Multiple sequence alignment - TraesCS2D01G173800

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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 TraesCS2D01G173800 chr2D 100.000 2408 0 0 1 2408 117234723 117232316 0.000000e+00 4447
1 TraesCS2D01G173800 chr2D 94.231 104 6 0 2305 2408 487937004 487936901 2.480000e-35 159
2 TraesCS2D01G173800 chr2D 92.523 107 8 0 2302 2408 552138214 552138320 1.150000e-33 154
3 TraesCS2D01G173800 chr6D 97.789 1447 28 4 1 1444 120728938 120727493 0.000000e+00 2492
4 TraesCS2D01G173800 chr6D 93.269 104 7 0 2305 2408 307788298 307788195 1.150000e-33 154
5 TraesCS2D01G173800 chr6D 92.308 104 8 0 2305 2408 472504093 472503990 5.360000e-32 148
6 TraesCS2D01G173800 chr1D 97.901 1429 28 2 1 1428 455118477 455119904 0.000000e+00 2471
7 TraesCS2D01G173800 chr7D 97.765 1432 28 3 1 1429 636675830 636677260 0.000000e+00 2464
8 TraesCS2D01G173800 chr7D 92.523 107 8 0 2302 2408 602026746 602026852 1.150000e-33 154
9 TraesCS2D01G173800 chr7D 92.308 104 8 0 2305 2408 591859823 591859720 5.360000e-32 148
10 TraesCS2D01G173800 chr4B 95.284 1442 64 2 1 1438 464151043 464149602 0.000000e+00 2283
11 TraesCS2D01G173800 chr7A 93.958 1440 76 3 1 1429 109235649 109234210 0.000000e+00 2167
12 TraesCS2D01G173800 chr3B 94.089 1421 79 2 1 1420 605288451 605289867 0.000000e+00 2154
13 TraesCS2D01G173800 chr2A 93.846 1430 87 1 1 1429 602700146 602698717 0.000000e+00 2152
14 TraesCS2D01G173800 chr2A 94.071 253 13 2 2053 2303 118675974 118675722 1.350000e-102 383
15 TraesCS2D01G173800 chr2A 86.919 344 7 12 1618 1929 118676383 118676046 3.810000e-93 351
16 TraesCS2D01G173800 chr1B 94.862 1265 61 2 180 1440 442104724 442103460 0.000000e+00 1973
17 TraesCS2D01G173800 chr5A 84.658 1434 206 10 1 1429 169971270 169969846 0.000000e+00 1417
18 TraesCS2D01G173800 chr2B 89.109 404 18 14 1434 1829 167803349 167802964 1.670000e-131 479
19 TraesCS2D01G173800 chr2B 91.193 352 22 5 1955 2301 167802884 167802537 1.010000e-128 470
20 TraesCS2D01G173800 chr3D 94.231 104 6 0 2305 2408 16258352 16258249 2.480000e-35 159
21 TraesCS2D01G173800 chr5D 93.269 104 7 0 2305 2408 410393880 410393777 1.150000e-33 154
22 TraesCS2D01G173800 chr5D 92.523 107 8 0 2302 2408 510829470 510829576 1.150000e-33 154


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 TraesCS2D01G173800 chr2D 117232316 117234723 2407 True 4447.0 4447 100.000 1 2408 1 chr2D.!!$R1 2407
1 TraesCS2D01G173800 chr6D 120727493 120728938 1445 True 2492.0 2492 97.789 1 1444 1 chr6D.!!$R1 1443
2 TraesCS2D01G173800 chr1D 455118477 455119904 1427 False 2471.0 2471 97.901 1 1428 1 chr1D.!!$F1 1427
3 TraesCS2D01G173800 chr7D 636675830 636677260 1430 False 2464.0 2464 97.765 1 1429 1 chr7D.!!$F2 1428
4 TraesCS2D01G173800 chr4B 464149602 464151043 1441 True 2283.0 2283 95.284 1 1438 1 chr4B.!!$R1 1437
