Multiple sequence alignment - TraesCS4A01G133900

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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 TraesCS4A01G133900 chr4A 100.000 4400 0 0 1 4400 182056491 182060890 0.000000e+00 8126.0
1 TraesCS4A01G133900 chr4D 91.479 2441 154 20 1962 4366 300855346 300852924 0.000000e+00 3306.0
2 TraesCS4A01G133900 chr4D 92.201 1295 47 20 715 1970 300858935 300857656 0.000000e+00 1783.0
3 TraesCS4A01G133900 chr4D 93.909 394 16 4 303 689 300860898 300860506 4.900000e-164 588.0
4 TraesCS4A01G133900 chr4D 93.785 177 7 3 1 174 300861032 300860857 3.370000e-66 263.0
5 TraesCS4A01G133900 chr4D 85.577 208 23 4 2640 2847 300854727 300854527 1.240000e-50 211.0
6 TraesCS4A01G133900 chr4D 87.402 127 9 2 2722 2848 300854727 300854608 5.930000e-29 139.0
7 TraesCS4A01G133900 chr4B 90.916 2488 166 26 1909 4366 374214835 374212378 0.000000e+00 3288.0
8 TraesCS4A01G133900 chr4B 91.721 1679 65 27 303 1919 374216935 374215269 0.000000e+00 2263.0
9 TraesCS4A01G133900 chr4B 93.182 176 12 0 1 176 374217067 374216892 4.370000e-65 259.0
10 TraesCS4A01G133900 chr4B 89.000 100 11 0 2722 2821 374214180 374214081 1.660000e-24 124.0
11 TraesCS4A01G133900 chr3D 97.479 119 3 0 182 300 1909139 1909257 2.070000e-48 204.0
12 TraesCS4A01G133900 chr3D 94.215 121 4 3 182 300 599314930 599314811 9.720000e-42 182.0
13 TraesCS4A01G133900 chr2D 97.479 119 3 0 182 300 423164804 423164686 2.070000e-48 204.0
14 TraesCS4A01G133900 chr2D 96.694 121 4 0 180 300 54666301 54666181 7.460000e-48 202.0
15 TraesCS4A01G133900 chr2D 85.345 116 12 4 1999 2109 532496827 532496942 1.000000e-21 115.0
16 TraesCS4A01G133900 chr7D 96.639 119 4 0 182 300 2488325 2488207 9.650000e-47 198.0
17 TraesCS4A01G133900 chr6B 96.610 118 3 1 183 300 712188434 712188318 1.250000e-45 195.0
18 TraesCS4A01G133900 chr6B 93.548 124 8 0 182 305 595948819 595948696 7.520000e-43 185.0
19 TraesCS4A01G133900 chr3A 96.581 117 4 0 184 300 15432020 15431904 1.250000e-45 195.0
20 TraesCS4A01G133900 chr1B 95.041 121 6 0 180 300 576519767 576519887 1.620000e-44 191.0
21 TraesCS4A01G133900 chr1B 89.888 89 9 0 2473 2561 593515760 593515672 1.000000e-21 115.0
22 TraesCS4A01G133900 chr1B 81.356 118 17 5 2474 2588 402110448 402110333 1.690000e-14 91.6
23 TraesCS4A01G133900 chr5A 92.391 92 6 1 2473 2564 19104992 19105082 3.570000e-26 130.0
24 TraesCS4A01G133900 chr5D 91.304 92 7 1 2473 2564 28479949 28480039 1.660000e-24 124.0
25 TraesCS4A01G133900 chr7B 89.888 89 9 0 2473 2561 23992734 23992646 1.000000e-21 115.0
26 TraesCS4A01G133900 chr6A 88.372 86 10 0 2474 2559 263872801 263872886 2.160000e-18 104.0
27 TraesCS4A01G133900 chr5B 88.235 85 9 1 2474 2558 517366209 517366292 2.800000e-17 100.0
28 TraesCS4A01G133900 chr2B 78.218 101 16 6 1405 1502 733077545 733077448 4.750000e-05 60.2


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 TraesCS4A01G133900 chr4A 182056491 182060890 4399 False 8126.000000 8126 100.00000 1 4400 1 chr4A.!!$F1 4399
1 TraesCS4A01G133900 chr4D 300852924 300861032 8108 True 1048.333333 3306 90.72550 1 4366 6 chr4D.!!$R1 4365
2 TraesCS4A01G133900 chr4B 374212378 374217067 4689 True 1483.500000 3288 91.20475 1 4366 4 chr4B.!!$R1 4365

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
294 297 0.037326 CCACACAGCCGTGATACACT 60.037 55.0 7.16 0.0 46.80 3.55 F
362 366 0.445829 TGGCGTATTGATTGTGTGCG 59.554 50.0 0.00 0.0 0.00 5.34 F
575 586 0.613572 TGCATCCTCGGTACAGGTCA 60.614 55.0 0.00 0.0 34.76 4.02 F
2164 6537 0.106894 TTCACGTGTGTGCCCATACA 59.893 50.0 16.51 0.0 46.01 2.29 F
3201 7600 0.449388 CGACTTACTACCGCCTCGTT 59.551 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 2857 0.109342 CAAAGTGAGGGACTGCCACT 59.891 55.000 0.00 0.00 43.95 4.00 R
1923 3533 0.682209 TAGTGGGGCCGTGAGTAGTC 60.682 60.000 0.00 0.00 0.00 2.59 R
2292 6666 1.272592 TGCATGGAAAAGGCTCATCCA 60.273 47.619 19.75 19.75 46.60 3.41 R
3357 7756 0.642156 TCCTGATCTCCCCCTTGCTA 59.358 55.000 0.00 0.00 0.00 3.49 R
4284 8697 0.043940 ATCCAGAGAGGCCCTGTTCT 59.956 55.000 0.00 0.00 37.29 3.01 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
74 75 1.799181 CGACTACCTGACGGAAGCATG 60.799 57.143 0.00 0.00 0.00 4.06
149 152 6.344500 TCCTTCATCTTATGCTCAACTCTTC 58.656 40.000 0.00 0.00 0.00 2.87
150 153 6.155910 TCCTTCATCTTATGCTCAACTCTTCT 59.844 38.462 0.00 0.00 0.00 2.85
151 154 7.343057 TCCTTCATCTTATGCTCAACTCTTCTA 59.657 37.037 0.00 0.00 0.00 2.10
152 155 7.984050 CCTTCATCTTATGCTCAACTCTTCTAA 59.016 37.037 0.00 0.00 0.00 2.10
153 156 9.545105 CTTCATCTTATGCTCAACTCTTCTAAT 57.455 33.333 0.00 0.00 0.00 1.73
154 157 9.896645 TTCATCTTATGCTCAACTCTTCTAATT 57.103 29.630 0.00 0.00 0.00 1.40
155 158 9.896645 TCATCTTATGCTCAACTCTTCTAATTT 57.103 29.630 0.00 0.00 0.00 1.82
158 161 9.950496 TCTTATGCTCAACTCTTCTAATTTTCT 57.050 29.630 0.00 0.00 0.00 2.52
