Multiple sequence alignment - TraesCS5B01G421900

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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 TraesCS5B01G421900 chr5B 100.000 2356 0 0 1 2356 597145641 597147996 0.000000e+00 4351.0
1 TraesCS5B01G421900 chr5B 100.000 301 0 0 2711 3011 597148351 597148651 9.430000e-155 556.0
2 TraesCS5B01G421900 chr5A 92.900 1662 72 21 707 2342 606840865 606842506 0.000000e+00 2374.0
3 TraesCS5B01G421900 chr5A 85.691 608 35 18 1 606 606840108 606840665 7.190000e-166 593.0
4 TraesCS5B01G421900 chr5A 79.558 362 33 22 1968 2318 606842694 606843025 1.410000e-53 220.0
5 TraesCS5B01G421900 chr5A 96.629 89 3 0 604 692 606840715 606840803 6.730000e-32 148.0
6 TraesCS5B01G421900 chr5A 93.069 101 6 1 2715 2815 606844773 606844872 2.420000e-31 147.0
7 TraesCS5B01G421900 chr5D 92.003 1388 66 15 968 2337 486100274 486101634 0.000000e+00 1906.0
8 TraesCS5B01G421900 chr5D 88.293 615 41 12 3 606 486099199 486099793 0.000000e+00 708.0
9 TraesCS5B01G421900 chr5D 93.085 188 12 1 708 895 486099993 486100179 1.060000e-69 274.0
10 TraesCS5B01G421900 chr5D 92.391 92 4 1 604 692 486099843 486099934 8.760000e-26 128.0
11 TraesCS5B01G421900 chr4B 92.887 239 11 3 1557 1795 26331078 26330846 2.870000e-90 342.0
12 TraesCS5B01G421900 chr3A 86.364 88 6 4 2725 2810 623941091 623941008 1.150000e-14 91.6
13 TraesCS5B01G421900 chrUn 85.882 85 9 1 2725 2809 103530590 103530509 1.490000e-13 87.9
14 TraesCS5B01G421900 chr6A 84.615 91 10 2 2720 2808 29079536 29079624 1.490000e-13 87.9


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 TraesCS5B01G421900 chr5B 597145641 597148651 3010 False 2453.5 4351 100.0000 1 3011 2 chr5B.!!$F1 3010
1 TraesCS5B01G421900 chr5A 606840108 606844872 4764 False 696.4 2374 89.5694 1 2815 5 chr5A.!!$F1 2814
2 TraesCS5B01G421900 chr5D 486099199 486101634 2435 False 754.0 1906 91.4430 3 2337 4 chr5D.!!$F1 2334

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
302 310 0.321919 CAGCAGCAGGAGGTAAAGCA 60.322 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2459 0.041535 TCCCAATGGCCAGCTTGATT 59.958 50.0 18.76 0.72 0.0 2.57 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
76 77 0.517316 AAGCGCTTCCAATGAACGAC 59.483 50.000 18.98 0.00 31.22 4.34
115 116 1.425825 CGATCCGATCCGATCCGAG 59.574 63.158 15.61 2.04 36.13 4.63
151 152 3.418619 CACACGCACGAAAGAAAGAAATG 59.581 43.478 0.00 0.00 0.00 2.32
219 220 2.789409 GGAGGCCACATCCCATATAC 57.211 55.000 5.01 0.00 0.00 1.47
242 243 3.363724 GCCGCTAATGCTTTTGTGTTTAC 59.636 43.478 6.59 0.00 36.97 2.01
243 244 4.794169 CCGCTAATGCTTTTGTGTTTACT 58.206 39.130 6.59 0.00 36.97 2.24
244 245 4.616802 CCGCTAATGCTTTTGTGTTTACTG 59.383 41.667 6.59 0.00 36.97 2.74
245 246 5.212194 CGCTAATGCTTTTGTGTTTACTGT 58.788 37.500 0.00 0.00 36.97 3.55
246 247 5.339611 CGCTAATGCTTTTGTGTTTACTGTC 59.660 40.000 0.00 0.00 36.97 3.51
247 248 5.339611 GCTAATGCTTTTGTGTTTACTGTCG 59.660 40.000 0.00 0.00 36.03 4.35
248 249 3.059634 TGCTTTTGTGTTTACTGTCGC 57.940 42.857 0.00 0.00 0.00 5.19
249 250 2.420372 TGCTTTTGTGTTTACTGTCGCA 59.580 40.909 0.00 0.00 0.00 5.10
250 251 3.035942 GCTTTTGTGTTTACTGTCGCAG 58.964 45.455 5.47 5.47 37.52 5.18
251 252 2.748461 TTTGTGTTTACTGTCGCAGC 57.252 45.000 6.74 0.00 34.37 5.25
288 296 3.003480 GAGTGGGTAACTAAAGCAGCAG 58.997 50.000 0.00 0.00 40.07 4.24
289 297 1.468914 GTGGGTAACTAAAGCAGCAGC 59.531 52.381 0.00 0.00 42.56 5.25
290 298 1.073125 TGGGTAACTAAAGCAGCAGCA 59.927 47.619 3.17 0.00 45.49 4.41
291 299 1.740025 GGGTAACTAAAGCAGCAGCAG 59.260 52.381 3.17 0.00 45.49 4.24
302 310 0.321919 CAGCAGCAGGAGGTAAAGCA 60.322 55.000 0.00 0.00 0.00 3.91
340 348 4.251103 GACCAAATCCATCCCCTTTACT 57.749 45.455 0.00 0.00 0.00 2.24
367 375 4.023021 GCCCGGTTCTGTTAAACAAATGTA 60.023 41.667 0.00 0.00 0.00 2.29
406 414 2.335712 GCTTTTGTCGGCCCCTCTG 61.336 63.158 0.00 0.00 0.00 3.35
436 444 1.109920 GCCCGTCAGATCCAGCTCTA 61.110 60.000 0.00 0.00 0.00 2.43
442 450 4.320861 CCGTCAGATCCAGCTCTACATTAG 60.321 50.000 0.00 0.00 0.00 1.73
469 477 9.325198 CTTAATCATTAAGCACTACCATGTACA 57.675 33.333 4.17 0.00 36.54 2.90
472 480 5.584649 TCATTAAGCACTACCATGTACAAGC 59.415 40.000 0.00 0.00 0.00 4.01
473 481 2.403252 AGCACTACCATGTACAAGCC 57.597 50.000 0.00 0.00 0.00 4.35
474 482 1.909302 AGCACTACCATGTACAAGCCT 59.091 47.619 0.00 0.00 0.00 4.58
478 486 4.442706 CACTACCATGTACAAGCCTAAGG 58.557 47.826 0.00 0.00 0.00 2.69
479 487 3.454812 ACTACCATGTACAAGCCTAAGGG 59.545 47.826 0.00 0.00 0.00 3.95
512 520 1.290955 CATTGCTGCAACTGTGGGG 59.709 57.895 18.51 0.00 0.00 4.96
529 537 2.024846 TGGGGTGGTGAAAAGAAGTGAA 60.025 45.455 0.00 0.00 0.00 3.18
530 538 2.623416 GGGGTGGTGAAAAGAAGTGAAG 59.377 50.000 0.00 0.00 0.00 3.02
533 551 3.945285 GGTGGTGAAAAGAAGTGAAGTGA 59.055 43.478 0.00 0.00 0.00 3.41
565 583 8.824781 TCAAAACCATATGTCAAAATTGTGTTG 58.175 29.630 1.24 2.10 0.00 3.33
569 587 5.577945 CCATATGTCAAAATTGTGTTGAGGC 59.422 40.000 1.24 0.00 35.71 4.70
593 611 1.670967 GGCATTGCAGGTTTTCAGAGC 60.671 52.381 11.39 0.00 0.00 4.09
634 704 4.410492 AGATTTAGCGTTGCAACTGAAG 57.590 40.909 26.09 12.40 0.00 3.02
655 725 1.421268 TGTGATTCAGTGGGAGTGCTT 59.579 47.619 0.00 0.00 0.00 3.91
