Multiple sequence alignment - TraesCS5D01G233100

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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 TraesCS5D01G233100 chr5D 100.000 3537 0 0 1 3537 340747134 340743598 0.000000e+00 6532.0
1 TraesCS5D01G233100 chr5B 91.401 2954 144 55 281 3186 399779886 399776995 0.000000e+00 3947.0
2 TraesCS5D01G233100 chr5B 86.029 272 18 5 3286 3537 399776885 399776614 1.250000e-69 274.0
3 TraesCS5D01G233100 chr5B 97.980 99 2 0 1161 1259 446421600 446421502 4.690000e-39 172.0
4 TraesCS5D01G233100 chr5B 96.078 102 4 0 1158 1259 447194770 447194871 2.180000e-37 167.0
5 TraesCS5D01G233100 chr5B 90.083 121 12 0 163 283 55460256 55460136 1.310000e-34 158.0
6 TraesCS5D01G233100 chr5A 94.339 2208 80 14 652 2816 441675275 441673070 0.000000e+00 3343.0
7 TraesCS5D01G233100 chr5A 86.019 515 26 23 3047 3537 441671973 441671481 8.760000e-141 510.0
8 TraesCS5D01G233100 chr5A 91.720 314 15 7 282 584 441675670 441675357 3.260000e-115 425.0
9 TraesCS5D01G233100 chr5A 100.000 38 0 0 2957 2994 441673027 441672990 1.760000e-08 71.3
10 TraesCS5D01G233100 chr5A 93.023 43 3 0 1785 1827 364148068 364148026 2.950000e-06 63.9
11 TraesCS5D01G233100 chr1D 82.961 358 52 1 1916 2273 480010405 480010753 7.370000e-82 315.0
12 TraesCS5D01G233100 chr1D 89.837 246 13 2 1713 1956 422597236 422597471 4.440000e-79 305.0
13 TraesCS5D01G233100 chr2D 96.129 155 6 0 1143 1297 624648667 624648821 1.630000e-63 254.0
14 TraesCS5D01G233100 chr2D 85.020 247 13 5 1682 1925 624648925 624649150 2.750000e-56 230.0
15 TraesCS5D01G233100 chr2D 97.727 44 1 0 1622 1665 624648884 624648927 3.790000e-10 76.8
16 TraesCS5D01G233100 chr6D 94.872 117 4 1 1143 1259 409578590 409578704 7.800000e-42 182.0
17 TraesCS5D01G233100 chr7A 90.370 135 11 2 1177 1310 491964328 491964461 3.630000e-40 176.0
18 TraesCS5D01G233100 chr7D 95.370 108 5 0 1152 1259 609272691 609272584 4.690000e-39 172.0
19 TraesCS5D01G233100 chr6B 97.059 102 3 0 1158 1259 142988850 142988749 4.690000e-39 172.0
20 TraesCS5D01G233100 chr6B 90.244 123 11 1 160 282 363665580 363665459 3.650000e-35 159.0
21 TraesCS5D01G233100 chr6B 91.304 115 10 0 168 282 692579569 692579455 1.310000e-34 158.0
22 TraesCS5D01G233100 chr4B 91.525 118 10 0 168 285 564374052 564373935 2.830000e-36 163.0
23 TraesCS5D01G233100 chr4B 91.304 115 10 0 168 282 467274988 467274874 1.310000e-34 158.0
24 TraesCS5D01G233100 chr3B 88.976 127 14 0 156 282 747704598 747704472 1.310000e-34 158.0
25 TraesCS5D01G233100 chr3B 88.710 124 13 1 159 282 816002762 816002640 2.200000e-32 150.0
26 TraesCS5D01G233100 chr1B 91.304 115 10 0 168 282 49729208 49729094 1.310000e-34 158.0
27 TraesCS5D01G233100 chr1B 88.800 125 14 0 158 282 583854089 583853965 1.700000e-33 154.0
28 TraesCS5D01G233100 chr4A 92.982 57 3 1 1370 1425 684087567 684087623 8.140000e-12 82.4


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 TraesCS5D01G233100 chr5D 340743598 340747134 3536 True 6532.000 6532 100.0000 1 3537 1 chr5D.!!$R1 3536
1 TraesCS5D01G233100 chr5B 399776614 399779886 3272 True 2110.500 3947 88.7150 281 3537 2 chr5B.!!$R3 3256
2 TraesCS5D01G233100 chr5A 441671481 441675670 4189 True 1087.325 3343 93.0195 282 3537 4 chr5A.!!$R2 3255

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
503 508 0.108615 ACGCCTCATCACTCTTTCCG 60.109 55.0 0.00 0.00 0.0 4.30 F
1536 1613 0.249699 TCGGCAATGACACGTGAGTT 60.250 50.0 25.01 10.61 46.4 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 2606 1.751143 TTGGAGGTGGAGGAGGAGGT 61.751 60.0 0.00 0.0 0.00 3.85 R
3005 3835 0.035458 CGACCAAAGTGGAGAAGGCT 59.965 55.0 0.18 0.0 40.96 4.58 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
39 40 9.541143 ACAAAGTGGAAATTAAGTTAATTGTGG 57.459 29.630 19.15 7.96 38.32 4.17
40 41 9.541143 CAAAGTGGAAATTAAGTTAATTGTGGT 57.459 29.630 19.15 5.92 38.32 4.16
43 44 9.802039 AGTGGAAATTAAGTTAATTGTGGTAGA 57.198 29.630 19.15 0.73 38.32 2.59
44 45 9.836076 GTGGAAATTAAGTTAATTGTGGTAGAC 57.164 33.333 19.15 7.86 38.32 2.59
45 46 8.723311 TGGAAATTAAGTTAATTGTGGTAGACG 58.277 33.333 19.15 0.00 38.32 4.18
46 47 7.695201 GGAAATTAAGTTAATTGTGGTAGACGC 59.305 37.037 19.15 2.72 38.32 5.19
47 48 7.916914 AATTAAGTTAATTGTGGTAGACGCT 57.083 32.000 18.02 0.00 37.03 5.07
48 49 6.715344 TTAAGTTAATTGTGGTAGACGCTG 57.285 37.500 0.00 0.00 0.00 5.18
49 50 3.000727 AGTTAATTGTGGTAGACGCTGC 58.999 45.455 0.00 0.00 0.00 5.25
50 51 2.739913 GTTAATTGTGGTAGACGCTGCA 59.260 45.455 0.00 0.00 0.00 4.41
51 52 1.156736 AATTGTGGTAGACGCTGCAC 58.843 50.000 0.00 0.00 0.00 4.57
52 53 0.673644 ATTGTGGTAGACGCTGCACC 60.674 55.000 0.00 0.00 0.00 5.01
53 54 2.809601 GTGGTAGACGCTGCACCG 60.810 66.667 0.00 0.00 34.94 4.94
54 55 4.735132 TGGTAGACGCTGCACCGC 62.735 66.667 0.25 0.00 34.94 5.68
55 56 4.436998 GGTAGACGCTGCACCGCT 62.437 66.667 0.25 2.72 0.00 5.52
56 57 3.181967 GTAGACGCTGCACCGCTG 61.182 66.667 0.25 0.00 0.00 5.18
65 66 2.745884 GCACCGCTGCACATGGTA 60.746 61.111 0.00 0.00 43.62 3.25
66 67 2.114670 GCACCGCTGCACATGGTAT 61.115 57.895 0.00 0.00 43.62 2.73
67 68 0.813610 GCACCGCTGCACATGGTATA 60.814 55.000 0.00 0.00 43.62 1.47
68 69 1.882912 CACCGCTGCACATGGTATAT 58.117 50.000 0.00 0.00 33.82 0.86
69 70 2.870035 GCACCGCTGCACATGGTATATA 60.870 50.000 0.00 0.00 43.62 0.86
70 71 2.736721 CACCGCTGCACATGGTATATAC 59.263 50.000 4.14 4.14 33.82 1.47
