Multiple sequence alignment - TraesCS3B01G469500

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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 TraesCS3B01G469500 chr3B 100.000 2255 0 0 1 2255 716303434 716301180 0.000000e+00 4165.0
1 TraesCS3B01G469500 chr3B 100.000 35 0 0 2146 2180 716301231 716301197 5.200000e-07 65.8
2 TraesCS3B01G469500 chr3B 100.000 35 0 0 2204 2238 716301289 716301255 5.200000e-07 65.8
3 TraesCS3B01G469500 chr3D 94.002 1834 55 22 438 2255 540158537 540156743 0.000000e+00 2726.0
4 TraesCS3B01G469500 chr3D 100.000 35 0 0 2204 2238 540156852 540156818 5.200000e-07 65.8
5 TraesCS3B01G469500 chr3A 92.432 925 45 10 692 1599 675290351 675289435 0.000000e+00 1297.0
6 TraesCS3B01G469500 chr3A 93.578 218 6 4 438 655 675290564 675290355 3.610000e-83 318.0
7 TraesCS3B01G469500 chr3A 84.946 279 35 4 1933 2206 675266906 675266630 2.210000e-70 276.0
8 TraesCS3B01G469500 chr3A 88.983 118 10 3 1583 1698 675233284 675233168 2.330000e-30 143.0
9 TraesCS3B01G469500 chr3A 88.983 118 10 3 1583 1698 675279234 675279118 2.330000e-30 143.0
10 TraesCS3B01G469500 chr3A 88.136 118 11 3 1583 1698 675267060 675266944 1.090000e-28 137.0
11 TraesCS3B01G469500 chr3A 87.288 118 12 3 1583 1698 675245694 675245578 5.050000e-27 132.0
12 TraesCS3B01G469500 chr1D 90.076 393 28 5 1 392 409574754 409574372 1.200000e-137 499.0
13 TraesCS3B01G469500 chr4D 88.917 397 34 6 1 392 256577962 256577571 4.360000e-132 481.0
14 TraesCS3B01G469500 chr4D 88.804 393 38 4 1 392 257935512 257935125 5.630000e-131 477.0
15 TraesCS3B01G469500 chr4D 89.496 238 21 4 1699 1933 51076340 51076104 4.710000e-77 298.0
16 TraesCS3B01G469500 chr4D 80.676 207 38 2 1050 1255 446749516 446749311 2.320000e-35 159.0
17 TraesCS3B01G469500 chr1B 88.684 380 37 3 16 392 105202573 105202197 2.040000e-125 459.0
18 TraesCS3B01G469500 chr1B 87.295 244 24 3 1696 1933 433423058 433422816 2.850000e-69 272.0
19 TraesCS3B01G469500 chr5D 87.277 393 47 3 1 393 394109126 394108737 1.590000e-121 446.0
20 TraesCS3B01G469500 chr5D 86.831 243 31 1 1692 1933 44622974 44623216 1.030000e-68 270.0
21 TraesCS3B01G469500 chr5D 87.083 240 23 7 1697 1933 494082937 494083171 4.780000e-67 265.0
22 TraesCS3B01G469500 chr1A 85.496 393 44 10 7 393 462138264 462137879 4.510000e-107 398.0
23 TraesCS3B01G469500 chr1A 83.459 399 56 8 1 393 351589047 351588653 1.650000e-96 363.0
24 TraesCS3B01G469500 chr1A 84.739 249 25 4 594 836 186369621 186369380 1.040000e-58 237.0
25 TraesCS3B01G469500 chr5A 84.596 396 50 9 1 390 290468008 290467618 1.260000e-102 383.0
26 TraesCS3B01G469500 chr5A 87.764 237 26 3 1702 1936 663303783 663304018 7.930000e-70 274.0
27 TraesCS3B01G469500 chr2A 84.131 397 55 7 1 396 131698390 131698779 5.880000e-101 377.0
28 TraesCS3B01G469500 chr7D 88.085 235 28 0 1699 1933 339118579 339118813 1.710000e-71 279.0
29 TraesCS3B01G469500 chr7D 88.983 118 12 1 1419 1536 61751714 61751598 6.490000e-31 145.0
30 TraesCS3B01G469500 chr2D 87.395 238 27 3 1697 1933 649755389 649755154 1.030000e-68 270.0
31 TraesCS3B01G469500 chr2D 85.950 242 30 4 1697 1936 641623736 641623497 2.870000e-64 255.0
32 TraesCS3B01G469500 chr6D 85.380 171 17 2 1101 1263 418176462 418176632 1.070000e-38 171.0
33 TraesCS3B01G469500 chr4B 81.159 207 37 2 1050 1255 558753848 558753643 4.980000e-37 165.0
34 TraesCS3B01G469500 chr4A 80.193 207 39 2 1050 1255 21025198 21025403 1.080000e-33 154.0


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 TraesCS3B01G469500 chr3B 716301180 716303434 2254 True 1432.2 4165 100.000 1 2255 3 chr3B.!!$R1 2254
1 TraesCS3B01G469500 chr3D 540156743 540158537 1794 True 1395.9 2726 97.001 438 2255 2 chr3D.!!$R1 1817
2 TraesCS3B01G469500 chr3A 675289435 675290564 1129 True 807.5 1297 93.005 438 1599 2 chr3A.!!$R5 1161

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
281 282 0.036952 AGGTCAGAGTTGGATGCACG 60.037 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 1946 0.884704 CAGTGGCCCGATAAATCCCG 60.885 60.0 0.0 0.0 0.0 5.14 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
17 18 2.125512 ATGACGGCGCTCTGGAAC 60.126 61.111 6.90 0.00 0.00 3.62
18 19 2.942796 ATGACGGCGCTCTGGAACA 61.943 57.895 6.90 0.00 0.00 3.18
19 20 3.112709 GACGGCGCTCTGGAACAC 61.113 66.667 6.90 0.00 0.00 3.32
25 26 2.665185 GCTCTGGAACACGGCGTT 60.665 61.111 11.19 0.00 41.86 4.84
26 27 2.251642 GCTCTGGAACACGGCGTTT 61.252 57.895 11.19 8.59 38.19 3.60
27 28 1.569493 CTCTGGAACACGGCGTTTG 59.431 57.895 11.19 2.00 38.19 2.93
28 29 2.051345 CTGGAACACGGCGTTTGC 60.051 61.111 11.19 14.04 38.19 3.68
58 59 4.492160 GGCACCGACGCTCATCGA 62.492 66.667 3.74 0.00 45.13 3.59
59 60 3.248171 GCACCGACGCTCATCGAC 61.248 66.667 3.74 0.00 45.13 4.20
60 61 2.579787 CACCGACGCTCATCGACC 60.580 66.667 3.74 0.00 45.13 4.79
61 62 2.750637 ACCGACGCTCATCGACCT 60.751 61.111 3.74 0.00 45.13 3.85
62 63 2.024871 CCGACGCTCATCGACCTC 59.975 66.667 3.74 0.00 45.13 3.85
63 64 2.761195 CCGACGCTCATCGACCTCA 61.761 63.158 3.74 0.00 45.13 3.86
64 65 1.583967 CGACGCTCATCGACCTCAC 60.584 63.158 0.00 0.00 45.13 3.51
65 66 1.583967 GACGCTCATCGACCTCACG 60.584 63.158 0.00 0.00 41.67 4.35
66 67 2.278206 CGCTCATCGACCTCACGG 60.278 66.667 0.00 0.00 41.67 4.94
67 68 2.761195 CGCTCATCGACCTCACGGA 61.761 63.158 0.00 0.00 41.67 4.69
68 69 1.226717 GCTCATCGACCTCACGGAC 60.227 63.158 0.00 0.00 0.00 4.79
69 70 1.433879 CTCATCGACCTCACGGACC 59.566 63.158 0.00 0.00 0.00 4.46
