Multiple sequence alignment - TraesCS3A01G303200

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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 TraesCS3A01G303200 chr3A 100.000 3270 0 0 1 3270 537506634 537509903 0.000000e+00 6039.0
1 TraesCS3A01G303200 chr3A 90.437 732 31 15 1692 2413 483816990 483817692 0.000000e+00 928.0
2 TraesCS3A01G303200 chr3D 91.486 3042 118 39 326 3270 412786819 412783822 0.000000e+00 4052.0
3 TraesCS3A01G303200 chr3B 92.600 2392 83 40 320 2672 539562163 539559827 0.000000e+00 3350.0
4 TraesCS3A01G303200 chr3B 92.857 224 14 1 92 313 16893139 16893362 1.130000e-84 324.0
5 TraesCS3A01G303200 chr3B 86.813 91 3 8 1 91 539562240 539562159 3.470000e-15 93.5
6 TraesCS3A01G303200 chr6A 92.769 733 22 13 1692 2414 204306262 204305551 0.000000e+00 1031.0
7 TraesCS3A01G303200 chr6A 91.940 732 29 10 1692 2414 328876597 328877307 0.000000e+00 998.0
8 TraesCS3A01G303200 chr6A 91.803 732 29 11 1692 2414 473515808 473516517 0.000000e+00 990.0
9 TraesCS3A01G303200 chr6A 91.667 732 31 11 1692 2414 136163650 136162940 0.000000e+00 987.0
10 TraesCS3A01G303200 chr6A 90.984 732 36 11 1692 2414 518074968 518074258 0.000000e+00 959.0
11 TraesCS3A01G303200 chr2D 92.730 729 24 15 1696 2414 628411931 628412640 0.000000e+00 1026.0
12 TraesCS3A01G303200 chr2D 94.137 307 18 0 1005 1311 126739430 126739124 4.940000e-128 468.0
13 TraesCS3A01G303200 chr1A 92.350 732 26 12 1692 2414 465252065 465252775 0.000000e+00 1014.0
14 TraesCS3A01G303200 chr1A 94.009 217 11 1 97 311 530170187 530169971 8.750000e-86 327.0
15 TraesCS3A01G303200 chr5A 92.202 731 26 11 1692 2413 268344977 268345685 0.000000e+00 1005.0
16 TraesCS3A01G303200 chr5A 91.940 732 28 11 1692 2414 109668279 109668988 0.000000e+00 996.0
17 TraesCS3A01G303200 chr2A 91.667 732 31 11 1692 2414 616455680 616454970 0.000000e+00 987.0
18 TraesCS3A01G303200 chr2A 90.301 732 32 11 1692 2414 154894069 154893368 0.000000e+00 922.0
19 TraesCS3A01G303200 chr2A 93.485 307 20 0 1005 1311 133346362 133346056 1.070000e-124 457.0
20 TraesCS3A01G303200 chr2A 99.095 221 0 1 92 310 222194896 222194676 2.360000e-106 396.0
21 TraesCS3A01G303200 chr2B 93.811 307 19 0 1005 1311 180423771 180423465 2.300000e-126 462.0
22 TraesCS3A01G303200 chr2B 94.737 228 10 1 88 313 529109554 529109781 1.440000e-93 353.0
23 TraesCS3A01G303200 chr4A 92.131 305 24 0 1005 1309 409035615 409035919 6.480000e-117 431.0
24 TraesCS3A01G303200 chr4D 91.803 305 25 0 1005 1309 179312503 179312807 3.020000e-115 425.0
25 TraesCS3A01G303200 chr5B 93.665 221 12 1 93 311 440262732 440262952 2.430000e-86 329.0
26 TraesCS3A01G303200 chr5B 92.411 224 14 2 93 314 537903902 537904124 1.890000e-82 316.0
27 TraesCS3A01G303200 chr1B 92.889 225 12 3 94 316 362883 363105 1.130000e-84 324.0
28 TraesCS3A01G303200 chr1B 92.444 225 12 4 94 315 62411339 62411561 1.890000e-82 316.0
29 TraesCS3A01G303200 chr7B 93.213 221 11 3 92 310 529726344 529726126 4.070000e-84 322.0


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 TraesCS3A01G303200 chr3A 537506634 537509903 3269 False 6039.00 6039 100.0000 1 3270 1 chr3A.!!$F2 3269
1 TraesCS3A01G303200 chr3A 483816990 483817692 702 False 928.00 928 90.4370 1692 2413 1 chr3A.!!$F1 721
2 TraesCS3A01G303200 chr3D 412783822 412786819 2997 True 4052.00 4052 91.4860 326 3270 1 chr3D.!!$R1 2944
3 TraesCS3A01G303200 chr3B 539559827 539562240 2413 True 1721.75 3350 89.7065 1 2672 2 chr3B.!!$R1 2671
4 TraesCS3A01G303200 chr6A 204305551 204306262 711 True 1031.00 1031 92.7690 1692 2414 1 chr6A.!!$R2 722
5 TraesCS3A01G303200 chr6A 328876597 328877307 710 False 998.00 998 91.9400 1692 2414 1 chr6A.!!$F1 722
6 TraesCS3A01G303200 chr6A 473515808 473516517 709 False 990.00 990 91.8030 1692 2414 1 chr6A.!!$F2 722
7 TraesCS3A01G303200 chr6A 136162940 136163650 710 True 987.00 987 91.6670 1692 2414 1 chr6A.!!$R1 722
8 TraesCS3A01G303200 chr6A 518074258 518074968 710 True 959.00 959 90.9840 1692 2414 1 chr6A.!!$R3 722
9 TraesCS3A01G303200 chr2D 628411931 628412640 709 False 1026.00 1026 92.7300 1696 2414 1 chr2D.!!$F1 718
10 TraesCS3A01G303200 chr1A 465252065 465252775 710 False 1014.00 1014 92.3500 1692 2414 1 chr1A.!!$F1 722
11 TraesCS3A01G303200 chr5A 268344977 268345685 708 False 1005.00 1005 92.2020 1692 2413 1 chr5A.!!$F2 721
12 TraesCS3A01G303200 chr5A 109668279 109668988 709 False 996.00 996 91.9400 1692 2414 1 chr5A.!!$F1 722
13 TraesCS3A01G303200 chr2A 616454970 616455680 710 True 987.00 987 91.6670 1692 2414 1 chr2A.!!$R4 722
14 TraesCS3A01G303200 chr2A 154893368 154894069 701 True 922.00 922 90.3010 1692 2414 1 chr2A.!!$R2 722

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
148 149 0.036952 CAAGTGAGACCCGTGCTGAT 60.037 55.0 0.0 0.0 0.00 2.90 F
157 158 0.179037 CCCGTGCTGATGGATGACAT 60.179 55.0 0.0 0.0 44.18 3.06 F
535 541 0.179078 TTACCGTTGCCGTCACAAGT 60.179 50.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2192 0.531753 GATCTTGCCGAGCTTCTCCC 60.532 60.000 0.00 0.0 0.00 4.30 R
2227 2295 4.821589 GCGTCGGCCTCCTTGGAG 62.822 72.222 9.60 9.6 38.35 3.86 R
2590 2668 0.311790 CACGGACAGTTGCAATGCTT 59.688 50.000 6.82 0.0 0.00 3.91 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
52 53 8.585471 ACTACTAGTAGTAAATGGCTTGTGTA 57.415 34.615 29.96 0.00 43.98 2.90
