Multiple sequence alignment - TraesCS3B01G554600

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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 TraesCS3B01G554600 chr3B 100.000 2453 0 0 1 2453 788407175 788404723 0.000000e+00 4530.0
1 TraesCS3B01G554600 chr3B 90.812 1306 99 13 564 1858 809059582 809058287 0.000000e+00 1727.0
2 TraesCS3B01G554600 chr3B 89.452 1223 112 15 540 1749 818053326 818052108 0.000000e+00 1528.0
3 TraesCS3B01G554600 chr3B 88.721 1259 107 16 590 1837 813307664 813306430 0.000000e+00 1506.0
4 TraesCS3B01G554600 chr3B 90.582 945 50 16 540 1471 825572773 825571855 0.000000e+00 1216.0
5 TraesCS3B01G554600 chr3B 91.516 884 72 2 954 1836 788510557 788511438 0.000000e+00 1214.0
6 TraesCS3B01G554600 chr3B 89.868 908 87 5 932 1837 27487922 27487018 0.000000e+00 1162.0
7 TraesCS3B01G554600 chr3B 95.588 544 23 1 1 544 825580625 825580083 0.000000e+00 870.0
8 TraesCS3B01G554600 chr3B 88.922 668 48 7 540 1204 813269855 813269211 0.000000e+00 800.0
9 TraesCS3B01G554600 chr3B 84.925 199 26 2 1388 1584 813267011 813266815 5.350000e-47 198.0
10 TraesCS3B01G554600 chrUn 96.971 1684 30 2 791 2453 364044718 364046401 0.000000e+00 2808.0
11 TraesCS3B01G554600 chrUn 98.475 918 12 2 1538 2453 430928043 430928960 0.000000e+00 1616.0
12 TraesCS3B01G554600 chrUn 98.634 659 9 0 1795 2453 461533110 461533768 0.000000e+00 1168.0
13 TraesCS3B01G554600 chrUn 91.518 731 46 9 756 1471 232147738 232147009 0.000000e+00 992.0
14 TraesCS3B01G554600 chrUn 91.518 731 46 9 756 1471 291110909 291111638 0.000000e+00 992.0
15 TraesCS3B01G554600 chrUn 88.390 646 48 4 1193 1837 380530548 380529929 0.000000e+00 752.0
16 TraesCS3B01G554600 chrUn 88.576 604 42 4 1193 1795 342673372 342672795 0.000000e+00 708.0
17 TraesCS3B01G554600 chrUn 85.331 634 71 7 570 1200 342674454 342673840 9.570000e-179 636.0
18 TraesCS3B01G554600 chrUn 99.118 340 3 0 2114 2453 473248865 473248526 1.610000e-171 612.0
19 TraesCS3B01G554600 chr2D 86.018 565 43 16 1 544 179346816 179347365 7.610000e-160 573.0
20 TraesCS3B01G554600 chr2D 85.487 565 42 13 1 544 229634739 229635284 9.910000e-154 553.0
21 TraesCS3B01G554600 chr7A 85.455 550 42 14 1 528 487729902 487729369 2.780000e-149 538.0
22 TraesCS3B01G554600 chr7A 76.190 378 67 18 1861 2224 273618156 273618524 6.970000e-41 178.0
23 TraesCS3B01G554600 chr7A 79.200 125 21 5 1859 1980 160417323 160417201 5.620000e-12 82.4
24 TraesCS3B01G554600 chr2A 84.821 560 49 14 1 539 309721043 309720499 4.640000e-147 531.0
25 TraesCS3B01G554600 chr2A 84.921 126 16 3 1859 1982 250837762 250837638 9.210000e-25 124.0
26 TraesCS3B01G554600 chr2B 85.096 416 27 15 150 544 175533328 175532927 2.290000e-105 392.0
27 TraesCS3B01G554600 chr2B 93.939 99 6 0 1 99 175533425 175533327 1.520000e-32 150.0
28 TraesCS3B01G554600 chr2B 85.714 77 11 0 1859 1935 694935699 694935775 5.620000e-12 82.4
29 TraesCS3B01G554600 chr1A 84.058 414 31 16 152 544 525190427 525190028 1.390000e-97 366.0
30 TraesCS3B01G554600 chr1A 93.750 96 6 0 1 96 525190726 525190631 7.070000e-31 145.0
31 TraesCS3B01G554600 chr1A 78.846 208 31 6 1858 2064 534528970 534529165 7.120000e-26 128.0
32 TraesCS3B01G554600 chr6B 73.748 579 115 31 1859 2425 352248269 352247716 2.490000e-45 193.0
33 TraesCS3B01G554600 chr3D 77.391 230 28 17 554 780 113816423 113816631 5.540000e-22 115.0
34 TraesCS3B01G554600 chr3A 88.525 61 5 2 722 780 109269512 109269572 3.380000e-09 73.1
35 TraesCS3B01G554600 chr7B 97.297 37 1 0 2287 2323 10196527 10196563 2.040000e-06 63.9


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 TraesCS3B01G554600 chr3B 788404723 788407175 2452 True 4530.0 4530 100.0000 1 2453 1 chr3B.!!$R2 2452
1 TraesCS3B01G554600 chr3B 809058287 809059582 1295 True 1727.0 1727 90.8120 564 1858 1 chr3B.!!$R3 1294
2 TraesCS3B01G554600 chr3B 818052108 818053326 1218 True 1528.0 1528 89.4520 540 1749 1 chr3B.!!$R5 1209
3 TraesCS3B01G554600 chr3B 813306430 813307664 1234 True 1506.0 1506 88.7210 590 1837 1 chr3B.!!$R4 1247
4 TraesCS3B01G554600 chr3B 825571855 825572773 918 True 1216.0 1216 90.5820 540 1471 1 chr3B.!!$R6 931
5 TraesCS3B01G554600 chr3B 788510557 788511438 881 False 1214.0 1214 91.5160 954 1836 1 chr3B.!!$F1 882
6 TraesCS3B01G554600 chr3B 27487018 27487922 904 True 1162.0 1162 89.8680 932 1837 1 chr3B.!!$R1 905
7 TraesCS3B01G554600 chr3B 825580083 825580625 542 True 870.0 870 95.5880 1 544 1 chr3B.!!$R7 543
8 TraesCS3B01G554600 chr3B 813266815 813269855 3040 True 499.0 800 86.9235 540 1584 2 chr3B.!!$R8 1044
9 TraesCS3B01G554600 chrUn 364044718 364046401 1683 False 2808.0 2808 96.9710 791 2453 1 chrUn.!!$F2 1662
10 TraesCS3B01G554600 chrUn 430928043 430928960 917 False 1616.0 1616 98.4750 1538 2453 1 chrUn.!!$F3 915
11 TraesCS3B01G554600 chrUn 461533110 461533768 658 False 1168.0 1168 98.6340 1795 2453 1 chrUn.!!$F4 658
