Multiple sequence alignment - TraesCS6A01G391400

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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 TraesCS6A01G391400 chr6A 100.000 2546 0 0 1 2546 606130628 606128083 0.000000e+00 4702
1 TraesCS6A01G391400 chr6A 93.556 2002 119 8 554 2546 484400728 484402728 0.000000e+00 2974
2 TraesCS6A01G391400 chr7A 94.416 1988 98 7 565 2546 150203039 150201059 0.000000e+00 3044
3 TraesCS6A01G391400 chr7A 93.508 1987 122 6 565 2546 15645802 15647786 0.000000e+00 2948
4 TraesCS6A01G391400 chr5A 94.011 1987 108 8 565 2546 91049246 91051226 0.000000e+00 3000
5 TraesCS6A01G391400 chr5A 93.910 1987 112 8 566 2546 14186781 14184798 0.000000e+00 2990
6 TraesCS6A01G391400 chr5A 93.763 1988 108 8 565 2546 90997657 90999634 0.000000e+00 2970
7 TraesCS6A01G391400 chr4A 93.709 1987 112 7 565 2546 626934247 626932269 0.000000e+00 2964
8 TraesCS6A01G391400 chr2B 93.461 1988 116 7 566 2546 4739876 4741856 0.000000e+00 2939
9 TraesCS6A01G391400 chr3A 93.373 1992 119 7 561 2546 722406051 722404067 0.000000e+00 2935
10 TraesCS6A01G391400 chr1B 95.165 393 17 2 173 565 577186155 577185765 1.000000e-173 619
11 TraesCS6A01G391400 chr1B 93.793 145 7 2 1 144 577186298 577186155 1.530000e-52 217
12 TraesCS6A01G391400 chr7B 91.463 164 14 0 105 268 94756724 94756887 2.550000e-55 226
13 TraesCS6A01G391400 chr7B 89.017 173 12 5 293 465 94758252 94758417 9.230000e-50 207
14 TraesCS6A01G391400 chr7B 90.476 84 4 1 486 565 94758414 94758497 9.630000e-20 108


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 TraesCS6A01G391400 chr6A 606128083 606130628 2545 True 4702 4702 100.000 1 2546 1 chr6A.!!$R1 2545
1 TraesCS6A01G391400 chr6A 484400728 484402728 2000 False 2974 2974 93.556 554 2546 1 chr6A.!!$F1 1992
2 TraesCS6A01G391400 chr7A 150201059 150203039 1980 True 3044 3044 94.416 565 2546 1 chr7A.!!$R1 1981
3 TraesCS6A01G391400 chr7A 15645802 15647786 1984 False 2948 2948 93.508 565 2546 1 chr7A.!!$F1 1981
4 TraesCS6A01G391400 chr5A 91049246 91051226 1980 False 3000 3000 94.011 565 2546 1 chr5A.!!$F2 1981
5 TraesCS6A01G391400 chr5A 14184798 14186781 1983 True 2990 2990 93.910 566 2546 1 chr5A.!!$R1 1980
6 TraesCS6A01G391400 chr5A 90997657 90999634 1977 False 2970 2970 93.763 565 2546 1 chr5A.!!$F1 1981
7 TraesCS6A01G391400 chr4A 626932269 626934247 1978 True 2964 2964 93.709 565 2546 1 chr4A.!!$R1 1981
8 TraesCS6A01G391400 chr2B 4739876 4741856 1980 False 2939 2939 93.461 566 2546 1 chr2B.!!$F1 1980
9 TraesCS6A01G391400 chr3A 722404067 722406051 1984 True 2935 2935 93.373 561 2546 1 chr3A.!!$R1 1985
10 TraesCS6A01G391400 chr1B 577185765 577186298 533 True 418 619 94.479 1 565 2 chr1B.!!$R1 564

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
47 48 0.657368 GCGTTGCACTTGCTGTACAC 60.657 55.0 2.33 0.0 42.66 2.90 F
150 151 0.663269 CGTAGCAGTCGACACAAGCA 60.663 55.0 19.50 4.7 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1190 1204 0.036388 GCTCAAAGATCCCGACCACA 60.036 55.0 0.0 0.0 0.00 4.17 R
1824 1844 0.618458 CAAGAGAACCCCCGATTGGA 59.382 55.0 0.0 0.0 37.49 3.53 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
24 25 6.668645 ACTCTAGCTGAATCTCCTTTCTCTA 58.331 40.000 0.00 0.00 0.00 2.43
47 48 0.657368 GCGTTGCACTTGCTGTACAC 60.657 55.000 2.33 0.00 42.66 2.90
53 54 1.676014 GCACTTGCTGTACACTAGGGG 60.676 57.143 0.00 0.00 38.21 4.79
54 55 1.899814 CACTTGCTGTACACTAGGGGA 59.100 52.381 0.00 0.00 0.00 4.81
55 56 2.093973 CACTTGCTGTACACTAGGGGAG 60.094 54.545 0.00 0.00 0.00 4.30
56 57 0.902531 TTGCTGTACACTAGGGGAGC 59.097 55.000 0.00 1.18 0.00 4.70
57 58 1.320344 TGCTGTACACTAGGGGAGCG 61.320 60.000 0.00 0.00 0.00 5.03
96 97 4.120331 GAGCCGTTGTGCCATGCC 62.120 66.667 0.00 0.00 0.00 4.40
98 99 4.424566 GCCGTTGTGCCATGCCTG 62.425 66.667 0.00 0.00 0.00 4.85
140 141 2.314647 TTTGCCGCACGTAGCAGTC 61.315 57.895 7.10 0.00 46.13 3.51
142 143 4.771356 GCCGCACGTAGCAGTCGA 62.771 66.667 9.95 0.00 46.13 4.20
143 144 2.874780 CCGCACGTAGCAGTCGAC 60.875 66.667 7.70 7.70 46.13 4.20
144 145 2.127003 CGCACGTAGCAGTCGACA 60.127 61.111 19.50 0.00 46.13 4.35
145 146 2.426183 CGCACGTAGCAGTCGACAC 61.426 63.158 19.50 9.51 46.13 3.67
146 147 1.371267 GCACGTAGCAGTCGACACA 60.371 57.895 19.50 0.00 44.79 3.72
147 148 0.937699 GCACGTAGCAGTCGACACAA 60.938 55.000 19.50 0.00 44.79 3.33
148 149 1.053048 CACGTAGCAGTCGACACAAG 58.947 55.000 19.50 5.66 0.00 3.16
