Multiple sequence alignment - TraesCS3B01G609700

Loading Multiple Alignment...

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 TraesCS3B01G609700 chr3B 100.000 2843 0 0 1 2843 828768835 828765993 0.000000e+00 5251.0
1 TraesCS3B01G609700 chr3B 97.163 2080 36 2 773 2843 828417291 828419356 0.000000e+00 3493.0
2 TraesCS3B01G609700 chr3B 88.768 276 21 5 445 711 828416680 828416954 2.110000e-86 329.0
3 TraesCS3B01G609700 chr3B 94.017 117 4 1 1 117 828416524 828416637 1.050000e-39 174.0
4 TraesCS3B01G609700 chr3B 95.918 49 2 0 633 681 828768106 828768058 2.350000e-11 80.5
5 TraesCS3B01G609700 chr3B 95.918 49 2 0 730 778 828768203 828768155 2.350000e-11 80.5
6 TraesCS3B01G609700 chr3D 92.843 1970 101 25 773 2725 610800551 610802497 0.000000e+00 2820.0
7 TraesCS3B01G609700 chr3D 88.727 275 22 6 445 711 610799944 610800217 7.590000e-86 327.0
8 TraesCS3B01G609700 chr3D 86.275 153 14 5 2692 2838 610802518 610802669 2.930000e-35 159.0
9 TraesCS3B01G609700 chr3D 88.136 118 8 2 1 118 610799819 610799930 4.940000e-28 135.0
10 TraesCS3B01G609700 chr3A 89.079 1108 68 11 773 1851 745509095 745510178 0.000000e+00 1327.0
11 TraesCS3B01G609700 chr3A 85.714 420 31 13 285 683 745508304 745508715 1.580000e-112 416.0
12 TraesCS3B01G609700 chr5A 81.353 1094 163 30 776 1852 382291843 382292912 0.000000e+00 852.0
13 TraesCS3B01G609700 chr5D 81.244 1093 160 29 776 1852 288818281 288819344 0.000000e+00 841.0
14 TraesCS3B01G609700 chr5D 80.568 1091 177 25 781 1852 289008410 289009484 0.000000e+00 808.0
15 TraesCS3B01G609700 chr5B 80.716 1089 181 20 776 1851 328233848 328234920 0.000000e+00 821.0


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 TraesCS3B01G609700 chr3B 828765993 828768835 2842 True 1804.00 5251 97.278667 1 2843 3 chr3B.!!$R1 2842
1 TraesCS3B01G609700 chr3B 828416524 828419356 2832 False 1332.00 3493 93.316000 1 2843 3 chr3B.!!$F1 2842
2 TraesCS3B01G609700 chr3D 610799819 610802669 2850 False 860.25 2820 88.995250 1 2838 4 chr3D.!!$F1 2837
3 TraesCS3B01G609700 chr3A 745508304 745510178 1874 False 871.50 1327 87.396500 285 1851 2 chr3A.!!$F1 1566
4 TraesCS3B01G609700 chr5A 382291843 382292912 1069 False 852.00 852 81.353000 776 1852 1 chr5A.!!$F1 1076
5 TraesCS3B01G609700 chr5D 288818281 288819344 1063 False 841.00 841 81.244000 776 1852 1 chr5D.!!$F1 1076
6 TraesCS3B01G609700 chr5D 289008410 289009484 1074 False 808.00 808 80.568000 781 1852 1 chr5D.!!$F2 1071
7 TraesCS3B01G609700 chr5B 328233848 328234920 1072 False 821.00 821 80.716000 776 1851 1 chr5B.!!$F1 1075

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
117 118 0.099791 CTCCTCCTCGCGAAGAAGAC 59.900 60.0 11.33 0.0 0.00 3.01 F
131 132 0.107459 GAAGACTGGGTGGAGATGCC 60.107 60.0 0.00 0.0 37.10 4.40 F
734 764 0.107508 GCACAGAGCCAGCATTAGGA 60.108 55.0 0.00 0.0 37.23 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 1854 1.667151 GCCTTGCCACAAAGATGCA 59.333 52.632 0.00 0.00 0.00 3.96 R
1509 1886 1.898472 CTCTTCTGAAGCTCCCAGTCA 59.102 52.381 12.54 1.03 33.57 3.41 R
2217 2608 0.175531 CAACCATCAATTTCCGGGCC 59.824 55.000 0.00 0.00 0.00 5.80 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
56 57 3.740044 TTTGCCGCTTTCTATTTCTCG 57.260 42.857 0.00 0.00 0.00 4.04
94 95 1.263356 TCTAGTTTAGCCGCCACACT 58.737 50.000 0.00 0.00 0.00 3.55
95 96 2.449464 TCTAGTTTAGCCGCCACACTA 58.551 47.619 0.00 0.00 0.00 2.74
96 97 3.028850 TCTAGTTTAGCCGCCACACTAT 58.971 45.455 0.00 0.00 0.00 2.12
105 106 0.757188 CGCCACACTATCCTCCTCCT 60.757 60.000 0.00 0.00 0.00 3.69
