Multiple sequence alignment - TraesCS2A01G084900

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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 TraesCS2A01G084900 chr2A 100.000 5294 0 0 1 5294 38964042 38969335 0.000000e+00 9777.0
1 TraesCS2A01G084900 chr2A 98.462 195 3 0 1989 2183 38965841 38966035 1.410000e-90 344.0
2 TraesCS2A01G084900 chr2A 98.462 195 3 0 1800 1994 38966030 38966224 1.410000e-90 344.0
3 TraesCS2A01G084900 chr2A 94.792 96 3 2 4376 4470 161948591 161948685 1.190000e-31 148.0
4 TraesCS2A01G084900 chr2B 96.830 4795 138 6 1 4785 58974926 58979716 0.000000e+00 8000.0
5 TraesCS2A01G084900 chr2B 97.949 195 4 0 1989 2183 58976728 58976922 6.570000e-89 339.0
6 TraesCS2A01G084900 chr2B 96.410 195 7 0 1800 1994 58976917 58977111 6.610000e-84 322.0
7 TraesCS2A01G084900 chr2B 90.438 251 10 3 4770 5006 58979736 58979986 8.560000e-83 318.0
8 TraesCS2A01G084900 chr2B 84.568 162 15 9 5005 5163 640768532 640768378 9.180000e-33 152.0
9 TraesCS2A01G084900 chr2D 97.224 4106 90 9 281 4372 35780356 35784451 0.000000e+00 6929.0
10 TraesCS2A01G084900 chr2D 95.683 556 14 1 4463 5008 35784450 35785005 0.000000e+00 885.0
11 TraesCS2A01G084900 chr2D 97.333 300 8 0 1 300 35779987 35780286 1.320000e-140 510.0
12 TraesCS2A01G084900 chr2D 98.462 195 3 0 1989 2183 35781873 35782067 1.410000e-90 344.0
13 TraesCS2A01G084900 chr2D 98.462 195 3 0 1800 1994 35782062 35782256 1.410000e-90 344.0
14 TraesCS2A01G084900 chr2D 86.842 76 2 4 5217 5292 7284842 7284909 1.580000e-10 78.7
15 TraesCS2A01G084900 chr2D 95.745 47 1 1 5247 5292 490047565 490047611 2.040000e-09 75.0
16 TraesCS2A01G084900 chr5D 85.762 302 25 12 4720 5003 433390674 433390975 2.400000e-78 303.0
17 TraesCS2A01G084900 chr5D 89.950 199 14 6 5005 5200 563595340 563595145 8.800000e-63 252.0
18 TraesCS2A01G084900 chr5D 94.737 95 4 1 4374 4468 128577586 128577679 4.270000e-31 147.0
19 TraesCS2A01G084900 chr5D 94.737 95 4 1 4374 4468 350331951 350331858 4.270000e-31 147.0
20 TraesCS2A01G084900 chr5D 90.411 73 0 3 5220 5292 563595328 563595263 7.300000e-14 89.8
21 TraesCS2A01G084900 chr3B 74.085 683 167 8 2746 3420 385465317 385464637 6.760000e-69 272.0
22 TraesCS2A01G084900 chr3B 89.041 73 1 3 5220 5292 239917416 239917481 3.400000e-12 84.2
23 TraesCS2A01G084900 chr3A 74.015 685 164 9 2746 3420 387297800 387298480 3.140000e-67 267.0
24 TraesCS2A01G084900 chr3A 84.980 253 20 12 5003 5250 489314323 489314562 1.910000e-59 241.0
25 TraesCS2A01G084900 chr3A 89.041 73 0 1 5220 5292 489314337 489314401 3.400000e-12 84.2
26 TraesCS2A01G084900 chr3D 73.607 682 172 6 2746 3420 292028461 292027781 6.800000e-64 255.0
27 TraesCS2A01G084900 chr3D 89.041 73 1 2 5220 5292 468378923 468378858 3.400000e-12 84.2
28 TraesCS2A01G084900 chr3D 87.671 73 2 3 5220 5292 531846137 531846072 1.580000e-10 78.7
29 TraesCS2A01G084900 chr4B 73.412 677 150 25 2792 3447 107237198 107237865 5.330000e-55 226.0
30 TraesCS2A01G084900 chr4B 89.011 182 14 6 5000 5177 529299954 529300133 2.480000e-53 220.0
31 TraesCS2A01G084900 chr4B 97.872 47 0 1 5247 5292 299556219 299556173 4.390000e-11 80.5
32 TraesCS2A01G084900 chr4D 87.317 205 13 10 5005 5201 449823157 449822958 6.900000e-54 222.0
33 TraesCS2A01G084900 chr7A 87.047 193 18 5 5015 5204 543445434 543445246 1.490000e-50 211.0
34 TraesCS2A01G084900 chr4A 85.222 203 24 5 5005 5201 7735311 7735513 2.500000e-48 204.0
35 TraesCS2A01G084900 chr4A 72.214 673 157 23 2796 3447 512580706 512580043 4.210000e-41 180.0
36 TraesCS2A01G084900 chr1B 84.211 190 16 13 5015 5201 381500060 381499882 7.050000e-39 172.0
37 TraesCS2A01G084900 chr6B 97.701 87 2 0 4376 4462 472612145 472612059 3.300000e-32 150.0
38 TraesCS2A01G084900 chr6B 80.447 179 18 5 5013 5177 21800386 21800211 2.590000e-23 121.0
39 TraesCS2A01G084900 chr5B 97.701 87 2 0 4375 4461 62940322 62940408 3.300000e-32 150.0
40 TraesCS2A01G084900 chr5B 94.737 95 4 1 4374 4468 140965928 140966021 4.270000e-31 147.0
41 TraesCS2A01G084900 chr5A 94.737 95 4 1 4374 4468 450750794 450750701 4.270000e-31 147.0
42 TraesCS2A01G084900 chr6D 90.476 105 8 2 4367 4471 283795863 283795761 2.570000e-28 137.0
43 TraesCS2A01G084900 chr7B 89.041 73 1 3 5220 5292 418045012 418044947 3.400000e-12 84.2
44 TraesCS2A01G084900 chr7B 86.842 76 2 4 5217 5292 47729294 47729227 1.580000e-10 78.7