159 162 9.985318 CTTATGCTCAACTCTTCTAATTTTCTG 57.015 33.333 0.00 0.00 0.00 3.02
160 163 7.992754 ATGCTCAACTCTTCTAATTTTCTGT 57.007 32.000 0.00 0.00 0.00 3.41
162 165 8.902540 TGCTCAACTCTTCTAATTTTCTGTAA 57.097 30.769 0.00 0.00 0.00 2.41
163 166 9.337396 TGCTCAACTCTTCTAATTTTCTGTAAA 57.663 29.630 0.00 0.00 0.00 2.01
207 210 6.976636 TTTTTGCGATGAAAAAGGAGTTTT 57.023 29.167 0.00 0.00 42.28 2.43
209 212 8.655651 TTTTTGCGATGAAAAAGGAGTTTTAT 57.344 26.923 0.00 0.00 39.60 1.40
210 213 8.655651 TTTTGCGATGAAAAAGGAGTTTTATT 57.344 26.923 0.00 0.00 39.60 1.40
211 214 7.867445 TTGCGATGAAAAAGGAGTTTTATTC 57.133 32.000 0.00 0.00 39.60 1.75
212 215 6.386654 TGCGATGAAAAAGGAGTTTTATTCC 58.613 36.000 0.00 0.00 39.60 3.01
213 216 6.015856 TGCGATGAAAAAGGAGTTTTATTCCA 60.016 34.615 0.00 0.00 39.60 3.53
214 217 6.866248 GCGATGAAAAAGGAGTTTTATTCCAA 59.134 34.615 0.00 0.00 39.60 3.53
215 218 7.383843 GCGATGAAAAAGGAGTTTTATTCCAAA 59.616 33.333 0.00 0.00 39.60 3.28
216 219 9.423061 CGATGAAAAAGGAGTTTTATTCCAAAT 57.577 29.630 0.00 0.00 39.60 2.32
225 228 9.981460 AGGAGTTTTATTCCAAATTGATAGAGT 57.019 29.630 0.00 0.00 37.18 3.24
234 237 9.739276 ATTCCAAATTGATAGAGTTACAGTCAA 57.261 29.630 0.00 0.00 33.82 3.18
235 238 8.777865 TCCAAATTGATAGAGTTACAGTCAAG 57.222 34.615 0.00 0.00 32.93 3.02
236 239 8.593679 TCCAAATTGATAGAGTTACAGTCAAGA 58.406 33.333 0.00 0.00 32.93 3.02
237 240 8.877779 CCAAATTGATAGAGTTACAGTCAAGAG 58.122 37.037 0.00 0.00 32.93 2.85
238 241 8.877779 CAAATTGATAGAGTTACAGTCAAGAGG 58.122 37.037 0.00 0.00 32.93 3.69
239 242 5.584253 TGATAGAGTTACAGTCAAGAGGC 57.416 43.478 0.00 0.00 0.00 4.70
240 243 5.016831 TGATAGAGTTACAGTCAAGAGGCA 58.983 41.667 0.00 0.00 0.00 4.75
241 244 5.480422 TGATAGAGTTACAGTCAAGAGGCAA 59.520 40.000 0.00 0.00 0.00 4.52
242 245 4.689612 AGAGTTACAGTCAAGAGGCAAA 57.310 40.909 0.00 0.00 0.00 3.68
243 246 5.036117 AGAGTTACAGTCAAGAGGCAAAA 57.964 39.130 0.00 0.00 0.00 2.44
244 247 5.059833 AGAGTTACAGTCAAGAGGCAAAAG 58.940 41.667 0.00 0.00 0.00 2.27
245 248 5.036117 AGTTACAGTCAAGAGGCAAAAGA 57.964 39.130 0.00 0.00 0.00 2.52
246 249 5.625150 AGTTACAGTCAAGAGGCAAAAGAT 58.375 37.500 0.00 0.00 0.00 2.40
247 250 5.703130 AGTTACAGTCAAGAGGCAAAAGATC 59.297 40.000 0.00 0.00 0.00 2.75
248 251 3.416156 ACAGTCAAGAGGCAAAAGATCC 58.584 45.455 0.00 0.00 0.00 3.36
249 252 3.073650 ACAGTCAAGAGGCAAAAGATCCT 59.926 43.478 0.00 0.00 34.90 3.24
256 259 4.060038 GAGGCAAAAGATCCTCGATACA 57.940 45.455 0.00 0.00 39.43 2.29
257 260 4.636249 GAGGCAAAAGATCCTCGATACAT 58.364 43.478 0.00 0.00 39.43 2.29
258 261 4.384056 AGGCAAAAGATCCTCGATACATG 58.616 43.478 0.00 0.00 0.00 3.21
259 262 3.499918 GGCAAAAGATCCTCGATACATGG 59.500 47.826 0.00 0.00 0.00 3.66
260 263 4.130118 GCAAAAGATCCTCGATACATGGT 58.870 43.478 0.00 0.00 0.00 3.55
261 264 4.024556 GCAAAAGATCCTCGATACATGGTG 60.025 45.833 0.00 0.00 0.00 4.17
262 265 4.342862 AAAGATCCTCGATACATGGTGG 57.657 45.455 0.00 0.00 0.00 4.61
263 266 2.964209 AGATCCTCGATACATGGTGGT 58.036 47.619 0.00 0.00 0.00 4.16
264 267 2.894126 AGATCCTCGATACATGGTGGTC 59.106 50.000 0.00 0.00 0.00 4.02
265 268 1.410004 TCCTCGATACATGGTGGTCC 58.590 55.000 0.00 0.00 0.00 4.46
266 269 1.063190 TCCTCGATACATGGTGGTCCT 60.063 52.381 0.00 0.00 34.23 3.85
267 270 2.176148 TCCTCGATACATGGTGGTCCTA 59.824 50.000 0.00 0.00 34.23 2.94
268 271 2.558795 CCTCGATACATGGTGGTCCTAG 59.441 54.545 0.00 0.00 34.23 3.02
269 272 3.487372 CTCGATACATGGTGGTCCTAGA 58.513 50.000 0.00 0.00 34.23 2.43
270 273 4.082845 CTCGATACATGGTGGTCCTAGAT 58.917 47.826 0.00 0.00 34.23 1.98
271 274 3.826729 TCGATACATGGTGGTCCTAGATG 59.173 47.826 0.00 0.00 34.23 2.90
272 275 3.615110 CGATACATGGTGGTCCTAGATGC 60.615 52.174 0.00 0.00 34.23 3.91
273 276 1.583556 ACATGGTGGTCCTAGATGCA 58.416 50.000 0.00 0.00 34.23 3.96
274 277 2.130193 ACATGGTGGTCCTAGATGCAT 58.870 47.619 0.00 0.00 34.23 3.96
275 278 2.105477 ACATGGTGGTCCTAGATGCATC 59.895 50.000 19.37 19.37 34.23 3.91
276 279 1.131638 TGGTGGTCCTAGATGCATCC 58.868 55.000 23.06 7.99 34.23 3.51
277 280 1.131638 GGTGGTCCTAGATGCATCCA 58.868 55.000 23.06 10.72 0.00 3.41
278 281 1.202698 GGTGGTCCTAGATGCATCCAC 60.203 57.143 23.06 21.12 42.87 4.02
279 282 1.486310 GTGGTCCTAGATGCATCCACA 59.514 52.381 23.06 10.22 43.03 4.17
280 283 1.486310 TGGTCCTAGATGCATCCACAC 59.514 52.381 23.06 13.85 0.00 3.82
281 284 1.486310 GGTCCTAGATGCATCCACACA 59.514 52.381 23.06 0.98 0.00 3.72
282 285 2.484417 GGTCCTAGATGCATCCACACAG 60.484 54.545 23.06 11.91 0.00 3.66
283 286 1.139654 TCCTAGATGCATCCACACAGC 59.860 52.381 23.06 0.00 0.00 4.40
284 287 1.590932 CTAGATGCATCCACACAGCC 58.409 55.000 23.06 0.00 0.00 4.85
285 288 0.179076 TAGATGCATCCACACAGCCG 60.179 55.000 23.06 0.00 0.00 5.52
286 289 1.746615 GATGCATCCACACAGCCGT 60.747 57.895 16.23 0.00 0.00 5.68
288 291 2.358615 GCATCCACACAGCCGTGA 60.359 61.111 7.16 0.00 46.80 4.35
289 292 1.746615 GCATCCACACAGCCGTGAT 60.747 57.895 7.16 0.00 46.80 3.06