70 71 2.005960 CTCATCGACCTCACGGACCC 62.006 65.000 0.00 0.00 0.00 4.46
71 72 2.758737 ATCGACCTCACGGACCCC 60.759 66.667 0.00 0.00 0.00 4.95
98 99 4.549516 GGCGACGACGTCTAGGGC 62.550 72.222 24.36 19.20 41.20 5.19
99 100 3.807538 GCGACGACGTCTAGGGCA 61.808 66.667 24.36 0.00 41.98 5.36
100 101 2.403987 CGACGACGTCTAGGGCAG 59.596 66.667 24.36 4.53 34.56 4.85
101 102 2.102553 GACGACGTCTAGGGCAGC 59.897 66.667 20.52 0.00 0.00 5.25
102 103 3.412879 GACGACGTCTAGGGCAGCC 62.413 68.421 20.52 1.26 0.00 4.85
103 104 4.208686 CGACGTCTAGGGCAGCCC 62.209 72.222 24.90 24.90 45.90 5.19
118 119 4.446413 CCCGCCGCCTCGTAGTTT 62.446 66.667 0.00 0.00 0.00 2.66
119 120 2.491152 CCGCCGCCTCGTAGTTTA 59.509 61.111 0.00 0.00 0.00 2.01
120 121 1.588139 CCGCCGCCTCGTAGTTTAG 60.588 63.158 0.00 0.00 0.00 1.85
121 122 1.138247 CGCCGCCTCGTAGTTTAGT 59.862 57.895 0.00 0.00 0.00 2.24
122 123 0.378257 CGCCGCCTCGTAGTTTAGTA 59.622 55.000 0.00 0.00 0.00 1.82
123 124 1.596464 CGCCGCCTCGTAGTTTAGTAG 60.596 57.143 0.00 0.00 0.00 2.57
124 125 1.268948 GCCGCCTCGTAGTTTAGTAGG 60.269 57.143 0.00 0.00 0.00 3.18
150 151 4.981389 TTTTTAATGCAAATGTGGACGC 57.019 36.364 0.00 0.00 0.00 5.19
151 152 2.254918 TTAATGCAAATGTGGACGCG 57.745 45.000 3.53 3.53 0.00 6.01
152 153 1.160989 TAATGCAAATGTGGACGCGT 58.839 45.000 13.85 13.85 0.00 6.01
153 154 0.387112 AATGCAAATGTGGACGCGTG 60.387 50.000 20.70 0.00 0.00 5.34
154 155 2.126888 GCAAATGTGGACGCGTGG 60.127 61.111 20.70 0.00 0.00 4.94
155 156 2.612567 GCAAATGTGGACGCGTGGA 61.613 57.895 20.70 0.00 0.00 4.02
156 157 1.206578 CAAATGTGGACGCGTGGAC 59.793 57.895 20.70 13.83 0.00 4.02
157 158 1.070786 AAATGTGGACGCGTGGACT 59.929 52.632 20.70 0.00 0.00 3.85
158 159 1.227999 AAATGTGGACGCGTGGACTG 61.228 55.000 20.70 0.00 0.00 3.51
159 160 2.377628 AATGTGGACGCGTGGACTGT 62.378 55.000 20.70 3.23 0.00 3.55
160 161 2.733593 GTGGACGCGTGGACTGTC 60.734 66.667 20.70 0.00 0.00 3.51
161 162 4.337060 TGGACGCGTGGACTGTCG 62.337 66.667 20.70 0.00 33.45 4.35
183 184 2.046700 CCTTCGTGGCCGGCTTTA 60.047 61.111 28.56 10.66 33.95 1.85
184 185 1.673009 CCTTCGTGGCCGGCTTTAA 60.673 57.895 28.56 14.43 33.95 1.52
185 186 1.029947 CCTTCGTGGCCGGCTTTAAT 61.030 55.000 28.56 0.00 33.95 1.40
186 187 0.098728 CTTCGTGGCCGGCTTTAATG 59.901 55.000 28.56 14.81 33.95 1.90
187 188 0.606944 TTCGTGGCCGGCTTTAATGT 60.607 50.000 28.56 0.00 33.95 2.71
188 189 0.606944 TCGTGGCCGGCTTTAATGTT 60.607 50.000 28.56 0.00 33.95 2.71
189 190 0.242555 CGTGGCCGGCTTTAATGTTT 59.757 50.000 28.56 0.00 0.00 2.83
190 191 1.469308 CGTGGCCGGCTTTAATGTTTA 59.531 47.619 28.56 0.00 0.00 2.01
191 192 2.095161 CGTGGCCGGCTTTAATGTTTAA 60.095 45.455 28.56 0.00 0.00 1.52
192 193 3.428316 CGTGGCCGGCTTTAATGTTTAAT 60.428 43.478 28.56 0.00 0.00 1.40
193 194 4.500127 GTGGCCGGCTTTAATGTTTAATT 58.500 39.130 28.56 0.00 0.00 1.40
194 195 5.652518 GTGGCCGGCTTTAATGTTTAATTA 58.347 37.500 28.56 0.00 0.00 1.40
195 196 6.100668 GTGGCCGGCTTTAATGTTTAATTAA 58.899 36.000 28.56 0.00 0.00 1.40
196 197 6.759356 GTGGCCGGCTTTAATGTTTAATTAAT 59.241 34.615 28.56 0.00 0.00 1.40
197 198 6.758886 TGGCCGGCTTTAATGTTTAATTAATG 59.241 34.615 28.56 0.00 0.00 1.90
198 199 6.292649 GGCCGGCTTTAATGTTTAATTAATGC 60.293 38.462 28.56 15.16 40.69 3.56
199 200 6.478673 GCCGGCTTTAATGTTTAATTAATGCT 59.521 34.615 22.15 0.00 40.95 3.79
200 201 7.516627 GCCGGCTTTAATGTTTAATTAATGCTG 60.517 37.037 22.15 20.13 43.34 4.41
201 202 7.336975 CGGCTTTAATGTTTAATTAATGCTGC 58.663 34.615 19.49 0.00 40.63 5.25
202 203 7.222611 CGGCTTTAATGTTTAATTAATGCTGCT 59.777 33.333 19.49 0.00 40.63 4.24
203 204 8.882736 GGCTTTAATGTTTAATTAATGCTGCTT 58.117 29.630 19.49 0.00 40.95 3.91
250 251 3.669354 AAAAATTTTGGCGCCGTCA 57.331 42.105 23.90 7.98 0.00 4.35
251 252 1.941325 AAAAATTTTGGCGCCGTCAA 58.059 40.000 23.90 14.67 0.00 3.18
252 253 1.941325 AAAATTTTGGCGCCGTCAAA 58.059 40.000 23.90 20.18 35.24 2.69
255 256 2.892305 TTTTGGCGCCGTCAAAATG 58.108 47.368 24.06 0.00 41.28 2.32
256 257 0.598680 TTTTGGCGCCGTCAAAATGG 60.599 50.000 24.06 0.00 41.28 3.16
257 258 2.427540 TTTGGCGCCGTCAAAATGGG 62.428 55.000 23.90 0.00 34.07 4.00
258 259 3.370231 GGCGCCGTCAAAATGGGT 61.370 61.111 12.58 0.00 31.56 4.51
259 260 2.178273 GCGCCGTCAAAATGGGTC 59.822 61.111 0.00 0.00 31.56 4.46
260 261 2.332654 GCGCCGTCAAAATGGGTCT 61.333 57.895 0.00 0.00 31.56 3.85
261 262 1.794222 CGCCGTCAAAATGGGTCTC 59.206 57.895 0.00 0.00 31.56 3.36
262 263 0.953471 CGCCGTCAAAATGGGTCTCA 60.953 55.000 0.00 0.00 31.56 3.27
263 264 0.804989 GCCGTCAAAATGGGTCTCAG 59.195 55.000 0.00 0.00 31.56 3.35
264 265 1.453155 CCGTCAAAATGGGTCTCAGG 58.547 55.000 0.00 0.00 0.00 3.86
265 266 1.271379 CCGTCAAAATGGGTCTCAGGT 60.271 52.381 0.00 0.00 0.00 4.00
266 267 2.076863 CGTCAAAATGGGTCTCAGGTC 58.923 52.381 0.00 0.00 0.00 3.85
267 268 2.549992 CGTCAAAATGGGTCTCAGGTCA 60.550 50.000 0.00 0.00 0.00 4.02
268 269 3.077359 GTCAAAATGGGTCTCAGGTCAG 58.923 50.000 0.00 0.00 0.00 3.51
269 270 2.978978 TCAAAATGGGTCTCAGGTCAGA 59.021 45.455 0.00 0.00 0.00 3.27
270 271 3.008375 TCAAAATGGGTCTCAGGTCAGAG 59.992 47.826 0.00 0.00 36.97 3.35
271 272 2.334006 AATGGGTCTCAGGTCAGAGT 57.666 50.000 0.00 0.00 36.97 3.24
272 273 2.334006 ATGGGTCTCAGGTCAGAGTT 57.666 50.000 0.00 0.00 36.97 3.01
273 274 1.342074 TGGGTCTCAGGTCAGAGTTG 58.658 55.000 0.00 0.00 36.97 3.16
274 275 0.610687 GGGTCTCAGGTCAGAGTTGG 59.389 60.000 0.00 0.00 36.97 3.77
275 276 1.633774 GGTCTCAGGTCAGAGTTGGA 58.366 55.000 0.00 0.00 36.97 3.53
