Multiple sequence alignment - TraesCS6D01G289300

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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 TraesCS6D01G289300 chr6D 100.000 3233 0 0 1 3233 400091102 400087870 0.000000e+00 5971.0
1 TraesCS6D01G289300 chr6D 86.567 201 20 4 1098 1291 400090050 400089850 7.020000e-52 215.0
2 TraesCS6D01G289300 chr6A 97.824 1195 20 2 1098 2286 545884642 545883448 0.000000e+00 2058.0
3 TraesCS6D01G289300 chr6A 95.390 564 16 3 679 1235 545885017 545884457 0.000000e+00 889.0
4 TraesCS6D01G289300 chr6A 93.137 408 17 5 2285 2690 545883412 545883014 3.590000e-164 588.0
5 TraesCS6D01G289300 chr6A 87.571 177 12 3 511 677 545885501 545885325 2.540000e-46 196.0
6 TraesCS6D01G289300 chr6B 96.460 1243 35 2 1053 2286 599123113 599121871 0.000000e+00 2043.0
7 TraesCS6D01G289300 chr6B 92.079 808 41 6 507 1291 599123720 599122913 0.000000e+00 1116.0
8 TraesCS6D01G289300 chr6B 90.164 183 15 1 1098 1277 599123158 599122976 5.390000e-58 235.0
9 TraesCS6D01G289300 chr6B 90.968 155 10 4 2411 2561 599121748 599121594 4.230000e-49 206.0
10 TraesCS6D01G289300 chr4A 95.992 499 20 0 1 499 545766190 545766688 0.000000e+00 811.0
11 TraesCS6D01G289300 chr7B 92.986 499 35 0 1 499 421039121 421038623 0.000000e+00 728.0
12 TraesCS6D01G289300 chr5A 92.986 499 32 1 1 499 69238935 69238440 0.000000e+00 725.0
13 TraesCS6D01G289300 chr5B 90.146 548 50 4 2689 3233 302836862 302836316 0.000000e+00 710.0
14 TraesCS6D01G289300 chr5D 89.706 544 53 3 2692 3233 501430665 501431207 0.000000e+00 691.0
15 TraesCS6D01G289300 chrUn 87.766 564 62 7 2672 3233 134450633 134451191 0.000000e+00 652.0
16 TraesCS6D01G289300 chrUn 87.589 564 64 6 2672 3233 30575259 30575818 0.000000e+00 649.0
17 TraesCS6D01G289300 chrUn 87.411 564 67 4 2672 3233 30607057 30607618 0.000000e+00 645.0
18 TraesCS6D01G289300 chrUn 87.057 564 67 6 2672 3233 134430594 134431153 1.640000e-177 632.0
19 TraesCS6D01G289300 chr3D 88.398 543 57 5 2692 3233 280279664 280280201 0.000000e+00 649.0
20 TraesCS6D01G289300 chr3D 86.905 504 60 3 1 499 129005414 129005916 7.830000e-156 560.0
21 TraesCS6D01G289300 chr1B 88.235 544 58 5 2692 3233 158547416 158546877 0.000000e+00 645.0
22 TraesCS6D01G289300 chr2A 87.545 554 65 4 2682 3233 372383850 372383299 3.520000e-179 638.0
23 TraesCS6D01G289300 chr2A 100.000 44 0 0 2030 2073 595832130 595832087 7.430000e-12 82.4
24 TraesCS6D01G289300 chr2A 100.000 44 0 0 2030 2073 595872816 595872773 7.430000e-12 82.4
25 TraesCS6D01G289300 chr2A 83.721 86 10 2 2609 2690 148597620 148597535 9.620000e-11 78.7
26 TraesCS6D01G289300 chr7D 88.577 499 57 0 1 499 37968802 37968304 9.920000e-170 606.0
27 TraesCS6D01G289300 chr7D 86.364 66 6 3 2630 2693 181630747 181630811 5.790000e-08 69.4
28 TraesCS6D01G289300 chr7D 94.737 38 2 0 2653 2690 426726574 426726611 3.480000e-05 60.2
29 TraesCS6D01G289300 chr1A 87.097 62 6 2 2630 2690 347334778 347334718 5.790000e-08 69.4
30 TraesCS6D01G289300 chr3A 93.182 44 3 0 1779 1822 730116437 730116394 7.490000e-07 65.8
31 TraesCS6D01G289300 chr1D 89.796 49 3 1 500 548 487627444 487627398 9.680000e-06 62.1
32 TraesCS6D01G289300 chr3B 90.909 44 4 0 1779 1822 807976520 807976563 3.480000e-05 60.2


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 TraesCS6D01G289300 chr6D 400087870 400091102 3232 True 3093.00 5971 93.28350 1 3233 2 chr6D.!!$R1 3232
1 TraesCS6D01G289300 chr6A 545883014 545885501 2487 True 932.75 2058 93.48050 511 2690 4 chr6A.!!$R1 2179
2 TraesCS6D01G289300 chr6B 599121594 599123720 2126 True 900.00 2043 92.41775 507 2561 4 chr6B.!!$R1 2054
3 TraesCS6D01G289300 chr5B 302836316 302836862 546 True 710.00 710 90.14600 2689 3233 1 chr5B.!!$R1 544
4 TraesCS6D01G289300 chr5D 501430665 501431207 542 False 691.00 691 89.70600 2692 3233 1 chr5D.!!$F1 541
5 TraesCS6D01G289300 chrUn 134450633 134451191 558 False 652.00 652 87.76600 2672 3233 1 chrUn.!!$F4 561
6 TraesCS6D01G289300 chrUn 30575259 30575818 559 False 649.00 649 87.58900 2672 3233 1 chrUn.!!$F1 561
