Multiple sequence alignment - TraesCS5B01G423400

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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 TraesCS5B01G423400 chr5B 100.000 4185 0 0 1 4185 599750921 599755105 0.000000e+00 7729
1 TraesCS5B01G423400 chr5B 95.037 1753 81 4 1305 3054 426111338 426109589 0.000000e+00 2750
2 TraesCS5B01G423400 chr5B 94.467 1753 91 4 1305 3054 485851974 485850225 0.000000e+00 2695
3 TraesCS5B01G423400 chr3B 95.094 1753 78 5 1305 3054 781322908 781324655 0.000000e+00 2754
4 TraesCS5B01G423400 chr3B 94.818 1756 82 6 1305 3055 781329902 781331653 0.000000e+00 2730
5 TraesCS5B01G423400 chr3B 97.352 1133 25 2 3054 4185 201539371 201540499 0.000000e+00 1921
6 TraesCS5B01G423400 chr2B 94.587 1755 86 7 1304 3053 56904699 56902949 0.000000e+00 2706
7 TraesCS5B01G423400 chr6B 94.435 1761 87 8 1302 3054 591565728 591563971 0.000000e+00 2699
8 TraesCS5B01G423400 chr6B 94.517 1751 89 5 1307 3054 668042640 668044386 0.000000e+00 2695
9 TraesCS5B01G423400 chr7B 94.530 1755 82 11 1305 3054 59418545 59420290 0.000000e+00 2697
10 TraesCS5B01G423400 chr7B 97.264 1133 26 2 3054 4185 662726253 662727381 0.000000e+00 1916
11 TraesCS5B01G423400 chr7B 97.087 1133 28 2 3054 4185 663099576 663098448 0.000000e+00 1905
12 TraesCS5B01G423400 chr7B 96.975 1058 28 2 251 1304 663100629 663099572 0.000000e+00 1773
13 TraesCS5B01G423400 chr7B 95.385 260 11 1 5 263 663100761 663100502 3.010000e-111 412
14 TraesCS5B01G423400 chr3D 94.305 1756 90 8 1304 3053 130988629 130986878 0.000000e+00 2680
15 TraesCS5B01G423400 chr3D 97.176 1133 27 2 3054 4185 589263677 589262549 0.000000e+00 1910
16 TraesCS5B01G423400 chr3D 96.970 1056 29 3 251 1304 589264727 589263673 0.000000e+00 1770
17 TraesCS5B01G423400 chr6D 97.352 1133 25 2 3054 4185 389245973 389244845 0.000000e+00 1921
18 TraesCS5B01G423400 chr6D 97.070 1058 27 2 251 1304 389247026 389245969 0.000000e+00 1779
19 TraesCS5B01G423400 chr6D 95.385 260 11 1 5 263 389247158 389246899 3.010000e-111 412
20 TraesCS5B01G423400 chr7D 97.264 1133 26 2 3054 4185 231554577 231553449 0.000000e+00 1916
21 TraesCS5B01G423400 chr7D 97.033 1045 29 1 262 1304 231555617 231554573 0.000000e+00 1757
22 TraesCS5B01G423400 chr2D 97.264 1133 26 2 3054 4185 591984458 591985586 0.000000e+00 1916
23 TraesCS5B01G423400 chr2D 96.109 257 9 1 5 260 272554445 272554701 6.470000e-113 418
24 TraesCS5B01G423400 chr1D 97.087 1133 30 2 3054 4185 254525454 254526584 0.000000e+00 1906
25 TraesCS5B01G423400 chr3A 97.087 1133 28 2 3054 4185 66005284 66004156 0.000000e+00 1905
26 TraesCS5B01G423400 chr3A 96.973 1057 29 2 251 1304 66006336 66005280 0.000000e+00 1772
27 TraesCS5B01G423400 chr3A 96.109 257 9 1 5 260 695639052 695639308 6.470000e-113 418
28 TraesCS5B01G423400 chr5D 97.159 1056 28 2 251 1304 503266507 503265452 0.000000e+00 1783
29 TraesCS5B01G423400 chr5D 97.070 1058 27 2 251 1304 503244068 503245125 0.000000e+00 1779
30 TraesCS5B01G423400 chr5D 96.109 257 9 1 5 260 503243936 503244192 6.470000e-113 418
31 TraesCS5B01G423400 chr5D 95.769 260 10 1 5 263 503266639 503266380 6.470000e-113 418
32 TraesCS5B01G423400 chr2A 97.070 1058 27 2 251 1304 726907659 726906602 0.000000e+00 1779
33 TraesCS5B01G423400 chrUn 96.509 1060 31 2 251 1304 388831695 388830636 0.000000e+00 1748
34 TraesCS5B01G423400 chrUn 95.385 260 11 1 5 263 43672196 43671937 3.010000e-111 412
35 TraesCS5B01G423400 chrUn 95.385 260 11 1 5 263 216507454 216507195 3.010000e-111 412
