Multiple sequence alignment - TraesCS5B01G169100

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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 TraesCS5B01G169100 chr5B 100.000 2636 0 0 1 2636 313214081 313211446 0.000000e+00 4868.0
1 TraesCS5B01G169100 chr5B 91.156 147 3 1 331 467 283999783 283999637 9.630000e-45 191.0
2 TraesCS5B01G169100 chr5B 92.143 140 1 1 333 462 638677466 638677327 3.460000e-44 189.0
3 TraesCS5B01G169100 chr5B 89.726 146 5 1 331 466 77852777 77852922 7.500000e-41 178.0
4 TraesCS5B01G169100 chr5D 91.380 1485 79 20 462 1910 276468646 276467175 0.000000e+00 1988.0
5 TraesCS5B01G169100 chr5D 88.829 743 54 11 1905 2636 276456377 276455653 0.000000e+00 885.0
6 TraesCS5B01G169100 chr5D 93.694 333 20 1 1 333 276468975 276468644 5.070000e-137 497.0
7 TraesCS5B01G169100 chr5D 76.923 585 84 24 1044 1582 276546957 276546378 4.290000e-73 285.0
8 TraesCS5B01G169100 chr5A 85.866 1316 120 25 1034 2306 364962135 364960843 0.000000e+00 1339.0
9 TraesCS5B01G169100 chr5A 93.846 325 16 2 10 333 364963072 364962751 1.100000e-133 486.0
10 TraesCS5B01G169100 chr5A 85.751 393 22 12 643 1035 364962529 364962171 4.120000e-103 385.0
11 TraesCS5B01G169100 chr5A 95.238 168 5 1 463 627 364962751 364962584 2.010000e-66 263.0
12 TraesCS5B01G169100 chr5A 90.083 121 11 1 2340 2459 364960844 364960724 3.510000e-34 156.0
13 TraesCS5B01G169100 chr2B 95.620 137 5 1 333 468 104827217 104827353 4.420000e-53 219.0
14 TraesCS5B01G169100 chr2B 90.476 147 4 2 330 466 86538269 86538415 4.480000e-43 185.0
15 TraesCS5B01G169100 chr2B 89.333 150 5 2 330 468 422983822 422983971 7.500000e-41 178.0
16 TraesCS5B01G169100 chr3B 91.724 145 2 1 330 464 127906589 127906733 2.680000e-45 193.0
17 TraesCS5B01G169100 chr3B 89.189 148 6 1 332 469 210461702 210461555 2.700000e-40 176.0
18 TraesCS5B01G169100 chr3B 83.815 173 15 6 309 470 827097963 827098133 4.540000e-33 152.0
19 TraesCS5B01G169100 chr7B 89.744 156 4 6 324 468 665423227 665423381 3.460000e-44 189.0
20 TraesCS5B01G169100 chr7B 87.647 170 6 6 327 483 297161180 297161347 1.610000e-42 183.0
21 TraesCS5B01G169100 chr7B 91.429 140 2 1 333 462 370208141 370208280 1.610000e-42 183.0
22 TraesCS5B01G169100 chr7B 89.051 137 14 1 330 465 436214214 436214078 4.510000e-38 169.0
23 TraesCS5B01G169100 chr4B 91.096 146 3 3 331 466 503494306 503494161 3.460000e-44 189.0
24 TraesCS5B01G169100 chr4B 87.582 153 8 2 325 466 512553387 512553235 1.620000e-37 167.0
25 TraesCS5B01G169100 chr4B 87.143 70 6 2 2152 2221 601789298 601789364 2.810000e-10 76.8
26 TraesCS5B01G169100 chr1B 89.744 156 4 3 326 470 58325289 58325135 3.460000e-44 189.0
27 TraesCS5B01G169100 chr1B 88.961 154 6 2 328 470 456300922 456301075 2.080000e-41 180.0
28 TraesCS5B01G169100 chr1B 72.530 506 111 18 2017 2515 90310222 90309738 3.540000e-29 139.0
29 TraesCS5B01G169100 chr6A 89.726 146 5 1 327 462 172616207 172616352 7.500000e-41 178.0
30 TraesCS5B01G169100 chr6B 77.404 208 43 4 2017 2221 213389246 213389452 1.280000e-23 121.0
31 TraesCS5B01G169100 chr4A 75.355 211 44 6 2017 2225 698325795 698325591 7.770000e-16 95.3
32 TraesCS5B01G169100 chr4A 72.043 279 64 10 2072 2338 724516357 724516633 1.310000e-08 71.3
33 TraesCS5B01G169100 chr2A 77.108 166 33 5 2067 2230 558654459 558654621 1.000000e-14 91.6
34 TraesCS5B01G169100 chr2A 76.829 164 33 5 2069 2230 558661845 558662005 1.300000e-13 87.9
35 TraesCS5B01G169100 chr7D 77.632 152 27 6 2088 2237 175654285 175654431 4.670000e-13 86.1
36 TraesCS5B01G169100 chr2D 78.862 123 23 2 2067 2187 429052750 429052629 2.170000e-11 80.5


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 TraesCS5B01G169100 chr5B 313211446 313214081 2635 True 4868.0 4868 100.0000 1 2636 1 chr5B.!!$R2 2635
1 TraesCS5B01G169100 chr5D 276467175 276468975 1800 True 1242.5 1988 92.5370 1 1910 2 chr5D.!!$R3 1909
2 TraesCS5B01G169100 chr5D 276455653 276456377 724 True 885.0 885 88.8290 1905 2636 1 chr5D.!!$R1 731
3 TraesCS5B01G169100 chr5D 276546378 276546957 579 True 285.0 285 76.9230 1044 1582 1 chr5D.!!$R2 538
4 TraesCS5B01G169100 chr5A 364960724 364963072 2348 True 525.8 1339 90.1568 10 2459 5 chr5A.!!$R1 2449

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
355 358 0.036306 CTTGTTCGGTTAGGCAGGGT 59.964 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2499 0.03759 TTAGCATTGTTGGAGGGCGT 59.962 50.0 0.0 0.0 0.0 5.68 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
49 50 1.679898 CCACCTTCACCTCTGACCC 59.320 63.158 0.00 0.00 0.00 4.46
124 125 3.130693 AGGACAAGTCTATCGCTAACCAC 59.869 47.826 0.00 0.00 0.00 4.16
127 128 3.119101 ACAAGTCTATCGCTAACCACAGG 60.119 47.826 0.00 0.00 0.00 4.00
172 174 8.795513 TCCAAATCACAGCATAATAATGTATGG 58.204 33.333 0.00 0.00 35.38 2.74