117 118 0.099791 CTCCTCCTCGCGAAGAAGAC 59.900 60.000 11.33 0.00 0.00 3.01
118 119 0.322636 TCCTCCTCGCGAAGAAGACT 60.323 55.000 11.33 0.00 0.00 3.24
119 120 0.179150 CCTCCTCGCGAAGAAGACTG 60.179 60.000 11.33 0.00 0.00 3.51
120 121 0.179150 CTCCTCGCGAAGAAGACTGG 60.179 60.000 11.33 5.21 0.00 4.00
121 122 1.153745 CCTCGCGAAGAAGACTGGG 60.154 63.158 11.33 0.00 0.00 4.45
122 123 1.587054 CTCGCGAAGAAGACTGGGT 59.413 57.895 11.33 0.00 0.00 4.51
123 124 0.734253 CTCGCGAAGAAGACTGGGTG 60.734 60.000 11.33 0.00 0.00 4.61
124 125 1.738099 CGCGAAGAAGACTGGGTGG 60.738 63.158 0.00 0.00 0.00 4.61
125 126 1.671742 GCGAAGAAGACTGGGTGGA 59.328 57.895 0.00 0.00 0.00 4.02
126 127 0.390472 GCGAAGAAGACTGGGTGGAG 60.390 60.000 0.00 0.00 0.00 3.86
127 128 1.257743 CGAAGAAGACTGGGTGGAGA 58.742 55.000 0.00 0.00 0.00 3.71
128 129 1.827969 CGAAGAAGACTGGGTGGAGAT 59.172 52.381 0.00 0.00 0.00 2.75
129 130 2.417924 CGAAGAAGACTGGGTGGAGATG 60.418 54.545 0.00 0.00 0.00 2.90
130 131 0.908198 AGAAGACTGGGTGGAGATGC 59.092 55.000 0.00 0.00 0.00 3.91
131 132 0.107459 GAAGACTGGGTGGAGATGCC 60.107 60.000 0.00 0.00 37.10 4.40
132 133 1.903877 AAGACTGGGTGGAGATGCCG 61.904 60.000 0.00 0.00 40.66 5.69
133 134 2.607750 ACTGGGTGGAGATGCCGT 60.608 61.111 0.00 0.00 40.66 5.68
141 142 1.220749 GGAGATGCCGTACCTTGCA 59.779 57.895 2.32 2.32 42.52 4.08
146 147 1.089481 ATGCCGTACCTTGCATGTCG 61.089 55.000 10.40 0.00 45.96 4.35
154 155 1.204941 ACCTTGCATGTCGTCCTAGTC 59.795 52.381 0.00 0.00 0.00 2.59
159 160 1.202582 GCATGTCGTCCTAGTCTGTGT 59.797 52.381 0.00 0.00 0.00 3.72
163 164 1.154016 CGTCCTAGTCTGTGTGCCG 60.154 63.158 0.00 0.00 0.00 5.69
165 166 0.818296 GTCCTAGTCTGTGTGCCGAT 59.182 55.000 0.00 0.00 0.00 4.18
166 167 1.103803 TCCTAGTCTGTGTGCCGATC 58.896 55.000 0.00 0.00 0.00 3.69
178 179 3.380671 CCGATCACACGGCGTTAC 58.619 61.111 11.19 0.00 46.20 2.50
179 180 2.162754 CCGATCACACGGCGTTACC 61.163 63.158 11.19 0.00 46.20 2.85
180 181 1.444724 CGATCACACGGCGTTACCA 60.445 57.895 11.19 0.00 39.03 3.25
181 182 1.009903 CGATCACACGGCGTTACCAA 61.010 55.000 11.19 0.00 39.03 3.67
182 183 1.149987 GATCACACGGCGTTACCAAA 58.850 50.000 11.19 0.00 39.03 3.28
183 184 0.869730 ATCACACGGCGTTACCAAAC 59.130 50.000 11.19 0.00 39.03 2.93
184 185 0.179078 TCACACGGCGTTACCAAACT 60.179 50.000 11.19 0.00 39.03 2.66
185 186 1.068281 TCACACGGCGTTACCAAACTA 59.932 47.619 11.19 0.00 39.03 2.24
186 187 1.865970 CACACGGCGTTACCAAACTAA 59.134 47.619 11.19 0.00 39.03 2.24
187 188 2.481185 CACACGGCGTTACCAAACTAAT 59.519 45.455 11.19 0.00 39.03 1.73
188 189 2.738314 ACACGGCGTTACCAAACTAATC 59.262 45.455 11.19 0.00 39.03 1.75
189 190 2.094734 CACGGCGTTACCAAACTAATCC 59.905 50.000 11.19 0.00 39.03 3.01
190 191 1.667212 CGGCGTTACCAAACTAATCCC 59.333 52.381 0.00 0.00 39.03 3.85
191 192 2.713877 GGCGTTACCAAACTAATCCCA 58.286 47.619 0.00 0.00 38.86 4.37
192 193 2.421073 GGCGTTACCAAACTAATCCCAC 59.579 50.000 0.00 0.00 38.86 4.61
193 194 3.075884 GCGTTACCAAACTAATCCCACA 58.924 45.455 0.00 0.00 33.15 4.17
194 195 3.120095 GCGTTACCAAACTAATCCCACAC 60.120 47.826 0.00 0.00 33.15 3.82
195 196 4.066490 CGTTACCAAACTAATCCCACACA 58.934 43.478 0.00 0.00 33.15 3.72
196 197 4.698304 CGTTACCAAACTAATCCCACACAT 59.302 41.667 0.00 0.00 33.15 3.21
197 198 5.391523 CGTTACCAAACTAATCCCACACATG 60.392 44.000 0.00 0.00 33.15 3.21
198 199 3.430453 ACCAAACTAATCCCACACATGG 58.570 45.455 0.00 0.00 46.81 3.66
199 200 7.249219 GTTACCAAACTAATCCCACACATGGA 61.249 42.308 0.00 0.00 39.33 3.41
200 201 8.968055 GTTACCAAACTAATCCCACACATGGAG 61.968 44.444 0.00 0.00 39.33 3.86
