Multiple sequence alignment - TraesCS3A01G357500

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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 TraesCS3A01G357500 chr3A 100.000 1905 0 0 739 2643 605241594 605239690 0.000000e+00 3518.0
1 TraesCS3A01G357500 chr3A 87.035 941 85 24 748 1669 605180531 605179609 0.000000e+00 1027.0
2 TraesCS3A01G357500 chr3A 100.000 344 0 0 1 344 605242332 605241989 1.030000e-178 636.0
3 TraesCS3A01G357500 chr3A 76.939 477 81 20 2010 2476 605176049 605175592 7.310000e-61 244.0
4 TraesCS3A01G357500 chr3A 81.780 236 31 10 2250 2481 605179032 605178805 1.250000e-43 187.0
5 TraesCS3A01G357500 chr3A 80.786 229 32 4 2259 2481 605176823 605176601 4.520000e-38 169.0
6 TraesCS3A01G357500 chr3A 100.000 28 0 0 2584 2611 63180274 63180247 5.000000e-03 52.8
7 TraesCS3A01G357500 chr3D 92.489 1864 99 19 807 2643 462455671 462453822 0.000000e+00 2628.0
8 TraesCS3A01G357500 chr3D 90.782 933 69 11 746 1669 462246974 462246050 0.000000e+00 1230.0
9 TraesCS3A01G357500 chr3D 78.616 477 83 14 2010 2476 462245559 462245092 5.530000e-77 298.0
10 TraesCS3A01G357500 chr3D 93.243 74 4 1 739 811 462458139 462458066 1.000000e-19 108.0
11 TraesCS3A01G357500 chr3B 89.247 1832 143 26 843 2643 614252141 614250333 0.000000e+00 2242.0
12 TraesCS3A01G357500 chr3B 89.362 940 79 18 742 1669 614266646 614265716 0.000000e+00 1162.0
13 TraesCS3A01G357500 chr3B 86.754 921 81 27 766 1669 613812189 613811293 0.000000e+00 987.0
14 TraesCS3A01G357500 chr3B 77.312 573 56 41 1804 2311 614265521 614264958 1.210000e-68 270.0
15 TraesCS3A01G357500 chr3B 78.140 430 63 14 2073 2481 613808620 613808201 7.310000e-61 244.0
16 TraesCS3A01G357500 chr3B 91.860 172 11 3 89 258 571752692 571752522 1.220000e-58 237.0
17 TraesCS3A01G357500 chr3B 80.339 295 46 10 2159 2447 613810734 613810446 2.060000e-51 213.0
18 TraesCS3A01G357500 chr3B 91.935 62 5 0 2377 2438 614264959 614264898 1.300000e-13 87.9
19 TraesCS3A01G357500 chr3B 96.970 33 1 0 2585 2617 571535892 571535860 3.680000e-04 56.5
20 TraesCS3A01G357500 chr3B 92.308 39 3 0 2537 2575 613810342 613810304 3.680000e-04 56.5
21 TraesCS3A01G357500 chr7D 90.284 422 31 7 1091 1504 588409310 588409729 6.430000e-151 544.0
22 TraesCS3A01G357500 chr7D 98.630 73 1 0 3 75 68921120 68921192 2.130000e-26 130.0
23 TraesCS3A01G357500 chr7B 90.284 422 31 7 1091 1504 661716684 661717103 6.430000e-151 544.0
24 TraesCS3A01G357500 chr7A 90.238 420 31 7 1091 1502 680264523 680264106 8.320000e-150 540.0
25 TraesCS3A01G357500 chr7A 90.503 179 12 5 85 258 320981163 320981341 5.690000e-57 231.0
26 TraesCS3A01G357500 chr7A 100.000 28 0 0 2583 2610 88945525 88945498 5.000000e-03 52.8
27 TraesCS3A01G357500 chr2D 91.329 173 13 2 85 255 516708484 516708312 4.400000e-58 235.0
28 TraesCS3A01G357500 chr2D 97.333 75 2 0 4 78 429202900 429202974 7.680000e-26 128.0
29 TraesCS3A01G357500 chr5D 90.857 175 14 2 83 255 321901904 321902078 1.580000e-57 233.0
30 TraesCS3A01G357500 chr5D 89.617 183 14 5 87 265 96007293 96007112 7.360000e-56 228.0
31 TraesCS3A01G357500 chr5D 95.000 80 3 1 3 81 44159693 44159614 9.930000e-25 124.0
32 TraesCS3A01G357500 chr5D 92.105 38 1 2 2581 2617 378153169 378153205 5.000000e-03 52.8
33 TraesCS3A01G357500 chr5A 89.730 185 15 4 90 270 290391865 290391681 1.580000e-57 233.0
34 TraesCS3A01G357500 chr5A 90.503 179 13 4 93 268 651496822 651496999 1.580000e-57 233.0
35 TraesCS3A01G357500 chr5A 97.260 73 2 0 3 75 276114762 276114690 9.930000e-25 124.0
