Multiple sequence alignment - TraesCS5D01G325000

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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 TraesCS5D01G325000 chr5D 100.000 5528 0 0 1 5528 416595561 416601088 0.000000e+00 10209.0
1 TraesCS5D01G325000 chr5B 93.799 4967 198 56 635 5526 503323137 503328068 0.000000e+00 7365.0
2 TraesCS5D01G325000 chr5B 90.187 214 19 1 2 215 503314728 503314939 1.520000e-70 278.0
3 TraesCS5D01G325000 chr5B 89.247 186 18 2 1888 2072 586789123 586789307 1.200000e-56 231.0
4 TraesCS5D01G325000 chr5A 93.676 4791 160 50 612 5354 529364568 529369263 0.000000e+00 7036.0
5 TraesCS5D01G325000 chr5A 88.557 201 22 1 16 215 529364178 529364378 5.530000e-60 243.0
6 TraesCS5D01G325000 chr5A 94.017 117 7 0 448 564 529364452 529364568 1.580000e-40 178.0
7 TraesCS5D01G325000 chr1D 88.568 761 52 15 1332 2072 59075671 59074926 0.000000e+00 891.0
8 TraesCS5D01G325000 chr4B 90.598 117 9 1 239 353 644679929 644679813 2.670000e-33 154.0
9 TraesCS5D01G325000 chr3D 90.598 117 9 1 239 353 606952360 606952244 2.670000e-33 154.0
10 TraesCS5D01G325000 chr3D 86.765 136 13 4 239 370 13983906 13983772 4.460000e-31 147.0
11 TraesCS5D01G325000 chr7D 90.598 117 8 2 239 353 33478455 33478570 9.590000e-33 152.0
12 TraesCS5D01G325000 chr7D 89.655 58 6 0 1327 1384 117261126 117261183 2.140000e-09 75.0
13 TraesCS5D01G325000 chr4A 87.879 132 13 2 239 367 618561554 618561423 9.590000e-33 152.0
14 TraesCS5D01G325000 chr3B 89.916 119 10 1 239 355 786786516 786786634 9.590000e-33 152.0
15 TraesCS5D01G325000 chr7B 87.407 135 12 3 239 369 733479625 733479758 3.450000e-32 150.0
16 TraesCS5D01G325000 chr7B 85.333 75 8 3 5454 5526 202102973 202103046 2.140000e-09 75.0
17 TraesCS5D01G325000 chrUn 88.189 127 12 2 239 362 51032725 51032599 1.240000e-31 148.0
18 TraesCS5D01G325000 chr6B 85.926 135 15 3 220 352 365540 365672 2.080000e-29 141.0
19 TraesCS5D01G325000 chr7A 76.056 142 30 4 5387 5526 569442717 569442856 2.760000e-08 71.3


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 TraesCS5D01G325000 chr5D 416595561 416601088 5527 False 10209.000000 10209 100.000000 1 5528 1 chr5D.!!$F1 5527
1 TraesCS5D01G325000 chr5B 503323137 503328068 4931 False 7365.000000 7365 93.799000 635 5526 1 chr5B.!!$F2 4891
2 TraesCS5D01G325000 chr5A 529364178 529369263 5085 False 2485.666667 7036 92.083333 16 5354 3 chr5A.!!$F1 5338
3 TraesCS5D01G325000 chr1D 59074926 59075671 745 True 891.000000 891 88.568000 1332 2072 1 chr1D.!!$R1 740

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
252 254 0.032515 TAAGCACTCCCTCCATCCGA 60.033 55.000 0.00 0.0 0.0 4.55 F
255 257 0.035439 GCACTCCCTCCATCCGAAAA 60.035 55.000 0.00 0.0 0.0 2.29 F
608 611 0.108520 AATTGGCTGGAAATGCTGCG 60.109 50.000 0.00 0.0 0.0 5.18 F
2033 2125 0.601841 TCGCCGGAGAAAGGTTCAAC 60.602 55.000 5.05 0.0 0.0 3.18 F
2456 2550 1.212751 CGGTGTCGATGTGCTCTCA 59.787 57.895 0.00 0.0 39.0 3.27 F
3714 3820 1.312371 GCCCGGCTGCAGTAAAATCA 61.312 55.000 16.64 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1082 1126 0.802607 GCAACGGTAGCTCGAGAAGG 60.803 60.000 18.75 2.17 0.00 3.46 R
1084 1128 1.154093 CGCAACGGTAGCTCGAGAA 60.154 57.895 18.75 0.00 0.00 2.87 R
2435 2529 1.080772 GAGCACATCGACACCGTCA 60.081 57.895 0.00 0.00 37.05 4.35 R
3428 3534 1.610673 GGTGGTCAGCTGAGGGAGA 60.611 63.158 18.89 0.00 0.00 3.71 R
3790 3896 2.037902 TCACGGACATTGGCTACAAAGA 59.962 45.455 0.00 0.00 40.55 2.52 R
5141 5257 0.980231 GCCCACTCATCCACCTCTCT 60.980 60.000 0.00 0.00 0.00 3.10 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
76 78 7.225931 TGCACCCTAATTTTGTCGAGATATAAC 59.774 37.037 0.00 0.00 0.00 1.89
77 79 7.307811 GCACCCTAATTTTGTCGAGATATAACC 60.308 40.741 0.00 0.00 0.00 2.85
85 87 8.738199 TTTTGTCGAGATATAACCGCTAATAG 57.262 34.615 0.00 0.00 0.00 1.73
140 142 9.784376 TGTTATTATCTCCTACCTTATATGCCT 57.216 33.333 0.00 0.00 0.00 4.75
148 150 4.702131 CCTACCTTATATGCCTGGAAATGC 59.298 45.833 0.00 0.00 0.00 3.56
150 152 3.140895 ACCTTATATGCCTGGAAATGCCT 59.859 43.478 0.00 0.00 37.63 4.75
158 160 2.938451 GCCTGGAAATGCCTTATTTTGC 59.062 45.455 0.00 0.00 39.06 3.68
191 193 9.699410 AAGACAAATCTTGGACCATATATTTGA 57.301 29.630 27.11 8.90 43.86 2.69
192 194 9.872684 AGACAAATCTTGGACCATATATTTGAT 57.127 29.630 27.11 18.38 37.61 2.57
215 217 9.409312 TGATTTGTATTTGTGATGTGAAATCAC 57.591 29.630 8.81 8.81 46.28 3.06
216 218 8.761575 ATTTGTATTTGTGATGTGAAATCACC 57.238 30.769 12.93 0.00 45.70 4.02
217 219 6.266168 TGTATTTGTGATGTGAAATCACCC 57.734 37.500 12.93 4.04 45.70 4.61
218 220 5.772169 TGTATTTGTGATGTGAAATCACCCA 59.228 36.000 12.93 6.40 45.70 4.51
219 221 5.804944 ATTTGTGATGTGAAATCACCCAA 57.195 34.783 12.93 6.61 45.70 4.12
220 222 5.804944 TTTGTGATGTGAAATCACCCAAT 57.195 34.783 12.93 0.00 45.70 3.16
221 223 5.389859 TTGTGATGTGAAATCACCCAATC 57.610 39.130 12.93 7.94 45.70 2.67
223 225 5.018149 TGTGATGTGAAATCACCCAATCAT 58.982 37.500 12.93 1.45 45.70 2.45
225 227 6.662663 TGTGATGTGAAATCACCCAATCATAA 59.337 34.615 12.93 7.15 45.70 1.90
226 228 7.342541 TGTGATGTGAAATCACCCAATCATAAT 59.657 33.333 12.93 0.00 45.70 1.28
