Multiple sequence alignment - TraesCS5A01G278500

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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 TraesCS5A01G278500 chr5A 100.000 2264 0 0 1 2264 487949969 487947706 0.000000e+00 4181.0
1 TraesCS5A01G278500 chr5A 86.536 765 64 10 665 1396 487918998 487918240 0.000000e+00 806.0
2 TraesCS5A01G278500 chr5A 85.505 752 72 24 663 1403 487941162 487940437 0.000000e+00 750.0
3 TraesCS5A01G278500 chr5A 88.772 570 47 7 792 1345 487985127 487984559 0.000000e+00 682.0
4 TraesCS5A01G278500 chr5A 88.929 560 34 7 875 1407 487925068 487924510 0.000000e+00 665.0
5 TraesCS5A01G278500 chr5A 89.385 179 12 6 14 187 487943151 487942975 3.790000e-53 219.0
6 TraesCS5A01G278500 chr5A 90.826 109 10 0 721 829 487925189 487925081 1.810000e-31 147.0
7 TraesCS5A01G278500 chr1A 96.105 873 25 2 1401 2264 248363323 248362451 0.000000e+00 1415.0
8 TraesCS5A01G278500 chr5B 87.517 721 47 13 726 1407 463918987 463918271 0.000000e+00 793.0
9 TraesCS5A01G278500 chr5B 92.193 538 30 6 880 1405 463912520 463911983 0.000000e+00 750.0
10 TraesCS5A01G278500 chr5B 88.585 622 52 7 721 1331 463945364 463944751 0.000000e+00 737.0
11 TraesCS5A01G278500 chr5B 88.384 594 40 10 767 1339 463937962 463937377 0.000000e+00 688.0
12 TraesCS5A01G278500 chr5B 87.755 49 4 2 20 66 463913134 463913086 3.140000e-04 56.5
13 TraesCS5A01G278500 chr5D 89.028 638 42 9 721 1345 386036129 386035507 0.000000e+00 765.0
14 TraesCS5A01G278500 chr5D 87.676 641 60 7 687 1314 386067700 386067066 0.000000e+00 728.0
15 TraesCS5A01G278500 chr5D 89.362 564 41 6 767 1311 386046322 386045759 0.000000e+00 691.0
16 TraesCS5A01G278500 chr5D 93.261 371 16 4 984 1345 385978550 385978180 2.560000e-149 538.0
17 TraesCS5A01G278500 chr5D 89.340 197 10 7 1 187 386036508 386036313 1.050000e-58 237.0
18 TraesCS5A01G278500 chr5D 88.384 198 12 5 1 187 385979182 385978985 6.290000e-56 228.0
19 TraesCS5A01G278500 chr5D 85.333 150 11 7 1 140 386046472 386046324 6.520000e-31 145.0
20 TraesCS5A01G278500 chr5D 88.596 114 6 4 14 121 386060810 386060698 5.070000e-27 132.0
21 TraesCS5A01G278500 chr5D 97.368 38 1 0 657 694 386067769 386067732 5.220000e-07 65.8
22 TraesCS5A01G278500 chr3D 86.310 336 39 6 181 514 553042917 553043247 2.140000e-95 359.0
23 TraesCS5A01G278500 chr3D 85.119 336 43 6 181 514 553080953 553081283 1.000000e-88 337.0
24 TraesCS5A01G278500 chrUn 86.012 336 40 6 181 514 241684153 241683823 9.950000e-94 353.0
25 TraesCS5A01G278500 chrUn 85.417 336 42 6 181 514 344549968 344550298 2.150000e-90 342.0
26 TraesCS5A01G278500 chr6D 84.195 329 44 8 190 516 5904762 5904440 1.690000e-81 313.0
27 TraesCS5A01G278500 chr6D 81.500 200 35 2 317 515 34925934 34926132 1.800000e-36 163.0
28 TraesCS5A01G278500 chr6D 80.000 180 31 5 314 491 134745118 134744942 6.560000e-26 128.0
29 TraesCS5A01G278500 chr4B 81.271 299 30 11 224 520 61290056 61289782 3.790000e-53 219.0
30 TraesCS5A01G278500 chr1B 78.698 338 60 11 187 519 616127218 616127548 4.900000e-52 215.0
31 TraesCS5A01G278500 chr7A 97.727 44 1 0 1404 1447 232336371 232336414 2.410000e-10 76.8
32 TraesCS5A01G278500 chr4A 85.714 63 9 0 1408 1470 687380087 687380149 1.450000e-07 67.6
33 TraesCS5A01G278500 chr2A 84.127 63 10 0 1408 1470 767794649 767794711 6.750000e-06 62.1


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 TraesCS5A01G278500 chr5A 487947706 487949969 2263 True 4181.00 4181 100.0000 1 2264 1 chr5A.!!$R2 2263
1 TraesCS5A01G278500 chr5A 487918240 487918998 758 True 806.00 806 86.5360 665 1396 1 chr5A.!!$R1 731
2 TraesCS5A01G278500 chr5A 487984559 487985127 568 True 682.00 682 88.7720 792 1345 1 chr5A.!!$R3 553
3 TraesCS5A01G278500 chr5A 487940437 487943151 2714 True 484.50 750 87.4450 14 1403 2 chr5A.!!$R5 1389
4 TraesCS5A01G278500 chr5A 487924510 487925189 679 True 406.00 665 89.8775 721 1407 2 chr5A.!!$R4 686
5 TraesCS5A01G278500 chr1A 248362451 248363323 872 True 1415.00 1415 96.1050 1401 2264 1 chr1A.!!$R1 863
6 TraesCS5A01G278500 chr5B 463918271 463918987 716 True 793.00 793 87.5170 726 1407 1 chr5B.!!$R1 681
7 TraesCS5A01G278500 chr5B 463944751 463945364 613 True 737.00 737 88.5850 721 1331 1 chr5B.!!$R3 610
8 TraesCS5A01G278500 chr5B 463937377 463937962 585 True 688.00 688 88.3840 767 1339 1 chr5B.!!$R2 572
9 TraesCS5A01G278500 chr5B 463911983 463913134 1151 True 403.25 750 89.9740 20 1405 2 chr5B.!!$R4 1385
10 TraesCS5A01G278500 chr5D 386035507 386036508 1001 True 501.00 765 89.1840 1 1345 2 chr5D.!!$R3 1344
11 TraesCS5A01G278500 chr5D 386045759 386046472 713 True 418.00 691 87.3475 1 1311 2 chr5D.!!$R4 1310
12 TraesCS5A01G278500 chr5D 386067066 386067769 703 True 396.90 728 92.5220 657 1314 2 chr5D.!!$R5 657