213 214 5.954335 CACACATGGAGGAAAAGAAATACC 58.046 41.667 0.00 0.00 0.00 2.73
214 215 4.700213 ACACATGGAGGAAAAGAAATACCG 59.300 41.667 0.00 0.00 0.00 4.02
215 216 3.694566 ACATGGAGGAAAAGAAATACCGC 59.305 43.478 0.00 0.00 0.00 5.68
216 217 2.718563 TGGAGGAAAAGAAATACCGCC 58.281 47.619 0.00 0.00 41.52 6.13
217 218 1.669265 GGAGGAAAAGAAATACCGCCG 59.331 52.381 0.00 0.00 33.30 6.46
218 219 2.624636 GAGGAAAAGAAATACCGCCGA 58.375 47.619 0.00 0.00 0.00 5.54
219 220 3.203716 GAGGAAAAGAAATACCGCCGAT 58.796 45.455 0.00 0.00 0.00 4.18
220 221 2.943033 AGGAAAAGAAATACCGCCGATG 59.057 45.455 0.00 0.00 0.00 3.84
221 222 2.540973 GGAAAAGAAATACCGCCGATGC 60.541 50.000 0.00 0.00 0.00 3.91
222 223 1.745232 AAAGAAATACCGCCGATGCA 58.255 45.000 0.00 0.00 37.32 3.96
223 224 1.967319 AAGAAATACCGCCGATGCAT 58.033 45.000 0.00 0.00 37.32 3.96
224 225 1.967319 AGAAATACCGCCGATGCATT 58.033 45.000 0.00 0.00 37.32 3.56
225 226 1.603802 AGAAATACCGCCGATGCATTG 59.396 47.619 6.99 6.99 37.32 2.82
226 227 0.667993 AAATACCGCCGATGCATTGG 59.332 50.000 26.56 26.56 37.32 3.16
227 228 0.465460 AATACCGCCGATGCATTGGT 60.465 50.000 29.87 21.95 37.32 3.67
228 229 1.165907 ATACCGCCGATGCATTGGTG 61.166 55.000 31.95 31.95 40.76 4.17
229 230 2.529454 TACCGCCGATGCATTGGTGT 62.529 55.000 34.37 29.25 39.69 4.16
230 231 1.817520 CCGCCGATGCATTGGTGTA 60.818 57.895 34.37 0.00 39.69 2.90
231 232 1.165907 CCGCCGATGCATTGGTGTAT 61.166 55.000 34.37 0.00 39.69 2.29
232 233 0.662619 CGCCGATGCATTGGTGTATT 59.337 50.000 30.96 0.00 37.13 1.89
233 234 1.334059 CGCCGATGCATTGGTGTATTC 60.334 52.381 30.96 15.08 37.13 1.75
234 235 1.001378 GCCGATGCATTGGTGTATTCC 60.001 52.381 29.87 11.11 37.47 3.01
235 236 2.575532 CCGATGCATTGGTGTATTCCT 58.424 47.619 23.23 0.00 30.30 3.36
236 237 2.549754 CCGATGCATTGGTGTATTCCTC 59.450 50.000 23.23 0.00 30.30 3.71
237 238 2.549754 CGATGCATTGGTGTATTCCTCC 59.450 50.000 5.98 0.00 30.30 4.30
238 239 3.554934 GATGCATTGGTGTATTCCTCCA 58.445 45.455 0.00 0.00 30.30 3.86
239 240 3.668141 TGCATTGGTGTATTCCTCCAT 57.332 42.857 0.00 0.00 0.00 3.41
240 241 4.787135 TGCATTGGTGTATTCCTCCATA 57.213 40.909 0.00 0.00 0.00 2.74
241 242 4.717877 TGCATTGGTGTATTCCTCCATAG 58.282 43.478 0.00 0.00 0.00 2.23
242 243 4.165950 TGCATTGGTGTATTCCTCCATAGT 59.834 41.667 0.00 0.00 0.00 2.12
243 244 5.133221 GCATTGGTGTATTCCTCCATAGTT 58.867 41.667 0.00 0.00 0.00 2.24
244 245 5.594317 GCATTGGTGTATTCCTCCATAGTTT 59.406 40.000 0.00 0.00 0.00 2.66
245 246 6.238759 GCATTGGTGTATTCCTCCATAGTTTC 60.239 42.308 0.00 0.00 0.00 2.78
246 247 6.381498 TTGGTGTATTCCTCCATAGTTTCA 57.619 37.500 0.00 0.00 0.00 2.69
247 248 5.989477 TGGTGTATTCCTCCATAGTTTCAG 58.011 41.667 0.00 0.00 0.00 3.02
248 249 5.487488 TGGTGTATTCCTCCATAGTTTCAGT 59.513 40.000 0.00 0.00 0.00 3.41
249 250 6.049790 GGTGTATTCCTCCATAGTTTCAGTC 58.950 44.000 0.00 0.00 0.00 3.51
250 251 6.351881 GGTGTATTCCTCCATAGTTTCAGTCA 60.352 42.308 0.00 0.00 0.00 3.41
251 252 6.535508 GTGTATTCCTCCATAGTTTCAGTCAC 59.464 42.308 0.00 0.00 0.00 3.67
252 253 5.762179 ATTCCTCCATAGTTTCAGTCACA 57.238 39.130 0.00 0.00 0.00 3.58
253 254 4.808414 TCCTCCATAGTTTCAGTCACAG 57.192 45.455 0.00 0.00 0.00 3.66
254 255 4.416516 TCCTCCATAGTTTCAGTCACAGA 58.583 43.478 0.00 0.00 0.00 3.41
255 256 4.464244 TCCTCCATAGTTTCAGTCACAGAG 59.536 45.833 0.00 0.00 0.00 3.35
256 257 4.382470 CCTCCATAGTTTCAGTCACAGAGG 60.382 50.000 0.00 0.00 0.00 3.69
257 258 4.416516 TCCATAGTTTCAGTCACAGAGGA 58.583 43.478 0.00 0.00 0.00 3.71
258 259 4.464244 TCCATAGTTTCAGTCACAGAGGAG 59.536 45.833 0.00 0.00 0.00 3.69
