Multiple sequence alignment - TraesCS3A01G231100

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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 TraesCS3A01G231100 chr3A 100.000 2302 0 0 1 2302 431129334 431127033 0.000000e+00 4252.0
1 TraesCS3A01G231100 chr3B 93.570 1524 47 16 443 1945 418065551 418064058 0.000000e+00 2224.0
2 TraesCS3A01G231100 chr3B 96.262 107 4 0 1991 2097 418064055 418063949 2.350000e-40 176.0
3 TraesCS3A01G231100 chr3B 94.495 109 6 0 2194 2302 427338347 427338239 3.930000e-38 169.0
4 TraesCS3A01G231100 chr3B 85.897 156 9 6 84 234 418066129 418065982 1.100000e-33 154.0
5 TraesCS3A01G231100 chr3D 93.605 1376 61 14 335 1698 303396993 303398353 0.000000e+00 2028.0
6 TraesCS3A01G231100 chr3D 87.559 426 40 8 1733 2146 303398355 303398779 4.450000e-132 481.0
7 TraesCS3A01G231100 chr3D 90.446 157 6 2 84 234 303396844 303396997 5.020000e-47 198.0
8 TraesCS3A01G231100 chr3D 97.590 83 2 0 1 83 303396789 303396871 2.380000e-30 143.0
9 TraesCS3A01G231100 chr2B 100.000 107 0 0 232 338 157756758 157756864 5.020000e-47 198.0
10 TraesCS3A01G231100 chr2B 97.619 42 0 1 420 460 115721037 115720996 1.140000e-08 71.3
11 TraesCS3A01G231100 chr4A 97.391 115 3 0 225 339 467233721 467233835 1.800000e-46 196.0
12 TraesCS3A01G231100 chr4A 93.651 126 7 1 224 348 1725399 1725524 1.090000e-43 187.0
13 TraesCS3A01G231100 chr6B 96.581 117 4 0 229 345 156651437 156651553 6.490000e-46 195.0
14 TraesCS3A01G231100 chr6B 100.000 103 0 0 2200 2302 489453736 489453838 8.390000e-45 191.0
15 TraesCS3A01G231100 chr6B 93.277 119 7 1 2185 2302 27997270 27997388 8.450000e-40 174.0
16 TraesCS3A01G231100 chr5B 97.368 114 3 0 230 343 167283534 167283421 6.490000e-46 195.0
17 TraesCS3A01G231100 chr5B 95.082 122 3 1 218 339 473194842 473194724 3.020000e-44 189.0
18 TraesCS3A01G231100 chr5B 92.982 114 8 0 2189 2302 157044232 157044119 1.410000e-37 167.0
19 TraesCS3A01G231100 chr6D 96.581 117 3 1 226 341 112344370 112344486 2.330000e-45 193.0
20 TraesCS3A01G231100 chr7D 97.321 112 3 0 232 343 126669804 126669693 8.390000e-45 191.0
21 TraesCS3A01G231100 chr1A 99.020 102 1 0 2201 2302 372550143 372550042 1.400000e-42 183.0
22 TraesCS3A01G231100 chr2D 91.667 132 9 2 232 361 45681104 45680973 5.050000e-42 182.0
23 TraesCS3A01G231100 chr7B 97.115 104 3 0 2199 2302 450588139 450588036 2.350000e-40 176.0
24 TraesCS3A01G231100 chr7B 96.078 102 4 0 2201 2302 583388921 583388820 1.410000e-37 167.0
25 TraesCS3A01G231100 chr4D 96.262 107 4 0 2196 2302 73597644 73597750 2.350000e-40 176.0
26 TraesCS3A01G231100 chr4D 97.059 34 1 0 427 460 72677902 72677935 8.880000e-05 58.4
27 TraesCS3A01G231100 chr4B 97.115 104 3 0 2199 2302 240145349 240145452 2.350000e-40 176.0
28 TraesCS3A01G231100 chr4B 97.059 34 1 0 427 460 105711578 105711611 8.880000e-05 58.4
29 TraesCS3A01G231100 chr7A 88.889 81 7 2 8 87 683092640 683092561 5.230000e-17 99.0
30 TraesCS3A01G231100 chr6A 95.238 42 1 1 420 460 330136500 330136459 5.310000e-07 65.8
31 TraesCS3A01G231100 chr1B 95.238 42 1 1 420 460 417423535 417423576 5.310000e-07 65.8
32 TraesCS3A01G231100 chrUn 93.023 43 2 1 419 460 323126398 323126440 6.870000e-06 62.1
33 TraesCS3A01G231100 chrUn 93.023 43 2 1 419 460 323129614 323129656 6.870000e-06 62.1
34 TraesCS3A01G231100 chrUn 93.023 43 2 1 419 460 353153147 353153105 6.870000e-06 62.1


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 TraesCS3A01G231100 chr3A 431127033 431129334 2301 True 4252.000000 4252 100.000000 1 2302 1 chr3A.!!$R1 2301
1 TraesCS3A01G231100 chr3B 418063949 418066129 2180 True 851.333333 2224 91.909667 84 2097 3 chr3B.!!$R2 2013
2 TraesCS3A01G231100 chr3D 303396789 303398779 1990 False 712.500000 2028 92.300000 1 2146 4 chr3D.!!$F1 2145

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
247 254 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.0 13.34 13.34 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2506 0.037975 GCACTTTCCTGGCATGTTGG 60.038 55.0 0.0 0.0 0.0 3.77 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
63 64 3.213506 TGCGCATAATCTAGCCAAACAT 58.786 40.909 5.66 0.00 0.00 2.71
80 81 5.299148 CAAACATTCCCTTTTGCTTGATCA 58.701 37.500 0.00 0.00 0.00 2.92
81 82 4.796038 ACATTCCCTTTTGCTTGATCAG 57.204 40.909 0.00 0.00 0.00 2.90
82 83 3.512724 ACATTCCCTTTTGCTTGATCAGG 59.487 43.478 0.00 0.00 0.00 3.86
91 92 1.188863 GCTTGATCAGGGCCAAACAT 58.811 50.000 6.18 0.00 0.00 2.71
188 195 2.363306 TCAATCAAGTGTTGGCACCT 57.637 45.000 0.00 0.00 46.35 4.00
191 198 2.191128 ATCAAGTGTTGGCACCTCTC 57.809 50.000 0.00 0.00 46.35 3.20
193 200 1.211703 TCAAGTGTTGGCACCTCTCAA 59.788 47.619 0.00 0.00 46.35 3.02
227 234 4.983671 AAAACAGTCCCTCAACAGAAAC 57.016 40.909 0.00 0.00 0.00 2.78
234 241 4.409247 AGTCCCTCAACAGAAACAAGTACT 59.591 41.667 0.00 0.00 0.00 2.73
235 242 4.750598 GTCCCTCAACAGAAACAAGTACTC 59.249 45.833 0.00 0.00 0.00 2.59
236 243 4.065789 CCCTCAACAGAAACAAGTACTCC 58.934 47.826 0.00 0.00 0.00 3.85
237 244 4.065789 CCTCAACAGAAACAAGTACTCCC 58.934 47.826 0.00 0.00 0.00 4.30
238 245 4.202367 CCTCAACAGAAACAAGTACTCCCT 60.202 45.833 0.00 0.00 0.00 4.20
239 246 4.957296 TCAACAGAAACAAGTACTCCCTC 58.043 43.478 0.00 0.00 0.00 4.30
240 247 4.065789 CAACAGAAACAAGTACTCCCTCC 58.934 47.826 0.00 0.00 0.00 4.30
