 2607 3.393941 ACGGGCTAGTAGTAGGAGTATGT 59.606 47.826 6.73 0.00 0.00 2.29
2464 2608 4.018484 ACGGGCTAGTAGTAGGAGTATG 57.982 50.000 6.73 0.00 0.00 2.39
2470 2614 3.759581 TGGATTACGGGCTAGTAGTAGG 58.240 50.000 6.73 0.00 0.00 3.18
2512 2663 2.187685 CAGCATGCACTAGCCGGA 59.812 61.111 21.98 0.00 41.13 5.14
2524 2675 0.535102 GGGGCTTATACGTGCAGCAT 60.535 55.000 14.94 0.00 35.05 3.79
2525 2676 1.153249 GGGGCTTATACGTGCAGCA 60.153 57.895 14.94 0.00 35.05 4.41
2526 2677 2.244651 CGGGGCTTATACGTGCAGC 61.245 63.158 0.00 2.25 0.00 5.25
2527 2678 2.244651 GCGGGGCTTATACGTGCAG 61.245 63.158 0.00 0.00 0.00 4.41
2528 2679 2.202960 GCGGGGCTTATACGTGCA 60.203 61.111 0.00 0.00 0.00 4.57
2530 2681 2.280592 GGGCGGGGCTTATACGTG 60.281 66.667 0.00 0.00 0.00 4.49
2532 2683 3.530910 CTGGGGCGGGGCTTATACG 62.531 68.421 0.00 0.00 0.00 3.06
2534 2685 2.852075 CCTGGGGCGGGGCTTATA 60.852 66.667 0.00 0.00 0.00 0.98
2535 2686 4.835456 TCCTGGGGCGGGGCTTAT 62.835 66.667 0.00 0.00 0.00 1.73
2623 2774 0.176449 CCATCGATCACCACTCTGCA 59.824 55.000 0.00 0.00 0.00 4.41
2862 3026 0.107508 CCGTGGAATGCATGTCTCCT 60.108 55.000 15.32 0.00 0.00 3.69
2867 3031 2.689785 CGTGCCGTGGAATGCATGT 61.690 57.895 0.00 0.00 40.07 3.21
3004 3189 5.012328 AGCTGCCAGTAGTTGATTAGTAC 57.988 43.478 0.00 0.00 33.57 2.73
3007 3192 3.119291 CGAGCTGCCAGTAGTTGATTAG 58.881 50.000 0.00 0.00 0.00 1.73
3009 3194 2.009042 GCGAGCTGCCAGTAGTTGATT 61.009 52.381 0.00 0.00 37.76 2.57
3121 3314 3.005539 ACCTCCGCCAGCAGTGAT 61.006 61.111 0.00 0.00 0.00 3.06
3124 3317 3.005539 ATCACCTCCGCCAGCAGT 61.006 61.111 0.00 0.00 0.00 4.40
3660 3853 6.093357 TCAGCTGATAGATAGATCATCACGTC 59.907 42.308 13.74 0.00 35.32 4.34
3695 3888 0.576328 TTTCGTTTCGTTCCGTTCCG 59.424 50.000 0.00 0.00 0.00 4.30
3696 3889 1.654501 CGTTTCGTTTCGTTCCGTTCC 60.655 52.381 0.00 0.00 0.00 3.62
3697 3890 1.255084 TCGTTTCGTTTCGTTCCGTTC 59.745 47.619 0.00 0.00 0.00 3.95
3698 3891 1.276415 TCGTTTCGTTTCGTTCCGTT 58.724 45.000 0.00 0.00 0.00 4.44
3699 3892 1.276415 TTCGTTTCGTTTCGTTCCGT 58.724 45.000 0.00 0.00 0.00 4.69
3846 4039 2.872858 ACGAGAAGAGGTGAAAAACAGC 59.127 45.455 0.00 0.00 46.00 4.40
3901 4094 5.235186 CACACACCACACAAACAAAAGAAAA 59.765 36.000 0.00 0.00 0.00 2.29
3939 4134 1.612469 CGCCGAGATCGATCACATGC 61.612 60.000 26.47 21.68 43.02 4.06
3944 4139 1.786049 CTGACCGCCGAGATCGATCA 61.786 60.000 26.47 3.81 43.02 2.92
3955 4150 1.003718 AAGCCTTGTACTGACCGCC 60.004 57.895 0.00 0.00 0.00 6.13