71 72 2.632996 ACCGCTGCACATGGTATATACT 59.367 45.455 12.54 0.00 33.25 2.12
72 73 3.254060 CCGCTGCACATGGTATATACTC 58.746 50.000 12.54 3.99 0.00 2.59
73 74 3.306019 CCGCTGCACATGGTATATACTCA 60.306 47.826 12.54 9.20 0.00 3.41
74 75 3.675225 CGCTGCACATGGTATATACTCAC 59.325 47.826 12.54 0.00 0.00 3.51
75 76 3.997021 GCTGCACATGGTATATACTCACC 59.003 47.826 12.54 0.00 35.24 4.02
84 85 5.063204 TGGTATATACTCACCAGCAAATGC 58.937 41.667 12.54 0.00 39.91 3.56
85 86 6.253670 TGGTATATACTCACCAGCAAATGCG 61.254 44.000 12.54 0.00 39.91 4.73
86 87 8.583450 TGGTATATACTCACCAGCAAATGCGT 62.583 42.308 12.54 0.00 39.91 5.24
99 100 5.852738 GCAAATGCGTCTGATAGATGTAT 57.147 39.130 0.00 0.00 38.03 2.29
100 101 6.951256 GCAAATGCGTCTGATAGATGTATA 57.049 37.500 2.75 0.00 35.88 1.47
101 102 7.351414 GCAAATGCGTCTGATAGATGTATAA 57.649 36.000 2.75 0.00 35.88 0.98
102 103 7.796838 GCAAATGCGTCTGATAGATGTATAAA 58.203 34.615 2.75 0.00 35.88 1.40
103 104 8.446273 GCAAATGCGTCTGATAGATGTATAAAT 58.554 33.333 2.75 0.00 35.88 1.40
104 105 9.964253 CAAATGCGTCTGATAGATGTATAAATC 57.036 33.333 0.00 0.00 35.88 2.17
105 106 9.710900 AAATGCGTCTGATAGATGTATAAATCA 57.289 29.630 5.68 0.00 35.88 2.57
106 107 9.881649 AATGCGTCTGATAGATGTATAAATCAT 57.118 29.630 5.68 0.00 35.88 2.45
107 108 8.693542 TGCGTCTGATAGATGTATAAATCATG 57.306 34.615 5.68 0.00 33.82 3.07
108 109 7.276438 TGCGTCTGATAGATGTATAAATCATGC 59.724 37.037 5.68 1.65 33.82 4.06
109 110 7.514280 GCGTCTGATAGATGTATAAATCATGCG 60.514 40.741 5.68 1.95 33.82 4.73
110 111 7.486232 CGTCTGATAGATGTATAAATCATGCGT 59.514 37.037 5.68 0.00 0.00 5.24
111 112 8.590470 GTCTGATAGATGTATAAATCATGCGTG 58.410 37.037 5.68 0.00 0.00 5.34
112 113 8.522830 TCTGATAGATGTATAAATCATGCGTGA 58.477 33.333 11.83 11.83 39.04 4.35
113 114 9.310716 CTGATAGATGTATAAATCATGCGTGAT 57.689 33.333 15.87 15.87 46.91 3.06
117 118 8.694975 AGATGTATAAATCATGCGTGATAGAC 57.305 34.615 21.49 14.31 44.20 2.59
144 145 7.981102 AGTATTGATCATACTACGTGCTAGA 57.019 36.000 13.07 0.00 45.56 2.43
145 146 8.392372 AGTATTGATCATACTACGTGCTAGAA 57.608 34.615 13.07 0.00 45.56 2.10
146 147 9.015367 AGTATTGATCATACTACGTGCTAGAAT 57.985 33.333 13.07 0.00 45.56 2.40
147 148 9.627395 GTATTGATCATACTACGTGCTAGAATT 57.373 33.333 0.00 0.00 35.66 2.17
148 149 7.930513 TTGATCATACTACGTGCTAGAATTG 57.069 36.000 0.00 0.00 0.00 2.32
149 150 5.920840 TGATCATACTACGTGCTAGAATTGC 59.079 40.000 0.00 0.00 0.00 3.56
150 151 5.257082 TCATACTACGTGCTAGAATTGCA 57.743 39.130 0.00 0.00 38.19 4.08
151 152 5.656480 TCATACTACGTGCTAGAATTGCAA 58.344 37.500 0.00 0.00 42.41 4.08
152 153 6.280643 TCATACTACGTGCTAGAATTGCAAT 58.719 36.000 5.99 5.99 42.41 3.56
153 154 4.864916 ACTACGTGCTAGAATTGCAATG 57.135 40.909 13.82 1.00 42.41 2.82
154 155 2.549633 ACGTGCTAGAATTGCAATGC 57.450 45.000 13.82 11.67 42.41 3.56
155 156 2.086869 ACGTGCTAGAATTGCAATGCT 58.913 42.857 23.48 23.48 42.41 3.79
156 157 2.096496 ACGTGCTAGAATTGCAATGCTC 59.904 45.455 23.65 15.60 42.41 4.26
157 158 2.096335 CGTGCTAGAATTGCAATGCTCA 59.904 45.455 23.65 13.51 42.41 4.26
158 159 3.242969 CGTGCTAGAATTGCAATGCTCAT 60.243 43.478 23.65 1.07 42.41 2.90
159 160 4.024641 CGTGCTAGAATTGCAATGCTCATA 60.025 41.667 23.65 5.69 42.41 2.15
160 161 5.210715 GTGCTAGAATTGCAATGCTCATAC 58.789 41.667 23.65 15.71 42.41 2.39
161 162 4.883006 TGCTAGAATTGCAATGCTCATACA 59.117 37.500 23.65 14.02 37.51 2.29
162 163 5.533528 TGCTAGAATTGCAATGCTCATACAT 59.466 36.000 23.65 0.57 37.51 2.29
163 164 6.711645 TGCTAGAATTGCAATGCTCATACATA 59.288 34.615 23.65 3.42 37.51 2.29
164 165 7.392393 TGCTAGAATTGCAATGCTCATACATAT 59.608 33.333 23.65 0.00 37.51 1.78
165 166 8.242053 GCTAGAATTGCAATGCTCATACATATT 58.758 33.333 23.65 0.00 0.00 1.28
166 167 9.770503 CTAGAATTGCAATGCTCATACATATTC 57.229 33.333 23.65 7.76 0.00 1.75
167 168 7.600065 AGAATTGCAATGCTCATACATATTCC 58.400 34.615 14.67 0.00 0.00 3.01
168 169 7.450634 AGAATTGCAATGCTCATACATATTCCT 59.549 33.333 14.67 0.00 0.00 3.36
169 170 6.564709 TTGCAATGCTCATACATATTCCTC 57.435 37.500 6.82 0.00 0.00 3.71
170 171 5.872963 TGCAATGCTCATACATATTCCTCT 58.127 37.500 6.82 0.00 0.00 3.69
171 172 5.936372 TGCAATGCTCATACATATTCCTCTC 59.064 40.000 6.82 0.00 0.00 3.20
172 173 6.171921 GCAATGCTCATACATATTCCTCTCT 58.828 40.000 0.00 0.00 0.00 3.10
173 174 6.313411 GCAATGCTCATACATATTCCTCTCTC 59.687 42.308 0.00 0.00 0.00 3.20
174 175 5.991933 TGCTCATACATATTCCTCTCTCC 57.008 43.478 0.00 0.00 0.00 3.71
175 176 4.460731 TGCTCATACATATTCCTCTCTCCG 59.539 45.833 0.00 0.00 0.00 4.63
176 177 4.461081 GCTCATACATATTCCTCTCTCCGT 59.539 45.833 0.00 0.00 0.00 4.69
177 178 5.392595 GCTCATACATATTCCTCTCTCCGTC 60.393 48.000 0.00 0.00 0.00 4.79
178 179 5.882040 TCATACATATTCCTCTCTCCGTCT 58.118 41.667 0.00 0.00 0.00 4.18
179 180 5.707764 TCATACATATTCCTCTCTCCGTCTG 59.292 44.000 0.00 0.00 0.00 3.51
180 181 3.226777 ACATATTCCTCTCTCCGTCTGG 58.773 50.000 0.00 0.00 0.00 3.86
181 182 3.117474 ACATATTCCTCTCTCCGTCTGGA 60.117 47.826 0.00 0.00 43.88 3.86
182 183 2.534042 ATTCCTCTCTCCGTCTGGAA 57.466 50.000 0.00 0.00 45.87 3.53
183 184 2.304221 TTCCTCTCTCCGTCTGGAAA 57.696 50.000 0.00 0.00 45.87 3.13
184 185 2.534042 TCCTCTCTCCGTCTGGAAAT 57.466 50.000 0.00 0.00 45.87 2.17
185 186 3.664551 TCCTCTCTCCGTCTGGAAATA 57.335 47.619 0.00 0.00 45.87 1.40
186 187 3.288964 TCCTCTCTCCGTCTGGAAATAC 58.711 50.000 0.00 0.00 45.87 1.89
