Multiple sequence alignment - TraesCS1D01G058700

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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 TraesCS1D01G058700 chr1D 100.000 3644 0 0 1 3644 38660114 38656471 0.000000e+00 6730
1 TraesCS1D01G058700 chr1A 92.107 2572 122 40 469 2974 38369168 38366612 0.000000e+00 3550
2 TraesCS1D01G058700 chr1A 95.954 519 21 0 3126 3644 38360954 38360436 0.000000e+00 843
3 TraesCS1D01G058700 chr1B 92.465 2150 132 18 632 2759 58546756 58544615 0.000000e+00 3046
4 TraesCS1D01G058700 chr1B 95.117 901 40 2 2748 3644 58542269 58541369 0.000000e+00 1417
5 TraesCS1D01G058700 chr3D 94.703 472 22 2 1 469 67014720 67014249 0.000000e+00 730
6 TraesCS1D01G058700 chr5D 93.220 472 28 3 1 469 1627019 1627489 0.000000e+00 691
7 TraesCS1D01G058700 chr2D 94.092 457 24 2 16 469 94443607 94444063 0.000000e+00 691
8 TraesCS1D01G058700 chr2D 90.890 472 38 3 1 469 469968754 469968285 2.390000e-176 628
9 TraesCS1D01G058700 chr7D 92.797 472 31 2 1 469 281327167 281327638 0.000000e+00 680
10 TraesCS1D01G058700 chr4D 92.373 472 33 2 1 469 177098475 177098946 0.000000e+00 669
11 TraesCS1D01G058700 chr4D 92.161 472 34 2 1 469 477361139 477361610 0.000000e+00 664
12 TraesCS1D01G058700 chr4D 90.678 472 41 2 1 469 191930538 191931009 3.090000e-175 625
13 TraesCS1D01G058700 chr6D 92.560 457 31 2 16 469 395365364 395365820 0.000000e+00 652


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 TraesCS1D01G058700 chr1D 38656471 38660114 3643 True 6730.0 6730 100.000 1 3644 1 chr1D.!!$R1 3643
1 TraesCS1D01G058700 chr1A 38366612 38369168 2556 True 3550.0 3550 92.107 469 2974 1 chr1A.!!$R2 2505
2 TraesCS1D01G058700 chr1A 38360436 38360954 518 True 843.0 843 95.954 3126 3644 1 chr1A.!!$R1 518
3 TraesCS1D01G058700 chr1B 58541369 58546756 5387 True 2231.5 3046 93.791 632 3644 2 chr1B.!!$R1 3012

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
452 453 0.036294 GGCCTCCTCCGGTTATATGC 60.036 60.0 0.00 0.00 0.00 3.14 F
600 609 0.038892 AGGCTTTTCGTCGCGACTTA 60.039 50.0 33.94 20.74 34.89 2.24 F
980 1050 0.391793 GGGCCTTGGTTCTCTTCTCG 60.392 60.0 0.84 0.00 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1469 0.322098 TCACCTGTACCCATTTGCCG 60.322 55.0 0.00 0.0 0.00 5.69 R
1897 1973 0.613853 TCGTCCTTCAGGTTCGGGAT 60.614 55.0 11.17 0.0 35.64 3.85 R
2739 2818 0.033601 TGGAGTTTGCACTGGTTGGT 60.034 50.0 0.00 0.0 31.22 3.67 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
29 30 4.771356 CGTCGTCATCGGTGCGGT 62.771 66.667 11.54 0.00 37.69 5.68
30 31 3.179265 GTCGTCATCGGTGCGGTG 61.179 66.667 11.54 0.00 39.56 4.94
31 32 3.366915 TCGTCATCGGTGCGGTGA 61.367 61.111 11.54 0.00 45.01 4.02
34 35 3.770040 TCATCGGTGCGGTGAGGG 61.770 66.667 0.00 0.00 42.26 4.30
35 36 3.770040 CATCGGTGCGGTGAGGGA 61.770 66.667 0.00 0.00 40.81 4.20
36 37 2.764128 ATCGGTGCGGTGAGGGAT 60.764 61.111 0.00 0.00 0.00 3.85
37 38 3.094062 ATCGGTGCGGTGAGGGATG 62.094 63.158 0.00 0.00 0.00 3.51
38 39 4.838152 CGGTGCGGTGAGGGATGG 62.838 72.222 0.00 0.00 0.00 3.51
47 48 4.241555 GAGGGATGGCGCCGTCAT 62.242 66.667 41.19 31.63 41.33 3.06
48 49 4.241555 AGGGATGGCGCCGTCATC 62.242 66.667 41.19 32.52 43.12 2.92
49 50 4.545706 GGGATGGCGCCGTCATCA 62.546 66.667 41.19 17.59 45.33 3.07
50 51 2.281070 GGATGGCGCCGTCATCAT 60.281 61.111 41.19 21.63 45.33 2.45
51 52 2.320587 GGATGGCGCCGTCATCATC 61.321 63.158 41.19 27.40 45.33 2.92
52 53 2.661566 GATGGCGCCGTCATCATCG 61.662 63.158 37.82 0.00 43.31 3.84
58 59 3.333189 CCGTCATCATCGGCGCAG 61.333 66.667 10.83 5.07 41.48 5.18
59 60 2.583319 CGTCATCATCGGCGCAGT 60.583 61.111 10.83 0.00 0.00 4.40
60 61 2.863853 CGTCATCATCGGCGCAGTG 61.864 63.158 10.83 6.76 0.00 3.66
61 62 2.202919 TCATCATCGGCGCAGTGG 60.203 61.111 10.83 1.93 0.00 4.00
62 63 2.202919 CATCATCGGCGCAGTGGA 60.203 61.111 10.83 8.09 0.00 4.02
63 64 2.107750 ATCATCGGCGCAGTGGAG 59.892 61.111 10.83 0.00 0.00 3.86
64 65 4.819761 TCATCGGCGCAGTGGAGC 62.820 66.667 10.83 0.00 39.33 4.70
71 72 3.826754 CGCAGTGGAGCCGCTAGA 61.827 66.667 1.69 0.00 34.71 2.43
72 73 2.579201 GCAGTGGAGCCGCTAGAA 59.421 61.111 1.69 0.00 34.71 2.10
73 74 1.079127 GCAGTGGAGCCGCTAGAAA 60.079 57.895 1.69 0.00 34.71 2.52
74 75 1.086634 GCAGTGGAGCCGCTAGAAAG 61.087 60.000 1.69 0.00 34.71 2.62
75 76 1.086634 CAGTGGAGCCGCTAGAAAGC 61.087 60.000 1.69 0.00 45.86 3.51
100 101 4.927782 GTGGTGGTGGCAGCGACA 62.928 66.667 12.58 10.45 0.00 4.35
101 102 3.952508 TGGTGGTGGCAGCGACAT 61.953 61.111 12.58 0.00 0.00 3.06
102 103 3.434319 GGTGGTGGCAGCGACATG 61.434 66.667 12.58 0.00 0.00 3.21
103 104 2.358615 GTGGTGGCAGCGACATGA 60.359 61.111 12.58 0.00 0.00 3.07
104 105 1.746615 GTGGTGGCAGCGACATGAT 60.747 57.895 12.58 0.00 0.00 2.45
105 106 1.450134 TGGTGGCAGCGACATGATC 60.450 57.895 12.58 0.00 0.00 2.92
115 116 3.694364 GACATGATCGGAGCATGGT 57.306 52.632 32.19 20.93 45.62 3.55
116 117 1.506493 GACATGATCGGAGCATGGTC 58.494 55.000 32.19 23.84 45.62 4.02
117 118 1.069823 GACATGATCGGAGCATGGTCT 59.930 52.381 32.19 17.02 45.62 3.85
118 119 1.069823 ACATGATCGGAGCATGGTCTC 59.930 52.381 32.19 14.09 45.62 3.36
119 120 1.343789 CATGATCGGAGCATGGTCTCT 59.656 52.381 24.62 9.15 39.48 3.10
