Multiple sequence alignment - TraesCS4A01G496500

Loading Multiple Alignment...

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 TraesCS4A01G496500 chr4A 100.000 3892 0 0 1 3892 742889714 742893605 0.000000e+00 7188.0
1 TraesCS4A01G496500 chr4A 95.722 1683 43 12 2237 3892 743868030 743869710 0.000000e+00 2682.0
2 TraesCS4A01G496500 chr4A 96.393 915 24 4 1015 1929 743866870 743867775 0.000000e+00 1498.0
3 TraesCS4A01G496500 chr4A 85.537 242 13 4 1927 2168 743867805 743868024 2.340000e-57 233.0
4 TraesCS4A01G496500 chrUn 95.765 1700 57 5 2199 3892 295470456 295472146 0.000000e+00 2726.0
5 TraesCS4A01G496500 chrUn 89.225 1290 55 34 939 2199 292914260 292915494 0.000000e+00 1535.0
6 TraesCS4A01G496500 chrUn 97.297 37 1 0 904 940 209480608 209480572 3.250000e-06 63.9
7 TraesCS4A01G496500 chr7D 93.627 1726 74 18 2195 3892 1414523 1412806 0.000000e+00 2545.0
8 TraesCS4A01G496500 chr7D 92.771 996 51 8 939 1929 1419565 1418586 0.000000e+00 1421.0
9 TraesCS4A01G496500 chr7D 94.970 338 15 2 2 339 618704784 618704449 2.660000e-146 529.0
10 TraesCS4A01G496500 chr7D 86.395 441 15 9 422 827 1420054 1419624 1.280000e-119 440.0
11 TraesCS4A01G496500 chr6B 84.345 939 122 13 998 1936 620283980 620283067 0.000000e+00 896.0
12 TraesCS4A01G496500 chr6B 84.454 714 108 3 2266 2977 620281941 620281229 0.000000e+00 701.0
13 TraesCS4A01G496500 chr6A 83.755 948 113 22 998 1936 557921315 557920400 0.000000e+00 859.0
14 TraesCS4A01G496500 chr6A 83.636 935 126 13 998 1929 557402224 557401314 0.000000e+00 854.0
15 TraesCS4A01G496500 chr6A 84.174 714 110 3 2266 2977 557792949 557792237 0.000000e+00 689.0
16 TraesCS4A01G496500 chr6A 83.239 710 114 4 2272 2977 557398597 557397889 0.000000e+00 647.0
17 TraesCS4A01G496500 chr6D 83.631 953 115 18 995 1944 412180331 412179417 0.000000e+00 857.0
18 TraesCS4A01G496500 chr6D 82.821 943 132 16 998 1936 412626533 412627449 0.000000e+00 817.0
19 TraesCS4A01G496500 chr6D 84.841 818 106 10 1115 1929 412010402 412009600 0.000000e+00 808.0
20 TraesCS4A01G496500 chr6D 85.434 714 101 3 2266 2977 412628585 412629297 0.000000e+00 739.0
21 TraesCS4A01G496500 chr6D 83.333 714 107 6 2266 2977 412178599 412177896 0.000000e+00 649.0
22 TraesCS4A01G496500 chr6D 82.817 710 117 3 2272 2977 412006679 412005971 7.100000e-177 630.0
23 TraesCS4A01G496500 chr3B 93.294 343 19 1 1 339 661743439 661743097 1.610000e-138 503.0
24 TraesCS4A01G496500 chr3B 92.711 343 21 1 1 339 661776469 661776127 3.490000e-135 492.0
25 TraesCS4A01G496500 chr2B 93.023 344 23 1 1 343 67074759 67075102 5.810000e-138 501.0
26 TraesCS4A01G496500 chr2B 93.023 344 19 1 1 339 484608759 484608416 7.510000e-137 497.0
27 TraesCS4A01G496500 chr2B 91.837 49 2 2 892 940 5847115 5847161 2.510000e-07 67.6
28 TraesCS4A01G496500 chr7B 92.982 342 24 0 1 342 26027755 26028096 2.090000e-137 499.0
29 TraesCS4A01G496500 chr7B 93.333 45 3 0 894 938 191632411 191632455 2.510000e-07 67.6
30 TraesCS4A01G496500 chr1D 92.982 342 23 1 1 342 13469263 13469603 7.510000e-137 497.0
31 TraesCS4A01G496500 chr5B 92.920 339 24 0 1 339 303587805 303587467 9.710000e-136 494.0
32 TraesCS4A01G496500 chr1B 92.625 339 25 0 1 339 531871491 531871829 4.520000e-134 488.0
33 TraesCS4A01G496500 chr7A 90.385 52 5 0 894 945 103006553 103006604 6.980000e-08 69.4
34 TraesCS4A01G496500 chr7A 91.667 48 3 1 893 940 243266896 243266942 9.030000e-07 65.8
35 TraesCS4A01G496500 chr5D 93.478 46 3 0 893 938 563120487 563120532 6.980000e-08 69.4
36 TraesCS4A01G496500 chr5A 87.500 56 5 2 890 945 434615697 434615644 3.250000e-06 63.9
37 TraesCS4A01G496500 chr3A 89.796 49 3 2 890 938 703715546 703715592 1.170000e-05 62.1
38 TraesCS4A01G496500 chr2A 89.796 49 3 2 890 938 96775324 96775370 1.170000e-05 62.1


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 TraesCS4A01G496500 chr4A 742889714 742893605 3891 False 7188.0 7188 100.000000 1 3892 1 chr4A.!!$F1 3891
1 TraesCS4A01G496500 chr4A 743866870 743869710 2840 False 1471.0 2682 92.550667 1015 3892 3 chr4A.!!$F2 2877
2 TraesCS4A01G496500 chrUn 295470456 295472146 1690 False 2726.0 2726 95.765000 2199 3892 1 chrUn.!!$F2 1693
3 TraesCS4A01G496500 chrUn 292914260 292915494 1234 False 1535.0 1535 89.225000 939 2199 1 chrUn.!!$F1 1260
4 TraesCS4A01G496500 chr7D 1412806 1414523 1717 True 2545.0 2545 93.627000 2195 3892 1 chr7D.!!$R1 1697
5 TraesCS4A01G496500 chr7D 1418586 1420054 1468 True 930.5 1421 89.583000 422 1929 2 chr7D.!!$R3 1507
6 TraesCS4A01G496500 chr6B 620281229 620283980 2751 True 798.5 896 84.399500 998 2977 2 chr6B.!!$R1 1979
7 TraesCS4A01G496500 chr6A 557920400 557921315 915 True 859.0 859 83.755000 998 1936 1 chr6A.!!$R2 938
8 TraesCS4A01G496500 chr6A 557397889 557402224 4335 True 750.5 854 83.437500 998 2977 2 chr6A.!!$R3 1979
9 TraesCS4A01G496500 chr6A 557792237 557792949 712 True 689.0 689 84.174000 2266 2977 1 chr6A.!!$R1 711
10 TraesCS4A01G496500 chr6D 412626533 412629297 2764 False 778.0 817 84.127500 998 2977 2 chr6D.!!$F1 1979
11 TraesCS4A01G496500 chr6D 412177896 412180331 2435 True 753.0 857 83.482000 995 2977 2 chr6D.!!$R2 1982
12 TraesCS4A01G496500 chr6D 412005971 412010402 4431 True 719.0 808 83.829000 1115 2977 2 chr6D.!!$R1 1862

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
659 673 0.036105 TGTCCAATCTGAGCACGCAT 60.036 50.000 0.0 0.0 0.00 4.73 F
