Multiple sequence alignment - TraesCS2B01G293100

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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 TraesCS2B01G293100 chr2B 100.000 2400 0 0 1 2400 408291357 408293756 0.000000e+00 4433.0
1 TraesCS2B01G293100 chr2A 91.871 1058 60 6 481 1537 453515690 453516722 0.000000e+00 1454.0
2 TraesCS2B01G293100 chr2A 98.491 464 7 0 1 464 768554999 768555462 0.000000e+00 819.0
3 TraesCS2B01G293100 chr3D 90.057 875 70 14 1534 2398 573450876 573450009 0.000000e+00 1118.0
4 TraesCS2B01G293100 chr3D 90.011 871 75 10 1535 2398 105127643 105128508 0.000000e+00 1116.0
5 TraesCS2B01G293100 chr3D 83.886 422 60 6 25 440 508191027 508191446 1.730000e-106 396.0
6 TraesCS2B01G293100 chr6B 89.588 874 76 12 1535 2400 213156724 213155858 0.000000e+00 1096.0
7 TraesCS2B01G293100 chr3B 89.576 873 77 12 1535 2398 532225735 532224868 0.000000e+00 1096.0
8 TraesCS2B01G293100 chr6A 89.462 873 76 13 1535 2398 613602669 613601804 0.000000e+00 1088.0
9 TraesCS2B01G293100 chr6A 99.138 464 4 0 1 464 184711183 184710720 0.000000e+00 835.0
10 TraesCS2B01G293100 chr6A 80.523 421 62 12 26 440 119336365 119336771 3.000000e-79 305.0
11 TraesCS2B01G293100 chr4D 89.462 873 77 13 1535 2398 306402579 306401713 0.000000e+00 1088.0
12 TraesCS2B01G293100 chr1B 89.450 872 79 11 1535 2398 4080431 4079565 0.000000e+00 1088.0
13 TraesCS2B01G293100 chr1B 93.333 60 2 2 685 743 655858079 655858021 1.180000e-13 87.9
14 TraesCS2B01G293100 chr5D 89.359 874 80 12 1534 2398 510617350 510616481 0.000000e+00 1086.0
15 TraesCS2B01G293100 chr6D 89.335 872 79 12 1535 2398 351974154 351975019 0.000000e+00 1083.0
16 TraesCS2B01G293100 chr5B 98.462 455 7 0 1 455 373221407 373220953 0.000000e+00 802.0
17 TraesCS2B01G293100 chr7D 97.386 459 11 1 1 458 106624124 106623666 0.000000e+00 780.0
18 TraesCS2B01G293100 chr7D 84.123 422 59 6 25 440 425723806 425723387 3.720000e-108 401.0
19 TraesCS2B01G293100 chr7D 83.886 422 60 6 25 440 489162731 489163150 1.730000e-106 396.0
20 TraesCS2B01G293100 chr2D 88.929 551 42 6 1001 1537 343167978 343168523 0.000000e+00 662.0
21 TraesCS2B01G293100 chr2D 94.751 381 20 0 1 381 559820362 559820742 5.710000e-166 593.0
22 TraesCS2B01G293100 chr2D 93.396 212 9 3 481 687 343160875 343161086 2.320000e-80 309.0
23 TraesCS2B01G293100 chr2D 93.204 103 6 1 892 994 343162255 343162356 1.490000e-32 150.0


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 TraesCS2B01G293100 chr2B 408291357 408293756 2399 False 4433.0 4433 100.000 1 2400 1 chr2B.!!$F1 2399
1 TraesCS2B01G293100 chr2A 453515690 453516722 1032 False 1454.0 1454 91.871 481 1537 1 chr2A.!!$F1 1056
2 TraesCS2B01G293100 chr3D 573450009 573450876 867 True 1118.0 1118 90.057 1534 2398 1 chr3D.!!$R1 864
3 TraesCS2B01G293100 chr3D 105127643 105128508 865 False 1116.0 1116 90.011 1535 2398 1 chr3D.!!$F1 863
4 TraesCS2B01G293100 chr6B 213155858 213156724 866 True 1096.0 1096 89.588 1535 2400 1 chr6B.!!$R1 865
5 TraesCS2B01G293100 chr3B 532224868 532225735 867 True 1096.0 1096 89.576 1535 2398 1 chr3B.!!$R1 863
6 TraesCS2B01G293100 chr6A 613601804 613602669 865 True 1088.0 1088 89.462 1535 2398 1 chr6A.!!$R2 863
7 TraesCS2B01G293100 chr4D 306401713 306402579 866 True 1088.0 1088 89.462 1535 2398 1 chr4D.!!$R1 863
8 TraesCS2B01G293100 chr1B 4079565 4080431 866 True 1088.0 1088 89.450 1535 2398 1 chr1B.!!$R1 863
9 TraesCS2B01G293100 chr5D 510616481 510617350 869 True 1086.0 1086 89.359 1534 2398 1 chr5D.!!$R1 864
10 TraesCS2B01G293100 chr6D 351974154 351975019 865 False 1083.0 1083 89.335 1535 2398 1 chr6D.!!$F1 863
11 TraesCS2B01G293100 chr2D 343167978 343168523 545 False 662.0 662 88.929 1001 1537 1 chr2D.!!$F1 536
12 TraesCS2B01G293100 chr2D 343160875 343162356 1481 False 229.5 309 93.300 481 994 2 chr2D.!!$F3 513

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
292 293 0.03601 CCTTCCCATCTGCTTGACGT 60.036 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 2632 0.105039 CATAGTCAAGCCCCGGAGAC 59.895 60.0 0.73 2.78 0.0 3.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.655364 CACGACGCTATCAGCCCG 60.655 66.667 0.00 6.20 38.18 6.13
18 19 3.900892 ACGACGCTATCAGCCCGG 61.901 66.667 0.00 0.00 38.18 5.73
19 20 4.647615 CGACGCTATCAGCCCGGG 62.648 72.222 19.09 19.09 38.18 5.73
20 21 3.224324 GACGCTATCAGCCCGGGA 61.224 66.667 29.31 2.74 38.18 5.14
21 22 2.524394 ACGCTATCAGCCCGGGAT 60.524 61.111 29.31 18.54 38.18 3.85
22 23 2.047844 CGCTATCAGCCCGGGATG 60.048 66.667 33.26 33.26 38.18 3.51