7 TraesCS6D01G289300 chrUn 30607057 30607618 561 False 645.00 645 87.41100 2672 3233 1 chrUn.!!$F2 561
8 TraesCS6D01G289300 chrUn 134430594 134431153 559 False 632.00 632 87.05700 2672 3233 1 chrUn.!!$F3 561
9 TraesCS6D01G289300 chr3D 280279664 280280201 537 False 649.00 649 88.39800 2692 3233 1 chr3D.!!$F2 541
10 TraesCS6D01G289300 chr3D 129005414 129005916 502 False 560.00 560 86.90500 1 499 1 chr3D.!!$F1 498
11 TraesCS6D01G289300 chr1B 158546877 158547416 539 True 645.00 645 88.23500 2692 3233 1 chr1B.!!$R1 541
12 TraesCS6D01G289300 chr2A 372383299 372383850 551 True 638.00 638 87.54500 2682 3233 1 chr2A.!!$R2 551

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
109 110 0.027455 TTGTTGTTCTGAAGTGCGCG 59.973 50.0 0.00 0.00 0.00 6.86 F
158 159 0.029567 GTGAGATCCTGGCGTAGACG 59.970 60.0 0.00 0.00 41.59 4.18 F
159 160 0.107361 TGAGATCCTGGCGTAGACGA 60.107 55.0 6.19 0.00 41.59 4.20 F
668 690 0.107459 AGGGCAGCTTAGCAGTTAGC 60.107 55.0 7.07 2.13 46.19 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1672 2.583685 GAAATCGGGCGACAGCTTGC 62.584 60.000 0.00 0.00 44.37 4.01 R
1815 2198 3.426568 GCGAACTCCTGGCAGTGC 61.427 66.667 14.43 6.55 0.00 4.40 R
2128 2511 4.161295 CTTCTCCATGGCGCGGGA 62.161 66.667 8.83 12.64 0.00 5.14 R
2310 2730 1.372997 CGCACCCGAAGATATCCCG 60.373 63.158 0.00 3.68 36.29 5.14 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
23 24 4.710695 CGCACCGTAGCCACACGA 62.711 66.667 4.81 0.00 44.69 4.35
24 25 2.125673 GCACCGTAGCCACACGAT 60.126 61.111 4.81 0.00 44.69 3.73
34 35 1.142748 CCACACGATCCCAGAGCTC 59.857 63.158 5.27 5.27 0.00 4.09
56 57 3.645884 GAAGAATTGAAGCAAAGCAGCA 58.354 40.909 0.00 0.00 36.85 4.41
60 61 1.113788 TTGAAGCAAAGCAGCAGGTT 58.886 45.000 0.00 0.00 36.96 3.50
61 62 0.386476 TGAAGCAAAGCAGCAGGTTG 59.614 50.000 0.00 0.00 35.26 3.77
98 99 1.112916 CCCCCACCCAGTTGTTGTTC 61.113 60.000 0.00 0.00 0.00 3.18
100 101 1.032014 CCCACCCAGTTGTTGTTCTG 58.968 55.000 0.00 0.00 0.00 3.02
104 105 3.016736 CACCCAGTTGTTGTTCTGAAGT 58.983 45.455 0.00 0.00 34.02 3.01
109 110 0.027455 TTGTTGTTCTGAAGTGCGCG 59.973 50.000 0.00 0.00 0.00 6.86
127 128 1.705337 CGCGCCACCATTTTCGATCT 61.705 55.000 0.00 0.00 0.00 2.75
129 130 1.135402 GCGCCACCATTTTCGATCTTT 60.135 47.619 0.00 0.00 0.00 2.52
139 140 7.912250 CACCATTTTCGATCTTTTGATTCTAGG 59.088 37.037 0.00 0.00 39.67 3.02
140 141 7.611855 ACCATTTTCGATCTTTTGATTCTAGGT 59.388 33.333 0.00 0.00 39.67 3.08
155 156 1.883275 CTAGGTGAGATCCTGGCGTAG 59.117 57.143 0.00 0.00 38.41 3.51
157 158 0.386113 GGTGAGATCCTGGCGTAGAC 59.614 60.000 0.00 0.00 0.00 2.59
158 159 0.029567 GTGAGATCCTGGCGTAGACG 59.970 60.000 0.00 0.00 41.59 4.18
159 160 0.107361 TGAGATCCTGGCGTAGACGA 60.107 55.000 6.19 0.00 41.59 4.20
161 162 0.180642 AGATCCTGGCGTAGACGAGA 59.819 55.000 6.19 0.00 41.59 4.04
166 171 3.902086 GGCGTAGACGAGAGGGGC 61.902 72.222 6.19 0.00 43.02 5.80
168 173 3.584052 CGTAGACGAGAGGGGCCG 61.584 72.222 0.00 0.00 43.02 6.13
200 205 0.606604 GACACCCGAGAAGCCACTTA 59.393 55.000 0.00 0.00 0.00 2.24
203 208 1.207089 CACCCGAGAAGCCACTTATCA 59.793 52.381 3.22 0.00 32.00 2.15
214 219 3.782523 AGCCACTTATCATCCCAGAAGAA 59.217 43.478 0.00 0.00 0.00 2.52
216 221 4.141620 GCCACTTATCATCCCAGAAGAAGA 60.142 45.833 0.00 0.00 0.00 2.87
220 225 5.907662 ACTTATCATCCCAGAAGAAGATGGA 59.092 40.000 0.00 0.00 39.02 3.41
221 226 4.703379 ATCATCCCAGAAGAAGATGGAC 57.297 45.455 0.00 0.00 39.02 4.02
239 244 4.436998 GTCCCGTCGCCCACAGAG 62.437 72.222 0.00 0.00 0.00 3.35
245 250 1.078759 CGTCGCCCACAGAGATGTTC 61.079 60.000 0.00 0.00 0.00 3.18
256 261 0.654683 GAGATGTTCACTGCCGCATC 59.345 55.000 0.00 0.00 38.30 3.91
260 265 1.965930 GTTCACTGCCGCATCCACA 60.966 57.895 0.00 0.00 0.00 4.17
291 296 8.049721 CCAGAGATTCTTTAGGTACCTTGATTT 58.950 37.037 22.11 7.22 0.00 2.17
308 313 0.887933 TTTGAAATTCGCTCCAGGGC 59.112 50.000 0.00 0.00 0.00 5.19
312 317 2.142292 AAATTCGCTCCAGGGCCTGT 62.142 55.000 30.68 8.83 0.00 4.00
314 319 4.704103 TCGCTCCAGGGCCTGTCT 62.704 66.667 30.68 0.00 0.00 3.41
341 346 2.904866 TTCTGCAACCACGGCCAC 60.905 61.111 2.24 0.00 0.00 5.01
