Multiple sequence alignment - TraesCS1A01G219900

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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 TraesCS1A01G219900 chr1A 100.000 5288 0 0 1 5288 388837833 388843120 0.000000e+00 9766
1 TraesCS1A01G219900 chr1D 97.775 4719 85 7 1 4700 309077560 309082277 0.000000e+00 8115
2 TraesCS1A01G219900 chr1D 94.488 381 21 0 4908 5288 309082286 309082666 5.900000e-164 588
3 TraesCS1A01G219900 chr1B 95.077 5099 192 21 108 5160 418809490 418814575 0.000000e+00 7971
4 TraesCS1A01G219900 chr1B 96.063 127 5 0 1 127 418809249 418809375 1.930000e-49 207
5 TraesCS1A01G219900 chr1B 89.691 97 8 1 5192 5288 418814576 418814670 7.190000e-24 122
6 TraesCS1A01G219900 chr2A 86.653 3394 439 12 916 4301 95991724 95995111 0.000000e+00 3746
7 TraesCS1A01G219900 chr2B 86.959 3328 425 8 978 4301 148237503 148240825 0.000000e+00 3733
8 TraesCS1A01G219900 chr3D 86.637 3360 433 15 950 4301 147817819 147821170 0.000000e+00 3703
9 TraesCS1A01G219900 chr2D 86.685 3327 435 7 978 4301 97220116 97223437 0.000000e+00 3683
10 TraesCS1A01G219900 chr3A 86.561 3356 432 18 956 4301 165420136 165416790 0.000000e+00 3681
11 TraesCS1A01G219900 chr3B 86.549 3353 436 14 956 4301 214563663 214560319 0.000000e+00 3679
12 TraesCS1A01G219900 chr5D 80.501 3313 593 36 993 4280 46319055 46322339 0.000000e+00 2490


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 TraesCS1A01G219900 chr1A 388837833 388843120 5287 False 9766.000000 9766 100.000000 1 5288 1 chr1A.!!$F1 5287
1 TraesCS1A01G219900 chr1D 309077560 309082666 5106 False 4351.500000 8115 96.131500 1 5288 2 chr1D.!!$F1 5287
2 TraesCS1A01G219900 chr1B 418809249 418814670 5421 False 2766.666667 7971 93.610333 1 5288 3 chr1B.!!$F1 5287
3 TraesCS1A01G219900 chr2A 95991724 95995111 3387 False 3746.000000 3746 86.653000 916 4301 1 chr2A.!!$F1 3385
4 TraesCS1A01G219900 chr2B 148237503 148240825 3322 False 3733.000000 3733 86.959000 978 4301 1 chr2B.!!$F1 3323
5 TraesCS1A01G219900 chr3D 147817819 147821170 3351 False 3703.000000 3703 86.637000 950 4301 1 chr3D.!!$F1 3351
6 TraesCS1A01G219900 chr2D 97220116 97223437 3321 False 3683.000000 3683 86.685000 978 4301 1 chr2D.!!$F1 3323
7 TraesCS1A01G219900 chr3A 165416790 165420136 3346 True 3681.000000 3681 86.561000 956 4301 1 chr3A.!!$R1 3345
8 TraesCS1A01G219900 chr3B 214560319 214563663 3344 True 3679.000000 3679 86.549000 956 4301 1 chr3B.!!$R1 3345
9 TraesCS1A01G219900 chr5D 46319055 46322339 3284 False 2490.000000 2490 80.501000 993 4280 1 chr5D.!!$F1 3287

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
803 965 1.105457 TCGTATGGTTCCGGTACCTG 58.895 55.000 28.09 16.25 39.04 4.00 F
1808 1978 0.664166 GGTGAAAATGCACAGCCACG 60.664 55.000 0.00 0.00 40.52 4.94 F
2068 2238 2.650778 CCGAAAAGCCAACCTGCC 59.349 61.111 0.00 0.00 0.00 4.85 F
3450 3620 0.605589 CCGAGAAGAGCCACAGTTCT 59.394 55.000 0.00 0.00 34.61 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2238 2.105006 TTGCCAGAAAGCTCAGCTAG 57.895 50.0 0.0 0.0 38.25 3.42 R
3206 3376 2.234661 CTGGTGGCATCTGAAGAGTACA 59.765 50.0 0.0 0.0 0.00 2.90 R
3808 3978 0.601311 GTGAGCTTGTTCTCTGCGGT 60.601 55.0 0.0 0.0 34.29 5.68 R
4718 5126 0.036164 ATAAGGCTGACAACGGTGCA 59.964 50.0 0.0 0.0 0.00 4.57 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
68 70 6.405731 GCATGCTTGTTTAGTTCATATGGGAA 60.406 38.462 11.37 0.00 0.00 3.97
137 273 7.337942 ACATTGATGGATTCCTGTCTTTTCTAC 59.662 37.037 3.95 0.00 0.00 2.59
192 328 7.805163 TGGGATTTGAGAATGATTCTTAGCTA 58.195 34.615 9.35 0.00 40.87 3.32
206 342 5.880054 TCTTAGCTATTTTCAGTTGCCAC 57.120 39.130 0.00 0.00 0.00 5.01
214 350 4.734398 TTTTCAGTTGCCACTTTGTCAT 57.266 36.364 0.00 0.00 0.00 3.06
216 352 5.843673 TTTCAGTTGCCACTTTGTCATTA 57.156 34.783 0.00 0.00 0.00 1.90
455 600 1.795286 GTGTTCTTGTTCAGGCTCTCG 59.205 52.381 0.00 0.00 0.00 4.04
515 660 3.070748 TCGCGAGAAAATGATGTTTGGA 58.929 40.909 3.71 0.00 37.03 3.53
803 965 1.105457 TCGTATGGTTCCGGTACCTG 58.895 55.000 28.09 16.25 39.04 4.00
1074 1241 3.710165 TCAAGATCCAGTCAGATGCTCAT 59.290 43.478 0.00 0.00 0.00 2.90
1648 1818 2.088423 GGCGTTCATTCATAACCACCA 58.912 47.619 0.00 0.00 0.00 4.17
1808 1978 0.664166 GGTGAAAATGCACAGCCACG 60.664 55.000 0.00 0.00 40.52 4.94
2068 2238 2.650778 CCGAAAAGCCAACCTGCC 59.349 61.111 0.00 0.00 0.00 4.85
2388 2558 8.488764 GTTGATCTTAAGATTACGAGCCAATAC 58.511 37.037 18.88 3.76 34.37 1.89
3087 3257 5.089970 TCAGCATTTACACTCATACAGCT 57.910 39.130 0.00 0.00 0.00 4.24
3088 3258 6.220726 TCAGCATTTACACTCATACAGCTA 57.779 37.500 0.00 0.00 0.00 3.32
3168 3338 5.296151 ACTCTGAGAAAATGTCCAAGTCA 57.704 39.130 12.44 0.00 0.00 3.41
3206 3376 1.077005 TCTTGGGCAGGCCATTAAAGT 59.923 47.619 18.18 0.00 37.98 2.66
3442 3612 2.416893 GTGAATGAAACCGAGAAGAGCC 59.583 50.000 0.00 0.00 0.00 4.70
