Multiple sequence alignment - TraesCS7B01G211100

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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 TraesCS7B01G211100 chr7B 100.000 3098 0 0 1 3098 385621876 385618779 0.000000e+00 5722.0
1 TraesCS7B01G211100 chr7B 91.724 290 16 5 1 282 10057081 10056792 2.240000e-106 396.0
2 TraesCS7B01G211100 chr7B 78.526 312 41 13 1 287 694309765 694310075 6.820000e-42 182.0
3 TraesCS7B01G211100 chr7B 85.714 161 11 8 139 290 675046105 675045948 3.200000e-35 159.0
4 TraesCS7B01G211100 chr7D 97.740 2124 42 3 903 3020 390157344 390155221 0.000000e+00 3651.0
5 TraesCS7B01G211100 chr7D 97.526 485 6 4 382 864 390157821 390157341 0.000000e+00 824.0
6 TraesCS7B01G211100 chr7D 96.429 84 3 0 3015 3098 390087166 390087083 4.170000e-29 139.0
7 TraesCS7B01G211100 chr7D 93.333 45 2 1 864 907 459945146 459945102 7.170000e-07 65.8
8 TraesCS7B01G211100 chr7A 94.382 2225 79 12 903 3098 441198112 441195905 0.000000e+00 3374.0
9 TraesCS7B01G211100 chr7A 93.277 476 28 3 382 857 441198583 441198112 0.000000e+00 699.0
10 TraesCS7B01G211100 chr7A 91.549 71 4 2 312 381 441198693 441198624 2.540000e-16 97.1
11 TraesCS7B01G211100 chr1B 91.065 291 21 4 1 287 484265782 484266071 3.750000e-104 388.0
12 TraesCS7B01G211100 chr1B 87.821 312 21 8 1 296 190314022 190313712 1.770000e-92 350.0
13 TraesCS7B01G211100 chr1B 80.364 275 31 6 6 257 62532451 62532725 1.470000e-43 187.0
14 TraesCS7B01G211100 chr2D 87.667 300 24 4 1 287 461294976 461295275 1.380000e-88 337.0
15 TraesCS7B01G211100 chr6B 82.724 301 24 11 3 287 29279305 29279017 3.090000e-60 243.0
16 TraesCS7B01G211100 chr6B 89.796 49 4 1 859 906 119844425 119844377 9.280000e-06 62.1
17 TraesCS7B01G211100 chr2B 77.817 284 34 14 24 288 764142567 764142294 6.920000e-32 148.0
18 TraesCS7B01G211100 chr2B 85.556 90 4 1 207 287 794338467 794338378 5.500000e-13 86.1
19 TraesCS7B01G211100 chrUn 87.255 102 3 2 195 287 131412830 131412730 1.170000e-19 108.0
20 TraesCS7B01G211100 chrUn 94.872 39 2 0 870 908 382894094 382894132 9.280000e-06 62.1
21 TraesCS7B01G211100 chr6D 87.755 98 3 1 199 287 80151969 80151872 4.230000e-19 106.0
22 TraesCS7B01G211100 chr1A 95.745 47 2 0 864 910 85841971 85841925 3.310000e-10 76.8
23 TraesCS7B01G211100 chr5D 97.561 41 1 0 866 906 456610971 456610931 1.540000e-08 71.3
24 TraesCS7B01G211100 chr3D 97.561 41 1 0 867 907 2692177 2692217 1.540000e-08 71.3
25 TraesCS7B01G211100 chr2A 92.000 50 2 2 860 907 367675082 367675131 5.540000e-08 69.4
26 TraesCS7B01G211100 chr2A 97.500 40 1 0 867 906 570013462 570013501 5.540000e-08 69.4
27 TraesCS7B01G211100 chr2A 89.091 55 3 3 854 906 54110377 54110324 7.170000e-07 65.8


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 TraesCS7B01G211100 chr7B 385618779 385621876 3097 True 5722.000000 5722 100.000000 1 3098 1 chr7B.!!$R2 3097
1 TraesCS7B01G211100 chr7D 390155221 390157821 2600 True 2237.500000 3651 97.633000 382 3020 2 chr7D.!!$R3 2638
2 TraesCS7B01G211100 chr7A 441195905 441198693 2788 True 1390.033333 3374 93.069333 312 3098 3 chr7A.!!$R1 2786

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
227 228 0.035598 TTTTCTCGTCGATTGGGCCA 59.964 50.000 0.00 0.0 0.0 5.36 F
228 229 0.391130 TTTCTCGTCGATTGGGCCAG 60.391 55.000 6.23 0.0 0.0 4.85 F
475 518 0.463116 CGGCCCGCTTATAAACAGGT 60.463 55.000 0.00 0.0 0.0 4.00 F
911 958 1.477558 GGGACGGAGGGAGTACGATTA 60.478 57.143 0.00 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 1375 1.414181 TCGAAATGGCTCCTCATCCTC 59.586 52.381 0.00 0.00 0.00 3.71 R
1325 1376 1.500474 TCGAAATGGCTCCTCATCCT 58.500 50.000 0.00 0.00 0.00 3.24 R
1557 1608 1.729470 CTGCTGCGGACGTATCCTCT 61.729 60.000 1.17 0.00 43.73 3.69 R
2187 2241 2.294791 AGCACAGGATCTAGATACGCAC 59.705 50.000 9.38 1.25 0.00 5.34 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
60 61 8.990163 TCTTTTTCAAATAACTAACTCTGGGT 57.010 30.769 0.00 0.00 0.00 4.51
90 91 9.877222 TTATATATCTGTAGAGGAGTGGTCAAA 57.123 33.333 0.00 0.00 0.00 2.69
91 92 4.810191 ATCTGTAGAGGAGTGGTCAAAC 57.190 45.455 0.00 0.00 0.00 2.93
92 93 2.897969 TCTGTAGAGGAGTGGTCAAACC 59.102 50.000 0.00 0.00 39.22 3.27
93 94 2.900546 CTGTAGAGGAGTGGTCAAACCT 59.099 50.000 0.00 0.00 39.58 3.50
94 95 4.087182 CTGTAGAGGAGTGGTCAAACCTA 58.913 47.826 0.00 0.00 39.58 3.08
95 96 3.830755 TGTAGAGGAGTGGTCAAACCTAC 59.169 47.826 0.00 0.00 39.58 3.18
96 97 2.972348 AGAGGAGTGGTCAAACCTACA 58.028 47.619 0.00 0.00 39.58 2.74
97 98 3.521727 AGAGGAGTGGTCAAACCTACAT 58.478 45.455 0.00 0.00 39.58 2.29
98 99 3.515901 AGAGGAGTGGTCAAACCTACATC 59.484 47.826 0.00 0.00 39.58 3.06
99 100 2.233922 AGGAGTGGTCAAACCTACATCG 59.766 50.000 0.00 0.00 39.58 3.84