149 150 0.663568 ACGTAGCAGTCGACACAAGC 60.664 55.000 19.50 15.34 0.00 4.01
150 151 0.663269 CGTAGCAGTCGACACAAGCA 60.663 55.000 19.50 4.70 0.00 3.91
151 152 1.063806 GTAGCAGTCGACACAAGCAG 58.936 55.000 19.50 0.00 0.00 4.24
152 153 0.667487 TAGCAGTCGACACAAGCAGC 60.667 55.000 19.50 9.41 0.00 5.25
153 154 2.849007 CAGTCGACACAAGCAGCG 59.151 61.111 19.50 0.00 0.00 5.18
154 155 2.356313 AGTCGACACAAGCAGCGG 60.356 61.111 19.50 0.00 0.00 5.52
155 156 2.661866 GTCGACACAAGCAGCGGT 60.662 61.111 11.55 0.00 0.00 5.68
156 157 2.661537 TCGACACAAGCAGCGGTG 60.662 61.111 10.98 10.98 40.78 4.94
157 158 3.716006 CGACACAAGCAGCGGTGG 61.716 66.667 17.54 1.98 39.31 4.61
158 159 2.280797 GACACAAGCAGCGGTGGA 60.281 61.111 17.54 0.00 39.31 4.02
159 160 2.281070 ACACAAGCAGCGGTGGAG 60.281 61.111 17.54 0.99 39.31 3.86
160 161 2.031012 CACAAGCAGCGGTGGAGA 59.969 61.111 17.54 0.00 0.00 3.71
161 162 1.597854 CACAAGCAGCGGTGGAGAA 60.598 57.895 17.54 0.00 0.00 2.87
162 163 1.302033 ACAAGCAGCGGTGGAGAAG 60.302 57.895 17.54 0.00 0.00 2.85
163 164 2.359230 AAGCAGCGGTGGAGAAGC 60.359 61.111 17.54 0.00 0.00 3.86
192 193 2.358737 CACGGCCCACCAAGACTC 60.359 66.667 0.00 0.00 34.57 3.36
234 235 4.201656 CGAGCACAAGATGAACATGTACAG 60.202 45.833 0.00 0.00 0.00 2.74
274 275 3.181463 ACATTGACCATTGTTTTGCTGCT 60.181 39.130 0.00 0.00 0.00 4.24
280 281 3.763360 ACCATTGTTTTGCTGCTGCTATA 59.237 39.130 17.00 1.57 40.48 1.31
350 351 3.132646 ACTTGATGTTGCTGCAGGAAAAA 59.867 39.130 23.11 14.23 0.00 1.94
359 360 2.485814 GCTGCAGGAAAAAGAGTACTGG 59.514 50.000 17.12 0.00 0.00 4.00
372 373 5.913137 AGAGTACTGGTCTCTTCTTCATG 57.087 43.478 0.00 0.00 38.91 3.07
373 374 5.329399 AGAGTACTGGTCTCTTCTTCATGT 58.671 41.667 0.00 0.00 38.91 3.21
374 375 5.777732 AGAGTACTGGTCTCTTCTTCATGTT 59.222 40.000 0.00 0.00 38.91 2.71
375 376 6.268847 AGAGTACTGGTCTCTTCTTCATGTTT 59.731 38.462 0.00 0.00 38.91 2.83
376 377 6.459923 AGTACTGGTCTCTTCTTCATGTTTC 58.540 40.000 0.00 0.00 0.00 2.78
377 378 5.559148 ACTGGTCTCTTCTTCATGTTTCT 57.441 39.130 0.00 0.00 0.00 2.52
378 379 5.934781 ACTGGTCTCTTCTTCATGTTTCTT 58.065 37.500 0.00 0.00 0.00 2.52
379 380 6.360618 ACTGGTCTCTTCTTCATGTTTCTTT 58.639 36.000 0.00 0.00 0.00 2.52
380 381 6.830838 ACTGGTCTCTTCTTCATGTTTCTTTT 59.169 34.615 0.00 0.00 0.00 2.27
381 382 7.340487 ACTGGTCTCTTCTTCATGTTTCTTTTT 59.660 33.333 0.00 0.00 0.00 1.94
405 406 6.956299 TTACGTTGCTACTTTTATGTCTCC 57.044 37.500 0.00 0.00 0.00 3.71
406 407 4.890088 ACGTTGCTACTTTTATGTCTCCA 58.110 39.130 0.00 0.00 0.00 3.86
407 408 4.689345 ACGTTGCTACTTTTATGTCTCCAC 59.311 41.667 0.00 0.00 0.00 4.02
408 409 4.092968 CGTTGCTACTTTTATGTCTCCACC 59.907 45.833 0.00 0.00 0.00 4.61
409 410 5.246307 GTTGCTACTTTTATGTCTCCACCT 58.754 41.667 0.00 0.00 0.00 4.00
410 411 6.403878 GTTGCTACTTTTATGTCTCCACCTA 58.596 40.000 0.00 0.00 0.00 3.08
411 412 6.222038 TGCTACTTTTATGTCTCCACCTAG 57.778 41.667 0.00 0.00 0.00 3.02
412 413 5.955959 TGCTACTTTTATGTCTCCACCTAGA 59.044 40.000 0.00 0.00 0.00 2.43
413 414 6.096987 TGCTACTTTTATGTCTCCACCTAGAG 59.903 42.308 0.00 0.00 35.04 2.43
414 415 6.097129 GCTACTTTTATGTCTCCACCTAGAGT 59.903 42.308 0.00 0.00 35.28 3.24
415 416 7.284944 GCTACTTTTATGTCTCCACCTAGAGTA 59.715 40.741 0.00 0.00 35.28 2.59
416 417 7.407393 ACTTTTATGTCTCCACCTAGAGTAC 57.593 40.000 0.00 0.00 35.28 2.73
417 418 6.952358 ACTTTTATGTCTCCACCTAGAGTACA 59.048 38.462 0.00 0.00 35.28 2.90
418 419 7.453752 ACTTTTATGTCTCCACCTAGAGTACAA 59.546 37.037 0.00 0.00 35.28 2.41
419 420 7.406031 TTTATGTCTCCACCTAGAGTACAAG 57.594 40.000 0.00 0.00 35.28 3.16
420 421 3.090037 TGTCTCCACCTAGAGTACAAGC 58.910 50.000 0.00 0.00 35.28 4.01
421 422 3.090037 GTCTCCACCTAGAGTACAAGCA 58.910 50.000 0.00 0.00 35.28 3.91
422 423 3.090037 TCTCCACCTAGAGTACAAGCAC 58.910 50.000 0.00 0.00 35.28 4.40
423 424 2.826128 CTCCACCTAGAGTACAAGCACA 59.174 50.000 0.00 0.00 0.00 4.57
424 425 3.441101 TCCACCTAGAGTACAAGCACAT 58.559 45.455 0.00 0.00 0.00 3.21
425 426 3.838317 TCCACCTAGAGTACAAGCACATT 59.162 43.478 0.00 0.00 0.00 2.71
426 427 5.020795 TCCACCTAGAGTACAAGCACATTA 58.979 41.667 0.00 0.00 0.00 1.90
427 428 5.105473 TCCACCTAGAGTACAAGCACATTAC 60.105 44.000 0.00 0.00 0.00 1.89
428 429 5.337250 CCACCTAGAGTACAAGCACATTACA 60.337 44.000 0.00 0.00 0.00 2.41
429 430 5.577164 CACCTAGAGTACAAGCACATTACAC 59.423 44.000 0.00 0.00 0.00 2.90
430 431 5.245301 ACCTAGAGTACAAGCACATTACACA 59.755 40.000 0.00 0.00 0.00 3.72
