Multiple sequence alignment - TraesCS5D01G420200

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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 TraesCS5D01G420200 chr5D 100.000 3092 0 0 1 3092 480824534 480821443 0 5710
1 TraesCS5D01G420200 chr5D 98.470 2810 36 2 284 3092 244414324 244411521 0 4944
2 TraesCS5D01G420200 chr5D 97.800 2818 54 6 281 3092 565815802 565818617 0 4854
3 TraesCS5D01G420200 chr5D 97.729 2818 56 6 281 3092 260689962 260687147 0 4843
4 TraesCS5D01G420200 chr6D 98.614 2813 38 1 281 3092 472510963 472513775 0 4977
5 TraesCS5D01G420200 chr6D 98.084 2818 48 2 276 3092 367564542 367561730 0 4900
6 TraesCS5D01G420200 chr6D 97.658 2818 58 6 281 3092 51499464 51502279 0 4831
7 TraesCS5D01G420200 chr3D 98.401 2815 43 2 279 3092 574856807 574853994 0 4948
8 TraesCS5D01G420200 chr4D 98.191 2820 42 4 281 3092 398986367 398983549 0 4916
9 TraesCS5D01G420200 chr7D 97.906 2818 52 5 281 3092 245402431 245399615 0 4870


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 TraesCS5D01G420200 chr5D 480821443 480824534 3091 True 5710 5710 100.000 1 3092 1 chr5D.!!$R3 3091
1 TraesCS5D01G420200 chr5D 244411521 244414324 2803 True 4944 4944 98.470 284 3092 1 chr5D.!!$R1 2808
2 TraesCS5D01G420200 chr5D 565815802 565818617 2815 False 4854 4854 97.800 281 3092 1 chr5D.!!$F1 2811
3 TraesCS5D01G420200 chr5D 260687147 260689962 2815 True 4843 4843 97.729 281 3092 1 chr5D.!!$R2 2811
4 TraesCS5D01G420200 chr6D 472510963 472513775 2812 False 4977 4977 98.614 281 3092 1 chr6D.!!$F2 2811
5 TraesCS5D01G420200 chr6D 367561730 367564542 2812 True 4900 4900 98.084 276 3092 1 chr6D.!!$R1 2816
6 TraesCS5D01G420200 chr6D 51499464 51502279 2815 False 4831 4831 97.658 281 3092 1 chr6D.!!$F1 2811
7 TraesCS5D01G420200 chr3D 574853994 574856807 2813 True 4948 4948 98.401 279 3092 1 chr3D.!!$R1 2813
8 TraesCS5D01G420200 chr4D 398983549 398986367 2818 True 4916 4916 98.191 281 3092 1 chr4D.!!$R1 2811
9 TraesCS5D01G420200 chr7D 245399615 245402431 2816 True 4870 4870 97.906 281 3092 1 chr7D.!!$R1 2811

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
175 176 0.031449 AACGGCATGAAAAACGGTGG 59.969 50.0 0.0 0.0 0.00 4.61 F
277 278 0.249073 GAGTCGATCCCCACATCGTG 60.249 60.0 3.0 0.0 44.99 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 1994 5.619220 CTTGGCCTTCTCTATCTTAAGCAT 58.381 41.667 3.32 0.00 0.0 3.79 R
2734 2749 1.685517 TGATGATCTTCCCTGAGCTCG 59.314 52.381 9.64 3.88 0.0 5.03 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
24 25 3.824806 CGATCGACGCGGTATTCC 58.175 61.111 10.26 0.00 34.51 3.01
25 26 1.009335 CGATCGACGCGGTATTCCA 60.009 57.895 10.26 0.00 34.51 3.53
26 27 0.997226 CGATCGACGCGGTATTCCAG 60.997 60.000 10.26 0.00 34.51 3.86
27 28 0.663568 GATCGACGCGGTATTCCAGG 60.664 60.000 12.47 0.00 0.00 4.45
28 29 2.083835 ATCGACGCGGTATTCCAGGG 62.084 60.000 12.47 0.00 0.00 4.45
29 30 2.588034 GACGCGGTATTCCAGGGC 60.588 66.667 12.47 0.00 0.00 5.19
32 33 4.547367 GCGGTATTCCAGGGCGCT 62.547 66.667 7.64 0.00 0.00 5.92
33 34 2.280186 CGGTATTCCAGGGCGCTC 60.280 66.667 7.64 1.48 0.00 5.03
34 35 2.908015 GGTATTCCAGGGCGCTCA 59.092 61.111 11.40 0.00 0.00 4.26
35 36 1.451936 GGTATTCCAGGGCGCTCAT 59.548 57.895 11.40 0.00 0.00 2.90
36 37 0.886490 GGTATTCCAGGGCGCTCATG 60.886 60.000 11.40 6.82 0.00 3.07
38 39 2.055689 TATTCCAGGGCGCTCATGGG 62.056 60.000 23.18 15.93 46.59 4.00
40 41 4.559063 CCAGGGCGCTCATGGGAG 62.559 72.222 11.40 0.00 43.17 4.30
41 42 3.473647 CAGGGCGCTCATGGGAGA 61.474 66.667 11.40 0.00 44.26 3.71
42 43 2.447379 AGGGCGCTCATGGGAGAT 60.447 61.111 11.40 0.00 44.26 2.75
43 44 1.152247 AGGGCGCTCATGGGAGATA 60.152 57.895 11.40 0.00 44.26 1.98
44 45 1.190833 AGGGCGCTCATGGGAGATAG 61.191 60.000 11.40 0.00 44.26 2.08
45 46 1.476007 GGGCGCTCATGGGAGATAGT 61.476 60.000 7.64 0.00 44.26 2.12
46 47 0.394565 GGCGCTCATGGGAGATAGTT 59.605 55.000 7.64 0.00 44.26 2.24
