Multiple sequence alignment - TraesCS1B01G159300

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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 TraesCS1B01G159300 chr1B 100.000 2318 0 0 1 2318 270328150 270330467 0.000000e+00 4281
1 TraesCS1B01G159300 chr1B 95.395 152 4 2 2168 2318 582799196 582799345 2.980000e-59 239
2 TraesCS1B01G159300 chr2B 92.899 1352 86 3 1 1344 217269680 217268331 0.000000e+00 1956
3 TraesCS1B01G159300 chr2B 96.000 150 4 1 2169 2318 355166752 355166605 2.300000e-60 243
4 TraesCS1B01G159300 chr2B 95.973 149 4 1 2170 2318 582332465 582332319 8.280000e-60 241
5 TraesCS1B01G159300 chr2B 95.333 150 5 2 2170 2318 379686014 379686162 1.070000e-58 237
6 TraesCS1B01G159300 chr4D 91.057 1353 109 5 1 1344 486555473 486556822 0.000000e+00 1818
7 TraesCS1B01G159300 chr7A 85.314 1355 184 12 1 1344 580627219 580628569 0.000000e+00 1386
8 TraesCS1B01G159300 chr6B 92.897 901 54 2 1 891 152381355 152380455 0.000000e+00 1301
9 TraesCS1B01G159300 chr6B 94.298 456 24 2 889 1344 152376010 152375557 0.000000e+00 697
10 TraesCS1B01G159300 chr7D 88.511 1088 95 13 1 1078 154937595 154936528 0.000000e+00 1290
11 TraesCS1B01G159300 chr7D 81.370 1358 230 19 1 1344 609177419 609178767 0.000000e+00 1085
12 TraesCS1B01G159300 chr1A 93.502 831 50 4 1341 2169 243605094 243604266 0.000000e+00 1232
13 TraesCS1B01G159300 chr3D 83.222 1353 216 6 1 1344 565242811 565244161 0.000000e+00 1230
14 TraesCS1B01G159300 chr3D 89.313 524 55 1 825 1348 28585406 28584884 0.000000e+00 656
15 TraesCS1B01G159300 chr3D 86.296 270 34 3 373 641 28585895 28585628 8.100000e-75 291
16 TraesCS1B01G159300 chr3A 81.987 1349 230 6 3 1343 21354198 21352855 0.000000e+00 1133
17 TraesCS1B01G159300 chr3A 82.425 734 115 7 621 1344 112923285 112924014 1.510000e-176 628
18 TraesCS1B01G159300 chr5A 80.987 1357 231 15 1 1344 608863736 608862394 0.000000e+00 1051
19 TraesCS1B01G159300 chr1D 92.453 371 26 2 1799 2169 195184381 195184013 1.580000e-146 529
20 TraesCS1B01G159300 chr5B 95.973 149 4 1 2170 2318 58314366 58314512 8.280000e-60 241
21 TraesCS1B01G159300 chr5B 94.667 150 6 1 2169 2318 215955789 215955642 4.980000e-57 231
22 TraesCS1B01G159300 chr7B 95.302 149 5 1 2170 2318 227065545 227065399 3.850000e-58 235
23 TraesCS1B01G159300 chr4B 95.302 149 5 1 2170 2318 471424934 471424788 3.850000e-58 235
24 TraesCS1B01G159300 chr3B 95.302 149 5 1 2170 2318 303829693 303829547 3.850000e-58 235


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 TraesCS1B01G159300 chr1B 270328150 270330467 2317 False 4281.0 4281 100.0000 1 2318 1 chr1B.!!$F1 2317
1 TraesCS1B01G159300 chr2B 217268331 217269680 1349 True 1956.0 1956 92.8990 1 1344 1 chr2B.!!$R1 1343
2 TraesCS1B01G159300 chr4D 486555473 486556822 1349 False 1818.0 1818 91.0570 1 1344 1 chr4D.!!$F1 1343
