Multiple sequence alignment - TraesCS5B01G552500

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 TraesCS5B01G552500 chr5B 100.000 2348 0 0 1 2348 703253330 703255677 0.000000e+00 4337.0
1 TraesCS5B01G552500 chrUn 91.316 2326 144 27 1 2276 19256551 19254234 0.000000e+00 3123.0
2 TraesCS5B01G552500 chrUn 90.382 2329 163 32 1 2276 250751158 250753478 0.000000e+00 3003.0
3 TraesCS5B01G552500 chrUn 90.382 2329 163 32 1 2276 258530552 258528232 0.000000e+00 3003.0
4 TraesCS5B01G552500 chr5A 90.976 2327 151 29 1 2276 674162609 674160291 0.000000e+00 3079.0
5 TraesCS5B01G552500 chr4B 90.757 2326 157 28 1 2276 566961079 566963396 0.000000e+00 3051.0
6 TraesCS5B01G552500 chr2D 90.757 2326 154 25 1 2276 485032072 485034386 0.000000e+00 3048.0
7 TraesCS5B01G552500 chr2B 91.403 2210 157 19 1 2184 200529041 200531243 0.000000e+00 2998.0
8 TraesCS5B01G552500 chr2B 82.432 74 5 4 2199 2264 200531276 200531349 9.060000e-05 58.4
9 TraesCS5B01G552500 chr7A 90.444 2208 176 18 4 2187 156239420 156237224 0.000000e+00 2876.0
10 TraesCS5B01G552500 chr2A 89.901 2020 169 16 112 2109 579874173 579872167 0.000000e+00 2567.0
11 TraesCS5B01G552500 chr7B 90.103 970 60 19 1338 2276 570909326 570908362 0.000000e+00 1227.0
12 TraesCS5B01G552500 chr1B 90.319 878 65 9 1 858 49860039 49859162 0.000000e+00 1133.0
13 TraesCS5B01G552500 chr1D 91.453 117 5 2 2152 2266 46322730 46322617 3.120000e-34 156.0


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 TraesCS5B01G552500 chr5B 703253330 703255677 2347 False 4337.0 4337 100.0000 1 2348 1 chr5B.!!$F1 2347
1 TraesCS5B01G552500 chrUn 19254234 19256551 2317 True 3123.0 3123 91.3160 1 2276 1 chrUn.!!$R1 2275
2 TraesCS5B01G552500 chrUn 250751158 250753478 2320 False 3003.0 3003 90.3820 1 2276 1 chrUn.!!$F1 2275
3 TraesCS5B01G552500 chrUn 258528232 258530552 2320 True 3003.0 3003 90.3820 1 2276 1 chrUn.!!$R2 2275
4 TraesCS5B01G552500 chr5A 674160291 674162609 2318 True 3079.0 3079 90.9760 1 2276 1 chr5A.!!$R1 2275
5 TraesCS5B01G552500 chr4B 566961079 566963396 2317 False 3051.0 3051 90.7570 1 2276 1 chr4B.!!$F1 2275
6 TraesCS5B01G552500 chr2D 485032072 485034386 2314 False 3048.0 3048 90.7570 1 2276 1 chr2D.!!$F1 2275
7 TraesCS5B01G552500 chr2B 200529041 200531349 2308 False 1528.2 2998 86.9175 1 2264 2 chr2B.!!$F1 2263
8 TraesCS5B01G552500 chr7A 156237224 156239420 2196 True 2876.0 2876 90.4440 4 2187 1 chr7A.!!$R1 2183
9 TraesCS5B01G552500 chr2A 579872167 579874173 2006 True 2567.0 2567 89.9010 112 2109 1 chr2A.!!$R1 1997
10 TraesCS5B01G552500 chr7B 570908362 570909326 964 True 1227.0 1227 90.1030 1338 2276 1 chr7B.!!$R1 938
11 TraesCS5B01G552500 chr1B 49859162 49860039 877 True 1133.0 1133 90.3190 1 858 1 chr1B.!!$R1 857

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
26 27 0.832135 AGAGGTGGTTGCCGAGAGAA 60.832 55.000 0.00 0.0 0.00 2.87 F
988 1012 1.064758 TCCGGCTATGGCAGAAATGTT 60.065 47.619 2.58 0.0 40.87 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1258 1284 0.457851 GCCAGCTCATAGTCGTCAGT 59.542 55.000 0.0 0.0 0.0 3.41 R
2035 2063 1.205655 TCAGCCCTCAACTCTTCATCG 59.794 52.381 0.0 0.0 0.0 3.84 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
