Multiple sequence alignment - TraesCS5D01G209000

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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 TraesCS5D01G209000 chr5D 100.000 2781 0 0 1 2781 315690445 315687665 0.000000e+00 5136.0
1 TraesCS5D01G209000 chr5D 89.049 347 23 11 186 520 465679630 465679973 1.540000e-112 416.0
2 TraesCS5D01G209000 chr5D 88.921 343 26 9 187 520 347478052 347477713 1.990000e-111 412.0
3 TraesCS5D01G209000 chr1D 85.532 1963 197 44 563 2468 135664172 135666104 0.000000e+00 1971.0
4 TraesCS5D01G209000 chr1D 88.655 238 14 5 2495 2720 135666958 135667194 7.590000e-71 278.0
5 TraesCS5D01G209000 chr6D 87.543 1734 167 25 767 2468 156810483 156812199 0.000000e+00 1960.0
6 TraesCS5D01G209000 chr6D 96.089 179 7 0 1 179 58444039 58443861 2.710000e-75 292.0
7 TraesCS5D01G209000 chr6D 90.698 43 1 2 501 541 472451954 472451913 1.000000e-03 54.7
8 TraesCS5D01G209000 chr2D 87.428 1734 169 26 767 2468 37860652 37862368 0.000000e+00 1949.0
9 TraesCS5D01G209000 chr2D 96.648 179 6 0 1 179 494064156 494063978 5.820000e-77 298.0
10 TraesCS5D01G209000 chr3B 87.370 1734 166 27 767 2468 819905200 819906912 0.000000e+00 1940.0
11 TraesCS5D01G209000 chr3B 87.117 1731 169 28 770 2468 728862519 728860811 0.000000e+00 1912.0
12 TraesCS5D01G209000 chr3B 81.174 494 78 13 1300 1788 174987290 174986807 1.560000e-102 383.0
13 TraesCS5D01G209000 chr1A 87.233 1731 169 26 770 2468 287582578 287580868 0.000000e+00 1925.0
14 TraesCS5D01G209000 chr1A 87.140 1734 165 27 767 2468 551173644 551175351 0.000000e+00 1914.0
15 TraesCS5D01G209000 chr1A 88.201 339 27 10 189 520 558093082 558092750 2.600000e-105 392.0
16 TraesCS5D01G209000 chr1A 86.008 243 21 5 2490 2720 382730852 382731093 5.950000e-62 248.0
17 TraesCS5D01G209000 chr6B 87.340 1643 155 27 858 2468 381180430 381182051 0.000000e+00 1832.0
18 TraesCS5D01G209000 chr6B 88.916 1218 111 16 1289 2497 705423930 705425132 0.000000e+00 1480.0
19 TraesCS5D01G209000 chr6B 85.316 790 78 19 563 1323 673074516 673075296 0.000000e+00 782.0
20 TraesCS5D01G209000 chr6B 89.076 238 13 5 2495 2720 52454498 52454262 1.630000e-72 283.0
21 TraesCS5D01G209000 chr3D 88.160 1250 122 19 1232 2468 583611499 583612735 0.000000e+00 1465.0
22 TraesCS5D01G209000 chr3D 86.940 536 53 8 684 1216 583610806 583611327 1.110000e-163 586.0
23 TraesCS5D01G209000 chr3D 87.603 242 13 6 2495 2720 583613456 583613696 5.910000e-67 265.0
24 TraesCS5D01G209000 chr2A 95.294 765 22 4 1968 2720 47676218 47675456 0.000000e+00 1201.0
25 TraesCS5D01G209000 chr2A 89.579 499 36 10 280 773 47677166 47676679 1.090000e-173 619.0
26 TraesCS5D01G209000 chr2A 87.316 339 32 8 189 520 76500138 76500472 7.270000e-101 377.0
27 TraesCS5D01G209000 chr2A 95.722 187 8 0 1 187 47677101 47676915 4.500000e-78 302.0
28 TraesCS5D01G209000 chr2A 86.307 241 17 7 2495 2720 16579485 16579724 5.950000e-62 248.0
29 TraesCS5D01G209000 chr2A 96.429 56 2 0 823 878 47676267 47676212 2.950000e-15 93.5
30 TraesCS5D01G209000 chr4D 88.270 341 28 8 190 520 442394110 442393772 5.580000e-107 398.0
31 TraesCS5D01G209000 chr4D 87.189 281 25 8 1 275 306378070 306378345 2.690000e-80 309.0
32 TraesCS5D01G209000 chr4D 97.207 179 5 0 1 179 374626127 374625949 1.250000e-78 303.0
33 TraesCS5D01G209000 chr4D 96.648 179 6 0 1 179 342884862 342884684 5.820000e-77 298.0
34 TraesCS5D01G209000 chr7A 87.390 341 31 9 189 520 694642668 694643005 5.620000e-102 381.0
35 TraesCS5D01G209000 chr4A 87.316 339 32 8 189 520 66585903 66586237 7.270000e-101 377.0
36 TraesCS5D01G209000 chr4A 89.381 226 12 4 2495 2708 658148785 658148560 9.810000e-70 274.0
37 TraesCS5D01G209000 chr3A 86.610 351 32 12 180 520 723470010 723470355 9.410000e-100 374.0
38 TraesCS5D01G209000 chr7D 96.648 179 6 0 1 179 536431794 536431972 5.820000e-77 298.0
39 TraesCS5D01G209000 chr7D 96.648 179 6 0 1 179 597064890 597065068 5.820000e-77 298.0
40 TraesCS5D01G209000 chr7B 96.111 180 6 1 1 179 703986937 703987116 2.710000e-75 292.0
41 TraesCS5D01G209000 chr7B 82.008 239 26 7 2495 2720 725757834 725757600 1.320000e-43 187.0
42 TraesCS5D01G209000 chr4B 83.043 230 23 6 2495 2711 408998379 408998153 7.860000e-46 195.0
43 TraesCS5D01G209000 chr5B 95.122 41 1 1 501 541 322562878 322562917 2.310000e-06 63.9
44 TraesCS5D01G209000 chrUn 97.143 35 1 0 501 535 83972127 83972161 2.990000e-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 TraesCS5D01G209000 chr5D 315687665 315690445 2780 True 5136.000 5136 100.000000 1 2781 1 chr5D.!!$R1 2780
1 TraesCS5D01G209000 chr1D 135664172 135667194 3022 False 1124.500 1971 87.093500 563 2720 2 chr1D.!!$F1 2157
2 TraesCS5D01G209000 chr6D 156810483 156812199 1716 False 1960.000 1960 87.543000 767 2468 1 chr6D.!!$F1 1701
3 TraesCS5D01G209000 chr2D 37860652 37862368 1716 False 1949.000 1949 87.428000 767 2468 1 chr2D.!!$F1 1701
4 TraesCS5D01G209000 chr3B 819905200 819906912 1712 False 1940.000 1940 87.370000 767 2468 1 chr3B.!!$F1 1701
5 TraesCS5D01G209000 chr3B 728860811 728862519 1708 True 1912.000 1912 87.117000 770 2468 1 chr3B.!!$R2 1698
6 TraesCS5D01G209000 chr1A 287580868 287582578 1710 True 1925.000 1925 87.233000 770 2468 1 chr1A.!!$R1 1698
