Multiple sequence alignment - TraesCS3B01G347700

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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 TraesCS3B01G347700 chr3B 100.000 2240 0 0 1 2240 556880342 556878103 0.000000e+00 4137
1 TraesCS3B01G347700 chr3A 92.352 1739 61 20 305 2015 559526130 559527824 0.000000e+00 2409
2 TraesCS3B01G347700 chr3A 96.460 226 8 0 2014 2239 559527919 559528144 7.550000e-100 374
3 TraesCS3B01G347700 chr3D 93.097 1666 49 15 268 1884 427228901 427227253 0.000000e+00 2379
4 TraesCS3B01G347700 chr3D 95.706 326 14 0 1914 2239 427227248 427226923 1.970000e-145 525
5 TraesCS3B01G347700 chr2B 97.183 213 6 0 1 213 403549246 403549034 5.880000e-96 361
6 TraesCS3B01G347700 chr5A 87.313 268 26 3 1 262 21069344 21069609 1.300000e-77 300


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 TraesCS3B01G347700 chr3B 556878103 556880342 2239 True 4137.0 4137 100.0000 1 2240 1 chr3B.!!$R1 2239
1 TraesCS3B01G347700 chr3A 559526130 559528144 2014 False 1391.5 2409 94.4060 305 2239 2 chr3A.!!$F1 1934
2 TraesCS3B01G347700 chr3D 427226923 427228901 1978 True 1452.0 2379 94.4015 268 2239 2 chr3D.!!$R1 1971

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
61 62 0.110486 GCAGTTCCTCCTCCCAAACA 59.89 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1700 1.009829 ATTCGGCTTCAAGCGATCAC 58.99 50.0 2.54 0.0 43.62 3.06 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
47 48 3.322466 CTCCCAGGTCCGGCAGTT 61.322 66.667 0.00 0.00 0.00 3.16
48 49 3.316573 CTCCCAGGTCCGGCAGTTC 62.317 68.421 0.00 0.00 0.00 3.01
49 50 4.410400 CCCAGGTCCGGCAGTTCC 62.410 72.222 0.00 0.00 0.00 3.62
50 51 3.322466 CCAGGTCCGGCAGTTCCT 61.322 66.667 0.00 0.00 0.00 3.36
51 52 2.266055 CAGGTCCGGCAGTTCCTC 59.734 66.667 0.00 0.00 0.00 3.71
52 53 3.003763 AGGTCCGGCAGTTCCTCC 61.004 66.667 0.00 0.00 0.00 4.30
53 54 3.003763 GGTCCGGCAGTTCCTCCT 61.004 66.667 0.00 0.00 0.00 3.69
54 55 2.579738 GTCCGGCAGTTCCTCCTC 59.420 66.667 0.00 0.00 0.00 3.71
55 56 2.683933 TCCGGCAGTTCCTCCTCC 60.684 66.667 0.00 0.00 0.00 4.30
56 57 3.787001 CCGGCAGTTCCTCCTCCC 61.787 72.222 0.00 0.00 0.00 4.30
57 58 3.003173 CGGCAGTTCCTCCTCCCA 61.003 66.667 0.00 0.00 0.00 4.37
58 59 2.592993 CGGCAGTTCCTCCTCCCAA 61.593 63.158 0.00 0.00 0.00 4.12
59 60 1.767692 GGCAGTTCCTCCTCCCAAA 59.232 57.895 0.00 0.00 0.00 3.28
60 61 0.609406 GGCAGTTCCTCCTCCCAAAC 60.609 60.000 0.00 0.00 0.00 2.93
61 62 0.110486 GCAGTTCCTCCTCCCAAACA 59.890 55.000 0.00 0.00 0.00 2.83
62 63 1.478654 GCAGTTCCTCCTCCCAAACAA 60.479 52.381 0.00 0.00 0.00 2.83
63 64 2.944129 CAGTTCCTCCTCCCAAACAAA 58.056 47.619 0.00 0.00 0.00 2.83
64 65 3.295973 CAGTTCCTCCTCCCAAACAAAA 58.704 45.455 0.00 0.00 0.00 2.44
65 66 3.319122 CAGTTCCTCCTCCCAAACAAAAG 59.681 47.826 0.00 0.00 0.00 2.27
66 67 1.995376 TCCTCCTCCCAAACAAAAGC 58.005 50.000 0.00 0.00 0.00 3.51
67 68 1.216678 TCCTCCTCCCAAACAAAAGCA 59.783 47.619 0.00 0.00 0.00 3.91
68 69 2.158325 TCCTCCTCCCAAACAAAAGCAT 60.158 45.455 0.00 0.00 0.00 3.79
69 70 2.232208 CCTCCTCCCAAACAAAAGCATC 59.768 50.000 0.00 0.00 0.00 3.91
70 71 2.892852 CTCCTCCCAAACAAAAGCATCA 59.107 45.455 0.00 0.00 0.00 3.07
71 72 3.509442 TCCTCCCAAACAAAAGCATCAT 58.491 40.909 0.00 0.00 0.00 2.45
72 73 3.511146 TCCTCCCAAACAAAAGCATCATC 59.489 43.478 0.00 0.00 0.00 2.92
73 74 3.368739 CCTCCCAAACAAAAGCATCATCC 60.369 47.826 0.00 0.00 0.00 3.51
74 75 3.509442 TCCCAAACAAAAGCATCATCCT 58.491 40.909 0.00 0.00 0.00 3.24
75 76 3.511146 TCCCAAACAAAAGCATCATCCTC 59.489 43.478 0.00 0.00 0.00 3.71
76 77 3.368739 CCCAAACAAAAGCATCATCCTCC 60.369 47.826 0.00 0.00 0.00 4.30
77 78 3.512724 CCAAACAAAAGCATCATCCTCCT 59.487 43.478 0.00 0.00 0.00 3.69
78 79 4.381292 CCAAACAAAAGCATCATCCTCCTC 60.381 45.833 0.00 0.00 0.00 3.71
79 80 4.313020 AACAAAAGCATCATCCTCCTCT 57.687 40.909 0.00 0.00 0.00 3.69
80 81 4.313020 ACAAAAGCATCATCCTCCTCTT 57.687 40.909 0.00 0.00 0.00 2.85
81 82 4.268359 ACAAAAGCATCATCCTCCTCTTC 58.732 43.478 0.00 0.00 0.00 2.87
82 83 3.574354 AAAGCATCATCCTCCTCTTCC 57.426 47.619 0.00 0.00 0.00 3.46
83 84 2.493099 AGCATCATCCTCCTCTTCCT 57.507 50.000 0.00 0.00 0.00 3.36
84 85 2.048601 AGCATCATCCTCCTCTTCCTG 58.951 52.381 0.00 0.00 0.00 3.86