431 432 6.070767 ACCTAGAGTACAAGCACATTACACAT 60.071 38.462 0.00 0.00 0.00 3.21
432 433 6.818644 CCTAGAGTACAAGCACATTACACATT 59.181 38.462 0.00 0.00 0.00 2.71
433 434 7.334421 CCTAGAGTACAAGCACATTACACATTT 59.666 37.037 0.00 0.00 0.00 2.32
434 435 6.902341 AGAGTACAAGCACATTACACATTTG 58.098 36.000 0.00 0.00 0.00 2.32
435 436 5.460646 AGTACAAGCACATTACACATTTGC 58.539 37.500 0.00 0.00 0.00 3.68
436 437 4.319139 ACAAGCACATTACACATTTGCA 57.681 36.364 0.00 0.00 35.57 4.08
437 438 4.300803 ACAAGCACATTACACATTTGCAG 58.699 39.130 0.00 0.00 35.57 4.41
438 439 4.037803 ACAAGCACATTACACATTTGCAGA 59.962 37.500 0.00 0.00 35.57 4.26
439 440 4.430137 AGCACATTACACATTTGCAGAG 57.570 40.909 0.00 0.00 35.57 3.35
440 441 3.822735 AGCACATTACACATTTGCAGAGT 59.177 39.130 0.00 0.00 35.57 3.24
441 442 5.003160 AGCACATTACACATTTGCAGAGTA 58.997 37.500 0.00 0.00 35.57 2.59
442 443 5.122869 AGCACATTACACATTTGCAGAGTAG 59.877 40.000 0.00 0.00 35.57 2.57
443 444 5.122239 GCACATTACACATTTGCAGAGTAGA 59.878 40.000 0.00 0.00 33.24 2.59
444 445 6.348458 GCACATTACACATTTGCAGAGTAGAA 60.348 38.462 0.00 0.00 33.24 2.10
445 446 7.017645 CACATTACACATTTGCAGAGTAGAAC 58.982 38.462 0.00 0.00 0.00 3.01
446 447 6.936900 ACATTACACATTTGCAGAGTAGAACT 59.063 34.615 0.00 0.00 0.00 3.01
447 448 7.445402 ACATTACACATTTGCAGAGTAGAACTT 59.555 33.333 0.00 0.00 0.00 2.66
448 449 5.931441 ACACATTTGCAGAGTAGAACTTC 57.069 39.130 0.00 0.00 0.00 3.01
449 450 5.615289 ACACATTTGCAGAGTAGAACTTCT 58.385 37.500 0.00 0.00 0.00 2.85
450 451 5.468072 ACACATTTGCAGAGTAGAACTTCTG 59.532 40.000 1.17 0.00 31.25 3.02
451 452 4.453819 ACATTTGCAGAGTAGAACTTCTGC 59.546 41.667 17.07 17.07 43.33 4.26
452 453 3.751479 TTGCAGAGTAGAACTTCTGCA 57.249 42.857 21.29 21.29 46.82 4.41
453 454 3.969287 TGCAGAGTAGAACTTCTGCAT 57.031 42.857 21.29 0.00 45.35 3.96
454 455 4.277515 TGCAGAGTAGAACTTCTGCATT 57.722 40.909 21.29 0.00 45.35 3.56
455 456 4.248859 TGCAGAGTAGAACTTCTGCATTC 58.751 43.478 21.29 0.76 45.35 2.67
456 457 4.248859 GCAGAGTAGAACTTCTGCATTCA 58.751 43.478 18.53 0.00 42.95 2.57
457 458 4.874966 GCAGAGTAGAACTTCTGCATTCAT 59.125 41.667 18.53 0.00 42.95 2.57
458 459 5.006552 GCAGAGTAGAACTTCTGCATTCATC 59.993 44.000 18.53 0.00 42.95 2.92
459 460 6.339730 CAGAGTAGAACTTCTGCATTCATCT 58.660 40.000 9.28 0.87 31.12 2.90
460 461 6.476380 CAGAGTAGAACTTCTGCATTCATCTC 59.524 42.308 9.28 11.08 31.12 2.75
461 462 6.154192 AGAGTAGAACTTCTGCATTCATCTCA 59.846 38.462 9.28 0.00 33.38 3.27
462 463 6.705302 AGTAGAACTTCTGCATTCATCTCAA 58.295 36.000 9.28 0.00 31.12 3.02
463 464 7.164122 AGTAGAACTTCTGCATTCATCTCAAA 58.836 34.615 9.28 0.00 31.12 2.69
464 465 7.828223 AGTAGAACTTCTGCATTCATCTCAAAT 59.172 33.333 9.28 0.00 31.12 2.32
465 466 7.463961 AGAACTTCTGCATTCATCTCAAATT 57.536 32.000 0.94 0.00 0.00 1.82
466 467 7.893658 AGAACTTCTGCATTCATCTCAAATTT 58.106 30.769 0.94 0.00 0.00 1.82
467 468 8.365647 AGAACTTCTGCATTCATCTCAAATTTT 58.634 29.630 0.94 0.00 0.00 1.82
468 469 8.897872 AACTTCTGCATTCATCTCAAATTTTT 57.102 26.923 0.00 0.00 0.00 1.94
469 470 9.985730 AACTTCTGCATTCATCTCAAATTTTTA 57.014 25.926 0.00 0.00 0.00 1.52
470 471 9.635520 ACTTCTGCATTCATCTCAAATTTTTAG 57.364 29.630 0.00 0.00 0.00 1.85
471 472 8.470040 TTCTGCATTCATCTCAAATTTTTAGC 57.530 30.769 0.00 0.00 0.00 3.09
472 473 7.833786 TCTGCATTCATCTCAAATTTTTAGCT 58.166 30.769 0.00 0.00 0.00 3.32
473 474 7.758076 TCTGCATTCATCTCAAATTTTTAGCTG 59.242 33.333 0.00 0.00 0.00 4.24
474 475 7.380536 TGCATTCATCTCAAATTTTTAGCTGT 58.619 30.769 0.00 0.00 0.00 4.40
475 476 7.874016 TGCATTCATCTCAAATTTTTAGCTGTT 59.126 29.630 0.00 0.00 0.00 3.16
476 477 8.715088 GCATTCATCTCAAATTTTTAGCTGTTT 58.285 29.630 0.00 0.00 0.00 2.83
506 507 9.578576 ACCATAAATCATTCATATAGCACACTT 57.421 29.630 0.00 0.00 0.00 3.16
510 511 8.638685 AAATCATTCATATAGCACACTTTTGC 57.361 30.769 0.00 0.00 43.34 3.68
511 512 6.756299 TCATTCATATAGCACACTTTTGCA 57.244 33.333 0.00 0.00 45.62 4.08
512 513 6.554419 TCATTCATATAGCACACTTTTGCAC 58.446 36.000 0.00 0.00 45.62 4.57
513 514 6.375174 TCATTCATATAGCACACTTTTGCACT 59.625 34.615 0.00 0.00 45.62 4.40
514 515 7.552330 TCATTCATATAGCACACTTTTGCACTA 59.448 33.333 0.00 0.00 45.62 2.74
515 516 6.908870 TCATATAGCACACTTTTGCACTAG 57.091 37.500 0.00 0.00 45.62 2.57
516 517 6.639563 TCATATAGCACACTTTTGCACTAGA 58.360 36.000 0.00 0.00 45.62 2.43
517 518 7.102993 TCATATAGCACACTTTTGCACTAGAA 58.897 34.615 0.00 0.00 45.62 2.10