7 TraesCS5D01G209000 chr1A 551173644 551175351 1707 False 1914.000 1914 87.140000 767 2468 1 chr1A.!!$F2 1701
8 TraesCS5D01G209000 chr6B 381180430 381182051 1621 False 1832.000 1832 87.340000 858 2468 1 chr6B.!!$F1 1610
9 TraesCS5D01G209000 chr6B 705423930 705425132 1202 False 1480.000 1480 88.916000 1289 2497 1 chr6B.!!$F3 1208
10 TraesCS5D01G209000 chr6B 673074516 673075296 780 False 782.000 782 85.316000 563 1323 1 chr6B.!!$F2 760
11 TraesCS5D01G209000 chr3D 583610806 583613696 2890 False 772.000 1465 87.567667 684 2720 3 chr3D.!!$F1 2036
12 TraesCS5D01G209000 chr2A 47675456 47677166 1710 True 553.875 1201 94.256000 1 2720 4 chr2A.!!$R1 2719

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
894 1263 0.179 GATCCAGCCATCGTTGACCT 59.821 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2721 4162 0.039978 ATGATCGACTAAGCGCCTCG 60.04 55.0 2.29 5.87 0.0 4.63 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
34 35 8.253810 TGAACAGATCAGAACTTTCTATACTGG 58.746 37.037 15.94 0.00 35.34 4.00
35 36 6.578023 ACAGATCAGAACTTTCTATACTGGC 58.422 40.000 15.94 0.00 35.34 4.85
36 37 5.689514 CAGATCAGAACTTTCTATACTGGCG 59.310 44.000 0.00 0.00 35.34 5.69
37 38 3.782046 TCAGAACTTTCTATACTGGCGC 58.218 45.455 0.00 0.00 35.34 6.53
38 39 3.194755 TCAGAACTTTCTATACTGGCGCA 59.805 43.478 10.83 0.00 35.34 6.09
39 40 3.932710 CAGAACTTTCTATACTGGCGCAA 59.067 43.478 10.83 0.00 35.34 4.85
40 41 4.391830 CAGAACTTTCTATACTGGCGCAAA 59.608 41.667 10.83 0.00 35.34 3.68
41 42 5.065218 CAGAACTTTCTATACTGGCGCAAAT 59.935 40.000 10.83 0.00 35.34 2.32
42 43 5.648092 AGAACTTTCTATACTGGCGCAAATT 59.352 36.000 10.83 0.00 35.34 1.82
43 44 6.821665 AGAACTTTCTATACTGGCGCAAATTA 59.178 34.615 10.83 0.00 35.34 1.40
44 45 7.499232 AGAACTTTCTATACTGGCGCAAATTAT 59.501 33.333 10.83 3.60 35.34 1.28
45 46 7.568199 ACTTTCTATACTGGCGCAAATTATT 57.432 32.000 10.83 0.00 0.00 1.40
46 47 7.996385 ACTTTCTATACTGGCGCAAATTATTT 58.004 30.769 10.83 0.00 0.00 1.40
47 48 9.116067 ACTTTCTATACTGGCGCAAATTATTTA 57.884 29.630 10.83 0.00 0.00 1.40
48 49 9.599322 CTTTCTATACTGGCGCAAATTATTTAG 57.401 33.333 10.83 0.00 0.00 1.85
49 50 8.671384 TTCTATACTGGCGCAAATTATTTAGT 57.329 30.769 10.83 1.53 0.00 2.24
50 51 9.767228 TTCTATACTGGCGCAAATTATTTAGTA 57.233 29.630 10.83 3.74 0.00 1.82
51 52 9.767228 TCTATACTGGCGCAAATTATTTAGTAA 57.233 29.630 10.83 0.00 0.00 2.24
54 55 7.095695 ACTGGCGCAAATTATTTAGTAATGT 57.904 32.000 10.83 0.00 33.32 2.71
55 56 8.215926 ACTGGCGCAAATTATTTAGTAATGTA 57.784 30.769 10.83 0.00 33.32 2.29
56 57 8.342634 ACTGGCGCAAATTATTTAGTAATGTAG 58.657 33.333 10.83 0.00 33.32 2.74
57 58 8.439993 TGGCGCAAATTATTTAGTAATGTAGA 57.560 30.769 10.83 0.00 33.32 2.59
58 59 8.894731 TGGCGCAAATTATTTAGTAATGTAGAA 58.105 29.630 10.83 0.00 33.32 2.10
59 60 9.893305 GGCGCAAATTATTTAGTAATGTAGAAT 57.107 29.630 10.83 0.00 33.32 2.40
71 72 9.863845 TTAGTAATGTAGAATCAATCACGAACA 57.136 29.630 0.00 0.00 0.00 3.18
72 73 8.771920 AGTAATGTAGAATCAATCACGAACAA 57.228 30.769 0.00 0.00 0.00 2.83
73 74 9.383519 AGTAATGTAGAATCAATCACGAACAAT 57.616 29.630 0.00 0.00 0.00 2.71
74 75 9.638300 GTAATGTAGAATCAATCACGAACAATC 57.362 33.333 0.00 0.00 0.00 2.67
75 76 8.498054 AATGTAGAATCAATCACGAACAATCT 57.502 30.769 0.00 0.00 0.00 2.40
76 77 7.525688 TGTAGAATCAATCACGAACAATCTC 57.474 36.000 0.00 0.00 0.00 2.75
77 78 7.323420 TGTAGAATCAATCACGAACAATCTCT 58.677 34.615 0.00 0.00 0.00 3.10
78 79 8.466798 TGTAGAATCAATCACGAACAATCTCTA 58.533 33.333 0.00 0.00 0.00 2.43
79 80 9.302345 GTAGAATCAATCACGAACAATCTCTAA 57.698 33.333 0.00 0.00 0.00 2.10
80 81 8.777865 AGAATCAATCACGAACAATCTCTAAA 57.222 30.769 0.00 0.00 0.00 1.85
81 82 8.877779 AGAATCAATCACGAACAATCTCTAAAG 58.122 33.333 0.00 0.00 0.00 1.85
82 83 8.777865 AATCAATCACGAACAATCTCTAAAGA 57.222 30.769 0.00 0.00 35.54 2.52
83 84 8.954950 ATCAATCACGAACAATCTCTAAAGAT 57.045 30.769 0.00 0.00 44.37 2.40
125 126 7.923414 ACCTTACCTTAAATCACTCAATCAC 57.077 36.000 0.00 0.00 0.00 3.06
126 127 7.458397 ACCTTACCTTAAATCACTCAATCACA 58.542 34.615 0.00 0.00 0.00 3.58
127 128 8.109634 ACCTTACCTTAAATCACTCAATCACAT 58.890 33.333 0.00 0.00 0.00 3.21
128 129 8.960591 CCTTACCTTAAATCACTCAATCACATT 58.039 33.333 0.00 0.00 0.00 2.71
172 173 8.809159 TGATTTTAACAAAAATCGCTCAATCA 57.191 26.923 15.18 0.00 46.72 2.57
173 174 8.698854 TGATTTTAACAAAAATCGCTCAATCAC 58.301 29.630 15.18 0.00 46.72 3.06
174 175 7.993821 TTTTAACAAAAATCGCTCAATCACA 57.006 28.000 0.00 0.00 0.00 3.58
175 176 8.586570 TTTTAACAAAAATCGCTCAATCACAT 57.413 26.923 0.00 0.00 0.00 3.21
176 177 8.586570 TTTAACAAAAATCGCTCAATCACATT 57.413 26.923 0.00 0.00 0.00 2.71
177 178 9.684448 TTTAACAAAAATCGCTCAATCACATTA 57.316 25.926 0.00 0.00 0.00 1.90
178 179 9.684448 TTAACAAAAATCGCTCAATCACATTAA 57.316 25.926 0.00 0.00 0.00 1.40
179 180 8.761575 AACAAAAATCGCTCAATCACATTAAT 57.238 26.923 0.00 0.00 0.00 1.40
180 181 8.761575 ACAAAAATCGCTCAATCACATTAATT 57.238 26.923 0.00 0.00 0.00 1.40
181 182 9.853555 ACAAAAATCGCTCAATCACATTAATTA 57.146 25.926 0.00 0.00 0.00 1.40
183 184 9.520204 AAAAATCGCTCAATCACATTAATTAGG 57.480 29.630 0.00 0.00 0.00 2.69
184 185 8.450578 AAATCGCTCAATCACATTAATTAGGA 57.549 30.769 0.00 0.00 0.00 2.94
185 186 8.450578 AATCGCTCAATCACATTAATTAGGAA 57.549 30.769 0.00 0.00 0.00 3.36
186 187 7.857734 TCGCTCAATCACATTAATTAGGAAA 57.142 32.000 0.00 0.00 0.00 3.13