368 373 1.358787 TGGAGGGATTTGTTCAGCCAT 59.641 47.619 0.00 0.00 0.00 4.40
371 376 2.827921 GAGGGATTTGTTCAGCCATTGT 59.172 45.455 0.00 0.00 0.00 2.71
375 380 3.763897 GGATTTGTTCAGCCATTGTAGGT 59.236 43.478 0.00 0.00 0.00 3.08
376 381 4.220602 GGATTTGTTCAGCCATTGTAGGTT 59.779 41.667 0.00 0.00 0.00 3.50
377 382 4.582701 TTTGTTCAGCCATTGTAGGTTG 57.417 40.909 0.00 0.00 40.81 3.77
378 383 2.513753 TGTTCAGCCATTGTAGGTTGG 58.486 47.619 0.00 0.00 39.98 3.77
379 384 1.818674 GTTCAGCCATTGTAGGTTGGG 59.181 52.381 0.00 0.00 39.98 4.12
380 385 0.331278 TCAGCCATTGTAGGTTGGGG 59.669 55.000 0.00 0.00 39.98 4.96
381 386 0.331278 CAGCCATTGTAGGTTGGGGA 59.669 55.000 0.00 0.00 36.37 4.81
382 387 1.063717 CAGCCATTGTAGGTTGGGGAT 60.064 52.381 0.00 0.00 36.37 3.85
383 388 1.645919 AGCCATTGTAGGTTGGGGATT 59.354 47.619 0.00 0.00 33.40 3.01
384 389 2.031870 GCCATTGTAGGTTGGGGATTC 58.968 52.381 0.00 0.00 33.40 2.52
385 390 2.666317 CCATTGTAGGTTGGGGATTCC 58.334 52.381 0.00 0.00 0.00 3.01
386 391 2.297701 CATTGTAGGTTGGGGATTCCG 58.702 52.381 0.00 0.00 38.76 4.30
387 392 1.659022 TTGTAGGTTGGGGATTCCGA 58.341 50.000 0.00 0.00 38.76 4.55
388 393 1.200519 TGTAGGTTGGGGATTCCGAG 58.799 55.000 0.00 0.00 38.76 4.63
389 394 0.468648 GTAGGTTGGGGATTCCGAGG 59.531 60.000 0.00 0.00 38.76 4.63
390 395 1.342672 TAGGTTGGGGATTCCGAGGC 61.343 60.000 0.00 0.00 38.76 4.70
391 396 2.124278 GTTGGGGATTCCGAGGCC 60.124 66.667 0.00 0.00 38.76 5.19
392 397 2.612430 TTGGGGATTCCGAGGCCA 60.612 61.111 5.01 0.00 38.76 5.36
393 398 2.978946 TTGGGGATTCCGAGGCCAC 61.979 63.158 5.01 0.00 38.76 5.01
394 399 4.191015 GGGGATTCCGAGGCCACC 62.191 72.222 5.01 0.00 0.00 4.61
395 400 4.547367 GGGATTCCGAGGCCACCG 62.547 72.222 5.01 8.22 0.00 4.94
406 411 2.833121 GCCACCGGCCCATTTAGG 60.833 66.667 0.00 0.00 44.06 2.69
407 412 2.680965 CCACCGGCCCATTTAGGT 59.319 61.111 0.00 0.00 37.49 3.08
408 413 1.000145 CCACCGGCCCATTTAGGTT 60.000 57.895 0.00 0.00 34.25 3.50
409 414 0.613572 CCACCGGCCCATTTAGGTTT 60.614 55.000 0.00 0.00 34.25 3.27
410 415 0.530288 CACCGGCCCATTTAGGTTTG 59.470 55.000 0.00 0.00 34.25 2.93
411 416 1.254975 ACCGGCCCATTTAGGTTTGC 61.255 55.000 0.00 0.00 32.17 3.68
412 417 1.254284 CCGGCCCATTTAGGTTTGCA 61.254 55.000 0.00 0.00 34.66 4.08
413 418 0.823460 CGGCCCATTTAGGTTTGCAT 59.177 50.000 0.00 0.00 34.66 3.96
414 419 2.028130 CGGCCCATTTAGGTTTGCATA 58.972 47.619 0.00 0.00 34.66 3.14
415 420 2.223711 CGGCCCATTTAGGTTTGCATAC 60.224 50.000 0.00 0.00 34.66 2.39
416 421 2.763448 GGCCCATTTAGGTTTGCATACA 59.237 45.455 9.57 0.00 34.66 2.29
417 422 3.181476 GGCCCATTTAGGTTTGCATACAG 60.181 47.826 9.57 0.00 34.66 2.74
418 423 3.699038 GCCCATTTAGGTTTGCATACAGA 59.301 43.478 9.57 0.00 34.66 3.41
419 424 4.342092 GCCCATTTAGGTTTGCATACAGAT 59.658 41.667 9.57 0.00 34.66 2.90
420 425 5.163416 GCCCATTTAGGTTTGCATACAGATT 60.163 40.000 9.57 0.00 34.66 2.40
421 426 6.507023 CCCATTTAGGTTTGCATACAGATTC 58.493 40.000 9.57 0.00 34.66 2.52
422 427 6.461509 CCCATTTAGGTTTGCATACAGATTCC 60.462 42.308 9.57 0.00 34.66 3.01
423 428 6.461509 CCATTTAGGTTTGCATACAGATTCCC 60.462 42.308 9.57 0.00 0.00 3.97
424 429 3.737559 AGGTTTGCATACAGATTCCCA 57.262 42.857 9.57 0.00 0.00 4.37
425 430 4.046286 AGGTTTGCATACAGATTCCCAA 57.954 40.909 9.57 0.00 0.00 4.12
426 431 4.019174 AGGTTTGCATACAGATTCCCAAG 58.981 43.478 9.57 0.00 0.00 3.61
427 432 3.429410 GGTTTGCATACAGATTCCCAAGC 60.429 47.826 9.57 0.00 0.00 4.01
428 433 2.057137 TGCATACAGATTCCCAAGCC 57.943 50.000 0.00 0.00 0.00 4.35
429 434 1.284491 TGCATACAGATTCCCAAGCCA 59.716 47.619 0.00 0.00 0.00 4.75
430 435 1.678101 GCATACAGATTCCCAAGCCAC 59.322 52.381 0.00 0.00 0.00 5.01
431 436 2.945440 GCATACAGATTCCCAAGCCACA 60.945 50.000 0.00 0.00 0.00 4.17
432 437 3.355378 CATACAGATTCCCAAGCCACAA 58.645 45.455 0.00 0.00 0.00 3.33
433 438 2.380064 ACAGATTCCCAAGCCACAAA 57.620 45.000 0.00 0.00 0.00 2.83
434 439 2.242043 ACAGATTCCCAAGCCACAAAG 58.758 47.619 0.00 0.00 0.00 2.77
435 440 1.067354 CAGATTCCCAAGCCACAAAGC 60.067 52.381 0.00 0.00 0.00 3.51
436 441 0.968405 GATTCCCAAGCCACAAAGCA 59.032 50.000 0.00 0.00 34.23 3.91
