Multiple sequence alignment - TraesCS3B01G008800

Loading Multiple Alignment...

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 TraesCS3B01G008800 chr3B 100.000 2448 0 0 1 2448 4333563 4331116 0.000000e+00 4521.0
1 TraesCS3B01G008800 chr3B 96.089 179 5 2 202 379 461200407 461200584 8.560000e-75 291.0
2 TraesCS3B01G008800 chr3B 80.198 101 16 2 1364 1460 5099841 5099941 3.380000e-09 73.1
3 TraesCS3B01G008800 chr3B 79.208 101 17 2 1364 1460 4228421 4228521 1.570000e-07 67.6
4 TraesCS3B01G008800 chr3B 94.118 34 2 0 1413 1446 5105639 5105672 4.000000e-03 52.8
5 TraesCS3B01G008800 chr3A 90.647 973 54 24 1481 2444 1919260 1920204 0.000000e+00 1258.0
6 TraesCS3B01G008800 chr3A 91.327 392 29 2 368 759 1905331 1905717 4.630000e-147 531.0
7 TraesCS3B01G008800 chr3A 94.961 258 12 1 1023 1279 1909438 1909695 1.050000e-108 403.0
8 TraesCS3B01G008800 chr3A 95.973 149 6 0 1 149 1905170 1905318 2.430000e-60 243.0
9 TraesCS3B01G008800 chr3A 89.855 138 9 3 1366 1499 1918892 1919028 3.240000e-39 172.0
10 TraesCS3B01G008800 chr3A 95.122 82 4 0 1281 1362 1918739 1918820 1.980000e-26 130.0
11 TraesCS3B01G008800 chr3A 83.471 121 15 2 2327 2447 95843325 95843210 9.260000e-20 108.0
12 TraesCS3B01G008800 chr3D 85.989 1092 69 43 1372 2448 2150834 2149812 0.000000e+00 1092.0
13 TraesCS3B01G008800 chr3D 90.728 604 48 2 761 1362 2151509 2150912 0.000000e+00 798.0
14 TraesCS3B01G008800 chr3D 85.882 85 12 0 1364 1448 1908944 1909028 9.320000e-15 91.6
15 TraesCS3B01G008800 chrUn 91.711 374 26 2 368 741 351354635 351354267 4.670000e-142 514.0
16 TraesCS3B01G008800 chrUn 80.083 482 59 19 1822 2298 306110515 306110964 8.440000e-85 324.0
17 TraesCS3B01G008800 chrUn 95.973 149 6 0 1 149 351354796 351354648 2.430000e-60 243.0
18 TraesCS3B01G008800 chr2A 81.923 520 67 17 1820 2331 20809384 20809884 4.870000e-112 414.0
19 TraesCS3B01G008800 chr2A 97.041 169 5 0 201 369 632622108 632622276 3.980000e-73 285.0
20 TraesCS3B01G008800 chr2B 81.092 513 78 11 1822 2331 31630853 31630357 2.280000e-105 392.0
21 TraesCS3B01G008800 chr2B 79.845 516 60 23 1822 2331 31678100 31677623 1.080000e-88 337.0
22 TraesCS3B01G008800 chr2B 79.457 516 61 23 1822 2331 31656839 31656363 8.440000e-85 324.0
23 TraesCS3B01G008800 chr2B 93.264 193 9 4 206 397 161144169 161143980 5.150000e-72 281.0
24 TraesCS3B01G008800 chr5B 97.605 167 4 0 206 372 276913960 276913794 1.110000e-73 287.0
25 TraesCS3B01G008800 chr5B 93.514 185 10 2 201 384 124898874 124898691 8.620000e-70 274.0
26 TraesCS3B01G008800 chr5B 85.897 234 25 5 1786 2015 670366439 670366210 2.430000e-60 243.0
27 TraesCS3B01G008800 chr1A 97.059 170 5 0 204 373 526575520 526575689 1.110000e-73 287.0
28 TraesCS3B01G008800 chr1A 97.024 168 5 0 205 372 328799032 328799199 1.430000e-72 283.0
29 TraesCS3B01G008800 chr1A 90.123 81 8 0 2367 2447 80620334 80620254 3.330000e-19 106.0
30 TraesCS3B01G008800 chr4A 95.954 173 6 1 201 373 669439499 669439670 1.850000e-71 279.0
31 TraesCS3B01G008800 chr4A 95.455 176 6 2 200 373 735482008 735481833 1.850000e-71 279.0
32 TraesCS3B01G008800 chr4A 90.123 81 8 0 2367 2447 50889617 50889697 3.330000e-19 106.0
33 TraesCS3B01G008800 chr5D 89.529 191 19 1 1786 1976 12873425 12873236 8.750000e-60 241.0
34 TraesCS3B01G008800 chr5D 84.211 247 36 3 2087 2331 12872122 12871877 1.130000e-58 237.0
35 TraesCS3B01G008800 chr5D 85.124 121 13 2 2327 2447 227771915 227772030 4.280000e-23 119.0
36 TraesCS3B01G008800 chr7A 83.117 231 21 9 1790 2015 594164071 594163854 6.910000e-46 195.0
37 TraesCS3B01G008800 chr7B 83.582 134 19 3 2201 2331 60993276 60993409 3.310000e-24 122.0
38 TraesCS3B01G008800 chr6A 92.593 81 6 0 2367 2447 31918718 31918798 1.540000e-22 117.0
39 TraesCS3B01G008800 chr6B 84.211 114 13 2 2334 2447 22055632 22055524 3.330000e-19 106.0
40 TraesCS3B01G008800 chr4B 88.889 81 9 0 2367 2447 584687428 584687508 1.550000e-17 100.0


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 TraesCS3B01G008800 chr3B 4331116 4333563 2447 True 4521.000000 4521 100.000000 1 2448 1 chr3B.!!$R1 2447
1 TraesCS3B01G008800 chr3A 1918739 1920204 1465 False 520.000000 1258 91.874667 1281 2444 3 chr3A.!!$F2 1163
2 TraesCS3B01G008800 chr3A 1905170 1909695 4525 False 392.333333 531 94.087000 1 1279 3 chr3A.!!$F1 1278
3 TraesCS3B01G008800 chr3D 2149812 2151509 1697 True 945.000000 1092 88.358500 761 2448 2 chr3D.!!$R1 1687
4 TraesCS3B01G008800 chrUn 351354267 351354796 529 True 378.500000 514 93.842000 1 741 2 chrUn.!!$R1 740
5 TraesCS3B01G008800 chr2A 20809384 20809884 500 False 414.000000 414 81.923000 1820 2331 1 chr2A.!!$F1 511
6 TraesCS3B01G008800 chr5D 12871877 12873425 1548 True 239.000000 241 86.870000 1786 2331 2 chr5D.!!$R1 545

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