290 293 0.461870 GCATCCACACAGCCGTGATA 60.462 55.000 7.16 0.00 46.80 2.15
291 294 1.290203 CATCCACACAGCCGTGATAC 58.710 55.000 7.16 0.00 46.80 2.24
292 295 0.901827 ATCCACACAGCCGTGATACA 59.098 50.000 7.16 0.00 46.80 2.29
293 296 0.037697 TCCACACAGCCGTGATACAC 60.038 55.000 7.16 0.00 46.80 2.90
294 297 0.037326 CCACACAGCCGTGATACACT 60.037 55.000 7.16 0.00 46.80 3.55
295 298 1.350193 CACACAGCCGTGATACACTC 58.650 55.000 7.16 0.00 46.80 3.51
296 299 1.067565 CACACAGCCGTGATACACTCT 60.068 52.381 7.16 0.00 46.80 3.24
297 300 2.163613 CACACAGCCGTGATACACTCTA 59.836 50.000 7.16 0.00 46.80 2.43
298 301 2.163815 ACACAGCCGTGATACACTCTAC 59.836 50.000 7.16 0.00 46.80 2.59
299 302 1.400846 ACAGCCGTGATACACTCTACG 59.599 52.381 0.00 0.00 36.39 3.51
300 303 1.400846 CAGCCGTGATACACTCTACGT 59.599 52.381 0.00 0.00 34.96 3.57
312 315 3.355270 CACTCTACGTGTCTTATGCTCG 58.645 50.000 0.00 0.00 38.84 5.03
313 316 3.063588 CACTCTACGTGTCTTATGCTCGA 59.936 47.826 0.00 0.00 38.84 4.04
314 317 3.063725 ACTCTACGTGTCTTATGCTCGAC 59.936 47.826 0.00 0.00 0.00 4.20
315 318 3.268330 TCTACGTGTCTTATGCTCGACT 58.732 45.455 0.00 0.00 0.00 4.18
316 319 2.546195 ACGTGTCTTATGCTCGACTC 57.454 50.000 0.00 0.00 0.00 3.36
317 320 2.085320 ACGTGTCTTATGCTCGACTCT 58.915 47.619 0.00 0.00 0.00 3.24
318 321 2.488545 ACGTGTCTTATGCTCGACTCTT 59.511 45.455 0.00 0.00 0.00 2.85
319 322 3.102276 CGTGTCTTATGCTCGACTCTTC 58.898 50.000 0.00 0.00 0.00 2.87
322 325 5.447413 CGTGTCTTATGCTCGACTCTTCTAA 60.447 44.000 0.00 0.00 0.00 2.10
327 330 8.536407 GTCTTATGCTCGACTCTTCTAATTTTC 58.464 37.037 0.00 0.00 0.00 2.29
362 366 0.445829 TGGCGTATTGATTGTGTGCG 59.554 50.000 0.00 0.00 0.00 5.34
383 387 2.163010 GTCGTGTTATGAAGAGACGGGA 59.837 50.000 0.00 0.00 34.90 5.14
390 394 0.976641 TGAAGAGACGGGAGCACAAT 59.023 50.000 0.00 0.00 0.00 2.71
420 424 4.188247 ACGGTTGTATCATCCGGATATG 57.812 45.455 18.63 7.82 46.94 1.78
551 562 4.718774 AGCAGGATATATATCACTGGGGTG 59.281 45.833 26.09 14.16 44.23 4.61
575 586 0.613572 TGCATCCTCGGTACAGGTCA 60.614 55.000 0.00 0.00 34.76 4.02
579 590 1.191535 TCCTCGGTACAGGTCATTGG 58.808 55.000 0.00 0.00 34.76 3.16
699 712 2.522185 ACCGAAGTAGCAGTGGAGTAA 58.478 47.619 0.00 0.00 0.00 2.24
700 713 2.230750 ACCGAAGTAGCAGTGGAGTAAC 59.769 50.000 0.00 0.00 0.00 2.50
702 715 3.119101 CCGAAGTAGCAGTGGAGTAACAT 60.119 47.826 0.00 0.00 0.00 2.71
704 717 5.221263 CCGAAGTAGCAGTGGAGTAACATAT 60.221 44.000 0.00 0.00 0.00 1.78
706 719 7.309255 CCGAAGTAGCAGTGGAGTAACATATAT 60.309 40.741 0.00 0.00 0.00 0.86
708 721 9.843334 GAAGTAGCAGTGGAGTAACATATATAC 57.157 37.037 0.00 0.00 0.00 1.47
709 722 8.041829 AGTAGCAGTGGAGTAACATATATACG 57.958 38.462 0.00 0.00 0.00 3.06
710 723 6.896021 AGCAGTGGAGTAACATATATACGT 57.104 37.500 0.00 0.00 0.00 3.57
711 724 7.991084 AGCAGTGGAGTAACATATATACGTA 57.009 36.000 0.00 0.00 0.00 3.57
712 725 8.577048 AGCAGTGGAGTAACATATATACGTAT 57.423 34.615 13.54 13.54 0.00 3.06
713 726 9.676861 AGCAGTGGAGTAACATATATACGTATA 57.323 33.333 17.24 17.24 0.00 1.47
807 2368 1.211709 CCATGACGGCCGGAAAAAC 59.788 57.895 31.76 13.25 0.00 2.43
808 2369 1.154301 CATGACGGCCGGAAAAACG 60.154 57.895 31.76 6.93 0.00 3.60
809 2370 1.301874 ATGACGGCCGGAAAAACGA 60.302 52.632 31.76 3.52 35.47 3.85
810 2371 1.571215 ATGACGGCCGGAAAAACGAC 61.571 55.000 31.76 9.06 35.47 4.34
811 2372 3.285776 GACGGCCGGAAAAACGACG 62.286 63.158 31.76 0.00 38.98 5.12
812 2373 4.729798 CGGCCGGAAAAACGACGC 62.730 66.667 20.10 0.00 35.47 5.19
813 2374 3.351416 GGCCGGAAAAACGACGCT 61.351 61.111 5.05 0.00 35.47 5.07
814 2375 2.172659 GCCGGAAAAACGACGCTC 59.827 61.111 5.05 0.00 35.47 5.03
815 2376 2.315386 GCCGGAAAAACGACGCTCT 61.315 57.895 5.05 0.00 35.47 4.09
816 2377 1.838568 GCCGGAAAAACGACGCTCTT 61.839 55.000 5.05 0.00 35.47 2.85
817 2378 1.421382 CCGGAAAAACGACGCTCTTA 58.579 50.000 0.00 0.00 35.47 2.10
818 2379 1.794116 CCGGAAAAACGACGCTCTTAA 59.206 47.619 0.00 0.00 35.47 1.85
819 2380 2.414138 CCGGAAAAACGACGCTCTTAAT 59.586 45.455 0.00 0.00 35.47 1.40
820 2381 3.613737 CCGGAAAAACGACGCTCTTAATA 59.386 43.478 0.00 0.00 35.47 0.98
821 2382 4.091800 CCGGAAAAACGACGCTCTTAATAA 59.908 41.667 0.00 0.00 35.47 1.40
836 2397 7.386299 CGCTCTTAATAATTAGTCAATGCTCCT 59.614 37.037 0.00 0.00 0.00 3.69
852 2413 3.381908 TGCTCCTTTTAGATCTCGGAGAC 59.618 47.826 23.71 17.61 43.02 3.36
888 2449 1.299541 CTTTATCGCCGGCAACTCAT 58.700 50.000 28.98 11.85 0.00 2.90
1122 2690 1.066430 GTCGGGTTCTACAGGCAATCA 60.066 52.381 0.00 0.00 0.00 2.57
1185 2753 2.271800 GCTGTGGAAGATGACCTAACG 58.728 52.381 0.00 0.00 0.00 3.18
1238 2806 3.410631 TGATTGCTTCGTCAGGGTAAA 57.589 42.857 0.00 0.00 0.00 2.01
1240 2808 4.331968 TGATTGCTTCGTCAGGGTAAAAT 58.668 39.130 0.00 0.00 0.00 1.82
1241 2809 4.155826 TGATTGCTTCGTCAGGGTAAAATG 59.844 41.667 0.00 0.00 0.00 2.32
1242 2810 1.810151 TGCTTCGTCAGGGTAAAATGC 59.190 47.619 0.00 0.00 0.00 3.56