85 86 1.542987 GCATCATCCTCCTCTTCCTGC 60.543 57.143 0.00 0.00 0.00 4.85
86 87 1.767088 CATCATCCTCCTCTTCCTGCA 59.233 52.381 0.00 0.00 0.00 4.41
87 88 1.493861 TCATCCTCCTCTTCCTGCAG 58.506 55.000 6.78 6.78 0.00 4.41
88 89 1.007600 TCATCCTCCTCTTCCTGCAGA 59.992 52.381 17.39 0.00 0.00 4.26
89 90 2.048601 CATCCTCCTCTTCCTGCAGAT 58.951 52.381 17.39 0.00 0.00 2.90
90 91 2.260639 TCCTCCTCTTCCTGCAGATT 57.739 50.000 17.39 0.00 0.00 2.40
91 92 3.404869 TCCTCCTCTTCCTGCAGATTA 57.595 47.619 17.39 0.00 0.00 1.75
92 93 3.724478 TCCTCCTCTTCCTGCAGATTAA 58.276 45.455 17.39 5.62 0.00 1.40
93 94 3.708631 TCCTCCTCTTCCTGCAGATTAAG 59.291 47.826 17.39 15.20 0.00 1.85
94 95 3.465871 CTCCTCTTCCTGCAGATTAAGC 58.534 50.000 17.39 0.00 0.00 3.09
95 96 2.171448 TCCTCTTCCTGCAGATTAAGCC 59.829 50.000 17.39 0.00 0.00 4.35
96 97 2.208431 CTCTTCCTGCAGATTAAGCCG 58.792 52.381 17.39 6.70 0.00 5.52
97 98 1.555075 TCTTCCTGCAGATTAAGCCGT 59.445 47.619 17.39 0.00 0.00 5.68
98 99 1.667724 CTTCCTGCAGATTAAGCCGTG 59.332 52.381 17.39 0.00 0.00 4.94
99 100 0.744414 TCCTGCAGATTAAGCCGTGC 60.744 55.000 17.39 0.00 36.42 5.34
100 101 1.026182 CCTGCAGATTAAGCCGTGCA 61.026 55.000 17.39 7.34 43.50 4.57
101 102 0.804364 CTGCAGATTAAGCCGTGCAA 59.196 50.000 8.42 0.00 44.93 4.08
102 103 0.804364 TGCAGATTAAGCCGTGCAAG 59.196 50.000 5.28 0.00 42.79 4.01
103 104 0.804989 GCAGATTAAGCCGTGCAAGT 59.195 50.000 0.00 0.00 35.91 3.16
104 105 2.006888 GCAGATTAAGCCGTGCAAGTA 58.993 47.619 0.00 0.00 35.91 2.24
105 106 2.418628 GCAGATTAAGCCGTGCAAGTAA 59.581 45.455 0.00 0.00 35.91 2.24
106 107 3.727970 GCAGATTAAGCCGTGCAAGTAAC 60.728 47.826 0.00 0.00 35.91 2.50
107 108 3.684788 CAGATTAAGCCGTGCAAGTAACT 59.315 43.478 0.00 0.00 0.00 2.24
108 109 3.933332 AGATTAAGCCGTGCAAGTAACTC 59.067 43.478 0.00 0.00 0.00 3.01
109 110 3.396260 TTAAGCCGTGCAAGTAACTCT 57.604 42.857 0.00 0.00 0.00 3.24
110 111 2.256117 AAGCCGTGCAAGTAACTCTT 57.744 45.000 0.00 0.00 36.75 2.85
111 112 1.797025 AGCCGTGCAAGTAACTCTTC 58.203 50.000 0.00 0.00 33.63 2.87
112 113 0.796927 GCCGTGCAAGTAACTCTTCC 59.203 55.000 0.00 0.00 33.63 3.46
113 114 1.068474 CCGTGCAAGTAACTCTTCCG 58.932 55.000 0.00 0.00 33.63 4.30
114 115 1.068474 CGTGCAAGTAACTCTTCCGG 58.932 55.000 0.00 0.00 33.63 5.14
115 116 0.796927 GTGCAAGTAACTCTTCCGGC 59.203 55.000 0.00 0.00 33.63 6.13
116 117 0.669318 TGCAAGTAACTCTTCCGGCG 60.669 55.000 0.00 0.00 33.63 6.46
117 118 0.389426 GCAAGTAACTCTTCCGGCGA 60.389 55.000 9.30 0.00 33.63 5.54
118 119 1.347320 CAAGTAACTCTTCCGGCGAC 58.653 55.000 9.30 0.00 33.63 5.19
119 120 1.067776 CAAGTAACTCTTCCGGCGACT 60.068 52.381 9.30 0.00 33.63 4.18
120 121 0.810016 AGTAACTCTTCCGGCGACTC 59.190 55.000 9.30 0.00 0.00 3.36
121 122 0.179142 GTAACTCTTCCGGCGACTCC 60.179 60.000 9.30 0.00 0.00 3.85
122 123 1.318158 TAACTCTTCCGGCGACTCCC 61.318 60.000 9.30 0.00 0.00 4.30
123 124 2.756283 CTCTTCCGGCGACTCCCT 60.756 66.667 9.30 0.00 0.00 4.20
124 125 2.283676 TCTTCCGGCGACTCCCTT 60.284 61.111 9.30 0.00 0.00 3.95
125 126 2.125512 CTTCCGGCGACTCCCTTG 60.126 66.667 9.30 0.00 0.00 3.61
126 127 4.388499 TTCCGGCGACTCCCTTGC 62.388 66.667 9.30 0.00 0.00 4.01
149 150 2.499685 GCCCCTGCGTACTCGATT 59.500 61.111 0.00 0.00 39.71 3.34
150 151 1.591863 GCCCCTGCGTACTCGATTC 60.592 63.158 0.00 0.00 39.71 2.52
151 152 1.299165 CCCCTGCGTACTCGATTCG 60.299 63.158 0.00 0.00 39.71 3.34
152 153 1.299165 CCCTGCGTACTCGATTCGG 60.299 63.158 6.18 0.00 39.71 4.30
153 154 1.944676 CCTGCGTACTCGATTCGGC 60.945 63.158 6.18 1.80 39.71 5.54
154 155 1.944676 CTGCGTACTCGATTCGGCC 60.945 63.158 6.18 0.00 39.71 6.13
155 156 3.022914 GCGTACTCGATTCGGCCG 61.023 66.667 22.12 22.12 39.71 6.13
156 157 3.022914 CGTACTCGATTCGGCCGC 61.023 66.667 23.51 5.56 39.71 6.53
157 158 2.657620 GTACTCGATTCGGCCGCC 60.658 66.667 23.51 11.21 0.00 6.13
158 159 3.142162 TACTCGATTCGGCCGCCA 61.142 61.111 23.51 10.28 0.00 5.69
159 160 2.495409 TACTCGATTCGGCCGCCAT 61.495 57.895 23.51 15.43 0.00 4.40
160 161 2.416244 TACTCGATTCGGCCGCCATC 62.416 60.000 23.51 22.12 0.00 3.51
161 162 3.506059 CTCGATTCGGCCGCCATCT 62.506 63.158 23.51 1.84 0.00 2.90
162 163 2.588877 CGATTCGGCCGCCATCTT 60.589 61.111 23.51 0.00 0.00 2.40
163 164 2.598632 CGATTCGGCCGCCATCTTC 61.599 63.158 23.51 9.32 0.00 2.87