100 101 2.028385 GGAGTGGTCAAACCTACATCGT 60.028 50.000 0.00 0.00 39.58 3.73
101 102 3.556423 GGAGTGGTCAAACCTACATCGTT 60.556 47.826 0.00 0.00 39.58 3.85
102 103 4.062991 GAGTGGTCAAACCTACATCGTTT 58.937 43.478 0.00 0.00 39.58 3.60
103 104 4.062991 AGTGGTCAAACCTACATCGTTTC 58.937 43.478 0.00 0.00 39.58 2.78
104 105 4.062991 GTGGTCAAACCTACATCGTTTCT 58.937 43.478 0.00 0.00 39.58 2.52
105 106 4.062293 TGGTCAAACCTACATCGTTTCTG 58.938 43.478 0.00 0.00 39.58 3.02
106 107 3.435671 GGTCAAACCTACATCGTTTCTGG 59.564 47.826 0.00 0.00 34.73 3.86
107 108 4.062991 GTCAAACCTACATCGTTTCTGGT 58.937 43.478 0.00 0.00 31.11 4.00
108 109 5.232463 GTCAAACCTACATCGTTTCTGGTA 58.768 41.667 0.00 0.00 31.11 3.25
109 110 5.347907 GTCAAACCTACATCGTTTCTGGTAG 59.652 44.000 0.00 0.00 31.11 3.18
110 111 5.011329 TCAAACCTACATCGTTTCTGGTAGT 59.989 40.000 0.00 0.00 33.14 2.73
111 112 5.479124 AACCTACATCGTTTCTGGTAGTT 57.521 39.130 0.00 0.00 33.14 2.24
112 113 5.069501 ACCTACATCGTTTCTGGTAGTTC 57.930 43.478 0.00 0.00 33.14 3.01
113 114 4.525487 ACCTACATCGTTTCTGGTAGTTCA 59.475 41.667 0.00 0.00 33.14 3.18
114 115 4.863131 CCTACATCGTTTCTGGTAGTTCAC 59.137 45.833 0.00 0.00 33.14 3.18
115 116 4.330944 ACATCGTTTCTGGTAGTTCACA 57.669 40.909 0.00 0.00 0.00 3.58
116 117 4.699637 ACATCGTTTCTGGTAGTTCACAA 58.300 39.130 0.00 0.00 0.00 3.33
117 118 4.750098 ACATCGTTTCTGGTAGTTCACAAG 59.250 41.667 0.00 0.00 0.00 3.16
118 119 3.128349 TCGTTTCTGGTAGTTCACAAGC 58.872 45.455 0.00 0.00 0.00 4.01
119 120 3.131396 CGTTTCTGGTAGTTCACAAGCT 58.869 45.455 0.00 0.00 0.00 3.74
120 121 3.059597 CGTTTCTGGTAGTTCACAAGCTG 60.060 47.826 0.00 0.00 0.00 4.24
121 122 4.127171 GTTTCTGGTAGTTCACAAGCTGA 58.873 43.478 0.00 0.00 0.00 4.26
122 123 3.667497 TCTGGTAGTTCACAAGCTGAG 57.333 47.619 0.00 0.00 0.00 3.35
123 124 2.072298 CTGGTAGTTCACAAGCTGAGC 58.928 52.381 0.00 0.00 0.00 4.26
124 125 1.694150 TGGTAGTTCACAAGCTGAGCT 59.306 47.619 0.00 0.00 42.68 4.09
125 126 2.289072 TGGTAGTTCACAAGCTGAGCTC 60.289 50.000 7.72 6.82 39.55 4.09
126 127 2.342179 GTAGTTCACAAGCTGAGCTCC 58.658 52.381 7.72 0.00 39.55 4.70
127 128 1.055040 AGTTCACAAGCTGAGCTCCT 58.945 50.000 7.72 0.00 35.64 3.69
128 129 1.001860 AGTTCACAAGCTGAGCTCCTC 59.998 52.381 7.72 2.47 35.64 3.71
129 130 1.001860 GTTCACAAGCTGAGCTCCTCT 59.998 52.381 7.72 5.07 38.25 3.69
130 131 0.607112 TCACAAGCTGAGCTCCTCTG 59.393 55.000 7.72 4.65 38.25 3.35
131 132 0.391395 CACAAGCTGAGCTCCTCTGG 60.391 60.000 7.72 8.15 38.25 3.86
132 133 0.835543 ACAAGCTGAGCTCCTCTGGT 60.836 55.000 7.72 8.82 38.25 4.00
133 134 0.391395 CAAGCTGAGCTCCTCTGGTG 60.391 60.000 7.72 0.00 38.25 4.17
134 135 1.551908 AAGCTGAGCTCCTCTGGTGG 61.552 60.000 7.72 0.00 38.25 4.61
135 136 2.289532 GCTGAGCTCCTCTGGTGGT 61.290 63.158 12.15 0.00 31.52 4.16
136 137 1.835927 GCTGAGCTCCTCTGGTGGTT 61.836 60.000 12.15 0.00 31.52 3.67
137 138 0.689623 CTGAGCTCCTCTGGTGGTTT 59.310 55.000 12.15 0.00 0.00 3.27
138 139 0.397941 TGAGCTCCTCTGGTGGTTTG 59.602 55.000 12.15 0.00 0.00 2.93
139 140 0.322008 GAGCTCCTCTGGTGGTTTGG 60.322 60.000 0.87 0.00 0.00 3.28
140 141 1.303643 GCTCCTCTGGTGGTTTGGG 60.304 63.158 0.00 0.00 0.00 4.12
141 142 2.069165 GCTCCTCTGGTGGTTTGGGT 62.069 60.000 0.00 0.00 0.00 4.51
142 143 0.250901 CTCCTCTGGTGGTTTGGGTG 60.251 60.000 0.00 0.00 0.00 4.61
143 144 0.991355 TCCTCTGGTGGTTTGGGTGT 60.991 55.000 0.00 0.00 0.00 4.16
144 145 0.106217 CCTCTGGTGGTTTGGGTGTT 60.106 55.000 0.00 0.00 0.00 3.32
145 146 1.144093 CCTCTGGTGGTTTGGGTGTTA 59.856 52.381 0.00 0.00 0.00 2.41
146 147 2.504367 CTCTGGTGGTTTGGGTGTTAG 58.496 52.381 0.00 0.00 0.00 2.34
147 148 1.144093 TCTGGTGGTTTGGGTGTTAGG 59.856 52.381 0.00 0.00 0.00 2.69
148 149 0.927767 TGGTGGTTTGGGTGTTAGGT 59.072 50.000 0.00 0.00 0.00 3.08
149 150 1.288335 TGGTGGTTTGGGTGTTAGGTT 59.712 47.619 0.00 0.00 0.00 3.50
150 151 1.684450 GGTGGTTTGGGTGTTAGGTTG 59.316 52.381 0.00 0.00 0.00 3.77
151 152 1.067974 GTGGTTTGGGTGTTAGGTTGC 59.932 52.381 0.00 0.00 0.00 4.17
152 153 1.063567 TGGTTTGGGTGTTAGGTTGCT 60.064 47.619 0.00 0.00 0.00 3.91
153 154 2.175069 TGGTTTGGGTGTTAGGTTGCTA 59.825 45.455 0.00 0.00 0.00 3.49
154 155 3.181427 TGGTTTGGGTGTTAGGTTGCTAT 60.181 43.478 0.00 0.00 0.00 2.97
155 156 3.830178 GGTTTGGGTGTTAGGTTGCTATT 59.170 43.478 0.00 0.00 0.00 1.73
156 157 4.082408 GGTTTGGGTGTTAGGTTGCTATTC 60.082 45.833 0.00 0.00 0.00 1.75
157 158 3.359695 TGGGTGTTAGGTTGCTATTCC 57.640 47.619 0.00 0.00 0.00 3.01
158 159 2.916934 TGGGTGTTAGGTTGCTATTCCT 59.083 45.455 0.00 0.00 37.80 3.36
159 160 3.332485 TGGGTGTTAGGTTGCTATTCCTT 59.668 43.478 0.00 0.00 35.51 3.36
160 161 4.536888 TGGGTGTTAGGTTGCTATTCCTTA 59.463 41.667 0.00 0.00 35.51 2.69
