Multiple sequence alignment - TraesCS4A01G136500

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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 TraesCS4A01G136500 chr4A 100.000 2426 0 0 1 2426 191118648 191121073 0.000000e+00 4481
1 TraesCS4A01G136500 chr4A 100.000 1066 0 0 2711 3776 191121358 191122423 0.000000e+00 1969
2 TraesCS4A01G136500 chr4A 87.538 995 121 1 2785 3776 730103544 730104538 0.000000e+00 1147
3 TraesCS4A01G136500 chr4A 91.071 112 10 0 357 468 699975419 699975308 6.530000e-33 152
4 TraesCS4A01G136500 chr4D 96.330 1962 63 3 466 2424 297207332 297205377 0.000000e+00 3216
5 TraesCS4A01G136500 chrUn 93.077 1979 85 21 466 2425 214476089 214474144 0.000000e+00 2848
6 TraesCS4A01G136500 chrUn 82.490 988 169 4 2787 3772 313308020 313309005 0.000000e+00 863
7 TraesCS4A01G136500 chrUn 82.490 988 169 4 2787 3772 313311799 313312784 0.000000e+00 863
8 TraesCS4A01G136500 chrUn 96.658 389 12 1 1111 1499 480243844 480243457 0.000000e+00 645
9 TraesCS4A01G136500 chrUn 90.052 191 14 4 1 191 214476270 214476085 3.770000e-60 243
10 TraesCS4A01G136500 chrUn 91.964 112 7 1 357 468 326063689 326063798 5.050000e-34 156
11 TraesCS4A01G136500 chr4B 92.926 1979 88 21 466 2425 367928336 367926391 0.000000e+00 2832
12 TraesCS4A01G136500 chr4B 90.052 191 14 4 1 191 367928517 367928332 3.770000e-60 243
13 TraesCS4A01G136500 chr7A 96.060 1066 37 1 2711 3776 47627960 47629020 0.000000e+00 1731
14 TraesCS4A01G136500 chr7A 84.211 304 32 4 185 472 709761759 709761456 7.990000e-72 281
15 TraesCS4A01G136500 chr7A 90.062 161 16 0 200 360 134481016 134480856 3.820000e-50 209
16 TraesCS4A01G136500 chr7A 89.744 117 11 1 357 473 712364445 712364330 8.450000e-32 148
17 TraesCS4A01G136500 chr2B 87.816 1067 121 7 2711 3776 309091926 309092984 0.000000e+00 1242
18 TraesCS4A01G136500 chr2B 81.912 1067 179 11 2711 3772 753946669 753947726 0.000000e+00 889
19 TraesCS4A01G136500 chr2B 92.035 113 7 2 359 469 105846817 105846929 1.400000e-34 158
20 TraesCS4A01G136500 chr1B 87.016 1032 134 0 2745 3776 626666201 626665170 0.000000e+00 1164
21 TraesCS4A01G136500 chr1B 86.919 1032 135 0 2745 3776 6111165 6110134 0.000000e+00 1158
22 TraesCS4A01G136500 chr1B 89.286 168 17 1 194 360 667744599 667744766 3.820000e-50 209
23 TraesCS4A01G136500 chr3B 81.921 1062 181 9 2711 3769 34556698 34557751 0.000000e+00 887
24 TraesCS4A01G136500 chr2D 76.290 1337 285 26 1001 2312 59007073 59008402 0.000000e+00 684
25 TraesCS4A01G136500 chr2D 90.728 151 14 0 210 360 556411543 556411393 6.400000e-48 202
26 TraesCS4A01G136500 chr2D 91.071 112 10 0 357 468 558721336 558721447 6.530000e-33 152
27 TraesCS4A01G136500 chr2D 91.346 104 9 0 369 472 186810820 186810717 3.930000e-30 143
28 TraesCS4A01G136500 chr6D 90.244 164 12 4 199 360 30072477 30072638 1.060000e-50 211
29 TraesCS4A01G136500 chr6D 88.957 163 17 1 199 360 368209402 368209240 2.300000e-47 200
30 TraesCS4A01G136500 chr6D 91.150 113 10 0 357 469 98746320 98746432 1.820000e-33 154
31 TraesCS4A01G136500 chr6D 91.071 112 10 0 357 468 368209213 368209102 6.530000e-33 152
32 TraesCS4A01G136500 chr1D 90.184 163 15 1 199 360 348801107 348801269 1.060000e-50 211
33 TraesCS4A01G136500 chr3D 89.506 162 17 0 199 360 529122029 529121868 4.940000e-49 206
34 TraesCS4A01G136500 chr5D 87.222 180 22 1 182 360 2621719 2621898 1.780000e-48 204
35 TraesCS4A01G136500 chr5D 92.523 107 8 0 366 472 32158338 32158444 1.820000e-33 154
36 TraesCS4A01G136500 chr5A 86.592 179 23 1 183 360 85270642 85270464 2.980000e-46 196
37 TraesCS4A01G136500 chr5A 88.889 117 11 2 357 472 608804229 608804344 3.930000e-30 143
38 TraesCS4A01G136500 chr5A 86.777 121 16 0 357 477 456100414 456100534 6.580000e-28 135
39 TraesCS4A01G136500 chr5B 92.727 110 8 0 357 466 398159699 398159808 3.900000e-35 159
40 TraesCS4A01G136500 chr3A 91.818 110 9 0 357 466 649812875 649812984 1.820000e-33 154
41 TraesCS4A01G136500 chr6B 89.655 116 11 1 357 472 706342475 706342361 3.040000e-31 147
42 TraesCS4A01G136500 chr7B 90.654 107 10 0 366 472 663974287 663974181 3.930000e-30 143


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 TraesCS4A01G136500 chr4A 191118648 191122423 3775 False 3225.0 4481 100.0000 1 3776 2 chr4A.!!$F2 3775
1 TraesCS4A01G136500 chr4A 730103544 730104538 994 False 1147.0 1147 87.5380 2785 3776 1 chr4A.!!$F1 991
2 TraesCS4A01G136500 chr4D 297205377 297207332 1955 True 3216.0 3216 96.3300 466 2424 1 chr4D.!!$R1 1958
3 TraesCS4A01G136500 chrUn 214474144 214476270 2126 True 1545.5 2848 91.5645 1 2425 2 chrUn.!!$R2 2424
