Multiple sequence alignment - TraesCS4A01G133800

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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 TraesCS4A01G133800 chr4A 100.000 4673 0 0 1 4673 181706922 181711594 0.000000e+00 8630.0
1 TraesCS4A01G133800 chr4D 96.526 3771 94 16 338 4096 301009663 301005918 0.000000e+00 6204.0
2 TraesCS4A01G133800 chr4D 90.353 539 19 9 4151 4673 301005799 301005278 0.000000e+00 676.0
3 TraesCS4A01G133800 chr4D 91.860 86 3 1 1 82 301009762 301009677 2.950000e-22 117.0
4 TraesCS4A01G133800 chr4B 95.938 3791 94 21 338 4097 374630508 374626747 0.000000e+00 6093.0
5 TraesCS4A01G133800 chr4B 84.872 390 18 13 4151 4529 374626579 374626220 5.750000e-94 355.0
6 TraesCS4A01G133800 chr4B 93.023 86 2 1 1 82 374630603 374630518 6.350000e-24 122.0
7 TraesCS4A01G133800 chr4B 95.161 62 3 0 4547 4608 374626223 374626162 1.070000e-16 99.0
8 TraesCS4A01G133800 chr4B 97.959 49 0 1 4625 4673 374626105 374626058 3.000000e-12 84.2
9 TraesCS4A01G133800 chr1D 89.345 3313 267 51 767 4033 316856464 316859736 0.000000e+00 4084.0
10 TraesCS4A01G133800 chr1A 89.640 3224 268 33 841 4033 398050442 398053630 0.000000e+00 4043.0
11 TraesCS4A01G133800 chr1A 93.878 245 15 0 99 343 531651544 531651300 2.050000e-98 370.0
12 TraesCS4A01G133800 chr1B 90.196 3111 242 30 841 3928 429002009 429005079 0.000000e+00 3997.0
13 TraesCS4A01G133800 chr1B 93.173 249 16 1 95 342 99529329 99529577 9.560000e-97 364.0
14 TraesCS4A01G133800 chr1B 93.469 245 16 0 97 341 479408024 479408268 9.560000e-97 364.0
15 TraesCS4A01G133800 chrUn 100.000 419 0 0 2213 2631 476932637 476932219 0.000000e+00 774.0
16 TraesCS4A01G133800 chr3B 94.215 242 14 0 99 340 742449919 742450160 2.050000e-98 370.0
17 TraesCS4A01G133800 chr7A 93.827 243 15 0 97 339 722869442 722869200 2.660000e-97 366.0
18 TraesCS4A01G133800 chr6B 92.885 253 16 1 98 348 716477635 716477383 2.660000e-97 366.0
19 TraesCS4A01G133800 chr5A 93.469 245 16 0 97 341 678227649 678227893 9.560000e-97 364.0
20 TraesCS4A01G133800 chr3A 93.117 247 17 0 93 339 44724401 44724647 3.440000e-96 363.0
21 TraesCS4A01G133800 chr2A 92.857 252 15 3 90 339 84977519 84977769 3.440000e-96 363.0


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 TraesCS4A01G133800 chr4A 181706922 181711594 4672 False 8630.000000 8630 100.0000 1 4673 1 chr4A.!!$F1 4672
1 TraesCS4A01G133800 chr4D 301005278 301009762 4484 True 2332.333333 6204 92.9130 1 4673 3 chr4D.!!$R1 4672
2 TraesCS4A01G133800 chr4B 374626058 374630603 4545 True 1350.640000 6093 93.3906 1 4673 5 chr4B.!!$R1 4672
3 TraesCS4A01G133800 chr1D 316856464 316859736 3272 False 4084.000000 4084 89.3450 767 4033 1 chr1D.!!$F1 3266
4 TraesCS4A01G133800 chr1A 398050442 398053630 3188 False 4043.000000 4043 89.6400 841 4033 1 chr1A.!!$F1 3192
5 TraesCS4A01G133800 chr1B 429002009 429005079 3070 False 3997.000000 3997 90.1960 841 3928 1 chr1B.!!$F2 3087

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
271 276 0.165944 GTCGCAATTGGTCTCGTTGG 59.834 55.0 7.72 0.00 0.00 3.77 F
499 508 0.242825 TGACGGTACCGAAGAAGCTG 59.757 55.0 39.52 8.75 42.83 4.24 F
1890 1963 0.527817 CTTCGGATGTCTACGCCACC 60.528 60.0 0.00 0.00 0.00 4.61 F
2631 2704 0.179000 ATGAGTCACGGATCCTTGGC 59.821 55.0 14.77 14.77 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 1911 0.249120 CGGCACATTGTCAGGGTAGA 59.751 55.000 0.00 0.0 0.00 2.59 R
2161 2234 1.075601 AGAGCCACCCAGAAATCCAA 58.924 50.000 0.00 0.0 0.00 3.53 R
3477 3550 1.070445 GCCCTCATCTGACATCCCG 59.930 63.158 0.00 0.0 0.00 5.14 R
4373 4593 0.894141 CAGAGGGAGAGTGGACACTG 59.106 60.000 10.08 0.0 42.66 3.66 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
86 91 2.815722 GAATCTATCGGCTGACGGC 58.184 57.895 1.72 0.00 44.45 5.68
87 92 0.315568 GAATCTATCGGCTGACGGCT 59.684 55.000 1.72 0.00 44.45 5.52
93 98 4.457496 CGGCTGACGGCTGTCCAT 62.457 66.667 22.81 0.00 44.86 3.41
102 107 5.386958 TGACGGCTGTCCATATTATACTC 57.613 43.478 22.81 0.00 44.86 2.59
103 108 4.219944 TGACGGCTGTCCATATTATACTCC 59.780 45.833 22.81 0.00 44.86 3.85
104 109 3.514309 ACGGCTGTCCATATTATACTCCC 59.486 47.826 0.00 0.00 0.00 4.30
105 110 3.769844 CGGCTGTCCATATTATACTCCCT 59.230 47.826 0.00 0.00 0.00 4.20
106 111 4.142138 CGGCTGTCCATATTATACTCCCTC 60.142 50.000 0.00 0.00 0.00 4.30
107 112 4.162509 GGCTGTCCATATTATACTCCCTCC 59.837 50.000 0.00 0.00 0.00 4.30
108 113 4.777896 GCTGTCCATATTATACTCCCTCCA 59.222 45.833 0.00 0.00 0.00 3.86
109 114 5.426833 GCTGTCCATATTATACTCCCTCCAT 59.573 44.000 0.00 0.00 0.00 3.41
110 115 6.069963 GCTGTCCATATTATACTCCCTCCATT 60.070 42.308 0.00 0.00 0.00 3.16
111 116 7.496346 TGTCCATATTATACTCCCTCCATTC 57.504 40.000 0.00 0.00 0.00 2.67
112 117 6.154534 TGTCCATATTATACTCCCTCCATTCG 59.845 42.308 0.00 0.00 0.00 3.34
113 118 6.380274 GTCCATATTATACTCCCTCCATTCGA 59.620 42.308 0.00 0.00 0.00 3.71
