Multiple sequence alignment - TraesCS1A01G208000

Loading Multiple Alignment...

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 TraesCS1A01G208000 chr1A 100.000 5207 0 0 1 5207 369693947 369699153 0.000000e+00 9616.0
1 TraesCS1A01G208000 chr1A 86.885 122 12 4 412 533 146970978 146971095 3.270000e-27 134.0
2 TraesCS1A01G208000 chr1D 96.123 3946 97 8 638 4539 297162665 297166598 0.000000e+00 6388.0
3 TraesCS1A01G208000 chr1D 83.568 426 55 8 4 425 297162069 297162483 8.180000e-103 385.0
4 TraesCS1A01G208000 chr1B 95.232 3943 118 16 638 4532 399332651 399336571 0.000000e+00 6176.0
5 TraesCS1A01G208000 chr1B 89.264 652 43 15 4583 5207 681932977 681932326 0.000000e+00 791.0
6 TraesCS1A01G208000 chr1B 89.789 284 28 1 2010 2293 612222087 612222369 3.830000e-96 363.0
7 TraesCS1A01G208000 chr1B 81.628 430 59 13 4 427 399332061 399332476 6.460000e-89 339.0
8 TraesCS1A01G208000 chr1B 89.076 119 7 6 414 529 51880940 51881055 5.440000e-30 143.0
9 TraesCS1A01G208000 chr6D 91.562 640 36 10 4585 5207 17142643 17142005 0.000000e+00 867.0
10 TraesCS1A01G208000 chr7D 91.420 641 37 7 4585 5207 88020699 88021339 0.000000e+00 863.0
11 TraesCS1A01G208000 chr3D 90.358 643 42 9 4585 5207 505991961 505992603 0.000000e+00 826.0
12 TraesCS1A01G208000 chr2B 89.877 652 39 12 4583 5207 763502409 763501758 0.000000e+00 813.0
13 TraesCS1A01G208000 chr6B 89.862 651 39 12 4583 5207 504137117 504136468 0.000000e+00 811.0
14 TraesCS1A01G208000 chr7A 89.231 650 43 14 4583 5207 47350570 47349923 0.000000e+00 787.0
15 TraesCS1A01G208000 chr5A 85.948 612 46 16 4594 5196 26578749 26579329 7.410000e-173 617.0
16 TraesCS1A01G208000 chr5A 95.833 48 2 0 4535 4582 26578616 26578663 1.550000e-10 78.7
17 TraesCS1A01G208000 chr5D 86.667 255 20 5 4585 4825 563696154 563695900 2.390000e-68 270.0
18 TraesCS1A01G208000 chr3B 90.265 113 8 3 412 523 757960026 757959916 1.510000e-30 145.0
19 TraesCS1A01G208000 chr3B 88.136 118 11 3 407 523 653137415 653137300 2.530000e-28 137.0
20 TraesCS1A01G208000 chr7B 89.381 113 10 2 412 524 214076594 214076484 1.950000e-29 141.0
21 TraesCS1A01G208000 chr4B 89.908 109 10 1 428 536 664943610 664943503 7.030000e-29 139.0
22 TraesCS1A01G208000 chr4B 89.908 109 10 1 428 536 665002974 665002867 7.030000e-29 139.0
23 TraesCS1A01G208000 chr4B 91.111 45 4 0 4494 4538 412774509 412774465 1.570000e-05 62.1
24 TraesCS1A01G208000 chr6A 85.496 131 15 3 402 530 150961345 150961473 3.270000e-27 134.0
25 TraesCS1A01G208000 chr4A 87.395 119 12 3 407 524 317070358 317070242 3.270000e-27 134.0
26 TraesCS1A01G208000 chr4D 88.542 96 6 5 4592 4686 453135959 453135868 1.530000e-20 111.0


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 TraesCS1A01G208000 chr1A 369693947 369699153 5206 False 9616.00 9616 100.0000 1 5207 1 chr1A.!!$F2 5206
1 TraesCS1A01G208000 chr1D 297162069 297166598 4529 False 3386.50 6388 89.8455 4 4539 2 chr1D.!!$F1 4535
2 TraesCS1A01G208000 chr1B 399332061 399336571 4510 False 3257.50 6176 88.4300 4 4532 2 chr1B.!!$F3 4528
3 TraesCS1A01G208000 chr1B 681932326 681932977 651 True 791.00 791 89.2640 4583 5207 1 chr1B.!!$R1 624
4 TraesCS1A01G208000 chr6D 17142005 17142643 638 True 867.00 867 91.5620 4585 5207 1 chr6D.!!$R1 622
5 TraesCS1A01G208000 chr7D 88020699 88021339 640 False 863.00 863 91.4200 4585 5207 1 chr7D.!!$F1 622
6 TraesCS1A01G208000 chr3D 505991961 505992603 642 False 826.00 826 90.3580 4585 5207 1 chr3D.!!$F1 622
7 TraesCS1A01G208000 chr2B 763501758 763502409 651 True 813.00 813 89.8770 4583 5207 1 chr2B.!!$R1 624
8 TraesCS1A01G208000 chr6B 504136468 504137117 649 True 811.00 811 89.8620 4583 5207 1 chr6B.!!$R1 624
9 TraesCS1A01G208000 chr7A 47349923 47350570 647 True 787.00 787 89.2310 4583 5207 1 chr7A.!!$R1 624
10 TraesCS1A01G208000 chr5A 26578616 26579329 713 False 347.85 617 90.8905 4535 5196 2 chr5A.!!$F1 661

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
300 304 0.039074 GACCGGCGATCTACTGATGG 60.039 60.0 9.30 0.0 32.19 3.51 F
1945 2053 0.033208 TAATGGCCCCTCTTTGCTGG 60.033 55.0 0.00 0.0 0.00 4.85 F
3219 3327 0.399454 ATGCGCAGAGGAAGGCATAT 59.601 50.0 18.32 0.0 43.74 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 2357 0.179100 TGCTATCTCTTGTGCTCGGC 60.179 55.000 0.00 0.00 0.00 5.54 R
3347 3455 1.132834 TGCCATCGTCATCAACATTGC 59.867 47.619 0.00 0.00 0.00 3.56 R
4539 4658 0.389948 ACTGAGTTTTAGCGCCTCCG 60.390 55.000 2.29 1.84 37.57 4.63 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
52 54 3.759086 TGCCGCCATAGAAAACACAATTA 59.241 39.130 0.00 0.00 0.00 1.40
