Multiple sequence alignment - TraesCS3D01G482700

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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 TraesCS3D01G482700 chr3D 100.000 2798 0 0 1 2798 580319570 580316773 0.000000e+00 5168
1 TraesCS3D01G482700 chr3D 86.179 369 51 0 1423 1791 582620028 582619660 1.560000e-107 399
2 TraesCS3D01G482700 chr3D 77.642 246 55 0 1053 1298 596896457 596896702 1.740000e-32 150
3 TraesCS3D01G482700 chr3B 92.780 1385 58 12 716 2100 775446039 775444697 0.000000e+00 1965
4 TraesCS3D01G482700 chr3B 88.711 1249 97 25 692 1920 775563138 775561914 0.000000e+00 1485
5 TraesCS3D01G482700 chr3B 91.931 347 23 5 2454 2798 775443489 775443146 5.420000e-132 481
6 TraesCS3D01G482700 chr3B 95.736 258 10 1 1 258 784527487 784527231 5.580000e-112 414
7 TraesCS3D01G482700 chr3B 95.349 258 11 1 1 258 784456350 784456094 2.590000e-110 409
8 TraesCS3D01G482700 chr3B 83.740 369 60 0 1423 1791 778660659 778661027 1.590000e-92 350
9 TraesCS3D01G482700 chr3A 89.372 1402 92 27 729 2093 715595128 715593747 0.000000e+00 1711
10 TraesCS3D01G482700 chr3A 89.726 730 45 15 2088 2798 715586484 715585766 0.000000e+00 905
11 TraesCS3D01G482700 chr3A 89.091 495 32 11 258 732 715595867 715595375 1.860000e-166 595
12 TraesCS3D01G482700 chr5D 94.677 263 10 4 1 260 361403127 361403388 3.360000e-109 405
13 TraesCS3D01G482700 chr6B 92.937 269 12 3 1 268 162619014 162618752 4.370000e-103 385
14 TraesCS3D01G482700 chr1B 91.954 261 15 2 1 261 15207380 15207126 7.370000e-96 361
15 TraesCS3D01G482700 chr4B 82.545 275 35 8 1055 1318 552028401 552028129 2.170000e-56 230
16 TraesCS3D01G482700 chr7D 76.608 342 68 11 1425 1760 46523858 46524193 7.960000e-41 178
17 TraesCS3D01G482700 chr7D 76.959 217 40 7 1122 1330 579536162 579535948 6.330000e-22 115
18 TraesCS3D01G482700 chr7B 78.199 211 36 7 1122 1324 645256259 645256467 2.930000e-25 126


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 TraesCS3D01G482700 chr3D 580316773 580319570 2797 True 5168 5168 100.0000 1 2798 1 chr3D.!!$R1 2797
1 TraesCS3D01G482700 chr3B 775561914 775563138 1224 True 1485 1485 88.7110 692 1920 1 chr3B.!!$R1 1228
2 TraesCS3D01G482700 chr3B 775443146 775446039 2893 True 1223 1965 92.3555 716 2798 2 chr3B.!!$R4 2082
3 TraesCS3D01G482700 chr3A 715593747 715595867 2120 True 1153 1711 89.2315 258 2093 2 chr3A.!!$R2 1835
4 TraesCS3D01G482700 chr3A 715585766 715586484 718 True 905 905 89.7260 2088 2798 1 chr3A.!!$R1 710

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
145 146 0.038310 AAGAAGGGGAAAAGGCGAGG 59.962 55.0 0.00 0.0 0.00 4.63 F
158 159 0.101219 GGCGAGGCAGCAAATTAAGG 59.899 55.0 7.25 0.0 39.27 2.69 F
1404 1693 0.108992 TCGTGGTTATGCACGGACTC 60.109 55.0 0.00 0.0 44.03 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1693 1.101331 GCTCTCCCTCAGCCAAAATG 58.899 55.000 0.00 0.00 0.00 2.32 R
1557 1846 1.806623 GCTATGTCGACGAGGCCAATT 60.807 52.381 11.62 0.00 0.00 2.32 R
2322 3717 3.906014 TCGTTTTTCGCCATGAATTCA 57.094 38.095 11.26 11.26 36.22 2.57 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
21 22 4.005487 CAAGTGGGGATGCAAAAATTGA 57.995 40.909 0.00 0.00 0.00 2.57
22 23 4.387598 CAAGTGGGGATGCAAAAATTGAA 58.612 39.130 0.00 0.00 0.00 2.69
23 24 4.276058 AGTGGGGATGCAAAAATTGAAG 57.724 40.909 0.00 0.00 0.00 3.02
24 25 3.903090 AGTGGGGATGCAAAAATTGAAGA 59.097 39.130 0.00 0.00 0.00 2.87
25 26 4.020839 AGTGGGGATGCAAAAATTGAAGAG 60.021 41.667 0.00 0.00 0.00 2.85
26 27 4.021192 GTGGGGATGCAAAAATTGAAGAGA 60.021 41.667 0.00 0.00 0.00 3.10
27 28 4.221262 TGGGGATGCAAAAATTGAAGAGAG 59.779 41.667 0.00 0.00 0.00 3.20
28 29 4.382362 GGGGATGCAAAAATTGAAGAGAGG 60.382 45.833 0.00 0.00 0.00 3.69
29 30 4.382362 GGGATGCAAAAATTGAAGAGAGGG 60.382 45.833 0.00 0.00 0.00 4.30
30 31 4.463891 GGATGCAAAAATTGAAGAGAGGGA 59.536 41.667 0.00 0.00 0.00 4.20
31 32 4.853924 TGCAAAAATTGAAGAGAGGGAC 57.146 40.909 0.00 0.00 0.00 4.46
32 33 3.253188 TGCAAAAATTGAAGAGAGGGACG 59.747 43.478 0.00 0.00 0.00 4.79
33 34 3.366374 GCAAAAATTGAAGAGAGGGACGG 60.366 47.826 0.00 0.00 0.00 4.79
34 35 4.072131 CAAAAATTGAAGAGAGGGACGGA 58.928 43.478 0.00 0.00 0.00 4.69
