Multiple sequence alignment - TraesCS4A01G359600

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 TraesCS4A01G359600 chr4A 100.000 4397 0 0 1 4397 632938746 632934350 0.000000e+00 8120.0
1 TraesCS4A01G359600 chr4A 88.289 2297 246 11 978 3255 668179034 668181326 0.000000e+00 2730.0
2 TraesCS4A01G359600 chr4A 96.000 75 3 0 376 450 632933370 632933444 5.970000e-24 122.0
3 TraesCS4A01G359600 chr1A 99.282 3482 15 1 916 4397 555687990 555691461 0.000000e+00 6283.0
4 TraesCS4A01G359600 chr1A 98.638 514 7 0 368 881 555687359 555687872 0.000000e+00 911.0
5 TraesCS4A01G359600 chr1A 94.048 84 5 0 367 450 555692503 555692420 1.280000e-25 128.0
6 TraesCS4A01G359600 chr3B 98.742 3498 27 6 916 4397 752213084 752216580 0.000000e+00 6200.0
7 TraesCS4A01G359600 chr3B 99.027 514 5 0 368 881 752212452 752212965 0.000000e+00 922.0
8 TraesCS4A01G359600 chr3B 85.397 315 17 15 1 314 661319693 661319407 2.570000e-77 300.0
9 TraesCS4A01G359600 chr3B 83.178 214 35 1 1 213 464391701 464391914 1.250000e-45 195.0
10 TraesCS4A01G359600 chr3B 94.845 97 5 0 4285 4381 816817115 816817211 7.620000e-33 152.0
11 TraesCS4A01G359600 chr3B 96.386 83 3 0 368 450 752217622 752217540 2.130000e-28 137.0
12 TraesCS4A01G359600 chr3B 96.429 56 2 0 310 365 661287222 661287167 4.680000e-15 93.5
13 TraesCS4A01G359600 chr3B 100.000 30 0 0 888 917 752212957 752212986 6.140000e-04 56.5
14 TraesCS4A01G359600 chr2B 99.551 3344 15 0 916 4259 245811435 245808092 0.000000e+00 6093.0
15 TraesCS4A01G359600 chr2B 98.835 515 6 0 367 881 245812068 245811554 0.000000e+00 918.0
16 TraesCS4A01G359600 chr2B 94.231 104 5 1 4286 4388 554296036 554296139 1.640000e-34 158.0
17 TraesCS4A01G359600 chr2B 95.181 83 4 0 368 450 245794262 245794344 9.920000e-27 132.0
18 TraesCS4A01G359600 chr2B 100.000 30 0 0 888 917 245811562 245811533 6.140000e-04 56.5
19 TraesCS4A01G359600 chr6D 96.092 1996 77 1 916 2911 140326897 140324903 0.000000e+00 3253.0
20 TraesCS4A01G359600 chr6D 89.383 810 28 22 3508 4293 140324881 140324106 0.000000e+00 966.0
21 TraesCS4A01G359600 chr6D 91.103 517 41 3 367 881 140327530 140327017 0.000000e+00 695.0
22 TraesCS4A01G359600 chr6D 76.058 827 158 29 3231 4032 200875909 200875098 1.150000e-105 394.0
23 TraesCS4A01G359600 chr6D 93.976 83 3 1 368 450 140317083 140317163 1.660000e-24 124.0
24 TraesCS4A01G359600 chr7B 87.813 2314 271 10 947 3252 711534106 711536416 0.000000e+00 2700.0
25 TraesCS4A01G359600 chr7B 87.989 2273 266 6 985 3252 685276858 685274588 0.000000e+00 2678.0
26 TraesCS4A01G359600 chr7B 77.978 999 151 41 3276 4253 28304912 28303962 2.970000e-156 562.0
27 TraesCS4A01G359600 chr7B 77.366 1025 163 42 3276 4274 28000685 27999704 1.080000e-150 544.0
28 TraesCS4A01G359600 chr7B 81.194 335 48 9 1 324 594042649 594042319 5.640000e-64 255.0
29 TraesCS4A01G359600 chr1B 88.165 2273 262 6 985 3252 366294502 366292232 0.000000e+00 2700.0
30 TraesCS4A01G359600 chr1B 87.770 2314 272 10 947 3252 365014549 365016859 0.000000e+00 2695.0
31 TraesCS4A01G359600 chr5A 87.066 2273 284 8 985 3252 221344698 221346965 0.000000e+00 2560.0
32 TraesCS4A01G359600 chr5A 94.949 99 3 2 4283 4380 413843513 413843416 2.120000e-33 154.0