518 519 7.606073 TCATATAGCACACTTTTGCACTAGAAA 59.394 33.333 0.00 0.00 45.62 2.52
519 520 4.981806 AGCACACTTTTGCACTAGAAAA 57.018 36.364 0.00 0.00 45.62 2.29
520 521 4.672409 AGCACACTTTTGCACTAGAAAAC 58.328 39.130 0.00 0.00 45.62 2.43
521 522 4.157656 AGCACACTTTTGCACTAGAAAACA 59.842 37.500 0.00 0.00 45.62 2.83
522 523 4.265320 GCACACTTTTGCACTAGAAAACAC 59.735 41.667 0.00 0.00 42.49 3.32
523 524 4.495472 CACACTTTTGCACTAGAAAACACG 59.505 41.667 0.00 0.00 0.00 4.49
524 525 4.035017 CACTTTTGCACTAGAAAACACGG 58.965 43.478 0.00 0.00 0.00 4.94
525 526 3.942748 ACTTTTGCACTAGAAAACACGGA 59.057 39.130 0.00 0.00 0.00 4.69
526 527 4.396790 ACTTTTGCACTAGAAAACACGGAA 59.603 37.500 0.00 0.00 0.00 4.30
527 528 5.067283 ACTTTTGCACTAGAAAACACGGAAT 59.933 36.000 0.00 0.00 0.00 3.01
528 529 5.508200 TTTGCACTAGAAAACACGGAATT 57.492 34.783 0.00 0.00 0.00 2.17
529 530 4.742438 TGCACTAGAAAACACGGAATTC 57.258 40.909 0.00 0.00 0.00 2.17
530 531 4.385825 TGCACTAGAAAACACGGAATTCT 58.614 39.130 5.23 0.00 37.23 2.40
531 532 4.451096 TGCACTAGAAAACACGGAATTCTC 59.549 41.667 5.23 0.00 35.22 2.87
532 533 4.691216 GCACTAGAAAACACGGAATTCTCT 59.309 41.667 5.23 1.06 35.22 3.10
533 534 5.179555 GCACTAGAAAACACGGAATTCTCTT 59.820 40.000 5.23 0.00 35.22 2.85
534 535 6.593978 CACTAGAAAACACGGAATTCTCTTG 58.406 40.000 5.23 2.98 35.22 3.02
535 536 4.489679 AGAAAACACGGAATTCTCTTGC 57.510 40.909 5.23 0.00 0.00 4.01
536 537 3.882888 AGAAAACACGGAATTCTCTTGCA 59.117 39.130 5.23 0.00 0.00 4.08
537 538 4.338118 AGAAAACACGGAATTCTCTTGCAA 59.662 37.500 5.23 0.00 0.00 4.08
538 539 4.647424 AAACACGGAATTCTCTTGCAAA 57.353 36.364 5.23 0.00 0.00 3.68
539 540 4.647424 AACACGGAATTCTCTTGCAAAA 57.353 36.364 5.23 0.00 0.00 2.44
540 541 4.853924 ACACGGAATTCTCTTGCAAAAT 57.146 36.364 5.23 0.00 0.00 1.82
541 542 5.200368 ACACGGAATTCTCTTGCAAAATT 57.800 34.783 5.23 7.19 0.00 1.82
542 543 4.984161 ACACGGAATTCTCTTGCAAAATTG 59.016 37.500 11.36 2.39 0.00 2.32
543 544 5.221224 ACACGGAATTCTCTTGCAAAATTGA 60.221 36.000 11.36 0.00 0.00 2.57
544 545 5.865552 CACGGAATTCTCTTGCAAAATTGAT 59.134 36.000 11.36 0.00 0.00 2.57
545 546 5.865552 ACGGAATTCTCTTGCAAAATTGATG 59.134 36.000 11.36 4.93 0.00 3.07
546 547 6.094719 CGGAATTCTCTTGCAAAATTGATGA 58.905 36.000 11.36 0.00 0.00 2.92
547 548 6.587226 CGGAATTCTCTTGCAAAATTGATGAA 59.413 34.615 11.36 6.56 0.00 2.57
548 549 7.411157 CGGAATTCTCTTGCAAAATTGATGAAC 60.411 37.037 11.36 0.00 0.00 3.18
549 550 7.148523 GGAATTCTCTTGCAAAATTGATGAACC 60.149 37.037 11.36 3.41 0.00 3.62
550 551 4.797471 TCTCTTGCAAAATTGATGAACCG 58.203 39.130 0.00 0.00 0.00 4.44
551 552 4.278170 TCTCTTGCAAAATTGATGAACCGT 59.722 37.500 0.00 0.00 0.00 4.83
552 553 4.297510 TCTTGCAAAATTGATGAACCGTG 58.702 39.130 0.00 0.00 0.00 4.94
561 562 9.566530 CAAAATTGATGAACCGTGTATATGAAA 57.433 29.630 0.00 0.00 0.00 2.69
591 592 6.831868 GGTTAATTATCCTTTTGCCCTCAGTA 59.168 38.462 5.46 0.00 0.00 2.74
605 606 3.769844 CCCTCAGTAGTGTCCATGTACTT 59.230 47.826 0.00 0.00 0.00 2.24
636 637 2.417586 CTCAGATGCGAATTGTGCTCAA 59.582 45.455 3.31 3.31 37.98 3.02
661 662 2.048023 CCCTAGTCCGTGCGTACCA 61.048 63.158 0.00 0.00 0.00 3.25
680 681 2.996621 CCAACTCATTCCGTGAACTCTC 59.003 50.000 0.00 0.00 36.14 3.20
684 685 1.084370 CATTCCGTGAACTCTCCCGC 61.084 60.000 0.00 0.00 0.00 6.13
756 757 3.120580 GCAGAAATGGCCAATTTTGTTCG 60.121 43.478 21.51 4.48 38.64 3.95
769 770 2.963320 GTTCGGACCGTTGCACGT 60.963 61.111 14.79 0.00 40.58 4.49
788 789 2.776526 TGGCTTGTGGGACCCAGT 60.777 61.111 15.52 0.00 32.34 4.00
930 943 2.266055 GCGGGAAGCTAGCTGTGT 59.734 61.111 20.16 1.61 44.04 3.72
966 979 3.775654 GCTAGCAGTGGAGGGCGT 61.776 66.667 10.63 0.00 34.54 5.68
992 1006 0.827368 GTTGAGATCCCTTCGGCTCT 59.173 55.000 0.00 0.00 37.33 4.09
1016 1030 2.169352 GCTCCATGTCTTCCTCAAGCTA 59.831 50.000 0.00 0.00 0.00 3.32
1061 1075 3.422303 GGCGCGAGTGAACATGCA 61.422 61.111 12.10 0.00 0.00 3.96
1117 1131 1.938585 TCGGAGGGTTTCTCAGACAT 58.061 50.000 0.00 0.00 44.19 3.06
1125 1139 3.118592 GGGTTTCTCAGACATCGAGGAAT 60.119 47.826 3.06 0.00 30.73 3.01
1135 1149 4.098654 AGACATCGAGGAATCAGAATCGTT 59.901 41.667 3.06 0.00 36.58 3.85
1183 1197 1.488390 AAGAATCGGGGCAATTGCAT 58.512 45.000 30.32 13.52 44.36 3.96
1190 1204 2.027377 TCGGGGCAATTGCATCATTTTT 60.027 40.909 30.32 0.00 44.36 1.94
1239 1253 3.827876 TGATCTGTTTGGTGTTCATGCAT 59.172 39.130 0.00 0.00 0.00 3.96
1300 1314 5.311265 AGACTCTGATGAATGAACTGCAAA 58.689 37.500 0.00 0.00 0.00 3.68