3 TraesCS1B01G159300 chr7A 580627219 580628569 1350 False 1386.0 1386 85.3140 1 1344 1 chr7A.!!$F1 1343
4 TraesCS1B01G159300 chr6B 152380455 152381355 900 True 1301.0 1301 92.8970 1 891 1 chr6B.!!$R2 890
5 TraesCS1B01G159300 chr7D 154936528 154937595 1067 True 1290.0 1290 88.5110 1 1078 1 chr7D.!!$R1 1077
6 TraesCS1B01G159300 chr7D 609177419 609178767 1348 False 1085.0 1085 81.3700 1 1344 1 chr7D.!!$F1 1343
7 TraesCS1B01G159300 chr1A 243604266 243605094 828 True 1232.0 1232 93.5020 1341 2169 1 chr1A.!!$R1 828
8 TraesCS1B01G159300 chr3D 565242811 565244161 1350 False 1230.0 1230 83.2220 1 1344 1 chr3D.!!$F1 1343
9 TraesCS1B01G159300 chr3D 28584884 28585895 1011 True 473.5 656 87.8045 373 1348 2 chr3D.!!$R1 975
10 TraesCS1B01G159300 chr3A 21352855 21354198 1343 True 1133.0 1133 81.9870 3 1343 1 chr3A.!!$R1 1340
11 TraesCS1B01G159300 chr3A 112923285 112924014 729 False 628.0 628 82.4250 621 1344 1 chr3A.!!$F1 723
12 TraesCS1B01G159300 chr5A 608862394 608863736 1342 True 1051.0 1051 80.9870 1 1344 1 chr5A.!!$R1 1343


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
89 90 0.181824 ATATAAACGGGGCTTGGCGT 59.818 50.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1741 0.389166 CAACTCTCCTCACCACGAGC 60.389 60.0 0.0 0.0 40.78 5.03 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
89 90 0.181824 ATATAAACGGGGCTTGGCGT 59.818 50.000 0.00 0.00 0.00 5.68
217 220 5.541098 AAAAGCGGTCTATTTTCGGTAAG 57.459 39.130 0.00 0.00 34.15 2.34
240 243 2.158755 AGTGCTTACAGACTTGCAACCT 60.159 45.455 0.00 0.00 37.17 3.50
401 404 3.131933 TGGCTACACAAAAGTGCAAACAT 59.868 39.130 0.00 0.00 0.00 2.71
403 406 3.421888 GCTACACAAAAGTGCAAACATCG 59.578 43.478 0.00 0.00 0.00 3.84
405 408 2.165437 ACACAAAAGTGCAAACATCGGT 59.835 40.909 0.00 0.00 0.00 4.69
425 428 1.565156 GACACTTGCCAACGCGATCA 61.565 55.000 15.93 1.15 38.08 2.92
436 439 0.670239 ACGCGATCAACATGTGCTCA 60.670 50.000 15.93 0.00 0.00 4.26
456 459 0.468226 TTGTGGCGTTGAGGAAGAGT 59.532 50.000 0.00 0.00 0.00 3.24
496 499 2.276201 TGTATGTACGCATGCAAGGAC 58.724 47.619 19.57 9.81 43.07 3.85
590 593 4.249661 GGTTTTTGTCCTTGTTGAGCAAA 58.750 39.130 0.00 0.00 36.53 3.68
783 794 3.366883 GCAAGATGACTATCCTAGAGGCG 60.367 52.174 0.00 0.00 33.64 5.52
879 920 1.002069 TGGATGGTTCCTTCCAGCAT 58.998 50.000 18.53 0.00 44.58 3.79
945 986 2.863740 TGGTACAATTATCTTCGCAGCG 59.136 45.455 9.06 9.06 31.92 5.18
1146 1187 5.189180 GTGCTGGAGATTAAGGATCTGTTT 58.811 41.667 0.00 0.00 45.17 2.83
1379 1421 3.678072 AGATACACAAACACGGATGAACG 59.322 43.478 0.00 0.00 40.31 3.95
1390 1432 1.726791 CGGATGAACGAGGACAAACAG 59.273 52.381 0.00 0.00 35.47 3.16
1394 1436 0.507358 GAACGAGGACAAACAGCGAC 59.493 55.000 0.00 0.00 0.00 5.19
1413 1455 1.207089 ACCGAATCTTGCGAGATCCAA 59.793 47.619 17.02 0.00 41.78 3.53
1422 1464 0.103208 GCGAGATCCAACGGAGACAT 59.897 55.000 6.67 0.00 34.05 3.06
1424 1466 2.859032 GCGAGATCCAACGGAGACATAC 60.859 54.545 6.67 0.00 34.05 2.39