981 1007 0.034059 AGTGCAAAGTGCTAGCGAGT 59.966 50.0 10.77 0.0 45.31 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 7098 2.554032 CAAGCAACTTTGTAGGTGAGGG 59.446 50.0 0.0 0.0 41.9 4.3 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 6.636454 ACATGATAGGGTTGTTCCTTTCTA 57.364 37.500 0.00 0.00 38.30 2.10
151 152 9.871238 ATACACTTCGTATCAACTTTCATTAGT 57.129 29.630 0.00 0.00 35.87 2.24
153 154 9.701098 ACACTTCGTATCAACTTTCATTAGTAA 57.299 29.630 0.00 0.00 0.00 2.24
190 191 9.787435 ATTTGTAGTTGGTACTTCATTAGTTGA 57.213 29.630 0.00 0.00 38.33 3.18
191 192 8.597662 TTGTAGTTGGTACTTCATTAGTTGAC 57.402 34.615 0.00 0.00 38.33 3.18
192 193 7.959175 TGTAGTTGGTACTTCATTAGTTGACT 58.041 34.615 0.00 0.00 38.33 3.41
193 194 7.870954 TGTAGTTGGTACTTCATTAGTTGACTG 59.129 37.037 0.00 0.00 38.33 3.51
194 195 6.827727 AGTTGGTACTTCATTAGTTGACTGT 58.172 36.000 0.00 0.00 38.33 3.55
195 196 6.929606 AGTTGGTACTTCATTAGTTGACTGTC 59.070 38.462 0.00 0.00 38.33 3.51
196 197 6.665992 TGGTACTTCATTAGTTGACTGTCT 57.334 37.500 9.51 0.00 38.33 3.41
197 198 6.688578 TGGTACTTCATTAGTTGACTGTCTC 58.311 40.000 9.51 2.72 38.33 3.36
198 199 6.100668 GGTACTTCATTAGTTGACTGTCTCC 58.899 44.000 9.51 0.00 38.33 3.71
199 200 5.808366 ACTTCATTAGTTGACTGTCTCCA 57.192 39.130 9.51 0.00 31.29 3.86
200 201 6.365970 ACTTCATTAGTTGACTGTCTCCAT 57.634 37.500 9.51 0.00 31.29 3.41
201 202 6.773638 ACTTCATTAGTTGACTGTCTCCATT 58.226 36.000 9.51 0.00 31.29 3.16
202 203 7.227156 ACTTCATTAGTTGACTGTCTCCATTT 58.773 34.615 9.51 0.00 31.29 2.32
203 204 8.375506 ACTTCATTAGTTGACTGTCTCCATTTA 58.624 33.333 9.51 0.00 31.29 1.40
204 205 9.388506 CTTCATTAGTTGACTGTCTCCATTTAT 57.611 33.333 9.51 0.00 32.84 1.40
205 206 9.739276 TTCATTAGTTGACTGTCTCCATTTATT 57.261 29.630 9.51 0.00 32.84 1.40
209 210 9.871238 TTAGTTGACTGTCTCCATTTATTACTC 57.129 33.333 9.51 0.00 0.00 2.59
210 211 7.331791 AGTTGACTGTCTCCATTTATTACTCC 58.668 38.462 9.51 0.00 0.00 3.85
211 212 6.235231 TGACTGTCTCCATTTATTACTCCC 57.765 41.667 9.51 0.00 0.00 4.30
212 213 5.964477 TGACTGTCTCCATTTATTACTCCCT 59.036 40.000 9.51 0.00 0.00 4.20
213 214 6.098409 TGACTGTCTCCATTTATTACTCCCTC 59.902 42.308 9.51 0.00 0.00 4.30
214 215 5.367060 ACTGTCTCCATTTATTACTCCCTCC 59.633 44.000 0.00 0.00 0.00 4.30
215 216 4.344102 TGTCTCCATTTATTACTCCCTCCG 59.656 45.833 0.00 0.00 0.00 4.63
216 217 4.344390 GTCTCCATTTATTACTCCCTCCGT 59.656 45.833 0.00 0.00 0.00 4.69
217 218 4.966805 TCTCCATTTATTACTCCCTCCGTT 59.033 41.667 0.00 0.00 0.00 4.44
218 219 5.070047 TCTCCATTTATTACTCCCTCCGTTC 59.930 44.000 0.00 0.00 0.00 3.95
219 220 4.102054 TCCATTTATTACTCCCTCCGTTCC 59.898 45.833 0.00 0.00 0.00 3.62
220 221 4.386711 CATTTATTACTCCCTCCGTTCCC 58.613 47.826 0.00 0.00 0.00 3.97
221 222 2.852714 TATTACTCCCTCCGTTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
222 223 1.961133 ATTACTCCCTCCGTTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
223 224 1.732117 TTACTCCCTCCGTTCCCAAA 58.268 50.000 0.00 0.00 0.00 3.28
224 225 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
225 226 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
226 227 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
227 228 1.838077 CTCCCTCCGTTCCCAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
228 229 2.238898 CTCCCTCCGTTCCCAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
229 230 2.026636 TCCCTCCGTTCCCAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
230 231 2.290705 CCCTCCGTTCCCAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
231 232 3.007635 CCTCCGTTCCCAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
232 233 3.307480 CCTCCGTTCCCAAATACTTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
233 234 4.324267 CTCCGTTCCCAAATACTTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
234 235 4.721132 TCCGTTCCCAAATACTTGTCTTT 58.279 39.130 0.00 0.00 0.00 2.52
235 236 4.758165 TCCGTTCCCAAATACTTGTCTTTC 59.242 41.667 0.00 0.00 0.00 2.62
236 237 4.760204 CCGTTCCCAAATACTTGTCTTTCT 59.240 41.667 0.00 0.00 0.00 2.52
237 238 5.935789 CCGTTCCCAAATACTTGTCTTTCTA 59.064 40.000 0.00 0.00 0.00 2.10
238 239 6.092259 CCGTTCCCAAATACTTGTCTTTCTAG 59.908 42.308 0.00 0.00 0.00 2.43
239 240 6.092259 CGTTCCCAAATACTTGTCTTTCTAGG 59.908 42.308 0.00 0.00 0.00 3.02
240 241 5.497474 TCCCAAATACTTGTCTTTCTAGGC 58.503 41.667 0.00 0.00 0.00 3.93
241 242 5.013704 TCCCAAATACTTGTCTTTCTAGGCA 59.986 40.000 0.00 0.00 33.22 4.75
242 243 5.888161 CCCAAATACTTGTCTTTCTAGGCAT 59.112 40.000 0.00 0.00 35.56 4.40
243 244 6.378280 CCCAAATACTTGTCTTTCTAGGCATT 59.622 38.462 0.00 0.00 35.56 3.56
244 245 7.093771 CCCAAATACTTGTCTTTCTAGGCATTT 60.094 37.037 0.00 0.00 35.56 2.32
245 246 7.970614 CCAAATACTTGTCTTTCTAGGCATTTC 59.029 37.037 0.00 0.00 35.56 2.17
246 247 8.514594 CAAATACTTGTCTTTCTAGGCATTTCA 58.485 33.333 0.00 0.00 35.56 2.69