164 165 1.227674 GATTCGGCCGCCATCTTCT 60.228 57.895 23.51 0.00 0.00 2.85
165 166 0.815615 GATTCGGCCGCCATCTTCTT 60.816 55.000 23.51 0.00 0.00 2.52
166 167 0.394352 ATTCGGCCGCCATCTTCTTT 60.394 50.000 23.51 0.00 0.00 2.52
167 168 1.024579 TTCGGCCGCCATCTTCTTTC 61.025 55.000 23.51 0.00 0.00 2.62
168 169 1.450312 CGGCCGCCATCTTCTTTCT 60.450 57.895 14.67 0.00 0.00 2.52
169 170 1.709147 CGGCCGCCATCTTCTTTCTG 61.709 60.000 14.67 0.00 0.00 3.02
170 171 0.392998 GGCCGCCATCTTCTTTCTGA 60.393 55.000 3.91 0.00 0.00 3.27
171 172 1.673168 GCCGCCATCTTCTTTCTGAT 58.327 50.000 0.00 0.00 0.00 2.90
172 173 1.601430 GCCGCCATCTTCTTTCTGATC 59.399 52.381 0.00 0.00 0.00 2.92
173 174 2.744494 GCCGCCATCTTCTTTCTGATCT 60.744 50.000 0.00 0.00 0.00 2.75
174 175 2.871022 CCGCCATCTTCTTTCTGATCTG 59.129 50.000 0.00 0.00 0.00 2.90
175 176 2.871022 CGCCATCTTCTTTCTGATCTGG 59.129 50.000 0.00 0.00 0.00 3.86
176 177 3.431346 CGCCATCTTCTTTCTGATCTGGA 60.431 47.826 0.00 0.00 0.00 3.86
177 178 3.876320 GCCATCTTCTTTCTGATCTGGAC 59.124 47.826 0.00 0.00 0.00 4.02
178 179 4.118410 CCATCTTCTTTCTGATCTGGACG 58.882 47.826 0.00 0.00 0.00 4.79
179 180 4.382470 CCATCTTCTTTCTGATCTGGACGT 60.382 45.833 0.00 0.00 0.00 4.34
180 181 4.873746 TCTTCTTTCTGATCTGGACGTT 57.126 40.909 0.00 0.00 0.00 3.99
181 182 4.810790 TCTTCTTTCTGATCTGGACGTTC 58.189 43.478 0.00 0.00 0.00 3.95
182 183 4.524714 TCTTCTTTCTGATCTGGACGTTCT 59.475 41.667 0.00 0.00 0.00 3.01
183 184 4.873746 TCTTTCTGATCTGGACGTTCTT 57.126 40.909 0.00 0.00 0.00 2.52
184 185 4.810790 TCTTTCTGATCTGGACGTTCTTC 58.189 43.478 0.00 0.00 0.00 2.87
185 186 4.280929 TCTTTCTGATCTGGACGTTCTTCA 59.719 41.667 0.00 0.00 0.00 3.02
186 187 3.577649 TCTGATCTGGACGTTCTTCAC 57.422 47.619 0.00 0.00 0.00 3.18
187 188 2.890945 TCTGATCTGGACGTTCTTCACA 59.109 45.455 0.00 0.00 0.00 3.58
188 189 3.320826 TCTGATCTGGACGTTCTTCACAA 59.679 43.478 0.00 0.00 0.00 3.33
189 190 4.058124 CTGATCTGGACGTTCTTCACAAA 58.942 43.478 0.00 0.00 0.00 2.83
190 191 3.807622 TGATCTGGACGTTCTTCACAAAC 59.192 43.478 0.00 0.00 0.00 2.93
191 192 2.557317 TCTGGACGTTCTTCACAAACC 58.443 47.619 0.00 0.00 0.00 3.27
192 193 1.602377 CTGGACGTTCTTCACAAACCC 59.398 52.381 0.00 0.00 0.00 4.11
193 194 1.210967 TGGACGTTCTTCACAAACCCT 59.789 47.619 0.00 0.00 0.00 4.34
194 195 2.435069 TGGACGTTCTTCACAAACCCTA 59.565 45.455 0.00 0.00 0.00 3.53
195 196 3.064931 GGACGTTCTTCACAAACCCTAG 58.935 50.000 0.00 0.00 0.00 3.02
196 197 2.479275 GACGTTCTTCACAAACCCTAGC 59.521 50.000 0.00 0.00 0.00 3.42
197 198 2.158871 ACGTTCTTCACAAACCCTAGCA 60.159 45.455 0.00 0.00 0.00 3.49
198 199 2.223377 CGTTCTTCACAAACCCTAGCAC 59.777 50.000 0.00 0.00 0.00 4.40
199 200 3.477530 GTTCTTCACAAACCCTAGCACT 58.522 45.455 0.00 0.00 0.00 4.40
200 201 3.402628 TCTTCACAAACCCTAGCACTC 57.597 47.619 0.00 0.00 0.00 3.51
201 202 2.972713 TCTTCACAAACCCTAGCACTCT 59.027 45.455 0.00 0.00 0.00 3.24
202 203 3.006967 TCTTCACAAACCCTAGCACTCTC 59.993 47.826 0.00 0.00 0.00 3.20
203 204 1.623811 TCACAAACCCTAGCACTCTCC 59.376 52.381 0.00 0.00 0.00 3.71
204 205 0.984995 ACAAACCCTAGCACTCTCCC 59.015 55.000 0.00 0.00 0.00 4.30
205 206 1.280457 CAAACCCTAGCACTCTCCCT 58.720 55.000 0.00 0.00 0.00 4.20
206 207 1.208293 CAAACCCTAGCACTCTCCCTC 59.792 57.143 0.00 0.00 0.00 4.30
207 208 0.684805 AACCCTAGCACTCTCCCTCG 60.685 60.000 0.00 0.00 0.00 4.63
208 209 1.227664 CCCTAGCACTCTCCCTCGA 59.772 63.158 0.00 0.00 0.00 4.04
209 210 0.178975 CCCTAGCACTCTCCCTCGAT 60.179 60.000 0.00 0.00 0.00 3.59
210 211 1.074084 CCCTAGCACTCTCCCTCGATA 59.926 57.143 0.00 0.00 0.00 2.92
211 212 2.489255 CCCTAGCACTCTCCCTCGATAA 60.489 54.545 0.00 0.00 0.00 1.75
212 213 2.554893 CCTAGCACTCTCCCTCGATAAC 59.445 54.545 0.00 0.00 0.00 1.89
213 214 1.404843 AGCACTCTCCCTCGATAACC 58.595 55.000 0.00 0.00 0.00 2.85
214 215 0.389757 GCACTCTCCCTCGATAACCC 59.610 60.000 0.00 0.00 0.00 4.11
215 216 2.030045 GCACTCTCCCTCGATAACCCT 61.030 57.143 0.00 0.00 0.00 4.34
216 217 2.752154 GCACTCTCCCTCGATAACCCTA 60.752 54.545 0.00 0.00 0.00 3.53
217 218 3.150767 CACTCTCCCTCGATAACCCTAG 58.849 54.545 0.00 0.00 0.00 3.02
218 219 2.164338 CTCTCCCTCGATAACCCTAGC 58.836 57.143 0.00 0.00 0.00 3.42
219 220 0.882474 CTCCCTCGATAACCCTAGCG 59.118 60.000 0.00 0.00 38.28 4.26