437 442 0.971386 ATTCCCAAGCCACAAAGCAG 59.029 50.000 0.00 0.00 34.23 4.24
438 443 0.396974 TTCCCAAGCCACAAAGCAGT 60.397 50.000 0.00 0.00 34.23 4.40
439 444 0.396974 TCCCAAGCCACAAAGCAGTT 60.397 50.000 0.00 0.00 34.23 3.16
440 445 0.249573 CCCAAGCCACAAAGCAGTTG 60.250 55.000 0.00 0.00 43.43 3.16
441 446 0.877213 CCAAGCCACAAAGCAGTTGC 60.877 55.000 0.00 0.00 41.31 4.17
442 447 0.877213 CAAGCCACAAAGCAGTTGCC 60.877 55.000 0.00 0.00 41.31 4.52
443 448 2.354074 AAGCCACAAAGCAGTTGCCG 62.354 55.000 0.00 0.00 41.31 5.69
444 449 2.355009 CCACAAAGCAGTTGCCGC 60.355 61.111 0.00 0.00 41.31 6.53
445 450 2.723746 CACAAAGCAGTTGCCGCT 59.276 55.556 0.00 0.00 41.31 5.52
446 451 1.659335 CACAAAGCAGTTGCCGCTG 60.659 57.895 0.00 0.79 41.31 5.18
447 452 2.120909 ACAAAGCAGTTGCCGCTGT 61.121 52.632 0.00 0.00 41.31 4.40
448 453 1.066257 CAAAGCAGTTGCCGCTGTT 59.934 52.632 0.00 0.00 43.38 3.16
449 454 0.936297 CAAAGCAGTTGCCGCTGTTC 60.936 55.000 0.00 0.00 43.38 3.18
450 455 2.392613 AAAGCAGTTGCCGCTGTTCG 62.393 55.000 0.00 0.00 43.38 3.95
452 457 3.349006 CAGTTGCCGCTGTTCGCT 61.349 61.111 0.00 0.00 36.73 4.93
453 458 2.591715 AGTTGCCGCTGTTCGCTT 60.592 55.556 0.00 0.00 36.73 4.68
454 459 2.127232 GTTGCCGCTGTTCGCTTC 60.127 61.111 0.00 0.00 36.73 3.86
455 460 2.280797 TTGCCGCTGTTCGCTTCT 60.281 55.556 0.00 0.00 36.73 2.85
456 461 1.891919 TTGCCGCTGTTCGCTTCTT 60.892 52.632 0.00 0.00 36.73 2.52
457 462 1.444119 TTGCCGCTGTTCGCTTCTTT 61.444 50.000 0.00 0.00 36.73 2.52
458 463 1.154395 GCCGCTGTTCGCTTCTTTC 60.154 57.895 0.00 0.00 36.73 2.62
459 464 1.569479 GCCGCTGTTCGCTTCTTTCT 61.569 55.000 0.00 0.00 36.73 2.52
460 465 0.868406 CCGCTGTTCGCTTCTTTCTT 59.132 50.000 0.00 0.00 36.73 2.52
461 466 2.066262 CCGCTGTTCGCTTCTTTCTTA 58.934 47.619 0.00 0.00 36.73 2.10
462 467 2.159827 CCGCTGTTCGCTTCTTTCTTAC 60.160 50.000 0.00 0.00 36.73 2.34
463 468 2.159827 CGCTGTTCGCTTCTTTCTTACC 60.160 50.000 0.00 0.00 36.13 2.85
464 469 2.806244 GCTGTTCGCTTCTTTCTTACCA 59.194 45.455 0.00 0.00 35.14 3.25
465 470 3.364068 GCTGTTCGCTTCTTTCTTACCAC 60.364 47.826 0.00 0.00 35.14 4.16
466 471 3.799366 TGTTCGCTTCTTTCTTACCACA 58.201 40.909 0.00 0.00 0.00 4.17
467 472 3.558418 TGTTCGCTTCTTTCTTACCACAC 59.442 43.478 0.00 0.00 0.00 3.82
468 473 2.762745 TCGCTTCTTTCTTACCACACC 58.237 47.619 0.00 0.00 0.00 4.16
469 474 2.103432 TCGCTTCTTTCTTACCACACCA 59.897 45.455 0.00 0.00 0.00 4.17
470 475 2.875933 CGCTTCTTTCTTACCACACCAA 59.124 45.455 0.00 0.00 0.00 3.67
471 476 3.314080 CGCTTCTTTCTTACCACACCAAA 59.686 43.478 0.00 0.00 0.00 3.28
472 477 4.554723 CGCTTCTTTCTTACCACACCAAAG 60.555 45.833 0.00 0.00 0.00 2.77
473 478 4.261614 GCTTCTTTCTTACCACACCAAAGG 60.262 45.833 0.00 0.00 0.00 3.11
474 479 4.781775 TCTTTCTTACCACACCAAAGGA 57.218 40.909 0.00 0.00 0.00 3.36
475 480 5.118729 TCTTTCTTACCACACCAAAGGAA 57.881 39.130 0.00 0.00 0.00 3.36
476 481 5.130350 TCTTTCTTACCACACCAAAGGAAG 58.870 41.667 0.00 0.00 37.24 3.46
477 482 3.502123 TCTTACCACACCAAAGGAAGG 57.498 47.619 0.00 0.00 0.00 3.46
478 483 1.886542 CTTACCACACCAAAGGAAGGC 59.113 52.381 0.00 0.00 0.00 4.35
479 484 0.847373 TACCACACCAAAGGAAGGCA 59.153 50.000 0.00 0.00 0.00 4.75
480 485 0.755327 ACCACACCAAAGGAAGGCAC 60.755 55.000 0.00 0.00 0.00 5.01
481 486 1.654220 CACACCAAAGGAAGGCACG 59.346 57.895 0.00 0.00 0.00 5.34
482 487 0.817634 CACACCAAAGGAAGGCACGA 60.818 55.000 0.00 0.00 0.00 4.35
483 488 0.818040 ACACCAAAGGAAGGCACGAC 60.818 55.000 0.00 0.00 0.00 4.34
484 489 0.817634 CACCAAAGGAAGGCACGACA 60.818 55.000 0.00 0.00 0.00 4.35
485 490 0.110486 ACCAAAGGAAGGCACGACAT 59.890 50.000 0.00 0.00 0.00 3.06
486 491 1.349688 ACCAAAGGAAGGCACGACATA 59.650 47.619 0.00 0.00 0.00 2.29
487 492 2.026262 ACCAAAGGAAGGCACGACATAT 60.026 45.455 0.00 0.00 0.00 1.78
488 493 2.614057 CCAAAGGAAGGCACGACATATC 59.386 50.000 0.00 0.00 0.00 1.63
489 494 3.535561 CAAAGGAAGGCACGACATATCT 58.464 45.455 0.00 0.00 0.00 1.98
490 495 3.914426 AAGGAAGGCACGACATATCTT 57.086 42.857 0.00 0.00 0.00 2.40
491 496 3.185246 AGGAAGGCACGACATATCTTG 57.815 47.619 0.00 0.00 0.00 3.02
