Multiple sequence alignment - TraesCS1A01G162400

Loading Multiple Alignment...

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 TraesCS1A01G162400 chr1A 100.000 3113 0 0 1 3113 291566838 291563726 0.000000e+00 5749.0
1 TraesCS1A01G162400 chr1B 95.119 2438 65 20 704 3113 324600874 324603285 0.000000e+00 3794.0
2 TraesCS1A01G162400 chr1B 90.234 256 17 4 261 511 324583971 324584223 8.320000e-86 327.0
3 TraesCS1A01G162400 chr1D 98.795 1577 17 2 874 2449 224575364 224573789 0.000000e+00 2806.0
4 TraesCS1A01G162400 chr1D 85.915 710 28 17 2431 3113 224573253 224572589 0.000000e+00 691.0
5 TraesCS1A01G162400 chr1D 93.662 284 10 5 601 879 224575860 224575580 4.800000e-113 418.0
6 TraesCS1A01G162400 chr1D 87.869 305 29 6 261 560 224576240 224575939 4.940000e-93 351.0
7 TraesCS1A01G162400 chr5D 97.436 39 1 0 199 237 461909343 461909381 2.000000e-07 67.6
8 TraesCS1A01G162400 chr3D 84.058 69 8 3 180 246 19118424 19118357 2.590000e-06 63.9
9 TraesCS1A01G162400 chr4D 83.333 66 9 2 182 246 473132473 473132409 3.350000e-05 60.2
10 TraesCS1A01G162400 chr4B 97.059 34 1 0 204 237 505556956 505556989 1.210000e-04 58.4
11 TraesCS1A01G162400 chr2B 94.444 36 2 0 200 235 17372644 17372609 4.340000e-04 56.5


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 TraesCS1A01G162400 chr1A 291563726 291566838 3112 True 5749.0 5749 100.00000 1 3113 1 chr1A.!!$R1 3112
1 TraesCS1A01G162400 chr1B 324600874 324603285 2411 False 3794.0 3794 95.11900 704 3113 1 chr1B.!!$F2 2409
2 TraesCS1A01G162400 chr1D 224572589 224576240 3651 True 1066.5 2806 91.56025 261 3113 4 chr1D.!!$R1 2852

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
152 153 0.177836 CGGGCACTATGGATCACACA 59.822 55.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2443 6.067217 AGTCTACCAAGTAAATTGCATCCT 57.933 37.5 0.0 0.0 37.6 3.24 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
27 28 3.926003 TTTTTGCACGGACTGCCA 58.074 50.000 0.00 0.00 46.51 4.92
28 29 1.732917 TTTTTGCACGGACTGCCAG 59.267 52.632 0.00 0.00 46.51 4.85
29 30 0.749818 TTTTTGCACGGACTGCCAGA 60.750 50.000 0.00 0.00 46.51 3.86
30 31 1.444119 TTTTGCACGGACTGCCAGAC 61.444 55.000 0.00 0.00 46.51 3.51
31 32 2.324014 TTTGCACGGACTGCCAGACT 62.324 55.000 0.00 0.00 46.51 3.24
32 33 2.740055 GCACGGACTGCCAGACTG 60.740 66.667 0.00 0.00 40.42 3.51
33 34 3.051210 CACGGACTGCCAGACTGA 58.949 61.111 9.98 0.00 0.00 3.41
34 35 1.367471 CACGGACTGCCAGACTGAA 59.633 57.895 9.98 0.00 0.00 3.02
35 36 0.249868 CACGGACTGCCAGACTGAAA 60.250 55.000 9.98 0.00 0.00 2.69
36 37 0.687354 ACGGACTGCCAGACTGAAAT 59.313 50.000 9.98 0.00 0.00 2.17
37 38 1.072331 ACGGACTGCCAGACTGAAATT 59.928 47.619 9.98 0.00 0.00 1.82
38 39 1.734465 CGGACTGCCAGACTGAAATTC 59.266 52.381 3.32 0.00 0.00 2.17
39 40 2.613977 CGGACTGCCAGACTGAAATTCT 60.614 50.000 3.32 0.00 0.00 2.40
40 41 3.416156 GGACTGCCAGACTGAAATTCTT 58.584 45.455 3.32 0.00 0.00 2.52
41 42 3.823304 GGACTGCCAGACTGAAATTCTTT 59.177 43.478 3.32 0.00 0.00 2.52
42 43 4.279420 GGACTGCCAGACTGAAATTCTTTT 59.721 41.667 3.32 0.00 0.00 2.27
43 44 5.192327 ACTGCCAGACTGAAATTCTTTTG 57.808 39.130 3.32 0.00 0.00 2.44
44 45 3.981211 TGCCAGACTGAAATTCTTTTGC 58.019 40.909 3.32 0.00 0.00 3.68
45 46 2.982470 GCCAGACTGAAATTCTTTTGCG 59.018 45.455 3.32 0.00 0.00 4.85
46 47 3.304659 GCCAGACTGAAATTCTTTTGCGA 60.305 43.478 3.32 0.00 0.00 5.10
47 48 4.616835 GCCAGACTGAAATTCTTTTGCGAT 60.617 41.667 3.32 0.00 0.00 4.58
48 49 5.091431 CCAGACTGAAATTCTTTTGCGATC 58.909 41.667 3.32 0.00 0.00 3.69
49 50 4.785055 CAGACTGAAATTCTTTTGCGATCG 59.215 41.667 11.69 11.69 0.00 3.69
50 51 4.083581 ACTGAAATTCTTTTGCGATCGG 57.916 40.909 18.30 0.00 0.00 4.18
51 52 3.119849 ACTGAAATTCTTTTGCGATCGGG 60.120 43.478 18.30 0.00 0.00 5.14
52 53 3.078097 TGAAATTCTTTTGCGATCGGGA 58.922 40.909 18.30 0.00 0.00 5.14
53 54 3.694072 TGAAATTCTTTTGCGATCGGGAT 59.306 39.130 18.30 0.00 0.00 3.85
54 55 3.971032 AATTCTTTTGCGATCGGGATC 57.029 42.857 18.30 0.00 34.56 3.36
55 56 2.394930 TTCTTTTGCGATCGGGATCA 57.605 45.000 18.30 2.85 37.69 2.92
56 57 1.939974 TCTTTTGCGATCGGGATCAG 58.060 50.000 18.30 3.52 37.69 2.90
57 58 0.940126 CTTTTGCGATCGGGATCAGG 59.060 55.000 18.30 0.00 37.69 3.86
58 59 1.095228 TTTTGCGATCGGGATCAGGC 61.095 55.000 18.30 5.72 37.69 4.85
59 60 2.250741 TTTGCGATCGGGATCAGGCA 62.251 55.000 18.30 8.01 37.69 4.75
60 61 2.043604 TTGCGATCGGGATCAGGCAT 62.044 55.000 18.30 0.00 35.30 4.40