161 162 5.123936 GGGTGTTAGGTTGCTATTCCTTAG 58.876 45.833 0.00 0.00 35.51 2.18
162 163 5.123936 GGTGTTAGGTTGCTATTCCTTAGG 58.876 45.833 0.00 0.00 35.51 2.69
163 164 5.338953 GGTGTTAGGTTGCTATTCCTTAGGT 60.339 44.000 0.00 0.00 35.51 3.08
164 165 5.585047 GTGTTAGGTTGCTATTCCTTAGGTG 59.415 44.000 0.00 0.00 35.51 4.00
165 166 5.486063 TGTTAGGTTGCTATTCCTTAGGTGA 59.514 40.000 0.00 0.00 35.51 4.02
166 167 6.157994 TGTTAGGTTGCTATTCCTTAGGTGAT 59.842 38.462 0.00 0.00 35.51 3.06
167 168 5.041191 AGGTTGCTATTCCTTAGGTGATG 57.959 43.478 0.00 0.00 0.00 3.07
168 169 4.137543 GGTTGCTATTCCTTAGGTGATGG 58.862 47.826 0.00 0.00 0.00 3.51
169 170 4.137543 GTTGCTATTCCTTAGGTGATGGG 58.862 47.826 0.00 0.00 0.00 4.00
170 171 3.393687 TGCTATTCCTTAGGTGATGGGT 58.606 45.455 0.00 0.00 0.00 4.51
171 172 3.785887 TGCTATTCCTTAGGTGATGGGTT 59.214 43.478 0.00 0.00 0.00 4.11
172 173 4.141482 TGCTATTCCTTAGGTGATGGGTTC 60.141 45.833 0.00 0.00 0.00 3.62
173 174 3.560636 ATTCCTTAGGTGATGGGTTCG 57.439 47.619 0.00 0.00 0.00 3.95
174 175 2.241281 TCCTTAGGTGATGGGTTCGA 57.759 50.000 0.00 0.00 0.00 3.71
175 176 2.108168 TCCTTAGGTGATGGGTTCGAG 58.892 52.381 0.00 0.00 0.00 4.04
176 177 1.831736 CCTTAGGTGATGGGTTCGAGT 59.168 52.381 0.00 0.00 0.00 4.18
177 178 2.236395 CCTTAGGTGATGGGTTCGAGTT 59.764 50.000 0.00 0.00 0.00 3.01
178 179 3.522553 CTTAGGTGATGGGTTCGAGTTC 58.477 50.000 0.00 0.00 0.00 3.01
179 180 0.613777 AGGTGATGGGTTCGAGTTCC 59.386 55.000 0.00 0.00 0.00 3.62
180 181 0.323629 GGTGATGGGTTCGAGTTCCA 59.676 55.000 6.03 6.03 34.79 3.53
181 182 1.676014 GGTGATGGGTTCGAGTTCCAG 60.676 57.143 8.90 0.00 33.68 3.86
182 183 1.002087 GTGATGGGTTCGAGTTCCAGT 59.998 52.381 8.90 0.00 33.68 4.00
183 184 1.697432 TGATGGGTTCGAGTTCCAGTT 59.303 47.619 8.90 0.00 33.68 3.16
184 185 2.105821 TGATGGGTTCGAGTTCCAGTTT 59.894 45.455 8.90 0.00 33.68 2.66
185 186 2.721425 TGGGTTCGAGTTCCAGTTTT 57.279 45.000 5.90 0.00 0.00 2.43
186 187 3.007473 TGGGTTCGAGTTCCAGTTTTT 57.993 42.857 5.90 0.00 0.00 1.94
187 188 2.685897 TGGGTTCGAGTTCCAGTTTTTG 59.314 45.455 5.90 0.00 0.00 2.44
188 189 2.543031 GGGTTCGAGTTCCAGTTTTTGC 60.543 50.000 5.90 0.00 0.00 3.68
189 190 2.098443 GGTTCGAGTTCCAGTTTTTGCA 59.902 45.455 0.00 0.00 0.00 4.08
190 191 3.243401 GGTTCGAGTTCCAGTTTTTGCAT 60.243 43.478 0.00 0.00 0.00 3.96
191 192 3.896648 TCGAGTTCCAGTTTTTGCATC 57.103 42.857 0.00 0.00 0.00 3.91
192 193 2.223144 TCGAGTTCCAGTTTTTGCATCG 59.777 45.455 0.00 0.00 0.00 3.84
193 194 2.032030 CGAGTTCCAGTTTTTGCATCGT 60.032 45.455 0.00 0.00 0.00 3.73
194 195 3.185594 CGAGTTCCAGTTTTTGCATCGTA 59.814 43.478 0.00 0.00 0.00 3.43
195 196 4.666655 CGAGTTCCAGTTTTTGCATCGTAG 60.667 45.833 0.00 0.00 0.00 3.51
196 197 4.134563 AGTTCCAGTTTTTGCATCGTAGT 58.865 39.130 0.00 0.00 0.00 2.73
197 198 4.213482 AGTTCCAGTTTTTGCATCGTAGTC 59.787 41.667 0.00 0.00 0.00 2.59
198 199 4.002906 TCCAGTTTTTGCATCGTAGTCT 57.997 40.909 0.00 0.00 0.00 3.24
199 200 4.385825 TCCAGTTTTTGCATCGTAGTCTT 58.614 39.130 0.00 0.00 0.00 3.01
200 201 4.819630 TCCAGTTTTTGCATCGTAGTCTTT 59.180 37.500 0.00 0.00 0.00 2.52
201 202 5.298276 TCCAGTTTTTGCATCGTAGTCTTTT 59.702 36.000 0.00 0.00 0.00 2.27
202 203 6.483974 TCCAGTTTTTGCATCGTAGTCTTTTA 59.516 34.615 0.00 0.00 0.00 1.52
203 204 6.577427 CCAGTTTTTGCATCGTAGTCTTTTAC 59.423 38.462 0.00 0.00 0.00 2.01
204 205 7.352739 CAGTTTTTGCATCGTAGTCTTTTACT 58.647 34.615 0.00 0.00 42.62 2.24
205 206 7.321271 CAGTTTTTGCATCGTAGTCTTTTACTG 59.679 37.037 0.00 0.00 39.39 2.74
206 207 6.854496 TTTTGCATCGTAGTCTTTTACTGT 57.146 33.333 0.00 0.00 39.39 3.55
207 208 6.854496 TTTGCATCGTAGTCTTTTACTGTT 57.146 33.333 0.00 0.00 39.39 3.16
208 209 6.854496 TTGCATCGTAGTCTTTTACTGTTT 57.146 33.333 0.00 0.00 39.39 2.83
209 210 6.854496 TGCATCGTAGTCTTTTACTGTTTT 57.146 33.333 0.00 0.00 39.39 2.43
210 211 7.254227 TGCATCGTAGTCTTTTACTGTTTTT 57.746 32.000 0.00 0.00 39.39 1.94
226 227 1.161843 TTTTTCTCGTCGATTGGGCC 58.838 50.000 0.00 0.00 0.00 5.80
227 228 0.035598 TTTTCTCGTCGATTGGGCCA 59.964 50.000 0.00 0.00 0.00 5.36
228 229 0.391130 TTTCTCGTCGATTGGGCCAG 60.391 55.000 6.23 0.00 0.00 4.85
229 230 2.852495 TTCTCGTCGATTGGGCCAGC 62.852 60.000 6.23 1.89 0.00 4.85
230 231 4.467084 TCGTCGATTGGGCCAGCC 62.467 66.667 6.23 0.00 0.00 4.85
268 269 4.166011 GCTAACCGGCGCTTGCAG 62.166 66.667 7.64 0.00 41.71 4.41
269 270 4.166011 CTAACCGGCGCTTGCAGC 62.166 66.667 7.64 0.00 41.71 5.25
278 279 3.558411 GCTTGCAGCGCCGACTAG 61.558 66.667 2.29 0.98 0.00 2.57
279 280 2.887568 CTTGCAGCGCCGACTAGG 60.888 66.667 2.29 0.00 44.97 3.02
280 281 3.356639 CTTGCAGCGCCGACTAGGA 62.357 63.158 2.29 0.00 45.00 2.94
281 282 3.356639 TTGCAGCGCCGACTAGGAG 62.357 63.158 2.29 0.00 45.00 3.69
286 287 3.597728 CGCCGACTAGGAGCTCCC 61.598 72.222 29.54 12.87 45.00 4.30