333 336 3.262135 ACAACGACGCAAACCATTAAG 57.738 42.857 0.00 0.00 0.00 1.85
334 337 2.031508 ACAACGACGCAAACCATTAAGG 60.032 45.455 0.00 0.00 45.67 2.69
335 338 0.519961 ACGACGCAAACCATTAAGGC 59.480 50.000 0.00 0.00 43.14 4.35
336 339 0.179174 CGACGCAAACCATTAAGGCC 60.179 55.000 0.00 0.00 43.14 5.19
337 340 1.173913 GACGCAAACCATTAAGGCCT 58.826 50.000 0.00 0.00 43.14 5.19
338 341 1.544246 GACGCAAACCATTAAGGCCTT 59.456 47.619 24.18 24.18 43.14 4.35
339 342 1.272212 ACGCAAACCATTAAGGCCTTG 59.728 47.619 28.77 13.66 43.14 3.61
340 343 1.272212 CGCAAACCATTAAGGCCTTGT 59.728 47.619 28.77 14.38 43.14 3.16
341 344 2.288763 CGCAAACCATTAAGGCCTTGTT 60.289 45.455 28.77 19.54 43.14 2.83
342 345 3.325870 GCAAACCATTAAGGCCTTGTTC 58.674 45.455 28.77 8.56 43.14 3.18
343 346 3.574614 CAAACCATTAAGGCCTTGTTCG 58.425 45.455 28.77 14.68 43.14 3.95
344 347 1.834188 ACCATTAAGGCCTTGTTCGG 58.166 50.000 28.77 22.61 43.14 4.30
345 348 1.074889 ACCATTAAGGCCTTGTTCGGT 59.925 47.619 28.77 23.23 43.14 4.69
346 349 2.167662 CCATTAAGGCCTTGTTCGGTT 58.832 47.619 28.77 0.57 0.00 4.44
347 350 3.244981 ACCATTAAGGCCTTGTTCGGTTA 60.245 43.478 28.77 1.62 43.14 2.85
348 351 3.377172 CCATTAAGGCCTTGTTCGGTTAG 59.623 47.826 28.77 7.08 0.00 2.34
349 352 2.773993 TAAGGCCTTGTTCGGTTAGG 57.226 50.000 28.77 0.00 0.00 2.69
353 356 2.854522 CCTTGTTCGGTTAGGCAGG 58.145 57.895 0.00 0.00 0.00 4.85
354 357 0.676782 CCTTGTTCGGTTAGGCAGGG 60.677 60.000 0.00 0.00 0.00 4.45
355 358 0.036306 CTTGTTCGGTTAGGCAGGGT 59.964 55.000 0.00 0.00 0.00 4.34
356 359 0.475044 TTGTTCGGTTAGGCAGGGTT 59.525 50.000 0.00 0.00 0.00 4.11
357 360 0.475044 TGTTCGGTTAGGCAGGGTTT 59.525 50.000 0.00 0.00 0.00 3.27
358 361 0.879090 GTTCGGTTAGGCAGGGTTTG 59.121 55.000 0.00 0.00 0.00 2.93
359 362 0.250989 TTCGGTTAGGCAGGGTTTGG 60.251 55.000 0.00 0.00 0.00 3.28
360 363 1.128809 TCGGTTAGGCAGGGTTTGGA 61.129 55.000 0.00 0.00 0.00 3.53
361 364 0.676782 CGGTTAGGCAGGGTTTGGAG 60.677 60.000 0.00 0.00 0.00 3.86
362 365 0.696501 GGTTAGGCAGGGTTTGGAGA 59.303 55.000 0.00 0.00 0.00 3.71
363 366 1.340114 GGTTAGGCAGGGTTTGGAGAG 60.340 57.143 0.00 0.00 0.00 3.20
364 367 0.991920 TTAGGCAGGGTTTGGAGAGG 59.008 55.000 0.00 0.00 0.00 3.69
365 368 0.178873 TAGGCAGGGTTTGGAGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
366 369 1.068352 AGGCAGGGTTTGGAGAGGTT 61.068 55.000 0.00 0.00 0.00 3.50
367 370 0.178961 GGCAGGGTTTGGAGAGGTTT 60.179 55.000 0.00 0.00 0.00 3.27
368 371 0.961753 GCAGGGTTTGGAGAGGTTTG 59.038 55.000 0.00 0.00 0.00 2.93
369 372 1.478654 GCAGGGTTTGGAGAGGTTTGA 60.479 52.381 0.00 0.00 0.00 2.69
370 373 2.944129 CAGGGTTTGGAGAGGTTTGAA 58.056 47.619 0.00 0.00 0.00 2.69
371 374 3.295973 CAGGGTTTGGAGAGGTTTGAAA 58.704 45.455 0.00 0.00 0.00 2.69
372 375 3.319122 CAGGGTTTGGAGAGGTTTGAAAG 59.681 47.826 0.00 0.00 0.00 2.62
373 376 2.628178 GGGTTTGGAGAGGTTTGAAAGG 59.372 50.000 0.00 0.00 0.00 3.11
374 377 2.628178 GGTTTGGAGAGGTTTGAAAGGG 59.372 50.000 0.00 0.00 0.00 3.95
375 378 3.562182 GTTTGGAGAGGTTTGAAAGGGA 58.438 45.455 0.00 0.00 0.00 4.20
376 379 4.152647 GTTTGGAGAGGTTTGAAAGGGAT 58.847 43.478 0.00 0.00 0.00 3.85
377 380 4.469469 TTGGAGAGGTTTGAAAGGGATT 57.531 40.909 0.00 0.00 0.00 3.01
378 381 3.766545 TGGAGAGGTTTGAAAGGGATTG 58.233 45.455 0.00 0.00 0.00 2.67
379 382 3.092301 GGAGAGGTTTGAAAGGGATTGG 58.908 50.000 0.00 0.00 0.00 3.16
380 383 3.245264 GGAGAGGTTTGAAAGGGATTGGA 60.245 47.826 0.00 0.00 0.00 3.53
381 384 4.013050 GAGAGGTTTGAAAGGGATTGGAG 58.987 47.826 0.00 0.00 0.00 3.86
382 385 3.092301 GAGGTTTGAAAGGGATTGGAGG 58.908 50.000 0.00 0.00 0.00 4.30
383 386 2.179427 GGTTTGAAAGGGATTGGAGGG 58.821 52.381 0.00 0.00 0.00 4.30
384 387 2.179427 GTTTGAAAGGGATTGGAGGGG 58.821 52.381 0.00 0.00 0.00 4.79
385 388 1.766951 TTGAAAGGGATTGGAGGGGA 58.233 50.000 0.00 0.00 0.00 4.81
386 389 2.000290 TGAAAGGGATTGGAGGGGAT 58.000 50.000 0.00 0.00 0.00 3.85
387 390 2.297044 TGAAAGGGATTGGAGGGGATT 58.703 47.619 0.00 0.00 0.00 3.01
388 391 3.480012 TGAAAGGGATTGGAGGGGATTA 58.520 45.455 0.00 0.00 0.00 1.75
389 392 3.861695 TGAAAGGGATTGGAGGGGATTAA 59.138 43.478 0.00 0.00 0.00 1.40
390 393 4.296313 TGAAAGGGATTGGAGGGGATTAAA 59.704 41.667 0.00 0.00 0.00 1.52
391 394 5.042676 TGAAAGGGATTGGAGGGGATTAAAT 60.043 40.000 0.00 0.00 0.00 1.40
392 395 5.503605 AAGGGATTGGAGGGGATTAAATT 57.496 39.130 0.00 0.00 0.00 1.82
393 396 5.079998 AGGGATTGGAGGGGATTAAATTC 57.920 43.478 0.00 0.00 0.00 2.17
394 397 4.140686 AGGGATTGGAGGGGATTAAATTCC 60.141 45.833 0.00 0.00 34.83 3.01
395 398 4.140686 GGGATTGGAGGGGATTAAATTCCT 60.141 45.833 0.00 0.00 35.97 3.36
396 399 5.467738 GGATTGGAGGGGATTAAATTCCTT 58.532 41.667 0.00 0.00 35.97 3.36
397 400 5.305386 GGATTGGAGGGGATTAAATTCCTTG 59.695 44.000 0.00 0.00 35.97 3.61
398 401 3.642141 TGGAGGGGATTAAATTCCTTGC 58.358 45.455 0.00 0.00 35.97 4.01
399 402 3.012274 TGGAGGGGATTAAATTCCTTGCA 59.988 43.478 0.00 0.00 35.97 4.08