241 248 2.299297 ACAGAAACAAGTACTCCCTCCG 59.701 50.000 0.00 0.00 0.00 4.63
242 249 2.299297 CAGAAACAAGTACTCCCTCCGT 59.701 50.000 0.00 0.00 0.00 4.69
243 250 2.970640 AGAAACAAGTACTCCCTCCGTT 59.029 45.455 0.00 0.00 0.00 4.44
244 251 3.006644 AGAAACAAGTACTCCCTCCGTTC 59.993 47.826 0.00 0.00 0.00 3.95
245 252 0.886563 ACAAGTACTCCCTCCGTTCG 59.113 55.000 0.00 0.00 0.00 3.95
246 253 0.172803 CAAGTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
247 254 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
248 255 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
249 256 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
250 257 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
251 258 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
252 259 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
253 260 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
254 261 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
255 262 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
256 263 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
257 264 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
258 265 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
259 266 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
260 267 3.256383 TCCGTTCGGAATTACTTGTCTCA 59.744 43.478 11.66 0.00 0.00 3.27
261 268 3.612860 CCGTTCGGAATTACTTGTCTCAG 59.387 47.826 5.19 0.00 0.00 3.35
262 269 4.482386 CGTTCGGAATTACTTGTCTCAGA 58.518 43.478 0.00 0.00 0.00 3.27
263 270 4.921515 CGTTCGGAATTACTTGTCTCAGAA 59.078 41.667 0.00 0.00 0.00 3.02
264 271 5.404366 CGTTCGGAATTACTTGTCTCAGAAA 59.596 40.000 0.00 0.00 0.00 2.52
265 272 6.090898 CGTTCGGAATTACTTGTCTCAGAAAT 59.909 38.462 0.00 0.00 0.00 2.17
266 273 6.968131 TCGGAATTACTTGTCTCAGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
267 274 5.874810 TCGGAATTACTTGTCTCAGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
268 275 5.874810 CGGAATTACTTGTCTCAGAAATGGA 59.125 40.000 0.00 0.00 0.00 3.41
269 276 6.540189 CGGAATTACTTGTCTCAGAAATGGAT 59.460 38.462 0.00 0.00 0.00 3.41
270 277 7.466455 CGGAATTACTTGTCTCAGAAATGGATG 60.466 40.741 0.00 0.00 0.00 3.51
271 278 6.690194 ATTACTTGTCTCAGAAATGGATGC 57.310 37.500 0.00 0.00 0.00 3.91
272 279 4.025040 ACTTGTCTCAGAAATGGATGCA 57.975 40.909 0.00 0.00 0.00 3.96
273 280 4.597004 ACTTGTCTCAGAAATGGATGCAT 58.403 39.130 0.00 0.00 0.00 3.96
274 281 4.639310 ACTTGTCTCAGAAATGGATGCATC 59.361 41.667 18.81 18.81 0.00 3.91
275 282 4.498894 TGTCTCAGAAATGGATGCATCT 57.501 40.909 25.28 6.25 0.00 2.90
276 283 5.619132 TGTCTCAGAAATGGATGCATCTA 57.381 39.130 25.28 20.79 0.00 1.98
277 284 5.608449 TGTCTCAGAAATGGATGCATCTAG 58.392 41.667 25.28 8.17 0.00 2.43
278 285 5.364735 TGTCTCAGAAATGGATGCATCTAGA 59.635 40.000 25.28 11.92 0.00 2.43
279 286 6.126968 TGTCTCAGAAATGGATGCATCTAGAA 60.127 38.462 25.28 10.04 0.00 2.10
280 287 6.202570 GTCTCAGAAATGGATGCATCTAGAAC 59.797 42.308 25.28 14.10 0.00 3.01
281 288 6.099413 TCTCAGAAATGGATGCATCTAGAACT 59.901 38.462 25.28 15.90 0.00 3.01
282 289 7.288621 TCTCAGAAATGGATGCATCTAGAACTA 59.711 37.037 25.28 5.34 0.00 2.24
283 290 7.795047 TCAGAAATGGATGCATCTAGAACTAA 58.205 34.615 25.28 4.56 0.00 2.24
284 291 8.267183 TCAGAAATGGATGCATCTAGAACTAAA 58.733 33.333 25.28 9.10 0.00 1.85
285 292 8.896744 CAGAAATGGATGCATCTAGAACTAAAA 58.103 33.333 25.28 0.70 0.00 1.52
286 293 9.638176 AGAAATGGATGCATCTAGAACTAAAAT 57.362 29.630 25.28 0.00 0.00 1.82
289 296 7.946655 TGGATGCATCTAGAACTAAAATACG 57.053 36.000 25.28 0.00 0.00 3.06
290 297 7.497595 TGGATGCATCTAGAACTAAAATACGT 58.502 34.615 25.28 0.00 0.00 3.57
291 298 7.652105 TGGATGCATCTAGAACTAAAATACGTC 59.348 37.037 25.28 3.59 0.00 4.34
292 299 7.868415 GGATGCATCTAGAACTAAAATACGTCT 59.132 37.037 25.28 0.00 0.00 4.18
293 300 9.894783 GATGCATCTAGAACTAAAATACGTCTA 57.105 33.333 19.70 0.00 0.00 2.59
294 301 9.900710 ATGCATCTAGAACTAAAATACGTCTAG 57.099 33.333 0.00 0.00 0.00 2.43
295 302 9.117183 TGCATCTAGAACTAAAATACGTCTAGA 57.883 33.333 10.27 10.27 38.94 2.43
309 316 9.698309 AAATACGTCTAGATACATCCATTTCTG 57.302 33.333 0.00 0.00 0.00 3.02
310 317 5.533482 ACGTCTAGATACATCCATTTCTGC 58.467 41.667 0.00 0.00 0.00 4.26
311 318 4.618912 CGTCTAGATACATCCATTTCTGCG 59.381 45.833 0.00 0.00 0.00 5.18
312 319 5.562890 CGTCTAGATACATCCATTTCTGCGA 60.563 44.000 0.00 0.00 0.00 5.10
313 320 5.631512 GTCTAGATACATCCATTTCTGCGAC 59.368 44.000 0.00 0.00 0.00 5.19
314 321 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
315 322 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
316 323 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
317 324 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
318 325 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
319 326 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
320 327 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
321 328 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
322 329 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
323 330 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
324 331 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
325 332 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
326 333 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
