Multiple sequence alignment - TraesCS7D01G296900

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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 TraesCS7D01G296900 chr7D 100.000 5910 0 0 1 5910 374428473 374434382 0.000000e+00 10914.0
1 TraesCS7D01G296900 chr7A 94.489 5716 195 49 244 5887 420664078 420669745 0.000000e+00 8700.0
2 TraesCS7D01G296900 chr7A 94.118 51 2 1 3602 3652 420667494 420667543 6.350000e-10 76.8
3 TraesCS7D01G296900 chr7A 87.931 58 7 0 139 196 85696470 85696413 1.060000e-07 69.4
4 TraesCS7D01G296900 chr7B 95.748 3222 89 23 460 3652 369105581 369108783 0.000000e+00 5147.0
5 TraesCS7D01G296900 chr7B 96.150 2208 58 13 3653 5838 369108735 369110937 0.000000e+00 3581.0
6 TraesCS7D01G296900 chr7B 97.101 69 0 2 5824 5891 369110957 369111024 1.350000e-21 115.0


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 TraesCS7D01G296900 chr7D 374428473 374434382 5909 False 10914.000000 10914 100.0000 1 5910 1 chr7D.!!$F1 5909
1 TraesCS7D01G296900 chr7A 420664078 420669745 5667 False 4388.400000 8700 94.3035 244 5887 2 chr7A.!!$F1 5643
2 TraesCS7D01G296900 chr7B 369105581 369111024 5443 False 2947.666667 5147 96.3330 460 5891 3 chr7B.!!$F1 5431

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
84 85 0.036858 GGAGCTGAGAGTTGGACACC 60.037 60.000 0.00 0.0 0.00 4.16 F
129 130 0.109342 AGCAAATGGATCCGCTAGGG 59.891 55.000 9.85 0.0 38.33 3.53 F
334 335 0.177373 GGACCGTCTACCCCAATGTC 59.823 60.000 0.00 0.0 0.00 3.06 F
337 338 0.178068 CCGTCTACCCCAATGTCTGG 59.822 60.000 0.00 0.0 45.97 3.86 F
952 967 0.532573 TTCTCTCTCCGCTGCGAATT 59.467 50.000 25.45 0.0 0.00 2.17 F
953 968 0.532573 TCTCTCTCCGCTGCGAATTT 59.467 50.000 25.45 0.0 0.00 1.82 F
1800 1827 0.921347 CTCGCAAATAAGACCGACCG 59.079 55.000 0.00 0.0 0.00 4.79 F
2287 2314 1.413445 TGCTCCTTGCTGCATTTGTTT 59.587 42.857 1.84 0.0 43.37 2.83 F
3056 3096 1.656587 TGTGCCCCTTCAGTCAGTAT 58.343 50.000 0.00 0.0 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 1989 1.740296 CCCAGGAAGTACAACGCCG 60.740 63.158 0.00 0.00 0.00 6.46 R
2024 2051 7.436376 GCTTTTCTTTTCACTGAGCTGTTTATT 59.564 33.333 0.00 0.00 0.00 1.40 R
2139 2166 2.275318 GTCCTTACACTGCAGATCAGC 58.725 52.381 23.35 2.62 46.76 4.26 R
2287 2314 5.490159 TGACATGATGATGTGCTAGAAACA 58.510 37.500 1.30 0.00 43.22 2.83 R
2733 2768 4.526970 ACCAGTTGTTCACTCATTCTTGT 58.473 39.130 0.00 0.00 30.92 3.16 R
3056 3096 5.964477 ACCTCATAATAACAGAGAAGGGTGA 59.036 40.000 0.00 0.00 0.00 4.02 R
3675 3725 2.308866 AGTAGCCAATACCACCAAAGCT 59.691 45.455 0.00 0.00 34.67 3.74 R
3838 3888 2.359900 AGCTTGGAAATCATGGACGTC 58.640 47.619 7.13 7.13 0.00 4.34 R
4952 5024 0.469917 AGGGATGTTGCTGGTATCCG 59.530 55.000 0.00 0.00 41.00 4.18 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
18 19 3.223661 GAGAGGAGTGTTGTGCTGG 57.776 57.895 0.00 0.00 0.00 4.85
19 20 0.952984 GAGAGGAGTGTTGTGCTGGC 60.953 60.000 0.00 0.00 0.00 4.85
20 21 2.281070 AGGAGTGTTGTGCTGGCG 60.281 61.111 0.00 0.00 0.00 5.69
21 22 4.030452 GGAGTGTTGTGCTGGCGC 62.030 66.667 0.00 0.00 0.00 6.53
22 23 2.974698 GAGTGTTGTGCTGGCGCT 60.975 61.111 7.64 0.00 36.97 5.92
23 24 3.245948 GAGTGTTGTGCTGGCGCTG 62.246 63.158 7.64 1.33 36.97 5.18
24 25 4.332637 GTGTTGTGCTGGCGCTGG 62.333 66.667 7.64 0.93 36.97 4.85
37 38 4.385405 GCTGGCGTCACAGAGGCT 62.385 66.667 10.91 0.00 42.20 4.58
38 39 2.125753 CTGGCGTCACAGAGGCTC 60.126 66.667 6.34 6.34 42.20 4.70
39 40 3.978723 CTGGCGTCACAGAGGCTCG 62.979 68.421 9.22 6.83 42.20 5.03
40 41 4.803426 GGCGTCACAGAGGCTCGG 62.803 72.222 13.28 13.28 42.20 4.63
41 42 3.749064 GCGTCACAGAGGCTCGGA 61.749 66.667 21.56 11.65 39.86 4.55
42 43 2.962569 CGTCACAGAGGCTCGGAA 59.037 61.111 21.56 6.06 0.00 4.30
43 44 1.444553 CGTCACAGAGGCTCGGAAC 60.445 63.158 21.56 16.00 0.00 3.62
76 77 3.444805 GGCGACGGAGCTGAGAGT 61.445 66.667 0.00 0.00 37.29 3.24
77 78 2.569134 GCGACGGAGCTGAGAGTT 59.431 61.111 0.00 0.00 0.00 3.01
78 79 1.803519 GCGACGGAGCTGAGAGTTG 60.804 63.158 0.00 0.00 0.00 3.16
79 80 1.153939 CGACGGAGCTGAGAGTTGG 60.154 63.158 0.00 0.00 0.00 3.77
80 81 1.587043 CGACGGAGCTGAGAGTTGGA 61.587 60.000 0.00 0.00 0.00 3.53
81 82 0.109039 GACGGAGCTGAGAGTTGGAC 60.109 60.000 0.00 0.00 0.00 4.02
82 83 0.827925 ACGGAGCTGAGAGTTGGACA 60.828 55.000 0.00 0.00 0.00 4.02
83 84 0.389166 CGGAGCTGAGAGTTGGACAC 60.389 60.000 0.00 0.00 0.00 3.67
84 85 0.036858 GGAGCTGAGAGTTGGACACC 60.037 60.000 0.00 0.00 0.00 4.16
85 86 0.389166 GAGCTGAGAGTTGGACACCG 60.389 60.000 0.00 0.00 0.00 4.94
86 87 2.029844 GCTGAGAGTTGGACACCGC 61.030 63.158 0.00 0.00 0.00 5.68
87 88 1.734477 CTGAGAGTTGGACACCGCG 60.734 63.158 0.00 0.00 0.00 6.46
88 89 2.432628 GAGAGTTGGACACCGCGG 60.433 66.667 26.86 26.86 0.00 6.46
89 90 2.915659 AGAGTTGGACACCGCGGA 60.916 61.111 35.90 5.52 0.00 5.54
90 91 2.432628 GAGTTGGACACCGCGGAG 60.433 66.667 35.90 28.39 0.00 4.63
92 93 3.998672 GTTGGACACCGCGGAGGA 61.999 66.667 35.90 9.84 45.00 3.71
93 94 3.691342 TTGGACACCGCGGAGGAG 61.691 66.667 35.90 20.23 45.00 3.69
96 97 3.379445 GACACCGCGGAGGAGGAA 61.379 66.667 35.90 0.00 45.00 3.36
97 98 3.358076 GACACCGCGGAGGAGGAAG 62.358 68.421 35.90 12.55 45.00 3.46
98 99 3.068691 CACCGCGGAGGAGGAAGA 61.069 66.667 35.90 0.00 45.00 2.87
99 100 2.283676 ACCGCGGAGGAGGAAGAA 60.284 61.111 35.90 0.00 45.00 2.52