3446 3616 1.270305 TGAAACCGAGAAGAGCCACAG 60.270 52.381 0.00 0.00 0.00 3.66
3450 3620 0.605589 CCGAGAAGAGCCACAGTTCT 59.394 55.000 0.00 0.00 34.61 3.01
3639 3809 3.808728 TGTGTGGCAGAATATCCTAAGC 58.191 45.455 0.00 0.00 0.00 3.09
3729 3899 6.842163 AGCAAACAAGTATTTACAGGATTCG 58.158 36.000 0.00 0.00 0.00 3.34
3782 3952 1.988107 AGGATCAGGCTCCAAGAAACA 59.012 47.619 0.00 0.00 37.81 2.83
3915 4091 6.887368 TCAATCGAATTATGATAGCCAAACG 58.113 36.000 0.00 0.00 0.00 3.60
4314 4493 6.209361 TCAGCTTCATCGATGTAAGTCATAC 58.791 40.000 24.09 12.38 36.83 2.39
4404 4583 8.892723 TGAGAATAAATGTAGGTTGTATTGCAG 58.107 33.333 0.00 0.00 0.00 4.41
4413 4592 2.360801 GGTTGTATTGCAGTGTTGTGGT 59.639 45.455 0.00 0.00 0.00 4.16
4465 4644 5.178797 TGCTCTACTGTTAAGGCTCAATTC 58.821 41.667 0.00 0.00 0.00 2.17
4567 4752 6.486657 TGAAACCAAGTTCTAGAATGTTCAGG 59.513 38.462 8.75 7.90 0.00 3.86
4585 4772 4.016444 TCAGGAAAAACAAGTTCTGCACT 58.984 39.130 0.00 0.00 37.30 4.40
4661 4848 1.965930 TCGTGGCAATCCTGTGTGC 60.966 57.895 0.00 0.00 40.14 4.57
4716 5124 8.715191 AATGAGTGATTTGTGTCTAGAATCTC 57.285 34.615 0.00 0.00 32.41 2.75
4717 5125 6.634805 TGAGTGATTTGTGTCTAGAATCTCC 58.365 40.000 0.00 0.00 32.41 3.71
4718 5126 6.438741 TGAGTGATTTGTGTCTAGAATCTCCT 59.561 38.462 0.00 0.00 32.41 3.69
4719 5127 6.638610 AGTGATTTGTGTCTAGAATCTCCTG 58.361 40.000 0.00 0.00 32.41 3.86
4720 5128 5.293079 GTGATTTGTGTCTAGAATCTCCTGC 59.707 44.000 0.00 0.00 32.41 4.85
4721 5129 4.890158 TTTGTGTCTAGAATCTCCTGCA 57.110 40.909 0.00 0.00 0.00 4.41
4722 5130 3.876274 TGTGTCTAGAATCTCCTGCAC 57.124 47.619 0.00 0.00 0.00 4.57
4723 5131 2.497675 TGTGTCTAGAATCTCCTGCACC 59.502 50.000 0.00 0.00 0.00 5.01
4724 5132 1.751351 TGTCTAGAATCTCCTGCACCG 59.249 52.381 0.00 0.00 0.00 4.94
4725 5133 1.751924 GTCTAGAATCTCCTGCACCGT 59.248 52.381 0.00 0.00 0.00 4.83
4726 5134 2.166664 GTCTAGAATCTCCTGCACCGTT 59.833 50.000 0.00 0.00 0.00 4.44
4727 5135 2.166459 TCTAGAATCTCCTGCACCGTTG 59.834 50.000 0.00 0.00 0.00 4.10
4728 5136 0.687354 AGAATCTCCTGCACCGTTGT 59.313 50.000 0.00 0.00 0.00 3.32
4729 5137 1.079503 GAATCTCCTGCACCGTTGTC 58.920 55.000 0.00 0.00 0.00 3.18
4730 5138 0.396435 AATCTCCTGCACCGTTGTCA 59.604 50.000 0.00 0.00 0.00 3.58
4731 5139 0.036952 ATCTCCTGCACCGTTGTCAG 60.037 55.000 0.00 0.00 0.00 3.51
4732 5140 2.280797 TCCTGCACCGTTGTCAGC 60.281 61.111 0.13 0.00 0.00 4.26
4733 5141 3.357079 CCTGCACCGTTGTCAGCC 61.357 66.667 0.13 0.00 0.00 4.85
4734 5142 2.281070 CTGCACCGTTGTCAGCCT 60.281 61.111 0.00 0.00 0.00 4.58
4735 5143 1.893808 CTGCACCGTTGTCAGCCTT 60.894 57.895 0.00 0.00 0.00 4.35
4736 5144 0.602638 CTGCACCGTTGTCAGCCTTA 60.603 55.000 0.00 0.00 0.00 2.69
4737 5145 0.036164 TGCACCGTTGTCAGCCTTAT 59.964 50.000 0.00 0.00 0.00 1.73
4738 5146 1.165270 GCACCGTTGTCAGCCTTATT 58.835 50.000 0.00 0.00 0.00 1.40
4739 5147 2.289756 TGCACCGTTGTCAGCCTTATTA 60.290 45.455 0.00 0.00 0.00 0.98
4740 5148 2.745281 GCACCGTTGTCAGCCTTATTAA 59.255 45.455 0.00 0.00 0.00 1.40
4741 5149 3.189702 GCACCGTTGTCAGCCTTATTAAA 59.810 43.478 0.00 0.00 0.00 1.52
4742 5150 4.671766 GCACCGTTGTCAGCCTTATTAAAG 60.672 45.833 0.00 0.00 0.00 1.85
4743 5151 4.693566 CACCGTTGTCAGCCTTATTAAAGA 59.306 41.667 0.00 0.00 34.37 2.52
4744 5152 5.354234 CACCGTTGTCAGCCTTATTAAAGAT 59.646 40.000 0.00 0.00 34.37 2.40
4745 5153 6.537301 CACCGTTGTCAGCCTTATTAAAGATA 59.463 38.462 0.00 0.00 34.37 1.98
4746 5154 6.761714 ACCGTTGTCAGCCTTATTAAAGATAG 59.238 38.462 0.00 0.00 34.37 2.08
4747 5155 6.984474 CCGTTGTCAGCCTTATTAAAGATAGA 59.016 38.462 0.00 0.00 34.37 1.98
4748 5156 7.494625 CCGTTGTCAGCCTTATTAAAGATAGAA 59.505 37.037 0.00 0.00 34.37 2.10
4749 5157 8.879759 CGTTGTCAGCCTTATTAAAGATAGAAA 58.120 33.333 0.00 0.00 34.37 2.52
4750 5158 9.989869 GTTGTCAGCCTTATTAAAGATAGAAAC 57.010 33.333 0.00 0.00 34.37 2.78
4751 5159 9.959721 TTGTCAGCCTTATTAAAGATAGAAACT 57.040 29.630 0.00 0.00 34.37 2.66
4752 5160 9.601217 TGTCAGCCTTATTAAAGATAGAAACTC 57.399 33.333 0.00 0.00 34.37 3.01
4753 5161 9.825109 GTCAGCCTTATTAAAGATAGAAACTCT 57.175 33.333 0.00 0.00 34.37 3.24
4754 5162 9.823647 TCAGCCTTATTAAAGATAGAAACTCTG 57.176 33.333 0.00 0.00 34.37 3.35
4755 5163 8.555361 CAGCCTTATTAAAGATAGAAACTCTGC 58.445 37.037 0.00 0.00 34.37 4.26
4756 5164 7.717436 AGCCTTATTAAAGATAGAAACTCTGCC 59.283 37.037 0.00 0.00 34.37 4.85
4757 5165 7.499232 GCCTTATTAAAGATAGAAACTCTGCCA 59.501 37.037 0.00 0.00 34.37 4.92
4758 5166 8.831550 CCTTATTAAAGATAGAAACTCTGCCAC 58.168 37.037 0.00 0.00 34.37 5.01
4759 5167 9.606631 CTTATTAAAGATAGAAACTCTGCCACT 57.393 33.333 0.00 0.00 34.37 4.00
4760 5168 9.959721 TTATTAAAGATAGAAACTCTGCCACTT 57.040 29.630 0.00 0.00 0.00 3.16
4761 5169 7.672983 TTAAAGATAGAAACTCTGCCACTTG 57.327 36.000 0.00 0.00 0.00 3.16
