Multiple sequence alignment - TraesCS1A01G303500

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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 TraesCS1A01G303500 chr1A 100.000 1470 0 0 993 2462 497182702 497181233 0.000000e+00 2715.0
1 TraesCS1A01G303500 chr1A 100.000 710 0 0 1 710 497183694 497182985 0.000000e+00 1312.0
2 TraesCS1A01G303500 chr1A 96.111 180 7 0 50 229 23394933 23395112 6.660000e-76 294.0
3 TraesCS1A01G303500 chr1B 93.145 1488 63 12 993 2462 538155879 538154413 0.000000e+00 2146.0
4 TraesCS1A01G303500 chr1B 93.673 490 22 4 221 709 538156423 538155942 0.000000e+00 725.0
5 TraesCS1A01G303500 chr1B 94.643 56 3 0 5 60 538156477 538156422 1.210000e-13 87.9
6 TraesCS1A01G303500 chr1D 92.565 1493 66 16 993 2462 400951128 400949658 0.000000e+00 2100.0
7 TraesCS1A01G303500 chr1D 94.493 454 16 4 221 674 400951597 400951153 0.000000e+00 691.0
8 TraesCS1A01G303500 chr1D 96.429 56 2 0 5 60 400951651 400951596 2.610000e-15 93.5
9 TraesCS1A01G303500 chr3B 98.256 172 3 0 51 222 788213265 788213094 3.980000e-78 302.0
10 TraesCS1A01G303500 chr3B 98.817 169 1 1 58 226 178399087 178399254 1.430000e-77 300.0
11 TraesCS1A01G303500 chr3B 98.810 168 2 0 59 226 731267038 731267205 1.430000e-77 300.0
12 TraesCS1A01G303500 chr3B 97.159 176 4 1 48 223 520149834 520150008 1.850000e-76 296.0
13 TraesCS1A01G303500 chr5B 98.802 167 2 0 59 225 276913797 276913963 5.150000e-77 298.0
14 TraesCS1A01G303500 chr4B 97.110 173 5 0 51 223 167364988 167364816 2.390000e-75 292.0
15 TraesCS1A01G303500 chr7A 96.067 178 6 1 56 232 13105263 13105440 3.100000e-74 289.0
16 TraesCS1A01G303500 chr7A 95.556 180 5 2 59 238 109364047 109364223 4.010000e-73 285.0


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 TraesCS1A01G303500 chr1A 497181233 497183694 2461 True 2013.5 2715 100.000000 1 2462 2 chr1A.!!$R1 2461
1 TraesCS1A01G303500 chr1B 538154413 538156477 2064 True 986.3 2146 93.820333 5 2462 3 chr1B.!!$R1 2457
2 TraesCS1A01G303500 chr1D 400949658 400951651 1993 True 961.5 2100 94.495667 5 2462 3 chr1D.!!$R1 2457

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
224 225 0.03918 TGGGAACGGAGAGAGTAGCA 59.961 55.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1493 0.460311 ATTAGGGCACTTCCTCGTCG 59.54 55.0 0.0 0.0 38.3 5.12 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
23 24 1.930567 TAGGCATCGCGGTTTTCTAC 58.069 50.000 6.13 0.00 0.00 2.59
24 25 0.249398 AGGCATCGCGGTTTTCTACT 59.751 50.000 6.13 0.00 0.00 2.57
62 63 6.362632 CAACGCTTAAGTTGCAAAATACTC 57.637 37.500 0.00 0.00 43.87 2.59
63 64 5.043189 ACGCTTAAGTTGCAAAATACTCC 57.957 39.130 0.00 0.00 0.00 3.85
64 65 4.082949 ACGCTTAAGTTGCAAAATACTCCC 60.083 41.667 0.00 0.00 0.00 4.30
65 66 4.156008 CGCTTAAGTTGCAAAATACTCCCT 59.844 41.667 0.00 0.00 0.00 4.20
66 67 5.641709 GCTTAAGTTGCAAAATACTCCCTC 58.358 41.667 0.00 0.00 0.00 4.30
67 68 5.393135 GCTTAAGTTGCAAAATACTCCCTCC 60.393 44.000 0.00 0.00 0.00 4.30
68 69 2.711542 AGTTGCAAAATACTCCCTCCG 58.288 47.619 0.00 0.00 0.00 4.63
69 70 2.039879 AGTTGCAAAATACTCCCTCCGT 59.960 45.455 0.00 0.00 0.00 4.69
70 71 2.817844 GTTGCAAAATACTCCCTCCGTT 59.182 45.455 0.00 0.00 0.00 4.44
71 72 2.706890 TGCAAAATACTCCCTCCGTTC 58.293 47.619 0.00 0.00 0.00 3.95
72 73 2.014857 GCAAAATACTCCCTCCGTTCC 58.985 52.381 0.00 0.00 0.00 3.62
73 74 2.355818 GCAAAATACTCCCTCCGTTCCT 60.356 50.000 0.00 0.00 0.00 3.36
74 75 3.118519 GCAAAATACTCCCTCCGTTCCTA 60.119 47.826 0.00 0.00 0.00 2.94