100 101 2.352032 ACCGCGGAGGAGGAAGAAG 61.352 63.158 35.90 0.00 45.00 2.85
101 102 2.052690 CCGCGGAGGAGGAAGAAGA 61.053 63.158 24.07 0.00 45.00 2.87
102 103 1.435515 CGCGGAGGAGGAAGAAGAG 59.564 63.158 0.00 0.00 0.00 2.85
103 104 1.032657 CGCGGAGGAGGAAGAAGAGA 61.033 60.000 0.00 0.00 0.00 3.10
104 105 0.744281 GCGGAGGAGGAAGAAGAGAG 59.256 60.000 0.00 0.00 0.00 3.20
105 106 1.958069 GCGGAGGAGGAAGAAGAGAGT 60.958 57.143 0.00 0.00 0.00 3.24
106 107 2.452505 CGGAGGAGGAAGAAGAGAGTT 58.547 52.381 0.00 0.00 0.00 3.01
107 108 2.165437 CGGAGGAGGAAGAAGAGAGTTG 59.835 54.545 0.00 0.00 0.00 3.16
108 109 3.436243 GGAGGAGGAAGAAGAGAGTTGA 58.564 50.000 0.00 0.00 0.00 3.18
109 110 3.447229 GGAGGAGGAAGAAGAGAGTTGAG 59.553 52.174 0.00 0.00 0.00 3.02
110 111 4.340617 GAGGAGGAAGAAGAGAGTTGAGA 58.659 47.826 0.00 0.00 0.00 3.27
111 112 4.344104 AGGAGGAAGAAGAGAGTTGAGAG 58.656 47.826 0.00 0.00 0.00 3.20
112 113 3.119137 GGAGGAAGAAGAGAGTTGAGAGC 60.119 52.174 0.00 0.00 0.00 4.09
113 114 3.505386 AGGAAGAAGAGAGTTGAGAGCA 58.495 45.455 0.00 0.00 0.00 4.26
114 115 3.900601 AGGAAGAAGAGAGTTGAGAGCAA 59.099 43.478 0.00 0.00 0.00 3.91
115 116 4.346418 AGGAAGAAGAGAGTTGAGAGCAAA 59.654 41.667 0.00 0.00 35.42 3.68
116 117 5.012975 AGGAAGAAGAGAGTTGAGAGCAAAT 59.987 40.000 0.00 0.00 35.42 2.32
117 118 5.122082 GGAAGAAGAGAGTTGAGAGCAAATG 59.878 44.000 0.00 0.00 35.42 2.32
118 119 4.577875 AGAAGAGAGTTGAGAGCAAATGG 58.422 43.478 0.00 0.00 35.42 3.16
119 120 4.285517 AGAAGAGAGTTGAGAGCAAATGGA 59.714 41.667 0.00 0.00 35.42 3.41
120 121 4.840716 AGAGAGTTGAGAGCAAATGGAT 57.159 40.909 0.00 0.00 35.42 3.41
121 122 4.768583 AGAGAGTTGAGAGCAAATGGATC 58.231 43.478 0.00 0.00 35.42 3.36
122 123 3.876320 GAGAGTTGAGAGCAAATGGATCC 59.124 47.826 4.20 4.20 35.42 3.36
123 124 2.611292 GAGTTGAGAGCAAATGGATCCG 59.389 50.000 7.39 0.00 35.42 4.18
124 125 1.064654 GTTGAGAGCAAATGGATCCGC 59.935 52.381 7.39 4.08 35.42 5.54
125 126 0.543277 TGAGAGCAAATGGATCCGCT 59.457 50.000 11.21 11.21 37.44 5.52
126 127 1.762370 TGAGAGCAAATGGATCCGCTA 59.238 47.619 11.35 0.00 34.12 4.26
127 128 2.224137 TGAGAGCAAATGGATCCGCTAG 60.224 50.000 11.35 1.22 34.12 3.42
128 129 1.071385 AGAGCAAATGGATCCGCTAGG 59.929 52.381 11.35 0.00 34.12 3.02
129 130 0.109342 AGCAAATGGATCCGCTAGGG 59.891 55.000 9.85 0.00 38.33 3.53
130 131 1.518903 GCAAATGGATCCGCTAGGGC 61.519 60.000 7.39 2.22 38.33 5.19
141 142 4.475444 CTAGGGCGAGGGGGTGGA 62.475 72.222 0.00 0.00 0.00 4.02
142 143 3.774336 TAGGGCGAGGGGGTGGAT 61.774 66.667 0.00 0.00 0.00 3.41
143 144 3.341469 TAGGGCGAGGGGGTGGATT 62.341 63.158 0.00 0.00 0.00 3.01
144 145 2.850851 TAGGGCGAGGGGGTGGATTT 62.851 60.000 0.00 0.00 0.00 2.17
145 146 2.440247 GGCGAGGGGGTGGATTTG 60.440 66.667 0.00 0.00 0.00 2.32
146 147 2.440247 GCGAGGGGGTGGATTTGG 60.440 66.667 0.00 0.00 0.00 3.28
147 148 3.087065 CGAGGGGGTGGATTTGGT 58.913 61.111 0.00 0.00 0.00 3.67
148 149 1.378514 CGAGGGGGTGGATTTGGTG 60.379 63.158 0.00 0.00 0.00 4.17
149 150 1.682344 GAGGGGGTGGATTTGGTGC 60.682 63.158 0.00 0.00 0.00 5.01
150 151 2.119391 GGGGGTGGATTTGGTGCA 59.881 61.111 0.00 0.00 0.00 4.57
151 152 1.535202 GGGGGTGGATTTGGTGCAA 60.535 57.895 0.00 0.00 0.00 4.08
152 153 1.124477 GGGGGTGGATTTGGTGCAAA 61.124 55.000 0.00 0.00 37.75 3.68
153 154 0.983467 GGGGTGGATTTGGTGCAAAT 59.017 50.000 0.00 0.00 45.25 2.32
154 155 1.350684 GGGGTGGATTTGGTGCAAATT 59.649 47.619 0.00 0.00 43.05 1.82
155 156 2.569404 GGGGTGGATTTGGTGCAAATTA 59.431 45.455 0.00 0.00 43.05 1.40
156 157 3.199727 GGGGTGGATTTGGTGCAAATTAT 59.800 43.478 0.00 0.00 43.05 1.28
157 158 4.190772 GGGTGGATTTGGTGCAAATTATG 58.809 43.478 0.00 0.00 43.05 1.90
158 159 4.081198 GGGTGGATTTGGTGCAAATTATGA 60.081 41.667 0.00 0.00 43.05 2.15
159 160 5.396660 GGGTGGATTTGGTGCAAATTATGAT 60.397 40.000 0.00 0.00 43.05 2.45
160 161 5.524646 GGTGGATTTGGTGCAAATTATGATG 59.475 40.000 0.00 0.00 43.05 3.07
161 162 5.524646 GTGGATTTGGTGCAAATTATGATGG 59.475 40.000 0.00 0.00 43.05 3.51
162 163 5.058490 GGATTTGGTGCAAATTATGATGGG 58.942 41.667 0.00 0.00 43.05 4.00
163 164 4.484537 TTTGGTGCAAATTATGATGGGG 57.515 40.909 0.00 0.00 0.00 4.96
164 165 3.113191 TGGTGCAAATTATGATGGGGT 57.887 42.857 0.00 0.00 0.00 4.95
165 166 4.256983 TGGTGCAAATTATGATGGGGTA 57.743 40.909 0.00 0.00 0.00 3.69
166 167 4.214310 TGGTGCAAATTATGATGGGGTAG 58.786 43.478 0.00 0.00 0.00 3.18
167 168 3.573967 GGTGCAAATTATGATGGGGTAGG 59.426 47.826 0.00 0.00 0.00 3.18
168 169 3.573967 GTGCAAATTATGATGGGGTAGGG 59.426 47.826 0.00 0.00 0.00 3.53
169 170 3.206412 TGCAAATTATGATGGGGTAGGGT 59.794 43.478 0.00 0.00 0.00 4.34
170 171 3.826729 GCAAATTATGATGGGGTAGGGTC 59.173 47.826 0.00 0.00 0.00 4.46
171 172 4.072131 CAAATTATGATGGGGTAGGGTCG 58.928 47.826 0.00 0.00 0.00 4.79
172 173 2.482414 TTATGATGGGGTAGGGTCGT 57.518 50.000 0.00 0.00 0.00 4.34
173 174 2.482414 TATGATGGGGTAGGGTCGTT 57.518 50.000 0.00 0.00 0.00 3.85
174 175 0.837272 ATGATGGGGTAGGGTCGTTG 59.163 55.000 0.00 0.00 0.00 4.10
175 176 1.268992 TGATGGGGTAGGGTCGTTGG 61.269 60.000 0.00 0.00 0.00 3.77
176 177 1.979619 GATGGGGTAGGGTCGTTGGG 61.980 65.000 0.00 0.00 0.00 4.12
177 178 2.608678 GGGGTAGGGTCGTTGGGT 60.609 66.667 0.00 0.00 0.00 4.51
178 179 2.663075 GGGGTAGGGTCGTTGGGTC 61.663 68.421 0.00 0.00 0.00 4.46
179 180 1.611556 GGGTAGGGTCGTTGGGTCT 60.612 63.158 0.00 0.00 0.00 3.85
180 181 1.595357 GGTAGGGTCGTTGGGTCTG 59.405 63.158 0.00 0.00 0.00 3.51