53 54 9.198475 ACTACTAGTAGTAAATGGCTTGTGTAT 57.802 33.333 29.96 3.18 43.98 2.29
91 92 7.389232 TGCAATATACGCTAGTACTCCTACTA 58.611 38.462 0.00 0.00 34.79 1.82
92 93 7.332926 TGCAATATACGCTAGTACTCCTACTAC 59.667 40.741 0.00 0.00 34.79 2.73
93 94 7.463913 GCAATATACGCTAGTACTCCTACTACG 60.464 44.444 0.00 0.00 36.76 3.51
94 95 3.104843 ACGCTAGTACTCCTACTACGG 57.895 52.381 0.00 0.00 35.96 4.02
95 96 2.224161 ACGCTAGTACTCCTACTACGGG 60.224 54.545 0.00 7.04 35.96 5.28
96 97 2.036475 CGCTAGTACTCCTACTACGGGA 59.964 54.545 0.00 0.00 34.79 5.14
97 98 3.493350 CGCTAGTACTCCTACTACGGGAA 60.493 52.174 0.00 0.00 34.79 3.97
98 99 4.455606 GCTAGTACTCCTACTACGGGAAA 58.544 47.826 0.00 0.00 34.79 3.13
99 100 4.884164 GCTAGTACTCCTACTACGGGAAAA 59.116 45.833 0.00 0.00 34.79 2.29
100 101 5.358160 GCTAGTACTCCTACTACGGGAAAAA 59.642 44.000 0.00 0.00 34.79 1.94
132 133 6.240549 AGACCAGGTCTCATATAAACCAAG 57.759 41.667 17.31 0.00 38.71 3.61
133 134 5.726793 AGACCAGGTCTCATATAAACCAAGT 59.273 40.000 17.31 0.00 38.71 3.16
134 135 5.745227 ACCAGGTCTCATATAAACCAAGTG 58.255 41.667 0.00 0.00 35.43 3.16
135 136 5.487488 ACCAGGTCTCATATAAACCAAGTGA 59.513 40.000 0.00 0.00 35.43 3.41
136 137 6.051717 CCAGGTCTCATATAAACCAAGTGAG 58.948 44.000 0.00 0.00 38.07 3.51
137 138 6.127054 CCAGGTCTCATATAAACCAAGTGAGA 60.127 42.308 0.00 0.00 41.99 3.27
140 141 6.235231 TCTCATATAAACCAAGTGAGACCC 57.765 41.667 0.00 0.00 40.06 4.46
141 142 5.018539 TCATATAAACCAAGTGAGACCCG 57.981 43.478 0.00 0.00 0.00 5.28
142 143 4.468510 TCATATAAACCAAGTGAGACCCGT 59.531 41.667 0.00 0.00 0.00 5.28
143 144 2.536761 TAAACCAAGTGAGACCCGTG 57.463 50.000 0.00 0.00 0.00 4.94
144 145 0.818040 AAACCAAGTGAGACCCGTGC 60.818 55.000 0.00 0.00 0.00 5.34
145 146 1.696097 AACCAAGTGAGACCCGTGCT 61.696 55.000 0.00 0.00 0.00 4.40
146 147 1.669115 CCAAGTGAGACCCGTGCTG 60.669 63.158 0.00 0.00 0.00 4.41
147 148 1.367471 CAAGTGAGACCCGTGCTGA 59.633 57.895 0.00 0.00 0.00 4.26
148 149 0.036952 CAAGTGAGACCCGTGCTGAT 60.037 55.000 0.00 0.00 0.00 2.90
149 150 0.036952 AAGTGAGACCCGTGCTGATG 60.037 55.000 0.00 0.00 0.00 3.07
150 151 1.448540 GTGAGACCCGTGCTGATGG 60.449 63.158 0.00 0.00 0.00 3.51
151 152 1.609210 TGAGACCCGTGCTGATGGA 60.609 57.895 0.00 0.00 0.00 3.41
152 153 0.977627 TGAGACCCGTGCTGATGGAT 60.978 55.000 0.00 0.00 0.00 3.41
153 154 0.531532 GAGACCCGTGCTGATGGATG 60.532 60.000 0.00 0.00 0.00 3.51
154 155 0.977627 AGACCCGTGCTGATGGATGA 60.978 55.000 0.00 0.00 0.00 2.92
155 156 0.811616 GACCCGTGCTGATGGATGAC 60.812 60.000 0.00 0.00 0.00 3.06
156 157 1.221566 CCCGTGCTGATGGATGACA 59.778 57.895 0.00 0.00 0.00 3.58
157 158 0.179037 CCCGTGCTGATGGATGACAT 60.179 55.000 0.00 0.00 44.18 3.06
158 159 0.942252 CCGTGCTGATGGATGACATG 59.058 55.000 0.00 0.00 40.72 3.21
159 160 1.660167 CGTGCTGATGGATGACATGT 58.340 50.000 0.00 0.00 40.72 3.21
160 161 1.329599 CGTGCTGATGGATGACATGTG 59.670 52.381 1.15 0.00 40.72 3.21
161 162 1.674441 GTGCTGATGGATGACATGTGG 59.326 52.381 1.15 0.00 40.72 4.17
162 163 0.666913 GCTGATGGATGACATGTGGC 59.333 55.000 1.15 0.00 40.72 5.01
163 164 2.020181 GCTGATGGATGACATGTGGCA 61.020 52.381 1.15 0.00 40.72 4.92
165 166 2.956333 CTGATGGATGACATGTGGCATT 59.044 45.455 1.15 0.00 45.42 3.56
166 167 2.953648 TGATGGATGACATGTGGCATTC 59.046 45.455 1.15 1.06 45.42 2.67
167 168 2.510928 TGGATGACATGTGGCATTCA 57.489 45.000 1.15 5.70 46.54 2.57
168 169 2.093890 TGGATGACATGTGGCATTCAC 58.906 47.619 1.15 0.00 43.95 3.18
179 180 3.391965 GTGGCATTCACAAATCAAAGCA 58.608 40.909 0.00 0.00 45.39 3.91
180 181 3.998341 GTGGCATTCACAAATCAAAGCAT 59.002 39.130 0.00 0.00 45.39 3.79
181 182 5.170021 GTGGCATTCACAAATCAAAGCATA 58.830 37.500 0.00 0.00 45.39 3.14
182 183 5.813672 GTGGCATTCACAAATCAAAGCATAT 59.186 36.000 0.00 0.00 45.39 1.78
183 184 6.979817 GTGGCATTCACAAATCAAAGCATATA 59.020 34.615 0.00 0.00 45.39 0.86
184 185 7.492020 GTGGCATTCACAAATCAAAGCATATAA 59.508 33.333 0.00 0.00 45.39 0.98
185 186 8.205512 TGGCATTCACAAATCAAAGCATATAAT 58.794 29.630 0.00 0.00 0.00 1.28
186 187 8.706035 GGCATTCACAAATCAAAGCATATAATC 58.294 33.333 0.00 0.00 0.00 1.75
187 188 9.472361 GCATTCACAAATCAAAGCATATAATCT 57.528 29.630 0.00 0.00 0.00 2.40
191 192 9.060347 TCACAAATCAAAGCATATAATCTCTCC 57.940 33.333 0.00 0.00 0.00 3.71
192 193 8.295288 CACAAATCAAAGCATATAATCTCTCCC 58.705 37.037 0.00 0.00 0.00 4.30
193 194 7.449704 ACAAATCAAAGCATATAATCTCTCCCC 59.550 37.037 0.00 0.00 0.00 4.81
194 195 5.505181 TCAAAGCATATAATCTCTCCCCC 57.495 43.478 0.00 0.00 0.00 5.40
211 212 2.653234 CCCCCTGATTTCAGATGAGG 57.347 55.000 9.15 1.93 46.59 3.86
212 213 1.144503 CCCCCTGATTTCAGATGAGGG 59.855 57.143 9.15 10.17 46.59 4.30
213 214 2.130193 CCCCTGATTTCAGATGAGGGA 58.870 52.381 11.52 0.00 46.59 4.20
214 215 2.715336 CCCCTGATTTCAGATGAGGGAT 59.285 50.000 11.52 0.00 46.59 3.85
215 216 3.498121 CCCCTGATTTCAGATGAGGGATG 60.498 52.174 11.52 0.00 46.59 3.51
216 217 3.498121 CCCTGATTTCAGATGAGGGATGG 60.498 52.174 9.15 0.00 46.59 3.51
217 218 3.498121 CCTGATTTCAGATGAGGGATGGG 60.498 52.174 9.15 0.00 46.59 4.00
218 219 2.444388 TGATTTCAGATGAGGGATGGGG 59.556 50.000 0.00 0.00 0.00 4.96
219 220 1.985622 TTTCAGATGAGGGATGGGGT 58.014 50.000 0.00 0.00 0.00 4.95
220 221 1.216064 TTCAGATGAGGGATGGGGTG 58.784 55.000 0.00 0.00 0.00 4.61
