Multiple sequence alignment - TraesCS1D01G148800

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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 TraesCS1D01G148800 chr1D 100.000 6972 0 0 1 6972 204627641 204634612 0.000000e+00 12875.0
1 TraesCS1D01G148800 chr1B 96.055 4892 128 30 368 5221 300571284 300576148 0.000000e+00 7904.0
2 TraesCS1D01G148800 chr1B 95.279 932 40 4 5371 6299 300576144 300577074 0.000000e+00 1474.0
3 TraesCS1D01G148800 chr1B 96.648 179 6 0 6794 6972 300581348 300581526 1.470000e-76 298.0
4 TraesCS1D01G148800 chr1B 90.608 181 9 5 6286 6458 300580523 300580703 4.200000e-57 233.0
5 TraesCS1D01G148800 chr1B 89.076 119 13 0 1 119 300570591 300570709 1.570000e-31 148.0
6 TraesCS1D01G148800 chr1B 95.000 60 3 0 5311 5370 645049264 645049205 2.070000e-15 95.3
7 TraesCS1D01G148800 chr1A 93.362 2094 107 15 1 2073 261129886 261131968 0.000000e+00 3068.0
8 TraesCS1D01G148800 chr1A 92.219 1568 93 12 2086 3625 261132230 261133796 0.000000e+00 2193.0
9 TraesCS1D01G148800 chr1A 91.735 1343 64 23 5371 6681 261135194 261136521 0.000000e+00 1821.0
10 TraesCS1D01G148800 chr1A 92.364 1100 58 13 3658 4747 261133789 261134872 0.000000e+00 1543.0
11 TraesCS1D01G148800 chr1A 94.709 189 7 2 6784 6972 261137274 261137459 2.460000e-74 291.0
12 TraesCS1D01G148800 chr1A 91.558 154 6 3 5074 5221 261135046 261135198 9.170000e-49 206.0
13 TraesCS1D01G148800 chr4D 93.548 93 6 0 5236 5328 281181342 281181434 9.430000e-29 139.0
14 TraesCS1D01G148800 chr4D 83.117 77 10 3 5237 5311 344812605 344812530 4.510000e-07 67.6
15 TraesCS1D01G148800 chr4D 92.683 41 2 1 5229 5268 287555594 287555634 2.720000e-04 58.4
16 TraesCS1D01G148800 chr4B 92.553 94 6 1 5236 5328 285617584 285617491 4.390000e-27 134.0
17 TraesCS1D01G148800 chr4B 95.082 61 2 1 5311 5371 206790047 206789988 2.070000e-15 95.3
18 TraesCS1D01G148800 chr4B 92.683 41 2 1 5229 5268 302853689 302853649 2.720000e-04 58.4
19 TraesCS1D01G148800 chr6B 88.172 93 11 0 5236 5328 31158369 31158461 2.060000e-20 111.0
20 TraesCS1D01G148800 chr6B 95.000 60 3 0 5311 5370 233682549 233682490 2.070000e-15 95.3
21 TraesCS1D01G148800 chr6B 91.489 47 3 1 5229 5274 695664629 695664675 5.840000e-06 63.9
22 TraesCS1D01G148800 chr7D 96.667 60 2 0 5311 5370 336302459 336302400 4.450000e-17 100.0
23 TraesCS1D01G148800 chr7D 95.000 60 3 0 5311 5370 330835582 330835523 2.070000e-15 95.3
24 TraesCS1D01G148800 chr3D 80.147 136 24 3 5236 5370 323277024 323276891 1.600000e-16 99.0
25 TraesCS1D01G148800 chr3D 91.176 68 6 0 5315 5382 598457977 598458044 7.450000e-15 93.5
26 TraesCS1D01G148800 chr7A 93.548 62 4 0 5311 5372 379061430 379061369 7.450000e-15 93.5
27 TraesCS1D01G148800 chr5A 78.261 138 27 3 5236 5372 349476524 349476389 1.250000e-12 86.1
28 TraesCS1D01G148800 chr2A 83.562 73 9 3 5237 5307 364472243 364472172 1.620000e-06 65.8
29 TraesCS1D01G148800 chr6D 84.058 69 8 3 5237 5303 174380549 174380616 5.840000e-06 63.9
30 TraesCS1D01G148800 chr6A 84.058 69 8 3 5237 5303 30442175 30442108 5.840000e-06 63.9
31 TraesCS1D01G148800 chr4A 92.683 41 2 1 5229 5268 207374203 207374243 2.720000e-04 58.4
32 TraesCS1D01G148800 chr3B 94.595 37 2 0 5238 5274 323324967 323324931 2.720000e-04 58.4


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 TraesCS1D01G148800 chr1D 204627641 204634612 6971 False 12875.000000 12875 100.000000 1 6972 1 chr1D.!!$F1 6971
1 TraesCS1D01G148800 chr1B 300570591 300581526 10935 False 2011.400000 7904 93.533200 1 6972 5 chr1B.!!$F1 6971
2 TraesCS1D01G148800 chr1A 261129886 261137459 7573 False 1520.333333 3068 92.657833 1 6972 6 chr1A.!!$F1 6971

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
291 349 0.175760 GAACGTGCAGGAGGCTGATA 59.824 55.000 14.38 0.0 45.15 2.15 F
741 1095 1.002624 TCCACCCGGTCTGCAATTC 60.003 57.895 0.00 0.0 0.00 2.17 F
2265 2876 0.037232 ACTACAGCTGGTTCTTCCGC 60.037 55.000 19.93 0.0 39.52 5.54 F
2280 2891 0.391661 TCCGCTGATGGACAAGCTTC 60.392 55.000 0.00 0.0 31.53 3.86 F
3457 4092 1.065251 GTAGATCCCGTGTTCGTCTCC 59.935 57.143 0.00 0.0 35.01 3.71 F