181 182 1.595357 GTAGGGTCGTTGGGTCTGG 59.405 63.158 0.00 0.00 0.00 3.86
182 183 2.288025 TAGGGTCGTTGGGTCTGGC 61.288 63.158 0.00 0.00 0.00 4.85
184 185 4.309950 GGTCGTTGGGTCTGGCGT 62.310 66.667 0.00 0.00 0.00 5.68
185 186 3.041940 GTCGTTGGGTCTGGCGTG 61.042 66.667 0.00 0.00 0.00 5.34
186 187 3.228017 TCGTTGGGTCTGGCGTGA 61.228 61.111 0.00 0.00 0.00 4.35
187 188 2.047274 CGTTGGGTCTGGCGTGAT 60.047 61.111 0.00 0.00 0.00 3.06
188 189 2.390599 CGTTGGGTCTGGCGTGATG 61.391 63.158 0.00 0.00 0.00 3.07
189 190 2.040544 GTTGGGTCTGGCGTGATGG 61.041 63.158 0.00 0.00 0.00 3.51
190 191 2.220586 TTGGGTCTGGCGTGATGGA 61.221 57.895 0.00 0.00 0.00 3.41
191 192 2.125106 GGGTCTGGCGTGATGGAC 60.125 66.667 0.00 0.00 0.00 4.02
199 200 3.545481 CGTGATGGACGCGCTCAC 61.545 66.667 14.76 14.76 45.14 3.51
200 201 3.545481 GTGATGGACGCGCTCACG 61.545 66.667 5.73 0.00 44.07 4.35
211 212 4.077188 GCTCACGCGTGCCTTGAC 62.077 66.667 33.63 14.66 0.00 3.18
212 213 3.767230 CTCACGCGTGCCTTGACG 61.767 66.667 33.63 8.60 42.42 4.35
215 216 3.980989 ACGCGTGCCTTGACGGTA 61.981 61.111 12.93 0.00 39.81 4.02
216 217 3.475774 CGCGTGCCTTGACGGTAC 61.476 66.667 0.00 0.00 44.13 3.34
217 218 2.048503 GCGTGCCTTGACGGTACT 60.049 61.111 0.00 0.00 45.25 2.73
218 219 1.213537 GCGTGCCTTGACGGTACTA 59.786 57.895 0.00 0.00 45.25 1.82
219 220 0.179119 GCGTGCCTTGACGGTACTAT 60.179 55.000 0.00 0.00 45.25 2.12
220 221 1.066002 GCGTGCCTTGACGGTACTATA 59.934 52.381 0.00 0.00 45.25 1.31
221 222 2.288030 GCGTGCCTTGACGGTACTATAT 60.288 50.000 0.00 0.00 45.25 0.86
222 223 3.562505 CGTGCCTTGACGGTACTATATC 58.437 50.000 0.00 0.00 45.25 1.63
223 224 3.252701 CGTGCCTTGACGGTACTATATCT 59.747 47.826 0.00 0.00 45.25 1.98
224 225 4.547532 GTGCCTTGACGGTACTATATCTG 58.452 47.826 0.00 0.00 44.19 2.90
225 226 3.005472 TGCCTTGACGGTACTATATCTGC 59.995 47.826 0.00 0.00 34.25 4.26
226 227 3.256136 GCCTTGACGGTACTATATCTGCT 59.744 47.826 0.00 0.00 34.25 4.24
227 228 4.458295 GCCTTGACGGTACTATATCTGCTA 59.542 45.833 0.00 0.00 34.25 3.49
228 229 5.619533 GCCTTGACGGTACTATATCTGCTAC 60.620 48.000 0.00 0.00 34.25 3.58
229 230 5.472478 CCTTGACGGTACTATATCTGCTACA 59.528 44.000 0.00 0.00 0.00 2.74
230 231 6.151312 CCTTGACGGTACTATATCTGCTACAT 59.849 42.308 0.00 0.00 0.00 2.29
231 232 7.336176 CCTTGACGGTACTATATCTGCTACATA 59.664 40.741 0.00 0.00 0.00 2.29
232 233 8.803397 TTGACGGTACTATATCTGCTACATAT 57.197 34.615 0.00 0.00 0.00 1.78
233 234 8.803397 TGACGGTACTATATCTGCTACATATT 57.197 34.615 0.00 0.00 0.00 1.28
234 235 9.239551 TGACGGTACTATATCTGCTACATATTT 57.760 33.333 0.00 0.00 0.00 1.40
235 236 9.504710 GACGGTACTATATCTGCTACATATTTG 57.495 37.037 0.00 0.00 0.00 2.32
236 237 8.467598 ACGGTACTATATCTGCTACATATTTGG 58.532 37.037 0.00 0.00 0.00 3.28
237 238 8.683615 CGGTACTATATCTGCTACATATTTGGA 58.316 37.037 0.00 0.00 0.00 3.53
238 239 9.804758 GGTACTATATCTGCTACATATTTGGAC 57.195 37.037 0.00 0.00 0.00 4.02
241 242 8.535335 ACTATATCTGCTACATATTTGGACTGG 58.465 37.037 0.00 0.00 0.00 4.00
242 243 5.894298 ATCTGCTACATATTTGGACTGGA 57.106 39.130 0.00 0.00 0.00 3.86
243 244 5.894298 TCTGCTACATATTTGGACTGGAT 57.106 39.130 0.00 0.00 0.00 3.41
244 245 6.994421 TCTGCTACATATTTGGACTGGATA 57.006 37.500 0.00 0.00 0.00 2.59
245 246 7.559335 TCTGCTACATATTTGGACTGGATAT 57.441 36.000 0.00 0.00 0.00 1.63
251 252 7.823745 ACATATTTGGACTGGATATTCAACC 57.176 36.000 1.17 1.17 0.00 3.77
257 258 3.403038 GACTGGATATTCAACCCGGATG 58.597 50.000 0.73 0.97 0.00 3.51
260 261 3.550820 TGGATATTCAACCCGGATGTTG 58.449 45.455 15.23 15.23 45.51 3.33
267 268 1.539827 CAACCCGGATGTTGAAAGTCC 59.460 52.381 16.08 0.00 46.77 3.85
278 279 7.368059 GGATGTTGAAAGTCCGTTTAGAAAAT 58.632 34.615 0.00 0.00 0.00 1.82
284 285 6.150474 TGAAAGTCCGTTTAGAAAATCCATCC 59.850 38.462 0.00 0.00 0.00 3.51
290 291 4.868171 CGTTTAGAAAATCCATCCGAGTCA 59.132 41.667 0.00 0.00 0.00 3.41
301 302 1.790755 TCCGAGTCACATTTTCGTGG 58.209 50.000 0.00 0.00 37.50 4.94
322 323 1.447314 GGTCAATGACCGGACCGTC 60.447 63.158 17.46 10.94 43.14 4.79
328 329 3.143515 GACCGGACCGTCTACCCC 61.144 72.222 9.46 0.00 0.00 4.95
332 333 1.143183 CGGACCGTCTACCCCAATG 59.857 63.158 5.48 0.00 0.00 2.82
334 335 0.177373 GGACCGTCTACCCCAATGTC 59.823 60.000 0.00 0.00 0.00 3.06
336 337 0.902531 ACCGTCTACCCCAATGTCTG 59.097 55.000 0.00 0.00 0.00 3.51
337 338 0.178068 CCGTCTACCCCAATGTCTGG 59.822 60.000 0.00 0.00 45.97 3.86
346 347 2.465860 CCAATGTCTGGGACACGTTA 57.534 50.000 2.34 0.00 45.65 3.18
347 348 2.773487 CCAATGTCTGGGACACGTTAA 58.227 47.619 2.34 0.00 45.65 2.01
348 349 2.482721 CCAATGTCTGGGACACGTTAAC 59.517 50.000 2.34 0.00 45.65 2.01
349 350 3.399330 CAATGTCTGGGACACGTTAACT 58.601 45.455 3.71 0.00 45.65 2.24
350 351 2.519377 TGTCTGGGACACGTTAACTG 57.481 50.000 3.71 4.01 37.67 3.16
351 352 1.758280 TGTCTGGGACACGTTAACTGT 59.242 47.619 3.71 7.17 37.67 3.55
352 353 2.132762 GTCTGGGACACGTTAACTGTG 58.867 52.381 21.14 21.14 42.99 3.66
365 376 4.327357 CGTTAACTGTGGATGCTCTTACAG 59.673 45.833 3.71 0.00 44.52 2.74
373 384 4.337555 GTGGATGCTCTTACAGATTGCAAT 59.662 41.667 12.83 12.83 37.20 3.56
386 397 7.452880 ACAGATTGCAATCTAAAACTTAGCA 57.547 32.000 35.25 0.00 43.65 3.49
396 407 8.905702 CAATCTAAAACTTAGCATCAAACACAC 58.094 33.333 0.00 0.00 0.00 3.82
404 416 1.537990 GCATCAAACACACGCCCTTTT 60.538 47.619 0.00 0.00 0.00 2.27