12 TraesCS3B01G554600 chrUn 232147009 232147738 729 True 992.0 992 91.5180 756 1471 1 chrUn.!!$R1 715
13 TraesCS3B01G554600 chrUn 291110909 291111638 729 False 992.0 992 91.5180 756 1471 1 chrUn.!!$F1 715
14 TraesCS3B01G554600 chrUn 380529929 380530548 619 True 752.0 752 88.3900 1193 1837 1 chrUn.!!$R2 644
15 TraesCS3B01G554600 chrUn 342672795 342674454 1659 True 672.0 708 86.9535 570 1795 2 chrUn.!!$R4 1225
16 TraesCS3B01G554600 chr2D 179346816 179347365 549 False 573.0 573 86.0180 1 544 1 chr2D.!!$F1 543
17 TraesCS3B01G554600 chr2D 229634739 229635284 545 False 553.0 553 85.4870 1 544 1 chr2D.!!$F2 543
18 TraesCS3B01G554600 chr7A 487729369 487729902 533 True 538.0 538 85.4550 1 528 1 chr7A.!!$R2 527
19 TraesCS3B01G554600 chr2A 309720499 309721043 544 True 531.0 531 84.8210 1 539 1 chr2A.!!$R2 538
20 TraesCS3B01G554600 chr1A 525190028 525190726 698 True 255.5 366 88.9040 1 544 2 chr1A.!!$R1 543

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
373 374 0.105039 CCTCCGCCTAAAGCTGGTAG 59.895 60.000 0.00 0.00 40.39 3.18 F
375 376 1.067821 CTCCGCCTAAAGCTGGTAGAG 59.932 57.143 6.32 2.08 40.39 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1196 0.319900 GTGTGAGCGCCTTCTTCTGA 60.320 55.0 2.29 0.0 0.0 3.27 R
1920 4757 0.322456 TTCCTTTGGCCCATCACGAG 60.322 55.0 0.00 0.0 0.0 4.18 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
33 34 4.584874 TGAGAAATGAAGGCGGAACAATA 58.415 39.130 0.00 0.00 0.00 1.90
109 110 8.527567 AAGAAAGAAGAGACTGAAGATTTACG 57.472 34.615 0.00 0.00 0.00 3.18
149 150 9.396022 ACATACTAATAATATATGTTGGCAGCC 57.604 33.333 3.66 3.66 36.37 4.85
156 157 8.704849 ATAATATATGTTGGCAGCCTAACAAA 57.295 30.769 24.42 16.62 39.89 2.83
197 198 6.257630 GCAATAAGCACAAAAGGAAACAAGAA 59.742 34.615 0.00 0.00 44.79 2.52
198 199 7.201600 GCAATAAGCACAAAAGGAAACAAGAAA 60.202 33.333 0.00 0.00 44.79 2.52
199 200 8.663911 CAATAAGCACAAAAGGAAACAAGAAAA 58.336 29.630 0.00 0.00 0.00 2.29
200 201 8.785329 ATAAGCACAAAAGGAAACAAGAAAAA 57.215 26.923 0.00 0.00 0.00 1.94
201 202 6.726258 AGCACAAAAGGAAACAAGAAAAAG 57.274 33.333 0.00 0.00 0.00 2.27
202 203 6.230472 AGCACAAAAGGAAACAAGAAAAAGT 58.770 32.000 0.00 0.00 0.00 2.66
203 204 7.382898 AGCACAAAAGGAAACAAGAAAAAGTA 58.617 30.769 0.00 0.00 0.00 2.24
204 205 7.875554 AGCACAAAAGGAAACAAGAAAAAGTAA 59.124 29.630 0.00 0.00 0.00 2.24
205 206 7.955324 GCACAAAAGGAAACAAGAAAAAGTAAC 59.045 33.333 0.00 0.00 0.00 2.50
206 207 8.983724 CACAAAAGGAAACAAGAAAAAGTAACA 58.016 29.630 0.00 0.00 0.00 2.41
207 208 9.203421 ACAAAAGGAAACAAGAAAAAGTAACAG 57.797 29.630 0.00 0.00 0.00 3.16
208 209 9.203421 CAAAAGGAAACAAGAAAAAGTAACAGT 57.797 29.630 0.00 0.00 0.00 3.55
209 210 8.981724 AAAGGAAACAAGAAAAAGTAACAGTC 57.018 30.769 0.00 0.00 0.00 3.51
210 211 7.939784 AGGAAACAAGAAAAAGTAACAGTCT 57.060 32.000 0.00 0.00 0.00 3.24
211 212 7.762382 AGGAAACAAGAAAAAGTAACAGTCTG 58.238 34.615 0.00 0.00 0.00 3.51
212 213 7.610305 AGGAAACAAGAAAAAGTAACAGTCTGA 59.390 33.333 6.91 0.00 0.00 3.27
213 214 8.241367 GGAAACAAGAAAAAGTAACAGTCTGAA 58.759 33.333 6.91 0.00 0.00 3.02
214 215 9.278734 GAAACAAGAAAAAGTAACAGTCTGAAG 57.721 33.333 6.91 0.00 0.00 3.02
215 216 8.561738 AACAAGAAAAAGTAACAGTCTGAAGA 57.438 30.769 6.91 0.00 0.00 2.87
216 217 8.561738 ACAAGAAAAAGTAACAGTCTGAAGAA 57.438 30.769 6.91 0.00 0.00 2.52
217 218 9.010029 ACAAGAAAAAGTAACAGTCTGAAGAAA 57.990 29.630 6.91 0.00 0.00 2.52
218 219 9.840427 CAAGAAAAAGTAACAGTCTGAAGAAAA 57.160 29.630 6.91 0.00 0.00 2.29
220 221 9.841880 AGAAAAAGTAACAGTCTGAAGAAAAAC 57.158 29.630 6.91 0.00 0.00 2.43
221 222 9.841880 GAAAAAGTAACAGTCTGAAGAAAAACT 57.158 29.630 6.91 0.00 0.00 2.66
229 230 9.620259 AACAGTCTGAAGAAAAACTATTTCTCT 57.380 29.630 6.91 0.00 37.75 3.10
246 247 9.712305 CTATTTCTCTATATAAAGTGTGGTGGG 57.288 37.037 0.00 0.00 0.00 4.61
247 248 7.743116 TTTCTCTATATAAAGTGTGGTGGGA 57.257 36.000 0.00 0.00 0.00 4.37
248 249 7.931015 TTCTCTATATAAAGTGTGGTGGGAT 57.069 36.000 0.00 0.00 0.00 3.85
249 250 7.540474 TCTCTATATAAAGTGTGGTGGGATC 57.460 40.000 0.00 0.00 0.00 3.36
250 251 7.073208 TCTCTATATAAAGTGTGGTGGGATCA 58.927 38.462 0.00 0.00 0.00 2.92
251 252 7.233553 TCTCTATATAAAGTGTGGTGGGATCAG 59.766 40.741 0.00 0.00 0.00 2.90
252 253 7.073208 TCTATATAAAGTGTGGTGGGATCAGA 58.927 38.462 0.00 0.00 0.00 3.27
253 254 4.927267 ATAAAGTGTGGTGGGATCAGAA 57.073 40.909 0.00 0.00 0.00 3.02
254 255 3.593442 AAAGTGTGGTGGGATCAGAAA 57.407 42.857 0.00 0.00 0.00 2.52
255 256 3.593442 AAGTGTGGTGGGATCAGAAAA 57.407 42.857 0.00 0.00 0.00 2.29
256 257 3.593442 AGTGTGGTGGGATCAGAAAAA 57.407 42.857 0.00 0.00 0.00 1.94
283 284 8.747538 ATATTTACAAGTCCAACTAATCCACC 57.252 34.615 0.00 0.00 0.00 4.61
284 285 5.570205 TTACAAGTCCAACTAATCCACCA 57.430 39.130 0.00 0.00 0.00 4.17
285 286 4.447138 ACAAGTCCAACTAATCCACCAA 57.553 40.909 0.00 0.00 0.00 3.67
286 287 4.798882 ACAAGTCCAACTAATCCACCAAA 58.201 39.130 0.00 0.00 0.00 3.28