400 403 4.030216 GGAGGGGATTAAATTCCTTGCAA 58.970 43.478 0.00 0.00 35.97 4.08
401 404 4.100035 GGAGGGGATTAAATTCCTTGCAAG 59.900 45.833 19.93 19.93 35.97 4.01
402 405 4.687976 AGGGGATTAAATTCCTTGCAAGT 58.312 39.130 24.35 8.64 35.97 3.16
403 406 4.711846 AGGGGATTAAATTCCTTGCAAGTC 59.288 41.667 24.35 12.49 35.97 3.01
404 407 4.466015 GGGGATTAAATTCCTTGCAAGTCA 59.534 41.667 24.35 11.21 35.97 3.41
405 408 5.046663 GGGGATTAAATTCCTTGCAAGTCAA 60.047 40.000 24.35 16.56 35.97 3.18
406 409 6.463360 GGGATTAAATTCCTTGCAAGTCAAA 58.537 36.000 24.35 15.47 35.97 2.69
407 410 6.934083 GGGATTAAATTCCTTGCAAGTCAAAA 59.066 34.615 24.35 13.17 35.97 2.44
408 411 7.607607 GGGATTAAATTCCTTGCAAGTCAAAAT 59.392 33.333 24.35 14.96 35.97 1.82
409 412 8.659491 GGATTAAATTCCTTGCAAGTCAAAATC 58.341 33.333 24.35 20.70 33.65 2.17
410 413 7.961325 TTAAATTCCTTGCAAGTCAAAATCC 57.039 32.000 24.35 0.00 33.65 3.01
411 414 5.813513 AATTCCTTGCAAGTCAAAATCCT 57.186 34.783 24.35 3.37 33.65 3.24
412 415 5.813513 ATTCCTTGCAAGTCAAAATCCTT 57.186 34.783 24.35 0.00 33.65 3.36
413 416 4.589216 TCCTTGCAAGTCAAAATCCTTG 57.411 40.909 24.35 5.25 40.77 3.61
414 417 3.960102 TCCTTGCAAGTCAAAATCCTTGT 59.040 39.130 24.35 0.00 40.13 3.16
415 418 4.037923 TCCTTGCAAGTCAAAATCCTTGTC 59.962 41.667 24.35 0.00 40.13 3.18
416 419 4.202141 CCTTGCAAGTCAAAATCCTTGTCA 60.202 41.667 24.35 0.00 40.13 3.58
417 420 4.998671 TGCAAGTCAAAATCCTTGTCAA 57.001 36.364 0.00 0.00 40.13 3.18
418 421 5.336150 TGCAAGTCAAAATCCTTGTCAAA 57.664 34.783 0.00 0.00 40.13 2.69
419 422 5.108517 TGCAAGTCAAAATCCTTGTCAAAC 58.891 37.500 0.00 0.00 40.13 2.93
420 423 4.507756 GCAAGTCAAAATCCTTGTCAAACC 59.492 41.667 0.00 0.00 40.13 3.27
421 424 5.682212 GCAAGTCAAAATCCTTGTCAAACCT 60.682 40.000 0.00 0.00 40.13 3.50
422 425 5.774498 AGTCAAAATCCTTGTCAAACCTC 57.226 39.130 0.00 0.00 0.00 3.85
423 426 5.449553 AGTCAAAATCCTTGTCAAACCTCT 58.550 37.500 0.00 0.00 0.00 3.69
424 427 5.532779 AGTCAAAATCCTTGTCAAACCTCTC 59.467 40.000 0.00 0.00 0.00 3.20
425 428 4.827284 TCAAAATCCTTGTCAAACCTCTCC 59.173 41.667 0.00 0.00 0.00 3.71
426 429 4.453480 AAATCCTTGTCAAACCTCTCCA 57.547 40.909 0.00 0.00 0.00 3.86
427 430 4.453480 AATCCTTGTCAAACCTCTCCAA 57.547 40.909 0.00 0.00 0.00 3.53
428 431 4.664688 ATCCTTGTCAAACCTCTCCAAT 57.335 40.909 0.00 0.00 0.00 3.16
429 432 4.021102 TCCTTGTCAAACCTCTCCAATC 57.979 45.455 0.00 0.00 0.00 2.67
430 433 3.084786 CCTTGTCAAACCTCTCCAATCC 58.915 50.000 0.00 0.00 0.00 3.01
431 434 2.879103 TGTCAAACCTCTCCAATCCC 57.121 50.000 0.00 0.00 0.00 3.85
432 435 2.348472 TGTCAAACCTCTCCAATCCCT 58.652 47.619 0.00 0.00 0.00 4.20
433 436 2.040278 TGTCAAACCTCTCCAATCCCTG 59.960 50.000 0.00 0.00 0.00 4.45
434 437 2.040412 GTCAAACCTCTCCAATCCCTGT 59.960 50.000 0.00 0.00 0.00 4.00
435 438 2.040278 TCAAACCTCTCCAATCCCTGTG 59.960 50.000 0.00 0.00 0.00 3.66
436 439 0.995024 AACCTCTCCAATCCCTGTGG 59.005 55.000 0.00 0.00 37.51 4.17
437 440 1.225704 CCTCTCCAATCCCTGTGGC 59.774 63.158 0.00 0.00 35.99 5.01
438 441 1.153289 CTCTCCAATCCCTGTGGCG 60.153 63.158 0.00 0.00 35.99 5.69
439 442 1.612146 TCTCCAATCCCTGTGGCGA 60.612 57.895 0.00 0.00 35.99 5.54
440 443 1.153289 CTCCAATCCCTGTGGCGAG 60.153 63.158 0.00 0.00 35.99 5.03
441 444 2.124570 CCAATCCCTGTGGCGAGG 60.125 66.667 0.00 0.00 0.00 4.63
447 450 3.642078 CCTGTGGCGAGGGGATTA 58.358 61.111 0.00 0.00 0.00 1.75
448 451 1.912220 CCTGTGGCGAGGGGATTAA 59.088 57.895 0.00 0.00 0.00 1.40
449 452 0.254747 CCTGTGGCGAGGGGATTAAA 59.745 55.000 0.00 0.00 0.00 1.52
450 453 1.379527 CTGTGGCGAGGGGATTAAAC 58.620 55.000 0.00 0.00 0.00 2.01
451 454 0.391927 TGTGGCGAGGGGATTAAACG 60.392 55.000 0.00 0.00 0.00 3.60
452 455 0.108041 GTGGCGAGGGGATTAAACGA 60.108 55.000 0.00 0.00 0.00 3.85
453 456 0.614294 TGGCGAGGGGATTAAACGAA 59.386 50.000 0.00 0.00 0.00 3.85
454 457 1.012086 GGCGAGGGGATTAAACGAAC 58.988 55.000 0.00 0.00 0.00 3.95
455 458 1.676615 GGCGAGGGGATTAAACGAACA 60.677 52.381 0.00 0.00 0.00 3.18
456 459 1.664151 GCGAGGGGATTAAACGAACAG 59.336 52.381 0.00 0.00 0.00 3.16
457 460 2.277084 CGAGGGGATTAAACGAACAGG 58.723 52.381 0.00 0.00 0.00 4.00
458 461 2.640184 GAGGGGATTAAACGAACAGGG 58.360 52.381 0.00 0.00 0.00 4.45
459 462 1.100510 GGGGATTAAACGAACAGGGC 58.899 55.000 0.00 0.00 0.00 5.19
460 463 1.100510 GGGATTAAACGAACAGGGCC 58.899 55.000 0.00 0.00 0.00 5.80
461 464 1.340697 GGGATTAAACGAACAGGGCCT 60.341 52.381 0.00 0.00 0.00 5.19
462 465 2.092807 GGGATTAAACGAACAGGGCCTA 60.093 50.000 5.28 0.00 0.00 3.93
463 466 3.613030 GGATTAAACGAACAGGGCCTAA 58.387 45.455 5.28 0.00 0.00 2.69
545 548 0.907486 TGCTAGTGCCAGCAGATCTT 59.093 50.000 0.00 0.00 46.41 2.40
599 605 7.627298 ACTACACTAGTATACTTGTCACTGG 57.373 40.000 15.79 8.21 37.23 4.00
640 691 3.914645 TGGAGCCTACCAGCCAAA 58.085 55.556 0.00 0.00 34.77 3.28