406 418 3.797184 GCATCAAACACACGCCCTTTTAA 60.797 43.478 0.00 0.00 0.00 1.52
410 422 4.806247 TCAAACACACGCCCTTTTAATTTG 59.194 37.500 0.00 0.00 0.00 2.32
414 426 2.297880 ACACGCCCTTTTAATTTGTCCC 59.702 45.455 0.00 0.00 0.00 4.46
427 439 0.658897 TTGTCCCAACTTTCGCGTTC 59.341 50.000 5.77 0.00 0.00 3.95
469 481 2.170607 TCCTCTCGGGGCTTAATCTTTG 59.829 50.000 0.00 0.00 35.33 2.77
951 966 0.749649 ATTCTCTCTCCGCTGCGAAT 59.250 50.000 25.45 10.29 0.00 3.34
952 967 0.532573 TTCTCTCTCCGCTGCGAATT 59.467 50.000 25.45 0.00 0.00 2.17
953 968 0.532573 TCTCTCTCCGCTGCGAATTT 59.467 50.000 25.45 0.00 0.00 1.82
998 1013 1.327303 TTTGTTTGCGAGGAAGCCAT 58.673 45.000 0.00 0.00 36.02 4.40
1205 1225 1.664965 GCCTATCGGATCCGTGTGC 60.665 63.158 32.15 24.60 40.74 4.57
1241 1261 6.936900 TGCTTTGTCTAGTGCTCTTTTAGATT 59.063 34.615 0.00 0.00 0.00 2.40
1276 1296 1.086634 GGACCATTGCGTGCTCTCTC 61.087 60.000 0.00 0.00 0.00 3.20
1325 1345 2.879103 TTCTTGTGGGATCTTGGACC 57.121 50.000 0.00 0.00 0.00 4.46
1326 1346 1.741028 TCTTGTGGGATCTTGGACCA 58.259 50.000 0.00 0.00 0.00 4.02
1355 1382 3.552875 CTTCCTGATGCACATGGAATCT 58.447 45.455 14.06 0.00 36.24 2.40
1475 1502 8.498358 CAAATATGTATGTCATCGCTACATTGT 58.502 33.333 4.65 0.00 38.49 2.71
1663 1690 7.883391 TCAATGTTTGTCTGGGTTAGTTTAA 57.117 32.000 0.00 0.00 0.00 1.52
1665 1692 9.575868 TCAATGTTTGTCTGGGTTAGTTTAATA 57.424 29.630 0.00 0.00 0.00 0.98
1726 1753 8.587608 TCTTTCTTAATCAAAATGTGCCTGAAT 58.412 29.630 0.00 0.00 0.00 2.57
1729 1756 9.558396 TTCTTAATCAAAATGTGCCTGAATTTT 57.442 25.926 0.00 0.00 36.63 1.82
1800 1827 0.921347 CTCGCAAATAAGACCGACCG 59.079 55.000 0.00 0.00 0.00 4.79
1962 1989 2.240493 ACTGTGTGCGCCCTAATATC 57.760 50.000 4.18 0.00 0.00 1.63
2009 2036 3.576550 TGTGATGTTACAGGTAGCTGTCA 59.423 43.478 29.64 22.16 38.64 3.58
2024 2051 6.663953 GGTAGCTGTCAGTCCATTATATAGGA 59.336 42.308 0.00 0.00 0.00 2.94
2139 2166 2.435586 CGCAGAGGGAAGCACCTG 60.436 66.667 0.00 0.00 42.10 4.00
2233 2260 4.561500 TTAGTGCAGCAATGGTACCTAA 57.438 40.909 14.36 0.42 0.00 2.69
2287 2314 1.413445 TGCTCCTTGCTGCATTTGTTT 59.587 42.857 1.84 0.00 43.37 2.83
2524 2551 6.982141 TCACTGAGTTAGCTCTTTCGTTTTTA 59.018 34.615 8.15 0.00 42.13 1.52
2525 2552 7.656137 TCACTGAGTTAGCTCTTTCGTTTTTAT 59.344 33.333 8.15 0.00 42.13 1.40
2526 2553 8.283291 CACTGAGTTAGCTCTTTCGTTTTTATT 58.717 33.333 8.15 0.00 42.13 1.40
2527 2554 8.837389 ACTGAGTTAGCTCTTTCGTTTTTATTT 58.163 29.630 8.15 0.00 42.13 1.40
2636 2671 3.726557 TCTGGTGAAGCATCAAAGGAT 57.273 42.857 0.00 0.00 37.30 3.24
2733 2768 4.465886 TGAGGTAAAAAGGCTGCAAGTTA 58.534 39.130 0.50 0.00 35.30 2.24
2854 2889 5.055642 TGGACTGTAGTACTGATTGTTCG 57.944 43.478 13.54 0.00 0.00 3.95
2856 2891 5.242171 TGGACTGTAGTACTGATTGTTCGAA 59.758 40.000 13.54 0.00 0.00 3.71
2857 2892 6.154445 GGACTGTAGTACTGATTGTTCGAAA 58.846 40.000 13.54 0.00 0.00 3.46
2858 2893 6.643770 GGACTGTAGTACTGATTGTTCGAAAA 59.356 38.462 13.54 0.00 0.00 2.29
2859 2894 7.170320 GGACTGTAGTACTGATTGTTCGAAAAA 59.830 37.037 13.54 2.60 0.00 1.94
3056 3096 1.656587 TGTGCCCCTTCAGTCAGTAT 58.343 50.000 0.00 0.00 0.00 2.12
3065 3105 3.772025 CCTTCAGTCAGTATCACCCTTCT 59.228 47.826 0.00 0.00 0.00 2.85
3443 3493 3.241322 GCACATACGCAAGCAAAATCATC 59.759 43.478 0.00 0.00 45.62 2.92
3548 3598 2.594592 GCCTGTGCGTGGGAACTT 60.595 61.111 0.00 0.00 0.00 2.66
3662 3712 4.458951 GCTACTGTATGCCAATTCGAAG 57.541 45.455 3.35 0.00 0.00 3.79
3665 3715 5.064707 GCTACTGTATGCCAATTCGAAGAAA 59.935 40.000 3.35 0.00 45.90 2.52
3770 3820 8.333908 GCATGATCTCTTACTTAGTTGTCAATG 58.666 37.037 0.00 0.00 0.00 2.82
3814 3864 9.739786 GAAGTTTTATGTTTTGATAAAATGGCG 57.260 29.630 0.00 0.00 39.07 5.69
3838 3888 3.203716 GGTTGGTTATTCCTTCTAGGCG 58.796 50.000 0.00 0.00 34.61 5.52
3841 3891 2.100252 TGGTTATTCCTTCTAGGCGACG 59.900 50.000 0.00 0.00 34.61 5.12
3961 4011 6.595326 CAGTTCTGAACCAATGCTGTATTCTA 59.405 38.462 16.48 0.00 0.00 2.10
4113 4163 9.462606 CTCCCCTCTTTGTACTTTATGTTTATT 57.537 33.333 0.00 0.00 0.00 1.40
4179 4230 3.265791 CTTCTTGCTTGCTCGTCCTAAT 58.734 45.455 0.00 0.00 0.00 1.73
4278 4329 9.817365 GATTTATCAATTGATGTAATGACGAGG 57.183 33.333 27.59 0.00 36.05 4.63
4325 4377 6.038936 AGCATAAAGTTAAGACGGTGTTTGTT 59.961 34.615 0.00 0.00 0.00 2.83
4416 4473 3.133003 AGCTGTGTGTTGTAGAGTGAACT 59.867 43.478 0.00 0.00 0.00 3.01
4562 4630 9.899661 ATAGTTTTGGCACATGTAAATAGAGTA 57.100 29.630 0.00 0.00 39.30 2.59
4600 4668 5.465724 GGGTCTCTGGCAAGTTAAATATACG 59.534 44.000 0.00 0.00 0.00 3.06
4604 4672 8.328864 GTCTCTGGCAAGTTAAATATACGAAAG 58.671 37.037 0.00 0.00 0.00 2.62
4716 4787 6.986904 CATGATGATGCATATGCTTCTAGT 57.013 37.500 31.83 22.15 43.23 2.57
4952 5024 4.302559 AGTTACATTCCCAGGAAAGGAC 57.697 45.455 2.65 3.25 37.69 3.85
4961 5033 1.139058 CCAGGAAAGGACGGATACCAG 59.861 57.143 0.00 0.00 0.00 4.00
5155 5240 8.292444 TCACCATAACCTTTAATTCATTCTGG 57.708 34.615 0.00 0.00 0.00 3.86
5165 5250 7.148171 CCTTTAATTCATTCTGGTCTCACCTTC 60.148 40.741 0.00 0.00 39.58 3.46
5181 5268 2.158755 ACCTTCCTTGTGACTTGGTGAG 60.159 50.000 0.00 0.00 0.00 3.51
5306 5393 1.203052 CAGTACGCGGAAGGAAAGGTA 59.797 52.381 12.47 0.00 0.00 3.08
5309 5396 0.743345 ACGCGGAAGGAAAGGTATGC 60.743 55.000 12.47 0.00 0.00 3.14
5354 5441 5.295292 GGTGATGAGTCTGAATACAACATGG 59.705 44.000 0.00 0.00 0.00 3.66
