Multiple sequence alignment - TraesCS2A01G400100

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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 TraesCS2A01G400100 chr2A 100.000 2950 0 0 1 2950 653374084 653371135 0.000000e+00 5448.0
1 TraesCS2A01G400100 chr2A 100.000 1652 0 0 3316 4967 653370769 653369118 0.000000e+00 3051.0
2 TraesCS2A01G400100 chr2A 92.035 113 6 3 211 322 331305207 331305317 6.660000e-34 156.0
3 TraesCS2A01G400100 chr2D 95.133 1726 46 13 384 2076 509742206 509740486 0.000000e+00 2687.0
4 TraesCS2A01G400100 chr2D 92.312 1665 74 22 3317 4954 509739658 509738021 0.000000e+00 2316.0
5 TraesCS2A01G400100 chr2D 94.990 499 25 0 2156 2654 509740489 509739991 0.000000e+00 784.0
6 TraesCS2A01G400100 chr2D 86.473 207 17 5 1 207 509742532 509742337 3.010000e-52 217.0
7 TraesCS2A01G400100 chr2D 91.946 149 4 1 2810 2950 509739992 509739844 8.430000e-48 202.0
8 TraesCS2A01G400100 chr2D 91.892 111 9 0 211 321 113794481 113794591 6.660000e-34 156.0
9 TraesCS2A01G400100 chr2B 92.828 1715 66 29 386 2076 598966771 598965090 0.000000e+00 2433.0
10 TraesCS2A01G400100 chr2B 93.584 1278 36 9 3316 4550 598964124 598962850 0.000000e+00 1864.0
11 TraesCS2A01G400100 chr2B 95.381 801 29 5 2156 2950 598965093 598964295 0.000000e+00 1267.0
12 TraesCS2A01G400100 chr2B 94.239 243 14 0 4588 4830 598962859 598962617 6.070000e-99 372.0
13 TraesCS2A01G400100 chr2B 94.872 156 8 0 4797 4952 598962620 598962465 1.380000e-60 244.0
14 TraesCS2A01G400100 chr2B 88.517 209 15 5 1 209 598967149 598966950 1.380000e-60 244.0
15 TraesCS2A01G400100 chr5A 93.578 109 7 0 211 319 655993959 655994067 3.980000e-36 163.0
16 TraesCS2A01G400100 chr5A 93.519 108 7 0 211 318 389062730 389062623 1.430000e-35 161.0
17 TraesCS2A01G400100 chr7A 95.000 100 5 0 2058 2157 735734264 735734165 1.850000e-34 158.0
18 TraesCS2A01G400100 chr7B 91.304 115 8 2 211 324 332242869 332242756 6.660000e-34 156.0
19 TraesCS2A01G400100 chr7B 91.964 112 7 2 211 321 629047168 629047278 6.660000e-34 156.0
20 TraesCS2A01G400100 chr3D 94.175 103 4 2 2064 2165 526827513 526827412 6.660000e-34 156.0
21 TraesCS2A01G400100 chr3A 94.175 103 4 2 2064 2165 661044389 661044288 6.660000e-34 156.0
22 TraesCS2A01G400100 chr3A 94.792 96 5 0 2064 2159 205416784 205416879 3.100000e-32 150.0
23 TraesCS2A01G400100 chr3A 97.059 34 1 0 4779 4812 311915700 311915733 1.930000e-04 58.4
24 TraesCS2A01G400100 chr5D 97.778 90 1 1 2073 2161 448145015 448145104 2.390000e-33 154.0
25 TraesCS2A01G400100 chr5B 90.598 117 10 1 211 326 42698119 42698003 2.390000e-33 154.0
26 TraesCS2A01G400100 chr6A 93.204 103 5 2 2064 2165 137273683 137273582 3.100000e-32 150.0
27 TraesCS2A01G400100 chr6A 94.792 96 5 0 2064 2159 445839005 445839100 3.100000e-32 150.0
28 TraesCS2A01G400100 chr4A 93.939 99 5 1 2069 2167 647219961 647219864 1.110000e-31 148.0
29 TraesCS2A01G400100 chr4A 97.059 34 1 0 4779 4812 303862808 303862841 1.930000e-04 58.4
30 TraesCS2A01G400100 chr4B 90.909 110 8 2 211 319 408719144 408719252 4.010000e-31 147.0
31 TraesCS2A01G400100 chr7D 85.034 147 16 5 211 352 54967164 54967019 1.440000e-30 145.0
32 TraesCS2A01G400100 chr1B 93.750 96 6 0 2073 2168 582741286 582741381 1.440000e-30 145.0


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 TraesCS2A01G400100 chr2A 653369118 653374084 4966 True 4249.500000 5448 100.000000 1 4967 2 chr2A.!!$R1 4966
1 TraesCS2A01G400100 chr2D 509738021 509742532 4511 True 1241.200000 2687 92.170800 1 4954 5 chr2D.!!$R1 4953
2 TraesCS2A01G400100 chr2B 598962465 598967149 4684 True 1070.666667 2433 93.236833 1 4952 6 chr2B.!!$R1 4951