56 58 6.027749 CCGCCATAGAAAACACAATTAAGAC 58.972 40.000 0.00 0.00 0.00 3.01
57 59 6.348950 CCGCCATAGAAAACACAATTAAGACA 60.349 38.462 0.00 0.00 0.00 3.41
70 73 8.030692 ACACAATTAAGACATGAATGTTGATGG 58.969 33.333 0.00 0.00 41.95 3.51
87 90 1.265236 TGGTGAATGATTGGTTGGGC 58.735 50.000 0.00 0.00 0.00 5.36
122 125 1.269778 ACATCTATGATGCGTCACCGG 60.270 52.381 11.65 0.00 37.14 5.28
124 127 1.682740 TCTATGATGCGTCACCGGTA 58.317 50.000 11.65 0.00 37.14 4.02
140 143 6.646240 GTCACCGGTAAAGACTTTATTGTACA 59.354 38.462 6.87 0.00 0.00 2.90
141 144 7.332678 GTCACCGGTAAAGACTTTATTGTACAT 59.667 37.037 6.87 0.00 0.00 2.29
147 150 7.277098 GGTAAAGACTTTATTGTACATCGCTGA 59.723 37.037 10.76 0.00 0.00 4.26
152 155 5.232202 ACTTTATTGTACATCGCTGACATCG 59.768 40.000 0.00 0.00 0.00 3.84
166 169 1.883084 CATCGCCGCTGGAAGGTAC 60.883 63.158 0.00 0.00 0.00 3.34
167 170 3.426117 ATCGCCGCTGGAAGGTACG 62.426 63.158 0.00 0.00 0.00 3.67
170 173 1.810030 GCCGCTGGAAGGTACGAAG 60.810 63.158 0.00 0.00 0.00 3.79
178 181 0.645868 GAAGGTACGAAGCGATGCAC 59.354 55.000 0.00 0.00 0.00 4.57
182 185 1.277326 GTACGAAGCGATGCACATCA 58.723 50.000 11.00 0.00 37.69 3.07
189 192 1.434696 CGATGCACATCAAAGGCCC 59.565 57.895 11.00 0.00 37.69 5.80
194 197 0.458669 GCACATCAAAGGCCCATCTG 59.541 55.000 0.00 0.00 0.00 2.90
201 204 3.575805 TCAAAGGCCCATCTGAAAACTT 58.424 40.909 0.00 0.00 0.00 2.66
208 211 3.735746 GCCCATCTGAAAACTTCAAAACG 59.264 43.478 0.00 0.00 39.58 3.60
240 244 9.482175 AACTATCTTCATCTAGTAAACCAGAGT 57.518 33.333 0.00 0.00 0.00 3.24
256 260 0.248843 GAGTCTCCTTGCACTCCCAG 59.751 60.000 0.00 0.00 34.09 4.45
259 263 0.471780 TCTCCTTGCACTCCCAGACA 60.472 55.000 0.00 0.00 0.00 3.41
265 269 1.963338 GCACTCCCAGACAGCACAC 60.963 63.158 0.00 0.00 0.00 3.82
267 271 1.766059 ACTCCCAGACAGCACACCA 60.766 57.895 0.00 0.00 0.00 4.17
269 273 0.886490 CTCCCAGACAGCACACCAAC 60.886 60.000 0.00 0.00 0.00 3.77
270 274 2.253758 CCCAGACAGCACACCAACG 61.254 63.158 0.00 0.00 0.00 4.10
271 275 1.523711 CCAGACAGCACACCAACGT 60.524 57.895 0.00 0.00 0.00 3.99
272 276 1.643292 CAGACAGCACACCAACGTG 59.357 57.895 0.00 0.00 46.11 4.49
273 277 1.523711 AGACAGCACACCAACGTGG 60.524 57.895 0.00 0.00 44.86 4.94
274 278 2.515991 ACAGCACACCAACGTGGG 60.516 61.111 7.67 7.67 46.96 4.61
300 304 0.039074 GACCGGCGATCTACTGATGG 60.039 60.000 9.30 0.00 32.19 3.51
313 317 0.179089 CTGATGGCGAAGGAGAGGTG 60.179 60.000 0.00 0.00 0.00 4.00
344 348 4.141937 CCCTCTAAAATCACCACTCGATGA 60.142 45.833 0.00 0.00 0.00 2.92
346 350 5.163509 CCTCTAAAATCACCACTCGATGAGA 60.164 44.000 0.00 0.00 33.32 3.27
351 355 6.471233 AAATCACCACTCGATGAGATTAGA 57.529 37.500 0.00 0.00 34.03 2.10
359 363 5.516696 CACTCGATGAGATTAGAAGCGAAAA 59.483 40.000 0.00 0.00 33.32 2.29
367 371 7.743104 TGAGATTAGAAGCGAAAAGTTTCATC 58.257 34.615 4.76 0.28 41.74 2.92
369 373 8.329203 AGATTAGAAGCGAAAAGTTTCATCTT 57.671 30.769 4.76 6.36 41.74 2.40
370 374 8.787852 AGATTAGAAGCGAAAAGTTTCATCTTT 58.212 29.630 4.76 0.00 41.74 2.52
371 375 9.399403 GATTAGAAGCGAAAAGTTTCATCTTTT 57.601 29.630 4.76 4.45 46.14 2.27
372 376 8.560576 TTAGAAGCGAAAAGTTTCATCTTTTG 57.439 30.769 8.76 4.08 44.36 2.44
373 377 6.564328 AGAAGCGAAAAGTTTCATCTTTTGT 58.436 32.000 8.76 0.00 44.36 2.83
374 378 6.473455 AGAAGCGAAAAGTTTCATCTTTTGTG 59.527 34.615 8.76 3.76 44.36 3.33
375 379 5.650543 AGCGAAAAGTTTCATCTTTTGTGT 58.349 33.333 8.76 0.00 44.36 3.72
376 380 5.516339 AGCGAAAAGTTTCATCTTTTGTGTG 59.484 36.000 8.76 0.00 44.36 3.82
390 394 7.994425 TCTTTTGTGTGGATCAAGCTTATTA 57.006 32.000 0.00 0.00 0.00 0.98
403 407 5.483937 TCAAGCTTATTAGAGTTGGACCTGA 59.516 40.000 0.00 0.00 0.00 3.86
409 413 5.878406 ATTAGAGTTGGACCTGATACCAG 57.122 43.478 0.00 0.00 40.09 4.00
430 434 5.152097 CAGATCAATCTGTTGAAAGTGTGC 58.848 41.667 11.14 0.00 46.67 4.57
431 435 5.048921 CAGATCAATCTGTTGAAAGTGTGCT 60.049 40.000 11.14 0.00 46.67 4.40
432 436 4.818534 TCAATCTGTTGAAAGTGTGCTC 57.181 40.909 0.00 0.00 41.22 4.26
433 437 4.198530 TCAATCTGTTGAAAGTGTGCTCA 58.801 39.130 0.00 0.00 41.22 4.26
434 438 4.823442 TCAATCTGTTGAAAGTGTGCTCAT 59.177 37.500 0.00 0.00 41.22 2.90
435 439 5.997129 TCAATCTGTTGAAAGTGTGCTCATA 59.003 36.000 0.00 0.00 41.22 2.15
436 440 6.486320 TCAATCTGTTGAAAGTGTGCTCATAA 59.514 34.615 0.00 0.00 41.22 1.90
437 441 5.929697 TCTGTTGAAAGTGTGCTCATAAG 57.070 39.130 0.00 0.00 0.00 1.73
438 442 4.756642 TCTGTTGAAAGTGTGCTCATAAGG 59.243 41.667 0.00 0.00 0.00 2.69
439 443 4.713553 TGTTGAAAGTGTGCTCATAAGGA 58.286 39.130 0.00 0.00 0.00 3.36
440 444 5.316167 TGTTGAAAGTGTGCTCATAAGGAT 58.684 37.500 0.00 0.00 0.00 3.24
441 445 6.472016 TGTTGAAAGTGTGCTCATAAGGATA 58.528 36.000 0.00 0.00 0.00 2.59