1441 1483 3.197766 ACATACCTCTTCATGCCTTTCGA 59.802 43.478 0.00 0.00 0.00 3.71
1446 1488 1.000394 TCTTCATGCCTTTCGACGACA 60.000 47.619 0.00 0.00 0.00 4.35
1452 1494 1.068748 TGCCTTTCGACGACACTAGTC 60.069 52.381 0.00 0.00 41.46 2.59
1482 1524 3.917760 CGGGGGCTAGGCGAAGAG 61.918 72.222 10.58 0.00 0.00 2.85
1485 1527 1.411651 GGGGGCTAGGCGAAGAGAAT 61.412 60.000 10.58 0.00 0.00 2.40
1490 1532 3.560481 GGGCTAGGCGAAGAGAATTTTAC 59.440 47.826 10.58 0.00 0.00 2.01
1493 1535 5.006844 GGCTAGGCGAAGAGAATTTTACTTC 59.993 44.000 0.00 0.00 37.32 3.01
1506 1548 9.995957 GAGAATTTTACTTCATCTTTAGGAAGC 57.004 33.333 0.00 0.00 45.31 3.86
1514 1556 3.773119 TCATCTTTAGGAAGCCGTTACCT 59.227 43.478 0.00 0.00 37.76 3.08
1525 1567 1.202545 GCCGTTACCTCCTCATCTTCC 60.203 57.143 0.00 0.00 0.00 3.46
1529 1571 4.038162 CCGTTACCTCCTCATCTTCCTAAG 59.962 50.000 0.00 0.00 0.00 2.18
1552 1594 5.046950 AGCAGGACACAAACCTTAAACAAAA 60.047 36.000 0.00 0.00 35.35 2.44
1556 1598 8.726068 CAGGACACAAACCTTAAACAAAATTTT 58.274 29.630 0.00 0.00 35.35 1.82
1590 1632 0.619832 TGAAGCAGGAGCCCTCTCAT 60.620 55.000 0.00 0.00 43.56 2.90
1655 1697 2.902486 ACATGAGGCATGGTAGATCGAT 59.098 45.455 11.61 0.00 45.16 3.59
1684 1726 4.086457 ACCAATGATAGGTGTGAAAACCC 58.914 43.478 0.00 0.00 41.54 4.11
1686 1728 2.483014 TGATAGGTGTGAAAACCCCG 57.517 50.000 0.00 0.00 41.54 5.73
1699 1741 2.358247 CCCCGGTTGTTGGAGTCG 60.358 66.667 0.00 0.00 0.00 4.18
1711 1753 2.179517 GAGTCGCTCGTGGTGAGG 59.820 66.667 0.00 0.00 45.38 3.86
1763 1805 2.106511 AGGTTAGGTGTGTGCATGTTCT 59.893 45.455 0.00 0.00 0.00 3.01
1775 1817 2.815503 TGCATGTTCTTGAGACCACATG 59.184 45.455 16.21 16.21 42.13 3.21
1801 1843 4.753233 CTGACTATTGTGAGACTTGGGAG 58.247 47.826 0.00 0.00 28.51 4.30
1872 1914 2.254152 TGATCCAAGGGCTGTAGACT 57.746 50.000 0.00 0.00 0.00 3.24
1913 1955 9.582431 CATTCTAAGACGTAAGATTACTTCCAA 57.418 33.333 5.81 0.00 43.62 3.53
1999 2043 3.911868 TGCACAAATTAGCATCACCAAC 58.088 40.909 0.00 0.00 35.51 3.77
2002 2046 4.622740 GCACAAATTAGCATCACCAACTTC 59.377 41.667 0.00 0.00 0.00 3.01
2040 2084 8.356000 ACCCAAGAATTTTCCGTGAATAAATA 57.644 30.769 0.00 0.00 0.00 1.40
2060 2104 7.578458 AAATACCCATCTTTATATACCCCGT 57.422 36.000 0.00 0.00 0.00 5.28
2112 2156 9.520204 AGCTCATCAAAATAAATACAAATTCCG 57.480 29.630 0.00 0.00 0.00 4.30
2157 2201 8.889717 TCAACTTGTTTCTTAACTCCTTAGTTG 58.110 33.333 0.00 0.00 45.63 3.16
2165 2209 7.171630 TCTTAACTCCTTAGTTGTCCAGATC 57.828 40.000 1.11 0.00 45.63 2.75
2169 2213 5.833340 ACTCCTTAGTTGTCCAGATCTACT 58.167 41.667 0.00 0.00 29.00 2.57
2170 2214 5.654650 ACTCCTTAGTTGTCCAGATCTACTG 59.345 44.000 5.51 0.00 38.38 2.74
2171 2215 5.580998 TCCTTAGTTGTCCAGATCTACTGT 58.419 41.667 5.51 0.00 44.40 3.55
2172 2216 6.728411 TCCTTAGTTGTCCAGATCTACTGTA 58.272 40.000 5.51 0.00 44.40 2.74
2173 2217 7.179966 TCCTTAGTTGTCCAGATCTACTGTAA 58.820 38.462 5.51 0.00 44.40 2.41