247 248 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
248 249 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
249 250 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
250 251 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
251 252 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
252 253 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
253 254 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
254 255 6.151817 GTCTTTCTAGGCATTTCAAATGGACT 59.848 38.462 12.14 3.08 0.00 3.85
255 256 6.375455 TCTTTCTAGGCATTTCAAATGGACTC 59.625 38.462 12.14 0.00 0.00 3.36
256 257 5.178096 TCTAGGCATTTCAAATGGACTCA 57.822 39.130 12.14 0.00 0.00 3.41
257 258 5.569355 TCTAGGCATTTCAAATGGACTCAA 58.431 37.500 12.14 0.00 0.00 3.02
258 259 4.525912 AGGCATTTCAAATGGACTCAAC 57.474 40.909 12.14 0.00 0.00 3.18
259 260 3.896888 AGGCATTTCAAATGGACTCAACA 59.103 39.130 12.14 0.00 0.00 3.33
260 261 4.529377 AGGCATTTCAAATGGACTCAACAT 59.471 37.500 12.14 0.00 0.00 2.71
261 262 5.716228 AGGCATTTCAAATGGACTCAACATA 59.284 36.000 12.14 0.00 0.00 2.29
262 263 5.807011 GGCATTTCAAATGGACTCAACATAC 59.193 40.000 12.14 0.00 0.00 2.39
263 264 5.512788 GCATTTCAAATGGACTCAACATACG 59.487 40.000 12.14 0.00 0.00 3.06
264 265 5.621197 TTTCAAATGGACTCAACATACGG 57.379 39.130 0.00 0.00 0.00 4.02
265 266 4.545208 TCAAATGGACTCAACATACGGA 57.455 40.909 0.00 0.00 0.00 4.69
266 267 5.097742 TCAAATGGACTCAACATACGGAT 57.902 39.130 0.00 0.00 0.00 4.18
267 268 4.875536 TCAAATGGACTCAACATACGGATG 59.124 41.667 5.94 5.94 39.16 3.51
269 270 5.607939 AATGGACTCAACATACGGATGTA 57.392 39.130 15.10 0.00 45.93 2.29
270 271 4.380841 TGGACTCAACATACGGATGTAC 57.619 45.455 15.10 3.73 45.93 2.90
271 272 3.764972 TGGACTCAACATACGGATGTACA 59.235 43.478 15.10 2.32 45.93 2.90
272 273 4.404394 TGGACTCAACATACGGATGTACAT 59.596 41.667 15.10 8.43 45.93 2.29
273 274 5.595133 TGGACTCAACATACGGATGTACATA 59.405 40.000 15.10 0.00 45.93 2.29
274 275 6.150318 GGACTCAACATACGGATGTACATAG 58.850 44.000 15.10 11.28 45.93 2.23
275 276 6.016527 GGACTCAACATACGGATGTACATAGA 60.017 42.308 15.10 6.65 45.93 1.98
276 277 6.736123 ACTCAACATACGGATGTACATAGAC 58.264 40.000 15.10 1.53 45.93 2.59
277 278 6.320418 ACTCAACATACGGATGTACATAGACA 59.680 38.462 15.10 1.12 45.93 3.41
278 279 7.014326 ACTCAACATACGGATGTACATAGACAT 59.986 37.037 15.10 0.00 45.93 3.06
279 280 8.398878 TCAACATACGGATGTACATAGACATA 57.601 34.615 15.10 0.00 45.93 2.29
280 281 9.020731 TCAACATACGGATGTACATAGACATAT 57.979 33.333 15.10 0.00 45.93 1.78
281 282 9.639601 CAACATACGGATGTACATAGACATATT 57.360 33.333 15.10 0.00 45.93 1.28
307 308 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
308 309 5.536554 AGTGTAGATTCACTCATTTTGCG 57.463 39.130 0.00 0.00 44.07 4.85
309 310 4.091424 GTGTAGATTCACTCATTTTGCGC 58.909 43.478 0.00 0.00 35.68 6.09
310 311 2.927553 AGATTCACTCATTTTGCGCC 57.072 45.000 4.18 0.00 0.00 6.53
311 312 1.131126 AGATTCACTCATTTTGCGCCG 59.869 47.619 4.18 0.00 0.00 6.46
312 313 0.881118 ATTCACTCATTTTGCGCCGT 59.119 45.000 4.18 0.00 0.00 5.68
313 314 1.514003 TTCACTCATTTTGCGCCGTA 58.486 45.000 4.18 0.00 0.00 4.02
314 315 1.732941 TCACTCATTTTGCGCCGTAT 58.267 45.000 4.18 0.00 0.00 3.06
315 316 1.396648 TCACTCATTTTGCGCCGTATG 59.603 47.619 4.18 5.63 0.00 2.39
316 317 1.130373 CACTCATTTTGCGCCGTATGT 59.870 47.619 4.18 0.00 0.00 2.29
317 318 2.350192 CACTCATTTTGCGCCGTATGTA 59.650 45.455 4.18 0.00 0.00 2.29
318 319 2.607635 ACTCATTTTGCGCCGTATGTAG 59.392 45.455 4.18 7.56 0.00 2.74
319 320 2.607635 CTCATTTTGCGCCGTATGTAGT 59.392 45.455 4.18 0.00 0.00 2.73
320 321 2.605818 TCATTTTGCGCCGTATGTAGTC 59.394 45.455 4.18 0.00 0.00 2.59
321 322 2.081725 TTTTGCGCCGTATGTAGTCA 57.918 45.000 4.18 0.00 0.00 3.41
322 323 1.352114 TTTGCGCCGTATGTAGTCAC 58.648 50.000 4.18 0.00 0.00 3.67
323 324 0.528924 TTGCGCCGTATGTAGTCACT 59.471 50.000 4.18 0.00 0.00 3.41
324 325 0.528924 TGCGCCGTATGTAGTCACTT 59.471 50.000 4.18 0.00 0.00 3.16
325 326 0.921347 GCGCCGTATGTAGTCACTTG 59.079 55.000 0.00 0.00 0.00 3.16
326 327 1.734707 GCGCCGTATGTAGTCACTTGT 60.735 52.381 0.00 0.00 0.00 3.16
327 328 2.602878 CGCCGTATGTAGTCACTTGTT 58.397 47.619 0.00 0.00 0.00 2.83
328 329 3.761657 CGCCGTATGTAGTCACTTGTTA 58.238 45.455 0.00 0.00 0.00 2.41
329 330 4.168014 CGCCGTATGTAGTCACTTGTTAA 58.832 43.478 0.00 0.00 0.00 2.01
330 331 4.622313 CGCCGTATGTAGTCACTTGTTAAA 59.378 41.667 0.00 0.00 0.00 1.52
331 332 5.118971 CGCCGTATGTAGTCACTTGTTAAAA 59.881 40.000 0.00 0.00 0.00 1.52
332 333 6.183360 CGCCGTATGTAGTCACTTGTTAAAAT 60.183 38.462 0.00 0.00 0.00 1.82
333 334 7.178074 GCCGTATGTAGTCACTTGTTAAAATC 58.822 38.462 0.00 0.00 0.00 2.17
334 335 7.064253 GCCGTATGTAGTCACTTGTTAAAATCT 59.936 37.037 0.00 0.00 0.00 2.40
335 336 8.592998 CCGTATGTAGTCACTTGTTAAAATCTC 58.407 37.037 0.00 0.00 0.00 2.75