26 27 0.832135 AGAGGTGGTTGCCGAGAGAA 60.832 55.000 0.00 0.00 0.00 2.87
92 93 8.424133 ACAAGAAGACAAAGGAGCAAAAATATT 58.576 29.630 0.00 0.00 0.00 1.28
206 209 4.423625 AGGGCAGTATGGTTCTGATTAC 57.576 45.455 0.00 0.00 35.86 1.89
260 268 4.217118 GCTTGAGAAGGCAAAGATCAAGAA 59.783 41.667 15.38 0.00 46.22 2.52
270 278 4.906437 GCAAAGATCAAGAACGACAACTTC 59.094 41.667 0.00 0.00 0.00 3.01
303 311 5.517770 GCATGAAGTTGCATGGAAAGAATAC 59.482 40.000 0.00 0.00 44.47 1.89
308 316 4.522789 AGTTGCATGGAAAGAATACGGTTT 59.477 37.500 0.00 0.00 0.00 3.27
333 341 1.208776 CTCATGTCAGATGGCTGGACA 59.791 52.381 0.00 0.00 42.53 4.02
335 343 1.065636 CATGTCAGATGGCTGGACAGT 60.066 52.381 0.82 0.00 42.53 3.55
342 350 2.450992 TGGCTGGACAGTCATGACA 58.549 52.632 27.02 5.71 38.26 3.58
374 382 5.869888 ACTTGATCAACTTCCTCGTCAATAC 59.130 40.000 3.38 0.00 0.00 1.89
418 426 3.330701 AGGGACAGCCAATGTTTCTTCTA 59.669 43.478 0.00 0.00 44.17 2.10
422 430 6.152379 GGACAGCCAATGTTTCTTCTAAAAG 58.848 40.000 0.00 0.00 44.17 2.27
444 464 2.954318 AGTTGATGCAAAGCTGTTGAGT 59.046 40.909 11.34 1.26 0.00 3.41
457 477 5.766222 AGCTGTTGAGTGAACAAATTGATC 58.234 37.500 0.00 0.00 44.14 2.92
475 495 4.095211 TGATCCAATTGGCCTTGAATTGA 58.905 39.130 22.38 12.36 41.44 2.57
482 502 4.591321 TTGGCCTTGAATTGATAGTCCT 57.409 40.909 3.32 0.00 0.00 3.85
493 513 8.762481 TGAATTGATAGTCCTAGTAGTTAGCA 57.238 34.615 0.00 0.00 0.00 3.49
549 569 9.495382 AGACTTCTAATGGAAAAGTATCCTACT 57.505 33.333 0.00 0.00 40.35 2.57
623 643 6.537355 ACATCAGGAAGATCAAAGAGTTCAA 58.463 36.000 0.00 0.00 33.72 2.69
625 645 6.179906 TCAGGAAGATCAAAGAGTTCAACT 57.820 37.500 0.00 0.00 0.00 3.16
742 763 2.035442 GGCCTGGAGCAACTCGTTC 61.035 63.158 0.00 0.00 46.50 3.95
769 790 4.415596 ACATCATTCCTTACTTTGGCCAA 58.584 39.130 16.05 16.05 0.00 4.52
798 821 4.024641 GGAAGCAAAGCCAAACATTGAAAG 60.025 41.667 0.00 0.00 0.00 2.62
852 876 6.068473 ACAAATTAAAGGACAACGAAGGAC 57.932 37.500 0.00 0.00 0.00 3.85
918 942 1.676916 CGGTGGAGTGTTGCATGAGAT 60.677 52.381 0.00 0.00 0.00 2.75
926 950 4.001652 AGTGTTGCATGAGATCTTCACAG 58.998 43.478 0.00 0.00 38.99 3.66
946 970 4.260170 CAGCCACTTCTTAGAGCTTTGAT 58.740 43.478 0.00 0.00 34.04 2.57
988 1012 1.064758 TCCGGCTATGGCAGAAATGTT 60.065 47.619 2.58 0.00 40.87 2.71
1039 1065 7.665559 ACATAAAGGAAGCTTTGACACATAAGA 59.334 33.333 0.00 0.00 0.00 2.10
1073 1099 3.689649 GGTCAAGTGGTAGCTATTGTTGG 59.310 47.826 0.00 0.00 0.00 3.77
1074 1100 4.564821 GGTCAAGTGGTAGCTATTGTTGGA 60.565 45.833 0.00 0.00 0.00 3.53
1157 1183 9.942850 CCCAAATAAATTCTTTGTCATTAAGGT 57.057 29.630 10.73 0.00 32.83 3.50
1199 1225 1.726791 CCGTCTCCGTTCAATGTTCAG 59.273 52.381 0.00 0.00 0.00 3.02
1202 1228 2.480419 GTCTCCGTTCAATGTTCAGTGG 59.520 50.000 0.63 0.00 0.00 4.00
1222 1248 2.356125 GGTGTGCTATGGAAGATGGTGT 60.356 50.000 0.00 0.00 0.00 4.16
1258 1284 7.722285 AGCAACAAACAACTATAAGTAGGGAAA 59.278 33.333 0.00 0.00 31.96 3.13
1299 1325 3.002862 CGGAAGGTGAATGTTTGTCGAAA 59.997 43.478 0.00 0.00 0.00 3.46
1351 1377 2.932261 AGCCCCCGTCAGAATAAATTC 58.068 47.619 0.00 0.00 37.06 2.17
1367 1393 9.461312 AGAATAAATTCTATGGCAACTTGTGTA 57.539 29.630 3.36 0.00 44.80 2.90
1405 1431 7.881142 TCAATTACTCCACTAATTGTTGGTTG 58.119 34.615 10.12 4.80 41.74 3.77
