Multiple sequence alignment - TraesCS2B01G581200

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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 TraesCS2B01G581200 chr2B 100.000 3735 0 0 1 3735 768808057 768804323 0.000000e+00 6898.0
1 TraesCS2B01G581200 chr2B 96.583 3278 101 7 465 3735 768930013 768926740 0.000000e+00 5422.0
2 TraesCS2B01G581200 chr2B 85.681 1704 236 7 873 2569 12422128 12423830 0.000000e+00 1788.0
3 TraesCS2B01G581200 chr2B 85.069 1748 243 17 873 2610 11518503 11516764 0.000000e+00 1766.0
4 TraesCS2B01G581200 chr2B 96.897 290 8 1 183 471 111009129 111009418 5.610000e-133 484.0
5 TraesCS2B01G581200 chr2B 81.663 469 79 7 2111 2576 11420051 11420515 2.100000e-102 383.0
6 TraesCS2B01G581200 chr2B 97.814 183 4 0 1 183 768930193 768930011 2.170000e-82 316.0
7 TraesCS2B01G581200 chr2B 89.189 148 13 2 730 875 12421954 12422100 8.240000e-42 182.0
8 TraesCS2B01G581200 chr2B 88.514 148 14 2 730 875 11518677 11518531 3.830000e-40 176.0
9 TraesCS2B01G581200 chr2B 88.060 134 16 0 538 671 11420808 11420941 3.860000e-35 159.0
10 TraesCS2B01G581200 chr2B 80.769 208 31 4 665 863 13347888 13347681 1.800000e-33 154.0
11 TraesCS2B01G581200 chr2B 100.000 29 0 0 2831 2859 719128202 719128230 2.000000e-03 54.7
12 TraesCS2B01G581200 chr2A 85.379 1703 236 11 873 2566 8707210 8708908 0.000000e+00 1753.0
13 TraesCS2B01G581200 chr2A 83.225 1532 246 8 1051 2576 9395122 9396648 0.000000e+00 1395.0
14 TraesCS2B01G581200 chr2A 83.235 1533 244 10 1051 2576 9847599 9849125 0.000000e+00 1395.0
15 TraesCS2B01G581200 chr2A 84.103 195 24 3 685 872 9941439 9941633 8.240000e-42 182.0
16 TraesCS2B01G581200 chr2A 93.182 44 3 0 2831 2874 551817971 551818014 8.660000e-07 65.8
17 TraesCS2B01G581200 chr2D 85.270 1704 238 7 885 2576 8695491 8697193 0.000000e+00 1744.0
18 TraesCS2B01G581200 chr2D 84.620 1775 237 25 879 2644 85929755 85928008 0.000000e+00 1733.0
19 TraesCS2B01G581200 chr2D 85.192 1695 238 9 875 2563 19586831 19588518 0.000000e+00 1727.0
20 TraesCS2B01G581200 chr2D 96.013 301 10 2 167 467 540821525 540821227 4.340000e-134 488.0
21 TraesCS2B01G581200 chr2D 86.395 147 19 1 730 875 9604387 9604533 3.860000e-35 159.0
22 TraesCS2B01G581200 chr4B 97.561 287 7 0 181 467 609511819 609511533 3.350000e-135 492.0
23 TraesCS2B01G581200 chr4A 96.528 288 9 1 181 468 11843046 11842760 3.380000e-130 475.0
24 TraesCS2B01G581200 chr4A 90.265 113 10 1 3133 3244 514415037 514415149 3.010000e-31 147.0
25 TraesCS2B01G581200 chr7B 94.444 306 15 2 163 468 652987961 652987658 1.570000e-128 470.0
26 TraesCS2B01G581200 chr3D 96.167 287 11 0 181 467 536025872 536025586 1.570000e-128 470.0
27 TraesCS2B01G581200 chr3D 78.689 305 51 12 2952 3245 28378326 28378025 1.370000e-44 191.0
28 TraesCS2B01G581200 chr3B 96.167 287 11 0 181 467 17350287 17350573 1.570000e-128 470.0
29 TraesCS2B01G581200 chr1D 96.154 286 11 0 181 466 79046795 79046510 5.650000e-128 468.0
30 TraesCS2B01G581200 chr1D 82.886 298 38 8 2956 3244 31413927 31413634 4.790000e-64 255.0
31 TraesCS2B01G581200 chr4D 95.848 289 11 1 179 467 149919572 149919285 2.030000e-127 466.0
32 TraesCS2B01G581200 chrUn 86.325 351 38 9 531 877 273227869 273227525 1.270000e-99 374.0
33 TraesCS2B01G581200 chrUn 86.158 354 39 9 528 877 292881980 292882327 1.270000e-99 374.0
34 TraesCS2B01G581200 chr6D 84.385 301 31 10 2956 3244 283554339 283554043 7.900000e-72 281.0
35 TraesCS2B01G581200 chr6D 83.509 285 34 4 2964 3235 373392771 373393055 1.720000e-63 254.0
36 TraesCS2B01G581200 chr6A 83.228 316 34 9 2950 3250 403323312 403323001 4.750000e-69 272.0
37 TraesCS2B01G581200 chr6B 83.553 304 32 9 2956 3244 444541115 444540815 6.150000e-68 268.0
38 TraesCS2B01G581200 chr6B 78.502 307 51 10 2956 3250 75963585 75963282 1.770000e-43 187.0
39 TraesCS2B01G581200 chr5B 82.595 316 30 10 2956 3248 534487004 534486691 4.790000e-64 255.0
40 TraesCS2B01G581200 chr7A 82.143 308 39 8 2955 3250 97912064 97911761 2.230000e-62 250.0
41 TraesCS2B01G581200 chr5D 81.788 302 40 6 2956 3244 439979394 439979095 4.820000e-59 239.0
42 TraesCS2B01G581200 chr5D 90.476 42 4 0 2833 2874 503875292 503875333 5.210000e-04 56.5
43 TraesCS2B01G581200 chr7D 80.968 310 38 15 2954 3244 567797276 567796969 3.750000e-55 226.0
44 TraesCS2B01G581200 chr7D 83.893 149 16 7 2953 3096 265008939 265008794 6.510000e-28 135.0
45 TraesCS2B01G581200 chr3A 79.805 307 36 14 2962 3244 740389361 740389057 2.280000e-47 200.0
46 TraesCS2B01G581200 chr3A 90.265 113 10 1 3133 3244 497657982 497658094 3.010000e-31 147.0
47 TraesCS2B01G581200 chr3A 90.476 42 4 0 2831 2872 510299822 510299781 5.210000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G581200 chr2B 768804323 768808057 3734 True 6898 6898 100.0000 1 3735 1 chr2B.!!$R2 3734
1 TraesCS2B01G581200 chr2B 768926740 768930193 3453 True 2869 5422 97.1985 1 3735 2 chr2B.!!$R4 3734
2 TraesCS2B01G581200 chr2B 12421954 12423830 1876 False 985 1788 87.4350 730 2569 2 chr2B.!!$F4 1839
