Multiple sequence alignment - TraesCS2A01G178100

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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 TraesCS2A01G178100 chr2A 100.000 2441 0 0 1 2441 137211785 137214225 0.000000e+00 4508.0
1 TraesCS2A01G178100 chr2A 77.764 787 92 34 839 1590 137129085 137129823 8.130000e-110 407.0
2 TraesCS2A01G178100 chr2D 88.060 1918 158 34 464 2338 131123931 131125820 0.000000e+00 2207.0
3 TraesCS2A01G178100 chr2D 89.655 1276 101 18 1187 2441 131134472 131135737 0.000000e+00 1596.0
4 TraesCS2A01G178100 chr2D 89.293 495 49 4 845 1337 131134187 131134679 3.450000e-173 617.0
5 TraesCS2A01G178100 chr2D 83.686 472 65 8 1129 1593 130987998 130988464 3.730000e-118 435.0
6 TraesCS2A01G178100 chr2D 92.884 267 13 3 36 298 131123681 131123945 1.370000e-102 383.0
7 TraesCS2A01G178100 chr2D 81.716 443 75 5 1129 1570 131114681 131115118 4.960000e-97 364.0
8 TraesCS2A01G178100 chr2D 80.964 415 54 10 1187 1592 131042998 131043396 3.050000e-79 305.0
9 TraesCS2A01G178100 chr2D 87.302 126 5 5 2317 2441 131128332 131128447 1.520000e-27 134.0
10 TraesCS2A01G178100 chr2D 79.333 150 28 2 628 774 131041770 131041919 4.290000e-18 102.0
11 TraesCS2A01G178100 chrUn 90.615 618 36 9 464 1068 428032985 428033593 0.000000e+00 800.0
12 TraesCS2A01G178100 chrUn 89.423 624 43 13 1831 2441 17495898 17495285 0.000000e+00 765.0
13 TraesCS2A01G178100 chrUn 89.423 624 43 13 1831 2441 302454850 302455463 0.000000e+00 765.0
14 TraesCS2A01G178100 chrUn 89.423 624 43 13 1831 2441 330584554 330585167 0.000000e+00 765.0
15 TraesCS2A01G178100 chrUn 85.594 715 82 13 1129 1837 17496759 17496060 0.000000e+00 730.0
16 TraesCS2A01G178100 chrUn 85.594 715 82 13 1129 1837 302453989 302454688 0.000000e+00 730.0
17 TraesCS2A01G178100 chrUn 85.594 715 82 13 1129 1837 330583693 330584392 0.000000e+00 730.0
18 TraesCS2A01G178100 chrUn 93.258 267 10 5 36 298 428032737 428032999 1.060000e-103 387.0
19 TraesCS2A01G178100 chrUn 94.355 248 14 0 1073 1320 17496872 17496625 4.930000e-102 381.0
20 TraesCS2A01G178100 chrUn 94.355 248 14 0 1073 1320 302453876 302454123 4.930000e-102 381.0
21 TraesCS2A01G178100 chrUn 94.355 248 14 0 1073 1320 330583580 330583827 4.930000e-102 381.0
22 TraesCS2A01G178100 chr2B 89.246 623 45 13 1831 2441 184593037 184593649 0.000000e+00 760.0
23 TraesCS2A01G178100 chr2B 84.509 652 72 16 1200 1837 184592239 184592875 3.450000e-173 617.0
24 TraesCS2A01G178100 chr2B 85.559 367 45 6 1220 1579 184494991 184495356 6.370000e-101 377.0
25 TraesCS2A01G178100 chr2B 85.484 186 9 1 1077 1262 184578917 184579084 6.940000e-41 178.0
26 TraesCS2A01G178100 chr2B 90.588 85 3 4 172 251 184578793 184578877 9.230000e-20 108.0
27 TraesCS2A01G178100 chr7A 100.000 29 0 0 136 164 720949390 720949362 1.000000e-03 54.7


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 TraesCS2A01G178100 chr2A 137211785 137214225 2440 False 4508.000000 4508 100.000000 1 2441 1 chr2A.!!$F2 2440
1 TraesCS2A01G178100 chr2A 137129085 137129823 738 False 407.000000 407 77.764000 839 1590 1 chr2A.!!$F1 751
2 TraesCS2A01G178100 chr2D 131134187 131135737 1550 False 1106.500000 1596 89.474000 845 2441 2 chr2D.!!$F5 1596
3 TraesCS2A01G178100 chr2D 131123681 131128447 4766 False 908.000000 2207 89.415333 36 2441 3 chr2D.!!$F4 2405
4 TraesCS2A01G178100 chr2D 131041770 131043396 1626 False 203.500000 305 80.148500 628 1592 2 chr2D.!!$F3 964
5 TraesCS2A01G178100 chrUn 17495285 17496872 1587 True 625.333333 765 89.790667 1073 2441 3 chrUn.!!$R1 1368
6 TraesCS2A01G178100 chrUn 302453876 302455463 1587 False 625.333333 765 89.790667 1073 2441 3 chrUn.!!$F1 1368
7 TraesCS2A01G178100 chrUn 330583580 330585167 1587 False 625.333333 765 89.790667 1073 2441 3 chrUn.!!$F2 1368
8 TraesCS2A01G178100 chrUn 428032737 428033593 856 False 593.500000 800 91.936500 36 1068 2 chrUn.!!$F3 1032
9 TraesCS2A01G178100 chr2B 184592239 184593649 1410 False 688.500000 760 86.877500 1200 2441 2 chr2B.!!$F3 1241

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
343 348 0.034186 GGGAATGTGATGCCACCTGA 60.034 55.0 0.0 0.0 42.53 3.86 F
417 422 0.035439 ATGGGGAAGGTACAAGTGCG 60.035 55.0 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1660 0.038166 GGGTGGTTCTCATGGCTTGA 59.962 55.0 2.86 2.86 0.0 3.02 R
1538 1776 0.249447 TCACTCACAACACTCGCTGG 60.249 55.0 0.00 0.00 0.0 4.85 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
29 30 5.697473 CGAGAGCTGAGGAAGTATATTCA 57.303 43.478 0.00 0.00 0.00 2.57
30 31 6.266168 CGAGAGCTGAGGAAGTATATTCAT 57.734 41.667 0.00 0.00 0.00 2.57