227 229 8.199449 GTGATGTGAAATCACCCAATCATAATT 58.801 33.333 14.39 0.00 45.88 1.40
228 230 9.418839 TGATGTGAAATCACCCAATCATAATTA 57.581 29.630 10.83 0.00 45.88 1.40
246 248 9.959721 TCATAATTATAAATAAGCACTCCCTCC 57.040 33.333 0.00 0.00 0.00 4.30
247 249 9.739276 CATAATTATAAATAAGCACTCCCTCCA 57.261 33.333 0.00 0.00 0.00 3.86
249 251 8.870075 AATTATAAATAAGCACTCCCTCCATC 57.130 34.615 0.00 0.00 0.00 3.51
250 252 3.584733 AAATAAGCACTCCCTCCATCC 57.415 47.619 0.00 0.00 0.00 3.51
251 253 1.051812 ATAAGCACTCCCTCCATCCG 58.948 55.000 0.00 0.00 0.00 4.18
252 254 0.032515 TAAGCACTCCCTCCATCCGA 60.033 55.000 0.00 0.00 0.00 4.55
253 255 0.909610 AAGCACTCCCTCCATCCGAA 60.910 55.000 0.00 0.00 0.00 4.30
254 256 0.909610 AGCACTCCCTCCATCCGAAA 60.910 55.000 0.00 0.00 0.00 3.46
255 257 0.035439 GCACTCCCTCCATCCGAAAA 60.035 55.000 0.00 0.00 0.00 2.29
256 258 1.408822 GCACTCCCTCCATCCGAAAAT 60.409 52.381 0.00 0.00 0.00 1.82
257 259 2.158813 GCACTCCCTCCATCCGAAAATA 60.159 50.000 0.00 0.00 0.00 1.40
258 260 3.467803 CACTCCCTCCATCCGAAAATAC 58.532 50.000 0.00 0.00 0.00 1.89
259 261 2.102588 ACTCCCTCCATCCGAAAATACG 59.897 50.000 0.00 0.00 0.00 3.06
260 262 1.202604 TCCCTCCATCCGAAAATACGC 60.203 52.381 0.00 0.00 0.00 4.42
261 263 0.859232 CCTCCATCCGAAAATACGCG 59.141 55.000 3.53 3.53 0.00 6.01
262 264 1.567504 CTCCATCCGAAAATACGCGT 58.432 50.000 19.17 19.17 0.00 6.01
263 265 1.521423 CTCCATCCGAAAATACGCGTC 59.479 52.381 18.63 0.00 0.00 5.19
264 266 0.228742 CCATCCGAAAATACGCGTCG 59.771 55.000 18.63 13.36 34.58 5.12
269 271 2.490697 CGAAAATACGCGTCGGAAAA 57.509 45.000 18.63 0.00 0.00 2.29
270 272 2.825189 CGAAAATACGCGTCGGAAAAA 58.175 42.857 18.63 0.00 0.00 1.94
271 273 3.409949 CGAAAATACGCGTCGGAAAAAT 58.590 40.909 18.63 0.00 0.00 1.82
272 274 3.234284 CGAAAATACGCGTCGGAAAAATG 59.766 43.478 18.63 0.00 0.00 2.32
273 275 2.817538 AATACGCGTCGGAAAAATGG 57.182 45.000 18.63 0.00 0.00 3.16
274 276 2.012937 ATACGCGTCGGAAAAATGGA 57.987 45.000 18.63 0.00 0.00 3.41
275 277 2.012937 TACGCGTCGGAAAAATGGAT 57.987 45.000 18.63 0.00 0.00 3.41
276 278 2.012937 ACGCGTCGGAAAAATGGATA 57.987 45.000 5.58 0.00 0.00 2.59
277 279 2.348660 ACGCGTCGGAAAAATGGATAA 58.651 42.857 5.58 0.00 0.00 1.75
278 280 2.743126 ACGCGTCGGAAAAATGGATAAA 59.257 40.909 5.58 0.00 0.00 1.40
279 281 3.188873 ACGCGTCGGAAAAATGGATAAAA 59.811 39.130 5.58 0.00 0.00 1.52
280 282 4.159857 CGCGTCGGAAAAATGGATAAAAA 58.840 39.130 0.00 0.00 0.00 1.94
281 283 4.796312 CGCGTCGGAAAAATGGATAAAAAT 59.204 37.500 0.00 0.00 0.00 1.82
282 284 5.275695 CGCGTCGGAAAAATGGATAAAAATG 60.276 40.000 0.00 0.00 0.00 2.32
283 285 5.005299 GCGTCGGAAAAATGGATAAAAATGG 59.995 40.000 0.00 0.00 0.00 3.16
284 286 6.326375 CGTCGGAAAAATGGATAAAAATGGA 58.674 36.000 0.00 0.00 0.00 3.41
285 287 6.978080 CGTCGGAAAAATGGATAAAAATGGAT 59.022 34.615 0.00 0.00 0.00 3.41
286 288 7.043458 CGTCGGAAAAATGGATAAAAATGGATG 60.043 37.037 0.00 0.00 0.00 3.51
287 289 7.763985 GTCGGAAAAATGGATAAAAATGGATGT 59.236 33.333 0.00 0.00 0.00 3.06
288 290 7.978975 TCGGAAAAATGGATAAAAATGGATGTC 59.021 33.333 0.00 0.00 0.00 3.06
289 291 7.981225 CGGAAAAATGGATAAAAATGGATGTCT 59.019 33.333 0.00 0.00 0.00 3.41
295 297 9.927081 AATGGATAAAAATGGATGTCTAGAACT 57.073 29.630 0.00 0.00 0.00 3.01
325 327 5.902681 TGTCTAGGTACATCCATTTCTTCG 58.097 41.667 0.00 0.00 39.02 3.79
326 328 5.655090 TGTCTAGGTACATCCATTTCTTCGA 59.345 40.000 0.00 0.00 39.02 3.71
327 329 5.978322 GTCTAGGTACATCCATTTCTTCGAC 59.022 44.000 0.00 0.00 39.02 4.20
328 330 4.819105 AGGTACATCCATTTCTTCGACA 57.181 40.909 0.00 0.00 39.02 4.35
329 331 5.160607 AGGTACATCCATTTCTTCGACAA 57.839 39.130 0.00 0.00 39.02 3.18
330 332 5.178797 AGGTACATCCATTTCTTCGACAAG 58.821 41.667 0.00 0.00 39.02 3.16
331 333 4.935808 GGTACATCCATTTCTTCGACAAGT 59.064 41.667 0.00 0.00 35.97 3.16
332 334 6.070995 AGGTACATCCATTTCTTCGACAAGTA 60.071 38.462 0.00 0.00 39.02 2.24
333 335 6.761714 GGTACATCCATTTCTTCGACAAGTAT 59.238 38.462 0.00 0.00 35.97 2.12
334 336 7.280205 GGTACATCCATTTCTTCGACAAGTATT 59.720 37.037 0.00 0.00 35.97 1.89
335 337 7.687941 ACATCCATTTCTTCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
336 338 8.110860 ACATCCATTTCTTCGACAAGTATTTT 57.889 30.769 0.00 0.00 0.00 1.82
337 339 8.237267 ACATCCATTTCTTCGACAAGTATTTTC 58.763 33.333 0.00 0.00 0.00 2.29
338 340 6.827641 TCCATTTCTTCGACAAGTATTTTCG 58.172 36.000 0.00 0.00 0.00 3.46
339 341 6.021596 CCATTTCTTCGACAAGTATTTTCGG 58.978 40.000 0.00 0.00 33.50 4.30
340 342 6.128391 CCATTTCTTCGACAAGTATTTTCGGA 60.128 38.462 0.00 0.00 33.50 4.55
341 343 5.834239 TTCTTCGACAAGTATTTTCGGAC 57.166 39.130 0.00 0.00 33.50 4.79
342 344 3.916172 TCTTCGACAAGTATTTTCGGACG 59.084 43.478 0.00 0.00 33.50 4.79
343 345 2.598589 TCGACAAGTATTTTCGGACGG 58.401 47.619 0.00 0.00 33.50 4.79
344 346 2.228582 TCGACAAGTATTTTCGGACGGA 59.771 45.455 0.00 0.00 33.50 4.69
345 347 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
346 348 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
347 349 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