220 221 0.475475 TCCCTCGATAACCCTAGCGA 59.525 55.000 0.00 0.00 43.29 4.93
221 222 1.133699 TCCCTCGATAACCCTAGCGAA 60.134 52.381 0.00 0.00 44.68 4.70
222 223 1.684983 CCCTCGATAACCCTAGCGAAA 59.315 52.381 0.00 0.00 44.68 3.46
223 224 2.545322 CCCTCGATAACCCTAGCGAAAC 60.545 54.545 0.00 0.00 44.68 2.78
224 225 2.545322 CCTCGATAACCCTAGCGAAACC 60.545 54.545 0.00 0.00 44.68 3.27
225 226 1.410153 TCGATAACCCTAGCGAAACCC 59.590 52.381 0.00 0.00 42.61 4.11
226 227 1.137479 CGATAACCCTAGCGAAACCCA 59.863 52.381 0.00 0.00 39.28 4.51
227 228 2.802057 CGATAACCCTAGCGAAACCCAG 60.802 54.545 0.00 0.00 39.28 4.45
228 229 0.906775 TAACCCTAGCGAAACCCAGG 59.093 55.000 0.00 0.00 0.00 4.45
229 230 2.124695 CCCTAGCGAAACCCAGGC 60.125 66.667 0.00 0.00 0.00 4.85
230 231 2.511600 CCTAGCGAAACCCAGGCG 60.512 66.667 0.00 0.00 0.00 5.52
231 232 2.511600 CTAGCGAAACCCAGGCGG 60.512 66.667 0.00 0.00 37.81 6.13
241 242 4.883354 CCAGGCGGGGGCAAGATC 62.883 72.222 0.00 0.00 0.00 2.75
242 243 4.113815 CAGGCGGGGGCAAGATCA 62.114 66.667 0.00 0.00 0.00 2.92
243 244 4.115199 AGGCGGGGGCAAGATCAC 62.115 66.667 0.00 0.00 0.00 3.06
244 245 4.424711 GGCGGGGGCAAGATCACA 62.425 66.667 0.00 0.00 0.00 3.58
245 246 2.825836 GCGGGGGCAAGATCACAG 60.826 66.667 0.00 0.00 0.00 3.66
246 247 2.989639 CGGGGGCAAGATCACAGA 59.010 61.111 0.00 0.00 0.00 3.41
247 248 1.153289 CGGGGGCAAGATCACAGAG 60.153 63.158 0.00 0.00 0.00 3.35
248 249 1.225704 GGGGGCAAGATCACAGAGG 59.774 63.158 0.00 0.00 0.00 3.69
249 250 1.274703 GGGGGCAAGATCACAGAGGA 61.275 60.000 0.00 0.00 0.00 3.71
250 251 0.842635 GGGGCAAGATCACAGAGGAT 59.157 55.000 0.00 0.00 0.00 3.24
251 252 1.202746 GGGGCAAGATCACAGAGGATC 60.203 57.143 0.00 0.00 43.21 3.36
252 253 1.202746 GGGCAAGATCACAGAGGATCC 60.203 57.143 2.48 2.48 43.79 3.36
253 254 1.202746 GGCAAGATCACAGAGGATCCC 60.203 57.143 8.55 0.00 43.79 3.85
254 255 1.202746 GCAAGATCACAGAGGATCCCC 60.203 57.143 8.55 0.00 43.79 4.81
255 256 1.419387 CAAGATCACAGAGGATCCCCC 59.581 57.143 8.55 0.14 43.79 5.40
269 270 4.519610 CCCCCTTTGTCACCCTTG 57.480 61.111 0.00 0.00 0.00 3.61
270 271 1.850549 CCCCCTTTGTCACCCTTGA 59.149 57.895 0.00 0.00 0.00 3.02
271 272 0.187361 CCCCCTTTGTCACCCTTGAA 59.813 55.000 0.00 0.00 31.90 2.69
272 273 1.412361 CCCCCTTTGTCACCCTTGAAA 60.412 52.381 0.00 0.00 31.90 2.69
273 274 2.608623 CCCCTTTGTCACCCTTGAAAT 58.391 47.619 0.00 0.00 31.90 2.17
274 275 3.501385 CCCCCTTTGTCACCCTTGAAATA 60.501 47.826 0.00 0.00 31.90 1.40
275 276 3.763897 CCCCTTTGTCACCCTTGAAATAG 59.236 47.826 0.00 0.00 31.90 1.73
276 277 4.407365 CCCTTTGTCACCCTTGAAATAGT 58.593 43.478 0.00 0.00 31.90 2.12
283 284 5.949354 TGTCACCCTTGAAATAGTTTATGGG 59.051 40.000 14.69 14.69 39.26 4.00
290 291 7.255942 CCCTTGAAATAGTTTATGGGCTTATGG 60.256 40.741 5.84 0.00 0.00 2.74
291 292 7.287696 CCTTGAAATAGTTTATGGGCTTATGGT 59.712 37.037 0.00 0.00 0.00 3.55
303 304 2.162408 GGCTTATGGTGCACTTCACTTC 59.838 50.000 17.98 0.00 44.98 3.01
408 409 1.072505 AATCCGTTGGCGTTCAGGT 59.927 52.632 0.00 0.00 36.15 4.00
518 524 1.073199 CCGGCTTTTGTCCTGACCT 59.927 57.895 0.00 0.00 0.00 3.85
519 525 1.237285 CCGGCTTTTGTCCTGACCTG 61.237 60.000 0.00 0.00 0.00 4.00
520 526 0.250295 CGGCTTTTGTCCTGACCTGA 60.250 55.000 0.00 0.00 0.00 3.86
521 527 1.239347 GGCTTTTGTCCTGACCTGAC 58.761 55.000 0.00 0.00 0.00 3.51
522 528 1.239347 GCTTTTGTCCTGACCTGACC 58.761 55.000 0.00 0.00 31.60 4.02
594 600 0.179045 CATCAATCACCGTCCCCTCC 60.179 60.000 0.00 0.00 0.00 4.30
595 601 1.345715 ATCAATCACCGTCCCCTCCC 61.346 60.000 0.00 0.00 0.00 4.30
596 602 3.081409 AATCACCGTCCCCTCCCG 61.081 66.667 0.00 0.00 0.00 5.14
995 1034 4.329545 GTCGCCAGGCCTTGTCCA 62.330 66.667 0.00 0.00 0.00 4.02
1321 1369 0.389426 ATGTGTACGTGTTCTCGGCC 60.389 55.000 0.00 0.00 34.94 6.13
1353 1405 3.845259 GTCCGCCCCGCTGTGATA 61.845 66.667 0.00 0.00 0.00 2.15
1508 1560 1.688793 CATTGTGCAATCGTGTGTGG 58.311 50.000 0.00 0.00 0.00 4.17
1513 1565 1.137404 GCAATCGTGTGTGGCCATC 59.863 57.895 9.72 6.30 0.00 3.51
1806 1858 6.879458 GTCCACCTTTATGTACTCATCAAAGT 59.121 38.462 0.00 0.00 35.70 2.66
1888 1940 4.096681 AGGTCATATATCTTGCGGATCCA 58.903 43.478 13.41 0.00 35.98 3.41
1892 1944 4.160439 TCATATATCTTGCGGATCCAGGAC 59.840 45.833 13.41 0.00 35.98 3.85