31 32 6.686630 CGAGAGCTGAGGAAGTATATTCATT 58.313 40.000 0.00 0.00 0.00 2.57
32 33 6.585702 CGAGAGCTGAGGAAGTATATTCATTG 59.414 42.308 0.00 0.00 0.00 2.82
33 34 7.522889 CGAGAGCTGAGGAAGTATATTCATTGA 60.523 40.741 0.00 0.00 0.00 2.57
34 35 8.204903 AGAGCTGAGGAAGTATATTCATTGAT 57.795 34.615 0.00 0.00 0.00 2.57
61 62 6.701400 GGTTCTGTTTCATAACTGCACAAAAT 59.299 34.615 0.00 0.00 33.36 1.82
113 114 7.728083 TGGGGAGAATTTTTGTAATCTCTTCAA 59.272 33.333 0.00 0.00 38.64 2.69
295 300 3.684908 TCGTTTGATGGGAATGTGATGT 58.315 40.909 0.00 0.00 0.00 3.06
296 301 4.078537 TCGTTTGATGGGAATGTGATGTT 58.921 39.130 0.00 0.00 0.00 2.71
297 302 4.082841 TCGTTTGATGGGAATGTGATGTTG 60.083 41.667 0.00 0.00 0.00 3.33
298 303 3.872511 TTGATGGGAATGTGATGTTGC 57.127 42.857 0.00 0.00 0.00 4.17
299 304 3.090210 TGATGGGAATGTGATGTTGCT 57.910 42.857 0.00 0.00 0.00 3.91
300 305 3.433343 TGATGGGAATGTGATGTTGCTT 58.567 40.909 0.00 0.00 0.00 3.91
301 306 3.833650 TGATGGGAATGTGATGTTGCTTT 59.166 39.130 0.00 0.00 0.00 3.51
302 307 4.283978 TGATGGGAATGTGATGTTGCTTTT 59.716 37.500 0.00 0.00 0.00 2.27
303 308 4.686191 TGGGAATGTGATGTTGCTTTTT 57.314 36.364 0.00 0.00 0.00 1.94
321 326 3.529216 TTTTTAAGGTCACGGGGGATT 57.471 42.857 0.00 0.00 0.00 3.01
322 327 4.654389 TTTTTAAGGTCACGGGGGATTA 57.346 40.909 0.00 0.00 0.00 1.75
323 328 4.866327 TTTTAAGGTCACGGGGGATTAT 57.134 40.909 0.00 0.00 0.00 1.28
324 329 3.849563 TTAAGGTCACGGGGGATTATG 57.150 47.619 0.00 0.00 0.00 1.90
325 330 0.843984 AAGGTCACGGGGGATTATGG 59.156 55.000 0.00 0.00 0.00 2.74
326 331 1.060163 AGGTCACGGGGGATTATGGG 61.060 60.000 0.00 0.00 0.00 4.00
327 332 1.057851 GGTCACGGGGGATTATGGGA 61.058 60.000 0.00 0.00 0.00 4.37
328 333 0.841289 GTCACGGGGGATTATGGGAA 59.159 55.000 0.00 0.00 0.00 3.97
329 334 1.423921 GTCACGGGGGATTATGGGAAT 59.576 52.381 0.00 0.00 0.00 3.01
330 335 1.423541 TCACGGGGGATTATGGGAATG 59.576 52.381 0.00 0.00 0.00 2.67
331 336 1.144913 CACGGGGGATTATGGGAATGT 59.855 52.381 0.00 0.00 0.00 2.71
332 337 1.144913 ACGGGGGATTATGGGAATGTG 59.855 52.381 0.00 0.00 0.00 3.21
333 338 1.423541 CGGGGGATTATGGGAATGTGA 59.576 52.381 0.00 0.00 0.00 3.58
334 339 2.041620 CGGGGGATTATGGGAATGTGAT 59.958 50.000 0.00 0.00 0.00 3.06
335 340 3.434309 GGGGGATTATGGGAATGTGATG 58.566 50.000 0.00 0.00 0.00 3.07
336 341 2.827921 GGGGATTATGGGAATGTGATGC 59.172 50.000 0.00 0.00 0.00 3.91
337 342 2.827921 GGGATTATGGGAATGTGATGCC 59.172 50.000 0.00 0.00 0.00 4.40
338 343 3.499338 GGATTATGGGAATGTGATGCCA 58.501 45.455 0.00 0.00 45.47 4.92
339 344 3.256631 GGATTATGGGAATGTGATGCCAC 59.743 47.826 0.00 0.00 44.11 5.01
340 345 2.363306 TATGGGAATGTGATGCCACC 57.637 50.000 0.00 0.00 44.11 4.61
341 346 0.632835 ATGGGAATGTGATGCCACCT 59.367 50.000 0.00 0.00 44.11 4.00
342 347 0.323633 TGGGAATGTGATGCCACCTG 60.324 55.000 0.00 0.00 42.53 4.00
343 348 0.034186 GGGAATGTGATGCCACCTGA 60.034 55.000 0.00 0.00 42.53 3.86
344 349 1.616725 GGGAATGTGATGCCACCTGAA 60.617 52.381 0.00 0.00 42.53 3.02
345 350 2.381911 GGAATGTGATGCCACCTGAAT 58.618 47.619 0.00 0.00 42.53 2.57
346 351 2.762327 GGAATGTGATGCCACCTGAATT 59.238 45.455 0.00 0.00 42.53 2.17
347 352 3.953612 GGAATGTGATGCCACCTGAATTA 59.046 43.478 0.00 0.00 42.53 1.40
348 353 4.586001 GGAATGTGATGCCACCTGAATTAT 59.414 41.667 0.00 0.00 42.53 1.28
349 354 5.069516 GGAATGTGATGCCACCTGAATTATT 59.930 40.000 0.00 0.00 42.53 1.40
350 355 6.407299 GGAATGTGATGCCACCTGAATTATTT 60.407 38.462 0.00 0.00 42.53 1.40
351 356 5.999205 TGTGATGCCACCTGAATTATTTT 57.001 34.783 0.00 0.00 42.53 1.82
352 357 5.964758 TGTGATGCCACCTGAATTATTTTC 58.035 37.500 0.00 0.00 42.53 2.29
353 358 5.105392 TGTGATGCCACCTGAATTATTTTCC 60.105 40.000 0.00 0.00 42.53 3.13
354 359 5.022122 TGATGCCACCTGAATTATTTTCCA 58.978 37.500 0.00 0.00 0.00 3.53
355 360 5.662208 TGATGCCACCTGAATTATTTTCCAT 59.338 36.000 0.00 0.00 0.00 3.41
356 361 6.156602 TGATGCCACCTGAATTATTTTCCATT 59.843 34.615 0.00 0.00 0.00 3.16
357 362 6.371595 TGCCACCTGAATTATTTTCCATTT 57.628 33.333 0.00 0.00 0.00 2.32
358 363 6.777782 TGCCACCTGAATTATTTTCCATTTT 58.222 32.000 0.00 0.00 0.00 1.82
359 364 7.230027 TGCCACCTGAATTATTTTCCATTTTT 58.770 30.769 0.00 0.00 0.00 1.94
383 388 8.996024 TTTATTTGATGATCAGAGACGTAACA 57.004 30.769 0.09 0.00 0.00 2.41
384 389 8.634475 TTATTTGATGATCAGAGACGTAACAG 57.366 34.615 0.09 0.00 0.00 3.16
385 390 5.897377 TTGATGATCAGAGACGTAACAGA 57.103 39.130 0.09 0.00 0.00 3.41
386 391 5.491635 TGATGATCAGAGACGTAACAGAG 57.508 43.478 0.09 0.00 0.00 3.35
387 392 4.944317 TGATGATCAGAGACGTAACAGAGT 59.056 41.667 0.09 0.00 0.00 3.24