187 188 3.053544 TCCTCTCTCCGTCTGGAAATACT 60.054 47.826 0.00 0.00 45.87 2.12
188 189 3.702045 CCTCTCTCCGTCTGGAAATACTT 59.298 47.826 0.00 0.00 45.87 2.24
189 190 4.440802 CCTCTCTCCGTCTGGAAATACTTG 60.441 50.000 0.00 0.00 45.87 3.16
190 191 4.087182 TCTCTCCGTCTGGAAATACTTGT 58.913 43.478 0.00 0.00 45.87 3.16
191 192 4.158025 TCTCTCCGTCTGGAAATACTTGTC 59.842 45.833 0.00 0.00 45.87 3.18
192 193 3.119602 TCTCCGTCTGGAAATACTTGTCG 60.120 47.826 0.00 0.00 45.87 4.35
193 194 1.659098 CCGTCTGGAAATACTTGTCGC 59.341 52.381 0.00 0.00 37.49 5.19
194 195 2.333926 CGTCTGGAAATACTTGTCGCA 58.666 47.619 0.00 0.00 0.00 5.10
195 196 2.345641 CGTCTGGAAATACTTGTCGCAG 59.654 50.000 0.00 0.00 0.00 5.18
196 197 3.585862 GTCTGGAAATACTTGTCGCAGA 58.414 45.455 0.00 0.00 0.00 4.26
197 198 3.994392 GTCTGGAAATACTTGTCGCAGAA 59.006 43.478 0.00 0.00 39.69 3.02
198 199 4.451096 GTCTGGAAATACTTGTCGCAGAAA 59.549 41.667 0.00 0.00 39.69 2.52
199 200 5.122396 GTCTGGAAATACTTGTCGCAGAAAT 59.878 40.000 0.00 0.00 39.69 2.17
200 201 5.122239 TCTGGAAATACTTGTCGCAGAAATG 59.878 40.000 0.00 0.00 39.69 2.32
201 202 4.759693 TGGAAATACTTGTCGCAGAAATGT 59.240 37.500 0.00 0.00 39.69 2.71
202 203 5.935206 TGGAAATACTTGTCGCAGAAATGTA 59.065 36.000 0.00 0.00 38.48 2.29
203 204 6.597672 TGGAAATACTTGTCGCAGAAATGTAT 59.402 34.615 0.00 0.00 43.96 2.29
204 205 7.766738 TGGAAATACTTGTCGCAGAAATGTATA 59.233 33.333 7.30 0.00 42.11 1.47
205 206 8.609176 GGAAATACTTGTCGCAGAAATGTATAA 58.391 33.333 7.30 0.00 42.11 0.98
206 207 9.982291 GAAATACTTGTCGCAGAAATGTATAAA 57.018 29.630 7.30 0.00 42.11 1.40
210 211 8.673626 ACTTGTCGCAGAAATGTATAAAAATG 57.326 30.769 0.00 0.00 39.69 2.32
211 212 7.754924 ACTTGTCGCAGAAATGTATAAAAATGG 59.245 33.333 0.00 0.00 39.69 3.16
212 213 7.384439 TGTCGCAGAAATGTATAAAAATGGA 57.616 32.000 0.00 0.00 39.69 3.41
213 214 7.995289 TGTCGCAGAAATGTATAAAAATGGAT 58.005 30.769 0.00 0.00 39.69 3.41
214 215 7.914871 TGTCGCAGAAATGTATAAAAATGGATG 59.085 33.333 0.00 0.00 39.69 3.51
215 216 7.915397 GTCGCAGAAATGTATAAAAATGGATGT 59.085 33.333 0.00 0.00 39.69 3.06
216 217 9.114952 TCGCAGAAATGTATAAAAATGGATGTA 57.885 29.630 0.00 0.00 0.00 2.29
217 218 9.897744 CGCAGAAATGTATAAAAATGGATGTAT 57.102 29.630 0.00 0.00 0.00 2.29
254 255 5.966742 TGTCTAGATACATCCATTCCTCG 57.033 43.478 0.00 0.00 0.00 4.63
255 256 4.767409 TGTCTAGATACATCCATTCCTCGG 59.233 45.833 0.00 0.00 0.00 4.63
256 257 5.010933 GTCTAGATACATCCATTCCTCGGA 58.989 45.833 0.00 0.00 36.84 4.55
257 258 5.010933 TCTAGATACATCCATTCCTCGGAC 58.989 45.833 0.00 0.00 34.69 4.79
258 259 3.576861 AGATACATCCATTCCTCGGACA 58.423 45.455 0.00 0.00 34.69 4.02
259 260 3.967326 AGATACATCCATTCCTCGGACAA 59.033 43.478 0.00 0.00 34.69 3.18
260 261 2.698855 ACATCCATTCCTCGGACAAG 57.301 50.000 0.00 0.00 34.69 3.16
261 262 1.909302 ACATCCATTCCTCGGACAAGT 59.091 47.619 0.00 0.00 34.69 3.16
262 263 3.104512 ACATCCATTCCTCGGACAAGTA 58.895 45.455 0.00 0.00 34.69 2.24
263 264 3.711704 ACATCCATTCCTCGGACAAGTAT 59.288 43.478 0.00 0.00 34.69 2.12
264 265 4.164221 ACATCCATTCCTCGGACAAGTATT 59.836 41.667 0.00 0.00 34.69 1.89
265 266 4.837093 TCCATTCCTCGGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
266 267 5.174037 TCCATTCCTCGGACAAGTATTTT 57.826 39.130 0.00 0.00 0.00 1.82
267 268 4.941263 TCCATTCCTCGGACAAGTATTTTG 59.059 41.667 0.00 0.00 0.00 2.44
268 269 4.096382 CCATTCCTCGGACAAGTATTTTGG 59.904 45.833 0.00 0.00 0.00 3.28
269 270 3.343941 TCCTCGGACAAGTATTTTGGG 57.656 47.619 0.00 0.00 0.00 4.12
270 271 2.907696 TCCTCGGACAAGTATTTTGGGA 59.092 45.455 0.00 0.00 0.00 4.37
271 272 3.007635 CCTCGGACAAGTATTTTGGGAC 58.992 50.000 0.00 0.00 0.00 4.46
272 273 3.007635 CTCGGACAAGTATTTTGGGACC 58.992 50.000 0.00 0.00 0.00 4.46
273 274 1.735571 CGGACAAGTATTTTGGGACCG 59.264 52.381 0.00 0.00 0.00 4.79
274 275 2.613474 CGGACAAGTATTTTGGGACCGA 60.613 50.000 0.00 0.00 37.12 4.69
275 276 3.007635 GGACAAGTATTTTGGGACCGAG 58.992 50.000 0.00 0.00 0.00 4.63
276 277 3.307199 GGACAAGTATTTTGGGACCGAGA 60.307 47.826 0.00 0.00 0.00 4.04
277 278 3.933332 GACAAGTATTTTGGGACCGAGAG 59.067 47.826 0.00 0.00 0.00 3.20
278 279 3.581332 ACAAGTATTTTGGGACCGAGAGA 59.419 43.478 0.00 0.00 0.00 3.10
279 280 4.184629 CAAGTATTTTGGGACCGAGAGAG 58.815 47.826 0.00 0.00 0.00 3.20
359 360 0.687757 AGAGCCAATCAGCGGGAGTA 60.688 55.000 0.00 0.00 38.01 2.59
386 387 5.692928 TGGTAGTAGGAGTATCTTGGACTC 58.307 45.833 0.00 0.00 42.24 3.36
499 504 4.017808 AGTAACTACGCCTCATCACTCTT 58.982 43.478 0.00 0.00 0.00 2.85
500 505 3.963428 AACTACGCCTCATCACTCTTT 57.037 42.857 0.00 0.00 0.00 2.52
501 506 3.512033 ACTACGCCTCATCACTCTTTC 57.488 47.619 0.00 0.00 0.00 2.62
503 508 0.108615 ACGCCTCATCACTCTTTCCG 60.109 55.000 0.00 0.00 0.00 4.30
506 511 1.945819 GCCTCATCACTCTTTCCGCAA 60.946 52.381 0.00 0.00 0.00 4.85
514 524 2.028930 CACTCTTTCCGCAACTACTCCT 60.029 50.000 0.00 0.00 0.00 3.69
550 560 3.495100 GCCACGATAGATCCCAGATTTGT 60.495 47.826 0.00 0.00 41.38 2.83
556 566 5.279206 CGATAGATCCCAGATTTGTACTGCT 60.279 44.000 0.00 0.00 39.76 4.24
560 570 0.729116 CCAGATTTGTACTGCTGCCG 59.271 55.000 0.00 0.00 34.47 5.69
561 571 1.675714 CCAGATTTGTACTGCTGCCGA 60.676 52.381 0.00 0.00 34.47 5.54
586 602 7.229581 ACTTTCGGAGTAACAGAGATAAACT 57.770 36.000 0.00 0.00 36.65 2.66
612 657 1.228521 CCACCATCCTGCACACCAA 60.229 57.895 0.00 0.00 0.00 3.67
633 678 7.756722 CACCAAGCCTGATCAAATACTTTTAAG 59.243 37.037 0.00 0.00 0.00 1.85