35 36 4.576330 AAAATTGAAGAGAGGGACGGAT 57.424 40.909 0.00 0.00 0.00 4.18
36 37 3.550437 AATTGAAGAGAGGGACGGATG 57.450 47.619 0.00 0.00 0.00 3.51
37 38 1.938585 TTGAAGAGAGGGACGGATGT 58.061 50.000 0.00 0.00 0.00 3.06
38 39 1.186200 TGAAGAGAGGGACGGATGTG 58.814 55.000 0.00 0.00 0.00 3.21
39 40 1.272480 TGAAGAGAGGGACGGATGTGA 60.272 52.381 0.00 0.00 0.00 3.58
40 41 1.407258 GAAGAGAGGGACGGATGTGAG 59.593 57.143 0.00 0.00 0.00 3.51
41 42 0.626382 AGAGAGGGACGGATGTGAGA 59.374 55.000 0.00 0.00 0.00 3.27
42 43 1.028905 GAGAGGGACGGATGTGAGAG 58.971 60.000 0.00 0.00 0.00 3.20
43 44 0.396417 AGAGGGACGGATGTGAGAGG 60.396 60.000 0.00 0.00 0.00 3.69
44 45 1.381872 AGGGACGGATGTGAGAGGG 60.382 63.158 0.00 0.00 0.00 4.30
45 46 2.435693 GGGACGGATGTGAGAGGGG 61.436 68.421 0.00 0.00 0.00 4.79
46 47 2.501610 GACGGATGTGAGAGGGGC 59.498 66.667 0.00 0.00 0.00 5.80
47 48 2.039624 ACGGATGTGAGAGGGGCT 59.960 61.111 0.00 0.00 0.00 5.19
48 49 0.755698 GACGGATGTGAGAGGGGCTA 60.756 60.000 0.00 0.00 0.00 3.93
49 50 0.757188 ACGGATGTGAGAGGGGCTAG 60.757 60.000 0.00 0.00 0.00 3.42
50 51 1.751563 GGATGTGAGAGGGGCTAGC 59.248 63.158 6.04 6.04 0.00 3.42
51 52 1.751563 GATGTGAGAGGGGCTAGCC 59.248 63.158 26.55 26.55 0.00 3.93
52 53 2.093537 GATGTGAGAGGGGCTAGCCG 62.094 65.000 27.24 0.00 36.85 5.52
53 54 3.541713 GTGAGAGGGGCTAGCCGG 61.542 72.222 27.24 0.00 36.85 6.13
71 72 4.722700 CCACGGTGGAGGGCAAGG 62.723 72.222 22.77 0.00 40.96 3.61
72 73 3.953775 CACGGTGGAGGGCAAGGT 61.954 66.667 0.00 0.00 0.00 3.50
73 74 3.175710 ACGGTGGAGGGCAAGGTT 61.176 61.111 0.00 0.00 0.00 3.50
74 75 2.672996 CGGTGGAGGGCAAGGTTG 60.673 66.667 0.00 0.00 0.00 3.77
75 76 2.283173 GGTGGAGGGCAAGGTTGG 60.283 66.667 0.00 0.00 0.00 3.77
76 77 2.283173 GTGGAGGGCAAGGTTGGG 60.283 66.667 0.00 0.00 0.00 4.12
77 78 4.299796 TGGAGGGCAAGGTTGGGC 62.300 66.667 0.00 0.00 0.00 5.36
78 79 4.299796 GGAGGGCAAGGTTGGGCA 62.300 66.667 0.00 0.00 0.00 5.36
79 80 2.991540 GAGGGCAAGGTTGGGCAC 60.992 66.667 0.00 0.00 0.00 5.01
103 104 2.047274 GGCCGTGAAGCTGCTGTA 60.047 61.111 1.35 0.00 0.00 2.74
104 105 2.103042 GGCCGTGAAGCTGCTGTAG 61.103 63.158 1.35 0.00 0.00 2.74
113 114 4.746361 CTGCTGTAGCTAGCGCAT 57.254 55.556 11.47 0.00 46.61 4.73
114 115 2.223509 CTGCTGTAGCTAGCGCATG 58.776 57.895 11.47 2.04 46.61 4.06
115 116 1.220169 CTGCTGTAGCTAGCGCATGG 61.220 60.000 11.47 6.40 46.61 3.66
116 117 1.068083 GCTGTAGCTAGCGCATGGA 59.932 57.895 11.47 0.00 39.10 3.41
117 118 0.320247 GCTGTAGCTAGCGCATGGAT 60.320 55.000 11.47 0.00 39.10 3.41
118 119 1.067565 GCTGTAGCTAGCGCATGGATA 60.068 52.381 11.47 0.00 39.10 2.59
119 120 2.873609 CTGTAGCTAGCGCATGGATAG 58.126 52.381 11.47 2.77 37.69 2.08
120 121 2.230025 CTGTAGCTAGCGCATGGATAGT 59.770 50.000 11.47 0.00 36.98 2.12
121 122 2.029918 TGTAGCTAGCGCATGGATAGTG 60.030 50.000 11.47 0.00 36.98 2.74
122 123 0.319728 AGCTAGCGCATGGATAGTGG 59.680 55.000 11.47 0.00 36.98 4.00
123 124 0.671781 GCTAGCGCATGGATAGTGGG 60.672 60.000 11.47 0.00 36.98 4.61
127 128 4.876701 GCATGGATAGTGGGCGAA 57.123 55.556 0.00 0.00 0.00 4.70
128 129 2.621763 GCATGGATAGTGGGCGAAG 58.378 57.895 0.00 0.00 0.00 3.79
129 130 0.106708 GCATGGATAGTGGGCGAAGA 59.893 55.000 0.00 0.00 0.00 2.87
130 131 1.475034 GCATGGATAGTGGGCGAAGAA 60.475 52.381 0.00 0.00 0.00 2.52
131 132 2.487934 CATGGATAGTGGGCGAAGAAG 58.512 52.381 0.00 0.00 0.00 2.85
132 133 0.830648 TGGATAGTGGGCGAAGAAGG 59.169 55.000 0.00 0.00 0.00 3.46
133 134 0.106894 GGATAGTGGGCGAAGAAGGG 59.893 60.000 0.00 0.00 0.00 3.95
134 135 0.106894 GATAGTGGGCGAAGAAGGGG 59.893 60.000 0.00 0.00 0.00 4.79
135 136 0.326238 ATAGTGGGCGAAGAAGGGGA 60.326 55.000 0.00 0.00 0.00 4.81
136 137 0.545787 TAGTGGGCGAAGAAGGGGAA 60.546 55.000 0.00 0.00 0.00 3.97
137 138 1.074248 GTGGGCGAAGAAGGGGAAA 59.926 57.895 0.00 0.00 0.00 3.13
138 139 0.538746 GTGGGCGAAGAAGGGGAAAA 60.539 55.000 0.00 0.00 0.00 2.29
139 140 0.251165 TGGGCGAAGAAGGGGAAAAG 60.251 55.000 0.00 0.00 0.00 2.27
140 141 0.965866 GGGCGAAGAAGGGGAAAAGG 60.966 60.000 0.00 0.00 0.00 3.11
141 142 1.595993 GGCGAAGAAGGGGAAAAGGC 61.596 60.000 0.00 0.00 0.00 4.35
142 143 1.923227 GCGAAGAAGGGGAAAAGGCG 61.923 60.000 0.00 0.00 0.00 5.52