221 222 0.695462 TCAGATGAGGGATGGGGTGG 60.695 60.000 0.00 0.00 0.00 4.61
222 223 0.695462 CAGATGAGGGATGGGGTGGA 60.695 60.000 0.00 0.00 0.00 4.02
223 224 0.273161 AGATGAGGGATGGGGTGGAT 59.727 55.000 0.00 0.00 0.00 3.41
224 225 0.403271 GATGAGGGATGGGGTGGATG 59.597 60.000 0.00 0.00 0.00 3.51
225 226 1.723128 ATGAGGGATGGGGTGGATGC 61.723 60.000 0.00 0.00 0.00 3.91
226 227 2.045132 AGGGATGGGGTGGATGCT 59.955 61.111 0.00 0.00 0.00 3.79
227 228 1.623686 AGGGATGGGGTGGATGCTT 60.624 57.895 0.00 0.00 0.00 3.91
228 229 1.224003 AGGGATGGGGTGGATGCTTT 61.224 55.000 0.00 0.00 0.00 3.51
229 230 1.044790 GGGATGGGGTGGATGCTTTG 61.045 60.000 0.00 0.00 0.00 2.77
230 231 0.324645 GGATGGGGTGGATGCTTTGT 60.325 55.000 0.00 0.00 0.00 2.83
231 232 0.819582 GATGGGGTGGATGCTTTGTG 59.180 55.000 0.00 0.00 0.00 3.33
232 233 0.409092 ATGGGGTGGATGCTTTGTGA 59.591 50.000 0.00 0.00 0.00 3.58
233 234 0.409092 TGGGGTGGATGCTTTGTGAT 59.591 50.000 0.00 0.00 0.00 3.06
234 235 1.203162 TGGGGTGGATGCTTTGTGATT 60.203 47.619 0.00 0.00 0.00 2.57
235 236 1.901833 GGGGTGGATGCTTTGTGATTT 59.098 47.619 0.00 0.00 0.00 2.17
236 237 2.354003 GGGGTGGATGCTTTGTGATTTG 60.354 50.000 0.00 0.00 0.00 2.32
237 238 2.299867 GGGTGGATGCTTTGTGATTTGT 59.700 45.455 0.00 0.00 0.00 2.83
238 239 3.319755 GGTGGATGCTTTGTGATTTGTG 58.680 45.455 0.00 0.00 0.00 3.33
239 240 3.005684 GGTGGATGCTTTGTGATTTGTGA 59.994 43.478 0.00 0.00 0.00 3.58
240 241 4.501229 GGTGGATGCTTTGTGATTTGTGAA 60.501 41.667 0.00 0.00 0.00 3.18
241 242 5.232463 GTGGATGCTTTGTGATTTGTGAAT 58.768 37.500 0.00 0.00 0.00 2.57
242 243 5.119588 GTGGATGCTTTGTGATTTGTGAATG 59.880 40.000 0.00 0.00 0.00 2.67
243 244 5.010820 TGGATGCTTTGTGATTTGTGAATGA 59.989 36.000 0.00 0.00 0.00 2.57
244 245 5.346822 GGATGCTTTGTGATTTGTGAATGAC 59.653 40.000 0.00 0.00 31.04 3.06
245 246 5.259832 TGCTTTGTGATTTGTGAATGACA 57.740 34.783 0.00 0.00 37.55 3.58
261 262 2.654749 GACACGTGTCATCCATCAGA 57.345 50.000 37.16 0.00 44.18 3.27
262 263 2.959516 GACACGTGTCATCCATCAGAA 58.040 47.619 37.16 0.00 44.18 3.02
263 264 3.525537 GACACGTGTCATCCATCAGAAT 58.474 45.455 37.16 4.46 44.18 2.40
264 265 3.264947 ACACGTGTCATCCATCAGAATG 58.735 45.455 17.22 0.00 37.54 2.67
265 266 5.735023 GACACGTGTCATCCATCAGAATGG 61.735 50.000 37.16 0.00 46.98 3.16
268 269 3.209410 GTGTCATCCATCAGAATGGGTC 58.791 50.000 4.68 0.00 43.29 4.46
269 270 3.117745 TGTCATCCATCAGAATGGGTCT 58.882 45.455 4.68 0.00 43.29 3.85
270 271 3.135348 TGTCATCCATCAGAATGGGTCTC 59.865 47.826 4.68 0.00 43.29 3.36
271 272 3.135348 GTCATCCATCAGAATGGGTCTCA 59.865 47.826 4.68 0.00 43.29 3.27
272 273 3.135348 TCATCCATCAGAATGGGTCTCAC 59.865 47.826 4.68 0.00 43.29 3.51
273 274 2.441001 ATCCATCAGAATGGGTCTCACC 59.559 50.000 4.68 0.00 43.29 4.02
274 275 3.893100 ATCCATCAGAATGGGTCTCACCT 60.893 47.826 4.68 0.00 43.29 4.00
275 276 2.915349 CATCAGAATGGGTCTCACCTG 58.085 52.381 0.00 0.00 38.64 4.00
276 277 0.615331 TCAGAATGGGTCTCACCTGC 59.385 55.000 0.22 0.00 38.64 4.85
277 278 0.617413 CAGAATGGGTCTCACCTGCT 59.383 55.000 0.00 0.00 38.64 4.24
278 279 1.833630 CAGAATGGGTCTCACCTGCTA 59.166 52.381 0.00 0.00 38.64 3.49
279 280 2.237143 CAGAATGGGTCTCACCTGCTAA 59.763 50.000 0.00 0.00 38.64 3.09
280 281 3.118112 CAGAATGGGTCTCACCTGCTAAT 60.118 47.826 0.00 0.00 38.64 1.73
281 282 3.135530 AGAATGGGTCTCACCTGCTAATC 59.864 47.826 0.00 0.00 38.64 1.75
282 283 1.204146 TGGGTCTCACCTGCTAATCC 58.796 55.000 0.00 0.00 38.64 3.01
283 284 1.204146 GGGTCTCACCTGCTAATCCA 58.796 55.000 0.00 0.00 38.64 3.41
284 285 1.771255 GGGTCTCACCTGCTAATCCAT 59.229 52.381 0.00 0.00 38.64 3.41
285 286 2.486191 GGGTCTCACCTGCTAATCCATG 60.486 54.545 0.00 0.00 38.64 3.66
286 287 2.435805 GGTCTCACCTGCTAATCCATGA 59.564 50.000 0.00 0.00 34.73 3.07
287 288 3.494048 GGTCTCACCTGCTAATCCATGAG 60.494 52.174 0.00 0.00 34.73 2.90
288 289 3.386078 GTCTCACCTGCTAATCCATGAGA 59.614 47.826 0.00 0.00 40.09 3.27
289 290 3.386078 TCTCACCTGCTAATCCATGAGAC 59.614 47.826 0.00 0.00 38.08 3.36
290 291 2.435805 TCACCTGCTAATCCATGAGACC 59.564 50.000 0.00 0.00 0.00 3.85
291 292 2.437281 CACCTGCTAATCCATGAGACCT 59.563 50.000 0.00 0.00 0.00 3.85
292 293 2.437281 ACCTGCTAATCCATGAGACCTG 59.563 50.000 0.00 0.00 0.00 4.00
293 294 2.224475 CCTGCTAATCCATGAGACCTGG 60.224 54.545 0.00 0.00 34.93 4.45
294 295 2.437281 CTGCTAATCCATGAGACCTGGT 59.563 50.000 0.00 0.00 35.19 4.00
295 296 2.435805 TGCTAATCCATGAGACCTGGTC 59.564 50.000 19.20 19.20 35.19 4.02
296 297 2.703007 GCTAATCCATGAGACCTGGTCT 59.297 50.000 28.70 28.70 46.42 3.85
332 333 5.479124 TTCCTCCTACTACTTTCAACACC 57.521 43.478 0.00 0.00 0.00 4.16
501 507 2.431942 GCACCGACACCACTACCG 60.432 66.667 0.00 0.00 0.00 4.02
533 539 1.159098 GGTTACCGTTGCCGTCACAA 61.159 55.000 0.00 0.00 0.00 3.33
534 540 0.233848 GTTACCGTTGCCGTCACAAG 59.766 55.000 0.00 0.00 0.00 3.16
535 541 0.179078 TTACCGTTGCCGTCACAAGT 60.179 50.000 0.00 0.00 0.00 3.16
536 542 0.672889 TACCGTTGCCGTCACAAGTA 59.327 50.000 0.00 0.00 0.00 2.24
537 543 0.877213 ACCGTTGCCGTCACAAGTAC 60.877 55.000 0.00 0.00 0.00 2.73
538 544 0.599204 CCGTTGCCGTCACAAGTACT 60.599 55.000 0.00 0.00 0.00 2.73
539 545 1.336148 CCGTTGCCGTCACAAGTACTA 60.336 52.381 0.00 0.00 0.00 1.82
540 546 1.983605 CGTTGCCGTCACAAGTACTAG 59.016 52.381 0.00 0.00 0.00 2.57
541 547 2.606308 CGTTGCCGTCACAAGTACTAGT 60.606 50.000 0.00 0.00 0.00 2.57