287 288 5.393866 ACAAGTCCAACTAATCCACCAAAT 58.606 37.500 0.00 0.00 0.00 2.32
288 289 5.838521 ACAAGTCCAACTAATCCACCAAATT 59.161 36.000 0.00 0.00 0.00 1.82
289 290 5.982890 AGTCCAACTAATCCACCAAATTG 57.017 39.130 0.00 0.00 0.00 2.32
290 291 4.220602 AGTCCAACTAATCCACCAAATTGC 59.779 41.667 0.00 0.00 0.00 3.56
291 292 4.021544 GTCCAACTAATCCACCAAATTGCA 60.022 41.667 0.00 0.00 0.00 4.08
292 293 4.776837 TCCAACTAATCCACCAAATTGCAT 59.223 37.500 0.00 0.00 0.00 3.96
293 294 5.954752 TCCAACTAATCCACCAAATTGCATA 59.045 36.000 0.00 0.00 0.00 3.14
294 295 6.438741 TCCAACTAATCCACCAAATTGCATAA 59.561 34.615 0.00 0.00 0.00 1.90
295 296 7.038729 TCCAACTAATCCACCAAATTGCATAAA 60.039 33.333 0.00 0.00 0.00 1.40
296 297 7.605691 CCAACTAATCCACCAAATTGCATAAAA 59.394 33.333 0.00 0.00 0.00 1.52
297 298 9.165035 CAACTAATCCACCAAATTGCATAAAAT 57.835 29.630 0.00 0.00 0.00 1.82
298 299 9.737844 AACTAATCCACCAAATTGCATAAAATT 57.262 25.926 0.00 0.00 0.00 1.82
304 305 9.381033 TCCACCAAATTGCATAAAATTATCTTG 57.619 29.630 0.00 0.00 0.00 3.02
305 306 9.165035 CCACCAAATTGCATAAAATTATCTTGT 57.835 29.630 0.00 0.00 0.00 3.16
313 314 8.464770 TGCATAAAATTATCTTGTTGTTCAGC 57.535 30.769 0.00 0.00 0.00 4.26
314 315 7.545265 TGCATAAAATTATCTTGTTGTTCAGCC 59.455 33.333 0.00 0.00 0.00 4.85
315 316 7.010460 GCATAAAATTATCTTGTTGTTCAGCCC 59.990 37.037 0.00 0.00 0.00 5.19
316 317 6.418057 AAAATTATCTTGTTGTTCAGCCCA 57.582 33.333 0.00 0.00 0.00 5.36
317 318 5.391312 AATTATCTTGTTGTTCAGCCCAC 57.609 39.130 0.00 0.00 0.00 4.61
318 319 1.620822 ATCTTGTTGTTCAGCCCACC 58.379 50.000 0.00 0.00 0.00 4.61
319 320 0.550914 TCTTGTTGTTCAGCCCACCT 59.449 50.000 0.00 0.00 0.00 4.00
320 321 0.670162 CTTGTTGTTCAGCCCACCTG 59.330 55.000 0.00 0.00 43.17 4.00
321 322 1.391157 TTGTTGTTCAGCCCACCTGC 61.391 55.000 0.00 0.00 41.50 4.85
322 323 1.827789 GTTGTTCAGCCCACCTGCA 60.828 57.895 0.00 0.00 41.50 4.41
323 324 1.529010 TTGTTCAGCCCACCTGCAG 60.529 57.895 6.78 6.78 41.50 4.41
324 325 1.993701 TTGTTCAGCCCACCTGCAGA 61.994 55.000 17.39 0.00 41.50 4.26
325 326 1.673665 GTTCAGCCCACCTGCAGAG 60.674 63.158 17.39 8.04 41.50 3.35
326 327 1.842920 TTCAGCCCACCTGCAGAGA 60.843 57.895 17.39 0.00 41.50 3.10
327 328 1.834856 TTCAGCCCACCTGCAGAGAG 61.835 60.000 17.39 0.15 41.50 3.20
328 329 3.715097 AGCCCACCTGCAGAGAGC 61.715 66.667 17.39 12.37 45.96 4.09
329 330 4.792804 GCCCACCTGCAGAGAGCC 62.793 72.222 17.39 0.00 44.83 4.70
330 331 4.106925 CCCACCTGCAGAGAGCCC 62.107 72.222 17.39 0.00 44.83 5.19
331 332 3.324930 CCACCTGCAGAGAGCCCA 61.325 66.667 17.39 0.00 44.83 5.36
332 333 2.268280 CACCTGCAGAGAGCCCAG 59.732 66.667 17.39 0.00 44.83 4.45
334 335 3.795041 CCTGCAGAGAGCCCAGGG 61.795 72.222 17.39 0.00 44.83 4.45
335 336 2.686470 CTGCAGAGAGCCCAGGGA 60.686 66.667 10.89 0.00 44.83 4.20
336 337 2.203983 TGCAGAGAGCCCAGGGAA 60.204 61.111 10.89 0.00 44.83 3.97
337 338 1.845627 CTGCAGAGAGCCCAGGGAAA 61.846 60.000 10.89 0.00 44.83 3.13
338 339 1.380302 GCAGAGAGCCCAGGGAAAA 59.620 57.895 10.89 0.00 37.23 2.29
339 340 0.679321 GCAGAGAGCCCAGGGAAAAG 60.679 60.000 10.89 0.00 37.23 2.27
340 341 0.695347 CAGAGAGCCCAGGGAAAAGT 59.305 55.000 10.89 0.00 0.00 2.66
341 342 0.988063 AGAGAGCCCAGGGAAAAGTC 59.012 55.000 10.89 0.00 0.00 3.01
342 343 0.693049 GAGAGCCCAGGGAAAAGTCA 59.307 55.000 10.89 0.00 0.00 3.41
343 344 1.073923 GAGAGCCCAGGGAAAAGTCAA 59.926 52.381 10.89 0.00 0.00 3.18
344 345 1.499007 AGAGCCCAGGGAAAAGTCAAA 59.501 47.619 10.89 0.00 0.00 2.69
345 346 2.110721 AGAGCCCAGGGAAAAGTCAAAT 59.889 45.455 10.89 0.00 0.00 2.32
346 347 2.899900 GAGCCCAGGGAAAAGTCAAATT 59.100 45.455 10.89 0.00 0.00 1.82
347 348 4.086457 GAGCCCAGGGAAAAGTCAAATTA 58.914 43.478 10.89 0.00 0.00 1.40
348 349 4.089361 AGCCCAGGGAAAAGTCAAATTAG 58.911 43.478 10.89 0.00 0.00 1.73
349 350 4.086457 GCCCAGGGAAAAGTCAAATTAGA 58.914 43.478 10.89 0.00 0.00 2.10
350 351 4.711846 GCCCAGGGAAAAGTCAAATTAGAT 59.288 41.667 10.89 0.00 0.00 1.98
351 352 5.394553 GCCCAGGGAAAAGTCAAATTAGATG 60.395 44.000 10.89 0.00 0.00 2.90
352 353 5.127682 CCCAGGGAAAAGTCAAATTAGATGG 59.872 44.000 0.00 0.00 0.00 3.51
353 354 5.951747 CCAGGGAAAAGTCAAATTAGATGGA 59.048 40.000 0.00 0.00 0.00 3.41
354 355 6.127619 CCAGGGAAAAGTCAAATTAGATGGAC 60.128 42.308 0.00 0.00 0.00 4.02
355 356 5.952347 AGGGAAAAGTCAAATTAGATGGACC 59.048 40.000 0.00 0.00 0.00 4.46
356 357 5.952347 GGGAAAAGTCAAATTAGATGGACCT 59.048 40.000 0.00 0.00 0.00 3.85
357 358 6.095580 GGGAAAAGTCAAATTAGATGGACCTC 59.904 42.308 0.00 0.00 0.00 3.85
358 359 6.095580 GGAAAAGTCAAATTAGATGGACCTCC 59.904 42.308 0.00 0.00 0.00 4.30
359 360 4.408182 AGTCAAATTAGATGGACCTCCG 57.592 45.455 0.00 0.00 39.43 4.63
360 361 2.872858 GTCAAATTAGATGGACCTCCGC 59.127 50.000 0.00 0.00 39.43 5.54
361 362 2.158813 TCAAATTAGATGGACCTCCGCC 60.159 50.000 0.00 0.00 39.43 6.13
362 363 1.807814 AATTAGATGGACCTCCGCCT 58.192 50.000 0.00 0.00 39.43 5.52
363 364 2.696526 ATTAGATGGACCTCCGCCTA 57.303 50.000 0.00 0.00 39.43 3.93