388 393 4.948608 TGATCAGAGACGTAACAGAGTC 57.051 45.455 0.00 0.00 37.63 3.36
389 394 3.690139 TGATCAGAGACGTAACAGAGTCC 59.310 47.826 0.00 0.00 38.08 3.85
390 395 3.136009 TCAGAGACGTAACAGAGTCCA 57.864 47.619 0.00 0.00 38.08 4.02
391 396 3.687125 TCAGAGACGTAACAGAGTCCAT 58.313 45.455 0.00 0.00 38.08 3.41
392 397 3.440522 TCAGAGACGTAACAGAGTCCATG 59.559 47.826 0.00 0.00 38.08 3.66
393 398 3.440522 CAGAGACGTAACAGAGTCCATGA 59.559 47.826 0.00 0.00 38.08 3.07
394 399 3.692101 AGAGACGTAACAGAGTCCATGAG 59.308 47.826 0.00 0.00 38.08 2.90
395 400 3.687125 AGACGTAACAGAGTCCATGAGA 58.313 45.455 0.00 0.00 38.08 3.27
396 401 4.274147 AGACGTAACAGAGTCCATGAGAT 58.726 43.478 0.00 0.00 38.08 2.75
397 402 4.707448 AGACGTAACAGAGTCCATGAGATT 59.293 41.667 0.00 0.00 38.08 2.40
398 403 5.886474 AGACGTAACAGAGTCCATGAGATTA 59.114 40.000 0.00 0.00 38.08 1.75
399 404 6.547880 AGACGTAACAGAGTCCATGAGATTAT 59.452 38.462 0.00 0.00 38.08 1.28
400 405 6.507900 ACGTAACAGAGTCCATGAGATTATG 58.492 40.000 0.00 0.00 30.30 1.90
402 407 4.970860 ACAGAGTCCATGAGATTATGGG 57.029 45.455 4.00 0.00 46.16 4.00
403 408 3.649981 ACAGAGTCCATGAGATTATGGGG 59.350 47.826 4.00 0.00 46.16 4.96
404 409 3.906218 CAGAGTCCATGAGATTATGGGGA 59.094 47.826 4.00 0.00 46.16 4.81
405 410 4.349048 CAGAGTCCATGAGATTATGGGGAA 59.651 45.833 4.00 0.00 46.16 3.97
406 411 4.596643 AGAGTCCATGAGATTATGGGGAAG 59.403 45.833 4.00 0.00 46.16 3.46
407 412 3.654806 AGTCCATGAGATTATGGGGAAGG 59.345 47.826 4.00 0.00 46.16 3.46
408 413 3.395941 GTCCATGAGATTATGGGGAAGGT 59.604 47.826 4.00 0.00 46.16 3.50
409 414 4.597507 GTCCATGAGATTATGGGGAAGGTA 59.402 45.833 4.00 0.00 46.16 3.08
410 415 4.597507 TCCATGAGATTATGGGGAAGGTAC 59.402 45.833 4.00 0.00 46.16 3.34
411 416 4.350816 CCATGAGATTATGGGGAAGGTACA 59.649 45.833 0.00 0.00 43.16 2.90
412 417 5.163099 CCATGAGATTATGGGGAAGGTACAA 60.163 44.000 0.00 0.00 43.16 2.41
413 418 5.630415 TGAGATTATGGGGAAGGTACAAG 57.370 43.478 0.00 0.00 0.00 3.16
414 419 5.036916 TGAGATTATGGGGAAGGTACAAGT 58.963 41.667 0.00 0.00 0.00 3.16
415 420 5.104527 TGAGATTATGGGGAAGGTACAAGTG 60.105 44.000 0.00 0.00 0.00 3.16
416 421 3.359695 TTATGGGGAAGGTACAAGTGC 57.640 47.619 0.00 0.00 0.00 4.40
417 422 0.035439 ATGGGGAAGGTACAAGTGCG 60.035 55.000 0.00 0.00 0.00 5.34
418 423 1.373812 GGGGAAGGTACAAGTGCGT 59.626 57.895 0.00 0.00 0.00 5.24
419 424 0.953960 GGGGAAGGTACAAGTGCGTG 60.954 60.000 0.00 0.00 0.00 5.34
420 425 1.574702 GGGAAGGTACAAGTGCGTGC 61.575 60.000 0.00 0.00 0.00 5.34
421 426 1.491563 GAAGGTACAAGTGCGTGCG 59.508 57.895 0.00 0.00 0.00 5.34
422 427 0.942410 GAAGGTACAAGTGCGTGCGA 60.942 55.000 0.00 0.00 0.00 5.10
423 428 0.944311 AAGGTACAAGTGCGTGCGAG 60.944 55.000 0.00 0.00 0.00 5.03
424 429 1.372499 GGTACAAGTGCGTGCGAGA 60.372 57.895 0.00 0.00 0.00 4.04
425 430 1.344942 GGTACAAGTGCGTGCGAGAG 61.345 60.000 0.00 0.00 0.00 3.20
426 431 0.386858 GTACAAGTGCGTGCGAGAGA 60.387 55.000 0.00 0.00 0.00 3.10
427 432 0.109735 TACAAGTGCGTGCGAGAGAG 60.110 55.000 0.00 0.00 0.00 3.20
428 433 1.081175 CAAGTGCGTGCGAGAGAGA 60.081 57.895 0.00 0.00 0.00 3.10
429 434 1.069924 CAAGTGCGTGCGAGAGAGAG 61.070 60.000 0.00 0.00 0.00 3.20
430 435 1.237954 AAGTGCGTGCGAGAGAGAGA 61.238 55.000 0.00 0.00 0.00 3.10
431 436 1.226267 GTGCGTGCGAGAGAGAGAG 60.226 63.158 0.00 0.00 0.00 3.20
432 437 1.376037 TGCGTGCGAGAGAGAGAGA 60.376 57.895 0.00 0.00 0.00 3.10
433 438 1.351707 GCGTGCGAGAGAGAGAGAG 59.648 63.158 0.00 0.00 0.00 3.20
434 439 1.087202 GCGTGCGAGAGAGAGAGAGA 61.087 60.000 0.00 0.00 0.00 3.10
435 440 0.930310 CGTGCGAGAGAGAGAGAGAG 59.070 60.000 0.00 0.00 0.00 3.20
436 441 1.470805 CGTGCGAGAGAGAGAGAGAGA 60.471 57.143 0.00 0.00 0.00 3.10
437 442 2.205074 GTGCGAGAGAGAGAGAGAGAG 58.795 57.143 0.00 0.00 0.00 3.20
438 443 1.138859 TGCGAGAGAGAGAGAGAGAGG 59.861 57.143 0.00 0.00 0.00 3.69
439 444 1.541233 GCGAGAGAGAGAGAGAGAGGG 60.541 61.905 0.00 0.00 0.00 4.30
440 445 2.039418 CGAGAGAGAGAGAGAGAGGGA 58.961 57.143 0.00 0.00 0.00 4.20
441 446 2.036475 CGAGAGAGAGAGAGAGAGGGAG 59.964 59.091 0.00 0.00 0.00 4.30
442 447 2.370189 GAGAGAGAGAGAGAGAGGGAGG 59.630 59.091 0.00 0.00 0.00 4.30
443 448 2.127708 GAGAGAGAGAGAGAGGGAGGT 58.872 57.143 0.00 0.00 0.00 3.85
444 449 3.051341 AGAGAGAGAGAGAGAGGGAGGTA 60.051 52.174 0.00 0.00 0.00 3.08
445 450 3.046374 AGAGAGAGAGAGAGGGAGGTAC 58.954 54.545 0.00 0.00 0.00 3.34
446 451 2.775384 GAGAGAGAGAGAGGGAGGTACA 59.225 54.545 0.00 0.00 0.00 2.90
447 452 3.194620 AGAGAGAGAGAGGGAGGTACAA 58.805 50.000 0.00 0.00 0.00 2.41
448 453 3.594232 AGAGAGAGAGAGGGAGGTACAAA 59.406 47.826 0.00 0.00 0.00 2.83