33 TraesCS4A01G359600 chrUn 99.717 706 2 0 3692 4397 335557051 335557756 0.000000e+00 1293.0
34 TraesCS4A01G359600 chr7D 77.996 1018 161 38 3276 4274 80780878 80779905 8.200000e-162 580.0
35 TraesCS4A01G359600 chr7A 78.287 829 134 26 3276 4094 83532456 83531664 3.950000e-135 492.0
36 TraesCS4A01G359600 chr2D 89.071 366 35 3 1 365 644488504 644488865 2.410000e-122 449.0
37 TraesCS4A01G359600 chr2D 96.970 99 2 1 4284 4382 476839032 476839129 9.780000e-37 165.0
38 TraesCS4A01G359600 chr5B 91.566 166 11 2 200 365 391056226 391056388 4.420000e-55 226.0
39 TraesCS4A01G359600 chr3A 80.357 280 39 8 1 266 478082459 478082736 9.650000e-47 198.0
40 TraesCS4A01G359600 chr5D 94.898 98 5 0 4285 4382 21789110 21789207 2.120000e-33 154.0
41 TraesCS4A01G359600 chr3D 93.939 99 6 0 4285 4383 571378041 571377943 2.740000e-32 150.0


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 TraesCS4A01G359600 chr4A 632934350 632938746 4396 True 8120.000000 8120 100.000000 1 4397 1 chr4A.!!$R1 4396
1 TraesCS4A01G359600 chr4A 668179034 668181326 2292 False 2730.000000 2730 88.289000 978 3255 1 chr4A.!!$F2 2277
2 TraesCS4A01G359600 chr1A 555687359 555691461 4102 False 3597.000000 6283 98.960000 368 4397 2 chr1A.!!$F1 4029
3 TraesCS4A01G359600 chr3B 752212452 752216580 4128 False 2392.833333 6200 99.256333 368 4397 3 chr3B.!!$F3 4029
4 TraesCS4A01G359600 chr2B 245808092 245812068 3976 True 2355.833333 6093 99.462000 367 4259 3 chr2B.!!$R1 3892
5 TraesCS4A01G359600 chr6D 140324106 140327530 3424 True 1638.000000 3253 92.192667 367 4293 3 chr6D.!!$R2 3926
6 TraesCS4A01G359600 chr6D 200875098 200875909 811 True 394.000000 394 76.058000 3231 4032 1 chr6D.!!$R1 801
7 TraesCS4A01G359600 chr7B 711534106 711536416 2310 False 2700.000000 2700 87.813000 947 3252 1 chr7B.!!$F1 2305
8 TraesCS4A01G359600 chr7B 685274588 685276858 2270 True 2678.000000 2678 87.989000 985 3252 1 chr7B.!!$R4 2267
9 TraesCS4A01G359600 chr7B 28303962 28304912 950 True 562.000000 562 77.978000 3276 4253 1 chr7B.!!$R2 977
10 TraesCS4A01G359600 chr7B 27999704 28000685 981 True 544.000000 544 77.366000 3276 4274 1 chr7B.!!$R1 998
11 TraesCS4A01G359600 chr1B 366292232 366294502 2270 True 2700.000000 2700 88.165000 985 3252 1 chr1B.!!$R1 2267
12 TraesCS4A01G359600 chr1B 365014549 365016859 2310 False 2695.000000 2695 87.770000 947 3252 1 chr1B.!!$F1 2305
13 TraesCS4A01G359600 chr5A 221344698 221346965 2267 False 2560.000000 2560 87.066000 985 3252 1 chr5A.!!$F1 2267
14 TraesCS4A01G359600 chrUn 335557051 335557756 705 False 1293.000000 1293 99.717000 3692 4397 1 chrUn.!!$F1 705
15 TraesCS4A01G359600 chr7D 80779905 80780878 973 True 580.000000 580 77.996000 3276 4274 1 chr7D.!!$R1 998
16 TraesCS4A01G359600 chr7A 83531664 83532456 792 True 492.000000 492 78.287000 3276 4094 1 chr7A.!!$R1 818

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
215 216 0.034896 AAGGAAGCAACGACGTCCAT 59.965 50.000 10.58 0.00 40.29 3.41 F
243 244 0.035881 CTGACTCCACCACACATGCT 59.964 55.000 0.00 0.00 0.00 3.79 F
296 297 0.036952 CAACATGCCAGTCCGAGACT 60.037 55.000 0.00 1.23 44.44 3.24 F
297 298 0.247736 AACATGCCAGTCCGAGACTC 59.752 55.000 3.87 0.00 41.37 3.36 F