61 62 2.031516 GCGATCGGGATCAGGCATG 61.032 63.158 18.30 0.00 37.69 4.06
62 63 1.368950 CGATCGGGATCAGGCATGT 59.631 57.895 7.38 0.00 37.69 3.21
63 64 0.603065 CGATCGGGATCAGGCATGTA 59.397 55.000 7.38 0.00 37.69 2.29
64 65 1.000843 CGATCGGGATCAGGCATGTAA 59.999 52.381 7.38 0.00 37.69 2.41
65 66 2.547855 CGATCGGGATCAGGCATGTAAA 60.548 50.000 7.38 0.00 37.69 2.01
66 67 3.476552 GATCGGGATCAGGCATGTAAAA 58.523 45.455 0.00 0.00 37.74 1.52
67 68 3.358111 TCGGGATCAGGCATGTAAAAA 57.642 42.857 0.00 0.00 0.00 1.94
90 91 9.996554 AAAAATTTAAGCATACTAGCCACTTTT 57.003 25.926 0.00 0.00 34.23 2.27
91 92 9.996554 AAAATTTAAGCATACTAGCCACTTTTT 57.003 25.926 0.00 0.00 34.23 1.94
92 93 8.986477 AATTTAAGCATACTAGCCACTTTTTG 57.014 30.769 0.00 0.00 34.23 2.44
93 94 7.753309 TTTAAGCATACTAGCCACTTTTTGA 57.247 32.000 0.00 0.00 34.23 2.69
94 95 7.938140 TTAAGCATACTAGCCACTTTTTGAT 57.062 32.000 0.00 0.00 34.23 2.57
95 96 6.840780 AAGCATACTAGCCACTTTTTGATT 57.159 33.333 0.00 0.00 34.23 2.57
96 97 6.199937 AGCATACTAGCCACTTTTTGATTG 57.800 37.500 0.00 0.00 34.23 2.67
97 98 5.711976 AGCATACTAGCCACTTTTTGATTGT 59.288 36.000 0.00 0.00 34.23 2.71
98 99 6.884295 AGCATACTAGCCACTTTTTGATTGTA 59.116 34.615 0.00 0.00 34.23 2.41
99 100 7.393234 AGCATACTAGCCACTTTTTGATTGTAA 59.607 33.333 0.00 0.00 34.23 2.41
100 101 8.190784 GCATACTAGCCACTTTTTGATTGTAAT 58.809 33.333 0.00 0.00 0.00 1.89
103 104 7.378181 ACTAGCCACTTTTTGATTGTAATTGG 58.622 34.615 0.00 0.00 0.00 3.16
104 105 6.418057 AGCCACTTTTTGATTGTAATTGGA 57.582 33.333 0.00 0.00 0.00 3.53
105 106 6.223120 AGCCACTTTTTGATTGTAATTGGAC 58.777 36.000 0.00 0.00 0.00 4.02
106 107 5.988561 GCCACTTTTTGATTGTAATTGGACA 59.011 36.000 0.00 0.00 0.00 4.02
107 108 6.650390 GCCACTTTTTGATTGTAATTGGACAT 59.350 34.615 0.00 0.00 0.00 3.06
108 109 7.360269 GCCACTTTTTGATTGTAATTGGACATG 60.360 37.037 0.00 0.00 0.00 3.21
109 110 7.656948 CCACTTTTTGATTGTAATTGGACATGT 59.343 33.333 0.00 0.00 0.00 3.21
110 111 8.489559 CACTTTTTGATTGTAATTGGACATGTG 58.510 33.333 1.15 0.00 0.00 3.21
111 112 8.420222 ACTTTTTGATTGTAATTGGACATGTGA 58.580 29.630 1.15 0.00 0.00 3.58
112 113 9.426837 CTTTTTGATTGTAATTGGACATGTGAT 57.573 29.630 1.15 0.00 0.00 3.06
113 114 8.984891 TTTTGATTGTAATTGGACATGTGATC 57.015 30.769 1.15 0.00 0.00 2.92
114 115 6.698008 TGATTGTAATTGGACATGTGATCC 57.302 37.500 1.15 0.00 36.70 3.36
115 116 5.296531 TGATTGTAATTGGACATGTGATCCG 59.703 40.000 1.15 0.00 39.30 4.18
116 117 3.540617 TGTAATTGGACATGTGATCCGG 58.459 45.455 1.15 0.00 39.30 5.14
117 118 1.392589 AATTGGACATGTGATCCGGC 58.607 50.000 1.15 0.00 39.30 6.13
118 119 0.815213 ATTGGACATGTGATCCGGCG 60.815 55.000 1.15 0.00 39.30 6.46
119 120 3.272334 GGACATGTGATCCGGCGC 61.272 66.667 1.15 0.00 0.00 6.53
120 121 2.202932 GACATGTGATCCGGCGCT 60.203 61.111 7.64 0.00 0.00 5.92
121 122 2.512286 ACATGTGATCCGGCGCTG 60.512 61.111 9.96 9.96 0.00 5.18
122 123 3.274586 CATGTGATCCGGCGCTGG 61.275 66.667 30.18 30.18 0.00 4.85
123 124 4.552365 ATGTGATCCGGCGCTGGG 62.552 66.667 34.26 22.33 0.00 4.45
142 143 2.645567 CGATCTCGCGGGCACTAT 59.354 61.111 6.13 0.00 0.00 2.12
143 144 1.730902 CGATCTCGCGGGCACTATG 60.731 63.158 6.13 0.00 0.00 2.23
144 145 1.373497 GATCTCGCGGGCACTATGG 60.373 63.158 6.13 0.00 0.00 2.74
145 146 1.806461 GATCTCGCGGGCACTATGGA 61.806 60.000 6.13 0.00 0.00 3.41
146 147 1.188219 ATCTCGCGGGCACTATGGAT 61.188 55.000 6.13 0.00 0.00 3.41
147 148 1.373497 CTCGCGGGCACTATGGATC 60.373 63.158 6.13 0.00 0.00 3.36
148 149 2.087462 CTCGCGGGCACTATGGATCA 62.087 60.000 6.13 0.00 0.00 2.92
149 150 1.956170 CGCGGGCACTATGGATCAC 60.956 63.158 0.00 0.00 0.00 3.06
150 151 1.146041 GCGGGCACTATGGATCACA 59.854 57.895 0.00 0.00 0.00 3.58
151 152 1.160329 GCGGGCACTATGGATCACAC 61.160 60.000 0.00 0.00 0.00 3.82
152 153 0.177836 CGGGCACTATGGATCACACA 59.822 55.000 0.00 0.00 0.00 3.72
153 154 1.406751 CGGGCACTATGGATCACACAA 60.407 52.381 0.00 0.00 0.00 3.33
154 155 2.292267 GGGCACTATGGATCACACAAG 58.708 52.381 0.00 0.00 0.00 3.16
155 156 2.092968 GGGCACTATGGATCACACAAGA 60.093 50.000 0.00 0.00 0.00 3.02
156 157 3.434167 GGGCACTATGGATCACACAAGAT 60.434 47.826 0.00 0.00 0.00 2.40
157 158 4.202441 GGCACTATGGATCACACAAGATT 58.798 43.478 0.00 0.00 0.00 2.40
158 159 4.641989 GGCACTATGGATCACACAAGATTT 59.358 41.667 0.00 0.00 0.00 2.17
159 160 5.449588 GGCACTATGGATCACACAAGATTTG 60.450 44.000 0.00 0.00 0.00 2.32
