Multiple sequence alignment - TraesCS1B01G372200

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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 TraesCS1B01G372200 chr1B 100.000 2288 0 0 1 2288 602896618 602898905 0.000000e+00 4226
1 TraesCS1B01G372200 chr2B 91.859 1167 93 2 562 1726 46495173 46494007 0.000000e+00 1628
2 TraesCS1B01G372200 chr2B 90.419 1169 110 2 557 1724 479889430 479888263 0.000000e+00 1537
3 TraesCS1B01G372200 chr2B 89.820 1169 114 4 560 1723 181981444 181980276 0.000000e+00 1495
4 TraesCS1B01G372200 chr2B 85.398 452 34 18 1 426 417309373 417308928 7.500000e-120 440
5 TraesCS1B01G372200 chr2B 85.078 449 37 15 3 426 218691238 218691681 4.520000e-117 431
6 TraesCS1B01G372200 chr2B 82.944 428 56 14 4 426 358203882 358203467 9.980000e-99 370
7 TraesCS1B01G372200 chr2B 81.416 452 45 13 4 426 312506199 312505758 1.310000e-87 333
8 TraesCS1B01G372200 chr2B 93.233 133 9 0 425 557 479889598 479889466 1.790000e-46 196
9 TraesCS1B01G372200 chr5B 90.995 1166 102 3 560 1723 641300047 641298883 0.000000e+00 1568
10 TraesCS1B01G372200 chr5B 87.416 445 33 7 1 428 225597145 225597583 7.350000e-135 490
11 TraesCS1B01G372200 chr5B 86.261 444 30 14 9 426 225575251 225575689 9.640000e-124 453
12 TraesCS1B01G372200 chr5B 93.985 133 8 0 425 557 470217627 470217759 3.850000e-48 202
13 TraesCS1B01G372200 chr6B 88.279 1331 119 23 425 1719 189103946 189105275 0.000000e+00 1559
14 TraesCS1B01G372200 chr6B 84.738 439 35 16 425 831 577462922 577463360 5.880000e-111 411
15 TraesCS1B01G372200 chr6B 83.217 429 56 11 5 426 378999381 378998962 1.660000e-101 379
16 TraesCS1B01G372200 chr4D 90.468 1175 106 5 560 1729 102106356 102105183 0.000000e+00 1544
17 TraesCS1B01G372200 chr6D 90.136 1176 113 3 557 1730 450906512 450907686 0.000000e+00 1526
18 TraesCS1B01G372200 chr4B 90.094 1171 111 4 557 1723 551785268 551786437 0.000000e+00 1515
19 TraesCS1B01G372200 chr4B 86.283 452 30 15 2 426 382614649 382615095 1.600000e-126 462
20 TraesCS1B01G372200 chr4B 85.366 451 35 8 1 426 373031329 373030885 2.700000e-119 438
21 TraesCS1B01G372200 chr4B 86.461 421 26 14 2 396 382622963 382623378 1.260000e-117 433
22 TraesCS1B01G372200 chr4B 81.879 447 38 15 4 426 181262755 181262328 1.010000e-88 337
23 TraesCS1B01G372200 chr4B 81.797 434 45 15 22 427 48291402 48291829 1.310000e-87 333
24 TraesCS1B01G372200 chr4B 93.985 133 8 0 425 557 633911141 633911009 3.850000e-48 202
25 TraesCS1B01G372200 chr7B 90.163 1169 106 7 557 1723 150842667 150843828 0.000000e+00 1513
26 TraesCS1B01G372200 chr7B 85.714 455 30 15 2 426 233395278 233395727 4.480000e-122 448
27 TraesCS1B01G372200 chr7B 83.040 454 38 15 4 427 318444586 318445030 2.150000e-100 375
28 TraesCS1B01G372200 chr7B 88.991 218 20 4 210 426 293694129 293694343 1.350000e-67 267
29 TraesCS1B01G372200 chr7B 92.424 132 10 0 426 557 679358025 679358156 3.000000e-44 189
30 TraesCS1B01G372200 chr1A 86.458 576 45 12 1723 2288 535504031 535503479 3.250000e-168 601
31 TraesCS1B01G372200 chr1A 90.476 399 35 2 1723 2118 539736846 539736448 7.240000e-145 523
32 TraesCS1B01G372200 chr1A 79.188 197 23 7 2110 2288 539735831 539735635 1.110000e-23 121
33 TraesCS1B01G372200 chr3B 86.161 448 31 15 4 426 191071599 191071158 2.680000e-124 455
34 TraesCS1B01G372200 chr1D 92.337 261 19 1 1723 1982 443304971 443305231 9.980000e-99 370
35 TraesCS1B01G372200 chr1D 84.821 336 31 2 1973 2288 443368430 443368765 1.020000e-83 320
36 TraesCS1B01G372200 chr4A 92.481 133 10 0 425 557 418072588 418072456 8.340000e-45 191
37 TraesCS1B01G372200 chr4A 91.791 134 11 0 424 557 588659726 588659593 1.080000e-43 187
38 TraesCS1B01G372200 chr5A 92.481 133 9 1 425 557 604231675 604231544 3.000000e-44 189


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 TraesCS1B01G372200 chr1B 602896618 602898905 2287 False 4226.0 4226 100.000 1 2288 1 chr1B.!!$F1 2287
1 TraesCS1B01G372200 chr2B 46494007 46495173 1166 True 1628.0 1628 91.859 562 1726 1 chr2B.!!$R1 1164
2 TraesCS1B01G372200 chr2B 181980276 181981444 1168 True 1495.0 1495 89.820 560 1723 1 chr2B.!!$R2 1163
3 TraesCS1B01G372200 chr2B 479888263 479889598 1335 True 866.5 1537 91.826 425 1724 2 chr2B.!!$R6 1299
4 TraesCS1B01G372200 chr5B 641298883 641300047 1164 True 1568.0 1568 90.995 560 1723 1 chr5B.!!$R1 1163