36 TraesCS5B01G423400 chrUn 95.385 260 11 1 5 263 388831827 388831568 3.010000e-111 412


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 TraesCS5B01G423400 chr5B 599750921 599755105 4184 False 7729.000000 7729 100.000000 1 4185 1 chr5B.!!$F1 4184
1 TraesCS5B01G423400 chr5B 426109589 426111338 1749 True 2750.000000 2750 95.037000 1305 3054 1 chr5B.!!$R1 1749
2 TraesCS5B01G423400 chr5B 485850225 485851974 1749 True 2695.000000 2695 94.467000 1305 3054 1 chr5B.!!$R2 1749
3 TraesCS5B01G423400 chr3B 781322908 781324655 1747 False 2754.000000 2754 95.094000 1305 3054 1 chr3B.!!$F2 1749
4 TraesCS5B01G423400 chr3B 781329902 781331653 1751 False 2730.000000 2730 94.818000 1305 3055 1 chr3B.!!$F3 1750
5 TraesCS5B01G423400 chr3B 201539371 201540499 1128 False 1921.000000 1921 97.352000 3054 4185 1 chr3B.!!$F1 1131
6 TraesCS5B01G423400 chr2B 56902949 56904699 1750 True 2706.000000 2706 94.587000 1304 3053 1 chr2B.!!$R1 1749
7 TraesCS5B01G423400 chr6B 591563971 591565728 1757 True 2699.000000 2699 94.435000 1302 3054 1 chr6B.!!$R1 1752
8 TraesCS5B01G423400 chr6B 668042640 668044386 1746 False 2695.000000 2695 94.517000 1307 3054 1 chr6B.!!$F1 1747
9 TraesCS5B01G423400 chr7B 59418545 59420290 1745 False 2697.000000 2697 94.530000 1305 3054 1 chr7B.!!$F1 1749
10 TraesCS5B01G423400 chr7B 662726253 662727381 1128 False 1916.000000 1916 97.264000 3054 4185 1 chr7B.!!$F2 1131
11 TraesCS5B01G423400 chr7B 663098448 663100761 2313 True 1363.333333 1905 96.482333 5 4185 3 chr7B.!!$R1 4180
12 TraesCS5B01G423400 chr3D 130986878 130988629 1751 True 2680.000000 2680 94.305000 1304 3053 1 chr3D.!!$R1 1749
13 TraesCS5B01G423400 chr3D 589262549 589264727 2178 True 1840.000000 1910 97.073000 251 4185 2 chr3D.!!$R2 3934
14 TraesCS5B01G423400 chr6D 389244845 389247158 2313 True 1370.666667 1921 96.602333 5 4185 3 chr6D.!!$R1 4180
15 TraesCS5B01G423400 chr7D 231553449 231555617 2168 True 1836.500000 1916 97.148500 262 4185 2 chr7D.!!$R1 3923
16 TraesCS5B01G423400 chr2D 591984458 591985586 1128 False 1916.000000 1916 97.264000 3054 4185 1 chr2D.!!$F2 1131
17 TraesCS5B01G423400 chr1D 254525454 254526584 1130 False 1906.000000 1906 97.087000 3054 4185 1 chr1D.!!$F1 1131
18 TraesCS5B01G423400 chr3A 66004156 66006336 2180 True 1838.500000 1905 97.030000 251 4185 2 chr3A.!!$R1 3934
19 TraesCS5B01G423400 chr5D 503265452 503266639 1187 True 1100.500000 1783 96.464000 5 1304 2 chr5D.!!$R1 1299
20 TraesCS5B01G423400 chr5D 503243936 503245125 1189 False 1098.500000 1779 96.589500 5 1304 2 chr5D.!!$F1 1299
21 TraesCS5B01G423400 chr2A 726906602 726907659 1057 True 1779.000000 1779 97.070000 251 1304 1 chr2A.!!$R1 1053
22 TraesCS5B01G423400 chrUn 388830636 388831827 1191 True 1080.000000 1748 95.947000 5 1304 2 chrUn.!!$R3 1299

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
876 877 0.105039 ACGGGCTATTAGCTCAGTGC 59.895 55.000 15.64 0.0 43.44 4.40 F
1005 1006 0.818938 CAAGGCACATTAGCATGGCA 59.181 50.000 0.00 0.0 43.55 4.92 F
2329 2343 1.072505 GGAGAAAACCGGAGTGCCA 59.927 57.895 9.46 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2137 0.538118 TTTAAGCGTGCGGACCCTAT 59.462 50.0 0.0 0.0 0.00 2.57 R
3003 3022 0.735978 TCCTACGCACACGCAAGATG 60.736 55.0 0.0 0.0 45.53 2.90 R
3357 3380 0.532862 CCTTCCCGAACGCAGCATAT 60.533 55.0 0.0 0.0 0.00 1.78 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
37 38 6.146510 CGTGTTTAGTTGCCACTATGAGTTTA 59.853 38.462 0.00 0.00 35.32 2.01
57 58 2.391724 GAACCCTGAACAGACCGCCA 62.392 60.000 3.19 0.00 0.00 5.69