45 TraesCS2A01G084900 chr7B 85.915 71 3 4 5220 5290 198946433 198946370 9.510000e-08 69.4
46 TraesCS2A01G084900 chr1D 97.727 44 0 1 5250 5292 58983356 58983313 2.040000e-09 75.0


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 TraesCS2A01G084900 chr2A 38964042 38969335 5293 False 3488.333333 9777 98.974667 1 5294 3 chr2A.!!$F2 5293
1 TraesCS2A01G084900 chr2B 58974926 58979986 5060 False 2244.750000 8000 95.406750 1 5006 4 chr2B.!!$F1 5005
2 TraesCS2A01G084900 chr2D 35779987 35785005 5018 False 1802.400000 6929 97.432800 1 5008 5 chr2D.!!$F3 5007
3 TraesCS2A01G084900 chr3B 385464637 385465317 680 True 272.000000 272 74.085000 2746 3420 1 chr3B.!!$R1 674
4 TraesCS2A01G084900 chr3A 387297800 387298480 680 False 267.000000 267 74.015000 2746 3420 1 chr3A.!!$F1 674
5 TraesCS2A01G084900 chr3D 292027781 292028461 680 True 255.000000 255 73.607000 2746 3420 1 chr3D.!!$R1 674
6 TraesCS2A01G084900 chr4B 107237198 107237865 667 False 226.000000 226 73.412000 2792 3447 1 chr4B.!!$F1 655

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
918 1018 0.875908 TGCGCATCCGTTATCTGCTC 60.876 55.000 5.66 0.0 36.67 4.26 F
1570 1670 1.078848 ATCCGCTGTCTGAACTGCC 60.079 57.895 2.47 0.0 44.84 4.85 F
2069 2169 0.447801 GCTGTACCGACTGCAAATGG 59.552 55.000 2.51 0.0 46.67 3.16 F
2298 2398 2.161808 CGAGAAGGAAGCTAACGAGTCA 59.838 50.000 0.00 0.0 0.00 3.41 F
3240 3358 2.229784 GGTCAGGATTGAAGGCTTTGTG 59.770 50.000 0.00 0.0 34.49 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1951 1.534163 GTCGGTACAGCAGGTTTTTCC 59.466 52.381 0.00 0.0 0.00 3.13 R
3540 3658 2.686915 GGGATTTCTCTGCAAGGATGTG 59.313 50.000 0.00 0.0 0.00 3.21 R
3771 3889 3.084786 AGCTTCAAGCCAGGTCAAATAC 58.915 45.455 5.53 0.0 43.77 1.89 R
4095 4213 0.802494 CCGCTGTGTAACCATTGACC 59.198 55.000 0.00 0.0 34.36 4.02 R
5236 5414 0.035439 GCTGGTTAGCTAGTTGGCCA 60.035 55.000 0.00 0.0 46.57 5.36 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
73 74 2.978156 TGGGCTCATCAAACTCCTTT 57.022 45.000 0.00 0.00 0.00 3.11
190 191 4.374689 TTGTTTCTAGTGGGTTATGCCA 57.625 40.909 0.00 0.00 39.65 4.92
391 485 5.596845 GCTCTTCCTTACTCTAATCAGTGG 58.403 45.833 0.00 0.00 0.00 4.00
392 486 5.128008 GCTCTTCCTTACTCTAATCAGTGGT 59.872 44.000 0.00 0.00 0.00 4.16
393 487 6.531503 TCTTCCTTACTCTAATCAGTGGTG 57.468 41.667 0.00 0.00 0.00 4.17
680 780 1.996191 GACTGCACGCTTTCTAGGAAG 59.004 52.381 6.39 6.39 0.00 3.46
742 842 5.742926 GTCTCGTATACTAGGTTTTGCACTC 59.257 44.000 4.70 0.00 0.00 3.51
743 843 5.416639 TCTCGTATACTAGGTTTTGCACTCA 59.583 40.000 4.70 0.00 0.00 3.41
859 959 5.435686 TTTGTAGGTCCTGATGCAGTAAT 57.564 39.130 0.00 0.00 0.00 1.89
918 1018 0.875908 TGCGCATCCGTTATCTGCTC 60.876 55.000 5.66 0.00 36.67 4.26
1008 1108 6.602410 TTTTTGGCAGTGATTATGATGGAA 57.398 33.333 0.00 0.00 0.00 3.53
1345 1445 3.423539 AGTTGGTTGCTGAAGCTCATA 57.576 42.857 3.61 0.00 42.66 2.15
1570 1670 1.078848 ATCCGCTGTCTGAACTGCC 60.079 57.895 2.47 0.00 44.84 4.85
1851 1951 7.884816 AAGTCAATTTTCAGCAATGAATCAG 57.115 32.000 0.00 0.00 0.00 2.90
2069 2169 0.447801 GCTGTACCGACTGCAAATGG 59.552 55.000 2.51 0.00 46.67 3.16
2298 2398 2.161808 CGAGAAGGAAGCTAACGAGTCA 59.838 50.000 0.00 0.00 0.00 3.41
2351 2451 6.860023 CCAGCAAAGACTCAAAGTAAATCTTG 59.140 38.462 0.00 0.00 36.40 3.02
2354 2454 7.067494 AGCAAAGACTCAAAGTAAATCTTGTGT 59.933 33.333 0.00 0.00 36.40 3.72
2399 2499 5.801947 CAGGTGTTTTTGACAGAAAGAACTG 59.198 40.000 16.14 16.14 38.28 3.16
2400 2500 8.871033 ACAGGTGTTTTTGACAGAAAGAACTGT 61.871 37.037 24.96 24.96 46.86 3.55
2433 2536 4.864916 ATCTACAGTGTTAAATGCTGCG 57.135 40.909 0.00 0.00 33.87 5.18
3240 3358 2.229784 GGTCAGGATTGAAGGCTTTGTG 59.770 50.000 0.00 0.00 34.49 3.33
3243 3361 6.391495 GTCAGGATTGAAGGCTTTGTGAGC 62.391 50.000 0.00 0.00 42.12 4.26
3523 3641 7.798596 AGCAGTAGAGGAAAACATGAATATG 57.201 36.000 0.00 0.00 40.24 1.78
3540 3658 6.913170 TGAATATGTTTCTTCTGAGCCAAAC 58.087 36.000 0.00 0.00 0.00 2.93
3771 3889 4.150804 GTCGAGCTAGAACCTTTCAAAGTG 59.849 45.833 0.00 0.00 0.00 3.16
3840 3958 2.438021 GTGGTTGGAGCAGGATATACCA 59.562 50.000 0.00 0.00 42.04 3.25
3869 3987 8.638565 CAGCTGTGGTAAATTTAAAATTCGAAG 58.361 33.333 5.25 0.00 0.00 3.79
3875 3993 8.361139 TGGTAAATTTAAAATTCGAAGCTGGAA 58.639 29.630 3.35 3.24 0.00 3.53