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
135 137 0.609957 TGCACTTGGGCATGGAGAAG 60.610 55.0 0.00 0.00 39.25 2.85 F
412 522 0.716108 GAAGCCACGTTCAGATCACG 59.284 55.0 2.79 2.79 43.52 4.35 F
1927 2083 0.034337 GCCACCTTACCACAGACGAA 59.966 55.0 0.00 0.00 0.00 3.85 F
2189 2346 0.674581 TTGAGCATGGCAGAACGGAG 60.675 55.0 0.00 0.00 0.00 4.63 F
2258 2415 0.687354 AAGTCTTCCGATGCCTGTGT 59.313 50.0 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 2020 0.377203 CGGTAATCGCCAAAGCCTTC 59.623 55.000 0.00 0.0 34.57 3.46 R
2258 2415 0.522626 CAGTGGCGCACATGAATGAA 59.477 50.000 10.83 0.0 36.74 2.57 R
2786 2945 0.040425 GTGGCGCTAGGTGTTGTTTG 60.040 55.000 7.64 0.0 0.00 2.93 R
3897 4083 2.430921 GAGTCGACACACAGGCCG 60.431 66.667 19.50 0.0 0.00 6.13 R
4032 4218 3.068560 CAACGGGTTTTGGACGAGAATA 58.931 45.455 0.00 0.0 0.00 1.75 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
35 37 4.079446 TTTTTCTGGCTGCCCGAG 57.921 55.556 17.53 8.04 0.00 4.63
135 137 0.609957 TGCACTTGGGCATGGAGAAG 60.610 55.000 0.00 0.00 39.25 2.85
182 184 6.780706 TTAAGAGAAAGACAAAACCTAGCG 57.219 37.500 0.00 0.00 0.00 4.26
188 190 7.660208 AGAGAAAGACAAAACCTAGCGAAATTA 59.340 33.333 0.00 0.00 0.00 1.40
211 213 5.208463 TGAGCATCAACACTTGTGTAGTA 57.792 39.130 6.84 0.00 45.97 1.82
214 265 5.611374 AGCATCAACACTTGTGTAGTACTT 58.389 37.500 0.00 0.00 34.56 2.24
215 266 5.466728 AGCATCAACACTTGTGTAGTACTTG 59.533 40.000 0.00 1.26 34.56 3.16
216 267 5.236478 GCATCAACACTTGTGTAGTACTTGT 59.764 40.000 0.00 0.00 34.56 3.16
217 268 6.564125 GCATCAACACTTGTGTAGTACTTGTC 60.564 42.308 0.00 0.00 34.56 3.18
218 269 5.968254 TCAACACTTGTGTAGTACTTGTCA 58.032 37.500 0.00 0.00 34.56 3.58
219 270 6.578944 TCAACACTTGTGTAGTACTTGTCAT 58.421 36.000 0.00 0.00 34.56 3.06
220 271 6.700081 TCAACACTTGTGTAGTACTTGTCATC 59.300 38.462 0.00 0.00 34.56 2.92
221 272 6.156748 ACACTTGTGTAGTACTTGTCATCA 57.843 37.500 0.00 0.00 34.56 3.07
222 273 6.578944 ACACTTGTGTAGTACTTGTCATCAA 58.421 36.000 0.00 5.75 34.56 2.57
223 274 7.045416 ACACTTGTGTAGTACTTGTCATCAAA 58.955 34.615 0.00 0.00 34.56 2.69
224 275 7.551262 ACACTTGTGTAGTACTTGTCATCAAAA 59.449 33.333 0.00 0.00 34.56 2.44
225 276 8.559536 CACTTGTGTAGTACTTGTCATCAAAAT 58.440 33.333 0.00 0.00 34.56 1.82
226 277 8.559536 ACTTGTGTAGTACTTGTCATCAAAATG 58.440 33.333 0.00 0.00 34.56 2.32
227 278 8.669946 TTGTGTAGTACTTGTCATCAAAATGA 57.330 30.769 0.00 0.00 39.63 2.57
228 279 8.669946 TGTGTAGTACTTGTCATCAAAATGAA 57.330 30.769 0.00 0.00 43.42 2.57
229 280 9.283768 TGTGTAGTACTTGTCATCAAAATGAAT 57.716 29.630 0.00 0.00 43.42 2.57
305 356 8.741101 TTCAATTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
306 357 8.105097 TCAATTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
307 358 8.020819 TCAATTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
308 359 6.869315 TTTGATGACAAGTATTTTCGGACA 57.131 33.333 0.00 0.00 37.32 4.02
309 360 6.480524 TTGATGACAAGTATTTTCGGACAG 57.519 37.500 0.00 0.00 0.00 3.51
310 361 5.789521 TGATGACAAGTATTTTCGGACAGA 58.210 37.500 0.00 0.00 0.00 3.41
311 362 5.869344 TGATGACAAGTATTTTCGGACAGAG 59.131 40.000 0.00 0.00 0.00 3.35
312 363 4.566004 TGACAAGTATTTTCGGACAGAGG 58.434 43.478 0.00 0.00 0.00 3.69
313 364 4.282449 TGACAAGTATTTTCGGACAGAGGA 59.718 41.667 0.00 0.00 0.00 3.71
314 365 5.221561 TGACAAGTATTTTCGGACAGAGGAA 60.222 40.000 0.00 0.00 0.00 3.36
315 366 5.238583 ACAAGTATTTTCGGACAGAGGAAG 58.761 41.667 0.00 0.00 0.00 3.46
316 367 5.221661 ACAAGTATTTTCGGACAGAGGAAGT 60.222 40.000 0.00 0.00 0.00 3.01
317 368 6.014840 ACAAGTATTTTCGGACAGAGGAAGTA 60.015 38.462 0.00 0.00 0.00 2.24