47 48 1.618837 GGCGCTCATGGGAGATAGTTA 59.381 52.381 7.64 0.00 44.26 2.24
48 49 2.037251 GGCGCTCATGGGAGATAGTTAA 59.963 50.000 7.64 0.00 44.26 2.01
49 50 3.307059 GGCGCTCATGGGAGATAGTTAAT 60.307 47.826 7.64 0.00 44.26 1.40
50 51 3.681897 GCGCTCATGGGAGATAGTTAATG 59.318 47.826 0.00 0.00 44.26 1.90
51 52 3.681897 CGCTCATGGGAGATAGTTAATGC 59.318 47.826 0.00 0.00 44.26 3.56
52 53 3.681897 GCTCATGGGAGATAGTTAATGCG 59.318 47.826 0.00 0.00 44.26 4.73
53 54 4.800914 GCTCATGGGAGATAGTTAATGCGT 60.801 45.833 0.00 0.00 44.26 5.24
54 55 5.566826 GCTCATGGGAGATAGTTAATGCGTA 60.567 44.000 0.00 0.00 44.26 4.42
55 56 5.779922 TCATGGGAGATAGTTAATGCGTAC 58.220 41.667 0.00 0.00 0.00 3.67
56 57 5.303333 TCATGGGAGATAGTTAATGCGTACA 59.697 40.000 0.00 0.00 0.00 2.90
57 58 5.196341 TGGGAGATAGTTAATGCGTACAG 57.804 43.478 0.00 0.00 0.00 2.74
58 59 4.647853 TGGGAGATAGTTAATGCGTACAGT 59.352 41.667 0.00 0.00 0.00 3.55
59 60 5.128171 TGGGAGATAGTTAATGCGTACAGTT 59.872 40.000 0.00 0.00 0.00 3.16
60 61 5.462398 GGGAGATAGTTAATGCGTACAGTTG 59.538 44.000 0.00 0.00 0.00 3.16
61 62 5.462398 GGAGATAGTTAATGCGTACAGTTGG 59.538 44.000 0.00 0.00 0.00 3.77
62 63 6.216801 AGATAGTTAATGCGTACAGTTGGA 57.783 37.500 0.00 0.00 0.00 3.53
63 64 6.040878 AGATAGTTAATGCGTACAGTTGGAC 58.959 40.000 0.00 0.00 0.00 4.02
64 65 2.991190 AGTTAATGCGTACAGTTGGACG 59.009 45.455 12.38 12.38 41.97 4.79
65 66 1.999048 TAATGCGTACAGTTGGACGG 58.001 50.000 17.70 1.18 39.46 4.79
66 67 0.319083 AATGCGTACAGTTGGACGGA 59.681 50.000 17.70 15.66 43.63 4.69
67 68 0.108804 ATGCGTACAGTTGGACGGAG 60.109 55.000 17.70 0.00 42.74 4.63
68 69 1.445582 GCGTACAGTTGGACGGAGG 60.446 63.158 17.70 0.00 39.46 4.30
69 70 1.445582 CGTACAGTTGGACGGAGGC 60.446 63.158 8.99 0.00 35.43 4.70
70 71 1.079336 GTACAGTTGGACGGAGGCC 60.079 63.158 0.00 0.00 0.00 5.19
71 72 2.288025 TACAGTTGGACGGAGGCCC 61.288 63.158 0.00 0.00 0.00 5.80
81 82 3.384532 GGAGGCCCGACGGTTGTA 61.385 66.667 13.94 0.00 0.00 2.41
82 83 2.125793 GAGGCCCGACGGTTGTAC 60.126 66.667 13.94 0.00 0.00 2.90
83 84 3.976902 GAGGCCCGACGGTTGTACG 62.977 68.421 13.94 0.00 40.31 3.67
85 86 4.362476 GCCCGACGGTTGTACGGT 62.362 66.667 13.94 0.00 44.34 4.83
86 87 2.431260 CCCGACGGTTGTACGGTG 60.431 66.667 13.94 0.00 44.34 4.94
87 88 2.336088 CCGACGGTTGTACGGTGT 59.664 61.111 5.48 0.00 41.47 4.16
88 89 2.017783 CCGACGGTTGTACGGTGTG 61.018 63.158 5.48 0.00 41.47 3.82
89 90 1.299316 CGACGGTTGTACGGTGTGT 60.299 57.895 0.00 0.00 38.39 3.72
90 91 1.542272 CGACGGTTGTACGGTGTGTG 61.542 60.000 0.00 0.00 38.39 3.82
91 92 0.528249 GACGGTTGTACGGTGTGTGT 60.528 55.000 0.00 0.00 38.39 3.72
92 93 0.806884 ACGGTTGTACGGTGTGTGTG 60.807 55.000 0.00 0.00 38.39 3.82
93 94 0.806884 CGGTTGTACGGTGTGTGTGT 60.807 55.000 0.00 0.00 0.00 3.72
94 95 1.535649 CGGTTGTACGGTGTGTGTGTA 60.536 52.381 0.00 0.00 0.00 2.90
95 96 2.129607 GGTTGTACGGTGTGTGTGTAG 58.870 52.381 0.00 0.00 0.00 2.74
96 97 2.223782 GGTTGTACGGTGTGTGTGTAGA 60.224 50.000 0.00 0.00 0.00 2.59
97 98 2.780065 TGTACGGTGTGTGTGTAGAC 57.220 50.000 0.00 0.00 0.00 2.59
98 99 1.002576 TGTACGGTGTGTGTGTAGACG 60.003 52.381 0.00 0.00 0.00 4.18
99 100 0.592637 TACGGTGTGTGTGTAGACGG 59.407 55.000 0.00 0.00 0.00 4.79
100 101 2.019951 CGGTGTGTGTGTAGACGGC 61.020 63.158 0.00 0.00 0.00 5.68
101 102 1.666872 GGTGTGTGTGTAGACGGCC 60.667 63.158 0.00 0.00 0.00 6.13
102 103 2.019951 GTGTGTGTGTAGACGGCCG 61.020 63.158 26.86 26.86 0.00 6.13
103 104 2.337532 GTGTGTGTAGACGGCCGT 59.662 61.111 34.89 34.89 0.00 5.68
104 105 2.019951 GTGTGTGTAGACGGCCGTG 61.020 63.158 39.65 5.58 0.00 4.94
105 106 3.110178 GTGTGTAGACGGCCGTGC 61.110 66.667 39.65 26.09 0.00 5.34
106 107 4.710695 TGTGTAGACGGCCGTGCG 62.711 66.667 39.65 7.13 0.00 5.34
117 118 4.849329 CCGTGCGGGACTAGCGAC 62.849 72.222 2.15 0.00 38.47 5.19
119 120 4.849329 GTGCGGGACTAGCGACGG 62.849 72.222 0.00 0.00 37.44 4.79
123 124 4.125695 GGGACTAGCGACGGCGTT 62.126 66.667 16.19 9.69 46.35 4.84