3921 4039 6.893958 ACTTTCTCTCATTTAGTATGCACG 57.106 37.500 0.00 0.00 0.00 5.34
3930 4048 4.415881 TTTAGTATGCACGGGACATGAT 57.584 40.909 0.00 0.00 0.00 2.45
4095 4213 7.011857 AGCACAAAAGTTTCTCTTCTTACTCAG 59.988 37.037 0.00 0.00 35.02 3.35
4159 4277 5.197451 AGAGAGTTGTGGAGATACCTACAG 58.803 45.833 0.00 0.00 32.92 2.74
4362 4480 2.029739 TCGTGTCTTATTCCGCTGTCAA 60.030 45.455 0.00 0.00 0.00 3.18
4386 4504 3.446442 TTTCTACAGTACTCCCTCCGT 57.554 47.619 0.00 0.00 0.00 4.69
4531 4649 3.664495 CAGACTTGCAGTGCCCTG 58.336 61.111 13.72 10.63 41.91 4.45
4736 4855 2.154462 AGCGCAAAGTTTAGCACATCT 58.846 42.857 11.47 3.26 0.00 2.90
4941 5119 2.572104 AGATTAGTTGCTTCCCCTTCGT 59.428 45.455 0.00 0.00 0.00 3.85
5025 5203 8.983702 TTATATTAAACCCATTAAGAGGCGTT 57.016 30.769 0.00 0.00 36.94 4.84
5027 5205 6.937436 ATTAAACCCATTAAGAGGCGTTAG 57.063 37.500 0.00 0.00 36.94 2.34
5028 5206 4.563140 AAACCCATTAAGAGGCGTTAGA 57.437 40.909 0.00 0.00 0.00 2.10
5029 5207 4.563140 AACCCATTAAGAGGCGTTAGAA 57.437 40.909 0.00 0.00 0.00 2.10
5030 5208 4.772886 ACCCATTAAGAGGCGTTAGAAT 57.227 40.909 0.00 0.00 0.00 2.40
5031 5209 4.451900 ACCCATTAAGAGGCGTTAGAATG 58.548 43.478 0.00 0.00 0.00 2.67
5032 5210 3.815401 CCCATTAAGAGGCGTTAGAATGG 59.185 47.826 15.08 15.08 41.90 3.16
5033 5211 4.451900 CCATTAAGAGGCGTTAGAATGGT 58.548 43.478 14.32 0.00 38.88 3.55
5034 5212 4.273480 CCATTAAGAGGCGTTAGAATGGTG 59.727 45.833 14.32 0.00 38.88 4.17
5035 5213 2.403252 AAGAGGCGTTAGAATGGTGG 57.597 50.000 0.00 0.00 0.00 4.61
5036 5214 0.107654 AGAGGCGTTAGAATGGTGGC 60.108 55.000 0.00 0.00 0.00 5.01
5037 5215 1.077716 AGGCGTTAGAATGGTGGCC 60.078 57.895 0.00 0.00 40.80 5.36
5038 5216 1.377987 GGCGTTAGAATGGTGGCCA 60.378 57.895 0.00 0.00 40.24 5.36
5039 5217 0.963355 GGCGTTAGAATGGTGGCCAA 60.963 55.000 7.24 0.00 40.24 4.52
5040 5218 0.170339 GCGTTAGAATGGTGGCCAAC 59.830 55.000 15.99 15.99 36.95 3.77
5041 5219 1.821216 CGTTAGAATGGTGGCCAACT 58.179 50.000 24.13 0.98 36.95 3.16
5042 5220 2.937873 GCGTTAGAATGGTGGCCAACTA 60.938 50.000 24.13 9.02 36.95 2.24
5043 5221 2.936498 CGTTAGAATGGTGGCCAACTAG 59.064 50.000 24.13 0.21 36.95 2.57
5044 5222 2.683362 GTTAGAATGGTGGCCAACTAGC 59.317 50.000 24.13 10.79 36.95 3.42
5045 5223 0.995024 AGAATGGTGGCCAACTAGCT 59.005 50.000 24.13 13.06 36.95 3.32
5046 5224 2.196595 AGAATGGTGGCCAACTAGCTA 58.803 47.619 24.13 0.00 36.95 3.32
5047 5225 2.092914 AGAATGGTGGCCAACTAGCTAC 60.093 50.000 24.13 7.54 42.98 3.58
5048 5226 0.178068 ATGGTGGCCAACTAGCTACG 59.822 55.000 24.13 0.00 44.50 3.51
5049 5227 1.814169 GGTGGCCAACTAGCTACGC 60.814 63.158 15.48 0.00 44.50 4.42
5050 5228 1.814169 GTGGCCAACTAGCTACGCC 60.814 63.158 7.24 8.72 40.16 5.68
5051 5229 2.582436 GGCCAACTAGCTACGCCA 59.418 61.111 0.00 0.00 39.50 5.69
5052 5230 1.146263 GGCCAACTAGCTACGCCAT 59.854 57.895 0.00 0.00 39.50 4.40
5053 5231 1.160329 GGCCAACTAGCTACGCCATG 61.160 60.000 0.00 0.00 39.50 3.66
5054 5232 0.462047 GCCAACTAGCTACGCCATGT 60.462 55.000 0.00 0.00 0.00 3.21
5055 5233 1.290203 CCAACTAGCTACGCCATGTG 58.710 55.000 0.00 0.00 0.00 3.21
5056 5234 1.290203 CAACTAGCTACGCCATGTGG 58.710 55.000 0.00 0.00 38.53 4.17
5068 5246 3.929002 ATGTGGCGCATGCTGATT 58.071 50.000 17.13 0.00 42.25 2.57
5069 5247 1.435925 ATGTGGCGCATGCTGATTG 59.564 52.632 17.13 0.00 42.25 2.67
5070 5248 2.011741 ATGTGGCGCATGCTGATTGG 62.012 55.000 17.13 0.00 42.25 3.16
5071 5249 2.361483 TGGCGCATGCTGATTGGT 60.361 55.556 17.13 0.00 42.25 3.67
5072 5250 2.409055 TGGCGCATGCTGATTGGTC 61.409 57.895 17.13 0.34 42.25 4.02
5073 5251 2.409055 GGCGCATGCTGATTGGTCA 61.409 57.895 17.13 0.00 42.25 4.02
5074 5252 1.226491 GCGCATGCTGATTGGTCAC 60.226 57.895 17.13 0.00 38.39 3.67
5075 5253 1.061411 CGCATGCTGATTGGTCACG 59.939 57.895 17.13 0.00 0.00 4.35
5076 5254 1.430632 GCATGCTGATTGGTCACGG 59.569 57.895 11.37 0.00 0.00 4.94
5077 5255 1.308069 GCATGCTGATTGGTCACGGT 61.308 55.000 11.37 0.00 0.00 4.83
5078 5256 0.448990 CATGCTGATTGGTCACGGTG 59.551 55.000 0.56 0.56 0.00 4.94
5079 5257 0.324614 ATGCTGATTGGTCACGGTGA 59.675 50.000 6.76 6.76 0.00 4.02
5080 5258 0.320683 TGCTGATTGGTCACGGTGAG 60.321 55.000 11.83 0.00 0.00 3.51
5081 5259 0.037326 GCTGATTGGTCACGGTGAGA 60.037 55.000 11.83 1.11 0.00 3.27
5082 5260 1.608025 GCTGATTGGTCACGGTGAGAA 60.608 52.381 11.83 7.96 0.00 2.87
5083 5261 2.766313 CTGATTGGTCACGGTGAGAAA 58.234 47.619 11.83 9.31 0.00 2.52