5358 5445 4.929211 TGAGTCTGAATACAACATGGTTCG 59.071 41.667 0.00 0.00 0.00 3.95
5727 5817 1.967535 CCGTCTCTTCTGCAGACCA 59.032 57.895 18.03 4.62 37.58 4.02
5765 5855 2.095282 ATGTCGTCGTCGTCGTCG 59.905 61.111 14.18 14.18 46.06 5.12
5766 5856 2.661566 ATGTCGTCGTCGTCGTCGT 61.662 57.895 18.44 5.06 45.27 4.34
5767 5857 2.539972 ATGTCGTCGTCGTCGTCGTC 62.540 60.000 18.44 14.46 45.27 4.20
5768 5858 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
5769 5859 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
5770 5860 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
5771 5861 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
5772 5862 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
5773 5863 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
5774 5864 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
5775 5865 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
5776 5866 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
5779 5869 2.553268 GTCGTCGTCGTCGTCCTT 59.447 61.111 11.41 0.00 38.33 3.36
5853 5985 6.314400 GCACCAGTTTCTCCGTATATGTAAAA 59.686 38.462 0.00 0.00 0.00 1.52
5854 5986 7.465513 GCACCAGTTTCTCCGTATATGTAAAAG 60.466 40.741 0.00 0.00 0.00 2.27
5856 5988 8.316214 ACCAGTTTCTCCGTATATGTAAAAGAA 58.684 33.333 0.00 0.00 0.00 2.52
5891 6023 3.195825 ACAGTTTCTCCGTATCTTCCCTG 59.804 47.826 0.00 0.00 0.00 4.45
5892 6024 3.195825 CAGTTTCTCCGTATCTTCCCTGT 59.804 47.826 0.00 0.00 0.00 4.00
5893 6025 3.838903 AGTTTCTCCGTATCTTCCCTGTT 59.161 43.478 0.00 0.00 0.00 3.16
5894 6026 5.021458 AGTTTCTCCGTATCTTCCCTGTTA 58.979 41.667 0.00 0.00 0.00 2.41
5895 6027 5.127356 AGTTTCTCCGTATCTTCCCTGTTAG 59.873 44.000 0.00 0.00 0.00 2.34
5896 6028 3.563223 TCTCCGTATCTTCCCTGTTAGG 58.437 50.000 0.00 0.00 34.30 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.952984 GCCAGCACAACACTCCTCTC 60.953 60.000 0.00 0.00 0.00 3.20
3 4 2.281070 CGCCAGCACAACACTCCT 60.281 61.111 0.00 0.00 0.00 3.69
4 5 4.030452 GCGCCAGCACAACACTCC 62.030 66.667 0.00 0.00 44.35 3.85
20 21 4.385405 AGCCTCTGTGACGCCAGC 62.385 66.667 0.00 0.00 32.32 4.85
21 22 2.125753 GAGCCTCTGTGACGCCAG 60.126 66.667 0.00 0.00 0.00 4.85
22 23 4.056125 CGAGCCTCTGTGACGCCA 62.056 66.667 0.00 0.00 0.00 5.69
23 24 4.803426 CCGAGCCTCTGTGACGCC 62.803 72.222 0.00 0.00 0.00 5.68
24 25 3.282745 TTCCGAGCCTCTGTGACGC 62.283 63.158 0.00 0.00 0.00 5.19
25 26 1.444553 GTTCCGAGCCTCTGTGACG 60.445 63.158 0.00 0.00 0.00 4.35
26 27 1.444553 CGTTCCGAGCCTCTGTGAC 60.445 63.158 0.00 0.00 0.00 3.67
27 28 2.636412 CCGTTCCGAGCCTCTGTGA 61.636 63.158 0.00 0.00 0.00 3.58
28 29 2.125912 CCGTTCCGAGCCTCTGTG 60.126 66.667 0.00 0.00 0.00 3.66
29 30 2.207924 AACCGTTCCGAGCCTCTGT 61.208 57.895 0.00 0.00 0.00 3.41
30 31 1.738099 CAACCGTTCCGAGCCTCTG 60.738 63.158 0.00 0.00 0.00 3.35
31 32 0.896940 TACAACCGTTCCGAGCCTCT 60.897 55.000 0.00 0.00 0.00 3.69
32 33 0.458025 CTACAACCGTTCCGAGCCTC 60.458 60.000 0.00 0.00 0.00 4.70
33 34 0.896940 TCTACAACCGTTCCGAGCCT 60.897 55.000 0.00 0.00 0.00 4.58
34 35 0.458025 CTCTACAACCGTTCCGAGCC 60.458 60.000 0.00 0.00 0.00 4.70
35 36 1.077089 GCTCTACAACCGTTCCGAGC 61.077 60.000 9.10 9.10 37.35 5.03
36 37 0.797249 CGCTCTACAACCGTTCCGAG 60.797 60.000 0.00 0.00 0.00 4.63
37 38 1.210931 CGCTCTACAACCGTTCCGA 59.789 57.895 0.00 0.00 0.00 4.55
38 39 1.804326 CCGCTCTACAACCGTTCCG 60.804 63.158 0.00 0.00 0.00 4.30
39 40 1.447314 CCCGCTCTACAACCGTTCC 60.447 63.158 0.00 0.00 0.00 3.62
40 41 2.098831 GCCCGCTCTACAACCGTTC 61.099 63.158 0.00 0.00 0.00 3.95
41 42 2.047560 GCCCGCTCTACAACCGTT 60.048 61.111 0.00 0.00 0.00 4.44
42 43 4.430765 CGCCCGCTCTACAACCGT 62.431 66.667 0.00 0.00 0.00 4.83
58 59 4.544689 CTCTCAGCTCCGTCGCCG 62.545 72.222 0.00 0.00 0.00 6.46
59 60 2.995872 AACTCTCAGCTCCGTCGCC 61.996 63.158 0.00 0.00 0.00 5.54
60 61 1.803519 CAACTCTCAGCTCCGTCGC 60.804 63.158 0.00 0.00 0.00 5.19
61 62 1.153939 CCAACTCTCAGCTCCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
62 63 0.109039 GTCCAACTCTCAGCTCCGTC 60.109 60.000 0.00 0.00 0.00 4.79
63 64 0.827925 TGTCCAACTCTCAGCTCCGT 60.828 55.000 0.00 0.00 0.00 4.69
64 65 0.389166 GTGTCCAACTCTCAGCTCCG 60.389 60.000 0.00 0.00 0.00 4.63
65 66 0.036858 GGTGTCCAACTCTCAGCTCC 60.037 60.000 0.00 0.00 0.00 4.70
66 67 0.389166 CGGTGTCCAACTCTCAGCTC 60.389 60.000 0.00 0.00 0.00 4.09
67 68 1.668294 CGGTGTCCAACTCTCAGCT 59.332 57.895 0.00 0.00 0.00 4.24
68 69 2.029844 GCGGTGTCCAACTCTCAGC 61.030 63.158 0.00 0.00 0.00 4.26
69 70 1.734477 CGCGGTGTCCAACTCTCAG 60.734 63.158 0.00 0.00 0.00 3.35
70 71 2.338620 CGCGGTGTCCAACTCTCA 59.661 61.111 0.00 0.00 0.00 3.27
71 72 2.432628 CCGCGGTGTCCAACTCTC 60.433 66.667 19.50 0.00 0.00 3.20
72 73 2.915659 TCCGCGGTGTCCAACTCT 60.916 61.111 27.15 0.00 0.00 3.24
73 74 2.432628 CTCCGCGGTGTCCAACTC 60.433 66.667 27.15 0.00 0.00 3.01
74 75 4.003788 CCTCCGCGGTGTCCAACT 62.004 66.667 27.15 0.00 0.00 3.16
75 76 3.934391 CTCCTCCGCGGTGTCCAAC 62.934 68.421 27.15 0.00 0.00 3.77
76 77 3.691342 CTCCTCCGCGGTGTCCAA 61.691 66.667 27.15 2.82 0.00 3.53
79 80 3.358076 CTTCCTCCTCCGCGGTGTC 62.358 68.421 27.15 0.00 0.00 3.67
80 81 3.382832 CTTCCTCCTCCGCGGTGT 61.383 66.667 27.15 0.00 0.00 4.16
81 82 2.564553 CTTCTTCCTCCTCCGCGGTG 62.565 65.000 27.15 23.40 0.00 4.94
82 83 2.283676 TTCTTCCTCCTCCGCGGT 60.284 61.111 27.15 0.00 0.00 5.68
