Multiple sequence alignment - TraesCS1D01G372500

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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 TraesCS1D01G372500 chr1D 100.000 3380 0 0 1 3380 450738235 450741614 0.000000e+00 6242.0
1 TraesCS1D01G372500 chr1D 88.908 1713 152 24 732 2423 450578930 450580625 0.000000e+00 2076.0
2 TraesCS1D01G372500 chr1D 86.182 1252 146 16 1009 2257 451035700 451034473 0.000000e+00 1328.0
3 TraesCS1D01G372500 chr1D 87.456 1148 119 19 1009 2154 450757612 450756488 0.000000e+00 1299.0
4 TraesCS1D01G372500 chr1D 84.438 1298 164 28 744 2018 451044222 451042940 0.000000e+00 1243.0
5 TraesCS1D01G372500 chr1D 88.024 334 25 5 2972 3294 365711923 365712252 6.840000e-102 381.0
6 TraesCS1D01G372500 chr1D 90.541 296 14 5 1 294 450576221 450576504 2.460000e-101 379.0
7 TraesCS1D01G372500 chr1D 87.600 250 20 2 2972 3210 62870705 62870456 2.570000e-71 279.0
8 TraesCS1D01G372500 chr1D 85.502 269 19 7 362 630 450578530 450578778 2.590000e-66 263.0
9 TraesCS1D01G372500 chr1D 91.935 62 5 0 385 446 451063958 451063897 1.670000e-13 87.9
10 TraesCS1D01G372500 chr1D 94.231 52 3 0 592 643 451063695 451063644 2.800000e-11 80.5
11 TraesCS1D01G372500 chr1B 87.796 2155 169 39 739 2823 618316577 618318707 0.000000e+00 2436.0
12 TraesCS1D01G372500 chr1B 88.061 1893 124 29 960 2800 618196934 618198776 0.000000e+00 2150.0
13 TraesCS1D01G372500 chr1B 85.989 2077 210 51 391 2420 618542365 618544407 0.000000e+00 2148.0
14 TraesCS1D01G372500 chr1B 83.125 1440 179 44 731 2151 618908317 618906923 0.000000e+00 1254.0
15 TraesCS1D01G372500 chr1B 86.806 288 24 7 31 317 618195933 618196207 3.280000e-80 309.0
16 TraesCS1D01G372500 chr1B 91.327 196 15 2 344 537 618196367 618196562 2.000000e-67 267.0
17 TraesCS1D01G372500 chr1B 88.406 207 20 3 112 317 618542134 618542337 2.600000e-61 246.0
18 TraesCS1D01G372500 chr1B 82.955 264 16 9 666 918 618196677 618196922 9.500000e-51 211.0
19 TraesCS1D01G372500 chr1B 90.968 155 14 0 2692 2846 618550028 618550182 3.420000e-50 209.0
20 TraesCS1D01G372500 chr1B 86.228 167 16 5 2593 2758 618906478 618906318 1.250000e-39 174.0
21 TraesCS1D01G372500 chr1B 97.030 101 3 0 2590 2690 618544519 618544619 1.610000e-38 171.0
22 TraesCS1D01G372500 chr1B 88.710 62 7 0 385 446 619096261 619096200 3.620000e-10 76.8
23 TraesCS1D01G372500 chr1A 87.210 2072 193 39 491 2532 545751514 545753543 0.000000e+00 2292.0
24 TraesCS1D01G372500 chr1A 82.754 1438 182 47 731 2139 545764212 545762812 0.000000e+00 1221.0
25 TraesCS1D01G372500 chr1A 89.011 273 11 5 2563 2819 545753538 545753807 1.510000e-83 320.0
26 TraesCS1D01G372500 chr1A 80.467 471 38 27 37 465 545751059 545751517 9.110000e-81 311.0
27 TraesCS1D01G372500 chr1A 95.122 41 2 0 385 425 545859946 545859906 7.830000e-07 65.8
28 TraesCS1D01G372500 chr5B 86.127 346 39 8 2972 3308 546541906 546542251 6.890000e-97 364.0
29 TraesCS1D01G372500 chr5B 82.550 298 41 7 2972 3266 476789708 476789419 5.600000e-63 252.0
30 TraesCS1D01G372500 chr6B 82.816 419 59 6 2975 3380 175329229 175328811 2.480000e-96 363.0
31 TraesCS1D01G372500 chr7A 84.697 379 33 11 2972 3343 9151537 9151897 4.150000e-94 355.0
32 TraesCS1D01G372500 chr7A 83.586 396 42 12 2972 3344 558156473 558156078 1.930000e-92 350.0
33 TraesCS1D01G372500 chr3A 83.586 396 42 9 2972 3344 227924532 227924927 1.930000e-92 350.0
34 TraesCS1D01G372500 chr2D 82.946 387 47 10 2972 3344 388002057 388002438 6.990000e-87 331.0
35 TraesCS1D01G372500 chr3B 82.143 336 53 4 2972 3301 352578961 352578627 7.140000e-72 281.0
36 TraesCS1D01G372500 chr4B 82.583 333 37 12 2972 3296 660537095 660537414 1.190000e-69 274.0
37 TraesCS1D01G372500 chr6D 78.723 423 58 11 2856 3266 210768377 210767975 1.560000e-63 254.0
38 TraesCS1D01G372500 chr4D 79.275 386 53 16 2972 3344 2827293 2826922 9.370000e-61 244.0


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 TraesCS1D01G372500 chr1D 450738235 450741614 3379 False 6242.000000 6242 100.000000 1 3380 1 chr1D.!!$F2 3379
1 TraesCS1D01G372500 chr1D 451034473 451035700 1227 True 1328.000000 1328 86.182000 1009 2257 1 chr1D.!!$R3 1248
2 TraesCS1D01G372500 chr1D 450756488 450757612 1124 True 1299.000000 1299 87.456000 1009 2154 1 chr1D.!!$R2 1145
3 TraesCS1D01G372500 chr1D 451042940 451044222 1282 True 1243.000000 1243 84.438000 744 2018 1 chr1D.!!$R4 1274
4 TraesCS1D01G372500 chr1D 450576221 450580625 4404 False 906.000000 2076 88.317000 1 2423 3 chr1D.!!$F3 2422
5 TraesCS1D01G372500 chr1B 618316577 618318707 2130 False 2436.000000 2436 87.796000 739 2823 1 chr1B.!!$F1 2084
6 TraesCS1D01G372500 chr1B 618542134 618544619 2485 False 855.000000 2148 90.475000 112 2690 3 chr1B.!!$F4 2578
7 TraesCS1D01G372500 chr1B 618195933 618198776 2843 False 734.250000 2150 87.287250 31 2800 4 chr1B.!!$F3 2769
8 TraesCS1D01G372500 chr1B 618906318 618908317 1999 True 714.000000 1254 84.676500 731 2758 2 chr1B.!!$R2 2027
9 TraesCS1D01G372500 chr1A 545762812 545764212 1400 True 1221.000000 1221 82.754000 731 2139 1 chr1A.!!$R1 1408
10 TraesCS1D01G372500 chr1A 545751059 545753807 2748 False 974.333333 2292 85.562667 37 2819 3 chr1A.!!$F1 2782

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