2174 2218 7.122353 TCCTTAGTTGTCCAGATCTACTGTAAC 59.878 40.741 5.51 3.89 44.40 2.50
2175 2219 7.093902 CCTTAGTTGTCCAGATCTACTGTAACA 60.094 40.741 5.51 0.00 44.40 2.41
2176 2220 6.859112 AGTTGTCCAGATCTACTGTAACAT 57.141 37.500 0.00 0.00 44.40 2.71
2177 2221 6.868622 AGTTGTCCAGATCTACTGTAACATC 58.131 40.000 0.00 0.00 44.40 3.06
2178 2222 5.854010 TGTCCAGATCTACTGTAACATCC 57.146 43.478 0.00 0.00 44.40 3.51
2179 2223 4.649674 TGTCCAGATCTACTGTAACATCCC 59.350 45.833 0.00 0.00 44.40 3.85
2180 2224 4.649674 GTCCAGATCTACTGTAACATCCCA 59.350 45.833 0.00 0.00 44.40 4.37
2181 2225 5.305644 GTCCAGATCTACTGTAACATCCCAT 59.694 44.000 0.00 0.00 44.40 4.00
2182 2226 5.905331 TCCAGATCTACTGTAACATCCCATT 59.095 40.000 0.00 0.00 44.40 3.16
2183 2227 6.386927 TCCAGATCTACTGTAACATCCCATTT 59.613 38.462 0.00 0.00 44.40 2.32
2184 2228 7.056635 CCAGATCTACTGTAACATCCCATTTT 58.943 38.462 0.00 0.00 44.40 1.82
2185 2229 7.557719 CCAGATCTACTGTAACATCCCATTTTT 59.442 37.037 0.00 0.00 44.40 1.94
2212 2256 9.913310 TTCAATTTGGATGTTATACATAGGTCA 57.087 29.630 0.00 0.00 39.27 4.02
2220 2264 9.265901 GGATGTTATACATAGGTCATCATATGC 57.734 37.037 8.58 0.00 39.27 3.14
2221 2265 9.822185 GATGTTATACATAGGTCATCATATGCA 57.178 33.333 0.00 0.00 39.27 3.96
2254 2298 8.761575 TTTATTCTTGCATTTGTTTGAGATCC 57.238 30.769 0.00 0.00 0.00 3.36
2255 2299 6.600882 ATTCTTGCATTTGTTTGAGATCCT 57.399 33.333 0.00 0.00 0.00 3.24
2256 2300 7.707624 ATTCTTGCATTTGTTTGAGATCCTA 57.292 32.000 0.00 0.00 0.00 2.94
2257 2301 6.748333 TCTTGCATTTGTTTGAGATCCTAG 57.252 37.500 0.00 0.00 0.00 3.02
2258 2302 6.475504 TCTTGCATTTGTTTGAGATCCTAGA 58.524 36.000 0.00 0.00 0.00 2.43
2259 2303 6.942005 TCTTGCATTTGTTTGAGATCCTAGAA 59.058 34.615 0.00 0.00 0.00 2.10
2260 2304 7.448161 TCTTGCATTTGTTTGAGATCCTAGAAA 59.552 33.333 0.00 0.00 0.00 2.52
2261 2305 7.707624 TGCATTTGTTTGAGATCCTAGAAAT 57.292 32.000 0.00 0.00 0.00 2.17
2262 2306 7.765307 TGCATTTGTTTGAGATCCTAGAAATC 58.235 34.615 0.00 0.00 0.00 2.17
2263 2307 7.613022 TGCATTTGTTTGAGATCCTAGAAATCT 59.387 33.333 7.17 7.17 36.19 2.40
2264 2308 8.465201 GCATTTGTTTGAGATCCTAGAAATCTT 58.535 33.333 8.47 0.00 33.64 2.40
2268 2312 8.723942 TGTTTGAGATCCTAGAAATCTTAAGC 57.276 34.615 13.91 13.91 33.64 3.09
2269 2313 8.321353 TGTTTGAGATCCTAGAAATCTTAAGCA 58.679 33.333 16.92 16.92 37.50 3.91
2270 2314 9.167311 GTTTGAGATCCTAGAAATCTTAAGCAA 57.833 33.333 14.98 9.86 33.25 3.91
2271 2315 8.723942 TTGAGATCCTAGAAATCTTAAGCAAC 57.276 34.615 0.00 0.00 33.64 4.17
2272 2316 8.083828 TGAGATCCTAGAAATCTTAAGCAACT 57.916 34.615 0.00 0.00 33.64 3.16
2273 2317 8.200792 TGAGATCCTAGAAATCTTAAGCAACTC 58.799 37.037 0.00 0.00 33.64 3.01
2274 2318 8.083828 AGATCCTAGAAATCTTAAGCAACTCA 57.916 34.615 0.00 0.00 29.01 3.41
2275 2319 8.543774 AGATCCTAGAAATCTTAAGCAACTCAA 58.456 33.333 0.00 0.00 29.01 3.02
2276 2320 8.729805 ATCCTAGAAATCTTAAGCAACTCAAG 57.270 34.615 0.00 0.00 0.00 3.02
