Multiple sequence alignment - TraesCS1A01G315200

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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 TraesCS1A01G315200 chr1A 100.000 5824 0 0 1 5824 506558775 506552952 0.000000e+00 10756.0
1 TraesCS1A01G315200 chr1A 100.000 151 0 0 6201 6351 506552575 506552425 4.850000e-71 279.0
2 TraesCS1A01G315200 chr1A 94.444 108 5 1 422 528 53905034 53905141 1.420000e-36 165.0
3 TraesCS1A01G315200 chr1A 100.000 36 0 0 5426 5461 506553323 506553288 4.110000e-07 67.6
4 TraesCS1A01G315200 chr1A 100.000 36 0 0 5453 5488 506553350 506553315 4.110000e-07 67.6
5 TraesCS1A01G315200 chr1D 97.339 4510 93 15 524 5023 410511484 410506992 0.000000e+00 7638.0
6 TraesCS1A01G315200 chr1D 99.129 804 7 0 5021 5824 410506967 410506164 0.000000e+00 1447.0
7 TraesCS1A01G315200 chr1D 89.680 281 26 3 4 281 410511942 410511662 7.830000e-94 355.0
8 TraesCS1A01G315200 chr1D 99.138 116 1 0 6236 6351 410505865 410505750 6.450000e-50 209.0
9 TraesCS1A01G315200 chr1D 88.506 174 19 1 154 326 410511663 410511490 6.450000e-50 209.0
10 TraesCS1A01G315200 chr1D 92.241 116 8 1 422 536 48024730 48024615 5.090000e-36 163.0
11 TraesCS1A01G315200 chr1D 100.000 36 0 0 5453 5488 410506562 410506527 4.110000e-07 67.6
12 TraesCS1A01G315200 chr1B 95.778 4524 125 26 524 5023 553156501 553152020 0.000000e+00 7236.0
13 TraesCS1A01G315200 chr1B 98.555 623 7 2 5021 5642 553151995 553151374 0.000000e+00 1099.0
14 TraesCS1A01G315200 chr1B 97.546 163 4 0 5662 5824 553151387 553151225 4.850000e-71 279.0
15 TraesCS1A01G315200 chr1B 93.421 152 9 1 6201 6351 553150742 553150591 2.300000e-54 224.0
16 TraesCS1A01G315200 chr1B 100.000 36 0 0 5426 5461 553151564 553151529 4.110000e-07 67.6
17 TraesCS1A01G315200 chr1B 100.000 36 0 0 5453 5488 553151591 553151556 4.110000e-07 67.6
18 TraesCS1A01G315200 chr5D 95.370 108 4 1 422 528 391376988 391376881 3.040000e-38 171.0
19 TraesCS1A01G315200 chr5D 90.833 120 9 2 422 539 135657964 135658083 6.590000e-35 159.0
20 TraesCS1A01G315200 chr7B 95.327 107 4 1 423 528 470986836 470986942 1.100000e-37 169.0
21 TraesCS1A01G315200 chr5B 92.373 118 5 4 423 539 21363008 21363122 1.420000e-36 165.0
22 TraesCS1A01G315200 chr5B 90.323 124 9 3 416 536 531200076 531199953 6.590000e-35 159.0
23 TraesCS1A01G315200 chr3B 92.241 116 8 1 414 528 449159935 449159820 5.090000e-36 163.0
24 TraesCS1A01G315200 chr2B 92.241 116 7 2 414 528 44067114 44067228 5.090000e-36 163.0


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 TraesCS1A01G315200 chr1A 506552425 506558775 6350 True 5517.500000 10756 100.000 1 6351 2 chr1A.!!$R1 6350
1 TraesCS1A01G315200 chr1D 410505750 410511942 6192 True 1654.266667 7638 95.632 4 6351 6 chr1D.!!$R2 6347
2 TraesCS1A01G315200 chr1B 553150591 553156501 5910 True 1495.533333 7236 97.550 524 6351 6 chr1B.!!$R1 5827

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
384 469 0.238289 CGCGCAAAGTCATGAAAGGT 59.762 50.000 8.75 0.00 0.00 3.50 F
438 523 0.549950 AGATACTCCCTCCGTTCGGA 59.450 55.000 13.34 13.34 0.00 4.55 F
833 926 0.597568 CGAGGGCAGCTGAGATAGAG 59.402 60.000 20.43 0.00 0.00 2.43 F
1185 1281 1.369091 CGCCCTCTAAACGCATGCTT 61.369 55.000 17.13 2.67 0.00 3.91 F
1684 1782 1.528129 AAGTAGGTGAAGCAGCTTGC 58.472 50.000 13.91 5.03 42.44 4.01 F
1724 1822 2.257974 TCGTAGCTCGACACAATGTC 57.742 50.000 0.00 0.00 44.01 3.06 F
3154 3263 2.858745 TGGAGCCTGTTAACAGTTTCC 58.141 47.619 30.38 30.38 42.27 3.13 F
4199 4308 0.621571 AGCTACTTGGATGGCAGGGA 60.622 55.000 0.00 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1571 0.033366 ACCATTGAAAAACAGGCGCC 59.967 50.000 21.89 21.89 0.00 6.53 R
1682 1780 0.108186 AGTTGCTGCTATACTGCGCA 60.108 50.000 10.98 10.98 45.63 6.09 R
1956 2054 0.515564 CCGTTGGTTGACTAAAGCGG 59.484 55.000 0.00 0.00 39.22 5.52 R
2549 2651 6.949352 ATTCAGCCAAGAATAATGGTACAG 57.051 37.500 0.00 0.00 37.98 2.74 R