1436 1462 5.335976 CCTTCTCTTTAATGTTGGACTTGCC 60.336 44.000 0.00 0.00 37.10 4.52
1503 1529 2.952310 GACCTCCAAACTCTTGCAAAGT 59.048 45.455 0.00 4.56 46.34 2.66
1529 1555 6.834959 ATCATTAGTCTATGTTGTTCAGCG 57.165 37.500 0.00 0.00 0.00 5.18
1533 1559 2.299013 AGTCTATGTTGTTCAGCGTCCA 59.701 45.455 0.00 0.00 0.00 4.02
1610 1638 5.125417 TGGTTTGATAGGCTAATTTCAGCAC 59.875 40.000 0.00 0.00 43.67 4.40
1612 1640 3.466836 TGATAGGCTAATTTCAGCACCG 58.533 45.455 0.00 0.00 43.67 4.94
1618 1646 2.742053 GCTAATTTCAGCACCGTCTCAA 59.258 45.455 0.00 0.00 41.40 3.02
1619 1647 3.375299 GCTAATTTCAGCACCGTCTCAAT 59.625 43.478 0.00 0.00 41.40 2.57
1644 1672 0.520404 GTGTGCTTGCAGATCCACAG 59.480 55.000 9.93 0.00 38.70 3.66
1709 1737 2.359848 TCATATGTCTCGTACAACCGGG 59.640 50.000 6.32 0.00 42.70 5.73
1729 1757 4.086457 GGGAAATGGAAGCTAGGTTTCAA 58.914 43.478 19.19 3.90 32.04 2.69
1738 1766 2.162408 AGCTAGGTTTCAAAATCTGCGC 59.838 45.455 0.00 0.00 32.31 6.09
1790 1818 7.929941 AATCCACTTGTCCTAGAAGAATTTC 57.070 36.000 0.00 0.00 0.00 2.17
1792 1820 6.467677 TCCACTTGTCCTAGAAGAATTTCAG 58.532 40.000 0.00 0.00 35.70 3.02
1794 1822 7.234782 TCCACTTGTCCTAGAAGAATTTCAGTA 59.765 37.037 0.00 0.00 35.70 2.74
1826 1854 6.040054 TGAATGGGTTGATATCAATGCTGAAG 59.960 38.462 20.65 0.00 38.24 3.02
1858 1886 4.774660 AGATCAAGCTCAAGTCATGGAT 57.225 40.909 0.00 0.00 0.00 3.41
2035 2063 0.249031 GAACAAGGCTGGTTGTGCAC 60.249 55.000 13.07 10.75 39.82 4.57
2109 2137 3.464907 AGAGCAATGATGAAGACGATGG 58.535 45.455 0.00 0.00 0.00 3.51
2110 2138 1.945394 AGCAATGATGAAGACGATGGC 59.055 47.619 0.00 0.00 0.00 4.40
2113 2141 2.804527 CAATGATGAAGACGATGGCGAT 59.195 45.455 0.00 0.00 41.64 4.58
2114 2142 1.856802 TGATGAAGACGATGGCGATG 58.143 50.000 0.00 0.00 41.64 3.84
2115 2143 1.408702 TGATGAAGACGATGGCGATGA 59.591 47.619 0.00 0.00 41.64 2.92
2116 2144 2.036346 TGATGAAGACGATGGCGATGAT 59.964 45.455 0.00 0.00 41.64 2.45
2138 2166 3.176411 TCACCAGATGATGAAGACACCT 58.824 45.455 0.00 0.00 29.99 4.00
2146 2174 7.201679 CCAGATGATGAAGACACCTATTTTCAC 60.202 40.741 0.00 0.00 32.90 3.18
2161 2189 6.434028 CCTATTTTCACCTTGAAGACATGGAA 59.566 38.462 0.00 0.00 41.88 3.53
2164 2192 4.008074 TCACCTTGAAGACATGGAACTC 57.992 45.455 0.00 0.00 41.88 3.01
2184 2214 2.421073 TCGGCTTGATTGCTTGAAGATG 59.579 45.455 0.00 0.00 0.00 2.90
2187 2217 3.057033 GGCTTGATTGCTTGAAGATGTGT 60.057 43.478 0.00 0.00 0.00 3.72
2188 2218 4.553323 GCTTGATTGCTTGAAGATGTGTT 58.447 39.130 0.00 0.00 0.00 3.32
2189 2219 4.620184 GCTTGATTGCTTGAAGATGTGTTC 59.380 41.667 0.00 0.00 0.00 3.18
2192 2222 5.765176 TGATTGCTTGAAGATGTGTTCTTG 58.235 37.500 0.00 0.00 44.88 3.02
2194 2224 5.581126 TTGCTTGAAGATGTGTTCTTGTT 57.419 34.783 0.00 0.00 44.88 2.83
2195 2225 5.581126 TGCTTGAAGATGTGTTCTTGTTT 57.419 34.783 0.00 0.00 44.88 2.83
2196 2226 5.581605 TGCTTGAAGATGTGTTCTTGTTTC 58.418 37.500 0.00 0.00 44.88 2.78
2197 2227 5.357878 TGCTTGAAGATGTGTTCTTGTTTCT 59.642 36.000 0.00 0.00 44.88 2.52
2231 2287 4.592485 TGTTTTGGTGTTGAAGTGTTGT 57.408 36.364 0.00 0.00 0.00 3.32
2250 2306 9.893305 AGTGTTGTACTTATTTACTTGCATTTC 57.107 29.630 0.00 0.00 35.67 2.17
2264 2320 3.591023 TGCATTTCAATCTGGTTGCATG 58.409 40.909 0.00 2.49 37.74 4.06
