Multiple sequence alignment - TraesCS7D01G208800

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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 TraesCS7D01G208800 chr7D 100.000 3458 0 0 1 3458 167059358 167055901 0.000000e+00 6386.0
1 TraesCS7D01G208800 chr7D 84.413 1328 192 10 998 2313 166928024 166926700 0.000000e+00 1291.0
2 TraesCS7D01G208800 chr7D 85.776 1160 155 8 1283 2434 166887091 166885934 0.000000e+00 1219.0
3 TraesCS7D01G208800 chr7D 92.188 64 3 2 2549 2612 513211546 513211607 4.750000e-14 89.8
4 TraesCS7D01G208800 chr7D 84.416 77 11 1 2536 2612 566988840 566988915 1.330000e-09 75.0
5 TraesCS7D01G208800 chr1A 87.268 1453 170 9 998 2441 20919536 20918090 0.000000e+00 1644.0
6 TraesCS7D01G208800 chr1D 86.944 1440 174 8 1009 2441 18995453 18994021 0.000000e+00 1605.0
7 TraesCS7D01G208800 chr1B 85.744 1452 194 6 998 2441 28163252 28161806 0.000000e+00 1522.0
8 TraesCS7D01G208800 chr1B 85.458 1451 200 5 998 2441 28166256 28164810 0.000000e+00 1500.0
9 TraesCS7D01G208800 chr7B 90.985 1076 73 12 262 1321 131074855 131073788 0.000000e+00 1428.0
10 TraesCS7D01G208800 chr7B 93.432 944 42 7 2190 3116 131067241 131066301 0.000000e+00 1382.0
11 TraesCS7D01G208800 chr7B 83.760 1447 220 11 1000 2434 130898363 130896920 0.000000e+00 1356.0
12 TraesCS7D01G208800 chr7B 93.895 344 20 1 3116 3458 131065459 131065116 5.120000e-143 518.0
13 TraesCS7D01G208800 chr7B 84.615 130 16 3 1 127 131074984 131074856 3.620000e-25 126.0
14 TraesCS7D01G208800 chr7A 84.342 1437 210 11 1009 2433 167987329 167985896 0.000000e+00 1393.0
15 TraesCS7D01G208800 chr7A 90.493 852 61 17 2611 3458 168257471 168256636 0.000000e+00 1107.0
16 TraesCS7D01G208800 chr6B 83.378 1480 224 14 1034 2502 21093098 21091630 0.000000e+00 1351.0
17 TraesCS7D01G208800 chr6B 93.750 64 3 1 2554 2617 610952839 610952777 1.020000e-15 95.3
18 TraesCS7D01G208800 chr6D 84.872 390 51 6 1034 1419 11192287 11191902 1.510000e-103 387.0
19 TraesCS7D01G208800 chr4D 93.333 60 3 1 2554 2612 466669438 466669379 1.710000e-13 87.9
20 TraesCS7D01G208800 chr2A 90.769 65 5 1 2548 2612 688224995 688224932 6.150000e-13 86.1
21 TraesCS7D01G208800 chr2A 89.231 65 6 1 2548 2612 688203513 688203450 2.860000e-11 80.5
22 TraesCS7D01G208800 chr2A 89.231 65 6 1 2548 2612 688214256 688214193 2.860000e-11 80.5
23 TraesCS7D01G208800 chrUn 87.500 72 6 3 2555 2625 351402398 351402329 2.860000e-11 80.5
24 TraesCS7D01G208800 chr5D 74.775 222 35 18 2616 2831 305208385 305208179 2.860000e-11 80.5


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 TraesCS7D01G208800 chr7D 167055901 167059358 3457 True 6386 6386 100.0000 1 3458 1 chr7D.!!$R3 3457
1 TraesCS7D01G208800 chr7D 166926700 166928024 1324 True 1291 1291 84.4130 998 2313 1 chr7D.!!$R2 1315
2 TraesCS7D01G208800 chr7D 166885934 166887091 1157 True 1219 1219 85.7760 1283 2434 1 chr7D.!!$R1 1151
3 TraesCS7D01G208800 chr1A 20918090 20919536 1446 True 1644 1644 87.2680 998 2441 1 chr1A.!!$R1 1443
4 TraesCS7D01G208800 chr1D 18994021 18995453 1432 True 1605 1605 86.9440 1009 2441 1 chr1D.!!$R1 1432
5 TraesCS7D01G208800 chr1B 28161806 28166256 4450 True 1511 1522 85.6010 998 2441 2 chr1B.!!$R1 1443
6 TraesCS7D01G208800 chr7B 130896920 130898363 1443 True 1356 1356 83.7600 1000 2434 1 chr7B.!!$R1 1434
7 TraesCS7D01G208800 chr7B 131065116 131067241 2125 True 950 1382 93.6635 2190 3458 2 chr7B.!!$R2 1268
8 TraesCS7D01G208800 chr7B 131073788 131074984 1196 True 777 1428 87.8000 1 1321 2 chr7B.!!$R3 1320
9 TraesCS7D01G208800 chr7A 167985896 167987329 1433 True 1393 1393 84.3420 1009 2433 1 chr7A.!!$R1 1424
10 TraesCS7D01G208800 chr7A 168256636 168257471 835 True 1107 1107 90.4930 2611 3458 1 chr7A.!!$R2 847
11 TraesCS7D01G208800 chr6B 21091630 21093098 1468 True 1351 1351 83.3780 1034 2502 1 chr6B.!!$R1 1468


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
604 608 0.033601 TCACCCATATTGCCACCCAC 60.034 55.0 0.0 0.0 0.0 4.61 F
1352 4378 0.104120 TACCTCGATGATGGCGGTTG 59.896 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 4928 0.250727 TGGACAAGCACAGGTAAGCC 60.251 55.0 0.0 0.0 0.0 4.35 R
2918 5968 0.532573 GATGGTCCACGAAGCTCTCA 59.467 55.0 0.0 0.0 0.0 3.27 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
127 131 9.905713 TTTATAATACTTTTCACCTGAGCTCAT 57.094 29.630 18.63 0.00 0.00 2.90