627 633 1.135460 GGTAAACACGAGGAGACGAGG 60.135 57.143 0.00 0.00 37.03 4.63
743 749 3.790437 CTCCCGCCAGCACTCCAT 61.790 66.667 0.00 0.00 0.00 3.41
744 750 2.364973 TCCCGCCAGCACTCCATA 60.365 61.111 0.00 0.00 0.00 2.74
807 813 0.951040 GTTCACTGGAGCACTTCCCG 60.951 60.000 0.00 0.00 46.19 5.14
862 868 1.445410 CCGCGCCGCAGCTTATATA 60.445 57.895 10.75 0.00 36.60 0.86
928 934 2.594592 AGCCGAAAGCCACACACC 60.595 61.111 0.00 0.00 45.47 4.16
929 935 2.594592 GCCGAAAGCCACACACCT 60.595 61.111 0.00 0.00 34.35 4.00
930 936 2.193536 GCCGAAAGCCACACACCTT 61.194 57.895 0.00 0.00 34.35 3.50
951 964 1.680522 TTCCTCCTCTGCTCGCATCC 61.681 60.000 0.00 0.00 0.00 3.51
1059 1072 1.437986 GACGATCCGGAACCTGGAG 59.562 63.158 9.01 0.00 39.30 3.86
1087 1100 3.976701 ATGTGGCGGCCCTTCTTCG 62.977 63.158 17.97 0.00 0.00 3.79
1352 1365 8.215926 TCTTTCTTTTTCACTTCCGTTATCAA 57.784 30.769 0.00 0.00 0.00 2.57
1353 1366 8.846211 TCTTTCTTTTTCACTTCCGTTATCAAT 58.154 29.630 0.00 0.00 0.00 2.57
1372 1395 7.856145 ATCAATTCTTCTTGGAGTCACATAC 57.144 36.000 0.00 0.00 0.00 2.39
1374 1397 6.875726 TCAATTCTTCTTGGAGTCACATACTG 59.124 38.462 0.00 0.00 39.07 2.74
1375 1398 6.611613 ATTCTTCTTGGAGTCACATACTGA 57.388 37.500 0.00 0.00 39.07 3.41
1376 1399 6.419484 TTCTTCTTGGAGTCACATACTGAA 57.581 37.500 0.00 0.00 39.07 3.02
1826 1877 2.033194 GGCTGGTGCGTCAAGGTAC 61.033 63.158 0.00 0.00 40.82 3.34
1833 1886 2.671396 GGTGCGTCAAGGTACATAACTG 59.329 50.000 0.00 0.00 0.00 3.16
1847 1900 8.154856 AGGTACATAACTGAACTAAACACACAT 58.845 33.333 0.00 0.00 0.00 3.21
1852 1905 5.779806 ACTGAACTAAACACACATATCGC 57.220 39.130 0.00 0.00 0.00 4.58
1866 1919 5.415701 ACACATATCGCCTTTGAGTTTGATT 59.584 36.000 0.00 0.00 0.00 2.57
1867 1920 6.071952 ACACATATCGCCTTTGAGTTTGATTT 60.072 34.615 0.00 0.00 0.00 2.17
1868 1921 6.252015 CACATATCGCCTTTGAGTTTGATTTG 59.748 38.462 0.00 0.00 0.00 2.32
1869 1922 3.641437 TCGCCTTTGAGTTTGATTTGG 57.359 42.857 0.00 0.00 0.00 3.28
1870 1923 2.955660 TCGCCTTTGAGTTTGATTTGGT 59.044 40.909 0.00 0.00 0.00 3.67
1871 1924 3.383185 TCGCCTTTGAGTTTGATTTGGTT 59.617 39.130 0.00 0.00 0.00 3.67
2157 2225 2.738964 GCAAGATCGACCCCTACTTCAC 60.739 54.545 0.00 0.00 0.00 3.18
2227 2295 1.353091 ACTCCAAGGACTCCAAGGAC 58.647 55.000 4.76 0.00 0.00 3.85
2228 2296 1.132689 ACTCCAAGGACTCCAAGGACT 60.133 52.381 4.76 0.00 0.00 3.85
2231 2299 1.352083 CAAGGACTCCAAGGACTCCA 58.648 55.000 14.66 0.00 32.04 3.86
2233 2301 1.650528 AGGACTCCAAGGACTCCAAG 58.349 55.000 14.66 0.00 32.04 3.61
2234 2302 0.615850 GGACTCCAAGGACTCCAAGG 59.384 60.000 9.20 0.00 30.65 3.61
2235 2303 1.645710 GACTCCAAGGACTCCAAGGA 58.354 55.000 7.95 7.95 0.00 3.36
2236 2304 1.552792 GACTCCAAGGACTCCAAGGAG 59.447 57.143 24.27 24.27 45.81 3.69
2237 2305 0.908198 CTCCAAGGACTCCAAGGAGG 59.092 60.000 19.62 2.50 45.88 4.30
2315 2392 0.824109 TTAGCATACTGAGCAGGCGT 59.176 50.000 2.20 0.00 0.00 5.68
2316 2393 0.103026 TAGCATACTGAGCAGGCGTG 59.897 55.000 1.01 1.01 0.00 5.34
2607 2685 3.492421 AATAAGCATTGCAACTGTCCG 57.508 42.857 11.91 0.00 0.00 4.79
2621 2699 2.823747 ACTGTCCGTGTGTATGCTTCTA 59.176 45.455 0.00 0.00 0.00 2.10
2641 2719 6.158023 TCTATTCCCTCCGTCTGAATTTAC 57.842 41.667 0.00 0.00 31.55 2.01
2649 2727 4.963373 TCCGTCTGAATTTACTGAACCAA 58.037 39.130 0.00 0.00 0.00 3.67
2652 2730 6.017440 TCCGTCTGAATTTACTGAACCAAAAG 60.017 38.462 0.00 0.00 0.00 2.27
2659 2737 4.513406 TTACTGAACCAAAAGGTCACCT 57.487 40.909 0.00 0.00 33.87 4.00
2662 2740 4.652822 ACTGAACCAAAAGGTCACCTATC 58.347 43.478 0.00 0.00 31.13 2.08
2689 2767 3.192466 ACGTATGTCGGTTATTCCTTGC 58.808 45.455 0.00 0.00 44.69 4.01
2732 2811 0.978151 TTGCCTGCATTGAAGCCAAT 59.022 45.000 0.00 0.00 43.37 3.16
2750 2829 2.661054 TGCATTGCATCAACCTGCT 58.339 47.368 7.38 0.00 42.75 4.24
2751 2830 0.528924 TGCATTGCATCAACCTGCTC 59.471 50.000 7.38 0.00 42.75 4.26
2752 2831 0.524816 GCATTGCATCAACCTGCTCG 60.525 55.000 3.15 0.00 42.75 5.03
2759 2838 2.481969 GCATCAACCTGCTCGACATAGA 60.482 50.000 0.00 0.00 39.12 1.98
2776 2855 6.980978 CGACATAGATTAATATCAGCCCGATT 59.019 38.462 0.00 0.00 35.39 3.34
2777 2856 8.135529 CGACATAGATTAATATCAGCCCGATTA 58.864 37.037 0.00 0.00 35.39 1.75
2778 2857 9.250624 GACATAGATTAATATCAGCCCGATTAC 57.749 37.037 0.00 0.00 35.39 1.89
2791 2870 3.434299 GCCCGATTACCATAATAACCGTG 59.566 47.826 0.00 0.00 0.00 4.94
2793 2872 5.299148 CCCGATTACCATAATAACCGTGAA 58.701 41.667 0.00 0.00 0.00 3.18
2794 2873 5.935789 CCCGATTACCATAATAACCGTGAAT 59.064 40.000 0.00 0.00 0.00 2.57
2795 2874 7.098477 CCCGATTACCATAATAACCGTGAATA 58.902 38.462 0.00 0.00 0.00 1.75
2796 2875 7.767198 CCCGATTACCATAATAACCGTGAATAT 59.233 37.037 0.00 0.00 0.00 1.28
2797 2876 8.600625 CCGATTACCATAATAACCGTGAATATG 58.399 37.037 0.00 0.00 0.00 1.78
2798 2877 9.361315 CGATTACCATAATAACCGTGAATATGA 57.639 33.333 0.00 0.00 0.00 2.15
2800 2879 8.523523 TTACCATAATAACCGTGAATATGACG 57.476 34.615 1.40 1.40 36.56 4.35
2808 2887 5.978934 ACCGTGAATATGACGATTTTACC 57.021 39.130 8.70 0.00 39.21 2.85
2812 2891 6.256975 CCGTGAATATGACGATTTTACCAGAA 59.743 38.462 8.70 0.00 39.21 3.02
2823 2902 1.241315 TTACCAGAAAAGGCCAGCGC 61.241 55.000 5.01 0.00 0.00 5.92
2838 2943 2.633657 CGCGGCCACTATTGATGC 59.366 61.111 2.24 0.00 0.00 3.91
2865 2970 2.496871 CACCAGGAAGCATGCCAATTAA 59.503 45.455 15.66 0.00 34.43 1.40