4762 5170 5.489792 AAGATAGAAACTCTGCCACTTGA 57.510 39.130 0.00 0.00 0.00 3.02
4763 5171 5.690464 AGATAGAAACTCTGCCACTTGAT 57.310 39.130 0.00 0.00 0.00 2.57
4764 5172 5.426504 AGATAGAAACTCTGCCACTTGATG 58.573 41.667 0.00 0.00 0.00 3.07
4765 5173 3.498774 AGAAACTCTGCCACTTGATGT 57.501 42.857 0.00 0.00 0.00 3.06
4766 5174 3.825328 AGAAACTCTGCCACTTGATGTT 58.175 40.909 0.00 0.00 0.00 2.71
4767 5175 4.973168 AGAAACTCTGCCACTTGATGTTA 58.027 39.130 0.00 0.00 0.00 2.41
4768 5176 4.757149 AGAAACTCTGCCACTTGATGTTAC 59.243 41.667 0.00 0.00 0.00 2.50
4769 5177 4.357918 AACTCTGCCACTTGATGTTACT 57.642 40.909 0.00 0.00 0.00 2.24
4770 5178 3.668447 ACTCTGCCACTTGATGTTACTG 58.332 45.455 0.00 0.00 0.00 2.74
4771 5179 2.417933 CTCTGCCACTTGATGTTACTGC 59.582 50.000 0.00 0.00 0.00 4.40
4772 5180 2.038952 TCTGCCACTTGATGTTACTGCT 59.961 45.455 0.00 0.00 0.00 4.24
4773 5181 2.153645 TGCCACTTGATGTTACTGCTG 58.846 47.619 0.00 0.00 0.00 4.41
4774 5182 1.135575 GCCACTTGATGTTACTGCTGC 60.136 52.381 0.00 0.00 0.00 5.25
4775 5183 2.153645 CCACTTGATGTTACTGCTGCA 58.846 47.619 0.88 0.88 0.00 4.41
4776 5184 2.553602 CCACTTGATGTTACTGCTGCAA 59.446 45.455 3.02 0.00 0.00 4.08
4777 5185 3.558505 CACTTGATGTTACTGCTGCAAC 58.441 45.455 3.02 0.00 0.00 4.17
4778 5186 3.003585 CACTTGATGTTACTGCTGCAACA 59.996 43.478 11.28 11.28 38.89 3.33
4779 5187 3.251729 ACTTGATGTTACTGCTGCAACAG 59.748 43.478 15.51 15.51 43.59 3.16
4780 5188 3.124578 TGATGTTACTGCTGCAACAGA 57.875 42.857 23.44 4.77 40.25 3.41
4781 5189 3.475575 TGATGTTACTGCTGCAACAGAA 58.524 40.909 23.44 10.37 40.25 3.02
4782 5190 3.882288 TGATGTTACTGCTGCAACAGAAA 59.118 39.130 23.44 8.31 40.25 2.52
4783 5191 4.520111 TGATGTTACTGCTGCAACAGAAAT 59.480 37.500 23.44 10.41 40.25 2.17
4784 5192 4.227512 TGTTACTGCTGCAACAGAAATG 57.772 40.909 23.44 0.00 40.25 2.32
4785 5193 3.631686 TGTTACTGCTGCAACAGAAATGT 59.368 39.130 23.44 4.22 40.25 2.71
4786 5194 4.097741 TGTTACTGCTGCAACAGAAATGTT 59.902 37.500 23.44 2.61 40.25 2.71
4794 5202 3.996150 CAACAGAAATGTTGTCAGGCT 57.004 42.857 11.93 0.00 42.87 4.58
4795 5203 4.311816 CAACAGAAATGTTGTCAGGCTT 57.688 40.909 11.93 0.00 42.87 4.35
4796 5204 5.437289 CAACAGAAATGTTGTCAGGCTTA 57.563 39.130 11.93 0.00 42.87 3.09
4797 5205 5.215160 CAACAGAAATGTTGTCAGGCTTAC 58.785 41.667 11.93 0.00 42.87 2.34
4798 5206 4.718961 ACAGAAATGTTGTCAGGCTTACT 58.281 39.130 0.00 0.00 0.00 2.24
4799 5207 4.757149 ACAGAAATGTTGTCAGGCTTACTC 59.243 41.667 0.00 0.00 0.00 2.59
4800 5208 4.756642 CAGAAATGTTGTCAGGCTTACTCA 59.243 41.667 0.00 0.78 0.00 3.41
4801 5209 5.239306 CAGAAATGTTGTCAGGCTTACTCAA 59.761 40.000 0.00 0.00 0.00 3.02
4802 5210 5.471456 AGAAATGTTGTCAGGCTTACTCAAG 59.529 40.000 0.00 0.00 34.66 3.02
4803 5211 4.623932 ATGTTGTCAGGCTTACTCAAGA 57.376 40.909 0.00 0.00 33.20 3.02
4804 5212 4.623932 TGTTGTCAGGCTTACTCAAGAT 57.376 40.909 0.00 0.00 33.20 2.40
4805 5213 4.318332 TGTTGTCAGGCTTACTCAAGATG 58.682 43.478 0.00 0.00 33.20 2.90
4806 5214 3.616956 TGTCAGGCTTACTCAAGATGG 57.383 47.619 0.00 0.00 33.20 3.51
4807 5215 2.906389 TGTCAGGCTTACTCAAGATGGT 59.094 45.455 0.00 0.00 33.20 3.55
4808 5216 3.055819 TGTCAGGCTTACTCAAGATGGTC 60.056 47.826 0.00 0.00 33.20 4.02
4809 5217 3.055819 GTCAGGCTTACTCAAGATGGTCA 60.056 47.826 0.00 0.00 33.20 4.02
4810 5218 3.055819 TCAGGCTTACTCAAGATGGTCAC 60.056 47.826 0.00 0.00 33.20 3.67
4811 5219 3.055530 CAGGCTTACTCAAGATGGTCACT 60.056 47.826 0.00 0.00 33.20 3.41
4812 5220 4.160439 CAGGCTTACTCAAGATGGTCACTA 59.840 45.833 0.00 0.00 33.20 2.74
4813 5221 4.404073 AGGCTTACTCAAGATGGTCACTAG 59.596 45.833 0.00 0.00 33.20 2.57
4814 5222 4.402793 GGCTTACTCAAGATGGTCACTAGA 59.597 45.833 0.00 0.00 33.20 2.43
4815 5223 5.069781 GGCTTACTCAAGATGGTCACTAGAT 59.930 44.000 0.00 0.00 33.20 1.98
4816 5224 6.212955 GCTTACTCAAGATGGTCACTAGATC 58.787 44.000 0.00 0.00 33.20 2.75
4817 5225 6.183360 GCTTACTCAAGATGGTCACTAGATCA 60.183 42.308 0.00 0.00 34.14 2.92
4818 5226 5.590530 ACTCAAGATGGTCACTAGATCAC 57.409 43.478 0.00 0.00 37.79 3.06
4819 5227 5.268387 ACTCAAGATGGTCACTAGATCACT 58.732 41.667 0.00 0.00 37.79 3.41
4820 5228 5.359576 ACTCAAGATGGTCACTAGATCACTC 59.640 44.000 0.00 0.00 37.79 3.51
4821 5229 4.646945 TCAAGATGGTCACTAGATCACTCC 59.353 45.833 0.00 0.00 37.79 3.85
4822 5230 4.256983 AGATGGTCACTAGATCACTCCA 57.743 45.455 0.00 0.00 37.79 3.86
4823 5231 4.813809 AGATGGTCACTAGATCACTCCAT 58.186 43.478 0.00 1.85 37.79 3.41
4824 5232 4.588106 AGATGGTCACTAGATCACTCCATG 59.412 45.833 0.00 0.00 37.79 3.66
4825 5233 2.432146 TGGTCACTAGATCACTCCATGC 59.568 50.000 0.00 0.00 27.47 4.06
4826 5234 2.697751 GGTCACTAGATCACTCCATGCT 59.302 50.000 0.00 0.00 0.00 3.79
4827 5235 3.492309 GGTCACTAGATCACTCCATGCTG 60.492 52.174 0.00 0.00 0.00 4.41
4828 5236 2.697229 TCACTAGATCACTCCATGCTGG 59.303 50.000 0.00 0.00 39.43 4.85
