Multiple sequence alignment - TraesCS5A01G073000

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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 TraesCS5A01G073000 chr5A 100.000 3546 0 0 1 3546 84897271 84893726 0.000000e+00 6549.0
1 TraesCS5A01G073000 chr5A 83.846 130 11 3 2820 2940 687277984 687277856 8.040000e-22 115.0
2 TraesCS5A01G073000 chr5B 93.858 2426 99 23 419 2809 96490942 96488532 0.000000e+00 3609.0
3 TraesCS5A01G073000 chr5B 88.737 293 26 4 1 289 96491236 96490947 5.630000e-93 351.0
4 TraesCS5A01G073000 chr5B 77.883 529 93 22 2820 3334 417662840 417663358 1.240000e-79 307.0
5 TraesCS5A01G073000 chr5B 83.432 169 7 4 3375 3523 96488530 96488363 1.720000e-28 137.0
6 TraesCS5A01G073000 chr5D 93.560 2407 99 27 442 2826 91343322 91340950 0.000000e+00 3535.0
7 TraesCS5A01G073000 chr5D 89.453 256 16 7 494 743 91345294 91345044 2.660000e-81 313.0
8 TraesCS5A01G073000 chr5D 86.161 224 20 9 616 838 91345001 91344788 7.660000e-57 231.0
9 TraesCS5A01G073000 chr5D 83.333 174 23 6 2933 3105 404614665 404614833 4.740000e-34 156.0
10 TraesCS5A01G073000 chr2B 78.571 448 56 21 2897 3334 632999754 633000171 3.510000e-65 259.0
11 TraesCS5A01G073000 chr2B 88.136 177 17 4 2821 2994 416857142 416856967 1.290000e-49 207.0
12 TraesCS5A01G073000 chr2B 88.158 76 9 0 2821 2896 632999651 632999726 1.360000e-14 91.6
13 TraesCS5A01G073000 chr2B 76.068 117 26 2 3221 3336 153902540 153902425 3.820000e-05 60.2
14 TraesCS5A01G073000 chr2B 100.000 29 0 0 365 393 642793097 642793125 2.000000e-03 54.7
15 TraesCS5A01G073000 chr2D 87.013 231 27 3 2869 3098 643464533 643464305 1.260000e-64 257.0
16 TraesCS5A01G073000 chr2D 79.932 294 30 14 2815 3105 588243591 588243858 4.670000e-44 189.0
17 TraesCS5A01G073000 chr2D 86.061 165 18 5 2935 3098 104850242 104850402 4.710000e-39 172.0
18 TraesCS5A01G073000 chr2D 83.333 174 24 5 2933 3105 421996757 421996926 4.740000e-34 156.0
19 TraesCS5A01G073000 chr2D 90.909 77 7 0 2820 2896 533169520 533169596 1.740000e-18 104.0
20 TraesCS5A01G073000 chr3B 83.275 287 32 8 2821 3105 169258548 169258276 2.110000e-62 250.0
21 TraesCS5A01G073000 chr4B 83.394 277 25 11 3062 3334 4557675 4557416 1.650000e-58 237.0
22 TraesCS5A01G073000 chr4B 85.714 168 18 6 2933 3099 539880141 539880303 4.710000e-39 172.0
23 TraesCS5A01G073000 chr4B 85.030 167 20 5 2933 3098 105861257 105861419 7.880000e-37 165.0
24 TraesCS5A01G073000 chr6B 87.079 178 19 3 2820 2994 480372192 480372016 7.760000e-47 198.0
25 TraesCS5A01G073000 chr6B 82.270 141 23 2 3198 3336 623343859 623343999 1.730000e-23 121.0
26 TraesCS5A01G073000 chr1D 85.311 177 21 4 2933 3108 71839341 71839169 1.010000e-40 178.0
27 TraesCS5A01G073000 chr3D 84.483 174 22 4 2933 3105 80755666 80755497 2.190000e-37 167.0
28 TraesCS5A01G073000 chr4D 84.940 166 21 3 2933 3098 494675470 494675309 7.880000e-37 165.0
29 TraesCS5A01G073000 chrUn 89.655 87 9 0 3249 3335 108759782 108759696 1.040000e-20 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G073000 chr5A 84893726 84897271 3545 True 6549.000000 6549 100.000000 1 3546 1 chr5A.!!$R1 3545
1 TraesCS5A01G073000 chr5B 96488363 96491236 2873 True 1365.666667 3609 88.675667 1 3523 3 chr5B.!!$R1 3522
2 TraesCS5A01G073000 chr5B 417662840 417663358 518 False 307.000000 307 77.883000 2820 3334 1 chr5B.!!$F1 514
3 TraesCS5A01G073000 chr5D 91340950 91345294 4344 True 1359.666667 3535 89.724667 442 2826 3 chr5D.!!$R1 2384

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
944 2489 0.035056 CACCAGACCAATCCCCTGAC 60.035 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2913 4489 0.911769 TGATGACCGAAGCCCATTCT 59.088 50.0 0.0 0.0 35.61 2.4 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
99 100 2.151202 TGGAGAATTTGGACTCAACGC 58.849 47.619 0.00 0.00 35.17 4.84
110 111 1.470098 GACTCAACGCAATGGCAAGAT 59.530 47.619 0.00 0.00 41.24 2.40
111 112 1.470098 ACTCAACGCAATGGCAAGATC 59.530 47.619 0.00 0.00 41.24 2.75
114 115 2.162208 TCAACGCAATGGCAAGATCTTC 59.838 45.455 4.57 0.75 41.24 2.87
116 117 2.161855 ACGCAATGGCAAGATCTTCAA 58.838 42.857 4.57 0.00 41.24 2.69
117 118 2.163010 ACGCAATGGCAAGATCTTCAAG 59.837 45.455 4.57 0.00 41.24 3.02
118 119 2.537401 GCAATGGCAAGATCTTCAAGC 58.463 47.619 4.57 6.35 40.72 4.01
119 120 2.094390 GCAATGGCAAGATCTTCAAGCA 60.094 45.455 15.73 5.22 40.72 3.91
122 123 3.144657 TGGCAAGATCTTCAAGCAAGA 57.855 42.857 15.73 0.00 45.60 3.02
124 125 3.504906 TGGCAAGATCTTCAAGCAAGAAG 59.495 43.478 15.73 10.84 44.66 2.85
126 127 4.474113 GCAAGATCTTCAAGCAAGAAGTG 58.526 43.478 4.57 9.07 44.66 3.16
128 129 5.106237 GCAAGATCTTCAAGCAAGAAGTGAT 60.106 40.000 4.57 5.64 44.66 3.06
130 131 4.395542 AGATCTTCAAGCAAGAAGTGATGC 59.604 41.667 15.13 0.00 44.66 3.91
203 207 6.403866 AGGCAAAACATTTGATGTGACTAA 57.596 33.333 6.99 0.00 44.07 2.24
217 221 8.450578 TGATGTGACTAAATGAATGGATTACC 57.549 34.615 0.00 0.00 0.00 2.85
