Multiple sequence alignment - TraesCS7D01G413100

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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 TraesCS7D01G413100 chr7D 100.000 2669 0 0 1 2669 531581047 531578379 0.000000e+00 4929.0
1 TraesCS7D01G413100 chr7D 81.410 312 50 6 1 306 543087329 543087638 5.710000e-62 248.0
2 TraesCS7D01G413100 chr7D 85.897 78 9 2 299 375 13342851 13342927 6.120000e-12 82.4
3 TraesCS7D01G413100 chr7B 90.265 1582 115 16 1094 2639 571893008 571891430 0.000000e+00 2032.0
4 TraesCS7D01G413100 chr7B 82.288 271 24 13 483 747 571893770 571893518 2.080000e-51 213.0
5 TraesCS7D01G413100 chr7A 84.649 2039 172 64 3 1939 611805905 611803906 0.000000e+00 1901.0
6 TraesCS7D01G413100 chr7A 85.641 195 19 5 1594 1782 612026305 612026114 2.100000e-46 196.0
7 TraesCS7D01G413100 chr7A 89.256 121 8 1 1481 1596 612027537 612027417 2.140000e-31 147.0
8 TraesCS7D01G413100 chr7A 89.157 83 6 1 1860 1939 612026044 612025962 1.690000e-17 100.0
9 TraesCS7D01G413100 chr2B 83.766 308 42 7 1 306 471323701 471323400 4.350000e-73 285.0
10 TraesCS7D01G413100 chr2B 82.520 246 43 0 5 250 385215877 385215632 1.610000e-52 217.0
11 TraesCS7D01G413100 chr2B 87.500 72 7 2 305 375 550939926 550939856 6.120000e-12 82.4
12 TraesCS7D01G413100 chr2B 87.324 71 7 2 306 375 496141863 496141932 2.200000e-11 80.5
13 TraesCS7D01G413100 chr3A 83.513 279 46 0 4 282 399702400 399702122 7.330000e-66 261.0
14 TraesCS7D01G413100 chr3A 81.017 295 50 6 13 306 511080735 511080446 2.070000e-56 230.0
15 TraesCS7D01G413100 chr3A 88.462 78 7 2 299 375 422994129 422994205 2.830000e-15 93.5
16 TraesCS7D01G413100 chr2D 86.555 238 31 1 13 250 317599655 317599419 7.330000e-66 261.0
17 TraesCS7D01G413100 chr3B 81.373 306 56 1 1 306 395862793 395862489 5.710000e-62 248.0
18 TraesCS7D01G413100 chr1A 80.412 291 48 9 20 306 299234496 299234211 2.080000e-51 213.0
19 TraesCS7D01G413100 chr1A 79.612 103 13 4 305 405 573384074 573384170 1.710000e-07 67.6
20 TraesCS7D01G413100 chr5D 83.417 199 25 5 2407 2603 549654587 549654395 7.590000e-41 178.0
21 TraesCS7D01G413100 chr4D 87.838 74 5 2 305 375 49162164 49162236 1.700000e-12 84.2
22 TraesCS7D01G413100 chr4D 87.671 73 6 3 305 375 464181284 464181213 6.120000e-12 82.4
23 TraesCS7D01G413100 chr4B 78.788 132 15 5 1990 2121 559545407 559545289 2.850000e-10 76.8
24 TraesCS7D01G413100 chr4B 81.000 100 7 4 2022 2121 559544791 559544704 4.770000e-08 69.4
25 TraesCS7D01G413100 chr6B 83.544 79 10 2 299 375 693433158 693433235 1.330000e-08 71.3


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 TraesCS7D01G413100 chr7D 531578379 531581047 2668 True 4929.0 4929 100.0000 1 2669 1 chr7D.!!$R1 2668
1 TraesCS7D01G413100 chr7B 571891430 571893770 2340 True 1122.5 2032 86.2765 483 2639 2 chr7B.!!$R1 2156
2 TraesCS7D01G413100 chr7A 611803906 611805905 1999 True 1901.0 1901 84.6490 3 1939 1 chr7A.!!$R1 1936

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