4217 4856 2.215451 AAATCACCGGATGGCCTGCT 62.215 55.000 9.46 0.0 39.70 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2876 2.630158 CTGAGGAAGCTTGTCCATCAG 58.370 52.381 2.10 8.85 40.48 2.90 R
2384 3001 1.179152 CAACCTGCATTGCTCATCCA 58.821 50.000 10.49 0.00 0.00 3.41 R
4205 4844 0.536687 AATCATGAGCAGGCCATCCG 60.537 55.000 5.01 0.00 37.47 4.18 R
4217 4856 1.487976 GAGCTGACAGGGGAATCATGA 59.512 52.381 4.26 0.00 0.00 3.07 R
5275 5935 0.106268 TGCTGGTTTTGGCCTCTCAA 60.106 50.000 3.32 0.00 0.00 3.02 R
6017 6680 0.035630 GAGCAGCACTCCATGGAACT 60.036 55.000 17.00 10.70 39.75 3.01 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
26 27 8.715191 TTAATGGATCAATGCAAACATTAACC 57.285 30.769 12.55 0.00 44.83 2.85
27 28 5.999205 TGGATCAATGCAAACATTAACCT 57.001 34.783 0.00 0.00 44.83 3.50
75 76 3.763902 TCGAAGCTCTCTTGATTCTTCG 58.236 45.455 14.24 14.24 45.51 3.79
111 112 4.909696 TTTTGCTCAATCCGTTCAAGAA 57.090 36.364 0.00 0.00 0.00 2.52
153 211 7.915293 TTGAGAATCTTCGGCTTTGTATTTA 57.085 32.000 0.00 0.00 34.92 1.40
162 220 6.827586 TCGGCTTTGTATTTACTGGAATTT 57.172 33.333 0.00 0.00 0.00 1.82
178 236 2.885135 ATTTGTGGATGTGCCTGAGA 57.115 45.000 0.00 0.00 37.63 3.27
189 247 2.970639 CCTGAGAGGCCGACGAAA 59.029 61.111 0.00 0.00 0.00 3.46
196 254 0.456221 GAGGCCGACGAAAGAGATCA 59.544 55.000 0.00 0.00 0.00 2.92
217 275 7.607607 AGATCAATGTTGCAGTGTGAATACTAA 59.392 33.333 0.00 0.00 31.07 2.24
258 316 3.244078 TGTGAAACTCTAGCGGTGACAAT 60.244 43.478 0.00 0.00 38.04 2.71
275 333 6.455646 GGTGACAATATCAACGTCATCAGAAC 60.456 42.308 0.00 0.00 41.39 3.01
284 342 1.354040 GTCATCAGAACGTGCAGGAG 58.646 55.000 14.38 0.00 0.00 3.69
285 343 0.247460 TCATCAGAACGTGCAGGAGG 59.753 55.000 14.38 0.00 0.00 4.30
286 344 1.078848 ATCAGAACGTGCAGGAGGC 60.079 57.895 14.38 1.76 45.13 4.70
291 349 0.175760 GAACGTGCAGGAGGCTGATA 59.824 55.000 14.38 0.00 45.15 2.15
381 715 7.416154 TTGATTAATATAAGCCTTCCGTTCG 57.584 36.000 0.00 0.00 0.00 3.95
397 731 4.453136 TCCGTTCGTTTGGGAAAAGAATAG 59.547 41.667 0.00 0.00 40.13 1.73
499 837 4.320870 CCCGTACCTGTACATTTCTTTGT 58.679 43.478 8.09 0.00 35.87 2.83
504 842 7.255001 CCGTACCTGTACATTTCTTTGTTCTTT 60.255 37.037 8.09 0.00 35.87 2.52
509 847 7.229506 CCTGTACATTTCTTTGTTCTTTCTCCT 59.770 37.037 0.00 0.00 0.00 3.69
591 929 4.814294 ACCGCCGACGCCTCAATC 62.814 66.667 0.00 0.00 38.22 2.67
666 1020 3.771160 CCCCAGCCTCTAACGCGT 61.771 66.667 5.58 5.58 0.00 6.01
719 1073 3.554692 CGACATCGCGTTCCTGCC 61.555 66.667 5.77 0.00 0.00 4.85
741 1095 1.002624 TCCACCCGGTCTGCAATTC 60.003 57.895 0.00 0.00 0.00 2.17
817 1171 1.200020 CCACTTGCCTCGACAATTTCC 59.800 52.381 0.00 0.00 0.00 3.13
965 1319 9.396022 TGCTTAAACTTTTATGCTCTTAGCTAT 57.604 29.630 16.28 0.00 42.97 2.97
1278 1632 2.159226 ACTGGAGCAGTCAGTATTACGC 60.159 50.000 5.07 0.00 41.21 4.42
1424 1778 1.338579 GCCTTCTAGTGCTCTGTTGCT 60.339 52.381 0.00 0.00 0.00 3.91
1726 2080 3.280295 TCTTGTTGACCGCCAAACTAAA 58.720 40.909 0.00 0.00 36.36 1.85
1803 2158 7.649306 GCTCTTTTGAAGATTAGCACTGAAAAA 59.351 33.333 0.00 0.00 36.82 1.94
1928 2283 7.182817 TGAGAAGGTAAAGCTATGCTCTTTA 57.817 36.000 0.00 0.00 38.25 1.85
1929 2284 7.620880 TGAGAAGGTAAAGCTATGCTCTTTAA 58.379 34.615 0.00 0.00 38.25 1.52
2158 2769 4.989168 AGAGTTTTTACGAATCTCAAGCGT 59.011 37.500 0.00 0.00 41.58 5.07
2162 2773 6.089150 AGTTTTTACGAATCTCAAGCGTCTAC 59.911 38.462 0.00 0.00 39.24 2.59
2265 2876 0.037232 ACTACAGCTGGTTCTTCCGC 60.037 55.000 19.93 0.00 39.52 5.54
2280 2891 0.391661 TCCGCTGATGGACAAGCTTC 60.392 55.000 0.00 0.00 31.53 3.86
2329 2946 5.548406 ACTTCAAGTATACAGGGTGTTGAC 58.452 41.667 5.50 0.00 0.00 3.18
2374 2991 9.070149 GTAAAATCAAGAGATGAGAAATTGTGC 57.930 33.333 0.00 0.00 42.53 4.57
2384 3001 5.947228 TGAGAAATTGTGCGATTCTTCTT 57.053 34.783 0.00 0.00 33.73 2.52
2537 3167 4.037565 TGGTCTGCCGACATAAGTACATAG 59.962 45.833 10.60 0.00 42.05 2.23
2569 3199 5.804639 TCCCATCAACCATTCTAATATCCG 58.195 41.667 0.00 0.00 0.00 4.18
2611 3241 6.603237 TGCTTCACCGAACATATATTTCTG 57.397 37.500 0.00 0.00 0.00 3.02
2619 3249 9.787532 CACCGAACATATATTTCTGTTTTGATT 57.212 29.630 0.00 0.00 35.80 2.57
3098 3732 1.709578 ACTGTGGAGCTGAAGTCAGA 58.290 50.000 12.54 0.00 46.59 3.27