124 125 2.764314 GGGACTAGCGACGGCGTTA 61.764 63.158 16.19 10.57 46.35 3.18
125 126 1.584742 GGACTAGCGACGGCGTTAC 60.585 63.158 16.19 9.80 46.35 2.50
126 127 1.135315 GACTAGCGACGGCGTTACA 59.865 57.895 16.19 0.00 46.35 2.41
127 128 0.454957 GACTAGCGACGGCGTTACAA 60.455 55.000 16.19 0.00 46.35 2.41
128 129 0.730494 ACTAGCGACGGCGTTACAAC 60.730 55.000 16.19 0.00 46.35 3.32
129 130 0.730155 CTAGCGACGGCGTTACAACA 60.730 55.000 16.19 0.00 46.35 3.33
130 131 1.003262 TAGCGACGGCGTTACAACAC 61.003 55.000 16.19 0.00 46.35 3.32
131 132 2.305127 GCGACGGCGTTACAACACT 61.305 57.895 16.19 0.00 40.36 3.55
132 133 1.485514 CGACGGCGTTACAACACTG 59.514 57.895 16.19 0.00 0.00 3.66
133 134 1.210545 CGACGGCGTTACAACACTGT 61.211 55.000 16.19 0.00 39.75 3.55
134 135 1.769733 GACGGCGTTACAACACTGTA 58.230 50.000 16.19 0.00 36.96 2.74
135 136 1.453148 GACGGCGTTACAACACTGTAC 59.547 52.381 16.19 0.00 37.77 2.90
136 137 1.067516 ACGGCGTTACAACACTGTACT 59.932 47.619 6.77 0.00 37.77 2.73
137 138 2.293122 ACGGCGTTACAACACTGTACTA 59.707 45.455 6.77 0.00 37.77 1.82
138 139 3.243367 ACGGCGTTACAACACTGTACTAA 60.243 43.478 6.77 0.00 37.77 2.24
139 140 3.120121 CGGCGTTACAACACTGTACTAAC 59.880 47.826 0.00 0.00 37.77 2.34
140 141 4.050553 GGCGTTACAACACTGTACTAACA 58.949 43.478 0.00 0.00 37.77 2.41
141 142 4.687483 GGCGTTACAACACTGTACTAACAT 59.313 41.667 0.00 0.00 37.77 2.71
142 143 5.389098 GGCGTTACAACACTGTACTAACATG 60.389 44.000 0.00 0.00 37.77 3.21
143 144 5.389098 GCGTTACAACACTGTACTAACATGG 60.389 44.000 0.00 0.00 37.77 3.66
144 145 5.119588 CGTTACAACACTGTACTAACATGGG 59.880 44.000 0.00 0.00 37.77 4.00
145 146 3.408634 ACAACACTGTACTAACATGGGC 58.591 45.455 0.00 0.00 34.37 5.36
146 147 2.747446 CAACACTGTACTAACATGGGCC 59.253 50.000 0.00 0.00 34.37 5.80
147 148 1.066430 ACACTGTACTAACATGGGCCG 60.066 52.381 0.00 0.00 34.37 6.13
148 149 1.066430 CACTGTACTAACATGGGCCGT 60.066 52.381 0.00 0.00 34.37 5.68
149 150 2.166870 CACTGTACTAACATGGGCCGTA 59.833 50.000 0.00 0.00 34.37 4.02
150 151 2.429610 ACTGTACTAACATGGGCCGTAG 59.570 50.000 0.00 0.00 34.37 3.51
151 152 2.223971 CTGTACTAACATGGGCCGTAGG 60.224 54.545 0.00 0.00 43.53 3.18
152 153 4.501959 CTGTACTAACATGGGCCGTAGGA 61.502 52.174 0.00 0.00 43.41 2.94
153 154 5.950380 CTGTACTAACATGGGCCGTAGGAA 61.950 50.000 0.00 0.00 43.41 3.36
154 155 7.908458 CTGTACTAACATGGGCCGTAGGAAC 62.908 52.000 0.00 1.84 43.41 3.62
164 165 3.967734 CGTAGGAACAAACGGCATG 57.032 52.632 0.00 0.00 36.56 4.06
165 166 1.434555 CGTAGGAACAAACGGCATGA 58.565 50.000 0.00 0.00 36.56 3.07
166 167 1.801771 CGTAGGAACAAACGGCATGAA 59.198 47.619 0.00 0.00 36.56 2.57
167 168 2.224549 CGTAGGAACAAACGGCATGAAA 59.775 45.455 0.00 0.00 36.56 2.69
168 169 3.304123 CGTAGGAACAAACGGCATGAAAA 60.304 43.478 0.00 0.00 36.56 2.29
169 170 3.810310 AGGAACAAACGGCATGAAAAA 57.190 38.095 0.00 0.00 0.00 1.94
170 171 3.453424 AGGAACAAACGGCATGAAAAAC 58.547 40.909 0.00 0.00 0.00 2.43
171 172 2.217620 GGAACAAACGGCATGAAAAACG 59.782 45.455 0.00 0.00 0.00 3.60
172 173 1.846541 ACAAACGGCATGAAAAACGG 58.153 45.000 0.00 0.00 0.00 4.44
173 174 1.135333 ACAAACGGCATGAAAAACGGT 59.865 42.857 0.00 0.00 0.00 4.83
174 175 1.520590 CAAACGGCATGAAAAACGGTG 59.479 47.619 0.00 0.00 0.00 4.94
175 176 0.031449 AACGGCATGAAAAACGGTGG 59.969 50.000 0.00 0.00 0.00 4.61
176 177 1.080839 CGGCATGAAAAACGGTGGG 60.081 57.895 0.00 0.00 0.00 4.61
177 178 1.519751 CGGCATGAAAAACGGTGGGA 61.520 55.000 0.00 0.00 0.00 4.37
178 179 0.894835 GGCATGAAAAACGGTGGGAT 59.105 50.000 0.00 0.00 0.00 3.85
179 180 1.135112 GGCATGAAAAACGGTGGGATC 60.135 52.381 0.00 0.00 0.00 3.36
180 181 1.135112 GCATGAAAAACGGTGGGATCC 60.135 52.381 1.92 1.92 0.00 3.36
214 215 4.382320 GCGTCGGCCCACCAACTA 62.382 66.667 0.00 0.00 34.57 2.24
215 216 2.433664 CGTCGGCCCACCAACTAC 60.434 66.667 0.00 0.00 34.57 2.73
216 217 2.745037 GTCGGCCCACCAACTACA 59.255 61.111 0.00 0.00 34.57 2.74