335 336 1.071471 CACCTCCGTTCTTGGCAGT 59.929 57.895 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1624 2.264813 GTTTACTCGTATTCCAGCGCA 58.735 47.619 11.47 0.00 0.00 6.09 R
2164 2285 6.634436 GCAACTTCAAACTCTGTAATTGTCAG 59.366 38.462 6.25 6.25 0.00 3.51 R
2300 2421 7.776933 CTACGTTGTGTAGTAGACATACCTA 57.223 40.000 0.29 0.00 44.64 3.08 R
3022 3143 5.163322 TGCCAACCTGATTCTTGTCATTTTT 60.163 36.000 0.00 0.00 0.00 1.94 R
3460 3625 6.590292 ACAAGAATTAGATACCGCATAATCCG 59.410 38.462 0.00 0.00 0.00 4.18 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
17 18 4.814294 GGCCGCCTCGATGTCGTT 62.814 66.667 0.71 0.00 40.80 3.85
18 19 2.813908 GCCGCCTCGATGTCGTTT 60.814 61.111 2.04 0.00 40.80 3.60
19 20 3.081133 CCGCCTCGATGTCGTTTG 58.919 61.111 2.04 0.00 40.80 2.93
20 21 2.452813 CCGCCTCGATGTCGTTTGG 61.453 63.158 2.04 5.20 40.80 3.28
21 22 2.452813 CGCCTCGATGTCGTTTGGG 61.453 63.158 2.04 3.02 40.80 4.12
22 23 2.106683 GCCTCGATGTCGTTTGGGG 61.107 63.158 2.04 0.88 40.80 4.96
23 24 1.449601 CCTCGATGTCGTTTGGGGG 60.450 63.158 2.04 0.00 40.80 5.40
24 25 2.046700 TCGATGTCGTTTGGGGGC 60.047 61.111 2.04 0.00 40.80 5.80
25 26 3.496131 CGATGTCGTTTGGGGGCG 61.496 66.667 0.00 0.00 34.11 6.13
26 27 3.131478 GATGTCGTTTGGGGGCGG 61.131 66.667 0.00 0.00 0.00 6.13
27 28 3.615509 GATGTCGTTTGGGGGCGGA 62.616 63.158 0.00 0.00 0.00 5.54
28 29 2.886730 GATGTCGTTTGGGGGCGGAT 62.887 60.000 0.00 0.00 0.00 4.18
29 30 3.131478 GTCGTTTGGGGGCGGATG 61.131 66.667 0.00 0.00 0.00 3.51
30 31 3.323286 TCGTTTGGGGGCGGATGA 61.323 61.111 0.00 0.00 0.00 2.92
31 32 2.360600 CGTTTGGGGGCGGATGAA 60.361 61.111 0.00 0.00 0.00 2.57
32 33 2.406616 CGTTTGGGGGCGGATGAAG 61.407 63.158 0.00 0.00 0.00 3.02
33 34 2.362375 TTTGGGGGCGGATGAAGC 60.362 61.111 0.00 0.00 0.00 3.86
121 122 4.742201 CGGCTGACCCACGACCAG 62.742 72.222 0.00 0.00 0.00 4.00
123 124 4.008933 GCTGACCCACGACCAGCT 62.009 66.667 0.00 0.00 46.96 4.24
124 125 2.262915 CTGACCCACGACCAGCTC 59.737 66.667 0.00 0.00 0.00 4.09
125 126 3.302347 CTGACCCACGACCAGCTCC 62.302 68.421 0.00 0.00 0.00 4.70
126 127 2.997897 GACCCACGACCAGCTCCT 60.998 66.667 0.00 0.00 0.00 3.69
127 128 2.526873 ACCCACGACCAGCTCCTT 60.527 61.111 0.00 0.00 0.00 3.36
128 129 2.113243 GACCCACGACCAGCTCCTTT 62.113 60.000 0.00 0.00 0.00 3.11
129 130 1.672356 CCCACGACCAGCTCCTTTG 60.672 63.158 0.00 0.00 0.00 2.77
130 131 1.672356 CCACGACCAGCTCCTTTGG 60.672 63.158 0.00 0.00 41.60 3.28
135 136 1.071471 ACCAGCTCCTTTGGTGACG 59.929 57.895 0.00 0.00 46.85 4.35
136 137 1.672356 CCAGCTCCTTTGGTGACGG 60.672 63.158 0.00 0.00 37.61 4.79
137 138 2.032681 AGCTCCTTTGGTGACGGC 59.967 61.111 0.00 0.00 0.00 5.68
138 139 3.056328 GCTCCTTTGGTGACGGCC 61.056 66.667 0.00 0.00 0.00 6.13
139 140 2.429930 CTCCTTTGGTGACGGCCA 59.570 61.111 2.24 0.00 36.62 5.36
140 141 1.966451 CTCCTTTGGTGACGGCCAC 60.966 63.158 2.24 0.00 44.95 5.01
193 194 1.733526 GCAATCGGCATGTTACCCC 59.266 57.895 0.00 0.00 43.97 4.95
194 195 1.034838 GCAATCGGCATGTTACCCCA 61.035 55.000 0.00 0.00 43.97 4.96
195 196 0.738389 CAATCGGCATGTTACCCCAC 59.262 55.000 0.00 0.00 0.00 4.61
196 197 0.329931 AATCGGCATGTTACCCCACA 59.670 50.000 0.00 0.00 0.00 4.17
197 198 0.329931 ATCGGCATGTTACCCCACAA 59.670 50.000 0.00 0.00 0.00 3.33