1245 2813 3.057526 GCTTCGTCAGGGTAAAATGCTTT 60.058 43.478 0.00 0.00 0.00 3.51
1246 2814 4.475944 CTTCGTCAGGGTAAAATGCTTTG 58.524 43.478 0.00 0.00 0.00 2.77
1247 2815 2.227865 TCGTCAGGGTAAAATGCTTTGC 59.772 45.455 0.00 0.00 0.00 3.68
1248 2816 2.671070 CGTCAGGGTAAAATGCTTTGCC 60.671 50.000 0.00 0.00 44.29 4.52
1272 2857 4.367039 AGCTTGGGTCTTTAACTGCTAA 57.633 40.909 0.00 0.00 0.00 3.09
1295 2880 1.230324 GCAGTCCCTCACTTTGTGAC 58.770 55.000 0.00 0.00 37.67 3.67
1296 2881 1.475034 GCAGTCCCTCACTTTGTGACA 60.475 52.381 0.00 0.00 37.67 3.58
1297 2882 2.811873 GCAGTCCCTCACTTTGTGACAT 60.812 50.000 0.00 0.00 37.67 3.06
1298 2883 2.810274 CAGTCCCTCACTTTGTGACATG 59.190 50.000 0.00 0.00 37.67 3.21
1347 2933 1.265365 GCTGCTCAACTCAACCAAGAC 59.735 52.381 0.00 0.00 0.00 3.01
1408 2994 1.007336 ACGCCTTCAACGTGATCGAC 61.007 55.000 0.00 0.00 43.23 4.20
1430 3016 1.836166 CCATCAAGGAGAAGCTGGAGA 59.164 52.381 0.00 0.00 41.22 3.71
1532 3118 3.526841 AGCCTCTTTTCCTCCATTCAGAT 59.473 43.478 0.00 0.00 0.00 2.90
1542 3128 5.205821 TCCTCCATTCAGATTGCATCAAAT 58.794 37.500 0.00 0.00 0.00 2.32
1595 3181 1.192146 AGCTAGCGTTGACTTGGGGA 61.192 55.000 9.55 0.00 0.00 4.81
1606 3216 1.005450 GACTTGGGGATTAACCAGGCA 59.995 52.381 0.00 0.00 38.54 4.75
1634 3244 0.681243 GGTGACCAAGGGAGAATGGC 60.681 60.000 0.00 0.00 40.51 4.40
1852 3462 7.544566 AGTTTCTATTTTCGAATCTTGCGAGTA 59.455 33.333 0.00 0.00 39.14 2.59
1859 3469 8.420374 TTTTCGAATCTTGCGAGTATTCTATT 57.580 30.769 17.09 4.52 39.14 1.73
1867 3477 5.608676 TGCGAGTATTCTATTCTAGGACG 57.391 43.478 0.00 0.00 0.00 4.79
1878 3488 6.736123 TCTATTCTAGGACGAGTTGCATTAC 58.264 40.000 0.00 0.00 0.00 1.89
1922 3532 2.357637 CGGTTGCCCCAATTGTATGTAG 59.642 50.000 4.43 0.00 0.00 2.74
1923 3533 2.693074 GGTTGCCCCAATTGTATGTAGG 59.307 50.000 4.43 0.00 0.00 3.18
1934 3985 5.769484 ATTGTATGTAGGACTACTCACGG 57.231 43.478 10.51 0.00 37.00 4.94
1947 3998 0.744414 CTCACGGCCCCACTACATTG 60.744 60.000 0.00 0.00 0.00 2.82
2164 6537 0.106894 TTCACGTGTGTGCCCATACA 59.893 50.000 16.51 0.00 46.01 2.29
2214 6587 6.868864 TCTTCTCTCTTAATGAAAAGACACGG 59.131 38.462 0.00 0.00 32.18 4.94
2225 6598 3.485463 AAAGACACGGAAACCTCATGA 57.515 42.857 0.00 0.00 0.00 3.07
2372 6771 5.348833 AGGGGACATGCTAGATGATATCTT 58.651 41.667 3.98 0.00 40.76 2.40
2380 6779 9.836864 ACATGCTAGATGATATCTTGTGTTTTA 57.163 29.630 3.98 0.00 40.76 1.52
2429 6828 7.792374 TCTATGAGATTTGTTTGTATGGAGC 57.208 36.000 0.00 0.00 0.00 4.70
2573 6972 9.007901 CAGAGGGAGTATGATTTATGGAATTTC 57.992 37.037 0.00 0.00 0.00 2.17
2592 6991 9.903682 GGAATTTCATCATGGTGAATATAAGTG 57.096 33.333 21.71 0.00 37.88 3.16
2602 7001 7.744087 TGGTGAATATAAGTGGCATGATAAC 57.256 36.000 0.00 0.00 0.00 1.89
2615 7014 8.850156 AGTGGCATGATAACTTGGAAATAATAC 58.150 33.333 0.00 0.00 0.00 1.89
2760 7159 8.601845 TTTGATCATGGTGAATATAAGTACCG 57.398 34.615 0.00 0.00 35.98 4.02
2872 7271 7.988737 ACAATCGAAATTCTTTCTCATGCATA 58.011 30.769 0.00 0.00 37.52 3.14
2898 7297 7.503230 AGTTGCATATTGATGTGATATGGTTCA 59.497 33.333 0.00 0.00 37.74 3.18
2900 7299 8.411991 TGCATATTGATGTGATATGGTTCAAT 57.588 30.769 6.32 0.00 39.58 2.57
2901 7300 9.517868 TGCATATTGATGTGATATGGTTCAATA 57.482 29.630 6.23 6.23 41.14 1.90
2910 7309 7.492524 TGTGATATGGTTCAATAGTGAGAGAC 58.507 38.462 0.00 0.00 34.49 3.36
2926 7325 8.834749 AGTGAGAGACTTAATTTAGTGGAAAC 57.165 34.615 1.04 0.00 0.00 2.78
2932 7331 8.567285 AGACTTAATTTAGTGGAAACCATCAG 57.433 34.615 1.04 0.00 35.28 2.90
3201 7600 0.449388 CGACTTACTACCGCCTCGTT 59.551 55.000 0.00 0.00 0.00 3.85
3377 7776 0.029267 AGCAAGGGGGAGATCAGGAT 60.029 55.000 0.00 0.00 0.00 3.24
3402 7801 4.630069 ACATGTGCCGTTCTCAACTAATAC 59.370 41.667 0.00 0.00 0.00 1.89
3442 7841 5.931724 TCTACTGTGTATGTGGTGTTCAATG 59.068 40.000 0.00 0.00 0.00 2.82
3479 7878 8.178313 GCTTTTCTTCAATAGATGTGTAGGAAC 58.822 37.037 0.00 0.00 31.54 3.62
3502 7901 8.634475 AACTAAAGTTTTGACTTCAGAATTGC 57.366 30.769 4.00 0.00 33.93 3.56
3509 7908 3.225104 TGACTTCAGAATTGCCAGCTTT 58.775 40.909 0.00 0.00 0.00 3.51
3601 8004 4.571984 TCTTCGTTACGGATCTATCGTGAA 59.428 41.667 4.53 1.41 41.24 3.18
3605 8009 7.137490 TCGTTACGGATCTATCGTGAATAAT 57.863 36.000 4.53 0.00 41.24 1.28
3648 8052 6.923508 TGATTGAGTACCTAGTATTTGCATCG 59.076 38.462 0.00 0.00 0.00 3.84
3691 8097 3.746045 ATTGCATGCCATCAATCCTTC 57.254 42.857 16.68 0.00 0.00 3.46
3702 8108 7.345691 TGCCATCAATCCTTCTAAGAAATGTA 58.654 34.615 0.00 0.00 0.00 2.29
3797 8204 9.378551 CCTATTGCTAGACAACAATACAAACTA 57.621 33.333 0.00 0.00 42.27 2.24
3834 8241 2.766263 TGTACCATCTCTAAGTGCCTGG 59.234 50.000 0.00 0.00 0.00 4.45
3842 8249 3.205507 TCTCTAAGTGCCTGGACCTAGAT 59.794 47.826 0.00 0.00 0.00 1.98
3856 8263 4.645588 GGACCTAGATACCAGAATATCCCG 59.354 50.000 0.00 0.00 32.76 5.14
3867 8274 5.894393 ACCAGAATATCCCGTATCTCCATAG 59.106 44.000 0.00 0.00 0.00 2.23