259 260 4.464244 CCATAGTTTCAGTCACAGAGGAGA 59.536 45.833 0.00 0.00 0.00 3.71
260 261 5.128499 CCATAGTTTCAGTCACAGAGGAGAT 59.872 44.000 0.00 0.00 0.00 2.75
261 262 4.533919 AGTTTCAGTCACAGAGGAGATG 57.466 45.455 0.00 0.00 0.00 2.90
262 263 2.999355 GTTTCAGTCACAGAGGAGATGC 59.001 50.000 0.00 0.00 0.00 3.91
263 264 1.189752 TCAGTCACAGAGGAGATGCC 58.810 55.000 0.00 0.00 0.00 4.40
271 272 2.898738 AGGAGATGCCTCGTGCTG 59.101 61.111 1.74 0.00 46.97 4.41
272 273 2.202987 GGAGATGCCTCGTGCTGG 60.203 66.667 1.74 0.00 40.33 4.85
273 274 2.202987 GAGATGCCTCGTGCTGGG 60.203 66.667 1.74 0.00 42.00 4.45
274 275 3.746949 GAGATGCCTCGTGCTGGGG 62.747 68.421 1.74 0.00 42.00 4.96
294 295 2.942796 CGCACCTGTGGCTCCACTA 61.943 63.158 18.72 5.95 46.30 2.74
313 314 1.859302 ACCTCTTCTCAGCCTGGTAG 58.141 55.000 0.00 0.00 0.00 3.18
324 325 0.610687 GCCTGGTAGAGCTCACAAGT 59.389 55.000 17.77 0.00 0.00 3.16
325 326 1.825474 GCCTGGTAGAGCTCACAAGTA 59.175 52.381 17.77 0.00 0.00 2.24
326 327 2.432510 GCCTGGTAGAGCTCACAAGTAT 59.567 50.000 17.77 0.00 0.00 2.12
327 328 3.637229 GCCTGGTAGAGCTCACAAGTATA 59.363 47.826 17.77 0.00 0.00 1.47
336 337 6.696411 AGAGCTCACAAGTATATATGAAGCC 58.304 40.000 17.77 5.09 32.88 4.35
414 416 0.616395 TGGCGGGGTACTGAAGATGA 60.616 55.000 0.00 0.00 0.00 2.92
419 421 2.101582 CGGGGTACTGAAGATGAGGAAG 59.898 54.545 0.00 0.00 0.00 3.46
425 446 6.317391 GGGTACTGAAGATGAGGAAGATTTTG 59.683 42.308 0.00 0.00 0.00 2.44
490 511 2.420022 ACATAGTCGCATGGCTTTGTTC 59.580 45.455 0.00 0.00 0.00 3.18
495 516 1.052287 CGCATGGCTTTGTTCGTTTC 58.948 50.000 0.00 0.00 0.00 2.78
502 523 3.181501 TGGCTTTGTTCGTTTCAAGTCTG 60.182 43.478 0.00 0.00 0.00 3.51
534 555 1.331756 ACAGAGTTACGCGTATACCCG 59.668 52.381 21.30 11.43 0.00 5.28
547 568 6.478344 ACGCGTATACCCGAAATACAATTAAA 59.522 34.615 11.67 0.00 31.43 1.52
555 576 6.596106 ACCCGAAATACAATTAAAATTTGGGC 59.404 34.615 14.24 0.00 37.23 5.36
571 592 1.527380 GGCAAGGAACCCGTTGACA 60.527 57.895 0.00 0.00 43.65 3.58
578 599 1.269051 GGAACCCGTTGACAAGCAAAG 60.269 52.381 0.00 0.00 38.44 2.77
609 630 4.710324 TCTAACCACAACAACTACTTGGG 58.290 43.478 0.00 0.00 0.00 4.12
619 640 3.264450 ACAACTACTTGGGAGGGATTCAG 59.736 47.826 0.00 0.00 0.00 3.02
625 646 3.311702 ACTTGGGAGGGATTCAGACCTAT 60.312 47.826 0.00 0.00 37.18 2.57
683 705 2.372852 GACCTACTTGGAGGGCACA 58.627 57.895 0.00 0.00 45.09 4.57
684 706 0.250513 GACCTACTTGGAGGGCACAG 59.749 60.000 0.00 0.00 45.09 3.66
701 731 3.011818 CACAGAGCCAGCATTATGACAA 58.988 45.455 0.00 0.00 0.00 3.18
711 741 5.817296 CCAGCATTATGACAAAGCTAGTGTA 59.183 40.000 3.07 0.00 33.59 2.90
712 742 6.238211 CCAGCATTATGACAAAGCTAGTGTAC 60.238 42.308 3.07 0.00 33.59 2.90
714 744 5.584649 GCATTATGACAAAGCTAGTGTACCA 59.415 40.000 3.07 0.00 0.00 3.25
715 745 6.238211 GCATTATGACAAAGCTAGTGTACCAG 60.238 42.308 3.07 0.00 0.00 4.00
716 746 3.040147 TGACAAAGCTAGTGTACCAGC 57.960 47.619 3.07 3.65 38.09 4.85
718 748 2.737252 GACAAAGCTAGTGTACCAGCAC 59.263 50.000 12.18 0.00 40.36 4.40
720 750 2.738846 CAAAGCTAGTGTACCAGCACAG 59.261 50.000 12.18 0.00 41.52 3.66
722 752 1.821753 AGCTAGTGTACCAGCACAGAG 59.178 52.381 12.18 0.00 41.52 3.35
723 753 1.737363 GCTAGTGTACCAGCACAGAGC 60.737 57.143 6.39 0.00 41.52 4.09
734 764 0.107508 GCACAGAGCCAGCATTAGGA 60.108 55.000 0.00 0.00 37.23 2.94
735 765 1.476471 GCACAGAGCCAGCATTAGGAT 60.476 52.381 0.00 0.00 37.23 3.24
736 766 2.224378 GCACAGAGCCAGCATTAGGATA 60.224 50.000 0.00 0.00 37.23 2.59
738 768 4.454678 CACAGAGCCAGCATTAGGATAAA 58.545 43.478 0.00 0.00 0.00 1.40
740 770 5.357878 CACAGAGCCAGCATTAGGATAAAAA 59.642 40.000 0.00 0.00 0.00 1.94