449 454 4.231890 AGAGAGAGAGAGGGAGGTACAAAT 59.768 45.833 0.00 0.00 0.00 2.32
450 455 4.542697 AGAGAGAGAGGGAGGTACAAATC 58.457 47.826 0.00 0.00 0.00 2.17
451 456 3.639561 GAGAGAGAGGGAGGTACAAATCC 59.360 52.174 0.00 0.00 34.64 3.01
452 457 3.012959 AGAGAGAGGGAGGTACAAATCCA 59.987 47.826 11.72 0.00 37.33 3.41
453 458 3.379452 AGAGAGGGAGGTACAAATCCAG 58.621 50.000 11.72 0.00 37.33 3.86
454 459 2.436173 GAGAGGGAGGTACAAATCCAGG 59.564 54.545 11.72 0.00 37.33 4.45
455 460 1.490910 GAGGGAGGTACAAATCCAGGG 59.509 57.143 11.72 0.00 37.33 4.45
456 461 0.551396 GGGAGGTACAAATCCAGGGG 59.449 60.000 11.72 0.00 37.33 4.79
457 462 1.591768 GGAGGTACAAATCCAGGGGA 58.408 55.000 6.22 0.00 35.54 4.81
458 463 2.136026 GGAGGTACAAATCCAGGGGAT 58.864 52.381 6.22 0.00 45.46 3.85
467 472 2.549694 ATCCAGGGGATTATGGGGAA 57.450 50.000 0.00 0.00 39.79 3.97
468 473 2.549694 TCCAGGGGATTATGGGGAAT 57.450 50.000 0.00 0.00 37.19 3.01
469 474 2.072973 TCCAGGGGATTATGGGGAATG 58.927 52.381 0.00 0.00 37.19 2.67
470 475 1.788915 CCAGGGGATTATGGGGAATGT 59.211 52.381 0.00 0.00 32.63 2.71
471 476 2.491455 CCAGGGGATTATGGGGAATGTG 60.491 54.545 0.00 0.00 32.63 3.21
472 477 2.446666 CAGGGGATTATGGGGAATGTGA 59.553 50.000 0.00 0.00 0.00 3.58
473 478 3.076484 CAGGGGATTATGGGGAATGTGAT 59.924 47.826 0.00 0.00 0.00 3.06
474 479 3.076484 AGGGGATTATGGGGAATGTGATG 59.924 47.826 0.00 0.00 0.00 3.07
617 622 2.706190 GGCCTATGTAGACTCCCACAAT 59.294 50.000 0.00 0.00 0.00 2.71
629 634 4.036518 ACTCCCACAATGAGAAGCTATCT 58.963 43.478 0.00 0.00 42.61 1.98
631 636 5.045286 ACTCCCACAATGAGAAGCTATCTTT 60.045 40.000 0.00 0.00 38.96 2.52
751 758 9.420551 GACCTAACAGCTATATGTTATTGTACC 57.579 37.037 0.21 0.00 42.97 3.34
755 762 7.046292 ACAGCTATATGTTATTGTACCGTCA 57.954 36.000 0.00 0.00 0.00 4.35
767 777 1.959282 GTACCGTCATACCTACCCTGG 59.041 57.143 0.00 0.00 0.00 4.45
774 784 0.337428 ATACCTACCCTGGACGTGGT 59.663 55.000 0.00 0.00 38.69 4.16
785 807 3.132289 CCTGGACGTGGTATCACTACAAT 59.868 47.826 4.28 0.00 41.53 2.71
794 844 7.033791 CGTGGTATCACTACAATCTAAACAGT 58.966 38.462 4.28 0.00 41.53 3.55
810 860 2.627945 ACAGTCAAACGTTGAGCAGAA 58.372 42.857 0.00 0.00 41.01 3.02
822 872 4.328440 CGTTGAGCAGAAATAGACTCCAAG 59.672 45.833 0.00 0.00 0.00 3.61
825 875 4.528206 TGAGCAGAAATAGACTCCAAGACA 59.472 41.667 0.00 0.00 0.00 3.41
831 881 5.703130 AGAAATAGACTCCAAGACAAAGTGC 59.297 40.000 0.00 0.00 0.00 4.40
832 882 4.623932 ATAGACTCCAAGACAAAGTGCA 57.376 40.909 0.00 0.00 0.00 4.57
833 883 3.498774 AGACTCCAAGACAAAGTGCAT 57.501 42.857 0.00 0.00 0.00 3.96
834 884 4.623932 AGACTCCAAGACAAAGTGCATA 57.376 40.909 0.00 0.00 0.00 3.14
869 919 3.699038 TGACCTAACTTGTTGCAAAGCTT 59.301 39.130 0.00 0.00 0.00 3.74
933 984 3.874383 AGTAGGAGCTGCTATCTCTCA 57.126 47.619 18.63 0.00 0.00 3.27
935 986 1.317613 AGGAGCTGCTATCTCTCACG 58.682 55.000 5.69 0.00 0.00 4.35
941 1000 0.378610 TGCTATCTCTCACGCACTCG 59.621 55.000 0.00 0.00 42.43 4.18
998 1057 2.671177 GCTGCACACGTCGAGCAAT 61.671 57.895 0.00 0.00 37.89 3.56
1004 1063 2.267426 CACACGTCGAGCAATTATGGA 58.733 47.619 0.00 0.00 0.00 3.41
1012 1071 6.183360 ACGTCGAGCAATTATGGATTTGAAAT 60.183 34.615 0.00 0.00 0.00 2.17
1042 1101 3.741249 GTTTTCCTCCTCGGTCTTCTTT 58.259 45.455 0.00 0.00 0.00 2.52
1138 1197 1.377202 GTGCCATCGCTTCCCAAGA 60.377 57.895 0.00 0.00 35.36 3.02
1144 1203 1.134280 CATCGCTTCCCAAGATGGAGT 60.134 52.381 0.00 0.00 40.96 3.85
1179 1238 0.405585 AAGTGCACCTGCCACCTAAT 59.594 50.000 14.63 0.00 41.18 1.73
1188 1247 2.042464 CTGCCACCTAATCCTGAGCTA 58.958 52.381 0.00 0.00 0.00 3.32
1236 1361 2.837291 GTGCACCTGCCACCCAAA 60.837 61.111 5.22 0.00 41.18 3.28
1239 1364 3.294493 CACCTGCCACCCAAACCG 61.294 66.667 0.00 0.00 0.00 4.44
1406 1636 1.899437 GAGATGCCCACTGTTCCCGA 61.899 60.000 0.00 0.00 0.00 5.14
1413 1643 0.613260 CCACTGTTCCCGAGATCCAA 59.387 55.000 0.00 0.00 0.00 3.53
1426 1656 0.389391 GATCCAATTCTCGGAGCCGA 59.611 55.000 11.55 11.55 46.87 5.54
1446 1676 1.067295 AGGTCAAGCCATGAGAACCA 58.933 50.000 0.00 0.00 39.19 3.67
1481 1718 2.997986 TGTTATTTCGTTCTTCCTCGCC 59.002 45.455 0.00 0.00 0.00 5.54
1487 1724 1.515736 GTTCTTCCTCGCCCGTACG 60.516 63.158 8.69 8.69 0.00 3.67
1533 1771 7.387673 TGTCGATGATCTGATTGTTTAGTTGTT 59.612 33.333 0.00 0.00 0.00 2.83
1538 1776 9.683069 ATGATCTGATTGTTTAGTTGTTGTTTC 57.317 29.630 0.00 0.00 0.00 2.78
1559 1797 1.458445 CAGCGAGTGTTGTGAGTGATG 59.542 52.381 0.00 0.00 0.00 3.07
1564 1802 3.653344 GAGTGTTGTGAGTGATGTGCTA 58.347 45.455 0.00 0.00 0.00 3.49
1607 1858 6.436843 AGAAATATACTTTCGCACCCTTTG 57.563 37.500 0.00 0.00 33.86 2.77