3190 3824 4.664150 TTTTCCACACCATTTCACCTTC 57.336 40.909 0.00 0.00 0.00 3.46
3457 4092 1.065251 GTAGATCCCGTGTTCGTCTCC 59.935 57.143 0.00 0.00 35.01 3.71
3829 4465 4.202567 TGGAAGCCTCTGGTACTGATTTTT 60.203 41.667 0.00 0.00 35.31 1.94
3860 4496 5.098663 TCAACCCCTTATCTTGAACCTAGT 58.901 41.667 0.00 0.00 0.00 2.57
4051 4689 9.127277 GGTATCCTTTTATTATGTTAACTGCCA 57.873 33.333 7.22 0.00 0.00 4.92
4205 4844 3.003480 GTCTGCTGGTCTACAAATCACC 58.997 50.000 0.00 0.00 0.00 4.02
4217 4856 2.215451 AAATCACCGGATGGCCTGCT 62.215 55.000 9.46 0.00 39.70 4.24
4339 4978 9.655769 CATAAATGCAACTCTGTTGATGTATAC 57.344 33.333 13.75 0.00 0.00 1.47
4340 4979 7.928307 AAATGCAACTCTGTTGATGTATACT 57.072 32.000 13.75 0.00 0.00 2.12
4341 4980 6.915544 ATGCAACTCTGTTGATGTATACTG 57.084 37.500 13.75 0.00 0.00 2.74
4342 4981 5.793817 TGCAACTCTGTTGATGTATACTGT 58.206 37.500 13.75 0.00 0.00 3.55
4343 4982 6.930731 TGCAACTCTGTTGATGTATACTGTA 58.069 36.000 13.75 0.00 0.00 2.74
4452 5104 6.017357 GCTTTAGGCAAAGTAACAACTGTAGT 60.017 38.462 9.90 0.00 42.71 2.73
4551 5203 4.698304 GGCTTAGCTTGTGTGGTTGTATTA 59.302 41.667 3.59 0.00 0.00 0.98
4751 5403 7.672983 TTTCTTTCACATATGTTCTCACTCC 57.327 36.000 5.37 0.00 0.00 3.85
4792 5444 5.240183 GGGAGTGGAAAAGGTGTTTAAGTAC 59.760 44.000 0.00 0.00 0.00 2.73
4800 5452 8.118607 GGAAAAGGTGTTTAAGTACGCATATAC 58.881 37.037 0.00 0.00 0.00 1.47
4818 5470 9.290483 CGCATATACTATAAATCTGTGTACCAG 57.710 37.037 5.31 5.31 42.97 4.00
4819 5471 9.088512 GCATATACTATAAATCTGTGTACCAGC 57.911 37.037 6.51 0.00 41.25 4.85
4828 5480 2.700371 TCTGTGTACCAGCCATATCCAG 59.300 50.000 6.51 0.00 41.25 3.86
4873 5525 4.853924 TTTTCAGCCAATCCAAAGAGAC 57.146 40.909 0.00 0.00 0.00 3.36
4955 5607 2.419673 TGTGCTCCTATGCATTTTCGTG 59.580 45.455 3.54 0.00 45.23 4.35
4959 5611 3.009723 CTCCTATGCATTTTCGTGTGGT 58.990 45.455 3.54 0.00 0.00 4.16
5047 5701 5.060662 GGAAAACCAGTATTCCTTGAAGC 57.939 43.478 0.00 0.00 41.54 3.86
5048 5702 4.767409 GGAAAACCAGTATTCCTTGAAGCT 59.233 41.667 0.00 0.00 41.54 3.74
5052 5706 5.966742 ACCAGTATTCCTTGAAGCTTTTC 57.033 39.130 0.00 0.00 0.00 2.29
5062 5716 7.079451 TCCTTGAAGCTTTTCCTATATAGGG 57.921 40.000 25.54 12.54 43.79 3.53
5238 5898 8.193250 TCTAATGTTGTTAGGAAATACGAAGC 57.807 34.615 0.00 0.00 0.00 3.86
5239 5899 8.038944 TCTAATGTTGTTAGGAAATACGAAGCT 58.961 33.333 0.00 0.00 0.00 3.74
5240 5900 6.663944 ATGTTGTTAGGAAATACGAAGCTC 57.336 37.500 0.00 0.00 0.00 4.09
5241 5901 5.790593 TGTTGTTAGGAAATACGAAGCTCT 58.209 37.500 0.00 0.00 0.00 4.09
5242 5902 6.927416 TGTTGTTAGGAAATACGAAGCTCTA 58.073 36.000 0.00 0.00 0.00 2.43
5243 5903 7.380536 TGTTGTTAGGAAATACGAAGCTCTAA 58.619 34.615 0.00 0.00 0.00 2.10
5244 5904 8.038944 TGTTGTTAGGAAATACGAAGCTCTAAT 58.961 33.333 0.00 0.00 0.00 1.73
5245 5905 9.525409 GTTGTTAGGAAATACGAAGCTCTAATA 57.475 33.333 0.00 0.00 0.00 0.98
5246 5906 9.525409 TTGTTAGGAAATACGAAGCTCTAATAC 57.475 33.333 0.00 0.00 0.00 1.89
5247 5907 8.139989 TGTTAGGAAATACGAAGCTCTAATACC 58.860 37.037 0.00 0.00 0.00 2.73
5248 5908 6.726490 AGGAAATACGAAGCTCTAATACCA 57.274 37.500 0.00 0.00 0.00 3.25
5249 5909 7.304497 AGGAAATACGAAGCTCTAATACCAT 57.696 36.000 0.00 0.00 0.00 3.55
5250 5910 7.155328 AGGAAATACGAAGCTCTAATACCATG 58.845 38.462 0.00 0.00 0.00 3.66
5251 5911 6.929606 GGAAATACGAAGCTCTAATACCATGT 59.070 38.462 0.00 0.00 0.00 3.21
5252 5912 7.441458 GGAAATACGAAGCTCTAATACCATGTT 59.559 37.037 0.00 0.00 0.00 2.71
5253 5913 9.472361 GAAATACGAAGCTCTAATACCATGTTA 57.528 33.333 0.00 0.00 0.00 2.41
5254 5914 9.477484 AAATACGAAGCTCTAATACCATGTTAG 57.523 33.333 0.00 0.00 0.00 2.34
5255 5915 5.844004 ACGAAGCTCTAATACCATGTTAGG 58.156 41.667 0.00 0.00 31.59 2.69
5256 5916 5.597182 ACGAAGCTCTAATACCATGTTAGGA 59.403 40.000 0.00 0.00 31.59 2.94
5257 5917 6.097839 ACGAAGCTCTAATACCATGTTAGGAA 59.902 38.462 0.00 0.00 31.59 3.36
5258 5918 6.984474 CGAAGCTCTAATACCATGTTAGGAAA 59.016 38.462 0.00 0.00 31.59 3.13
5259 5919 7.657761 CGAAGCTCTAATACCATGTTAGGAAAT 59.342 37.037 0.00 0.00 31.59 2.17
5260 5920 9.998106 GAAGCTCTAATACCATGTTAGGAAATA 57.002 33.333 0.00 0.00 31.59 1.40
5262 5922 9.950496 AGCTCTAATACCATGTTAGGAAATATG 57.050 33.333 0.00 0.00 34.82 1.78