938 976 0.523072 GCACGGGTTGACGACTAGTA 59.477 55.000 0.0 0.0 37.61 1.82 F
939 977 1.133790 GCACGGGTTGACGACTAGTAT 59.866 52.381 0.0 0.0 37.61 2.12 F
982 1020 1.582502 GTCTGTTGTAGATACGCACGC 59.417 52.381 0.0 0.0 37.83 5.34 F
1830 1892 1.680735 AGAGATGGAGATGACGAGCAC 59.319 52.381 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1730 0.251253 ACGACGAAGGGAAGAGGTCT 60.251 55.000 0.00 0.00 0.00 3.85 R
2101 2974 0.326264 AAGGGTGTGGCTAGCTCTTG 59.674 55.000 15.72 0.00 0.00 3.02 R
2646 7292 1.153289 CCATGCCTCTCAAGTCGGG 60.153 63.158 0.00 0.00 0.00 5.14 R
2843 7489 3.219281 ACGCACAAATAGGTTGACCTTT 58.781 40.909 8.18 0.00 46.09 3.11 R
2989 7646 1.538047 AAACTACGGAGTGCGTAGGA 58.462 50.000 36.77 12.83 45.73 2.94 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
25 26 2.269241 GCCGAACAGGGGAGGAAG 59.731 66.667 0.00 0.00 41.48 3.46
26 27 2.990479 CCGAACAGGGGAGGAAGG 59.010 66.667 0.00 0.00 35.97 3.46
27 28 2.670148 CCGAACAGGGGAGGAAGGG 61.670 68.421 0.00 0.00 35.97 3.95
28 29 1.612442 CGAACAGGGGAGGAAGGGA 60.612 63.158 0.00 0.00 0.00 4.20
29 30 1.900545 CGAACAGGGGAGGAAGGGAC 61.901 65.000 0.00 0.00 0.00 4.46
30 31 1.900545 GAACAGGGGAGGAAGGGACG 61.901 65.000 0.00 0.00 0.00 4.79
31 32 3.787001 CAGGGGAGGAAGGGACGC 61.787 72.222 0.00 0.00 0.00 5.19
36 37 4.388499 GAGGAAGGGACGCGCCAA 62.388 66.667 18.87 0.00 38.95 4.52
37 38 3.894547 GAGGAAGGGACGCGCCAAA 62.895 63.158 18.87 0.00 38.95 3.28
38 39 2.750237 GGAAGGGACGCGCCAAAT 60.750 61.111 18.87 6.36 38.95 2.32
39 40 2.761195 GGAAGGGACGCGCCAAATC 61.761 63.158 18.87 13.22 38.95 2.17
40 41 3.095898 GAAGGGACGCGCCAAATCG 62.096 63.158 18.87 0.00 38.95 3.34
50 51 3.418913 CCAAATCGCGCACACCGA 61.419 61.111 8.75 0.00 40.02 4.69
51 52 2.202171 CAAATCGCGCACACCGAC 60.202 61.111 8.75 0.00 40.02 4.79
52 53 3.419759 AAATCGCGCACACCGACC 61.420 61.111 8.75 0.00 40.02 4.79
60 61 4.805231 CACACCGACCGCCGCATA 62.805 66.667 0.00 0.00 36.84 3.14
61 62 4.071875 ACACCGACCGCCGCATAA 62.072 61.111 0.00 0.00 36.84 1.90
62 63 3.261951 CACCGACCGCCGCATAAG 61.262 66.667 0.00 0.00 36.84 1.73
64 65 4.891727 CCGACCGCCGCATAAGCT 62.892 66.667 0.00 0.00 39.10 3.74
65 66 3.630148 CGACCGCCGCATAAGCTG 61.630 66.667 0.00 0.00 39.10 4.24
91 92 4.404098 GGCCAACGACCACCGGAT 62.404 66.667 9.46 0.00 43.93 4.18
92 93 2.818274 GCCAACGACCACCGGATC 60.818 66.667 9.46 1.08 43.93 3.36
93 94 2.125269 CCAACGACCACCGGATCC 60.125 66.667 9.46 0.00 43.93 3.36
94 95 2.508439 CAACGACCACCGGATCCG 60.508 66.667 27.65 27.65 43.93 4.18
127 128 3.006728 GGGACACCGGATCCACCA 61.007 66.667 24.72 0.00 38.06 4.17
128 129 2.267961 GGACACCGGATCCACCAC 59.732 66.667 20.46 0.00 38.90 4.16
129 130 2.267961 GACACCGGATCCACCACC 59.732 66.667 9.46 0.00 38.90 4.61
130 131 3.325201 GACACCGGATCCACCACCC 62.325 68.421 9.46 0.00 38.90 4.61
131 132 4.467084 CACCGGATCCACCACCCG 62.467 72.222 9.46 0.00 42.64 5.28
142 143 4.690719 CCACCCGCACGGCTGTTA 62.691 66.667 2.83 0.00 33.26 2.41
143 144 3.118454 CACCCGCACGGCTGTTAG 61.118 66.667 2.83 0.00 33.26 2.34
153 154 3.892581 GCTGTTAGCCGGCCATGC 61.893 66.667 26.15 16.92 39.74 4.06
154 155 3.211963 CTGTTAGCCGGCCATGCC 61.212 66.667 26.15 7.58 46.75 4.40
163 164 2.188469 GGCCATGCCTTGCCAATG 59.812 61.111 0.00 0.00 46.69 2.82
164 165 2.188469 GCCATGCCTTGCCAATGG 59.812 61.111 0.00 0.00 35.59 3.16
165 166 2.360767 GCCATGCCTTGCCAATGGA 61.361 57.895 2.05 0.00 34.46 3.41
166 167 1.820581 CCATGCCTTGCCAATGGAG 59.179 57.895 2.05 0.00 34.46 3.86
167 168 1.143183 CATGCCTTGCCAATGGAGC 59.857 57.895 2.05 0.00 0.00 4.70
168 169 2.062177 ATGCCTTGCCAATGGAGCC 61.062 57.895 2.05 0.00 0.00 4.70
169 170 3.830192 GCCTTGCCAATGGAGCCG 61.830 66.667 2.05 0.00 0.00 5.52
170 171 3.830192 CCTTGCCAATGGAGCCGC 61.830 66.667 2.05 0.00 0.00 6.53
171 172 2.753043 CTTGCCAATGGAGCCGCT 60.753 61.111 2.05 0.00 0.00 5.52
172 173 3.060020 CTTGCCAATGGAGCCGCTG 62.060 63.158 2.05 0.00 0.00 5.18
183 184 4.166888 GCCGCTGCTCCAGATCCA 62.167 66.667 0.00 0.00 32.44 3.41
184 185 2.108566 CCGCTGCTCCAGATCCAG 59.891 66.667 0.00 0.00 32.44 3.86
185 186 2.108566 CGCTGCTCCAGATCCAGG 59.891 66.667 0.00 0.00 32.44 4.45
186 187 2.509916 GCTGCTCCAGATCCAGGG 59.490 66.667 2.24 0.00 32.44 4.45
187 188 2.373707 GCTGCTCCAGATCCAGGGT 61.374 63.158 2.24 0.00 32.44 4.34
188 189 1.919600 GCTGCTCCAGATCCAGGGTT 61.920 60.000 2.24 0.00 32.44 4.11
189 190 0.179936 CTGCTCCAGATCCAGGGTTC 59.820 60.000 2.24 0.00 32.44 3.62
190 191 1.274703 TGCTCCAGATCCAGGGTTCC 61.275 60.000 2.24 0.00 0.00 3.62
191 192 1.826024 CTCCAGATCCAGGGTTCCG 59.174 63.158 2.24 0.00 0.00 4.30
192 193 2.190578 CCAGATCCAGGGTTCCGC 59.809 66.667 0.00 0.00 0.00 5.54
193 194 2.669133 CCAGATCCAGGGTTCCGCA 61.669 63.158 0.00 0.00 0.00 5.69
194 195 1.450312 CAGATCCAGGGTTCCGCAC 60.450 63.158 0.00 0.00 0.00 5.34
195 196 1.918293 AGATCCAGGGTTCCGCACA 60.918 57.895 0.00 0.00 0.00 4.57
196 197 1.745489 GATCCAGGGTTCCGCACAC 60.745 63.158 0.00 0.00 0.00 3.82
197 198 2.463589 GATCCAGGGTTCCGCACACA 62.464 60.000 0.00 0.00 0.00 3.72
198 199 1.852157 ATCCAGGGTTCCGCACACAT 61.852 55.000 0.00 0.00 0.00 3.21
199 200 2.334946 CCAGGGTTCCGCACACATG 61.335 63.158 0.00 0.00 0.00 3.21
200 201 1.302431 CAGGGTTCCGCACACATGA 60.302 57.895 0.00 0.00 0.00 3.07
201 202 1.003355 AGGGTTCCGCACACATGAG 60.003 57.895 0.00 0.00 0.00 2.90
202 203 2.690778 GGGTTCCGCACACATGAGC 61.691 63.158 0.00 0.00 0.00 4.26
203 204 1.965930 GGTTCCGCACACATGAGCA 60.966 57.895 0.00 0.00 0.00 4.26
