Multiple sequence alignment - TraesCS2B01G276200

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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 TraesCS2B01G276200 chr2B 100.000 2552 0 0 1 2552 381915697 381913146 0.000000e+00 4713.0
1 TraesCS2B01G276200 chr2B 99.132 922 8 0 714 1635 382731858 382732779 0.000000e+00 1659.0
2 TraesCS2B01G276200 chr2B 92.780 928 51 10 1635 2552 165514804 165515725 0.000000e+00 1328.0
3 TraesCS2B01G276200 chr2B 97.059 34 1 0 1630 1663 93182857 93182824 9.860000e-05 58.4
4 TraesCS2B01G276200 chr6A 99.347 919 6 0 1634 2552 207823877 207824795 0.000000e+00 1664.0
5 TraesCS2B01G276200 chr3D 94.800 923 43 3 1635 2552 353152690 353153612 0.000000e+00 1434.0
6 TraesCS2B01G276200 chr1A 94.258 923 48 3 1635 2552 84276518 84277440 0.000000e+00 1406.0
7 TraesCS2B01G276200 chr1A 90.698 559 41 9 1995 2552 492722216 492722764 0.000000e+00 734.0
8 TraesCS2B01G276200 chr1A 91.797 256 10 3 1753 2008 492720647 492720891 1.880000e-91 346.0
9 TraesCS2B01G276200 chr2A 94.048 924 44 7 1635 2552 447300853 447299935 0.000000e+00 1391.0
10 TraesCS2B01G276200 chr2A 93.966 928 41 4 714 1630 421060738 421059815 0.000000e+00 1389.0
11 TraesCS2B01G276200 chr2A 92.449 927 51 8 714 1630 422102867 422103784 0.000000e+00 1306.0
12 TraesCS2B01G276200 chr2A 92.102 937 56 7 713 1635 422221558 422222490 0.000000e+00 1304.0
13 TraesCS2B01G276200 chr2A 89.312 814 62 6 1634 2441 398448036 398447242 0.000000e+00 998.0
14 TraesCS2B01G276200 chr2A 89.351 770 62 5 1673 2441 398867993 398868743 0.000000e+00 950.0
15 TraesCS2B01G276200 chr2A 90.909 88 5 1 2466 2550 398447125 398447038 5.770000e-22 115.0
16 TraesCS2B01G276200 chr2A 89.655 87 6 1 2466 2549 398868860 398868946 9.650000e-20 108.0
17 TraesCS2B01G276200 chr2A 95.745 47 2 0 1634 1680 398867559 398867605 2.720000e-10 76.8
18 TraesCS2B01G276200 chr2D 93.960 596 31 2 714 1304 314054104 314053509 0.000000e+00 896.0
19 TraesCS2B01G276200 chr2D 93.929 593 31 2 714 1301 314565194 314565786 0.000000e+00 891.0
20 TraesCS2B01G276200 chr2D 93.929 593 31 2 714 1301 314794853 314795445 0.000000e+00 891.0
21 TraesCS2B01G276200 chr2D 91.607 417 31 1 1197 1613 314795302 314795714 7.920000e-160 573.0
22 TraesCS2B01G276200 chr2D 90.045 442 37 3 1192 1630 314053660 314053223 1.330000e-157 566.0
23 TraesCS2B01G276200 chr2D 91.127 417 33 1 1197 1613 314565643 314566055 1.710000e-156 562.0
24 TraesCS2B01G276200 chrUn 88.462 52 5 1 131 182 51450373 51450423 7.620000e-06 62.1
25 TraesCS2B01G276200 chr1D 100.000 30 0 0 1634 1663 246038514 246038543 3.550000e-04 56.5


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 TraesCS2B01G276200 chr2B 381913146 381915697 2551 True 4713.000000 4713 100.000000 1 2552 1 chr2B.!!$R2 2551
1 TraesCS2B01G276200 chr2B 382731858 382732779 921 False 1659.000000 1659 99.132000 714 1635 1 chr2B.!!$F2 921
2 TraesCS2B01G276200 chr2B 165514804 165515725 921 False 1328.000000 1328 92.780000 1635 2552 1 chr2B.!!$F1 917
3 TraesCS2B01G276200 chr6A 207823877 207824795 918 False 1664.000000 1664 99.347000 1634 2552 1 chr6A.!!$F1 918
4 TraesCS2B01G276200 chr3D 353152690 353153612 922 False 1434.000000 1434 94.800000 1635 2552 1 chr3D.!!$F1 917
5 TraesCS2B01G276200 chr1A 84276518 84277440 922 False 1406.000000 1406 94.258000 1635 2552 1 chr1A.!!$F1 917
6 TraesCS2B01G276200 chr1A 492720647 492722764 2117 False 540.000000 734 91.247500 1753 2552 2 chr1A.!!$F2 799
7 TraesCS2B01G276200 chr2A 447299935 447300853 918 True 1391.000000 1391 94.048000 1635 2552 1 chr2A.!!$R2 917
8 TraesCS2B01G276200 chr2A 421059815 421060738 923 True 1389.000000 1389 93.966000 714 1630 1 chr2A.!!$R1 916
9 TraesCS2B01G276200 chr2A 422102867 422103784 917 False 1306.000000 1306 92.449000 714 1630 1 chr2A.!!$F1 916
10 TraesCS2B01G276200 chr2A 422221558 422222490 932 False 1304.000000 1304 92.102000 713 1635 1 chr2A.!!$F2 922
11 TraesCS2B01G276200 chr2A 398447038 398448036 998 True 556.500000 998 90.110500 1634 2550 2 chr2A.!!$R3 916
12 TraesCS2B01G276200 chr2A 398867559 398868946 1387 False 378.266667 950 91.583667 1634 2549 3 chr2A.!!$F3 915
13 TraesCS2B01G276200 chr2D 314794853 314795714 861 False 732.000000 891 92.768000 714 1613 2 chr2D.!!$F2 899
14 TraesCS2B01G276200 chr2D 314053223 314054104 881 True 731.000000 896 92.002500 714 1630 2 chr2D.!!$R1 916
15 TraesCS2B01G276200 chr2D 314565194 314566055 861 False 726.500000 891 92.528000 714 1613 2 chr2D.!!$F1 899

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
44 45 0.033090 GGTTCGGGTTCTGAGACGTT 59.967 55.0 0.00 0.00 0.00 3.99 F
704 705 0.039074 CCCACGCAGATCCGATCTAC 60.039 60.0 10.65 4.61 37.58 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1059 1065 1.154016 CGTCCGCGATGTCTTGAGT 60.154 57.895 8.23 0.0 41.33 3.41 R
1706 2157 6.372659 GGCGTACATGATAATCAATGAGGAAT 59.627 38.462 0.00 0.0 0.00 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
20 21 3.744238 AGGTTTTTCCCATCGGTTTTG 57.256 42.857 0.00 0.00 36.75 2.44