327 334 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
328 335 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
329 336 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
330 337 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
331 338 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
332 339 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
333 340 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
334 341 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
335 342 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
336 343 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
337 344 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
338 345 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
339 346 0.251297 TTCCGAACGGAGGGAGTACA 60.251 55.000 15.34 0.00 46.06 2.90
415 457 6.157211 CCACTATCCCATAACATAAGACGTC 58.843 44.000 7.70 7.70 0.00 4.34
474 572 4.217983 AGGGAGTACGAAACAGAGTACAAG 59.782 45.833 8.22 0.00 43.98 3.16
478 576 3.402628 ACGAAACAGAGTACAAGCCAT 57.597 42.857 0.00 0.00 0.00 4.40
505 847 4.515191 TCTCAAGGACACATGCAACTAAAC 59.485 41.667 0.00 0.00 0.00 2.01
660 1008 6.980397 CAGCAAACCTTCTTGTACAAGATTTT 59.020 34.615 33.02 26.86 45.78 1.82
661 1009 8.134895 CAGCAAACCTTCTTGTACAAGATTTTA 58.865 33.333 33.02 20.03 45.78 1.52
1072 1427 0.743345 GCCTACCAAGGTTAGTGCCG 60.743 60.000 0.00 0.00 45.64 5.69
1207 1562 5.795972 CAGCTGATGTCATATTGAGATCCT 58.204 41.667 8.42 1.48 43.97 3.24
1432 1792 4.017877 GGCGCTGACAGTGTGTGC 62.018 66.667 17.01 5.45 36.59 4.57
1543 1903 4.260011 CCATTTTACGTGTGTTTGTTTGGC 60.260 41.667 0.00 0.00 0.00 4.52
1546 1906 2.734276 ACGTGTGTTTGTTTGGCTTT 57.266 40.000 0.00 0.00 0.00 3.51
1579 1939 9.254133 CAAATACAATAACACAAACACCAATCA 57.746 29.630 0.00 0.00 0.00 2.57
1606 1966 5.476599 CGAGACCCTAAGAATCATCATCTCT 59.523 44.000 0.00 0.00 0.00 3.10
1608 1968 6.142498 AGACCCTAAGAATCATCATCTCTGT 58.858 40.000 0.00 0.00 0.00 3.41
1651 2012 1.999024 GCAAAACCCATTATGCCAACG 59.001 47.619 0.00 0.00 32.73 4.10
1710 2071 2.360483 ACACAACCGCAATCATCAAACA 59.640 40.909 0.00 0.00 0.00 2.83
1717 2078 4.202101 ACCGCAATCATCAAACAAACAGAA 60.202 37.500 0.00 0.00 0.00 3.02
1744 2105 5.492895 TCAGGACACAGAACTGTTACAAAA 58.507 37.500 4.63 0.00 42.83 2.44
1762 2123 4.161189 ACAAAATCACACAACCAATCACCA 59.839 37.500 0.00 0.00 0.00 4.17
1797 2158 7.402811 TGATGTCTCAAAAAGTAACACTACG 57.597 36.000 0.00 0.00 32.87 3.51
1881 2243 0.846693 AGTCAAAGGTGGGCACTTCT 59.153 50.000 0.00 0.00 0.00 2.85
1889 2251 4.322057 AGGTGGGCACTTCTGAAATTAT 57.678 40.909 0.00 0.00 0.00 1.28
1894 2256 3.633986 GGGCACTTCTGAAATTATCCTGG 59.366 47.826 0.00 0.00 0.00 4.45
1895 2257 3.067320 GGCACTTCTGAAATTATCCTGGC 59.933 47.826 0.00 0.00 0.00 4.85
1913 2275 4.046938 TGGCGCATTTAGAAACAACAAA 57.953 36.364 10.83 0.00 0.00 2.83
1973 2336 6.202954 CAGTGACTTCCTAGTTTTTGTTCGAT 59.797 38.462 0.00 0.00 33.84 3.59
2011 2381 2.689983 CAGAACCCATGATTACAAGCCC 59.310 50.000 0.00 0.00 0.00 5.19
2097 2467 3.921677 TGTTTCGACTCATGTAGGTTCC 58.078 45.455 0.00 0.00 0.00 3.62
2102 2472 2.761208 CGACTCATGTAGGTTCCTCCTT 59.239 50.000 0.00 0.00 45.67 3.36
2103 2473 3.952323 CGACTCATGTAGGTTCCTCCTTA 59.048 47.826 0.00 0.00 45.67 2.69
2104 2474 4.401519 CGACTCATGTAGGTTCCTCCTTAA 59.598 45.833 0.00 0.00 45.67 1.85
2105 2475 5.105473 CGACTCATGTAGGTTCCTCCTTAAA 60.105 44.000 0.00 0.00 45.67 1.52
2106 2476 6.051179 ACTCATGTAGGTTCCTCCTTAAAC 57.949 41.667 0.00 0.00 45.67 2.01
2124 2497 6.258068 CCTTAAACGGATAGCAGGTAAAGAAG 59.742 42.308 0.00 0.00 0.00 2.85
2133 2506 2.742589 GCAGGTAAAGAAGTGTACAGGC 59.257 50.000 0.00 0.00 0.00 4.85
2135 2508 2.976882 AGGTAAAGAAGTGTACAGGCCA 59.023 45.455 5.01 0.00 0.00 5.36
2139 2512 3.508845 AAGAAGTGTACAGGCCAACAT 57.491 42.857 5.01 0.00 0.00 2.71
2150 2523 2.354902 GCCAACATGCCAGGAAAGT 58.645 52.632 0.00 0.00 0.00 2.66
2151 2524 0.037975 GCCAACATGCCAGGAAAGTG 60.038 55.000 0.00 0.00 0.00 3.16
2152 2525 0.037975 CCAACATGCCAGGAAAGTGC 60.038 55.000 0.00 0.00 0.00 4.40
2153 2526 0.675083 CAACATGCCAGGAAAGTGCA 59.325 50.000 0.00 0.00 39.68 4.57
2154 2527 0.675633 AACATGCCAGGAAAGTGCAC 59.324 50.000 9.40 9.40 37.92 4.57
2155 2528 0.467844 ACATGCCAGGAAAGTGCACA 60.468 50.000 21.04 0.00 37.92 4.57
2156 2529 0.038892 CATGCCAGGAAAGTGCACAC 60.039 55.000 21.04 9.77 37.92 3.82
2157 2530 1.181098 ATGCCAGGAAAGTGCACACC 61.181 55.000 21.04 18.23 37.92 4.16
2158 2531 1.827789 GCCAGGAAAGTGCACACCA 60.828 57.895 21.04 0.00 0.00 4.17
2159 2532 1.391157 GCCAGGAAAGTGCACACCAA 61.391 55.000 21.04 0.00 0.00 3.67
2160 2533 0.385390 CCAGGAAAGTGCACACCAAC 59.615 55.000 21.04 5.04 0.00 3.77
2161 2534 1.102154 CAGGAAAGTGCACACCAACA 58.898 50.000 21.04 0.00 0.00 3.33
2162 2535 1.476085 CAGGAAAGTGCACACCAACAA 59.524 47.619 21.04 0.00 0.00 2.83
2163 2536 2.094286 CAGGAAAGTGCACACCAACAAA 60.094 45.455 21.04 0.00 0.00 2.83
2164 2537 2.166254 AGGAAAGTGCACACCAACAAAG 59.834 45.455 21.04 0.00 0.00 2.77
2165 2538 2.094234 GGAAAGTGCACACCAACAAAGT 60.094 45.455 21.04 0.00 0.00 2.66
2166 2539 3.584834 GAAAGTGCACACCAACAAAGTT 58.415 40.909 21.04 0.00 0.00 2.66
2167 2540 2.652941 AGTGCACACCAACAAAGTTG 57.347 45.000 21.04 3.00 0.00 3.16
2168 2541 2.166829 AGTGCACACCAACAAAGTTGA 58.833 42.857 21.04 0.00 0.00 3.18