920 3122 0.521735 AAAAAGAACTCATCGCCGGC 59.478 50.0 19.07 19.07 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2834 5207 0.036483 TGCGCACTAAATGGAGAGCA 60.036 50.0 5.66 0.0 33.14 4.26 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
61 66 1.061131 GCATGTGTTGTACGCTAGCTG 59.939 52.381 13.93 9.03 0.00 4.24
62 67 2.337583 CATGTGTTGTACGCTAGCTGT 58.662 47.619 13.93 14.47 0.00 4.40
207 222 2.789409 GGGATCGAATATTCCCCCTG 57.211 55.000 20.02 4.97 45.08 4.45
208 223 1.340114 GGGATCGAATATTCCCCCTGC 60.340 57.143 20.02 6.24 45.08 4.85
209 224 1.340114 GGATCGAATATTCCCCCTGCC 60.340 57.143 9.87 0.27 0.00 4.85
210 225 1.351017 GATCGAATATTCCCCCTGCCA 59.649 52.381 9.87 0.00 0.00 4.92
231 246 6.666113 TGCCATCCTATTCCTATTCGTATGTA 59.334 38.462 0.00 0.00 0.00 2.29
233 248 7.147880 GCCATCCTATTCCTATTCGTATGTACT 60.148 40.741 0.00 0.00 0.00 2.73
234 249 9.404848 CCATCCTATTCCTATTCGTATGTACTA 57.595 37.037 0.00 0.00 0.00 1.82
252 282 5.417894 TGTACTAGTATGTGTGGAAGTGGAG 59.582 44.000 5.75 0.00 0.00 3.86
300 334 1.160329 GCGCCAGATATTTGCTCGGT 61.160 55.000 0.00 0.00 0.00 4.69
318 352 3.325425 TCGGTATTTTCTGTCAGGTCCAA 59.675 43.478 0.00 0.00 0.00 3.53
331 365 3.136443 TCAGGTCCAAGAGCTTTCTTTCA 59.864 43.478 0.00 0.00 38.40 2.69
332 366 3.501445 CAGGTCCAAGAGCTTTCTTTCAG 59.499 47.826 0.00 0.00 38.40 3.02
333 367 3.137360 AGGTCCAAGAGCTTTCTTTCAGT 59.863 43.478 0.00 0.00 37.04 3.41
334 368 3.500299 GGTCCAAGAGCTTTCTTTCAGTC 59.500 47.826 0.00 0.00 0.00 3.51
335 369 3.500299 GTCCAAGAGCTTTCTTTCAGTCC 59.500 47.826 0.00 0.00 0.00 3.85
338 372 3.971245 AGAGCTTTCTTTCAGTCCGAT 57.029 42.857 0.00 0.00 0.00 4.18
339 373 3.594134 AGAGCTTTCTTTCAGTCCGATG 58.406 45.455 0.00 0.00 0.00 3.84
340 374 2.675348 GAGCTTTCTTTCAGTCCGATGG 59.325 50.000 0.00 0.00 0.00 3.51
341 375 1.131315 GCTTTCTTTCAGTCCGATGGC 59.869 52.381 0.00 0.00 0.00 4.40
348 2380 1.878522 CAGTCCGATGGCGCAGTAC 60.879 63.158 10.83 0.00 35.83 2.73
351 2383 2.184322 CCGATGGCGCAGTACAGT 59.816 61.111 10.83 0.00 35.83 3.55
367 2399 1.909781 AGTGGTGGGCTTTGGCATG 60.910 57.895 0.00 0.00 40.87 4.06
370 2402 0.544833 TGGTGGGCTTTGGCATGAAT 60.545 50.000 0.00 0.00 40.87 2.57
428 2462 2.435059 GACCAGCTCCGTTCAGGC 60.435 66.667 0.00 0.00 40.77 4.85
492 2526 4.696899 TGATCTGTTTCATACGACTCGT 57.303 40.909 9.45 9.45 44.35 4.18
512 2546 2.664851 CCCAGCGCGACTTTGACA 60.665 61.111 12.10 0.00 0.00 3.58
630 2687 5.764686 GGTTTTTACCTTTTCCGACTCCTAA 59.235 40.000 0.00 0.00 0.00 2.69
650 2757 5.518847 CCTAAACGAGATTATTTGACGCAGA 59.481 40.000 0.00 0.00 0.00 4.26
654 2762 5.035443 ACGAGATTATTTGACGCAGACTAC 58.965 41.667 0.00 0.00 0.00 2.73
699 2835 2.430244 CGTTCCCACTCACCGTCG 60.430 66.667 0.00 0.00 0.00 5.12
714 2850 1.762222 CGTCGAACCCAATCCATCGC 61.762 60.000 0.00 0.00 35.39 4.58
715 2851 1.153249 TCGAACCCAATCCATCGCC 60.153 57.895 0.00 0.00 35.39 5.54
716 2852 2.534019 CGAACCCAATCCATCGCCG 61.534 63.158 0.00 0.00 0.00 6.46
717 2853 2.828549 AACCCAATCCATCGCCGC 60.829 61.111 0.00 0.00 0.00 6.53
718 2854 3.636929 AACCCAATCCATCGCCGCA 62.637 57.895 0.00 0.00 0.00 5.69
719 2855 3.282157 CCCAATCCATCGCCGCAG 61.282 66.667 0.00 0.00 0.00 5.18
791 2950 1.977009 CCCACGCCTTTTCCCTTCC 60.977 63.158 0.00 0.00 0.00 3.46
793 2952 1.599797 CACGCCTTTTCCCTTCCGT 60.600 57.895 0.00 0.00 0.00 4.69
920 3122 0.521735 AAAAAGAACTCATCGCCGGC 59.478 50.000 19.07 19.07 0.00 6.13
921 3123 0.605319 AAAAGAACTCATCGCCGGCA 60.605 50.000 28.98 14.46 0.00 5.69
922 3124 1.298859 AAAGAACTCATCGCCGGCAC 61.299 55.000 28.98 6.51 0.00 5.01
923 3125 3.195698 GAACTCATCGCCGGCACC 61.196 66.667 28.98 0.00 0.00 5.01
955 3168 1.873591 GCTCGACACAACAGAAACCAT 59.126 47.619 0.00 0.00 0.00 3.55
975 3188 2.495866 CATCCCAATTGCCACCGC 59.504 61.111 0.00 0.00 0.00 5.68
1567 3787 4.794439 CGCTCGGATGCACGGTCA 62.794 66.667 0.00 0.00 0.00 4.02
1860 4086 2.268920 GCGGCATTCTGGGAGTCA 59.731 61.111 0.00 0.00 0.00 3.41
1870 4096 1.649390 CTGGGAGTCAGAGTCCGACG 61.649 65.000 16.92 5.21 46.18 5.12
1878 4116 4.517703 GAGTCCGACGCCGACGAG 62.518 72.222 11.04 0.87 43.93 4.18
2056 4309 1.153289 AGGACTGGCATCATCGTGC 60.153 57.895 0.00 0.00 44.31 5.34
2085 4338 1.248486 TCACCAGTGAAGAGGAGTCG 58.752 55.000 0.00 0.00 36.53 4.18
2096 4352 4.194720 GGAGTCGATCGGCGCAGT 62.195 66.667 24.43 1.83 40.61 4.40
2168 4424 1.534595 CGCAGGGCAAGAAACATATGC 60.535 52.381 1.58 0.00 39.33 3.14
2204 4469 1.222936 GGCACAGTAGGCATCAGCT 59.777 57.895 0.00 0.00 41.70 4.24
2206 4471 0.107993 GCACAGTAGGCATCAGCTCA 60.108 55.000 0.00 0.00 41.70 4.26
2207 4472 1.474677 GCACAGTAGGCATCAGCTCAT 60.475 52.381 0.00 0.00 41.70 2.90
2208 4473 2.224137 GCACAGTAGGCATCAGCTCATA 60.224 50.000 0.00 0.00 41.70 2.15
2213 4478 1.407936 AGGCATCAGCTCATACTCGT 58.592 50.000 0.00 0.00 41.70 4.18
2215 4480 0.857935 GCATCAGCTCATACTCGTGC 59.142 55.000 0.00 0.00 37.91 5.34
2448 4745 2.873609 CTGTGACTTCGATGGACTGAG 58.126 52.381 3.12 0.00 0.00 3.35
2486 4810 3.431725 CTTGCCCGCGGAAAGGAC 61.432 66.667 30.73 9.02 0.00 3.85
2571 4895 1.199327 CTCGACGGAAAGTACTGCTGA 59.801 52.381 10.81 0.00 0.00 4.26
2791 5164 1.735376 CTCCATGCTGCTCCATTGCC 61.735 60.000 0.00 0.00 0.00 4.52
2823 5196 1.271982 TGACGAGAACTGGTAGAGGCT 60.272 52.381 0.00 0.00 0.00 4.58