13 TraesCS5A01G278500 chr5D 385978180 385979182 1002 True 383.00 538 90.8225 1 1345 2 chr5D.!!$R2 1344

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
500 672 0.040067 GAGCAGTTTTCGGGCACTTG 60.04 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 3809 0.100861 GTCATCCTTCTCGTCGACCC 59.899 60.0 10.58 0.0 0.0 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
18 25 1.373497 CGCTCGATCCATAGCACCC 60.373 63.158 9.32 0.00 38.70 4.61
121 293 1.153862 GAGCAGCTCGAGAGTGTGG 60.154 63.158 18.75 0.00 0.00 4.17
126 298 0.250945 AGCTCGAGAGTGTGGAGACA 60.251 55.000 18.75 0.00 32.82 3.41
187 359 1.300311 CGCCACGTTGGTGTAGTGA 60.300 57.895 8.79 0.00 42.85 3.41
189 361 0.249741 GCCACGTTGGTGTAGTGACT 60.250 55.000 6.02 0.00 42.80 3.41
190 362 1.000060 GCCACGTTGGTGTAGTGACTA 60.000 52.381 6.02 0.00 42.80 2.59
191 363 2.546373 GCCACGTTGGTGTAGTGACTAA 60.546 50.000 0.00 0.00 42.80 2.24
195 367 3.243336 CGTTGGTGTAGTGACTAAGAGC 58.757 50.000 0.00 0.00 0.00 4.09
197 369 4.618460 CGTTGGTGTAGTGACTAAGAGCAT 60.618 45.833 0.00 0.00 0.00 3.79
198 370 4.720649 TGGTGTAGTGACTAAGAGCATC 57.279 45.455 0.00 0.00 0.00 3.91
212 384 1.129437 GAGCATCTCCAACAAAGTCGC 59.871 52.381 0.00 0.00 0.00 5.19
213 385 0.874390 GCATCTCCAACAAAGTCGCA 59.126 50.000 0.00 0.00 0.00 5.10
214 386 1.266718 GCATCTCCAACAAAGTCGCAA 59.733 47.619 0.00 0.00 0.00 4.85
215 387 2.287547 GCATCTCCAACAAAGTCGCAAA 60.288 45.455 0.00 0.00 0.00 3.68
216 388 3.795150 GCATCTCCAACAAAGTCGCAAAA 60.795 43.478 0.00 0.00 0.00 2.44
217 389 4.358851 CATCTCCAACAAAGTCGCAAAAA 58.641 39.130 0.00 0.00 0.00 1.94
245 417 8.669394 ATTGAGCGTTAAAATAGTTTTACAGC 57.331 30.769 5.75 8.76 37.70 4.40
246 418 6.301108 TGAGCGTTAAAATAGTTTTACAGCG 58.699 36.000 5.75 0.00 40.07 5.18
247 419 6.073657 TGAGCGTTAAAATAGTTTTACAGCGT 60.074 34.615 5.75 1.68 40.07 5.07
248 420 6.301861 AGCGTTAAAATAGTTTTACAGCGTC 58.698 36.000 5.75 0.00 40.07 5.19
249 421 6.072733 GCGTTAAAATAGTTTTACAGCGTCA 58.927 36.000 5.75 0.00 35.03 4.35
250 422 6.030693 GCGTTAAAATAGTTTTACAGCGTCAC 59.969 38.462 5.75 1.13 35.03 3.67
251 423 7.285788 CGTTAAAATAGTTTTACAGCGTCACT 58.714 34.615 5.75 0.00 35.03 3.41
252 424 7.265495 CGTTAAAATAGTTTTACAGCGTCACTG 59.735 37.037 5.75 0.00 41.88 3.66
262 434 3.542712 CAGCGTCACTGTAGCATTTTT 57.457 42.857 5.20 0.00 41.86 1.94
263 435 4.661993 CAGCGTCACTGTAGCATTTTTA 57.338 40.909 5.20 0.00 41.86 1.52
264 436 4.641954 CAGCGTCACTGTAGCATTTTTAG 58.358 43.478 5.20 0.00 41.86 1.85
265 437 3.125316 AGCGTCACTGTAGCATTTTTAGC 59.875 43.478 5.20 0.00 0.00 3.09
266 438 3.659735 CGTCACTGTAGCATTTTTAGCG 58.340 45.455 0.00 0.00 37.01 4.26
267 439 3.417185 GTCACTGTAGCATTTTTAGCGC 58.583 45.455 0.00 0.00 37.01 5.92
268 440 2.093625 TCACTGTAGCATTTTTAGCGCG 59.906 45.455 0.00 0.00 37.01 6.86
269 441 1.202031 ACTGTAGCATTTTTAGCGCGC 60.202 47.619 26.66 26.66 37.01 6.86
270 442 1.062587 CTGTAGCATTTTTAGCGCGCT 59.937 47.619 38.01 38.01 37.01 5.92
271 443 1.202020 TGTAGCATTTTTAGCGCGCTG 60.202 47.619 41.85 26.18 37.01 5.18
272 444 0.248054 TAGCATTTTTAGCGCGCTGC 60.248 50.000 41.85 33.81 46.98 5.25
296 468 4.471157 CCAACATTGGTTTTTCACATGC 57.529 40.909 2.22 0.00 43.43 4.06
297 469 3.250521 CCAACATTGGTTTTTCACATGCC 59.749 43.478 2.22 0.00 43.43 4.40
298 470 3.124578 ACATTGGTTTTTCACATGCCC 57.875 42.857 0.00 0.00 0.00 5.36
299 471 2.437281 ACATTGGTTTTTCACATGCCCA 59.563 40.909 0.00 0.00 0.00 5.36
300 472 3.118112 ACATTGGTTTTTCACATGCCCAA 60.118 39.130 0.00 0.00 36.49 4.12
301 473 3.634397 TTGGTTTTTCACATGCCCAAA 57.366 38.095 0.00 0.00 0.00 3.28
302 474 3.634397 TGGTTTTTCACATGCCCAAAA 57.366 38.095 0.00 0.00 0.00 2.44
303 475 3.955471 TGGTTTTTCACATGCCCAAAAA 58.045 36.364 0.00 0.00 0.00 1.94
341 513 1.578915 CACGCGTGCAAATTATGAAGC 59.421 47.619 28.16 0.00 0.00 3.86
342 514 0.833264 CGCGTGCAAATTATGAAGCG 59.167 50.000 0.00 3.79 39.73 4.68
343 515 0.567509 GCGTGCAAATTATGAAGCGC 59.432 50.000 0.00 0.00 37.61 5.92
345 517 0.567509 GTGCAAATTATGAAGCGCGC 59.432 50.000 26.66 26.66 0.00 6.86
346 518 0.861034 TGCAAATTATGAAGCGCGCG 60.861 50.000 28.44 28.44 0.00 6.86
347 519 1.832913 CAAATTATGAAGCGCGCGC 59.167 52.632 45.10 45.10 42.33 6.86
366 538 3.370231 GTCCGGCGCCCAACATTT 61.370 61.111 23.46 0.00 0.00 2.32
367 539 3.369400 TCCGGCGCCCAACATTTG 61.369 61.111 23.46 3.38 0.00 2.32
368 540 3.679738 CCGGCGCCCAACATTTGT 61.680 61.111 23.46 0.00 0.00 2.83
369 541 2.336478 CCGGCGCCCAACATTTGTA 61.336 57.895 23.46 0.00 0.00 2.41
370 542 1.136565 CGGCGCCCAACATTTGTAG 59.863 57.895 23.46 0.00 0.00 2.74
371 543 1.153842 GGCGCCCAACATTTGTAGC 60.154 57.895 18.11 0.00 0.00 3.58
372 544 1.583986 GCGCCCAACATTTGTAGCA 59.416 52.632 0.00 0.00 0.00 3.49
373 545 0.173255 GCGCCCAACATTTGTAGCAT 59.827 50.000 0.00 0.00 0.00 3.79
374 546 1.912001 CGCCCAACATTTGTAGCATG 58.088 50.000 0.00 0.00 0.00 4.06