198 199 0.322098 TCGGCATGTTACCCCACAAG 60.322 55.000 0.00 0.00 0.00 3.16
199 200 1.312371 CGGCATGTTACCCCACAAGG 61.312 60.000 0.00 0.00 0.00 3.61
200 201 0.039035 GGCATGTTACCCCACAAGGA 59.961 55.000 0.00 0.00 38.24 3.36
201 202 1.549037 GGCATGTTACCCCACAAGGAA 60.549 52.381 0.00 0.00 38.24 3.36
202 203 1.818674 GCATGTTACCCCACAAGGAAG 59.181 52.381 0.00 0.00 38.24 3.46
203 204 1.818674 CATGTTACCCCACAAGGAAGC 59.181 52.381 0.00 0.00 38.24 3.86
204 205 0.847373 TGTTACCCCACAAGGAAGCA 59.153 50.000 0.00 0.00 38.24 3.91
205 206 1.215673 TGTTACCCCACAAGGAAGCAA 59.784 47.619 0.00 0.00 38.24 3.91
206 207 1.611977 GTTACCCCACAAGGAAGCAAC 59.388 52.381 0.00 0.00 38.24 4.17
207 208 0.250553 TACCCCACAAGGAAGCAACG 60.251 55.000 0.00 0.00 38.24 4.10
208 209 1.228124 CCCCACAAGGAAGCAACGA 60.228 57.895 0.00 0.00 38.24 3.85
209 210 1.515521 CCCCACAAGGAAGCAACGAC 61.516 60.000 0.00 0.00 38.24 4.34
210 211 1.569493 CCACAAGGAAGCAACGACG 59.431 57.895 0.00 0.00 36.89 5.12
211 212 1.157870 CCACAAGGAAGCAACGACGT 61.158 55.000 0.00 0.00 36.89 4.34
212 213 0.232303 CACAAGGAAGCAACGACGTC 59.768 55.000 5.18 5.18 0.00 4.34
213 214 0.878961 ACAAGGAAGCAACGACGTCC 60.879 55.000 10.58 0.00 38.36 4.79
214 215 0.878523 CAAGGAAGCAACGACGTCCA 60.879 55.000 10.58 0.00 40.29 4.02
215 216 0.034896 AAGGAAGCAACGACGTCCAT 59.965 50.000 10.58 0.00 40.29 3.41
216 217 0.670546 AGGAAGCAACGACGTCCATG 60.671 55.000 10.58 10.31 40.29 3.66
217 218 1.635663 GGAAGCAACGACGTCCATGG 61.636 60.000 10.58 4.97 38.03 3.66
218 219 2.240612 GAAGCAACGACGTCCATGGC 62.241 60.000 10.58 7.87 0.00 4.40
219 220 4.147322 GCAACGACGTCCATGGCG 62.147 66.667 21.83 21.83 0.00 5.69
220 221 3.487202 CAACGACGTCCATGGCGG 61.487 66.667 25.35 14.80 0.00 6.13
230 231 4.864334 CATGGCGGCCCCTGACTC 62.864 72.222 17.97 0.00 0.00 3.36
236 237 4.035102 GGCCCCTGACTCCACCAC 62.035 72.222 0.00 0.00 0.00 4.16
237 238 3.249189 GCCCCTGACTCCACCACA 61.249 66.667 0.00 0.00 0.00 4.17
238 239 2.750350 CCCCTGACTCCACCACAC 59.250 66.667 0.00 0.00 0.00 3.82
239 240 2.146724 CCCCTGACTCCACCACACA 61.147 63.158 0.00 0.00 0.00 3.72
240 241 1.492133 CCCCTGACTCCACCACACAT 61.492 60.000 0.00 0.00 0.00 3.21
241 242 0.321919 CCCTGACTCCACCACACATG 60.322 60.000 0.00 0.00 0.00 3.21
242 243 0.957395 CCTGACTCCACCACACATGC 60.957 60.000 0.00 0.00 0.00 4.06
243 244 0.035881 CTGACTCCACCACACATGCT 59.964 55.000 0.00 0.00 0.00 3.79
244 245 0.250424 TGACTCCACCACACATGCTG 60.250 55.000 0.00 0.00 0.00 4.41
245 246 1.580845 GACTCCACCACACATGCTGC 61.581 60.000 0.00 0.00 0.00 5.25
246 247 2.282391 TCCACCACACATGCTGCC 60.282 61.111 0.00 0.00 0.00 4.85
247 248 3.740397 CCACCACACATGCTGCCG 61.740 66.667 0.00 0.00 0.00 5.69
248 249 4.409218 CACCACACATGCTGCCGC 62.409 66.667 0.00 0.00 0.00 6.53
262 263 4.493747 CCGCCGACTCCGTCCTTC 62.494 72.222 0.00 0.00 0.00 3.46
263 264 4.493747 CGCCGACTCCGTCCTTCC 62.494 72.222 0.00 0.00 0.00 3.46
264 265 3.379445 GCCGACTCCGTCCTTCCA 61.379 66.667 0.00 0.00 0.00 3.53
265 266 2.572284 CCGACTCCGTCCTTCCAC 59.428 66.667 0.00 0.00 0.00 4.02
266 267 1.977544 CCGACTCCGTCCTTCCACT 60.978 63.158 0.00 0.00 0.00 4.00
267 268 1.213013 CGACTCCGTCCTTCCACTG 59.787 63.158 0.00 0.00 0.00 3.66
268 269 1.079750 GACTCCGTCCTTCCACTGC 60.080 63.158 0.00 0.00 0.00 4.40