2824 5197 1.402613 GACGAGAACTGGTAGAGGCTC 59.597 57.143 6.34 6.34 0.00 4.70
2825 5198 1.004979 ACGAGAACTGGTAGAGGCTCT 59.995 52.381 22.48 22.48 0.00 4.09
2826 5199 1.403679 CGAGAACTGGTAGAGGCTCTG 59.596 57.143 26.95 12.45 0.00 3.35
2827 5200 1.754226 GAGAACTGGTAGAGGCTCTGG 59.246 57.143 26.95 15.33 0.00 3.86
2828 5201 1.077993 AGAACTGGTAGAGGCTCTGGT 59.922 52.381 26.95 15.93 0.00 4.00
2829 5202 1.903183 GAACTGGTAGAGGCTCTGGTT 59.097 52.381 26.95 22.15 0.00 3.67
2830 5203 2.031495 ACTGGTAGAGGCTCTGGTTT 57.969 50.000 26.95 2.57 0.00 3.27
2831 5204 3.185880 ACTGGTAGAGGCTCTGGTTTA 57.814 47.619 26.95 3.24 0.00 2.01
2832 5205 3.725634 ACTGGTAGAGGCTCTGGTTTAT 58.274 45.455 26.95 5.30 0.00 1.40
2833 5206 4.880164 ACTGGTAGAGGCTCTGGTTTATA 58.120 43.478 26.95 1.60 0.00 0.98
2834 5207 5.468658 ACTGGTAGAGGCTCTGGTTTATAT 58.531 41.667 26.95 0.00 0.00 0.86
2835 5208 5.305644 ACTGGTAGAGGCTCTGGTTTATATG 59.694 44.000 26.95 9.24 0.00 1.78
2836 5209 4.040461 TGGTAGAGGCTCTGGTTTATATGC 59.960 45.833 26.95 0.67 0.00 3.14
2837 5210 4.284746 GGTAGAGGCTCTGGTTTATATGCT 59.715 45.833 26.95 0.00 0.00 3.79
2838 5211 4.615588 AGAGGCTCTGGTTTATATGCTC 57.384 45.455 17.96 0.00 0.00 4.26
2839 5212 4.230455 AGAGGCTCTGGTTTATATGCTCT 58.770 43.478 17.96 0.00 0.00 4.09
2840 5213 4.283212 AGAGGCTCTGGTTTATATGCTCTC 59.717 45.833 17.96 0.00 0.00 3.20
2841 5214 3.326297 AGGCTCTGGTTTATATGCTCTCC 59.674 47.826 0.00 0.00 0.00 3.71
2842 5215 3.071602 GGCTCTGGTTTATATGCTCTCCA 59.928 47.826 0.00 0.00 0.00 3.86
2843 5216 4.263243 GGCTCTGGTTTATATGCTCTCCAT 60.263 45.833 0.00 0.00 37.97 3.41
2844 5217 5.312079 GCTCTGGTTTATATGCTCTCCATT 58.688 41.667 0.00 0.00 35.34 3.16
2845 5218 5.767168 GCTCTGGTTTATATGCTCTCCATTT 59.233 40.000 0.00 0.00 35.34 2.32
2846 5219 6.936900 GCTCTGGTTTATATGCTCTCCATTTA 59.063 38.462 0.00 0.00 35.34 1.40
2847 5220 7.118971 GCTCTGGTTTATATGCTCTCCATTTAG 59.881 40.741 0.00 0.00 35.34 1.85
2848 5221 8.034313 TCTGGTTTATATGCTCTCCATTTAGT 57.966 34.615 0.00 0.00 35.34 2.24
2849 5222 7.933577 TCTGGTTTATATGCTCTCCATTTAGTG 59.066 37.037 0.00 0.00 35.34 2.74
2850 5223 6.486657 TGGTTTATATGCTCTCCATTTAGTGC 59.513 38.462 0.00 0.00 36.70 4.40
2851 5224 6.347725 GGTTTATATGCTCTCCATTTAGTGCG 60.348 42.308 0.00 0.00 38.51 5.34
2852 5225 1.303309 ATGCTCTCCATTTAGTGCGC 58.697 50.000 0.00 0.00 38.51 6.09
2853 5226 0.036483 TGCTCTCCATTTAGTGCGCA 60.036 50.000 5.66 5.66 38.51 6.09
2854 5227 0.654683 GCTCTCCATTTAGTGCGCAG 59.345 55.000 12.22 0.00 0.00 5.18
2855 5228 1.293924 CTCTCCATTTAGTGCGCAGG 58.706 55.000 12.22 7.74 0.00 4.85
2856 5229 0.901827 TCTCCATTTAGTGCGCAGGA 59.098 50.000 12.22 12.48 0.00 3.86
2857 5230 1.134699 TCTCCATTTAGTGCGCAGGAG 60.135 52.381 26.84 26.84 43.05 3.69
2858 5231 0.744414 TCCATTTAGTGCGCAGGAGC 60.744 55.000 12.22 0.00 37.71 4.70
2859 5232 1.026182 CCATTTAGTGCGCAGGAGCA 61.026 55.000 12.22 0.00 45.96 4.26
2905 5278 5.638596 AAAAATACCTAGCTTTTGGACCG 57.361 39.130 0.00 0.00 0.00 4.79
2906 5279 3.994931 AATACCTAGCTTTTGGACCGT 57.005 42.857 0.00 0.00 0.00 4.83
2907 5280 5.425196 AAATACCTAGCTTTTGGACCGTA 57.575 39.130 0.00 0.00 0.00 4.02
2908 5281 5.625568 AATACCTAGCTTTTGGACCGTAT 57.374 39.130 0.00 0.00 0.00 3.06
2909 5282 3.261981 ACCTAGCTTTTGGACCGTATG 57.738 47.619 0.00 0.00 0.00 2.39
2910 5283 2.835764 ACCTAGCTTTTGGACCGTATGA 59.164 45.455 0.00 0.00 0.00 2.15
2911 5284 3.118738 ACCTAGCTTTTGGACCGTATGAG 60.119 47.826 0.00 0.00 0.00 2.90
2912 5285 2.403252 AGCTTTTGGACCGTATGAGG 57.597 50.000 0.00 0.00 37.30 3.86
2913 5286 0.733150 GCTTTTGGACCGTATGAGGC 59.267 55.000 0.00 0.00 33.69 4.70
2914 5287 1.948611 GCTTTTGGACCGTATGAGGCA 60.949 52.381 0.00 0.00 33.69 4.75
2915 5288 2.432444 CTTTTGGACCGTATGAGGCAA 58.568 47.619 0.00 0.00 33.69 4.52
2916 5289 2.570415 TTTGGACCGTATGAGGCAAA 57.430 45.000 0.00 0.00 33.69 3.68
2917 5290 2.570415 TTGGACCGTATGAGGCAAAA 57.430 45.000 0.00 0.00 33.69 2.44
2918 5291 2.570415 TGGACCGTATGAGGCAAAAA 57.430 45.000 0.00 0.00 33.69 1.94
2936 5309 4.856115 AAAAATGCTGTTCCAACAAACG 57.144 36.364 0.00 0.00 38.66 3.60
2937 5310 2.507339 AATGCTGTTCCAACAAACGG 57.493 45.000 0.00 0.00 38.66 4.44
2938 5311 1.398692 ATGCTGTTCCAACAAACGGT 58.601 45.000 0.00 0.00 38.66 4.83
2939 5312 0.736053 TGCTGTTCCAACAAACGGTC 59.264 50.000 0.00 0.00 38.66 4.79
2940 5313 0.736053 GCTGTTCCAACAAACGGTCA 59.264 50.000 0.00 0.00 38.66 4.02
2941 5314 1.336755 GCTGTTCCAACAAACGGTCAT 59.663 47.619 0.00 0.00 38.66 3.06
2942 5315 2.550606 GCTGTTCCAACAAACGGTCATA 59.449 45.455 0.00 0.00 38.66 2.15
2943 5316 3.190535 GCTGTTCCAACAAACGGTCATAT 59.809 43.478 0.00 0.00 38.66 1.78
2944 5317 4.722194 CTGTTCCAACAAACGGTCATATG 58.278 43.478 0.00 0.00 38.66 1.78
2945 5318 4.138290 TGTTCCAACAAACGGTCATATGT 58.862 39.130 1.90 0.00 35.67 2.29
2946 5319 5.306394 TGTTCCAACAAACGGTCATATGTA 58.694 37.500 1.90 0.00 35.67 2.29
2947 5320 5.763698 TGTTCCAACAAACGGTCATATGTAA 59.236 36.000 1.90 0.00 35.67 2.41
2948 5321 6.262496 TGTTCCAACAAACGGTCATATGTAAA 59.738 34.615 1.90 0.00 35.67 2.01
2949 5322 6.879276 TCCAACAAACGGTCATATGTAAAA 57.121 33.333 1.90 0.00 0.00 1.52
2950 5323 7.273320 TCCAACAAACGGTCATATGTAAAAA 57.727 32.000 1.90 0.00 0.00 1.94
2968 5341 2.823924 AAAAATTAAACCGCGGCCTT 57.176 40.000 28.58 21.43 0.00 4.35