310 311 0.036010 CATATCCATGTCCGCCTCCC 60.036 60.0 0.0 0.0 0.00 4.30 F
720 726 0.040499 TTGCTGGTTATTCCCCACCC 59.960 55.0 0.0 0.0 34.77 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1437 0.107214 TTCTTGGCCCCGCTATTCTG 60.107 55.0 0.0 0.0 0.0 3.02 R
2071 2347 0.379316 GCACCGCCCCTTAAATTACG 59.621 55.0 0.0 0.0 0.0 3.18 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
32 33 2.184579 GACACGGAGGCTGCCTAC 59.815 66.667 23.44 22.41 31.76 3.18
65 66 1.954927 CACCTCCTTAATCGGGAAGC 58.045 55.000 0.00 0.00 31.92 3.86
82 83 3.721793 GCATCTTGCTAGGATGGCT 57.278 52.632 8.86 0.00 46.01 4.75
148 149 4.873746 TTTGGATTCCGGCATGTAAAAA 57.126 36.364 0.00 0.00 0.00 1.94
152 153 4.396790 TGGATTCCGGCATGTAAAAACTAC 59.603 41.667 0.00 0.00 0.00 2.73
162 163 6.750039 GGCATGTAAAAACTACGCATATTTGT 59.250 34.615 0.00 0.00 0.00 2.83
175 176 7.151999 ACGCATATTTGTCTCATTTTGGTTA 57.848 32.000 0.00 0.00 0.00 2.85
185 186 4.165180 TCTCATTTTGGTTATGATCGGGGA 59.835 41.667 0.00 0.00 32.00 4.81
188 189 3.943671 TTTGGTTATGATCGGGGATGT 57.056 42.857 0.00 0.00 0.00 3.06
224 225 2.817834 GCTGGCGCGTTATGTGGA 60.818 61.111 8.43 0.00 0.00 4.02
228 229 0.391793 TGGCGCGTTATGTGGATCAA 60.392 50.000 8.43 0.00 0.00 2.57
230 231 0.724549 GCGCGTTATGTGGATCAACA 59.275 50.000 5.12 5.12 0.00 3.33
237 238 6.292865 CGCGTTATGTGGATCAACATAGATTT 60.293 38.462 19.88 0.48 42.44 2.17
238 239 7.095816 CGCGTTATGTGGATCAACATAGATTTA 60.096 37.037 19.88 5.45 42.44 1.40
264 265 8.791355 AATTTAAATTTGTTGACGGACAGTAC 57.209 30.769 7.64 0.00 0.00 2.73
282 283 2.202878 GCGGCTAGCGTTGGATGA 60.203 61.111 9.00 0.00 35.41 2.92
290 291 1.078848 GCGTTGGATGACTGCCTCT 60.079 57.895 0.00 0.00 0.00 3.69
292 293 0.247460 CGTTGGATGACTGCCTCTCA 59.753 55.000 0.00 0.00 0.00 3.27
293 294 1.134580 CGTTGGATGACTGCCTCTCAT 60.135 52.381 0.00 0.00 0.00 2.90
303 304 2.636893 ACTGCCTCTCATATCCATGTCC 59.363 50.000 0.00 0.00 33.57 4.02
305 306 1.674221 GCCTCTCATATCCATGTCCGC 60.674 57.143 0.00 0.00 33.57 5.54
306 307 1.066573 CCTCTCATATCCATGTCCGCC 60.067 57.143 0.00 0.00 33.57 6.13
307 308 1.898472 CTCTCATATCCATGTCCGCCT 59.102 52.381 0.00 0.00 33.57 5.52
308 309 1.895798 TCTCATATCCATGTCCGCCTC 59.104 52.381 0.00 0.00 33.57 4.70
309 310 0.976641 TCATATCCATGTCCGCCTCC 59.023 55.000 0.00 0.00 33.57 4.30
310 311 0.036010 CATATCCATGTCCGCCTCCC 60.036 60.000 0.00 0.00 0.00 4.30
311 312 0.473694 ATATCCATGTCCGCCTCCCA 60.474 55.000 0.00 0.00 0.00 4.37
312 313 1.407656 TATCCATGTCCGCCTCCCAC 61.408 60.000 0.00 0.00 0.00 4.61
313 314 4.489771 CCATGTCCGCCTCCCACC 62.490 72.222 0.00 0.00 0.00 4.61
314 315 3.402681 CATGTCCGCCTCCCACCT 61.403 66.667 0.00 0.00 0.00 4.00
315 316 3.083997 ATGTCCGCCTCCCACCTC 61.084 66.667 0.00 0.00 0.00 3.85
318 319 4.414956 TCCGCCTCCCACCTCCAT 62.415 66.667 0.00 0.00 0.00 3.41
319 320 4.181010 CCGCCTCCCACCTCCATG 62.181 72.222 0.00 0.00 0.00 3.66
320 321 3.402681 CGCCTCCCACCTCCATGT 61.403 66.667 0.00 0.00 0.00 3.21
321 322 2.592308 GCCTCCCACCTCCATGTC 59.408 66.667 0.00 0.00 0.00 3.06