2277 2321 7.106239 TCCTAGAAATCTTAAGCAACTCAAGG 58.894 38.462 0.00 0.00 0.00 3.61
2278 2322 7.038302 TCCTAGAAATCTTAAGCAACTCAAGGA 60.038 37.037 0.00 2.34 0.00 3.36
2279 2323 6.809630 AGAAATCTTAAGCAACTCAAGGAC 57.190 37.500 0.00 0.00 0.00 3.85
2280 2324 5.707764 AGAAATCTTAAGCAACTCAAGGACC 59.292 40.000 0.00 0.00 0.00 4.46
2281 2325 3.418684 TCTTAAGCAACTCAAGGACCC 57.581 47.619 0.00 0.00 0.00 4.46
2282 2326 2.708861 TCTTAAGCAACTCAAGGACCCA 59.291 45.455 0.00 0.00 0.00 4.51
2283 2327 3.137544 TCTTAAGCAACTCAAGGACCCAA 59.862 43.478 0.00 0.00 0.00 4.12
2284 2328 1.986882 AAGCAACTCAAGGACCCAAG 58.013 50.000 0.00 0.00 0.00 3.61
2285 2329 0.111253 AGCAACTCAAGGACCCAAGG 59.889 55.000 0.00 0.00 0.00 3.61
2286 2330 0.110486 GCAACTCAAGGACCCAAGGA 59.890 55.000 0.00 0.00 0.00 3.36
2287 2331 1.884067 GCAACTCAAGGACCCAAGGAG 60.884 57.143 0.00 0.00 0.00 3.69
2288 2332 1.699634 CAACTCAAGGACCCAAGGAGA 59.300 52.381 6.37 0.00 0.00 3.71
2289 2333 1.650528 ACTCAAGGACCCAAGGAGAG 58.349 55.000 6.37 0.00 0.00 3.20
2290 2334 1.150135 ACTCAAGGACCCAAGGAGAGA 59.850 52.381 6.37 0.00 0.00 3.10
2291 2335 1.830477 CTCAAGGACCCAAGGAGAGAG 59.170 57.143 0.00 0.00 0.00 3.20
2292 2336 1.150135 TCAAGGACCCAAGGAGAGAGT 59.850 52.381 0.00 0.00 0.00 3.24
2293 2337 1.981495 CAAGGACCCAAGGAGAGAGTT 59.019 52.381 0.00 0.00 0.00 3.01
2294 2338 3.173965 CAAGGACCCAAGGAGAGAGTTA 58.826 50.000 0.00 0.00 0.00 2.24
2295 2339 3.108847 AGGACCCAAGGAGAGAGTTAG 57.891 52.381 0.00 0.00 0.00 2.34
2296 2340 2.655407 AGGACCCAAGGAGAGAGTTAGA 59.345 50.000 0.00 0.00 0.00 2.10
2297 2341 3.028130 GGACCCAAGGAGAGAGTTAGAG 58.972 54.545 0.00 0.00 0.00 2.43
2298 2342 3.028130 GACCCAAGGAGAGAGTTAGAGG 58.972 54.545 0.00 0.00 0.00 3.69
2299 2343 2.384029 ACCCAAGGAGAGAGTTAGAGGT 59.616 50.000 0.00 0.00 0.00 3.85
2300 2344 3.181405 ACCCAAGGAGAGAGTTAGAGGTT 60.181 47.826 0.00 0.00 0.00 3.50
2301 2345 3.841255 CCCAAGGAGAGAGTTAGAGGTTT 59.159 47.826 0.00 0.00 0.00 3.27
2302 2346 4.081365 CCCAAGGAGAGAGTTAGAGGTTTC 60.081 50.000 0.00 0.00 0.00 2.78
2303 2347 4.528596 CCAAGGAGAGAGTTAGAGGTTTCA 59.471 45.833 0.00 0.00 0.00 2.69
2304 2348 5.474825 CAAGGAGAGAGTTAGAGGTTTCAC 58.525 45.833 0.00 0.00 0.00 3.18
2305 2349 4.742012 AGGAGAGAGTTAGAGGTTTCACA 58.258 43.478 0.00 0.00 0.00 3.58
2306 2350 5.148502 AGGAGAGAGTTAGAGGTTTCACAA 58.851 41.667 0.00 0.00 0.00 3.33
2307 2351 5.602978 AGGAGAGAGTTAGAGGTTTCACAAA 59.397 40.000 0.00 0.00 0.00 2.83
2308 2352 6.099845 AGGAGAGAGTTAGAGGTTTCACAAAA 59.900 38.462 0.00 0.00 0.00 2.44
2309 2353 6.766467 GGAGAGAGTTAGAGGTTTCACAAAAA 59.234 38.462 0.00 0.00 0.00 1.94
2310 2354 7.445707 GGAGAGAGTTAGAGGTTTCACAAAAAT 59.554 37.037 0.00 0.00 0.00 1.82
2311 2355 8.384607 AGAGAGTTAGAGGTTTCACAAAAATC 57.615 34.615 0.00 0.00 0.00 2.17
2312 2356 7.993183 AGAGAGTTAGAGGTTTCACAAAAATCA 59.007 33.333 0.00 0.00 0.00 2.57