276 277 2.183679 GGTCTCAGGTCAGAGTTGGAT 58.816 52.381 0.00 0.00 36.97 3.41
277 278 2.093764 GGTCTCAGGTCAGAGTTGGATG 60.094 54.545 0.00 0.00 36.97 3.51
278 279 1.552337 TCTCAGGTCAGAGTTGGATGC 59.448 52.381 0.00 0.00 36.97 3.91
279 280 1.277273 CTCAGGTCAGAGTTGGATGCA 59.723 52.381 0.00 0.00 0.00 3.96
280 281 1.002430 TCAGGTCAGAGTTGGATGCAC 59.998 52.381 0.00 0.00 0.00 4.57
281 282 0.036952 AGGTCAGAGTTGGATGCACG 60.037 55.000 0.00 0.00 0.00 5.34
282 283 1.639298 GGTCAGAGTTGGATGCACGC 61.639 60.000 0.00 0.00 0.00 5.34
283 284 1.737735 TCAGAGTTGGATGCACGCG 60.738 57.895 3.53 3.53 0.00 6.01
284 285 3.121030 AGAGTTGGATGCACGCGC 61.121 61.111 5.73 0.00 39.24 6.86
285 286 4.166011 GAGTTGGATGCACGCGCC 62.166 66.667 5.73 0.00 37.32 6.53
295 296 4.459331 CACGCGCCGACCCAAATG 62.459 66.667 5.73 0.00 0.00 2.32
297 298 4.459331 CGCGCCGACCCAAATGTG 62.459 66.667 0.00 0.00 0.00 3.21
298 299 3.053291 GCGCCGACCCAAATGTGA 61.053 61.111 0.00 0.00 0.00 3.58
299 300 2.622011 GCGCCGACCCAAATGTGAA 61.622 57.895 0.00 0.00 0.00 3.18
300 301 1.953017 CGCCGACCCAAATGTGAAA 59.047 52.632 0.00 0.00 0.00 2.69
301 302 0.109781 CGCCGACCCAAATGTGAAAG 60.110 55.000 0.00 0.00 0.00 2.62
302 303 0.388520 GCCGACCCAAATGTGAAAGC 60.389 55.000 0.00 0.00 0.00 3.51
303 304 0.109781 CCGACCCAAATGTGAAAGCG 60.110 55.000 0.00 0.00 0.00 4.68
304 305 0.109781 CGACCCAAATGTGAAAGCGG 60.110 55.000 0.00 0.00 0.00 5.52
305 306 0.243636 GACCCAAATGTGAAAGCGGG 59.756 55.000 0.00 0.00 39.72 6.13
306 307 1.079888 CCCAAATGTGAAAGCGGGC 60.080 57.895 0.00 0.00 0.00 6.13
307 308 1.664873 CCAAATGTGAAAGCGGGCA 59.335 52.632 0.00 0.00 0.00 5.36
308 309 0.247185 CCAAATGTGAAAGCGGGCAT 59.753 50.000 0.00 0.00 0.00 4.40
309 310 1.632422 CAAATGTGAAAGCGGGCATC 58.368 50.000 0.00 0.00 0.00 3.91
310 311 0.532115 AAATGTGAAAGCGGGCATCC 59.468 50.000 0.00 0.00 0.00 3.51
320 321 3.771160 GGGCATCCGTGTCCGTCT 61.771 66.667 0.00 0.00 40.95 4.18
321 322 2.509336 GGCATCCGTGTCCGTCTG 60.509 66.667 0.00 0.00 0.00 3.51
322 323 2.571757 GCATCCGTGTCCGTCTGA 59.428 61.111 0.00 0.00 0.00 3.27
323 324 1.805945 GCATCCGTGTCCGTCTGAC 60.806 63.158 0.00 0.00 44.72 3.51
324 325 1.153823 CATCCGTGTCCGTCTGACC 60.154 63.158 1.55 0.00 43.78 4.02
325 326 2.697761 ATCCGTGTCCGTCTGACCG 61.698 63.158 1.55 0.00 43.78 4.79
326 327 3.359523 CCGTGTCCGTCTGACCGA 61.360 66.667 1.55 0.00 43.78 4.69
327 328 2.126965 CGTGTCCGTCTGACCGAC 60.127 66.667 18.37 18.37 43.78 4.79
328 329 2.257676 GTGTCCGTCTGACCGACC 59.742 66.667 21.05 11.99 43.78 4.79
329 330 2.987547 TGTCCGTCTGACCGACCC 60.988 66.667 21.05 4.05 43.78 4.46
330 331 2.987547 GTCCGTCTGACCGACCCA 60.988 66.667 15.50 0.00 39.56 4.51
331 332 2.203523 TCCGTCTGACCGACCCAA 60.204 61.111 1.55 0.00 39.56 4.12
332 333 1.833492 TCCGTCTGACCGACCCAAA 60.833 57.895 1.55 0.00 39.56 3.28
333 334 1.666872 CCGTCTGACCGACCCAAAC 60.667 63.158 1.55 0.00 39.56 2.93
334 335 2.019951 CGTCTGACCGACCCAAACG 61.020 63.158 1.55 0.00 39.56 3.60
335 336 1.364901 GTCTGACCGACCCAAACGA 59.635 57.895 0.00 0.00 36.62 3.85
336 337 0.249573 GTCTGACCGACCCAAACGAA 60.250 55.000 0.00 0.00 36.62 3.85
337 338 0.682852 TCTGACCGACCCAAACGAAT 59.317 50.000 0.00 0.00 0.00 3.34
338 339 1.894466 TCTGACCGACCCAAACGAATA 59.106 47.619 0.00 0.00 0.00 1.75
339 340 2.299582 TCTGACCGACCCAAACGAATAA 59.700 45.455 0.00 0.00 0.00 1.40
340 341 3.068560 CTGACCGACCCAAACGAATAAA 58.931 45.455 0.00 0.00 0.00 1.40
341 342 3.474600 TGACCGACCCAAACGAATAAAA 58.525 40.909 0.00 0.00 0.00 1.52
342 343 3.881688 TGACCGACCCAAACGAATAAAAA 59.118 39.130 0.00 0.00 0.00 1.94
343 344 4.023878 TGACCGACCCAAACGAATAAAAAG 60.024 41.667 0.00 0.00 0.00 2.27
344 345 3.239254 CCGACCCAAACGAATAAAAAGC 58.761 45.455 0.00 0.00 0.00 3.51
345 346 3.304794 CCGACCCAAACGAATAAAAAGCA 60.305 43.478 0.00 0.00 0.00 3.91
346 347 3.911964 CGACCCAAACGAATAAAAAGCAG 59.088 43.478 0.00 0.00 0.00 4.24
347 348 4.319911 CGACCCAAACGAATAAAAAGCAGA 60.320 41.667 0.00 0.00 0.00 4.26
348 349 4.866921 ACCCAAACGAATAAAAAGCAGAC 58.133 39.130 0.00 0.00 0.00 3.51
349 350 3.911964 CCCAAACGAATAAAAAGCAGACG 59.088 43.478 0.00 0.00 0.00 4.18
350 351 4.319911 CCCAAACGAATAAAAAGCAGACGA 60.320 41.667 0.00 0.00 0.00 4.20
351 352 5.209240 CCAAACGAATAAAAAGCAGACGAA 58.791 37.500 0.00 0.00 0.00 3.85
352 353 5.683743 CCAAACGAATAAAAAGCAGACGAAA 59.316 36.000 0.00 0.00 0.00 3.46
353 354 6.362283 CCAAACGAATAAAAAGCAGACGAAAT 59.638 34.615 0.00 0.00 0.00 2.17
354 355 7.096230 CCAAACGAATAAAAAGCAGACGAAATT 60.096 33.333 0.00 0.00 0.00 1.82
355 356 8.897809 CAAACGAATAAAAAGCAGACGAAATTA 58.102 29.630 0.00 0.00 0.00 1.40
356 357 8.431020 AACGAATAAAAAGCAGACGAAATTAC 57.569 30.769 0.00 0.00 0.00 1.89
357 358 7.019418 ACGAATAAAAAGCAGACGAAATTACC 58.981 34.615 0.00 0.00 0.00 2.85
358 359 6.192137 CGAATAAAAAGCAGACGAAATTACCG 59.808 38.462 0.00 0.00 0.00 4.02
359 360 4.823790 AAAAAGCAGACGAAATTACCGT 57.176 36.364 5.63 5.63 43.56 4.83
367 368 2.753296 ACGAAATTACCGTCCGTTTGA 58.247 42.857 0.00 0.00 34.97 2.69
368 369 3.129871 ACGAAATTACCGTCCGTTTGAA 58.870 40.909 0.00 0.00 34.97 2.69
369 370 3.747529 ACGAAATTACCGTCCGTTTGAAT 59.252 39.130 0.00 0.00 34.97 2.57
370 371 4.143052 ACGAAATTACCGTCCGTTTGAATC 60.143 41.667 0.00 0.00 34.97 2.52
371 372 4.328667 GAAATTACCGTCCGTTTGAATCG 58.671 43.478 0.00 0.00 0.00 3.34
373 374 0.737019 TACCGTCCGTTTGAATCGGC 60.737 55.000 9.70 4.78 46.49 5.54
374 375 2.746803 CCGTCCGTTTGAATCGGCC 61.747 63.158 9.70 0.00 46.49 6.13