143 144 0.321298 CGAAGAAGGGGAAAAGGCGA 60.321 55.000 0.00 0.00 0.00 5.54
144 145 1.454201 GAAGAAGGGGAAAAGGCGAG 58.546 55.000 0.00 0.00 0.00 5.03
145 146 0.038310 AAGAAGGGGAAAAGGCGAGG 59.962 55.000 0.00 0.00 0.00 4.63
146 147 2.035783 AAGGGGAAAAGGCGAGGC 59.964 61.111 0.00 0.00 0.00 4.70
147 148 2.764637 GAAGGGGAAAAGGCGAGGCA 62.765 60.000 0.00 0.00 0.00 4.75
148 149 2.751837 GGGGAAAAGGCGAGGCAG 60.752 66.667 0.00 0.00 0.00 4.85
149 150 3.443925 GGGAAAAGGCGAGGCAGC 61.444 66.667 0.00 0.00 0.00 5.25
150 151 2.672996 GGAAAAGGCGAGGCAGCA 60.673 61.111 7.25 0.00 39.27 4.41
151 152 2.268076 GGAAAAGGCGAGGCAGCAA 61.268 57.895 7.25 0.00 39.27 3.91
152 153 1.659794 GAAAAGGCGAGGCAGCAAA 59.340 52.632 7.25 0.00 39.27 3.68
153 154 0.244721 GAAAAGGCGAGGCAGCAAAT 59.755 50.000 7.25 0.00 39.27 2.32
154 155 0.681175 AAAAGGCGAGGCAGCAAATT 59.319 45.000 7.25 0.00 39.27 1.82
155 156 1.544724 AAAGGCGAGGCAGCAAATTA 58.455 45.000 7.25 0.00 39.27 1.40
156 157 1.544724 AAGGCGAGGCAGCAAATTAA 58.455 45.000 7.25 0.00 39.27 1.40
157 158 1.098050 AGGCGAGGCAGCAAATTAAG 58.902 50.000 7.25 0.00 39.27 1.85
158 159 0.101219 GGCGAGGCAGCAAATTAAGG 59.899 55.000 7.25 0.00 39.27 2.69
159 160 1.094785 GCGAGGCAGCAAATTAAGGA 58.905 50.000 0.00 0.00 37.05 3.36
160 161 1.472480 GCGAGGCAGCAAATTAAGGAA 59.528 47.619 0.00 0.00 37.05 3.36
161 162 2.478539 GCGAGGCAGCAAATTAAGGAAG 60.479 50.000 0.00 0.00 37.05 3.46
162 163 3.009723 CGAGGCAGCAAATTAAGGAAGA 58.990 45.455 0.00 0.00 0.00 2.87
163 164 3.440173 CGAGGCAGCAAATTAAGGAAGAA 59.560 43.478 0.00 0.00 0.00 2.52
164 165 4.437930 CGAGGCAGCAAATTAAGGAAGAAG 60.438 45.833 0.00 0.00 0.00 2.85
165 166 4.666512 AGGCAGCAAATTAAGGAAGAAGA 58.333 39.130 0.00 0.00 0.00 2.87
166 167 4.460731 AGGCAGCAAATTAAGGAAGAAGAC 59.539 41.667 0.00 0.00 0.00 3.01
167 168 4.218417 GGCAGCAAATTAAGGAAGAAGACA 59.782 41.667 0.00 0.00 0.00 3.41
168 169 5.157067 GCAGCAAATTAAGGAAGAAGACAC 58.843 41.667 0.00 0.00 0.00 3.67
169 170 5.703876 CAGCAAATTAAGGAAGAAGACACC 58.296 41.667 0.00 0.00 0.00 4.16
170 171 4.767409 AGCAAATTAAGGAAGAAGACACCC 59.233 41.667 0.00 0.00 0.00 4.61
171 172 4.522789 GCAAATTAAGGAAGAAGACACCCA 59.477 41.667 0.00 0.00 0.00 4.51
172 173 5.564848 GCAAATTAAGGAAGAAGACACCCAC 60.565 44.000 0.00 0.00 0.00 4.61
173 174 3.396260 TTAAGGAAGAAGACACCCACG 57.604 47.619 0.00 0.00 0.00 4.94
174 175 1.420430 AAGGAAGAAGACACCCACGA 58.580 50.000 0.00 0.00 0.00 4.35
175 176 1.420430 AGGAAGAAGACACCCACGAA 58.580 50.000 0.00 0.00 0.00 3.85
176 177 1.344763 AGGAAGAAGACACCCACGAAG 59.655 52.381 0.00 0.00 0.00 3.79
177 178 1.608283 GGAAGAAGACACCCACGAAGG 60.608 57.143 0.00 0.00 37.03 3.46
187 188 3.780624 CCACGAAGGGATAAGGTGG 57.219 57.895 0.00 0.00 41.81 4.61
188 189 0.180406 CCACGAAGGGATAAGGTGGG 59.820 60.000 0.65 0.00 43.39 4.61
189 190 0.463833 CACGAAGGGATAAGGTGGGC 60.464 60.000 0.00 0.00 0.00 5.36
190 191 1.148498 CGAAGGGATAAGGTGGGCC 59.852 63.158 0.00 0.00 0.00 5.80
192 193 0.183731 GAAGGGATAAGGTGGGCCTG 59.816 60.000 4.53 0.00 46.33 4.85
193 194 1.937924 AAGGGATAAGGTGGGCCTGC 61.938 60.000 4.53 0.00 46.33 4.85
194 195 2.689691 GGGATAAGGTGGGCCTGCA 61.690 63.158 4.53 0.00 46.33 4.41
195 196 1.152881 GGATAAGGTGGGCCTGCAG 60.153 63.158 6.78 6.78 46.33 4.41
196 197 1.825622 GATAAGGTGGGCCTGCAGC 60.826 63.158 8.66 2.30 46.33 5.25
197 198 3.704231 ATAAGGTGGGCCTGCAGCG 62.704 63.158 8.66 2.70 46.33 5.18
201 202 4.704833 GTGGGCCTGCAGCGAGAA 62.705 66.667 8.66 0.00 45.17 2.87
202 203 4.704833 TGGGCCTGCAGCGAGAAC 62.705 66.667 8.66 0.00 45.17 3.01
204 205 4.742201 GGCCTGCAGCGAGAACGA 62.742 66.667 8.66 0.00 45.17 3.85
205 206 3.184683 GCCTGCAGCGAGAACGAG 61.185 66.667 8.66 0.00 42.66 4.18
206 207 3.184683 CCTGCAGCGAGAACGAGC 61.185 66.667 8.66 0.00 42.66 5.03
207 208 3.540014 CTGCAGCGAGAACGAGCG 61.540 66.667 0.00 0.00 42.02 5.03
213 214 4.753877 CGAGAACGAGCGGTGCGA 62.754 66.667 12.17 0.00 42.66 5.10
214 215 3.173240 GAGAACGAGCGGTGCGAC 61.173 66.667 12.17 6.80 0.00 5.19
215 216 4.719369 AGAACGAGCGGTGCGACC 62.719 66.667 12.17 0.00 34.05 4.79
251 252 2.262572 GGTCGACCGTATGTAAACGT 57.737 50.000 20.85 0.00 41.27 3.99
252 253 2.595386 GGTCGACCGTATGTAAACGTT 58.405 47.619 20.85 0.00 41.27 3.99