4 TraesCS4A01G136500 chrUn 313308020 313312784 4764 False 863.0 863 82.4900 2787 3772 2 chrUn.!!$F2 985
5 TraesCS4A01G136500 chr4B 367926391 367928517 2126 True 1537.5 2832 91.4890 1 2425 2 chr4B.!!$R1 2424
6 TraesCS4A01G136500 chr7A 47627960 47629020 1060 False 1731.0 1731 96.0600 2711 3776 1 chr7A.!!$F1 1065
7 TraesCS4A01G136500 chr2B 309091926 309092984 1058 False 1242.0 1242 87.8160 2711 3776 1 chr2B.!!$F2 1065
8 TraesCS4A01G136500 chr2B 753946669 753947726 1057 False 889.0 889 81.9120 2711 3772 1 chr2B.!!$F3 1061
9 TraesCS4A01G136500 chr1B 626665170 626666201 1031 True 1164.0 1164 87.0160 2745 3776 1 chr1B.!!$R2 1031
10 TraesCS4A01G136500 chr1B 6110134 6111165 1031 True 1158.0 1158 86.9190 2745 3776 1 chr1B.!!$R1 1031
11 TraesCS4A01G136500 chr3B 34556698 34557751 1053 False 887.0 887 81.9210 2711 3769 1 chr3B.!!$F1 1058
12 TraesCS4A01G136500 chr2D 59007073 59008402 1329 False 684.0 684 76.2900 1001 2312 1 chr2D.!!$F1 1311

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
298 299 0.247695 AAAAGATTTAGAGCGCGCGC 60.248 50.0 45.1 45.10 42.33 6.86 F
1305 1324 0.235926 GCGAGCTGTTCAACAAGGTC 59.764 55.0 0.0 0.76 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 1384 0.536006 GGCTGTGGCAGAAGTCAACT 60.536 55.0 0.0 0.0 40.87 3.16 R
2999 3037 0.250858 CATGAACTGTGGGACTGCCA 60.251 55.0 0.0 0.0 35.15 4.92 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
60 61 7.659390 AGTTTTCTCTTCTAGAACAAGGATGTG 59.341 37.037 0.00 0.00 44.02 3.21
61 62 6.918067 TTCTCTTCTAGAACAAGGATGTGA 57.082 37.500 0.00 0.00 39.36 3.58
63 64 6.871844 TCTCTTCTAGAACAAGGATGTGATG 58.128 40.000 0.00 0.00 40.46 3.07
83 84 6.539826 GTGATGTTCACAGATCATGTTCCATA 59.460 38.462 2.85 0.00 46.22 2.74
88 89 7.227910 TGTTCACAGATCATGTTCCATATCATG 59.772 37.037 0.00 0.00 41.41 3.07
117 118 5.877012 TCTCTCTGCCTTGATATGTTTGTTC 59.123 40.000 0.00 0.00 0.00 3.18
119 120 6.003326 TCTCTGCCTTGATATGTTTGTTCAA 58.997 36.000 0.00 0.00 0.00 2.69
125 126 6.695292 CTTGATATGTTTGTTCAAGGCAAC 57.305 37.500 4.40 0.00 41.58 4.17
143 144 3.846023 GCAACGAGAAACACACACATCTG 60.846 47.826 0.00 0.00 0.00 2.90
166 167 6.778821 TGGATAGTTCAGACCAAAAGATGAA 58.221 36.000 0.00 0.00 0.00 2.57
167 168 7.405292 TGGATAGTTCAGACCAAAAGATGAAT 58.595 34.615 0.00 0.00 34.45 2.57
168 169 7.337689 TGGATAGTTCAGACCAAAAGATGAATG 59.662 37.037 0.00 0.00 34.45 2.67
169 170 7.554118 GGATAGTTCAGACCAAAAGATGAATGA 59.446 37.037 0.00 0.00 34.45 2.57
206 207 8.926710 AGTTCATAAGACTATTTTCAACAGACG 58.073 33.333 0.00 0.00 0.00 4.18
207 208 7.290857 TCATAAGACTATTTTCAACAGACGC 57.709 36.000 0.00 0.00 0.00 5.19
208 209 7.097192 TCATAAGACTATTTTCAACAGACGCT 58.903 34.615 0.00 0.00 0.00 5.07
209 210 5.847670 AAGACTATTTTCAACAGACGCTC 57.152 39.130 0.00 0.00 0.00 5.03
210 211 4.883083 AGACTATTTTCAACAGACGCTCA 58.117 39.130 0.00 0.00 0.00 4.26
211 212 5.297547 AGACTATTTTCAACAGACGCTCAA 58.702 37.500 0.00 0.00 0.00 3.02
212 213 5.758296 AGACTATTTTCAACAGACGCTCAAA 59.242 36.000 0.00 0.00 0.00 2.69
213 214 6.260050 AGACTATTTTCAACAGACGCTCAAAA 59.740 34.615 0.00 0.00 0.00 2.44
214 215 6.791303 ACTATTTTCAACAGACGCTCAAAAA 58.209 32.000 0.00 0.00 0.00 1.94
234 235 5.582689 AAAAAGCTCTGCACACTAAAAGT 57.417 34.783 0.00 0.00 0.00 2.66
235 236 5.582689 AAAAGCTCTGCACACTAAAAGTT 57.417 34.783 0.00 0.00 0.00 2.66
236 237 5.582689 AAAGCTCTGCACACTAAAAGTTT 57.417 34.783 0.00 0.00 0.00 2.66
237 238 4.558538 AGCTCTGCACACTAAAAGTTTG 57.441 40.909 0.00 0.00 0.00 2.93
238 239 3.947834 AGCTCTGCACACTAAAAGTTTGT 59.052 39.130 0.00 0.00 29.08 2.83
239 240 4.399303 AGCTCTGCACACTAAAAGTTTGTT 59.601 37.500 0.00 0.00 29.08 2.83
240 241 5.102313 GCTCTGCACACTAAAAGTTTGTTT 58.898 37.500 0.00 0.00 29.08 2.83
241 242 5.576774 GCTCTGCACACTAAAAGTTTGTTTT 59.423 36.000 0.00 0.00 29.08 2.43
242 243 6.090763 GCTCTGCACACTAAAAGTTTGTTTTT 59.909 34.615 0.00 0.00 34.78 1.94
258 259 2.499214 TTTTTGGCACGGAACAGCT 58.501 47.368 0.00 0.00 0.00 4.24
259 260 0.383949 TTTTTGGCACGGAACAGCTC 59.616 50.000 0.00 0.00 0.00 4.09
260 261 1.452145 TTTTGGCACGGAACAGCTCC 61.452 55.000 0.00 0.00 41.40 4.70
261 262 2.616797 TTTGGCACGGAACAGCTCCA 62.617 55.000 0.00 0.00 45.74 3.86
262 263 2.743928 GGCACGGAACAGCTCCAG 60.744 66.667 0.00 0.00 45.74 3.86
263 264 3.426568 GCACGGAACAGCTCCAGC 61.427 66.667 0.00 0.00 45.74 4.85
264 265 2.031012 CACGGAACAGCTCCAGCA 59.969 61.111 0.48 0.00 45.74 4.41
265 266 2.031516 CACGGAACAGCTCCAGCAG 61.032 63.158 0.48 0.00 45.74 4.24
266 267 2.210013 ACGGAACAGCTCCAGCAGA 61.210 57.895 0.48 0.00 45.74 4.26
267 268 1.739562 CGGAACAGCTCCAGCAGAC 60.740 63.158 0.48 0.00 45.74 3.51