21 22 2.367241 AGGTTTTTCCCATCGGTTTTGG 59.633 45.455 0.00 0.00 36.75 3.28
27 28 3.356814 CCATCGGTTTTGGGAAGGT 57.643 52.632 0.00 0.00 0.00 3.50
28 29 1.627864 CCATCGGTTTTGGGAAGGTT 58.372 50.000 0.00 0.00 0.00 3.50
29 30 1.544246 CCATCGGTTTTGGGAAGGTTC 59.456 52.381 0.00 0.00 0.00 3.62
30 31 1.199097 CATCGGTTTTGGGAAGGTTCG 59.801 52.381 0.00 0.00 0.00 3.95
31 32 0.535553 TCGGTTTTGGGAAGGTTCGG 60.536 55.000 0.00 0.00 0.00 4.30
32 33 1.520600 CGGTTTTGGGAAGGTTCGGG 61.521 60.000 0.00 0.00 0.00 5.14
33 34 0.468585 GGTTTTGGGAAGGTTCGGGT 60.469 55.000 0.00 0.00 0.00 5.28
34 35 1.405872 GTTTTGGGAAGGTTCGGGTT 58.594 50.000 0.00 0.00 0.00 4.11
35 36 1.338973 GTTTTGGGAAGGTTCGGGTTC 59.661 52.381 0.00 0.00 0.00 3.62
36 37 0.848053 TTTGGGAAGGTTCGGGTTCT 59.152 50.000 0.00 0.00 0.00 3.01
37 38 0.109723 TTGGGAAGGTTCGGGTTCTG 59.890 55.000 0.00 0.00 0.00 3.02
38 39 0.765135 TGGGAAGGTTCGGGTTCTGA 60.765 55.000 0.00 0.00 0.00 3.27
39 40 0.036294 GGGAAGGTTCGGGTTCTGAG 60.036 60.000 0.00 0.00 0.00 3.35
40 41 0.974383 GGAAGGTTCGGGTTCTGAGA 59.026 55.000 0.00 0.00 0.00 3.27
41 42 1.337917 GGAAGGTTCGGGTTCTGAGAC 60.338 57.143 0.00 0.00 0.00 3.36
42 43 0.317479 AAGGTTCGGGTTCTGAGACG 59.683 55.000 0.00 0.00 0.00 4.18
43 44 0.826672 AGGTTCGGGTTCTGAGACGT 60.827 55.000 0.00 0.00 0.00 4.34
44 45 0.033090 GGTTCGGGTTCTGAGACGTT 59.967 55.000 0.00 0.00 0.00 3.99
45 46 1.539712 GGTTCGGGTTCTGAGACGTTT 60.540 52.381 0.00 0.00 0.00 3.60
46 47 2.207590 GTTCGGGTTCTGAGACGTTTT 58.792 47.619 0.00 0.00 0.00 2.43
47 48 2.607631 TCGGGTTCTGAGACGTTTTT 57.392 45.000 0.00 0.00 0.00 1.94
151 152 9.956720 TTTTGTGAACATTGTTTTGAAATTTGT 57.043 22.222 3.08 0.00 0.00 2.83
152 153 8.945758 TTGTGAACATTGTTTTGAAATTTGTG 57.054 26.923 3.08 0.00 0.00 3.33
153 154 7.524912 TGTGAACATTGTTTTGAAATTTGTGG 58.475 30.769 3.08 0.00 0.00 4.17
154 155 7.388776 TGTGAACATTGTTTTGAAATTTGTGGA 59.611 29.630 3.08 0.00 0.00 4.02
155 156 7.691877 GTGAACATTGTTTTGAAATTTGTGGAC 59.308 33.333 3.08 0.00 0.00 4.02
156 157 7.388776 TGAACATTGTTTTGAAATTTGTGGACA 59.611 29.630 3.08 0.00 0.00 4.02
157 158 7.678947 ACATTGTTTTGAAATTTGTGGACAA 57.321 28.000 0.00 2.59 0.00 3.18
158 159 8.278729 ACATTGTTTTGAAATTTGTGGACAAT 57.721 26.923 0.00 4.81 37.05 2.71
159 160 8.738106 ACATTGTTTTGAAATTTGTGGACAATT 58.262 25.926 12.95 6.48 35.11 2.32
160 161 9.570488 CATTGTTTTGAAATTTGTGGACAATTT 57.430 25.926 12.95 0.00 35.11 1.82
162 163 9.971922 TTGTTTTGAAATTTGTGGACAATTTTT 57.028 22.222 11.63 7.06 38.64 1.94
163 164 9.403110 TGTTTTGAAATTTGTGGACAATTTTTG 57.597 25.926 11.63 0.00 38.64 2.44
164 165 9.617975 GTTTTGAAATTTGTGGACAATTTTTGA 57.382 25.926 11.63 0.87 38.64 2.69
168 169 9.784680 TGAAATTTGTGGACAATTTTTGAATTG 57.215 25.926 11.63 9.61 43.77 2.32
170 171 9.786105 AAATTTGTGGACAATTTTTGAATTGAC 57.214 25.926 16.26 10.96 41.44 3.18
171 172 6.580963 TTGTGGACAATTTTTGAATTGACG 57.419 33.333 16.26 0.00 41.44 4.35
172 173 5.046529 TGTGGACAATTTTTGAATTGACGG 58.953 37.500 16.26 0.00 41.44 4.79
173 174 5.163509 TGTGGACAATTTTTGAATTGACGGA 60.164 36.000 16.26 1.47 41.44 4.69
174 175 5.174943 GTGGACAATTTTTGAATTGACGGAC 59.825 40.000 16.26 8.32 41.44 4.79
175 176 5.163509 TGGACAATTTTTGAATTGACGGACA 60.164 36.000 16.26 4.19 41.44 4.02
176 177 5.925969 GGACAATTTTTGAATTGACGGACAT 59.074 36.000 16.26 0.00 41.44 3.06
177 178 7.087639 GGACAATTTTTGAATTGACGGACATA 58.912 34.615 16.26 0.00 41.44 2.29
178 179 7.759433 GGACAATTTTTGAATTGACGGACATAT 59.241 33.333 16.26 0.00 41.44 1.78
179 180 9.139174 GACAATTTTTGAATTGACGGACATATT 57.861 29.630 16.26 0.00 41.44 1.28
180 181 9.487790 ACAATTTTTGAATTGACGGACATATTT 57.512 25.926 16.26 0.00 41.44 1.40
183 184 8.527567 TTTTTGAATTGACGGACATATTTTCC 57.472 30.769 0.00 0.00 0.00 3.13
184 185 6.825944 TTGAATTGACGGACATATTTTCCA 57.174 33.333 1.82 0.00 31.94 3.53
185 186 6.189677 TGAATTGACGGACATATTTTCCAC 57.810 37.500 1.82 0.00 31.94 4.02
186 187 5.707764 TGAATTGACGGACATATTTTCCACA 59.292 36.000 1.82 0.00 31.94 4.17
187 188 6.376864 TGAATTGACGGACATATTTTCCACAT 59.623 34.615 1.82 0.00 31.94 3.21
188 189 7.554476 TGAATTGACGGACATATTTTCCACATA 59.446 33.333 1.82 0.00 31.94 2.29
189 190 8.463930 AATTGACGGACATATTTTCCACATAT 57.536 30.769 1.82 0.00 31.94 1.78
190 191 6.859420 TGACGGACATATTTTCCACATATG 57.141 37.500 0.00 0.00 39.57 1.78
191 192 6.353323 TGACGGACATATTTTCCACATATGT 58.647 36.000 1.41 1.41 46.21 2.29
192 193 6.259829 TGACGGACATATTTTCCACATATGTG 59.740 38.462 26.02 26.02 44.43 3.21
210 211 9.352784 ACATATGTGAATGTGTTTTAAAATCCG 57.647 29.630 7.78 0.00 38.65 4.18
211 212 9.352784 CATATGTGAATGTGTTTTAAAATCCGT 57.647 29.630 3.52 0.00 0.00 4.69
214 215 9.751542 ATGTGAATGTGTTTTAAAATCCGTAAA 57.248 25.926 3.52 0.00 0.00 2.01
215 216 9.751542 TGTGAATGTGTTTTAAAATCCGTAAAT 57.248 25.926 3.52 0.00 0.00 1.40
230 231 8.994429 AATCCGTAAATATTTTTGAATGTGCA 57.006 26.923 5.91 0.00 0.00 4.57
231 232 8.994429 ATCCGTAAATATTTTTGAATGTGCAA 57.006 26.923 5.91 0.00 0.00 4.08
232 233 8.818141 TCCGTAAATATTTTTGAATGTGCAAA 57.182 26.923 5.91 0.00 36.08 3.68