1899 1951 2.362369 CGGATCCAGGACACAGCCT 61.362 63.158 13.41 0.00 39.37 4.58
2180 2331 8.239314 TCAATAAGTGATTTGACATTTCTCTGC 58.761 33.333 0.00 0.00 0.00 4.26
2239 2390 7.413548 CGTTAATGCCAAAACCTTTTGTCTTTT 60.414 33.333 9.17 0.00 44.52 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.319198 GAACTGCCGGACCTGGGA 61.319 66.667 5.05 1.23 0.00 4.37
32 33 4.410400 GGAACTGCCGGACCTGGG 62.410 72.222 5.05 0.00 0.00 4.45
33 34 3.316573 GAGGAACTGCCGGACCTGG 62.317 68.421 5.05 0.00 41.55 4.45
34 35 2.266055 GAGGAACTGCCGGACCTG 59.734 66.667 5.05 0.00 41.55 4.00
35 36 3.003763 GGAGGAACTGCCGGACCT 61.004 66.667 5.05 4.83 42.57 3.85
43 44 2.656947 TTGTTTGGGAGGAGGAACTG 57.343 50.000 0.00 0.00 41.55 3.16
45 46 2.035961 GCTTTTGTTTGGGAGGAGGAAC 59.964 50.000 0.00 0.00 0.00 3.62
46 47 2.316108 GCTTTTGTTTGGGAGGAGGAA 58.684 47.619 0.00 0.00 0.00 3.36
47 48 1.216678 TGCTTTTGTTTGGGAGGAGGA 59.783 47.619 0.00 0.00 0.00 3.71
48 49 1.703411 TGCTTTTGTTTGGGAGGAGG 58.297 50.000 0.00 0.00 0.00 4.30
49 50 2.892852 TGATGCTTTTGTTTGGGAGGAG 59.107 45.455 0.00 0.00 0.00 3.69
50 51 2.956132 TGATGCTTTTGTTTGGGAGGA 58.044 42.857 0.00 0.00 0.00 3.71
51 52 3.368739 GGATGATGCTTTTGTTTGGGAGG 60.369 47.826 0.00 0.00 0.00 4.30
52 53 3.512724 AGGATGATGCTTTTGTTTGGGAG 59.487 43.478 0.00 0.00 0.00 4.30
53 54 3.509442 AGGATGATGCTTTTGTTTGGGA 58.491 40.909 0.00 0.00 0.00 4.37
54 55 3.368739 GGAGGATGATGCTTTTGTTTGGG 60.369 47.826 0.00 0.00 0.00 4.12
55 56 3.512724 AGGAGGATGATGCTTTTGTTTGG 59.487 43.478 0.00 0.00 0.00 3.28
56 57 4.461781 AGAGGAGGATGATGCTTTTGTTTG 59.538 41.667 0.00 0.00 0.00 2.93
57 58 4.670765 AGAGGAGGATGATGCTTTTGTTT 58.329 39.130 0.00 0.00 0.00 2.83
58 59 4.313020 AGAGGAGGATGATGCTTTTGTT 57.687 40.909 0.00 0.00 0.00 2.83
59 60 4.268359 GAAGAGGAGGATGATGCTTTTGT 58.732 43.478 0.00 0.00 0.00 2.83
60 61 3.631227 GGAAGAGGAGGATGATGCTTTTG 59.369 47.826 0.00 0.00 0.00 2.44
61 62 3.526841 AGGAAGAGGAGGATGATGCTTTT 59.473 43.478 0.00 0.00 0.00 2.27
62 63 3.117963 CAGGAAGAGGAGGATGATGCTTT 60.118 47.826 0.00 0.00 0.00 3.51
63 64 2.438763 CAGGAAGAGGAGGATGATGCTT 59.561 50.000 0.00 0.00 0.00 3.91
64 65 2.048601 CAGGAAGAGGAGGATGATGCT 58.951 52.381 0.00 0.00 0.00 3.79
65 66 1.542987 GCAGGAAGAGGAGGATGATGC 60.543 57.143 0.00 0.00 0.00 3.91
66 67 1.767088 TGCAGGAAGAGGAGGATGATG 59.233 52.381 0.00 0.00 0.00 3.07
67 68 2.048601 CTGCAGGAAGAGGAGGATGAT 58.951 52.381 5.57 0.00 0.00 2.45
68 69 1.007600 TCTGCAGGAAGAGGAGGATGA 59.992 52.381 15.13 0.00 0.00 2.92
69 70 1.493861 TCTGCAGGAAGAGGAGGATG 58.506 55.000 15.13 0.00 0.00 3.51
70 71 2.493099 ATCTGCAGGAAGAGGAGGAT 57.507 50.000 15.13 0.00 0.00 3.24
71 72 2.260639 AATCTGCAGGAAGAGGAGGA 57.739 50.000 15.13 0.00 0.00 3.71
72 73 3.743899 GCTTAATCTGCAGGAAGAGGAGG 60.744 52.174 21.06 4.59 0.00 4.30
73 74 3.465871 GCTTAATCTGCAGGAAGAGGAG 58.534 50.000 21.06 10.08 0.00 3.69
74 75 2.171448 GGCTTAATCTGCAGGAAGAGGA 59.829 50.000 21.06 0.72 0.00 3.71
75 76 2.570135 GGCTTAATCTGCAGGAAGAGG 58.430 52.381 21.06 8.10 0.00 3.69
76 77 2.208431 CGGCTTAATCTGCAGGAAGAG 58.792 52.381 21.06 13.23 0.00 2.85
77 78 1.555075 ACGGCTTAATCTGCAGGAAGA 59.445 47.619 21.06 2.41 0.00 2.87
78 79 1.667724 CACGGCTTAATCTGCAGGAAG 59.332 52.381 15.13 15.37 0.00 3.46
79 80 1.737838 CACGGCTTAATCTGCAGGAA 58.262 50.000 15.13 5.20 0.00 3.36
80 81 0.744414 GCACGGCTTAATCTGCAGGA 60.744 55.000 15.13 0.57 0.00 3.86
81 82 1.026182 TGCACGGCTTAATCTGCAGG 61.026 55.000 15.13 0.00 34.73 4.85
82 83 0.804364 TTGCACGGCTTAATCTGCAG 59.196 50.000 7.63 7.63 40.59 4.41
83 84 0.804364 CTTGCACGGCTTAATCTGCA 59.196 50.000 0.00 0.00 37.86 4.41
84 85 0.804989 ACTTGCACGGCTTAATCTGC 59.195 50.000 0.00 0.00 0.00 4.26
85 86 3.684788 AGTTACTTGCACGGCTTAATCTG 59.315 43.478 0.00 0.00 0.00 2.90
86 87 3.933332 GAGTTACTTGCACGGCTTAATCT 59.067 43.478 0.00 0.00 0.00 2.40
87 88 3.933332 AGAGTTACTTGCACGGCTTAATC 59.067 43.478 0.00 0.00 0.00 1.75
88 89 3.939066 AGAGTTACTTGCACGGCTTAAT 58.061 40.909 0.00 0.00 0.00 1.40
89 90 3.396260 AGAGTTACTTGCACGGCTTAA 57.604 42.857 0.00 0.00 0.00 1.85
90 91 3.323243 GAAGAGTTACTTGCACGGCTTA 58.677 45.455 0.00 0.00 39.13 3.09
91 92 2.143925 GAAGAGTTACTTGCACGGCTT 58.856 47.619 0.00 0.00 39.13 4.35