375 547 1.202114 CGCCCAACATTTGTAGCATGT 59.798 47.619 0.00 0.00 36.36 3.21
376 548 2.609350 GCCCAACATTTGTAGCATGTG 58.391 47.619 0.00 0.00 34.97 3.21
377 549 2.230992 GCCCAACATTTGTAGCATGTGA 59.769 45.455 0.00 0.00 34.97 3.58
378 550 3.119029 GCCCAACATTTGTAGCATGTGAT 60.119 43.478 0.00 0.00 34.97 3.06
379 551 4.097741 GCCCAACATTTGTAGCATGTGATA 59.902 41.667 0.00 0.00 34.97 2.15
380 552 5.734220 GCCCAACATTTGTAGCATGTGATAG 60.734 44.000 0.00 0.00 34.97 2.08
381 553 5.276270 CCAACATTTGTAGCATGTGATAGC 58.724 41.667 0.00 0.00 34.97 2.97
382 554 4.801147 ACATTTGTAGCATGTGATAGCG 57.199 40.909 0.00 0.00 33.42 4.26
383 555 3.002656 ACATTTGTAGCATGTGATAGCGC 59.997 43.478 0.00 0.00 33.42 5.92
384 556 2.602257 TTGTAGCATGTGATAGCGCT 57.398 45.000 17.26 17.26 38.51 5.92
385 557 2.602257 TGTAGCATGTGATAGCGCTT 57.398 45.000 18.68 2.89 35.93 4.68
386 558 2.905075 TGTAGCATGTGATAGCGCTTT 58.095 42.857 18.68 8.03 35.93 3.51
387 559 3.270027 TGTAGCATGTGATAGCGCTTTT 58.730 40.909 18.68 3.01 35.93 2.27
388 560 4.438148 TGTAGCATGTGATAGCGCTTTTA 58.562 39.130 18.68 0.20 35.93 1.52
389 561 4.873259 TGTAGCATGTGATAGCGCTTTTAA 59.127 37.500 18.68 0.00 35.93 1.52
390 562 4.542662 AGCATGTGATAGCGCTTTTAAG 57.457 40.909 18.68 1.01 35.48 1.85
411 583 4.629527 GCAGGTGCGTTAAATTCTTTTG 57.370 40.909 0.00 0.00 0.00 2.44
412 584 4.048504 GCAGGTGCGTTAAATTCTTTTGT 58.951 39.130 0.00 0.00 0.00 2.83
413 585 4.085107 GCAGGTGCGTTAAATTCTTTTGTG 60.085 41.667 0.00 0.00 0.00 3.33
414 586 4.048504 AGGTGCGTTAAATTCTTTTGTGC 58.951 39.130 0.00 0.00 0.00 4.57
415 587 3.121496 GGTGCGTTAAATTCTTTTGTGCG 60.121 43.478 0.00 0.00 0.00 5.34
416 588 3.484285 GTGCGTTAAATTCTTTTGTGCGT 59.516 39.130 0.00 0.00 0.00 5.24
417 589 3.483922 TGCGTTAAATTCTTTTGTGCGTG 59.516 39.130 0.00 0.00 0.00 5.34
418 590 3.658088 GCGTTAAATTCTTTTGTGCGTGC 60.658 43.478 0.00 0.00 0.00 5.34
419 591 3.483922 CGTTAAATTCTTTTGTGCGTGCA 59.516 39.130 0.00 0.00 0.00 4.57
420 592 4.148000 CGTTAAATTCTTTTGTGCGTGCAT 59.852 37.500 0.00 0.00 0.00 3.96
421 593 5.332205 CGTTAAATTCTTTTGTGCGTGCATT 60.332 36.000 0.00 0.00 0.00 3.56
422 594 6.129326 CGTTAAATTCTTTTGTGCGTGCATTA 60.129 34.615 0.00 0.00 0.00 1.90
423 595 7.410300 CGTTAAATTCTTTTGTGCGTGCATTAT 60.410 33.333 0.00 0.00 0.00 1.28
424 596 6.783892 AAATTCTTTTGTGCGTGCATTATT 57.216 29.167 0.00 0.00 0.00 1.40
425 597 6.783892 AATTCTTTTGTGCGTGCATTATTT 57.216 29.167 0.00 0.00 0.00 1.40
426 598 6.783892 ATTCTTTTGTGCGTGCATTATTTT 57.216 29.167 0.00 0.00 0.00 1.82
427 599 5.573296 TCTTTTGTGCGTGCATTATTTTG 57.427 34.783 0.00 0.00 0.00 2.44
428 600 3.784883 TTTGTGCGTGCATTATTTTGC 57.215 38.095 0.00 0.00 43.07 3.68
439 611 5.138800 GCATTATTTTGCAGCATCTGTTG 57.861 39.130 0.00 0.00 42.31 3.33
440 612 4.865925 GCATTATTTTGCAGCATCTGTTGA 59.134 37.500 0.00 0.00 42.31 3.18
441 613 5.349270 GCATTATTTTGCAGCATCTGTTGAA 59.651 36.000 0.00 0.00 42.31 2.69
442 614 6.455113 GCATTATTTTGCAGCATCTGTTGAAG 60.455 38.462 0.00 0.00 42.31 3.02
443 615 2.427232 TTTGCAGCATCTGTTGAAGC 57.573 45.000 0.00 0.00 37.19 3.86
444 616 0.599558 TTGCAGCATCTGTTGAAGCC 59.400 50.000 0.00 0.00 37.60 4.35
445 617 0.251033 TGCAGCATCTGTTGAAGCCT 60.251 50.000 0.00 0.00 37.60 4.58
446 618 0.450983 GCAGCATCTGTTGAAGCCTC 59.549 55.000 0.00 0.00 37.60 4.70
447 619 1.949547 GCAGCATCTGTTGAAGCCTCT 60.950 52.381 0.00 0.00 37.60 3.69
448 620 2.008329 CAGCATCTGTTGAAGCCTCTC 58.992 52.381 0.00 0.00 37.60 3.20
449 621 1.065564 AGCATCTGTTGAAGCCTCTCC 60.066 52.381 0.00 0.00 37.60 3.71
450 622 1.649664 CATCTGTTGAAGCCTCTCCG 58.350 55.000 0.00 0.00 0.00 4.63
451 623 0.539051 ATCTGTTGAAGCCTCTCCGG 59.461 55.000 0.00 0.00 0.00 5.14
460 632 2.582436 CCTCTCCGGCGCCTAAAA 59.418 61.111 26.68 6.57 0.00 1.52
461 633 1.078708 CCTCTCCGGCGCCTAAAAA 60.079 57.895 26.68 5.00 0.00 1.94
462 634 1.090052 CCTCTCCGGCGCCTAAAAAG 61.090 60.000 26.68 14.59 0.00 2.27
463 635 0.108329 CTCTCCGGCGCCTAAAAAGA 60.108 55.000 26.68 17.18 0.00 2.52
464 636 0.322322 TCTCCGGCGCCTAAAAAGAA 59.678 50.000 26.68 0.00 0.00 2.52
465 637 0.446616 CTCCGGCGCCTAAAAAGAAC 59.553 55.000 26.68 0.00 0.00 3.01
466 638 1.133869 CCGGCGCCTAAAAAGAACG 59.866 57.895 26.68 6.63 0.00 3.95
467 639 1.133869 CGGCGCCTAAAAAGAACGG 59.866 57.895 26.68 0.00 0.00 4.44
468 640 1.154093 GGCGCCTAAAAAGAACGGC 60.154 57.895 22.15 0.00 42.04 5.68
469 641 1.583495 GGCGCCTAAAAAGAACGGCT 61.583 55.000 22.15 0.00 44.73 5.52
470 642 0.240145 GCGCCTAAAAAGAACGGCTT 59.760 50.000 0.00 0.00 40.34 4.35
480 652 3.963383 AAGAACGGCTTTTAGTGTGTG 57.037 42.857 0.00 0.00 31.11 3.82
481 653 2.218603 AGAACGGCTTTTAGTGTGTGG 58.781 47.619 0.00 0.00 0.00 4.17
482 654 2.158871 AGAACGGCTTTTAGTGTGTGGA 60.159 45.455 0.00 0.00 0.00 4.02
483 655 1.878953 ACGGCTTTTAGTGTGTGGAG 58.121 50.000 0.00 0.00 0.00 3.86
484 656 0.517316 CGGCTTTTAGTGTGTGGAGC 59.483 55.000 0.00 0.00 0.00 4.70