114 119 6.380274 TCCATATTATACTCCCTCCATTCGAC 59.620 42.308 0.00 0.00 0.00 4.20
115 120 6.154534 CCATATTATACTCCCTCCATTCGACA 59.845 42.308 0.00 0.00 0.00 4.35
116 121 7.310423 CCATATTATACTCCCTCCATTCGACAA 60.310 40.741 0.00 0.00 0.00 3.18
117 122 6.688073 ATTATACTCCCTCCATTCGACAAT 57.312 37.500 0.00 0.00 0.00 2.71
118 123 2.698855 ACTCCCTCCATTCGACAATG 57.301 50.000 0.00 0.00 39.45 2.82
119 124 1.909302 ACTCCCTCCATTCGACAATGT 59.091 47.619 0.00 0.00 38.22 2.71
120 125 3.104512 ACTCCCTCCATTCGACAATGTA 58.895 45.455 0.00 0.00 38.22 2.29
121 126 3.133003 ACTCCCTCCATTCGACAATGTAG 59.867 47.826 0.00 0.00 38.22 2.74
122 127 3.104512 TCCCTCCATTCGACAATGTAGT 58.895 45.455 0.00 0.00 38.22 2.73
123 128 3.118775 TCCCTCCATTCGACAATGTAGTG 60.119 47.826 0.00 0.00 38.22 2.74
124 129 2.609459 CCTCCATTCGACAATGTAGTGC 59.391 50.000 0.00 0.00 38.22 4.40
125 130 3.525537 CTCCATTCGACAATGTAGTGCT 58.474 45.455 0.00 0.00 38.22 4.40
126 131 3.935203 CTCCATTCGACAATGTAGTGCTT 59.065 43.478 0.00 0.00 38.22 3.91
127 132 3.932710 TCCATTCGACAATGTAGTGCTTC 59.067 43.478 0.00 0.00 38.22 3.86
128 133 3.063997 CCATTCGACAATGTAGTGCTTCC 59.936 47.826 0.00 0.00 38.22 3.46
129 134 3.678056 TTCGACAATGTAGTGCTTCCT 57.322 42.857 0.00 0.00 0.00 3.36
130 135 3.232213 TCGACAATGTAGTGCTTCCTC 57.768 47.619 0.00 0.00 0.00 3.71
131 136 2.826128 TCGACAATGTAGTGCTTCCTCT 59.174 45.455 0.00 0.00 0.00 3.69
132 137 4.014406 TCGACAATGTAGTGCTTCCTCTA 58.986 43.478 0.00 0.00 0.00 2.43
133 138 4.645136 TCGACAATGTAGTGCTTCCTCTAT 59.355 41.667 0.00 0.00 0.00 1.98
134 139 4.979197 CGACAATGTAGTGCTTCCTCTATC 59.021 45.833 0.00 0.00 0.00 2.08
135 140 5.283457 ACAATGTAGTGCTTCCTCTATCC 57.717 43.478 0.00 0.00 0.00 2.59
136 141 4.716784 ACAATGTAGTGCTTCCTCTATCCA 59.283 41.667 0.00 0.00 0.00 3.41
137 142 4.946478 ATGTAGTGCTTCCTCTATCCAC 57.054 45.455 0.00 0.00 0.00 4.02
138 143 2.688446 TGTAGTGCTTCCTCTATCCACG 59.312 50.000 0.00 0.00 0.00 4.94
139 144 1.853963 AGTGCTTCCTCTATCCACGT 58.146 50.000 0.00 0.00 0.00 4.49
140 145 1.478510 AGTGCTTCCTCTATCCACGTG 59.521 52.381 9.08 9.08 0.00 4.49
141 146 0.175760 TGCTTCCTCTATCCACGTGC 59.824 55.000 10.91 0.00 0.00 5.34
142 147 0.461961 GCTTCCTCTATCCACGTGCT 59.538 55.000 10.91 1.67 0.00 4.40
143 148 1.134670 GCTTCCTCTATCCACGTGCTT 60.135 52.381 10.91 1.47 0.00 3.91
144 149 2.815478 CTTCCTCTATCCACGTGCTTC 58.185 52.381 10.91 0.00 0.00 3.86
145 150 1.847328 TCCTCTATCCACGTGCTTCA 58.153 50.000 10.91 0.00 0.00 3.02
146 151 2.176045 TCCTCTATCCACGTGCTTCAA 58.824 47.619 10.91 0.00 0.00 2.69
147 152 2.766263 TCCTCTATCCACGTGCTTCAAT 59.234 45.455 10.91 0.68 0.00 2.57
148 153 3.197766 TCCTCTATCCACGTGCTTCAATT 59.802 43.478 10.91 0.00 0.00 2.32
149 154 3.941483 CCTCTATCCACGTGCTTCAATTT 59.059 43.478 10.91 0.00 0.00 1.82
150 155 4.396166 CCTCTATCCACGTGCTTCAATTTT 59.604 41.667 10.91 0.00 0.00 1.82
151 156 5.295431 TCTATCCACGTGCTTCAATTTTG 57.705 39.130 10.91 0.00 0.00 2.44
152 157 5.000591 TCTATCCACGTGCTTCAATTTTGA 58.999 37.500 10.91 0.00 34.92 2.69
153 158 3.347958 TCCACGTGCTTCAATTTTGAC 57.652 42.857 10.91 0.00 36.83 3.18
154 159 2.034053 TCCACGTGCTTCAATTTTGACC 59.966 45.455 10.91 0.00 36.83 4.02
155 160 2.043411 CACGTGCTTCAATTTTGACCG 58.957 47.619 0.82 0.00 36.83 4.79
156 161 1.673920 ACGTGCTTCAATTTTGACCGT 59.326 42.857 0.00 0.00 36.83 4.83
157 162 2.873472 ACGTGCTTCAATTTTGACCGTA 59.127 40.909 0.00 0.00 36.83 4.02
158 163 3.312973 ACGTGCTTCAATTTTGACCGTAA 59.687 39.130 0.00 0.00 36.83 3.18
159 164 4.201930 ACGTGCTTCAATTTTGACCGTAAA 60.202 37.500 0.00 0.00 36.83 2.01
160 165 4.915085 CGTGCTTCAATTTTGACCGTAAAT 59.085 37.500 0.00 0.00 36.83 1.40
161 166 5.401079 CGTGCTTCAATTTTGACCGTAAATT 59.599 36.000 0.00 0.00 36.83 1.82
162 167 6.074569 CGTGCTTCAATTTTGACCGTAAATTT 60.075 34.615 0.00 0.00 36.83 1.82
163 168 7.113684 CGTGCTTCAATTTTGACCGTAAATTTA 59.886 33.333 0.00 0.00 36.83 1.40
164 169 8.756864 GTGCTTCAATTTTGACCGTAAATTTAA 58.243 29.630 0.00 0.00 36.83 1.52
165 170 8.756864 TGCTTCAATTTTGACCGTAAATTTAAC 58.243 29.630 0.00 0.00 36.83 2.01
166 171 8.974408 GCTTCAATTTTGACCGTAAATTTAACT 58.026 29.630 0.00 0.00 36.83 2.24
169 174 9.896263 TCAATTTTGACCGTAAATTTAACTACC 57.104 29.630 0.00 0.00 34.01 3.18
170 175 9.680315 CAATTTTGACCGTAAATTTAACTACCA 57.320 29.630 0.00 0.00 34.01 3.25
172 177 9.902196 ATTTTGACCGTAAATTTAACTACCAAG 57.098 29.630 0.00 0.00 0.00 3.61
173 178 8.674263 TTTGACCGTAAATTTAACTACCAAGA 57.326 30.769 0.00 0.00 0.00 3.02
174 179 7.656707 TGACCGTAAATTTAACTACCAAGAC 57.343 36.000 0.00 0.00 0.00 3.01
175 180 6.650390 TGACCGTAAATTTAACTACCAAGACC 59.350 38.462 0.00 0.00 0.00 3.85
176 181 5.639082 ACCGTAAATTTAACTACCAAGACCG 59.361 40.000 0.00 0.00 0.00 4.79
177 182 5.868801 CCGTAAATTTAACTACCAAGACCGA 59.131 40.000 0.00 0.00 0.00 4.69
178 183 6.536224 CCGTAAATTTAACTACCAAGACCGAT 59.464 38.462 0.00 0.00 0.00 4.18
