Multiple sequence alignment - TraesCS5D01G214200

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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 TraesCS5D01G214200 chr5D 100.000 3892 0 0 1 3892 323906312 323910203 0.000000e+00 7188
1 TraesCS5D01G214200 chr5D 85.535 318 45 1 3160 3477 323917031 323917347 9.010000e-87 331
2 TraesCS5D01G214200 chr5D 100.000 141 0 0 4207 4347 323910518 323910658 1.200000e-65 261
3 TraesCS5D01G214200 chr5A 92.316 1809 94 25 1898 3692 421825250 421827027 0.000000e+00 2529
4 TraesCS5D01G214200 chr5A 91.284 1044 46 10 893 1909 421823340 421824365 0.000000e+00 1382
5 TraesCS5D01G214200 chr5A 87.500 312 37 2 3160 3470 421834243 421834553 4.130000e-95 359
6 TraesCS5D01G214200 chr5A 90.071 282 18 5 18 295 421822422 421822697 1.490000e-94 357
7 TraesCS5D01G214200 chr5A 80.372 484 71 16 2708 3182 421833768 421834236 3.220000e-91 346
8 TraesCS5D01G214200 chr5A 93.966 116 4 3 3690 3803 421827186 421827300 5.780000e-39 172
9 TraesCS5D01G214200 chr5A 95.062 81 3 1 4267 4347 421827474 421827553 4.560000e-25 126
10 TraesCS5D01G214200 chr5A 98.276 58 1 0 3835 3892 421827298 421827355 7.690000e-18 102
11 TraesCS5D01G214200 chr5B 93.199 1588 77 13 2238 3809 375617333 375618905 0.000000e+00 2305
12 TraesCS5D01G214200 chr5B 92.655 1375 51 16 891 2239 375615938 375617288 0.000000e+00 1934
13 TraesCS5D01G214200 chr5B 79.361 877 136 25 2325 3181 375643471 375644322 3.770000e-160 575
14 TraesCS5D01G214200 chr5B 87.338 308 34 3 3167 3470 375644366 375644672 8.950000e-92 348
15 TraesCS5D01G214200 chr5B 96.970 66 1 1 3828 3892 375619774 375619839 4.600000e-20 110
16 TraesCS5D01G214200 chr2B 79.007 1067 140 46 1697 2722 736726334 736727357 0.000000e+00 652
17 TraesCS5D01G214200 chr2B 85.065 616 80 8 949 1560 736725608 736726215 6.180000e-173 617
18 TraesCS5D01G214200 chr2B 82.683 589 75 15 2747 3325 736727357 736727928 8.400000e-137 497
19 TraesCS5D01G214200 chr2D 80.986 852 108 36 1899 2722 605829211 605830036 1.030000e-175 627
20 TraesCS5D01G214200 chr2D 83.225 614 74 14 949 1560 605828293 605828879 1.780000e-148 536
21 TraesCS5D01G214200 chr2D 82.792 616 79 14 2747 3350 605830036 605830636 3.850000e-145 525
22 TraesCS5D01G214200 chr2A 80.742 862 116 33 1887 2722 737235635 737236472 1.030000e-175 627
23 TraesCS5D01G214200 chr2A 84.765 617 81 9 949 1560 737234707 737235315 1.340000e-169 606
24 TraesCS5D01G214200 chr2A 82.955 616 78 13 2747 3350 737236472 737237072 8.280000e-147 531
25 TraesCS5D01G214200 chr7A 96.053 76 2 1 296 371 686714863 686714789 5.900000e-24 122
26 TraesCS5D01G214200 chr7A 94.737 76 3 1 296 371 673307693 673307619 2.750000e-22 117
27 TraesCS5D01G214200 chr3A 96.053 76 2 1 296 371 171785911 171785985 5.900000e-24 122
28 TraesCS5D01G214200 chr6B 95.775 71 3 0 296 366 71082309 71082239 9.880000e-22 115


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 TraesCS5D01G214200 chr5D 323906312 323910658 4346 False 3724.500000 7188 100.000000 1 4347 2 chr5D.!!$F2 4346
1 TraesCS5D01G214200 chr5A 421822422 421827553 5131 False 778.000000 2529 93.495833 18 4347 6 chr5A.!!$F1 4329
2 TraesCS5D01G214200 chr5A 421833768 421834553 785 False 352.500000 359 83.936000 2708 3470 2 chr5A.!!$F2 762
3 TraesCS5D01G214200 chr5B 375615938 375619839 3901 False 1449.666667 2305 94.274667 891 3892 3 chr5B.!!$F1 3001
4 TraesCS5D01G214200 chr5B 375643471 375644672 1201 False 461.500000 575 83.349500 2325 3470 2 chr5B.!!$F2 1145
5 TraesCS5D01G214200 chr2B 736725608 736727928 2320 False 588.666667 652 82.251667 949 3325 3 chr2B.!!$F1 2376
6 TraesCS5D01G214200 chr2D 605828293 605830636 2343 False 562.666667 627 82.334333 949 3350 3 chr2D.!!$F1 2401
7 TraesCS5D01G214200 chr2A 737234707 737237072 2365 False 588.000000 627 82.820667 949 3350 3 chr2A.!!$F1 2401

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
374 378 0.327095 AACTTGTGGGGGCCCTTTTT 60.327 50.000 24.38 4.57 36.94 1.94 F
1452 1685 0.037232 CCTCAACTTCGAGGTCACCC 60.037 60.000 0.00 0.00 46.48 4.61 F
1467 1700 1.423921 TCACCCTTGTTTCCTTCCCTC 59.576 52.381 0.00 0.00 0.00 4.30 F
2620 3908 2.079925 GATCCACACCTTTCTCTGTGC 58.920 52.381 0.00 0.00 37.12 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 1890 0.603065 GACTGGTTCAACAATGGGGC 59.397 55.0 0.00 0.00 0.00 5.80 R
3079 4387 0.179059 TTCGTGTCAGCCTTGCAAGA 60.179 50.0 28.05 4.89 0.00 3.02 R
3205 4571 1.294659 GACCAGGCAGCGACTTCTTG 61.295 60.0 0.00 0.00 0.00 3.02 R
3851 6235 0.106868 CCCATTTAGGAACGGGGTCC 60.107 60.0 0.00 0.00 41.22 4.46 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
62 63 7.348080 TCGATTTGTCAATACCTATGAGACT 57.652 36.000 0.00 0.00 0.00 3.24
69 70 8.547481 TGTCAATACCTATGAGACTAAATGGA 57.453 34.615 0.00 0.00 0.00 3.41
157 159 5.441718 ACTCTAACCACATCACATCCAAT 57.558 39.130 0.00 0.00 0.00 3.16