375 376 2.746803 CGTCCGTTTGAATCGGCCC 61.747 63.158 9.70 2.64 46.49 5.80
376 377 2.435234 TCCGTTTGAATCGGCCCG 60.435 61.111 9.70 0.00 46.49 6.13
377 378 2.744709 CCGTTTGAATCGGCCCGT 60.745 61.111 1.63 0.00 41.48 5.28
378 379 2.329614 CCGTTTGAATCGGCCCGTT 61.330 57.895 1.63 0.00 41.48 4.44
379 380 1.154301 CGTTTGAATCGGCCCGTTG 60.154 57.895 1.63 0.00 0.00 4.10
380 381 1.211709 GTTTGAATCGGCCCGTTGG 59.788 57.895 1.63 0.00 0.00 3.77
381 382 1.073373 TTTGAATCGGCCCGTTGGA 59.927 52.632 1.63 0.00 0.00 3.53
382 383 0.958382 TTTGAATCGGCCCGTTGGAG 60.958 55.000 1.63 0.00 0.00 3.86
383 384 2.119484 TTGAATCGGCCCGTTGGAGT 62.119 55.000 1.63 0.00 0.00 3.85
384 385 1.376812 GAATCGGCCCGTTGGAGTT 60.377 57.895 1.63 0.00 0.00 3.01
385 386 1.644786 GAATCGGCCCGTTGGAGTTG 61.645 60.000 1.63 0.00 0.00 3.16
388 389 3.056328 GGCCCGTTGGAGTTGCTC 61.056 66.667 0.00 0.00 0.00 4.26
389 390 2.032681 GCCCGTTGGAGTTGCTCT 59.967 61.111 0.00 0.00 0.00 4.09
390 391 1.295423 GCCCGTTGGAGTTGCTCTA 59.705 57.895 0.00 0.00 0.00 2.43
391 392 0.321298 GCCCGTTGGAGTTGCTCTAA 60.321 55.000 0.00 0.00 0.00 2.10
392 393 1.679032 GCCCGTTGGAGTTGCTCTAAT 60.679 52.381 0.00 0.00 33.81 1.73
393 394 2.419574 GCCCGTTGGAGTTGCTCTAATA 60.420 50.000 0.00 0.00 33.81 0.98
394 395 3.869065 CCCGTTGGAGTTGCTCTAATAA 58.131 45.455 0.00 0.00 33.81 1.40
395 396 4.451900 CCCGTTGGAGTTGCTCTAATAAT 58.548 43.478 0.00 0.00 33.81 1.28
396 397 4.273480 CCCGTTGGAGTTGCTCTAATAATG 59.727 45.833 0.00 0.00 33.81 1.90
397 398 4.876107 CCGTTGGAGTTGCTCTAATAATGT 59.124 41.667 0.00 0.00 33.81 2.71
398 399 5.006746 CCGTTGGAGTTGCTCTAATAATGTC 59.993 44.000 0.00 0.00 33.81 3.06
399 400 5.276395 CGTTGGAGTTGCTCTAATAATGTCG 60.276 44.000 0.00 0.00 33.81 4.35
400 401 5.339008 TGGAGTTGCTCTAATAATGTCGT 57.661 39.130 0.00 0.00 0.00 4.34
401 402 5.109210 TGGAGTTGCTCTAATAATGTCGTG 58.891 41.667 0.00 0.00 0.00 4.35
402 403 4.025647 GGAGTTGCTCTAATAATGTCGTGC 60.026 45.833 0.00 0.00 0.00 5.34
403 404 3.551890 AGTTGCTCTAATAATGTCGTGCG 59.448 43.478 0.00 0.00 0.00 5.34
404 405 1.858458 TGCTCTAATAATGTCGTGCGC 59.142 47.619 0.00 0.00 0.00 6.09
405 406 1.858458 GCTCTAATAATGTCGTGCGCA 59.142 47.619 5.66 5.66 0.00 6.09
406 407 2.284150 GCTCTAATAATGTCGTGCGCAA 59.716 45.455 14.00 0.00 0.00 4.85
407 408 3.242284 GCTCTAATAATGTCGTGCGCAAA 60.242 43.478 14.00 0.00 0.00 3.68
408 409 4.552767 GCTCTAATAATGTCGTGCGCAAAT 60.553 41.667 14.00 0.14 0.00 2.32
409 410 5.078153 TCTAATAATGTCGTGCGCAAATC 57.922 39.130 14.00 5.78 0.00 2.17
410 411 2.367399 ATAATGTCGTGCGCAAATCG 57.633 45.000 14.00 12.89 42.12 3.34
411 412 1.072391 TAATGTCGTGCGCAAATCGT 58.928 45.000 14.00 3.53 41.07 3.73
412 413 0.179225 AATGTCGTGCGCAAATCGTC 60.179 50.000 14.00 10.58 41.07 4.20
413 414 1.966493 ATGTCGTGCGCAAATCGTCC 61.966 55.000 14.00 7.94 41.07 4.79
414 415 3.474904 TCGTGCGCAAATCGTCCG 61.475 61.111 14.00 10.25 41.07 4.79
415 416 3.773630 CGTGCGCAAATCGTCCGT 61.774 61.111 14.00 0.00 41.07 4.69
416 417 2.095843 GTGCGCAAATCGTCCGTC 59.904 61.111 14.00 0.00 41.07 4.79
417 418 2.356433 TGCGCAAATCGTCCGTCA 60.356 55.556 8.16 0.00 41.07 4.35
418 419 1.956678 TGCGCAAATCGTCCGTCAA 60.957 52.632 8.16 0.00 41.07 3.18
419 420 1.509162 GCGCAAATCGTCCGTCAAC 60.509 57.895 0.30 0.00 41.07 3.18
420 421 1.856688 CGCAAATCGTCCGTCAACA 59.143 52.632 0.00 0.00 0.00 3.33
421 422 0.179250 CGCAAATCGTCCGTCAACAG 60.179 55.000 0.00 0.00 0.00 3.16
422 423 1.144969 GCAAATCGTCCGTCAACAGA 58.855 50.000 0.00 0.00 0.00 3.41
423 424 1.732259 GCAAATCGTCCGTCAACAGAT 59.268 47.619 0.00 0.00 0.00 2.90
424 425 2.222819 GCAAATCGTCCGTCAACAGATC 60.223 50.000 0.00 0.00 0.00 2.75
425 426 1.909376 AATCGTCCGTCAACAGATCG 58.091 50.000 0.00 0.00 0.00 3.69
426 427 0.809385 ATCGTCCGTCAACAGATCGT 59.191 50.000 0.00 0.00 0.00 3.73
427 428 0.109919 TCGTCCGTCAACAGATCGTG 60.110 55.000 0.00 0.00 0.00 4.35
428 429 0.386858 CGTCCGTCAACAGATCGTGT 60.387 55.000 0.00 0.00 43.24 4.49
429 430 1.060713 GTCCGTCAACAGATCGTGTG 58.939 55.000 0.00 0.00 40.26 3.82
430 431 0.671796 TCCGTCAACAGATCGTGTGT 59.328 50.000 0.00 0.00 40.26 3.72
431 432 0.784178 CCGTCAACAGATCGTGTGTG 59.216 55.000 0.00 1.92 40.26 3.82
432 433 0.161658 CGTCAACAGATCGTGTGTGC 59.838 55.000 0.00 0.00 40.26 4.57
433 434 1.217001 GTCAACAGATCGTGTGTGCA 58.783 50.000 0.00 0.00 40.26 4.57
434 435 1.193203 GTCAACAGATCGTGTGTGCAG 59.807 52.381 0.00 0.00 40.26 4.41
435 436 0.110509 CAACAGATCGTGTGTGCAGC 60.111 55.000 0.00 0.00 40.26 5.25
436 437 0.532640 AACAGATCGTGTGTGCAGCA 60.533 50.000 0.00 0.00 40.26 4.41
452 453 1.220749 GCAGTGTCGGGGCATCTAA 59.779 57.895 0.00 0.00 0.00 2.10
455 456 0.907704 AGTGTCGGGGCATCTAACCA 60.908 55.000 0.00 0.00 0.00 3.67
511 512 3.884091 TGTAAAAAGCCGCAGTAGGAAAA 59.116 39.130 0.00 0.00 0.00 2.29
516 517 0.952010 GCCGCAGTAGGAAAAACGGA 60.952 55.000 3.02 0.00 43.19 4.69
552 553 1.064832 AGAAGAGGGGAAAGCATCAGC 60.065 52.381 0.00 0.00 42.56 4.26
655 656 0.606401 CTTCCTCTTGCTTTCGGCCA 60.606 55.000 2.24 0.00 40.92 5.36
656 657 0.606401 TTCCTCTTGCTTTCGGCCAG 60.606 55.000 2.24 0.00 40.92 4.85
657 658 1.003355 CCTCTTGCTTTCGGCCAGA 60.003 57.895 2.24 0.00 39.88 3.86
658 659 0.606401 CCTCTTGCTTTCGGCCAGAA 60.606 55.000 2.24 4.57 41.27 3.02
659 660 0.519077 CTCTTGCTTTCGGCCAGAAC 59.481 55.000 2.24 0.00 41.27 3.01
660 661 0.108585 TCTTGCTTTCGGCCAGAACT 59.891 50.000 2.24 0.00 39.34 3.01
661 662 1.346395 TCTTGCTTTCGGCCAGAACTA 59.654 47.619 2.24 0.00 39.34 2.24
662 663 1.464997 CTTGCTTTCGGCCAGAACTAC 59.535 52.381 2.24 0.62 38.83 2.73