492 497 2.766263 AGGAAGGCACGACATATCTTGA 59.234 45.455 0.00 0.00 0.00 3.02
493 498 2.866762 GGAAGGCACGACATATCTTGAC 59.133 50.000 0.00 0.00 32.09 3.18
494 499 2.209838 AGGCACGACATATCTTGACG 57.790 50.000 0.00 0.00 46.63 4.35
495 500 1.749063 AGGCACGACATATCTTGACGA 59.251 47.619 4.64 0.00 44.56 4.20
496 501 2.120232 GGCACGACATATCTTGACGAG 58.880 52.381 4.64 0.00 44.56 4.18
497 502 2.223502 GGCACGACATATCTTGACGAGA 60.224 50.000 4.64 0.00 44.56 4.04
498 503 3.039405 GCACGACATATCTTGACGAGAG 58.961 50.000 4.64 0.00 44.56 3.20
499 504 3.242772 GCACGACATATCTTGACGAGAGA 60.243 47.826 4.64 0.00 44.56 3.10
500 505 4.730903 GCACGACATATCTTGACGAGAGAA 60.731 45.833 4.64 0.00 44.56 2.87
501 506 5.515184 CACGACATATCTTGACGAGAGAAT 58.485 41.667 4.64 0.00 44.56 2.40
502 507 5.974158 CACGACATATCTTGACGAGAGAATT 59.026 40.000 4.64 0.00 44.56 2.17
503 508 6.141527 CACGACATATCTTGACGAGAGAATTC 59.858 42.308 0.00 0.00 44.56 2.17
504 509 6.038825 ACGACATATCTTGACGAGAGAATTCT 59.961 38.462 7.95 7.95 44.56 2.40
505 510 7.226918 ACGACATATCTTGACGAGAGAATTCTA 59.773 37.037 8.25 0.00 44.56 2.10
550 555 8.792830 TGTATTTTCTTGGGTCTTAGATCAAG 57.207 34.615 16.48 16.48 38.26 3.02
563 568 7.943447 GGTCTTAGATCAAGATAGGTGTACCTA 59.057 40.741 12.85 12.85 44.22 3.08
592 597 8.385111 ACAATTACGAATGTGAATAAAGGTACG 58.615 33.333 0.00 0.00 0.00 3.67
665 687 0.111253 AACAGGGCAGCTTAGCAGTT 59.889 50.000 7.07 0.00 35.83 3.16
668 690 0.107459 AGGGCAGCTTAGCAGTTAGC 60.107 55.000 7.07 2.13 46.19 3.09
771 1100 3.641017 GCTCTCCAGCCTCTTGTTT 57.359 52.632 0.00 0.00 40.14 2.83
1815 2198 3.114616 CACACGCTGGGCTTCTCG 61.115 66.667 0.00 0.00 0.00 4.04
2128 2511 0.109689 CGCCTTCTTCGACGACTTCT 60.110 55.000 0.00 0.00 0.00 2.85
2441 2864 8.186178 TCGATTGAGTAATCTCTTTAGTTTGC 57.814 34.615 0.00 0.00 40.43 3.68
2555 2980 5.800941 CAGCTTTTGGTTTTTACACGTGTTA 59.199 36.000 28.55 16.01 0.00 2.41
2556 2981 5.801444 AGCTTTTGGTTTTTACACGTGTTAC 59.199 36.000 28.55 18.29 0.00 2.50
2574 2999 8.443160 ACGTGTTACTGTTCTTGATTTATCATG 58.557 33.333 0.00 0.00 36.56 3.07
2619 3044 7.564793 TGGTCATAGTAAGAAGTAACATGCAT 58.435 34.615 0.00 0.00 0.00 3.96
2653 3078 7.332926 GCATGTTACTATCTTCATGATGGGTAG 59.667 40.741 8.60 10.72 39.68 3.18
2667 3092 8.585018 TCATGATGGGTAGTAACATATGTGTAG 58.415 37.037 9.63 0.00 37.67 2.74
2696 3121 6.627395 TGCAAACCATTATTTATAGGTCCG 57.373 37.500 0.00 0.00 32.05 4.79
2739 3165 0.034337 TAAAGGGTCTGACCACACGC 59.966 55.000 26.94 10.24 41.02 5.34
2742 3168 2.280552 GGGTCTGACCACACGCCTA 61.281 63.158 26.94 0.00 41.02 3.93
2762 3188 5.622914 GCCTACGTGTGGTATCTAAAGAACA 60.623 44.000 0.00 0.00 0.00 3.18
2800 3226 2.032722 TGTAGGCAAAACAAGTAACGCG 60.033 45.455 3.53 3.53 0.00 6.01
2819 3245 1.890041 CACACGCCCGGTCTTTTGA 60.890 57.895 0.00 0.00 0.00 2.69
2836 3263 0.039764 TGACTCGTGGTCCCTCTCAT 59.960 55.000 8.31 0.00 43.89 2.90
2856 3283 1.156736 ATGCCTACGTGTGAGCAAAC 58.843 50.000 0.00 0.00 38.99 2.93
2864 3291 6.273825 CCTACGTGTGAGCAAACTAGATAAT 58.726 40.000 0.00 0.00 0.00 1.28
2916 3343 3.036084 CGCGTGACAGTCACCACC 61.036 66.667 25.11 13.96 44.20 4.61
2918 3345 2.818841 CGTGACAGTCACCACCCA 59.181 61.111 25.11 0.00 44.20 4.51
2956 3383 0.976073 TCCGGACCCTCTTCCATGTC 60.976 60.000 0.00 0.00 35.04 3.06
2974 3401 1.200020 GTCCGTTTAATTGCAGCTGCT 59.800 47.619 36.61 21.18 42.66 4.24
3227 3659 6.145338 TGTTCGAGTAAAGAGAGAGTTGTT 57.855 37.500 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.023949 GCTCTGGGATCGTGTGGCT 62.024 63.158 0.00 0.00 0.00 4.75
22 23 3.129871 CAATTCTTCGAGCTCTGGGATC 58.870 50.000 12.85 0.00 0.00 3.36
23 24 2.768527 TCAATTCTTCGAGCTCTGGGAT 59.231 45.455 12.85 0.00 0.00 3.85
24 25 2.179427 TCAATTCTTCGAGCTCTGGGA 58.821 47.619 12.85 3.80 0.00 4.37
34 35 2.660236 GCTGCTTTGCTTCAATTCTTCG 59.340 45.455 0.00 0.00 0.00 3.79
74 75 1.000896 CAACTGGGTGGGGGACATC 60.001 63.158 0.00 0.00 0.00 3.06
80 81 0.106217 AGAACAACAACTGGGTGGGG 60.106 55.000 0.00 0.00 0.00 4.96
109 110 0.451783 AAGATCGAAAATGGTGGCGC 59.548 50.000 0.00 0.00 0.00 6.53
117 118 8.792830 TCACCTAGAATCAAAAGATCGAAAAT 57.207 30.769 0.00 0.00 0.00 1.82