1305 1319 7.041635 TCTGATGAATGAACTGCAAAAAGAA 57.958 32.000 0.00 0.00 0.00 2.52
1375 1389 2.028130 GAGCTCCGGAAGAAGAGATGA 58.972 52.381 5.23 0.00 0.00 2.92
1433 1450 5.942826 AGCTTAGAATGTTGAAGAAGAAGGG 59.057 40.000 0.00 0.00 0.00 3.95
1466 1483 8.659925 CTTGAAGATCAAGCACTATCAATACT 57.340 34.615 7.13 0.00 46.03 2.12
1479 1496 9.903682 GCACTATCAATACTCATTTGCAAATAT 57.096 29.630 23.69 14.58 0.00 1.28
1510 1527 5.181245 GCATTTGTAGGTATGGTAATCGCAT 59.819 40.000 0.00 0.00 0.00 4.73
1626 1644 8.443937 TGTTGGTTAAAGTTGTTTAAATGTTGC 58.556 29.630 0.00 0.00 39.34 4.17
1655 1673 6.625873 AAAGAGAAGAAGTGACCAACATTC 57.374 37.500 0.00 0.00 0.00 2.67
1791 1811 3.465990 GCATAGAGCCAAGTGCAGA 57.534 52.632 0.00 0.00 44.83 4.26
1806 1826 2.432510 GTGCAGACTAGACTAATGGGCT 59.567 50.000 0.00 0.00 37.00 5.19
1821 1841 2.101783 TGGGCTAACTGCATCCAATTG 58.898 47.619 0.00 0.00 45.15 2.32
1824 1844 2.102578 GCTAACTGCATCCAATTGGGT 58.897 47.619 24.29 15.50 42.31 4.51
1828 1848 1.203162 ACTGCATCCAATTGGGTCCAA 60.203 47.619 24.29 4.87 40.47 3.53
1910 1930 6.647334 TCATAATGCTGGAACTTTTTGTGA 57.353 33.333 0.00 0.00 0.00 3.58
1931 1951 8.275015 TGTGAAAGCTAATTGAATTATTCCGA 57.725 30.769 2.22 0.00 0.00 4.55
1954 1975 7.142680 CGAAGCCAAACAATTAAGGTTAGAAA 58.857 34.615 0.00 0.00 0.00 2.52
2036 2063 3.765381 TCTCATGGAAAATGTGCCTCAA 58.235 40.909 0.00 0.00 0.00 3.02
2062 2089 1.547372 GTAGAGGTTTACGCCAGGTGA 59.453 52.381 7.13 0.00 0.00 4.02
2182 2210 4.367023 CTCGAACCCGGAACCGCA 62.367 66.667 0.73 0.00 38.24 5.69
2185 2213 2.046700 GAACCCGGAACCGCATGA 60.047 61.111 0.73 0.00 38.24 3.07
2260 2288 6.012508 ACTTTGACATGAATAGGGAAGGAAGA 60.013 38.462 0.00 0.00 0.00 2.87
2412 2444 3.255395 TGCACTACCACATGATTTTGGTG 59.745 43.478 14.36 9.54 46.03 4.17
2465 2497 5.479027 GGCACTTGGTTTAGGATTTAAAGGA 59.521 40.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.883354 CATTCTCCCCCAGCCCGC 62.883 72.222 0.00 0.00 0.00 6.13
56 57 3.411517 ACATTCTCCCCCAGCCCG 61.412 66.667 0.00 0.00 0.00 6.13
57 58 2.276740 CACATTCTCCCCCAGCCC 59.723 66.667 0.00 0.00 0.00 5.19
66 67 0.247736 ACGGCTCACTCCACATTCTC 59.752 55.000 0.00 0.00 0.00 2.87
98 99 4.115287 CACTAAAAGTGCACGCGC 57.885 55.556 12.01 0.00 39.62 6.86
140 141 3.716006 CCACCGCTGCTTGTGTCG 61.716 66.667 15.07 1.44 0.00 4.35
141 142 2.280797 TCCACCGCTGCTTGTGTC 60.281 61.111 15.07 0.00 0.00 3.67
142 143 2.281070 CTCCACCGCTGCTTGTGT 60.281 61.111 15.07 0.00 0.00 3.72
143 144 1.572085 CTTCTCCACCGCTGCTTGTG 61.572 60.000 10.96 10.96 0.00 3.33
144 145 1.302033 CTTCTCCACCGCTGCTTGT 60.302 57.895 0.00 0.00 0.00 3.16
145 146 2.684843 GCTTCTCCACCGCTGCTTG 61.685 63.158 0.00 0.00 0.00 4.01
146 147 2.359230 GCTTCTCCACCGCTGCTT 60.359 61.111 0.00 0.00 0.00 3.91
147 148 4.749310 CGCTTCTCCACCGCTGCT 62.749 66.667 0.00 0.00 0.00 4.24
152 153 3.793144 GCTTGCGCTTCTCCACCG 61.793 66.667 9.73 0.00 0.00 4.94
153 154 3.793144 CGCTTGCGCTTCTCCACC 61.793 66.667 9.73 0.00 0.00 4.61
154 155 3.793144 CCGCTTGCGCTTCTCCAC 61.793 66.667 9.73 0.00 0.00 4.02
176 177 2.847234 TGAGTCTTGGTGGGCCGT 60.847 61.111 0.00 0.00 37.67 5.68
192 193 1.596260 CGACAGTATTCAGCATGCCTG 59.404 52.381 15.66 15.39 43.17 4.85
234 235 5.124457 TCAATGTAGCAAAAGGATTCAGAGC 59.876 40.000 0.00 0.00 0.00 4.09
274 275 5.972935 TCGTCTGAACTCCAATTTATAGCA 58.027 37.500 0.00 0.00 0.00 3.49
280 281 6.763610 GGAAGATATCGTCTGAACTCCAATTT 59.236 38.462 16.67 0.00 37.23 1.82
350 351 5.329399 ACATGAAGAAGAGACCAGTACTCT 58.671 41.667 0.00 0.00 45.13 3.24
379 380 8.284693 GGAGACATAAAAGTAGCAACGTAAAAA 58.715 33.333 0.00 0.00 0.00 1.94
380 381 7.441760 TGGAGACATAAAAGTAGCAACGTAAAA 59.558 33.333 0.00 0.00 33.40 1.52
381 382 6.930164 TGGAGACATAAAAGTAGCAACGTAAA 59.070 34.615 0.00 0.00 33.40 2.01
382 383 6.366877 GTGGAGACATAAAAGTAGCAACGTAA 59.633 38.462 0.00 0.00 46.14 3.18
383 384 5.865552 GTGGAGACATAAAAGTAGCAACGTA 59.134 40.000 0.00 0.00 46.14 3.57
384 385 4.689345 GTGGAGACATAAAAGTAGCAACGT 59.311 41.667 0.00 0.00 46.14 3.99
385 386 4.092968 GGTGGAGACATAAAAGTAGCAACG 59.907 45.833 0.00 0.00 46.14 4.10
386 387 5.246307 AGGTGGAGACATAAAAGTAGCAAC 58.754 41.667 0.00 0.00 46.14 4.17
387 388 5.499004 AGGTGGAGACATAAAAGTAGCAA 57.501 39.130 0.00 0.00 46.14 3.91
388 389 5.955959 TCTAGGTGGAGACATAAAAGTAGCA 59.044 40.000 0.00 0.00 46.14 3.49
389 390 6.097129 ACTCTAGGTGGAGACATAAAAGTAGC 59.903 42.308 0.00 0.00 46.14 3.58
390 391 7.648039 ACTCTAGGTGGAGACATAAAAGTAG 57.352 40.000 0.00 0.00 46.14 2.57