23 24 2.348998 GCTATCAGCCCGGGATGG 59.651 66.667 36.99 22.81 34.48 3.51
32 33 4.240103 CCGGGATGGCGATGCAGA 62.240 66.667 2.14 0.00 0.00 4.26
33 34 2.969238 CGGGATGGCGATGCAGAC 60.969 66.667 2.14 0.00 0.00 3.51
34 35 2.969238 GGGATGGCGATGCAGACG 60.969 66.667 10.94 10.94 0.00 4.18
35 36 2.969238 GGATGGCGATGCAGACGG 60.969 66.667 15.72 0.00 0.00 4.79
54 55 4.373116 GGAAGGACGACGGCTGCA 62.373 66.667 0.00 0.00 0.00 4.41
55 56 2.357034 GAAGGACGACGGCTGCAA 60.357 61.111 0.00 0.00 0.00 4.08
56 57 2.665185 AAGGACGACGGCTGCAAC 60.665 61.111 0.00 0.00 0.00 4.17
57 58 3.454587 AAGGACGACGGCTGCAACA 62.455 57.895 0.00 0.00 0.00 3.33
58 59 3.414700 GGACGACGGCTGCAACAG 61.415 66.667 0.00 0.00 34.12 3.16
111 112 4.959596 GCCTCCTCGAGCGGCATC 62.960 72.222 28.56 8.55 43.25 3.91
112 113 4.637489 CCTCCTCGAGCGGCATCG 62.637 72.222 6.99 13.26 44.07 3.84
154 155 4.803426 GCGCTGAGGACGTGGGAG 62.803 72.222 0.00 0.00 0.00 4.30
155 156 3.062466 CGCTGAGGACGTGGGAGA 61.062 66.667 0.00 0.00 0.00 3.71
156 157 2.888863 GCTGAGGACGTGGGAGAG 59.111 66.667 0.00 0.00 0.00 3.20
157 158 2.888863 CTGAGGACGTGGGAGAGC 59.111 66.667 0.00 0.00 0.00 4.09
158 159 3.057547 CTGAGGACGTGGGAGAGCG 62.058 68.421 0.00 0.00 0.00 5.03
159 160 4.500116 GAGGACGTGGGAGAGCGC 62.500 72.222 0.00 0.00 0.00 5.92
264 265 4.059459 CACTTGCACGGACGCGAC 62.059 66.667 15.93 6.56 33.35 5.19
265 266 4.578898 ACTTGCACGGACGCGACA 62.579 61.111 15.93 0.00 33.35 4.35
266 267 3.767230 CTTGCACGGACGCGACAG 61.767 66.667 15.93 10.84 33.35 3.51
273 274 3.188786 GGACGCGACAGCACCATC 61.189 66.667 15.93 0.00 45.49 3.51
274 275 3.188786 GACGCGACAGCACCATCC 61.189 66.667 15.93 0.00 45.49 3.51
275 276 3.649277 GACGCGACAGCACCATCCT 62.649 63.158 15.93 0.00 45.49 3.24
276 277 2.434884 CGCGACAGCACCATCCTT 60.435 61.111 0.00 0.00 45.49 3.36
277 278 2.456119 CGCGACAGCACCATCCTTC 61.456 63.158 0.00 0.00 45.49 3.46
278 279 2.109126 GCGACAGCACCATCCTTCC 61.109 63.158 0.00 0.00 44.35 3.46
279 280 1.450312 CGACAGCACCATCCTTCCC 60.450 63.158 0.00 0.00 0.00 3.97
280 281 1.685224 GACAGCACCATCCTTCCCA 59.315 57.895 0.00 0.00 0.00 4.37
281 282 0.257039 GACAGCACCATCCTTCCCAT 59.743 55.000 0.00 0.00 0.00 4.00
282 283 0.257039 ACAGCACCATCCTTCCCATC 59.743 55.000 0.00 0.00 0.00 3.51
283 284 0.549950 CAGCACCATCCTTCCCATCT 59.450 55.000 0.00 0.00 0.00 2.90
284 285 0.549950 AGCACCATCCTTCCCATCTG 59.450 55.000 0.00 0.00 0.00 2.90
285 286 1.105759 GCACCATCCTTCCCATCTGC 61.106 60.000 0.00 0.00 0.00 4.26
286 287 0.549950 CACCATCCTTCCCATCTGCT 59.450 55.000 0.00 0.00 0.00 4.24
287 288 1.064166 CACCATCCTTCCCATCTGCTT 60.064 52.381 0.00 0.00 0.00 3.91
288 289 1.064166 ACCATCCTTCCCATCTGCTTG 60.064 52.381 0.00 0.00 0.00 4.01
289 290 1.213678 CCATCCTTCCCATCTGCTTGA 59.786 52.381 0.00 0.00 0.00 3.02
290 291 2.295885 CATCCTTCCCATCTGCTTGAC 58.704 52.381 0.00 0.00 0.00 3.18
291 292 0.250234 TCCTTCCCATCTGCTTGACG 59.750 55.000 0.00 0.00 0.00 4.35
292 293 0.036010 CCTTCCCATCTGCTTGACGT 60.036 55.000 0.00 0.00 0.00 4.34
293 294 1.363744 CTTCCCATCTGCTTGACGTC 58.636 55.000 9.11 9.11 0.00 4.34
294 295 0.389817 TTCCCATCTGCTTGACGTCG 60.390 55.000 11.62 0.00 0.00 5.12
295 296 1.811266 CCCATCTGCTTGACGTCGG 60.811 63.158 11.62 7.51 0.00 4.79
296 297 1.811266 CCATCTGCTTGACGTCGGG 60.811 63.158 11.62 7.13 0.00 5.14
297 298 2.125512 ATCTGCTTGACGTCGGGC 60.126 61.111 20.66 20.66 0.00 6.13
298 299 2.650116 ATCTGCTTGACGTCGGGCT 61.650 57.895 25.20 9.54 0.00 5.19
299 300 2.842394 ATCTGCTTGACGTCGGGCTG 62.842 60.000 25.20 24.14 0.00 4.85
300 301 3.573772 CTGCTTGACGTCGGGCTGA 62.574 63.158 25.20 11.38 0.00 4.26
301 302 2.811317 GCTTGACGTCGGGCTGAG 60.811 66.667 20.33 9.07 0.00 3.35
302 303 2.811317 CTTGACGTCGGGCTGAGC 60.811 66.667 11.62 0.00 0.00 4.26
316 317 4.168291 GAGCCTCGCAGGGGGAAG 62.168 72.222 4.65 0.00 35.37 3.46
317 318 4.722535 AGCCTCGCAGGGGGAAGA 62.723 66.667 4.65 0.00 35.37 2.87
318 319 4.168291 GCCTCGCAGGGGGAAGAG 62.168 72.222 4.65 0.00 35.37 2.85
319 320 2.364317 CCTCGCAGGGGGAAGAGA 60.364 66.667 0.00 0.00 32.84 3.10
320 321 2.430610 CCTCGCAGGGGGAAGAGAG 61.431 68.421 0.00 0.00 32.84 3.20
321 322 1.380515 CTCGCAGGGGGAAGAGAGA 60.381 63.158 0.00 0.00 34.17 3.10
322 323 1.380515 TCGCAGGGGGAAGAGAGAG 60.381 63.158 0.00 0.00 0.00 3.20
323 324 2.430610 CGCAGGGGGAAGAGAGAGG 61.431 68.421 0.00 0.00 0.00 3.69
324 325 2.069430 GCAGGGGGAAGAGAGAGGG 61.069 68.421 0.00 0.00 0.00 4.30
325 326 2.069430 CAGGGGGAAGAGAGAGGGC 61.069 68.421 0.00 0.00 0.00 5.19
326 327 2.041265 GGGGGAAGAGAGAGGGCA 59.959 66.667 0.00 0.00 0.00 5.36