160 161 5.355071 GCACTATGGATCACACAAGATTTGA 59.645 40.000 0.00 0.00 0.00 2.69
161 162 6.127925 GCACTATGGATCACACAAGATTTGAA 60.128 38.462 0.00 0.00 0.00 2.69
162 163 7.246311 CACTATGGATCACACAAGATTTGAAC 58.754 38.462 0.00 0.00 0.00 3.18
163 164 7.120285 CACTATGGATCACACAAGATTTGAACT 59.880 37.037 0.00 0.00 0.00 3.01
164 165 6.906157 ATGGATCACACAAGATTTGAACTT 57.094 33.333 0.00 0.00 0.00 2.66
165 166 6.317789 TGGATCACACAAGATTTGAACTTC 57.682 37.500 0.00 0.00 0.00 3.01
166 167 5.827267 TGGATCACACAAGATTTGAACTTCA 59.173 36.000 0.00 0.00 0.00 3.02
167 168 6.320926 TGGATCACACAAGATTTGAACTTCAA 59.679 34.615 0.00 0.00 34.03 2.69
168 169 7.014518 TGGATCACACAAGATTTGAACTTCAAT 59.985 33.333 5.03 0.00 36.11 2.57
169 170 7.869429 GGATCACACAAGATTTGAACTTCAATT 59.131 33.333 5.03 2.13 36.11 2.32
170 171 9.252962 GATCACACAAGATTTGAACTTCAATTT 57.747 29.630 5.03 0.00 36.11 1.82
172 173 9.515020 TCACACAAGATTTGAACTTCAATTTAC 57.485 29.630 5.03 0.00 36.11 2.01
173 174 9.520204 CACACAAGATTTGAACTTCAATTTACT 57.480 29.630 5.03 1.12 36.11 2.24
183 184 8.865590 TGAACTTCAATTTACTTTTTACTGGC 57.134 30.769 0.00 0.00 0.00 4.85
184 185 7.646130 TGAACTTCAATTTACTTTTTACTGGCG 59.354 33.333 0.00 0.00 0.00 5.69
185 186 6.443792 ACTTCAATTTACTTTTTACTGGCGG 58.556 36.000 0.00 0.00 0.00 6.13
186 187 6.263617 ACTTCAATTTACTTTTTACTGGCGGA 59.736 34.615 0.00 0.00 0.00 5.54
187 188 6.004408 TCAATTTACTTTTTACTGGCGGAC 57.996 37.500 0.00 0.00 0.00 4.79
188 189 5.531659 TCAATTTACTTTTTACTGGCGGACA 59.468 36.000 0.00 0.00 0.00 4.02
189 190 6.207810 TCAATTTACTTTTTACTGGCGGACAT 59.792 34.615 0.00 0.00 0.00 3.06
190 191 7.390996 TCAATTTACTTTTTACTGGCGGACATA 59.609 33.333 0.00 0.00 0.00 2.29
191 192 7.875327 ATTTACTTTTTACTGGCGGACATAT 57.125 32.000 0.00 0.00 0.00 1.78
192 193 8.967664 ATTTACTTTTTACTGGCGGACATATA 57.032 30.769 0.00 0.00 0.00 0.86
193 194 8.967664 TTTACTTTTTACTGGCGGACATATAT 57.032 30.769 0.00 0.00 0.00 0.86
196 197 8.547967 ACTTTTTACTGGCGGACATATATATG 57.452 34.615 19.21 19.21 39.55 1.78
197 198 8.372459 ACTTTTTACTGGCGGACATATATATGA 58.628 33.333 26.05 4.81 37.15 2.15
198 199 9.383519 CTTTTTACTGGCGGACATATATATGAT 57.616 33.333 26.05 12.31 37.15 2.45
201 202 6.090483 ACTGGCGGACATATATATGATAGC 57.910 41.667 26.05 23.21 37.15 2.97
202 203 5.598417 ACTGGCGGACATATATATGATAGCA 59.402 40.000 26.05 15.78 37.15 3.49
203 204 6.268617 ACTGGCGGACATATATATGATAGCAT 59.731 38.462 26.05 13.99 37.15 3.79
204 205 7.066307 TGGCGGACATATATATGATAGCATT 57.934 36.000 26.05 4.78 37.15 3.56
205 206 7.154656 TGGCGGACATATATATGATAGCATTC 58.845 38.462 26.05 12.61 37.15 2.67
206 207 6.309009 GGCGGACATATATATGATAGCATTCG 59.691 42.308 26.05 15.04 37.15 3.34
207 208 7.084486 GCGGACATATATATGATAGCATTCGA 58.916 38.462 26.05 0.00 37.15 3.71
208 209 7.757173 GCGGACATATATATGATAGCATTCGAT 59.243 37.037 26.05 2.24 37.15 3.59
209 210 9.070149 CGGACATATATATGATAGCATTCGATG 57.930 37.037 26.05 1.45 37.15 3.84
210 211 9.363763 GGACATATATATGATAGCATTCGATGG 57.636 37.037 26.05 0.00 37.15 3.51
211 212 8.768957 ACATATATATGATAGCATTCGATGGC 57.231 34.615 26.05 0.87 37.15 4.40
212 213 7.821359 ACATATATATGATAGCATTCGATGGCC 59.179 37.037 26.05 0.00 37.15 5.36
213 214 1.730501 ATGATAGCATTCGATGGCCG 58.269 50.000 0.00 0.00 40.25 6.13
214 215 0.320683 TGATAGCATTCGATGGCCGG 60.321 55.000 0.00 0.00 39.14 6.13
215 216 1.639298 GATAGCATTCGATGGCCGGC 61.639 60.000 21.18 21.18 39.14 6.13
216 217 2.116983 ATAGCATTCGATGGCCGGCT 62.117 55.000 28.56 7.30 37.18 5.52
217 218 2.715532 TAGCATTCGATGGCCGGCTC 62.716 60.000 28.56 16.48 35.50 4.70
218 219 2.974698 CATTCGATGGCCGGCTCC 60.975 66.667 28.56 11.61 39.14 4.70
219 220 4.256180 ATTCGATGGCCGGCTCCC 62.256 66.667 28.56 10.74 39.14 4.30
229 230 4.457496 CGGCTCCCGCATCAGTGT 62.457 66.667 0.00 0.00 41.17 3.55
230 231 2.512515 GGCTCCCGCATCAGTGTC 60.513 66.667 0.00 0.00 38.10 3.67
231 232 2.512515 GCTCCCGCATCAGTGTCC 60.513 66.667 0.00 0.00 35.78 4.02
232 233 2.202797 CTCCCGCATCAGTGTCCG 60.203 66.667 0.00 0.00 0.00 4.79
233 234 4.451150 TCCCGCATCAGTGTCCGC 62.451 66.667 0.00 0.00 0.00 5.54
236 237 4.794439 CGCATCAGTGTCCGCGGA 62.794 66.667 27.28 27.28 43.84 5.54
237 238 2.202932 GCATCAGTGTCCGCGGAT 60.203 61.111 33.58 13.52 0.00 4.18
238 239 1.815421 GCATCAGTGTCCGCGGATT 60.815 57.895 33.58 17.47 0.00 3.01
239 240 2.009108 CATCAGTGTCCGCGGATTG 58.991 57.895 33.58 27.29 0.00 2.67
240 241 0.460109 CATCAGTGTCCGCGGATTGA 60.460 55.000 33.58 31.05 0.00 2.57