268 269 1.739562 GGAACAGCTCCAGCAGACG 60.740 63.158 0.48 0.00 44.67 4.18
269 270 2.358003 AACAGCTCCAGCAGACGC 60.358 61.111 0.48 0.00 45.16 5.19
270 271 3.890936 AACAGCTCCAGCAGACGCC 62.891 63.158 0.48 0.00 45.16 5.68
273 274 4.129737 GCTCCAGCAGACGCCGTA 62.130 66.667 0.00 0.00 41.59 4.02
274 275 2.103143 CTCCAGCAGACGCCGTAG 59.897 66.667 0.00 0.00 39.83 3.51
275 276 4.129737 TCCAGCAGACGCCGTAGC 62.130 66.667 6.08 6.08 39.83 3.58
289 290 4.116713 GCCGTAGCGCTAAAAGATTTAG 57.883 45.455 20.73 5.67 0.00 1.85
290 291 3.800506 GCCGTAGCGCTAAAAGATTTAGA 59.199 43.478 20.73 0.00 0.00 2.10
291 292 4.085004 GCCGTAGCGCTAAAAGATTTAGAG 60.085 45.833 20.73 10.60 0.00 2.43
292 293 4.085004 CCGTAGCGCTAAAAGATTTAGAGC 60.085 45.833 20.73 22.66 44.52 4.09
295 296 2.880456 CGCTAAAAGATTTAGAGCGCG 58.120 47.619 16.64 0.00 42.09 6.86
296 297 2.630090 GCTAAAAGATTTAGAGCGCGC 58.370 47.619 26.66 26.66 0.00 6.86
297 298 2.880456 CTAAAAGATTTAGAGCGCGCG 58.120 47.619 28.44 28.44 0.00 6.86
298 299 0.247695 AAAAGATTTAGAGCGCGCGC 60.248 50.000 45.10 45.10 42.33 6.86
314 315 2.828784 CGCTGAAAAACGCTATCGC 58.171 52.632 0.00 0.00 39.84 4.58
335 336 2.763249 CGCAGCATATTTTGGACTCC 57.237 50.000 0.00 0.00 0.00 3.85
336 337 1.003545 CGCAGCATATTTTGGACTCCG 60.004 52.381 0.00 0.00 0.00 4.63
337 338 1.334869 GCAGCATATTTTGGACTCCGG 59.665 52.381 0.00 0.00 0.00 5.14
338 339 2.917933 CAGCATATTTTGGACTCCGGA 58.082 47.619 2.93 2.93 0.00 5.14
339 340 3.480470 CAGCATATTTTGGACTCCGGAT 58.520 45.455 3.57 0.00 0.00 4.18
340 341 3.885297 CAGCATATTTTGGACTCCGGATT 59.115 43.478 3.57 0.00 0.00 3.01
341 342 3.885297 AGCATATTTTGGACTCCGGATTG 59.115 43.478 3.57 0.00 0.00 2.67
342 343 3.550842 GCATATTTTGGACTCCGGATTGC 60.551 47.826 3.57 5.21 0.00 3.56
343 344 1.094785 ATTTTGGACTCCGGATTGCG 58.905 50.000 3.57 0.00 0.00 4.85
344 345 1.582610 TTTTGGACTCCGGATTGCGC 61.583 55.000 3.57 0.00 0.00 6.09
345 346 4.812476 TGGACTCCGGATTGCGCG 62.812 66.667 3.57 0.00 0.00 6.86
358 359 4.285291 GCGCGCGCTTCATAATTT 57.715 50.000 44.38 0.00 38.26 1.82
359 360 1.832913 GCGCGCGCTTCATAATTTG 59.167 52.632 44.38 10.35 38.26 2.32
360 361 0.861450 GCGCGCGCTTCATAATTTGT 60.861 50.000 44.38 0.00 38.26 2.83
361 362 0.833264 CGCGCGCTTCATAATTTGTG 59.167 50.000 30.48 4.24 0.00 3.33
362 363 0.567509 GCGCGCTTCATAATTTGTGC 59.432 50.000 26.67 0.00 0.00 4.57
363 364 1.893759 CGCGCTTCATAATTTGTGCA 58.106 45.000 5.56 0.00 35.91 4.57
364 365 1.578915 CGCGCTTCATAATTTGTGCAC 59.421 47.619 10.75 10.75 35.91 4.57
365 366 1.919918 GCGCTTCATAATTTGTGCACC 59.080 47.619 15.69 0.00 36.16 5.01
366 367 2.415893 GCGCTTCATAATTTGTGCACCT 60.416 45.455 15.69 0.00 36.16 4.00
367 368 3.173599 CGCTTCATAATTTGTGCACCTG 58.826 45.455 15.69 2.57 0.00 4.00
368 369 2.925563 GCTTCATAATTTGTGCACCTGC 59.074 45.455 15.69 0.16 42.50 4.85
369 370 3.367703 GCTTCATAATTTGTGCACCTGCT 60.368 43.478 15.69 0.00 42.66 4.24
370 371 4.142403 GCTTCATAATTTGTGCACCTGCTA 60.142 41.667 15.69 1.23 42.66 3.49
371 372 5.622007 GCTTCATAATTTGTGCACCTGCTAA 60.622 40.000 15.69 0.00 42.66 3.09
372 373 5.973899 TCATAATTTGTGCACCTGCTAAA 57.026 34.783 15.69 8.09 42.66 1.85
373 374 5.953183 TCATAATTTGTGCACCTGCTAAAG 58.047 37.500 15.69 0.00 42.66 1.85
374 375 2.730550 ATTTGTGCACCTGCTAAAGC 57.269 45.000 15.69 0.00 42.66 3.51
386 387 2.654749 GCTAAAGCAATGTTGGTCCC 57.345 50.000 0.00 0.00 41.59 4.46
387 388 1.135402 GCTAAAGCAATGTTGGTCCCG 60.135 52.381 0.00 0.00 41.59 5.14
388 389 1.472480 CTAAAGCAATGTTGGTCCCGG 59.528 52.381 0.00 0.00 38.04 5.73
389 390 1.815817 AAAGCAATGTTGGTCCCGGC 61.816 55.000 0.00 0.00 38.04 6.13
390 391 4.114997 GCAATGTTGGTCCCGGCG 62.115 66.667 0.00 0.00 0.00 6.46
391 392 4.114997 CAATGTTGGTCCCGGCGC 62.115 66.667 0.00 0.00 0.00 6.53
392 393 4.652131 AATGTTGGTCCCGGCGCA 62.652 61.111 10.83 0.00 0.00 6.09
393 394 3.936772 AATGTTGGTCCCGGCGCAT 62.937 57.895 10.83 0.00 0.00 4.73
394 395 3.936772 ATGTTGGTCCCGGCGCATT 62.937 57.895 10.83 0.00 0.00 3.56
395 396 2.437002 GTTGGTCCCGGCGCATTA 60.437 61.111 10.83 0.00 0.00 1.90
396 397 2.041686 GTTGGTCCCGGCGCATTAA 61.042 57.895 10.83 0.00 0.00 1.40
397 398 1.303398 TTGGTCCCGGCGCATTAAA 60.303 52.632 10.83 0.00 0.00 1.52
398 399 0.894184 TTGGTCCCGGCGCATTAAAA 60.894 50.000 10.83 0.00 0.00 1.52
399 400 0.894184 TGGTCCCGGCGCATTAAAAA 60.894 50.000 10.83 0.00 0.00 1.94
400 401 0.458260 GGTCCCGGCGCATTAAAAAT 59.542 50.000 10.83 0.00 0.00 1.82
401 402 1.677052 GGTCCCGGCGCATTAAAAATA 59.323 47.619 10.83 0.00 0.00 1.40
402 403 2.542205 GGTCCCGGCGCATTAAAAATAC 60.542 50.000 10.83 0.00 0.00 1.89
403 404 2.356695 GTCCCGGCGCATTAAAAATACT 59.643 45.455 10.83 0.00 0.00 2.12