164 166 5.332743 ACCACATCACATCCAATTTTACCT 58.667 37.500 0.00 0.00 0.00 3.08
166 168 6.101332 CCACATCACATCCAATTTTACCTTG 58.899 40.000 0.00 0.00 0.00 3.61
172 174 7.653647 TCACATCCAATTTTACCTTGTTACAC 58.346 34.615 0.00 0.00 0.00 2.90
174 176 6.487331 ACATCCAATTTTACCTTGTTACACGA 59.513 34.615 0.00 0.00 0.00 4.35
199 201 3.367630 GGATGCCACAAAATGTAAAAGCG 59.632 43.478 0.00 0.00 0.00 4.68
216 218 5.597813 AAAGCGATGCTATGTATAGTTGC 57.402 39.130 0.00 0.00 38.25 4.17
250 253 4.691685 GCATGAAGCCAATTTTGATCAACA 59.308 37.500 7.89 1.31 37.23 3.33
261 264 8.489559 CCAATTTTGATCAACAATGTTGTAGTG 58.510 33.333 23.41 12.63 41.31 2.74
292 296 9.926158 ACAAATGATAATGTAAATCAACTTGCA 57.074 25.926 9.43 0.00 36.95 4.08
303 307 9.677567 TGTAAATCAACTTGCAATACTTTTCTC 57.322 29.630 0.00 0.00 0.00 2.87
304 308 7.858052 AAATCAACTTGCAATACTTTTCTCG 57.142 32.000 0.00 0.00 0.00 4.04
305 309 6.560253 ATCAACTTGCAATACTTTTCTCGT 57.440 33.333 0.00 0.00 0.00 4.18
306 310 6.371809 TCAACTTGCAATACTTTTCTCGTT 57.628 33.333 0.00 0.00 0.00 3.85
307 311 6.198687 TCAACTTGCAATACTTTTCTCGTTG 58.801 36.000 0.00 7.05 0.00 4.10
308 312 6.037720 TCAACTTGCAATACTTTTCTCGTTGA 59.962 34.615 15.41 15.41 35.91 3.18
309 313 5.990408 ACTTGCAATACTTTTCTCGTTGAG 58.010 37.500 0.00 0.00 0.00 3.02
310 314 5.758296 ACTTGCAATACTTTTCTCGTTGAGA 59.242 36.000 0.00 0.00 36.86 3.27
311 315 6.260050 ACTTGCAATACTTTTCTCGTTGAGAA 59.740 34.615 0.00 5.19 45.45 2.87
312 316 6.801539 TGCAATACTTTTCTCGTTGAGAAT 57.198 33.333 9.83 0.00 46.20 2.40
313 317 7.899178 TGCAATACTTTTCTCGTTGAGAATA 57.101 32.000 9.83 5.06 46.20 1.75
314 318 8.317891 TGCAATACTTTTCTCGTTGAGAATAA 57.682 30.769 9.83 6.93 46.20 1.40
315 319 8.443160 TGCAATACTTTTCTCGTTGAGAATAAG 58.557 33.333 9.83 15.59 46.20 1.73
316 320 8.443937 GCAATACTTTTCTCGTTGAGAATAAGT 58.556 33.333 23.90 23.90 46.20 2.24
317 321 9.959775 CAATACTTTTCTCGTTGAGAATAAGTC 57.040 33.333 24.01 0.00 46.20 3.01
318 322 8.705048 ATACTTTTCTCGTTGAGAATAAGTCC 57.295 34.615 24.01 0.00 46.20 3.85
319 323 6.760291 ACTTTTCTCGTTGAGAATAAGTCCT 58.240 36.000 19.62 8.08 46.20 3.85
320 324 7.217906 ACTTTTCTCGTTGAGAATAAGTCCTT 58.782 34.615 19.62 7.87 46.20 3.36
321 325 7.385478 ACTTTTCTCGTTGAGAATAAGTCCTTC 59.615 37.037 19.62 0.00 46.20 3.46
322 326 5.326200 TCTCGTTGAGAATAAGTCCTTCC 57.674 43.478 0.00 0.00 35.59 3.46
323 327 4.106029 TCGTTGAGAATAAGTCCTTCCG 57.894 45.455 0.00 0.00 0.00 4.30
324 328 3.508793 TCGTTGAGAATAAGTCCTTCCGT 59.491 43.478 0.00 0.00 0.00 4.69
325 329 4.021719 TCGTTGAGAATAAGTCCTTCCGTT 60.022 41.667 0.00 0.00 0.00 4.44
326 330 4.689345 CGTTGAGAATAAGTCCTTCCGTTT 59.311 41.667 0.00 0.00 0.00 3.60
327 331 5.178809 CGTTGAGAATAAGTCCTTCCGTTTT 59.821 40.000 0.00 0.00 0.00 2.43
328 332 6.371389 GTTGAGAATAAGTCCTTCCGTTTTG 58.629 40.000 0.00 0.00 0.00 2.44
329 333 5.617252 TGAGAATAAGTCCTTCCGTTTTGT 58.383 37.500 0.00 0.00 0.00 2.83
330 334 5.468746 TGAGAATAAGTCCTTCCGTTTTGTG 59.531 40.000 0.00 0.00 0.00 3.33
331 335 5.374071 AGAATAAGTCCTTCCGTTTTGTGT 58.626 37.500 0.00 0.00 0.00 3.72
332 336 5.238650 AGAATAAGTCCTTCCGTTTTGTGTG 59.761 40.000 0.00 0.00 0.00 3.82
333 337 2.702592 AGTCCTTCCGTTTTGTGTGA 57.297 45.000 0.00 0.00 0.00 3.58
334 338 2.993937 AGTCCTTCCGTTTTGTGTGAA 58.006 42.857 0.00 0.00 0.00 3.18
335 339 3.551846 AGTCCTTCCGTTTTGTGTGAAT 58.448 40.909 0.00 0.00 0.00 2.57
336 340 3.951680 AGTCCTTCCGTTTTGTGTGAATT 59.048 39.130 0.00 0.00 0.00 2.17
337 341 4.036380 AGTCCTTCCGTTTTGTGTGAATTC 59.964 41.667 0.00 0.00 0.00 2.17
338 342 3.316868 TCCTTCCGTTTTGTGTGAATTCC 59.683 43.478 2.27 0.00 0.00 3.01
339 343 3.552068 CCTTCCGTTTTGTGTGAATTCCC 60.552 47.826 2.27 0.00 0.00 3.97
340 344 1.957877 TCCGTTTTGTGTGAATTCCCC 59.042 47.619 2.27 0.00 0.00 4.81
341 345 1.683917 CCGTTTTGTGTGAATTCCCCA 59.316 47.619 2.27 0.00 0.00 4.96
342 346 2.288152 CCGTTTTGTGTGAATTCCCCAG 60.288 50.000 2.27 0.00 0.00 4.45
343 347 2.360801 CGTTTTGTGTGAATTCCCCAGT 59.639 45.455 2.27 0.00 0.00 4.00
344 348 3.716601 GTTTTGTGTGAATTCCCCAGTG 58.283 45.455 2.27 0.00 0.00 3.66
345 349 1.993956 TTGTGTGAATTCCCCAGTGG 58.006 50.000 0.63 0.63 0.00 4.00
346 350 0.539438 TGTGTGAATTCCCCAGTGGC 60.539 55.000 2.61 0.00 0.00 5.01
347 351 1.303236 TGTGAATTCCCCAGTGGCG 60.303 57.895 2.61 0.00 0.00 5.69
348 352 1.002624 GTGAATTCCCCAGTGGCGA 60.003 57.895 2.61 0.00 0.00 5.54
349 353 0.608035 GTGAATTCCCCAGTGGCGAA 60.608 55.000 11.63 11.63 0.00 4.70
350 354 0.331278 TGAATTCCCCAGTGGCGAAT 59.669 50.000 15.11 15.11 34.76 3.34
351 355 1.272425 TGAATTCCCCAGTGGCGAATT 60.272 47.619 27.44 27.44 40.87 2.17
352 356 2.025793 TGAATTCCCCAGTGGCGAATTA 60.026 45.455 27.24 16.29 39.54 1.40
353 357 2.818751 ATTCCCCAGTGGCGAATTAA 57.181 45.000 15.11 0.00 31.41 1.40
354 358 1.828979 TTCCCCAGTGGCGAATTAAC 58.171 50.000 5.09 0.00 0.00 2.01
355 359 0.693622 TCCCCAGTGGCGAATTAACA 59.306 50.000 2.61 0.00 0.00 2.41
356 360 1.074084 TCCCCAGTGGCGAATTAACAA 59.926 47.619 2.61 0.00 0.00 2.83