322 323 3.049080 GCCTCCCACCTCCATGTCC 62.049 68.421 0.00 0.00 0.00 4.02
323 324 2.735772 CCTCCCACCTCCATGTCCG 61.736 68.421 0.00 0.00 0.00 4.79
324 325 3.391665 CTCCCACCTCCATGTCCGC 62.392 68.421 0.00 0.00 0.00 5.54
325 326 3.716195 CCCACCTCCATGTCCGCA 61.716 66.667 0.00 0.00 0.00 5.69
326 327 2.124983 CCACCTCCATGTCCGCAG 60.125 66.667 0.00 0.00 0.00 5.18
332 333 0.459237 CTCCATGTCCGCAGACTGAC 60.459 60.000 6.65 0.00 43.91 3.51
335 336 2.660064 ATGTCCGCAGACTGACCCC 61.660 63.158 6.65 0.00 43.91 4.95
343 344 4.083862 GACTGACCCCCTGTCCGC 62.084 72.222 0.00 0.00 43.78 5.54
379 380 3.218974 TTTTTGGCGGGTTGGGTTA 57.781 47.368 0.00 0.00 0.00 2.85
403 404 6.779860 ACCGTTATAGATGCCCTTATTCAAT 58.220 36.000 0.00 0.00 0.00 2.57
438 439 6.687081 TTTGTTCCCACGGAATATATTCAC 57.313 37.500 23.54 13.25 44.04 3.18
476 477 2.158813 ACTTGATTGACACTTGACCCGT 60.159 45.455 0.00 0.00 0.00 5.28
520 521 2.996621 GTCCATCAGTCCGTCTTGAAAG 59.003 50.000 0.00 0.00 0.00 2.62
694 700 3.950397 ACAAGAGAAGGAACAACACACA 58.050 40.909 0.00 0.00 0.00 3.72
720 726 0.040499 TTGCTGGTTATTCCCCACCC 59.960 55.000 0.00 0.00 34.77 4.61
748 755 1.216064 CCACCAATCATCCTCCTCCA 58.784 55.000 0.00 0.00 0.00 3.86
765 775 1.586154 CCACCACAACTCCGGATTGC 61.586 60.000 19.99 0.00 0.00 3.56
843 884 3.809905 AGCTTGTTCTTCGTTTTCCTCT 58.190 40.909 0.00 0.00 0.00 3.69
855 896 2.687935 GTTTTCCTCTTGCTTGTCACCA 59.312 45.455 0.00 0.00 0.00 4.17
868 909 1.067974 TGTCACCACAAGAACGATCGT 59.932 47.619 16.60 16.60 0.00 3.73
874 915 1.194547 CACAAGAACGATCGTGGTTGG 59.805 52.381 30.91 21.61 39.09 3.77
893 935 0.672342 GCCTGCACCAATCATCATCC 59.328 55.000 0.00 0.00 0.00 3.51
894 936 1.325355 CCTGCACCAATCATCATCCC 58.675 55.000 0.00 0.00 0.00 3.85
909 960 1.570857 ATCCCTTCCCAATGCCGTCA 61.571 55.000 0.00 0.00 0.00 4.35
1032 1187 4.450976 CGGACATAGATTTCACCAATCCA 58.549 43.478 0.00 0.00 42.31 3.41
1043 1198 1.134788 CACCAATCCAGAGACGTACCC 60.135 57.143 0.00 0.00 0.00 3.69
1075 1266 0.520827 GGACAGCTACTTCGACGACG 60.521 60.000 0.00 0.00 41.26 5.12
1090 1281 1.606350 CGACGTCCTGAAAGACACGC 61.606 60.000 10.58 0.00 41.83 5.34
1135 1356 3.901797 GAGGACCTTGCCCACCACG 62.902 68.421 0.00 0.00 0.00 4.94
1161 1382 1.004560 CTGCGTCCATGTCCACACT 60.005 57.895 0.00 0.00 0.00 3.55
1169 1390 3.197766 GTCCATGTCCACACTAAGATCCA 59.802 47.826 0.00 0.00 0.00 3.41
1172 1393 1.906574 TGTCCACACTAAGATCCACCC 59.093 52.381 0.00 0.00 0.00 4.61
1175 1396 0.462047 CACACTAAGATCCACCCGGC 60.462 60.000 0.00 0.00 0.00 6.13
1176 1397 0.907704 ACACTAAGATCCACCCGGCA 60.908 55.000 0.00 0.00 0.00 5.69
1182 1403 3.083997 ATCCACCCGGCAGAGTCC 61.084 66.667 0.00 0.00 0.00 3.85
1216 1437 3.554692 CATCCGAGTCGCCGCAAC 61.555 66.667 7.12 0.00 0.00 4.17
1223 1444 0.924090 GAGTCGCCGCAACAGAATAG 59.076 55.000 0.00 0.00 0.00 1.73
1251 1475 3.478540 GAAGCGCCCTTCTGGTAAT 57.521 52.632 2.29 0.00 43.31 1.89
1254 1478 1.143183 GCGCCCTTCTGGTAATCGA 59.857 57.895 0.00 0.00 36.04 3.59
1268 1492 0.175302 AATCGAGCAGCTGTGAGGAG 59.825 55.000 16.64 1.70 0.00 3.69
