Multiple sequence alignment - TraesCS3D01G313000

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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 TraesCS3D01G313000 chr3D 100.000 2243 0 0 1 2243 427229148 427226906 0.000000e+00 4143
1 TraesCS3D01G313000 chr3B 93.097 1666 49 15 248 1896 556880075 556878459 0.000000e+00 2379
2 TraesCS3D01G313000 chr3B 95.335 343 15 1 1901 2242 556878429 556878087 5.450000e-151 544
3 TraesCS3D01G313000 chr3A 93.437 1615 50 17 284 1896 559526131 559527691 0.000000e+00 2344
4 TraesCS3D01G313000 chr3A 94.650 243 12 1 2001 2242 559527919 559528161 2.100000e-100 375
5 TraesCS3D01G313000 chr6D 92.377 223 17 0 2 224 6552451 6552673 3.590000e-83 318
6 TraesCS3D01G313000 chr6D 91.364 220 19 0 2 221 94749607 94749826 3.620000e-78 302
7 TraesCS3D01G313000 chr6D 91.071 224 19 1 1 224 431854116 431854338 3.620000e-78 302
8 TraesCS3D01G313000 chr4D 91.518 224 18 1 1 224 396622333 396622111 7.780000e-80 307
9 TraesCS3D01G313000 chr4D 90.991 222 19 1 1 222 22556856 22556636 4.680000e-77 298
10 TraesCS3D01G313000 chr2D 91.441 222 19 0 1 222 627585881 627586102 2.800000e-79 305
11 TraesCS3D01G313000 chr1D 90.476 231 18 3 2 229 433297524 433297295 3.620000e-78 302
12 TraesCS3D01G313000 chr7D 90.991 222 19 1 1 222 71621134 71621354 4.680000e-77 298
13 TraesCS3D01G313000 chr6A 90.667 225 20 1 1 225 153514397 153514620 4.680000e-77 298


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 TraesCS3D01G313000 chr3D 427226906 427229148 2242 True 4143.0 4143 100.0000 1 2243 1 chr3D.!!$R1 2242
1 TraesCS3D01G313000 chr3B 556878087 556880075 1988 True 1461.5 2379 94.2160 248 2242 2 chr3B.!!$R1 1994
2 TraesCS3D01G313000 chr3A 559526131 559528161 2030 False 1359.5 2344 94.0435 284 2242 2 chr3A.!!$F1 1958

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
84 85 0.024619 GATCTAAAACGCACGCGGTC 59.975 55.0 16.7 0.0 44.69 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1383 0.100682 GAGCTAACGATCACAGCGGA 59.899 55.0 0.0 0.0 40.29 5.54 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
40 41 3.294493 GCTGGAGCGCCAAAACCA 61.294 61.111 11.38 5.74 45.41 3.67
41 42 2.956987 CTGGAGCGCCAAAACCAG 59.043 61.111 11.38 11.97 45.41 4.00
42 43 2.597217 TGGAGCGCCAAAACCAGG 60.597 61.111 6.75 0.00 42.49 4.45
43 44 3.373565 GGAGCGCCAAAACCAGGG 61.374 66.667 2.29 0.00 0.00 4.45
44 45 4.056125 GAGCGCCAAAACCAGGGC 62.056 66.667 2.29 0.00 46.80 5.19
48 49 4.038080 GCCAAAACCAGGGCGACG 62.038 66.667 0.00 0.00 40.93 5.12
49 50 3.361977 CCAAAACCAGGGCGACGG 61.362 66.667 0.00 0.00 0.00 4.79
50 51 4.038080 CAAAACCAGGGCGACGGC 62.038 66.667 13.84 13.84 38.90 5.68
51 52 4.572571 AAAACCAGGGCGACGGCA 62.573 61.111 23.66 0.00 42.47 5.69
52 53 3.860930 AAAACCAGGGCGACGGCAT 62.861 57.895 23.66 14.13 42.47 4.40
74 75 2.763249 CCGCTGGCATGATCTAAAAC 57.237 50.000 0.00 0.00 0.00 2.43
75 76 1.003545 CCGCTGGCATGATCTAAAACG 60.004 52.381 0.00 0.00 0.00 3.60
76 77 1.595489 CGCTGGCATGATCTAAAACGC 60.595 52.381 0.00 0.00 0.00 4.84
77 78 1.401552 GCTGGCATGATCTAAAACGCA 59.598 47.619 0.00 0.00 0.00 5.24
78 79 2.792542 GCTGGCATGATCTAAAACGCAC 60.793 50.000 0.00 0.00 0.00 5.34
79 80 1.396648 TGGCATGATCTAAAACGCACG 59.603 47.619 0.00 0.00 0.00 5.34
80 81 1.456732 GCATGATCTAAAACGCACGC 58.543 50.000 0.00 0.00 0.00 5.34
81 82 1.718504 CATGATCTAAAACGCACGCG 58.281 50.000 10.36 10.36 46.03 6.01
82 83 0.650512 ATGATCTAAAACGCACGCGG 59.349 50.000 16.70 0.00 44.69 6.46
83 84 0.668096 TGATCTAAAACGCACGCGGT 60.668 50.000 16.70 6.19 44.69 5.68