2908 3031 2.615240 GGCCATTTCCCACCACATTTTC 60.615 50.000 0.00 0.00 0.00 2.29
2942 3065 1.000884 CGGCGGCTACGAAAATGTTA 58.999 50.000 7.61 0.00 44.60 2.41
2946 3069 2.536803 GCGGCTACGAAAATGTTATCGA 59.463 45.455 1.84 0.00 44.60 3.59
2969 3092 0.733150 GGCCGAATAACTCACAAGCC 59.267 55.000 0.00 0.00 0.00 4.35
2970 3093 0.733150 GCCGAATAACTCACAAGCCC 59.267 55.000 0.00 0.00 0.00 5.19
2972 3095 1.006832 CGAATAACTCACAAGCCCCG 58.993 55.000 0.00 0.00 0.00 5.73
2977 3100 1.990160 AACTCACAAGCCCCGGTTCA 61.990 55.000 0.00 0.00 0.00 3.18
2995 3118 2.795329 TCAAATGCCTCCACCTTTCTC 58.205 47.619 0.00 0.00 0.00 2.87
3000 3123 1.559682 TGCCTCCACCTTTCTCCATAC 59.440 52.381 0.00 0.00 0.00 2.39
3001 3124 1.134068 GCCTCCACCTTTCTCCATACC 60.134 57.143 0.00 0.00 0.00 2.73
3008 3131 1.134098 CCTTTCTCCATACCGCCATGT 60.134 52.381 0.00 0.00 0.00 3.21
3010 3133 1.496060 TTCTCCATACCGCCATGTCT 58.504 50.000 0.00 0.00 0.00 3.41
3011 3134 2.375014 TCTCCATACCGCCATGTCTA 57.625 50.000 0.00 0.00 0.00 2.59
3012 3135 2.673258 TCTCCATACCGCCATGTCTAA 58.327 47.619 0.00 0.00 0.00 2.10
3034 3157 0.905337 AGCTCTTGTCCCGCCTAGTT 60.905 55.000 0.00 0.00 0.00 2.24
3061 3184 2.046314 CTCCCCATCGCCACGTTT 60.046 61.111 0.00 0.00 0.00 3.60
3079 3202 3.060895 CGTTTGAATAGCTCTTCACCGTC 59.939 47.826 13.61 4.88 34.96 4.79
3080 3203 3.953712 TTGAATAGCTCTTCACCGTCA 57.046 42.857 13.61 0.00 34.96 4.35
3081 3204 4.471904 TTGAATAGCTCTTCACCGTCAT 57.528 40.909 13.61 0.00 34.96 3.06
3106 3229 1.203013 TCGTCCACTCTTGAAGGAGGA 60.203 52.381 0.00 0.00 42.22 3.71
3107 3230 1.203523 CGTCCACTCTTGAAGGAGGAG 59.796 57.143 0.00 0.00 39.10 3.69
3110 3233 0.979665 CACTCTTGAAGGAGGAGGCA 59.020 55.000 0.00 0.00 37.63 4.75
3111 3234 1.066286 CACTCTTGAAGGAGGAGGCAG 60.066 57.143 0.00 0.00 37.63 4.85
3112 3235 1.274712 CTCTTGAAGGAGGAGGCAGT 58.725 55.000 0.00 0.00 0.00 4.40
3121 3244 1.075600 AGGAGGCAGTAGAGGAGGC 60.076 63.158 0.00 0.00 0.00 4.70
3192 3315 0.529992 GGCCACGTAGAAAGATCCCG 60.530 60.000 0.00 0.00 0.00 5.14
3212 3335 2.105128 CTCGATGAGTGGCCGGAC 59.895 66.667 5.05 0.56 0.00 4.79
3214 3337 2.202797 CGATGAGTGGCCGGACTG 60.203 66.667 9.82 0.00 0.00 3.51
3215 3338 2.710902 CGATGAGTGGCCGGACTGA 61.711 63.158 9.82 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.198475 ACACAAGCCATTTACTACTAGTAGTAT 57.802 33.333 33.08 22.49 45.07 2.12
30 31 8.974238 TGTATACACAAGCCATTTACTACTAGT 58.026 33.333 0.08 0.00 0.00 2.57
31 32 9.982651 ATGTATACACAAGCCATTTACTACTAG 57.017 33.333 7.96 0.00 38.42 2.57
33 34 9.760077 GTATGTATACACAAGCCATTTACTACT 57.240 33.333 7.96 0.00 38.42 2.57
34 35 9.537192 TGTATGTATACACAAGCCATTTACTAC 57.463 33.333 7.96 2.92 38.28 2.73
52 53 8.135529 AGCGTATATTGCATCGTATGTATGTAT 58.864 33.333 0.00 0.00 33.85 2.29
53 54 7.477494 AGCGTATATTGCATCGTATGTATGTA 58.523 34.615 0.00 0.00 33.85 2.29
54 55 6.330278 AGCGTATATTGCATCGTATGTATGT 58.670 36.000 0.00 0.00 33.85 2.29
55 56 6.812481 AGCGTATATTGCATCGTATGTATG 57.188 37.500 0.00 0.00 33.85 2.39
109 110 5.726793 ACTTGGTTTATATGAGACCTGGTCT 59.273 40.000 28.70 28.70 46.42 3.85
110 111 5.817816 CACTTGGTTTATATGAGACCTGGTC 59.182 44.000 19.20 19.20 34.52 4.02
111 112 5.487488 TCACTTGGTTTATATGAGACCTGGT 59.513 40.000 0.00 0.00 34.52 4.00
112 113 5.989477 TCACTTGGTTTATATGAGACCTGG 58.011 41.667 0.00 0.00 34.52 4.45
113 114 6.878317 TCTCACTTGGTTTATATGAGACCTG 58.122 40.000 0.00 2.72 40.59 4.00
117 118 5.163447 CGGGTCTCACTTGGTTTATATGAGA 60.163 44.000 0.00 0.00 42.63 3.27
118 119 5.050490 CGGGTCTCACTTGGTTTATATGAG 58.950 45.833 0.00 0.00 38.51 2.90
119 120 4.468510 ACGGGTCTCACTTGGTTTATATGA 59.531 41.667 0.00 0.00 0.00 2.15
120 121 4.570772 CACGGGTCTCACTTGGTTTATATG 59.429 45.833 0.00 0.00 0.00 1.78
121 122 4.766375 CACGGGTCTCACTTGGTTTATAT 58.234 43.478 0.00 0.00 0.00 0.86
122 123 3.618019 GCACGGGTCTCACTTGGTTTATA 60.618 47.826 0.00 0.00 0.00 0.98
123 124 2.874457 GCACGGGTCTCACTTGGTTTAT 60.874 50.000 0.00 0.00 0.00 1.40
124 125 1.541670 GCACGGGTCTCACTTGGTTTA 60.542 52.381 0.00 0.00 0.00 2.01
125 126 0.818040 GCACGGGTCTCACTTGGTTT 60.818 55.000 0.00 0.00 0.00 3.27
126 127 1.227853 GCACGGGTCTCACTTGGTT 60.228 57.895 0.00 0.00 0.00 3.67
127 128 2.140792 AGCACGGGTCTCACTTGGT 61.141 57.895 0.00 0.00 0.00 3.67
128 129 1.669115 CAGCACGGGTCTCACTTGG 60.669 63.158 0.00 0.00 0.00 3.61
129 130 0.036952 ATCAGCACGGGTCTCACTTG 60.037 55.000 0.00 0.00 0.00 3.16
130 131 0.036952 CATCAGCACGGGTCTCACTT 60.037 55.000 0.00 0.00 0.00 3.16
131 132 1.593787 CATCAGCACGGGTCTCACT 59.406 57.895 0.00 0.00 0.00 3.41
132 133 1.448540 CCATCAGCACGGGTCTCAC 60.449 63.158 0.00 0.00 0.00 3.51
133 134 0.977627 ATCCATCAGCACGGGTCTCA 60.978 55.000 0.00 0.00 0.00 3.27
134 135 0.531532 CATCCATCAGCACGGGTCTC 60.532 60.000 0.00 0.00 0.00 3.36
135 136 0.977627 TCATCCATCAGCACGGGTCT 60.978 55.000 0.00 0.00 0.00 3.85
136 137 0.811616 GTCATCCATCAGCACGGGTC 60.812 60.000 0.00 0.00 0.00 4.46
137 138 1.221840 GTCATCCATCAGCACGGGT 59.778 57.895 0.00 0.00 0.00 5.28
138 139 0.179037 ATGTCATCCATCAGCACGGG 60.179 55.000 0.00 0.00 0.00 5.28
139 140 0.942252 CATGTCATCCATCAGCACGG 59.058 55.000 0.00 0.00 0.00 4.94
140 141 1.329599 CACATGTCATCCATCAGCACG 59.670 52.381 0.00 0.00 0.00 5.34
141 142 1.674441 CCACATGTCATCCATCAGCAC 59.326 52.381 0.00 0.00 0.00 4.40