2969 5342 2.357327 AAAATTAAACCGCGGCCTTC 57.643 45.000 28.58 0.00 0.00 3.46
2970 5343 0.528924 AAATTAAACCGCGGCCTTCC 59.471 50.000 28.58 0.00 0.00 3.46
2980 5353 3.680156 GGCCTTCCGTGATGCAAA 58.320 55.556 0.00 0.00 0.00 3.68
2981 5354 2.192605 GGCCTTCCGTGATGCAAAT 58.807 52.632 0.00 0.00 0.00 2.32
2982 5355 0.532115 GGCCTTCCGTGATGCAAATT 59.468 50.000 0.00 0.00 0.00 1.82
2983 5356 1.066929 GGCCTTCCGTGATGCAAATTT 60.067 47.619 0.00 0.00 0.00 1.82
2984 5357 2.165437 GGCCTTCCGTGATGCAAATTTA 59.835 45.455 0.00 0.00 0.00 1.40
2985 5358 3.179048 GCCTTCCGTGATGCAAATTTAC 58.821 45.455 0.00 0.00 0.00 2.01
2986 5359 3.366883 GCCTTCCGTGATGCAAATTTACA 60.367 43.478 0.00 0.00 0.00 2.41
2987 5360 4.677779 GCCTTCCGTGATGCAAATTTACAT 60.678 41.667 3.46 3.46 0.00 2.29
2988 5361 5.036737 CCTTCCGTGATGCAAATTTACATC 58.963 41.667 20.21 20.21 42.46 3.06
2995 5368 6.682423 TGATGCAAATTTACATCACGAGAT 57.318 33.333 24.14 0.00 45.79 2.75
3005 5378 3.856104 CATCACGAGATGCAACTGATC 57.144 47.619 9.93 0.00 44.61 2.92
3006 5379 2.299993 TCACGAGATGCAACTGATCC 57.700 50.000 0.00 0.00 0.00 3.36
3007 5380 1.550072 TCACGAGATGCAACTGATCCA 59.450 47.619 0.00 0.00 0.00 3.41
3008 5381 2.028203 TCACGAGATGCAACTGATCCAA 60.028 45.455 0.00 0.00 0.00 3.53
3009 5382 2.743664 CACGAGATGCAACTGATCCAAA 59.256 45.455 0.00 0.00 0.00 3.28
3010 5383 3.189080 CACGAGATGCAACTGATCCAAAA 59.811 43.478 0.00 0.00 0.00 2.44
3011 5384 3.189287 ACGAGATGCAACTGATCCAAAAC 59.811 43.478 0.00 0.00 0.00 2.43
3012 5385 3.426695 CGAGATGCAACTGATCCAAAACC 60.427 47.826 0.00 0.00 0.00 3.27
3013 5386 2.489329 AGATGCAACTGATCCAAAACCG 59.511 45.455 0.00 0.00 0.00 4.44
3014 5387 0.313672 TGCAACTGATCCAAAACCGC 59.686 50.000 0.00 0.00 0.00 5.68
3015 5388 0.729140 GCAACTGATCCAAAACCGCG 60.729 55.000 0.00 0.00 0.00 6.46
3016 5389 0.109781 CAACTGATCCAAAACCGCGG 60.110 55.000 26.86 26.86 0.00 6.46
3017 5390 1.862602 AACTGATCCAAAACCGCGGC 61.863 55.000 28.58 6.62 0.00 6.53
3018 5391 3.051392 CTGATCCAAAACCGCGGCC 62.051 63.158 28.58 4.77 0.00 6.13
3019 5392 4.174129 GATCCAAAACCGCGGCCG 62.174 66.667 28.58 24.05 0.00 6.13
3042 5415 4.639171 CAAACGCCCAACCGCCAC 62.639 66.667 0.00 0.00 0.00 5.01
3043 5416 4.887190 AAACGCCCAACCGCCACT 62.887 61.111 0.00 0.00 0.00 4.00
3044 5417 4.887190 AACGCCCAACCGCCACTT 62.887 61.111 0.00 0.00 0.00 3.16
3047 5420 2.676471 GCCCAACCGCCACTTCAT 60.676 61.111 0.00 0.00 0.00 2.57
3048 5421 2.275380 GCCCAACCGCCACTTCATT 61.275 57.895 0.00 0.00 0.00 2.57
3049 5422 1.883021 CCCAACCGCCACTTCATTC 59.117 57.895 0.00 0.00 0.00 2.67
3050 5423 1.595093 CCCAACCGCCACTTCATTCC 61.595 60.000 0.00 0.00 0.00 3.01
3051 5424 1.501741 CAACCGCCACTTCATTCCG 59.498 57.895 0.00 0.00 0.00 4.30
3052 5425 2.332654 AACCGCCACTTCATTCCGC 61.333 57.895 0.00 0.00 0.00 5.54
3053 5426 2.436646 CCGCCACTTCATTCCGCT 60.437 61.111 0.00 0.00 0.00 5.52
3054 5427 2.040544 CCGCCACTTCATTCCGCTT 61.041 57.895 0.00 0.00 0.00 4.68
3055 5428 1.425428 CGCCACTTCATTCCGCTTC 59.575 57.895 0.00 0.00 0.00 3.86
3056 5429 1.803289 GCCACTTCATTCCGCTTCC 59.197 57.895 0.00 0.00 0.00 3.46
3057 5430 1.982073 GCCACTTCATTCCGCTTCCG 61.982 60.000 0.00 0.00 0.00 4.30
3058 5431 1.425428 CACTTCATTCCGCTTCCGC 59.575 57.895 0.00 0.00 0.00 5.54
3059 5432 1.745489 ACTTCATTCCGCTTCCGCC 60.745 57.895 0.00 0.00 0.00 6.13
3060 5433 1.450312 CTTCATTCCGCTTCCGCCT 60.450 57.895 0.00 0.00 0.00 5.52
3061 5434 1.709147 CTTCATTCCGCTTCCGCCTG 61.709 60.000 0.00 0.00 0.00 4.85
3062 5435 3.204827 CATTCCGCTTCCGCCTGG 61.205 66.667 0.00 0.00 0.00 4.45
3098 5471 4.641645 CCAGCACCAGCCACCGAA 62.642 66.667 0.00 0.00 43.56 4.30
3099 5472 2.594303 CAGCACCAGCCACCGAAA 60.594 61.111 0.00 0.00 43.56 3.46
3100 5473 2.192861 CAGCACCAGCCACCGAAAA 61.193 57.895 0.00 0.00 43.56 2.29
3101 5474 1.228552 AGCACCAGCCACCGAAAAT 60.229 52.632 0.00 0.00 43.56 1.82
3102 5475 0.827507 AGCACCAGCCACCGAAAATT 60.828 50.000 0.00 0.00 43.56 1.82
3103 5476 0.667184 GCACCAGCCACCGAAAATTG 60.667 55.000 0.00 0.00 33.58 2.32
3104 5477 0.667184 CACCAGCCACCGAAAATTGC 60.667 55.000 0.00 0.00 0.00 3.56
3105 5478 1.079888 CCAGCCACCGAAAATTGCC 60.080 57.895 0.00 0.00 0.00 4.52
3106 5479 1.444212 CAGCCACCGAAAATTGCCG 60.444 57.895 0.00 0.00 0.00 5.69
3107 5480 2.809174 GCCACCGAAAATTGCCGC 60.809 61.111 0.00 0.00 0.00 6.53
3108 5481 2.126110 CCACCGAAAATTGCCGCC 60.126 61.111 0.00 0.00 0.00 6.13
3109 5482 2.503809 CACCGAAAATTGCCGCCG 60.504 61.111 0.00 0.00 0.00 6.46
3110 5483 4.413800 ACCGAAAATTGCCGCCGC 62.414 61.111 0.00 0.00 0.00 6.53
3135 5508 3.470567 CAAGTCGCCGTCGCTGTC 61.471 66.667 0.00 0.00 35.26 3.51
3153 5526 4.554036 GCCGCCACCTCCCTCATC 62.554 72.222 0.00 0.00 0.00 2.92
3154 5527 4.227134 CCGCCACCTCCCTCATCG 62.227 72.222 0.00 0.00 0.00 3.84
3155 5528 4.899239 CGCCACCTCCCTCATCGC 62.899 72.222 0.00 0.00 0.00 4.58
3156 5529 4.554036 GCCACCTCCCTCATCGCC 62.554 72.222 0.00 0.00 0.00 5.54
3157 5530 4.227134 CCACCTCCCTCATCGCCG 62.227 72.222 0.00 0.00 0.00 6.46
3158 5531 3.461773 CACCTCCCTCATCGCCGT 61.462 66.667 0.00 0.00 0.00 5.68
3159 5532 3.148279 ACCTCCCTCATCGCCGTC 61.148 66.667 0.00 0.00 0.00 4.79
3160 5533 4.271816 CCTCCCTCATCGCCGTCG 62.272 72.222 0.00 0.00 0.00 5.12
3161 5534 4.933064 CTCCCTCATCGCCGTCGC 62.933 72.222 0.00 0.00 35.26 5.19