5 TraesCS1B01G372200 chr6B 189103946 189105275 1329 False 1559.0 1559 88.279 425 1719 1 chr6B.!!$F1 1294
6 TraesCS1B01G372200 chr4D 102105183 102106356 1173 True 1544.0 1544 90.468 560 1729 1 chr4D.!!$R1 1169
7 TraesCS1B01G372200 chr6D 450906512 450907686 1174 False 1526.0 1526 90.136 557 1730 1 chr6D.!!$F1 1173
8 TraesCS1B01G372200 chr4B 551785268 551786437 1169 False 1515.0 1515 90.094 557 1723 1 chr4B.!!$F4 1166
9 TraesCS1B01G372200 chr7B 150842667 150843828 1161 False 1513.0 1513 90.163 557 1723 1 chr7B.!!$F1 1166
10 TraesCS1B01G372200 chr1A 535503479 535504031 552 True 601.0 601 86.458 1723 2288 1 chr1A.!!$R1 565
11 TraesCS1B01G372200 chr1A 539735635 539736846 1211 True 322.0 523 84.832 1723 2288 2 chr1A.!!$R2 565

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
820 862 0.032217 GCCCCTTCATCCAATTCCCA 60.032 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2814 0.110486 ACGGTGTGCAAATCCTTCCT 59.89 50.0 0.0 0.0 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
28 29 6.824958 ATGGCCTTCTTAATAACCTAGTGA 57.175 37.500 3.32 0.00 0.00 3.41
29 30 6.630203 TGGCCTTCTTAATAACCTAGTGAA 57.370 37.500 3.32 0.00 0.00 3.18
30 31 6.412214 TGGCCTTCTTAATAACCTAGTGAAC 58.588 40.000 3.32 0.00 0.00 3.18
31 32 6.013206 TGGCCTTCTTAATAACCTAGTGAACA 60.013 38.462 3.32 0.00 0.00 3.18
32 33 7.054751 GGCCTTCTTAATAACCTAGTGAACAT 58.945 38.462 0.00 0.00 0.00 2.71
33 34 7.556635 GGCCTTCTTAATAACCTAGTGAACATT 59.443 37.037 0.00 0.00 0.00 2.71
34 35 8.957466 GCCTTCTTAATAACCTAGTGAACATTT 58.043 33.333 0.00 0.00 0.00 2.32
41 42 7.703058 ATAACCTAGTGAACATTTTTCTGGG 57.297 36.000 0.00 0.00 33.90 4.45
42 43 3.826729 ACCTAGTGAACATTTTTCTGGGC 59.173 43.478 0.00 0.00 31.47 5.36
43 44 3.193479 CCTAGTGAACATTTTTCTGGGCC 59.807 47.826 0.00 0.00 0.00 5.80
44 45 2.962859 AGTGAACATTTTTCTGGGCCT 58.037 42.857 4.53 0.00 0.00 5.19
45 46 4.112634 AGTGAACATTTTTCTGGGCCTA 57.887 40.909 4.53 0.00 0.00 3.93
46 47 4.479158 AGTGAACATTTTTCTGGGCCTAA 58.521 39.130 4.53 0.00 0.00 2.69
47 48 4.898861 AGTGAACATTTTTCTGGGCCTAAA 59.101 37.500 4.53 2.50 0.00 1.85
48 49 5.543790 AGTGAACATTTTTCTGGGCCTAAAT 59.456 36.000 4.53 3.03 0.00 1.40
49 50 5.639082 GTGAACATTTTTCTGGGCCTAAATG 59.361 40.000 21.32 21.32 41.44 2.32
50 51 4.206477 ACATTTTTCTGGGCCTAAATGC 57.794 40.909 22.15 0.00 40.09 3.56
66 67 8.596271 GCCTAAATGCCTAAACTAAAAACAAA 57.404 30.769 0.00 0.00 0.00 2.83
67 68 8.492748 GCCTAAATGCCTAAACTAAAAACAAAC 58.507 33.333 0.00 0.00 0.00 2.93
68 69 9.758651 CCTAAATGCCTAAACTAAAAACAAACT 57.241 29.630 0.00 0.00 0.00 2.66
199 200 9.853177 TTTTGAAGAAGTCCTTTTATCTTCTCT 57.147 29.630 13.59 0.00 44.43 3.10
200 201 9.495572 TTTGAAGAAGTCCTTTTATCTTCTCTC 57.504 33.333 13.59 7.71 44.43 3.20
201 202 8.429237 TGAAGAAGTCCTTTTATCTTCTCTCT 57.571 34.615 13.59 0.00 44.43 3.10
202 203 8.875168 TGAAGAAGTCCTTTTATCTTCTCTCTT 58.125 33.333 13.59 0.00 44.43 2.85
203 204 9.719355 GAAGAAGTCCTTTTATCTTCTCTCTTT 57.281 33.333 7.04 0.00 44.43 2.52
249 250 9.968870 ACAAATTGATCCAATTTCCAAATTTTG 57.031 25.926 12.98 1.99 46.82 2.44
274 275 9.686683 TGAAAAATTAAAAATGGACTTTTGGGA 57.313 25.926 0.00 0.00 37.14 4.37
279 280 9.639563 AATTAAAAATGGACTTTTGGGAAATGT 57.360 25.926 0.00 0.00 37.14 2.71
280 281 8.669946 TTAAAAATGGACTTTTGGGAAATGTC 57.330 30.769 0.00 0.00 41.94 3.06
293 294 4.278975 GGAAATGTCCAACTCTCTCAGT 57.721 45.455 0.00 0.00 44.26 3.41
295 296 5.066593 GGAAATGTCCAACTCTCTCAGTTT 58.933 41.667 0.00 0.00 44.14 2.66
296 297 5.049129 GGAAATGTCCAACTCTCTCAGTTTG 60.049 44.000 0.00 0.00 44.14 2.93
297 298 3.475566 TGTCCAACTCTCTCAGTTTGG 57.524 47.619 0.00 0.00 43.38 3.28
298 299 2.771943 TGTCCAACTCTCTCAGTTTGGT 59.228 45.455 0.00 0.00 43.38 3.67
299 300 3.181465 TGTCCAACTCTCTCAGTTTGGTC 60.181 47.826 0.00 0.00 43.38 4.02
300 301 2.368875 TCCAACTCTCTCAGTTTGGTCC 59.631 50.000 0.00 0.00 43.38 4.46
301 302 2.370189 CCAACTCTCTCAGTTTGGTCCT 59.630 50.000 0.00 0.00 43.38 3.85
302 303 3.181450 CCAACTCTCTCAGTTTGGTCCTT 60.181 47.826 0.00 0.00 43.38 3.36
303 304 3.760580 ACTCTCTCAGTTTGGTCCTTG 57.239 47.619 0.00 0.00 26.56 3.61
304 305 3.309296 ACTCTCTCAGTTTGGTCCTTGA 58.691 45.455 0.00 0.00 26.56 3.02
305 306 3.323403 ACTCTCTCAGTTTGGTCCTTGAG 59.677 47.826 0.00 0.00 38.67 3.02