142 143 2.020181 GCCACATGTCATCCATCAGCA 61.020 52.381 0.00 0.00 0.00 4.41
143 144 0.666913 GCCACATGTCATCCATCAGC 59.333 55.000 0.00 0.00 0.00 4.26
144 145 2.047002 TGCCACATGTCATCCATCAG 57.953 50.000 0.00 0.00 0.00 2.90
145 146 2.740506 ATGCCACATGTCATCCATCA 57.259 45.000 0.00 0.00 0.00 3.07
146 147 2.953648 TGAATGCCACATGTCATCCATC 59.046 45.455 0.00 0.00 0.00 3.51
147 148 2.691526 GTGAATGCCACATGTCATCCAT 59.308 45.455 0.00 0.00 45.03 3.41
148 149 2.093890 GTGAATGCCACATGTCATCCA 58.906 47.619 0.00 0.00 45.03 3.41
149 150 2.857592 GTGAATGCCACATGTCATCC 57.142 50.000 0.00 0.00 45.03 3.51
158 159 3.391965 TGCTTTGATTTGTGAATGCCAC 58.608 40.909 0.00 0.00 45.88 5.01
159 160 3.747854 TGCTTTGATTTGTGAATGCCA 57.252 38.095 0.00 0.00 0.00 4.92
160 161 8.597662 ATTATATGCTTTGATTTGTGAATGCC 57.402 30.769 0.00 0.00 0.00 4.40
161 162 9.472361 AGATTATATGCTTTGATTTGTGAATGC 57.528 29.630 0.00 0.00 0.00 3.56
165 166 9.060347 GGAGAGATTATATGCTTTGATTTGTGA 57.940 33.333 0.00 0.00 0.00 3.58
166 167 8.295288 GGGAGAGATTATATGCTTTGATTTGTG 58.705 37.037 0.00 0.00 0.00 3.33
167 168 7.449704 GGGGAGAGATTATATGCTTTGATTTGT 59.550 37.037 0.00 0.00 0.00 2.83
168 169 7.094032 GGGGGAGAGATTATATGCTTTGATTTG 60.094 40.741 0.00 0.00 0.00 2.32
169 170 6.950619 GGGGGAGAGATTATATGCTTTGATTT 59.049 38.462 0.00 0.00 0.00 2.17
170 171 6.488715 GGGGGAGAGATTATATGCTTTGATT 58.511 40.000 0.00 0.00 0.00 2.57
171 172 6.072199 GGGGGAGAGATTATATGCTTTGAT 57.928 41.667 0.00 0.00 0.00 2.57
172 173 5.505181 GGGGGAGAGATTATATGCTTTGA 57.495 43.478 0.00 0.00 0.00 2.69
192 193 1.144503 CCCTCATCTGAAATCAGGGGG 59.855 57.143 10.37 12.02 43.91 5.40
193 194 2.130193 TCCCTCATCTGAAATCAGGGG 58.870 52.381 13.40 13.40 43.91 4.79
194 195 3.498121 CCATCCCTCATCTGAAATCAGGG 60.498 52.174 10.37 4.68 43.91 4.45
195 196 3.498121 CCCATCCCTCATCTGAAATCAGG 60.498 52.174 10.37 0.00 43.91 3.86
196 197 3.498121 CCCCATCCCTCATCTGAAATCAG 60.498 52.174 3.99 3.99 45.08 2.90
197 198 2.444388 CCCCATCCCTCATCTGAAATCA 59.556 50.000 0.00 0.00 0.00 2.57
198 199 2.444766 ACCCCATCCCTCATCTGAAATC 59.555 50.000 0.00 0.00 0.00 2.17
199 200 2.176364 CACCCCATCCCTCATCTGAAAT 59.824 50.000 0.00 0.00 0.00 2.17
200 201 1.565759 CACCCCATCCCTCATCTGAAA 59.434 52.381 0.00 0.00 0.00 2.69
201 202 1.216064 CACCCCATCCCTCATCTGAA 58.784 55.000 0.00 0.00 0.00 3.02
202 203 0.695462 CCACCCCATCCCTCATCTGA 60.695 60.000 0.00 0.00 0.00 3.27
203 204 0.695462 TCCACCCCATCCCTCATCTG 60.695 60.000 0.00 0.00 0.00 2.90
204 205 0.273161 ATCCACCCCATCCCTCATCT 59.727 55.000 0.00 0.00 0.00 2.90
205 206 0.403271 CATCCACCCCATCCCTCATC 59.597 60.000 0.00 0.00 0.00 2.92
206 207 1.723128 GCATCCACCCCATCCCTCAT 61.723 60.000 0.00 0.00 0.00 2.90
207 208 2.386100 GCATCCACCCCATCCCTCA 61.386 63.158 0.00 0.00 0.00 3.86
208 209 1.649271 AAGCATCCACCCCATCCCTC 61.649 60.000 0.00 0.00 0.00 4.30
209 210 1.224003 AAAGCATCCACCCCATCCCT 61.224 55.000 0.00 0.00 0.00 4.20
210 211 1.044790 CAAAGCATCCACCCCATCCC 61.045 60.000 0.00 0.00 0.00 3.85
211 212 0.324645 ACAAAGCATCCACCCCATCC 60.325 55.000 0.00 0.00 0.00 3.51
212 213 0.819582 CACAAAGCATCCACCCCATC 59.180 55.000 0.00 0.00 0.00 3.51
213 214 0.409092 TCACAAAGCATCCACCCCAT 59.591 50.000 0.00 0.00 0.00 4.00
214 215 0.409092 ATCACAAAGCATCCACCCCA 59.591 50.000 0.00 0.00 0.00 4.96
215 216 1.560505 AATCACAAAGCATCCACCCC 58.439 50.000 0.00 0.00 0.00 4.95
216 217 2.299867 ACAAATCACAAAGCATCCACCC 59.700 45.455 0.00 0.00 0.00 4.61
217 218 3.005684 TCACAAATCACAAAGCATCCACC 59.994 43.478 0.00 0.00 0.00 4.61
218 219 4.241590 TCACAAATCACAAAGCATCCAC 57.758 40.909 0.00 0.00 0.00 4.02
219 220 4.933505 TTCACAAATCACAAAGCATCCA 57.066 36.364 0.00 0.00 0.00 3.41
220 221 5.346822 GTCATTCACAAATCACAAAGCATCC 59.653 40.000 0.00 0.00 0.00 3.51
221 222 5.921976 TGTCATTCACAAATCACAAAGCATC 59.078 36.000 0.00 0.00 29.30 3.91
222 223 5.693104 GTGTCATTCACAAATCACAAAGCAT 59.307 36.000 0.00 0.00 45.51 3.79
223 224 5.042593 GTGTCATTCACAAATCACAAAGCA 58.957 37.500 0.00 0.00 45.51 3.91
224 225 4.146961 CGTGTCATTCACAAATCACAAAGC 59.853 41.667 0.00 0.00 46.44 3.51
225 226 5.171874 CACGTGTCATTCACAAATCACAAAG 59.828 40.000 7.58 0.00 46.44 2.77
226 227 5.033507 CACGTGTCATTCACAAATCACAAA 58.966 37.500 7.58 0.00 46.44 2.83
227 228 4.095632 ACACGTGTCATTCACAAATCACAA 59.904 37.500 17.22 0.00 46.44 3.33
228 229 3.625313 ACACGTGTCATTCACAAATCACA 59.375 39.130 17.22 0.00 46.44 3.58
229 230 4.209452 ACACGTGTCATTCACAAATCAC 57.791 40.909 17.22 0.00 46.44 3.06
230 231 4.466567 GACACGTGTCATTCACAAATCA 57.533 40.909 37.16 0.00 46.44 2.57
242 243 2.654749 TCTGATGGATGACACGTGTC 57.345 50.000 36.01 36.01 44.97 3.67
243 244 3.264947 CATTCTGATGGATGACACGTGT 58.735 45.455 23.64 23.64 0.00 4.49
244 245 3.938778 CATTCTGATGGATGACACGTG 57.061 47.619 15.48 15.48 0.00 4.49
255 256 2.915349 CAGGTGAGACCCATTCTGATG 58.085 52.381 0.00 0.00 39.75 3.07
256 257 1.211457 GCAGGTGAGACCCATTCTGAT 59.789 52.381 0.00 0.00 39.75 2.90
257 258 0.615331 GCAGGTGAGACCCATTCTGA 59.385 55.000 0.00 0.00 39.75 3.27
258 259 0.617413 AGCAGGTGAGACCCATTCTG 59.383 55.000 0.00 0.00 39.75 3.02
259 260 2.254152 TAGCAGGTGAGACCCATTCT 57.746 50.000 0.00 0.00 39.75 2.40
260 261 3.471680 GATTAGCAGGTGAGACCCATTC 58.528 50.000 0.00 0.00 39.75 2.67
261 262 2.173569 GGATTAGCAGGTGAGACCCATT 59.826 50.000 0.00 0.00 39.75 3.16