357 361 1.201414 CCCCAGTGGCGAATTAACAAC 59.799 52.381 2.61 0.00 0.00 3.32
358 362 2.159382 CCCAGTGGCGAATTAACAACT 58.841 47.619 2.61 0.00 0.00 3.16
359 363 2.556622 CCCAGTGGCGAATTAACAACTT 59.443 45.455 2.61 0.00 0.00 2.66
360 364 3.564511 CCAGTGGCGAATTAACAACTTG 58.435 45.455 0.00 0.00 0.00 3.16
361 365 3.004315 CCAGTGGCGAATTAACAACTTGT 59.996 43.478 0.00 0.00 0.00 3.16
362 366 3.974401 CAGTGGCGAATTAACAACTTGTG 59.026 43.478 0.00 0.00 0.00 3.33
363 367 3.004315 AGTGGCGAATTAACAACTTGTGG 59.996 43.478 0.00 0.00 0.00 4.17
364 368 2.294791 TGGCGAATTAACAACTTGTGGG 59.705 45.455 0.00 0.00 0.00 4.61
365 369 2.352323 GGCGAATTAACAACTTGTGGGG 60.352 50.000 0.00 0.00 0.00 4.96
366 370 2.352323 GCGAATTAACAACTTGTGGGGG 60.352 50.000 0.00 0.00 0.00 5.40
367 371 2.352323 CGAATTAACAACTTGTGGGGGC 60.352 50.000 0.00 0.00 0.00 5.80
368 372 1.639722 ATTAACAACTTGTGGGGGCC 58.360 50.000 0.00 0.00 0.00 5.80
369 373 0.470268 TTAACAACTTGTGGGGGCCC 60.470 55.000 15.76 15.76 0.00 5.80
370 374 1.365105 TAACAACTTGTGGGGGCCCT 61.365 55.000 24.38 0.00 36.94 5.19
371 375 2.201210 CAACTTGTGGGGGCCCTT 59.799 61.111 24.38 4.27 36.94 3.95
372 376 1.459348 CAACTTGTGGGGGCCCTTT 60.459 57.895 24.38 3.43 36.94 3.11
373 377 1.053835 CAACTTGTGGGGGCCCTTTT 61.054 55.000 24.38 3.81 36.94 2.27
374 378 0.327095 AACTTGTGGGGGCCCTTTTT 60.327 50.000 24.38 4.57 36.94 1.94
375 379 1.053835 ACTTGTGGGGGCCCTTTTTG 61.054 55.000 24.38 12.80 36.94 2.44
383 387 0.467804 GGGCCCTTTTTGTGCAAGAA 59.532 50.000 17.04 0.00 0.00 2.52
388 392 4.497842 GGCCCTTTTTGTGCAAGAAAAATG 60.498 41.667 14.73 12.58 46.08 2.32
392 396 7.482474 CCCTTTTTGTGCAAGAAAAATGAAAT 58.518 30.769 14.73 0.00 46.08 2.17
394 398 7.969508 CCTTTTTGTGCAAGAAAAATGAAATGT 59.030 29.630 14.73 0.00 46.08 2.71
412 422 7.411274 TGAAATGTAGTTAAGTCGTTTGGTTG 58.589 34.615 0.00 0.00 0.00 3.77
433 443 4.941657 TGCATTGCATAGTTGTTCACAAA 58.058 34.783 7.38 0.00 33.46 2.83
434 444 5.539979 TGCATTGCATAGTTGTTCACAAAT 58.460 33.333 7.38 0.00 33.46 2.32
435 445 5.405873 TGCATTGCATAGTTGTTCACAAATG 59.594 36.000 7.38 2.12 33.46 2.32
436 446 5.634439 GCATTGCATAGTTGTTCACAAATGA 59.366 36.000 3.15 0.00 37.63 2.57
437 447 6.145858 GCATTGCATAGTTGTTCACAAATGAA 59.854 34.615 3.15 0.00 42.73 2.57
438 448 7.148540 GCATTGCATAGTTGTTCACAAATGAAT 60.149 33.333 3.15 1.57 46.43 2.57
439 449 9.356433 CATTGCATAGTTGTTCACAAATGAATA 57.644 29.630 2.94 0.00 46.43 1.75
441 451 8.914328 TGCATAGTTGTTCACAAATGAATATG 57.086 30.769 2.94 0.63 46.43 1.78
442 452 8.738106 TGCATAGTTGTTCACAAATGAATATGA 58.262 29.630 2.94 0.00 46.43 2.15
443 453 9.013490 GCATAGTTGTTCACAAATGAATATGAC 57.987 33.333 2.94 0.00 46.43 3.06
447 457 8.084073 AGTTGTTCACAAATGAATATGACTTGG 58.916 33.333 0.00 0.00 46.43 3.61
448 458 7.523293 TGTTCACAAATGAATATGACTTGGT 57.477 32.000 0.00 0.00 46.43 3.67
449 459 8.628630 TGTTCACAAATGAATATGACTTGGTA 57.371 30.769 0.00 0.00 46.43 3.25
450 460 9.072375 TGTTCACAAATGAATATGACTTGGTAA 57.928 29.630 0.00 0.00 46.43 2.85
451 461 9.559958 GTTCACAAATGAATATGACTTGGTAAG 57.440 33.333 0.00 0.00 46.43 2.34
452 462 8.862325 TCACAAATGAATATGACTTGGTAAGT 57.138 30.769 0.00 0.00 46.38 2.24
453 463 9.295825 TCACAAATGAATATGACTTGGTAAGTT 57.704 29.630 0.00 0.00 43.03 2.66
454 464 9.559958 CACAAATGAATATGACTTGGTAAGTTC 57.440 33.333 0.00 0.00 43.03 3.01
455 465 9.295825 ACAAATGAATATGACTTGGTAAGTTCA 57.704 29.630 0.00 0.00 43.03 3.18
458 468 9.685276 AATGAATATGACTTGGTAAGTTCATCA 57.315 29.630 6.39 4.04 43.03 3.07
459 469 9.685276 ATGAATATGACTTGGTAAGTTCATCAA 57.315 29.630 8.72 0.00 43.03 2.57
460 470 9.513906 TGAATATGACTTGGTAAGTTCATCAAA 57.486 29.630 8.72 0.00 43.03 2.69
461 471 9.994432 GAATATGACTTGGTAAGTTCATCAAAG 57.006 33.333 8.72 0.00 43.03 2.77
462 472 9.739276 AATATGACTTGGTAAGTTCATCAAAGA 57.261 29.630 8.72 0.00 43.03 2.52
463 473 7.678947 ATGACTTGGTAAGTTCATCAAAGAG 57.321 36.000 0.00 0.00 43.03 2.85
464 474 6.826668 TGACTTGGTAAGTTCATCAAAGAGA 58.173 36.000 0.00 0.00 43.03 3.10
465 475 7.279615 TGACTTGGTAAGTTCATCAAAGAGAA 58.720 34.615 0.00 0.00 43.03 2.87
466 476 7.939039 TGACTTGGTAAGTTCATCAAAGAGAAT 59.061 33.333 0.00 0.00 43.03 2.40
467 477 9.436957 GACTTGGTAAGTTCATCAAAGAGAATA 57.563 33.333 0.00 0.00 43.03 1.75
468 478 9.965902 ACTTGGTAAGTTCATCAAAGAGAATAT 57.034 29.630 0.00 0.00 39.04 1.28
470 480 9.958180 TTGGTAAGTTCATCAAAGAGAATATGA 57.042 29.630 0.00 0.00 0.00 2.15
475 485 9.605275 AAGTTCATCAAAGAGAATATGATTCGA 57.395 29.630 0.00 0.00 31.65 3.71
476 486 9.775854 AGTTCATCAAAGAGAATATGATTCGAT 57.224 29.630 0.00 0.00 31.65 3.59
584 602 9.755804 TGATATGATTAGATAATGATTCGGCTC 57.244 33.333 0.00 0.00 0.00 4.70
585 603 8.809159 ATATGATTAGATAATGATTCGGCTCG 57.191 34.615 0.00 0.00 0.00 5.03
608 626 9.619727 CTCGAATATACGTTGTTTAGTGATTTG 57.380 33.333 0.00 0.00 34.70 2.32
704 723 9.840427 ATTTGTTCACGTAATTCTAGGAAAATG 57.160 29.630 0.00 0.00 0.00 2.32