269 270 2.266055 CTCCGTCCTTCCACTGCC 59.734 66.667 0.00 0.00 0.00 4.85
270 271 3.649277 CTCCGTCCTTCCACTGCCG 62.649 68.421 0.00 0.00 0.00 5.69
293 294 3.181367 GCAACATGCCAGTCCGAG 58.819 61.111 0.00 0.00 37.42 4.63
294 295 1.375908 GCAACATGCCAGTCCGAGA 60.376 57.895 0.00 0.00 37.42 4.04
295 296 1.639298 GCAACATGCCAGTCCGAGAC 61.639 60.000 0.00 0.00 37.42 3.36
296 297 0.036952 CAACATGCCAGTCCGAGACT 60.037 55.000 0.00 1.23 44.44 3.24
297 298 0.247736 AACATGCCAGTCCGAGACTC 59.752 55.000 3.87 0.00 41.37 3.36
298 299 1.142748 CATGCCAGTCCGAGACTCC 59.857 63.158 3.87 0.65 41.37 3.85
299 300 2.060980 ATGCCAGTCCGAGACTCCC 61.061 63.158 3.87 0.36 41.37 4.30
300 301 2.680352 GCCAGTCCGAGACTCCCA 60.680 66.667 3.87 0.00 41.37 4.37
301 302 2.060980 GCCAGTCCGAGACTCCCAT 61.061 63.158 3.87 0.00 41.37 4.00
302 303 1.819229 CCAGTCCGAGACTCCCATG 59.181 63.158 3.87 0.00 41.37 3.66
303 304 1.680522 CCAGTCCGAGACTCCCATGG 61.681 65.000 4.14 4.14 41.37 3.66
304 305 2.060980 AGTCCGAGACTCCCATGGC 61.061 63.158 6.09 0.00 38.71 4.40
305 306 3.147595 TCCGAGACTCCCATGGCG 61.148 66.667 6.09 2.90 0.00 5.69
306 307 4.899239 CCGAGACTCCCATGGCGC 62.899 72.222 6.09 0.00 0.00 6.53
307 308 3.842923 CGAGACTCCCATGGCGCT 61.843 66.667 6.09 0.00 0.00 5.92
308 309 2.107953 GAGACTCCCATGGCGCTC 59.892 66.667 6.09 5.96 0.00 5.03
309 310 3.781770 GAGACTCCCATGGCGCTCG 62.782 68.421 6.09 0.00 0.00 5.03
328 329 4.003788 CGCACCCACCTCCGTTCT 62.004 66.667 0.00 0.00 0.00 3.01
329 330 2.430367 GCACCCACCTCCGTTCTT 59.570 61.111 0.00 0.00 0.00 2.52
330 331 1.966451 GCACCCACCTCCGTTCTTG 60.966 63.158 0.00 0.00 0.00 3.02
331 332 1.302511 CACCCACCTCCGTTCTTGG 60.303 63.158 0.00 0.00 0.00 3.61
332 333 2.359975 CCCACCTCCGTTCTTGGC 60.360 66.667 0.00 0.00 0.00 4.52
333 334 2.429930 CCACCTCCGTTCTTGGCA 59.570 61.111 0.00 0.00 0.00 4.92
334 335 1.672356 CCACCTCCGTTCTTGGCAG 60.672 63.158 0.00 0.00 0.00 4.85
335 336 1.071471 CACCTCCGTTCTTGGCAGT 59.929 57.895 0.00 0.00 0.00 4.40
336 337 1.071471 ACCTCCGTTCTTGGCAGTG 59.929 57.895 0.00 0.00 0.00 3.66
337 338 1.672356 CCTCCGTTCTTGGCAGTGG 60.672 63.158 0.00 0.00 0.00 4.00
338 339 2.281484 TCCGTTCTTGGCAGTGGC 60.281 61.111 10.30 10.30 40.13 5.01
353 354 2.050442 GGCCGCGTGGTCAAAAAG 60.050 61.111 16.28 0.00 40.65 2.27
354 355 2.729491 GCCGCGTGGTCAAAAAGC 60.729 61.111 17.91 0.00 37.67 3.51
355 356 2.718731 CCGCGTGGTCAAAAAGCA 59.281 55.556 6.91 0.00 0.00 3.91
546 548 3.567478 AAACAGAAACAGAGAGGCAGT 57.433 42.857 0.00 0.00 0.00 4.40
872 875 2.299867 GGGTTCTTGTGAATGTTGGCAT 59.700 45.455 0.00 0.00 36.80 4.40
873 876 3.509575 GGGTTCTTGTGAATGTTGGCATA 59.490 43.478 0.00 0.00 34.39 3.14
874 877 4.160252 GGGTTCTTGTGAATGTTGGCATAT 59.840 41.667 0.00 0.00 34.39 1.78
875 878 5.337491 GGGTTCTTGTGAATGTTGGCATATT 60.337 40.000 0.00 0.00 34.39 1.28
876 879 6.165577 GGTTCTTGTGAATGTTGGCATATTT 58.834 36.000 0.00 0.00 34.39 1.40
877 880 6.311200 GGTTCTTGTGAATGTTGGCATATTTC 59.689 38.462 0.00 0.00 34.39 2.17
878 881 6.587206 TCTTGTGAATGTTGGCATATTTCA 57.413 33.333 0.00 0.00 34.39 2.69
879 882 7.172868 TCTTGTGAATGTTGGCATATTTCAT 57.827 32.000 8.95 0.00 34.39 2.57
880 883 7.259882 TCTTGTGAATGTTGGCATATTTCATC 58.740 34.615 8.95 5.32 34.39 2.92