36 TraesCS3A01G357500 chr5A 91.860 86 5 1 1 86 64984442 64984525 4.620000e-23 119.0
37 TraesCS3A01G357500 chr4D 88.060 201 19 5 85 280 352606336 352606536 1.580000e-57 233.0
38 TraesCS3A01G357500 chr4D 82.996 247 30 11 1425 1669 6776545 6776309 2.060000e-51 213.0
39 TraesCS3A01G357500 chr4D 93.478 46 0 1 1092 1137 352755519 352755477 6.110000e-07 65.8
40 TraesCS3A01G357500 chr1D 90.503 179 14 3 87 262 238940209 238940387 1.580000e-57 233.0
41 TraesCS3A01G357500 chr1D 100.000 28 0 0 2585 2612 403336642 403336669 5.000000e-03 52.8
42 TraesCS3A01G357500 chr1A 83.978 181 23 6 2208 2385 242688846 242688669 4.520000e-38 169.0
43 TraesCS3A01G357500 chr1A 97.222 72 2 0 3 74 585986577 585986648 3.570000e-24 122.0
44 TraesCS3A01G357500 chr1A 94.118 34 2 0 2584 2617 291896583 291896550 5.000000e-03 52.8
45 TraesCS3A01G357500 chr6A 97.297 74 2 0 1 74 516162219 516162146 2.760000e-25 126.0
46 TraesCS3A01G357500 chr2A 97.297 74 2 0 1 74 570733879 570733806 2.760000e-25 126.0
47 TraesCS3A01G357500 chr5B 97.297 74 1 1 5 78 658539510 658539438 9.930000e-25 124.0
48 TraesCS3A01G357500 chr4B 93.478 46 0 1 1092 1137 436312303 436312261 6.110000e-07 65.8
49 TraesCS3A01G357500 chr4B 100.000 29 0 0 2584 2612 2210911 2210939 1.000000e-03 54.7
50 TraesCS3A01G357500 chr4B 100.000 29 0 0 2584 2612 2240901 2240929 1.000000e-03 54.7


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 TraesCS3A01G357500 chr3A 605239690 605242332 2642 True 2077.000000 3518 100.00000 1 2643 2 chr3A.!!$R3 2642
1 TraesCS3A01G357500 chr3A 605175592 605180531 4939 True 406.750000 1027 81.63500 748 2481 4 chr3A.!!$R2 1733
2 TraesCS3A01G357500 chr3D 462453822 462458139 4317 True 1368.000000 2628 92.86600 739 2643 2 chr3D.!!$R2 1904
3 TraesCS3A01G357500 chr3D 462245092 462246974 1882 True 764.000000 1230 84.69900 746 2476 2 chr3D.!!$R1 1730
4 TraesCS3A01G357500 chr3B 614250333 614252141 1808 True 2242.000000 2242 89.24700 843 2643 1 chr3B.!!$R3 1800
5 TraesCS3A01G357500 chr3B 614264898 614266646 1748 True 506.633333 1162 86.20300 742 2438 3 chr3B.!!$R5 1696
6 TraesCS3A01G357500 chr3B 613808201 613812189 3988 True 375.125000 987 84.38525 766 2575 4 chr3B.!!$R4 1809

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
27 28 0.101579 ACCCAAACGGACAAAAAGCG 59.898 50.0 0.0 0.0 34.64 4.68 F
73 74 0.321298 GCCCGTTGGAGTTGCTCTAA 60.321 55.0 0.0 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 3928 0.872021 GACGGACGGCAGCAATCTAG 60.872 60.000 0.0 0.0 0.0 2.43 R
1721 5748 1.416030 TCAGAGCAGCTTACACAACCA 59.584 47.619 0.0 0.0 0.0 3.67 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
25 26 2.113910 CGACCCAAACGGACAAAAAG 57.886 50.000 0.00 0.00 34.64 2.27
26 27 1.847818 GACCCAAACGGACAAAAAGC 58.152 50.000 0.00 0.00 34.64 3.51
27 28 0.101579 ACCCAAACGGACAAAAAGCG 59.898 50.000 0.00 0.00 34.64 4.68
28 29 0.596341 CCCAAACGGACAAAAAGCGG 60.596 55.000 0.00 0.00 0.00 5.52
29 30 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.000 0.00 0.00 0.00 5.54
30 31 1.472990 CAAACGGACAAAAAGCGGAC 58.527 50.000 0.00 0.00 0.00 4.79
31 32 1.096416 AAACGGACAAAAAGCGGACA 58.904 45.000 0.00 0.00 0.00 4.02
32 33 1.096416 AACGGACAAAAAGCGGACAA 58.904 45.000 0.00 0.00 0.00 3.18
33 34 1.096416 ACGGACAAAAAGCGGACAAA 58.904 45.000 0.00 0.00 0.00 2.83
34 35 1.473278 ACGGACAAAAAGCGGACAAAA 59.527 42.857 0.00 0.00 0.00 2.44
35 36 2.094649 ACGGACAAAAAGCGGACAAAAA 60.095 40.909 0.00 0.00 0.00 1.94
36 37 2.280445 CGGACAAAAAGCGGACAAAAAC 59.720 45.455 0.00 0.00 0.00 2.43