75 76 4.624604 GCAAAATACTCCCTCCGTTCCTAA 60.625 45.833 0.00 0.00 0.00 2.69
76 77 5.493809 CAAAATACTCCCTCCGTTCCTAAA 58.506 41.667 0.00 0.00 0.00 1.85
77 78 5.970501 AAATACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
78 79 7.277396 CAAAATACTCCCTCCGTTCCTAAATA 58.723 38.462 0.00 0.00 0.00 1.40
79 80 6.416631 AATACTCCCTCCGTTCCTAAATAC 57.583 41.667 0.00 0.00 0.00 1.89
80 81 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
81 82 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
82 83 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
83 84 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
84 85 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
85 86 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
86 87 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
87 88 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
88 89 6.653740 CCTCCGTTCCTAAATACTTGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
89 90 7.174426 CCTCCGTTCCTAAATACTTGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
90 91 9.211485 CTCCGTTCCTAAATACTTGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
91 92 9.211485 TCCGTTCCTAAATACTTGTCTTTTTAG 57.789 33.333 0.00 0.00 33.47 1.85
92 93 9.211485 CCGTTCCTAAATACTTGTCTTTTTAGA 57.789 33.333 0.00 0.00 34.90 2.10
106 107 9.787532 TTGTCTTTTTAGAGATTTCAACAAGTG 57.212 29.630 0.00 0.00 0.00 3.16
107 108 9.173021 TGTCTTTTTAGAGATTTCAACAAGTGA 57.827 29.630 0.00 0.00 0.00 3.41
108 109 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
109 110 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
112 113 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
113 114 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
115 116 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
116 117 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
117 118 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
118 119 3.581755 TCAACAAGTGACTACATACGGC 58.418 45.455 0.00 0.00 0.00 5.68
119 120 2.273370 ACAAGTGACTACATACGGCG 57.727 50.000 4.80 4.80 0.00 6.46
120 121 0.921347 CAAGTGACTACATACGGCGC 59.079 55.000 6.90 0.00 0.00 6.53
121 122 0.528924 AAGTGACTACATACGGCGCA 59.471 50.000 10.83 0.00 0.00 6.09
122 123 0.528924 AGTGACTACATACGGCGCAA 59.471 50.000 10.83 0.00 0.00 4.85
123 124 1.067425 AGTGACTACATACGGCGCAAA 60.067 47.619 10.83 0.00 0.00 3.68
124 125 1.727880 GTGACTACATACGGCGCAAAA 59.272 47.619 10.83 0.00 0.00 2.44
125 126 2.350498 GTGACTACATACGGCGCAAAAT 59.650 45.455 10.83 0.00 0.00 1.82
126 127 2.350192 TGACTACATACGGCGCAAAATG 59.650 45.455 10.83 11.57 0.00 2.32
127 128 2.605818 GACTACATACGGCGCAAAATGA 59.394 45.455 10.83 0.00 0.00 2.57
128 129 2.607635 ACTACATACGGCGCAAAATGAG 59.392 45.455 10.83 10.39 0.00 2.90
129 130 1.448985 ACATACGGCGCAAAATGAGT 58.551 45.000 10.83 0.00 0.00 3.41
130 131 1.130373 ACATACGGCGCAAAATGAGTG 59.870 47.619 10.83 0.00 0.00 3.51
131 132 1.396648 CATACGGCGCAAAATGAGTGA 59.603 47.619 10.83 0.00 0.00 3.41
132 133 1.514003 TACGGCGCAAAATGAGTGAA 58.486 45.000 10.83 0.00 0.00 3.18
133 134 0.881118 ACGGCGCAAAATGAGTGAAT 59.119 45.000 10.83 0.00 0.00 2.57
134 135 1.135689 ACGGCGCAAAATGAGTGAATC 60.136 47.619 10.83 0.00 0.00 2.52
135 136 1.131126 CGGCGCAAAATGAGTGAATCT 59.869 47.619 10.83 0.00 0.00 2.40
136 137 2.351418 CGGCGCAAAATGAGTGAATCTA 59.649 45.455 10.83 0.00 0.00 1.98
137 138 3.685058 GGCGCAAAATGAGTGAATCTAC 58.315 45.455 10.83 0.00 0.00 2.59
138 139 3.126858 GGCGCAAAATGAGTGAATCTACA 59.873 43.478 10.83 0.00 0.00 2.74
