Multiple sequence alignment - TraesCS3D01G190700

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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 TraesCS3D01G190700 chr3D 100.000 2746 0 0 1 2746 179169554 179166809 0.000000e+00 5072.0
1 TraesCS3D01G190700 chr3B 94.322 2219 56 16 564 2746 257245373 257243189 0.000000e+00 3336.0
2 TraesCS3D01G190700 chr3A 92.801 1667 58 16 443 2068 221932065 221930420 0.000000e+00 2357.0
3 TraesCS3D01G190700 chr3A 95.327 642 23 4 2111 2746 221930418 221929778 0.000000e+00 1013.0
4 TraesCS3D01G190700 chr3A 92.188 64 5 0 335 398 221937494 221937431 1.050000e-14 91.6
5 TraesCS3D01G190700 chr5B 80.788 203 31 4 225 426 586733308 586733113 4.740000e-33 152.0
6 TraesCS3D01G190700 chr5A 79.661 177 30 2 225 400 597786327 597786156 3.710000e-24 122.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G190700 chr3D 179166809 179169554 2745 True 5072 5072 100.000 1 2746 1 chr3D.!!$R1 2745
1 TraesCS3D01G190700 chr3B 257243189 257245373 2184 True 3336 3336 94.322 564 2746 1 chr3B.!!$R1 2182
2 TraesCS3D01G190700 chr3A 221929778 221932065 2287 True 1685 2357 94.064 443 2746 2 chr3A.!!$R2 2303

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
500 510 0.027324 GTCCTACGCGTCTACGGAAG 59.973 60.0 18.63 5.29 40.23 3.46 F
675 685 0.037975 TTAAACCGCCTCGTCACCTC 60.038 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 1348 0.512952 GTTGCAGGACACACGATCAC 59.487 55.000 0.0 0.0 0.0 3.06 R
2642 2709 2.069273 GTCACTGACCAGGTTCATTCG 58.931 52.381 0.0 0.0 0.0 3.34 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 2.105128 CGACCAGAGGATGTCGCC 59.895 66.667 0.00 0.00 46.41 5.54
25 26 2.710902 CGACCAGAGGATGTCGCCA 61.711 63.158 0.00 0.00 46.41 5.69
26 27 1.826024 GACCAGAGGATGTCGCCAT 59.174 57.895 0.00 0.00 0.00 4.40
27 28 1.040646 GACCAGAGGATGTCGCCATA 58.959 55.000 0.00 0.00 0.00 2.74
28 29 1.000283 GACCAGAGGATGTCGCCATAG 60.000 57.143 0.00 0.00 0.00 2.23
29 30 1.332195 CCAGAGGATGTCGCCATAGA 58.668 55.000 0.00 0.00 0.00 1.98
30 31 1.000283 CCAGAGGATGTCGCCATAGAC 60.000 57.143 0.00 0.00 41.30 2.59
31 32 1.000283 CAGAGGATGTCGCCATAGACC 60.000 57.143 0.00 0.00 40.26 3.85
32 33 0.039074 GAGGATGTCGCCATAGACCG 60.039 60.000 0.00 0.00 40.26 4.79
33 34 0.467474 AGGATGTCGCCATAGACCGA 60.467 55.000 0.00 0.00 40.26 4.69
34 35 0.603569 GGATGTCGCCATAGACCGAT 59.396 55.000 0.00 0.00 40.26 4.18
35 36 1.402984 GGATGTCGCCATAGACCGATC 60.403 57.143 0.00 0.00 40.26 3.69
36 37 1.269723 GATGTCGCCATAGACCGATCA 59.730 52.381 0.00 0.00 40.26 2.92
37 38 0.668535 TGTCGCCATAGACCGATCAG 59.331 55.000 0.00 0.00 40.26 2.90
38 39 0.669077 GTCGCCATAGACCGATCAGT 59.331 55.000 0.00 0.00 35.76 3.41
39 40 0.952280 TCGCCATAGACCGATCAGTC 59.048 55.000 0.44 0.44 37.01 3.51
41 42 1.068885 CGCCATAGACCGATCAGTCTC 60.069 57.143 14.89 0.59 43.76 3.36
42 43 1.271102 GCCATAGACCGATCAGTCTCC 59.729 57.143 14.89 0.01 43.76 3.71
43 44 1.537638 CCATAGACCGATCAGTCTCCG 59.462 57.143 14.89 7.62 43.76 4.63
44 45 2.222886 CATAGACCGATCAGTCTCCGT 58.777 52.381 14.89 0.89 43.76 4.69
45 46 1.664873 TAGACCGATCAGTCTCCGTG 58.335 55.000 14.89 0.00 43.76 4.94
46 47 0.322636 AGACCGATCAGTCTCCGTGT 60.323 55.000 5.73 0.00 43.76 4.49
47 48 0.526662 GACCGATCAGTCTCCGTGTT 59.473 55.000 1.61 0.00 33.79 3.32
48 49 0.243907 ACCGATCAGTCTCCGTGTTG 59.756 55.000 0.00 0.00 0.00 3.33
49 50 1.078759 CCGATCAGTCTCCGTGTTGC 61.079 60.000 0.00 0.00 0.00 4.17
50 51 1.078759 CGATCAGTCTCCGTGTTGCC 61.079 60.000 0.00 0.00 0.00 4.52
51 52 0.741221 GATCAGTCTCCGTGTTGCCC 60.741 60.000 0.00 0.00 0.00 5.36
52 53 2.185310 ATCAGTCTCCGTGTTGCCCC 62.185 60.000 0.00 0.00 0.00 5.80
53 54 2.847234 AGTCTCCGTGTTGCCCCA 60.847 61.111 0.00 0.00 0.00 4.96
54 55 2.668550 GTCTCCGTGTTGCCCCAC 60.669 66.667 0.00 0.00 0.00 4.61
55 56 3.164977 TCTCCGTGTTGCCCCACA 61.165 61.111 4.06 0.00 34.98 4.17
56 57 2.203280 CTCCGTGTTGCCCCACAA 60.203 61.111 4.06 0.00 34.98 3.33
57 58 1.826054 CTCCGTGTTGCCCCACAAA 60.826 57.895 4.06 0.00 40.82 2.83
58 59 1.152652 TCCGTGTTGCCCCACAAAT 60.153 52.632 4.06 0.00 40.82 2.32
59 60 1.006337 CCGTGTTGCCCCACAAATG 60.006 57.895 4.06 0.00 40.82 2.32
60 61 1.459455 CCGTGTTGCCCCACAAATGA 61.459 55.000 4.06 0.00 40.82 2.57
61 62 0.039256 CGTGTTGCCCCACAAATGAG 60.039 55.000 4.06 0.00 40.82 2.90
62 63 1.327303 GTGTTGCCCCACAAATGAGA 58.673 50.000 0.00 0.00 40.82 3.27
63 64 1.895131 GTGTTGCCCCACAAATGAGAT 59.105 47.619 0.00 0.00 40.82 2.75
64 65 2.094545 GTGTTGCCCCACAAATGAGATC 60.095 50.000 0.00 0.00 40.82 2.75