641 692 1.685224 TGGAGCCTACCAGCCAAAG 59.315 57.895 0.00 0.00 34.77 2.77
743 794 3.960102 TGCCAATTATTCTCCCACCATTC 59.040 43.478 0.00 0.00 0.00 2.67
769 820 1.335872 GCTGATTGGTGGTTTGTTCCG 60.336 52.381 0.00 0.00 0.00 4.30
777 828 3.508793 TGGTGGTTTGTTCCGTTTGTTAA 59.491 39.130 0.00 0.00 0.00 2.01
836 887 0.908198 CCCTCTCTCCCTCCTTTGTG 59.092 60.000 0.00 0.00 0.00 3.33
837 888 1.650528 CCTCTCTCCCTCCTTTGTGT 58.349 55.000 0.00 0.00 0.00 3.72
847 898 2.632996 CCTCCTTTGTGTGTGTCCTCTA 59.367 50.000 0.00 0.00 0.00 2.43
878 929 5.543790 TCTCTGTCTGCATATAAATAGGCCA 59.456 40.000 5.01 0.00 39.14 5.36
879 930 5.551233 TCTGTCTGCATATAAATAGGCCAC 58.449 41.667 5.01 2.50 39.14 5.01
893 944 4.596585 CCACCCGGGGCAACTTGT 62.597 66.667 27.92 0.00 0.00 3.16
907 958 3.503748 GCAACTTGTTGCTGATAAGAGGT 59.496 43.478 25.56 0.00 44.15 3.85
939 990 2.495409 TGCACTGTCAAATTGCACAG 57.505 45.000 17.62 17.62 41.29 3.66
991 1042 2.545526 ACAGCTCGTGAGAAACATTGTG 59.454 45.455 0.00 0.00 41.32 3.33
1012 1063 2.352127 GCAAGCAAGATGGTCAAGGTTC 60.352 50.000 0.00 0.00 0.00 3.62
1063 1151 1.082756 GCTCAGTTTTGTGCGTCGG 60.083 57.895 0.00 0.00 34.54 4.79
1078 1166 1.325338 CGTCGGTCTGAACGTGTTTTT 59.675 47.619 15.48 0.00 0.00 1.94
1136 1224 0.690192 TTGGATGGCGAGAGGAACAA 59.310 50.000 0.00 0.00 0.00 2.83
1219 1307 9.334693 GATCATGACAAACAACAGTTTATCTTC 57.665 33.333 0.00 0.00 33.90 2.87
1221 1309 8.902806 TCATGACAAACAACAGTTTATCTTCTT 58.097 29.630 0.00 0.00 33.90 2.52
1228 1316 9.878599 AAACAACAGTTTATCTTCTTATGTTCG 57.121 29.630 0.00 0.00 33.90 3.95
1229 1317 8.603242 ACAACAGTTTATCTTCTTATGTTCGT 57.397 30.769 0.00 0.00 0.00 3.85
1239 1355 8.842358 ATCTTCTTATGTTCGTTGGTTCTTAA 57.158 30.769 0.00 0.00 0.00 1.85
1243 1359 7.218614 TCTTATGTTCGTTGGTTCTTAAAGGA 58.781 34.615 0.00 0.00 0.00 3.36
1258 1380 7.324388 TCTTAAAGGAAGGTGGTGAATTCTA 57.676 36.000 7.05 0.00 35.67 2.10
1263 1385 3.009143 GGAAGGTGGTGAATTCTACAGGT 59.991 47.826 7.05 0.00 0.00 4.00
1359 1481 3.458163 CTCCGGCGCAACCTAGGA 61.458 66.667 17.98 6.76 35.61 2.94
1437 1580 1.435577 GCTACGGCGGAGAAAAGAAA 58.564 50.000 26.08 0.00 0.00 2.52
1584 1751 1.895238 GTCCTACCCTGCTTACGCA 59.105 57.895 0.00 0.00 45.60 5.24
1655 1830 0.389426 GCTAAGGTGCCGACGAGAAA 60.389 55.000 0.00 0.00 0.00 2.52
1679 1854 3.090037 CTCGGGGAGACTCAAAGACTTA 58.910 50.000 4.53 0.00 0.00 2.24
1686 1861 4.081917 GGAGACTCAAAGACTTAGTCCAGG 60.082 50.000 8.96 0.00 40.42 4.45
1687 1862 4.742012 AGACTCAAAGACTTAGTCCAGGA 58.258 43.478 8.96 3.32 40.42 3.86
1688 1863 4.525100 AGACTCAAAGACTTAGTCCAGGAC 59.475 45.833 12.25 12.25 40.42 3.85
1689 1864 4.223953 ACTCAAAGACTTAGTCCAGGACA 58.776 43.478 22.31 5.02 34.60 4.02
1690 1865 4.654262 ACTCAAAGACTTAGTCCAGGACAA 59.346 41.667 22.31 12.36 34.60 3.18
1722 1897 9.428097 GCTTTCATTTCAAAATAAGTTCAGGAT 57.572 29.630 0.00 0.00 0.00 3.24
1754 1929 2.964740 TCCTGAACTGATCAAGCGAAG 58.035 47.619 0.00 0.00 37.67 3.79
1773 1948 4.800993 CGAAGTACGATGAAGCAAGAGATT 59.199 41.667 0.00 0.00 45.77 2.40
1774 1949 5.971792 CGAAGTACGATGAAGCAAGAGATTA 59.028 40.000 0.00 0.00 45.77 1.75
1818 1993 5.232202 CGTACATGTACATAGCTTGTGGAAG 59.768 44.000 30.17 9.45 39.48 3.46
1865 2040 1.346068 AGGGCTTCAGTTCAGAGTGTC 59.654 52.381 0.00 0.00 0.00 3.67
1879 2054 2.628657 AGAGTGTCCTAGTGTTGTGGTC 59.371 50.000 0.00 0.00 0.00 4.02
1951 2127 0.525242 TGCGCAAAAGCACACTGAAC 60.525 50.000 8.16 0.00 42.92 3.18
1956 2132 3.000773 CGCAAAAGCACACTGAACTTTTC 60.001 43.478 9.43 6.10 40.63 2.29
2003 2180 3.568007 TCATTGCAGTACAAAGAACACCC 59.432 43.478 0.00 0.00 42.86 4.61
2033 2226 0.963962 AAAGACCACCTAGCGACGAA 59.036 50.000 0.00 0.00 0.00 3.85
2067 2260 3.386867 GAGTTGAAGGCATGCCGCG 62.387 63.158 30.50 0.00 43.84 6.46
2068 2261 3.737172 GTTGAAGGCATGCCGCGT 61.737 61.111 30.50 19.91 43.84 6.01
2072 2266 3.294493 AAGGCATGCCGCGTTGTT 61.294 55.556 30.50 15.71 46.57 2.83
2087 2281 4.410400 GTTGCCCCTCCCTCACCG 62.410 72.222 0.00 0.00 0.00 4.94
2109 2303 2.794350 GAGCCGGACAAAATTTGTTGTG 59.206 45.455 13.00 5.98 45.52 3.33
2126 2320 1.154197 GTGGTAGACGGTTGGAAAGC 58.846 55.000 0.00 0.00 41.84 3.51
2157 2351 2.360350 CCGGCAAGACCAGTGCAT 60.360 61.111 0.00 0.00 44.07 3.96
2165 2359 2.880268 CAAGACCAGTGCATCAGAACAA 59.120 45.455 0.00 0.00 0.00 2.83
2188 2382 4.142271 ACAACCGTTGCTGATGAAGAAAAA 60.142 37.500 11.29 0.00 0.00 1.94
2190 2384 5.957842 ACCGTTGCTGATGAAGAAAAATA 57.042 34.783 0.00 0.00 0.00 1.40
2235 2429 4.322080 AGACACATGAAACGAAGACTGA 57.678 40.909 0.00 0.00 0.00 3.41
2248 2442 4.629200 ACGAAGACTGAATTCAAGCAGATC 59.371 41.667 9.88 3.13 36.07 2.75
2261 2455 5.377478 TCAAGCAGATCTATCGAAGACCTA 58.623 41.667 0.00 0.00 42.51 3.08
2276 2470 6.015688 TCGAAGACCTACACTAACTGAATTGT 60.016 38.462 0.00 0.00 0.00 2.71
2304 2498 0.523966 CGTCAGAGACAGACCTCCAC 59.476 60.000 0.00 0.00 33.76 4.02