139 140 4.091424 GCGCAAAATGAGTGAATCTACAC 58.909 43.478 0.30 0.00 40.60 2.90
177 178 4.944048 CATACATCCGTATGTTGAGTCCA 58.056 43.478 0.00 0.00 46.70 4.02
178 179 5.541845 CATACATCCGTATGTTGAGTCCAT 58.458 41.667 0.00 0.00 46.70 3.41
179 180 4.487714 ACATCCGTATGTTGAGTCCATT 57.512 40.909 0.00 0.00 44.07 3.16
180 181 4.843728 ACATCCGTATGTTGAGTCCATTT 58.156 39.130 0.00 0.00 44.07 2.32
181 182 4.635765 ACATCCGTATGTTGAGTCCATTTG 59.364 41.667 0.00 0.00 44.07 2.32
182 183 4.545208 TCCGTATGTTGAGTCCATTTGA 57.455 40.909 0.00 0.00 0.00 2.69
183 184 4.900684 TCCGTATGTTGAGTCCATTTGAA 58.099 39.130 0.00 0.00 0.00 2.69
184 185 5.309638 TCCGTATGTTGAGTCCATTTGAAA 58.690 37.500 0.00 0.00 0.00 2.69
185 186 5.943416 TCCGTATGTTGAGTCCATTTGAAAT 59.057 36.000 0.00 0.00 0.00 2.17
186 187 6.029607 CCGTATGTTGAGTCCATTTGAAATG 58.970 40.000 10.84 10.84 0.00 2.32
187 188 5.512788 CGTATGTTGAGTCCATTTGAAATGC 59.487 40.000 12.26 0.23 0.00 3.56
188 189 4.255833 TGTTGAGTCCATTTGAAATGCC 57.744 40.909 12.26 5.23 0.00 4.40
189 190 3.896888 TGTTGAGTCCATTTGAAATGCCT 59.103 39.130 12.26 9.70 0.00 4.75
190 191 5.076182 TGTTGAGTCCATTTGAAATGCCTA 58.924 37.500 12.26 0.00 0.00 3.93
191 192 5.183713 TGTTGAGTCCATTTGAAATGCCTAG 59.816 40.000 12.26 0.00 0.00 3.02
192 193 5.178096 TGAGTCCATTTGAAATGCCTAGA 57.822 39.130 12.26 1.83 0.00 2.43
193 194 5.569355 TGAGTCCATTTGAAATGCCTAGAA 58.431 37.500 12.26 0.00 0.00 2.10
194 195 6.009589 TGAGTCCATTTGAAATGCCTAGAAA 58.990 36.000 12.26 0.00 0.00 2.52
195 196 6.151648 TGAGTCCATTTGAAATGCCTAGAAAG 59.848 38.462 12.26 0.00 0.00 2.62
196 197 6.248433 AGTCCATTTGAAATGCCTAGAAAGA 58.752 36.000 12.26 0.00 0.00 2.52
197 198 6.151817 AGTCCATTTGAAATGCCTAGAAAGAC 59.848 38.462 12.26 10.86 0.00 3.01
198 199 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
199 200 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
200 201 6.810182 CCATTTGAAATGCCTAGAAAGACAAG 59.190 38.462 12.26 0.00 0.00 3.16
201 202 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
202 203 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
203 204 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
204 205 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
205 206 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
206 207 8.514594 TGAAATGCCTAGAAAGACAAGTATTTG 58.485 33.333 0.00 0.00 40.24 2.32
207 208 7.396540 AATGCCTAGAAAGACAAGTATTTGG 57.603 36.000 2.81 0.00 38.66 3.28
208 209 5.253330 TGCCTAGAAAGACAAGTATTTGGG 58.747 41.667 2.81 0.00 38.66 4.12
209 210 5.013704 TGCCTAGAAAGACAAGTATTTGGGA 59.986 40.000 2.81 0.00 38.66 4.37
210 211 5.944007 GCCTAGAAAGACAAGTATTTGGGAA 59.056 40.000 2.81 0.00 38.66 3.97
211 212 6.127980 GCCTAGAAAGACAAGTATTTGGGAAC 60.128 42.308 2.81 0.00 38.66 3.62
212 213 5.941948 AGAAAGACAAGTATTTGGGAACG 57.058 39.130 2.81 0.00 38.66 3.95
213 214 4.760204 AGAAAGACAAGTATTTGGGAACGG 59.240 41.667 2.81 0.00 38.66 4.44
214 215 4.360951 AAGACAAGTATTTGGGAACGGA 57.639 40.909 2.81 0.00 38.66 4.69
215 216 3.939066 AGACAAGTATTTGGGAACGGAG 58.061 45.455 2.81 0.00 38.66 4.63
216 217 3.581332 AGACAAGTATTTGGGAACGGAGA 59.419 43.478 2.81 0.00 38.66 3.71
217 218 3.933332 GACAAGTATTTGGGAACGGAGAG 59.067 47.826 2.81 0.00 38.66 3.20
218 219 3.581332 ACAAGTATTTGGGAACGGAGAGA 59.419 43.478 2.81 0.00 38.66 3.10
219 220 4.184629 CAAGTATTTGGGAACGGAGAGAG 58.815 47.826 0.00 0.00 0.00 3.20
224 225 0.039180 TGGGAACGGAGAGAGTAGCA 59.961 55.000 0.00 0.00 0.00 3.49
255 256 7.768582 CCATGACCAAACACTATCTATGTTGTA 59.231 37.037 0.00 0.00 40.16 2.41