128 132 9.905713 TTATAATACTTTTCACCTGAGCTCATT 57.094 29.630 18.63 4.31 0.00 2.57
129 133 8.814038 ATAATACTTTTCACCTGAGCTCATTT 57.186 30.769 18.63 3.90 0.00 2.32
130 134 4.843220 ACTTTTCACCTGAGCTCATTTG 57.157 40.909 18.63 16.74 0.00 2.32
131 135 4.464008 ACTTTTCACCTGAGCTCATTTGA 58.536 39.130 18.63 18.77 0.00 2.69
132 136 4.518211 ACTTTTCACCTGAGCTCATTTGAG 59.482 41.667 18.63 12.54 44.75 3.02
145 149 5.633830 CTCATTTGAGCTTTGCCTAAGAA 57.366 39.130 0.00 0.00 35.48 2.52
146 150 6.017400 CTCATTTGAGCTTTGCCTAAGAAA 57.983 37.500 0.00 0.00 35.48 2.52
147 151 5.772521 TCATTTGAGCTTTGCCTAAGAAAC 58.227 37.500 0.00 0.00 35.80 2.78
148 152 5.536161 TCATTTGAGCTTTGCCTAAGAAACT 59.464 36.000 0.00 0.00 35.80 2.66
149 153 5.438761 TTTGAGCTTTGCCTAAGAAACTC 57.561 39.130 0.00 0.00 35.80 3.01
150 154 3.412386 TGAGCTTTGCCTAAGAAACTCC 58.588 45.455 0.00 0.00 35.80 3.85
151 155 3.181445 TGAGCTTTGCCTAAGAAACTCCA 60.181 43.478 0.00 0.00 35.80 3.86
152 156 3.149981 AGCTTTGCCTAAGAAACTCCAC 58.850 45.455 0.22 0.00 35.80 4.02
153 157 2.095718 GCTTTGCCTAAGAAACTCCACG 60.096 50.000 0.22 0.00 35.80 4.94
154 158 2.922740 TTGCCTAAGAAACTCCACGT 57.077 45.000 0.00 0.00 0.00 4.49
155 159 2.450609 TGCCTAAGAAACTCCACGTC 57.549 50.000 0.00 0.00 0.00 4.34
156 160 1.001633 TGCCTAAGAAACTCCACGTCC 59.998 52.381 0.00 0.00 0.00 4.79
157 161 1.675116 GCCTAAGAAACTCCACGTCCC 60.675 57.143 0.00 0.00 0.00 4.46
158 162 1.621814 CCTAAGAAACTCCACGTCCCA 59.378 52.381 0.00 0.00 0.00 4.37
159 163 2.612221 CCTAAGAAACTCCACGTCCCAC 60.612 54.545 0.00 0.00 0.00 4.61
160 164 0.834612 AAGAAACTCCACGTCCCACA 59.165 50.000 0.00 0.00 0.00 4.17
161 165 1.056660 AGAAACTCCACGTCCCACAT 58.943 50.000 0.00 0.00 0.00 3.21
162 166 2.253610 AGAAACTCCACGTCCCACATA 58.746 47.619 0.00 0.00 0.00 2.29
163 167 2.233922 AGAAACTCCACGTCCCACATAG 59.766 50.000 0.00 0.00 0.00 2.23
164 168 0.249398 AACTCCACGTCCCACATAGC 59.751 55.000 0.00 0.00 0.00 2.97
165 169 0.614979 ACTCCACGTCCCACATAGCT 60.615 55.000 0.00 0.00 0.00 3.32
166 170 0.179100 CTCCACGTCCCACATAGCTG 60.179 60.000 0.00 0.00 0.00 4.24
167 171 1.815421 CCACGTCCCACATAGCTGC 60.815 63.158 0.00 0.00 0.00 5.25
168 172 1.079197 CACGTCCCACATAGCTGCA 60.079 57.895 1.02 0.00 0.00 4.41
169 173 1.079127 ACGTCCCACATAGCTGCAC 60.079 57.895 1.02 0.00 0.00 4.57
170 174 1.815421 CGTCCCACATAGCTGCACC 60.815 63.158 1.02 0.00 0.00 5.01
171 175 1.452108 GTCCCACATAGCTGCACCC 60.452 63.158 1.02 0.00 0.00 4.61
172 176 1.616327 TCCCACATAGCTGCACCCT 60.616 57.895 1.02 0.00 0.00 4.34
173 177 1.153086 CCCACATAGCTGCACCCTC 60.153 63.158 1.02 0.00 0.00 4.30
174 178 1.522355 CCACATAGCTGCACCCTCG 60.522 63.158 1.02 0.00 0.00 4.63
175 179 1.219124 CACATAGCTGCACCCTCGT 59.781 57.895 1.02 0.00 0.00 4.18
176 180 1.086067 CACATAGCTGCACCCTCGTG 61.086 60.000 1.02 0.00 43.35 4.35
177 181 1.219124 CATAGCTGCACCCTCGTGT 59.781 57.895 1.02 0.00 42.39 4.49
178 182 0.391661 CATAGCTGCACCCTCGTGTT 60.392 55.000 1.02 0.00 42.39 3.32
179 183 0.324943 ATAGCTGCACCCTCGTGTTT 59.675 50.000 1.02 0.00 42.39 2.83
180 184 0.320421 TAGCTGCACCCTCGTGTTTC 60.320 55.000 1.02 0.00 42.39 2.78
181 185 1.598130 GCTGCACCCTCGTGTTTCT 60.598 57.895 0.00 0.00 42.39 2.52
182 186 1.569479 GCTGCACCCTCGTGTTTCTC 61.569 60.000 0.00 0.00 42.39 2.87
183 187 0.249868 CTGCACCCTCGTGTTTCTCA 60.250 55.000 0.00 0.00 42.39 3.27
184 188 0.179234 TGCACCCTCGTGTTTCTCAA 59.821 50.000 0.00 0.00 42.39 3.02
185 189 1.305201 GCACCCTCGTGTTTCTCAAA 58.695 50.000 0.00 0.00 42.39 2.69
186 190 1.673920 GCACCCTCGTGTTTCTCAAAA 59.326 47.619 0.00 0.00 42.39 2.44
187 191 2.098443 GCACCCTCGTGTTTCTCAAAAA 59.902 45.455 0.00 0.00 42.39 1.94
188 192 3.792124 GCACCCTCGTGTTTCTCAAAAAG 60.792 47.826 0.00 0.00 42.39 2.27
189 193 3.625764 CACCCTCGTGTTTCTCAAAAAGA 59.374 43.478 0.00 0.00 35.10 2.52
190 194 4.095782 CACCCTCGTGTTTCTCAAAAAGAA 59.904 41.667 0.00 0.00 42.35 2.52
191 195 8.761811 GCACCCTCGTGTTTCTCAAAAAGAAA 62.762 42.308 0.00 0.00 44.04 2.52
199 203 3.078594 TCTCAAAAAGAAAAGCCACGC 57.921 42.857 0.00 0.00 0.00 5.34
200 204 2.127251 CTCAAAAAGAAAAGCCACGCC 58.873 47.619 0.00 0.00 0.00 5.68
201 205 1.202475 TCAAAAAGAAAAGCCACGCCC 60.202 47.619 0.00 0.00 0.00 6.13
202 206 0.827368 AAAAAGAAAAGCCACGCCCA 59.173 45.000 0.00 0.00 0.00 5.36
203 207 0.389025 AAAAGAAAAGCCACGCCCAG 59.611 50.000 0.00 0.00 0.00 4.45