92 93 1.608283 GGAAGAGTTACTTGCACGGCT 60.608 52.381 0.00 0.00 44.50 5.52
93 94 0.796927 GGAAGAGTTACTTGCACGGC 59.203 55.000 0.00 0.00 44.50 5.68
94 95 1.068474 CGGAAGAGTTACTTGCACGG 58.932 55.000 0.00 0.00 45.19 4.94
95 96 1.068474 CCGGAAGAGTTACTTGCACG 58.932 55.000 0.00 0.00 45.19 5.34
96 97 0.796927 GCCGGAAGAGTTACTTGCAC 59.203 55.000 5.05 0.00 45.19 4.57
97 98 0.669318 CGCCGGAAGAGTTACTTGCA 60.669 55.000 5.05 0.00 45.19 4.08
98 99 0.389426 TCGCCGGAAGAGTTACTTGC 60.389 55.000 5.05 0.00 42.26 4.01
99 100 1.067776 AGTCGCCGGAAGAGTTACTTG 60.068 52.381 5.05 0.00 39.13 3.16
100 101 1.201880 GAGTCGCCGGAAGAGTTACTT 59.798 52.381 5.05 0.00 42.03 2.24
101 102 0.810016 GAGTCGCCGGAAGAGTTACT 59.190 55.000 5.05 0.00 0.00 2.24
102 103 0.179142 GGAGTCGCCGGAAGAGTTAC 60.179 60.000 5.05 0.54 0.00 2.50
103 104 1.318158 GGGAGTCGCCGGAAGAGTTA 61.318 60.000 5.05 0.00 37.63 2.24
104 105 2.647158 GGGAGTCGCCGGAAGAGTT 61.647 63.158 5.05 0.00 37.63 3.01
105 106 3.069318 GGGAGTCGCCGGAAGAGT 61.069 66.667 5.05 6.51 37.63 3.24
106 107 2.352032 AAGGGAGTCGCCGGAAGAG 61.352 63.158 5.05 0.00 37.63 2.85
107 108 2.283676 AAGGGAGTCGCCGGAAGA 60.284 61.111 5.05 0.00 37.63 2.87
108 109 2.125512 CAAGGGAGTCGCCGGAAG 60.126 66.667 5.05 0.00 37.63 3.46
109 110 4.388499 GCAAGGGAGTCGCCGGAA 62.388 66.667 5.05 0.00 37.63 4.30
132 133 1.591863 GAATCGAGTACGCAGGGGC 60.592 63.158 0.00 0.00 39.58 5.80
133 134 1.299165 CGAATCGAGTACGCAGGGG 60.299 63.158 0.00 0.00 39.58 4.79
134 135 1.299165 CCGAATCGAGTACGCAGGG 60.299 63.158 3.36 0.00 39.58 4.45
135 136 1.944676 GCCGAATCGAGTACGCAGG 60.945 63.158 3.36 0.00 39.58 4.85
136 137 1.944676 GGCCGAATCGAGTACGCAG 60.945 63.158 3.36 0.00 39.58 5.18
137 138 2.103538 GGCCGAATCGAGTACGCA 59.896 61.111 3.36 0.00 39.58 5.24
138 139 3.022914 CGGCCGAATCGAGTACGC 61.023 66.667 24.07 0.00 39.58 4.42
139 140 3.022914 GCGGCCGAATCGAGTACG 61.023 66.667 33.48 4.10 41.26 3.67
140 141 2.657620 GGCGGCCGAATCGAGTAC 60.658 66.667 33.48 7.28 0.00 2.73
141 142 2.416244 GATGGCGGCCGAATCGAGTA 62.416 60.000 33.48 4.86 0.00 2.59
142 143 3.792053 GATGGCGGCCGAATCGAGT 62.792 63.158 33.48 6.30 0.00 4.18
143 144 2.978452 AAGATGGCGGCCGAATCGAG 62.978 60.000 33.48 0.00 0.00 4.04
144 145 2.971428 GAAGATGGCGGCCGAATCGA 62.971 60.000 33.48 9.21 0.00 3.59
145 146 2.588877 AAGATGGCGGCCGAATCG 60.589 61.111 33.48 0.95 0.00 3.34
146 147 0.815615 AAGAAGATGGCGGCCGAATC 60.816 55.000 33.48 28.59 0.00 2.52
147 148 0.394352 AAAGAAGATGGCGGCCGAAT 60.394 50.000 33.48 22.03 0.00 3.34
148 149 1.002624 AAAGAAGATGGCGGCCGAA 60.003 52.632 33.48 17.52 0.00 4.30
149 150 1.449601 GAAAGAAGATGGCGGCCGA 60.450 57.895 33.48 9.86 0.00 5.54
150 151 1.450312 AGAAAGAAGATGGCGGCCG 60.450 57.895 24.05 24.05 0.00 6.13
151 152 0.392998 TCAGAAAGAAGATGGCGGCC 60.393 55.000 13.32 13.32 0.00 6.13
152 153 1.601430 GATCAGAAAGAAGATGGCGGC 59.399 52.381 0.00 0.00 0.00 6.53
153 154 2.871022 CAGATCAGAAAGAAGATGGCGG 59.129 50.000 0.00 0.00 0.00 6.13
154 155 2.871022 CCAGATCAGAAAGAAGATGGCG 59.129 50.000 0.00 0.00 0.00 5.69
155 156 3.876320 GTCCAGATCAGAAAGAAGATGGC 59.124 47.826 0.00 0.00 31.02 4.40
156 157 4.118410 CGTCCAGATCAGAAAGAAGATGG 58.882 47.826 0.00 0.00 0.00 3.51
157 158 4.753233 ACGTCCAGATCAGAAAGAAGATG 58.247 43.478 0.00 0.00 0.00 2.90
158 159 5.186797 AGAACGTCCAGATCAGAAAGAAGAT 59.813 40.000 0.00 0.00 0.00 2.40
159 160 4.524714 AGAACGTCCAGATCAGAAAGAAGA 59.475 41.667 0.00 0.00 0.00 2.87
160 161 4.815269 AGAACGTCCAGATCAGAAAGAAG 58.185 43.478 0.00 0.00 0.00 2.85
161 162 4.873746 AGAACGTCCAGATCAGAAAGAA 57.126 40.909 0.00 0.00 0.00 2.52
162 163 4.280929 TGAAGAACGTCCAGATCAGAAAGA 59.719 41.667 0.00 0.00 0.00 2.52
163 164 4.387256 GTGAAGAACGTCCAGATCAGAAAG 59.613 45.833 0.00 0.00 0.00 2.62
164 165 4.202212 TGTGAAGAACGTCCAGATCAGAAA 60.202 41.667 0.00 0.00 0.00 2.52
165 166 3.320826 TGTGAAGAACGTCCAGATCAGAA 59.679 43.478 0.00 0.00 0.00 3.02
166 167 2.890945 TGTGAAGAACGTCCAGATCAGA 59.109 45.455 0.00 0.00 0.00 3.27
167 168 3.303881 TGTGAAGAACGTCCAGATCAG 57.696 47.619 0.00 0.00 0.00 2.90
168 169 3.744238 TTGTGAAGAACGTCCAGATCA 57.256 42.857 0.00 0.00 0.00 2.92
169 170 3.186613 GGTTTGTGAAGAACGTCCAGATC 59.813 47.826 0.00 0.00 0.00 2.75