881 884 5.904941 TGTGAATGTTGGCATATTTCATCC 58.095 37.500 8.95 0.97 34.39 3.51
882 885 5.421374 TGTGAATGTTGGCATATTTCATCCA 59.579 36.000 8.95 2.96 34.39 3.41
883 886 6.070938 TGTGAATGTTGGCATATTTCATCCAA 60.071 34.615 8.95 0.00 36.35 3.53
884 887 6.987992 GTGAATGTTGGCATATTTCATCCAAT 59.012 34.615 8.95 0.00 40.29 3.16
885 888 7.496591 GTGAATGTTGGCATATTTCATCCAATT 59.503 33.333 8.95 0.00 40.29 2.32
886 889 7.496263 TGAATGTTGGCATATTTCATCCAATTG 59.504 33.333 0.00 0.00 40.29 2.32
941 1045 2.128771 TCCAGCATTTAGGCCACTTC 57.871 50.000 5.01 0.00 0.00 3.01
1519 1624 2.305343 AGAAGGCTTGAGCTGAATGACT 59.695 45.455 3.46 0.00 41.70 3.41
2300 2421 1.425066 TGTGAAAGATGCCTTCTGGGT 59.575 47.619 0.00 0.00 33.93 4.51
3022 3143 8.349568 TGAGTACTCTAGCAACTCAATTTCTA 57.650 34.615 23.01 0.00 44.89 2.10
4127 4333 7.232127 CCCATGATTGATAGCTTCCAGTTTATT 59.768 37.037 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.106683 CCCCAAACGACATCGAGGC 61.107 63.158 8.54 0.00 43.02 4.70
5 6 1.449601 CCCCCAAACGACATCGAGG 60.450 63.158 8.54 0.00 43.02 4.63
6 7 2.106683 GCCCCCAAACGACATCGAG 61.107 63.158 8.54 0.00 43.02 4.04
7 8 2.046700 GCCCCCAAACGACATCGA 60.047 61.111 8.54 0.00 43.02 3.59
8 9 3.496131 CGCCCCCAAACGACATCG 61.496 66.667 0.00 0.00 46.33 3.84
9 10 2.886730 ATCCGCCCCCAAACGACATC 62.887 60.000 0.00 0.00 0.00 3.06
11 12 3.642503 ATCCGCCCCCAAACGACA 61.643 61.111 0.00 0.00 0.00 4.35
12 13 3.131478 CATCCGCCCCCAAACGAC 61.131 66.667 0.00 0.00 0.00 4.34
13 14 2.813226 CTTCATCCGCCCCCAAACGA 62.813 60.000 0.00 0.00 0.00 3.85
14 15 2.360600 TTCATCCGCCCCCAAACG 60.361 61.111 0.00 0.00 0.00 3.60
15 16 2.710902 GCTTCATCCGCCCCCAAAC 61.711 63.158 0.00 0.00 0.00 2.93
16 17 2.362375 GCTTCATCCGCCCCCAAA 60.362 61.111 0.00 0.00 0.00 3.28
17 18 4.440829 GGCTTCATCCGCCCCCAA 62.441 66.667 0.00 0.00 41.73 4.12
104 105 4.742201 CTGGTCGTGGGTCAGCCG 62.742 72.222 0.00 0.00 34.97 5.52
107 108 2.262915 GAGCTGGTCGTGGGTCAG 59.737 66.667 0.00 0.00 0.00 3.51
108 109 3.311110 GGAGCTGGTCGTGGGTCA 61.311 66.667 0.00 0.00 0.00 4.02
109 110 2.113243 AAAGGAGCTGGTCGTGGGTC 62.113 60.000 2.56 0.00 0.00 4.46
110 111 2.147387 AAAGGAGCTGGTCGTGGGT 61.147 57.895 2.56 0.00 0.00 4.51
111 112 1.672356 CAAAGGAGCTGGTCGTGGG 60.672 63.158 2.56 0.00 0.00 4.61
112 113 1.672356 CCAAAGGAGCTGGTCGTGG 60.672 63.158 2.56 5.76 0.00 4.94
113 114 1.071471 ACCAAAGGAGCTGGTCGTG 59.929 57.895 2.56 0.46 44.05 4.35
114 115 1.071471 CACCAAAGGAGCTGGTCGT 59.929 57.895 0.00 0.00 44.05 4.34
115 116 0.951040 GTCACCAAAGGAGCTGGTCG 60.951 60.000 0.00 0.00 44.05 4.79
116 117 0.951040 CGTCACCAAAGGAGCTGGTC 60.951 60.000 0.00 0.00 44.05 4.02
118 119 1.672356 CCGTCACCAAAGGAGCTGG 60.672 63.158 0.00 0.00 40.05 4.85
119 120 2.328099 GCCGTCACCAAAGGAGCTG 61.328 63.158 0.00 0.00 0.00 4.24
120 121 2.032681 GCCGTCACCAAAGGAGCT 59.967 61.111 0.00 0.00 0.00 4.09
121 122 3.056328 GGCCGTCACCAAAGGAGC 61.056 66.667 0.00 0.00 0.00 4.70
122 123 1.966451 GTGGCCGTCACCAAAGGAG 60.966 63.158 0.00 0.00 42.70 3.69
123 124 2.112297 GTGGCCGTCACCAAAGGA 59.888 61.111 0.00 0.00 42.70 3.36
175 176 1.034838 TGGGGTAACATGCCGATTGC 61.035 55.000 0.00 0.00 38.70 3.56
176 177 0.738389 GTGGGGTAACATGCCGATTG 59.262 55.000 0.00 0.00 39.74 2.67