3543 3652 7.862372 TGAATCAAATGACTGTTTAAGAAGTGC 59.138 33.333 0.00 0.00 0.00 4.40 R
3822 3931 8.925161 TTGTGGCTGCAAGATATTATTTAAAC 57.075 30.769 0.50 0.00 34.07 2.01 R
4229 4338 0.169672 CAGATCCGGCAACAGCTTTG 59.830 55.000 0.00 0.00 0.00 2.77 R
6203 6369 0.108520 CATTGCATGGCACTTCACCC 60.109 55.000 0.00 0.00 38.71 4.61 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
46 47 0.859232 AAACATGCTCGACACACGTC 59.141 50.000 0.00 0.00 43.13 4.34
84 85 3.684788 AGAAAGTCGTCATTACATGTGGC 59.315 43.478 9.11 0.00 0.00 5.01
87 88 1.588404 GTCGTCATTACATGTGGCTCG 59.412 52.381 9.11 7.21 0.00 5.03
126 127 0.953960 TTTTCCTCCGCGCCTCTTTC 60.954 55.000 0.00 0.00 0.00 2.62
146 148 2.306219 TCACCATCCCACGTAAATGGAA 59.694 45.455 22.74 11.77 43.02 3.53
152 154 1.673920 CCCACGTAAATGGAAATCCCG 59.326 52.381 0.00 0.00 43.02 5.14
160 162 3.973206 AATGGAAATCCCGAAAAACCC 57.027 42.857 0.00 0.00 37.93 4.11
165 167 1.919240 AATCCCGAAAAACCCAGGTC 58.081 50.000 0.00 0.00 0.00 3.85
181 184 4.393155 TCTGCAAGCCGCCATCGT 62.393 61.111 0.00 0.00 41.33 3.73
190 193 2.480555 CGCCATCGTCCAAGCAAC 59.519 61.111 0.00 0.00 0.00 4.17
195 198 1.026718 CATCGTCCAAGCAACCCCTC 61.027 60.000 0.00 0.00 0.00 4.30
219 222 2.029918 GCCCTCCATTTTCACACAACTC 60.030 50.000 0.00 0.00 0.00 3.01
222 225 1.606668 TCCATTTTCACACAACTCCGC 59.393 47.619 0.00 0.00 0.00 5.54
237 240 4.016706 CGCGGGTTCCCTCCTTGT 62.017 66.667 0.00 0.00 0.00 3.16
239 242 2.593956 GCGGGTTCCCTCCTTGTCT 61.594 63.158 6.31 0.00 0.00 3.41
244 247 1.610886 GGTTCCCTCCTTGTCTTTCCG 60.611 57.143 0.00 0.00 0.00 4.30
245 248 1.346722 GTTCCCTCCTTGTCTTTCCGA 59.653 52.381 0.00 0.00 0.00 4.55
277 280 7.931578 AATACTTCATTAAAATCACCCACGA 57.068 32.000 0.00 0.00 0.00 4.35
281 284 7.145323 ACTTCATTAAAATCACCCACGAAAAG 58.855 34.615 0.00 0.00 0.00 2.27
282 285 5.465935 TCATTAAAATCACCCACGAAAAGC 58.534 37.500 0.00 0.00 0.00 3.51
288 373 1.454295 ACCCACGAAAAGCCCGTTT 60.454 52.632 0.00 0.00 38.29 3.60
295 380 0.663269 GAAAAGCCCGTTTCGCTTGG 60.663 55.000 0.00 0.00 45.69 3.61
300 385 0.806241 GCCCGTTTCGCTTGGAATAA 59.194 50.000 0.00 0.00 33.85 1.40
303 388 3.252458 GCCCGTTTCGCTTGGAATAATAT 59.748 43.478 0.00 0.00 33.85 1.28
323 408 1.065345 TCCCATTAAAATCACCCGCGA 60.065 47.619 8.23 0.00 0.00 5.87
337 422 3.351416 GCGAAAAGCCCGTTCCGT 61.351 61.111 0.00 0.00 40.81 4.69
361 446 9.863845 CGTTTGGAATAATACCCTGTTAAAATT 57.136 29.630 0.00 0.00 0.00 1.82
372 457 3.566523 CTGTTAAAATTACCCGCGCAAA 58.433 40.909 8.75 0.00 0.00 3.68
373 458 3.566523 TGTTAAAATTACCCGCGCAAAG 58.433 40.909 8.75 0.00 0.00 2.77
374 459 3.004524 TGTTAAAATTACCCGCGCAAAGT 59.995 39.130 8.75 3.35 0.00 2.66
375 460 2.341318 AAAATTACCCGCGCAAAGTC 57.659 45.000 8.75 0.00 0.00 3.01
376 461 1.240256 AAATTACCCGCGCAAAGTCA 58.760 45.000 8.75 0.00 0.00 3.41
377 462 1.459450 AATTACCCGCGCAAAGTCAT 58.541 45.000 8.75 0.00 0.00 3.06
378 463 0.732571 ATTACCCGCGCAAAGTCATG 59.267 50.000 8.75 0.00 0.00 3.07
379 464 0.320858 TTACCCGCGCAAAGTCATGA 60.321 50.000 8.75 0.00 0.00 3.07
380 465 0.320858 TACCCGCGCAAAGTCATGAA 60.321 50.000 8.75 0.00 0.00 2.57
381 466 1.169661 ACCCGCGCAAAGTCATGAAA 61.170 50.000 8.75 0.00 0.00 2.69
382 467 0.454957 CCCGCGCAAAGTCATGAAAG 60.455 55.000 8.75 0.00 0.00 2.62
383 468 0.454957 CCGCGCAAAGTCATGAAAGG 60.455 55.000 8.75 0.00 0.00 3.11
384 469 0.238289 CGCGCAAAGTCATGAAAGGT 59.762 50.000 8.75 0.00 0.00 3.50
385 470 1.334960 CGCGCAAAGTCATGAAAGGTT 60.335 47.619 8.75 0.00 0.00 3.50
386 471 2.319472 GCGCAAAGTCATGAAAGGTTC 58.681 47.619 0.30 0.00 0.00 3.62
387 472 2.922335 GCGCAAAGTCATGAAAGGTTCC 60.922 50.000 0.30 0.00 0.00 3.62
388 473 2.665519 CGCAAAGTCATGAAAGGTTCCG 60.666 50.000 0.00 0.00 0.00 4.30
389 474 2.922335 GCAAAGTCATGAAAGGTTCCGC 60.922 50.000 0.00 0.00 0.00 5.54
390 475 2.270352 AAGTCATGAAAGGTTCCGCA 57.730 45.000 0.00 0.00 0.00 5.69