262 263 1.771255 GGATTAGCAGGTGAGACCCAT 59.229 52.381 0.00 0.00 39.75 4.00
263 264 1.204146 GGATTAGCAGGTGAGACCCA 58.796 55.000 0.00 0.00 39.75 4.51
264 265 1.204146 TGGATTAGCAGGTGAGACCC 58.796 55.000 0.00 0.00 39.75 4.46
265 266 2.435805 TCATGGATTAGCAGGTGAGACC 59.564 50.000 0.00 0.00 38.99 3.85
266 267 3.386078 TCTCATGGATTAGCAGGTGAGAC 59.614 47.826 0.00 0.00 37.69 3.36
267 268 3.386078 GTCTCATGGATTAGCAGGTGAGA 59.614 47.826 0.00 0.00 39.59 3.27
268 269 3.494048 GGTCTCATGGATTAGCAGGTGAG 60.494 52.174 0.00 0.00 35.58 3.51
269 270 2.435805 GGTCTCATGGATTAGCAGGTGA 59.564 50.000 0.00 0.00 0.00 4.02
270 271 2.437281 AGGTCTCATGGATTAGCAGGTG 59.563 50.000 0.00 0.00 0.00 4.00
271 272 2.437281 CAGGTCTCATGGATTAGCAGGT 59.563 50.000 0.00 0.00 0.00 4.00
272 273 2.224475 CCAGGTCTCATGGATTAGCAGG 60.224 54.545 0.00 0.00 40.51 4.85
273 274 2.437281 ACCAGGTCTCATGGATTAGCAG 59.563 50.000 7.43 0.00 40.51 4.24
274 275 2.435805 GACCAGGTCTCATGGATTAGCA 59.564 50.000 12.94 0.00 40.51 3.49
275 276 2.703007 AGACCAGGTCTCATGGATTAGC 59.297 50.000 17.31 0.00 38.71 3.09
307 308 6.769341 GGTGTTGAAAGTAGTAGGAGGAAAAA 59.231 38.462 0.00 0.00 0.00 1.94
308 309 6.100714 AGGTGTTGAAAGTAGTAGGAGGAAAA 59.899 38.462 0.00 0.00 0.00 2.29
309 310 5.605488 AGGTGTTGAAAGTAGTAGGAGGAAA 59.395 40.000 0.00 0.00 0.00 3.13
310 311 5.152934 AGGTGTTGAAAGTAGTAGGAGGAA 58.847 41.667 0.00 0.00 0.00 3.36
311 312 4.748701 AGGTGTTGAAAGTAGTAGGAGGA 58.251 43.478 0.00 0.00 0.00 3.71
312 313 5.238583 CAAGGTGTTGAAAGTAGTAGGAGG 58.761 45.833 0.00 0.00 35.46 4.30
313 314 5.221661 ACCAAGGTGTTGAAAGTAGTAGGAG 60.222 44.000 0.00 0.00 35.46 3.69
314 315 4.657039 ACCAAGGTGTTGAAAGTAGTAGGA 59.343 41.667 0.00 0.00 35.46 2.94
315 316 4.755123 CACCAAGGTGTTGAAAGTAGTAGG 59.245 45.833 11.08 0.00 40.91 3.18
316 317 5.924475 CACCAAGGTGTTGAAAGTAGTAG 57.076 43.478 11.08 0.00 40.91 2.57
401 404 3.118482 CGTACGTTGAAAGTTAGGTCGTG 59.882 47.826 7.22 0.00 0.00 4.35
438 441 7.826260 TTTGATTTCTTTCAAGTGTGGTTTC 57.174 32.000 0.00 0.00 36.97 2.78
533 539 4.759782 TCGCCGAACTTACTACTAGTACT 58.240 43.478 0.00 0.00 28.93 2.73
534 540 5.470845 TTCGCCGAACTTACTACTAGTAC 57.529 43.478 0.00 0.00 28.93 2.73
535 541 5.643777 ACTTTCGCCGAACTTACTACTAGTA 59.356 40.000 0.00 1.89 0.00 1.82
536 542 4.457257 ACTTTCGCCGAACTTACTACTAGT 59.543 41.667 0.00 0.00 0.00 2.57
537 543 4.979388 ACTTTCGCCGAACTTACTACTAG 58.021 43.478 0.00 0.00 0.00 2.57
538 544 6.494893 TTACTTTCGCCGAACTTACTACTA 57.505 37.500 0.00 0.00 0.00 1.82
539 545 3.930634 ACTTTCGCCGAACTTACTACT 57.069 42.857 0.00 0.00 0.00 2.57
540 546 4.031089 GCTTACTTTCGCCGAACTTACTAC 59.969 45.833 0.00 0.00 0.00 2.73
541 547 4.168760 GCTTACTTTCGCCGAACTTACTA 58.831 43.478 0.00 0.00 0.00 1.82
743 749 3.371063 GGATCGGGATCGCGGCTA 61.371 66.667 28.92 12.93 38.69 3.93
862 868 4.083862 GAGGAGGAGGCGCCGTTT 62.084 66.667 23.20 10.39 43.43 3.60
916 922 1.215423 AGGAAGAAGGTGTGTGGCTTT 59.785 47.619 0.00 0.00 0.00 3.51
928 934 0.179113 GCGAGCAGAGGAGGAAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
929 935 0.900182 TGCGAGCAGAGGAGGAAGAA 60.900 55.000 0.00 0.00 0.00 2.52
930 936 0.685785 ATGCGAGCAGAGGAGGAAGA 60.686 55.000 3.58 0.00 0.00 2.87
1008 1021 1.254284 CCAGCTCGTCCTTGAGGAGT 61.254 60.000 13.45 1.18 46.49 3.85
1011 1024 1.216710 GTCCAGCTCGTCCTTGAGG 59.783 63.158 0.00 0.00 36.47 3.86
1059 1072 1.519455 CCGCCACATCTCGAGGAAC 60.519 63.158 13.56 0.00 0.00 3.62
1087 1100 0.753262 ATGATGAGGTGGTACGGCTC 59.247 55.000 0.00 0.00 0.00 4.70
1352 1365 6.611613 TCAGTATGTGACTCCAAGAAGAAT 57.388 37.500 0.00 0.00 35.64 2.40
1353 1366 6.223852 GTTCAGTATGTGACTCCAAGAAGAA 58.776 40.000 0.00 0.00 35.64 2.52
1372 1395 1.669115 CGCAGGGTCACAGGTTCAG 60.669 63.158 0.00 0.00 0.00 3.02
1374 1397 1.021390 CATCGCAGGGTCACAGGTTC 61.021 60.000 0.00 0.00 0.00 3.62
1375 1398 1.003355 CATCGCAGGGTCACAGGTT 60.003 57.895 0.00 0.00 0.00 3.50
1376 1399 2.665000 CATCGCAGGGTCACAGGT 59.335 61.111 0.00 0.00 0.00 4.00
1423 1474 2.507102 AGCGCGTCGATGTCCTTG 60.507 61.111 8.43 0.00 0.00 3.61
1826 1877 7.846107 GCGATATGTGTGTTTAGTTCAGTTATG 59.154 37.037 0.00 0.00 0.00 1.90
1833 1886 5.796350 AAGGCGATATGTGTGTTTAGTTC 57.204 39.130 0.00 0.00 0.00 3.01
1847 1900 4.764823 ACCAAATCAAACTCAAAGGCGATA 59.235 37.500 0.00 0.00 0.00 2.92
1852 1905 4.298332 CCGAACCAAATCAAACTCAAAGG 58.702 43.478 0.00 0.00 0.00 3.11
1866 1919 1.414919 AGTTCAGTACAGCCGAACCAA 59.585 47.619 11.52 0.00 39.89 3.67
1867 1920 1.045407 AGTTCAGTACAGCCGAACCA 58.955 50.000 11.52 0.00 39.89 3.67
1868 1921 2.165319 AAGTTCAGTACAGCCGAACC 57.835 50.000 11.52 0.00 39.89 3.62
1869 1922 4.748600 AGTAAAAGTTCAGTACAGCCGAAC 59.251 41.667 0.00 2.71 39.44 3.95
1870 1923 4.748102 CAGTAAAAGTTCAGTACAGCCGAA 59.252 41.667 0.00 0.00 0.00 4.30
1871 1924 4.038282 TCAGTAAAAGTTCAGTACAGCCGA 59.962 41.667 0.00 0.00 0.00 5.54
2124 2192 0.531753 GATCTTGCCGAGCTTCTCCC 60.532 60.000 0.00 0.00 0.00 4.30
2227 2295 4.821589 GCGTCGGCCTCCTTGGAG 62.822 72.222 9.60 9.60 38.35 3.86
2315 2392 2.788640 GGTATACGCCGCCTCACCA 61.789 63.158 0.00 0.00 0.00 4.17
2316 2393 2.028631 GGTATACGCCGCCTCACC 59.971 66.667 0.00 0.00 0.00 4.02
2481 2559 2.021457 ACCCTTGAGAAAACAACACCG 58.979 47.619 0.00 0.00 0.00 4.94
2588 2666 2.162208 CACGGACAGTTGCAATGCTTAT 59.838 45.455 6.82 0.00 0.00 1.73