65 66 1.133025 GTTGCCCCACAAATGAGATCG 59.867 52.381 0.00 0.00 40.82 3.69
66 67 0.617935 TGCCCCACAAATGAGATCGA 59.382 50.000 0.00 0.00 0.00 3.59
67 68 1.017387 GCCCCACAAATGAGATCGAC 58.983 55.000 0.00 0.00 0.00 4.20
68 69 1.290203 CCCCACAAATGAGATCGACG 58.710 55.000 0.00 0.00 0.00 5.12
69 70 1.290203 CCCACAAATGAGATCGACGG 58.710 55.000 0.00 0.00 0.00 4.79
70 71 1.290203 CCACAAATGAGATCGACGGG 58.710 55.000 0.00 0.00 0.00 5.28
71 72 0.652592 CACAAATGAGATCGACGGGC 59.347 55.000 0.00 0.00 0.00 6.13
72 73 0.806102 ACAAATGAGATCGACGGGCG 60.806 55.000 0.00 0.00 42.69 6.13
73 74 1.883084 AAATGAGATCGACGGGCGC 60.883 57.895 0.00 0.00 40.61 6.53
74 75 3.792053 AATGAGATCGACGGGCGCC 62.792 63.158 21.18 21.18 40.61 6.53
88 89 4.025401 CGCCGCCACAAAGTCCAC 62.025 66.667 0.00 0.00 0.00 4.02
89 90 3.670377 GCCGCCACAAAGTCCACC 61.670 66.667 0.00 0.00 0.00 4.61
90 91 2.983592 CCGCCACAAAGTCCACCC 60.984 66.667 0.00 0.00 0.00 4.61
91 92 2.113139 CGCCACAAAGTCCACCCT 59.887 61.111 0.00 0.00 0.00 4.34
92 93 1.966451 CGCCACAAAGTCCACCCTC 60.966 63.158 0.00 0.00 0.00 4.30
93 94 1.150536 GCCACAAAGTCCACCCTCA 59.849 57.895 0.00 0.00 0.00 3.86
94 95 0.467290 GCCACAAAGTCCACCCTCAA 60.467 55.000 0.00 0.00 0.00 3.02
95 96 2.026905 GCCACAAAGTCCACCCTCAAA 61.027 52.381 0.00 0.00 0.00 2.69
96 97 2.383855 CCACAAAGTCCACCCTCAAAA 58.616 47.619 0.00 0.00 0.00 2.44
97 98 2.100749 CCACAAAGTCCACCCTCAAAAC 59.899 50.000 0.00 0.00 0.00 2.43
98 99 2.100749 CACAAAGTCCACCCTCAAAACC 59.899 50.000 0.00 0.00 0.00 3.27
99 100 1.686587 CAAAGTCCACCCTCAAAACCC 59.313 52.381 0.00 0.00 0.00 4.11
100 101 1.231963 AAGTCCACCCTCAAAACCCT 58.768 50.000 0.00 0.00 0.00 4.34
101 102 0.478507 AGTCCACCCTCAAAACCCTG 59.521 55.000 0.00 0.00 0.00 4.45
102 103 0.539669 GTCCACCCTCAAAACCCTGG 60.540 60.000 0.00 0.00 0.00 4.45
103 104 1.228862 CCACCCTCAAAACCCTGGG 60.229 63.158 12.28 12.28 44.89 4.45
104 105 1.228862 CACCCTCAAAACCCTGGGG 60.229 63.158 18.88 7.87 43.72 4.96
115 116 3.922366 CCTGGGGTCTCCTGGTTT 58.078 61.111 6.51 0.00 46.21 3.27
116 117 2.164393 CCTGGGGTCTCCTGGTTTT 58.836 57.895 6.51 0.00 46.21 2.43
117 118 0.482887 CCTGGGGTCTCCTGGTTTTT 59.517 55.000 6.51 0.00 46.21 1.94
118 119 1.547901 CCTGGGGTCTCCTGGTTTTTC 60.548 57.143 6.51 0.00 46.21 2.29
119 120 1.144913 CTGGGGTCTCCTGGTTTTTCA 59.855 52.381 0.00 0.00 36.20 2.69
120 121 1.571457 TGGGGTCTCCTGGTTTTTCAA 59.429 47.619 0.00 0.00 36.20 2.69
121 122 2.023888 TGGGGTCTCCTGGTTTTTCAAA 60.024 45.455 0.00 0.00 36.20 2.69
122 123 2.628178 GGGGTCTCCTGGTTTTTCAAAG 59.372 50.000 0.00 0.00 0.00 2.77
123 124 2.628178 GGGTCTCCTGGTTTTTCAAAGG 59.372 50.000 0.00 0.00 0.00 3.11
124 125 3.562182 GGTCTCCTGGTTTTTCAAAGGA 58.438 45.455 0.00 0.00 37.29 3.36
125 126 3.958147 GGTCTCCTGGTTTTTCAAAGGAA 59.042 43.478 0.00 0.00 38.34 3.36
126 127 4.404394 GGTCTCCTGGTTTTTCAAAGGAAA 59.596 41.667 0.00 0.00 41.13 3.13
143 144 9.965824 TCAAAGGAAAAACTATTGACTTTCATC 57.034 29.630 0.00 0.00 30.89 2.92
144 145 9.196552 CAAAGGAAAAACTATTGACTTTCATCC 57.803 33.333 0.00 0.00 30.89 3.51
145 146 8.477419 AAGGAAAAACTATTGACTTTCATCCA 57.523 30.769 0.00 0.00 30.89 3.41
146 147 7.886338 AGGAAAAACTATTGACTTTCATCCAC 58.114 34.615 0.00 0.00 30.89 4.02
147 148 7.505585 AGGAAAAACTATTGACTTTCATCCACA 59.494 33.333 0.00 0.00 30.89 4.17
148 149 8.306761 GGAAAAACTATTGACTTTCATCCACAT 58.693 33.333 0.00 0.00 30.89 3.21
149 150 9.132521 GAAAAACTATTGACTTTCATCCACATG 57.867 33.333 0.00 0.00 0.00 3.21
150 151 5.824904 ACTATTGACTTTCATCCACATGC 57.175 39.130 0.00 0.00 0.00 4.06
151 152 5.255687 ACTATTGACTTTCATCCACATGCA 58.744 37.500 0.00 0.00 0.00 3.96
152 153 4.713824 ATTGACTTTCATCCACATGCAG 57.286 40.909 0.00 0.00 0.00 4.41
153 154 1.814394 TGACTTTCATCCACATGCAGC 59.186 47.619 0.00 0.00 0.00 5.25
154 155 1.814394 GACTTTCATCCACATGCAGCA 59.186 47.619 0.00 0.00 0.00 4.41
155 156 2.426024 GACTTTCATCCACATGCAGCAT 59.574 45.455 0.52 0.52 0.00 3.79
156 157 2.165641 ACTTTCATCCACATGCAGCATG 59.834 45.455 30.34 30.34 46.18 4.06
157 158 2.131776 TTCATCCACATGCAGCATGA 57.868 45.000 36.91 18.71 43.81 3.07
158 159 1.385528 TCATCCACATGCAGCATGAC 58.614 50.000 36.91 0.00 43.81 3.06
159 160 0.384309 CATCCACATGCAGCATGACC 59.616 55.000 36.91 0.00 43.81 4.02
160 161 0.257905 ATCCACATGCAGCATGACCT 59.742 50.000 36.91 16.03 43.81 3.85
161 162 0.678684 TCCACATGCAGCATGACCTG 60.679 55.000 36.91 25.13 43.81 4.00
179 180 3.965660 CCGTAGGCCACCCACTAT 58.034 61.111 5.01 0.00 46.14 2.12
180 181 3.136620 CCGTAGGCCACCCACTATA 57.863 57.895 5.01 0.00 46.14 1.31
181 182 0.677842 CCGTAGGCCACCCACTATAC 59.322 60.000 5.01 0.00 46.14 1.47