391 476 2.270352 AGTCATGAAAGGTTCCGCAA 57.730 45.000 0.00 0.00 0.00 4.85
392 477 2.582052 AGTCATGAAAGGTTCCGCAAA 58.418 42.857 0.00 0.00 0.00 3.68
393 478 2.955660 AGTCATGAAAGGTTCCGCAAAA 59.044 40.909 0.00 0.00 0.00 2.44
394 479 3.049912 GTCATGAAAGGTTCCGCAAAAC 58.950 45.455 0.00 0.00 0.00 2.43
401 486 2.517650 GGTTCCGCAAAACCATGAAA 57.482 45.000 11.40 0.00 46.62 2.69
402 487 2.403259 GGTTCCGCAAAACCATGAAAG 58.597 47.619 11.40 0.00 46.62 2.62
403 488 2.035321 GGTTCCGCAAAACCATGAAAGA 59.965 45.455 11.40 0.00 46.62 2.52
404 489 3.306019 GGTTCCGCAAAACCATGAAAGAT 60.306 43.478 11.40 0.00 46.62 2.40
405 490 3.848272 TCCGCAAAACCATGAAAGATC 57.152 42.857 0.00 0.00 0.00 2.75
406 491 3.153130 TCCGCAAAACCATGAAAGATCA 58.847 40.909 0.00 0.00 40.57 2.92
408 493 4.107622 CCGCAAAACCATGAAAGATCATC 58.892 43.478 0.00 0.00 44.53 2.92
409 494 4.107622 CGCAAAACCATGAAAGATCATCC 58.892 43.478 0.00 0.00 44.53 3.51
410 495 4.142315 CGCAAAACCATGAAAGATCATCCT 60.142 41.667 0.00 0.00 44.53 3.24
411 496 5.107133 GCAAAACCATGAAAGATCATCCTG 58.893 41.667 0.00 0.00 44.53 3.86
412 497 5.337009 GCAAAACCATGAAAGATCATCCTGT 60.337 40.000 0.00 0.00 44.53 4.00
424 509 8.729805 AAAGATCATCCTGTTTTCTGAGATAC 57.270 34.615 0.00 0.00 0.00 2.24
425 510 7.673641 AGATCATCCTGTTTTCTGAGATACT 57.326 36.000 0.00 0.00 0.00 2.12
426 511 7.725251 AGATCATCCTGTTTTCTGAGATACTC 58.275 38.462 0.00 0.00 0.00 2.59
427 512 6.227298 TCATCCTGTTTTCTGAGATACTCC 57.773 41.667 0.00 0.00 0.00 3.85
428 513 5.129485 TCATCCTGTTTTCTGAGATACTCCC 59.871 44.000 0.00 0.00 0.00 4.30
429 514 4.689062 TCCTGTTTTCTGAGATACTCCCT 58.311 43.478 0.00 0.00 0.00 4.20
430 515 4.712337 TCCTGTTTTCTGAGATACTCCCTC 59.288 45.833 0.00 0.00 0.00 4.30
431 516 4.141824 CCTGTTTTCTGAGATACTCCCTCC 60.142 50.000 0.00 0.00 0.00 4.30
432 517 3.447586 TGTTTTCTGAGATACTCCCTCCG 59.552 47.826 0.00 0.00 0.00 4.63
433 518 3.383698 TTTCTGAGATACTCCCTCCGT 57.616 47.619 0.00 0.00 0.00 4.69
434 519 3.383698 TTCTGAGATACTCCCTCCGTT 57.616 47.619 0.00 0.00 0.00 4.44
435 520 2.933573 TCTGAGATACTCCCTCCGTTC 58.066 52.381 0.00 0.00 0.00 3.95
436 521 1.604755 CTGAGATACTCCCTCCGTTCG 59.395 57.143 0.00 0.00 0.00 3.95
437 522 0.953003 GAGATACTCCCTCCGTTCGG 59.047 60.000 4.74 4.74 0.00 4.30
438 523 0.549950 AGATACTCCCTCCGTTCGGA 59.450 55.000 13.34 13.34 0.00 4.55
439 524 1.064166 AGATACTCCCTCCGTTCGGAA 60.064 52.381 14.79 0.00 33.41 4.30
440 525 1.962100 GATACTCCCTCCGTTCGGAAT 59.038 52.381 14.79 4.68 33.41 3.01
441 526 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
442 527 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
443 528 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
444 529 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
445 530 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
446 531 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
447 532 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
448 533 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
449 534 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
450 535 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
451 536 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
452 537 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
453 538 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
454 539 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
455 540 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
456 541 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
457 542 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
458 543 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
459 544 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
460 545 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
461 546 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
462 547 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
463 548 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