2589 2667 1.535028 CACGGACAGTTGCAATGCTTA 59.465 47.619 6.82 0.00 0.00 3.09
2590 2668 0.311790 CACGGACAGTTGCAATGCTT 59.688 50.000 6.82 0.00 0.00 3.91
2607 2685 4.381411 GGAGGGAATAGAAGCATACACAC 58.619 47.826 0.00 0.00 0.00 3.82
2621 2699 4.469945 TCAGTAAATTCAGACGGAGGGAAT 59.530 41.667 0.00 0.00 32.90 3.01
2649 2727 5.416271 ACGTACATTGATAGGTGACCTTT 57.584 39.130 10.53 0.27 34.61 3.11
2652 2730 5.839621 ACATACGTACATTGATAGGTGACC 58.160 41.667 0.00 0.00 0.00 4.02
2659 2737 7.809331 GGAATAACCGACATACGTACATTGATA 59.191 37.037 0.00 0.00 40.78 2.15
2662 2740 5.981315 AGGAATAACCGACATACGTACATTG 59.019 40.000 0.00 0.00 44.74 2.82
2689 2767 4.285292 GCAACACACAAACAGAGAGATTG 58.715 43.478 0.00 0.00 36.21 2.67
2741 2820 5.592104 TTAATCTATGTCGAGCAGGTTGA 57.408 39.130 0.00 0.00 0.00 3.18
2747 2826 6.333416 GGCTGATATTAATCTATGTCGAGCA 58.667 40.000 0.00 0.00 32.93 4.26
2748 2827 5.751028 GGGCTGATATTAATCTATGTCGAGC 59.249 44.000 0.00 0.00 32.93 5.03
2749 2828 5.974158 CGGGCTGATATTAATCTATGTCGAG 59.026 44.000 0.00 0.00 32.93 4.04
2750 2829 5.650703 TCGGGCTGATATTAATCTATGTCGA 59.349 40.000 0.00 0.00 32.93 4.20
2751 2830 5.891451 TCGGGCTGATATTAATCTATGTCG 58.109 41.667 0.00 0.00 32.93 4.35
2752 2831 9.250624 GTAATCGGGCTGATATTAATCTATGTC 57.749 37.037 9.70 0.00 35.84 3.06
2776 2855 7.884257 TCGTCATATTCACGGTTATTATGGTA 58.116 34.615 4.52 0.00 37.85 3.25
2777 2856 6.751157 TCGTCATATTCACGGTTATTATGGT 58.249 36.000 4.52 0.00 37.85 3.55
2778 2857 7.827819 ATCGTCATATTCACGGTTATTATGG 57.172 36.000 4.52 0.00 37.85 2.74
2791 2870 7.644157 GCCTTTTCTGGTAAAATCGTCATATTC 59.356 37.037 0.00 0.00 0.00 1.75
2793 2872 6.039382 GGCCTTTTCTGGTAAAATCGTCATAT 59.961 38.462 0.00 0.00 0.00 1.78
2794 2873 5.355910 GGCCTTTTCTGGTAAAATCGTCATA 59.644 40.000 0.00 0.00 0.00 2.15
2795 2874 4.157840 GGCCTTTTCTGGTAAAATCGTCAT 59.842 41.667 0.00 0.00 0.00 3.06
2796 2875 3.504520 GGCCTTTTCTGGTAAAATCGTCA 59.495 43.478 0.00 0.00 0.00 4.35
2797 2876 3.504520 TGGCCTTTTCTGGTAAAATCGTC 59.495 43.478 3.32 0.00 0.00 4.20
2798 2877 3.492337 TGGCCTTTTCTGGTAAAATCGT 58.508 40.909 3.32 0.00 0.00 3.73
2799 2878 3.673323 GCTGGCCTTTTCTGGTAAAATCG 60.673 47.826 3.32 0.00 0.00 3.34
2800 2879 3.673323 CGCTGGCCTTTTCTGGTAAAATC 60.673 47.826 3.32 0.00 0.00 2.17
2807 2886 4.107051 CGCGCTGGCCTTTTCTGG 62.107 66.667 5.56 0.00 35.02 3.86
2808 2887 4.107051 CCGCGCTGGCCTTTTCTG 62.107 66.667 5.56 0.00 35.02 3.02
2838 2943 1.380785 ATGCTTCCTGGTGCCATGG 60.381 57.895 7.63 7.63 0.00 3.66
2865 2970 2.103537 GGTACGTAGCAAACCACCAT 57.896 50.000 19.43 0.00 32.34 3.55
2924 3047 2.348218 CGATAACATTTTCGTAGCCGCC 60.348 50.000 0.00 0.00 0.00 6.13
2925 3048 2.536803 TCGATAACATTTTCGTAGCCGC 59.463 45.455 4.73 0.00 36.74 6.53
2933 3056 3.372822 TCGGCCAAGTCGATAACATTTTC 59.627 43.478 2.24 0.00 33.73 2.29
2936 3059 2.684001 TCGGCCAAGTCGATAACATT 57.316 45.000 2.24 0.00 33.73 2.71
2942 3065 2.167693 TGAGTTATTCGGCCAAGTCGAT 59.832 45.455 2.24 0.00 40.05 3.59
2946 3069 2.851263 TGTGAGTTATTCGGCCAAGT 57.149 45.000 2.24 0.00 0.00 3.16
2969 3092 1.304052 TGGAGGCATTTGAACCGGG 60.304 57.895 6.32 0.00 0.00 5.73
2970 3093 1.595093 GGTGGAGGCATTTGAACCGG 61.595 60.000 0.00 0.00 0.00 5.28
2972 3095 1.632589 AAGGTGGAGGCATTTGAACC 58.367 50.000 0.00 0.00 0.00 3.62
2977 3100 1.428912 TGGAGAAAGGTGGAGGCATTT 59.571 47.619 0.00 0.00 0.00 2.32
2995 3118 3.684788 GCTATTTAGACATGGCGGTATGG 59.315 47.826 0.00 0.00 32.32 2.74
3000 3123 3.393089 AGAGCTATTTAGACATGGCGG 57.607 47.619 0.00 0.00 35.84 6.13
3001 3124 4.122776 ACAAGAGCTATTTAGACATGGCG 58.877 43.478 0.00 0.00 35.84 5.69
3008 3131 2.102588 GGCGGGACAAGAGCTATTTAGA 59.897 50.000 0.00 0.00 0.00 2.10
3010 3133 2.116238 AGGCGGGACAAGAGCTATTTA 58.884 47.619 0.00 0.00 0.00 1.40
3011 3134 0.912486 AGGCGGGACAAGAGCTATTT 59.088 50.000 0.00 0.00 0.00 1.40
3012 3135 1.689273 CTAGGCGGGACAAGAGCTATT 59.311 52.381 0.00 0.00 0.00 1.73
3034 3157 4.369591 ATGGGGAGGGAGGTGGCA 62.370 66.667 0.00 0.00 0.00 4.92
3061 3184 3.447229 TGATGACGGTGAAGAGCTATTCA 59.553 43.478 19.51 19.51 36.85 2.57
3079 3202 3.236632 TCAAGAGTGGACGACATGATG 57.763 47.619 0.00 0.00 0.00 3.07
3080 3203 3.368843 CCTTCAAGAGTGGACGACATGAT 60.369 47.826 0.00 0.00 0.00 2.45
3081 3204 2.029020 CCTTCAAGAGTGGACGACATGA 60.029 50.000 0.00 0.00 0.00 3.07
3106 3229 2.443016 CCGCCTCCTCTACTGCCT 60.443 66.667 0.00 0.00 0.00 4.75
3107 3230 4.228567 GCCGCCTCCTCTACTGCC 62.229 72.222 0.00 0.00 0.00 4.85
3110 3233 1.755008 GTCAGCCGCCTCCTCTACT 60.755 63.158 0.00 0.00 0.00 2.57
3111 3234 2.787567 GGTCAGCCGCCTCCTCTAC 61.788 68.421 0.00 0.00 0.00 2.59
3112 3235 2.442272 GGTCAGCCGCCTCCTCTA 60.442 66.667 0.00 0.00 0.00 2.43
3132 3255 0.681564 TCCTCCTTCTCCTCAGCGAC 60.682 60.000 0.00 0.00 0.00 5.19
3137 3260 1.133637 CGATCCTCCTCCTTCTCCTCA 60.134 57.143 0.00 0.00 0.00 3.86
3170 3293 1.202545 GGATCTTTCTACGTGGCCTCC 60.203 57.143 3.32 0.00 0.00 4.30
3180 3303 1.758936 TCGAGTGCGGGATCTTTCTA 58.241 50.000 0.00 0.00 38.28 2.10
3212 3335 3.636300 TGGAGTGTGTTTTGGGATTTCAG 59.364 43.478 0.00 0.00 0.00 3.02
3214 3337 4.615912 CGATGGAGTGTGTTTTGGGATTTC 60.616 45.833 0.00 0.00 0.00 2.17
3215 3338 3.255642 CGATGGAGTGTGTTTTGGGATTT 59.744 43.478 0.00 0.00 0.00 2.17
3243 3366 0.818938 TCTTAGCCGCCGTGTGAATA 59.181 50.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.