120 121 0.749049 TGATCGGAGCATGGTCTCTG 59.251 55.000 23.24 12.93 40.08 3.35
121 122 4.764143 TCGGAGCATGGTCTCTGA 57.236 55.556 23.24 14.93 43.96 3.27
122 123 2.976099 TCGGAGCATGGTCTCTGAA 58.024 52.632 23.24 3.46 43.41 3.02
123 124 1.489481 TCGGAGCATGGTCTCTGAAT 58.511 50.000 23.24 0.00 43.41 2.57
124 125 2.666317 TCGGAGCATGGTCTCTGAATA 58.334 47.619 23.24 0.50 43.41 1.75
125 126 2.362397 TCGGAGCATGGTCTCTGAATAC 59.638 50.000 23.24 4.37 43.41 1.89
126 127 2.546795 CGGAGCATGGTCTCTGAATACC 60.547 54.545 23.24 4.27 40.97 2.73
146 147 4.586306 CCAAATTGGTAGGACTAGGGTT 57.414 45.455 3.34 0.00 31.35 4.11
147 148 4.524053 CCAAATTGGTAGGACTAGGGTTC 58.476 47.826 3.34 0.00 31.35 3.62
148 149 4.524053 CAAATTGGTAGGACTAGGGTTCC 58.476 47.826 0.00 0.00 0.00 3.62
149 150 3.797671 ATTGGTAGGACTAGGGTTCCT 57.202 47.619 5.75 5.75 37.71 3.36
150 151 4.913154 ATTGGTAGGACTAGGGTTCCTA 57.087 45.455 3.95 3.95 34.61 2.94
153 154 2.580962 GTAGGACTAGGGTTCCTACCG 58.419 57.143 20.22 0.00 46.18 4.02
154 155 0.261109 AGGACTAGGGTTCCTACCGG 59.739 60.000 0.00 0.00 46.04 5.28
155 156 1.398174 GGACTAGGGTTCCTACCGGC 61.398 65.000 0.00 0.00 46.04 6.13
156 157 0.396835 GACTAGGGTTCCTACCGGCT 60.397 60.000 0.00 0.00 46.04 5.52
157 158 0.396835 ACTAGGGTTCCTACCGGCTC 60.397 60.000 0.00 0.00 46.04 4.70
158 159 0.106116 CTAGGGTTCCTACCGGCTCT 60.106 60.000 0.00 0.00 46.04 4.09
159 160 1.144503 CTAGGGTTCCTACCGGCTCTA 59.855 57.143 0.00 0.00 46.04 2.43
160 161 0.396835 AGGGTTCCTACCGGCTCTAC 60.397 60.000 0.00 0.00 46.04 2.59
161 162 0.396835 GGGTTCCTACCGGCTCTACT 60.397 60.000 0.00 0.00 46.04 2.57
162 163 1.031235 GGTTCCTACCGGCTCTACTC 58.969 60.000 0.00 0.00 34.01 2.59
163 164 1.031235 GTTCCTACCGGCTCTACTCC 58.969 60.000 0.00 0.00 0.00 3.85
164 165 0.924823 TTCCTACCGGCTCTACTCCT 59.075 55.000 0.00 0.00 0.00 3.69
165 166 0.924823 TCCTACCGGCTCTACTCCTT 59.075 55.000 0.00 0.00 0.00 3.36
166 167 2.130193 TCCTACCGGCTCTACTCCTTA 58.870 52.381 0.00 0.00 0.00 2.69
167 168 2.106166 TCCTACCGGCTCTACTCCTTAG 59.894 54.545 0.00 0.00 0.00 2.18
168 169 2.506444 CTACCGGCTCTACTCCTTAGG 58.494 57.143 0.00 0.00 0.00 2.69
169 170 0.630134 ACCGGCTCTACTCCTTAGGT 59.370 55.000 0.00 0.00 0.00 3.08
170 171 1.006878 ACCGGCTCTACTCCTTAGGTT 59.993 52.381 0.00 0.00 0.00 3.50
171 172 2.243221 ACCGGCTCTACTCCTTAGGTTA 59.757 50.000 0.00 0.00 0.00 2.85
172 173 3.117208 ACCGGCTCTACTCCTTAGGTTAT 60.117 47.826 0.00 0.00 0.00 1.89
173 174 4.105377 ACCGGCTCTACTCCTTAGGTTATA 59.895 45.833 0.00 0.00 0.00 0.98
174 175 5.075493 CCGGCTCTACTCCTTAGGTTATAA 58.925 45.833 0.00 0.00 0.00 0.98
175 176 5.715753 CCGGCTCTACTCCTTAGGTTATAAT 59.284 44.000 0.00 0.00 0.00 1.28
176 177 6.350277 CCGGCTCTACTCCTTAGGTTATAATG 60.350 46.154 0.00 0.00 0.00 1.90
177 178 6.350277 CGGCTCTACTCCTTAGGTTATAATGG 60.350 46.154 0.00 0.00 0.00 3.16
178 179 6.399743 GCTCTACTCCTTAGGTTATAATGGC 58.600 44.000 0.00 0.00 0.00 4.40
179 180 6.014499 GCTCTACTCCTTAGGTTATAATGGCA 60.014 42.308 0.00 0.00 0.00 4.92
180 181 7.540474 TCTACTCCTTAGGTTATAATGGCAG 57.460 40.000 0.00 0.00 0.00 4.85
181 182 7.302948 TCTACTCCTTAGGTTATAATGGCAGA 58.697 38.462 0.00 0.00 0.00 4.26
182 183 6.824958 ACTCCTTAGGTTATAATGGCAGAA 57.175 37.500 0.00 0.00 0.00 3.02
183 184 6.592870 ACTCCTTAGGTTATAATGGCAGAAC 58.407 40.000 0.00 0.00 0.00 3.01
184 185 6.157994 ACTCCTTAGGTTATAATGGCAGAACA 59.842 38.462 0.00 0.00 0.00 3.18
185 186 6.591935 TCCTTAGGTTATAATGGCAGAACAG 58.408 40.000 0.00 0.00 0.00 3.16
186 187 5.239525 CCTTAGGTTATAATGGCAGAACAGC 59.760 44.000 0.00 0.00 0.00 4.40
187 188 3.206150 AGGTTATAATGGCAGAACAGCG 58.794 45.455 0.00 0.00 34.64 5.18
188 189 2.290641 GGTTATAATGGCAGAACAGCGG 59.709 50.000 0.00 0.00 34.64 5.52
189 190 3.202906 GTTATAATGGCAGAACAGCGGA 58.797 45.455 0.00 0.00 34.64 5.54
190 191 1.959042 ATAATGGCAGAACAGCGGAG 58.041 50.000 0.00 0.00 34.64 4.63
191 192 0.107703 TAATGGCAGAACAGCGGAGG 60.108 55.000 0.00 0.00 34.64 4.30
192 193 2.129555 AATGGCAGAACAGCGGAGGT 62.130 55.000 0.00 0.00 41.48 3.85
193 194 2.032681 GGCAGAACAGCGGAGGTT 59.967 61.111 0.00 0.00 33.74 3.50
194 195 2.328099 GGCAGAACAGCGGAGGTTG 61.328 63.158 0.00 0.00 33.74 3.77
195 196 2.328099 GCAGAACAGCGGAGGTTGG 61.328 63.158 0.00 0.00 33.74 3.77
196 197 1.672356 CAGAACAGCGGAGGTTGGG 60.672 63.158 0.00 0.00 33.74 4.12
197 198 2.359975 GAACAGCGGAGGTTGGGG 60.360 66.667 0.00 0.00 33.74 4.96
198 199 3.920093 GAACAGCGGAGGTTGGGGG 62.920 68.421 0.00 0.00 33.74 5.40
242 243 3.796443 CGTCGTCGCGAGGGAAGA 61.796 66.667 26.64 10.93 37.97 2.87
243 244 2.100603 GTCGTCGCGAGGGAAGAG 59.899 66.667 26.64 5.38 36.23 2.85
244 245 3.132139 TCGTCGCGAGGGAAGAGG 61.132 66.667 26.64 2.00 0.00 3.69
245 246 3.132139 CGTCGCGAGGGAAGAGGA 61.132 66.667 20.58 0.00 0.00 3.71
246 247 2.802106 GTCGCGAGGGAAGAGGAG 59.198 66.667 10.24 0.00 0.00 3.69
247 248 2.440430 TCGCGAGGGAAGAGGAGG 60.440 66.667 3.71 0.00 0.00 4.30
248 249 3.532155 CGCGAGGGAAGAGGAGGG 61.532 72.222 0.00 0.00 0.00 4.30
249 250 3.855853 GCGAGGGAAGAGGAGGGC 61.856 72.222 0.00 0.00 0.00 5.19
250 251 3.532155 CGAGGGAAGAGGAGGGCG 61.532 72.222 0.00 0.00 0.00 6.13
251 252 3.157949 GAGGGAAGAGGAGGGCGG 61.158 72.222 0.00 0.00 0.00 6.13
252 253 4.806339 AGGGAAGAGGAGGGCGGG 62.806 72.222 0.00 0.00 0.00 6.13