224 228 4.836125 AATGAATGGATTACCGCACATC 57.164 40.909 0.00 0.00 39.42 3.06
241 245 1.741706 CATCTGTGATGTTGGTCAGCC 59.258 52.381 0.00 0.00 0.00 4.85
242 246 0.036732 TCTGTGATGTTGGTCAGCCC 59.963 55.000 0.00 0.00 0.00 5.19
243 247 0.250858 CTGTGATGTTGGTCAGCCCA 60.251 55.000 0.00 0.00 43.27 5.36
256 260 1.065199 TCAGCCCAATCAGATCACCAC 60.065 52.381 0.00 0.00 0.00 4.16
260 264 2.100252 GCCCAATCAGATCACCACATTG 59.900 50.000 0.00 0.00 0.00 2.82
290 294 4.402155 CCATGTTTCCTAAGCAAGGCATTA 59.598 41.667 0.26 0.00 46.10 1.90
291 295 5.450965 CCATGTTTCCTAAGCAAGGCATTAG 60.451 44.000 0.26 0.00 46.10 1.73
292 296 4.662278 TGTTTCCTAAGCAAGGCATTAGT 58.338 39.130 0.26 0.00 46.10 2.24
293 297 5.076873 TGTTTCCTAAGCAAGGCATTAGTT 58.923 37.500 0.26 0.00 46.10 2.24
294 298 5.048083 TGTTTCCTAAGCAAGGCATTAGTTG 60.048 40.000 0.26 0.00 46.10 3.16
295 299 3.620488 TCCTAAGCAAGGCATTAGTTGG 58.380 45.455 0.26 0.00 46.10 3.77
367 371 9.952188 TTATTGTAACGTTTTGTGATTTGATGA 57.048 25.926 5.91 0.00 0.00 2.92
369 373 8.689251 TTGTAACGTTTTGTGATTTGATGAAA 57.311 26.923 5.91 0.00 0.00 2.69
371 375 9.307121 TGTAACGTTTTGTGATTTGATGAAAAT 57.693 25.926 5.91 0.00 41.33 1.82
375 379 8.760569 ACGTTTTGTGATTTGATGAAAATTACC 58.239 29.630 4.04 0.00 41.69 2.85
376 380 7.944120 CGTTTTGTGATTTGATGAAAATTACCG 59.056 33.333 4.04 0.00 41.69 4.02
377 381 8.760569 GTTTTGTGATTTGATGAAAATTACCGT 58.239 29.630 4.04 0.00 41.69 4.83
379 383 9.619316 TTTGTGATTTGATGAAAATTACCGTAG 57.381 29.630 4.04 0.00 41.69 3.51
380 384 8.554835 TGTGATTTGATGAAAATTACCGTAGA 57.445 30.769 4.04 0.00 41.69 2.59
381 385 9.004717 TGTGATTTGATGAAAATTACCGTAGAA 57.995 29.630 4.04 0.00 41.69 2.10
382 386 9.274065 GTGATTTGATGAAAATTACCGTAGAAC 57.726 33.333 0.00 0.00 38.30 3.01
383 387 9.004717 TGATTTGATGAAAATTACCGTAGAACA 57.995 29.630 0.00 0.00 38.64 3.18
384 388 9.490663 GATTTGATGAAAATTACCGTAGAACAG 57.509 33.333 0.00 0.00 38.64 3.16
386 390 7.972832 TGATGAAAATTACCGTAGAACAGTT 57.027 32.000 0.00 0.00 0.00 3.16
387 391 7.802738 TGATGAAAATTACCGTAGAACAGTTG 58.197 34.615 0.00 0.00 0.00 3.16
388 392 7.442969 TGATGAAAATTACCGTAGAACAGTTGT 59.557 33.333 0.00 0.00 0.00 3.32
401 405 4.732285 AACAGTTGTTCTACAATCTGCG 57.268 40.909 15.51 0.00 40.59 5.18
403 407 2.416547 CAGTTGTTCTACAATCTGCGGG 59.583 50.000 0.00 0.00 40.59 6.13
404 408 2.038557 AGTTGTTCTACAATCTGCGGGT 59.961 45.455 0.00 0.00 40.59 5.28
405 409 2.380084 TGTTCTACAATCTGCGGGTC 57.620 50.000 0.00 0.00 0.00 4.46
406 410 1.621317 TGTTCTACAATCTGCGGGTCA 59.379 47.619 0.00 0.00 0.00 4.02
407 411 2.037902 TGTTCTACAATCTGCGGGTCAA 59.962 45.455 0.00 0.00 0.00 3.18
408 412 3.071479 GTTCTACAATCTGCGGGTCAAA 58.929 45.455 0.00 0.00 0.00 2.69
409 413 3.410631 TCTACAATCTGCGGGTCAAAA 57.589 42.857 0.00 0.00 0.00 2.44
410 414 3.334691 TCTACAATCTGCGGGTCAAAAG 58.665 45.455 0.00 0.00 0.00 2.27
411 415 0.598065 ACAATCTGCGGGTCAAAAGC 59.402 50.000 0.00 0.00 0.00 3.51
412 416 0.597568 CAATCTGCGGGTCAAAAGCA 59.402 50.000 0.00 0.00 39.25 3.91
413 417 1.000385 CAATCTGCGGGTCAAAAGCAA 60.000 47.619 0.00 0.00 40.63 3.91
414 418 0.598065 ATCTGCGGGTCAAAAGCAAC 59.402 50.000 0.00 0.00 40.63 4.17
417 421 0.749649 TGCGGGTCAAAAGCAACAAT 59.250 45.000 0.00 0.00 38.01 2.71
426 430 7.254590 CGGGTCAAAAGCAACAATTTAATTGAA 60.255 33.333 22.53 0.00 42.83 2.69
439 443 7.598493 ACAATTTAATTGAAGTGGAATTGGTCG 59.402 33.333 22.53 0.00 42.83 4.79
456 1988 7.765695 ATTGGTCGATTTATAGCAATTCCAT 57.234 32.000 0.00 0.00 39.99 3.41
543 2077 7.819644 TCTTAACATGCATGATTATGGCATAC 58.180 34.615 32.75 0.00 33.09 2.39
550 2087 7.848223 TGCATGATTATGGCATACAGTATAC 57.152 36.000 6.72 0.00 34.79 1.47
553 2090 7.225538 GCATGATTATGGCATACAGTATACTCC 59.774 40.741 6.72 1.37 34.79 3.85
554 2091 8.481314 CATGATTATGGCATACAGTATACTCCT 58.519 37.037 6.72 0.00 0.00 3.69
621 2158 6.330004 TCATCAATTGTATGGCGCAAATAT 57.670 33.333 10.83 0.00 0.00 1.28
713 2251 3.534554 TGGCTATACACTGACATTGCTG 58.465 45.455 0.00 0.00 0.00 4.41
715 2253 4.161377 TGGCTATACACTGACATTGCTGTA 59.839 41.667 0.00 0.00 35.14 2.74
719 2257 7.201732 GGCTATACACTGACATTGCTGTAAAAT 60.202 37.037 0.00 0.00 35.14 1.82
725 2264 7.862372 ACACTGACATTGCTGTAAAATAAACTG 59.138 33.333 0.00 0.00 35.14 3.16
797 2342 1.448013 GCGGACCCTGTCTAACTGC 60.448 63.158 0.00 0.00 32.47 4.40
861 2406 1.886253 TTGCCATGCCCAAATCACCG 61.886 55.000 0.00 0.00 0.00 4.94
944 2489 0.035056 CACCAGACCAATCCCCTGAC 60.035 60.000 0.00 0.00 0.00 3.51
959 2504 0.391927 CTGACCCGTCTCTCTCGTCT 60.392 60.000 0.00 0.00 0.00 4.18
1194 2739 1.984570 CCTCTGGTCGCTCCCTGAA 60.985 63.158 0.95 0.00 32.77 3.02
1473 3018 4.180946 CACCTCGTCGGCCTCTCG 62.181 72.222 0.00 2.70 35.61 4.04
1743 3288 3.473647 CTCATCCCGCTCCTGGCA 61.474 66.667 0.00 0.00 41.91 4.92
1770 3315 4.819761 GCGCTGCCATCGGAGACA 62.820 66.667 0.00 0.00 42.51 3.41
1992 3554 0.304705 CGAAATCCAATCTTCCCGCG 59.695 55.000 0.00 0.00 0.00 6.46
2210 3772 0.581529 CGTCAAGCTGCGTTTCAAGA 59.418 50.000 0.00 0.00 0.00 3.02