217 218 1.298667 GTCGGCCCACCAACTACAT 59.701 57.895 0.00 0.00 34.57 2.29
218 219 1.024579 GTCGGCCCACCAACTACATG 61.025 60.000 0.00 0.00 34.57 3.21
219 220 1.195442 TCGGCCCACCAACTACATGA 61.195 55.000 0.00 0.00 34.57 3.07
220 221 0.322098 CGGCCCACCAACTACATGAA 60.322 55.000 0.00 0.00 34.57 2.57
221 222 1.463674 GGCCCACCAACTACATGAAG 58.536 55.000 0.00 0.00 35.26 3.02
222 223 1.271926 GGCCCACCAACTACATGAAGT 60.272 52.381 0.00 0.00 35.26 3.01
223 224 1.812571 GCCCACCAACTACATGAAGTG 59.187 52.381 0.00 0.00 0.00 3.16
224 225 1.812571 CCCACCAACTACATGAAGTGC 59.187 52.381 0.00 0.00 0.00 4.40
225 226 1.464608 CCACCAACTACATGAAGTGCG 59.535 52.381 0.00 0.00 0.00 5.34
226 227 2.143122 CACCAACTACATGAAGTGCGT 58.857 47.619 0.00 0.00 0.00 5.24
227 228 2.157668 CACCAACTACATGAAGTGCGTC 59.842 50.000 0.00 0.00 0.00 5.19
228 229 2.037251 ACCAACTACATGAAGTGCGTCT 59.963 45.455 0.00 0.00 0.00 4.18
229 230 2.413112 CCAACTACATGAAGTGCGTCTG 59.587 50.000 0.00 0.00 0.00 3.51
230 231 1.714794 ACTACATGAAGTGCGTCTGC 58.285 50.000 0.00 0.00 43.20 4.26
240 241 3.766691 GCGTCTGCGGGACCCTAA 61.767 66.667 9.41 0.00 41.64 2.69
241 242 2.494918 CGTCTGCGGGACCCTAAG 59.505 66.667 9.41 5.96 41.64 2.18
242 243 2.348888 CGTCTGCGGGACCCTAAGT 61.349 63.158 9.41 0.00 41.64 2.24
243 244 1.516423 GTCTGCGGGACCCTAAGTC 59.484 63.158 9.41 0.00 45.51 3.01
256 257 5.915175 GACCCTAAGTCGATCCATTTAACT 58.085 41.667 0.00 0.00 35.30 2.24
257 258 5.915175 ACCCTAAGTCGATCCATTTAACTC 58.085 41.667 0.00 0.00 0.00 3.01
258 259 4.982916 CCCTAAGTCGATCCATTTAACTCG 59.017 45.833 0.00 0.00 0.00 4.18
259 260 5.221185 CCCTAAGTCGATCCATTTAACTCGA 60.221 44.000 0.00 0.00 37.77 4.04
260 261 5.915758 CCTAAGTCGATCCATTTAACTCGAG 59.084 44.000 11.84 11.84 40.44 4.04
261 262 4.985538 AGTCGATCCATTTAACTCGAGT 57.014 40.909 13.58 13.58 40.44 4.18
262 263 4.922719 AGTCGATCCATTTAACTCGAGTC 58.077 43.478 20.33 1.53 38.97 3.36
263 264 3.724751 GTCGATCCATTTAACTCGAGTCG 59.275 47.826 20.33 14.37 40.44 4.18
264 265 3.624410 TCGATCCATTTAACTCGAGTCGA 59.376 43.478 20.33 16.50 35.41 4.20
265 266 4.275196 TCGATCCATTTAACTCGAGTCGAT 59.725 41.667 20.33 12.27 35.41 3.59
266 267 4.613448 CGATCCATTTAACTCGAGTCGATC 59.387 45.833 20.33 18.17 34.61 3.69
267 268 4.303086 TCCATTTAACTCGAGTCGATCC 57.697 45.455 20.33 0.00 34.61 3.36
268 269 3.067742 TCCATTTAACTCGAGTCGATCCC 59.932 47.826 20.33 0.00 34.61 3.85
269 270 3.381949 CATTTAACTCGAGTCGATCCCC 58.618 50.000 20.33 0.00 34.61 4.81
270 271 2.133281 TTAACTCGAGTCGATCCCCA 57.867 50.000 20.33 0.00 34.61 4.96
271 272 1.386533 TAACTCGAGTCGATCCCCAC 58.613 55.000 20.33 0.00 34.61 4.61
272 273 0.611062 AACTCGAGTCGATCCCCACA 60.611 55.000 20.33 0.00 34.61 4.17
273 274 0.395862 ACTCGAGTCGATCCCCACAT 60.396 55.000 16.94 0.00 34.61 3.21
274 275 0.312416 CTCGAGTCGATCCCCACATC 59.688 60.000 16.94 0.00 34.61 3.06
275 276 1.008424 CGAGTCGATCCCCACATCG 60.008 63.158 6.73 0.00 45.91 3.84
276 277 1.725557 CGAGTCGATCCCCACATCGT 61.726 60.000 6.73 0.00 44.99 3.73
277 278 0.249073 GAGTCGATCCCCACATCGTG 60.249 60.000 3.00 0.00 44.99 4.35
788 801 1.409427 CTGAGCTAGGGTTAGGGTTCG 59.591 57.143 0.00 0.00 0.00 3.95
883 896 2.890945 AGGGTTATGGTTGCTGTTTGAC 59.109 45.455 0.00 0.00 0.00 3.18
890 903 3.146066 TGGTTGCTGTTTGACCTATGTC 58.854 45.455 0.00 0.00 42.12 3.06
934 947 1.145571 TGGGTTAGGGTTCTTGCTGT 58.854 50.000 0.00 0.00 0.00 4.40
1737 1750 4.384940 TGTGCATTGAGTACACAAAGCTA 58.615 39.130 25.85 16.15 42.43 3.32
1981 1994 4.017037 AGGAGGTTGAACAGGAGAGAGATA 60.017 45.833 0.00 0.00 0.00 1.98
2830 2845 2.160013 GGTGTCGTTTCTTCGATCGTTG 60.160 50.000 15.94 9.24 41.78 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.997226 CTGGAATACCGCGTCGATCG 60.997 60.000 9.36 9.36 43.12 3.69
8 9 0.663568 CCTGGAATACCGCGTCGATC 60.664 60.000 4.92 0.00 39.42 3.69
9 10 1.362717 CCTGGAATACCGCGTCGAT 59.637 57.895 4.92 0.00 39.42 3.59