37 38 2.280445 GGACAAAAAGCGGACAAAAACG 59.720 45.455 0.00 0.00 0.00 3.60
43 44 4.199130 CGGACAAAAACGCCGTTC 57.801 55.556 1.60 0.00 40.17 3.95
44 45 1.719766 CGGACAAAAACGCCGTTCG 60.720 57.895 1.60 0.00 45.38 3.95
53 54 4.067016 CGCCGTTCGTTTGGGTCG 62.067 66.667 0.00 0.00 0.00 4.79
54 55 3.719144 GCCGTTCGTTTGGGTCGG 61.719 66.667 0.00 0.00 43.37 4.79
55 56 3.719144 CCGTTCGTTTGGGTCGGC 61.719 66.667 0.00 0.00 35.01 5.54
56 57 3.719144 CGTTCGTTTGGGTCGGCC 61.719 66.667 0.00 0.00 0.00 6.13
66 67 4.324991 GGTCGGCCCGTTGGAGTT 62.325 66.667 1.63 0.00 0.00 3.01
67 68 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
70 71 3.056328 GGCCCGTTGGAGTTGCTC 61.056 66.667 0.00 0.00 0.00 4.26
71 72 2.032681 GCCCGTTGGAGTTGCTCT 59.967 61.111 0.00 0.00 0.00 4.09
72 73 1.295423 GCCCGTTGGAGTTGCTCTA 59.705 57.895 0.00 0.00 0.00 2.43
73 74 0.321298 GCCCGTTGGAGTTGCTCTAA 60.321 55.000 0.00 0.00 0.00 2.10
74 75 1.726853 CCCGTTGGAGTTGCTCTAAG 58.273 55.000 0.00 0.00 31.92 2.18
75 76 1.079503 CCGTTGGAGTTGCTCTAAGC 58.920 55.000 0.00 0.00 42.82 3.09
103 104 8.749026 TCAGTCTTTATTATTACTCTCTCCGT 57.251 34.615 0.00 0.00 0.00 4.69
104 105 9.186837 TCAGTCTTTATTATTACTCTCTCCGTT 57.813 33.333 0.00 0.00 0.00 4.44
105 106 9.453325 CAGTCTTTATTATTACTCTCTCCGTTC 57.547 37.037 0.00 0.00 0.00 3.95
106 107 9.411189 AGTCTTTATTATTACTCTCTCCGTTCT 57.589 33.333 0.00 0.00 0.00 3.01
118 119 8.705048 ACTCTCTCCGTTCTTAAATATTTGTC 57.295 34.615 11.05 0.00 0.00 3.18
119 120 8.532819 ACTCTCTCCGTTCTTAAATATTTGTCT 58.467 33.333 11.05 0.00 0.00 3.41
120 121 9.372369 CTCTCTCCGTTCTTAAATATTTGTCTT 57.628 33.333 11.05 0.00 0.00 3.01
121 122 9.720769 TCTCTCCGTTCTTAAATATTTGTCTTT 57.279 29.630 11.05 0.00 0.00 2.52
140 141 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
141 142 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
188 189 9.747898 ATACATTTTAAAGTGTAGATTCACCCA 57.252 29.630 22.85 4.48 38.91 4.51
189 190 8.650143 ACATTTTAAAGTGTAGATTCACCCAT 57.350 30.769 14.06 0.00 38.91 4.00
190 191 9.088987 ACATTTTAAAGTGTAGATTCACCCATT 57.911 29.630 14.06 0.00 38.91 3.16
191 192 9.927668 CATTTTAAAGTGTAGATTCACCCATTT 57.072 29.630 2.68 0.00 38.91 2.32
193 194 9.757227 TTTTAAAGTGTAGATTCACCCATTTTG 57.243 29.630 0.00 0.00 38.91 2.44
194 195 5.391312 AAGTGTAGATTCACCCATTTTGC 57.609 39.130 0.00 0.00 38.91 3.68
195 196 4.666512 AGTGTAGATTCACCCATTTTGCT 58.333 39.130 0.00 0.00 38.91 3.91
196 197 5.079643 AGTGTAGATTCACCCATTTTGCTT 58.920 37.500 0.00 0.00 38.91 3.91
197 198 5.183904 AGTGTAGATTCACCCATTTTGCTTC 59.816 40.000 0.00 0.00 38.91 3.86
198 199 3.855689 AGATTCACCCATTTTGCTTCG 57.144 42.857 0.00 0.00 0.00 3.79
199 200 3.157087 AGATTCACCCATTTTGCTTCGT 58.843 40.909 0.00 0.00 0.00 3.85
200 201 4.331968 AGATTCACCCATTTTGCTTCGTA 58.668 39.130 0.00 0.00 0.00 3.43
201 202 4.949856 AGATTCACCCATTTTGCTTCGTAT 59.050 37.500 0.00 0.00 0.00 3.06
202 203 4.433186 TTCACCCATTTTGCTTCGTATG 57.567 40.909 0.00 0.00 0.00 2.39
203 204 3.417101 TCACCCATTTTGCTTCGTATGT 58.583 40.909 0.00 0.00 0.00 2.29
204 205 4.580868 TCACCCATTTTGCTTCGTATGTA 58.419 39.130 0.00 0.00 0.00 2.29
205 206 5.004448 TCACCCATTTTGCTTCGTATGTAA 58.996 37.500 0.00 0.00 0.00 2.41
206 207 5.650266 TCACCCATTTTGCTTCGTATGTAAT 59.350 36.000 0.00 0.00 0.00 1.89
207 208 5.971202 CACCCATTTTGCTTCGTATGTAATC 59.029 40.000 0.00 0.00 0.00 1.75
208 209 5.650266 ACCCATTTTGCTTCGTATGTAATCA 59.350 36.000 0.00 0.00 0.00 2.57
209 210 5.971202 CCCATTTTGCTTCGTATGTAATCAC 59.029 40.000 0.00 0.00 0.00 3.06