2353 3915 0.108662 TCAACATCATCGTGCTCGCT 60.109 50.000 2.69 0.00 36.96 4.93
2530 4092 1.920325 CCAGGAGGAGGAAGTGGCA 60.920 63.158 0.00 0.00 36.89 4.92
2582 4144 1.361793 GCGGTCGCAATTTGTACCTA 58.638 50.000 10.67 0.00 41.49 3.08
2583 4145 1.326548 GCGGTCGCAATTTGTACCTAG 59.673 52.381 10.67 7.22 41.49 3.02
2589 4151 4.630069 GTCGCAATTTGTACCTAGACACAT 59.370 41.667 0.00 0.00 0.00 3.21
2590 4152 5.808540 GTCGCAATTTGTACCTAGACACATA 59.191 40.000 0.00 0.00 0.00 2.29
2591 4153 5.808540 TCGCAATTTGTACCTAGACACATAC 59.191 40.000 0.00 0.00 0.00 2.39
2592 4154 5.810587 CGCAATTTGTACCTAGACACATACT 59.189 40.000 0.00 0.00 0.00 2.12
2593 4155 6.237835 CGCAATTTGTACCTAGACACATACTG 60.238 42.308 0.00 0.00 0.00 2.74
2660 4229 7.504238 TGGGTATATTTGTCATACACCAATTCC 59.496 37.037 0.00 0.00 32.31 3.01
2670 4245 6.260936 GTCATACACCAATTCCTTCATACCAG 59.739 42.308 0.00 0.00 0.00 4.00
2687 4262 7.827701 TCATACCAGAGTTAGTTGAGTTGTAG 58.172 38.462 0.00 0.00 0.00 2.74
2688 4263 7.450634 TCATACCAGAGTTAGTTGAGTTGTAGT 59.549 37.037 0.00 0.00 0.00 2.73
2689 4264 8.737175 CATACCAGAGTTAGTTGAGTTGTAGTA 58.263 37.037 0.00 0.00 0.00 1.82
2715 4290 1.679032 CCCCGACTTTTCAGGGTGATC 60.679 57.143 0.00 0.00 43.58 2.92
2743 4318 3.057315 AGTTGCTTCATGTTTGGGATTCG 60.057 43.478 0.00 0.00 0.00 3.34
2746 4321 3.320541 TGCTTCATGTTTGGGATTCGTTT 59.679 39.130 0.00 0.00 0.00 3.60
2751 4326 4.022416 TCATGTTTGGGATTCGTTTCAAGG 60.022 41.667 0.00 0.00 0.00 3.61
2769 4344 1.836802 AGGGTTTGAGCTCTGGATCTC 59.163 52.381 16.19 1.30 0.00 2.75
2780 4355 1.361632 TGGATCTCGATGCAGAGCG 59.638 57.895 0.00 0.00 38.12 5.03
2802 4377 3.213506 CAGTGGGTTGATTGACTGAACA 58.786 45.455 0.00 0.00 38.49 3.18
2809 4384 6.206634 TGGGTTGATTGACTGAACAGAAATAC 59.793 38.462 8.87 4.78 0.00 1.89
2810 4385 6.431234 GGGTTGATTGACTGAACAGAAATACT 59.569 38.462 8.87 0.00 0.00 2.12
2811 4386 7.361286 GGGTTGATTGACTGAACAGAAATACTC 60.361 40.741 8.87 1.93 0.00 2.59
2812 4387 7.389053 GGTTGATTGACTGAACAGAAATACTCT 59.611 37.037 8.87 0.00 33.23 3.24
2813 4388 9.424319 GTTGATTGACTGAACAGAAATACTCTA 57.576 33.333 8.87 0.00 31.12 2.43
2814 4389 9.645059 TTGATTGACTGAACAGAAATACTCTAG 57.355 33.333 8.87 0.00 31.12 2.43
2815 4390 8.807118 TGATTGACTGAACAGAAATACTCTAGT 58.193 33.333 8.87 0.00 31.12 2.57
2816 4391 9.646427 GATTGACTGAACAGAAATACTCTAGTT 57.354 33.333 8.87 0.00 31.12 2.24
2818 4393 9.832445 TTGACTGAACAGAAATACTCTAGTTTT 57.168 29.630 8.87 0.00 31.12 2.43
2836 4411 9.635520 TCTAGTTTTCAGTTTAGGTAGATTTCG 57.364 33.333 0.00 0.00 0.00 3.46
2841 4416 6.540438 TCAGTTTAGGTAGATTTCGGTCAT 57.460 37.500 0.00 0.00 0.00 3.06
2846 4421 4.657436 AGGTAGATTTCGGTCATCTGAC 57.343 45.455 1.59 1.59 44.04 3.51
2850 4425 5.520649 GGTAGATTTCGGTCATCTGACTTTC 59.479 44.000 9.98 1.81 44.20 2.62
2851 4426 4.508662 AGATTTCGGTCATCTGACTTTCC 58.491 43.478 9.98 0.00 44.20 3.13
2853 4428 5.422331 AGATTTCGGTCATCTGACTTTCCTA 59.578 40.000 9.98 0.00 44.20 2.94
2854 4429 4.720649 TTCGGTCATCTGACTTTCCTAG 57.279 45.455 9.98 0.00 44.20 3.02
2861 4437 2.885616 TCTGACTTTCCTAGTTCGGGT 58.114 47.619 0.00 0.00 37.17 5.28
2873 4449 3.121738 AGTTCGGGTCAGTCGATTTTT 57.878 42.857 0.00 0.00 36.49 1.94
2874 4450 2.806244 AGTTCGGGTCAGTCGATTTTTG 59.194 45.455 0.00 0.00 36.49 2.44
2876 4452 3.114668 TCGGGTCAGTCGATTTTTGAA 57.885 42.857 0.00 0.00 0.00 2.69
2877 4453 3.670625 TCGGGTCAGTCGATTTTTGAAT 58.329 40.909 0.00 0.00 0.00 2.57
2878 4454 3.682858 TCGGGTCAGTCGATTTTTGAATC 59.317 43.478 0.00 0.00 0.00 2.52
2880 4456 4.094887 CGGGTCAGTCGATTTTTGAATCAT 59.905 41.667 0.00 0.00 0.00 2.45
2886 4462 6.032094 CAGTCGATTTTTGAATCATGGAAGG 58.968 40.000 0.00 0.00 0.00 3.46
2908 4484 1.151810 AGGAAGGGCCTCACCAGAA 60.152 57.895 24.82 0.00 46.97 3.02
2913 4489 1.149101 AGGGCCTCACCAGAAAGAAA 58.851 50.000 0.00 0.00 42.05 2.52
2917 4493 3.425659 GGCCTCACCAGAAAGAAAGAAT 58.574 45.455 0.00 0.00 38.86 2.40
2923 4499 3.575687 CACCAGAAAGAAAGAATGGGCTT 59.424 43.478 0.00 0.00 35.26 4.35
2924 4500 3.829026 ACCAGAAAGAAAGAATGGGCTTC 59.171 43.478 0.00 0.00 35.26 3.86
2925 4501 3.119708 CCAGAAAGAAAGAATGGGCTTCG 60.120 47.826 0.00 0.00 38.98 3.79
2946 4523 4.844085 TCGGTCATCACCCCATTATCTATT 59.156 41.667 0.00 0.00 40.01 1.73
2950 4527 7.663905 CGGTCATCACCCCATTATCTATTTTAA 59.336 37.037 0.00 0.00 40.01 1.52
2952 4529 9.014297 GTCATCACCCCATTATCTATTTTAAGG 57.986 37.037 0.00 0.00 0.00 2.69
3020 4597 1.581447 GCGGTGGCTGGAGAAAAAG 59.419 57.895 0.00 0.00 35.83 2.27
3023 4600 0.884514 GGTGGCTGGAGAAAAAGCTC 59.115 55.000 0.00 0.00 39.46 4.09
3025 4602 0.606401 TGGCTGGAGAAAAAGCTCGG 60.606 55.000 0.00 0.00 39.46 4.63
3026 4603 1.503994 GCTGGAGAAAAAGCTCGGC 59.496 57.895 0.00 0.00 36.47 5.54
3028 4605 0.951040 CTGGAGAAAAAGCTCGGCGT 60.951 55.000 6.85 0.00 35.74 5.68
3032 4609 1.964373 GAAAAAGCTCGGCGTGGGA 60.964 57.895 6.85 0.00 0.00 4.37
3033 4610 1.912371 GAAAAAGCTCGGCGTGGGAG 61.912 60.000 6.85 0.00 34.62 4.30