687 760 7.981225 AGTTGAACCATATAAAAATCCATGCAC 59.019 33.333 0.00 0.00 0.00 4.57
692 765 9.683870 AACCATATAAAAATCCATGCACAAAAT 57.316 25.926 0.00 0.00 0.00 1.82
695 768 4.769859 AAAAATCCATGCACAAAATGGC 57.230 36.364 0.00 0.00 43.70 4.40
696 769 3.706600 AAATCCATGCACAAAATGGCT 57.293 38.095 0.00 0.00 43.70 4.75
697 770 2.684001 ATCCATGCACAAAATGGCTG 57.316 45.000 0.00 0.00 43.70 4.85
699 772 1.546923 TCCATGCACAAAATGGCTGAG 59.453 47.619 0.00 0.00 43.70 3.35
704 777 2.957680 TGCACAAAATGGCTGAGAGAAA 59.042 40.909 0.00 0.00 0.00 2.52
705 778 3.384146 TGCACAAAATGGCTGAGAGAAAA 59.616 39.130 0.00 0.00 0.00 2.29
795 916 5.062934 CGGAAAAGGTGAAAGTTTGAAAACC 59.937 40.000 0.00 0.00 39.71 3.27
796 917 5.353123 GGAAAAGGTGAAAGTTTGAAAACCC 59.647 40.000 0.00 0.00 39.71 4.11
895 1017 1.003696 AGGAGAAGCAAGTTGGTAGCC 59.996 52.381 8.21 9.89 0.00 3.93
945 1101 2.672307 GCAAGCAGCAGCAGGTCT 60.672 61.111 3.17 0.00 45.49 3.85
946 1102 2.979197 GCAAGCAGCAGCAGGTCTG 61.979 63.158 3.17 0.00 45.49 3.51
964 1126 7.576666 GCAGGTCTGGTATACTGAATCTATCTG 60.577 44.444 2.25 0.08 32.86 2.90
983 1145 1.589716 GACCCTGCATTGCACTCCAC 61.590 60.000 7.38 0.00 33.79 4.02
984 1146 2.345760 CCCTGCATTGCACTCCACC 61.346 63.158 7.38 0.00 33.79 4.61
985 1147 2.693762 CCTGCATTGCACTCCACCG 61.694 63.158 7.38 0.00 33.79 4.94
986 1148 2.672651 TGCATTGCACTCCACCGG 60.673 61.111 7.38 0.00 31.71 5.28
987 1149 4.120331 GCATTGCACTCCACCGGC 62.120 66.667 0.00 0.00 0.00 6.13
995 1157 3.866582 CTCCACCGGCCAGGGATC 61.867 72.222 16.44 0.00 46.96 3.36
1068 1230 0.391793 GCTACCTCAACCTGCTCACC 60.392 60.000 0.00 0.00 0.00 4.02
1398 1560 2.117156 GGACTACTCGCCGTGGCTA 61.117 63.158 9.55 0.00 39.32 3.93
1863 2025 2.100197 CGATGGGACTACTTCTGGTCA 58.900 52.381 0.00 0.00 34.49 4.02
1884 2046 1.151908 CCTCCTCGCCCTAGCTACT 59.848 63.158 0.00 0.00 36.60 2.57
1885 2047 1.175983 CCTCCTCGCCCTAGCTACTG 61.176 65.000 0.00 0.00 36.60 2.74
1886 2048 0.466555 CTCCTCGCCCTAGCTACTGT 60.467 60.000 0.00 0.00 36.60 3.55
1887 2049 0.841961 TCCTCGCCCTAGCTACTGTA 59.158 55.000 0.00 0.00 36.60 2.74
1888 2050 0.953003 CCTCGCCCTAGCTACTGTAC 59.047 60.000 0.00 0.00 36.60 2.90
1912 2083 2.981805 CGTTCAACTCACCATTTGCATG 59.018 45.455 0.00 0.00 0.00 4.06
2012 2191 6.374333 GGCCACAGAGAACAAATCTATTAACA 59.626 38.462 0.00 0.00 38.96 2.41
2013 2192 7.094377 GGCCACAGAGAACAAATCTATTAACAA 60.094 37.037 0.00 0.00 38.96 2.83
2041 2220 2.440409 CCTCCTTCCTTGGTTCACATG 58.560 52.381 0.00 0.00 0.00 3.21
2042 2221 2.440409 CTCCTTCCTTGGTTCACATGG 58.560 52.381 0.00 0.00 43.85 3.66
2043 2222 1.780309 TCCTTCCTTGGTTCACATGGT 59.220 47.619 0.00 0.00 43.18 3.55
2044 2223 1.888512 CCTTCCTTGGTTCACATGGTG 59.111 52.381 0.00 0.00 43.18 4.17
2045 2224 1.888512 CTTCCTTGGTTCACATGGTGG 59.111 52.381 0.00 0.00 43.18 4.61
2160 2358 8.442632 AAGAGTTTGATCCACATGTATGTATG 57.557 34.615 0.00 0.00 39.39 2.39
2161 2359 7.568349 AGAGTTTGATCCACATGTATGTATGT 58.432 34.615 0.00 0.00 41.77 2.29
2162 2360 8.704668 AGAGTTTGATCCACATGTATGTATGTA 58.295 33.333 0.00 0.00 39.17 2.29
2163 2361 8.893219 AGTTTGATCCACATGTATGTATGTAG 57.107 34.615 0.00 0.00 39.17 2.74
2164 2362 7.442364 AGTTTGATCCACATGTATGTATGTAGC 59.558 37.037 0.00 0.00 39.17 3.58
2165 2363 5.793817 TGATCCACATGTATGTATGTAGCC 58.206 41.667 0.00 0.00 39.17 3.93
2246 2445 7.329962 TGTCGTCGTGTATTCAATTCTTATTGT 59.670 33.333 0.00 0.00 41.54 2.71
2249 2448 8.380644 CGTCGTGTATTCAATTCTTATTGTTCT 58.619 33.333 0.00 0.00 41.54 3.01
2314 4701 2.544844 TTGGACCCTTATCTCCGTCT 57.455 50.000 0.00 0.00 0.00 4.18
2317 4704 1.411216 GGACCCTTATCTCCGTCTCCA 60.411 57.143 0.00 0.00 0.00 3.86
2337 4724 1.261938 CGACAGTCACCCCATACCCA 61.262 60.000 0.41 0.00 0.00 4.51
2342 4729 0.991355 GTCACCCCATACCCATCCCA 60.991 60.000 0.00 0.00 0.00 4.37
2347 4734 0.697511 CCCATACCCATCCCAGTCCA 60.698 60.000 0.00 0.00 0.00 4.02
2348 4735 0.474184 CCATACCCATCCCAGTCCAC 59.526 60.000 0.00 0.00 0.00 4.02
2349 4736 0.106708 CATACCCATCCCAGTCCACG 59.893 60.000 0.00 0.00 0.00 4.94
2350 4737 0.326238 ATACCCATCCCAGTCCACGT 60.326 55.000 0.00 0.00 0.00 4.49
2351 4738 0.335705 TACCCATCCCAGTCCACGTA 59.664 55.000 0.00 0.00 0.00 3.57
2352 4739 0.545787 ACCCATCCCAGTCCACGTAA 60.546 55.000 0.00 0.00 0.00 3.18
2354 4741 0.611200 CCATCCCAGTCCACGTAACA 59.389 55.000 0.00 0.00 0.00 2.41
2355 4742 1.209504 CCATCCCAGTCCACGTAACAT 59.790 52.381 0.00 0.00 0.00 2.71
2743 5130 4.997565 ACACAATCAACAACAACCTTCAG 58.002 39.130 0.00 0.00 0.00 3.02
2760 5147 9.612620 CAACCTTCAGTAGCATTTTAGTAAAAG 57.387 33.333 13.25 7.17 33.22 2.27
2786 5173 9.934190 GAAAAACAACATTTCAGCACAATAAAT 57.066 25.926 0.00 0.00 36.89 1.40
2810 5197 1.843368 TGTCGTCACTAGGTTAGGGG 58.157 55.000 0.00 0.00 0.00 4.79
2811 5198 1.355381 TGTCGTCACTAGGTTAGGGGA 59.645 52.381 0.00 0.00 0.00 4.81
2814 5201 3.450096 GTCGTCACTAGGTTAGGGGATTT 59.550 47.826 0.00 0.00 0.00 2.17
2815 5202 4.081254 GTCGTCACTAGGTTAGGGGATTTT 60.081 45.833 0.00 0.00 0.00 1.82
2816 5203 4.081309 TCGTCACTAGGTTAGGGGATTTTG 60.081 45.833 0.00 0.00 0.00 2.44
2817 5204 4.524053 GTCACTAGGTTAGGGGATTTTGG 58.476 47.826 0.00 0.00 0.00 3.28
2818 5205 4.018688 GTCACTAGGTTAGGGGATTTTGGT 60.019 45.833 0.00 0.00 0.00 3.67