364 365 2.464796 TTAGATGGACCTCCGCCTAA 57.535 50.000 0.00 2.72 39.43 2.69
365 366 2.464796 TAGATGGACCTCCGCCTAAA 57.535 50.000 0.00 0.00 39.43 1.85
366 367 1.123928 AGATGGACCTCCGCCTAAAG 58.876 55.000 0.00 0.00 39.43 1.85
367 368 0.533085 GATGGACCTCCGCCTAAAGC 60.533 60.000 0.00 0.00 39.43 3.51
368 369 0.983378 ATGGACCTCCGCCTAAAGCT 60.983 55.000 0.00 0.00 40.39 3.74
369 370 1.153349 GGACCTCCGCCTAAAGCTG 60.153 63.158 0.00 0.00 40.39 4.24
370 371 1.153349 GACCTCCGCCTAAAGCTGG 60.153 63.158 0.00 0.00 40.39 4.85
371 372 1.900545 GACCTCCGCCTAAAGCTGGT 61.901 60.000 0.00 0.00 40.39 4.00
372 373 0.616679 ACCTCCGCCTAAAGCTGGTA 60.617 55.000 0.00 0.00 40.39 3.25
373 374 0.105039 CCTCCGCCTAAAGCTGGTAG 59.895 60.000 0.00 0.00 40.39 3.18
374 375 1.112113 CTCCGCCTAAAGCTGGTAGA 58.888 55.000 6.32 0.00 40.39 2.59
375 376 1.067821 CTCCGCCTAAAGCTGGTAGAG 59.932 57.143 6.32 2.08 40.39 2.43
376 377 1.112113 CCGCCTAAAGCTGGTAGAGA 58.888 55.000 6.32 0.00 40.39 3.10
377 378 1.480954 CCGCCTAAAGCTGGTAGAGAA 59.519 52.381 6.32 0.00 40.39 2.87
378 379 2.093658 CCGCCTAAAGCTGGTAGAGAAA 60.094 50.000 6.32 0.00 40.39 2.52
379 380 3.596214 CGCCTAAAGCTGGTAGAGAAAA 58.404 45.455 6.32 0.00 40.39 2.29
380 381 3.619038 CGCCTAAAGCTGGTAGAGAAAAG 59.381 47.826 6.32 0.00 40.39 2.27
381 382 4.580868 GCCTAAAGCTGGTAGAGAAAAGT 58.419 43.478 6.32 0.00 38.99 2.66
382 383 5.623824 CGCCTAAAGCTGGTAGAGAAAAGTA 60.624 44.000 6.32 0.00 40.39 2.24
383 384 6.171213 GCCTAAAGCTGGTAGAGAAAAGTAA 58.829 40.000 6.32 0.00 38.99 2.24
384 385 6.314152 GCCTAAAGCTGGTAGAGAAAAGTAAG 59.686 42.308 6.32 0.00 38.99 2.34
385 386 7.387643 CCTAAAGCTGGTAGAGAAAAGTAAGT 58.612 38.462 6.32 0.00 0.00 2.24
386 387 7.546316 CCTAAAGCTGGTAGAGAAAAGTAAGTC 59.454 40.741 6.32 0.00 0.00 3.01
387 388 6.420913 AAGCTGGTAGAGAAAAGTAAGTCA 57.579 37.500 0.00 0.00 0.00 3.41
388 389 6.613153 AGCTGGTAGAGAAAAGTAAGTCAT 57.387 37.500 0.00 0.00 0.00 3.06
389 390 6.402222 AGCTGGTAGAGAAAAGTAAGTCATG 58.598 40.000 0.00 0.00 0.00 3.07
390 391 6.211584 AGCTGGTAGAGAAAAGTAAGTCATGA 59.788 38.462 0.00 0.00 0.00 3.07
391 392 6.311690 GCTGGTAGAGAAAAGTAAGTCATGAC 59.688 42.308 18.47 18.47 0.00 3.06
392 393 7.540474 TGGTAGAGAAAAGTAAGTCATGACT 57.460 36.000 22.89 22.89 44.94 3.41
393 394 8.645814 TGGTAGAGAAAAGTAAGTCATGACTA 57.354 34.615 28.10 13.76 41.58 2.59
394 395 9.085645 TGGTAGAGAAAAGTAAGTCATGACTAA 57.914 33.333 28.10 0.81 41.58 2.24
395 396 9.575783 GGTAGAGAAAAGTAAGTCATGACTAAG 57.424 37.037 28.10 0.00 41.58 2.18
403 404 9.628500 AAAGTAAGTCATGACTAAGAAAAACCT 57.372 29.630 28.10 11.26 41.58 3.50
404 405 9.628500 AAGTAAGTCATGACTAAGAAAAACCTT 57.372 29.630 28.10 14.95 41.58 3.50
405 406 9.628500 AGTAAGTCATGACTAAGAAAAACCTTT 57.372 29.630 28.10 10.56 41.58 3.11
440 441 9.662947 ACCCTATAGTGTAGTGAATTTTACAAC 57.337 33.333 0.00 0.00 32.08 3.32
441 442 9.106070 CCCTATAGTGTAGTGAATTTTACAACC 57.894 37.037 0.00 0.00 32.08 3.77
442 443 9.661563 CCTATAGTGTAGTGAATTTTACAACCA 57.338 33.333 0.00 0.00 32.08 3.67
447 448 9.361315 AGTGTAGTGAATTTTACAACCAAAAAC 57.639 29.630 0.00 0.00 32.08 2.43
448 449 8.597227 GTGTAGTGAATTTTACAACCAAAAACC 58.403 33.333 0.00 0.00 32.08 3.27
449 450 8.532819 TGTAGTGAATTTTACAACCAAAAACCT 58.467 29.630 0.00 0.00 31.54 3.50
450 451 9.373603 GTAGTGAATTTTACAACCAAAAACCTT 57.626 29.630 0.00 0.00 31.54 3.50
451 452 8.856153 AGTGAATTTTACAACCAAAAACCTTT 57.144 26.923 0.00 0.00 31.54 3.11
452 453 8.726068 AGTGAATTTTACAACCAAAAACCTTTG 58.274 29.630 0.00 0.00 41.45 2.77
453 454 8.508062 GTGAATTTTACAACCAAAAACCTTTGT 58.492 29.630 0.00 0.00 40.38 2.83
454 455 9.067986 TGAATTTTACAACCAAAAACCTTTGTT 57.932 25.926 0.00 0.00 40.38 2.83
455 456 9.900710 GAATTTTACAACCAAAAACCTTTGTTT 57.099 25.926 0.00 0.00 46.50 2.83
456 457 9.900710 AATTTTACAACCAAAAACCTTTGTTTC 57.099 25.926 0.00 0.00 43.80 2.78
457 458 7.436430 TTTACAACCAAAAACCTTTGTTTCC 57.564 32.000 0.00 0.00 43.80 3.13
458 459 4.328536 ACAACCAAAAACCTTTGTTTCCC 58.671 39.130 0.00 0.00 43.80 3.97
459 460 4.042311 ACAACCAAAAACCTTTGTTTCCCT 59.958 37.500 0.00 0.00 43.80 4.20
460 461 4.481368 ACCAAAAACCTTTGTTTCCCTC 57.519 40.909 0.00 0.00 43.80 4.30
461 462 4.101114 ACCAAAAACCTTTGTTTCCCTCT 58.899 39.130 0.00 0.00 43.80 3.69
462 463 5.274015 ACCAAAAACCTTTGTTTCCCTCTA 58.726 37.500 0.00 0.00 43.80 2.43
463 464 5.128171 ACCAAAAACCTTTGTTTCCCTCTAC 59.872 40.000 0.00 0.00 43.80 2.59
464 465 5.362717 CCAAAAACCTTTGTTTCCCTCTACT 59.637 40.000 0.00 0.00 43.80 2.57
465 466 6.548251 CCAAAAACCTTTGTTTCCCTCTACTA 59.452 38.462 0.00 0.00 43.80 1.82
466 467 7.232737 CCAAAAACCTTTGTTTCCCTCTACTAT 59.767 37.037 0.00 0.00 43.80 2.12
467 468 9.292195 CAAAAACCTTTGTTTCCCTCTACTATA 57.708 33.333 0.00 0.00 43.80 1.31
468 469 8.859236 AAAACCTTTGTTTCCCTCTACTATAC 57.141 34.615 0.00 0.00 43.80 1.47
469 470 7.809880 AACCTTTGTTTCCCTCTACTATACT 57.190 36.000 0.00 0.00 0.00 2.12
470 471 8.906238 AACCTTTGTTTCCCTCTACTATACTA 57.094 34.615 0.00 0.00 0.00 1.82