233 234 8.704234 TCCGTAAATATTTTTGAATGTGCAAAC 58.296 29.630 5.91 0.00 37.48 2.93
234 235 7.682055 CCGTAAATATTTTTGAATGTGCAAACG 59.318 33.333 5.91 5.32 37.48 3.60
235 236 8.211181 CGTAAATATTTTTGAATGTGCAAACGT 58.789 29.630 5.91 0.00 37.48 3.99
236 237 9.856803 GTAAATATTTTTGAATGTGCAAACGTT 57.143 25.926 5.91 0.00 37.48 3.99
238 239 9.780413 AAATATTTTTGAATGTGCAAACGTTTT 57.220 22.222 11.66 0.00 37.48 2.43
239 240 9.780413 AATATTTTTGAATGTGCAAACGTTTTT 57.220 22.222 11.66 2.35 37.48 1.94
251 252 9.692749 TGTGCAAACGTTTTTATAATTTATGGA 57.307 25.926 11.66 0.00 0.00 3.41
273 274 9.981114 ATGGAAATTTTAAAAACTCGAGAACAT 57.019 25.926 21.68 5.13 0.00 2.71
274 275 9.810545 TGGAAATTTTAAAAACTCGAGAACATT 57.189 25.926 21.68 10.64 0.00 2.71
284 285 9.586435 AAAAACTCGAGAACATTTCTTGAAATT 57.414 25.926 21.68 0.00 46.69 1.82
285 286 8.788409 AAACTCGAGAACATTTCTTGAAATTC 57.212 30.769 21.68 4.18 46.69 2.17
286 287 7.496529 ACTCGAGAACATTTCTTGAAATTCA 57.503 32.000 21.68 0.00 46.69 2.57
287 288 8.103948 ACTCGAGAACATTTCTTGAAATTCAT 57.896 30.769 21.68 0.00 46.69 2.57
288 289 8.019669 ACTCGAGAACATTTCTTGAAATTCATG 58.980 33.333 21.68 0.00 46.69 3.07
289 290 8.098220 TCGAGAACATTTCTTGAAATTCATGA 57.902 30.769 7.38 7.38 45.02 3.07
290 291 8.567104 TCGAGAACATTTCTTGAAATTCATGAA 58.433 29.630 16.98 16.98 45.02 2.57
291 292 9.350357 CGAGAACATTTCTTGAAATTCATGAAT 57.650 29.630 20.17 15.36 42.69 2.57
321 322 8.535066 TTTAATTTGCAAACGTTTTGTAATGC 57.465 26.923 15.41 12.05 41.47 3.56
322 323 5.725110 ATTTGCAAACGTTTTGTAATGCA 57.275 30.435 15.41 16.76 46.00 3.96
323 324 4.506838 TTGCAAACGTTTTGTAATGCAC 57.493 36.364 19.56 0.29 46.77 4.57
324 325 2.531912 TGCAAACGTTTTGTAATGCACG 59.468 40.909 16.76 1.82 44.11 5.34
325 326 2.097637 GCAAACGTTTTGTAATGCACGG 60.098 45.455 11.66 0.00 41.03 4.94
326 327 3.364062 CAAACGTTTTGTAATGCACGGA 58.636 40.909 11.66 0.00 36.95 4.69
327 328 2.673976 ACGTTTTGTAATGCACGGAC 57.326 45.000 0.00 0.00 36.95 4.79
328 329 1.941294 ACGTTTTGTAATGCACGGACA 59.059 42.857 0.00 0.00 36.95 4.02
329 330 2.550606 ACGTTTTGTAATGCACGGACAT 59.449 40.909 0.00 0.00 36.95 3.06
330 331 3.003897 ACGTTTTGTAATGCACGGACATT 59.996 39.130 9.68 9.68 42.73 2.71
331 332 3.978217 CGTTTTGTAATGCACGGACATTT 59.022 39.130 9.98 0.00 40.64 2.32
332 333 4.442733 CGTTTTGTAATGCACGGACATTTT 59.557 37.500 9.98 0.00 40.64 1.82
333 334 5.051374 CGTTTTGTAATGCACGGACATTTTT 60.051 36.000 9.98 0.00 40.64 1.94
385 386 9.833894 CAAGAACATGTTTTCAATTTAAGAACG 57.166 29.630 13.36 0.00 0.00 3.95
386 387 9.796120 AAGAACATGTTTTCAATTTAAGAACGA 57.204 25.926 13.36 0.00 0.00 3.85
387 388 9.796120 AGAACATGTTTTCAATTTAAGAACGAA 57.204 25.926 13.36 0.00 0.00 3.85
397 398 9.528018 TTCAATTTAAGAACGAATTTTCAAGCT 57.472 25.926 0.00 0.00 0.00 3.74
398 399 9.180678 TCAATTTAAGAACGAATTTTCAAGCTC 57.819 29.630 0.00 0.00 0.00 4.09
399 400 8.967218 CAATTTAAGAACGAATTTTCAAGCTCA 58.033 29.630 0.00 0.00 0.00 4.26
400 401 8.733857 ATTTAAGAACGAATTTTCAAGCTCAG 57.266 30.769 0.00 0.00 0.00 3.35
401 402 4.152607 AGAACGAATTTTCAAGCTCAGC 57.847 40.909 0.00 0.00 0.00 4.26
402 403 3.817647 AGAACGAATTTTCAAGCTCAGCT 59.182 39.130 0.00 0.00 42.56 4.24
403 404 4.997395 AGAACGAATTTTCAAGCTCAGCTA 59.003 37.500 0.00 0.00 38.25 3.32
404 405 5.470098 AGAACGAATTTTCAAGCTCAGCTAA 59.530 36.000 0.00 0.00 38.25 3.09
405 406 5.288543 ACGAATTTTCAAGCTCAGCTAAG 57.711 39.130 0.00 0.00 38.25 2.18
406 407 4.757149 ACGAATTTTCAAGCTCAGCTAAGT 59.243 37.500 0.00 0.00 38.25 2.24
407 408 5.239525 ACGAATTTTCAAGCTCAGCTAAGTT 59.760 36.000 0.00 0.00 38.25 2.66
408 409 6.145535 CGAATTTTCAAGCTCAGCTAAGTTT 58.854 36.000 0.00 0.00 38.25 2.66
409 410 6.638468 CGAATTTTCAAGCTCAGCTAAGTTTT 59.362 34.615 0.00 0.00 38.25 2.43
410 411 7.168135 CGAATTTTCAAGCTCAGCTAAGTTTTT 59.832 33.333 0.00 0.00 38.25 1.94
466 467 8.859517 AAATTGTGGAAATTTTTCAAATGCAG 57.140 26.923 5.48 0.00 38.92 4.41
467 468 6.998968 TTGTGGAAATTTTTCAAATGCAGT 57.001 29.167 5.48 0.00 38.92 4.40
468 469 8.674263 ATTGTGGAAATTTTTCAAATGCAGTA 57.326 26.923 5.48 0.00 38.92 2.74
469 470 7.475771 TGTGGAAATTTTTCAAATGCAGTAC 57.524 32.000 5.48 0.00 38.92 2.73
470 471 7.271511 TGTGGAAATTTTTCAAATGCAGTACT 58.728 30.769 5.48 0.00 38.92 2.73
471 472 7.768120 TGTGGAAATTTTTCAAATGCAGTACTT 59.232 29.630 0.00 0.00 38.92 2.24
472 473 8.611757 GTGGAAATTTTTCAAATGCAGTACTTT 58.388 29.630 0.00 0.00 38.92 2.66
473 474 9.171877 TGGAAATTTTTCAAATGCAGTACTTTT 57.828 25.926 0.00 0.00 38.92 2.27
474 475 9.437045 GGAAATTTTTCAAATGCAGTACTTTTG 57.563 29.630 10.89 10.89 42.12 2.44
482 483 7.077605 TCAAATGCAGTACTTTTGAAATCTCG 58.922 34.615 15.58 0.00 44.76 4.04
483 484 6.801539 AATGCAGTACTTTTGAAATCTCGA 57.198 33.333 0.00 0.00 0.00 4.04
484 485 6.801539 ATGCAGTACTTTTGAAATCTCGAA 57.198 33.333 0.00 0.00 0.00 3.71
485 486 6.801539 TGCAGTACTTTTGAAATCTCGAAT 57.198 33.333 0.00 0.00 0.00 3.34
486 487 7.899178 TGCAGTACTTTTGAAATCTCGAATA 57.101 32.000 0.00 0.00 0.00 1.75
487 488 8.492673 TGCAGTACTTTTGAAATCTCGAATAT 57.507 30.769 0.00 0.00 0.00 1.28
488 489 8.604035 TGCAGTACTTTTGAAATCTCGAATATC 58.396 33.333 0.00 0.00 0.00 1.63