84 85 0.024619 GATCTAAAACGCACGCGGTC 59.975 55.000 16.70 0.00 44.69 4.79
85 86 0.668096 ATCTAAAACGCACGCGGTCA 60.668 50.000 16.70 0.00 44.69 4.02
86 87 0.668096 TCTAAAACGCACGCGGTCAT 60.668 50.000 16.70 4.70 44.69 3.06
87 88 0.247145 CTAAAACGCACGCGGTCATC 60.247 55.000 16.70 0.00 44.69 2.92
88 89 1.946855 TAAAACGCACGCGGTCATCG 61.947 55.000 16.70 8.60 44.69 3.84
89 90 4.710695 AACGCACGCGGTCATCGA 62.711 61.111 16.70 0.00 44.69 3.59
90 91 4.710695 ACGCACGCGGTCATCGAA 62.711 61.111 16.70 0.00 44.69 3.71
91 92 3.254654 CGCACGCGGTCATCGAAT 61.255 61.111 12.47 0.00 42.43 3.34
92 93 2.321060 GCACGCGGTCATCGAATG 59.679 61.111 12.47 0.00 42.43 2.67
93 94 3.005898 CACGCGGTCATCGAATGG 58.994 61.111 12.47 0.00 42.43 3.16
94 95 2.202878 ACGCGGTCATCGAATGGG 60.203 61.111 12.47 0.00 42.43 4.00
95 96 2.202878 CGCGGTCATCGAATGGGT 60.203 61.111 0.00 0.00 42.43 4.51
96 97 2.237751 CGCGGTCATCGAATGGGTC 61.238 63.158 0.00 0.00 42.43 4.46
119 120 2.672996 GTTGGGTGCACTGCCGAT 60.673 61.111 17.98 0.00 0.00 4.18
120 121 2.359850 TTGGGTGCACTGCCGATC 60.360 61.111 17.98 0.00 0.00 3.69
121 122 3.918253 TTGGGTGCACTGCCGATCC 62.918 63.158 17.98 7.97 0.00 3.36
122 123 4.408821 GGGTGCACTGCCGATCCA 62.409 66.667 17.98 0.00 0.00 3.41
123 124 2.359850 GGTGCACTGCCGATCCAA 60.360 61.111 17.98 0.00 0.00 3.53
124 125 1.971167 GGTGCACTGCCGATCCAAA 60.971 57.895 17.98 0.00 0.00 3.28
125 126 1.523154 GGTGCACTGCCGATCCAAAA 61.523 55.000 17.98 0.00 0.00 2.44
126 127 0.387239 GTGCACTGCCGATCCAAAAC 60.387 55.000 10.32 0.00 0.00 2.43
127 128 0.537143 TGCACTGCCGATCCAAAACT 60.537 50.000 0.00 0.00 0.00 2.66
128 129 1.271108 TGCACTGCCGATCCAAAACTA 60.271 47.619 0.00 0.00 0.00 2.24
129 130 1.810151 GCACTGCCGATCCAAAACTAA 59.190 47.619 0.00 0.00 0.00 2.24
130 131 2.227865 GCACTGCCGATCCAAAACTAAA 59.772 45.455 0.00 0.00 0.00 1.85
131 132 3.305064 GCACTGCCGATCCAAAACTAAAA 60.305 43.478 0.00 0.00 0.00 1.52
132 133 4.475944 CACTGCCGATCCAAAACTAAAAG 58.524 43.478 0.00 0.00 0.00 2.27
133 134 4.215399 CACTGCCGATCCAAAACTAAAAGA 59.785 41.667 0.00 0.00 0.00 2.52
134 135 4.455877 ACTGCCGATCCAAAACTAAAAGAG 59.544 41.667 0.00 0.00 0.00 2.85
135 136 3.756434 TGCCGATCCAAAACTAAAAGAGG 59.244 43.478 0.00 0.00 0.00 3.69
136 137 3.128764 GCCGATCCAAAACTAAAAGAGGG 59.871 47.826 0.00 0.00 0.00 4.30
137 138 3.128764 CCGATCCAAAACTAAAAGAGGGC 59.871 47.826 0.00 0.00 0.00 5.19
138 139 3.181510 CGATCCAAAACTAAAAGAGGGCG 60.182 47.826 0.00 0.00 0.00 6.13
139 140 2.510613 TCCAAAACTAAAAGAGGGCGG 58.489 47.619 0.00 0.00 0.00 6.13
140 141 2.106857 TCCAAAACTAAAAGAGGGCGGA 59.893 45.455 0.00 0.00 0.00 5.54
141 142 2.228103 CCAAAACTAAAAGAGGGCGGAC 59.772 50.000 0.00 0.00 0.00 4.79
142 143 1.804601 AAACTAAAAGAGGGCGGACG 58.195 50.000 0.00 0.00 0.00 4.79
143 144 0.036671 AACTAAAAGAGGGCGGACGG 60.037 55.000 0.00 0.00 0.00 4.79
144 145 1.190178 ACTAAAAGAGGGCGGACGGT 61.190 55.000 0.00 0.00 0.00 4.83
145 146 0.819582 CTAAAAGAGGGCGGACGGTA 59.180 55.000 0.00 0.00 0.00 4.02
146 147 0.819582 TAAAAGAGGGCGGACGGTAG 59.180 55.000 0.00 0.00 0.00 3.18
147 148 1.896122 AAAAGAGGGCGGACGGTAGG 61.896 60.000 0.00 0.00 0.00 3.18
148 149 3.597086 AAGAGGGCGGACGGTAGGT 62.597 63.158 0.00 0.00 0.00 3.08
149 150 3.834799 GAGGGCGGACGGTAGGTG 61.835 72.222 0.00 0.00 0.00 4.00
174 175 3.837669 CGACCCAAACGGACAAAAG 57.162 52.632 0.00 0.00 34.64 2.27
175 176 0.309612 CGACCCAAACGGACAAAAGG 59.690 55.000 0.00 0.00 34.64 3.11
176 177 0.031585 GACCCAAACGGACAAAAGGC 59.968 55.000 0.00 0.00 34.64 4.35