2169 2542 2.760092 AGTGCACACCAACAAAGTTGAT 59.240 40.909 21.04 0.00 0.00 2.57
2170 2543 3.951037 AGTGCACACCAACAAAGTTGATA 59.049 39.130 21.04 0.00 0.00 2.15
2171 2544 4.041723 GTGCACACCAACAAAGTTGATAC 58.958 43.478 13.17 0.00 0.00 2.24
2172 2545 3.696548 TGCACACCAACAAAGTTGATACA 59.303 39.130 11.19 0.55 0.00 2.29
2173 2546 4.340666 TGCACACCAACAAAGTTGATACAT 59.659 37.500 11.19 0.00 0.00 2.29
2174 2547 5.163468 TGCACACCAACAAAGTTGATACATT 60.163 36.000 11.19 0.00 0.00 2.71
2175 2548 5.752955 GCACACCAACAAAGTTGATACATTT 59.247 36.000 11.19 0.00 0.00 2.32
2176 2549 6.257630 GCACACCAACAAAGTTGATACATTTT 59.742 34.615 11.19 0.00 0.00 1.82
2177 2550 7.620215 CACACCAACAAAGTTGATACATTTTG 58.380 34.615 11.19 0.00 36.77 2.44
2178 2551 6.760770 ACACCAACAAAGTTGATACATTTTGG 59.239 34.615 11.19 5.47 35.42 3.28
2179 2552 6.983307 CACCAACAAAGTTGATACATTTTGGA 59.017 34.615 11.19 0.00 35.42 3.53
2180 2553 7.493971 CACCAACAAAGTTGATACATTTTGGAA 59.506 33.333 11.19 0.00 35.42 3.53
2181 2554 7.494298 ACCAACAAAGTTGATACATTTTGGAAC 59.506 33.333 11.19 0.00 35.42 3.62
2182 2555 7.306515 CCAACAAAGTTGATACATTTTGGAACG 60.307 37.037 11.19 0.00 35.42 3.95
2183 2556 6.801575 ACAAAGTTGATACATTTTGGAACGT 58.198 32.000 0.00 0.00 35.42 3.99
2184 2557 7.262048 ACAAAGTTGATACATTTTGGAACGTT 58.738 30.769 0.00 0.00 35.42 3.99
2185 2558 7.434013 ACAAAGTTGATACATTTTGGAACGTTC 59.566 33.333 20.14 20.14 35.42 3.95
2186 2559 6.627395 AGTTGATACATTTTGGAACGTTCA 57.373 33.333 28.24 12.75 0.00 3.18
2187 2560 7.214467 AGTTGATACATTTTGGAACGTTCAT 57.786 32.000 28.24 11.48 0.00 2.57
2188 2561 7.657336 AGTTGATACATTTTGGAACGTTCATT 58.343 30.769 28.24 6.28 0.00 2.57
2189 2562 8.141268 AGTTGATACATTTTGGAACGTTCATTT 58.859 29.630 28.24 9.92 0.00 2.32
2190 2563 8.760569 GTTGATACATTTTGGAACGTTCATTTT 58.239 29.630 28.24 7.32 0.00 1.82
2191 2564 8.879342 TGATACATTTTGGAACGTTCATTTTT 57.121 26.923 28.24 8.36 0.00 1.94
2192 2565 8.973378 TGATACATTTTGGAACGTTCATTTTTC 58.027 29.630 28.24 11.34 0.00 2.29
2193 2566 9.191995 GATACATTTTGGAACGTTCATTTTTCT 57.808 29.630 28.24 9.10 0.00 2.52
2194 2567 7.232945 ACATTTTGGAACGTTCATTTTTCTG 57.767 32.000 28.24 17.40 0.00 3.02
2195 2568 6.816140 ACATTTTGGAACGTTCATTTTTCTGT 59.184 30.769 28.24 17.95 0.00 3.41
2196 2569 6.879188 TTTTGGAACGTTCATTTTTCTGTC 57.121 33.333 28.24 8.55 0.00 3.51
2197 2570 4.203950 TGGAACGTTCATTTTTCTGTCG 57.796 40.909 28.24 0.00 0.00 4.35
2198 2571 3.623960 TGGAACGTTCATTTTTCTGTCGT 59.376 39.130 28.24 0.00 32.73 4.34
2199 2572 4.809958 TGGAACGTTCATTTTTCTGTCGTA 59.190 37.500 28.24 0.00 31.82 3.43
2200 2573 5.467399 TGGAACGTTCATTTTTCTGTCGTAT 59.533 36.000 28.24 0.00 31.82 3.06
2201 2574 6.645827 TGGAACGTTCATTTTTCTGTCGTATA 59.354 34.615 28.24 0.00 31.82 1.47
2202 2575 6.952083 GGAACGTTCATTTTTCTGTCGTATAC 59.048 38.462 28.24 1.99 31.82 1.47
2203 2576 7.148689 GGAACGTTCATTTTTCTGTCGTATACT 60.149 37.037 28.24 0.00 31.82 2.12
2204 2577 7.274442 ACGTTCATTTTTCTGTCGTATACTC 57.726 36.000 0.56 0.00 0.00 2.59
2205 2578 6.309737 ACGTTCATTTTTCTGTCGTATACTCC 59.690 38.462 0.56 0.00 0.00 3.85
2206 2579 6.237755 CGTTCATTTTTCTGTCGTATACTCCC 60.238 42.308 0.56 0.00 0.00 4.30
2207 2580 6.540438 TCATTTTTCTGTCGTATACTCCCT 57.460 37.500 0.56 0.00 0.00 4.20
2208 2581 6.570692 TCATTTTTCTGTCGTATACTCCCTC 58.429 40.000 0.56 0.00 0.00 4.30
2209 2582 4.996788 TTTTCTGTCGTATACTCCCTCC 57.003 45.455 0.56 0.00 0.00 4.30
2210 2583 2.251409 TCTGTCGTATACTCCCTCCG 57.749 55.000 0.56 0.00 0.00 4.63
2211 2584 1.487976 TCTGTCGTATACTCCCTCCGT 59.512 52.381 0.56 0.00 0.00 4.69
2212 2585 2.092753 TCTGTCGTATACTCCCTCCGTT 60.093 50.000 0.56 0.00 0.00 4.44
2213 2586 2.290093 CTGTCGTATACTCCCTCCGTTC 59.710 54.545 0.56 0.00 0.00 3.95
2214 2587 1.262683 GTCGTATACTCCCTCCGTTCG 59.737 57.143 0.56 0.00 0.00 3.95
2215 2588 0.590195 CGTATACTCCCTCCGTTCGG 59.410 60.000 4.74 4.74 0.00 4.30
2216 2589 1.811558 CGTATACTCCCTCCGTTCGGA 60.812 57.143 13.34 13.34 0.00 4.55
2217 2590 2.301346 GTATACTCCCTCCGTTCGGAA 58.699 52.381 14.79 0.00 33.41 4.30
2218 2591 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
2219 2592 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2220 2593 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2221 2594 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2222 2595 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2223 2596 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2224 2597 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2225 2598 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2226 2599 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2227 2600 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2228 2601 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
2229 2602 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
2230 2603 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
2231 2604 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
2232 2605 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
2233 2606 5.343058 CGTTCGGAATTACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
2234 2607 6.034256 CGTTCGGAATTACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
2235 2608 7.389479 GTTCGGAATTACTTGTCGTAGAAATC 58.611 38.462 0.00 0.00 39.69 2.17