1666 1925 4.095334 AGTTTTCACCGTAAGCTTCGTTTT 59.905 37.500 0.00 0.00 0.00 2.43
1689 1949 4.005650 CACCTATCCATTTCCCATCGATG 58.994 47.826 18.76 18.76 0.00 3.84
1700 1960 7.927629 CCATTTCCCATCGATGAAACATAAAAT 59.072 33.333 26.86 15.56 33.64 1.82
1755 2024 5.067544 GTCGTCCTAGCTTTAGTACCTGATT 59.932 44.000 0.00 0.00 0.00 2.57
1879 2715 2.224314 TGCATGACTACTATCGAGCGAG 59.776 50.000 0.00 0.00 0.00 5.03
1884 2720 1.080298 CTACTATCGAGCGAGCGGAT 58.920 55.000 0.00 9.02 0.00 4.18
1886 2722 1.799519 CTATCGAGCGAGCGGATGC 60.800 63.158 12.56 0.00 43.24 3.91
1994 2835 3.788227 TCACTTCAGTGGGCAAATACT 57.212 42.857 7.11 0.00 45.65 2.12
2032 2873 2.673368 GGATGAAACTGACATGTCGACC 59.327 50.000 20.54 10.47 0.00 4.79
2033 2874 2.900716 TGAAACTGACATGTCGACCA 57.099 45.000 20.54 10.89 0.00 4.02
2034 2875 2.479837 TGAAACTGACATGTCGACCAC 58.520 47.619 20.54 12.09 0.00 4.16
2039 2880 2.807967 ACTGACATGTCGACCACAAATG 59.192 45.455 20.54 11.90 38.97 2.32
2077 2919 8.973835 ATAATAATACAACAACCAAACCAACG 57.026 30.769 0.00 0.00 0.00 4.10
2139 2984 2.476051 GCGCCGTGAACACATCAG 59.524 61.111 0.00 0.00 39.19 2.90
2153 2998 5.324784 ACACATCAGTAGTTAAGCGATCA 57.675 39.130 0.00 0.00 0.00 2.92
2169 3014 4.272018 AGCGATCAAGCAAGCAAACTATAG 59.728 41.667 0.00 0.00 40.15 1.31
2239 3085 1.006878 ACTTTAGGACCTCTAGGCGGT 59.993 52.381 0.00 4.56 39.32 5.68
2243 3089 1.516110 AGGACCTCTAGGCGGTAGTA 58.484 55.000 4.85 0.00 39.32 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.246086 ACTTCCTCAGCTCTCGCAAG 59.754 55.000 0.00 0.00 39.10 4.01
4 5 1.545841 TACTTCCTCAGCTCTCGCAA 58.454 50.000 0.00 0.00 39.10 4.85
6 7 4.022762 TGAATATACTTCCTCAGCTCTCGC 60.023 45.833 0.00 0.00 0.00 5.03
7 8 5.697473 TGAATATACTTCCTCAGCTCTCG 57.303 43.478 0.00 0.00 0.00 4.04
8 9 7.665690 TCAATGAATATACTTCCTCAGCTCTC 58.334 38.462 0.00 0.00 0.00 3.20
9 10 7.609097 TCAATGAATATACTTCCTCAGCTCT 57.391 36.000 0.00 0.00 0.00 4.09
10 11 8.719648 CAATCAATGAATATACTTCCTCAGCTC 58.280 37.037 0.00 0.00 0.00 4.09
11 12 7.664731 CCAATCAATGAATATACTTCCTCAGCT 59.335 37.037 0.00 0.00 0.00 4.24
12 13 7.446625 ACCAATCAATGAATATACTTCCTCAGC 59.553 37.037 0.00 0.00 0.00 4.26
13 14 8.915057 ACCAATCAATGAATATACTTCCTCAG 57.085 34.615 0.00 0.00 0.00 3.35
14 15 9.342308 GAACCAATCAATGAATATACTTCCTCA 57.658 33.333 0.00 0.00 0.00 3.86
15 16 9.566432 AGAACCAATCAATGAATATACTTCCTC 57.434 33.333 0.00 0.00 0.00 3.71
16 17 9.347240 CAGAACCAATCAATGAATATACTTCCT 57.653 33.333 0.00 0.00 0.00 3.36
17 18 9.125026 ACAGAACCAATCAATGAATATACTTCC 57.875 33.333 0.00 0.00 0.00 3.46
25 26 9.643693 GTTATGAAACAGAACCAATCAATGAAT 57.356 29.630 0.00 0.00 35.56 2.57
26 27 8.859090 AGTTATGAAACAGAACCAATCAATGAA 58.141 29.630 5.79 0.00 36.39 2.57
27 28 8.298854 CAGTTATGAAACAGAACCAATCAATGA 58.701 33.333 5.79 0.00 36.39 2.57
28 29 7.062605 GCAGTTATGAAACAGAACCAATCAATG 59.937 37.037 5.79 0.00 36.39 2.82
29 30 7.092716 GCAGTTATGAAACAGAACCAATCAAT 58.907 34.615 5.79 0.00 36.39 2.57
30 31 6.040278 TGCAGTTATGAAACAGAACCAATCAA 59.960 34.615 5.79 0.00 36.39 2.57
31 32 5.534278 TGCAGTTATGAAACAGAACCAATCA 59.466 36.000 5.79 0.00 36.39 2.57
32 33 5.858581 GTGCAGTTATGAAACAGAACCAATC 59.141 40.000 5.79 0.00 36.39 2.67
33 34 5.301551 TGTGCAGTTATGAAACAGAACCAAT 59.698 36.000 5.79 0.00 36.39 3.16
34 35 4.642437 TGTGCAGTTATGAAACAGAACCAA 59.358 37.500 5.79 0.00 36.39 3.67
88 89 7.703058 TGAAGAGATTACAAAAATTCTCCCC 57.297 36.000 0.00 0.00 0.00 4.81
89 90 8.797438 AGTTGAAGAGATTACAAAAATTCTCCC 58.203 33.333 0.00 0.00 0.00 4.30
90 91 9.617975 CAGTTGAAGAGATTACAAAAATTCTCC 57.382 33.333 0.00 0.00 0.00 3.71
113 114 6.717289 TGCTAAACCACCACTAATAATCAGT 58.283 36.000 0.00 0.00 0.00 3.41
166 167 6.893583 ACATATGAGCTAATCTGAACAAGGT 58.106 36.000 10.38 0.00 0.00 3.50
301 306 3.529216 AATCCCCCGTGACCTTAAAAA 57.471 42.857 0.00 0.00 0.00 1.94
302 307 4.528920 CATAATCCCCCGTGACCTTAAAA 58.471 43.478 0.00 0.00 0.00 1.52
303 308 3.117813 CCATAATCCCCCGTGACCTTAAA 60.118 47.826 0.00 0.00 0.00 1.52
304 309 2.440253 CCATAATCCCCCGTGACCTTAA 59.560 50.000 0.00 0.00 0.00 1.85
305 310 2.051692 CCATAATCCCCCGTGACCTTA 58.948 52.381 0.00 0.00 0.00 2.69
306 311 0.843984 CCATAATCCCCCGTGACCTT 59.156 55.000 0.00 0.00 0.00 3.50
307 312 1.060163 CCCATAATCCCCCGTGACCT 61.060 60.000 0.00 0.00 0.00 3.85
308 313 1.057851 TCCCATAATCCCCCGTGACC 61.058 60.000 0.00 0.00 0.00 4.02
309 314 0.841289 TTCCCATAATCCCCCGTGAC 59.159 55.000 0.00 0.00 0.00 3.67
310 315 1.423541 CATTCCCATAATCCCCCGTGA 59.576 52.381 0.00 0.00 0.00 4.35
311 316 1.144913 ACATTCCCATAATCCCCCGTG 59.855 52.381 0.00 0.00 0.00 4.94