5 TraesCS2D01G173800 chr7A 109234210 109235649 1439 True 2167.0 2167 93.958 1 1429 1 chr7A.!!$R1 1428
6 TraesCS2D01G173800 chr3B 605288451 605289867 1416 False 2154.0 2154 94.089 1 1420 1 chr3B.!!$F1 1419
7 TraesCS2D01G173800 chr2A 602698717 602700146 1429 True 2152.0 2152 93.846 1 1429 1 chr2A.!!$R1 1428
8 TraesCS2D01G173800 chr2A 118675722 118676383 661 True 367.0 383 90.495 1618 2303 2 chr2A.!!$R2 685
9 TraesCS2D01G173800 chr1B 442103460 442104724 1264 True 1973.0 1973 94.862 180 1440 1 chr1B.!!$R1 1260
10 TraesCS2D01G173800 chr5A 169969846 169971270 1424 True 1417.0 1417 84.658 1 1429 1 chr5A.!!$R1 1428
11 TraesCS2D01G173800 chr2B 167802537 167803349 812 True 474.5 479 90.151 1434 2301 2 chr2B.!!$R1 867

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
880 885 0.987613 TGGTGCATGATAGCCTCCCA 60.988 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2104 0.035534 TGCAGCGGAGGCAGAAAATA 60.036 50.0 0.0 0.0 43.41 1.4 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
695 698 1.069091 TGACAGAAACGACGCGTATGA 60.069 47.619 13.97 0.00 39.99 2.15
880 885 0.987613 TGGTGCATGATAGCCTCCCA 60.988 55.000 0.00 0.00 0.00 4.37
936 941 2.452114 CTGGACCCCTCCTCCACT 59.548 66.667 0.00 0.00 37.48 4.00
974 979 4.020396 TCAATACAAATGGCAGCCATGTTT 60.020 37.500 28.35 17.98 44.40 2.83
1138 1146 2.211619 TTACCGTACGAACCTGCCCG 62.212 60.000 18.76 0.00 0.00 6.13
1309 1317 4.119862 GCAGAATAAGGTTAGTCATGCGA 58.880 43.478 0.51 0.00 30.67 5.10
1368 1384 3.790437 CTGTGCTCGGGGCTGGAT 61.790 66.667 0.00 0.00 42.39 3.41
1420 1436 5.819991 TGCCTCCTTGAGTAATGAAATCTT 58.180 37.500 0.00 0.00 0.00 2.40
1429 1445 9.231297 CTTGAGTAATGAAATCTTCCTTTACCA 57.769 33.333 0.00 0.00 32.25 3.25
1471 1487 0.962356 CAGTGCACAGTCCCCATTCC 60.962 60.000 21.04 0.00 0.00 3.01
1480 1496 3.747579 CCCCATTCCCCTGCTGCT 61.748 66.667 0.00 0.00 0.00 4.24
1487 1503 0.251341 TTCCCCTGCTGCTTCTTTCC 60.251 55.000 0.00 0.00 0.00 3.13
1488 1504 2.042831 CCCCTGCTGCTTCTTTCCG 61.043 63.158 0.00 0.00 0.00 4.30
1511 1527 1.747956 CTGTCAGCGCTACAGTATCG 58.252 55.000 25.87 9.16 39.61 2.92
1512 1528 0.380733 TGTCAGCGCTACAGTATCGG 59.619 55.000 10.99 0.00 0.00 4.18
1524 1540 0.746923 AGTATCGGCGGCCCTTTTTC 60.747 55.000 14.55 0.00 0.00 2.29
1525 1541 0.746923 GTATCGGCGGCCCTTTTTCT 60.747 55.000 14.55 0.00 0.00 2.52
1553 1569 2.227626 GCTTCCAGACTCTGAAAAAGGC 59.772 50.000 7.69 0.00 32.44 4.35
1554 1570 2.568623 TCCAGACTCTGAAAAAGGCC 57.431 50.000 7.69 0.00 32.44 5.19
1555 1571 2.057922 TCCAGACTCTGAAAAAGGCCT 58.942 47.619 0.00 0.00 32.44 5.19
1556 1572 3.248024 TCCAGACTCTGAAAAAGGCCTA 58.752 45.455 5.16 0.00 32.44 3.93
1570 1586 3.103091 GCCTACCCTACCCCGCAAG 62.103 68.421 0.00 0.00 0.00 4.01
1571 1587 2.504519 CTACCCTACCCCGCAAGC 59.495 66.667 0.00 0.00 0.00 4.01
1572 1588 2.039951 TACCCTACCCCGCAAGCT 59.960 61.111 0.00 0.00 0.00 3.74