204 208 1.463553 AAAGAAAAGCCACGCCCAGG 61.464 55.000 0.00 0.00 0.00 4.45
211 215 3.443045 CCACGCCCAGGCATCAAC 61.443 66.667 9.78 0.00 42.06 3.18
212 216 2.360350 CACGCCCAGGCATCAACT 60.360 61.111 9.78 0.00 42.06 3.16
213 217 2.045926 ACGCCCAGGCATCAACTC 60.046 61.111 9.78 0.00 42.06 3.01
214 218 2.270205 CGCCCAGGCATCAACTCT 59.730 61.111 9.78 0.00 42.06 3.24
215 219 1.817099 CGCCCAGGCATCAACTCTC 60.817 63.158 9.78 0.00 42.06 3.20
216 220 1.452833 GCCCAGGCATCAACTCTCC 60.453 63.158 3.12 0.00 41.49 3.71
217 221 1.919600 GCCCAGGCATCAACTCTCCT 61.920 60.000 3.12 0.00 41.49 3.69
218 222 0.107312 CCCAGGCATCAACTCTCCTG 60.107 60.000 0.00 0.00 44.25 3.86
219 223 0.617413 CCAGGCATCAACTCTCCTGT 59.383 55.000 6.41 0.00 43.38 4.00
220 224 1.406614 CCAGGCATCAACTCTCCTGTC 60.407 57.143 6.41 0.00 43.38 3.51
221 225 0.534412 AGGCATCAACTCTCCTGTCG 59.466 55.000 0.00 0.00 0.00 4.35
222 226 0.247736 GGCATCAACTCTCCTGTCGT 59.752 55.000 0.00 0.00 0.00 4.34
223 227 1.634702 GCATCAACTCTCCTGTCGTC 58.365 55.000 0.00 0.00 0.00 4.20
224 228 1.203523 GCATCAACTCTCCTGTCGTCT 59.796 52.381 0.00 0.00 0.00 4.18
225 229 2.873609 CATCAACTCTCCTGTCGTCTG 58.126 52.381 0.00 0.00 0.00 3.51
226 230 1.248486 TCAACTCTCCTGTCGTCTGG 58.752 55.000 0.00 0.00 0.00 3.86
227 231 0.962489 CAACTCTCCTGTCGTCTGGT 59.038 55.000 5.57 0.00 34.80 4.00
228 232 1.341531 CAACTCTCCTGTCGTCTGGTT 59.658 52.381 5.57 0.00 34.80 3.67
229 233 1.249407 ACTCTCCTGTCGTCTGGTTC 58.751 55.000 5.57 0.00 34.80 3.62
230 234 0.169230 CTCTCCTGTCGTCTGGTTCG 59.831 60.000 5.57 0.00 34.80 3.95
231 235 0.250597 TCTCCTGTCGTCTGGTTCGA 60.251 55.000 5.57 0.00 34.80 3.71
232 236 0.811915 CTCCTGTCGTCTGGTTCGAT 59.188 55.000 5.57 0.00 39.45 3.59
233 237 1.202582 CTCCTGTCGTCTGGTTCGATT 59.797 52.381 5.57 0.00 39.45 3.34
234 238 1.067846 TCCTGTCGTCTGGTTCGATTG 60.068 52.381 5.57 0.00 39.45 2.67
235 239 1.067846 CCTGTCGTCTGGTTCGATTGA 60.068 52.381 0.00 0.00 39.45 2.57
236 240 1.986378 CTGTCGTCTGGTTCGATTGAC 59.014 52.381 0.00 0.00 39.45 3.18
237 241 1.338655 TGTCGTCTGGTTCGATTGACA 59.661 47.619 0.00 0.00 39.45 3.58
238 242 2.029380 TGTCGTCTGGTTCGATTGACAT 60.029 45.455 0.00 0.00 39.45 3.06
239 243 2.993899 GTCGTCTGGTTCGATTGACATT 59.006 45.455 0.00 0.00 39.45 2.71
240 244 2.993220 TCGTCTGGTTCGATTGACATTG 59.007 45.455 0.00 0.00 32.30 2.82
241 245 2.993220 CGTCTGGTTCGATTGACATTGA 59.007 45.455 0.00 0.00 0.00 2.57
242 246 3.181530 CGTCTGGTTCGATTGACATTGAC 60.182 47.826 0.00 0.00 0.00 3.18
243 247 2.993220 TCTGGTTCGATTGACATTGACG 59.007 45.455 0.00 0.00 0.00 4.35
244 248 2.993220 CTGGTTCGATTGACATTGACGA 59.007 45.455 0.00 0.00 0.00 4.20
245 249 2.734606 TGGTTCGATTGACATTGACGAC 59.265 45.455 0.00 0.00 32.89 4.34
246 250 2.222508 GGTTCGATTGACATTGACGACG 60.223 50.000 0.00 0.00 32.89 5.12
247 251 2.341318 TCGATTGACATTGACGACGT 57.659 45.000 0.00 0.00 0.00 4.34
248 252 2.247637 TCGATTGACATTGACGACGTC 58.752 47.619 20.97 20.97 0.00 4.34
249 253 1.982913 CGATTGACATTGACGACGTCA 59.017 47.619 26.04 26.04 41.09 4.35
250 254 2.222289 CGATTGACATTGACGACGTCAC 60.222 50.000 29.22 18.16 42.60 3.67
251 255 1.493772 TTGACATTGACGACGTCACC 58.506 50.000 29.22 18.09 42.60 4.02
252 256 0.671796 TGACATTGACGACGTCACCT 59.328 50.000 29.22 17.05 42.60 4.00
253 257 1.335597 TGACATTGACGACGTCACCTC 60.336 52.381 29.22 21.62 42.60 3.85
254 258 0.038526 ACATTGACGACGTCACCTCC 60.039 55.000 29.22 2.46 42.60 4.30
255 259 0.038618 CATTGACGACGTCACCTCCA 60.039 55.000 29.22 15.47 42.60 3.86
256 260 0.038526 ATTGACGACGTCACCTCCAC 60.039 55.000 29.22 0.88 42.60 4.02
257 261 2.079020 TTGACGACGTCACCTCCACC 62.079 60.000 29.22 0.10 42.60 4.61
258 262 2.520020 ACGACGTCACCTCCACCA 60.520 61.111 17.16 0.00 0.00 4.17
259 263 2.079020 GACGACGTCACCTCCACCAA 62.079 60.000 22.66 0.00 32.09 3.67
260 264 1.663702 CGACGTCACCTCCACCAAC 60.664 63.158 17.16 0.00 0.00 3.77
272 276 1.589461 CACCAACAACGTCGACGGA 60.589 57.895 37.89 0.00 44.95 4.69
297 301 4.514577 CAGGCGCCGGACTTCGAT 62.515 66.667 23.19 0.00 42.43 3.59
386 390 5.527951 TGTGTCCACTTTTATTTGATGCAC 58.472 37.500 0.00 0.00 0.00 4.57
390 394 5.048083 GTCCACTTTTATTTGATGCACCTGA 60.048 40.000 0.00 0.00 0.00 3.86
398 402 8.523915 TTTATTTGATGCACCTGATTAGATGT 57.476 30.769 0.00 0.00 0.00 3.06
516 520 1.550524 TCACTCTTGTCCTTCCATCGG 59.449 52.381 0.00 0.00 0.00 4.18