1278 1502 0.526662 CTGTGAGGAGGTACCGTGAC 59.473 60.000 6.18 0.37 44.74 3.67
1283 1507 1.473278 GAGGAGGTACCGTGACAAGAG 59.527 57.143 6.18 0.00 44.74 2.85
1292 1516 1.376037 GTGACAAGAGGAAGGCCCG 60.376 63.158 0.00 0.00 40.87 6.13
1296 1520 3.249189 AAGAGGAAGGCCCGCACA 61.249 61.111 0.00 0.00 40.87 4.57
1297 1521 3.259633 AAGAGGAAGGCCCGCACAG 62.260 63.158 0.00 0.00 40.87 3.66
1355 1579 1.758440 AACAGGCAGCTCGTGAGGAA 61.758 55.000 11.20 0.00 34.80 3.36
1357 1581 1.607756 AGGCAGCTCGTGAGGAAGA 60.608 57.895 0.00 0.00 0.00 2.87
1377 1601 1.806461 TTCAGAGTCACTCGGCGCTT 61.806 55.000 7.64 0.00 35.36 4.68
1378 1602 1.803519 CAGAGTCACTCGGCGCTTC 60.804 63.158 7.64 0.00 35.36 3.86
1443 1667 0.958822 GGAGGATCGAAGGAGAGCTC 59.041 60.000 5.27 5.27 34.37 4.09
1446 1670 0.820074 GGATCGAAGGAGAGCTCGGA 60.820 60.000 8.37 0.81 35.76 4.55
1448 1672 0.106918 ATCGAAGGAGAGCTCGGAGT 60.107 55.000 8.37 0.00 35.76 3.85
1457 1681 1.002544 AGAGCTCGGAGTTTTCCCTTG 59.997 52.381 8.37 0.00 40.67 3.61
1516 1740 1.681264 GAAGTTTCCTTGGTGGTGGTG 59.319 52.381 0.00 0.00 37.07 4.17
1561 1785 3.358076 GAGCCGCTCTACCGCAGTT 62.358 63.158 13.42 0.00 0.00 3.16
1663 1892 4.299796 TGGCTCCCAGGTTTGCCC 62.300 66.667 10.90 0.00 44.32 5.36
1721 1950 7.050970 ACTTATCTTGTGTGTTCAGTAGACA 57.949 36.000 0.00 0.00 0.00 3.41
1892 2148 5.385198 AGCATTACTGAACCTTTTCCAGAA 58.615 37.500 0.00 0.00 0.00 3.02
1959 2215 2.656422 CCACTGAAAAATAAAGCGCACG 59.344 45.455 11.47 0.00 0.00 5.34
1961 2217 4.158384 CACTGAAAAATAAAGCGCACGAT 58.842 39.130 11.47 0.00 0.00 3.73
1977 2233 0.456142 CGATAGCGCCGCTAATAGCA 60.456 55.000 23.98 0.09 44.62 3.49
1978 2234 1.799181 CGATAGCGCCGCTAATAGCAT 60.799 52.381 23.98 6.15 44.62 3.79
2043 2319 9.884636 AGTTTACAATGTATCACTAATAGCACA 57.115 29.630 4.49 0.00 0.00 4.57
2071 2347 3.368236 GTGCGCTATACCTTGCTAATAGC 59.632 47.826 9.73 5.12 42.95 2.97
2102 2378 3.117813 AGGGGCGGTGCTATTTTGTATAA 60.118 43.478 0.00 0.00 0.00 0.98
2103 2379 3.824443 GGGGCGGTGCTATTTTGTATAAT 59.176 43.478 0.00 0.00 0.00 1.28
2104 2380 4.279922 GGGGCGGTGCTATTTTGTATAATT 59.720 41.667 0.00 0.00 0.00 1.40
2171 2447 3.700539 CCCATGAACTTCATAATGCACCA 59.299 43.478 3.88 0.00 34.28 4.17
2244 2520 4.875544 TGAACGGCTTTCATTAGTATGC 57.124 40.909 1.83 0.00 39.45 3.14
2246 2522 2.210116 ACGGCTTTCATTAGTATGCGG 58.790 47.619 0.00 0.00 0.00 5.69
2260 2536 4.880759 AGTATGCGGATCTGATTCTCAAG 58.119 43.478 5.48 0.00 0.00 3.02
2306 2582 9.084164 GGTAATAACTAATGACGGCATATAGTG 57.916 37.037 19.96 6.98 33.10 2.74
2338 2614 6.931281 TGTCTCCTTGATTCTTTCTTGTACAG 59.069 38.462 0.00 0.00 0.00 2.74
2411 2687 8.373981 ACATCTCAGGTATAGGAAGATGATTTG 58.626 37.037 15.43 0.00 36.50 2.32
2422 2698 3.287867 AGATGATTTGTAGCACCTGGG 57.712 47.619 0.00 0.00 0.00 4.45
2446 2722 3.881713 GCTCCACCCCCTAAATGAACATT 60.882 47.826 0.00 0.00 0.00 2.71
2522 2800 6.126863 TCAAACTTGGGTGTCTGATCTATT 57.873 37.500 0.00 0.00 0.00 1.73
2530 2808 3.865745 GGTGTCTGATCTATTTCCGTGTG 59.134 47.826 0.00 0.00 0.00 3.82