3868 8275 5.894393 CCAGAATATCCCGTATCTCCATAGT 59.106 44.000 0.00 0.00 0.00 2.12
3869 8276 7.061054 CCAGAATATCCCGTATCTCCATAGTA 58.939 42.308 0.00 0.00 0.00 1.82
3921 8331 8.043113 TCAAGTGATTAGTATTGACAATCTGCT 58.957 33.333 3.36 4.75 31.37 4.24
3930 8340 7.318141 AGTATTGACAATCTGCTGAAAATTGG 58.682 34.615 3.36 0.00 35.24 3.16
3931 8341 5.787953 TTGACAATCTGCTGAAAATTGGA 57.212 34.783 9.38 0.00 35.24 3.53
3973 8383 6.177663 AGATATCCCTCTCATAATCCCACT 57.822 41.667 0.00 0.00 0.00 4.00
3974 8384 6.579214 AGATATCCCTCTCATAATCCCACTT 58.421 40.000 0.00 0.00 0.00 3.16
3988 8398 8.820831 CATAATCCCACTTGATCCTCTACTTAT 58.179 37.037 0.00 0.00 0.00 1.73
4067 8477 6.065374 TGACTAAGAATACAAAAGTTGCCCA 58.935 36.000 0.00 0.00 0.00 5.36
4068 8478 6.547880 TGACTAAGAATACAAAAGTTGCCCAA 59.452 34.615 0.00 0.00 0.00 4.12
4072 8482 9.921637 CTAAGAATACAAAAGTTGCCCAATAAA 57.078 29.630 0.00 0.00 0.00 1.40
4085 8495 3.554129 GCCCAATAAAACCGAGCAAAACT 60.554 43.478 0.00 0.00 0.00 2.66
4087 8497 4.261825 CCCAATAAAACCGAGCAAAACTCA 60.262 41.667 0.00 0.00 46.63 3.41
4092 8502 1.148310 ACCGAGCAAAACTCATCACG 58.852 50.000 0.00 0.00 46.63 4.35
4103 8513 1.753649 ACTCATCACGACCCTCTGATG 59.246 52.381 5.35 5.35 43.53 3.07
4111 8521 3.096852 ACGACCCTCTGATGATACACAA 58.903 45.455 0.00 0.00 0.00 3.33
4112 8522 3.513912 ACGACCCTCTGATGATACACAAA 59.486 43.478 0.00 0.00 0.00 2.83
4138 8548 8.475331 AAAAGTATAAATCACTCACCACTACG 57.525 34.615 0.00 0.00 0.00 3.51
4139 8549 7.400599 AAGTATAAATCACTCACCACTACGA 57.599 36.000 0.00 0.00 0.00 3.43
4140 8550 7.584122 AGTATAAATCACTCACCACTACGAT 57.416 36.000 0.00 0.00 0.00 3.73
4174 8587 0.240678 GTTGCATGTTGGCGTCATCA 59.759 50.000 2.81 2.81 36.28 3.07
4177 8590 1.425031 CATGTTGGCGTCATCACCG 59.575 57.895 2.30 0.00 0.00 4.94
4190 8603 2.507110 ATCACCGCCACTTCTCCACG 62.507 60.000 0.00 0.00 0.00 4.94
4247 8660 2.668212 CTCGAACCGCAAAGGCCA 60.668 61.111 5.01 0.00 46.52 5.36
4249 8662 4.383602 CGAACCGCAAAGGCCACG 62.384 66.667 5.01 2.55 46.52 4.94
4274 8687 2.943690 AGTCACATGCAGATCAATCAGC 59.056 45.455 0.00 0.82 39.44 4.26
4279 8692 1.456296 TGCAGATCAATCAGCCACAC 58.544 50.000 5.11 0.00 38.39 3.82
4284 8697 2.076100 GATCAATCAGCCACACGTCAA 58.924 47.619 0.00 0.00 0.00 3.18
4299 8712 0.980423 GTCAAGAACAGGGCCTCTCT 59.020 55.000 0.95 5.88 0.00 3.10
4321 8734 2.164624 GGATCCGGGATTGATCTACGAG 59.835 54.545 11.57 0.00 38.89 4.18
4343 8756 6.017440 CGAGGGAGAACTATGAAAGACTAGAG 60.017 46.154 0.00 0.00 0.00 2.43
4348 8761 2.362717 ACTATGAAAGACTAGAGCCGCC 59.637 50.000 0.00 0.00 0.00 6.13
4369 8782 1.584724 AGGATCACCTAGGTGTTGGG 58.415 55.000 35.34 15.07 45.83 4.12
4370 8783 1.080498 AGGATCACCTAGGTGTTGGGA 59.920 52.381 35.34 20.27 45.83 4.37
4371 8784 1.913419 GGATCACCTAGGTGTTGGGAA 59.087 52.381 35.34 19.58 45.55 3.97
4372 8785 2.307686 GGATCACCTAGGTGTTGGGAAA 59.692 50.000 35.34 18.89 45.55 3.13
4373 8786 2.943036 TCACCTAGGTGTTGGGAAAC 57.057 50.000 35.34 0.00 45.55 2.78
4374 8787 2.128535 TCACCTAGGTGTTGGGAAACA 58.871 47.619 35.34 14.90 45.55 2.83
4375 8788 2.714250 TCACCTAGGTGTTGGGAAACAT 59.286 45.455 35.34 0.00 45.55 2.71
4376 8789 3.911260 TCACCTAGGTGTTGGGAAACATA 59.089 43.478 35.34 13.70 45.55 2.29
4377 8790 4.019681 TCACCTAGGTGTTGGGAAACATAG 60.020 45.833 35.34 10.39 45.55 2.23
4378 8791 3.914435 ACCTAGGTGTTGGGAAACATAGT 59.086 43.478 15.42 0.00 34.86 2.12
4379 8792 5.046159 CACCTAGGTGTTGGGAAACATAGTA 60.046 44.000 30.57 0.00 40.91 1.82
4380 8793 5.189145 ACCTAGGTGTTGGGAAACATAGTAG 59.811 44.000 15.42 0.00 34.86 2.57
4381 8794 4.569719 AGGTGTTGGGAAACATAGTAGG 57.430 45.455 0.00 0.00 34.86 3.18
4382 8795 4.172807 AGGTGTTGGGAAACATAGTAGGA 58.827 43.478 0.00 0.00 34.86 2.94
4383 8796 4.600111 AGGTGTTGGGAAACATAGTAGGAA 59.400 41.667 0.00 0.00 34.86 3.36
4384 8797 5.073965 AGGTGTTGGGAAACATAGTAGGAAA 59.926 40.000 0.00 0.00 34.86 3.13
4385 8798 5.771165 GGTGTTGGGAAACATAGTAGGAAAA 59.229 40.000 0.00 0.00 34.86 2.29
4386 8799 6.265876 GGTGTTGGGAAACATAGTAGGAAAAA 59.734 38.462 0.00 0.00 34.86 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 94 6.317140 CCGAAGATTATACATCAATGATGGGG 59.683 42.308 24.99 3.00 43.60 4.96
184 187 6.976636 AAAACTCCTTTTTCATCGCAAAAA 57.023 29.167 0.00 0.00 31.23 1.94
185 188 8.655651 AATAAAACTCCTTTTTCATCGCAAAA 57.344 26.923 0.00 0.00 38.43 2.44
186 189 7.383843 GGAATAAAACTCCTTTTTCATCGCAAA 59.616 33.333 0.00 0.00 38.43 3.68
187 190 6.866248 GGAATAAAACTCCTTTTTCATCGCAA 59.134 34.615 0.00 0.00 38.43 4.85
188 191 6.015856 TGGAATAAAACTCCTTTTTCATCGCA 60.016 34.615 0.00 0.00 38.43 5.10
189 192 6.386654 TGGAATAAAACTCCTTTTTCATCGC 58.613 36.000 0.00 0.00 38.43 4.58
190 193 8.810652 TTTGGAATAAAACTCCTTTTTCATCG 57.189 30.769 0.00 0.00 38.43 3.84
199 202 9.981460 ACTCTATCAATTTGGAATAAAACTCCT 57.019 29.630 0.00 0.00 33.77 3.69
208 211 9.739276 TTGACTGTAACTCTATCAATTTGGAAT 57.261 29.630 0.00 0.00 0.00 3.01
209 212 9.219603 CTTGACTGTAACTCTATCAATTTGGAA 57.780 33.333 0.00 0.00 0.00 3.53