2313 2357 8.697507 AGAGTTAGAGGTTTCACAAAAATCAT 57.302 30.769 0.00 0.00 0.00 2.45
2314 2358 9.793259 AGAGTTAGAGGTTTCACAAAAATCATA 57.207 29.630 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 220 2.169832 TGCAAGTCTGTAAGCACTCC 57.830 50.000 0.00 0.00 31.05 3.85
240 243 4.065088 GTGAAGACAGAATTGTGTGCCTA 58.935 43.478 13.71 0.00 37.76 3.93
401 404 1.885388 CGTTGGCAAGTGTCACCGA 60.885 57.895 0.00 0.00 37.78 4.69
403 406 2.331451 GCGTTGGCAAGTGTCACC 59.669 61.111 0.00 0.00 39.62 4.02
405 408 1.565156 GATCGCGTTGGCAAGTGTCA 61.565 55.000 5.77 0.00 39.92 3.58
425 428 0.241749 CGCCACAATGAGCACATGTT 59.758 50.000 0.00 0.00 36.79 2.71
436 439 1.072331 ACTCTTCCTCAACGCCACAAT 59.928 47.619 0.00 0.00 0.00 2.71
456 459 2.850806 ATCAGCGCATGGTACGTGCA 62.851 55.000 11.47 3.30 42.62 4.57
496 499 0.036952 ACGCATGTTCACCCAGAGAG 60.037 55.000 0.00 0.00 0.00 3.20
590 593 1.561076 TCCCTTACATCAGCAGTGCAT 59.439 47.619 19.20 0.00 0.00 3.96
879 920 0.108186 CTGCCGCAGTACCATCTTCA 60.108 55.000 12.54 0.00 0.00 3.02
909 950 2.969950 TGTACCATCCGGATTCCTTAGG 59.030 50.000 16.19 14.46 35.59 2.69
945 986 5.718649 TGCAGTGAAAGATAAAGCGATAC 57.281 39.130 0.00 0.00 0.00 2.24
960 1001 1.661509 CAGCGAGTCGTTGCAGTGA 60.662 57.895 16.53 0.00 35.18 3.41
1320 1362 1.428718 TTTGCGGGGGTAAAGGGAGT 61.429 55.000 0.00 0.00 0.00 3.85
1379 1421 0.599204 TTCGGTCGCTGTTTGTCCTC 60.599 55.000 0.00 0.00 0.00 3.71
1413 1455 2.101582 GCATGAAGAGGTATGTCTCCGT 59.898 50.000 0.00 0.00 34.46 4.69
1422 1464 2.416836 CGTCGAAAGGCATGAAGAGGTA 60.417 50.000 0.00 0.00 33.27 3.08
1424 1466 1.002366 CGTCGAAAGGCATGAAGAGG 58.998 55.000 0.00 0.00 33.27 3.69
1446 1488 3.760035 CCCAGCGGTGCGACTAGT 61.760 66.667 9.63 0.00 0.00 2.57
1466 1508 1.411651 ATTCTCTTCGCCTAGCCCCC 61.412 60.000 0.00 0.00 0.00 5.40
1482 1524 7.910683 CGGCTTCCTAAAGATGAAGTAAAATTC 59.089 37.037 0.00 0.00 40.07 2.17
1485 1527 6.235664 ACGGCTTCCTAAAGATGAAGTAAAA 58.764 36.000 0.00 0.00 40.07 1.52
1490 1532 4.571176 GGTAACGGCTTCCTAAAGATGAAG 59.429 45.833 0.00 0.00 40.72 3.02
1493 1535 4.120589 GAGGTAACGGCTTCCTAAAGATG 58.879 47.826 0.00 0.00 46.39 2.90
1506 1548 2.389715 AGGAAGATGAGGAGGTAACGG 58.610 52.381 0.00 0.00 46.39 4.44
1514 1556 3.034635 GTCCTGCTTAGGAAGATGAGGA 58.965 50.000 0.00 0.00 40.06 3.71
1525 1567 5.298276 TGTTTAAGGTTTGTGTCCTGCTTAG 59.702 40.000 0.00 0.00 35.27 2.18
1529 1571 4.379339 TTGTTTAAGGTTTGTGTCCTGC 57.621 40.909 0.00 0.00 35.27 4.85
1556 1598 7.362056 GCTCCTGCTTCATTCTTATGTGTTTTA 60.362 37.037 0.00 0.00 36.03 1.52
1573 1615 1.684386 CGATGAGAGGGCTCCTGCTT 61.684 60.000 0.00 0.00 40.55 3.91
1578 1620 2.657102 CTTGGCGATGAGAGGGCTCC 62.657 65.000 0.00 0.00 40.55 4.70
1590 1632 3.467226 GATCCCGTCCCTTGGCGA 61.467 66.667 0.00 0.00 0.00 5.54
1613 1655 4.181010 CTCAGGACCATGGGGGCG 62.181 72.222 18.09 1.66 46.61 6.13
1617 1659 0.982852 TGTAGCCTCAGGACCATGGG 60.983 60.000 18.09 0.00 0.00 4.00