4036 4231 7.731054 AGGTGAATGAGACCAAACTATATCTC 58.269 38.462 0.00 0.00 38.46 2.75
4037 4232 7.682787 AGGTGAATGAGACCAAACTATATCT 57.317 36.000 0.00 0.00 35.76 1.98
4038 4233 8.738645 AAAGGTGAATGAGACCAAACTATATC 57.261 34.615 0.00 0.00 35.76 1.63
4042 4237 9.667107 CTATAAAAGGTGAATGAGACCAAACTA 57.333 33.333 0.00 0.00 35.76 2.24
4043 4238 7.121315 GCTATAAAAGGTGAATGAGACCAAACT 59.879 37.037 0.00 0.00 35.76 2.66
4044 4239 7.251281 GCTATAAAAGGTGAATGAGACCAAAC 58.749 38.462 0.00 0.00 35.76 2.93
4045 4240 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
4046 4241 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
4047 4242 5.045213 TGGCTATAAAAGGTGAATGAGACCA 60.045 40.000 0.00 0.00 35.76 4.02
4048 4243 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
4049 4244 7.420800 CAATGGCTATAAAAGGTGAATGAGAC 58.579 38.462 0.00 0.00 0.00 3.36
4050 4245 6.547141 CCAATGGCTATAAAAGGTGAATGAGA 59.453 38.462 0.00 0.00 0.00 3.27
4051 4246 6.547141 TCCAATGGCTATAAAAGGTGAATGAG 59.453 38.462 0.00 0.00 0.00 2.90
4052 4247 6.430864 TCCAATGGCTATAAAAGGTGAATGA 58.569 36.000 0.00 0.00 0.00 2.57
4053 4248 6.713762 TCCAATGGCTATAAAAGGTGAATG 57.286 37.500 0.00 0.00 0.00 2.67
4054 4249 6.840705 ACATCCAATGGCTATAAAAGGTGAAT 59.159 34.615 0.00 0.00 33.60 2.57
4055 4250 6.096705 CACATCCAATGGCTATAAAAGGTGAA 59.903 38.462 0.00 0.00 33.60 3.18
4056 4251 5.593909 CACATCCAATGGCTATAAAAGGTGA 59.406 40.000 0.00 0.00 33.60 4.02
4057 4252 5.593909 TCACATCCAATGGCTATAAAAGGTG 59.406 40.000 0.00 0.00 33.60 4.00
4058 4253 5.765510 TCACATCCAATGGCTATAAAAGGT 58.234 37.500 0.00 0.00 33.60 3.50
4059 4254 6.266103 ACATCACATCCAATGGCTATAAAAGG 59.734 38.462 0.00 0.00 33.60 3.11
4060 4255 7.281040 ACATCACATCCAATGGCTATAAAAG 57.719 36.000 0.00 0.00 33.60 2.27
4061 4256 7.658525 AACATCACATCCAATGGCTATAAAA 57.341 32.000 0.00 0.00 33.60 1.52
4062 4257 8.938801 ATAACATCACATCCAATGGCTATAAA 57.061 30.769 0.00 0.00 33.60 1.40
4064 4259 9.671279 CTTATAACATCACATCCAATGGCTATA 57.329 33.333 0.00 0.00 33.60 1.31
4065 4260 8.385491 TCTTATAACATCACATCCAATGGCTAT 58.615 33.333 0.00 0.00 33.60 2.97
4066 4261 7.744733 TCTTATAACATCACATCCAATGGCTA 58.255 34.615 0.00 0.00 33.60 3.93
4067 4262 6.604171 TCTTATAACATCACATCCAATGGCT 58.396 36.000 0.00 0.00 33.60 4.75
4068 4263 6.882610 TCTTATAACATCACATCCAATGGC 57.117 37.500 0.00 0.00 33.60 4.40
4069 4264 7.310664 GCATCTTATAACATCACATCCAATGG 58.689 38.462 0.00 0.00 33.60 3.16