182 183 1.405872 CGTAGGCCACCCACTATACA 58.594 55.000 5.01 0.00 0.00 2.29
183 184 1.968493 CGTAGGCCACCCACTATACAT 59.032 52.381 5.01 0.00 0.00 2.29
184 185 2.288825 CGTAGGCCACCCACTATACATG 60.289 54.545 5.01 0.00 0.00 3.21
185 186 1.140312 AGGCCACCCACTATACATGG 58.860 55.000 5.01 0.00 36.94 3.66
187 188 3.725754 CCACCCACTATACATGGCC 57.274 57.895 0.00 0.00 35.74 5.36
188 189 0.843309 CCACCCACTATACATGGCCA 59.157 55.000 8.56 8.56 35.74 5.36
189 190 1.476833 CCACCCACTATACATGGCCAC 60.477 57.143 8.16 0.00 35.74 5.01
190 191 0.468226 ACCCACTATACATGGCCACG 59.532 55.000 8.16 0.08 35.74 4.94
191 192 0.250295 CCCACTATACATGGCCACGG 60.250 60.000 8.16 6.04 35.74 4.94
192 193 0.250295 CCACTATACATGGCCACGGG 60.250 60.000 8.16 2.83 0.00 5.28
193 194 0.756294 CACTATACATGGCCACGGGA 59.244 55.000 8.16 0.00 0.00 5.14
194 195 1.347707 CACTATACATGGCCACGGGAT 59.652 52.381 8.16 8.63 0.00 3.85
195 196 2.565391 CACTATACATGGCCACGGGATA 59.435 50.000 8.16 9.45 0.00 2.59
196 197 2.565834 ACTATACATGGCCACGGGATAC 59.434 50.000 8.16 0.00 0.00 2.24
224 225 3.760035 CGACCCGACCAGACCCTG 61.760 72.222 0.00 0.00 0.00 4.45
225 226 4.083862 GACCCGACCAGACCCTGC 62.084 72.222 0.00 0.00 0.00 4.85
229 230 4.087892 CGACCAGACCCTGCCCAG 62.088 72.222 0.00 0.00 0.00 4.45
230 231 2.930562 GACCAGACCCTGCCCAGT 60.931 66.667 0.00 0.00 0.00 4.00
231 232 2.930562 ACCAGACCCTGCCCAGTC 60.931 66.667 0.00 0.00 0.00 3.51
232 233 2.608988 CCAGACCCTGCCCAGTCT 60.609 66.667 0.00 0.00 44.12 3.24
233 234 2.227036 CCAGACCCTGCCCAGTCTT 61.227 63.158 0.00 0.00 41.38 3.01
234 235 1.002868 CAGACCCTGCCCAGTCTTG 60.003 63.158 0.00 0.00 41.38 3.02
235 236 2.360475 GACCCTGCCCAGTCTTGC 60.360 66.667 0.00 0.00 0.00 4.01
236 237 3.927481 GACCCTGCCCAGTCTTGCC 62.927 68.421 0.00 0.00 0.00 4.52
237 238 4.748144 CCCTGCCCAGTCTTGCCC 62.748 72.222 0.00 0.00 0.00 5.36
238 239 3.970410 CCTGCCCAGTCTTGCCCA 61.970 66.667 0.00 0.00 0.00 5.36
239 240 2.674380 CTGCCCAGTCTTGCCCAC 60.674 66.667 0.00 0.00 0.00 4.61
240 241 3.496309 CTGCCCAGTCTTGCCCACA 62.496 63.158 0.00 0.00 0.00 4.17
241 242 2.674380 GCCCAGTCTTGCCCACAG 60.674 66.667 0.00 0.00 0.00 3.66
242 243 2.034687 CCCAGTCTTGCCCACAGG 59.965 66.667 0.00 0.00 0.00 4.00
271 272 4.932060 CCTGAGATCTAGGCCCGA 57.068 61.111 0.00 0.00 0.00 5.14
272 273 3.372557 CCTGAGATCTAGGCCCGAT 57.627 57.895 0.00 0.95 0.00 4.18
273 274 0.894141 CCTGAGATCTAGGCCCGATG 59.106 60.000 9.69 0.00 0.00 3.84
274 275 0.894141 CTGAGATCTAGGCCCGATGG 59.106 60.000 9.69 0.00 0.00 3.51
314 315 8.757164 GCTTAGGCTTGTAATATTTGTGTTTT 57.243 30.769 0.00 0.00 35.22 2.43
315 316 9.849166 GCTTAGGCTTGTAATATTTGTGTTTTA 57.151 29.630 0.00 0.00 35.22 1.52
318 319 7.836842 AGGCTTGTAATATTTGTGTTTTAGGG 58.163 34.615 0.00 0.00 0.00 3.53
319 320 7.672239 AGGCTTGTAATATTTGTGTTTTAGGGA 59.328 33.333 0.00 0.00 0.00 4.20
320 321 7.973944 GGCTTGTAATATTTGTGTTTTAGGGAG 59.026 37.037 0.00 0.00 0.00 4.30
321 322 7.973944 GCTTGTAATATTTGTGTTTTAGGGAGG 59.026 37.037 0.00 0.00 0.00 4.30
322 323 7.948034 TGTAATATTTGTGTTTTAGGGAGGG 57.052 36.000 0.00 0.00 0.00 4.30
323 324 6.893005 TGTAATATTTGTGTTTTAGGGAGGGG 59.107 38.462 0.00 0.00 0.00 4.79
324 325 2.003937 TTTGTGTTTTAGGGAGGGGC 57.996 50.000 0.00 0.00 0.00 5.80
325 326 0.113580 TTGTGTTTTAGGGAGGGGCC 59.886 55.000 0.00 0.00 0.00 5.80
342 343 4.278513 CCGACCCAAGGCCCAACA 62.279 66.667 0.00 0.00 0.00 3.33
343 344 2.672996 CGACCCAAGGCCCAACAG 60.673 66.667 0.00 0.00 0.00 3.16
344 345 2.283173 GACCCAAGGCCCAACAGG 60.283 66.667 0.00 0.00 39.47 4.00
356 357 3.473923 CCCAACAGGCTTTTTCATTGT 57.526 42.857 0.00 0.00 0.00 2.71
357 358 3.807553 CCCAACAGGCTTTTTCATTGTT 58.192 40.909 0.00 0.00 32.60 2.83
358 359 3.560896 CCCAACAGGCTTTTTCATTGTTG 59.439 43.478 8.29 8.29 44.92 3.33
359 360 4.799419 CAACAGGCTTTTTCATTGTTGG 57.201 40.909 7.56 0.00 42.84 3.77
360 361 3.473923 ACAGGCTTTTTCATTGTTGGG 57.526 42.857 0.00 0.00 0.00 4.12
361 362 2.771372 ACAGGCTTTTTCATTGTTGGGT 59.229 40.909 0.00 0.00 0.00 4.51
362 363 3.181466 ACAGGCTTTTTCATTGTTGGGTC 60.181 43.478 0.00 0.00 0.00 4.46
363 364 2.035832 AGGCTTTTTCATTGTTGGGTCG 59.964 45.455 0.00 0.00 0.00 4.79
364 365 2.403259 GCTTTTTCATTGTTGGGTCGG 58.597 47.619 0.00 0.00 0.00 4.79
365 366 2.866065 GCTTTTTCATTGTTGGGTCGGG 60.866 50.000 0.00 0.00 0.00 5.14
366 367 0.676736 TTTTCATTGTTGGGTCGGGC 59.323 50.000 0.00 0.00 0.00 6.13
367 368 1.182385 TTTCATTGTTGGGTCGGGCC 61.182 55.000 0.00 0.00 0.00 5.80
368 369 2.035626 CATTGTTGGGTCGGGCCT 59.964 61.111 0.84 0.00 37.43 5.19