663 664 0.669318 TGCTTTCGGCCAGAACTACG 60.669 55.000 2.24 0.00 38.83 3.51
664 665 1.967597 GCTTTCGGCCAGAACTACGC 61.968 60.000 2.24 4.34 38.83 4.42
665 666 1.683790 CTTTCGGCCAGAACTACGCG 61.684 60.000 3.53 3.53 38.83 6.01
666 667 2.144833 TTTCGGCCAGAACTACGCGA 62.145 55.000 15.93 0.00 38.83 5.87
667 668 2.126228 CGGCCAGAACTACGCGAA 60.126 61.111 15.93 0.00 0.00 4.70
668 669 1.735198 CGGCCAGAACTACGCGAAA 60.735 57.895 15.93 0.00 0.00 3.46
669 670 1.683790 CGGCCAGAACTACGCGAAAG 61.684 60.000 15.93 12.73 0.00 2.62
670 671 0.389426 GGCCAGAACTACGCGAAAGA 60.389 55.000 15.93 0.00 0.00 2.52
671 672 0.992802 GCCAGAACTACGCGAAAGAG 59.007 55.000 15.93 6.84 0.00 2.85
672 673 0.992802 CCAGAACTACGCGAAAGAGC 59.007 55.000 15.93 7.46 0.00 4.09
727 728 1.673033 CCCTCTCACACTGTAAAGCCG 60.673 57.143 0.00 0.00 0.00 5.52
744 745 4.766088 GCAGAAAAGCGGCGGCAG 62.766 66.667 19.21 0.00 43.41 4.85
745 746 3.357079 CAGAAAAGCGGCGGCAGT 61.357 61.111 19.21 2.67 43.41 4.40
746 747 2.032634 CAGAAAAGCGGCGGCAGTA 61.033 57.895 19.21 0.00 43.41 2.74
936 953 1.032657 ACAGGTCGGATCAGAGGTCG 61.033 60.000 0.00 0.00 0.00 4.79
941 958 1.826054 CGGATCAGAGGTCGGAGCT 60.826 63.158 9.87 9.87 0.00 4.09
946 963 3.444805 AGAGGTCGGAGCTCGTGC 61.445 66.667 26.20 8.29 46.62 5.34
962 979 1.464687 CGTGCACAGTTTGATAGCTGC 60.465 52.381 18.64 0.00 36.26 5.25
994 1011 1.006805 GTGGCGAGAGGATCATCGG 60.007 63.158 13.79 6.71 37.82 4.18
1224 1241 2.176055 CTCACCCTCGTCGTCGTG 59.824 66.667 1.33 0.00 38.33 4.35
1352 1379 3.799755 GGCCGGCTGTAAACTGCG 61.800 66.667 28.56 2.52 41.04 5.18
1387 1414 7.170998 GCTGGCTGAAAACAGTACGTATATAAT 59.829 37.037 0.00 0.00 37.07 1.28
1508 1535 4.095483 CCAACTATTCACTGAATCAGCACC 59.905 45.833 10.62 0.00 34.37 5.01
1544 1571 7.930217 TCCTCTACTTCAGATTTTGTTTTGTG 58.070 34.615 0.00 0.00 31.13 3.33
1545 1572 7.556275 TCCTCTACTTCAGATTTTGTTTTGTGT 59.444 33.333 0.00 0.00 31.13 3.72
1562 1589 9.081997 TGTTTTGTGTTTTGTTAAAGAGCATAG 57.918 29.630 0.00 0.00 0.00 2.23
1590 1617 4.797275 GCTGCAATTTTGGAAAGTGCTACT 60.797 41.667 21.35 0.00 34.05 2.57
1736 1763 4.714851 CGAACGTTCGGATTTTAACCATT 58.285 39.130 36.53 0.00 46.30 3.16
1740 1767 3.851403 CGTTCGGATTTTAACCATTGCAG 59.149 43.478 0.00 0.00 0.00 4.41
1745 1772 3.442273 GGATTTTAACCATTGCAGTCCGA 59.558 43.478 0.00 0.00 0.00 4.55
1775 1802 1.082756 GGCAACTTGAGTTCACGCG 60.083 57.895 3.53 3.53 35.83 6.01
1879 1906 5.123186 CCTCGTGTCAACTAAAATTGCCATA 59.877 40.000 0.00 0.00 0.00 2.74
1919 1946 4.719040 ACATGCTTAAAATCCGAACGTTC 58.281 39.130 18.47 18.47 0.00 3.95
1930 1957 2.897658 CGAACGTTCGGGATTTATCG 57.102 50.000 36.53 13.23 46.30 2.92
1938 1965 0.884704 CGGGATTTATCGGGCCACTG 60.885 60.000 4.39 0.00 0.00 3.66
1976 2003 8.984891 TCACACATTTTAGCATTCTATTTTGG 57.015 30.769 0.00 0.00 0.00 3.28
2211 2238 7.270365 CAGTACGGCAAACACTTTATACATTTG 59.730 37.037 0.00 0.00 34.17 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.125512 GTTCCAGAGCGCCGTCAT 60.126 61.111 2.29 0.00 0.00 3.06
1 2 3.611674 TGTTCCAGAGCGCCGTCA 61.612 61.111 2.29 0.00 0.00 4.35
2 3 3.112709 GTGTTCCAGAGCGCCGTC 61.113 66.667 2.29 0.00 0.00 4.79
8 9 2.251642 AAACGCCGTGTTCCAGAGC 61.252 57.895 0.00 0.00 40.84 4.09
9 10 1.569493 CAAACGCCGTGTTCCAGAG 59.431 57.895 0.00 0.00 40.84 3.35
10 11 2.539338 GCAAACGCCGTGTTCCAGA 61.539 57.895 0.00 0.00 40.84 3.86
11 12 2.051345 GCAAACGCCGTGTTCCAG 60.051 61.111 0.00 0.00 40.84 3.86
12 13 3.587933 GGCAAACGCCGTGTTCCA 61.588 61.111 0.00 0.00 40.84 3.53
41 42 4.492160 TCGATGAGCGTCGGTGCC 62.492 66.667 0.00 0.00 41.74 5.01
42 43 3.248171 GTCGATGAGCGTCGGTGC 61.248 66.667 0.00 0.00 41.74 5.01
43 44 2.579787 GGTCGATGAGCGTCGGTG 60.580 66.667 0.00 0.00 41.74 4.94
44 45 2.750637 AGGTCGATGAGCGTCGGT 60.751 61.111 11.67 0.00 41.74 4.69
45 46 2.024871 GAGGTCGATGAGCGTCGG 59.975 66.667 11.67 0.00 41.74 4.79
46 47 1.583967 GTGAGGTCGATGAGCGTCG 60.584 63.158 5.78 5.78 42.74 5.12
47 48 1.583967 CGTGAGGTCGATGAGCGTC 60.584 63.158 0.00 0.00 41.80 5.19
48 49 2.485582 CGTGAGGTCGATGAGCGT 59.514 61.111 0.00 0.00 41.80 5.07
72 73 4.808238 GTCGTCGCCGTCGTCCTC 62.808 72.222 3.41 0.00 36.96 3.71
79 80 3.494336 CCTAGACGTCGTCGCCGT 61.494 66.667 19.11 0.00 42.06 5.68
80 81 4.233635 CCCTAGACGTCGTCGCCG 62.234 72.222 19.11 11.30 41.18 6.46
81 82 4.549516 GCCCTAGACGTCGTCGCC 62.550 72.222 19.11 4.24 41.18 5.54
82 83 3.736482 CTGCCCTAGACGTCGTCGC 62.736 68.421 19.11 16.21 41.18 5.19
83 84 2.403987 CTGCCCTAGACGTCGTCG 59.596 66.667 19.11 6.52 37.67 5.12
84 85 2.102553 GCTGCCCTAGACGTCGTC 59.897 66.667 17.70 17.70 0.00 4.20
85 86 3.450115 GGCTGCCCTAGACGTCGT 61.450 66.667 7.66 0.00 0.00 4.34
86 87 4.208686 GGGCTGCCCTAGACGTCG 62.209 72.222 30.42 0.00 41.34 5.12
87 88 4.208686 CGGGCTGCCCTAGACGTC 62.209 72.222 33.39 7.70 42.67 4.34
101 102 2.948840 CTAAACTACGAGGCGGCGGG 62.949 65.000 9.78 1.46 35.12 6.13
102 103 1.588139 CTAAACTACGAGGCGGCGG 60.588 63.158 9.78 1.88 35.12 6.13
103 104 0.378257 TACTAAACTACGAGGCGGCG 59.622 55.000 0.51 0.51 37.29 6.46
104 105 1.268948 CCTACTAAACTACGAGGCGGC 60.269 57.143 0.00 0.00 0.00 6.53
105 106 1.268948 GCCTACTAAACTACGAGGCGG 60.269 57.143 0.00 0.00 43.05 6.13
106 107 2.116787 GCCTACTAAACTACGAGGCG 57.883 55.000 0.00 0.00 43.05 5.52
129 130 3.426859 CGCGTCCACATTTGCATTAAAAA 59.573 39.130 0.00 0.00 0.00 1.94
130 131 2.983136 CGCGTCCACATTTGCATTAAAA 59.017 40.909 0.00 0.00 0.00 1.52
131 132 2.030717 ACGCGTCCACATTTGCATTAAA 60.031 40.909 5.58 0.00 0.00 1.52