520 524 2.100584 CTCTTGTCCTTCCATCGGAGAG 59.899 54.545 0.00 0.00 43.63 3.20
547 551 4.099419 ACAAAATTGTCGCTCCTTTTCCTT 59.901 37.500 0.00 0.00 36.50 3.36
548 552 4.937201 AAATTGTCGCTCCTTTTCCTTT 57.063 36.364 0.00 0.00 0.00 3.11
549 553 4.505313 AATTGTCGCTCCTTTTCCTTTC 57.495 40.909 0.00 0.00 0.00 2.62
550 554 1.892209 TGTCGCTCCTTTTCCTTTCC 58.108 50.000 0.00 0.00 0.00 3.13
551 555 1.420138 TGTCGCTCCTTTTCCTTTCCT 59.580 47.619 0.00 0.00 0.00 3.36
558 562 4.281941 GCTCCTTTTCCTTTCCTGAACAAT 59.718 41.667 0.00 0.00 0.00 2.71
565 569 4.204012 TCCTTTCCTGAACAATGAAACGT 58.796 39.130 0.00 0.00 0.00 3.99
566 570 5.369833 TCCTTTCCTGAACAATGAAACGTA 58.630 37.500 0.00 0.00 0.00 3.57
584 588 7.648112 TGAAACGTATTAGTGCATAGATCACTC 59.352 37.037 0.00 0.00 43.13 3.51
594 598 5.046735 GTGCATAGATCACTCTCACCCATAT 60.047 44.000 0.00 0.00 32.66 1.78
598 602 3.072184 AGATCACTCTCACCCATATTGCC 59.928 47.826 0.00 0.00 0.00 4.52
599 603 2.195727 TCACTCTCACCCATATTGCCA 58.804 47.619 0.00 0.00 0.00 4.92
600 604 2.092968 TCACTCTCACCCATATTGCCAC 60.093 50.000 0.00 0.00 0.00 5.01
601 605 1.212935 ACTCTCACCCATATTGCCACC 59.787 52.381 0.00 0.00 0.00 4.61
602 606 0.550914 TCTCACCCATATTGCCACCC 59.449 55.000 0.00 0.00 0.00 4.61
603 607 0.258484 CTCACCCATATTGCCACCCA 59.742 55.000 0.00 0.00 0.00 4.51
604 608 0.033601 TCACCCATATTGCCACCCAC 60.034 55.000 0.00 0.00 0.00 4.61
606 610 1.309347 CCCATATTGCCACCCACCA 59.691 57.895 0.00 0.00 0.00 4.17
607 611 0.325110 CCCATATTGCCACCCACCAA 60.325 55.000 0.00 0.00 0.00 3.67
608 612 0.823460 CCATATTGCCACCCACCAAC 59.177 55.000 0.00 0.00 0.00 3.77
609 613 1.554836 CATATTGCCACCCACCAACA 58.445 50.000 0.00 0.00 0.00 3.33
621 625 4.340950 CACCCACCAACAACTGATTAAAGT 59.659 41.667 0.00 0.00 0.00 2.66
648 652 8.613482 GCTATAATGTTCTTTGGTAGGAAAGAC 58.387 37.037 0.00 0.00 40.80 3.01
652 656 5.617252 TGTTCTTTGGTAGGAAAGACGAAT 58.383 37.500 0.00 0.00 40.80 3.34
681 685 4.340950 TCCGATACACATCAACAGCTCATA 59.659 41.667 0.00 0.00 0.00 2.15
692 696 4.692155 TCAACAGCTCATACAAGACACATG 59.308 41.667 0.00 0.00 0.00 3.21
711 715 6.974932 ACATGATCATGTGTTCTGTAAGAC 57.025 37.500 34.83 0.00 46.81 3.01
725 729 6.419484 TCTGTAAGACTGGAAACATGAGAA 57.581 37.500 0.00 0.00 38.67 2.87
755 759 8.122952 GGAAATAATGAAGTTTGTATCCACGAG 58.877 37.037 0.00 0.00 0.00 4.18
847 851 4.336889 TCGAGTGAGAATGGTTTCTTGT 57.663 40.909 0.00 0.00 42.34 3.16
858 862 6.207417 AGAATGGTTTCTTGTAATGGTGACAG 59.793 38.462 0.00 0.00 41.14 3.51
877 881 2.691409 GCATGGGCTACAACTAGTCA 57.309 50.000 0.00 0.00 36.96 3.41
878 882 2.985896 GCATGGGCTACAACTAGTCAA 58.014 47.619 0.00 0.00 36.96 3.18
879 883 2.678336 GCATGGGCTACAACTAGTCAAC 59.322 50.000 0.00 0.00 36.96 3.18
880 884 3.619979 GCATGGGCTACAACTAGTCAACT 60.620 47.826 0.00 0.00 36.96 3.16
882 886 4.796038 TGGGCTACAACTAGTCAACTAC 57.204 45.455 0.00 0.00 0.00 2.73
884 888 4.589798 TGGGCTACAACTAGTCAACTACAA 59.410 41.667 0.00 0.00 0.00 2.41
886 890 4.626172 GGCTACAACTAGTCAACTACAAGC 59.374 45.833 0.00 0.00 0.00 4.01
887 891 4.323868 GCTACAACTAGTCAACTACAAGCG 59.676 45.833 0.00 0.00 0.00 4.68
888 892 3.057734 ACAACTAGTCAACTACAAGCGC 58.942 45.455 0.00 0.00 0.00 5.92
889 893 3.057019 CAACTAGTCAACTACAAGCGCA 58.943 45.455 11.47 0.00 0.00 6.09
915 934 3.404141 AACGTTGCGGCGTGCTTTT 62.404 52.632 9.37 0.00 45.00 2.27
954 973 4.113354 GACACCTTCATCACCTACGAATC 58.887 47.826 0.00 0.00 0.00 2.52
1093 1115 4.758251 TCATCGCCGCACCACTGG 62.758 66.667 0.00 0.00 0.00 4.00
1164 1186 3.764160 CTCCCGGCTCCATGGCTTC 62.764 68.421 6.96 0.00 39.32 3.86
1176 1198 1.074775 TGGCTTCCGGCAAGTTCAT 59.925 52.632 13.06 0.00 43.40 2.57
1290 4316 3.214328 CAGGCCTAAATCTAATTGCCGT 58.786 45.455 3.98 0.00 43.56 5.68
1332 4358 0.531974 AGAACGTTCGCTTCTTGCCA 60.532 50.000 21.87 0.00 38.78 4.92
1352 4378 0.104120 TACCTCGATGATGGCGGTTG 59.896 55.000 0.00 0.00 0.00 3.77
1354 4380 1.815003 CTCGATGATGGCGGTTGCA 60.815 57.895 0.00 0.00 45.35 4.08
1451 4477 2.482374 GCGCTGCTGCTTAAGTGG 59.518 61.111 14.03 0.00 36.97 4.00
1497 4523 2.048597 TTTGCAGCCGTCGACGAT 60.049 55.556 37.65 23.10 43.02 3.73
1527 4553 0.617820 AGACGGGCATAAGTCCTGGT 60.618 55.000 0.00 0.00 37.38 4.00
1532 4558 2.482326 GCATAAGTCCTGGTGCCAC 58.518 57.895 0.00 0.00 0.00 5.01
1559 4585 0.106708 ATCGTCACCAACTGCAGTGT 59.893 50.000 22.49 12.43 35.45 3.55
1564 4590 1.486310 TCACCAACTGCAGTGTCTTCT 59.514 47.619 22.49 0.00 35.45 2.85