306 307 3.309296 TCTCTCAGTTTGGTCCTTGAGT 58.691 45.455 10.81 0.00 38.50 3.41
307 308 3.711704 TCTCTCAGTTTGGTCCTTGAGTT 59.288 43.478 10.81 0.00 38.50 3.01
308 309 3.808728 TCTCAGTTTGGTCCTTGAGTTG 58.191 45.455 10.81 0.00 38.50 3.16
309 310 2.291741 CTCAGTTTGGTCCTTGAGTTGC 59.708 50.000 0.00 0.00 33.95 4.17
310 311 2.092429 TCAGTTTGGTCCTTGAGTTGCT 60.092 45.455 0.00 0.00 0.00 3.91
311 312 2.689983 CAGTTTGGTCCTTGAGTTGCTT 59.310 45.455 0.00 0.00 0.00 3.91
312 313 3.882888 CAGTTTGGTCCTTGAGTTGCTTA 59.117 43.478 0.00 0.00 0.00 3.09
313 314 4.338118 CAGTTTGGTCCTTGAGTTGCTTAA 59.662 41.667 0.00 0.00 0.00 1.85
314 315 4.580580 AGTTTGGTCCTTGAGTTGCTTAAG 59.419 41.667 0.00 0.00 0.00 1.85
315 316 3.140325 TGGTCCTTGAGTTGCTTAAGG 57.860 47.619 11.93 11.93 45.11 2.69
316 317 2.441750 TGGTCCTTGAGTTGCTTAAGGT 59.558 45.455 16.02 0.00 44.40 3.50
317 318 3.117663 TGGTCCTTGAGTTGCTTAAGGTT 60.118 43.478 16.02 0.00 44.40 3.50
318 319 3.889538 GGTCCTTGAGTTGCTTAAGGTTT 59.110 43.478 16.02 0.00 44.40 3.27
319 320 4.023107 GGTCCTTGAGTTGCTTAAGGTTTC 60.023 45.833 16.02 9.84 44.40 2.78
320 321 4.822350 GTCCTTGAGTTGCTTAAGGTTTCT 59.178 41.667 16.02 0.00 44.40 2.52
321 322 5.995897 GTCCTTGAGTTGCTTAAGGTTTCTA 59.004 40.000 16.02 0.00 44.40 2.10
322 323 6.147985 GTCCTTGAGTTGCTTAAGGTTTCTAG 59.852 42.308 16.02 0.00 44.40 2.43
323 324 5.412904 CCTTGAGTTGCTTAAGGTTTCTAGG 59.587 44.000 4.29 0.00 40.80 3.02
324 325 5.818678 TGAGTTGCTTAAGGTTTCTAGGA 57.181 39.130 4.29 0.00 0.00 2.94
325 326 6.374417 TGAGTTGCTTAAGGTTTCTAGGAT 57.626 37.500 4.29 0.00 0.00 3.24
326 327 6.407202 TGAGTTGCTTAAGGTTTCTAGGATC 58.593 40.000 4.29 0.00 0.00 3.36
327 328 6.013725 TGAGTTGCTTAAGGTTTCTAGGATCA 60.014 38.462 4.29 0.00 0.00 2.92
328 329 6.779860 AGTTGCTTAAGGTTTCTAGGATCAA 58.220 36.000 4.29 0.00 0.00 2.57
329 330 7.231467 AGTTGCTTAAGGTTTCTAGGATCAAA 58.769 34.615 4.29 0.00 0.00 2.69
330 331 7.724061 AGTTGCTTAAGGTTTCTAGGATCAAAA 59.276 33.333 4.29 0.00 0.00 2.44
331 332 8.523658 GTTGCTTAAGGTTTCTAGGATCAAAAT 58.476 33.333 4.29 0.00 0.00 1.82
332 333 8.650143 TGCTTAAGGTTTCTAGGATCAAAATT 57.350 30.769 4.29 0.00 0.00 1.82
333 334 8.739972 TGCTTAAGGTTTCTAGGATCAAAATTC 58.260 33.333 4.29 0.00 0.00 2.17
334 335 8.739972 GCTTAAGGTTTCTAGGATCAAAATTCA 58.260 33.333 4.29 0.00 0.00 2.57
337 338 8.712228 AAGGTTTCTAGGATCAAAATTCAACT 57.288 30.769 0.00 0.00 0.00 3.16
338 339 9.807921 AAGGTTTCTAGGATCAAAATTCAACTA 57.192 29.630 0.00 0.00 0.00 2.24
339 340 9.807921 AGGTTTCTAGGATCAAAATTCAACTAA 57.192 29.630 0.00 0.00 0.00 2.24
357 358 9.868277 TTCAACTAAAAGAAATGAGAGCAAAAA 57.132 25.926 0.00 0.00 0.00 1.94
360 361 8.302965 ACTAAAAGAAATGAGAGCAAAAATGC 57.697 30.769 0.00 0.00 0.00 3.56
361 362 7.927629 ACTAAAAGAAATGAGAGCAAAAATGCA 59.072 29.630 3.41 0.00 37.25 3.96
362 363 7.739498 AAAAGAAATGAGAGCAAAAATGCAT 57.261 28.000 0.00 0.00 37.25 3.96
363 364 8.836268 AAAAGAAATGAGAGCAAAAATGCATA 57.164 26.923 0.00 0.00 37.25 3.14
364 365 8.836268 AAAGAAATGAGAGCAAAAATGCATAA 57.164 26.923 0.00 0.00 37.25 1.90
365 366 8.836268 AAGAAATGAGAGCAAAAATGCATAAA 57.164 26.923 0.00 0.00 37.25 1.40
366 367 9.444600 AAGAAATGAGAGCAAAAATGCATAAAT 57.555 25.926 0.00 0.00 37.25 1.40
367 368 9.095065 AGAAATGAGAGCAAAAATGCATAAATC 57.905 29.630 0.00 0.00 37.25 2.17
368 369 8.780846 AAATGAGAGCAAAAATGCATAAATCA 57.219 26.923 0.00 0.00 37.25 2.57
369 370 8.958119 AATGAGAGCAAAAATGCATAAATCAT 57.042 26.923 0.00 0.00 37.25 2.45
370 371 7.764695 TGAGAGCAAAAATGCATAAATCATG 57.235 32.000 0.00 0.00 37.73 3.07
371 372 6.759356 TGAGAGCAAAAATGCATAAATCATGG 59.241 34.615 0.00 0.00 34.97 3.66
372 373 6.880484 AGAGCAAAAATGCATAAATCATGGA 58.120 32.000 0.00 0.00 39.56 3.41
373 374 7.506114 AGAGCAAAAATGCATAAATCATGGAT 58.494 30.769 0.00 0.00 46.71 3.41
374 375 8.644216 AGAGCAAAAATGCATAAATCATGGATA 58.356 29.630 0.00 0.00 44.23 2.59
375 376 8.597662 AGCAAAAATGCATAAATCATGGATAC 57.402 30.769 0.00 0.00 44.23 2.24
376 377 8.205512 AGCAAAAATGCATAAATCATGGATACA 58.794 29.630 0.00 0.00 44.23 2.29
377 378 8.995220 GCAAAAATGCATAAATCATGGATACAT 58.005 29.630 0.00 0.00 44.23 2.29
417 418 8.726870 AATAGCATCCAAATTGAAAAATCAGG 57.273 30.769 0.00 0.00 0.00 3.86
418 419 6.363167 AGCATCCAAATTGAAAAATCAGGA 57.637 33.333 0.00 0.00 0.00 3.86
419 420 6.954232 AGCATCCAAATTGAAAAATCAGGAT 58.046 32.000 0.00 0.00 35.13 3.24