179 184 7.064966 CCGTAAATTTAACTACCAAGACCGATT 59.935 37.037 0.00 0.00 0.00 3.34
180 185 7.901377 CGTAAATTTAACTACCAAGACCGATTG 59.099 37.037 0.00 0.00 0.00 2.67
181 186 5.813080 ATTTAACTACCAAGACCGATTGC 57.187 39.130 0.00 0.00 0.00 3.56
182 187 1.722011 AACTACCAAGACCGATTGCG 58.278 50.000 0.00 0.00 37.24 4.85
207 212 6.618287 CGGGAGCAAAAATTATATCAGTGA 57.382 37.500 0.00 0.00 0.00 3.41
208 213 7.026631 CGGGAGCAAAAATTATATCAGTGAA 57.973 36.000 0.00 0.00 0.00 3.18
209 214 7.651808 CGGGAGCAAAAATTATATCAGTGAAT 58.348 34.615 0.00 0.00 0.00 2.57
210 215 8.137437 CGGGAGCAAAAATTATATCAGTGAATT 58.863 33.333 0.00 0.00 0.00 2.17
211 216 9.468532 GGGAGCAAAAATTATATCAGTGAATTC 57.531 33.333 0.00 0.00 0.00 2.17
212 217 9.173939 GGAGCAAAAATTATATCAGTGAATTCG 57.826 33.333 0.00 0.00 0.00 3.34
213 218 9.722056 GAGCAAAAATTATATCAGTGAATTCGT 57.278 29.630 0.00 0.00 0.00 3.85
261 266 2.697431 TTTTTCTCCCGTCGCAATTG 57.303 45.000 0.00 0.00 0.00 2.32
262 267 0.878416 TTTTCTCCCGTCGCAATTGG 59.122 50.000 7.72 0.00 0.00 3.16
263 268 0.250553 TTTCTCCCGTCGCAATTGGT 60.251 50.000 7.72 0.00 0.00 3.67
264 269 0.672401 TTCTCCCGTCGCAATTGGTC 60.672 55.000 7.72 0.00 0.00 4.02
265 270 1.079127 CTCCCGTCGCAATTGGTCT 60.079 57.895 7.72 0.00 0.00 3.85
266 271 1.079405 TCCCGTCGCAATTGGTCTC 60.079 57.895 7.72 0.00 0.00 3.36
267 272 2.452813 CCCGTCGCAATTGGTCTCG 61.453 63.158 7.72 2.11 0.00 4.04
268 273 1.736645 CCGTCGCAATTGGTCTCGT 60.737 57.895 7.72 0.00 0.00 4.18
269 274 1.289109 CCGTCGCAATTGGTCTCGTT 61.289 55.000 7.72 0.00 0.00 3.85
270 275 0.179250 CGTCGCAATTGGTCTCGTTG 60.179 55.000 7.72 0.00 0.00 4.10
271 276 0.165944 GTCGCAATTGGTCTCGTTGG 59.834 55.000 7.72 0.00 0.00 3.77
272 277 0.250124 TCGCAATTGGTCTCGTTGGT 60.250 50.000 7.72 0.00 0.00 3.67
273 278 0.591170 CGCAATTGGTCTCGTTGGTT 59.409 50.000 7.72 0.00 0.00 3.67
274 279 1.801771 CGCAATTGGTCTCGTTGGTTA 59.198 47.619 7.72 0.00 0.00 2.85
275 280 2.224549 CGCAATTGGTCTCGTTGGTTAA 59.775 45.455 7.72 0.00 0.00 2.01
276 281 3.304123 CGCAATTGGTCTCGTTGGTTAAA 60.304 43.478 7.72 0.00 0.00 1.52
277 282 4.614993 CGCAATTGGTCTCGTTGGTTAAAT 60.615 41.667 7.72 0.00 0.00 1.40
278 283 5.227152 GCAATTGGTCTCGTTGGTTAAATT 58.773 37.500 7.72 0.00 0.00 1.82
279 284 5.694458 GCAATTGGTCTCGTTGGTTAAATTT 59.306 36.000 7.72 0.00 0.00 1.82
280 285 6.864165 GCAATTGGTCTCGTTGGTTAAATTTA 59.136 34.615 7.72 0.00 0.00 1.40
281 286 7.148869 GCAATTGGTCTCGTTGGTTAAATTTAC 60.149 37.037 7.72 0.00 0.00 2.01
282 287 5.594724 TGGTCTCGTTGGTTAAATTTACG 57.405 39.130 0.00 0.61 0.00 3.18
283 288 4.451774 TGGTCTCGTTGGTTAAATTTACGG 59.548 41.667 9.79 2.88 33.37 4.02
284 289 4.452114 GGTCTCGTTGGTTAAATTTACGGT 59.548 41.667 9.79 0.00 33.37 4.83
285 290 5.389830 GGTCTCGTTGGTTAAATTTACGGTC 60.390 44.000 9.79 2.84 33.37 4.79
286 291 5.177327 GTCTCGTTGGTTAAATTTACGGTCA 59.823 40.000 9.79 0.00 33.37 4.02
287 292 5.757320 TCTCGTTGGTTAAATTTACGGTCAA 59.243 36.000 9.79 4.76 33.37 3.18
288 293 6.259608 TCTCGTTGGTTAAATTTACGGTCAAA 59.740 34.615 9.79 0.00 33.37 2.69
289 294 6.428799 TCGTTGGTTAAATTTACGGTCAAAG 58.571 36.000 9.79 8.60 33.37 2.77
290 295 6.038050 TCGTTGGTTAAATTTACGGTCAAAGT 59.962 34.615 9.79 0.00 33.37 2.66
291 296 6.692249 CGTTGGTTAAATTTACGGTCAAAGTT 59.308 34.615 0.00 0.00 31.36 2.66
292 297 7.305533 CGTTGGTTAAATTTACGGTCAAAGTTG 60.306 37.037 0.00 0.00 29.44 3.16
293 298 7.330900 TGGTTAAATTTACGGTCAAAGTTGA 57.669 32.000 0.00 0.00 34.20 3.18
294 299 7.769220 TGGTTAAATTTACGGTCAAAGTTGAA 58.231 30.769 0.00 0.00 39.21 2.69
295 300 8.414778 TGGTTAAATTTACGGTCAAAGTTGAAT 58.585 29.630 0.00 0.00 39.21 2.57
296 301 8.908678 GGTTAAATTTACGGTCAAAGTTGAATC 58.091 33.333 0.00 0.00 39.21 2.52
297 302 9.673454 GTTAAATTTACGGTCAAAGTTGAATCT 57.327 29.630 0.00 0.00 39.21 2.40
298 303 9.887406 TTAAATTTACGGTCAAAGTTGAATCTC 57.113 29.630 0.00 0.00 39.21 2.75
299 304 5.585500 TTTACGGTCAAAGTTGAATCTCG 57.415 39.130 0.00 1.51 39.21 4.04
300 305 2.413837 ACGGTCAAAGTTGAATCTCGG 58.586 47.619 0.00 0.00 39.21 4.63
301 306 2.036733 ACGGTCAAAGTTGAATCTCGGA 59.963 45.455 0.00 0.00 39.21 4.55
302 307 3.064207 CGGTCAAAGTTGAATCTCGGAA 58.936 45.455 0.00 0.00 39.21 4.30
303 308 3.496884 CGGTCAAAGTTGAATCTCGGAAA 59.503 43.478 0.00 0.00 39.21 3.13
304 309 4.377431 CGGTCAAAGTTGAATCTCGGAAAG 60.377 45.833 0.00 0.00 39.21 2.62
305 310 4.467735 GTCAAAGTTGAATCTCGGAAAGC 58.532 43.478 0.00 0.00 39.21 3.51
306 311 4.024048 GTCAAAGTTGAATCTCGGAAAGCA 60.024 41.667 0.00 0.00 39.21 3.91
307 312 4.761739 TCAAAGTTGAATCTCGGAAAGCAT 59.238 37.500 0.00 0.00 33.55 3.79
308 313 4.691860 AAGTTGAATCTCGGAAAGCATG 57.308 40.909 0.00 0.00 0.00 4.06
309 314 3.012518 AGTTGAATCTCGGAAAGCATGG 58.987 45.455 0.00 0.00 0.00 3.66
310 315 3.009723 GTTGAATCTCGGAAAGCATGGA 58.990 45.455 0.00 0.00 0.00 3.41
311 316 2.632377 TGAATCTCGGAAAGCATGGAC 58.368 47.619 0.00 0.00 0.00 4.02