254 255 4.798682 GGAAGAGGAGGGCGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
255 256 3.471806 GAAGAGGAGGGCGGGGAC 61.472 72.222 0.00 0.00 0.00 4.46
267 268 3.793888 GGGGACGGTTAGGGCTGG 61.794 72.222 0.00 0.00 0.00 4.85
268 269 4.484872 GGGACGGTTAGGGCTGGC 62.485 72.222 0.00 0.00 0.00 4.85
269 270 4.832608 GGACGGTTAGGGCTGGCG 62.833 72.222 0.00 0.00 0.00 5.69
270 271 4.832608 GACGGTTAGGGCTGGCGG 62.833 72.222 0.00 0.00 0.00 6.13
285 286 4.530857 CGGCGGCTAGGGTTCCAG 62.531 72.222 7.61 0.00 0.00 3.86
286 287 4.858680 GGCGGCTAGGGTTCCAGC 62.859 72.222 0.00 0.00 37.05 4.85
287 288 3.787001 GCGGCTAGGGTTCCAGCT 61.787 66.667 0.00 0.00 37.91 4.24
288 289 2.501610 CGGCTAGGGTTCCAGCTC 59.498 66.667 0.00 0.00 37.91 4.09
289 290 2.911928 GGCTAGGGTTCCAGCTCC 59.088 66.667 0.00 0.00 37.91 4.70
290 291 1.690985 GGCTAGGGTTCCAGCTCCT 60.691 63.158 0.00 0.00 37.91 3.69
291 292 1.691195 GGCTAGGGTTCCAGCTCCTC 61.691 65.000 0.00 0.00 37.91 3.71
292 293 0.689412 GCTAGGGTTCCAGCTCCTCT 60.689 60.000 0.00 0.00 34.86 3.69
293 294 1.118838 CTAGGGTTCCAGCTCCTCTG 58.881 60.000 0.00 0.00 42.49 3.35
312 313 3.686045 GAGCCGGGCGAGGGATAG 61.686 72.222 14.39 0.00 0.00 2.08
315 316 2.523412 CCGGGCGAGGGATAGGAA 60.523 66.667 0.00 0.00 0.00 3.36
316 317 2.138179 CCGGGCGAGGGATAGGAAA 61.138 63.158 0.00 0.00 0.00 3.13
317 318 1.481056 CCGGGCGAGGGATAGGAAAT 61.481 60.000 0.00 0.00 0.00 2.17
318 319 1.263356 CGGGCGAGGGATAGGAAATA 58.737 55.000 0.00 0.00 0.00 1.40
319 320 1.831736 CGGGCGAGGGATAGGAAATAT 59.168 52.381 0.00 0.00 0.00 1.28
320 321 2.159085 CGGGCGAGGGATAGGAAATATC 60.159 54.545 0.00 0.00 39.78 1.63
321 322 3.108376 GGGCGAGGGATAGGAAATATCT 58.892 50.000 0.00 0.00 40.29 1.98
322 323 3.519913 GGGCGAGGGATAGGAAATATCTT 59.480 47.826 0.00 0.00 40.29 2.40
323 324 4.019231 GGGCGAGGGATAGGAAATATCTTT 60.019 45.833 0.00 0.00 40.29 2.52
324 325 5.189145 GGGCGAGGGATAGGAAATATCTTTA 59.811 44.000 0.00 0.00 40.29 1.85
325 326 6.126739 GGGCGAGGGATAGGAAATATCTTTAT 60.127 42.308 0.00 0.00 40.29 1.40
326 327 7.339482 GGCGAGGGATAGGAAATATCTTTATT 58.661 38.462 0.00 0.00 40.29 1.40
327 328 7.281100 GGCGAGGGATAGGAAATATCTTTATTG 59.719 40.741 0.00 0.00 40.29 1.90
328 329 7.201652 GCGAGGGATAGGAAATATCTTTATTGC 60.202 40.741 0.00 0.00 40.29 3.56
329 330 8.043710 CGAGGGATAGGAAATATCTTTATTGCT 58.956 37.037 0.00 0.00 40.29 3.91
330 331 9.746457 GAGGGATAGGAAATATCTTTATTGCTT 57.254 33.333 0.00 0.00 40.29 3.91
345 346 9.010029 TCTTTATTGCTTAATTCCGAAAAGAGT 57.990 29.630 0.00 0.00 0.00 3.24
346 347 9.278734 CTTTATTGCTTAATTCCGAAAAGAGTC 57.721 33.333 0.00 0.00 0.00 3.36
347 348 8.561738 TTATTGCTTAATTCCGAAAAGAGTCT 57.438 30.769 0.00 0.00 0.00 3.24
348 349 6.877611 TTGCTTAATTCCGAAAAGAGTCTT 57.122 33.333 0.00 0.00 0.00 3.01
349 350 7.972832 TTGCTTAATTCCGAAAAGAGTCTTA 57.027 32.000 5.65 0.00 0.00 2.10
350 351 7.360575 TGCTTAATTCCGAAAAGAGTCTTAC 57.639 36.000 5.65 3.06 0.00 2.34
351 352 6.932400 TGCTTAATTCCGAAAAGAGTCTTACA 59.068 34.615 5.65 0.00 0.00 2.41
352 353 7.117812 TGCTTAATTCCGAAAAGAGTCTTACAG 59.882 37.037 5.65 0.36 0.00 2.74
353 354 5.864628 AATTCCGAAAAGAGTCTTACAGC 57.135 39.130 5.65 0.00 0.00 4.40
354 355 3.314541 TCCGAAAAGAGTCTTACAGCC 57.685 47.619 5.65 0.00 0.00 4.85
355 356 2.897969 TCCGAAAAGAGTCTTACAGCCT 59.102 45.455 5.65 0.00 0.00 4.58
356 357 4.084287 TCCGAAAAGAGTCTTACAGCCTA 58.916 43.478 5.65 0.00 0.00 3.93
357 358 4.710375 TCCGAAAAGAGTCTTACAGCCTAT 59.290 41.667 5.65 0.00 0.00 2.57
358 359 5.889853 TCCGAAAAGAGTCTTACAGCCTATA 59.110 40.000 5.65 0.00 0.00 1.31
359 360 6.550108 TCCGAAAAGAGTCTTACAGCCTATAT 59.450 38.462 5.65 0.00 0.00 0.86
360 361 7.069578 TCCGAAAAGAGTCTTACAGCCTATATT 59.930 37.037 5.65 0.00 0.00 1.28
361 362 7.711339 CCGAAAAGAGTCTTACAGCCTATATTT 59.289 37.037 5.65 0.00 0.00 1.40
362 363 9.745880 CGAAAAGAGTCTTACAGCCTATATTTA 57.254 33.333 5.65 0.00 0.00 1.40
409 410 7.640597 AATTAACCTAAGATAACTTGTGGGC 57.359 36.000 9.98 0.00 37.53 5.36
410 411 3.646736 ACCTAAGATAACTTGTGGGCC 57.353 47.619 0.00 0.00 37.53 5.80
411 412 2.916934 ACCTAAGATAACTTGTGGGCCA 59.083 45.455 0.00 0.00 37.53 5.36
412 413 3.332485 ACCTAAGATAACTTGTGGGCCAA 59.668 43.478 8.40 0.00 37.53 4.52
426 427 0.179070 GGCCAAGCCTCTACTACTGC 60.179 60.000 0.00 0.00 46.69 4.40
427 428 0.179070 GCCAAGCCTCTACTACTGCC 60.179 60.000 0.00 0.00 0.00 4.85
428 429 0.466124 CCAAGCCTCTACTACTGCCC 59.534 60.000 0.00 0.00 0.00 5.36
429 430 1.195115 CAAGCCTCTACTACTGCCCA 58.805 55.000 0.00 0.00 0.00 5.36
430 431 1.137872 CAAGCCTCTACTACTGCCCAG 59.862 57.143 0.00 0.00 0.00 4.45
431 432 0.336737 AGCCTCTACTACTGCCCAGT 59.663 55.000 6.17 6.17 45.02 4.00
432 433 0.461961 GCCTCTACTACTGCCCAGTG 59.538 60.000 11.02 4.22 42.52 3.66
433 434 1.115467 CCTCTACTACTGCCCAGTGG 58.885 60.000 11.02 10.40 44.31 4.00
446 447 4.658786 AGTGGGCCTCCTCCGGTT 62.659 66.667 4.53 0.00 0.00 4.44
447 448 2.686106 GTGGGCCTCCTCCGGTTA 60.686 66.667 4.53 0.00 0.00 2.85
448 449 2.070650 GTGGGCCTCCTCCGGTTAT 61.071 63.158 4.53 0.00 0.00 1.89
449 450 0.761702 GTGGGCCTCCTCCGGTTATA 60.762 60.000 4.53 0.00 0.00 0.98
450 451 0.192566 TGGGCCTCCTCCGGTTATAT 59.807 55.000 4.53 0.00 0.00 0.86
451 452 0.613777 GGGCCTCCTCCGGTTATATG 59.386 60.000 0.84 0.00 0.00 1.78