318 369 5.963594 AGTATTTTCGGACAGAGGAAGTAC 58.036 41.667 0.00 0.00 0.00 2.73
324 375 5.515797 TCGGACAGAGGAAGTACATATTG 57.484 43.478 0.00 0.00 0.00 1.90
336 387 9.823647 AGGAAGTACATATTGTTACTTCATCTG 57.176 33.333 20.31 0.00 46.00 2.90
367 462 9.398921 ACTCCCATAATATTCTGAAAGTAGGAT 57.601 33.333 2.54 0.00 33.76 3.24
378 473 7.113658 TCTGAAAGTAGGATTACTGCTAAGG 57.886 40.000 0.00 0.00 41.66 2.69
412 522 0.716108 GAAGCCACGTTCAGATCACG 59.284 55.000 2.79 2.79 43.52 4.35
598 715 3.334910 AATTCCCCCATCCAGAAATCC 57.665 47.619 0.00 0.00 0.00 3.01
711 843 2.158959 CGATTCGGTGCCGTGTCTC 61.159 63.158 10.60 3.20 40.74 3.36
729 862 2.370445 CCCCGAGAATCTGTGGCCT 61.370 63.158 3.32 0.00 0.00 5.19
731 864 1.617018 CCCGAGAATCTGTGGCCTGA 61.617 60.000 3.32 0.00 0.00 3.86
899 1035 3.164269 ATAGGCGCCCACCTGGAG 61.164 66.667 26.15 0.00 41.34 3.86
1399 1546 4.630894 TTCAACTTGTACTTGTTGCAGG 57.369 40.909 19.49 4.47 42.11 4.85
1549 1697 4.048504 GGTAGATTTGGTTTGTGTGCAAC 58.951 43.478 0.00 0.00 33.82 4.17
1562 1710 1.733912 TGTGCAACGAATCTGAGATGC 59.266 47.619 0.00 0.00 42.39 3.91
1571 1719 1.719529 ATCTGAGATGCTGAGAGGGG 58.280 55.000 0.00 0.00 25.67 4.79
1590 1738 4.352893 AGGGGTTTGTTAACTATGACTGGT 59.647 41.667 7.22 0.00 34.59 4.00
1604 1752 7.551585 ACTATGACTGGTAATGTTTCTGAGAG 58.448 38.462 0.00 0.00 0.00 3.20
1671 1827 7.271511 GCTCATAAAGACCCAGATATATGGAG 58.728 42.308 18.18 10.19 43.57 3.86
1700 1856 5.066505 AGTTTTCCTTTCATGTGTCAGTGTC 59.933 40.000 0.00 0.00 0.00 3.67
1763 1919 4.046286 TGGATGGTGTTTATTCTTGGCT 57.954 40.909 0.00 0.00 0.00 4.75
1864 2020 1.938577 CTTTGCATGTCCATCTCCTCG 59.061 52.381 0.00 0.00 0.00 4.63
1927 2083 0.034337 GCCACCTTACCACAGACGAA 59.966 55.000 0.00 0.00 0.00 3.85
1930 2086 2.028476 CCACCTTACCACAGACGAATCA 60.028 50.000 0.00 0.00 0.00 2.57
2037 2194 6.378564 TGTGGAAACCTGTTCAGATTTTTGTA 59.621 34.615 1.00 0.00 0.00 2.41
2082 2239 6.546428 TTTTCCTAGAACATACTCCCTCTG 57.454 41.667 0.00 0.00 0.00 3.35
2083 2240 4.883021 TCCTAGAACATACTCCCTCTGT 57.117 45.455 0.00 0.00 0.00 3.41
2084 2241 4.794334 TCCTAGAACATACTCCCTCTGTC 58.206 47.826 0.00 0.00 0.00 3.51
2085 2242 3.892588 CCTAGAACATACTCCCTCTGTCC 59.107 52.174 0.00 0.00 0.00 4.02
2086 2243 2.753247 AGAACATACTCCCTCTGTCCC 58.247 52.381 0.00 0.00 0.00 4.46
2087 2244 2.044492 AGAACATACTCCCTCTGTCCCA 59.956 50.000 0.00 0.00 0.00 4.37
2088 2245 2.166907 ACATACTCCCTCTGTCCCAG 57.833 55.000 0.00 0.00 0.00 4.45
2089 2246 1.646447 ACATACTCCCTCTGTCCCAGA 59.354 52.381 0.00 0.00 38.25 3.86
2090 2247 2.044492 ACATACTCCCTCTGTCCCAGAA 59.956 50.000 0.00 0.00 40.18 3.02
2091 2248 3.310954 ACATACTCCCTCTGTCCCAGAAT 60.311 47.826 0.00 0.00 40.18 2.40
2092 2249 4.078571 ACATACTCCCTCTGTCCCAGAATA 60.079 45.833 0.00 0.00 40.18 1.75
2093 2250 3.715648 ACTCCCTCTGTCCCAGAATAT 57.284 47.619 0.00 0.00 40.18 1.28
2094 2251 4.834406 ACTCCCTCTGTCCCAGAATATA 57.166 45.455 0.00 0.00 40.18 0.86
2095 2252 5.157770 ACTCCCTCTGTCCCAGAATATAA 57.842 43.478 0.00 0.00 40.18 0.98
2096 2253 5.151454 ACTCCCTCTGTCCCAGAATATAAG 58.849 45.833 0.00 0.00 40.18 1.73
2097 2254 5.103043 ACTCCCTCTGTCCCAGAATATAAGA 60.103 44.000 0.00 0.00 40.18 2.10
2098 2255 5.788430 TCCCTCTGTCCCAGAATATAAGAA 58.212 41.667 0.00 0.00 40.18 2.52
2099 2256 5.602978 TCCCTCTGTCCCAGAATATAAGAAC 59.397 44.000 0.00 0.00 40.18 3.01
2100 2257 5.509840 CCCTCTGTCCCAGAATATAAGAACG 60.510 48.000 0.00 0.00 40.18 3.95
2101 2258 5.069251 CCTCTGTCCCAGAATATAAGAACGT 59.931 44.000 0.00 0.00 40.18 3.99
2102 2259 6.407074 CCTCTGTCCCAGAATATAAGAACGTT 60.407 42.308 0.00 0.00 40.18 3.99