485 657 1.604604 GGCTTTTAGTGTGTGGAGCA 58.395 50.000 0.00 0.00 32.01 4.26
486 658 1.537202 GGCTTTTAGTGTGTGGAGCAG 59.463 52.381 0.00 0.00 32.01 4.24
487 659 2.222027 GCTTTTAGTGTGTGGAGCAGT 58.778 47.619 0.00 0.00 0.00 4.40
488 660 2.618709 GCTTTTAGTGTGTGGAGCAGTT 59.381 45.455 0.00 0.00 0.00 3.16
489 661 3.066760 GCTTTTAGTGTGTGGAGCAGTTT 59.933 43.478 0.00 0.00 0.00 2.66
490 662 4.440112 GCTTTTAGTGTGTGGAGCAGTTTT 60.440 41.667 0.00 0.00 0.00 2.43
491 663 4.893424 TTTAGTGTGTGGAGCAGTTTTC 57.107 40.909 0.00 0.00 0.00 2.29
492 664 1.299541 AGTGTGTGGAGCAGTTTTCG 58.700 50.000 0.00 0.00 0.00 3.46
493 665 0.307760 GTGTGTGGAGCAGTTTTCGG 59.692 55.000 0.00 0.00 0.00 4.30
494 666 0.817634 TGTGTGGAGCAGTTTTCGGG 60.818 55.000 0.00 0.00 0.00 5.14
495 667 1.896660 TGTGGAGCAGTTTTCGGGC 60.897 57.895 0.00 0.00 0.00 6.13
496 668 1.896660 GTGGAGCAGTTTTCGGGCA 60.897 57.895 0.00 0.00 0.00 5.36
497 669 1.896660 TGGAGCAGTTTTCGGGCAC 60.897 57.895 0.00 0.00 0.00 5.01
498 670 1.600916 GGAGCAGTTTTCGGGCACT 60.601 57.895 0.00 0.00 0.00 4.40
499 671 1.172812 GGAGCAGTTTTCGGGCACTT 61.173 55.000 0.00 0.00 0.00 3.16
500 672 0.040067 GAGCAGTTTTCGGGCACTTG 60.040 55.000 0.00 0.00 0.00 3.16
501 673 0.751643 AGCAGTTTTCGGGCACTTGT 60.752 50.000 0.00 0.00 0.00 3.16
502 674 0.102300 GCAGTTTTCGGGCACTTGTT 59.898 50.000 0.00 0.00 0.00 2.83
503 675 1.838913 CAGTTTTCGGGCACTTGTTG 58.161 50.000 0.00 0.00 0.00 3.33
504 676 0.744281 AGTTTTCGGGCACTTGTTGG 59.256 50.000 0.00 0.00 0.00 3.77
505 677 0.741915 GTTTTCGGGCACTTGTTGGA 59.258 50.000 0.00 0.00 0.00 3.53
506 678 1.028905 TTTTCGGGCACTTGTTGGAG 58.971 50.000 0.00 0.00 0.00 3.86
507 679 0.181587 TTTCGGGCACTTGTTGGAGA 59.818 50.000 0.00 0.00 0.00 3.71
508 680 0.400213 TTCGGGCACTTGTTGGAGAT 59.600 50.000 0.00 0.00 0.00 2.75
509 681 0.321564 TCGGGCACTTGTTGGAGATG 60.322 55.000 0.00 0.00 0.00 2.90
511 683 0.610232 GGGCACTTGTTGGAGATGCT 60.610 55.000 0.00 0.00 36.52 3.79
515 2391 3.338249 GCACTTGTTGGAGATGCTCTAA 58.662 45.455 0.00 0.00 33.44 2.10
521 2397 4.318332 TGTTGGAGATGCTCTAACTGTTG 58.682 43.478 19.61 0.00 46.98 3.33
539 2423 8.697507 AACTGTTGGACTTTTGAATCTTATCT 57.302 30.769 0.00 0.00 0.00 1.98
541 2426 7.391833 ACTGTTGGACTTTTGAATCTTATCTCC 59.608 37.037 0.00 0.00 0.00 3.71
587 2474 1.003696 CCCCTGGAAACCTGACTCTTC 59.996 57.143 0.00 0.00 0.00 2.87
591 2478 1.000955 TGGAAACCTGACTCTTCGCTC 59.999 52.381 0.00 0.00 0.00 5.03
594 2481 0.318762 AACCTGACTCTTCGCTCCAC 59.681 55.000 0.00 0.00 0.00 4.02
598 2485 0.318699 TGACTCTTCGCTCCACGTTG 60.319 55.000 0.00 0.00 44.19 4.10
599 2486 1.618640 GACTCTTCGCTCCACGTTGC 61.619 60.000 0.00 0.00 44.19 4.17
600 2487 1.664649 CTCTTCGCTCCACGTTGCA 60.665 57.895 5.91 0.00 44.19 4.08
601 2488 1.005037 TCTTCGCTCCACGTTGCAT 60.005 52.632 0.00 0.00 44.19 3.96
602 2489 1.014044 TCTTCGCTCCACGTTGCATC 61.014 55.000 0.00 0.00 44.19 3.91
603 2490 1.005037 TTCGCTCCACGTTGCATCT 60.005 52.632 0.00 0.00 44.19 2.90
604 2491 1.291184 TTCGCTCCACGTTGCATCTG 61.291 55.000 0.00 0.00 44.19 2.90
605 2492 2.482374 GCTCCACGTTGCATCTGC 59.518 61.111 0.00 0.00 42.50 4.26
616 2503 3.271250 GCATCTGCAAGGGAAGGAA 57.729 52.632 0.00 0.00 41.59 3.36
617 2504 1.549203 GCATCTGCAAGGGAAGGAAA 58.451 50.000 0.00 0.00 41.59 3.13
618 2505 1.203287 GCATCTGCAAGGGAAGGAAAC 59.797 52.381 0.00 0.00 41.59 2.78
619 2506 2.517959 CATCTGCAAGGGAAGGAAACA 58.482 47.619 0.00 0.00 0.00 2.83
620 2507 2.746279 TCTGCAAGGGAAGGAAACAA 57.254 45.000 0.00 0.00 0.00 2.83
621 2508 2.306847 TCTGCAAGGGAAGGAAACAAC 58.693 47.619 0.00 0.00 0.00 3.32
622 2509 2.031120 CTGCAAGGGAAGGAAACAACA 58.969 47.619 0.00 0.00 0.00 3.33
623 2510 1.754226 TGCAAGGGAAGGAAACAACAC 59.246 47.619 0.00 0.00 0.00 3.32
624 2511 1.269051 GCAAGGGAAGGAAACAACACG 60.269 52.381 0.00 0.00 0.00 4.49
625 2512 1.336755 CAAGGGAAGGAAACAACACGG 59.663 52.381 0.00 0.00 0.00 4.94
626 2513 0.549469 AGGGAAGGAAACAACACGGT 59.451 50.000 0.00 0.00 0.00 4.83
627 2514 1.064240 AGGGAAGGAAACAACACGGTT 60.064 47.619 0.00 0.00 0.00 4.44
636 2523 4.924462 GGAAACAACACGGTTCAAGAAAAA 59.076 37.500 0.00 0.00 0.00 1.94
637 2524 5.061684 GGAAACAACACGGTTCAAGAAAAAG 59.938 40.000 0.00 0.00 0.00 2.27
660 2547 1.322442 AAAGAAGGAGCCAGTTGCAC 58.678 50.000 0.00 0.00 44.83 4.57
710 2638 5.220043 GGATCGATCAATTATGCGTACTTCG 60.220 44.000 25.93 0.00 43.12 3.79
752 2680 4.002982 TCGCAGCAACAGAATCTACATTT 58.997 39.130 0.00 0.00 0.00 2.32
763 2691 6.128172 ACAGAATCTACATTTCAAAGGAAGCG 60.128 38.462 0.00 0.00 33.82 4.68
765 2693 3.674997 TCTACATTTCAAAGGAAGCGCT 58.325 40.909 2.64 2.64 33.82 5.92
778 2706 3.259123 AGGAAGCGCTTTCATCCAAAAAT 59.741 39.130 29.55 5.04 37.54 1.82
808 2751 7.930325 CAGAATCAGAATCTAATTAGCCTCACA 59.070 37.037 7.67 0.00 0.00 3.58
856 2805 2.574006 TCCCTATACCATACGAGCGT 57.426 50.000 0.00 0.00 0.00 5.07