452 453 0.036294 GGCCTCCTCCGGTTATATGC 60.036 60.000 0.00 0.00 0.00 3.14
453 454 0.977395 GCCTCCTCCGGTTATATGCT 59.023 55.000 0.00 0.00 0.00 3.79
454 455 2.176889 GCCTCCTCCGGTTATATGCTA 58.823 52.381 0.00 0.00 0.00 3.49
455 456 2.565834 GCCTCCTCCGGTTATATGCTAA 59.434 50.000 0.00 0.00 0.00 3.09
456 457 3.007614 GCCTCCTCCGGTTATATGCTAAA 59.992 47.826 0.00 0.00 0.00 1.85
457 458 4.566987 CCTCCTCCGGTTATATGCTAAAC 58.433 47.826 0.00 0.00 0.00 2.01
458 459 4.562963 CCTCCTCCGGTTATATGCTAAACC 60.563 50.000 0.00 0.00 41.48 3.27
467 468 7.125536 GGTTATATGCTAAACCGGTCATAAC 57.874 40.000 8.04 9.09 36.12 1.89
490 491 1.327303 TTGGGTGAATGACTTGTGGC 58.673 50.000 0.00 0.00 0.00 5.01
504 505 1.605165 GTGGCCCCCATGAACGAAA 60.605 57.895 0.00 0.00 35.28 3.46
524 525 5.225129 CGAAAATCTAGCAACAACGCATTAC 59.775 40.000 0.00 0.00 0.00 1.89
527 528 3.259064 TCTAGCAACAACGCATTACTCC 58.741 45.455 0.00 0.00 0.00 3.85
528 529 2.185004 AGCAACAACGCATTACTCCT 57.815 45.000 0.00 0.00 0.00 3.69
546 547 4.160065 ACTCCTCTGTCATGTCTTGATCAG 59.840 45.833 0.00 9.86 36.54 2.90
547 548 3.118847 TCCTCTGTCATGTCTTGATCAGC 60.119 47.826 0.00 0.00 36.54 4.26
548 549 3.369157 CCTCTGTCATGTCTTGATCAGCA 60.369 47.826 0.00 0.00 36.54 4.41
549 550 4.443621 CTCTGTCATGTCTTGATCAGCAT 58.556 43.478 0.00 0.00 36.54 3.79
550 551 5.452917 CCTCTGTCATGTCTTGATCAGCATA 60.453 44.000 0.00 0.00 36.54 3.14
552 553 4.114794 TGTCATGTCTTGATCAGCATACG 58.885 43.478 0.00 0.00 36.54 3.06
578 586 5.067674 AGCACACAGAATCTTTACTTGCAAA 59.932 36.000 0.00 0.00 0.00 3.68
592 600 2.202295 TGCAAACAAGGCTTTTCGTC 57.798 45.000 0.00 0.00 0.00 4.20
600 609 0.038892 AGGCTTTTCGTCGCGACTTA 60.039 50.000 33.94 20.74 34.89 2.24
635 674 4.487714 AGAAAAGCTCGGTCATGGAATA 57.512 40.909 0.00 0.00 0.00 1.75
734 779 4.380531 GAATAATAGTGGCAGTAGCAGCA 58.619 43.478 8.22 0.00 44.61 4.41
798 843 2.949644 ACTTGTTAACGAGGCAAAAGCT 59.050 40.909 23.81 0.80 0.00 3.74
848 893 2.852495 TTTCGTGCCTCGCTCCATCC 62.852 60.000 0.00 0.00 39.67 3.51
866 913 5.604650 TCCATCCCTCTCTTTCTATCTTTCC 59.395 44.000 0.00 0.00 0.00 3.13
939 1005 6.812160 AGAACATAAGCTTGTAAGTTAGACGG 59.188 38.462 9.86 0.00 0.00 4.79
956 1022 1.009675 GGCATAAGGTTGCGCATCG 60.010 57.895 12.75 0.00 43.71 3.84
963 1033 1.154035 GGTTGCGCATCGAAAAGGG 60.154 57.895 12.75 0.00 0.00 3.95
980 1050 0.391793 GGGCCTTGGTTCTCTTCTCG 60.392 60.000 0.84 0.00 0.00 4.04
982 1052 1.355066 GCCTTGGTTCTCTTCTCGCG 61.355 60.000 0.00 0.00 0.00 5.87
988 1058 1.733041 TTCTCTTCTCGCGCGGTTG 60.733 57.895 31.69 19.90 0.00 3.77
1259 1334 2.899339 GAAGATCAGGGCAGCGGC 60.899 66.667 0.00 0.00 40.13 6.53
1366 1442 4.939439 TGACCTGTGAATGTGATCATGAAG 59.061 41.667 0.00 0.00 34.19 3.02
1393 1469 5.684704 TGAATGTGGAGTTGATATCTTCCC 58.315 41.667 14.74 7.61 0.00 3.97
1419 1495 5.594317 GCAAATGGGTACAGGTGAAGAATAT 59.406 40.000 0.00 0.00 0.00 1.28
1422 1498 5.353394 TGGGTACAGGTGAAGAATATGAC 57.647 43.478 0.00 0.00 0.00 3.06
1494 1570 2.904434 GGAGGAAGAGAAGTTACCACCA 59.096 50.000 0.00 0.00 32.97 4.17
1614 1690 0.968405 GTGGAAGCATGAAAAGGCCA 59.032 50.000 5.01 0.00 0.00 5.36
1755 1831 8.501580 CACTATATGGCAAATCAAGTATGACAG 58.498 37.037 0.00 0.00 38.69 3.51
1769 1845 8.984764 TCAAGTATGACAGTGTGTTTTATGTAC 58.015 33.333 0.00 0.00 0.00 2.90
1770 1846 8.769891 CAAGTATGACAGTGTGTTTTATGTACA 58.230 33.333 0.00 0.00 0.00 2.90
1791 1867 6.466885 ACATTCTACTACTAAATCGTGGCT 57.533 37.500 0.00 0.00 0.00 4.75
1793 1869 7.424001 ACATTCTACTACTAAATCGTGGCTAC 58.576 38.462 0.00 0.00 0.00 3.58
1889 1965 2.120737 AACGTGGTAGGGAAGGTGGC 62.121 60.000 0.00 0.00 0.00 5.01
1897 1973 3.319198 GGAAGGTGGCCGACTCCA 61.319 66.667 0.00 0.00 35.15 3.86
1927 2003 2.668457 CTGAAGGACGATCCAAGTTTCG 59.332 50.000 6.78 0.00 39.61 3.46
1941 2017 0.658897 GTTTCGCGAGGAAAACACCA 59.341 50.000 9.59 0.00 45.74 4.17
1953 2029 4.164221 AGGAAAACACCAGACAAGAAGAGA 59.836 41.667 0.00 0.00 0.00 3.10
1984 2060 2.592102 TGAGCAGGAGGAAGCAAATT 57.408 45.000 0.00 0.00 0.00 1.82
1985 2061 2.165167 TGAGCAGGAGGAAGCAAATTG 58.835 47.619 0.00 0.00 0.00 2.32
1988 2064 1.895131 GCAGGAGGAAGCAAATTGGAA 59.105 47.619 0.00 0.00 0.00 3.53
1995 2071 2.599659 GAAGCAAATTGGAAGGCGAAG 58.400 47.619 0.00 0.00 0.00 3.79
2032 2108 1.715993 GACCTCGTTTCCAGAAGAGC 58.284 55.000 0.00 0.00 0.00 4.09
2454 2532 0.681175 GGCTGTTTTGATTGCAGGGT 59.319 50.000 0.00 0.00 0.00 4.34
2499 2577 0.456221 CGCTGGAGGAGTACAACGAT 59.544 55.000 0.00 0.00 0.00 3.73
2529 2607 3.984193 GATCAGCAAGGTGGCCGCT 62.984 63.158 17.49 6.21 36.10 5.52
2607 2685 3.059386 GCGGCCAAAATCCGGTCA 61.059 61.111 2.24 0.00 46.51 4.02
2678 2756 5.132502 CACATAATGTGGGCCAAGAATCTA 58.867 41.667 8.40 0.00 44.27 1.98
2685 2763 1.745653 GGGCCAAGAATCTAGTTGTGC 59.254 52.381 4.39 0.00 0.00 4.57
2739 2818 4.257731 TCGCCTAAATGAAGTACATTGCA 58.742 39.130 0.00 0.00 46.90 4.08
2777 5213 1.194547 CACGTGGTGGAATTTCGACAG 59.805 52.381 7.95 6.62 0.00 3.51
2792 5228 3.621558 TCGACAGGACTCATAGTGTGAT 58.378 45.455 0.00 0.00 35.97 3.06
2800 5236 5.934625 AGGACTCATAGTGTGATGAAACAAC 59.065 40.000 0.00 0.00 35.44 3.32
2900 5336 2.821969 ACGAGCTAACCTTCGTTTCCTA 59.178 45.455 0.00 0.00 35.08 2.94
2903 5339 1.925185 GCTAACCTTCGTTTCCTAGCG 59.075 52.381 0.00 0.00 33.17 4.26