369 370 2.035626 ATTGTTGGGTCGGGCCTG 59.964 61.111 4.71 4.71 37.43 4.85
370 371 3.583882 ATTGTTGGGTCGGGCCTGG 62.584 63.158 12.87 0.00 37.43 4.45
415 416 4.798682 CCGGGTCCAGGCCTAGGT 62.799 72.222 3.98 0.00 0.00 3.08
416 417 2.687566 CGGGTCCAGGCCTAGGTT 60.688 66.667 3.98 0.00 0.00 3.50
417 418 2.298661 CGGGTCCAGGCCTAGGTTT 61.299 63.158 3.98 0.00 0.00 3.27
418 419 1.848886 CGGGTCCAGGCCTAGGTTTT 61.849 60.000 3.98 0.00 0.00 2.43
419 420 0.034380 GGGTCCAGGCCTAGGTTTTC 60.034 60.000 3.98 3.05 0.00 2.29
420 421 0.992695 GGTCCAGGCCTAGGTTTTCT 59.007 55.000 3.98 0.51 0.00 2.52
421 422 1.340114 GGTCCAGGCCTAGGTTTTCTG 60.340 57.143 3.98 12.48 0.00 3.02
422 423 0.328258 TCCAGGCCTAGGTTTTCTGC 59.672 55.000 3.98 0.00 0.00 4.26
423 424 0.329596 CCAGGCCTAGGTTTTCTGCT 59.670 55.000 3.98 0.00 0.00 4.24
424 425 1.559682 CCAGGCCTAGGTTTTCTGCTA 59.440 52.381 3.98 0.00 0.00 3.49
425 426 2.633488 CAGGCCTAGGTTTTCTGCTAC 58.367 52.381 3.98 0.00 0.00 3.58
426 427 2.027192 CAGGCCTAGGTTTTCTGCTACA 60.027 50.000 3.98 0.00 0.00 2.74
427 428 2.237392 AGGCCTAGGTTTTCTGCTACAG 59.763 50.000 1.29 0.00 0.00 2.74
428 429 2.633488 GCCTAGGTTTTCTGCTACAGG 58.367 52.381 11.31 0.00 31.51 4.00
429 430 2.236395 GCCTAGGTTTTCTGCTACAGGA 59.764 50.000 11.31 0.00 31.51 3.86
430 431 3.680196 GCCTAGGTTTTCTGCTACAGGAG 60.680 52.174 11.31 0.00 34.56 3.69
431 432 3.769844 CCTAGGTTTTCTGCTACAGGAGA 59.230 47.826 0.00 0.00 40.83 3.71
438 439 3.685139 TCTGCTACAGGAGAAAACCAG 57.315 47.619 0.00 0.00 39.60 4.00
439 440 2.303022 TCTGCTACAGGAGAAAACCAGG 59.697 50.000 0.00 0.00 39.60 4.45
440 441 2.039084 CTGCTACAGGAGAAAACCAGGT 59.961 50.000 0.00 0.00 35.31 4.00
441 442 3.244582 TGCTACAGGAGAAAACCAGGTA 58.755 45.455 0.00 0.00 0.00 3.08
475 476 2.026641 GTATACCACCCACTCGTAGCA 58.973 52.381 0.00 0.00 0.00 3.49
498 508 0.807667 GAGTCCTACGCGTCTACGGA 60.808 60.000 18.63 15.18 40.23 4.69
500 510 0.027324 GTCCTACGCGTCTACGGAAG 59.973 60.000 18.63 5.29 40.23 3.46
540 550 2.644418 CGTACACACGTTCCCCGA 59.356 61.111 0.00 0.00 43.31 5.14
607 617 3.517901 ACATACTCCCCGTCTTCAAATCA 59.482 43.478 0.00 0.00 0.00 2.57
608 618 4.019681 ACATACTCCCCGTCTTCAAATCAA 60.020 41.667 0.00 0.00 0.00 2.57
609 619 3.502123 ACTCCCCGTCTTCAAATCAAA 57.498 42.857 0.00 0.00 0.00 2.69
612 622 3.006940 TCCCCGTCTTCAAATCAAATCG 58.993 45.455 0.00 0.00 0.00 3.34
675 685 0.037975 TTAAACCGCCTCGTCACCTC 60.038 55.000 0.00 0.00 0.00 3.85
698 708 3.717294 CCCACGTCCCCCTCCTTG 61.717 72.222 0.00 0.00 0.00 3.61
794 804 5.015178 ACCTCCATCATCAAAGGGAAGTTAA 59.985 40.000 0.00 0.00 32.97 2.01
907 917 1.226547 CGGAGCAACGAGAGAGAGC 60.227 63.158 0.00 0.00 35.47 4.09
1052 1078 4.316823 TGTGCTCCTCCTCCCCGT 62.317 66.667 0.00 0.00 0.00 5.28
1231 1257 0.107945 GCTCTGTGAGTCATCCACCC 60.108 60.000 0.00 0.00 33.80 4.61
1243 1270 4.167502 AGTCATCCACCCATCTCATCATTT 59.832 41.667 0.00 0.00 0.00 2.32
1299 1341 3.603857 GCGTACTTGTGTTGTGTGTGATC 60.604 47.826 0.00 0.00 0.00 2.92
1304 1346 2.142319 TGTGTTGTGTGTGATCCATCG 58.858 47.619 0.00 0.00 0.00 3.84
1306 1348 0.095245 GTTGTGTGTGATCCATCGCG 59.905 55.000 0.00 0.00 40.07 5.87
1326 1372 0.392706 TGATCGTGTGTCCTGCAACT 59.607 50.000 0.00 0.00 0.00 3.16
1328 1374 2.036604 TGATCGTGTGTCCTGCAACTTA 59.963 45.455 0.00 0.00 0.00 2.24
1834 1882 2.758979 AGTTCATCCGGTGGTACTAGTG 59.241 50.000 5.39 0.00 0.00 2.74
2025 2089 7.533900 CGAGTTTACATCAATGGTTACAAGTTG 59.466 37.037 0.00 0.00 0.00 3.16
2085 2149 5.079406 CGAGTTTACATTTGTCGTGATTGG 58.921 41.667 0.00 0.00 0.00 3.16
2117 2181 4.214437 CACAAGTCGAGAAAGATGCAAAC 58.786 43.478 0.00 0.00 0.00 2.93
2297 2364 3.701532 TTTTTGGTCCAGTAACTTGCG 57.298 42.857 0.00 0.00 0.00 4.85
2304 2371 0.889186 CCAGTAACTTGCGGCAGGTT 60.889 55.000 29.24 29.24 37.44 3.50
2478 2545 7.116075 AGTATTTACAATGGCTGAATGCAAT 57.884 32.000 0.00 0.00 45.15 3.56
2642 2709 2.292569 CTGCCATCAAGATGCATGGTAC 59.707 50.000 2.46 0.00 41.63 3.34
2704 2771 6.049955 TGGAGAAACCAGGACTTAATACAG 57.950 41.667 0.00 0.00 44.64 2.74
2705 2772 5.546499 TGGAGAAACCAGGACTTAATACAGT 59.454 40.000 0.00 0.00 44.64 3.55
2706 2773 5.875359 GGAGAAACCAGGACTTAATACAGTG 59.125 44.000 0.00 0.00 38.79 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.298958 TGGCGACATCCTCTGGTC 58.701 61.111 0.00 0.00 33.40 4.02
18 19 3.897308 GACTGATCGGTCTATGGCGACA 61.897 54.545 24.73 0.00 37.76 4.35
19 20 0.669077 ACTGATCGGTCTATGGCGAC 59.331 55.000 0.00 0.00 0.00 5.19
20 21 0.952280 GACTGATCGGTCTATGGCGA 59.048 55.000 24.73 0.00 33.81 5.54
21 22 0.955178 AGACTGATCGGTCTATGGCG 59.045 55.000 31.57 0.00 43.76 5.69