422 423 8.556213 CATCCAAATTGAAAAATCAGGATGTT 57.444 30.769 16.37 0.00 43.78 2.71
423 424 9.656040 CATCCAAATTGAAAAATCAGGATGTTA 57.344 29.630 16.37 0.00 43.78 2.41
457 458 5.764192 AGATTCTTTCTGCATCTTAGCCATC 59.236 40.000 0.00 0.00 31.79 3.51
499 500 5.629079 CCTCCATGGTGTTCTAAAACTTC 57.371 43.478 12.58 0.00 36.30 3.01
553 555 1.363530 CCCTCCAGCCAATACCCCAT 61.364 60.000 0.00 0.00 0.00 4.00
603 642 0.336737 GAGAGAAGAGAGGGGTGGGA 59.663 60.000 0.00 0.00 0.00 4.37
617 656 1.076513 GGTGGGAAAATAGTGGTGGGT 59.923 52.381 0.00 0.00 0.00 4.51
623 662 4.079385 GGGAAAATAGTGGTGGGTAGGATT 60.079 45.833 0.00 0.00 0.00 3.01
625 664 6.183361 GGGAAAATAGTGGTGGGTAGGATTAT 60.183 42.308 0.00 0.00 0.00 1.28
707 748 6.051717 GCTCTTCAATAAGCCATGAACTCTA 58.948 40.000 0.00 0.00 32.46 2.43
740 781 2.816087 ACTCCATGAATTGTGTGCAGAC 59.184 45.455 7.12 7.12 0.00 3.51
786 827 2.045926 GTGCTCCCGGCTGTTGAT 60.046 61.111 0.00 0.00 42.39 2.57
799 841 2.094545 GCTGTTGATAACAAGGGCAAGG 60.095 50.000 5.41 0.00 41.61 3.61
820 862 0.032217 GCCCCTTCATCCAATTCCCA 60.032 55.000 0.00 0.00 0.00 4.37
837 879 1.529010 CAAGGAGGTTGTGCTGCCA 60.529 57.895 0.00 0.00 0.00 4.92
856 899 4.052229 CCACCGCCGACGAAGACT 62.052 66.667 0.00 0.00 43.93 3.24
874 917 2.818432 GACTCGAAGACACCTGAGGTTA 59.182 50.000 0.00 0.00 31.02 2.85
897 940 1.005275 CGATGAGCGCATGGAGGAT 60.005 57.895 11.47 0.00 34.11 3.24
917 962 2.835431 CCCCAACAACAACCGCCA 60.835 61.111 0.00 0.00 0.00 5.69
940 985 1.358103 ACTACAGCCACTACCAGGAGA 59.642 52.381 0.00 0.00 0.00 3.71
948 993 2.626950 CCACTACCAGGAGAAGGATGGA 60.627 54.545 0.00 0.00 37.54 3.41
1027 1072 3.209410 CTGAACTTCACCAAGCACTTCT 58.791 45.455 0.00 0.00 32.09 2.85
1056 1101 4.683432 ACGGAGTTCAAGCTCAGC 57.317 55.556 0.00 0.00 37.78 4.26
1074 1120 1.580845 GCAACAACATCGGCTGCTCT 61.581 55.000 0.00 0.00 0.00 4.09
1101 1147 2.615493 GGTGACGGTGAAGGTGATGAAT 60.615 50.000 0.00 0.00 0.00 2.57
1110 1156 1.595311 AGGTGATGAATGGCAGGGTA 58.405 50.000 0.00 0.00 0.00 3.69
1134 1180 2.763215 GATCAGGGTTGGGCCACA 59.237 61.111 5.23 0.00 39.65 4.17
1161 1207 3.875727 CAGCCGTTCATCAGATCAAGATT 59.124 43.478 0.00 0.00 0.00 2.40
1222 1268 3.118992 CCTCAAGGTCATCATCTTCGACA 60.119 47.826 0.00 0.00 0.00 4.35
1252 1299 0.464036 TGAGGTCGTCAACAAGTGCT 59.536 50.000 0.00 0.00 29.64 4.40
1384 1432 5.187772 TGAAGTGTGGTACTGCTTATCTGAT 59.812 40.000 0.00 0.00 40.26 2.90
1465 1514 0.820871 TGGTTGTGCCAAAGTGTTCC 59.179 50.000 0.00 0.00 45.94 3.62
1468 1517 1.388065 TTGTGCCAAAGTGTTCCGGG 61.388 55.000 0.00 0.00 0.00 5.73
1504 1553 2.748465 GCCAAAGAGGTTACCACACACT 60.748 50.000 3.51 0.00 40.61 3.55
1557 1606 2.625790 GGGTTTGTCCACTAACATGCAA 59.374 45.455 0.00 0.00 38.11 4.08
1576 1625 0.975040 AGCAACCAAACACCAGGCAA 60.975 50.000 0.00 0.00 0.00 4.52
1581 1630 1.039068 CCAAACACCAGGCAATGTGA 58.961 50.000 7.86 0.00 36.35 3.58
1597 1646 1.352017 TGTGATTCAGTCCATGCAGGT 59.648 47.619 0.00 0.00 39.02 4.00
1719 1768 2.709170 CCTACGGCAACCAAACACA 58.291 52.632 0.00 0.00 0.00 3.72
1798 1847 1.184431 TAGGTTGTCCAATCCGCGTA 58.816 50.000 4.92 0.00 35.89 4.42
1839 1888 1.227586 CGAGCATGATCCTGCAGCT 60.228 57.895 22.67 9.50 44.77 4.24
1840 1889 0.814410 CGAGCATGATCCTGCAGCTT 60.814 55.000 22.67 4.14 44.77 3.74
1844 1893 2.172082 AGCATGATCCTGCAGCTTAGAA 59.828 45.455 22.67 0.00 44.77 2.10
1846 1895 3.806380 CATGATCCTGCAGCTTAGAACT 58.194 45.455 8.66 0.00 0.00 3.01
1848 1897 5.363101 CATGATCCTGCAGCTTAGAACTTA 58.637 41.667 8.66 0.00 0.00 2.24
1857 1906 4.624125 GCAGCTTAGAACTTATGGGAGTGT 60.624 45.833 0.00 0.00 0.00 3.55
1862 1918 2.092323 GAACTTATGGGAGTGTTGGGC 58.908 52.381 0.00 0.00 0.00 5.36
1893 1949 2.094417 GTGTAGATTGTTCGCTTGGCTC 59.906 50.000 0.00 0.00 0.00 4.70
1911 1967 2.802816 GCTCGCATATAAGAACAGGTGG 59.197 50.000 0.00 0.00 0.00 4.61
1970 2026 3.423154 GGACGAGTGCCCGCTTTG 61.423 66.667 0.00 0.00 0.00 2.77
2008 2064 3.261580 CAATCGATCACTTGCTGGTGTA 58.738 45.455 0.00 0.00 38.28 2.90
2011 2067 3.086282 TCGATCACTTGCTGGTGTACTA 58.914 45.455 8.87 0.00 38.28 1.82
2023 2079 0.179205 GTGTACTACGTCTTCGCGCT 60.179 55.000 5.56 0.00 41.18 5.92
2031 2087 2.095252 GTCTTCGCGCTCTTGGTCC 61.095 63.158 5.56 0.00 0.00 4.46
2032 2088 2.048222 CTTCGCGCTCTTGGTCCA 60.048 61.111 5.56 0.00 0.00 4.02