210 211 6.183360 CCCATTTTGCTTCGTATGTAATCACT 60.183 38.462 0.00 0.00 0.00 3.41
211 212 7.250569 CCATTTTGCTTCGTATGTAATCACTT 58.749 34.615 0.00 0.00 0.00 3.16
212 213 7.218773 CCATTTTGCTTCGTATGTAATCACTTG 59.781 37.037 0.00 0.00 0.00 3.16
213 214 6.795098 TTTGCTTCGTATGTAATCACTTGT 57.205 33.333 0.00 0.00 0.00 3.16
214 215 6.795098 TTGCTTCGTATGTAATCACTTGTT 57.205 33.333 0.00 0.00 0.00 2.83
215 216 6.164408 TGCTTCGTATGTAATCACTTGTTG 57.836 37.500 0.00 0.00 0.00 3.33
216 217 5.929415 TGCTTCGTATGTAATCACTTGTTGA 59.071 36.000 0.00 0.00 39.11 3.18
217 218 6.425417 TGCTTCGTATGTAATCACTTGTTGAA 59.575 34.615 0.00 0.00 37.92 2.69
218 219 7.041712 TGCTTCGTATGTAATCACTTGTTGAAA 60.042 33.333 0.00 0.00 37.92 2.69
219 220 7.962918 GCTTCGTATGTAATCACTTGTTGAAAT 59.037 33.333 0.00 0.00 37.92 2.17
220 221 9.478019 CTTCGTATGTAATCACTTGTTGAAATC 57.522 33.333 0.00 0.00 37.92 2.17
221 222 8.771920 TCGTATGTAATCACTTGTTGAAATCT 57.228 30.769 0.00 0.00 37.92 2.40
222 223 8.655970 TCGTATGTAATCACTTGTTGAAATCTG 58.344 33.333 0.00 0.00 37.92 2.90
223 224 8.443160 CGTATGTAATCACTTGTTGAAATCTGT 58.557 33.333 0.00 0.00 37.92 3.41
226 227 9.725019 ATGTAATCACTTGTTGAAATCTGTAGA 57.275 29.630 0.00 0.00 37.92 2.59
227 228 9.554395 TGTAATCACTTGTTGAAATCTGTAGAA 57.446 29.630 0.00 0.00 37.92 2.10
230 231 8.908786 ATCACTTGTTGAAATCTGTAGAAAGA 57.091 30.769 0.00 0.00 37.92 2.52
231 232 8.142994 TCACTTGTTGAAATCTGTAGAAAGAC 57.857 34.615 0.00 0.00 0.00 3.01
232 233 7.768582 TCACTTGTTGAAATCTGTAGAAAGACA 59.231 33.333 0.00 0.00 0.00 3.41
233 234 8.397906 CACTTGTTGAAATCTGTAGAAAGACAA 58.602 33.333 0.00 0.00 0.00 3.18
234 235 8.956426 ACTTGTTGAAATCTGTAGAAAGACAAA 58.044 29.630 0.00 0.00 0.00 2.83
235 236 9.956720 CTTGTTGAAATCTGTAGAAAGACAAAT 57.043 29.630 0.00 0.00 0.00 2.32
298 299 7.610580 AATTTTGGGAAAGATAACTGTTCCA 57.389 32.000 0.00 2.08 42.26 3.53
299 300 7.610580 ATTTTGGGAAAGATAACTGTTCCAA 57.389 32.000 0.00 0.00 42.26 3.53
300 301 7.425224 TTTTGGGAAAGATAACTGTTCCAAA 57.575 32.000 10.91 10.91 42.26 3.28
301 302 7.610580 TTTGGGAAAGATAACTGTTCCAAAT 57.389 32.000 10.91 0.00 42.26 2.32
302 303 8.713708 TTTGGGAAAGATAACTGTTCCAAATA 57.286 30.769 10.91 0.00 42.26 1.40
303 304 7.696992 TGGGAAAGATAACTGTTCCAAATAC 57.303 36.000 0.00 0.00 42.26 1.89
304 305 6.661805 TGGGAAAGATAACTGTTCCAAATACC 59.338 38.462 0.00 0.00 42.26 2.73
305 306 6.890268 GGGAAAGATAACTGTTCCAAATACCT 59.110 38.462 0.00 0.00 42.26 3.08
306 307 7.067129 GGGAAAGATAACTGTTCCAAATACCTC 59.933 40.741 0.00 0.00 42.26 3.85
307 308 7.829706 GGAAAGATAACTGTTCCAAATACCTCT 59.170 37.037 0.00 0.00 40.53 3.69
308 309 9.886132 GAAAGATAACTGTTCCAAATACCTCTA 57.114 33.333 0.00 0.00 0.00 2.43
336 337 9.574516 AAAAATCCTGAGCTTACTCTAAAAGAA 57.425 29.630 0.00 0.00 43.85 2.52
337 338 8.554835 AAATCCTGAGCTTACTCTAAAAGAAC 57.445 34.615 0.00 0.00 43.85 3.01
338 339 6.665992 TCCTGAGCTTACTCTAAAAGAACA 57.334 37.500 0.00 0.00 43.85 3.18
339 340 6.456501 TCCTGAGCTTACTCTAAAAGAACAC 58.543 40.000 0.00 0.00 43.85 3.32
340 341 5.639931 CCTGAGCTTACTCTAAAAGAACACC 59.360 44.000 0.00 0.00 43.85 4.16
341 342 5.548406 TGAGCTTACTCTAAAAGAACACCC 58.452 41.667 0.00 0.00 43.85 4.61
342 343 4.907809 AGCTTACTCTAAAAGAACACCCC 58.092 43.478 0.00 0.00 0.00 4.95
343 344 4.008330 GCTTACTCTAAAAGAACACCCCC 58.992 47.826 0.00 0.00 0.00 5.40
799 802 2.126110 CGCCACCAAATTTCCGCC 60.126 61.111 0.00 0.00 0.00 6.13
985 3387 1.692762 CCCTATATATCCCCAGCGCCT 60.693 57.143 2.29 0.00 0.00 5.52
1016 3429 1.302511 CCAACACCTCGAACCCCAG 60.303 63.158 0.00 0.00 0.00 4.45