4829 5237 2.433604 CACTAGATCACTCCATGCTGGT 59.566 50.000 0.00 0.00 39.03 4.00
4830 5238 3.638627 CACTAGATCACTCCATGCTGGTA 59.361 47.826 0.00 0.00 39.03 3.25
4831 5239 3.894427 ACTAGATCACTCCATGCTGGTAG 59.106 47.826 0.00 2.57 39.03 3.18
4832 5240 2.756907 AGATCACTCCATGCTGGTAGT 58.243 47.619 0.00 3.06 39.03 2.73
4833 5241 2.433604 AGATCACTCCATGCTGGTAGTG 59.566 50.000 17.98 17.98 42.12 2.74
4834 5242 1.644509 TCACTCCATGCTGGTAGTGT 58.355 50.000 20.42 9.00 41.79 3.55
4835 5243 1.977854 TCACTCCATGCTGGTAGTGTT 59.022 47.619 20.42 0.47 41.79 3.32
4836 5244 2.079158 CACTCCATGCTGGTAGTGTTG 58.921 52.381 16.93 0.00 39.08 3.33
4837 5245 1.699634 ACTCCATGCTGGTAGTGTTGT 59.300 47.619 2.68 0.00 39.03 3.32
4838 5246 2.903784 ACTCCATGCTGGTAGTGTTGTA 59.096 45.455 2.68 0.00 39.03 2.41
4839 5247 3.055819 ACTCCATGCTGGTAGTGTTGTAG 60.056 47.826 2.68 0.00 39.03 2.74
4840 5248 2.009774 CCATGCTGGTAGTGTTGTAGC 58.990 52.381 0.00 0.00 31.35 3.58
4841 5249 2.615240 CCATGCTGGTAGTGTTGTAGCA 60.615 50.000 0.00 0.00 46.90 3.49
4842 5250 2.455674 TGCTGGTAGTGTTGTAGCAG 57.544 50.000 5.86 5.86 46.75 4.24
4843 5251 1.967779 TGCTGGTAGTGTTGTAGCAGA 59.032 47.619 12.95 0.00 46.91 4.26
4844 5252 2.367241 TGCTGGTAGTGTTGTAGCAGAA 59.633 45.455 12.95 0.92 46.91 3.02
4845 5253 2.996621 GCTGGTAGTGTTGTAGCAGAAG 59.003 50.000 12.95 0.00 46.91 2.85
4846 5254 3.306088 GCTGGTAGTGTTGTAGCAGAAGA 60.306 47.826 12.95 0.00 46.91 2.87
4847 5255 4.621747 GCTGGTAGTGTTGTAGCAGAAGAT 60.622 45.833 12.95 0.00 46.91 2.40
4848 5256 4.820897 TGGTAGTGTTGTAGCAGAAGATG 58.179 43.478 0.00 0.00 0.00 2.90
4849 5257 4.184629 GGTAGTGTTGTAGCAGAAGATGG 58.815 47.826 0.00 0.00 0.00 3.51
4850 5258 3.340814 AGTGTTGTAGCAGAAGATGGG 57.659 47.619 0.00 0.00 0.00 4.00
4851 5259 2.639839 AGTGTTGTAGCAGAAGATGGGT 59.360 45.455 0.00 0.00 0.00 4.51
4852 5260 3.003480 GTGTTGTAGCAGAAGATGGGTC 58.997 50.000 0.00 0.00 0.00 4.46
4853 5261 2.637382 TGTTGTAGCAGAAGATGGGTCA 59.363 45.455 0.00 0.00 0.00 4.02
4854 5262 3.265791 GTTGTAGCAGAAGATGGGTCAG 58.734 50.000 0.00 0.00 0.00 3.51
4855 5263 2.540383 TGTAGCAGAAGATGGGTCAGT 58.460 47.619 0.00 0.00 0.00 3.41
4856 5264 3.708451 TGTAGCAGAAGATGGGTCAGTA 58.292 45.455 0.00 0.00 0.00 2.74
4857 5265 3.701542 TGTAGCAGAAGATGGGTCAGTAG 59.298 47.826 0.00 0.00 0.00 2.57
4858 5266 1.484240 AGCAGAAGATGGGTCAGTAGC 59.516 52.381 0.00 0.00 0.00 3.58
4859 5267 1.208052 GCAGAAGATGGGTCAGTAGCA 59.792 52.381 0.00 0.00 0.00 3.49
4860 5268 2.158842 GCAGAAGATGGGTCAGTAGCAT 60.159 50.000 0.00 0.00 0.00 3.79
4861 5269 3.683847 GCAGAAGATGGGTCAGTAGCATT 60.684 47.826 0.00 0.00 0.00 3.56
4862 5270 4.443457 GCAGAAGATGGGTCAGTAGCATTA 60.443 45.833 0.00 0.00 0.00 1.90
4863 5271 5.053145 CAGAAGATGGGTCAGTAGCATTAC 58.947 45.833 0.00 0.00 0.00 1.89
4864 5272 4.965532 AGAAGATGGGTCAGTAGCATTACT 59.034 41.667 0.00 0.00 40.79 2.24
4875 5283 4.504858 AGTAGCATTACTGTAGTTGTGCC 58.495 43.478 13.94 4.63 38.69 5.01
4876 5284 3.703001 AGCATTACTGTAGTTGTGCCT 57.297 42.857 13.94 4.02 37.68 4.75
4877 5285 4.021102 AGCATTACTGTAGTTGTGCCTT 57.979 40.909 13.94 0.20 37.68 4.35
4878 5286 5.160607 AGCATTACTGTAGTTGTGCCTTA 57.839 39.130 13.94 0.00 37.68 2.69
4879 5287 4.935808 AGCATTACTGTAGTTGTGCCTTAC 59.064 41.667 13.94 0.00 37.68 2.34
4880 5288 4.201685 GCATTACTGTAGTTGTGCCTTACG 60.202 45.833 9.02 0.00 33.77 3.18
4881 5289 4.589216 TTACTGTAGTTGTGCCTTACGT 57.411 40.909 0.00 0.00 0.00 3.57
4882 5290 3.022607 ACTGTAGTTGTGCCTTACGTC 57.977 47.619 0.00 0.00 0.00 4.34
4883 5291 1.983605 CTGTAGTTGTGCCTTACGTCG 59.016 52.381 0.00 0.00 0.00 5.12
4884 5292 0.712222 GTAGTTGTGCCTTACGTCGC 59.288 55.000 0.00 0.00 0.00 5.19
4885 5293 0.314618 TAGTTGTGCCTTACGTCGCA 59.685 50.000 0.00 0.00 0.00 5.10
4886 5294 0.944311 AGTTGTGCCTTACGTCGCAG 60.944 55.000 5.24 0.00 35.20 5.18
4887 5295 1.666553 TTGTGCCTTACGTCGCAGG 60.667 57.895 5.24 6.69 35.20 4.85
4888 5296 2.813908 GTGCCTTACGTCGCAGGG 60.814 66.667 11.97 1.35 35.20 4.45
4889 5297 3.307906 TGCCTTACGTCGCAGGGT 61.308 61.111 11.97 0.00 0.00 4.34
4890 5298 1.978080 TGCCTTACGTCGCAGGGTA 60.978 57.895 11.97 0.00 0.00 3.69
4891 5299 1.216178 GCCTTACGTCGCAGGGTAA 59.784 57.895 11.97 0.00 0.00 2.85
4892 5300 0.179092 GCCTTACGTCGCAGGGTAAT 60.179 55.000 11.97 0.00 0.00 1.89
4893 5301 1.741394 GCCTTACGTCGCAGGGTAATT 60.741 52.381 11.97 0.00 0.00 1.40
4894 5302 1.931172 CCTTACGTCGCAGGGTAATTG 59.069 52.381 0.00 0.00 0.00 2.32
4895 5303 1.931172 CTTACGTCGCAGGGTAATTGG 59.069 52.381 0.00 0.00 0.00 3.16
4896 5304 0.460635 TACGTCGCAGGGTAATTGGC 60.461 55.000 0.00 0.00 0.00 4.52
4897 5305 1.449601 CGTCGCAGGGTAATTGGCT 60.450 57.895 0.00 0.00 0.00 4.75
4898 5306 1.429148 CGTCGCAGGGTAATTGGCTC 61.429 60.000 0.00 0.00 0.00 4.70
4899 5307 0.392461 GTCGCAGGGTAATTGGCTCA 60.392 55.000 0.00 0.00 0.00 4.26
4900 5308 0.546122 TCGCAGGGTAATTGGCTCAT 59.454 50.000 0.00 0.00 0.00 2.90