391 392 8.111545 TGTACTCTAGGTGGAGACATAAAAGTA 58.888 37.037 0.00 0.00 46.14 2.24
392 393 6.952358 TGTACTCTAGGTGGAGACATAAAAGT 59.048 38.462 0.00 0.00 46.14 2.66
393 394 7.406031 TGTACTCTAGGTGGAGACATAAAAG 57.594 40.000 0.00 0.00 46.14 2.27
394 395 7.578955 GCTTGTACTCTAGGTGGAGACATAAAA 60.579 40.741 0.00 0.00 46.14 1.52
395 396 6.127423 GCTTGTACTCTAGGTGGAGACATAAA 60.127 42.308 0.00 0.00 46.14 1.40
396 397 5.360144 GCTTGTACTCTAGGTGGAGACATAA 59.640 44.000 0.00 0.00 46.14 1.90
397 398 4.888239 GCTTGTACTCTAGGTGGAGACATA 59.112 45.833 0.00 0.00 46.14 2.29
398 399 3.702045 GCTTGTACTCTAGGTGGAGACAT 59.298 47.826 0.00 0.00 46.14 3.06
399 400 3.090037 GCTTGTACTCTAGGTGGAGACA 58.910 50.000 0.00 0.00 37.13 3.41
400 401 3.090037 TGCTTGTACTCTAGGTGGAGAC 58.910 50.000 0.00 0.00 37.13 3.36
401 402 3.090037 GTGCTTGTACTCTAGGTGGAGA 58.910 50.000 0.00 0.00 37.13 3.71
402 403 2.826128 TGTGCTTGTACTCTAGGTGGAG 59.174 50.000 0.00 0.00 39.09 3.86
403 404 2.884320 TGTGCTTGTACTCTAGGTGGA 58.116 47.619 0.00 0.00 0.00 4.02
404 405 3.895232 ATGTGCTTGTACTCTAGGTGG 57.105 47.619 0.00 0.00 0.00 4.61
405 406 5.577164 GTGTAATGTGCTTGTACTCTAGGTG 59.423 44.000 0.00 0.00 0.00 4.00
406 407 5.245301 TGTGTAATGTGCTTGTACTCTAGGT 59.755 40.000 0.00 0.00 0.00 3.08
407 408 5.720202 TGTGTAATGTGCTTGTACTCTAGG 58.280 41.667 0.00 0.00 0.00 3.02
408 409 7.834068 AATGTGTAATGTGCTTGTACTCTAG 57.166 36.000 0.00 0.00 0.00 2.43
409 410 7.360861 GCAAATGTGTAATGTGCTTGTACTCTA 60.361 37.037 0.00 0.00 32.43 2.43
410 411 6.568462 GCAAATGTGTAATGTGCTTGTACTCT 60.568 38.462 0.00 0.00 32.43 3.24
411 412 5.569059 GCAAATGTGTAATGTGCTTGTACTC 59.431 40.000 0.00 0.00 32.43 2.59
412 413 5.009510 TGCAAATGTGTAATGTGCTTGTACT 59.990 36.000 2.43 0.00 36.18 2.73
413 414 5.218885 TGCAAATGTGTAATGTGCTTGTAC 58.781 37.500 2.43 0.00 36.18 2.90
414 415 5.240403 TCTGCAAATGTGTAATGTGCTTGTA 59.760 36.000 2.43 0.00 36.18 2.41
415 416 4.037803 TCTGCAAATGTGTAATGTGCTTGT 59.962 37.500 2.43 0.00 36.18 3.16
416 417 4.548494 TCTGCAAATGTGTAATGTGCTTG 58.452 39.130 2.43 0.00 36.18 4.01
417 418 4.279169 ACTCTGCAAATGTGTAATGTGCTT 59.721 37.500 2.43 0.00 36.18 3.91
418 419 3.822735 ACTCTGCAAATGTGTAATGTGCT 59.177 39.130 2.43 0.00 36.18 4.40
419 420 4.164822 ACTCTGCAAATGTGTAATGTGC 57.835 40.909 0.00 0.00 35.75 4.57
420 421 6.726258 TCTACTCTGCAAATGTGTAATGTG 57.274 37.500 0.00 0.00 0.00 3.21
421 422 6.936900 AGTTCTACTCTGCAAATGTGTAATGT 59.063 34.615 0.00 0.00 0.00 2.71
422 423 7.369803 AGTTCTACTCTGCAAATGTGTAATG 57.630 36.000 0.00 0.00 0.00 1.90
423 424 7.880195 AGAAGTTCTACTCTGCAAATGTGTAAT 59.120 33.333 2.75 0.00 0.00 1.89
424 425 7.171508 CAGAAGTTCTACTCTGCAAATGTGTAA 59.828 37.037 4.74 0.00 0.00 2.41
425 426 6.646653 CAGAAGTTCTACTCTGCAAATGTGTA 59.353 38.462 4.74 0.00 0.00 2.90
426 427 5.468072 CAGAAGTTCTACTCTGCAAATGTGT 59.532 40.000 4.74 0.00 0.00 3.72
427 428 5.616424 GCAGAAGTTCTACTCTGCAAATGTG 60.616 44.000 16.93 0.00 42.95 3.21
428 429 4.453819 GCAGAAGTTCTACTCTGCAAATGT 59.546 41.667 16.93 0.00 42.95 2.71
429 430 4.453478 TGCAGAAGTTCTACTCTGCAAATG 59.547 41.667 21.01 0.00 46.22 2.32
430 431 4.645535 TGCAGAAGTTCTACTCTGCAAAT 58.354 39.130 21.01 0.00 46.22 2.32
431 432 4.071961 TGCAGAAGTTCTACTCTGCAAA 57.928 40.909 21.01 2.68 46.22 3.68
432 433 3.751479 TGCAGAAGTTCTACTCTGCAA 57.249 42.857 21.01 7.85 46.22 4.08
434 435 4.248859 TGAATGCAGAAGTTCTACTCTGC 58.751 43.478 15.40 15.40 43.33 4.26
435 436 6.339730 AGATGAATGCAGAAGTTCTACTCTG 58.660 40.000 4.74 0.00 31.25 3.35
436 437 6.154192 TGAGATGAATGCAGAAGTTCTACTCT 59.846 38.462 4.74 0.00 33.29 3.24
437 438 6.336566 TGAGATGAATGCAGAAGTTCTACTC 58.663 40.000 4.74 5.42 33.04 2.59
438 439 6.291648 TGAGATGAATGCAGAAGTTCTACT 57.708 37.500 4.74 0.00 0.00 2.57
439 440 6.974932 TTGAGATGAATGCAGAAGTTCTAC 57.025 37.500 4.74 0.00 0.00 2.59
440 441 8.571461 AATTTGAGATGAATGCAGAAGTTCTA 57.429 30.769 4.74 0.00 0.00 2.10
441 442 7.463961 AATTTGAGATGAATGCAGAAGTTCT 57.536 32.000 0.00 0.00 0.00 3.01
442 443 8.530269 AAAATTTGAGATGAATGCAGAAGTTC 57.470 30.769 0.00 0.00 0.00 3.01
443 444 8.897872 AAAAATTTGAGATGAATGCAGAAGTT 57.102 26.923 0.00 0.00 0.00 2.66
444 445 9.635520 CTAAAAATTTGAGATGAATGCAGAAGT 57.364 29.630 0.00 0.00 0.00 3.01
445 446 8.592998 GCTAAAAATTTGAGATGAATGCAGAAG 58.407 33.333 0.00 0.00 0.00 2.85
446 447 8.308931 AGCTAAAAATTTGAGATGAATGCAGAA 58.691 29.630 0.00 0.00 0.00 3.02