177 178 1.007849 CCCAAACGGACAAAAGGCG 60.008 57.895 0.00 0.00 0.00 5.52
178 179 1.448922 CCCAAACGGACAAAAGGCGA 61.449 55.000 0.00 0.00 0.00 5.54
179 180 0.382515 CCAAACGGACAAAAGGCGAA 59.617 50.000 0.00 0.00 0.00 4.70
180 181 1.472990 CAAACGGACAAAAGGCGAAC 58.527 50.000 0.00 0.00 0.00 3.95
181 182 1.096416 AAACGGACAAAAGGCGAACA 58.904 45.000 0.00 0.00 0.00 3.18
182 183 1.096416 AACGGACAAAAGGCGAACAA 58.904 45.000 0.00 0.00 0.00 2.83
183 184 1.096416 ACGGACAAAAGGCGAACAAA 58.904 45.000 0.00 0.00 0.00 2.83
184 185 1.473278 ACGGACAAAAGGCGAACAAAA 59.527 42.857 0.00 0.00 0.00 2.44
185 186 2.094649 ACGGACAAAAGGCGAACAAAAA 60.095 40.909 0.00 0.00 0.00 1.94
186 187 2.280445 CGGACAAAAGGCGAACAAAAAC 59.720 45.455 0.00 0.00 0.00 2.43
187 188 2.280445 GGACAAAAGGCGAACAAAAACG 59.720 45.455 0.00 0.00 0.00 3.60
188 189 2.918600 GACAAAAGGCGAACAAAAACGT 59.081 40.909 0.00 0.00 0.00 3.99
189 190 2.918600 ACAAAAGGCGAACAAAAACGTC 59.081 40.909 0.00 0.00 0.00 4.34
190 191 1.817609 AAAGGCGAACAAAAACGTCG 58.182 45.000 0.00 0.00 39.16 5.12
191 192 0.728542 AAGGCGAACAAAAACGTCGT 59.271 45.000 0.00 0.00 39.16 4.34
192 193 0.302589 AGGCGAACAAAAACGTCGTC 59.697 50.000 0.00 0.00 39.16 4.20
193 194 0.302589 GGCGAACAAAAACGTCGTCT 59.697 50.000 0.00 0.00 0.00 4.18
194 195 1.372656 GCGAACAAAAACGTCGTCTG 58.627 50.000 0.00 0.00 0.00 3.51
195 196 1.267186 GCGAACAAAAACGTCGTCTGT 60.267 47.619 0.00 0.00 0.00 3.41
196 197 2.785342 GCGAACAAAAACGTCGTCTGTT 60.785 45.455 16.03 16.03 33.07 3.16
197 198 3.409949 CGAACAAAAACGTCGTCTGTTT 58.590 40.909 16.75 8.26 41.07 2.83
198 199 3.234284 CGAACAAAAACGTCGTCTGTTTG 59.766 43.478 19.48 19.48 39.36 2.93
199 200 3.125698 ACAAAAACGTCGTCTGTTTGG 57.874 42.857 22.54 11.73 39.36 3.28
200 201 2.159490 ACAAAAACGTCGTCTGTTTGGG 60.159 45.455 22.54 10.51 39.36 4.12
201 202 1.741528 AAAACGTCGTCTGTTTGGGT 58.258 45.000 0.00 0.00 39.36 4.51
202 203 1.292992 AAACGTCGTCTGTTTGGGTC 58.707 50.000 0.00 0.00 38.08 4.46
203 204 0.872881 AACGTCGTCTGTTTGGGTCG 60.873 55.000 0.00 0.00 0.00 4.79
204 205 2.019951 CGTCGTCTGTTTGGGTCGG 61.020 63.158 0.00 0.00 0.00 4.79
205 206 2.029964 TCGTCTGTTTGGGTCGGC 59.970 61.111 0.00 0.00 0.00 5.54
206 207 3.047877 CGTCTGTTTGGGTCGGCC 61.048 66.667 0.00 0.00 0.00 6.13
216 217 4.324991 GGTCGGCCCGTTGGAGTT 62.325 66.667 1.63 0.00 0.00 3.01
217 218 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
220 221 3.056328 GGCCCGTTGGAGTTGCTC 61.056 66.667 0.00 0.00 0.00 4.26
221 222 2.032681 GCCCGTTGGAGTTGCTCT 59.967 61.111 0.00 0.00 0.00 4.09
222 223 1.295423 GCCCGTTGGAGTTGCTCTA 59.705 57.895 0.00 0.00 0.00 2.43
223 224 0.321298 GCCCGTTGGAGTTGCTCTAA 60.321 55.000 0.00 0.00 0.00 2.10
224 225 1.439679 CCCGTTGGAGTTGCTCTAAC 58.560 55.000 13.14 13.14 44.66 2.34
235 236 3.246619 GTTGCTCTAACTTCAGAGACGG 58.753 50.000 4.35 0.00 44.11 4.79
236 237 1.819288 TGCTCTAACTTCAGAGACGGG 59.181 52.381 4.35 0.00 44.11 5.28
237 238 1.135333 GCTCTAACTTCAGAGACGGGG 59.865 57.143 4.35 0.00 44.11 5.73
238 239 2.724454 CTCTAACTTCAGAGACGGGGA 58.276 52.381 0.00 0.00 44.11 4.81
239 240 3.090037 CTCTAACTTCAGAGACGGGGAA 58.910 50.000 0.00 0.00 44.11 3.97
240 241 3.503365 TCTAACTTCAGAGACGGGGAAA 58.497 45.455 0.00 0.00 0.00 3.13
241 242 3.899360 TCTAACTTCAGAGACGGGGAAAA 59.101 43.478 0.00 0.00 0.00 2.29
242 243 2.841442 ACTTCAGAGACGGGGAAAAG 57.159 50.000 0.00 0.00 0.00 2.27
243 244 1.348036 ACTTCAGAGACGGGGAAAAGG 59.652 52.381 0.00 0.00 0.00 3.11
244 245 1.623811 CTTCAGAGACGGGGAAAAGGA 59.376 52.381 0.00 0.00 0.00 3.36