336 337 9.355215 CGTATGTAGTCACTTGTTAAAATCTCT 57.645 33.333 0.00 0.00 0.00 3.10
360 361 9.582431 TCTAGAAAGACAAGTATTTATGAACGG 57.418 33.333 0.00 0.00 0.00 4.44
361 362 9.582431 CTAGAAAGACAAGTATTTATGAACGGA 57.418 33.333 0.00 0.00 0.00 4.69
362 363 8.480643 AGAAAGACAAGTATTTATGAACGGAG 57.519 34.615 0.00 0.00 0.00 4.63
363 364 7.549488 AGAAAGACAAGTATTTATGAACGGAGG 59.451 37.037 0.00 0.00 0.00 4.30
364 365 5.671493 AGACAAGTATTTATGAACGGAGGG 58.329 41.667 0.00 0.00 0.00 4.30
365 366 5.424252 AGACAAGTATTTATGAACGGAGGGA 59.576 40.000 0.00 0.00 0.00 4.20
366 367 5.671493 ACAAGTATTTATGAACGGAGGGAG 58.329 41.667 0.00 0.00 0.00 4.30
377 378 1.831736 ACGGAGGGAGTACATTCTTGG 59.168 52.381 0.00 0.00 0.00 3.61
404 405 2.787473 TTCCGACTCATGGAAAGCAT 57.213 45.000 0.00 0.00 42.37 3.79
407 408 4.422073 TCCGACTCATGGAAAGCATAAT 57.578 40.909 0.00 0.00 30.98 1.28
409 410 4.129380 CCGACTCATGGAAAGCATAATGA 58.871 43.478 0.00 0.00 0.00 2.57
447 448 7.928908 TCTTGATTTGCAAAACAATCTGTAC 57.071 32.000 28.20 7.49 38.31 2.90
450 451 7.640616 TGATTTGCAAAACAATCTGTACATG 57.359 32.000 18.57 0.00 38.31 3.21
459 460 9.333497 CAAAACAATCTGTACATGTATTCACTG 57.667 33.333 9.18 7.17 0.00 3.66
482 483 9.249053 ACTGATGAATTCAAGAGACTTAGAGTA 57.751 33.333 13.09 0.00 32.78 2.59
483 484 9.515020 CTGATGAATTCAAGAGACTTAGAGTAC 57.485 37.037 13.09 0.00 32.78 2.73
484 485 9.249053 TGATGAATTCAAGAGACTTAGAGTACT 57.751 33.333 13.09 0.00 0.00 2.73
485 486 9.730420 GATGAATTCAAGAGACTTAGAGTACTC 57.270 37.037 15.41 15.41 0.00 2.59
501 502 5.897050 GAGTACTCACTCGATCCTTCATTT 58.103 41.667 18.20 0.00 41.79 2.32
503 504 6.797454 AGTACTCACTCGATCCTTCATTTAC 58.203 40.000 0.00 0.00 0.00 2.01
633 634 8.895141 AAGTATATACTCCATGCCACTACATA 57.105 34.615 15.72 0.00 34.99 2.29
636 637 8.967918 GTATATACTCCATGCCACTACATAAGA 58.032 37.037 5.58 0.00 0.00 2.10
637 638 6.747414 ATACTCCATGCCACTACATAAGAA 57.253 37.500 0.00 0.00 0.00 2.52
721 722 7.094205 GCATTTTTCCTCTCATGAAGAAGGTAA 60.094 37.037 14.80 10.61 32.23 2.85
776 777 7.341512 TGCATTGGACATTTAATAACTGGATCA 59.658 33.333 0.00 0.00 0.00 2.92
778 779 8.906867 CATTGGACATTTAATAACTGGATCACT 58.093 33.333 0.00 0.00 0.00 3.41
781 782 8.768397 TGGACATTTAATAACTGGATCACTACT 58.232 33.333 0.00 0.00 0.00 2.57
814 815 8.755028 TGATTTGCTAGTAGTACCACTCATTTA 58.245 33.333 0.00 0.00 0.00 1.40
815 816 9.595823 GATTTGCTAGTAGTACCACTCATTTAA 57.404 33.333 0.00 0.00 0.00 1.52
816 817 8.767478 TTTGCTAGTAGTACCACTCATTTAAC 57.233 34.615 0.00 0.00 0.00 2.01
884 908 7.177878 AGGCGGATCATATCATAAGGATTTTT 58.822 34.615 0.00 0.00 37.44 1.94
885 909 7.337942 AGGCGGATCATATCATAAGGATTTTTC 59.662 37.037 0.00 0.00 37.44 2.29
893 917 8.689972 CATATCATAAGGATTTTTCCCCATAGC 58.310 37.037 0.00 0.00 37.44 2.97
929 953 8.774546 ATAGATATGTAGAGTCCCCATGTATG 57.225 38.462 3.08 0.00 0.00 2.39
937 961 2.852449 AGTCCCCATGTATGACACCAAT 59.148 45.455 8.60 0.00 0.00 3.16
941 965 4.415179 TCCCCATGTATGACACCAATACAT 59.585 41.667 3.76 3.76 40.82 2.29
947 971 4.331443 TGTATGACACCAATACATCAACGC 59.669 41.667 0.00 0.00 0.00 4.84
970 994 6.073765 CGCCTAGGTATATACAAAGTGCAAAG 60.074 42.308 14.70 0.00 0.00 2.77
974 998 6.180472 AGGTATATACAAAGTGCAAAGTGCT 58.820 36.000 14.70 0.00 45.31 4.40
981 1007 0.034059 AGTGCAAAGTGCTAGCGAGT 59.966 50.000 10.77 0.00 45.31 4.18
1005 1441 3.808728 TGCAACATCCTTAGCTATGGTC 58.191 45.455 21.63 8.74 0.00 4.02
1014 1450 2.916702 TAGCTATGGTCCTCGTCGTA 57.083 50.000 0.00 0.00 0.00 3.43
1021 4490 2.046988 TCCTCGTCGTACTCGCCA 60.047 61.111 0.00 0.00 36.96 5.69
1107 4576 1.595929 CACTAACCCCGCGTTGTGT 60.596 57.895 4.92 0.00 35.79 3.72
1114 4583 4.312231 CCGCGTTGTGTGTGGCTG 62.312 66.667 4.92 0.00 0.00 4.85
1193 4662 2.703798 CCCTGCAAATCGCCACCAG 61.704 63.158 0.00 0.00 41.33 4.00
1212 4681 1.961277 CACCGCCAAGAAGAACGCT 60.961 57.895 0.00 0.00 0.00 5.07
1215 4684 2.606961 CGCCAAGAAGAACGCTGCA 61.607 57.895 0.00 0.00 0.00 4.41
1347 4816 2.192861 CAGCTTCAACGGTGGGCAA 61.193 57.895 18.32 0.00 0.00 4.52
1364 4833 2.487934 GCAATATGCCGAGACACTCAT 58.512 47.619 0.00 0.00 37.42 2.90
1450 4987 0.764271 TGCTCATCACCAAGTGACCA 59.236 50.000 0.00 0.00 45.65 4.02
1588 5378 1.559682 CTAGAAGGCAAGCCCACCTTA 59.440 52.381 7.62 0.00 46.33 2.69
1589 5379 1.002857 AGAAGGCAAGCCCACCTTAT 58.997 50.000 7.62 0.00 46.33 1.73
1654 5444 2.793831 GGCACGGCATTTATGGTCT 58.206 52.632 0.00 0.00 0.00 3.85
1660 5450 3.034635 ACGGCATTTATGGTCTCTCTCT 58.965 45.455 0.00 0.00 0.00 3.10
1662 5452 3.320541 CGGCATTTATGGTCTCTCTCTCT 59.679 47.826 0.00 0.00 0.00 3.10
1663 5453 4.558496 CGGCATTTATGGTCTCTCTCTCTC 60.558 50.000 0.00 0.00 0.00 3.20
1664 5454 4.588528 GGCATTTATGGTCTCTCTCTCTCT 59.411 45.833 0.00 0.00 0.00 3.10
1665 5455 5.278957 GGCATTTATGGTCTCTCTCTCTCTC 60.279 48.000 0.00 0.00 0.00 3.20