241 242 0.465705 ATCAGTGTCCGCGGATTGAT 59.534 50.000 33.58 31.72 0.00 2.57
242 243 0.249120 TCAGTGTCCGCGGATTGATT 59.751 50.000 33.58 12.46 0.00 2.57
243 244 0.652592 CAGTGTCCGCGGATTGATTC 59.347 55.000 33.58 17.93 0.00 2.52
244 245 0.462047 AGTGTCCGCGGATTGATTCC 60.462 55.000 33.58 17.12 41.59 3.01
245 246 1.153249 TGTCCGCGGATTGATTCCC 60.153 57.895 33.58 16.31 42.06 3.97
246 247 1.146263 GTCCGCGGATTGATTCCCT 59.854 57.895 33.58 0.00 42.06 4.20
247 248 0.880718 GTCCGCGGATTGATTCCCTC 60.881 60.000 33.58 10.49 42.06 4.30
248 249 1.048724 TCCGCGGATTGATTCCCTCT 61.049 55.000 27.28 0.00 42.06 3.69
249 250 0.179045 CCGCGGATTGATTCCCTCTT 60.179 55.000 24.07 0.00 42.06 2.85
250 251 1.070134 CCGCGGATTGATTCCCTCTTA 59.930 52.381 24.07 0.00 42.06 2.10
251 252 2.408050 CGCGGATTGATTCCCTCTTAG 58.592 52.381 0.00 0.00 42.06 2.18
252 253 2.772287 GCGGATTGATTCCCTCTTAGG 58.228 52.381 0.00 0.00 42.06 2.69
253 254 2.772287 CGGATTGATTCCCTCTTAGGC 58.228 52.381 0.00 0.00 42.06 3.93
254 255 2.104792 CGGATTGATTCCCTCTTAGGCA 59.895 50.000 0.00 0.00 42.06 4.75
255 256 3.433598 CGGATTGATTCCCTCTTAGGCAA 60.434 47.826 0.00 0.00 42.06 4.52
256 257 4.536765 GGATTGATTCCCTCTTAGGCAAA 58.463 43.478 0.00 0.00 38.75 3.68
257 258 4.339530 GGATTGATTCCCTCTTAGGCAAAC 59.660 45.833 0.00 0.00 38.75 2.93
258 259 2.985896 TGATTCCCTCTTAGGCAAACG 58.014 47.619 0.00 0.00 32.73 3.60
259 260 2.289565 GATTCCCTCTTAGGCAAACGG 58.710 52.381 0.00 0.00 32.73 4.44
297 298 1.600957 GCATGTCAACGATGGAGATGG 59.399 52.381 12.09 0.00 36.75 3.51
368 373 9.275398 ACTTTTGCAATCAATTCACATAATGTT 57.725 25.926 0.00 0.00 31.33 2.71
405 410 7.010367 ACAAAACTTTCACACAACATATTGCTG 59.990 33.333 0.00 0.00 39.66 4.41
407 412 3.574284 TTCACACAACATATTGCTGCC 57.426 42.857 0.00 0.00 39.66 4.85
408 413 1.818060 TCACACAACATATTGCTGCCC 59.182 47.619 0.00 0.00 39.66 5.36
409 414 0.810648 ACACAACATATTGCTGCCCG 59.189 50.000 0.00 0.00 39.66 6.13
411 416 0.810648 ACAACATATTGCTGCCCGTG 59.189 50.000 0.00 0.00 39.66 4.94
449 454 3.559655 GCCTTTTTCCACAAACCATCAAC 59.440 43.478 0.00 0.00 0.00 3.18
460 466 5.047188 ACAAACCATCAACGGTGAAAATTC 58.953 37.500 7.51 0.00 39.95 2.17
462 468 3.496331 ACCATCAACGGTGAAAATTCCT 58.504 40.909 7.51 0.00 38.07 3.36
510 516 8.630278 AGATAATTAAGTTATATACGCGCTGG 57.370 34.615 5.73 0.00 33.16 4.85
515 521 1.909532 GTTATATACGCGCTGGCTACG 59.090 52.381 5.73 3.94 36.88 3.51
521 527 2.736995 GCGCTGGCTACGTGTCAA 60.737 61.111 0.00 0.00 35.83 3.18
549 555 1.069427 TGTTTGCAACATGGCCTGC 59.931 52.632 3.32 5.93 36.25 4.85
554 560 1.154035 GCAACATGGCCTGCGTTAC 60.154 57.895 3.32 0.00 0.00 2.50
575 592 3.573538 ACAAACTCATGCCTAATGTTGCA 59.426 39.130 0.00 0.00 42.52 4.08
594 611 5.843673 TGCAAACTTGTTGGTCAATCTTA 57.156 34.783 0.00 0.00 35.35 2.10
598 615 6.682861 GCAAACTTGTTGGTCAATCTTACCTT 60.683 38.462 0.00 0.00 37.91 3.50
599 616 6.391227 AACTTGTTGGTCAATCTTACCTTG 57.609 37.500 0.00 0.00 37.91 3.61
608 652 5.064834 GGTCAATCTTACCTTGAATCGAACC 59.935 44.000 0.00 0.00 34.59 3.62
629 673 1.486310 GCCACTGAGGTGATGGATACA 59.514 52.381 0.00 0.00 45.79 2.29
654 698 1.347707 AGTCATCAGCCGGTTGAAAGA 59.652 47.619 25.48 21.41 0.00 2.52
657 701 3.938963 GTCATCAGCCGGTTGAAAGATAA 59.061 43.478 25.48 0.00 0.00 1.75
659 703 3.695830 TCAGCCGGTTGAAAGATAACT 57.304 42.857 19.64 0.00 0.00 2.24
660 704 4.015872 TCAGCCGGTTGAAAGATAACTT 57.984 40.909 19.64 0.00 38.05 2.66
663 707 5.300792 TCAGCCGGTTGAAAGATAACTTTTT 59.699 36.000 19.64 0.00 44.97 1.94
666 710 6.713450 AGCCGGTTGAAAGATAACTTTTTCTA 59.287 34.615 1.90 0.00 44.97 2.10
667 711 7.229907 AGCCGGTTGAAAGATAACTTTTTCTAA 59.770 33.333 1.90 0.00 44.97 2.10
668 712 7.863877 GCCGGTTGAAAGATAACTTTTTCTAAA 59.136 33.333 1.90 0.00 44.97 1.85
702 751 5.028375 GTGAAAATACCAGTAAATCGCTGC 58.972 41.667 0.00 0.00 32.93 5.25
760 811 3.596310 TGACACGAAATCAACCCGATA 57.404 42.857 0.00 0.00 32.51 2.92
771 822 7.460896 CGAAATCAACCCGATAAACAAAATTCG 60.461 37.037 0.00 0.00 32.51 3.34
834 885 7.845066 AATCAATCGGAAACTAACTAACCTC 57.155 36.000 0.00 0.00 0.00 3.85
835 886 6.600882 TCAATCGGAAACTAACTAACCTCT 57.399 37.500 0.00 0.00 0.00 3.69
836 887 6.628185 TCAATCGGAAACTAACTAACCTCTC 58.372 40.000 0.00 0.00 0.00 3.20
951 1224 2.838202 AGAGCCGAAGACCTAAATTCCA 59.162 45.455 0.00 0.00 0.00 3.53
1161 1434 2.037527 GAGGAGGTCACCGTCCCT 59.962 66.667 5.30 5.30 45.01 4.20