3177 5550 4.858680 GCCGCCCTAGCCCTTGTC 62.859 72.222 0.00 0.00 34.57 3.18
3178 5551 4.530857 CCGCCCTAGCCCTTGTCG 62.531 72.222 0.00 0.00 34.57 4.35
3180 5553 4.858680 GCCCTAGCCCTTGTCGCC 62.859 72.222 0.00 0.00 0.00 5.54
3181 5554 3.083997 CCCTAGCCCTTGTCGCCT 61.084 66.667 0.00 0.00 0.00 5.52
3182 5555 2.501610 CCTAGCCCTTGTCGCCTC 59.498 66.667 0.00 0.00 0.00 4.70
3183 5556 2.501610 CTAGCCCTTGTCGCCTCC 59.498 66.667 0.00 0.00 0.00 4.30
3184 5557 3.081409 TAGCCCTTGTCGCCTCCC 61.081 66.667 0.00 0.00 0.00 4.30
3237 5610 2.273449 CCATTTCGGGAGGCAGCT 59.727 61.111 0.00 0.00 0.00 4.24
3238 5611 2.117156 CCATTTCGGGAGGCAGCTG 61.117 63.158 10.11 10.11 0.00 4.24
3239 5612 2.439156 ATTTCGGGAGGCAGCTGC 60.439 61.111 30.88 30.88 41.14 5.25
3257 5630 2.586357 GGCTGGATTCGCCGACTC 60.586 66.667 0.00 0.00 40.66 3.36
3258 5631 2.586357 GCTGGATTCGCCGACTCC 60.586 66.667 15.84 15.84 40.66 3.85
3259 5632 2.278857 CTGGATTCGCCGACTCCG 60.279 66.667 17.26 9.34 40.66 4.63
3277 5650 3.394836 GCGGTCTGCCTCCCTTCT 61.395 66.667 0.00 0.00 37.76 2.85
3278 5651 2.896443 CGGTCTGCCTCCCTTCTC 59.104 66.667 0.00 0.00 0.00 2.87
3279 5652 2.726351 CGGTCTGCCTCCCTTCTCC 61.726 68.421 0.00 0.00 0.00 3.71
3280 5653 1.306568 GGTCTGCCTCCCTTCTCCT 60.307 63.158 0.00 0.00 0.00 3.69
3281 5654 1.334384 GGTCTGCCTCCCTTCTCCTC 61.334 65.000 0.00 0.00 0.00 3.71
3282 5655 0.325203 GTCTGCCTCCCTTCTCCTCT 60.325 60.000 0.00 0.00 0.00 3.69
3283 5656 0.325110 TCTGCCTCCCTTCTCCTCTG 60.325 60.000 0.00 0.00 0.00 3.35
3284 5657 0.617249 CTGCCTCCCTTCTCCTCTGT 60.617 60.000 0.00 0.00 0.00 3.41
3285 5658 0.906756 TGCCTCCCTTCTCCTCTGTG 60.907 60.000 0.00 0.00 0.00 3.66
3286 5659 1.904032 CCTCCCTTCTCCTCTGTGC 59.096 63.158 0.00 0.00 0.00 4.57
3287 5660 1.621672 CCTCCCTTCTCCTCTGTGCC 61.622 65.000 0.00 0.00 0.00 5.01
3288 5661 1.954362 CTCCCTTCTCCTCTGTGCCG 61.954 65.000 0.00 0.00 0.00 5.69
3289 5662 2.125350 CCTTCTCCTCTGTGCCGC 60.125 66.667 0.00 0.00 0.00 6.53
3290 5663 2.125350 CTTCTCCTCTGTGCCGCC 60.125 66.667 0.00 0.00 0.00 6.13
3291 5664 3.997064 CTTCTCCTCTGTGCCGCCG 62.997 68.421 0.00 0.00 0.00 6.46
3311 5684 3.942439 GCCCTCCGCCTCCCATAC 61.942 72.222 0.00 0.00 0.00 2.39
3312 5685 3.242291 CCCTCCGCCTCCCATACC 61.242 72.222 0.00 0.00 0.00 2.73
3313 5686 3.616721 CCTCCGCCTCCCATACCG 61.617 72.222 0.00 0.00 0.00 4.02
3314 5687 3.616721 CTCCGCCTCCCATACCGG 61.617 72.222 0.00 0.00 41.97 5.28
3315 5688 4.146156 TCCGCCTCCCATACCGGA 62.146 66.667 9.46 0.00 46.50 5.14
3316 5689 2.923035 CCGCCTCCCATACCGGAT 60.923 66.667 9.46 0.00 43.20 4.18
3317 5690 2.343758 CGCCTCCCATACCGGATG 59.656 66.667 9.46 7.74 36.56 3.51
3324 5697 4.846551 CATACCGGATGGCGTCAA 57.153 55.556 9.46 0.00 39.70 3.18
3325 5698 2.605094 CATACCGGATGGCGTCAAG 58.395 57.895 9.46 1.30 39.70 3.02
3353 5726 4.179579 GGTGCCGCGGCTGAAATC 62.180 66.667 45.79 26.41 42.51 2.17
3354 5727 4.520846 GTGCCGCGGCTGAAATCG 62.521 66.667 45.79 10.45 42.51 3.34
3361 5734 3.202706 GGCTGAAATCGCCGACCC 61.203 66.667 0.00 0.00 37.87 4.46
3362 5735 2.125106 GCTGAAATCGCCGACCCT 60.125 61.111 0.00 0.00 0.00 4.34
3363 5736 2.464459 GCTGAAATCGCCGACCCTG 61.464 63.158 0.00 0.00 0.00 4.45
3364 5737 1.815421 CTGAAATCGCCGACCCTGG 60.815 63.158 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.856688 GTACAACACATGCACGCGA 59.143 52.632 15.93 0.00 0.00 5.87
204 219 3.261897 ACGAATAGGAATAGGATGGCAGG 59.738 47.826 0.00 0.00 0.00 4.85
205 220 4.543590 ACGAATAGGAATAGGATGGCAG 57.456 45.455 0.00 0.00 0.00 4.85
207 222 5.978814 ACATACGAATAGGAATAGGATGGC 58.021 41.667 0.00 0.00 0.00 4.40
208 223 8.294954 AGTACATACGAATAGGAATAGGATGG 57.705 38.462 0.00 0.00 0.00 3.51
231 246 3.195825 GCTCCACTTCCACACATACTAGT 59.804 47.826 0.00 0.00 0.00 2.57
233 248 2.165641 CGCTCCACTTCCACACATACTA 59.834 50.000 0.00 0.00 0.00 1.82
234 249 1.066858 CGCTCCACTTCCACACATACT 60.067 52.381 0.00 0.00 0.00 2.12
237 252 1.672356 GCGCTCCACTTCCACACAT 60.672 57.895 0.00 0.00 0.00 3.21
300 334 4.287067 AGCTCTTGGACCTGACAGAAAATA 59.713 41.667 3.32 0.00 0.00 1.40
318 352 3.594134 CATCGGACTGAAAGAAAGCTCT 58.406 45.455 0.00 0.00 37.43 4.09
331 365 2.284798 CTGTACTGCGCCATCGGACT 62.285 60.000 4.18 0.00 35.95 3.85
332 366 1.878522 CTGTACTGCGCCATCGGAC 60.879 63.158 4.18 0.00 35.95 4.79
333 367 2.348104 ACTGTACTGCGCCATCGGA 61.348 57.895 4.18 0.00 35.95 4.55
334 368 2.167219 CACTGTACTGCGCCATCGG 61.167 63.158 4.18 0.28 35.95 4.18
335 369 2.167219 CCACTGTACTGCGCCATCG 61.167 63.158 4.18 0.00 39.07 3.84
338 372 2.030412 CACCACTGTACTGCGCCA 59.970 61.111 4.18 0.00 0.00 5.69
339 373 2.742372 CCACCACTGTACTGCGCC 60.742 66.667 4.18 0.00 0.00 6.53
340 374 2.742372 CCCACCACTGTACTGCGC 60.742 66.667 0.00 0.00 0.00 6.09
341 375 2.731691 AAGCCCACCACTGTACTGCG 62.732 60.000 0.00 0.00 0.00 5.18
348 2380 1.909781 ATGCCAAAGCCCACCACTG 60.910 57.895 0.00 0.00 38.69 3.66
351 2383 0.544833 ATTCATGCCAAAGCCCACCA 60.545 50.000 0.00 0.00 38.69 4.17
367 2399 5.458015 GTTGGTACTTTTACACTGGCATTC 58.542 41.667 0.00 0.00 0.00 2.67
370 2402 3.215975 GGTTGGTACTTTTACACTGGCA 58.784 45.455 0.00 0.00 0.00 4.92
492 2526 2.664851 CAAAGTCGCGCTGGGTCA 60.665 61.111 5.56 0.00 0.00 4.02
512 2546 3.439129 GGGAGCAAGCAATTTACGTACTT 59.561 43.478 0.00 0.00 0.00 2.24