327 328 1.616628 GGGGGAAGAGAGAGGGCAA 60.617 63.158 0.00 0.00 0.00 4.52
328 329 1.631071 GGGGGAAGAGAGAGGGCAAG 61.631 65.000 0.00 0.00 0.00 4.01
329 330 1.223211 GGGAAGAGAGAGGGCAAGC 59.777 63.158 0.00 0.00 0.00 4.01
330 331 1.557269 GGGAAGAGAGAGGGCAAGCA 61.557 60.000 0.00 0.00 0.00 3.91
331 332 0.107752 GGAAGAGAGAGGGCAAGCAG 60.108 60.000 0.00 0.00 0.00 4.24
332 333 0.107752 GAAGAGAGAGGGCAAGCAGG 60.108 60.000 0.00 0.00 0.00 4.85
333 334 1.560866 AAGAGAGAGGGCAAGCAGGG 61.561 60.000 0.00 0.00 0.00 4.45
334 335 3.013932 AGAGAGGGCAAGCAGGGG 61.014 66.667 0.00 0.00 0.00 4.79
335 336 3.011517 GAGAGGGCAAGCAGGGGA 61.012 66.667 0.00 0.00 0.00 4.81
336 337 3.334054 AGAGGGCAAGCAGGGGAC 61.334 66.667 0.00 0.00 0.00 4.46
337 338 3.334054 GAGGGCAAGCAGGGGACT 61.334 66.667 0.00 0.00 46.44 3.85
338 339 3.334054 AGGGCAAGCAGGGGACTC 61.334 66.667 0.00 0.00 40.21 3.36
339 340 4.432741 GGGCAAGCAGGGGACTCC 62.433 72.222 0.00 0.00 40.21 3.85
340 341 4.785453 GGCAAGCAGGGGACTCCG 62.785 72.222 0.00 0.00 40.21 4.63
341 342 4.785453 GCAAGCAGGGGACTCCGG 62.785 72.222 0.00 0.00 40.21 5.14
342 343 3.003173 CAAGCAGGGGACTCCGGA 61.003 66.667 2.93 2.93 40.21 5.14
343 344 2.041265 AAGCAGGGGACTCCGGAT 59.959 61.111 3.57 0.00 40.21 4.18
344 345 2.066999 AAGCAGGGGACTCCGGATC 61.067 63.158 3.57 4.89 40.21 3.36
345 346 2.444895 GCAGGGGACTCCGGATCT 60.445 66.667 3.57 0.00 40.21 2.75
346 347 2.801631 GCAGGGGACTCCGGATCTG 61.802 68.421 3.57 9.34 40.21 2.90
347 348 2.136878 CAGGGGACTCCGGATCTGG 61.137 68.421 15.09 15.09 40.21 3.86
348 349 3.551407 GGGGACTCCGGATCTGGC 61.551 72.222 16.48 0.00 0.00 4.85
349 350 3.551407 GGGACTCCGGATCTGGCC 61.551 72.222 16.48 4.69 0.00 5.36
350 351 2.444895 GGACTCCGGATCTGGCCT 60.445 66.667 16.48 2.42 0.00 5.19
351 352 2.503382 GGACTCCGGATCTGGCCTC 61.503 68.421 16.48 11.64 0.00 4.70
352 353 2.835431 ACTCCGGATCTGGCCTCG 60.835 66.667 16.48 6.58 0.00 4.63
353 354 3.610669 CTCCGGATCTGGCCTCGG 61.611 72.222 16.48 7.61 43.42 4.63
368 369 4.845580 CGGCAGCTGCAGGGGTAG 62.846 72.222 37.63 16.31 44.36 3.18
374 375 3.854669 CTGCAGGGGTAGCCGGAG 61.855 72.222 5.05 0.00 0.00 4.63
375 376 4.392166 TGCAGGGGTAGCCGGAGA 62.392 66.667 5.05 0.00 0.00 3.71
376 377 3.081409 GCAGGGGTAGCCGGAGAA 61.081 66.667 5.05 0.00 0.00 2.87
377 378 3.095347 GCAGGGGTAGCCGGAGAAG 62.095 68.421 5.05 0.00 0.00 2.85
378 379 2.041819 AGGGGTAGCCGGAGAAGG 60.042 66.667 5.05 0.00 0.00 3.46
379 380 3.162154 GGGGTAGCCGGAGAAGGG 61.162 72.222 5.05 0.00 0.00 3.95
380 381 2.042230 GGGTAGCCGGAGAAGGGA 60.042 66.667 5.05 0.00 0.00 4.20
381 382 2.134933 GGGTAGCCGGAGAAGGGAG 61.135 68.421 5.05 0.00 0.00 4.30
382 383 1.076192 GGTAGCCGGAGAAGGGAGA 60.076 63.158 5.05 0.00 0.00 3.71
383 384 0.470268 GGTAGCCGGAGAAGGGAGAT 60.470 60.000 5.05 0.00 0.00 2.75
384 385 0.963225 GTAGCCGGAGAAGGGAGATC 59.037 60.000 5.05 0.00 0.00 2.75
385 386 0.537600 TAGCCGGAGAAGGGAGATCG 60.538 60.000 5.05 0.00 0.00 3.69
386 387 1.828660 GCCGGAGAAGGGAGATCGA 60.829 63.158 5.05 0.00 0.00 3.59
387 388 1.801309 GCCGGAGAAGGGAGATCGAG 61.801 65.000 5.05 0.00 0.00 4.04
388 389 0.466555 CCGGAGAAGGGAGATCGAGT 60.467 60.000 0.00 0.00 0.00 4.18
389 390 0.948678 CGGAGAAGGGAGATCGAGTC 59.051 60.000 0.00 0.00 0.00 3.36
390 391 0.948678 GGAGAAGGGAGATCGAGTCG 59.051 60.000 6.09 6.09 0.00 4.18
391 392 0.309612 GAGAAGGGAGATCGAGTCGC 59.690 60.000 7.92 6.53 0.00 5.19
392 393 1.104577 AGAAGGGAGATCGAGTCGCC 61.105 60.000 7.92 2.74 45.24 5.54
393 394 2.395367 GAAGGGAGATCGAGTCGCCG 62.395 65.000 7.92 0.00 46.76 6.46
394 395 3.967335 GGGAGATCGAGTCGCCGG 61.967 72.222 7.92 0.00 46.76 6.13
395 396 4.632458 GGAGATCGAGTCGCCGGC 62.632 72.222 19.07 19.07 37.05 6.13
396 397 4.965858 GAGATCGAGTCGCCGGCG 62.966 72.222 42.13 42.13 41.35 6.46
452 453 4.569180 CCCATGGGCACTAGCGGG 62.569 72.222 20.41 0.00 43.41 6.13
454 455 4.488136 CATGGGCACTAGCGGGCA 62.488 66.667 10.17 0.00 43.41 5.36
455 456 4.181010 ATGGGCACTAGCGGGCAG 62.181 66.667 10.17 0.00 43.41 4.85
457 458 4.840005 GGGCACTAGCGGGCAGTC 62.840 72.222 10.17 0.00 43.41 3.51
460 461 3.449227 CACTAGCGGGCAGTCGGA 61.449 66.667 0.00 0.00 0.00 4.55
461 462 2.678934 ACTAGCGGGCAGTCGGAA 60.679 61.111 0.00 0.00 0.00 4.30
462 463 2.105128 CTAGCGGGCAGTCGGAAG 59.895 66.667 0.00 0.00 0.00 3.46
463 464 2.678934 TAGCGGGCAGTCGGAAGT 60.679 61.111 0.00 0.00 0.00 3.01
464 465 1.378911 TAGCGGGCAGTCGGAAGTA 60.379 57.895 0.00 0.00 0.00 2.24
465 466 0.754217 TAGCGGGCAGTCGGAAGTAT 60.754 55.000 0.00 0.00 0.00 2.12
466 467 1.883084 GCGGGCAGTCGGAAGTATG 60.883 63.158 0.00 0.00 0.00 2.39