1239 1512 3.288290 CCGTCCCGATCCTCCTCG 61.288 72.222 0.00 0.00 38.37 4.63
1242 1515 1.453379 GTCCCGATCCTCCTCGTCA 60.453 63.158 0.00 0.00 36.93 4.35
1246 1519 1.576920 CGATCCTCCTCGTCATCCG 59.423 63.158 0.00 0.00 34.00 4.18
2170 2443 8.839343 CATCATATAACACAGCCTTTTGTATCA 58.161 33.333 0.00 0.00 0.00 2.15
2386 2660 5.230306 GCTATAGTACAAACTTGACTGCTCG 59.770 44.000 0.84 0.00 37.15 5.03
2439 2713 6.304126 GTGGTTTTGTGTCATTGTAGTATCG 58.696 40.000 0.00 0.00 0.00 2.92
2442 2716 3.173668 TGTGTCATTGTAGTATCGGCC 57.826 47.619 0.00 0.00 0.00 6.13
2710 3560 8.626526 GGAAGAGGAACAACATAGTTTTAACAA 58.373 33.333 0.00 0.00 0.00 2.83
2753 3603 1.147824 CAGGGATGAGCTTCGCCAT 59.852 57.895 0.00 0.00 0.00 4.40
2777 3627 2.365635 GCACCTGGGAGCCCTAGA 60.366 66.667 7.16 0.00 36.94 2.43
2902 3754 2.770589 GCCTGTGTGTTGCAACGGT 61.771 57.895 23.79 0.00 0.00 4.83
2948 3800 5.718801 TTACCTGCCCATATTTGGTAAGA 57.281 39.130 1.26 0.00 41.91 2.10
3022 3874 4.475135 GGCAGGGAGGCGGTCTTC 62.475 72.222 0.00 0.00 33.57 2.87
3029 3881 1.219393 GAGGCGGTCTTCAGGGAAG 59.781 63.158 0.00 0.00 40.65 3.46
3052 3905 4.770795 ACCGATAGAAAAACCAGAGATGG 58.229 43.478 0.00 0.00 39.76 3.51
3086 3947 1.119684 GAAGAGGGAGAGGAAGGAGC 58.880 60.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.249868 TTTCAGTCTGGCAGTCCGTG 60.250 55.000 15.27 7.95 34.14 4.94
17 18 0.687354 ATTTCAGTCTGGCAGTCCGT 59.313 50.000 15.27 0.00 34.14 4.69
18 19 1.734465 GAATTTCAGTCTGGCAGTCCG 59.266 52.381 15.27 0.99 34.14 4.79
19 20 3.064900 AGAATTTCAGTCTGGCAGTCC 57.935 47.619 15.27 6.61 0.00 3.85
20 21 5.218139 CAAAAGAATTTCAGTCTGGCAGTC 58.782 41.667 15.27 9.24 37.28 3.51
21 22 4.500375 GCAAAAGAATTTCAGTCTGGCAGT 60.500 41.667 15.27 0.00 37.28 4.40
22 23 3.985925 GCAAAAGAATTTCAGTCTGGCAG 59.014 43.478 8.58 8.58 37.28 4.85
23 24 3.550639 CGCAAAAGAATTTCAGTCTGGCA 60.551 43.478 0.00 0.00 37.28 4.92
24 25 2.982470 CGCAAAAGAATTTCAGTCTGGC 59.018 45.455 0.00 0.00 37.28 4.85
25 26 4.488126 TCGCAAAAGAATTTCAGTCTGG 57.512 40.909 0.00 0.00 37.28 3.86
26 27 4.785055 CGATCGCAAAAGAATTTCAGTCTG 59.215 41.667 0.26 0.00 37.28 3.51
27 28 4.142816 CCGATCGCAAAAGAATTTCAGTCT 60.143 41.667 10.32 0.00 37.28 3.24
28 29 4.091424 CCGATCGCAAAAGAATTTCAGTC 58.909 43.478 10.32 0.00 37.28 3.51
29 30 3.119849 CCCGATCGCAAAAGAATTTCAGT 60.120 43.478 10.32 0.00 37.28 3.41
30 31 3.126858 TCCCGATCGCAAAAGAATTTCAG 59.873 43.478 10.32 0.00 37.28 3.02
31 32 3.078097 TCCCGATCGCAAAAGAATTTCA 58.922 40.909 10.32 0.00 37.28 2.69
32 33 3.757745 TCCCGATCGCAAAAGAATTTC 57.242 42.857 10.32 0.00 37.28 2.17
33 34 3.694072 TGATCCCGATCGCAAAAGAATTT 59.306 39.130 10.32 0.00 39.50 1.82
34 35 3.278574 TGATCCCGATCGCAAAAGAATT 58.721 40.909 10.32 0.00 40.63 2.17
35 36 2.874701 CTGATCCCGATCGCAAAAGAAT 59.125 45.455 10.32 0.00 40.63 2.40
36 37 2.279741 CTGATCCCGATCGCAAAAGAA 58.720 47.619 10.32 0.00 40.63 2.52
37 38 1.473257 CCTGATCCCGATCGCAAAAGA 60.473 52.381 10.32 1.04 40.63 2.52
38 39 0.940126 CCTGATCCCGATCGCAAAAG 59.060 55.000 10.32 2.97 40.63 2.27
39 40 1.095228 GCCTGATCCCGATCGCAAAA 61.095 55.000 10.32 0.00 40.63 2.44
40 41 1.523711 GCCTGATCCCGATCGCAAA 60.524 57.895 10.32 0.00 40.63 3.68
41 42 2.043604 ATGCCTGATCCCGATCGCAA 62.044 55.000 10.32 0.00 40.63 4.85
42 43 2.510551 ATGCCTGATCCCGATCGCA 61.511 57.895 10.32 8.94 40.63 5.10
43 44 2.031516 CATGCCTGATCCCGATCGC 61.032 63.158 10.32 0.00 40.63 4.58
44 45 0.603065 TACATGCCTGATCCCGATCG 59.397 55.000 8.51 8.51 40.63 3.69
45 46 2.839486 TTACATGCCTGATCCCGATC 57.161 50.000 0.00 0.00 38.29 3.69
46 47 3.576078 TTTTACATGCCTGATCCCGAT 57.424 42.857 0.00 0.00 0.00 4.18
47 48 3.358111 TTTTTACATGCCTGATCCCGA 57.642 42.857 0.00 0.00 0.00 5.14
64 65 9.996554 AAAAGTGGCTAGTATGCTTAAATTTTT 57.003 25.926 0.00 0.00 0.00 1.94
65 66 9.996554 AAAAAGTGGCTAGTATGCTTAAATTTT 57.003 25.926 0.00 0.00 0.00 1.82
66 67 9.423061 CAAAAAGTGGCTAGTATGCTTAAATTT 57.577 29.630 0.00 0.00 0.00 1.82
67 68 8.802267 TCAAAAAGTGGCTAGTATGCTTAAATT 58.198 29.630 0.00 0.00 0.00 1.82
68 69 8.348285 TCAAAAAGTGGCTAGTATGCTTAAAT 57.652 30.769 0.00 0.00 0.00 1.40
69 70 7.753309 TCAAAAAGTGGCTAGTATGCTTAAA 57.247 32.000 0.00 0.00 0.00 1.52
70 71 7.938140 ATCAAAAAGTGGCTAGTATGCTTAA 57.062 32.000 0.00 0.00 0.00 1.85
71 72 7.393234 ACAATCAAAAAGTGGCTAGTATGCTTA 59.607 33.333 0.00 0.00 0.00 3.09
72 73 6.209391 ACAATCAAAAAGTGGCTAGTATGCTT 59.791 34.615 0.00 0.00 0.00 3.91
73 74 5.711976 ACAATCAAAAAGTGGCTAGTATGCT 59.288 36.000 0.00 0.00 0.00 3.79