3096 4675 2.271173 GTGGTTTAGGGGAGGGCG 59.729 66.667 0.00 0.00 0.00 6.13
3098 4677 4.501285 GGTTTAGGGGAGGGCGGC 62.501 72.222 0.00 0.00 0.00 6.53
3185 4769 1.374252 GCGTGCGGGAAGAAGAAGA 60.374 57.895 0.00 0.00 0.00 2.87
3187 4771 0.790814 CGTGCGGGAAGAAGAAGAAC 59.209 55.000 0.00 0.00 0.00 3.01
3193 4777 1.346722 GGGAAGAAGAAGAACACCCGA 59.653 52.381 0.00 0.00 0.00 5.14
3194 4778 2.613223 GGGAAGAAGAAGAACACCCGAG 60.613 54.545 0.00 0.00 0.00 4.63
3195 4779 2.070028 GAAGAAGAAGAACACCCGAGC 58.930 52.381 0.00 0.00 0.00 5.03
3196 4780 1.048601 AGAAGAAGAACACCCGAGCA 58.951 50.000 0.00 0.00 0.00 4.26
3197 4781 1.416401 AGAAGAAGAACACCCGAGCAA 59.584 47.619 0.00 0.00 0.00 3.91
3199 4783 2.100605 AGAAGAACACCCGAGCAATC 57.899 50.000 0.00 0.00 0.00 2.67
3201 4785 1.734465 GAAGAACACCCGAGCAATCTG 59.266 52.381 0.00 0.00 0.00 2.90
3206 4790 3.350219 ACACCCGAGCAATCTGTTTAT 57.650 42.857 0.00 0.00 0.00 1.40
3209 4793 1.949525 CCCGAGCAATCTGTTTATGGG 59.050 52.381 0.00 0.00 0.00 4.00
3212 4796 3.694072 CCGAGCAATCTGTTTATGGGAAA 59.306 43.478 0.00 0.00 0.00 3.13
3213 4797 4.201950 CCGAGCAATCTGTTTATGGGAAAG 60.202 45.833 0.00 0.00 0.00 2.62
3214 4798 4.396166 CGAGCAATCTGTTTATGGGAAAGT 59.604 41.667 0.00 0.00 0.00 2.66
3238 4822 1.909302 TGGGAGGAGGAAGACACAATC 59.091 52.381 0.00 0.00 0.00 2.67
3241 4825 2.834549 GGAGGAGGAAGACACAATCTGA 59.165 50.000 0.00 0.00 37.88 3.27
3247 4831 1.996191 GAAGACACAATCTGAGCCGTC 59.004 52.381 0.00 0.00 37.88 4.79
3248 4832 0.247736 AGACACAATCTGAGCCGTCC 59.752 55.000 0.00 0.00 35.81 4.79
3252 4836 0.389948 ACAATCTGAGCCGTCCGTTC 60.390 55.000 0.00 0.00 0.00 3.95
3258 4842 1.002251 CTGAGCCGTCCGTTCTCTATC 60.002 57.143 7.41 0.00 0.00 2.08
3269 4853 3.581755 CGTTCTCTATCCAACGGTTCAA 58.418 45.455 0.00 0.00 41.36 2.69
3277 4861 4.718940 ATCCAACGGTTCAAATTCATCC 57.281 40.909 0.00 0.00 0.00 3.51
3278 4862 2.823154 TCCAACGGTTCAAATTCATCCC 59.177 45.455 0.00 0.00 0.00 3.85
3279 4863 2.560542 CCAACGGTTCAAATTCATCCCA 59.439 45.455 0.00 0.00 0.00 4.37
3282 4866 1.134946 CGGTTCAAATTCATCCCAGCC 59.865 52.381 0.00 0.00 0.00 4.85
3287 4871 5.247862 GTTCAAATTCATCCCAGCCAAATT 58.752 37.500 0.00 0.00 0.00 1.82
3288 4872 4.834534 TCAAATTCATCCCAGCCAAATTG 58.165 39.130 0.00 0.00 0.00 2.32
3294 4878 2.905415 TCCCAGCCAAATTGACTGAT 57.095 45.000 10.88 0.00 33.10 2.90
3297 4881 2.167075 CCCAGCCAAATTGACTGATTCC 59.833 50.000 10.88 0.00 33.10 3.01
3301 4885 4.687483 CAGCCAAATTGACTGATTCCAAAC 59.313 41.667 3.06 0.00 33.10 2.93
3302 4886 3.674753 GCCAAATTGACTGATTCCAAACG 59.325 43.478 0.00 0.00 0.00 3.60
3303 4887 4.558496 GCCAAATTGACTGATTCCAAACGA 60.558 41.667 0.00 0.00 0.00 3.85
3304 4888 5.156355 CCAAATTGACTGATTCCAAACGAG 58.844 41.667 0.00 0.00 0.00 4.18
3305 4889 5.048782 CCAAATTGACTGATTCCAAACGAGA 60.049 40.000 0.00 0.00 0.00 4.04
3338 4922 3.064900 GCTCCTAGCCATTCCCAATAG 57.935 52.381 0.00 0.00 34.48 1.73
3339 4923 2.373502 GCTCCTAGCCATTCCCAATAGT 59.626 50.000 0.00 0.00 34.48 2.12
3340 4924 3.181439 GCTCCTAGCCATTCCCAATAGTT 60.181 47.826 0.00 0.00 34.48 2.24
3341 4925 4.689983 GCTCCTAGCCATTCCCAATAGTTT 60.690 45.833 0.00 0.00 34.48 2.66
3342 4926 5.449553 CTCCTAGCCATTCCCAATAGTTTT 58.550 41.667 0.00 0.00 0.00 2.43
3343 4927 5.837829 TCCTAGCCATTCCCAATAGTTTTT 58.162 37.500 0.00 0.00 0.00 1.94
3344 4928 5.891551 TCCTAGCCATTCCCAATAGTTTTTC 59.108 40.000 0.00 0.00 0.00 2.29
3345 4929 5.893824 CCTAGCCATTCCCAATAGTTTTTCT 59.106 40.000 0.00 0.00 0.00 2.52
3346 4930 6.381133 CCTAGCCATTCCCAATAGTTTTTCTT 59.619 38.462 0.00 0.00 0.00 2.52
3347 4931 6.286240 AGCCATTCCCAATAGTTTTTCTTC 57.714 37.500 0.00 0.00 0.00 2.87
3348 4932 5.779771 AGCCATTCCCAATAGTTTTTCTTCA 59.220 36.000 0.00 0.00 0.00 3.02
3349 4933 6.071165 AGCCATTCCCAATAGTTTTTCTTCAG 60.071 38.462 0.00 0.00 0.00 3.02
3350 4934 6.101997 CCATTCCCAATAGTTTTTCTTCAGC 58.898 40.000 0.00 0.00 0.00 4.26
3351 4935 6.295236 CCATTCCCAATAGTTTTTCTTCAGCA 60.295 38.462 0.00 0.00 0.00 4.41
3352 4936 6.723298 TTCCCAATAGTTTTTCTTCAGCAA 57.277 33.333 0.00 0.00 0.00 3.91
3353 4937 6.723298 TCCCAATAGTTTTTCTTCAGCAAA 57.277 33.333 0.00 0.00 0.00 3.68
3354 4938 6.748132 TCCCAATAGTTTTTCTTCAGCAAAG 58.252 36.000 0.00 0.00 36.22 2.77
3355 4939 6.323739 TCCCAATAGTTTTTCTTCAGCAAAGT 59.676 34.615 0.00 0.00 36.31 2.66
3356 4940 6.421801 CCCAATAGTTTTTCTTCAGCAAAGTG 59.578 38.462 0.00 0.00 36.31 3.16
3357 4941 6.074142 CCAATAGTTTTTCTTCAGCAAAGTGC 60.074 38.462 0.00 0.00 45.46 4.40
3370 4954 3.248266 GCAAAGTGCATGAAGATTGTCC 58.752 45.455 0.00 0.00 44.26 4.02
3371 4955 3.057033 GCAAAGTGCATGAAGATTGTCCT 60.057 43.478 0.00 0.00 44.26 3.85
3372 4956 4.482386 CAAAGTGCATGAAGATTGTCCTG 58.518 43.478 0.00 0.00 0.00 3.86
3373 4957 2.089980 AGTGCATGAAGATTGTCCTGC 58.910 47.619 0.00 0.00 39.00 4.85
3401 4985 2.979813 GTTCCATTTAAAGTGCAGCACG 59.020 45.455 19.96 3.67 39.64 5.34
3444 5028 2.222213 CGACAGCAAACATGTTCCGTTA 59.778 45.455 12.39 0.00 0.00 3.18
3452 5038 5.455525 GCAAACATGTTCCGTTATGCTATTC 59.544 40.000 18.83 0.00 32.52 1.75