204 205 1.499056 GTTCCGCACACATGAGCAG 59.501 57.895 0.00 0.00 0.00 4.24
205 206 1.672030 TTCCGCACACATGAGCAGG 60.672 57.895 0.00 6.86 0.00 4.85
206 207 3.129502 CCGCACACATGAGCAGGG 61.130 66.667 0.00 0.00 0.00 4.45
207 208 3.807538 CGCACACATGAGCAGGGC 61.808 66.667 0.00 0.00 0.00 5.19
208 209 2.674033 GCACACATGAGCAGGGCA 60.674 61.111 0.00 0.00 0.00 5.36
209 210 2.270257 GCACACATGAGCAGGGCAA 61.270 57.895 0.00 0.00 0.00 4.52
210 211 1.582968 CACACATGAGCAGGGCAAC 59.417 57.895 0.00 0.00 0.00 4.17
234 235 3.861797 CCCGCCGCTACCATCCTT 61.862 66.667 0.00 0.00 0.00 3.36
235 236 2.588877 CCGCCGCTACCATCCTTG 60.589 66.667 0.00 0.00 0.00 3.61
291 292 4.548513 CGAGGGAGGGAGGAGGGG 62.549 77.778 0.00 0.00 0.00 4.79
292 293 3.036959 GAGGGAGGGAGGAGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
293 294 3.039526 AGGGAGGGAGGAGGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
294 295 4.179599 GGGAGGGAGGAGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
295 296 4.179599 GGAGGGAGGAGGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
296 297 4.179599 GAGGGAGGAGGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
299 300 4.825679 GGAGGAGGGGAGGGGGTG 62.826 77.778 0.00 0.00 0.00 4.61
300 301 3.695825 GAGGAGGGGAGGGGGTGA 61.696 72.222 0.00 0.00 0.00 4.02
301 302 3.700350 AGGAGGGGAGGGGGTGAG 61.700 72.222 0.00 0.00 0.00 3.51
302 303 4.825679 GGAGGGGAGGGGGTGAGG 62.826 77.778 0.00 0.00 0.00 3.86
303 304 3.695825 GAGGGGAGGGGGTGAGGA 61.696 72.222 0.00 0.00 0.00 3.71
304 305 3.700350 AGGGGAGGGGGTGAGGAG 61.700 72.222 0.00 0.00 0.00 3.69
305 306 4.825679 GGGGAGGGGGTGAGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
306 307 3.695825 GGGAGGGGGTGAGGAGGA 61.696 72.222 0.00 0.00 0.00 3.71
307 308 2.041405 GGAGGGGGTGAGGAGGAG 60.041 72.222 0.00 0.00 0.00 3.69
308 309 2.041405 GAGGGGGTGAGGAGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
309 310 3.700350 AGGGGGTGAGGAGGAGGG 61.700 72.222 0.00 0.00 0.00 4.30
310 311 4.825679 GGGGGTGAGGAGGAGGGG 62.826 77.778 0.00 0.00 0.00 4.79
316 317 4.541648 GAGGAGGAGGGGCGGCTA 62.542 72.222 9.56 0.00 0.00 3.93
317 318 4.548513 AGGAGGAGGGGCGGCTAG 62.549 72.222 9.56 0.00 0.00 3.42
322 323 4.176752 GAGGGGCGGCTAGGGTTG 62.177 72.222 9.56 0.00 0.00 3.77
326 327 4.176752 GGCGGCTAGGGTTGGGAG 62.177 72.222 0.00 0.00 0.00 4.30
327 328 4.176752 GCGGCTAGGGTTGGGAGG 62.177 72.222 0.00 0.00 0.00 4.30
328 329 2.365105 CGGCTAGGGTTGGGAGGA 60.365 66.667 0.00 0.00 0.00 3.71
329 330 2.435693 CGGCTAGGGTTGGGAGGAG 61.436 68.421 0.00 0.00 0.00 3.69
330 331 2.073101 GGCTAGGGTTGGGAGGAGG 61.073 68.421 0.00 0.00 0.00 4.30
331 332 1.003051 GCTAGGGTTGGGAGGAGGA 59.997 63.158 0.00 0.00 0.00 3.71
332 333 1.051556 GCTAGGGTTGGGAGGAGGAG 61.052 65.000 0.00 0.00 0.00 3.69
333 334 0.399233 CTAGGGTTGGGAGGAGGAGG 60.399 65.000 0.00 0.00 0.00 4.30
334 335 2.547123 TAGGGTTGGGAGGAGGAGGC 62.547 65.000 0.00 0.00 0.00 4.70
335 336 3.787001 GGTTGGGAGGAGGAGGCG 61.787 72.222 0.00 0.00 0.00 5.52
336 337 3.787001 GTTGGGAGGAGGAGGCGG 61.787 72.222 0.00 0.00 0.00 6.13
340 341 4.851214 GGAGGAGGAGGCGGCTCT 62.851 72.222 34.35 22.03 0.00 4.09
341 342 3.535962 GAGGAGGAGGCGGCTCTG 61.536 72.222 34.35 0.00 0.00 3.35
342 343 4.390556 AGGAGGAGGCGGCTCTGT 62.391 66.667 34.35 23.60 0.00 3.41
343 344 2.442272 GGAGGAGGCGGCTCTGTA 60.442 66.667 34.35 0.00 0.00 2.74
344 345 2.787567 GGAGGAGGCGGCTCTGTAC 61.788 68.421 34.35 21.04 0.00 2.90
345 346 2.037367 AGGAGGCGGCTCTGTACA 59.963 61.111 34.35 0.00 0.00 2.90
346 347 1.381872 AGGAGGCGGCTCTGTACAT 60.382 57.895 34.35 13.70 0.00 2.29
347 348 0.978146 AGGAGGCGGCTCTGTACATT 60.978 55.000 34.35 11.77 0.00 2.71
348 349 0.750850 GGAGGCGGCTCTGTACATTA 59.249 55.000 34.35 0.00 0.00 1.90
349 350 1.344763 GGAGGCGGCTCTGTACATTAT 59.655 52.381 34.35 0.00 0.00 1.28
350 351 2.224305 GGAGGCGGCTCTGTACATTATT 60.224 50.000 34.35 0.00 0.00 1.40
351 352 3.467803 GAGGCGGCTCTGTACATTATTT 58.532 45.455 30.02 0.00 0.00 1.40
352 353 4.502604 GGAGGCGGCTCTGTACATTATTTA 60.503 45.833 34.35 0.00 0.00 1.40
353 354 5.031066 AGGCGGCTCTGTACATTATTTAA 57.969 39.130 5.25 0.00 0.00 1.52
354 355 5.621193 AGGCGGCTCTGTACATTATTTAAT 58.379 37.500 5.25 0.00 0.00 1.40
355 356 6.765403 AGGCGGCTCTGTACATTATTTAATA 58.235 36.000 5.25 0.00 0.00 0.98
356 357 6.649557 AGGCGGCTCTGTACATTATTTAATAC 59.350 38.462 5.25 0.00 0.00 1.89
357 358 6.425721 GGCGGCTCTGTACATTATTTAATACA 59.574 38.462 0.00 0.00 0.00 2.29
358 359 7.119262 GGCGGCTCTGTACATTATTTAATACAT 59.881 37.037 0.00 0.00 0.00 2.29
359 360 9.146984 GCGGCTCTGTACATTATTTAATACATA 57.853 33.333 0.00 0.00 0.00 2.29
381 382 9.308000 ACATAGGGAATTTGAGTATTTTTGACA 57.692 29.630 0.00 0.00 0.00 3.58
382 383 9.573133 CATAGGGAATTTGAGTATTTTTGACAC 57.427 33.333 0.00 0.00 0.00 3.67
383 384 7.595819 AGGGAATTTGAGTATTTTTGACACA 57.404 32.000 0.00 0.00 0.00 3.72
384 385 8.017418 AGGGAATTTGAGTATTTTTGACACAA 57.983 30.769 0.00 0.00 0.00 3.33
385 386 8.482128 AGGGAATTTGAGTATTTTTGACACAAA 58.518 29.630 0.00 0.00 40.19 2.83
386 387 9.271828 GGGAATTTGAGTATTTTTGACACAAAT 57.728 29.630 5.02 5.02 44.61 2.32
390 391 9.927668 ATTTGAGTATTTTTGACACAAATAGGG 57.072 29.630 6.96 0.00 42.49 3.53
391 392 8.698973 TTGAGTATTTTTGACACAAATAGGGA 57.301 30.769 6.96 0.00 28.77 4.20
392 393 8.877864 TGAGTATTTTTGACACAAATAGGGAT 57.122 30.769 6.96 0.00 28.77 3.85
393 394 9.967451 TGAGTATTTTTGACACAAATAGGGATA 57.033 29.630 6.96 0.00 28.77 2.59