1666 5456 5.536161 GCATTTATGGTCTCTCTCTCTCTCT 59.464 44.000 0.00 0.00 0.00 3.10
1667 5457 6.294176 GCATTTATGGTCTCTCTCTCTCTCTC 60.294 46.154 0.00 0.00 0.00 3.20
1668 5458 3.864789 ATGGTCTCTCTCTCTCTCTCC 57.135 52.381 0.00 0.00 0.00 3.71
1669 5459 2.845659 TGGTCTCTCTCTCTCTCTCCT 58.154 52.381 0.00 0.00 0.00 3.69
1670 5460 4.002256 TGGTCTCTCTCTCTCTCTCCTA 57.998 50.000 0.00 0.00 0.00 2.94
1671 5461 3.967326 TGGTCTCTCTCTCTCTCTCCTAG 59.033 52.174 0.00 0.00 0.00 3.02
1672 5462 3.967987 GGTCTCTCTCTCTCTCTCCTAGT 59.032 52.174 0.00 0.00 0.00 2.57
1673 5463 4.039366 GGTCTCTCTCTCTCTCTCCTAGTC 59.961 54.167 0.00 0.00 0.00 2.59
1674 5464 4.649674 GTCTCTCTCTCTCTCTCCTAGTCA 59.350 50.000 0.00 0.00 0.00 3.41
1675 5465 5.305644 GTCTCTCTCTCTCTCTCCTAGTCAT 59.694 48.000 0.00 0.00 0.00 3.06
1676 5466 5.905331 TCTCTCTCTCTCTCTCCTAGTCATT 59.095 44.000 0.00 0.00 0.00 2.57
1677 5467 6.042093 TCTCTCTCTCTCTCTCCTAGTCATTC 59.958 46.154 0.00 0.00 0.00 2.67
1678 5468 5.905331 TCTCTCTCTCTCTCCTAGTCATTCT 59.095 44.000 0.00 0.00 0.00 2.40
1679 5469 6.386927 TCTCTCTCTCTCTCCTAGTCATTCTT 59.613 42.308 0.00 0.00 0.00 2.52
1680 5470 6.591935 TCTCTCTCTCTCCTAGTCATTCTTC 58.408 44.000 0.00 0.00 0.00 2.87
1681 5471 6.386927 TCTCTCTCTCTCCTAGTCATTCTTCT 59.613 42.308 0.00 0.00 0.00 2.85
1682 5472 6.591935 TCTCTCTCTCCTAGTCATTCTTCTC 58.408 44.000 0.00 0.00 0.00 2.87
1683 5473 5.690865 TCTCTCTCCTAGTCATTCTTCTCC 58.309 45.833 0.00 0.00 0.00 3.71
1684 5474 4.456535 TCTCTCCTAGTCATTCTTCTCCG 58.543 47.826 0.00 0.00 0.00 4.63
1685 5475 4.164413 TCTCTCCTAGTCATTCTTCTCCGA 59.836 45.833 0.00 0.00 0.00 4.55
1686 5476 5.055265 TCTCCTAGTCATTCTTCTCCGAT 57.945 43.478 0.00 0.00 0.00 4.18
1714 5504 1.152839 CCCCGTCTCTCCCTCTCTC 60.153 68.421 0.00 0.00 0.00 3.20
1716 5506 1.525077 CCGTCTCTCCCTCTCTCCG 60.525 68.421 0.00 0.00 0.00 4.63
1717 5507 1.523046 CGTCTCTCCCTCTCTCCGA 59.477 63.158 0.00 0.00 0.00 4.55
1718 5508 0.812412 CGTCTCTCCCTCTCTCCGAC 60.812 65.000 0.00 0.00 0.00 4.79
1720 5510 0.914902 TCTCTCCCTCTCTCCGACCA 60.915 60.000 0.00 0.00 0.00 4.02
1726 5529 0.103208 CCTCTCTCCGACCAAATCCG 59.897 60.000 0.00 0.00 0.00 4.18
1915 5720 3.430497 TCCCTCTCCTCCCTCCCG 61.430 72.222 0.00 0.00 0.00 5.14
1983 5789 2.527951 CTTTCTCACTCCCCCGCCAG 62.528 65.000 0.00 0.00 0.00 4.85
2274 7098 6.983906 ATGAAGGGTATCCAAAATTCATCC 57.016 37.500 0.00 0.00 33.32 3.51
2331 7158 6.611381 TGCTGCTCATAAACTTATGTTGTTC 58.389 36.000 0.00 0.51 40.97 3.18
2332 7159 6.206438 TGCTGCTCATAAACTTATGTTGTTCA 59.794 34.615 0.00 2.53 40.97 3.18
2342 7169 1.901591 ATGTTGTTCACCTGCTCCTG 58.098 50.000 0.00 0.00 0.00 3.86
2357 7184 2.113433 CCTGGCAGCTGTCATGCTC 61.113 63.158 23.50 0.00 41.98 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.626045 CAATTAAGAACATAGAAAGGAACAACC 57.374 33.333 0.00 0.00 39.35 3.77
82 83 9.703892 CACCACCTAAATTTTATCATTCAACAA 57.296 29.630 0.00 0.00 0.00 2.83
87 88 7.654022 TCCCACCACCTAAATTTTATCATTC 57.346 36.000 0.00 0.00 0.00 2.67
164 165 9.787435 TCAACTAATGAAGTACCAACTACAAAT 57.213 29.630 0.00 0.00 37.50 2.32
165 166 9.048446 GTCAACTAATGAAGTACCAACTACAAA 57.952 33.333 0.00 0.00 40.50 2.83
166 167 8.426489 AGTCAACTAATGAAGTACCAACTACAA 58.574 33.333 0.00 0.00 40.50 2.41
167 168 7.870954 CAGTCAACTAATGAAGTACCAACTACA 59.129 37.037 0.00 0.00 40.50 2.74
168 169 7.871463 ACAGTCAACTAATGAAGTACCAACTAC 59.129 37.037 0.00 0.00 40.50 2.73
169 170 7.959175 ACAGTCAACTAATGAAGTACCAACTA 58.041 34.615 0.00 0.00 40.50 2.24
170 171 6.827727 ACAGTCAACTAATGAAGTACCAACT 58.172 36.000 0.00 0.00 40.50 3.16
171 172 6.929606 AGACAGTCAACTAATGAAGTACCAAC 59.070 38.462 2.66 0.00 40.50 3.77
172 173 7.062749 AGACAGTCAACTAATGAAGTACCAA 57.937 36.000 2.66 0.00 40.50 3.67
173 174 6.295123 GGAGACAGTCAACTAATGAAGTACCA 60.295 42.308 2.66 0.00 40.50 3.25
174 175 6.100668 GGAGACAGTCAACTAATGAAGTACC 58.899 44.000 2.66 0.00 40.50 3.34
175 176 6.688578 TGGAGACAGTCAACTAATGAAGTAC 58.311 40.000 2.66 0.00 35.73 2.73
176 177 6.911250 TGGAGACAGTCAACTAATGAAGTA 57.089 37.500 2.66 0.00 35.73 2.24
177 178 5.808366 TGGAGACAGTCAACTAATGAAGT 57.192 39.130 2.66 0.00 35.73 3.01
193 194 4.344390 ACGGAGGGAGTAATAAATGGAGAC 59.656 45.833 0.00 0.00 0.00 3.36
194 195 4.553678 ACGGAGGGAGTAATAAATGGAGA 58.446 43.478 0.00 0.00 0.00 3.71
195 196 4.957684 ACGGAGGGAGTAATAAATGGAG 57.042 45.455 0.00 0.00 0.00 3.86
196 197 4.102054 GGAACGGAGGGAGTAATAAATGGA 59.898 45.833 0.00 0.00 0.00 3.41
197 198 4.386711 GGAACGGAGGGAGTAATAAATGG 58.613 47.826 0.00 0.00 0.00 3.16
198 199 4.141574 TGGGAACGGAGGGAGTAATAAATG 60.142 45.833 0.00 0.00 0.00 2.32
199 200 4.042174 TGGGAACGGAGGGAGTAATAAAT 58.958 43.478 0.00 0.00 0.00 1.40
200 201 3.452878 TGGGAACGGAGGGAGTAATAAA 58.547 45.455 0.00 0.00 0.00 1.40
201 202 3.119009 TGGGAACGGAGGGAGTAATAA 57.881 47.619 0.00 0.00 0.00 1.40
202 203 2.852714 TGGGAACGGAGGGAGTAATA 57.147 50.000 0.00 0.00 0.00 0.98