467 468 1.813859 CGGGCAGTCGGAAGTATGA 59.186 57.895 0.00 0.00 0.00 2.15
468 469 0.249073 CGGGCAGTCGGAAGTATGAG 60.249 60.000 0.00 0.00 0.00 2.90
469 470 0.530870 GGGCAGTCGGAAGTATGAGC 60.531 60.000 0.00 0.00 0.00 4.26
470 471 0.872021 GGCAGTCGGAAGTATGAGCG 60.872 60.000 0.00 0.00 0.00 5.03
471 472 0.872021 GCAGTCGGAAGTATGAGCGG 60.872 60.000 0.00 0.00 0.00 5.52
472 473 0.456221 CAGTCGGAAGTATGAGCGGT 59.544 55.000 0.00 0.00 0.00 5.68
473 474 0.739561 AGTCGGAAGTATGAGCGGTC 59.260 55.000 7.89 7.89 0.00 4.79
474 475 0.739561 GTCGGAAGTATGAGCGGTCT 59.260 55.000 16.64 4.07 0.00 3.85
475 476 1.134560 GTCGGAAGTATGAGCGGTCTT 59.865 52.381 16.64 12.19 0.00 3.01
476 477 1.822990 TCGGAAGTATGAGCGGTCTTT 59.177 47.619 16.64 6.04 0.00 2.52
477 478 2.232941 TCGGAAGTATGAGCGGTCTTTT 59.767 45.455 16.64 1.68 0.00 2.27
478 479 2.603560 CGGAAGTATGAGCGGTCTTTTC 59.396 50.000 16.64 10.60 0.00 2.29
479 480 2.937149 GGAAGTATGAGCGGTCTTTTCC 59.063 50.000 16.64 15.34 0.00 3.13
487 488 2.763651 CGGTCTTTTCCCGTCCATC 58.236 57.895 0.00 0.00 40.59 3.51
504 505 3.353836 CACCCTTTGGCGACCACG 61.354 66.667 0.00 0.00 42.93 4.94
613 619 1.154413 CCGATGCACAACTTCGCAC 60.154 57.895 1.12 0.00 42.83 5.34
670 676 8.105097 TCATATTCTTCGGTTTGACATGAAAA 57.895 30.769 0.00 0.00 0.00 2.29
733 771 1.301479 AGGTTTCCGCGACACTTCC 60.301 57.895 8.23 2.04 0.00 3.46
738 776 0.389817 TTCCGCGACACTTCCTCATG 60.390 55.000 8.23 0.00 0.00 3.07
763 801 1.669049 CCGCGTACCCATACCTGACA 61.669 60.000 4.92 0.00 0.00 3.58
849 887 0.184933 CAACTCCAACTGAACCCCCA 59.815 55.000 0.00 0.00 0.00 4.96
910 1885 1.599667 GCAGAGAACACGAACGAGTCA 60.600 52.381 0.14 0.00 0.00 3.41
1084 2059 1.331756 CACAAGAAGCGCACTTGAAGT 59.668 47.619 35.66 20.97 44.92 3.01
1090 2065 2.556287 CGCACTTGAAGTTCCGGC 59.444 61.111 0.00 0.00 0.00 6.13
1091 2066 2.954611 GCACTTGAAGTTCCGGCC 59.045 61.111 0.00 0.00 0.00 6.13
1092 2067 2.966309 GCACTTGAAGTTCCGGCCG 61.966 63.158 21.04 21.04 0.00 6.13
1093 2068 2.032071 ACTTGAAGTTCCGGCCGG 59.968 61.111 39.13 39.13 0.00 6.13
1127 2119 3.333804 CTCTTTCCCTTCTCAGCTGAAC 58.666 50.000 18.85 0.00 0.00 3.18
1129 2121 1.434188 TTCCCTTCTCAGCTGAACCA 58.566 50.000 18.85 1.43 0.00 3.67
1218 2210 0.607217 TGCTGCTCCTGTTGGTCATG 60.607 55.000 0.00 0.00 34.23 3.07
1221 2213 0.178995 TGCTCCTGTTGGTCATGCAA 60.179 50.000 0.00 0.00 34.23 4.08
1222 2214 0.961019 GCTCCTGTTGGTCATGCAAA 59.039 50.000 0.00 0.00 34.23 3.68
1228 2220 2.821378 CTGTTGGTCATGCAAATCCTCA 59.179 45.455 0.00 0.00 0.00 3.86
1231 2223 1.272037 TGGTCATGCAAATCCTCAGCA 60.272 47.619 0.00 0.00 43.14 4.41
1234 2226 2.686405 GTCATGCAAATCCTCAGCATCA 59.314 45.455 0.00 0.00 46.39 3.07
1453 2446 8.143835 TCAAAAGAAAAAGATGGATCAACCTTC 58.856 33.333 0.00 0.00 41.42 3.46
1483 2476 6.100792 GAAACATGATCGAGTTTCTTCTCC 57.899 41.667 24.32 7.79 46.15 3.71
1491 2484 6.645415 TGATCGAGTTTCTTCTCCTTTTGTAC 59.355 38.462 0.00 0.00 0.00 2.90
1505 2498 7.974501 TCTCCTTTTGTACTTCTATCGTGATTC 59.025 37.037 0.00 0.00 0.00 2.52
1509 2502 5.806366 TGTACTTCTATCGTGATTCGTGA 57.194 39.130 0.00 0.00 40.80 4.35
1523 2516 7.758076 TCGTGATTCGTGAAATGTATAGTTTCT 59.242 33.333 10.32 0.00 40.80 2.52
1552 2545 9.681062 ATCCCTTTTGTTAGAATAAATTCGAGA 57.319 29.630 0.00 0.00 41.56 4.04
1572 2565 5.926542 CGAGACATACCGTTAATCATCCAAT 59.073 40.000 0.00 0.00 0.00 3.16
1585 2578 4.898829 TCATCCAATAACCAAGCAATCG 57.101 40.909 0.00 0.00 0.00 3.34
1594 2590 1.426621 CAAGCAATCGCACGAGCAT 59.573 52.632 5.50 0.00 42.27 3.79
1596 2592 2.588146 AAGCAATCGCACGAGCATGC 62.588 55.000 10.51 10.51 41.82 4.06
1597 2593 2.786584 CAATCGCACGAGCATGCA 59.213 55.556 21.98 0.00 46.47 3.96
1607 2603 0.302890 CGAGCATGCAACCGAGATTC 59.697 55.000 21.98 4.00 0.00 2.52
1613 2609 3.242739 GCATGCAACCGAGATTCGTTAAT 60.243 43.478 14.21 0.00 38.40 1.40
1614 2610 4.025229 GCATGCAACCGAGATTCGTTAATA 60.025 41.667 14.21 0.00 38.40 0.98
1616 2612 5.459110 TGCAACCGAGATTCGTTAATAAC 57.541 39.130 0.00 0.00 38.40 1.89
1636 2632 3.305964 ACGTTCATCGATATTGGCTACG 58.694 45.455 0.00 3.40 42.86 3.51
1639 2635 4.547532 GTTCATCGATATTGGCTACGTCT 58.452 43.478 0.00 0.00 0.00 4.18
1778 2776 3.428532 AGGTTACATCGTGTGTCTACCT 58.571 45.455 16.76 16.76 44.67 3.08
1837 2835 3.392616 ACTTGGACATGACTCCATATCCC 59.607 47.826 5.92 0.00 44.00 3.85
1851 2849 7.586349 ACTCCATATCCCATCTAAACACAATT 58.414 34.615 0.00 0.00 0.00 2.32
1894 2892 8.595421 TGTAACCTACCTTGTACACAATATTCA 58.405 33.333 0.00 0.00 35.02 2.57
1914 2912 7.865706 ATTCAACACAACTCTAACAAACTCT 57.134 32.000 0.00 0.00 0.00 3.24