634 679 7.451566 ACCAAGCCTGATCAAATACTTTTAAGT 59.548 33.333 0.00 0.29 42.91 2.24
635 680 8.306761 CCAAGCCTGATCAAATACTTTTAAGTT 58.693 33.333 0.00 0.00 40.37 2.66
636 681 9.696917 CAAGCCTGATCAAATACTTTTAAGTTT 57.303 29.630 0.00 0.00 40.37 2.66
720 766 3.866582 CACCTCCTCGATGGCCCC 61.867 72.222 0.00 0.00 35.26 5.80
747 793 5.146010 TGCAAAATCCAACTGTAAATCCC 57.854 39.130 0.00 0.00 0.00 3.85
775 825 3.019933 TGGCGTCCAGTTTTTAATTGC 57.980 42.857 0.00 0.00 0.00 3.56
824 877 4.135153 CCGCCCTGTCAGTCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
944 1001 2.359975 CCTTCGCCAAGTGTCCCC 60.360 66.667 0.00 0.00 0.00 4.81
1095 1160 1.163554 GGAAGCTTCTTGAGGTGCTG 58.836 55.000 25.05 0.00 35.94 4.41
1536 1613 0.249699 TCGGCAATGACACGTGAGTT 60.250 50.000 25.01 10.61 46.40 3.01
1605 1691 0.742281 GCTCGGCTTCTGATTCTGCA 60.742 55.000 0.00 0.00 0.00 4.41
1874 1961 1.880340 CTCAACCTCTCCATCGCGC 60.880 63.158 0.00 0.00 0.00 6.86
2349 2451 2.445654 CCAGGAGGAGGAGGAGGC 60.446 72.222 0.00 0.00 36.89 4.70
2676 2792 5.240891 CCACTGTCATGTCAATGTTCTACT 58.759 41.667 1.03 0.00 35.15 2.57
2692 2808 5.179368 TGTTCTACTGTAGCATTTTGTCTGC 59.821 40.000 9.98 0.00 39.97 4.26
2804 2921 0.626382 TGACAGGACCCACCAAAACA 59.374 50.000 0.00 0.00 42.04 2.83
2809 2926 3.118445 ACAGGACCCACCAAAACAAAATG 60.118 43.478 0.00 0.00 42.04 2.32
2811 2928 4.100189 CAGGACCCACCAAAACAAAATGTA 59.900 41.667 0.00 0.00 42.04 2.29
2816 2933 6.110033 ACCCACCAAAACAAAATGTAGTTTC 58.890 36.000 0.00 0.00 36.98 2.78
2819 2936 6.238076 CCACCAAAACAAAATGTAGTTTCTGC 60.238 38.462 0.00 0.00 36.98 4.26
2828 2945 9.630098 ACAAAATGTAGTTTCTGCATTAATCTG 57.370 29.630 11.94 9.97 43.76 2.90
2834 2951 9.317936 TGTAGTTTCTGCATTAATCTGATAGTG 57.682 33.333 0.00 0.00 0.00 2.74
2836 2953 7.341805 AGTTTCTGCATTAATCTGATAGTGGT 58.658 34.615 0.00 0.00 0.00 4.16
2837 2954 7.497249 AGTTTCTGCATTAATCTGATAGTGGTC 59.503 37.037 0.00 0.00 0.00 4.02
2838 2955 5.532557 TCTGCATTAATCTGATAGTGGTCG 58.467 41.667 0.00 0.00 0.00 4.79
2839 2956 5.069119 TCTGCATTAATCTGATAGTGGTCGT 59.931 40.000 0.00 0.00 0.00 4.34
2844 2961 7.096023 GCATTAATCTGATAGTGGTCGTACAAG 60.096 40.741 0.00 0.00 0.00 3.16
2854 2971 4.038883 AGTGGTCGTACAAGTTAAGAGCTT 59.961 41.667 0.00 0.00 0.00 3.74
2857 2974 5.474532 TGGTCGTACAAGTTAAGAGCTTCTA 59.525 40.000 0.00 0.00 0.00 2.10
2861 2978 7.904461 GTCGTACAAGTTAAGAGCTTCTAGTAG 59.096 40.741 0.00 0.00 0.00 2.57
2862 2979 7.605691 TCGTACAAGTTAAGAGCTTCTAGTAGT 59.394 37.037 0.00 0.00 0.00 2.73
2863 2980 8.877779 CGTACAAGTTAAGAGCTTCTAGTAGTA 58.122 37.037 0.00 0.00 0.00 1.82
2865 2982 8.866970 ACAAGTTAAGAGCTTCTAGTAGTAGT 57.133 34.615 4.51 0.00 0.00 2.73
2866 2983 8.732531 ACAAGTTAAGAGCTTCTAGTAGTAGTG 58.267 37.037 4.51 1.21 0.00 2.74
2867 2984 8.732531 CAAGTTAAGAGCTTCTAGTAGTAGTGT 58.267 37.037 4.51 0.00 0.00 3.55
2891 3008 0.525311 CCACACAACACAGCACACAA 59.475 50.000 0.00 0.00 0.00 3.33
2893 3010 1.199789 CACACAACACAGCACACAAGT 59.800 47.619 0.00 0.00 0.00 3.16
2903 3020 3.153364 CACACAAGTGCAAAGCTCG 57.847 52.632 0.00 0.00 39.21 5.03
2904 3021 0.657312 CACACAAGTGCAAAGCTCGA 59.343 50.000 0.00 0.00 39.21 4.04
2905 3022 1.265095 CACACAAGTGCAAAGCTCGAT 59.735 47.619 0.00 0.00 39.21 3.59
2906 3023 1.532868 ACACAAGTGCAAAGCTCGATC 59.467 47.619 0.00 0.00 0.00 3.69
2907 3024 0.792640 ACAAGTGCAAAGCTCGATCG 59.207 50.000 9.36 9.36 0.00 3.69
2909 3027 0.320771 AAGTGCAAAGCTCGATCGGT 60.321 50.000 16.41 0.00 0.00 4.69
2923 3041 8.209917 AGCTCGATCGGTTTTAATAAAGAAAT 57.790 30.769 16.41 0.00 0.00 2.17
2944 3063 2.093500 TCGAGTGTCATCCATTTCCCAG 60.093 50.000 0.00 0.00 0.00 4.45
2947 3066 3.424703 AGTGTCATCCATTTCCCAGTTG 58.575 45.455 0.00 0.00 0.00 3.16
3004 3834 1.051812 AGCAGGGTCAATCCTATCCG 58.948 55.000 0.00 0.00 34.92 4.18
3005 3835 1.048601 GCAGGGTCAATCCTATCCGA 58.951 55.000 0.00 0.00 34.92 4.55
3006 3836 1.001406 GCAGGGTCAATCCTATCCGAG 59.999 57.143 0.00 0.00 34.92 4.63
3009 3839 1.343069 GGTCAATCCTATCCGAGCCT 58.657 55.000 0.00 0.00 0.00 4.58
3015 3845 0.556258 TCCTATCCGAGCCTTCTCCA 59.444 55.000 0.00 0.00 35.94 3.86
3026 3856 0.955919 CCTTCTCCACTTTGGTCGGC 60.956 60.000 0.00 0.00 39.03 5.54
3035 3865 4.595538 TTGGTCGGCGTCGTGCTT 62.596 61.111 10.18 0.00 45.43 3.91
3067 4150 3.113745 CCATGGCCATCGTTGCTC 58.886 61.111 17.61 0.00 0.00 4.26
3175 4258 0.595053 AGGACATCATAACGCTCGCG 60.595 55.000 10.06 10.06 46.03 5.87
3190 4273 2.726691 CGCGTTTGGACTACCGCTG 61.727 63.158 0.00 0.00 43.70 5.18
3191 4274 2.388232 GCGTTTGGACTACCGCTGG 61.388 63.158 0.00 0.00 42.66 4.85
3192 4275 1.005394 CGTTTGGACTACCGCTGGT 60.005 57.895 5.58 5.58 40.16 4.00
3193 4276 0.244450 CGTTTGGACTACCGCTGGTA 59.756 55.000 7.15 7.15 37.09 3.25
3194 4277 1.718396 GTTTGGACTACCGCTGGTAC 58.282 55.000 3.72 0.00 37.09 3.34
3195 4278 1.274447 GTTTGGACTACCGCTGGTACT 59.726 52.381 3.72 0.00 37.09 2.73
3196 4279 0.892755 TTGGACTACCGCTGGTACTG 59.107 55.000 3.72 0.00 37.09 2.74
3197 4280 0.968901 TGGACTACCGCTGGTACTGG 60.969 60.000 3.72 0.00 37.09 4.00
3198 4281 0.682209 GGACTACCGCTGGTACTGGA 60.682 60.000 3.72 0.00 37.09 3.86
3199 4282 0.739561 GACTACCGCTGGTACTGGAG 59.260 60.000 3.72 0.00 37.09 3.86
3200 4283 0.039326 ACTACCGCTGGTACTGGAGT 59.961 55.000 3.72 0.18 37.09 3.85
3201 4284 1.283029 ACTACCGCTGGTACTGGAGTA 59.717 52.381 3.72 0.00 37.09 2.59
3227 4310 4.756084 ACTGGTACTCGTACAACACTAC 57.244 45.455 9.22 0.00 37.78 2.73