83 84 2.010582 CTCTTCTTCCTCCTCCGCGG 62.011 65.000 22.12 22.12 0.00 6.46
84 85 1.032657 TCTCTTCTTCCTCCTCCGCG 61.033 60.000 0.00 0.00 0.00 6.46
85 86 0.744281 CTCTCTTCTTCCTCCTCCGC 59.256 60.000 0.00 0.00 0.00 5.54
86 87 2.137810 ACTCTCTTCTTCCTCCTCCG 57.862 55.000 0.00 0.00 0.00 4.63
87 88 3.436243 TCAACTCTCTTCTTCCTCCTCC 58.564 50.000 0.00 0.00 0.00 4.30
88 89 4.340617 TCTCAACTCTCTTCTTCCTCCTC 58.659 47.826 0.00 0.00 0.00 3.71
89 90 4.344104 CTCTCAACTCTCTTCTTCCTCCT 58.656 47.826 0.00 0.00 0.00 3.69
90 91 3.119137 GCTCTCAACTCTCTTCTTCCTCC 60.119 52.174 0.00 0.00 0.00 4.30
91 92 3.509575 TGCTCTCAACTCTCTTCTTCCTC 59.490 47.826 0.00 0.00 0.00 3.71
92 93 3.505386 TGCTCTCAACTCTCTTCTTCCT 58.495 45.455 0.00 0.00 0.00 3.36
93 94 3.951775 TGCTCTCAACTCTCTTCTTCC 57.048 47.619 0.00 0.00 0.00 3.46
94 95 5.122082 CCATTTGCTCTCAACTCTCTTCTTC 59.878 44.000 0.00 0.00 30.75 2.87
95 96 5.002516 CCATTTGCTCTCAACTCTCTTCTT 58.997 41.667 0.00 0.00 30.75 2.52
96 97 4.285517 TCCATTTGCTCTCAACTCTCTTCT 59.714 41.667 0.00 0.00 30.75 2.85
97 98 4.573900 TCCATTTGCTCTCAACTCTCTTC 58.426 43.478 0.00 0.00 30.75 2.87
98 99 4.630644 TCCATTTGCTCTCAACTCTCTT 57.369 40.909 0.00 0.00 30.75 2.85
99 100 4.383989 GGATCCATTTGCTCTCAACTCTCT 60.384 45.833 6.95 0.00 30.75 3.10
100 101 3.876320 GGATCCATTTGCTCTCAACTCTC 59.124 47.826 6.95 0.00 30.75 3.20
101 102 3.681034 CGGATCCATTTGCTCTCAACTCT 60.681 47.826 13.41 0.00 30.75 3.24
102 103 2.611292 CGGATCCATTTGCTCTCAACTC 59.389 50.000 13.41 0.00 30.75 3.01
103 104 2.636830 CGGATCCATTTGCTCTCAACT 58.363 47.619 13.41 0.00 30.75 3.16
104 105 1.064654 GCGGATCCATTTGCTCTCAAC 59.935 52.381 13.41 0.00 30.75 3.18
105 106 1.065199 AGCGGATCCATTTGCTCTCAA 60.065 47.619 13.41 0.00 30.37 3.02
106 107 0.543277 AGCGGATCCATTTGCTCTCA 59.457 50.000 13.41 0.00 30.37 3.27
107 108 2.411904 CTAGCGGATCCATTTGCTCTC 58.588 52.381 14.31 0.00 38.82 3.20
108 109 1.071385 CCTAGCGGATCCATTTGCTCT 59.929 52.381 14.31 1.16 38.82 4.09
109 110 1.517242 CCTAGCGGATCCATTTGCTC 58.483 55.000 14.31 0.00 38.82 4.26
110 111 0.109342 CCCTAGCGGATCCATTTGCT 59.891 55.000 13.41 14.40 41.32 3.91
111 112 1.518903 GCCCTAGCGGATCCATTTGC 61.519 60.000 13.41 6.92 0.00 3.68
112 113 2.633860 GCCCTAGCGGATCCATTTG 58.366 57.895 13.41 0.00 0.00 2.32
124 125 3.776016 ATCCACCCCCTCGCCCTAG 62.776 68.421 0.00 0.00 0.00 3.02
125 126 2.850851 AAATCCACCCCCTCGCCCTA 62.851 60.000 0.00 0.00 0.00 3.53
126 127 4.760220 AATCCACCCCCTCGCCCT 62.760 66.667 0.00 0.00 0.00 5.19
127 128 3.739613 AAATCCACCCCCTCGCCC 61.740 66.667 0.00 0.00 0.00 6.13
128 129 2.440247 CAAATCCACCCCCTCGCC 60.440 66.667 0.00 0.00 0.00 5.54
129 130 2.440247 CCAAATCCACCCCCTCGC 60.440 66.667 0.00 0.00 0.00 5.03
130 131 1.378514 CACCAAATCCACCCCCTCG 60.379 63.158 0.00 0.00 0.00 4.63
131 132 1.682344 GCACCAAATCCACCCCCTC 60.682 63.158 0.00 0.00 0.00 4.30
132 133 2.029892 TTGCACCAAATCCACCCCCT 62.030 55.000 0.00 0.00 0.00 4.79
133 134 1.124477 TTTGCACCAAATCCACCCCC 61.124 55.000 0.00 0.00 0.00 5.40
134 135 0.983467 ATTTGCACCAAATCCACCCC 59.017 50.000 0.00 0.00 39.50 4.95
135 136 2.857186 AATTTGCACCAAATCCACCC 57.143 45.000 3.90 0.00 42.32 4.61
136 137 5.083533 TCATAATTTGCACCAAATCCACC 57.916 39.130 3.90 0.00 42.32 4.61
137 138 5.524646 CCATCATAATTTGCACCAAATCCAC 59.475 40.000 3.90 0.00 42.32 4.02
138 139 5.396548 CCCATCATAATTTGCACCAAATCCA 60.397 40.000 3.90 0.00 42.32 3.41
139 140 5.058490 CCCATCATAATTTGCACCAAATCC 58.942 41.667 3.90 0.00 42.32 3.01
140 141 5.058490 CCCCATCATAATTTGCACCAAATC 58.942 41.667 3.90 0.00 42.32 2.17
141 142 4.474287 ACCCCATCATAATTTGCACCAAAT 59.526 37.500 0.00 0.00 44.62 2.32
142 143 3.843027 ACCCCATCATAATTTGCACCAAA 59.157 39.130 0.00 0.00 37.75 3.28
143 144 3.448934 ACCCCATCATAATTTGCACCAA 58.551 40.909 0.00 0.00 0.00 3.67
144 145 3.113191 ACCCCATCATAATTTGCACCA 57.887 42.857 0.00 0.00 0.00 4.17
145 146 3.573967 CCTACCCCATCATAATTTGCACC 59.426 47.826 0.00 0.00 0.00 5.01
146 147 3.573967 CCCTACCCCATCATAATTTGCAC 59.426 47.826 0.00 0.00 0.00 4.57
147 148 3.206412 ACCCTACCCCATCATAATTTGCA 59.794 43.478 0.00 0.00 0.00 4.08
148 149 3.826729 GACCCTACCCCATCATAATTTGC 59.173 47.826 0.00 0.00 0.00 3.68
149 150 4.072131 CGACCCTACCCCATCATAATTTG 58.928 47.826 0.00 0.00 0.00 2.32
150 151 3.720002 ACGACCCTACCCCATCATAATTT 59.280 43.478 0.00 0.00 0.00 1.82
151 152 3.323775 ACGACCCTACCCCATCATAATT 58.676 45.455 0.00 0.00 0.00 1.40
152 153 2.986050 ACGACCCTACCCCATCATAAT 58.014 47.619 0.00 0.00 0.00 1.28
153 154 2.436542 CAACGACCCTACCCCATCATAA 59.563 50.000 0.00 0.00 0.00 1.90
154 155 2.043992 CAACGACCCTACCCCATCATA 58.956 52.381 0.00 0.00 0.00 2.15
155 156 0.837272 CAACGACCCTACCCCATCAT 59.163 55.000 0.00 0.00 0.00 2.45
156 157 1.268992 CCAACGACCCTACCCCATCA 61.269 60.000 0.00 0.00 0.00 3.07
157 158 1.525442 CCAACGACCCTACCCCATC 59.475 63.158 0.00 0.00 0.00 3.51
158 159 1.999002 CCCAACGACCCTACCCCAT 60.999 63.158 0.00 0.00 0.00 4.00
159 160 2.608368 CCCAACGACCCTACCCCA 60.608 66.667 0.00 0.00 0.00 4.96
160 161 2.608678 ACCCAACGACCCTACCCC 60.609 66.667 0.00 0.00 0.00 4.95
161 162 1.611556 AGACCCAACGACCCTACCC 60.612 63.158 0.00 0.00 0.00 3.69
162 163 1.595357 CAGACCCAACGACCCTACC 59.405 63.158 0.00 0.00 0.00 3.18
163 164 1.595357 CCAGACCCAACGACCCTAC 59.405 63.158 0.00 0.00 0.00 3.18
164 165 2.288025 GCCAGACCCAACGACCCTA 61.288 63.158 0.00 0.00 0.00 3.53