253 254 2.986479 GGTCGACCGTATGTAAACGTTT 59.014 45.455 20.85 18.90 41.27 3.60
254 255 3.059438 GGTCGACCGTATGTAAACGTTTC 59.941 47.826 20.85 9.90 41.27 2.78
255 256 3.059438 GTCGACCGTATGTAAACGTTTCC 59.941 47.826 18.42 6.75 41.27 3.13
256 257 2.345341 CGACCGTATGTAAACGTTTCCC 59.655 50.000 18.42 10.10 41.27 3.97
261 262 7.054491 ACCGTATGTAAACGTTTCCCTATAT 57.946 36.000 18.42 6.41 41.27 0.86
282 283 3.940335 TCTAATGGATGGATGGTGGAGA 58.060 45.455 0.00 0.00 0.00 3.71
370 373 5.362717 TGAGCCGATAGAGAAAAATGAGGTA 59.637 40.000 0.00 0.00 39.76 3.08
374 377 5.694006 CCGATAGAGAAAAATGAGGTAGCAG 59.306 44.000 0.00 0.00 39.76 4.24
376 379 6.640499 CGATAGAGAAAAATGAGGTAGCAGAG 59.360 42.308 0.00 0.00 39.76 3.35
382 385 4.640771 AAATGAGGTAGCAGAGACCAAA 57.359 40.909 0.00 0.00 39.65 3.28
385 388 0.608640 AGGTAGCAGAGACCAAACCG 59.391 55.000 0.00 0.00 39.65 4.44
390 393 1.899814 AGCAGAGACCAAACCGTATCA 59.100 47.619 0.00 0.00 0.00 2.15
396 399 4.162320 AGAGACCAAACCGTATCATGTCAT 59.838 41.667 0.00 0.00 0.00 3.06
401 404 4.438608 CCAAACCGTATCATGTCATTGTGG 60.439 45.833 0.00 0.00 0.00 4.17
402 405 3.627395 ACCGTATCATGTCATTGTGGT 57.373 42.857 0.00 0.00 0.00 4.16
403 406 3.950397 ACCGTATCATGTCATTGTGGTT 58.050 40.909 0.00 0.00 0.00 3.67
404 407 5.092554 ACCGTATCATGTCATTGTGGTTA 57.907 39.130 0.00 0.00 0.00 2.85
405 408 4.873827 ACCGTATCATGTCATTGTGGTTAC 59.126 41.667 0.00 0.00 0.00 2.50
406 409 4.026062 CCGTATCATGTCATTGTGGTTACG 60.026 45.833 0.00 0.00 32.64 3.18
407 410 4.801516 CGTATCATGTCATTGTGGTTACGA 59.198 41.667 0.00 0.00 33.63 3.43
417 435 3.120321 TGTGGTTACGAGCAGACATTT 57.880 42.857 0.00 0.00 33.20 2.32
426 444 4.130118 ACGAGCAGACATTTTTGAAGTCT 58.870 39.130 0.00 0.00 42.97 3.24
447 465 4.080863 TCTGAGGAGGAGTTTTAGAATGCC 60.081 45.833 0.00 0.00 0.00 4.40
472 490 2.093869 GCAACCGGAGATGTGGTAGTAA 60.094 50.000 9.46 0.00 37.54 2.24
475 493 3.288964 ACCGGAGATGTGGTAGTAAGAG 58.711 50.000 9.46 0.00 36.50 2.85
479 497 3.315749 GGAGATGTGGTAGTAAGAGACCG 59.684 52.174 0.00 0.00 38.69 4.79
501 519 1.069358 CTAGAGATCGGGGCAAAGGAC 59.931 57.143 0.00 0.00 0.00 3.85
522 540 3.259876 ACGGTGAAGATGGTAACTGCTTA 59.740 43.478 0.00 0.00 32.20 3.09
528 547 8.903820 GGTGAAGATGGTAACTGCTTAATTATT 58.096 33.333 0.00 0.00 32.20 1.40
569 588 6.872020 AGTTCATTTTAGTCTTAAGCTACGCA 59.128 34.615 0.00 0.00 0.00 5.24
667 687 1.027357 GCATCAGACGCCCATTCATT 58.973 50.000 0.00 0.00 0.00 2.57
681 701 3.434299 CCATTCATTTTGGCTTGCTGTTC 59.566 43.478 0.00 0.00 0.00 3.18
836 1106 6.597672 GGGGAAACAAAAACAATCTGTTCTTT 59.402 34.615 0.00 0.00 40.14 2.52
839 1109 7.201609 GGAAACAAAAACAATCTGTTCTTTCCC 60.202 37.037 13.57 0.00 40.14 3.97
878 1148 5.696724 CCAACTCGATTAAAATAGCCTCGAT 59.303 40.000 0.00 0.00 37.68 3.59
967 1237 6.100859 ACCTCACAATCTCACCATCAATCTAT 59.899 38.462 0.00 0.00 0.00 1.98
1050 1320 2.861006 GCTTTCGACAGCCCGTTC 59.139 61.111 12.62 0.00 33.21 3.95
1248 1518 3.677527 GAGACCTTCGACGGACCA 58.322 61.111 15.91 0.00 0.00 4.02
1261 1531 1.676967 GGACCACGACTCCTACCGT 60.677 63.158 0.00 0.00 39.88 4.83
1337 1607 2.158957 AGGTACGTACATGCCCTGATTG 60.159 50.000 26.02 0.00 0.00 2.67
1339 1609 2.779755 ACGTACATGCCCTGATTGAA 57.220 45.000 0.00 0.00 0.00 2.69
1343 1628 3.804325 CGTACATGCCCTGATTGAACTAG 59.196 47.826 0.00 0.00 0.00 2.57
1345 1630 5.451381 CGTACATGCCCTGATTGAACTAGTA 60.451 44.000 0.00 0.00 0.00 1.82
1381 1670 3.495100 CCTTGTTTCAGCTGTCCTGTACT 60.495 47.826 14.67 0.00 42.38 2.73
1404 1693 0.108992 TCGTGGTTATGCACGGACTC 60.109 55.000 0.00 0.00 44.03 3.36
1557 1846 4.287781 TTCTTCGGCGGCGACACA 62.288 61.111 34.85 18.96 0.00 3.72
1632 1921 4.065281 GAGGTGTCCGGGGTGACG 62.065 72.222 0.00 0.00 38.11 4.35
1936 2237 6.038603 CCATCGGATGAATGTATCAACTTTGT 59.961 38.462 19.30 0.00 42.54 2.83
1955 2256 8.771920 ACTTTGTTATATCGAATTGAGTCACA 57.228 30.769 0.00 0.00 0.00 3.58
1991 2300 2.609459 CTCGCAACACTTGACAGAACTT 59.391 45.455 0.00 0.00 0.00 2.66
1992 2301 2.607635 TCGCAACACTTGACAGAACTTC 59.392 45.455 0.00 0.00 0.00 3.01
1993 2302 2.597505 CGCAACACTTGACAGAACTTCG 60.598 50.000 0.00 0.00 0.00 3.79
1998 2307 3.617263 ACACTTGACAGAACTTCGTTGTC 59.383 43.478 4.82 4.82 41.15 3.18