442 446 6.939730 TGTTGAAAGTGTGCTCATAAGGATAA 59.060 34.615 0.00 0.00 0.00 1.75
443 447 7.446931 TGTTGAAAGTGTGCTCATAAGGATAAA 59.553 33.333 0.00 0.00 0.00 1.40
444 448 8.462016 GTTGAAAGTGTGCTCATAAGGATAAAT 58.538 33.333 0.00 0.00 0.00 1.40
445 449 8.579850 TGAAAGTGTGCTCATAAGGATAAATT 57.420 30.769 0.00 0.00 0.00 1.82
446 450 8.461222 TGAAAGTGTGCTCATAAGGATAAATTG 58.539 33.333 0.00 0.00 0.00 2.32
447 451 7.944729 AAGTGTGCTCATAAGGATAAATTGT 57.055 32.000 0.00 0.00 0.00 2.71
448 452 7.325660 AGTGTGCTCATAAGGATAAATTGTG 57.674 36.000 0.00 0.00 0.00 3.33
449 453 5.973565 GTGTGCTCATAAGGATAAATTGTGC 59.026 40.000 0.00 0.00 0.00 4.57
450 454 5.207768 GTGCTCATAAGGATAAATTGTGCG 58.792 41.667 0.00 0.00 31.40 5.34
451 455 4.881273 TGCTCATAAGGATAAATTGTGCGT 59.119 37.500 0.00 0.00 31.40 5.24
452 456 5.207768 GCTCATAAGGATAAATTGTGCGTG 58.792 41.667 0.00 0.00 0.00 5.34
453 457 5.220854 GCTCATAAGGATAAATTGTGCGTGT 60.221 40.000 0.00 0.00 0.00 4.49
454 458 6.117911 TCATAAGGATAAATTGTGCGTGTG 57.882 37.500 0.00 0.00 0.00 3.82
455 459 5.645929 TCATAAGGATAAATTGTGCGTGTGT 59.354 36.000 0.00 0.00 0.00 3.72
456 460 3.829886 AGGATAAATTGTGCGTGTGTG 57.170 42.857 0.00 0.00 0.00 3.82
457 461 2.095263 AGGATAAATTGTGCGTGTGTGC 60.095 45.455 0.00 0.00 0.00 4.57
458 462 1.904412 GATAAATTGTGCGTGTGTGCG 59.096 47.619 0.00 0.00 37.81 5.34
459 463 0.658368 TAAATTGTGCGTGTGTGCGT 59.342 45.000 0.00 0.00 37.81 5.24
460 464 0.179150 AAATTGTGCGTGTGTGCGTT 60.179 45.000 0.00 0.00 37.81 4.84
461 465 0.591236 AATTGTGCGTGTGTGCGTTC 60.591 50.000 0.00 0.00 37.81 3.95
462 466 1.710103 ATTGTGCGTGTGTGCGTTCA 61.710 50.000 0.00 0.00 37.81 3.18
463 467 1.710103 TTGTGCGTGTGTGCGTTCAT 61.710 50.000 0.00 0.00 37.81 2.57
464 468 0.876342 TGTGCGTGTGTGCGTTCATA 60.876 50.000 0.00 0.00 37.81 2.15
465 469 0.233590 GTGCGTGTGTGCGTTCATAA 59.766 50.000 0.00 0.00 37.81 1.90
466 470 0.510790 TGCGTGTGTGCGTTCATAAG 59.489 50.000 0.00 0.00 37.81 1.73
467 471 0.179225 GCGTGTGTGCGTTCATAAGG 60.179 55.000 0.00 0.00 0.00 2.69
468 472 1.424403 CGTGTGTGCGTTCATAAGGA 58.576 50.000 0.00 0.00 0.00 3.36
469 473 1.999735 CGTGTGTGCGTTCATAAGGAT 59.000 47.619 0.00 0.00 0.00 3.24
470 474 2.222796 CGTGTGTGCGTTCATAAGGATG 60.223 50.000 0.00 0.00 0.00 3.51
471 475 3.000041 GTGTGTGCGTTCATAAGGATGA 59.000 45.455 0.00 0.00 40.45 2.92
472 476 3.062639 GTGTGTGCGTTCATAAGGATGAG 59.937 47.826 0.00 0.00 43.03 2.90
473 477 3.262420 GTGTGCGTTCATAAGGATGAGT 58.738 45.455 0.00 0.00 43.03 3.41
474 478 3.062639 GTGTGCGTTCATAAGGATGAGTG 59.937 47.826 0.00 0.00 43.03 3.51
475 479 3.262420 GTGCGTTCATAAGGATGAGTGT 58.738 45.455 0.00 0.00 43.03 3.55
476 480 4.081917 TGTGCGTTCATAAGGATGAGTGTA 60.082 41.667 0.00 0.00 43.03 2.90
477 481 5.050490 GTGCGTTCATAAGGATGAGTGTAT 58.950 41.667 0.00 0.00 43.03 2.29
478 482 5.049828 TGCGTTCATAAGGATGAGTGTATG 58.950 41.667 0.00 0.00 43.03 2.39
479 483 4.084328 GCGTTCATAAGGATGAGTGTATGC 60.084 45.833 0.00 0.00 43.03 3.14
480 484 4.148871 CGTTCATAAGGATGAGTGTATGCG 59.851 45.833 0.00 0.00 43.03 4.73
481 485 3.653344 TCATAAGGATGAGTGTATGCGC 58.347 45.455 0.00 0.00 37.15 6.09
482 486 2.134201 TAAGGATGAGTGTATGCGCG 57.866 50.000 0.00 0.00 0.00 6.86
483 487 0.175760 AAGGATGAGTGTATGCGCGT 59.824 50.000 8.43 7.55 0.00 6.01
484 488 1.029681 AGGATGAGTGTATGCGCGTA 58.970 50.000 8.43 4.92 0.00 4.42
485 489 1.613925 AGGATGAGTGTATGCGCGTAT 59.386 47.619 15.52 15.52 0.00 3.06
486 490 2.817844 AGGATGAGTGTATGCGCGTATA 59.182 45.455 13.13 13.13 0.00 1.47
487 491 3.444034 AGGATGAGTGTATGCGCGTATAT 59.556 43.478 19.79 4.31 0.00 0.86
488 492 4.638865 AGGATGAGTGTATGCGCGTATATA 59.361 41.667 19.79 14.59 0.00 0.86
489 493 5.299531 AGGATGAGTGTATGCGCGTATATAT 59.700 40.000 19.79 9.03 0.00 0.86
490 494 5.399596 GGATGAGTGTATGCGCGTATATATG 59.600 44.000 19.79 0.00 0.00 1.78
491 495 5.554822 TGAGTGTATGCGCGTATATATGA 57.445 39.130 19.79 3.29 0.00 2.15
492 496 5.569413 TGAGTGTATGCGCGTATATATGAG 58.431 41.667 19.79 3.76 0.00 2.90
493 497 4.352039 AGTGTATGCGCGTATATATGAGC 58.648 43.478 19.79 20.14 38.31 4.26
498 502 2.959586 CGCGTATATATGAGCGCTTG 57.040 50.000 13.26 7.35 46.56 4.01
499 503 2.251040 CGCGTATATATGAGCGCTTGT 58.749 47.619 13.26 5.98 46.56 3.16
500 504 2.026860 CGCGTATATATGAGCGCTTGTG 59.973 50.000 13.26 6.56 46.56 3.33
501 505 2.987149 GCGTATATATGAGCGCTTGTGT 59.013 45.455 13.26 4.27 45.48 3.72
502 506 3.059570 GCGTATATATGAGCGCTTGTGTC 59.940 47.826 13.26 0.00 45.48 3.67
503 507 4.476862 CGTATATATGAGCGCTTGTGTCT 58.523 43.478 13.26 0.00 0.00 3.41
504 508 4.322009 CGTATATATGAGCGCTTGTGTCTG 59.678 45.833 13.26 0.00 0.00 3.51
505 509 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