464 549 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
465 550 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
466 551 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
467 552 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
468 553 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
469 554 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
470 555 5.631512 GTCGCAGAAATGGATGTATCTAGAC 59.368 44.000 0.00 0.00 39.69 2.59
471 556 4.618912 CGCAGAAATGGATGTATCTAGACG 59.381 45.833 0.00 0.00 0.00 4.18
472 557 5.533482 GCAGAAATGGATGTATCTAGACGT 58.467 41.667 0.00 0.00 0.00 4.34
473 558 6.567891 CGCAGAAATGGATGTATCTAGACGTA 60.568 42.308 0.00 0.00 0.00 3.57
474 559 7.316640 GCAGAAATGGATGTATCTAGACGTAT 58.683 38.462 0.00 0.00 0.00 3.06
475 560 7.815068 GCAGAAATGGATGTATCTAGACGTATT 59.185 37.037 0.00 0.00 0.00 1.89
476 561 9.698309 CAGAAATGGATGTATCTAGACGTATTT 57.302 33.333 0.00 0.00 0.00 1.40
504 589 9.690913 AATTCTAGATCATCCATTTTTGAGACA 57.309 29.630 0.00 0.00 0.00 3.41
505 590 9.690913 ATTCTAGATCATCCATTTTTGAGACAA 57.309 29.630 0.00 0.00 0.00 3.18
506 591 8.728337 TCTAGATCATCCATTTTTGAGACAAG 57.272 34.615 0.00 0.00 0.00 3.16
507 592 8.324306 TCTAGATCATCCATTTTTGAGACAAGT 58.676 33.333 0.00 0.00 0.00 3.16
508 593 9.605275 CTAGATCATCCATTTTTGAGACAAGTA 57.395 33.333 0.00 0.00 0.00 2.24
509 594 8.868522 AGATCATCCATTTTTGAGACAAGTAA 57.131 30.769 0.00 0.00 0.00 2.24
510 595 9.471702 AGATCATCCATTTTTGAGACAAGTAAT 57.528 29.630 0.00 0.00 0.00 1.89
511 596 9.512435 GATCATCCATTTTTGAGACAAGTAATG 57.488 33.333 0.00 0.00 0.00 1.90
512 597 7.315142 TCATCCATTTTTGAGACAAGTAATGC 58.685 34.615 0.00 0.00 0.00 3.56
513 598 6.899393 TCCATTTTTGAGACAAGTAATGCT 57.101 33.333 0.00 0.00 0.00 3.79
514 599 6.680810 TCCATTTTTGAGACAAGTAATGCTG 58.319 36.000 0.00 0.00 0.00 4.41
515 600 6.489700 TCCATTTTTGAGACAAGTAATGCTGA 59.510 34.615 0.00 0.00 0.00 4.26
516 601 7.014134 TCCATTTTTGAGACAAGTAATGCTGAA 59.986 33.333 0.00 0.00 0.00 3.02
517 602 7.115378 CCATTTTTGAGACAAGTAATGCTGAAC 59.885 37.037 0.00 0.00 0.00 3.18
518 603 4.990543 TTGAGACAAGTAATGCTGAACG 57.009 40.909 0.00 0.00 0.00 3.95
519 604 3.325870 TGAGACAAGTAATGCTGAACGG 58.674 45.455 0.00 0.00 0.00 4.44
520 605 3.006430 TGAGACAAGTAATGCTGAACGGA 59.994 43.478 0.00 0.00 0.00 4.69
521 606 3.994392 GAGACAAGTAATGCTGAACGGAA 59.006 43.478 0.00 0.00 0.00 4.30
522 607 3.997021 AGACAAGTAATGCTGAACGGAAG 59.003 43.478 0.00 0.00 0.00 3.46
523 608 3.074412 ACAAGTAATGCTGAACGGAAGG 58.926 45.455 0.00 0.00 0.00 3.46
524 609 3.244422 ACAAGTAATGCTGAACGGAAGGA 60.244 43.478 0.00 0.00 0.00 3.36
525 610 3.252974 AGTAATGCTGAACGGAAGGAG 57.747 47.619 0.00 0.00 0.00 3.69
526 611 2.567615 AGTAATGCTGAACGGAAGGAGT 59.432 45.455 0.00 0.00 0.00 3.85
527 612 3.767673 AGTAATGCTGAACGGAAGGAGTA 59.232 43.478 0.00 0.00 0.00 2.59
667 755 1.477553 TGGGAGCAATGAATGAAGGC 58.522 50.000 0.00 0.00 0.00 4.35
691 779 4.339247 CCTTTATTGATGGATTTGCGTCCT 59.661 41.667 4.52 0.00 39.12 3.85
832 925 1.459455 GCGAGGGCAGCTGAGATAGA 61.459 60.000 20.43 0.00 39.62 1.98
833 926 0.597568 CGAGGGCAGCTGAGATAGAG 59.402 60.000 20.43 0.00 0.00 2.43
846 939 4.518283 TGAGATAGAGATAGGAGAGGGGT 58.482 47.826 0.00 0.00 0.00 4.95
1185 1281 1.369091 CGCCCTCTAAACGCATGCTT 61.369 55.000 17.13 2.67 0.00 3.91
1202 1298 5.729454 GCATGCTTTACCGGTTAATGTACTG 60.729 44.000 15.04 4.91 0.00 2.74
1302 1398 2.674747 CGGGGAAAATGCACATCCTTTG 60.675 50.000 12.50 2.02 33.61 2.77
1327 1423 8.046107 TGTGTGGTTGATTGATGATTGATACTA 58.954 33.333 0.00 0.00 0.00 1.82
1328 1424 9.060347 GTGTGGTTGATTGATGATTGATACTAT 57.940 33.333 0.00 0.00 0.00 2.12
1473 1571 6.035327 GCTTGAATTGCATAACTTAGCCTTTG 59.965 38.462 0.00 0.00 0.00 2.77
1489 1587 2.482864 CTTTGGCGCCTGTTTTTCAAT 58.517 42.857 29.70 0.00 0.00 2.57
1500 1598 4.216687 CCTGTTTTTCAATGGTAGCCGTTA 59.783 41.667 0.00 0.00 30.71 3.18