555 2607 2.127232 GCGCGAGTGTTTTGAGCC 60.127 61.111 12.10 0.00 30.39 4.70
590 2646 2.814280 AACCGTGTCAAATCTCTCGT 57.186 45.000 0.00 0.00 0.00 4.18
630 2687 4.495422 AGTCTGCGTCAAATAATCTCGTT 58.505 39.130 0.00 0.00 0.00 3.85
650 2757 2.432510 GCTTGACCTGCCTATGAGTAGT 59.567 50.000 0.00 0.00 0.00 2.73
654 2762 2.408271 TTGCTTGACCTGCCTATGAG 57.592 50.000 0.00 0.00 0.00 2.90
699 2835 2.834618 GCGGCGATGGATTGGGTTC 61.835 63.158 12.98 0.00 0.00 3.62
714 2850 3.775654 GGGTGGAGACTCCTGCGG 61.776 72.222 22.14 0.00 43.63 5.69
715 2851 4.135153 CGGGTGGAGACTCCTGCG 62.135 72.222 22.14 1.05 42.96 5.18
751 2906 1.007387 CAAGCTGTTTGGGTTCGCC 60.007 57.895 0.00 0.00 32.95 5.54
753 2908 0.385390 AAGCAAGCTGTTTGGGTTCG 59.615 50.000 6.38 0.00 37.26 3.95
791 2950 4.619760 TGCGCGATAAAGATAGGAAATACG 59.380 41.667 12.10 0.00 0.00 3.06
793 2952 4.619760 CGTGCGCGATAAAGATAGGAAATA 59.380 41.667 16.08 0.00 41.33 1.40
920 3122 3.259425 GAGCTTGCTTGTGGCGGTG 62.259 63.158 0.00 0.00 45.43 4.94
921 3123 2.980233 GAGCTTGCTTGTGGCGGT 60.980 61.111 0.00 0.00 45.43 5.68
922 3124 4.093952 CGAGCTTGCTTGTGGCGG 62.094 66.667 0.00 0.00 45.43 6.13
923 3125 3.043713 TCGAGCTTGCTTGTGGCG 61.044 61.111 9.41 2.55 45.43 5.69
924 3126 2.253758 TGTCGAGCTTGCTTGTGGC 61.254 57.895 9.41 0.00 42.22 5.01
925 3127 1.159713 TGTGTCGAGCTTGCTTGTGG 61.160 55.000 9.41 0.00 0.00 4.17
926 3128 0.657312 TTGTGTCGAGCTTGCTTGTG 59.343 50.000 9.41 0.00 0.00 3.33
955 3168 2.051518 GGTGGCAATTGGGATGCGA 61.052 57.895 7.72 0.00 44.75 5.10
975 3188 2.416162 CGTCTTCTTTTCTCTCCTCCGG 60.416 54.545 0.00 0.00 0.00 5.14
977 3190 3.367600 GGTCGTCTTCTTTTCTCTCCTCC 60.368 52.174 0.00 0.00 0.00 4.30
1268 3485 0.321919 GTTGCTCATCACCTGCTCCA 60.322 55.000 0.00 0.00 0.00 3.86
1279 3496 4.115199 GAGGCCCCCGTTGCTCAT 62.115 66.667 0.00 0.00 0.00 2.90
1316 3533 4.508128 CCACATCGGCCGCGTAGT 62.508 66.667 23.51 13.07 0.00 2.73
1557 3777 0.249615 CCATCTCGATGACCGTGCAT 60.250 55.000 8.42 0.00 41.20 3.96
1567 3787 4.241555 GCCGGTGGCCATCTCGAT 62.242 66.667 15.59 0.00 44.06 3.59
2039 4289 1.450134 TGCACGATGATGCCAGTCC 60.450 57.895 0.00 0.00 45.50 3.85
2056 4309 2.126463 ACTGGTGATCGCGTCGTG 60.126 61.111 5.77 0.00 0.00 4.35
2085 4338 3.554692 CCGAACACTGCGCCGATC 61.555 66.667 4.18 0.00 0.00 3.69
2096 4352 0.317160 AATGTCGAGAGCACCGAACA 59.683 50.000 0.00 0.00 37.81 3.18
2213 4478 8.513199 CACTAACTGGTGAGATGCTAGAAGCA 62.513 46.154 3.76 3.76 46.40 3.91
2215 4480 5.105554 ACACTAACTGGTGAGATGCTAGAAG 60.106 44.000 0.00 0.00 40.13 2.85
2258 4529 7.517614 TTACTGATTCTGTTGCCAAATAACA 57.482 32.000 1.28 0.00 36.66 2.41
2322 4597 0.390340 TAAACAGAGGAGCAGCGCTG 60.390 55.000 32.83 32.83 39.88 5.18
2448 4745 3.380637 AGCTTGTGAATTCATGCTGGATC 59.619 43.478 23.34 7.00 43.66 3.36
2486 4810 2.874780 CTTTCCGCGTCGACTCCG 60.875 66.667 14.70 15.29 37.07 4.63
2616 4971 2.997986 TCGCTTGTCGATAAAGGTTTCC 59.002 45.455 11.45 0.00 43.16 3.13
2791 5164 5.574830 CCAGTTCTCGTCAATCTAGAAACAG 59.425 44.000 0.00 0.00 31.32 3.16
2823 5196 7.933577 CACTAAATGGAGAGCATATAAACCAGA 59.066 37.037 0.00 0.00 0.00 3.86
2824 5197 7.308229 GCACTAAATGGAGAGCATATAAACCAG 60.308 40.741 0.00 0.00 33.70 4.00
2825 5198 6.486657 GCACTAAATGGAGAGCATATAAACCA 59.513 38.462 0.00 0.00 33.70 3.67
2826 5199 6.347725 CGCACTAAATGGAGAGCATATAAACC 60.348 42.308 0.00 0.00 33.14 3.27
2827 5200 6.593978 CGCACTAAATGGAGAGCATATAAAC 58.406 40.000 0.00 0.00 33.14 2.01
2828 5201 5.179368 GCGCACTAAATGGAGAGCATATAAA 59.821 40.000 0.30 0.00 33.14 1.40
2829 5202 4.690748 GCGCACTAAATGGAGAGCATATAA 59.309 41.667 0.30 0.00 33.14 0.98
2830 5203 4.245660 GCGCACTAAATGGAGAGCATATA 58.754 43.478 0.30 0.00 33.14 0.86
2831 5204 3.070018 GCGCACTAAATGGAGAGCATAT 58.930 45.455 0.30 0.00 33.14 1.78
2832 5205 2.158971 TGCGCACTAAATGGAGAGCATA 60.159 45.455 5.66 0.00 33.14 3.14
2833 5206 1.303309 GCGCACTAAATGGAGAGCAT 58.697 50.000 0.30 0.00 33.14 3.79
2834 5207 0.036483 TGCGCACTAAATGGAGAGCA 60.036 50.000 5.66 0.00 33.14 4.26
2835 5208 0.654683 CTGCGCACTAAATGGAGAGC 59.345 55.000 5.66 0.00 0.00 4.09
2836 5209 1.134699 TCCTGCGCACTAAATGGAGAG 60.135 52.381 5.66 0.00 0.00 3.20
2837 5210 0.901827 TCCTGCGCACTAAATGGAGA 59.098 50.000 5.66 0.00 0.00 3.71
2838 5211 1.293924 CTCCTGCGCACTAAATGGAG 58.706 55.000 22.08 22.08 35.72 3.86
2839 5212 0.744414 GCTCCTGCGCACTAAATGGA 60.744 55.000 5.66 10.14 0.00 3.41
2840 5213 1.026182 TGCTCCTGCGCACTAAATGG 61.026 55.000 5.66 5.13 43.34 3.16
2841 5214 1.003116 GATGCTCCTGCGCACTAAATG 60.003 52.381 5.66 0.00 43.61 2.32
2842 5215 1.134280 AGATGCTCCTGCGCACTAAAT 60.134 47.619 5.66 0.00 43.61 1.40
2843 5216 0.250234 AGATGCTCCTGCGCACTAAA 59.750 50.000 5.66 0.00 43.61 1.85
2844 5217 0.179100 GAGATGCTCCTGCGCACTAA 60.179 55.000 5.66 0.00 43.61 2.24
2845 5218 1.439228 GAGATGCTCCTGCGCACTA 59.561 57.895 5.66 0.00 43.61 2.74
2846 5219 2.186384 GAGATGCTCCTGCGCACT 59.814 61.111 5.66 0.00 43.61 4.40
2847 5220 2.894387 GGAGATGCTCCTGCGCAC 60.894 66.667 5.66 0.00 46.41 5.34
2879 5252 9.063615 CGGTCCAAAAGCTAGGTATTTTTATAT 57.936 33.333 0.00 0.00 0.00 0.86
2880 5253 8.048514 ACGGTCCAAAAGCTAGGTATTTTTATA 58.951 33.333 0.00 0.00 0.00 0.98
2881 5254 6.888088 ACGGTCCAAAAGCTAGGTATTTTTAT 59.112 34.615 0.00 0.00 0.00 1.40