187 188 8.450578 TCGCTCAATCACATTAATTAGGAAAT 57.549 30.769 0.00 0.00 0.00 2.17
188 189 9.554395 TCGCTCAATCACATTAATTAGGAAATA 57.446 29.630 0.00 0.00 0.00 1.40
212 213 7.595819 ATCTCTACTCCTAATTCTCAGTTGG 57.404 40.000 0.00 0.00 0.00 3.77
213 214 6.494952 TCTCTACTCCTAATTCTCAGTTGGT 58.505 40.000 0.00 0.00 0.00 3.67
214 215 7.640313 TCTCTACTCCTAATTCTCAGTTGGTA 58.360 38.462 0.00 0.00 0.00 3.25
215 216 8.114102 TCTCTACTCCTAATTCTCAGTTGGTAA 58.886 37.037 0.00 0.00 0.00 2.85
216 217 8.840200 TCTACTCCTAATTCTCAGTTGGTAAT 57.160 34.615 0.00 0.00 0.00 1.89
217 218 9.268282 TCTACTCCTAATTCTCAGTTGGTAATT 57.732 33.333 0.00 0.00 0.00 1.40
218 219 9.892130 CTACTCCTAATTCTCAGTTGGTAATTT 57.108 33.333 0.00 0.00 0.00 1.82
220 221 9.232473 ACTCCTAATTCTCAGTTGGTAATTTTC 57.768 33.333 0.00 0.00 0.00 2.29
221 222 8.263940 TCCTAATTCTCAGTTGGTAATTTTCG 57.736 34.615 0.00 0.00 0.00 3.46
222 223 6.967199 CCTAATTCTCAGTTGGTAATTTTCGC 59.033 38.462 0.00 0.00 0.00 4.70
223 224 4.398549 TTCTCAGTTGGTAATTTTCGCG 57.601 40.909 0.00 0.00 0.00 5.87
224 225 2.739913 TCTCAGTTGGTAATTTTCGCGG 59.260 45.455 6.13 0.00 0.00 6.46
225 226 2.482721 CTCAGTTGGTAATTTTCGCGGT 59.517 45.455 6.13 0.00 0.00 5.68
226 227 2.879646 TCAGTTGGTAATTTTCGCGGTT 59.120 40.909 6.13 0.00 0.00 4.44
227 228 4.063689 TCAGTTGGTAATTTTCGCGGTTA 58.936 39.130 6.13 0.00 0.00 2.85
228 229 4.514441 TCAGTTGGTAATTTTCGCGGTTAA 59.486 37.500 6.13 0.00 0.00 2.01
229 230 5.181622 TCAGTTGGTAATTTTCGCGGTTAAT 59.818 36.000 6.13 0.47 0.00 1.40
230 231 5.859648 CAGTTGGTAATTTTCGCGGTTAATT 59.140 36.000 6.13 12.10 0.00 1.40
231 232 6.363896 CAGTTGGTAATTTTCGCGGTTAATTT 59.636 34.615 6.13 4.36 0.00 1.82
232 233 6.924612 AGTTGGTAATTTTCGCGGTTAATTTT 59.075 30.769 6.13 0.00 0.00 1.82
233 234 6.931243 TGGTAATTTTCGCGGTTAATTTTC 57.069 33.333 6.13 6.95 0.00 2.29
234 235 6.444633 TGGTAATTTTCGCGGTTAATTTTCA 58.555 32.000 6.13 8.71 0.00 2.69
235 236 7.091443 TGGTAATTTTCGCGGTTAATTTTCAT 58.909 30.769 6.13 0.00 0.00 2.57
236 237 7.273815 TGGTAATTTTCGCGGTTAATTTTCATC 59.726 33.333 6.13 0.00 0.00 2.92
237 238 6.641176 AATTTTCGCGGTTAATTTTCATCC 57.359 33.333 6.13 0.00 0.00 3.51
238 239 3.768468 TTCGCGGTTAATTTTCATCCC 57.232 42.857 6.13 0.00 0.00 3.85
239 240 2.712709 TCGCGGTTAATTTTCATCCCA 58.287 42.857 6.13 0.00 0.00 4.37
240 241 2.420722 TCGCGGTTAATTTTCATCCCAC 59.579 45.455 6.13 0.00 0.00 4.61
241 242 2.422127 CGCGGTTAATTTTCATCCCACT 59.578 45.455 0.00 0.00 0.00 4.00
242 243 3.119637 CGCGGTTAATTTTCATCCCACTT 60.120 43.478 0.00 0.00 0.00 3.16
243 244 4.095185 CGCGGTTAATTTTCATCCCACTTA 59.905 41.667 0.00 0.00 0.00 2.24
244 245 5.220970 CGCGGTTAATTTTCATCCCACTTAT 60.221 40.000 0.00 0.00 0.00 1.73
245 246 6.206498 GCGGTTAATTTTCATCCCACTTATC 58.794 40.000 0.00 0.00 0.00 1.75
246 247 6.183360 GCGGTTAATTTTCATCCCACTTATCA 60.183 38.462 0.00 0.00 0.00 2.15
247 248 7.470009 GCGGTTAATTTTCATCCCACTTATCAT 60.470 37.037 0.00 0.00 0.00 2.45
248 249 7.862372 CGGTTAATTTTCATCCCACTTATCATG 59.138 37.037 0.00 0.00 0.00 3.07
249 250 8.912988 GGTTAATTTTCATCCCACTTATCATGA 58.087 33.333 0.00 0.00 0.00 3.07
271 272 2.857087 TTTTTCGTCCCTCCTCCCA 58.143 52.632 0.00 0.00 0.00 4.37
272 273 0.399075 TTTTTCGTCCCTCCTCCCAC 59.601 55.000 0.00 0.00 0.00 4.61
273 274 1.486145 TTTTCGTCCCTCCTCCCACC 61.486 60.000 0.00 0.00 0.00 4.61
274 275 2.396651 TTTCGTCCCTCCTCCCACCT 62.397 60.000 0.00 0.00 0.00 4.00
275 276 2.284699 CGTCCCTCCTCCCACCTT 60.285 66.667 0.00 0.00 0.00 3.50
276 277 1.918800 CGTCCCTCCTCCCACCTTT 60.919 63.158 0.00 0.00 0.00 3.11
277 278 1.685820 GTCCCTCCTCCCACCTTTG 59.314 63.158 0.00 0.00 0.00 2.77
278 279 2.231380 TCCCTCCTCCCACCTTTGC 61.231 63.158 0.00 0.00 0.00 3.68
279 280 2.234296 CCCTCCTCCCACCTTTGCT 61.234 63.158 0.00 0.00 0.00 3.91
280 281 1.001641 CCTCCTCCCACCTTTGCTG 60.002 63.158 0.00 0.00 0.00 4.41
281 282 1.001641 CTCCTCCCACCTTTGCTGG 60.002 63.158 0.00 0.00 0.00 4.85
282 283 1.774217 TCCTCCCACCTTTGCTGGT 60.774 57.895 0.00 0.00 41.77 4.00
283 284 1.153756 CCTCCCACCTTTGCTGGTT 59.846 57.895 0.00 0.00 38.45 3.67
357 359 5.678483 CACACAACGAAAGAAATCTGAACAG 59.322 40.000 0.00 0.00 0.00 3.16
379 381 4.225942 AGATCAGAACTTTCCATACTGGCA 59.774 41.667 0.00 0.00 37.47 4.92
380 382 4.574674 TCAGAACTTTCCATACTGGCAT 57.425 40.909 0.00 0.00 37.47 4.40
389 391 9.914834 AACTTTCCATACTGGCATAAGTTATTA 57.085 29.630 14.00 0.00 39.36 0.98
470 472 7.390718 ACCTTACCTTAAATCACTCAATCACAC 59.609 37.037 0.00 0.00 0.00 3.82
528 533 8.450578 TCGCTCAATCACATTAATTAGGAAAT 57.549 30.769 0.00 0.00 0.00 2.17
558 563 7.741554 ATCTAATGAAGGAGTTGGTAGTCTT 57.258 36.000 0.00 0.00 0.00 3.01
559 564 7.554959 TCTAATGAAGGAGTTGGTAGTCTTT 57.445 36.000 0.00 0.00 0.00 2.52
658 664 5.365021 AAAAACATCCTCTCTCGATCCAT 57.635 39.130 0.00 0.00 0.00 3.41
735 741 2.759149 CCGATTGCCCCAATGCCA 60.759 61.111 0.00 0.00 33.90 4.92
750 756 3.072468 CCACCTGCAAGCCATGGG 61.072 66.667 15.13 0.00 0.00 4.00
775 782 1.601759 CCCCTAGATGCATTGCCGG 60.602 63.158 6.12 0.00 0.00 6.13
808 818 2.494918 CACCGCCTCCCTTACGAG 59.505 66.667 0.00 0.00 0.00 4.18
815 825 2.200052 CTCCCTTACGAGGACACCC 58.800 63.158 0.00 0.00 46.74 4.61
832 1201 2.671070 CCGCCATGGGTCTCAGTT 59.329 61.111 15.13 0.00 0.00 3.16
880 1249 2.824546 GCCGATGCTCCAGATCCA 59.175 61.111 0.00 0.00 33.53 3.41