5084 5262 2.738846 CTGATTGGTCACGGTGAGAAAG 59.261 50.000 11.83 0.45 0.00 2.62
5085 5263 2.104111 TGATTGGTCACGGTGAGAAAGT 59.896 45.455 11.83 0.00 0.00 2.66
5086 5264 2.702592 TTGGTCACGGTGAGAAAGTT 57.297 45.000 11.83 0.00 0.00 2.66
5087 5265 1.948104 TGGTCACGGTGAGAAAGTTG 58.052 50.000 11.83 0.00 0.00 3.16
5088 5266 1.208535 TGGTCACGGTGAGAAAGTTGT 59.791 47.619 11.83 0.00 0.00 3.32
5089 5267 2.285977 GGTCACGGTGAGAAAGTTGTT 58.714 47.619 11.83 0.00 0.00 2.83
5090 5268 2.681344 GGTCACGGTGAGAAAGTTGTTT 59.319 45.455 11.83 0.00 0.00 2.83
5091 5269 3.128068 GGTCACGGTGAGAAAGTTGTTTT 59.872 43.478 11.83 0.00 0.00 2.43
5092 5270 4.333372 GGTCACGGTGAGAAAGTTGTTTTA 59.667 41.667 11.83 0.00 0.00 1.52
5093 5271 5.499047 GTCACGGTGAGAAAGTTGTTTTAG 58.501 41.667 11.83 0.00 0.00 1.85
5094 5272 5.292589 GTCACGGTGAGAAAGTTGTTTTAGA 59.707 40.000 11.83 0.00 0.00 2.10
5095 5273 5.522460 TCACGGTGAGAAAGTTGTTTTAGAG 59.478 40.000 6.76 0.00 0.00 2.43
5096 5274 5.293569 CACGGTGAGAAAGTTGTTTTAGAGT 59.706 40.000 0.74 0.00 0.00 3.24
5097 5275 5.878669 ACGGTGAGAAAGTTGTTTTAGAGTT 59.121 36.000 0.00 0.00 0.00 3.01
5098 5276 6.373495 ACGGTGAGAAAGTTGTTTTAGAGTTT 59.627 34.615 0.00 0.00 0.00 2.66
5099 5277 7.094506 ACGGTGAGAAAGTTGTTTTAGAGTTTT 60.095 33.333 0.00 0.00 0.00 2.43
5100 5278 7.753580 CGGTGAGAAAGTTGTTTTAGAGTTTTT 59.246 33.333 0.00 0.00 0.00 1.94
5122 5300 8.533569 TTTTTGAATGGTAGGAAGACTCTTTT 57.466 30.769 0.00 0.00 0.00 2.27
5123 5301 8.533569 TTTTGAATGGTAGGAAGACTCTTTTT 57.466 30.769 0.00 0.00 0.00 1.94
5176 5354 9.912634 TTTTCTTTTTAAGATGGATGTGATGTC 57.087 29.630 0.00 0.00 37.38 3.06
5177 5355 8.868522 TTCTTTTTAAGATGGATGTGATGTCT 57.131 30.769 0.00 0.00 37.38 3.41
5178 5356 9.958180 TTCTTTTTAAGATGGATGTGATGTCTA 57.042 29.630 0.00 0.00 37.38 2.59
5179 5357 9.383519 TCTTTTTAAGATGGATGTGATGTCTAC 57.616 33.333 0.00 0.00 31.20 2.59
5180 5358 9.166173 CTTTTTAAGATGGATGTGATGTCTACA 57.834 33.333 0.00 0.00 0.00 2.74
5181 5359 9.685276 TTTTTAAGATGGATGTGATGTCTACAT 57.315 29.630 0.00 0.00 41.21 2.29
5183 5361 9.987272 TTTAAGATGGATGTGATGTCTACATAG 57.013 33.333 0.00 0.00 38.78 2.23
5184 5362 7.609097 AAGATGGATGTGATGTCTACATAGT 57.391 36.000 0.00 0.00 38.78 2.12
5185 5363 6.990798 AGATGGATGTGATGTCTACATAGTG 58.009 40.000 0.00 0.00 38.78 2.74
5186 5364 4.948847 TGGATGTGATGTCTACATAGTGC 58.051 43.478 0.00 0.00 38.78 4.40
5187 5365 3.983988 GGATGTGATGTCTACATAGTGCG 59.016 47.826 0.00 0.00 38.78 5.34
5188 5366 4.261614 GGATGTGATGTCTACATAGTGCGA 60.262 45.833 0.00 0.00 38.78 5.10
5189 5367 4.292977 TGTGATGTCTACATAGTGCGAG 57.707 45.455 0.00 0.00 36.57 5.03
5190 5368 3.945285 TGTGATGTCTACATAGTGCGAGA 59.055 43.478 0.00 0.00 36.57 4.04
5191 5369 4.398044 TGTGATGTCTACATAGTGCGAGAA 59.602 41.667 0.00 0.00 36.57 2.87
5192 5370 5.067805 TGTGATGTCTACATAGTGCGAGAAT 59.932 40.000 0.00 0.00 36.57 2.40
5193 5371 6.262273 TGTGATGTCTACATAGTGCGAGAATA 59.738 38.462 0.00 0.00 36.57 1.75
5194 5372 7.040409 TGTGATGTCTACATAGTGCGAGAATAT 60.040 37.037 0.00 0.00 36.57 1.28
5195 5373 7.810282 GTGATGTCTACATAGTGCGAGAATATT 59.190 37.037 0.00 0.00 36.57 1.28
5196 5374 8.360390 TGATGTCTACATAGTGCGAGAATATTT 58.640 33.333 0.00 0.00 36.57 1.40
5197 5375 9.197694 GATGTCTACATAGTGCGAGAATATTTT 57.802 33.333 0.00 0.00 36.57 1.82
5198 5376 8.942338 TGTCTACATAGTGCGAGAATATTTTT 57.058 30.769 0.00 0.00 0.00 1.94
5219 5397 7.825331 TTTTTACATGATGGTGAGGTGTTAA 57.175 32.000 0.00 0.00 0.00 2.01
5220 5398 7.825331 TTTTACATGATGGTGAGGTGTTAAA 57.175 32.000 0.00 0.00 0.00 1.52
5221 5399 7.447374 TTTACATGATGGTGAGGTGTTAAAG 57.553 36.000 0.00 0.00 0.00 1.85
5222 5400 5.241403 ACATGATGGTGAGGTGTTAAAGA 57.759 39.130 0.00 0.00 0.00 2.52
5223 5401 5.248640 ACATGATGGTGAGGTGTTAAAGAG 58.751 41.667 0.00 0.00 0.00 2.85
5224 5402 4.286297 TGATGGTGAGGTGTTAAAGAGG 57.714 45.455 0.00 0.00 0.00 3.69
5225 5403 2.561478 TGGTGAGGTGTTAAAGAGGC 57.439 50.000 0.00 0.00 0.00 4.70
5226 5404 1.270625 TGGTGAGGTGTTAAAGAGGCG 60.271 52.381 0.00 0.00 0.00 5.52
5227 5405 0.796927 GTGAGGTGTTAAAGAGGCGC 59.203 55.000 0.00 0.00 0.00 6.53
5228 5406 0.685097 TGAGGTGTTAAAGAGGCGCT 59.315 50.000 7.64 0.00 0.00 5.92
5229 5407 1.897133 TGAGGTGTTAAAGAGGCGCTA 59.103 47.619 7.64 0.00 0.00 4.26
5230 5408 2.094182 TGAGGTGTTAAAGAGGCGCTAG 60.094 50.000 7.64 0.00 0.00 3.42