22 23 1.271102 GGAGACTGATCGGTCTATGGC 59.729 57.143 32.36 21.11 45.32 4.40
23 24 1.537638 CGGAGACTGATCGGTCTATGG 59.462 57.143 32.36 21.28 45.32 2.74
24 25 2.031595 CACGGAGACTGATCGGTCTATG 60.032 54.545 32.36 27.66 45.32 2.23
25 26 2.222886 CACGGAGACTGATCGGTCTAT 58.777 52.381 32.36 19.96 45.32 1.98
26 27 1.065636 ACACGGAGACTGATCGGTCTA 60.066 52.381 32.36 0.00 45.32 2.59
28 29 0.526662 AACACGGAGACTGATCGGTC 59.473 55.000 24.65 24.65 36.56 4.79
29 30 0.243907 CAACACGGAGACTGATCGGT 59.756 55.000 6.97 6.97 33.47 4.69
30 31 1.078759 GCAACACGGAGACTGATCGG 61.079 60.000 0.00 0.00 0.00 4.18
31 32 1.078759 GGCAACACGGAGACTGATCG 61.079 60.000 0.00 0.00 0.00 3.69
32 33 0.741221 GGGCAACACGGAGACTGATC 60.741 60.000 0.00 0.00 39.74 2.92
33 34 1.296715 GGGCAACACGGAGACTGAT 59.703 57.895 0.00 0.00 39.74 2.90
34 35 2.741092 GGGCAACACGGAGACTGA 59.259 61.111 0.00 0.00 39.74 3.41
35 36 2.358737 GGGGCAACACGGAGACTG 60.359 66.667 0.00 0.00 39.74 3.51
43 44 1.327303 TCTCATTTGTGGGGCAACAC 58.673 50.000 4.80 4.80 44.44 3.32
44 45 2.170166 GATCTCATTTGTGGGGCAACA 58.830 47.619 0.00 0.00 36.72 3.33
45 46 1.133025 CGATCTCATTTGTGGGGCAAC 59.867 52.381 0.00 0.00 36.72 4.17
46 47 1.004161 TCGATCTCATTTGTGGGGCAA 59.996 47.619 0.00 0.00 34.87 4.52
47 48 0.617935 TCGATCTCATTTGTGGGGCA 59.382 50.000 0.00 0.00 0.00 5.36
48 49 1.017387 GTCGATCTCATTTGTGGGGC 58.983 55.000 0.00 0.00 0.00 5.80
49 50 1.290203 CGTCGATCTCATTTGTGGGG 58.710 55.000 0.00 0.00 0.00 4.96
50 51 1.290203 CCGTCGATCTCATTTGTGGG 58.710 55.000 0.00 0.00 0.00 4.61
51 52 1.290203 CCCGTCGATCTCATTTGTGG 58.710 55.000 0.00 0.00 0.00 4.17
52 53 0.652592 GCCCGTCGATCTCATTTGTG 59.347 55.000 0.00 0.00 0.00 3.33
53 54 0.806102 CGCCCGTCGATCTCATTTGT 60.806 55.000 0.00 0.00 41.67 2.83
54 55 1.927210 CGCCCGTCGATCTCATTTG 59.073 57.895 0.00 0.00 41.67 2.32
55 56 1.883084 GCGCCCGTCGATCTCATTT 60.883 57.895 0.00 0.00 41.67 2.32
56 57 2.279517 GCGCCCGTCGATCTCATT 60.280 61.111 0.00 0.00 41.67 2.57
57 58 4.286320 GGCGCCCGTCGATCTCAT 62.286 66.667 18.11 0.00 41.67 2.90
71 72 4.025401 GTGGACTTTGTGGCGGCG 62.025 66.667 0.51 0.51 0.00 6.46
72 73 3.670377 GGTGGACTTTGTGGCGGC 61.670 66.667 0.00 0.00 0.00 6.53
73 74 2.983592 GGGTGGACTTTGTGGCGG 60.984 66.667 0.00 0.00 0.00 6.13
74 75 1.966451 GAGGGTGGACTTTGTGGCG 60.966 63.158 0.00 0.00 0.00 5.69
75 76 0.467290 TTGAGGGTGGACTTTGTGGC 60.467 55.000 0.00 0.00 0.00 5.01
76 77 2.065899 TTTGAGGGTGGACTTTGTGG 57.934 50.000 0.00 0.00 0.00 4.17
77 78 2.100749 GGTTTTGAGGGTGGACTTTGTG 59.899 50.000 0.00 0.00 0.00 3.33
78 79 2.384828 GGTTTTGAGGGTGGACTTTGT 58.615 47.619 0.00 0.00 0.00 2.83
79 80 1.686587 GGGTTTTGAGGGTGGACTTTG 59.313 52.381 0.00 0.00 0.00 2.77
80 81 1.573857 AGGGTTTTGAGGGTGGACTTT 59.426 47.619 0.00 0.00 0.00 2.66
81 82 1.133482 CAGGGTTTTGAGGGTGGACTT 60.133 52.381 0.00 0.00 0.00 3.01
82 83 0.478507 CAGGGTTTTGAGGGTGGACT 59.521 55.000 0.00 0.00 0.00 3.85
83 84 0.539669 CCAGGGTTTTGAGGGTGGAC 60.540 60.000 0.00 0.00 0.00 4.02
84 85 1.725169 CCCAGGGTTTTGAGGGTGGA 61.725 60.000 0.00 0.00 36.52 4.02
85 86 1.228862 CCCAGGGTTTTGAGGGTGG 60.229 63.158 0.00 0.00 36.52 4.61
86 87 1.228862 CCCCAGGGTTTTGAGGGTG 60.229 63.158 4.22 0.00 39.76 4.61
87 88 3.272017 CCCCAGGGTTTTGAGGGT 58.728 61.111 4.22 0.00 39.76 4.34
97 98 1.435346 AAAACCAGGAGACCCCAGGG 61.435 60.000 0.00 0.00 45.32 4.45
98 99 0.482887 AAAAACCAGGAGACCCCAGG 59.517 55.000 0.00 0.00 46.38 4.45
99 100 1.144913 TGAAAAACCAGGAGACCCCAG 59.855 52.381 0.00 0.00 37.41 4.45
100 101 1.227249 TGAAAAACCAGGAGACCCCA 58.773 50.000 0.00 0.00 37.41 4.96
101 102 2.375014 TTGAAAAACCAGGAGACCCC 57.625 50.000 0.00 0.00 0.00 4.95
102 103 2.628178 CCTTTGAAAAACCAGGAGACCC 59.372 50.000 0.00 0.00 0.00 4.46
103 104 3.562182 TCCTTTGAAAAACCAGGAGACC 58.438 45.455 0.00 0.00 31.45 3.85
104 105 5.592104 TTTCCTTTGAAAAACCAGGAGAC 57.408 39.130 0.00 0.00 37.53 3.36
117 118 9.965824 GATGAAAGTCAATAGTTTTTCCTTTGA 57.034 29.630 0.00 0.00 0.00 2.69
118 119 9.196552 GGATGAAAGTCAATAGTTTTTCCTTTG 57.803 33.333 0.00 0.00 32.77 2.77
119 120 8.923270 TGGATGAAAGTCAATAGTTTTTCCTTT 58.077 29.630 0.00 0.00 34.63 3.11
120 121 8.360390 GTGGATGAAAGTCAATAGTTTTTCCTT 58.640 33.333 0.00 0.00 34.63 3.36
121 122 7.505585 TGTGGATGAAAGTCAATAGTTTTTCCT 59.494 33.333 0.00 0.00 34.63 3.36
122 123 7.657336 TGTGGATGAAAGTCAATAGTTTTTCC 58.343 34.615 0.00 0.00 34.39 3.13
123 124 9.132521 CATGTGGATGAAAGTCAATAGTTTTTC 57.867 33.333 0.00 0.00 0.00 2.29
124 125 7.599998 GCATGTGGATGAAAGTCAATAGTTTTT 59.400 33.333 0.00 0.00 0.00 1.94