2236 2609 5.740569 TCGGAATTACTTGTCGTAGAAATCG 59.259 40.000 0.00 0.00 39.69 3.34
2237 2610 5.740569 CGGAATTACTTGTCGTAGAAATCGA 59.259 40.000 0.00 0.00 39.69 3.59
2238 2611 6.417044 CGGAATTACTTGTCGTAGAAATCGAT 59.583 38.462 0.00 0.00 39.69 3.59
2239 2612 7.556433 GGAATTACTTGTCGTAGAAATCGATG 58.444 38.462 0.00 0.00 39.69 3.84
2240 2613 7.222224 GGAATTACTTGTCGTAGAAATCGATGT 59.778 37.037 0.00 0.00 39.69 3.06
2241 2614 9.229784 GAATTACTTGTCGTAGAAATCGATGTA 57.770 33.333 0.00 0.00 39.69 2.29
2242 2615 9.745880 AATTACTTGTCGTAGAAATCGATGTAT 57.254 29.630 0.00 0.00 39.69 2.29
2243 2616 8.778141 TTACTTGTCGTAGAAATCGATGTATC 57.222 34.615 0.00 0.00 39.69 2.24
2244 2617 7.028926 ACTTGTCGTAGAAATCGATGTATCT 57.971 36.000 0.00 6.28 39.69 1.98
2245 2618 8.151141 ACTTGTCGTAGAAATCGATGTATCTA 57.849 34.615 0.00 5.26 39.69 1.98
2246 2619 8.283992 ACTTGTCGTAGAAATCGATGTATCTAG 58.716 37.037 13.26 7.49 39.69 2.43
2247 2620 7.958053 TGTCGTAGAAATCGATGTATCTAGA 57.042 36.000 13.26 0.00 39.69 2.43
2248 2621 8.549338 TGTCGTAGAAATCGATGTATCTAGAT 57.451 34.615 10.73 10.73 39.69 1.98
2249 2622 8.443937 TGTCGTAGAAATCGATGTATCTAGATG 58.556 37.037 15.79 0.00 39.69 2.90
2250 2623 8.444715 GTCGTAGAAATCGATGTATCTAGATGT 58.555 37.037 15.79 1.25 39.69 3.06
2251 2624 9.649167 TCGTAGAAATCGATGTATCTAGATGTA 57.351 33.333 15.79 4.44 32.30 2.29
2281 2654 8.774546 AGTTCTAGATACATCCATTTCTGAGA 57.225 34.615 0.00 0.00 0.00 3.27
2282 2655 8.637986 AGTTCTAGATACATCCATTTCTGAGAC 58.362 37.037 0.00 0.00 0.00 3.36
2283 2656 8.417106 GTTCTAGATACATCCATTTCTGAGACA 58.583 37.037 0.00 0.00 0.00 3.41
2284 2657 8.539117 TCTAGATACATCCATTTCTGAGACAA 57.461 34.615 0.00 0.00 0.00 3.18
2285 2658 8.637099 TCTAGATACATCCATTTCTGAGACAAG 58.363 37.037 0.00 0.00 0.00 3.16
2286 2659 7.192852 AGATACATCCATTTCTGAGACAAGT 57.807 36.000 0.00 0.00 0.00 3.16
2287 2660 8.311395 AGATACATCCATTTCTGAGACAAGTA 57.689 34.615 0.00 0.00 0.00 2.24
2288 2661 8.762645 AGATACATCCATTTCTGAGACAAGTAA 58.237 33.333 0.00 0.00 0.00 2.24
2289 2662 9.553064 GATACATCCATTTCTGAGACAAGTAAT 57.447 33.333 0.00 0.00 0.00 1.89
2290 2663 9.911788 ATACATCCATTTCTGAGACAAGTAATT 57.088 29.630 0.00 0.00 0.00 1.40
2291 2664 8.273780 ACATCCATTTCTGAGACAAGTAATTC 57.726 34.615 0.00 0.00 0.00 2.17
2292 2665 7.337942 ACATCCATTTCTGAGACAAGTAATTCC 59.662 37.037 0.00 0.00 0.00 3.01
2293 2666 5.874810 TCCATTTCTGAGACAAGTAATTCCG 59.125 40.000 0.00 0.00 0.00 4.30
2294 2667 5.874810 CCATTTCTGAGACAAGTAATTCCGA 59.125 40.000 0.00 0.00 0.00 4.55
2295 2668 6.371548 CCATTTCTGAGACAAGTAATTCCGAA 59.628 38.462 0.00 0.00 0.00 4.30
2296 2669 6.780706 TTTCTGAGACAAGTAATTCCGAAC 57.219 37.500 0.00 0.00 0.00 3.95
2297 2670 4.482386 TCTGAGACAAGTAATTCCGAACG 58.518 43.478 0.00 0.00 0.00 3.95
2298 2671 3.581755 TGAGACAAGTAATTCCGAACGG 58.418 45.455 6.94 6.94 0.00 4.44
2299 2672 3.256383 TGAGACAAGTAATTCCGAACGGA 59.744 43.478 12.04 12.04 43.52 4.69
2300 2673 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2301 2674 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 1.881925 GCAAAAGGGAATGTTTGGCCC 60.882 52.381 0.00 0.00 42.37 5.80
82 83 1.072173 AGCAAAAGGGAATGTTTGGCC 59.928 47.619 0.00 0.00 35.66 5.36
227 234 0.172803 CCGAACGGAGGGAGTACTTG 59.827 60.000 7.53 0.00 37.50 3.16
234 241 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
235 242 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
236 243 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
237 244 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
238 245 3.256383 TGAGACAAGTAATTCCGAACGGA 59.744 43.478 12.04 12.04 43.52 4.69
239 246 3.581755 TGAGACAAGTAATTCCGAACGG 58.418 45.455 6.94 6.94 0.00 4.44
240 247 4.482386 TCTGAGACAAGTAATTCCGAACG 58.518 43.478 0.00 0.00 0.00 3.95
241 248 6.780706 TTTCTGAGACAAGTAATTCCGAAC 57.219 37.500 0.00 0.00 0.00 3.95
242 249 6.371548 CCATTTCTGAGACAAGTAATTCCGAA 59.628 38.462 0.00 0.00 0.00 4.30
243 250 5.874810 CCATTTCTGAGACAAGTAATTCCGA 59.125 40.000 0.00 0.00 0.00 4.55
244 251 5.874810 TCCATTTCTGAGACAAGTAATTCCG 59.125 40.000 0.00 0.00 0.00 4.30
245 252 7.680588 GCATCCATTTCTGAGACAAGTAATTCC 60.681 40.741 0.00 0.00 0.00 3.01
246 253 7.148188 TGCATCCATTTCTGAGACAAGTAATTC 60.148 37.037 0.00 0.00 0.00 2.17
247 254 6.660521 TGCATCCATTTCTGAGACAAGTAATT 59.339 34.615 0.00 0.00 0.00 1.40
248 255 6.182627 TGCATCCATTTCTGAGACAAGTAAT 58.817 36.000 0.00 0.00 0.00 1.89
249 256 5.559770 TGCATCCATTTCTGAGACAAGTAA 58.440 37.500 0.00 0.00 0.00 2.24
250 257 5.164620 TGCATCCATTTCTGAGACAAGTA 57.835 39.130 0.00 0.00 0.00 2.24
251 258 4.025040 TGCATCCATTTCTGAGACAAGT 57.975 40.909 0.00 0.00 0.00 3.16
252 259 4.882427 AGATGCATCCATTTCTGAGACAAG 59.118 41.667 23.06 0.00 0.00 3.16
253 260 4.851843 AGATGCATCCATTTCTGAGACAA 58.148 39.130 23.06 0.00 0.00 3.18
254 261 4.498894 AGATGCATCCATTTCTGAGACA 57.501 40.909 23.06 0.00 0.00 3.41
255 262 5.851720 TCTAGATGCATCCATTTCTGAGAC 58.148 41.667 23.06 0.00 0.00 3.36
256 263 6.099413 AGTTCTAGATGCATCCATTTCTGAGA 59.901 38.462 23.06 9.83 0.00 3.27
257 264 6.289834 AGTTCTAGATGCATCCATTTCTGAG 58.710 40.000 23.06 7.85 0.00 3.35
258 265 6.244552 AGTTCTAGATGCATCCATTTCTGA 57.755 37.500 23.06 8.13 0.00 3.27
259 266 8.442632 TTTAGTTCTAGATGCATCCATTTCTG 57.557 34.615 23.06 6.03 0.00 3.02