489 490 8.821894 GCAGTACTTTTGAAATCTCGAATATCT 58.178 33.333 0.00 0.00 0.00 1.98
547 548 5.547181 GGAACGAAAAACATTAGGAGAGG 57.453 43.478 0.00 0.00 0.00 3.69
548 549 4.142665 GGAACGAAAAACATTAGGAGAGGC 60.143 45.833 0.00 0.00 0.00 4.70
549 550 3.344515 ACGAAAAACATTAGGAGAGGCC 58.655 45.455 0.00 0.00 0.00 5.19
550 551 2.683362 CGAAAAACATTAGGAGAGGCCC 59.317 50.000 0.00 0.00 37.37 5.80
551 552 2.420058 AAAACATTAGGAGAGGCCCG 57.580 50.000 0.00 0.00 37.37 6.13
552 553 1.580059 AAACATTAGGAGAGGCCCGA 58.420 50.000 0.00 0.00 37.37 5.14
553 554 0.831307 AACATTAGGAGAGGCCCGAC 59.169 55.000 0.00 0.00 37.37 4.79
554 555 1.049289 ACATTAGGAGAGGCCCGACC 61.049 60.000 0.00 0.00 37.37 4.79
555 556 1.459730 ATTAGGAGAGGCCCGACCC 60.460 63.158 0.00 0.00 40.58 4.46
556 557 4.517934 TAGGAGAGGCCCGACCCG 62.518 72.222 0.00 0.00 40.58 5.28
558 559 4.828296 GGAGAGGCCCGACCCGTA 62.828 72.222 0.00 0.00 40.58 4.02
559 560 3.525545 GAGAGGCCCGACCCGTAC 61.526 72.222 0.00 0.00 40.58 3.67
573 574 3.712907 GTACCTGGGCTGGCCGAA 61.713 66.667 16.08 0.00 36.85 4.30
574 575 3.399181 TACCTGGGCTGGCCGAAG 61.399 66.667 16.08 8.16 36.85 3.79
576 577 4.351054 CCTGGGCTGGCCGAAGTT 62.351 66.667 16.08 0.00 36.85 2.66
577 578 2.282462 CTGGGCTGGCCGAAGTTT 60.282 61.111 16.08 0.00 36.85 2.66
578 579 2.597217 TGGGCTGGCCGAAGTTTG 60.597 61.111 16.08 0.00 36.85 2.93
579 580 4.056125 GGGCTGGCCGAAGTTTGC 62.056 66.667 3.84 0.00 36.85 3.68
580 581 4.404654 GGCTGGCCGAAGTTTGCG 62.405 66.667 0.00 0.00 0.00 4.85
582 583 4.741781 CTGGCCGAAGTTTGCGCG 62.742 66.667 0.00 0.00 0.00 6.86
586 587 4.383602 CCGAAGTTTGCGCGTGGG 62.384 66.667 8.43 0.00 0.00 4.61
587 588 4.383602 CGAAGTTTGCGCGTGGGG 62.384 66.667 8.43 0.00 0.00 4.96
588 589 4.038080 GAAGTTTGCGCGTGGGGG 62.038 66.667 8.43 0.00 0.00 5.40
589 590 4.572571 AAGTTTGCGCGTGGGGGA 62.573 61.111 8.43 0.00 0.00 4.81
604 605 2.188207 GGAGCGAGGCCTCCTTTC 59.812 66.667 27.20 19.84 46.39 2.62
605 606 2.188207 GAGCGAGGCCTCCTTTCC 59.812 66.667 27.20 10.17 31.76 3.13
606 607 2.607750 AGCGAGGCCTCCTTTCCA 60.608 61.111 27.20 0.00 31.76 3.53
607 608 2.436824 GCGAGGCCTCCTTTCCAC 60.437 66.667 27.20 0.00 31.76 4.02
608 609 2.269241 CGAGGCCTCCTTTCCACC 59.731 66.667 27.20 0.00 31.76 4.61
609 610 2.592993 CGAGGCCTCCTTTCCACCA 61.593 63.158 27.20 0.00 31.76 4.17
610 611 1.002011 GAGGCCTCCTTTCCACCAC 60.002 63.158 23.19 0.00 31.76 4.16
611 612 1.774217 AGGCCTCCTTTCCACCACA 60.774 57.895 0.00 0.00 0.00 4.17
612 613 1.603739 GGCCTCCTTTCCACCACAC 60.604 63.158 0.00 0.00 0.00 3.82
613 614 1.966451 GCCTCCTTTCCACCACACG 60.966 63.158 0.00 0.00 0.00 4.49
614 615 1.302511 CCTCCTTTCCACCACACGG 60.303 63.158 0.00 0.00 38.77 4.94
615 616 1.302511 CTCCTTTCCACCACACGGG 60.303 63.158 0.00 0.00 44.81 5.28
616 617 2.983592 CCTTTCCACCACACGGGC 60.984 66.667 0.00 0.00 42.05 6.13
617 618 2.203280 CTTTCCACCACACGGGCA 60.203 61.111 0.00 0.00 42.05 5.36
618 619 2.203280 TTTCCACCACACGGGCAG 60.203 61.111 0.00 0.00 42.05 4.85
619 620 3.783362 TTTCCACCACACGGGCAGG 62.783 63.158 0.00 0.00 42.05 4.85
621 622 4.263572 CCACCACACGGGCAGGAA 62.264 66.667 3.43 0.00 42.05 3.36
622 623 2.203280 CACCACACGGGCAGGAAA 60.203 61.111 3.43 0.00 42.05 3.13
623 624 2.203294 ACCACACGGGCAGGAAAC 60.203 61.111 3.43 0.00 42.05 2.78
624 625 2.203280 CCACACGGGCAGGAAACA 60.203 61.111 0.00 0.00 0.00 2.83
625 626 2.260869 CCACACGGGCAGGAAACAG 61.261 63.158 0.00 0.00 0.00 3.16
626 627 1.227823 CACACGGGCAGGAAACAGA 60.228 57.895 0.00 0.00 0.00 3.41
627 628 0.817634 CACACGGGCAGGAAACAGAA 60.818 55.000 0.00 0.00 0.00 3.02
628 629 0.818040 ACACGGGCAGGAAACAGAAC 60.818 55.000 0.00 0.00 0.00 3.01
629 630 0.817634 CACGGGCAGGAAACAGAACA 60.818 55.000 0.00 0.00 0.00 3.18
630 631 0.535102 ACGGGCAGGAAACAGAACAG 60.535 55.000 0.00 0.00 0.00 3.16
631 632 0.250295 CGGGCAGGAAACAGAACAGA 60.250 55.000 0.00 0.00 0.00 3.41
632 633 1.813862 CGGGCAGGAAACAGAACAGAA 60.814 52.381 0.00 0.00 0.00 3.02
633 634 1.882623 GGGCAGGAAACAGAACAGAAG 59.117 52.381 0.00 0.00 0.00 2.85
634 635 2.576615 GGCAGGAAACAGAACAGAAGT 58.423 47.619 0.00 0.00 0.00 3.01
635 636 2.952310 GGCAGGAAACAGAACAGAAGTT 59.048 45.455 0.00 0.00 41.64 2.66
651 652 4.983671 GAAGTTCCCTTCTCTCTCTCTC 57.016 50.000 0.00 0.00 43.18 3.20
652 653 4.340617 GAAGTTCCCTTCTCTCTCTCTCA 58.659 47.826 0.00 0.00 43.18 3.27
653 654 4.396357 AGTTCCCTTCTCTCTCTCTCAA 57.604 45.455 0.00 0.00 0.00 3.02
654 655 4.746466 AGTTCCCTTCTCTCTCTCTCAAA 58.254 43.478 0.00 0.00 0.00 2.69
655 656 5.151454 AGTTCCCTTCTCTCTCTCTCAAAA 58.849 41.667 0.00 0.00 0.00 2.44
656 657 5.604650 AGTTCCCTTCTCTCTCTCTCAAAAA 59.395 40.000 0.00 0.00 0.00 1.94
689 690 6.665992 AAAAAGGAAATAGAAGTTCCCCAC 57.334 37.500 0.00 0.00 44.90 4.61
690 691 3.629142 AGGAAATAGAAGTTCCCCACG 57.371 47.619 0.00 0.00 44.90 4.94
691 692 2.014857 GGAAATAGAAGTTCCCCACGC 58.985 52.381 0.00 0.00 38.95 5.34
692 693 2.617021 GGAAATAGAAGTTCCCCACGCA 60.617 50.000 0.00 0.00 38.95 5.24
693 694 2.403252 AATAGAAGTTCCCCACGCAG 57.597 50.000 0.00 0.00 0.00 5.18