312 317 1.144913 CACATTCCCATAATCCCCCGT 59.855 52.381 0.00 0.00 0.00 5.28
313 318 1.423541 TCACATTCCCATAATCCCCCG 59.576 52.381 0.00 0.00 0.00 5.73
314 319 3.434309 CATCACATTCCCATAATCCCCC 58.566 50.000 0.00 0.00 0.00 5.40
315 320 2.827921 GCATCACATTCCCATAATCCCC 59.172 50.000 0.00 0.00 0.00 4.81
316 321 2.827921 GGCATCACATTCCCATAATCCC 59.172 50.000 0.00 0.00 0.00 3.85
317 322 3.256631 GTGGCATCACATTCCCATAATCC 59.743 47.826 0.00 0.00 43.13 3.01
318 323 3.256631 GGTGGCATCACATTCCCATAATC 59.743 47.826 0.00 0.00 45.32 1.75
319 324 3.117016 AGGTGGCATCACATTCCCATAAT 60.117 43.478 0.00 0.00 45.32 1.28
320 325 2.244510 AGGTGGCATCACATTCCCATAA 59.755 45.455 0.00 0.00 45.32 1.90
321 326 1.852309 AGGTGGCATCACATTCCCATA 59.148 47.619 0.00 0.00 45.32 2.74
322 327 0.632835 AGGTGGCATCACATTCCCAT 59.367 50.000 0.00 0.00 45.32 4.00
323 328 0.323633 CAGGTGGCATCACATTCCCA 60.324 55.000 0.00 0.00 45.32 4.37
324 329 0.034186 TCAGGTGGCATCACATTCCC 60.034 55.000 0.00 0.00 45.32 3.97
325 330 1.838112 TTCAGGTGGCATCACATTCC 58.162 50.000 0.00 0.00 45.32 3.01
326 331 5.779529 ATAATTCAGGTGGCATCACATTC 57.220 39.130 0.00 0.00 45.32 2.67
327 332 6.549433 AAATAATTCAGGTGGCATCACATT 57.451 33.333 0.00 0.00 45.32 2.71
328 333 6.407299 GGAAAATAATTCAGGTGGCATCACAT 60.407 38.462 0.00 0.00 45.32 3.21
329 334 5.105392 GGAAAATAATTCAGGTGGCATCACA 60.105 40.000 0.00 0.00 45.32 3.58
330 335 5.105392 TGGAAAATAATTCAGGTGGCATCAC 60.105 40.000 0.00 0.00 42.91 3.06
331 336 5.022122 TGGAAAATAATTCAGGTGGCATCA 58.978 37.500 0.00 0.00 0.00 3.07
332 337 5.596836 TGGAAAATAATTCAGGTGGCATC 57.403 39.130 0.00 0.00 0.00 3.91
333 338 6.564557 AATGGAAAATAATTCAGGTGGCAT 57.435 33.333 0.00 0.00 0.00 4.40
334 339 6.371595 AAATGGAAAATAATTCAGGTGGCA 57.628 33.333 0.00 0.00 0.00 4.92
335 340 7.686438 AAAAATGGAAAATAATTCAGGTGGC 57.314 32.000 0.00 0.00 0.00 5.01
357 362 9.430623 TGTTACGTCTCTGATCATCAAATAAAA 57.569 29.630 0.00 0.00 0.00 1.52
358 363 8.996024 TGTTACGTCTCTGATCATCAAATAAA 57.004 30.769 0.00 0.00 0.00 1.40
359 364 8.466798 TCTGTTACGTCTCTGATCATCAAATAA 58.533 33.333 0.00 0.00 0.00 1.40
360 365 7.996385 TCTGTTACGTCTCTGATCATCAAATA 58.004 34.615 0.00 0.00 0.00 1.40
361 366 6.867550 TCTGTTACGTCTCTGATCATCAAAT 58.132 36.000 0.00 0.00 0.00 2.32
362 367 6.071896 ACTCTGTTACGTCTCTGATCATCAAA 60.072 38.462 0.00 0.00 0.00 2.69
363 368 5.416013 ACTCTGTTACGTCTCTGATCATCAA 59.584 40.000 0.00 0.00 0.00 2.57
364 369 4.944317 ACTCTGTTACGTCTCTGATCATCA 59.056 41.667 0.00 0.00 0.00 3.07
365 370 5.493133 ACTCTGTTACGTCTCTGATCATC 57.507 43.478 0.00 0.00 0.00 2.92
366 371 4.336993 GGACTCTGTTACGTCTCTGATCAT 59.663 45.833 0.00 0.00 0.00 2.45
367 372 3.690139 GGACTCTGTTACGTCTCTGATCA 59.310 47.826 0.00 0.00 0.00 2.92
368 373 3.690139 TGGACTCTGTTACGTCTCTGATC 59.310 47.826 0.00 0.00 0.00 2.92
369 374 3.687125 TGGACTCTGTTACGTCTCTGAT 58.313 45.455 0.00 0.00 0.00 2.90
370 375 3.136009 TGGACTCTGTTACGTCTCTGA 57.864 47.619 0.00 0.00 0.00 3.27
371 376 3.440522 TCATGGACTCTGTTACGTCTCTG 59.559 47.826 0.00 0.00 0.00 3.35
372 377 3.687125 TCATGGACTCTGTTACGTCTCT 58.313 45.455 0.00 0.00 0.00 3.10
373 378 3.690139 TCTCATGGACTCTGTTACGTCTC 59.310 47.826 0.00 0.00 0.00 3.36
374 379 3.687125 TCTCATGGACTCTGTTACGTCT 58.313 45.455 0.00 0.00 0.00 4.18
375 380 4.640789 ATCTCATGGACTCTGTTACGTC 57.359 45.455 0.00 0.00 0.00 4.34
376 381 6.507900 CATAATCTCATGGACTCTGTTACGT 58.492 40.000 0.00 0.00 0.00 3.57
377 382 6.999956 CATAATCTCATGGACTCTGTTACG 57.000 41.667 0.00 0.00 0.00 3.18
388 393 4.350816 TGTACCTTCCCCATAATCTCATGG 59.649 45.833 0.00 0.00 44.44 3.66
389 394 5.567037 TGTACCTTCCCCATAATCTCATG 57.433 43.478 0.00 0.00 0.00 3.07
390 395 5.672194 ACTTGTACCTTCCCCATAATCTCAT 59.328 40.000 0.00 0.00 0.00 2.90
391 396 5.036916 ACTTGTACCTTCCCCATAATCTCA 58.963 41.667 0.00 0.00 0.00 3.27
392 397 5.368989 CACTTGTACCTTCCCCATAATCTC 58.631 45.833 0.00 0.00 0.00 2.75
393 398 4.385310 GCACTTGTACCTTCCCCATAATCT 60.385 45.833 0.00 0.00 0.00 2.40
394 399 3.883489 GCACTTGTACCTTCCCCATAATC 59.117 47.826 0.00 0.00 0.00 1.75
395 400 3.684413 CGCACTTGTACCTTCCCCATAAT 60.684 47.826 0.00 0.00 0.00 1.28
396 401 2.355310 CGCACTTGTACCTTCCCCATAA 60.355 50.000 0.00 0.00 0.00 1.90
397 402 1.208535 CGCACTTGTACCTTCCCCATA 59.791 52.381 0.00 0.00 0.00 2.74
398 403 0.035439 CGCACTTGTACCTTCCCCAT 60.035 55.000 0.00 0.00 0.00 4.00
399 404 1.373435 CGCACTTGTACCTTCCCCA 59.627 57.895 0.00 0.00 0.00 4.96
400 405 0.953960 CACGCACTTGTACCTTCCCC 60.954 60.000 0.00 0.00 0.00 4.81
401 406 1.574702 GCACGCACTTGTACCTTCCC 61.575 60.000 0.00 0.00 0.00 3.97