395 396 9.747898 AGTATTTTTGACACAAATAGGGATACA 57.252 29.630 6.96 0.00 39.74 2.29
398 399 7.825331 TTTTGACACAAATAGGGATACAACA 57.175 32.000 0.00 0.00 39.74 3.33
399 400 8.415950 TTTTGACACAAATAGGGATACAACAT 57.584 30.769 0.00 0.00 39.74 2.71
400 401 9.521841 TTTTGACACAAATAGGGATACAACATA 57.478 29.630 0.00 0.00 39.74 2.29
401 402 9.693739 TTTGACACAAATAGGGATACAACATAT 57.306 29.630 0.00 0.00 39.74 1.78
402 403 8.675705 TGACACAAATAGGGATACAACATATG 57.324 34.615 0.00 0.00 39.74 1.78
403 404 7.719193 TGACACAAATAGGGATACAACATATGG 59.281 37.037 7.80 0.00 39.74 2.74
404 405 7.582719 ACACAAATAGGGATACAACATATGGT 58.417 34.615 7.80 0.00 39.74 3.55
405 406 8.719596 ACACAAATAGGGATACAACATATGGTA 58.280 33.333 7.80 0.99 39.74 3.25
406 407 9.567776 CACAAATAGGGATACAACATATGGTAA 57.432 33.333 7.80 0.00 39.74 2.85
407 408 9.793259 ACAAATAGGGATACAACATATGGTAAG 57.207 33.333 7.80 0.00 39.74 2.34
408 409 8.730680 CAAATAGGGATACAACATATGGTAAGC 58.269 37.037 7.80 0.00 39.74 3.09
409 410 5.904984 AGGGATACAACATATGGTAAGCA 57.095 39.130 7.80 0.00 39.74 3.91
410 411 6.454223 AGGGATACAACATATGGTAAGCAT 57.546 37.500 7.80 0.00 39.74 3.79
411 412 6.852404 AGGGATACAACATATGGTAAGCATT 58.148 36.000 7.80 0.00 39.74 3.56
412 413 6.942576 AGGGATACAACATATGGTAAGCATTC 59.057 38.462 7.80 0.00 39.74 2.67
413 414 6.942576 GGGATACAACATATGGTAAGCATTCT 59.057 38.462 7.80 0.00 39.74 2.40
414 415 8.100791 GGGATACAACATATGGTAAGCATTCTA 58.899 37.037 7.80 0.00 39.74 2.10
415 416 9.502091 GGATACAACATATGGTAAGCATTCTAA 57.498 33.333 7.80 0.00 0.00 2.10
417 418 7.246674 ACAACATATGGTAAGCATTCTAACG 57.753 36.000 7.80 0.00 0.00 3.18
418 419 6.821665 ACAACATATGGTAAGCATTCTAACGT 59.178 34.615 7.80 0.00 0.00 3.99
419 420 7.011109 ACAACATATGGTAAGCATTCTAACGTC 59.989 37.037 7.80 0.00 0.00 4.34
420 421 6.578944 ACATATGGTAAGCATTCTAACGTCA 58.421 36.000 7.80 0.00 0.00 4.35
439 440 4.083003 CGTCATTTAGTTGGGCTTAAAGCA 60.083 41.667 0.00 0.00 44.75 3.91
440 441 5.393027 CGTCATTTAGTTGGGCTTAAAGCAT 60.393 40.000 0.00 0.00 44.75 3.79
463 464 7.469043 GCATCTATGACATTTGCAGGTTATGAA 60.469 37.037 10.92 0.00 33.58 2.57
464 465 8.573885 CATCTATGACATTTGCAGGTTATGAAT 58.426 33.333 0.00 4.14 0.00 2.57
565 579 7.776030 TGGACTTTAAGAACATCACCAAAGTAA 59.224 33.333 0.00 0.00 36.60 2.24
611 625 9.574516 AGAGTGTTCTGTTTATTAGGTTTTCAT 57.425 29.630 0.00 0.00 30.72 2.57
659 673 0.036105 TGTCCAATCTGAGCACGCAT 60.036 50.000 0.00 0.00 0.00 4.73
672 686 1.798223 GCACGCATGTTGTACTCTCAA 59.202 47.619 0.00 0.00 0.00 3.02
741 779 2.098614 TGTTTGTGCACATGGTGAGTT 58.901 42.857 22.39 0.00 35.23 3.01
751 789 2.362077 ACATGGTGAGTTCTTGCCAAAC 59.638 45.455 0.00 0.00 34.39 2.93
758 796 4.154195 GTGAGTTCTTGCCAAACGACATAT 59.846 41.667 0.00 0.00 0.00 1.78
759 797 5.350365 GTGAGTTCTTGCCAAACGACATATA 59.650 40.000 0.00 0.00 0.00 0.86
763 801 7.250569 AGTTCTTGCCAAACGACATATAATTG 58.749 34.615 0.00 0.00 0.00 2.32
769 807 8.627487 TGCCAAACGACATATAATTGATTTTC 57.373 30.769 0.00 0.00 0.00 2.29
836 874 9.788960 AACAGAAGAATGTTAAAAGAAGTGTTC 57.211 29.630 0.00 0.00 41.53 3.18
837 875 9.178758 ACAGAAGAATGTTAAAAGAAGTGTTCT 57.821 29.630 0.00 0.00 43.15 3.01
838 876 9.657121 CAGAAGAATGTTAAAAGAAGTGTTCTC 57.343 33.333 0.00 0.00 39.61 2.87
839 877 9.396022 AGAAGAATGTTAAAAGAAGTGTTCTCA 57.604 29.630 0.00 0.00 39.61 3.27
852 890 9.495572 AAGAAGTGTTCTCAATTAAAGACTAGG 57.504 33.333 0.00 0.00 39.61 3.02
853 891 7.604545 AGAAGTGTTCTCAATTAAAGACTAGGC 59.395 37.037 0.00 0.00 34.07 3.93
854 892 7.010339 AGTGTTCTCAATTAAAGACTAGGCT 57.990 36.000 0.00 0.00 28.24 4.58
855 893 8.135382 AGTGTTCTCAATTAAAGACTAGGCTA 57.865 34.615 0.00 0.00 28.24 3.93
856 894 8.763601 AGTGTTCTCAATTAAAGACTAGGCTAT 58.236 33.333 0.00 0.00 28.24 2.97
892 930 9.838975 CTACTCATGTTTATAAAAATGTGTGCA 57.161 29.630 29.61 18.31 39.41 4.57
911 949 9.353999 TGTGTGCATATTAATAATACTAGCTCG 57.646 33.333 0.00 0.00 0.00 5.03
912 950 9.355215 GTGTGCATATTAATAATACTAGCTCGT 57.645 33.333 0.00 0.00 0.00 4.18
913 951 9.353999 TGTGCATATTAATAATACTAGCTCGTG 57.646 33.333 0.22 0.00 0.00 4.35
914 952 8.321716 GTGCATATTAATAATACTAGCTCGTGC 58.678 37.037 0.07 0.07 40.05 5.34
915 953 8.032451 TGCATATTAATAATACTAGCTCGTGCA 58.968 33.333 12.58 8.64 42.74 4.57
916 954 8.869897 GCATATTAATAATACTAGCTCGTGCAA 58.130 33.333 12.58 0.00 42.74 4.08
919 957 7.694388 TTAATAATACTAGCTCGTGCAACTG 57.306 36.000 12.58 1.34 42.74 3.16
920 958 1.927895 ATACTAGCTCGTGCAACTGC 58.072 50.000 12.58 0.00 42.74 4.40
930 968 2.331451 GCAACTGCACGGGTTGAC 59.669 61.111 18.50 8.20 44.58 3.18
931 969 2.631428 CAACTGCACGGGTTGACG 59.369 61.111 10.89 0.00 44.58 4.35
932 970 1.885388 CAACTGCACGGGTTGACGA 60.885 57.895 10.89 0.00 44.58 4.20
933 971 1.885850 AACTGCACGGGTTGACGAC 60.886 57.895 0.00 0.00 37.61 4.34
934 972 2.029073 CTGCACGGGTTGACGACT 59.971 61.111 0.00 0.00 37.61 4.18
935 973 1.287815 CTGCACGGGTTGACGACTA 59.712 57.895 0.00 0.00 37.61 2.59
936 974 0.732880 CTGCACGGGTTGACGACTAG 60.733 60.000 0.00 0.00 37.61 2.57
937 975 1.288127 GCACGGGTTGACGACTAGT 59.712 57.895 0.00 0.00 37.61 2.57
938 976 0.523072 GCACGGGTTGACGACTAGTA 59.477 55.000 0.00 0.00 37.61 1.82
939 977 1.133790 GCACGGGTTGACGACTAGTAT 59.866 52.381 0.00 0.00 37.61 2.12
940 978 2.355756 GCACGGGTTGACGACTAGTATA 59.644 50.000 0.00 0.00 37.61 1.47
941 979 3.181497 GCACGGGTTGACGACTAGTATAA 60.181 47.826 0.00 0.00 37.61 0.98
942 980 4.675146 GCACGGGTTGACGACTAGTATAAA 60.675 45.833 0.00 0.00 37.61 1.40