694 695 1.568504 ATAGAAGTTCCCCACGCAGA 58.431 50.000 0.00 0.00 0.00 4.26
695 696 1.568504 TAGAAGTTCCCCACGCAGAT 58.431 50.000 0.00 0.00 0.00 2.90
696 697 0.250513 AGAAGTTCCCCACGCAGATC 59.749 55.000 0.00 0.00 0.00 2.75
697 698 0.744771 GAAGTTCCCCACGCAGATCC 60.745 60.000 0.00 0.00 0.00 3.36
698 699 2.511600 GTTCCCCACGCAGATCCG 60.512 66.667 0.00 0.00 0.00 4.18
699 700 2.682136 TTCCCCACGCAGATCCGA 60.682 61.111 0.00 0.00 0.00 4.55
700 701 2.063979 TTCCCCACGCAGATCCGAT 61.064 57.895 0.00 0.00 0.00 4.18
701 702 2.028125 TTCCCCACGCAGATCCGATC 62.028 60.000 0.00 0.00 0.00 3.69
702 703 2.502492 CCCCACGCAGATCCGATCT 61.502 63.158 4.96 4.96 41.15 2.75
703 704 1.179174 CCCCACGCAGATCCGATCTA 61.179 60.000 10.65 0.00 37.58 1.98
704 705 0.039074 CCCACGCAGATCCGATCTAC 60.039 60.000 10.65 4.61 37.58 2.59
705 706 0.668535 CCACGCAGATCCGATCTACA 59.331 55.000 10.65 0.00 37.58 2.74
706 707 1.067060 CCACGCAGATCCGATCTACAA 59.933 52.381 10.65 0.00 37.58 2.41
707 708 2.481276 CCACGCAGATCCGATCTACAAA 60.481 50.000 10.65 0.00 37.58 2.83
708 709 3.384668 CACGCAGATCCGATCTACAAAT 58.615 45.455 10.65 0.00 37.58 2.32
709 710 4.546570 CACGCAGATCCGATCTACAAATA 58.453 43.478 10.65 0.00 37.58 1.40
710 711 4.383052 CACGCAGATCCGATCTACAAATAC 59.617 45.833 10.65 0.00 37.58 1.89
711 712 3.921021 CGCAGATCCGATCTACAAATACC 59.079 47.826 10.65 0.00 37.58 2.73
749 750 1.159713 ACGACGTACAGACACGACCA 61.160 55.000 0.00 0.00 44.69 4.02
1059 1065 0.748450 CGGCCCCAATCTCTACGTTA 59.252 55.000 0.00 0.00 0.00 3.18
1080 1086 1.226974 CAAGACATCGCGGACGGAT 60.227 57.895 6.13 0.00 40.63 4.18
1118 1124 4.593864 GGCGAGCCGGAGATGGAC 62.594 72.222 5.05 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.367241 CCAAAACCGATGGGAAAAACCT 59.633 45.455 0.00 0.00 38.98 3.50
1 2 2.761559 CCAAAACCGATGGGAAAAACC 58.238 47.619 0.00 0.00 36.97 3.27
9 10 1.544246 GAACCTTCCCAAAACCGATGG 59.456 52.381 0.00 0.00 37.71 3.51
10 11 1.199097 CGAACCTTCCCAAAACCGATG 59.801 52.381 0.00 0.00 0.00 3.84
11 12 1.530323 CGAACCTTCCCAAAACCGAT 58.470 50.000 0.00 0.00 0.00 4.18
12 13 0.535553 CCGAACCTTCCCAAAACCGA 60.536 55.000 0.00 0.00 0.00 4.69
13 14 1.520600 CCCGAACCTTCCCAAAACCG 61.521 60.000 0.00 0.00 0.00 4.44
14 15 0.468585 ACCCGAACCTTCCCAAAACC 60.469 55.000 0.00 0.00 0.00 3.27
15 16 1.338973 GAACCCGAACCTTCCCAAAAC 59.661 52.381 0.00 0.00 0.00 2.43
16 17 1.215924 AGAACCCGAACCTTCCCAAAA 59.784 47.619 0.00 0.00 0.00 2.44
17 18 0.848053 AGAACCCGAACCTTCCCAAA 59.152 50.000 0.00 0.00 0.00 3.28
18 19 0.109723 CAGAACCCGAACCTTCCCAA 59.890 55.000 0.00 0.00 0.00 4.12
19 20 0.765135 TCAGAACCCGAACCTTCCCA 60.765 55.000 0.00 0.00 0.00 4.37
20 21 0.036294 CTCAGAACCCGAACCTTCCC 60.036 60.000 0.00 0.00 0.00 3.97
21 22 0.974383 TCTCAGAACCCGAACCTTCC 59.026 55.000 0.00 0.00 0.00 3.46
22 23 1.669211 CGTCTCAGAACCCGAACCTTC 60.669 57.143 0.00 0.00 0.00 3.46
23 24 0.317479 CGTCTCAGAACCCGAACCTT 59.683 55.000 0.00 0.00 0.00 3.50
24 25 0.826672 ACGTCTCAGAACCCGAACCT 60.827 55.000 0.00 0.00 0.00 3.50
25 26 0.033090 AACGTCTCAGAACCCGAACC 59.967 55.000 0.00 0.00 0.00 3.62
26 27 1.861971 AAACGTCTCAGAACCCGAAC 58.138 50.000 0.00 0.00 0.00 3.95
27 28 2.607631 AAAACGTCTCAGAACCCGAA 57.392 45.000 0.00 0.00 0.00 4.30
28 29 2.607631 AAAAACGTCTCAGAACCCGA 57.392 45.000 0.00 0.00 0.00 5.14
125 126 9.956720 ACAAATTTCAAAACAATGTTCACAAAA 57.043 22.222 0.00 0.00 0.00 2.44
126 127 9.390795 CACAAATTTCAAAACAATGTTCACAAA 57.609 25.926 0.00 0.00 0.00 2.83
127 128 8.019669 CCACAAATTTCAAAACAATGTTCACAA 58.980 29.630 0.00 0.00 0.00 3.33
128 129 7.388776 TCCACAAATTTCAAAACAATGTTCACA 59.611 29.630 0.00 0.00 0.00 3.58
129 130 7.691877 GTCCACAAATTTCAAAACAATGTTCAC 59.308 33.333 0.00 0.00 0.00 3.18
130 131 7.388776 TGTCCACAAATTTCAAAACAATGTTCA 59.611 29.630 0.00 0.00 0.00 3.18
131 132 7.746929 TGTCCACAAATTTCAAAACAATGTTC 58.253 30.769 0.00 0.00 0.00 3.18
132 133 7.678947 TGTCCACAAATTTCAAAACAATGTT 57.321 28.000 0.00 0.00 0.00 2.71
133 134 7.678947 TTGTCCACAAATTTCAAAACAATGT 57.321 28.000 0.00 0.00 32.11 2.71
134 135 9.570488 AAATTGTCCACAAATTTCAAAACAATG 57.430 25.926 14.44 0.00 39.55 2.82
136 137 9.971922 AAAAATTGTCCACAAATTTCAAAACAA 57.028 22.222 6.05 7.69 37.81 2.83
137 138 9.403110 CAAAAATTGTCCACAAATTTCAAAACA 57.597 25.926 6.05 0.00 37.81 2.83
138 139 9.617975 TCAAAAATTGTCCACAAATTTCAAAAC 57.382 25.926 6.05 0.00 37.81 2.43
142 143 9.784680 CAATTCAAAAATTGTCCACAAATTTCA 57.215 25.926 6.05 0.00 44.43 2.69
157 158 9.150348 GGAAAATATGTCCGTCAATTCAAAAAT 57.850 29.630 0.00 0.00 0.00 1.82
158 159 8.144478 TGGAAAATATGTCCGTCAATTCAAAAA 58.856 29.630 2.15 0.00 38.06 1.94
159 160 7.596995 GTGGAAAATATGTCCGTCAATTCAAAA 59.403 33.333 2.15 0.00 38.06 2.44
160 161 7.087639 GTGGAAAATATGTCCGTCAATTCAAA 58.912 34.615 2.15 0.00 38.06 2.69
161 162 6.207614 TGTGGAAAATATGTCCGTCAATTCAA 59.792 34.615 2.15 0.00 38.06 2.69
162 163 5.707764 TGTGGAAAATATGTCCGTCAATTCA 59.292 36.000 2.15 0.00 38.06 2.57
163 164 6.189677 TGTGGAAAATATGTCCGTCAATTC 57.810 37.500 2.15 0.00 38.06 2.17
164 165 6.773976 ATGTGGAAAATATGTCCGTCAATT 57.226 33.333 2.15 0.00 38.06 2.32