312 317 1.594862 GAATCTCGGAAAGCATGGACG 59.405 52.381 0.00 0.00 0.00 4.79
313 318 0.811616 ATCTCGGAAAGCATGGACGC 60.812 55.000 0.00 0.00 0.00 5.19
314 319 1.741401 CTCGGAAAGCATGGACGCA 60.741 57.895 0.00 0.00 0.00 5.24
315 320 1.298157 CTCGGAAAGCATGGACGCAA 61.298 55.000 0.00 0.00 0.00 4.85
316 321 0.676466 TCGGAAAGCATGGACGCAAT 60.676 50.000 0.00 0.00 0.00 3.56
317 322 1.013596 CGGAAAGCATGGACGCAATA 58.986 50.000 0.00 0.00 0.00 1.90
318 323 1.603802 CGGAAAGCATGGACGCAATAT 59.396 47.619 0.00 0.00 0.00 1.28
319 324 2.805671 CGGAAAGCATGGACGCAATATA 59.194 45.455 0.00 0.00 0.00 0.86
320 325 3.436704 CGGAAAGCATGGACGCAATATAT 59.563 43.478 0.00 0.00 0.00 0.86
321 326 4.083324 CGGAAAGCATGGACGCAATATATT 60.083 41.667 0.00 0.00 0.00 1.28
322 327 5.562696 CGGAAAGCATGGACGCAATATATTT 60.563 40.000 0.00 0.00 0.00 1.40
323 328 6.215845 GGAAAGCATGGACGCAATATATTTT 58.784 36.000 0.00 0.00 0.00 1.82
324 329 7.367285 GGAAAGCATGGACGCAATATATTTTA 58.633 34.615 0.00 0.00 0.00 1.52
325 330 7.538678 GGAAAGCATGGACGCAATATATTTTAG 59.461 37.037 0.00 0.00 0.00 1.85
326 331 7.744087 AAGCATGGACGCAATATATTTTAGA 57.256 32.000 0.00 0.00 0.00 2.10
327 332 7.744087 AGCATGGACGCAATATATTTTAGAA 57.256 32.000 0.00 0.00 0.00 2.10
328 333 8.340618 AGCATGGACGCAATATATTTTAGAAT 57.659 30.769 0.00 0.00 0.00 2.40
329 334 8.239314 AGCATGGACGCAATATATTTTAGAATG 58.761 33.333 0.00 0.00 0.00 2.67
330 335 7.485913 GCATGGACGCAATATATTTTAGAATGG 59.514 37.037 0.00 0.00 0.00 3.16
331 336 8.729756 CATGGACGCAATATATTTTAGAATGGA 58.270 33.333 0.00 0.00 0.00 3.41
332 337 8.322906 TGGACGCAATATATTTTAGAATGGAG 57.677 34.615 0.00 0.00 0.00 3.86
333 338 8.154203 TGGACGCAATATATTTTAGAATGGAGA 58.846 33.333 0.00 0.00 0.00 3.71
334 339 8.660373 GGACGCAATATATTTTAGAATGGAGAG 58.340 37.037 0.00 0.00 0.00 3.20
335 340 9.424319 GACGCAATATATTTTAGAATGGAGAGA 57.576 33.333 0.00 0.00 0.00 3.10
336 341 9.429359 ACGCAATATATTTTAGAATGGAGAGAG 57.571 33.333 0.00 0.00 0.00 3.20
419 424 1.816863 AACAGTCCATGACGAGCGGT 61.817 55.000 0.00 0.00 37.67 5.68
467 473 0.386476 GGTTCCCACCACCGAAAAAC 59.614 55.000 0.00 0.00 43.61 2.43
469 475 0.259356 TTCCCACCACCGAAAAACCT 59.741 50.000 0.00 0.00 0.00 3.50
499 508 0.242825 TGACGGTACCGAAGAAGCTG 59.757 55.000 39.52 8.75 42.83 4.24
643 652 3.357079 CTGGCCAGCGGAACACAC 61.357 66.667 22.33 0.00 0.00 3.82
644 653 4.182433 TGGCCAGCGGAACACACA 62.182 61.111 0.00 0.00 0.00 3.72
645 654 2.672996 GGCCAGCGGAACACACAT 60.673 61.111 0.00 0.00 0.00 3.21
646 655 2.690778 GGCCAGCGGAACACACATC 61.691 63.158 0.00 0.00 0.00 3.06
648 657 1.915614 GCCAGCGGAACACACATCAG 61.916 60.000 0.00 0.00 0.00 2.90
649 658 1.300971 CCAGCGGAACACACATCAGG 61.301 60.000 0.00 0.00 0.00 3.86
650 659 1.672356 AGCGGAACACACATCAGGC 60.672 57.895 0.00 0.00 0.00 4.85
651 660 2.690778 GCGGAACACACATCAGGCC 61.691 63.158 0.00 0.00 0.00 5.19
652 661 1.302431 CGGAACACACATCAGGCCA 60.302 57.895 5.01 0.00 0.00 5.36
653 662 1.577328 CGGAACACACATCAGGCCAC 61.577 60.000 5.01 0.00 0.00 5.01
654 663 1.577328 GGAACACACATCAGGCCACG 61.577 60.000 5.01 0.00 0.00 4.94
655 664 0.602638 GAACACACATCAGGCCACGA 60.603 55.000 5.01 0.06 0.00 4.35
656 665 0.603707 AACACACATCAGGCCACGAG 60.604 55.000 5.01 0.00 0.00 4.18
746 759 1.000771 AGCTGAGCGGAGTAGGTCA 60.001 57.895 0.00 0.00 45.06 4.02
835 850 4.410400 CCTCCTTGACGCCACCCC 62.410 72.222 0.00 0.00 0.00 4.95
836 851 3.322466 CTCCTTGACGCCACCCCT 61.322 66.667 0.00 0.00 0.00 4.79
837 852 3.612247 CTCCTTGACGCCACCCCTG 62.612 68.421 0.00 0.00 0.00 4.45
838 853 4.722700 CCTTGACGCCACCCCTGG 62.723 72.222 0.00 0.00 41.13 4.45
901 947 3.288308 CTCCGCCACGCACTTCTCT 62.288 63.158 0.00 0.00 0.00 3.10
1605 1678 2.684735 GAGGTCGTCTCCTCCCCT 59.315 66.667 11.06 0.00 45.84 4.79
1616 1689 0.547712 TCCTCCCCTGACCTCTTTGG 60.548 60.000 0.00 0.00 42.93 3.28
1618 1691 1.463214 TCCCCTGACCTCTTTGGCA 60.463 57.895 0.00 0.00 40.22 4.92
1647 1720 1.358725 CGCAATTCGTCACCGGTGAT 61.359 55.000 38.11 21.20 42.18 3.06
1838 1911 3.889815 ACGATCCCAATGTCACAATCAT 58.110 40.909 0.00 0.00 0.00 2.45
1884 1957 0.535335 TGGCACCTTCGGATGTCTAC 59.465 55.000 0.00 0.00 0.00 2.59
1890 1963 0.527817 CTTCGGATGTCTACGCCACC 60.528 60.000 0.00 0.00 0.00 4.61
2067 2140 2.233271 CTCAACAACCAGACTGCCATT 58.767 47.619 0.00 0.00 0.00 3.16
2161 2234 1.823250 GCACTGTGGGTTCTGGGATTT 60.823 52.381 10.21 0.00 0.00 2.17
2631 2704 0.179000 ATGAGTCACGGATCCTTGGC 59.821 55.000 14.77 14.77 0.00 4.52
3929 4033 6.418946 TGCTATGTGTTATTGACCCAACATA 58.581 36.000 0.00 0.00 37.04 2.29
3962 4066 4.676546 TGAGAAAGATAGAGTGATGTGCG 58.323 43.478 0.00 0.00 0.00 5.34
4029 4133 2.093500 TCCGAATCCTGGTGATTGACAG 60.093 50.000 0.00 0.00 43.81 3.51
4073 4177 6.653020 TCTCAGAGCAATTTATTCTGCCTTA 58.347 36.000 0.00 0.00 39.47 2.69
4074 4178 6.540189 TCTCAGAGCAATTTATTCTGCCTTAC 59.460 38.462 0.00 0.00 39.47 2.34