2267 2323 5.170021 GCATTTCAATCTGGTTGCATGTAA 58.830 37.500 11.79 0.00 37.74 2.41
2268 2324 5.062558 GCATTTCAATCTGGTTGCATGTAAC 59.937 40.000 17.37 17.37 37.74 2.50
2270 2326 6.403866 TTTCAATCTGGTTGCATGTAACTT 57.596 33.333 23.33 9.37 37.74 2.66
2273 2329 7.701539 TCAATCTGGTTGCATGTAACTTATT 57.298 32.000 23.33 16.97 37.74 1.40
2274 2330 7.537715 TCAATCTGGTTGCATGTAACTTATTG 58.462 34.615 23.33 24.33 37.74 1.90
2275 2331 7.176515 TCAATCTGGTTGCATGTAACTTATTGT 59.823 33.333 26.96 12.37 37.74 2.71
2276 2332 6.892658 TCTGGTTGCATGTAACTTATTGTT 57.107 33.333 23.33 0.00 42.31 2.83
2277 2333 6.676950 TCTGGTTGCATGTAACTTATTGTTG 58.323 36.000 23.33 7.64 39.55 3.33
2278 2334 5.777802 TGGTTGCATGTAACTTATTGTTGG 58.222 37.500 23.33 0.00 39.55 3.77
2279 2335 5.536538 TGGTTGCATGTAACTTATTGTTGGA 59.463 36.000 23.33 0.00 39.55 3.53
2280 2336 5.861787 GGTTGCATGTAACTTATTGTTGGAC 59.138 40.000 23.33 1.75 39.55 4.02
2281 2337 5.637006 TGCATGTAACTTATTGTTGGACC 57.363 39.130 0.00 0.00 39.55 4.46
2282 2338 5.321102 TGCATGTAACTTATTGTTGGACCT 58.679 37.500 0.00 0.00 39.55 3.85
2283 2339 6.477253 TGCATGTAACTTATTGTTGGACCTA 58.523 36.000 0.00 0.00 39.55 3.08
2284 2340 7.116075 TGCATGTAACTTATTGTTGGACCTAT 58.884 34.615 0.00 0.00 39.55 2.57
2285 2341 7.613801 TGCATGTAACTTATTGTTGGACCTATT 59.386 33.333 0.00 0.00 39.55 1.73
2286 2342 7.915397 GCATGTAACTTATTGTTGGACCTATTG 59.085 37.037 0.00 0.00 39.55 1.90
2287 2343 8.956426 CATGTAACTTATTGTTGGACCTATTGT 58.044 33.333 0.00 0.00 39.55 2.71
2288 2344 8.330466 TGTAACTTATTGTTGGACCTATTGTG 57.670 34.615 0.00 0.00 39.55 3.33
2289 2345 7.940137 TGTAACTTATTGTTGGACCTATTGTGT 59.060 33.333 0.00 0.00 39.55 3.72
2290 2346 7.833285 AACTTATTGTTGGACCTATTGTGTT 57.167 32.000 0.00 0.00 37.52 3.32
2291 2347 7.833285 ACTTATTGTTGGACCTATTGTGTTT 57.167 32.000 0.00 0.00 0.00 2.83
2292 2348 8.927675 ACTTATTGTTGGACCTATTGTGTTTA 57.072 30.769 0.00 0.00 0.00 2.01
2293 2349 9.357161 ACTTATTGTTGGACCTATTGTGTTTAA 57.643 29.630 0.00 0.00 0.00 1.52
2298 2354 9.535878 TTGTTGGACCTATTGTGTTTAAATTTC 57.464 29.630 0.00 0.00 0.00 2.17
2299 2355 8.696374 TGTTGGACCTATTGTGTTTAAATTTCA 58.304 29.630 0.00 0.00 0.00 2.69
2300 2356 9.705290 GTTGGACCTATTGTGTTTAAATTTCAT 57.295 29.630 0.00 0.00 0.00 2.57
2301 2357 9.921637 TTGGACCTATTGTGTTTAAATTTCATC 57.078 29.630 0.00 0.00 0.00 2.92
2302 2358 8.240682 TGGACCTATTGTGTTTAAATTTCATCG 58.759 33.333 0.00 0.00 0.00 3.84
2303 2359 8.241367 GGACCTATTGTGTTTAAATTTCATCGT 58.759 33.333 0.00 0.00 0.00 3.73
2304 2360 9.620660 GACCTATTGTGTTTAAATTTCATCGTT 57.379 29.630 0.00 0.00 0.00 3.85
2305 2361 9.405587 ACCTATTGTGTTTAAATTTCATCGTTG 57.594 29.630 0.00 0.00 0.00 4.10
2306 2362 9.619316 CCTATTGTGTTTAAATTTCATCGTTGA 57.381 29.630 0.00 0.00 0.00 3.18
2309 2365 7.687005 TGTGTTTAAATTTCATCGTTGAACC 57.313 32.000 8.41 0.00 41.50 3.62
2310 2366 7.484975 TGTGTTTAAATTTCATCGTTGAACCT 58.515 30.769 8.41 0.00 41.50 3.50
2311 2367 7.646130 TGTGTTTAAATTTCATCGTTGAACCTC 59.354 33.333 8.41 0.00 41.50 3.85
2312 2368 7.860872 GTGTTTAAATTTCATCGTTGAACCTCT 59.139 33.333 8.41 0.00 41.50 3.69
2313 2369 8.410141 TGTTTAAATTTCATCGTTGAACCTCTT 58.590 29.630 8.41 3.35 41.50 2.85