3 TraesCS2B01G581200 chr2B 11516764 11518677 1913 True 971 1766 86.7915 730 2610 2 chr2B.!!$R3 1880
4 TraesCS2B01G581200 chr2B 11420051 11420941 890 False 271 383 84.8615 538 2576 2 chr2B.!!$F3 2038
5 TraesCS2B01G581200 chr2A 8707210 8708908 1698 False 1753 1753 85.3790 873 2566 1 chr2A.!!$F1 1693
6 TraesCS2B01G581200 chr2A 9395122 9396648 1526 False 1395 1395 83.2250 1051 2576 1 chr2A.!!$F2 1525
7 TraesCS2B01G581200 chr2A 9847599 9849125 1526 False 1395 1395 83.2350 1051 2576 1 chr2A.!!$F3 1525
8 TraesCS2B01G581200 chr2D 8695491 8697193 1702 False 1744 1744 85.2700 885 2576 1 chr2D.!!$F1 1691
9 TraesCS2B01G581200 chr2D 85928008 85929755 1747 True 1733 1733 84.6200 879 2644 1 chr2D.!!$R1 1765
10 TraesCS2B01G581200 chr2D 19586831 19588518 1687 False 1727 1727 85.1920 875 2563 1 chr2D.!!$F3 1688

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
137 138 0.721718 GAAGAACGCCGATGGTTCAG 59.278 55.000 13.19 0.0 44.78 3.02 F
203 204 0.930726 AGGGTGTTTGTTTCCAGGGA 59.069 50.000 0.00 0.0 0.00 4.20 F
204 205 1.037493 GGGTGTTTGTTTCCAGGGAC 58.963 55.000 0.00 0.0 0.00 4.46 F
1194 1239 1.133790 GATTGCAACACCTCCTGATGC 59.866 52.381 0.00 0.0 46.39 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1239 0.028110 TCGATGACGATGCTGACTCG 59.972 55.000 0.0 0.0 43.81 4.18 R
2018 2066 0.606401 CACTCCCGAATGCCAGTGTT 60.606 55.000 0.0 0.0 33.03 3.32 R
2323 2374 6.655003 TGGTGATTCTTCCTTGATAGAAACAC 59.345 38.462 13.5 13.5 45.64 3.32 R
2955 3052 0.176219 TATACTTTCGTGCGGGGGTG 59.824 55.000 0.0 0.0 0.00 4.61 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
77 78 1.737793 GGTTTACCATTGTGGAGAGCG 59.262 52.381 2.45 0.00 40.96 5.03
134 135 1.086696 CATGAAGAACGCCGATGGTT 58.913 50.000 0.00 0.00 0.00 3.67
137 138 0.721718 GAAGAACGCCGATGGTTCAG 59.278 55.000 13.19 0.00 44.78 3.02
145 146 1.522668 CCGATGGTTCAGCAGTTTCA 58.477 50.000 0.00 0.00 0.00 2.69
191 192 6.742559 TTACTCAAGAAGTAAGAGGGTGTT 57.257 37.500 0.00 0.00 43.89 3.32
192 193 5.632034 ACTCAAGAAGTAAGAGGGTGTTT 57.368 39.130 0.00 0.00 36.07 2.83
193 194 5.368989 ACTCAAGAAGTAAGAGGGTGTTTG 58.631 41.667 0.00 0.00 36.07 2.93
194 195 5.104485 ACTCAAGAAGTAAGAGGGTGTTTGT 60.104 40.000 0.00 0.00 36.07 2.83
195 196 5.751586 TCAAGAAGTAAGAGGGTGTTTGTT 58.248 37.500 0.00 0.00 0.00 2.83
196 197 6.184789 TCAAGAAGTAAGAGGGTGTTTGTTT 58.815 36.000 0.00 0.00 0.00 2.83
197 198 6.317893 TCAAGAAGTAAGAGGGTGTTTGTTTC 59.682 38.462 0.00 0.00 0.00 2.78
198 199 5.131067 AGAAGTAAGAGGGTGTTTGTTTCC 58.869 41.667 0.00 0.00 0.00 3.13
199 200 4.513406 AGTAAGAGGGTGTTTGTTTCCA 57.487 40.909 0.00 0.00 0.00 3.53
200 201 4.461198 AGTAAGAGGGTGTTTGTTTCCAG 58.539 43.478 0.00 0.00 0.00 3.86
201 202 2.364972 AGAGGGTGTTTGTTTCCAGG 57.635 50.000 0.00 0.00 0.00 4.45
202 203 1.133482 AGAGGGTGTTTGTTTCCAGGG 60.133 52.381 0.00 0.00 0.00 4.45
203 204 0.930726 AGGGTGTTTGTTTCCAGGGA 59.069 50.000 0.00 0.00 0.00 4.20
204 205 1.037493 GGGTGTTTGTTTCCAGGGAC 58.963 55.000 0.00 0.00 0.00 4.46
205 206 1.411074 GGGTGTTTGTTTCCAGGGACT 60.411 52.381 0.00 0.00 43.88 3.85
206 207 2.384828 GGTGTTTGTTTCCAGGGACTT 58.615 47.619 0.00 0.00 34.60 3.01
207 208 3.558033 GGTGTTTGTTTCCAGGGACTTA 58.442 45.455 0.00 0.00 34.60 2.24
208 209 4.149598 GGTGTTTGTTTCCAGGGACTTAT 58.850 43.478 0.00 0.00 34.60 1.73
209 210 4.587262 GGTGTTTGTTTCCAGGGACTTATT 59.413 41.667 0.00 0.00 34.60 1.40
210 211 5.508994 GGTGTTTGTTTCCAGGGACTTATTG 60.509 44.000 0.00 0.00 34.60 1.90
211 212 4.586841 TGTTTGTTTCCAGGGACTTATTGG 59.413 41.667 0.00 0.00 34.60 3.16
212 213 4.463050 TTGTTTCCAGGGACTTATTGGT 57.537 40.909 0.00 0.00 34.60 3.67
213 214 4.463050 TGTTTCCAGGGACTTATTGGTT 57.537 40.909 0.00 0.00 34.60 3.67
214 215 4.810345 TGTTTCCAGGGACTTATTGGTTT 58.190 39.130 0.00 0.00 34.60 3.27
215 216 5.954757 TGTTTCCAGGGACTTATTGGTTTA 58.045 37.500 0.00 0.00 34.60 2.01
216 217 6.007703 TGTTTCCAGGGACTTATTGGTTTAG 58.992 40.000 0.00 0.00 34.60 1.85
217 218 4.855298 TCCAGGGACTTATTGGTTTAGG 57.145 45.455 0.00 0.00 34.60 2.69
218 219 3.526019 TCCAGGGACTTATTGGTTTAGGG 59.474 47.826 0.00 0.00 34.60 3.53
219 220 3.526019 CCAGGGACTTATTGGTTTAGGGA 59.474 47.826 0.00 0.00 34.60 4.20
220 221 4.524053 CAGGGACTTATTGGTTTAGGGAC 58.476 47.826 0.00 0.00 34.60 4.46
221 222 4.227527 CAGGGACTTATTGGTTTAGGGACT 59.772 45.833 0.00 0.00 39.39 3.85
222 223 4.856182 AGGGACTTATTGGTTTAGGGACTT 59.144 41.667 0.00 0.00 34.75 3.01
223 224 6.034003 AGGGACTTATTGGTTTAGGGACTTA 58.966 40.000 0.00 0.00 34.75 2.24
224 225 6.506413 AGGGACTTATTGGTTTAGGGACTTAA 59.494 38.462 0.00 0.00 34.75 1.85
225 226 7.018851 AGGGACTTATTGGTTTAGGGACTTAAA 59.981 37.037 0.00 0.00 34.75 1.52
226 227 7.670979 GGGACTTATTGGTTTAGGGACTTAAAA 59.329 37.037 0.00 0.00 41.75 1.52
227 228 9.081204 GGACTTATTGGTTTAGGGACTTAAAAA 57.919 33.333 0.00 0.00 41.75 1.94
247 248 5.941555 AAAAGTCCCGATAAGTCTCATCT 57.058 39.130 0.00 0.00 0.00 2.90
248 249 7.419711 AAAAAGTCCCGATAAGTCTCATCTA 57.580 36.000 0.00 0.00 0.00 1.98