2819 5206 4.604490 TCACTAGGTTAGGGGATTTTGGTT 59.396 41.667 0.00 0.00 0.00 3.67
2820 5207 4.705023 CACTAGGTTAGGGGATTTTGGTTG 59.295 45.833 0.00 0.00 0.00 3.77
2821 5208 4.604490 ACTAGGTTAGGGGATTTTGGTTGA 59.396 41.667 0.00 0.00 0.00 3.18
2822 5209 4.479156 AGGTTAGGGGATTTTGGTTGAA 57.521 40.909 0.00 0.00 0.00 2.69
2823 5210 4.416516 AGGTTAGGGGATTTTGGTTGAAG 58.583 43.478 0.00 0.00 0.00 3.02
2824 5211 3.513912 GGTTAGGGGATTTTGGTTGAAGG 59.486 47.826 0.00 0.00 0.00 3.46
2825 5212 4.412843 GTTAGGGGATTTTGGTTGAAGGA 58.587 43.478 0.00 0.00 0.00 3.36
2826 5213 3.628832 AGGGGATTTTGGTTGAAGGAA 57.371 42.857 0.00 0.00 0.00 3.36
2827 5214 3.510459 AGGGGATTTTGGTTGAAGGAAG 58.490 45.455 0.00 0.00 0.00 3.46
2828 5215 3.142028 AGGGGATTTTGGTTGAAGGAAGA 59.858 43.478 0.00 0.00 0.00 2.87
2829 5216 4.096681 GGGGATTTTGGTTGAAGGAAGAT 58.903 43.478 0.00 0.00 0.00 2.40
2830 5217 4.532126 GGGGATTTTGGTTGAAGGAAGATT 59.468 41.667 0.00 0.00 0.00 2.40
2831 5218 5.719563 GGGGATTTTGGTTGAAGGAAGATTA 59.280 40.000 0.00 0.00 0.00 1.75
2832 5219 6.127338 GGGGATTTTGGTTGAAGGAAGATTAG 60.127 42.308 0.00 0.00 0.00 1.73
2833 5220 6.127338 GGGATTTTGGTTGAAGGAAGATTAGG 60.127 42.308 0.00 0.00 0.00 2.69
2834 5221 5.722021 TTTTGGTTGAAGGAAGATTAGGC 57.278 39.130 0.00 0.00 0.00 3.93
2835 5222 2.985896 TGGTTGAAGGAAGATTAGGCG 58.014 47.619 0.00 0.00 0.00 5.52
2836 5223 2.569853 TGGTTGAAGGAAGATTAGGCGA 59.430 45.455 0.00 0.00 0.00 5.54
2837 5224 3.199946 TGGTTGAAGGAAGATTAGGCGAT 59.800 43.478 0.00 0.00 0.00 4.58
2838 5225 4.200092 GGTTGAAGGAAGATTAGGCGATT 58.800 43.478 0.00 0.00 0.00 3.34
2839 5226 4.640647 GGTTGAAGGAAGATTAGGCGATTT 59.359 41.667 0.00 0.00 0.00 2.17
2840 5227 5.220873 GGTTGAAGGAAGATTAGGCGATTTC 60.221 44.000 0.00 0.00 0.00 2.17
2841 5228 5.097742 TGAAGGAAGATTAGGCGATTTCA 57.902 39.130 0.00 0.00 0.00 2.69
2842 5229 4.876107 TGAAGGAAGATTAGGCGATTTCAC 59.124 41.667 0.00 0.00 0.00 3.18
2843 5230 3.458189 AGGAAGATTAGGCGATTTCACG 58.542 45.455 0.00 0.00 0.00 4.35
2844 5231 2.544267 GGAAGATTAGGCGATTTCACGG 59.456 50.000 0.00 0.00 0.00 4.94
2845 5232 2.240493 AGATTAGGCGATTTCACGGG 57.760 50.000 0.00 0.00 0.00 5.28
2846 5233 1.760613 AGATTAGGCGATTTCACGGGA 59.239 47.619 0.00 0.00 0.00 5.14
2847 5234 2.368875 AGATTAGGCGATTTCACGGGAT 59.631 45.455 0.00 0.00 0.00 3.85
2848 5235 2.702592 TTAGGCGATTTCACGGGATT 57.297 45.000 0.00 0.00 0.00 3.01
2849 5236 1.948104 TAGGCGATTTCACGGGATTG 58.052 50.000 0.00 0.00 0.00 2.67
2850 5237 0.748005 AGGCGATTTCACGGGATTGG 60.748 55.000 0.00 0.00 0.00 3.16
2851 5238 1.724582 GGCGATTTCACGGGATTGGG 61.725 60.000 0.00 0.00 0.00 4.12
2852 5239 1.029947 GCGATTTCACGGGATTGGGT 61.030 55.000 0.00 0.00 0.00 4.51
2853 5240 1.459450 CGATTTCACGGGATTGGGTT 58.541 50.000 0.00 0.00 0.00 4.11
2854 5241 1.132262 CGATTTCACGGGATTGGGTTG 59.868 52.381 0.00 0.00 0.00 3.77
2855 5242 2.442413 GATTTCACGGGATTGGGTTGA 58.558 47.619 0.00 0.00 0.00 3.18
2856 5243 2.366640 TTTCACGGGATTGGGTTGAA 57.633 45.000 0.00 0.00 0.00 2.69
2857 5244 1.904287 TTCACGGGATTGGGTTGAAG 58.096 50.000 0.00 0.00 0.00 3.02
2858 5245 1.060729 TCACGGGATTGGGTTGAAGA 58.939 50.000 0.00 0.00 0.00 2.87
2859 5246 1.003118 TCACGGGATTGGGTTGAAGAG 59.997 52.381 0.00 0.00 0.00 2.85
2860 5247 1.003118 CACGGGATTGGGTTGAAGAGA 59.997 52.381 0.00 0.00 0.00 3.10
2861 5248 1.279271 ACGGGATTGGGTTGAAGAGAG 59.721 52.381 0.00 0.00 0.00 3.20
2862 5249 1.407437 CGGGATTGGGTTGAAGAGAGG 60.407 57.143 0.00 0.00 0.00 3.69
2863 5250 1.064389 GGGATTGGGTTGAAGAGAGGG 60.064 57.143 0.00 0.00 0.00 4.30
2864 5251 1.916181 GGATTGGGTTGAAGAGAGGGA 59.084 52.381 0.00 0.00 0.00 4.20
2865 5252 2.511637 GGATTGGGTTGAAGAGAGGGAT 59.488 50.000 0.00 0.00 0.00 3.85
2866 5253 3.434310 GGATTGGGTTGAAGAGAGGGATC 60.434 52.174 0.00 0.00 0.00 3.36
2867 5254 2.342406 TGGGTTGAAGAGAGGGATCA 57.658 50.000 0.00 0.00 0.00 2.92
2868 5255 2.850833 TGGGTTGAAGAGAGGGATCAT 58.149 47.619 0.00 0.00 0.00 2.45
2869 5256 2.774234 TGGGTTGAAGAGAGGGATCATC 59.226 50.000 0.00 0.00 0.00 2.92
2870 5257 2.774234 GGGTTGAAGAGAGGGATCATCA 59.226 50.000 0.00 0.00 0.00 3.07
2871 5258 3.200825 GGGTTGAAGAGAGGGATCATCAA 59.799 47.826 0.00 0.00 35.26 2.57
2872 5259 4.324563 GGGTTGAAGAGAGGGATCATCAAA 60.325 45.833 0.00 0.00 38.29 2.69
2873 5260 5.444176 GGTTGAAGAGAGGGATCATCAAAT 58.556 41.667 0.00 0.00 38.29 2.32
2874 5261 5.530543 GGTTGAAGAGAGGGATCATCAAATC 59.469 44.000 0.00 0.00 38.29 2.17
2875 5262 5.301835 TGAAGAGAGGGATCATCAAATCC 57.698 43.478 0.00 0.00 43.90 3.01
2876 5263 4.973856 TGAAGAGAGGGATCATCAAATCCT 59.026 41.667 0.00 0.00 44.06 3.24
2877 5264 5.071519 TGAAGAGAGGGATCATCAAATCCTC 59.928 44.000 4.29 4.29 44.06 3.71
2878 5265 4.830138 AGAGAGGGATCATCAAATCCTCT 58.170 43.478 12.61 12.61 44.06 3.69
2879 5266 5.226015 AGAGAGGGATCATCAAATCCTCTT 58.774 41.667 13.61 4.34 44.06 2.85
2880 5267 6.388814 AGAGAGGGATCATCAAATCCTCTTA 58.611 40.000 13.61 0.00 44.06 2.10
2881 5268 6.848631 AGAGAGGGATCATCAAATCCTCTTAA 59.151 38.462 13.61 0.00 44.06 1.85
2882 5269 7.349330 AGAGAGGGATCATCAAATCCTCTTAAA 59.651 37.037 13.61 0.00 44.06 1.52
2883 5270 8.054931 AGAGGGATCATCAAATCCTCTTAAAT 57.945 34.615 8.23 0.00 44.06 1.40