1565 4591 1.600957 CACCAACTGCAGTGTCTTCTG 59.399 52.381 22.49 13.55 38.35 3.02
1605 4631 4.245660 CAGACATGGTCGTGAACAAGTAT 58.754 43.478 0.00 0.00 37.67 2.12
1608 4634 6.367695 CAGACATGGTCGTGAACAAGTATAAA 59.632 38.462 0.00 0.00 37.67 1.40
1617 4643 5.220043 CGTGAACAAGTATAAACTCAGAGCG 60.220 44.000 0.00 0.00 33.75 5.03
1641 4667 1.029681 TCCGTAGCGTGCACATATCT 58.970 50.000 18.64 10.07 0.00 1.98
1835 4867 0.304705 GTGCTGTTGTCAACGTCCAG 59.695 55.000 11.03 4.16 0.00 3.86
1868 4900 4.794439 CCGGCTCACGCACATCGA 62.794 66.667 0.00 0.00 42.52 3.59
1973 5005 2.270986 CCAAGGACCTTGTGGCAGC 61.271 63.158 28.45 0.00 39.58 5.25
2014 5046 1.873591 CTAACATCACGGCAATAGGGC 59.126 52.381 0.00 0.00 39.06 5.19
2046 5078 2.186384 CCCTCGGAGAAGCTGCTG 59.814 66.667 0.00 0.00 34.09 4.41
2107 5139 7.179338 GGAGAAAGATCAAGCTATATGTCCCTA 59.821 40.741 0.00 0.00 0.00 3.53
2184 5216 1.154413 CGCGGTGCAAACTAGCTTG 60.154 57.895 0.00 1.31 34.99 4.01
2272 5312 3.498397 CAGTTCATTGTGGTACGAGCTTT 59.502 43.478 0.00 0.00 0.00 3.51
2452 5497 3.695060 TCCTCTGAACATCTCGGAAGTAC 59.305 47.826 0.00 0.00 39.04 2.73
2543 5591 6.255215 CAACAACGAACAATACTTTCACAGT 58.745 36.000 0.00 0.00 39.87 3.55
2575 5623 4.938575 TTTATGGGTGTGGTTAGGTCAT 57.061 40.909 0.00 0.00 0.00 3.06
2580 5628 2.159142 GGGTGTGGTTAGGTCATAGTCG 60.159 54.545 0.00 0.00 0.00 4.18
2619 5668 5.440610 AGTCTCAGTCAAGTGACCATTTTT 58.559 37.500 7.82 0.00 45.85 1.94
2622 5671 7.556275 AGTCTCAGTCAAGTGACCATTTTTAAA 59.444 33.333 7.82 0.00 45.85 1.52
2623 5672 8.188139 GTCTCAGTCAAGTGACCATTTTTAAAA 58.812 33.333 7.82 0.00 45.85 1.52
2768 5817 8.125728 TCCGAAACACTTTTCAAAATTCATTC 57.874 30.769 0.00 0.00 41.22 2.67
2938 5988 0.179097 GAGAGCTTCGTGGACCATCC 60.179 60.000 0.00 0.00 36.96 3.51
2947 5997 1.408683 CGTGGACCATCCCATGTGAAT 60.409 52.381 0.00 0.00 38.66 2.57
3127 7020 7.409697 CACCCAACATGATATACGAAGAAAAG 58.590 38.462 0.00 0.00 0.00 2.27
3232 7126 2.975799 GGGTGAAAAGTGGCGCGA 60.976 61.111 12.10 0.00 0.00 5.87
3233 7127 2.548295 GGGTGAAAAGTGGCGCGAA 61.548 57.895 12.10 0.00 0.00 4.70
3274 7170 7.287927 CCTCTAATTGGACATGACTAGGAACTA 59.712 40.741 0.00 0.00 41.75 2.24
3286 7182 7.330900 TGACTAGGAACTATAAGACCTTTCG 57.669 40.000 0.00 0.00 41.70 3.46
3387 7283 9.903682 ACAAATGATGAAAGTGTCTCTTAAATG 57.096 29.630 0.00 0.00 35.02 2.32
3432 7328 5.901276 ACCTAGTGTTAAGATAATCCGGGAA 59.099 40.000 0.00 0.00 0.00 3.97
3439 7335 6.155565 TGTTAAGATAATCCGGGAAGAGTGAA 59.844 38.462 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 111 6.240894 TCAAATGAGCTCAGGTGAAAAGTAT 58.759 36.000 22.96 0.00 0.00 2.12
127 131 4.278419 GGAGTTTCTTAGGCAAAGCTCAAA 59.722 41.667 0.00 0.00 34.97 2.69
128 132 3.821033 GGAGTTTCTTAGGCAAAGCTCAA 59.179 43.478 0.00 0.00 34.97 3.02
129 133 3.181445 TGGAGTTTCTTAGGCAAAGCTCA 60.181 43.478 0.00 0.00 34.97 4.26
130 134 3.189495 GTGGAGTTTCTTAGGCAAAGCTC 59.811 47.826 0.00 0.00 34.97 4.09
131 135 3.149981 GTGGAGTTTCTTAGGCAAAGCT 58.850 45.455 0.00 0.00 34.97 3.74
132 136 2.095718 CGTGGAGTTTCTTAGGCAAAGC 60.096 50.000 0.00 0.00 34.97 3.51
133 137 3.139077 ACGTGGAGTTTCTTAGGCAAAG 58.861 45.455 0.00 0.00 36.45 2.77
134 138 3.135994 GACGTGGAGTTTCTTAGGCAAA 58.864 45.455 0.00 0.00 0.00 3.68
135 139 2.549349 GGACGTGGAGTTTCTTAGGCAA 60.549 50.000 0.00 0.00 0.00 4.52
136 140 1.001633 GGACGTGGAGTTTCTTAGGCA 59.998 52.381 0.00 0.00 0.00 4.75
137 141 1.675116 GGGACGTGGAGTTTCTTAGGC 60.675 57.143 0.00 0.00 0.00 3.93
138 142 1.621814 TGGGACGTGGAGTTTCTTAGG 59.378 52.381 0.00 0.00 0.00 2.69
139 143 2.036733 TGTGGGACGTGGAGTTTCTTAG 59.963 50.000 0.00 0.00 0.00 2.18
140 144 2.040939 TGTGGGACGTGGAGTTTCTTA 58.959 47.619 0.00 0.00 0.00 2.10
141 145 0.834612 TGTGGGACGTGGAGTTTCTT 59.165 50.000 0.00 0.00 0.00 2.52
142 146 1.056660 ATGTGGGACGTGGAGTTTCT 58.943 50.000 0.00 0.00 0.00 2.52
143 147 2.618053 CTATGTGGGACGTGGAGTTTC 58.382 52.381 0.00 0.00 0.00 2.78
144 148 1.338769 GCTATGTGGGACGTGGAGTTT 60.339 52.381 0.00 0.00 0.00 2.66
145 149 0.249398 GCTATGTGGGACGTGGAGTT 59.751 55.000 0.00 0.00 0.00 3.01
146 150 0.614979 AGCTATGTGGGACGTGGAGT 60.615 55.000 0.00 0.00 0.00 3.85
147 151 0.179100 CAGCTATGTGGGACGTGGAG 60.179 60.000 0.00 0.00 0.00 3.86
148 152 1.897423 CAGCTATGTGGGACGTGGA 59.103 57.895 0.00 0.00 0.00 4.02
149 153 1.815421 GCAGCTATGTGGGACGTGG 60.815 63.158 0.00 0.00 0.00 4.94