245 246 1.952621 TCAGAGACGGGGAAAAGGAT 58.047 50.000 0.00 0.00 0.00 3.24
246 247 2.266279 TCAGAGACGGGGAAAAGGATT 58.734 47.619 0.00 0.00 0.00 3.01
247 248 2.642807 TCAGAGACGGGGAAAAGGATTT 59.357 45.455 0.00 0.00 42.41 2.17
282 283 3.123621 GGACTTATGACGCACTTCACTTG 59.876 47.826 0.00 0.00 0.00 3.16
305 307 0.447801 CGGAGCAAAAGGATGGAACG 59.552 55.000 0.00 0.00 0.00 3.95
382 385 0.312729 AAACAATCCGTTGGCGTTCC 59.687 50.000 0.00 0.00 39.70 3.62
465 468 2.017782 CGAGACGAGAGGATGGAAAGA 58.982 52.381 0.00 0.00 0.00 2.52
469 472 2.619177 GACGAGAGGATGGAAAGATCGA 59.381 50.000 0.00 0.00 33.23 3.59
470 473 3.226777 ACGAGAGGATGGAAAGATCGAT 58.773 45.455 0.00 0.00 33.23 3.59
471 474 4.399219 ACGAGAGGATGGAAAGATCGATA 58.601 43.478 0.00 0.00 33.23 2.92
472 475 5.013547 ACGAGAGGATGGAAAGATCGATAT 58.986 41.667 0.00 0.00 33.23 1.63
473 476 5.124776 ACGAGAGGATGGAAAGATCGATATC 59.875 44.000 0.00 0.00 33.23 1.63
566 574 1.697432 AGGAACCTTCAATCACCGTCA 59.303 47.619 0.00 0.00 0.00 4.35
602 617 4.386867 TCACGACTAGACATTCCATTCC 57.613 45.455 0.00 0.00 0.00 3.01
603 618 3.116300 CACGACTAGACATTCCATTCCG 58.884 50.000 0.00 0.00 0.00 4.30
604 619 2.758979 ACGACTAGACATTCCATTCCGT 59.241 45.455 0.00 0.00 0.00 4.69
605 620 3.194968 ACGACTAGACATTCCATTCCGTT 59.805 43.478 0.00 0.00 0.00 4.44
606 621 3.797256 CGACTAGACATTCCATTCCGTTC 59.203 47.826 0.00 0.00 0.00 3.95
607 622 4.120589 GACTAGACATTCCATTCCGTTCC 58.879 47.826 0.00 0.00 0.00 3.62
608 623 3.517901 ACTAGACATTCCATTCCGTTCCA 59.482 43.478 0.00 0.00 0.00 3.53
609 624 3.652057 AGACATTCCATTCCGTTCCAT 57.348 42.857 0.00 0.00 0.00 3.41
610 625 3.968265 AGACATTCCATTCCGTTCCATT 58.032 40.909 0.00 0.00 0.00 3.16
611 626 3.947834 AGACATTCCATTCCGTTCCATTC 59.052 43.478 0.00 0.00 0.00 2.67
652 667 4.760047 ACCAGGATGTCGCGCCAC 62.760 66.667 0.00 0.00 0.00 5.01
719 745 2.262915 CGCTCCACAGTCCACTCC 59.737 66.667 0.00 0.00 0.00 3.85
720 746 2.665603 GCTCCACAGTCCACTCCC 59.334 66.667 0.00 0.00 0.00 4.30
721 747 2.960688 GCTCCACAGTCCACTCCCC 61.961 68.421 0.00 0.00 0.00 4.81
722 748 1.536418 CTCCACAGTCCACTCCCCA 60.536 63.158 0.00 0.00 0.00 4.96
723 749 0.911525 CTCCACAGTCCACTCCCCAT 60.912 60.000 0.00 0.00 0.00 4.00
724 750 0.909610 TCCACAGTCCACTCCCCATC 60.910 60.000 0.00 0.00 0.00 3.51
725 751 1.219124 CACAGTCCACTCCCCATCG 59.781 63.158 0.00 0.00 0.00 3.84
726 752 2.187946 CAGTCCACTCCCCATCGC 59.812 66.667 0.00 0.00 0.00 4.58
727 753 3.083997 AGTCCACTCCCCATCGCC 61.084 66.667 0.00 0.00 0.00 5.54
728 754 3.083997 GTCCACTCCCCATCGCCT 61.084 66.667 0.00 0.00 0.00 5.52
729 755 2.285368 TCCACTCCCCATCGCCTT 60.285 61.111 0.00 0.00 0.00 4.35
918 945 0.321298 AACACCAGAACCCGATTCCG 60.321 55.000 0.00 0.00 38.16 4.30
1368 1397 2.507102 CGCTCCGCTGTGATCGTT 60.507 61.111 0.00 0.00 0.00 3.85
1461 1490 8.718102 TTCTATAAGCTGGTACATTTGTTCTC 57.282 34.615 0.00 0.00 38.20 2.87
1589 1618 7.698550 CAGACTATGTACTACACTACAGCAAAG 59.301 40.741 0.00 0.00 30.12 2.77
1896 1925 4.271696 TCAAGGTCATATATCTTGCGGG 57.728 45.455 7.47 0.00 38.13 6.13
1897 1926 3.901222 TCAAGGTCATATATCTTGCGGGA 59.099 43.478 7.47 0.00 38.13 5.14
1898 1927 4.346709 TCAAGGTCATATATCTTGCGGGAA 59.653 41.667 7.47 0.00 38.13 3.97
1899 1928 4.974645 AGGTCATATATCTTGCGGGAAA 57.025 40.909 0.00 0.00 0.00 3.13
1941 1995 5.096849 CCTCGAAACGGAACTTTTGAAAAA 58.903 37.500 0.00 0.00 27.14 1.94
1945 1999 5.478233 AAACGGAACTTTTGAAAAATGCC 57.522 34.783 0.00 0.00 0.00 4.40
1955 2009 7.334858 ACTTTTGAAAAATGCCCTAGTTTTGA 58.665 30.769 0.00 0.00 36.76 2.69
1987 2044 2.865551 CGGCTTGCTTTTTGTTTCATGT 59.134 40.909 0.00 0.00 0.00 3.21