932 2889 4.079665 CGCAGCCATCATCAAATCATAG 57.920 45.455 0.00 0.00 0.00 2.23
934 2891 3.254903 GCAGCCATCATCAAATCATAGCA 59.745 43.478 0.00 0.00 0.00 3.49
963 2933 4.584325 AGCTTCTGAAGTGCAAAAACCATA 59.416 37.500 17.97 0.00 0.00 2.74
967 2937 4.340666 TCTGAAGTGCAAAAACCATAAGCA 59.659 37.500 0.00 0.00 0.00 3.91
1017 3026 0.820871 AGATGTCTTCTGGGTCGAGC 59.179 55.000 5.93 5.93 31.79 5.03
1028 3037 2.430610 GGTCGAGCAGCTCATCCCT 61.431 63.158 22.49 0.00 0.00 4.20
1030 3039 2.130426 TCGAGCAGCTCATCCCTCC 61.130 63.158 22.49 0.00 0.00 4.30
1179 3188 4.530857 GAGGTGCGCCGCCACTAT 62.531 66.667 18.38 0.00 40.50 2.12
1272 3287 3.129988 GGGCTTGGAACTGATTCATCAAG 59.870 47.826 11.49 11.49 37.26 3.02
1427 3454 8.846943 ATTATGAGATATTTTACGGTGCATCA 57.153 30.769 0.00 0.00 0.00 3.07
1436 3463 2.890808 ACGGTGCATCATACTACCAG 57.109 50.000 0.00 0.00 32.75 4.00
1443 3470 6.650807 CGGTGCATCATACTACCAGATTTAAT 59.349 38.462 0.00 0.00 32.75 1.40
1509 3536 2.099141 TTGGCTCGAGGACAGATTTG 57.901 50.000 15.58 0.00 32.68 2.32
1514 3541 3.804873 GGCTCGAGGACAGATTTGTAATC 59.195 47.826 15.58 0.00 37.76 1.75
1563 3590 6.443849 TGATTTACCTTGATAGGACTTCACCT 59.556 38.462 0.00 0.00 45.05 4.00
1607 3634 5.564259 GCCAGATTCAATGCCTATGATCAAC 60.564 44.000 0.00 0.00 0.00 3.18
1634 3661 7.224753 CGAGGGAAAAAGAAAGATAATCGATCA 59.775 37.037 0.00 0.00 36.98 2.92
1678 3705 4.135153 CACGCCCTCAGGTCCTCG 62.135 72.222 0.00 0.00 34.57 4.63
1999 4035 3.863424 CGGCGTATCAATTGTGAAGTAGT 59.137 43.478 5.13 0.00 37.30 2.73
2245 4281 1.611851 CCCTCTCTCCAGCCACAGT 60.612 63.158 0.00 0.00 0.00 3.55
2249 4285 2.503356 CCTCTCTCCAGCCACAGTAATT 59.497 50.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 25 2.982470 GCAGAAATTCGCCTTTCTTGTG 59.018 45.455 8.71 2.65 41.55 3.33
121 293 3.728268 CGACGAGTTGGTGACTATGTCTC 60.728 52.174 0.00 0.00 39.72 3.36
126 298 0.172803 GGCGACGAGTTGGTGACTAT 59.827 55.000 0.00 0.00 39.19 2.12
181 353 5.105716 TGTTGGAGATGCTCTTAGTCACTAC 60.106 44.000 0.00 0.00 0.00 2.73
182 354 5.016831 TGTTGGAGATGCTCTTAGTCACTA 58.983 41.667 0.00 0.00 0.00 2.74
187 359 5.234466 ACTTTGTTGGAGATGCTCTTAGT 57.766 39.130 0.00 0.00 0.00 2.24
189 361 4.245660 CGACTTTGTTGGAGATGCTCTTA 58.754 43.478 0.00 0.00 0.00 2.10
190 362 3.070018 CGACTTTGTTGGAGATGCTCTT 58.930 45.455 0.00 0.00 0.00 2.85
191 363 2.693069 CGACTTTGTTGGAGATGCTCT 58.307 47.619 0.00 0.00 0.00 4.09
195 367 3.624326 TTTGCGACTTTGTTGGAGATG 57.376 42.857 0.00 0.00 0.00 2.90
219 391 9.763465 GCTGTAAAACTATTTTAACGCTCAATA 57.237 29.630 0.00 0.00 36.91 1.90
220 392 7.480542 CGCTGTAAAACTATTTTAACGCTCAAT 59.519 33.333 11.08 0.00 36.91 2.57
221 393 6.793203 CGCTGTAAAACTATTTTAACGCTCAA 59.207 34.615 11.08 0.00 36.91 3.02
222 394 6.073657 ACGCTGTAAAACTATTTTAACGCTCA 60.074 34.615 10.08 0.00 36.91 4.26
223 395 6.301861 ACGCTGTAAAACTATTTTAACGCTC 58.698 36.000 10.08 0.00 36.91 5.03
224 396 6.073657 TGACGCTGTAAAACTATTTTAACGCT 60.074 34.615 10.08 0.00 36.91 5.07
225 397 6.030693 GTGACGCTGTAAAACTATTTTAACGC 59.969 38.462 10.08 8.11 36.91 4.84
226 398 7.265495 CAGTGACGCTGTAAAACTATTTTAACG 59.735 37.037 7.89 9.19 40.27 3.18
227 399 8.418267 CAGTGACGCTGTAAAACTATTTTAAC 57.582 34.615 7.89 0.00 40.27 2.01
243 415 3.125316 GCTAAAAATGCTACAGTGACGCT 59.875 43.478 0.00 0.00 0.00 5.07
244 416 3.417185 GCTAAAAATGCTACAGTGACGC 58.583 45.455 0.00 0.00 0.00 5.19
245 417 3.659735 CGCTAAAAATGCTACAGTGACG 58.340 45.455 0.00 0.00 0.00 4.35
246 418 3.417185 GCGCTAAAAATGCTACAGTGAC 58.583 45.455 0.00 0.00 0.00 3.67
247 419 2.093625 CGCGCTAAAAATGCTACAGTGA 59.906 45.455 5.56 0.00 0.00 3.41
248 420 2.430956 CGCGCTAAAAATGCTACAGTG 58.569 47.619 5.56 0.00 0.00 3.66
249 421 1.202031 GCGCGCTAAAAATGCTACAGT 60.202 47.619 26.67 0.00 0.00 3.55
250 422 1.062587 AGCGCGCTAAAAATGCTACAG 59.937 47.619 35.79 0.00 33.37 2.74
251 423 1.083489 AGCGCGCTAAAAATGCTACA 58.917 45.000 35.79 0.00 33.37 2.74
252 424 1.456732 CAGCGCGCTAAAAATGCTAC 58.543 50.000 36.02 0.00 33.90 3.58
253 425 0.248054 GCAGCGCGCTAAAAATGCTA 60.248 50.000 36.02 0.00 37.77 3.49
254 426 1.514873 GCAGCGCGCTAAAAATGCT 60.515 52.632 36.02 5.36 37.77 3.79
255 427 2.989948 GCAGCGCGCTAAAAATGC 59.010 55.556 36.02 28.15 37.77 3.56
267 439 4.781959 CCAATGTTGGCCGCAGCG 62.782 66.667 8.18 8.18 42.21 5.18
276 448 3.250521 GGGCATGTGAAAAACCAATGTTG 59.749 43.478 0.00 0.00 34.13 3.33
277 449 3.118112 TGGGCATGTGAAAAACCAATGTT 60.118 39.130 0.00 0.00 35.82 2.71
278 450 2.437281 TGGGCATGTGAAAAACCAATGT 59.563 40.909 0.00 0.00 0.00 2.71
279 451 3.123157 TGGGCATGTGAAAAACCAATG 57.877 42.857 0.00 0.00 0.00 2.82
280 452 3.853355 TTGGGCATGTGAAAAACCAAT 57.147 38.095 0.00 0.00 33.43 3.16
281 453 3.634397 TTTGGGCATGTGAAAAACCAA 57.366 38.095 0.00 0.00 36.30 3.67
282 454 3.634397 TTTTGGGCATGTGAAAAACCA 57.366 38.095 0.00 0.00 0.00 3.67