260 267 9.638176 ATTTTAGTTCTAGATGCATCCATTTCT 57.362 29.630 23.06 17.09 0.00 2.52
263 270 8.993121 CGTATTTTAGTTCTAGATGCATCCATT 58.007 33.333 23.06 7.62 0.00 3.16
264 271 8.150945 ACGTATTTTAGTTCTAGATGCATCCAT 58.849 33.333 23.06 8.39 0.00 3.41
265 272 7.497595 ACGTATTTTAGTTCTAGATGCATCCA 58.502 34.615 23.06 9.05 0.00 3.41
266 273 7.868415 AGACGTATTTTAGTTCTAGATGCATCC 59.132 37.037 23.06 7.42 0.00 3.51
267 274 8.804688 AGACGTATTTTAGTTCTAGATGCATC 57.195 34.615 19.37 19.37 0.00 3.91
268 275 9.900710 CTAGACGTATTTTAGTTCTAGATGCAT 57.099 33.333 0.00 0.00 0.00 3.96
269 276 9.117183 TCTAGACGTATTTTAGTTCTAGATGCA 57.883 33.333 0.00 0.00 32.48 3.96
283 290 9.698309 CAGAAATGGATGTATCTAGACGTATTT 57.302 33.333 0.00 0.00 0.00 1.40
284 291 7.815068 GCAGAAATGGATGTATCTAGACGTATT 59.185 37.037 0.00 0.00 0.00 1.89
285 292 7.316640 GCAGAAATGGATGTATCTAGACGTAT 58.683 38.462 0.00 0.00 0.00 3.06
286 293 6.567891 CGCAGAAATGGATGTATCTAGACGTA 60.568 42.308 0.00 0.00 0.00 3.57
287 294 5.533482 GCAGAAATGGATGTATCTAGACGT 58.467 41.667 0.00 0.00 0.00 4.34
288 295 4.618912 CGCAGAAATGGATGTATCTAGACG 59.381 45.833 0.00 0.00 0.00 4.18
289 296 5.631512 GTCGCAGAAATGGATGTATCTAGAC 59.368 44.000 0.00 0.00 39.69 2.59
290 297 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
291 298 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
292 299 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
293 300 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
294 301 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
295 302 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
296 303 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
297 304 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
298 305 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
299 306 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
300 307 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
301 308 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
302 309 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
303 310 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
304 311 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
305 312 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
306 313 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
307 314 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
308 315 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
309 316 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
310 317 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
311 318 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
312 319 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
313 320 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
314 321 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
315 322 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
316 323 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
317 324 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
318 325 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
319 326 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
320 327 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
321 328 0.251297 TTGTACTCCCTCCGTTCGGA 60.251 55.000 13.34 13.34 0.00 4.55
322 329 0.604578 TTTGTACTCCCTCCGTTCGG 59.395 55.000 4.74 4.74 0.00 4.30
323 330 2.064014 GTTTTGTACTCCCTCCGTTCG 58.936 52.381 0.00 0.00 0.00 3.95
324 331 3.064931 CTGTTTTGTACTCCCTCCGTTC 58.935 50.000 0.00 0.00 0.00 3.95
325 332 2.701951 TCTGTTTTGTACTCCCTCCGTT 59.298 45.455 0.00 0.00 0.00 4.44
326 333 2.299297 CTCTGTTTTGTACTCCCTCCGT 59.701 50.000 0.00 0.00 0.00 4.69
327 334 2.299297 ACTCTGTTTTGTACTCCCTCCG 59.701 50.000 0.00 0.00 0.00 4.63
328 335 4.282703 TGTACTCTGTTTTGTACTCCCTCC 59.717 45.833 0.00 0.00 39.57 4.30
329 336 5.464030 TGTACTCTGTTTTGTACTCCCTC 57.536 43.478 0.00 0.00 39.57 4.30
330 337 5.221661 CCTTGTACTCTGTTTTGTACTCCCT 60.222 44.000 0.00 0.00 39.57 4.20
331 338 4.995487 CCTTGTACTCTGTTTTGTACTCCC 59.005 45.833 0.00 0.00 39.57 4.30
332 339 5.850614 TCCTTGTACTCTGTTTTGTACTCC 58.149 41.667 0.00 0.00 39.57 3.85
333 340 5.927115 CCTCCTTGTACTCTGTTTTGTACTC 59.073 44.000 0.00 0.00 39.57 2.59
334 341 5.742255 GCCTCCTTGTACTCTGTTTTGTACT 60.742 44.000 0.00 0.00 39.57 2.73
335 342 4.451435 GCCTCCTTGTACTCTGTTTTGTAC 59.549 45.833 0.00 0.00 39.37 2.90
336 343 4.101898 TGCCTCCTTGTACTCTGTTTTGTA 59.898 41.667 0.00 0.00 0.00 2.41
337 344 3.118038 TGCCTCCTTGTACTCTGTTTTGT 60.118 43.478 0.00 0.00 0.00 2.83
338 345 3.251004 GTGCCTCCTTGTACTCTGTTTTG 59.749 47.826 0.00 0.00 0.00 2.44
339 346 3.136626 AGTGCCTCCTTGTACTCTGTTTT 59.863 43.478 0.00 0.00 0.00 2.43
395 415 9.976511 CTAAAAGACGTCTTATGTTATGGGATA 57.023 33.333 29.91 4.65 34.61 2.59
437 535 0.035458 CTCCCTCCGTCCCATAATGC 59.965 60.000 0.00 0.00 0.00 3.56
505 847 8.853077 TGCTGATTCTATGGGATTTGTAATAG 57.147 34.615 0.00 0.00 0.00 1.73
1086 1441 3.426568 GCCGTGGCACTGAGCTTC 61.427 66.667 16.72 0.00 44.79 3.86
1143 1498 1.738099 CTCCCGTGGCTTTGACTCG 60.738 63.158 0.00 0.00 0.00 4.18
1207 1562 4.599041 AGCATGCAAGGTGAAGGTTATAA 58.401 39.130 21.98 0.00 0.00 0.98
1432 1792 4.472691 AATATTCGTCACATGGATTGCG 57.527 40.909 0.00 0.00 0.00 4.85
1543 1903 8.531622 TGTGTTATTGTATTTGCCAATCAAAG 57.468 30.769 0.00 0.00 46.68 2.77