132 133 1.537638 ACGCGTCCACATTTGCATTAA 59.462 42.857 5.58 0.00 0.00 1.40
133 134 1.135831 CACGCGTCCACATTTGCATTA 60.136 47.619 9.86 0.00 0.00 1.90
134 135 0.387112 CACGCGTCCACATTTGCATT 60.387 50.000 9.86 0.00 0.00 3.56
135 136 1.209898 CACGCGTCCACATTTGCAT 59.790 52.632 9.86 0.00 0.00 3.96
136 137 2.636462 CACGCGTCCACATTTGCA 59.364 55.556 9.86 0.00 0.00 4.08
137 138 2.126888 CCACGCGTCCACATTTGC 60.127 61.111 9.86 0.00 0.00 3.68
138 139 1.206578 GTCCACGCGTCCACATTTG 59.793 57.895 9.86 0.00 0.00 2.32
139 140 1.070786 AGTCCACGCGTCCACATTT 59.929 52.632 9.86 0.00 0.00 2.32
140 141 1.667830 CAGTCCACGCGTCCACATT 60.668 57.895 9.86 0.00 0.00 2.71
141 142 2.048222 CAGTCCACGCGTCCACAT 60.048 61.111 9.86 0.00 0.00 3.21
142 143 3.493830 GACAGTCCACGCGTCCACA 62.494 63.158 9.86 0.00 0.00 4.17
143 144 2.733593 GACAGTCCACGCGTCCAC 60.734 66.667 9.86 9.15 0.00 4.02
144 145 4.337060 CGACAGTCCACGCGTCCA 62.337 66.667 9.86 0.00 0.00 4.02
166 167 1.029947 ATTAAAGCCGGCCACGAAGG 61.030 55.000 26.15 0.00 44.60 3.46
167 168 0.098728 CATTAAAGCCGGCCACGAAG 59.901 55.000 26.15 5.89 44.60 3.79
168 169 0.606944 ACATTAAAGCCGGCCACGAA 60.607 50.000 26.15 13.16 44.60 3.85
169 170 0.606944 AACATTAAAGCCGGCCACGA 60.607 50.000 26.15 7.86 44.60 4.35
170 171 0.242555 AAACATTAAAGCCGGCCACG 59.757 50.000 26.15 8.66 40.55 4.94
171 172 3.579335 TTAAACATTAAAGCCGGCCAC 57.421 42.857 26.15 0.00 0.00 5.01
172 173 4.810191 AATTAAACATTAAAGCCGGCCA 57.190 36.364 26.15 5.71 0.00 5.36
173 174 6.292649 GCATTAATTAAACATTAAAGCCGGCC 60.293 38.462 26.15 5.07 34.20 6.13
174 175 6.478673 AGCATTAATTAAACATTAAAGCCGGC 59.521 34.615 21.89 21.89 38.31 6.13
175 176 7.516627 GCAGCATTAATTAAACATTAAAGCCGG 60.517 37.037 1.21 0.00 38.31 6.13
176 177 7.222611 AGCAGCATTAATTAAACATTAAAGCCG 59.777 33.333 1.21 3.37 38.31 5.52
177 178 8.424274 AGCAGCATTAATTAAACATTAAAGCC 57.576 30.769 1.21 0.00 38.31 4.35
232 233 1.941325 TTGACGGCGCCAAAATTTTT 58.059 40.000 28.98 0.00 0.00 1.94
233 234 1.941325 TTTGACGGCGCCAAAATTTT 58.059 40.000 28.98 0.00 31.36 1.82
234 235 1.941325 TTTTGACGGCGCCAAAATTT 58.059 40.000 26.30 1.82 38.23 1.82
235 236 1.797635 CATTTTGACGGCGCCAAAATT 59.202 42.857 33.88 21.14 46.18 1.82
236 237 3.904586 ATTTTGACGGCGCCAAAAT 57.095 42.105 31.83 31.83 44.30 1.82
237 238 0.598680 CCATTTTGACGGCGCCAAAA 60.599 50.000 30.52 30.52 44.44 2.44
238 239 1.006805 CCATTTTGACGGCGCCAAA 60.007 52.632 28.98 17.33 0.00 3.28
239 240 2.647875 CCATTTTGACGGCGCCAA 59.352 55.556 28.98 13.47 0.00 4.52
240 241 3.369400 CCCATTTTGACGGCGCCA 61.369 61.111 28.98 5.63 0.00 5.69
241 242 3.336715 GACCCATTTTGACGGCGCC 62.337 63.158 19.07 19.07 0.00 6.53
242 243 2.178273 GACCCATTTTGACGGCGC 59.822 61.111 6.90 0.00 0.00 6.53
243 244 0.953471 TGAGACCCATTTTGACGGCG 60.953 55.000 4.80 4.80 0.00 6.46
244 245 0.804989 CTGAGACCCATTTTGACGGC 59.195 55.000 0.00 0.00 0.00 5.68
245 246 1.271379 ACCTGAGACCCATTTTGACGG 60.271 52.381 0.00 0.00 0.00 4.79
246 247 2.076863 GACCTGAGACCCATTTTGACG 58.923 52.381 0.00 0.00 0.00 4.35
247 248 3.077359 CTGACCTGAGACCCATTTTGAC 58.923 50.000 0.00 0.00 0.00 3.18
248 249 2.978978 TCTGACCTGAGACCCATTTTGA 59.021 45.455 0.00 0.00 0.00 2.69
249 250 3.244700 ACTCTGACCTGAGACCCATTTTG 60.245 47.826 10.28 0.00 37.50 2.44
250 251 2.982488 ACTCTGACCTGAGACCCATTTT 59.018 45.455 10.28 0.00 37.50 1.82
251 252 2.625639 ACTCTGACCTGAGACCCATTT 58.374 47.619 10.28 0.00 37.50 2.32
252 253 2.304180 CAACTCTGACCTGAGACCCATT 59.696 50.000 10.28 0.00 37.50 3.16
253 254 1.905215 CAACTCTGACCTGAGACCCAT 59.095 52.381 10.28 0.00 37.50 4.00
254 255 1.342074 CAACTCTGACCTGAGACCCA 58.658 55.000 10.28 0.00 37.50 4.51
255 256 0.610687 CCAACTCTGACCTGAGACCC 59.389 60.000 10.28 0.00 37.50 4.46
256 257 1.633774 TCCAACTCTGACCTGAGACC 58.366 55.000 10.28 0.00 37.50 3.85
257 258 2.676463 GCATCCAACTCTGACCTGAGAC 60.676 54.545 10.28 0.00 37.50 3.36
258 259 1.552337 GCATCCAACTCTGACCTGAGA 59.448 52.381 10.28 0.00 37.50 3.27
259 260 1.277273 TGCATCCAACTCTGACCTGAG 59.723 52.381 2.89 2.89 39.78 3.35
260 261 1.002430 GTGCATCCAACTCTGACCTGA 59.998 52.381 0.00 0.00 0.00 3.86
261 262 1.446907 GTGCATCCAACTCTGACCTG 58.553 55.000 0.00 0.00 0.00 4.00
262 263 0.036952 CGTGCATCCAACTCTGACCT 60.037 55.000 0.00 0.00 0.00 3.85
263 264 1.639298 GCGTGCATCCAACTCTGACC 61.639 60.000 0.00 0.00 0.00 4.02
264 265 1.790387 GCGTGCATCCAACTCTGAC 59.210 57.895 0.00 0.00 0.00 3.51
265 266 1.737735 CGCGTGCATCCAACTCTGA 60.738 57.895 0.00 0.00 0.00 3.27
266 267 2.780643 CGCGTGCATCCAACTCTG 59.219 61.111 0.00 0.00 0.00 3.35
267 268 3.121030 GCGCGTGCATCCAACTCT 61.121 61.111 17.66 0.00 42.15 3.24
268 269 4.166011 GGCGCGTGCATCCAACTC 62.166 66.667 24.18 0.00 45.35 3.01
278 279 4.459331 CATTTGGGTCGGCGCGTG 62.459 66.667 8.43 0.00 0.00 5.34
280 281 4.459331 CACATTTGGGTCGGCGCG 62.459 66.667 0.00 0.00 0.00 6.86
281 282 2.136196 TTTCACATTTGGGTCGGCGC 62.136 55.000 0.00 0.00 0.00 6.53
282 283 0.109781 CTTTCACATTTGGGTCGGCG 60.110 55.000 0.00 0.00 0.00 6.46
283 284 0.388520 GCTTTCACATTTGGGTCGGC 60.389 55.000 0.00 0.00 0.00 5.54
284 285 0.109781 CGCTTTCACATTTGGGTCGG 60.110 55.000 0.00 0.00 0.00 4.79
285 286 0.109781 CCGCTTTCACATTTGGGTCG 60.110 55.000 0.00 0.00 0.00 4.79
286 287 0.243636 CCCGCTTTCACATTTGGGTC 59.756 55.000 0.00 0.00 31.82 4.46
287 288 1.815817 GCCCGCTTTCACATTTGGGT 61.816 55.000 0.00 0.00 38.93 4.51
288 289 1.079888 GCCCGCTTTCACATTTGGG 60.080 57.895 0.00 0.00 39.72 4.12