3474 5077 4.780021 TCCAGAGCCAGAGTCTTTTTCTAT 59.220 41.667 0.00 0.00 0.00 1.98
3476 5079 4.803088 CAGAGCCAGAGTCTTTTTCTATCG 59.197 45.833 0.00 0.00 0.00 2.92
3480 5083 5.104735 AGCCAGAGTCTTTTTCTATCGGATT 60.105 40.000 0.00 0.00 0.00 3.01
3526 5129 7.553881 AATGAAACGAAAACTTCTTCTGAGA 57.446 32.000 0.00 0.00 0.00 3.27
3527 5130 6.978343 TGAAACGAAAACTTCTTCTGAGAA 57.022 33.333 0.00 0.00 39.54 2.87
3528 5131 7.553881 TGAAACGAAAACTTCTTCTGAGAAT 57.446 32.000 0.00 0.00 40.93 2.40
3529 5132 7.409697 TGAAACGAAAACTTCTTCTGAGAATG 58.590 34.615 0.00 0.00 40.93 2.67
3530 5133 7.279981 TGAAACGAAAACTTCTTCTGAGAATGA 59.720 33.333 0.00 0.00 40.93 2.57
3531 5134 7.553881 AACGAAAACTTCTTCTGAGAATGAA 57.446 32.000 0.00 1.56 40.93 2.57
3532 5135 7.553881 ACGAAAACTTCTTCTGAGAATGAAA 57.446 32.000 0.00 0.00 40.93 2.69
3533 5136 7.634522 ACGAAAACTTCTTCTGAGAATGAAAG 58.365 34.615 0.00 3.28 40.93 2.62
3534 5137 6.576684 CGAAAACTTCTTCTGAGAATGAAAGC 59.423 38.462 0.00 0.00 40.93 3.51
3535 5138 7.519649 CGAAAACTTCTTCTGAGAATGAAAGCT 60.520 37.037 0.00 0.00 40.93 3.74
3536 5139 6.799926 AACTTCTTCTGAGAATGAAAGCTC 57.200 37.500 0.00 0.00 40.93 4.09
3537 5140 5.862845 ACTTCTTCTGAGAATGAAAGCTCA 58.137 37.500 0.00 0.00 40.93 4.26
3538 5141 5.700373 ACTTCTTCTGAGAATGAAAGCTCAC 59.300 40.000 0.00 0.00 40.93 3.51
3539 5142 4.573900 TCTTCTGAGAATGAAAGCTCACC 58.426 43.478 0.00 0.00 36.31 4.02
3540 5143 4.040829 TCTTCTGAGAATGAAAGCTCACCA 59.959 41.667 0.00 0.00 36.31 4.17
3541 5144 4.564782 TCTGAGAATGAAAGCTCACCAT 57.435 40.909 0.00 0.00 36.31 3.55
3542 5145 5.682234 TCTGAGAATGAAAGCTCACCATA 57.318 39.130 0.00 0.00 36.31 2.74
3543 5146 5.423015 TCTGAGAATGAAAGCTCACCATAC 58.577 41.667 0.00 0.00 36.31 2.39
3544 5147 5.188555 TCTGAGAATGAAAGCTCACCATACT 59.811 40.000 0.00 0.00 36.31 2.12
3545 5148 6.381133 TCTGAGAATGAAAGCTCACCATACTA 59.619 38.462 0.00 0.00 36.31 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.028284 TGAAGAGTGTATGAGCATGATATCATA 57.972 33.333 17.77 3.14 34.26 2.15
80 81 2.151202 TGCGTTGAGTCCAAATTCTCC 58.849 47.619 0.00 0.00 33.49 3.71
99 100 3.861276 TGCTTGAAGATCTTGCCATTG 57.139 42.857 14.00 3.48 0.00 2.82
110 111 3.501062 CAGCATCACTTCTTGCTTGAAGA 59.499 43.478 20.43 3.91 46.71 2.87
111 112 3.366070 CCAGCATCACTTCTTGCTTGAAG 60.366 47.826 14.61 14.61 46.71 3.02
114 115 2.156917 TCCAGCATCACTTCTTGCTTG 58.843 47.619 0.00 0.00 46.71 4.01
117 118 3.863142 ATTTCCAGCATCACTTCTTGC 57.137 42.857 0.00 0.00 39.17 4.01
118 119 5.381174 TGAATTTCCAGCATCACTTCTTG 57.619 39.130 0.00 0.00 0.00 3.02
119 120 4.461781 CCTGAATTTCCAGCATCACTTCTT 59.538 41.667 0.00 0.00 32.97 2.52
122 123 3.771216 ACCTGAATTTCCAGCATCACTT 58.229 40.909 0.00 0.00 32.97 3.16
124 125 3.507233 TGAACCTGAATTTCCAGCATCAC 59.493 43.478 0.00 0.00 32.97 3.06
126 127 4.381292 CCTTGAACCTGAATTTCCAGCATC 60.381 45.833 0.00 0.00 32.97 3.91
128 129 2.892852 CCTTGAACCTGAATTTCCAGCA 59.107 45.455 0.00 0.00 32.97 4.41
130 131 5.072741 TCTTCCTTGAACCTGAATTTCCAG 58.927 41.667 0.00 0.00 0.00 3.86
133 134 7.661040 TCAAATCTTCCTTGAACCTGAATTTC 58.339 34.615 0.00 0.00 29.93 2.17
203 207 4.276678 CAGATGTGCGGTAATCCATTCATT 59.723 41.667 0.00 0.00 0.00 2.57
217 221 1.129251 GACCAACATCACAGATGTGCG 59.871 52.381 12.86 8.73 45.25 5.34
224 228 2.559785 GGGCTGACCAACATCACAG 58.440 57.895 0.00 0.00 39.85 3.66
341 345 9.952188 TCATCAAATCACAAAACGTTACAATAA 57.048 25.926 0.00 0.00 0.00 1.40
342 346 9.952188 TTCATCAAATCACAAAACGTTACAATA 57.048 25.926 0.00 0.00 0.00 1.90
343 347 8.864069 TTCATCAAATCACAAAACGTTACAAT 57.136 26.923 0.00 0.00 0.00 2.71
345 349 8.689251 TTTTCATCAAATCACAAAACGTTACA 57.311 26.923 0.00 0.00 0.00 2.41
349 353 8.760569 GGTAATTTTCATCAAATCACAAAACGT 58.239 29.630 0.00 0.00 33.60 3.99
350 354 7.944120 CGGTAATTTTCATCAAATCACAAAACG 59.056 33.333 0.00 0.00 33.60 3.60
351 355 8.760569 ACGGTAATTTTCATCAAATCACAAAAC 58.239 29.630 0.00 0.00 33.60 2.43
352 356 8.879342 ACGGTAATTTTCATCAAATCACAAAA 57.121 26.923 0.00 0.00 33.60 2.44
353 357 9.619316 CTACGGTAATTTTCATCAAATCACAAA 57.381 29.630 0.00 0.00 33.60 2.83
355 359 8.554835 TCTACGGTAATTTTCATCAAATCACA 57.445 30.769 0.00 0.00 33.60 3.58
356 360 9.274065 GTTCTACGGTAATTTTCATCAAATCAC 57.726 33.333 0.00 0.00 33.60 3.06
357 361 9.004717 TGTTCTACGGTAATTTTCATCAAATCA 57.995 29.630 0.00 0.00 33.60 2.57
358 362 9.490663 CTGTTCTACGGTAATTTTCATCAAATC 57.509 33.333 0.00 0.00 33.60 2.17
359 363 9.010029 ACTGTTCTACGGTAATTTTCATCAAAT 57.990 29.630 0.00 0.00 35.60 2.32
361 365 7.972832 ACTGTTCTACGGTAATTTTCATCAA 57.027 32.000 0.00 0.00 35.60 2.57
362 366 7.442969 ACAACTGTTCTACGGTAATTTTCATCA 59.557 33.333 0.00 0.00 36.53 3.07
363 367 7.803724 ACAACTGTTCTACGGTAATTTTCATC 58.196 34.615 0.00 0.00 36.53 2.92
364 368 7.739498 ACAACTGTTCTACGGTAATTTTCAT 57.261 32.000 0.00 0.00 36.53 2.57
365 369 7.556733 AACAACTGTTCTACGGTAATTTTCA 57.443 32.000 0.00 0.00 36.53 2.69