1546 1906 7.928167 TGTTTGTGTTATTGTATTTGCCAATCA 59.072 29.630 0.00 0.00 34.51 2.57
1579 1939 2.544844 TGATTCTTAGGGTCTCGGGT 57.455 50.000 0.00 0.00 0.00 5.28
1628 1989 3.608316 TGGCATAATGGGTTTTGCTTC 57.392 42.857 4.18 0.00 40.66 3.86
1651 2012 9.477484 AATCGTTTGTCATGTACTCCTATTATC 57.523 33.333 0.00 0.00 0.00 1.75
1710 2071 6.378280 AGTTCTGTGTCCTGAAATTTCTGTTT 59.622 34.615 18.64 0.00 31.36 2.83
1717 2078 6.119536 TGTAACAGTTCTGTGTCCTGAAATT 58.880 36.000 6.22 0.00 31.36 1.82
1744 2105 5.335583 CGTTTATGGTGATTGGTTGTGTGAT 60.336 40.000 0.00 0.00 0.00 3.06
1762 2123 6.741992 TTTTGAGACATCATCAGCGTTTAT 57.258 33.333 0.00 0.00 34.73 1.40
1797 2158 1.609208 AAGTGTGGCTGGTCATTCAC 58.391 50.000 0.00 0.00 0.00 3.18
1881 2243 5.129634 TCTAAATGCGCCAGGATAATTTCA 58.870 37.500 4.18 0.00 0.00 2.69
1889 2251 2.192664 TGTTTCTAAATGCGCCAGGA 57.807 45.000 4.18 0.00 0.00 3.86
1973 2336 6.491745 TGGGTTCTGCAATGTTCTAATTTGTA 59.508 34.615 0.00 0.00 0.00 2.41
2011 2381 8.251026 TGAGGTGTACTTTATATCACTCACAAG 58.749 37.037 0.00 0.00 0.00 3.16
2045 2415 6.869695 TCTTTTACCCCTTCTGTTTTTGAAC 58.130 36.000 0.00 0.00 0.00 3.18
2097 2467 3.821421 ACCTGCTATCCGTTTAAGGAG 57.179 47.619 0.00 0.00 44.55 3.69
2101 2471 6.592607 CACTTCTTTACCTGCTATCCGTTTAA 59.407 38.462 0.00 0.00 0.00 1.52
2102 2472 6.103997 CACTTCTTTACCTGCTATCCGTTTA 58.896 40.000 0.00 0.00 0.00 2.01
2103 2473 4.935808 CACTTCTTTACCTGCTATCCGTTT 59.064 41.667 0.00 0.00 0.00 3.60
2104 2474 4.020485 ACACTTCTTTACCTGCTATCCGTT 60.020 41.667 0.00 0.00 0.00 4.44
2105 2475 3.514309 ACACTTCTTTACCTGCTATCCGT 59.486 43.478 0.00 0.00 0.00 4.69
2106 2476 4.124851 ACACTTCTTTACCTGCTATCCG 57.875 45.455 0.00 0.00 0.00 4.18
2133 2506 0.037975 GCACTTTCCTGGCATGTTGG 60.038 55.000 0.00 0.00 0.00 3.77
2135 2508 0.675633 GTGCACTTTCCTGGCATGTT 59.324 50.000 10.32 0.00 40.05 2.71
2139 2512 1.827789 GGTGTGCACTTTCCTGGCA 60.828 57.895 19.41 0.00 34.70 4.92
2146 2519 3.006323 TCAACTTTGTTGGTGTGCACTTT 59.994 39.130 19.41 0.00 0.00 2.66
2147 2520 2.560542 TCAACTTTGTTGGTGTGCACTT 59.439 40.909 19.41 0.00 0.00 3.16
2148 2521 2.166829 TCAACTTTGTTGGTGTGCACT 58.833 42.857 19.41 0.00 0.00 4.40
2149 2522 2.645730 TCAACTTTGTTGGTGTGCAC 57.354 45.000 10.75 10.75 0.00 4.57
2150 2523 3.696548 TGTATCAACTTTGTTGGTGTGCA 59.303 39.130 10.05 0.00 0.00 4.57
2151 2524 4.300189 TGTATCAACTTTGTTGGTGTGC 57.700 40.909 10.05 2.88 0.00 4.57
2152 2525 7.254387 CCAAAATGTATCAACTTTGTTGGTGTG 60.254 37.037 10.05 0.00 33.01 3.82
2153 2526 6.760770 CCAAAATGTATCAACTTTGTTGGTGT 59.239 34.615 10.05 1.37 33.01 4.16
2154 2527 6.983307 TCCAAAATGTATCAACTTTGTTGGTG 59.017 34.615 10.05 0.00 35.43 4.17
2155 2528 7.118496 TCCAAAATGTATCAACTTTGTTGGT 57.882 32.000 10.05 6.08 35.43 3.67
2156 2529 7.306515 CGTTCCAAAATGTATCAACTTTGTTGG 60.307 37.037 10.05 0.00 35.35 3.77
2157 2530 7.221838 ACGTTCCAAAATGTATCAACTTTGTTG 59.778 33.333 4.25 4.25 32.78 3.33
2158 2531 7.262048 ACGTTCCAAAATGTATCAACTTTGTT 58.738 30.769 0.00 0.00 32.78 2.83
2159 2532 6.801575 ACGTTCCAAAATGTATCAACTTTGT 58.198 32.000 0.00 0.00 32.78 2.83
2160 2533 7.433719 TGAACGTTCCAAAATGTATCAACTTTG 59.566 33.333 24.78 0.00 33.42 2.77
2161 2534 7.484975 TGAACGTTCCAAAATGTATCAACTTT 58.515 30.769 24.78 0.00 33.42 2.66
2162 2535 7.033530 TGAACGTTCCAAAATGTATCAACTT 57.966 32.000 24.78 0.00 33.42 2.66
2163 2536 6.627395 TGAACGTTCCAAAATGTATCAACT 57.373 33.333 24.78 0.00 33.42 3.16
2164 2537 7.867445 AATGAACGTTCCAAAATGTATCAAC 57.133 32.000 24.78 0.00 33.42 3.18
2165 2538 8.879342 AAAATGAACGTTCCAAAATGTATCAA 57.121 26.923 24.78 2.23 33.42 2.57
2166 2539 8.879342 AAAAATGAACGTTCCAAAATGTATCA 57.121 26.923 24.78 3.15 33.42 2.15
2167 2540 9.191995 AGAAAAATGAACGTTCCAAAATGTATC 57.808 29.630 24.78 11.34 33.42 2.24
2168 2541 8.977505 CAGAAAAATGAACGTTCCAAAATGTAT 58.022 29.630 24.78 6.74 33.42 2.29
2169 2542 7.976734 ACAGAAAAATGAACGTTCCAAAATGTA 59.023 29.630 24.78 4.49 33.42 2.29
2170 2543 6.816140 ACAGAAAAATGAACGTTCCAAAATGT 59.184 30.769 24.78 16.58 36.14 2.71
2171 2544 7.232945 ACAGAAAAATGAACGTTCCAAAATG 57.767 32.000 24.78 16.02 0.00 2.32
2172 2545 6.198216 CGACAGAAAAATGAACGTTCCAAAAT 59.802 34.615 24.78 9.31 0.00 1.82
2173 2546 5.513495 CGACAGAAAAATGAACGTTCCAAAA 59.487 36.000 24.78 7.18 0.00 2.44
2174 2547 5.031578 CGACAGAAAAATGAACGTTCCAAA 58.968 37.500 24.78 7.56 0.00 3.28
2175 2548 4.095185 ACGACAGAAAAATGAACGTTCCAA 59.905 37.500 24.78 8.34 34.99 3.53
2176 2549 3.623960 ACGACAGAAAAATGAACGTTCCA 59.376 39.130 24.78 13.50 34.99 3.53
2177 2550 4.205323 ACGACAGAAAAATGAACGTTCC 57.795 40.909 24.78 8.72 34.99 3.62
2178 2551 7.727017 AGTATACGACAGAAAAATGAACGTTC 58.273 34.615 21.42 21.42 37.65 3.95
2179 2552 7.148689 GGAGTATACGACAGAAAAATGAACGTT 60.149 37.037 0.00 0.00 37.65 3.99
2180 2553 6.309737 GGAGTATACGACAGAAAAATGAACGT 59.690 38.462 0.00 0.00 38.92 3.99
2181 2554 6.237755 GGGAGTATACGACAGAAAAATGAACG 60.238 42.308 0.00 0.00 0.00 3.95
2182 2555 6.817140 AGGGAGTATACGACAGAAAAATGAAC 59.183 38.462 0.00 0.00 0.00 3.18
2183 2556 6.942976 AGGGAGTATACGACAGAAAAATGAA 58.057 36.000 0.00 0.00 0.00 2.57
2184 2557 6.406624 GGAGGGAGTATACGACAGAAAAATGA 60.407 42.308 0.00 0.00 0.00 2.57
2185 2558 5.753921 GGAGGGAGTATACGACAGAAAAATG 59.246 44.000 0.00 0.00 0.00 2.32
2186 2559 5.451520 CGGAGGGAGTATACGACAGAAAAAT 60.452 44.000 0.00 0.00 0.00 1.82