3243 4326 4.011023 ACACTACACTAGCAGTAGGAGTG 58.989 47.826 20.70 16.41 44.98 3.51
3286 4388 3.118482 ACATCTTCTGCCCATCTACTGTG 60.118 47.826 0.00 0.00 0.00 3.66
3330 4454 8.064814 GCAGATTAAAATAAACCGATCTCTGAC 58.935 37.037 0.00 0.00 30.49 3.51
3385 4520 1.252904 GCATGACAGTGGGCAATGGT 61.253 55.000 0.00 0.00 0.00 3.55
3477 4623 2.898738 CTCTGCCATGACGGAGCT 59.101 61.111 4.80 0.00 36.31 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.541143 CCACAATTAACTTAATTTCCACTTTGT 57.459 29.630 4.30 0.00 36.29 2.83
14 15 9.541143 ACCACAATTAACTTAATTTCCACTTTG 57.459 29.630 4.30 0.00 36.29 2.77
17 18 9.802039 TCTACCACAATTAACTTAATTTCCACT 57.198 29.630 4.30 0.00 36.29 4.00
18 19 9.836076 GTCTACCACAATTAACTTAATTTCCAC 57.164 33.333 4.30 0.00 36.29 4.02
19 20 8.723311 CGTCTACCACAATTAACTTAATTTCCA 58.277 33.333 4.30 0.00 36.29 3.53
20 21 7.695201 GCGTCTACCACAATTAACTTAATTTCC 59.305 37.037 4.30 0.00 36.29 3.13
21 22 8.448615 AGCGTCTACCACAATTAACTTAATTTC 58.551 33.333 4.30 0.00 36.29 2.17
22 23 8.234546 CAGCGTCTACCACAATTAACTTAATTT 58.765 33.333 4.30 0.00 36.29 1.82
23 24 7.625606 GCAGCGTCTACCACAATTAACTTAATT 60.626 37.037 1.48 1.48 38.84 1.40
24 25 6.183360 GCAGCGTCTACCACAATTAACTTAAT 60.183 38.462 0.00 0.00 0.00 1.40
25 26 5.121142 GCAGCGTCTACCACAATTAACTTAA 59.879 40.000 0.00 0.00 0.00 1.85
26 27 4.628333 GCAGCGTCTACCACAATTAACTTA 59.372 41.667 0.00 0.00 0.00 2.24
27 28 3.435671 GCAGCGTCTACCACAATTAACTT 59.564 43.478 0.00 0.00 0.00 2.66
28 29 3.000727 GCAGCGTCTACCACAATTAACT 58.999 45.455 0.00 0.00 0.00 2.24
29 30 2.739913 TGCAGCGTCTACCACAATTAAC 59.260 45.455 0.00 0.00 0.00 2.01
30 31 2.739913 GTGCAGCGTCTACCACAATTAA 59.260 45.455 0.00 0.00 0.00 1.40
31 32 2.343101 GTGCAGCGTCTACCACAATTA 58.657 47.619 0.00 0.00 0.00 1.40
32 33 1.156736 GTGCAGCGTCTACCACAATT 58.843 50.000 0.00 0.00 0.00 2.32
33 34 0.673644 GGTGCAGCGTCTACCACAAT 60.674 55.000 0.00 0.00 34.61 2.71
34 35 1.301401 GGTGCAGCGTCTACCACAA 60.301 57.895 0.00 0.00 34.61 3.33
35 36 2.342279 GGTGCAGCGTCTACCACA 59.658 61.111 0.00 0.00 34.61 4.17
36 37 2.809601 CGGTGCAGCGTCTACCAC 60.810 66.667 29.05 0.00 34.10 4.16
37 38 4.735132 GCGGTGCAGCGTCTACCA 62.735 66.667 35.36 0.00 34.10 3.25
38 39 4.436998 AGCGGTGCAGCGTCTACC 62.437 66.667 35.36 20.48 43.00 3.18
39 40 3.181967 CAGCGGTGCAGCGTCTAC 61.182 66.667 35.36 20.84 43.00 2.59
49 50 1.882912 ATATACCATGTGCAGCGGTG 58.117 50.000 10.98 10.98 34.12 4.94
50 51 2.632996 AGTATATACCATGTGCAGCGGT 59.367 45.455 9.32 6.82 36.79 5.68
51 52 3.254060 GAGTATATACCATGTGCAGCGG 58.746 50.000 9.32 0.00 0.00 5.52
52 53 3.675225 GTGAGTATATACCATGTGCAGCG 59.325 47.826 9.32 0.00 0.00 5.18
53 54 3.997021 GGTGAGTATATACCATGTGCAGC 59.003 47.826 9.32 5.01 36.94 5.25
54 55 5.213891 TGGTGAGTATATACCATGTGCAG 57.786 43.478 9.32 0.00 41.80 4.41
55 56 4.503123 GCTGGTGAGTATATACCATGTGCA 60.503 45.833 9.32 0.00 45.28 4.57
56 57 3.997021 GCTGGTGAGTATATACCATGTGC 59.003 47.826 9.32 4.35 45.28 4.57
57 58 5.213891 TGCTGGTGAGTATATACCATGTG 57.786 43.478 9.32 0.00 45.28 3.21
58 59 5.887214 TTGCTGGTGAGTATATACCATGT 57.113 39.130 9.32 0.00 45.28 3.21
59 60 6.348786 GCATTTGCTGGTGAGTATATACCATG 60.349 42.308 9.32 0.00 45.28 3.66
60 61 5.707298 GCATTTGCTGGTGAGTATATACCAT 59.293 40.000 9.32 0.00 45.28 3.55
61 62 5.063204 GCATTTGCTGGTGAGTATATACCA 58.937 41.667 9.32 2.13 44.31 3.25
62 63 4.152402 CGCATTTGCTGGTGAGTATATACC 59.848 45.833 9.32 0.00 39.32 2.73
63 64 4.750098 ACGCATTTGCTGGTGAGTATATAC 59.250 41.667 4.60 4.60 39.32 1.47
64 65 4.956085 ACGCATTTGCTGGTGAGTATATA 58.044 39.130 0.51 0.00 39.32 0.86
65 66 3.808728 ACGCATTTGCTGGTGAGTATAT 58.191 40.909 0.51 0.00 39.32 0.86
66 67 3.118775 AGACGCATTTGCTGGTGAGTATA 60.119 43.478 0.51 0.00 39.32 1.47
67 68 2.009774 GACGCATTTGCTGGTGAGTAT 58.990 47.619 0.51 0.00 39.32 2.12
68 69 1.001974 AGACGCATTTGCTGGTGAGTA 59.998 47.619 0.51 0.00 39.32 2.59
69 70 0.250467 AGACGCATTTGCTGGTGAGT 60.250 50.000 0.51 0.00 39.32 3.41
70 71 0.167470 CAGACGCATTTGCTGGTGAG 59.833 55.000 0.51 0.00 39.32 3.51
71 72 0.250252 TCAGACGCATTTGCTGGTGA 60.250 50.000 0.51 0.00 39.32 4.02
72 73 0.806868 ATCAGACGCATTTGCTGGTG 59.193 50.000 0.51 0.00 39.32 4.17
73 74 2.093500 TCTATCAGACGCATTTGCTGGT 60.093 45.455 0.51 0.00 39.32 4.00
74 75 2.554142 TCTATCAGACGCATTTGCTGG 58.446 47.619 0.51 0.00 39.32 4.85
75 76 3.558829 ACATCTATCAGACGCATTTGCTG 59.441 43.478 0.51 0.00 39.32 4.41
76 77 3.801698 ACATCTATCAGACGCATTTGCT 58.198 40.909 0.51 0.00 39.32 3.91
77 78 5.852738 ATACATCTATCAGACGCATTTGC 57.147 39.130 0.00 0.00 37.78 3.68
78 79 9.964253 GATTTATACATCTATCAGACGCATTTG 57.036 33.333 0.00 0.00 0.00 2.32
79 80 9.710900 TGATTTATACATCTATCAGACGCATTT 57.289 29.630 0.82 0.00 0.00 2.32
80 81 9.881649 ATGATTTATACATCTATCAGACGCATT 57.118 29.630 0.82 0.00 31.20 3.56
81 82 9.310716 CATGATTTATACATCTATCAGACGCAT 57.689 33.333 0.82 0.00 31.20 4.73
82 83 7.276438 GCATGATTTATACATCTATCAGACGCA 59.724 37.037 0.00 0.00 31.20 5.24
83 84 7.514280 CGCATGATTTATACATCTATCAGACGC 60.514 40.741 0.00 0.00 31.20 5.19
84 85 7.486232 ACGCATGATTTATACATCTATCAGACG 59.514 37.037 0.00 0.00 36.33 4.18
85 86 8.590470 CACGCATGATTTATACATCTATCAGAC 58.410 37.037 0.00 0.00 31.20 3.51
86 87 8.522830 TCACGCATGATTTATACATCTATCAGA 58.477 33.333 0.00 0.00 31.20 3.27
87 88 8.693542 TCACGCATGATTTATACATCTATCAG 57.306 34.615 0.00 0.00 31.20 2.90
91 92 9.788960 GTCTATCACGCATGATTTATACATCTA 57.211 33.333 0.00 0.00 43.40 1.98