2314 2370 9.244799 GTTTAAATTTCATCGTTGAACCTCTTT 57.755 29.630 8.41 8.67 41.50 2.52
2318 2374 9.981114 AAATTTCATCGTTGAACCTCTTTATTT 57.019 25.926 8.41 7.45 41.50 1.40
2319 2375 8.970691 ATTTCATCGTTGAACCTCTTTATTTG 57.029 30.769 8.41 0.00 41.50 2.32
2320 2376 5.938322 TCATCGTTGAACCTCTTTATTTGC 58.062 37.500 0.00 0.00 0.00 3.68
2321 2377 5.705441 TCATCGTTGAACCTCTTTATTTGCT 59.295 36.000 0.00 0.00 0.00 3.91
2322 2378 6.876789 TCATCGTTGAACCTCTTTATTTGCTA 59.123 34.615 0.00 0.00 0.00 3.49
2323 2379 6.476243 TCGTTGAACCTCTTTATTTGCTAC 57.524 37.500 0.00 0.00 0.00 3.58
2324 2380 5.410439 TCGTTGAACCTCTTTATTTGCTACC 59.590 40.000 0.00 0.00 0.00 3.18
2325 2381 5.391629 CGTTGAACCTCTTTATTTGCTACCC 60.392 44.000 0.00 0.00 0.00 3.69
2326 2382 5.514500 TGAACCTCTTTATTTGCTACCCT 57.486 39.130 0.00 0.00 0.00 4.34
2327 2383 6.630203 TGAACCTCTTTATTTGCTACCCTA 57.370 37.500 0.00 0.00 0.00 3.53
2328 2384 7.208064 TGAACCTCTTTATTTGCTACCCTAT 57.792 36.000 0.00 0.00 0.00 2.57
2329 2385 7.639378 TGAACCTCTTTATTTGCTACCCTATT 58.361 34.615 0.00 0.00 0.00 1.73
2330 2386 8.113462 TGAACCTCTTTATTTGCTACCCTATTT 58.887 33.333 0.00 0.00 0.00 1.40
2331 2387 7.881775 ACCTCTTTATTTGCTACCCTATTTG 57.118 36.000 0.00 0.00 0.00 2.32
2332 2388 7.410991 ACCTCTTTATTTGCTACCCTATTTGT 58.589 34.615 0.00 0.00 0.00 2.83
2333 2389 7.339466 ACCTCTTTATTTGCTACCCTATTTGTG 59.661 37.037 0.00 0.00 0.00 3.33
2334 2390 7.339466 CCTCTTTATTTGCTACCCTATTTGTGT 59.661 37.037 0.00 0.00 0.00 3.72
2335 2391 8.644374 TCTTTATTTGCTACCCTATTTGTGTT 57.356 30.769 0.00 0.00 0.00 3.32
2336 2392 9.742144 TCTTTATTTGCTACCCTATTTGTGTTA 57.258 29.630 0.00 0.00 0.00 2.41
2339 2395 7.954666 ATTTGCTACCCTATTTGTGTTATGT 57.045 32.000 0.00 0.00 0.00 2.29
2340 2396 7.768807 TTTGCTACCCTATTTGTGTTATGTT 57.231 32.000 0.00 0.00 0.00 2.71
2341 2397 7.768807 TTGCTACCCTATTTGTGTTATGTTT 57.231 32.000 0.00 0.00 0.00 2.83
2342 2398 7.385778 TGCTACCCTATTTGTGTTATGTTTC 57.614 36.000 0.00 0.00 0.00 2.78
2343 2399 6.943146 TGCTACCCTATTTGTGTTATGTTTCA 59.057 34.615 0.00 0.00 0.00 2.69
2344 2400 7.613801 TGCTACCCTATTTGTGTTATGTTTCAT 59.386 33.333 0.00 0.00 0.00 2.57
2345 2401 7.915397 GCTACCCTATTTGTGTTATGTTTCATG 59.085 37.037 0.00 0.00 0.00 3.07
2346 2402 7.775053 ACCCTATTTGTGTTATGTTTCATGT 57.225 32.000 0.00 0.00 0.00 3.21
2347 2403 8.189119 ACCCTATTTGTGTTATGTTTCATGTT 57.811 30.769 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.774690 TCTTTTGAGTGCCCTTTGACATATT 59.225 36.000 0.00 0.00 0.00 1.28
92 93 8.414629 AAGTCAGCTACATGATCATCTACATA 57.585 34.615 4.86 0.00 0.00 2.29
102 103 8.043113 TCTCATACAAAAAGTCAGCTACATGAT 58.957 33.333 0.00 0.00 0.00 2.45
206 209 9.050601 GTTCCCTCACTTGAAGATAAAGATATG 57.949 37.037 0.00 0.00 0.00 1.78
218 226 2.158475 AGCAATGGTTCCCTCACTTGAA 60.158 45.455 0.00 0.00 0.00 2.69
270 278 2.036217 TGCAACTTCATGCTTCCCTTTG 59.964 45.455 0.67 0.00 46.54 2.77
303 311 3.303881 TCTGACATGAGTGAGAAACCG 57.696 47.619 0.00 0.00 34.97 4.44
308 316 2.167900 CAGCCATCTGACATGAGTGAGA 59.832 50.000 0.00 0.00 42.22 3.27
333 341 3.321648 TGCCGCCCTGTCATGACT 61.322 61.111 25.55 0.00 0.00 3.41
335 343 2.894257 AAGTGCCGCCCTGTCATGA 61.894 57.895 0.00 0.00 0.00 3.07
342 350 1.675641 GTTGATCAAGTGCCGCCCT 60.676 57.895 8.80 0.00 0.00 5.19