368 369 5.221342 TGGGAAACAACAAATCTTTATGCGT 60.221 36.000 0.00 0.00 0.00 5.24
373 374 9.123709 GAAACAACAAATCTTTATGCGTATTCA 57.876 29.630 0.00 0.00 0.00 2.57
377 378 9.288124 CAACAAATCTTTATGCGTATTCATTGA 57.712 29.630 0.00 0.00 0.00 2.57
442 443 7.070571 TGGGATGGACTACAAATTTGAAAAACT 59.929 33.333 24.64 3.62 0.00 2.66
456 457 9.481340 AATTTGAAAAACTAAATCTTGCTCCTC 57.519 29.630 0.00 0.00 0.00 3.71
497 498 2.022934 GGTCGAGTTAGGAATCCTCGT 58.977 52.381 4.42 0.00 46.10 4.18
612 613 7.613585 TCACCCTACGATACTTCAAACAATAA 58.386 34.615 0.00 0.00 0.00 1.40
613 614 7.546667 TCACCCTACGATACTTCAAACAATAAC 59.453 37.037 0.00 0.00 0.00 1.89
614 615 7.332430 CACCCTACGATACTTCAAACAATAACA 59.668 37.037 0.00 0.00 0.00 2.41
615 616 7.879160 ACCCTACGATACTTCAAACAATAACAA 59.121 33.333 0.00 0.00 0.00 2.83
616 617 8.889717 CCCTACGATACTTCAAACAATAACAAT 58.110 33.333 0.00 0.00 0.00 2.71
617 618 9.702726 CCTACGATACTTCAAACAATAACAATG 57.297 33.333 0.00 0.00 0.00 2.82
692 694 7.834803 TCATCACACATATCTAGATAGCTTGG 58.165 38.462 17.22 7.63 0.00 3.61
709 711 1.070786 GGACACTCCAAGCGGAACA 59.929 57.895 0.00 0.00 42.21 3.18
1041 1043 5.523552 CCACCTTGTTTTCATTTTCCTTGTC 59.476 40.000 0.00 0.00 0.00 3.18
1078 1080 2.710096 ACCTGCATTTGGTATACGCT 57.290 45.000 0.00 0.00 35.80 5.07
1079 1081 2.288666 ACCTGCATTTGGTATACGCTG 58.711 47.619 0.00 0.00 35.80 5.18
1242 1245 0.111253 CTGGCTCCCAGTCCAAGTTT 59.889 55.000 3.09 0.00 45.82 2.66
1244 1247 0.178990 GGCTCCCAGTCCAAGTTTGT 60.179 55.000 0.00 0.00 0.00 2.83
1291 1294 7.863901 AAGTAAGCATATGGGAGTAGATTCT 57.136 36.000 4.56 0.00 0.00 2.40
1322 1325 6.182507 TCTTGGATGTTGTTAAGTACCACT 57.817 37.500 0.00 0.00 0.00 4.00
1343 1346 5.995282 CACTGATGTTCTGGGTTAACACTTA 59.005 40.000 9.72 0.00 39.51 2.24
1393 1396 4.590850 TCATTGATCTCGGTGGACTATG 57.409 45.455 0.00 0.00 0.00 2.23
1506 1509 2.600769 ACGACGAGGAAGTGCCCT 60.601 61.111 0.00 0.00 39.77 5.19
1600 1603 7.998383 AGCGGGCCATTTTATATGATATATCAA 59.002 33.333 19.03 9.29 40.69 2.57
1646 1649 6.715280 AGTGAATGTGTGTCTTTATGGATCT 58.285 36.000 0.00 0.00 0.00 2.75
1751 1761 0.031994 AAAGTGTCGCCAACCATTGC 59.968 50.000 0.00 0.00 0.00 3.56
1853 1863 5.872963 TCCTCAAATCCATCATCCATGTAG 58.127 41.667 0.00 0.00 0.00 2.74
1854 1864 5.008331 CCTCAAATCCATCATCCATGTAGG 58.992 45.833 0.00 0.00 39.47 3.18
1855 1865 4.989277 TCAAATCCATCATCCATGTAGGG 58.011 43.478 0.00 0.00 38.24 3.53
1856 1866 4.084287 CAAATCCATCATCCATGTAGGGG 58.916 47.826 0.00 0.00 38.24 4.79
1857 1867 1.746157 TCCATCATCCATGTAGGGGG 58.254 55.000 0.00 0.00 38.24 5.40
1882 1893 2.823747 GGGGGTTGACCATCTTTACAAC 59.176 50.000 2.12 0.00 42.91 3.32
1941 1952 5.181811 TGTTCCTTCATCACATCATCAACAC 59.818 40.000 0.00 0.00 0.00 3.32
1991 2005 2.337583 TCTCTCGCTTCCAACATTTCG 58.662 47.619 0.00 0.00 0.00 3.46
1992 2006 2.029380 TCTCTCGCTTCCAACATTTCGA 60.029 45.455 0.00 0.00 0.00 3.71
1993 2007 2.066262 TCTCGCTTCCAACATTTCGAC 58.934 47.619 0.00 0.00 0.00 4.20
2013 2027 1.138661 CATCCCTTCCTCTCTCTGCAC 59.861 57.143 0.00 0.00 0.00 4.57
2047 2061 1.739562 GCTCCGAAGCCACTGTCTG 60.740 63.158 0.00 0.00 43.10 3.51
2076 2090 1.955778 CCACTCCATGTTTCAGTGCAA 59.044 47.619 0.00 0.00 36.91 4.08
2097 2111 2.293399 ACTCGTTCACCTTCATTTTGCC 59.707 45.455 0.00 0.00 0.00 4.52
2099 2113 3.745799 TCGTTCACCTTCATTTTGCCTA 58.254 40.909 0.00 0.00 0.00 3.93
2103 2117 1.472480 CACCTTCATTTTGCCTACCCG 59.528 52.381 0.00 0.00 0.00 5.28
2143 2157 4.243007 AGCATAACAAACAAACTCAGCC 57.757 40.909 0.00 0.00 0.00 4.85