92 93 7.486232 CGTCTATCACGCATGATTTATACATCT 59.514 37.037 0.00 0.00 43.40 2.90
93 94 7.604386 CGTCTATCACGCATGATTTATACATC 58.396 38.462 0.00 0.00 43.40 3.06
94 95 7.511809 CGTCTATCACGCATGATTTATACAT 57.488 36.000 0.00 0.00 43.40 2.29
95 96 6.927933 CGTCTATCACGCATGATTTATACA 57.072 37.500 0.00 0.00 43.40 2.29
107 108 7.425882 GTATGATCAATACTACGTCTATCACGC 59.574 40.741 0.00 0.00 43.78 5.34
108 109 8.808861 GTATGATCAATACTACGTCTATCACG 57.191 38.462 0.00 0.00 44.58 4.35
121 122 9.627395 AATTCTAGCACGTAGTATGATCAATAC 57.373 33.333 0.00 3.48 41.61 1.89
122 123 9.626045 CAATTCTAGCACGTAGTATGATCAATA 57.374 33.333 0.00 0.00 41.61 1.90
123 124 7.116948 GCAATTCTAGCACGTAGTATGATCAAT 59.883 37.037 0.00 0.00 41.61 2.57
124 125 6.420903 GCAATTCTAGCACGTAGTATGATCAA 59.579 38.462 0.00 0.00 41.61 2.57
125 126 5.920840 GCAATTCTAGCACGTAGTATGATCA 59.079 40.000 0.00 0.00 41.61 2.92
126 127 5.920840 TGCAATTCTAGCACGTAGTATGATC 59.079 40.000 0.00 0.00 41.61 2.92
127 128 5.842907 TGCAATTCTAGCACGTAGTATGAT 58.157 37.500 0.00 0.00 41.61 2.45
128 129 5.257082 TGCAATTCTAGCACGTAGTATGA 57.743 39.130 0.00 0.00 41.61 2.15
129 130 5.966636 TTGCAATTCTAGCACGTAGTATG 57.033 39.130 0.00 0.00 41.61 2.39
130 131 5.050091 GCATTGCAATTCTAGCACGTAGTAT 60.050 40.000 9.83 0.00 41.61 2.12
131 132 4.270084 GCATTGCAATTCTAGCACGTAGTA 59.730 41.667 9.83 0.00 41.61 1.82
133 134 3.310774 AGCATTGCAATTCTAGCACGTAG 59.689 43.478 18.41 2.23 42.54 3.51
134 135 3.270027 AGCATTGCAATTCTAGCACGTA 58.730 40.909 18.41 0.00 42.54 3.57
135 136 2.086869 AGCATTGCAATTCTAGCACGT 58.913 42.857 18.41 0.00 42.54 4.49
136 137 2.096335 TGAGCATTGCAATTCTAGCACG 59.904 45.455 11.71 0.00 42.54 5.34
137 138 3.770263 TGAGCATTGCAATTCTAGCAC 57.230 42.857 11.71 10.20 42.54 4.40
138 139 4.883006 TGTATGAGCATTGCAATTCTAGCA 59.117 37.500 11.71 7.20 40.85 3.49
139 140 5.428496 TGTATGAGCATTGCAATTCTAGC 57.572 39.130 11.71 11.11 0.00 3.42
140 141 9.770503 GAATATGTATGAGCATTGCAATTCTAG 57.229 33.333 11.71 0.79 0.00 2.43
141 142 8.733458 GGAATATGTATGAGCATTGCAATTCTA 58.267 33.333 11.71 1.78 0.00 2.10
142 143 7.450634 AGGAATATGTATGAGCATTGCAATTCT 59.549 33.333 11.56 11.56 0.00 2.40
143 144 7.600065 AGGAATATGTATGAGCATTGCAATTC 58.400 34.615 9.83 4.81 0.00 2.17
144 145 7.450634 AGAGGAATATGTATGAGCATTGCAATT 59.549 33.333 9.83 0.00 0.00 2.32
145 146 6.946583 AGAGGAATATGTATGAGCATTGCAAT 59.053 34.615 11.91 5.99 0.00 3.56
146 147 6.301486 AGAGGAATATGTATGAGCATTGCAA 58.699 36.000 11.91 0.00 0.00 4.08
147 148 5.872963 AGAGGAATATGTATGAGCATTGCA 58.127 37.500 11.91 0.00 0.00 4.08
148 149 6.171921 AGAGAGGAATATGTATGAGCATTGC 58.828 40.000 0.00 0.00 0.00 3.56
149 150 6.817641 GGAGAGAGGAATATGTATGAGCATTG 59.182 42.308 0.00 0.00 0.00 2.82
150 151 6.350864 CGGAGAGAGGAATATGTATGAGCATT 60.351 42.308 0.00 0.00 0.00 3.56
151 152 5.126869 CGGAGAGAGGAATATGTATGAGCAT 59.873 44.000 0.00 0.00 0.00 3.79
152 153 4.460731 CGGAGAGAGGAATATGTATGAGCA 59.539 45.833 0.00 0.00 0.00 4.26
153 154 4.461081 ACGGAGAGAGGAATATGTATGAGC 59.539 45.833 0.00 0.00 0.00 4.26
154 155 5.943416 AGACGGAGAGAGGAATATGTATGAG 59.057 44.000 0.00 0.00 0.00 2.90
155 156 5.707764 CAGACGGAGAGAGGAATATGTATGA 59.292 44.000 0.00 0.00 0.00 2.15
156 157 5.105957 CCAGACGGAGAGAGGAATATGTATG 60.106 48.000 0.00 0.00 0.00 2.39
157 158 5.013547 CCAGACGGAGAGAGGAATATGTAT 58.986 45.833 0.00 0.00 0.00 2.29
158 159 4.104261 TCCAGACGGAGAGAGGAATATGTA 59.896 45.833 0.00 0.00 35.91 2.29
159 160 3.117474 TCCAGACGGAGAGAGGAATATGT 60.117 47.826 0.00 0.00 35.91 2.29
160 161 3.491342 TCCAGACGGAGAGAGGAATATG 58.509 50.000 0.00 0.00 35.91 1.78
161 162 3.885976 TCCAGACGGAGAGAGGAATAT 57.114 47.619 0.00 0.00 35.91 1.28
162 163 3.664551 TTCCAGACGGAGAGAGGAATA 57.335 47.619 0.00 0.00 44.10 1.75
163 164 2.534042 TTCCAGACGGAGAGAGGAAT 57.466 50.000 0.00 0.00 44.10 3.01
164 165 2.304221 TTTCCAGACGGAGAGAGGAA 57.696 50.000 0.00 0.00 44.10 3.36
165 166 2.534042 ATTTCCAGACGGAGAGAGGA 57.466 50.000 0.00 0.00 44.10 3.71
166 167 3.292460 AGTATTTCCAGACGGAGAGAGG 58.708 50.000 0.00 0.00 44.10 3.69
167 168 4.158764 ACAAGTATTTCCAGACGGAGAGAG 59.841 45.833 0.00 0.00 44.10 3.20
168 169 4.087182 ACAAGTATTTCCAGACGGAGAGA 58.913 43.478 0.00 0.00 44.10 3.10
169 170 4.425520 GACAAGTATTTCCAGACGGAGAG 58.574 47.826 0.00 0.00 44.10 3.20
170 171 3.119602 CGACAAGTATTTCCAGACGGAGA 60.120 47.826 0.00 0.00 44.10 3.71
171 172 3.179830 CGACAAGTATTTCCAGACGGAG 58.820 50.000 0.00 0.00 44.10 4.63
172 173 2.673043 GCGACAAGTATTTCCAGACGGA 60.673 50.000 0.00 0.00 40.60 4.69
173 174 1.659098 GCGACAAGTATTTCCAGACGG 59.341 52.381 0.00 0.00 0.00 4.79
174 175 2.333926 TGCGACAAGTATTTCCAGACG 58.666 47.619 0.00 0.00 0.00 4.18
175 176 3.585862 TCTGCGACAAGTATTTCCAGAC 58.414 45.455 0.00 0.00 0.00 3.51
176 177 3.953712 TCTGCGACAAGTATTTCCAGA 57.046 42.857 0.00 0.00 0.00 3.86
177 178 5.106555 ACATTTCTGCGACAAGTATTTCCAG 60.107 40.000 0.00 0.00 0.00 3.86
178 179 4.759693 ACATTTCTGCGACAAGTATTTCCA 59.240 37.500 0.00 0.00 0.00 3.53
179 180 5.296813 ACATTTCTGCGACAAGTATTTCC 57.703 39.130 0.00 0.00 0.00 3.13
180 181 9.982291 TTTATACATTTCTGCGACAAGTATTTC 57.018 29.630 0.00 0.00 0.00 2.17
184 185 9.767684 CATTTTTATACATTTCTGCGACAAGTA 57.232 29.630 0.00 0.00 0.00 2.24
185 186 7.754924 CCATTTTTATACATTTCTGCGACAAGT 59.245 33.333 0.00 0.00 0.00 3.16
186 187 7.967854 TCCATTTTTATACATTTCTGCGACAAG 59.032 33.333 0.00 0.00 0.00 3.16