2129 3518 2.757894 ATTGGGTTTGGGTGTGTGTA 57.242 45.000 0.00 0.00 0.00 2.90
2168 3557 4.448395 CGCCAATATGCCATGGTTTAATTG 59.552 41.667 14.67 16.42 39.00 2.32
2200 3589 2.419436 GCCCTAAAGTCCTCTTCTGCTC 60.419 54.545 0.00 0.00 32.90 4.26
2229 3618 4.614946 TCATCTGAGCATACGATGAACAG 58.385 43.478 0.00 2.97 40.20 3.16
2238 3627 8.194769 TGAGCATACGATGAACAGTAAAATCTA 58.805 33.333 0.00 0.00 0.00 1.98
2240 3629 9.378551 AGCATACGATGAACAGTAAAATCTAAA 57.621 29.630 0.00 0.00 0.00 1.85
2241 3630 9.982291 GCATACGATGAACAGTAAAATCTAAAA 57.018 29.630 0.00 0.00 0.00 1.52
2304 3699 5.293560 TGTTTTAGGTGCTTGGCAATTAAC 58.706 37.500 0.00 0.00 41.47 2.01
2322 3717 7.201461 GCAATTAACGATGAAATGACATTTGCT 60.201 33.333 18.00 4.98 35.50 3.91
2348 3743 3.820689 TCATGGCGAAAAACGAAATCAG 58.179 40.909 0.00 0.00 45.77 2.90
2352 3747 2.604614 GGCGAAAAACGAAATCAGCACT 60.605 45.455 0.00 0.00 45.77 4.40
2364 3759 9.774742 AACGAAATCAGCACTCTAAAATATTTC 57.225 29.630 0.10 0.00 0.00 2.17
2445 3859 9.520204 AACTTCTACAGAAATGTTGTTGAAATG 57.480 29.630 4.42 0.00 38.90 2.32
2483 3897 7.827819 TCCATACAAGTTGAAATCTACTTCG 57.172 36.000 10.54 6.51 39.28 3.79
2691 4105 9.599866 CACTTTCATACACACCAGAATATCTTA 57.400 33.333 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.005487 TCAATTTTTGCATCCCCACTTG 57.995 40.909 0.00 0.00 0.00 3.16
1 2 4.347583 TCTTCAATTTTTGCATCCCCACTT 59.652 37.500 0.00 0.00 0.00 3.16
2 3 3.903090 TCTTCAATTTTTGCATCCCCACT 59.097 39.130 0.00 0.00 0.00 4.00
3 4 4.021192 TCTCTTCAATTTTTGCATCCCCAC 60.021 41.667 0.00 0.00 0.00 4.61
4 5 4.158786 TCTCTTCAATTTTTGCATCCCCA 58.841 39.130 0.00 0.00 0.00 4.96
5 6 4.382362 CCTCTCTTCAATTTTTGCATCCCC 60.382 45.833 0.00 0.00 0.00 4.81
6 7 4.382362 CCCTCTCTTCAATTTTTGCATCCC 60.382 45.833 0.00 0.00 0.00 3.85
7 8 4.463891 TCCCTCTCTTCAATTTTTGCATCC 59.536 41.667 0.00 0.00 0.00 3.51
8 9 5.405797 GTCCCTCTCTTCAATTTTTGCATC 58.594 41.667 0.00 0.00 0.00 3.91
9 10 4.082571 CGTCCCTCTCTTCAATTTTTGCAT 60.083 41.667 0.00 0.00 0.00 3.96
10 11 3.253188 CGTCCCTCTCTTCAATTTTTGCA 59.747 43.478 0.00 0.00 0.00 4.08
11 12 3.366374 CCGTCCCTCTCTTCAATTTTTGC 60.366 47.826 0.00 0.00 0.00 3.68
12 13 4.072131 TCCGTCCCTCTCTTCAATTTTTG 58.928 43.478 0.00 0.00 0.00 2.44
13 14 4.367039 TCCGTCCCTCTCTTCAATTTTT 57.633 40.909 0.00 0.00 0.00 1.94
14 15 4.263506 ACATCCGTCCCTCTCTTCAATTTT 60.264 41.667 0.00 0.00 0.00 1.82
15 16 3.264450 ACATCCGTCCCTCTCTTCAATTT 59.736 43.478 0.00 0.00 0.00 1.82
16 17 2.840651 ACATCCGTCCCTCTCTTCAATT 59.159 45.455 0.00 0.00 0.00 2.32
17 18 2.169352 CACATCCGTCCCTCTCTTCAAT 59.831 50.000 0.00 0.00 0.00 2.57
18 19 1.550524 CACATCCGTCCCTCTCTTCAA 59.449 52.381 0.00 0.00 0.00 2.69
19 20 1.186200 CACATCCGTCCCTCTCTTCA 58.814 55.000 0.00 0.00 0.00 3.02
20 21 1.407258 CTCACATCCGTCCCTCTCTTC 59.593 57.143 0.00 0.00 0.00 2.87
21 22 1.006043 TCTCACATCCGTCCCTCTCTT 59.994 52.381 0.00 0.00 0.00 2.85
22 23 0.626382 TCTCACATCCGTCCCTCTCT 59.374 55.000 0.00 0.00 0.00 3.10
23 24 1.028905 CTCTCACATCCGTCCCTCTC 58.971 60.000 0.00 0.00 0.00 3.20
24 25 0.396417 CCTCTCACATCCGTCCCTCT 60.396 60.000 0.00 0.00 0.00 3.69
25 26 1.395826 CCCTCTCACATCCGTCCCTC 61.396 65.000 0.00 0.00 0.00 4.30
26 27 1.381872 CCCTCTCACATCCGTCCCT 60.382 63.158 0.00 0.00 0.00 4.20
27 28 2.435693 CCCCTCTCACATCCGTCCC 61.436 68.421 0.00 0.00 0.00 4.46
28 29 3.095347 GCCCCTCTCACATCCGTCC 62.095 68.421 0.00 0.00 0.00 4.79
29 30 0.755698 TAGCCCCTCTCACATCCGTC 60.756 60.000 0.00 0.00 0.00 4.79
30 31 0.757188 CTAGCCCCTCTCACATCCGT 60.757 60.000 0.00 0.00 0.00 4.69
31 32 2.045280 CTAGCCCCTCTCACATCCG 58.955 63.158 0.00 0.00 0.00 4.18
32 33 1.751563 GCTAGCCCCTCTCACATCC 59.248 63.158 2.29 0.00 0.00 3.51
33 34 1.751563 GGCTAGCCCCTCTCACATC 59.248 63.158 24.19 0.00 0.00 3.06
34 35 2.136878 CGGCTAGCCCCTCTCACAT 61.137 63.158 28.09 0.00 0.00 3.21
35 36 2.759973 CGGCTAGCCCCTCTCACA 60.760 66.667 28.09 0.00 0.00 3.58
36 37 3.541713 CCGGCTAGCCCCTCTCAC 61.542 72.222 28.09 0.36 0.00 3.51
54 55 4.722700 CCTTGCCCTCCACCGTGG 62.723 72.222 11.73 11.73 39.43 4.94
55 56 3.491598 AACCTTGCCCTCCACCGTG 62.492 63.158 0.00 0.00 0.00 4.94
56 57 3.175710 AACCTTGCCCTCCACCGT 61.176 61.111 0.00 0.00 0.00 4.83