210 213 8.593679 TCTTGACTGTAACTCTATCAATTTGGA 58.406 33.333 0.00 0.00 0.00 3.53
211 214 8.777865 TCTTGACTGTAACTCTATCAATTTGG 57.222 34.615 0.00 0.00 0.00 3.28
212 215 8.877779 CCTCTTGACTGTAACTCTATCAATTTG 58.122 37.037 0.00 0.00 0.00 2.32
213 216 7.550906 GCCTCTTGACTGTAACTCTATCAATTT 59.449 37.037 0.00 0.00 0.00 1.82
214 217 7.044798 GCCTCTTGACTGTAACTCTATCAATT 58.955 38.462 0.00 0.00 0.00 2.32
215 218 6.155221 TGCCTCTTGACTGTAACTCTATCAAT 59.845 38.462 0.00 0.00 0.00 2.57
216 219 5.480422 TGCCTCTTGACTGTAACTCTATCAA 59.520 40.000 0.00 0.00 0.00 2.57
217 220 5.016831 TGCCTCTTGACTGTAACTCTATCA 58.983 41.667 0.00 0.00 0.00 2.15
218 221 5.584253 TGCCTCTTGACTGTAACTCTATC 57.416 43.478 0.00 0.00 0.00 2.08
219 222 6.360370 TTTGCCTCTTGACTGTAACTCTAT 57.640 37.500 0.00 0.00 0.00 1.98
220 223 5.801531 TTTGCCTCTTGACTGTAACTCTA 57.198 39.130 0.00 0.00 0.00 2.43
221 224 4.689612 TTTGCCTCTTGACTGTAACTCT 57.310 40.909 0.00 0.00 0.00 3.24
222 225 5.057149 TCTTTTGCCTCTTGACTGTAACTC 58.943 41.667 0.00 0.00 0.00 3.01
223 226 5.036117 TCTTTTGCCTCTTGACTGTAACT 57.964 39.130 0.00 0.00 0.00 2.24
224 227 5.106515 GGATCTTTTGCCTCTTGACTGTAAC 60.107 44.000 0.00 0.00 0.00 2.50
225 228 5.003804 GGATCTTTTGCCTCTTGACTGTAA 58.996 41.667 0.00 0.00 0.00 2.41
226 229 4.287067 AGGATCTTTTGCCTCTTGACTGTA 59.713 41.667 0.00 0.00 0.00 2.74
227 230 3.073650 AGGATCTTTTGCCTCTTGACTGT 59.926 43.478 0.00 0.00 0.00 3.55
228 231 3.683802 AGGATCTTTTGCCTCTTGACTG 58.316 45.455 0.00 0.00 0.00 3.51
229 232 3.618507 CGAGGATCTTTTGCCTCTTGACT 60.619 47.826 0.00 0.00 46.75 3.41
230 233 2.675348 CGAGGATCTTTTGCCTCTTGAC 59.325 50.000 0.00 0.00 46.75 3.18
231 234 2.567169 TCGAGGATCTTTTGCCTCTTGA 59.433 45.455 0.00 0.00 46.75 3.02
232 235 2.977914 TCGAGGATCTTTTGCCTCTTG 58.022 47.619 0.00 0.00 46.75 3.02
233 236 3.922171 ATCGAGGATCTTTTGCCTCTT 57.078 42.857 0.00 0.00 46.75 2.85
234 237 3.706594 TGTATCGAGGATCTTTTGCCTCT 59.293 43.478 0.00 0.00 46.75 3.69
235 238 4.060038 TGTATCGAGGATCTTTTGCCTC 57.940 45.455 0.00 0.00 45.73 4.70
236 239 4.384056 CATGTATCGAGGATCTTTTGCCT 58.616 43.478 0.00 0.00 37.18 4.75
237 240 3.499918 CCATGTATCGAGGATCTTTTGCC 59.500 47.826 0.00 0.00 0.00 4.52
238 241 4.024556 CACCATGTATCGAGGATCTTTTGC 60.025 45.833 0.00 0.00 0.00 3.68
239 242 4.512944 CCACCATGTATCGAGGATCTTTTG 59.487 45.833 0.00 0.00 0.00 2.44
240 243 4.164221 ACCACCATGTATCGAGGATCTTTT 59.836 41.667 0.00 0.00 0.00 2.27
241 244 3.711704 ACCACCATGTATCGAGGATCTTT 59.288 43.478 0.00 0.00 0.00 2.52
242 245 3.309296 ACCACCATGTATCGAGGATCTT 58.691 45.455 0.00 0.00 0.00 2.40
243 246 2.894126 GACCACCATGTATCGAGGATCT 59.106 50.000 0.00 0.00 0.00 2.75
244 247 2.028930 GGACCACCATGTATCGAGGATC 60.029 54.545 0.00 0.00 35.97 3.36
245 248 1.971357 GGACCACCATGTATCGAGGAT 59.029 52.381 0.00 0.00 35.97 3.24
246 249 1.063190 AGGACCACCATGTATCGAGGA 60.063 52.381 0.00 0.00 38.94 3.71
247 250 1.414158 AGGACCACCATGTATCGAGG 58.586 55.000 0.00 0.00 38.94 4.63
248 251 3.487372 TCTAGGACCACCATGTATCGAG 58.513 50.000 0.00 0.00 38.94 4.04
249 252 3.588210 TCTAGGACCACCATGTATCGA 57.412 47.619 0.00 0.00 38.94 3.59
250 253 3.615110 GCATCTAGGACCACCATGTATCG 60.615 52.174 0.00 0.00 38.94 2.92
251 254 3.324846 TGCATCTAGGACCACCATGTATC 59.675 47.826 0.00 0.00 38.94 2.24
252 255 3.317406 TGCATCTAGGACCACCATGTAT 58.683 45.455 0.00 0.00 38.94 2.29
253 256 2.758130 TGCATCTAGGACCACCATGTA 58.242 47.619 0.00 0.00 38.94 2.29
254 257 1.583556 TGCATCTAGGACCACCATGT 58.416 50.000 0.00 0.00 38.94 3.21
255 258 2.551721 GGATGCATCTAGGACCACCATG 60.552 54.545 25.28 0.00 38.94 3.66
256 259 1.701847 GGATGCATCTAGGACCACCAT 59.298 52.381 25.28 0.00 38.94 3.55
257 260 1.131638 GGATGCATCTAGGACCACCA 58.868 55.000 25.28 0.00 38.94 4.17
258 261 1.131638 TGGATGCATCTAGGACCACC 58.868 55.000 25.28 7.45 0.00 4.61
259 262 1.486310 TGTGGATGCATCTAGGACCAC 59.514 52.381 25.28 22.65 45.16 4.16
260 263 1.486310 GTGTGGATGCATCTAGGACCA 59.514 52.381 25.28 12.29 0.00 4.02
261 264 1.486310 TGTGTGGATGCATCTAGGACC 59.514 52.381 25.28 9.67 0.00 4.46
262 265 2.831333 CTGTGTGGATGCATCTAGGAC 58.169 52.381 25.28 18.21 0.00 3.85
263 266 1.139654 GCTGTGTGGATGCATCTAGGA 59.860 52.381 25.28 7.11 0.00 2.94
264 267 1.590932 GCTGTGTGGATGCATCTAGG 58.409 55.000 25.28 11.23 0.00 3.02
265 268 1.590932 GGCTGTGTGGATGCATCTAG 58.409 55.000 25.28 15.92 0.00 2.43
266 269 0.179076 CGGCTGTGTGGATGCATCTA 60.179 55.000 25.28 17.90 0.00 1.98
267 270 1.450848 CGGCTGTGTGGATGCATCT 60.451 57.895 25.28 0.00 0.00 2.90
268 271 1.746615 ACGGCTGTGTGGATGCATC 60.747 57.895 18.81 18.81 0.00 3.91
269 272 2.042259 CACGGCTGTGTGGATGCAT 61.042 57.895 17.96 0.00 41.34 3.96
270 273 2.467993 ATCACGGCTGTGTGGATGCA 62.468 55.000 24.61 4.45 46.49 3.96
271 274 0.461870 TATCACGGCTGTGTGGATGC 60.462 55.000 24.61 0.00 46.49 3.91
272 275 1.290203 GTATCACGGCTGTGTGGATG 58.710 55.000 24.61 0.00 46.49 3.51