66 67 1.045407 ACAGACCGCCAGTGTTAAGA 58.955 50.000 0.00 0.00 0.00 2.10
143 144 2.112815 GTGCTACAATGGGCGGGAC 61.113 63.158 0.00 0.00 0.00 4.46
144 145 2.270850 GCTACAATGGGCGGGACA 59.729 61.111 0.00 0.00 0.00 4.02
145 146 1.377987 GCTACAATGGGCGGGACAA 60.378 57.895 0.00 0.00 0.00 3.18
146 147 0.963355 GCTACAATGGGCGGGACAAA 60.963 55.000 0.00 0.00 0.00 2.83
147 148 1.094785 CTACAATGGGCGGGACAAAG 58.905 55.000 0.00 0.00 0.00 2.77
148 149 0.322997 TACAATGGGCGGGACAAAGG 60.323 55.000 0.00 0.00 0.00 3.11
149 150 2.037208 AATGGGCGGGACAAAGGG 59.963 61.111 0.00 0.00 0.00 3.95
150 151 2.852281 AATGGGCGGGACAAAGGGT 61.852 57.895 0.00 0.00 0.00 4.34
151 152 2.781431 AATGGGCGGGACAAAGGGTC 62.781 60.000 0.00 0.00 46.20 4.46
158 159 4.913126 GACAAAGGGTCGCGATCT 57.087 55.556 20.42 13.95 36.65 2.75
159 160 3.139029 GACAAAGGGTCGCGATCTT 57.861 52.632 20.42 18.93 36.65 2.40
160 161 0.721718 GACAAAGGGTCGCGATCTTG 59.278 55.000 20.42 18.47 36.65 3.02
161 162 1.298859 ACAAAGGGTCGCGATCTTGC 61.299 55.000 20.42 2.22 0.00 4.01
169 170 2.184322 GCGATCTTGCGAGGGTGA 59.816 61.111 0.00 0.00 0.00 4.02
170 171 1.880340 GCGATCTTGCGAGGGTGAG 60.880 63.158 0.00 0.00 0.00 3.51
171 172 1.880340 CGATCTTGCGAGGGTGAGC 60.880 63.158 0.00 0.00 0.00 4.26
172 173 1.519719 GATCTTGCGAGGGTGAGCT 59.480 57.895 0.00 0.00 0.00 4.09
173 174 0.747255 GATCTTGCGAGGGTGAGCTA 59.253 55.000 0.00 0.00 0.00 3.32
174 175 1.137086 GATCTTGCGAGGGTGAGCTAA 59.863 52.381 0.00 0.00 0.00 3.09
175 176 0.246635 TCTTGCGAGGGTGAGCTAAC 59.753 55.000 0.00 0.00 0.00 2.34
176 177 0.247736 CTTGCGAGGGTGAGCTAACT 59.752 55.000 0.00 0.00 0.00 2.24
177 178 0.246635 TTGCGAGGGTGAGCTAACTC 59.753 55.000 0.00 0.00 43.76 3.01
178 179 1.142097 GCGAGGGTGAGCTAACTCC 59.858 63.158 0.00 0.00 42.74 3.85
179 180 1.605058 GCGAGGGTGAGCTAACTCCA 61.605 60.000 0.00 0.00 42.74 3.86
180 181 0.895530 CGAGGGTGAGCTAACTCCAA 59.104 55.000 0.00 0.00 42.74 3.53
181 182 1.275291 CGAGGGTGAGCTAACTCCAAA 59.725 52.381 0.00 0.00 42.74 3.28
182 183 2.289444 CGAGGGTGAGCTAACTCCAAAA 60.289 50.000 0.00 0.00 42.74 2.44
183 184 3.751518 GAGGGTGAGCTAACTCCAAAAA 58.248 45.455 0.00 0.00 42.74 1.94
184 185 3.487372 AGGGTGAGCTAACTCCAAAAAC 58.513 45.455 0.00 0.00 42.74 2.43
185 186 2.557056 GGGTGAGCTAACTCCAAAAACC 59.443 50.000 0.00 0.00 42.74 3.27
186 187 2.557056 GGTGAGCTAACTCCAAAAACCC 59.443 50.000 0.00 0.00 42.74 4.11
187 188 2.225727 GTGAGCTAACTCCAAAAACCCG 59.774 50.000 0.00 0.00 42.74 5.28
188 189 2.158726 TGAGCTAACTCCAAAAACCCGT 60.159 45.455 0.00 0.00 42.74 5.28
189 190 2.483106 GAGCTAACTCCAAAAACCCGTC 59.517 50.000 0.00 0.00 36.90 4.79
190 191 1.538512 GCTAACTCCAAAAACCCGTCC 59.461 52.381 0.00 0.00 0.00 4.79
191 192 2.812983 GCTAACTCCAAAAACCCGTCCT 60.813 50.000 0.00 0.00 0.00 3.85
192 193 1.977056 AACTCCAAAAACCCGTCCTC 58.023 50.000 0.00 0.00 0.00 3.71
193 194 0.841289 ACTCCAAAAACCCGTCCTCA 59.159 50.000 0.00 0.00 0.00 3.86
194 195 1.202770 ACTCCAAAAACCCGTCCTCAG 60.203 52.381 0.00 0.00 0.00 3.35
195 196 0.841289 TCCAAAAACCCGTCCTCAGT 59.159 50.000 0.00 0.00 0.00 3.41
196 197 1.213430 TCCAAAAACCCGTCCTCAGTT 59.787 47.619 0.00 0.00 0.00 3.16
197 198 2.028876 CCAAAAACCCGTCCTCAGTTT 58.971 47.619 0.00 0.00 35.29 2.66
198 199 2.223711 CCAAAAACCCGTCCTCAGTTTG 60.224 50.000 0.00 0.00 34.12 2.93
199 200 1.687563 AAAACCCGTCCTCAGTTTGG 58.312 50.000 0.00 0.00 34.12 3.28
200 201 0.841289 AAACCCGTCCTCAGTTTGGA 59.159 50.000 0.00 0.00 32.67 3.53
201 202 1.064825 AACCCGTCCTCAGTTTGGAT 58.935 50.000 0.00 0.00 35.87 3.41