4075 4179 5.590259 TCAGAGCAATTTATTCTGCCTTACC 59.410 40.000 5.96 0.00 39.47 2.85
4213 4433 0.392706 TGCTGTGTTCCATGTCGTCT 59.607 50.000 0.00 0.00 0.00 4.18
4225 4445 4.750098 TCCATGTCGTCTTTGTCTTTTCTC 59.250 41.667 0.00 0.00 0.00 2.87
4282 4502 5.174398 GCAGACATCAATTGTTTGTGAGTTG 59.826 40.000 17.47 12.23 41.37 3.16
4283 4503 6.267817 CAGACATCAATTGTTTGTGAGTTGT 58.732 36.000 17.47 5.10 39.18 3.32
4284 4504 6.753279 CAGACATCAATTGTTTGTGAGTTGTT 59.247 34.615 17.47 0.00 39.18 2.83
4285 4505 6.753279 AGACATCAATTGTTTGTGAGTTGTTG 59.247 34.615 17.47 0.00 39.18 3.33
4286 4506 6.397272 ACATCAATTGTTTGTGAGTTGTTGT 58.603 32.000 13.51 0.00 33.74 3.32
4287 4507 7.542890 ACATCAATTGTTTGTGAGTTGTTGTA 58.457 30.769 13.51 0.00 33.74 2.41
4288 4508 7.487829 ACATCAATTGTTTGTGAGTTGTTGTAC 59.512 33.333 13.51 0.00 33.74 2.90
4289 4509 7.151999 TCAATTGTTTGTGAGTTGTTGTACT 57.848 32.000 5.13 0.00 34.32 2.73
4290 4510 7.598278 TCAATTGTTTGTGAGTTGTTGTACTT 58.402 30.769 5.13 0.00 34.32 2.24
4291 4511 8.731605 TCAATTGTTTGTGAGTTGTTGTACTTA 58.268 29.630 5.13 0.00 34.32 2.24
4320 4540 1.275421 TGCCATTATCCGGACACCCA 61.275 55.000 6.12 0.00 0.00 4.51
4339 4559 3.005554 CCATTGTCTGTCTACTTGCAGG 58.994 50.000 0.00 0.00 33.81 4.85
4373 4593 6.560253 TGTTTAAGTTTCTTGATCCAGAGC 57.440 37.500 0.00 0.00 0.00 4.09
4444 4674 0.179134 AGCGCATGAACTAGGACGTC 60.179 55.000 11.47 7.13 0.00 4.34
4664 4940 3.559655 CGTTTCGGGAAGCATTGATCATA 59.440 43.478 0.00 0.00 0.00 2.15
4665 4941 4.319046 CGTTTCGGGAAGCATTGATCATAG 60.319 45.833 0.00 0.00 0.00 2.23
4666 4942 4.687901 TTCGGGAAGCATTGATCATAGA 57.312 40.909 0.00 0.00 0.00 1.98
4667 4943 4.897509 TCGGGAAGCATTGATCATAGAT 57.102 40.909 0.00 0.00 0.00 1.98
4668 4944 4.572909 TCGGGAAGCATTGATCATAGATG 58.427 43.478 0.00 0.00 0.00 2.90
4669 4945 3.126514 CGGGAAGCATTGATCATAGATGC 59.873 47.826 18.97 18.97 44.89 3.91
4672 4948 2.539346 GCATTGATCATAGATGCGGC 57.461 50.000 13.56 0.00 37.09 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.267121 TAGCACCAGAACAGGGTCTC 58.733 55.000 0.00 0.00 36.19 3.36
82 87 3.514309 GGGAGTATAATATGGACAGCCGT 59.486 47.826 0.00 0.00 36.79 5.68
83 88 3.769844 AGGGAGTATAATATGGACAGCCG 59.230 47.826 0.00 0.00 36.79 5.52
84 89 4.162509 GGAGGGAGTATAATATGGACAGCC 59.837 50.000 0.00 0.00 0.00 4.85
85 90 4.777896 TGGAGGGAGTATAATATGGACAGC 59.222 45.833 0.00 0.00 0.00 4.40
86 91 7.502060 AATGGAGGGAGTATAATATGGACAG 57.498 40.000 0.00 0.00 0.00 3.51
87 92 6.154534 CGAATGGAGGGAGTATAATATGGACA 59.845 42.308 0.00 0.00 0.00 4.02
88 93 6.380274 TCGAATGGAGGGAGTATAATATGGAC 59.620 42.308 0.00 0.00 0.00 4.02
93 98 7.234782 ACATTGTCGAATGGAGGGAGTATAATA 59.765 37.037 2.35 0.00 43.00 0.98
105 110 3.610040 AGCACTACATTGTCGAATGGA 57.390 42.857 2.35 0.00 43.00 3.41
106 111 3.063997 GGAAGCACTACATTGTCGAATGG 59.936 47.826 2.35 0.00 43.00 3.16
107 112 3.935203 AGGAAGCACTACATTGTCGAATG 59.065 43.478 0.00 0.00 44.11 2.67
108 113 4.081420 AGAGGAAGCACTACATTGTCGAAT 60.081 41.667 0.00 0.00 0.00 3.34
109 114 3.258372 AGAGGAAGCACTACATTGTCGAA 59.742 43.478 0.00 0.00 0.00 3.71
110 115 2.826128 AGAGGAAGCACTACATTGTCGA 59.174 45.455 0.00 0.00 0.00 4.20
111 116 3.238108 AGAGGAAGCACTACATTGTCG 57.762 47.619 0.00 0.00 0.00 4.35
112 117 5.163405 TGGATAGAGGAAGCACTACATTGTC 60.163 44.000 0.00 0.00 0.00 3.18
113 118 4.716784 TGGATAGAGGAAGCACTACATTGT 59.283 41.667 0.00 0.00 0.00 2.71
114 119 5.053145 GTGGATAGAGGAAGCACTACATTG 58.947 45.833 0.00 0.00 0.00 2.82
115 120 4.202161 CGTGGATAGAGGAAGCACTACATT 60.202 45.833 0.00 0.00 0.00 2.71
116 121 3.319405 CGTGGATAGAGGAAGCACTACAT 59.681 47.826 0.00 0.00 0.00 2.29
117 122 2.688446 CGTGGATAGAGGAAGCACTACA 59.312 50.000 0.00 0.00 0.00 2.74
118 123 2.688958 ACGTGGATAGAGGAAGCACTAC 59.311 50.000 0.00 0.00 0.00 2.73
119 124 2.688446 CACGTGGATAGAGGAAGCACTA 59.312 50.000 7.95 0.00 0.00 2.74
120 125 1.478510 CACGTGGATAGAGGAAGCACT 59.521 52.381 7.95 0.00 0.00 4.40
121 126 1.927895 CACGTGGATAGAGGAAGCAC 58.072 55.000 7.95 0.00 0.00 4.40
122 127 0.175760 GCACGTGGATAGAGGAAGCA 59.824 55.000 18.88 0.00 0.00 3.91
123 128 0.461961 AGCACGTGGATAGAGGAAGC 59.538 55.000 18.88 0.00 0.00 3.86
124 129 2.166459 TGAAGCACGTGGATAGAGGAAG 59.834 50.000 18.88 0.00 0.00 3.46
125 130 2.176045 TGAAGCACGTGGATAGAGGAA 58.824 47.619 18.88 0.00 0.00 3.36
126 131 1.847328 TGAAGCACGTGGATAGAGGA 58.153 50.000 18.88 0.00 0.00 3.71
127 132 2.672961 TTGAAGCACGTGGATAGAGG 57.327 50.000 18.88 0.00 0.00 3.69
128 133 5.122239 TCAAAATTGAAGCACGTGGATAGAG 59.878 40.000 18.88 0.00 33.55 2.43
129 134 5.000591 TCAAAATTGAAGCACGTGGATAGA 58.999 37.500 18.88 0.00 33.55 1.98
130 135 5.088739 GTCAAAATTGAAGCACGTGGATAG 58.911 41.667 18.88 0.00 39.21 2.08
131 136 4.083003 GGTCAAAATTGAAGCACGTGGATA 60.083 41.667 18.88 0.00 39.21 2.59
132 137 3.305335 GGTCAAAATTGAAGCACGTGGAT 60.305 43.478 18.88 0.00 39.21 3.41