943 981 5.585390 CACGGGTTGACGACTAGTATAAAT 58.415 41.667 0.00 0.00 37.61 1.40
979 1017 3.692593 TGCTAGTCTGTTGTAGATACGCA 59.307 43.478 0.00 0.00 37.83 5.24
980 1018 4.036352 GCTAGTCTGTTGTAGATACGCAC 58.964 47.826 0.00 0.00 37.83 5.34
981 1019 3.132629 AGTCTGTTGTAGATACGCACG 57.867 47.619 0.00 0.00 37.83 5.34
982 1020 1.582502 GTCTGTTGTAGATACGCACGC 59.417 52.381 0.00 0.00 37.83 5.34
1584 1634 1.802960 GAGTTCGTGACAGACTCGGTA 59.197 52.381 0.53 0.00 36.37 4.02
1680 1730 5.291858 CCTGTCATCGATTTTTGATCTTCGA 59.708 40.000 0.00 0.00 43.82 3.71
1830 1892 1.680735 AGAGATGGAGATGACGAGCAC 59.319 52.381 0.00 0.00 0.00 4.40
2013 2253 2.710377 TGCATTTAGATCCGTGCAGTT 58.290 42.857 7.55 0.00 42.13 3.16
2014 2254 3.081061 TGCATTTAGATCCGTGCAGTTT 58.919 40.909 7.55 0.00 42.13 2.66
2015 2255 3.505680 TGCATTTAGATCCGTGCAGTTTT 59.494 39.130 7.55 0.00 42.13 2.43
2016 2256 4.022416 TGCATTTAGATCCGTGCAGTTTTT 60.022 37.500 7.55 0.00 42.13 1.94
2101 2974 8.882415 TTGATTAAATCCCAGTCGACTAATAC 57.118 34.615 19.57 7.41 0.00 1.89
2230 6782 9.917887 TCTCTACTACTAATAGTTTTACAGCCT 57.082 33.333 0.00 0.00 41.99 4.58
2404 7050 1.743321 GCTCTCGCAGGACAGGCTAT 61.743 60.000 0.00 0.00 35.78 2.97
2416 7062 4.079096 AGGACAGGCTATAGTACAAGAGGT 60.079 45.833 0.84 0.00 0.00 3.85
2646 7292 2.654877 TCGAAGGCGAGGGTGTTC 59.345 61.111 0.00 0.00 42.51 3.18
2717 7363 1.864669 GGATTTGCCCTGGGATTGAA 58.135 50.000 19.27 4.94 0.00 2.69
2843 7489 0.605589 TCGGAGTCACTGCTCGAAGA 60.606 55.000 0.00 0.00 36.41 2.87
2910 7562 6.815089 AGATGAATTACACTTGCAAAACCAA 58.185 32.000 0.00 0.00 0.00 3.67
2989 7646 9.185680 GTATTTGTATCAAACCCCAAGAATACT 57.814 33.333 0.00 0.00 0.00 2.12
2999 7656 2.431057 CCCAAGAATACTCCTACGCACT 59.569 50.000 0.00 0.00 0.00 4.40
3501 8163 2.608261 CCTCACCTCGAACTGTTCAGAC 60.608 54.545 19.56 0.00 0.00 3.51
3581 8243 3.878086 TCATGCGAACAAGACAGAAAC 57.122 42.857 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.760047 CCTCCCCTGTTCGGCGTG 62.760 72.222 6.85 0.00 0.00 5.34
7 8 3.665675 CTTCCTCCCCTGTTCGGCG 62.666 68.421 0.00 0.00 0.00 6.46
8 9 2.269241 CTTCCTCCCCTGTTCGGC 59.731 66.667 0.00 0.00 0.00 5.54
9 10 2.670148 CCCTTCCTCCCCTGTTCGG 61.670 68.421 0.00 0.00 0.00 4.30
10 11 1.612442 TCCCTTCCTCCCCTGTTCG 60.612 63.158 0.00 0.00 0.00 3.95
11 12 1.900545 CGTCCCTTCCTCCCCTGTTC 61.901 65.000 0.00 0.00 0.00 3.18
12 13 1.918800 CGTCCCTTCCTCCCCTGTT 60.919 63.158 0.00 0.00 0.00 3.16
13 14 2.284699 CGTCCCTTCCTCCCCTGT 60.285 66.667 0.00 0.00 0.00 4.00
14 15 3.787001 GCGTCCCTTCCTCCCCTG 61.787 72.222 0.00 0.00 0.00 4.45
19 20 3.894547 TTTGGCGCGTCCCTTCCTC 62.895 63.158 8.89 0.00 0.00 3.71
20 21 3.268103 ATTTGGCGCGTCCCTTCCT 62.268 57.895 8.89 0.00 0.00 3.36
21 22 2.750237 ATTTGGCGCGTCCCTTCC 60.750 61.111 8.89 0.00 0.00 3.46
22 23 2.791927 GATTTGGCGCGTCCCTTC 59.208 61.111 8.89 0.00 0.00 3.46
23 24 3.124921 CGATTTGGCGCGTCCCTT 61.125 61.111 8.89 0.00 0.00 3.95
33 34 3.418913 TCGGTGTGCGCGATTTGG 61.419 61.111 12.10 0.00 0.00 3.28
34 35 2.202171 GTCGGTGTGCGCGATTTG 60.202 61.111 12.10 0.00 0.00 2.32
35 36 3.419759 GGTCGGTGTGCGCGATTT 61.420 61.111 12.10 0.00 0.00 2.17
43 44 4.805231 TATGCGGCGGTCGGTGTG 62.805 66.667 9.78 0.00 39.69 3.82
44 45 4.071875 TTATGCGGCGGTCGGTGT 62.072 61.111 9.78 0.00 39.69 4.16
45 46 3.261951 CTTATGCGGCGGTCGGTG 61.262 66.667 9.78 0.00 39.69 4.94
47 48 4.891727 AGCTTATGCGGCGGTCGG 62.892 66.667 9.78 0.00 45.42 4.79
48 49 3.630148 CAGCTTATGCGGCGGTCG 61.630 66.667 9.78 0.00 45.42 4.79
57 58 3.945434 CGCCGGCAGCAGCTTATG 61.945 66.667 28.98 0.98 44.04 1.90
74 75 4.404098 ATCCGGTGGTCGTTGGCC 62.404 66.667 0.00 0.00 37.11 5.36
75 76 2.818274 GATCCGGTGGTCGTTGGC 60.818 66.667 0.00 0.00 37.11 4.52
76 77 2.125269 GGATCCGGTGGTCGTTGG 60.125 66.667 0.00 0.00 37.11 3.77
77 78 2.508439 CGGATCCGGTGGTCGTTG 60.508 66.667 26.95 0.00 37.11 4.10
110 111 3.006728 TGGTGGATCCGGTGTCCC 61.007 66.667 20.82 13.91 39.52 4.46
111 112 2.267961 GTGGTGGATCCGGTGTCC 59.732 66.667 18.08 18.08 39.52 4.02
112 113 2.267961 GGTGGTGGATCCGGTGTC 59.732 66.667 7.39 0.57 39.52 3.67
113 114 3.327404 GGGTGGTGGATCCGGTGT 61.327 66.667 7.39 0.00 39.52 4.16
114 115 4.467084 CGGGTGGTGGATCCGGTG 62.467 72.222 7.39 0.00 45.57 4.94
136 137 3.892581 GCATGGCCGGCTAACAGC 61.893 66.667 28.56 21.73 41.46 4.40
137 138 3.211963 GGCATGGCCGGCTAACAG 61.212 66.667 28.56 15.84 39.62 3.16
148 149 1.820581 CTCCATTGGCAAGGCATGG 59.179 57.895 6.33 8.80 39.17 3.66
149 150 1.143183 GCTCCATTGGCAAGGCATG 59.857 57.895 6.33 0.00 0.00 4.06
150 151 2.062177 GGCTCCATTGGCAAGGCAT 61.062 57.895 6.33 0.00 35.78 4.40
151 152 2.681064 GGCTCCATTGGCAAGGCA 60.681 61.111 6.33 0.00 35.78 4.75
152 153 3.830192 CGGCTCCATTGGCAAGGC 61.830 66.667 6.33 3.22 0.00 4.35
153 154 3.830192 GCGGCTCCATTGGCAAGG 61.830 66.667 5.96 5.28 0.00 3.61
154 155 2.753043 AGCGGCTCCATTGGCAAG 60.753 61.111 5.96 0.00 0.00 4.01
155 156 3.063704 CAGCGGCTCCATTGGCAA 61.064 61.111 0.68 0.68 0.00 4.52
166 167 4.166888 TGGATCTGGAGCAGCGGC 62.167 66.667 0.00 0.00 41.61 6.53
167 168 2.108566 CTGGATCTGGAGCAGCGG 59.891 66.667 0.00 0.00 0.00 5.52
168 169 2.108566 CCTGGATCTGGAGCAGCG 59.891 66.667 0.00 0.00 0.00 5.18
169 170 1.919600 AACCCTGGATCTGGAGCAGC 61.920 60.000 0.00 0.00 0.00 5.25
170 171 0.179936 GAACCCTGGATCTGGAGCAG 59.820 60.000 0.00 0.00 0.00 4.24
171 172 1.274703 GGAACCCTGGATCTGGAGCA 61.275 60.000 0.00 0.00 0.00 4.26
172 173 1.529309 GGAACCCTGGATCTGGAGC 59.471 63.158 0.00 0.00 0.00 4.70