5231 5409 2.165845 GAGGTGTTAAAGAGGCGCTAGA 59.834 50.000 7.64 0.00 0.00 2.43
5232 5410 2.565834 AGGTGTTAAAGAGGCGCTAGAA 59.434 45.455 7.64 0.00 0.00 2.10
5233 5411 3.197983 AGGTGTTAAAGAGGCGCTAGAAT 59.802 43.478 7.64 0.00 0.00 2.40
5234 5412 3.309954 GGTGTTAAAGAGGCGCTAGAATG 59.690 47.826 7.64 0.00 0.00 2.67
5235 5413 3.309954 GTGTTAAAGAGGCGCTAGAATGG 59.690 47.826 7.64 0.00 0.00 3.16
5236 5414 3.055385 TGTTAAAGAGGCGCTAGAATGGT 60.055 43.478 7.64 0.00 0.00 3.55
5237 5415 2.029838 AAAGAGGCGCTAGAATGGTG 57.970 50.000 7.64 0.00 0.00 4.17
5238 5416 0.179000 AAGAGGCGCTAGAATGGTGG 59.821 55.000 7.64 0.00 0.00 4.61
5240 5418 2.902343 GGCGCTAGAATGGTGGCC 60.902 66.667 7.64 0.00 46.79 5.36
5241 5419 2.124736 GCGCTAGAATGGTGGCCA 60.125 61.111 0.00 0.00 38.19 5.36
5242 5420 1.748879 GCGCTAGAATGGTGGCCAA 60.749 57.895 7.24 0.00 36.95 4.52
5243 5421 1.993369 GCGCTAGAATGGTGGCCAAC 61.993 60.000 15.99 15.99 36.95 3.77
5244 5422 0.392998 CGCTAGAATGGTGGCCAACT 60.393 55.000 24.13 0.98 36.95 3.16
5245 5423 1.134521 CGCTAGAATGGTGGCCAACTA 60.135 52.381 24.13 9.02 36.95 2.24
5246 5424 2.565841 GCTAGAATGGTGGCCAACTAG 58.434 52.381 24.13 20.75 42.04 2.57
5247 5425 2.565841 CTAGAATGGTGGCCAACTAGC 58.434 52.381 24.13 10.79 37.56 3.42
5248 5426 0.995024 AGAATGGTGGCCAACTAGCT 59.005 50.000 24.13 13.06 36.95 3.32
5249 5427 2.196595 AGAATGGTGGCCAACTAGCTA 58.803 47.619 24.13 0.00 36.95 3.32
5250 5428 2.576191 AGAATGGTGGCCAACTAGCTAA 59.424 45.455 24.13 0.00 36.95 3.09
5251 5429 2.420058 ATGGTGGCCAACTAGCTAAC 57.580 50.000 24.13 0.00 36.95 2.34
5252 5430 0.326927 TGGTGGCCAACTAGCTAACC 59.673 55.000 24.13 9.45 38.88 2.85
5253 5431 0.326927 GGTGGCCAACTAGCTAACCA 59.673 55.000 15.48 0.47 38.53 3.67
5254 5432 1.679032 GGTGGCCAACTAGCTAACCAG 60.679 57.143 15.48 0.00 38.53 4.00
5265 5443 1.668419 GCTAACCAGCTACCCATGTG 58.332 55.000 0.00 0.00 44.93 3.21
5266 5444 1.747206 GCTAACCAGCTACCCATGTGG 60.747 57.143 0.00 0.00 44.93 4.17
5271 5449 2.516930 GCTACCCATGTGGCGCAT 60.517 61.111 10.83 7.93 39.28 4.73
5278 5456 2.677524 ATGTGGCGCATGCTGGTT 60.678 55.556 17.13 0.00 42.25 3.67
5279 5457 2.997075 ATGTGGCGCATGCTGGTTG 61.997 57.895 17.13 0.00 42.25 3.77
5280 5458 4.424566 GTGGCGCATGCTGGTTGG 62.425 66.667 17.13 0.00 42.25 3.77
5281 5459 4.972733 TGGCGCATGCTGGTTGGT 62.973 61.111 17.13 0.00 42.25 3.67
5282 5460 4.120331 GGCGCATGCTGGTTGGTC 62.120 66.667 17.13 0.00 42.25 4.02
5283 5461 3.364441 GCGCATGCTGGTTGGTCA 61.364 61.111 17.13 0.00 38.39 4.02
5284 5462 2.562912 CGCATGCTGGTTGGTCAC 59.437 61.111 17.13 0.00 0.00 3.67
5285 5463 2.562912 GCATGCTGGTTGGTCACG 59.437 61.111 11.37 0.00 0.00 4.35
5286 5464 2.981560 GCATGCTGGTTGGTCACGG 61.982 63.158 11.37 0.00 0.00 4.94
5287 5465 1.600636 CATGCTGGTTGGTCACGGT 60.601 57.895 0.00 0.00 0.00 4.83
5288 5466 1.600636 ATGCTGGTTGGTCACGGTG 60.601 57.895 0.56 0.56 0.00 4.94
5289 5467 2.050836 ATGCTGGTTGGTCACGGTGA 62.051 55.000 6.76 6.76 0.00 4.02
5290 5468 1.961277 GCTGGTTGGTCACGGTGAG 60.961 63.158 11.83 0.00 0.00 3.51
5291 5469 1.745890 CTGGTTGGTCACGGTGAGA 59.254 57.895 11.83 0.00 0.00 3.27
5292 5470 0.319900 CTGGTTGGTCACGGTGAGAG 60.320 60.000 11.83 0.00 0.00 3.20
5293 5471 1.046472 TGGTTGGTCACGGTGAGAGT 61.046 55.000 11.83 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.966875 GCCATGTTCCCATGTGCAGA 60.967 55.000 0.00 0.00 45.83 4.26
101 102 6.819397 TCTCGACAACTCTAGATGAAAAGA 57.181 37.500 0.29 0.00 0.00 2.52
190 191 4.036380 GTGACAAAAGAATGACCGGAAAGT 59.964 41.667 9.46 0.00 0.00 2.66
273 274 5.843673 TCACCAGAAAATGTTTGTAGCAA 57.156 34.783 0.00 0.00 0.00 3.91
391 485 9.831737 GATATATTTCACATCAACCTTATGCAC 57.168 33.333 0.00 0.00 0.00 4.57
392 486 9.797642 AGATATATTTCACATCAACCTTATGCA 57.202 29.630 0.00 0.00 0.00 3.96
680 780 4.765856 TCCCTCCGTTCATAAGTAGATAGC 59.234 45.833 0.00 0.00 0.00 2.97
692 792 7.364673 CCACATATGATATATTCCCTCCGTTCA 60.365 40.741 10.38 0.00 0.00 3.18
743 843 8.579850 TCCATAACAATAAGTCAAGATTGCTT 57.420 30.769 7.20 7.20 36.67 3.91
877 977 5.008415 GCACATCTGGATCAATTTCTCGAAT 59.992 40.000 0.00 0.00 0.00 3.34
880 980 3.302935 CGCACATCTGGATCAATTTCTCG 60.303 47.826 0.00 0.00 0.00 4.04
918 1018 3.891422 ATCCTCTGACTCAAGCTTCAG 57.109 47.619 6.78 6.78 40.65 3.02
1008 1108 2.617532 GGAAGCCTCTTCTCTGTTGCAT 60.618 50.000 6.54 0.00 0.00 3.96