119 120 7.611770 TCTCACCTAGAATCAAAAGATCGAAA 58.388 34.615 0.00 0.00 0.00 3.46
127 128 5.630069 GCCAGGATCTCACCTAGAATCAAAA 60.630 44.000 0.00 0.00 37.89 2.44
129 130 3.389329 GCCAGGATCTCACCTAGAATCAA 59.611 47.826 0.00 0.00 37.89 2.57
139 140 0.029567 CGTCTACGCCAGGATCTCAC 59.970 60.000 0.00 0.00 0.00 3.51
140 141 0.107361 TCGTCTACGCCAGGATCTCA 60.107 55.000 0.00 0.00 39.60 3.27
155 156 3.607661 GATCCGGCCCCTCTCGTC 61.608 72.222 0.00 0.00 0.00 4.20
185 190 2.548920 GGATGATAAGTGGCTTCTCGGG 60.549 54.545 0.00 0.00 0.00 5.14
188 193 3.389329 TCTGGGATGATAAGTGGCTTCTC 59.611 47.826 0.00 0.00 0.00 2.87
189 194 3.387962 TCTGGGATGATAAGTGGCTTCT 58.612 45.455 0.00 0.00 0.00 2.85
200 205 3.070734 CGTCCATCTTCTTCTGGGATGAT 59.929 47.826 0.00 0.00 39.12 2.45
203 208 2.432510 GACGTCCATCTTCTTCTGGGAT 59.567 50.000 3.51 0.00 33.13 3.85
239 244 1.026182 TGGATGCGGCAGTGAACATC 61.026 55.000 9.25 10.40 38.53 3.06
245 250 1.968017 ACTTGTGGATGCGGCAGTG 60.968 57.895 9.25 0.00 0.00 3.66
256 261 2.486472 AGAATCTCTGGCACTTGTGG 57.514 50.000 2.81 0.00 0.00 4.17
260 265 4.917906 ACCTAAAGAATCTCTGGCACTT 57.082 40.909 0.00 0.00 0.00 3.16
291 296 1.378514 GGCCCTGGAGCGAATTTCA 60.379 57.895 0.00 0.00 0.00 2.69
296 301 3.706373 GACAGGCCCTGGAGCGAA 61.706 66.667 16.70 0.00 35.51 4.70
308 313 4.318332 TGCAGAAGTATGACAAAGACAGG 58.682 43.478 0.00 0.00 0.00 4.00
312 317 4.515191 GTGGTTGCAGAAGTATGACAAAGA 59.485 41.667 0.00 0.00 0.00 2.52
314 319 3.249799 CGTGGTTGCAGAAGTATGACAAA 59.750 43.478 0.00 0.00 0.00 2.83
341 346 1.076485 CAAATCCCTCCAGGCCAGG 60.076 63.158 8.15 8.15 34.51 4.45
368 373 1.557832 CTCGGAATCCCCAACCTACAA 59.442 52.381 0.00 0.00 34.14 2.41
371 376 1.342672 GCCTCGGAATCCCCAACCTA 61.343 60.000 0.00 0.00 34.14 3.08
375 380 2.612430 TGGCCTCGGAATCCCCAA 60.612 61.111 3.32 0.00 34.14 4.12
376 381 3.407967 GTGGCCTCGGAATCCCCA 61.408 66.667 3.32 0.00 34.14 4.96
377 382 4.191015 GGTGGCCTCGGAATCCCC 62.191 72.222 3.32 0.00 0.00 4.81
378 383 4.547367 CGGTGGCCTCGGAATCCC 62.547 72.222 3.32 0.00 0.00 3.85
390 395 0.613572 AAACCTAAATGGGCCGGTGG 60.614 55.000 1.90 0.00 41.11 4.61
391 396 0.530288 CAAACCTAAATGGGCCGGTG 59.470 55.000 1.90 0.00 41.11 4.94
392 397 1.254975 GCAAACCTAAATGGGCCGGT 61.255 55.000 1.90 0.00 41.11 5.28
393 398 1.254284 TGCAAACCTAAATGGGCCGG 61.254 55.000 0.00 0.00 41.11 6.13
394 399 0.823460 ATGCAAACCTAAATGGGCCG 59.177 50.000 0.00 0.00 41.11 6.13
395 400 2.763448 TGTATGCAAACCTAAATGGGCC 59.237 45.455 0.00 0.00 41.11 5.80
396 401 3.699038 TCTGTATGCAAACCTAAATGGGC 59.301 43.478 0.00 0.00 41.11 5.36
397 402 6.461509 GGAATCTGTATGCAAACCTAAATGGG 60.462 42.308 0.00 0.00 41.11 4.00
398 403 6.461509 GGGAATCTGTATGCAAACCTAAATGG 60.462 42.308 0.00 0.00 42.93 3.16
399 404 6.096705 TGGGAATCTGTATGCAAACCTAAATG 59.903 38.462 0.00 0.00 0.00 2.32
400 405 6.194235 TGGGAATCTGTATGCAAACCTAAAT 58.806 36.000 0.00 0.00 0.00 1.40
401 406 5.575157 TGGGAATCTGTATGCAAACCTAAA 58.425 37.500 0.00 0.00 0.00 1.85
402 407 5.186256 TGGGAATCTGTATGCAAACCTAA 57.814 39.130 0.00 0.00 0.00 2.69
403 408 4.853468 TGGGAATCTGTATGCAAACCTA 57.147 40.909 0.00 0.00 0.00 3.08
404 409 3.737559 TGGGAATCTGTATGCAAACCT 57.262 42.857 0.00 0.00 0.00 3.50
405 410 3.429410 GCTTGGGAATCTGTATGCAAACC 60.429 47.826 0.00 0.00 0.00 3.27
406 411 3.429410 GGCTTGGGAATCTGTATGCAAAC 60.429 47.826 0.00 0.00 0.00 2.93
407 412 2.760092 GGCTTGGGAATCTGTATGCAAA 59.240 45.455 0.00 0.00 0.00 3.68
408 413 2.291475 TGGCTTGGGAATCTGTATGCAA 60.291 45.455 0.00 0.00 0.00 4.08
409 414 1.284491 TGGCTTGGGAATCTGTATGCA 59.716 47.619 0.00 0.00 0.00 3.96
410 415 1.678101 GTGGCTTGGGAATCTGTATGC 59.322 52.381 0.00 0.00 0.00 3.14
411 416 3.003394 TGTGGCTTGGGAATCTGTATG 57.997 47.619 0.00 0.00 0.00 2.39
412 417 3.737559 TTGTGGCTTGGGAATCTGTAT 57.262 42.857 0.00 0.00 0.00 2.29
413 418 3.420893 CTTTGTGGCTTGGGAATCTGTA 58.579 45.455 0.00 0.00 0.00 2.74
414 419 2.242043 CTTTGTGGCTTGGGAATCTGT 58.758 47.619 0.00 0.00 0.00 3.41
415 420 1.067354 GCTTTGTGGCTTGGGAATCTG 60.067 52.381 0.00 0.00 0.00 2.90