506 510 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
507 511 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
508 512 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
509 513 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
510 514 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
511 515 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
512 516 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
513 517 2.677199 CGCTTGTGTCTGTACTGATGT 58.323 47.619 5.69 0.00 0.00 3.06
514 518 3.059884 CGCTTGTGTCTGTACTGATGTT 58.940 45.455 5.69 0.00 0.00 2.71
515 519 4.234574 CGCTTGTGTCTGTACTGATGTTA 58.765 43.478 5.69 0.00 0.00 2.41
516 520 4.684242 CGCTTGTGTCTGTACTGATGTTAA 59.316 41.667 5.69 0.07 0.00 2.01
517 521 5.176774 CGCTTGTGTCTGTACTGATGTTAAA 59.823 40.000 5.69 0.00 0.00 1.52
547 551 8.937634 ATCAAACATTAAATCATCTGCCTTTC 57.062 30.769 0.00 0.00 0.00 2.62
587 592 1.952990 TGCAAAAAGTTGAGGCATCGA 59.047 42.857 0.00 0.00 36.83 3.59
595 600 8.547069 CAAAAAGTTGAGGCATCGAAAATAAAA 58.453 29.630 0.00 0.00 36.83 1.52
624 632 8.871686 ATATATTTCCTGCGAAACCAAATTTC 57.128 30.769 0.00 0.00 40.74 2.17
642 650 7.201266 CCAAATTTCGAGCGTCTTGAAAATAAG 60.201 37.037 19.38 12.59 44.06 1.73
644 652 5.763444 TTCGAGCGTCTTGAAAATAAGAG 57.237 39.130 6.96 0.00 37.36 2.85
645 653 4.806330 TCGAGCGTCTTGAAAATAAGAGT 58.194 39.130 0.00 0.00 37.36 3.24
647 655 6.384224 TCGAGCGTCTTGAAAATAAGAGTAA 58.616 36.000 0.00 0.00 37.36 2.24
679 748 3.452474 GATCTTGTCATCAGGGTTCTCG 58.548 50.000 0.00 0.00 0.00 4.04
680 749 2.525368 TCTTGTCATCAGGGTTCTCGA 58.475 47.619 0.00 0.00 0.00 4.04
684 753 2.831526 TGTCATCAGGGTTCTCGATTCA 59.168 45.455 0.00 0.00 0.00 2.57
716 785 2.125106 GCAAGCCTACAGGGACCG 60.125 66.667 0.00 0.00 37.23 4.79
717 786 2.584608 CAAGCCTACAGGGACCGG 59.415 66.667 0.00 0.00 37.23 5.28
718 787 2.687566 AAGCCTACAGGGACCGGG 60.688 66.667 6.32 0.00 37.23 5.73
719 788 3.248248 AAGCCTACAGGGACCGGGA 62.248 63.158 6.32 0.00 37.23 5.14
720 789 3.468140 GCCTACAGGGACCGGGAC 61.468 72.222 6.32 0.00 37.23 4.46
721 790 2.762875 CCTACAGGGACCGGGACC 60.763 72.222 6.32 7.62 37.23 4.46
1248 1338 0.393077 AGGTCAGACAAAGGGACGTG 59.607 55.000 2.17 0.00 32.39 4.49
1269 1359 1.906824 TGTCGAGGAGGTGGTGTCC 60.907 63.158 0.00 0.00 0.00 4.02
1307 1397 1.669115 CGACCATGGATCCATCGGC 60.669 63.158 28.90 23.51 33.90 5.54
1309 1399 0.604780 GACCATGGATCCATCGGCAG 60.605 60.000 28.90 18.04 33.90 4.85
1389 1497 1.808945 GCTGATCTGTTTGTGGAGGTG 59.191 52.381 1.27 0.00 0.00 4.00
1539 1647 2.580470 CGAGGATGATGCGCACGAC 61.580 63.158 14.90 8.31 0.00 4.34
1670 1778 4.712476 GAAGATGTTCCTGCCTGTGATAT 58.288 43.478 0.00 0.00 0.00 1.63
1781 1889 0.621571 AAGGGAGATACTGCTGCCCA 60.622 55.000 0.00 0.00 46.52 5.36
1796 1904 1.064537 TGCCCATGATAGCAAGCTTGA 60.065 47.619 30.39 10.67 35.69 3.02
1865 1973 4.226427 TGGATGATTCAAACTCCTCTGG 57.774 45.455 6.40 0.00 0.00 3.86
1945 2053 0.033208 TAATGGCCCCTCTTTGCTGG 60.033 55.000 0.00 0.00 0.00 4.85
1966 2074 2.045536 GTCCTGCTGGCCTTGGAG 60.046 66.667 3.32 7.61 0.00 3.86
2022 2130 1.078426 GCAGGTCCGTGCTAATGGT 60.078 57.895 4.81 0.00 40.54 3.55
2181 2289 2.826428 CCTCACAATATGGTGGTCTCG 58.174 52.381 10.43 0.00 39.27 4.04
2226 2334 5.391416 GCTGGCAGAACAGATTAGAAGAAAC 60.391 44.000 20.86 0.00 40.97 2.78
2249 2357 4.106909 GGTCGTGGTGTTTTTAACTTTGG 58.893 43.478 0.00 0.00 0.00 3.28
2265 2373 0.901827 TTGGCCGAGCACAAGAGATA 59.098 50.000 0.00 0.00 0.00 1.98
2320 2428 4.440525 CCCTTGATTTGTCATGCACCATAC 60.441 45.833 0.00 0.00 0.00 2.39
2455 2563 3.053619 AGTTGGTATGGTTGAGGGAATCC 60.054 47.826 0.00 0.00 0.00 3.01
2469 2577 6.552008 TGAGGGAATCCAAGTAAAAGTGATT 58.448 36.000 0.09 0.00 34.83 2.57
2508 2616 1.829849 TCCTCATCTTCAGACCAGCAG 59.170 52.381 0.00 0.00 0.00 4.24
2556 2664 7.765360 TCTGTGAAGAAAATTGTGAGCAAAAAT 59.235 29.630 0.00 0.00 38.21 1.82
2601 2709 0.613292 ACCGACTGGATCTGCAGAGT 60.613 55.000 22.96 14.23 39.21 3.24
2826 2934 2.688446 TCGTCTTATGAATCCAGTCGCT 59.312 45.455 0.00 0.00 0.00 4.93
2931 3039 1.733912 CTATTGCTCTGCTTTGCGTCA 59.266 47.619 0.00 0.00 0.00 4.35
3021 3129 1.217942 AGGGTTGCTCCACTTCCTTTT 59.782 47.619 1.43 0.00 38.11 2.27
3081 3189 2.747855 CCCGAGGAGCAGTTTGGC 60.748 66.667 0.00 0.00 0.00 4.52
3084 3192 1.448540 CGAGGAGCAGTTTGGCGAT 60.449 57.895 0.00 0.00 39.27 4.58
3119 3227 6.144078 TGAAGATGATTTGGCAGATGATTG 57.856 37.500 0.00 0.00 0.00 2.67
3122 3230 5.198207 AGATGATTTGGCAGATGATTGTGA 58.802 37.500 0.00 0.00 0.00 3.58
3171 3279 0.676782 TGCCTCCTTTTAAGCGCCTC 60.677 55.000 2.29 0.00 0.00 4.70
3219 3327 0.399454 ATGCGCAGAGGAAGGCATAT 59.601 50.000 18.32 0.00 43.74 1.78