1345 1445 6.363088 CGCTTTGTTTGATCACACAATATTGT 59.637 34.615 24.07 15.47 43.36 2.71
1851 1951 1.534163 GTCGGTACAGCAGGTTTTTCC 59.466 52.381 0.00 0.00 0.00 3.13
2069 2169 3.576078 TTGACCATCCACCCATATGTC 57.424 47.619 1.24 0.00 0.00 3.06
2351 2451 5.741982 GTGTTCATGTTTACAGTTTGGACAC 59.258 40.000 9.53 9.53 36.39 3.67
2354 2454 5.067153 CCTGTGTTCATGTTTACAGTTTGGA 59.933 40.000 17.88 0.00 39.02 3.53
2399 2499 6.945938 ACACTGTAGATACATCCTCTACAC 57.054 41.667 8.65 0.00 46.23 2.90
2501 2604 8.015658 TCTTTCTTCGCTTCTTTTTGCTATTAC 58.984 33.333 0.00 0.00 0.00 1.89
2636 2739 3.244911 TGGAGTTTTAGCTTCCTCTTGGG 60.245 47.826 0.00 0.00 0.00 4.12
3240 3358 4.630069 TCCTTAACTGTCGCAAATAAGCTC 59.370 41.667 0.00 0.00 0.00 4.09
3243 3361 6.721571 TTCTCCTTAACTGTCGCAAATAAG 57.278 37.500 0.00 0.00 0.00 1.73
3523 3641 4.540824 GATGTGTTTGGCTCAGAAGAAAC 58.459 43.478 0.00 0.00 0.00 2.78
3540 3658 2.686915 GGGATTTCTCTGCAAGGATGTG 59.313 50.000 0.00 0.00 0.00 3.21
3771 3889 3.084786 AGCTTCAAGCCAGGTCAAATAC 58.915 45.455 5.53 0.00 43.77 1.89
3840 3958 7.807907 CGAATTTTAAATTTACCACAGCTGACT 59.192 33.333 23.35 4.17 0.00 3.41
3875 3993 4.879104 TCGTTTGTTTCGTACATGGTTT 57.121 36.364 0.00 0.00 36.44 3.27
3930 4048 4.344679 ACAATTTCAATCTGCTGGTTTGGA 59.655 37.500 7.13 0.00 0.00 3.53
4095 4213 0.802494 CCGCTGTGTAACCATTGACC 59.198 55.000 0.00 0.00 34.36 4.02
4159 4277 3.006247 GAGAGAACTTCAGATTGTGCCC 58.994 50.000 0.00 0.00 0.00 5.36
4228 4346 1.596477 CCAGCTCATAGAAGCCGCC 60.596 63.158 0.00 0.00 43.56 6.13
4343 4461 4.946784 AATTGACAGCGGAATAAGACAC 57.053 40.909 0.00 0.00 0.00 3.67
4531 4649 2.104281 ACTTCACCACCACCAGTAAGAC 59.896 50.000 0.00 0.00 0.00 3.01
4736 4855 6.916387 CAGTAAAGAACAACTCGAGTAGAACA 59.084 38.462 20.39 0.00 0.00 3.18
4931 5105 1.462627 AGGGACCAACGAAGGGGAA 60.463 57.895 0.00 0.00 0.00 3.97
4941 5119 2.018515 GTTGTTCGTTTCAGGGACCAA 58.981 47.619 0.00 0.00 0.00 3.67
4972 5150 8.657387 AGATAGCCTTATTAGCAACAGATCTA 57.343 34.615 0.00 0.00 0.00 1.98
5008 5186 4.563140 TTCTAACGCCTCTTAATGGGTT 57.437 40.909 0.00 0.00 40.27 4.11
5009 5187 4.451900 CATTCTAACGCCTCTTAATGGGT 58.548 43.478 0.00 0.00 0.00 4.51
5010 5188 3.815401 CCATTCTAACGCCTCTTAATGGG 59.185 47.826 0.00 0.00 39.65 4.00
5011 5189 4.273480 CACCATTCTAACGCCTCTTAATGG 59.727 45.833 9.70 9.70 45.67 3.16
5012 5190 4.273480 CCACCATTCTAACGCCTCTTAATG 59.727 45.833 0.00 0.00 0.00 1.90
5013 5191 4.451900 CCACCATTCTAACGCCTCTTAAT 58.548 43.478 0.00 0.00 0.00 1.40
5014 5192 3.869065 CCACCATTCTAACGCCTCTTAA 58.131 45.455 0.00 0.00 0.00 1.85
5015 5193 2.419574 GCCACCATTCTAACGCCTCTTA 60.420 50.000 0.00 0.00 0.00 2.10
5016 5194 1.679032 GCCACCATTCTAACGCCTCTT 60.679 52.381 0.00 0.00 0.00 2.85
5017 5195 0.107654 GCCACCATTCTAACGCCTCT 60.108 55.000 0.00 0.00 0.00 3.69
5018 5196 1.095807 GGCCACCATTCTAACGCCTC 61.096 60.000 0.00 0.00 33.50 4.70
5019 5197 1.077716 GGCCACCATTCTAACGCCT 60.078 57.895 0.00 0.00 33.50 5.52
5020 5198 0.963355 TTGGCCACCATTCTAACGCC 60.963 55.000 3.88 0.00 36.91 5.68
5021 5199 0.170339 GTTGGCCACCATTCTAACGC 59.830 55.000 3.88 0.00 31.53 4.84
5022 5200 1.821216 AGTTGGCCACCATTCTAACG 58.179 50.000 3.88 0.00 31.53 3.18
5023 5201 2.683362 GCTAGTTGGCCACCATTCTAAC 59.317 50.000 3.88 0.00 31.53 2.34
5024 5202 2.576191 AGCTAGTTGGCCACCATTCTAA 59.424 45.455 3.88 0.00 31.53 2.10
5025 5203 2.196595 AGCTAGTTGGCCACCATTCTA 58.803 47.619 3.88 2.86 31.53 2.10
5026 5204 0.995024 AGCTAGTTGGCCACCATTCT 59.005 50.000 3.88 1.66 31.53 2.40
5027 5205 2.289565 GTAGCTAGTTGGCCACCATTC 58.710 52.381 3.88 0.00 31.53 2.67
5028 5206 1.406887 CGTAGCTAGTTGGCCACCATT 60.407 52.381 3.88 0.00 31.53 3.16
5029 5207 0.178068 CGTAGCTAGTTGGCCACCAT 59.822 55.000 3.88 0.00 31.53 3.55
5030 5208 1.594833 CGTAGCTAGTTGGCCACCA 59.405 57.895 3.88 0.00 0.00 4.17
5031 5209 4.515404 CGTAGCTAGTTGGCCACC 57.485 61.111 3.88 0.00 0.00 4.61
5051 5229 1.435925 CAATCAGCATGCGCCACAT 59.564 52.632 13.01 0.00 40.66 3.21
5052 5230 2.702788 CCAATCAGCATGCGCCACA 61.703 57.895 13.01 0.00 39.83 4.17
5053 5231 2.103538 CCAATCAGCATGCGCCAC 59.896 61.111 13.01 0.00 39.83 5.01
5054 5232 2.361483 ACCAATCAGCATGCGCCA 60.361 55.556 13.01 0.00 39.83 5.69
5055 5233 2.409055 TGACCAATCAGCATGCGCC 61.409 57.895 13.01 0.00 39.83 6.53
5056 5234 1.226491 GTGACCAATCAGCATGCGC 60.226 57.895 13.01 0.00 34.75 6.09