2229 2243 2.092914 AGCACCTAAACCTACCATCAGC 60.093 50.000 0.00 0.00 0.00 4.26
2322 2336 3.944055 AGGACCGATGCATCTACATAC 57.056 47.619 23.73 7.66 0.00 2.39
2327 2341 3.059884 CCGATGCATCTACATACCACAC 58.940 50.000 23.73 0.00 0.00 3.82
2328 2342 2.726241 CGATGCATCTACATACCACACG 59.274 50.000 23.73 3.24 0.00 4.49
2329 2343 3.717707 GATGCATCTACATACCACACGT 58.282 45.455 19.70 0.00 0.00 4.49
2376 2404 5.186992 TGACGAATATTCTCAAACTCTGGGA 59.813 40.000 13.45 0.00 30.28 4.37
2394 2423 6.081356 TCTGGGAAAAATGATACAAAGGGTT 58.919 36.000 0.00 0.00 0.00 4.11
2433 2462 4.097551 TGATCATGTTGTCTTTGGTGGA 57.902 40.909 0.00 0.00 0.00 4.02
2456 2485 4.996788 ATGACATTCCAAAGCCAGATTC 57.003 40.909 0.00 0.00 0.00 2.52
2457 2486 4.038271 TGACATTCCAAAGCCAGATTCT 57.962 40.909 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.527311 GAAAACCGCGATGCCTATCTC 59.473 52.381 8.23 0.00 0.00 2.75
1 2 1.139058 AGAAAACCGCGATGCCTATCT 59.861 47.619 8.23 0.00 0.00 1.98
2 3 1.583054 AGAAAACCGCGATGCCTATC 58.417 50.000 8.23 0.00 0.00 2.08
3 4 2.102588 AGTAGAAAACCGCGATGCCTAT 59.897 45.455 8.23 0.00 0.00 2.57
23 24 4.945246 AGCGTTGTATACTACCCAATCAG 58.055 43.478 11.15 0.00 0.00 2.90
24 25 5.347620 AAGCGTTGTATACTACCCAATCA 57.652 39.130 11.15 0.00 0.00 2.57
58 59 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
59 60 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
60 61 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
61 62 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
62 63 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
63 64 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
64 65 7.668525 AAAAGACAAGTATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
65 66 9.211485 CTAAAAAGACAAGTATTTAGGAACGGA 57.789 33.333 0.00 0.00 33.69 4.69
66 67 9.211485 TCTAAAAAGACAAGTATTTAGGAACGG 57.789 33.333 0.00 0.00 36.48 4.44
80 81 9.787532 CACTTGTTGAAATCTCTAAAAAGACAA 57.212 29.630 0.00 0.00 0.00 3.18
81 82 9.173021 TCACTTGTTGAAATCTCTAAAAAGACA 57.827 29.630 0.00 0.00 0.00 3.41
82 83 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
83 84 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
86 87 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
87 88 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
89 90 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
90 91 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
91 92 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
92 93 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
93 94 6.672357 GCCGTATGTAGTCACTTGTTGAAATC 60.672 42.308 0.00 0.00 35.39 2.17
94 95 5.121768 GCCGTATGTAGTCACTTGTTGAAAT 59.878 40.000 0.00 0.00 35.39 2.17
95 96 4.449743 GCCGTATGTAGTCACTTGTTGAAA 59.550 41.667 0.00 0.00 35.39 2.69
96 97 3.991773 GCCGTATGTAGTCACTTGTTGAA 59.008 43.478 0.00 0.00 35.39 2.69
97 98 3.581755 GCCGTATGTAGTCACTTGTTGA 58.418 45.455 0.00 0.00 0.00 3.18
98 99 2.344441 CGCCGTATGTAGTCACTTGTTG 59.656 50.000 0.00 0.00 0.00 3.33
99 100 2.602878 CGCCGTATGTAGTCACTTGTT 58.397 47.619 0.00 0.00 0.00 2.83
100 101 1.734707 GCGCCGTATGTAGTCACTTGT 60.735 52.381 0.00 0.00 0.00 3.16
101 102 0.921347 GCGCCGTATGTAGTCACTTG 59.079 55.000 0.00 0.00 0.00 3.16
102 103 0.528924 TGCGCCGTATGTAGTCACTT 59.471 50.000 4.18 0.00 0.00 3.16
103 104 0.528924 TTGCGCCGTATGTAGTCACT 59.471 50.000 4.18 0.00 0.00 3.41
104 105 1.352114 TTTGCGCCGTATGTAGTCAC 58.648 50.000 4.18 0.00 0.00 3.67
105 106 2.081725 TTTTGCGCCGTATGTAGTCA 57.918 45.000 4.18 0.00 0.00 3.41