741 771 6.040166 CACAGAGCCAGCATTAGGATAAAAAT 59.960 38.462 0.00 0.00 0.00 1.82
744 774 8.078596 CAGAGCCAGCATTAGGATAAAAATTAC 58.921 37.037 0.00 0.00 0.00 1.89
745 775 8.001292 AGAGCCAGCATTAGGATAAAAATTACT 58.999 33.333 0.00 0.00 0.00 2.24
746 776 8.539117 AGCCAGCATTAGGATAAAAATTACTT 57.461 30.769 0.00 0.00 0.00 2.24
747 777 9.640952 AGCCAGCATTAGGATAAAAATTACTTA 57.359 29.630 0.00 0.00 0.00 2.24
748 778 9.678941 GCCAGCATTAGGATAAAAATTACTTAC 57.321 33.333 0.00 0.00 0.00 2.34
757 787 8.842764 AGGATAAAAATTACTTACTTGGAGGGA 58.157 33.333 0.00 0.00 0.00 4.20
758 788 9.642343 GGATAAAAATTACTTACTTGGAGGGAT 57.358 33.333 0.00 0.00 0.00 3.85
761 791 8.950007 AAAAATTACTTACTTGGAGGGATTCA 57.050 30.769 0.00 0.00 0.00 2.57
762 792 8.581253 AAAATTACTTACTTGGAGGGATTCAG 57.419 34.615 0.00 0.00 0.00 3.02
764 794 4.828072 ACTTACTTGGAGGGATTCAGAC 57.172 45.455 0.00 0.00 0.00 3.51
765 795 3.519913 ACTTACTTGGAGGGATTCAGACC 59.480 47.826 0.00 0.00 0.00 3.85
766 796 2.350863 ACTTGGAGGGATTCAGACCT 57.649 50.000 0.00 0.00 40.54 3.85
767 797 3.491766 ACTTGGAGGGATTCAGACCTA 57.508 47.619 0.00 0.00 37.18 3.08
769 799 3.246167 ACTTGGAGGGATTCAGACCTACT 60.246 47.826 0.00 0.00 38.59 2.57
770 800 3.491766 TGGAGGGATTCAGACCTACTT 57.508 47.619 0.00 0.00 38.59 2.24
771 801 3.375699 TGGAGGGATTCAGACCTACTTC 58.624 50.000 0.00 0.00 38.59 3.01
1339 1707 2.832838 TGCAAGATGACCCTTCCTCTA 58.167 47.619 0.00 0.00 0.00 2.43
1422 1790 0.539986 GAGGATCGGCTTTGTGGGTA 59.460 55.000 0.00 0.00 0.00 3.69
1477 1854 1.454847 TTGCAGGGCGACAACCTTT 60.455 52.632 0.00 0.00 35.78 3.11
1533 1910 1.273267 TGGGAGCTTCAGAAGAGCCTA 60.273 52.381 14.86 8.78 0.00 3.93
1591 1968 1.751924 AGGATGAGTACTTCCGTCAGC 59.248 52.381 7.77 0.00 42.74 4.26
2217 2608 4.098960 AGTTCCATTGCTTCATGCCTATTG 59.901 41.667 0.00 0.00 42.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.514781 AGAACCGCAATAAAACCTTTCC 57.485 40.909 0.00 0.00 0.00 3.13
94 95 0.472898 TCTTCGCGAGGAGGAGGATA 59.527 55.000 17.79 0.00 37.31 2.59
95 96 0.395862 TTCTTCGCGAGGAGGAGGAT 60.396 55.000 20.61 0.00 37.31 3.24
96 97 1.001269 TTCTTCGCGAGGAGGAGGA 60.001 57.895 20.61 3.11 37.31 3.71
105 106 1.289066 CACCCAGTCTTCTTCGCGA 59.711 57.895 3.71 3.71 0.00 5.87
117 118 1.144057 GTACGGCATCTCCACCCAG 59.856 63.158 0.00 0.00 34.01 4.45
118 119 2.363975 GGTACGGCATCTCCACCCA 61.364 63.158 0.00 0.00 34.01 4.51
119 120 1.623542 AAGGTACGGCATCTCCACCC 61.624 60.000 0.00 0.00 32.64 4.61
120 121 0.462047 CAAGGTACGGCATCTCCACC 60.462 60.000 0.00 0.00 32.45 4.61
121 122 1.090052 GCAAGGTACGGCATCTCCAC 61.090 60.000 0.00 0.00 33.90 4.02
122 123 1.220749 GCAAGGTACGGCATCTCCA 59.779 57.895 0.00 0.00 33.90 3.86
123 124 1.220749 TGCAAGGTACGGCATCTCC 59.779 57.895 1.87 0.00 38.47 3.71
124 125 4.932789 TGCAAGGTACGGCATCTC 57.067 55.556 1.87 0.00 38.47 2.75
128 129 1.739929 CGACATGCAAGGTACGGCA 60.740 57.895 7.76 7.76 46.10 5.69
129 130 1.693083 GACGACATGCAAGGTACGGC 61.693 60.000 0.00 0.00 0.00 5.68
130 131 1.082117 GGACGACATGCAAGGTACGG 61.082 60.000 0.00 0.00 0.00 4.02
131 132 0.108804 AGGACGACATGCAAGGTACG 60.109 55.000 0.00 1.60 0.00 3.67
132 133 2.165845 ACTAGGACGACATGCAAGGTAC 59.834 50.000 0.00 0.00 0.00 3.34
133 134 2.426024 GACTAGGACGACATGCAAGGTA 59.574 50.000 0.00 0.00 0.00 3.08
141 142 1.202582 GCACACAGACTAGGACGACAT 59.797 52.381 0.00 0.00 0.00 3.06
144 145 1.583495 CGGCACACAGACTAGGACGA 61.583 60.000 0.00 0.00 0.00 4.20
146 147 0.818296 ATCGGCACACAGACTAGGAC 59.182 55.000 0.00 0.00 0.00 3.85
163 164 1.136169 GTTTGGTAACGCCGTGTGATC 60.136 52.381 0.00 0.00 41.21 2.92