1575 1591 1.749258 CCCTACCCCGCAAGCTTTC 60.749 63.158 0.00 0.00 0.00 2.62
1576 1592 1.299976 CCTACCCCGCAAGCTTTCT 59.700 57.895 0.00 0.00 0.00 2.52
1577 1593 0.539986 CCTACCCCGCAAGCTTTCTA 59.460 55.000 0.00 0.00 0.00 2.10
1578 1594 1.653151 CTACCCCGCAAGCTTTCTAC 58.347 55.000 0.00 0.00 0.00 2.59
1579 1595 0.251073 TACCCCGCAAGCTTTCTACC 59.749 55.000 0.00 0.00 0.00 3.18
1604 1620 1.675007 TGGGACAGGAGAGAGAGAGA 58.325 55.000 0.00 0.00 0.00 3.10
1605 1621 1.563879 TGGGACAGGAGAGAGAGAGAG 59.436 57.143 0.00 0.00 0.00 3.20
1607 1623 2.421529 GGGACAGGAGAGAGAGAGAGAC 60.422 59.091 0.00 0.00 0.00 3.36
1608 1624 2.238646 GGACAGGAGAGAGAGAGAGACA 59.761 54.545 0.00 0.00 0.00 3.41
1609 1625 3.535561 GACAGGAGAGAGAGAGAGACAG 58.464 54.545 0.00 0.00 0.00 3.51
1611 1627 1.915489 AGGAGAGAGAGAGAGACAGCA 59.085 52.381 0.00 0.00 0.00 4.41
1612 1628 2.017049 GGAGAGAGAGAGAGACAGCAC 58.983 57.143 0.00 0.00 0.00 4.40
1613 1629 2.356125 GGAGAGAGAGAGAGACAGCACT 60.356 54.545 0.00 0.00 0.00 4.40
1710 1733 3.771160 CTCCTCGTGTTCCCCCGG 61.771 72.222 0.00 0.00 0.00 5.73
1833 1881 2.669569 GTCCACATGCGTGCCACT 60.670 61.111 5.64 0.00 42.17 4.00
1846 1894 1.217244 GCCACTGGATCGTTACGGT 59.783 57.895 4.53 0.00 0.00 4.83
1866 1914 2.536761 TTGTTTGGTACTCCGGTCAG 57.463 50.000 0.00 0.00 36.30 3.51
1879 1927 2.179517 GTCAGAGGCTCCACGACG 59.820 66.667 11.71 0.00 0.00 5.12
1881 1929 4.135153 CAGAGGCTCCACGACGGG 62.135 72.222 11.71 0.00 34.36 5.28
1928 1982 1.080093 CGTGTTCGCTGGAGCCTAA 60.080 57.895 0.00 0.00 37.91 2.69
1929 1983 1.352156 CGTGTTCGCTGGAGCCTAAC 61.352 60.000 5.10 5.10 37.91 2.34
1930 1984 1.080093 TGTTCGCTGGAGCCTAACG 60.080 57.895 6.90 0.00 36.67 3.18
1931 1985 2.125673 TTCGCTGGAGCCTAACGC 60.126 61.111 0.00 0.00 37.91 4.84
1932 1986 3.659089 TTCGCTGGAGCCTAACGCC 62.659 63.158 0.00 0.00 38.78 5.68
1942 1996 2.105128 CTAACGCCGCTCCCTCTG 59.895 66.667 0.00 0.00 0.00 3.35
1943 1997 4.143333 TAACGCCGCTCCCTCTGC 62.143 66.667 0.00 0.00 0.00 4.26
1947 2001 2.835431 GCCGCTCCCTCTGCTCTA 60.835 66.667 0.00 0.00 0.00 2.43
1948 2002 2.206536 GCCGCTCCCTCTGCTCTAT 61.207 63.158 0.00 0.00 0.00 1.98
1949 2003 1.963679 CCGCTCCCTCTGCTCTATC 59.036 63.158 0.00 0.00 0.00 2.08
1950 2004 1.531739 CCGCTCCCTCTGCTCTATCC 61.532 65.000 0.00 0.00 0.00 2.59
1951 2005 0.825425 CGCTCCCTCTGCTCTATCCA 60.825 60.000 0.00 0.00 0.00 3.41
1952 2006 0.968405 GCTCCCTCTGCTCTATCCAG 59.032 60.000 0.00 0.00 0.00 3.86
1953 2007 0.968405 CTCCCTCTGCTCTATCCAGC 59.032 60.000 0.00 0.00 40.13 4.85
1957 2011 0.680618 CTCTGCTCTATCCAGCCCAG 59.319 60.000 0.00 0.00 38.80 4.45
1973 2027 0.179000 CCAGCCATCCAGACAGGTAC 59.821 60.000 0.00 0.00 39.02 3.34
1976 2030 1.226974 CCATCCAGACAGGTACGCG 60.227 63.158 3.53 3.53 39.02 6.01
2024 2079 1.313091 GGAGGCGAAAATGTGGGACC 61.313 60.000 0.00 0.00 0.00 4.46
2027 2082 0.322546 GGCGAAAATGTGGGACCTCT 60.323 55.000 0.00 0.00 0.00 3.69