10 11 2.777972 CCCTGGAATACCGCGTCGA 61.778 63.158 4.92 0.00 39.42 4.20
11 12 2.279252 CCCTGGAATACCGCGTCG 60.279 66.667 4.92 0.00 39.42 5.12
12 13 2.588034 GCCCTGGAATACCGCGTC 60.588 66.667 4.92 0.00 39.42 5.19
13 14 4.524318 CGCCCTGGAATACCGCGT 62.524 66.667 4.92 0.00 38.22 6.01
15 16 4.547367 AGCGCCCTGGAATACCGC 62.547 66.667 2.29 1.44 44.47 5.68
16 17 2.280186 GAGCGCCCTGGAATACCG 60.280 66.667 2.29 0.00 39.42 4.02
17 18 0.886490 CATGAGCGCCCTGGAATACC 60.886 60.000 2.29 0.00 0.00 2.73
18 19 0.886490 CCATGAGCGCCCTGGAATAC 60.886 60.000 13.66 0.00 31.38 1.89
19 20 1.451504 CCATGAGCGCCCTGGAATA 59.548 57.895 13.66 0.00 31.38 1.75
20 21 2.194056 CCATGAGCGCCCTGGAAT 59.806 61.111 13.66 0.00 31.38 3.01
21 22 4.113815 CCCATGAGCGCCCTGGAA 62.114 66.667 19.00 0.00 31.38 3.53
23 24 4.559063 CTCCCATGAGCGCCCTGG 62.559 72.222 2.29 8.79 0.00 4.45
24 25 1.475169 TATCTCCCATGAGCGCCCTG 61.475 60.000 2.29 0.00 38.58 4.45
25 26 1.152247 TATCTCCCATGAGCGCCCT 60.152 57.895 2.29 0.00 38.58 5.19
26 27 1.294780 CTATCTCCCATGAGCGCCC 59.705 63.158 2.29 0.00 38.58 6.13
27 28 0.394565 AACTATCTCCCATGAGCGCC 59.605 55.000 2.29 0.00 38.58 6.53
28 29 3.386768 TTAACTATCTCCCATGAGCGC 57.613 47.619 0.00 0.00 38.58 5.92
29 30 3.681897 GCATTAACTATCTCCCATGAGCG 59.318 47.826 0.00 0.00 38.58 5.03
30 31 3.681897 CGCATTAACTATCTCCCATGAGC 59.318 47.826 0.00 0.00 38.58 4.26
31 32 4.887748 ACGCATTAACTATCTCCCATGAG 58.112 43.478 0.00 0.00 40.17 2.90
32 33 4.955811 ACGCATTAACTATCTCCCATGA 57.044 40.909 0.00 0.00 0.00 3.07
33 34 5.538118 TGTACGCATTAACTATCTCCCATG 58.462 41.667 0.00 0.00 0.00 3.66
34 35 5.304614 ACTGTACGCATTAACTATCTCCCAT 59.695 40.000 0.00 0.00 0.00 4.00
35 36 4.647853 ACTGTACGCATTAACTATCTCCCA 59.352 41.667 0.00 0.00 0.00 4.37
36 37 5.197682 ACTGTACGCATTAACTATCTCCC 57.802 43.478 0.00 0.00 0.00 4.30
37 38 5.462398 CCAACTGTACGCATTAACTATCTCC 59.538 44.000 0.00 0.00 0.00 3.71
38 39 6.198591 GTCCAACTGTACGCATTAACTATCTC 59.801 42.308 0.00 0.00 0.00 2.75
39 40 6.040878 GTCCAACTGTACGCATTAACTATCT 58.959 40.000 0.00 0.00 0.00 1.98
40 41 5.051907 CGTCCAACTGTACGCATTAACTATC 60.052 44.000 0.00 0.00 31.66 2.08
41 42 4.802039 CGTCCAACTGTACGCATTAACTAT 59.198 41.667 0.00 0.00 31.66 2.12
42 43 4.168014 CGTCCAACTGTACGCATTAACTA 58.832 43.478 0.00 0.00 31.66 2.24
43 44 2.991190 CGTCCAACTGTACGCATTAACT 59.009 45.455 0.00 0.00 31.66 2.24
44 45 2.093152 CCGTCCAACTGTACGCATTAAC 59.907 50.000 0.00 0.00 37.78 2.01
45 46 2.029200 TCCGTCCAACTGTACGCATTAA 60.029 45.455 0.00 0.00 37.78 1.40
46 47 1.545136 TCCGTCCAACTGTACGCATTA 59.455 47.619 0.00 0.00 37.78 1.90
47 48 0.319083 TCCGTCCAACTGTACGCATT 59.681 50.000 0.00 0.00 37.78 3.56
48 49 0.108804 CTCCGTCCAACTGTACGCAT 60.109 55.000 0.00 0.00 37.78 4.73
49 50 1.287815 CTCCGTCCAACTGTACGCA 59.712 57.895 0.00 0.00 37.78 5.24
50 51 1.445582 CCTCCGTCCAACTGTACGC 60.446 63.158 0.00 0.00 37.78 4.42
51 52 1.445582 GCCTCCGTCCAACTGTACG 60.446 63.158 0.00 0.00 38.80 3.67
52 53 1.079336 GGCCTCCGTCCAACTGTAC 60.079 63.158 0.00 0.00 0.00 2.90
53 54 2.288025 GGGCCTCCGTCCAACTGTA 61.288 63.158 0.84 0.00 0.00 2.74
54 55 3.637273 GGGCCTCCGTCCAACTGT 61.637 66.667 0.84 0.00 0.00 3.55
64 65 3.384532 TACAACCGTCGGGCCTCC 61.385 66.667 17.28 0.00 36.48 4.30
65 66 2.125793 GTACAACCGTCGGGCCTC 60.126 66.667 17.28 0.00 36.48 4.70
66 67 4.060038 CGTACAACCGTCGGGCCT 62.060 66.667 17.28 0.00 36.48 5.19
71 72 1.299316 ACACACCGTACAACCGTCG 60.299 57.895 0.00 0.00 0.00 5.12
72 73 0.528249 ACACACACCGTACAACCGTC 60.528 55.000 0.00 0.00 0.00 4.79
73 74 0.806884 CACACACACCGTACAACCGT 60.807 55.000 0.00 0.00 0.00 4.83
74 75 0.806884 ACACACACACCGTACAACCG 60.807 55.000 0.00 0.00 0.00 4.44
75 76 2.129607 CTACACACACACCGTACAACC 58.870 52.381 0.00 0.00 0.00 3.77
76 77 2.791004 GTCTACACACACACCGTACAAC 59.209 50.000 0.00 0.00 0.00 3.32
77 78 2.541383 CGTCTACACACACACCGTACAA 60.541 50.000 0.00 0.00 0.00 2.41