321 493 1.578915 GCTTCATAATTTGCACGCGTG 59.421 47.619 34.01 34.01 0.00 5.34
322 494 1.790123 CGCTTCATAATTTGCACGCGT 60.790 47.619 5.58 5.58 33.41 6.01
323 495 0.833264 CGCTTCATAATTTGCACGCG 59.167 50.000 3.53 3.53 0.00 6.01
324 496 0.567509 GCGCTTCATAATTTGCACGC 59.432 50.000 0.00 0.00 34.92 5.34
325 497 0.833264 CGCGCTTCATAATTTGCACG 59.167 50.000 5.56 0.00 0.00 5.34
326 498 0.567509 GCGCGCTTCATAATTTGCAC 59.432 50.000 26.67 0.00 0.00 4.57
327 499 0.861034 CGCGCGCTTCATAATTTGCA 60.861 50.000 30.48 0.00 0.00 4.08
328 500 1.832913 CGCGCGCTTCATAATTTGC 59.167 52.632 30.48 0.00 0.00 3.68
329 501 1.832913 GCGCGCGCTTCATAATTTG 59.167 52.632 44.38 10.35 38.26 2.32
330 502 1.651132 CGCGCGCGCTTCATAATTT 60.651 52.632 45.97 0.00 39.32 1.82
331 503 2.053116 CGCGCGCGCTTCATAATT 60.053 55.556 45.97 0.00 39.32 1.40
332 504 4.000557 CCGCGCGCGCTTCATAAT 62.001 61.111 45.97 0.00 39.32 1.28
349 521 3.370231 AAATGTTGGGCGCCGGAC 61.370 61.111 22.54 21.20 0.00 4.79
350 522 2.749706 TACAAATGTTGGGCGCCGGA 62.750 55.000 22.54 8.55 34.12 5.14
351 523 2.265073 CTACAAATGTTGGGCGCCGG 62.265 60.000 22.54 0.00 34.12 6.13
352 524 1.136565 CTACAAATGTTGGGCGCCG 59.863 57.895 22.54 6.21 34.12 6.46
353 525 1.153842 GCTACAAATGTTGGGCGCC 60.154 57.895 21.18 21.18 34.12 6.53
354 526 0.173255 ATGCTACAAATGTTGGGCGC 59.827 50.000 0.00 0.00 36.68 6.53
355 527 1.202114 ACATGCTACAAATGTTGGGCG 59.798 47.619 0.00 0.00 34.60 6.13
356 528 2.230992 TCACATGCTACAAATGTTGGGC 59.769 45.455 0.00 0.00 36.10 5.36
357 529 4.724074 ATCACATGCTACAAATGTTGGG 57.276 40.909 0.00 0.00 36.10 4.12
358 530 5.276270 GCTATCACATGCTACAAATGTTGG 58.724 41.667 0.00 0.00 36.10 3.77
359 531 4.965762 CGCTATCACATGCTACAAATGTTG 59.034 41.667 0.00 0.00 36.10 3.33
360 532 4.496341 GCGCTATCACATGCTACAAATGTT 60.496 41.667 0.00 0.00 36.10 2.71
361 533 3.002656 GCGCTATCACATGCTACAAATGT 59.997 43.478 0.00 0.00 38.81 2.71
362 534 3.249320 AGCGCTATCACATGCTACAAATG 59.751 43.478 8.99 0.00 35.56 2.32
363 535 3.470709 AGCGCTATCACATGCTACAAAT 58.529 40.909 8.99 0.00 35.56 2.32
364 536 2.905075 AGCGCTATCACATGCTACAAA 58.095 42.857 8.99 0.00 35.56 2.83
365 537 2.602257 AGCGCTATCACATGCTACAA 57.398 45.000 8.99 0.00 35.56 2.41
366 538 2.602257 AAGCGCTATCACATGCTACA 57.398 45.000 12.05 0.00 36.49 2.74
367 539 3.951979 AAAAGCGCTATCACATGCTAC 57.048 42.857 12.05 0.00 36.49 3.58
368 540 4.024893 GCTTAAAAGCGCTATCACATGCTA 60.025 41.667 12.05 0.00 42.88 3.49
369 541 3.242870 GCTTAAAAGCGCTATCACATGCT 60.243 43.478 12.05 0.00 42.88 3.79
370 542 3.038710 GCTTAAAAGCGCTATCACATGC 58.961 45.455 12.05 6.15 42.88 4.06
383 555 6.149633 AGAATTTAACGCACCTGCTTAAAAG 58.850 36.000 13.67 0.00 37.28 2.27
384 556 6.079424 AGAATTTAACGCACCTGCTTAAAA 57.921 33.333 13.67 5.21 37.28 1.52
385 557 5.699097 AGAATTTAACGCACCTGCTTAAA 57.301 34.783 12.76 12.76 37.66 1.52
386 558 5.699097 AAGAATTTAACGCACCTGCTTAA 57.301 34.783 0.00 0.00 39.32 1.85
387 559 5.699097 AAAGAATTTAACGCACCTGCTTA 57.301 34.783 0.00 0.00 35.86 3.09
388 560 4.584327 AAAGAATTTAACGCACCTGCTT 57.416 36.364 0.00 0.00 35.86 3.91
389 561 4.202111 ACAAAAGAATTTAACGCACCTGCT 60.202 37.500 0.00 0.00 37.28 4.24
390 562 4.048504 ACAAAAGAATTTAACGCACCTGC 58.951 39.130 0.00 0.00 37.28 4.85
391 563 4.085107 GCACAAAAGAATTTAACGCACCTG 60.085 41.667 0.00 0.00 37.28 4.00
392 564 4.048504 GCACAAAAGAATTTAACGCACCT 58.951 39.130 0.00 0.00 37.28 4.00
393 565 3.121496 CGCACAAAAGAATTTAACGCACC 60.121 43.478 0.00 0.00 37.28 5.01
394 566 3.484285 ACGCACAAAAGAATTTAACGCAC 59.516 39.130 0.00 0.00 37.28 5.34
395 567 3.483922 CACGCACAAAAGAATTTAACGCA 59.516 39.130 0.00 0.00 37.28 5.24
396 568 3.658088 GCACGCACAAAAGAATTTAACGC 60.658 43.478 0.00 0.00 37.28 4.84
397 569 3.483922 TGCACGCACAAAAGAATTTAACG 59.516 39.130 0.00 0.00 37.28 3.18
398 570 5.574815 ATGCACGCACAAAAGAATTTAAC 57.425 34.783 0.00 0.00 37.28 2.01
399 571 7.881643 ATAATGCACGCACAAAAGAATTTAA 57.118 28.000 0.00 0.00 37.28 1.52
400 572 7.881643 AATAATGCACGCACAAAAGAATTTA 57.118 28.000 0.00 0.00 37.28 1.40
401 573 6.783892 AATAATGCACGCACAAAAGAATTT 57.216 29.167 0.00 0.00 42.41 1.82
402 574 6.783892 AAATAATGCACGCACAAAAGAATT 57.216 29.167 0.00 0.00 0.00 2.17
403 575 6.592166 CAAAATAATGCACGCACAAAAGAAT 58.408 32.000 0.00 0.00 0.00 2.40
404 576 5.557893 GCAAAATAATGCACGCACAAAAGAA 60.558 36.000 0.00 0.00 45.70 2.52
405 577 4.084641 GCAAAATAATGCACGCACAAAAGA 60.085 37.500 0.00 0.00 45.70 2.52
406 578 4.143116 GCAAAATAATGCACGCACAAAAG 58.857 39.130 0.00 0.00 45.70 2.27
407 579 4.125912 GCAAAATAATGCACGCACAAAA 57.874 36.364 0.00 0.00 45.70 2.44
408 580 3.784883 GCAAAATAATGCACGCACAAA 57.215 38.095 0.00 0.00 45.70 2.83
417 589 4.865925 TCAACAGATGCTGCAAAATAATGC 59.134 37.500 6.36 0.00 46.58 3.56
418 590 6.455113 GCTTCAACAGATGCTGCAAAATAATG 60.455 38.462 6.36 2.47 34.37 1.90