2047 2105 1.202675 GGTCCAACCCTGTGTTCGTTA 60.203 52.381 0.00 0.00 34.00 3.18
2070 2128 0.861155 GGGGAGGAGAGGAGTGGATA 59.139 60.000 0.00 0.00 0.00 2.59
2104 2162 2.436417 GAAGATTACTGCCTTGGTGCA 58.564 47.619 0.00 0.00 39.37 4.57
2121 2804 0.665369 GCACTTCATTGCAGCCACAC 60.665 55.000 0.00 0.00 42.49 3.82
2122 2805 0.956633 CACTTCATTGCAGCCACACT 59.043 50.000 0.00 0.00 0.00 3.55
2124 2807 1.241165 CTTCATTGCAGCCACACTCA 58.759 50.000 0.00 0.00 0.00 3.41
2160 2843 2.333938 CACACCGTCGTCGTCCTT 59.666 61.111 0.71 0.00 35.01 3.36
2202 2885 6.017687 GGAAACACCGTAACACAATAGTCTTT 60.018 38.462 0.00 0.00 0.00 2.52
2208 2891 6.708949 ACCGTAACACAATAGTCTTTGTCAAT 59.291 34.615 0.00 0.00 37.73 2.57
2240 2941 1.272816 TGGGATCTACGACAAGGGACA 60.273 52.381 0.00 0.00 0.00 4.02
2244 2945 1.542492 TCTACGACAAGGGACAGACC 58.458 55.000 0.00 0.00 38.08 3.85
2251 2952 0.607489 CAAGGGACAGACCTGGCAAG 60.607 60.000 5.12 0.00 41.42 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.945193 TCACTAGGTTATTAAGAAGGCCATATT 58.055 33.333 5.01 0.00 0.00 1.28
4 5 7.924358 TCACTAGGTTATTAAGAAGGCCATA 57.076 36.000 5.01 0.00 0.00 2.74
5 6 6.824958 TCACTAGGTTATTAAGAAGGCCAT 57.175 37.500 5.01 0.00 0.00 4.40
6 7 6.013206 TGTTCACTAGGTTATTAAGAAGGCCA 60.013 38.462 5.01 0.00 0.00 5.36
7 8 6.412214 TGTTCACTAGGTTATTAAGAAGGCC 58.588 40.000 0.00 0.00 0.00 5.19
8 9 8.507524 AATGTTCACTAGGTTATTAAGAAGGC 57.492 34.615 0.00 0.00 0.00 4.35
15 16 9.238368 CCCAGAAAAATGTTCACTAGGTTATTA 57.762 33.333 0.00 0.00 0.00 0.98
16 17 7.309805 GCCCAGAAAAATGTTCACTAGGTTATT 60.310 37.037 0.00 0.00 0.00 1.40
17 18 6.152831 GCCCAGAAAAATGTTCACTAGGTTAT 59.847 38.462 0.00 0.00 0.00 1.89
18 19 5.475564 GCCCAGAAAAATGTTCACTAGGTTA 59.524 40.000 0.00 0.00 0.00 2.85
19 20 4.280929 GCCCAGAAAAATGTTCACTAGGTT 59.719 41.667 0.00 0.00 0.00 3.50
20 21 3.826729 GCCCAGAAAAATGTTCACTAGGT 59.173 43.478 0.00 0.00 0.00 3.08
21 22 3.193479 GGCCCAGAAAAATGTTCACTAGG 59.807 47.826 0.00 0.00 0.00 3.02
22 23 4.082125 AGGCCCAGAAAAATGTTCACTAG 58.918 43.478 0.00 0.00 0.00 2.57
23 24 4.112634 AGGCCCAGAAAAATGTTCACTA 57.887 40.909 0.00 0.00 0.00 2.74
24 25 2.962859 AGGCCCAGAAAAATGTTCACT 58.037 42.857 0.00 0.00 0.00 3.41
25 26 4.864704 TTAGGCCCAGAAAAATGTTCAC 57.135 40.909 0.00 0.00 0.00 3.18
26 27 5.792741 CATTTAGGCCCAGAAAAATGTTCA 58.207 37.500 0.00 0.00 35.55 3.18
27 28 4.631377 GCATTTAGGCCCAGAAAAATGTTC 59.369 41.667 18.49 6.83 40.05 3.18
28 29 4.578871 GCATTTAGGCCCAGAAAAATGTT 58.421 39.130 18.49 0.00 40.05 2.71
29 30 4.206477 GCATTTAGGCCCAGAAAAATGT 57.794 40.909 18.49 0.00 40.05 2.71
41 42 8.492748 GTTTGTTTTTAGTTTAGGCATTTAGGC 58.507 33.333 0.00 0.00 44.61 3.93
42 43 9.758651 AGTTTGTTTTTAGTTTAGGCATTTAGG 57.241 29.630 0.00 0.00 0.00 2.69
173 174 9.853177 AGAGAAGATAAAAGGACTTCTTCAAAA 57.147 29.630 12.50 0.00 46.49 2.44
174 175 9.495572 GAGAGAAGATAAAAGGACTTCTTCAAA 57.504 33.333 12.50 0.00 46.49 2.69
175 176 8.875168 AGAGAGAAGATAAAAGGACTTCTTCAA 58.125 33.333 12.50 0.00 46.49 2.69
176 177 8.429237 AGAGAGAAGATAAAAGGACTTCTTCA 57.571 34.615 12.50 0.00 46.49 3.02
177 178 9.719355 AAAGAGAGAAGATAAAAGGACTTCTTC 57.281 33.333 0.00 3.87 46.49 2.87
248 249 9.686683 TCCCAAAAGTCCATTTTTAATTTTTCA 57.313 25.926 0.00 0.00 39.11 2.69
253 254 9.639563 ACATTTCCCAAAAGTCCATTTTTAATT 57.360 25.926 0.00 0.00 39.11 1.40
254 255 9.283768 GACATTTCCCAAAAGTCCATTTTTAAT 57.716 29.630 0.00 0.00 39.11 1.40
255 256 7.717436 GGACATTTCCCAAAAGTCCATTTTTAA 59.283 33.333 15.31 0.00 39.69 1.52
256 257 7.147479 TGGACATTTCCCAAAAGTCCATTTTTA 60.147 33.333 17.85 0.23 41.95 1.52
257 258 6.061441 GGACATTTCCCAAAAGTCCATTTTT 58.939 36.000 15.31 0.00 39.69 1.94
258 259 5.131809 TGGACATTTCCCAAAAGTCCATTTT 59.868 36.000 17.85 0.00 41.95 1.82
259 260 4.657969 TGGACATTTCCCAAAAGTCCATTT 59.342 37.500 17.85 0.00 41.95 2.32
260 261 4.230455 TGGACATTTCCCAAAAGTCCATT 58.770 39.130 17.85 0.00 41.95 3.16
261 262 3.855668 TGGACATTTCCCAAAAGTCCAT 58.144 40.909 17.85 0.00 41.95 3.41
262 263 3.320610 TGGACATTTCCCAAAAGTCCA 57.679 42.857 17.85 17.85 43.11 4.02
263 264 3.641436 AGTTGGACATTTCCCAAAAGTCC 59.359 43.478 13.92 13.92 44.41 3.85
264 265 4.584743 AGAGTTGGACATTTCCCAAAAGTC 59.415 41.667 0.00 0.00 44.41 3.01
265 266 4.546674 AGAGTTGGACATTTCCCAAAAGT 58.453 39.130 0.00 0.00 44.41 2.66
266 267 4.829492 AGAGAGTTGGACATTTCCCAAAAG 59.171 41.667 0.00 0.00 44.41 2.27