273 276 0.901827 TGTATCACGGCTGTGTGGAT 59.098 50.000 24.61 13.77 46.49 3.41
274 277 0.037697 GTGTATCACGGCTGTGTGGA 60.038 55.000 24.61 6.79 46.49 4.02
275 278 0.037326 AGTGTATCACGGCTGTGTGG 60.037 55.000 24.61 0.00 46.49 4.17
276 279 1.067565 AGAGTGTATCACGGCTGTGTG 60.068 52.381 24.61 11.33 46.49 3.82
277 280 1.257743 AGAGTGTATCACGGCTGTGT 58.742 50.000 24.61 14.52 46.49 3.72
279 282 1.400846 CGTAGAGTGTATCACGGCTGT 59.599 52.381 0.00 0.00 39.64 4.40
280 283 1.400846 ACGTAGAGTGTATCACGGCTG 59.599 52.381 0.00 0.00 39.64 4.85
281 284 1.400846 CACGTAGAGTGTATCACGGCT 59.599 52.381 0.00 0.00 45.51 5.52
282 285 1.823828 CACGTAGAGTGTATCACGGC 58.176 55.000 0.00 0.00 45.51 5.68
292 295 3.063725 GTCGAGCATAAGACACGTAGAGT 59.936 47.826 0.00 0.00 37.34 3.24
293 296 3.310227 AGTCGAGCATAAGACACGTAGAG 59.690 47.826 0.00 0.00 39.67 2.43
294 297 3.268330 AGTCGAGCATAAGACACGTAGA 58.732 45.455 0.00 0.00 39.67 2.59
295 298 3.310227 AGAGTCGAGCATAAGACACGTAG 59.690 47.826 0.00 0.00 39.67 3.51
296 299 3.268330 AGAGTCGAGCATAAGACACGTA 58.732 45.455 0.00 0.00 39.67 3.57
297 300 2.085320 AGAGTCGAGCATAAGACACGT 58.915 47.619 0.00 0.00 39.67 4.49
298 301 2.834574 AGAGTCGAGCATAAGACACG 57.165 50.000 0.00 0.00 39.67 4.49
299 302 4.364415 AGAAGAGTCGAGCATAAGACAC 57.636 45.455 0.00 0.00 39.67 3.67
300 303 6.701145 ATTAGAAGAGTCGAGCATAAGACA 57.299 37.500 0.00 0.00 39.67 3.41
301 304 7.995463 AAATTAGAAGAGTCGAGCATAAGAC 57.005 36.000 0.00 0.00 37.63 3.01
302 305 8.470805 AGAAAATTAGAAGAGTCGAGCATAAGA 58.529 33.333 0.00 0.00 0.00 2.10
303 306 8.538856 CAGAAAATTAGAAGAGTCGAGCATAAG 58.461 37.037 0.00 0.00 0.00 1.73
304 307 8.035394 ACAGAAAATTAGAAGAGTCGAGCATAA 58.965 33.333 0.00 0.00 0.00 1.90
305 308 7.548097 ACAGAAAATTAGAAGAGTCGAGCATA 58.452 34.615 0.00 0.00 0.00 3.14
306 309 6.402222 ACAGAAAATTAGAAGAGTCGAGCAT 58.598 36.000 0.00 0.00 0.00 3.79
307 310 5.784177 ACAGAAAATTAGAAGAGTCGAGCA 58.216 37.500 0.00 0.00 0.00 4.26
308 311 7.813852 TTACAGAAAATTAGAAGAGTCGAGC 57.186 36.000 0.00 0.00 0.00 5.03
362 366 2.163010 TCCCGTCTCTTCATAACACGAC 59.837 50.000 0.00 0.00 32.08 4.34
420 424 7.098477 TGACATTTCCATTCAATTCAATCCAC 58.902 34.615 0.00 0.00 0.00 4.02
551 562 0.461870 TGTACCGAGGATGCATGCAC 60.462 55.000 25.37 16.53 0.00 4.57
575 586 3.585856 CGGTTAGTTGCCGCCAAT 58.414 55.556 0.00 0.00 42.82 3.16
807 2368 7.004225 GCATTGACTAATTATTAAGAGCGTCG 58.996 38.462 0.00 0.00 0.00 5.12
808 2369 8.077836 AGCATTGACTAATTATTAAGAGCGTC 57.922 34.615 0.00 0.00 0.00 5.19
809 2370 7.171678 GGAGCATTGACTAATTATTAAGAGCGT 59.828 37.037 0.00 0.00 0.00 5.07
810 2371 7.386299 AGGAGCATTGACTAATTATTAAGAGCG 59.614 37.037 0.00 0.00 0.00 5.03
811 2372 8.614469 AGGAGCATTGACTAATTATTAAGAGC 57.386 34.615 0.00 0.00 0.00 4.09
820 2381 9.336171 GAGATCTAAAAGGAGCATTGACTAATT 57.664 33.333 0.00 0.00 0.00 1.40
821 2382 7.655328 CGAGATCTAAAAGGAGCATTGACTAAT 59.345 37.037 0.00 0.00 0.00 1.73
836 2397 2.097036 TGCCGTCTCCGAGATCTAAAA 58.903 47.619 0.33 0.00 35.63 1.52
882 2443 5.588648 TGAAAAGTCCTCGTTTTCATGAGTT 59.411 36.000 6.86 0.00 44.89 3.01
888 2449 4.638421 ACATGTGAAAAGTCCTCGTTTTCA 59.362 37.500 0.00 6.86 46.62 2.69
1238 2806 1.551883 CCCAAGCTAAGGCAAAGCATT 59.448 47.619 12.75 0.00 42.62 3.56
1240 2808 0.178964 ACCCAAGCTAAGGCAAAGCA 60.179 50.000 12.75 0.00 42.62 3.91
1241 2809 0.528017 GACCCAAGCTAAGGCAAAGC 59.472 55.000 1.84 3.14 41.70 3.51
1242 2810 2.206576 AGACCCAAGCTAAGGCAAAG 57.793 50.000 1.84 0.00 41.70 2.77
1245 2813 3.073946 AGTTAAAGACCCAAGCTAAGGCA 59.926 43.478 1.84 0.00 41.70 4.75
1246 2814 3.440522 CAGTTAAAGACCCAAGCTAAGGC 59.559 47.826 1.84 0.00 39.06 4.35
1247 2815 3.440522 GCAGTTAAAGACCCAAGCTAAGG 59.559 47.826 0.37 0.37 0.00 2.69
1248 2816 4.327680 AGCAGTTAAAGACCCAAGCTAAG 58.672 43.478 0.00 0.00 0.00 2.18
1272 2857 0.109342 CAAAGTGAGGGACTGCCACT 59.891 55.000 0.00 0.00 43.95 4.00
1281 2866 3.678289 TCATCATGTCACAAAGTGAGGG 58.322 45.455 0.00 0.00 43.57 4.30
1282 2867 3.688185 CCTCATCATGTCACAAAGTGAGG 59.312 47.826 16.72 16.72 43.57 3.86
1295 2880 1.100510 CAACCCTGCACCTCATCATG 58.899 55.000 0.00 0.00 0.00 3.07
1296 2881 3.583054 CAACCCTGCACCTCATCAT 57.417 52.632 0.00 0.00 0.00 2.45
1347 2933 2.202932 CCCTCTCCGCGATGTTGG 60.203 66.667 8.23 2.65 0.00 3.77
1408 2994 1.094073 CCAGCTTCTCCTTGATGGCG 61.094 60.000 0.00 0.00 32.85 5.69
1459 3045 4.194720 GCGACGGCGAGGATGTCT 62.195 66.667 18.90 0.00 40.82 3.41
1489 3075 4.448060 GCTTAATTGTATACCAGCGAGACC 59.552 45.833 0.00 0.00 0.00 3.85
1502 3088 6.134535 TGGAGGAAAAGAGGCTTAATTGTA 57.865 37.500 0.00 0.00 0.00 2.41
1506 3092 5.831103 TGAATGGAGGAAAAGAGGCTTAAT 58.169 37.500 0.00 0.00 0.00 1.40
1561 3147 3.357897 GCTAGCTTTGATTGACGCATTC 58.642 45.455 7.70 0.00 0.00 2.67
1567 3153 3.433615 AGTCAACGCTAGCTTTGATTGAC 59.566 43.478 31.68 27.07 43.94 3.18
1595 3181 2.247358 CACCTTGGTTGCCTGGTTAAT 58.753 47.619 0.00 0.00 31.30 1.40