2305 2499 1.621992 GTCAGAGACAGACCTCCACA 58.378 55.000 0.00 0.00 33.76 4.17
2306 2500 1.271102 GTCAGAGACAGACCTCCACAC 59.729 57.143 0.00 0.00 33.76 3.82
2307 2501 0.242286 CAGAGACAGACCTCCACACG 59.758 60.000 0.00 0.00 33.76 4.49
2308 2502 1.080434 GAGACAGACCTCCACACGC 60.080 63.158 0.00 0.00 0.00 5.34
2309 2503 2.048127 GACAGACCTCCACACGCC 60.048 66.667 0.00 0.00 0.00 5.68
2310 2504 3.591254 GACAGACCTCCACACGCCC 62.591 68.421 0.00 0.00 0.00 6.13
2311 2505 3.314331 CAGACCTCCACACGCCCT 61.314 66.667 0.00 0.00 0.00 5.19
2312 2506 2.997897 AGACCTCCACACGCCCTC 60.998 66.667 0.00 0.00 0.00 4.30
2313 2507 4.083862 GACCTCCACACGCCCTCC 62.084 72.222 0.00 0.00 0.00 4.30
2314 2508 4.954118 ACCTCCACACGCCCTCCA 62.954 66.667 0.00 0.00 0.00 3.86
2315 2509 3.636231 CCTCCACACGCCCTCCAA 61.636 66.667 0.00 0.00 0.00 3.53
2316 2510 2.358737 CTCCACACGCCCTCCAAC 60.359 66.667 0.00 0.00 0.00 3.77
2317 2511 3.164977 TCCACACGCCCTCCAACA 61.165 61.111 0.00 0.00 0.00 3.33
2318 2512 2.203280 CCACACGCCCTCCAACAA 60.203 61.111 0.00 0.00 0.00 2.83
2319 2513 1.603455 CCACACGCCCTCCAACAAT 60.603 57.895 0.00 0.00 0.00 2.71
2320 2514 1.580942 CACACGCCCTCCAACAATG 59.419 57.895 0.00 0.00 0.00 2.82
2321 2515 2.268076 ACACGCCCTCCAACAATGC 61.268 57.895 0.00 0.00 0.00 3.56
2322 2516 1.973281 CACGCCCTCCAACAATGCT 60.973 57.895 0.00 0.00 0.00 3.79
2323 2517 0.676466 CACGCCCTCCAACAATGCTA 60.676 55.000 0.00 0.00 0.00 3.49
2324 2518 0.037590 ACGCCCTCCAACAATGCTAA 59.962 50.000 0.00 0.00 0.00 3.09
2325 2519 1.173043 CGCCCTCCAACAATGCTAAA 58.827 50.000 0.00 0.00 0.00 1.85
2326 2520 1.750778 CGCCCTCCAACAATGCTAAAT 59.249 47.619 0.00 0.00 0.00 1.40
2327 2521 2.480073 CGCCCTCCAACAATGCTAAATG 60.480 50.000 0.00 0.00 0.00 2.32
2328 2522 2.739609 GCCCTCCAACAATGCTAAATGC 60.740 50.000 0.00 0.00 43.25 3.56
2338 2532 3.557207 GCTAAATGCATTGCCGAGG 57.443 52.632 13.82 1.45 42.31 4.63
2375 2604 6.388100 TGAGGAGAAACTTATCCCATCTTCAT 59.612 38.462 0.00 0.00 39.36 2.57
2406 2641 1.139058 CGGCCTCACCTTACTAAGCAT 59.861 52.381 0.00 0.00 35.61 3.79
2415 2651 5.700832 TCACCTTACTAAGCATGACACAAAG 59.299 40.000 0.00 0.00 0.00 2.77
2492 2728 4.394712 GGGTCCACCACGCCTCAG 62.395 72.222 0.00 0.00 39.85 3.35
2493 2729 3.626924 GGTCCACCACGCCTCAGT 61.627 66.667 0.00 0.00 35.64 3.41
2515 2751 1.208165 CCCTAGGGCCACCAAAGACT 61.208 60.000 16.90 0.00 40.13 3.24
2567 2806 0.324943 TTTCTTTGGAGAGGAGGCGG 59.675 55.000 0.00 0.00 32.44 6.13
2573 2812 4.200283 GAGAGGAGGCGGCGACTG 62.200 72.222 25.55 0.00 0.00 3.51
2596 2835 6.568869 TGTGTAAAGCAACATGTTAAAAGCT 58.431 32.000 11.53 12.82 0.00 3.74
2597 2836 6.695278 TGTGTAAAGCAACATGTTAAAAGCTC 59.305 34.615 18.28 9.28 0.00 4.09
2600 2839 8.572185 TGTAAAGCAACATGTTAAAAGCTCATA 58.428 29.630 18.28 12.90 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.128764 GCCGTCAAGGGAAAAATAAGAGG 59.871 47.826 0.00 0.00 41.48 3.69
124 125 1.069906 GCTGCTGTGTACGTTTTCCTG 60.070 52.381 0.00 0.00 0.00 3.86
127 128 2.412847 GGATGCTGCTGTGTACGTTTTC 60.413 50.000 0.00 0.00 0.00 2.29
172 174 1.626654 CGGTCGAGTGGCATGTTCAC 61.627 60.000 11.64 11.64 35.51 3.18
335 338 0.676782 CCCTGCCTAACCGAACAAGG 60.677 60.000 0.00 0.00 37.30 3.61
336 339 0.036306 ACCCTGCCTAACCGAACAAG 59.964 55.000 0.00 0.00 0.00 3.16
337 340 0.475044 AACCCTGCCTAACCGAACAA 59.525 50.000 0.00 0.00 0.00 2.83
338 341 0.475044 AAACCCTGCCTAACCGAACA 59.525 50.000 0.00 0.00 0.00 3.18
339 342 0.879090 CAAACCCTGCCTAACCGAAC 59.121 55.000 0.00 0.00 0.00 3.95
340 343 0.250989 CCAAACCCTGCCTAACCGAA 60.251 55.000 0.00 0.00 0.00 4.30
341 344 1.128809 TCCAAACCCTGCCTAACCGA 61.129 55.000 0.00 0.00 0.00 4.69
342 345 0.676782 CTCCAAACCCTGCCTAACCG 60.677 60.000 0.00 0.00 0.00 4.44
343 346 0.696501 TCTCCAAACCCTGCCTAACC 59.303 55.000 0.00 0.00 0.00 2.85
344 347 1.340114 CCTCTCCAAACCCTGCCTAAC 60.340 57.143 0.00 0.00 0.00 2.34
345 348 0.991920 CCTCTCCAAACCCTGCCTAA 59.008 55.000 0.00 0.00 0.00 2.69
346 349 0.178873 ACCTCTCCAAACCCTGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
347 350 1.068352 AACCTCTCCAAACCCTGCCT 61.068 55.000 0.00 0.00 0.00 4.75
348 351 0.178961 AAACCTCTCCAAACCCTGCC 60.179 55.000 0.00 0.00 0.00 4.85
349 352 0.961753 CAAACCTCTCCAAACCCTGC 59.038 55.000 0.00 0.00 0.00 4.85
350 353 2.656947 TCAAACCTCTCCAAACCCTG 57.343 50.000 0.00 0.00 0.00 4.45
351 354 3.566351 CTTTCAAACCTCTCCAAACCCT 58.434 45.455 0.00 0.00 0.00 4.34
352 355 2.628178 CCTTTCAAACCTCTCCAAACCC 59.372 50.000 0.00 0.00 0.00 4.11
353 356 2.628178 CCCTTTCAAACCTCTCCAAACC 59.372 50.000 0.00 0.00 0.00 3.27
354 357 3.562182 TCCCTTTCAAACCTCTCCAAAC 58.438 45.455 0.00 0.00 0.00 2.93
355 358 3.963476 TCCCTTTCAAACCTCTCCAAA 57.037 42.857 0.00 0.00 0.00 3.28
356 359 4.151883 CAATCCCTTTCAAACCTCTCCAA 58.848 43.478 0.00 0.00 0.00 3.53
357 360 3.500289 CCAATCCCTTTCAAACCTCTCCA 60.500 47.826 0.00 0.00 0.00 3.86