150 154 1.079197 TGCAGCTATGTGGGACGTG 60.079 57.895 0.00 0.00 0.00 4.49
151 155 1.079127 GTGCAGCTATGTGGGACGT 60.079 57.895 0.00 0.00 0.00 4.34
152 156 1.815421 GGTGCAGCTATGTGGGACG 60.815 63.158 9.07 0.00 0.00 4.79
153 157 1.452108 GGGTGCAGCTATGTGGGAC 60.452 63.158 16.65 0.00 0.00 4.46
154 158 1.616327 AGGGTGCAGCTATGTGGGA 60.616 57.895 16.65 0.00 0.00 4.37
155 159 1.153086 GAGGGTGCAGCTATGTGGG 60.153 63.158 16.65 0.00 0.00 4.61
156 160 1.522355 CGAGGGTGCAGCTATGTGG 60.522 63.158 16.65 0.00 0.00 4.17
157 161 1.086067 CACGAGGGTGCAGCTATGTG 61.086 60.000 16.65 16.37 37.35 3.21
158 162 1.219124 CACGAGGGTGCAGCTATGT 59.781 57.895 16.65 8.62 37.35 2.29
159 163 4.115279 CACGAGGGTGCAGCTATG 57.885 61.111 16.65 7.97 37.35 2.23
166 170 7.387016 TTCTTTTTGAGAAACACGAGGGTGC 62.387 44.000 0.00 0.00 42.41 5.01
167 171 4.095782 TTCTTTTTGAGAAACACGAGGGTG 59.904 41.667 0.00 0.00 43.34 4.61
168 172 3.881220 TCTTTTTGAGAAACACGAGGGT 58.119 40.909 0.00 0.00 0.00 4.34
169 173 4.893424 TTCTTTTTGAGAAACACGAGGG 57.107 40.909 0.00 0.00 41.34 4.30
178 182 3.443976 GCGTGGCTTTTCTTTTTGAGAA 58.556 40.909 0.00 0.00 42.56 2.87
179 183 2.223711 GGCGTGGCTTTTCTTTTTGAGA 60.224 45.455 0.00 0.00 0.00 3.27
180 184 2.127251 GGCGTGGCTTTTCTTTTTGAG 58.873 47.619 0.00 0.00 0.00 3.02
181 185 1.202475 GGGCGTGGCTTTTCTTTTTGA 60.202 47.619 0.00 0.00 0.00 2.69
182 186 1.217001 GGGCGTGGCTTTTCTTTTTG 58.783 50.000 0.00 0.00 0.00 2.44
183 187 0.827368 TGGGCGTGGCTTTTCTTTTT 59.173 45.000 0.00 0.00 0.00 1.94
184 188 0.389025 CTGGGCGTGGCTTTTCTTTT 59.611 50.000 0.00 0.00 0.00 2.27
185 189 1.463553 CCTGGGCGTGGCTTTTCTTT 61.464 55.000 0.00 0.00 0.00 2.52
186 190 1.903404 CCTGGGCGTGGCTTTTCTT 60.903 57.895 0.00 0.00 0.00 2.52
187 191 2.282462 CCTGGGCGTGGCTTTTCT 60.282 61.111 0.00 0.00 0.00 2.52
188 192 4.056125 GCCTGGGCGTGGCTTTTC 62.056 66.667 11.39 0.00 46.38 2.29
194 198 3.443045 GTTGATGCCTGGGCGTGG 61.443 66.667 11.37 0.00 45.51 4.94
195 199 2.360350 AGTTGATGCCTGGGCGTG 60.360 61.111 11.37 0.00 45.51 5.34
196 200 2.045926 GAGTTGATGCCTGGGCGT 60.046 61.111 5.98 5.98 45.51 5.68
197 201 1.817099 GAGAGTTGATGCCTGGGCG 60.817 63.158 7.14 0.00 45.51 6.13
198 202 1.452833 GGAGAGTTGATGCCTGGGC 60.453 63.158 4.43 4.43 42.35 5.36
199 203 0.107312 CAGGAGAGTTGATGCCTGGG 60.107 60.000 0.00 0.00 43.22 4.45
200 204 3.473147 CAGGAGAGTTGATGCCTGG 57.527 57.895 0.00 0.00 43.22 4.45
202 206 0.534412 CGACAGGAGAGTTGATGCCT 59.466 55.000 0.00 0.00 0.00 4.75
203 207 0.247736 ACGACAGGAGAGTTGATGCC 59.752 55.000 0.00 0.00 0.00 4.40
204 208 1.203523 AGACGACAGGAGAGTTGATGC 59.796 52.381 0.00 0.00 0.00 3.91
205 209 2.416566 CCAGACGACAGGAGAGTTGATG 60.417 54.545 0.00 0.00 0.00 3.07
206 210 1.821753 CCAGACGACAGGAGAGTTGAT 59.178 52.381 0.00 0.00 0.00 2.57
207 211 1.248486 CCAGACGACAGGAGAGTTGA 58.752 55.000 0.00 0.00 0.00 3.18
208 212 0.962489 ACCAGACGACAGGAGAGTTG 59.038 55.000 2.94 0.00 0.00 3.16
209 213 1.614413 GAACCAGACGACAGGAGAGTT 59.386 52.381 2.94 0.00 0.00 3.01
210 214 1.249407 GAACCAGACGACAGGAGAGT 58.751 55.000 2.94 0.00 0.00 3.24
211 215 0.169230 CGAACCAGACGACAGGAGAG 59.831 60.000 2.94 0.00 0.00 3.20
212 216 0.250597 TCGAACCAGACGACAGGAGA 60.251 55.000 2.94 0.00 34.85 3.71
213 217 0.811915 ATCGAACCAGACGACAGGAG 59.188 55.000 2.94 0.00 42.37 3.69
214 218 1.067846 CAATCGAACCAGACGACAGGA 60.068 52.381 2.94 0.00 42.37 3.86
215 219 1.067846 TCAATCGAACCAGACGACAGG 60.068 52.381 0.00 0.00 42.37 4.00
216 220 1.986378 GTCAATCGAACCAGACGACAG 59.014 52.381 0.00 0.00 42.37 3.51
217 221 1.338655 TGTCAATCGAACCAGACGACA 59.661 47.619 0.00 0.00 42.37 4.35
218 222 2.060326 TGTCAATCGAACCAGACGAC 57.940 50.000 0.00 0.00 42.37 4.34
219 223 2.993220 CAATGTCAATCGAACCAGACGA 59.007 45.455 0.00 0.00 43.65 4.20
220 224 2.993220 TCAATGTCAATCGAACCAGACG 59.007 45.455 0.00 0.00 33.83 4.18
221 225 3.181530 CGTCAATGTCAATCGAACCAGAC 60.182 47.826 0.00 0.00 0.00 3.51
222 226 2.993220 CGTCAATGTCAATCGAACCAGA 59.007 45.455 0.00 0.00 0.00 3.86
223 227 2.993220 TCGTCAATGTCAATCGAACCAG 59.007 45.455 0.00 0.00 0.00 4.00
224 228 2.734606 GTCGTCAATGTCAATCGAACCA 59.265 45.455 0.00 0.00 32.56 3.67
225 229 2.222508 CGTCGTCAATGTCAATCGAACC 60.223 50.000 0.00 0.00 32.56 3.62
226 230 2.407361 ACGTCGTCAATGTCAATCGAAC 59.593 45.455 0.00 0.00 32.56 3.95