419 591 5.579511 GCTTCAACAGATGCTGCAAAATAAT 59.420 36.000 6.36 0.00 34.37 1.28
420 592 4.925054 GCTTCAACAGATGCTGCAAAATAA 59.075 37.500 6.36 0.00 34.37 1.40
421 593 4.487948 GCTTCAACAGATGCTGCAAAATA 58.512 39.130 6.36 0.00 34.37 1.40
422 594 3.323243 GCTTCAACAGATGCTGCAAAAT 58.677 40.909 6.36 0.00 34.37 1.82
423 595 2.546373 GGCTTCAACAGATGCTGCAAAA 60.546 45.455 6.36 0.00 34.37 2.44
424 596 1.000060 GGCTTCAACAGATGCTGCAAA 60.000 47.619 6.36 0.00 34.37 3.68
425 597 0.599558 GGCTTCAACAGATGCTGCAA 59.400 50.000 6.36 0.00 34.37 4.08
426 598 0.251033 AGGCTTCAACAGATGCTGCA 60.251 50.000 4.13 4.13 34.37 4.41
427 599 0.450983 GAGGCTTCAACAGATGCTGC 59.549 55.000 0.00 0.00 34.37 5.25
428 600 2.008329 GAGAGGCTTCAACAGATGCTG 58.992 52.381 0.00 0.00 37.52 4.41
429 601 1.065564 GGAGAGGCTTCAACAGATGCT 60.066 52.381 0.00 0.00 34.07 3.79
430 602 1.377536 GGAGAGGCTTCAACAGATGC 58.622 55.000 0.00 0.00 0.00 3.91
431 603 1.649664 CGGAGAGGCTTCAACAGATG 58.350 55.000 0.00 0.00 0.00 2.90
432 604 0.539051 CCGGAGAGGCTTCAACAGAT 59.461 55.000 0.00 0.00 0.00 2.90
433 605 1.975327 CCGGAGAGGCTTCAACAGA 59.025 57.895 0.00 0.00 0.00 3.41
434 606 4.606071 CCGGAGAGGCTTCAACAG 57.394 61.111 0.00 0.00 0.00 3.16
443 615 1.078708 TTTTTAGGCGCCGGAGAGG 60.079 57.895 23.20 0.00 44.97 3.69
444 616 0.108329 TCTTTTTAGGCGCCGGAGAG 60.108 55.000 23.20 16.32 0.00 3.20
445 617 0.322322 TTCTTTTTAGGCGCCGGAGA 59.678 50.000 23.20 17.27 0.00 3.71
446 618 0.446616 GTTCTTTTTAGGCGCCGGAG 59.553 55.000 23.20 15.22 0.00 4.63
447 619 1.293267 CGTTCTTTTTAGGCGCCGGA 61.293 55.000 23.20 10.93 0.00 5.14
448 620 1.133869 CGTTCTTTTTAGGCGCCGG 59.866 57.895 23.20 8.43 0.00 6.13
449 621 1.133869 CCGTTCTTTTTAGGCGCCG 59.866 57.895 23.20 5.45 0.00 6.46
450 622 1.154093 GCCGTTCTTTTTAGGCGCC 60.154 57.895 21.89 21.89 40.17 6.53
451 623 4.452753 GCCGTTCTTTTTAGGCGC 57.547 55.556 0.00 0.00 40.17 6.53
459 631 3.066203 CCACACACTAAAAGCCGTTCTTT 59.934 43.478 0.00 0.00 46.42 2.52
460 632 2.616842 CCACACACTAAAAGCCGTTCTT 59.383 45.455 0.00 0.00 36.34 2.52
461 633 2.158871 TCCACACACTAAAAGCCGTTCT 60.159 45.455 0.00 0.00 0.00 3.01
462 634 2.215196 TCCACACACTAAAAGCCGTTC 58.785 47.619 0.00 0.00 0.00 3.95
463 635 2.218603 CTCCACACACTAAAAGCCGTT 58.781 47.619 0.00 0.00 0.00 4.44
464 636 1.878953 CTCCACACACTAAAAGCCGT 58.121 50.000 0.00 0.00 0.00 5.68
465 637 0.517316 GCTCCACACACTAAAAGCCG 59.483 55.000 0.00 0.00 0.00 5.52
466 638 1.537202 CTGCTCCACACACTAAAAGCC 59.463 52.381 0.00 0.00 0.00 4.35
467 639 2.222027 ACTGCTCCACACACTAAAAGC 58.778 47.619 0.00 0.00 0.00 3.51
468 640 4.900635 AAACTGCTCCACACACTAAAAG 57.099 40.909 0.00 0.00 0.00 2.27
469 641 4.201871 CGAAAACTGCTCCACACACTAAAA 60.202 41.667 0.00 0.00 0.00 1.52
470 642 3.311322 CGAAAACTGCTCCACACACTAAA 59.689 43.478 0.00 0.00 0.00 1.85
471 643 2.869801 CGAAAACTGCTCCACACACTAA 59.130 45.455 0.00 0.00 0.00 2.24
472 644 2.479837 CGAAAACTGCTCCACACACTA 58.520 47.619 0.00 0.00 0.00 2.74
473 645 1.299541 CGAAAACTGCTCCACACACT 58.700 50.000 0.00 0.00 0.00 3.55
474 646 0.307760 CCGAAAACTGCTCCACACAC 59.692 55.000 0.00 0.00 0.00 3.82
475 647 0.817634 CCCGAAAACTGCTCCACACA 60.818 55.000 0.00 0.00 0.00 3.72
476 648 1.949257 CCCGAAAACTGCTCCACAC 59.051 57.895 0.00 0.00 0.00 3.82
477 649 1.896660 GCCCGAAAACTGCTCCACA 60.897 57.895 0.00 0.00 0.00 4.17
478 650 1.896660 TGCCCGAAAACTGCTCCAC 60.897 57.895 0.00 0.00 0.00 4.02
479 651 1.896660 GTGCCCGAAAACTGCTCCA 60.897 57.895 0.00 0.00 0.00 3.86
480 652 1.172812 AAGTGCCCGAAAACTGCTCC 61.173 55.000 0.00 0.00 0.00 4.70
481 653 0.040067 CAAGTGCCCGAAAACTGCTC 60.040 55.000 0.00 0.00 0.00 4.26
482 654 0.751643 ACAAGTGCCCGAAAACTGCT 60.752 50.000 0.00 0.00 0.00 4.24
483 655 0.102300 AACAAGTGCCCGAAAACTGC 59.898 50.000 0.00 0.00 0.00 4.40
484 656 1.535860 CCAACAAGTGCCCGAAAACTG 60.536 52.381 0.00 0.00 0.00 3.16
485 657 0.744281 CCAACAAGTGCCCGAAAACT 59.256 50.000 0.00 0.00 0.00 2.66
486 658 0.741915 TCCAACAAGTGCCCGAAAAC 59.258 50.000 0.00 0.00 0.00 2.43
487 659 1.028905 CTCCAACAAGTGCCCGAAAA 58.971 50.000 0.00 0.00 0.00 2.29
488 660 0.181587 TCTCCAACAAGTGCCCGAAA 59.818 50.000 0.00 0.00 0.00 3.46
489 661 0.400213 ATCTCCAACAAGTGCCCGAA 59.600 50.000 0.00 0.00 0.00 4.30
490 662 0.321564 CATCTCCAACAAGTGCCCGA 60.322 55.000 0.00 0.00 0.00 5.14
491 663 1.926511 GCATCTCCAACAAGTGCCCG 61.927 60.000 0.00 0.00 0.00 6.13
492 664 0.610232 AGCATCTCCAACAAGTGCCC 60.610 55.000 0.00 0.00 36.50 5.36
493 665 0.807496 GAGCATCTCCAACAAGTGCC 59.193 55.000 0.00 0.00 36.50 5.01
506 678 5.470098 TCAAAAGTCCAACAGTTAGAGCATC 59.530 40.000 0.00 0.00 0.00 3.91
507 679 5.376625 TCAAAAGTCCAACAGTTAGAGCAT 58.623 37.500 0.00 0.00 0.00 3.79
508 680 4.776349 TCAAAAGTCCAACAGTTAGAGCA 58.224 39.130 0.00 0.00 0.00 4.26
509 681 5.751243 TTCAAAAGTCCAACAGTTAGAGC 57.249 39.130 0.00 0.00 0.00 4.09