705 724 7.972832 TGTTCACGTAATTCTAGGAAAATGT 57.027 32.000 0.00 0.00 0.00 2.71
830 851 7.881775 TTTTTAGAAGAATAGGGAAGATGGC 57.118 36.000 0.00 0.00 0.00 4.40
832 853 2.713708 AGAAGAATAGGGAAGATGGCCC 59.286 50.000 0.00 0.00 46.40 5.80
867 1093 3.861689 GCAAGTGAGATTTAGCATTTGGC 59.138 43.478 0.00 0.00 45.30 4.52
879 1105 2.454055 GCATTTGGCGTTCAAGATAGC 58.546 47.619 0.00 0.00 36.62 2.97
885 1111 3.113260 GGCGTTCAAGATAGCCTATGT 57.887 47.619 8.47 0.00 45.67 2.29
886 1112 4.252971 GGCGTTCAAGATAGCCTATGTA 57.747 45.455 8.47 0.00 45.67 2.29
887 1113 3.988517 GGCGTTCAAGATAGCCTATGTAC 59.011 47.826 8.47 0.00 45.67 2.90
888 1114 3.669122 GCGTTCAAGATAGCCTATGTACG 59.331 47.826 0.00 0.00 38.87 3.67
889 1115 4.792057 GCGTTCAAGATAGCCTATGTACGT 60.792 45.833 0.00 0.00 38.36 3.57
913 1139 3.010200 AGAAGGAATCTCACATTGCCC 57.990 47.619 0.00 0.00 30.46 5.36
940 1166 4.329545 GCCCGCACCCTGTGAAGA 62.330 66.667 0.00 0.00 35.23 2.87
941 1167 2.358737 CCCGCACCCTGTGAAGAC 60.359 66.667 0.00 0.00 35.23 3.01
942 1168 2.743718 CCGCACCCTGTGAAGACT 59.256 61.111 0.00 0.00 35.23 3.24
943 1169 1.374758 CCGCACCCTGTGAAGACTC 60.375 63.158 0.00 0.00 35.23 3.36
944 1170 1.734477 CGCACCCTGTGAAGACTCG 60.734 63.158 0.00 0.00 35.23 4.18
1343 1576 1.075896 CCCCGGGCTCTACTTCTCT 60.076 63.158 17.73 0.00 0.00 3.10
1352 1585 2.486592 GCTCTACTTCTCTATCCTCCGC 59.513 54.545 0.00 0.00 0.00 5.54
1452 1685 0.037232 CCTCAACTTCGAGGTCACCC 60.037 60.000 0.00 0.00 46.48 4.61
1467 1700 1.423921 TCACCCTTGTTTCCTTCCCTC 59.576 52.381 0.00 0.00 0.00 4.30
1575 1832 6.670695 AATTGTTGAACCTCAGCCTAATTT 57.329 33.333 0.00 0.00 0.00 1.82
1598 1855 2.881074 TCAAGCGATTCACACTAGCTC 58.119 47.619 0.00 0.00 37.15 4.09
1602 1859 2.159310 AGCGATTCACACTAGCTCAGTC 60.159 50.000 0.00 0.00 34.26 3.51
1615 1872 7.815068 ACACTAGCTCAGTCAAACTAATTACAG 59.185 37.037 0.00 0.00 34.26 2.74
1627 1884 7.336931 TCAAACTAATTACAGAAGGCAGGAATC 59.663 37.037 0.00 0.00 0.00 2.52
1633 1890 3.152341 ACAGAAGGCAGGAATCAAACTG 58.848 45.455 0.00 0.00 37.76 3.16
1660 1917 6.239572 CCCATTGTTGAACCAGTCCTTAAATT 60.240 38.462 0.00 0.00 0.00 1.82
1709 1968 4.156556 GCATGGTTTTACATCTCTCAAGCA 59.843 41.667 0.00 0.00 0.00 3.91
1751 2011 2.237143 CCATCTACCAGCTTCCAGTTCA 59.763 50.000 0.00 0.00 0.00 3.18
1815 2079 6.907212 GTGATCGACGAAAATTTGCATAGAAT 59.093 34.615 0.00 0.00 0.00 2.40
1893 2179 8.678199 CCTCATTTTGTCCTAGATACTTTTTCC 58.322 37.037 0.00 0.00 0.00 3.13
2102 3284 5.409712 TGAGAGGAATCATGATGGAGGTAT 58.590 41.667 9.46 0.00 0.00 2.73
2163 3355 7.653767 CCCTGTTGGTCTTAATCGTATATTC 57.346 40.000 0.00 0.00 0.00 1.75
2184 3376 7.630242 ATTCGTATGGACTCATTGATTGTTT 57.370 32.000 0.00 0.00 34.96 2.83
2282 3520 9.832445 CTGAGTACTGTTAATATAACAATGGGT 57.168 33.333 0.00 2.43 0.00 4.51
2287 3525 8.996024 ACTGTTAATATAACAATGGGTTTTGC 57.004 30.769 4.68 0.00 40.96 3.68
2288 3526 8.811994 ACTGTTAATATAACAATGGGTTTTGCT 58.188 29.630 4.68 0.00 40.96 3.91
2289 3527 8.994429 TGTTAATATAACAATGGGTTTTGCTG 57.006 30.769 0.66 0.00 40.96 4.41
2290 3528 7.547370 TGTTAATATAACAATGGGTTTTGCTGC 59.453 33.333 0.66 0.00 40.96 5.25
2295 3535 3.230134 ACAATGGGTTTTGCTGCTAGAA 58.770 40.909 0.00 0.00 0.00 2.10
2441 3703 8.494016 ACCTATGTTGAGCTTGATTAACTTAC 57.506 34.615 0.00 0.00 0.00 2.34
2487 3766 8.872845 GCACCTACATGATTTTATTTTTGAAGG 58.127 33.333 0.00 0.00 0.00 3.46
2521 3801 6.819397 AGCTTTAAATTCGTAAGGCTCTTT 57.181 33.333 1.73 0.00 41.14 2.52
2556 3836 4.273318 AGCAATAGTTCAAAGGGTCATCC 58.727 43.478 0.00 0.00 0.00 3.51
2620 3908 2.079925 GATCCACACCTTTCTCTGTGC 58.920 52.381 0.00 0.00 37.12 4.57
2838 4132 6.024049 AGAAATTTCGAAAATAGCGCTCAAG 58.976 36.000 16.34 0.45 0.00 3.02
2853 4148 4.320202 GCGCTCAAGGTTGTTGAATCTAAA 60.320 41.667 0.00 0.00 0.00 1.85
2921 4219 3.196685 AGCACCAAAACCTGCAAAACTTA 59.803 39.130 0.00 0.00 35.73 2.24
2962 4268 3.668141 TTCTGTGGCATGGATAATGGT 57.332 42.857 0.00 0.00 36.71 3.55
3055 4363 5.064452 CACTGAGAAATCCAGTATTCAGTGC 59.936 44.000 16.47 0.00 42.44 4.40
3079 4387 2.787473 TGTCCAAGATCATTTCCGCT 57.213 45.000 0.00 0.00 0.00 5.52
3114 4422 4.606961 ACACGAAGGTTTATGTTGCTTTG 58.393 39.130 0.00 0.00 0.00 2.77
3205 4571 0.392461 TATGGCAGGAAACACTCGCC 60.392 55.000 0.00 0.00 43.28 5.54
3238 4604 2.487934 CCTGGTCGATTCATCCATGTC 58.512 52.381 0.00 0.00 0.00 3.06
3325 4694 2.151202 GCTACCTGCTTGCAACAACTA 58.849 47.619 0.00 0.00 38.95 2.24
3352 4721 1.759445 GCTGTGAGGGCTTAGATCTGA 59.241 52.381 5.18 0.00 0.00 3.27
3511 4880 6.036083 CCTCTACCATGTTTGAGATGTTAACG 59.964 42.308 3.36 0.00 0.00 3.18
3555 4924 4.095483 GCAAGTTGTAATGGTCATCTGAGG 59.905 45.833 4.48 0.00 0.00 3.86
3626 4995 5.160641 GCTGGGTAATGTTGTTGTACAATG 58.839 41.667 12.26 0.00 40.59 2.82
3651 5020 5.970317 TTTGAACATGAACATCTGATGCT 57.030 34.783 17.24 5.32 0.00 3.79
3654 5023 5.490159 TGAACATGAACATCTGATGCTGTA 58.510 37.500 17.24 2.66 0.00 2.74