894 1263 0.179000 GATCCAGCCATCGTTGACCT 59.821 55.000 0.00 0.00 0.00 3.85
899 1268 0.616111 AGCCATCGTTGACCTCCTCT 60.616 55.000 0.00 0.00 0.00 3.69
908 1277 3.193691 CGTTGACCTCCTCTACATCAGTT 59.806 47.826 0.00 0.00 0.00 3.16
912 1281 5.141182 TGACCTCCTCTACATCAGTTATCC 58.859 45.833 0.00 0.00 0.00 2.59
927 1297 0.761702 TATCCGTCAAGGTAGGGGGC 60.762 60.000 0.00 0.00 41.99 5.80
938 1308 1.074775 TAGGGGGCGTGGCTCTATT 60.075 57.895 0.00 0.00 0.00 1.73
953 1323 2.731976 CTCTATTTATCTTCCCGCGTGC 59.268 50.000 4.92 0.00 0.00 5.34
972 1342 1.097232 CACCGTGTCCGTGTATCCTA 58.903 55.000 0.00 0.00 0.00 2.94
1043 1413 3.331889 AGATCCATGGTTGGGGATACATC 59.668 47.826 12.58 3.14 43.82 3.06
1060 1442 1.138859 CATCCAACGACCTAGGCATCA 59.861 52.381 9.30 0.00 0.00 3.07
1087 1473 2.104331 CGTACTCGAAGCCCGCAT 59.896 61.111 0.00 0.00 39.71 4.73
1091 1477 2.292794 TACTCGAAGCCCGCATCCAC 62.293 60.000 0.00 0.00 38.37 4.02
1115 1501 5.211973 TGCCTCCTCAATCTATGTTAGTCT 58.788 41.667 0.00 0.00 0.00 3.24
1133 1519 4.099170 GCAGCAGCAAGGTCAGCG 62.099 66.667 0.00 0.00 41.58 5.18
1154 1540 4.743955 GCGCCCCACTCTATATTTTCTTCT 60.744 45.833 0.00 0.00 0.00 2.85
1155 1541 5.368989 CGCCCCACTCTATATTTTCTTCTT 58.631 41.667 0.00 0.00 0.00 2.52
1156 1542 5.467063 CGCCCCACTCTATATTTTCTTCTTC 59.533 44.000 0.00 0.00 0.00 2.87
1157 1543 6.357367 GCCCCACTCTATATTTTCTTCTTCA 58.643 40.000 0.00 0.00 0.00 3.02
1158 1544 6.828785 GCCCCACTCTATATTTTCTTCTTCAA 59.171 38.462 0.00 0.00 0.00 2.69
1178 1565 1.753930 ATCTTGCATCGCATGGTGAA 58.246 45.000 0.00 0.00 38.76 3.18
1203 1590 8.765488 ATCCACAAAATATGTACATCCATTGA 57.235 30.769 23.39 10.51 41.46 2.57
1230 1617 9.144747 CGATGTTGGTATTTATTCAGGAGATAG 57.855 37.037 0.00 0.00 0.00 2.08
1245 1788 3.034635 GAGATAGAAAGGAGGGTCAGCA 58.965 50.000 0.00 0.00 0.00 4.41
1283 1826 0.040646 TTCCAGAGGACTCGCCCTAA 59.959 55.000 0.00 0.00 36.49 2.69
1301 1844 1.896122 AACTAGCCTGCACGGTACCC 61.896 60.000 6.25 0.00 34.25 3.69
1325 1868 3.445008 TCATTAGCACTTCTCCCAGTCT 58.555 45.455 0.00 0.00 0.00 3.24
1326 1869 3.840666 TCATTAGCACTTCTCCCAGTCTT 59.159 43.478 0.00 0.00 0.00 3.01
1335 1878 4.466015 ACTTCTCCCAGTCTTTTTGCAAAA 59.534 37.500 20.46 20.46 0.00 2.44
1343 1886 7.338957 TCCCAGTCTTTTTGCAAAATTTGAATT 59.661 29.630 24.39 11.90 0.00 2.17
1365 1908 5.125100 TCACCACTTTTGAATCATGCTTC 57.875 39.130 2.26 2.26 0.00 3.86
1371 1916 2.617250 TTGAATCATGCTTCGTGTGC 57.383 45.000 4.92 0.00 0.00 4.57
1480 2040 4.460263 TGTGGTATTTCAAAGTGCTCTGT 58.540 39.130 0.00 0.00 0.00 3.41
1486 2046 8.264347 TGGTATTTCAAAGTGCTCTGTATGATA 58.736 33.333 0.00 0.00 0.00 2.15
1530 2098 1.217882 GACGACTGGTGGTTGTTCTG 58.782 55.000 0.00 0.00 42.21 3.02
1535 2103 3.813166 CGACTGGTGGTTGTTCTGTTTAT 59.187 43.478 0.00 0.00 0.00 1.40
1549 2117 4.523083 TCTGTTTATACCTGGCATGGTTC 58.477 43.478 12.73 2.72 41.22 3.62
1558 2126 1.142465 CTGGCATGGTTCAGAGGCTAT 59.858 52.381 0.00 0.00 33.11 2.97
1563 2131 2.550277 TGGTTCAGAGGCTATGGAGA 57.450 50.000 9.58 0.00 0.00 3.71
1569 2137 0.397816 AGAGGCTATGGAGAAGGCGT 60.398 55.000 0.00 0.00 43.86 5.68
1608 2182 6.312141 TGGTCAGTGATGGAGATGAATTTA 57.688 37.500 0.00 0.00 0.00 1.40
1621 2195 6.183361 GGAGATGAATTTAGGAGAGATGTGGT 60.183 42.308 0.00 0.00 0.00 4.16
1638 2212 0.604511 GGTTGGGAGTTGTACCGGTG 60.605 60.000 19.93 0.00 0.00 4.94
1660 2234 6.536941 GGTGATTTTTCTGTCCTCTCTATGTC 59.463 42.308 0.00 0.00 0.00 3.06
1723 2297 2.453521 AGGGTAGCGTACATGAACAGA 58.546 47.619 0.00 0.00 0.00 3.41
1751 2325 2.160721 AGAAGGCGAGGAGGACAATA 57.839 50.000 0.00 0.00 0.00 1.90
1759 2333 2.351253 CGAGGAGGACAATATGAGCGAG 60.351 54.545 0.00 0.00 0.00 5.03
1763 2337 3.198068 GAGGACAATATGAGCGAGCAAA 58.802 45.455 0.00 0.00 0.00 3.68
1796 2371 6.097839 TGGGTATTGAGATGTAGGTAAGACAC 59.902 42.308 0.00 0.00 0.00 3.67
1823 2398 8.768955 GTGTAATCTGAATTGAGACATATGGAC 58.231 37.037 7.80 0.88 0.00 4.02
1825 2400 5.852282 TCTGAATTGAGACATATGGACGA 57.148 39.130 7.80 0.00 0.00 4.20
1845 2420 8.403236 TGGACGACATATATAGTACATATGTGC 58.597 37.037 16.92 17.04 45.30 4.57
1846 2421 7.586664 GGACGACATATATAGTACATATGTGCG 59.413 40.741 16.92 18.83 45.30 5.34
1897 2472 1.683917 CTCTAGATCCACCTTCACCGG 59.316 57.143 0.00 0.00 0.00 5.28
1903 2478 1.077501 CCACCTTCACCGGCATCAT 60.078 57.895 0.00 0.00 0.00 2.45
2091 2668 0.904865 AGGGAAGACACTCGCATGGA 60.905 55.000 0.00 0.00 0.00 3.41
2277 2863 7.123547 AGTTGTCCATTTGGTTCTAAACTTTGA 59.876 33.333 0.00 0.00 36.34 2.69
2281 2867 9.974980 GTCCATTTGGTTCTAAACTTTGATAAA 57.025 29.630 0.00 0.00 36.34 1.40
2288 2874 8.792633 TGGTTCTAAACTTTGATAAATGACAGG 58.207 33.333 0.00 0.00 0.00 4.00
2725 4166 9.379791 AGTTAAAGACTATGAATTAAACCGAGG 57.620 33.333 0.00 0.00 36.65 4.63
2726 4167 6.679327 AAAGACTATGAATTAAACCGAGGC 57.321 37.500 0.00 0.00 0.00 4.70
2727 4168 4.369182 AGACTATGAATTAAACCGAGGCG 58.631 43.478 0.00 0.00 0.00 5.52
2728 4169 2.870411 ACTATGAATTAAACCGAGGCGC 59.130 45.455 0.00 0.00 0.00 6.53
2729 4170 2.038387 ATGAATTAAACCGAGGCGCT 57.962 45.000 7.64 0.00 0.00 5.92
2730 4171 1.816074 TGAATTAAACCGAGGCGCTT 58.184 45.000 7.64 0.00 0.00 4.68
2731 4172 2.975266 TGAATTAAACCGAGGCGCTTA 58.025 42.857 7.64 0.00 0.00 3.09
2732 4173 2.933906 TGAATTAAACCGAGGCGCTTAG 59.066 45.455 7.64 0.00 0.00 2.18