380 384 3.498397 CCGCAGATTGTAGAACAACTGTT 59.502 43.478 16.42 0.00 41.40 3.16
381 385 3.067106 CCGCAGATTGTAGAACAACTGT 58.933 45.455 16.42 0.00 41.40 3.55
382 386 2.416547 CCCGCAGATTGTAGAACAACTG 59.583 50.000 13.37 13.37 41.40 3.16
383 387 2.038557 ACCCGCAGATTGTAGAACAACT 59.961 45.455 0.00 0.00 41.40 3.16
384 388 2.415512 GACCCGCAGATTGTAGAACAAC 59.584 50.000 0.00 0.00 41.40 3.32
386 390 1.621317 TGACCCGCAGATTGTAGAACA 59.379 47.619 0.00 0.00 0.00 3.18
387 391 2.380084 TGACCCGCAGATTGTAGAAC 57.620 50.000 0.00 0.00 0.00 3.01
388 392 3.410631 TTTGACCCGCAGATTGTAGAA 57.589 42.857 0.00 0.00 0.00 2.10
390 394 2.159517 GCTTTTGACCCGCAGATTGTAG 60.160 50.000 0.00 0.00 0.00 2.74
391 395 1.810151 GCTTTTGACCCGCAGATTGTA 59.190 47.619 0.00 0.00 0.00 2.41
393 397 0.597568 TGCTTTTGACCCGCAGATTG 59.402 50.000 0.00 0.00 0.00 2.67
394 398 1.000274 GTTGCTTTTGACCCGCAGATT 60.000 47.619 0.00 0.00 34.82 2.40
397 401 0.102120 TTGTTGCTTTTGACCCGCAG 59.898 50.000 0.00 0.00 34.82 5.18
398 402 0.749649 ATTGTTGCTTTTGACCCGCA 59.250 45.000 0.00 0.00 0.00 5.69
399 403 1.864565 AATTGTTGCTTTTGACCCGC 58.135 45.000 0.00 0.00 0.00 6.13
401 405 7.489574 TCAATTAAATTGTTGCTTTTGACCC 57.510 32.000 0.00 0.00 41.02 4.46
403 407 9.424659 CACTTCAATTAAATTGTTGCTTTTGAC 57.575 29.630 0.00 0.00 41.02 3.18
404 408 8.610896 CCACTTCAATTAAATTGTTGCTTTTGA 58.389 29.630 0.00 0.00 41.02 2.69
405 409 8.610896 TCCACTTCAATTAAATTGTTGCTTTTG 58.389 29.630 0.00 0.00 41.02 2.44
406 410 8.729805 TCCACTTCAATTAAATTGTTGCTTTT 57.270 26.923 0.00 0.00 41.02 2.27
407 411 8.729805 TTCCACTTCAATTAAATTGTTGCTTT 57.270 26.923 0.00 0.00 41.02 3.51
408 412 8.907222 ATTCCACTTCAATTAAATTGTTGCTT 57.093 26.923 0.00 0.00 41.02 3.91
409 413 8.776470 CAATTCCACTTCAATTAAATTGTTGCT 58.224 29.630 0.00 0.00 41.02 3.91
410 414 8.016801 CCAATTCCACTTCAATTAAATTGTTGC 58.983 33.333 0.00 0.00 41.02 4.17
411 415 9.054922 ACCAATTCCACTTCAATTAAATTGTTG 57.945 29.630 0.00 0.00 41.02 3.33
412 416 9.271828 GACCAATTCCACTTCAATTAAATTGTT 57.728 29.630 0.00 0.00 41.02 2.83
413 417 7.598493 CGACCAATTCCACTTCAATTAAATTGT 59.402 33.333 0.00 0.00 41.02 2.71
414 418 7.812191 TCGACCAATTCCACTTCAATTAAATTG 59.188 33.333 0.00 0.00 41.57 2.32
417 421 6.885952 TCGACCAATTCCACTTCAATTAAA 57.114 33.333 0.00 0.00 0.00 1.52
426 430 5.680619 TGCTATAAATCGACCAATTCCACT 58.319 37.500 0.00 0.00 0.00 4.00
439 443 9.507329 TCTTGGAGTATGGAATTGCTATAAATC 57.493 33.333 0.00 0.00 0.00 2.17
456 1988 5.949354 CCCATTTGGTTTATGTCTTGGAGTA 59.051 40.000 0.00 0.00 0.00 2.59
663 2201 8.325477 AGCTTATTTTCTAGTAGGACTTCCAT 57.675 34.615 0.00 0.00 38.89 3.41
713 2251 9.821662 GGAATGTCAGTGTACAGTTTATTTTAC 57.178 33.333 0.00 0.00 31.70 2.01
715 2253 7.724061 AGGGAATGTCAGTGTACAGTTTATTTT 59.276 33.333 0.00 0.00 31.70 1.82
719 2257 5.818678 AGGGAATGTCAGTGTACAGTTTA 57.181 39.130 0.00 0.00 31.70 2.01
725 2264 7.573283 GCTTTTTCTAAGGGAATGTCAGTGTAC 60.573 40.741 0.00 0.00 33.53 2.90
797 2342 6.410942 TCTGGTGATGATACTCCTGTATTG 57.589 41.667 0.00 0.00 39.29 1.90
805 2350 4.065321 CAGGGTTCTGGTGATGATACTC 57.935 50.000 0.00 0.00 37.36 2.59
861 2406 4.254492 GGAAGTTGCGGGAGATATTATCC 58.746 47.826 0.00 0.28 35.99 2.59
944 2489 1.820481 GGGAGACGAGAGAGACGGG 60.820 68.421 0.00 0.00 34.93 5.28
1523 3068 3.466791 ATCTTGGGGATGGCGAGCG 62.467 63.158 0.00 0.00 32.69 5.03
1623 3168 1.295423 GCTCGCCTTGTCCCAGTAA 59.705 57.895 0.00 0.00 0.00 2.24
1948 3493 3.665675 ATCACCTGCGGGCGAAGAC 62.666 63.158 12.89 0.00 35.63 3.01
1970 3515 2.741878 GCGGGAAGATTGGATTTCGAGA 60.742 50.000 0.00 0.00 0.00 4.04
1971 3516 1.599542 GCGGGAAGATTGGATTTCGAG 59.400 52.381 0.00 0.00 0.00 4.04
2508 4070 2.685380 CTTCCTCCTCCTGGGCGT 60.685 66.667 0.00 0.00 34.39 5.68
2530 4092 2.125512 CGCTACTCGGCCTTGCTT 60.126 61.111 0.00 0.00 33.78 3.91
2582 4144 6.758886 GTACTAGGTACGTACAGTATGTGTCT 59.241 42.308 26.02 13.06 38.48 3.41
2583 4145 6.535150 TGTACTAGGTACGTACAGTATGTGTC 59.465 42.308 26.02 13.46 45.42 3.67
2592 4154 5.530915 ACAACAACTGTACTAGGTACGTACA 59.469 40.000 26.02 6.47 43.41 2.90
2593 4155 6.002062 ACAACAACTGTACTAGGTACGTAC 57.998 41.667 17.56 17.56 41.41 3.67
2660 4229 7.155328 ACAACTCAACTAACTCTGGTATGAAG 58.845 38.462 0.00 0.00 0.00 3.02
2670 4245 9.363763 GGGTTTATACTACAACTCAACTAACTC 57.636 37.037 0.00 0.00 0.00 3.01
2687 4262 3.943381 CCTGAAAAGTCGGGGGTTTATAC 59.057 47.826 0.00 0.00 45.56 1.47
2688 4263 4.224991 CCTGAAAAGTCGGGGGTTTATA 57.775 45.455 0.00 0.00 45.56 0.98
2689 4264 3.081710 CCTGAAAAGTCGGGGGTTTAT 57.918 47.619 0.00 0.00 45.56 1.40
2715 4290 4.925054 CCCAAACATGAAGCAACTACAATG 59.075 41.667 0.00 0.00 0.00 2.82
2743 4318 2.294512 CCAGAGCTCAAACCCTTGAAAC 59.705 50.000 17.77 0.00 41.05 2.78
2746 4321 1.434188 TCCAGAGCTCAAACCCTTGA 58.566 50.000 17.77 0.00 39.30 3.02
2751 4326 1.478510 TCGAGATCCAGAGCTCAAACC 59.521 52.381 17.77 0.73 43.57 3.27
2780 4355 1.896220 TCAGTCAATCAACCCACTGC 58.104 50.000 0.00 0.00 36.90 4.40
2782 4357 3.136443 TCTGTTCAGTCAATCAACCCACT 59.864 43.478 0.00 0.00 0.00 4.00