1067 3488 2.499685 CAACCCGATCCCTCGTCC 59.500 66.667 0.00 0.00 43.49 4.79
1089 3513 4.675029 CACCTCCGCCGAAACCGT 62.675 66.667 0.00 0.00 0.00 4.83
1498 3928 1.056660 TCACCAAGTTCACCTCCTCC 58.943 55.000 0.00 0.00 0.00 4.30
1529 5517 0.728466 CGTCCGTCCGAGTCTGTTTC 60.728 60.000 0.00 0.00 0.00 2.78
1531 5519 0.596577 TCCGTCCGAGTCTGTTTCTG 59.403 55.000 0.00 0.00 0.00 3.02
1560 5548 2.621526 GGTCTGAATTTGTTCCCGTGTT 59.378 45.455 0.00 0.00 0.00 3.32
1614 5603 4.951254 TCGAACAGTGTAAAATGAGTCCA 58.049 39.130 0.00 0.00 0.00 4.02
1709 5736 7.364522 TCTTTACTTGGATGATTTCGTTGAG 57.635 36.000 0.00 0.00 0.00 3.02
1719 5746 4.447290 TGATTTCGTTGAGACAAACCTCA 58.553 39.130 0.00 0.00 41.06 3.86
1741 5771 1.416030 TGGTTGTGTAAGCTGCTCTGA 59.584 47.619 1.00 0.00 35.38 3.27
1891 6181 5.409826 CAGATTGTTCTACAGGTGGAAAGTC 59.590 44.000 0.00 0.32 31.87 3.01
2046 7271 9.427127 GTCTGAATTTTATAACTTTGCGATCTC 57.573 33.333 0.00 0.00 0.00 2.75
2049 7274 9.773328 TGAATTTTATAACTTTGCGATCTCTTG 57.227 29.630 0.00 0.00 0.00 3.02
2050 7275 9.988350 GAATTTTATAACTTTGCGATCTCTTGA 57.012 29.630 0.00 0.00 0.00 3.02
2086 7321 2.430465 TCTGAATGTGCTTCTGCCTTC 58.570 47.619 0.00 0.00 38.71 3.46
2214 8504 1.457346 CAACTGAGGTTGGGAGATGC 58.543 55.000 1.43 0.00 46.37 3.91
2298 8602 1.918262 TCAGGGGCAAGATCTCATTGT 59.082 47.619 0.00 0.00 0.00 2.71
2341 8646 7.449704 ACTCATTAGAAAATTCAGAAAGCCAGT 59.550 33.333 0.00 0.00 0.00 4.00
2342 8647 7.820648 TCATTAGAAAATTCAGAAAGCCAGTC 58.179 34.615 0.00 0.00 0.00 3.51
2343 8648 4.756084 AGAAAATTCAGAAAGCCAGTCG 57.244 40.909 0.00 0.00 0.00 4.18
2409 8718 9.738832 GAAATGTCTACTTCTAGAGGAATACAC 57.261 37.037 9.14 0.00 33.01 2.90
2445 8754 5.641209 GTCATCCCTGTAGCTTAATATGCTG 59.359 44.000 10.45 0.00 41.32 4.41
2460 8769 5.686159 ATATGCTGCTCTGCAATAAGTTC 57.314 39.130 0.00 0.00 46.61 3.01
2466 8775 4.252878 TGCTCTGCAATAAGTTCGATTCA 58.747 39.130 0.00 0.00 34.76 2.57
2612 8923 7.754625 TCCCTTTGTAAACAAATATAAGACGC 58.245 34.615 8.62 0.00 43.92 5.19
2629 8940 2.230750 GACGCTTTACAGTGGGAGTAGT 59.769 50.000 0.00 0.00 34.49 2.73
2630 8941 2.631545 ACGCTTTACAGTGGGAGTAGTT 59.368 45.455 0.00 0.00 34.49 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
4 5 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
6 7 1.862411 GCTTTTTGTCCGTTTGGGTCG 60.862 52.381 0.00 0.00 37.00 4.79
7 8 1.847818 GCTTTTTGTCCGTTTGGGTC 58.152 50.000 0.00 0.00 37.00 4.46
8 9 0.101579 CGCTTTTTGTCCGTTTGGGT 59.898 50.000 0.00 0.00 37.00 4.51
9 10 0.596341 CCGCTTTTTGTCCGTTTGGG 60.596 55.000 0.00 0.00 35.24 4.12
10 11 0.382515 TCCGCTTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
11 12 1.202200 TGTCCGCTTTTTGTCCGTTTG 60.202 47.619 0.00 0.00 0.00 2.93
12 13 1.096416 TGTCCGCTTTTTGTCCGTTT 58.904 45.000 0.00 0.00 0.00 3.60
13 14 1.096416 TTGTCCGCTTTTTGTCCGTT 58.904 45.000 0.00 0.00 0.00 4.44
14 15 1.096416 TTTGTCCGCTTTTTGTCCGT 58.904 45.000 0.00 0.00 0.00 4.69
15 16 2.196295 TTTTGTCCGCTTTTTGTCCG 57.804 45.000 0.00 0.00 0.00 4.79
16 17 2.280445 CGTTTTTGTCCGCTTTTTGTCC 59.720 45.455 0.00 0.00 0.00 4.02
17 18 2.284798 GCGTTTTTGTCCGCTTTTTGTC 60.285 45.455 0.00 0.00 46.08 3.18
18 19 1.656594 GCGTTTTTGTCCGCTTTTTGT 59.343 42.857 0.00 0.00 46.08 2.83
19 20 2.345469 GCGTTTTTGTCCGCTTTTTG 57.655 45.000 0.00 0.00 46.08 2.44
25 26 2.007114 GAACGGCGTTTTTGTCCGC 61.007 57.895 27.48 7.42 46.49 5.54
27 28 4.199130 CGAACGGCGTTTTTGTCC 57.801 55.556 27.48 11.66 34.64 4.02
37 38 3.719144 CCGACCCAAACGAACGGC 61.719 66.667 0.00 0.00 37.32 5.68
38 39 3.719144 GCCGACCCAAACGAACGG 61.719 66.667 0.00 0.00 45.26 4.44