203 204 1.961133 TTGGGAACGGAGGGAGTAAT 58.039 50.000 0.00 0.00 0.00 1.89
204 205 1.732117 TTTGGGAACGGAGGGAGTAA 58.268 50.000 0.00 0.00 0.00 2.24
205 206 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
206 207 1.558294 GTATTTGGGAACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
207 208 1.838077 AGTATTTGGGAACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
208 209 1.961133 AGTATTTGGGAACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
209 210 2.290705 ACAAGTATTTGGGAACGGAGGG 60.291 50.000 2.81 0.00 38.66 4.30
210 211 3.007635 GACAAGTATTTGGGAACGGAGG 58.992 50.000 2.81 0.00 38.66 4.30
211 212 3.939066 AGACAAGTATTTGGGAACGGAG 58.061 45.455 2.81 0.00 38.66 4.63
212 213 4.360951 AAGACAAGTATTTGGGAACGGA 57.639 40.909 2.81 0.00 38.66 4.69
213 214 4.760204 AGAAAGACAAGTATTTGGGAACGG 59.240 41.667 2.81 0.00 38.66 4.44
214 215 5.941948 AGAAAGACAAGTATTTGGGAACG 57.058 39.130 2.81 0.00 38.66 3.95
215 216 6.127980 GCCTAGAAAGACAAGTATTTGGGAAC 60.128 42.308 2.81 0.00 38.66 3.62
216 217 5.944007 GCCTAGAAAGACAAGTATTTGGGAA 59.056 40.000 2.81 0.00 38.66 3.97
217 218 5.013704 TGCCTAGAAAGACAAGTATTTGGGA 59.986 40.000 2.81 0.00 38.66 4.37
218 219 5.253330 TGCCTAGAAAGACAAGTATTTGGG 58.747 41.667 2.81 0.00 38.66 4.12
219 220 7.396540 AATGCCTAGAAAGACAAGTATTTGG 57.603 36.000 2.81 0.00 38.66 3.28
220 221 8.514594 TGAAATGCCTAGAAAGACAAGTATTTG 58.485 33.333 0.00 0.00 40.24 2.32
221 222 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
222 223 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
223 224 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
224 225 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
225 226 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
226 227 6.810182 CCATTTGAAATGCCTAGAAAGACAAG 59.190 38.462 12.26 0.00 0.00 3.16
227 228 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
228 229 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
229 230 6.151817 AGTCCATTTGAAATGCCTAGAAAGAC 59.848 38.462 12.26 10.86 0.00 3.01
230 231 6.248433 AGTCCATTTGAAATGCCTAGAAAGA 58.752 36.000 12.26 0.00 0.00 2.52
231 232 6.151648 TGAGTCCATTTGAAATGCCTAGAAAG 59.848 38.462 12.26 0.00 0.00 2.62
232 233 6.009589 TGAGTCCATTTGAAATGCCTAGAAA 58.990 36.000 12.26 0.00 0.00 2.52
233 234 5.569355 TGAGTCCATTTGAAATGCCTAGAA 58.431 37.500 12.26 0.00 0.00 2.10
234 235 5.178096 TGAGTCCATTTGAAATGCCTAGA 57.822 39.130 12.26 1.83 0.00 2.43
235 236 5.183713 TGTTGAGTCCATTTGAAATGCCTAG 59.816 40.000 12.26 0.00 0.00 3.02
236 237 5.076182 TGTTGAGTCCATTTGAAATGCCTA 58.924 37.500 12.26 0.00 0.00 3.93
237 238 3.896888 TGTTGAGTCCATTTGAAATGCCT 59.103 39.130 12.26 9.70 0.00 4.75
238 239 4.255833 TGTTGAGTCCATTTGAAATGCC 57.744 40.909 12.26 5.23 0.00 4.40
239 240 5.512788 CGTATGTTGAGTCCATTTGAAATGC 59.487 40.000 12.26 0.23 0.00 3.56
240 241 6.029607 CCGTATGTTGAGTCCATTTGAAATG 58.970 40.000 10.84 10.84 0.00 2.32
241 242 5.943416 TCCGTATGTTGAGTCCATTTGAAAT 59.057 36.000 0.00 0.00 0.00 2.17
242 243 5.309638 TCCGTATGTTGAGTCCATTTGAAA 58.690 37.500 0.00 0.00 0.00 2.69
243 244 4.900684 TCCGTATGTTGAGTCCATTTGAA 58.099 39.130 0.00 0.00 0.00 2.69
244 245 4.545208 TCCGTATGTTGAGTCCATTTGA 57.455 40.909 0.00 0.00 0.00 2.69
245 246 4.635765 ACATCCGTATGTTGAGTCCATTTG 59.364 41.667 0.00 0.00 44.07 2.32
246 247 4.843728 ACATCCGTATGTTGAGTCCATTT 58.156 39.130 0.00 0.00 44.07 2.32
247 248 4.487714 ACATCCGTATGTTGAGTCCATT 57.512 40.909 0.00 0.00 44.07 3.16
248 249 4.404394 TGTACATCCGTATGTTGAGTCCAT 59.596 41.667 0.00 0.00 44.07 3.41
249 250 3.764972 TGTACATCCGTATGTTGAGTCCA 59.235 43.478 0.00 0.00 44.07 4.02
250 251 4.380841 TGTACATCCGTATGTTGAGTCC 57.619 45.455 0.00 0.00 44.07 3.85
251 252 6.856938 GTCTATGTACATCCGTATGTTGAGTC 59.143 42.308 12.68 0.00 44.07 3.36
252 253 6.320418 TGTCTATGTACATCCGTATGTTGAGT 59.680 38.462 12.68 0.00 44.07 3.41
253 254 6.735130 TGTCTATGTACATCCGTATGTTGAG 58.265 40.000 12.68 0.00 44.07 3.02
254 255 6.702716 TGTCTATGTACATCCGTATGTTGA 57.297 37.500 12.68 0.00 44.07 3.18
255 256 9.639601 AATATGTCTATGTACATCCGTATGTTG 57.360 33.333 12.68 0.00 44.07 3.33
287 288 4.091424 GCGCAAAATGAGTGAATCTACAC 58.909 43.478 0.30 0.00 40.60 2.90
288 289 3.126858 GGCGCAAAATGAGTGAATCTACA 59.873 43.478 10.83 0.00 0.00 2.74
289 290 3.685058 GGCGCAAAATGAGTGAATCTAC 58.315 45.455 10.83 0.00 0.00 2.59
290 291 2.351418 CGGCGCAAAATGAGTGAATCTA 59.649 45.455 10.83 0.00 0.00 1.98
291 292 1.131126 CGGCGCAAAATGAGTGAATCT 59.869 47.619 10.83 0.00 0.00 2.40
292 293 1.135689 ACGGCGCAAAATGAGTGAATC 60.136 47.619 10.83 0.00 0.00 2.52
293 294 0.881118 ACGGCGCAAAATGAGTGAAT 59.119 45.000 10.83 0.00 0.00 2.57
294 295 1.514003 TACGGCGCAAAATGAGTGAA 58.486 45.000 10.83 0.00 0.00 3.18
295 296 1.396648 CATACGGCGCAAAATGAGTGA 59.603 47.619 10.83 0.00 0.00 3.41