165 166 7.874940 CATATGTGGAAAATATGTCCGTCAAT 58.125 34.615 0.00 0.00 39.26 2.57
166 167 7.258022 CATATGTGGAAAATATGTCCGTCAA 57.742 36.000 0.00 0.00 39.26 3.18
167 168 6.859420 CATATGTGGAAAATATGTCCGTCA 57.141 37.500 0.00 4.39 39.26 4.35
184 185 9.352784 CGGATTTTAAAACACATTCACATATGT 57.647 29.630 1.41 1.41 39.27 2.29
185 186 9.352784 ACGGATTTTAAAACACATTCACATATG 57.647 29.630 1.97 0.00 0.00 1.78
188 189 9.751542 TTTACGGATTTTAAAACACATTCACAT 57.248 25.926 1.97 0.00 0.00 3.21
189 190 9.751542 ATTTACGGATTTTAAAACACATTCACA 57.248 25.926 1.97 0.00 0.00 3.58
204 205 9.429359 TGCACATTCAAAAATATTTACGGATTT 57.571 25.926 0.01 0.00 0.00 2.17
205 206 8.994429 TGCACATTCAAAAATATTTACGGATT 57.006 26.923 0.01 0.00 0.00 3.01
206 207 8.994429 TTGCACATTCAAAAATATTTACGGAT 57.006 26.923 0.01 0.00 0.00 4.18
207 208 8.704234 GTTTGCACATTCAAAAATATTTACGGA 58.296 29.630 0.01 0.00 37.65 4.69
208 209 7.682055 CGTTTGCACATTCAAAAATATTTACGG 59.318 33.333 0.01 0.00 37.65 4.02
209 210 8.211181 ACGTTTGCACATTCAAAAATATTTACG 58.789 29.630 0.01 5.57 37.65 3.18
210 211 9.856803 AACGTTTGCACATTCAAAAATATTTAC 57.143 25.926 0.01 0.00 37.65 2.01
212 213 9.780413 AAAACGTTTGCACATTCAAAAATATTT 57.220 22.222 15.46 0.00 37.65 1.40
213 214 9.780413 AAAAACGTTTGCACATTCAAAAATATT 57.220 22.222 15.46 0.00 37.65 1.28
225 226 9.692749 TCCATAAATTATAAAAACGTTTGCACA 57.307 25.926 15.46 0.42 0.00 4.57
247 248 9.981114 ATGTTCTCGAGTTTTTAAAATTTCCAT 57.019 25.926 13.13 0.00 0.00 3.41
248 249 9.810545 AATGTTCTCGAGTTTTTAAAATTTCCA 57.189 25.926 13.13 0.00 0.00 3.53
258 259 9.586435 AATTTCAAGAAATGTTCTCGAGTTTTT 57.414 25.926 13.13 8.13 40.57 1.94
259 260 9.237846 GAATTTCAAGAAATGTTCTCGAGTTTT 57.762 29.630 13.13 8.47 40.57 2.43
260 261 8.405531 TGAATTTCAAGAAATGTTCTCGAGTTT 58.594 29.630 13.13 5.34 40.57 2.66
261 262 7.930217 TGAATTTCAAGAAATGTTCTCGAGTT 58.070 30.769 13.13 0.00 40.57 3.01
262 263 7.496529 TGAATTTCAAGAAATGTTCTCGAGT 57.503 32.000 13.13 0.00 40.57 4.18
263 264 8.232513 TCATGAATTTCAAGAAATGTTCTCGAG 58.767 33.333 5.93 5.93 40.57 4.04
264 265 8.098220 TCATGAATTTCAAGAAATGTTCTCGA 57.902 30.769 8.66 3.82 40.57 4.04
265 266 8.732413 TTCATGAATTTCAAGAAATGTTCTCG 57.268 30.769 13.14 1.96 40.57 4.04
295 296 9.000018 GCATTACAAAACGTTTGCAAATTAAAA 58.000 25.926 16.21 3.97 36.22 1.52
296 297 8.175069 TGCATTACAAAACGTTTGCAAATTAAA 58.825 25.926 18.01 4.29 40.51 1.52
297 298 7.636359 GTGCATTACAAAACGTTTGCAAATTAA 59.364 29.630 20.97 10.29 43.19 1.40
298 299 7.119997 GTGCATTACAAAACGTTTGCAAATTA 58.880 30.769 20.97 7.84 43.19 1.40
299 300 5.962423 GTGCATTACAAAACGTTTGCAAATT 59.038 32.000 20.97 3.46 43.19 1.82
300 301 5.497273 GTGCATTACAAAACGTTTGCAAAT 58.503 33.333 20.97 14.30 43.19 2.32
301 302 4.490959 CGTGCATTACAAAACGTTTGCAAA 60.491 37.500 20.97 8.05 43.19 3.68
302 303 3.000674 CGTGCATTACAAAACGTTTGCAA 60.001 39.130 20.97 12.91 43.19 4.08
303 304 2.531912 CGTGCATTACAAAACGTTTGCA 59.468 40.909 15.46 16.22 40.92 4.08
304 305 2.097637 CCGTGCATTACAAAACGTTTGC 60.098 45.455 15.46 13.64 36.54 3.68
305 306 3.178814 GTCCGTGCATTACAAAACGTTTG 59.821 43.478 15.46 11.16 34.30 2.93
306 307 3.181499 TGTCCGTGCATTACAAAACGTTT 60.181 39.130 7.96 7.96 34.30 3.60
307 308 2.355132 TGTCCGTGCATTACAAAACGTT 59.645 40.909 0.00 0.00 34.30 3.99
308 309 1.941294 TGTCCGTGCATTACAAAACGT 59.059 42.857 0.00 0.00 34.30 3.99
309 310 2.672188 TGTCCGTGCATTACAAAACG 57.328 45.000 0.00 0.00 35.85 3.60
310 311 5.898630 AAAATGTCCGTGCATTACAAAAC 57.101 34.783 0.00 0.00 38.03 2.43
359 360 9.833894 CGTTCTTAAATTGAAAACATGTTCTTG 57.166 29.630 12.39 0.00 0.00 3.02
360 361 9.796120 TCGTTCTTAAATTGAAAACATGTTCTT 57.204 25.926 12.39 8.48 0.00 2.52
361 362 9.796120 TTCGTTCTTAAATTGAAAACATGTTCT 57.204 25.926 12.39 0.00 0.00 3.01
371 372 9.528018 AGCTTGAAAATTCGTTCTTAAATTGAA 57.472 25.926 0.00 0.00 0.00 2.69
372 373 9.180678 GAGCTTGAAAATTCGTTCTTAAATTGA 57.819 29.630 0.00 0.00 0.00 2.57
373 374 8.967218 TGAGCTTGAAAATTCGTTCTTAAATTG 58.033 29.630 0.00 0.00 0.00 2.32
374 375 9.185192 CTGAGCTTGAAAATTCGTTCTTAAATT 57.815 29.630 0.00 0.00 0.00 1.82
375 376 7.327032 GCTGAGCTTGAAAATTCGTTCTTAAAT 59.673 33.333 0.00 0.00 0.00 1.40
376 377 6.636850 GCTGAGCTTGAAAATTCGTTCTTAAA 59.363 34.615 0.00 0.00 0.00 1.52
377 378 6.017109 AGCTGAGCTTGAAAATTCGTTCTTAA 60.017 34.615 0.00 0.00 33.89 1.85
378 379 5.470098 AGCTGAGCTTGAAAATTCGTTCTTA 59.530 36.000 0.00 0.00 33.89 2.10
379 380 4.276926 AGCTGAGCTTGAAAATTCGTTCTT 59.723 37.500 0.00 0.00 33.89 2.52
380 381 3.817647 AGCTGAGCTTGAAAATTCGTTCT 59.182 39.130 0.00 0.00 33.89 3.01
381 382 4.152607 AGCTGAGCTTGAAAATTCGTTC 57.847 40.909 0.00 0.00 33.89 3.95
382 383 5.239525 ACTTAGCTGAGCTTGAAAATTCGTT 59.760 36.000 14.14 0.00 40.44 3.85
383 384 4.757149 ACTTAGCTGAGCTTGAAAATTCGT 59.243 37.500 14.14 0.00 40.44 3.85
384 385 5.288543 ACTTAGCTGAGCTTGAAAATTCG 57.711 39.130 14.14 0.00 40.44 3.34
385 386 7.936950 AAAACTTAGCTGAGCTTGAAAATTC 57.063 32.000 14.14 0.00 40.44 2.17
440 441 9.947669 CTGCATTTGAAAAATTTCCACAATTTA 57.052 25.926 3.60 0.00 36.36 1.40