511 683 9.793259 ATAAGATTCAAAAGTCCAACAGTTAGA 57.207 29.630 0.00 0.00 0.00 2.10
515 2391 7.391833 GGAGATAAGATTCAAAAGTCCAACAGT 59.608 37.037 0.00 0.00 0.00 3.55
521 2397 9.784531 TCATATGGAGATAAGATTCAAAAGTCC 57.215 33.333 2.13 0.00 0.00 3.85
539 2423 3.503363 GCCTTGCATTTCGATCATATGGA 59.497 43.478 2.13 0.00 0.00 3.41
541 2426 4.473199 CTGCCTTGCATTTCGATCATATG 58.527 43.478 0.00 0.00 38.13 1.78
587 2474 3.372676 GCAGATGCAACGTGGAGCG 62.373 63.158 0.00 0.00 43.24 5.03
598 2485 1.203287 GTTTCCTTCCCTTGCAGATGC 59.797 52.381 0.00 0.00 42.50 3.91
599 2486 2.517959 TGTTTCCTTCCCTTGCAGATG 58.482 47.619 0.00 0.00 0.00 2.90
600 2487 2.893489 GTTGTTTCCTTCCCTTGCAGAT 59.107 45.455 0.00 0.00 0.00 2.90
601 2488 2.306847 GTTGTTTCCTTCCCTTGCAGA 58.693 47.619 0.00 0.00 0.00 4.26
602 2489 2.031120 TGTTGTTTCCTTCCCTTGCAG 58.969 47.619 0.00 0.00 0.00 4.41
603 2490 1.754226 GTGTTGTTTCCTTCCCTTGCA 59.246 47.619 0.00 0.00 0.00 4.08
604 2491 1.269051 CGTGTTGTTTCCTTCCCTTGC 60.269 52.381 0.00 0.00 0.00 4.01
605 2492 1.336755 CCGTGTTGTTTCCTTCCCTTG 59.663 52.381 0.00 0.00 0.00 3.61
606 2493 1.064240 ACCGTGTTGTTTCCTTCCCTT 60.064 47.619 0.00 0.00 0.00 3.95
607 2494 0.549469 ACCGTGTTGTTTCCTTCCCT 59.451 50.000 0.00 0.00 0.00 4.20
608 2495 1.335810 GAACCGTGTTGTTTCCTTCCC 59.664 52.381 0.00 0.00 0.00 3.97
609 2496 2.018515 TGAACCGTGTTGTTTCCTTCC 58.981 47.619 0.00 0.00 0.00 3.46
610 2497 3.375922 TCTTGAACCGTGTTGTTTCCTTC 59.624 43.478 0.00 0.00 0.00 3.46
611 2498 3.349022 TCTTGAACCGTGTTGTTTCCTT 58.651 40.909 0.00 0.00 0.00 3.36
612 2499 2.993937 TCTTGAACCGTGTTGTTTCCT 58.006 42.857 0.00 0.00 0.00 3.36
613 2500 3.768468 TTCTTGAACCGTGTTGTTTCC 57.232 42.857 0.00 0.00 0.00 3.13
614 2501 5.859648 TCTTTTTCTTGAACCGTGTTGTTTC 59.140 36.000 0.00 0.00 0.00 2.78
615 2502 5.774630 TCTTTTTCTTGAACCGTGTTGTTT 58.225 33.333 0.00 0.00 0.00 2.83
616 2503 5.379732 TCTTTTTCTTGAACCGTGTTGTT 57.620 34.783 0.00 0.00 0.00 2.83
617 2504 5.379732 TTCTTTTTCTTGAACCGTGTTGT 57.620 34.783 0.00 0.00 0.00 3.32
618 2505 6.698359 TTTTCTTTTTCTTGAACCGTGTTG 57.302 33.333 0.00 0.00 0.00 3.33
643 2530 4.809070 GTGCAACTGGCTCCTTCT 57.191 55.556 0.00 0.00 45.15 2.85
660 2547 0.806868 ACGTCTCAAATGCATGGCAG 59.193 50.000 0.00 0.00 43.65 4.85
710 2638 2.740714 GCGCTTGGGTCGACACATC 61.741 63.158 23.39 15.35 0.00 3.06
752 2680 1.812571 GGATGAAAGCGCTTCCTTTGA 59.187 47.619 25.24 1.35 35.31 2.69
763 2691 7.385752 TGATTCTGAACATTTTTGGATGAAAGC 59.614 33.333 0.00 0.00 0.00 3.51
765 2693 8.640651 TCTGATTCTGAACATTTTTGGATGAAA 58.359 29.630 0.00 0.00 0.00 2.69
778 2706 8.489489 AGGCTAATTAGATTCTGATTCTGAACA 58.511 33.333 16.85 0.00 0.00 3.18
808 2751 0.603975 GCTTGGCGACTGAAAGGTCT 60.604 55.000 0.00 0.00 39.30 3.85
841 2790 2.030540 GCCTTGACGCTCGTATGGTATA 60.031 50.000 0.00 0.00 0.00 1.47
907 2864 0.961857 TTTGATGATGGCTGCGCTGT 60.962 50.000 16.05 0.00 0.00 4.40
912 2869 3.254903 TGCTATGATTTGATGATGGCTGC 59.745 43.478 0.00 0.00 32.00 5.25
917 2874 4.516321 TCCGGTTGCTATGATTTGATGATG 59.484 41.667 0.00 0.00 0.00 3.07
927 2884 1.134699 CAGAAGCTCCGGTTGCTATGA 60.135 52.381 21.04 0.00 40.22 2.15
932 2889 0.603975 ACTTCAGAAGCTCCGGTTGC 60.604 55.000 10.33 12.89 0.00 4.17
934 2891 0.603975 GCACTTCAGAAGCTCCGGTT 60.604 55.000 10.33 0.00 0.00 4.44
963 2933 3.679824 AACCGAGCTAAGTTAGTGCTT 57.320 42.857 11.51 0.00 37.16 3.91
1017 3026 4.598894 CCGCGGAGGGATGAGCTG 62.599 72.222 24.07 0.00 46.37 4.24
1179 3188 1.248101 TGTCGCCGTCAAGGATCTCA 61.248 55.000 0.00 0.00 45.00 3.27
1272 3287 2.484065 GGTTGGGTTTTGGTTACCTTGC 60.484 50.000 2.07 0.00 35.92 4.01
1336 3361 2.123409 GCTCTGAGCTAGGACCTGG 58.877 63.158 21.93 1.29 38.45 4.45
1363 3390 6.041511 AGAAGTGATTGAGTTGAGATCGATG 58.958 40.000 0.54 0.00 0.00 3.84
1443 3470 6.205464 CCGTCGGATGAACTTAATACTACCTA 59.795 42.308 4.91 0.00 0.00 3.08
1529 3556 8.144478 TCCTATCAAGGTAAATCAGATCGAAAG 58.856 37.037 0.00 0.00 44.09 2.62
1563 3590 1.335597 CGCTCGTGACCTCTAAACACA 60.336 52.381 0.00 0.00 34.69 3.72
1607 3634 5.815740 TCGATTATCTTTCTTTTTCCCTCGG 59.184 40.000 0.00 0.00 0.00 4.63
1678 3705 1.996292 TGCAGATTAGTGTCAGTCGC 58.004 50.000 0.00 0.00 0.00 5.19
1782 3809 0.100861 GTCATCCTTCTCGTCGACCC 59.899 60.000 10.58 0.00 0.00 4.46
1847 3876 3.057315 CGTTCTGCATGGATTCCAAGTTT 60.057 43.478 9.98 0.00 36.95 2.66
1853 3882 3.438781 TGTTAACGTTCTGCATGGATTCC 59.561 43.478 2.82 0.00 0.00 3.01
1865 3894 7.532884 GGTTGATGTTTCATAGTGTTAACGTTC 59.467 37.037 2.82 0.00 0.00 3.95
1999 4035 0.817013 GCCGCTTCCATTTTCCATCA 59.183 50.000 0.00 0.00 0.00 3.07
2113 4149 1.153939 CGTCAACGAGGAGCTGGAG 60.154 63.158 0.00 0.00 43.02 3.86
2192 4228 1.833434 TTTACGTTGCCGGCGAAGTG 61.833 55.000 36.40 23.53 38.78 3.16


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

AutoCloner maintained by Alex Coulton.