404 405 3.560896 GTCCCGGCGCATTAAAAATACTA 59.439 43.478 10.83 0.00 0.00 1.82
405 406 3.560896 TCCCGGCGCATTAAAAATACTAC 59.439 43.478 10.83 0.00 0.00 2.73
406 407 3.312973 CCCGGCGCATTAAAAATACTACA 59.687 43.478 10.83 0.00 0.00 2.74
407 408 4.201930 CCCGGCGCATTAAAAATACTACAA 60.202 41.667 10.83 0.00 0.00 2.41
408 409 5.506649 CCCGGCGCATTAAAAATACTACAAT 60.507 40.000 10.83 0.00 0.00 2.71
409 410 5.398122 CCGGCGCATTAAAAATACTACAATG 59.602 40.000 10.83 0.00 0.00 2.82
410 411 5.398122 CGGCGCATTAAAAATACTACAATGG 59.602 40.000 10.83 0.00 0.00 3.16
411 412 5.689961 GGCGCATTAAAAATACTACAATGGG 59.310 40.000 10.83 0.00 40.50 4.00
412 413 5.689961 GCGCATTAAAAATACTACAATGGGG 59.310 40.000 0.30 0.00 38.95 4.96
413 414 5.689961 CGCATTAAAAATACTACAATGGGGC 59.310 40.000 0.00 0.00 36.47 5.80
414 415 5.689961 GCATTAAAAATACTACAATGGGGCG 59.310 40.000 0.00 0.00 0.00 6.13
415 416 3.793797 AAAAATACTACAATGGGGCGC 57.206 42.857 0.00 0.00 0.00 6.53
416 417 2.729028 AAATACTACAATGGGGCGCT 57.271 45.000 7.64 0.00 0.00 5.92
417 418 3.849563 AAATACTACAATGGGGCGCTA 57.150 42.857 7.64 0.00 0.00 4.26
418 419 3.849563 AATACTACAATGGGGCGCTAA 57.150 42.857 7.64 0.00 0.00 3.09
419 420 3.849563 ATACTACAATGGGGCGCTAAA 57.150 42.857 7.64 0.00 0.00 1.85
420 421 2.500392 ACTACAATGGGGCGCTAAAA 57.500 45.000 7.64 0.00 0.00 1.52
421 422 2.089201 ACTACAATGGGGCGCTAAAAC 58.911 47.619 7.64 0.00 0.00 2.43
422 423 2.290705 ACTACAATGGGGCGCTAAAACT 60.291 45.455 7.64 0.00 0.00 2.66
423 424 1.627864 ACAATGGGGCGCTAAAACTT 58.372 45.000 7.64 0.00 0.00 2.66
424 425 1.967779 ACAATGGGGCGCTAAAACTTT 59.032 42.857 7.64 0.00 0.00 2.66
425 426 2.367241 ACAATGGGGCGCTAAAACTTTT 59.633 40.909 7.64 0.00 0.00 2.27
426 427 3.574826 ACAATGGGGCGCTAAAACTTTTA 59.425 39.130 7.64 0.00 0.00 1.52
427 428 4.221924 ACAATGGGGCGCTAAAACTTTTAT 59.778 37.500 7.64 0.00 0.00 1.40
428 429 5.175127 CAATGGGGCGCTAAAACTTTTATT 58.825 37.500 7.64 0.00 0.00 1.40
429 430 4.181309 TGGGGCGCTAAAACTTTTATTG 57.819 40.909 7.64 0.00 0.00 1.90
430 431 3.056465 TGGGGCGCTAAAACTTTTATTGG 60.056 43.478 7.64 0.00 0.00 3.16
431 432 3.517602 GGGCGCTAAAACTTTTATTGGG 58.482 45.455 7.64 0.00 0.00 4.12
432 433 2.927477 GGCGCTAAAACTTTTATTGGGC 59.073 45.455 7.64 11.28 0.00 5.36
433 434 2.596862 GCGCTAAAACTTTTATTGGGCG 59.403 45.455 15.85 15.85 42.37 6.13
434 435 2.596862 CGCTAAAACTTTTATTGGGCGC 59.403 45.455 0.00 0.00 34.19 6.53
435 436 2.596862 GCTAAAACTTTTATTGGGCGCG 59.403 45.455 0.00 0.00 0.00 6.86
436 437 3.671164 GCTAAAACTTTTATTGGGCGCGA 60.671 43.478 12.10 0.00 0.00 5.87
437 438 3.372660 AAAACTTTTATTGGGCGCGAA 57.627 38.095 12.10 0.00 0.00 4.70
438 439 3.372660 AAACTTTTATTGGGCGCGAAA 57.627 38.095 12.10 0.00 0.00 3.46
439 440 3.586100 AACTTTTATTGGGCGCGAAAT 57.414 38.095 12.10 8.89 0.00 2.17
440 441 3.586100 ACTTTTATTGGGCGCGAAATT 57.414 38.095 12.10 0.00 0.00 1.82
441 442 3.920446 ACTTTTATTGGGCGCGAAATTT 58.080 36.364 12.10 0.00 0.00 1.82
442 443 4.311606 ACTTTTATTGGGCGCGAAATTTT 58.688 34.783 12.10 0.00 0.00 1.82
443 444 4.752604 ACTTTTATTGGGCGCGAAATTTTT 59.247 33.333 12.10 0.00 0.00 1.94
444 445 4.653806 TTTATTGGGCGCGAAATTTTTG 57.346 36.364 12.10 0.00 0.00 2.44
445 446 2.162319 ATTGGGCGCGAAATTTTTGT 57.838 40.000 12.10 0.00 0.00 2.83
446 447 1.212616 TTGGGCGCGAAATTTTTGTG 58.787 45.000 12.10 5.69 0.00 3.33
447 448 1.218230 TGGGCGCGAAATTTTTGTGC 61.218 50.000 21.55 21.55 38.36 4.57
450 451 1.127620 CGCGAAATTTTTGTGCGGC 59.872 52.632 0.00 0.00 44.65 6.53
451 452 1.491127 GCGAAATTTTTGTGCGGCC 59.509 52.632 0.00 0.00 0.00 6.13
452 453 1.772268 CGAAATTTTTGTGCGGCCG 59.228 52.632 24.05 24.05 0.00 6.13
453 454 0.937231 CGAAATTTTTGTGCGGCCGT 60.937 50.000 28.70 1.15 0.00 5.68
454 455 1.213491 GAAATTTTTGTGCGGCCGTT 58.787 45.000 28.70 9.54 0.00 4.44
455 456 0.933796 AAATTTTTGTGCGGCCGTTG 59.066 45.000 28.70 0.00 0.00 4.10
456 457 0.878086 AATTTTTGTGCGGCCGTTGG 60.878 50.000 28.70 0.00 0.00 3.77
457 458 1.739338 ATTTTTGTGCGGCCGTTGGA 61.739 50.000 28.70 8.23 0.00 3.53
458 459 2.343163 TTTTTGTGCGGCCGTTGGAG 62.343 55.000 28.70 0.00 0.00 3.86
459 460 3.758973 TTTGTGCGGCCGTTGGAGA 62.759 57.895 28.70 6.06 0.00 3.71
460 461 3.545124 TTGTGCGGCCGTTGGAGAT 62.545 57.895 28.70 0.00 0.00 2.75
461 462 3.499737 GTGCGGCCGTTGGAGATG 61.500 66.667 28.70 0.00 0.00 2.90
464 465 2.892425 CGGCCGTTGGAGATGCTC 60.892 66.667 19.50 0.00 0.00 4.26
475 476 6.461648 CCGTTGGAGATGCTCTAAGAAATCTA 60.462 42.308 0.00 0.00 31.92 1.98
544 545 9.750125 TTCTTTTTCTTTAAGAGGCAAGAATTC 57.250 29.630 15.31 0.00 38.51 2.17
550 551 5.705609 TTAAGAGGCAAGAATTCGCTTTT 57.294 34.783 0.00 0.00 0.00 2.27