2906 5342 1.153901 CCTTCGTTTCCTAGCGCGA 60.154 57.895 12.10 0.00 0.00 5.87
2937 5373 7.823665 TCTCCATCATTTGATCTTGAAACTTG 58.176 34.615 0.00 0.00 31.21 3.16
3034 5473 6.664428 TTCATTAGCAAAACTAGGCCTTTT 57.336 33.333 12.58 2.84 30.79 2.27
3110 5549 7.588497 AATCTTTAGTTGGAAGCAGAGTTTT 57.412 32.000 0.00 0.00 0.00 2.43
3259 5698 4.864916 ACATTCATTCGATCCAGTTTCG 57.135 40.909 0.00 0.00 37.94 3.46
3335 5775 6.501781 AGTCAAAAGCAAAGCATCATATAGC 58.498 36.000 0.00 0.00 0.00 2.97
3346 5786 3.369892 GCATCATATAGCCCCAGGTGTAG 60.370 52.174 0.00 0.00 0.00 2.74
3426 5866 8.986847 GTGAGATCTTATCCACAAACAGATATG 58.013 37.037 0.00 0.00 33.49 1.78
3428 5868 9.202273 GAGATCTTATCCACAAACAGATATGAC 57.798 37.037 0.00 0.00 34.11 3.06
3432 5872 7.552687 TCTTATCCACAAACAGATATGACCAAC 59.447 37.037 0.00 0.00 29.20 3.77
3485 5925 6.349300 TGAGCCTAAGAAAGACATGTAATCC 58.651 40.000 0.00 0.00 0.00 3.01
3633 6073 5.941948 ATTTACACAAGGTAGTTCAGCAC 57.058 39.130 0.00 0.00 32.49 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.771356 ACCGCACCGATGACGACG 62.771 66.667 0.00 0.00 42.66 5.12
13 14 3.179265 CACCGCACCGATGACGAC 61.179 66.667 0.00 0.00 42.66 4.34
14 15 3.336715 CTCACCGCACCGATGACGA 62.337 63.158 0.00 0.00 42.66 4.20
15 16 2.880879 CTCACCGCACCGATGACG 60.881 66.667 0.00 0.00 39.43 4.35
16 17 2.509336 CCTCACCGCACCGATGAC 60.509 66.667 0.00 0.00 0.00 3.06
17 18 3.770040 CCCTCACCGCACCGATGA 61.770 66.667 0.00 0.00 0.00 2.92
18 19 3.094062 ATCCCTCACCGCACCGATG 62.094 63.158 0.00 0.00 0.00 3.84
19 20 2.764128 ATCCCTCACCGCACCGAT 60.764 61.111 0.00 0.00 0.00 4.18
20 21 3.770040 CATCCCTCACCGCACCGA 61.770 66.667 0.00 0.00 0.00 4.69
21 22 4.838152 CCATCCCTCACCGCACCG 62.838 72.222 0.00 0.00 0.00 4.94
30 31 4.241555 ATGACGGCGCCATCCCTC 62.242 66.667 28.98 12.31 0.00 4.30
31 32 4.241555 GATGACGGCGCCATCCCT 62.242 66.667 28.98 11.22 35.56 4.20
32 33 3.832237 ATGATGACGGCGCCATCCC 62.832 63.158 28.88 15.91 39.60 3.85
33 34 2.281070 ATGATGACGGCGCCATCC 60.281 61.111 28.88 14.96 39.60 3.51
34 35 2.661566 CGATGATGACGGCGCCATC 61.662 63.158 26.21 26.21 40.48 3.51
35 36 2.662857 CGATGATGACGGCGCCAT 60.663 61.111 28.98 12.81 0.00 4.40
36 37 4.889856 CCGATGATGACGGCGCCA 62.890 66.667 28.98 7.49 43.74 5.69
42 43 2.583319 ACTGCGCCGATGATGACG 60.583 61.111 4.18 0.00 0.00 4.35
43 44 2.528743 CCACTGCGCCGATGATGAC 61.529 63.158 4.18 0.00 0.00 3.06
44 45 2.202919 CCACTGCGCCGATGATGA 60.203 61.111 4.18 0.00 0.00 2.92
45 46 2.202919 TCCACTGCGCCGATGATG 60.203 61.111 4.18 0.00 0.00 3.07
46 47 2.107750 CTCCACTGCGCCGATGAT 59.892 61.111 4.18 0.00 0.00 2.45
47 48 4.819761 GCTCCACTGCGCCGATGA 62.820 66.667 4.18 0.00 0.00 2.92
56 57 1.086634 GCTTTCTAGCGGCTCCACTG 61.087 60.000 5.39 0.00 37.71 3.66
57 58 1.219393 GCTTTCTAGCGGCTCCACT 59.781 57.895 5.39 0.00 37.71 4.00
58 59 3.801129 GCTTTCTAGCGGCTCCAC 58.199 61.111 5.39 0.00 37.71 4.02
67 68 4.814294 ACCGCCGGCGCTTTCTAG 62.814 66.667 42.39 28.27 38.24 2.43
83 84 4.927782 TGTCGCTGCCACCACCAC 62.928 66.667 0.00 0.00 0.00 4.16
84 85 3.952508 ATGTCGCTGCCACCACCA 61.953 61.111 0.00 0.00 0.00 4.17
85 86 3.434319 CATGTCGCTGCCACCACC 61.434 66.667 0.00 0.00 0.00 4.61
86 87 1.709147 GATCATGTCGCTGCCACCAC 61.709 60.000 0.00 0.00 0.00 4.16
87 88 1.450134 GATCATGTCGCTGCCACCA 60.450 57.895 0.00 0.00 0.00 4.17
88 89 2.528743 CGATCATGTCGCTGCCACC 61.529 63.158 5.07 0.00 44.33 4.61
89 90 3.009140 CGATCATGTCGCTGCCAC 58.991 61.111 5.07 0.00 44.33 5.01
97 98 1.069823 AGACCATGCTCCGATCATGTC 59.930 52.381 10.53 8.35 39.60 3.06
98 99 1.069823 GAGACCATGCTCCGATCATGT 59.930 52.381 10.53 0.76 39.60 3.21
99 100 1.343789 AGAGACCATGCTCCGATCATG 59.656 52.381 5.39 5.39 40.60 3.07
100 101 1.343789 CAGAGACCATGCTCCGATCAT 59.656 52.381 0.00 0.00 35.49 2.45
101 102 0.749049 CAGAGACCATGCTCCGATCA 59.251 55.000 0.00 0.00 35.49 2.92
102 103 1.035923 TCAGAGACCATGCTCCGATC 58.964 55.000 0.00 0.00 35.49 3.69
103 104 1.489481 TTCAGAGACCATGCTCCGAT 58.511 50.000 0.00 0.00 35.49 4.18
104 105 1.489481 ATTCAGAGACCATGCTCCGA 58.511 50.000 0.00 0.00 35.49 4.55
105 106 2.546795 GGTATTCAGAGACCATGCTCCG 60.547 54.545 0.00 0.00 37.12 4.63
106 107 2.435805 TGGTATTCAGAGACCATGCTCC 59.564 50.000 2.70 0.00 42.04 4.70
107 108 3.827008 TGGTATTCAGAGACCATGCTC 57.173 47.619 2.70 0.00 42.04 4.26
108 109 4.574674 TTTGGTATTCAGAGACCATGCT 57.425 40.909 7.03 0.00 45.94 3.79
109 110 5.450965 CCAATTTGGTATTCAGAGACCATGC 60.451 44.000 7.31 0.00 45.94 4.06
110 111 6.140303 CCAATTTGGTATTCAGAGACCATG 57.860 41.667 7.31 3.81 45.94 3.66
123 124 9.863898 AGGAACCCTAGTCCTACCAATTTGGTA 62.864 44.444 23.53 23.53 40.03 3.25
124 125 9.863898 TAGGAACCCTAGTCCTACCAATTTGGT 62.864 44.444 23.83 23.83 43.88 3.67
125 126 4.524053 GAACCCTAGTCCTACCAATTTGG 58.476 47.826 14.02 14.02 45.02 3.28
126 127 4.227527 AGGAACCCTAGTCCTACCAATTTG 59.772 45.833 0.00 0.00 31.06 2.32
127 128 4.445564 AGGAACCCTAGTCCTACCAATTT 58.554 43.478 0.00 0.00 31.06 1.82
128 129 4.090027 AGGAACCCTAGTCCTACCAATT 57.910 45.455 0.00 0.00 31.06 2.32
129 130 3.797671 AGGAACCCTAGTCCTACCAAT 57.202 47.619 0.00 0.00 31.06 3.16
130 131 3.986435 GTAGGAACCCTAGTCCTACCAA 58.014 50.000 20.22 0.00 46.18 3.67
131 132 3.677156 GTAGGAACCCTAGTCCTACCA 57.323 52.381 20.22 0.00 46.18 3.25