227 231 2.659757 GACGTCGTCAATGTCAATCGAA 59.340 45.455 20.28 0.00 42.52 3.71
228 232 2.247637 GACGTCGTCAATGTCAATCGA 58.752 47.619 20.28 0.00 42.52 3.59
229 233 2.678443 GACGTCGTCAATGTCAATCG 57.322 50.000 20.28 0.00 42.52 3.34
234 238 1.337821 GAGGTGACGTCGTCAATGTC 58.662 55.000 28.48 20.03 44.49 3.06
235 239 0.038526 GGAGGTGACGTCGTCAATGT 60.039 55.000 28.48 16.12 44.49 2.71
236 240 0.038618 TGGAGGTGACGTCGTCAATG 60.039 55.000 28.48 0.00 44.49 2.82
237 241 0.038526 GTGGAGGTGACGTCGTCAAT 60.039 55.000 28.48 20.03 44.49 2.57
238 242 1.361271 GTGGAGGTGACGTCGTCAA 59.639 57.895 28.48 11.02 44.49 3.18
239 243 2.558286 GGTGGAGGTGACGTCGTCA 61.558 63.158 23.70 23.70 40.50 4.35
240 244 2.079020 TTGGTGGAGGTGACGTCGTC 62.079 60.000 18.51 18.51 0.00 4.20
241 245 2.129146 TTGGTGGAGGTGACGTCGT 61.129 57.895 11.62 0.00 0.00 4.34
242 246 1.663702 GTTGGTGGAGGTGACGTCG 60.664 63.158 11.62 0.00 0.00 5.12
243 247 0.179067 TTGTTGGTGGAGGTGACGTC 60.179 55.000 9.11 9.11 0.00 4.34
244 248 0.463116 GTTGTTGGTGGAGGTGACGT 60.463 55.000 0.00 0.00 0.00 4.34
245 249 1.495584 CGTTGTTGGTGGAGGTGACG 61.496 60.000 0.00 0.00 0.00 4.35
246 250 0.463116 ACGTTGTTGGTGGAGGTGAC 60.463 55.000 0.00 0.00 0.00 3.67
247 251 0.179067 GACGTTGTTGGTGGAGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
248 252 1.495584 CGACGTTGTTGGTGGAGGTG 61.496 60.000 0.00 0.00 0.00 4.00
249 253 1.227438 CGACGTTGTTGGTGGAGGT 60.227 57.895 0.00 0.00 0.00 3.85
250 254 1.068417 TCGACGTTGTTGGTGGAGG 59.932 57.895 1.96 0.00 0.00 4.30
251 255 1.545614 CGTCGACGTTGTTGGTGGAG 61.546 60.000 29.08 0.00 34.11 3.86
252 256 1.589461 CGTCGACGTTGTTGGTGGA 60.589 57.895 29.08 0.00 34.11 4.02
253 257 2.591311 CCGTCGACGTTGTTGGTGG 61.591 63.158 33.49 13.35 37.74 4.61
254 258 1.589461 TCCGTCGACGTTGTTGGTG 60.589 57.895 33.49 17.32 37.74 4.17
255 259 1.589727 GTCCGTCGACGTTGTTGGT 60.590 57.895 33.49 0.00 37.74 3.67
256 260 3.227667 GTCCGTCGACGTTGTTGG 58.772 61.111 33.49 18.72 37.74 3.77
280 284 4.514577 ATCGAAGTCCGGCGCCTG 62.515 66.667 26.68 19.63 39.14 4.85
288 292 5.237779 CCTAGTCTACTCTTCATCGAAGTCC 59.762 48.000 3.81 0.00 40.24 3.85
293 297 4.706035 GACCCTAGTCTACTCTTCATCGA 58.294 47.826 0.00 0.00 40.10 3.59
297 301 2.575279 ACCGACCCTAGTCTACTCTTCA 59.425 50.000 0.00 0.00 41.16 3.02
359 363 8.363390 TGCATCAAATAAAAGTGGACACAATAA 58.637 29.630 5.14 0.00 0.00 1.40
386 390 3.006752 GGAGAGCTGGACATCTAATCAGG 59.993 52.174 0.00 0.00 0.00 3.86
390 394 5.221621 GCTTTAGGAGAGCTGGACATCTAAT 60.222 44.000 0.00 0.00 37.18 1.73
516 520 4.606457 AGCGACAATTTTGTATGCTCTC 57.394 40.909 13.78 0.00 44.62 3.20
520 524 3.764885 AGGAGCGACAATTTTGTATGC 57.235 42.857 10.52 10.52 42.43 3.14
547 551 7.572353 GCACTAATACGTTTCATTGTTCAGGAA 60.572 37.037 0.00 0.00 0.00 3.36
548 552 6.128391 GCACTAATACGTTTCATTGTTCAGGA 60.128 38.462 0.00 0.00 0.00 3.86
549 553 6.021596 GCACTAATACGTTTCATTGTTCAGG 58.978 40.000 0.00 0.00 0.00 3.86
550 554 6.598525 TGCACTAATACGTTTCATTGTTCAG 58.401 36.000 0.00 0.00 0.00 3.02
551 555 6.546972 TGCACTAATACGTTTCATTGTTCA 57.453 33.333 0.00 0.00 0.00 3.18
558 562 7.489160 AGTGATCTATGCACTAATACGTTTCA 58.511 34.615 0.00 0.00 44.27 2.69
565 569 6.209589 GGGTGAGAGTGATCTATGCACTAATA 59.790 42.308 0.00 0.00 45.94 0.98
566 570 5.011533 GGGTGAGAGTGATCTATGCACTAAT 59.988 44.000 0.00 0.00 45.94 1.73
584 588 0.258484 TGGGTGGCAATATGGGTGAG 59.742 55.000 0.00 0.00 0.00 3.51
594 598 1.000993 AGTTGTTGGTGGGTGGCAA 59.999 52.632 0.00 0.00 0.00 4.52
598 602 4.340950 ACTTTAATCAGTTGTTGGTGGGTG 59.659 41.667 0.00 0.00 0.00 4.61
599 603 4.340950 CACTTTAATCAGTTGTTGGTGGGT 59.659 41.667 0.00 0.00 0.00 4.51
600 604 4.795962 GCACTTTAATCAGTTGTTGGTGGG 60.796 45.833 0.00 0.00 0.00 4.61
601 605 4.037923 AGCACTTTAATCAGTTGTTGGTGG 59.962 41.667 0.00 0.00 0.00 4.61
602 606 5.186996 AGCACTTTAATCAGTTGTTGGTG 57.813 39.130 0.00 0.00 0.00 4.17
603 607 8.630054 TTATAGCACTTTAATCAGTTGTTGGT 57.370 30.769 0.00 0.00 0.00 3.67
604 608 9.507280 CATTATAGCACTTTAATCAGTTGTTGG 57.493 33.333 0.00 0.00 0.00 3.77
621 625 8.325787 TCTTTCCTACCAAAGAACATTATAGCA 58.674 33.333 0.00 0.00 39.06 3.49
648 652 5.758924 TGATGTGTATCGGAGACTAATTCG 58.241 41.667 4.23 0.00 42.51 3.34
652 656 5.678871 GCTGTTGATGTGTATCGGAGACTAA 60.679 44.000 4.23 0.00 42.51 2.24
692 696 5.724328 TCCAGTCTTACAGAACACATGATC 58.276 41.667 0.00 0.00 0.00 2.92