1599 1697 4.929808 GGTTGACTTGATGACTTGTATCGT 59.070 41.667 0.00 0.00 0.00 3.73
1682 1780 6.371825 GTGTATTTAAGTAGGTGAAGCAGCTT 59.628 38.462 7.60 7.60 42.44 3.74
1684 1782 1.528129 AAGTAGGTGAAGCAGCTTGC 58.472 50.000 13.91 5.03 42.44 4.01
1724 1822 2.257974 TCGTAGCTCGACACAATGTC 57.742 50.000 0.00 0.00 44.01 3.06
2225 2327 5.481105 CAACAGGTTTTCATGGCATGTTAT 58.519 37.500 25.62 6.05 35.77 1.89
2549 2651 3.771577 TCCTTTCACTTGGACTCCTTC 57.228 47.619 0.00 0.00 0.00 3.46
2787 2890 5.414789 TGGTAAAGCTAACACTCTATGCA 57.585 39.130 0.00 0.00 0.00 3.96
3154 3263 2.858745 TGGAGCCTGTTAACAGTTTCC 58.141 47.619 30.38 30.38 42.27 3.13
3219 3328 9.640963 ATGGCTAGTACGAATAAGTTGAATATC 57.359 33.333 0.00 0.00 0.00 1.63
3995 4104 2.227388 CCCTCATTCATTCTTATGGCGC 59.773 50.000 0.00 0.00 32.40 6.53
4199 4308 0.621571 AGCTACTTGGATGGCAGGGA 60.622 55.000 0.00 0.00 0.00 4.20
4229 4338 6.874288 AAGTAGATTGCATTTAGATGGAGC 57.126 37.500 0.00 0.00 34.92 4.70
4257 4366 1.153086 GCCGGATCTGAATGTGGCT 60.153 57.895 5.05 0.00 39.38 4.75
4531 4640 5.302059 CGAGGAATTACTCACCTAGGAATGA 59.698 44.000 17.98 8.96 37.82 2.57
4774 4883 1.977854 ACCCACTTGCTGACAGTATGA 59.022 47.619 12.41 0.00 39.69 2.15
4875 4984 5.071788 TGGGAATGGTGTTATAGATGGAGAC 59.928 44.000 0.00 0.00 0.00 3.36
5275 5441 4.098807 TGCAATTCAATGATGCACATAGCT 59.901 37.500 7.37 0.00 44.52 3.32
6272 6725 5.041940 GTGTACTTTTATCTGCTCTACCGG 58.958 45.833 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.268999 TGTGTCGAGCATGTTTTTGGC 60.269 47.619 0.00 0.00 0.00 4.52
46 47 1.533625 TTCTGCAAATGGTTCCCGAG 58.466 50.000 0.00 0.00 0.00 4.63
84 85 1.464734 TCAAGTCAGGCTAGACCGAG 58.535 55.000 11.72 4.86 46.52 4.63
87 88 6.261158 GGAAAATATTCAAGTCAGGCTAGACC 59.739 42.308 11.72 0.00 36.95 3.85
126 127 2.411628 TCCATTTACGTGGGATGGTG 57.588 50.000 19.56 2.60 40.89 4.17
146 148 1.427753 AGACCTGGGTTTTTCGGGATT 59.572 47.619 0.00 0.00 34.80 3.01
152 154 1.269778 GCTTGCAGACCTGGGTTTTTC 60.270 52.381 0.00 0.00 0.00 2.29
175 178 2.046285 GGGGTTGCTTGGACGATGG 61.046 63.158 0.00 0.00 0.00 3.51
177 180 1.299976 GAGGGGTTGCTTGGACGAT 59.700 57.895 0.00 0.00 0.00 3.73
181 184 3.068881 CTCGAGGGGTTGCTTGGA 58.931 61.111 3.91 0.00 0.00 3.53
190 193 1.926426 AAAATGGAGGGCTCGAGGGG 61.926 60.000 15.58 0.00 0.00 4.79
195 198 0.804989 GTGTGAAAATGGAGGGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
258 261 5.923684 GCTTTTCGTGGGTGATTTTAATGAA 59.076 36.000 0.00 0.00 0.00 2.57
259 262 5.465935 GCTTTTCGTGGGTGATTTTAATGA 58.534 37.500 0.00 0.00 0.00 2.57
260 263 4.625311 GGCTTTTCGTGGGTGATTTTAATG 59.375 41.667 0.00 0.00 0.00 1.90
262 265 3.006003 GGGCTTTTCGTGGGTGATTTTAA 59.994 43.478 0.00 0.00 0.00 1.52
281 284 0.806241 TTATTCCAAGCGAAACGGGC 59.194 50.000 0.00 0.00 33.08 6.13
282 285 4.083484 GGATATTATTCCAAGCGAAACGGG 60.083 45.833 0.00 0.00 35.72 5.28
288 373 8.698973 TTTTAATGGGATATTATTCCAAGCGA 57.301 30.769 7.80 0.00 37.53 4.93
295 380 7.973944 GCGGGTGATTTTAATGGGATATTATTC 59.026 37.037 0.00 0.00 0.00 1.75
300 385 3.756434 CGCGGGTGATTTTAATGGGATAT 59.244 43.478 0.00 0.00 0.00 1.63
303 388 1.065345 TCGCGGGTGATTTTAATGGGA 60.065 47.619 6.13 0.00 0.00 4.37
352 437 3.004524 ACTTTGCGCGGGTAATTTTAACA 59.995 39.130 8.83 0.00 0.00 2.41
361 446 0.320858 TTCATGACTTTGCGCGGGTA 60.321 50.000 8.83 0.00 0.00 3.69
372 457 2.270352 TTGCGGAACCTTTCATGACT 57.730 45.000 0.00 0.00 0.00 3.41
373 458 3.049912 GTTTTGCGGAACCTTTCATGAC 58.950 45.455 0.00 0.00 0.00 3.06
374 459 2.035321 GGTTTTGCGGAACCTTTCATGA 59.965 45.455 12.41 0.00 44.55 3.07
375 460 2.403259 GGTTTTGCGGAACCTTTCATG 58.597 47.619 12.41 0.00 44.55 3.07
376 461 2.812358 GGTTTTGCGGAACCTTTCAT 57.188 45.000 12.41 0.00 44.55 2.57
382 467 8.727889 ATGATCTTTCATGGTTTTGCGGAACC 62.728 42.308 12.71 12.71 41.12 3.62
383 468 3.363341 TCTTTCATGGTTTTGCGGAAC 57.637 42.857 0.00 0.00 0.00 3.62
384 469 3.571828 TGATCTTTCATGGTTTTGCGGAA 59.428 39.130 0.00 0.00 0.00 4.30