165 166 0.179078 AGTTTGGTAACGCCGTGTGA 60.179 50.000 0.00 0.00 41.21 3.58
166 167 1.500108 TAGTTTGGTAACGCCGTGTG 58.500 50.000 0.00 0.00 41.21 3.82
170 171 1.667212 GGGATTAGTTTGGTAACGCCG 59.333 52.381 0.00 0.00 41.21 6.46
174 175 5.105917 CCATGTGTGGGATTAGTTTGGTAAC 60.106 44.000 0.00 0.00 42.11 2.50
175 176 5.013547 CCATGTGTGGGATTAGTTTGGTAA 58.986 41.667 0.00 0.00 42.11 2.85
176 177 4.289934 TCCATGTGTGGGATTAGTTTGGTA 59.710 41.667 0.00 0.00 46.06 3.25
177 178 3.075283 TCCATGTGTGGGATTAGTTTGGT 59.925 43.478 0.00 0.00 46.06 3.67
178 179 3.696045 TCCATGTGTGGGATTAGTTTGG 58.304 45.455 0.00 0.00 46.06 3.28
179 180 3.696051 CCTCCATGTGTGGGATTAGTTTG 59.304 47.826 0.00 0.00 46.06 2.93
180 181 3.591527 TCCTCCATGTGTGGGATTAGTTT 59.408 43.478 0.00 0.00 46.06 2.66
181 182 3.189606 TCCTCCATGTGTGGGATTAGTT 58.810 45.455 0.00 0.00 46.06 2.24
182 183 2.845659 TCCTCCATGTGTGGGATTAGT 58.154 47.619 0.00 0.00 46.06 2.24
183 184 3.931907 TTCCTCCATGTGTGGGATTAG 57.068 47.619 0.00 0.00 46.06 1.73
184 185 4.290985 TCTTTTCCTCCATGTGTGGGATTA 59.709 41.667 0.00 0.00 46.06 1.75
185 186 3.075882 TCTTTTCCTCCATGTGTGGGATT 59.924 43.478 0.00 0.00 46.06 3.01
186 187 2.649312 TCTTTTCCTCCATGTGTGGGAT 59.351 45.455 0.00 0.00 46.06 3.85
187 188 2.061848 TCTTTTCCTCCATGTGTGGGA 58.938 47.619 0.00 0.00 46.06 4.37
188 189 2.584835 TCTTTTCCTCCATGTGTGGG 57.415 50.000 0.00 0.00 46.06 4.61
190 191 5.391950 CGGTATTTCTTTTCCTCCATGTGTG 60.392 44.000 0.00 0.00 0.00 3.82
191 192 4.700213 CGGTATTTCTTTTCCTCCATGTGT 59.300 41.667 0.00 0.00 0.00 3.72
192 193 4.438744 GCGGTATTTCTTTTCCTCCATGTG 60.439 45.833 0.00 0.00 0.00 3.21
193 194 3.694566 GCGGTATTTCTTTTCCTCCATGT 59.305 43.478 0.00 0.00 0.00 3.21
194 195 3.066760 GGCGGTATTTCTTTTCCTCCATG 59.933 47.826 0.00 0.00 0.00 3.66
195 196 3.288092 GGCGGTATTTCTTTTCCTCCAT 58.712 45.455 0.00 0.00 0.00 3.41
196 197 2.718563 GGCGGTATTTCTTTTCCTCCA 58.281 47.619 0.00 0.00 0.00 3.86
197 198 1.669265 CGGCGGTATTTCTTTTCCTCC 59.331 52.381 0.00 0.00 0.00 4.30
198 199 2.624636 TCGGCGGTATTTCTTTTCCTC 58.375 47.619 7.21 0.00 0.00 3.71
199 200 2.773993 TCGGCGGTATTTCTTTTCCT 57.226 45.000 7.21 0.00 0.00 3.36
200 201 2.540973 GCATCGGCGGTATTTCTTTTCC 60.541 50.000 7.21 0.00 0.00 3.13
201 202 2.096819 TGCATCGGCGGTATTTCTTTTC 59.903 45.455 7.21 0.00 45.35 2.29
202 203 2.088423 TGCATCGGCGGTATTTCTTTT 58.912 42.857 7.21 0.00 45.35 2.27
203 204 1.745232 TGCATCGGCGGTATTTCTTT 58.255 45.000 7.21 0.00 45.35 2.52
204 205 1.967319 ATGCATCGGCGGTATTTCTT 58.033 45.000 7.21 0.00 45.35 2.52
205 206 1.603802 CAATGCATCGGCGGTATTTCT 59.396 47.619 7.21 0.00 45.35 2.52
206 207 1.334960 CCAATGCATCGGCGGTATTTC 60.335 52.381 7.21 0.00 45.35 2.17
207 208 0.667993 CCAATGCATCGGCGGTATTT 59.332 50.000 7.21 0.00 45.35 1.40
208 209 0.465460 ACCAATGCATCGGCGGTATT 60.465 50.000 2.74 0.00 45.35 1.89
209 210 1.148273 ACCAATGCATCGGCGGTAT 59.852 52.632 2.74 0.00 45.35 2.73
210 211 1.817520 CACCAATGCATCGGCGGTA 60.818 57.895 2.74 0.00 45.35 4.02
211 212 2.529454 TACACCAATGCATCGGCGGT 62.529 55.000 2.74 5.18 45.35 5.68
212 213 1.165907 ATACACCAATGCATCGGCGG 61.166 55.000 2.74 3.24 45.35 6.13
213 214 0.662619 AATACACCAATGCATCGGCG 59.337 50.000 2.74 0.00 45.35 6.46
214 215 1.001378 GGAATACACCAATGCATCGGC 60.001 52.381 2.74 0.00 41.68 5.54
215 216 2.549754 GAGGAATACACCAATGCATCGG 59.450 50.000 0.88 0.88 0.00 4.18
216 217 2.549754 GGAGGAATACACCAATGCATCG 59.450 50.000 0.00 0.00 0.00 3.84
217 218 3.554934 TGGAGGAATACACCAATGCATC 58.445 45.455 0.00 0.00 0.00 3.91
218 219 3.668141 TGGAGGAATACACCAATGCAT 57.332 42.857 0.00 0.00 0.00 3.96