2103 2260 6.942976 TCTGTCCCAGAATATAAGAACGTTT 58.057 36.000 0.46 0.00 37.57 3.60
2104 2261 7.391620 TCTGTCCCAGAATATAAGAACGTTTT 58.608 34.615 0.46 0.00 37.57 2.43
2105 2262 7.881232 TCTGTCCCAGAATATAAGAACGTTTTT 59.119 33.333 9.22 9.22 37.57 1.94
2106 2263 7.812648 TGTCCCAGAATATAAGAACGTTTTTG 58.187 34.615 13.87 0.00 0.00 2.44
2107 2264 7.662258 TGTCCCAGAATATAAGAACGTTTTTGA 59.338 33.333 13.87 2.81 0.00 2.69
2108 2265 8.674607 GTCCCAGAATATAAGAACGTTTTTGAT 58.325 33.333 13.87 4.93 0.00 2.57
2109 2266 9.893634 TCCCAGAATATAAGAACGTTTTTGATA 57.106 29.630 13.87 8.23 0.00 2.15
2110 2267 9.931210 CCCAGAATATAAGAACGTTTTTGATAC 57.069 33.333 13.87 2.84 0.00 2.24
2119 2276 8.773404 AAGAACGTTTTTGATACTATGCTAGT 57.227 30.769 0.46 2.19 42.68 2.57
2120 2277 8.186178 AGAACGTTTTTGATACTATGCTAGTG 57.814 34.615 0.46 0.00 39.81 2.74
2121 2278 7.817962 AGAACGTTTTTGATACTATGCTAGTGT 59.182 33.333 0.46 0.61 39.81 3.55
2122 2279 7.900782 ACGTTTTTGATACTATGCTAGTGTT 57.099 32.000 6.21 0.00 39.81 3.32
2123 2280 8.991243 ACGTTTTTGATACTATGCTAGTGTTA 57.009 30.769 6.21 0.00 39.81 2.41
2124 2281 9.426837 ACGTTTTTGATACTATGCTAGTGTTAA 57.573 29.630 6.21 1.48 39.81 2.01
2130 2287 8.991243 TGATACTATGCTAGTGTTAAAAACGT 57.009 30.769 6.21 0.00 39.81 3.99
2131 2288 9.426837 TGATACTATGCTAGTGTTAAAAACGTT 57.573 29.630 0.00 0.00 39.81 3.99
2132 2289 9.897349 GATACTATGCTAGTGTTAAAAACGTTC 57.103 33.333 0.00 0.00 39.81 3.95
2133 2290 7.958053 ACTATGCTAGTGTTAAAAACGTTCT 57.042 32.000 0.00 0.00 37.69 3.01
2134 2291 8.374327 ACTATGCTAGTGTTAAAAACGTTCTT 57.626 30.769 0.00 0.00 37.69 2.52
2135 2292 9.480053 ACTATGCTAGTGTTAAAAACGTTCTTA 57.520 29.630 0.00 0.00 37.69 2.10
2149 2306 8.776376 AAAACGTTCTTATATTTTAGGACGGA 57.224 30.769 0.00 0.00 45.45 4.69
2150 2307 7.998753 AACGTTCTTATATTTTAGGACGGAG 57.001 36.000 13.99 0.00 45.45 4.63
2151 2308 6.510536 ACGTTCTTATATTTTAGGACGGAGG 58.489 40.000 13.99 0.00 45.45 4.30
2152 2309 5.924825 CGTTCTTATATTTTAGGACGGAGGG 59.075 44.000 0.00 0.00 39.22 4.30
2153 2310 6.239120 CGTTCTTATATTTTAGGACGGAGGGA 60.239 42.308 0.00 0.00 39.22 4.20
2154 2311 6.912951 TCTTATATTTTAGGACGGAGGGAG 57.087 41.667 0.00 0.00 0.00 4.30
2155 2312 6.379579 TCTTATATTTTAGGACGGAGGGAGT 58.620 40.000 0.00 0.00 0.00 3.85
2156 2313 7.529555 TCTTATATTTTAGGACGGAGGGAGTA 58.470 38.462 0.00 0.00 0.00 2.59
2157 2314 7.449704 TCTTATATTTTAGGACGGAGGGAGTAC 59.550 40.741 0.00 0.00 0.00 2.73
2158 2315 3.463048 TTTTAGGACGGAGGGAGTACT 57.537 47.619 0.00 0.00 36.60 2.73
2189 2346 0.674581 TTGAGCATGGCAGAACGGAG 60.675 55.000 0.00 0.00 0.00 4.63
2196 2353 1.112113 TGGCAGAACGGAGTATCTCC 58.888 55.000 5.79 5.79 45.00 3.71
2211 2368 5.892568 AGTATCTCCGTTGTGTCATAGTTC 58.107 41.667 0.00 0.00 0.00 3.01
2247 2404 4.553330 TTGTATGGAGGTGAAGTCTTCC 57.447 45.455 10.12 1.81 0.00 3.46
2258 2415 0.687354 AAGTCTTCCGATGCCTGTGT 59.313 50.000 0.00 0.00 0.00 3.72
2265 2422 1.003003 TCCGATGCCTGTGTTCATTCA 59.997 47.619 0.00 0.00 0.00 2.57
2270 2427 1.270274 TGCCTGTGTTCATTCATGTGC 59.730 47.619 0.00 0.00 0.00 4.57
2366 2525 0.830648 CGACAAGGCCCTATTCCTCA 59.169 55.000 0.00 0.00 32.45 3.86
2403 2562 7.495279 TGTTTTGACTTTCAATTCTTTCCCATG 59.505 33.333 0.00 0.00 36.11 3.66
2469 2628 4.225942 AGAGAATGCTGACTTGGGAATGTA 59.774 41.667 0.00 0.00 0.00 2.29
2573 2732 2.284263 TGTGCACTCTAAGAGATGCG 57.716 50.000 19.41 0.00 38.52 4.73
2575 2734 2.159324 TGTGCACTCTAAGAGATGCGAG 60.159 50.000 19.41 0.00 38.52 5.03
2595 2754 5.093457 CGAGAAAGCTCATAGTCGTAACAA 58.907 41.667 0.00 0.00 41.36 2.83
2671 2830 1.888436 TTCAGTGGCGGTGCTAGGAG 61.888 60.000 0.00 0.00 0.00 3.69