2882 5255 6.240145 ACGGTCCAAAAGCTAGGTATTTTTA 58.760 36.000 0.00 0.00 0.00 1.52
2883 5256 5.074804 ACGGTCCAAAAGCTAGGTATTTTT 58.925 37.500 0.00 0.00 0.00 1.94
2884 5257 4.659115 ACGGTCCAAAAGCTAGGTATTTT 58.341 39.130 0.00 0.00 0.00 1.82
2885 5258 4.296621 ACGGTCCAAAAGCTAGGTATTT 57.703 40.909 0.00 0.00 0.00 1.40
2886 5259 3.994931 ACGGTCCAAAAGCTAGGTATT 57.005 42.857 0.00 0.00 0.00 1.89
2887 5260 4.652421 TCATACGGTCCAAAAGCTAGGTAT 59.348 41.667 0.00 0.00 0.00 2.73
2888 5261 4.025360 TCATACGGTCCAAAAGCTAGGTA 58.975 43.478 0.00 0.00 0.00 3.08
2889 5262 2.835764 TCATACGGTCCAAAAGCTAGGT 59.164 45.455 0.00 0.00 0.00 3.08
2890 5263 3.458189 CTCATACGGTCCAAAAGCTAGG 58.542 50.000 0.00 0.00 0.00 3.02
2891 5264 3.458189 CCTCATACGGTCCAAAAGCTAG 58.542 50.000 0.00 0.00 0.00 3.42
2892 5265 2.419574 GCCTCATACGGTCCAAAAGCTA 60.420 50.000 0.00 0.00 0.00 3.32
2893 5266 1.679032 GCCTCATACGGTCCAAAAGCT 60.679 52.381 0.00 0.00 0.00 3.74
2894 5267 0.733150 GCCTCATACGGTCCAAAAGC 59.267 55.000 0.00 0.00 0.00 3.51
2895 5268 2.107950 TGCCTCATACGGTCCAAAAG 57.892 50.000 0.00 0.00 0.00 2.27
2896 5269 2.570415 TTGCCTCATACGGTCCAAAA 57.430 45.000 0.00 0.00 0.00 2.44
2897 5270 2.570415 TTTGCCTCATACGGTCCAAA 57.430 45.000 0.00 0.00 0.00 3.28
2898 5271 2.570415 TTTTGCCTCATACGGTCCAA 57.430 45.000 0.00 0.00 0.00 3.53
2899 5272 2.570415 TTTTTGCCTCATACGGTCCA 57.430 45.000 0.00 0.00 0.00 4.02
2921 5294 0.736053 TGACCGTTTGTTGGAACAGC 59.264 50.000 0.00 0.00 42.39 4.40
2922 5295 4.215399 ACATATGACCGTTTGTTGGAACAG 59.785 41.667 10.38 0.00 42.39 3.16
2923 5296 4.138290 ACATATGACCGTTTGTTGGAACA 58.862 39.130 10.38 0.00 37.08 3.18
2924 5297 4.759516 ACATATGACCGTTTGTTGGAAC 57.240 40.909 10.38 0.00 0.00 3.62
2925 5298 6.879276 TTTACATATGACCGTTTGTTGGAA 57.121 33.333 10.38 0.00 0.00 3.53
2926 5299 6.879276 TTTTACATATGACCGTTTGTTGGA 57.121 33.333 10.38 0.00 0.00 3.53
2949 5322 2.610976 GGAAGGCCGCGGTTTAATTTTT 60.611 45.455 28.70 9.42 0.00 1.94
2950 5323 1.067425 GGAAGGCCGCGGTTTAATTTT 60.067 47.619 28.70 10.49 0.00 1.82
2951 5324 0.528924 GGAAGGCCGCGGTTTAATTT 59.471 50.000 28.70 11.93 0.00 1.82
2952 5325 2.186155 GGAAGGCCGCGGTTTAATT 58.814 52.632 28.70 14.17 0.00 1.40
2953 5326 3.914094 GGAAGGCCGCGGTTTAAT 58.086 55.556 28.70 8.97 0.00 1.40
2963 5336 0.532115 AATTTGCATCACGGAAGGCC 59.468 50.000 0.00 0.00 0.00 5.19
2964 5337 2.368655 AAATTTGCATCACGGAAGGC 57.631 45.000 0.00 0.00 0.00 4.35
2965 5338 4.433186 TGTAAATTTGCATCACGGAAGG 57.567 40.909 4.71 0.00 0.00 3.46
2973 5346 6.964677 CATCTCGTGATGTAAATTTGCATC 57.035 37.500 30.97 30.97 46.34 3.91
2974 5347 6.625520 TTGCATCTCGTGATGTAAATTTGCAT 60.626 34.615 22.90 20.00 46.80 3.96
2975 5348 5.335504 TTGCATCTCGTGATGTAAATTTGCA 60.336 36.000 22.90 11.51 46.80 4.08
2976 5349 5.094812 TTGCATCTCGTGATGTAAATTTGC 58.905 37.500 22.90 11.98 46.80 3.68
2986 5359 2.169144 TGGATCAGTTGCATCTCGTGAT 59.831 45.455 0.00 0.00 0.00 3.06
2987 5360 1.550072 TGGATCAGTTGCATCTCGTGA 59.450 47.619 0.00 0.00 0.00 4.35
2988 5361 2.014335 TGGATCAGTTGCATCTCGTG 57.986 50.000 0.00 0.00 0.00 4.35
2989 5362 2.768253 TTGGATCAGTTGCATCTCGT 57.232 45.000 0.00 0.00 0.00 4.18
2990 5363 3.426695 GGTTTTGGATCAGTTGCATCTCG 60.427 47.826 0.00 0.00 0.00 4.04
2991 5364 3.426695 CGGTTTTGGATCAGTTGCATCTC 60.427 47.826 0.00 0.00 0.00 2.75
2992 5365 2.489329 CGGTTTTGGATCAGTTGCATCT 59.511 45.455 0.00 0.00 0.00 2.90
2993 5366 2.867429 CGGTTTTGGATCAGTTGCATC 58.133 47.619 0.00 0.00 0.00 3.91
2994 5367 1.067635 GCGGTTTTGGATCAGTTGCAT 60.068 47.619 0.00 0.00 0.00 3.96
2995 5368 0.313672 GCGGTTTTGGATCAGTTGCA 59.686 50.000 0.00 0.00 0.00 4.08
2996 5369 0.729140 CGCGGTTTTGGATCAGTTGC 60.729 55.000 0.00 0.00 0.00 4.17
2997 5370 0.109781 CCGCGGTTTTGGATCAGTTG 60.110 55.000 19.50 0.00 0.00 3.16
2998 5371 1.862602 GCCGCGGTTTTGGATCAGTT 61.863 55.000 28.70 0.00 0.00 3.16
2999 5372 2.332654 GCCGCGGTTTTGGATCAGT 61.333 57.895 28.70 0.00 0.00 3.41
3000 5373 2.485122 GCCGCGGTTTTGGATCAG 59.515 61.111 28.70 0.00 0.00 2.90
3001 5374 3.059386 GGCCGCGGTTTTGGATCA 61.059 61.111 28.70 0.00 0.00 2.92
3002 5375 4.174129 CGGCCGCGGTTTTGGATC 62.174 66.667 28.70 6.82 0.00 3.36
3025 5398 4.639171 GTGGCGGTTGGGCGTTTG 62.639 66.667 0.00 0.00 46.04 2.93
3026 5399 4.887190 AGTGGCGGTTGGGCGTTT 62.887 61.111 0.00 0.00 46.04 3.60
3027 5400 4.887190 AAGTGGCGGTTGGGCGTT 62.887 61.111 0.00 0.00 46.04 4.84
3030 5403 2.212900 GAATGAAGTGGCGGTTGGGC 62.213 60.000 0.00 0.00 42.69 5.36
3031 5404 1.595093 GGAATGAAGTGGCGGTTGGG 61.595 60.000 0.00 0.00 0.00 4.12
3032 5405 1.883021 GGAATGAAGTGGCGGTTGG 59.117 57.895 0.00 0.00 0.00 3.77
3033 5406 1.501741 CGGAATGAAGTGGCGGTTG 59.498 57.895 0.00 0.00 0.00 3.77
3034 5407 2.332654 GCGGAATGAAGTGGCGGTT 61.333 57.895 0.00 0.00 0.00 4.44
3035 5408 2.746277 GCGGAATGAAGTGGCGGT 60.746 61.111 0.00 0.00 0.00 5.68
3036 5409 1.982073 GAAGCGGAATGAAGTGGCGG 61.982 60.000 0.00 0.00 0.00 6.13
3037 5410 1.425428 GAAGCGGAATGAAGTGGCG 59.575 57.895 0.00 0.00 0.00 5.69
3038 5411 1.803289 GGAAGCGGAATGAAGTGGC 59.197 57.895 0.00 0.00 0.00 5.01
3039 5412 2.089854 CGGAAGCGGAATGAAGTGG 58.910 57.895 0.00 0.00 0.00 4.00
3081 5454 4.641645 TTCGGTGGCTGGTGCTGG 62.642 66.667 0.00 0.00 39.59 4.85
3082 5455 1.526575 ATTTTCGGTGGCTGGTGCTG 61.527 55.000 0.00 0.00 39.59 4.41