74 75 5.954335 ACAATCAAAAAGTGGCTAGTATGC 58.046 37.500 0.00 0.00 0.00 3.14
77 78 8.519526 CCAATTACAATCAAAAAGTGGCTAGTA 58.480 33.333 0.00 0.00 32.35 1.82
78 79 7.232534 TCCAATTACAATCAAAAAGTGGCTAGT 59.767 33.333 0.00 0.00 38.05 2.57
79 80 7.542130 GTCCAATTACAATCAAAAAGTGGCTAG 59.458 37.037 0.00 0.00 38.05 3.42
80 81 7.014711 TGTCCAATTACAATCAAAAAGTGGCTA 59.985 33.333 0.00 0.00 38.05 3.93
81 82 6.183360 TGTCCAATTACAATCAAAAAGTGGCT 60.183 34.615 0.00 0.00 38.05 4.75
82 83 5.988561 TGTCCAATTACAATCAAAAAGTGGC 59.011 36.000 0.00 0.00 38.05 5.01
83 84 7.656948 ACATGTCCAATTACAATCAAAAAGTGG 59.343 33.333 0.00 0.00 39.18 4.00
84 85 8.489559 CACATGTCCAATTACAATCAAAAAGTG 58.510 33.333 0.00 0.00 32.02 3.16
85 86 8.420222 TCACATGTCCAATTACAATCAAAAAGT 58.580 29.630 0.00 0.00 32.02 2.66
86 87 8.815141 TCACATGTCCAATTACAATCAAAAAG 57.185 30.769 0.00 0.00 32.02 2.27
87 88 9.421806 GATCACATGTCCAATTACAATCAAAAA 57.578 29.630 0.00 0.00 32.02 1.94
88 89 8.034215 GGATCACATGTCCAATTACAATCAAAA 58.966 33.333 0.00 0.00 35.76 2.44
89 90 7.546358 GGATCACATGTCCAATTACAATCAAA 58.454 34.615 0.00 0.00 35.76 2.69
90 91 6.183360 CGGATCACATGTCCAATTACAATCAA 60.183 38.462 0.00 0.00 35.41 2.57
91 92 5.296531 CGGATCACATGTCCAATTACAATCA 59.703 40.000 0.00 0.00 35.41 2.57
92 93 5.277974 CCGGATCACATGTCCAATTACAATC 60.278 44.000 0.00 0.00 35.41 2.67
93 94 4.580167 CCGGATCACATGTCCAATTACAAT 59.420 41.667 0.00 0.00 35.41 2.71
94 95 3.944650 CCGGATCACATGTCCAATTACAA 59.055 43.478 0.00 0.00 35.41 2.41
95 96 3.540617 CCGGATCACATGTCCAATTACA 58.459 45.455 0.00 0.00 35.41 2.41
96 97 2.290641 GCCGGATCACATGTCCAATTAC 59.709 50.000 5.05 0.00 35.41 1.89
97 98 2.571212 GCCGGATCACATGTCCAATTA 58.429 47.619 5.05 0.00 35.41 1.40
98 99 1.392589 GCCGGATCACATGTCCAATT 58.607 50.000 5.05 0.00 35.41 2.32
99 100 0.815213 CGCCGGATCACATGTCCAAT 60.815 55.000 5.05 0.00 35.41 3.16
100 101 1.449423 CGCCGGATCACATGTCCAA 60.449 57.895 5.05 0.00 35.41 3.53
101 102 2.186644 CGCCGGATCACATGTCCA 59.813 61.111 5.05 0.00 35.41 4.02
102 103 3.272334 GCGCCGGATCACATGTCC 61.272 66.667 5.05 0.00 0.00 4.02
103 104 2.202932 AGCGCCGGATCACATGTC 60.203 61.111 5.05 0.00 0.00 3.06
104 105 2.512286 CAGCGCCGGATCACATGT 60.512 61.111 5.05 0.00 0.00 3.21
105 106 3.274586 CCAGCGCCGGATCACATG 61.275 66.667 5.05 0.00 0.00 3.21
106 107 4.552365 CCCAGCGCCGGATCACAT 62.552 66.667 12.38 0.00 0.00 3.21
125 126 1.730902 CATAGTGCCCGCGAGATCG 60.731 63.158 8.23 0.00 43.27 3.69
126 127 1.373497 CCATAGTGCCCGCGAGATC 60.373 63.158 8.23 0.00 0.00 2.75
127 128 1.188219 ATCCATAGTGCCCGCGAGAT 61.188 55.000 8.23 0.00 0.00 2.75
128 129 1.806461 GATCCATAGTGCCCGCGAGA 61.806 60.000 8.23 0.00 0.00 4.04
129 130 1.373497 GATCCATAGTGCCCGCGAG 60.373 63.158 8.23 0.00 0.00 5.03
130 131 2.131067 TGATCCATAGTGCCCGCGA 61.131 57.895 8.23 0.00 0.00 5.87
131 132 1.956170 GTGATCCATAGTGCCCGCG 60.956 63.158 0.00 0.00 0.00 6.46
132 133 1.146041 TGTGATCCATAGTGCCCGC 59.854 57.895 0.00 0.00 0.00 6.13
133 134 0.177836 TGTGTGATCCATAGTGCCCG 59.822 55.000 0.00 0.00 0.00 6.13
134 135 2.092968 TCTTGTGTGATCCATAGTGCCC 60.093 50.000 0.00 0.00 0.00 5.36
135 136 3.266510 TCTTGTGTGATCCATAGTGCC 57.733 47.619 0.00 0.00 0.00 5.01
136 137 5.355071 TCAAATCTTGTGTGATCCATAGTGC 59.645 40.000 0.00 0.00 0.00 4.40
137 138 6.990341 TCAAATCTTGTGTGATCCATAGTG 57.010 37.500 0.00 0.00 0.00 2.74
138 139 7.170965 AGTTCAAATCTTGTGTGATCCATAGT 58.829 34.615 0.00 0.00 0.00 2.12
139 140 7.621428 AGTTCAAATCTTGTGTGATCCATAG 57.379 36.000 0.00 0.00 0.00 2.23
140 141 7.665145 TGAAGTTCAAATCTTGTGTGATCCATA 59.335 33.333 2.20 0.00 0.00 2.74
141 142 6.491062 TGAAGTTCAAATCTTGTGTGATCCAT 59.509 34.615 2.20 0.00 0.00 3.41
142 143 5.827267 TGAAGTTCAAATCTTGTGTGATCCA 59.173 36.000 2.20 0.00 0.00 3.41
143 144 6.317789 TGAAGTTCAAATCTTGTGTGATCC 57.682 37.500 2.20 0.00 0.00 3.36
144 145 8.807667 AATTGAAGTTCAAATCTTGTGTGATC 57.192 30.769 21.57 0.00 40.12 2.92
146 147 9.515020 GTAAATTGAAGTTCAAATCTTGTGTGA 57.485 29.630 21.57 0.00 40.12 3.58
147 148 9.520204 AGTAAATTGAAGTTCAAATCTTGTGTG 57.480 29.630 21.57 0.00 40.12 3.82
157 158 9.308318 GCCAGTAAAAAGTAAATTGAAGTTCAA 57.692 29.630 20.14 20.14 41.09 2.69
158 159 7.646130 CGCCAGTAAAAAGTAAATTGAAGTTCA 59.354 33.333 0.08 0.08 0.00 3.18
159 160 7.114388 CCGCCAGTAAAAAGTAAATTGAAGTTC 59.886 37.037 0.00 0.00 0.00 3.01
160 161 6.921307 CCGCCAGTAAAAAGTAAATTGAAGTT 59.079 34.615 0.00 0.00 0.00 2.66