5263 5923 8.669243 GCTCTAATACCATGTTAGGAAATATGC 58.331 37.037 0.00 0.00 33.98 3.14
5264 5924 9.725019 CTCTAATACCATGTTAGGAAATATGCA 57.275 33.333 0.00 0.00 33.98 3.96
5267 5927 8.766994 AATACCATGTTAGGAAATATGCAACT 57.233 30.769 0.00 0.00 33.98 3.16
5268 5928 9.860650 AATACCATGTTAGGAAATATGCAACTA 57.139 29.630 0.00 0.00 33.98 2.24
5269 5929 9.860650 ATACCATGTTAGGAAATATGCAACTAA 57.139 29.630 0.00 0.00 33.98 2.24
5270 5930 8.766994 ACCATGTTAGGAAATATGCAACTAAT 57.233 30.769 0.00 0.00 33.98 1.73
5271 5931 9.860650 ACCATGTTAGGAAATATGCAACTAATA 57.139 29.630 0.00 0.00 33.98 0.98
5284 5944 7.693969 ATGCAACTAATATTATTGAGAGGCC 57.306 36.000 15.78 0.00 0.00 5.19
5285 5945 6.600388 TGCAACTAATATTATTGAGAGGCCA 58.400 36.000 5.01 0.00 0.00 5.36
5286 5946 7.059788 TGCAACTAATATTATTGAGAGGCCAA 58.940 34.615 5.01 0.00 0.00 4.52
5287 5947 7.559533 TGCAACTAATATTATTGAGAGGCCAAA 59.440 33.333 5.01 0.00 0.00 3.28
5288 5948 8.413229 GCAACTAATATTATTGAGAGGCCAAAA 58.587 33.333 5.01 0.00 0.00 2.44
5289 5949 9.736023 CAACTAATATTATTGAGAGGCCAAAAC 57.264 33.333 5.01 0.00 0.00 2.43
5290 5950 8.465273 ACTAATATTATTGAGAGGCCAAAACC 57.535 34.615 5.01 0.00 0.00 3.27
5291 5951 8.058847 ACTAATATTATTGAGAGGCCAAAACCA 58.941 33.333 5.01 0.00 0.00 3.67
5292 5952 6.966534 ATATTATTGAGAGGCCAAAACCAG 57.033 37.500 5.01 0.00 0.00 4.00
5293 5953 1.260544 ATTGAGAGGCCAAAACCAGC 58.739 50.000 5.01 0.00 0.00 4.85
5294 5954 0.106268 TTGAGAGGCCAAAACCAGCA 60.106 50.000 5.01 0.00 0.00 4.41
5295 5955 0.112995 TGAGAGGCCAAAACCAGCAT 59.887 50.000 5.01 0.00 0.00 3.79
5296 5956 0.529378 GAGAGGCCAAAACCAGCATG 59.471 55.000 5.01 0.00 0.00 4.06
5297 5957 0.178953 AGAGGCCAAAACCAGCATGT 60.179 50.000 5.01 0.00 0.00 3.21
5298 5958 1.075374 AGAGGCCAAAACCAGCATGTA 59.925 47.619 5.01 0.00 0.00 2.29
5299 5959 2.102578 GAGGCCAAAACCAGCATGTAT 58.897 47.619 5.01 0.00 0.00 2.29
5300 5960 3.053693 AGAGGCCAAAACCAGCATGTATA 60.054 43.478 5.01 0.00 0.00 1.47
5301 5961 3.023832 AGGCCAAAACCAGCATGTATAC 58.976 45.455 5.01 0.00 0.00 1.47
5302 5962 2.757868 GGCCAAAACCAGCATGTATACA 59.242 45.455 8.27 8.27 0.00 2.29
5303 5963 3.428862 GGCCAAAACCAGCATGTATACAC 60.429 47.826 7.96 0.00 0.00 2.90
5304 5964 3.192422 GCCAAAACCAGCATGTATACACA 59.808 43.478 7.96 0.00 39.52 3.72
5305 5965 4.142182 GCCAAAACCAGCATGTATACACAT 60.142 41.667 7.96 0.00 46.58 3.21
5317 5977 4.698780 ATGTATACACATGCATGAGGATGC 59.301 41.667 32.75 27.75 46.38 3.91
5318 5978 6.321815 ATGTATACACATGCATGAGGATGCC 61.322 44.000 32.75 20.12 46.38 4.40
5319 5979 8.660838 ATGTATACACATGCATGAGGATGCCA 62.661 42.308 32.75 24.28 46.38 4.92
5328 5988 3.992643 CATGAGGATGCCAAGAGACTAG 58.007 50.000 0.00 0.00 0.00 2.57
5329 5989 3.388552 TGAGGATGCCAAGAGACTAGA 57.611 47.619 0.00 0.00 0.00 2.43
5330 5990 3.295093 TGAGGATGCCAAGAGACTAGAG 58.705 50.000 0.00 0.00 0.00 2.43
5331 5991 3.295973 GAGGATGCCAAGAGACTAGAGT 58.704 50.000 0.00 0.00 0.00 3.24
5332 5992 3.030291 AGGATGCCAAGAGACTAGAGTG 58.970 50.000 0.00 0.00 0.00 3.51
5333 5993 2.482839 GGATGCCAAGAGACTAGAGTGC 60.483 54.545 0.00 0.00 0.00 4.40
5334 5994 1.632589 TGCCAAGAGACTAGAGTGCA 58.367 50.000 0.00 0.00 0.00 4.57
5335 5995 1.547820 TGCCAAGAGACTAGAGTGCAG 59.452 52.381 0.00 0.00 0.00 4.41
5336 5996 1.821753 GCCAAGAGACTAGAGTGCAGA 59.178 52.381 0.00 0.00 0.00 4.26
5337 5997 2.232452 GCCAAGAGACTAGAGTGCAGAA 59.768 50.000 0.00 0.00 0.00 3.02
5338 5998 3.675775 GCCAAGAGACTAGAGTGCAGAAG 60.676 52.174 0.00 0.00 0.00 2.85
5339 5999 3.119173 CCAAGAGACTAGAGTGCAGAAGG 60.119 52.174 0.00 0.00 0.00 3.46
5340 6000 3.449746 AGAGACTAGAGTGCAGAAGGT 57.550 47.619 0.00 0.00 0.00 3.50
5341 6001 3.352648 AGAGACTAGAGTGCAGAAGGTC 58.647 50.000 0.00 0.00 0.00 3.85
5342 6002 3.085533 GAGACTAGAGTGCAGAAGGTCA 58.914 50.000 0.00 0.00 0.00 4.02
5343 6003 3.501349 AGACTAGAGTGCAGAAGGTCAA 58.499 45.455 0.00 0.00 0.00 3.18
5344 6004 3.898123 AGACTAGAGTGCAGAAGGTCAAA 59.102 43.478 0.00 0.00 0.00 2.69
5345 6005 4.345257 AGACTAGAGTGCAGAAGGTCAAAA 59.655 41.667 0.00 0.00 0.00 2.44
5346 6006 4.636249 ACTAGAGTGCAGAAGGTCAAAAG 58.364 43.478 0.00 0.00 0.00 2.27
5347 6007 3.845781 AGAGTGCAGAAGGTCAAAAGA 57.154 42.857 0.00 0.00 0.00 2.52