2733 4174 2.685850 ATTAAACCGAGGCGCTTAGT 57.314 45.000 7.64 0.00 0.00 2.24
2734 4175 2.000429 TTAAACCGAGGCGCTTAGTC 58.000 50.000 7.64 0.00 0.00 2.59
2735 4176 0.179156 TAAACCGAGGCGCTTAGTCG 60.179 55.000 7.64 11.00 0.00 4.18
2736 4177 1.870055 AAACCGAGGCGCTTAGTCGA 61.870 55.000 18.79 0.00 35.70 4.20
2737 4178 1.664321 AACCGAGGCGCTTAGTCGAT 61.664 55.000 18.79 3.80 35.70 3.59
2738 4179 1.370657 CCGAGGCGCTTAGTCGATC 60.371 63.158 18.79 0.00 35.70 3.69
2739 4180 1.355563 CGAGGCGCTTAGTCGATCA 59.644 57.895 7.64 0.00 35.70 2.92
2740 4181 0.039978 CGAGGCGCTTAGTCGATCAT 60.040 55.000 7.64 0.00 35.70 2.45
2741 4182 1.692296 GAGGCGCTTAGTCGATCATC 58.308 55.000 7.64 0.00 0.00 2.92
2742 4183 0.039978 AGGCGCTTAGTCGATCATCG 60.040 55.000 7.64 0.00 42.10 3.84
2743 4184 1.004277 GGCGCTTAGTCGATCATCGG 61.004 60.000 7.33 0.00 40.88 4.18
2744 4185 0.040336 GCGCTTAGTCGATCATCGGA 60.040 55.000 7.33 0.00 40.88 4.55
2745 4186 1.957089 CGCTTAGTCGATCATCGGAG 58.043 55.000 7.33 2.08 40.88 4.63
2746 4187 1.531578 CGCTTAGTCGATCATCGGAGA 59.468 52.381 7.33 0.00 40.88 3.71
2747 4188 2.031944 CGCTTAGTCGATCATCGGAGAA 60.032 50.000 7.33 0.00 43.58 2.87
2748 4189 3.548214 CGCTTAGTCGATCATCGGAGAAA 60.548 47.826 7.33 0.00 43.58 2.52
2749 4190 3.731717 GCTTAGTCGATCATCGGAGAAAC 59.268 47.826 7.33 0.00 43.58 2.78
2750 4191 4.733815 GCTTAGTCGATCATCGGAGAAACA 60.734 45.833 7.33 0.00 43.58 2.83
2751 4192 3.868757 AGTCGATCATCGGAGAAACAA 57.131 42.857 7.33 0.00 43.58 2.83
2752 4193 3.775202 AGTCGATCATCGGAGAAACAAG 58.225 45.455 7.33 0.00 43.58 3.16
2753 4194 2.282820 GTCGATCATCGGAGAAACAAGC 59.717 50.000 7.33 0.00 43.58 4.01
2754 4195 2.094234 TCGATCATCGGAGAAACAAGCA 60.094 45.455 7.33 0.00 43.58 3.91
2755 4196 2.672874 CGATCATCGGAGAAACAAGCAA 59.327 45.455 0.00 0.00 43.58 3.91
2756 4197 3.310774 CGATCATCGGAGAAACAAGCAAT 59.689 43.478 0.00 0.00 43.58 3.56
2757 4198 4.551603 CGATCATCGGAGAAACAAGCAATC 60.552 45.833 0.00 0.00 43.58 2.67
2758 4199 3.673902 TCATCGGAGAAACAAGCAATCA 58.326 40.909 0.00 0.00 43.58 2.57
2759 4200 4.264253 TCATCGGAGAAACAAGCAATCAT 58.736 39.130 0.00 0.00 43.58 2.45
2760 4201 5.427378 TCATCGGAGAAACAAGCAATCATA 58.573 37.500 0.00 0.00 43.58 2.15
2761 4202 5.879777 TCATCGGAGAAACAAGCAATCATAA 59.120 36.000 0.00 0.00 43.58 1.90
2762 4203 5.801350 TCGGAGAAACAAGCAATCATAAG 57.199 39.130 0.00 0.00 0.00 1.73
2763 4204 5.487433 TCGGAGAAACAAGCAATCATAAGA 58.513 37.500 0.00 0.00 0.00 2.10
2764 4205 5.582269 TCGGAGAAACAAGCAATCATAAGAG 59.418 40.000 0.00 0.00 0.00 2.85
2765 4206 5.220739 CGGAGAAACAAGCAATCATAAGAGG 60.221 44.000 0.00 0.00 0.00 3.69
2766 4207 5.449725 GGAGAAACAAGCAATCATAAGAGGC 60.450 44.000 0.00 0.00 0.00 4.70
2767 4208 5.012239 AGAAACAAGCAATCATAAGAGGCA 58.988 37.500 0.00 0.00 32.25 4.75
2768 4209 4.708726 AACAAGCAATCATAAGAGGCAC 57.291 40.909 0.00 0.00 32.25 5.01
2769 4210 2.679837 ACAAGCAATCATAAGAGGCACG 59.320 45.455 0.00 0.00 32.25 5.34
2770 4211 2.938451 CAAGCAATCATAAGAGGCACGA 59.062 45.455 0.00 0.00 32.25 4.35
2771 4212 2.555199 AGCAATCATAAGAGGCACGAC 58.445 47.619 0.00 0.00 32.25 4.34
2772 4213 2.093500 AGCAATCATAAGAGGCACGACA 60.093 45.455 0.00 0.00 32.25 4.35
2773 4214 2.030946 GCAATCATAAGAGGCACGACAC 59.969 50.000 0.00 0.00 0.00 3.67
2774 4215 2.604046 ATCATAAGAGGCACGACACC 57.396 50.000 0.00 0.00 0.00 4.16
2775 4216 0.172578 TCATAAGAGGCACGACACCG 59.827 55.000 0.00 0.00 42.50 4.94
2776 4217 0.172578 CATAAGAGGCACGACACCGA 59.827 55.000 0.00 0.00 39.50 4.69
2777 4218 0.456221 ATAAGAGGCACGACACCGAG 59.544 55.000 0.00 0.00 39.50 4.63
2778 4219 0.607217 TAAGAGGCACGACACCGAGA 60.607 55.000 0.00 0.00 39.50 4.04
2779 4220 1.251527 AAGAGGCACGACACCGAGAT 61.252 55.000 0.00 0.00 39.50 2.75
2780 4221 1.215647 GAGGCACGACACCGAGATT 59.784 57.895 0.00 0.00 39.50 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.253810 CCAGTATAGAAAGTTCTGATCTGTTCA 58.746 37.037 3.76 0.00 38.19 3.18
9 10 7.223777 GCCAGTATAGAAAGTTCTGATCTGTTC 59.776 40.741 3.76 0.00 38.19 3.18
10 11 7.044798 GCCAGTATAGAAAGTTCTGATCTGTT 58.955 38.462 3.76 0.00 38.19 3.16
11 12 6.578023 GCCAGTATAGAAAGTTCTGATCTGT 58.422 40.000 3.76 0.00 38.19 3.41
12 13 5.689514 CGCCAGTATAGAAAGTTCTGATCTG 59.310 44.000 3.76 8.40 38.19 2.90
13 14 5.737635 GCGCCAGTATAGAAAGTTCTGATCT 60.738 44.000 0.00 0.00 38.19 2.75
14 15 4.446051 GCGCCAGTATAGAAAGTTCTGATC 59.554 45.833 0.00 0.00 38.19 2.92
15 16 4.141937 TGCGCCAGTATAGAAAGTTCTGAT 60.142 41.667 4.18 0.00 38.19 2.90
16 17 3.194755 TGCGCCAGTATAGAAAGTTCTGA 59.805 43.478 4.18 0.00 38.19 3.27
17 18 3.521560 TGCGCCAGTATAGAAAGTTCTG 58.478 45.455 4.18 0.00 38.19 3.02
18 19 3.887621 TGCGCCAGTATAGAAAGTTCT 57.112 42.857 4.18 0.00 41.24 3.01
19 20 4.939509 TTTGCGCCAGTATAGAAAGTTC 57.060 40.909 4.18 0.00 0.00 3.01
20 21 5.897377 AATTTGCGCCAGTATAGAAAGTT 57.103 34.783 4.18 0.00 0.00 2.66
21 22 7.568199 AATAATTTGCGCCAGTATAGAAAGT 57.432 32.000 4.18 0.00 0.00 2.66
22 23 9.599322 CTAAATAATTTGCGCCAGTATAGAAAG 57.401 33.333 4.18 0.00 0.00 2.62
23 24 9.116067 ACTAAATAATTTGCGCCAGTATAGAAA 57.884 29.630 4.18 0.00 0.00 2.52
24 25 8.671384 ACTAAATAATTTGCGCCAGTATAGAA 57.329 30.769 4.18 0.00 0.00 2.10
25 26 9.767228 TTACTAAATAATTTGCGCCAGTATAGA 57.233 29.630 4.18 0.00 0.00 1.98
28 29 8.846211 ACATTACTAAATAATTTGCGCCAGTAT 58.154 29.630 4.18 0.00 30.54 2.12