4070 4265 7.019418 CGCATCTTATAACATCACATCCAATG 58.981 38.462 0.00 0.00 0.00 2.82
4071 4266 6.712095 ACGCATCTTATAACATCACATCCAAT 59.288 34.615 0.00 0.00 0.00 3.16
4072 4267 6.018016 CACGCATCTTATAACATCACATCCAA 60.018 38.462 0.00 0.00 0.00 3.53
4073 4268 5.466393 CACGCATCTTATAACATCACATCCA 59.534 40.000 0.00 0.00 0.00 3.41
4074 4269 5.466728 ACACGCATCTTATAACATCACATCC 59.533 40.000 0.00 0.00 0.00 3.51
4075 4270 6.018751 ACACACGCATCTTATAACATCACATC 60.019 38.462 0.00 0.00 0.00 3.06
4076 4271 5.817296 ACACACGCATCTTATAACATCACAT 59.183 36.000 0.00 0.00 0.00 3.21
4077 4272 5.175127 ACACACGCATCTTATAACATCACA 58.825 37.500 0.00 0.00 0.00 3.58
4078 4273 5.276868 GGACACACGCATCTTATAACATCAC 60.277 44.000 0.00 0.00 0.00 3.06
4079 4274 4.808895 GGACACACGCATCTTATAACATCA 59.191 41.667 0.00 0.00 0.00 3.07
4080 4275 5.050490 AGGACACACGCATCTTATAACATC 58.950 41.667 0.00 0.00 0.00 3.06
4081 4276 4.811024 CAGGACACACGCATCTTATAACAT 59.189 41.667 0.00 0.00 0.00 2.71
4082 4277 4.081917 TCAGGACACACGCATCTTATAACA 60.082 41.667 0.00 0.00 0.00 2.41
4083 4278 4.267928 GTCAGGACACACGCATCTTATAAC 59.732 45.833 0.00 0.00 0.00 1.89
4084 4279 4.430007 GTCAGGACACACGCATCTTATAA 58.570 43.478 0.00 0.00 0.00 0.98
4085 4280 3.488553 CGTCAGGACACACGCATCTTATA 60.489 47.826 0.00 0.00 0.00 0.98
4086 4281 2.735444 CGTCAGGACACACGCATCTTAT 60.735 50.000 0.00 0.00 0.00 1.73
4087 4282 1.402325 CGTCAGGACACACGCATCTTA 60.402 52.381 0.00 0.00 0.00 2.10
4088 4283 0.667487 CGTCAGGACACACGCATCTT 60.667 55.000 0.00 0.00 0.00 2.40
4089 4284 1.080501 CGTCAGGACACACGCATCT 60.081 57.895 0.00 0.00 0.00 2.90
4090 4285 1.372997 ACGTCAGGACACACGCATC 60.373 57.895 0.00 0.00 39.73 3.91
4091 4286 1.664649 CACGTCAGGACACACGCAT 60.665 57.895 0.00 0.00 39.73 4.73
4092 4287 2.279186 CACGTCAGGACACACGCA 60.279 61.111 0.00 0.00 39.73 5.24
4093 4288 3.036084 CCACGTCAGGACACACGC 61.036 66.667 0.00 0.00 39.73 5.34
4094 4289 2.355837 CCCACGTCAGGACACACG 60.356 66.667 0.00 0.00 41.90 4.49
4095 4290 1.145377 AACCCACGTCAGGACACAC 59.855 57.895 8.14 0.00 0.00 3.82
4096 4291 1.145156 CAACCCACGTCAGGACACA 59.855 57.895 8.14 0.00 0.00 3.72
4097 4292 0.390124 TACAACCCACGTCAGGACAC 59.610 55.000 8.14 0.00 0.00 3.67
4098 4293 0.390124 GTACAACCCACGTCAGGACA 59.610 55.000 8.14 0.00 0.00 4.02
4099 4294 0.320160 GGTACAACCCACGTCAGGAC 60.320 60.000 8.14 0.00 30.04 3.85
4100 4295 0.470456 AGGTACAACCCACGTCAGGA 60.470 55.000 8.14 0.00 39.75 3.86