5057 5235 1.061411 CGTGACCAATCAGCATGCG 59.939 57.895 13.01 7.64 34.75 4.73
5058 5236 1.308069 ACCGTGACCAATCAGCATGC 61.308 55.000 10.51 10.51 34.75 4.06
5059 5237 0.448990 CACCGTGACCAATCAGCATG 59.551 55.000 0.00 0.00 34.75 4.06
5060 5238 0.324614 TCACCGTGACCAATCAGCAT 59.675 50.000 0.00 0.00 34.75 3.79
5061 5239 0.320683 CTCACCGTGACCAATCAGCA 60.321 55.000 0.00 0.00 34.75 4.41
5062 5240 0.037326 TCTCACCGTGACCAATCAGC 60.037 55.000 0.00 0.00 34.75 4.26
5063 5241 2.455674 TTCTCACCGTGACCAATCAG 57.544 50.000 0.00 0.00 34.75 2.90
5064 5242 2.104111 ACTTTCTCACCGTGACCAATCA 59.896 45.455 0.00 0.00 0.00 2.57
5065 5243 2.767505 ACTTTCTCACCGTGACCAATC 58.232 47.619 0.00 0.00 0.00 2.67
5066 5244 2.878406 CAACTTTCTCACCGTGACCAAT 59.122 45.455 0.00 0.00 0.00 3.16
5067 5245 2.285083 CAACTTTCTCACCGTGACCAA 58.715 47.619 0.00 0.00 0.00 3.67
5068 5246 1.208535 ACAACTTTCTCACCGTGACCA 59.791 47.619 0.00 0.00 0.00 4.02
5069 5247 1.949465 ACAACTTTCTCACCGTGACC 58.051 50.000 0.00 0.00 0.00 4.02
5070 5248 4.351131 AAAACAACTTTCTCACCGTGAC 57.649 40.909 0.00 0.00 0.00 3.67
5071 5249 5.421277 TCTAAAACAACTTTCTCACCGTGA 58.579 37.500 0.29 0.29 0.00 4.35
5072 5250 5.293569 ACTCTAAAACAACTTTCTCACCGTG 59.706 40.000 0.00 0.00 0.00 4.94
5073 5251 5.425630 ACTCTAAAACAACTTTCTCACCGT 58.574 37.500 0.00 0.00 0.00 4.83
5074 5252 5.986004 ACTCTAAAACAACTTTCTCACCG 57.014 39.130 0.00 0.00 0.00 4.94
5075 5253 8.981724 AAAAACTCTAAAACAACTTTCTCACC 57.018 30.769 0.00 0.00 0.00 4.02
5097 5275 8.533569 AAAAGAGTCTTCCTACCATTCAAAAA 57.466 30.769 5.70 0.00 0.00 1.94
5098 5276 8.533569 AAAAAGAGTCTTCCTACCATTCAAAA 57.466 30.769 5.70 0.00 0.00 2.44
5150 5328 9.912634 GACATCACATCCATCTTAAAAAGAAAA 57.087 29.630 0.00 0.00 41.63 2.29
5151 5329 9.300681 AGACATCACATCCATCTTAAAAAGAAA 57.699 29.630 0.00 0.00 41.63 2.52
5152 5330 8.868522 AGACATCACATCCATCTTAAAAAGAA 57.131 30.769 0.00 0.00 41.63 2.52
5153 5331 9.383519 GTAGACATCACATCCATCTTAAAAAGA 57.616 33.333 0.00 0.00 42.69 2.52
5154 5332 9.166173 TGTAGACATCACATCCATCTTAAAAAG 57.834 33.333 0.00 0.00 0.00 2.27
5155 5333 9.685276 ATGTAGACATCACATCCATCTTAAAAA 57.315 29.630 0.00 0.00 30.82 1.94
5157 5335 9.987272 CTATGTAGACATCACATCCATCTTAAA 57.013 33.333 0.00 0.00 37.74 1.52
5158 5336 9.147732 ACTATGTAGACATCACATCCATCTTAA 57.852 33.333 0.00 0.00 37.74 1.85
5159 5337 8.579863 CACTATGTAGACATCACATCCATCTTA 58.420 37.037 0.00 0.00 37.74 2.10
5160 5338 7.440198 CACTATGTAGACATCACATCCATCTT 58.560 38.462 0.00 0.00 37.74 2.40
5161 5339 6.518032 GCACTATGTAGACATCACATCCATCT 60.518 42.308 0.00 0.00 37.74 2.90
5162 5340 5.636965 GCACTATGTAGACATCACATCCATC 59.363 44.000 0.00 0.00 37.74 3.51
5163 5341 5.545588 GCACTATGTAGACATCACATCCAT 58.454 41.667 0.00 0.00 37.74 3.41
5164 5342 4.499696 CGCACTATGTAGACATCACATCCA 60.500 45.833 0.00 0.00 37.74 3.41
5165 5343 3.983988 CGCACTATGTAGACATCACATCC 59.016 47.826 0.00 0.00 37.74 3.51
5166 5344 4.860072 TCGCACTATGTAGACATCACATC 58.140 43.478 0.00 0.00 37.74 3.06
5167 5345 4.580580 TCTCGCACTATGTAGACATCACAT 59.419 41.667 0.00 0.00 39.82 3.21
5168 5346 3.945285 TCTCGCACTATGTAGACATCACA 59.055 43.478 0.00 0.00 37.76 3.58
5169 5347 4.553756 TCTCGCACTATGTAGACATCAC 57.446 45.455 0.00 0.00 37.76 3.06
5170 5348 5.774498 ATTCTCGCACTATGTAGACATCA 57.226 39.130 0.00 0.00 37.76 3.07
5171 5349 8.749841 AAATATTCTCGCACTATGTAGACATC 57.250 34.615 0.00 0.00 37.76 3.06
5172 5350 9.547753 AAAAATATTCTCGCACTATGTAGACAT 57.452 29.630 0.08 0.08 40.22 3.06
5173 5351 8.942338 AAAAATATTCTCGCACTATGTAGACA 57.058 30.769 0.00 0.00 0.00 3.41
5195 5373 7.825331 TTAACACCTCACCATCATGTAAAAA 57.175 32.000 0.00 0.00 0.00 1.94
5196 5374 7.721842 TCTTTAACACCTCACCATCATGTAAAA 59.278 33.333 0.00 0.00 0.00 1.52
5197 5375 7.227873 TCTTTAACACCTCACCATCATGTAAA 58.772 34.615 0.00 0.00 0.00 2.01
5198 5376 6.774673 TCTTTAACACCTCACCATCATGTAA 58.225 36.000 0.00 0.00 0.00 2.41
5199 5377 6.367374 TCTTTAACACCTCACCATCATGTA 57.633 37.500 0.00 0.00 0.00 2.29
5200 5378 5.241403 TCTTTAACACCTCACCATCATGT 57.759 39.130 0.00 0.00 0.00 3.21
5201 5379 4.637534 CCTCTTTAACACCTCACCATCATG 59.362 45.833 0.00 0.00 0.00 3.07
5202 5380 4.848357 CCTCTTTAACACCTCACCATCAT 58.152 43.478 0.00 0.00 0.00 2.45
5203 5381 3.559171 GCCTCTTTAACACCTCACCATCA 60.559 47.826 0.00 0.00 0.00 3.07
5204 5382 3.010420 GCCTCTTTAACACCTCACCATC 58.990 50.000 0.00 0.00 0.00 3.51