39 40 3.719144 GGCCGACCCAAACGAACG 61.719 66.667 0.00 0.00 0.00 3.95
49 50 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
50 51 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
53 54 2.180159 TAGAGCAACTCCAACGGGCC 62.180 60.000 0.00 0.00 0.00 5.80
54 55 0.321298 TTAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
55 56 1.726853 CTTAGAGCAACTCCAACGGG 58.273 55.000 0.00 0.00 0.00 5.28
56 57 1.079503 GCTTAGAGCAACTCCAACGG 58.920 55.000 0.00 0.00 41.89 4.44
77 78 9.357161 ACGGAGAGAGTAATAATAAAGACTGAT 57.643 33.333 0.00 0.00 0.00 2.90
78 79 8.749026 ACGGAGAGAGTAATAATAAAGACTGA 57.251 34.615 0.00 0.00 0.00 3.41
79 80 9.453325 GAACGGAGAGAGTAATAATAAAGACTG 57.547 37.037 0.00 0.00 0.00 3.51
80 81 9.411189 AGAACGGAGAGAGTAATAATAAAGACT 57.589 33.333 0.00 0.00 0.00 3.24
92 93 9.798994 GACAAATATTTAAGAACGGAGAGAGTA 57.201 33.333 0.00 0.00 0.00 2.59
93 94 8.532819 AGACAAATATTTAAGAACGGAGAGAGT 58.467 33.333 0.00 0.00 0.00 3.24
94 95 8.934507 AGACAAATATTTAAGAACGGAGAGAG 57.065 34.615 0.00 0.00 0.00 3.20
95 96 9.720769 AAAGACAAATATTTAAGAACGGAGAGA 57.279 29.630 0.00 0.00 0.00 3.10
114 115 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
115 116 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
119 120 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
120 121 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
121 122 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
122 123 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
123 124 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
124 125 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
125 126 8.562892 CATATGTGGTAGTCCATTTGAAATCTC 58.437 37.037 0.00 0.00 46.20 2.75
126 127 7.503566 CCATATGTGGTAGTCCATTTGAAATCT 59.496 37.037 0.00 0.00 46.20 2.40
127 128 7.502226 TCCATATGTGGTAGTCCATTTGAAATC 59.498 37.037 8.51 0.00 46.20 2.17
128 129 7.353525 TCCATATGTGGTAGTCCATTTGAAAT 58.646 34.615 8.51 0.00 46.20 2.17
129 130 6.726379 TCCATATGTGGTAGTCCATTTGAAA 58.274 36.000 8.51 0.00 46.20 2.69
130 131 6.320434 TCCATATGTGGTAGTCCATTTGAA 57.680 37.500 8.51 0.00 46.20 2.69
131 132 5.966853 TCCATATGTGGTAGTCCATTTGA 57.033 39.130 8.51 0.00 46.20 2.69
132 133 6.064060 ACATCCATATGTGGTAGTCCATTTG 58.936 40.000 8.51 0.00 44.79 2.32
133 134 6.266131 ACATCCATATGTGGTAGTCCATTT 57.734 37.500 8.51 0.00 44.79 2.32
134 135 5.912149 ACATCCATATGTGGTAGTCCATT 57.088 39.130 8.51 0.00 44.79 3.16
135 136 7.574021 AATACATCCATATGTGGTAGTCCAT 57.426 36.000 8.51 0.00 45.99 3.41
136 137 7.953493 TCTAATACATCCATATGTGGTAGTCCA 59.047 37.037 8.51 0.00 45.99 4.02
137 138 8.362464 TCTAATACATCCATATGTGGTAGTCC 57.638 38.462 8.51 0.00 45.99 3.85
162 163 9.747898 TGGGTGAATCTACACTTTAAAATGTAT 57.252 29.630 9.73 0.00 40.22 2.29
163 164 9.747898 ATGGGTGAATCTACACTTTAAAATGTA 57.252 29.630 9.02 9.02 40.22 2.29
164 165 8.650143 ATGGGTGAATCTACACTTTAAAATGT 57.350 30.769 7.53 7.53 40.22 2.71
165 166 9.927668 AAATGGGTGAATCTACACTTTAAAATG 57.072 29.630 0.00 0.00 40.22 2.32
167 168 9.757227 CAAAATGGGTGAATCTACACTTTAAAA 57.243 29.630 0.00 0.00 40.22 1.52
168 169 7.870445 GCAAAATGGGTGAATCTACACTTTAAA 59.130 33.333 0.00 0.00 40.22 1.52
169 170 7.232534 AGCAAAATGGGTGAATCTACACTTTAA 59.767 33.333 0.00 0.00 40.22 1.52
170 171 6.719370 AGCAAAATGGGTGAATCTACACTTTA 59.281 34.615 0.00 0.00 40.22 1.85
171 172 5.539955 AGCAAAATGGGTGAATCTACACTTT 59.460 36.000 0.00 0.00 40.22 2.66
172 173 5.079643 AGCAAAATGGGTGAATCTACACTT 58.920 37.500 0.00 0.00 40.22 3.16