187 188 7.821652 TCCATTTTTATACATTTCTGCGACAA 58.178 30.769 0.00 0.00 0.00 3.18
188 189 7.384439 TCCATTTTTATACATTTCTGCGACA 57.616 32.000 0.00 0.00 0.00 4.35
189 190 7.915397 ACATCCATTTTTATACATTTCTGCGAC 59.085 33.333 0.00 0.00 0.00 5.19
190 191 7.995289 ACATCCATTTTTATACATTTCTGCGA 58.005 30.769 0.00 0.00 0.00 5.10
191 192 9.897744 ATACATCCATTTTTATACATTTCTGCG 57.102 29.630 0.00 0.00 0.00 5.18
228 229 8.690884 CGAGGAATGGATGTATCTAGACATATT 58.309 37.037 0.00 0.00 40.18 1.28
229 230 7.286546 CCGAGGAATGGATGTATCTAGACATAT 59.713 40.741 0.00 0.00 40.18 1.78
230 231 6.603599 CCGAGGAATGGATGTATCTAGACATA 59.396 42.308 0.00 0.00 40.18 2.29
231 232 5.420421 CCGAGGAATGGATGTATCTAGACAT 59.580 44.000 0.00 0.00 42.82 3.06
232 233 4.767409 CCGAGGAATGGATGTATCTAGACA 59.233 45.833 0.00 0.00 0.00 3.41
233 234 5.010933 TCCGAGGAATGGATGTATCTAGAC 58.989 45.833 0.00 0.00 0.00 2.59
234 235 5.010933 GTCCGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 37.93 2.43
235 236 4.767409 TGTCCGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 37.93 2.43
236 237 4.736473 TGTCCGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 37.93 1.98
237 238 3.576861 TGTCCGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 37.93 1.98
238 239 4.202264 ACTTGTCCGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 37.93 2.24
239 240 3.711704 ACTTGTCCGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 37.93 2.29
240 241 3.104512 ACTTGTCCGAGGAATGGATGTA 58.895 45.455 0.00 0.00 37.93 2.29
241 242 1.909302 ACTTGTCCGAGGAATGGATGT 59.091 47.619 0.00 0.00 37.93 3.06
242 243 2.698855 ACTTGTCCGAGGAATGGATG 57.301 50.000 0.00 0.00 37.93 3.51
243 244 5.373812 AAATACTTGTCCGAGGAATGGAT 57.626 39.130 0.00 0.00 37.93 3.41
244 245 4.837093 AAATACTTGTCCGAGGAATGGA 57.163 40.909 0.00 0.00 0.00 3.41
245 246 4.096382 CCAAAATACTTGTCCGAGGAATGG 59.904 45.833 0.00 0.00 0.00 3.16
246 247 4.096382 CCCAAAATACTTGTCCGAGGAATG 59.904 45.833 0.00 0.00 0.00 2.67
247 248 4.018779 TCCCAAAATACTTGTCCGAGGAAT 60.019 41.667 0.00 0.00 0.00 3.01
248 249 3.328343 TCCCAAAATACTTGTCCGAGGAA 59.672 43.478 0.00 0.00 0.00 3.36
249 250 2.907696 TCCCAAAATACTTGTCCGAGGA 59.092 45.455 0.00 0.00 0.00 3.71
250 251 3.007635 GTCCCAAAATACTTGTCCGAGG 58.992 50.000 0.00 0.00 0.00 4.63
251 252 3.007635 GGTCCCAAAATACTTGTCCGAG 58.992 50.000 0.00 0.00 0.00 4.63
252 253 2.613474 CGGTCCCAAAATACTTGTCCGA 60.613 50.000 0.00 0.00 38.03 4.55
253 254 1.735571 CGGTCCCAAAATACTTGTCCG 59.264 52.381 0.00 0.00 0.00 4.79
254 255 3.007635 CTCGGTCCCAAAATACTTGTCC 58.992 50.000 0.00 0.00 0.00 4.02
255 256 3.933332 CTCTCGGTCCCAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
256 257 3.581332 TCTCTCGGTCCCAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
257 258 4.184629 CTCTCTCGGTCCCAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
258 259 3.838903 ACTCTCTCGGTCCCAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
259 260 3.442076 ACTCTCTCGGTCCCAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
260 261 3.889520 ACTCTCTCGGTCCCAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
261 262 6.041296 GGTATTACTCTCTCGGTCCCAAAATA 59.959 42.308 0.00 0.00 0.00 1.40
262 263 5.163332 GGTATTACTCTCTCGGTCCCAAAAT 60.163 44.000 0.00 0.00 0.00 1.82
263 264 4.161001 GGTATTACTCTCTCGGTCCCAAAA 59.839 45.833 0.00 0.00 0.00 2.44
264 265 3.703052 GGTATTACTCTCTCGGTCCCAAA 59.297 47.826 0.00 0.00 0.00 3.28
265 266 3.294214 GGTATTACTCTCTCGGTCCCAA 58.706 50.000 0.00 0.00 0.00 4.12
266 267 2.423947 GGGTATTACTCTCTCGGTCCCA 60.424 54.545 0.00 0.00 33.33 4.37
267 268 2.237643 GGGTATTACTCTCTCGGTCCC 58.762 57.143 0.00 0.00 0.00 4.46
268 269 2.941480 TGGGTATTACTCTCTCGGTCC 58.059 52.381 0.00 0.00 0.00 4.46
269 270 4.142790 TGATGGGTATTACTCTCTCGGTC 58.857 47.826 0.00 0.00 0.00 4.79
270 271 4.145807 CTGATGGGTATTACTCTCTCGGT 58.854 47.826 0.00 0.00 0.00 4.69
271 272 3.057174 GCTGATGGGTATTACTCTCTCGG 60.057 52.174 0.00 0.00 0.00 4.63
272 273 3.570125 TGCTGATGGGTATTACTCTCTCG 59.430 47.826 0.00 0.00 0.00 4.04
273 274 5.537300 TTGCTGATGGGTATTACTCTCTC 57.463 43.478 0.00 0.00 0.00 3.20
274 275 5.957771 TTTGCTGATGGGTATTACTCTCT 57.042 39.130 0.00 0.00 0.00 3.10
275 276 5.049129 GCATTTGCTGATGGGTATTACTCTC 60.049 44.000 0.00 0.00 38.21 3.20
276 277 4.823989 GCATTTGCTGATGGGTATTACTCT 59.176 41.667 0.00 0.00 38.21 3.24
277 278 4.319766 CGCATTTGCTGATGGGTATTACTC 60.320 45.833 0.51 0.00 39.32 2.59
278 279 3.565482 CGCATTTGCTGATGGGTATTACT 59.435 43.478 0.51 0.00 39.32 2.24
279 280 3.853307 GCGCATTTGCTGATGGGTATTAC 60.853 47.826 0.30 0.00 40.80 1.89
359 360 5.432390 TCCAAGATACTCCTACTACCAGTCT 59.568 44.000 0.00 0.00 0.00 3.24
386 387 2.829003 TAGCTCCGCCGACAGAGG 60.829 66.667 0.00 0.00 0.00 3.69
499 504 2.753452 CAGTCTAGGAGTAGTTGCGGAA 59.247 50.000 0.00 0.00 0.00 4.30
500 505 2.290768 ACAGTCTAGGAGTAGTTGCGGA 60.291 50.000 0.00 0.00 0.00 5.54
501 506 2.093106 ACAGTCTAGGAGTAGTTGCGG 58.907 52.381 0.00 0.00 0.00 5.69
503 508 6.864342 TCATTTACAGTCTAGGAGTAGTTGC 58.136 40.000 0.00 0.00 0.00 4.17
506 511 5.595133 GGCTCATTTACAGTCTAGGAGTAGT 59.405 44.000 0.00 0.00 0.00 2.73
514 524 5.826208 TCTATCGTGGCTCATTTACAGTCTA 59.174 40.000 0.00 0.00 0.00 2.59
550 560 2.822306 CGAAAGTTCGGCAGCAGTA 58.178 52.632 5.53 0.00 46.30 2.74
560 570 7.813627 AGTTTATCTCTGTTACTCCGAAAGTTC 59.186 37.037 0.00 0.00 39.55 3.01