134 135 1.496429 CCGGTAGGAACCCTAGTCCTA 59.504 57.143 3.95 3.95 43.54 2.94
135 136 0.261109 CCGGTAGGAACCCTAGTCCT 59.739 60.000 5.75 5.75 43.54 3.85
136 137 1.398174 GCCGGTAGGAACCCTAGTCC 61.398 65.000 1.90 0.00 43.54 3.85
137 138 0.396835 AGCCGGTAGGAACCCTAGTC 60.397 60.000 1.90 0.00 43.54 2.59
138 139 0.396835 GAGCCGGTAGGAACCCTAGT 60.397 60.000 1.90 0.00 43.54 2.57
139 140 0.106116 AGAGCCGGTAGGAACCCTAG 60.106 60.000 1.90 0.00 43.54 3.02
140 141 1.133668 GTAGAGCCGGTAGGAACCCTA 60.134 57.143 1.90 0.00 43.54 3.53
141 142 0.396835 GTAGAGCCGGTAGGAACCCT 60.397 60.000 1.90 0.00 43.54 4.34
142 143 0.396835 AGTAGAGCCGGTAGGAACCC 60.397 60.000 1.90 0.00 43.54 4.11
143 144 1.031235 GAGTAGAGCCGGTAGGAACC 58.969 60.000 1.90 0.00 42.95 3.62
144 145 1.031235 GGAGTAGAGCCGGTAGGAAC 58.969 60.000 1.90 0.00 41.02 3.62
145 146 0.924823 AGGAGTAGAGCCGGTAGGAA 59.075 55.000 1.90 0.00 41.02 3.36
146 147 0.924823 AAGGAGTAGAGCCGGTAGGA 59.075 55.000 1.90 0.00 41.02 2.94
147 148 2.506444 CTAAGGAGTAGAGCCGGTAGG 58.494 57.143 1.90 0.00 34.31 3.18
148 149 2.158638 ACCTAAGGAGTAGAGCCGGTAG 60.159 54.545 1.90 0.00 30.50 3.18
149 150 1.849039 ACCTAAGGAGTAGAGCCGGTA 59.151 52.381 1.90 0.00 30.50 4.02
150 151 0.630134 ACCTAAGGAGTAGAGCCGGT 59.370 55.000 1.90 0.00 30.50 5.28
151 152 1.777941 AACCTAAGGAGTAGAGCCGG 58.222 55.000 0.00 0.00 30.50 6.13
152 153 6.350277 CCATTATAACCTAAGGAGTAGAGCCG 60.350 46.154 0.00 0.00 30.50 5.52
153 154 6.574662 GCCATTATAACCTAAGGAGTAGAGCC 60.575 46.154 0.00 0.00 30.50 4.70
154 155 6.014499 TGCCATTATAACCTAAGGAGTAGAGC 60.014 42.308 0.00 0.00 30.50 4.09
155 156 7.451877 TCTGCCATTATAACCTAAGGAGTAGAG 59.548 40.741 0.00 0.00 30.50 2.43
156 157 7.302948 TCTGCCATTATAACCTAAGGAGTAGA 58.697 38.462 0.00 0.00 30.50 2.59
157 158 7.540474 TCTGCCATTATAACCTAAGGAGTAG 57.460 40.000 0.00 0.00 0.00 2.57
158 159 7.346175 TGTTCTGCCATTATAACCTAAGGAGTA 59.654 37.037 0.00 0.00 0.00 2.59
159 160 6.157994 TGTTCTGCCATTATAACCTAAGGAGT 59.842 38.462 0.00 0.00 0.00 3.85
160 161 6.591935 TGTTCTGCCATTATAACCTAAGGAG 58.408 40.000 0.00 0.00 0.00 3.69
161 162 6.569127 TGTTCTGCCATTATAACCTAAGGA 57.431 37.500 0.00 0.00 0.00 3.36
162 163 5.239525 GCTGTTCTGCCATTATAACCTAAGG 59.760 44.000 0.00 0.00 0.00 2.69
163 164 5.050091 CGCTGTTCTGCCATTATAACCTAAG 60.050 44.000 0.00 0.00 0.00 2.18
164 165 4.814234 CGCTGTTCTGCCATTATAACCTAA 59.186 41.667 0.00 0.00 0.00 2.69
165 166 4.377021 CGCTGTTCTGCCATTATAACCTA 58.623 43.478 0.00 0.00 0.00 3.08
166 167 3.206150 CGCTGTTCTGCCATTATAACCT 58.794 45.455 0.00 0.00 0.00 3.50
167 168 2.290641 CCGCTGTTCTGCCATTATAACC 59.709 50.000 0.00 0.00 0.00 2.85
168 169 3.202906 TCCGCTGTTCTGCCATTATAAC 58.797 45.455 0.00 0.00 0.00 1.89
169 170 3.466836 CTCCGCTGTTCTGCCATTATAA 58.533 45.455 0.00 0.00 0.00 0.98
170 171 2.224281 CCTCCGCTGTTCTGCCATTATA 60.224 50.000 0.00 0.00 0.00 0.98
171 172 1.475751 CCTCCGCTGTTCTGCCATTAT 60.476 52.381 0.00 0.00 0.00 1.28
172 173 0.107703 CCTCCGCTGTTCTGCCATTA 60.108 55.000 0.00 0.00 0.00 1.90
173 174 1.377725 CCTCCGCTGTTCTGCCATT 60.378 57.895 0.00 0.00 0.00 3.16
174 175 2.129555 AACCTCCGCTGTTCTGCCAT 62.130 55.000 0.00 0.00 0.00 4.40
175 176 2.818169 AACCTCCGCTGTTCTGCCA 61.818 57.895 0.00 0.00 0.00 4.92
176 177 2.032681 AACCTCCGCTGTTCTGCC 59.967 61.111 0.00 0.00 0.00 4.85
177 178 2.328099 CCAACCTCCGCTGTTCTGC 61.328 63.158 0.00 0.00 0.00 4.26
178 179 1.672356 CCCAACCTCCGCTGTTCTG 60.672 63.158 0.00 0.00 0.00 3.02
179 180 2.750350 CCCAACCTCCGCTGTTCT 59.250 61.111 0.00 0.00 0.00 3.01
180 181 2.359975 CCCCAACCTCCGCTGTTC 60.360 66.667 0.00 0.00 0.00 3.18
181 182 3.966543 CCCCCAACCTCCGCTGTT 61.967 66.667 0.00 0.00 0.00 3.16
225 226 3.720106 CTCTTCCCTCGCGACGACG 62.720 68.421 3.71 2.12 42.93 5.12
226 227 2.100603 CTCTTCCCTCGCGACGAC 59.899 66.667 3.71 0.00 0.00 4.34
227 228 3.132139 CCTCTTCCCTCGCGACGA 61.132 66.667 3.71 0.00 0.00 4.20
228 229 3.114647 CTCCTCTTCCCTCGCGACG 62.115 68.421 3.71 0.04 0.00 5.12
229 230 2.776913 CCTCCTCTTCCCTCGCGAC 61.777 68.421 3.71 0.00 0.00 5.19
230 231 2.440430 CCTCCTCTTCCCTCGCGA 60.440 66.667 9.26 9.26 0.00 5.87
231 232 3.532155 CCCTCCTCTTCCCTCGCG 61.532 72.222 0.00 0.00 0.00 5.87
232 233 3.855853 GCCCTCCTCTTCCCTCGC 61.856 72.222 0.00 0.00 0.00 5.03
233 234 3.532155 CGCCCTCCTCTTCCCTCG 61.532 72.222 0.00 0.00 0.00 4.63
234 235 3.157949 CCGCCCTCCTCTTCCCTC 61.158 72.222 0.00 0.00 0.00 4.30
235 236 4.806339 CCCGCCCTCCTCTTCCCT 62.806 72.222 0.00 0.00 0.00 4.20
237 238 4.798682 TCCCCGCCCTCCTCTTCC 62.799 72.222 0.00 0.00 0.00 3.46
238 239 3.471806 GTCCCCGCCCTCCTCTTC 61.472 72.222 0.00 0.00 0.00 2.87
244 245 3.846430 CTAACCGTCCCCGCCCTC 61.846 72.222 0.00 0.00 0.00 4.30
249 250 4.157120 CAGCCCTAACCGTCCCCG 62.157 72.222 0.00 0.00 0.00 5.73
250 251 3.793888 CCAGCCCTAACCGTCCCC 61.794 72.222 0.00 0.00 0.00 4.81
251 252 4.484872 GCCAGCCCTAACCGTCCC 62.485 72.222 0.00 0.00 0.00 4.46
252 253 4.832608 CGCCAGCCCTAACCGTCC 62.833 72.222 0.00 0.00 0.00 4.79
253 254 4.832608 CCGCCAGCCCTAACCGTC 62.833 72.222 0.00 0.00 0.00 4.79
268 269 4.530857 CTGGAACCCTAGCCGCCG 62.531 72.222 0.00 0.00 0.00 6.46
269 270 4.858680 GCTGGAACCCTAGCCGCC 62.859 72.222 0.00 0.00 33.89 6.13
270 271 3.741830 GAGCTGGAACCCTAGCCGC 62.742 68.421 0.00 0.00 40.76 6.53