2884 5271 8.162746 AGAGGGATCATCAAATCCTCTTAAATC 58.837 37.037 8.23 0.00 44.06 2.17
2885 5272 7.237255 AGGGATCATCAAATCCTCTTAAATCC 58.763 38.462 0.00 0.00 44.06 3.01
2886 5273 6.435591 GGGATCATCAAATCCTCTTAAATCCC 59.564 42.308 0.00 0.00 44.06 3.85
2887 5274 6.435591 GGATCATCAAATCCTCTTAAATCCCC 59.564 42.308 0.00 0.00 41.78 4.81
2888 5275 6.339999 TCATCAAATCCTCTTAAATCCCCA 57.660 37.500 0.00 0.00 0.00 4.96
2889 5276 6.129179 TCATCAAATCCTCTTAAATCCCCAC 58.871 40.000 0.00 0.00 0.00 4.61
2890 5277 4.867086 TCAAATCCTCTTAAATCCCCACC 58.133 43.478 0.00 0.00 0.00 4.61
2891 5278 3.960755 CAAATCCTCTTAAATCCCCACCC 59.039 47.826 0.00 0.00 0.00 4.61
2892 5279 1.603634 TCCTCTTAAATCCCCACCCC 58.396 55.000 0.00 0.00 0.00 4.95
2893 5280 1.083912 TCCTCTTAAATCCCCACCCCT 59.916 52.381 0.00 0.00 0.00 4.79
2894 5281 1.930204 CCTCTTAAATCCCCACCCCTT 59.070 52.381 0.00 0.00 0.00 3.95
2895 5282 2.314852 CCTCTTAAATCCCCACCCCTTT 59.685 50.000 0.00 0.00 0.00 3.11
2896 5283 3.245984 CCTCTTAAATCCCCACCCCTTTT 60.246 47.826 0.00 0.00 0.00 2.27
2897 5284 3.769300 CTCTTAAATCCCCACCCCTTTTG 59.231 47.826 0.00 0.00 0.00 2.44
2898 5285 2.632763 TAAATCCCCACCCCTTTTGG 57.367 50.000 0.00 0.00 39.97 3.28
2910 5297 0.904649 CCTTTTGGGGCTGGAAATCC 59.095 55.000 0.00 0.00 35.46 3.01
2911 5298 0.904649 CTTTTGGGGCTGGAAATCCC 59.095 55.000 0.00 0.00 41.87 3.85
2915 5302 2.603580 GGGCTGGAAATCCCCCTC 59.396 66.667 6.55 0.00 35.37 4.30
2916 5303 2.009302 GGGCTGGAAATCCCCCTCT 61.009 63.158 6.55 0.00 35.37 3.69
2917 5304 1.228510 GGCTGGAAATCCCCCTCTG 59.771 63.158 0.00 0.00 34.29 3.35
2918 5305 1.454663 GCTGGAAATCCCCCTCTGC 60.455 63.158 0.00 0.00 34.29 4.26
2919 5306 1.228510 CTGGAAATCCCCCTCTGCC 59.771 63.158 0.00 0.00 34.29 4.85
2920 5307 1.543642 TGGAAATCCCCCTCTGCCA 60.544 57.895 0.00 0.00 34.29 4.92
2921 5308 1.145900 TGGAAATCCCCCTCTGCCAA 61.146 55.000 0.00 0.00 34.29 4.52
2922 5309 0.041090 GGAAATCCCCCTCTGCCAAA 59.959 55.000 0.00 0.00 0.00 3.28
2923 5310 1.186200 GAAATCCCCCTCTGCCAAAC 58.814 55.000 0.00 0.00 0.00 2.93
2924 5311 0.611896 AAATCCCCCTCTGCCAAACG 60.612 55.000 0.00 0.00 0.00 3.60
2925 5312 1.497309 AATCCCCCTCTGCCAAACGA 61.497 55.000 0.00 0.00 0.00 3.85
2926 5313 1.915078 ATCCCCCTCTGCCAAACGAG 61.915 60.000 0.00 0.00 0.00 4.18
2927 5314 2.045926 CCCCTCTGCCAAACGAGG 60.046 66.667 0.00 0.00 45.10 4.63
2935 5322 3.365535 CCAAACGAGGCCAAAGGG 58.634 61.111 5.01 0.00 37.18 3.95
2936 5323 2.275380 CCAAACGAGGCCAAAGGGG 61.275 63.158 5.01 0.00 40.85 4.79
2937 5324 1.530655 CAAACGAGGCCAAAGGGGT 60.531 57.895 5.01 0.00 39.65 4.95
2938 5325 1.530655 AAACGAGGCCAAAGGGGTG 60.531 57.895 5.01 0.00 39.65 4.61
2939 5326 2.292785 AAACGAGGCCAAAGGGGTGT 62.293 55.000 5.01 0.00 39.65 4.16
2940 5327 2.672996 CGAGGCCAAAGGGGTGTG 60.673 66.667 5.01 0.00 39.65 3.82
2941 5328 2.520968 GAGGCCAAAGGGGTGTGT 59.479 61.111 5.01 0.00 39.65 3.72
2942 5329 1.152546 GAGGCCAAAGGGGTGTGTT 60.153 57.895 5.01 0.00 39.65 3.32
2943 5330 0.759060 GAGGCCAAAGGGGTGTGTTT 60.759 55.000 5.01 0.00 39.65 2.83
2944 5331 0.326143 AGGCCAAAGGGGTGTGTTTT 60.326 50.000 5.01 0.00 39.65 2.43
2945 5332 0.105964 GGCCAAAGGGGTGTGTTTTC 59.894 55.000 0.00 0.00 39.65 2.29
2946 5333 0.105964 GCCAAAGGGGTGTGTTTTCC 59.894 55.000 0.00 0.00 39.65 3.13
2947 5334 1.490574 CCAAAGGGGTGTGTTTTCCA 58.509 50.000 0.00 0.00 0.00 3.53
2948 5335 1.412343 CCAAAGGGGTGTGTTTTCCAG 59.588 52.381 0.00 0.00 0.00 3.86
2949 5336 2.383855 CAAAGGGGTGTGTTTTCCAGA 58.616 47.619 0.00 0.00 0.00 3.86
2950 5337 2.763448 CAAAGGGGTGTGTTTTCCAGAA 59.237 45.455 0.00 0.00 0.00 3.02
2951 5338 2.838637 AGGGGTGTGTTTTCCAGAAA 57.161 45.000 0.00 0.00 0.00 2.52
2952 5339 3.328535 AGGGGTGTGTTTTCCAGAAAT 57.671 42.857 0.00 0.00 0.00 2.17
2953 5340 2.965147 AGGGGTGTGTTTTCCAGAAATG 59.035 45.455 0.00 0.00 0.00 2.32
2954 5341 2.547855 GGGGTGTGTTTTCCAGAAATGC 60.548 50.000 0.00 0.00 0.00 3.56
2955 5342 2.365293 GGGTGTGTTTTCCAGAAATGCT 59.635 45.455 0.00 0.00 0.00 3.79
2956 5343 3.572255 GGGTGTGTTTTCCAGAAATGCTA 59.428 43.478 0.00 0.00 0.00 3.49
2957 5344 4.220602 GGGTGTGTTTTCCAGAAATGCTAT 59.779 41.667 0.00 0.00 0.00 2.97
2958 5345 5.279456 GGGTGTGTTTTCCAGAAATGCTATT 60.279 40.000 0.00 0.00 0.00 1.73
2959 5346 6.071616 GGGTGTGTTTTCCAGAAATGCTATTA 60.072 38.462 0.00 0.00 0.00 0.98
2960 5347 6.806739 GGTGTGTTTTCCAGAAATGCTATTAC 59.193 38.462 0.00 0.00 0.00 1.89
2961 5348 6.806739 GTGTGTTTTCCAGAAATGCTATTACC 59.193 38.462 0.00 0.00 0.00 2.85
2962 5349 6.491745 TGTGTTTTCCAGAAATGCTATTACCA 59.508 34.615 0.00 0.00 0.00 3.25
2963 5350 7.014711 TGTGTTTTCCAGAAATGCTATTACCAA 59.985 33.333 0.00 0.00 0.00 3.67
2964 5351 7.542130 GTGTTTTCCAGAAATGCTATTACCAAG 59.458 37.037 0.00 0.00 0.00 3.61
2965 5352 7.232534 TGTTTTCCAGAAATGCTATTACCAAGT 59.767 33.333 0.00 0.00 0.00 3.16
2966 5353 6.757897 TTCCAGAAATGCTATTACCAAGTG 57.242 37.500 0.00 0.00 0.00 3.16
2967 5354 5.815581 TCCAGAAATGCTATTACCAAGTGT 58.184 37.500 0.00 0.00 0.00 3.55
2968 5355 6.953101 TCCAGAAATGCTATTACCAAGTGTA 58.047 36.000 0.00 0.00 0.00 2.90
2969 5356 7.047891 TCCAGAAATGCTATTACCAAGTGTAG 58.952 38.462 0.00 0.00 0.00 2.74
2970 5357 6.238484 CCAGAAATGCTATTACCAAGTGTAGC 60.238 42.308 0.00 0.00 39.88 3.58