296 297 1.130373 ACATACGGCGCAAAATGAGTG 59.870 47.619 10.83 0.00 0.00 3.51
297 298 1.448985 ACATACGGCGCAAAATGAGT 58.551 45.000 10.83 0.00 0.00 3.41
298 299 2.607635 ACTACATACGGCGCAAAATGAG 59.392 45.455 10.83 10.39 0.00 2.90
299 300 2.605818 GACTACATACGGCGCAAAATGA 59.394 45.455 10.83 0.00 0.00 2.57
300 301 2.350192 TGACTACATACGGCGCAAAATG 59.650 45.455 10.83 11.57 0.00 2.32
301 302 2.350498 GTGACTACATACGGCGCAAAAT 59.650 45.455 10.83 0.00 0.00 1.82
302 303 1.727880 GTGACTACATACGGCGCAAAA 59.272 47.619 10.83 0.00 0.00 2.44
303 304 1.067425 AGTGACTACATACGGCGCAAA 60.067 47.619 10.83 0.00 0.00 3.68
304 305 0.528924 AGTGACTACATACGGCGCAA 59.471 50.000 10.83 0.00 0.00 4.85
305 306 0.528924 AAGTGACTACATACGGCGCA 59.471 50.000 10.83 0.00 0.00 6.09
306 307 0.921347 CAAGTGACTACATACGGCGC 59.079 55.000 6.90 0.00 0.00 6.53
307 308 2.273370 ACAAGTGACTACATACGGCG 57.727 50.000 4.80 4.80 0.00 6.46
308 309 6.470557 TTTTAACAAGTGACTACATACGGC 57.529 37.500 0.00 0.00 0.00 5.68
309 310 8.475331 AGATTTTAACAAGTGACTACATACGG 57.525 34.615 0.00 0.00 0.00 4.02
310 311 9.355215 AGAGATTTTAACAAGTGACTACATACG 57.645 33.333 0.00 0.00 0.00 3.06
334 335 9.582431 CCGTTCATAAATACTTGTCTTTCTAGA 57.418 33.333 0.00 0.00 0.00 2.43
335 336 9.582431 TCCGTTCATAAATACTTGTCTTTCTAG 57.418 33.333 0.00 0.00 0.00 2.43
336 337 9.582431 CTCCGTTCATAAATACTTGTCTTTCTA 57.418 33.333 0.00 0.00 0.00 2.10
337 338 7.549488 CCTCCGTTCATAAATACTTGTCTTTCT 59.451 37.037 0.00 0.00 0.00 2.52
338 339 7.201617 CCCTCCGTTCATAAATACTTGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
339 340 6.598064 CCCTCCGTTCATAAATACTTGTCTTT 59.402 38.462 0.00 0.00 0.00 2.52
340 341 6.070424 TCCCTCCGTTCATAAATACTTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
341 342 5.424252 TCCCTCCGTTCATAAATACTTGTCT 59.576 40.000 0.00 0.00 0.00 3.41
342 343 5.667466 TCCCTCCGTTCATAAATACTTGTC 58.333 41.667 0.00 0.00 0.00 3.18
343 344 5.189145 ACTCCCTCCGTTCATAAATACTTGT 59.811 40.000 0.00 0.00 0.00 3.16
344 345 5.671493 ACTCCCTCCGTTCATAAATACTTG 58.329 41.667 0.00 0.00 0.00 3.16
345 346 5.952347 ACTCCCTCCGTTCATAAATACTT 57.048 39.130 0.00 0.00 0.00 2.24
346 347 5.895534 TGTACTCCCTCCGTTCATAAATACT 59.104 40.000 0.00 0.00 0.00 2.12
347 348 6.152932 TGTACTCCCTCCGTTCATAAATAC 57.847 41.667 0.00 0.00 0.00 1.89
348 349 6.989155 ATGTACTCCCTCCGTTCATAAATA 57.011 37.500 0.00 0.00 0.00 1.40
349 350 5.888982 ATGTACTCCCTCCGTTCATAAAT 57.111 39.130 0.00 0.00 0.00 1.40
350 351 5.424252 AGAATGTACTCCCTCCGTTCATAAA 59.576 40.000 0.00 0.00 0.00 1.40
351 352 4.960469 AGAATGTACTCCCTCCGTTCATAA 59.040 41.667 0.00 0.00 0.00 1.90
352 353 4.543689 AGAATGTACTCCCTCCGTTCATA 58.456 43.478 0.00 0.00 0.00 2.15
353 354 3.375699 AGAATGTACTCCCTCCGTTCAT 58.624 45.455 0.00 0.00 0.00 2.57
354 355 2.816411 AGAATGTACTCCCTCCGTTCA 58.184 47.619 0.00 0.00 0.00 3.18
355 356 3.522553 CAAGAATGTACTCCCTCCGTTC 58.477 50.000 0.00 0.00 0.00 3.95
356 357 2.236395 CCAAGAATGTACTCCCTCCGTT 59.764 50.000 0.00 0.00 0.00 4.44
357 358 1.831736 CCAAGAATGTACTCCCTCCGT 59.168 52.381 0.00 0.00 0.00 4.69
358 359 2.108168 TCCAAGAATGTACTCCCTCCG 58.892 52.381 0.00 0.00 0.00 4.63
359 360 3.263425 TGTTCCAAGAATGTACTCCCTCC 59.737 47.826 0.00 0.00 0.00 4.30
360 361 4.553330 TGTTCCAAGAATGTACTCCCTC 57.447 45.455 0.00 0.00 0.00 4.30
361 362 4.993705 TTGTTCCAAGAATGTACTCCCT 57.006 40.909 0.00 0.00 0.00 4.20
362 363 6.590234 ATTTTGTTCCAAGAATGTACTCCC 57.410 37.500 0.00 0.00 0.00 4.30
363 364 7.090808 GGAATTTTGTTCCAAGAATGTACTCC 58.909 38.462 2.07 0.00 38.45 3.85
364 365 6.801862 CGGAATTTTGTTCCAAGAATGTACTC 59.198 38.462 7.51 0.00 38.49 2.59
365 366 6.488683 TCGGAATTTTGTTCCAAGAATGTACT 59.511 34.615 7.51 0.00 38.49 2.73
366 367 6.581166 GTCGGAATTTTGTTCCAAGAATGTAC 59.419 38.462 7.51 0.00 38.49 2.90
377 378 5.371115 TTCCATGAGTCGGAATTTTGTTC 57.629 39.130 0.00 0.00 37.62 3.18
424 425 7.697352 TGTACAGATTGTTTTGCAAATCAAG 57.303 32.000 29.39 21.77 40.91 3.02
438 439 8.652810 TCATCAGTGAATACATGTACAGATTG 57.347 34.615 7.96 5.09 0.00 2.67
459 460 9.730420 GAGTACTCTAAGTCTCTTGAATTCATC 57.270 37.037 15.91 0.00 32.45 2.92
482 483 5.923733 AGTAAATGAAGGATCGAGTGAGT 57.076 39.130 0.00 0.00 0.00 3.41
483 484 8.879342 AATAAGTAAATGAAGGATCGAGTGAG 57.121 34.615 0.00 0.00 0.00 3.51
484 485 9.098355 CAAATAAGTAAATGAAGGATCGAGTGA 57.902 33.333 0.00 0.00 0.00 3.41
485 486 9.098355 TCAAATAAGTAAATGAAGGATCGAGTG 57.902 33.333 0.00 0.00 0.00 3.51
556 557 9.678260 AATCCTTATGATATGATCTGCCTTAAC 57.322 33.333 0.00 0.00 31.83 2.01
619 620 6.455360 AAACATTCTTATGTAGTGGCATGG 57.545 37.500 0.00 0.00 44.14 3.66
685 686 7.092137 TGAGAGGAAAAATGCATGTTGATAG 57.908 36.000 1.98 0.00 0.00 2.08
695 696 5.184671 ACCTTCTTCATGAGAGGAAAAATGC 59.815 40.000 21.74 0.00 39.08 3.56
696 697 6.830873 ACCTTCTTCATGAGAGGAAAAATG 57.169 37.500 21.74 6.87 39.08 2.32