106 107 2.605818 TCATTTTGCGCCGTATGTAGTC 59.394 45.455 4.18 0.00 0.00 2.59
107 108 2.607635 CTCATTTTGCGCCGTATGTAGT 59.392 45.455 4.18 0.00 0.00 2.73
108 109 2.607635 ACTCATTTTGCGCCGTATGTAG 59.392 45.455 4.18 7.56 0.00 2.74
109 110 2.350192 CACTCATTTTGCGCCGTATGTA 59.650 45.455 4.18 0.00 0.00 2.29
110 111 1.130373 CACTCATTTTGCGCCGTATGT 59.870 47.619 4.18 0.00 0.00 2.29
111 112 1.396648 TCACTCATTTTGCGCCGTATG 59.603 47.619 4.18 5.63 0.00 2.39
112 113 1.732941 TCACTCATTTTGCGCCGTAT 58.267 45.000 4.18 0.00 0.00 3.06
113 114 1.514003 TTCACTCATTTTGCGCCGTA 58.486 45.000 4.18 0.00 0.00 4.02
114 115 0.881118 ATTCACTCATTTTGCGCCGT 59.119 45.000 4.18 0.00 0.00 5.68
115 116 1.131126 AGATTCACTCATTTTGCGCCG 59.869 47.619 4.18 0.00 0.00 6.46
116 117 2.927553 AGATTCACTCATTTTGCGCC 57.072 45.000 4.18 0.00 0.00 6.53
117 118 4.091424 GTGTAGATTCACTCATTTTGCGC 58.909 43.478 0.00 0.00 35.68 6.09
118 119 5.536554 AGTGTAGATTCACTCATTTTGCG 57.463 39.130 0.00 0.00 44.07 4.85
119 120 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
156 157 5.808366 ATGGACTCAACATACGGATGTAT 57.192 39.130 15.10 0.00 45.93 2.29
157 158 5.607939 AATGGACTCAACATACGGATGTA 57.392 39.130 15.10 0.00 45.93 2.29
159 160 4.875536 TCAAATGGACTCAACATACGGATG 59.124 41.667 5.94 5.94 39.16 3.51
160 161 5.097742 TCAAATGGACTCAACATACGGAT 57.902 39.130 0.00 0.00 0.00 4.18
161 162 4.545208 TCAAATGGACTCAACATACGGA 57.455 40.909 0.00 0.00 0.00 4.69
162 163 5.621197 TTTCAAATGGACTCAACATACGG 57.379 39.130 0.00 0.00 0.00 4.02
163 164 5.512788 GCATTTCAAATGGACTCAACATACG 59.487 40.000 12.14 0.00 0.00 3.06
164 165 5.807011 GGCATTTCAAATGGACTCAACATAC 59.193 40.000 12.14 0.00 0.00 2.39
165 166 5.716228 AGGCATTTCAAATGGACTCAACATA 59.284 36.000 12.14 0.00 0.00 2.29
166 167 4.529377 AGGCATTTCAAATGGACTCAACAT 59.471 37.500 12.14 0.00 0.00 2.71
167 168 3.896888 AGGCATTTCAAATGGACTCAACA 59.103 39.130 12.14 0.00 0.00 3.33
168 169 4.525912 AGGCATTTCAAATGGACTCAAC 57.474 40.909 12.14 0.00 0.00 3.18
169 170 5.569355 TCTAGGCATTTCAAATGGACTCAA 58.431 37.500 12.14 0.00 0.00 3.02
170 171 5.178096 TCTAGGCATTTCAAATGGACTCA 57.822 39.130 12.14 0.00 0.00 3.41
171 172 6.375455 TCTTTCTAGGCATTTCAAATGGACTC 59.625 38.462 12.14 0.00 0.00 3.36
172 173 6.151817 GTCTTTCTAGGCATTTCAAATGGACT 59.848 38.462 12.14 3.08 0.00 3.85
173 174 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
174 175 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
175 176 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
176 177 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
177 178 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
178 179 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
179 180 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
180 181 8.514594 CAAATACTTGTCTTTCTAGGCATTTCA 58.485 33.333 0.00 0.00 35.56 2.69
181 182 7.970614 CCAAATACTTGTCTTTCTAGGCATTTC 59.029 37.037 0.00 0.00 35.56 2.17
182 183 7.093771 CCCAAATACTTGTCTTTCTAGGCATTT 60.094 37.037 0.00 0.00 35.56 2.32
183 184 6.378280 CCCAAATACTTGTCTTTCTAGGCATT 59.622 38.462 0.00 0.00 35.56 3.56
184 185 5.888161 CCCAAATACTTGTCTTTCTAGGCAT 59.112 40.000 0.00 0.00 35.56 4.40
185 186 5.013704 TCCCAAATACTTGTCTTTCTAGGCA 59.986 40.000 0.00 0.00 33.22 4.75
186 187 5.497474 TCCCAAATACTTGTCTTTCTAGGC 58.503 41.667 0.00 0.00 0.00 3.93
187 188 6.092259 CGTTCCCAAATACTTGTCTTTCTAGG 59.908 42.308 0.00 0.00 0.00 3.02
188 189 6.092259 CCGTTCCCAAATACTTGTCTTTCTAG 59.908 42.308 0.00 0.00 0.00 2.43