358 361 3.092301 CCAATCCCTTTCAAACCTCTCC 58.908 50.000 0.00 0.00 0.00 3.71
359 362 4.013050 CTCCAATCCCTTTCAAACCTCTC 58.987 47.826 0.00 0.00 0.00 3.20
360 363 3.245407 CCTCCAATCCCTTTCAAACCTCT 60.245 47.826 0.00 0.00 0.00 3.69
361 364 3.092301 CCTCCAATCCCTTTCAAACCTC 58.908 50.000 0.00 0.00 0.00 3.85
362 365 2.225369 CCCTCCAATCCCTTTCAAACCT 60.225 50.000 0.00 0.00 0.00 3.50
363 366 2.179427 CCCTCCAATCCCTTTCAAACC 58.821 52.381 0.00 0.00 0.00 3.27
364 367 2.179427 CCCCTCCAATCCCTTTCAAAC 58.821 52.381 0.00 0.00 0.00 2.93
365 368 2.077803 TCCCCTCCAATCCCTTTCAAA 58.922 47.619 0.00 0.00 0.00 2.69
366 369 1.766951 TCCCCTCCAATCCCTTTCAA 58.233 50.000 0.00 0.00 0.00 2.69
367 370 2.000290 ATCCCCTCCAATCCCTTTCA 58.000 50.000 0.00 0.00 0.00 2.69
368 371 4.536295 TTAATCCCCTCCAATCCCTTTC 57.464 45.455 0.00 0.00 0.00 2.62
369 372 4.984642 TTTAATCCCCTCCAATCCCTTT 57.015 40.909 0.00 0.00 0.00 3.11
370 373 5.467738 GAATTTAATCCCCTCCAATCCCTT 58.532 41.667 0.00 0.00 0.00 3.95
371 374 4.140686 GGAATTTAATCCCCTCCAATCCCT 60.141 45.833 0.00 0.00 33.05 4.20
372 375 4.140686 AGGAATTTAATCCCCTCCAATCCC 60.141 45.833 0.00 0.00 40.59 3.85
373 376 5.079998 AGGAATTTAATCCCCTCCAATCC 57.920 43.478 0.00 0.00 40.59 3.01
374 377 5.221521 GCAAGGAATTTAATCCCCTCCAATC 60.222 44.000 0.53 0.00 40.59 2.67
375 378 4.655649 GCAAGGAATTTAATCCCCTCCAAT 59.344 41.667 0.53 0.00 40.59 3.16
376 379 4.030216 GCAAGGAATTTAATCCCCTCCAA 58.970 43.478 0.53 0.00 40.59 3.53
377 380 3.012274 TGCAAGGAATTTAATCCCCTCCA 59.988 43.478 0.00 0.03 40.59 3.86
378 381 3.642141 TGCAAGGAATTTAATCCCCTCC 58.358 45.455 0.00 0.00 40.59 4.30
379 382 4.711846 ACTTGCAAGGAATTTAATCCCCTC 59.288 41.667 29.18 0.00 40.59 4.30
380 383 4.687976 ACTTGCAAGGAATTTAATCCCCT 58.312 39.130 29.18 0.93 40.59 4.79
381 384 4.466015 TGACTTGCAAGGAATTTAATCCCC 59.534 41.667 29.18 3.92 40.59 4.81
382 385 5.659440 TGACTTGCAAGGAATTTAATCCC 57.341 39.130 29.18 5.19 40.59 3.85
383 386 7.961325 TTTTGACTTGCAAGGAATTTAATCC 57.039 32.000 29.18 6.57 37.87 3.01
384 387 8.659491 GGATTTTGACTTGCAAGGAATTTAATC 58.341 33.333 29.18 23.91 37.87 1.75
385 388 8.377799 AGGATTTTGACTTGCAAGGAATTTAAT 58.622 29.630 29.18 18.73 37.87 1.40
386 389 7.734942 AGGATTTTGACTTGCAAGGAATTTAA 58.265 30.769 29.18 15.31 37.87 1.52
387 390 7.301868 AGGATTTTGACTTGCAAGGAATTTA 57.698 32.000 29.18 11.01 37.87 1.40
388 391 6.178607 AGGATTTTGACTTGCAAGGAATTT 57.821 33.333 29.18 8.87 37.87 1.82
389 392 5.813513 AGGATTTTGACTTGCAAGGAATT 57.186 34.783 29.18 16.15 37.87 2.17
390 393 5.070847 ACAAGGATTTTGACTTGCAAGGAAT 59.929 36.000 29.18 21.01 46.03 3.01
391 394 4.405358 ACAAGGATTTTGACTTGCAAGGAA 59.595 37.500 29.18 18.39 46.03 3.36
392 395 3.960102 ACAAGGATTTTGACTTGCAAGGA 59.040 39.130 29.18 13.46 46.03 3.36
393 396 4.202141 TGACAAGGATTTTGACTTGCAAGG 60.202 41.667 29.18 12.28 46.03 3.61
394 397 4.935702 TGACAAGGATTTTGACTTGCAAG 58.064 39.130 24.84 24.84 46.03 4.01
395 398 4.998671 TGACAAGGATTTTGACTTGCAA 57.001 36.364 0.00 0.00 46.03 4.08
396 399 4.998671 TTGACAAGGATTTTGACTTGCA 57.001 36.364 4.48 0.00 46.03 4.08
397 400 4.507756 GGTTTGACAAGGATTTTGACTTGC 59.492 41.667 4.48 0.00 46.03 4.01
399 402 5.893824 AGAGGTTTGACAAGGATTTTGACTT 59.106 36.000 0.00 0.00 0.00 3.01
400 403 5.449553 AGAGGTTTGACAAGGATTTTGACT 58.550 37.500 0.00 0.00 0.00 3.41
401 404 5.278512 GGAGAGGTTTGACAAGGATTTTGAC 60.279 44.000 0.00 0.00 0.00 3.18
402 405 4.827284 GGAGAGGTTTGACAAGGATTTTGA 59.173 41.667 0.00 0.00 0.00 2.69
403 406 4.584325 TGGAGAGGTTTGACAAGGATTTTG 59.416 41.667 0.00 0.00 0.00 2.44
404 407 4.803452 TGGAGAGGTTTGACAAGGATTTT 58.197 39.130 0.00 0.00 0.00 1.82
405 408 4.453480 TGGAGAGGTTTGACAAGGATTT 57.547 40.909 0.00 0.00 0.00 2.17
406 409 4.453480 TTGGAGAGGTTTGACAAGGATT 57.547 40.909 0.00 0.00 0.00 3.01
407 410 4.568592 GGATTGGAGAGGTTTGACAAGGAT 60.569 45.833 0.00 0.00 0.00 3.24
408 411 3.244911 GGATTGGAGAGGTTTGACAAGGA 60.245 47.826 0.00 0.00 0.00 3.36
409 412 3.084786 GGATTGGAGAGGTTTGACAAGG 58.915 50.000 0.00 0.00 0.00 3.61
410 413 3.084786 GGGATTGGAGAGGTTTGACAAG 58.915 50.000 0.00 0.00 0.00 3.16
411 414 2.716424 AGGGATTGGAGAGGTTTGACAA 59.284 45.455 0.00 0.00 0.00 3.18
412 415 2.040278 CAGGGATTGGAGAGGTTTGACA 59.960 50.000 0.00 0.00 0.00 3.58
413 416 2.040412 ACAGGGATTGGAGAGGTTTGAC 59.960 50.000 0.00 0.00 0.00 3.18
414 417 2.040278 CACAGGGATTGGAGAGGTTTGA 59.960 50.000 0.00 0.00 0.00 2.69
415 418 2.440409 CACAGGGATTGGAGAGGTTTG 58.560 52.381 0.00 0.00 0.00 2.93
416 419 1.355720 CCACAGGGATTGGAGAGGTTT 59.644 52.381 0.00 0.00 36.02 3.27
417 420 0.995024 CCACAGGGATTGGAGAGGTT 59.005 55.000 0.00 0.00 36.02 3.50
418 421 1.566298 GCCACAGGGATTGGAGAGGT 61.566 60.000 0.00 0.00 36.02 3.85
419 422 1.225704 GCCACAGGGATTGGAGAGG 59.774 63.158 0.00 0.00 36.02 3.69
420 423 1.153289 CGCCACAGGGATTGGAGAG 60.153 63.158 0.00 0.00 36.07 3.20