202 203 1.064825 ACCCGTCCTCAGTTTGGATT 58.935 50.000 0.00 0.00 35.87 3.01
203 204 1.271379 ACCCGTCCTCAGTTTGGATTG 60.271 52.381 0.00 0.00 35.87 2.67
204 205 0.804989 CCGTCCTCAGTTTGGATTGC 59.195 55.000 0.00 0.00 35.87 3.56
205 206 1.522668 CGTCCTCAGTTTGGATTGCA 58.477 50.000 0.00 0.00 35.87 4.08
206 207 1.466167 CGTCCTCAGTTTGGATTGCAG 59.534 52.381 0.00 0.00 35.87 4.41
207 208 1.815003 GTCCTCAGTTTGGATTGCAGG 59.185 52.381 0.00 0.00 35.87 4.85
208 209 0.529378 CCTCAGTTTGGATTGCAGGC 59.471 55.000 0.00 0.00 0.00 4.85
209 210 1.542492 CTCAGTTTGGATTGCAGGCT 58.458 50.000 0.00 0.00 0.00 4.58
210 211 1.201647 CTCAGTTTGGATTGCAGGCTG 59.798 52.381 10.94 10.94 0.00 4.85
211 212 0.389426 CAGTTTGGATTGCAGGCTGC 60.389 55.000 31.91 31.91 45.29 5.25
225 226 3.506096 CTGCACCTCGCCTGCATG 61.506 66.667 2.51 0.00 43.61 4.06
226 227 3.963687 CTGCACCTCGCCTGCATGA 62.964 63.158 0.00 0.00 43.61 3.07
227 228 2.747460 GCACCTCGCCTGCATGAA 60.747 61.111 0.00 0.00 34.56 2.57
228 229 2.758089 GCACCTCGCCTGCATGAAG 61.758 63.158 0.00 0.00 34.56 3.02
229 230 2.437359 ACCTCGCCTGCATGAAGC 60.437 61.111 0.00 0.00 45.96 3.86
239 240 2.401967 GCATGAAGCAGGAATCGCT 58.598 52.632 0.00 0.00 44.79 4.93
240 241 1.586422 GCATGAAGCAGGAATCGCTA 58.414 50.000 0.00 0.00 44.79 4.26
241 242 1.530293 GCATGAAGCAGGAATCGCTAG 59.470 52.381 0.00 0.00 44.79 3.42
242 243 2.831333 CATGAAGCAGGAATCGCTAGT 58.169 47.619 0.00 0.00 39.29 2.57
243 244 3.800261 GCATGAAGCAGGAATCGCTAGTA 60.800 47.826 0.00 0.00 44.79 1.82
244 245 4.371786 CATGAAGCAGGAATCGCTAGTAA 58.628 43.478 0.00 0.00 39.29 2.24
245 246 4.672587 TGAAGCAGGAATCGCTAGTAAT 57.327 40.909 0.00 0.00 39.29 1.89
246 247 4.621991 TGAAGCAGGAATCGCTAGTAATC 58.378 43.478 0.00 0.00 39.29 1.75
247 248 3.290308 AGCAGGAATCGCTAGTAATCG 57.710 47.619 0.00 0.00 38.15 3.34
248 249 2.623889 AGCAGGAATCGCTAGTAATCGT 59.376 45.455 0.00 0.00 38.15 3.73
249 250 2.981140 GCAGGAATCGCTAGTAATCGTC 59.019 50.000 0.00 0.00 0.00 4.20
250 251 3.227147 CAGGAATCGCTAGTAATCGTCG 58.773 50.000 0.00 0.00 0.00 5.12
251 252 2.225963 AGGAATCGCTAGTAATCGTCGG 59.774 50.000 0.00 0.00 0.00 4.79
252 253 1.977412 GAATCGCTAGTAATCGTCGGC 59.023 52.381 0.00 0.00 0.00 5.54
253 254 0.110328 ATCGCTAGTAATCGTCGGCG 60.110 55.000 1.15 1.15 43.22 6.46
254 255 1.724929 CGCTAGTAATCGTCGGCGG 60.725 63.158 10.62 0.00 39.12 6.13
255 256 2.015090 GCTAGTAATCGTCGGCGGC 61.015 63.158 10.62 3.25 38.89 6.53
258 259 1.457823 TAGTAATCGTCGGCGGCCAT 61.458 55.000 20.71 0.00 38.89 4.40
272 273 1.367840 GCCATAGGGTCGCGATCTT 59.632 57.895 20.42 15.14 36.17 2.40
367 368 0.578683 TCGCTAGTAATCGTCGGTCG 59.421 55.000 0.00 0.00 41.41 4.79
377 378 3.830192 GTCGGTCGGCCATACGGT 61.830 66.667 6.96 0.00 34.09 4.83
392 393 1.004320 CGGTGGTGAATCCGTTCCA 60.004 57.895 0.00 0.00 41.58 3.53
412 413 2.032071 GCCTTGTACACACCGCCT 59.968 61.111 0.00 0.00 0.00 5.52
428 429 2.025155 CGCCTGTCACACTATAGGAGT 58.975 52.381 4.43 0.00 39.82 3.85
566 567 3.983044 TCCTTTTCAGGGAGAGCTAAC 57.017 47.619 0.00 0.00 41.25 2.34
663 664 7.020827 ACTTGGATATGGAAGTCTTCTTTCA 57.979 36.000 12.31 2.81 42.55 2.69
876 877 0.105039 ACGGGCTATTAGCTCAGTGC 59.895 55.000 15.64 0.00 43.44 4.40
921 922 1.827789 GTTGTGCCTGGGCTGTGAA 60.828 57.895 13.05 0.00 42.51 3.18
942 943 2.855209 GCTCTCAGCCACATGGATAT 57.145 50.000 0.87 0.00 34.48 1.63
1005 1006 0.818938 CAAGGCACATTAGCATGGCA 59.181 50.000 0.00 0.00 43.55 4.92
1053 1054 7.469537 TTTGAAACCAAACAAACTTCTCCTA 57.530 32.000 0.00 0.00 32.26 2.94
1071 1072 2.907892 CTAAGGAGGATAGATGGGGCA 58.092 52.381 0.00 0.00 0.00 5.36