133 138 2.034053 GGTCAAAATTGAAGCACGTGGA 59.966 45.455 18.88 0.00 39.21 4.02
134 139 2.393764 GGTCAAAATTGAAGCACGTGG 58.606 47.619 18.88 0.00 39.21 4.94
135 140 2.043411 CGGTCAAAATTGAAGCACGTG 58.957 47.619 12.28 12.28 39.21 4.49
136 141 1.673920 ACGGTCAAAATTGAAGCACGT 59.326 42.857 0.00 4.44 39.21 4.49
137 142 2.399396 ACGGTCAAAATTGAAGCACG 57.601 45.000 0.00 3.88 39.21 5.34
138 143 6.763303 AATTTACGGTCAAAATTGAAGCAC 57.237 33.333 0.00 0.00 39.21 4.40
139 144 8.756864 GTTAAATTTACGGTCAAAATTGAAGCA 58.243 29.630 0.00 0.00 39.21 3.91
140 145 8.974408 AGTTAAATTTACGGTCAAAATTGAAGC 58.026 29.630 0.00 0.00 39.21 3.86
143 148 9.896263 GGTAGTTAAATTTACGGTCAAAATTGA 57.104 29.630 0.00 0.00 36.81 2.57
144 149 9.680315 TGGTAGTTAAATTTACGGTCAAAATTG 57.320 29.630 0.00 0.00 36.81 2.32
146 151 9.902196 CTTGGTAGTTAAATTTACGGTCAAAAT 57.098 29.630 0.00 0.00 0.00 1.82
147 152 9.118300 TCTTGGTAGTTAAATTTACGGTCAAAA 57.882 29.630 0.00 0.00 0.00 2.44
148 153 8.558700 GTCTTGGTAGTTAAATTTACGGTCAAA 58.441 33.333 0.00 0.00 0.00 2.69
149 154 7.173047 GGTCTTGGTAGTTAAATTTACGGTCAA 59.827 37.037 0.00 0.00 0.00 3.18
150 155 6.650390 GGTCTTGGTAGTTAAATTTACGGTCA 59.350 38.462 0.00 0.00 0.00 4.02
151 156 6.183360 CGGTCTTGGTAGTTAAATTTACGGTC 60.183 42.308 0.00 0.00 0.00 4.79
152 157 5.639082 CGGTCTTGGTAGTTAAATTTACGGT 59.361 40.000 0.00 0.00 0.00 4.83
153 158 5.868801 TCGGTCTTGGTAGTTAAATTTACGG 59.131 40.000 0.00 0.00 0.00 4.02
154 159 6.949578 TCGGTCTTGGTAGTTAAATTTACG 57.050 37.500 0.00 0.00 0.00 3.18
155 160 7.695201 GCAATCGGTCTTGGTAGTTAAATTTAC 59.305 37.037 0.00 0.00 0.00 2.01
156 161 7.413219 CGCAATCGGTCTTGGTAGTTAAATTTA 60.413 37.037 0.00 0.00 0.00 1.40
157 162 6.617879 GCAATCGGTCTTGGTAGTTAAATTT 58.382 36.000 0.00 0.00 0.00 1.82
158 163 5.163794 CGCAATCGGTCTTGGTAGTTAAATT 60.164 40.000 0.00 0.00 0.00 1.82
159 164 4.331717 CGCAATCGGTCTTGGTAGTTAAAT 59.668 41.667 0.00 0.00 0.00 1.40
160 165 3.680937 CGCAATCGGTCTTGGTAGTTAAA 59.319 43.478 0.00 0.00 0.00 1.52
161 166 3.255725 CGCAATCGGTCTTGGTAGTTAA 58.744 45.455 0.00 0.00 0.00 2.01
162 167 2.883574 CGCAATCGGTCTTGGTAGTTA 58.116 47.619 0.00 0.00 0.00 2.24
163 168 1.722011 CGCAATCGGTCTTGGTAGTT 58.278 50.000 0.00 0.00 0.00 2.24
164 169 3.436001 CGCAATCGGTCTTGGTAGT 57.564 52.632 0.00 0.00 0.00 2.73
176 181 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
177 182 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
178 183 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
179 184 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
180 185 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
181 186 3.252215 TGATATAATTTTTGCTCCCGCCG 59.748 43.478 0.00 0.00 34.43 6.46
182 187 4.278419 ACTGATATAATTTTTGCTCCCGCC 59.722 41.667 0.00 0.00 34.43 6.13
183 188 5.008613 TCACTGATATAATTTTTGCTCCCGC 59.991 40.000 0.00 0.00 0.00 6.13
184 189 6.618287 TCACTGATATAATTTTTGCTCCCG 57.382 37.500 0.00 0.00 0.00 5.14
185 190 9.468532 GAATTCACTGATATAATTTTTGCTCCC 57.531 33.333 0.00 0.00 0.00 4.30
186 191 9.173939 CGAATTCACTGATATAATTTTTGCTCC 57.826 33.333 6.22 0.00 0.00 4.70
187 192 9.722056 ACGAATTCACTGATATAATTTTTGCTC 57.278 29.630 6.22 0.00 0.00 4.26
242 247 1.268352 CCAATTGCGACGGGAGAAAAA 59.732 47.619 0.00 0.00 0.00 1.94
243 248 0.878416 CCAATTGCGACGGGAGAAAA 59.122 50.000 0.00 0.00 0.00 2.29
244 249 0.250553 ACCAATTGCGACGGGAGAAA 60.251 50.000 0.00 0.00 0.00 2.52
245 250 0.672401 GACCAATTGCGACGGGAGAA 60.672 55.000 0.00 0.00 0.00 2.87
246 251 1.079405 GACCAATTGCGACGGGAGA 60.079 57.895 0.00 0.00 0.00 3.71
247 252 1.079127 AGACCAATTGCGACGGGAG 60.079 57.895 0.00 0.00 0.00 4.30
248 253 1.079405 GAGACCAATTGCGACGGGA 60.079 57.895 0.00 0.00 0.00 5.14
249 254 2.452813 CGAGACCAATTGCGACGGG 61.453 63.158 0.00 0.00 0.00 5.28
250 255 1.289109 AACGAGACCAATTGCGACGG 61.289 55.000 9.68 0.00 0.00 4.79
251 256 0.179250 CAACGAGACCAATTGCGACG 60.179 55.000 9.68 9.65 0.00 5.12
252 257 0.165944 CCAACGAGACCAATTGCGAC 59.834 55.000 9.68 0.37 0.00 5.19
253 258 0.250124 ACCAACGAGACCAATTGCGA 60.250 50.000 9.68 0.00 0.00 5.10
254 259 0.591170 AACCAACGAGACCAATTGCG 59.409 50.000 0.00 0.47 0.00 4.85
255 260 3.907894 TTAACCAACGAGACCAATTGC 57.092 42.857 0.00 0.00 0.00 3.56
256 261 7.060174 CGTAAATTTAACCAACGAGACCAATTG 59.940 37.037 4.77 0.00 35.66 2.32
257 262 7.079475 CGTAAATTTAACCAACGAGACCAATT 58.921 34.615 4.77 0.00 35.66 2.32
258 263 6.348704 CCGTAAATTTAACCAACGAGACCAAT 60.349 38.462 11.09 0.00 35.66 3.16
259 264 5.049543 CCGTAAATTTAACCAACGAGACCAA 60.050 40.000 11.09 0.00 35.66 3.67
260 265 4.451774 CCGTAAATTTAACCAACGAGACCA 59.548 41.667 11.09 0.00 35.66 4.02
261 266 4.452114 ACCGTAAATTTAACCAACGAGACC 59.548 41.667 11.09 0.00 35.66 3.85
262 267 5.177327 TGACCGTAAATTTAACCAACGAGAC 59.823 40.000 11.09 4.23 35.66 3.36
263 268 5.295950 TGACCGTAAATTTAACCAACGAGA 58.704 37.500 11.09 0.00 35.66 4.04