5348 6008 3.471680 AGAGTGCAGAAGGTCAAAAGAC 58.528 45.455 0.00 0.00 0.00 3.01
5349 6009 3.118261 AGAGTGCAGAAGGTCAAAAGACA 60.118 43.478 0.00 0.00 0.00 3.41
5350 6010 3.817647 GAGTGCAGAAGGTCAAAAGACAT 59.182 43.478 0.00 0.00 0.00 3.06
5351 6011 3.817647 AGTGCAGAAGGTCAAAAGACATC 59.182 43.478 0.00 0.00 0.00 3.06
5352 6012 3.565482 GTGCAGAAGGTCAAAAGACATCA 59.435 43.478 0.00 0.00 0.00 3.07
5353 6013 3.565482 TGCAGAAGGTCAAAAGACATCAC 59.435 43.478 0.00 0.00 0.00 3.06
5354 6014 3.817647 GCAGAAGGTCAAAAGACATCACT 59.182 43.478 0.00 0.00 0.00 3.41
5355 6015 4.997395 GCAGAAGGTCAAAAGACATCACTA 59.003 41.667 0.00 0.00 0.00 2.74
5356 6016 5.470098 GCAGAAGGTCAAAAGACATCACTAA 59.530 40.000 0.00 0.00 0.00 2.24
5357 6017 6.150140 GCAGAAGGTCAAAAGACATCACTAAT 59.850 38.462 0.00 0.00 0.00 1.73
5358 6018 7.334421 GCAGAAGGTCAAAAGACATCACTAATA 59.666 37.037 0.00 0.00 0.00 0.98
5359 6019 9.388506 CAGAAGGTCAAAAGACATCACTAATAT 57.611 33.333 0.00 0.00 0.00 1.28
5418 6078 8.887036 ATTAGGTGAAAATTTGAAAGGAACAC 57.113 30.769 0.00 0.00 0.00 3.32
5442 6102 8.391106 CACTGTTATTTGTGTAGGATTAAGCTC 58.609 37.037 0.00 0.00 0.00 4.09
5531 6194 5.641209 ACTGCTAAACTACTTGAATGCTCTG 59.359 40.000 0.00 0.00 0.00 3.35
5584 6247 5.588648 AGCATGGTATATTGTGTTGGTGTAC 59.411 40.000 0.00 0.00 0.00 2.90
5647 6310 3.279434 GTCTTCTGTCACCAGGTTTTGT 58.721 45.455 0.00 0.00 39.31 2.83
5670 6333 4.164843 ACCCTGAGAGCTTTAACAAACA 57.835 40.909 0.00 0.00 0.00 2.83
5810 6473 4.697514 TGCTGAAGTAGATAGATGCCAAC 58.302 43.478 0.00 0.00 0.00 3.77
6017 6680 5.010922 CCCTTGAGATTTTGTTGATTGTCCA 59.989 40.000 0.00 0.00 0.00 4.02
6018 6681 6.154445 CCTTGAGATTTTGTTGATTGTCCAG 58.846 40.000 0.00 0.00 0.00 3.86
6020 6683 6.713762 TGAGATTTTGTTGATTGTCCAGTT 57.286 33.333 0.00 0.00 0.00 3.16
6022 6685 6.089249 AGATTTTGTTGATTGTCCAGTTCC 57.911 37.500 0.00 0.00 0.00 3.62
6024 6687 5.867903 TTTTGTTGATTGTCCAGTTCCAT 57.132 34.783 0.00 0.00 0.00 3.41
6025 6688 4.852134 TTGTTGATTGTCCAGTTCCATG 57.148 40.909 0.00 0.00 0.00 3.66
6026 6689 3.156293 TGTTGATTGTCCAGTTCCATGG 58.844 45.455 4.97 4.97 42.11 3.66
6159 6824 3.759086 TGTTTGTGTTTGTAGACTTGGCA 59.241 39.130 0.00 0.00 0.00 4.92
6221 6886 6.194967 TCTGTGATCTCTTTACATGGTAGGA 58.805 40.000 0.00 0.00 0.00 2.94
6230 6895 4.487282 TTACATGGTAGGAGCCTAGGAT 57.513 45.455 14.75 5.88 0.00 3.24
6402 10537 2.862597 TGGGGCCAATTAGGGTTCTATT 59.137 45.455 4.39 0.00 38.09 1.73
6414 10549 5.441718 AGGGTTCTATTTCAAGCATCTCA 57.558 39.130 0.00 0.00 0.00 3.27
6415 10550 5.435291 AGGGTTCTATTTCAAGCATCTCAG 58.565 41.667 0.00 0.00 0.00 3.35
6418 10553 5.007528 GGTTCTATTTCAAGCATCTCAGAGC 59.992 44.000 0.00 0.00 0.00 4.09
6421 10556 0.248565 TTCAAGCATCTCAGAGCGCT 59.751 50.000 11.27 11.27 35.90 5.92
6427 10564 1.005557 GCATCTCAGAGCGCTTTTACG 60.006 52.381 13.26 0.00 0.00 3.18
6478 10615 3.952967 ACTAGTCGATTTACAGAGTCCCC 59.047 47.826 0.00 0.00 0.00 4.81
6513 10890 4.202161 GGTGTACTGGTGTCTATCCATCTG 60.202 50.000 0.00 0.00 34.26 2.90
6518 10895 3.703556 CTGGTGTCTATCCATCTGTGACT 59.296 47.826 0.00 0.00 34.26 3.41
6638 11028 4.612264 ATTGATTGCCTTTGACTTGCTT 57.388 36.364 0.00 0.00 0.00 3.91
6654 11044 5.245531 ACTTGCTTGGATCGAAACTTCATA 58.754 37.500 0.00 0.00 0.00 2.15
6681 11071 9.107177 TCAAACAAAGTGCAATGAATTTATTGT 57.893 25.926 20.34 2.56 39.62 2.71
6791 11883 9.546909 CACAATTCAGCAAGTACTGTATTAAAG 57.453 33.333 0.00 0.00 36.04 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.479724 TGAGGTTAATGTTTGCATTGATCCA 59.520 36.000 3.39 0.00 44.32 3.41
27 28 6.382282 AGAGTTGTGGAGACTCATATTCATGA 59.618 38.462 4.53 0.00 44.65 3.07
128 186 6.817765 AATACAAAGCCGAAGATTCTCAAA 57.182 33.333 0.00 0.00 0.00 2.69
140 198 6.307800 CACAAATTCCAGTAAATACAAAGCCG 59.692 38.462 0.00 0.00 0.00 5.52
142 200 7.375053 TCCACAAATTCCAGTAAATACAAAGC 58.625 34.615 0.00 0.00 0.00 3.51
153 211 1.895131 GGCACATCCACAAATTCCAGT 59.105 47.619 0.00 0.00 34.01 4.00
162 220 1.985614 CCTCTCAGGCACATCCACA 59.014 57.895 0.00 0.00 37.29 4.17
178 236 0.895530 TTGATCTCTTTCGTCGGCCT 59.104 50.000 0.00 0.00 0.00 5.19
185 243 4.083643 ACACTGCAACATTGATCTCTTTCG 60.084 41.667 0.00 0.00 0.00 3.46