416 421 1.260544 GCTTTGTGGCTTGGGAATCT 58.739 50.000 0.00 0.00 0.00 2.40
417 422 0.968405 TGCTTTGTGGCTTGGGAATC 59.032 50.000 0.00 0.00 0.00 2.52
418 423 0.971386 CTGCTTTGTGGCTTGGGAAT 59.029 50.000 0.00 0.00 0.00 3.01
419 424 0.396974 ACTGCTTTGTGGCTTGGGAA 60.397 50.000 0.00 0.00 0.00 3.97
420 425 0.396974 AACTGCTTTGTGGCTTGGGA 60.397 50.000 0.00 0.00 0.00 4.37
421 426 0.249573 CAACTGCTTTGTGGCTTGGG 60.250 55.000 0.00 0.00 0.00 4.12
422 427 0.877213 GCAACTGCTTTGTGGCTTGG 60.877 55.000 0.00 0.00 37.54 3.61
423 428 0.877213 GGCAACTGCTTTGTGGCTTG 60.877 55.000 1.06 0.00 41.70 4.01
424 429 1.442987 GGCAACTGCTTTGTGGCTT 59.557 52.632 1.06 0.00 41.70 4.35
425 430 2.848858 CGGCAACTGCTTTGTGGCT 61.849 57.895 1.06 0.00 41.70 4.75
426 431 2.355009 CGGCAACTGCTTTGTGGC 60.355 61.111 1.06 0.00 41.70 5.01
427 432 2.355009 GCGGCAACTGCTTTGTGG 60.355 61.111 1.06 0.00 41.70 4.17
428 433 1.659335 CAGCGGCAACTGCTTTGTG 60.659 57.895 1.45 0.00 42.95 3.33
429 434 1.666209 AACAGCGGCAACTGCTTTGT 61.666 50.000 1.45 1.68 42.95 2.83
430 435 0.936297 GAACAGCGGCAACTGCTTTG 60.936 55.000 1.45 1.10 42.95 2.77
431 436 1.360192 GAACAGCGGCAACTGCTTT 59.640 52.632 1.45 0.00 42.95 3.51
432 437 2.896801 CGAACAGCGGCAACTGCTT 61.897 57.895 1.45 0.27 42.95 3.91
433 438 3.349006 CGAACAGCGGCAACTGCT 61.349 61.111 1.45 0.00 45.07 4.24
444 449 3.807622 TGTGGTAAGAAAGAAGCGAACAG 59.192 43.478 0.00 0.00 0.00 3.16
445 450 3.558418 GTGTGGTAAGAAAGAAGCGAACA 59.442 43.478 0.00 0.00 0.00 3.18
446 451 3.059120 GGTGTGGTAAGAAAGAAGCGAAC 60.059 47.826 0.00 0.00 0.00 3.95
447 452 3.135994 GGTGTGGTAAGAAAGAAGCGAA 58.864 45.455 0.00 0.00 0.00 4.70
448 453 2.103432 TGGTGTGGTAAGAAAGAAGCGA 59.897 45.455 0.00 0.00 0.00 4.93
449 454 2.489971 TGGTGTGGTAAGAAAGAAGCG 58.510 47.619 0.00 0.00 0.00 4.68
450 455 4.261614 CCTTTGGTGTGGTAAGAAAGAAGC 60.262 45.833 0.00 0.00 0.00 3.86
451 456 5.130350 TCCTTTGGTGTGGTAAGAAAGAAG 58.870 41.667 0.00 0.00 0.00 2.85
452 457 5.118729 TCCTTTGGTGTGGTAAGAAAGAA 57.881 39.130 0.00 0.00 0.00 2.52
453 458 4.781775 TCCTTTGGTGTGGTAAGAAAGA 57.218 40.909 0.00 0.00 0.00 2.52
454 459 4.278419 CCTTCCTTTGGTGTGGTAAGAAAG 59.722 45.833 0.00 0.00 0.00 2.62
455 460 4.211920 CCTTCCTTTGGTGTGGTAAGAAA 58.788 43.478 0.00 0.00 0.00 2.52
456 461 3.827722 CCTTCCTTTGGTGTGGTAAGAA 58.172 45.455 0.00 0.00 0.00 2.52
457 462 2.488347 GCCTTCCTTTGGTGTGGTAAGA 60.488 50.000 0.00 0.00 0.00 2.10
458 463 1.886542 GCCTTCCTTTGGTGTGGTAAG 59.113 52.381 0.00 0.00 0.00 2.34
459 464 1.215673 TGCCTTCCTTTGGTGTGGTAA 59.784 47.619 0.00 0.00 0.00 2.85
460 465 0.847373 TGCCTTCCTTTGGTGTGGTA 59.153 50.000 0.00 0.00 0.00 3.25
461 466 0.755327 GTGCCTTCCTTTGGTGTGGT 60.755 55.000 0.00 0.00 0.00 4.16
462 467 1.795170 CGTGCCTTCCTTTGGTGTGG 61.795 60.000 0.00 0.00 0.00 4.17
463 468 0.817634 TCGTGCCTTCCTTTGGTGTG 60.818 55.000 0.00 0.00 0.00 3.82
464 469 0.818040 GTCGTGCCTTCCTTTGGTGT 60.818 55.000 0.00 0.00 0.00 4.16
465 470 0.817634 TGTCGTGCCTTCCTTTGGTG 60.818 55.000 0.00 0.00 0.00 4.17
466 471 0.110486 ATGTCGTGCCTTCCTTTGGT 59.890 50.000 0.00 0.00 0.00 3.67
467 472 2.107950 TATGTCGTGCCTTCCTTTGG 57.892 50.000 0.00 0.00 0.00 3.28
468 473 3.535561 AGATATGTCGTGCCTTCCTTTG 58.464 45.455 0.00 0.00 0.00 2.77
469 474 3.914426 AGATATGTCGTGCCTTCCTTT 57.086 42.857 0.00 0.00 0.00 3.11
470 475 3.197766 TCAAGATATGTCGTGCCTTCCTT 59.802 43.478 0.52 0.00 34.38 3.36
471 476 2.766263 TCAAGATATGTCGTGCCTTCCT 59.234 45.455 0.52 0.00 34.38 3.36
472 477 2.866762 GTCAAGATATGTCGTGCCTTCC 59.133 50.000 0.52 0.00 34.38 3.46
473 478 2.535984 CGTCAAGATATGTCGTGCCTTC 59.464 50.000 0.52 0.00 36.12 3.46
474 479 2.165641 TCGTCAAGATATGTCGTGCCTT 59.834 45.455 0.52 0.00 40.69 4.35
475 480 1.749063 TCGTCAAGATATGTCGTGCCT 59.251 47.619 0.52 0.00 40.69 4.75
476 481 2.120232 CTCGTCAAGATATGTCGTGCC 58.880 52.381 0.52 0.00 40.69 5.01
477 482 3.039405 CTCTCGTCAAGATATGTCGTGC 58.961 50.000 0.52 0.00 40.69 5.34
478 483 4.537936 TCTCTCGTCAAGATATGTCGTG 57.462 45.455 0.00 0.00 40.69 4.35
479 484 5.759506 ATTCTCTCGTCAAGATATGTCGT 57.240 39.130 0.00 0.00 40.69 4.34