360 362 3.558533 GGACGGAGGGAGTATGTTTTTGT 60.559 47.826 0.00 0.00 0.00 2.83
361 363 4.322953 GGACGGAGGGAGTATGTTTTTGTA 60.323 45.833 0.00 0.00 0.00 2.41
362 364 4.572909 ACGGAGGGAGTATGTTTTTGTAC 58.427 43.478 0.00 0.00 0.00 2.90
363 365 4.285260 ACGGAGGGAGTATGTTTTTGTACT 59.715 41.667 0.00 0.00 34.02 2.73
364 366 5.481473 ACGGAGGGAGTATGTTTTTGTACTA 59.519 40.000 0.00 0.00 31.61 1.82
365 367 5.809051 CGGAGGGAGTATGTTTTTGTACTAC 59.191 44.000 0.00 0.00 31.61 2.73
366 368 6.350780 CGGAGGGAGTATGTTTTTGTACTACT 60.351 42.308 0.00 0.00 33.24 2.57
367 369 7.148018 CGGAGGGAGTATGTTTTTGTACTACTA 60.148 40.741 0.00 0.00 33.24 1.82
368 370 8.702819 GGAGGGAGTATGTTTTTGTACTACTAT 58.297 37.037 0.00 0.00 33.24 2.12
370 372 9.886132 AGGGAGTATGTTTTTGTACTACTATTG 57.114 33.333 0.00 0.00 33.24 1.90
396 399 0.242017 ATTTGCTGCACGGAGAAAGC 59.758 50.000 0.00 0.00 36.18 3.51
397 400 1.100463 TTTGCTGCACGGAGAAAGCA 61.100 50.000 0.00 0.00 43.60 3.91
409 412 3.431486 CGGAGAAAGCAATAAGAGGCTCT 60.431 47.826 12.24 12.24 40.01 4.09
410 413 4.126437 GGAGAAAGCAATAAGAGGCTCTC 58.874 47.826 19.03 4.64 40.01 3.20
411 414 4.383552 GGAGAAAGCAATAAGAGGCTCTCA 60.384 45.833 19.03 2.73 40.01 3.27
412 415 4.768583 AGAAAGCAATAAGAGGCTCTCAG 58.231 43.478 19.03 9.09 40.01 3.35
413 416 4.224818 AGAAAGCAATAAGAGGCTCTCAGT 59.775 41.667 19.03 0.00 40.01 3.41
414 417 5.423610 AGAAAGCAATAAGAGGCTCTCAGTA 59.576 40.000 19.03 7.20 40.01 2.74
415 418 5.683876 AAGCAATAAGAGGCTCTCAGTAA 57.316 39.130 19.03 1.78 40.01 2.24
416 419 5.017294 AGCAATAAGAGGCTCTCAGTAAC 57.983 43.478 19.03 6.40 34.76 2.50
417 420 4.714308 AGCAATAAGAGGCTCTCAGTAACT 59.286 41.667 19.03 8.64 34.76 2.24
418 421 5.188751 AGCAATAAGAGGCTCTCAGTAACTT 59.811 40.000 19.03 1.54 34.76 2.66
419 422 5.522097 GCAATAAGAGGCTCTCAGTAACTTC 59.478 44.000 19.03 0.00 32.06 3.01
420 423 6.634805 CAATAAGAGGCTCTCAGTAACTTCA 58.365 40.000 19.03 0.00 32.06 3.02
421 424 6.859112 ATAAGAGGCTCTCAGTAACTTCAA 57.141 37.500 19.03 0.00 32.06 2.69
422 425 4.529109 AGAGGCTCTCAGTAACTTCAAC 57.471 45.455 12.24 0.00 32.06 3.18
423 426 3.898123 AGAGGCTCTCAGTAACTTCAACA 59.102 43.478 12.24 0.00 32.06 3.33
424 427 4.345257 AGAGGCTCTCAGTAACTTCAACAA 59.655 41.667 12.24 0.00 32.06 2.83
425 428 5.036117 AGGCTCTCAGTAACTTCAACAAA 57.964 39.130 0.00 0.00 0.00 2.83
426 429 5.625150 AGGCTCTCAGTAACTTCAACAAAT 58.375 37.500 0.00 0.00 0.00 2.32
427 430 5.703130 AGGCTCTCAGTAACTTCAACAAATC 59.297 40.000 0.00 0.00 0.00 2.17
428 431 5.106515 GGCTCTCAGTAACTTCAACAAATCC 60.107 44.000 0.00 0.00 0.00 3.01
429 432 5.389935 GCTCTCAGTAACTTCAACAAATCCG 60.390 44.000 0.00 0.00 0.00 4.18
430 433 4.451096 TCTCAGTAACTTCAACAAATCCGC 59.549 41.667 0.00 0.00 0.00 5.54
431 434 4.130857 TCAGTAACTTCAACAAATCCGCA 58.869 39.130 0.00 0.00 0.00 5.69
432 435 4.576873 TCAGTAACTTCAACAAATCCGCAA 59.423 37.500 0.00 0.00 0.00 4.85
433 436 5.066634 TCAGTAACTTCAACAAATCCGCAAA 59.933 36.000 0.00 0.00 0.00 3.68
434 437 5.746245 CAGTAACTTCAACAAATCCGCAAAA 59.254 36.000 0.00 0.00 0.00 2.44
435 438 5.746721 AGTAACTTCAACAAATCCGCAAAAC 59.253 36.000 0.00 0.00 0.00 2.43
436 439 4.116747 ACTTCAACAAATCCGCAAAACA 57.883 36.364 0.00 0.00 0.00 2.83
437 440 4.499183 ACTTCAACAAATCCGCAAAACAA 58.501 34.783 0.00 0.00 0.00 2.83
438 441 4.932200 ACTTCAACAAATCCGCAAAACAAA 59.068 33.333 0.00 0.00 0.00 2.83
439 442 5.409826 ACTTCAACAAATCCGCAAAACAAAA 59.590 32.000 0.00 0.00 0.00 2.44
440 443 5.862924 TCAACAAATCCGCAAAACAAAAA 57.137 30.435 0.00 0.00 0.00 1.94
495 498 0.108585 AGAGTTGCTTCCGCCTTTGA 59.891 50.000 0.00 0.00 34.43 2.69
499 502 2.029918 AGTTGCTTCCGCCTTTGAAATC 60.030 45.455 0.00 0.00 34.43 2.17
507 510 2.533266 CGCCTTTGAAATCAGCCAATC 58.467 47.619 0.00 0.00 0.00 2.67
549 552 9.586435 GGAATTCGAATTTCACCAAATATCTTT 57.414 29.630 23.49 0.00 31.51 2.52
594 597 5.582689 GGTAGTCCCATGAAGAAAATTGG 57.417 43.478 0.00 0.00 0.00 3.16
595 598 4.142160 GGTAGTCCCATGAAGAAAATTGGC 60.142 45.833 0.00 0.00 0.00 4.52
596 599 3.782992 AGTCCCATGAAGAAAATTGGCT 58.217 40.909 0.00 0.00 0.00 4.75
597 600 3.512724 AGTCCCATGAAGAAAATTGGCTG 59.487 43.478 0.00 0.00 0.00 4.85
598 601 2.833338 TCCCATGAAGAAAATTGGCTGG 59.167 45.455 0.00 0.00 0.00 4.85
599 602 2.833338 CCCATGAAGAAAATTGGCTGGA 59.167 45.455 0.00 0.00 0.00 3.86
600 603 3.261390 CCCATGAAGAAAATTGGCTGGAA 59.739 43.478 0.00 0.00 0.00 3.53
601 604 4.262981 CCCATGAAGAAAATTGGCTGGAAA 60.263 41.667 0.00 0.00 0.00 3.13
602 605 5.493809 CCATGAAGAAAATTGGCTGGAAAT 58.506 37.500 0.00 0.00 0.00 2.17
603 606 5.353123 CCATGAAGAAAATTGGCTGGAAATG 59.647 40.000 0.00 0.00 0.00 2.32
604 607 4.317488 TGAAGAAAATTGGCTGGAAATGC 58.683 39.130 0.00 0.00 0.00 3.56
605 608 4.040706 TGAAGAAAATTGGCTGGAAATGCT 59.959 37.500 0.00 0.00 0.00 3.79
606 609 3.934068 AGAAAATTGGCTGGAAATGCTG 58.066 40.909 0.00 0.00 0.00 4.41
607 610 2.103537 AAATTGGCTGGAAATGCTGC 57.896 45.000 0.00 0.00 0.00 5.25
608 611 0.108520 AATTGGCTGGAAATGCTGCG 60.109 50.000 0.00 0.00 0.00 5.18
609 612 1.952102 ATTGGCTGGAAATGCTGCGG 61.952 55.000 0.00 0.00 0.00 5.69
610 613 4.503314 GGCTGGAAATGCTGCGGC 62.503 66.667 11.65 11.65 46.67 6.53
728 755 3.918328 AACGGGTCGAGGGTGGGAT 62.918 63.158 0.00 0.00 0.00 3.85