173 174 1.826024 CGGAACCCTGGATCTGGAG 59.174 63.158 0.00 1.27 0.00 3.86
174 175 2.367202 GCGGAACCCTGGATCTGGA 61.367 63.158 0.00 0.00 0.00 3.86
175 176 2.190578 GCGGAACCCTGGATCTGG 59.809 66.667 0.00 0.00 0.00 3.86
176 177 1.450312 GTGCGGAACCCTGGATCTG 60.450 63.158 0.00 0.00 0.00 2.90
177 178 1.918293 TGTGCGGAACCCTGGATCT 60.918 57.895 0.00 0.00 0.00 2.75
178 179 1.745489 GTGTGCGGAACCCTGGATC 60.745 63.158 0.00 0.00 0.00 3.36
179 180 1.852157 ATGTGTGCGGAACCCTGGAT 61.852 55.000 0.00 0.00 0.00 3.41
180 181 2.525124 ATGTGTGCGGAACCCTGGA 61.525 57.895 0.00 0.00 0.00 3.86
181 182 2.034066 ATGTGTGCGGAACCCTGG 59.966 61.111 0.00 0.00 0.00 4.45
182 183 1.300971 CTCATGTGTGCGGAACCCTG 61.301 60.000 0.00 0.00 0.00 4.45
183 184 1.003355 CTCATGTGTGCGGAACCCT 60.003 57.895 0.00 0.00 0.00 4.34
184 185 2.690778 GCTCATGTGTGCGGAACCC 61.691 63.158 0.00 0.00 0.00 4.11
185 186 1.915614 CTGCTCATGTGTGCGGAACC 61.916 60.000 9.63 0.00 41.88 3.62
186 187 1.499056 CTGCTCATGTGTGCGGAAC 59.501 57.895 9.63 0.00 41.88 3.62
187 188 1.672030 CCTGCTCATGTGTGCGGAA 60.672 57.895 15.34 0.00 41.88 4.30
188 189 2.046988 CCTGCTCATGTGTGCGGA 60.047 61.111 15.34 0.00 41.88 5.54
189 190 3.129502 CCCTGCTCATGTGTGCGG 61.130 66.667 8.51 8.51 39.77 5.69
190 191 3.807538 GCCCTGCTCATGTGTGCG 61.808 66.667 0.00 0.00 37.35 5.34
191 192 2.270257 TTGCCCTGCTCATGTGTGC 61.270 57.895 0.00 0.40 35.32 4.57
192 193 1.582968 GTTGCCCTGCTCATGTGTG 59.417 57.895 0.00 0.00 0.00 3.82
193 194 1.604593 GGTTGCCCTGCTCATGTGT 60.605 57.895 0.00 0.00 0.00 3.72
194 195 2.693762 CGGTTGCCCTGCTCATGTG 61.694 63.158 0.00 0.00 0.00 3.21
195 196 2.360350 CGGTTGCCCTGCTCATGT 60.360 61.111 0.00 0.00 0.00 3.21
196 197 2.046023 TCGGTTGCCCTGCTCATG 60.046 61.111 0.00 0.00 0.00 3.07
197 198 2.270205 CTCGGTTGCCCTGCTCAT 59.730 61.111 0.00 0.00 0.00 2.90
198 199 4.020617 CCTCGGTTGCCCTGCTCA 62.021 66.667 0.00 0.00 0.00 4.26
217 218 3.861797 AAGGATGGTAGCGGCGGG 61.862 66.667 9.78 0.00 0.00 6.13
218 219 2.588877 CAAGGATGGTAGCGGCGG 60.589 66.667 9.78 0.00 0.00 6.13
219 220 2.588877 CCAAGGATGGTAGCGGCG 60.589 66.667 0.51 0.51 42.18 6.46
274 275 4.548513 CCCCTCCTCCCTCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
275 276 3.036959 TCCCCTCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
276 277 3.039526 CTCCCCTCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
277 278 4.179599 CCTCCCCTCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
278 279 4.179599 CCCTCCCCTCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
279 280 4.179599 CCCCTCCCCTCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
282 283 4.825679 CACCCCCTCCCCTCCTCC 62.826 77.778 0.00 0.00 0.00 4.30
283 284 3.695825 TCACCCCCTCCCCTCCTC 61.696 72.222 0.00 0.00 0.00 3.71
284 285 3.700350 CTCACCCCCTCCCCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
285 286 4.825679 CCTCACCCCCTCCCCTCC 62.826 77.778 0.00 0.00 0.00 4.30
286 287 3.695825 TCCTCACCCCCTCCCCTC 61.696 72.222 0.00 0.00 0.00 4.30
287 288 3.700350 CTCCTCACCCCCTCCCCT 61.700 72.222 0.00 0.00 0.00 4.79
288 289 4.825679 CCTCCTCACCCCCTCCCC 62.826 77.778 0.00 0.00 0.00 4.81
289 290 3.695825 TCCTCCTCACCCCCTCCC 61.696 72.222 0.00 0.00 0.00 4.30
290 291 2.041405 CTCCTCCTCACCCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
291 292 2.041405 CCTCCTCCTCACCCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
292 293 3.700350 CCCTCCTCCTCACCCCCT 61.700 72.222 0.00 0.00 0.00 4.79
293 294 4.825679 CCCCTCCTCCTCACCCCC 62.826 77.778 0.00 0.00 0.00 5.40
299 300 4.541648 TAGCCGCCCCTCCTCCTC 62.542 72.222 0.00 0.00 0.00 3.71
300 301 4.548513 CTAGCCGCCCCTCCTCCT 62.549 72.222 0.00 0.00 0.00 3.69
305 306 4.176752 CAACCCTAGCCGCCCCTC 62.177 72.222 0.00 0.00 0.00 4.30
309 310 4.176752 CTCCCAACCCTAGCCGCC 62.177 72.222 0.00 0.00 0.00 6.13
310 311 4.176752 CCTCCCAACCCTAGCCGC 62.177 72.222 0.00 0.00 0.00 6.53
311 312 2.365105 TCCTCCCAACCCTAGCCG 60.365 66.667 0.00 0.00 0.00 5.52
312 313 2.073101 CCTCCTCCCAACCCTAGCC 61.073 68.421 0.00 0.00 0.00 3.93
313 314 1.003051 TCCTCCTCCCAACCCTAGC 59.997 63.158 0.00 0.00 0.00 3.42
314 315 0.399233 CCTCCTCCTCCCAACCCTAG 60.399 65.000 0.00 0.00 0.00 3.02
315 316 1.710341 CCTCCTCCTCCCAACCCTA 59.290 63.158 0.00 0.00 0.00 3.53
316 317 2.456840 CCTCCTCCTCCCAACCCT 59.543 66.667 0.00 0.00 0.00 4.34
317 318 3.412408 GCCTCCTCCTCCCAACCC 61.412 72.222 0.00 0.00 0.00 4.11
318 319 3.787001 CGCCTCCTCCTCCCAACC 61.787 72.222 0.00 0.00 0.00 3.77
319 320 3.787001 CCGCCTCCTCCTCCCAAC 61.787 72.222 0.00 0.00 0.00 3.77
323 324 4.851214 AGAGCCGCCTCCTCCTCC 62.851 72.222 0.00 0.00 38.96 4.30
324 325 2.912987 TACAGAGCCGCCTCCTCCTC 62.913 65.000 0.00 0.00 38.96 3.71
325 326 2.997584 TACAGAGCCGCCTCCTCCT 61.998 63.158 0.00 0.00 38.96 3.69
326 327 2.442272 TACAGAGCCGCCTCCTCC 60.442 66.667 0.00 0.00 38.96 4.30
327 328 1.395826 ATGTACAGAGCCGCCTCCTC 61.396 60.000 0.33 0.00 38.96 3.71
328 329 0.978146 AATGTACAGAGCCGCCTCCT 60.978 55.000 0.33 0.00 38.96 3.69
329 330 0.750850 TAATGTACAGAGCCGCCTCC 59.249 55.000 0.33 0.00 38.96 4.30
330 331 2.821991 ATAATGTACAGAGCCGCCTC 57.178 50.000 0.33 0.00 38.42 4.70
331 332 3.560636 AAATAATGTACAGAGCCGCCT 57.439 42.857 0.33 0.00 0.00 5.52
332 333 5.941948 ATTAAATAATGTACAGAGCCGCC 57.058 39.130 0.33 0.00 0.00 6.13
333 334 7.416154 TGTATTAAATAATGTACAGAGCCGC 57.584 36.000 0.33 0.00 0.00 6.53