267 268 4.803452 AGAGAGTTGGACATTTCCCAAAA 58.197 39.130 0.00 0.00 44.41 2.44
268 269 4.141274 TGAGAGAGTTGGACATTTCCCAAA 60.141 41.667 0.00 0.00 44.41 3.28
269 270 3.394274 TGAGAGAGTTGGACATTTCCCAA 59.606 43.478 0.00 0.00 42.01 4.12
270 271 2.978978 TGAGAGAGTTGGACATTTCCCA 59.021 45.455 0.00 0.00 42.01 4.37
271 272 3.008485 ACTGAGAGAGTTGGACATTTCCC 59.992 47.826 0.00 0.00 42.01 3.97
272 273 4.278975 ACTGAGAGAGTTGGACATTTCC 57.721 45.455 0.00 0.00 43.19 3.13
273 274 5.049129 CCAAACTGAGAGAGTTGGACATTTC 60.049 44.000 0.00 0.00 44.68 2.17
274 275 4.823989 CCAAACTGAGAGAGTTGGACATTT 59.176 41.667 0.00 0.00 44.68 2.32
275 276 4.141390 ACCAAACTGAGAGAGTTGGACATT 60.141 41.667 8.22 0.00 44.68 2.71
276 277 3.392616 ACCAAACTGAGAGAGTTGGACAT 59.607 43.478 8.22 0.00 44.68 3.06
277 278 2.771943 ACCAAACTGAGAGAGTTGGACA 59.228 45.455 8.22 0.00 44.68 4.02
278 279 3.394719 GACCAAACTGAGAGAGTTGGAC 58.605 50.000 8.22 0.00 44.68 4.02
279 280 2.368875 GGACCAAACTGAGAGAGTTGGA 59.631 50.000 8.22 0.00 44.68 3.53
280 281 2.370189 AGGACCAAACTGAGAGAGTTGG 59.630 50.000 0.00 0.00 44.68 3.77
281 282 3.760580 AGGACCAAACTGAGAGAGTTG 57.239 47.619 0.00 0.00 44.68 3.16
283 284 3.309296 TCAAGGACCAAACTGAGAGAGT 58.691 45.455 0.00 0.00 35.94 3.24
284 285 3.323403 ACTCAAGGACCAAACTGAGAGAG 59.677 47.826 15.75 0.00 0.00 3.20
285 286 3.309296 ACTCAAGGACCAAACTGAGAGA 58.691 45.455 15.75 0.00 0.00 3.10
286 287 3.760580 ACTCAAGGACCAAACTGAGAG 57.239 47.619 15.75 0.00 0.00 3.20
287 288 3.808728 CAACTCAAGGACCAAACTGAGA 58.191 45.455 15.75 0.00 0.00 3.27
288 289 2.291741 GCAACTCAAGGACCAAACTGAG 59.708 50.000 9.95 9.95 0.00 3.35
289 290 2.092429 AGCAACTCAAGGACCAAACTGA 60.092 45.455 0.00 0.00 0.00 3.41
290 291 2.301346 AGCAACTCAAGGACCAAACTG 58.699 47.619 0.00 0.00 0.00 3.16
291 292 2.736670 AGCAACTCAAGGACCAAACT 57.263 45.000 0.00 0.00 0.00 2.66
292 293 4.261614 CCTTAAGCAACTCAAGGACCAAAC 60.262 45.833 0.00 0.00 41.18 2.93
293 294 3.888930 CCTTAAGCAACTCAAGGACCAAA 59.111 43.478 0.00 0.00 41.18 3.28
294 295 3.117663 ACCTTAAGCAACTCAAGGACCAA 60.118 43.478 3.47 0.00 41.18 3.67
295 296 2.441750 ACCTTAAGCAACTCAAGGACCA 59.558 45.455 3.47 0.00 41.18 4.02
296 297 3.141767 ACCTTAAGCAACTCAAGGACC 57.858 47.619 3.47 0.00 41.18 4.46
297 298 4.822350 AGAAACCTTAAGCAACTCAAGGAC 59.178 41.667 3.47 0.00 41.18 3.85
298 299 5.048846 AGAAACCTTAAGCAACTCAAGGA 57.951 39.130 3.47 0.00 41.18 3.36
299 300 5.412904 CCTAGAAACCTTAAGCAACTCAAGG 59.587 44.000 0.00 0.00 43.73 3.61
300 301 6.231211 TCCTAGAAACCTTAAGCAACTCAAG 58.769 40.000 0.00 0.00 0.00 3.02
301 302 6.182507 TCCTAGAAACCTTAAGCAACTCAA 57.817 37.500 0.00 0.00 0.00 3.02
302 303 5.818678 TCCTAGAAACCTTAAGCAACTCA 57.181 39.130 0.00 0.00 0.00 3.41
303 304 6.407202 TGATCCTAGAAACCTTAAGCAACTC 58.593 40.000 0.00 0.00 0.00 3.01
304 305 6.374417 TGATCCTAGAAACCTTAAGCAACT 57.626 37.500 0.00 0.00 0.00 3.16
305 306 7.448748 TTTGATCCTAGAAACCTTAAGCAAC 57.551 36.000 0.00 0.00 0.00 4.17
306 307 8.650143 ATTTTGATCCTAGAAACCTTAAGCAA 57.350 30.769 0.00 0.00 0.00 3.91
307 308 8.650143 AATTTTGATCCTAGAAACCTTAAGCA 57.350 30.769 0.00 0.00 0.00 3.91
308 309 8.739972 TGAATTTTGATCCTAGAAACCTTAAGC 58.260 33.333 0.00 0.00 0.00 3.09
311 312 9.807921 AGTTGAATTTTGATCCTAGAAACCTTA 57.192 29.630 0.00 0.00 0.00 2.69
312 313 8.712228 AGTTGAATTTTGATCCTAGAAACCTT 57.288 30.769 0.00 0.00 0.00 3.50
313 314 9.807921 TTAGTTGAATTTTGATCCTAGAAACCT 57.192 29.630 0.00 0.00 0.00 3.50
331 332 9.868277 TTTTTGCTCTCATTTCTTTTAGTTGAA 57.132 25.926 0.00 0.00 0.00 2.69
334 335 8.768019 GCATTTTTGCTCTCATTTCTTTTAGTT 58.232 29.630 0.00 0.00 0.00 2.24
335 336 7.927629 TGCATTTTTGCTCTCATTTCTTTTAGT 59.072 29.630 0.00 0.00 35.49 2.24
336 337 8.301730 TGCATTTTTGCTCTCATTTCTTTTAG 57.698 30.769 0.00 0.00 35.49 1.85
337 338 8.836268 ATGCATTTTTGCTCTCATTTCTTTTA 57.164 26.923 0.00 0.00 35.49 1.52
338 339 7.739498 ATGCATTTTTGCTCTCATTTCTTTT 57.261 28.000 0.00 0.00 35.49 2.27
339 340 8.836268 TTATGCATTTTTGCTCTCATTTCTTT 57.164 26.923 3.54 0.00 35.49 2.52
340 341 8.836268 TTTATGCATTTTTGCTCTCATTTCTT 57.164 26.923 3.54 0.00 35.49 2.52
341 342 9.095065 GATTTATGCATTTTTGCTCTCATTTCT 57.905 29.630 3.54 0.00 35.49 2.52
342 343 8.875803 TGATTTATGCATTTTTGCTCTCATTTC 58.124 29.630 3.54 0.00 35.49 2.17