219 220 3.668141 ATGGAGGAATACACCAATGCA 57.332 42.857 0.00 0.00 37.24 3.96
220 221 4.718961 ACTATGGAGGAATACACCAATGC 58.281 43.478 0.00 0.00 37.24 3.56
221 222 6.828273 TGAAACTATGGAGGAATACACCAATG 59.172 38.462 0.00 0.00 37.24 2.82
222 223 6.969043 TGAAACTATGGAGGAATACACCAAT 58.031 36.000 0.00 0.00 37.24 3.16
223 224 6.012858 ACTGAAACTATGGAGGAATACACCAA 60.013 38.462 0.00 0.00 37.24 3.67
224 225 5.487488 ACTGAAACTATGGAGGAATACACCA 59.513 40.000 0.00 0.00 38.09 4.17
225 226 5.990668 ACTGAAACTATGGAGGAATACACC 58.009 41.667 0.00 0.00 0.00 4.16
226 227 6.535508 GTGACTGAAACTATGGAGGAATACAC 59.464 42.308 0.00 0.00 0.00 2.90
227 228 6.212589 TGTGACTGAAACTATGGAGGAATACA 59.787 38.462 0.00 0.00 0.00 2.29
228 229 6.640518 TGTGACTGAAACTATGGAGGAATAC 58.359 40.000 0.00 0.00 0.00 1.89
229 230 6.667848 TCTGTGACTGAAACTATGGAGGAATA 59.332 38.462 0.00 0.00 0.00 1.75
230 231 5.485353 TCTGTGACTGAAACTATGGAGGAAT 59.515 40.000 0.00 0.00 0.00 3.01
231 232 4.838423 TCTGTGACTGAAACTATGGAGGAA 59.162 41.667 0.00 0.00 0.00 3.36
232 233 4.416516 TCTGTGACTGAAACTATGGAGGA 58.583 43.478 0.00 0.00 0.00 3.71
233 234 4.382470 CCTCTGTGACTGAAACTATGGAGG 60.382 50.000 0.00 0.00 0.00 4.30
234 235 4.464244 TCCTCTGTGACTGAAACTATGGAG 59.536 45.833 0.00 0.00 0.00 3.86
235 236 4.416516 TCCTCTGTGACTGAAACTATGGA 58.583 43.478 0.00 0.00 0.00 3.41
236 237 4.464244 TCTCCTCTGTGACTGAAACTATGG 59.536 45.833 0.00 0.00 0.00 2.74
237 238 5.651387 TCTCCTCTGTGACTGAAACTATG 57.349 43.478 0.00 0.00 0.00 2.23
238 239 5.395103 GCATCTCCTCTGTGACTGAAACTAT 60.395 44.000 0.00 0.00 0.00 2.12
239 240 4.081972 GCATCTCCTCTGTGACTGAAACTA 60.082 45.833 0.00 0.00 0.00 2.24
240 241 3.306641 GCATCTCCTCTGTGACTGAAACT 60.307 47.826 0.00 0.00 0.00 2.66
241 242 2.999355 GCATCTCCTCTGTGACTGAAAC 59.001 50.000 0.00 0.00 0.00 2.78
242 243 2.027745 GGCATCTCCTCTGTGACTGAAA 60.028 50.000 0.00 0.00 0.00 2.69
243 244 1.552337 GGCATCTCCTCTGTGACTGAA 59.448 52.381 0.00 0.00 0.00 3.02
244 245 1.189752 GGCATCTCCTCTGTGACTGA 58.810 55.000 0.00 0.00 0.00 3.41
245 246 1.193323 AGGCATCTCCTCTGTGACTG 58.807 55.000 0.00 0.00 43.20 3.51
246 247 3.707821 AGGCATCTCCTCTGTGACT 57.292 52.632 0.00 0.00 43.20 3.41
283 284 1.478916 GAGAAGAGGTAGTGGAGCCAC 59.521 57.143 11.67 11.67 46.50 5.01
294 295 1.359474 TCTACCAGGCTGAGAAGAGGT 59.641 52.381 17.94 5.81 0.00 3.85
313 314 5.574830 CGGCTTCATATATACTTGTGAGCTC 59.425 44.000 6.82 6.82 0.00 4.09
325 326 9.277783 GCAATATTTATCCTCGGCTTCATATAT 57.722 33.333 0.00 0.00 0.00 0.86
326 327 7.715249 GGCAATATTTATCCTCGGCTTCATATA 59.285 37.037 0.00 0.00 0.00 0.86
327 328 6.543831 GGCAATATTTATCCTCGGCTTCATAT 59.456 38.462 0.00 0.00 0.00 1.78
336 337 5.163513 GCAATTGGGCAATATTTATCCTCG 58.836 41.667 7.72 0.00 0.00 4.63
435 456 9.905713 ATATTCTTACCTGTGAACATGTACATT 57.094 29.630 5.37 0.00 28.98 2.71
436 457 9.905713 AATATTCTTACCTGTGAACATGTACAT 57.094 29.630 1.41 1.41 28.98 2.29
490 511 4.342772 CAGTTTGAACCAGACTTGAAACG 58.657 43.478 0.00 0.00 0.00 3.60
495 516 2.423185 TGTGCAGTTTGAACCAGACTTG 59.577 45.455 0.00 0.00 0.00 3.16
502 523 3.303132 CGTAACTCTGTGCAGTTTGAACC 60.303 47.826 0.00 0.00 37.75 3.62
534 555 9.225436 TCCTTGCCCAAATTTTAATTGTATTTC 57.775 29.630 0.00 0.00 0.00 2.17
547 568 0.471022 ACGGGTTCCTTGCCCAAATT 60.471 50.000 1.07 0.00 46.40 1.82
555 576 0.310854 GCTTGTCAACGGGTTCCTTG 59.689 55.000 0.00 0.00 0.00 3.61
578 599 7.611213 AGTTGTTGTGGTTAGATTAGCATAC 57.389 36.000 0.00 0.00 0.00 2.39
589 610 4.445162 CCTCCCAAGTAGTTGTTGTGGTTA 60.445 45.833 9.42 0.00 30.95 2.85