441 442 8.468399 ACTGCATTTGAAAAATTTCCACAATTT 58.532 25.926 3.60 0.00 36.36 1.82
442 443 7.998580 ACTGCATTTGAAAAATTTCCACAATT 58.001 26.923 3.60 0.00 36.36 2.32
443 444 7.571080 ACTGCATTTGAAAAATTTCCACAAT 57.429 28.000 3.60 0.00 36.36 2.71
444 445 6.998968 ACTGCATTTGAAAAATTTCCACAA 57.001 29.167 3.60 0.00 36.36 3.33
445 446 7.271511 AGTACTGCATTTGAAAAATTTCCACA 58.728 30.769 0.00 0.00 36.36 4.17
446 447 7.713764 AGTACTGCATTTGAAAAATTTCCAC 57.286 32.000 0.00 0.00 36.36 4.02
447 448 8.729805 AAAGTACTGCATTTGAAAAATTTCCA 57.270 26.923 0.00 0.00 36.36 3.53
448 449 9.437045 CAAAAGTACTGCATTTGAAAAATTTCC 57.563 29.630 11.50 0.00 37.82 3.13
456 457 7.591057 CGAGATTTCAAAAGTACTGCATTTGAA 59.409 33.333 21.73 21.73 46.46 2.69
457 458 7.041440 TCGAGATTTCAAAAGTACTGCATTTGA 60.041 33.333 14.43 14.43 41.30 2.69
458 459 7.077605 TCGAGATTTCAAAAGTACTGCATTTG 58.922 34.615 10.89 10.89 37.18 2.32
459 460 7.202016 TCGAGATTTCAAAAGTACTGCATTT 57.798 32.000 0.00 0.00 0.00 2.32
460 461 6.801539 TCGAGATTTCAAAAGTACTGCATT 57.198 33.333 0.00 0.00 0.00 3.56
461 462 6.801539 TTCGAGATTTCAAAAGTACTGCAT 57.198 33.333 0.00 0.00 0.00 3.96
462 463 6.801539 ATTCGAGATTTCAAAAGTACTGCA 57.198 33.333 0.00 0.00 0.00 4.41
463 464 8.821894 AGATATTCGAGATTTCAAAAGTACTGC 58.178 33.333 0.00 0.00 0.00 4.40
519 520 6.562518 TCCTAATGTTTTTCGTTCCGTTTTT 58.437 32.000 0.00 0.00 0.00 1.94
520 521 6.038492 TCTCCTAATGTTTTTCGTTCCGTTTT 59.962 34.615 0.00 0.00 0.00 2.43
521 522 5.528320 TCTCCTAATGTTTTTCGTTCCGTTT 59.472 36.000 0.00 0.00 0.00 3.60
522 523 5.058490 TCTCCTAATGTTTTTCGTTCCGTT 58.942 37.500 0.00 0.00 0.00 4.44
523 524 4.634199 TCTCCTAATGTTTTTCGTTCCGT 58.366 39.130 0.00 0.00 0.00 4.69
524 525 4.092968 CCTCTCCTAATGTTTTTCGTTCCG 59.907 45.833 0.00 0.00 0.00 4.30
525 526 4.142665 GCCTCTCCTAATGTTTTTCGTTCC 60.143 45.833 0.00 0.00 0.00 3.62
526 527 4.142665 GGCCTCTCCTAATGTTTTTCGTTC 60.143 45.833 0.00 0.00 0.00 3.95
527 528 3.756963 GGCCTCTCCTAATGTTTTTCGTT 59.243 43.478 0.00 0.00 0.00 3.85
528 529 3.344515 GGCCTCTCCTAATGTTTTTCGT 58.655 45.455 0.00 0.00 0.00 3.85
529 530 2.683362 GGGCCTCTCCTAATGTTTTTCG 59.317 50.000 0.84 0.00 34.39 3.46
530 531 2.683362 CGGGCCTCTCCTAATGTTTTTC 59.317 50.000 0.84 0.00 34.39 2.29
531 532 2.307686 TCGGGCCTCTCCTAATGTTTTT 59.692 45.455 0.84 0.00 34.39 1.94
532 533 1.913419 TCGGGCCTCTCCTAATGTTTT 59.087 47.619 0.84 0.00 34.39 2.43
533 534 1.209747 GTCGGGCCTCTCCTAATGTTT 59.790 52.381 0.84 0.00 34.39 2.83
534 535 0.831307 GTCGGGCCTCTCCTAATGTT 59.169 55.000 0.84 0.00 34.39 2.71
535 536 1.049289 GGTCGGGCCTCTCCTAATGT 61.049 60.000 0.84 0.00 34.39 2.71
536 537 1.749033 GGTCGGGCCTCTCCTAATG 59.251 63.158 0.84 0.00 34.39 1.90
537 538 1.459730 GGGTCGGGCCTCTCCTAAT 60.460 63.158 0.84 0.00 37.43 1.73
538 539 2.042230 GGGTCGGGCCTCTCCTAA 60.042 66.667 0.84 0.00 37.43 2.69
539 540 4.517934 CGGGTCGGGCCTCTCCTA 62.518 72.222 0.84 0.00 37.43 2.94
541 542 4.828296 TACGGGTCGGGCCTCTCC 62.828 72.222 0.84 2.09 37.43 3.71
542 543 3.525545 GTACGGGTCGGGCCTCTC 61.526 72.222 0.84 0.00 37.43 3.20
556 557 3.682292 CTTCGGCCAGCCCAGGTAC 62.682 68.421 2.24 0.00 0.00 3.34
557 558 3.399181 CTTCGGCCAGCCCAGGTA 61.399 66.667 2.24 0.00 0.00 3.08
559 560 3.868200 AAACTTCGGCCAGCCCAGG 62.868 63.158 2.24 0.00 0.00 4.45
560 561 2.282462 AAACTTCGGCCAGCCCAG 60.282 61.111 2.24 1.99 0.00 4.45
561 562 2.597217 CAAACTTCGGCCAGCCCA 60.597 61.111 2.24 0.00 0.00 5.36
562 563 4.056125 GCAAACTTCGGCCAGCCC 62.056 66.667 2.24 0.00 0.00 5.19
563 564 4.404654 CGCAAACTTCGGCCAGCC 62.405 66.667 2.24 0.00 0.00 4.85
565 566 4.741781 CGCGCAAACTTCGGCCAG 62.742 66.667 8.75 0.00 0.00 4.85
569 570 4.383602 CCCACGCGCAAACTTCGG 62.384 66.667 5.73 0.00 0.00 4.30
570 571 4.383602 CCCCACGCGCAAACTTCG 62.384 66.667 5.73 0.00 0.00 3.79
571 572 4.038080 CCCCCACGCGCAAACTTC 62.038 66.667 5.73 0.00 0.00 3.01
572 573 4.572571 TCCCCCACGCGCAAACTT 62.573 61.111 5.73 0.00 0.00 2.66
586 587 3.393149 GAAAGGAGGCCTCGCTCCC 62.393 68.421 26.36 13.15 40.49 4.30
587 588 2.188207 GAAAGGAGGCCTCGCTCC 59.812 66.667 26.36 13.80 39.93 4.70
588 589 2.188207 GGAAAGGAGGCCTCGCTC 59.812 66.667 26.36 20.20 30.89 5.03
589 590 2.607750 TGGAAAGGAGGCCTCGCT 60.608 61.111 26.36 20.50 30.89 4.93
590 591 2.436824 GTGGAAAGGAGGCCTCGC 60.437 66.667 26.36 18.59 30.89 5.03
591 592 2.269241 GGTGGAAAGGAGGCCTCG 59.731 66.667 26.36 0.00 30.89 4.63
592 593 1.002011 GTGGTGGAAAGGAGGCCTC 60.002 63.158 25.59 25.59 30.89 4.70
593 594 1.774217 TGTGGTGGAAAGGAGGCCT 60.774 57.895 3.86 3.86 33.87 5.19
594 595 1.603739 GTGTGGTGGAAAGGAGGCC 60.604 63.158 0.00 0.00 0.00 5.19
595 596 1.966451 CGTGTGGTGGAAAGGAGGC 60.966 63.158 0.00 0.00 0.00 4.70
596 597 1.302511 CCGTGTGGTGGAAAGGAGG 60.303 63.158 0.00 0.00 0.00 4.30
597 598 1.302511 CCCGTGTGGTGGAAAGGAG 60.303 63.158 0.00 0.00 0.00 3.69
598 599 2.833227 CCCGTGTGGTGGAAAGGA 59.167 61.111 0.00 0.00 0.00 3.36
599 600 2.983592 GCCCGTGTGGTGGAAAGG 60.984 66.667 0.00 0.00 36.04 3.11
600 601 2.203280 TGCCCGTGTGGTGGAAAG 60.203 61.111 0.00 0.00 36.04 2.62