343 344 8.780846 TGATTTATGCATTTTTGCTCTCATTT 57.219 26.923 3.54 0.00 35.49 2.32
344 345 8.826710 CATGATTTATGCATTTTTGCTCTCATT 58.173 29.630 3.54 0.00 35.49 2.57
345 346 7.441157 CCATGATTTATGCATTTTTGCTCTCAT 59.559 33.333 3.54 0.45 35.37 2.90
346 347 6.759356 CCATGATTTATGCATTTTTGCTCTCA 59.241 34.615 3.54 0.00 35.37 3.27
347 348 6.982141 TCCATGATTTATGCATTTTTGCTCTC 59.018 34.615 3.54 0.00 35.37 3.20
348 349 6.880484 TCCATGATTTATGCATTTTTGCTCT 58.120 32.000 3.54 0.00 35.37 4.09
349 350 7.724305 ATCCATGATTTATGCATTTTTGCTC 57.276 32.000 3.54 0.00 35.37 4.26
350 351 8.205512 TGTATCCATGATTTATGCATTTTTGCT 58.794 29.630 3.54 0.00 35.37 3.91
351 352 8.367943 TGTATCCATGATTTATGCATTTTTGC 57.632 30.769 3.54 0.00 35.37 3.68
391 392 9.169592 CCTGATTTTTCAATTTGGATGCTATTT 57.830 29.630 0.00 0.00 0.00 1.40
392 393 8.542080 TCCTGATTTTTCAATTTGGATGCTATT 58.458 29.630 0.00 0.00 0.00 1.73
393 394 8.081517 TCCTGATTTTTCAATTTGGATGCTAT 57.918 30.769 0.00 0.00 0.00 2.97
394 395 7.479352 TCCTGATTTTTCAATTTGGATGCTA 57.521 32.000 0.00 0.00 0.00 3.49
395 396 6.363167 TCCTGATTTTTCAATTTGGATGCT 57.637 33.333 0.00 0.00 0.00 3.79
396 397 6.596497 ACATCCTGATTTTTCAATTTGGATGC 59.404 34.615 19.30 0.00 45.23 3.91
397 398 8.556213 AACATCCTGATTTTTCAATTTGGATG 57.444 30.769 18.51 18.51 45.87 3.51
398 399 9.657419 GTAACATCCTGATTTTTCAATTTGGAT 57.343 29.630 0.00 0.00 36.23 3.41
399 400 8.646004 TGTAACATCCTGATTTTTCAATTTGGA 58.354 29.630 0.00 0.00 32.23 3.53
400 401 8.711457 GTGTAACATCCTGATTTTTCAATTTGG 58.289 33.333 0.00 0.00 36.32 3.28
401 402 9.480053 AGTGTAACATCCTGATTTTTCAATTTG 57.520 29.630 0.00 0.00 41.43 2.32
402 403 9.480053 CAGTGTAACATCCTGATTTTTCAATTT 57.520 29.630 0.00 0.00 41.43 1.82
403 404 7.599998 GCAGTGTAACATCCTGATTTTTCAATT 59.400 33.333 0.00 0.00 41.43 2.32
404 405 7.092716 GCAGTGTAACATCCTGATTTTTCAAT 58.907 34.615 0.00 0.00 41.43 2.57
405 406 6.040278 TGCAGTGTAACATCCTGATTTTTCAA 59.960 34.615 0.00 0.00 41.43 2.69
406 407 5.534278 TGCAGTGTAACATCCTGATTTTTCA 59.466 36.000 0.00 0.00 41.43 2.69
407 408 6.012658 TGCAGTGTAACATCCTGATTTTTC 57.987 37.500 0.00 0.00 41.43 2.29
408 409 6.209192 TGATGCAGTGTAACATCCTGATTTTT 59.791 34.615 0.00 0.00 41.63 1.94
409 410 5.711506 TGATGCAGTGTAACATCCTGATTTT 59.288 36.000 0.00 0.00 41.63 1.82
410 411 5.255687 TGATGCAGTGTAACATCCTGATTT 58.744 37.500 0.00 0.00 41.63 2.17
411 412 4.847198 TGATGCAGTGTAACATCCTGATT 58.153 39.130 0.00 0.00 41.63 2.57
412 413 4.162888 TCTGATGCAGTGTAACATCCTGAT 59.837 41.667 0.00 0.00 41.63 2.90
413 414 3.515104 TCTGATGCAGTGTAACATCCTGA 59.485 43.478 0.00 3.63 41.63 3.86
414 415 3.865446 TCTGATGCAGTGTAACATCCTG 58.135 45.455 0.00 0.00 41.63 3.86
415 416 4.767578 ATCTGATGCAGTGTAACATCCT 57.232 40.909 0.00 0.00 41.63 3.24
416 417 5.121811 AGAATCTGATGCAGTGTAACATCC 58.878 41.667 0.00 0.00 41.63 3.51
417 418 6.674694 AAGAATCTGATGCAGTGTAACATC 57.325 37.500 0.00 3.10 41.43 3.06
418 419 6.883217 AGAAAGAATCTGATGCAGTGTAACAT 59.117 34.615 0.00 0.00 36.55 2.71
419 420 6.233434 AGAAAGAATCTGATGCAGTGTAACA 58.767 36.000 0.00 0.00 36.55 2.41
420 421 6.734104 AGAAAGAATCTGATGCAGTGTAAC 57.266 37.500 0.00 0.00 36.88 2.50
450 451 0.102481 GAACTTCGGCTCGATGGCTA 59.898 55.000 12.62 0.00 39.32 3.93
457 458 2.126463 TGCTCGAACTTCGGCTCG 60.126 61.111 19.00 0.03 40.88 5.03
492 493 0.745128 TGGTGACCGCACGAAGTTTT 60.745 50.000 0.00 0.00 46.09 2.43
493 494 1.153329 TGGTGACCGCACGAAGTTT 60.153 52.632 0.00 0.00 46.09 2.66
517 519 2.593956 GGCCTTCTTCCTCGGGTGT 61.594 63.158 0.00 0.00 0.00 4.16
553 555 1.003442 CCTCCTCTCCATCACCCCA 59.997 63.158 0.00 0.00 0.00 4.96
617 656 7.870954 CCATCGCGCCTATATTTAATAATCCTA 59.129 37.037 0.00 0.00 0.00 2.94
623 662 6.459670 TCTCCATCGCGCCTATATTTAATA 57.540 37.500 0.00 0.00 0.00 0.98
625 664 4.381612 CCTCTCCATCGCGCCTATATTTAA 60.382 45.833 0.00 0.00 0.00 1.52
707 748 3.144657 TCATGGAGTCAAGCACAACAT 57.855 42.857 0.00 0.00 0.00 2.71
740 781 1.270199 CCATCTCATTGCTCTCCTCGG 60.270 57.143 0.00 0.00 0.00 4.63
799 841 1.697284 GGAATTGGATGAAGGGGCTC 58.303 55.000 0.00 0.00 0.00 4.70
820 862 1.529244 GTGGCAGCACAACCTCCTT 60.529 57.895 0.00 0.00 0.00 3.36
856 899 1.544691 GCTAACCTCAGGTGTCTTCGA 59.455 52.381 0.00 0.00 35.34 3.71
912 957 2.031919 TGGCTGTAGTTGTGGCGG 59.968 61.111 0.00 0.00 0.00 6.13
917 962 1.623811 CCTGGTAGTGGCTGTAGTTGT 59.376 52.381 0.00 0.00 0.00 3.32