471 472 8.906238 ACCTTTGTTTCCCTCTACTATACTAA 57.094 34.615 0.00 0.00 0.00 2.24
472 473 9.330220 ACCTTTGTTTCCCTCTACTATACTAAA 57.670 33.333 0.00 0.00 0.00 1.85
506 507 8.127150 AGAAAAATCTTCCTTTTCCTATGTGG 57.873 34.615 4.80 0.00 41.63 4.17
507 508 7.950124 AGAAAAATCTTCCTTTTCCTATGTGGA 59.050 33.333 4.80 0.00 41.63 4.02
508 509 8.670521 AAAAATCTTCCTTTTCCTATGTGGAT 57.329 30.769 0.00 0.00 45.68 3.41
509 510 8.670521 AAAATCTTCCTTTTCCTATGTGGATT 57.329 30.769 0.00 0.00 45.68 3.01
510 511 9.768215 AAAATCTTCCTTTTCCTATGTGGATTA 57.232 29.630 0.00 0.00 45.68 1.75
511 512 8.986929 AATCTTCCTTTTCCTATGTGGATTAG 57.013 34.615 0.00 0.00 45.68 1.73
512 513 7.749377 TCTTCCTTTTCCTATGTGGATTAGA 57.251 36.000 0.00 0.00 45.68 2.10
513 514 8.337118 TCTTCCTTTTCCTATGTGGATTAGAT 57.663 34.615 0.00 0.00 45.68 1.98
514 515 8.213679 TCTTCCTTTTCCTATGTGGATTAGATG 58.786 37.037 0.00 0.00 45.68 2.90
515 516 7.690454 TCCTTTTCCTATGTGGATTAGATGA 57.310 36.000 0.00 0.00 45.68 2.92
516 517 8.280258 TCCTTTTCCTATGTGGATTAGATGAT 57.720 34.615 0.00 0.00 45.68 2.45
517 518 8.378565 TCCTTTTCCTATGTGGATTAGATGATC 58.621 37.037 0.00 0.00 45.68 2.92
518 519 8.381636 CCTTTTCCTATGTGGATTAGATGATCT 58.618 37.037 0.00 0.00 45.68 2.75
519 520 9.790344 CTTTTCCTATGTGGATTAGATGATCTT 57.210 33.333 0.00 0.00 45.68 2.40
520 521 9.565090 TTTTCCTATGTGGATTAGATGATCTTG 57.435 33.333 0.00 0.00 45.68 3.02
521 522 7.862274 TCCTATGTGGATTAGATGATCTTGT 57.138 36.000 0.00 0.00 40.56 3.16
522 523 7.674120 TCCTATGTGGATTAGATGATCTTGTG 58.326 38.462 0.00 0.00 40.56 3.33
523 524 7.510343 TCCTATGTGGATTAGATGATCTTGTGA 59.490 37.037 0.00 0.00 40.56 3.58
524 525 8.152898 CCTATGTGGATTAGATGATCTTGTGAA 58.847 37.037 0.00 0.00 38.35 3.18
525 526 9.722184 CTATGTGGATTAGATGATCTTGTGAAT 57.278 33.333 0.00 0.00 0.00 2.57
526 527 8.991783 ATGTGGATTAGATGATCTTGTGAATT 57.008 30.769 0.00 0.00 0.00 2.17
538 539 9.754382 ATGATCTTGTGAATTATTTGTTATGCC 57.246 29.630 0.00 0.00 0.00 4.40
568 569 4.873746 TCTATTAGTACCAGCAGCATCC 57.126 45.455 0.00 0.00 0.00 3.51
598 600 3.265995 ACCCAGGTCAAGGAAAATCGTAT 59.734 43.478 0.00 0.00 0.00 3.06
660 666 1.475441 GACGCGTGCTAGCATCACTC 61.475 60.000 22.51 9.91 36.85 3.51
692 698 3.465122 AATTTAACTACCAGCAACGCG 57.535 42.857 3.53 3.53 0.00 6.01
709 715 1.589630 CGATTCCATCCGCCCGATA 59.410 57.895 0.00 0.00 0.00 2.92
783 789 5.680619 TCAAGTTCAGACCTTTGCTTTCTA 58.319 37.500 0.00 0.00 0.00 2.10
837 851 8.867935 CAGTGAACATCAGTAGTAGAATTTCTG 58.132 37.037 9.22 0.00 0.00 3.02
876 890 1.279271 CCTATAAATCAGCCCCTCCCG 59.721 57.143 0.00 0.00 0.00 5.14
1034 1051 4.245660 GTGATCGAGGTGAACAGAAATGA 58.754 43.478 0.00 0.00 28.98 2.57
1203 1728 2.591715 AAGGCGCTCACACACACC 60.592 61.111 7.64 0.00 0.00 4.16
1206 1731 2.607892 GGCGCTCACACACACCTTC 61.608 63.158 7.64 0.00 0.00 3.46
1209 1734 0.583438 CGCTCACACACACCTTCAAG 59.417 55.000 0.00 0.00 0.00 3.02
1210 1735 0.308993 GCTCACACACACCTTCAAGC 59.691 55.000 0.00 0.00 0.00 4.01
1212 1737 1.600957 CTCACACACACCTTCAAGCAG 59.399 52.381 0.00 0.00 0.00 4.24
1215 1740 2.225019 CACACACACCTTCAAGCAGATC 59.775 50.000 0.00 0.00 0.00 2.75
1216 1741 1.462283 CACACACCTTCAAGCAGATCG 59.538 52.381 0.00 0.00 0.00 3.69
1220 1745 0.392193 ACCTTCAAGCAGATCGGCAG 60.392 55.000 20.15 11.73 35.83 4.85
1221 1746 1.094073 CCTTCAAGCAGATCGGCAGG 61.094 60.000 20.15 13.29 35.83 4.85
1222 1747 1.712977 CTTCAAGCAGATCGGCAGGC 61.713 60.000 20.15 4.59 35.83 4.85
1223 1748 2.124819 CAAGCAGATCGGCAGGCT 60.125 61.111 20.15 6.81 38.45 4.58
1225 1750 3.694058 AAGCAGATCGGCAGGCTGG 62.694 63.158 20.15 0.00 36.58 4.85
1226 1751 4.479993 GCAGATCGGCAGGCTGGT 62.480 66.667 17.64 0.00 0.00 4.00
1228 1753 2.364842 AGATCGGCAGGCTGGTCT 60.365 61.111 17.64 10.05 37.92 3.85
1229 1754 2.107953 GATCGGCAGGCTGGTCTC 59.892 66.667 17.64 0.00 30.13 3.36
1230 1755 3.781770 GATCGGCAGGCTGGTCTCG 62.782 68.421 17.64 6.65 30.13 4.04
1232 1757 3.449227 CGGCAGGCTGGTCTCGTA 61.449 66.667 17.64 0.00 0.00 3.43
1233 1758 2.786495 CGGCAGGCTGGTCTCGTAT 61.786 63.158 17.64 0.00 0.00 3.06
1234 1759 1.227380 GGCAGGCTGGTCTCGTATG 60.227 63.158 17.64 0.00 0.00 2.39
1235 1760 1.884926 GCAGGCTGGTCTCGTATGC 60.885 63.158 17.64 0.00 0.00 3.14
1674 4511 5.927115 GGCTCCTTAAATCATAGTAAGTCGG 59.073 44.000 0.00 0.00 0.00 4.79
1705 4542 1.454847 AAAGGCCAACTCCAACGCA 60.455 52.632 5.01 0.00 0.00 5.24
1852 4689 3.726291 TGCATGTCTTATAGCGTGCTA 57.274 42.857 3.73 3.73 45.07 3.49
1920 4757 1.811266 ACGTCGTCAGATGCATGCC 60.811 57.895 16.68 0.00 36.88 4.40
1987 4824 6.388435 ACGTGGAACATATACTACTTCCTC 57.612 41.667 0.00 0.00 44.52 3.71
2204 5042 1.026718 ACGAGCCAACATTAGCCAGC 61.027 55.000 0.00 0.00 0.00 4.85
2270 5108 1.410517 TCTCATCGTTCCAGATCTGCC 59.589 52.381 17.76 6.23 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.930693 CTTCACTATTTCAGTAAGTACCTTCTT 57.069 33.333 0.00 0.00 34.98 2.52
109 110 5.616488 TTAGTATGTTGCGGTTCTTTTCC 57.384 39.130 0.00 0.00 0.00 3.13