289 290 0.247185 ATGCCCGCTTTCACATTTGG 59.753 50.000 0.00 0.00 0.00 3.28
290 291 1.632422 GATGCCCGCTTTCACATTTG 58.368 50.000 0.00 0.00 0.00 2.32
291 292 0.532115 GGATGCCCGCTTTCACATTT 59.468 50.000 0.00 0.00 0.00 2.32
292 293 2.192605 GGATGCCCGCTTTCACATT 58.807 52.632 0.00 0.00 0.00 2.71
293 294 3.924507 GGATGCCCGCTTTCACAT 58.075 55.556 0.00 0.00 0.00 3.21
303 304 3.771160 AGACGGACACGGATGCCC 61.771 66.667 0.00 0.00 46.48 5.36
304 305 2.509336 CAGACGGACACGGATGCC 60.509 66.667 0.00 0.00 46.48 4.40
305 306 1.805945 GTCAGACGGACACGGATGC 60.806 63.158 0.42 0.00 46.19 3.91
306 307 4.478195 GTCAGACGGACACGGATG 57.522 61.111 0.42 0.00 46.19 3.51
318 319 0.682852 ATTCGTTTGGGTCGGTCAGA 59.317 50.000 0.00 0.00 0.00 3.27
319 320 2.373540 TATTCGTTTGGGTCGGTCAG 57.626 50.000 0.00 0.00 0.00 3.51
320 321 2.835580 TTATTCGTTTGGGTCGGTCA 57.164 45.000 0.00 0.00 0.00 4.02
321 322 4.469552 CTTTTTATTCGTTTGGGTCGGTC 58.530 43.478 0.00 0.00 0.00 4.79
322 323 3.304861 GCTTTTTATTCGTTTGGGTCGGT 60.305 43.478 0.00 0.00 0.00 4.69
323 324 3.239254 GCTTTTTATTCGTTTGGGTCGG 58.761 45.455 0.00 0.00 0.00 4.79
324 325 3.891324 TGCTTTTTATTCGTTTGGGTCG 58.109 40.909 0.00 0.00 0.00 4.79
325 326 4.915667 GTCTGCTTTTTATTCGTTTGGGTC 59.084 41.667 0.00 0.00 0.00 4.46
326 327 4.555906 CGTCTGCTTTTTATTCGTTTGGGT 60.556 41.667 0.00 0.00 0.00 4.51
327 328 3.911964 CGTCTGCTTTTTATTCGTTTGGG 59.088 43.478 0.00 0.00 0.00 4.12
328 329 4.778904 TCGTCTGCTTTTTATTCGTTTGG 58.221 39.130 0.00 0.00 0.00 3.28
329 330 6.726035 TTTCGTCTGCTTTTTATTCGTTTG 57.274 33.333 0.00 0.00 0.00 2.93
330 331 7.924103 AATTTCGTCTGCTTTTTATTCGTTT 57.076 28.000 0.00 0.00 0.00 3.60
331 332 7.536281 GGTAATTTCGTCTGCTTTTTATTCGTT 59.464 33.333 0.00 0.00 0.00 3.85
332 333 7.019418 GGTAATTTCGTCTGCTTTTTATTCGT 58.981 34.615 0.00 0.00 0.00 3.85
333 334 6.192137 CGGTAATTTCGTCTGCTTTTTATTCG 59.808 38.462 0.00 0.00 0.00 3.34
334 335 7.019418 ACGGTAATTTCGTCTGCTTTTTATTC 58.981 34.615 1.45 0.00 35.87 1.75
335 336 6.905578 ACGGTAATTTCGTCTGCTTTTTATT 58.094 32.000 1.45 0.00 35.87 1.40
336 337 6.490566 ACGGTAATTTCGTCTGCTTTTTAT 57.509 33.333 1.45 0.00 35.87 1.40
337 338 5.927954 ACGGTAATTTCGTCTGCTTTTTA 57.072 34.783 1.45 0.00 35.87 1.52
338 339 4.823790 ACGGTAATTTCGTCTGCTTTTT 57.176 36.364 1.45 0.00 35.87 1.94
347 348 2.753296 TCAAACGGACGGTAATTTCGT 58.247 42.857 6.29 6.29 44.03 3.85
348 349 3.791993 TTCAAACGGACGGTAATTTCG 57.208 42.857 0.00 0.00 0.00 3.46
349 350 4.328667 CGATTCAAACGGACGGTAATTTC 58.671 43.478 0.00 0.00 0.00 2.17
350 351 4.330740 CGATTCAAACGGACGGTAATTT 57.669 40.909 0.00 0.00 0.00 1.82
361 362 1.154301 CAACGGGCCGATTCAAACG 60.154 57.895 35.78 3.33 0.00 3.60
362 363 1.211709 CCAACGGGCCGATTCAAAC 59.788 57.895 35.78 0.00 0.00 2.93
363 364 0.958382 CTCCAACGGGCCGATTCAAA 60.958 55.000 35.78 11.43 0.00 2.69
364 365 1.376683 CTCCAACGGGCCGATTCAA 60.377 57.895 35.78 12.55 0.00 2.69
365 366 2.119484 AACTCCAACGGGCCGATTCA 62.119 55.000 35.78 12.53 0.00 2.57
366 367 1.376812 AACTCCAACGGGCCGATTC 60.377 57.895 35.78 0.00 0.00 2.52
367 368 1.674322 CAACTCCAACGGGCCGATT 60.674 57.895 35.78 19.99 0.00 3.34
368 369 2.046314 CAACTCCAACGGGCCGAT 60.046 61.111 35.78 20.37 0.00 4.18
371 372 2.180159 TAGAGCAACTCCAACGGGCC 62.180 60.000 0.00 0.00 0.00 5.80
372 373 0.321298 TTAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
373 374 2.403252 ATTAGAGCAACTCCAACGGG 57.597 50.000 0.00 0.00 0.00 5.28
374 375 4.876107 ACATTATTAGAGCAACTCCAACGG 59.124 41.667 0.00 0.00 0.00 4.44
375 376 5.276395 CGACATTATTAGAGCAACTCCAACG 60.276 44.000 0.00 0.00 0.00 4.10
376 377 5.581085 ACGACATTATTAGAGCAACTCCAAC 59.419 40.000 0.00 0.00 0.00 3.77
377 378 5.580691 CACGACATTATTAGAGCAACTCCAA 59.419 40.000 0.00 0.00 0.00 3.53
378 379 5.109210 CACGACATTATTAGAGCAACTCCA 58.891 41.667 0.00 0.00 0.00 3.86
379 380 4.025647 GCACGACATTATTAGAGCAACTCC 60.026 45.833 0.00 0.00 0.00 3.85
380 381 4.317418 CGCACGACATTATTAGAGCAACTC 60.317 45.833 0.00 0.00 0.00 3.01
381 382 3.551890 CGCACGACATTATTAGAGCAACT 59.448 43.478 0.00 0.00 0.00 3.16
382 383 3.841372 GCGCACGACATTATTAGAGCAAC 60.841 47.826 0.30 0.00 0.00 4.17
383 384 2.284150 GCGCACGACATTATTAGAGCAA 59.716 45.455 0.30 0.00 0.00 3.91
384 385 1.858458 GCGCACGACATTATTAGAGCA 59.142 47.619 0.30 0.00 0.00 4.26
385 386 1.858458 TGCGCACGACATTATTAGAGC 59.142 47.619 5.66 0.00 0.00 4.09
386 387 4.514545 TTTGCGCACGACATTATTAGAG 57.485 40.909 11.12 0.00 0.00 2.43
387 388 4.317769 CGATTTGCGCACGACATTATTAGA 60.318 41.667 11.12 0.00 0.00 2.10
388 389 3.894288 CGATTTGCGCACGACATTATTAG 59.106 43.478 11.12 0.00 0.00 1.73
389 390 3.307512 ACGATTTGCGCACGACATTATTA 59.692 39.130 23.36 0.00 46.04 0.98
390 391 2.095213 ACGATTTGCGCACGACATTATT 59.905 40.909 23.36 0.00 46.04 1.40
391 392 1.663643 ACGATTTGCGCACGACATTAT 59.336 42.857 23.36 3.47 46.04 1.28
392 393 1.059979 GACGATTTGCGCACGACATTA 59.940 47.619 23.36 0.00 46.04 1.90
393 394 0.179225 GACGATTTGCGCACGACATT 60.179 50.000 23.36 2.88 46.04 2.71
394 395 1.419922 GACGATTTGCGCACGACAT 59.580 52.632 23.36 7.98 46.04 3.06
395 396 2.663478 GGACGATTTGCGCACGACA 61.663 57.895 23.36 0.00 46.04 4.35
396 397 2.095843 GGACGATTTGCGCACGAC 59.904 61.111 23.36 17.28 46.04 4.34
397 398 3.474904 CGGACGATTTGCGCACGA 61.475 61.111 23.36 10.39 46.04 4.35
398 399 3.680072 GACGGACGATTTGCGCACG 62.680 63.158 11.12 14.32 44.28 5.34
399 400 2.095843 GACGGACGATTTGCGCAC 59.904 61.111 11.12 0.00 44.28 5.34
400 401 1.956678 TTGACGGACGATTTGCGCA 60.957 52.632 5.66 5.66 44.28 6.09