1618 1660 1.135094 ATGTAGCCTCAGGACCATGG 58.865 55.000 11.19 11.19 0.00 3.66
1684 1726 2.027625 GAGCGACTCCAACAACCGG 61.028 63.158 0.00 0.00 0.00 5.28
1686 1728 1.300697 ACGAGCGACTCCAACAACC 60.301 57.895 0.00 0.00 0.00 3.77
1699 1741 0.389166 CAACTCTCCTCACCACGAGC 60.389 60.000 0.00 0.00 40.78 5.03
1775 1817 3.601443 AGTCTCACAATAGTCAGCACC 57.399 47.619 0.00 0.00 0.00 5.01
1872 1914 7.095313 CGTCTTAGAATGTAAGAGGTCGCTATA 60.095 40.741 10.51 0.00 35.74 1.31
1913 1955 8.845413 TGCCTACAAAATAATCTTGCATTTTT 57.155 26.923 0.00 0.00 33.23 1.94
2040 2084 4.495565 TCACGGGGTATATAAAGATGGGT 58.504 43.478 0.00 0.00 0.00 4.51
2143 2187 7.894364 AGTAGATCTGGACAACTAAGGAGTTAA 59.106 37.037 5.18 0.00 44.39 2.01
2186 2230 9.913310 TGACCTATGTATAACATCCAAATTGAA 57.087 29.630 0.00 0.00 39.88 2.69
2194 2238 9.265901 GCATATGATGACCTATGTATAACATCC 57.734 37.037 6.97 0.00 39.88 3.51
2195 2239 9.822185 TGCATATGATGACCTATGTATAACATC 57.178 33.333 6.97 0.00 39.88 3.06
2228 2272 9.374838 GGATCTCAAACAAATGCAAGAATAAAT 57.625 29.630 0.00 0.00 0.00 1.40
2229 2273 8.587608 AGGATCTCAAACAAATGCAAGAATAAA 58.412 29.630 0.00 0.00 0.00 1.40
2230 2274 8.125978 AGGATCTCAAACAAATGCAAGAATAA 57.874 30.769 0.00 0.00 0.00 1.40
2231 2275 7.707624 AGGATCTCAAACAAATGCAAGAATA 57.292 32.000 0.00 0.00 0.00 1.75
2232 2276 6.600882 AGGATCTCAAACAAATGCAAGAAT 57.399 33.333 0.00 0.00 0.00 2.40
2233 2277 6.942005 TCTAGGATCTCAAACAAATGCAAGAA 59.058 34.615 0.00 0.00 0.00 2.52
2234 2278 6.475504 TCTAGGATCTCAAACAAATGCAAGA 58.524 36.000 0.00 0.00 0.00 3.02
2235 2279 6.748333 TCTAGGATCTCAAACAAATGCAAG 57.252 37.500 0.00 0.00 0.00 4.01
2236 2280 7.523293 TTTCTAGGATCTCAAACAAATGCAA 57.477 32.000 0.00 0.00 0.00 4.08
2237 2281 7.613022 AGATTTCTAGGATCTCAAACAAATGCA 59.387 33.333 0.00 0.00 0.00 3.96
2238 2282 7.994194 AGATTTCTAGGATCTCAAACAAATGC 58.006 34.615 4.33 0.00 0.00 3.56
2242 2286 9.167311 GCTTAAGATTTCTAGGATCTCAAACAA 57.833 33.333 6.67 1.75 32.86 2.83
2243 2287 8.321353 TGCTTAAGATTTCTAGGATCTCAAACA 58.679 33.333 6.67 2.51 32.86 2.83
2244 2288 8.723942 TGCTTAAGATTTCTAGGATCTCAAAC 57.276 34.615 6.67 0.45 32.86 2.93
2245 2289 9.167311 GTTGCTTAAGATTTCTAGGATCTCAAA 57.833 33.333 6.67 7.05 32.86 2.69
2246 2290 8.543774 AGTTGCTTAAGATTTCTAGGATCTCAA 58.456 33.333 6.67 7.13 32.86 3.02
2247 2291 8.083828 AGTTGCTTAAGATTTCTAGGATCTCA 57.916 34.615 6.67 2.67 32.86 3.27
2248 2292 8.200792 TGAGTTGCTTAAGATTTCTAGGATCTC 58.799 37.037 6.67 0.00 32.86 2.75
2249 2293 8.083828 TGAGTTGCTTAAGATTTCTAGGATCT 57.916 34.615 6.67 4.33 35.43 2.75
2250 2294 8.723942 TTGAGTTGCTTAAGATTTCTAGGATC 57.276 34.615 6.67 0.00 0.00 3.36
2251 2295 7.772757 CCTTGAGTTGCTTAAGATTTCTAGGAT 59.227 37.037 6.67 0.00 30.08 3.24
2252 2296 7.038302 TCCTTGAGTTGCTTAAGATTTCTAGGA 60.038 37.037 6.67 14.03 34.39 2.94
2253 2297 7.065204 GTCCTTGAGTTGCTTAAGATTTCTAGG 59.935 40.741 6.67 12.22 30.08 3.02