189 190 5.935789 CCGTTCCCAAATACTTGTCTTTCTA 59.064 40.000 0.00 0.00 0.00 2.10
190 191 4.760204 CCGTTCCCAAATACTTGTCTTTCT 59.240 41.667 0.00 0.00 0.00 2.52
191 192 4.758165 TCCGTTCCCAAATACTTGTCTTTC 59.242 41.667 0.00 0.00 0.00 2.62
192 193 4.721132 TCCGTTCCCAAATACTTGTCTTT 58.279 39.130 0.00 0.00 0.00 2.52
193 194 4.041198 TCTCCGTTCCCAAATACTTGTCTT 59.959 41.667 0.00 0.00 0.00 3.01
194 195 3.581332 TCTCCGTTCCCAAATACTTGTCT 59.419 43.478 0.00 0.00 0.00 3.41
195 196 3.933332 CTCTCCGTTCCCAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
196 197 3.581332 TCTCTCCGTTCCCAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
197 198 4.184629 CTCTCTCCGTTCCCAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
198 199 3.838903 ACTCTCTCCGTTCCCAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
199 200 3.442076 ACTCTCTCCGTTCCCAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
200 201 3.889520 ACTCTCTCCGTTCCCAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
201 202 3.383825 GCTACTCTCTCCGTTCCCAAATA 59.616 47.826 0.00 0.00 0.00 1.40
202 203 2.168728 GCTACTCTCTCCGTTCCCAAAT 59.831 50.000 0.00 0.00 0.00 2.32
203 204 1.549170 GCTACTCTCTCCGTTCCCAAA 59.451 52.381 0.00 0.00 0.00 3.28
204 205 1.183549 GCTACTCTCTCCGTTCCCAA 58.816 55.000 0.00 0.00 0.00 4.12
205 206 0.039180 TGCTACTCTCTCCGTTCCCA 59.961 55.000 0.00 0.00 0.00 4.37
206 207 1.338655 GATGCTACTCTCTCCGTTCCC 59.661 57.143 0.00 0.00 0.00 3.97
207 208 2.303175 AGATGCTACTCTCTCCGTTCC 58.697 52.381 0.00 0.00 0.00 3.62
208 209 3.243267 GGAAGATGCTACTCTCTCCGTTC 60.243 52.174 0.00 0.00 0.00 3.95
209 210 2.691011 GGAAGATGCTACTCTCTCCGTT 59.309 50.000 0.00 0.00 0.00 4.44
210 211 2.303175 GGAAGATGCTACTCTCTCCGT 58.697 52.381 0.00 0.00 0.00 4.69
211 212 2.302260 TGGAAGATGCTACTCTCTCCG 58.698 52.381 0.00 0.00 30.98 4.63
212 213 3.894427 TCATGGAAGATGCTACTCTCTCC 59.106 47.826 0.00 0.00 0.00 3.71
213 214 4.261994 GGTCATGGAAGATGCTACTCTCTC 60.262 50.000 0.00 0.00 0.00 3.20
214 215 3.640967 GGTCATGGAAGATGCTACTCTCT 59.359 47.826 0.00 0.00 0.00 3.10
215 216 3.386078 TGGTCATGGAAGATGCTACTCTC 59.614 47.826 0.00 0.00 0.00 3.20
216 217 3.378512 TGGTCATGGAAGATGCTACTCT 58.621 45.455 0.00 0.00 0.00 3.24
217 218 3.827008 TGGTCATGGAAGATGCTACTC 57.173 47.619 0.00 0.00 0.00 2.59
218 219 4.263462 TGTTTGGTCATGGAAGATGCTACT 60.263 41.667 0.00 0.00 0.00 2.57
219 220 4.009675 TGTTTGGTCATGGAAGATGCTAC 58.990 43.478 0.00 0.00 0.00 3.58
224 225 6.319048 AGATAGTGTTTGGTCATGGAAGAT 57.681 37.500 0.00 0.00 0.00 2.40
304 305 4.068599 TGTGCATGGTTCGTTCTAATGAA 58.931 39.130 0.00 0.00 0.00 2.57
364 365 6.037062 ACGATTTGAAGATCAATGAATACGCA 59.963 34.615 0.00 0.00 36.11 5.24
368 369 8.504812 TGGAACGATTTGAAGATCAATGAATA 57.495 30.769 0.00 0.00 36.11 1.75
373 374 6.573664 TGTTGGAACGATTTGAAGATCAAT 57.426 33.333 0.00 0.00 36.11 2.57
377 378 8.400947 CAAGATATGTTGGAACGATTTGAAGAT 58.599 33.333 4.68 0.00 0.00 2.40
442 443 3.674997 AGCAAACGAGGAGCAAGATTTA 58.325 40.909 0.00 0.00 0.00 1.40
456 457 5.525199 ACCCACTGTATTTAAAAGCAAACG 58.475 37.500 0.00 0.00 0.00 3.60
580 581 6.942976 TGAAGTATCGTAGGGTGAAATCTTT 58.057 36.000 0.00 0.00 0.00 2.52
612 613 1.885157 CGGAAGGCATGCACATTGT 59.115 52.632 21.36 0.00 0.00 2.71
613 614 1.517694 GCGGAAGGCATGCACATTG 60.518 57.895 21.36 7.07 42.87 2.82
614 615 2.887360 GCGGAAGGCATGCACATT 59.113 55.556 21.36 10.91 42.87 2.71
615 616 3.511595 CGCGGAAGGCATGCACAT 61.512 61.111 21.36 4.19 43.84 3.21
617 618 4.465512 CACGCGGAAGGCATGCAC 62.466 66.667 21.36 9.10 43.84 4.57