125 126 7.092716 GCATGTGGATGAAAGTCAATAGTTTT 58.907 34.615 0.00 0.00 0.00 2.43
126 127 6.209192 TGCATGTGGATGAAAGTCAATAGTTT 59.791 34.615 0.00 0.00 0.00 2.66
127 128 5.711506 TGCATGTGGATGAAAGTCAATAGTT 59.288 36.000 0.00 0.00 0.00 2.24
128 129 5.255687 TGCATGTGGATGAAAGTCAATAGT 58.744 37.500 0.00 0.00 0.00 2.12
129 130 5.732528 GCTGCATGTGGATGAAAGTCAATAG 60.733 44.000 0.00 0.00 0.00 1.73
130 131 4.096833 GCTGCATGTGGATGAAAGTCAATA 59.903 41.667 0.00 0.00 0.00 1.90
131 132 3.119245 GCTGCATGTGGATGAAAGTCAAT 60.119 43.478 0.00 0.00 0.00 2.57
132 133 2.229543 GCTGCATGTGGATGAAAGTCAA 59.770 45.455 0.00 0.00 0.00 3.18
133 134 1.814394 GCTGCATGTGGATGAAAGTCA 59.186 47.619 0.00 0.00 0.00 3.41
134 135 1.814394 TGCTGCATGTGGATGAAAGTC 59.186 47.619 0.00 0.00 0.00 3.01
135 136 1.913778 TGCTGCATGTGGATGAAAGT 58.086 45.000 0.00 0.00 0.00 2.66
136 137 2.425668 TCATGCTGCATGTGGATGAAAG 59.574 45.455 34.14 11.78 41.98 2.62
137 138 2.164827 GTCATGCTGCATGTGGATGAAA 59.835 45.455 34.14 15.60 42.29 2.69
138 139 1.746787 GTCATGCTGCATGTGGATGAA 59.253 47.619 34.14 16.27 42.29 2.57
139 140 1.385528 GTCATGCTGCATGTGGATGA 58.614 50.000 34.14 17.93 41.98 2.92
140 141 0.384309 GGTCATGCTGCATGTGGATG 59.616 55.000 34.14 16.00 41.98 3.51
141 142 0.257905 AGGTCATGCTGCATGTGGAT 59.742 50.000 34.14 19.82 41.98 3.41
142 143 0.678684 CAGGTCATGCTGCATGTGGA 60.679 55.000 34.14 18.26 41.98 4.02
143 144 1.807226 CAGGTCATGCTGCATGTGG 59.193 57.895 34.14 21.03 41.98 4.17
162 163 0.677842 GTATAGTGGGTGGCCTACGG 59.322 60.000 3.32 0.00 40.06 4.02
163 164 1.405872 TGTATAGTGGGTGGCCTACG 58.594 55.000 3.32 0.00 40.06 3.51
164 165 2.038557 CCATGTATAGTGGGTGGCCTAC 59.961 54.545 3.32 0.00 35.11 3.18
165 166 2.334977 CCATGTATAGTGGGTGGCCTA 58.665 52.381 3.32 0.00 32.98 3.93
166 167 1.140312 CCATGTATAGTGGGTGGCCT 58.860 55.000 3.32 0.00 32.98 5.19
167 168 3.725754 CCATGTATAGTGGGTGGCC 57.274 57.895 0.00 0.00 32.98 5.36
169 170 0.843309 TGGCCATGTATAGTGGGTGG 59.157 55.000 0.00 0.00 37.22 4.61
170 171 1.810031 CGTGGCCATGTATAGTGGGTG 60.810 57.143 17.42 0.00 37.22 4.61
171 172 0.468226 CGTGGCCATGTATAGTGGGT 59.532 55.000 17.42 0.00 37.22 4.51
172 173 0.250295 CCGTGGCCATGTATAGTGGG 60.250 60.000 23.39 1.68 37.22 4.61
173 174 0.250295 CCCGTGGCCATGTATAGTGG 60.250 60.000 23.39 12.30 39.80 4.00
174 175 0.756294 TCCCGTGGCCATGTATAGTG 59.244 55.000 23.39 6.92 0.00 2.74
175 176 1.729586 ATCCCGTGGCCATGTATAGT 58.270 50.000 23.39 2.24 0.00 2.12
176 177 2.093658 GGTATCCCGTGGCCATGTATAG 60.094 54.545 23.39 8.03 0.00 1.31
177 178 1.903860 GGTATCCCGTGGCCATGTATA 59.096 52.381 23.39 16.64 0.00 1.47
178 179 0.690762 GGTATCCCGTGGCCATGTAT 59.309 55.000 23.39 17.60 0.00 2.29
179 180 1.412453 GGGTATCCCGTGGCCATGTA 61.412 60.000 23.39 11.69 32.13 2.29
180 181 2.752807 GGGTATCCCGTGGCCATGT 61.753 63.158 23.39 7.98 32.13 3.21
181 182 2.113139 GGGTATCCCGTGGCCATG 59.887 66.667 18.73 18.73 32.13 3.66
207 208 3.760035 CAGGGTCTGGTCGGGTCG 61.760 72.222 0.00 0.00 0.00 4.79
208 209 4.083862 GCAGGGTCTGGTCGGGTC 62.084 72.222 0.00 0.00 31.21 4.46
212 213 4.087892 CTGGGCAGGGTCTGGTCG 62.088 72.222 0.00 0.00 31.21 4.79
213 214 2.930562 ACTGGGCAGGGTCTGGTC 60.931 66.667 0.00 0.00 31.21 4.02
214 215 2.930562 GACTGGGCAGGGTCTGGT 60.931 66.667 0.00 0.00 31.21 4.00
215 216 2.227036 AAGACTGGGCAGGGTCTGG 61.227 63.158 6.94 0.00 41.28 3.86
216 217 1.002868 CAAGACTGGGCAGGGTCTG 60.003 63.158 6.94 0.00 41.28 3.51
217 218 2.900106 GCAAGACTGGGCAGGGTCT 61.900 63.158 0.00 0.00 43.60 3.85
218 219 2.360475 GCAAGACTGGGCAGGGTC 60.360 66.667 0.00 0.00 0.00 4.46
219 220 3.971702 GGCAAGACTGGGCAGGGT 61.972 66.667 0.00 0.00 0.00 4.34
220 221 4.748144 GGGCAAGACTGGGCAGGG 62.748 72.222 5.65 0.00 0.00 4.45
221 222 3.970410 TGGGCAAGACTGGGCAGG 61.970 66.667 5.65 0.00 0.00 4.85
222 223 2.674380 GTGGGCAAGACTGGGCAG 60.674 66.667 5.65 0.00 0.00 4.85
223 224 3.496309 CTGTGGGCAAGACTGGGCA 62.496 63.158 5.65 0.00 0.00 5.36
224 225 2.674380 CTGTGGGCAAGACTGGGC 60.674 66.667 0.00 0.00 0.00 5.36
225 226 2.034687 CCTGTGGGCAAGACTGGG 59.965 66.667 0.00 0.00 0.00 4.45
247 248 1.555967 CCTAGATCTCAGGCCTAGGC 58.444 60.000 26.55 26.55 41.91 3.93
254 255 0.894141 CATCGGGCCTAGATCTCAGG 59.106 60.000 0.84 6.20 36.16 3.86
255 256 0.894141 CCATCGGGCCTAGATCTCAG 59.106 60.000 0.84 0.00 0.00 3.35
256 257 3.057749 CCATCGGGCCTAGATCTCA 57.942 57.895 0.84 0.00 0.00 3.27
277 278 4.222847 CTAAGCTCGGCCCGACCC 62.223 72.222 0.00 0.00 33.26 4.46
278 279 4.222847 CCTAAGCTCGGCCCGACC 62.223 72.222 0.00 0.00 0.00 4.79