3083 5456 0.827507 AATTTTCGGTGGCTGGTGCT 60.828 50.000 0.00 0.00 39.59 4.40
3084 5457 0.667184 CAATTTTCGGTGGCTGGTGC 60.667 55.000 0.00 0.00 38.76 5.01
3085 5458 0.667184 GCAATTTTCGGTGGCTGGTG 60.667 55.000 0.00 0.00 0.00 4.17
3086 5459 1.665442 GCAATTTTCGGTGGCTGGT 59.335 52.632 0.00 0.00 0.00 4.00
3087 5460 1.079888 GGCAATTTTCGGTGGCTGG 60.080 57.895 0.00 0.00 37.34 4.85
3088 5461 1.444212 CGGCAATTTTCGGTGGCTG 60.444 57.895 0.00 0.00 38.12 4.85
3089 5462 2.961768 CGGCAATTTTCGGTGGCT 59.038 55.556 0.00 0.00 38.12 4.75
3090 5463 2.809174 GCGGCAATTTTCGGTGGC 60.809 61.111 0.00 0.00 36.98 5.01
3091 5464 2.126110 GGCGGCAATTTTCGGTGG 60.126 61.111 3.07 0.00 0.00 4.61
3092 5465 2.503809 CGGCGGCAATTTTCGGTG 60.504 61.111 10.53 0.00 0.00 4.94
3093 5466 4.413800 GCGGCGGCAATTTTCGGT 62.414 61.111 9.78 0.00 39.62 4.69
3118 5491 3.470567 GACAGCGACGGCGACTTG 61.471 66.667 18.90 12.29 46.35 3.16
3136 5509 4.554036 GATGAGGGAGGTGGCGGC 62.554 72.222 0.00 0.00 0.00 6.53
3137 5510 4.227134 CGATGAGGGAGGTGGCGG 62.227 72.222 0.00 0.00 0.00 6.13
3138 5511 4.899239 GCGATGAGGGAGGTGGCG 62.899 72.222 0.00 0.00 0.00 5.69
3139 5512 4.554036 GGCGATGAGGGAGGTGGC 62.554 72.222 0.00 0.00 0.00 5.01
3140 5513 4.227134 CGGCGATGAGGGAGGTGG 62.227 72.222 0.00 0.00 0.00 4.61
3141 5514 3.432051 GACGGCGATGAGGGAGGTG 62.432 68.421 16.62 0.00 0.00 4.00
3142 5515 3.148279 GACGGCGATGAGGGAGGT 61.148 66.667 16.62 0.00 0.00 3.85
3143 5516 4.271816 CGACGGCGATGAGGGAGG 62.272 72.222 16.62 0.00 40.82 4.30
3144 5517 4.933064 GCGACGGCGATGAGGGAG 62.933 72.222 18.90 0.00 40.82 4.30
3160 5533 4.858680 GACAAGGGCTAGGGCGGC 62.859 72.222 0.00 0.00 39.81 6.53
3161 5534 4.530857 CGACAAGGGCTAGGGCGG 62.531 72.222 0.00 0.00 39.81 6.13
3163 5536 4.858680 GGCGACAAGGGCTAGGGC 62.859 72.222 0.00 0.00 37.82 5.19
3164 5537 3.083997 AGGCGACAAGGGCTAGGG 61.084 66.667 0.00 0.00 41.57 3.53
3165 5538 2.501610 GAGGCGACAAGGGCTAGG 59.498 66.667 0.00 0.00 43.66 3.02
3166 5539 2.501610 GGAGGCGACAAGGGCTAG 59.498 66.667 0.00 0.00 43.66 3.42
3167 5540 3.081409 GGGAGGCGACAAGGGCTA 61.081 66.667 0.00 0.00 43.66 3.93
3219 5592 3.521796 GCTGCCTCCCGAAATGGC 61.522 66.667 0.00 0.00 46.26 4.40
3220 5593 2.117156 CAGCTGCCTCCCGAAATGG 61.117 63.158 0.00 0.00 37.55 3.16
3221 5594 2.768492 GCAGCTGCCTCCCGAAATG 61.768 63.158 28.76 0.00 34.31 2.32
3222 5595 2.439156 GCAGCTGCCTCCCGAAAT 60.439 61.111 28.76 0.00 34.31 2.17
3241 5614 2.586357 GGAGTCGGCGAATCCAGC 60.586 66.667 41.25 21.23 44.94 4.85
3242 5615 2.278857 CGGAGTCGGCGAATCCAG 60.279 66.667 42.81 33.45 45.75 3.86
3260 5633 3.378399 GAGAAGGGAGGCAGACCGC 62.378 68.421 0.00 0.00 42.76 5.68
3261 5634 2.726351 GGAGAAGGGAGGCAGACCG 61.726 68.421 0.00 0.00 42.76 4.79
3262 5635 1.306568 AGGAGAAGGGAGGCAGACC 60.307 63.158 0.00 0.00 0.00 3.85
3263 5636 0.325203 AGAGGAGAAGGGAGGCAGAC 60.325 60.000 0.00 0.00 0.00 3.51
3264 5637 0.325110 CAGAGGAGAAGGGAGGCAGA 60.325 60.000 0.00 0.00 0.00 4.26
3265 5638 0.617249 ACAGAGGAGAAGGGAGGCAG 60.617 60.000 0.00 0.00 0.00 4.85
3266 5639 0.906756 CACAGAGGAGAAGGGAGGCA 60.907 60.000 0.00 0.00 0.00 4.75
3267 5640 1.904032 CACAGAGGAGAAGGGAGGC 59.096 63.158 0.00 0.00 0.00 4.70
3268 5641 1.621672 GGCACAGAGGAGAAGGGAGG 61.622 65.000 0.00 0.00 0.00 4.30
3269 5642 1.904032 GGCACAGAGGAGAAGGGAG 59.096 63.158 0.00 0.00 0.00 4.30
3270 5643 1.984570 CGGCACAGAGGAGAAGGGA 60.985 63.158 0.00 0.00 0.00 4.20
3271 5644 2.581354 CGGCACAGAGGAGAAGGG 59.419 66.667 0.00 0.00 0.00 3.95
3272 5645 2.125350 GCGGCACAGAGGAGAAGG 60.125 66.667 0.00 0.00 0.00 3.46
3273 5646 2.125350 GGCGGCACAGAGGAGAAG 60.125 66.667 3.07 0.00 0.00 2.85
3274 5647 4.069232 CGGCGGCACAGAGGAGAA 62.069 66.667 10.53 0.00 0.00 2.87
3294 5667 3.942439 GTATGGGAGGCGGAGGGC 61.942 72.222 0.00 0.00 42.51 5.19
3295 5668 3.242291 GGTATGGGAGGCGGAGGG 61.242 72.222 0.00 0.00 0.00 4.30
3296 5669 3.616721 CGGTATGGGAGGCGGAGG 61.617 72.222 0.00 0.00 0.00 4.30
3297 5670 3.616721 CCGGTATGGGAGGCGGAG 61.617 72.222 0.00 0.00 0.00 4.63
3298 5671 3.462056 ATCCGGTATGGGAGGCGGA 62.462 63.158 0.00 0.00 40.02 5.54
3299 5672 2.923035 ATCCGGTATGGGAGGCGG 60.923 66.667 0.00 0.00 40.02 6.13
3300 5673 2.343758 CATCCGGTATGGGAGGCG 59.656 66.667 0.00 0.00 40.02 5.52
3307 5680 1.498865 GCTTGACGCCATCCGGTATG 61.499 60.000 0.00 4.03 42.52 2.39
3308 5681 1.227556 GCTTGACGCCATCCGGTAT 60.228 57.895 0.00 0.00 42.52 2.73
3309 5682 2.185867 GCTTGACGCCATCCGGTA 59.814 61.111 0.00 0.00 42.52 4.02
3310 5683 3.958147 CTGCTTGACGCCATCCGGT 62.958 63.158 0.00 0.00 42.52 5.28
3311 5684 3.197790 CTGCTTGACGCCATCCGG 61.198 66.667 0.00 0.00 42.52 5.14
3312 5685 3.869272 GCTGCTTGACGCCATCCG 61.869 66.667 0.00 0.00 44.21 4.18
3313 5686 3.512516 GGCTGCTTGACGCCATCC 61.513 66.667 0.00 0.00 45.59 3.51
3314 5687 3.869272 CGGCTGCTTGACGCCATC 61.869 66.667 0.00 0.00 46.62 3.51
3345 5718 2.125106 AGGGTCGGCGATTTCAGC 60.125 61.111 14.79 0.00 0.00 4.26
3346 5719 1.815421 CCAGGGTCGGCGATTTCAG 60.815 63.158 14.79 2.47 0.00 3.02
3347 5720 2.267642 CCAGGGTCGGCGATTTCA 59.732 61.111 14.79 0.00 0.00 2.69
3348 5721 3.202706 GCCAGGGTCGGCGATTTC 61.203 66.667 14.79 6.07 43.52 2.17


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

AutoCloner maintained by Alex Coulton.