385 470 3.153130 TGATCTTTCATGGTTTTGCGGA 58.847 40.909 0.00 0.00 0.00 5.54
386 471 3.574284 TGATCTTTCATGGTTTTGCGG 57.426 42.857 0.00 0.00 0.00 5.69
387 472 4.107622 GGATGATCTTTCATGGTTTTGCG 58.892 43.478 0.00 0.00 42.73 4.85
388 473 5.107133 CAGGATGATCTTTCATGGTTTTGC 58.893 41.667 0.00 0.00 42.73 3.68
389 474 6.276832 ACAGGATGATCTTTCATGGTTTTG 57.723 37.500 13.04 0.00 42.73 2.44
390 475 6.923199 AACAGGATGATCTTTCATGGTTTT 57.077 33.333 13.04 0.19 42.73 2.43
391 476 6.923199 AAACAGGATGATCTTTCATGGTTT 57.077 33.333 13.04 7.00 42.73 3.27
392 477 6.723052 AGAAAACAGGATGATCTTTCATGGTT 59.277 34.615 13.04 10.58 42.73 3.67
393 478 6.152323 CAGAAAACAGGATGATCTTTCATGGT 59.848 38.462 13.04 5.92 42.73 3.55
394 479 6.376299 TCAGAAAACAGGATGATCTTTCATGG 59.624 38.462 13.04 1.10 42.73 3.66
395 480 7.336176 TCTCAGAAAACAGGATGATCTTTCATG 59.664 37.037 8.65 8.65 42.73 3.07
396 481 7.400439 TCTCAGAAAACAGGATGATCTTTCAT 58.600 34.615 7.38 0.00 45.39 2.57
397 482 6.772605 TCTCAGAAAACAGGATGATCTTTCA 58.227 36.000 7.38 0.00 39.69 2.69
398 483 7.862512 ATCTCAGAAAACAGGATGATCTTTC 57.137 36.000 0.00 0.00 39.69 2.62
399 484 8.547173 AGTATCTCAGAAAACAGGATGATCTTT 58.453 33.333 0.00 0.00 39.69 2.52
400 485 8.088463 AGTATCTCAGAAAACAGGATGATCTT 57.912 34.615 0.00 0.00 39.69 2.40
401 486 7.201992 GGAGTATCTCAGAAAACAGGATGATCT 60.202 40.741 0.00 0.00 35.19 2.75
402 487 6.928492 GGAGTATCTCAGAAAACAGGATGATC 59.072 42.308 0.00 0.00 35.19 2.92
403 488 6.183361 GGGAGTATCTCAGAAAACAGGATGAT 60.183 42.308 0.00 0.00 35.34 2.45
404 489 5.129485 GGGAGTATCTCAGAAAACAGGATGA 59.871 44.000 0.00 0.00 35.34 2.92
405 490 5.130145 AGGGAGTATCTCAGAAAACAGGATG 59.870 44.000 0.00 0.00 38.91 3.51
406 491 5.284582 AGGGAGTATCTCAGAAAACAGGAT 58.715 41.667 0.00 0.00 38.91 3.24
407 492 4.689062 AGGGAGTATCTCAGAAAACAGGA 58.311 43.478 0.00 0.00 38.91 3.86
408 493 4.141824 GGAGGGAGTATCTCAGAAAACAGG 60.142 50.000 0.00 0.00 38.91 4.00
409 494 4.440802 CGGAGGGAGTATCTCAGAAAACAG 60.441 50.000 0.00 0.00 38.91 3.16
410 495 3.447586 CGGAGGGAGTATCTCAGAAAACA 59.552 47.826 0.00 0.00 38.91 2.83
411 496 3.447944 ACGGAGGGAGTATCTCAGAAAAC 59.552 47.826 0.00 0.00 38.91 2.43
412 497 3.709587 ACGGAGGGAGTATCTCAGAAAA 58.290 45.455 0.00 0.00 38.91 2.29
424 509 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
425 510 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
426 511 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
427 512 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
428 513 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
429 514 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
430 515 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
431 516 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
432 517 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
433 518 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
434 519 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
435 520 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
436 521 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
437 522 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
438 523 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
439 524 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
440 525 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
441 526 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
442 527 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
443 528 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
444 529 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
445 530 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
446 531 5.631512 GTCTAGATACATCCATTTCTGCGAC 59.368 44.000 0.00 0.00 0.00 5.19
447 532 5.562890 CGTCTAGATACATCCATTTCTGCGA 60.563 44.000 0.00 0.00 0.00 5.10
448 533 4.618912 CGTCTAGATACATCCATTTCTGCG 59.381 45.833 0.00 0.00 0.00 5.18