156 157 9.573133 GTGCTTATTGCTCTAAATGTTAAATGT 57.427 29.630 0.00 0.00 43.37 2.71
203 204 9.620259 AGAGAAATAGTTTTTCTTCAGACTGTT 57.380 29.630 9.55 0.00 38.73 3.16
220 221 9.712305 CCCACCACACTTTATATAGAGAAATAG 57.288 37.037 7.26 0.00 0.00 1.73
221 222 9.442062 TCCCACCACACTTTATATAGAGAAATA 57.558 33.333 7.26 0.00 0.00 1.40
222 223 8.331931 TCCCACCACACTTTATATAGAGAAAT 57.668 34.615 7.26 0.00 0.00 2.17
223 224 7.743116 TCCCACCACACTTTATATAGAGAAA 57.257 36.000 7.26 0.00 0.00 2.52
224 225 7.567250 TGATCCCACCACACTTTATATAGAGAA 59.433 37.037 7.26 0.00 0.00 2.87
225 226 7.073208 TGATCCCACCACACTTTATATAGAGA 58.927 38.462 7.26 0.00 0.00 3.10
226 227 7.233553 TCTGATCCCACCACACTTTATATAGAG 59.766 40.741 0.00 0.00 0.00 2.43
227 228 7.073208 TCTGATCCCACCACACTTTATATAGA 58.927 38.462 0.00 0.00 0.00 1.98
228 229 7.303182 TCTGATCCCACCACACTTTATATAG 57.697 40.000 0.00 0.00 0.00 1.31
229 230 7.684317 TTCTGATCCCACCACACTTTATATA 57.316 36.000 0.00 0.00 0.00 0.86
230 231 6.575244 TTCTGATCCCACCACACTTTATAT 57.425 37.500 0.00 0.00 0.00 0.86
231 232 6.381498 TTTCTGATCCCACCACACTTTATA 57.619 37.500 0.00 0.00 0.00 0.98
232 233 4.927267 TTCTGATCCCACCACACTTTAT 57.073 40.909 0.00 0.00 0.00 1.40
233 234 4.715534 TTTCTGATCCCACCACACTTTA 57.284 40.909 0.00 0.00 0.00 1.85
234 235 3.593442 TTTCTGATCCCACCACACTTT 57.407 42.857 0.00 0.00 0.00 2.66
235 236 3.593442 TTTTCTGATCCCACCACACTT 57.407 42.857 0.00 0.00 0.00 3.16
236 237 3.593442 TTTTTCTGATCCCACCACACT 57.407 42.857 0.00 0.00 0.00 3.55
257 258 9.185680 GGTGGATTAGTTGGACTTGTAAATATT 57.814 33.333 0.00 0.00 0.00 1.28
258 259 8.333235 TGGTGGATTAGTTGGACTTGTAAATAT 58.667 33.333 0.00 0.00 0.00 1.28
259 260 7.691213 TGGTGGATTAGTTGGACTTGTAAATA 58.309 34.615 0.00 0.00 0.00 1.40
260 261 6.548321 TGGTGGATTAGTTGGACTTGTAAAT 58.452 36.000 0.00 0.00 0.00 1.40
261 262 5.942961 TGGTGGATTAGTTGGACTTGTAAA 58.057 37.500 0.00 0.00 0.00 2.01
262 263 5.570205 TGGTGGATTAGTTGGACTTGTAA 57.430 39.130 0.00 0.00 0.00 2.41
263 264 5.570205 TTGGTGGATTAGTTGGACTTGTA 57.430 39.130 0.00 0.00 0.00 2.41
264 265 4.447138 TTGGTGGATTAGTTGGACTTGT 57.553 40.909 0.00 0.00 0.00 3.16
265 266 5.982890 ATTTGGTGGATTAGTTGGACTTG 57.017 39.130 0.00 0.00 0.00 3.16
266 267 5.279456 GCAATTTGGTGGATTAGTTGGACTT 60.279 40.000 0.00 0.00 0.00 3.01
267 268 4.220602 GCAATTTGGTGGATTAGTTGGACT 59.779 41.667 0.00 0.00 0.00 3.85
268 269 4.021544 TGCAATTTGGTGGATTAGTTGGAC 60.022 41.667 0.00 0.00 0.00 4.02
269 270 4.155709 TGCAATTTGGTGGATTAGTTGGA 58.844 39.130 0.00 0.00 0.00 3.53
270 271 4.533919 TGCAATTTGGTGGATTAGTTGG 57.466 40.909 0.00 0.00 0.00 3.77
271 272 8.545229 TTTTATGCAATTTGGTGGATTAGTTG 57.455 30.769 0.00 0.00 31.34 3.16
272 273 9.737844 AATTTTATGCAATTTGGTGGATTAGTT 57.262 25.926 0.00 0.00 31.34 2.24
278 279 9.381033 CAAGATAATTTTATGCAATTTGGTGGA 57.619 29.630 0.00 0.00 0.00 4.02
279 280 9.165035 ACAAGATAATTTTATGCAATTTGGTGG 57.835 29.630 0.00 0.00 0.00 4.61
287 288 8.924691 GCTGAACAACAAGATAATTTTATGCAA 58.075 29.630 0.00 0.00 0.00 4.08
288 289 7.545265 GGCTGAACAACAAGATAATTTTATGCA 59.455 33.333 0.00 0.00 0.00 3.96
289 290 7.010460 GGGCTGAACAACAAGATAATTTTATGC 59.990 37.037 0.00 0.00 0.00 3.14
290 291 8.034215 TGGGCTGAACAACAAGATAATTTTATG 58.966 33.333 0.00 0.00 0.00 1.90
291 292 8.034804 GTGGGCTGAACAACAAGATAATTTTAT 58.965 33.333 0.00 0.00 0.00 1.40
292 293 7.375053 GTGGGCTGAACAACAAGATAATTTTA 58.625 34.615 0.00 0.00 0.00 1.52
293 294 6.223120 GTGGGCTGAACAACAAGATAATTTT 58.777 36.000 0.00 0.00 0.00 1.82
294 295 5.279456 GGTGGGCTGAACAACAAGATAATTT 60.279 40.000 0.00 0.00 0.00 1.82
295 296 4.220602 GGTGGGCTGAACAACAAGATAATT 59.779 41.667 0.00 0.00 0.00 1.40
296 297 3.763897 GGTGGGCTGAACAACAAGATAAT 59.236 43.478 0.00 0.00 0.00 1.28
297 298 3.153919 GGTGGGCTGAACAACAAGATAA 58.846 45.455 0.00 0.00 0.00 1.75
298 299 2.375174 AGGTGGGCTGAACAACAAGATA 59.625 45.455 0.00 0.00 0.00 1.98
299 300 1.145738 AGGTGGGCTGAACAACAAGAT 59.854 47.619 0.00 0.00 0.00 2.40
300 301 0.550914 AGGTGGGCTGAACAACAAGA 59.449 50.000 0.00 0.00 0.00 3.02
301 302 0.670162 CAGGTGGGCTGAACAACAAG 59.330 55.000 0.00 0.00 0.00 3.16
302 303 1.391157 GCAGGTGGGCTGAACAACAA 61.391 55.000 0.00 0.00 0.00 2.83
303 304 1.827789 GCAGGTGGGCTGAACAACA 60.828 57.895 0.00 0.00 0.00 3.33
304 305 1.799258 CTGCAGGTGGGCTGAACAAC 61.799 60.000 5.57 0.00 35.02 3.32
305 306 1.529010 CTGCAGGTGGGCTGAACAA 60.529 57.895 5.57 0.00 35.02 2.83
306 307 2.113774 CTGCAGGTGGGCTGAACA 59.886 61.111 5.57 0.00 35.02 3.18
307 308 1.673665 CTCTGCAGGTGGGCTGAAC 60.674 63.158 15.13 0.00 40.52 3.18
308 309 1.834856 CTCTCTGCAGGTGGGCTGAA 61.835 60.000 15.13 0.00 40.52 3.02
309 310 2.203832 TCTCTGCAGGTGGGCTGA 60.204 61.111 15.13 0.00 39.08 4.26
310 311 2.268280 CTCTCTGCAGGTGGGCTG 59.732 66.667 15.13 0.00 34.04 4.85
311 312 3.715097 GCTCTCTGCAGGTGGGCT 61.715 66.667 20.22 0.00 42.31 5.19
312 313 4.792804 GGCTCTCTGCAGGTGGGC 62.793 72.222 19.61 19.61 45.15 5.36