177 178 0.329931 TGTGGGGTAACATGCCGATT 59.670 50.000 0.00 0.00 39.74 3.34
178 179 0.329931 TTGTGGGGTAACATGCCGAT 59.670 50.000 0.00 0.00 39.74 4.18
179 180 0.322098 CTTGTGGGGTAACATGCCGA 60.322 55.000 0.00 0.00 39.74 5.54
180 181 1.312371 CCTTGTGGGGTAACATGCCG 61.312 60.000 0.00 0.00 39.74 5.69
181 182 0.039035 TCCTTGTGGGGTAACATGCC 59.961 55.000 0.00 0.00 39.74 4.40
182 183 1.818674 CTTCCTTGTGGGGTAACATGC 59.181 52.381 0.00 0.00 39.74 4.06
183 184 1.818674 GCTTCCTTGTGGGGTAACATG 59.181 52.381 0.00 0.00 39.74 3.21
184 185 1.427368 TGCTTCCTTGTGGGGTAACAT 59.573 47.619 0.00 0.00 39.74 2.71
185 186 0.847373 TGCTTCCTTGTGGGGTAACA 59.153 50.000 0.00 0.00 39.74 2.41
186 187 1.611977 GTTGCTTCCTTGTGGGGTAAC 59.388 52.381 0.00 0.00 35.33 2.50
187 188 1.816183 CGTTGCTTCCTTGTGGGGTAA 60.816 52.381 0.00 0.00 35.33 2.85
188 189 0.250553 CGTTGCTTCCTTGTGGGGTA 60.251 55.000 0.00 0.00 35.33 3.69
189 190 1.528309 CGTTGCTTCCTTGTGGGGT 60.528 57.895 0.00 0.00 35.33 4.95
190 191 1.228124 TCGTTGCTTCCTTGTGGGG 60.228 57.895 0.00 0.00 35.33 4.96
191 192 1.841663 CGTCGTTGCTTCCTTGTGGG 61.842 60.000 0.00 0.00 0.00 4.61
192 193 1.157870 ACGTCGTTGCTTCCTTGTGG 61.158 55.000 0.00 0.00 0.00 4.17
193 194 0.232303 GACGTCGTTGCTTCCTTGTG 59.768 55.000 0.00 0.00 0.00 3.33
194 195 0.878961 GGACGTCGTTGCTTCCTTGT 60.879 55.000 9.92 0.00 0.00 3.16
195 196 0.878523 TGGACGTCGTTGCTTCCTTG 60.879 55.000 9.92 0.00 0.00 3.61
196 197 0.034896 ATGGACGTCGTTGCTTCCTT 59.965 50.000 9.92 0.00 0.00 3.36
197 198 0.670546 CATGGACGTCGTTGCTTCCT 60.671 55.000 9.92 0.00 0.00 3.36
198 199 1.635663 CCATGGACGTCGTTGCTTCC 61.636 60.000 5.56 0.00 0.00 3.46
199 200 1.787847 CCATGGACGTCGTTGCTTC 59.212 57.895 5.56 0.00 0.00 3.86
200 201 2.325082 GCCATGGACGTCGTTGCTT 61.325 57.895 18.40 0.00 0.00 3.91
201 202 2.742372 GCCATGGACGTCGTTGCT 60.742 61.111 18.40 0.00 0.00 3.91
202 203 4.147322 CGCCATGGACGTCGTTGC 62.147 66.667 18.40 8.55 0.00 4.17
203 204 3.487202 CCGCCATGGACGTCGTTG 61.487 66.667 18.40 9.30 42.00 4.10
213 214 4.864334 GAGTCAGGGGCCGCCATG 62.864 72.222 17.56 9.57 0.00 3.66
219 220 4.035102 GTGGTGGAGTCAGGGGCC 62.035 72.222 0.00 0.00 0.00 5.80
220 221 3.249189 TGTGGTGGAGTCAGGGGC 61.249 66.667 0.00 0.00 0.00 5.80
221 222 1.492133 ATGTGTGGTGGAGTCAGGGG 61.492 60.000 0.00 0.00 0.00 4.79
222 223 0.321919 CATGTGTGGTGGAGTCAGGG 60.322 60.000 0.00 0.00 0.00 4.45
223 224 0.957395 GCATGTGTGGTGGAGTCAGG 60.957 60.000 0.00 0.00 0.00 3.86
224 225 0.035881 AGCATGTGTGGTGGAGTCAG 59.964 55.000 0.00 0.00 34.14 3.51
225 226 2.144952 AGCATGTGTGGTGGAGTCA 58.855 52.632 0.00 0.00 34.14 3.41
252 253 2.266055 GGCAGTGGAAGGACGGAG 59.734 66.667 0.00 0.00 0.00 4.63
253 254 3.691342 CGGCAGTGGAAGGACGGA 61.691 66.667 0.00 0.00 0.00 4.69
276 277 1.375908 TCTCGGACTGGCATGTTGC 60.376 57.895 0.00 0.00 44.08 4.17
277 278 0.036952 AGTCTCGGACTGGCATGTTG 60.037 55.000 5.85 0.00 41.76 3.33
278 279 0.247736 GAGTCTCGGACTGGCATGTT 59.752 55.000 10.72 0.00 43.53 2.71
279 280 1.608717 GGAGTCTCGGACTGGCATGT 61.609 60.000 10.72 0.00 43.53 3.21
280 281 1.142748 GGAGTCTCGGACTGGCATG 59.857 63.158 10.72 0.00 43.53 4.06
281 282 2.060980 GGGAGTCTCGGACTGGCAT 61.061 63.158 10.72 0.00 43.53 4.40
282 283 2.680352 GGGAGTCTCGGACTGGCA 60.680 66.667 10.72 0.00 43.53 4.92