449 534 5.533482 ACGTCTAGATACATCCATTTCTGC 58.467 41.667 0.00 0.00 0.00 4.26
450 535 9.698309 AAATACGTCTAGATACATCCATTTCTG 57.302 33.333 0.00 0.00 0.00 3.02
478 563 9.690913 TGTCTCAAAAATGGATGATCTAGAATT 57.309 29.630 0.00 0.00 0.00 2.17
479 564 9.690913 TTGTCTCAAAAATGGATGATCTAGAAT 57.309 29.630 0.00 0.00 0.00 2.40
480 565 9.170734 CTTGTCTCAAAAATGGATGATCTAGAA 57.829 33.333 0.00 0.00 0.00 2.10
481 566 8.324306 ACTTGTCTCAAAAATGGATGATCTAGA 58.676 33.333 0.00 0.00 0.00 2.43
482 567 8.503458 ACTTGTCTCAAAAATGGATGATCTAG 57.497 34.615 0.00 0.00 0.00 2.43
483 568 9.958180 TTACTTGTCTCAAAAATGGATGATCTA 57.042 29.630 0.00 0.00 0.00 1.98
484 569 8.868522 TTACTTGTCTCAAAAATGGATGATCT 57.131 30.769 0.00 0.00 0.00 2.75
485 570 9.512435 CATTACTTGTCTCAAAAATGGATGATC 57.488 33.333 0.00 0.00 0.00 2.92
486 571 7.977853 GCATTACTTGTCTCAAAAATGGATGAT 59.022 33.333 13.75 0.00 0.00 2.45
487 572 7.177216 AGCATTACTTGTCTCAAAAATGGATGA 59.823 33.333 13.75 0.00 0.00 2.92
488 573 7.274904 CAGCATTACTTGTCTCAAAAATGGATG 59.725 37.037 13.75 0.00 0.00 3.51
489 574 7.177216 TCAGCATTACTTGTCTCAAAAATGGAT 59.823 33.333 13.75 0.00 0.00 3.41
490 575 6.489700 TCAGCATTACTTGTCTCAAAAATGGA 59.510 34.615 13.75 6.11 0.00 3.41
491 576 6.680810 TCAGCATTACTTGTCTCAAAAATGG 58.319 36.000 13.75 4.70 0.00 3.16
492 577 7.149080 CGTTCAGCATTACTTGTCTCAAAAATG 60.149 37.037 10.31 10.31 0.00 2.32
493 578 6.857964 CGTTCAGCATTACTTGTCTCAAAAAT 59.142 34.615 0.00 0.00 0.00 1.82
494 579 6.198687 CGTTCAGCATTACTTGTCTCAAAAA 58.801 36.000 0.00 0.00 0.00 1.94
495 580 5.277779 CCGTTCAGCATTACTTGTCTCAAAA 60.278 40.000 0.00 0.00 0.00 2.44
496 581 4.213270 CCGTTCAGCATTACTTGTCTCAAA 59.787 41.667 0.00 0.00 0.00 2.69
497 582 3.745975 CCGTTCAGCATTACTTGTCTCAA 59.254 43.478 0.00 0.00 0.00 3.02
498 583 3.006430 TCCGTTCAGCATTACTTGTCTCA 59.994 43.478 0.00 0.00 0.00 3.27
499 584 3.585862 TCCGTTCAGCATTACTTGTCTC 58.414 45.455 0.00 0.00 0.00 3.36
500 585 3.678056 TCCGTTCAGCATTACTTGTCT 57.322 42.857 0.00 0.00 0.00 3.41
501 586 3.125316 CCTTCCGTTCAGCATTACTTGTC 59.875 47.826 0.00 0.00 0.00 3.18
502 587 3.074412 CCTTCCGTTCAGCATTACTTGT 58.926 45.455 0.00 0.00 0.00 3.16
503 588 3.334691 TCCTTCCGTTCAGCATTACTTG 58.665 45.455 0.00 0.00 0.00 3.16
504 589 3.008049 ACTCCTTCCGTTCAGCATTACTT 59.992 43.478 0.00 0.00 0.00 2.24
505 590 2.567615 ACTCCTTCCGTTCAGCATTACT 59.432 45.455 0.00 0.00 0.00 2.24
506 591 2.973945 ACTCCTTCCGTTCAGCATTAC 58.026 47.619 0.00 0.00 0.00 1.89
507 592 4.020928 TGTTACTCCTTCCGTTCAGCATTA 60.021 41.667 0.00 0.00 0.00 1.90
508 593 3.244422 TGTTACTCCTTCCGTTCAGCATT 60.244 43.478 0.00 0.00 0.00 3.56
509 594 2.301870 TGTTACTCCTTCCGTTCAGCAT 59.698 45.455 0.00 0.00 0.00 3.79
510 595 1.689813 TGTTACTCCTTCCGTTCAGCA 59.310 47.619 0.00 0.00 0.00 4.41
511 596 2.029290 TCTGTTACTCCTTCCGTTCAGC 60.029 50.000 0.00 0.00 0.00 4.26
512 597 3.005472 TGTCTGTTACTCCTTCCGTTCAG 59.995 47.826 0.00 0.00 0.00 3.02
513 598 2.960384 TGTCTGTTACTCCTTCCGTTCA 59.040 45.455 0.00 0.00 0.00 3.18
514 599 3.576648 CTGTCTGTTACTCCTTCCGTTC 58.423 50.000 0.00 0.00 0.00 3.95
515 600 2.288886 GCTGTCTGTTACTCCTTCCGTT 60.289 50.000 0.00 0.00 0.00 4.44
516 601 1.272769 GCTGTCTGTTACTCCTTCCGT 59.727 52.381 0.00 0.00 0.00 4.69
517 602 1.272490 TGCTGTCTGTTACTCCTTCCG 59.728 52.381 0.00 0.00 0.00 4.30
518 603 3.526534 GATGCTGTCTGTTACTCCTTCC 58.473 50.000 0.00 0.00 0.00 3.46
519 604 3.526534 GGATGCTGTCTGTTACTCCTTC 58.473 50.000 0.00 0.00 0.00 3.46
520 605 2.237392 GGGATGCTGTCTGTTACTCCTT 59.763 50.000 0.00 0.00 0.00 3.36
521 606 1.834263 GGGATGCTGTCTGTTACTCCT 59.166 52.381 0.00 0.00 0.00 3.69
522 607 1.555075 TGGGATGCTGTCTGTTACTCC 59.445 52.381 0.00 0.00 0.00 3.85
523 608 3.265791 CTTGGGATGCTGTCTGTTACTC 58.734 50.000 0.00 0.00 0.00 2.59
524 609 2.639839 ACTTGGGATGCTGTCTGTTACT 59.360 45.455 0.00 0.00 0.00 2.24
525 610 3.059352 ACTTGGGATGCTGTCTGTTAC 57.941 47.619 0.00 0.00 0.00 2.50