4101 4296 1.259609 TAGGTACAACCCACGTCAGG 58.740 55.000 0.00 0.00 39.75 3.86
4102 4297 3.604875 AATAGGTACAACCCACGTCAG 57.395 47.619 0.00 0.00 39.75 3.51
4103 4298 4.354893 AAAATAGGTACAACCCACGTCA 57.645 40.909 0.00 0.00 39.75 4.35
4104 4299 4.516321 ACAAAAATAGGTACAACCCACGTC 59.484 41.667 0.00 0.00 39.75 4.34
4105 4300 4.463070 ACAAAAATAGGTACAACCCACGT 58.537 39.130 0.00 0.00 39.75 4.49
4106 4301 5.441709 AACAAAAATAGGTACAACCCACG 57.558 39.130 0.00 0.00 39.75 4.94
4107 4302 7.266400 TGAAAACAAAAATAGGTACAACCCAC 58.734 34.615 0.00 0.00 39.75 4.61
4108 4303 7.419711 TGAAAACAAAAATAGGTACAACCCA 57.580 32.000 0.00 0.00 39.75 4.51
4109 4304 7.439955 CCTTGAAAACAAAAATAGGTACAACCC 59.560 37.037 0.00 0.00 39.75 4.11
4110 4305 7.982919 ACCTTGAAAACAAAAATAGGTACAACC 59.017 33.333 0.00 0.00 38.99 3.77
4111 4306 8.813282 CACCTTGAAAACAAAAATAGGTACAAC 58.187 33.333 0.00 0.00 33.44 3.32
4112 4307 8.750298 TCACCTTGAAAACAAAAATAGGTACAA 58.250 29.630 0.00 0.00 33.44 2.41
4113 4308 8.294954 TCACCTTGAAAACAAAAATAGGTACA 57.705 30.769 0.00 0.00 33.44 2.90
4114 4309 9.758651 ATTCACCTTGAAAACAAAAATAGGTAC 57.241 29.630 0.00 0.00 40.12 3.34
4115 4310 9.757227 CATTCACCTTGAAAACAAAAATAGGTA 57.243 29.630 0.00 0.00 40.12 3.08
4116 4311 8.482128 TCATTCACCTTGAAAACAAAAATAGGT 58.518 29.630 0.00 0.00 40.12 3.08
4117 4312 8.885494 TCATTCACCTTGAAAACAAAAATAGG 57.115 30.769 0.00 0.00 40.12 2.57
4118 4313 9.748708 TCTCATTCACCTTGAAAACAAAAATAG 57.251 29.630 0.00 0.00 40.12 1.73
4119 4314 9.528018 GTCTCATTCACCTTGAAAACAAAAATA 57.472 29.630 0.00 0.00 40.12 1.40
4120 4315 7.495606 GGTCTCATTCACCTTGAAAACAAAAAT 59.504 33.333 0.00 0.00 40.12 1.82
4121 4316 6.816140 GGTCTCATTCACCTTGAAAACAAAAA 59.184 34.615 0.00 0.00 40.12 1.94
4122 4317 6.071108 TGGTCTCATTCACCTTGAAAACAAAA 60.071 34.615 0.00 0.00 40.12 2.44
4123 4318 5.420421 TGGTCTCATTCACCTTGAAAACAAA 59.580 36.000 0.00 0.00 40.12 2.83
4124 4319 4.952957 TGGTCTCATTCACCTTGAAAACAA 59.047 37.500 0.00 0.00 40.12 2.83
4125 4320 4.531854 TGGTCTCATTCACCTTGAAAACA 58.468 39.130 0.00 0.00 40.12 2.83
4126 4321 5.514274 TTGGTCTCATTCACCTTGAAAAC 57.486 39.130 0.00 0.00 40.12 2.43
4127 4322 6.729690 ATTTGGTCTCATTCACCTTGAAAA 57.270 33.333 0.00 0.00 40.12 2.29
4128 4323 6.729690 AATTTGGTCTCATTCACCTTGAAA 57.270 33.333 0.00 0.00 40.12 2.69
4129 4324 9.699410 ATATAATTTGGTCTCATTCACCTTGAA 57.301 29.630 0.00 0.00 41.09 2.69
4130 4325 9.342308 GATATAATTTGGTCTCATTCACCTTGA 57.658 33.333 0.00 0.00 34.66 3.02