402 407 1.866925 GCACGCACTTGTACCTTCC 59.133 57.895 0.00 0.00 0.00 3.46
403 408 0.942410 TCGCACGCACTTGTACCTTC 60.942 55.000 0.00 0.00 0.00 3.46
404 409 0.944311 CTCGCACGCACTTGTACCTT 60.944 55.000 0.00 0.00 0.00 3.50
405 410 1.372997 CTCGCACGCACTTGTACCT 60.373 57.895 0.00 0.00 0.00 3.08
406 411 1.344942 CTCTCGCACGCACTTGTACC 61.345 60.000 0.00 0.00 0.00 3.34
407 412 0.386858 TCTCTCGCACGCACTTGTAC 60.387 55.000 0.00 0.00 0.00 2.90
408 413 0.109735 CTCTCTCGCACGCACTTGTA 60.110 55.000 0.00 0.00 0.00 2.41
409 414 1.372251 CTCTCTCGCACGCACTTGT 60.372 57.895 0.00 0.00 0.00 3.16
410 415 1.069924 CTCTCTCTCGCACGCACTTG 61.070 60.000 0.00 0.00 0.00 3.16
411 416 1.211449 CTCTCTCTCGCACGCACTT 59.789 57.895 0.00 0.00 0.00 3.16
412 417 1.643868 CTCTCTCTCTCGCACGCACT 61.644 60.000 0.00 0.00 0.00 4.40
413 418 1.226267 CTCTCTCTCTCGCACGCAC 60.226 63.158 0.00 0.00 0.00 5.34
414 419 1.365368 CTCTCTCTCTCTCGCACGCA 61.365 60.000 0.00 0.00 0.00 5.24
415 420 1.087202 TCTCTCTCTCTCTCGCACGC 61.087 60.000 0.00 0.00 0.00 5.34
416 421 0.930310 CTCTCTCTCTCTCTCGCACG 59.070 60.000 0.00 0.00 0.00 5.34
417 422 2.205074 CTCTCTCTCTCTCTCTCGCAC 58.795 57.143 0.00 0.00 0.00 5.34
418 423 1.138859 CCTCTCTCTCTCTCTCTCGCA 59.861 57.143 0.00 0.00 0.00 5.10
419 424 1.541233 CCCTCTCTCTCTCTCTCTCGC 60.541 61.905 0.00 0.00 0.00 5.03
420 425 2.036475 CTCCCTCTCTCTCTCTCTCTCG 59.964 59.091 0.00 0.00 0.00 4.04
421 426 2.370189 CCTCCCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
422 427 2.293856 ACCTCCCTCTCTCTCTCTCTCT 60.294 54.545 0.00 0.00 0.00 3.10
423 428 2.127708 ACCTCCCTCTCTCTCTCTCTC 58.872 57.143 0.00 0.00 0.00 3.20
424 429 2.286935 ACCTCCCTCTCTCTCTCTCT 57.713 55.000 0.00 0.00 0.00 3.10
425 430 2.775384 TGTACCTCCCTCTCTCTCTCTC 59.225 54.545 0.00 0.00 0.00 3.20
426 431 2.853430 TGTACCTCCCTCTCTCTCTCT 58.147 52.381 0.00 0.00 0.00 3.10
427 432 3.655615 TTGTACCTCCCTCTCTCTCTC 57.344 52.381 0.00 0.00 0.00 3.20
428 433 4.542697 GATTTGTACCTCCCTCTCTCTCT 58.457 47.826 0.00 0.00 0.00 3.10
429 434 3.639561 GGATTTGTACCTCCCTCTCTCTC 59.360 52.174 0.00 0.00 0.00 3.20
430 435 3.012959 TGGATTTGTACCTCCCTCTCTCT 59.987 47.826 4.34 0.00 0.00 3.10
431 436 3.375699 TGGATTTGTACCTCCCTCTCTC 58.624 50.000 4.34 0.00 0.00 3.20
432 437 3.379452 CTGGATTTGTACCTCCCTCTCT 58.621 50.000 4.34 0.00 0.00 3.10
433 438 2.436173 CCTGGATTTGTACCTCCCTCTC 59.564 54.545 0.00 0.00 0.00 3.20
434 439 2.482494 CCTGGATTTGTACCTCCCTCT 58.518 52.381 0.00 0.00 0.00 3.69
435 440 1.490910 CCCTGGATTTGTACCTCCCTC 59.509 57.143 0.00 0.00 0.00 4.30
436 441 1.596496 CCCTGGATTTGTACCTCCCT 58.404 55.000 0.00 0.00 0.00 4.20
437 442 0.551396 CCCCTGGATTTGTACCTCCC 59.449 60.000 0.00 0.00 0.00 4.30
438 443 1.591768 TCCCCTGGATTTGTACCTCC 58.408 55.000 0.00 0.00 0.00 4.30
448 453 2.549694 TTCCCCATAATCCCCTGGAT 57.450 50.000 0.00 0.00 45.46 3.41
449 454 2.072973 CATTCCCCATAATCCCCTGGA 58.927 52.381 0.00 0.00 34.24 3.86
450 455 1.788915 ACATTCCCCATAATCCCCTGG 59.211 52.381 0.00 0.00 0.00 4.45
451 456 2.446666 TCACATTCCCCATAATCCCCTG 59.553 50.000 0.00 0.00 0.00 4.45
452 457 2.800656 TCACATTCCCCATAATCCCCT 58.199 47.619 0.00 0.00 0.00 4.79
453 458 3.181418 ACATCACATTCCCCATAATCCCC 60.181 47.826 0.00 0.00 0.00 4.81
454 459 4.118168 ACATCACATTCCCCATAATCCC 57.882 45.455 0.00 0.00 0.00 3.85
455 460 4.895297 ACAACATCACATTCCCCATAATCC 59.105 41.667 0.00 0.00 0.00 3.01
456 461 6.294176 GCTACAACATCACATTCCCCATAATC 60.294 42.308 0.00 0.00 0.00 1.75
457 462 5.536161 GCTACAACATCACATTCCCCATAAT 59.464 40.000 0.00 0.00 0.00 1.28
458 463 4.887071 GCTACAACATCACATTCCCCATAA 59.113 41.667 0.00 0.00 0.00 1.90
459 464 4.080072 TGCTACAACATCACATTCCCCATA 60.080 41.667 0.00 0.00 0.00 2.74
460 465 3.290710 GCTACAACATCACATTCCCCAT 58.709 45.455 0.00 0.00 0.00 4.00
461 466 2.040947 TGCTACAACATCACATTCCCCA 59.959 45.455 0.00 0.00 0.00 4.96
462 467 2.722094 TGCTACAACATCACATTCCCC 58.278 47.619 0.00 0.00 0.00 4.81
463 468 3.316308 GGATGCTACAACATCACATTCCC 59.684 47.826 6.82 0.00 46.81 3.97
464 469 3.947196 TGGATGCTACAACATCACATTCC 59.053 43.478 6.82 0.00 46.81 3.01
465 470 5.297527 TCATGGATGCTACAACATCACATTC 59.702 40.000 6.82 0.00 46.81 2.67
466 471 5.195185 TCATGGATGCTACAACATCACATT 58.805 37.500 6.82 0.00 46.81 2.71
467 472 4.784177 TCATGGATGCTACAACATCACAT 58.216 39.130 6.82 5.18 46.81 3.21
468 473 4.219264 TCATGGATGCTACAACATCACA 57.781 40.909 6.82 3.30 46.81 3.58
469 474 4.395854 TGTTCATGGATGCTACAACATCAC 59.604 41.667 6.82 0.00 46.81 3.06
470 475 4.587891 TGTTCATGGATGCTACAACATCA 58.412 39.130 6.82 0.00 46.81 3.07
471 476 4.497006 GCTGTTCATGGATGCTACAACATC 60.497 45.833 0.00 0.00 44.73 3.06