1933 2931 4.896482 ACTCTACCTTGGCGAATATTCTCT 59.104 41.667 13.45 0.00 0.00 3.10
1962 2960 4.418013 TGAATTCGTCAATGCGTCAAAT 57.582 36.364 0.04 0.00 31.51 2.32
1993 2992 5.520748 ACATTGGACTTGAGTTTATCCCT 57.479 39.130 0.00 0.00 0.00 4.20
2054 3054 5.826208 CACCTACAACTTGTAGTCCCTTTTT 59.174 40.000 22.12 0.40 46.68 1.94
2096 3096 2.030579 GCTCGAGCGAAATTAAGTTCCC 59.969 50.000 23.61 1.22 0.00 3.97
2105 3106 5.293814 GCGAAATTAAGTTCCCCTTACTCTC 59.706 44.000 9.88 0.00 35.36 3.20
2200 3202 0.867746 CTCACATGTTGGGTGTCACG 59.132 55.000 0.00 0.00 37.52 4.35
2211 3215 3.225104 TGGGTGTCACGTAAGAGTTACT 58.775 45.455 0.00 0.00 43.62 2.24
2227 3231 3.990469 AGTTACTTGAACTCAGCATCACG 59.010 43.478 0.00 0.00 45.81 4.35
2230 3234 0.955428 TTGAACTCAGCATCACGGCC 60.955 55.000 0.00 0.00 0.00 6.13
2231 3235 1.078848 GAACTCAGCATCACGGCCT 60.079 57.895 0.00 0.00 0.00 5.19
2248 3252 1.301677 CCTCTTTCTTGACCGCCTGC 61.302 60.000 0.00 0.00 0.00 4.85
2251 3255 1.580845 CTTTCTTGACCGCCTGCCTG 61.581 60.000 0.00 0.00 0.00 4.85
2282 3287 5.070180 TGAAGGAATTTCACCATTGCTTGAA 59.930 36.000 5.07 0.00 42.87 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.900892 CCGGGCTGATAGCGTCGT 61.901 66.667 0.00 0.00 43.62 4.34
2 3 4.647615 CCCGGGCTGATAGCGTCG 62.648 72.222 8.08 7.77 43.62 5.12
4 5 2.524394 ATCCCGGGCTGATAGCGT 60.524 61.111 18.49 0.00 43.62 5.07
5 6 2.047844 CATCCCGGGCTGATAGCG 60.048 66.667 19.99 0.00 43.62 4.26
6 7 2.348998 CCATCCCGGGCTGATAGC 59.651 66.667 26.02 0.00 41.46 2.97
15 16 4.240103 TCTGCATCGCCATCCCGG 62.240 66.667 0.00 0.00 38.11 5.73
16 17 2.969238 GTCTGCATCGCCATCCCG 60.969 66.667 0.00 0.00 0.00 5.14
17 18 2.969238 CGTCTGCATCGCCATCCC 60.969 66.667 0.00 0.00 0.00 3.85
18 19 2.969238 CCGTCTGCATCGCCATCC 60.969 66.667 6.01 0.00 0.00 3.51
19 20 3.643978 GCCGTCTGCATCGCCATC 61.644 66.667 6.01 0.00 40.77 3.51
24 25 3.257561 CTTCCGCCGTCTGCATCG 61.258 66.667 4.75 4.75 41.33 3.84
25 26 2.892425 CCTTCCGCCGTCTGCATC 60.892 66.667 0.00 0.00 41.33 3.91
26 27 3.390521 TCCTTCCGCCGTCTGCAT 61.391 61.111 0.00 0.00 41.33 3.96
27 28 4.373116 GTCCTTCCGCCGTCTGCA 62.373 66.667 0.00 0.00 41.33 4.41
29 30 3.744719 TCGTCCTTCCGCCGTCTG 61.745 66.667 0.00 0.00 0.00 3.51
30 31 3.745803 GTCGTCCTTCCGCCGTCT 61.746 66.667 0.00 0.00 0.00 4.18
37 38 3.876589 TTGCAGCCGTCGTCCTTCC 62.877 63.158 0.00 0.00 0.00 3.46
38 39 2.357034 TTGCAGCCGTCGTCCTTC 60.357 61.111 0.00 0.00 0.00 3.46
39 40 2.665185 GTTGCAGCCGTCGTCCTT 60.665 61.111 0.00 0.00 0.00 3.36
40 41 3.865929 CTGTTGCAGCCGTCGTCCT 62.866 63.158 0.00 0.00 0.00 3.85
41 42 3.414700 CTGTTGCAGCCGTCGTCC 61.415 66.667 0.00 0.00 0.00 4.79
95 96 4.637489 CGATGCCGCTCGAGGAGG 62.637 72.222 15.58 7.39 41.12 4.30
137 138 4.803426 CTCCCACGTCCTCAGCGC 62.803 72.222 0.00 0.00 0.00 5.92
138 139 3.057547 CTCTCCCACGTCCTCAGCG 62.058 68.421 0.00 0.00 0.00 5.18
139 140 2.888863 CTCTCCCACGTCCTCAGC 59.111 66.667 0.00 0.00 0.00 4.26
140 141 2.888863 GCTCTCCCACGTCCTCAG 59.111 66.667 0.00 0.00 0.00 3.35
141 142 3.062466 CGCTCTCCCACGTCCTCA 61.062 66.667 0.00 0.00 0.00 3.86
142 143 4.500116 GCGCTCTCCCACGTCCTC 62.500 72.222 0.00 0.00 0.00 3.71
201 202 4.593864 GATCTCCGGCCTCCGTGC 62.594 72.222 0.00 0.00 46.80 5.34
202 203 3.917760 GGATCTCCGGCCTCCGTG 61.918 72.222 0.00 0.00 46.80 4.94
247 248 4.059459 GTCGCGTCCGTGCAAGTG 62.059 66.667 5.77 0.00 35.54 3.16
248 249 4.578898 TGTCGCGTCCGTGCAAGT 62.579 61.111 5.77 0.00 35.54 3.16
249 250 3.767230 CTGTCGCGTCCGTGCAAG 61.767 66.667 5.77 0.00 35.54 4.01
256 257 3.188786 GATGGTGCTGTCGCGTCC 61.189 66.667 5.77 0.00 39.65 4.79
257 258 3.188786 GGATGGTGCTGTCGCGTC 61.189 66.667 5.77 0.00 39.65 5.19
258 259 3.240134 AAGGATGGTGCTGTCGCGT 62.240 57.895 5.77 0.00 39.65 6.01
259 260 2.434884 AAGGATGGTGCTGTCGCG 60.435 61.111 0.00 0.00 39.65 5.87
260 261 2.109126 GGAAGGATGGTGCTGTCGC 61.109 63.158 0.00 0.00 0.00 5.19
261 262 1.450312 GGGAAGGATGGTGCTGTCG 60.450 63.158 0.00 0.00 0.00 4.35
262 263 0.257039 ATGGGAAGGATGGTGCTGTC 59.743 55.000 0.00 0.00 0.00 3.51
263 264 0.257039 GATGGGAAGGATGGTGCTGT 59.743 55.000 0.00 0.00 0.00 4.40
264 265 0.549950 AGATGGGAAGGATGGTGCTG 59.450 55.000 0.00 0.00 0.00 4.41
265 266 0.549950 CAGATGGGAAGGATGGTGCT 59.450 55.000 0.00 0.00 0.00 4.40
266 267 1.105759 GCAGATGGGAAGGATGGTGC 61.106 60.000 0.00 0.00 0.00 5.01
267 268 0.549950 AGCAGATGGGAAGGATGGTG 59.450 55.000 0.00 0.00 0.00 4.17
268 269 1.064166 CAAGCAGATGGGAAGGATGGT 60.064 52.381 0.00 0.00 0.00 3.55
269 270 1.213678 TCAAGCAGATGGGAAGGATGG 59.786 52.381 0.00 0.00 0.00 3.51