418 426 4.660789 ACAGCTTTGCATCAACTCTTTT 57.339 36.364 0.00 0.00 0.00 2.27
422 430 3.004106 ACTCAACAGCTTTGCATCAACTC 59.996 43.478 0.00 0.00 0.00 3.01
444 464 4.286549 AGGCCAATTGGATCAATTTGTTCA 59.713 37.500 29.02 0.00 40.60 3.18
457 477 5.452356 GGACTATCAATTCAAGGCCAATTGG 60.452 44.000 20.81 20.81 40.33 3.16
475 495 9.824216 TCCATTATTGCTAACTACTAGGACTAT 57.176 33.333 0.00 0.00 0.00 2.12
493 513 7.806180 ACTGCCTTGTAGTTAGATCCATTATT 58.194 34.615 0.00 0.00 0.00 1.40
549 569 4.517453 GCAACACAAGGTGTCCAATACTTA 59.483 41.667 2.07 0.00 46.79 2.24
551 571 2.884639 GCAACACAAGGTGTCCAATACT 59.115 45.455 2.07 0.00 46.79 2.12
597 617 6.013898 TGAACTCTTTGATCTTCCTGATGTCT 60.014 38.462 0.00 0.00 35.14 3.41
654 674 9.777008 AACCTTTCCATGGGAATAAATAAACTA 57.223 29.630 13.02 0.00 41.71 2.24
742 763 5.220931 GCCAAAGTAAGGAATGATGTAGCAG 60.221 44.000 0.00 0.00 0.00 4.24
749 770 4.415596 TGTTGGCCAAAGTAAGGAATGAT 58.584 39.130 22.47 0.00 0.00 2.45
769 790 1.412079 TTGGCTTTGCTTCCACATGT 58.588 45.000 0.00 0.00 30.97 3.21
785 806 5.594926 ACAAAGAGAGCTTTCAATGTTTGG 58.405 37.500 16.23 0.64 42.27 3.28
798 821 4.470462 CATTGTGTGCTAACAAAGAGAGC 58.530 43.478 8.52 0.00 42.98 4.09
865 889 1.073964 CACGGAGATCACAGTTGCTG 58.926 55.000 0.00 0.00 37.52 4.41
918 942 3.306364 GCTCTAAGAAGTGGCTGTGAAGA 60.306 47.826 0.00 0.00 0.00 2.87
926 950 4.256920 TCATCAAAGCTCTAAGAAGTGGC 58.743 43.478 0.00 0.00 0.00 5.01
946 970 2.034124 TCTCATCACCATCAGCGATCA 58.966 47.619 0.00 0.00 0.00 2.92
988 1012 2.352821 GCAACATCCATGGCTGCCA 61.353 57.895 25.65 25.65 35.78 4.92
1073 1099 5.072329 TCCATCTGATTATCCCACCTCTTTC 59.928 44.000 0.00 0.00 0.00 2.62
1074 1100 4.977739 TCCATCTGATTATCCCACCTCTTT 59.022 41.667 0.00 0.00 0.00 2.52
1157 1183 1.484038 AGCTTGTCTTTTGTTGGGCA 58.516 45.000 0.00 0.00 0.00 5.36
1159 1185 2.224042 GGGAAGCTTGTCTTTTGTTGGG 60.224 50.000 2.10 0.00 34.56 4.12
1199 1225 2.292267 CCATCTTCCATAGCACACCAC 58.708 52.381 0.00 0.00 0.00 4.16
1202 1228 2.939103 GACACCATCTTCCATAGCACAC 59.061 50.000 0.00 0.00 0.00 3.82
1222 1248 2.777094 TGTTTGTTGCTCATCATCGGA 58.223 42.857 0.00 0.00 0.00 4.55
1258 1284 0.457851 GCCAGCTCATAGTCGTCAGT 59.542 55.000 0.00 0.00 0.00 3.41
1299 1325 5.048991 GTCACGGTCTTTAATTGACAATGGT 60.049 40.000 0.34 0.00 37.20 3.55
1336 1362 6.260936 AGTTGCCATAGAATTTATTCTGACGG 59.739 38.462 13.83 11.71 46.01 4.79
1340 1366 8.246180 ACACAAGTTGCCATAGAATTTATTCTG 58.754 33.333 13.83 1.09 46.01 3.02
1351 1377 6.500684 ACAAGAATACACAAGTTGCCATAG 57.499 37.500 1.81 0.00 0.00 2.23
1367 1393 7.721399 AGTGGAGTAATTGAGTTGAACAAGAAT 59.279 33.333 0.00 0.00 0.00 2.40
1405 1431 5.696270 CCAACATTAAAGAGAAGGCCAAAAC 59.304 40.000 5.01 0.00 0.00 2.43
1436 1462 3.628487 TCCACCAAAGAACTACAAAACCG 59.372 43.478 0.00 0.00 0.00 4.44
1503 1529 7.010460 CGCTGAACAACATAGACTAATGATTCA 59.990 37.037 0.00 0.00 31.91 2.57
1529 1555 1.580845 AATTGCGCTCACAGCTGGAC 61.581 55.000 19.93 3.01 39.60 4.02
1533 1559 1.302752 TCCAATTGCGCTCACAGCT 60.303 52.632 9.73 0.00 39.60 4.24
1610 1638 4.685169 AGCACACAAATAATTGAGACGG 57.315 40.909 0.00 0.00 38.94 4.79
1612 1640 5.221880 TGCAAGCACACAAATAATTGAGAC 58.778 37.500 0.00 0.00 38.94 3.36