170 171 3.139077 GGTTTGTGAAGAACGTCCAGAT 58.861 45.455 0.00 0.00 0.00 2.90
171 172 2.557317 GGTTTGTGAAGAACGTCCAGA 58.443 47.619 0.00 0.00 0.00 3.86
172 173 1.602377 GGGTTTGTGAAGAACGTCCAG 59.398 52.381 0.00 0.00 0.00 3.86
173 174 1.210967 AGGGTTTGTGAAGAACGTCCA 59.789 47.619 0.00 0.00 0.00 4.02
174 175 1.963172 AGGGTTTGTGAAGAACGTCC 58.037 50.000 0.00 0.00 0.00 4.79
175 176 2.479275 GCTAGGGTTTGTGAAGAACGTC 59.521 50.000 0.00 0.00 0.00 4.34
176 177 2.158871 TGCTAGGGTTTGTGAAGAACGT 60.159 45.455 0.00 0.00 0.00 3.99
177 178 2.223377 GTGCTAGGGTTTGTGAAGAACG 59.777 50.000 0.00 0.00 0.00 3.95
178 179 3.477530 AGTGCTAGGGTTTGTGAAGAAC 58.522 45.455 0.00 0.00 0.00 3.01
179 180 3.391296 AGAGTGCTAGGGTTTGTGAAGAA 59.609 43.478 0.00 0.00 0.00 2.52
180 181 2.972713 AGAGTGCTAGGGTTTGTGAAGA 59.027 45.455 0.00 0.00 0.00 2.87
181 182 3.330267 GAGAGTGCTAGGGTTTGTGAAG 58.670 50.000 0.00 0.00 0.00 3.02
182 183 2.038557 GGAGAGTGCTAGGGTTTGTGAA 59.961 50.000 0.00 0.00 0.00 3.18
183 184 1.623811 GGAGAGTGCTAGGGTTTGTGA 59.376 52.381 0.00 0.00 0.00 3.58
184 185 1.339151 GGGAGAGTGCTAGGGTTTGTG 60.339 57.143 0.00 0.00 0.00 3.33
185 186 0.984995 GGGAGAGTGCTAGGGTTTGT 59.015 55.000 0.00 0.00 0.00 2.83
186 187 1.208293 GAGGGAGAGTGCTAGGGTTTG 59.792 57.143 0.00 0.00 0.00 2.93
187 188 1.574263 GAGGGAGAGTGCTAGGGTTT 58.426 55.000 0.00 0.00 0.00 3.27
188 189 0.684805 CGAGGGAGAGTGCTAGGGTT 60.685 60.000 0.00 0.00 0.00 4.11
189 190 1.076632 CGAGGGAGAGTGCTAGGGT 60.077 63.158 0.00 0.00 0.00 4.34
190 191 0.178975 ATCGAGGGAGAGTGCTAGGG 60.179 60.000 0.00 0.00 0.00 3.53
191 192 2.554893 GTTATCGAGGGAGAGTGCTAGG 59.445 54.545 0.00 0.00 0.00 3.02
192 193 2.554893 GGTTATCGAGGGAGAGTGCTAG 59.445 54.545 0.00 0.00 0.00 3.42
193 194 2.584236 GGTTATCGAGGGAGAGTGCTA 58.416 52.381 0.00 0.00 0.00 3.49
194 195 1.404843 GGTTATCGAGGGAGAGTGCT 58.595 55.000 0.00 0.00 0.00 4.40
195 196 0.389757 GGGTTATCGAGGGAGAGTGC 59.610 60.000 0.00 0.00 0.00 4.40
196 197 2.074729 AGGGTTATCGAGGGAGAGTG 57.925 55.000 0.00 0.00 0.00 3.51
197 198 2.489437 GCTAGGGTTATCGAGGGAGAGT 60.489 54.545 0.00 0.00 0.00 3.24
198 199 2.164338 GCTAGGGTTATCGAGGGAGAG 58.836 57.143 0.00 0.00 0.00 3.20
199 200 1.544982 CGCTAGGGTTATCGAGGGAGA 60.545 57.143 0.00 0.00 0.00 3.71
200 201 0.882474 CGCTAGGGTTATCGAGGGAG 59.118 60.000 0.00 0.00 0.00 4.30
201 202 0.475475 TCGCTAGGGTTATCGAGGGA 59.525 55.000 6.70 0.00 0.00 4.20
202 203 1.325355 TTCGCTAGGGTTATCGAGGG 58.675 55.000 6.70 0.00 30.16 4.30
203 204 2.545322 GGTTTCGCTAGGGTTATCGAGG 60.545 54.545 6.70 0.00 30.16 4.63
204 205 2.545322 GGGTTTCGCTAGGGTTATCGAG 60.545 54.545 6.70 0.00 30.16 4.04
205 206 1.410153 GGGTTTCGCTAGGGTTATCGA 59.590 52.381 6.70 0.00 0.00 3.59
206 207 1.137479 TGGGTTTCGCTAGGGTTATCG 59.863 52.381 6.70 0.00 0.00 2.92
207 208 2.484947 CCTGGGTTTCGCTAGGGTTATC 60.485 54.545 6.70 0.00 0.00 1.75
208 209 1.489230 CCTGGGTTTCGCTAGGGTTAT 59.511 52.381 6.70 0.00 0.00 1.89
209 210 0.906775 CCTGGGTTTCGCTAGGGTTA 59.093 55.000 6.70 0.00 0.00 2.85
210 211 1.683441 CCTGGGTTTCGCTAGGGTT 59.317 57.895 6.70 0.00 0.00 4.11
211 212 2.967946 GCCTGGGTTTCGCTAGGGT 61.968 63.158 6.70 0.00 0.00 4.34
212 213 2.124695 GCCTGGGTTTCGCTAGGG 60.125 66.667 0.00 0.00 0.00 3.53
213 214 2.511600 CGCCTGGGTTTCGCTAGG 60.512 66.667 0.00 0.00 0.00 3.02
214 215 2.511600 CCGCCTGGGTTTCGCTAG 60.512 66.667 0.00 0.00 0.00 3.42
224 225 4.883354 GATCTTGCCCCCGCCTGG 62.883 72.222 0.00 0.00 0.00 4.45
225 226 4.113815 TGATCTTGCCCCCGCCTG 62.114 66.667 0.00 0.00 0.00 4.85
226 227 4.115199 GTGATCTTGCCCCCGCCT 62.115 66.667 0.00 0.00 0.00 5.52
227 228 4.424711 TGTGATCTTGCCCCCGCC 62.425 66.667 0.00 0.00 0.00 6.13
228 229 2.825836 CTGTGATCTTGCCCCCGC 60.826 66.667 0.00 0.00 0.00 6.13
229 230 1.153289 CTCTGTGATCTTGCCCCCG 60.153 63.158 0.00 0.00 0.00 5.73
230 231 1.225704 CCTCTGTGATCTTGCCCCC 59.774 63.158 0.00 0.00 0.00 5.40
231 232 0.842635 ATCCTCTGTGATCTTGCCCC 59.157 55.000 0.00 0.00 0.00 5.80
232 233 1.202746 GGATCCTCTGTGATCTTGCCC 60.203 57.143 3.84 0.00 40.80 5.36
233 234 1.202746 GGGATCCTCTGTGATCTTGCC 60.203 57.143 12.58 0.00 40.80 4.52
234 235 1.202746 GGGGATCCTCTGTGATCTTGC 60.203 57.143 12.58 0.00 40.80 4.01
235 236 1.419387 GGGGGATCCTCTGTGATCTTG 59.581 57.143 12.53 0.00 40.80 3.02