1121 1122 5.422214 ACTTTCTATTCACTCGTGGGATT 57.578 39.130 0.00 0.00 0.00 3.01
1181 1189 6.726299 TCTCGAGAATCCATACATCCCTTATT 59.274 38.462 14.01 0.00 0.00 1.40
1185 1193 8.967918 CGAGAATCCATACATCCCTTATTAGTA 58.032 37.037 0.00 0.00 0.00 1.82
1264 1272 3.067106 CACCTAACAACGCATCTTCACT 58.933 45.455 0.00 0.00 0.00 3.41
1583 1595 2.560504 CCATTCCGTTAGCATAGCACA 58.439 47.619 0.00 0.00 0.00 4.57
1607 1619 7.916977 ACACGATCGTTTAGTATGTTGCTATTA 59.083 33.333 20.14 0.00 0.00 0.98
1610 1622 8.628279 CGATCGTTTAGTATGTTGCTATTACTC 58.372 37.037 7.03 0.00 0.00 2.59
1638 1650 9.778741 TTTCCATGACTTATACATGTTCCTATC 57.221 33.333 2.30 0.00 42.16 2.08
1695 1707 3.508012 AACACTTTGTGTGCTACCAAACA 59.492 39.130 4.01 0.00 46.79 2.83
1702 1714 3.888323 TGTGTGCTACCAAACATCACAAT 59.112 39.130 0.00 0.00 39.07 2.71
1769 1781 5.069383 GGTACTTGTTGGGTTGGTGTATTTT 59.931 40.000 0.00 0.00 0.00 1.82
1841 1853 5.109210 TCTCGGTAATGCACATCACTTAAG 58.891 41.667 0.00 0.00 0.00 1.85
1842 1854 5.079689 TCGGTAATGCACATCACTTAAGA 57.920 39.130 10.09 0.00 0.00 2.10
1979 1993 3.740115 GGGCAAGTAACATACCGATGAT 58.260 45.455 0.00 0.00 36.48 2.45
2008 2022 2.817538 AACGTATGTTGTTATGCGGC 57.182 45.000 0.00 0.00 39.90 6.53
2014 2028 1.890876 TGTTGTTATGCGGCTTGACT 58.109 45.000 11.17 0.00 0.00 3.41
2123 2137 4.338012 TGTCTACATAGTTCTCGAACCCA 58.662 43.478 6.20 0.00 42.06 4.51
2329 2343 1.072505 GGAGAAAACCGGAGTGCCA 59.927 57.895 9.46 0.00 0.00 4.92
2666 2685 6.431852 TGACACACAAGTTGATCATCATGATT 59.568 34.615 10.54 0.00 37.20 2.57
2778 2797 1.447663 CATCATCGTCACCACGCCA 60.448 57.895 0.00 0.00 46.28 5.69
2854 2873 2.162809 TCATCGAGCTAAACGTGTGCTA 59.837 45.455 9.63 0.00 37.16 3.49
2860 2879 3.724374 AGCTAAACGTGTGCTAAACTCA 58.276 40.909 8.18 0.00 35.05 3.41
2918 2937 3.089267 CGTGAAGACGTACGACTACATG 58.911 50.000 24.41 16.37 42.54 3.21
2925 2944 1.466192 CGTACGACTACATGAACCGCA 60.466 52.381 10.44 0.00 0.00 5.69
2984 3003 1.431633 TGGACAACACTCTCCCCTCTA 59.568 52.381 0.00 0.00 0.00 2.43
3003 3022 4.635223 TCTAGTTGCTATGCATCACCATC 58.365 43.478 0.19 0.00 38.76 3.51
3234 3257 4.399483 TCTTAGAGTGTCTAGGGTTGGT 57.601 45.455 0.00 0.00 29.56 3.67
3273 3296 1.625315 GCCTTCCTTTTTCTGCCCATT 59.375 47.619 0.00 0.00 0.00 3.16
3287 3310 2.314549 TGCCCATTGGAGTTATTTCCCT 59.685 45.455 3.62 0.00 36.35 4.20
3290 3313 4.141251 GCCCATTGGAGTTATTTCCCTAGA 60.141 45.833 3.62 0.00 36.35 2.43
3295 3318 7.615757 CCATTGGAGTTATTTCCCTAGAACTTT 59.384 37.037 0.00 0.00 36.35 2.66
3348 3371 2.738846 CACTTGAAGAGCGCAGTACAAT 59.261 45.455 11.47 0.00 0.00 2.71
3357 3380 1.406341 GCGCAGTACAATGGGGAGTTA 60.406 52.381 0.30 0.00 33.94 2.24
3389 3412 0.761802 GGGAAGGATGAATCGCTCCT 59.238 55.000 0.00 0.00 43.86 3.69
3452 3475 2.238646 AGGGGCGATGATTTACTTCACA 59.761 45.455 0.00 0.00 0.00 3.58
3453 3476 3.013921 GGGGCGATGATTTACTTCACAA 58.986 45.455 0.00 0.00 0.00 3.33
3550 3573 0.175760 GCATACTCCACTTGGCTCGA 59.824 55.000 0.00 0.00 34.44 4.04
3551 3574 1.804372 GCATACTCCACTTGGCTCGAG 60.804 57.143 8.45 8.45 34.44 4.04
3600 3623 0.539438 TCCGCTCTTGCAATTGGGTT 60.539 50.000 7.72 0.00 39.64 4.11
3665 3688 7.914427 ATGATAGTATCTTGTACCTGAACCA 57.086 36.000 11.40 0.00 0.00 3.67
3723 3746 3.316029 TGAAACATGCCACTGAAAGACTG 59.684 43.478 0.00 0.00 37.43 3.51
3744 3767 5.163195 ACTGTACTGAGACAAAAAGATGGGT 60.163 40.000 6.77 0.00 0.00 4.51
3755 3778 6.706295 ACAAAAAGATGGGTTGTCAAAAAGA 58.294 32.000 0.00 0.00 29.57 2.52
3761 3784 5.649831 AGATGGGTTGTCAAAAAGATAGAGC 59.350 40.000 0.00 0.00 0.00 4.09
3773 3796 4.477536 AAGATAGAGCAGGTAGGATGGA 57.522 45.455 0.00 0.00 0.00 3.41