421 424 1.612146 TCGCCACAGGGATTGGAGA 60.612 57.895 0.00 0.00 40.27 3.71
422 425 1.153289 CTCGCCACAGGGATTGGAG 60.153 63.158 0.00 0.00 36.02 3.86
423 426 2.669133 CCTCGCCACAGGGATTGGA 61.669 63.158 0.00 0.00 36.02 3.53
424 427 2.124570 CCTCGCCACAGGGATTGG 60.125 66.667 0.00 0.00 35.59 3.16
430 433 0.254747 TTTAATCCCCTCGCCACAGG 59.745 55.000 0.00 0.00 0.00 4.00
431 434 1.379527 GTTTAATCCCCTCGCCACAG 58.620 55.000 0.00 0.00 0.00 3.66
432 435 0.391927 CGTTTAATCCCCTCGCCACA 60.392 55.000 0.00 0.00 0.00 4.17
433 436 0.108041 TCGTTTAATCCCCTCGCCAC 60.108 55.000 0.00 0.00 0.00 5.01
434 437 0.614294 TTCGTTTAATCCCCTCGCCA 59.386 50.000 0.00 0.00 0.00 5.69
435 438 1.012086 GTTCGTTTAATCCCCTCGCC 58.988 55.000 0.00 0.00 0.00 5.54
436 439 1.664151 CTGTTCGTTTAATCCCCTCGC 59.336 52.381 0.00 0.00 0.00 5.03
437 440 2.277084 CCTGTTCGTTTAATCCCCTCG 58.723 52.381 0.00 0.00 0.00 4.63
438 441 2.640184 CCCTGTTCGTTTAATCCCCTC 58.360 52.381 0.00 0.00 0.00 4.30
439 442 1.340697 GCCCTGTTCGTTTAATCCCCT 60.341 52.381 0.00 0.00 0.00 4.79
440 443 1.100510 GCCCTGTTCGTTTAATCCCC 58.899 55.000 0.00 0.00 0.00 4.81
441 444 1.100510 GGCCCTGTTCGTTTAATCCC 58.899 55.000 0.00 0.00 0.00 3.85
442 445 2.124277 AGGCCCTGTTCGTTTAATCC 57.876 50.000 0.00 0.00 0.00 3.01
443 446 4.939439 TCTTTAGGCCCTGTTCGTTTAATC 59.061 41.667 0.00 0.00 0.00 1.75
444 447 4.913784 TCTTTAGGCCCTGTTCGTTTAAT 58.086 39.130 0.00 0.00 0.00 1.40
445 448 4.202388 ACTCTTTAGGCCCTGTTCGTTTAA 60.202 41.667 0.00 0.00 0.00 1.52
446 449 3.325716 ACTCTTTAGGCCCTGTTCGTTTA 59.674 43.478 0.00 0.00 0.00 2.01
447 450 2.105993 ACTCTTTAGGCCCTGTTCGTTT 59.894 45.455 0.00 0.00 0.00 3.60
448 451 1.697982 ACTCTTTAGGCCCTGTTCGTT 59.302 47.619 0.00 0.00 0.00 3.85
449 452 1.349067 ACTCTTTAGGCCCTGTTCGT 58.651 50.000 0.00 0.00 0.00 3.85
450 453 2.347731 GAACTCTTTAGGCCCTGTTCG 58.652 52.381 0.00 0.00 0.00 3.95
451 454 2.039879 TGGAACTCTTTAGGCCCTGTTC 59.960 50.000 0.00 5.41 34.74 3.18
452 455 2.062636 TGGAACTCTTTAGGCCCTGTT 58.937 47.619 0.00 0.00 0.00 3.16
453 456 1.742308 TGGAACTCTTTAGGCCCTGT 58.258 50.000 0.00 0.00 0.00 4.00
454 457 2.239654 TCATGGAACTCTTTAGGCCCTG 59.760 50.000 0.00 0.00 0.00 4.45
455 458 2.562296 TCATGGAACTCTTTAGGCCCT 58.438 47.619 0.00 0.00 0.00 5.19
456 459 3.117888 TCATCATGGAACTCTTTAGGCCC 60.118 47.826 0.00 0.00 0.00 5.80
457 460 4.133078 CTCATCATGGAACTCTTTAGGCC 58.867 47.826 0.00 0.00 0.00 5.19
458 461 3.563390 GCTCATCATGGAACTCTTTAGGC 59.437 47.826 0.00 0.00 0.00 3.93
459 462 5.033589 AGCTCATCATGGAACTCTTTAGG 57.966 43.478 0.00 0.00 0.00 2.69
460 463 6.815089 AGTAGCTCATCATGGAACTCTTTAG 58.185 40.000 0.00 0.00 0.00 1.85
461 464 6.798427 AGTAGCTCATCATGGAACTCTTTA 57.202 37.500 0.00 0.00 0.00 1.85
462 465 5.690464 AGTAGCTCATCATGGAACTCTTT 57.310 39.130 0.00 0.00 0.00 2.52
463 466 6.382570 ACTTAGTAGCTCATCATGGAACTCTT 59.617 38.462 0.00 0.00 0.00 2.85
545 548 6.496565 AGAGAAACAGAGAAGATCTTCCTCAA 59.503 38.462 28.01 0.00 40.33 3.02
559 562 8.038944 ACTAGTGTAGTAGAGAGAGAAACAGAG 58.961 40.741 0.00 0.00 37.23 3.35
599 605 4.730487 AGACATGTCTGGCTTGGC 57.270 55.556 27.37 0.00 37.52 4.52
636 687 0.443869 CGTCGAGTGATTGGCTTTGG 59.556 55.000 0.00 0.00 0.00 3.28
637 688 1.148310 ACGTCGAGTGATTGGCTTTG 58.852 50.000 0.00 0.00 0.00 2.77
638 689 1.531149 CAACGTCGAGTGATTGGCTTT 59.469 47.619 0.00 0.00 0.00 3.51
639 690 1.148310 CAACGTCGAGTGATTGGCTT 58.852 50.000 0.00 0.00 0.00 4.35
640 691 0.317160 TCAACGTCGAGTGATTGGCT 59.683 50.000 0.00 0.00 0.00 4.75
641 692 0.716108 CTCAACGTCGAGTGATTGGC 59.284 55.000 0.00 0.00 0.00 4.52
743 794 1.331214 AACCACCAATCAGCCAACAG 58.669 50.000 0.00 0.00 0.00 3.16
769 820 8.657729 GGCTATAGAGACAGAAAGTTAACAAAC 58.342 37.037 8.61 0.00 0.00 2.93
777 828 4.339814 CGGAAGGCTATAGAGACAGAAAGT 59.660 45.833 3.21 0.00 30.20 2.66
836 887 4.873827 CAGAGAGTAGAGTAGAGGACACAC 59.126 50.000 0.00 0.00 0.00 3.82
837 888 4.532916 ACAGAGAGTAGAGTAGAGGACACA 59.467 45.833 0.00 0.00 0.00 3.72
847 898 8.704849 ATTTATATGCAGACAGAGAGTAGAGT 57.295 34.615 0.00 0.00 0.00 3.24
878 929 2.520741 CAACAAGTTGCCCCGGGT 60.521 61.111 21.85 0.00 33.45 5.28
886 937 5.934625 ACTACCTCTTATCAGCAACAAGTTG 59.065 40.000 8.53 8.53 43.14 3.16
888 939 5.746990 ACTACCTCTTATCAGCAACAAGT 57.253 39.130 0.00 0.00 0.00 3.16
893 944 5.201243 TGAGCTACTACCTCTTATCAGCAA 58.799 41.667 0.00 0.00 0.00 3.91
907 958 3.763897 TGACAGTGCAAGATGAGCTACTA 59.236 43.478 0.00 0.00 0.00 1.82
939 990 1.002544 AGCTTGTCAGTAGAGTTGCCC 59.997 52.381 0.00 0.00 0.00 5.36
991 1042 1.251251 ACCTTGACCATCTTGCTTGC 58.749 50.000 0.00 0.00 0.00 4.01
1063 1151 3.181510 ACAGAGCAAAAACACGTTCAGAC 60.182 43.478 0.00 0.00 0.00 3.51
1219 1307 7.429636 TCCTTTAAGAACCAACGAACATAAG 57.570 36.000 0.00 0.00 0.00 1.73
1221 1309 6.428771 CCTTCCTTTAAGAACCAACGAACATA 59.571 38.462 0.00 0.00 37.38 2.29