874 914 4.840005 GGCTGCTGCGGGGTACTC 62.840 72.222 10.99 0.00 40.82 2.59
876 916 4.514577 CTGCTGCGGGGTACTCGG 62.515 72.222 0.00 3.82 0.00 4.63
879 919 4.814294 CTGCGGGGTACTCGGCAC 62.814 72.222 22.78 0.00 37.91 5.01
893 934 6.260936 GGTACTCGGCACTGTATTTACTACTA 59.739 42.308 0.00 0.00 0.00 1.82
1451 1539 2.522836 AGACTCAAGAGCTGTGTGTG 57.477 50.000 0.00 0.00 31.92 3.82
1452 1540 1.759445 AGACTCAAGAGCTGTGTGTGT 59.241 47.619 0.00 0.00 31.92 3.72
1453 1541 1.863454 GACTCAAGAGCTGTGTGTGTG 59.137 52.381 0.00 0.00 31.92 3.82
1454 1542 1.224075 CTCAAGAGCTGTGTGTGTGG 58.776 55.000 0.00 0.00 0.00 4.17
1455 1543 0.815213 TCAAGAGCTGTGTGTGTGGC 60.815 55.000 0.00 0.00 0.00 5.01
1456 1544 1.526917 AAGAGCTGTGTGTGTGGCC 60.527 57.895 0.00 0.00 0.00 5.36
1457 1545 1.987807 AAGAGCTGTGTGTGTGGCCT 61.988 55.000 3.32 0.00 0.00 5.19
1458 1546 1.526917 GAGCTGTGTGTGTGGCCTT 60.527 57.895 3.32 0.00 0.00 4.35
1459 1547 1.789078 GAGCTGTGTGTGTGGCCTTG 61.789 60.000 3.32 0.00 0.00 3.61
1460 1548 2.723746 CTGTGTGTGTGGCCTTGC 59.276 61.111 3.32 0.00 0.00 4.01
2033 2125 0.601841 TCGCCGGAGAAAGGTTCAAC 60.602 55.000 5.05 0.00 0.00 3.18
2092 2186 9.528018 CTTTTCTTTCAGTTTGCTTACCATTTA 57.472 29.630 0.00 0.00 0.00 1.40
2108 2202 9.436957 CTTACCATTTAGTTGTGAGAATGTACT 57.563 33.333 0.00 0.00 0.00 2.73
2384 2478 1.675641 CAAGGTGTGCTGGGCTACC 60.676 63.158 7.90 7.90 36.98 3.18
2387 2481 3.702048 GTGTGCTGGGCTACCGGA 61.702 66.667 9.46 0.00 46.80 5.14
2435 2529 1.888215 CCTTCGATGCTGCCATACAT 58.112 50.000 0.00 0.00 0.00 2.29
2456 2550 1.212751 CGGTGTCGATGTGCTCTCA 59.787 57.895 0.00 0.00 39.00 3.27
2531 2625 2.267961 GGATCCTTCCACGCCGTT 59.732 61.111 3.84 0.00 42.12 4.44
2558 2652 1.347707 GGGATCACTGTGGTCTGTTCA 59.652 52.381 19.60 0.00 0.00 3.18
2788 2882 1.774894 ATGTACCGTGGTTGCAGGGT 61.775 55.000 0.00 0.00 44.44 4.34
2803 2897 3.509575 TGCAGGGTCAAACAATGTATTCC 59.490 43.478 0.00 0.00 0.00 3.01
2890 2986 3.808728 TGATACTGATGCAAGGTAAGCC 58.191 45.455 0.00 0.00 0.00 4.35
2924 3020 9.401058 CCTTGTTCTGTTCTTTATTGATCCTAT 57.599 33.333 0.00 0.00 0.00 2.57
3209 3314 6.956202 ACTACTAGCACGAGGTACATAAAT 57.044 37.500 0.00 0.00 0.00 1.40
3217 3322 7.948357 AGCACGAGGTACATAAATCAGTATTA 58.052 34.615 0.00 0.00 0.00 0.98
3314 3420 9.758651 GTTTTTCTACATAAACAGAAACCCAAT 57.241 29.630 0.00 0.00 39.76 3.16
3428 3534 9.566432 GACTCCATCAATTCTGAAGGTAATTAT 57.434 33.333 0.00 0.00 40.63 1.28
3429 3535 9.566432 ACTCCATCAATTCTGAAGGTAATTATC 57.434 33.333 0.00 0.00 40.63 1.75
3460 3566 1.681264 GACCACCCAAGTTTGTCCTTG 59.319 52.381 0.00 0.00 41.21 3.61
3469 3575 4.262121 CCAAGTTTGTCCTTGATGCATTCA 60.262 41.667 0.00 0.00 43.65 2.57
3645 3751 1.547675 GGAACTTCAATGTCCTGCCCA 60.548 52.381 0.00 0.00 0.00 5.36
3714 3820 1.312371 GCCCGGCTGCAGTAAAATCA 61.312 55.000 16.64 0.00 0.00 2.57
3768 3874 5.566826 GCTTCACCTTGTCACACATACTCTA 60.567 44.000 0.00 0.00 0.00 2.43
3772 3878 3.769844 CCTTGTCACACATACTCTACCCT 59.230 47.826 0.00 0.00 0.00 4.34
3790 3896 7.416731 TCTACCCTTAACTAACAGGTCTACAT 58.583 38.462 0.00 0.00 31.89 2.29
4064 4170 0.991920 ACCTGAACGTCCCATCCATT 59.008 50.000 0.00 0.00 0.00 3.16
4247 4353 1.607178 CAAGGTGGCATTCCAGGCA 60.607 57.895 0.00 0.00 44.48 4.75
4404 4510 0.966875 AGTATGTACCGGTGCCGTCA 60.967 55.000 19.93 8.91 37.81 4.35
4614 4724 3.718434 TGATATCCAGGAGCATCTTTGGT 59.282 43.478 12.88 0.00 39.63 3.67
4624 4734 4.479619 GAGCATCTTTGGTGACACAAATC 58.520 43.478 8.08 0.00 42.67 2.17
4636 4746 6.048509 GGTGACACAAATCTGACCAATTTTT 58.951 36.000 8.08 0.00 0.00 1.94
4678 4790 4.120792 TGAATTGAACTGCTGCACAAAA 57.879 36.364 8.02 0.00 0.00 2.44
4679 4791 4.502016 TGAATTGAACTGCTGCACAAAAA 58.498 34.783 8.02 0.00 0.00 1.94
4680 4792 5.117584 TGAATTGAACTGCTGCACAAAAAT 58.882 33.333 8.02 0.37 0.00 1.82
4718 4830 1.002134 AGGGGCATCTTTGGTCACG 60.002 57.895 0.00 0.00 0.00 4.35
4781 4894 6.882140 ACGGTGAGAATACAATGGATGTTTAA 59.118 34.615 0.00 0.00 43.63 1.52
4833 4946 5.175859 TCTTACACGACCAAGAATCCAATC 58.824 41.667 0.00 0.00 0.00 2.67
4836 4949 3.007940 ACACGACCAAGAATCCAATCTGA 59.992 43.478 0.00 0.00 0.00 3.27
4844 4957 4.500499 AGAATCCAATCTGAGAACAGGG 57.500 45.455 0.00 0.00 43.60 4.45
4847 4960 2.631384 TCCAATCTGAGAACAGGGGAA 58.369 47.619 0.00 0.00 43.60 3.97
4990 5106 1.276622 GCCTTCTGGTAGTCCTGGAA 58.723 55.000 0.00 0.00 35.27 3.53
5156 5272 1.040339 GGCGAGAGAGGTGGATGAGT 61.040 60.000 0.00 0.00 0.00 3.41
5358 5474 3.186047 GGCGCGTCGTGTTGCTAT 61.186 61.111 8.43 0.00 0.00 2.97
5359 5475 2.020016 GCGCGTCGTGTTGCTATG 59.980 61.111 8.43 0.00 0.00 2.23
5360 5476 2.695055 CGCGTCGTGTTGCTATGG 59.305 61.111 0.00 0.00 0.00 2.74
5361 5477 2.399611 GCGTCGTGTTGCTATGGC 59.600 61.111 0.00 0.00 39.26 4.40
5381 5497 4.528531 GCAAAAACAAATTGCGAAGGAA 57.471 36.364 0.00 0.00 45.69 3.36
5433 5575 8.535690 AAGAGTTATAATCTGCTAAATACGGC 57.464 34.615 0.00 0.00 0.00 5.68
5442 5584 4.155280 TCTGCTAAATACGGCCAAAGAAAC 59.845 41.667 2.24 0.00 0.00 2.78
5449 5591 2.306847 ACGGCCAAAGAAACATTGTCT 58.693 42.857 2.24 0.00 0.00 3.41
5486 5628 1.246056 ACAAGCGGTGCTACCTCGTA 61.246 55.000 0.00 0.00 38.25 3.43