2974 5361 3.938963 TGCTATTACCAAGTGTAGCAAGC 59.061 43.478 11.71 0.00 44.52 4.01
2975 5362 3.001330 GCTATTACCAAGTGTAGCAAGCG 59.999 47.826 8.29 0.00 39.39 4.68
2976 5363 2.536761 TTACCAAGTGTAGCAAGCGT 57.463 45.000 0.00 0.00 0.00 5.07
2977 5364 2.536761 TACCAAGTGTAGCAAGCGTT 57.463 45.000 0.00 0.00 0.00 4.84
2978 5365 0.944386 ACCAAGTGTAGCAAGCGTTG 59.056 50.000 0.00 0.00 0.00 4.10
2979 5366 0.944386 CCAAGTGTAGCAAGCGTTGT 59.056 50.000 0.00 0.00 0.00 3.32
2980 5367 2.139917 CCAAGTGTAGCAAGCGTTGTA 58.860 47.619 0.00 0.00 0.00 2.41
2981 5368 2.157668 CCAAGTGTAGCAAGCGTTGTAG 59.842 50.000 0.00 0.00 0.00 2.74
2982 5369 2.080286 AGTGTAGCAAGCGTTGTAGG 57.920 50.000 0.00 0.00 0.00 3.18
2983 5370 1.076332 GTGTAGCAAGCGTTGTAGGG 58.924 55.000 0.00 0.00 0.00 3.53
2984 5371 0.036765 TGTAGCAAGCGTTGTAGGGG 60.037 55.000 0.00 0.00 0.00 4.79
2985 5372 0.248289 GTAGCAAGCGTTGTAGGGGA 59.752 55.000 0.00 0.00 0.00 4.81
2986 5373 0.535335 TAGCAAGCGTTGTAGGGGAG 59.465 55.000 0.00 0.00 0.00 4.30
2987 5374 1.003718 GCAAGCGTTGTAGGGGAGT 60.004 57.895 0.00 0.00 0.00 3.85
2988 5375 1.019805 GCAAGCGTTGTAGGGGAGTC 61.020 60.000 0.00 0.00 0.00 3.36
2989 5376 0.736325 CAAGCGTTGTAGGGGAGTCG 60.736 60.000 0.00 0.00 0.00 4.18
2990 5377 2.502692 AAGCGTTGTAGGGGAGTCGC 62.503 60.000 0.00 0.00 43.16 5.19
2991 5378 2.183555 CGTTGTAGGGGAGTCGCC 59.816 66.667 18.33 18.33 36.67 5.54
2993 5380 1.033746 CGTTGTAGGGGAGTCGCCTA 61.034 60.000 27.50 27.50 45.12 3.93
2997 5384 2.892025 TAGGGGAGTCGCCTACAAC 58.108 57.895 27.50 1.61 45.12 3.32
2998 5385 0.685458 TAGGGGAGTCGCCTACAACC 60.685 60.000 27.50 0.68 45.12 3.77
2999 5386 2.183555 GGGAGTCGCCTACAACCG 59.816 66.667 0.00 0.00 36.66 4.44
3000 5387 2.508663 GGAGTCGCCTACAACCGC 60.509 66.667 0.00 0.00 0.00 5.68
3001 5388 2.572284 GAGTCGCCTACAACCGCT 59.428 61.111 0.00 0.00 0.00 5.52
3002 5389 1.660560 GGAGTCGCCTACAACCGCTA 61.661 60.000 0.00 0.00 0.00 4.26
3003 5390 0.525029 GAGTCGCCTACAACCGCTAC 60.525 60.000 0.00 0.00 0.00 3.58
3004 5391 0.964358 AGTCGCCTACAACCGCTACT 60.964 55.000 0.00 0.00 0.00 2.57
3005 5392 0.734889 GTCGCCTACAACCGCTACTA 59.265 55.000 0.00 0.00 0.00 1.82
3006 5393 1.133025 GTCGCCTACAACCGCTACTAA 59.867 52.381 0.00 0.00 0.00 2.24
3007 5394 2.026641 TCGCCTACAACCGCTACTAAT 58.973 47.619 0.00 0.00 0.00 1.73
3008 5395 2.124903 CGCCTACAACCGCTACTAATG 58.875 52.381 0.00 0.00 0.00 1.90
3009 5396 2.480845 GCCTACAACCGCTACTAATGG 58.519 52.381 0.00 0.00 0.00 3.16
3010 5397 2.159000 GCCTACAACCGCTACTAATGGT 60.159 50.000 0.00 0.00 37.68 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 1.002468 GCGTGTGTATGAATGGATGGC 60.002 52.381 0.00 0.00 0.00 4.40
151 152 2.207788 AATGCCGCCTTTTACACGCC 62.208 55.000 0.00 0.00 0.00 5.68
288 296 1.541588 CCTGTTTGCTTTACCTCCTGC 59.458 52.381 0.00 0.00 0.00 4.85
289 297 2.162681 CCCTGTTTGCTTTACCTCCTG 58.837 52.381 0.00 0.00 0.00 3.86
290 298 1.547901 GCCCTGTTTGCTTTACCTCCT 60.548 52.381 0.00 0.00 0.00 3.69
291 299 0.888619 GCCCTGTTTGCTTTACCTCC 59.111 55.000 0.00 0.00 0.00 4.30
302 310 2.990967 CCATGCCACGCCCTGTTT 60.991 61.111 0.00 0.00 0.00 2.83
329 337 2.595655 GGCGCCAGTAAAGGGGAT 59.404 61.111 24.80 0.00 43.81 3.85
340 348 2.677765 TTTAACAGAACCGGGCGCCA 62.678 55.000 30.85 0.00 0.00 5.69
349 357 6.205784 TGCAGCTACATTTGTTTAACAGAAC 58.794 36.000 0.00 0.00 0.00 3.01
406 414 5.112686 GGATCTGACGGGCATATAAGAATC 58.887 45.833 0.00 0.00 0.00 2.52
472 480 1.072965 CATGGAGCCTTAGCCCTTAGG 59.927 57.143 0.00 0.00 41.25 2.69
473 481 2.050144 TCATGGAGCCTTAGCCCTTAG 58.950 52.381 0.00 0.00 41.25 2.18
474 482 1.768870 GTCATGGAGCCTTAGCCCTTA 59.231 52.381 0.00 0.00 41.25 2.69
478 486 1.952296 CAATGTCATGGAGCCTTAGCC 59.048 52.381 0.00 0.00 41.25 3.93
479 487 1.336125 GCAATGTCATGGAGCCTTAGC 59.664 52.381 0.00 0.00 40.32 3.09
512 520 4.394920 TGTCACTTCACTTCTTTTCACCAC 59.605 41.667 0.00 0.00 0.00 4.16
529 537 6.942005 TGACATATGGTTTTGAGAATGTCACT 59.058 34.615 7.80 0.00 44.84 3.41
530 538 7.144722 TGACATATGGTTTTGAGAATGTCAC 57.855 36.000 7.80 0.00 44.84 3.67
569 587 1.139163 GAAAACCTGCAATGCCGTTG 58.861 50.000 1.53 0.00 40.90 4.10
634 704 1.160137 GCACTCCCACTGAATCACAC 58.840 55.000 0.00 0.00 0.00 3.82
655 725 9.921637 GGATTTTTATATGGTTCAACTGTCAAA 57.078 29.630 0.00 0.00 0.00 2.69
704 777 5.989168 CCTTTTCTCCCGCAAAGTAATTTTT 59.011 36.000 0.00 0.00 0.00 1.94
705 778 5.069914 ACCTTTTCTCCCGCAAAGTAATTTT 59.930 36.000 0.00 0.00 0.00 1.82
808 929 3.691118 GTGTGTGTATGATCTGGCAATGT 59.309 43.478 0.00 0.00 0.00 2.71
809 930 3.242511 CGTGTGTGTATGATCTGGCAATG 60.243 47.826 0.00 0.00 0.00 2.82
811 932 2.345876 CGTGTGTGTATGATCTGGCAA 58.654 47.619 0.00 0.00 0.00 4.52
876 998 1.454201 GGCTACCAACTTGCTTCTCC 58.546 55.000 0.00 0.00 0.00 3.71
895 1017 0.179089 CATCACTCCTCCCTTGAGCG 60.179 60.000 0.00 0.00 37.29 5.03
942 1098 7.094118 GGGTCAGATAGATTCAGTATACCAGAC 60.094 44.444 0.00 0.00 0.00 3.51
943 1099 6.948886 GGGTCAGATAGATTCAGTATACCAGA 59.051 42.308 0.00 0.00 0.00 3.86
944 1100 6.951198 AGGGTCAGATAGATTCAGTATACCAG 59.049 42.308 0.00 0.00 0.00 4.00
945 1101 6.721668 CAGGGTCAGATAGATTCAGTATACCA 59.278 42.308 0.00 0.00 0.00 3.25
946 1102 6.350612 GCAGGGTCAGATAGATTCAGTATACC 60.351 46.154 0.00 0.00 0.00 2.73