249 250 7.419711 AAAAGTCCCGATAAGTCTCATCTAA 57.580 36.000 0.00 0.00 0.00 2.10
250 251 7.419711 AAAGTCCCGATAAGTCTCATCTAAA 57.580 36.000 0.00 0.00 0.00 1.85
251 252 6.394025 AGTCCCGATAAGTCTCATCTAAAC 57.606 41.667 0.00 0.00 0.00 2.01
252 253 5.302313 AGTCCCGATAAGTCTCATCTAAACC 59.698 44.000 0.00 0.00 0.00 3.27
253 254 5.068723 GTCCCGATAAGTCTCATCTAAACCA 59.931 44.000 0.00 0.00 0.00 3.67
254 255 5.659525 TCCCGATAAGTCTCATCTAAACCAA 59.340 40.000 0.00 0.00 0.00 3.67
255 256 6.155565 TCCCGATAAGTCTCATCTAAACCAAA 59.844 38.462 0.00 0.00 0.00 3.28
256 257 6.258068 CCCGATAAGTCTCATCTAAACCAAAC 59.742 42.308 0.00 0.00 0.00 2.93
257 258 6.816640 CCGATAAGTCTCATCTAAACCAAACA 59.183 38.462 0.00 0.00 0.00 2.83
258 259 7.010552 CCGATAAGTCTCATCTAAACCAAACAG 59.989 40.741 0.00 0.00 0.00 3.16
259 260 7.010552 CGATAAGTCTCATCTAAACCAAACAGG 59.989 40.741 0.00 0.00 45.67 4.00
260 261 5.825593 AGTCTCATCTAAACCAAACAGGA 57.174 39.130 0.00 0.00 41.22 3.86
261 262 5.799213 AGTCTCATCTAAACCAAACAGGAG 58.201 41.667 0.00 0.00 41.22 3.69
262 263 4.938226 GTCTCATCTAAACCAAACAGGAGG 59.062 45.833 0.00 0.00 41.22 4.30
263 264 4.019321 TCTCATCTAAACCAAACAGGAGGG 60.019 45.833 0.00 0.00 41.22 4.30
264 265 3.913799 TCATCTAAACCAAACAGGAGGGA 59.086 43.478 0.00 0.00 41.22 4.20
265 266 3.782656 TCTAAACCAAACAGGAGGGAC 57.217 47.619 0.00 0.00 41.22 4.46
267 268 3.720002 TCTAAACCAAACAGGAGGGACTT 59.280 43.478 0.00 0.00 41.55 3.01
268 269 4.909088 TCTAAACCAAACAGGAGGGACTTA 59.091 41.667 0.00 0.00 41.55 2.24
269 270 4.741928 AAACCAAACAGGAGGGACTTAT 57.258 40.909 0.00 0.00 41.55 1.73
270 271 5.853572 AAACCAAACAGGAGGGACTTATA 57.146 39.130 0.00 0.00 41.55 0.98
271 272 5.437191 AACCAAACAGGAGGGACTTATAG 57.563 43.478 0.00 0.00 41.55 1.31
272 273 3.780850 ACCAAACAGGAGGGACTTATAGG 59.219 47.826 0.00 0.00 41.55 2.57
273 274 3.136626 CCAAACAGGAGGGACTTATAGGG 59.863 52.174 0.00 0.00 41.55 3.53
274 275 4.037927 CAAACAGGAGGGACTTATAGGGA 58.962 47.826 0.00 0.00 41.55 4.20
275 276 3.331718 ACAGGAGGGACTTATAGGGAC 57.668 52.381 0.00 0.00 41.55 4.46
276 277 2.866454 ACAGGAGGGACTTATAGGGACT 59.134 50.000 0.00 0.00 41.55 3.85
277 278 3.275228 ACAGGAGGGACTTATAGGGACTT 59.725 47.826 0.00 0.00 41.55 3.01
278 279 4.485021 ACAGGAGGGACTTATAGGGACTTA 59.515 45.833 0.00 0.00 41.55 2.24
279 280 5.042827 ACAGGAGGGACTTATAGGGACTTAA 60.043 44.000 0.00 0.00 41.55 1.85
280 281 5.903589 CAGGAGGGACTTATAGGGACTTAAA 59.096 44.000 0.00 0.00 41.55 1.52
281 282 6.042208 CAGGAGGGACTTATAGGGACTTAAAG 59.958 46.154 0.00 0.00 41.55 1.85
282 283 5.904169 GGAGGGACTTATAGGGACTTAAAGT 59.096 44.000 0.00 0.00 42.31 2.66
283 284 6.183360 GGAGGGACTTATAGGGACTTAAAGTG 60.183 46.154 0.00 0.00 40.60 3.16
284 285 5.666265 AGGGACTTATAGGGACTTAAAGTGG 59.334 44.000 0.00 0.00 40.60 4.00
285 286 5.163227 GGGACTTATAGGGACTTAAAGTGGG 60.163 48.000 0.00 0.00 40.60 4.61
286 287 5.366460 GACTTATAGGGACTTAAAGTGGGC 58.634 45.833 0.00 0.00 40.60 5.36
287 288 4.786454 ACTTATAGGGACTTAAAGTGGGCA 59.214 41.667 0.00 0.00 39.58 5.36
288 289 5.432060 ACTTATAGGGACTTAAAGTGGGCAT 59.568 40.000 0.00 0.00 39.58 4.40
289 290 4.881157 ATAGGGACTTAAAGTGGGCATT 57.119 40.909 0.00 0.00 41.75 3.56
290 291 3.542969 AGGGACTTAAAGTGGGCATTT 57.457 42.857 0.00 0.00 27.25 2.32
291 292 3.165071 AGGGACTTAAAGTGGGCATTTG 58.835 45.455 0.00 0.00 27.25 2.32
292 293 2.897326 GGGACTTAAAGTGGGCATTTGT 59.103 45.455 0.00 0.00 0.00 2.83
293 294 4.083565 GGGACTTAAAGTGGGCATTTGTA 58.916 43.478 0.00 0.00 0.00 2.41
294 295 4.525100 GGGACTTAAAGTGGGCATTTGTAA 59.475 41.667 0.00 0.00 0.00 2.41
295 296 5.466819 GGACTTAAAGTGGGCATTTGTAAC 58.533 41.667 0.00 0.00 0.00 2.50
296 297 5.243060 GGACTTAAAGTGGGCATTTGTAACT 59.757 40.000 0.00 0.00 0.00 2.24
297 298 6.239204 GGACTTAAAGTGGGCATTTGTAACTT 60.239 38.462 0.00 0.00 32.60 2.66
298 299 7.040271 GGACTTAAAGTGGGCATTTGTAACTTA 60.040 37.037 0.00 0.00 31.09 2.24
299 300 8.417273 ACTTAAAGTGGGCATTTGTAACTTAT 57.583 30.769 0.00 0.00 31.09 1.73
300 301 8.303876 ACTTAAAGTGGGCATTTGTAACTTATG 58.696 33.333 0.00 0.00 31.09 1.90
301 302 6.909550 AAAGTGGGCATTTGTAACTTATGA 57.090 33.333 0.00 0.00 31.09 2.15
302 303 6.909550 AAGTGGGCATTTGTAACTTATGAA 57.090 33.333 0.00 0.00 29.56 2.57
303 304 6.909550 AGTGGGCATTTGTAACTTATGAAA 57.090 33.333 0.00 0.00 0.00 2.69
304 305 7.480760 AGTGGGCATTTGTAACTTATGAAAT 57.519 32.000 0.00 0.00 0.00 2.17
305 306 8.588290 AGTGGGCATTTGTAACTTATGAAATA 57.412 30.769 0.00 0.00 0.00 1.40
306 307 9.030452 AGTGGGCATTTGTAACTTATGAAATAA 57.970 29.630 0.00 0.00 36.20 1.40
332 333 5.996271 TCTCAAGGAGAGTCTTATAGGGA 57.004 43.478 0.00 0.00 44.98 4.20
333 334 5.697067 TCTCAAGGAGAGTCTTATAGGGAC 58.303 45.833 0.00 0.00 44.98 4.46
334 335 5.433712 TCTCAAGGAGAGTCTTATAGGGACT 59.566 44.000 9.30 9.30 45.37 3.85
335 336 6.068735 TCTCAAGGAGAGTCTTATAGGGACTT 60.069 42.308 10.43 3.61 43.13 3.01
336 337 7.129038 TCTCAAGGAGAGTCTTATAGGGACTTA 59.871 40.741 10.43 0.00 43.13 2.24