2630 2909 2.928116 GGACGGATTTTAGTTCGGACAG 59.072 50.000 0.00 0.00 0.00 3.51
2636 2915 6.312180 ACGGATTTTAGTTCGGACAGTATTTC 59.688 38.462 0.00 0.00 0.00 2.17
2639 2918 8.388853 GGATTTTAGTTCGGACAGTATTTCTTC 58.611 37.037 0.00 0.00 0.00 2.87
2640 2919 8.842358 ATTTTAGTTCGGACAGTATTTCTTCA 57.158 30.769 0.00 0.00 0.00 3.02
2641 2920 7.647907 TTTAGTTCGGACAGTATTTCTTCAC 57.352 36.000 0.00 0.00 0.00 3.18
2642 2921 4.566987 AGTTCGGACAGTATTTCTTCACC 58.433 43.478 0.00 0.00 0.00 4.02
2643 2922 4.039973 AGTTCGGACAGTATTTCTTCACCA 59.960 41.667 0.00 0.00 0.00 4.17
2644 2923 4.819105 TCGGACAGTATTTCTTCACCAT 57.181 40.909 0.00 0.00 0.00 3.55
2645 2924 5.925506 TCGGACAGTATTTCTTCACCATA 57.074 39.130 0.00 0.00 0.00 2.74
2646 2925 5.902681 TCGGACAGTATTTCTTCACCATAG 58.097 41.667 0.00 0.00 0.00 2.23
2647 2926 5.655090 TCGGACAGTATTTCTTCACCATAGA 59.345 40.000 0.00 0.00 0.00 1.98
2648 2927 6.323996 TCGGACAGTATTTCTTCACCATAGAT 59.676 38.462 0.00 0.00 0.00 1.98
2649 2928 7.504574 TCGGACAGTATTTCTTCACCATAGATA 59.495 37.037 0.00 0.00 0.00 1.98
2650 2929 7.595502 CGGACAGTATTTCTTCACCATAGATAC 59.404 40.741 0.00 0.00 0.00 2.24
2651 2930 7.595502 GGACAGTATTTCTTCACCATAGATACG 59.404 40.741 0.00 0.00 0.00 3.06
2652 2931 8.008513 ACAGTATTTCTTCACCATAGATACGT 57.991 34.615 0.00 0.00 0.00 3.57
2653 2932 8.475639 ACAGTATTTCTTCACCATAGATACGTT 58.524 33.333 0.00 0.00 0.00 3.99
2654 2933 9.314321 CAGTATTTCTTCACCATAGATACGTTT 57.686 33.333 0.00 0.00 0.00 3.60
2655 2934 9.886132 AGTATTTCTTCACCATAGATACGTTTT 57.114 29.630 0.00 0.00 0.00 2.43
2658 2937 7.827819 TTCTTCACCATAGATACGTTTTCTG 57.172 36.000 10.12 0.00 0.00 3.02
2659 2938 6.338146 TCTTCACCATAGATACGTTTTCTGG 58.662 40.000 10.12 7.60 0.00 3.86
2660 2939 5.670792 TCACCATAGATACGTTTTCTGGT 57.329 39.130 10.12 8.11 0.00 4.00
2661 2940 6.778834 TCACCATAGATACGTTTTCTGGTA 57.221 37.500 10.12 0.00 0.00 3.25
2662 2941 7.356089 TCACCATAGATACGTTTTCTGGTAT 57.644 36.000 10.12 0.00 32.27 2.73
2663 2942 7.788026 TCACCATAGATACGTTTTCTGGTATT 58.212 34.615 10.12 0.00 29.86 1.89
2664 2943 8.262227 TCACCATAGATACGTTTTCTGGTATTT 58.738 33.333 10.12 0.00 29.86 1.40
2665 2944 8.548721 CACCATAGATACGTTTTCTGGTATTTC 58.451 37.037 10.12 0.00 29.86 2.17
2666 2945 8.262227 ACCATAGATACGTTTTCTGGTATTTCA 58.738 33.333 10.12 0.00 29.86 2.69
2667 2946 8.548721 CCATAGATACGTTTTCTGGTATTTCAC 58.451 37.037 10.12 0.00 29.86 3.18
2668 2947 6.642683 AGATACGTTTTCTGGTATTTCACG 57.357 37.500 0.00 0.00 29.86 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.148498 CCCGATTAAGGAGGTGCCC 59.852 63.158 0.00 0.00 37.37 5.36
44 45 0.544697 TTCCCGATTAAGGAGGTGCC 59.455 55.000 0.00 0.00 34.08 5.01
65 66 2.924757 TCAGCCATCCTAGCAAGATG 57.075 50.000 4.20 4.20 40.71 2.90
82 83 1.925285 ATTTCTGCCCTGCCGGATCA 61.925 55.000 5.05 0.00 0.00 2.92
115 116 5.067805 GCCGGAATCCAAAAGAATATCAGTT 59.932 40.000 5.05 0.00 0.00 3.16
116 117 4.580580 GCCGGAATCCAAAAGAATATCAGT 59.419 41.667 5.05 0.00 0.00 3.41