78 79 1.002576 CGTCTACACACACACCGTACA 60.003 52.381 0.00 0.00 0.00 2.90
79 80 1.664016 CCGTCTACACACACACCGTAC 60.664 57.143 0.00 0.00 0.00 3.67
80 81 0.592637 CCGTCTACACACACACCGTA 59.407 55.000 0.00 0.00 0.00 4.02
81 82 1.361271 CCGTCTACACACACACCGT 59.639 57.895 0.00 0.00 0.00 4.83
82 83 2.019951 GCCGTCTACACACACACCG 61.020 63.158 0.00 0.00 0.00 4.94
83 84 1.666872 GGCCGTCTACACACACACC 60.667 63.158 0.00 0.00 0.00 4.16
84 85 2.019951 CGGCCGTCTACACACACAC 61.020 63.158 19.50 0.00 0.00 3.82
85 86 2.337170 CGGCCGTCTACACACACA 59.663 61.111 19.50 0.00 0.00 3.72
86 87 2.019951 CACGGCCGTCTACACACAC 61.020 63.158 31.80 0.00 0.00 3.82
87 88 2.337170 CACGGCCGTCTACACACA 59.663 61.111 31.80 0.00 0.00 3.72
88 89 3.110178 GCACGGCCGTCTACACAC 61.110 66.667 31.80 8.11 0.00 3.82
89 90 4.710695 CGCACGGCCGTCTACACA 62.711 66.667 31.80 0.00 0.00 3.72
100 101 4.849329 GTCGCTAGTCCCGCACGG 62.849 72.222 1.02 1.02 0.00 4.94
102 103 4.849329 CCGTCGCTAGTCCCGCAC 62.849 72.222 0.00 0.00 0.00 5.34
106 107 2.764314 TAACGCCGTCGCTAGTCCC 61.764 63.158 0.00 0.00 39.84 4.46
107 108 1.584742 GTAACGCCGTCGCTAGTCC 60.585 63.158 0.00 0.00 39.84 3.85
108 109 0.454957 TTGTAACGCCGTCGCTAGTC 60.455 55.000 0.00 0.00 39.84 2.59
109 110 0.730494 GTTGTAACGCCGTCGCTAGT 60.730 55.000 0.00 0.00 39.84 2.57
110 111 0.730155 TGTTGTAACGCCGTCGCTAG 60.730 55.000 0.00 0.00 39.84 3.42
111 112 1.003262 GTGTTGTAACGCCGTCGCTA 61.003 55.000 0.00 0.00 39.84 4.26
112 113 2.027897 TGTTGTAACGCCGTCGCT 59.972 55.556 0.00 0.00 39.84 4.93
113 114 2.169327 GTGTTGTAACGCCGTCGC 59.831 61.111 0.00 0.00 39.84 5.19
114 115 1.210545 ACAGTGTTGTAACGCCGTCG 61.211 55.000 4.80 0.00 40.18 5.12
115 116 1.453148 GTACAGTGTTGTAACGCCGTC 59.547 52.381 0.00 0.00 41.25 4.79
116 117 1.067516 AGTACAGTGTTGTAACGCCGT 59.932 47.619 0.00 3.91 41.25 5.68
117 118 1.774639 AGTACAGTGTTGTAACGCCG 58.225 50.000 0.00 0.00 41.25 6.46
118 119 4.050553 TGTTAGTACAGTGTTGTAACGCC 58.949 43.478 0.00 0.00 41.25 5.68
119 120 5.389098 CCATGTTAGTACAGTGTTGTAACGC 60.389 44.000 0.00 0.21 41.25 4.84
120 121 5.119588 CCCATGTTAGTACAGTGTTGTAACG 59.880 44.000 0.00 0.00 41.25 3.18
121 122 5.106830 GCCCATGTTAGTACAGTGTTGTAAC 60.107 44.000 15.61 15.61 41.25 2.50
122 123 4.998672 GCCCATGTTAGTACAGTGTTGTAA 59.001 41.667 0.00 0.00 41.25 2.41
123 124 4.563993 GGCCCATGTTAGTACAGTGTTGTA 60.564 45.833 0.00 0.00 37.77 2.41
124 125 3.408634 GCCCATGTTAGTACAGTGTTGT 58.591 45.455 0.00 0.00 37.77 3.32
125 126 2.747446 GGCCCATGTTAGTACAGTGTTG 59.253 50.000 0.00 0.00 37.77 3.33
126 127 2.614481 CGGCCCATGTTAGTACAGTGTT 60.614 50.000 0.00 0.00 37.77 3.32
127 128 1.066430 CGGCCCATGTTAGTACAGTGT 60.066 52.381 0.00 0.00 37.77 3.55
128 129 1.066430 ACGGCCCATGTTAGTACAGTG 60.066 52.381 0.00 0.00 37.77 3.66
129 130 1.272807 ACGGCCCATGTTAGTACAGT 58.727 50.000 0.00 0.00 37.77 3.55
130 131 2.223971 CCTACGGCCCATGTTAGTACAG 60.224 54.545 0.00 0.00 37.77 2.74
131 132 1.758280 CCTACGGCCCATGTTAGTACA 59.242 52.381 0.00 0.00 38.95 2.90
132 133 2.034124 TCCTACGGCCCATGTTAGTAC 58.966 52.381 0.00 0.00 0.00 2.73
133 134 2.431782 GTTCCTACGGCCCATGTTAGTA 59.568 50.000 0.00 0.00 0.00 1.82
134 135 1.208776 GTTCCTACGGCCCATGTTAGT 59.791 52.381 0.00 0.00 0.00 2.24
135 136 1.208535 TGTTCCTACGGCCCATGTTAG 59.791 52.381 0.00 0.00 0.00 2.34
136 137 1.277579 TGTTCCTACGGCCCATGTTA 58.722 50.000 0.00 0.00 0.00 2.41
137 138 0.402504 TTGTTCCTACGGCCCATGTT 59.597 50.000 0.00 0.00 0.00 2.71
138 139 0.402504 TTTGTTCCTACGGCCCATGT 59.597 50.000 0.00 0.00 0.00 3.21
139 140 0.808755 GTTTGTTCCTACGGCCCATG 59.191 55.000 0.00 0.00 0.00 3.66
140 141 0.675522 CGTTTGTTCCTACGGCCCAT 60.676 55.000 0.00 0.00 34.30 4.00
141 142 1.301874 CGTTTGTTCCTACGGCCCA 60.302 57.895 0.00 0.00 34.30 5.36
142 143 3.569902 CGTTTGTTCCTACGGCCC 58.430 61.111 0.00 0.00 34.30 5.80
146 147 1.434555 TCATGCCGTTTGTTCCTACG 58.565 50.000 0.00 0.00 37.50 3.51
147 148 3.907894 TTTCATGCCGTTTGTTCCTAC 57.092 42.857 0.00 0.00 0.00 3.18