189 247 4.011966 TCACACTGCAACATTGATCTCT 57.988 40.909 0.00 0.00 0.00 3.10
196 254 7.445402 AGAAGTTAGTATTCACACTGCAACATT 59.555 33.333 0.00 0.00 0.00 2.71
217 275 9.301153 GTTTCACATCATTACAAAACAAGAAGT 57.699 29.630 0.00 0.00 0.00 3.01
258 316 2.921121 GCACGTTCTGATGACGTTGATA 59.079 45.455 4.89 0.00 38.07 2.15
265 323 1.354040 CTCCTGCACGTTCTGATGAC 58.646 55.000 0.00 0.00 0.00 3.06
266 324 0.247460 CCTCCTGCACGTTCTGATGA 59.753 55.000 0.00 0.00 0.00 2.92
275 333 1.148157 CGTTATCAGCCTCCTGCACG 61.148 60.000 0.00 0.00 44.83 5.34
284 342 1.202545 GGGAGGTCTTCGTTATCAGCC 60.203 57.143 0.00 0.00 0.00 4.85
285 343 1.202545 GGGGAGGTCTTCGTTATCAGC 60.203 57.143 0.00 0.00 0.00 4.26
286 344 2.108168 TGGGGAGGTCTTCGTTATCAG 58.892 52.381 0.00 0.00 0.00 2.90
291 349 1.071857 GTTCTTGGGGAGGTCTTCGTT 59.928 52.381 0.00 0.00 0.00 3.85
353 411 6.204108 ACGGAAGGCTTATATTAATCAAACGG 59.796 38.462 0.00 0.00 0.00 4.44
499 837 5.545723 AGAGATTGGACTGAAGGAGAAAGAA 59.454 40.000 0.00 0.00 0.00 2.52
504 842 3.766591 GTGAGAGATTGGACTGAAGGAGA 59.233 47.826 0.00 0.00 0.00 3.71
509 847 5.127845 GGACTATGTGAGAGATTGGACTGAA 59.872 44.000 0.00 0.00 0.00 3.02
719 1073 2.184020 TTGCAGACCGGGTGGAGATG 62.184 60.000 3.30 0.00 39.21 2.90
741 1095 3.165071 ACCTCAAAACCTAATGGCCAAG 58.835 45.455 10.96 2.68 36.63 3.61
965 1319 8.637986 AGTGTTACTGCAAATGGAAAGAAATAA 58.362 29.630 0.00 0.00 0.00 1.40
1278 1632 9.241317 GATTTCAAGGCATTGACAACATAATAG 57.759 33.333 14.30 0.00 45.07 1.73
1424 1778 4.607293 AGTAGAAGCAGACACAATGTGA 57.393 40.909 21.34 0.00 36.96 3.58
1726 2080 8.956533 AAACAGTGTTTAAGCAAACCATAATT 57.043 26.923 19.59 0.00 42.88 1.40
1803 2158 4.401022 TCTTGAGGCACTTGATCATGTTT 58.599 39.130 11.33 1.41 41.55 2.83
2265 2876 2.630158 CTGAGGAAGCTTGTCCATCAG 58.370 52.381 2.10 8.85 40.48 2.90
2280 2891 3.316868 GGATTCTTCGTAGACTCCTGAGG 59.683 52.174 17.71 0.00 43.47 3.86
2374 2991 4.788840 GCATTGCTCATCCAAGAAGAATCG 60.789 45.833 0.16 0.00 0.00 3.34
2384 3001 1.179152 CAACCTGCATTGCTCATCCA 58.821 50.000 10.49 0.00 0.00 3.41
2527 3152 6.630203 TGGGAAAGAAAGGCTATGTACTTA 57.370 37.500 0.00 0.00 0.00 2.24
2528 3153 5.514500 TGGGAAAGAAAGGCTATGTACTT 57.486 39.130 0.00 0.00 0.00 2.24
2537 3167 2.247358 TGGTTGATGGGAAAGAAAGGC 58.753 47.619 0.00 0.00 0.00 4.35
2569 3199 7.062255 GTGAAGCATAAAAGTAATCCAAAGTGC 59.938 37.037 0.00 0.00 0.00 4.40
2977 3607 6.929606 TCAAAGTCTAGAAACTTCAGTTAGGC 59.070 38.462 0.00 0.00 38.52 3.93
3032 3666 4.242475 GTGTTGATGAGTCGTATGTCCAA 58.758 43.478 0.00 0.00 0.00 3.53
3098 3732 1.891150 CTGCATTCCCAAGAAAGTGCT 59.109 47.619 0.00 0.00 38.35 4.40
3457 4092 3.614659 CGTCTCGATGCAGCTGCG 61.615 66.667 32.11 19.09 45.83 5.18
3640 4275 3.784701 AGTTGTAGATAGGTCGTGCTG 57.215 47.619 0.00 0.00 0.00 4.41
3829 4465 7.906199 TCAAGATAAGGGGTTGAAAGAAAAA 57.094 32.000 0.00 0.00 0.00 1.94
3860 4496 3.097614 GGTTACTGGCTAGAGACTTCCA 58.902 50.000 3.17 0.00 0.00 3.53
4205 4844 0.536687 AATCATGAGCAGGCCATCCG 60.537 55.000 5.01 0.00 37.47 4.18
4217 4856 1.487976 GAGCTGACAGGGGAATCATGA 59.512 52.381 4.26 0.00 0.00 3.07
4818 5470 2.338577 ACTGCAAGACTGGATATGGC 57.661 50.000 0.00 0.00 37.43 4.40
4819 5471 4.753610 CACATACTGCAAGACTGGATATGG 59.246 45.833 0.00 0.00 37.43 2.74
4855 5507 4.908601 TTAGTCTCTTTGGATTGGCTGA 57.091 40.909 0.00 0.00 0.00 4.26
4873 5525 8.087750 TGCCTGAAACCAAATAGTTCAAATTAG 58.912 33.333 0.00 0.00 0.00 1.73
4976 5628 2.352225 GGTGTGCAAAGTGTGTGTGAAA 60.352 45.455 0.00 0.00 0.00 2.69
5037 5691 7.128883 ACCCTATATAGGAAAAGCTTCAAGGAA 59.871 37.037 27.58 0.00 46.63 3.36
5043 5697 7.068686 ACAGACCCTATATAGGAAAAGCTTC 57.931 40.000 27.58 12.38 46.63 3.86
5044 5698 8.011290 TCTACAGACCCTATATAGGAAAAGCTT 58.989 37.037 27.58 9.64 46.63 3.74
5046 5700 7.232941 TGTCTACAGACCCTATATAGGAAAAGC 59.767 40.741 27.58 12.56 43.06 3.51
5047 5701 8.707796 TGTCTACAGACCCTATATAGGAAAAG 57.292 38.462 27.58 16.88 43.06 2.27
5048 5702 8.287350 ACTGTCTACAGACCCTATATAGGAAAA 58.713 37.037 27.58 7.88 45.18 2.29
5052 5706 8.480133 AAAACTGTCTACAGACCCTATATAGG 57.520 38.462 20.43 20.43 46.59 2.57
5062 5716 7.976734 AGTATGCATCTAAAACTGTCTACAGAC 59.023 37.037 16.74 2.70 46.59 3.51