948 1104 6.314917 TGCAGGGTCAGATAGATTCAGTATA 58.685 40.000 0.00 0.00 0.00 1.47
964 1126 1.303561 TGGAGTGCAATGCAGGGTC 60.304 57.895 8.73 5.87 40.08 4.46
984 1146 2.851102 ATCCTGGATCCCTGGCCG 60.851 66.667 9.90 0.00 41.59 6.13
985 1147 1.355718 TTCATCCTGGATCCCTGGCC 61.356 60.000 9.90 0.00 41.59 5.36
986 1148 0.179006 GTTCATCCTGGATCCCTGGC 60.179 60.000 9.90 0.00 41.59 4.85
987 1149 0.475906 GGTTCATCCTGGATCCCTGG 59.524 60.000 9.90 11.85 42.93 4.45
995 1157 2.438434 GCCCGTGGTTCATCCTGG 60.438 66.667 0.00 0.00 37.07 4.45
1019 1181 2.512355 TTGCTCAGGTGGTACGGCA 61.512 57.895 0.00 0.00 0.00 5.69
1068 1230 4.247380 GGGATGGAGGCGAGCAGG 62.247 72.222 0.00 0.00 0.00 4.85
1863 2025 1.354168 TAGCTAGGGCGAGGAGGACT 61.354 60.000 0.00 0.00 44.37 3.85
1884 2046 3.804786 TGGTGAGTTGAACGAAGTACA 57.195 42.857 0.00 0.00 45.00 2.90
1885 2047 5.440685 CAAATGGTGAGTTGAACGAAGTAC 58.559 41.667 0.00 0.00 45.00 2.73
1886 2048 4.024387 GCAAATGGTGAGTTGAACGAAGTA 60.024 41.667 0.00 0.00 45.00 2.24
1888 2050 3.243035 TGCAAATGGTGAGTTGAACGAAG 60.243 43.478 0.00 0.00 28.10 3.79
1912 2083 6.040842 AGCAAATCAATGAATGTATACCACCC 59.959 38.462 0.00 0.00 0.00 4.61
1913 2084 7.042797 AGCAAATCAATGAATGTATACCACC 57.957 36.000 0.00 0.00 0.00 4.61
1914 2085 9.450807 GTAAGCAAATCAATGAATGTATACCAC 57.549 33.333 0.00 0.00 0.00 4.16
1915 2086 9.407380 AGTAAGCAAATCAATGAATGTATACCA 57.593 29.630 0.00 0.00 0.00 3.25
2012 2191 2.489802 CCAAGGAAGGAGGCTTGAGTTT 60.490 50.000 0.00 0.00 0.00 2.66
2013 2192 1.074566 CCAAGGAAGGAGGCTTGAGTT 59.925 52.381 0.00 0.00 0.00 3.01
2144 2342 4.322725 CGGGCTACATACATACATGTGGAT 60.323 45.833 9.11 0.00 39.12 3.41
2159 2357 5.449041 CGTACTTTACTTGATACGGGCTACA 60.449 44.000 0.00 0.00 37.38 2.74
2160 2358 4.972440 CGTACTTTACTTGATACGGGCTAC 59.028 45.833 0.00 0.00 37.38 3.58
2161 2359 4.640201 ACGTACTTTACTTGATACGGGCTA 59.360 41.667 7.47 0.00 43.58 3.93
2162 2360 3.445096 ACGTACTTTACTTGATACGGGCT 59.555 43.478 7.47 0.00 43.58 5.19
2163 2361 3.549070 CACGTACTTTACTTGATACGGGC 59.451 47.826 7.47 0.00 43.58 6.13
2164 2362 4.985413 TCACGTACTTTACTTGATACGGG 58.015 43.478 7.47 3.33 44.01 5.28
2165 2363 7.515957 AAATCACGTACTTTACTTGATACGG 57.484 36.000 5.92 0.00 43.99 4.02
2194 2392 7.616935 ACACATAATCACAATGGGAGAAAATCT 59.383 33.333 0.00 0.00 31.92 2.40
2195 2393 7.703621 CACACATAATCACAATGGGAGAAAATC 59.296 37.037 0.00 0.00 31.92 2.17
2260 2459 0.041535 TCCCAATGGCCAGCTTGATT 59.958 50.000 18.76 0.72 0.00 2.57
2261 2460 0.263765 ATCCCAATGGCCAGCTTGAT 59.736 50.000 18.76 11.75 0.00 2.57
2262 2461 0.041535 AATCCCAATGGCCAGCTTGA 59.958 50.000 18.76 10.01 0.00 3.02
2263 2462 1.410153 GTAATCCCAATGGCCAGCTTG 59.590 52.381 13.05 12.13 0.00 4.01
2301 3040 1.334243 GTCGTGGAGACGGAGATAAGG 59.666 57.143 0.00 0.00 46.11 2.69
2314 4701 0.251877 TATGGGGTGACTGTCGTGGA 60.252 55.000 2.98 0.00 0.00 4.02
2317 4704 1.262640 GGGTATGGGGTGACTGTCGT 61.263 60.000 2.98 0.00 0.00 4.34
2710 5097 2.212869 TGATTGTGTATACGGGCGTC 57.787 50.000 0.00 0.00 0.00 5.19
2711 5098 2.273557 GTTGATTGTGTATACGGGCGT 58.726 47.619 0.00 0.00 0.00 5.68
2712 5099 2.272678 TGTTGATTGTGTATACGGGCG 58.727 47.619 0.00 0.00 0.00 6.13
2713 5100 3.437395 TGTTGTTGATTGTGTATACGGGC 59.563 43.478 0.00 0.00 0.00 6.13
2760 5147 9.934190 ATTTATTGTGCTGAAATGTTGTTTTTC 57.066 25.926 0.00 0.00 34.40 2.29
2786 5173 5.771666 CCCCTAACCTAGTGACGACATATTA 59.228 44.000 0.00 0.00 0.00 0.98
2810 5197 6.333416 GCCTAATCTTCCTTCAACCAAAATC 58.667 40.000 0.00 0.00 0.00 2.17
2811 5198 5.105756 CGCCTAATCTTCCTTCAACCAAAAT 60.106 40.000 0.00 0.00 0.00 1.82
2814 5201 3.008594 TCGCCTAATCTTCCTTCAACCAA 59.991 43.478 0.00 0.00 0.00 3.67
2815 5202 2.569853 TCGCCTAATCTTCCTTCAACCA 59.430 45.455 0.00 0.00 0.00 3.67
2816 5203 3.261981 TCGCCTAATCTTCCTTCAACC 57.738 47.619 0.00 0.00 0.00 3.77
2817 5204 5.354234 TGAAATCGCCTAATCTTCCTTCAAC 59.646 40.000 0.00 0.00 0.00 3.18
2818 5205 5.354234 GTGAAATCGCCTAATCTTCCTTCAA 59.646 40.000 0.00 0.00 0.00 2.69
2819 5206 4.876107 GTGAAATCGCCTAATCTTCCTTCA 59.124 41.667 0.00 0.00 0.00 3.02
2820 5207 4.025647 CGTGAAATCGCCTAATCTTCCTTC 60.026 45.833 0.00 0.00 0.00 3.46
2821 5208 3.871594 CGTGAAATCGCCTAATCTTCCTT 59.128 43.478 0.00 0.00 0.00 3.36
2822 5209 3.458189 CGTGAAATCGCCTAATCTTCCT 58.542 45.455 0.00 0.00 0.00 3.36
2823 5210 2.544267 CCGTGAAATCGCCTAATCTTCC 59.456 50.000 0.00 0.00 0.00 3.46
2824 5211 2.544267 CCCGTGAAATCGCCTAATCTTC 59.456 50.000 0.00 0.00 0.00 2.87
2825 5212 2.169769 TCCCGTGAAATCGCCTAATCTT 59.830 45.455 0.00 0.00 0.00 2.40
2826 5213 1.760613 TCCCGTGAAATCGCCTAATCT 59.239 47.619 0.00 0.00 0.00 2.40
2827 5214 2.234300 TCCCGTGAAATCGCCTAATC 57.766 50.000 0.00 0.00 0.00 1.75
2828 5215 2.878406 CAATCCCGTGAAATCGCCTAAT 59.122 45.455 0.00 0.00 0.00 1.73
2829 5216 2.285083 CAATCCCGTGAAATCGCCTAA 58.715 47.619 0.00 0.00 0.00 2.69
2830 5217 1.474320 CCAATCCCGTGAAATCGCCTA 60.474 52.381 0.00 0.00 0.00 3.93
2831 5218 0.748005 CCAATCCCGTGAAATCGCCT 60.748 55.000 0.00 0.00 0.00 5.52
2832 5219 1.724582 CCCAATCCCGTGAAATCGCC 61.725 60.000 0.00 0.00 0.00 5.54
2833 5220 1.029947 ACCCAATCCCGTGAAATCGC 61.030 55.000 0.00 0.00 0.00 4.58
2834 5221 1.132262 CAACCCAATCCCGTGAAATCG 59.868 52.381 0.00 0.00 0.00 3.34