29 30 8.215926 ACATTACTAAATAATTTGCGCCAGTA 57.784 30.769 4.18 0.00 30.54 2.74
30 31 7.095695 ACATTACTAAATAATTTGCGCCAGT 57.904 32.000 4.18 0.00 30.54 4.00
31 32 8.556194 TCTACATTACTAAATAATTTGCGCCAG 58.444 33.333 4.18 0.00 30.54 4.85
32 33 8.439993 TCTACATTACTAAATAATTTGCGCCA 57.560 30.769 4.18 0.00 30.54 5.69
33 34 9.893305 ATTCTACATTACTAAATAATTTGCGCC 57.107 29.630 4.18 0.00 30.54 6.53
45 46 9.863845 TGTTCGTGATTGATTCTACATTACTAA 57.136 29.630 0.00 0.00 0.00 2.24
46 47 9.863845 TTGTTCGTGATTGATTCTACATTACTA 57.136 29.630 0.00 0.00 0.00 1.82
47 48 8.771920 TTGTTCGTGATTGATTCTACATTACT 57.228 30.769 0.00 0.00 0.00 2.24
48 49 9.638300 GATTGTTCGTGATTGATTCTACATTAC 57.362 33.333 0.00 0.00 0.00 1.89
49 50 9.599866 AGATTGTTCGTGATTGATTCTACATTA 57.400 29.630 0.00 0.00 0.00 1.90
50 51 8.498054 AGATTGTTCGTGATTGATTCTACATT 57.502 30.769 0.00 0.00 0.00 2.71
51 52 7.984050 AGAGATTGTTCGTGATTGATTCTACAT 59.016 33.333 0.00 0.00 0.00 2.29
52 53 7.323420 AGAGATTGTTCGTGATTGATTCTACA 58.677 34.615 0.00 0.00 0.00 2.74
53 54 7.763172 AGAGATTGTTCGTGATTGATTCTAC 57.237 36.000 0.00 0.00 0.00 2.59
54 55 9.869757 TTTAGAGATTGTTCGTGATTGATTCTA 57.130 29.630 0.00 0.00 0.00 2.10
55 56 8.777865 TTTAGAGATTGTTCGTGATTGATTCT 57.222 30.769 0.00 0.00 0.00 2.40
56 57 8.873830 TCTTTAGAGATTGTTCGTGATTGATTC 58.126 33.333 0.00 0.00 0.00 2.52
57 58 8.777865 TCTTTAGAGATTGTTCGTGATTGATT 57.222 30.769 0.00 0.00 0.00 2.57
58 59 8.954950 ATCTTTAGAGATTGTTCGTGATTGAT 57.045 30.769 0.00 0.00 39.63 2.57
99 100 9.444600 GTGATTGAGTGATTTAAGGTAAGGTTA 57.555 33.333 0.00 0.00 0.00 2.85
100 101 7.942341 TGTGATTGAGTGATTTAAGGTAAGGTT 59.058 33.333 0.00 0.00 0.00 3.50
101 102 7.458397 TGTGATTGAGTGATTTAAGGTAAGGT 58.542 34.615 0.00 0.00 0.00 3.50
102 103 7.921786 TGTGATTGAGTGATTTAAGGTAAGG 57.078 36.000 0.00 0.00 0.00 2.69
149 150 8.586570 TGTGATTGAGCGATTTTTGTTAAAAT 57.413 26.923 0.00 0.00 44.53 1.82
150 151 7.993821 TGTGATTGAGCGATTTTTGTTAAAA 57.006 28.000 0.00 0.00 37.62 1.52
151 152 8.586570 AATGTGATTGAGCGATTTTTGTTAAA 57.413 26.923 0.00 0.00 0.00 1.52
152 153 9.684448 TTAATGTGATTGAGCGATTTTTGTTAA 57.316 25.926 0.00 0.00 0.00 2.01
153 154 9.853555 ATTAATGTGATTGAGCGATTTTTGTTA 57.146 25.926 0.00 0.00 0.00 2.41
154 155 8.761575 ATTAATGTGATTGAGCGATTTTTGTT 57.238 26.923 0.00 0.00 0.00 2.83
155 156 8.761575 AATTAATGTGATTGAGCGATTTTTGT 57.238 26.923 0.00 0.00 0.00 2.83
157 158 9.520204 CCTAATTAATGTGATTGAGCGATTTTT 57.480 29.630 0.00 0.00 0.00 1.94
158 159 8.902806 TCCTAATTAATGTGATTGAGCGATTTT 58.097 29.630 0.00 0.00 0.00 1.82
159 160 8.450578 TCCTAATTAATGTGATTGAGCGATTT 57.549 30.769 0.00 0.00 0.00 2.17
160 161 8.450578 TTCCTAATTAATGTGATTGAGCGATT 57.549 30.769 0.00 0.00 0.00 3.34
161 162 8.450578 TTTCCTAATTAATGTGATTGAGCGAT 57.549 30.769 0.00 0.00 0.00 4.58
162 163 7.857734 TTTCCTAATTAATGTGATTGAGCGA 57.142 32.000 0.00 0.00 0.00 4.93
186 187 9.308000 CCAACTGAGAATTAGGAGTAGAGATAT 57.692 37.037 0.00 0.00 0.00 1.63
187 188 8.282982 ACCAACTGAGAATTAGGAGTAGAGATA 58.717 37.037 0.00 0.00 0.00 1.98
188 189 7.129425 ACCAACTGAGAATTAGGAGTAGAGAT 58.871 38.462 0.00 0.00 0.00 2.75
189 190 6.494952 ACCAACTGAGAATTAGGAGTAGAGA 58.505 40.000 0.00 0.00 0.00 3.10
190 191 6.783708 ACCAACTGAGAATTAGGAGTAGAG 57.216 41.667 0.00 0.00 0.00 2.43
191 192 8.840200 ATTACCAACTGAGAATTAGGAGTAGA 57.160 34.615 0.00 0.00 0.00 2.59
192 193 9.892130 AAATTACCAACTGAGAATTAGGAGTAG 57.108 33.333 0.00 0.00 0.00 2.57
194 195 9.232473 GAAAATTACCAACTGAGAATTAGGAGT 57.768 33.333 0.00 0.00 0.00 3.85
195 196 8.391106 CGAAAATTACCAACTGAGAATTAGGAG 58.609 37.037 0.00 0.00 0.00 3.69
196 197 7.148306 GCGAAAATTACCAACTGAGAATTAGGA 60.148 37.037 0.00 0.00 0.00 2.94
197 198 6.967199 GCGAAAATTACCAACTGAGAATTAGG 59.033 38.462 0.00 0.00 0.00 2.69
198 199 6.682863 CGCGAAAATTACCAACTGAGAATTAG 59.317 38.462 0.00 0.00 0.00 1.73
199 200 6.402766 CCGCGAAAATTACCAACTGAGAATTA 60.403 38.462 8.23 0.00 0.00 1.40
200 201 5.390613 CGCGAAAATTACCAACTGAGAATT 58.609 37.500 0.00 0.00 0.00 2.17
201 202 4.142687 CCGCGAAAATTACCAACTGAGAAT 60.143 41.667 8.23 0.00 0.00 2.40
202 203 3.187637 CCGCGAAAATTACCAACTGAGAA 59.812 43.478 8.23 0.00 0.00 2.87
203 204 2.739913 CCGCGAAAATTACCAACTGAGA 59.260 45.455 8.23 0.00 0.00 3.27
204 205 2.482721 ACCGCGAAAATTACCAACTGAG 59.517 45.455 8.23 0.00 0.00 3.35
205 206 2.496111 ACCGCGAAAATTACCAACTGA 58.504 42.857 8.23 0.00 0.00 3.41
206 207 2.981400 ACCGCGAAAATTACCAACTG 57.019 45.000 8.23 0.00 0.00 3.16
207 208 5.632244 ATTAACCGCGAAAATTACCAACT 57.368 34.783 8.23 0.00 0.00 3.16
208 209 6.693761 AAATTAACCGCGAAAATTACCAAC 57.306 33.333 8.23 0.00 0.00 3.77
209 210 6.921857 TGAAAATTAACCGCGAAAATTACCAA 59.078 30.769 8.23 0.00 0.00 3.67
210 211 6.444633 TGAAAATTAACCGCGAAAATTACCA 58.555 32.000 8.23 8.80 0.00 3.25
211 212 6.931243 TGAAAATTAACCGCGAAAATTACC 57.069 33.333 8.23 6.54 0.00 2.85
212 213 7.253850 GGGATGAAAATTAACCGCGAAAATTAC 60.254 37.037 8.23 8.77 0.00 1.89
213 214 6.752815 GGGATGAAAATTAACCGCGAAAATTA 59.247 34.615 8.23 0.00 0.00 1.40
214 215 5.579119 GGGATGAAAATTAACCGCGAAAATT 59.421 36.000 8.23 7.58 0.00 1.82
215 216 5.106442 GGGATGAAAATTAACCGCGAAAAT 58.894 37.500 8.23 0.55 0.00 1.82
216 217 4.022242 TGGGATGAAAATTAACCGCGAAAA 60.022 37.500 8.23 0.00 0.00 2.29