447 448 7.758076 CAGCTAAAAATTTGAGATGAATGCAGA 59.242 33.333 2.23 0.00 0.00 4.26
448 449 7.544566 ACAGCTAAAAATTTGAGATGAATGCAG 59.455 33.333 14.67 4.18 31.16 4.41
449 450 7.380536 ACAGCTAAAAATTTGAGATGAATGCA 58.619 30.769 14.67 0.00 31.16 3.96
450 451 7.823149 ACAGCTAAAAATTTGAGATGAATGC 57.177 32.000 14.67 4.44 31.16 3.56
480 481 9.578576 AAGTGTGCTATATGAATGATTTATGGT 57.421 29.630 0.00 0.00 0.00 3.55
484 485 9.734620 GCAAAAGTGTGCTATATGAATGATTTA 57.265 29.630 0.00 0.00 41.51 1.40
485 486 8.252417 TGCAAAAGTGTGCTATATGAATGATTT 58.748 29.630 0.00 0.00 45.17 2.17
486 487 7.703621 GTGCAAAAGTGTGCTATATGAATGATT 59.296 33.333 0.00 0.00 45.17 2.57
487 488 7.067859 AGTGCAAAAGTGTGCTATATGAATGAT 59.932 33.333 0.00 0.00 45.17 2.45
488 489 6.375174 AGTGCAAAAGTGTGCTATATGAATGA 59.625 34.615 0.00 0.00 45.17 2.57
489 490 6.558009 AGTGCAAAAGTGTGCTATATGAATG 58.442 36.000 0.00 0.00 45.17 2.67
490 491 6.764308 AGTGCAAAAGTGTGCTATATGAAT 57.236 33.333 0.00 0.00 45.17 2.57
491 492 7.102993 TCTAGTGCAAAAGTGTGCTATATGAA 58.897 34.615 0.00 0.00 45.17 2.57
492 493 6.639563 TCTAGTGCAAAAGTGTGCTATATGA 58.360 36.000 0.00 0.00 45.17 2.15
493 494 6.908870 TCTAGTGCAAAAGTGTGCTATATG 57.091 37.500 0.00 0.00 45.17 1.78
494 495 7.921786 TTTCTAGTGCAAAAGTGTGCTATAT 57.078 32.000 0.00 0.00 45.17 0.86
495 496 7.227711 TGTTTTCTAGTGCAAAAGTGTGCTATA 59.772 33.333 0.00 0.00 45.17 1.31
496 497 6.039270 TGTTTTCTAGTGCAAAAGTGTGCTAT 59.961 34.615 0.00 0.00 45.17 2.97
497 498 5.355630 TGTTTTCTAGTGCAAAAGTGTGCTA 59.644 36.000 0.00 0.00 45.17 3.49
498 499 4.157656 TGTTTTCTAGTGCAAAAGTGTGCT 59.842 37.500 0.00 0.00 45.17 4.40
499 500 4.265320 GTGTTTTCTAGTGCAAAAGTGTGC 59.735 41.667 0.00 0.00 45.15 4.57
500 501 4.495472 CGTGTTTTCTAGTGCAAAAGTGTG 59.505 41.667 0.00 0.00 0.00 3.82
501 502 4.438200 CCGTGTTTTCTAGTGCAAAAGTGT 60.438 41.667 0.00 0.00 0.00 3.55
502 503 4.035017 CCGTGTTTTCTAGTGCAAAAGTG 58.965 43.478 0.00 0.00 0.00 3.16
503 504 3.942748 TCCGTGTTTTCTAGTGCAAAAGT 59.057 39.130 0.00 0.00 0.00 2.66
504 505 4.545823 TCCGTGTTTTCTAGTGCAAAAG 57.454 40.909 0.00 0.00 0.00 2.27
505 506 4.966965 TTCCGTGTTTTCTAGTGCAAAA 57.033 36.364 0.00 0.00 0.00 2.44
506 507 5.298276 AGAATTCCGTGTTTTCTAGTGCAAA 59.702 36.000 0.65 0.00 0.00 3.68
507 508 4.819630 AGAATTCCGTGTTTTCTAGTGCAA 59.180 37.500 0.65 0.00 0.00 4.08
508 509 4.385825 AGAATTCCGTGTTTTCTAGTGCA 58.614 39.130 0.65 0.00 0.00 4.57
509 510 4.691216 AGAGAATTCCGTGTTTTCTAGTGC 59.309 41.667 0.65 0.00 30.11 4.40
510 511 6.593978 CAAGAGAATTCCGTGTTTTCTAGTG 58.406 40.000 0.65 0.00 30.11 2.74
511 512 5.179555 GCAAGAGAATTCCGTGTTTTCTAGT 59.820 40.000 0.65 0.00 30.11 2.57
512 513 5.179368 TGCAAGAGAATTCCGTGTTTTCTAG 59.821 40.000 0.65 0.00 30.11 2.43
513 514 5.060506 TGCAAGAGAATTCCGTGTTTTCTA 58.939 37.500 0.65 0.00 30.11 2.10
514 515 3.882888 TGCAAGAGAATTCCGTGTTTTCT 59.117 39.130 0.65 0.00 32.56 2.52
515 516 4.223320 TGCAAGAGAATTCCGTGTTTTC 57.777 40.909 0.65 0.00 0.00 2.29
516 517 4.647424 TTGCAAGAGAATTCCGTGTTTT 57.353 36.364 0.65 0.00 0.00 2.43
517 518 4.647424 TTTGCAAGAGAATTCCGTGTTT 57.353 36.364 0.65 0.00 0.00 2.83
518 519 4.647424 TTTTGCAAGAGAATTCCGTGTT 57.353 36.364 0.65 0.00 0.00 3.32
519 520 4.853924 ATTTTGCAAGAGAATTCCGTGT 57.146 36.364 0.65 0.00 0.00 4.49
520 521 5.221880 TCAATTTTGCAAGAGAATTCCGTG 58.778 37.500 0.65 3.92 0.00 4.94
521 522 5.452078 TCAATTTTGCAAGAGAATTCCGT 57.548 34.783 0.65 0.00 0.00 4.69
522 523 6.094719 TCATCAATTTTGCAAGAGAATTCCG 58.905 36.000 0.65 0.00 0.00 4.30
523 524 7.148523 GGTTCATCAATTTTGCAAGAGAATTCC 60.149 37.037 0.65 0.00 0.00 3.01
524 525 7.411157 CGGTTCATCAATTTTGCAAGAGAATTC 60.411 37.037 0.00 0.00 0.00 2.17
525 526 6.366877 CGGTTCATCAATTTTGCAAGAGAATT 59.633 34.615 0.00 0.14 0.00 2.17
526 527 5.865552 CGGTTCATCAATTTTGCAAGAGAAT 59.134 36.000 0.00 0.00 0.00 2.40
527 528 5.221224 ACGGTTCATCAATTTTGCAAGAGAA 60.221 36.000 0.00 0.00 0.00 2.87
528 529 4.278170 ACGGTTCATCAATTTTGCAAGAGA 59.722 37.500 0.00 0.00 0.00 3.10
529 530 4.383649 CACGGTTCATCAATTTTGCAAGAG 59.616 41.667 0.00 0.00 0.00 2.85
530 531 4.202101 ACACGGTTCATCAATTTTGCAAGA 60.202 37.500 0.00 0.00 0.00 3.02
531 532 4.050553 ACACGGTTCATCAATTTTGCAAG 58.949 39.130 0.00 0.00 0.00 4.01
532 533 4.052159 ACACGGTTCATCAATTTTGCAA 57.948 36.364 0.00 0.00 0.00 4.08
533 534 3.724508 ACACGGTTCATCAATTTTGCA 57.275 38.095 0.00 0.00 0.00 4.08
534 535 7.192913 TCATATACACGGTTCATCAATTTTGC 58.807 34.615 0.00 0.00 0.00 3.68