283 284 2.060980 ATGGGAGTCTCGGACTGGC 61.061 63.158 10.72 0.00 43.53 4.85
284 285 1.680522 CCATGGGAGTCTCGGACTGG 61.681 65.000 2.85 3.80 43.53 4.00
285 286 1.819229 CCATGGGAGTCTCGGACTG 59.181 63.158 2.85 0.00 43.53 3.51
286 287 2.060980 GCCATGGGAGTCTCGGACT 61.061 63.158 15.13 6.29 46.42 3.85
287 288 2.501610 GCCATGGGAGTCTCGGAC 59.498 66.667 15.13 0.00 0.00 4.79
288 289 3.147595 CGCCATGGGAGTCTCGGA 61.148 66.667 15.13 0.00 0.00 4.55
289 290 4.899239 GCGCCATGGGAGTCTCGG 62.899 72.222 15.13 0.00 0.00 4.63
290 291 3.781770 GAGCGCCATGGGAGTCTCG 62.782 68.421 15.13 8.40 0.00 4.04
291 292 2.107953 GAGCGCCATGGGAGTCTC 59.892 66.667 15.13 2.70 0.00 3.36
292 293 3.842923 CGAGCGCCATGGGAGTCT 61.843 66.667 15.13 0.00 0.00 3.24
311 312 3.530910 AAGAACGGAGGTGGGTGCG 62.531 63.158 0.00 0.00 37.29 5.34
312 313 1.966451 CAAGAACGGAGGTGGGTGC 60.966 63.158 0.00 0.00 0.00 5.01
313 314 1.302511 CCAAGAACGGAGGTGGGTG 60.303 63.158 0.00 0.00 0.00 4.61
314 315 3.157680 CCAAGAACGGAGGTGGGT 58.842 61.111 0.00 0.00 0.00 4.51
315 316 2.359975 GCCAAGAACGGAGGTGGG 60.360 66.667 0.00 0.00 0.00 4.61
316 317 1.672356 CTGCCAAGAACGGAGGTGG 60.672 63.158 0.00 0.00 0.00 4.61
317 318 1.071471 ACTGCCAAGAACGGAGGTG 59.929 57.895 0.00 0.00 0.00 4.00
318 319 1.071471 CACTGCCAAGAACGGAGGT 59.929 57.895 0.00 0.00 0.00 3.85
319 320 1.672356 CCACTGCCAAGAACGGAGG 60.672 63.158 0.00 0.00 0.00 4.30
320 321 2.328099 GCCACTGCCAAGAACGGAG 61.328 63.158 0.00 0.00 0.00 4.63
321 322 2.281484 GCCACTGCCAAGAACGGA 60.281 61.111 0.00 0.00 0.00 4.69
333 334 4.555709 TTTGACCACGCGGCCACT 62.556 61.111 12.47 0.00 34.57 4.00
334 335 2.999363 CTTTTTGACCACGCGGCCAC 62.999 60.000 12.47 0.00 34.57 5.01
335 336 2.829003 TTTTTGACCACGCGGCCA 60.829 55.556 12.47 0.00 34.57 5.36
336 337 2.050442 CTTTTTGACCACGCGGCC 60.050 61.111 12.47 0.00 34.57 6.13
337 338 2.729491 GCTTTTTGACCACGCGGC 60.729 61.111 12.47 0.00 34.57 6.53
338 339 1.657181 GTGCTTTTTGACCACGCGG 60.657 57.895 12.47 0.00 38.77 6.46
339 340 0.317770 ATGTGCTTTTTGACCACGCG 60.318 50.000 3.53 3.53 32.32 6.01
340 341 1.851658 AATGTGCTTTTTGACCACGC 58.148 45.000 0.00 0.00 32.32 5.34
341 342 6.305399 CACTATTAATGTGCTTTTTGACCACG 59.695 38.462 0.00 0.00 32.32 4.94
342 343 7.566858 CACTATTAATGTGCTTTTTGACCAC 57.433 36.000 0.00 0.00 0.00 4.16
546 548 2.295909 CTGGCAAATCAGGAAAAACGGA 59.704 45.455 0.00 0.00 0.00 4.69
874 877 9.699410 AGGTAGATGAAATACAATTGGATGAAA 57.301 29.630 3.26 0.00 0.00 2.69
875 878 9.699410 AAGGTAGATGAAATACAATTGGATGAA 57.301 29.630 3.26 0.00 0.00 2.57
876 879 9.699410 AAAGGTAGATGAAATACAATTGGATGA 57.301 29.630 3.26 0.00 0.00 2.92
941 1045 6.259638 TGAAGGCAAAACTAAAACTGTAACG 58.740 36.000 0.00 0.00 0.00 3.18
1519 1624 2.264813 GTTTACTCGTATTCCAGCGCA 58.735 47.619 11.47 0.00 0.00 6.09
2164 2285 6.634436 GCAACTTCAAACTCTGTAATTGTCAG 59.366 38.462 6.25 6.25 0.00 3.51
2300 2421 7.776933 CTACGTTGTGTAGTAGACATACCTA 57.223 40.000 0.29 0.00 44.64 3.08
3022 3143 5.163322 TGCCAACCTGATTCTTGTCATTTTT 60.163 36.000 0.00 0.00 0.00 1.94
3460 3625 6.590292 ACAAGAATTAGATACCGCATAATCCG 59.410 38.462 0.00 0.00 0.00 4.18
4127 4333 4.574674 AGAAAGCTCCCAATCATGTGTA 57.425 40.909 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.