2029 2182 1.068816 GCGTTTATTGTTGCCCGAACT 60.069 47.619 0.00 0.00 35.37 3.01
2149 2302 6.422776 TTCTCCAGTTTCGAATCAATAAGC 57.577 37.500 8.83 0.00 0.00 3.09
2200 2353 2.801679 CACGGCAATGTCAAAATGCTTT 59.198 40.909 8.09 0.00 39.94 3.51
2242 2396 6.085555 TGTCTTTCGACAAGAAGACACTAT 57.914 37.500 20.98 0.00 46.61 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.273080 CTGGTTTTGGCGCTCCAGC 62.273 63.158 7.64 0.00 44.53 4.85
24 25 2.629656 CCTGGTTTTGGCGCTCCAG 61.630 63.158 20.13 20.13 44.53 3.86
25 26 2.597217 CCTGGTTTTGGCGCTCCA 60.597 61.111 7.64 7.90 41.55 3.86
26 27 3.373565 CCCTGGTTTTGGCGCTCC 61.374 66.667 7.64 3.30 0.00 4.70
27 28 4.056125 GCCCTGGTTTTGGCGCTC 62.056 66.667 7.64 0.00 38.00 5.03
31 32 4.038080 CGTCGCCCTGGTTTTGGC 62.038 66.667 0.00 0.00 44.41 4.52
32 33 3.361977 CCGTCGCCCTGGTTTTGG 61.362 66.667 0.00 0.00 0.00 3.28
33 34 4.038080 GCCGTCGCCCTGGTTTTG 62.038 66.667 0.00 0.00 0.00 2.44
34 35 3.860930 ATGCCGTCGCCCTGGTTTT 62.861 57.895 0.00 0.00 0.00 2.43
35 36 4.344865 ATGCCGTCGCCCTGGTTT 62.345 61.111 0.00 0.00 0.00 3.27
55 56 1.003545 CGTTTTAGATCATGCCAGCGG 60.004 52.381 0.00 0.00 0.00 5.52
56 57 1.595489 GCGTTTTAGATCATGCCAGCG 60.595 52.381 0.00 0.00 0.00 5.18
57 58 1.401552 TGCGTTTTAGATCATGCCAGC 59.598 47.619 0.00 0.00 0.00 4.85
58 59 2.537529 CGTGCGTTTTAGATCATGCCAG 60.538 50.000 0.00 0.00 0.00 4.85
59 60 1.396648 CGTGCGTTTTAGATCATGCCA 59.603 47.619 0.00 0.00 0.00 4.92
60 61 1.856014 GCGTGCGTTTTAGATCATGCC 60.856 52.381 0.00 0.00 35.93 4.40
61 62 1.456732 GCGTGCGTTTTAGATCATGC 58.543 50.000 0.00 0.00 34.82 4.06
62 63 1.592110 CCGCGTGCGTTTTAGATCATG 60.592 52.381 13.70 0.00 37.81 3.07
63 64 0.650512 CCGCGTGCGTTTTAGATCAT 59.349 50.000 13.70 0.00 37.81 2.45
64 65 0.668096 ACCGCGTGCGTTTTAGATCA 60.668 50.000 13.70 0.00 37.81 2.92
65 66 0.024619 GACCGCGTGCGTTTTAGATC 59.975 55.000 13.70 0.00 37.81 2.75
66 67 0.668096 TGACCGCGTGCGTTTTAGAT 60.668 50.000 13.70 0.00 37.81 1.98
67 68 0.668096 ATGACCGCGTGCGTTTTAGA 60.668 50.000 13.70 0.00 37.81 2.10
68 69 0.247145 GATGACCGCGTGCGTTTTAG 60.247 55.000 13.70 0.00 37.81 1.85
69 70 1.782807 GATGACCGCGTGCGTTTTA 59.217 52.632 13.70 0.00 37.81 1.52
70 71 2.554272 GATGACCGCGTGCGTTTT 59.446 55.556 13.70 0.00 37.81 2.43
71 72 3.773630 CGATGACCGCGTGCGTTT 61.774 61.111 13.70 0.00 37.81 3.60
72 73 4.710695 TCGATGACCGCGTGCGTT 62.711 61.111 13.70 0.00 38.37 4.84
73 74 3.982372 ATTCGATGACCGCGTGCGT 62.982 57.895 13.70 0.00 38.37 5.24
74 75 3.254654 ATTCGATGACCGCGTGCG 61.255 61.111 4.92 7.38 38.37 5.34
75 76 2.321060 CATTCGATGACCGCGTGC 59.679 61.111 4.92 0.00 38.37 5.34
76 77 2.525248 CCCATTCGATGACCGCGTG 61.525 63.158 4.92 0.00 38.37 5.34
77 78 2.202878 CCCATTCGATGACCGCGT 60.203 61.111 4.92 0.00 38.37 6.01
78 79 2.202878 ACCCATTCGATGACCGCG 60.203 61.111 0.00 0.00 38.37 6.46
79 80 3.719214 GACCCATTCGATGACCGC 58.281 61.111 0.00 0.00 38.37 5.68
102 103 2.672996 ATCGGCAGTGCACCCAAC 60.673 61.111 18.61 0.00 0.00 3.77
103 104 2.359850 GATCGGCAGTGCACCCAA 60.360 61.111 18.61 0.00 0.00 4.12
104 105 4.408821 GGATCGGCAGTGCACCCA 62.409 66.667 18.61 0.22 0.00 4.51
105 106 3.918253 TTGGATCGGCAGTGCACCC 62.918 63.158 18.61 7.72 0.00 4.61
106 107 1.523154 TTTTGGATCGGCAGTGCACC 61.523 55.000 18.61 14.14 0.00 5.01
107 108 0.387239 GTTTTGGATCGGCAGTGCAC 60.387 55.000 18.61 9.40 0.00 4.57
108 109 0.537143 AGTTTTGGATCGGCAGTGCA 60.537 50.000 18.61 0.00 0.00 4.57
109 110 1.448985 TAGTTTTGGATCGGCAGTGC 58.551 50.000 6.55 6.55 0.00 4.40