480 485 6.434596 AGAATTCTCTCGTCAAGATATGTCG 58.565 40.000 0.88 0.00 41.11 4.35
481 486 8.564574 ACTAGAATTCTCTCGTCAAGATATGTC 58.435 37.037 12.24 0.00 32.19 3.06
482 487 8.458573 ACTAGAATTCTCTCGTCAAGATATGT 57.541 34.615 12.24 0.00 32.19 2.29
484 489 9.787435 ACTACTAGAATTCTCTCGTCAAGATAT 57.213 33.333 12.24 0.00 32.19 1.63
485 490 9.263538 GACTACTAGAATTCTCTCGTCAAGATA 57.736 37.037 12.24 0.00 32.19 1.98
486 491 7.771361 TGACTACTAGAATTCTCTCGTCAAGAT 59.229 37.037 12.24 0.00 32.19 2.40
487 492 7.104290 TGACTACTAGAATTCTCTCGTCAAGA 58.896 38.462 12.24 0.00 30.64 3.02
488 493 7.310072 TGACTACTAGAATTCTCTCGTCAAG 57.690 40.000 12.24 4.40 30.64 3.02
489 494 7.867305 ATGACTACTAGAATTCTCTCGTCAA 57.133 36.000 22.44 12.92 32.91 3.18
490 495 7.658167 CCTATGACTACTAGAATTCTCTCGTCA 59.342 40.741 21.58 21.58 33.31 4.35
491 496 7.874016 TCCTATGACTACTAGAATTCTCTCGTC 59.126 40.741 12.24 14.03 30.64 4.20
492 497 7.737869 TCCTATGACTACTAGAATTCTCTCGT 58.262 38.462 12.24 10.30 32.64 4.18
493 498 7.876068 ACTCCTATGACTACTAGAATTCTCTCG 59.124 40.741 12.24 4.58 32.70 4.04
494 499 9.569122 AACTCCTATGACTACTAGAATTCTCTC 57.431 37.037 12.24 1.16 32.70 3.20
500 505 9.787435 CAGAGTAACTCCTATGACTACTAGAAT 57.213 37.037 0.00 0.00 0.00 2.40
501 506 8.770322 ACAGAGTAACTCCTATGACTACTAGAA 58.230 37.037 0.00 0.00 0.00 2.10
502 507 8.321621 ACAGAGTAACTCCTATGACTACTAGA 57.678 38.462 0.00 0.00 0.00 2.43
505 510 9.924010 AAATACAGAGTAACTCCTATGACTACT 57.076 33.333 0.00 0.00 0.00 2.57
576 581 6.708949 AGAAACACACGTACCTTTATTCACAT 59.291 34.615 0.00 0.00 0.00 3.21
668 690 9.444600 TGTTTCCTTTACTACCTTTAGCATTAG 57.555 33.333 0.00 0.00 0.00 1.73
672 694 7.069877 TCTGTTTCCTTTACTACCTTTAGCA 57.930 36.000 0.00 0.00 0.00 3.49
688 1017 1.006571 TGTCCGTCGCTCTGTTTCC 60.007 57.895 0.00 0.00 0.00 3.13
771 1100 3.138798 GGGAGTGCTCGTAGGCGA 61.139 66.667 0.00 0.00 45.79 5.54
1289 1672 2.583685 GAAATCGGGCGACAGCTTGC 62.584 60.000 0.00 0.00 44.37 4.01
1815 2198 3.426568 GCGAACTCCTGGCAGTGC 61.427 66.667 14.43 6.55 0.00 4.40
2128 2511 4.161295 CTTCTCCATGGCGCGGGA 62.161 66.667 8.83 12.64 0.00 5.14
2310 2730 1.372997 CGCACCCGAAGATATCCCG 60.373 63.158 0.00 3.68 36.29 5.14
2510 2934 8.614469 AGCTGATTTAATTAGAGGCAAGATAC 57.386 34.615 0.71 0.00 0.00 2.24
2555 2980 7.458409 AGCAACATGATAAATCAAGAACAGT 57.542 32.000 0.00 0.00 40.69 3.55
2556 2981 8.886719 TCTAGCAACATGATAAATCAAGAACAG 58.113 33.333 0.00 0.00 40.69 3.16
2574 2999 9.712305 ATGACCATAATAACATAGTCTAGCAAC 57.288 33.333 0.00 0.00 0.00 4.17
2591 3016 9.542462 GCATGTTACTTCTTACTATGACCATAA 57.458 33.333 0.00 0.00 0.00 1.90
2646 3071 9.596308 TGATACTACACATATGTTACTACCCAT 57.404 33.333 5.37 0.00 40.48 4.00
2653 3078 9.864034 GTTTGCATGATACTACACATATGTTAC 57.136 33.333 5.37 0.00 40.48 2.50
2690 3115 2.344872 GTGGGCGTTAACGGACCT 59.655 61.111 27.82 0.00 40.23 3.85
2696 3121 1.277440 CACACGTGTGGGCGTTAAC 59.723 57.895 35.65 0.00 43.83 2.01
2739 3165 5.957798 TGTTCTTTAGATACCACACGTAGG 58.042 41.667 4.77 4.77 0.00 3.18
2742 3168 4.689345 GCTTGTTCTTTAGATACCACACGT 59.311 41.667 0.00 0.00 0.00 4.49
2762 3188 3.532896 CACGTAGATGTGTGGGCTT 57.467 52.632 0.00 0.00 35.12 4.35
2782 3208 0.317519 GCGCGTTACTTGTTTTGCCT 60.318 50.000 8.43 0.00 0.00 4.75
2800 3226 3.284449 AAAAGACCGGGCGTGTGC 61.284 61.111 6.32 0.00 41.71 4.57
2819 3245 2.311463 CATATGAGAGGGACCACGAGT 58.689 52.381 0.00 0.00 0.00 4.18
2836 3263 2.028476 AGTTTGCTCACACGTAGGCATA 60.028 45.455 0.00 0.00 34.59 3.14
2856 3283 1.512926 GGCGTGTGGGCATTATCTAG 58.487 55.000 0.00 0.00 41.77 2.43
2916 3343 4.738998 TGGCAACTGCGGGGATGG 62.739 66.667 0.00 0.00 43.26 3.51
2918 3345 2.440796 CATGGCAACTGCGGGGAT 60.441 61.111 0.00 0.00 43.26 3.85
2956 3383 3.181497 ACATAGCAGCTGCAATTAAACGG 60.181 43.478 38.24 18.78 45.16 4.44
3001 3428 5.116084 ACCATGGCAACTGTAGTTATCAT 57.884 39.130 13.04 2.37 36.32 2.45
3097 3528 4.606210 TGGCAACTGTAGTAGACCAGATA 58.394 43.478 0.00 0.00 37.61 1.98
3197 3629 7.711339 ACTCTCTCTTTACTCGAACATGTTTTT 59.289 33.333 13.36 0.24 0.00 1.94


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

AutoCloner maintained by Alex Coulton.