57 58 2.672996 CAACCTTGCCCTCCACCG 60.673 66.667 0.00 0.00 0.00 4.94
58 59 2.283173 CCAACCTTGCCCTCCACC 60.283 66.667 0.00 0.00 0.00 4.61
59 60 2.283173 CCCAACCTTGCCCTCCAC 60.283 66.667 0.00 0.00 0.00 4.02
60 61 4.299796 GCCCAACCTTGCCCTCCA 62.300 66.667 0.00 0.00 0.00 3.86
61 62 4.299796 TGCCCAACCTTGCCCTCC 62.300 66.667 0.00 0.00 0.00 4.30
62 63 2.991540 GTGCCCAACCTTGCCCTC 60.992 66.667 0.00 0.00 0.00 4.30
63 64 4.621087 GGTGCCCAACCTTGCCCT 62.621 66.667 0.00 0.00 46.55 5.19
85 86 3.605749 TACAGCAGCTTCACGGCCC 62.606 63.158 0.00 0.00 40.83 5.80
86 87 2.047274 TACAGCAGCTTCACGGCC 60.047 61.111 0.00 0.00 40.83 6.13
87 88 3.479370 CTACAGCAGCTTCACGGC 58.521 61.111 0.00 0.00 40.15 5.68
96 97 1.220169 CCATGCGCTAGCTACAGCAG 61.220 60.000 17.92 11.07 43.20 4.24
97 98 1.227350 CCATGCGCTAGCTACAGCA 60.227 57.895 15.85 15.85 45.16 4.41
98 99 0.320247 ATCCATGCGCTAGCTACAGC 60.320 55.000 13.93 9.29 45.42 4.40
99 100 2.230025 ACTATCCATGCGCTAGCTACAG 59.770 50.000 13.93 0.00 45.42 2.74
100 101 2.029918 CACTATCCATGCGCTAGCTACA 60.030 50.000 13.93 11.42 45.42 2.74
101 102 2.600731 CACTATCCATGCGCTAGCTAC 58.399 52.381 13.93 5.37 45.42 3.58
102 103 1.546029 CCACTATCCATGCGCTAGCTA 59.454 52.381 13.93 1.70 45.42 3.32
103 104 0.319728 CCACTATCCATGCGCTAGCT 59.680 55.000 13.93 0.00 45.42 3.32
104 105 0.671781 CCCACTATCCATGCGCTAGC 60.672 60.000 9.73 4.06 45.41 3.42
105 106 0.671781 GCCCACTATCCATGCGCTAG 60.672 60.000 9.73 3.75 0.00 3.42
106 107 1.371183 GCCCACTATCCATGCGCTA 59.629 57.895 9.73 0.00 0.00 4.26
107 108 2.111878 GCCCACTATCCATGCGCT 59.888 61.111 9.73 0.00 0.00 5.92
108 109 3.349006 CGCCCACTATCCATGCGC 61.349 66.667 0.00 0.00 38.69 6.09
109 110 1.224069 CTTCGCCCACTATCCATGCG 61.224 60.000 0.00 0.00 46.09 4.73
110 111 0.106708 TCTTCGCCCACTATCCATGC 59.893 55.000 0.00 0.00 0.00 4.06
111 112 2.487934 CTTCTTCGCCCACTATCCATG 58.512 52.381 0.00 0.00 0.00 3.66
112 113 1.417890 CCTTCTTCGCCCACTATCCAT 59.582 52.381 0.00 0.00 0.00 3.41
113 114 0.830648 CCTTCTTCGCCCACTATCCA 59.169 55.000 0.00 0.00 0.00 3.41
114 115 0.106894 CCCTTCTTCGCCCACTATCC 59.893 60.000 0.00 0.00 0.00 2.59
115 116 0.106894 CCCCTTCTTCGCCCACTATC 59.893 60.000 0.00 0.00 0.00 2.08
116 117 0.326238 TCCCCTTCTTCGCCCACTAT 60.326 55.000 0.00 0.00 0.00 2.12
117 118 0.545787 TTCCCCTTCTTCGCCCACTA 60.546 55.000 0.00 0.00 0.00 2.74
118 119 1.423794 TTTCCCCTTCTTCGCCCACT 61.424 55.000 0.00 0.00 0.00 4.00
119 120 0.538746 TTTTCCCCTTCTTCGCCCAC 60.539 55.000 0.00 0.00 0.00 4.61
120 121 0.251165 CTTTTCCCCTTCTTCGCCCA 60.251 55.000 0.00 0.00 0.00 5.36
121 122 0.965866 CCTTTTCCCCTTCTTCGCCC 60.966 60.000 0.00 0.00 0.00 6.13
122 123 1.595993 GCCTTTTCCCCTTCTTCGCC 61.596 60.000 0.00 0.00 0.00 5.54
123 124 1.883732 GCCTTTTCCCCTTCTTCGC 59.116 57.895 0.00 0.00 0.00 4.70
124 125 0.321298 TCGCCTTTTCCCCTTCTTCG 60.321 55.000 0.00 0.00 0.00 3.79
125 126 1.454201 CTCGCCTTTTCCCCTTCTTC 58.546 55.000 0.00 0.00 0.00 2.87
126 127 0.038310 CCTCGCCTTTTCCCCTTCTT 59.962 55.000 0.00 0.00 0.00 2.52
127 128 1.685820 CCTCGCCTTTTCCCCTTCT 59.314 57.895 0.00 0.00 0.00 2.85
128 129 2.046864 GCCTCGCCTTTTCCCCTTC 61.047 63.158 0.00 0.00 0.00 3.46
129 130 2.035783 GCCTCGCCTTTTCCCCTT 59.964 61.111 0.00 0.00 0.00 3.95
130 131 3.256960 TGCCTCGCCTTTTCCCCT 61.257 61.111 0.00 0.00 0.00 4.79
131 132 2.751837 CTGCCTCGCCTTTTCCCC 60.752 66.667 0.00 0.00 0.00 4.81
132 133 3.443925 GCTGCCTCGCCTTTTCCC 61.444 66.667 0.00 0.00 0.00 3.97
133 134 1.805428 TTTGCTGCCTCGCCTTTTCC 61.805 55.000 0.00 0.00 0.00 3.13
134 135 0.244721 ATTTGCTGCCTCGCCTTTTC 59.755 50.000 0.00 0.00 0.00 2.29
135 136 0.681175 AATTTGCTGCCTCGCCTTTT 59.319 45.000 0.00 0.00 0.00 2.27
136 137 1.544724 TAATTTGCTGCCTCGCCTTT 58.455 45.000 0.00 0.00 0.00 3.11
137 138 1.474077 CTTAATTTGCTGCCTCGCCTT 59.526 47.619 0.00 0.00 0.00 4.35
138 139 1.098050 CTTAATTTGCTGCCTCGCCT 58.902 50.000 0.00 0.00 0.00 5.52
139 140 0.101219 CCTTAATTTGCTGCCTCGCC 59.899 55.000 0.00 0.00 0.00 5.54
140 141 1.094785 TCCTTAATTTGCTGCCTCGC 58.905 50.000 0.00 0.00 0.00 5.03
141 142 3.009723 TCTTCCTTAATTTGCTGCCTCG 58.990 45.455 0.00 0.00 0.00 4.63
142 143 4.702131 TCTTCTTCCTTAATTTGCTGCCTC 59.298 41.667 0.00 0.00 0.00 4.70