535 536 9.566530 TTTCATATACACGGTTCATCAATTTTG 57.433 29.630 0.00 0.00 0.00 2.44
540 541 9.051679 CCTATTTTCATATACACGGTTCATCAA 57.948 33.333 0.00 0.00 0.00 2.57
541 542 7.659799 CCCTATTTTCATATACACGGTTCATCA 59.340 37.037 0.00 0.00 0.00 3.07
542 543 7.660208 ACCCTATTTTCATATACACGGTTCATC 59.340 37.037 0.00 0.00 0.00 2.92
543 544 7.514721 ACCCTATTTTCATATACACGGTTCAT 58.485 34.615 0.00 0.00 0.00 2.57
544 545 6.891388 ACCCTATTTTCATATACACGGTTCA 58.109 36.000 0.00 0.00 0.00 3.18
545 546 7.797038 AACCCTATTTTCATATACACGGTTC 57.203 36.000 0.00 0.00 0.00 3.62
546 547 9.856162 ATTAACCCTATTTTCATATACACGGTT 57.144 29.630 0.00 0.00 34.43 4.44
547 548 9.856162 AATTAACCCTATTTTCATATACACGGT 57.144 29.630 0.00 0.00 0.00 4.83
561 562 7.370238 AGGGCAAAAGGATAATTAACCCTATT 58.630 34.615 8.09 0.00 43.36 1.73
591 592 4.760204 GGCAAAACTAAGTACATGGACACT 59.240 41.667 11.55 0.68 0.00 3.55
605 606 1.277842 TCGCATCTGAGGGCAAAACTA 59.722 47.619 5.18 0.00 0.00 2.24
636 637 0.679960 GCACGGACTAGGGGCAAAAT 60.680 55.000 0.00 0.00 0.00 1.82
657 658 3.576982 AGAGTTCACGGAATGAGTTGGTA 59.423 43.478 0.00 0.00 38.99 3.25
661 662 2.028020 GGGAGAGTTCACGGAATGAGTT 60.028 50.000 0.00 0.00 38.99 3.01
769 770 3.099841 TGGGTCCCACAAGCCACA 61.100 61.111 6.47 0.00 41.74 4.17
788 789 1.098869 CTCTGCTCAACGGCTCTCTA 58.901 55.000 0.00 0.00 0.00 2.43
886 887 3.133721 GTGCTCTCTCTCTCTCTCTCTCT 59.866 52.174 0.00 0.00 0.00 3.10
966 979 4.467084 GGGATCTCAACGCCGCCA 62.467 66.667 0.00 0.00 0.00 5.69
992 1006 1.942776 TGAGGAAGACATGGAGCTCA 58.057 50.000 17.19 1.87 0.00 4.26
1050 1064 2.738846 GACGAAGACATGCATGTTCACT 59.261 45.455 31.82 21.58 41.95 3.41
1054 1068 2.738846 GACAGACGAAGACATGCATGTT 59.261 45.455 31.82 18.43 41.95 2.71
1061 1075 1.154016 CGCGGACAGACGAAGACAT 60.154 57.895 0.00 0.00 35.47 3.06
1117 1131 2.422479 ACGAACGATTCTGATTCCTCGA 59.578 45.455 18.00 0.00 35.24 4.04
1125 1139 3.058708 ACACGTAGAACGAACGATTCTGA 60.059 43.478 6.44 0.00 46.05 3.27
1135 1149 1.127397 CTCGCTACACACGTAGAACGA 59.873 52.381 6.44 3.65 46.98 3.85
1183 1197 3.433306 AGATCCCGACCACAAAAATGA 57.567 42.857 0.00 0.00 0.00 2.57
1190 1204 0.036388 GCTCAAAGATCCCGACCACA 60.036 55.000 0.00 0.00 0.00 4.17
1239 1253 3.318839 CCCAAAGAAAGAAGCATGTCACA 59.681 43.478 0.00 0.00 0.00 3.58
1300 1314 4.549458 CGCAACCATTCTTCATGTTCTTT 58.451 39.130 0.00 0.00 0.00 2.52
1305 1319 1.246649 TGCGCAACCATTCTTCATGT 58.753 45.000 8.16 0.00 0.00 3.21
1375 1389 1.003118 TCTAATGTGTGCTTCGCCCTT 59.997 47.619 0.00 0.00 0.00 3.95
1391 1405 3.791973 GCTCAACAGCTAGCTCTCTAA 57.208 47.619 16.15 0.00 43.09 2.10
1416 1433 5.843019 TCCTACCCTTCTTCTTCAACATT 57.157 39.130 0.00 0.00 0.00 2.71
1466 1483 7.463961 AATGCCCAAAAATATTTGCAAATGA 57.536 28.000 30.43 16.66 43.73 2.57
1479 1496 4.841246 ACCATACCTACAAATGCCCAAAAA 59.159 37.500 0.00 0.00 0.00 1.94
1535 1553 7.441903 AATTCCTCCATAATTCATGCCTTTT 57.558 32.000 0.00 0.00 32.84 2.27
1626 1644 6.194796 TGGTCACTTCTTCTCTTTTTGTTG 57.805 37.500 0.00 0.00 0.00 3.33
1761 1781 3.054139 TGGCTCTATGCTCTGAATTTGGT 60.054 43.478 0.00 0.00 42.39 3.67
1791 1811 4.030913 TGCAGTTAGCCCATTAGTCTAGT 58.969 43.478 0.00 0.00 44.83 2.57
1806 1826 2.042297 TGGACCCAATTGGATGCAGTTA 59.958 45.455 26.60 5.51 37.39 2.24
1821 1841 2.266816 GAGAACCCCCGATTGGACCC 62.267 65.000 0.00 0.00 37.49 4.46
1824 1844 0.618458 CAAGAGAACCCCCGATTGGA 59.382 55.000 0.00 0.00 37.49 3.53
1828 1848 0.974010 TACGCAAGAGAACCCCCGAT 60.974 55.000 0.00 0.00 43.62 4.18
1910 1930 7.147915 TGGCTTCGGAATAATTCAATTAGCTTT 60.148 33.333 0.00 0.00 0.00 3.51
1931 1951 9.845740 AAATTTCTAACCTTAATTGTTTGGCTT 57.154 25.926 0.00 0.00 0.00 4.35
2003 2024 8.869109 ACATTTTCCATGAGATTTTGGTCTTTA 58.131 29.630 0.00 0.00 34.48 1.85
2036 2063 1.823610 GGCGTAAACCTCTACCAGAGT 59.176 52.381 2.71 0.00 40.72 3.24
2174 2202 0.240945 CCACAAACTCATGCGGTTCC 59.759 55.000 4.77 0.00 0.00 3.62
2176 2204 0.667993 CACCACAAACTCATGCGGTT 59.332 50.000 0.00 0.00 33.55 4.44
2182 2210 2.890945 GCCCTAAACACCACAAACTCAT 59.109 45.455 0.00 0.00 0.00 2.90
2185 2213 2.306847 CAGCCCTAAACACCACAAACT 58.693 47.619 0.00 0.00 0.00 2.66
2412 2444 3.071167 ACCCTAAACCAAGTGTCACTCTC 59.929 47.826 5.82 0.00 0.00 3.20
2489 2521 8.729756 CCCTCTTTTTCATTCAAACAAAAAGTT 58.270 29.630 13.17 0.00 43.25 2.66
2509 2541 1.925972 GGGGGTGAGAAGCCCTCTT 60.926 63.158 12.46 0.00 43.38 2.85


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

AutoCloner maintained by Alex Coulton.