161 162 6.263617 TCCGCCAGTAAAAAGTAAATTGAAGT 59.736 34.615 0.00 0.00 0.00 3.01
162 163 6.581166 GTCCGCCAGTAAAAAGTAAATTGAAG 59.419 38.462 0.00 0.00 0.00 3.02
163 164 6.039493 TGTCCGCCAGTAAAAAGTAAATTGAA 59.961 34.615 0.00 0.00 0.00 2.69
164 165 5.531659 TGTCCGCCAGTAAAAAGTAAATTGA 59.468 36.000 0.00 0.00 0.00 2.57
165 166 5.764131 TGTCCGCCAGTAAAAAGTAAATTG 58.236 37.500 0.00 0.00 0.00 2.32
166 167 6.584185 ATGTCCGCCAGTAAAAAGTAAATT 57.416 33.333 0.00 0.00 0.00 1.82
167 168 7.875327 ATATGTCCGCCAGTAAAAAGTAAAT 57.125 32.000 0.00 0.00 0.00 1.40
168 169 8.967664 ATATATGTCCGCCAGTAAAAAGTAAA 57.032 30.769 0.00 0.00 0.00 2.01
170 171 9.647797 CATATATATGTCCGCCAGTAAAAAGTA 57.352 33.333 13.69 0.00 0.00 2.24
171 172 8.372459 TCATATATATGTCCGCCAGTAAAAAGT 58.628 33.333 19.78 0.00 35.26 2.66
172 173 8.771920 TCATATATATGTCCGCCAGTAAAAAG 57.228 34.615 19.78 0.00 35.26 2.27
175 176 8.141909 GCTATCATATATATGTCCGCCAGTAAA 58.858 37.037 19.78 0.00 35.26 2.01
176 177 7.286775 TGCTATCATATATATGTCCGCCAGTAA 59.713 37.037 19.78 0.20 35.26 2.24
177 178 6.775629 TGCTATCATATATATGTCCGCCAGTA 59.224 38.462 19.78 8.03 35.26 2.74
178 179 5.598417 TGCTATCATATATATGTCCGCCAGT 59.402 40.000 19.78 3.48 35.26 4.00
179 180 6.089249 TGCTATCATATATATGTCCGCCAG 57.911 41.667 19.78 11.06 35.26 4.85
180 181 6.670695 ATGCTATCATATATATGTCCGCCA 57.329 37.500 19.78 12.83 35.26 5.69
181 182 6.309009 CGAATGCTATCATATATATGTCCGCC 59.691 42.308 19.78 8.64 35.26 6.13
182 183 7.084486 TCGAATGCTATCATATATATGTCCGC 58.916 38.462 19.78 18.58 35.26 5.54
183 184 9.070149 CATCGAATGCTATCATATATATGTCCG 57.930 37.037 19.78 11.33 35.26 4.79
184 185 9.363763 CCATCGAATGCTATCATATATATGTCC 57.636 37.037 19.78 9.20 35.26 4.02
185 186 8.867935 GCCATCGAATGCTATCATATATATGTC 58.132 37.037 19.78 9.17 35.26 3.06
186 187 7.821359 GGCCATCGAATGCTATCATATATATGT 59.179 37.037 19.78 11.32 35.26 2.29
187 188 7.009907 CGGCCATCGAATGCTATCATATATATG 59.990 40.741 15.47 15.47 42.43 1.78
188 189 7.038048 CGGCCATCGAATGCTATCATATATAT 58.962 38.462 2.24 0.00 42.43 0.86
189 190 6.389906 CGGCCATCGAATGCTATCATATATA 58.610 40.000 2.24 0.00 42.43 0.86
190 191 5.233225 CGGCCATCGAATGCTATCATATAT 58.767 41.667 2.24 0.00 42.43 0.86
191 192 4.501400 CCGGCCATCGAATGCTATCATATA 60.501 45.833 2.24 0.00 42.43 0.86
192 193 3.461061 CGGCCATCGAATGCTATCATAT 58.539 45.455 2.24 0.00 42.43 1.78
193 194 2.418609 CCGGCCATCGAATGCTATCATA 60.419 50.000 2.24 0.00 42.43 2.15
194 195 1.676916 CCGGCCATCGAATGCTATCAT 60.677 52.381 2.24 0.00 42.43 2.45
195 196 0.320683 CCGGCCATCGAATGCTATCA 60.321 55.000 2.24 0.00 42.43 2.15
196 197 1.639298 GCCGGCCATCGAATGCTATC 61.639 60.000 18.11 0.00 42.43 2.08
197 198 1.672356 GCCGGCCATCGAATGCTAT 60.672 57.895 18.11 0.00 42.43 2.97
198 199 2.280797 GCCGGCCATCGAATGCTA 60.281 61.111 18.11 0.00 42.43 3.49
199 200 4.181010 AGCCGGCCATCGAATGCT 62.181 61.111 26.15 0.00 42.43 3.79
200 201 3.654020 GAGCCGGCCATCGAATGC 61.654 66.667 26.15 0.00 42.43 3.56
201 202 2.974698 GGAGCCGGCCATCGAATG 60.975 66.667 26.15 0.00 42.43 2.67
202 203 4.256180 GGGAGCCGGCCATCGAAT 62.256 66.667 26.15 0.94 42.43 3.34
215 216 2.202797 CGGACACTGATGCGGGAG 60.203 66.667 0.00 0.00 0.00 4.30
216 217 4.451150 GCGGACACTGATGCGGGA 62.451 66.667 0.00 0.00 0.00 5.14
220 221 1.815421 AATCCGCGGACACTGATGC 60.815 57.895 33.75 0.00 0.00 3.91
221 222 0.460109 TCAATCCGCGGACACTGATG 60.460 55.000 33.75 21.03 0.00 3.07
222 223 0.465705 ATCAATCCGCGGACACTGAT 59.534 50.000 33.75 31.19 0.00 2.90
223 224 0.249120 AATCAATCCGCGGACACTGA 59.751 50.000 33.75 30.46 0.00 3.41
224 225 0.652592 GAATCAATCCGCGGACACTG 59.347 55.000 33.75 26.45 0.00 3.66
225 226 0.462047 GGAATCAATCCGCGGACACT 60.462 55.000 33.75 15.76 38.79 3.55
226 227 2.014594 GGAATCAATCCGCGGACAC 58.985 57.895 33.75 17.03 38.79 3.67
227 228 4.532490 GGAATCAATCCGCGGACA 57.468 55.556 33.75 18.34 38.79 4.02
234 235 4.170468 TTGCCTAAGAGGGAATCAATCC 57.830 45.455 0.00 0.00 41.00 3.01
235 236 4.035675 CGTTTGCCTAAGAGGGAATCAATC 59.964 45.833 0.00 0.00 45.37 2.67
236 237 3.947834 CGTTTGCCTAAGAGGGAATCAAT 59.052 43.478 0.00 0.00 45.37 2.57
237 238 3.343617 CGTTTGCCTAAGAGGGAATCAA 58.656 45.455 0.00 0.00 45.37 2.57
238 239 2.355716 CCGTTTGCCTAAGAGGGAATCA 60.356 50.000 0.00 0.00 45.37 2.57
239 240 2.093128 TCCGTTTGCCTAAGAGGGAATC 60.093 50.000 0.00 0.00 45.37 2.52
240 241 1.913419 TCCGTTTGCCTAAGAGGGAAT 59.087 47.619 0.00 0.00 45.37 3.01