5221 5881 8.139989 GGTATTAGAGCTTCGTATTTCCTAACA 58.860 37.037 0.00 0.00 0.00 2.41
5222 5882 8.139989 TGGTATTAGAGCTTCGTATTTCCTAAC 58.860 37.037 0.00 0.00 0.00 2.34
5224 5884 7.828508 TGGTATTAGAGCTTCGTATTTCCTA 57.171 36.000 0.00 0.00 0.00 2.94
5225 5885 6.726490 TGGTATTAGAGCTTCGTATTTCCT 57.274 37.500 0.00 0.00 0.00 3.36
5226 5886 6.929606 ACATGGTATTAGAGCTTCGTATTTCC 59.070 38.462 0.00 0.00 0.00 3.13
5227 5887 7.948278 ACATGGTATTAGAGCTTCGTATTTC 57.052 36.000 0.00 0.00 0.00 2.17
5228 5888 9.477484 CTAACATGGTATTAGAGCTTCGTATTT 57.523 33.333 0.00 0.00 32.31 1.40
5229 5889 8.088981 CCTAACATGGTATTAGAGCTTCGTATT 58.911 37.037 0.00 0.00 32.31 1.89
5230 5890 7.450634 TCCTAACATGGTATTAGAGCTTCGTAT 59.549 37.037 0.00 0.00 32.31 3.06
5231 5891 6.774170 TCCTAACATGGTATTAGAGCTTCGTA 59.226 38.462 0.00 0.00 32.31 3.43
5232 5892 5.597182 TCCTAACATGGTATTAGAGCTTCGT 59.403 40.000 0.00 0.00 32.31 3.85
5233 5893 6.085555 TCCTAACATGGTATTAGAGCTTCG 57.914 41.667 0.00 0.00 32.31 3.79
5234 5894 8.910351 ATTTCCTAACATGGTATTAGAGCTTC 57.090 34.615 0.00 0.00 32.31 3.86
5236 5896 9.950496 CATATTTCCTAACATGGTATTAGAGCT 57.050 33.333 0.00 0.00 32.31 4.09
5237 5897 8.669243 GCATATTTCCTAACATGGTATTAGAGC 58.331 37.037 0.00 0.00 32.31 4.09
5238 5898 9.725019 TGCATATTTCCTAACATGGTATTAGAG 57.275 33.333 0.00 0.00 32.31 2.43
5241 5901 9.860650 AGTTGCATATTTCCTAACATGGTATTA 57.139 29.630 0.00 0.00 0.00 0.98
5242 5902 8.766994 AGTTGCATATTTCCTAACATGGTATT 57.233 30.769 0.00 0.00 0.00 1.89
5243 5903 9.860650 TTAGTTGCATATTTCCTAACATGGTAT 57.139 29.630 0.00 0.00 0.00 2.73
5244 5904 9.860650 ATTAGTTGCATATTTCCTAACATGGTA 57.139 29.630 0.00 0.00 0.00 3.25
5245 5905 8.766994 ATTAGTTGCATATTTCCTAACATGGT 57.233 30.769 0.00 0.00 0.00 3.55
5258 5918 9.401058 GGCCTCTCAATAATATTAGTTGCATAT 57.599 33.333 0.00 0.00 0.00 1.78
5259 5919 8.382405 TGGCCTCTCAATAATATTAGTTGCATA 58.618 33.333 3.32 0.00 0.00 3.14
5260 5920 7.233632 TGGCCTCTCAATAATATTAGTTGCAT 58.766 34.615 3.32 0.00 0.00 3.96
5261 5921 6.600388 TGGCCTCTCAATAATATTAGTTGCA 58.400 36.000 3.32 0.00 0.00 4.08
5262 5922 7.510549 TTGGCCTCTCAATAATATTAGTTGC 57.489 36.000 3.32 0.00 0.00 4.17
5263 5923 9.736023 GTTTTGGCCTCTCAATAATATTAGTTG 57.264 33.333 3.32 6.38 0.00 3.16
5264 5924 8.914011 GGTTTTGGCCTCTCAATAATATTAGTT 58.086 33.333 3.32 0.00 0.00 2.24
5265 5925 8.058847 TGGTTTTGGCCTCTCAATAATATTAGT 58.941 33.333 3.32 0.00 0.00 2.24
5266 5926 8.463930 TGGTTTTGGCCTCTCAATAATATTAG 57.536 34.615 3.32 0.00 0.00 1.73
5267 5927 7.014230 GCTGGTTTTGGCCTCTCAATAATATTA 59.986 37.037 3.32 0.00 0.00 0.98
5268 5928 6.183360 GCTGGTTTTGGCCTCTCAATAATATT 60.183 38.462 3.32 0.00 0.00 1.28
5269 5929 5.302823 GCTGGTTTTGGCCTCTCAATAATAT 59.697 40.000 3.32 0.00 0.00 1.28
5270 5930 4.644685 GCTGGTTTTGGCCTCTCAATAATA 59.355 41.667 3.32 0.00 0.00 0.98
5271 5931 3.448660 GCTGGTTTTGGCCTCTCAATAAT 59.551 43.478 3.32 0.00 0.00 1.28
5272 5932 2.825532 GCTGGTTTTGGCCTCTCAATAA 59.174 45.455 3.32 0.00 0.00 1.40
5273 5933 2.224992 TGCTGGTTTTGGCCTCTCAATA 60.225 45.455 3.32 0.00 0.00 1.90
5274 5934 1.260544 GCTGGTTTTGGCCTCTCAAT 58.739 50.000 3.32 0.00 0.00 2.57
5275 5935 0.106268 TGCTGGTTTTGGCCTCTCAA 60.106 50.000 3.32 0.00 0.00 3.02
5276 5936 0.112995 ATGCTGGTTTTGGCCTCTCA 59.887 50.000 3.32 0.00 0.00 3.27
5277 5937 0.529378 CATGCTGGTTTTGGCCTCTC 59.471 55.000 3.32 0.00 0.00 3.20
5278 5938 0.178953 ACATGCTGGTTTTGGCCTCT 60.179 50.000 3.32 0.00 0.00 3.69
5279 5939 1.544724 TACATGCTGGTTTTGGCCTC 58.455 50.000 3.32 0.00 0.00 4.70
5280 5940 2.236489 ATACATGCTGGTTTTGGCCT 57.764 45.000 3.32 0.00 0.00 5.19
5281 5941 2.757868 TGTATACATGCTGGTTTTGGCC 59.242 45.455 0.08 0.00 0.00 5.36
5282 5942 3.192422 TGTGTATACATGCTGGTTTTGGC 59.808 43.478 9.18 0.00 0.00 4.52
5283 5943 5.581126 ATGTGTATACATGCTGGTTTTGG 57.419 39.130 9.18 0.00 45.54 3.28
5307 5967 3.640498 TCTAGTCTCTTGGCATCCTCATG 59.360 47.826 0.00 0.00 0.00 3.07
5308 5968 3.896888 CTCTAGTCTCTTGGCATCCTCAT 59.103 47.826 0.00 0.00 0.00 2.90
5309 5969 3.295093 CTCTAGTCTCTTGGCATCCTCA 58.705 50.000 0.00 0.00 0.00 3.86
5310 5970 3.068024 CACTCTAGTCTCTTGGCATCCTC 59.932 52.174 0.00 0.00 0.00 3.71
5311 5971 3.030291 CACTCTAGTCTCTTGGCATCCT 58.970 50.000 0.00 0.00 0.00 3.24