4901 5309 1.765904 TCGCAGGGTAATTGGCTCATA 59.234 47.619 0.00 0.00 0.00 2.15
4902 5310 2.146342 CGCAGGGTAATTGGCTCATAG 58.854 52.381 0.00 0.00 0.00 2.23
4903 5311 2.485479 CGCAGGGTAATTGGCTCATAGT 60.485 50.000 0.00 0.00 0.00 2.12
4904 5312 2.880890 GCAGGGTAATTGGCTCATAGTG 59.119 50.000 0.00 0.00 0.00 2.74
4905 5313 2.880890 CAGGGTAATTGGCTCATAGTGC 59.119 50.000 0.00 0.00 0.00 4.40
4906 5314 2.780010 AGGGTAATTGGCTCATAGTGCT 59.220 45.455 0.00 0.00 0.00 4.40
4947 5355 3.637432 ACATTGTGTGTTTGTTATGCGG 58.363 40.909 0.00 0.00 38.01 5.69
4949 5357 2.765108 TGTGTGTTTGTTATGCGGTG 57.235 45.000 0.00 0.00 0.00 4.94
4958 5366 5.163703 TGTTTGTTATGCGGTGTATGGATTC 60.164 40.000 0.00 0.00 0.00 2.52
4969 5377 3.871006 GTGTATGGATTCATCTGTTGCGA 59.129 43.478 0.00 0.00 34.96 5.10
4980 5388 2.167662 TCTGTTGCGACACTCCTATGA 58.832 47.619 1.50 0.00 0.00 2.15
4982 5390 1.204704 TGTTGCGACACTCCTATGAGG 59.795 52.381 1.50 0.00 43.29 3.86
5006 5414 3.572632 ATGCTGCTTGAGGTCATGTAT 57.427 42.857 0.00 0.00 0.00 2.29
5056 5466 4.788075 TGGATGAATAGGTGAGGAAAGGAA 59.212 41.667 0.00 0.00 0.00 3.36
5059 5469 4.589908 TGAATAGGTGAGGAAAGGAAAGC 58.410 43.478 0.00 0.00 0.00 3.51
5094 5504 1.135333 GTGTGAGGATCCGAGAAGGTC 59.865 57.143 5.98 0.00 41.99 3.85
5118 5528 4.467769 AGGATTCAGAAATGGTAGGCATG 58.532 43.478 0.00 0.00 0.00 4.06
5127 5537 1.533625 TGGTAGGCATGCTGTTTGAC 58.466 50.000 18.92 6.63 0.00 3.18
5162 5572 3.260632 TCATGGGAGTGACTTCGAATTCA 59.739 43.478 13.60 13.60 0.00 2.57
5170 5580 5.043903 AGTGACTTCGAATTCATCATACGG 58.956 41.667 19.51 0.00 0.00 4.02
5190 5600 1.803555 GAAGAACTGAGGAAGTGCAGC 59.196 52.381 0.00 0.00 39.81 5.25
5206 5616 2.233431 TGCAGCCATTGGGAAATTGTAC 59.767 45.455 4.53 0.00 35.59 2.90
5219 5629 5.393027 GGGAAATTGTACCATACTTGCACAG 60.393 44.000 0.00 0.00 0.00 3.66
5230 5640 0.027979 CTTGCACAGGTTGACACGTG 59.972 55.000 15.48 15.48 43.28 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.721960 ACCAGGTCTACAGAAAGTATCACAT 59.278 40.000 0.00 0.00 30.93 3.21
68 70 2.296471 CGGTAAGGACAGTCACAGTTCT 59.704 50.000 2.17 0.00 0.00 3.01
137 273 3.486584 GCTCGAAGAAAAGCAATCACAG 58.513 45.455 0.00 0.00 38.42 3.66
192 328 4.734398 TGACAAAGTGGCAACTGAAAAT 57.266 36.364 0.00 0.00 36.51 1.82
195 331 4.278170 CCTAATGACAAAGTGGCAACTGAA 59.722 41.667 0.00 0.00 39.86 3.02
206 342 9.507280 CAAATTACTGCATACCTAATGACAAAG 57.493 33.333 0.00 0.00 37.86 2.77
214 350 7.885922 TCCAAAGACAAATTACTGCATACCTAA 59.114 33.333 0.00 0.00 0.00 2.69
216 352 6.245408 TCCAAAGACAAATTACTGCATACCT 58.755 36.000 0.00 0.00 0.00 3.08
340 484 2.185004 AAGTTCCACATCCTTGACCG 57.815 50.000 0.00 0.00 0.00 4.79
515 660 6.980397 GTGACACCAATCAAAGTGAAAAATCT 59.020 34.615 0.00 0.00 37.43 2.40
708 868 3.142174 AGACAAACTCTGCTGGCTAAAC 58.858 45.455 0.00 0.00 0.00 2.01
803 965 4.937620 TGAGATGAAGCCATTCTGTAACAC 59.062 41.667 0.00 0.00 36.33 3.32
946 1108 4.332268 CAGAGGCAAGCTTCTAGATTTCAC 59.668 45.833 6.36 0.00 30.96 3.18
1074 1241 4.288626 ACTTTGCTATCCTCCCAACACTTA 59.711 41.667 0.00 0.00 0.00 2.24
1424 1594 6.764560 GCTCTTAAATTTATCTGGGGTAACGA 59.235 38.462 0.00 0.00 37.60 3.85
1590 1760 4.804597 AGCCAAAGTCCTTAAGGTCTTTT 58.195 39.130 31.66 20.81 46.31 2.27
1648 1818 7.893124 AAGCATCATAGAAAGGATTCATGTT 57.107 32.000 0.00 0.00 38.06 2.71
1808 1978 8.295288 CCTCCATTTTAATCAGCACATATTCTC 58.705 37.037 0.00 0.00 0.00 2.87
1852 2022 3.954258 CCTTCCAAGACCTTCAACTTTGT 59.046 43.478 0.00 0.00 0.00 2.83
2068 2238 2.105006 TTGCCAGAAAGCTCAGCTAG 57.895 50.000 0.00 0.00 38.25 3.42
2388 2558 3.691049 TCAGCAAGTTTTTCCTTGTCG 57.309 42.857 0.00 0.00 43.03 4.35
2770 2940 5.972107 AGGAACTGTTCATCAAATGGAAG 57.028 39.130 21.01 0.00 37.18 3.46
3087 3257 3.497405 GCCAATGATGCTCTGGAAGGATA 60.497 47.826 0.00 0.00 35.96 2.59
3088 3258 2.752154 GCCAATGATGCTCTGGAAGGAT 60.752 50.000 0.00 0.00 39.02 3.24
3168 3338 5.535753 CAAGAGTTTGGAAATTCCCTGTT 57.464 39.130 9.87 1.70 35.03 3.16
3206 3376 2.234661 CTGGTGGCATCTGAAGAGTACA 59.765 50.000 0.00 0.00 0.00 2.90
3442 3612 7.020010 GCATCTCTGAACATAAAAGAACTGTG 58.980 38.462 0.00 0.00 0.00 3.66
3446 3616 6.749923 AGGCATCTCTGAACATAAAAGAAC 57.250 37.500 0.00 0.00 0.00 3.01
3450 3620 6.716628 ACTTCAAGGCATCTCTGAACATAAAA 59.283 34.615 0.00 0.00 0.00 1.52
3639 3809 4.452114 GCCTTTATTGCAAAACCTTCCTTG 59.548 41.667 1.71 0.00 0.00 3.61
3729 3899 4.171754 GCAGCTTCCTCATCAAAACAATC 58.828 43.478 0.00 0.00 0.00 2.67
3808 3978 0.601311 GTGAGCTTGTTCTCTGCGGT 60.601 55.000 0.00 0.00 34.29 5.68
3915 4091 0.657368 CGTCAGGAGCAAACAAACGC 60.657 55.000 0.00 0.00 0.00 4.84
4314 4493 5.973565 GCAAACATGTAAGGCAAGCTAATAG 59.026 40.000 0.00 0.00 0.00 1.73
4404 4583 2.365582 ACCAGTTTCAGACCACAACAC 58.634 47.619 0.00 0.00 0.00 3.32
4413 4592 2.777692 ACAAGGAGGAACCAGTTTCAGA 59.222 45.455 0.00 0.00 42.04 3.27