122 123 3.099141 ACATGCCGGAATCCAAAAGAAT 58.901 40.909 5.05 0.00 0.00 2.40
148 149 6.374333 ACCAAAATGAGACAAATATGCGTAGT 59.626 34.615 0.00 0.00 0.00 2.73
152 153 7.914871 TCATAACCAAAATGAGACAAATATGCG 59.085 33.333 0.00 0.00 0.00 4.73
162 163 4.165180 TCCCCGATCATAACCAAAATGAGA 59.835 41.667 0.00 0.00 36.82 3.27
238 239 9.240159 GTACTGTCCGTCAACAAATTTAAATTT 57.760 29.630 18.40 18.40 39.07 1.82
242 243 5.558653 GCGTACTGTCCGTCAACAAATTTAA 60.559 40.000 0.00 0.00 0.00 1.52
254 255 2.747460 TAGCCGCGTACTGTCCGT 60.747 61.111 4.92 0.00 0.00 4.69
255 256 2.024305 CTAGCCGCGTACTGTCCG 59.976 66.667 4.92 0.00 0.00 4.79
282 283 2.636893 GGACATGGATATGAGAGGCAGT 59.363 50.000 0.00 0.00 37.73 4.40
290 291 0.976641 GGAGGCGGACATGGATATGA 59.023 55.000 0.00 0.00 37.73 2.15
292 293 0.473694 TGGGAGGCGGACATGGATAT 60.474 55.000 0.00 0.00 0.00 1.63
293 294 1.074850 TGGGAGGCGGACATGGATA 60.075 57.895 0.00 0.00 0.00 2.59
303 304 3.391665 GACATGGAGGTGGGAGGCG 62.392 68.421 0.00 0.00 0.00 5.52
305 306 2.735772 CGGACATGGAGGTGGGAGG 61.736 68.421 0.00 0.00 0.00 4.30
306 307 2.903357 CGGACATGGAGGTGGGAG 59.097 66.667 0.00 0.00 0.00 4.30
307 308 3.399181 GCGGACATGGAGGTGGGA 61.399 66.667 0.00 0.00 0.00 4.37
308 309 3.687321 CTGCGGACATGGAGGTGGG 62.687 68.421 0.00 0.00 0.00 4.61
309 310 2.124983 CTGCGGACATGGAGGTGG 60.125 66.667 0.00 0.00 0.00 4.61
310 311 1.448540 GTCTGCGGACATGGAGGTG 60.449 63.158 21.02 0.00 41.75 4.00
311 312 1.610673 AGTCTGCGGACATGGAGGT 60.611 57.895 27.02 1.75 44.36 3.85
312 313 1.153489 CAGTCTGCGGACATGGAGG 60.153 63.158 27.02 5.86 44.36 4.30
313 314 0.459237 GTCAGTCTGCGGACATGGAG 60.459 60.000 27.02 11.29 44.36 3.86
314 315 1.591703 GTCAGTCTGCGGACATGGA 59.408 57.895 27.02 17.64 44.36 3.41
315 316 1.448540 GGTCAGTCTGCGGACATGG 60.449 63.158 27.02 15.70 44.36 3.66
316 317 1.448540 GGGTCAGTCTGCGGACATG 60.449 63.158 27.02 20.23 44.36 3.21
317 318 2.660064 GGGGTCAGTCTGCGGACAT 61.660 63.158 27.02 9.89 44.36 3.06
318 319 3.311110 GGGGTCAGTCTGCGGACA 61.311 66.667 27.02 4.93 44.36 4.02
319 320 4.083862 GGGGGTCAGTCTGCGGAC 62.084 72.222 18.39 18.39 42.41 4.79
320 321 4.316823 AGGGGGTCAGTCTGCGGA 62.317 66.667 0.00 0.00 0.00 5.54
321 322 4.087892 CAGGGGGTCAGTCTGCGG 62.088 72.222 0.00 0.00 0.00 5.69
322 323 3.302347 GACAGGGGGTCAGTCTGCG 62.302 68.421 0.00 0.00 46.19 5.18
323 324 2.665603 GACAGGGGGTCAGTCTGC 59.334 66.667 0.00 0.00 46.19 4.26
345 346 0.958876 AAAAACCTCCCGCATCCGTC 60.959 55.000 0.00 0.00 0.00 4.79
366 367 2.462125 TAACGGTAACCCAACCCGCC 62.462 60.000 0.00 0.00 45.49 6.13
370 371 3.811497 GCATCTATAACGGTAACCCAACC 59.189 47.826 0.00 0.00 36.08 3.77
379 380 5.818678 TGAATAAGGGCATCTATAACGGT 57.181 39.130 0.00 0.00 0.00 4.83
403 404 4.083749 CGTGGGAACAAAAACGACATCATA 60.084 41.667 0.00 0.00 46.06 2.15
453 454 3.679980 CGGGTCAAGTGTCAATCAAGTAG 59.320 47.826 0.00 0.00 0.00 2.57
476 477 2.056223 GTGCGGCTCTACTACCCCA 61.056 63.158 0.00 0.00 0.00 4.96
480 481 1.872679 GCGTGTGCGGCTCTACTAC 60.873 63.158 0.00 0.00 38.78 2.73