313 314 4.106925 GGGCTCTCTGCAGGTGGG 62.107 72.222 15.13 8.51 45.15 4.61
314 315 3.324930 TGGGCTCTCTGCAGGTGG 61.325 66.667 15.13 4.92 45.15 4.61
315 316 2.268280 CTGGGCTCTCTGCAGGTG 59.732 66.667 15.13 7.59 45.15 4.00
316 317 3.007920 CCTGGGCTCTCTGCAGGT 61.008 66.667 15.13 0.00 45.15 4.00
317 318 3.795041 CCCTGGGCTCTCTGCAGG 61.795 72.222 15.13 4.77 45.15 4.85
318 319 1.845627 TTTCCCTGGGCTCTCTGCAG 61.846 60.000 7.63 7.63 45.15 4.41
319 320 1.426251 TTTTCCCTGGGCTCTCTGCA 61.426 55.000 8.22 0.00 45.15 4.41
320 321 0.679321 CTTTTCCCTGGGCTCTCTGC 60.679 60.000 8.22 0.00 41.94 4.26
321 322 0.695347 ACTTTTCCCTGGGCTCTCTG 59.305 55.000 8.22 0.00 0.00 3.35
322 323 0.988063 GACTTTTCCCTGGGCTCTCT 59.012 55.000 8.22 0.00 0.00 3.10
323 324 0.693049 TGACTTTTCCCTGGGCTCTC 59.307 55.000 8.22 0.00 0.00 3.20
324 325 1.149101 TTGACTTTTCCCTGGGCTCT 58.851 50.000 8.22 0.00 0.00 4.09
325 326 1.995376 TTTGACTTTTCCCTGGGCTC 58.005 50.000 8.22 0.00 0.00 4.70
326 327 2.702270 ATTTGACTTTTCCCTGGGCT 57.298 45.000 8.22 0.00 0.00 5.19
327 328 4.086457 TCTAATTTGACTTTTCCCTGGGC 58.914 43.478 8.22 0.00 0.00 5.36
328 329 5.127682 CCATCTAATTTGACTTTTCCCTGGG 59.872 44.000 6.33 6.33 0.00 4.45
329 330 5.951747 TCCATCTAATTTGACTTTTCCCTGG 59.048 40.000 0.00 0.00 0.00 4.45
330 331 6.127619 GGTCCATCTAATTTGACTTTTCCCTG 60.128 42.308 0.00 0.00 0.00 4.45
331 332 5.952347 GGTCCATCTAATTTGACTTTTCCCT 59.048 40.000 0.00 0.00 0.00 4.20
332 333 5.952347 AGGTCCATCTAATTTGACTTTTCCC 59.048 40.000 0.00 0.00 0.00 3.97
333 334 6.095580 GGAGGTCCATCTAATTTGACTTTTCC 59.904 42.308 0.00 0.00 35.64 3.13
334 335 6.183360 CGGAGGTCCATCTAATTTGACTTTTC 60.183 42.308 0.00 0.00 35.14 2.29
335 336 5.648092 CGGAGGTCCATCTAATTTGACTTTT 59.352 40.000 0.00 0.00 35.14 2.27
336 337 5.186198 CGGAGGTCCATCTAATTTGACTTT 58.814 41.667 0.00 0.00 35.14 2.66
337 338 4.770795 CGGAGGTCCATCTAATTTGACTT 58.229 43.478 0.00 0.00 35.14 3.01
338 339 3.432326 GCGGAGGTCCATCTAATTTGACT 60.432 47.826 0.00 0.00 35.14 3.41
339 340 2.872858 GCGGAGGTCCATCTAATTTGAC 59.127 50.000 0.00 0.00 35.14 3.18
340 341 2.158813 GGCGGAGGTCCATCTAATTTGA 60.159 50.000 0.00 0.00 35.14 2.69
341 342 2.158755 AGGCGGAGGTCCATCTAATTTG 60.159 50.000 0.00 0.00 35.14 2.32
342 343 2.127708 AGGCGGAGGTCCATCTAATTT 58.872 47.619 0.00 0.00 35.14 1.82
343 344 1.807814 AGGCGGAGGTCCATCTAATT 58.192 50.000 0.00 0.00 35.14 1.40
344 345 2.696526 TAGGCGGAGGTCCATCTAAT 57.303 50.000 0.00 0.00 35.14 1.73
345 346 2.464796 TTAGGCGGAGGTCCATCTAA 57.535 50.000 0.00 1.12 35.14 2.10
346 347 2.317040 CTTTAGGCGGAGGTCCATCTA 58.683 52.381 0.00 0.00 35.14 1.98
347 348 1.123928 CTTTAGGCGGAGGTCCATCT 58.876 55.000 0.00 0.00 35.14 2.90
348 349 0.533085 GCTTTAGGCGGAGGTCCATC 60.533 60.000 0.00 0.00 35.14 3.51
349 350 1.527370 GCTTTAGGCGGAGGTCCAT 59.473 57.895 0.00 0.00 35.14 3.41
350 351 2.987125 GCTTTAGGCGGAGGTCCA 59.013 61.111 0.00 0.00 35.14 4.02
359 360 4.580868 ACTTTTCTCTACCAGCTTTAGGC 58.419 43.478 0.00 0.00 42.19 3.93
360 361 7.387643 ACTTACTTTTCTCTACCAGCTTTAGG 58.612 38.462 0.00 0.00 0.00 2.69
361 362 8.088981 TGACTTACTTTTCTCTACCAGCTTTAG 58.911 37.037 0.00 0.00 0.00 1.85
362 363 7.959175 TGACTTACTTTTCTCTACCAGCTTTA 58.041 34.615 0.00 0.00 0.00 1.85
363 364 6.827727 TGACTTACTTTTCTCTACCAGCTTT 58.172 36.000 0.00 0.00 0.00 3.51
364 365 6.420913 TGACTTACTTTTCTCTACCAGCTT 57.579 37.500 0.00 0.00 0.00 3.74
365 366 6.211584 TCATGACTTACTTTTCTCTACCAGCT 59.788 38.462 0.00 0.00 0.00 4.24
366 367 6.311690 GTCATGACTTACTTTTCTCTACCAGC 59.688 42.308 18.83 0.00 0.00 4.85
367 368 7.607250 AGTCATGACTTACTTTTCTCTACCAG 58.393 38.462 22.89 0.00 38.83 4.00
368 369 7.540474 AGTCATGACTTACTTTTCTCTACCA 57.460 36.000 22.89 0.00 38.83 3.25
369 370 9.575783 CTTAGTCATGACTTACTTTTCTCTACC 57.424 37.037 32.14 0.00 42.54 3.18
377 378 9.628500 AGGTTTTTCTTAGTCATGACTTACTTT 57.372 29.630 32.14 10.83 42.54 2.66
378 379 9.628500 AAGGTTTTTCTTAGTCATGACTTACTT 57.372 29.630 32.14 17.14 42.54 2.24
379 380 9.628500 AAAGGTTTTTCTTAGTCATGACTTACT 57.372 29.630 32.14 12.49 42.54 2.24
414 415 9.662947 GTTGTAAAATTCACTACACTATAGGGT 57.337 33.333 13.27 13.27 0.00 4.34
415 416 9.106070 GGTTGTAAAATTCACTACACTATAGGG 57.894 37.037 0.00 0.00 0.00 3.53
416 417 9.661563 TGGTTGTAAAATTCACTACACTATAGG 57.338 33.333 4.43 0.00 0.00 2.57
421 422 9.361315 GTTTTTGGTTGTAAAATTCACTACACT 57.639 29.630 6.92 0.00 30.39 3.55
422 423 8.597227 GGTTTTTGGTTGTAAAATTCACTACAC 58.403 33.333 6.92 0.00 30.39 2.90
423 424 8.532819 AGGTTTTTGGTTGTAAAATTCACTACA 58.467 29.630 6.92 0.83 30.39 2.74
424 425 8.936070 AGGTTTTTGGTTGTAAAATTCACTAC 57.064 30.769 0.00 0.00 30.39 2.73
425 426 9.945904 AAAGGTTTTTGGTTGTAAAATTCACTA 57.054 25.926 0.00 0.00 30.39 2.74
426 427 8.726068 CAAAGGTTTTTGGTTGTAAAATTCACT 58.274 29.630 0.00 0.00 39.98 3.41
427 428 8.508062 ACAAAGGTTTTTGGTTGTAAAATTCAC 58.492 29.630 5.17 0.00 46.33 3.18
428 429 8.622948 ACAAAGGTTTTTGGTTGTAAAATTCA 57.377 26.923 5.17 0.00 46.33 2.57