165 166 3.637273 GCCAGACCCAACGACCCT 61.637 66.667 0.00 0.00 0.00 4.34
167 168 4.309950 ACGCCAGACCCAACGACC 62.310 66.667 0.00 0.00 0.00 4.79
168 169 2.781595 ATCACGCCAGACCCAACGAC 62.782 60.000 0.00 0.00 0.00 4.34
169 170 2.579657 ATCACGCCAGACCCAACGA 61.580 57.895 0.00 0.00 0.00 3.85
170 171 2.047274 ATCACGCCAGACCCAACG 60.047 61.111 0.00 0.00 0.00 4.10
171 172 2.040544 CCATCACGCCAGACCCAAC 61.041 63.158 0.00 0.00 0.00 3.77
172 173 2.220586 TCCATCACGCCAGACCCAA 61.221 57.895 0.00 0.00 0.00 4.12
173 174 2.606213 TCCATCACGCCAGACCCA 60.606 61.111 0.00 0.00 0.00 4.51
174 175 2.125106 GTCCATCACGCCAGACCC 60.125 66.667 0.00 0.00 0.00 4.46
175 176 2.509336 CGTCCATCACGCCAGACC 60.509 66.667 0.00 0.00 42.87 3.85
183 184 3.545481 CGTGAGCGCGTCCATCAC 61.545 66.667 19.14 19.14 39.93 3.06
195 196 3.767230 CGTCAAGGCACGCGTGAG 61.767 66.667 41.19 25.53 31.96 3.51
198 199 3.980989 TACCGTCAAGGCACGCGT 61.981 61.111 5.58 5.58 46.52 6.01
199 200 2.531927 TAGTACCGTCAAGGCACGCG 62.532 60.000 3.53 3.53 46.52 6.01
200 201 0.179119 ATAGTACCGTCAAGGCACGC 60.179 55.000 0.00 0.00 46.52 5.34
201 202 3.252701 AGATATAGTACCGTCAAGGCACG 59.747 47.826 0.00 0.00 46.52 5.34
202 203 4.547532 CAGATATAGTACCGTCAAGGCAC 58.452 47.826 0.00 0.00 46.52 5.01
203 204 3.005472 GCAGATATAGTACCGTCAAGGCA 59.995 47.826 0.00 0.00 46.52 4.75
204 205 3.256136 AGCAGATATAGTACCGTCAAGGC 59.744 47.826 0.00 0.00 46.52 4.35
206 207 6.555812 TGTAGCAGATATAGTACCGTCAAG 57.444 41.667 0.00 0.00 0.00 3.02
207 208 8.803397 ATATGTAGCAGATATAGTACCGTCAA 57.197 34.615 0.00 0.00 0.00 3.18
208 209 8.803397 AATATGTAGCAGATATAGTACCGTCA 57.197 34.615 0.00 0.00 0.00 4.35
209 210 9.504710 CAAATATGTAGCAGATATAGTACCGTC 57.495 37.037 0.00 0.00 0.00 4.79
210 211 8.467598 CCAAATATGTAGCAGATATAGTACCGT 58.532 37.037 0.00 0.00 0.00 4.83
211 212 8.683615 TCCAAATATGTAGCAGATATAGTACCG 58.316 37.037 0.00 0.00 0.00 4.02
212 213 9.804758 GTCCAAATATGTAGCAGATATAGTACC 57.195 37.037 0.00 0.00 0.00 3.34
215 216 8.535335 CCAGTCCAAATATGTAGCAGATATAGT 58.465 37.037 0.00 0.00 0.00 2.12
216 217 8.753133 TCCAGTCCAAATATGTAGCAGATATAG 58.247 37.037 0.00 0.00 0.00 1.31
217 218 8.664669 TCCAGTCCAAATATGTAGCAGATATA 57.335 34.615 0.00 0.00 0.00 0.86
218 219 7.559335 TCCAGTCCAAATATGTAGCAGATAT 57.441 36.000 0.00 0.00 0.00 1.63
219 220 6.994421 TCCAGTCCAAATATGTAGCAGATA 57.006 37.500 0.00 0.00 0.00 1.98
220 221 5.894298 TCCAGTCCAAATATGTAGCAGAT 57.106 39.130 0.00 0.00 0.00 2.90
221 222 5.894298 ATCCAGTCCAAATATGTAGCAGA 57.106 39.130 0.00 0.00 0.00 4.26
222 223 7.879677 TGAATATCCAGTCCAAATATGTAGCAG 59.120 37.037 0.00 0.00 0.00 4.24
223 224 7.744733 TGAATATCCAGTCCAAATATGTAGCA 58.255 34.615 0.00 0.00 0.00 3.49
224 225 8.507249 GTTGAATATCCAGTCCAAATATGTAGC 58.493 37.037 0.00 0.00 0.00 3.58
225 226 9.003658 GGTTGAATATCCAGTCCAAATATGTAG 57.996 37.037 0.00 0.00 0.00 2.74
226 227 7.942341 GGGTTGAATATCCAGTCCAAATATGTA 59.058 37.037 0.00 0.00 0.00 2.29
227 228 6.777580 GGGTTGAATATCCAGTCCAAATATGT 59.222 38.462 0.00 0.00 0.00 2.29
228 229 6.072508 CGGGTTGAATATCCAGTCCAAATATG 60.073 42.308 0.00 0.00 0.00 1.78
229 230 6.003950 CGGGTTGAATATCCAGTCCAAATAT 58.996 40.000 0.00 0.00 0.00 1.28
230 231 5.373222 CGGGTTGAATATCCAGTCCAAATA 58.627 41.667 0.00 0.00 0.00 1.40
231 232 4.207165 CGGGTTGAATATCCAGTCCAAAT 58.793 43.478 0.00 0.00 0.00 2.32
232 233 3.616219 CGGGTTGAATATCCAGTCCAAA 58.384 45.455 0.00 0.00 0.00 3.28
233 234 2.092646 CCGGGTTGAATATCCAGTCCAA 60.093 50.000 0.00 0.00 0.00 3.53
234 235 1.488812 CCGGGTTGAATATCCAGTCCA 59.511 52.381 0.00 0.00 0.00 4.02
235 236 1.766496 TCCGGGTTGAATATCCAGTCC 59.234 52.381 0.00 0.00 0.00 3.85
236 237 3.181454 ACATCCGGGTTGAATATCCAGTC 60.181 47.826 11.95 0.00 0.00 3.51
237 238 2.777692 ACATCCGGGTTGAATATCCAGT 59.222 45.455 11.95 0.00 0.00 4.00
238 239 3.492102 ACATCCGGGTTGAATATCCAG 57.508 47.619 11.95 0.00 0.00 3.86
239 240 3.943671 AACATCCGGGTTGAATATCCA 57.056 42.857 11.95 0.00 0.00 3.41
257 258 6.731164 TGGATTTTCTAAACGGACTTTCAAC 58.269 36.000 0.00 0.00 0.00 3.18
260 261 6.552629 GGATGGATTTTCTAAACGGACTTTC 58.447 40.000 0.00 0.00 0.00 2.62
261 262 5.123344 CGGATGGATTTTCTAAACGGACTTT 59.877 40.000 0.00 0.00 0.00 2.66
265 266 4.081309 ACTCGGATGGATTTTCTAAACGGA 60.081 41.667 0.00 0.00 0.00 4.69
267 268 4.868171 TGACTCGGATGGATTTTCTAAACG 59.132 41.667 0.00 0.00 0.00 3.60
278 279 2.028476 ACGAAAATGTGACTCGGATGGA 60.028 45.455 0.00 0.00 36.90 3.41
284 285 0.165944 GGCCACGAAAATGTGACTCG 59.834 55.000 0.00 0.00 42.55 4.18
290 291 0.820074 TTGACCGGCCACGAAAATGT 60.820 50.000 0.00 0.00 44.60 2.71
328 329 3.186409 CAGTTAACGTGTCCCAGACATTG 59.814 47.826 0.05 0.13 44.63 2.82
332 333 2.132762 CACAGTTAACGTGTCCCAGAC 58.867 52.381 17.08 0.00 0.00 3.51
334 335 1.069513 TCCACAGTTAACGTGTCCCAG 59.930 52.381 20.98 11.00 32.26 4.45
336 337 2.073816 CATCCACAGTTAACGTGTCCC 58.926 52.381 20.98 0.00 32.26 4.46
337 338 1.463444 GCATCCACAGTTAACGTGTCC 59.537 52.381 20.98 8.99 32.26 4.02
365 376 8.915871 TTGATGCTAAGTTTTAGATTGCAATC 57.084 30.769 28.44 28.44 35.64 2.67
373 384 6.655062 CGTGTGTTTGATGCTAAGTTTTAGA 58.345 36.000 0.21 0.00 0.00 2.10
386 397 4.864704 ATTAAAAGGGCGTGTGTTTGAT 57.135 36.364 0.00 0.00 0.00 2.57
404 416 7.745741 CGAACGCGAAAGTTGGGACAAATTA 62.746 44.000 15.93 0.00 42.29 1.40
406 418 5.670433 CGAACGCGAAAGTTGGGACAAAT 62.670 47.826 15.93 0.00 42.29 2.32