173 174 4.666512 AGCAAAATGGGTGAATCTACACT 58.333 39.130 0.00 0.00 40.22 3.55
174 175 5.391312 AAGCAAAATGGGTGAATCTACAC 57.609 39.130 0.00 0.00 39.70 2.90
175 176 4.155826 CGAAGCAAAATGGGTGAATCTACA 59.844 41.667 0.00 0.00 0.00 2.74
176 177 4.156008 ACGAAGCAAAATGGGTGAATCTAC 59.844 41.667 0.00 0.00 0.00 2.59
177 178 4.331968 ACGAAGCAAAATGGGTGAATCTA 58.668 39.130 0.00 0.00 0.00 1.98
178 179 3.157087 ACGAAGCAAAATGGGTGAATCT 58.843 40.909 0.00 0.00 0.00 2.40
179 180 3.575965 ACGAAGCAAAATGGGTGAATC 57.424 42.857 0.00 0.00 0.00 2.52
180 181 4.462483 ACATACGAAGCAAAATGGGTGAAT 59.538 37.500 0.00 0.00 0.00 2.57
181 182 3.823873 ACATACGAAGCAAAATGGGTGAA 59.176 39.130 0.00 0.00 0.00 3.18
182 183 3.417101 ACATACGAAGCAAAATGGGTGA 58.583 40.909 0.00 0.00 0.00 4.02
183 184 3.848272 ACATACGAAGCAAAATGGGTG 57.152 42.857 0.00 0.00 0.00 4.61
184 185 5.650266 TGATTACATACGAAGCAAAATGGGT 59.350 36.000 0.00 0.00 0.00 4.51
185 186 5.971202 GTGATTACATACGAAGCAAAATGGG 59.029 40.000 0.00 0.00 0.00 4.00
186 187 6.785191 AGTGATTACATACGAAGCAAAATGG 58.215 36.000 0.00 0.00 0.00 3.16
187 188 7.750458 ACAAGTGATTACATACGAAGCAAAATG 59.250 33.333 0.00 0.00 0.00 2.32
188 189 7.816640 ACAAGTGATTACATACGAAGCAAAAT 58.183 30.769 0.00 0.00 0.00 1.82
189 190 7.197071 ACAAGTGATTACATACGAAGCAAAA 57.803 32.000 0.00 0.00 0.00 2.44
190 191 6.795098 ACAAGTGATTACATACGAAGCAAA 57.205 33.333 0.00 0.00 0.00 3.68
191 192 6.425417 TCAACAAGTGATTACATACGAAGCAA 59.575 34.615 0.00 0.00 0.00 3.91
192 193 5.929415 TCAACAAGTGATTACATACGAAGCA 59.071 36.000 0.00 0.00 0.00 3.91
193 194 6.403333 TCAACAAGTGATTACATACGAAGC 57.597 37.500 0.00 0.00 0.00 3.86
194 195 9.478019 GATTTCAACAAGTGATTACATACGAAG 57.522 33.333 0.00 0.00 35.70 3.79
195 196 9.214957 AGATTTCAACAAGTGATTACATACGAA 57.785 29.630 0.00 0.00 35.70 3.85
196 197 8.655970 CAGATTTCAACAAGTGATTACATACGA 58.344 33.333 0.00 0.00 35.70 3.43
197 198 8.443160 ACAGATTTCAACAAGTGATTACATACG 58.557 33.333 0.00 0.00 35.70 3.06
200 201 9.725019 TCTACAGATTTCAACAAGTGATTACAT 57.275 29.630 0.00 0.00 35.70 2.29
201 202 9.554395 TTCTACAGATTTCAACAAGTGATTACA 57.446 29.630 0.00 0.00 35.70 2.41
204 205 9.342308 TCTTTCTACAGATTTCAACAAGTGATT 57.658 29.630 0.00 0.00 35.70 2.57
205 206 8.778358 GTCTTTCTACAGATTTCAACAAGTGAT 58.222 33.333 0.00 0.00 35.70 3.06
206 207 7.768582 TGTCTTTCTACAGATTTCAACAAGTGA 59.231 33.333 0.00 0.00 0.00 3.41
207 208 7.919690 TGTCTTTCTACAGATTTCAACAAGTG 58.080 34.615 0.00 0.00 0.00 3.16
208 209 8.506168 TTGTCTTTCTACAGATTTCAACAAGT 57.494 30.769 0.00 0.00 0.00 3.16
209 210 9.956720 ATTTGTCTTTCTACAGATTTCAACAAG 57.043 29.630 0.00 0.00 0.00 3.16
272 273 9.320295 TGGAACAGTTATCTTTCCCAAAATTAT 57.680 29.630 0.00 0.00 38.46 1.28
273 274 8.713708 TGGAACAGTTATCTTTCCCAAAATTA 57.286 30.769 0.00 0.00 38.46 1.40
274 275 7.610580 TGGAACAGTTATCTTTCCCAAAATT 57.389 32.000 0.00 0.00 38.46 1.82
275 276 7.610580 TTGGAACAGTTATCTTTCCCAAAAT 57.389 32.000 0.00 0.00 42.39 1.82
276 277 7.425224 TTTGGAACAGTTATCTTTCCCAAAA 57.575 32.000 9.56 0.00 42.39 2.44
277 278 7.610580 ATTTGGAACAGTTATCTTTCCCAAA 57.389 32.000 12.92 12.92 42.39 3.28
278 279 7.177744 GGTATTTGGAACAGTTATCTTTCCCAA 59.822 37.037 0.00 0.00 42.39 4.12
279 280 6.661805 GGTATTTGGAACAGTTATCTTTCCCA 59.338 38.462 0.00 0.00 42.39 4.37
280 281 6.890268 AGGTATTTGGAACAGTTATCTTTCCC 59.110 38.462 0.00 0.00 42.39 3.97
281 282 7.829706 AGAGGTATTTGGAACAGTTATCTTTCC 59.170 37.037 0.00 0.00 42.39 3.13
282 283 8.794335 AGAGGTATTTGGAACAGTTATCTTTC 57.206 34.615 0.00 0.00 42.39 2.62