499 500 2.743636 TTCAAGACGGACTGATGGAC 57.256 50.000 0.00 0.00 0.00 4.02
563 566 3.427503 CGTGAAGACAAGCAAACCAGTTT 60.428 43.478 0.00 0.00 0.00 2.66
565 568 1.670811 CGTGAAGACAAGCAAACCAGT 59.329 47.619 0.00 0.00 0.00 4.00
566 569 1.670811 ACGTGAAGACAAGCAAACCAG 59.329 47.619 0.00 0.00 0.00 4.00
602 607 1.891011 CGTCATCGATGGATAGGGGGA 60.891 57.143 24.61 0.00 39.71 4.81
631 636 0.811281 CTCGGGTGGAATGCTTTTCC 59.189 55.000 10.93 10.93 39.03 3.13
694 700 3.243941 GGGGAATAACCAGCAACGTTTTT 60.244 43.478 0.00 0.00 41.20 1.94
720 726 0.107017 ATGATTGGTGGGCGGAGAAG 60.107 55.000 0.00 0.00 0.00 2.85
748 755 1.303317 GGCAATCCGGAGTTGTGGT 60.303 57.895 11.34 0.00 0.00 4.16
765 775 4.489771 GGTCCTGGATGGCCACGG 62.490 72.222 8.16 6.74 39.92 4.94
776 786 3.343788 GAGTCGCGTCCTGGTCCTG 62.344 68.421 5.77 0.00 0.00 3.86
855 896 1.508632 CCAACCACGATCGTTCTTGT 58.491 50.000 20.14 10.66 0.00 3.16
874 915 0.672342 GGATGATGATTGGTGCAGGC 59.328 55.000 0.00 0.00 0.00 4.85
893 935 1.135024 CAATTGACGGCATTGGGAAGG 60.135 52.381 0.00 0.00 0.00 3.46
894 936 1.736696 GCAATTGACGGCATTGGGAAG 60.737 52.381 10.34 0.00 0.00 3.46
934 985 7.928307 TGAGATGCTCTTGCTACTTATTTTT 57.072 32.000 0.00 0.00 40.48 1.94
937 988 7.730084 TGTATGAGATGCTCTTGCTACTTATT 58.270 34.615 0.00 0.00 40.48 1.40
938 989 7.295322 TGTATGAGATGCTCTTGCTACTTAT 57.705 36.000 0.00 0.00 40.48 1.73
939 990 6.715347 TGTATGAGATGCTCTTGCTACTTA 57.285 37.500 0.00 0.00 40.48 2.24
1010 1165 4.450976 TGGATTGGTGAAATCTATGTCCG 58.549 43.478 0.00 0.00 43.71 4.79
1075 1266 0.880278 TGCTGCGTGTCTTTCAGGAC 60.880 55.000 0.00 0.00 34.28 3.85
1116 1334 3.636231 TGGTGGGCAAGGTCCTCG 61.636 66.667 0.00 0.00 0.00 4.63
1117 1335 2.034221 GTGGTGGGCAAGGTCCTC 59.966 66.667 0.00 0.00 0.00 3.71
1118 1336 3.953775 CGTGGTGGGCAAGGTCCT 61.954 66.667 0.00 0.00 0.00 3.85
1140 1361 2.034879 GTGGACATGGACGCAGGTG 61.035 63.158 0.00 0.00 0.00 4.00
1161 1382 0.325296 ACTCTGCCGGGTGGATCTTA 60.325 55.000 2.18 0.00 37.49 2.10
1194 1415 2.413765 GGCGACTCGGATGTCTCC 59.586 66.667 0.00 0.00 35.14 3.71
1200 1421 3.989698 CTGTTGCGGCGACTCGGAT 62.990 63.158 20.38 0.00 0.00 4.18
1216 1437 0.107214 TTCTTGGCCCCGCTATTCTG 60.107 55.000 0.00 0.00 0.00 3.02
1228 1449 2.360475 AGAAGGGCGCTTCTTGGC 60.360 61.111 33.51 14.45 40.43 4.52
1242 1466 1.550524 ACAGCTGCTCGATTACCAGAA 59.449 47.619 15.27 0.00 0.00 3.02
1243 1467 1.134995 CACAGCTGCTCGATTACCAGA 60.135 52.381 15.27 0.00 0.00 3.86
1245 1469 0.894835 TCACAGCTGCTCGATTACCA 59.105 50.000 15.27 0.00 0.00 3.25
1251 1475 2.346541 CCTCCTCACAGCTGCTCGA 61.347 63.158 15.27 7.29 0.00 4.04
1254 1478 1.261238 GGTACCTCCTCACAGCTGCT 61.261 60.000 15.27 0.00 0.00 4.24
1268 1492 1.067071 CCTTCCTCTTGTCACGGTACC 60.067 57.143 0.16 0.16 0.00 3.34
1278 1502 2.747855 GTGCGGGCCTTCCTCTTG 60.748 66.667 0.84 0.00 0.00 3.02
1296 1520 1.294780 CTCTTCCTCCAGCAACGCT 59.705 57.895 0.00 0.00 40.77 5.07
1297 1521 1.743252 CCTCTTCCTCCAGCAACGC 60.743 63.158 0.00 0.00 0.00 4.84
1332 1556 1.728971 CTCACGAGCTGCCTGTTTAAG 59.271 52.381 0.00 0.00 0.00 1.85