3672 5042 5.050490 GCTGTAGTAACTATCATGGGTGTG 58.950 45.833 0.00 0.00 0.00 3.82
3795 5327 4.798882 ACATGTGGGTGAGAACCTTTTTA 58.201 39.130 0.00 0.00 0.00 1.52
3803 5336 4.098807 GGTGAGAACCTTTTTAGGCAAACA 59.901 41.667 0.00 0.00 0.00 2.83
3809 5342 3.709141 ACCTTTTTAGGCAAACATGTGGT 59.291 39.130 0.00 0.00 0.00 4.16
3851 6235 4.629200 GGTGAGAACTGCACAGAATAAGAG 59.371 45.833 4.31 0.00 37.99 2.85
4235 6619 0.518764 CGACGGCGAGATATAGCGAC 60.519 60.000 16.62 0.00 40.82 5.19
4264 6648 4.096003 GCCGCAGCCCTAGTTGGA 62.096 66.667 0.00 0.00 38.35 3.53
4265 6649 2.668632 CCGCAGCCCTAGTTGGAA 59.331 61.111 0.00 0.00 38.35 3.53
4266 6650 1.745489 CCGCAGCCCTAGTTGGAAC 60.745 63.158 0.00 0.00 38.35 3.62
4267 6651 2.100631 CGCAGCCCTAGTTGGAACG 61.101 63.158 0.00 0.00 38.35 3.95
4268 6652 1.745489 GCAGCCCTAGTTGGAACGG 60.745 63.158 0.00 0.00 38.35 4.44
4269 6653 1.078426 CAGCCCTAGTTGGAACGGG 60.078 63.158 0.00 0.00 38.35 5.28
4270 6654 1.229400 AGCCCTAGTTGGAACGGGA 60.229 57.895 6.66 0.00 39.08 5.14
4325 6709 2.356818 GACGGAGAGATGGCGGAAGG 62.357 65.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.078426 GTTGGACCCGGGAGACATG 60.078 63.158 32.02 0.00 0.00 3.21
1 2 1.537889 TGTTGGACCCGGGAGACAT 60.538 57.895 32.02 2.86 0.00 3.06
2 3 2.122769 TGTTGGACCCGGGAGACA 60.123 61.111 32.02 21.57 0.00 3.41
3 4 1.838073 ATGTGTTGGACCCGGGAGAC 61.838 60.000 32.02 19.20 0.00 3.36
4 5 1.537889 ATGTGTTGGACCCGGGAGA 60.538 57.895 32.02 7.20 0.00 3.71
5 6 1.377202 CATGTGTTGGACCCGGGAG 60.377 63.158 32.02 0.33 0.00 4.30
6 7 2.119484 GACATGTGTTGGACCCGGGA 62.119 60.000 32.02 0.04 0.00 5.14
7 8 1.674322 GACATGTGTTGGACCCGGG 60.674 63.158 22.25 22.25 0.00 5.73
8 9 1.072332 TGACATGTGTTGGACCCGG 59.928 57.895 1.15 0.00 0.00 5.73
9 10 1.234615 GGTGACATGTGTTGGACCCG 61.235 60.000 1.15 0.00 0.00 5.28
10 11 0.179004 TGGTGACATGTGTTGGACCC 60.179 55.000 1.15 0.00 33.16 4.46
11 12 3.412722 TGGTGACATGTGTTGGACC 57.587 52.632 1.15 1.85 34.19 4.46
39 40 9.529325 TTTAGTCTCATAGGTATTGACAAATCG 57.471 33.333 0.00 0.00 0.00 3.34
62 63 8.387813 ACTAGTCCCACAAAGTAATTCCATTTA 58.612 33.333 0.00 0.00 0.00 1.40
66 67 5.280317 GGACTAGTCCCACAAAGTAATTCCA 60.280 44.000 28.87 0.00 43.94 3.53
67 68 5.183969 GGACTAGTCCCACAAAGTAATTCC 58.816 45.833 28.87 0.44 43.94 3.01
119 121 9.982651 GTGGTTAGAGTACAATCATACATATGT 57.017 33.333 13.93 13.93 35.26 2.29
123 125 8.704668 TGATGTGGTTAGAGTACAATCATACAT 58.295 33.333 0.00 0.00 0.00 2.29
124 126 7.979537 GTGATGTGGTTAGAGTACAATCATACA 59.020 37.037 0.00 0.00 0.00 2.29
125 127 7.979537 TGTGATGTGGTTAGAGTACAATCATAC 59.020 37.037 0.00 0.00 0.00 2.39
126 128 8.073467 TGTGATGTGGTTAGAGTACAATCATA 57.927 34.615 0.00 0.00 0.00 2.15
127 129 6.946340 TGTGATGTGGTTAGAGTACAATCAT 58.054 36.000 0.00 0.00 0.00 2.45
128 130 6.353404 TGTGATGTGGTTAGAGTACAATCA 57.647 37.500 0.00 0.00 0.00 2.57
129 131 6.480320 GGATGTGATGTGGTTAGAGTACAATC 59.520 42.308 0.00 0.00 0.00 2.67
130 132 6.070251 TGGATGTGATGTGGTTAGAGTACAAT 60.070 38.462 0.00 0.00 0.00 2.71
131 133 5.247337 TGGATGTGATGTGGTTAGAGTACAA 59.753 40.000 0.00 0.00 0.00 2.41
157 159 6.513720 GCATCCTTTCGTGTAACAAGGTAAAA 60.514 38.462 0.00 0.00 35.74 1.52
164 166 2.550606 GTGGCATCCTTTCGTGTAACAA 59.449 45.455 0.00 0.00 35.74 2.83
166 168 2.147958 TGTGGCATCCTTTCGTGTAAC 58.852 47.619 0.00 0.00 0.00 2.50
172 174 3.302365 ACATTTTGTGGCATCCTTTCG 57.698 42.857 0.00 0.00 0.00 3.46
174 176 5.469760 GCTTTTACATTTTGTGGCATCCTTT 59.530 36.000 0.00 0.00 0.00 3.11
199 201 4.563184 GCCTACGCAACTATACATAGCATC 59.437 45.833 0.00 0.00 32.31 3.91
216 218 0.601311 GCTTCATGCCCTAGCCTACG 60.601 60.000 0.00 0.00 38.69 3.51
300 304 4.142447 CGGAAGGACTTATTCTCAACGAGA 60.142 45.833 0.00 0.00 36.86 4.04
301 305 4.106197 CGGAAGGACTTATTCTCAACGAG 58.894 47.826 0.00 0.00 0.00 4.18
302 306 3.508793 ACGGAAGGACTTATTCTCAACGA 59.491 43.478 0.00 0.00 0.00 3.85
303 307 3.846360 ACGGAAGGACTTATTCTCAACG 58.154 45.455 0.00 0.00 0.00 4.10
304 308 6.017357 ACAAAACGGAAGGACTTATTCTCAAC 60.017 38.462 0.00 0.00 0.00 3.18
305 309 6.017440 CACAAAACGGAAGGACTTATTCTCAA 60.017 38.462 0.00 0.00 0.00 3.02
306 310 5.468746 CACAAAACGGAAGGACTTATTCTCA 59.531 40.000 0.00 0.00 0.00 3.27
307 311 5.469084 ACACAAAACGGAAGGACTTATTCTC 59.531 40.000 0.00 0.00 0.00 2.87
308 312 5.238650 CACACAAAACGGAAGGACTTATTCT 59.761 40.000 0.00 0.00 0.00 2.40
309 313 5.237779 TCACACAAAACGGAAGGACTTATTC 59.762 40.000 0.00 0.00 0.00 1.75
310 314 5.127491 TCACACAAAACGGAAGGACTTATT 58.873 37.500 0.00 0.00 0.00 1.40
311 315 4.710324 TCACACAAAACGGAAGGACTTAT 58.290 39.130 0.00 0.00 0.00 1.73
312 316 4.139859 TCACACAAAACGGAAGGACTTA 57.860 40.909 0.00 0.00 0.00 2.24
313 317 2.993937 TCACACAAAACGGAAGGACTT 58.006 42.857 0.00 0.00 0.00 3.01
314 318 2.702592 TCACACAAAACGGAAGGACT 57.297 45.000 0.00 0.00 0.00 3.85
315 319 3.982576 ATTCACACAAAACGGAAGGAC 57.017 42.857 0.00 0.00 0.00 3.85