526 611 3.788227 AACTTGGGATGCTGTCTGTTA 57.212 42.857 0.00 0.00 0.00 2.41
527 612 2.664402 AACTTGGGATGCTGTCTGTT 57.336 45.000 0.00 0.00 0.00 3.16
645 733 3.094572 CCTTCATTCATTGCTCCCAACT 58.905 45.455 0.00 0.00 32.95 3.16
667 755 4.499696 GGACGCAAATCCATCAATAAAGGG 60.500 45.833 0.00 0.00 38.77 3.95
691 779 0.393820 GGTCCCGGCGGTATATTTCA 59.606 55.000 26.32 0.00 0.00 2.69
718 811 1.660264 GGGTTTTGCGTTTCTGCCG 60.660 57.895 0.00 0.00 0.00 5.69
719 812 0.874175 GTGGGTTTTGCGTTTCTGCC 60.874 55.000 0.00 0.00 0.00 4.85
824 917 4.518283 ACCCCTCTCCTATCTCTATCTCA 58.482 47.826 0.00 0.00 0.00 3.27
832 925 5.043281 TCAGTTTCTTACCCCTCTCCTATCT 60.043 44.000 0.00 0.00 0.00 1.98
833 926 5.209659 TCAGTTTCTTACCCCTCTCCTATC 58.790 45.833 0.00 0.00 0.00 2.08
846 939 2.352421 CCTCGGTCGCTTCAGTTTCTTA 60.352 50.000 0.00 0.00 0.00 2.10
1141 1237 2.173569 GAGGGGCAATACCATGAGAACT 59.826 50.000 0.00 0.00 42.05 3.01
1142 1238 2.576615 GAGGGGCAATACCATGAGAAC 58.423 52.381 0.00 0.00 42.05 3.01
1185 1281 3.261390 ACAGGCAGTACATTAACCGGTAA 59.739 43.478 8.00 2.91 0.00 2.85
1202 1298 0.741221 CCGAAACTAGGAGCACAGGC 60.741 60.000 0.00 0.00 41.61 4.85
1302 1398 7.325660 AGTATCAATCATCAATCAACCACAC 57.674 36.000 0.00 0.00 0.00 3.82
1327 1423 7.284489 TCTCCTACACAAGCAAAACAACTTAAT 59.716 33.333 0.00 0.00 0.00 1.40
1328 1424 6.600032 TCTCCTACACAAGCAAAACAACTTAA 59.400 34.615 0.00 0.00 0.00 1.85
1473 1571 0.033366 ACCATTGAAAAACAGGCGCC 59.967 50.000 21.89 21.89 0.00 6.53
1489 1587 1.447140 CAAGCGCTAACGGCTACCA 60.447 57.895 12.05 0.00 40.53 3.25
1500 1598 1.068333 CCAGCAACATAAACAAGCGCT 60.068 47.619 2.64 2.64 0.00 5.92
1599 1697 3.684305 CCAATGACGTCACAAGCATAGAA 59.316 43.478 22.71 0.00 0.00 2.10
1682 1780 0.108186 AGTTGCTGCTATACTGCGCA 60.108 50.000 10.98 10.98 45.63 6.09
1684 1782 3.355626 TCTAGTTGCTGCTATACTGCG 57.644 47.619 0.00 0.00 45.63 5.18
1724 1822 5.268118 TGCTCCACTGATCTACTACATTG 57.732 43.478 0.00 0.00 0.00 2.82
1954 2052 2.406130 CGTTGGTTGACTAAAGCGGTA 58.594 47.619 0.00 0.00 39.22 4.02
1955 2053 1.223187 CGTTGGTTGACTAAAGCGGT 58.777 50.000 0.00 0.00 39.22 5.68
1956 2054 0.515564 CCGTTGGTTGACTAAAGCGG 59.484 55.000 0.00 0.00 39.22 5.52
2549 2651 6.949352 ATTCAGCCAAGAATAATGGTACAG 57.051 37.500 0.00 0.00 37.98 2.74
3219 3328 8.830580 AGTGATCTTCATACAAAATTCATACCG 58.169 33.333 0.00 0.00 0.00 4.02
3543 3652 7.862372 TGAATCAAATGACTGTTTAAGAAGTGC 59.138 33.333 0.00 0.00 0.00 4.40
3822 3931 8.925161 TTGTGGCTGCAAGATATTATTTAAAC 57.075 30.769 0.50 0.00 34.07 2.01
3829 3938 6.588719 AAAGTTTGTGGCTGCAAGATATTA 57.411 33.333 0.50 0.00 34.07 0.98
3995 4104 1.132554 AGCCAGCCCCCTATGATCTG 61.133 60.000 0.00 0.00 0.00 2.90
4229 4338 0.169672 CAGATCCGGCAACAGCTTTG 59.830 55.000 0.00 0.00 0.00 2.77
4257 4366 3.417069 TCACTTAGGCTGCTTGCTTTA 57.583 42.857 0.00 0.00 42.39 1.85
4531 4640 3.556423 GGTGTTAACTGATGAAGGGACGT 60.556 47.826 7.22 0.00 0.00 4.34
5275 5441 8.698973 TGGAATCAAACATAGGAAAGTTAACA 57.301 30.769 8.61 0.00 0.00 2.41
5551 5717 9.083080 GCATACATTAAATTAAAACTCCACCAC 57.917 33.333 0.00 0.00 0.00 4.16
6201 6367 3.070576 GCATGGCACTTCACCCCC 61.071 66.667 0.00 0.00 0.00 5.40
6202 6368 1.259840 ATTGCATGGCACTTCACCCC 61.260 55.000 0.00 0.00 38.71 4.95
6203 6369 0.108520 CATTGCATGGCACTTCACCC 60.109 55.000 0.00 0.00 38.71 4.61
6204 6370 0.604578 ACATTGCATGGCACTTCACC 59.395 50.000 0.00 0.00 38.71 4.02
6205 6371 1.403249 GGACATTGCATGGCACTTCAC 60.403 52.381 0.00 0.00 41.20 3.18
6206 6372 0.889994 GGACATTGCATGGCACTTCA 59.110 50.000 0.00 0.00 41.20 3.02
6207 6373 1.180029 AGGACATTGCATGGCACTTC 58.820 50.000 0.00 0.00 41.20 3.01
6208 6374 2.493278 GTTAGGACATTGCATGGCACTT 59.507 45.455 0.00 0.00 41.20 3.16
6272 6725 1.541588 CAGAGCAGGGTTTTTACCAGC 59.458 52.381 0.00 0.00 34.08 4.85


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

AutoCloner maintained by Alex Coulton.