410 422 1.203313 CGAACGCGAAAGTTGGGAC 59.797 57.895 15.93 0.00 40.82 4.46
427 439 5.120830 AGGATCAAATTGAAAACGAGACTCG 59.879 40.000 22.97 22.97 46.93 4.18
469 481 0.872021 CGATCTGCTTGAGCCCGTAC 60.872 60.000 0.00 0.00 41.18 3.67
569 581 1.438814 GCGCTTTAATGGGCATGCT 59.561 52.632 18.92 0.00 43.95 3.79
703 716 4.676986 CGGATGAACTGTGATCGTTAGGAA 60.677 45.833 0.00 0.00 0.00 3.36
1205 1225 2.434428 AGACAAAGCAAGCTGATCAGG 58.566 47.619 23.89 8.85 0.00 3.86
1241 1261 1.825474 GGTCCAAGATCCTGAGTTCGA 59.175 52.381 0.00 0.00 0.00 3.71
1318 1338 3.379372 CAGGAAGCACATAATGGTCCAAG 59.621 47.826 0.00 0.00 38.37 3.61
1320 1340 2.575735 TCAGGAAGCACATAATGGTCCA 59.424 45.455 0.00 0.00 38.37 4.02
1321 1341 3.281727 TCAGGAAGCACATAATGGTCC 57.718 47.619 0.00 0.00 38.37 4.46
1323 1343 2.954318 GCATCAGGAAGCACATAATGGT 59.046 45.455 0.00 0.00 42.22 3.55
1324 1344 2.953648 TGCATCAGGAAGCACATAATGG 59.046 45.455 0.00 0.00 35.51 3.16
1475 1502 3.370840 AGCAACTCCATAATGCCAGAA 57.629 42.857 0.00 0.00 40.93 3.02
1665 1692 9.099071 ACCTCTAGATATTCAGTGCAAAGATAT 57.901 33.333 0.00 0.00 0.00 1.63
1800 1827 8.438676 ACTGATTACCTTGAATGCTACATAAC 57.561 34.615 0.00 0.00 0.00 1.89
1827 1854 8.537728 TGAGGCACATAGGATTGAAAATTTAT 57.462 30.769 0.00 0.00 0.00 1.40
1962 1989 1.740296 CCCAGGAAGTACAACGCCG 60.740 63.158 0.00 0.00 0.00 6.46
2024 2051 7.436376 GCTTTTCTTTTCACTGAGCTGTTTATT 59.564 33.333 0.00 0.00 0.00 1.40
2139 2166 2.275318 GTCCTTACACTGCAGATCAGC 58.725 52.381 23.35 2.62 46.76 4.26
2287 2314 5.490159 TGACATGATGATGTGCTAGAAACA 58.510 37.500 1.30 0.00 43.22 2.83
2530 2557 8.631797 CCCAGGAATTTCATTCAAAACAAAAAT 58.368 29.630 0.00 0.00 41.03 1.82
2531 2558 7.067981 CCCCAGGAATTTCATTCAAAACAAAAA 59.932 33.333 0.00 0.00 41.03 1.94
2733 2768 4.526970 ACCAGTTGTTCACTCATTCTTGT 58.473 39.130 0.00 0.00 30.92 3.16
3056 3096 5.964477 ACCTCATAATAACAGAGAAGGGTGA 59.036 40.000 0.00 0.00 0.00 4.02
3065 3105 7.194112 TCACCAATCACCTCATAATAACAGA 57.806 36.000 0.00 0.00 0.00 3.41
3443 3493 4.581824 CCACCCAATTATCATCAAGACCAG 59.418 45.833 0.00 0.00 0.00 4.00
3548 3598 3.669536 TGGATTACAATCACGCAAGACA 58.330 40.909 4.45 0.00 36.91 3.41
3665 3715 7.322664 CAATACCACCAAAGCTACATGATTTT 58.677 34.615 0.00 0.00 31.16 1.82
3671 3721 3.023832 GCCAATACCACCAAAGCTACAT 58.976 45.455 0.00 0.00 0.00 2.29
3675 3725 2.308866 AGTAGCCAATACCACCAAAGCT 59.691 45.455 0.00 0.00 34.67 3.74
3682 3732 7.170998 GTCAATACATACAGTAGCCAATACCAC 59.829 40.741 0.00 0.00 35.85 4.16
3814 3864 4.524053 CCTAGAAGGAATAACCAACCACC 58.476 47.826 0.00 0.00 37.67 4.61
3838 3888 2.359900 AGCTTGGAAATCATGGACGTC 58.640 47.619 7.13 7.13 0.00 4.34
3841 3891 4.943705 TCAGTTAGCTTGGAAATCATGGAC 59.056 41.667 0.00 0.00 0.00 4.02
3961 4011 8.758829 GGAAAACAAATTCCAGAATAATACCCT 58.241 33.333 1.30 0.00 46.70 4.34
4113 4163 5.801531 ACATTCCGCTATTCATGGTAGTA 57.198 39.130 0.00 0.00 0.00 1.82
4179 4230 6.713762 ATGGTGTGAACAAAGATTTCTTGA 57.286 33.333 0.00 0.00 36.12 3.02
4278 4329 6.427853 TGCTATGTGTAATTATGAGCATGACC 59.572 38.462 0.00 0.00 33.73 4.02
4341 4393 8.383318 TCTCCAACAAACAACAAATTTGAAAA 57.617 26.923 24.64 0.00 39.01 2.29
4393 4448 3.097877 TCACTCTACAACACACAGCTG 57.902 47.619 13.48 13.48 0.00 4.24
4562 4630 4.074970 CAGAGACCCAGCACAACTTTTAT 58.925 43.478 0.00 0.00 0.00 1.40
4600 4668 6.769512 TGATTATATCAGCAGGGGTACTTTC 58.230 40.000 0.00 0.00 33.59 2.62
4712 4783 7.840342 AAATTCTGATAAGCACACAGACTAG 57.160 36.000 0.00 0.00 39.80 2.57
4716 4787 7.828717 TCCATTAAATTCTGATAAGCACACAGA 59.171 33.333 0.00 0.00 38.61 3.41
4952 5024 0.469917 AGGGATGTTGCTGGTATCCG 59.530 55.000 0.00 0.00 41.00 4.18
4961 5033 4.944048 AGTAAAAACACAAGGGATGTTGC 58.056 39.130 0.00 0.00 41.46 4.17
5155 5240 3.134458 CAAGTCACAAGGAAGGTGAGAC 58.866 50.000 0.00 0.00 45.21 3.36
5165 5250 2.917933 TGAACTCACCAAGTCACAAGG 58.082 47.619 0.00 0.00 37.17 3.61
5181 5268 0.599558 TGGCAGAAGCAGCAATGAAC 59.400 50.000 0.00 0.00 44.61 3.18
5306 5393 4.445453 TGATGAATCGACAGCTTAAGCAT 58.555 39.130 28.39 16.48 45.16 3.79
5309 5396 3.806521 CCCTGATGAATCGACAGCTTAAG 59.193 47.826 0.00 0.00 0.00 1.85
5354 5441 3.088194 TGTAGGAACAGACACACGAAC 57.912 47.619 0.00 0.00 0.00 3.95
5727 5817 2.321263 TACGAGGGCGACGGAGAGAT 62.321 60.000 0.00 0.00 41.64 2.75
5765 5855 0.040603 ACAAGAAGGACGACGACGAC 60.041 55.000 15.32 7.84 42.66 4.34
5766 5856 0.664761 AACAAGAAGGACGACGACGA 59.335 50.000 15.32 0.00 42.66 4.20
5767 5857 2.240040 CTAACAAGAAGGACGACGACG 58.760 52.381 5.58 5.58 45.75 5.12
5768 5858 3.058363 AGACTAACAAGAAGGACGACGAC 60.058 47.826 0.00 0.00 0.00 4.34
5769 5859 3.144506 AGACTAACAAGAAGGACGACGA 58.855 45.455 0.00 0.00 0.00 4.20
5770 5860 3.490399 GAGACTAACAAGAAGGACGACG 58.510 50.000 0.00 0.00 0.00 5.12
5771 5861 3.490399 CGAGACTAACAAGAAGGACGAC 58.510 50.000 0.00 0.00 0.00 4.34
5772 5862 2.095364 GCGAGACTAACAAGAAGGACGA 60.095 50.000 0.00 0.00 0.00 4.20
5773 5863 2.251893 GCGAGACTAACAAGAAGGACG 58.748 52.381 0.00 0.00 0.00 4.79
5774 5864 2.251893 CGCGAGACTAACAAGAAGGAC 58.748 52.381 0.00 0.00 0.00 3.85
5775 5865 1.201647 CCGCGAGACTAACAAGAAGGA 59.798 52.381 8.23 0.00 0.00 3.36
5776 5866 1.067776 ACCGCGAGACTAACAAGAAGG 60.068 52.381 8.23 0.00 0.00 3.46
5779 5869 0.242825 CCACCGCGAGACTAACAAGA 59.757 55.000 8.23 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.