316 320 3.316868 GGAATTCACACAAAACGGAAGGA 59.683 43.478 7.93 0.00 0.00 3.36
317 321 3.552068 GGGAATTCACACAAAACGGAAGG 60.552 47.826 7.93 0.00 0.00 3.46
318 322 3.552068 GGGGAATTCACACAAAACGGAAG 60.552 47.826 10.48 0.00 0.00 3.46
319 323 2.362717 GGGGAATTCACACAAAACGGAA 59.637 45.455 10.48 0.00 0.00 4.30
320 324 1.957877 GGGGAATTCACACAAAACGGA 59.042 47.619 10.48 0.00 0.00 4.69
321 325 1.683917 TGGGGAATTCACACAAAACGG 59.316 47.619 10.48 0.00 0.00 4.44
322 326 2.360801 ACTGGGGAATTCACACAAAACG 59.639 45.455 10.48 0.00 0.00 3.60
323 327 3.492482 CCACTGGGGAATTCACACAAAAC 60.492 47.826 10.48 0.00 40.01 2.43
324 328 2.697751 CCACTGGGGAATTCACACAAAA 59.302 45.455 10.48 0.00 40.01 2.44
325 329 2.315176 CCACTGGGGAATTCACACAAA 58.685 47.619 10.48 0.00 40.01 2.83
326 330 1.993956 CCACTGGGGAATTCACACAA 58.006 50.000 10.48 0.00 40.01 3.33
327 331 0.539438 GCCACTGGGGAATTCACACA 60.539 55.000 10.48 4.44 40.01 3.72
328 332 1.586154 CGCCACTGGGGAATTCACAC 61.586 60.000 10.48 0.00 40.01 3.82
329 333 1.303236 CGCCACTGGGGAATTCACA 60.303 57.895 10.48 5.99 40.01 3.58
330 334 1.002624 TCGCCACTGGGGAATTCAC 60.003 57.895 12.34 2.76 41.69 3.18
331 335 3.489636 TCGCCACTGGGGAATTCA 58.510 55.556 12.34 0.00 41.69 2.57
336 340 0.693622 TGTTAATTCGCCACTGGGGA 59.306 50.000 10.76 10.76 42.93 4.81
337 341 1.201414 GTTGTTAATTCGCCACTGGGG 59.799 52.381 5.75 5.75 40.85 4.96
338 342 2.159382 AGTTGTTAATTCGCCACTGGG 58.841 47.619 0.00 0.00 37.18 4.45
339 343 3.004315 ACAAGTTGTTAATTCGCCACTGG 59.996 43.478 1.64 0.00 0.00 4.00
340 344 3.974401 CACAAGTTGTTAATTCGCCACTG 59.026 43.478 5.57 0.00 0.00 3.66
341 345 3.004315 CCACAAGTTGTTAATTCGCCACT 59.996 43.478 5.57 0.00 0.00 4.00
342 346 3.305110 CCACAAGTTGTTAATTCGCCAC 58.695 45.455 5.57 0.00 0.00 5.01
343 347 2.294791 CCCACAAGTTGTTAATTCGCCA 59.705 45.455 5.57 0.00 0.00 5.69
344 348 2.352323 CCCCACAAGTTGTTAATTCGCC 60.352 50.000 5.57 0.00 0.00 5.54
345 349 2.352323 CCCCCACAAGTTGTTAATTCGC 60.352 50.000 5.57 0.00 0.00 4.70
346 350 2.352323 GCCCCCACAAGTTGTTAATTCG 60.352 50.000 5.57 0.00 0.00 3.34
347 351 2.028476 GGCCCCCACAAGTTGTTAATTC 60.028 50.000 5.57 0.00 0.00 2.17
348 352 1.974957 GGCCCCCACAAGTTGTTAATT 59.025 47.619 5.57 0.00 0.00 1.40
349 353 1.639722 GGCCCCCACAAGTTGTTAAT 58.360 50.000 5.57 0.00 0.00 1.40
350 354 0.470268 GGGCCCCCACAAGTTGTTAA 60.470 55.000 12.23 0.00 35.81 2.01
351 355 1.154221 GGGCCCCCACAAGTTGTTA 59.846 57.895 12.23 0.00 35.81 2.41
352 356 2.123033 GGGCCCCCACAAGTTGTT 60.123 61.111 12.23 0.00 35.81 2.83
353 357 2.250635 AAAGGGCCCCCACAAGTTGT 62.251 55.000 21.43 1.64 38.92 3.32
354 358 1.053835 AAAAGGGCCCCCACAAGTTG 61.054 55.000 21.43 0.00 38.92 3.16
355 359 0.327095 AAAAAGGGCCCCCACAAGTT 60.327 50.000 21.43 0.00 38.92 2.66
356 360 1.053835 CAAAAAGGGCCCCCACAAGT 61.054 55.000 21.43 0.00 38.92 3.16
357 361 1.053835 ACAAAAAGGGCCCCCACAAG 61.054 55.000 21.43 7.22 38.92 3.16
358 362 1.003573 ACAAAAAGGGCCCCCACAA 59.996 52.632 21.43 0.00 38.92 3.33
359 363 1.764054 CACAAAAAGGGCCCCCACA 60.764 57.895 21.43 0.00 38.92 4.17
360 364 3.147132 CACAAAAAGGGCCCCCAC 58.853 61.111 21.43 0.00 38.92 4.61
361 365 2.846754 GCACAAAAAGGGCCCCCA 60.847 61.111 21.43 0.00 42.32 4.96
367 371 6.434018 TTCATTTTTCTTGCACAAAAAGGG 57.566 33.333 19.61 14.22 36.43 3.95
368 372 7.969508 ACATTTCATTTTTCTTGCACAAAAAGG 59.030 29.630 16.15 16.15 36.43 3.11
369 373 8.898983 ACATTTCATTTTTCTTGCACAAAAAG 57.101 26.923 16.62 10.99 36.43 2.27
370 374 9.985318 CTACATTTCATTTTTCTTGCACAAAAA 57.015 25.926 14.77 14.77 37.18 1.94
371 375 9.160496 ACTACATTTCATTTTTCTTGCACAAAA 57.840 25.926 0.00 0.00 0.00 2.44
372 376 8.715191 ACTACATTTCATTTTTCTTGCACAAA 57.285 26.923 0.00 0.00 0.00 2.83
373 377 8.715191 AACTACATTTCATTTTTCTTGCACAA 57.285 26.923 0.00 0.00 0.00 3.33
374 378 9.809096 TTAACTACATTTCATTTTTCTTGCACA 57.191 25.926 0.00 0.00 0.00 4.57
383 387 9.458374 CCAAACGACTTAACTACATTTCATTTT 57.542 29.630 0.00 0.00 0.00 1.82
388 392 6.358822 GCAACCAAACGACTTAACTACATTTC 59.641 38.462 0.00 0.00 0.00 2.17
392 396 4.190001 TGCAACCAAACGACTTAACTACA 58.810 39.130 0.00 0.00 0.00 2.74
394 398 5.753744 CAATGCAACCAAACGACTTAACTA 58.246 37.500 0.00 0.00 0.00 2.24
403 413 2.945278 ACTATGCAATGCAACCAAACG 58.055 42.857 13.45 0.00 43.62 3.60
412 422 5.634439 TCATTTGTGAACAACTATGCAATGC 59.366 36.000 0.00 0.00 35.28 3.56
433 443 9.685276 TTGATGAACTTACCAAGTCATATTCAT 57.315 29.630 0.00 0.00 41.91 2.57
434 444 9.513906 TTTGATGAACTTACCAAGTCATATTCA 57.486 29.630 0.00 0.00 41.91 2.57
435 445 9.994432 CTTTGATGAACTTACCAAGTCATATTC 57.006 33.333 0.00 0.00 41.91 1.75
436 446 9.739276 TCTTTGATGAACTTACCAAGTCATATT 57.261 29.630 0.00 0.00 41.91 1.28
437 447 9.388506 CTCTTTGATGAACTTACCAAGTCATAT 57.611 33.333 0.00 0.00 41.91 1.78
438 448 8.593679 TCTCTTTGATGAACTTACCAAGTCATA 58.406 33.333 0.00 0.00 41.91 2.15
439 449 7.453393 TCTCTTTGATGAACTTACCAAGTCAT 58.547 34.615 0.00 0.00 41.91 3.06