287 288 3.228017 GCCGACTAGGAGCTCCCC 61.228 72.222 29.54 14.65 45.00 4.81
288 289 2.522193 CCGACTAGGAGCTCCCCC 60.522 72.222 29.54 14.30 45.00 5.40
289 290 2.907917 CGACTAGGAGCTCCCCCG 60.908 72.222 29.54 21.51 36.42 5.73
290 291 2.601868 GACTAGGAGCTCCCCCGA 59.398 66.667 29.54 11.38 36.42 5.14
291 292 1.076192 GACTAGGAGCTCCCCCGAA 60.076 63.158 29.54 9.00 36.42 4.30
292 293 1.075896 ACTAGGAGCTCCCCCGAAG 60.076 63.158 29.54 19.50 36.42 3.79
293 294 1.230497 CTAGGAGCTCCCCCGAAGA 59.770 63.158 29.54 5.22 36.42 2.87
294 295 0.825840 CTAGGAGCTCCCCCGAAGAG 60.826 65.000 29.54 11.05 36.42 2.85
295 296 2.299727 TAGGAGCTCCCCCGAAGAGG 62.300 65.000 29.54 0.00 40.63 3.69
296 297 2.042843 GAGCTCCCCCGAAGAGGA 60.043 66.667 0.87 0.00 45.00 3.71
297 298 2.042435 AGCTCCCCCGAAGAGGAG 60.042 66.667 1.58 1.58 46.31 3.69
298 299 3.157949 GCTCCCCCGAAGAGGAGG 61.158 72.222 8.08 0.00 44.57 4.30
299 300 2.364961 CTCCCCCGAAGAGGAGGT 59.635 66.667 0.00 0.00 45.00 3.85
300 301 1.758906 CTCCCCCGAAGAGGAGGTC 60.759 68.421 0.00 0.00 45.00 3.85
301 302 2.231540 CTCCCCCGAAGAGGAGGTCT 62.232 65.000 0.00 0.00 45.00 3.85
302 303 1.758906 CCCCCGAAGAGGAGGTCTC 60.759 68.421 0.00 0.00 45.00 3.36
324 325 9.178758 GTCTCTGACATGGACCTTTATTTATTT 57.821 33.333 0.00 0.00 32.09 1.40
395 438 2.195123 GAAACCCGGCACACATTCCG 62.195 60.000 0.00 0.00 44.89 4.30
475 518 0.463116 CGGCCCGCTTATAAACAGGT 60.463 55.000 0.00 0.00 0.00 4.00
689 732 2.418197 CGCCGTCTTCTTTTGGATCCTA 60.418 50.000 14.23 1.56 0.00 2.94
868 915 7.192148 TGAGTTCGATCTATCTAGTAACAGC 57.808 40.000 0.00 0.00 0.00 4.40
869 916 6.993308 TGAGTTCGATCTATCTAGTAACAGCT 59.007 38.462 0.00 0.00 0.00 4.24
870 917 7.499563 TGAGTTCGATCTATCTAGTAACAGCTT 59.500 37.037 0.00 0.00 0.00 3.74
871 918 7.644490 AGTTCGATCTATCTAGTAACAGCTTG 58.356 38.462 0.00 0.00 0.00 4.01
872 919 6.003234 TCGATCTATCTAGTAACAGCTTGC 57.997 41.667 0.00 0.00 0.00 4.01
873 920 5.531287 TCGATCTATCTAGTAACAGCTTGCA 59.469 40.000 0.00 0.00 0.00 4.08
874 921 6.039382 TCGATCTATCTAGTAACAGCTTGCAA 59.961 38.462 0.00 0.00 0.00 4.08
875 922 6.143118 CGATCTATCTAGTAACAGCTTGCAAC 59.857 42.308 0.00 0.00 0.00 4.17
876 923 6.280855 TCTATCTAGTAACAGCTTGCAACA 57.719 37.500 0.00 0.00 0.00 3.33
877 924 6.100004 TCTATCTAGTAACAGCTTGCAACAC 58.900 40.000 0.00 0.00 0.00 3.32
878 925 3.057019 TCTAGTAACAGCTTGCAACACG 58.943 45.455 0.00 0.00 0.00 4.49
879 926 1.948104 AGTAACAGCTTGCAACACGA 58.052 45.000 0.00 0.00 0.00 4.35
880 927 2.494059 AGTAACAGCTTGCAACACGAT 58.506 42.857 0.00 0.00 0.00 3.73
881 928 2.480419 AGTAACAGCTTGCAACACGATC 59.520 45.455 0.00 0.00 0.00 3.69
882 929 1.597742 AACAGCTTGCAACACGATCT 58.402 45.000 0.00 0.00 0.00 2.75
883 930 1.597742 ACAGCTTGCAACACGATCTT 58.402 45.000 0.00 0.00 0.00 2.40
884 931 2.766313 ACAGCTTGCAACACGATCTTA 58.234 42.857 0.00 0.00 0.00 2.10
885 932 3.338249 ACAGCTTGCAACACGATCTTAT 58.662 40.909 0.00 0.00 0.00 1.73
886 933 4.503910 ACAGCTTGCAACACGATCTTATA 58.496 39.130 0.00 0.00 0.00 0.98
887 934 5.118990 ACAGCTTGCAACACGATCTTATAT 58.881 37.500 0.00 0.00 0.00 0.86
888 935 5.586243 ACAGCTTGCAACACGATCTTATATT 59.414 36.000 0.00 0.00 0.00 1.28
889 936 5.905733 CAGCTTGCAACACGATCTTATATTG 59.094 40.000 0.00 0.00 0.00 1.90
890 937 5.586243 AGCTTGCAACACGATCTTATATTGT 59.414 36.000 0.00 0.00 0.00 2.71
891 938 5.678483 GCTTGCAACACGATCTTATATTGTG 59.322 40.000 0.00 4.22 38.91 3.33
892 939 5.733226 TGCAACACGATCTTATATTGTGG 57.267 39.130 9.55 0.00 37.65 4.17
893 940 4.574421 TGCAACACGATCTTATATTGTGGG 59.426 41.667 9.55 3.64 37.65 4.61
894 941 4.814234 GCAACACGATCTTATATTGTGGGA 59.186 41.667 9.55 0.00 37.65 4.37
895 942 5.277345 GCAACACGATCTTATATTGTGGGAC 60.277 44.000 9.55 0.00 37.65 4.46
896 943 4.617959 ACACGATCTTATATTGTGGGACG 58.382 43.478 9.55 0.00 37.65 4.79
897 944 3.987868 CACGATCTTATATTGTGGGACGG 59.012 47.826 0.00 0.00 31.43 4.79
898 945 3.893200 ACGATCTTATATTGTGGGACGGA 59.107 43.478 0.00 0.00 0.00 4.69
899 946 4.022242 ACGATCTTATATTGTGGGACGGAG 60.022 45.833 0.00 0.00 0.00 4.63
900 947 4.618460 CGATCTTATATTGTGGGACGGAGG 60.618 50.000 0.00 0.00 0.00 4.30
901 948 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
911 958 1.477558 GGGACGGAGGGAGTACGATTA 60.478 57.143 0.00 0.00 0.00 1.75
1011 1059 2.930887 GCAGAGAGTAATGGCGTCAACA 60.931 50.000 0.00 0.00 0.00 3.33
1083 1131 3.827302 AGATCTGTCAGTTTAGTCACGGT 59.173 43.478 0.00 0.00 0.00 4.83
1240 1291 3.519107 TGAGTTCATGAGCAAGTATGGGA 59.481 43.478 12.41 0.00 0.00 4.37
1324 1375 9.318041 CGTTATTGTCAAGTGTATTCTTTGAAG 57.682 33.333 0.00 0.00 0.00 3.02
1338 1389 1.956869 TTGAAGAGGATGAGGAGCCA 58.043 50.000 0.00 0.00 0.00 4.75
1350 1401 3.684908 TGAGGAGCCATTTCGATTCAAA 58.315 40.909 0.00 0.00 0.00 2.69