271 272 2.501610 GAGCTGGAACCCTAGCCG 59.498 66.667 0.00 0.00 40.76 5.52
272 273 1.690985 AGGAGCTGGAACCCTAGCC 60.691 63.158 0.00 0.00 40.76 3.93
273 274 0.689412 AGAGGAGCTGGAACCCTAGC 60.689 60.000 0.00 0.00 40.18 3.42
274 275 1.118838 CAGAGGAGCTGGAACCCTAG 58.881 60.000 0.00 0.00 41.07 3.02
275 276 3.306902 CAGAGGAGCTGGAACCCTA 57.693 57.895 0.00 0.00 41.07 3.53
276 277 4.143740 CAGAGGAGCTGGAACCCT 57.856 61.111 0.00 0.00 41.07 4.34
295 296 3.686045 CTATCCCTCGCCCGGCTC 61.686 72.222 8.05 0.00 0.00 4.70
298 299 1.481056 ATTTCCTATCCCTCGCCCGG 61.481 60.000 0.00 0.00 0.00 5.73
299 300 1.263356 TATTTCCTATCCCTCGCCCG 58.737 55.000 0.00 0.00 0.00 6.13
300 301 3.108376 AGATATTTCCTATCCCTCGCCC 58.892 50.000 0.00 0.00 37.53 6.13
301 302 4.828072 AAGATATTTCCTATCCCTCGCC 57.172 45.455 0.00 0.00 37.53 5.54
302 303 7.201652 GCAATAAAGATATTTCCTATCCCTCGC 60.202 40.741 0.00 0.00 37.53 5.03
303 304 8.043710 AGCAATAAAGATATTTCCTATCCCTCG 58.956 37.037 0.00 0.00 37.53 4.63
304 305 9.746457 AAGCAATAAAGATATTTCCTATCCCTC 57.254 33.333 0.00 0.00 37.53 4.30
319 320 9.010029 ACTCTTTTCGGAATTAAGCAATAAAGA 57.990 29.630 0.00 0.00 29.48 2.52
320 321 9.278734 GACTCTTTTCGGAATTAAGCAATAAAG 57.721 33.333 0.00 0.00 0.00 1.85
321 322 9.010029 AGACTCTTTTCGGAATTAAGCAATAAA 57.990 29.630 0.00 0.00 0.00 1.40
322 323 8.561738 AGACTCTTTTCGGAATTAAGCAATAA 57.438 30.769 0.00 0.00 0.00 1.40
323 324 8.561738 AAGACTCTTTTCGGAATTAAGCAATA 57.438 30.769 0.00 0.00 0.00 1.90
324 325 7.454260 AAGACTCTTTTCGGAATTAAGCAAT 57.546 32.000 0.00 0.00 0.00 3.56
325 326 6.877611 AAGACTCTTTTCGGAATTAAGCAA 57.122 33.333 0.00 0.00 0.00 3.91
326 327 6.932400 TGTAAGACTCTTTTCGGAATTAAGCA 59.068 34.615 0.00 0.00 0.00 3.91
327 328 7.360575 TGTAAGACTCTTTTCGGAATTAAGC 57.639 36.000 0.00 0.00 0.00 3.09
328 329 7.413109 GGCTGTAAGACTCTTTTCGGAATTAAG 60.413 40.741 0.00 0.00 40.68 1.85
329 330 6.370718 GGCTGTAAGACTCTTTTCGGAATTAA 59.629 38.462 0.00 0.00 40.68 1.40
330 331 5.873164 GGCTGTAAGACTCTTTTCGGAATTA 59.127 40.000 0.00 0.00 40.68 1.40
331 332 4.695928 GGCTGTAAGACTCTTTTCGGAATT 59.304 41.667 0.00 0.00 40.68 2.17
332 333 4.254492 GGCTGTAAGACTCTTTTCGGAAT 58.746 43.478 0.00 0.00 40.68 3.01
333 334 3.660865 GGCTGTAAGACTCTTTTCGGAA 58.339 45.455 0.00 0.00 40.68 4.30
334 335 3.314541 GGCTGTAAGACTCTTTTCGGA 57.685 47.619 0.00 0.00 40.68 4.55
383 384 9.350951 GCCCACAAGTTATCTTAGGTTAATTAT 57.649 33.333 0.00 0.00 32.07 1.28
384 385 7.776500 GGCCCACAAGTTATCTTAGGTTAATTA 59.224 37.037 0.00 0.00 32.07 1.40
385 386 6.605995 GGCCCACAAGTTATCTTAGGTTAATT 59.394 38.462 0.00 0.00 32.07 1.40
386 387 6.127101 GGCCCACAAGTTATCTTAGGTTAAT 58.873 40.000 0.00 0.00 32.07 1.40
387 388 5.014333 TGGCCCACAAGTTATCTTAGGTTAA 59.986 40.000 0.00 0.00 32.07 2.01
388 389 4.536888 TGGCCCACAAGTTATCTTAGGTTA 59.463 41.667 0.00 0.00 32.07 2.85
389 390 3.332485 TGGCCCACAAGTTATCTTAGGTT 59.668 43.478 0.00 0.00 32.07 3.50
390 391 2.916934 TGGCCCACAAGTTATCTTAGGT 59.083 45.455 0.00 0.00 32.07 3.08
391 392 3.644966 TGGCCCACAAGTTATCTTAGG 57.355 47.619 0.00 0.00 32.07 2.69
408 409 0.179070 GGCAGTAGTAGAGGCTTGGC 60.179 60.000 0.00 0.00 0.00 4.52
409 410 0.466124 GGGCAGTAGTAGAGGCTTGG 59.534 60.000 0.00 0.00 0.00 3.61
410 411 1.137872 CTGGGCAGTAGTAGAGGCTTG 59.862 57.143 0.00 0.00 0.00 4.01
411 412 1.273324 ACTGGGCAGTAGTAGAGGCTT 60.273 52.381 0.00 0.00 40.43 4.35
412 413 0.336737 ACTGGGCAGTAGTAGAGGCT 59.663 55.000 0.00 0.00 40.43 4.58
413 414 0.461961 CACTGGGCAGTAGTAGAGGC 59.538 60.000 0.00 0.00 40.20 4.70
414 415 1.115467 CCACTGGGCAGTAGTAGAGG 58.885 60.000 0.00 0.00 40.20 3.69
415 416 1.115467 CCCACTGGGCAGTAGTAGAG 58.885 60.000 0.00 0.00 40.20 2.43
416 417 3.300032 CCCACTGGGCAGTAGTAGA 57.700 57.895 0.00 0.00 40.20 2.59
443 444 6.707161 TGTTATGACCGGTTTAGCATATAACC 59.293 38.462 9.42 1.84 40.31 2.85
444 445 7.440255 AGTGTTATGACCGGTTTAGCATATAAC 59.560 37.037 9.42 14.49 32.96 1.89
445 446 7.502696 AGTGTTATGACCGGTTTAGCATATAA 58.497 34.615 9.42 3.34 0.00 0.98
446 447 7.058023 AGTGTTATGACCGGTTTAGCATATA 57.942 36.000 9.42 1.80 0.00 0.86
447 448 5.925509 AGTGTTATGACCGGTTTAGCATAT 58.074 37.500 9.42 3.30 0.00 1.78
448 449 5.347620 AGTGTTATGACCGGTTTAGCATA 57.652 39.130 9.42 9.22 0.00 3.14
449 450 4.216411 AGTGTTATGACCGGTTTAGCAT 57.784 40.909 9.42 10.37 0.00 3.79
450 451 3.688694 AGTGTTATGACCGGTTTAGCA 57.311 42.857 9.42 9.71 0.00 3.49
451 452 4.379082 CCAAAGTGTTATGACCGGTTTAGC 60.379 45.833 9.42 6.98 0.00 3.09
452 453 4.155280 CCCAAAGTGTTATGACCGGTTTAG 59.845 45.833 9.42 0.00 0.00 1.85
453 454 4.073549 CCCAAAGTGTTATGACCGGTTTA 58.926 43.478 9.42 0.66 0.00 2.01
454 455 2.888414 CCCAAAGTGTTATGACCGGTTT 59.112 45.455 9.42 1.66 0.00 3.27
455 456 2.158579 ACCCAAAGTGTTATGACCGGTT 60.159 45.455 9.42 0.00 0.00 4.44
456 457 1.422402 ACCCAAAGTGTTATGACCGGT 59.578 47.619 6.92 6.92 0.00 5.28
457 458 1.810151 CACCCAAAGTGTTATGACCGG 59.190 52.381 0.00 0.00 41.93 5.28
481 482 1.076549 TTCATGGGGGCCACAAGTC 59.923 57.895 15.12 0.00 35.80 3.01
490 491 2.618709 GCTAGATTTTCGTTCATGGGGG 59.381 50.000 0.00 0.00 0.00 5.40
504 505 4.332819 GGAGTAATGCGTTGTTGCTAGATT 59.667 41.667 0.08 0.00 35.36 2.40
524 525 4.684877 CTGATCAAGACATGACAGAGGAG 58.315 47.826 0.00 0.00 41.93 3.69