657 659 7.506328 AGATATGTGTGATGATGAACAATGG 57.494 36.000 0.00 0.00 0.00 3.16
664 666 8.820153 AGCTATCTAGATATGTGTGATGATGA 57.180 34.615 12.86 0.00 0.00 2.92
692 694 4.771127 TGTTCCGCTTGGAGTGTC 57.229 55.556 0.00 0.00 44.35 3.67
992 994 6.634035 GCAAAATTGGCTCTTCATTTTTGTTC 59.366 34.615 17.95 6.73 43.04 3.18
993 995 6.497437 GCAAAATTGGCTCTTCATTTTTGTT 58.503 32.000 17.95 0.00 43.04 2.83
994 996 6.063640 GCAAAATTGGCTCTTCATTTTTGT 57.936 33.333 17.95 0.00 43.04 2.83
1010 1012 6.772360 AAATGAAAACAAGGTGGCAAAATT 57.228 29.167 0.00 0.00 0.00 1.82
1041 1043 4.498345 GCAGGTAAGGAACATAGAGAGACG 60.498 50.000 0.00 0.00 0.00 4.18
1078 1080 1.167851 CCTGATTGAAAGCTTCCGCA 58.832 50.000 0.00 0.00 39.10 5.69
1079 1081 1.168714 ACCTGATTGAAAGCTTCCGC 58.831 50.000 0.00 0.00 0.00 5.54
1204 1207 0.618458 GGTCCCTATGGTTCACTGCA 59.382 55.000 0.00 0.00 0.00 4.41
1242 1245 1.554836 CAGAGAAGGGAGCTCAGACA 58.445 55.000 17.19 0.00 34.85 3.41
1244 1247 0.975040 GCCAGAGAAGGGAGCTCAGA 60.975 60.000 17.19 0.00 34.85 3.27
1291 1294 8.528044 ACTTAACAACATCCAAGAACCTAAAA 57.472 30.769 0.00 0.00 0.00 1.52
1322 1325 6.597562 ACTTAAGTGTTAACCCAGAACATCA 58.402 36.000 7.48 0.00 38.94 3.07
1343 1346 1.681264 CACGGCCTGGAAAGAAAACTT 59.319 47.619 0.00 0.00 0.00 2.66
1393 1396 1.445582 CGTGTCCTTCTACACCGGC 60.446 63.158 0.00 0.00 45.66 6.13
1490 1493 0.460311 ATTAGGGCACTTCCTCGTCG 59.540 55.000 0.00 0.00 38.30 5.12
1751 1761 0.668096 ATTTGTTGCGGTGCATGCAG 60.668 50.000 23.41 11.99 44.28 4.41
1759 1769 6.485648 AGTTTCTTACTTCTATTTGTTGCGGT 59.514 34.615 0.00 0.00 31.29 5.68
1861 1871 2.823747 GTTGTAAAGATGGTCAACCCCC 59.176 50.000 0.00 0.00 35.56 5.40
1866 1877 7.517614 TTGCTAATGTTGTAAAGATGGTCAA 57.482 32.000 0.00 0.00 26.23 3.18
1878 1889 7.573710 TGATCCCTATAGTTTGCTAATGTTGT 58.426 34.615 0.00 0.00 0.00 3.32
1882 1893 8.682936 AACTTGATCCCTATAGTTTGCTAATG 57.317 34.615 0.00 0.00 0.00 1.90
1991 2005 1.412343 GCAGAGAGAGGAAGGGATGTC 59.588 57.143 0.00 0.00 0.00 3.06
1992 2006 1.273495 TGCAGAGAGAGGAAGGGATGT 60.273 52.381 0.00 0.00 0.00 3.06
1993 2007 1.138661 GTGCAGAGAGAGGAAGGGATG 59.861 57.143 0.00 0.00 0.00 3.51
2034 2048 2.143925 GGTTGTACAGACAGTGGCTTC 58.856 52.381 0.00 0.00 36.76 3.86
2047 2061 2.561478 ACATGGAGTGGTGGTTGTAC 57.439 50.000 0.00 0.00 0.00 2.90
2076 2090 2.293399 GGCAAAATGAAGGTGAACGAGT 59.707 45.455 0.00 0.00 0.00 4.18
2097 2111 2.167693 TCTTTCATGCACTACCGGGTAG 59.832 50.000 28.43 28.43 41.43 3.18
2099 2113 0.981183 TCTTTCATGCACTACCGGGT 59.019 50.000 6.32 4.46 0.00 5.28
2103 2117 3.253188 TGCTTGTTCTTTCATGCACTACC 59.747 43.478 0.00 0.00 41.30 3.18
2143 2157 3.134458 AGAAGAAACTTGTTGCTCCTCG 58.866 45.455 0.00 0.00 0.00 4.63
2244 2258 4.016444 GGTGGATTCTCAGTAATTTGCCA 58.984 43.478 0.00 0.00 0.00 4.92
2273 2287 9.679661 TTCTAGGCATACATGTTTCTCAAAATA 57.320 29.630 2.30 0.00 0.00 1.40
2308 2322 3.717707 ACGTGTGGTATGTAGATGCATC 58.282 45.455 19.37 19.37 0.00 3.91
2322 2336 4.804608 TTCATTGTTCAACTACGTGTGG 57.195 40.909 0.00 0.00 0.00 4.17
2327 2341 9.407514 CATTTTGTTTTTCATTGTTCAACTACG 57.592 29.630 0.00 0.00 0.00 3.51
2355 2383 6.985188 TTTCCCAGAGTTTGAGAATATTCG 57.015 37.500 9.78 0.00 0.00 3.34
2376 2404 5.559148 TGGCAACCCTTTGTATCATTTTT 57.441 34.783 0.00 0.00 34.90 1.94
2394 2423 2.461695 TCAAAAGAAAGTGGGTTGGCA 58.538 42.857 0.00 0.00 0.00 4.92
2407 2436 6.461370 CCACCAAAGACAACATGATCAAAAGA 60.461 38.462 0.00 0.00 0.00 2.52
2433 2462 5.482878 AGAATCTGGCTTTGGAATGTCATTT 59.517 36.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.