940 985 2.982488 AGAAGTGAGTTGGTCCATCCTT 59.018 45.455 0.00 0.00 37.07 3.36
948 993 1.212935 ACCTTGCAGAAGTGAGTTGGT 59.787 47.619 0.00 0.00 0.00 3.67
976 1021 1.881973 GATGCACTCAAGCTTTGGTGA 59.118 47.619 24.28 8.80 35.32 4.02
1009 1054 3.620488 TGAAGAAGTGCTTGGTGAAGTT 58.380 40.909 0.00 0.00 36.83 2.66
1027 1072 2.107041 AACTCCGTCGGCACCATGAA 62.107 55.000 6.34 0.00 0.00 2.57
1056 1101 0.877071 AAGAGCAGCCGATGTTGTTG 59.123 50.000 0.00 0.00 0.00 3.33
1074 1120 0.107831 CCTTCACCGTCACCTTCCAA 59.892 55.000 0.00 0.00 0.00 3.53
1101 1147 1.906105 GATCCACGGTTACCCTGCCA 61.906 60.000 0.00 0.00 0.00 4.92
1110 1156 1.378762 CCAACCCTGATCCACGGTT 59.621 57.895 3.08 3.08 40.55 4.44
1114 1160 2.043953 GGCCCAACCCTGATCCAC 60.044 66.667 0.00 0.00 0.00 4.02
1134 1180 0.459899 TCTGATGAACGGCTGCGTAT 59.540 50.000 0.00 0.00 0.00 3.06
1161 1207 0.682292 TGAACGTCACCATGTAGCCA 59.318 50.000 0.00 0.00 0.00 4.75
1222 1268 0.620556 ACGACCTCAATGCCATCCTT 59.379 50.000 0.00 0.00 0.00 3.36
1252 1299 2.357034 GGCTTCGTCGTGCTTCCA 60.357 61.111 11.32 0.00 0.00 3.53
1418 1467 4.445453 CACACATAATAAGCAGAGCAGGA 58.555 43.478 0.00 0.00 0.00 3.86
1433 1482 2.746904 GCACAACCATGTAGCACACATA 59.253 45.455 3.88 0.00 46.47 2.29
1463 1512 2.181975 CTAGTTGGTAAGGTTCCCGGA 58.818 52.381 0.73 0.00 0.00 5.14
1465 1514 1.406477 GGCTAGTTGGTAAGGTTCCCG 60.406 57.143 0.00 0.00 0.00 5.14
1468 1517 4.648651 TCTTTGGCTAGTTGGTAAGGTTC 58.351 43.478 0.00 0.00 0.00 3.62
1557 1606 0.975040 TTGCCTGGTGTTTGGTTGCT 60.975 50.000 0.00 0.00 0.00 3.91
1576 1625 2.025605 ACCTGCATGGACTGAATCACAT 60.026 45.455 8.91 0.00 39.71 3.21
1581 1630 3.118112 CCTCTTACCTGCATGGACTGAAT 60.118 47.826 8.91 0.00 39.71 2.57
1597 1646 0.680921 GTTGCCTGCATGCCCTCTTA 60.681 55.000 16.68 0.00 0.00 2.10
1663 1712 2.679059 GCATAGCCTTCTCAACTCAGCA 60.679 50.000 0.00 0.00 0.00 4.41
1719 1768 0.179056 CGAGTTGGTTCACTGTGGGT 60.179 55.000 8.11 0.00 0.00 4.51
1839 1888 4.566907 GCCCAACACTCCCATAAGTTCTAA 60.567 45.833 0.00 0.00 0.00 2.10
1840 1889 3.054655 GCCCAACACTCCCATAAGTTCTA 60.055 47.826 0.00 0.00 0.00 2.10
1844 1893 1.282157 GAGCCCAACACTCCCATAAGT 59.718 52.381 0.00 0.00 0.00 2.24
1846 1895 0.623723 GGAGCCCAACACTCCCATAA 59.376 55.000 0.00 0.00 46.81 1.90
1848 1897 3.090765 GGAGCCCAACACTCCCAT 58.909 61.111 0.00 0.00 46.81 4.00
1857 1906 4.776322 CACCGCGATGGAGCCCAA 62.776 66.667 8.23 0.00 42.00 4.12
1862 1918 1.202417 ACAATCTACACCGCGATGGAG 60.202 52.381 6.27 6.27 42.00 3.86
1868 1924 1.076533 AGCGAACAATCTACACCGCG 61.077 55.000 0.00 0.00 46.11 6.46
1893 1949 2.872245 CCACCACCTGTTCTTATATGCG 59.128 50.000 0.00 0.00 0.00 4.73
1911 1967 1.515521 CCAAACGCCCTCAAGTCCAC 61.516 60.000 0.00 0.00 0.00 4.02
1977 2033 3.009723 AGTGATCGATTGTTTCCGCATT 58.990 40.909 0.00 0.00 0.00 3.56
2011 2067 2.430921 CCAAGAGCGCGAAGACGT 60.431 61.111 12.10 0.00 41.98 4.34
2023 2079 0.923358 AACACAGGGTTGGACCAAGA 59.077 50.000 7.31 0.00 41.02 3.02
2031 2087 1.871039 CAGGTAACGAACACAGGGTTG 59.129 52.381 0.00 0.00 40.63 3.77
2032 2088 1.202722 CCAGGTAACGAACACAGGGTT 60.203 52.381 0.00 0.00 44.10 4.11
2047 2105 1.864559 ACTCCTCTCCTCCCCAGGT 60.865 63.158 0.00 0.00 41.28 4.00
2084 2142 2.162408 GTGCACCAAGGCAGTAATCTTC 59.838 50.000 5.22 0.00 45.96 2.87
2085 2143 2.162681 GTGCACCAAGGCAGTAATCTT 58.837 47.619 5.22 0.00 45.96 2.40
2104 2162 1.242076 GAGTGTGGCTGCAATGAAGT 58.758 50.000 0.50 0.00 0.00 3.01
2121 2804 3.341823 CAAATCCTTCCTGGTCACTGAG 58.658 50.000 0.00 0.00 37.07 3.35
2122 2805 2.553028 GCAAATCCTTCCTGGTCACTGA 60.553 50.000 0.00 0.00 37.07 3.41
2124 2807 1.425066 TGCAAATCCTTCCTGGTCACT 59.575 47.619 0.00 0.00 37.07 3.41
2128 2811 1.620822 GTGTGCAAATCCTTCCTGGT 58.379 50.000 0.00 0.00 37.07 4.00
2129 2812 0.890683 GGTGTGCAAATCCTTCCTGG 59.109 55.000 0.00 0.00 37.10 4.45
2131 2814 0.110486 ACGGTGTGCAAATCCTTCCT 59.890 50.000 0.00 0.00 0.00 3.36
2160 2843 1.414158 TCCAAATTTCCCGGCAAACA 58.586 45.000 0.00 0.00 0.00 2.83
2202 2885 2.356432 CCCAGATGGAGAAGCATTGACA 60.356 50.000 0.00 0.00 37.39 3.58
2240 2941 2.833913 CCCACCACTTGCCAGGTCT 61.834 63.158 0.00 0.00 35.52 3.85
2251 2952 1.750399 CATGTAGCAGGCCCACCAC 60.750 63.158 0.00 0.00 39.06 4.16


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

AutoCloner maintained by Alex Coulton.