4465 4644 8.407457 TGACTAAACACATTAATCTAGAAGCG 57.593 34.615 0.00 0.00 0.00 4.68
4567 4752 6.753744 AGATTTCAGTGCAGAACTTGTTTTTC 59.246 34.615 0.00 0.00 36.83 2.29
4585 4772 6.127647 GGCATGGTAAATGAACAGAGATTTCA 60.128 38.462 0.00 0.00 37.38 2.69
4661 4848 9.896645 ATACATGATTTCCCAAGCTACATATAG 57.103 33.333 0.00 0.00 0.00 1.31
4700 5108 4.563580 GGTGCAGGAGATTCTAGACACAAA 60.564 45.833 0.00 0.00 0.00 2.83
4702 5110 2.497675 GGTGCAGGAGATTCTAGACACA 59.502 50.000 0.00 0.00 0.00 3.72
4704 5112 1.751351 CGGTGCAGGAGATTCTAGACA 59.249 52.381 0.00 0.00 0.00 3.41
4705 5113 1.751924 ACGGTGCAGGAGATTCTAGAC 59.248 52.381 0.00 0.00 0.00 2.59
4706 5114 2.145397 ACGGTGCAGGAGATTCTAGA 57.855 50.000 0.00 0.00 0.00 2.43
4707 5115 2.093973 ACAACGGTGCAGGAGATTCTAG 60.094 50.000 0.00 0.00 0.00 2.43
4708 5116 1.899814 ACAACGGTGCAGGAGATTCTA 59.100 47.619 0.00 0.00 0.00 2.10
4709 5117 0.687354 ACAACGGTGCAGGAGATTCT 59.313 50.000 0.00 0.00 0.00 2.40
4710 5118 1.079503 GACAACGGTGCAGGAGATTC 58.920 55.000 0.00 0.00 0.00 2.52
4711 5119 0.396435 TGACAACGGTGCAGGAGATT 59.604 50.000 0.00 0.00 0.00 2.40
4712 5120 0.036952 CTGACAACGGTGCAGGAGAT 60.037 55.000 14.66 0.00 0.00 2.75
4713 5121 1.367471 CTGACAACGGTGCAGGAGA 59.633 57.895 14.66 0.00 0.00 3.71
4714 5122 2.320587 GCTGACAACGGTGCAGGAG 61.321 63.158 21.11 5.81 32.66 3.69
4715 5123 2.280797 GCTGACAACGGTGCAGGA 60.281 61.111 21.11 0.00 32.66 3.86
4716 5124 3.357079 GGCTGACAACGGTGCAGG 61.357 66.667 21.11 5.16 32.66 4.85
4717 5125 0.602638 TAAGGCTGACAACGGTGCAG 60.603 55.000 17.21 17.21 34.16 4.41
4718 5126 0.036164 ATAAGGCTGACAACGGTGCA 59.964 50.000 0.00 0.00 0.00 4.57
4719 5127 1.165270 AATAAGGCTGACAACGGTGC 58.835 50.000 0.00 0.00 0.00 5.01
4720 5128 4.693566 TCTTTAATAAGGCTGACAACGGTG 59.306 41.667 0.00 0.00 32.02 4.94
4721 5129 4.901868 TCTTTAATAAGGCTGACAACGGT 58.098 39.130 0.00 0.00 32.02 4.83
4722 5130 6.984474 TCTATCTTTAATAAGGCTGACAACGG 59.016 38.462 0.00 0.00 32.02 4.44
4723 5131 8.420374 TTCTATCTTTAATAAGGCTGACAACG 57.580 34.615 0.00 0.00 32.02 4.10
4724 5132 9.989869 GTTTCTATCTTTAATAAGGCTGACAAC 57.010 33.333 0.00 0.00 32.02 3.32
4725 5133 9.959721 AGTTTCTATCTTTAATAAGGCTGACAA 57.040 29.630 0.00 0.00 32.02 3.18
4726 5134 9.601217 GAGTTTCTATCTTTAATAAGGCTGACA 57.399 33.333 0.00 0.00 32.02 3.58
4727 5135 9.825109 AGAGTTTCTATCTTTAATAAGGCTGAC 57.175 33.333 0.00 0.00 32.02 3.51
4728 5136 9.823647 CAGAGTTTCTATCTTTAATAAGGCTGA 57.176 33.333 0.00 0.00 32.02 4.26
4729 5137 8.555361 GCAGAGTTTCTATCTTTAATAAGGCTG 58.445 37.037 0.00 0.00 32.02 4.85
4730 5138 7.717436 GGCAGAGTTTCTATCTTTAATAAGGCT 59.283 37.037 0.00 0.00 32.02 4.58
4731 5139 7.499232 TGGCAGAGTTTCTATCTTTAATAAGGC 59.501 37.037 0.00 0.00 32.02 4.35
4732 5140 8.831550 GTGGCAGAGTTTCTATCTTTAATAAGG 58.168 37.037 0.00 0.00 32.02 2.69
4733 5141 9.606631 AGTGGCAGAGTTTCTATCTTTAATAAG 57.393 33.333 0.00 0.00 0.00 1.73
4734 5142 9.959721 AAGTGGCAGAGTTTCTATCTTTAATAA 57.040 29.630 0.00 0.00 0.00 1.40
4735 5143 9.383519 CAAGTGGCAGAGTTTCTATCTTTAATA 57.616 33.333 0.00 0.00 0.00 0.98
4736 5144 8.103305 TCAAGTGGCAGAGTTTCTATCTTTAAT 58.897 33.333 0.00 0.00 0.00 1.40
4737 5145 7.450074 TCAAGTGGCAGAGTTTCTATCTTTAA 58.550 34.615 0.00 0.00 0.00 1.52
4738 5146 7.004555 TCAAGTGGCAGAGTTTCTATCTTTA 57.995 36.000 0.00 0.00 0.00 1.85
4739 5147 5.869579 TCAAGTGGCAGAGTTTCTATCTTT 58.130 37.500 0.00 0.00 0.00 2.52
4740 5148 5.489792 TCAAGTGGCAGAGTTTCTATCTT 57.510 39.130 0.00 0.00 0.00 2.40
4741 5149 5.046014 ACATCAAGTGGCAGAGTTTCTATCT 60.046 40.000 0.00 0.00 0.00 1.98
4742 5150 5.181748 ACATCAAGTGGCAGAGTTTCTATC 58.818 41.667 0.00 0.00 0.00 2.08
4743 5151 5.171339 ACATCAAGTGGCAGAGTTTCTAT 57.829 39.130 0.00 0.00 0.00 1.98
4744 5152 4.623932 ACATCAAGTGGCAGAGTTTCTA 57.376 40.909 0.00 0.00 0.00 2.10
4745 5153 3.498774 ACATCAAGTGGCAGAGTTTCT 57.501 42.857 0.00 0.00 0.00 2.52
4746 5154 4.757149 AGTAACATCAAGTGGCAGAGTTTC 59.243 41.667 0.00 0.00 0.00 2.78
4747 5155 4.516698 CAGTAACATCAAGTGGCAGAGTTT 59.483 41.667 0.00 0.00 0.00 2.66
4748 5156 4.067896 CAGTAACATCAAGTGGCAGAGTT 58.932 43.478 0.00 0.00 0.00 3.01
4749 5157 3.668447 CAGTAACATCAAGTGGCAGAGT 58.332 45.455 0.00 0.00 0.00 3.24
4750 5158 2.417933 GCAGTAACATCAAGTGGCAGAG 59.582 50.000 0.00 0.00 0.00 3.35
4751 5159 2.038952 AGCAGTAACATCAAGTGGCAGA 59.961 45.455 0.00 0.00 0.00 4.26
4752 5160 2.161012 CAGCAGTAACATCAAGTGGCAG 59.839 50.000 0.00 0.00 0.00 4.85
4753 5161 2.153645 CAGCAGTAACATCAAGTGGCA 58.846 47.619 0.00 0.00 0.00 4.92
4754 5162 1.135575 GCAGCAGTAACATCAAGTGGC 60.136 52.381 0.00 0.00 0.00 5.01
4755 5163 2.153645 TGCAGCAGTAACATCAAGTGG 58.846 47.619 0.00 0.00 0.00 4.00
4756 5164 3.003585 TGTTGCAGCAGTAACATCAAGTG 59.996 43.478 8.64 0.00 43.89 3.16
4757 5165 3.213506 TGTTGCAGCAGTAACATCAAGT 58.786 40.909 8.64 0.00 43.89 3.16