217 218 3.506455 TGGGATGAAAATTAACCGCGAAA 59.494 39.130 8.23 0.00 0.00 3.46
218 219 3.082548 TGGGATGAAAATTAACCGCGAA 58.917 40.909 8.23 0.00 0.00 4.70
219 220 2.420722 GTGGGATGAAAATTAACCGCGA 59.579 45.455 8.23 0.00 0.00 5.87
220 221 2.422127 AGTGGGATGAAAATTAACCGCG 59.578 45.455 0.00 0.00 33.93 6.46
221 222 4.450082 AAGTGGGATGAAAATTAACCGC 57.550 40.909 0.00 0.00 0.00 5.68
222 223 7.328277 TGATAAGTGGGATGAAAATTAACCG 57.672 36.000 0.00 0.00 0.00 4.44
223 224 8.912988 TCATGATAAGTGGGATGAAAATTAACC 58.087 33.333 0.00 0.00 0.00 2.85
253 254 0.399075 GTGGGAGGAGGGACGAAAAA 59.601 55.000 0.00 0.00 0.00 1.94
254 255 1.486145 GGTGGGAGGAGGGACGAAAA 61.486 60.000 0.00 0.00 0.00 2.29
255 256 1.916777 GGTGGGAGGAGGGACGAAA 60.917 63.158 0.00 0.00 0.00 3.46
256 257 2.284405 GGTGGGAGGAGGGACGAA 60.284 66.667 0.00 0.00 0.00 3.85
257 258 2.396651 AAAGGTGGGAGGAGGGACGA 62.397 60.000 0.00 0.00 0.00 4.20
258 259 1.918800 AAAGGTGGGAGGAGGGACG 60.919 63.158 0.00 0.00 0.00 4.79
259 260 1.685820 CAAAGGTGGGAGGAGGGAC 59.314 63.158 0.00 0.00 0.00 4.46
260 261 2.231380 GCAAAGGTGGGAGGAGGGA 61.231 63.158 0.00 0.00 0.00 4.20
261 262 2.234296 AGCAAAGGTGGGAGGAGGG 61.234 63.158 0.00 0.00 0.00 4.30
262 263 1.001641 CAGCAAAGGTGGGAGGAGG 60.002 63.158 0.00 0.00 0.00 4.30
263 264 1.001641 CCAGCAAAGGTGGGAGGAG 60.002 63.158 7.33 0.00 46.19 3.69
264 265 3.170362 CCAGCAAAGGTGGGAGGA 58.830 61.111 7.33 0.00 46.19 3.71
403 405 9.869757 TTGATCTTTAGAGATTGTTCGTGATTA 57.130 29.630 0.00 0.00 42.66 1.75
502 507 8.450578 TTTCCTAATTAATGTGATTGAGCGAT 57.549 30.769 0.00 0.00 0.00 4.58
658 664 1.984026 GGGTTCCGTCGTTAGGGGA 60.984 63.158 0.00 0.00 0.00 4.81
735 741 4.387343 CCCCCATGGCTTGCAGGT 62.387 66.667 6.09 0.00 0.00 4.00
761 768 0.546122 AAGGACCGGCAATGCATCTA 59.454 50.000 7.79 0.00 0.00 1.98
768 775 1.299976 GTGGAGAAGGACCGGCAAT 59.700 57.895 0.00 0.00 0.00 3.56
775 782 4.373116 TGGCGCGTGGAGAAGGAC 62.373 66.667 8.43 0.00 0.00 3.85
815 825 1.746615 CAACTGAGACCCATGGCGG 60.747 63.158 6.09 0.00 0.00 6.13
880 1249 0.616111 AGAGGAGGTCAACGATGGCT 60.616 55.000 0.00 0.00 0.00 4.75
894 1263 4.788679 TGACGGATAACTGATGTAGAGGA 58.211 43.478 0.00 0.00 0.00 3.71
899 1268 5.301045 CCTACCTTGACGGATAACTGATGTA 59.699 44.000 0.00 0.00 36.31 2.29
908 1277 0.761702 GCCCCCTACCTTGACGGATA 60.762 60.000 0.00 0.00 36.31 2.59
912 1281 3.387947 ACGCCCCCTACCTTGACG 61.388 66.667 0.00 0.00 0.00 4.35
927 1297 3.318017 CGGGAAGATAAATAGAGCCACG 58.682 50.000 0.00 0.00 0.00 4.94
938 1308 1.448893 GGTGCACGCGGGAAGATAA 60.449 57.895 15.48 0.00 0.00 1.75
953 1323 1.065102 CTAGGATACACGGACACGGTG 59.935 57.143 6.58 6.58 46.48 4.94
1043 1413 1.541233 GGATGATGCCTAGGTCGTTGG 60.541 57.143 11.31 0.00 0.00 3.77
1060 1442 3.448267 TCGAGTACGACGTCAGGAT 57.552 52.632 17.16 0.00 43.81 3.24
1087 1473 2.550277 TAGATTGAGGAGGCAGTGGA 57.450 50.000 0.00 0.00 0.00 4.02
1091 1477 5.304101 AGACTAACATAGATTGAGGAGGCAG 59.696 44.000 0.00 0.00 0.00 4.85
1133 1519 6.357367 TGAAGAAGAAAATATAGAGTGGGGC 58.643 40.000 0.00 0.00 0.00 5.80
1154 1540 2.492881 ACCATGCGATGCAAGATTTGAA 59.507 40.909 0.00 0.00 43.62 2.69
1155 1541 2.093890 ACCATGCGATGCAAGATTTGA 58.906 42.857 0.00 0.00 43.62 2.69
1156 1542 2.159352 TCACCATGCGATGCAAGATTTG 60.159 45.455 0.00 0.00 43.62 2.32
1157 1543 2.093890 TCACCATGCGATGCAAGATTT 58.906 42.857 0.00 0.00 43.62 2.17
1158 1544 1.753930 TCACCATGCGATGCAAGATT 58.246 45.000 0.00 0.00 43.62 2.40
1178 1565 8.632679 GTCAATGGATGTACATATTTTGTGGAT 58.367 33.333 8.71 0.00 39.48 3.41
1203 1590 6.884832 TCTCCTGAATAAATACCAACATCGT 58.115 36.000 0.00 0.00 0.00 3.73
1230 1617 2.496899 TTCATGCTGACCCTCCTTTC 57.503 50.000 0.00 0.00 0.00 2.62
1232 1619 1.064166 CCATTCATGCTGACCCTCCTT 60.064 52.381 0.00 0.00 0.00 3.36
1234 1621 0.548031 TCCATTCATGCTGACCCTCC 59.452 55.000 0.00 0.00 0.00 4.30
1235 1622 2.019984 GTTCCATTCATGCTGACCCTC 58.980 52.381 0.00 0.00 0.00 4.30
1283 1826 2.356780 GGGTACCGTGCAGGCTAGT 61.357 63.158 5.65 0.00 46.52 2.57
1301 1844 4.583871 ACTGGGAGAAGTGCTAATGAAAG 58.416 43.478 0.00 0.00 0.00 2.62
1325 1868 7.824672 AGTGGTGAATTCAAATTTTGCAAAAA 58.175 26.923 27.10 11.87 0.00 1.94
1326 1869 7.388460 AGTGGTGAATTCAAATTTTGCAAAA 57.612 28.000 25.76 25.76 0.00 2.44
1335 1878 8.995220 CATGATTCAAAAGTGGTGAATTCAAAT 58.005 29.630 10.35 2.84 43.96 2.32
1343 1886 4.320421 CGAAGCATGATTCAAAAGTGGTGA 60.320 41.667 22.50 0.00 0.00 4.02
1380 1925 3.264897 ATCACATTCCTCGCGCGC 61.265 61.111 27.95 23.91 0.00 6.86
1381 1926 2.622629 CATCACATTCCTCGCGCG 59.377 61.111 26.76 26.76 0.00 6.86
1392 1937 6.491062 ACATGATTCAGAGAAAAACCATCACA 59.509 34.615 0.00 0.00 0.00 3.58
1480 2040 3.880608 TCCCCATCCACCACATATCATA 58.119 45.455 0.00 0.00 0.00 2.15
1486 2046 1.307647 GCTTCCCCATCCACCACAT 59.692 57.895 0.00 0.00 0.00 3.21
1520 2088 4.076394 GCCAGGTATAAACAGAACAACCA 58.924 43.478 0.00 0.00 0.00 3.67
1530 2098 4.523083 TCTGAACCATGCCAGGTATAAAC 58.477 43.478 0.00 0.00 42.25 2.01
1535 2103 0.911769 CCTCTGAACCATGCCAGGTA 59.088 55.000 0.00 0.00 42.25 3.08
1549 2117 0.033228 CGCCTTCTCCATAGCCTCTG 59.967 60.000 0.00 0.00 0.00 3.35
1574 2142 4.494484 CATCACTGACCAAATACGAGTGA 58.506 43.478 0.00 0.00 45.24 3.41
1592 2166 7.291885 ACATCTCTCCTAAATTCATCTCCATCA 59.708 37.037 0.00 0.00 0.00 3.07
1608 2182 1.203364 ACTCCCAACCACATCTCTCCT 60.203 52.381 0.00 0.00 0.00 3.69