472 477 3.379372 GCTGTTCATGGATGCTACAACAT 59.621 43.478 0.00 0.00 0.00 2.71
473 478 2.749076 GCTGTTCATGGATGCTACAACA 59.251 45.455 0.00 0.00 0.00 3.33
474 479 3.012518 AGCTGTTCATGGATGCTACAAC 58.987 45.455 3.02 0.00 31.71 3.32
599 604 6.471233 TTCTCATTGTGGGAGTCTACATAG 57.529 41.667 2.41 2.34 34.35 2.23
601 606 4.383552 GCTTCTCATTGTGGGAGTCTACAT 60.384 45.833 2.41 0.00 34.35 2.29
686 693 2.498078 GTTGTGTCCAAGGGTCCAAAAA 59.502 45.455 0.00 0.00 0.00 1.94
751 758 0.666913 CGTCCAGGGTAGGTATGACG 59.333 60.000 0.00 0.00 39.44 4.35
755 762 0.337428 ACCACGTCCAGGGTAGGTAT 59.663 55.000 0.00 0.00 35.09 2.73
774 784 9.135843 CGTTTGACTGTTTAGATTGTAGTGATA 57.864 33.333 0.00 0.00 0.00 2.15
785 807 4.185394 TGCTCAACGTTTGACTGTTTAGA 58.815 39.130 0.00 0.00 35.46 2.10
794 844 5.297547 AGTCTATTTCTGCTCAACGTTTGA 58.702 37.500 0.00 0.00 38.17 2.69
810 860 4.973168 TGCACTTTGTCTTGGAGTCTATT 58.027 39.130 0.00 0.00 0.00 1.73
825 875 9.712305 GGTCATCTACTTGTATATATGCACTTT 57.288 33.333 2.64 0.00 0.00 2.66
869 919 0.748367 AGCATGCGTAGAGAGTCCGA 60.748 55.000 13.01 0.00 0.00 4.55
933 984 4.280494 AGTGCGGTTCGAGTGCGT 62.280 61.111 1.96 0.00 38.98 5.24
935 986 4.077188 GCAGTGCGGTTCGAGTGC 62.077 66.667 0.00 0.00 0.00 4.40
941 1000 2.959357 GCAGTGAGCAGTGCGGTTC 61.959 63.158 13.83 2.38 46.30 3.62
998 1057 4.513692 CGGCGGAGTATTTCAAATCCATAA 59.486 41.667 0.00 0.00 0.00 1.90
1004 1063 4.380128 GGAAAACGGCGGAGTATTTCAAAT 60.380 41.667 13.24 0.00 32.91 2.32
1012 1071 0.901580 AGGAGGAAAACGGCGGAGTA 60.902 55.000 13.24 0.00 0.00 2.59
1042 1101 3.246403 TCATGGCAACGCATGAGAA 57.754 47.368 2.50 0.00 42.51 2.87
1105 1164 4.335647 CACCTCGGGCTGGTGCTT 62.336 66.667 10.69 0.00 46.73 3.91
1144 1203 1.228124 CTTCTGGGAACGGTGGCAA 60.228 57.895 0.00 0.00 38.16 4.52
1179 1238 0.909610 CCACCTTGGGTAGCTCAGGA 60.910 60.000 14.57 0.00 32.11 3.86
1188 1247 2.895424 CGGAAGCTCCACCTTGGGT 61.895 63.158 0.00 0.00 38.32 4.51
1231 1347 2.440247 GGGCATCTCCGGTTTGGG 60.440 66.667 0.00 0.00 38.76 4.12
1236 1361 2.610859 ACCTTGGGCATCTCCGGT 60.611 61.111 0.00 0.00 34.94 5.28
1239 1364 1.225704 CTCCACCTTGGGCATCTCC 59.774 63.158 0.00 0.00 38.32 3.71
1265 1390 1.612199 GCATGTGTACCTCCGGGAAAA 60.612 52.381 0.00 0.00 36.25 2.29
1267 1392 1.600107 GCATGTGTACCTCCGGGAA 59.400 57.895 0.00 0.00 36.25 3.97
1278 1403 2.601367 GGCTTGGGTGGCATGTGT 60.601 61.111 0.00 0.00 0.00 3.72
1426 1656 1.425066 TGGTTCTCATGGCTTGACCTT 59.575 47.619 9.98 0.00 40.22 3.50
1430 1660 0.038166 GGGTGGTTCTCATGGCTTGA 59.962 55.000 2.86 2.86 0.00 3.02
1446 1676 5.771165 ACGAAATAACAATGTTGGTAAGGGT 59.229 36.000 9.15 0.00 33.45 4.34
1481 1718 2.159338 ACAGCAATAGGTACACGTACGG 60.159 50.000 21.06 11.05 36.94 4.02
1487 1724 3.813166 ACACAACACAGCAATAGGTACAC 59.187 43.478 0.00 0.00 0.00 2.90
1533 1771 1.013596 CACAACACTCGCTGGAAACA 58.986 50.000 0.00 0.00 39.59 2.83
1538 1776 0.249447 TCACTCACAACACTCGCTGG 60.249 55.000 0.00 0.00 0.00 4.85
1581 1821 4.117685 GGGTGCGAAAGTATATTTCTCGT 58.882 43.478 11.27 0.00 32.23 4.18
1582 1822 4.369182 AGGGTGCGAAAGTATATTTCTCG 58.631 43.478 0.00 7.62 0.00 4.04
1607 1858 5.713025 TGCTTTTGAAATGCTCTTATGACC 58.287 37.500 15.38 0.00 0.00 4.02
1640 1893 4.810491 ACGAAGCTTACGGTGAAAACTTAA 59.190 37.500 18.17 0.00 34.93 1.85
1666 1925 3.313791 TCGATGGGAAATGGATAGGTGA 58.686 45.455 0.00 0.00 0.00 4.02
1782 2051 0.460459 TCAGACCGTTGACGCAAACA 60.460 50.000 0.00 0.00 38.18 2.83
1879 2715 3.040763 GATCTCTGCCGCATCCGC 61.041 66.667 0.00 0.00 0.00 5.54
2067 2909 1.533731 ACTCGTAATGCGTTGGTTTGG 59.466 47.619 0.08 0.00 42.13 3.28
2071 2913 1.425412 GACACTCGTAATGCGTTGGT 58.575 50.000 0.08 0.00 42.13 3.67
2073 2915 1.424403 TGGACACTCGTAATGCGTTG 58.576 50.000 0.08 0.00 42.13 4.10
2139 2984 3.370978 TGCTTGCTTGATCGCTTAACTAC 59.629 43.478 0.00 0.00 0.00 2.73
2153 2998 3.019564 CCTGGCTATAGTTTGCTTGCTT 58.980 45.455 0.84 0.00 0.00 3.91
2169 3014 1.039856 TTTGAGCTTCAAACCCTGGC 58.960 50.000 7.09 0.00 41.02 4.85
2239 3085 3.756933 AAGCAAGTTTGGTCCGTACTA 57.243 42.857 0.00 0.00 38.04 1.82
2321 5709 6.826231 TGTAGGAGTTAGATGAGACTTCTCTG 59.174 42.308 7.74 0.00 43.25 3.35
2355 5743 5.067283 GTGTAGGAGTTTTCTTTTTGCAGGA 59.933 40.000 0.00 0.00 0.00 3.86
2358 5746 7.633193 TTAGTGTAGGAGTTTTCTTTTTGCA 57.367 32.000 0.00 0.00 0.00 4.08
2359 5747 8.968242 CAATTAGTGTAGGAGTTTTCTTTTTGC 58.032 33.333 0.00 0.00 0.00 3.68
2416 5813 7.771927 GGATTTTACATGGAGATTCATGGAT 57.228 36.000 6.08 0.00 46.33 3.41


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

AutoCloner maintained by Alex Coulton.