2672 2831 2.283966 AGTGGCGGTGCTAGGAGT 60.284 61.111 0.00 0.00 0.00 3.85
2796 2955 4.104776 CACTTGACATCACAAACAACACC 58.895 43.478 0.00 0.00 0.00 4.16
2801 2960 2.548057 ACATCACAAACAACACCTAGCG 59.452 45.455 0.00 0.00 0.00 4.26
2923 3094 6.595716 AGTCTTGTGATAAAACATCTAGGTGC 59.404 38.462 1.90 0.00 0.00 5.01
2938 3109 2.043227 AGGTGCATCCTAGCTTCTACC 58.957 52.381 6.10 0.00 46.10 3.18
3454 3625 6.597672 TCTTGACACTTGTAGTTTCACACATT 59.402 34.615 0.00 0.00 34.94 2.71
3897 4083 1.919918 GATTGCACGCATACAAAAGGC 59.080 47.619 0.00 0.00 0.00 4.35
3903 4089 1.139520 GCATACAAAAGGCGGCCTG 59.860 57.895 24.63 13.96 32.13 4.85
4032 4218 3.282885 GTGCCTAGCCTTTTTCATAGCT 58.717 45.455 0.00 0.00 39.37 3.32
4086 4289 3.689347 TCATTTGAACCTGGAGTCATGG 58.311 45.455 0.00 0.00 0.00 3.66
4089 4292 3.695830 TTGAACCTGGAGTCATGGTAC 57.304 47.619 0.00 0.00 33.17 3.34
4216 4419 6.253298 AGTTTCATTTGTTCGTCATTGTTGTG 59.747 34.615 0.00 0.00 0.00 3.33
4294 4497 9.141400 CCTAGTTATTTCTCAACACTTGTCTAC 57.859 37.037 0.00 0.00 0.00 2.59
4322 4527 8.706322 AAAATCACTTTGGATAAGTGTAACCT 57.294 30.769 15.04 0.00 45.75 3.50
4371 4577 0.688487 ACGAAACCGGAGATTGGGAA 59.312 50.000 9.46 0.00 0.00 3.97
4391 4597 1.073923 ACTCCAGCCTTTTGTGGGTAG 59.926 52.381 0.00 0.00 35.87 3.18
4482 4690 3.541632 AGTTTTCACATGTGTTCCTCGT 58.458 40.909 24.63 3.27 0.00 4.18
4487 4703 2.159028 TCACATGTGTTCCTCGTGTTCA 60.159 45.455 24.63 0.00 33.49 3.18
4515 4731 3.434299 AGGTAGGTTTGCGATTTTGTACG 59.566 43.478 0.00 0.00 0.00 3.67
4542 4758 4.023291 AGTGTTCTTTCCATGTTGGTGTT 58.977 39.130 0.00 0.00 39.03 3.32
4543 4759 4.466015 AGTGTTCTTTCCATGTTGGTGTTT 59.534 37.500 0.00 0.00 39.03 2.83
4561 4777 4.810491 GTGTTTGTACTTCCAGTTTCGGTA 59.190 41.667 0.00 0.00 0.00 4.02
4618 4834 1.678728 CCCACGAACATGGCAGTACAT 60.679 52.381 0.00 0.00 38.55 2.29
4651 4867 6.538021 TGTGTCACATCCCAAAATTTTCAAAG 59.462 34.615 0.18 0.00 0.00 2.77
4682 4898 8.398878 TGTGAACATGACATTCATATGCATAT 57.601 30.769 13.63 13.63 38.31 1.78
4697 4913 4.477302 TGCATATCATGATTTCAGTGCG 57.523 40.909 14.65 0.00 34.28 5.34
4745 4961 6.339587 TGGCTACTTTGGAAAACCTAATTG 57.660 37.500 0.00 0.00 0.00 2.32
4794 5010 7.218773 CACATTACGACCTCTTGCATAAAAATG 59.781 37.037 0.00 0.00 0.00 2.32
4825 5071 3.536956 ATTGCATCAATGGCTGGAAAG 57.463 42.857 0.00 0.00 32.39 2.62
4841 5087 8.632679 TGGCTGGAAAGATTTTTCATATGATAC 58.367 33.333 6.17 0.00 43.62 2.24
4843 5089 9.455847 GCTGGAAAGATTTTTCATATGATACAC 57.544 33.333 6.17 0.00 43.62 2.90
4907 5153 7.965718 AGAAATTGAACTGGAATGAATTTGGA 58.034 30.769 0.00 0.00 0.00 3.53
4930 5176 7.038160 TGGACCAATTCAAATTCAATTCCAGAT 60.038 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 2.034066 CCTCGGGCAGCCAGAAAA 59.966 61.111 15.79 0.00 0.00 2.29
20 22 2.351924 AAACCTCGGGCAGCCAGAAA 62.352 55.000 15.79 0.00 0.00 2.52
21 23 1.485294 TAAACCTCGGGCAGCCAGAA 61.485 55.000 15.79 0.00 0.00 3.02
22 24 1.899437 CTAAACCTCGGGCAGCCAGA 61.899 60.000 15.19 14.66 0.00 3.86
61 63 8.506168 TTAATAAAGCCTAGAGGATTGTTGTG 57.494 34.615 0.00 0.00 44.03 3.33
62 64 9.343539 GATTAATAAAGCCTAGAGGATTGTTGT 57.656 33.333 0.00 0.00 44.03 3.32
63 65 9.342308 TGATTAATAAAGCCTAGAGGATTGTTG 57.658 33.333 0.00 0.00 44.03 3.33
103 105 5.764686 TGCCCAAGTGCAAATAGTATATCTG 59.235 40.000 0.00 0.00 38.56 2.90
106 108 5.477984 CCATGCCCAAGTGCAAATAGTATAT 59.522 40.000 0.00 0.00 45.84 0.86
107 109 4.826733 CCATGCCCAAGTGCAAATAGTATA 59.173 41.667 0.00 0.00 45.84 1.47
108 110 3.638160 CCATGCCCAAGTGCAAATAGTAT 59.362 43.478 0.00 0.00 45.84 2.12
109 111 3.023119 CCATGCCCAAGTGCAAATAGTA 58.977 45.455 0.00 0.00 45.84 1.82
110 112 1.826720 CCATGCCCAAGTGCAAATAGT 59.173 47.619 0.00 0.00 45.84 2.12