527 528 3.858247 TGCTGATCAAGACATGACAGAG 58.142 45.455 0.00 0.00 41.93 3.35
528 529 3.967332 TGCTGATCAAGACATGACAGA 57.033 42.857 0.00 0.00 41.93 3.41
546 547 2.932614 AGATTCTGTGTGCTTCGTATGC 59.067 45.455 0.00 0.00 0.00 3.14
547 548 5.536554 AAAGATTCTGTGTGCTTCGTATG 57.463 39.130 0.00 0.00 0.00 2.39
548 549 6.398918 AGTAAAGATTCTGTGTGCTTCGTAT 58.601 36.000 0.00 0.00 0.00 3.06
549 550 5.779922 AGTAAAGATTCTGTGTGCTTCGTA 58.220 37.500 0.00 0.00 0.00 3.43
550 551 4.632153 AGTAAAGATTCTGTGTGCTTCGT 58.368 39.130 0.00 0.00 0.00 3.85
552 553 5.149977 GCAAGTAAAGATTCTGTGTGCTTC 58.850 41.667 0.00 0.00 0.00 3.86
578 586 1.593209 TCGCGACGAAAAGCCTTGT 60.593 52.632 3.71 0.00 31.06 3.16
619 628 2.171448 AGCTTTATTCCATGACCGAGCT 59.829 45.455 0.00 0.00 34.64 4.09
620 629 2.565841 AGCTTTATTCCATGACCGAGC 58.434 47.619 0.00 0.00 0.00 5.03
621 630 6.677781 TTTTAGCTTTATTCCATGACCGAG 57.322 37.500 0.00 0.00 0.00 4.63
622 631 7.012327 CAGATTTTAGCTTTATTCCATGACCGA 59.988 37.037 0.00 0.00 0.00 4.69
626 665 7.643569 TGCAGATTTTAGCTTTATTCCATGA 57.356 32.000 0.00 0.00 0.00 3.07
635 674 5.717119 CCTTGTCATGCAGATTTTAGCTTT 58.283 37.500 0.00 0.00 0.00 3.51
734 779 2.758736 TTTGCTTTGCAGTGTGGTTT 57.241 40.000 0.00 0.00 40.61 3.27
798 843 0.255890 GGAGGCAAGCAAGTGGGATA 59.744 55.000 0.00 0.00 0.00 2.59
848 893 7.506938 AGAGAGATGGAAAGATAGAAAGAGAGG 59.493 40.741 0.00 0.00 0.00 3.69
933 999 0.808453 GCGCAACCTTATGCCGTCTA 60.808 55.000 0.30 0.00 43.47 2.59
934 1000 2.106683 GCGCAACCTTATGCCGTCT 61.107 57.895 0.30 0.00 43.47 4.18
939 1005 0.376852 TTCGATGCGCAACCTTATGC 59.623 50.000 17.11 0.00 42.94 3.14
956 1022 2.294449 AGAGAACCAAGGCCCTTTTC 57.706 50.000 0.00 0.00 0.00 2.29
963 1033 1.355066 CGCGAGAAGAGAACCAAGGC 61.355 60.000 0.00 0.00 0.00 4.35
988 1058 3.747976 GTCCATGGCGCACAACCC 61.748 66.667 10.83 0.00 0.00 4.11
1007 1077 3.533606 ACCTCGATTGTCTCATTCCAG 57.466 47.619 0.00 0.00 0.00 3.86
1031 1101 1.073284 TGTAACAGGTTCCCTTGAGGC 59.927 52.381 0.00 0.00 34.51 4.70
1366 1442 8.348507 GGAAGATATCAACTCCACATTCATTTC 58.651 37.037 5.32 0.00 0.00 2.17
1393 1469 0.322098 TCACCTGTACCCATTTGCCG 60.322 55.000 0.00 0.00 0.00 5.69
1494 1570 0.835941 CTGGGATAGGCTTCTGCTGT 59.164 55.000 0.00 0.00 39.59 4.40
1614 1690 5.829924 TCTTGAGATTTTGCTTCCTTCAGTT 59.170 36.000 0.00 0.00 0.00 3.16
1769 1845 6.862090 GGTAGCCACGATTTAGTAGTAGAATG 59.138 42.308 0.00 0.00 0.00 2.67
1770 1846 6.776603 AGGTAGCCACGATTTAGTAGTAGAAT 59.223 38.462 0.00 0.00 0.00 2.40
1786 1862 1.519408 TTCGCTGAAAAGGTAGCCAC 58.481 50.000 0.00 0.00 36.60 5.01
1791 1867 4.398549 CGAAACATTCGCTGAAAAGGTA 57.601 40.909 0.00 0.00 46.97 3.08
1834 1910 1.302832 CTCCTGGCTTCTTTGGCGT 60.303 57.895 0.00 0.00 35.06 5.68
1889 1965 2.058595 AGGTTCGGGATGGAGTCGG 61.059 63.158 0.00 0.00 0.00 4.79
1897 1973 0.613853 TCGTCCTTCAGGTTCGGGAT 60.614 55.000 11.17 0.00 35.64 3.85
1927 2003 1.264288 CTTGTCTGGTGTTTTCCTCGC 59.736 52.381 0.00 0.00 0.00 5.03
1941 2017 5.289083 AGTTTCTGCTTCTCTTCTTGTCT 57.711 39.130 0.00 0.00 0.00 3.41
1953 2029 2.883386 CTCCTGCTCAAAGTTTCTGCTT 59.117 45.455 9.76 0.00 0.00 3.91
1995 2071 2.125391 GTCGGGTTAACCTCGGGC 60.125 66.667 23.69 16.19 36.97 6.13
2000 2076 1.589716 CGAGGTCGTCGGGTTAACCT 61.590 60.000 23.69 0.90 45.58 3.50
2027 2103 1.374758 CAGCTCCGTTTCCGCTCTT 60.375 57.895 0.00 0.00 0.00 2.85
2032 2108 2.391389 GCTTCCAGCTCCGTTTCCG 61.391 63.158 0.00 0.00 38.45 4.30
2039 2115 2.817396 GCTCGTGCTTCCAGCTCC 60.817 66.667 1.41 0.00 42.97 4.70
2139 2215 1.684049 CTCCTCCTTCTCCCACGCT 60.684 63.158 0.00 0.00 0.00 5.07
2454 2532 1.135915 GCTCGCTTCCTCTCTGAATCA 59.864 52.381 0.00 0.00 0.00 2.57
2499 2577 0.826062 TGCTGATCCGCTTCATCTCA 59.174 50.000 10.62 0.00 0.00 3.27
2529 2607 2.106938 GCCGACATCCTCGATGCA 59.893 61.111 1.54 0.00 46.14 3.96
2532 2610 1.459455 CCTCTGCCGACATCCTCGAT 61.459 60.000 0.00 0.00 46.14 3.59
2678 2756 1.605710 CAGTAAAGCAGCAGCACAACT 59.394 47.619 3.17 0.01 45.49 3.16
2685 2763 5.639506 ACAAGTATACACAGTAAAGCAGCAG 59.360 40.000 5.50 0.00 0.00 4.24
2739 2818 0.033601 TGGAGTTTGCACTGGTTGGT 60.034 50.000 0.00 0.00 31.22 3.67
2777 5213 5.934625 AGTTGTTTCATCACACTATGAGTCC 59.065 40.000 0.00 0.00 41.91 3.85
2792 5228 5.941647 GGGCTACTTGGTTATAGTTGTTTCA 59.058 40.000 0.00 0.00 0.00 2.69
2800 5236 3.314693 TCCAGGGGCTACTTGGTTATAG 58.685 50.000 9.25 0.00 0.00 1.31
2880 5316 2.365408 AGGAAACGAAGGTTAGCTCG 57.635 50.000 0.00 0.00 40.87 5.03
2900 5336 0.807667 GATGGAGATTGTGTCGCGCT 60.808 55.000 5.56 0.00 0.00 5.92
2903 5339 3.374988 TCAAATGATGGAGATTGTGTCGC 59.625 43.478 0.00 0.00 0.00 5.19
2906 5342 6.888088 TCAAGATCAAATGATGGAGATTGTGT 59.112 34.615 0.00 0.00 34.37 3.72
3058 5497 2.849318 AGATCCAGCTAGGCTTCCTTTT 59.151 45.455 0.00 0.00 36.40 2.27
3110 5549 2.037251 GCAGGTAGAGTGTTCCAACAGA 59.963 50.000 0.00 0.00 40.05 3.41
3259 5698 2.472695 TTCTCTGCATGTGTGGTACC 57.527 50.000 4.43 4.43 0.00 3.34
3311 5751 6.460676 GGCTATATGATGCTTTGCTTTTGACT 60.461 38.462 0.00 0.00 0.00 3.41
3335 5775 0.683504 ACTCTACGCTACACCTGGGG 60.684 60.000 0.00 0.00 0.00 4.96
3346 5786 4.151689 TGAGTTTGCATTACAACTCTACGC 59.848 41.667 22.92 4.74 38.23 4.42


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

AutoCloner maintained by Alex Coulton.