440 450 6.826668 TCTCTTTGATGAACTTACCAAGTCA 58.173 36.000 0.00 0.00 41.91 3.41
441 451 7.730364 TTCTCTTTGATGAACTTACCAAGTC 57.270 36.000 0.00 0.00 41.91 3.01
442 452 9.965902 ATATTCTCTTTGATGAACTTACCAAGT 57.034 29.630 0.00 0.00 45.46 3.16
444 454 9.958180 TCATATTCTCTTTGATGAACTTACCAA 57.042 29.630 0.00 0.00 0.00 3.67
449 459 9.605275 TCGAATCATATTCTCTTTGATGAACTT 57.395 29.630 0.00 0.00 32.34 2.66
450 460 9.775854 ATCGAATCATATTCTCTTTGATGAACT 57.224 29.630 0.00 0.00 32.34 3.01
500 510 7.312154 TGCACACCACAAAAATAGCTAATTAG 58.688 34.615 8.20 8.20 0.00 1.73
501 511 7.220741 TGCACACCACAAAAATAGCTAATTA 57.779 32.000 0.00 0.00 0.00 1.40
502 512 6.095432 TGCACACCACAAAAATAGCTAATT 57.905 33.333 0.00 0.00 0.00 1.40
503 513 5.720371 TGCACACCACAAAAATAGCTAAT 57.280 34.783 0.00 0.00 0.00 1.73
517 527 6.000840 TCATAGTAACTTTTCATGCACACCA 58.999 36.000 0.00 0.00 0.00 4.17
520 530 9.409312 CATTTTCATAGTAACTTTTCATGCACA 57.591 29.630 0.00 0.00 0.00 4.57
559 577 8.910666 CGAGCCGAATCATTATCTAATCATATC 58.089 37.037 0.00 0.00 0.00 1.63
680 699 8.385898 ACATTTTCCTAGAATTACGTGAACAA 57.614 30.769 0.00 0.00 0.00 2.83
806 827 6.833933 GGCCATCTTCCCTATTCTTCTAAAAA 59.166 38.462 0.00 0.00 0.00 1.94
809 830 4.351111 GGGCCATCTTCCCTATTCTTCTAA 59.649 45.833 4.39 0.00 40.66 2.10
810 831 3.910627 GGGCCATCTTCCCTATTCTTCTA 59.089 47.826 4.39 0.00 40.66 2.10
811 832 2.713708 GGGCCATCTTCCCTATTCTTCT 59.286 50.000 4.39 0.00 40.66 2.85
812 833 2.443255 TGGGCCATCTTCCCTATTCTTC 59.557 50.000 0.00 0.00 44.23 2.87
813 834 2.502745 TGGGCCATCTTCCCTATTCTT 58.497 47.619 0.00 0.00 44.23 2.52
814 835 2.212752 TGGGCCATCTTCCCTATTCT 57.787 50.000 0.00 0.00 44.23 2.40
816 837 3.999764 AAATGGGCCATCTTCCCTATT 57.000 42.857 21.48 4.60 44.23 1.73
819 840 2.647846 AAAAATGGGCCATCTTCCCT 57.352 45.000 21.48 0.00 44.23 4.20
835 856 1.774110 TCTCACTTGCTGCCCAAAAA 58.226 45.000 0.00 0.00 31.94 1.94
837 858 1.999648 AATCTCACTTGCTGCCCAAA 58.000 45.000 0.00 0.00 31.94 3.28
838 859 1.999648 AAATCTCACTTGCTGCCCAA 58.000 45.000 0.00 0.00 0.00 4.12
839 860 2.715046 CTAAATCTCACTTGCTGCCCA 58.285 47.619 0.00 0.00 0.00 5.36
840 861 1.403323 GCTAAATCTCACTTGCTGCCC 59.597 52.381 0.00 0.00 0.00 5.36
841 862 2.086869 TGCTAAATCTCACTTGCTGCC 58.913 47.619 0.00 0.00 0.00 4.85
842 863 4.367386 AATGCTAAATCTCACTTGCTGC 57.633 40.909 0.00 0.00 0.00 5.25
843 864 5.100259 CCAAATGCTAAATCTCACTTGCTG 58.900 41.667 0.00 0.00 0.00 4.41
845 866 3.861689 GCCAAATGCTAAATCTCACTTGC 59.138 43.478 0.00 0.00 36.87 4.01
846 867 4.100529 CGCCAAATGCTAAATCTCACTTG 58.899 43.478 0.00 0.00 38.05 3.16
867 1093 4.675565 CACGTACATAGGCTATCTTGAACG 59.324 45.833 3.47 11.83 0.00 3.95
876 1102 5.439721 TCCTTCTTACACGTACATAGGCTA 58.560 41.667 0.00 0.00 0.00 3.93
878 1104 4.644103 TCCTTCTTACACGTACATAGGC 57.356 45.455 0.00 0.00 0.00 3.93
879 1105 7.040473 AGATTCCTTCTTACACGTACATAGG 57.960 40.000 0.00 0.00 0.00 2.57
880 1106 7.644551 GTGAGATTCCTTCTTACACGTACATAG 59.355 40.741 0.00 0.00 39.97 2.23
881 1107 7.121611 TGTGAGATTCCTTCTTACACGTACATA 59.878 37.037 0.00 0.00 43.75 2.29
882 1108 6.071560 TGTGAGATTCCTTCTTACACGTACAT 60.072 38.462 0.00 0.00 43.75 2.29
883 1109 5.242171 TGTGAGATTCCTTCTTACACGTACA 59.758 40.000 0.00 0.00 43.75 2.90
884 1110 5.706916 TGTGAGATTCCTTCTTACACGTAC 58.293 41.667 0.00 0.00 43.75 3.67
885 1111 5.970317 TGTGAGATTCCTTCTTACACGTA 57.030 39.130 0.00 0.00 43.75 3.57
886 1112 4.866508 TGTGAGATTCCTTCTTACACGT 57.133 40.909 0.00 0.00 43.75 4.49
940 1166 0.875728 CGGTGTCTTGACTCTCGAGT 59.124 55.000 13.13 0.00 45.84 4.18
941 1167 0.455295 GCGGTGTCTTGACTCTCGAG 60.455 60.000 5.93 5.93 0.00 4.04
942 1168 1.579932 GCGGTGTCTTGACTCTCGA 59.420 57.895 13.47 0.00 0.00 4.04
943 1169 1.444553 GGCGGTGTCTTGACTCTCG 60.445 63.158 2.35 6.02 0.00 4.04
944 1170 1.444553 CGGCGGTGTCTTGACTCTC 60.445 63.158 0.00 0.00 0.00 3.20
1352 1585 4.379243 AGGACGAGGCGCTGGTTG 62.379 66.667 7.64 0.00 0.00 3.77
1452 1685 1.076438 AGGGGAGGGAAGGAAACAAG 58.924 55.000 0.00 0.00 0.00 3.16
1467 1700 3.209410 CATCAGAAGAAATCGGAAGGGG 58.791 50.000 0.00 0.00 35.82 4.79
1536 1792 2.418628 ACAATTAATCGCCACTGGTTCG 59.581 45.455 0.00 0.00 0.00 3.95
1575 1832 4.065088 AGCTAGTGTGAATCGCTTGAAAA 58.935 39.130 0.00 0.00 38.01 2.29
1595 1852 6.402658 GCCTTCTGTAATTAGTTTGACTGAGC 60.403 42.308 0.00 0.00 0.00 4.26
1598 1855 6.128172 CCTGCCTTCTGTAATTAGTTTGACTG 60.128 42.308 0.00 0.00 0.00 3.51
1602 1859 6.817765 TTCCTGCCTTCTGTAATTAGTTTG 57.182 37.500 0.00 0.00 0.00 2.93
1615 1872 2.643933 GCAGTTTGATTCCTGCCTTC 57.356 50.000 0.24 0.00 46.55 3.46
1627 1884 2.482864 GTTCAACAATGGGGCAGTTTG 58.517 47.619 0.00 0.00 0.00 2.93
1633 1890 0.603065 GACTGGTTCAACAATGGGGC 59.397 55.000 0.00 0.00 0.00 5.80
1709 1968 6.767524 TGGTCTATTTTGTCACTGTTGTTT 57.232 33.333 0.00 0.00 0.00 2.83
1751 2011 5.770162 CACCCACTTCCTGAAATTAGAAGTT 59.230 40.000 2.03 0.00 46.08 2.66