1618 1646 4.463539 TGGATCTGCAAGCACACAAATAAT 59.536 37.500 0.00 0.00 0.00 1.28
1619 1647 3.825585 TGGATCTGCAAGCACACAAATAA 59.174 39.130 0.00 0.00 0.00 1.40
1644 1672 2.028385 TCTAGACGGTTTCTCCCTTTGC 60.028 50.000 0.00 0.00 35.55 3.68
1709 1737 7.543520 CAGATTTTGAAACCTAGCTTCCATTTC 59.456 37.037 0.00 0.00 0.00 2.17
1790 1818 9.388506 GATATCAACCCATTCATTATCCTACTG 57.611 37.037 0.00 0.00 0.00 2.74
1792 1820 9.739276 TTGATATCAACCCATTCATTATCCTAC 57.261 33.333 14.23 0.00 0.00 3.18
1794 1822 9.251440 CATTGATATCAACCCATTCATTATCCT 57.749 33.333 20.19 0.00 38.86 3.24
1826 1854 2.941720 GAGCTTGATCTTCATGGACCAC 59.058 50.000 0.00 0.00 0.00 4.16
1870 1898 6.419484 TCATCAACTTGAGACCAAAGTAGA 57.581 37.500 0.00 0.00 0.00 2.59
2035 2063 1.205655 TCAGCCCTCAACTCTTCATCG 59.794 52.381 0.00 0.00 0.00 3.84
2109 2137 3.396560 TCATCATCTGGTGAATCATCGC 58.603 45.455 0.00 0.00 40.97 4.58
2110 2138 5.177142 GTCTTCATCATCTGGTGAATCATCG 59.823 44.000 6.35 0.00 40.97 3.84
2113 2141 5.181009 GTGTCTTCATCATCTGGTGAATCA 58.819 41.667 6.35 6.70 40.97 2.57
2114 2142 4.574013 GGTGTCTTCATCATCTGGTGAATC 59.426 45.833 6.35 4.53 40.97 2.52
2115 2143 4.226846 AGGTGTCTTCATCATCTGGTGAAT 59.773 41.667 6.35 0.00 40.97 2.57
2116 2144 3.584406 AGGTGTCTTCATCATCTGGTGAA 59.416 43.478 5.79 5.79 40.97 3.18
2138 2166 7.004086 AGTTCCATGTCTTCAAGGTGAAAATA 58.996 34.615 0.00 0.00 35.73 1.40
2146 2174 2.350522 CCGAGTTCCATGTCTTCAAGG 58.649 52.381 0.00 0.00 34.16 3.61
2161 2189 1.808945 CTTCAAGCAATCAAGCCGAGT 59.191 47.619 0.00 0.00 34.23 4.18
2164 2192 2.163010 ACATCTTCAAGCAATCAAGCCG 59.837 45.455 0.00 0.00 34.23 5.52
2184 2214 5.886960 ATGGCAGATAGAAACAAGAACAC 57.113 39.130 0.00 0.00 0.00 3.32
2187 2217 6.660521 ACATGAATGGCAGATAGAAACAAGAA 59.339 34.615 0.00 0.00 0.00 2.52
2188 2218 6.182627 ACATGAATGGCAGATAGAAACAAGA 58.817 36.000 0.00 0.00 0.00 3.02
2189 2219 6.446781 ACATGAATGGCAGATAGAAACAAG 57.553 37.500 0.00 0.00 0.00 3.16
2191 2221 6.839124 AAACATGAATGGCAGATAGAAACA 57.161 33.333 0.00 0.00 0.00 2.83
2192 2222 6.532657 CCAAAACATGAATGGCAGATAGAAAC 59.467 38.462 0.00 0.00 0.00 2.78
2194 2224 5.716228 ACCAAAACATGAATGGCAGATAGAA 59.284 36.000 0.00 0.00 37.77 2.10
2195 2225 5.125900 CACCAAAACATGAATGGCAGATAGA 59.874 40.000 0.00 0.00 37.77 1.98
2196 2226 5.105635 ACACCAAAACATGAATGGCAGATAG 60.106 40.000 0.00 0.00 37.77 2.08
2197 2227 4.771577 ACACCAAAACATGAATGGCAGATA 59.228 37.500 0.00 0.00 37.77 1.98
2240 2296 3.069872 TGCAACCAGATTGAAATGCAAGT 59.930 39.130 0.00 0.00 41.23 3.16
2250 2306 7.315142 ACAATAAGTTACATGCAACCAGATTG 58.685 34.615 17.89 17.89 41.69 2.67
2264 2320 8.331730 ACACAATAGGTCCAACAATAAGTTAC 57.668 34.615 0.00 0.00 38.74 2.50
2267 2323 7.833285 AAACACAATAGGTCCAACAATAAGT 57.167 32.000 0.00 0.00 0.00 2.24
2273 2329 8.696374 TGAAATTTAAACACAATAGGTCCAACA 58.304 29.630 0.00 0.00 0.00 3.33
2274 2330 9.705290 ATGAAATTTAAACACAATAGGTCCAAC 57.295 29.630 0.00 0.00 0.00 3.77
2275 2331 9.921637 GATGAAATTTAAACACAATAGGTCCAA 57.078 29.630 0.00 0.00 0.00 3.53
2276 2332 8.240682 CGATGAAATTTAAACACAATAGGTCCA 58.759 33.333 0.00 0.00 0.00 4.02
2277 2333 8.241367 ACGATGAAATTTAAACACAATAGGTCC 58.759 33.333 0.00 0.00 0.00 4.46
2278 2334 9.620660 AACGATGAAATTTAAACACAATAGGTC 57.379 29.630 0.00 0.00 0.00 3.85