2783 4358 3.476552 TCTGTTCAGTCAATCAACCCAC 58.523 45.455 0.00 0.00 0.00 4.61
2810 4385 9.635520 CGAAATCTACCTAAACTGAAAACTAGA 57.364 33.333 0.00 0.00 0.00 2.43
2811 4386 8.870879 CCGAAATCTACCTAAACTGAAAACTAG 58.129 37.037 0.00 0.00 0.00 2.57
2812 4387 8.370182 ACCGAAATCTACCTAAACTGAAAACTA 58.630 33.333 0.00 0.00 0.00 2.24
2813 4388 7.222161 ACCGAAATCTACCTAAACTGAAAACT 58.778 34.615 0.00 0.00 0.00 2.66
2814 4389 7.172019 TGACCGAAATCTACCTAAACTGAAAAC 59.828 37.037 0.00 0.00 0.00 2.43
2815 4390 7.218614 TGACCGAAATCTACCTAAACTGAAAA 58.781 34.615 0.00 0.00 0.00 2.29
2816 4391 6.761312 TGACCGAAATCTACCTAAACTGAAA 58.239 36.000 0.00 0.00 0.00 2.69
2817 4392 6.349243 TGACCGAAATCTACCTAAACTGAA 57.651 37.500 0.00 0.00 0.00 3.02
2818 4393 5.988310 TGACCGAAATCTACCTAAACTGA 57.012 39.130 0.00 0.00 0.00 3.41
2827 4402 5.520649 GGAAAGTCAGATGACCGAAATCTAC 59.479 44.000 9.31 0.00 45.85 2.59
2830 4405 4.508662 AGGAAAGTCAGATGACCGAAATC 58.491 43.478 9.31 1.96 45.85 2.17
2833 4408 4.087182 ACTAGGAAAGTCAGATGACCGAA 58.913 43.478 9.31 0.00 45.85 4.30
2834 4409 3.698289 ACTAGGAAAGTCAGATGACCGA 58.302 45.455 9.31 0.00 45.85 4.69
2835 4410 4.425520 GAACTAGGAAAGTCAGATGACCG 58.574 47.826 9.31 0.00 45.85 4.79
2836 4411 4.425520 CGAACTAGGAAAGTCAGATGACC 58.574 47.826 9.31 0.00 45.85 4.02
2841 4416 2.824341 GACCCGAACTAGGAAAGTCAGA 59.176 50.000 0.00 0.00 37.50 3.27
2846 4421 2.415625 CGACTGACCCGAACTAGGAAAG 60.416 54.545 0.00 0.00 0.00 2.62
2850 4425 1.390565 ATCGACTGACCCGAACTAGG 58.609 55.000 0.00 0.00 39.62 3.02
2851 4426 3.505464 AAATCGACTGACCCGAACTAG 57.495 47.619 0.00 0.00 39.62 2.57
2853 4428 2.806244 CAAAAATCGACTGACCCGAACT 59.194 45.455 0.00 0.00 39.62 3.01
2854 4429 2.803956 TCAAAAATCGACTGACCCGAAC 59.196 45.455 0.00 0.00 39.62 3.95
2861 4437 6.127925 CCTTCCATGATTCAAAAATCGACTGA 60.128 38.462 0.00 0.00 43.61 3.41
2873 4449 4.080129 CCTTCCTTCTCCTTCCATGATTCA 60.080 45.833 0.00 0.00 0.00 2.57
2874 4450 4.459330 CCTTCCTTCTCCTTCCATGATTC 58.541 47.826 0.00 0.00 0.00 2.52
2876 4452 2.782341 CCCTTCCTTCTCCTTCCATGAT 59.218 50.000 0.00 0.00 0.00 2.45
2877 4453 2.200081 CCCTTCCTTCTCCTTCCATGA 58.800 52.381 0.00 0.00 0.00 3.07
2878 4454 1.409381 GCCCTTCCTTCTCCTTCCATG 60.409 57.143 0.00 0.00 0.00 3.66
2880 4456 1.208165 GGCCCTTCCTTCTCCTTCCA 61.208 60.000 0.00 0.00 0.00 3.53
2905 4481 3.084786 CCGAAGCCCATTCTTTCTTTCT 58.915 45.455 0.00 0.00 35.61 2.52
2906 4482 2.820197 ACCGAAGCCCATTCTTTCTTTC 59.180 45.455 0.00 0.00 35.61 2.62
2908 4484 2.224769 TGACCGAAGCCCATTCTTTCTT 60.225 45.455 0.00 0.00 35.61 2.52
2913 4489 0.911769 TGATGACCGAAGCCCATTCT 59.088 50.000 0.00 0.00 35.61 2.40
2917 4493 2.668632 GGTGATGACCGAAGCCCA 59.331 61.111 0.00 0.00 30.61 5.36
2923 4499 2.689658 AGATAATGGGGTGATGACCGA 58.310 47.619 0.00 0.00 44.23 4.69
2924 4500 4.826274 ATAGATAATGGGGTGATGACCG 57.174 45.455 0.00 0.00 44.23 4.79
2925 4501 8.934023 TTAAAATAGATAATGGGGTGATGACC 57.066 34.615 0.00 0.00 42.27 4.02
2946 4523 0.781278 CCCCCACCCTGAACCTTAAA 59.219 55.000 0.00 0.00 0.00 1.52
3001 4578 1.866853 CTTTTTCTCCAGCCACCGCC 61.867 60.000 0.00 0.00 34.57 6.13
3002 4579 1.581447 CTTTTTCTCCAGCCACCGC 59.419 57.895 0.00 0.00 0.00 5.68
3003 4580 0.890996 AGCTTTTTCTCCAGCCACCG 60.891 55.000 0.00 0.00 36.62 4.94
3004 4581 0.884514 GAGCTTTTTCTCCAGCCACC 59.115 55.000 0.00 0.00 36.62 4.61
3006 4583 0.606401 CCGAGCTTTTTCTCCAGCCA 60.606 55.000 0.00 0.00 36.62 4.75
3007 4584 1.927608 GCCGAGCTTTTTCTCCAGCC 61.928 60.000 0.00 0.00 36.62 4.85
3009 4586 0.951040 ACGCCGAGCTTTTTCTCCAG 60.951 55.000 0.00 0.00 0.00 3.86
3010 4587 1.070786 ACGCCGAGCTTTTTCTCCA 59.929 52.632 0.00 0.00 0.00 3.86
3012 4589 1.497722 CCACGCCGAGCTTTTTCTC 59.502 57.895 0.00 0.00 0.00 2.87
3015 4592 1.966451 CTCCCACGCCGAGCTTTTT 60.966 57.895 0.00 0.00 0.00 1.94
3016 4593 2.358737 CTCCCACGCCGAGCTTTT 60.359 61.111 0.00 0.00 0.00 2.27
3037 4614 2.925170 CCCGGCCATCCCTCTAGG 60.925 72.222 2.24 0.00 0.00 3.02
3078 4657 2.681591 GCCCTCCCCTAAACCACC 59.318 66.667 0.00 0.00 0.00 4.61
3080 4659 3.012722 CCGCCCTCCCCTAAACCA 61.013 66.667 0.00 0.00 0.00 3.67
3098 4677 4.821589 GCTCCCTCAACCGCCTCG 62.822 72.222 0.00 0.00 0.00 4.63
3165 4749 4.735132 TCTTCTTCCCGCACGCCG 62.735 66.667 0.00 0.00 0.00 6.46
3168 4752 0.790814 GTTCTTCTTCTTCCCGCACG 59.209 55.000 0.00 0.00 0.00 5.34
3175 4759 2.070028 GCTCGGGTGTTCTTCTTCTTC 58.930 52.381 0.00 0.00 0.00 2.87
3177 4761 1.048601 TGCTCGGGTGTTCTTCTTCT 58.951 50.000 0.00 0.00 0.00 2.85
3185 4769 1.981256 AAACAGATTGCTCGGGTGTT 58.019 45.000 0.00 0.00 32.75 3.32
3187 4771 2.355756 CCATAAACAGATTGCTCGGGTG 59.644 50.000 0.00 0.00 0.00 4.61
3193 4777 5.539955 ACAACTTTCCCATAAACAGATTGCT 59.460 36.000 0.00 0.00 0.00 3.91
3194 4778 5.783111 ACAACTTTCCCATAAACAGATTGC 58.217 37.500 0.00 0.00 0.00 3.56
3195 4779 6.646240 CCAACAACTTTCCCATAAACAGATTG 59.354 38.462 0.00 0.00 0.00 2.67
3196 4780 6.239572 CCCAACAACTTTCCCATAAACAGATT 60.240 38.462 0.00 0.00 0.00 2.40