1449 1500 2.200067 CGAGATGACTGCCTTGTGATC 58.800 52.381 0.00 0.00 32.11 2.92
1494 1545 3.826729 GCCAATTAAGGGTGTCTGAAACT 59.173 43.478 0.00 0.00 0.00 2.66
1521 1572 4.308265 CATTGTGTGAAATTGATGTGCCA 58.692 39.130 0.00 0.00 0.00 4.92
1781 1835 3.018856 TGCCTGTGATGGATGATTTCAC 58.981 45.455 0.00 0.00 40.10 3.18
1867 1921 2.816087 AGGTTGAAGCTTATGTGTGCAG 59.184 45.455 0.00 0.00 0.00 4.41
2187 2241 7.226325 TGAAAGCAGTTCCACCAAAATTTATTG 59.774 33.333 0.00 0.00 35.12 1.90
2204 2258 8.539770 AATTTATTGTGCGTATCTAGATCCTG 57.460 34.615 8.95 1.48 0.00 3.86
2213 2267 5.592054 CGTATCTAGATCCTGTGCTTTGAA 58.408 41.667 8.95 0.00 0.00 2.69
2417 2472 6.775142 TGTTTTGATTTGGTCCATCTTACTCA 59.225 34.615 0.00 0.00 0.00 3.41
2477 2532 1.019278 CGCACGGTTCAGCTTACCAT 61.019 55.000 13.71 0.00 35.31 3.55
2591 2648 6.109156 TCTGCTGTTTTAGTTGATACTCCA 57.891 37.500 0.00 0.00 35.78 3.86
2823 2902 8.050778 TGTTCAAGTTGTCAATAACTTTGAGT 57.949 30.769 2.11 0.00 45.85 3.41
2877 2956 3.730715 GTGCATTTTCTGTTTTGACCGAG 59.269 43.478 0.00 0.00 0.00 4.63
2906 2985 5.283457 TGTGAAAACATTTAACTTGGGGG 57.717 39.130 0.00 0.00 0.00 5.40
2925 3004 4.202315 GGGGGTGTCTATTGTTTGCTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
2929 3008 5.523552 GGTGTCTATTGTTTGCTTTTTGCTT 59.476 36.000 0.00 0.00 43.37 3.91
3030 3110 5.008911 TCAGATGTTCTGGTTTGTTGATGTG 59.991 40.000 4.78 0.00 44.39 3.21
3031 3111 3.435105 TGTTCTGGTTTGTTGATGTGC 57.565 42.857 0.00 0.00 0.00 4.57
3067 3147 1.834896 TCCCGCTAGCTGATTACCAAA 59.165 47.619 13.93 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.416284 ACCCAGAGTTAGTTATTTGAAAAAGAA 57.584 29.630 0.00 0.00 0.00 2.52
35 36 8.990163 ACCCAGAGTTAGTTATTTGAAAAAGA 57.010 30.769 0.00 0.00 0.00 2.52
64 65 9.877222 TTTGACCACTCCTCTACAGATATATAA 57.123 33.333 0.00 0.00 0.00 0.98
65 66 9.298250 GTTTGACCACTCCTCTACAGATATATA 57.702 37.037 0.00 0.00 0.00 0.86
66 67 7.233757 GGTTTGACCACTCCTCTACAGATATAT 59.766 40.741 0.00 0.00 38.42 0.86
67 68 6.550108 GGTTTGACCACTCCTCTACAGATATA 59.450 42.308 0.00 0.00 38.42 0.86
68 69 5.364157 GGTTTGACCACTCCTCTACAGATAT 59.636 44.000 0.00 0.00 38.42 1.63
69 70 4.710375 GGTTTGACCACTCCTCTACAGATA 59.290 45.833 0.00 0.00 38.42 1.98
70 71 3.515901 GGTTTGACCACTCCTCTACAGAT 59.484 47.826 0.00 0.00 38.42 2.90
71 72 2.897969 GGTTTGACCACTCCTCTACAGA 59.102 50.000 0.00 0.00 38.42 3.41
72 73 2.900546 AGGTTTGACCACTCCTCTACAG 59.099 50.000 0.00 0.00 41.95 2.74
73 74 2.972348 AGGTTTGACCACTCCTCTACA 58.028 47.619 0.00 0.00 41.95 2.74
74 75 3.830755 TGTAGGTTTGACCACTCCTCTAC 59.169 47.826 0.00 0.00 41.95 2.59
75 76 4.122337 TGTAGGTTTGACCACTCCTCTA 57.878 45.455 0.00 0.00 41.95 2.43
76 77 2.972348 TGTAGGTTTGACCACTCCTCT 58.028 47.619 0.00 0.00 41.95 3.69
77 78 3.676324 CGATGTAGGTTTGACCACTCCTC 60.676 52.174 0.00 0.00 41.95 3.71
78 79 2.233922 CGATGTAGGTTTGACCACTCCT 59.766 50.000 0.00 0.00 41.95 3.69
79 80 2.028385 ACGATGTAGGTTTGACCACTCC 60.028 50.000 0.00 0.00 41.95 3.85
80 81 3.314541 ACGATGTAGGTTTGACCACTC 57.685 47.619 0.00 0.00 41.95 3.51
81 82 3.764237 AACGATGTAGGTTTGACCACT 57.236 42.857 0.00 0.00 41.95 4.00
82 83 4.062991 AGAAACGATGTAGGTTTGACCAC 58.937 43.478 0.00 0.00 41.95 4.16
83 84 4.062293 CAGAAACGATGTAGGTTTGACCA 58.938 43.478 0.00 0.00 41.95 4.02
84 85 3.435671 CCAGAAACGATGTAGGTTTGACC 59.564 47.826 0.00 0.00 37.70 4.02
85 86 4.062991 ACCAGAAACGATGTAGGTTTGAC 58.937 43.478 0.00 0.00 37.70 3.18
86 87 4.345859 ACCAGAAACGATGTAGGTTTGA 57.654 40.909 0.00 0.00 37.70 2.69
87 88 5.235516 ACTACCAGAAACGATGTAGGTTTG 58.764 41.667 0.00 0.00 37.70 2.93
88 89 5.479124 ACTACCAGAAACGATGTAGGTTT 57.521 39.130 0.00 0.00 40.11 3.27
89 90 5.011329 TGAACTACCAGAAACGATGTAGGTT 59.989 40.000 0.00 0.00 35.98 3.50
90 91 4.525487 TGAACTACCAGAAACGATGTAGGT 59.475 41.667 0.00 0.00 35.98 3.08
91 92 4.863131 GTGAACTACCAGAAACGATGTAGG 59.137 45.833 0.00 0.00 35.98 3.18
92 93 5.466819 TGTGAACTACCAGAAACGATGTAG 58.533 41.667 0.00 0.00 37.34 2.74
93 94 5.456548 TGTGAACTACCAGAAACGATGTA 57.543 39.130 0.00 0.00 0.00 2.29
94 95 4.330944 TGTGAACTACCAGAAACGATGT 57.669 40.909 0.00 0.00 0.00 3.06
95 96 4.377431 GCTTGTGAACTACCAGAAACGATG 60.377 45.833 0.00 0.00 0.00 3.84
96 97 3.746492 GCTTGTGAACTACCAGAAACGAT 59.254 43.478 0.00 0.00 0.00 3.73
97 98 3.128349 GCTTGTGAACTACCAGAAACGA 58.872 45.455 0.00 0.00 0.00 3.85
98 99 3.059597 CAGCTTGTGAACTACCAGAAACG 60.060 47.826 0.00 0.00 0.00 3.60
99 100 4.127171 TCAGCTTGTGAACTACCAGAAAC 58.873 43.478 0.00 0.00 29.64 2.78
100 101 4.380531 CTCAGCTTGTGAACTACCAGAAA 58.619 43.478 0.00 0.00 33.60 2.52
101 102 3.803715 GCTCAGCTTGTGAACTACCAGAA 60.804 47.826 0.00 0.00 33.60 3.02