1224 1312 4.577693 ACCTTCCTTTAAGAACCAACGAAC 59.422 41.667 0.00 0.00 37.38 3.95
1225 1313 4.577283 CACCTTCCTTTAAGAACCAACGAA 59.423 41.667 0.00 0.00 37.38 3.85
1226 1314 4.131596 CACCTTCCTTTAAGAACCAACGA 58.868 43.478 0.00 0.00 37.38 3.85
1227 1315 3.252458 CCACCTTCCTTTAAGAACCAACG 59.748 47.826 0.00 0.00 37.38 4.10
1228 1316 4.037565 CACCACCTTCCTTTAAGAACCAAC 59.962 45.833 0.00 0.00 37.38 3.77
1229 1317 4.079672 TCACCACCTTCCTTTAAGAACCAA 60.080 41.667 0.00 0.00 37.38 3.67
1239 1355 4.263506 CCTGTAGAATTCACCACCTTCCTT 60.264 45.833 8.44 0.00 0.00 3.36
1243 1359 3.394606 ACACCTGTAGAATTCACCACCTT 59.605 43.478 8.44 0.00 0.00 3.50
1258 1380 2.048222 CGCGGATGTCACACCTGT 60.048 61.111 0.00 0.00 0.00 4.00
1263 1385 2.019408 CAACGTCGCGGATGTCACA 61.019 57.895 6.13 0.00 29.72 3.58
1352 1474 0.537653 GAGCTCGGCTTTTCCTAGGT 59.462 55.000 9.08 0.00 39.88 3.08
1437 1580 1.514553 GTAGCCGTAGCCGTCCTTT 59.485 57.895 0.00 0.00 41.25 3.11
1477 1620 0.250553 TTACCCTTGGTGTCCTTGCG 60.251 55.000 0.00 0.00 36.19 4.85
1486 1629 1.479368 TAACCGCCGTTACCCTTGGT 61.479 55.000 0.00 0.00 40.16 3.67
1655 1830 0.610687 CTTTGAGTCTCCCCGAGCTT 59.389 55.000 0.00 0.00 0.00 3.74
1679 1854 1.428869 AGCTTGTCTTGTCCTGGACT 58.571 50.000 26.03 1.01 33.15 3.85
1686 1861 7.524294 TTTTGAAATGAAAGCTTGTCTTGTC 57.476 32.000 0.00 4.13 34.67 3.18
1687 1862 9.598517 TTATTTTGAAATGAAAGCTTGTCTTGT 57.401 25.926 0.00 0.00 34.67 3.16
1689 1864 9.822185 ACTTATTTTGAAATGAAAGCTTGTCTT 57.178 25.926 0.00 0.00 36.34 3.01
1690 1865 9.822185 AACTTATTTTGAAATGAAAGCTTGTCT 57.178 25.926 0.00 0.00 0.00 3.41
1724 1899 5.431765 TGATCAGTTCAGGATTTCTAAGCC 58.568 41.667 0.00 0.00 37.16 4.35
1754 1929 5.174761 CAGCTAATCTCTTGCTTCATCGTAC 59.825 44.000 0.00 0.00 34.51 3.67
1818 1993 0.520404 CAGACAACCACTGCAGATGC 59.480 55.000 23.35 9.55 42.50 3.91
1865 2040 1.202639 TGCACAGACCACAACACTAGG 60.203 52.381 0.00 0.00 0.00 3.02
1879 2054 3.553508 CCACCCTTTTCAATCTTGCACAG 60.554 47.826 0.00 0.00 0.00 3.66
1995 2172 6.373495 GGTCTTTTTATTACATCGGGTGTTCT 59.627 38.462 0.00 0.00 42.29 3.01
2003 2180 6.292168 CGCTAGGTGGTCTTTTTATTACATCG 60.292 42.308 0.00 0.00 0.00 3.84
2033 2226 6.372659 CCTTCAACTCACTTTAGTGCATGTAT 59.627 38.462 5.00 0.00 45.25 2.29
2067 2260 1.603739 GTGAGGGAGGGGCAACAAC 60.604 63.158 0.00 0.00 39.74 3.32
2068 2261 2.840753 GGTGAGGGAGGGGCAACAA 61.841 63.158 0.00 0.00 39.74 2.83
2087 2281 2.223947 ACAACAAATTTTGTCCGGCTCC 60.224 45.455 14.80 0.00 44.59 4.70
2109 2303 1.017701 CGGCTTTCCAACCGTCTACC 61.018 60.000 0.00 0.00 44.46 3.18
2165 2359 2.254546 TCTTCATCAGCAACGGTTGT 57.745 45.000 20.92 6.46 0.00 3.32
2235 2429 7.014711 TAGGTCTTCGATAGATCTGCTTGAATT 59.985 37.037 16.08 0.00 44.25 2.17
2248 2442 6.922247 TCAGTTAGTGTAGGTCTTCGATAG 57.078 41.667 0.00 0.00 0.00 2.08
2261 2455 6.535150 CGGATATCACACAATTCAGTTAGTGT 59.465 38.462 4.83 0.00 45.29 3.55
2276 2470 3.886123 TCTGTCTCTGACGGATATCACA 58.114 45.455 4.83 1.12 42.21 3.58
2304 2498 0.676466 TAGCATTGTTGGAGGGCGTG 60.676 55.000 0.00 0.00 0.00 5.34
2305 2499 0.037590 TTAGCATTGTTGGAGGGCGT 59.962 50.000 0.00 0.00 0.00 5.68
2306 2500 1.173043 TTTAGCATTGTTGGAGGGCG 58.827 50.000 0.00 0.00 0.00 6.13
2307 2501 2.739609 GCATTTAGCATTGTTGGAGGGC 60.740 50.000 0.00 0.00 44.79 5.19
2308 2502 3.169355 GCATTTAGCATTGTTGGAGGG 57.831 47.619 0.00 0.00 44.79 4.30
2320 2514 0.595825 GCCTCGGCAATGCATTTAGC 60.596 55.000 9.83 11.22 41.92 3.09
2321 2515 3.557207 GCCTCGGCAATGCATTTAG 57.443 52.632 9.83 4.23 41.49 1.85
2335 2529 3.672295 CTCACCGAGCCCTTGCCTC 62.672 68.421 0.00 0.00 38.69 4.70
2336 2530 3.710722 CTCACCGAGCCCTTGCCT 61.711 66.667 0.00 0.00 38.69 4.75
2337 2531 4.785453 CCTCACCGAGCCCTTGCC 62.785 72.222 0.00 0.00 38.69 4.52
2338 2532 3.672295 CTCCTCACCGAGCCCTTGC 62.672 68.421 0.00 0.00 37.95 4.01
2347 2576 2.500098 TGGGATAAGTTTCTCCTCACCG 59.500 50.000 4.66 0.00 0.00 4.94
2406 2641 8.911918 TCTAAGTTTATTTAGGCTTTGTGTCA 57.088 30.769 0.00 0.00 32.66 3.58
2449 2685 0.044092 TGCAGGTGGGAGGATTCCTA 59.956 55.000 4.86 0.00 43.49 2.94
2509 2745 5.265989 CTCTACCTCCTGGTCTTAGTCTTT 58.734 45.833 0.00 0.00 44.78 2.52
2515 2751 3.309701 GGTTCCTCTACCTCCTGGTCTTA 60.310 52.174 0.00 0.00 44.78 2.10
2550 2789 2.660064 GCCGCCTCCTCTCCAAAGA 61.660 63.158 0.00 0.00 0.00 2.52
2551 2790 2.124942 GCCGCCTCCTCTCCAAAG 60.125 66.667 0.00 0.00 0.00 2.77
2556 2795 4.200283 CAGTCGCCGCCTCCTCTC 62.200 72.222 0.00 0.00 0.00 3.20
2567 2806 2.032030 ACATGTTGCTTTACACAGTCGC 60.032 45.455 0.00 0.00 0.00 5.19
2570 2809 6.475402 GCTTTTAACATGTTGCTTTACACAGT 59.525 34.615 21.42 0.00 0.00 3.55
2573 2812 6.695278 TGAGCTTTTAACATGTTGCTTTACAC 59.305 34.615 21.42 8.85 0.00 2.90
2574 2813 6.800543 TGAGCTTTTAACATGTTGCTTTACA 58.199 32.000 21.42 11.72 0.00 2.41


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

AutoCloner maintained by Alex Coulton.