5489 5631 1.213537 GCGGTGCTACCTCGTAACA 59.786 57.895 4.21 0.00 35.66 2.41
5491 5633 0.457337 CGGTGCTACCTCGTAACACC 60.457 60.000 12.39 12.39 46.03 4.16
5507 5649 4.510167 AACACCATAGATTAGCAAGGCT 57.490 40.909 0.00 0.00 43.41 4.58
5508 5650 3.813443 ACACCATAGATTAGCAAGGCTG 58.187 45.455 0.07 0.00 40.10 4.85
5512 5654 3.812053 CCATAGATTAGCAAGGCTGTGAC 59.188 47.826 0.07 0.00 40.10 3.67
5526 5668 4.520492 AGGCTGTGACAAACTCTATTTTGG 59.480 41.667 0.00 0.00 40.25 3.28
5527 5669 4.278419 GGCTGTGACAAACTCTATTTTGGT 59.722 41.667 1.04 0.00 40.25 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.585471 ATTCTCAAGATGCAGGAATAGAAAAA 57.415 30.769 7.43 0.00 0.00 1.94
10 11 7.830697 TGATTCTCAAGATGCAGGAATAGAAAA 59.169 33.333 7.43 0.00 0.00 2.29
11 12 7.341030 TGATTCTCAAGATGCAGGAATAGAAA 58.659 34.615 7.43 0.00 0.00 2.52
12 13 6.892485 TGATTCTCAAGATGCAGGAATAGAA 58.108 36.000 0.00 0.00 0.00 2.10
13 14 6.490241 TGATTCTCAAGATGCAGGAATAGA 57.510 37.500 0.00 0.00 0.00 1.98
14 15 6.348622 GCATGATTCTCAAGATGCAGGAATAG 60.349 42.308 0.00 0.00 32.01 1.73
26 27 7.254117 GCATCTTTGATTTGCATGATTCTCAAG 60.254 37.037 0.00 0.00 36.40 3.02
40 41 7.452562 ACAAAATTAGGGTGCATCTTTGATTT 58.547 30.769 13.71 6.50 0.00 2.17
50 51 3.410631 TCTCGACAAAATTAGGGTGCA 57.589 42.857 0.00 0.00 0.00 4.57
134 136 5.684552 GCAAAATAAGGCATTTCCAGGCATA 60.685 40.000 0.00 0.00 35.74 3.14
135 137 4.773013 CAAAATAAGGCATTTCCAGGCAT 58.227 39.130 0.00 0.00 35.74 4.40
140 142 3.951775 ACGCAAAATAAGGCATTTCCA 57.048 38.095 0.00 0.00 35.74 3.53
148 150 9.274065 GATTTGTCTTAACTACGCAAAATAAGG 57.726 33.333 0.00 0.00 33.60 2.69
158 160 5.929992 TGGTCCAAGATTTGTCTTAACTACG 59.070 40.000 0.00 0.00 0.00 3.51
220 222 9.959721 GGAGGGAGTGCTTATTTATAATTATGA 57.040 33.333 8.28 0.00 0.00 2.15
221 223 9.739276 TGGAGGGAGTGCTTATTTATAATTATG 57.261 33.333 8.28 0.00 0.00 1.90
223 225 9.959721 GATGGAGGGAGTGCTTATTTATAATTA 57.040 33.333 0.00 0.00 0.00 1.40
225 227 7.406104 GGATGGAGGGAGTGCTTATTTATAAT 58.594 38.462 0.00 0.00 0.00 1.28
226 228 6.520061 CGGATGGAGGGAGTGCTTATTTATAA 60.520 42.308 0.00 0.00 0.00 0.98
227 229 5.046591 CGGATGGAGGGAGTGCTTATTTATA 60.047 44.000 0.00 0.00 0.00 0.98
228 230 4.263068 CGGATGGAGGGAGTGCTTATTTAT 60.263 45.833 0.00 0.00 0.00 1.40
229 231 3.071023 CGGATGGAGGGAGTGCTTATTTA 59.929 47.826 0.00 0.00 0.00 1.40
230 232 2.158755 CGGATGGAGGGAGTGCTTATTT 60.159 50.000 0.00 0.00 0.00 1.40
231 233 1.417890 CGGATGGAGGGAGTGCTTATT 59.582 52.381 0.00 0.00 0.00 1.40
232 234 1.051812 CGGATGGAGGGAGTGCTTAT 58.948 55.000 0.00 0.00 0.00 1.73
233 235 0.032515 TCGGATGGAGGGAGTGCTTA 60.033 55.000 0.00 0.00 0.00 3.09
234 236 0.909610 TTCGGATGGAGGGAGTGCTT 60.910 55.000 0.00 0.00 0.00 3.91
235 237 0.909610 TTTCGGATGGAGGGAGTGCT 60.910 55.000 0.00 0.00 0.00 4.40
236 238 0.035439 TTTTCGGATGGAGGGAGTGC 60.035 55.000 0.00 0.00 0.00 4.40
237 239 2.717639 ATTTTCGGATGGAGGGAGTG 57.282 50.000 0.00 0.00 0.00 3.51
238 240 2.102588 CGTATTTTCGGATGGAGGGAGT 59.897 50.000 0.00 0.00 0.00 3.85
239 241 2.755650 CGTATTTTCGGATGGAGGGAG 58.244 52.381 0.00 0.00 0.00 4.30
240 242 1.202604 GCGTATTTTCGGATGGAGGGA 60.203 52.381 0.00 0.00 0.00 4.20
241 243 1.226746 GCGTATTTTCGGATGGAGGG 58.773 55.000 0.00 0.00 0.00 4.30
242 244 0.859232 CGCGTATTTTCGGATGGAGG 59.141 55.000 0.00 0.00 0.00 4.30
243 245 1.521423 GACGCGTATTTTCGGATGGAG 59.479 52.381 13.97 0.00 0.00 3.86
244 246 1.563111 GACGCGTATTTTCGGATGGA 58.437 50.000 13.97 0.00 0.00 3.41
245 247 0.228742 CGACGCGTATTTTCGGATGG 59.771 55.000 13.97 0.00 0.00 3.51
246 248 3.684355 CGACGCGTATTTTCGGATG 57.316 52.632 13.97 0.00 0.00 3.51
250 252 2.490697 TTTTCCGACGCGTATTTTCG 57.509 45.000 13.97 11.54 0.00 3.46
251 253 3.540738 CCATTTTTCCGACGCGTATTTTC 59.459 43.478 13.97 0.00 0.00 2.29
252 254 3.188873 TCCATTTTTCCGACGCGTATTTT 59.811 39.130 13.97 0.00 0.00 1.82
253 255 2.743126 TCCATTTTTCCGACGCGTATTT 59.257 40.909 13.97 0.00 0.00 1.40
254 256 2.348660 TCCATTTTTCCGACGCGTATT 58.651 42.857 13.97 0.00 0.00 1.89
255 257 2.012937 TCCATTTTTCCGACGCGTAT 57.987 45.000 13.97 0.00 0.00 3.06
256 258 2.012937 ATCCATTTTTCCGACGCGTA 57.987 45.000 13.97 0.00 0.00 4.42
257 259 2.012937 TATCCATTTTTCCGACGCGT 57.987 45.000 13.85 13.85 0.00 6.01
258 260 3.392769 TTTATCCATTTTTCCGACGCG 57.607 42.857 3.53 3.53 0.00 6.01
259 261 5.005299 CCATTTTTATCCATTTTTCCGACGC 59.995 40.000 0.00 0.00 0.00 5.19
260 262 6.326375 TCCATTTTTATCCATTTTTCCGACG 58.674 36.000 0.00 0.00 0.00 5.12
261 263 7.763985 ACATCCATTTTTATCCATTTTTCCGAC 59.236 33.333 0.00 0.00 0.00 4.79
262 264 7.846066 ACATCCATTTTTATCCATTTTTCCGA 58.154 30.769 0.00 0.00 0.00 4.55
263 265 7.981225 AGACATCCATTTTTATCCATTTTTCCG 59.019 33.333 0.00 0.00 0.00 4.30
269 271 9.927081 AGTTCTAGACATCCATTTTTATCCATT 57.073 29.630 0.00 0.00 0.00 3.16
299 301 8.307483 CGAAGAAATGGATGTACCTAGACATAT 58.693 37.037 0.00 0.00 40.18 1.78
300 302 7.504574 TCGAAGAAATGGATGTACCTAGACATA 59.495 37.037 0.00 0.00 40.18 2.29
301 303 6.323996 TCGAAGAAATGGATGTACCTAGACAT 59.676 38.462 0.00 0.00 42.82 3.06
302 304 5.655090 TCGAAGAAATGGATGTACCTAGACA 59.345 40.000 0.00 0.00 39.86 3.41