337 338 7.827787 TCAAGGAGAGTCTTATAGGGACTTAT 58.172 38.462 10.43 4.90 43.13 1.73
338 339 8.956860 TCAAGGAGAGTCTTATAGGGACTTATA 58.043 37.037 10.43 0.00 43.13 0.98
339 340 9.238368 CAAGGAGAGTCTTATAGGGACTTATAG 57.762 40.741 10.43 0.00 43.13 1.31
340 341 8.528543 AGGAGAGTCTTATAGGGACTTATAGT 57.471 38.462 10.43 0.00 43.13 2.12
341 342 8.962205 AGGAGAGTCTTATAGGGACTTATAGTT 58.038 37.037 10.43 0.00 43.13 2.24
342 343 9.016438 GGAGAGTCTTATAGGGACTTATAGTTG 57.984 40.741 10.43 0.00 43.13 3.16
343 344 9.577222 GAGAGTCTTATAGGGACTTATAGTTGT 57.423 37.037 10.43 0.00 43.13 3.32
354 355 9.448587 AGGGACTTATAGTTGTAATATGGTCTT 57.551 33.333 0.00 0.00 27.25 3.01
364 365 9.448587 AGTTGTAATATGGTCTTATAGGGACTT 57.551 33.333 7.52 0.00 41.75 3.01
385 386 6.607019 ACTTATAAGTCCCAGAAACCAAACA 58.393 36.000 12.50 0.00 32.86 2.83
386 387 6.715264 ACTTATAAGTCCCAGAAACCAAACAG 59.285 38.462 12.50 0.00 32.86 3.16
387 388 2.364972 AGTCCCAGAAACCAAACAGG 57.635 50.000 0.00 0.00 45.67 4.00
402 403 6.803154 CCAAACAGGTAGAGACTTTTTAGG 57.197 41.667 0.00 0.00 0.00 2.69
403 404 5.705905 CCAAACAGGTAGAGACTTTTTAGGG 59.294 44.000 0.00 0.00 0.00 3.53
404 405 6.465321 CCAAACAGGTAGAGACTTTTTAGGGA 60.465 42.308 0.00 0.00 0.00 4.20
405 406 5.741962 ACAGGTAGAGACTTTTTAGGGAC 57.258 43.478 0.00 0.00 0.00 4.46
406 407 5.404395 ACAGGTAGAGACTTTTTAGGGACT 58.596 41.667 0.00 0.00 46.37 3.85
407 408 5.845065 ACAGGTAGAGACTTTTTAGGGACTT 59.155 40.000 0.00 0.00 41.75 3.01
408 409 6.166982 CAGGTAGAGACTTTTTAGGGACTTG 58.833 44.000 0.00 0.00 41.75 3.16
409 410 5.845065 AGGTAGAGACTTTTTAGGGACTTGT 59.155 40.000 0.00 0.00 41.75 3.16
410 411 5.932883 GGTAGAGACTTTTTAGGGACTTGTG 59.067 44.000 0.00 0.00 41.75 3.33
411 412 5.888982 AGAGACTTTTTAGGGACTTGTGA 57.111 39.130 0.00 0.00 41.75 3.58
412 413 5.612351 AGAGACTTTTTAGGGACTTGTGAC 58.388 41.667 0.00 0.00 41.75 3.67
413 414 5.367060 AGAGACTTTTTAGGGACTTGTGACT 59.633 40.000 0.00 0.00 41.75 3.41
414 415 6.002653 AGACTTTTTAGGGACTTGTGACTT 57.997 37.500 0.00 0.00 41.75 3.01
415 416 7.070821 AGAGACTTTTTAGGGACTTGTGACTTA 59.929 37.037 0.00 0.00 41.75 2.24
416 417 7.746703 AGACTTTTTAGGGACTTGTGACTTAT 58.253 34.615 0.00 0.00 41.75 1.73
417 418 8.877195 AGACTTTTTAGGGACTTGTGACTTATA 58.123 33.333 0.00 0.00 41.75 0.98
418 419 9.498176 GACTTTTTAGGGACTTGTGACTTATAA 57.502 33.333 0.00 0.00 41.75 0.98
419 420 9.503399 ACTTTTTAGGGACTTGTGACTTATAAG 57.497 33.333 11.05 11.05 41.75 1.73
420 421 9.503399 CTTTTTAGGGACTTGTGACTTATAAGT 57.497 33.333 18.05 18.05 42.57 2.24
421 422 9.856162 TTTTTAGGGACTTGTGACTTATAAGTT 57.144 29.630 18.96 2.29 40.34 2.66
422 423 8.842358 TTTAGGGACTTGTGACTTATAAGTTG 57.158 34.615 18.96 9.81 40.34 3.16
423 424 5.805728 AGGGACTTGTGACTTATAAGTTGG 58.194 41.667 18.96 10.07 40.34 3.77
424 425 4.941873 GGGACTTGTGACTTATAAGTTGGG 59.058 45.833 18.96 10.37 40.34 4.12
425 426 5.280317 GGGACTTGTGACTTATAAGTTGGGA 60.280 44.000 18.96 6.15 40.34 4.37
426 427 5.642491 GGACTTGTGACTTATAAGTTGGGAC 59.358 44.000 18.96 13.23 40.34 4.46
427 428 6.435292 ACTTGTGACTTATAAGTTGGGACT 57.565 37.500 18.96 0.00 37.44 3.85
428 429 7.310237 GGACTTGTGACTTATAAGTTGGGACTA 60.310 40.741 18.96 9.68 40.34 2.59
429 430 7.612677 ACTTGTGACTTATAAGTTGGGACTAG 58.387 38.462 18.96 18.05 37.44 2.57
430 431 7.453752 ACTTGTGACTTATAAGTTGGGACTAGA 59.546 37.037 18.96 5.07 37.44 2.43
431 432 7.786046 TGTGACTTATAAGTTGGGACTAGAA 57.214 36.000 18.96 0.00 39.88 2.10
432 433 8.197592 TGTGACTTATAAGTTGGGACTAGAAA 57.802 34.615 18.96 0.00 39.88 2.52
433 434 8.653191 TGTGACTTATAAGTTGGGACTAGAAAA 58.347 33.333 18.96 0.00 39.88 2.29
434 435 9.498176 GTGACTTATAAGTTGGGACTAGAAAAA 57.502 33.333 18.96 0.00 39.88 1.94
435 436 9.720769 TGACTTATAAGTTGGGACTAGAAAAAG 57.279 33.333 18.96 0.00 39.88 2.27
436 437 9.722184 GACTTATAAGTTGGGACTAGAAAAAGT 57.278 33.333 18.96 0.00 39.88 2.66
437 438 9.722184 ACTTATAAGTTGGGACTAGAAAAAGTC 57.278 33.333 12.50 0.00 39.73 3.01
458 459 5.801380 GTCCTAGGACTTATGAACCAAACA 58.199 41.667 31.12 0.00 41.57 2.83
459 460 5.875359 GTCCTAGGACTTATGAACCAAACAG 59.125 44.000 31.12 0.00 41.57 3.16
460 461 5.045869 TCCTAGGACTTATGAACCAAACAGG 60.046 44.000 7.62 0.00 45.67 4.00
461 462 4.034285 AGGACTTATGAACCAAACAGGG 57.966 45.455 0.00 0.00 43.89 4.45
462 463 2.492088 GGACTTATGAACCAAACAGGGC 59.508 50.000 0.00 0.00 43.89 5.19
463 464 2.492088 GACTTATGAACCAAACAGGGCC 59.508 50.000 0.00 0.00 43.89 5.80
464 465 2.110011 ACTTATGAACCAAACAGGGCCT 59.890 45.455 0.00 0.00 43.89 5.19
465 466 3.332485 ACTTATGAACCAAACAGGGCCTA 59.668 43.478 5.28 0.00 43.89 3.93
466 467 2.990740 ATGAACCAAACAGGGCCTAA 57.009 45.000 5.28 0.00 43.89 2.69
550 551 8.680903 ACAAATTGGTAGCATATCTTCTCAAAG 58.319 33.333 0.00 0.00 0.00 2.77
674 675 5.066593 GTCTTCTCAACCTGGATTCAAACT 58.933 41.667 0.00 0.00 0.00 2.66
680 681 4.515191 TCAACCTGGATTCAAACTTCTTCG 59.485 41.667 0.00 0.00 0.00 3.79
1194 1239 1.133790 GATTGCAACACCTCCTGATGC 59.866 52.381 0.00 0.00 46.39 3.91
1228 1273 4.519437 CGAGGAGGCAGATGCGCA 62.519 66.667 14.96 14.96 43.26 6.09