111 113 2.100252 CTCCATGCCCAAGTGCAAATAG 59.900 50.000 0.00 0.00 45.84 1.73
135 137 1.647084 GTCGTCACTTGTGGTTGGC 59.353 57.895 0.64 0.00 0.00 4.52
182 184 7.086376 ACACAAGTGTTGATGCTCATAATTTC 58.914 34.615 0.00 0.00 41.83 2.17
188 190 4.645535 ACTACACAAGTGTTGATGCTCAT 58.354 39.130 18.86 0.00 41.83 2.90
201 203 8.773645 TCATTTTGATGACAAGTACTACACAAG 58.226 33.333 0.00 0.00 37.32 3.16
279 330 9.357652 CCGAAAATACTTGTCATCAAATTGAAT 57.642 29.630 0.00 0.00 32.87 2.57
280 331 8.572185 TCCGAAAATACTTGTCATCAAATTGAA 58.428 29.630 0.00 0.00 32.87 2.69
281 332 8.020819 GTCCGAAAATACTTGTCATCAAATTGA 58.979 33.333 0.00 0.00 32.87 2.57
282 333 7.807433 TGTCCGAAAATACTTGTCATCAAATTG 59.193 33.333 0.00 0.00 32.87 2.32
283 334 7.881142 TGTCCGAAAATACTTGTCATCAAATT 58.119 30.769 0.00 0.00 32.87 1.82
284 335 7.390440 TCTGTCCGAAAATACTTGTCATCAAAT 59.610 33.333 0.00 0.00 32.87 2.32
285 336 6.708502 TCTGTCCGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
286 337 6.227522 TCTGTCCGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
287 338 5.789521 TCTGTCCGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
288 339 5.292101 CCTCTGTCCGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
289 340 5.046591 TCCTCTGTCCGAAAATACTTGTCAT 60.047 40.000 0.00 0.00 0.00 3.06
290 341 4.282449 TCCTCTGTCCGAAAATACTTGTCA 59.718 41.667 0.00 0.00 0.00 3.58
291 342 4.817517 TCCTCTGTCCGAAAATACTTGTC 58.182 43.478 0.00 0.00 0.00 3.18
292 343 4.884668 TCCTCTGTCCGAAAATACTTGT 57.115 40.909 0.00 0.00 0.00 3.16
293 344 5.238583 ACTTCCTCTGTCCGAAAATACTTG 58.761 41.667 0.00 0.00 0.00 3.16
294 345 5.485209 ACTTCCTCTGTCCGAAAATACTT 57.515 39.130 0.00 0.00 0.00 2.24
295 346 5.479375 TGTACTTCCTCTGTCCGAAAATACT 59.521 40.000 0.00 0.00 0.00 2.12
296 347 5.717119 TGTACTTCCTCTGTCCGAAAATAC 58.283 41.667 0.00 0.00 0.00 1.89
297 348 5.988310 TGTACTTCCTCTGTCCGAAAATA 57.012 39.130 0.00 0.00 0.00 1.40
298 349 4.884668 TGTACTTCCTCTGTCCGAAAAT 57.115 40.909 0.00 0.00 0.00 1.82
299 350 4.884668 ATGTACTTCCTCTGTCCGAAAA 57.115 40.909 0.00 0.00 0.00 2.29
300 351 6.070995 ACAATATGTACTTCCTCTGTCCGAAA 60.071 38.462 0.00 0.00 0.00 3.46
301 352 5.421056 ACAATATGTACTTCCTCTGTCCGAA 59.579 40.000 0.00 0.00 0.00 4.30
302 353 4.954202 ACAATATGTACTTCCTCTGTCCGA 59.046 41.667 0.00 0.00 0.00 4.55
303 354 5.263968 ACAATATGTACTTCCTCTGTCCG 57.736 43.478 0.00 0.00 0.00 4.79
304 355 7.783042 AGTAACAATATGTACTTCCTCTGTCC 58.217 38.462 0.00 0.00 0.00 4.02
305 356 9.303537 GAAGTAACAATATGTACTTCCTCTGTC 57.696 37.037 16.39 0.45 41.29 3.51
306 357 8.812972 TGAAGTAACAATATGTACTTCCTCTGT 58.187 33.333 20.68 0.00 44.52 3.41
307 358 9.823647 ATGAAGTAACAATATGTACTTCCTCTG 57.176 33.333 20.68 0.00 44.52 3.35
310 361 9.823647 CAGATGAAGTAACAATATGTACTTCCT 57.176 33.333 20.68 15.39 44.52 3.36
311 362 9.817809 TCAGATGAAGTAACAATATGTACTTCC 57.182 33.333 20.68 12.47 44.52 3.46
367 462 3.117398 TCGGGGATAGTCCTTAGCAGTAA 60.117 47.826 0.00 0.00 36.57 2.24
375 470 0.549950 TCGAGTCGGGGATAGTCCTT 59.450 55.000 13.54 0.00 36.57 3.36
376 471 0.549950 TTCGAGTCGGGGATAGTCCT 59.450 55.000 13.54 0.00 36.57 3.85
378 473 0.311477 GCTTCGAGTCGGGGATAGTC 59.689 60.000 13.54 0.00 0.00 2.59
412 522 8.483758 TGTTTATCTATTGGAGAAGGTAGGTTC 58.516 37.037 0.00 0.00 37.85 3.62
711 843 2.190578 GGCCACAGATTCTCGGGG 59.809 66.667 0.00 2.21 0.00 5.73
729 862 2.435938 GCGACCAAATCCGCCTCA 60.436 61.111 0.00 0.00 45.06 3.86
735 868 0.526211 GGAACTTGGCGACCAAATCC 59.474 55.000 18.45 18.45 43.44 3.01
831 967 2.174319 GCTTCGGATCAGCGAACCC 61.174 63.158 3.10 0.00 0.00 4.11