303 305 5.978322 GTCGAAGAAATGGATGTACCTAGAC 59.022 44.000 0.00 0.00 39.69 2.59
304 306 5.655090 TGTCGAAGAAATGGATGTACCTAGA 59.345 40.000 0.00 0.00 39.69 2.43
305 307 5.902681 TGTCGAAGAAATGGATGTACCTAG 58.097 41.667 0.00 0.00 39.69 3.02
306 308 5.925506 TGTCGAAGAAATGGATGTACCTA 57.074 39.130 0.00 0.00 39.69 3.08
307 309 4.819105 TGTCGAAGAAATGGATGTACCT 57.181 40.909 0.00 0.00 39.69 3.08
308 310 4.935808 ACTTGTCGAAGAAATGGATGTACC 59.064 41.667 0.00 0.00 39.69 3.34
309 311 7.772332 ATACTTGTCGAAGAAATGGATGTAC 57.228 36.000 0.00 0.00 39.69 2.90
310 312 8.786826 AAATACTTGTCGAAGAAATGGATGTA 57.213 30.769 0.00 0.00 39.69 2.29
311 313 7.687941 AAATACTTGTCGAAGAAATGGATGT 57.312 32.000 0.00 0.00 39.69 3.06
312 314 7.426456 CGAAAATACTTGTCGAAGAAATGGATG 59.574 37.037 0.00 0.00 39.69 3.51
313 315 7.414098 CCGAAAATACTTGTCGAAGAAATGGAT 60.414 37.037 1.13 0.00 39.69 3.41
314 316 6.128391 CCGAAAATACTTGTCGAAGAAATGGA 60.128 38.462 1.13 0.00 39.69 3.41
315 317 6.021596 CCGAAAATACTTGTCGAAGAAATGG 58.978 40.000 1.13 0.00 39.69 3.16
316 318 6.736853 GTCCGAAAATACTTGTCGAAGAAATG 59.263 38.462 1.13 0.00 39.69 2.32
317 319 6.400727 CGTCCGAAAATACTTGTCGAAGAAAT 60.401 38.462 1.13 0.00 39.69 2.17
318 320 5.107760 CGTCCGAAAATACTTGTCGAAGAAA 60.108 40.000 1.13 0.00 39.69 2.52
319 321 4.383649 CGTCCGAAAATACTTGTCGAAGAA 59.616 41.667 1.13 0.00 39.69 2.52
320 322 3.916172 CGTCCGAAAATACTTGTCGAAGA 59.084 43.478 1.13 0.00 36.92 2.87
321 323 3.060363 CCGTCCGAAAATACTTGTCGAAG 59.940 47.826 1.13 0.00 36.92 3.79
322 324 2.988493 CCGTCCGAAAATACTTGTCGAA 59.012 45.455 1.13 0.00 36.92 3.71
323 325 2.228582 TCCGTCCGAAAATACTTGTCGA 59.771 45.455 1.13 0.00 36.92 4.20
324 326 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
325 327 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
326 328 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
327 329 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
328 330 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
329 331 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
330 332 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
331 333 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
332 334 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
333 335 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
334 336 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
335 337 0.033796 ACATACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
336 338 0.033796 AACATACTCCCTCCGTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
337 339 0.822164 AAACATACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
338 340 3.007635 CAAAAACATACTCCCTCCGTCC 58.992 50.000 0.00 0.00 0.00 4.79
339 341 3.671716 ACAAAAACATACTCCCTCCGTC 58.328 45.455 0.00 0.00 0.00 4.79
340 342 3.782656 ACAAAAACATACTCCCTCCGT 57.217 42.857 0.00 0.00 0.00 4.69
341 343 4.828829 AGTACAAAAACATACTCCCTCCG 58.171 43.478 0.00 0.00 0.00 4.63
342 344 6.944096 AGTAGTACAAAAACATACTCCCTCC 58.056 40.000 2.52 0.00 33.65 4.30
344 346 9.886132 CAATAGTAGTACAAAAACATACTCCCT 57.114 33.333 2.52 0.00 33.65 4.20
345 347 9.880157 TCAATAGTAGTACAAAAACATACTCCC 57.120 33.333 2.52 0.00 33.65 4.30
360 362 8.038351 TGCAGCAAATTAGTGTCAATAGTAGTA 58.962 33.333 0.00 0.00 0.00 1.82
361 363 6.878923 TGCAGCAAATTAGTGTCAATAGTAGT 59.121 34.615 0.00 0.00 0.00 2.73
362 364 7.182761 GTGCAGCAAATTAGTGTCAATAGTAG 58.817 38.462 0.00 0.00 0.00 2.57
363 365 6.183360 CGTGCAGCAAATTAGTGTCAATAGTA 60.183 38.462 0.00 0.00 0.00 1.82
364 366 5.390885 CGTGCAGCAAATTAGTGTCAATAGT 60.391 40.000 0.00 0.00 0.00 2.12
365 367 5.023920 CGTGCAGCAAATTAGTGTCAATAG 58.976 41.667 0.00 0.00 0.00 1.73
366 368 4.142708 CCGTGCAGCAAATTAGTGTCAATA 60.143 41.667 0.00 0.00 0.00 1.90
367 369 3.366273 CCGTGCAGCAAATTAGTGTCAAT 60.366 43.478 0.00 0.00 0.00 2.57
368 370 2.031245 CCGTGCAGCAAATTAGTGTCAA 60.031 45.455 0.00 0.00 0.00 3.18
370 372 1.804151 TCCGTGCAGCAAATTAGTGTC 59.196 47.619 0.00 0.00 0.00 3.67
396 399 6.634805 TGAAGTTACTGAGAGCCTCTTATTG 58.365 40.000 0.00 0.00 0.00 1.90
397 400 6.859112 TGAAGTTACTGAGAGCCTCTTATT 57.141 37.500 0.00 0.00 0.00 1.40
409 412 4.130857 TGCGGATTTGTTGAAGTTACTGA 58.869 39.130 0.00 0.00 0.00 3.41
410 413 4.481930 TGCGGATTTGTTGAAGTTACTG 57.518 40.909 0.00 0.00 0.00 2.74
411 414 5.508200 TTTGCGGATTTGTTGAAGTTACT 57.492 34.783 0.00 0.00 0.00 2.24
412 415 5.517054 TGTTTTGCGGATTTGTTGAAGTTAC 59.483 36.000 0.00 0.00 0.00 2.50
413 416 5.651530 TGTTTTGCGGATTTGTTGAAGTTA 58.348 33.333 0.00 0.00 0.00 2.24
414 417 4.499183 TGTTTTGCGGATTTGTTGAAGTT 58.501 34.783 0.00 0.00 0.00 2.66
415 418 4.116747 TGTTTTGCGGATTTGTTGAAGT 57.883 36.364 0.00 0.00 0.00 3.01
416 419 5.462034 TTTGTTTTGCGGATTTGTTGAAG 57.538 34.783 0.00 0.00 0.00 3.02
417 420 5.862924 TTTTGTTTTGCGGATTTGTTGAA 57.137 30.435 0.00 0.00 0.00 2.69
418 421 5.862924 TTTTTGTTTTGCGGATTTGTTGA 57.137 30.435 0.00 0.00 0.00 3.18
495 498 5.049129 GCTATAAAGCGAGATTGGCTGATTT 60.049 40.000 0.00 0.00 41.39 2.17
499 502 3.802722 GCTATAAAGCGAGATTGGCTG 57.197 47.619 0.00 0.00 41.39 4.85