561 571 7.668492 AGTTTATCTCTGTTACTCCGAAAGTT 58.332 34.615 0.00 0.00 39.55 2.66
586 602 1.284491 TGCAGGATGGTGGAGCAATTA 59.716 47.619 0.00 0.00 35.86 1.40
633 678 1.253034 CGATCTGCGAGCGAGTTAAAC 59.747 52.381 9.95 0.00 44.55 2.01
634 679 1.131693 TCGATCTGCGAGCGAGTTAAA 59.868 47.619 13.29 0.00 45.37 1.52
635 680 0.730840 TCGATCTGCGAGCGAGTTAA 59.269 50.000 13.29 0.00 45.37 2.01
636 681 2.390427 TCGATCTGCGAGCGAGTTA 58.610 52.632 13.29 0.00 45.37 2.24
637 682 3.188011 TCGATCTGCGAGCGAGTT 58.812 55.556 13.29 0.00 45.37 3.01
654 699 2.086869 CCAGGTCATTTGCAGACGAAT 58.913 47.619 0.00 0.00 36.87 3.34
655 700 1.202758 ACCAGGTCATTTGCAGACGAA 60.203 47.619 0.00 0.00 36.87 3.85
720 766 1.688197 ACAGTTGGATTTTGCAGTGGG 59.312 47.619 0.00 0.00 0.00 4.61
763 813 6.686484 AAATGGAGGGAGCAATTAAAAACT 57.314 33.333 0.00 0.00 0.00 2.66
1605 1691 2.884639 CGAATCAAACCAAACACCTCCT 59.115 45.455 0.00 0.00 0.00 3.69
2501 2606 1.751143 TTGGAGGTGGAGGAGGAGGT 61.751 60.000 0.00 0.00 0.00 3.85
2692 2808 0.108615 GTCGACTGATCTGGTGGTGG 60.109 60.000 8.70 0.00 0.00 4.61
2791 2908 5.270893 ACTACATTTTGTTTTGGTGGGTC 57.729 39.130 0.00 0.00 0.00 4.46
2795 2912 6.312426 TGCAGAAACTACATTTTGTTTTGGTG 59.688 34.615 0.00 0.00 36.64 4.17
2809 2926 8.768955 CCACTATCAGATTAATGCAGAAACTAC 58.231 37.037 0.00 0.00 0.00 2.73
2811 2928 7.341805 ACCACTATCAGATTAATGCAGAAACT 58.658 34.615 0.00 0.00 0.00 2.66
2816 2933 5.292765 ACGACCACTATCAGATTAATGCAG 58.707 41.667 0.00 0.00 0.00 4.41
2819 2936 7.921214 ACTTGTACGACCACTATCAGATTAATG 59.079 37.037 0.00 0.00 0.00 1.90
2824 2941 5.916661 AACTTGTACGACCACTATCAGAT 57.083 39.130 0.00 0.00 0.00 2.90
2828 2945 5.742926 GCTCTTAACTTGTACGACCACTATC 59.257 44.000 0.00 0.00 0.00 2.08
2830 2947 4.763793 AGCTCTTAACTTGTACGACCACTA 59.236 41.667 0.00 0.00 0.00 2.74
2831 2948 3.573110 AGCTCTTAACTTGTACGACCACT 59.427 43.478 0.00 0.00 0.00 4.00
2832 2949 3.910648 AGCTCTTAACTTGTACGACCAC 58.089 45.455 0.00 0.00 0.00 4.16
2834 2951 4.807443 AGAAGCTCTTAACTTGTACGACC 58.193 43.478 0.00 0.00 0.00 4.79
2836 2953 6.814506 ACTAGAAGCTCTTAACTTGTACGA 57.185 37.500 0.00 0.00 0.00 3.43
2837 2954 7.750769 ACTACTAGAAGCTCTTAACTTGTACG 58.249 38.462 0.00 0.00 0.00 3.67
2839 2956 9.956640 ACTACTACTAGAAGCTCTTAACTTGTA 57.043 33.333 0.00 0.00 0.00 2.41
2865 2982 2.285083 GCTGTGTTGTGTGGACTAACA 58.715 47.619 0.00 0.00 32.39 2.41
2866 2983 2.031683 GTGCTGTGTTGTGTGGACTAAC 59.968 50.000 0.00 0.00 0.00 2.34
2867 2984 2.285083 GTGCTGTGTTGTGTGGACTAA 58.715 47.619 0.00 0.00 0.00 2.24
2891 3008 0.320771 AACCGATCGAGCTTTGCACT 60.321 50.000 18.66 0.00 0.00 4.40
2893 3010 1.234821 AAAACCGATCGAGCTTTGCA 58.765 45.000 18.66 0.00 0.00 4.08
2895 3012 7.461107 TCTTTATTAAAACCGATCGAGCTTTG 58.539 34.615 18.66 0.27 0.00 2.77
2896 3013 7.605410 TCTTTATTAAAACCGATCGAGCTTT 57.395 32.000 18.66 14.30 0.00 3.51
2897 3014 7.605410 TTCTTTATTAAAACCGATCGAGCTT 57.395 32.000 18.66 8.61 0.00 3.74
2900 3017 8.537223 TCGATTTCTTTATTAAAACCGATCGAG 58.463 33.333 18.66 9.42 31.91 4.04
2901 3018 8.410030 TCGATTTCTTTATTAAAACCGATCGA 57.590 30.769 18.66 15.21 32.93 3.59
2903 3020 9.422196 CACTCGATTTCTTTATTAAAACCGATC 57.578 33.333 0.00 0.00 30.38 3.69
2904 3021 8.943002 ACACTCGATTTCTTTATTAAAACCGAT 58.057 29.630 0.00 0.00 30.38 4.18
2905 3022 8.314143 ACACTCGATTTCTTTATTAAAACCGA 57.686 30.769 0.00 0.00 0.00 4.69
2906 3023 8.225107 TGACACTCGATTTCTTTATTAAAACCG 58.775 33.333 0.00 0.00 0.00 4.44
2923 3041 1.905894 TGGGAAATGGATGACACTCGA 59.094 47.619 0.00 0.00 0.00 4.04
3004 3834 1.814793 GACCAAAGTGGAGAAGGCTC 58.185 55.000 0.18 0.00 40.96 4.70
3005 3835 0.035458 CGACCAAAGTGGAGAAGGCT 59.965 55.000 0.18 0.00 40.96 4.58
3006 3836 0.955919 CCGACCAAAGTGGAGAAGGC 60.956 60.000 0.18 0.00 40.96 4.35
3009 3839 1.301401 CGCCGACCAAAGTGGAGAA 60.301 57.895 0.18 0.00 40.96 2.87
3015 3845 2.660552 CACGACGCCGACCAAAGT 60.661 61.111 0.00 0.00 39.50 2.66
3067 4150 2.785258 GCGCTTACTTTGCCGGAG 59.215 61.111 5.05 0.00 0.00 4.63
3175 4258 1.274447 AGTACCAGCGGTAGTCCAAAC 59.726 52.381 7.56 0.00 37.25 2.93
3190 4273 6.836242 AGTACCAGTATAGTACTCCAGTACC 58.164 44.000 12.40 0.00 45.70 3.34
3199 4282 7.278868 AGTGTTGTACGAGTACCAGTATAGTAC 59.721 40.741 10.48 10.68 40.34 2.73
3200 4283 7.331026 AGTGTTGTACGAGTACCAGTATAGTA 58.669 38.462 10.48 0.00 35.26 1.82
3201 4284 6.176183 AGTGTTGTACGAGTACCAGTATAGT 58.824 40.000 10.48 0.00 35.26 2.12
3202 4285 6.674694 AGTGTTGTACGAGTACCAGTATAG 57.325 41.667 10.48 0.00 35.26 1.31
3203 4286 7.064609 GTGTAGTGTTGTACGAGTACCAGTATA 59.935 40.741 10.48 5.72 35.26 1.47
3204 4287 5.939883 TGTAGTGTTGTACGAGTACCAGTAT 59.060 40.000 10.48 0.00 35.26 2.12
3205 4288 5.179368 GTGTAGTGTTGTACGAGTACCAGTA 59.821 44.000 10.48 6.92 35.26 2.74
3206 4289 4.023707 GTGTAGTGTTGTACGAGTACCAGT 60.024 45.833 10.48 7.73 35.26 4.00
3207 4290 4.214971 AGTGTAGTGTTGTACGAGTACCAG 59.785 45.833 10.48 0.00 35.26 4.00
3208 4291 4.136796 AGTGTAGTGTTGTACGAGTACCA 58.863 43.478 10.48 0.00 35.26 3.25
3209 4292 4.756084 AGTGTAGTGTTGTACGAGTACC 57.244 45.455 10.48 0.00 35.26 3.34
3227 4310 4.645136 TCCATAACACTCCTACTGCTAGTG 59.355 45.833 0.00 0.00 44.89 2.74
3286 4388 9.801873 TTAATCTGCTAAAAATGTAATCCAAGC 57.198 29.630 0.00 0.00 0.00 4.01
3385 4520 2.594303 CCTCCAACGCTTGCACCA 60.594 61.111 0.00 0.00 0.00 4.17
3446 4592 2.424601 TGGCAGAGCATAAACAAGCATC 59.575 45.455 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.