401 402 1.509162 GTTGACGGACGATTTGCGC 60.509 57.895 0.00 0.00 44.28 6.09
402 403 0.179250 CTGTTGACGGACGATTTGCG 60.179 55.000 0.00 0.00 46.25 4.85
403 404 1.144969 TCTGTTGACGGACGATTTGC 58.855 50.000 0.00 0.00 0.00 3.68
404 405 2.028045 CGATCTGTTGACGGACGATTTG 59.972 50.000 0.00 0.00 33.47 2.32
405 406 2.259618 CGATCTGTTGACGGACGATTT 58.740 47.619 0.00 0.00 33.47 2.17
406 407 1.201647 ACGATCTGTTGACGGACGATT 59.798 47.619 16.24 0.00 33.47 3.34
407 408 0.809385 ACGATCTGTTGACGGACGAT 59.191 50.000 16.24 0.00 33.47 3.73
408 409 0.109919 CACGATCTGTTGACGGACGA 60.110 55.000 16.24 0.00 33.47 4.20
409 410 0.386858 ACACGATCTGTTGACGGACG 60.387 55.000 0.00 10.96 33.47 4.79
410 411 1.060713 CACACGATCTGTTGACGGAC 58.939 55.000 0.00 0.00 33.47 4.79
411 412 0.671796 ACACACGATCTGTTGACGGA 59.328 50.000 0.00 0.00 35.43 4.69
412 413 0.784178 CACACACGATCTGTTGACGG 59.216 55.000 0.00 0.00 0.00 4.79
413 414 0.161658 GCACACACGATCTGTTGACG 59.838 55.000 0.00 0.00 0.00 4.35
414 415 1.193203 CTGCACACACGATCTGTTGAC 59.807 52.381 0.00 0.00 0.00 3.18
415 416 1.501169 CTGCACACACGATCTGTTGA 58.499 50.000 0.00 0.00 0.00 3.18
416 417 0.110509 GCTGCACACACGATCTGTTG 60.111 55.000 0.00 0.00 0.00 3.33
417 418 0.532640 TGCTGCACACACGATCTGTT 60.533 50.000 0.00 0.00 0.00 3.16
418 419 0.947660 CTGCTGCACACACGATCTGT 60.948 55.000 0.00 0.00 0.00 3.41
419 420 0.947660 ACTGCTGCACACACGATCTG 60.948 55.000 0.00 0.00 0.00 2.90
420 421 0.947660 CACTGCTGCACACACGATCT 60.948 55.000 0.00 0.00 0.00 2.75
421 422 1.224069 ACACTGCTGCACACACGATC 61.224 55.000 0.00 0.00 0.00 3.69
422 423 1.224069 GACACTGCTGCACACACGAT 61.224 55.000 0.00 0.00 0.00 3.73
423 424 1.882625 GACACTGCTGCACACACGA 60.883 57.895 0.00 0.00 0.00 4.35
424 425 2.628106 GACACTGCTGCACACACG 59.372 61.111 0.00 0.00 0.00 4.49
425 426 2.628106 CGACACTGCTGCACACAC 59.372 61.111 0.00 0.00 0.00 3.82
426 427 2.588596 CCGACACTGCTGCACACA 60.589 61.111 0.00 0.00 0.00 3.72
427 428 3.349006 CCCGACACTGCTGCACAC 61.349 66.667 0.00 0.00 0.00 3.82
428 429 4.624364 CCCCGACACTGCTGCACA 62.624 66.667 0.00 0.00 0.00 4.57
432 433 1.960040 TAGATGCCCCGACACTGCTG 61.960 60.000 0.00 0.00 0.00 4.41
433 434 1.264749 TTAGATGCCCCGACACTGCT 61.265 55.000 0.00 0.00 0.00 4.24
434 435 1.090052 GTTAGATGCCCCGACACTGC 61.090 60.000 0.00 0.00 0.00 4.40
435 436 0.462047 GGTTAGATGCCCCGACACTG 60.462 60.000 0.00 0.00 0.00 3.66
436 437 0.907704 TGGTTAGATGCCCCGACACT 60.908 55.000 0.00 0.00 0.00 3.55
452 453 0.537143 TTGCCGCAAGACAAGATGGT 60.537 50.000 0.38 0.00 43.02 3.55
455 456 1.878775 GCTTGCCGCAAGACAAGAT 59.121 52.632 32.61 0.00 44.89 2.40
511 512 1.226746 CGGTTCTTCTTGCTTCCGTT 58.773 50.000 0.00 0.00 34.38 4.44
516 517 2.368875 TCTTCTCCGGTTCTTCTTGCTT 59.631 45.455 0.00 0.00 0.00 3.91
673 674 3.922640 CTCCAGCTAGGGCCGCTC 61.923 72.222 2.64 0.00 39.73 5.03
698 699 3.086600 GTGAGAGGGGGCTCCAGG 61.087 72.222 5.99 0.00 38.24 4.45
727 728 4.766088 CTGCCGCCGCTTTTCTGC 62.766 66.667 0.00 0.00 35.36 4.26
741 742 4.448060 GGTACAAGAACTGAACAGTACTGC 59.552 45.833 22.90 8.13 41.58 4.40
744 745 5.211174 AGGGTACAAGAACTGAACAGTAC 57.789 43.478 7.90 1.93 41.58 2.73
745 746 5.221581 GGAAGGGTACAAGAACTGAACAGTA 60.222 44.000 7.90 0.00 41.58 2.74
746 747 4.444449 GGAAGGGTACAAGAACTGAACAGT 60.444 45.833 1.32 1.32 44.94 3.55
936 953 0.880278 TCAAACTGTGCACGAGCTCC 60.880 55.000 13.13 0.00 42.74 4.70
941 958 2.068519 CAGCTATCAAACTGTGCACGA 58.931 47.619 13.13 2.82 0.00 4.35
946 963 1.131883 GGCTGCAGCTATCAAACTGTG 59.868 52.381 35.82 0.00 41.70 3.66
974 991 1.738346 CGATGATCCTCTCGCCACCA 61.738 60.000 0.00 0.00 0.00 4.17
994 1011 2.516225 GCCCCCGTTCATGGCTAC 60.516 66.667 0.00 0.00 42.01 3.58
1236 1253 4.118995 TAGGCGGCGTACACGTGG 62.119 66.667 21.57 2.89 42.22 4.94
1352 1379 1.032014 TTTCAGCCAGCAGTGTTTCC 58.968 50.000 0.00 0.00 0.00 3.13
1387 1414 6.542821 ACTAATTCCTCATCCAAGAACACAA 58.457 36.000 0.00 0.00 0.00 3.33
1508 1535 1.872773 AGTAGAGGAGCCCTTGAAGG 58.127 55.000 3.69 3.69 31.76 3.46
1562 1589 4.060205 ACTTTCCAAAATTGCAGCATCAC 58.940 39.130 0.00 0.00 0.00 3.06
1590 1617 8.536175 GGACAAATATGTTTCTTAATTTCCCCA 58.464 33.333 0.00 0.00 40.74 4.96
1718 1745 3.827625 TGCAATGGTTAAAATCCGAACG 58.172 40.909 0.00 0.00 0.00 3.95
1719 1746 4.805219 ACTGCAATGGTTAAAATCCGAAC 58.195 39.130 0.00 0.00 0.00 3.95
1736 1763 3.305267 CCATGAAAAATGTTCGGACTGCA 60.305 43.478 0.00 0.00 0.00 4.41
1740 1767 3.296322 TGCCATGAAAAATGTTCGGAC 57.704 42.857 0.00 0.00 0.00 4.79
1745 1772 5.673514 ACTCAAGTTGCCATGAAAAATGTT 58.326 33.333 0.00 0.00 0.00 2.71
1775 1802 6.647895 AGAAAATTGCCATGTTTGTCAATCTC 59.352 34.615 0.00 0.00 0.00 2.75
1852 1879 4.024387 GCAATTTTAGTTGACACGAGGTGA 60.024 41.667 2.29 0.00 36.96 4.02
1889 1916 4.576053 CGGATTTTAAGCATGTCATCCTGA 59.424 41.667 0.00 0.00 0.00 3.86
1919 1946 0.884704 CAGTGGCCCGATAAATCCCG 60.885 60.000 0.00 0.00 0.00 5.14
1923 1950 0.923358 TTCCCAGTGGCCCGATAAAT 59.077 50.000 2.61 0.00 0.00 1.40
1930 1957 2.284515 AATCCGATTCCCAGTGGCCC 62.285 60.000 2.61 0.00 0.00 5.80
1938 1965 4.718940 AATGTGTGAAAATCCGATTCCC 57.281 40.909 0.00 0.00 0.00 3.97
1976 2003 7.491696 AGCCACTTCTAATACTAAAATGTCGTC 59.508 37.037 0.00 0.00 0.00 4.20
2050 2077 3.322828 AGCCTCTTTGTGAAATGCATGTT 59.677 39.130 0.00 0.00 0.00 2.71
2120 2147 9.612066 ATCCAAAATTGAGTTTTAAAGCTTTCA 57.388 25.926 16.57 0.92 37.93 2.69
2185 2212 5.849357 TGTATAAAGTGTTTGCCGTACTG 57.151 39.130 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.