567 568 5.068460 TCGCTTTTTGGATTCTTCTGGAAAA 59.932 36.000 0.00 0.00 37.49 2.29
683 684 8.681486 TTAGTAGCTACGTACCTAATCATTCA 57.319 34.615 17.99 0.00 0.00 2.57
687 688 7.520451 AGCTACGTACCTAATCATTCATGTA 57.480 36.000 0.00 0.00 0.00 2.29
757 761 1.031571 GGAATGCCGGAAGATGTGCA 61.032 55.000 5.05 0.00 38.23 4.57
760 764 1.731433 ATGCCGGAAGATGTGCATGC 61.731 55.000 11.82 11.82 42.48 4.06
791 795 1.886655 GCTACCTTGGTTGGGAACTGG 60.887 57.143 0.00 0.00 0.00 4.00
851 855 0.250424 CATGGGCATACGCAGGATGA 60.250 55.000 5.14 0.00 42.54 2.92
911 927 3.201290 ACGAATTGATCATCTGCAGGTC 58.799 45.455 15.13 8.00 0.00 3.85
948 964 1.211457 GTGCCCCTGATCAGTTCTGAT 59.789 52.381 21.11 14.13 0.00 2.90
990 1006 6.237901 TCACTGCCTTTTGTGTACATAAGAT 58.762 36.000 14.21 0.00 37.17 2.40
998 1014 4.406648 TGTGTACATAAGATCTGGCCAG 57.593 45.455 27.87 27.87 0.00 4.85
1131 1150 0.527565 GCGTTGCCATCAAGGTGATT 59.472 50.000 0.00 0.00 39.52 2.57
1146 1165 7.679783 TCAAGGTGATTGACAAAGAGAAGATA 58.320 34.615 0.00 0.00 43.09 1.98
1305 1324 0.235926 GCGAGCTGTTCAACAAGGTC 59.764 55.000 0.00 0.76 0.00 3.85
1365 1384 2.857186 TCCAACAGCTCAATAGTGCA 57.143 45.000 0.00 0.00 36.73 4.57
1841 1860 5.068723 AGGGACTGATTACCTATAACACACG 59.931 44.000 0.00 0.00 37.18 4.49
1887 1909 3.274393 GGATCCGACTTGTGATCCG 57.726 57.895 0.00 0.00 45.47 4.18
2100 2134 1.373570 GCTTGCGGCTAAGACTCATT 58.626 50.000 13.78 0.00 38.06 2.57
2135 2169 2.161211 GGTTGTTGAAGATGCAGAGCTC 59.839 50.000 5.27 5.27 0.00 4.09
2142 2176 1.742880 GATGCAGAGCTCGCAACCA 60.743 57.895 28.07 14.61 43.84 3.67
2254 2291 4.974368 ACTCTCGAGTATCAGAAGGTTG 57.026 45.455 13.13 0.00 40.43 3.77
2299 2336 2.380064 AGACATTGTTTGGGCTTGGA 57.620 45.000 0.00 0.00 0.00 3.53
2333 2370 5.828859 AGCCCTAGTAATAGTGTGACTACTG 59.171 44.000 0.00 0.00 32.84 2.74
2739 2777 2.366533 TGTAACCCAACGTTTGCTTGA 58.633 42.857 0.00 0.00 35.79 3.02
2740 2778 2.952978 TGTAACCCAACGTTTGCTTGAT 59.047 40.909 0.00 0.00 35.79 2.57
2741 2779 3.381908 TGTAACCCAACGTTTGCTTGATT 59.618 39.130 0.00 0.00 35.79 2.57
2742 2780 4.579340 TGTAACCCAACGTTTGCTTGATTA 59.421 37.500 0.00 0.00 35.79 1.75
2743 2781 3.636282 ACCCAACGTTTGCTTGATTAC 57.364 42.857 0.00 0.00 0.00 1.89
2890 2928 3.407698 TCGCTTCAAGGTGAAAATGCTA 58.592 40.909 0.00 0.00 35.73 3.49
2975 3013 3.798202 AGAAGTACGGAATGCCAGATTC 58.202 45.455 0.00 0.00 0.00 2.52
2999 3037 3.260100 CAACCTGGCAGGGGAGGT 61.260 66.667 35.34 14.13 44.94 3.85
3115 3153 2.664436 GGTCTCGCCGTCAAAACCG 61.664 63.158 0.00 0.00 0.00 4.44
3154 6971 3.478394 GCGACGATGTGCTTGCGA 61.478 61.111 0.00 0.00 0.00 5.10
3351 7168 2.207924 GGTCCGGTCCTGGCGATAT 61.208 63.158 10.82 0.00 0.00 1.63
3465 7282 3.750373 AAACCGCAGCCACACGAGT 62.750 57.895 0.00 0.00 0.00 4.18
3587 7404 6.431234 GGAGTTTGTGATAACAAAGGAGATGT 59.569 38.462 8.74 0.00 39.86 3.06
3655 7475 3.146066 GTGGCTGTTTTGTGGAGTGATA 58.854 45.455 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.402798 TGTTCTAGAACATATGGCAAAAGAAA 57.597 30.769 30.07 5.73 45.42 2.52
34 35 7.659390 CACATCCTTGTTCTAGAAGAGAAAACT 59.341 37.037 5.12 0.00 45.90 2.66
35 36 7.657761 TCACATCCTTGTTCTAGAAGAGAAAAC 59.342 37.037 5.12 0.00 45.90 2.43
117 118 1.400142 TGTGTGTTTCTCGTTGCCTTG 59.600 47.619 0.00 0.00 0.00 3.61
119 120 1.014352 GTGTGTGTTTCTCGTTGCCT 58.986 50.000 0.00 0.00 0.00 4.75
125 126 2.754472 TCCAGATGTGTGTGTTTCTCG 58.246 47.619 0.00 0.00 0.00 4.04
143 144 7.554118 TCATTCATCTTTTGGTCTGAACTATCC 59.446 37.037 0.00 0.00 31.00 2.59
181 182 7.688578 GCGTCTGTTGAAAATAGTCTTATGAAC 59.311 37.037 0.00 0.00 36.34 3.18
186 187 6.452242 TGAGCGTCTGTTGAAAATAGTCTTA 58.548 36.000 0.00 0.00 36.34 2.10
187 188 5.297547 TGAGCGTCTGTTGAAAATAGTCTT 58.702 37.500 0.00 0.00 36.34 3.01
188 189 4.883083 TGAGCGTCTGTTGAAAATAGTCT 58.117 39.130 0.00 0.00 36.34 3.24
189 190 5.591643 TTGAGCGTCTGTTGAAAATAGTC 57.408 39.130 0.00 0.00 36.34 2.59
190 191 6.371809 TTTTGAGCGTCTGTTGAAAATAGT 57.628 33.333 0.00 0.00 36.34 2.12
212 213 5.582689 ACTTTTAGTGTGCAGAGCTTTTT 57.417 34.783 0.00 0.00 0.00 1.94
213 214 5.582689 AACTTTTAGTGTGCAGAGCTTTT 57.417 34.783 0.00 0.00 0.00 2.27
214 215 5.105756 ACAAACTTTTAGTGTGCAGAGCTTT 60.106 36.000 0.00 0.00 36.93 3.51
215 216 4.399303 ACAAACTTTTAGTGTGCAGAGCTT 59.601 37.500 0.00 0.00 36.93 3.74
216 217 3.947834 ACAAACTTTTAGTGTGCAGAGCT 59.052 39.130 0.00 0.00 36.93 4.09
217 218 4.292977 ACAAACTTTTAGTGTGCAGAGC 57.707 40.909 0.00 0.00 36.93 4.09
218 219 7.581011 AAAAACAAACTTTTAGTGTGCAGAG 57.419 32.000 0.00 0.00 36.93 3.35
240 241 0.383949 GAGCTGTTCCGTGCCAAAAA 59.616 50.000 0.00 0.00 0.00 1.94