755 759 2.075338 ACGTCTTCTAGACTCGTGGTC 58.925 52.381 12.92 3.77 42.92 4.02
801 805 2.156917 CATGCACCATCTTGTGACAGT 58.843 47.619 0.00 0.00 38.55 3.55
847 851 3.189568 GCCCATGCTGTCACCATTA 57.810 52.632 0.00 0.00 33.53 1.90
858 862 2.678336 GTTGACTAGTTGTAGCCCATGC 59.322 50.000 0.00 0.00 37.95 4.06
874 878 1.606606 GCATTGCGCTTGTAGTTGAC 58.393 50.000 9.73 0.00 37.77 3.18
887 891 2.696521 CGCAACGTTCACGCATTGC 61.697 57.895 14.45 14.45 43.40 3.56
888 892 2.074353 CCGCAACGTTCACGCATTG 61.074 57.895 13.36 0.00 44.43 2.82
889 893 2.251075 CCGCAACGTTCACGCATT 59.749 55.556 13.36 0.00 44.43 3.56
897 916 2.049475 TAAAAGCACGCCGCAACGTT 62.049 50.000 0.00 0.00 45.75 3.99
915 934 5.021458 AGGTGTCGGAACTTAGGAGATTTA 58.979 41.667 0.00 0.00 0.00 1.40
954 973 0.315869 GTGTCGTGGCTTCGTTGTTG 60.316 55.000 3.16 0.00 0.00 3.33
990 1009 4.394300 GGTGAGATGACCATGTTTCTGAAG 59.606 45.833 0.00 0.00 35.88 3.02
1164 1186 1.813513 AGAAGACATGAACTTGCCGG 58.186 50.000 0.00 0.00 0.00 6.13
1170 1192 1.072331 ACGGCCAAGAAGACATGAACT 59.928 47.619 2.24 0.00 0.00 3.01
1176 1198 1.416401 AGAAAGACGGCCAAGAAGACA 59.584 47.619 2.24 0.00 0.00 3.41
1243 4269 3.441496 AGAGTAGTCGACGAGGTAGAG 57.559 52.381 10.46 0.00 0.00 2.43
1290 4316 4.205683 CCACCAAGGATCCTATGGAGACA 61.206 52.174 32.56 0.00 43.43 3.41
1332 4358 1.048601 AACCGCCATCATCGAGGTAT 58.951 50.000 0.00 0.00 34.35 2.73
1352 4378 1.135315 ATGCGCGTCATGAAGTTGC 59.865 52.632 8.43 16.65 33.26 4.17
1476 4502 1.710339 GTCGACGGCTGCAAAGATC 59.290 57.895 0.00 0.00 0.00 2.75
1497 4523 2.342279 CCCGTCTTGGCGAACAGA 59.658 61.111 0.00 0.00 35.87 3.41
1559 4585 4.689549 TCGGGGTCGGGCAGAAGA 62.690 66.667 0.00 0.00 36.95 2.87
1584 4610 2.910688 ACTTGTTCACGACCATGTCT 57.089 45.000 0.00 0.00 0.00 3.41
1605 4631 2.961526 GGATGTCCGCTCTGAGTTTA 57.038 50.000 6.53 0.00 0.00 2.01
1617 4643 2.165301 GTGCACGCTACGGATGTCC 61.165 63.158 0.00 0.00 0.00 4.02
1626 4652 1.408969 TCCCAGATATGTGCACGCTA 58.591 50.000 13.13 6.89 0.00 4.26
1747 4779 3.195661 GGTTCTTGCCGGTATAGTTGAG 58.804 50.000 1.90 0.00 0.00 3.02
1822 4854 1.068417 CGGACCTGGACGTTGACAA 59.932 57.895 0.00 0.00 0.00 3.18
1827 4859 2.732658 GACACGGACCTGGACGTT 59.267 61.111 16.02 9.55 42.04 3.99
1835 4867 4.754667 GGAAGCGGGACACGGACC 62.755 72.222 0.00 0.00 44.51 4.46
1896 4928 0.250727 TGGACAAGCACAGGTAAGCC 60.251 55.000 0.00 0.00 0.00 4.35
1991 5023 1.526887 CTATTGCCGTGATGTTAGCCG 59.473 52.381 0.00 0.00 0.00 5.52
1995 5027 1.476110 GGCCCTATTGCCGTGATGTTA 60.476 52.381 0.00 0.00 42.54 2.41
2046 5078 2.169179 GCAATGAACGAGATCGCAAAC 58.831 47.619 1.39 0.00 44.43 2.93
2082 5114 7.003402 AGGGACATATAGCTTGATCTTTCTC 57.997 40.000 0.00 0.00 0.00 2.87
2107 5139 2.340328 GGAAGGCCGTGCGGAAATT 61.340 57.895 15.45 5.05 37.50 1.82
2184 5216 3.553511 CCACGTCTTCATCTGATAAGCAC 59.446 47.826 0.00 0.00 0.00 4.40
2272 5312 1.770658 CCTCTTGGCCTCCATGTATGA 59.229 52.381 3.32 0.00 31.53 2.15
2452 5497 1.665679 ACGTGCATGATCCTTTTAGCG 59.334 47.619 14.17 0.00 0.00 4.26
2507 5552 6.503616 TGTTCGTTGTTGCAATAACAAATC 57.496 33.333 30.45 19.48 41.23 2.17
2565 5613 4.035441 GTCTCAGTCGACTATGACCTAACC 59.965 50.000 26.55 10.88 39.77 2.85
2566 5614 4.877251 AGTCTCAGTCGACTATGACCTAAC 59.123 45.833 30.05 16.84 42.19 2.34
2575 5623 5.068636 ACTTGGTTAAGTCTCAGTCGACTA 58.931 41.667 19.57 0.00 43.53 2.59
2858 5908 7.704899 GCTCCACTGTTAACTTGTAAAATGTTT 59.295 33.333 7.22 0.00 0.00 2.83
2918 5968 0.532573 GATGGTCCACGAAGCTCTCA 59.467 55.000 0.00 0.00 0.00 3.27
2938 5988 2.946990 TGCTGCTATGACATTCACATGG 59.053 45.455 0.00 0.00 34.27 3.66
2947 5997 3.018856 CCTTGGAATTGCTGCTATGACA 58.981 45.455 0.00 0.00 0.00 3.58
3093 6144 6.747414 ATATCATGTTGGGTGCTACTAGAA 57.253 37.500 0.00 0.00 0.00 2.10
3127 7020 6.128769 GGTTTTTAATTATGTTTCGGTGGTGC 60.129 38.462 0.00 0.00 0.00 5.01
3158 7052 7.721402 TGTGGTCTTTTTGTTTTATATGTGCT 58.279 30.769 0.00 0.00 0.00 4.40
3232 7126 1.140252 AGAGGCTAACGTGTGGTTGTT 59.860 47.619 0.00 0.00 39.75 2.83
3233 7127 0.756903 AGAGGCTAACGTGTGGTTGT 59.243 50.000 0.00 0.00 39.75 3.32
3274 7170 4.995487 GTGAAACACTCCGAAAGGTCTTAT 59.005 41.667 0.00 0.00 45.88 1.73
3286 7182 3.476552 TGATGTTGAGGTGAAACACTCC 58.523 45.455 0.00 0.00 40.16 3.85
3387 7283 2.580867 CGCCTGCGTGTAGAGCTC 60.581 66.667 5.27 5.27 35.28 4.09



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

AutoCloner maintained by Alex Coulton.