1297 1342 2.849943 AGGCCATGTACAAAGGATACCA 59.150 45.455 18.86 0.00 37.17 3.25
1632 1678 3.805108 GCTCTTGAGCTTCTTGTTGGAGA 60.805 47.826 14.65 0.00 0.00 3.71
1721 1769 6.403866 AAGAAAACATTGGTTGCTCATGTA 57.596 33.333 0.00 0.00 37.30 2.29
2018 2066 4.448210 ACGAGTTGAGCTACCTTTTCAAA 58.552 39.130 0.00 0.00 33.10 2.69
2323 2374 8.198109 ACTTACCATGACAAGTTATACTGCTAG 58.802 37.037 0.00 0.00 30.89 3.42
2652 2719 7.712205 ACGGGTTCATGTATACCATTTAACTAC 59.288 37.037 13.64 0.00 36.10 2.73
2688 2755 6.618811 ACCTCATTTAACACTACAGTAGACG 58.381 40.000 14.94 7.33 0.00 4.18
2731 2798 4.079253 ACAATTCCCGTGCAGTTCTTAAT 58.921 39.130 0.00 0.00 0.00 1.40
2738 2805 5.584649 TCCCGTGCAGTTCTTAATAAATCTG 59.415 40.000 0.00 0.00 0.00 2.90
2744 2811 9.677567 GTGCAGTTCTTAATAAATCTGAAACAA 57.322 29.630 0.00 0.00 0.00 2.83
2806 2903 9.490379 AGTAAGGAAACTGAAACATAACTACTG 57.510 33.333 0.00 0.00 42.68 2.74
2812 2909 3.857052 TGAAACATAACTACTGCCTCCG 58.143 45.455 0.00 0.00 0.00 4.63
2921 3018 5.528690 TCATCATTGCATACTTCTGGTTAGC 59.471 40.000 0.00 0.00 0.00 3.09
2955 3052 2.673368 CCGATGAGAGTAGTTTTGGTGC 59.327 50.000 0.00 0.00 0.00 5.01
3017 3114 6.983906 ATCTGAAACTTTGTGGGAAAGATT 57.016 33.333 0.00 0.00 0.00 2.40
3028 3125 8.830201 TTTGTGGGAAAGATTATGAACAAATG 57.170 30.769 0.00 0.00 32.89 2.32
3044 3141 3.636300 ACAAATGTTAGAGGTGCTTGCAA 59.364 39.130 0.00 0.00 0.00 4.08
3064 3161 4.211794 GCAAAGTTTGGTGGTCAAATGATG 59.788 41.667 17.11 0.00 45.79 3.07
3252 3390 3.634568 TTGATAGGTTTTTGTGCACCG 57.365 42.857 15.69 0.00 38.21 4.94
3254 3392 1.201414 GATAGGTTTTTGTGCACCGGG 59.799 52.381 15.69 0.00 38.21 5.73
3291 3493 7.948034 TTTTCCCTTCGTGGATATAATTGTT 57.052 32.000 0.00 0.00 38.35 2.83
3348 3550 5.163513 CAATGCTATGTTTTGTTCCACTCC 58.836 41.667 0.00 0.00 0.00 3.85
3352 3554 4.142381 GCTATGTTTTGTTCCACTCCATCC 60.142 45.833 0.00 0.00 0.00 3.51
3457 3659 1.529226 TATGTGGCCACGTTTCAAGG 58.471 50.000 34.54 0.00 0.00 3.61
3461 3663 1.135333 GTGGCCACGTTTCAAGGAAAA 59.865 47.619 22.49 0.00 33.14 2.29
3462 3664 2.035632 TGGCCACGTTTCAAGGAAAAT 58.964 42.857 0.00 0.00 33.14 1.82
3488 3690 3.120854 CGATTAAGAAATCTGCTAGGCGC 60.121 47.826 0.00 0.00 39.56 6.53
3550 3752 7.067737 TGTGAGATTTTCGGAAACCTAAAAAGT 59.932 33.333 1.96 0.00 0.00 2.66
3581 3783 2.510768 ATAACCGACCATCTCGAAGC 57.489 50.000 0.00 0.00 46.14 3.86
3599 3801 0.109412 GCACAGAGCACTCATTTGGC 60.109 55.000 0.00 0.00 44.79 4.52
3626 3828 2.857186 TACATCTGCAAGGCTCACAA 57.143 45.000 0.00 0.00 0.00 3.33
3637 3839 1.207593 GCTCACAACACATGTCGCC 59.792 57.895 0.00 0.00 41.46 5.54
3654 3856 2.040544 CCACCGTCAAGGCATCCAC 61.041 63.158 0.00 0.00 46.52 4.02
3661 3863 3.965258 AAGGCATCCACGCACCCA 61.965 61.111 0.00 0.00 0.00 4.51
3662 3864 3.286694 AAGGCATCCACGCACCCAT 62.287 57.895 0.00 0.00 0.00 4.00
3663 3865 3.520862 GGCATCCACGCACCCATG 61.521 66.667 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 6.115446 TCTATTGATGGACAAACCTGATGTC 58.885 40.000 0.00 0.00 45.08 3.06
134 135 2.275134 TCATGGCTTGAAACTGCTGA 57.725 45.000 0.00 0.00 0.00 4.26
137 138 4.503741 TTACTTCATGGCTTGAAACTGC 57.496 40.909 15.56 0.00 43.64 4.40
145 146 9.860898 GTAATCAAATCTTTTACTTCATGGCTT 57.139 29.630 0.00 0.00 0.00 4.35
183 184 1.133606 TCCCTGGAAACAAACACCCTC 60.134 52.381 0.00 0.00 42.06 4.30
184 185 0.930726 TCCCTGGAAACAAACACCCT 59.069 50.000 0.00 0.00 42.06 4.34
185 186 1.037493 GTCCCTGGAAACAAACACCC 58.963 55.000 0.00 0.00 42.06 4.61
186 187 2.067365 AGTCCCTGGAAACAAACACC 57.933 50.000 0.00 0.00 42.06 4.16
187 188 5.508994 CCAATAAGTCCCTGGAAACAAACAC 60.509 44.000 0.00 0.00 42.06 3.32
188 189 4.586841 CCAATAAGTCCCTGGAAACAAACA 59.413 41.667 0.00 0.00 42.06 2.83
189 190 4.587262 ACCAATAAGTCCCTGGAAACAAAC 59.413 41.667 0.00 0.00 42.06 2.93
190 191 4.810345 ACCAATAAGTCCCTGGAAACAAA 58.190 39.130 0.00 0.00 42.06 2.83
191 192 4.463050 ACCAATAAGTCCCTGGAAACAA 57.537 40.909 0.00 0.00 42.06 2.83
192 193 4.463050 AACCAATAAGTCCCTGGAAACA 57.537 40.909 0.00 0.00 39.59 2.83
193 194 5.417894 CCTAAACCAATAAGTCCCTGGAAAC 59.582 44.000 0.00 0.00 34.16 2.78
194 195 5.517655 CCCTAAACCAATAAGTCCCTGGAAA 60.518 44.000 0.00 0.00 34.16 3.13
195 196 4.017867 CCCTAAACCAATAAGTCCCTGGAA 60.018 45.833 0.00 0.00 34.16 3.53
196 197 3.526019 CCCTAAACCAATAAGTCCCTGGA 59.474 47.826 0.00 0.00 34.16 3.86
197 198 3.526019 TCCCTAAACCAATAAGTCCCTGG 59.474 47.826 0.00 0.00 36.24 4.45
198 199 4.227527 AGTCCCTAAACCAATAAGTCCCTG 59.772 45.833 0.00 0.00 0.00 4.45
199 200 4.445564 AGTCCCTAAACCAATAAGTCCCT 58.554 43.478 0.00 0.00 0.00 4.20
200 201 4.857130 AGTCCCTAAACCAATAAGTCCC 57.143 45.455 0.00 0.00 0.00 4.46
201 202 8.640063 TTTTAAGTCCCTAAACCAATAAGTCC 57.360 34.615 0.00 0.00 0.00 3.85
224 225 6.301169 AGATGAGACTTATCGGGACTTTTT 57.699 37.500 1.85 0.00 0.00 1.94
225 226 5.941555 AGATGAGACTTATCGGGACTTTT 57.058 39.130 1.85 0.00 0.00 2.27
226 227 7.266400 GTTTAGATGAGACTTATCGGGACTTT 58.734 38.462 1.85 0.00 0.00 2.66