264 269 5.594724 TGACCGTAAATTTAACCAACGAG 57.405 39.130 11.09 5.19 35.66 4.18
265 270 5.998454 TTGACCGTAAATTTAACCAACGA 57.002 34.783 11.09 0.00 35.66 3.85
266 271 6.200808 ACTTTGACCGTAAATTTAACCAACG 58.799 36.000 0.00 1.44 0.00 4.10
267 272 7.701501 TCAACTTTGACCGTAAATTTAACCAAC 59.298 33.333 0.00 0.00 31.01 3.77
268 273 7.769220 TCAACTTTGACCGTAAATTTAACCAA 58.231 30.769 0.00 0.05 31.01 3.67
269 274 7.330900 TCAACTTTGACCGTAAATTTAACCA 57.669 32.000 0.00 0.00 31.01 3.67
270 275 8.806177 ATTCAACTTTGACCGTAAATTTAACC 57.194 30.769 0.00 0.00 36.83 2.85
271 276 9.673454 AGATTCAACTTTGACCGTAAATTTAAC 57.327 29.630 0.00 0.00 36.83 2.01
272 277 9.887406 GAGATTCAACTTTGACCGTAAATTTAA 57.113 29.630 0.00 0.00 36.83 1.52
273 278 8.225107 CGAGATTCAACTTTGACCGTAAATTTA 58.775 33.333 0.00 0.00 36.83 1.40
274 279 7.075741 CGAGATTCAACTTTGACCGTAAATTT 58.924 34.615 0.00 0.00 36.83 1.82
275 280 6.348213 CCGAGATTCAACTTTGACCGTAAATT 60.348 38.462 0.00 0.00 36.83 1.82
276 281 5.121768 CCGAGATTCAACTTTGACCGTAAAT 59.878 40.000 0.00 0.00 36.83 1.40
277 282 4.449743 CCGAGATTCAACTTTGACCGTAAA 59.550 41.667 0.00 0.00 36.83 2.01
278 283 3.991773 CCGAGATTCAACTTTGACCGTAA 59.008 43.478 0.00 0.00 36.83 3.18
279 284 3.256383 TCCGAGATTCAACTTTGACCGTA 59.744 43.478 0.00 0.00 36.83 4.02
280 285 2.036733 TCCGAGATTCAACTTTGACCGT 59.963 45.455 0.00 0.00 36.83 4.83
281 286 2.683968 TCCGAGATTCAACTTTGACCG 58.316 47.619 0.00 0.00 36.83 4.79
282 287 4.613850 GCTTTCCGAGATTCAACTTTGACC 60.614 45.833 0.00 0.00 36.83 4.02
283 288 4.024048 TGCTTTCCGAGATTCAACTTTGAC 60.024 41.667 0.00 0.00 36.83 3.18
284 289 4.133820 TGCTTTCCGAGATTCAACTTTGA 58.866 39.130 0.00 0.00 34.92 2.69
285 290 4.488126 TGCTTTCCGAGATTCAACTTTG 57.512 40.909 0.00 0.00 0.00 2.77
286 291 4.082571 CCATGCTTTCCGAGATTCAACTTT 60.083 41.667 0.00 0.00 0.00 2.66
287 292 3.441572 CCATGCTTTCCGAGATTCAACTT 59.558 43.478 0.00 0.00 0.00 2.66
288 293 3.012518 CCATGCTTTCCGAGATTCAACT 58.987 45.455 0.00 0.00 0.00 3.16
289 294 3.009723 TCCATGCTTTCCGAGATTCAAC 58.990 45.455 0.00 0.00 0.00 3.18
290 295 3.009723 GTCCATGCTTTCCGAGATTCAA 58.990 45.455 0.00 0.00 0.00 2.69
291 296 2.632377 GTCCATGCTTTCCGAGATTCA 58.368 47.619 0.00 0.00 0.00 2.57
292 297 1.594862 CGTCCATGCTTTCCGAGATTC 59.405 52.381 0.00 0.00 0.00 2.52
293 298 1.656652 CGTCCATGCTTTCCGAGATT 58.343 50.000 0.00 0.00 0.00 2.40
294 299 0.811616 GCGTCCATGCTTTCCGAGAT 60.812 55.000 0.00 0.00 0.00 2.75
295 300 1.447838 GCGTCCATGCTTTCCGAGA 60.448 57.895 0.00 0.00 0.00 4.04
296 301 1.298157 TTGCGTCCATGCTTTCCGAG 61.298 55.000 0.00 0.00 35.36 4.63
297 302 0.676466 ATTGCGTCCATGCTTTCCGA 60.676 50.000 0.00 0.00 35.36 4.55
298 303 1.013596 TATTGCGTCCATGCTTTCCG 58.986 50.000 0.00 0.00 35.36 4.30
299 304 5.376854 AATATATTGCGTCCATGCTTTCC 57.623 39.130 0.00 0.00 35.36 3.13
300 305 8.289618 TCTAAAATATATTGCGTCCATGCTTTC 58.710 33.333 0.00 0.00 35.36 2.62
301 306 8.165239 TCTAAAATATATTGCGTCCATGCTTT 57.835 30.769 0.00 0.00 35.36 3.51
302 307 7.744087 TCTAAAATATATTGCGTCCATGCTT 57.256 32.000 0.00 0.00 35.36 3.91
303 308 7.744087 TTCTAAAATATATTGCGTCCATGCT 57.256 32.000 0.00 0.00 35.36 3.79
304 309 7.485913 CCATTCTAAAATATATTGCGTCCATGC 59.514 37.037 0.00 0.00 0.00 4.06
305 310 8.729756 TCCATTCTAAAATATATTGCGTCCATG 58.270 33.333 0.00 0.00 0.00 3.66
306 311 8.862325 TCCATTCTAAAATATATTGCGTCCAT 57.138 30.769 0.00 0.00 0.00 3.41
307 312 8.154203 TCTCCATTCTAAAATATATTGCGTCCA 58.846 33.333 0.00 0.00 0.00 4.02
308 313 8.547967 TCTCCATTCTAAAATATATTGCGTCC 57.452 34.615 0.00 0.00 0.00 4.79
309 314 9.424319 TCTCTCCATTCTAAAATATATTGCGTC 57.576 33.333 0.00 0.00 0.00 5.19
310 315 9.429359 CTCTCTCCATTCTAAAATATATTGCGT 57.571 33.333 0.00 0.00 0.00 5.24
311 316 9.429359 ACTCTCTCCATTCTAAAATATATTGCG 57.571 33.333 0.00 0.00 0.00 4.85
318 323 9.869667 AGCTAGTACTCTCTCCATTCTAAAATA 57.130 33.333 0.00 0.00 0.00 1.40
319 324 8.637986 CAGCTAGTACTCTCTCCATTCTAAAAT 58.362 37.037 0.00 0.00 0.00 1.82
320 325 7.834681 TCAGCTAGTACTCTCTCCATTCTAAAA 59.165 37.037 0.00 0.00 0.00 1.52
321 326 7.283580 GTCAGCTAGTACTCTCTCCATTCTAAA 59.716 40.741 0.00 0.00 0.00 1.85
322 327 6.768861 GTCAGCTAGTACTCTCTCCATTCTAA 59.231 42.308 0.00 0.00 0.00 2.10
323 328 6.292923 GTCAGCTAGTACTCTCTCCATTCTA 58.707 44.000 0.00 0.00 0.00 2.10
324 329 5.130350 GTCAGCTAGTACTCTCTCCATTCT 58.870 45.833 0.00 0.00 0.00 2.40
325 330 4.277423 GGTCAGCTAGTACTCTCTCCATTC 59.723 50.000 0.00 0.00 0.00 2.67
326 331 4.211920 GGTCAGCTAGTACTCTCTCCATT 58.788 47.826 0.00 0.00 0.00 3.16
327 332 3.435890 GGGTCAGCTAGTACTCTCTCCAT 60.436 52.174 0.00 0.00 0.00 3.41
328 333 2.092321 GGGTCAGCTAGTACTCTCTCCA 60.092 54.545 0.00 0.00 0.00 3.86
329 334 2.578786 GGGTCAGCTAGTACTCTCTCC 58.421 57.143 0.00 0.00 0.00 3.71
330 335 2.158928 TCGGGTCAGCTAGTACTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
331 336 1.838715 TCGGGTCAGCTAGTACTCTCT 59.161 52.381 0.00 0.00 0.00 3.10