241 242 1.354101 TCCGTTTGCCTAAGAGGGAA 58.646 50.000 0.00 0.00 44.34 3.97
242 243 1.209504 CATCCGTTTGCCTAAGAGGGA 59.790 52.381 0.00 0.00 35.37 4.20
243 244 1.668419 CATCCGTTTGCCTAAGAGGG 58.332 55.000 0.00 0.00 35.37 4.30
244 245 1.017387 GCATCCGTTTGCCTAAGAGG 58.983 55.000 0.00 0.00 38.80 3.69
252 253 1.006337 TGCTTTGGCATCCGTTTGC 60.006 52.632 0.00 0.00 44.28 3.68
279 280 1.475751 GGCCATCTCCATCGTTGACAT 60.476 52.381 0.00 0.00 0.00 3.06
280 281 0.107703 GGCCATCTCCATCGTTGACA 60.108 55.000 0.00 0.00 0.00 3.58
281 282 0.179000 AGGCCATCTCCATCGTTGAC 59.821 55.000 5.01 0.00 0.00 3.18
286 287 1.967066 AGTCTTAGGCCATCTCCATCG 59.033 52.381 5.01 0.00 0.00 3.84
297 298 6.932356 TCATCATGATTGAAAGTCTTAGGC 57.068 37.500 5.16 0.00 34.96 3.93
338 339 7.789273 ATGTGAATTGATTGCAAAAGTTTCA 57.211 28.000 1.71 8.54 37.59 2.69
342 347 8.836268 ACATTATGTGAATTGATTGCAAAAGT 57.164 26.923 1.71 0.00 37.59 2.66
368 373 7.600375 TGTGTGAAAGTTTTGTTTTGCTCAATA 59.400 29.630 0.00 0.00 0.00 1.90
407 412 2.267961 GTCTTGCCTACCCCACGG 59.732 66.667 0.00 0.00 0.00 4.94
408 413 1.375523 GTGTCTTGCCTACCCCACG 60.376 63.158 0.00 0.00 0.00 4.94
409 414 1.375523 CGTGTCTTGCCTACCCCAC 60.376 63.158 0.00 0.00 0.00 4.61
411 416 2.436115 GCGTGTCTTGCCTACCCC 60.436 66.667 0.00 0.00 0.00 4.95
449 454 9.632807 TTATTATTTTCACAGGAATTTTCACCG 57.367 29.630 0.00 0.00 31.93 4.94
484 490 9.084164 CCAGCGCGTATATAACTTAATTATCTT 57.916 33.333 8.43 0.00 35.08 2.40
485 491 7.222224 GCCAGCGCGTATATAACTTAATTATCT 59.778 37.037 8.43 0.00 35.08 1.98
486 492 7.222224 AGCCAGCGCGTATATAACTTAATTATC 59.778 37.037 8.43 0.00 41.18 1.75
489 495 5.235516 AGCCAGCGCGTATATAACTTAATT 58.764 37.500 8.43 0.00 41.18 1.40
501 507 3.672255 GACACGTAGCCAGCGCGTA 62.672 63.158 8.43 0.00 41.18 4.42
505 511 2.094659 CCTTGACACGTAGCCAGCG 61.095 63.158 0.00 0.00 0.00 5.18
510 516 0.736325 ACGATGCCTTGACACGTAGC 60.736 55.000 0.00 0.00 35.49 3.58
515 521 3.747193 CAAACATACGATGCCTTGACAC 58.253 45.455 0.00 0.00 31.54 3.67
544 550 2.247311 CATGAGTTTGTAACGCAGGC 57.753 50.000 2.70 0.00 44.25 4.85
547 553 1.890876 AGGCATGAGTTTGTAACGCA 58.109 45.000 0.00 0.00 45.09 5.24
549 555 5.545658 ACATTAGGCATGAGTTTGTAACG 57.454 39.130 0.00 0.00 36.24 3.18
554 560 4.177165 TGCAACATTAGGCATGAGTTTG 57.823 40.909 0.00 0.00 36.24 2.93
575 592 6.605594 TCAAGGTAAGATTGACCAACAAGTTT 59.394 34.615 0.00 0.00 42.02 2.66
578 595 6.633500 TTCAAGGTAAGATTGACCAACAAG 57.367 37.500 0.00 0.00 42.02 3.16
584 601 5.064834 GGTTCGATTCAAGGTAAGATTGACC 59.935 44.000 0.00 0.00 36.44 4.02
588 605 3.621715 GCGGTTCGATTCAAGGTAAGATT 59.378 43.478 0.00 0.00 0.00 2.40
589 606 3.195661 GCGGTTCGATTCAAGGTAAGAT 58.804 45.455 0.00 0.00 0.00 2.40
594 611 0.953960 GTGGCGGTTCGATTCAAGGT 60.954 55.000 0.00 0.00 0.00 3.50
598 615 0.389817 CTCAGTGGCGGTTCGATTCA 60.390 55.000 0.00 0.00 0.00 2.57
599 616 1.084370 CCTCAGTGGCGGTTCGATTC 61.084 60.000 0.00 0.00 0.00 2.52
608 652 0.752658 TATCCATCACCTCAGTGGCG 59.247 55.000 0.00 0.00 44.64 5.69
629 673 1.816863 AACCGGCTGATGACTCACGT 61.817 55.000 0.00 0.00 0.00 4.49
702 751 8.622948 ACTACCAGTATTCTCCTTTCTTTTTG 57.377 34.615 0.00 0.00 0.00 2.44
760 811 6.530181 GTCAGAGTTTGGTTCGAATTTTGTTT 59.470 34.615 0.00 0.00 0.00 2.83
771 822 0.868406 CAGGCGTCAGAGTTTGGTTC 59.132 55.000 0.00 0.00 0.00 3.62
836 887 4.479993 CTTGCGGCCCAGAGGAGG 62.480 72.222 0.00 0.00 33.47 4.30
951 1224 2.474816 GGCGATGCGAGTTTTCTCTAT 58.525 47.619 0.00 0.00 44.16 1.98
2170 2443 6.067217 AGTCTACCAAGTAAATTGCATCCT 57.933 37.500 0.00 0.00 37.60 3.24
2386 2660 7.387119 TCAGATATATGCCTGAAATTGATGC 57.613 36.000 2.43 0.00 36.58 3.91
2439 2713 0.819582 AAGCATATGCAACTGTGGCC 59.180 50.000 28.62 0.00 45.16 5.36
2442 2716 5.796935 GTCTTAACAAGCATATGCAACTGTG 59.203 40.000 28.62 18.68 45.16 3.66
2558 3389 9.939424 ACAAACCTCTATAAGTAGAAGATAGGT 57.061 33.333 0.00 0.00 36.54 3.08
2710 3560 1.270199 CGCCTAAGATCTGCATCAGCT 60.270 52.381 0.00 0.00 42.74 4.24
2777 3627 2.357154 GCCACCATGGGAACTTAGATGT 60.357 50.000 18.09 0.00 38.19 3.06
3022 3874 3.939592 GGTTTTTCTATCGGTCTTCCCTG 59.060 47.826 0.00 0.00 0.00 4.45
3029 3881 4.811557 CCATCTCTGGTTTTTCTATCGGTC 59.188 45.833 0.00 0.00 37.79 4.79
3067 3920 1.119684 GCTCCTTCCTCTCCCTCTTC 58.880 60.000 0.00 0.00 0.00 2.87
3086 3947 2.533266 GTCCAACCTTACGTACATCCG 58.467 52.381 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.