4758 5166 3.499537 TCTGTTGCAGCAGTAACATCAAG 59.500 43.478 27.01 2.51 46.76 3.02
4759 5167 3.475575 TCTGTTGCAGCAGTAACATCAA 58.524 40.909 27.01 5.41 46.76 2.57
4760 5168 3.124578 TCTGTTGCAGCAGTAACATCA 57.875 42.857 27.01 6.14 46.76 3.07
4761 5169 4.488126 TTTCTGTTGCAGCAGTAACATC 57.512 40.909 27.01 0.00 46.76 3.06
4762 5170 4.279169 ACATTTCTGTTGCAGCAGTAACAT 59.721 37.500 27.01 14.19 46.76 2.71
4763 5171 3.631686 ACATTTCTGTTGCAGCAGTAACA 59.368 39.130 27.01 11.93 46.03 2.41
4764 5172 4.228912 ACATTTCTGTTGCAGCAGTAAC 57.771 40.909 27.01 3.65 40.29 2.50
4765 5173 4.916983 AACATTTCTGTTGCAGCAGTAA 57.083 36.364 27.01 24.07 43.92 2.24
4775 5183 5.133221 AGTAAGCCTGACAACATTTCTGTT 58.867 37.500 0.00 0.00 46.54 3.16
4776 5184 4.718961 AGTAAGCCTGACAACATTTCTGT 58.281 39.130 0.00 0.00 37.12 3.41
4777 5185 4.756642 TGAGTAAGCCTGACAACATTTCTG 59.243 41.667 0.00 0.00 0.00 3.02
4778 5186 4.973168 TGAGTAAGCCTGACAACATTTCT 58.027 39.130 0.00 0.00 0.00 2.52
4779 5187 5.470098 TCTTGAGTAAGCCTGACAACATTTC 59.530 40.000 0.00 0.00 33.82 2.17
4780 5188 5.376625 TCTTGAGTAAGCCTGACAACATTT 58.623 37.500 0.00 0.00 33.82 2.32
4781 5189 4.973168 TCTTGAGTAAGCCTGACAACATT 58.027 39.130 0.00 0.00 33.82 2.71
4782 5190 4.623932 TCTTGAGTAAGCCTGACAACAT 57.376 40.909 0.00 0.00 33.82 2.71
4783 5191 4.318332 CATCTTGAGTAAGCCTGACAACA 58.682 43.478 0.00 0.00 33.82 3.33
4784 5192 3.686726 CCATCTTGAGTAAGCCTGACAAC 59.313 47.826 0.00 0.00 33.82 3.32
4785 5193 3.327757 ACCATCTTGAGTAAGCCTGACAA 59.672 43.478 0.00 0.00 33.82 3.18
4786 5194 2.906389 ACCATCTTGAGTAAGCCTGACA 59.094 45.455 0.00 0.00 33.82 3.58
4787 5195 3.055819 TGACCATCTTGAGTAAGCCTGAC 60.056 47.826 0.00 0.00 33.82 3.51
4788 5196 3.055819 GTGACCATCTTGAGTAAGCCTGA 60.056 47.826 0.00 0.00 33.82 3.86
4789 5197 3.055530 AGTGACCATCTTGAGTAAGCCTG 60.056 47.826 0.00 0.00 33.82 4.85
4790 5198 3.177228 AGTGACCATCTTGAGTAAGCCT 58.823 45.455 0.00 0.00 33.82 4.58
4791 5199 3.618690 AGTGACCATCTTGAGTAAGCC 57.381 47.619 0.00 0.00 33.82 4.35
4792 5200 5.584253 TCTAGTGACCATCTTGAGTAAGC 57.416 43.478 0.00 0.00 33.82 3.09
4793 5201 7.068103 AGTGATCTAGTGACCATCTTGAGTAAG 59.932 40.741 0.00 0.00 35.16 2.34
4794 5202 6.892456 AGTGATCTAGTGACCATCTTGAGTAA 59.108 38.462 0.00 0.00 0.00 2.24
4795 5203 6.427441 AGTGATCTAGTGACCATCTTGAGTA 58.573 40.000 0.00 0.00 0.00 2.59
4796 5204 5.268387 AGTGATCTAGTGACCATCTTGAGT 58.732 41.667 0.00 0.00 0.00 3.41
4797 5205 5.221224 GGAGTGATCTAGTGACCATCTTGAG 60.221 48.000 0.00 0.00 0.00 3.02
4798 5206 4.646945 GGAGTGATCTAGTGACCATCTTGA 59.353 45.833 0.00 0.00 0.00 3.02
4799 5207 4.403752 TGGAGTGATCTAGTGACCATCTTG 59.596 45.833 0.00 0.00 0.00 3.02
4800 5208 4.614475 TGGAGTGATCTAGTGACCATCTT 58.386 43.478 0.00 0.00 0.00 2.40
4801 5209 4.256983 TGGAGTGATCTAGTGACCATCT 57.743 45.455 0.00 0.00 0.00 2.90
4802 5210 4.798924 GCATGGAGTGATCTAGTGACCATC 60.799 50.000 0.00 0.00 34.96 3.51
4803 5211 3.070734 GCATGGAGTGATCTAGTGACCAT 59.929 47.826 0.00 0.00 37.16 3.55
4804 5212 2.432146 GCATGGAGTGATCTAGTGACCA 59.568 50.000 0.00 0.00 0.00 4.02
4805 5213 2.697751 AGCATGGAGTGATCTAGTGACC 59.302 50.000 0.00 0.00 0.00 4.02
4806 5214 3.715495 CAGCATGGAGTGATCTAGTGAC 58.285 50.000 0.00 0.00 0.00 3.67
4821 5229 2.674852 CTGCTACAACACTACCAGCATG 59.325 50.000 0.00 0.00 41.12 4.06
4822 5230 2.567169 TCTGCTACAACACTACCAGCAT 59.433 45.455 0.00 0.00 41.12 3.79
4823 5231 1.967779 TCTGCTACAACACTACCAGCA 59.032 47.619 0.00 0.00 39.79 4.41
4824 5232 2.743636 TCTGCTACAACACTACCAGC 57.256 50.000 0.00 0.00 0.00 4.85
4825 5233 4.521130 TCTTCTGCTACAACACTACCAG 57.479 45.455 0.00 0.00 0.00 4.00
4826 5234 4.322725 CCATCTTCTGCTACAACACTACCA 60.323 45.833 0.00 0.00 0.00 3.25
4827 5235 4.184629 CCATCTTCTGCTACAACACTACC 58.815 47.826 0.00 0.00 0.00 3.18
4828 5236 4.184629 CCCATCTTCTGCTACAACACTAC 58.815 47.826 0.00 0.00 0.00 2.73
4829 5237 3.838317 ACCCATCTTCTGCTACAACACTA 59.162 43.478 0.00 0.00 0.00 2.74
4830 5238 2.639839 ACCCATCTTCTGCTACAACACT 59.360 45.455 0.00 0.00 0.00 3.55
4831 5239 3.003480 GACCCATCTTCTGCTACAACAC 58.997 50.000 0.00 0.00 0.00 3.32
4832 5240 2.637382 TGACCCATCTTCTGCTACAACA 59.363 45.455 0.00 0.00 0.00 3.33
4833 5241 3.265791 CTGACCCATCTTCTGCTACAAC 58.734 50.000 0.00 0.00 0.00 3.32
4834 5242 2.906389 ACTGACCCATCTTCTGCTACAA 59.094 45.455 0.00 0.00 0.00 2.41
4835 5243 2.540383 ACTGACCCATCTTCTGCTACA 58.460 47.619 0.00 0.00 0.00 2.74
4836 5244 3.491792 GCTACTGACCCATCTTCTGCTAC 60.492 52.174 0.00 0.00 0.00 3.58
4837 5245 2.695666 GCTACTGACCCATCTTCTGCTA 59.304 50.000 0.00 0.00 0.00 3.49
4838 5246 1.484240 GCTACTGACCCATCTTCTGCT 59.516 52.381 0.00 0.00 0.00 4.24
4839 5247 1.208052 TGCTACTGACCCATCTTCTGC 59.792 52.381 0.00 0.00 0.00 4.26
4840 5248 3.834489 ATGCTACTGACCCATCTTCTG 57.166 47.619 0.00 0.00 0.00 3.02