241 242 1.452145 GGAGCTGTTCCGTGCCAAAA 61.452 55.000 0.00 0.00 35.91 2.44
242 243 1.896660 GGAGCTGTTCCGTGCCAAA 60.897 57.895 0.00 0.00 35.91 3.28
243 244 2.281484 GGAGCTGTTCCGTGCCAA 60.281 61.111 0.00 0.00 35.91 4.52
250 251 1.739562 CGTCTGCTGGAGCTGTTCC 60.740 63.158 3.27 3.27 46.98 3.62
251 252 2.386660 GCGTCTGCTGGAGCTGTTC 61.387 63.158 0.00 0.00 42.66 3.18
252 253 2.358003 GCGTCTGCTGGAGCTGTT 60.358 61.111 0.00 0.00 42.66 3.16
253 254 4.385405 GGCGTCTGCTGGAGCTGT 62.385 66.667 0.00 0.00 42.66 4.40
268 269 3.800506 TCTAAATCTTTTAGCGCTACGGC 59.199 43.478 18.63 0.00 0.00 5.68
269 270 4.085004 GCTCTAAATCTTTTAGCGCTACGG 60.085 45.833 18.63 10.21 31.93 4.02
270 271 4.374112 CGCTCTAAATCTTTTAGCGCTACG 60.374 45.833 18.63 8.72 41.26 3.51
271 272 4.995920 CGCTCTAAATCTTTTAGCGCTAC 58.004 43.478 18.63 0.00 41.26 3.58
275 276 2.880456 CGCGCTCTAAATCTTTTAGCG 58.120 47.619 19.41 19.41 45.80 4.26
276 277 2.630090 GCGCGCTCTAAATCTTTTAGC 58.370 47.619 26.67 0.00 0.00 3.09
277 278 2.880456 CGCGCGCTCTAAATCTTTTAG 58.120 47.619 30.48 3.74 0.00 1.85
278 279 1.005347 GCGCGCGCTCTAAATCTTTTA 60.005 47.619 44.38 0.00 38.26 1.52
279 280 0.247695 GCGCGCGCTCTAAATCTTTT 60.248 50.000 44.38 0.00 38.26 2.27
280 281 1.348594 GCGCGCGCTCTAAATCTTT 59.651 52.632 44.38 0.00 38.26 2.52
281 282 3.006706 GCGCGCGCTCTAAATCTT 58.993 55.556 44.38 0.00 38.26 2.40
308 309 0.439985 AAATATGCTGCGCGCGATAG 59.560 50.000 37.18 29.48 43.27 2.08
309 310 0.865111 AAAATATGCTGCGCGCGATA 59.135 45.000 37.18 22.34 43.27 2.92
310 311 0.658244 CAAAATATGCTGCGCGCGAT 60.658 50.000 37.18 20.72 43.27 4.58
311 312 1.297524 CAAAATATGCTGCGCGCGA 60.298 52.632 37.18 17.91 43.27 5.87
312 313 2.287965 CCAAAATATGCTGCGCGCG 61.288 57.895 28.44 28.44 43.27 6.86
313 314 1.063972 TCCAAAATATGCTGCGCGC 59.936 52.632 27.26 27.26 39.77 6.86
314 315 0.378257 AGTCCAAAATATGCTGCGCG 59.622 50.000 0.00 0.00 0.00 6.86
315 316 1.268743 GGAGTCCAAAATATGCTGCGC 60.269 52.381 3.60 0.00 0.00 6.09
316 317 1.003545 CGGAGTCCAAAATATGCTGCG 60.004 52.381 10.49 0.00 35.05 5.18
317 318 1.334869 CCGGAGTCCAAAATATGCTGC 59.665 52.381 10.49 0.00 0.00 5.25
318 319 2.917933 TCCGGAGTCCAAAATATGCTG 58.082 47.619 10.49 0.00 0.00 4.41
319 320 3.864789 ATCCGGAGTCCAAAATATGCT 57.135 42.857 11.34 0.00 0.00 3.79
320 321 3.550842 GCAATCCGGAGTCCAAAATATGC 60.551 47.826 11.34 7.83 0.00 3.14
321 322 3.303990 CGCAATCCGGAGTCCAAAATATG 60.304 47.826 11.34 1.37 0.00 1.78
322 323 2.878406 CGCAATCCGGAGTCCAAAATAT 59.122 45.455 11.34 0.00 0.00 1.28
323 324 2.285083 CGCAATCCGGAGTCCAAAATA 58.715 47.619 11.34 0.00 0.00 1.40
324 325 1.094785 CGCAATCCGGAGTCCAAAAT 58.905 50.000 11.34 0.00 0.00 1.82
325 326 1.582610 GCGCAATCCGGAGTCCAAAA 61.583 55.000 11.34 0.00 37.44 2.44
326 327 2.038269 GCGCAATCCGGAGTCCAAA 61.038 57.895 11.34 0.00 37.44 3.28
327 328 2.435938 GCGCAATCCGGAGTCCAA 60.436 61.111 11.34 0.00 37.44 3.53
328 329 4.812476 CGCGCAATCCGGAGTCCA 62.812 66.667 11.34 0.00 37.44 4.02
341 342 0.861450 ACAAATTATGAAGCGCGCGC 60.861 50.000 45.10 45.10 42.33 6.86
342 343 0.833264 CACAAATTATGAAGCGCGCG 59.167 50.000 28.44 28.44 0.00 6.86
343 344 0.567509 GCACAAATTATGAAGCGCGC 59.432 50.000 26.66 26.66 0.00 6.86
344 345 1.578915 GTGCACAAATTATGAAGCGCG 59.421 47.619 13.17 0.00 36.73 6.86
345 346 1.919918 GGTGCACAAATTATGAAGCGC 59.080 47.619 20.43 0.00 40.64 5.92
346 347 3.173599 CAGGTGCACAAATTATGAAGCG 58.826 45.455 20.43 0.00 36.73 4.68
347 348 2.925563 GCAGGTGCACAAATTATGAAGC 59.074 45.455 20.43 3.12 41.59 3.86
348 349 4.445452 AGCAGGTGCACAAATTATGAAG 57.555 40.909 20.43 0.00 45.16 3.02
349 350 5.973899 TTAGCAGGTGCACAAATTATGAA 57.026 34.783 20.43 0.00 45.16 2.57
350 351 5.622007 GCTTTAGCAGGTGCACAAATTATGA 60.622 40.000 20.43 0.00 45.16 2.15
351 352 4.563976 GCTTTAGCAGGTGCACAAATTATG 59.436 41.667 20.43 7.97 45.16 1.90
352 353 4.747810 GCTTTAGCAGGTGCACAAATTAT 58.252 39.130 20.43 1.42 45.16 1.28
353 354 4.173036 GCTTTAGCAGGTGCACAAATTA 57.827 40.909 20.43 2.74 45.16 1.40
354 355 3.030668 GCTTTAGCAGGTGCACAAATT 57.969 42.857 20.43 3.77 45.16 1.82
355 356 2.730550 GCTTTAGCAGGTGCACAAAT 57.269 45.000 20.43 0.20 45.16 2.32
367 368 1.135402 CGGGACCAACATTGCTTTAGC 60.135 52.381 0.00 0.00 42.50 3.09
368 369 1.472480 CCGGGACCAACATTGCTTTAG 59.528 52.381 0.00 0.00 0.00 1.85
369 370 1.540267 CCGGGACCAACATTGCTTTA 58.460 50.000 0.00 0.00 0.00 1.85
370 371 1.815817 GCCGGGACCAACATTGCTTT 61.816 55.000 2.18 0.00 0.00 3.51
371 372 2.275380 GCCGGGACCAACATTGCTT 61.275 57.895 2.18 0.00 0.00 3.91
372 373 2.676471 GCCGGGACCAACATTGCT 60.676 61.111 2.18 0.00 0.00 3.91