3197 4781 5.245977 CCCAACAACTTTCCCATAAACAGAT 59.754 40.000 0.00 0.00 0.00 2.90
3199 4783 4.586841 TCCCAACAACTTTCCCATAAACAG 59.413 41.667 0.00 0.00 0.00 3.16
3201 4785 4.021456 CCTCCCAACAACTTTCCCATAAAC 60.021 45.833 0.00 0.00 0.00 2.01
3206 4790 1.144913 CTCCTCCCAACAACTTTCCCA 59.855 52.381 0.00 0.00 0.00 4.37
3209 4793 2.951229 TCCTCCTCCCAACAACTTTC 57.049 50.000 0.00 0.00 0.00 2.62
3212 4796 1.700186 GTCTTCCTCCTCCCAACAACT 59.300 52.381 0.00 0.00 0.00 3.16
3213 4797 1.420138 TGTCTTCCTCCTCCCAACAAC 59.580 52.381 0.00 0.00 0.00 3.32
3214 4798 1.420138 GTGTCTTCCTCCTCCCAACAA 59.580 52.381 0.00 0.00 0.00 2.83
3238 4822 1.002251 GATAGAGAACGGACGGCTCAG 60.002 57.143 15.55 0.00 0.00 3.35
3241 4825 0.395311 TGGATAGAGAACGGACGGCT 60.395 55.000 0.00 0.00 0.00 5.52
3248 4832 3.226346 TGAACCGTTGGATAGAGAACG 57.774 47.619 0.00 0.00 43.59 3.95
3252 4836 6.238484 GGATGAATTTGAACCGTTGGATAGAG 60.238 42.308 0.00 0.00 0.00 2.43
3258 4842 2.560542 TGGGATGAATTTGAACCGTTGG 59.439 45.455 0.00 0.00 0.00 3.77
3264 4848 3.959535 TTGGCTGGGATGAATTTGAAC 57.040 42.857 0.00 0.00 0.00 3.18
3269 4853 4.081309 CAGTCAATTTGGCTGGGATGAATT 60.081 41.667 20.81 0.00 45.77 2.17
3279 4863 4.559300 CGTTTGGAATCAGTCAATTTGGCT 60.559 41.667 0.00 0.00 28.47 4.75
3282 4866 6.000891 TCTCGTTTGGAATCAGTCAATTTG 57.999 37.500 0.00 0.00 0.00 2.32
3287 4871 4.893608 TGAATCTCGTTTGGAATCAGTCA 58.106 39.130 0.00 0.00 0.00 3.41
3288 4872 4.932200 ACTGAATCTCGTTTGGAATCAGTC 59.068 41.667 8.15 0.00 38.06 3.51
3294 4878 3.005472 AGTCGACTGAATCTCGTTTGGAA 59.995 43.478 19.30 0.00 32.77 3.53
3297 4881 2.663602 CCAGTCGACTGAATCTCGTTTG 59.336 50.000 40.21 19.41 46.59 2.93
3301 4885 0.453793 AGCCAGTCGACTGAATCTCG 59.546 55.000 40.21 25.39 46.59 4.04
3302 4886 1.202359 GGAGCCAGTCGACTGAATCTC 60.202 57.143 40.21 35.00 46.59 2.75
3303 4887 0.820871 GGAGCCAGTCGACTGAATCT 59.179 55.000 40.21 31.43 46.59 2.40
3304 4888 0.820871 AGGAGCCAGTCGACTGAATC 59.179 55.000 40.21 33.24 46.59 2.52
3305 4889 2.028130 CTAGGAGCCAGTCGACTGAAT 58.972 52.381 40.21 29.07 46.59 2.57
3334 4918 6.572519 TGCACTTTGCTGAAGAAAAACTATT 58.427 32.000 7.30 0.00 45.31 1.73
3335 4919 6.147864 TGCACTTTGCTGAAGAAAAACTAT 57.852 33.333 7.30 0.00 45.31 2.12
3336 4920 5.574891 TGCACTTTGCTGAAGAAAAACTA 57.425 34.783 7.30 0.00 45.31 2.24
3337 4921 4.454728 TGCACTTTGCTGAAGAAAAACT 57.545 36.364 7.30 0.00 45.31 2.66
3338 4922 4.805192 TCATGCACTTTGCTGAAGAAAAAC 59.195 37.500 7.30 0.00 45.31 2.43
3339 4923 5.008619 TCATGCACTTTGCTGAAGAAAAA 57.991 34.783 7.30 0.00 45.31 1.94
3340 4924 4.652421 TCATGCACTTTGCTGAAGAAAA 57.348 36.364 7.30 0.00 45.31 2.29
3341 4925 4.652421 TTCATGCACTTTGCTGAAGAAA 57.348 36.364 7.30 0.00 45.31 2.52
3344 4928 3.909776 TCTTCATGCACTTTGCTGAAG 57.090 42.857 21.68 21.68 46.97 3.02
3345 4929 4.038282 ACAATCTTCATGCACTTTGCTGAA 59.962 37.500 0.00 6.35 45.31 3.02
3346 4930 3.570975 ACAATCTTCATGCACTTTGCTGA 59.429 39.130 0.00 0.00 45.31 4.26
3347 4931 3.909430 ACAATCTTCATGCACTTTGCTG 58.091 40.909 0.00 0.00 45.31 4.41
3348 4932 3.057033 GGACAATCTTCATGCACTTTGCT 60.057 43.478 0.00 0.00 45.31 3.91
3349 4933 3.057033 AGGACAATCTTCATGCACTTTGC 60.057 43.478 0.00 0.00 45.29 3.68
3350 4934 4.482386 CAGGACAATCTTCATGCACTTTG 58.518 43.478 0.00 0.00 0.00 2.77
3351 4935 4.778534 CAGGACAATCTTCATGCACTTT 57.221 40.909 0.00 0.00 0.00 2.66
3357 4941 3.340928 TGACTGCAGGACAATCTTCATG 58.659 45.455 19.93 0.00 0.00 3.07
3358 4942 3.607741 CTGACTGCAGGACAATCTTCAT 58.392 45.455 19.93 0.00 38.51 2.57
3359 4943 3.049708 CTGACTGCAGGACAATCTTCA 57.950 47.619 19.93 8.87 38.51 3.02
3370 4954 4.520492 ACTTTAAATGGAACCTGACTGCAG 59.480 41.667 13.48 13.48 41.93 4.41
3371 4955 4.278170 CACTTTAAATGGAACCTGACTGCA 59.722 41.667 0.00 0.00 0.00 4.41
3372 4956 4.798574 CACTTTAAATGGAACCTGACTGC 58.201 43.478 0.00 0.00 0.00 4.40
3373 4957 4.278170 TGCACTTTAAATGGAACCTGACTG 59.722 41.667 0.00 0.00 0.00 3.51
3401 4985 6.633634 GTCGTTGAGTCTTGCAGAGTATATAC 59.366 42.308 4.60 4.60 0.00 1.47
3444 5028 2.368221 GACTCTGGCTCTGGAATAGCAT 59.632 50.000 0.00 0.00 41.93 3.79
3452 5038 3.415457 AGAAAAAGACTCTGGCTCTGG 57.585 47.619 0.00 0.00 0.00 3.86
3474 5077 2.470983 TTGCTGTGATGTGAATCCGA 57.529 45.000 0.00 0.00 0.00 4.55
3500 5103 9.273016 TCTCAGAAGAAGTTTTCGTTTCATTAT 57.727 29.630 0.00 0.00 34.02 1.28
3501 5104 8.657074 TCTCAGAAGAAGTTTTCGTTTCATTA 57.343 30.769 0.00 0.00 34.02 1.90
3503 5106 7.553881 TTCTCAGAAGAAGTTTTCGTTTCAT 57.446 32.000 0.00 0.00 36.59 2.57
3504 5107 6.978343 TTCTCAGAAGAAGTTTTCGTTTCA 57.022 33.333 0.00 0.00 36.59 2.69
3505 5108 7.630924 TCATTCTCAGAAGAAGTTTTCGTTTC 58.369 34.615 0.00 0.00 44.53 2.78
3506 5109 7.553881 TCATTCTCAGAAGAAGTTTTCGTTT 57.446 32.000 0.00 0.00 44.53 3.60
3509 5112 6.576684 GCTTTCATTCTCAGAAGAAGTTTTCG 59.423 38.462 0.00 0.00 44.53 3.46


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

AutoCloner maintained by Alex Coulton.