102 103 2.289072 GCTCAGCTTGTGAACTACCAGA 60.289 50.000 0.00 0.00 33.60 3.86
103 104 2.072298 GCTCAGCTTGTGAACTACCAG 58.928 52.381 0.00 0.00 33.60 4.00
104 105 1.694150 AGCTCAGCTTGTGAACTACCA 59.306 47.619 0.00 0.00 33.89 3.25
105 106 2.342179 GAGCTCAGCTTGTGAACTACC 58.658 52.381 9.40 0.00 39.88 3.18
106 107 2.028567 AGGAGCTCAGCTTGTGAACTAC 60.029 50.000 17.19 0.00 39.88 2.73
107 108 2.232452 GAGGAGCTCAGCTTGTGAACTA 59.768 50.000 17.19 0.00 39.88 2.24
108 109 1.001860 GAGGAGCTCAGCTTGTGAACT 59.998 52.381 17.19 0.00 39.88 3.01
109 110 1.001860 AGAGGAGCTCAGCTTGTGAAC 59.998 52.381 17.19 0.00 39.88 3.18
110 111 1.001746 CAGAGGAGCTCAGCTTGTGAA 59.998 52.381 17.19 0.00 39.88 3.18
111 112 0.607112 CAGAGGAGCTCAGCTTGTGA 59.393 55.000 17.19 0.00 39.88 3.58
112 113 0.391395 CCAGAGGAGCTCAGCTTGTG 60.391 60.000 17.19 6.50 39.88 3.33
113 114 0.835543 ACCAGAGGAGCTCAGCTTGT 60.836 55.000 17.19 10.63 39.88 3.16
114 115 0.391395 CACCAGAGGAGCTCAGCTTG 60.391 60.000 17.19 9.99 39.88 4.01
115 116 1.551908 CCACCAGAGGAGCTCAGCTT 61.552 60.000 17.19 0.00 39.88 3.74
116 117 1.988956 CCACCAGAGGAGCTCAGCT 60.989 63.158 17.19 0.00 43.88 4.24
117 118 1.835927 AACCACCAGAGGAGCTCAGC 61.836 60.000 17.19 6.50 32.06 4.26
118 119 0.689623 AAACCACCAGAGGAGCTCAG 59.310 55.000 17.19 1.83 32.06 3.35
119 120 0.397941 CAAACCACCAGAGGAGCTCA 59.602 55.000 17.19 0.00 32.06 4.26
120 121 0.322008 CCAAACCACCAGAGGAGCTC 60.322 60.000 4.71 4.71 0.00 4.09
121 122 1.763770 CCAAACCACCAGAGGAGCT 59.236 57.895 0.00 0.00 0.00 4.09
122 123 1.303643 CCCAAACCACCAGAGGAGC 60.304 63.158 0.00 0.00 0.00 4.70
123 124 0.250901 CACCCAAACCACCAGAGGAG 60.251 60.000 0.00 0.00 0.00 3.69
124 125 0.991355 ACACCCAAACCACCAGAGGA 60.991 55.000 0.00 0.00 0.00 3.71
125 126 0.106217 AACACCCAAACCACCAGAGG 60.106 55.000 0.00 0.00 0.00 3.69
126 127 2.504367 CTAACACCCAAACCACCAGAG 58.496 52.381 0.00 0.00 0.00 3.35
127 128 1.144093 CCTAACACCCAAACCACCAGA 59.856 52.381 0.00 0.00 0.00 3.86
128 129 1.133606 ACCTAACACCCAAACCACCAG 60.134 52.381 0.00 0.00 0.00 4.00
129 130 0.927767 ACCTAACACCCAAACCACCA 59.072 50.000 0.00 0.00 0.00 4.17
130 131 1.684450 CAACCTAACACCCAAACCACC 59.316 52.381 0.00 0.00 0.00 4.61
131 132 1.067974 GCAACCTAACACCCAAACCAC 59.932 52.381 0.00 0.00 0.00 4.16
132 133 1.063567 AGCAACCTAACACCCAAACCA 60.064 47.619 0.00 0.00 0.00 3.67
133 134 1.699730 AGCAACCTAACACCCAAACC 58.300 50.000 0.00 0.00 0.00 3.27
134 135 4.082408 GGAATAGCAACCTAACACCCAAAC 60.082 45.833 0.00 0.00 0.00 2.93
135 136 4.083565 GGAATAGCAACCTAACACCCAAA 58.916 43.478 0.00 0.00 0.00 3.28
136 137 3.332485 AGGAATAGCAACCTAACACCCAA 59.668 43.478 0.00 0.00 34.47 4.12
137 138 2.916934 AGGAATAGCAACCTAACACCCA 59.083 45.455 0.00 0.00 34.47 4.51
138 139 3.646736 AGGAATAGCAACCTAACACCC 57.353 47.619 0.00 0.00 34.47 4.61
139 140 5.123936 CCTAAGGAATAGCAACCTAACACC 58.876 45.833 0.00 0.00 35.25 4.16
140 141 5.585047 CACCTAAGGAATAGCAACCTAACAC 59.415 44.000 0.00 0.00 35.25 3.32
141 142 5.486063 TCACCTAAGGAATAGCAACCTAACA 59.514 40.000 0.00 0.00 35.25 2.41
142 143 5.985911 TCACCTAAGGAATAGCAACCTAAC 58.014 41.667 0.00 0.00 35.25 2.34
143 144 6.409234 CCATCACCTAAGGAATAGCAACCTAA 60.409 42.308 0.00 0.00 35.25 2.69
144 145 5.071788 CCATCACCTAAGGAATAGCAACCTA 59.928 44.000 0.00 0.00 35.25 3.08
145 146 4.141390 CCATCACCTAAGGAATAGCAACCT 60.141 45.833 0.00 0.00 38.23 3.50
146 147 4.137543 CCATCACCTAAGGAATAGCAACC 58.862 47.826 0.00 0.00 0.00 3.77
147 148 4.137543 CCCATCACCTAAGGAATAGCAAC 58.862 47.826 0.00 0.00 0.00 4.17
148 149 3.785887 ACCCATCACCTAAGGAATAGCAA 59.214 43.478 0.00 0.00 0.00 3.91
149 150 3.393687 ACCCATCACCTAAGGAATAGCA 58.606 45.455 0.00 0.00 0.00 3.49
150 151 4.390264 GAACCCATCACCTAAGGAATAGC 58.610 47.826 0.00 0.00 0.00 2.97
151 152 4.344102 TCGAACCCATCACCTAAGGAATAG 59.656 45.833 0.00 0.00 0.00 1.73
152 153 4.291792 TCGAACCCATCACCTAAGGAATA 58.708 43.478 0.00 0.00 0.00 1.75
153 154 3.112263 TCGAACCCATCACCTAAGGAAT 58.888 45.455 0.00 0.00 0.00 3.01
154 155 2.500098 CTCGAACCCATCACCTAAGGAA 59.500 50.000 0.00 0.00 0.00 3.36
155 156 2.108168 CTCGAACCCATCACCTAAGGA 58.892 52.381 0.00 0.00 0.00 3.36
156 157 1.831736 ACTCGAACCCATCACCTAAGG 59.168 52.381 0.00 0.00 0.00 2.69
157 158 3.522553 GAACTCGAACCCATCACCTAAG 58.477 50.000 0.00 0.00 0.00 2.18
158 159 2.235402 GGAACTCGAACCCATCACCTAA 59.765 50.000 0.00 0.00 0.00 2.69
159 160 1.829222 GGAACTCGAACCCATCACCTA 59.171 52.381 0.00 0.00 0.00 3.08
160 161 0.613777 GGAACTCGAACCCATCACCT 59.386 55.000 0.00 0.00 0.00 4.00
161 162 0.323629 TGGAACTCGAACCCATCACC 59.676 55.000 0.00 0.00 0.00 4.02
162 163 1.002087 ACTGGAACTCGAACCCATCAC 59.998 52.381 1.25 0.00 0.00 3.06
163 164 1.348064 ACTGGAACTCGAACCCATCA 58.652 50.000 1.25 0.00 0.00 3.07