3246 3354 6.780901 TGAGGAACTAGACTACAGAGAGAAA 58.219 40.000 0.00 0.00 41.55 2.52
3249 3357 7.920227 AGGAACTAGACTACAGAGAGAAACTA 58.080 38.462 0.00 0.00 36.02 2.24
3338 3446 2.707791 CCAGGGCCAGAGAAGATGATTA 59.292 50.000 6.18 0.00 0.00 1.75
3339 3447 3.330110 CCAGGGCCAGAGAAGATGATTAT 59.670 47.826 6.18 0.00 0.00 1.28
3795 3903 2.016393 TATCTGCGACGCTCCTTGGG 62.016 60.000 22.08 2.84 0.00 4.12
3936 4044 3.582647 TGGAGGCTACATTGAGAGACAAA 59.417 43.478 0.00 0.00 42.03 2.83
4137 4245 2.186384 GAGCACCTGCAGATCGCT 59.814 61.111 17.39 19.05 45.16 4.93
4179 4287 6.727824 ATATTCAAGAACGTCAGGAAGTTG 57.272 37.500 5.35 0.00 33.35 3.16
4262 4370 6.777580 GGGAAGATCCTTAGGATTAATGCAAA 59.222 38.462 15.69 0.00 43.27 3.68
4419 4534 0.961019 CTGCTGGTGCTGCCTTTTTA 59.039 50.000 0.00 0.00 40.48 1.52
4442 4557 8.737168 TTATAGTTTCTGATATGCAAAGCTGT 57.263 30.769 0.00 0.00 0.00 4.40
4487 4602 0.373024 GCTTCTCGCATCTGAACTGC 59.627 55.000 0.00 0.00 38.92 4.40
4521 4640 4.537135 AAGACGGAGACATAAGCTTTGA 57.463 40.909 3.20 0.00 0.00 2.69
4540 4659 8.562892 AGCTTTGACTCATCCATTAATTAATCG 58.437 33.333 7.76 2.12 0.00 3.34
4541 4660 7.805071 GCTTTGACTCATCCATTAATTAATCGG 59.195 37.037 7.76 12.40 0.00 4.18
4542 4661 8.972458 TTTGACTCATCCATTAATTAATCGGA 57.028 30.769 21.45 21.45 31.95 4.55
4543 4662 8.607441 TTGACTCATCCATTAATTAATCGGAG 57.393 34.615 22.57 19.35 31.38 4.63
4603 4796 6.546403 TCTCTATATTCAAGTACAGGTCGCTT 59.454 38.462 0.00 0.00 0.00 4.68
4661 4863 8.792830 TCTTTCTTTCTTTTTCTTCACTCTGA 57.207 30.769 0.00 0.00 0.00 3.27
4689 4891 2.557490 GGTACGTGTTGGTCTTCTCTCT 59.443 50.000 0.00 0.00 0.00 3.10
4690 4892 3.366171 GGTACGTGTTGGTCTTCTCTCTC 60.366 52.174 0.00 0.00 0.00 3.20
4695 4898 4.025647 CGTGTTGGTCTTCTCTCTCAAAAC 60.026 45.833 0.00 0.00 0.00 2.43
4698 4901 5.119694 GTTGGTCTTCTCTCTCAAAACAGT 58.880 41.667 0.00 0.00 0.00 3.55
4701 4904 5.598830 TGGTCTTCTCTCTCAAAACAGTACT 59.401 40.000 0.00 0.00 0.00 2.73
4709 4912 4.751060 TCTCAAAACAGTACTCGTGTTGT 58.249 39.130 19.27 6.00 38.17 3.32
4710 4913 5.893687 TCTCAAAACAGTACTCGTGTTGTA 58.106 37.500 19.27 11.51 38.17 2.41
4816 5046 0.940126 CCATATGGCACGAGCTGTTC 59.060 55.000 9.29 0.00 41.70 3.18
4973 5210 6.035843 GGCATTTGCTAATTCTCAATCGAAA 58.964 36.000 2.12 0.00 41.70 3.46
5000 5244 4.659111 TTGGTCAAGTCTTAGTCGTTCA 57.341 40.909 0.00 0.00 0.00 3.18
5018 5262 7.121463 AGTCGTTCAGTAGTCATAAGATCTTGT 59.879 37.037 18.47 8.72 0.00 3.16
5021 5265 7.251994 GTTCAGTAGTCATAAGATCTTGTCGT 58.748 38.462 18.47 0.95 0.00 4.34
5061 5305 7.776107 TGTATCATTTTTCCTGTTTGTTGACA 58.224 30.769 0.00 0.00 0.00 3.58
5074 5318 1.739929 TTGACATTGACGCGCGGAT 60.740 52.632 35.22 21.18 0.00 4.18
5097 5341 4.143986 TGCCGTACACAATGGATGATAA 57.856 40.909 0.00 0.00 36.17 1.75
5197 5444 0.251634 TTGCGAGGGATGCACACATA 59.748 50.000 0.00 0.00 43.10 2.29
5198 5445 0.469494 TGCGAGGGATGCACACATAT 59.531 50.000 0.00 0.00 37.44 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.434013 GGCATCGATATTTTTGGACGTAAATTT 59.566 33.333 0.00 0.00 0.00 1.82
20 21 3.937814 TCTATGGCGGCATCGATATTTT 58.062 40.909 29.33 4.22 39.00 1.82
24 25 3.064207 GTTTTCTATGGCGGCATCGATA 58.936 45.455 29.33 19.06 39.00 2.92
25 26 1.873591 GTTTTCTATGGCGGCATCGAT 59.126 47.619 29.33 8.04 39.00 3.59
26 27 1.295792 GTTTTCTATGGCGGCATCGA 58.704 50.000 29.33 24.36 39.00 3.59
27 28 1.013596 TGTTTTCTATGGCGGCATCG 58.986 50.000 29.33 22.29 39.81 3.84
52 54 6.434965 TCATTCACCATCAACATTCATGTCTT 59.565 34.615 0.00 0.00 40.80 3.01
56 58 6.478673 CCAATCATTCACCATCAACATTCATG 59.521 38.462 0.00 0.00 0.00 3.07
57 59 6.155565 ACCAATCATTCACCATCAACATTCAT 59.844 34.615 0.00 0.00 0.00 2.57
70 73 3.066380 GTTTGCCCAACCAATCATTCAC 58.934 45.455 0.00 0.00 0.00 3.18
87 90 1.066908 AGATGTTTGTGGTGGCGTTTG 59.933 47.619 0.00 0.00 0.00 2.93
122 125 8.108782 GTCAGCGATGTACAATAAAGTCTTTAC 58.891 37.037 7.20 0.00 0.00 2.01
124 127 6.649141 TGTCAGCGATGTACAATAAAGTCTTT 59.351 34.615 0.00 2.81 0.00 2.52
140 143 4.212913 AGCGGCGATGTCAGCGAT 62.213 61.111 15.87 0.00 35.00 4.58
147 150 2.355986 TACCTTCCAGCGGCGATGT 61.356 57.895 24.41 7.45 0.00 3.06
152 155 1.810030 CTTCGTACCTTCCAGCGGC 60.810 63.158 0.00 0.00 0.00 6.53
159 162 0.645868 GTGCATCGCTTCGTACCTTC 59.354 55.000 0.00 0.00 0.00 3.46
166 169 1.530441 CCTTTGATGTGCATCGCTTCG 60.530 52.381 7.56 0.00 40.63 3.79
167 170 1.796617 GCCTTTGATGTGCATCGCTTC 60.797 52.381 7.56 0.00 40.63 3.86
170 173 1.226773 GGCCTTTGATGTGCATCGC 60.227 57.895 0.00 4.87 40.63 4.58
178 181 3.512724 AGTTTTCAGATGGGCCTTTGATG 59.487 43.478 4.53 0.00 0.00 3.07
182 185 3.575805 TGAAGTTTTCAGATGGGCCTTT 58.424 40.909 4.53 0.00 34.08 3.11