355 356 9.308000 TGTCAAAAATACTCAAATTCCCTATGT 57.692 29.630 0.00 0.00 0.00 2.29
356 357 9.573133 GTGTCAAAAATACTCAAATTCCCTATG 57.427 33.333 0.00 0.00 0.00 2.23
357 358 9.308000 TGTGTCAAAAATACTCAAATTCCCTAT 57.692 29.630 0.00 0.00 0.00 2.57
358 359 8.698973 TGTGTCAAAAATACTCAAATTCCCTA 57.301 30.769 0.00 0.00 0.00 3.53
359 360 7.595819 TGTGTCAAAAATACTCAAATTCCCT 57.404 32.000 0.00 0.00 0.00 4.20
360 361 8.655651 TTTGTGTCAAAAATACTCAAATTCCC 57.344 30.769 0.00 0.00 36.16 3.97
364 365 9.927668 CCCTATTTGTGTCAAAAATACTCAAAT 57.072 29.630 15.97 15.97 45.57 2.32
365 366 9.137459 TCCCTATTTGTGTCAAAAATACTCAAA 57.863 29.630 4.33 0.00 41.67 2.69
366 367 8.698973 TCCCTATTTGTGTCAAAAATACTCAA 57.301 30.769 4.33 0.00 0.00 3.02
367 368 8.877864 ATCCCTATTTGTGTCAAAAATACTCA 57.122 30.769 4.33 0.00 0.00 3.41
369 370 9.747898 TGTATCCCTATTTGTGTCAAAAATACT 57.252 29.630 4.33 0.00 0.00 2.12
372 373 8.865090 TGTTGTATCCCTATTTGTGTCAAAAAT 58.135 29.630 6.24 6.24 0.00 1.82
373 374 8.239038 TGTTGTATCCCTATTTGTGTCAAAAA 57.761 30.769 0.00 0.00 0.00 1.94
374 375 7.825331 TGTTGTATCCCTATTTGTGTCAAAA 57.175 32.000 0.00 0.00 0.00 2.44
375 376 9.693739 ATATGTTGTATCCCTATTTGTGTCAAA 57.306 29.630 0.00 0.00 0.00 2.69
376 377 9.119418 CATATGTTGTATCCCTATTTGTGTCAA 57.881 33.333 0.00 0.00 0.00 3.18
377 378 7.719193 CCATATGTTGTATCCCTATTTGTGTCA 59.281 37.037 1.24 0.00 0.00 3.58
378 379 7.719633 ACCATATGTTGTATCCCTATTTGTGTC 59.280 37.037 1.24 0.00 0.00 3.67
379 380 7.582719 ACCATATGTTGTATCCCTATTTGTGT 58.417 34.615 1.24 0.00 0.00 3.72
380 381 9.567776 TTACCATATGTTGTATCCCTATTTGTG 57.432 33.333 1.24 0.00 0.00 3.33
381 382 9.793259 CTTACCATATGTTGTATCCCTATTTGT 57.207 33.333 1.24 0.00 0.00 2.83
382 383 8.730680 GCTTACCATATGTTGTATCCCTATTTG 58.269 37.037 1.24 0.00 0.00 2.32
383 384 8.444783 TGCTTACCATATGTTGTATCCCTATTT 58.555 33.333 1.24 0.00 0.00 1.40
384 385 7.984475 TGCTTACCATATGTTGTATCCCTATT 58.016 34.615 1.24 0.00 0.00 1.73
385 386 7.568128 TGCTTACCATATGTTGTATCCCTAT 57.432 36.000 1.24 0.00 0.00 2.57
386 387 7.568128 ATGCTTACCATATGTTGTATCCCTA 57.432 36.000 1.24 0.00 30.69 3.53
387 388 5.904984 TGCTTACCATATGTTGTATCCCT 57.095 39.130 1.24 0.00 0.00 4.20
388 389 6.942576 AGAATGCTTACCATATGTTGTATCCC 59.057 38.462 1.24 0.00 32.67 3.85
389 390 7.986085 AGAATGCTTACCATATGTTGTATCC 57.014 36.000 1.24 0.00 32.67 2.59
391 392 8.988934 CGTTAGAATGCTTACCATATGTTGTAT 58.011 33.333 1.24 0.00 32.67 2.29
392 393 7.982919 ACGTTAGAATGCTTACCATATGTTGTA 59.017 33.333 1.24 0.00 32.67 2.41
393 394 6.821665 ACGTTAGAATGCTTACCATATGTTGT 59.178 34.615 1.24 0.00 32.67 3.32
394 395 7.011016 TGACGTTAGAATGCTTACCATATGTTG 59.989 37.037 1.24 0.00 32.67 3.33
395 396 7.045416 TGACGTTAGAATGCTTACCATATGTT 58.955 34.615 1.24 0.00 32.67 2.71
396 397 6.578944 TGACGTTAGAATGCTTACCATATGT 58.421 36.000 1.24 0.00 32.67 2.29
397 398 7.658179 ATGACGTTAGAATGCTTACCATATG 57.342 36.000 0.00 0.00 32.67 1.78
398 399 8.677148 AAATGACGTTAGAATGCTTACCATAT 57.323 30.769 0.00 0.00 32.67 1.78
399 400 9.256477 CTAAATGACGTTAGAATGCTTACCATA 57.744 33.333 0.00 0.00 33.62 2.74
400 401 7.769044 ACTAAATGACGTTAGAATGCTTACCAT 59.231 33.333 0.00 0.00 35.45 3.55
401 402 7.101054 ACTAAATGACGTTAGAATGCTTACCA 58.899 34.615 0.00 0.00 35.45 3.25
402 403 7.535489 ACTAAATGACGTTAGAATGCTTACC 57.465 36.000 0.00 0.00 35.45 2.85
403 404 7.903431 CCAACTAAATGACGTTAGAATGCTTAC 59.097 37.037 0.00 0.00 35.45 2.34
404 405 7.065324 CCCAACTAAATGACGTTAGAATGCTTA 59.935 37.037 0.00 0.00 35.45 3.09
405 406 6.128007 CCCAACTAAATGACGTTAGAATGCTT 60.128 38.462 0.00 0.00 35.45 3.91
406 407 5.354234 CCCAACTAAATGACGTTAGAATGCT 59.646 40.000 0.00 0.00 35.45 3.79
407 408 5.569413 CCCAACTAAATGACGTTAGAATGC 58.431 41.667 0.00 0.00 35.45 3.56
408 409 5.354234 AGCCCAACTAAATGACGTTAGAATG 59.646 40.000 0.00 0.00 35.45 2.67
409 410 5.497474 AGCCCAACTAAATGACGTTAGAAT 58.503 37.500 0.00 0.00 35.45 2.40
410 411 4.901868 AGCCCAACTAAATGACGTTAGAA 58.098 39.130 0.00 0.00 35.45 2.10
411 412 4.546829 AGCCCAACTAAATGACGTTAGA 57.453 40.909 0.00 0.00 35.45 2.10
412 413 6.730960 TTAAGCCCAACTAAATGACGTTAG 57.269 37.500 0.00 0.00 37.16 2.34
413 414 6.348704 GCTTTAAGCCCAACTAAATGACGTTA 60.349 38.462 5.52 0.00 34.48 3.18
414 415 5.564063 GCTTTAAGCCCAACTAAATGACGTT 60.564 40.000 5.52 0.00 34.48 3.99
415 416 4.082949 GCTTTAAGCCCAACTAAATGACGT 60.083 41.667 5.52 0.00 34.48 4.34
416 417 4.083003 TGCTTTAAGCCCAACTAAATGACG 60.083 41.667 14.80 0.00 41.51 4.35
417 418 5.385509 TGCTTTAAGCCCAACTAAATGAC 57.614 39.130 14.80 0.00 41.51 3.06
418 419 5.951747 AGATGCTTTAAGCCCAACTAAATGA 59.048 36.000 14.80 0.00 41.51 2.57
419 420 6.212888 AGATGCTTTAAGCCCAACTAAATG 57.787 37.500 14.80 0.00 41.51 2.32
420 421 7.779798 TCATAGATGCTTTAAGCCCAACTAAAT 59.220 33.333 14.80 0.00 41.51 1.40
439 440 8.701908 ATTCATAACCTGCAAATGTCATAGAT 57.298 30.769 0.00 0.00 0.00 1.98
440 441 8.523915 AATTCATAACCTGCAAATGTCATAGA 57.476 30.769 0.00 0.00 0.00 1.98
463 464 5.693961 ACAAAAAGAAGGCATGGGAAAAAT 58.306 33.333 0.00 0.00 0.00 1.82
464 465 5.109500 ACAAAAAGAAGGCATGGGAAAAA 57.891 34.783 0.00 0.00 0.00 1.94
537 551 7.123547 ACTTTGGTGATGTTCTTAAAGTCCAAA 59.876 33.333 0.00 0.00 39.18 3.28
565 579 9.520515 ACACTCTTTATGTAGAACATGGAAAAT 57.479 29.630 0.00 0.00 39.53 1.82
618 632 3.536956 TTACTCAAAGGAGCATACCCG 57.463 47.619 0.00 0.00 45.42 5.28
741 779 6.993786 TCAATTATATGTCGTTTGGCAAGA 57.006 33.333 0.00 0.00 0.00 3.02
763 801 9.396022 TCTCTTGGTTATTAGTCATGGAAAATC 57.604 33.333 0.00 0.00 0.00 2.17