5312 5972 2.482839 GCACTCTAGTCTCTTGGCATCC 60.483 54.545 0.00 0.00 0.00 3.51
5313 5973 2.167281 TGCACTCTAGTCTCTTGGCATC 59.833 50.000 0.00 0.00 0.00 3.91
5314 5974 2.168106 CTGCACTCTAGTCTCTTGGCAT 59.832 50.000 0.00 0.00 0.00 4.40
5315 5975 1.547820 CTGCACTCTAGTCTCTTGGCA 59.452 52.381 0.00 0.00 0.00 4.92
5316 5976 1.821753 TCTGCACTCTAGTCTCTTGGC 59.178 52.381 0.00 0.00 0.00 4.52
5317 5977 3.119173 CCTTCTGCACTCTAGTCTCTTGG 60.119 52.174 0.00 0.00 0.00 3.61
5318 5978 3.509575 ACCTTCTGCACTCTAGTCTCTTG 59.490 47.826 0.00 0.00 0.00 3.02
5319 5979 3.761752 GACCTTCTGCACTCTAGTCTCTT 59.238 47.826 0.00 0.00 0.00 2.85
5320 5980 3.245087 TGACCTTCTGCACTCTAGTCTCT 60.245 47.826 0.00 0.00 0.00 3.10
5321 5981 3.085533 TGACCTTCTGCACTCTAGTCTC 58.914 50.000 0.00 0.00 0.00 3.36
5322 5982 3.162147 TGACCTTCTGCACTCTAGTCT 57.838 47.619 0.00 0.00 0.00 3.24
5323 5983 3.944055 TTGACCTTCTGCACTCTAGTC 57.056 47.619 0.00 0.00 0.00 2.59
5324 5984 4.345257 TCTTTTGACCTTCTGCACTCTAGT 59.655 41.667 0.00 0.00 0.00 2.57
5325 5985 4.688413 GTCTTTTGACCTTCTGCACTCTAG 59.312 45.833 0.00 0.00 43.37 2.43
5326 5986 4.632153 GTCTTTTGACCTTCTGCACTCTA 58.368 43.478 0.00 0.00 43.37 2.43
5327 5987 3.471680 GTCTTTTGACCTTCTGCACTCT 58.528 45.455 0.00 0.00 43.37 3.24
5328 5988 3.887339 GTCTTTTGACCTTCTGCACTC 57.113 47.619 0.00 0.00 43.37 3.51
5418 6078 7.491372 TCGAGCTTAATCCTACACAAATAACAG 59.509 37.037 0.00 0.00 0.00 3.16
5442 6102 2.358267 ACTAGCCGGACTGTCTAAATCG 59.642 50.000 5.05 2.23 0.00 3.34
5531 6194 8.303876 TCTGGTAAAATAAAAGTTCAATCAGGC 58.696 33.333 0.00 0.00 0.00 4.85
5584 6247 2.540361 GGAATGCTTCGCAGTTGCATAG 60.540 50.000 4.84 1.97 43.65 2.23
5647 6310 5.529800 GTGTTTGTTAAAGCTCTCAGGGTTA 59.470 40.000 0.00 0.00 0.00 2.85
5670 6333 1.372582 CAACGCTACCTCATGCATGT 58.627 50.000 25.43 9.95 0.00 3.21
5717 6380 1.071814 CCCGAACCAAACCCGAAGA 59.928 57.895 0.00 0.00 0.00 2.87
5719 6382 2.595172 GCCCGAACCAAACCCGAA 60.595 61.111 0.00 0.00 0.00 4.30
5810 6473 2.968574 AGGGATATAGTGGACTGCTGTG 59.031 50.000 0.00 0.00 0.00 3.66
6017 6680 0.035630 GAGCAGCACTCCATGGAACT 60.036 55.000 17.00 10.70 39.75 3.01
6018 6681 2.475666 GAGCAGCACTCCATGGAAC 58.524 57.895 17.00 8.41 39.75 3.62
6026 6689 2.125753 CTCCACGGAGCAGCACTC 60.126 66.667 0.00 0.00 45.45 3.51
6027 6690 2.919856 ACTCCACGGAGCAGCACT 60.920 61.111 13.16 0.00 45.54 4.40
6118 6783 1.269448 CATGACCCAGTTTTCCAACGG 59.731 52.381 0.00 0.00 38.03 4.44
6159 6824 2.858745 ACAACATAGTTTCACCGGCTT 58.141 42.857 0.00 0.00 0.00 4.35
6221 6886 2.703007 CCTGCTGTAAAGATCCTAGGCT 59.297 50.000 2.96 0.00 0.00 4.58
6230 6895 2.708861 TGGGAGAAACCTGCTGTAAAGA 59.291 45.455 0.00 0.00 38.98 2.52
6320 10455 5.404366 CAGCAACACATCATTTTTCCTTCAG 59.596 40.000 0.00 0.00 0.00 3.02
6358 10493 6.828273 CCAAACCATCAACTGATAGGACAATA 59.172 38.462 12.35 0.00 32.63 1.90
6402 10537 0.248565 AGCGCTCTGAGATGCTTGAA 59.751 50.000 2.64 0.00 32.89 2.69
6414 10549 4.689345 ACAAGAATTACGTAAAAGCGCTCT 59.311 37.500 12.06 3.27 34.88 4.09
6415 10550 4.781528 CACAAGAATTACGTAAAAGCGCTC 59.218 41.667 12.06 0.00 34.88 5.03
6418 10553 7.007099 GGATTTCACAAGAATTACGTAAAAGCG 59.993 37.037 12.81 3.12 32.89 4.68
6463 10600 3.889520 AACTCGGGGACTCTGTAAATC 57.110 47.619 0.00 0.00 0.00 2.17
6470 10607 1.122019 ACTGCAAACTCGGGGACTCT 61.122 55.000 0.00 0.00 0.00 3.24
6478 10615 1.865865 AGTACACCACTGCAAACTCG 58.134 50.000 0.00 0.00 35.62 4.18
6638 11028 7.680442 TTGTTTGATATGAAGTTTCGATCCA 57.320 32.000 0.00 0.00 0.00 3.41
6677 11067 3.307199 CGTTGGTTGACCTACCCTACAAT 60.307 47.826 8.76 0.00 38.30 2.71
6681 11071 1.895131 GTCGTTGGTTGACCTACCCTA 59.105 52.381 8.76 0.00 38.30 3.53
6797 11889 0.668535 GCTCGCCAAACACTTCCTTT 59.331 50.000 0.00 0.00 0.00 3.11
6798 11890 0.465460 TGCTCGCCAAACACTTCCTT 60.465 50.000 0.00 0.00 0.00 3.36
6799 11891 0.465460 TTGCTCGCCAAACACTTCCT 60.465 50.000 0.00 0.00 0.00 3.36
6800 11892 0.383949 TTTGCTCGCCAAACACTTCC 59.616 50.000 0.00 0.00 38.46 3.46
6801 11893 2.422276 ATTTGCTCGCCAAACACTTC 57.578 45.000 3.69 0.00 45.52 3.01


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

AutoCloner maintained by Alex Coulton.