1340 1564 0.107945 AATCTTCCTCACGAGCTGCC 60.108 55.000 0.00 0.00 0.00 4.85
1355 1579 0.453793 CGCCGAGTGACTCTGAATCT 59.546 55.000 11.26 0.00 0.00 2.40
1357 1581 1.153745 GCGCCGAGTGACTCTGAAT 60.154 57.895 11.26 0.00 0.00 2.57
1403 1627 2.093973 CCTCTAATGTCGACAAGCAGGT 60.094 50.000 24.13 0.98 0.00 4.00
1443 1667 1.866853 GCTGGCAAGGGAAAACTCCG 61.867 60.000 0.00 0.00 0.00 4.63
1446 1670 1.903404 CCGCTGGCAAGGGAAAACT 60.903 57.895 6.76 0.00 38.63 2.66
1468 1692 2.416547 CAGCCGAATCGTTGTTTCTCAT 59.583 45.455 0.82 0.00 0.00 2.90
1472 1696 1.136057 GGTCAGCCGAATCGTTGTTTC 60.136 52.381 0.82 0.00 0.00 2.78
1473 1697 0.872388 GGTCAGCCGAATCGTTGTTT 59.128 50.000 0.82 0.00 0.00 2.83
1516 1740 4.792804 GAGCCTGACCTGCTGGGC 62.793 72.222 14.82 12.09 43.36 5.36
1527 1751 2.381109 CTCGTTGCATCTGAGCCTG 58.619 57.895 0.00 0.00 0.00 4.85
1561 1785 0.747644 CCATTGTCGTGGCCTGCATA 60.748 55.000 3.32 0.00 31.43 3.14
1663 1892 3.557595 GCCTTCACCTCTTTACATCATCG 59.442 47.826 0.00 0.00 0.00 3.84
1939 2195 3.550561 TCGTGCGCTTTATTTTTCAGTG 58.449 40.909 9.73 0.00 0.00 3.66
1959 2215 1.927895 ATGCTATTAGCGGCGCTATC 58.072 50.000 38.35 26.43 46.26 2.08
1961 2217 2.230508 AGTAATGCTATTAGCGGCGCTA 59.769 45.455 35.39 35.39 46.26 4.26
2043 2319 3.827302 AGCAAGGTATAGCGCACTATAGT 59.173 43.478 11.47 0.00 41.09 2.12
2049 2325 3.368236 GCTATTAGCAAGGTATAGCGCAC 59.632 47.826 11.47 0.00 41.89 5.34
2059 2335 6.072673 CCCCTTAAATTACGCTATTAGCAAGG 60.073 42.308 15.64 16.03 42.58 3.61
2061 2337 5.239963 GCCCCTTAAATTACGCTATTAGCAA 59.760 40.000 15.64 3.93 42.58 3.91
2071 2347 0.379316 GCACCGCCCCTTAAATTACG 59.621 55.000 0.00 0.00 0.00 3.18
2202 2478 7.259161 GTTCATAACGGCCCATTATAAAACAA 58.741 34.615 17.15 4.19 0.00 2.83
2260 2536 4.215109 ACCAATGGCATACTATTCCCAAC 58.785 43.478 0.00 0.00 0.00 3.77
2306 2582 4.278975 AGAATCAAGGAGACACTTGTCC 57.721 45.455 5.73 0.00 46.11 4.02
2338 2614 5.362430 AGACTAGAGATGGACAAAGGTCATC 59.638 44.000 0.00 0.00 46.17 2.92
2398 2674 4.521146 CAGGTGCTACAAATCATCTTCCT 58.479 43.478 0.00 0.00 0.00 3.36
2401 2677 3.010584 ACCCAGGTGCTACAAATCATCTT 59.989 43.478 0.00 0.00 0.00 2.40
2422 2698 0.623723 TCATTTAGGGGGTGGAGCAC 59.376 55.000 0.00 0.00 0.00 4.40
2489 2767 6.011981 AGACACCCAAGTTTGATATCCCTAAA 60.012 38.462 0.00 0.00 0.00 1.85
2636 2915 6.106673 ACCAGAAAACGTATCTATGGTGAAG 58.893 40.000 9.27 0.00 0.00 3.02
2639 2918 8.433421 AAATACCAGAAAACGTATCTATGGTG 57.567 34.615 16.69 2.23 29.11 4.17
2640 2919 8.262227 TGAAATACCAGAAAACGTATCTATGGT 58.738 33.333 13.32 13.32 30.72 3.55
2641 2920 8.548721 GTGAAATACCAGAAAACGTATCTATGG 58.451 37.037 3.70 3.94 0.00 2.74
2642 2921 8.266682 CGTGAAATACCAGAAAACGTATCTATG 58.733 37.037 3.70 2.15 0.00 2.23
2643 2922 8.348983 CGTGAAATACCAGAAAACGTATCTAT 57.651 34.615 3.70 0.00 0.00 1.98
2644 2923 7.745022 CGTGAAATACCAGAAAACGTATCTA 57.255 36.000 3.70 0.00 0.00 1.98
2645 2924 6.642683 CGTGAAATACCAGAAAACGTATCT 57.357 37.500 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.