769 807 9.838339 ATAGTTTCTCTTGGTTATTAGTCATGG 57.162 33.333 0.00 0.00 0.00 3.66
827 865 7.604545 GCCTAGTCTTTAATTGAGAACACTTCT 59.395 37.037 0.00 0.00 44.21 2.85
828 866 7.604545 AGCCTAGTCTTTAATTGAGAACACTTC 59.395 37.037 0.00 0.00 0.00 3.01
831 869 8.950208 ATAGCCTAGTCTTTAATTGAGAACAC 57.050 34.615 0.00 0.00 0.00 3.32
850 888 9.740710 AACATGAGTAGAAACTTTTAATAGCCT 57.259 29.630 0.00 0.00 35.56 4.58
887 925 9.353999 CACGAGCTAGTATTATTAATATGCACA 57.646 33.333 0.00 0.00 0.00 4.57
888 926 8.321716 GCACGAGCTAGTATTATTAATATGCAC 58.678 37.037 0.00 10.78 37.91 4.57
889 927 8.032451 TGCACGAGCTAGTATTATTAATATGCA 58.968 33.333 6.36 10.69 42.74 3.96
893 931 9.406828 CAGTTGCACGAGCTAGTATTATTAATA 57.593 33.333 6.36 0.00 42.74 0.98
894 932 7.095607 GCAGTTGCACGAGCTAGTATTATTAAT 60.096 37.037 6.36 0.00 42.74 1.40
896 934 5.690409 GCAGTTGCACGAGCTAGTATTATTA 59.310 40.000 6.36 0.00 42.74 0.98
897 935 4.508124 GCAGTTGCACGAGCTAGTATTATT 59.492 41.667 6.36 0.00 42.74 1.40
899 937 3.444916 GCAGTTGCACGAGCTAGTATTA 58.555 45.455 6.36 0.00 42.74 0.98
901 939 1.927895 GCAGTTGCACGAGCTAGTAT 58.072 50.000 6.36 0.00 42.74 2.12
902 940 3.418675 GCAGTTGCACGAGCTAGTA 57.581 52.632 6.36 0.00 42.74 1.82
913 951 2.331451 GTCAACCCGTGCAGTTGC 59.669 61.111 11.40 0.00 43.45 4.17
914 952 1.885388 TCGTCAACCCGTGCAGTTG 60.885 57.895 10.27 10.27 44.80 3.16
915 953 1.885850 GTCGTCAACCCGTGCAGTT 60.886 57.895 0.00 0.00 0.00 3.16
916 954 1.457823 TAGTCGTCAACCCGTGCAGT 61.458 55.000 0.00 0.00 0.00 4.40
917 955 0.732880 CTAGTCGTCAACCCGTGCAG 60.733 60.000 0.00 0.00 0.00 4.41
918 956 1.287815 CTAGTCGTCAACCCGTGCA 59.712 57.895 0.00 0.00 0.00 4.57
919 957 0.523072 TACTAGTCGTCAACCCGTGC 59.477 55.000 0.00 0.00 0.00 5.34
920 958 4.621068 TTATACTAGTCGTCAACCCGTG 57.379 45.455 0.00 0.00 0.00 4.94
921 959 5.841957 ATTTATACTAGTCGTCAACCCGT 57.158 39.130 0.00 0.00 0.00 5.28
922 960 6.728200 TGTATTTATACTAGTCGTCAACCCG 58.272 40.000 0.00 0.00 34.41 5.28
923 961 7.115947 GCATGTATTTATACTAGTCGTCAACCC 59.884 40.741 0.00 0.00 34.41 4.11
924 962 7.866393 AGCATGTATTTATACTAGTCGTCAACC 59.134 37.037 0.00 0.00 34.41 3.77
925 963 8.798748 AGCATGTATTTATACTAGTCGTCAAC 57.201 34.615 0.00 0.00 34.41 3.18
926 964 9.459640 GAAGCATGTATTTATACTAGTCGTCAA 57.540 33.333 0.00 0.00 34.41 3.18
927 965 7.801783 CGAAGCATGTATTTATACTAGTCGTCA 59.198 37.037 0.00 0.00 34.41 4.35
928 966 7.270793 CCGAAGCATGTATTTATACTAGTCGTC 59.729 40.741 0.00 0.00 34.41 4.20
929 967 7.082602 CCGAAGCATGTATTTATACTAGTCGT 58.917 38.462 0.00 0.00 34.41 4.34
930 968 7.082602 ACCGAAGCATGTATTTATACTAGTCG 58.917 38.462 0.00 0.00 34.41 4.18
931 969 8.298140 AGACCGAAGCATGTATTTATACTAGTC 58.702 37.037 0.00 0.00 34.41 2.59
932 970 8.082852 CAGACCGAAGCATGTATTTATACTAGT 58.917 37.037 0.00 0.00 34.41 2.57
933 971 7.062371 GCAGACCGAAGCATGTATTTATACTAG 59.938 40.741 0.00 0.00 34.41 2.57
934 972 6.866770 GCAGACCGAAGCATGTATTTATACTA 59.133 38.462 0.00 0.00 34.41 1.82
935 973 5.696724 GCAGACCGAAGCATGTATTTATACT 59.303 40.000 0.00 0.00 34.41 2.12
936 974 5.696724 AGCAGACCGAAGCATGTATTTATAC 59.303 40.000 0.00 0.00 0.00 1.47
937 975 5.853936 AGCAGACCGAAGCATGTATTTATA 58.146 37.500 0.00 0.00 0.00 0.98
938 976 4.708177 AGCAGACCGAAGCATGTATTTAT 58.292 39.130 0.00 0.00 0.00 1.40
939 977 4.137116 AGCAGACCGAAGCATGTATTTA 57.863 40.909 0.00 0.00 0.00 1.40
940 978 2.991250 AGCAGACCGAAGCATGTATTT 58.009 42.857 0.00 0.00 0.00 1.40
941 979 2.698855 AGCAGACCGAAGCATGTATT 57.301 45.000 0.00 0.00 0.00 1.89
942 980 2.695666 ACTAGCAGACCGAAGCATGTAT 59.304 45.455 0.00 0.00 0.00 2.29
943 981 2.099263 GACTAGCAGACCGAAGCATGTA 59.901 50.000 0.00 0.00 0.00 2.29
979 1017 3.045492 CGCCAAAGGGTTACGCGT 61.045 61.111 19.17 19.17 38.12 6.01
980 1018 4.454717 GCGCCAAAGGGTTACGCG 62.455 66.667 3.53 3.53 45.35 6.01
982 1020 1.582610 ATGTGCGCCAAAGGGTTACG 61.583 55.000 4.18 0.00 36.17 3.18
1584 1634 1.973281 CCCAAAGATGGCACGCACT 60.973 57.895 0.00 0.00 46.09 4.40
1627 1677 3.529533 CTTGCTTGACGATCCTCAGAAT 58.470 45.455 0.00 0.00 0.00 2.40
1680 1730 0.251253 ACGACGAAGGGAAGAGGTCT 60.251 55.000 0.00 0.00 0.00 3.85
1750 1806 3.000727 CCATAACGTTCAACACCTCCTC 58.999 50.000 2.82 0.00 0.00 3.71
1850 1918 5.447818 GCATCTTTTTGGATCCTGAGTAACG 60.448 44.000 14.23 0.00 0.00 3.18
1994 2234 3.764885 AAACTGCACGGATCTAAATGC 57.235 42.857 0.00 0.00 38.59 3.56
2087 2960 4.640789 AGCTCTTGTATTAGTCGACTGG 57.359 45.455 28.12 8.88 0.00 4.00
2101 2974 0.326264 AAGGGTGTGGCTAGCTCTTG 59.674 55.000 15.72 0.00 0.00 3.02
2404 7050 5.005740 TCTTTAGTGCGACCTCTTGTACTA 58.994 41.667 0.00 0.00 33.07 1.82
2416 7062 1.807139 TTGCATGCTCTTTAGTGCGA 58.193 45.000 20.33 0.00 40.34 5.10
2646 7292 1.153289 CCATGCCTCTCAAGTCGGG 60.153 63.158 0.00 0.00 0.00 5.14
2843 7489 3.219281 ACGCACAAATAGGTTGACCTTT 58.781 40.909 8.18 0.00 46.09 3.11
2910 7562 8.239038 TGTGAGCTACTTATAGTAAGAGCATT 57.761 34.615 16.20 0.00 29.00 3.56
2989 7646 1.538047 AAACTACGGAGTGCGTAGGA 58.462 50.000 36.77 12.83 45.73 2.94
2999 7656 4.319622 CGTTTTGCCACATAAAACTACGGA 60.320 41.667 10.44 0.00 42.76 4.69
3420 8082 5.667539 TTGATTGGTGAAGTTGGACAAAA 57.332 34.783 0.00 0.00 0.00 2.44
3438 8100 5.968254 TGCATTGAACTGCATAACATTGAT 58.032 33.333 0.00 0.00 46.76 2.57
3594 8256 5.247110 ACACCCCAATGCATTTACAAATACA 59.753 36.000 9.83 0.00 0.00 2.29
3612 8297 5.678955 ACTAGTTATTTCTCAGACACCCC 57.321 43.478 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.