439 440 4.101114 AGAGGGAAACAAAGGTTTTTGGT 58.899 39.130 5.17 0.00 46.84 3.67
440 441 4.753516 AGAGGGAAACAAAGGTTTTTGG 57.246 40.909 5.17 0.00 46.84 3.28
441 442 6.465439 AGTAGAGGGAAACAAAGGTTTTTG 57.535 37.500 0.00 0.00 46.84 2.44
442 443 9.293404 GTATAGTAGAGGGAAACAAAGGTTTTT 57.707 33.333 0.00 0.00 46.84 1.94
443 444 8.666821 AGTATAGTAGAGGGAAACAAAGGTTTT 58.333 33.333 0.00 0.00 46.84 2.43
445 446 7.809880 AGTATAGTAGAGGGAAACAAAGGTT 57.190 36.000 0.00 0.00 39.43 3.50
446 447 8.906238 TTAGTATAGTAGAGGGAAACAAAGGT 57.094 34.615 0.00 0.00 0.00 3.50
480 481 9.243105 CCACATAGGAAAAGGAAGATTTTTCTA 57.757 33.333 9.49 3.17 41.97 2.10
481 482 7.950124 TCCACATAGGAAAAGGAAGATTTTTCT 59.050 33.333 9.49 3.66 45.65 2.52
482 483 8.122472 TCCACATAGGAAAAGGAAGATTTTTC 57.878 34.615 2.67 2.67 45.65 2.29
498 499 7.674120 TCACAAGATCATCTAATCCACATAGG 58.326 38.462 0.00 0.00 39.47 2.57
499 500 9.722184 ATTCACAAGATCATCTAATCCACATAG 57.278 33.333 0.00 0.00 0.00 2.23
501 502 8.991783 AATTCACAAGATCATCTAATCCACAT 57.008 30.769 0.00 0.00 0.00 3.21
512 513 9.754382 GGCATAACAAATAATTCACAAGATCAT 57.246 29.630 0.00 0.00 0.00 2.45
513 514 7.914871 CGGCATAACAAATAATTCACAAGATCA 59.085 33.333 0.00 0.00 0.00 2.92
514 515 7.096477 GCGGCATAACAAATAATTCACAAGATC 60.096 37.037 0.00 0.00 0.00 2.75
515 516 6.697019 GCGGCATAACAAATAATTCACAAGAT 59.303 34.615 0.00 0.00 0.00 2.40
516 517 6.033341 GCGGCATAACAAATAATTCACAAGA 58.967 36.000 0.00 0.00 0.00 3.02
517 518 6.035843 AGCGGCATAACAAATAATTCACAAG 58.964 36.000 1.45 0.00 0.00 3.16
518 519 5.960113 AGCGGCATAACAAATAATTCACAA 58.040 33.333 1.45 0.00 0.00 3.33
519 520 5.574891 AGCGGCATAACAAATAATTCACA 57.425 34.783 1.45 0.00 0.00 3.58
520 521 5.619607 CGTAGCGGCATAACAAATAATTCAC 59.380 40.000 1.45 0.00 0.00 3.18
521 522 5.277586 CCGTAGCGGCATAACAAATAATTCA 60.278 40.000 1.45 0.00 41.17 2.57
522 523 5.144359 CCGTAGCGGCATAACAAATAATTC 58.856 41.667 1.45 0.00 41.17 2.17
523 524 5.103290 CCGTAGCGGCATAACAAATAATT 57.897 39.130 1.45 0.00 41.17 1.40
524 525 4.742438 CCGTAGCGGCATAACAAATAAT 57.258 40.909 1.45 0.00 41.17 1.28
538 539 4.437121 GCTGGTACTAATAGATCCGTAGCG 60.437 50.000 0.00 0.00 34.17 4.26
568 569 1.100510 CTTGACCTGGGTGATGCATG 58.899 55.000 2.46 0.00 0.00 4.06
598 600 4.323945 CCAGTGCAACCACCCTAGTTAATA 60.324 45.833 0.00 0.00 43.09 0.98
660 666 7.307219 GCTGGTAGTTAAATTAATACTCCTGCG 60.307 40.741 14.19 0.00 31.61 5.18
676 682 2.264813 GAATCGCGTTGCTGGTAGTTA 58.735 47.619 5.77 0.00 0.00 2.24
692 698 0.741221 GCTATCGGGCGGATGGAATC 60.741 60.000 20.03 1.49 44.55 2.52
709 715 1.442526 CGTGTCGTATACGGGGAGCT 61.443 60.000 24.18 0.00 40.29 4.09
783 789 2.348998 CTCTGGAGCAAGCGGGTT 59.651 61.111 0.00 0.00 0.00 4.11
837 851 3.878778 AGGCATTGACACCAACTATCTC 58.121 45.455 0.00 0.00 34.72 2.75
846 860 4.022849 GGCTGATTTATAGGCATTGACACC 60.023 45.833 0.00 0.00 40.17 4.16
876 890 1.460699 GGATACTGGGATTGGGGCC 59.539 63.158 0.00 0.00 0.00 5.80
1179 1196 0.319900 GTGTGAGCGCCTTCTTCTGA 60.320 55.000 2.29 0.00 0.00 3.27
1203 1728 1.712977 GCCTGCCGATCTGCTTGAAG 61.713 60.000 10.62 0.00 0.00 3.02
1206 1731 2.124819 AGCCTGCCGATCTGCTTG 60.125 61.111 10.62 2.79 0.00 4.01
1209 1734 4.479993 ACCAGCCTGCCGATCTGC 62.480 66.667 1.59 1.59 0.00 4.26
1210 1735 2.202987 GACCAGCCTGCCGATCTG 60.203 66.667 0.00 0.00 0.00 2.90
1212 1737 2.107953 GAGACCAGCCTGCCGATC 59.892 66.667 0.00 0.00 0.00 3.69
1215 1740 2.786495 ATACGAGACCAGCCTGCCG 61.786 63.158 0.00 0.00 0.00 5.69
1216 1741 1.227380 CATACGAGACCAGCCTGCC 60.227 63.158 0.00 0.00 0.00 4.85
1220 1745 1.521681 GTGGCATACGAGACCAGCC 60.522 63.158 0.00 0.00 45.41 4.85
1221 1746 1.521681 GGTGGCATACGAGACCAGC 60.522 63.158 0.00 0.00 43.92 4.85
1222 1747 1.226974 CGGTGGCATACGAGACCAG 60.227 63.158 8.59 0.00 33.12 4.00
1223 1748 1.679641 TCGGTGGCATACGAGACCA 60.680 57.895 12.24 0.00 34.67 4.02
1228 1753 1.040893 ATCACCTCGGTGGCATACGA 61.041 55.000 15.58 14.84 45.43 3.43
1229 1754 0.875908 CATCACCTCGGTGGCATACG 60.876 60.000 15.58 8.04 45.43 3.06
1230 1755 0.532862 CCATCACCTCGGTGGCATAC 60.533 60.000 15.58 0.00 45.43 2.39
1231 1756 1.829456 CCATCACCTCGGTGGCATA 59.171 57.895 15.58 0.00 45.43 3.14
1232 1757 2.591753 CCATCACCTCGGTGGCAT 59.408 61.111 15.58 0.67 45.43 4.40
1235 1760 2.484287 AAAGGCCATCACCTCGGTGG 62.484 60.000 15.58 1.70 45.43 4.61
1571 4407 7.597743 ACCAAAGTAGAGTATTACAAGTTCGTG 59.402 37.037 0.00 0.00 0.00 4.35
1705 4542 7.983484 ACTAAATTTATGTCCGTTTAGATCGGT 59.017 33.333 9.84 0.00 46.86 4.69
1852 4689 0.517316 GAAAGTGCGCTCCGAATGTT 59.483 50.000 9.73 0.00 0.00 2.71
1920 4757 0.322456 TTCCTTTGGCCCATCACGAG 60.322 55.000 0.00 0.00 0.00 4.18
1987 4824 1.121240 CGAAGTCAATAGCTACCGCG 58.879 55.000 0.00 0.00 42.32 6.46
2149 4987 3.002656 CCTACAGACAACTTGTTGCACTG 59.997 47.826 24.63 24.63 36.48 3.66
2204 5042 1.548719 TGGTCAACTATCACGTCCTGG 59.451 52.381 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.