227 228 6.183360 GGTTTAGATGAGACTTATCGGGACTT 60.183 42.308 1.85 0.00 0.00 3.01
228 229 5.302313 GGTTTAGATGAGACTTATCGGGACT 59.698 44.000 1.85 0.00 0.00 3.85
229 230 5.068723 TGGTTTAGATGAGACTTATCGGGAC 59.931 44.000 1.85 2.61 0.00 4.46
230 231 5.205821 TGGTTTAGATGAGACTTATCGGGA 58.794 41.667 1.85 0.00 0.00 5.14
231 232 5.531122 TGGTTTAGATGAGACTTATCGGG 57.469 43.478 1.85 0.00 0.00 5.14
232 233 6.816640 TGTTTGGTTTAGATGAGACTTATCGG 59.183 38.462 1.85 0.00 0.00 4.18
233 234 7.010552 CCTGTTTGGTTTAGATGAGACTTATCG 59.989 40.741 1.85 0.00 0.00 2.92
234 235 8.041323 TCCTGTTTGGTTTAGATGAGACTTATC 58.959 37.037 0.00 0.00 37.07 1.75
235 236 7.918076 TCCTGTTTGGTTTAGATGAGACTTAT 58.082 34.615 0.00 0.00 37.07 1.73
236 237 7.311092 TCCTGTTTGGTTTAGATGAGACTTA 57.689 36.000 0.00 0.00 37.07 2.24
237 238 6.187727 TCCTGTTTGGTTTAGATGAGACTT 57.812 37.500 0.00 0.00 37.07 3.01
238 239 5.280215 CCTCCTGTTTGGTTTAGATGAGACT 60.280 44.000 0.00 0.00 37.07 3.24
239 240 4.938226 CCTCCTGTTTGGTTTAGATGAGAC 59.062 45.833 0.00 0.00 37.07 3.36
240 241 4.019321 CCCTCCTGTTTGGTTTAGATGAGA 60.019 45.833 0.00 0.00 37.07 3.27
241 242 4.019321 TCCCTCCTGTTTGGTTTAGATGAG 60.019 45.833 0.00 0.00 37.07 2.90
242 243 3.913799 TCCCTCCTGTTTGGTTTAGATGA 59.086 43.478 0.00 0.00 37.07 2.92
243 244 4.010349 GTCCCTCCTGTTTGGTTTAGATG 58.990 47.826 0.00 0.00 37.07 2.90
244 245 3.916989 AGTCCCTCCTGTTTGGTTTAGAT 59.083 43.478 0.00 0.00 37.07 1.98
245 246 3.323775 AGTCCCTCCTGTTTGGTTTAGA 58.676 45.455 0.00 0.00 37.07 2.10
246 247 3.790089 AGTCCCTCCTGTTTGGTTTAG 57.210 47.619 0.00 0.00 37.07 1.85
247 248 5.853572 ATAAGTCCCTCCTGTTTGGTTTA 57.146 39.130 0.00 0.00 37.07 2.01
248 249 4.741928 ATAAGTCCCTCCTGTTTGGTTT 57.258 40.909 0.00 0.00 37.07 3.27
249 250 4.227527 CCTATAAGTCCCTCCTGTTTGGTT 59.772 45.833 0.00 0.00 37.07 3.67
250 251 3.780850 CCTATAAGTCCCTCCTGTTTGGT 59.219 47.826 0.00 0.00 37.07 3.67
251 252 3.136626 CCCTATAAGTCCCTCCTGTTTGG 59.863 52.174 0.00 0.00 37.10 3.28
252 253 4.037927 TCCCTATAAGTCCCTCCTGTTTG 58.962 47.826 0.00 0.00 0.00 2.93
253 254 4.038633 GTCCCTATAAGTCCCTCCTGTTT 58.961 47.826 0.00 0.00 0.00 2.83
254 255 3.275228 AGTCCCTATAAGTCCCTCCTGTT 59.725 47.826 0.00 0.00 0.00 3.16
255 256 2.866454 AGTCCCTATAAGTCCCTCCTGT 59.134 50.000 0.00 0.00 0.00 4.00
256 257 3.621682 AGTCCCTATAAGTCCCTCCTG 57.378 52.381 0.00 0.00 0.00 3.86
257 258 5.763239 TTAAGTCCCTATAAGTCCCTCCT 57.237 43.478 0.00 0.00 0.00 3.69
258 259 5.904169 ACTTTAAGTCCCTATAAGTCCCTCC 59.096 44.000 0.00 0.00 0.00 4.30
259 260 6.183360 CCACTTTAAGTCCCTATAAGTCCCTC 60.183 46.154 0.00 0.00 0.00 4.30
260 261 5.666265 CCACTTTAAGTCCCTATAAGTCCCT 59.334 44.000 0.00 0.00 0.00 4.20
261 262 5.163227 CCCACTTTAAGTCCCTATAAGTCCC 60.163 48.000 0.00 0.00 0.00 4.46
262 263 5.686913 GCCCACTTTAAGTCCCTATAAGTCC 60.687 48.000 0.00 0.00 0.00 3.85
263 264 5.104652 TGCCCACTTTAAGTCCCTATAAGTC 60.105 44.000 0.00 0.00 0.00 3.01
264 265 4.786454 TGCCCACTTTAAGTCCCTATAAGT 59.214 41.667 0.00 0.00 0.00 2.24
265 266 5.367945 TGCCCACTTTAAGTCCCTATAAG 57.632 43.478 0.00 0.00 0.00 1.73
266 267 5.987019 ATGCCCACTTTAAGTCCCTATAA 57.013 39.130 0.00 0.00 0.00 0.98
267 268 5.987019 AATGCCCACTTTAAGTCCCTATA 57.013 39.130 0.00 0.00 0.00 1.31
268 269 4.881157 AATGCCCACTTTAAGTCCCTAT 57.119 40.909 0.00 0.00 0.00 2.57
269 270 4.202631 ACAAATGCCCACTTTAAGTCCCTA 60.203 41.667 0.00 0.00 0.00 3.53
270 271 3.165071 CAAATGCCCACTTTAAGTCCCT 58.835 45.455 0.00 0.00 0.00 4.20
271 272 2.897326 ACAAATGCCCACTTTAAGTCCC 59.103 45.455 0.00 0.00 0.00 4.46
272 273 5.243060 AGTTACAAATGCCCACTTTAAGTCC 59.757 40.000 0.00 0.00 0.00 3.85
273 274 6.327279 AGTTACAAATGCCCACTTTAAGTC 57.673 37.500 0.00 0.00 0.00 3.01
274 275 6.724893 AAGTTACAAATGCCCACTTTAAGT 57.275 33.333 0.00 0.00 0.00 2.24
275 276 8.519526 TCATAAGTTACAAATGCCCACTTTAAG 58.480 33.333 0.00 0.00 0.00 1.85
276 277 8.410673 TCATAAGTTACAAATGCCCACTTTAA 57.589 30.769 0.00 0.00 0.00 1.52
277 278 8.410673 TTCATAAGTTACAAATGCCCACTTTA 57.589 30.769 0.00 0.00 0.00 1.85
278 279 6.909550 TCATAAGTTACAAATGCCCACTTT 57.090 33.333 0.00 0.00 0.00 2.66
279 280 6.909550 TTCATAAGTTACAAATGCCCACTT 57.090 33.333 0.00 0.00 0.00 3.16
280 281 6.909550 TTTCATAAGTTACAAATGCCCACT 57.090 33.333 0.00 0.00 0.00 4.00
281 282 9.301153 CTTATTTCATAAGTTACAAATGCCCAC 57.699 33.333 10.16 0.00 37.91 4.61
282 283 9.249053 TCTTATTTCATAAGTTACAAATGCCCA 57.751 29.630 10.16 0.00 42.21 5.36
283 284 9.516314 GTCTTATTTCATAAGTTACAAATGCCC 57.484 33.333 10.16 0.00 42.21 5.36
293 294 9.883142 CTCCTTGAGAGTCTTATTTCATAAGTT 57.117 33.333 0.00 0.00 37.60 2.66
294 295 9.261035 TCTCCTTGAGAGTCTTATTTCATAAGT 57.739 33.333 0.00 0.00 43.71 2.24
310 311 5.433712 AGTCCCTATAAGACTCTCCTTGAGA 59.566 44.000 0.00 0.00 45.39 3.27
311 312 5.701224 AGTCCCTATAAGACTCTCCTTGAG 58.299 45.833 0.24 0.00 40.61 3.02
312 313 5.735733 AGTCCCTATAAGACTCTCCTTGA 57.264 43.478 0.24 0.00 40.61 3.02
313 314 9.238368 CTATAAGTCCCTATAAGACTCTCCTTG 57.762 40.741 5.74 0.00 43.77 3.61