164 165 2.474410 AACTGGAACTCGAACCCATC 57.526 50.000 1.25 0.00 0.00 3.51
165 166 2.951229 AAACTGGAACTCGAACCCAT 57.049 45.000 1.25 0.00 0.00 4.00
166 167 2.685897 CAAAAACTGGAACTCGAACCCA 59.314 45.455 0.00 0.00 0.00 4.51
167 168 2.543031 GCAAAAACTGGAACTCGAACCC 60.543 50.000 0.00 0.00 0.00 4.11
168 169 2.098443 TGCAAAAACTGGAACTCGAACC 59.902 45.455 0.00 0.00 0.00 3.62
169 170 3.414549 TGCAAAAACTGGAACTCGAAC 57.585 42.857 0.00 0.00 0.00 3.95
170 171 3.303725 CGATGCAAAAACTGGAACTCGAA 60.304 43.478 0.00 0.00 31.61 3.71
171 172 2.223144 CGATGCAAAAACTGGAACTCGA 59.777 45.455 0.00 0.00 31.61 4.04
172 173 2.032030 ACGATGCAAAAACTGGAACTCG 60.032 45.455 0.00 0.00 34.94 4.18
173 174 3.626028 ACGATGCAAAAACTGGAACTC 57.374 42.857 0.00 0.00 0.00 3.01
174 175 4.134563 ACTACGATGCAAAAACTGGAACT 58.865 39.130 0.00 0.00 0.00 3.01
175 176 4.213482 AGACTACGATGCAAAAACTGGAAC 59.787 41.667 0.00 0.00 0.00 3.62
176 177 4.385825 AGACTACGATGCAAAAACTGGAA 58.614 39.130 0.00 0.00 0.00 3.53
177 178 4.002906 AGACTACGATGCAAAAACTGGA 57.997 40.909 0.00 0.00 0.00 3.86
178 179 4.749245 AAGACTACGATGCAAAAACTGG 57.251 40.909 0.00 0.00 0.00 4.00
179 180 7.321271 CAGTAAAAGACTACGATGCAAAAACTG 59.679 37.037 0.00 0.00 35.64 3.16
180 181 7.012044 ACAGTAAAAGACTACGATGCAAAAACT 59.988 33.333 0.00 0.00 35.64 2.66
181 182 7.130269 ACAGTAAAAGACTACGATGCAAAAAC 58.870 34.615 0.00 0.00 35.64 2.43
182 183 7.254227 ACAGTAAAAGACTACGATGCAAAAA 57.746 32.000 0.00 0.00 35.64 1.94
183 184 6.854496 ACAGTAAAAGACTACGATGCAAAA 57.146 33.333 0.00 0.00 35.64 2.44
184 185 6.854496 AACAGTAAAAGACTACGATGCAAA 57.146 33.333 0.00 0.00 35.64 3.68
185 186 6.854496 AAACAGTAAAAGACTACGATGCAA 57.146 33.333 0.00 0.00 35.64 4.08
186 187 6.854496 AAAACAGTAAAAGACTACGATGCA 57.146 33.333 0.00 0.00 35.64 3.96
207 208 1.161843 GGCCCAATCGACGAGAAAAA 58.838 50.000 3.01 0.00 0.00 1.94
208 209 0.035598 TGGCCCAATCGACGAGAAAA 59.964 50.000 0.00 0.00 0.00 2.29
209 210 0.391130 CTGGCCCAATCGACGAGAAA 60.391 55.000 0.00 0.00 0.00 2.52
210 211 1.218047 CTGGCCCAATCGACGAGAA 59.782 57.895 0.00 0.00 0.00 2.87
211 212 2.892640 CTGGCCCAATCGACGAGA 59.107 61.111 0.00 0.00 0.00 4.04
212 213 2.892425 GCTGGCCCAATCGACGAG 60.892 66.667 0.00 0.00 0.00 4.18
213 214 4.467084 GGCTGGCCCAATCGACGA 62.467 66.667 0.00 0.00 0.00 4.20
251 252 4.166011 CTGCAAGCGCCGGTTAGC 62.166 66.667 2.29 8.72 37.32 3.09
262 263 2.887568 CCTAGTCGGCGCTGCAAG 60.888 66.667 12.58 8.29 0.00 4.01
263 264 3.356639 CTCCTAGTCGGCGCTGCAA 62.357 63.158 12.58 0.00 0.00 4.08
264 265 3.826754 CTCCTAGTCGGCGCTGCA 61.827 66.667 12.58 0.00 0.00 4.41
268 269 4.273257 GGAGCTCCTAGTCGGCGC 62.273 72.222 26.25 0.00 43.98 6.53
269 270 3.597728 GGGAGCTCCTAGTCGGCG 61.598 72.222 31.36 0.00 35.95 6.46
270 271 3.228017 GGGGAGCTCCTAGTCGGC 61.228 72.222 31.36 13.25 35.95 5.54
271 272 2.522193 GGGGGAGCTCCTAGTCGG 60.522 72.222 31.36 0.00 35.95 4.79
272 273 2.905935 TTCGGGGGAGCTCCTAGTCG 62.906 65.000 31.36 25.73 35.95 4.18
273 274 1.076192 TTCGGGGGAGCTCCTAGTC 60.076 63.158 31.36 15.13 35.95 2.59
274 275 1.075896 CTTCGGGGGAGCTCCTAGT 60.076 63.158 31.36 0.00 35.95 2.57
275 276 0.825840 CTCTTCGGGGGAGCTCCTAG 60.826 65.000 31.36 21.57 35.95 3.02
276 277 1.230497 CTCTTCGGGGGAGCTCCTA 59.770 63.158 31.36 12.59 35.95 2.94
277 278 2.042435 CTCTTCGGGGGAGCTCCT 60.042 66.667 31.36 0.00 35.95 3.69
278 279 3.157949 CCTCTTCGGGGGAGCTCC 61.158 72.222 25.59 25.59 0.00 4.70
279 280 2.042843 TCCTCTTCGGGGGAGCTC 60.043 66.667 4.71 4.71 0.00 4.09
280 281 2.042435 CTCCTCTTCGGGGGAGCT 60.042 66.667 0.00 0.00 41.92 4.09
285 286 3.942601 GAGACCTCCTCTTCGGGG 58.057 66.667 0.00 0.00 38.86 5.73
292 293 1.754226 GTCCATGTCAGAGACCTCCTC 59.246 57.143 0.00 0.00 42.28 3.71
293 294 1.621072 GGTCCATGTCAGAGACCTCCT 60.621 57.143 14.20 0.00 45.49 3.69
294 295 0.827368 GGTCCATGTCAGAGACCTCC 59.173 60.000 14.20 0.00 45.49 4.30
298 299 8.738645 AATAAATAAAGGTCCATGTCAGAGAC 57.261 34.615 0.00 0.00 0.00 3.36
299 300 9.753674 AAAATAAATAAAGGTCCATGTCAGAGA 57.246 29.630 0.00 0.00 0.00 3.10
376 377 1.584495 GGAATGTGTGCCGGGTTTC 59.416 57.895 2.18 0.00 0.00 2.78
689 732 3.960102 ACGCATTGGTTCCAATAATCCAT 59.040 39.130 15.47 0.00 35.21 3.41
856 903 3.679980 CGTGTTGCAAGCTGTTACTAGAT 59.320 43.478 0.00 0.00 0.00 1.98
857 904 3.057019 CGTGTTGCAAGCTGTTACTAGA 58.943 45.455 0.00 0.00 0.00 2.43
858 905 3.057019 TCGTGTTGCAAGCTGTTACTAG 58.943 45.455 0.00 0.00 0.00 2.57
859 906 3.100658 TCGTGTTGCAAGCTGTTACTA 57.899 42.857 0.00 0.00 0.00 1.82
860 907 1.948104 TCGTGTTGCAAGCTGTTACT 58.052 45.000 0.00 0.00 0.00 2.24
861 908 2.480419 AGATCGTGTTGCAAGCTGTTAC 59.520 45.455 0.00 0.00 0.00 2.50
862 909 2.766313 AGATCGTGTTGCAAGCTGTTA 58.234 42.857 0.00 0.00 0.00 2.41