4841 5249 4.965532 AGTAATGCTACTGACCCATCTTCT 59.034 41.667 0.00 0.00 36.98 2.85
4842 5250 5.283457 AGTAATGCTACTGACCCATCTTC 57.717 43.478 0.00 0.00 36.98 2.87
4853 5261 4.223032 AGGCACAACTACAGTAATGCTACT 59.777 41.667 14.13 4.99 39.04 2.57
4854 5262 4.504858 AGGCACAACTACAGTAATGCTAC 58.495 43.478 14.13 3.32 38.41 3.58
4855 5263 4.819105 AGGCACAACTACAGTAATGCTA 57.181 40.909 14.13 0.00 38.41 3.49
4856 5264 3.703001 AGGCACAACTACAGTAATGCT 57.297 42.857 14.13 2.71 38.41 3.79
4857 5265 4.201685 CGTAAGGCACAACTACAGTAATGC 60.202 45.833 8.55 8.55 37.93 3.56
4858 5266 4.927425 ACGTAAGGCACAACTACAGTAATG 59.073 41.667 0.00 0.00 46.39 1.90
4859 5267 5.143376 ACGTAAGGCACAACTACAGTAAT 57.857 39.130 0.00 0.00 46.39 1.89
4860 5268 4.589216 ACGTAAGGCACAACTACAGTAA 57.411 40.909 0.00 0.00 46.39 2.24
4874 5282 1.931172 CAATTACCCTGCGACGTAAGG 59.069 52.381 10.72 10.72 46.39 2.69
4876 5284 2.008045 GCCAATTACCCTGCGACGTAA 61.008 52.381 0.00 0.00 0.00 3.18
4877 5285 0.460635 GCCAATTACCCTGCGACGTA 60.461 55.000 0.00 0.00 0.00 3.57
4878 5286 1.743995 GCCAATTACCCTGCGACGT 60.744 57.895 0.00 0.00 0.00 4.34
4879 5287 1.429148 GAGCCAATTACCCTGCGACG 61.429 60.000 0.00 0.00 0.00 5.12
4880 5288 0.392461 TGAGCCAATTACCCTGCGAC 60.392 55.000 0.00 0.00 0.00 5.19
4881 5289 0.546122 ATGAGCCAATTACCCTGCGA 59.454 50.000 0.00 0.00 0.00 5.10
4882 5290 2.146342 CTATGAGCCAATTACCCTGCG 58.854 52.381 0.00 0.00 0.00 5.18
4883 5291 2.880890 CACTATGAGCCAATTACCCTGC 59.119 50.000 0.00 0.00 0.00 4.85
4884 5292 2.880890 GCACTATGAGCCAATTACCCTG 59.119 50.000 0.00 0.00 0.00 4.45
4885 5293 2.780010 AGCACTATGAGCCAATTACCCT 59.220 45.455 0.00 0.00 0.00 4.34
4886 5294 2.880890 CAGCACTATGAGCCAATTACCC 59.119 50.000 0.00 0.00 0.00 3.69
4887 5295 3.808728 TCAGCACTATGAGCCAATTACC 58.191 45.455 0.00 0.00 0.00 2.85
4888 5296 3.812053 CCTCAGCACTATGAGCCAATTAC 59.188 47.826 0.00 0.00 44.47 1.89
4889 5297 3.455910 ACCTCAGCACTATGAGCCAATTA 59.544 43.478 0.00 0.00 44.47 1.40
4890 5298 2.240667 ACCTCAGCACTATGAGCCAATT 59.759 45.455 0.00 0.00 44.47 2.32
4891 5299 1.842562 ACCTCAGCACTATGAGCCAAT 59.157 47.619 0.00 0.00 44.47 3.16
4892 5300 1.279496 ACCTCAGCACTATGAGCCAA 58.721 50.000 0.00 0.00 44.47 4.52
4893 5301 2.159179 TACCTCAGCACTATGAGCCA 57.841 50.000 0.00 0.00 44.47 4.75
4894 5302 3.543680 TTTACCTCAGCACTATGAGCC 57.456 47.619 0.00 0.00 44.47 4.70
4895 5303 6.367422 GTGATATTTACCTCAGCACTATGAGC 59.633 42.308 0.00 0.00 44.47 4.26
4896 5304 7.665690 AGTGATATTTACCTCAGCACTATGAG 58.334 38.462 0.00 0.00 45.24 2.90
4897 5305 7.603180 AGTGATATTTACCTCAGCACTATGA 57.397 36.000 0.00 0.00 33.78 2.15
4898 5306 8.668510 AAAGTGATATTTACCTCAGCACTATG 57.331 34.615 0.00 0.00 34.38 2.23
4899 5307 9.113838 CAAAAGTGATATTTACCTCAGCACTAT 57.886 33.333 0.00 0.00 34.38 2.12
4900 5308 8.318412 TCAAAAGTGATATTTACCTCAGCACTA 58.682 33.333 0.00 0.00 34.38 2.74
4901 5309 7.119846 GTCAAAAGTGATATTTACCTCAGCACT 59.880 37.037 0.00 0.00 35.80 4.40
4902 5310 7.094805 TGTCAAAAGTGATATTTACCTCAGCAC 60.095 37.037 0.00 0.00 35.80 4.40
4903 5311 6.939730 TGTCAAAAGTGATATTTACCTCAGCA 59.060 34.615 0.00 0.00 35.80 4.41
4904 5312 7.377766 TGTCAAAAGTGATATTTACCTCAGC 57.622 36.000 0.00 0.00 35.80 4.26
4905 5313 9.778993 CAATGTCAAAAGTGATATTTACCTCAG 57.221 33.333 0.00 0.00 41.34 3.35
4906 5314 9.295825 ACAATGTCAAAAGTGATATTTACCTCA 57.704 29.630 0.00 0.00 41.34 3.86
4947 5355 3.871006 TCGCAACAGATGAATCCATACAC 59.129 43.478 0.00 0.00 32.09 2.90
4949 5357 3.871006 TGTCGCAACAGATGAATCCATAC 59.129 43.478 0.00 0.00 32.09 2.39
4958 5366 2.654749 TAGGAGTGTCGCAACAGATG 57.345 50.000 0.00 0.00 35.64 2.90
4969 5377 4.221703 GCAGCATATACCTCATAGGAGTGT 59.778 45.833 3.36 3.96 37.67 3.55
4980 5388 3.041211 TGACCTCAAGCAGCATATACCT 58.959 45.455 0.00 0.00 0.00 3.08
4982 5390 4.384056 ACATGACCTCAAGCAGCATATAC 58.616 43.478 0.00 0.00 0.00 1.47
5006 5414 4.090761 AGAAGAACCTCAGCACATTTCA 57.909 40.909 0.00 0.00 0.00 2.69
5073 5483 0.461961 CCTTCTCGGATCCTCACACC 59.538 60.000 10.75 0.00 33.16 4.16
5086 5496 5.356470 CCATTTCTGAATCCTTGACCTTCTC 59.644 44.000 0.00 0.00 0.00 2.87
5094 5504 4.272489 TGCCTACCATTTCTGAATCCTTG 58.728 43.478 0.00 0.00 0.00 3.61
5118 5528 0.317020 GAACAGCCACGTCAAACAGC 60.317 55.000 0.00 0.00 0.00 4.40
5127 5537 0.452987 CCCATGAATGAACAGCCACG 59.547 55.000 0.00 0.00 0.00 4.94
5162 5572 4.712337 ACTTCCTCAGTTCTTCCGTATGAT 59.288 41.667 0.00 0.00 27.32 2.45
5170 5580 1.803555 GCTGCACTTCCTCAGTTCTTC 59.196 52.381 0.00 0.00 30.92 2.87
5206 5616 2.226437 GTGTCAACCTGTGCAAGTATGG 59.774 50.000 0.00 0.00 0.00 2.74
5219 5629 3.343421 GCGTCCCACGTGTCAACC 61.343 66.667 15.65 0.00 44.73 3.77
5230 5640 3.718210 GACTGATCGTGGGCGTCCC 62.718 68.421 2.12 5.67 45.71 4.46


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

AutoCloner maintained by Alex Coulton.