148 149 4.612943 GTTTTTCATGCCGTTTGTTCCTA 58.387 39.130 0.00 0.00 0.00 2.94
149 150 3.453424 GTTTTTCATGCCGTTTGTTCCT 58.547 40.909 0.00 0.00 0.00 3.36
150 151 2.217620 CGTTTTTCATGCCGTTTGTTCC 59.782 45.455 0.00 0.00 0.00 3.62
151 152 2.217620 CCGTTTTTCATGCCGTTTGTTC 59.782 45.455 0.00 0.00 0.00 3.18
152 153 2.197577 CCGTTTTTCATGCCGTTTGTT 58.802 42.857 0.00 0.00 0.00 2.83
153 154 1.135333 ACCGTTTTTCATGCCGTTTGT 59.865 42.857 0.00 0.00 0.00 2.83
154 155 1.520590 CACCGTTTTTCATGCCGTTTG 59.479 47.619 0.00 0.00 0.00 2.93
155 156 1.537135 CCACCGTTTTTCATGCCGTTT 60.537 47.619 0.00 0.00 0.00 3.60
156 157 0.031449 CCACCGTTTTTCATGCCGTT 59.969 50.000 0.00 0.00 0.00 4.44
157 158 1.657556 CCACCGTTTTTCATGCCGT 59.342 52.632 0.00 0.00 0.00 5.68
158 159 1.080839 CCCACCGTTTTTCATGCCG 60.081 57.895 0.00 0.00 0.00 5.69
159 160 0.894835 ATCCCACCGTTTTTCATGCC 59.105 50.000 0.00 0.00 0.00 4.40
160 161 1.135112 GGATCCCACCGTTTTTCATGC 60.135 52.381 0.00 0.00 0.00 4.06
161 162 1.132262 CGGATCCCACCGTTTTTCATG 59.868 52.381 6.06 0.00 46.70 3.07
162 163 1.459450 CGGATCCCACCGTTTTTCAT 58.541 50.000 6.06 0.00 46.70 2.57
163 164 2.935505 CGGATCCCACCGTTTTTCA 58.064 52.632 6.06 0.00 46.70 2.69
171 172 2.590092 CTCCAACCGGATCCCACC 59.410 66.667 9.46 0.00 41.79 4.61
172 173 2.590092 CCTCCAACCGGATCCCAC 59.410 66.667 9.46 0.00 41.79 4.61
173 174 2.690881 CCCTCCAACCGGATCCCA 60.691 66.667 9.46 0.00 41.79 4.37
174 175 3.489513 CCCCTCCAACCGGATCCC 61.490 72.222 9.46 0.00 41.79 3.85
175 176 3.489513 CCCCCTCCAACCGGATCC 61.490 72.222 9.46 0.00 41.79 3.36
200 201 1.195442 TCATGTAGTTGGTGGGCCGA 61.195 55.000 0.00 0.00 37.67 5.54
201 202 0.322098 TTCATGTAGTTGGTGGGCCG 60.322 55.000 0.00 0.00 37.67 6.13
202 203 1.271926 ACTTCATGTAGTTGGTGGGCC 60.272 52.381 0.00 0.00 0.00 5.80
203 204 1.812571 CACTTCATGTAGTTGGTGGGC 59.187 52.381 1.68 0.00 0.00 5.36
204 205 1.812571 GCACTTCATGTAGTTGGTGGG 59.187 52.381 1.68 0.00 0.00 4.61
205 206 1.464608 CGCACTTCATGTAGTTGGTGG 59.535 52.381 1.68 0.00 0.00 4.61
206 207 2.143122 ACGCACTTCATGTAGTTGGTG 58.857 47.619 1.68 2.45 0.00 4.17
207 208 2.037251 AGACGCACTTCATGTAGTTGGT 59.963 45.455 1.68 3.80 0.00 3.67
208 209 2.413112 CAGACGCACTTCATGTAGTTGG 59.587 50.000 1.68 0.59 0.00 3.77
209 210 2.159787 GCAGACGCACTTCATGTAGTTG 60.160 50.000 1.68 1.48 38.36 3.16
210 211 2.069273 GCAGACGCACTTCATGTAGTT 58.931 47.619 1.68 0.00 38.36 2.24
211 212 1.714794 GCAGACGCACTTCATGTAGT 58.285 50.000 0.00 0.00 38.36 2.73
212 213 0.642291 CGCAGACGCACTTCATGTAG 59.358 55.000 0.00 0.00 38.40 2.74
213 214 0.735978 CCGCAGACGCACTTCATGTA 60.736 55.000 0.00 0.00 38.40 2.29
214 215 2.029288 CCGCAGACGCACTTCATGT 61.029 57.895 0.00 0.00 38.40 3.21
215 216 2.743752 CCCGCAGACGCACTTCATG 61.744 63.158 0.00 0.00 38.40 3.07
216 217 2.434884 CCCGCAGACGCACTTCAT 60.435 61.111 0.00 0.00 38.40 2.57
217 218 3.611674 TCCCGCAGACGCACTTCA 61.612 61.111 0.00 0.00 38.40 3.02
218 219 3.112709 GTCCCGCAGACGCACTTC 61.113 66.667 0.00 0.00 38.40 3.01
225 226 1.516423 GACTTAGGGTCCCGCAGAC 59.484 63.158 14.72 6.31 45.51 3.51
226 227 2.050350 CGACTTAGGGTCCCGCAGA 61.050 63.158 14.72 0.00 41.64 4.26
227 228 1.392710 ATCGACTTAGGGTCCCGCAG 61.393 60.000 0.99 5.01 41.64 5.18
228 229 1.380785 ATCGACTTAGGGTCCCGCA 60.381 57.895 0.99 0.00 41.64 5.69
229 230 1.363080 GATCGACTTAGGGTCCCGC 59.637 63.158 0.99 0.00 41.64 6.13
230 231 0.754217 TGGATCGACTTAGGGTCCCG 60.754 60.000 0.99 0.00 41.64 5.14
231 232 1.718280 ATGGATCGACTTAGGGTCCC 58.282 55.000 0.00 0.00 41.64 4.46
232 233 3.840124 AAATGGATCGACTTAGGGTCC 57.160 47.619 0.00 0.00 41.64 4.46
233 234 5.915175 AGTTAAATGGATCGACTTAGGGTC 58.085 41.667 0.00 0.00 41.28 4.46
234 235 5.451520 CGAGTTAAATGGATCGACTTAGGGT 60.452 44.000 0.00 0.00 37.35 4.34
235 236 4.982916 CGAGTTAAATGGATCGACTTAGGG 59.017 45.833 0.00 0.00 37.35 3.53
236 237 5.828747 TCGAGTTAAATGGATCGACTTAGG 58.171 41.667 0.00 0.00 39.11 2.69