143 144 4.460731 GTCTTCTTCCTTAATTTGCTGCCT 59.539 41.667 0.00 0.00 0.00 4.75
144 145 4.218417 TGTCTTCTTCCTTAATTTGCTGCC 59.782 41.667 0.00 0.00 0.00 4.85
145 146 5.157067 GTGTCTTCTTCCTTAATTTGCTGC 58.843 41.667 0.00 0.00 0.00 5.25
146 147 5.335976 GGGTGTCTTCTTCCTTAATTTGCTG 60.336 44.000 0.00 0.00 0.00 4.41
147 148 4.767409 GGGTGTCTTCTTCCTTAATTTGCT 59.233 41.667 0.00 0.00 0.00 3.91
148 149 4.522789 TGGGTGTCTTCTTCCTTAATTTGC 59.477 41.667 0.00 0.00 0.00 3.68
149 150 5.334879 CGTGGGTGTCTTCTTCCTTAATTTG 60.335 44.000 0.00 0.00 0.00 2.32
150 151 4.760204 CGTGGGTGTCTTCTTCCTTAATTT 59.240 41.667 0.00 0.00 0.00 1.82
151 152 4.041198 TCGTGGGTGTCTTCTTCCTTAATT 59.959 41.667 0.00 0.00 0.00 1.40
152 153 3.581332 TCGTGGGTGTCTTCTTCCTTAAT 59.419 43.478 0.00 0.00 0.00 1.40
153 154 2.967201 TCGTGGGTGTCTTCTTCCTTAA 59.033 45.455 0.00 0.00 0.00 1.85
154 155 2.600790 TCGTGGGTGTCTTCTTCCTTA 58.399 47.619 0.00 0.00 0.00 2.69
155 156 1.420430 TCGTGGGTGTCTTCTTCCTT 58.580 50.000 0.00 0.00 0.00 3.36
156 157 1.344763 CTTCGTGGGTGTCTTCTTCCT 59.655 52.381 0.00 0.00 0.00 3.36
157 158 1.608283 CCTTCGTGGGTGTCTTCTTCC 60.608 57.143 0.00 0.00 0.00 3.46
158 159 1.797025 CCTTCGTGGGTGTCTTCTTC 58.203 55.000 0.00 0.00 0.00 2.87
169 170 0.180406 CCCACCTTATCCCTTCGTGG 59.820 60.000 0.00 0.00 43.00 4.94
170 171 0.463833 GCCCACCTTATCCCTTCGTG 60.464 60.000 0.00 0.00 0.00 4.35
171 172 1.632965 GGCCCACCTTATCCCTTCGT 61.633 60.000 0.00 0.00 0.00 3.85
172 173 1.148498 GGCCCACCTTATCCCTTCG 59.852 63.158 0.00 0.00 0.00 3.79
184 185 4.704833 TTCTCGCTGCAGGCCCAC 62.705 66.667 17.12 0.00 37.74 4.61
185 186 4.704833 GTTCTCGCTGCAGGCCCA 62.705 66.667 17.12 0.00 37.74 5.36
187 188 4.742201 TCGTTCTCGCTGCAGGCC 62.742 66.667 17.12 0.00 37.74 5.19
188 189 3.184683 CTCGTTCTCGCTGCAGGC 61.185 66.667 17.12 6.97 36.96 4.85
189 190 3.184683 GCTCGTTCTCGCTGCAGG 61.185 66.667 17.12 5.82 36.72 4.85
190 191 3.540014 CGCTCGTTCTCGCTGCAG 61.540 66.667 10.11 10.11 36.60 4.41
193 194 3.175240 CACCGCTCGTTCTCGCTG 61.175 66.667 0.00 0.00 36.96 5.18
196 197 4.753877 TCGCACCGCTCGTTCTCG 62.754 66.667 0.00 0.00 38.55 4.04
197 198 3.173240 GTCGCACCGCTCGTTCTC 61.173 66.667 0.00 0.00 0.00 2.87
198 199 4.719369 GGTCGCACCGCTCGTTCT 62.719 66.667 0.00 0.00 0.00 3.01
232 233 2.262572 ACGTTTACATACGGTCGACC 57.737 50.000 25.28 25.28 45.44 4.79
233 234 3.059438 GGAAACGTTTACATACGGTCGAC 59.941 47.826 18.49 7.13 41.29 4.20
234 235 3.241701 GGAAACGTTTACATACGGTCGA 58.758 45.455 18.49 0.00 41.29 4.20
235 236 2.345341 GGGAAACGTTTACATACGGTCG 59.655 50.000 24.13 0.00 41.29 4.79
236 237 3.588955 AGGGAAACGTTTACATACGGTC 58.411 45.455 24.13 5.52 41.29 4.79
237 238 3.683365 AGGGAAACGTTTACATACGGT 57.317 42.857 24.13 0.00 44.63 4.83
238 239 7.373493 AGATATAGGGAAACGTTTACATACGG 58.627 38.462 24.13 0.00 45.44 4.02
239 240 9.897744 TTAGATATAGGGAAACGTTTACATACG 57.102 33.333 24.13 0.00 46.52 3.06
242 243 9.720769 CCATTAGATATAGGGAAACGTTTACAT 57.279 33.333 24.13 20.02 0.00 2.29
243 244 8.926374 TCCATTAGATATAGGGAAACGTTTACA 58.074 33.333 24.13 5.65 0.00 2.41
244 245 9.939802 ATCCATTAGATATAGGGAAACGTTTAC 57.060 33.333 15.19 15.19 31.60 2.01
245 246 9.938280 CATCCATTAGATATAGGGAAACGTTTA 57.062 33.333 14.65 0.00 32.37 2.01
246 247 7.883311 CCATCCATTAGATATAGGGAAACGTTT 59.117 37.037 14.57 14.57 32.37 3.60
247 248 7.236847 TCCATCCATTAGATATAGGGAAACGTT 59.763 37.037 0.00 0.00 32.37 3.99
248 249 6.729100 TCCATCCATTAGATATAGGGAAACGT 59.271 38.462 0.00 0.00 32.37 3.99
249 250 7.182817 TCCATCCATTAGATATAGGGAAACG 57.817 40.000 0.00 0.00 32.37 3.60
250 251 7.995488 CCATCCATCCATTAGATATAGGGAAAC 59.005 40.741 0.00 0.00 32.37 2.78
251 252 7.688534 ACCATCCATCCATTAGATATAGGGAAA 59.311 37.037 0.00 0.00 32.37 3.13
252 253 7.127801 CACCATCCATCCATTAGATATAGGGAA 59.872 40.741 0.00 0.00 32.37 3.97
253 254 6.616959 CACCATCCATCCATTAGATATAGGGA 59.383 42.308 0.00 0.00 32.37 4.20
254 255 6.183361 CCACCATCCATCCATTAGATATAGGG 60.183 46.154 0.00 0.00 32.37 3.53
255 256 6.616959 TCCACCATCCATCCATTAGATATAGG 59.383 42.308 0.00 0.00 32.37 2.57
256 257 7.566509 TCTCCACCATCCATCCATTAGATATAG 59.433 40.741 0.00 0.00 32.37 1.31