5205 5383 2.615493 CGCCTCTTTAACACCTCACCAT 60.615 50.000 0.00 0.00 0.00 3.55
5206 5384 1.270625 CGCCTCTTTAACACCTCACCA 60.271 52.381 0.00 0.00 0.00 4.17
5207 5385 1.439679 CGCCTCTTTAACACCTCACC 58.560 55.000 0.00 0.00 0.00 4.02
5208 5386 0.796927 GCGCCTCTTTAACACCTCAC 59.203 55.000 0.00 0.00 0.00 3.51
5209 5387 0.685097 AGCGCCTCTTTAACACCTCA 59.315 50.000 2.29 0.00 0.00 3.86
5210 5388 2.165845 TCTAGCGCCTCTTTAACACCTC 59.834 50.000 2.29 0.00 0.00 3.85
5211 5389 2.176889 TCTAGCGCCTCTTTAACACCT 58.823 47.619 2.29 0.00 0.00 4.00
5212 5390 2.667473 TCTAGCGCCTCTTTAACACC 57.333 50.000 2.29 0.00 0.00 4.16
5213 5391 3.309954 CCATTCTAGCGCCTCTTTAACAC 59.690 47.826 2.29 0.00 0.00 3.32
5214 5392 3.055385 ACCATTCTAGCGCCTCTTTAACA 60.055 43.478 2.29 0.00 0.00 2.41
5215 5393 3.309954 CACCATTCTAGCGCCTCTTTAAC 59.690 47.826 2.29 0.00 0.00 2.01
5216 5394 3.531538 CACCATTCTAGCGCCTCTTTAA 58.468 45.455 2.29 0.00 0.00 1.52
5217 5395 2.158957 CCACCATTCTAGCGCCTCTTTA 60.159 50.000 2.29 0.00 0.00 1.85
5218 5396 1.407437 CCACCATTCTAGCGCCTCTTT 60.407 52.381 2.29 0.00 0.00 2.52
5219 5397 0.179000 CCACCATTCTAGCGCCTCTT 59.821 55.000 2.29 0.00 0.00 2.85
5220 5398 1.826024 CCACCATTCTAGCGCCTCT 59.174 57.895 2.29 0.00 0.00 3.69
5221 5399 1.889573 GCCACCATTCTAGCGCCTC 60.890 63.158 2.29 0.00 0.00 4.70
5222 5400 2.190578 GCCACCATTCTAGCGCCT 59.809 61.111 2.29 0.00 0.00 5.52
5223 5401 2.902343 GGCCACCATTCTAGCGCC 60.902 66.667 2.29 0.00 0.00 6.53
5224 5402 1.748879 TTGGCCACCATTCTAGCGC 60.749 57.895 3.88 0.00 31.53 5.92
5225 5403 0.392998 AGTTGGCCACCATTCTAGCG 60.393 55.000 3.88 0.00 31.53 4.26
5226 5404 2.565841 CTAGTTGGCCACCATTCTAGC 58.434 52.381 3.88 0.00 34.49 3.42
5227 5405 2.171448 AGCTAGTTGGCCACCATTCTAG 59.829 50.000 3.88 13.35 39.27 2.43
5228 5406 2.196595 AGCTAGTTGGCCACCATTCTA 58.803 47.619 3.88 2.86 31.53 2.10
5229 5407 0.995024 AGCTAGTTGGCCACCATTCT 59.005 50.000 3.88 1.66 31.53 2.40
5230 5408 2.683362 GTTAGCTAGTTGGCCACCATTC 59.317 50.000 3.88 0.00 31.53 2.67
5231 5409 2.620627 GGTTAGCTAGTTGGCCACCATT 60.621 50.000 3.88 0.00 36.57 3.16
5232 5410 1.064685 GGTTAGCTAGTTGGCCACCAT 60.065 52.381 3.88 0.00 36.57 3.55
5233 5411 0.326927 GGTTAGCTAGTTGGCCACCA 59.673 55.000 3.88 0.00 36.57 4.17
5234 5412 0.326927 TGGTTAGCTAGTTGGCCACC 59.673 55.000 3.88 0.00 36.89 4.61
5235 5413 1.739067 CTGGTTAGCTAGTTGGCCAC 58.261 55.000 3.88 0.00 0.00 5.01
5236 5414 0.035439 GCTGGTTAGCTAGTTGGCCA 60.035 55.000 0.00 0.00 46.57 5.36
5237 5415 2.781911 GCTGGTTAGCTAGTTGGCC 58.218 57.895 0.00 0.00 46.57 5.36
5247 5425 1.747206 GCCACATGGGTAGCTGGTTAG 60.747 57.143 0.00 0.00 39.65 2.34
5248 5426 0.254747 GCCACATGGGTAGCTGGTTA 59.745 55.000 0.00 0.00 39.65 2.85
5249 5427 1.000896 GCCACATGGGTAGCTGGTT 60.001 57.895 0.00 0.00 39.65 3.67
5250 5428 2.677228 GCCACATGGGTAGCTGGT 59.323 61.111 0.00 0.00 39.65 4.00
5251 5429 2.514592 CGCCACATGGGTAGCTGG 60.515 66.667 0.00 0.00 39.65 4.85
5252 5430 3.204827 GCGCCACATGGGTAGCTG 61.205 66.667 0.00 0.00 38.71 4.24
5253 5431 3.047807 ATGCGCCACATGGGTAGCT 62.048 57.895 4.18 0.00 41.15 3.32
5254 5432 2.516930 ATGCGCCACATGGGTAGC 60.517 61.111 4.18 5.09 37.70 3.58
5261 5439 2.677524 AACCAGCATGCGCCACAT 60.678 55.556 13.01 0.00 40.66 3.21
5262 5440 3.672447 CAACCAGCATGCGCCACA 61.672 61.111 13.01 0.00 39.83 4.17
5263 5441 4.424566 CCAACCAGCATGCGCCAC 62.425 66.667 13.01 0.00 39.83 5.01
5264 5442 4.972733 ACCAACCAGCATGCGCCA 62.973 61.111 13.01 0.00 39.83 5.69
5265 5443 4.120331 GACCAACCAGCATGCGCC 62.120 66.667 13.01 0.00 39.83 6.53
5266 5444 3.364441 TGACCAACCAGCATGCGC 61.364 61.111 13.01 0.00 38.99 6.09
5267 5445 2.562912 GTGACCAACCAGCATGCG 59.437 61.111 13.01 7.31 31.97 4.73
5268 5446 2.562912 CGTGACCAACCAGCATGC 59.437 61.111 10.51 10.51 31.97 4.06
5269 5447 1.600636 ACCGTGACCAACCAGCATG 60.601 57.895 0.00 0.00 0.00 4.06
5270 5448 1.600636 CACCGTGACCAACCAGCAT 60.601 57.895 0.00 0.00 0.00 3.79
5271 5449 2.203139 CACCGTGACCAACCAGCA 60.203 61.111 0.00 0.00 0.00 4.41
5272 5450 1.961277 CTCACCGTGACCAACCAGC 60.961 63.158 0.00 0.00 0.00 4.85
5273 5451 0.319900 CTCTCACCGTGACCAACCAG 60.320 60.000 0.00 0.00 0.00 4.00
5274 5452 1.046472 ACTCTCACCGTGACCAACCA 61.046 55.000 0.00 0.00 0.00 3.67
5275 5453 1.746517 ACTCTCACCGTGACCAACC 59.253 57.895 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.