747 748 7.560991 TCCAGTTATTAAATGTCCAATGCATCT 59.439 33.333 0.00 0.00 0.00 2.90
814 815 8.569641 TCTTTTTGCTAACCGTAATTGTATGTT 58.430 29.630 0.00 0.00 0.00 2.71
815 816 8.101654 TCTTTTTGCTAACCGTAATTGTATGT 57.898 30.769 0.00 0.00 0.00 2.29
816 817 8.958175 TTCTTTTTGCTAACCGTAATTGTATG 57.042 30.769 0.00 0.00 0.00 2.39
884 908 1.552578 ATATACACGCGCTATGGGGA 58.447 50.000 5.73 0.00 34.15 4.81
885 909 3.728076 ATATATACACGCGCTATGGGG 57.272 47.619 5.73 0.00 34.15 4.96
920 944 5.375773 TGATGTATTGGTGTCATACATGGG 58.624 41.667 9.71 0.00 40.40 4.00
923 947 5.007626 GCGTTGATGTATTGGTGTCATACAT 59.992 40.000 5.45 5.45 42.27 2.29
929 953 2.356135 AGGCGTTGATGTATTGGTGTC 58.644 47.619 0.00 0.00 0.00 3.67
937 961 7.764141 TTGTATATACCTAGGCGTTGATGTA 57.236 36.000 9.30 0.00 0.00 2.29
941 965 6.509656 CACTTTGTATATACCTAGGCGTTGA 58.490 40.000 9.30 0.00 0.00 3.18
947 971 7.254795 GCACTTTGCACTTTGTATATACCTAGG 60.255 40.741 7.41 7.41 44.26 3.02
981 1007 3.208594 CATAGCTAAGGATGTTGCAGCA 58.791 45.455 5.46 5.46 34.65 4.41
1014 1450 0.537188 CATAGGACAAGGTGGCGAGT 59.463 55.000 0.00 0.00 0.00 4.18
1021 4490 0.988678 GGGAGGCCATAGGACAAGGT 60.989 60.000 5.01 0.00 29.21 3.50
1193 4662 2.556287 CGTTCTTCTTGGCGGTGC 59.444 61.111 0.00 0.00 0.00 5.01
1347 4816 2.560542 GGAGATGAGTGTCTCGGCATAT 59.439 50.000 0.00 0.00 44.43 1.78
1356 4825 1.153549 GCCACCGGAGATGAGTGTC 60.154 63.158 9.46 0.00 0.00 3.67
1450 4987 9.125026 AGACAAGGCGAGAAATGATTTATTATT 57.875 29.630 0.00 0.00 0.00 1.40
1588 5378 3.243724 GGGCTTGGACTCTACCAGATAT 58.756 50.000 0.00 0.00 41.19 1.63
1589 5379 2.023404 TGGGCTTGGACTCTACCAGATA 60.023 50.000 0.00 0.00 41.19 1.98
1626 5416 1.686325 ATGCCGTGCCGTTAGAGGAT 61.686 55.000 0.00 0.00 0.00 3.24
1642 5432 5.536161 AGAGAGAGAGAGAGACCATAAATGC 59.464 44.000 0.00 0.00 0.00 3.56
1647 5437 4.566837 AGGAGAGAGAGAGAGAGACCATA 58.433 47.826 0.00 0.00 0.00 2.74
1648 5438 3.397527 AGGAGAGAGAGAGAGAGACCAT 58.602 50.000 0.00 0.00 0.00 3.55
1649 5439 2.845659 AGGAGAGAGAGAGAGAGACCA 58.154 52.381 0.00 0.00 0.00 4.02
1651 5441 4.649674 TGACTAGGAGAGAGAGAGAGAGAC 59.350 50.000 0.00 0.00 0.00 3.36
1654 5444 5.905331 AGAATGACTAGGAGAGAGAGAGAGA 59.095 44.000 0.00 0.00 0.00 3.10
1660 5450 5.686387 CGGAGAAGAATGACTAGGAGAGAGA 60.686 48.000 0.00 0.00 0.00 3.10
1662 5452 4.164413 TCGGAGAAGAATGACTAGGAGAGA 59.836 45.833 0.00 0.00 0.00 3.10
1663 5453 4.456535 TCGGAGAAGAATGACTAGGAGAG 58.543 47.826 0.00 0.00 0.00 3.20
1664 5454 4.505324 TCGGAGAAGAATGACTAGGAGA 57.495 45.455 0.00 0.00 0.00 3.71
1665 5455 4.083537 CGATCGGAGAAGAATGACTAGGAG 60.084 50.000 7.38 0.00 43.58 3.69
1666 5456 3.815962 CGATCGGAGAAGAATGACTAGGA 59.184 47.826 7.38 0.00 43.58 2.94
1667 5457 3.610585 GCGATCGGAGAAGAATGACTAGG 60.611 52.174 18.30 0.00 43.58 3.02
1668 5458 3.252215 AGCGATCGGAGAAGAATGACTAG 59.748 47.826 18.30 0.00 43.58 2.57
1669 5459 3.003793 CAGCGATCGGAGAAGAATGACTA 59.996 47.826 18.30 0.00 43.58 2.59
1670 5460 2.028130 AGCGATCGGAGAAGAATGACT 58.972 47.619 18.30 0.00 43.58 3.41
1671 5461 2.123342 CAGCGATCGGAGAAGAATGAC 58.877 52.381 18.30 0.00 43.58 3.06
1672 5462 1.536922 GCAGCGATCGGAGAAGAATGA 60.537 52.381 18.30 0.00 43.58 2.57
1673 5463 0.857935 GCAGCGATCGGAGAAGAATG 59.142 55.000 18.30 0.00 43.58 2.67
1674 5464 0.249657 GGCAGCGATCGGAGAAGAAT 60.250 55.000 18.30 0.00 43.58 2.40
1675 5465 1.141881 GGCAGCGATCGGAGAAGAA 59.858 57.895 18.30 0.00 43.58 2.52
1676 5466 2.808315 GGCAGCGATCGGAGAAGA 59.192 61.111 18.30 0.00 43.58 2.87
1677 5467 2.656651 CGGCAGCGATCGGAGAAG 60.657 66.667 18.30 0.00 43.58 2.85
1678 5468 3.411418 GACGGCAGCGATCGGAGAA 62.411 63.158 18.30 0.00 43.58 2.87
1679 5469 3.889044 GACGGCAGCGATCGGAGA 61.889 66.667 18.30 0.00 45.75 3.71
1680 5470 4.933064 GGACGGCAGCGATCGGAG 62.933 72.222 18.30 1.88 0.00 4.63
1707 5497 0.103208 CGGATTTGGTCGGAGAGAGG 59.897 60.000 0.00 0.00 36.95 3.69
1753 5556 4.435436 TGCTCCGCCGTGTGCTAG 62.435 66.667 0.00 0.00 38.05 3.42
1754 5557 4.435436 CTGCTCCGCCGTGTGCTA 62.435 66.667 0.00 0.00 38.05 3.49
1780 5583 4.715523 ATGGTCGTGTTGGGCCGG 62.716 66.667 0.00 0.00 0.00 6.13
1782 5585 3.061848 CCATGGTCGTGTTGGGCC 61.062 66.667 2.57 0.00 0.00 5.80
1783 5586 3.747976 GCCATGGTCGTGTTGGGC 61.748 66.667 14.67 0.00 0.00 5.36
1786 5589 4.101790 GGCGCCATGGTCGTGTTG 62.102 66.667 24.80 4.78 0.00 3.33
1888 5693 4.219999 GAGAGGGAGCCGAGCAGC 62.220 72.222 0.00 0.00 0.00 5.25
1952 5757 6.072230 GGGGAGTGAGAAAGAAGAGAAATTTG 60.072 42.308 0.00 0.00 0.00 2.32
2227 7049 2.613977 CCGAGGAGCAGACTTTGTTGAT 60.614 50.000 0.00 0.00 0.00 2.57
2274 7098 2.554032 CAAGCAACTTTGTAGGTGAGGG 59.446 50.000 0.00 0.00 41.90 4.30
2342 7169 3.873883 GCGAGCATGACAGCTGCC 61.874 66.667 15.27 2.30 46.75 4.85


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

AutoCloner maintained by Alex Coulton.