2835 5222 2.442413 TCAACCCAATCCCGTGAAATC 58.558 47.619 0.00 0.00 0.00 2.17
2836 5223 2.595750 TCAACCCAATCCCGTGAAAT 57.404 45.000 0.00 0.00 0.00 2.17
2837 5224 2.158593 TCTTCAACCCAATCCCGTGAAA 60.159 45.455 0.00 0.00 0.00 2.69
2838 5225 1.422024 TCTTCAACCCAATCCCGTGAA 59.578 47.619 0.00 0.00 0.00 3.18
2839 5226 1.003118 CTCTTCAACCCAATCCCGTGA 59.997 52.381 0.00 0.00 0.00 4.35
2840 5227 1.003118 TCTCTTCAACCCAATCCCGTG 59.997 52.381 0.00 0.00 0.00 4.94
2841 5228 1.279271 CTCTCTTCAACCCAATCCCGT 59.721 52.381 0.00 0.00 0.00 5.28
2842 5229 1.407437 CCTCTCTTCAACCCAATCCCG 60.407 57.143 0.00 0.00 0.00 5.14
2843 5230 1.064389 CCCTCTCTTCAACCCAATCCC 60.064 57.143 0.00 0.00 0.00 3.85
2844 5231 1.916181 TCCCTCTCTTCAACCCAATCC 59.084 52.381 0.00 0.00 0.00 3.01
2845 5232 3.200825 TGATCCCTCTCTTCAACCCAATC 59.799 47.826 0.00 0.00 0.00 2.67
2846 5233 3.192944 TGATCCCTCTCTTCAACCCAAT 58.807 45.455 0.00 0.00 0.00 3.16
2847 5234 2.631384 TGATCCCTCTCTTCAACCCAA 58.369 47.619 0.00 0.00 0.00 4.12
2848 5235 2.342406 TGATCCCTCTCTTCAACCCA 57.658 50.000 0.00 0.00 0.00 4.51
2849 5236 2.774234 TGATGATCCCTCTCTTCAACCC 59.226 50.000 0.00 0.00 0.00 4.11
2850 5237 4.494091 TTGATGATCCCTCTCTTCAACC 57.506 45.455 0.00 0.00 35.55 3.77
2851 5238 5.530543 GGATTTGATGATCCCTCTCTTCAAC 59.469 44.000 0.00 0.00 39.79 3.18
2852 5239 5.431073 AGGATTTGATGATCCCTCTCTTCAA 59.569 40.000 0.46 0.00 45.56 2.69
2853 5240 4.973856 AGGATTTGATGATCCCTCTCTTCA 59.026 41.667 0.46 0.00 45.56 3.02
2854 5241 5.307716 AGAGGATTTGATGATCCCTCTCTTC 59.692 44.000 10.91 0.62 45.56 2.87
2855 5242 5.226015 AGAGGATTTGATGATCCCTCTCTT 58.774 41.667 10.91 0.00 45.56 2.85
2856 5243 4.830138 AGAGGATTTGATGATCCCTCTCT 58.170 43.478 10.91 4.37 45.56 3.10
2857 5244 5.565455 AAGAGGATTTGATGATCCCTCTC 57.435 43.478 15.37 4.93 45.56 3.20
2858 5245 7.457380 TTTAAGAGGATTTGATGATCCCTCT 57.543 36.000 10.91 10.91 45.56 3.69
2859 5246 7.392953 GGATTTAAGAGGATTTGATGATCCCTC 59.607 40.741 7.21 7.21 45.56 4.30
2860 5247 7.237255 GGATTTAAGAGGATTTGATGATCCCT 58.763 38.462 0.46 0.00 45.56 4.20
2861 5248 6.435591 GGGATTTAAGAGGATTTGATGATCCC 59.564 42.308 0.00 0.00 45.56 3.85
2862 5249 6.435591 GGGGATTTAAGAGGATTTGATGATCC 59.564 42.308 0.00 0.00 44.91 3.36
2863 5250 7.006509 TGGGGATTTAAGAGGATTTGATGATC 58.993 38.462 0.00 0.00 0.00 2.92
2864 5251 6.779539 GTGGGGATTTAAGAGGATTTGATGAT 59.220 38.462 0.00 0.00 0.00 2.45
2865 5252 6.129179 GTGGGGATTTAAGAGGATTTGATGA 58.871 40.000 0.00 0.00 0.00 2.92
2866 5253 5.302823 GGTGGGGATTTAAGAGGATTTGATG 59.697 44.000 0.00 0.00 0.00 3.07
2867 5254 5.458595 GGTGGGGATTTAAGAGGATTTGAT 58.541 41.667 0.00 0.00 0.00 2.57
2868 5255 4.325816 GGGTGGGGATTTAAGAGGATTTGA 60.326 45.833 0.00 0.00 0.00 2.69
2869 5256 3.960755 GGGTGGGGATTTAAGAGGATTTG 59.039 47.826 0.00 0.00 0.00 2.32
2870 5257 3.052109 GGGGTGGGGATTTAAGAGGATTT 60.052 47.826 0.00 0.00 0.00 2.17
2871 5258 2.518407 GGGGTGGGGATTTAAGAGGATT 59.482 50.000 0.00 0.00 0.00 3.01
2872 5259 2.144450 GGGGTGGGGATTTAAGAGGAT 58.856 52.381 0.00 0.00 0.00 3.24
2873 5260 1.083912 AGGGGTGGGGATTTAAGAGGA 59.916 52.381 0.00 0.00 0.00 3.71
2874 5261 1.608425 AGGGGTGGGGATTTAAGAGG 58.392 55.000 0.00 0.00 0.00 3.69
2875 5262 3.757947 AAAGGGGTGGGGATTTAAGAG 57.242 47.619 0.00 0.00 0.00 2.85
2876 5263 3.503227 CCAAAAGGGGTGGGGATTTAAGA 60.503 47.826 0.00 0.00 32.03 2.10
2877 5264 2.837591 CCAAAAGGGGTGGGGATTTAAG 59.162 50.000 0.00 0.00 32.03 1.85
2878 5265 2.909217 CCAAAAGGGGTGGGGATTTAA 58.091 47.619 0.00 0.00 32.03 1.52
2879 5266 2.632763 CCAAAAGGGGTGGGGATTTA 57.367 50.000 0.00 0.00 32.03 1.40
2880 5267 3.492686 CCAAAAGGGGTGGGGATTT 57.507 52.632 0.00 0.00 32.03 2.17
2891 5278 0.904649 GGATTTCCAGCCCCAAAAGG 59.095 55.000 0.00 0.00 35.64 3.11
2892 5279 0.904649 GGGATTTCCAGCCCCAAAAG 59.095 55.000 0.00 0.00 39.89 2.27
2893 5280 3.081048 GGGATTTCCAGCCCCAAAA 57.919 52.632 0.00 0.00 39.89 2.44
2894 5281 4.885709 GGGATTTCCAGCCCCAAA 57.114 55.556 0.00 0.00 39.89 3.28
2898 5285 2.009302 AGAGGGGGATTTCCAGCCC 61.009 63.158 3.38 3.38 43.91 5.19
2899 5286 1.228510 CAGAGGGGGATTTCCAGCC 59.771 63.158 0.00 0.00 37.91 4.85
2900 5287 1.454663 GCAGAGGGGGATTTCCAGC 60.455 63.158 0.00 0.00 37.91 4.85
2901 5288 1.228510 GGCAGAGGGGGATTTCCAG 59.771 63.158 0.00 0.00 37.91 3.86
2902 5289 1.145900 TTGGCAGAGGGGGATTTCCA 61.146 55.000 0.00 0.00 37.91 3.53
2903 5290 0.041090 TTTGGCAGAGGGGGATTTCC 59.959 55.000 0.00 0.00 0.00 3.13
2904 5291 1.186200 GTTTGGCAGAGGGGGATTTC 58.814 55.000 0.00 0.00 0.00 2.17
2905 5292 0.611896 CGTTTGGCAGAGGGGGATTT 60.612 55.000 0.00 0.00 0.00 2.17
2906 5293 1.000896 CGTTTGGCAGAGGGGGATT 60.001 57.895 0.00 0.00 0.00 3.01
2907 5294 1.915078 CTCGTTTGGCAGAGGGGGAT 61.915 60.000 0.00 0.00 0.00 3.85
2908 5295 2.528127 TCGTTTGGCAGAGGGGGA 60.528 61.111 0.00 0.00 0.00 4.81
2909 5296 2.045926 CTCGTTTGGCAGAGGGGG 60.046 66.667 0.00 0.00 0.00 5.40
2918 5305 2.275380 CCCCTTTGGCCTCGTTTGG 61.275 63.158 3.32 0.00 0.00 3.28
2919 5306 1.530655 ACCCCTTTGGCCTCGTTTG 60.531 57.895 3.32 0.00 37.83 2.93
2920 5307 1.530655 CACCCCTTTGGCCTCGTTT 60.531 57.895 3.32 0.00 37.83 3.60
2921 5308 2.115266 CACCCCTTTGGCCTCGTT 59.885 61.111 3.32 0.00 37.83 3.85