899 1035 2.825836 CGTCAGCCCTCAATGCCC 60.826 66.667 0.00 0.00 0.00 5.36
1399 1546 2.100605 AGCAAGCTGTACTAGTTGGC 57.899 50.000 0.00 3.46 0.00 4.52
1549 1697 2.288334 CCCTCTCAGCATCTCAGATTCG 60.288 54.545 0.00 0.00 0.00 3.34
1562 1710 5.875359 GTCATAGTTAACAAACCCCTCTCAG 59.125 44.000 8.61 0.00 0.00 3.35
1604 1752 6.476706 GCAACCAAGCAATCCATAATCTAAAC 59.523 38.462 0.00 0.00 0.00 2.01
1671 1827 5.008613 TGACACATGAAAGGAAAACTACTGC 59.991 40.000 0.00 0.00 0.00 4.40
1700 1856 7.229506 ACAAAGAAGGAAAACAGAGACCAATAG 59.770 37.037 0.00 0.00 0.00 1.73
1864 2020 0.377203 CGGTAATCGCCAAAGCCTTC 59.623 55.000 0.00 0.00 34.57 3.46
1885 2041 1.655597 CAATACCGCCGATCATCGATG 59.344 52.381 19.61 19.61 43.74 3.84
2081 2238 7.662258 TCAAAAACGTTCTTATATTCTGGGACA 59.338 33.333 0.00 0.00 0.00 4.02
2082 2239 8.036273 TCAAAAACGTTCTTATATTCTGGGAC 57.964 34.615 0.00 0.00 0.00 4.46
2083 2240 8.801882 ATCAAAAACGTTCTTATATTCTGGGA 57.198 30.769 0.00 0.00 0.00 4.37
2084 2241 9.931210 GTATCAAAAACGTTCTTATATTCTGGG 57.069 33.333 0.00 0.00 0.00 4.45
2123 2280 9.218440 TCCGTCCTAAAATATAAGAACGTTTTT 57.782 29.630 9.22 9.22 0.00 1.94
2124 2281 8.776376 TCCGTCCTAAAATATAAGAACGTTTT 57.224 30.769 0.46 0.00 0.00 2.43
2125 2282 7.493645 CCTCCGTCCTAAAATATAAGAACGTTT 59.506 37.037 0.46 0.00 0.00 3.60
2126 2283 6.982724 CCTCCGTCCTAAAATATAAGAACGTT 59.017 38.462 0.00 0.00 0.00 3.99
2127 2284 6.462067 CCCTCCGTCCTAAAATATAAGAACGT 60.462 42.308 0.00 0.00 0.00 3.99
2128 2285 5.924825 CCCTCCGTCCTAAAATATAAGAACG 59.075 44.000 0.00 0.00 0.00 3.95
2129 2286 7.059202 TCCCTCCGTCCTAAAATATAAGAAC 57.941 40.000 0.00 0.00 0.00 3.01
2130 2287 6.842807 ACTCCCTCCGTCCTAAAATATAAGAA 59.157 38.462 0.00 0.00 0.00 2.52
2131 2288 6.379579 ACTCCCTCCGTCCTAAAATATAAGA 58.620 40.000 0.00 0.00 0.00 2.10
2132 2289 6.667558 ACTCCCTCCGTCCTAAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2133 2290 7.300658 AGTACTCCCTCCGTCCTAAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2134 2291 6.856757 AGTACTCCCTCCGTCCTAAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2135 2292 5.713807 AGTACTCCCTCCGTCCTAAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2136 2293 5.134725 AGTACTCCCTCCGTCCTAAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2137 2294 3.991683 AGTACTCCCTCCGTCCTAAAAT 58.008 45.455 0.00 0.00 0.00 1.82
2138 2295 3.463048 AGTACTCCCTCCGTCCTAAAA 57.537 47.619 0.00 0.00 0.00 1.52
2139 2296 3.266772 TGTAGTACTCCCTCCGTCCTAAA 59.733 47.826 0.00 0.00 0.00 1.85
2140 2297 2.846206 TGTAGTACTCCCTCCGTCCTAA 59.154 50.000 0.00 0.00 0.00 2.69
2141 2298 2.481441 TGTAGTACTCCCTCCGTCCTA 58.519 52.381 0.00 0.00 0.00 2.94
2142 2299 1.293062 TGTAGTACTCCCTCCGTCCT 58.707 55.000 0.00 0.00 0.00 3.85
2143 2300 2.361643 ATGTAGTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
2144 2301 2.813172 GCTATGTAGTACTCCCTCCGTC 59.187 54.545 0.00 0.00 0.00 4.79
2145 2302 2.174210 TGCTATGTAGTACTCCCTCCGT 59.826 50.000 0.00 0.00 0.00 4.69
2146 2303 2.860009 TGCTATGTAGTACTCCCTCCG 58.140 52.381 0.00 0.00 0.00 4.63
2147 2304 5.810080 ATTTGCTATGTAGTACTCCCTCC 57.190 43.478 0.00 0.00 0.00 4.30
2148 2305 7.272978 TCAAATTTGCTATGTAGTACTCCCTC 58.727 38.462 13.54 0.00 0.00 4.30
2149 2306 7.195374 TCAAATTTGCTATGTAGTACTCCCT 57.805 36.000 13.54 0.00 0.00 4.20
2150 2307 6.017852 GCTCAAATTTGCTATGTAGTACTCCC 60.018 42.308 13.54 0.00 0.00 4.30
2151 2308 6.538742 TGCTCAAATTTGCTATGTAGTACTCC 59.461 38.462 13.54 0.00 0.00 3.85
2152 2309 7.539712 TGCTCAAATTTGCTATGTAGTACTC 57.460 36.000 13.54 0.00 0.00 2.59
2153 2310 7.012704 CCATGCTCAAATTTGCTATGTAGTACT 59.987 37.037 13.54 0.00 0.00 2.73