601 602 2.203280 CTGCCCGTGTGGTGGAAA 60.203 61.111 0.00 0.00 36.04 3.13
602 603 4.263572 CCTGCCCGTGTGGTGGAA 62.264 66.667 0.00 0.00 36.04 3.53
604 605 3.783362 TTTCCTGCCCGTGTGGTGG 62.783 63.158 0.00 0.00 36.04 4.61
605 606 2.203280 TTTCCTGCCCGTGTGGTG 60.203 61.111 0.00 0.00 36.04 4.17
606 607 2.203294 GTTTCCTGCCCGTGTGGT 60.203 61.111 0.00 0.00 36.04 4.16
607 608 2.203280 TGTTTCCTGCCCGTGTGG 60.203 61.111 0.00 0.00 37.09 4.17
608 609 0.817634 TTCTGTTTCCTGCCCGTGTG 60.818 55.000 0.00 0.00 0.00 3.82
609 610 0.818040 GTTCTGTTTCCTGCCCGTGT 60.818 55.000 0.00 0.00 0.00 4.49
610 611 0.817634 TGTTCTGTTTCCTGCCCGTG 60.818 55.000 0.00 0.00 0.00 4.94
611 612 0.535102 CTGTTCTGTTTCCTGCCCGT 60.535 55.000 0.00 0.00 0.00 5.28
612 613 0.250295 TCTGTTCTGTTTCCTGCCCG 60.250 55.000 0.00 0.00 0.00 6.13
613 614 1.882623 CTTCTGTTCTGTTTCCTGCCC 59.117 52.381 0.00 0.00 0.00 5.36
614 615 2.576615 ACTTCTGTTCTGTTTCCTGCC 58.423 47.619 0.00 0.00 0.00 4.85
615 616 4.216366 GAACTTCTGTTCTGTTTCCTGC 57.784 45.455 2.11 0.00 46.56 4.85
633 634 5.476091 TTTTGAGAGAGAGAGAAGGGAAC 57.524 43.478 0.00 0.00 0.00 3.62
666 667 5.243060 CGTGGGGAACTTCTATTTCCTTTTT 59.757 40.000 1.34 0.00 42.10 1.94
667 668 4.765339 CGTGGGGAACTTCTATTTCCTTTT 59.235 41.667 1.34 0.00 42.10 2.27
668 669 4.332828 CGTGGGGAACTTCTATTTCCTTT 58.667 43.478 1.34 0.00 42.10 3.11
669 670 3.872630 GCGTGGGGAACTTCTATTTCCTT 60.873 47.826 1.34 0.00 42.10 3.36
670 671 2.355818 GCGTGGGGAACTTCTATTTCCT 60.356 50.000 1.34 0.00 42.10 3.36
671 672 2.014857 GCGTGGGGAACTTCTATTTCC 58.985 52.381 0.00 0.00 41.76 3.13
672 673 2.678336 CTGCGTGGGGAACTTCTATTTC 59.322 50.000 0.00 0.00 0.00 2.17
673 674 2.304761 TCTGCGTGGGGAACTTCTATTT 59.695 45.455 0.00 0.00 0.00 1.40
674 675 1.906574 TCTGCGTGGGGAACTTCTATT 59.093 47.619 0.00 0.00 0.00 1.73
675 676 1.568504 TCTGCGTGGGGAACTTCTAT 58.431 50.000 0.00 0.00 0.00 1.98
676 677 1.480954 GATCTGCGTGGGGAACTTCTA 59.519 52.381 0.00 0.00 0.00 2.10
677 678 0.250513 GATCTGCGTGGGGAACTTCT 59.749 55.000 0.00 0.00 0.00 2.85
678 679 0.744771 GGATCTGCGTGGGGAACTTC 60.745 60.000 0.00 0.00 0.00 3.01
679 680 1.299976 GGATCTGCGTGGGGAACTT 59.700 57.895 0.00 0.00 0.00 2.66
680 681 2.990479 GGATCTGCGTGGGGAACT 59.010 61.111 0.00 0.00 0.00 3.01
681 682 2.311688 ATCGGATCTGCGTGGGGAAC 62.312 60.000 0.00 0.00 0.00 3.62
682 683 2.028125 GATCGGATCTGCGTGGGGAA 62.028 60.000 10.73 0.00 0.00 3.97
683 684 2.443952 ATCGGATCTGCGTGGGGA 60.444 61.111 0.00 0.00 0.00 4.81
684 685 1.179174 TAGATCGGATCTGCGTGGGG 61.179 60.000 26.72 0.00 40.51 4.96
685 686 0.039074 GTAGATCGGATCTGCGTGGG 60.039 60.000 26.72 0.00 40.51 4.61
686 687 0.668535 TGTAGATCGGATCTGCGTGG 59.331 55.000 26.72 0.00 43.82 4.94
687 688 2.492019 TTGTAGATCGGATCTGCGTG 57.508 50.000 26.72 0.00 43.82 5.34
688 689 3.735237 ATTTGTAGATCGGATCTGCGT 57.265 42.857 26.72 14.36 43.82 5.24
689 690 3.921021 GGTATTTGTAGATCGGATCTGCG 59.079 47.826 26.72 0.00 43.82 5.18
690 691 5.140747 AGGTATTTGTAGATCGGATCTGC 57.859 43.478 26.72 25.27 40.51 4.26
691 692 6.434652 ACCTAGGTATTTGTAGATCGGATCTG 59.565 42.308 26.72 10.30 40.51 2.90
692 693 6.553857 ACCTAGGTATTTGTAGATCGGATCT 58.446 40.000 22.96 22.96 43.33 2.75
693 694 6.127675 GGACCTAGGTATTTGTAGATCGGATC 60.128 46.154 16.29 10.02 0.00 3.36
694 695 5.715753 GGACCTAGGTATTTGTAGATCGGAT 59.284 44.000 16.29 0.00 0.00 4.18
695 696 5.075493 GGACCTAGGTATTTGTAGATCGGA 58.925 45.833 16.29 0.00 0.00 4.55
696 697 4.082895 CGGACCTAGGTATTTGTAGATCGG 60.083 50.000 16.29 0.00 0.00 4.18
697 698 4.758674 TCGGACCTAGGTATTTGTAGATCG 59.241 45.833 16.29 6.41 0.00 3.69
698 699 6.660094 AGATCGGACCTAGGTATTTGTAGATC 59.340 42.308 16.29 18.31 0.00 2.75
699 700 6.553857 AGATCGGACCTAGGTATTTGTAGAT 58.446 40.000 16.29 11.42 0.00 1.98
700 701 5.950023 AGATCGGACCTAGGTATTTGTAGA 58.050 41.667 16.29 7.09 0.00 2.59
701 702 7.166851 TCTAGATCGGACCTAGGTATTTGTAG 58.833 42.308 16.29 11.92 35.50 2.74
702 703 7.083062 TCTAGATCGGACCTAGGTATTTGTA 57.917 40.000 16.29 2.67 35.50 2.41
703 704 5.950023 TCTAGATCGGACCTAGGTATTTGT 58.050 41.667 16.29 0.00 35.50 2.83
704 705 6.896021 TTCTAGATCGGACCTAGGTATTTG 57.104 41.667 16.29 5.10 35.50 2.32
705 706 9.022884 GTATTTCTAGATCGGACCTAGGTATTT 57.977 37.037 16.29 2.79 35.50 1.40
706 707 7.336427 CGTATTTCTAGATCGGACCTAGGTATT 59.664 40.741 16.29 0.00 35.50 1.89
707 708 6.822676 CGTATTTCTAGATCGGACCTAGGTAT 59.177 42.308 16.29 4.62 35.50 2.73
708 709 6.014242 TCGTATTTCTAGATCGGACCTAGGTA 60.014 42.308 16.29 0.00 35.50 3.08
709 710 5.002516 CGTATTTCTAGATCGGACCTAGGT 58.997 45.833 16.26 16.26 35.50 3.08
710 711 5.122082 GTCGTATTTCTAGATCGGACCTAGG 59.878 48.000 7.41 7.41 35.50 3.02
711 712 5.163972 CGTCGTATTTCTAGATCGGACCTAG 60.164 48.000 0.00 0.00 35.97 3.02
1059 1065 1.154016 CGTCCGCGATGTCTTGAGT 60.154 57.895 8.23 0.00 41.33 3.41
1118 1124 7.446319 TGGCCAGAATCATAAATCTGTTATCTG 59.554 37.037 0.00 0.00 41.16 2.90
1456 1501 1.166531 GGACCAGCGAACAGTTGCTT 61.167 55.000 7.31 0.00 40.03 3.91
1706 2157 6.372659 GGCGTACATGATAATCAATGAGGAAT 59.627 38.462 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.