261 262 3.648067 GTCTCCACCATCCATCCATTAGA 59.352 47.826 0.00 0.00 0.00 2.10
370 373 1.899814 TGATACGGTTTGGTCTCTGCT 59.100 47.619 0.00 0.00 0.00 4.24
374 377 3.857052 TGACATGATACGGTTTGGTCTC 58.143 45.455 0.00 0.00 0.00 3.36
376 379 4.394920 ACAATGACATGATACGGTTTGGTC 59.605 41.667 0.00 0.00 0.00 4.02
382 385 3.627395 ACCACAATGACATGATACGGT 57.373 42.857 0.00 0.00 0.00 4.83
385 388 5.276868 GCTCGTAACCACAATGACATGATAC 60.277 44.000 0.00 0.00 0.00 2.24
390 393 3.002791 CTGCTCGTAACCACAATGACAT 58.997 45.455 0.00 0.00 0.00 3.06
396 399 2.831685 ATGTCTGCTCGTAACCACAA 57.168 45.000 0.00 0.00 0.00 3.33
401 404 5.748592 ACTTCAAAAATGTCTGCTCGTAAC 58.251 37.500 0.00 0.00 0.00 2.50
402 405 5.758296 AGACTTCAAAAATGTCTGCTCGTAA 59.242 36.000 0.00 0.00 39.29 3.18
403 406 5.177511 CAGACTTCAAAAATGTCTGCTCGTA 59.822 40.000 9.00 0.00 46.95 3.43
404 407 4.024556 CAGACTTCAAAAATGTCTGCTCGT 60.025 41.667 9.00 0.00 46.95 4.18
405 408 4.461405 CAGACTTCAAAAATGTCTGCTCG 58.539 43.478 9.00 0.00 46.95 5.03
417 435 5.373812 AAAACTCCTCCTCAGACTTCAAA 57.626 39.130 0.00 0.00 0.00 2.69
426 444 3.369471 CGGCATTCTAAAACTCCTCCTCA 60.369 47.826 0.00 0.00 0.00 3.86
447 465 2.047274 ACATCTCCGGTTGCCACG 60.047 61.111 0.00 0.00 0.00 4.94
479 497 1.069358 CCTTTGCCCCGATCTCTAGTC 59.931 57.143 0.00 0.00 0.00 2.59
501 519 2.386661 AGCAGTTACCATCTTCACCG 57.613 50.000 0.00 0.00 0.00 4.94
649 669 3.441163 CAAAATGAATGGGCGTCTGATG 58.559 45.455 0.00 0.00 0.00 3.07
667 687 4.662278 AGTTATAGGAACAGCAAGCCAAA 58.338 39.130 0.00 0.00 0.00 3.28
681 701 4.566987 GCCAAATCGTAGGGAGTTATAGG 58.433 47.826 0.00 0.00 30.54 2.57
836 1106 4.165372 AGTTGGTACTGAAACTTCTTGGGA 59.835 41.667 0.00 0.00 32.75 4.37
839 1109 5.047847 TCGAGTTGGTACTGAAACTTCTTG 58.952 41.667 9.47 3.48 36.77 3.02
878 1148 3.671079 TGGGTATGGGACTGGCTTAATA 58.329 45.455 0.00 0.00 0.00 0.98
967 1237 3.423539 AGCTGTGCTGGAAGTCAAATA 57.576 42.857 0.00 0.00 37.57 1.40
1248 1518 1.743252 GTCGGACGGTAGGAGTCGT 60.743 63.158 0.00 0.00 42.67 4.34
1261 1531 2.852180 CGCGGTCATATGGGTCGGA 61.852 63.158 0.00 0.00 0.00 4.55
1343 1628 5.754543 AACAAGGTCGCTACTAGAGATAC 57.245 43.478 0.00 0.00 0.00 2.24
1345 1630 4.705507 TGAAACAAGGTCGCTACTAGAGAT 59.294 41.667 0.00 0.00 0.00 2.75
1359 1648 1.972872 ACAGGACAGCTGAAACAAGG 58.027 50.000 23.35 5.37 0.00 3.61
1404 1693 1.101331 GCTCTCCCTCAGCCAAAATG 58.899 55.000 0.00 0.00 0.00 2.32
1479 1768 6.013032 AGTTCTCCTTGATCTCCTTCATGAAA 60.013 38.462 9.88 0.00 0.00 2.69
1557 1846 1.806623 GCTATGTCGACGAGGCCAATT 60.807 52.381 11.62 0.00 0.00 2.32
1608 1897 4.436998 CCGGACACCTCCTCGCAC 62.437 72.222 0.00 0.00 33.79 5.34
1632 1921 4.329545 TCCTTGGCGGTGACCAGC 62.330 66.667 1.11 6.15 41.82 4.85
1936 2237 7.543756 TGTGACTGTGACTCAATTCGATATAA 58.456 34.615 0.00 0.00 0.00 0.98
1955 2256 2.447443 TGCGAGAGGAGTAATGTGACT 58.553 47.619 0.00 0.00 0.00 3.41
1991 2300 2.420628 AAACCATACGACGACAACGA 57.579 45.000 0.00 0.00 42.66 3.85
1992 2301 3.059834 CCTTAAACCATACGACGACAACG 59.940 47.826 0.00 0.00 45.75 4.10
1993 2302 4.236935 TCCTTAAACCATACGACGACAAC 58.763 43.478 0.00 0.00 0.00 3.32
1998 2307 2.601763 GTGCTCCTTAAACCATACGACG 59.398 50.000 0.00 0.00 0.00 5.12
2129 3518 8.932791 GCATATTGGCGTGTACTATAATACTTT 58.067 33.333 0.00 0.00 0.00 2.66
2171 3560 0.328258 GGACTTTAGGGCCTTGCTCA 59.672 55.000 13.45 0.00 40.87 4.26
2266 3655 8.611757 GCACCTAAAACATTTGTCAAGAAAAAT 58.388 29.630 0.00 0.00 0.00 1.82
2283 3672 4.278669 TCGTTAATTGCCAAGCACCTAAAA 59.721 37.500 0.00 0.00 38.71 1.52
2291 3680 5.004726 GTCATTTCATCGTTAATTGCCAAGC 59.995 40.000 0.00 0.00 0.00 4.01
2304 3699 6.528774 TGAATTCAGCAAATGTCATTTCATCG 59.471 34.615 7.87 0.00 0.00 3.84
2322 3717 3.906014 TCGTTTTTCGCCATGAATTCA 57.094 38.095 11.26 11.26 36.22 2.57
2416 3811 8.506168 TCAACAACATTTCTGTAGAAGTTTCT 57.494 30.769 0.00 0.00 41.24 2.52
2417 3812 9.567848 TTTCAACAACATTTCTGTAGAAGTTTC 57.432 29.630 0.00 0.00 33.36 2.78
2636 4050 8.754080 CATGCTTTATAACTAGATAGGTAGGCT 58.246 37.037 0.00 0.00 0.00 4.58
2647 4061 8.492673 TGAAAGTGTCCATGCTTTATAACTAG 57.507 34.615 0.00 0.00 35.35 2.57


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

AutoCloner maintained by Alex Coulton.