2187 2560 4.142315 CGGAGGGAGTATACGACAGAAAAA 60.142 45.833 0.00 0.00 0.00 1.94
2188 2561 3.379372 CGGAGGGAGTATACGACAGAAAA 59.621 47.826 0.00 0.00 0.00 2.29
2189 2562 2.947652 CGGAGGGAGTATACGACAGAAA 59.052 50.000 0.00 0.00 0.00 2.52
2190 2563 2.092753 ACGGAGGGAGTATACGACAGAA 60.093 50.000 0.00 0.00 0.00 3.02
2191 2564 1.487976 ACGGAGGGAGTATACGACAGA 59.512 52.381 0.00 0.00 0.00 3.41
2192 2565 1.964552 ACGGAGGGAGTATACGACAG 58.035 55.000 0.00 0.00 0.00 3.51
2193 2566 2.292267 GAACGGAGGGAGTATACGACA 58.708 52.381 0.00 0.00 0.00 4.35
2194 2567 1.262683 CGAACGGAGGGAGTATACGAC 59.737 57.143 0.00 0.00 0.00 4.34
2195 2568 1.586422 CGAACGGAGGGAGTATACGA 58.414 55.000 0.00 0.00 0.00 3.43
2196 2569 0.590195 CCGAACGGAGGGAGTATACG 59.410 60.000 7.53 0.00 37.50 3.06
2197 2570 1.972872 TCCGAACGGAGGGAGTATAC 58.027 55.000 12.04 0.00 39.76 1.47
2198 2571 2.734755 TTCCGAACGGAGGGAGTATA 57.265 50.000 15.34 0.00 46.06 1.47
2199 2572 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
2200 2573 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2201 2574 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2202 2575 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2203 2576 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2204 2577 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2205 2578 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2206 2579 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2207 2580 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
2208 2581 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
2209 2582 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
2210 2583 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
2211 2584 6.252015 CGATTTCTACGACAAGTAATTCCGAA 59.748 38.462 0.00 0.00 34.45 4.30
2212 2585 5.740569 CGATTTCTACGACAAGTAATTCCGA 59.259 40.000 0.00 0.00 34.45 4.55
2213 2586 5.740569 TCGATTTCTACGACAAGTAATTCCG 59.259 40.000 0.00 0.00 34.45 4.30
2214 2587 7.222224 ACATCGATTTCTACGACAAGTAATTCC 59.778 37.037 0.00 0.00 42.37 3.01
2215 2588 8.116624 ACATCGATTTCTACGACAAGTAATTC 57.883 34.615 0.00 0.00 42.37 2.17
2216 2589 9.745880 ATACATCGATTTCTACGACAAGTAATT 57.254 29.630 0.00 0.00 42.37 1.40
2217 2590 9.395707 GATACATCGATTTCTACGACAAGTAAT 57.604 33.333 0.00 0.00 42.37 1.89
2218 2591 8.618677 AGATACATCGATTTCTACGACAAGTAA 58.381 33.333 0.00 0.00 42.37 2.24
2219 2592 8.151141 AGATACATCGATTTCTACGACAAGTA 57.849 34.615 0.00 0.00 42.37 2.24
2220 2593 7.028926 AGATACATCGATTTCTACGACAAGT 57.971 36.000 0.00 0.00 42.37 3.16
2221 2594 8.496751 TCTAGATACATCGATTTCTACGACAAG 58.503 37.037 0.00 0.00 42.37 3.16
2222 2595 8.374327 TCTAGATACATCGATTTCTACGACAA 57.626 34.615 0.00 0.00 42.37 3.18
2223 2596 7.958053 TCTAGATACATCGATTTCTACGACA 57.042 36.000 0.00 0.00 42.37 4.35
2224 2597 8.444715 ACATCTAGATACATCGATTTCTACGAC 58.555 37.037 4.54 0.00 42.37 4.34
2225 2598 8.549338 ACATCTAGATACATCGATTTCTACGA 57.451 34.615 4.54 0.00 43.65 3.43
2255 2628 9.868160 TCTCAGAAATGGATGTATCTAGAACTA 57.132 33.333 0.00 0.00 0.00 2.24
2256 2629 8.637986 GTCTCAGAAATGGATGTATCTAGAACT 58.362 37.037 0.00 0.00 0.00 3.01
2257 2630 8.417106 TGTCTCAGAAATGGATGTATCTAGAAC 58.583 37.037 0.00 0.00 0.00 3.01
2258 2631 8.539117 TGTCTCAGAAATGGATGTATCTAGAA 57.461 34.615 0.00 0.00 0.00 2.10
2259 2632 8.539117 TTGTCTCAGAAATGGATGTATCTAGA 57.461 34.615 0.00 0.00 0.00 2.43
2260 2633 8.420222 ACTTGTCTCAGAAATGGATGTATCTAG 58.580 37.037 0.00 0.00 0.00 2.43
2261 2634 8.311395 ACTTGTCTCAGAAATGGATGTATCTA 57.689 34.615 0.00 0.00 0.00 1.98
2262 2635 7.192852 ACTTGTCTCAGAAATGGATGTATCT 57.807 36.000 0.00 0.00 0.00 1.98
2263 2636 8.948631 TTACTTGTCTCAGAAATGGATGTATC 57.051 34.615 0.00 0.00 0.00 2.24
2264 2637 9.911788 AATTACTTGTCTCAGAAATGGATGTAT 57.088 29.630 0.00 0.00 0.00 2.29
2265 2638 9.383519 GAATTACTTGTCTCAGAAATGGATGTA 57.616 33.333 0.00 0.00 0.00 2.29
2266 2639 7.337942 GGAATTACTTGTCTCAGAAATGGATGT 59.662 37.037 0.00 0.00 0.00 3.06
2267 2640 7.466455 CGGAATTACTTGTCTCAGAAATGGATG 60.466 40.741 0.00 0.00 0.00 3.51
2268 2641 6.540189 CGGAATTACTTGTCTCAGAAATGGAT 59.460 38.462 0.00 0.00 0.00 3.41
2269 2642 5.874810 CGGAATTACTTGTCTCAGAAATGGA 59.125 40.000 0.00 0.00 0.00 3.41
2270 2643 5.874810 TCGGAATTACTTGTCTCAGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
2271 2644 6.968131 TCGGAATTACTTGTCTCAGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
2272 2645 6.090898 CGTTCGGAATTACTTGTCTCAGAAAT 59.909 38.462 0.00 0.00 0.00 2.17
2273 2646 5.404366 CGTTCGGAATTACTTGTCTCAGAAA 59.596 40.000 0.00 0.00 0.00 2.52
2274 2647 4.921515 CGTTCGGAATTACTTGTCTCAGAA 59.078 41.667 0.00 0.00 0.00 3.02
2275 2648 4.482386 CGTTCGGAATTACTTGTCTCAGA 58.518 43.478 0.00 0.00 0.00 3.27
2276 2649 3.612860 CCGTTCGGAATTACTTGTCTCAG 59.387 47.826 5.19 0.00 0.00 3.35
2277 2650 3.256383 TCCGTTCGGAATTACTTGTCTCA 59.744 43.478 11.66 0.00 0.00 3.27
2278 2651 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2279 2652 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2280 2653 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2281 2654 2.968675 CCTCCGTTCGGAATTACTTGT 58.031 47.619 14.79 0.00 33.41 3.16


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

AutoCloner maintained by Alex Coulton.