3906 3929 5.234972 TGCGAATAACTTGATGCACTATCTG 59.765 40.000 0.00 0.00 36.71 2.90
4042 4065 2.981859 GTCACGGACCAACCATAGAT 57.018 50.000 0.00 0.00 38.90 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.858745 ACTAAACACGAGGGTTGCATT 58.141 42.857 0.00 0.00 0.00 3.56
2 3 2.552315 CAACTAAACACGAGGGTTGCAT 59.448 45.455 0.00 0.00 32.50 3.96
3 4 1.944024 CAACTAAACACGAGGGTTGCA 59.056 47.619 0.00 0.00 32.50 4.08
37 38 1.371558 GCGGTCTGTTCAGGGTTCT 59.628 57.895 0.00 0.00 0.00 3.01
57 58 2.826725 CTCCTTCCTCCGTCTTAACACT 59.173 50.000 0.00 0.00 0.00 3.55
66 67 0.631753 TCATCCTCTCCTTCCTCCGT 59.368 55.000 0.00 0.00 0.00 4.69
118 119 1.234821 CCCATTGTAGCACGTGTGTT 58.765 50.000 18.38 6.02 0.00 3.32
143 144 1.425428 GCAAGATCGCGACCCTTTG 59.575 57.895 12.93 14.52 0.00 2.77
144 145 3.890674 GCAAGATCGCGACCCTTT 58.109 55.556 12.93 0.00 0.00 3.11
155 156 5.298265 GAGTTAGCTCACCCTCGCAAGAT 62.298 52.174 1.11 0.00 43.24 2.40
156 157 4.038588 GAGTTAGCTCACCCTCGCAAGA 62.039 54.545 1.11 0.00 42.50 3.02
157 158 0.247736 AGTTAGCTCACCCTCGCAAG 59.752 55.000 0.00 0.00 0.00 4.01
158 159 0.246635 GAGTTAGCTCACCCTCGCAA 59.753 55.000 1.11 0.00 41.29 4.85
159 160 1.605058 GGAGTTAGCTCACCCTCGCA 61.605 60.000 8.96 0.00 43.37 5.10
160 161 1.142097 GGAGTTAGCTCACCCTCGC 59.858 63.158 8.96 0.00 43.37 5.03
161 162 0.895530 TTGGAGTTAGCTCACCCTCG 59.104 55.000 8.96 0.00 43.37 4.63
162 163 3.418684 TTTTGGAGTTAGCTCACCCTC 57.581 47.619 8.96 0.00 43.37 4.30
163 164 3.487372 GTTTTTGGAGTTAGCTCACCCT 58.513 45.455 8.96 0.00 43.37 4.34
164 165 2.557056 GGTTTTTGGAGTTAGCTCACCC 59.443 50.000 8.96 0.00 43.37 4.61
165 166 2.557056 GGGTTTTTGGAGTTAGCTCACC 59.443 50.000 8.96 6.70 43.37 4.02
166 167 2.225727 CGGGTTTTTGGAGTTAGCTCAC 59.774 50.000 8.96 0.00 43.37 3.51
167 168 2.158726 ACGGGTTTTTGGAGTTAGCTCA 60.159 45.455 8.96 0.00 43.37 4.26
168 169 2.483106 GACGGGTTTTTGGAGTTAGCTC 59.517 50.000 0.00 0.00 40.93 4.09
169 170 2.501261 GACGGGTTTTTGGAGTTAGCT 58.499 47.619 0.00 0.00 0.00 3.32
170 171 1.538512 GGACGGGTTTTTGGAGTTAGC 59.461 52.381 0.00 0.00 0.00 3.09
171 172 3.072211 GAGGACGGGTTTTTGGAGTTAG 58.928 50.000 0.00 0.00 0.00 2.34
172 173 2.438763 TGAGGACGGGTTTTTGGAGTTA 59.561 45.455 0.00 0.00 0.00 2.24
173 174 1.213430 TGAGGACGGGTTTTTGGAGTT 59.787 47.619 0.00 0.00 0.00 3.01
174 175 0.841289 TGAGGACGGGTTTTTGGAGT 59.159 50.000 0.00 0.00 0.00 3.85
175 176 1.202770 ACTGAGGACGGGTTTTTGGAG 60.203 52.381 0.00 0.00 0.00 3.86
176 177 0.841289 ACTGAGGACGGGTTTTTGGA 59.159 50.000 0.00 0.00 0.00 3.53
177 178 1.687563 AACTGAGGACGGGTTTTTGG 58.312 50.000 0.00 0.00 0.00 3.28
178 179 2.223711 CCAAACTGAGGACGGGTTTTTG 60.224 50.000 0.00 0.00 31.87 2.44
179 180 2.028876 CCAAACTGAGGACGGGTTTTT 58.971 47.619 0.00 0.00 31.87 1.94
180 181 1.213430 TCCAAACTGAGGACGGGTTTT 59.787 47.619 0.00 0.00 31.87 2.43
181 182 0.841289 TCCAAACTGAGGACGGGTTT 59.159 50.000 0.00 0.00 34.10 3.27
182 183 1.064825 ATCCAAACTGAGGACGGGTT 58.935 50.000 0.00 0.00 38.13 4.11
183 184 1.064825 AATCCAAACTGAGGACGGGT 58.935 50.000 0.00 0.00 38.13 5.28
184 185 1.453155 CAATCCAAACTGAGGACGGG 58.547 55.000 0.00 0.00 38.13 5.28
185 186 0.804989 GCAATCCAAACTGAGGACGG 59.195 55.000 0.00 0.00 38.13 4.79
186 187 1.466167 CTGCAATCCAAACTGAGGACG 59.534 52.381 0.00 0.00 38.13 4.79
187 188 1.815003 CCTGCAATCCAAACTGAGGAC 59.185 52.381 0.00 0.00 38.13 3.85
188 189 1.887956 GCCTGCAATCCAAACTGAGGA 60.888 52.381 0.00 0.00 39.97 3.71
189 190 0.529378 GCCTGCAATCCAAACTGAGG 59.471 55.000 0.00 0.00 0.00 3.86