373 374 4.114997 CGCCGGGACCAACATTGC 62.115 66.667 2.18 0.00 0.00 3.56
374 375 4.114997 GCGCCGGGACCAACATTG 62.115 66.667 2.18 0.00 0.00 2.82
375 376 3.936772 ATGCGCCGGGACCAACATT 62.937 57.895 4.18 0.00 0.00 2.71
376 377 2.544590 TAATGCGCCGGGACCAACAT 62.545 55.000 4.18 0.00 0.00 2.71
377 378 2.749706 TTAATGCGCCGGGACCAACA 62.750 55.000 4.18 0.00 0.00 3.33
378 379 1.587933 TTTAATGCGCCGGGACCAAC 61.588 55.000 4.18 0.00 0.00 3.77
379 380 0.894184 TTTTAATGCGCCGGGACCAA 60.894 50.000 4.18 0.00 0.00 3.67
380 381 0.894184 TTTTTAATGCGCCGGGACCA 60.894 50.000 4.18 0.00 0.00 4.02
381 382 0.458260 ATTTTTAATGCGCCGGGACC 59.542 50.000 4.18 0.00 0.00 4.46
382 383 2.356695 AGTATTTTTAATGCGCCGGGAC 59.643 45.455 4.18 0.00 0.00 4.46
383 384 2.645802 AGTATTTTTAATGCGCCGGGA 58.354 42.857 4.18 0.00 0.00 5.14
384 385 3.312973 TGTAGTATTTTTAATGCGCCGGG 59.687 43.478 4.18 0.00 0.00 5.73
385 386 4.539509 TGTAGTATTTTTAATGCGCCGG 57.460 40.909 4.18 0.00 0.00 6.13
386 387 5.398122 CCATTGTAGTATTTTTAATGCGCCG 59.602 40.000 4.18 0.00 0.00 6.46
387 388 5.689961 CCCATTGTAGTATTTTTAATGCGCC 59.310 40.000 4.18 0.00 0.00 6.53
388 389 5.689961 CCCCATTGTAGTATTTTTAATGCGC 59.310 40.000 0.00 0.00 0.00 6.09
389 390 5.689961 GCCCCATTGTAGTATTTTTAATGCG 59.310 40.000 0.00 0.00 0.00 4.73
390 391 5.689961 CGCCCCATTGTAGTATTTTTAATGC 59.310 40.000 0.00 0.00 0.00 3.56
391 392 5.689961 GCGCCCCATTGTAGTATTTTTAATG 59.310 40.000 0.00 0.00 0.00 1.90
392 393 5.596772 AGCGCCCCATTGTAGTATTTTTAAT 59.403 36.000 2.29 0.00 0.00 1.40
393 394 4.951094 AGCGCCCCATTGTAGTATTTTTAA 59.049 37.500 2.29 0.00 0.00 1.52
394 395 4.528920 AGCGCCCCATTGTAGTATTTTTA 58.471 39.130 2.29 0.00 0.00 1.52
395 396 3.361786 AGCGCCCCATTGTAGTATTTTT 58.638 40.909 2.29 0.00 0.00 1.94
396 397 3.012934 AGCGCCCCATTGTAGTATTTT 57.987 42.857 2.29 0.00 0.00 1.82
397 398 2.729028 AGCGCCCCATTGTAGTATTT 57.271 45.000 2.29 0.00 0.00 1.40
398 399 3.849563 TTAGCGCCCCATTGTAGTATT 57.150 42.857 2.29 0.00 0.00 1.89
399 400 3.849563 TTTAGCGCCCCATTGTAGTAT 57.150 42.857 2.29 0.00 0.00 2.12
400 401 3.054948 AGTTTTAGCGCCCCATTGTAGTA 60.055 43.478 2.29 0.00 0.00 1.82
401 402 2.089201 GTTTTAGCGCCCCATTGTAGT 58.911 47.619 2.29 0.00 0.00 2.73
402 403 2.365582 AGTTTTAGCGCCCCATTGTAG 58.634 47.619 2.29 0.00 0.00 2.74
403 404 2.500392 AGTTTTAGCGCCCCATTGTA 57.500 45.000 2.29 0.00 0.00 2.41
404 405 1.627864 AAGTTTTAGCGCCCCATTGT 58.372 45.000 2.29 0.00 0.00 2.71
405 406 2.741759 AAAGTTTTAGCGCCCCATTG 57.258 45.000 2.29 0.00 0.00 2.82
406 407 5.175127 CAATAAAAGTTTTAGCGCCCCATT 58.825 37.500 13.25 0.00 0.00 3.16
407 408 4.382577 CCAATAAAAGTTTTAGCGCCCCAT 60.383 41.667 13.25 0.00 0.00 4.00
408 409 3.056465 CCAATAAAAGTTTTAGCGCCCCA 60.056 43.478 13.25 0.00 0.00 4.96
409 410 3.517602 CCAATAAAAGTTTTAGCGCCCC 58.482 45.455 13.25 0.00 0.00 5.80
410 411 3.517602 CCCAATAAAAGTTTTAGCGCCC 58.482 45.455 13.25 0.00 0.00 6.13
411 412 2.927477 GCCCAATAAAAGTTTTAGCGCC 59.073 45.455 13.25 0.00 0.00 6.53
412 413 2.596862 CGCCCAATAAAAGTTTTAGCGC 59.403 45.455 19.96 0.00 34.23 5.92
413 414 2.596862 GCGCCCAATAAAAGTTTTAGCG 59.403 45.455 24.25 24.25 43.58 4.26
414 415 2.596862 CGCGCCCAATAAAAGTTTTAGC 59.403 45.455 13.25 9.88 0.00 3.09
415 416 4.086199 TCGCGCCCAATAAAAGTTTTAG 57.914 40.909 13.25 1.68 0.00 1.85
416 417 4.500603 TTCGCGCCCAATAAAAGTTTTA 57.499 36.364 10.39 10.39 0.00 1.52
417 418 3.372660 TTCGCGCCCAATAAAAGTTTT 57.627 38.095 0.00 6.06 0.00 2.43
418 419 3.372660 TTTCGCGCCCAATAAAAGTTT 57.627 38.095 0.00 0.00 0.00 2.66
419 420 3.586100 ATTTCGCGCCCAATAAAAGTT 57.414 38.095 0.00 0.00 0.00 2.66
420 421 3.586100 AATTTCGCGCCCAATAAAAGT 57.414 38.095 0.00 0.00 0.00 2.66
421 422 4.919677 AAAATTTCGCGCCCAATAAAAG 57.080 36.364 0.00 0.00 0.00 2.27
422 423 4.511826 ACAAAAATTTCGCGCCCAATAAAA 59.488 33.333 0.00 0.00 0.00 1.52
423 424 4.058817 ACAAAAATTTCGCGCCCAATAAA 58.941 34.783 0.00 0.00 0.00 1.40
424 425 3.430218 CACAAAAATTTCGCGCCCAATAA 59.570 39.130 0.00 0.00 0.00 1.40
425 426 2.989840 CACAAAAATTTCGCGCCCAATA 59.010 40.909 0.00 0.00 0.00 1.90
426 427 1.797635 CACAAAAATTTCGCGCCCAAT 59.202 42.857 0.00 0.00 0.00 3.16
427 428 1.212616 CACAAAAATTTCGCGCCCAA 58.787 45.000 0.00 0.00 0.00 4.12
428 429 1.218230 GCACAAAAATTTCGCGCCCA 61.218 50.000 0.00 0.00 0.00 5.36
429 430 1.491127 GCACAAAAATTTCGCGCCC 59.509 52.632 0.00 0.00 0.00 6.13
430 431 1.127620 CGCACAAAAATTTCGCGCC 59.872 52.632 0.00 0.00 39.43 6.53
431 432 1.127620 CCGCACAAAAATTTCGCGC 59.872 52.632 0.00 0.00 44.36 6.86
432 433 1.127620 GCCGCACAAAAATTTCGCG 59.872 52.632 0.00 0.00 45.25 5.87
433 434 1.491127 GGCCGCACAAAAATTTCGC 59.509 52.632 0.00 0.00 0.00 4.70