279 280 4.893601 GCCTAAGCTCGGCCCGAC 62.894 72.222 14.42 0.00 41.73 4.79
289 290 8.757164 AAAACACAAATATTACAAGCCTAAGC 57.243 30.769 0.00 0.00 40.32 3.09
292 293 8.962679 CCCTAAAACACAAATATTACAAGCCTA 58.037 33.333 0.00 0.00 0.00 3.93
293 294 7.672239 TCCCTAAAACACAAATATTACAAGCCT 59.328 33.333 0.00 0.00 0.00 4.58
294 295 7.832769 TCCCTAAAACACAAATATTACAAGCC 58.167 34.615 0.00 0.00 0.00 4.35
295 296 7.973944 CCTCCCTAAAACACAAATATTACAAGC 59.026 37.037 0.00 0.00 0.00 4.01
296 297 8.466798 CCCTCCCTAAAACACAAATATTACAAG 58.533 37.037 0.00 0.00 0.00 3.16
297 298 7.397761 CCCCTCCCTAAAACACAAATATTACAA 59.602 37.037 0.00 0.00 0.00 2.41
298 299 6.893005 CCCCTCCCTAAAACACAAATATTACA 59.107 38.462 0.00 0.00 0.00 2.41
299 300 6.183360 GCCCCTCCCTAAAACACAAATATTAC 60.183 42.308 0.00 0.00 0.00 1.89
300 301 5.894964 GCCCCTCCCTAAAACACAAATATTA 59.105 40.000 0.00 0.00 0.00 0.98
301 302 4.714802 GCCCCTCCCTAAAACACAAATATT 59.285 41.667 0.00 0.00 0.00 1.28
302 303 4.286707 GCCCCTCCCTAAAACACAAATAT 58.713 43.478 0.00 0.00 0.00 1.28
303 304 3.564790 GGCCCCTCCCTAAAACACAAATA 60.565 47.826 0.00 0.00 0.00 1.40
304 305 2.536066 GCCCCTCCCTAAAACACAAAT 58.464 47.619 0.00 0.00 0.00 2.32
305 306 1.481615 GGCCCCTCCCTAAAACACAAA 60.482 52.381 0.00 0.00 0.00 2.83
306 307 0.113580 GGCCCCTCCCTAAAACACAA 59.886 55.000 0.00 0.00 0.00 3.33
307 308 1.771646 GGCCCCTCCCTAAAACACA 59.228 57.895 0.00 0.00 0.00 3.72
308 309 4.757773 GGCCCCTCCCTAAAACAC 57.242 61.111 0.00 0.00 0.00 3.32
325 326 4.278513 TGTTGGGCCTTGGGTCGG 62.279 66.667 4.53 0.00 0.00 4.79
326 327 2.672996 CTGTTGGGCCTTGGGTCG 60.673 66.667 4.53 0.00 0.00 4.79
327 328 2.283173 CCTGTTGGGCCTTGGGTC 60.283 66.667 4.53 0.00 0.00 4.46
336 337 3.473923 ACAATGAAAAAGCCTGTTGGG 57.526 42.857 0.00 0.00 38.36 4.12
337 338 4.799419 CAACAATGAAAAAGCCTGTTGG 57.201 40.909 5.53 0.00 41.91 3.77
338 339 3.560896 CCCAACAATGAAAAAGCCTGTTG 59.439 43.478 6.32 6.32 44.07 3.33
339 340 3.199727 ACCCAACAATGAAAAAGCCTGTT 59.800 39.130 0.00 0.00 0.00 3.16
340 341 2.771372 ACCCAACAATGAAAAAGCCTGT 59.229 40.909 0.00 0.00 0.00 4.00
341 342 3.392882 GACCCAACAATGAAAAAGCCTG 58.607 45.455 0.00 0.00 0.00 4.85
342 343 2.035832 CGACCCAACAATGAAAAAGCCT 59.964 45.455 0.00 0.00 0.00 4.58
343 344 2.403259 CGACCCAACAATGAAAAAGCC 58.597 47.619 0.00 0.00 0.00 4.35
344 345 2.403259 CCGACCCAACAATGAAAAAGC 58.597 47.619 0.00 0.00 0.00 3.51
345 346 2.866065 GCCCGACCCAACAATGAAAAAG 60.866 50.000 0.00 0.00 0.00 2.27
346 347 1.069358 GCCCGACCCAACAATGAAAAA 59.931 47.619 0.00 0.00 0.00 1.94
347 348 0.676736 GCCCGACCCAACAATGAAAA 59.323 50.000 0.00 0.00 0.00 2.29
348 349 1.182385 GGCCCGACCCAACAATGAAA 61.182 55.000 0.00 0.00 0.00 2.69
349 350 1.605165 GGCCCGACCCAACAATGAA 60.605 57.895 0.00 0.00 0.00 2.57
350 351 2.034999 GGCCCGACCCAACAATGA 59.965 61.111 0.00 0.00 0.00 2.57
351 352 2.035626 AGGCCCGACCCAACAATG 59.964 61.111 0.00 0.00 40.58 2.82
352 353 2.035626 CAGGCCCGACCCAACAAT 59.964 61.111 0.00 0.00 40.58 2.71
353 354 4.278513 CCAGGCCCGACCCAACAA 62.279 66.667 0.00 0.00 40.58 2.83
398 399 4.798682 ACCTAGGCCTGGACCCGG 62.799 72.222 19.36 9.34 0.00 5.73
399 400 1.848886 AAAACCTAGGCCTGGACCCG 61.849 60.000 19.36 2.81 0.00 5.28
400 401 0.034380 GAAAACCTAGGCCTGGACCC 60.034 60.000 19.36 5.13 0.00 4.46
401 402 0.992695 AGAAAACCTAGGCCTGGACC 59.007 55.000 19.36 7.91 0.00 4.46
402 403 1.950954 GCAGAAAACCTAGGCCTGGAC 60.951 57.143 19.36 0.00 0.00 4.02
403 404 0.328258 GCAGAAAACCTAGGCCTGGA 59.672 55.000 19.36 0.00 0.00 3.86
404 405 0.329596 AGCAGAAAACCTAGGCCTGG 59.670 55.000 17.99 13.68 0.00 4.45
405 406 2.027192 TGTAGCAGAAAACCTAGGCCTG 60.027 50.000 17.99 12.10 0.00 4.85
406 407 2.237392 CTGTAGCAGAAAACCTAGGCCT 59.763 50.000 11.78 11.78 32.44 5.19
407 408 2.633488 CTGTAGCAGAAAACCTAGGCC 58.367 52.381 9.30 0.00 32.44 5.19
408 409 2.236395 TCCTGTAGCAGAAAACCTAGGC 59.764 50.000 9.30 0.00 32.44 3.93
409 410 3.769844 TCTCCTGTAGCAGAAAACCTAGG 59.230 47.826 7.41 7.41 32.44 3.02
410 411 5.407407 TTCTCCTGTAGCAGAAAACCTAG 57.593 43.478 0.00 0.00 32.44 3.02
411 412 5.818678 TTTCTCCTGTAGCAGAAAACCTA 57.181 39.130 0.00 0.00 36.02 3.08
412 413 4.706842 TTTCTCCTGTAGCAGAAAACCT 57.293 40.909 0.00 0.00 36.02 3.50
415 416 4.787551 TGGTTTTCTCCTGTAGCAGAAAA 58.212 39.130 6.63 6.63 43.28 2.29
416 417 4.389374 CTGGTTTTCTCCTGTAGCAGAAA 58.611 43.478 0.00 0.00 38.12 2.52
417 418 3.244561 CCTGGTTTTCTCCTGTAGCAGAA 60.245 47.826 0.00 0.00 38.12 3.02
418 419 2.303022 CCTGGTTTTCTCCTGTAGCAGA 59.697 50.000 0.00 0.00 38.12 4.26