189 192 7.518731 TTTTCCGTTTTGAAGTTTTCAGATG 57.481 32.000 0.00 0.00 41.38 2.90
216 219 9.349713 AGACTCTGGTTTACTAGATGAAGATAG 57.650 37.037 0.00 0.00 32.93 2.08
217 220 9.344772 GAGACTCTGGTTTACTAGATGAAGATA 57.655 37.037 0.00 0.00 32.93 1.98
218 221 7.286775 GGAGACTCTGGTTTACTAGATGAAGAT 59.713 40.741 1.74 0.00 32.93 2.40
219 222 6.603997 GGAGACTCTGGTTTACTAGATGAAGA 59.396 42.308 1.74 0.00 32.93 2.87
220 223 6.605594 AGGAGACTCTGGTTTACTAGATGAAG 59.394 42.308 1.74 0.00 32.90 3.02
221 224 6.494952 AGGAGACTCTGGTTTACTAGATGAA 58.505 40.000 1.74 0.00 32.90 2.57
225 229 4.463186 GCAAGGAGACTCTGGTTTACTAGA 59.537 45.833 1.74 0.00 42.68 2.43
240 244 0.471780 TGTCTGGGAGTGCAAGGAGA 60.472 55.000 0.00 0.00 0.00 3.71
256 260 2.542907 CCCACGTTGGTGTGCTGTC 61.543 63.158 0.00 0.00 42.80 3.51
259 263 2.111043 CTCCCACGTTGGTGTGCT 59.889 61.111 5.46 0.00 42.80 4.40
265 269 2.606519 TCCCTCCTCCCACGTTGG 60.607 66.667 0.00 0.00 37.25 3.77
267 271 2.606826 GGTCCCTCCTCCCACGTT 60.607 66.667 0.00 0.00 0.00 3.99
274 278 2.693896 TAGATCGCCGGTCCCTCCTC 62.694 65.000 1.90 0.00 0.00 3.71
300 304 2.930682 GTTTGTATCACCTCTCCTTCGC 59.069 50.000 0.00 0.00 0.00 4.70
313 317 6.884836 AGTGGTGATTTTAGAGGGTTTGTATC 59.115 38.462 0.00 0.00 0.00 2.24
329 333 6.471233 TTCTAATCTCATCGAGTGGTGATT 57.529 37.500 13.02 13.02 36.33 2.57
344 348 7.913674 AGATGAAACTTTTCGCTTCTAATCT 57.086 32.000 0.00 0.00 40.01 2.40
346 350 9.185192 CAAAAGATGAAACTTTTCGCTTCTAAT 57.815 29.630 0.00 0.00 44.73 1.73
351 355 6.034898 CACACAAAAGATGAAACTTTTCGCTT 59.965 34.615 0.00 4.64 44.73 4.68
359 363 6.713762 TTGATCCACACAAAAGATGAAACT 57.286 33.333 0.00 0.00 0.00 2.66
367 371 8.044060 TCTAATAAGCTTGATCCACACAAAAG 57.956 34.615 9.86 0.00 0.00 2.27
369 373 7.168219 ACTCTAATAAGCTTGATCCACACAAA 58.832 34.615 9.86 0.00 0.00 2.83
370 374 6.711277 ACTCTAATAAGCTTGATCCACACAA 58.289 36.000 9.86 0.00 0.00 3.33
371 375 6.299805 ACTCTAATAAGCTTGATCCACACA 57.700 37.500 9.86 0.00 0.00 3.72
372 376 6.037610 CCAACTCTAATAAGCTTGATCCACAC 59.962 42.308 9.86 0.00 0.00 3.82
373 377 6.070251 TCCAACTCTAATAAGCTTGATCCACA 60.070 38.462 9.86 0.00 0.00 4.17
374 378 6.258947 GTCCAACTCTAATAAGCTTGATCCAC 59.741 42.308 9.86 0.00 0.00 4.02
375 379 6.349300 GTCCAACTCTAATAAGCTTGATCCA 58.651 40.000 9.86 0.00 0.00 3.41
376 380 5.760743 GGTCCAACTCTAATAAGCTTGATCC 59.239 44.000 9.86 0.00 0.00 3.36
390 394 3.474798 TCTGGTATCAGGTCCAACTCT 57.525 47.619 2.43 0.00 41.23 3.24
409 413 5.049198 TGAGCACACTTTCAACAGATTGATC 60.049 40.000 0.00 0.00 44.36 2.92
418 422 5.886960 ATCCTTATGAGCACACTTTCAAC 57.113 39.130 0.00 0.00 0.00 3.18
419 423 7.994425 TTTATCCTTATGAGCACACTTTCAA 57.006 32.000 0.00 0.00 0.00 2.69
422 426 8.246180 CACAATTTATCCTTATGAGCACACTTT 58.754 33.333 0.00 0.00 0.00 2.66
423 427 7.629222 GCACAATTTATCCTTATGAGCACACTT 60.629 37.037 0.00 0.00 0.00 3.16
424 428 6.183360 GCACAATTTATCCTTATGAGCACACT 60.183 38.462 0.00 0.00 0.00 3.55
425 429 5.973565 GCACAATTTATCCTTATGAGCACAC 59.026 40.000 0.00 0.00 0.00 3.82
426 430 5.220835 CGCACAATTTATCCTTATGAGCACA 60.221 40.000 0.00 0.00 0.00 4.57
427 431 5.207768 CGCACAATTTATCCTTATGAGCAC 58.792 41.667 0.00 0.00 0.00 4.40
428 432 4.881273 ACGCACAATTTATCCTTATGAGCA 59.119 37.500 0.00 0.00 0.00 4.26
429 433 5.207768 CACGCACAATTTATCCTTATGAGC 58.792 41.667 0.00 0.00 0.00 4.26
430 434 6.183360 ACACACGCACAATTTATCCTTATGAG 60.183 38.462 0.00 0.00 0.00 2.90
431 435 5.645929 ACACACGCACAATTTATCCTTATGA 59.354 36.000 0.00 0.00 0.00 2.15
432 436 5.738693 CACACACGCACAATTTATCCTTATG 59.261 40.000 0.00 0.00 0.00 1.90
433 437 5.676079 GCACACACGCACAATTTATCCTTAT 60.676 40.000 0.00 0.00 0.00 1.73
434 438 4.378978 GCACACACGCACAATTTATCCTTA 60.379 41.667 0.00 0.00 0.00 2.69
435 439 3.611530 GCACACACGCACAATTTATCCTT 60.612 43.478 0.00 0.00 0.00 3.36
436 440 2.095263 GCACACACGCACAATTTATCCT 60.095 45.455 0.00 0.00 0.00 3.24
437 441 2.250188 GCACACACGCACAATTTATCC 58.750 47.619 0.00 0.00 0.00 2.59
438 442 1.904412 CGCACACACGCACAATTTATC 59.096 47.619 0.00 0.00 0.00 1.75
439 443 1.265635 ACGCACACACGCACAATTTAT 59.734 42.857 0.00 0.00 36.19 1.40
440 444 0.658368 ACGCACACACGCACAATTTA 59.342 45.000 0.00 0.00 36.19 1.40
441 445 0.179150 AACGCACACACGCACAATTT 60.179 45.000 0.00 0.00 36.19 1.82
442 446 0.591236 GAACGCACACACGCACAATT 60.591 50.000 0.00 0.00 36.19 2.32
443 447 1.010125 GAACGCACACACGCACAAT 60.010 52.632 0.00 0.00 36.19 2.71
444 448 1.710103 ATGAACGCACACACGCACAA 61.710 50.000 0.00 0.00 36.19 3.33
445 449 0.876342 TATGAACGCACACACGCACA 60.876 50.000 0.00 0.00 36.19 4.57
446 450 0.233590 TTATGAACGCACACACGCAC 59.766 50.000 0.00 0.00 36.19 5.34