1778 3388 5.624159 TGACAGAACAACAAGATCCTTGAT 58.376 37.500 13.00 0.00 0.00 2.57
1852 3462 5.854010 TGCAACTCGTCCTAGAATAGAAT 57.146 39.130 0.00 0.00 42.77 2.40
1859 3469 2.429610 GGGTAATGCAACTCGTCCTAGA 59.570 50.000 0.00 0.00 0.00 2.43
1867 3477 2.928116 GAGTACACGGGTAATGCAACTC 59.072 50.000 0.80 0.72 0.00 3.01
1878 3488 5.332808 CGTAAAGAACTTTTGAGTACACGGG 60.333 44.000 5.14 0.00 34.23 5.28
1922 3532 2.682494 TGGGGCCGTGAGTAGTCC 60.682 66.667 0.00 0.00 0.00 3.85
1923 3533 0.682209 TAGTGGGGCCGTGAGTAGTC 60.682 60.000 0.00 0.00 0.00 2.59
1934 3985 4.076394 TCAAGTTAACAATGTAGTGGGGC 58.924 43.478 8.61 0.00 0.00 5.80
1947 3998 7.750903 GGCATTGTCTAATTCACTCAAGTTAAC 59.249 37.037 0.00 0.00 0.00 2.01
2139 6510 1.498865 GGCACACACGTGAAGAGGTG 61.499 60.000 25.01 20.23 46.80 4.00
2164 6537 7.681939 ATCGGTTCATACAATTGTTACAAGT 57.318 32.000 17.78 0.00 0.00 3.16
2165 6538 8.450964 AGAATCGGTTCATACAATTGTTACAAG 58.549 33.333 17.78 8.28 36.79 3.16
2214 6587 3.565482 TGCAAGAACACTCATGAGGTTTC 59.435 43.478 26.08 23.81 0.00 2.78
2292 6666 1.272592 TGCATGGAAAAGGCTCATCCA 60.273 47.619 19.75 19.75 46.60 3.41
2372 6771 1.944024 CACTTCCCGCAGTAAAACACA 59.056 47.619 0.00 0.00 0.00 3.72
2380 6779 2.594592 GCAACCACTTCCCGCAGT 60.595 61.111 0.00 0.00 0.00 4.40
2529 6928 6.706270 TCCCTCTGAATCAAAATATAAGTCGC 59.294 38.462 0.00 0.00 0.00 5.19
2573 6972 6.431852 TCATGCCACTTATATTCACCATGATG 59.568 38.462 0.00 0.00 34.60 3.07
2592 6991 8.094798 TCGTATTATTTCCAAGTTATCATGCC 57.905 34.615 0.00 0.00 0.00 4.40
2813 7212 8.083828 ACTTATACTCACCATGATCAAACTCT 57.916 34.615 0.00 0.00 0.00 3.24
2818 7217 7.360113 TGCTACTTATACTCACCATGATCAA 57.640 36.000 0.00 0.00 0.00 2.57
2872 7271 7.503230 TGAACCATATCACATCAATATGCAACT 59.497 33.333 0.00 0.00 36.29 3.16
2900 7299 9.924650 GTTTCCACTAAATTAAGTCTCTCACTA 57.075 33.333 0.00 0.00 32.30 2.74
2901 7300 7.878644 GGTTTCCACTAAATTAAGTCTCTCACT 59.121 37.037 0.00 0.00 36.64 3.41
3201 7600 4.149598 GGAAAAGGCCCTTGTTCTCTTTA 58.850 43.478 0.00 0.00 0.00 1.85
3357 7756 0.642156 TCCTGATCTCCCCCTTGCTA 59.358 55.000 0.00 0.00 0.00 3.49
3361 7760 1.010046 TGTCATCCTGATCTCCCCCTT 59.990 52.381 0.00 0.00 0.00 3.95
3377 7776 1.202639 AGTTGAGAACGGCACATGTCA 60.203 47.619 0.00 0.00 36.23 3.58
3421 7820 4.460263 ACATTGAACACCACATACACAGT 58.540 39.130 0.00 0.00 0.00 3.55
3422 7821 5.214417 CAACATTGAACACCACATACACAG 58.786 41.667 0.00 0.00 0.00 3.66
3442 7841 5.482686 TTGAAGAAAAGCAAATTGGCAAC 57.517 34.783 7.75 0.00 35.83 4.17
3479 7878 7.202526 TGGCAATTCTGAAGTCAAAACTTTAG 58.797 34.615 4.27 4.27 45.80 1.85
3502 7901 3.791245 TGCCAACAAAAAGTAAAGCTGG 58.209 40.909 0.00 0.00 0.00 4.85
3639 8043 7.877612 TGGTTATATGTATCACTCGATGCAAAT 59.122 33.333 0.00 0.00 45.71 2.32
3750 8156 9.816354 AATAGGGTTTGTGATGCATAAATTTAC 57.184 29.630 0.00 0.00 28.32 2.01
3834 8241 5.262804 ACGGGATATTCTGGTATCTAGGTC 58.737 45.833 0.00 0.00 32.78 3.85
3842 8249 5.265290 TGGAGATACGGGATATTCTGGTA 57.735 43.478 0.00 0.00 0.00 3.25
3856 8263 5.776173 ACTGCAGTGTACTATGGAGATAC 57.224 43.478 20.97 0.00 38.17 2.24
3973 8383 5.458595 TCTCAGGCATAAGTAGAGGATCAA 58.541 41.667 0.00 0.00 37.82 2.57
3974 8384 5.066913 TCTCAGGCATAAGTAGAGGATCA 57.933 43.478 0.00 0.00 37.82 2.92
4055 8465 4.372656 TCGGTTTTATTGGGCAACTTTTG 58.627 39.130 0.00 0.00 0.00 2.44
4056 8466 4.627058 CTCGGTTTTATTGGGCAACTTTT 58.373 39.130 0.00 0.00 0.00 2.27
4058 8468 2.029380 GCTCGGTTTTATTGGGCAACTT 60.029 45.455 0.00 0.00 0.00 2.66
4087 8497 3.319405 GTGTATCATCAGAGGGTCGTGAT 59.681 47.826 0.00 0.00 33.52 3.06
4112 8522 8.932791 CGTAGTGGTGAGTGATTTATACTTTTT 58.067 33.333 0.00 0.00 0.00 1.94
4137 8547 3.541516 GCAACCTCGACGATGTTTTATCG 60.542 47.826 14.72 7.66 46.02 2.92
4138 8548 3.369756 TGCAACCTCGACGATGTTTTATC 59.630 43.478 14.72 6.59 0.00 1.75
4139 8549 3.331150 TGCAACCTCGACGATGTTTTAT 58.669 40.909 14.72 0.00 0.00 1.40
4140 8550 2.756829 TGCAACCTCGACGATGTTTTA 58.243 42.857 14.72 5.56 0.00 1.52
4174 8587 2.915659 TCGTGGAGAAGTGGCGGT 60.916 61.111 0.00 0.00 0.00 5.68
4177 8590 1.294659 CTTGCTCGTGGAGAAGTGGC 61.295 60.000 0.00 0.00 0.00 5.01
4190 8603 0.319900 TGAAGCGGAGTCACTTGCTC 60.320 55.000 6.01 2.04 36.49 4.26
4247 8660 2.232208 TGATCTGCATGTGACTTCTCGT 59.768 45.455 0.00 0.00 0.00 4.18
4249 8662 4.874396 TGATTGATCTGCATGTGACTTCTC 59.126 41.667 0.00 0.00 0.00 2.87
4274 8687 1.507141 GCCCTGTTCTTGACGTGTGG 61.507 60.000 0.00 0.00 0.00 4.17
4279 8692 0.390472 GAGAGGCCCTGTTCTTGACG 60.390 60.000 0.00 0.00 0.00 4.35
4284 8697 0.043940 ATCCAGAGAGGCCCTGTTCT 59.956 55.000 0.00 0.00 37.29 3.01
4299 8712 1.893137 CGTAGATCAATCCCGGATCCA 59.107 52.381 13.41 0.00 41.64 3.41
4321 8734 5.221362 GGCTCTAGTCTTTCATAGTTCTCCC 60.221 48.000 0.00 0.00 0.00 4.30
4343 8756 1.227674 CTAGGTGATCCTTGGCGGC 60.228 63.158 0.00 0.00 42.12 6.53


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

AutoCloner maintained by Alex Coulton.