314 315 8.962205 ACTATAAGTCCCTATAAGACTCTCCTT 58.038 37.037 5.74 0.00 43.77 3.36
315 316 8.528543 ACTATAAGTCCCTATAAGACTCTCCT 57.471 38.462 5.74 0.00 43.77 3.69
316 317 9.016438 CAACTATAAGTCCCTATAAGACTCTCC 57.984 40.741 5.74 0.00 43.77 3.71
317 318 9.577222 ACAACTATAAGTCCCTATAAGACTCTC 57.423 37.037 5.74 0.00 43.77 3.20
328 329 9.448587 AAGACCATATTACAACTATAAGTCCCT 57.551 33.333 0.00 0.00 0.00 4.20
338 339 9.448587 AAGTCCCTATAAGACCATATTACAACT 57.551 33.333 0.09 0.00 34.67 3.16
361 362 6.607019 TGTTTGGTTTCTGGGACTTATAAGT 58.393 36.000 18.05 18.05 43.16 2.24
362 363 6.151144 CCTGTTTGGTTTCTGGGACTTATAAG 59.849 42.308 11.05 11.05 0.00 1.73
363 364 6.007703 CCTGTTTGGTTTCTGGGACTTATAA 58.992 40.000 0.00 0.00 0.00 0.98
364 365 5.566469 CCTGTTTGGTTTCTGGGACTTATA 58.434 41.667 0.00 0.00 0.00 0.98
365 366 4.407365 CCTGTTTGGTTTCTGGGACTTAT 58.593 43.478 0.00 0.00 0.00 1.73
366 367 3.827722 CCTGTTTGGTTTCTGGGACTTA 58.172 45.455 0.00 0.00 0.00 2.24
367 368 2.666317 CCTGTTTGGTTTCTGGGACTT 58.334 47.619 0.00 0.00 0.00 3.01
368 369 2.364972 CCTGTTTGGTTTCTGGGACT 57.635 50.000 0.00 0.00 0.00 3.85
379 380 5.705905 CCCTAAAAAGTCTCTACCTGTTTGG 59.294 44.000 0.00 0.00 42.93 3.28
380 381 6.427242 GTCCCTAAAAAGTCTCTACCTGTTTG 59.573 42.308 0.00 0.00 0.00 2.93
381 382 6.329460 AGTCCCTAAAAAGTCTCTACCTGTTT 59.671 38.462 0.00 0.00 0.00 2.83
382 383 5.845065 AGTCCCTAAAAAGTCTCTACCTGTT 59.155 40.000 0.00 0.00 0.00 3.16
383 384 5.404395 AGTCCCTAAAAAGTCTCTACCTGT 58.596 41.667 0.00 0.00 0.00 4.00
384 385 6.166982 CAAGTCCCTAAAAAGTCTCTACCTG 58.833 44.000 0.00 0.00 0.00 4.00
385 386 5.845065 ACAAGTCCCTAAAAAGTCTCTACCT 59.155 40.000 0.00 0.00 0.00 3.08
386 387 5.932883 CACAAGTCCCTAAAAAGTCTCTACC 59.067 44.000 0.00 0.00 0.00 3.18
387 388 6.645827 GTCACAAGTCCCTAAAAAGTCTCTAC 59.354 42.308 0.00 0.00 0.00 2.59
388 389 6.553852 AGTCACAAGTCCCTAAAAAGTCTCTA 59.446 38.462 0.00 0.00 0.00 2.43
389 390 5.367060 AGTCACAAGTCCCTAAAAAGTCTCT 59.633 40.000 0.00 0.00 0.00 3.10
390 391 5.612351 AGTCACAAGTCCCTAAAAAGTCTC 58.388 41.667 0.00 0.00 0.00 3.36
391 392 5.632034 AGTCACAAGTCCCTAAAAAGTCT 57.368 39.130 0.00 0.00 0.00 3.24
392 393 7.981102 ATAAGTCACAAGTCCCTAAAAAGTC 57.019 36.000 0.00 0.00 0.00 3.01
393 394 9.503399 CTTATAAGTCACAAGTCCCTAAAAAGT 57.497 33.333 4.18 0.00 0.00 2.66
394 395 9.503399 ACTTATAAGTCACAAGTCCCTAAAAAG 57.497 33.333 12.50 0.00 32.86 2.27
395 396 9.856162 AACTTATAAGTCACAAGTCCCTAAAAA 57.144 29.630 18.28 0.00 38.57 1.94
396 397 9.280174 CAACTTATAAGTCACAAGTCCCTAAAA 57.720 33.333 18.28 0.00 38.57 1.52
397 398 7.881232 CCAACTTATAAGTCACAAGTCCCTAAA 59.119 37.037 18.28 0.00 38.57 1.85
398 399 7.391620 CCAACTTATAAGTCACAAGTCCCTAA 58.608 38.462 18.28 0.00 38.57 2.69
399 400 6.070424 CCCAACTTATAAGTCACAAGTCCCTA 60.070 42.308 18.28 0.00 38.57 3.53
400 401 5.280521 CCCAACTTATAAGTCACAAGTCCCT 60.281 44.000 18.28 0.00 38.57 4.20
401 402 4.941873 CCCAACTTATAAGTCACAAGTCCC 59.058 45.833 18.28 0.00 38.57 4.46
402 403 5.642491 GTCCCAACTTATAAGTCACAAGTCC 59.358 44.000 18.28 0.00 38.57 3.85
403 404 6.465084 AGTCCCAACTTATAAGTCACAAGTC 58.535 40.000 18.28 6.78 38.57 3.01
404 405 6.435292 AGTCCCAACTTATAAGTCACAAGT 57.565 37.500 18.28 5.74 38.57 3.16
405 406 7.837863 TCTAGTCCCAACTTATAAGTCACAAG 58.162 38.462 18.28 9.78 38.57 3.16
406 407 7.786046 TCTAGTCCCAACTTATAAGTCACAA 57.214 36.000 18.28 3.05 38.57 3.33
407 408 7.786046 TTCTAGTCCCAACTTATAAGTCACA 57.214 36.000 18.28 1.06 38.57 3.58
408 409 9.498176 TTTTTCTAGTCCCAACTTATAAGTCAC 57.502 33.333 18.28 12.21 38.57 3.67
409 410 9.720769 CTTTTTCTAGTCCCAACTTATAAGTCA 57.279 33.333 18.28 1.07 38.57 3.41
410 411 9.722184 ACTTTTTCTAGTCCCAACTTATAAGTC 57.278 33.333 18.28 5.93 38.57 3.01
411 412 9.722184 GACTTTTTCTAGTCCCAACTTATAAGT 57.278 33.333 12.50 12.50 38.76 2.24
435 436 5.801380 TGTTTGGTTCATAAGTCCTAGGAC 58.199 41.667 31.29 31.29 44.86 3.85
436 437 5.045869 CCTGTTTGGTTCATAAGTCCTAGGA 60.046 44.000 7.62 7.62 0.00 2.94
437 438 5.186198 CCTGTTTGGTTCATAAGTCCTAGG 58.814 45.833 0.82 0.82 0.00 3.02
438 439 5.186198 CCCTGTTTGGTTCATAAGTCCTAG 58.814 45.833 0.00 0.00 0.00 3.02
439 440 4.566907 GCCCTGTTTGGTTCATAAGTCCTA 60.567 45.833 0.00 0.00 0.00 2.94
440 441 3.814316 GCCCTGTTTGGTTCATAAGTCCT 60.814 47.826 0.00 0.00 0.00 3.85
441 442 2.492088 GCCCTGTTTGGTTCATAAGTCC 59.508 50.000 0.00 0.00 0.00 3.85
442 443 2.492088 GGCCCTGTTTGGTTCATAAGTC 59.508 50.000 0.00 0.00 0.00 3.01
443 444 2.110011 AGGCCCTGTTTGGTTCATAAGT 59.890 45.455 0.00 0.00 0.00 2.24
444 445 2.807676 AGGCCCTGTTTGGTTCATAAG 58.192 47.619 0.00 0.00 0.00 1.73
445 446 2.990740 AGGCCCTGTTTGGTTCATAA 57.009 45.000 0.00 0.00 0.00 1.90
446 447 4.083565 GTTTAGGCCCTGTTTGGTTCATA 58.916 43.478 0.00 0.00 0.00 2.15
447 448 2.897326 GTTTAGGCCCTGTTTGGTTCAT 59.103 45.455 0.00 0.00 0.00 2.57
448 449 2.312390 GTTTAGGCCCTGTTTGGTTCA 58.688 47.619 0.00 0.00 0.00 3.18
449 450 1.616865 GGTTTAGGCCCTGTTTGGTTC 59.383 52.381 0.00 0.00 0.00 3.62
450 451 1.062810 TGGTTTAGGCCCTGTTTGGTT 60.063 47.619 0.00 0.00 0.00 3.67