2279 2335 9.405587 CAACGATGAAATTTAAACACAATAGGT 57.594 29.630 0.00 0.00 0.00 3.08
2280 2336 9.619316 TCAACGATGAAATTTAAACACAATAGG 57.381 29.630 0.00 0.00 30.99 2.57
2283 2339 8.760569 GGTTCAACGATGAAATTTAAACACAAT 58.239 29.630 9.90 0.00 46.66 2.71
2284 2340 7.976734 AGGTTCAACGATGAAATTTAAACACAA 59.023 29.630 9.90 0.00 46.66 3.33
2285 2341 7.484975 AGGTTCAACGATGAAATTTAAACACA 58.515 30.769 9.90 0.00 46.66 3.72
2286 2342 7.860872 AGAGGTTCAACGATGAAATTTAAACAC 59.139 33.333 9.90 0.00 46.66 3.32
2287 2343 7.936584 AGAGGTTCAACGATGAAATTTAAACA 58.063 30.769 9.90 0.00 46.66 2.83
2288 2344 8.797266 AAGAGGTTCAACGATGAAATTTAAAC 57.203 30.769 9.90 0.00 46.66 2.01
2292 2348 9.981114 AAATAAAGAGGTTCAACGATGAAATTT 57.019 25.926 9.90 7.71 46.66 1.82
2293 2349 9.410556 CAAATAAAGAGGTTCAACGATGAAATT 57.589 29.630 9.90 2.00 46.66 1.82
2294 2350 7.542130 GCAAATAAAGAGGTTCAACGATGAAAT 59.458 33.333 9.90 1.97 46.66 2.17
2295 2351 6.861055 GCAAATAAAGAGGTTCAACGATGAAA 59.139 34.615 9.90 0.00 46.66 2.69
2296 2352 6.206634 AGCAAATAAAGAGGTTCAACGATGAA 59.793 34.615 3.72 3.72 43.18 2.57
2297 2353 5.705441 AGCAAATAAAGAGGTTCAACGATGA 59.295 36.000 0.00 0.00 0.00 2.92
2298 2354 5.942872 AGCAAATAAAGAGGTTCAACGATG 58.057 37.500 0.00 0.00 0.00 3.84
2299 2355 6.093633 GGTAGCAAATAAAGAGGTTCAACGAT 59.906 38.462 0.00 0.00 0.00 3.73
2300 2356 5.410439 GGTAGCAAATAAAGAGGTTCAACGA 59.590 40.000 0.00 0.00 0.00 3.85
2301 2357 5.391629 GGGTAGCAAATAAAGAGGTTCAACG 60.392 44.000 0.00 0.00 0.00 4.10
2302 2358 5.710567 AGGGTAGCAAATAAAGAGGTTCAAC 59.289 40.000 0.00 0.00 0.00 3.18
2303 2359 5.887754 AGGGTAGCAAATAAAGAGGTTCAA 58.112 37.500 0.00 0.00 0.00 2.69
2304 2360 5.514500 AGGGTAGCAAATAAAGAGGTTCA 57.486 39.130 0.00 0.00 0.00 3.18
2305 2361 8.406297 CAAATAGGGTAGCAAATAAAGAGGTTC 58.594 37.037 0.00 0.00 0.00 3.62
2306 2362 7.893833 ACAAATAGGGTAGCAAATAAAGAGGTT 59.106 33.333 0.00 0.00 0.00 3.50
2307 2363 7.339466 CACAAATAGGGTAGCAAATAAAGAGGT 59.661 37.037 0.00 0.00 0.00 3.85
2308 2364 7.339466 ACACAAATAGGGTAGCAAATAAAGAGG 59.661 37.037 0.00 0.00 26.29 3.69
2309 2365 8.281212 ACACAAATAGGGTAGCAAATAAAGAG 57.719 34.615 0.00 0.00 26.29 2.85
2310 2366 8.644374 AACACAAATAGGGTAGCAAATAAAGA 57.356 30.769 0.00 0.00 29.80 2.52
2313 2369 9.469097 ACATAACACAAATAGGGTAGCAAATAA 57.531 29.630 0.00 0.00 29.80 1.40
2314 2370 9.469097 AACATAACACAAATAGGGTAGCAAATA 57.531 29.630 0.00 0.00 29.80 1.40
2315 2371 7.954666 ACATAACACAAATAGGGTAGCAAAT 57.045 32.000 0.00 0.00 29.80 2.32
2316 2372 7.768807 AACATAACACAAATAGGGTAGCAAA 57.231 32.000 0.00 0.00 29.80 3.68
2317 2373 7.448777 TGAAACATAACACAAATAGGGTAGCAA 59.551 33.333 0.00 0.00 29.80 3.91
2318 2374 6.943146 TGAAACATAACACAAATAGGGTAGCA 59.057 34.615 0.00 0.00 29.80 3.49
2319 2375 7.385778 TGAAACATAACACAAATAGGGTAGC 57.614 36.000 0.00 0.00 29.80 3.58
2320 2376 8.956426 ACATGAAACATAACACAAATAGGGTAG 58.044 33.333 0.00 0.00 29.80 3.18
2321 2377 8.871629 ACATGAAACATAACACAAATAGGGTA 57.128 30.769 0.00 0.00 29.80 3.69
2322 2378 7.775053 ACATGAAACATAACACAAATAGGGT 57.225 32.000 0.00 0.00 32.92 4.34


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

AutoCloner maintained by Alex Coulton.