434 435 0.937231 ACGGCCGCACAAAAATTTCG 60.937 50.000 28.58 0.00 0.00 3.46
435 436 1.070909 CAACGGCCGCACAAAAATTTC 60.071 47.619 28.58 0.00 0.00 2.17
436 437 0.933796 CAACGGCCGCACAAAAATTT 59.066 45.000 28.58 5.37 0.00 1.82
437 438 0.878086 CCAACGGCCGCACAAAAATT 60.878 50.000 28.58 6.25 0.00 1.82
438 439 1.300542 CCAACGGCCGCACAAAAAT 60.301 52.632 28.58 0.00 0.00 1.82
439 440 2.105128 CCAACGGCCGCACAAAAA 59.895 55.556 28.58 0.00 0.00 1.94
440 441 2.829003 TCCAACGGCCGCACAAAA 60.829 55.556 28.58 2.77 0.00 2.44
441 442 3.283684 CTCCAACGGCCGCACAAA 61.284 61.111 28.58 6.34 0.00 2.83
442 443 3.545124 ATCTCCAACGGCCGCACAA 62.545 57.895 28.58 7.99 0.00 3.33
443 444 4.015406 ATCTCCAACGGCCGCACA 62.015 61.111 28.58 5.68 0.00 4.57
444 445 3.499737 CATCTCCAACGGCCGCAC 61.500 66.667 28.58 0.00 0.00 5.34
447 448 2.892425 GAGCATCTCCAACGGCCG 60.892 66.667 26.86 26.86 0.00 6.13
458 459 9.650539 TGCATAGATTAGATTTCTTAGAGCATC 57.349 33.333 0.00 0.00 0.00 3.91
460 461 9.265901 GTTGCATAGATTAGATTTCTTAGAGCA 57.734 33.333 0.00 0.00 0.00 4.26
461 462 9.265901 TGTTGCATAGATTAGATTTCTTAGAGC 57.734 33.333 0.00 0.00 0.00 4.09
544 545 4.503741 TTCCAGAAGAATCCAAAAAGCG 57.496 40.909 0.00 0.00 0.00 4.68
683 684 5.012148 AGCCTAATACTGCGAGGAAATACAT 59.988 40.000 0.00 0.00 31.45 2.29
687 688 4.423625 AAGCCTAATACTGCGAGGAAAT 57.576 40.909 0.00 0.00 31.45 2.17
733 737 0.911769 ATCTTCCGGCATTCCTGTGA 59.088 50.000 0.00 0.00 0.00 3.58
757 761 1.742768 GTAGCCCTCTAGCACGCAT 59.257 57.895 0.00 0.00 34.23 4.73
760 764 0.103208 CAAGGTAGCCCTCTAGCACG 59.897 60.000 4.64 0.00 43.76 5.34
771 775 1.534729 CAGTTCCCAACCAAGGTAGC 58.465 55.000 0.00 0.00 0.00 3.58
791 795 6.102663 TCAGTATCTTCAAAAGCTAGACTGC 58.897 40.000 0.00 0.00 0.00 4.40
823 827 1.027357 GTATGCCCATGGAGCAACTG 58.973 55.000 25.44 4.94 44.83 3.16
851 855 2.057922 GATGGTAGGTGGTCCATGGAT 58.942 52.381 19.62 3.53 43.45 3.41
878 894 6.573664 TGATCAATTCGTTTCAACCATCTT 57.426 33.333 0.00 0.00 0.00 2.40
911 927 2.163010 GGCACTCAATGATGTGGACAAG 59.837 50.000 12.34 0.00 34.99 3.16
948 964 5.056480 CAGTGATGTTGTAACTTGAGGTGA 58.944 41.667 0.00 0.00 0.00 4.02
998 1014 1.207791 TCCCTTCTTCTCTGCCATCC 58.792 55.000 0.00 0.00 0.00 3.51
1131 1150 6.091305 CGCACTTGAATATCTTCTCTTTGTCA 59.909 38.462 0.00 0.00 32.29 3.58
1146 1165 1.064758 TCCATAAGCCCGCACTTGAAT 60.065 47.619 0.00 0.00 0.00 2.57
1305 1324 1.160137 CTTTCAGCCTTCCTCGTTGG 58.840 55.000 0.00 0.00 37.10 3.77
1365 1384 0.536006 GGCTGTGGCAGAAGTCAACT 60.536 55.000 0.00 0.00 40.87 3.16
1829 1848 2.480759 CCCTCCGTTCGTGTGTTATAGG 60.481 54.545 0.00 0.00 0.00 2.57
1887 1909 1.466167 TCGGTCGTACAGCTACTGAAC 59.534 52.381 0.78 0.00 35.18 3.18
1902 1924 3.585862 TGCTTCTTGTATTGTCTCGGTC 58.414 45.455 0.00 0.00 0.00 4.79
2100 2134 2.005370 ACAACCCACCGTCTCTCTTA 57.995 50.000 0.00 0.00 0.00 2.10
2135 2169 1.866853 GCCTTTCCTTCCTGGTTGCG 61.867 60.000 0.00 0.00 37.07 4.85
2142 2176 2.355818 GGACATTACGCCTTTCCTTCCT 60.356 50.000 0.00 0.00 0.00 3.36
2254 2291 3.393089 AGCCGGTCTCATATCATGTTC 57.607 47.619 1.90 0.00 0.00 3.18
2299 2336 1.952621 TACTAGGGCTGCTCACCTTT 58.047 50.000 0.74 0.00 38.30 3.11
2333 2370 5.779806 TCTTGCAATTTCTACGCTTACTC 57.220 39.130 0.00 0.00 0.00 2.59
2741 2779 9.158233 GCTTATGTAGTTCACCTTTGTAATGTA 57.842 33.333 0.00 0.00 0.00 2.29
2742 2780 7.663905 TGCTTATGTAGTTCACCTTTGTAATGT 59.336 33.333 0.00 0.00 0.00 2.71
2743 2781 7.962918 GTGCTTATGTAGTTCACCTTTGTAATG 59.037 37.037 0.00 0.00 0.00 1.90
2782 2820 3.265791 CTCATGGTGTTCCTACTTCTGC 58.734 50.000 0.00 0.00 34.23 4.26
2783 2821 4.248859 CACTCATGGTGTTCCTACTTCTG 58.751 47.826 6.25 0.00 40.79 3.02
2890 2928 2.363306 TCAAGCAACAGAACCACCAT 57.637 45.000 0.00 0.00 0.00 3.55
2975 3013 1.601419 CCCTGCCAGGTTGATGCAAG 61.601 60.000 10.47 0.00 34.06 4.01
2999 3037 0.250858 CATGAACTGTGGGACTGCCA 60.251 55.000 0.00 0.00 35.15 4.92
3076 3114 3.243805 CCAGCTCTCACATCTTCATCGAT 60.244 47.826 0.00 0.00 0.00 3.59
3115 3153 2.621055 AGACTCTCTATGTCCACGATGC 59.379 50.000 0.00 0.00 35.21 3.91
3154 6971 2.629617 CAACTCCAAATGCAACCTCCTT 59.370 45.455 0.00 0.00 0.00 3.36
3351 7168 3.055530 GTCTCTCTTGCAGGATTTCCAGA 60.056 47.826 0.00 0.00 38.89 3.86
3451 7268 3.108289 CTCACTCGTGTGGCTGCG 61.108 66.667 16.88 0.00 43.94 5.18
3465 7282 0.613260 GCATACCACCACACCTCTCA 59.387 55.000 0.00 0.00 0.00 3.27
3587 7404 2.567169 AGCAACTACCAGCACTACATGA 59.433 45.455 0.00 0.00 0.00 3.07
3655 7475 1.053264 TGCAACACCCAAATGCCCTT 61.053 50.000 0.00 0.00 39.31 3.95


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

AutoCloner maintained by Alex Coulton.