110 111 4.215399 TCTTTTAGTTTTGGATCGGCAGTG 59.785 41.667 0.00 0.00 0.00 3.66
111 112 4.394729 TCTTTTAGTTTTGGATCGGCAGT 58.605 39.130 0.00 0.00 0.00 4.40
112 113 4.142600 CCTCTTTTAGTTTTGGATCGGCAG 60.143 45.833 0.00 0.00 0.00 4.85
113 114 3.756434 CCTCTTTTAGTTTTGGATCGGCA 59.244 43.478 0.00 0.00 0.00 5.69
114 115 3.128764 CCCTCTTTTAGTTTTGGATCGGC 59.871 47.826 0.00 0.00 0.00 5.54
115 116 3.128764 GCCCTCTTTTAGTTTTGGATCGG 59.871 47.826 0.00 0.00 0.00 4.18
116 117 3.181510 CGCCCTCTTTTAGTTTTGGATCG 60.182 47.826 0.00 0.00 0.00 3.69
117 118 3.128764 CCGCCCTCTTTTAGTTTTGGATC 59.871 47.826 0.00 0.00 0.00 3.36
118 119 3.089284 CCGCCCTCTTTTAGTTTTGGAT 58.911 45.455 0.00 0.00 0.00 3.41
119 120 2.106857 TCCGCCCTCTTTTAGTTTTGGA 59.893 45.455 0.00 0.00 0.00 3.53
120 121 2.228103 GTCCGCCCTCTTTTAGTTTTGG 59.772 50.000 0.00 0.00 0.00 3.28
121 122 2.095919 CGTCCGCCCTCTTTTAGTTTTG 60.096 50.000 0.00 0.00 0.00 2.44
122 123 2.148768 CGTCCGCCCTCTTTTAGTTTT 58.851 47.619 0.00 0.00 0.00 2.43
123 124 1.609841 CCGTCCGCCCTCTTTTAGTTT 60.610 52.381 0.00 0.00 0.00 2.66
124 125 0.036671 CCGTCCGCCCTCTTTTAGTT 60.037 55.000 0.00 0.00 0.00 2.24
125 126 1.190178 ACCGTCCGCCCTCTTTTAGT 61.190 55.000 0.00 0.00 0.00 2.24
126 127 0.819582 TACCGTCCGCCCTCTTTTAG 59.180 55.000 0.00 0.00 0.00 1.85
127 128 0.819582 CTACCGTCCGCCCTCTTTTA 59.180 55.000 0.00 0.00 0.00 1.52
128 129 1.595357 CTACCGTCCGCCCTCTTTT 59.405 57.895 0.00 0.00 0.00 2.27
129 130 2.356780 CCTACCGTCCGCCCTCTTT 61.357 63.158 0.00 0.00 0.00 2.52
130 131 2.758737 CCTACCGTCCGCCCTCTT 60.759 66.667 0.00 0.00 0.00 2.85
131 132 4.057943 ACCTACCGTCCGCCCTCT 62.058 66.667 0.00 0.00 0.00 3.69
132 133 3.834799 CACCTACCGTCCGCCCTC 61.835 72.222 0.00 0.00 0.00 4.30
153 154 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
154 155 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
156 157 0.309612 CCTTTTGTCCGTTTGGGTCG 59.690 55.000 0.00 0.00 37.00 4.79
157 158 0.031585 GCCTTTTGTCCGTTTGGGTC 59.968 55.000 0.00 0.00 37.00 4.46
158 159 1.730451 CGCCTTTTGTCCGTTTGGGT 61.730 55.000 0.00 0.00 37.00 4.51
159 160 1.007849 CGCCTTTTGTCCGTTTGGG 60.008 57.895 0.00 0.00 35.24 4.12
160 161 0.382515 TTCGCCTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
161 162 1.202200 TGTTCGCCTTTTGTCCGTTTG 60.202 47.619 0.00 0.00 0.00 2.93
162 163 1.096416 TGTTCGCCTTTTGTCCGTTT 58.904 45.000 0.00 0.00 0.00 3.60
163 164 1.096416 TTGTTCGCCTTTTGTCCGTT 58.904 45.000 0.00 0.00 0.00 4.44
164 165 1.096416 TTTGTTCGCCTTTTGTCCGT 58.904 45.000 0.00 0.00 0.00 4.69
165 166 2.196295 TTTTGTTCGCCTTTTGTCCG 57.804 45.000 0.00 0.00 0.00 4.79
166 167 2.280445 CGTTTTTGTTCGCCTTTTGTCC 59.720 45.455 0.00 0.00 0.00 4.02
167 168 2.918600 ACGTTTTTGTTCGCCTTTTGTC 59.081 40.909 0.00 0.00 0.00 3.18
168 169 2.918600 GACGTTTTTGTTCGCCTTTTGT 59.081 40.909 0.00 0.00 0.00 2.83
169 170 2.036086 CGACGTTTTTGTTCGCCTTTTG 60.036 45.455 0.00 0.00 0.00 2.44
170 171 2.178783 CGACGTTTTTGTTCGCCTTTT 58.821 42.857 0.00 0.00 0.00 2.27
171 172 1.130938 ACGACGTTTTTGTTCGCCTTT 59.869 42.857 0.00 0.00 0.00 3.11
172 173 0.728542 ACGACGTTTTTGTTCGCCTT 59.271 45.000 0.00 0.00 0.00 4.35
173 174 0.302589 GACGACGTTTTTGTTCGCCT 59.697 50.000 0.13 0.00 0.00 5.52
174 175 0.302589 AGACGACGTTTTTGTTCGCC 59.697 50.000 0.13 0.00 0.00 5.54
175 176 1.267186 ACAGACGACGTTTTTGTTCGC 60.267 47.619 0.13 0.00 0.00 4.70
176 177 2.706760 ACAGACGACGTTTTTGTTCG 57.293 45.000 0.13 0.00 0.00 3.95
177 178 3.540738 CCAAACAGACGACGTTTTTGTTC 59.459 43.478 19.64 0.83 34.40 3.18