332 337 1.941975 GTCGGGTCAGCTAGTACTCTC 59.058 57.143 0.00 0.00 0.00 3.20
333 338 1.408544 GGTCGGGTCAGCTAGTACTCT 60.409 57.143 0.00 0.00 0.00 3.24
334 339 1.023502 GGTCGGGTCAGCTAGTACTC 58.976 60.000 0.00 0.00 0.00 2.59
335 340 0.624785 AGGTCGGGTCAGCTAGTACT 59.375 55.000 0.00 0.00 0.00 2.73
336 341 1.023502 GAGGTCGGGTCAGCTAGTAC 58.976 60.000 0.00 0.00 0.00 2.73
342 347 4.083862 GGGTGAGGTCGGGTCAGC 62.084 72.222 3.96 3.96 40.91 4.26
419 424 2.606519 CAGGGGAAGACGTGGGGA 60.607 66.667 0.00 0.00 0.00 4.81
627 636 3.490031 ATGTGTGTTCCGCTGGCCA 62.490 57.895 4.71 4.71 0.00 5.36
643 652 1.226802 CTCGTCTCGTGGCCTGATG 60.227 63.158 3.32 2.99 0.00 3.07
644 653 1.378646 TCTCGTCTCGTGGCCTGAT 60.379 57.895 3.32 0.00 0.00 2.90
645 654 2.033602 TCTCGTCTCGTGGCCTGA 59.966 61.111 3.32 0.33 0.00 3.86
646 655 2.336478 ACTCTCGTCTCGTGGCCTG 61.336 63.158 3.32 0.00 0.00 4.85
648 657 2.179517 CACTCTCGTCTCGTGGCC 59.820 66.667 0.00 0.00 0.00 5.36
649 658 1.154188 GTCACTCTCGTCTCGTGGC 60.154 63.158 0.00 0.00 0.00 5.01
650 659 0.110147 GTGTCACTCTCGTCTCGTGG 60.110 60.000 0.00 0.00 0.00 4.94
651 660 0.586802 TGTGTCACTCTCGTCTCGTG 59.413 55.000 4.27 0.00 0.00 4.35
652 661 0.587285 GTGTGTCACTCTCGTCTCGT 59.413 55.000 4.27 0.00 0.00 4.18
653 662 0.451299 CGTGTGTCACTCTCGTCTCG 60.451 60.000 4.27 0.00 31.34 4.04
654 663 0.726452 GCGTGTGTCACTCTCGTCTC 60.726 60.000 4.27 0.00 31.34 3.36
655 664 1.283181 GCGTGTGTCACTCTCGTCT 59.717 57.895 4.27 0.00 31.34 4.18
656 665 1.008881 TGCGTGTGTCACTCTCGTC 60.009 57.895 4.27 4.56 31.34 4.20
724 737 1.234821 CCTACTCCGCTCAGCTCTAG 58.765 60.000 0.00 0.00 0.00 2.43
894 930 1.005630 GCGTGCTGGTGAGAGAAGT 60.006 57.895 0.00 0.00 0.00 3.01
901 947 2.324330 CGGATTTGCGTGCTGGTGA 61.324 57.895 0.00 0.00 0.00 4.02
1605 1678 4.301505 GCGATGCCAAAGAGGTCA 57.698 55.556 0.00 0.00 40.61 4.02
1618 1691 3.876198 GAATTGCGGCGTGGCGAT 61.876 61.111 20.46 1.93 38.69 4.58
1838 1911 0.249120 CGGCACATTGTCAGGGTAGA 59.751 55.000 0.00 0.00 0.00 2.59
2067 2140 1.629861 TGGATCACATCAGCACCTTCA 59.370 47.619 0.00 0.00 0.00 3.02
2161 2234 1.075601 AGAGCCACCCAGAAATCCAA 58.924 50.000 0.00 0.00 0.00 3.53
2631 2704 0.869730 CTTTACCGAACCCACCAACG 59.130 55.000 0.00 0.00 0.00 4.10
3477 3550 1.070445 GCCCTCATCTGACATCCCG 59.930 63.158 0.00 0.00 0.00 5.14
3838 3942 5.104735 ACAACACTGAAGAAGAGGAAGAAGT 60.105 40.000 0.00 0.00 0.00 3.01
3947 4051 1.124462 GTCGCGCACATCACTCTATC 58.876 55.000 8.75 0.00 0.00 2.08
3949 4053 1.138883 GGTCGCGCACATCACTCTA 59.861 57.895 8.75 0.00 0.00 2.43
3951 4055 1.291877 AAAGGTCGCGCACATCACTC 61.292 55.000 8.75 0.00 0.00 3.51
3962 4066 1.037493 AAAAGGGGAACAAAGGTCGC 58.963 50.000 0.00 0.00 0.00 5.19
3995 4099 4.999311 CAGGATTCGGAAATGAGCATATGA 59.001 41.667 6.97 0.00 0.00 2.15
3997 4101 4.202503 ACCAGGATTCGGAAATGAGCATAT 60.203 41.667 0.00 0.00 0.00 1.78
3998 4102 3.136443 ACCAGGATTCGGAAATGAGCATA 59.864 43.478 0.00 0.00 0.00 3.14
4054 4158 6.456795 AAGGTAAGGCAGAATAAATTGCTC 57.543 37.500 0.00 0.00 40.15 4.26
4082 4187 8.941977 CAAGCACATACTGTATTTGTTTAGGTA 58.058 33.333 13.32 0.00 0.00 3.08
4134 4336 1.315690 CGTCTGGCCGACCTCTATAA 58.684 55.000 18.07 0.00 39.56 0.98
4253 4473 5.749588 CACAAACAATTGATGTCTGCAAGAA 59.250 36.000 13.59 0.00 41.59 2.52
4254 4474 5.067544 TCACAAACAATTGATGTCTGCAAGA 59.932 36.000 13.59 6.50 42.99 3.02
4255 4475 5.283294 TCACAAACAATTGATGTCTGCAAG 58.717 37.500 13.59 4.42 42.99 4.01
4256 4476 5.163530 ACTCACAAACAATTGATGTCTGCAA 60.164 36.000 13.59 0.00 42.99 4.08
4257 4477 4.338964 ACTCACAAACAATTGATGTCTGCA 59.661 37.500 13.59 0.00 42.99 4.41
4258 4478 4.863491 ACTCACAAACAATTGATGTCTGC 58.137 39.130 13.59 0.00 42.99 4.26
4259 4479 6.267817 ACAACTCACAAACAATTGATGTCTG 58.732 36.000 13.59 12.49 42.99 3.51
4260 4480 6.455360 ACAACTCACAAACAATTGATGTCT 57.545 33.333 13.59 0.00 42.99 3.41
4261 4481 6.531240 ACAACAACTCACAAACAATTGATGTC 59.469 34.615 13.59 0.00 42.99 3.06
4287 4507 9.010029 CCGGATAATGGCAATTAAATACTAAGT 57.990 33.333 0.00 0.00 32.06 2.24
4288 4508 9.226606 TCCGGATAATGGCAATTAAATACTAAG 57.773 33.333 0.00 0.00 32.06 2.18
4289 4509 9.005777 GTCCGGATAATGGCAATTAAATACTAA 57.994 33.333 7.81 0.00 32.06 2.24
4290 4510 8.158132 TGTCCGGATAATGGCAATTAAATACTA 58.842 33.333 7.81 0.00 32.06 1.82
4291 4511 7.001674 TGTCCGGATAATGGCAATTAAATACT 58.998 34.615 7.81 0.00 32.06 2.12
4320 4540 3.071602 ACACCTGCAAGTAGACAGACAAT 59.928 43.478 0.00 0.00 35.90 2.71
4329 4549 1.550524 TGCCTAGACACCTGCAAGTAG 59.449 52.381 0.00 0.00 0.00 2.57
4339 4559 6.803154 AGAAACTTAAACATGCCTAGACAC 57.197 37.500 0.00 0.00 0.00 3.67
4373 4593 0.894141 CAGAGGGAGAGTGGACACTG 59.106 60.000 10.08 0.00 42.66 3.66
4444 4674 1.203928 CGATCAAGCTTAGCCTCACG 58.796 55.000 0.00 0.00 0.00 4.35
4597 4833 3.196469 AGATTTCACGATGCTCTCTCCAA 59.804 43.478 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.