2922 5309 3.175710 ACACCCCTTTGGCCTCGT 61.176 61.111 3.32 0.00 37.83 4.18
2923 5310 2.672996 CACACCCCTTTGGCCTCG 60.673 66.667 3.32 0.00 37.83 4.63
2924 5311 0.759060 AAACACACCCCTTTGGCCTC 60.759 55.000 3.32 0.00 37.83 4.70
2925 5312 0.326143 AAAACACACCCCTTTGGCCT 60.326 50.000 3.32 0.00 37.83 5.19
2926 5313 0.105964 GAAAACACACCCCTTTGGCC 59.894 55.000 0.00 0.00 37.83 5.36
2927 5314 0.105964 GGAAAACACACCCCTTTGGC 59.894 55.000 0.00 0.00 37.83 4.52
2928 5315 1.412343 CTGGAAAACACACCCCTTTGG 59.588 52.381 0.00 0.00 41.37 3.28
2929 5316 2.383855 TCTGGAAAACACACCCCTTTG 58.616 47.619 0.00 0.00 0.00 2.77
2930 5317 2.838637 TCTGGAAAACACACCCCTTT 57.161 45.000 0.00 0.00 0.00 3.11
2931 5318 2.838637 TTCTGGAAAACACACCCCTT 57.161 45.000 0.00 0.00 0.00 3.95
2932 5319 2.838637 TTTCTGGAAAACACACCCCT 57.161 45.000 0.00 0.00 0.00 4.79
2933 5320 2.547855 GCATTTCTGGAAAACACACCCC 60.548 50.000 0.00 0.00 33.56 4.95
2934 5321 2.365293 AGCATTTCTGGAAAACACACCC 59.635 45.455 0.00 0.00 33.56 4.61
2935 5322 3.733443 AGCATTTCTGGAAAACACACC 57.267 42.857 0.00 0.00 33.56 4.16
2936 5323 6.806739 GGTAATAGCATTTCTGGAAAACACAC 59.193 38.462 0.00 0.00 33.56 3.82
2937 5324 6.491745 TGGTAATAGCATTTCTGGAAAACACA 59.508 34.615 0.00 0.00 33.56 3.72
2938 5325 6.919721 TGGTAATAGCATTTCTGGAAAACAC 58.080 36.000 0.00 0.00 33.56 3.32
2939 5326 7.232534 ACTTGGTAATAGCATTTCTGGAAAACA 59.767 33.333 0.00 0.00 33.56 2.83
2940 5327 7.542130 CACTTGGTAATAGCATTTCTGGAAAAC 59.458 37.037 0.00 0.00 33.56 2.43
2941 5328 7.232534 ACACTTGGTAATAGCATTTCTGGAAAA 59.767 33.333 0.00 0.00 33.56 2.29
2942 5329 6.719370 ACACTTGGTAATAGCATTTCTGGAAA 59.281 34.615 0.00 0.00 34.46 3.13
2943 5330 6.245408 ACACTTGGTAATAGCATTTCTGGAA 58.755 36.000 0.00 0.00 0.00 3.53
2944 5331 5.815581 ACACTTGGTAATAGCATTTCTGGA 58.184 37.500 0.00 0.00 0.00 3.86
2945 5332 6.238484 GCTACACTTGGTAATAGCATTTCTGG 60.238 42.308 0.00 0.00 39.87 3.86
2946 5333 6.316140 TGCTACACTTGGTAATAGCATTTCTG 59.684 38.462 0.78 0.00 43.83 3.02
2947 5334 6.414732 TGCTACACTTGGTAATAGCATTTCT 58.585 36.000 0.78 0.00 43.83 2.52
2948 5335 6.677781 TGCTACACTTGGTAATAGCATTTC 57.322 37.500 0.78 0.00 43.83 2.17
2949 5336 6.404734 GCTTGCTACACTTGGTAATAGCATTT 60.405 38.462 5.69 0.00 46.91 2.32
2950 5337 5.066505 GCTTGCTACACTTGGTAATAGCATT 59.933 40.000 5.69 0.00 46.91 3.56
2951 5338 4.576463 GCTTGCTACACTTGGTAATAGCAT 59.424 41.667 5.69 0.00 46.91 3.79
2952 5339 3.938963 GCTTGCTACACTTGGTAATAGCA 59.061 43.478 0.78 0.78 46.26 3.49
2953 5340 3.001330 CGCTTGCTACACTTGGTAATAGC 59.999 47.826 0.00 0.00 40.40 2.97
2954 5341 4.181578 ACGCTTGCTACACTTGGTAATAG 58.818 43.478 0.00 0.00 0.00 1.73
2955 5342 4.196626 ACGCTTGCTACACTTGGTAATA 57.803 40.909 0.00 0.00 0.00 0.98
2956 5343 3.053831 ACGCTTGCTACACTTGGTAAT 57.946 42.857 0.00 0.00 0.00 1.89
2957 5344 2.536761 ACGCTTGCTACACTTGGTAA 57.463 45.000 0.00 0.00 0.00 2.85
2958 5345 2.139917 CAACGCTTGCTACACTTGGTA 58.860 47.619 0.00 0.00 0.00 3.25
2959 5346 0.944386 CAACGCTTGCTACACTTGGT 59.056 50.000 0.00 0.00 0.00 3.67
2960 5347 0.944386 ACAACGCTTGCTACACTTGG 59.056 50.000 0.00 0.00 0.00 3.61
2961 5348 2.157668 CCTACAACGCTTGCTACACTTG 59.842 50.000 0.00 0.00 0.00 3.16
2962 5349 2.413837 CCTACAACGCTTGCTACACTT 58.586 47.619 0.00 0.00 0.00 3.16
2963 5350 1.337823 CCCTACAACGCTTGCTACACT 60.338 52.381 0.00 0.00 0.00 3.55
2964 5351 1.076332 CCCTACAACGCTTGCTACAC 58.924 55.000 0.00 0.00 0.00 2.90
2965 5352 0.036765 CCCCTACAACGCTTGCTACA 60.037 55.000 0.00 0.00 0.00 2.74
2966 5353 0.248289 TCCCCTACAACGCTTGCTAC 59.752 55.000 0.00 0.00 0.00 3.58
2967 5354 0.535335 CTCCCCTACAACGCTTGCTA 59.465 55.000 0.00 0.00 0.00 3.49
2968 5355 1.296715 CTCCCCTACAACGCTTGCT 59.703 57.895 0.00 0.00 0.00 3.91
2969 5356 1.003718 ACTCCCCTACAACGCTTGC 60.004 57.895 0.00 0.00 0.00 4.01
2970 5357 0.736325 CGACTCCCCTACAACGCTTG 60.736 60.000 0.00 0.00 0.00 4.01
2971 5358 1.590147 CGACTCCCCTACAACGCTT 59.410 57.895 0.00 0.00 0.00 4.68
2972 5359 3.003113 GCGACTCCCCTACAACGCT 62.003 63.158 0.00 0.00 42.19 5.07
2973 5360 2.508663 GCGACTCCCCTACAACGC 60.509 66.667 0.00 0.00 39.33 4.84
2974 5361 1.033746 TAGGCGACTCCCCTACAACG 61.034 60.000 0.00 0.00 43.67 4.10
2975 5362 2.892025 TAGGCGACTCCCCTACAAC 58.108 57.895 0.00 0.00 43.67 3.32
2979 5366 0.685458 GGTTGTAGGCGACTCCCCTA 60.685 60.000 0.00 0.00 43.67 3.53
2980 5367 1.988406 GGTTGTAGGCGACTCCCCT 60.988 63.158 0.00 0.00 43.67 4.79
2981 5368 2.582978 GGTTGTAGGCGACTCCCC 59.417 66.667 0.00 0.00 43.67 4.81
2982 5369 2.183555 CGGTTGTAGGCGACTCCC 59.816 66.667 0.00 0.00 43.67 4.30
2983 5370 1.660560 TAGCGGTTGTAGGCGACTCC 61.661 60.000 0.00 0.00 43.67 3.85
2984 5371 0.525029 GTAGCGGTTGTAGGCGACTC 60.525 60.000 0.00 0.00 43.67 3.36
2985 5372 1.679944 TAGTAGCGGTTGTAGGCGACT 60.680 52.381 0.00 0.00 45.15 4.18
2986 5373 0.734889 TAGTAGCGGTTGTAGGCGAC 59.265 55.000 0.00 0.00 35.39 5.19
2987 5374 1.462616 TTAGTAGCGGTTGTAGGCGA 58.537 50.000 0.00 0.00 0.00 5.54
2988 5375 2.124903 CATTAGTAGCGGTTGTAGGCG 58.875 52.381 0.00 0.00 0.00 5.52
2989 5376 2.159000 ACCATTAGTAGCGGTTGTAGGC 60.159 50.000 0.00 0.00 0.00 3.93
2990 5377 3.814005 ACCATTAGTAGCGGTTGTAGG 57.186 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.