178 179 3.494232 CCAAACAGACGACGTTTTTGTT 58.506 40.909 20.19 18.22 34.40 2.83
179 180 2.159490 CCCAAACAGACGACGTTTTTGT 60.159 45.455 20.19 14.75 34.40 2.83
180 181 2.159490 ACCCAAACAGACGACGTTTTTG 60.159 45.455 17.25 17.25 34.40 2.44
181 182 2.086094 ACCCAAACAGACGACGTTTTT 58.914 42.857 0.13 0.00 34.40 1.94
182 183 1.667212 GACCCAAACAGACGACGTTTT 59.333 47.619 0.13 0.00 34.40 2.43
183 184 1.292992 GACCCAAACAGACGACGTTT 58.707 50.000 0.13 0.00 37.04 3.60
184 185 0.872881 CGACCCAAACAGACGACGTT 60.873 55.000 0.13 0.00 0.00 3.99
185 186 1.299620 CGACCCAAACAGACGACGT 60.300 57.895 0.00 0.00 0.00 4.34
186 187 2.019951 CCGACCCAAACAGACGACG 61.020 63.158 0.00 0.00 0.00 5.12
187 188 2.315386 GCCGACCCAAACAGACGAC 61.315 63.158 0.00 0.00 0.00 4.34
188 189 2.029964 GCCGACCCAAACAGACGA 59.970 61.111 0.00 0.00 0.00 4.20
189 190 3.047877 GGCCGACCCAAACAGACG 61.048 66.667 0.00 0.00 0.00 4.18
199 200 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
200 201 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
203 204 2.180159 TAGAGCAACTCCAACGGGCC 62.180 60.000 0.00 0.00 0.00 5.80
204 205 0.321298 TTAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
205 206 1.002087 AGTTAGAGCAACTCCAACGGG 59.998 52.381 1.24 0.00 44.48 5.28
206 207 2.457366 AGTTAGAGCAACTCCAACGG 57.543 50.000 1.24 0.00 44.48 4.44
214 215 3.246619 CCGTCTCTGAAGTTAGAGCAAC 58.753 50.000 0.00 0.00 43.09 4.17
215 216 2.231478 CCCGTCTCTGAAGTTAGAGCAA 59.769 50.000 0.00 0.00 43.09 3.91
216 217 1.819288 CCCGTCTCTGAAGTTAGAGCA 59.181 52.381 0.00 0.00 43.09 4.26
217 218 1.135333 CCCCGTCTCTGAAGTTAGAGC 59.865 57.143 0.00 0.00 43.09 4.09
218 219 2.724454 TCCCCGTCTCTGAAGTTAGAG 58.276 52.381 0.00 0.00 44.42 2.43
219 220 2.893215 TCCCCGTCTCTGAAGTTAGA 57.107 50.000 0.00 0.00 0.00 2.10
220 221 3.955650 TTTCCCCGTCTCTGAAGTTAG 57.044 47.619 0.00 0.00 0.00 2.34
221 222 3.007614 CCTTTTCCCCGTCTCTGAAGTTA 59.992 47.826 0.00 0.00 0.00 2.24
222 223 2.224548 CCTTTTCCCCGTCTCTGAAGTT 60.225 50.000 0.00 0.00 0.00 2.66
223 224 1.348036 CCTTTTCCCCGTCTCTGAAGT 59.652 52.381 0.00 0.00 0.00 3.01
224 225 1.623811 TCCTTTTCCCCGTCTCTGAAG 59.376 52.381 0.00 0.00 0.00 3.02
225 226 1.724545 TCCTTTTCCCCGTCTCTGAA 58.275 50.000 0.00 0.00 0.00 3.02
226 227 1.952621 ATCCTTTTCCCCGTCTCTGA 58.047 50.000 0.00 0.00 0.00 3.27
227 228 2.789409 AATCCTTTTCCCCGTCTCTG 57.211 50.000 0.00 0.00 0.00 3.35
228 229 3.073946 TCAAAATCCTTTTCCCCGTCTCT 59.926 43.478 0.00 0.00 0.00 3.10
229 230 3.418047 TCAAAATCCTTTTCCCCGTCTC 58.582 45.455 0.00 0.00 0.00 3.36
230 231 3.073946 TCTCAAAATCCTTTTCCCCGTCT 59.926 43.478 0.00 0.00 0.00 4.18
231 232 3.418047 TCTCAAAATCCTTTTCCCCGTC 58.582 45.455 0.00 0.00 0.00 4.79
232 233 3.518992 TCTCAAAATCCTTTTCCCCGT 57.481 42.857 0.00 0.00 0.00 5.28
233 234 5.193679 ACTATCTCAAAATCCTTTTCCCCG 58.806 41.667 0.00 0.00 0.00 5.73
234 235 8.633561 CATAACTATCTCAAAATCCTTTTCCCC 58.366 37.037 0.00 0.00 0.00 4.81
235 236 8.633561 CCATAACTATCTCAAAATCCTTTTCCC 58.366 37.037 0.00 0.00 0.00 3.97
236 237 9.408648 TCCATAACTATCTCAAAATCCTTTTCC 57.591 33.333 0.00 0.00 0.00 3.13
238 239 9.981460 AGTCCATAACTATCTCAAAATCCTTTT 57.019 29.630 0.00 0.00 36.07 2.27
239 240 9.981460 AAGTCCATAACTATCTCAAAATCCTTT 57.019 29.630 0.00 0.00 37.17 3.11
245 246 9.529325 CGTCATAAGTCCATAACTATCTCAAAA 57.471 33.333 0.00 0.00 37.17 2.44
246 247 7.652105 GCGTCATAAGTCCATAACTATCTCAAA 59.348 37.037 0.00 0.00 37.17 2.69
247 248 7.145985 GCGTCATAAGTCCATAACTATCTCAA 58.854 38.462 0.00 0.00 37.17 3.02
248 249 6.264518 TGCGTCATAAGTCCATAACTATCTCA 59.735 38.462 0.00 0.00 37.17 3.27