1621 2195 1.354101 ATCACCGGTACAACTCCCAA 58.646 50.000 6.87 0.00 0.00 4.12
1638 2212 7.440856 GGATGACATAGAGAGGACAGAAAAATC 59.559 40.741 0.00 0.00 0.00 2.17
1660 2234 2.643551 ACCGATTAGTGCAAAGGGATG 58.356 47.619 0.00 0.00 0.00 3.51
1723 2297 4.010349 CCTCCTCGCCTTCTACAATTTTT 58.990 43.478 0.00 0.00 0.00 1.94
1751 2325 3.065786 CCACATAATGTTTGCTCGCTCAT 59.934 43.478 0.00 0.00 0.00 2.90
1759 2333 6.449635 TCTCAATACCCACATAATGTTTGC 57.550 37.500 0.00 0.00 0.00 3.68
1763 2337 7.072454 ACCTACATCTCAATACCCACATAATGT 59.928 37.037 0.00 0.00 0.00 2.71
1796 2371 7.653311 TCCATATGTCTCAATTCAGATTACACG 59.347 37.037 1.24 0.00 0.00 4.49
1823 2398 6.910433 TGCGCACATATGTACTATATATGTCG 59.090 38.462 5.66 19.45 45.26 4.35
1825 2400 7.772166 ACTGCGCACATATGTACTATATATGT 58.228 34.615 5.66 11.00 46.97 2.29
1863 2438 7.607991 GGTGGATCTAGAGAACAAGAATTCAAA 59.392 37.037 8.44 0.00 0.00 2.69
1897 2472 2.029728 GTCACAGACAAGCGTATGATGC 59.970 50.000 0.00 0.00 36.41 3.91
1903 2478 0.601558 GGAGGTCACAGACAAGCGTA 59.398 55.000 0.00 0.00 33.68 4.42
2091 2668 4.574674 TCTGGTGTATTTCCTTGAGCAT 57.425 40.909 0.00 0.00 0.00 3.79
2320 2906 1.065401 CAAACCAACTCACGTGTGCAT 59.935 47.619 16.51 3.00 0.00 3.96
2442 3029 9.173939 CACTCTGAAACACAAAAAGATCATTAC 57.826 33.333 0.00 0.00 0.00 1.89
2638 4079 4.039245 TCCGAGCATTTCTACCCTGAATAG 59.961 45.833 0.00 0.00 0.00 1.73
2713 4154 2.934553 GACTAAGCGCCTCGGTTTAATT 59.065 45.455 2.29 0.00 45.20 1.40
2714 4155 2.547826 GACTAAGCGCCTCGGTTTAAT 58.452 47.619 2.29 0.00 45.20 1.40
2716 4157 0.179156 CGACTAAGCGCCTCGGTTTA 60.179 55.000 2.29 0.00 45.20 2.01
2719 4160 2.061182 GATCGACTAAGCGCCTCGGT 62.061 60.000 2.29 1.07 40.00 4.69
2720 4161 1.370657 GATCGACTAAGCGCCTCGG 60.371 63.158 2.29 0.00 0.00 4.63
2721 4162 0.039978 ATGATCGACTAAGCGCCTCG 60.040 55.000 2.29 5.87 0.00 4.63
2722 4163 1.692296 GATGATCGACTAAGCGCCTC 58.308 55.000 2.29 0.00 0.00 4.70
2723 4164 0.039978 CGATGATCGACTAAGCGCCT 60.040 55.000 9.62 0.00 43.74 5.52
2724 4165 1.004277 CCGATGATCGACTAAGCGCC 61.004 60.000 17.52 0.00 43.74 6.53
2725 4166 0.040336 TCCGATGATCGACTAAGCGC 60.040 55.000 17.52 0.00 43.74 5.92
2726 4167 1.531578 TCTCCGATGATCGACTAAGCG 59.468 52.381 17.52 0.00 43.74 4.68
2727 4168 3.627732 TTCTCCGATGATCGACTAAGC 57.372 47.619 17.52 0.00 43.74 3.09
2728 4169 4.921547 TGTTTCTCCGATGATCGACTAAG 58.078 43.478 17.52 8.10 43.74 2.18
2729 4170 4.976224 TGTTTCTCCGATGATCGACTAA 57.024 40.909 17.52 4.12 43.74 2.24
2730 4171 4.733815 GCTTGTTTCTCCGATGATCGACTA 60.734 45.833 17.52 2.20 43.74 2.59
2731 4172 3.775202 CTTGTTTCTCCGATGATCGACT 58.225 45.455 17.52 0.00 43.74 4.18
2732 4173 2.282820 GCTTGTTTCTCCGATGATCGAC 59.717 50.000 17.52 6.54 43.74 4.20
2733 4174 2.094234 TGCTTGTTTCTCCGATGATCGA 60.094 45.455 17.52 1.63 43.74 3.59
2734 4175 2.270923 TGCTTGTTTCTCCGATGATCG 58.729 47.619 8.05 8.05 40.07 3.69
2735 4176 4.333649 TGATTGCTTGTTTCTCCGATGATC 59.666 41.667 0.00 0.00 0.00 2.92
2736 4177 4.264253 TGATTGCTTGTTTCTCCGATGAT 58.736 39.130 0.00 0.00 0.00 2.45
2737 4178 3.673902 TGATTGCTTGTTTCTCCGATGA 58.326 40.909 0.00 0.00 0.00 2.92
2738 4179 4.627611 ATGATTGCTTGTTTCTCCGATG 57.372 40.909 0.00 0.00 0.00 3.84
2739 4180 6.115446 TCTTATGATTGCTTGTTTCTCCGAT 58.885 36.000 0.00 0.00 0.00 4.18
2740 4181 5.487433 TCTTATGATTGCTTGTTTCTCCGA 58.513 37.500 0.00 0.00 0.00 4.55
2741 4182 5.220739 CCTCTTATGATTGCTTGTTTCTCCG 60.221 44.000 0.00 0.00 0.00 4.63
2742 4183 5.449725 GCCTCTTATGATTGCTTGTTTCTCC 60.450 44.000 0.00 0.00 0.00 3.71
2743 4184 5.124457 TGCCTCTTATGATTGCTTGTTTCTC 59.876 40.000 0.00 0.00 0.00 2.87
2744 4185 5.012239 TGCCTCTTATGATTGCTTGTTTCT 58.988 37.500 0.00 0.00 0.00 2.52
2745 4186 5.098211 GTGCCTCTTATGATTGCTTGTTTC 58.902 41.667 0.00 0.00 0.00 2.78
2746 4187 4.379813 CGTGCCTCTTATGATTGCTTGTTT 60.380 41.667 0.00 0.00 0.00 2.83
2747 4188 3.127548 CGTGCCTCTTATGATTGCTTGTT 59.872 43.478 0.00 0.00 0.00 2.83
2748 4189 2.679837 CGTGCCTCTTATGATTGCTTGT 59.320 45.455 0.00 0.00 0.00 3.16
2749 4190 2.938451 TCGTGCCTCTTATGATTGCTTG 59.062 45.455 0.00 0.00 0.00 4.01
2750 4191 2.939103 GTCGTGCCTCTTATGATTGCTT 59.061 45.455 0.00 0.00 0.00 3.91
2751 4192 2.093500 TGTCGTGCCTCTTATGATTGCT 60.093 45.455 0.00 0.00 0.00 3.91
2752 4193 2.030946 GTGTCGTGCCTCTTATGATTGC 59.969 50.000 0.00 0.00 0.00 3.56
2753 4194 2.609459 GGTGTCGTGCCTCTTATGATTG 59.391 50.000 0.00 0.00 0.00 2.67
2754 4195 2.738643 CGGTGTCGTGCCTCTTATGATT 60.739 50.000 0.00 0.00 0.00 2.57
2755 4196 1.202417 CGGTGTCGTGCCTCTTATGAT 60.202 52.381 0.00 0.00 0.00 2.45
2756 4197 0.172578 CGGTGTCGTGCCTCTTATGA 59.827 55.000 0.00 0.00 0.00 2.15
2757 4198 0.172578 TCGGTGTCGTGCCTCTTATG 59.827 55.000 0.00 0.00 37.69 1.90
2758 4199 0.456221 CTCGGTGTCGTGCCTCTTAT 59.544 55.000 0.00 0.00 37.69 1.73
2759 4200 0.607217 TCTCGGTGTCGTGCCTCTTA 60.607 55.000 0.00 0.00 37.69 2.10
2760 4201 1.251527 ATCTCGGTGTCGTGCCTCTT 61.252 55.000 0.00 0.00 37.69 2.85
2761 4202 1.251527 AATCTCGGTGTCGTGCCTCT 61.252 55.000 0.00 0.00 37.69 3.69
2762 4203 1.215647 AATCTCGGTGTCGTGCCTC 59.784 57.895 0.00 0.00 37.69 4.70
2763 4204 3.377656 AATCTCGGTGTCGTGCCT 58.622 55.556 0.00 0.00 37.69 4.75


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

AutoCloner maintained by Alex Coulton.