521 524 8.917088 AGATATTTGGTGAAATTCGAATTCCAT 58.083 29.630 22.93 13.96 33.63 3.41
572 575 4.142160 GCCAATTTTCTTCATGGGACTACC 60.142 45.833 0.00 0.00 40.81 3.18
573 576 4.706962 AGCCAATTTTCTTCATGGGACTAC 59.293 41.667 0.00 0.00 33.45 2.73
574 577 4.706476 CAGCCAATTTTCTTCATGGGACTA 59.294 41.667 0.00 0.00 33.45 2.59
575 578 3.512724 CAGCCAATTTTCTTCATGGGACT 59.487 43.478 0.00 0.00 33.45 3.85
576 579 3.368739 CCAGCCAATTTTCTTCATGGGAC 60.369 47.826 0.00 0.00 33.45 4.46
577 580 2.833338 CCAGCCAATTTTCTTCATGGGA 59.167 45.455 0.00 0.00 33.45 4.37
578 581 2.833338 TCCAGCCAATTTTCTTCATGGG 59.167 45.455 0.00 0.00 33.45 4.00
579 582 4.540359 TTCCAGCCAATTTTCTTCATGG 57.460 40.909 0.00 0.00 36.00 3.66
580 583 5.163794 GCATTTCCAGCCAATTTTCTTCATG 60.164 40.000 0.00 0.00 0.00 3.07
581 584 4.939439 GCATTTCCAGCCAATTTTCTTCAT 59.061 37.500 0.00 0.00 0.00 2.57
582 585 4.040706 AGCATTTCCAGCCAATTTTCTTCA 59.959 37.500 0.00 0.00 0.00 3.02
583 586 4.390909 CAGCATTTCCAGCCAATTTTCTTC 59.609 41.667 0.00 0.00 0.00 2.87
584 587 4.320870 CAGCATTTCCAGCCAATTTTCTT 58.679 39.130 0.00 0.00 0.00 2.52
585 588 3.867216 GCAGCATTTCCAGCCAATTTTCT 60.867 43.478 0.00 0.00 0.00 2.52
586 589 2.417586 GCAGCATTTCCAGCCAATTTTC 59.582 45.455 0.00 0.00 0.00 2.29
587 590 2.429478 GCAGCATTTCCAGCCAATTTT 58.571 42.857 0.00 0.00 0.00 1.82
588 591 1.673626 CGCAGCATTTCCAGCCAATTT 60.674 47.619 0.00 0.00 0.00 1.82
589 592 0.108520 CGCAGCATTTCCAGCCAATT 60.109 50.000 0.00 0.00 0.00 2.32
590 593 1.514087 CGCAGCATTTCCAGCCAAT 59.486 52.632 0.00 0.00 0.00 3.16
591 594 2.638354 CCGCAGCATTTCCAGCCAA 61.638 57.895 0.00 0.00 0.00 4.52
592 595 3.063704 CCGCAGCATTTCCAGCCA 61.064 61.111 0.00 0.00 0.00 4.75
593 596 4.503314 GCCGCAGCATTTCCAGCC 62.503 66.667 0.00 0.00 39.53 4.85
594 597 3.751246 TGCCGCAGCATTTCCAGC 61.751 61.111 0.00 0.00 46.52 4.85
608 611 2.335712 CCCTTTGCTTCGGAGTGCC 61.336 63.158 0.00 0.00 0.00 5.01
609 612 2.982744 GCCCTTTGCTTCGGAGTGC 61.983 63.158 0.00 0.00 36.87 4.40
610 613 1.172180 TTGCCCTTTGCTTCGGAGTG 61.172 55.000 0.00 0.00 42.00 3.51
611 614 0.890996 CTTGCCCTTTGCTTCGGAGT 60.891 55.000 0.00 0.00 42.00 3.85
612 615 0.606401 TCTTGCCCTTTGCTTCGGAG 60.606 55.000 0.00 0.00 42.00 4.63
613 616 0.179004 TTCTTGCCCTTTGCTTCGGA 60.179 50.000 0.00 0.00 42.00 4.55
728 755 3.311110 GTCGTGCTCCCACTCCCA 61.311 66.667 0.00 0.00 39.86 4.37
870 910 7.011763 CAGTAGTAGTAAATACAGTGCCGAGTA 59.988 40.741 0.00 0.00 36.79 2.59
874 914 5.163581 ACCAGTAGTAGTAAATACAGTGCCG 60.164 44.000 0.00 0.00 36.79 5.69
875 915 6.218108 ACCAGTAGTAGTAAATACAGTGCC 57.782 41.667 0.00 0.00 36.79 5.01
876 916 7.284034 TCCTACCAGTAGTAGTAAATACAGTGC 59.716 40.741 4.23 0.00 46.15 4.40
877 917 8.743085 TCCTACCAGTAGTAGTAAATACAGTG 57.257 38.462 4.23 0.00 46.15 3.66
878 918 8.776119 TCTCCTACCAGTAGTAGTAAATACAGT 58.224 37.037 4.23 0.00 46.15 3.55
879 919 9.796180 ATCTCCTACCAGTAGTAGTAAATACAG 57.204 37.037 4.23 0.00 46.15 2.74
893 934 4.712337 ACTCGATTCAAATCTCCTACCAGT 59.288 41.667 1.58 0.00 33.24 4.00
969 1010 2.281276 GGGGGTTGGTGTCGTGTC 60.281 66.667 0.00 0.00 0.00 3.67
1007 1051 0.898320 TTGAAAGGCGAGAGGAGGAG 59.102 55.000 0.00 0.00 0.00 3.69
1080 1124 1.096416 AACGGTAGCTCGAGAAGGAG 58.904 55.000 18.75 6.36 37.11 3.69
1081 1125 0.809385 CAACGGTAGCTCGAGAAGGA 59.191 55.000 18.75 0.00 0.00 3.36
1082 1126 0.802607 GCAACGGTAGCTCGAGAAGG 60.803 60.000 18.75 2.17 0.00 3.46
1084 1128 1.154093 CGCAACGGTAGCTCGAGAA 60.154 57.895 18.75 0.00 0.00 2.87
1460 1548 1.226211 CCTGCTTGCTGCGAAATCG 60.226 57.895 0.00 0.00 46.63 3.34
1798 1889 2.683933 TCCTCCCCGAACCTGCTC 60.684 66.667 0.00 0.00 0.00 4.26
1904 1995 5.810095 AGATCCCAAGAAAACCTTAGTCAG 58.190 41.667 0.00 0.00 32.86 3.51
2033 2125 1.283793 CCTGTTGCAGTTGGAAGCG 59.716 57.895 0.00 0.00 0.00 4.68
2092 2186 5.721960 ACCAGGATAGTACATTCTCACAACT 59.278 40.000 0.00 0.00 0.00 3.16
2108 2202 3.184382 TCTGAAGTCACCACCAGGATA 57.816 47.619 0.00 0.00 38.69 2.59
2339 2433 2.284699 AACCTAGCCCTCGGTGCT 60.285 61.111 4.71 4.71 42.81 4.40
2384 2478 1.751351 TCTGCAGAGGTACAATCTCCG 59.249 52.381 13.74 0.00 31.96 4.63
2387 2481 3.133721 GGATGTCTGCAGAGGTACAATCT 59.866 47.826 18.89 0.00 0.00 2.40
2435 2529 1.080772 GAGCACATCGACACCGTCA 60.081 57.895 0.00 0.00 37.05 4.35
2456 2550 4.021925 GCTTGGCCGAGGGACACT 62.022 66.667 22.06 0.00 42.46 3.55
2531 2625 1.269958 CCACAGTGATCCCTCTCACA 58.730 55.000 0.62 0.00 46.45 3.58
2558 2652 3.003763 GGACCGGAGTTCCCTGCT 61.004 66.667 9.46 0.00 0.00 4.24
2630 2724 2.621998 GAGGAAAGTCCGATCGATGGTA 59.378 50.000 18.66 0.00 42.75 3.25
2636 2730 0.457853 TTGCGAGGAAAGTCCGATCG 60.458 55.000 8.51 8.51 42.75 3.69
2788 2882 3.442273 GCTTCCCGGAATACATTGTTTGA 59.558 43.478 0.73 0.00 0.00 2.69
2890 2986 3.919216 AGAACAGAACAAGGATGACGAG 58.081 45.455 0.00 0.00 0.00 4.18
2924 3020 5.005628 AGCCAAAAGGGGAGTGTATTTTA 57.994 39.130 0.00 0.00 37.04 1.52
2925 3021 3.856900 AGCCAAAAGGGGAGTGTATTTT 58.143 40.909 0.00 0.00 37.04 1.82
3217 3322 7.956420 TTTTCGCAACTACGGAATCATATAT 57.044 32.000 0.00 0.00 28.88 0.86
3314 3420 4.473643 CGGAGCCAAACTGAACCA 57.526 55.556 0.00 0.00 0.00 3.67