270 271 2.295885 GTCAAGCAGATGGGAAGGATG 58.704 52.381 0.00 0.00 0.00 3.51
271 272 1.134280 CGTCAAGCAGATGGGAAGGAT 60.134 52.381 0.00 0.00 0.00 3.24
272 273 0.250234 CGTCAAGCAGATGGGAAGGA 59.750 55.000 0.00 0.00 0.00 3.36
273 274 0.036010 ACGTCAAGCAGATGGGAAGG 60.036 55.000 3.83 0.00 37.58 3.46
274 275 1.363744 GACGTCAAGCAGATGGGAAG 58.636 55.000 11.55 0.00 37.58 3.46
275 276 0.389817 CGACGTCAAGCAGATGGGAA 60.390 55.000 17.16 0.00 37.58 3.97
276 277 1.215382 CGACGTCAAGCAGATGGGA 59.785 57.895 17.16 0.00 37.58 4.37
277 278 1.811266 CCGACGTCAAGCAGATGGG 60.811 63.158 17.16 0.88 37.58 4.00
278 279 1.811266 CCCGACGTCAAGCAGATGG 60.811 63.158 17.16 5.62 37.58 3.51
279 280 2.456119 GCCCGACGTCAAGCAGATG 61.456 63.158 17.16 0.00 39.25 2.90
280 281 2.125512 GCCCGACGTCAAGCAGAT 60.126 61.111 17.16 0.00 0.00 2.90
281 282 3.303135 AGCCCGACGTCAAGCAGA 61.303 61.111 23.92 0.00 0.00 4.26
282 283 3.114616 CAGCCCGACGTCAAGCAG 61.115 66.667 23.92 15.06 0.00 4.24
283 284 3.573772 CTCAGCCCGACGTCAAGCA 62.574 63.158 23.92 7.81 0.00 3.91
284 285 2.811317 CTCAGCCCGACGTCAAGC 60.811 66.667 17.16 16.95 0.00 4.01
285 286 2.811317 GCTCAGCCCGACGTCAAG 60.811 66.667 17.16 6.92 0.00 3.02
286 287 4.373116 GGCTCAGCCCGACGTCAA 62.373 66.667 17.16 0.00 44.06 3.18
299 300 4.168291 CTTCCCCCTGCGAGGCTC 62.168 72.222 3.87 3.87 32.73 4.70
300 301 4.722535 TCTTCCCCCTGCGAGGCT 62.723 66.667 0.00 0.00 32.73 4.58
301 302 4.168291 CTCTTCCCCCTGCGAGGC 62.168 72.222 0.00 0.00 32.73 4.70
302 303 2.364317 TCTCTTCCCCCTGCGAGG 60.364 66.667 0.00 0.00 34.30 4.63
303 304 1.380515 TCTCTCTTCCCCCTGCGAG 60.381 63.158 0.00 0.00 0.00 5.03
304 305 1.380515 CTCTCTCTTCCCCCTGCGA 60.381 63.158 0.00 0.00 0.00 5.10
305 306 2.430610 CCTCTCTCTTCCCCCTGCG 61.431 68.421 0.00 0.00 0.00 5.18
306 307 2.069430 CCCTCTCTCTTCCCCCTGC 61.069 68.421 0.00 0.00 0.00 4.85
307 308 2.069430 GCCCTCTCTCTTCCCCCTG 61.069 68.421 0.00 0.00 0.00 4.45
308 309 2.125066 TTGCCCTCTCTCTTCCCCCT 62.125 60.000 0.00 0.00 0.00 4.79
309 310 1.616628 TTGCCCTCTCTCTTCCCCC 60.617 63.158 0.00 0.00 0.00 5.40
310 311 1.911471 CTTGCCCTCTCTCTTCCCC 59.089 63.158 0.00 0.00 0.00 4.81
311 312 1.223211 GCTTGCCCTCTCTCTTCCC 59.777 63.158 0.00 0.00 0.00 3.97
312 313 0.107752 CTGCTTGCCCTCTCTCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
313 314 0.107752 CCTGCTTGCCCTCTCTCTTC 60.108 60.000 0.00 0.00 0.00 2.87
314 315 1.560866 CCCTGCTTGCCCTCTCTCTT 61.561 60.000 0.00 0.00 0.00 2.85
315 316 1.994507 CCCTGCTTGCCCTCTCTCT 60.995 63.158 0.00 0.00 0.00 3.10
316 317 2.588989 CCCTGCTTGCCCTCTCTC 59.411 66.667 0.00 0.00 0.00 3.20
317 318 3.013932 CCCCTGCTTGCCCTCTCT 61.014 66.667 0.00 0.00 0.00 3.10
318 319 3.011517 TCCCCTGCTTGCCCTCTC 61.012 66.667 0.00 0.00 0.00 3.20
319 320 3.334054 GTCCCCTGCTTGCCCTCT 61.334 66.667 0.00 0.00 0.00 3.69
320 321 3.334054 AGTCCCCTGCTTGCCCTC 61.334 66.667 0.00 0.00 0.00 4.30
321 322 3.334054 GAGTCCCCTGCTTGCCCT 61.334 66.667 0.00 0.00 0.00 5.19
322 323 4.432741 GGAGTCCCCTGCTTGCCC 62.433 72.222 0.00 0.00 0.00 5.36
323 324 4.785453 CGGAGTCCCCTGCTTGCC 62.785 72.222 2.80 0.00 0.00 4.52
324 325 4.785453 CCGGAGTCCCCTGCTTGC 62.785 72.222 2.80 0.00 0.00 4.01
325 326 2.317149 GATCCGGAGTCCCCTGCTTG 62.317 65.000 11.34 0.00 0.00 4.01
326 327 2.041265 ATCCGGAGTCCCCTGCTT 59.959 61.111 11.34 0.00 0.00 3.91
327 328 2.444895 GATCCGGAGTCCCCTGCT 60.445 66.667 11.34 0.00 0.00 4.24
328 329 2.444895 AGATCCGGAGTCCCCTGC 60.445 66.667 11.34 0.00 0.00 4.85
329 330 2.136878 CCAGATCCGGAGTCCCCTG 61.137 68.421 11.34 11.35 0.00 4.45
330 331 2.283809 CCAGATCCGGAGTCCCCT 59.716 66.667 11.34 0.00 0.00 4.79
331 332 3.551407 GCCAGATCCGGAGTCCCC 61.551 72.222 11.34 0.00 0.00 4.81
332 333 3.551407 GGCCAGATCCGGAGTCCC 61.551 72.222 11.34 1.76 0.00 4.46
333 334 2.444895 AGGCCAGATCCGGAGTCC 60.445 66.667 11.34 6.22 0.00 3.85
334 335 2.851071 CGAGGCCAGATCCGGAGTC 61.851 68.421 11.34 8.03 0.00 3.36
335 336 2.835431 CGAGGCCAGATCCGGAGT 60.835 66.667 11.34 0.00 0.00 3.85
336 337 3.610669 CCGAGGCCAGATCCGGAG 61.611 72.222 11.34 0.00 44.29 4.63
339 340 4.598894 CTGCCGAGGCCAGATCCG 62.599 72.222 12.05 0.00 41.09 4.18
340 341 4.925861 GCTGCCGAGGCCAGATCC 62.926 72.222 12.05 0.00 41.09 3.36
341 342 3.859414 AGCTGCCGAGGCCAGATC 61.859 66.667 12.05 0.00 41.09 2.75
342 343 4.172512 CAGCTGCCGAGGCCAGAT 62.173 66.667 12.05 5.18 41.09 2.90
351 352 4.845580 CTACCCCTGCAGCTGCCG 62.846 72.222 34.64 28.21 41.18 5.69
354 355 4.845580 CGGCTACCCCTGCAGCTG 62.846 72.222 10.11 10.11 37.91 4.24