447 451 0.510790 CTTATGAACGCACACACGCA 59.489 50.000 0.00 0.00 36.19 5.24
448 452 0.179225 CCTTATGAACGCACACACGC 60.179 55.000 0.00 0.00 36.19 5.34
449 453 1.424403 TCCTTATGAACGCACACACG 58.576 50.000 0.00 0.00 39.50 4.49
450 454 3.000041 TCATCCTTATGAACGCACACAC 59.000 45.455 0.00 0.00 39.20 3.82
451 455 3.261580 CTCATCCTTATGAACGCACACA 58.738 45.455 0.00 0.00 41.57 3.72
452 456 3.062639 CACTCATCCTTATGAACGCACAC 59.937 47.826 0.00 0.00 41.57 3.82
453 457 3.261580 CACTCATCCTTATGAACGCACA 58.738 45.455 0.00 0.00 41.57 4.57
454 458 3.262420 ACACTCATCCTTATGAACGCAC 58.738 45.455 0.00 0.00 41.57 5.34
455 459 3.610040 ACACTCATCCTTATGAACGCA 57.390 42.857 0.00 0.00 41.57 5.24
456 460 4.084328 GCATACACTCATCCTTATGAACGC 60.084 45.833 0.00 0.00 41.57 4.84
457 461 4.148871 CGCATACACTCATCCTTATGAACG 59.851 45.833 0.00 0.00 41.57 3.95
458 462 4.084328 GCGCATACACTCATCCTTATGAAC 60.084 45.833 0.30 0.00 41.57 3.18
459 463 4.058124 GCGCATACACTCATCCTTATGAA 58.942 43.478 0.30 0.00 41.57 2.57
460 464 3.653344 GCGCATACACTCATCCTTATGA 58.347 45.455 0.30 0.00 39.87 2.15
461 465 2.409715 CGCGCATACACTCATCCTTATG 59.590 50.000 8.75 0.00 0.00 1.90
462 466 2.035961 ACGCGCATACACTCATCCTTAT 59.964 45.455 5.73 0.00 0.00 1.73
463 467 1.407618 ACGCGCATACACTCATCCTTA 59.592 47.619 5.73 0.00 0.00 2.69
464 468 0.175760 ACGCGCATACACTCATCCTT 59.824 50.000 5.73 0.00 0.00 3.36
465 469 1.029681 TACGCGCATACACTCATCCT 58.970 50.000 5.73 0.00 0.00 3.24
466 470 2.065993 ATACGCGCATACACTCATCC 57.934 50.000 5.73 0.00 0.00 3.51
467 471 6.199393 TCATATATACGCGCATACACTCATC 58.801 40.000 5.73 0.00 0.00 2.92
468 472 6.131544 TCATATATACGCGCATACACTCAT 57.868 37.500 5.73 0.00 0.00 2.90
469 473 5.554822 TCATATATACGCGCATACACTCA 57.445 39.130 5.73 0.00 0.00 3.41
470 474 4.438145 GCTCATATATACGCGCATACACTC 59.562 45.833 5.73 0.00 0.00 3.51
471 475 4.352039 GCTCATATATACGCGCATACACT 58.648 43.478 5.73 0.00 0.00 3.55
472 476 3.177838 CGCTCATATATACGCGCATACAC 59.822 47.826 5.73 0.00 39.11 2.90
473 477 3.359654 CGCTCATATATACGCGCATACA 58.640 45.455 5.73 0.00 39.11 2.29
481 485 4.322009 CAGACACAAGCGCTCATATATACG 59.678 45.833 12.06 0.00 0.00 3.06
482 486 5.223382 ACAGACACAAGCGCTCATATATAC 58.777 41.667 12.06 0.00 0.00 1.47
483 487 5.453567 ACAGACACAAGCGCTCATATATA 57.546 39.130 12.06 0.00 0.00 0.86
484 488 4.327982 ACAGACACAAGCGCTCATATAT 57.672 40.909 12.06 0.00 0.00 0.86
485 489 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
486 490 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
487 491 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
488 492 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
489 493 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
490 494 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
491 495 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
492 496 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
493 497 2.677199 ACATCAGTACAGACACAAGCG 58.323 47.619 0.00 0.00 0.00 4.68
494 498 6.539649 TTTAACATCAGTACAGACACAAGC 57.460 37.500 0.00 0.00 0.00 4.01
522 526 8.533657 TGAAAGGCAGATGATTTAATGTTTGAT 58.466 29.630 0.00 0.00 0.00 2.57
567 572 1.952990 TCGATGCCTCAACTTTTTGCA 59.047 42.857 0.00 0.00 36.23 4.08
570 575 8.655651 TTTTATTTTCGATGCCTCAACTTTTT 57.344 26.923 0.00 0.00 0.00 1.94
621 629 5.694910 ACTCTTATTTTCAAGACGCTCGAAA 59.305 36.000 0.00 0.00 31.34 3.46
624 632 6.627690 TTACTCTTATTTTCAAGACGCTCG 57.372 37.500 0.00 0.00 31.34 5.03
647 655 7.066284 CCCTGATGACAAGATCGAACTTTTTAT 59.934 37.037 5.03 1.95 0.00 1.40
679 748 2.418083 CCGCTTTGGGGGCTGAATC 61.418 63.158 0.00 0.00 38.70 2.52
680 749 2.362889 CCGCTTTGGGGGCTGAAT 60.363 61.111 0.00 0.00 38.70 2.57
716 785 0.545548 AGAGAAGGTGGTCAGGTCCC 60.546 60.000 0.00 0.00 0.00 4.46
717 786 0.899019 GAGAGAAGGTGGTCAGGTCC 59.101 60.000 0.00 0.00 0.00 4.46
718 787 1.931635 AGAGAGAAGGTGGTCAGGTC 58.068 55.000 0.00 0.00 0.00 3.85
719 788 2.252714 GAAGAGAGAAGGTGGTCAGGT 58.747 52.381 0.00 0.00 0.00 4.00
720 789 1.552792 GGAAGAGAGAAGGTGGTCAGG 59.447 57.143 0.00 0.00 0.00 3.86
721 790 2.495669 GAGGAAGAGAGAAGGTGGTCAG 59.504 54.545 0.00 0.00 0.00 3.51
1140 1230 1.658717 CAAGATCTCGCCGCTACCG 60.659 63.158 0.00 0.00 0.00 4.02
1248 1338 2.603776 ACCACCTCCTCGACACCC 60.604 66.667 0.00 0.00 0.00 4.61
1269 1359 4.100084 TCAGCCCAGGCCACATCG 62.100 66.667 5.01 0.00 43.17 3.84
1307 1397 2.219458 CAGCCTGTTGATCATAGCCTG 58.781 52.381 0.00 0.09 0.00 4.85
1309 1399 0.950116 GCAGCCTGTTGATCATAGCC 59.050 55.000 0.00 0.00 0.00 3.93
1368 1476 1.421268 ACCTCCACAAACAGATCAGCA 59.579 47.619 0.00 0.00 0.00 4.41