3428 3534 1.610673 GGTGGTCAGCTGAGGGAGA 60.611 63.158 18.89 0.00 0.00 3.71
3429 3535 2.664081 GGGTGGTCAGCTGAGGGAG 61.664 68.421 18.89 0.00 0.00 4.30
3460 3566 6.969473 GGAGTTTAAGCTTAGTTGAATGCATC 59.031 38.462 6.24 0.00 0.00 3.91
3469 3575 9.961265 GTGTTTATTTGGAGTTTAAGCTTAGTT 57.039 29.630 6.24 0.00 0.00 2.24
3645 3751 2.268076 GGCCACGCCTGAAATGTGT 61.268 57.895 0.00 0.00 46.69 3.72
3714 3820 2.949177 TACCTGTTGTGACCATTGCT 57.051 45.000 0.00 0.00 0.00 3.91
3768 3874 6.262207 AGATGTAGACCTGTTAGTTAAGGGT 58.738 40.000 0.00 0.00 37.94 4.34
3790 3896 2.037902 TCACGGACATTGGCTACAAAGA 59.962 45.455 0.00 0.00 40.55 2.52
4064 4170 2.196595 CCCCTCAGTTCAGGAATGGTA 58.803 52.381 0.00 0.00 35.20 3.25
4277 4383 2.934932 TCCCATGTCAGGCTGCCA 60.935 61.111 22.65 4.75 0.00 4.92
4404 4510 3.313012 TCGTTTGTTCTCATGACCGAT 57.687 42.857 0.00 0.00 0.00 4.18
4597 4707 1.003580 GTCACCAAAGATGCTCCTGGA 59.996 52.381 0.00 0.00 32.97 3.86
4614 4724 5.523188 GCAAAAATTGGTCAGATTTGTGTCA 59.477 36.000 0.00 0.00 35.23 3.58
4624 4734 3.460103 ACTTGCTGCAAAAATTGGTCAG 58.540 40.909 16.74 2.89 0.00 3.51
4636 4746 1.680207 TGTTTGCACATACTTGCTGCA 59.320 42.857 0.00 0.00 43.41 4.41
4678 4790 6.607198 CCCTGGTTATGAATACAAGTTCCATT 59.393 38.462 0.00 0.00 0.00 3.16
4679 4791 6.129179 CCCTGGTTATGAATACAAGTTCCAT 58.871 40.000 0.00 0.00 0.00 3.41
4680 4792 5.505780 CCCTGGTTATGAATACAAGTTCCA 58.494 41.667 0.00 0.00 0.00 3.53
4718 4830 5.557891 ACTTACTGCTCATCATTCTTTGC 57.442 39.130 0.00 0.00 0.00 3.68
4781 4894 4.633126 CAGCATTACTCACAGCATTACAGT 59.367 41.667 0.00 0.00 0.00 3.55
4833 4946 3.406764 CTTTGACTTCCCCTGTTCTCAG 58.593 50.000 0.00 0.00 41.01 3.35
4836 4949 1.494721 TGCTTTGACTTCCCCTGTTCT 59.505 47.619 0.00 0.00 0.00 3.01
4844 4957 4.034048 CCGTATGTGTATGCTTTGACTTCC 59.966 45.833 0.00 0.00 0.00 3.46
4847 4960 3.055385 ACCCGTATGTGTATGCTTTGACT 60.055 43.478 0.00 0.00 0.00 3.41
4990 5106 2.093288 TGGGACATCTACTACGACGAGT 60.093 50.000 0.00 3.47 0.00 4.18
5141 5257 0.980231 GCCCACTCATCCACCTCTCT 60.980 60.000 0.00 0.00 0.00 3.10
5304 5420 3.188100 CTCGATCGCTTGCGCCAA 61.188 61.111 11.09 0.00 0.00 4.52
5354 5470 3.431572 TCGCAATTTGTTTTTGCCATAGC 59.568 39.130 3.08 0.00 45.19 2.97
5355 5471 5.389725 CCTTCGCAATTTGTTTTTGCCATAG 60.390 40.000 3.08 0.00 45.19 2.23
5356 5472 4.450419 CCTTCGCAATTTGTTTTTGCCATA 59.550 37.500 3.08 0.00 45.19 2.74
5357 5473 3.250521 CCTTCGCAATTTGTTTTTGCCAT 59.749 39.130 3.08 0.00 45.19 4.40
5358 5474 2.611292 CCTTCGCAATTTGTTTTTGCCA 59.389 40.909 3.08 0.00 45.19 4.92
5359 5475 2.869192 TCCTTCGCAATTTGTTTTTGCC 59.131 40.909 3.08 0.00 45.19 4.52
5360 5476 4.528531 TTCCTTCGCAATTTGTTTTTGC 57.471 36.364 0.00 0.00 44.68 3.68
5361 5477 7.406799 ACTATTCCTTCGCAATTTGTTTTTG 57.593 32.000 0.00 0.00 0.00 2.44
5363 5479 7.882179 ACTACTATTCCTTCGCAATTTGTTTT 58.118 30.769 0.00 0.00 0.00 2.43
5364 5480 7.448748 ACTACTATTCCTTCGCAATTTGTTT 57.551 32.000 0.00 0.00 0.00 2.83
5365 5481 8.556213 TTACTACTATTCCTTCGCAATTTGTT 57.444 30.769 0.00 0.00 0.00 2.83
5366 5482 7.822822 ACTTACTACTATTCCTTCGCAATTTGT 59.177 33.333 0.00 0.00 0.00 2.83
5367 5483 8.197988 ACTTACTACTATTCCTTCGCAATTTG 57.802 34.615 0.00 0.00 0.00 2.32
5372 5488 9.347240 ACTAATACTTACTACTATTCCTTCGCA 57.653 33.333 0.00 0.00 0.00 5.10
5373 5489 9.824534 GACTAATACTTACTACTATTCCTTCGC 57.175 37.037 0.00 0.00 0.00 4.70
5407 5549 8.989980 GCCGTATTTAGCAGATTATAACTCTTT 58.010 33.333 0.00 0.00 0.00 2.52
5408 5550 7.603024 GGCCGTATTTAGCAGATTATAACTCTT 59.397 37.037 0.00 0.00 0.00 2.85
5409 5551 7.097834 GGCCGTATTTAGCAGATTATAACTCT 58.902 38.462 0.00 0.00 0.00 3.24
5410 5552 6.872020 TGGCCGTATTTAGCAGATTATAACTC 59.128 38.462 0.00 0.00 0.00 3.01
5411 5553 6.765403 TGGCCGTATTTAGCAGATTATAACT 58.235 36.000 0.00 0.00 0.00 2.24
5412 5554 7.429636 TTGGCCGTATTTAGCAGATTATAAC 57.570 36.000 0.00 0.00 0.00 1.89
5413 5555 7.934665 TCTTTGGCCGTATTTAGCAGATTATAA 59.065 33.333 0.00 0.00 0.00 0.98
5414 5556 7.446769 TCTTTGGCCGTATTTAGCAGATTATA 58.553 34.615 0.00 0.00 0.00 0.98
5415 5557 6.296026 TCTTTGGCCGTATTTAGCAGATTAT 58.704 36.000 0.00 0.00 0.00 1.28
5416 5558 5.676552 TCTTTGGCCGTATTTAGCAGATTA 58.323 37.500 0.00 0.00 0.00 1.75
5417 5559 4.523083 TCTTTGGCCGTATTTAGCAGATT 58.477 39.130 0.00 0.00 0.00 2.40
5418 5560 4.150897 TCTTTGGCCGTATTTAGCAGAT 57.849 40.909 0.00 0.00 0.00 2.90
5419 5561 3.620427 TCTTTGGCCGTATTTAGCAGA 57.380 42.857 0.00 0.00 0.00 4.26
5420 5562 4.083003 TGTTTCTTTGGCCGTATTTAGCAG 60.083 41.667 0.00 0.00 0.00 4.24
5433 5575 3.181477 TGTGCCAGACAATGTTTCTTTGG 60.181 43.478 0.00 0.00 0.00 3.28
5442 5584 1.138036 CGCCATGTGCCAGACAATG 59.862 57.895 0.00 0.00 38.36 2.82
5467 5609 1.246056 TACGAGGTAGCACCGCTTGT 61.246 55.000 6.64 0.00 44.90 3.16
5486 5628 4.202441 CAGCCTTGCTAATCTATGGTGTT 58.798 43.478 0.00 0.00 36.40 3.32
5489 5631 3.455910 TCACAGCCTTGCTAATCTATGGT 59.544 43.478 0.00 0.00 36.40 3.55
5491 5633 4.445453 TGTCACAGCCTTGCTAATCTATG 58.555 43.478 0.00 0.00 36.40 2.23
5492 5634 4.760530 TGTCACAGCCTTGCTAATCTAT 57.239 40.909 0.00 0.00 36.40 1.98


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

AutoCloner maintained by Alex Coulton.