1815 2079 5.263599 AGCAACATCCAATGATCAGGTAAA 58.736 37.500 0.09 0.00 0.00 2.01
1849 2135 3.330701 TGAGGGGTTAACAGAGCAGAAAT 59.669 43.478 8.10 0.00 0.00 2.17
2102 3284 7.447374 TCGAAAAGGAAGAAAATGATAGCAA 57.553 32.000 0.00 0.00 0.00 3.91
2156 3348 9.424319 ACAATCAATGAGTCCATACGAATATAC 57.576 33.333 0.00 0.00 31.59 1.47
2157 3349 9.996554 AACAATCAATGAGTCCATACGAATATA 57.003 29.630 0.00 0.00 31.59 0.86
2158 3350 8.908786 AACAATCAATGAGTCCATACGAATAT 57.091 30.769 0.00 0.00 31.59 1.28
2159 3351 8.731275 AAACAATCAATGAGTCCATACGAATA 57.269 30.769 0.00 0.00 31.59 1.75
2160 3352 7.630242 AAACAATCAATGAGTCCATACGAAT 57.370 32.000 0.00 0.00 31.59 3.34
2161 3353 7.822334 AGTAAACAATCAATGAGTCCATACGAA 59.178 33.333 0.00 0.00 31.59 3.85
2162 3354 7.327975 AGTAAACAATCAATGAGTCCATACGA 58.672 34.615 0.00 0.00 31.59 3.43
2163 3355 7.539712 AGTAAACAATCAATGAGTCCATACG 57.460 36.000 0.00 0.00 31.59 3.06
2287 3525 6.100404 AGAATTAGGCTGAGATTCTAGCAG 57.900 41.667 16.16 7.43 41.63 4.24
2288 3526 6.098838 TCAAGAATTAGGCTGAGATTCTAGCA 59.901 38.462 17.31 7.00 38.74 3.49
2289 3527 6.520272 TCAAGAATTAGGCTGAGATTCTAGC 58.480 40.000 17.31 6.60 38.74 3.42
2290 3528 8.149647 ACATCAAGAATTAGGCTGAGATTCTAG 58.850 37.037 17.31 12.33 38.74 2.43
2295 3535 6.497624 AGACATCAAGAATTAGGCTGAGAT 57.502 37.500 0.00 0.00 0.00 2.75
2441 3703 5.804473 GGTGCGATAGATCATCTTCTACATG 59.196 44.000 0.00 0.00 39.76 3.21
2458 3736 8.465999 TCAAAAATAAAATCATGTAGGTGCGAT 58.534 29.630 0.00 0.00 0.00 4.58
2487 3766 5.179555 ACGAATTTAAAGCTCAGAAGGTGTC 59.820 40.000 0.00 0.00 32.35 3.67
2604 3890 3.996150 AATTGCACAGAGAAAGGTGTG 57.004 42.857 0.00 0.00 45.75 3.82
2783 4077 3.595190 AATATTGGTAGGGGCCAGAAC 57.405 47.619 4.39 0.00 40.01 3.01
2838 4132 7.206687 TGGTCAACATTTTAGATTCAACAACC 58.793 34.615 0.00 0.00 0.00 3.77
2921 4219 3.814504 ATGTTCATCTCCTTTGGTGGT 57.185 42.857 0.00 0.00 0.00 4.16
2962 4268 8.217131 TCGCTACTGTAGTATTGAAAGTATCA 57.783 34.615 15.71 0.00 35.85 2.15
2983 4289 5.684184 GGAACGTTTTGAAAGTAAAATCGCT 59.316 36.000 0.46 0.00 32.71 4.93
2993 4299 3.775661 ACCAGTGGAACGTTTTGAAAG 57.224 42.857 18.40 0.00 45.86 2.62
3055 4363 5.297776 AGCGGAAATGATCTTGGACATAAAG 59.702 40.000 0.00 0.00 0.00 1.85
3079 4387 0.179059 TTCGTGTCAGCCTTGCAAGA 60.179 50.000 28.05 4.89 0.00 3.02
3114 4422 3.261137 GGGATAATACTCTACCTGCACCC 59.739 52.174 0.00 0.00 0.00 4.61
3205 4571 1.294659 GACCAGGCAGCGACTTCTTG 61.295 60.000 0.00 0.00 0.00 3.02
3238 4604 6.138761 GCCATACTCTGCAAAATTAGATTCG 58.861 40.000 0.00 0.00 0.00 3.34
3325 4694 2.362120 GCCCTCACAGCTGCCATT 60.362 61.111 15.27 0.00 0.00 3.16
3386 4755 6.543465 TGATGTTATCATGATCTTGGGAACAC 59.457 38.462 17.46 13.08 35.18 3.32
3511 4880 7.761249 ACTTGCTATTCCTTGCAAATAAATCAC 59.239 33.333 0.00 0.00 46.55 3.06
3555 4924 2.165319 AAAACACAGCTACTCGGTCC 57.835 50.000 0.00 0.00 0.00 4.46
3626 4995 6.643770 AGCATCAGATGTTCATGTTCAAAAAC 59.356 34.615 12.18 0.00 35.85 2.43
3651 5020 7.783119 AGATACACACCCATGATAGTTACTACA 59.217 37.037 0.00 0.00 0.00 2.74
3654 5023 7.419057 CCAAGATACACACCCATGATAGTTACT 60.419 40.741 0.00 0.00 0.00 2.24
3820 5353 0.877071 GCAGTTCTCACCCACATGTG 59.123 55.000 19.31 19.31 37.59 3.21
3821 5354 0.473755 TGCAGTTCTCACCCACATGT 59.526 50.000 0.00 0.00 0.00 3.21
3822 5355 0.877071 GTGCAGTTCTCACCCACATG 59.123 55.000 0.00 0.00 0.00 3.21
3823 5356 0.473755 TGTGCAGTTCTCACCCACAT 59.526 50.000 0.00 0.00 33.18 3.21
3824 5357 0.179048 CTGTGCAGTTCTCACCCACA 60.179 55.000 0.00 0.00 35.49 4.17
3826 5359 0.836606 TTCTGTGCAGTTCTCACCCA 59.163 50.000 0.00 0.00 33.71 4.51
3851 6235 0.106868 CCCATTTAGGAACGGGGTCC 60.107 60.000 0.00 0.00 41.22 4.46
4226 6610 1.082300 CGCCGTCGTGTCGCTATAT 60.082 57.895 0.00 0.00 0.00 0.86
4227 6611 2.325511 CGCCGTCGTGTCGCTATA 59.674 61.111 0.00 0.00 0.00 1.31
4228 6612 4.547905 CCGCCGTCGTGTCGCTAT 62.548 66.667 0.00 0.00 0.00 2.97
4248 6632 1.745489 GTTCCAACTAGGGCTGCGG 60.745 63.158 0.00 0.00 38.24 5.69
4249 6633 2.100631 CGTTCCAACTAGGGCTGCG 61.101 63.158 0.00 0.00 38.24 5.18
4250 6634 1.745489 CCGTTCCAACTAGGGCTGC 60.745 63.158 0.00 0.00 38.24 5.25
4251 6635 1.078426 CCCGTTCCAACTAGGGCTG 60.078 63.158 0.00 0.00 37.07 4.85
4252 6636 1.229400 TCCCGTTCCAACTAGGGCT 60.229 57.895 0.00 0.00 43.46 5.19
4253 6637 1.078637 GTCCCGTTCCAACTAGGGC 60.079 63.158 0.00 0.00 43.46 5.19
4254 6638 0.688487 TTGTCCCGTTCCAACTAGGG 59.312 55.000 0.00 0.00 45.10 3.53
4255 6639 1.609841 GGTTGTCCCGTTCCAACTAGG 60.610 57.143 0.00 0.00 40.56 3.02
4256 6640 1.804601 GGTTGTCCCGTTCCAACTAG 58.195 55.000 0.00 0.00 40.56 2.57
4258 6642 4.892002 GGTTGTCCCGTTCCAACT 57.108 55.556 0.00 0.00 40.56 3.16
4306 6690 1.066587 CTTCCGCCATCTCTCCGTC 59.933 63.158 0.00 0.00 0.00 4.79
4325 6709 4.908877 GACGACCGGAGCTAGCGC 62.909 72.222 9.46 10.35 0.00 5.92


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

AutoCloner maintained by Alex Coulton.