863 910 1.597742 AGATCGTGTTGCAAGCTGTT 58.402 45.000 0.00 0.00 0.00 3.16
864 911 1.597742 AAGATCGTGTTGCAAGCTGT 58.402 45.000 0.00 0.00 0.00 4.40
865 912 5.663795 ATATAAGATCGTGTTGCAAGCTG 57.336 39.130 0.00 0.00 0.00 4.24
866 913 5.586243 ACAATATAAGATCGTGTTGCAAGCT 59.414 36.000 0.00 0.00 0.00 3.74
867 914 5.678483 CACAATATAAGATCGTGTTGCAAGC 59.322 40.000 0.00 0.00 0.00 4.01
868 915 6.194463 CCACAATATAAGATCGTGTTGCAAG 58.806 40.000 0.00 0.00 0.00 4.01
869 916 5.065859 CCCACAATATAAGATCGTGTTGCAA 59.934 40.000 0.00 0.00 0.00 4.08
870 917 4.574421 CCCACAATATAAGATCGTGTTGCA 59.426 41.667 0.00 0.00 0.00 4.08
871 918 4.814234 TCCCACAATATAAGATCGTGTTGC 59.186 41.667 0.00 0.00 0.00 4.17
872 919 5.051039 CGTCCCACAATATAAGATCGTGTTG 60.051 44.000 0.00 0.00 0.00 3.33
873 920 5.047847 CGTCCCACAATATAAGATCGTGTT 58.952 41.667 0.00 0.00 0.00 3.32
874 921 4.500887 CCGTCCCACAATATAAGATCGTGT 60.501 45.833 0.00 0.00 0.00 4.49
875 922 3.987868 CCGTCCCACAATATAAGATCGTG 59.012 47.826 0.00 0.00 0.00 4.35
876 923 3.893200 TCCGTCCCACAATATAAGATCGT 59.107 43.478 0.00 0.00 0.00 3.73
877 924 4.486090 CTCCGTCCCACAATATAAGATCG 58.514 47.826 0.00 0.00 0.00 3.69
878 925 4.322801 CCCTCCGTCCCACAATATAAGATC 60.323 50.000 0.00 0.00 0.00 2.75
879 926 3.583086 CCCTCCGTCCCACAATATAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
880 927 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
881 928 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
882 929 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
883 930 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
884 931 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
885 932 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
886 933 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
887 934 0.901580 GTACTCCCTCCGTCCCACAA 60.902 60.000 0.00 0.00 0.00 3.33
888 935 1.304713 GTACTCCCTCCGTCCCACA 60.305 63.158 0.00 0.00 0.00 4.17
889 936 2.413142 CGTACTCCCTCCGTCCCAC 61.413 68.421 0.00 0.00 0.00 4.61
890 937 1.929860 ATCGTACTCCCTCCGTCCCA 61.930 60.000 0.00 0.00 0.00 4.37
891 938 0.754587 AATCGTACTCCCTCCGTCCC 60.755 60.000 0.00 0.00 0.00 4.46
892 939 1.972872 TAATCGTACTCCCTCCGTCC 58.027 55.000 0.00 0.00 0.00 4.79
893 940 2.287487 GCTTAATCGTACTCCCTCCGTC 60.287 54.545 0.00 0.00 0.00 4.79
894 941 1.680207 GCTTAATCGTACTCCCTCCGT 59.320 52.381 0.00 0.00 0.00 4.69
895 942 1.334779 CGCTTAATCGTACTCCCTCCG 60.335 57.143 0.00 0.00 0.00 4.63
896 943 1.952296 TCGCTTAATCGTACTCCCTCC 59.048 52.381 0.00 0.00 0.00 4.30
897 944 3.919223 ATCGCTTAATCGTACTCCCTC 57.081 47.619 0.00 0.00 0.00 4.30
898 945 3.635373 TCAATCGCTTAATCGTACTCCCT 59.365 43.478 0.00 0.00 0.00 4.20
899 946 3.973657 TCAATCGCTTAATCGTACTCCC 58.026 45.455 0.00 0.00 0.00 4.30
900 947 6.421202 AGAAATCAATCGCTTAATCGTACTCC 59.579 38.462 0.00 0.00 0.00 3.85
901 948 7.396190 AGAAATCAATCGCTTAATCGTACTC 57.604 36.000 0.00 0.00 0.00 2.59
942 990 5.162794 ACATTAGCACATTCGTGTACGTTA 58.837 37.500 0.00 0.00 45.50 3.18
946 994 4.088648 GCAACATTAGCACATTCGTGTAC 58.911 43.478 0.00 0.00 45.50 2.90
1050 1098 3.193263 CTGACAGATCTTCAATCGGTGG 58.807 50.000 0.00 0.00 0.00 4.61
1083 1131 2.481289 TGACGTCCATGCCAACAATA 57.519 45.000 14.12 0.00 0.00 1.90
1324 1375 1.414181 TCGAAATGGCTCCTCATCCTC 59.586 52.381 0.00 0.00 0.00 3.71
1325 1376 1.500474 TCGAAATGGCTCCTCATCCT 58.500 50.000 0.00 0.00 0.00 3.24
1338 1389 6.506500 AAGCTGTCAGATTTGAATCGAAAT 57.493 33.333 3.32 0.00 40.35 2.17
1494 1545 6.423302 GCACATCAATTTCACACAATGGTTTA 59.577 34.615 0.00 0.00 0.00 2.01
1521 1572 1.896122 GCTGTAGTGCGTTAGGGGGT 61.896 60.000 0.00 0.00 0.00 4.95
1557 1608 1.729470 CTGCTGCGGACGTATCCTCT 61.729 60.000 1.17 0.00 43.73 3.69
1781 1835 3.008330 ACAGCATTGCTTTCAGCTCTAG 58.992 45.455 8.83 0.00 42.97 2.43
1959 2013 3.103742 GGAAGGGGCCATAAAATTGACA 58.896 45.455 4.39 0.00 0.00 3.58
2187 2241 2.294791 AGCACAGGATCTAGATACGCAC 59.705 50.000 9.38 1.25 0.00 5.34
2204 2258 6.865205 ACTGCTTAGATGATTTTTCAAAGCAC 59.135 34.615 8.66 0.00 41.93 4.40
2417 2472 4.875536 GGACCAAAGCAATTCAAAAAGTGT 59.124 37.500 0.00 0.00 33.10 3.55
2591 2648 7.348080 TCTTCTTTATCATACACGGAGTCAT 57.652 36.000 0.00 0.00 41.61 3.06
2877 2956 4.917415 AGTTAAATGTTTTCACATGAGCGC 59.083 37.500 0.00 0.00 43.34 5.92
2925 3004 3.320673 AACCGTTTTGTGGAAAAAGCA 57.679 38.095 0.00 0.00 32.81 3.91
2929 3008 3.040147 TGCAAACCGTTTTGTGGAAAA 57.960 38.095 7.30 0.00 43.62 2.29
3030 3110 2.480416 CGGGATAGAGAGGATTATGCGC 60.480 54.545 0.00 0.00 0.00 6.09
3031 3111 2.480416 GCGGGATAGAGAGGATTATGCG 60.480 54.545 0.00 0.00 0.00 4.73
3067 3147 3.175594 ACCATGCCACAAAATCTTCCAT 58.824 40.909 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.