310 311 9.574516 TTCTTTTAGAGTAAGCTCAGGATTTTT 57.425 29.630 0.00 0.00 44.00 1.94
311 312 9.004717 GTTCTTTTAGAGTAAGCTCAGGATTTT 57.995 33.333 0.00 0.00 44.00 1.82
312 313 8.157476 TGTTCTTTTAGAGTAAGCTCAGGATTT 58.843 33.333 0.00 0.00 44.00 2.17
313 314 7.604545 GTGTTCTTTTAGAGTAAGCTCAGGATT 59.395 37.037 0.00 0.00 44.00 3.01
314 315 7.100409 GTGTTCTTTTAGAGTAAGCTCAGGAT 58.900 38.462 0.00 0.00 44.00 3.24
315 316 6.456501 GTGTTCTTTTAGAGTAAGCTCAGGA 58.543 40.000 0.00 0.00 44.00 3.86
316 317 5.639931 GGTGTTCTTTTAGAGTAAGCTCAGG 59.360 44.000 0.00 0.00 44.00 3.86
317 318 5.639931 GGGTGTTCTTTTAGAGTAAGCTCAG 59.360 44.000 0.00 0.00 44.00 3.35
318 319 5.512576 GGGGTGTTCTTTTAGAGTAAGCTCA 60.513 44.000 0.00 0.00 44.00 4.26
319 320 4.936411 GGGGTGTTCTTTTAGAGTAAGCTC 59.064 45.833 0.00 0.00 41.94 4.09
320 321 4.263374 GGGGGTGTTCTTTTAGAGTAAGCT 60.263 45.833 0.00 0.00 0.00 3.74
321 322 4.008330 GGGGGTGTTCTTTTAGAGTAAGC 58.992 47.826 0.00 0.00 0.00 3.09
785 787 2.126110 GCGGGCGGAAATTTGGTG 60.126 61.111 0.00 0.00 0.00 4.17
985 3387 4.646877 GTTGGTTTCCGGGGGCGA 62.647 66.667 0.00 0.00 0.00 5.54
1016 3429 1.078143 AGGACTGGAGGATTTGCGC 60.078 57.895 0.00 0.00 0.00 6.09
1067 3488 2.646175 TTTCGGCGGAGGTGGAGAG 61.646 63.158 7.21 0.00 0.00 3.20
1498 3928 0.872021 GACGGACGGCAGCAATCTAG 60.872 60.000 0.00 0.00 0.00 2.43
1529 5517 4.330250 ACAAATTCAGACCAGACCATCAG 58.670 43.478 0.00 0.00 0.00 2.90
1531 5519 4.156739 GGAACAAATTCAGACCAGACCATC 59.843 45.833 0.00 0.00 36.46 3.51
1560 5548 9.856162 GAATCTAACCCCCTGTAATATGTTTTA 57.144 33.333 0.00 0.00 0.00 1.52
1614 5603 7.617225 TGGATGATTCTTTGATTCAGCAAATT 58.383 30.769 9.02 0.00 37.16 1.82
1680 5669 5.447818 CGAAATCATCCAAGTAAAGAGGTGC 60.448 44.000 0.00 0.00 0.00 5.01
1682 5671 5.805728 ACGAAATCATCCAAGTAAAGAGGT 58.194 37.500 0.00 0.00 0.00 3.85
1689 5678 5.789521 TGTCTCAACGAAATCATCCAAGTA 58.210 37.500 0.00 0.00 0.00 2.24
1719 5746 2.816087 CAGAGCAGCTTACACAACCATT 59.184 45.455 0.00 0.00 0.00 3.16
1721 5748 1.416030 TCAGAGCAGCTTACACAACCA 59.584 47.619 0.00 0.00 0.00 3.67
1722 5749 2.169832 TCAGAGCAGCTTACACAACC 57.830 50.000 0.00 0.00 0.00 3.77
1723 5750 6.428385 AATTATCAGAGCAGCTTACACAAC 57.572 37.500 0.00 0.00 0.00 3.32
1896 6190 8.925700 CCTGAAAATAAAGTTAACAAATCAGGC 58.074 33.333 18.71 3.09 42.43 4.85
1927 6235 4.962151 GCGTTAAAAGCTCGGAATGAATAC 59.038 41.667 0.00 0.00 0.00 1.89
1928 6236 4.034742 GGCGTTAAAAGCTCGGAATGAATA 59.965 41.667 0.00 0.00 34.52 1.75
1929 6237 3.181500 GGCGTTAAAAGCTCGGAATGAAT 60.181 43.478 0.00 0.00 34.52 2.57
2037 7262 2.408271 ATTGGCTCAAGAGATCGCAA 57.592 45.000 0.32 0.00 0.00 4.85
2086 7321 3.842428 CGTGAATTCAACGCAATCTTCAG 59.158 43.478 10.35 0.00 0.00 3.02
2341 8646 4.895224 ACAGAATCACTAGAATACGCGA 57.105 40.909 15.93 0.00 0.00 5.87
2342 8647 7.295930 TGTATACAGAATCACTAGAATACGCG 58.704 38.462 3.53 3.53 0.00 6.01
2343 8648 9.627395 ATTGTATACAGAATCACTAGAATACGC 57.373 33.333 5.56 0.00 0.00 4.42
2409 8718 6.072286 GCTACAGGGATGACCAAAATATCATG 60.072 42.308 0.00 0.00 43.89 3.07
2445 8754 4.864916 TGAATCGAACTTATTGCAGAGC 57.135 40.909 0.00 0.00 0.00 4.09
2494 8803 8.208903 ACTATTGTCGTACAGGGCTATAAATTT 58.791 33.333 0.00 0.00 0.00 1.82
2500 8809 5.128171 TCAAACTATTGTCGTACAGGGCTAT 59.872 40.000 0.00 0.00 37.79 2.97
2539 8850 4.038642 GGGTGCTAATTGGTTTGAAGTTGA 59.961 41.667 0.00 0.00 0.00 3.18
2542 8853 3.573967 CAGGGTGCTAATTGGTTTGAAGT 59.426 43.478 0.00 0.00 0.00 3.01
2612 8923 7.439381 TGAAACTAACTACTCCCACTGTAAAG 58.561 38.462 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.