249 250 6.583050 GTGCGTCATAAGTCCATAACTATCTC 59.417 42.308 0.00 0.00 37.17 2.75
250 251 6.265649 AGTGCGTCATAAGTCCATAACTATCT 59.734 38.462 0.00 0.00 37.17 1.98
251 252 6.448006 AGTGCGTCATAAGTCCATAACTATC 58.552 40.000 0.00 0.00 37.17 2.08
252 253 6.406692 AGTGCGTCATAAGTCCATAACTAT 57.593 37.500 0.00 0.00 37.17 2.12
253 254 5.847111 AGTGCGTCATAAGTCCATAACTA 57.153 39.130 0.00 0.00 37.17 2.24
254 255 4.737855 AGTGCGTCATAAGTCCATAACT 57.262 40.909 0.00 0.00 41.10 2.24
255 256 4.868171 TGAAGTGCGTCATAAGTCCATAAC 59.132 41.667 0.00 0.00 0.00 1.89
262 263 3.728845 ACAAGTGAAGTGCGTCATAAGT 58.271 40.909 0.00 0.00 0.00 2.24
269 270 1.351707 CGCAACAAGTGAAGTGCGT 59.648 52.632 8.62 0.00 40.33 5.24
270 271 1.369209 CCGCAACAAGTGAAGTGCG 60.369 57.895 9.75 9.75 44.10 5.34
291 293 0.454957 CAGCGCGTTCCATCCTTTTG 60.455 55.000 8.43 0.00 0.00 2.44
300 302 1.944676 CTCCGTATCAGCGCGTTCC 60.945 63.158 8.43 0.00 0.00 3.62
304 306 0.863799 TACTACTCCGTATCAGCGCG 59.136 55.000 0.00 0.00 0.00 6.86
305 307 2.032550 TGTTACTACTCCGTATCAGCGC 59.967 50.000 0.00 0.00 0.00 5.92
465 468 3.891977 AGCCGGTAGCATATGATATCGAT 59.108 43.478 29.86 17.48 42.48 3.59
553 561 0.323629 GGGAGGTGACGGTGATTGAA 59.676 55.000 0.00 0.00 0.00 2.69
602 617 2.426522 AGTGTGTGATGGAATGGAACG 58.573 47.619 0.00 0.00 0.00 3.95
603 618 4.154195 GTGTAGTGTGTGATGGAATGGAAC 59.846 45.833 0.00 0.00 0.00 3.62
604 619 4.041567 AGTGTAGTGTGTGATGGAATGGAA 59.958 41.667 0.00 0.00 0.00 3.53
605 620 3.582647 AGTGTAGTGTGTGATGGAATGGA 59.417 43.478 0.00 0.00 0.00 3.41
606 621 3.942829 AGTGTAGTGTGTGATGGAATGG 58.057 45.455 0.00 0.00 0.00 3.16
607 622 5.111989 CCTAGTGTAGTGTGTGATGGAATG 58.888 45.833 0.00 0.00 0.00 2.67
608 623 4.383118 GCCTAGTGTAGTGTGTGATGGAAT 60.383 45.833 0.00 0.00 0.00 3.01
609 624 3.056107 GCCTAGTGTAGTGTGTGATGGAA 60.056 47.826 0.00 0.00 0.00 3.53
610 625 2.496070 GCCTAGTGTAGTGTGTGATGGA 59.504 50.000 0.00 0.00 0.00 3.41
611 626 2.233676 TGCCTAGTGTAGTGTGTGATGG 59.766 50.000 0.00 0.00 0.00 3.51
811 838 1.377333 GGGTCACTAGGCTGGTTGC 60.377 63.158 0.00 0.00 41.94 4.17
888 915 0.608035 TCTGGTGTTTTCCGGGATGC 60.608 55.000 0.00 0.00 34.81 3.91
918 945 0.098200 GCATAAAAGGGCGACGGAAC 59.902 55.000 0.00 0.00 0.00 3.62
940 967 4.087892 CTCTGTCCACCCGGCCAG 62.088 72.222 2.24 0.00 0.00 4.85
1354 1383 0.100682 GAGCTAACGATCACAGCGGA 59.899 55.000 0.00 0.00 40.29 5.54
1368 1397 7.555965 ACAAGTATGTACATTCACATGAGCTA 58.444 34.615 14.77 0.00 39.46 3.32
1461 1490 6.095300 TGGAGTAACCATGTGATGCTATTTTG 59.905 38.462 0.00 0.00 44.64 2.44
1497 1526 2.095768 ACACACGATTGCACAATGCTAC 60.096 45.455 0.00 0.00 45.31 3.58
1589 1618 7.097192 TGGACTGACATACTACATGTTCTTTC 58.903 38.462 2.30 0.00 31.52 2.62
1707 1736 1.299392 CGATCGCCGAAGCTGATCA 60.299 57.895 0.26 0.00 43.28 2.92
1877 1906 4.974645 TTCCCGCAAGATATATGACCTT 57.025 40.909 0.00 0.00 43.02 3.50
1918 1972 3.955771 TTCAAAAGTTCCGTTTCGAGG 57.044 42.857 0.00 0.00 0.00 4.63
1941 1995 1.710809 AGTGGGTCAAAACTAGGGCAT 59.289 47.619 0.00 0.00 0.00 4.40
1945 1999 3.252458 CGGAAAAGTGGGTCAAAACTAGG 59.748 47.826 0.00 0.00 0.00 3.02
1955 2009 2.200337 GCAAGCCGGAAAAGTGGGT 61.200 57.895 5.05 0.00 37.64 4.51
2007 2160 2.096220 TCGGGCAACAATAAACGCTA 57.904 45.000 0.00 0.00 39.74 4.26
2013 2166 3.821600 TGCTTTAGTTCGGGCAACAATAA 59.178 39.130 0.00 0.00 37.48 1.40
2029 2182 2.163010 CGAGTCCGAGGTAAGTGCTTTA 59.837 50.000 0.00 0.00 38.22 1.85


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

AutoCloner maintained by Alex Coulton.