190 191 1.201647 CAGCCTGCAATCCAAACTGAG 59.798 52.381 0.00 0.00 31.38 3.35
191 192 1.250328 CAGCCTGCAATCCAAACTGA 58.750 50.000 0.00 0.00 31.38 3.41
192 193 0.389426 GCAGCCTGCAATCCAAACTG 60.389 55.000 12.82 0.00 44.26 3.16
193 194 1.969862 GCAGCCTGCAATCCAAACT 59.030 52.632 12.82 0.00 44.26 2.66
194 195 4.584688 GCAGCCTGCAATCCAAAC 57.415 55.556 12.82 0.00 44.26 2.93
210 211 2.747460 TTCATGCAGGCGAGGTGC 60.747 61.111 0.00 0.00 45.38 5.01
211 212 2.758089 GCTTCATGCAGGCGAGGTG 61.758 63.158 0.00 0.00 42.31 4.00
212 213 2.437359 GCTTCATGCAGGCGAGGT 60.437 61.111 0.00 0.00 42.31 3.85
221 222 1.530293 CTAGCGATTCCTGCTTCATGC 59.470 52.381 0.00 0.00 43.71 4.06
222 223 2.831333 ACTAGCGATTCCTGCTTCATG 58.169 47.619 0.00 0.00 43.71 3.07
223 224 4.672587 TTACTAGCGATTCCTGCTTCAT 57.327 40.909 0.00 0.00 43.71 2.57
224 225 4.621991 GATTACTAGCGATTCCTGCTTCA 58.378 43.478 0.00 0.00 43.71 3.02
225 226 3.670991 CGATTACTAGCGATTCCTGCTTC 59.329 47.826 0.00 0.00 43.71 3.86
226 227 3.068307 ACGATTACTAGCGATTCCTGCTT 59.932 43.478 0.00 0.00 43.71 3.91
227 228 2.623889 ACGATTACTAGCGATTCCTGCT 59.376 45.455 0.00 0.00 46.29 4.24
228 229 2.981140 GACGATTACTAGCGATTCCTGC 59.019 50.000 0.00 0.00 36.50 4.85
229 230 3.227147 CGACGATTACTAGCGATTCCTG 58.773 50.000 0.00 0.00 36.50 3.86
230 231 2.225963 CCGACGATTACTAGCGATTCCT 59.774 50.000 0.00 0.00 36.50 3.36
231 232 2.582687 CCGACGATTACTAGCGATTCC 58.417 52.381 0.00 0.00 36.50 3.01
232 233 1.977412 GCCGACGATTACTAGCGATTC 59.023 52.381 0.00 0.00 36.50 2.52
233 234 1.662309 CGCCGACGATTACTAGCGATT 60.662 52.381 6.56 0.00 46.03 3.34
234 235 0.110328 CGCCGACGATTACTAGCGAT 60.110 55.000 6.56 0.00 46.03 4.58
235 236 1.277739 CGCCGACGATTACTAGCGA 59.722 57.895 6.56 0.00 46.03 4.93
236 237 1.724929 CCGCCGACGATTACTAGCG 60.725 63.158 0.00 0.29 43.93 4.26
237 238 2.015090 GCCGCCGACGATTACTAGC 61.015 63.158 0.00 0.00 43.93 3.42
238 239 1.371389 GGCCGCCGACGATTACTAG 60.371 63.158 0.00 0.00 43.93 2.57
239 240 1.457823 ATGGCCGCCGACGATTACTA 61.458 55.000 4.58 0.00 43.93 1.82
240 241 1.457823 TATGGCCGCCGACGATTACT 61.458 55.000 4.58 0.00 43.93 2.24
241 242 1.007038 TATGGCCGCCGACGATTAC 60.007 57.895 4.58 0.00 43.93 1.89
242 243 1.287815 CTATGGCCGCCGACGATTA 59.712 57.895 4.58 0.00 43.93 1.75
243 244 2.029073 CTATGGCCGCCGACGATT 59.971 61.111 4.58 0.00 43.93 3.34
244 245 3.991051 CCTATGGCCGCCGACGAT 61.991 66.667 4.58 0.00 43.93 3.73
247 248 4.603946 GACCCTATGGCCGCCGAC 62.604 72.222 4.58 0.00 33.59 4.79
252 253 3.916392 GATCGCGACCCTATGGCCG 62.916 68.421 12.93 0.00 33.59 6.13
253 254 2.048127 GATCGCGACCCTATGGCC 60.048 66.667 12.93 0.00 33.59 5.36
254 255 0.946221 CAAGATCGCGACCCTATGGC 60.946 60.000 12.93 0.00 33.59 4.40
255 256 0.946221 GCAAGATCGCGACCCTATGG 60.946 60.000 12.93 6.59 37.80 2.74
272 273 1.605058 GGAGTTAGCTCACCCTCGCA 61.605 60.000 8.96 0.00 43.37 5.10
377 378 1.682849 CCCTGGAACGGATTCACCA 59.317 57.895 0.00 0.00 36.46 4.17
392 393 2.747686 CGGTGTGTACAAGGCCCT 59.252 61.111 0.00 0.00 0.00 5.19
412 413 2.500098 GGCCAACTCCTATAGTGTGACA 59.500 50.000 0.00 0.00 38.88 3.58
428 429 4.021544 GGTAATGACTTCAAACATGGCCAA 60.022 41.667 10.96 0.00 0.00 4.52
663 664 5.014228 AGCTTGGTCTTACTTCACCCTAAAT 59.986 40.000 0.00 0.00 0.00 1.40
876 877 1.806461 TTATCAGGGGCGCGCTCTAG 61.806 60.000 32.56 23.07 0.00 2.43
942 943 1.135603 GCGCTGATGAGCACATTGAAA 60.136 47.619 4.68 0.00 46.62 2.69
1005 1006 4.030913 TCCGATTCAAACAGGAGGAGTAT 58.969 43.478 0.00 0.00 0.00 2.12
1053 1054 2.212752 TTGCCCCATCTATCCTCCTT 57.787 50.000 0.00 0.00 0.00 3.36