357 358 3.854669 CTCCGGCTACCCCTGCAG 61.855 72.222 6.78 6.78 0.00 4.41
358 359 3.916438 TTCTCCGGCTACCCCTGCA 62.916 63.158 0.00 0.00 0.00 4.41
359 360 3.081409 TTCTCCGGCTACCCCTGC 61.081 66.667 0.00 0.00 0.00 4.85
360 361 2.435693 CCTTCTCCGGCTACCCCTG 61.436 68.421 0.00 0.00 0.00 4.45
361 362 2.041819 CCTTCTCCGGCTACCCCT 60.042 66.667 0.00 0.00 0.00 4.79
362 363 3.162154 CCCTTCTCCGGCTACCCC 61.162 72.222 0.00 0.00 0.00 4.95
363 364 2.042230 TCCCTTCTCCGGCTACCC 60.042 66.667 0.00 0.00 0.00 3.69
364 365 0.470268 ATCTCCCTTCTCCGGCTACC 60.470 60.000 0.00 0.00 0.00 3.18
365 366 0.963225 GATCTCCCTTCTCCGGCTAC 59.037 60.000 0.00 0.00 0.00 3.58
366 367 0.537600 CGATCTCCCTTCTCCGGCTA 60.538 60.000 0.00 0.00 0.00 3.93
367 368 1.830408 CGATCTCCCTTCTCCGGCT 60.830 63.158 0.00 0.00 0.00 5.52
368 369 1.801309 CTCGATCTCCCTTCTCCGGC 61.801 65.000 0.00 0.00 0.00 6.13
369 370 0.466555 ACTCGATCTCCCTTCTCCGG 60.467 60.000 0.00 0.00 0.00 5.14
370 371 0.948678 GACTCGATCTCCCTTCTCCG 59.051 60.000 0.00 0.00 0.00 4.63
371 372 0.948678 CGACTCGATCTCCCTTCTCC 59.051 60.000 0.00 0.00 0.00 3.71
372 373 0.309612 GCGACTCGATCTCCCTTCTC 59.690 60.000 1.63 0.00 0.00 2.87
373 374 1.104577 GGCGACTCGATCTCCCTTCT 61.105 60.000 1.63 0.00 0.00 2.85
374 375 1.360911 GGCGACTCGATCTCCCTTC 59.639 63.158 1.63 0.00 0.00 3.46
375 376 2.482333 CGGCGACTCGATCTCCCTT 61.482 63.158 0.00 0.00 0.00 3.95
376 377 2.902846 CGGCGACTCGATCTCCCT 60.903 66.667 0.00 0.00 0.00 4.20
377 378 3.967335 CCGGCGACTCGATCTCCC 61.967 72.222 9.30 0.00 0.00 4.30
378 379 4.632458 GCCGGCGACTCGATCTCC 62.632 72.222 12.58 0.00 0.00 3.71
379 380 4.965858 CGCCGGCGACTCGATCTC 62.966 72.222 44.86 0.00 42.83 2.75
435 436 4.569180 CCCGCTAGTGCCCATGGG 62.569 72.222 27.87 27.87 35.36 4.00
437 438 4.488136 TGCCCGCTAGTGCCCATG 62.488 66.667 0.00 0.00 35.36 3.66
438 439 4.181010 CTGCCCGCTAGTGCCCAT 62.181 66.667 0.00 0.00 35.36 4.00
440 441 4.840005 GACTGCCCGCTAGTGCCC 62.840 72.222 0.00 0.00 35.36 5.36
443 444 2.890847 CTTCCGACTGCCCGCTAGTG 62.891 65.000 0.00 0.00 0.00 2.74
444 445 2.678934 TTCCGACTGCCCGCTAGT 60.679 61.111 0.00 0.00 0.00 2.57
445 446 1.381928 TACTTCCGACTGCCCGCTAG 61.382 60.000 0.00 0.00 0.00 3.42
446 447 0.754217 ATACTTCCGACTGCCCGCTA 60.754 55.000 0.00 0.00 0.00 4.26
447 448 2.058595 ATACTTCCGACTGCCCGCT 61.059 57.895 0.00 0.00 0.00 5.52
448 449 1.883084 CATACTTCCGACTGCCCGC 60.883 63.158 0.00 0.00 0.00 6.13
449 450 0.249073 CTCATACTTCCGACTGCCCG 60.249 60.000 0.00 0.00 0.00 6.13
450 451 0.530870 GCTCATACTTCCGACTGCCC 60.531 60.000 0.00 0.00 0.00 5.36
451 452 0.872021 CGCTCATACTTCCGACTGCC 60.872 60.000 0.00 0.00 0.00 4.85
452 453 0.872021 CCGCTCATACTTCCGACTGC 60.872 60.000 0.00 0.00 0.00 4.40
453 454 0.456221 ACCGCTCATACTTCCGACTG 59.544 55.000 0.00 0.00 0.00 3.51
454 455 0.739561 GACCGCTCATACTTCCGACT 59.260 55.000 0.00 0.00 0.00 4.18
455 456 0.739561 AGACCGCTCATACTTCCGAC 59.260 55.000 0.00 0.00 0.00 4.79
456 457 1.471119 AAGACCGCTCATACTTCCGA 58.529 50.000 0.00 0.00 0.00 4.55
457 458 2.295253 AAAGACCGCTCATACTTCCG 57.705 50.000 0.00 0.00 0.00 4.30
458 459 2.937149 GGAAAAGACCGCTCATACTTCC 59.063 50.000 0.00 0.00 0.00 3.46
459 460 2.937149 GGGAAAAGACCGCTCATACTTC 59.063 50.000 0.00 0.00 0.00 3.01
460 461 2.677037 CGGGAAAAGACCGCTCATACTT 60.677 50.000 0.00 0.00 45.34 2.24
461 462 1.134788 CGGGAAAAGACCGCTCATACT 60.135 52.381 0.00 0.00 45.34 2.12
462 463 1.287425 CGGGAAAAGACCGCTCATAC 58.713 55.000 0.00 0.00 45.34 2.39
463 464 3.752796 CGGGAAAAGACCGCTCATA 57.247 52.632 0.00 0.00 45.34 2.15
464 465 4.617875 CGGGAAAAGACCGCTCAT 57.382 55.556 0.00 0.00 45.34 2.90
470 471 1.450025 GTGATGGACGGGAAAAGACC 58.550 55.000 0.00 0.00 0.00 3.85
471 472 1.450025 GGTGATGGACGGGAAAAGAC 58.550 55.000 0.00 0.00 0.00 3.01
472 473 0.326927 GGGTGATGGACGGGAAAAGA 59.673 55.000 0.00 0.00 0.00 2.52
473 474 0.328258 AGGGTGATGGACGGGAAAAG 59.672 55.000 0.00 0.00 0.00 2.27
474 475 0.774908 AAGGGTGATGGACGGGAAAA 59.225 50.000 0.00 0.00 0.00 2.29
475 476 0.774908 AAAGGGTGATGGACGGGAAA 59.225 50.000 0.00 0.00 0.00 3.13
476 477 0.037590 CAAAGGGTGATGGACGGGAA 59.962 55.000 0.00 0.00 0.00 3.97
477 478 1.682849 CAAAGGGTGATGGACGGGA 59.317 57.895 0.00 0.00 0.00 5.14
478 479 1.378514 CCAAAGGGTGATGGACGGG 60.379 63.158 0.00 0.00 39.12 5.28
479 480 2.046285 GCCAAAGGGTGATGGACGG 61.046 63.158 0.00 0.00 39.12 4.79
487 488 3.353836 CGTGGTCGCCAAAGGGTG 61.354 66.667 0.00 0.00 46.45 4.61
560 566 1.815421 CACCCACGCTGGTAGCATC 60.815 63.158 0.00 0.00 42.58 3.91
664 670 0.881159 TCCGCGGTTCGTGTTTTCAT 60.881 50.000 27.15 0.00 35.46 2.57