2154 2311 7.134815 CCATGCTCAAATTTGCTATGTAGTAC 58.865 38.462 13.54 0.00 0.00 2.73
2155 2312 6.238731 GCCATGCTCAAATTTGCTATGTAGTA 60.239 38.462 13.54 4.61 0.00 1.82
2156 2313 5.450965 GCCATGCTCAAATTTGCTATGTAGT 60.451 40.000 13.54 0.00 0.00 2.73
2157 2314 4.980434 GCCATGCTCAAATTTGCTATGTAG 59.020 41.667 13.54 5.70 0.00 2.74
2158 2315 4.401837 TGCCATGCTCAAATTTGCTATGTA 59.598 37.500 13.54 3.90 0.00 2.29
2189 2346 5.892568 AGAACTATGACACAACGGAGATAC 58.107 41.667 0.00 0.00 0.00 2.24
2196 2353 8.018677 ACATTTTAGAGAACTATGACACAACG 57.981 34.615 0.00 0.00 0.00 4.10
2211 2368 8.432805 ACCTCCATACAATAGGACATTTTAGAG 58.567 37.037 0.00 0.00 34.34 2.43
2247 2404 2.421073 ACATGAATGAACACAGGCATCG 59.579 45.455 0.00 0.00 0.00 3.84
2258 2415 0.522626 CAGTGGCGCACATGAATGAA 59.477 50.000 10.83 0.00 36.74 2.57
2265 2422 2.279741 CAACTATACAGTGGCGCACAT 58.720 47.619 10.83 1.10 36.74 3.21
2270 2427 4.049186 GTCATACCAACTATACAGTGGCG 58.951 47.826 0.00 0.00 34.36 5.69
2403 2562 3.550437 ACTCTGATGCACCTTATGGTC 57.450 47.619 0.00 0.00 46.60 4.02
2469 2628 4.735369 TCAACCACCAAGACATACCAATT 58.265 39.130 0.00 0.00 0.00 2.32
2573 2732 6.323266 TCTTGTTACGACTATGAGCTTTCTC 58.677 40.000 0.00 0.00 39.78 2.87
2575 2734 5.004916 GCTCTTGTTACGACTATGAGCTTTC 59.995 44.000 0.00 0.00 38.60 2.62
2595 2754 6.059787 ACCTTTATCACAGAAATGAGCTCT 57.940 37.500 16.19 0.00 30.46 4.09
2671 2830 4.378874 GCTTTGACATCACTAGCTTCCAAC 60.379 45.833 0.00 0.00 33.47 3.77
2672 2831 3.753272 GCTTTGACATCACTAGCTTCCAA 59.247 43.478 0.00 0.00 33.47 3.53
2786 2945 0.040425 GTGGCGCTAGGTGTTGTTTG 60.040 55.000 7.64 0.00 0.00 2.93
2796 2955 0.391661 ATGACAAGTGGTGGCGCTAG 60.392 55.000 7.64 0.00 38.59 3.42
2801 2960 1.620822 AAGGAATGACAAGTGGTGGC 58.379 50.000 0.00 0.00 34.82 5.01
2923 3094 2.683768 ACCAGGGTAGAAGCTAGGATG 58.316 52.381 0.00 0.00 0.00 3.51
3897 4083 2.430921 GAGTCGACACACAGGCCG 60.431 66.667 19.50 0.00 0.00 6.13
3903 4089 4.795970 AATGAAAACAGAGTCGACACAC 57.204 40.909 19.50 8.73 0.00 3.82
4032 4218 3.068560 CAACGGGTTTTGGACGAGAATA 58.931 45.455 0.00 0.00 0.00 1.75
4371 4577 1.073923 CTACCCACAAAAGGCTGGAGT 59.926 52.381 0.00 0.00 0.00 3.85
4378 4584 5.301805 ACACAAAGAATCTACCCACAAAAGG 59.698 40.000 0.00 0.00 0.00 3.11
4482 4690 4.273969 CGCAAACCTACCTAGTTTTGAACA 59.726 41.667 6.55 0.00 37.75 3.18
4487 4703 6.040054 ACAAAATCGCAAACCTACCTAGTTTT 59.960 34.615 0.00 0.00 35.28 2.43
4504 4720 3.247563 ACACTTGCACGTACAAAATCG 57.752 42.857 2.29 0.00 0.00 3.34
4515 4731 3.715628 ACATGGAAAGAACACTTGCAC 57.284 42.857 0.00 0.00 0.00 4.57
4542 4758 4.487948 CGATACCGAAACTGGAAGTACAA 58.512 43.478 0.00 0.00 43.00 2.41
4543 4759 3.674138 GCGATACCGAAACTGGAAGTACA 60.674 47.826 0.00 0.00 43.00 2.90
4561 4777 5.220854 GCTAACATAAATTGACACAGGCGAT 60.221 40.000 0.00 0.00 0.00 4.58
4618 4834 2.039613 TGGGATGTGACACAAGTGCATA 59.960 45.455 13.23 0.00 0.00 3.14
4651 4867 4.930963 TGAATGTCATGTTCACAACCAAC 58.069 39.130 0.00 0.00 31.07 3.77
4682 4898 3.567585 TCCAAAACGCACTGAAATCATGA 59.432 39.130 0.00 0.00 0.00 3.07
4775 4991 7.009540 GGAAATTCATTTTTATGCAAGAGGTCG 59.990 37.037 0.00 0.00 0.00 4.79
4794 5010 6.031471 GCCATTGATGCAATTTTGGAAATTC 58.969 36.000 11.90 0.00 31.05 2.17
4815 5031 7.664552 ATCATATGAAAAATCTTTCCAGCCA 57.335 32.000 9.99 0.00 40.31 4.75
4825 5071 7.072030 GGCTCACGTGTATCATATGAAAAATC 58.928 38.462 16.51 0.00 0.00 2.17
4841 5087 1.148310 CAAACACTAGGGCTCACGTG 58.852 55.000 9.94 9.94 0.00 4.49
4843 5089 1.878953 AACAAACACTAGGGCTCACG 58.121 50.000 0.00 0.00 0.00 4.35
4907 5153 9.039165 ACTATCTGGAATTGAATTTGAATTGGT 57.961 29.630 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.