644 666 5.189145 GGTCTGAATCCCTCCAAGTAAGTAA 59.811 44.000 0.00 0.00 0.00 2.24
648 670 3.803340 AGGTCTGAATCCCTCCAAGTAA 58.197 45.455 0.00 0.00 0.00 2.24
683 705 2.686915 GCTTTGTCATAATGCTGGCTCT 59.313 45.455 0.00 0.00 0.00 4.09
684 706 2.686915 AGCTTTGTCATAATGCTGGCTC 59.313 45.455 0.00 0.00 32.32 4.70
711 741 2.421923 AATGCTGGCTCTGTGCTGGT 62.422 55.000 1.44 0.00 42.39 4.00
712 742 0.393402 TAATGCTGGCTCTGTGCTGG 60.393 55.000 1.44 0.00 42.39 4.85
714 744 0.107312 CCTAATGCTGGCTCTGTGCT 60.107 55.000 1.44 0.00 42.39 4.40
715 745 0.107508 TCCTAATGCTGGCTCTGTGC 60.108 55.000 0.00 0.00 41.94 4.57
716 746 2.634815 ATCCTAATGCTGGCTCTGTG 57.365 50.000 0.00 0.00 0.00 3.66
718 748 6.645790 ATTTTTATCCTAATGCTGGCTCTG 57.354 37.500 0.00 0.00 0.00 3.35
720 750 8.171164 AGTAATTTTTATCCTAATGCTGGCTC 57.829 34.615 0.00 0.00 0.00 4.70
722 752 9.678941 GTAAGTAATTTTTATCCTAATGCTGGC 57.321 33.333 0.00 0.00 0.00 4.85
732 762 9.642343 ATCCCTCCAAGTAAGTAATTTTTATCC 57.358 33.333 0.00 0.00 0.00 2.59
736 766 8.950007 TGAATCCCTCCAAGTAAGTAATTTTT 57.050 30.769 0.00 0.00 0.00 1.94
738 768 7.829706 GTCTGAATCCCTCCAAGTAAGTAATTT 59.170 37.037 0.00 0.00 0.00 1.82
740 770 6.126739 GGTCTGAATCCCTCCAAGTAAGTAAT 60.127 42.308 0.00 0.00 0.00 1.89
741 771 5.189145 GGTCTGAATCCCTCCAAGTAAGTAA 59.811 44.000 0.00 0.00 0.00 2.24
744 774 3.777522 AGGTCTGAATCCCTCCAAGTAAG 59.222 47.826 0.00 0.00 0.00 2.34
745 775 3.803340 AGGTCTGAATCCCTCCAAGTAA 58.197 45.455 0.00 0.00 0.00 2.24
746 776 3.491766 AGGTCTGAATCCCTCCAAGTA 57.508 47.619 0.00 0.00 0.00 2.24
747 777 2.350863 AGGTCTGAATCCCTCCAAGT 57.649 50.000 0.00 0.00 0.00 3.16
748 778 3.379452 AGTAGGTCTGAATCCCTCCAAG 58.621 50.000 0.00 0.00 32.08 3.61
749 779 3.491766 AGTAGGTCTGAATCCCTCCAA 57.508 47.619 0.00 0.00 32.08 3.53
750 780 3.375699 GAAGTAGGTCTGAATCCCTCCA 58.624 50.000 0.00 0.00 32.08 3.86
751 781 2.362717 CGAAGTAGGTCTGAATCCCTCC 59.637 54.545 0.00 0.00 32.08 4.30
752 782 3.067040 GTCGAAGTAGGTCTGAATCCCTC 59.933 52.174 0.00 0.00 32.08 4.30
754 784 2.223525 CGTCGAAGTAGGTCTGAATCCC 60.224 54.545 0.00 0.00 0.00 3.85
755 785 2.223525 CCGTCGAAGTAGGTCTGAATCC 60.224 54.545 0.00 0.00 0.00 3.01
756 786 2.795331 GCCGTCGAAGTAGGTCTGAATC 60.795 54.545 0.00 0.00 0.00 2.52
757 787 1.134560 GCCGTCGAAGTAGGTCTGAAT 59.865 52.381 0.00 0.00 0.00 2.57
758 788 0.524862 GCCGTCGAAGTAGGTCTGAA 59.475 55.000 0.00 0.00 0.00 3.02
759 789 1.310933 GGCCGTCGAAGTAGGTCTGA 61.311 60.000 0.00 0.00 0.00 3.27
760 790 1.139095 GGCCGTCGAAGTAGGTCTG 59.861 63.158 0.00 0.00 0.00 3.51
761 791 2.404995 CGGCCGTCGAAGTAGGTCT 61.405 63.158 19.50 0.00 42.43 3.85
762 792 2.101770 CGGCCGTCGAAGTAGGTC 59.898 66.667 19.50 0.00 42.43 3.85
764 794 4.867599 GGCGGCCGTCGAAGTAGG 62.868 72.222 28.70 0.00 42.43 3.18
1339 1707 7.149202 TCCACTGGAAATTATAGGTTAGCAT 57.851 36.000 0.00 0.00 0.00 3.79
1422 1790 4.112634 CCATGTCGTCGTTGATATTGAGT 58.887 43.478 0.00 0.00 0.00 3.41
1477 1854 1.667151 GCCTTGCCACAAAGATGCA 59.333 52.632 0.00 0.00 0.00 3.96
1509 1886 1.898472 CTCTTCTGAAGCTCCCAGTCA 59.102 52.381 12.54 1.03 33.57 3.41
1533 1910 4.442706 CACGAGTAGCCTCCATTAATTGT 58.557 43.478 0.00 0.00 33.93 2.71
1591 1968 4.177026 CTGGTTGAGACAATCTTCGTAGG 58.823 47.826 0.00 0.00 0.00 3.18
2017 2408 9.739276 TCAAAAGATTTATGGACACAGTTAGAT 57.261 29.630 0.00 0.00 0.00 1.98
2217 2608 0.175531 CAACCATCAATTTCCGGGCC 59.824 55.000 0.00 0.00 0.00 5.80
2686 3083 9.865484 GATCAAAGTTCTCAGTTTGTAACTAAC 57.135 33.333 3.15 0.00 42.10 2.34


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

AutoCloner maintained by Alex Coulton.