236 237 1.813102 GGGGGATCCTCTGTGATCTT 58.187 55.000 12.53 0.00 40.80 2.40
237 238 3.567902 GGGGGATCCTCTGTGATCT 57.432 57.895 12.53 0.00 40.80 2.75
252 253 0.187361 TTCAAGGGTGACAAAGGGGG 59.813 55.000 0.00 0.00 31.90 5.40
253 254 2.080654 TTTCAAGGGTGACAAAGGGG 57.919 50.000 0.00 0.00 31.90 4.79
254 255 4.407365 ACTATTTCAAGGGTGACAAAGGG 58.593 43.478 0.00 0.00 31.90 3.95
255 256 6.405278 AAACTATTTCAAGGGTGACAAAGG 57.595 37.500 0.00 0.00 31.90 3.11
256 257 8.028938 CCATAAACTATTTCAAGGGTGACAAAG 58.971 37.037 0.00 0.00 31.90 2.77
257 258 7.039363 CCCATAAACTATTTCAAGGGTGACAAA 60.039 37.037 0.00 0.00 31.90 2.83
258 259 6.435904 CCCATAAACTATTTCAAGGGTGACAA 59.564 38.462 0.00 0.00 31.90 3.18
259 260 5.949354 CCCATAAACTATTTCAAGGGTGACA 59.051 40.000 0.00 0.00 31.90 3.58
260 261 5.163550 GCCCATAAACTATTTCAAGGGTGAC 60.164 44.000 0.00 0.00 37.38 3.67
261 262 4.953579 GCCCATAAACTATTTCAAGGGTGA 59.046 41.667 0.00 0.00 37.38 4.02
262 263 4.956075 AGCCCATAAACTATTTCAAGGGTG 59.044 41.667 0.00 0.00 37.38 4.61
263 264 5.206905 AGCCCATAAACTATTTCAAGGGT 57.793 39.130 0.00 0.00 37.38 4.34
264 265 7.255942 CCATAAGCCCATAAACTATTTCAAGGG 60.256 40.741 0.00 0.00 38.10 3.95
265 266 7.287696 ACCATAAGCCCATAAACTATTTCAAGG 59.712 37.037 0.00 0.00 0.00 3.61
266 267 8.137437 CACCATAAGCCCATAAACTATTTCAAG 58.863 37.037 0.00 0.00 0.00 3.02
267 268 7.417342 GCACCATAAGCCCATAAACTATTTCAA 60.417 37.037 0.00 0.00 0.00 2.69
268 269 6.040391 GCACCATAAGCCCATAAACTATTTCA 59.960 38.462 0.00 0.00 0.00 2.69
269 270 6.040391 TGCACCATAAGCCCATAAACTATTTC 59.960 38.462 0.00 0.00 0.00 2.17
270 271 5.896678 TGCACCATAAGCCCATAAACTATTT 59.103 36.000 0.00 0.00 0.00 1.40
271 272 5.301805 GTGCACCATAAGCCCATAAACTATT 59.698 40.000 5.22 0.00 0.00 1.73
272 273 4.827284 GTGCACCATAAGCCCATAAACTAT 59.173 41.667 5.22 0.00 0.00 2.12
273 274 4.080015 AGTGCACCATAAGCCCATAAACTA 60.080 41.667 14.63 0.00 0.00 2.24
274 275 3.023832 GTGCACCATAAGCCCATAAACT 58.976 45.455 5.22 0.00 0.00 2.66
275 276 3.023832 AGTGCACCATAAGCCCATAAAC 58.976 45.455 14.63 0.00 0.00 2.01
276 277 3.380471 AGTGCACCATAAGCCCATAAA 57.620 42.857 14.63 0.00 0.00 1.40
291 292 0.662619 CCGCAAAGAAGTGAAGTGCA 59.337 50.000 0.00 0.00 34.87 4.57
303 304 6.148811 TGTTTCTATCCTTTTACTCCGCAAAG 59.851 38.462 0.00 0.00 0.00 2.77
596 602 1.442148 GTGATCCACTCCGGTAGCC 59.558 63.158 0.00 0.00 35.57 3.93
597 603 1.065928 CGTGATCCACTCCGGTAGC 59.934 63.158 0.00 0.00 35.57 3.58
600 606 0.034767 TAGTCGTGATCCACTCCGGT 60.035 55.000 0.00 0.00 35.57 5.28
896 935 1.810755 GGAATCGGGTTCTGGTGTTTC 59.189 52.381 0.36 0.00 37.01 2.78
995 1034 4.415150 CCGGGTGGCACATGCTCT 62.415 66.667 20.82 0.00 44.52 4.09
1115 1157 1.300931 CACACGCAGTAGTGGTGCT 60.301 57.895 15.17 4.72 45.80 4.40
1267 1309 2.431942 CGGCGTAGGTGTCACCAC 60.432 66.667 24.02 17.19 41.95 4.16
1297 1344 1.126113 GAGAACACGTACACATTGCGG 59.874 52.381 0.00 0.00 0.00 5.69
1299 1346 1.126113 CCGAGAACACGTACACATTGC 59.874 52.381 0.00 0.00 0.00 3.56
1321 1369 2.484062 GGACAAGATGGCGCCATGG 61.484 63.158 44.96 32.59 36.70 3.66
1353 1405 4.541973 TGTACATTCACATGAGCTGACT 57.458 40.909 0.00 0.00 34.11 3.41
1481 1533 4.033019 CACGATTGCACAATGCTATTCTG 58.967 43.478 0.00 0.00 45.31 3.02
1508 1560 6.019318 CCAATTTTGATTGATTTCTCGATGGC 60.019 38.462 0.92 0.00 33.55 4.40
1513 1565 6.867816 TGAACCCAATTTTGATTGATTTCTCG 59.132 34.615 0.92 0.00 33.55 4.04
1648 1700 1.009829 ATTCGGCTTCAAGCGATCAC 58.990 50.000 2.54 0.00 43.62 3.06
1685 1737 1.678970 GGCTGATCCGCCCAAAACT 60.679 57.895 16.84 0.00 44.41 2.66
1857 1909 5.107453 GCAAGATATATGACCTCGAAAACCG 60.107 44.000 0.00 0.00 40.25 4.44
1859 1911 5.107453 CCGCAAGATATATGACCTCGAAAAC 60.107 44.000 0.00 0.00 43.02 2.43
1907 1959 6.767524 AAACACATCACTCTTTTTACCACA 57.232 33.333 0.00 0.00 0.00 4.17
1908 1960 7.480810 AGAAAACACATCACTCTTTTTACCAC 58.519 34.615 0.00 0.00 0.00 4.16
1910 1962 6.851330 CGAGAAAACACATCACTCTTTTTACC 59.149 38.462 0.00 0.00 0.00 2.85
1912 1964 7.780008 TCGAGAAAACACATCACTCTTTTTA 57.220 32.000 0.00 0.00 0.00 1.52
1940 1992 9.435688 AAAACTAGTGCAATTTTCAAAAGTTCT 57.564 25.926 0.00 0.00 0.00 3.01
2180 2331 2.430546 TTGCCGTGTTTTGCTTATGG 57.569 45.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.