2254 2298 7.065204 GGTCCTTGAGTTGCTTAAGATTTCTAG 59.935 40.741 6.67 4.36 30.08 2.43
2255 2299 6.879458 GGTCCTTGAGTTGCTTAAGATTTCTA 59.121 38.462 6.67 0.00 30.08 2.10
2256 2300 5.707764 GGTCCTTGAGTTGCTTAAGATTTCT 59.292 40.000 6.67 0.00 30.08 2.52
2257 2301 5.106118 GGGTCCTTGAGTTGCTTAAGATTTC 60.106 44.000 6.67 0.00 30.08 2.17
2258 2302 4.767409 GGGTCCTTGAGTTGCTTAAGATTT 59.233 41.667 6.67 0.00 30.08 2.17
2259 2303 4.202567 TGGGTCCTTGAGTTGCTTAAGATT 60.203 41.667 6.67 0.00 30.08 2.40
2260 2304 3.330701 TGGGTCCTTGAGTTGCTTAAGAT 59.669 43.478 6.67 0.00 30.08 2.40
2261 2305 2.708861 TGGGTCCTTGAGTTGCTTAAGA 59.291 45.455 6.67 0.00 30.08 2.10
2262 2306 3.140325 TGGGTCCTTGAGTTGCTTAAG 57.860 47.619 0.00 0.00 0.00 1.85
2263 2307 3.486383 CTTGGGTCCTTGAGTTGCTTAA 58.514 45.455 0.00 0.00 0.00 1.85
2264 2308 2.224769 CCTTGGGTCCTTGAGTTGCTTA 60.225 50.000 0.00 0.00 0.00 3.09
2265 2309 1.479389 CCTTGGGTCCTTGAGTTGCTT 60.479 52.381 0.00 0.00 0.00 3.91
2266 2310 0.111253 CCTTGGGTCCTTGAGTTGCT 59.889 55.000 0.00 0.00 0.00 3.91
2267 2311 0.110486 TCCTTGGGTCCTTGAGTTGC 59.890 55.000 0.00 0.00 0.00 4.17
2268 2312 1.699634 TCTCCTTGGGTCCTTGAGTTG 59.300 52.381 0.00 0.00 0.00 3.16
2269 2313 1.981495 CTCTCCTTGGGTCCTTGAGTT 59.019 52.381 0.00 0.00 0.00 3.01
2270 2314 1.150135 TCTCTCCTTGGGTCCTTGAGT 59.850 52.381 0.00 0.00 0.00 3.41
2271 2315 1.830477 CTCTCTCCTTGGGTCCTTGAG 59.170 57.143 0.00 0.00 0.00 3.02
2272 2316 1.150135 ACTCTCTCCTTGGGTCCTTGA 59.850 52.381 0.00 0.00 0.00 3.02
2273 2317 1.650528 ACTCTCTCCTTGGGTCCTTG 58.349 55.000 0.00 0.00 0.00 3.61
2274 2318 2.424684 AACTCTCTCCTTGGGTCCTT 57.575 50.000 0.00 0.00 0.00 3.36
2275 2319 2.655407 TCTAACTCTCTCCTTGGGTCCT 59.345 50.000 0.00 0.00 0.00 3.85
2276 2320 3.028130 CTCTAACTCTCTCCTTGGGTCC 58.972 54.545 0.00 0.00 0.00 4.46
2277 2321 3.028130 CCTCTAACTCTCTCCTTGGGTC 58.972 54.545 0.00 0.00 0.00 4.46
2278 2322 2.384029 ACCTCTAACTCTCTCCTTGGGT 59.616 50.000 0.00 0.00 0.00 4.51
2279 2323 3.108847 ACCTCTAACTCTCTCCTTGGG 57.891 52.381 0.00 0.00 0.00 4.12
2280 2324 4.528596 TGAAACCTCTAACTCTCTCCTTGG 59.471 45.833 0.00 0.00 0.00 3.61
2281 2325 5.011125 TGTGAAACCTCTAACTCTCTCCTTG 59.989 44.000 0.00 0.00 34.36 3.61
2282 2326 5.148502 TGTGAAACCTCTAACTCTCTCCTT 58.851 41.667 0.00 0.00 34.36 3.36
2283 2327 4.742012 TGTGAAACCTCTAACTCTCTCCT 58.258 43.478 0.00 0.00 34.36 3.69
2284 2328 5.470047 TTGTGAAACCTCTAACTCTCTCC 57.530 43.478 0.00 0.00 34.36 3.71
2285 2329 7.787725 TTTTTGTGAAACCTCTAACTCTCTC 57.212 36.000 0.00 0.00 34.36 3.20
2286 2330 7.993183 TGATTTTTGTGAAACCTCTAACTCTCT 59.007 33.333 0.00 0.00 34.36 3.10
2287 2331 8.154649 TGATTTTTGTGAAACCTCTAACTCTC 57.845 34.615 0.00 0.00 34.36 3.20
2288 2332 8.697507 ATGATTTTTGTGAAACCTCTAACTCT 57.302 30.769 0.00 0.00 34.36 3.24



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

AutoCloner maintained by Alex Coulton.