670 676 0.881159 TTTGAATCCGCGGTTCGTGT 60.881 50.000 27.15 0.49 35.46 4.49
733 771 2.104928 TACGCGGCAGCTCATGAG 59.895 61.111 18.84 18.84 42.32 2.90
738 776 3.146726 TATGGGTACGCGGCAGCTC 62.147 63.158 12.47 0.00 42.32 4.09
849 887 4.363990 CTGCCGGTCTCACACGCT 62.364 66.667 1.90 0.00 0.00 5.07
876 914 6.599437 GTGTTCTCTGCGCTTAAATTTCTAA 58.401 36.000 9.73 0.00 0.00 2.10
910 1885 1.207791 AGGAGGGAGAAATCGTGCAT 58.792 50.000 0.00 0.00 0.00 3.96
991 1966 7.550712 TGAGCTCGTTTATATAGATGCATCAT 58.449 34.615 27.81 19.70 0.00 2.45
1102 2094 2.499693 AGCTGAGAAGGGAAAGAGCTAC 59.500 50.000 0.00 0.00 35.05 3.58
1103 2095 2.499289 CAGCTGAGAAGGGAAAGAGCTA 59.501 50.000 8.42 0.00 35.05 3.32
1113 2105 1.338579 GGACTGGTTCAGCTGAGAAGG 60.339 57.143 17.43 11.23 34.37 3.46
1144 2136 1.933041 CGACGTGGTATCTCGCACG 60.933 63.158 9.04 9.04 42.18 5.34
1146 2138 2.767445 CCCGACGTGGTATCTCGCA 61.767 63.158 0.00 0.00 35.15 5.10
1218 2210 1.945394 ACGATGATGCTGAGGATTTGC 59.055 47.619 0.00 0.00 0.00 3.68
1221 2213 1.269988 CCGACGATGATGCTGAGGATT 60.270 52.381 0.00 0.00 0.00 3.01
1222 2214 0.316522 CCGACGATGATGCTGAGGAT 59.683 55.000 0.00 0.00 0.00 3.24
1295 2287 1.226802 CTGAGCATCTCCGTCACCG 60.227 63.158 0.00 0.00 34.92 4.94
1409 2401 6.214615 TCTTTTGACCTGTGATCCACCTTATA 59.785 38.462 0.00 0.00 32.73 0.98
1410 2402 4.927267 TTTGACCTGTGATCCACCTTAT 57.073 40.909 0.00 0.00 32.73 1.73
1411 2403 4.349636 TCTTTTGACCTGTGATCCACCTTA 59.650 41.667 0.00 0.00 32.73 2.69
1412 2404 3.138283 TCTTTTGACCTGTGATCCACCTT 59.862 43.478 0.00 0.00 32.73 3.50
1413 2405 2.711009 TCTTTTGACCTGTGATCCACCT 59.289 45.455 0.00 0.00 32.73 4.00
1453 2446 7.269435 GAAACTCGATCATGTTTCCATTTTG 57.731 36.000 20.81 0.00 43.44 2.44
1479 2472 6.829229 TCACGATAGAAGTACAAAAGGAGA 57.171 37.500 0.00 0.00 41.38 3.71
1483 2476 7.272731 TCACGAATCACGATAGAAGTACAAAAG 59.727 37.037 0.00 0.00 45.77 2.27
1491 2484 6.575083 ACATTTCACGAATCACGATAGAAG 57.425 37.500 0.00 0.00 45.77 2.85
1505 2498 9.326413 AGGGATAAAGAAACTATACATTTCACG 57.674 33.333 7.24 0.00 38.32 4.35
1552 2545 7.284074 TGGTTATTGGATGATTAACGGTATGT 58.716 34.615 0.00 0.00 0.00 2.29
1562 2555 5.737063 GCGATTGCTTGGTTATTGGATGATT 60.737 40.000 0.00 0.00 38.39 2.57
1572 2565 1.075542 CTCGTGCGATTGCTTGGTTA 58.924 50.000 6.47 0.00 43.34 2.85
1585 2578 3.372676 CTCGGTTGCATGCTCGTGC 62.373 63.158 20.33 1.71 45.25 5.34
1594 2590 5.459110 GTTATTAACGAATCTCGGTTGCA 57.541 39.130 0.67 0.00 35.55 4.08
1613 2609 4.913345 CGTAGCCAATATCGATGAACGTTA 59.087 41.667 8.54 0.00 43.13 3.18
1614 2610 3.734231 CGTAGCCAATATCGATGAACGTT 59.266 43.478 8.54 0.00 43.13 3.99
1616 2612 3.305964 ACGTAGCCAATATCGATGAACG 58.694 45.455 8.54 9.29 44.09 3.95
1636 2632 0.105039 CATAGTCAAGCCCCGGAGAC 59.895 60.000 0.73 2.78 0.00 3.36
1639 2635 2.070039 CCCATAGTCAAGCCCCGGA 61.070 63.158 0.73 0.00 0.00 5.14
1720 2718 0.107703 CAGGAACGCATAGGAAGCCA 60.108 55.000 0.00 0.00 0.00 4.75
1728 2726 4.956085 ACATAATAGCACAGGAACGCATA 58.044 39.130 0.00 0.00 0.00 3.14
1729 2727 3.808728 ACATAATAGCACAGGAACGCAT 58.191 40.909 0.00 0.00 0.00 4.73
1778 2776 6.910259 TCTAGGCCTCTCATATATAGTGGA 57.090 41.667 9.68 0.00 30.69 4.02
1824 2822 5.665360 TGTGTTTAGATGGGATATGGAGTCA 59.335 40.000 0.00 0.00 0.00 3.41
1837 2835 9.599322 GACTTGTAGTTGAATTGTGTTTAGATG 57.401 33.333 0.00 0.00 0.00 2.90
1851 2849 5.129815 AGGTTACAGTTGGACTTGTAGTTGA 59.870 40.000 0.00 0.00 0.00 3.18
1894 2892 6.885922 AGGTAGAGTTTGTTAGAGTTGTGTT 58.114 36.000 0.00 0.00 0.00 3.32
1914 2912 4.897076 TGGTAGAGAATATTCGCCAAGGTA 59.103 41.667 14.69 0.00 0.00 3.08
2054 3054 4.396790 AGCGTTGACTGTGGTTAAGAAAAA 59.603 37.500 0.00 0.00 0.00 1.94
2105 3106 0.310854 GGAAGTTGGGAGCACAAACG 59.689 55.000 0.00 0.00 31.17 3.60
2133 3134 3.749226 TCAGTGTGTGATGGCATTAACA 58.251 40.909 11.57 11.57 0.00 2.41
2188 3190 2.521105 ACTCTTACGTGACACCCAAC 57.479 50.000 0.00 0.00 0.00 3.77
2211 3215 0.955428 GGCCGTGATGCTGAGTTCAA 60.955 55.000 0.00 0.00 0.00 2.69
2220 3224 0.449388 CAAGAAAGAGGCCGTGATGC 59.551 55.000 0.00 0.00 0.00 3.91
2227 3231 2.041115 GGCGGTCAAGAAAGAGGCC 61.041 63.158 0.00 0.00 33.03 5.19
2230 3234 1.301677 GGCAGGCGGTCAAGAAAGAG 61.302 60.000 0.00 0.00 0.00 2.85
2231 3235 1.302511 GGCAGGCGGTCAAGAAAGA 60.303 57.895 0.00 0.00 0.00 2.52
2248 3252 5.509670 GGTGAAATTCCTTCAAGTTTCCAGG 60.510 44.000 0.00 0.00 45.67 4.45
2251 3255 5.529581 TGGTGAAATTCCTTCAAGTTTCC 57.470 39.130 0.00 0.00 45.67 3.13
2282 3287 2.039746 TGTGAATTTGACTCGGGGTGAT 59.960 45.455 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.