451 452 0.558712 TGGTTTAGGCCCTGTTTGGT 59.441 50.000 0.00 0.00 0.00 3.67
452 453 0.966179 GTGGTTTAGGCCCTGTTTGG 59.034 55.000 0.00 0.00 0.00 3.28
453 454 1.698506 TGTGGTTTAGGCCCTGTTTG 58.301 50.000 0.00 0.00 0.00 2.93
454 455 2.247358 CATGTGGTTTAGGCCCTGTTT 58.753 47.619 0.00 0.00 0.00 2.83
455 456 1.923356 CATGTGGTTTAGGCCCTGTT 58.077 50.000 0.00 0.00 0.00 3.16
456 457 0.611896 GCATGTGGTTTAGGCCCTGT 60.612 55.000 0.00 0.00 0.00 4.00
457 458 0.611618 TGCATGTGGTTTAGGCCCTG 60.612 55.000 0.00 0.00 0.00 4.45
458 459 0.323725 CTGCATGTGGTTTAGGCCCT 60.324 55.000 0.00 0.00 0.00 5.19
459 460 0.323360 TCTGCATGTGGTTTAGGCCC 60.323 55.000 0.00 0.00 0.00 5.80
460 461 0.811281 GTCTGCATGTGGTTTAGGCC 59.189 55.000 0.00 0.00 0.00 5.19
461 462 1.533625 TGTCTGCATGTGGTTTAGGC 58.466 50.000 0.00 0.00 0.00 3.93
462 463 3.309682 CGTATGTCTGCATGTGGTTTAGG 59.690 47.826 0.00 0.00 36.58 2.69
463 464 3.309682 CCGTATGTCTGCATGTGGTTTAG 59.690 47.826 0.00 0.00 36.58 1.85
464 465 3.055747 TCCGTATGTCTGCATGTGGTTTA 60.056 43.478 0.00 0.00 36.58 2.01
465 466 2.083774 CCGTATGTCTGCATGTGGTTT 58.916 47.619 0.00 0.00 36.58 3.27
466 467 1.277842 TCCGTATGTCTGCATGTGGTT 59.722 47.619 0.00 0.00 36.58 3.67
640 641 5.417266 CAGGTTGAGAAGACAGAGTCTATCA 59.583 44.000 0.39 5.66 42.59 2.15
642 643 4.709397 CCAGGTTGAGAAGACAGAGTCTAT 59.291 45.833 0.00 0.00 42.59 1.98
646 647 2.964209 TCCAGGTTGAGAAGACAGAGT 58.036 47.619 0.00 0.00 0.00 3.24
715 716 6.173427 ACTAACCTGTTTTTGCAATTGGAT 57.827 33.333 7.72 0.00 0.00 3.41
1194 1239 0.028110 TCGATGACGATGCTGACTCG 59.972 55.000 0.00 0.00 43.81 4.18
1228 1273 7.669722 ACAACATCCCAGAATTTGTTATGTACT 59.330 33.333 0.00 0.00 32.80 2.73
1632 1678 0.768221 TCACCAGGAGGGCTGTTCTT 60.768 55.000 0.00 0.00 42.05 2.52
1721 1769 1.534729 GAACCCTTTCTTCGCCACAT 58.465 50.000 0.00 0.00 0.00 3.21
2018 2066 0.606401 CACTCCCGAATGCCAGTGTT 60.606 55.000 0.00 0.00 33.03 3.32
2323 2374 6.655003 TGGTGATTCTTCCTTGATAGAAACAC 59.345 38.462 13.50 13.50 45.64 3.32
2652 2719 9.383519 AGTGTTAAATGAGGTCTGTAATACATG 57.616 33.333 0.00 0.00 0.00 3.21
2658 2725 7.959175 ACTGTAGTGTTAAATGAGGTCTGTAA 58.041 34.615 0.00 0.00 0.00 2.41
2665 2732 6.527023 CACGTCTACTGTAGTGTTAAATGAGG 59.473 42.308 14.11 1.42 0.00 3.86
2675 2742 8.795341 CATAAAACATACACGTCTACTGTAGTG 58.205 37.037 14.11 9.01 40.17 2.74
2688 2755 5.960113 TGTTGGATGCCATAAAACATACAC 58.040 37.500 1.58 0.00 36.85 2.90
2864 2961 3.275228 ACCCCTTACTTGATACTCCCTCT 59.725 47.826 0.00 0.00 0.00 3.69
2921 3018 4.984161 ACTCTCATCGGCAAAAACAAAATG 59.016 37.500 0.00 0.00 0.00 2.32
2955 3052 0.176219 TATACTTTCGTGCGGGGGTG 59.824 55.000 0.00 0.00 0.00 4.61
3017 3114 6.349280 GCAAGCACCTCTAACATTTGTTCATA 60.349 38.462 0.00 0.00 39.31 2.15
3028 3125 3.990318 AACTTTGCAAGCACCTCTAAC 57.010 42.857 0.00 0.00 0.00 2.34
3044 3141 5.600696 GAACATCATTTGACCACCAAACTT 58.399 37.500 0.00 0.00 46.41 2.66
3099 3202 9.838975 TTTTACTCAAACACTGCACATATATTG 57.161 29.630 0.00 0.00 0.00 1.90
3128 3231 6.753913 TGACATCCAGGAGCTCTATAATTT 57.246 37.500 14.64 0.00 0.00 1.82
3129 3232 6.949117 ATGACATCCAGGAGCTCTATAATT 57.051 37.500 14.64 0.00 0.00 1.40
3134 3237 4.033009 TCAAATGACATCCAGGAGCTCTA 58.967 43.478 14.64 0.00 0.00 2.43
3143 3246 2.967745 TGGTGGTCAAATGACATCCA 57.032 45.000 18.29 18.29 46.47 3.41
3238 3376 1.962321 AACCCCGGTGCACAAAAACC 61.962 55.000 20.43 0.00 0.00 3.27
3244 3382 4.947147 GCTGAACCCCGGTGCACA 62.947 66.667 20.43 0.00 29.27 4.57
3252 3390 2.100197 GGAAAATAGTGGCTGAACCCC 58.900 52.381 0.00 0.00 37.83 4.95
3254 3392 3.087370 AGGGAAAATAGTGGCTGAACC 57.913 47.619 0.00 0.00 39.84 3.62
3291 3493 8.783093 GTCAATTACAAGCTTATATGTATGCCA 58.217 33.333 0.00 0.00 32.46 4.92
3348 3550 3.256383 TGTTGTCCTTGCTTGATTGGATG 59.744 43.478 0.00 0.00 0.00 3.51
3352 3554 3.996150 AGTGTTGTCCTTGCTTGATTG 57.004 42.857 0.00 0.00 0.00 2.67
3457 3659 8.902040 AGCAGATTTCTTAATCGAACATTTTC 57.098 30.769 0.00 0.00 43.99 2.29
3461 3663 6.203723 GCCTAGCAGATTTCTTAATCGAACAT 59.796 38.462 0.00 0.00 43.99 2.71
3462 3664 5.523916 GCCTAGCAGATTTCTTAATCGAACA 59.476 40.000 0.00 0.00 43.99 3.18
3550 3752 9.849166 GAGATGGTCGGTTATTTTAATTCAAAA 57.151 29.630 0.00 0.00 40.34 2.44
3581 3783 0.167470 CGCCAAATGAGTGCTCTGTG 59.833 55.000 0.00 0.00 0.00 3.66
3626 3828 2.357034 GACGGTGGCGACATGTGT 60.357 61.111 1.15 0.00 46.14 3.72
3637 3839 2.390599 CGTGGATGCCTTGACGGTG 61.391 63.158 0.00 0.00 34.25 4.94
3650 3852 4.408821 GGCTCATGGGTGCGTGGA 62.409 66.667 0.00 0.00 34.40 4.02
3654 3856 3.136123 CAAGGGCTCATGGGTGCG 61.136 66.667 0.00 0.00 34.40 5.34
3661 3863 3.832175 AGCACCTCAAGGGCTCAT 58.168 55.556 0.29 0.00 37.20 2.90
3663 3865 1.605058 TACGAGCACCTCAAGGGCTC 61.605 60.000 20.71 20.71 46.14 4.70
3709 3911 1.065491 TGCGCCAAGTTCTATCACCAT 60.065 47.619 4.18 0.00 0.00 3.55
3715 3917 0.802494 CCGTTTGCGCCAAGTTCTAT 59.198 50.000 4.18 0.00 36.67 1.98


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

AutoCloner maintained by Alex Coulton.