1071 1072 4.971282 TCTACATGGGATCTCACCTGAATT 59.029 41.667 0.00 0.00 0.00 2.17
1264 1272 3.192844 GGTGATCTCGTAGTTCTTGGTCA 59.807 47.826 0.00 0.00 0.00 4.02
1499 1510 9.047371 TCGTTAATCAAATGACAACTCTTTGTA 57.953 29.630 7.65 0.00 46.43 2.41
1583 1595 8.133627 AGTAATAGCAACATACTAAACGATCGT 58.866 33.333 16.60 16.60 0.00 3.73
1607 1619 9.167311 GAACATGTATAAGTCATGGAAAAGAGT 57.833 33.333 0.00 0.00 44.57 3.24
1610 1622 8.511604 AGGAACATGTATAAGTCATGGAAAAG 57.488 34.615 0.00 0.00 44.57 2.27
1612 1624 9.778741 GATAGGAACATGTATAAGTCATGGAAA 57.221 33.333 0.00 0.00 44.57 3.13
1615 1627 8.370940 AGTGATAGGAACATGTATAAGTCATGG 58.629 37.037 0.00 0.00 44.57 3.66
1638 1650 4.687948 CGGGAGTTGCATAATCTCATAGTG 59.312 45.833 0.00 0.00 0.00 2.74
1695 1707 9.693739 TTTATAATCACCCAGTTACATTGTGAT 57.306 29.630 0.00 7.50 45.77 3.06
1702 1714 5.883673 GCACCTTTATAATCACCCAGTTACA 59.116 40.000 0.00 0.00 0.00 2.41
1769 1781 4.709886 TCGGAGTGACAAATCCTAATCTCA 59.290 41.667 6.43 0.00 33.12 3.27
2008 2022 9.743057 ATTCTACGAAGATCTTTATCAGTCAAG 57.257 33.333 9.87 2.08 34.28 3.02
2123 2137 0.538118 TTTAAGCGTGCGGACCCTAT 59.462 50.000 0.00 0.00 0.00 2.57
2208 2222 2.029380 TCGTCAAGTCCGTGATCACATT 60.029 45.455 24.93 11.01 0.00 2.71
2269 2283 3.564644 CCGGTGTCTGAATATAGTCGTCT 59.435 47.826 0.00 0.00 0.00 4.18
2634 2653 2.439880 TCAACTTGTGTGTCATGGGGTA 59.560 45.455 0.00 0.00 0.00 3.69
2666 2685 1.666553 CGCACACGGCTAAGGAACA 60.667 57.895 0.00 0.00 41.67 3.18
2843 2862 3.131396 CCTCTGAGTTTAGCACACGTTT 58.869 45.455 3.66 0.00 0.00 3.60
2854 2873 1.623811 ACATACGGCACCTCTGAGTTT 59.376 47.619 3.66 0.00 0.00 2.66
2860 2879 1.515954 CCGAACATACGGCACCTCT 59.484 57.895 0.00 0.00 46.20 3.69
2882 2901 0.822121 TCACGATCCGACCGATCCAT 60.822 55.000 0.00 0.00 44.07 3.41
2984 3003 3.286329 TGATGGTGATGCATAGCAACT 57.714 42.857 0.00 0.00 43.62 3.16
3003 3022 0.735978 TCCTACGCACACGCAAGATG 60.736 55.000 0.00 0.00 45.53 2.90
3234 3257 1.848652 CGTTAAGAGACCCTCCTGGA 58.151 55.000 0.00 0.00 38.00 3.86
3273 3296 6.273730 TGGAAAGTTCTAGGGAAATAACTCCA 59.726 38.462 0.00 0.00 37.20 3.86
3287 3310 5.347124 TCCCTCTTACCATGGAAAGTTCTA 58.653 41.667 21.47 0.00 0.00 2.10
3290 3313 4.175962 TCTCCCTCTTACCATGGAAAGTT 58.824 43.478 21.47 0.00 0.00 2.66
3295 3318 2.629639 CCCTTCTCCCTCTTACCATGGA 60.630 54.545 21.47 0.00 0.00 3.41
3348 3371 1.128200 ACGCAGCATATAACTCCCCA 58.872 50.000 0.00 0.00 0.00 4.96
3357 3380 0.532862 CCTTCCCGAACGCAGCATAT 60.533 55.000 0.00 0.00 0.00 1.78
3389 3412 7.365117 GGGAGAGAATCAATAGACTCCTTTTCA 60.365 40.741 0.00 0.00 42.17 2.69
3452 3475 1.001406 CTTGAACCAGAGACCTCGCTT 59.999 52.381 0.00 0.00 34.09 4.68
3453 3476 0.605589 CTTGAACCAGAGACCTCGCT 59.394 55.000 0.00 0.00 34.09 4.93
3488 3511 2.091541 CTATTCTTTTCCCTGGCGCAA 58.908 47.619 10.83 0.00 0.00 4.85
3600 3623 1.579084 GCCAACCCGTAATCGCAACA 61.579 55.000 0.00 0.00 35.54 3.33
3723 3746 5.531287 ACAACCCATCTTTTTGTCTCAGTAC 59.469 40.000 0.00 0.00 0.00 2.73
3744 3767 6.013725 TCCTACCTGCTCTATCTTTTTGACAA 60.014 38.462 0.00 0.00 0.00 3.18
3755 3778 3.116939 ACTGTCCATCCTACCTGCTCTAT 60.117 47.826 0.00 0.00 0.00 1.98
3761 3784 1.909302 ACCAACTGTCCATCCTACCTG 59.091 52.381 0.00 0.00 0.00 4.00
3773 3796 5.023452 TCCATACTAGATGTGACCAACTGT 58.977 41.667 0.00 0.00 0.00 3.55
3784 3807 6.556212 GTCCATGTACGATCCATACTAGATG 58.444 44.000 0.00 0.00 0.00 2.90
3906 3929 0.889186 TCGCTCAAAGGGTTGAAGGC 60.889 55.000 0.00 0.00 43.18 4.35
4033 4056 7.056635 CCACTTATTGAACAGGATCTATGGTT 58.943 38.462 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.