1539 1647 3.484742 TAAGCGCTCCCGATGCTCG 62.485 63.158 12.06 0.00 38.17 5.03
1589 1697 2.330440 AACAGCATCTGTCACACACA 57.670 45.000 0.00 0.00 44.62 3.72
1670 1778 0.841961 CATGGGGAGCTCAGGATTGA 59.158 55.000 17.19 0.00 0.00 2.57
1781 1889 2.158696 GGGACCTCAAGCTTGCTATCAT 60.159 50.000 21.99 3.53 0.00 2.45
1796 1904 2.472029 CTCCAGATTGTGTAGGGACCT 58.528 52.381 0.00 0.00 0.00 3.85
1865 1973 5.229423 CAGAGCTAGCCTTATTCTCATCAC 58.771 45.833 12.13 0.00 0.00 3.06
1966 2074 0.813821 GGCAACAAGGAAGAGGATGC 59.186 55.000 0.00 0.00 0.00 3.91
1971 2079 0.674895 CCGGAGGCAACAAGGAAGAG 60.675 60.000 0.00 0.00 46.14 2.85
2022 2130 3.051210 CTGTCCACAGCGACTGGA 58.949 61.111 10.80 2.47 37.15 3.86
2044 2152 2.363680 CAGATTCAGTATCCTGCCGAGT 59.636 50.000 0.00 0.00 38.66 4.18
2226 2334 3.678915 AAGTTAAAAACACCACGACCG 57.321 42.857 0.00 0.00 0.00 4.79
2249 2357 0.179100 TGCTATCTCTTGTGCTCGGC 60.179 55.000 0.00 0.00 0.00 5.54
2265 2373 1.072159 AGCTTCAAGCCGTTCTGCT 59.928 52.632 5.53 0.00 43.77 4.24
2320 2428 2.890945 CCCCAGTTTTACCAAGAACCAG 59.109 50.000 0.00 0.00 0.00 4.00
2455 2563 7.530010 CCAGGTGTATCAATCACTTTTACTTG 58.470 38.462 0.00 0.00 36.25 3.16
2469 2577 2.092429 GGATGAAAGGCCAGGTGTATCA 60.092 50.000 5.01 0.00 0.00 2.15
2508 2616 7.012421 ACAGAATTGAGAACTTTCTGGTTGTAC 59.988 37.037 14.35 0.00 46.75 2.90
2556 2664 9.973661 TCAAAATAAAGAACAATATCAGGAGGA 57.026 29.630 0.00 0.00 0.00 3.71
2844 2952 2.040278 TGACCTATTTGTCCTGCAAGCT 59.960 45.455 0.00 0.00 38.47 3.74
3021 3129 4.735369 ACTGAAGAAGTGAAGAGAGGAGA 58.265 43.478 0.00 0.00 37.88 3.71
3081 3189 7.835634 ATCATCTTCAAGATCATCATCATCG 57.164 36.000 0.00 0.00 31.32 3.84
3084 3192 7.255486 GCCAAATCATCTTCAAGATCATCATCA 60.255 37.037 0.00 0.00 31.32 3.07
3119 3227 5.426504 AGTCTGAACCATCATCTGAATCAC 58.573 41.667 0.00 0.00 34.37 3.06
3122 3230 7.370905 TCATAGTCTGAACCATCATCTGAAT 57.629 36.000 0.00 0.00 34.37 2.57
3171 3279 6.136541 AGTTTTGAAAGTTGAGCCTTAGTG 57.863 37.500 0.00 0.00 0.00 2.74
3219 3327 6.213802 TCTCTCTGTAGTCTAGTTCCTCAAGA 59.786 42.308 0.00 0.00 0.00 3.02
3338 3446 4.142622 CGTCATCAACATTGCTGTTACCAT 60.143 41.667 0.00 0.00 43.76 3.55
3339 3447 3.188254 CGTCATCAACATTGCTGTTACCA 59.812 43.478 0.00 0.00 43.76 3.25
3347 3455 1.132834 TGCCATCGTCATCAACATTGC 59.867 47.619 0.00 0.00 0.00 3.56
3729 3837 5.453567 TGAAGTTCTTGAATCTCGACTCA 57.546 39.130 4.17 0.00 0.00 3.41
3795 3903 3.388024 TCACACCAGCTGATAAGGTATCC 59.612 47.826 17.39 0.00 34.26 2.59
3801 3909 5.181009 TCAATCTTCACACCAGCTGATAAG 58.819 41.667 17.39 10.67 0.00 1.73
3810 3918 4.101585 AGTCTGTCTTCAATCTTCACACCA 59.898 41.667 0.00 0.00 0.00 4.17
3918 4026 4.826556 AGTCTTTGTCTCTCAATGTAGCC 58.173 43.478 0.00 0.00 35.84 3.93
3921 4029 5.105877 CGGGTAGTCTTTGTCTCTCAATGTA 60.106 44.000 0.00 0.00 35.84 2.29
4054 4162 3.076621 TCACATTCAGACTGGCAATCAC 58.923 45.455 1.81 0.00 0.00 3.06
4179 4287 4.509600 GCAGATTCATAGTAGTTGTCCAGC 59.490 45.833 0.00 0.00 0.00 4.85
4262 4370 7.639113 ACAAATGTATGGTTCCGATTTATGT 57.361 32.000 0.00 0.00 0.00 2.29
4419 4534 7.478322 CAACAGCTTTGCATATCAGAAACTAT 58.522 34.615 0.00 0.00 0.00 2.12
4456 4571 2.493713 CGAGAAGCAGGTATTACGCT 57.506 50.000 0.00 0.00 37.68 5.07
4502 4621 3.851098 AGTCAAAGCTTATGTCTCCGTC 58.149 45.455 0.00 0.00 0.00 4.79
4521 4640 5.940470 GCCTCCGATTAATTAATGGATGAGT 59.060 40.000 18.62 0.00 0.00 3.41
4539 4658 0.389948 ACTGAGTTTTAGCGCCTCCG 60.390 55.000 2.29 1.84 37.57 4.63
4540 4659 1.464997 CAACTGAGTTTTAGCGCCTCC 59.535 52.381 2.29 0.00 0.00 4.30
4541 4660 2.157863 GTCAACTGAGTTTTAGCGCCTC 59.842 50.000 2.29 3.32 0.00 4.70
4542 4661 2.143925 GTCAACTGAGTTTTAGCGCCT 58.856 47.619 2.29 0.00 0.00 5.52
4543 4662 2.143925 AGTCAACTGAGTTTTAGCGCC 58.856 47.619 2.29 0.00 0.00 6.53
4603 4796 0.604243 AGAAACGGCAATACGGTGCA 60.604 50.000 9.73 0.00 46.81 4.57
4661 4863 1.274447 GACCAACACGTACCTAAGGCT 59.726 52.381 0.00 0.00 0.00 4.58
4689 4891 5.954434 GTACAACACGAGTACTGTTTTGA 57.046 39.130 20.99 9.61 38.95 2.69
4792 5022 1.065491 AGCTCGTGCCATATGGAACAA 60.065 47.619 29.00 13.40 44.37 2.83
4951 5187 7.642978 CCTCTTTCGATTGAGAATTAGCAAATG 59.357 37.037 14.37 0.00 32.44 2.32
4973 5210 4.158764 CGACTAAGACTTGACCAATCCTCT 59.841 45.833 0.00 0.00 0.00 3.69
5000 5244 9.175312 TCTTTACGACAAGATCTTATGACTACT 57.825 33.333 7.86 0.00 0.00 2.57
5018 5262 5.808030 TGATACATTGCACGAATCTTTACGA 59.192 36.000 0.00 0.00 0.00 3.43
5021 5265 9.853555 AAAAATGATACATTGCACGAATCTTTA 57.146 25.926 0.00 0.00 0.00 1.85
5061 5305 3.864686 GCACATCCGCGCGTCAAT 61.865 61.111 29.95 16.06 0.00 2.57
5097 5341 2.304761 TCACTCGCCCATAGAAAAAGGT 59.695 45.455 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.