237 238 6.496571 ACTCGAGTTAAATGGATCGACTTAG 58.503 40.000 13.58 0.00 39.11 2.18
238 239 6.446781 ACTCGAGTTAAATGGATCGACTTA 57.553 37.500 13.58 0.00 39.11 2.24
239 240 5.326200 ACTCGAGTTAAATGGATCGACTT 57.674 39.130 13.58 0.00 39.11 3.01
240 241 4.496010 CGACTCGAGTTAAATGGATCGACT 60.496 45.833 21.08 0.00 39.11 4.18
241 242 3.724751 CGACTCGAGTTAAATGGATCGAC 59.275 47.826 21.08 0.55 39.11 4.20
242 243 3.624410 TCGACTCGAGTTAAATGGATCGA 59.376 43.478 21.08 16.84 41.51 3.59
243 244 3.948851 TCGACTCGAGTTAAATGGATCG 58.051 45.455 21.08 14.75 36.54 3.69
244 245 4.918583 GGATCGACTCGAGTTAAATGGATC 59.081 45.833 21.08 20.56 39.91 3.36
245 246 4.262079 GGGATCGACTCGAGTTAAATGGAT 60.262 45.833 21.08 14.53 39.91 3.41
246 247 3.067742 GGGATCGACTCGAGTTAAATGGA 59.932 47.826 21.08 10.59 39.91 3.41
247 248 3.381949 GGGATCGACTCGAGTTAAATGG 58.618 50.000 21.08 5.54 39.91 3.16
248 249 3.181479 TGGGGATCGACTCGAGTTAAATG 60.181 47.826 21.08 7.84 39.91 2.32
249 250 3.028850 TGGGGATCGACTCGAGTTAAAT 58.971 45.455 21.08 13.23 39.91 1.40
250 251 2.165030 GTGGGGATCGACTCGAGTTAAA 59.835 50.000 21.08 8.70 39.91 1.52
251 252 1.747355 GTGGGGATCGACTCGAGTTAA 59.253 52.381 21.08 11.38 39.91 2.01
252 253 1.340308 TGTGGGGATCGACTCGAGTTA 60.340 52.381 21.08 11.76 39.91 2.24
253 254 0.611062 TGTGGGGATCGACTCGAGTT 60.611 55.000 21.08 3.21 39.91 3.01
254 255 0.395862 ATGTGGGGATCGACTCGAGT 60.396 55.000 20.18 20.18 39.91 4.18
255 256 0.312416 GATGTGGGGATCGACTCGAG 59.688 60.000 11.84 11.84 39.91 4.04
256 257 1.444917 CGATGTGGGGATCGACTCGA 61.445 60.000 3.06 3.06 46.72 4.04
257 258 1.008424 CGATGTGGGGATCGACTCG 60.008 63.158 0.00 0.00 46.72 4.18
258 259 0.249073 CACGATGTGGGGATCGACTC 60.249 60.000 9.73 0.00 46.72 3.36
259 260 0.970937 ACACGATGTGGGGATCGACT 60.971 55.000 9.73 0.00 46.72 4.18
260 261 0.527817 GACACGATGTGGGGATCGAC 60.528 60.000 9.73 0.00 46.72 4.20
261 262 1.813859 GACACGATGTGGGGATCGA 59.186 57.895 9.73 0.00 46.72 3.59
263 264 0.249073 CTCGACACGATGTGGGGATC 60.249 60.000 1.64 0.00 37.94 3.36
264 265 0.970937 ACTCGACACGATGTGGGGAT 60.971 55.000 6.94 0.00 37.94 3.85
265 266 0.322726 TACTCGACACGATGTGGGGA 60.323 55.000 6.94 0.00 37.94 4.81
266 267 0.528924 TTACTCGACACGATGTGGGG 59.471 55.000 1.64 0.00 37.94 4.96
267 268 2.357327 TTTACTCGACACGATGTGGG 57.643 50.000 1.64 0.00 37.94 4.61
268 269 3.486108 GCTATTTACTCGACACGATGTGG 59.514 47.826 1.64 0.00 37.94 4.17
269 270 4.102649 TGCTATTTACTCGACACGATGTG 58.897 43.478 0.00 0.00 39.75 3.21
270 271 4.365899 TGCTATTTACTCGACACGATGT 57.634 40.909 0.00 0.00 34.61 3.06
271 272 6.986424 TTATGCTATTTACTCGACACGATG 57.014 37.500 0.00 0.00 34.61 3.84
272 273 7.705325 AGTTTTATGCTATTTACTCGACACGAT 59.295 33.333 0.00 0.00 34.61 3.73
273 274 7.031372 AGTTTTATGCTATTTACTCGACACGA 58.969 34.615 0.00 0.00 0.00 4.35
274 275 7.218145 AGTTTTATGCTATTTACTCGACACG 57.782 36.000 0.00 0.00 0.00 4.49
275 276 8.538039 GGTAGTTTTATGCTATTTACTCGACAC 58.462 37.037 0.00 0.00 0.00 3.67
276 277 8.252417 TGGTAGTTTTATGCTATTTACTCGACA 58.748 33.333 0.00 0.00 0.00 4.35
277 278 8.538039 GTGGTAGTTTTATGCTATTTACTCGAC 58.462 37.037 0.00 0.00 0.00 4.20
528 530 1.019278 ACCACTTAATGAGCGCACGG 61.019 55.000 11.47 0.00 0.00 4.94
721 734 2.494471 CCATGTCCATGCTTGTGATGTT 59.506 45.455 1.64 0.00 37.49 2.71
788 801 6.999871 ACACTAACCTAATCTAGCTCCTAGAC 59.000 42.308 4.23 0.00 44.47 2.59
883 896 8.668510 AGTTTTCAAGCATACATAGACATAGG 57.331 34.615 0.00 0.00 0.00 2.57
890 903 7.865706 AACCCTAGTTTTCAAGCATACATAG 57.134 36.000 0.00 0.00 29.61 2.23
1981 1994 5.619220 CTTGGCCTTCTCTATCTTAAGCAT 58.381 41.667 3.32 0.00 0.00 3.79
2734 2749 1.685517 TGATGATCTTCCCTGAGCTCG 59.314 52.381 9.64 3.88 0.00 5.03
2830 2845 2.996621 ACTAGCAACAACTCTCAATCGC 59.003 45.455 0.00 0.00 0.00 4.58
2864 2879 6.482898 ACATAGCTCAGACTCTCATTCATT 57.517 37.500 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.