419 420 2.039084 ACCTGGTTTTCTCCTGTAGCAG 59.961 50.000 0.00 0.00 36.24 4.24
420 421 2.054799 ACCTGGTTTTCTCCTGTAGCA 58.945 47.619 0.00 0.00 0.00 3.49
421 422 2.861147 ACCTGGTTTTCTCCTGTAGC 57.139 50.000 0.00 0.00 0.00 3.58
422 423 4.527038 TGTCTACCTGGTTTTCTCCTGTAG 59.473 45.833 3.84 0.00 36.18 2.74
423 424 4.485875 TGTCTACCTGGTTTTCTCCTGTA 58.514 43.478 3.84 0.00 0.00 2.74
424 425 3.314693 TGTCTACCTGGTTTTCTCCTGT 58.685 45.455 3.84 0.00 0.00 4.00
425 426 4.559862 ATGTCTACCTGGTTTTCTCCTG 57.440 45.455 3.84 0.00 0.00 3.86
426 427 5.131142 CCATATGTCTACCTGGTTTTCTCCT 59.869 44.000 3.84 0.00 0.00 3.69
427 428 5.368989 CCATATGTCTACCTGGTTTTCTCC 58.631 45.833 3.84 0.00 0.00 3.71
428 429 4.816925 GCCATATGTCTACCTGGTTTTCTC 59.183 45.833 3.84 0.00 0.00 2.87
429 430 4.385310 GGCCATATGTCTACCTGGTTTTCT 60.385 45.833 3.84 0.00 0.00 2.52
430 431 3.883489 GGCCATATGTCTACCTGGTTTTC 59.117 47.826 3.84 0.00 0.00 2.29
431 432 3.268334 TGGCCATATGTCTACCTGGTTTT 59.732 43.478 0.00 0.00 0.00 2.43
432 433 2.849943 TGGCCATATGTCTACCTGGTTT 59.150 45.455 0.00 0.00 0.00 3.27
433 434 2.439507 CTGGCCATATGTCTACCTGGTT 59.560 50.000 5.51 0.00 0.00 3.67
434 435 2.050144 CTGGCCATATGTCTACCTGGT 58.950 52.381 5.51 4.05 0.00 4.00
435 436 1.349026 CCTGGCCATATGTCTACCTGG 59.651 57.143 5.51 7.27 33.83 4.45
436 437 2.050144 ACCTGGCCATATGTCTACCTG 58.950 52.381 5.51 2.31 0.00 4.00
437 438 2.496679 ACCTGGCCATATGTCTACCT 57.503 50.000 5.51 0.00 0.00 3.08
438 439 4.161754 GGTATACCTGGCCATATGTCTACC 59.838 50.000 19.79 19.79 0.00 3.18
439 440 4.775780 TGGTATACCTGGCCATATGTCTAC 59.224 45.833 22.41 10.96 36.82 2.59
440 441 4.775780 GTGGTATACCTGGCCATATGTCTA 59.224 45.833 22.41 0.00 36.82 2.59
441 442 3.583086 GTGGTATACCTGGCCATATGTCT 59.417 47.826 22.41 0.00 36.82 3.41
475 476 2.765122 GTAGACGCGTAGGACTCCTAT 58.235 52.381 13.97 0.00 38.48 2.57
498 508 7.062605 CGTTTTTCCGTATGTATACTGTGTCTT 59.937 37.037 4.17 0.00 0.00 3.01
500 510 6.308766 ACGTTTTTCCGTATGTATACTGTGTC 59.691 38.462 4.17 0.00 39.73 3.67
506 516 7.383361 GTGTGTACGTTTTTCCGTATGTATAC 58.617 38.462 0.00 0.00 44.27 1.47
540 550 4.072839 GTTTGAATCTTTTCTCCTCGGGT 58.927 43.478 0.00 0.00 32.78 5.28
607 617 0.026803 GCGCGCTCTTGATTCGATTT 59.973 50.000 26.67 0.00 0.00 2.17
608 618 1.638467 GCGCGCTCTTGATTCGATT 59.362 52.632 26.67 0.00 0.00 3.34
609 619 2.580470 CGCGCGCTCTTGATTCGAT 61.580 57.895 30.48 0.00 0.00 3.59
612 622 4.909056 CGCGCGCGCTCTTGATTC 62.909 66.667 45.97 19.75 39.32 2.52
634 644 4.963276 TTTCCGCTGATTACCTTTGATG 57.037 40.909 0.00 0.00 0.00 3.07
675 685 4.109675 GGGGGACGTGGGATGTGG 62.110 72.222 0.00 0.00 0.00 4.17
698 708 1.017177 TGCCACGGACGTGCTTAATC 61.017 55.000 18.57 4.46 44.16 1.75
1052 1078 2.032528 CAAGGACGAAGGCCAGCA 59.967 61.111 5.01 0.00 0.00 4.41
1231 1257 6.550108 AGGGAAATGGAAGAAATGATGAGATG 59.450 38.462 0.00 0.00 0.00 2.90
1243 1270 4.290985 TGACATGGTAAGGGAAATGGAAGA 59.709 41.667 0.00 0.00 0.00 2.87
1299 1341 1.742900 GACACACGATCACGCGATGG 61.743 60.000 15.93 0.00 43.96 3.51
1304 1346 2.730672 GCAGGACACACGATCACGC 61.731 63.158 0.00 0.00 43.96 5.34
1306 1348 0.512952 GTTGCAGGACACACGATCAC 59.487 55.000 0.00 0.00 0.00 3.06
1326 1372 9.442047 GAAGTCTGGAATCAAAAGAAGATCTAA 57.558 33.333 0.00 0.00 0.00 2.10
1328 1374 7.456725 TGAAGTCTGGAATCAAAAGAAGATCT 58.543 34.615 0.00 0.00 0.00 2.75
1505 1553 3.847602 CTCTGGCCCTCCTCGCAG 61.848 72.222 0.00 0.00 0.00 5.18
2025 2089 6.018180 AGTCTTTTCAGTTATGTTCACCGAAC 60.018 38.462 0.00 0.00 42.26 3.95
2056 2120 5.060077 CACGACAAATGTAAACTCGTATCGT 59.940 40.000 0.00 0.00 39.46 3.73
2117 2181 5.575957 GTTCTCACATGTTTGATATGGCAG 58.424 41.667 0.00 0.00 0.00 4.85
2297 2364 2.564721 GGACAGCCACAAACCTGCC 61.565 63.158 0.00 0.00 32.37 4.85
2417 2484 5.282055 TGCCACTCTACATCTATTCCTTG 57.718 43.478 0.00 0.00 0.00 3.61
2478 2545 7.894753 TGCCATGGTATTTCATCTTCAAATA 57.105 32.000 14.67 0.00 0.00 1.40
2642 2709 2.069273 GTCACTGACCAGGTTCATTCG 58.931 52.381 0.00 0.00 0.00 3.34
2691 2758 7.665974 CCTTTCTTTTCCACTGTATTAAGTCCT 59.334 37.037 0.00 0.00 0.00 3.85
2699 2766 5.047092 CCATTGCCTTTCTTTTCCACTGTAT 60.047 40.000 0.00 0.00 0.00 2.29
2700 2767 4.280677 CCATTGCCTTTCTTTTCCACTGTA 59.719 41.667 0.00 0.00 0.00 2.74
2701 2768 3.070015 CCATTGCCTTTCTTTTCCACTGT 59.930 43.478 0.00 0.00 0.00 3.55
2702 2769 3.656559 CCATTGCCTTTCTTTTCCACTG 58.343 45.455 0.00 0.00 0.00 3.66
2704 2771 2.416747 GCCATTGCCTTTCTTTTCCAC 58.583 47.619 0.00 0.00 0.00 4.02
2705 2772 2.837532 GCCATTGCCTTTCTTTTCCA 57.162 45.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.