4131 4326 9.347240 AGATATAATTTGGTCTCATTCACCTTG 57.653 33.333 0.00 0.00 34.66 3.61
4132 4327 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
4133 4328 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
4134 4329 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
4157 4352 6.544928 TGTGCCTAGAACTCATTTAGATGA 57.455 37.500 0.00 0.00 39.92 2.92
4160 4355 9.143155 TGTATATGTGCCTAGAACTCATTTAGA 57.857 33.333 0.00 0.00 0.00 2.10
4161 4356 9.935241 ATGTATATGTGCCTAGAACTCATTTAG 57.065 33.333 0.00 0.00 0.00 1.85
4163 4358 9.277783 GAATGTATATGTGCCTAGAACTCATTT 57.722 33.333 0.00 0.00 0.00 2.32
4164 4359 8.432013 TGAATGTATATGTGCCTAGAACTCATT 58.568 33.333 0.00 0.00 0.00 2.57
4165 4360 7.966812 TGAATGTATATGTGCCTAGAACTCAT 58.033 34.615 0.00 0.00 0.00 2.90
4166 4361 7.360113 TGAATGTATATGTGCCTAGAACTCA 57.640 36.000 0.00 0.00 0.00 3.41
4167 4362 7.928706 AGTTGAATGTATATGTGCCTAGAACTC 59.071 37.037 0.00 0.00 0.00 3.01
4168 4363 7.796054 AGTTGAATGTATATGTGCCTAGAACT 58.204 34.615 0.00 0.00 0.00 3.01
4169 4364 8.438676 AAGTTGAATGTATATGTGCCTAGAAC 57.561 34.615 0.00 0.00 0.00 3.01
4170 4365 8.486210 AGAAGTTGAATGTATATGTGCCTAGAA 58.514 33.333 0.00 0.00 0.00 2.10
4171 4366 8.023021 AGAAGTTGAATGTATATGTGCCTAGA 57.977 34.615 0.00 0.00 0.00 2.43
4172 4367 7.928167 TGAGAAGTTGAATGTATATGTGCCTAG 59.072 37.037 0.00 0.00 0.00 3.02
4173 4368 7.791029 TGAGAAGTTGAATGTATATGTGCCTA 58.209 34.615 0.00 0.00 0.00 3.93
4174 4369 6.653020 TGAGAAGTTGAATGTATATGTGCCT 58.347 36.000 0.00 0.00 0.00 4.75
4175 4370 6.763135 TCTGAGAAGTTGAATGTATATGTGCC 59.237 38.462 0.00 0.00 0.00 5.01
4176 4371 7.493971 AGTCTGAGAAGTTGAATGTATATGTGC 59.506 37.037 0.00 0.00 0.00 4.57
4177 4372 8.815189 CAGTCTGAGAAGTTGAATGTATATGTG 58.185 37.037 0.00 0.00 0.00 3.21
4178 4373 7.493971 GCAGTCTGAGAAGTTGAATGTATATGT 59.506 37.037 3.32 0.00 0.00 2.29
4253 4448 8.488651 TGAGCGACAAGTAATATAGATCGATA 57.511 34.615 0.00 0.00 0.00 2.92
4254 4449 7.379098 TGAGCGACAAGTAATATAGATCGAT 57.621 36.000 0.00 0.00 0.00 3.59
4255 4450 6.796705 TGAGCGACAAGTAATATAGATCGA 57.203 37.500 0.00 0.00 0.00 3.59
4314 4513 8.611757 CAATCCATATTACTTGTCGATCAAACA 58.388 33.333 0.00 0.00 35.48 2.83
4321 4520 5.221641 CCCTCCAATCCATATTACTTGTCGA 60.222 44.000 0.00 0.00 0.00 4.20
4346 4545 8.612619 CCATACTTACATGTCAAATCAGTTACC 58.387 37.037 0.00 0.00 0.00 2.85
4398 4635 0.601558 ACCGTGCAATACTGTCTCGT 59.398 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.