2036 2091 1.203087 TGTGGGACCTCTTCTCCGTTA 60.203 52.381 0.00 0.00 0.00 3.18
2048 2103 6.017852 CCTCTTCTCCGTTAAATAATTCAGCC 60.018 42.308 0.00 0.00 0.00 4.85
2049 2104 6.650120 TCTTCTCCGTTAAATAATTCAGCCT 58.350 36.000 0.00 0.00 0.00 4.58
2252 2312 2.052104 CCCCCTTCCACGCCAAATC 61.052 63.158 0.00 0.00 0.00 2.17
2307 2368 7.478520 AATTATTGCAAAGTAGTACTAGCGG 57.521 36.000 17.74 5.14 33.66 5.52
2308 2369 2.288961 TGCAAAGTAGTACTAGCGGC 57.711 50.000 17.74 12.92 33.66 6.53
2309 2370 1.134907 TGCAAAGTAGTACTAGCGGCC 60.135 52.381 17.74 0.00 33.66 6.13
2310 2371 1.836383 CAAAGTAGTACTAGCGGCCG 58.164 55.000 24.05 24.05 0.00 6.13
2311 2372 1.133790 CAAAGTAGTACTAGCGGCCGT 59.866 52.381 28.70 16.08 0.00 5.68
2312 2373 1.020437 AAGTAGTACTAGCGGCCGTC 58.980 55.000 28.70 19.09 0.00 4.79
2313 2374 0.817229 AGTAGTACTAGCGGCCGTCC 60.817 60.000 28.70 11.34 0.00 4.79
2314 2375 1.097547 GTAGTACTAGCGGCCGTCCA 61.098 60.000 28.70 11.20 0.00 4.02
2315 2376 0.394216 TAGTACTAGCGGCCGTCCAA 60.394 55.000 28.70 8.85 0.00 3.53
2316 2377 1.517913 GTACTAGCGGCCGTCCAAC 60.518 63.158 28.70 14.90 0.00 3.77
2317 2378 1.679977 TACTAGCGGCCGTCCAACT 60.680 57.895 28.70 17.19 0.00 3.16
2318 2379 0.394216 TACTAGCGGCCGTCCAACTA 60.394 55.000 28.70 17.41 0.00 2.24
2319 2380 1.226888 CTAGCGGCCGTCCAACTAC 60.227 63.158 28.70 7.06 0.00 2.73
2320 2381 2.931713 CTAGCGGCCGTCCAACTACG 62.932 65.000 28.70 8.96 42.49 3.51
2321 2382 4.424566 GCGGCCGTCCAACTACGA 62.425 66.667 28.70 0.00 45.68 3.43
2322 2383 2.505557 CGGCCGTCCAACTACGAC 60.506 66.667 19.50 0.00 45.68 4.34
2328 2389 3.871775 GTCCAACTACGACGGTCAA 57.128 52.632 9.10 0.00 0.00 3.18
2329 2390 1.412387 GTCCAACTACGACGGTCAAC 58.588 55.000 9.10 0.00 0.00 3.18
2330 2391 1.031235 TCCAACTACGACGGTCAACA 58.969 50.000 9.10 0.00 0.00 3.33
2331 2392 1.614903 TCCAACTACGACGGTCAACAT 59.385 47.619 9.10 0.00 0.00 2.71
2332 2393 2.819019 TCCAACTACGACGGTCAACATA 59.181 45.455 9.10 0.00 0.00 2.29
2333 2394 3.255395 TCCAACTACGACGGTCAACATAA 59.745 43.478 9.10 0.00 0.00 1.90
2334 2395 4.082081 TCCAACTACGACGGTCAACATAAT 60.082 41.667 9.10 0.00 0.00 1.28
2335 2396 4.628333 CCAACTACGACGGTCAACATAATT 59.372 41.667 9.10 0.00 0.00 1.40
2336 2397 5.121142 CCAACTACGACGGTCAACATAATTT 59.879 40.000 9.10 0.00 0.00 1.82
2337 2398 6.310956 CCAACTACGACGGTCAACATAATTTA 59.689 38.462 9.10 0.00 0.00 1.40
2338 2399 7.010738 CCAACTACGACGGTCAACATAATTTAT 59.989 37.037 9.10 0.00 0.00 1.40
2339 2400 7.459394 ACTACGACGGTCAACATAATTTATG 57.541 36.000 13.64 13.64 41.88 1.90
2340 2401 7.259882 ACTACGACGGTCAACATAATTTATGA 58.740 34.615 20.54 0.00 39.45 2.15
2341 2402 7.924412 ACTACGACGGTCAACATAATTTATGAT 59.076 33.333 20.54 8.19 39.45 2.45
2342 2403 6.943981 ACGACGGTCAACATAATTTATGATG 58.056 36.000 20.54 18.35 39.47 3.07
2343 2404 6.759356 ACGACGGTCAACATAATTTATGATGA 59.241 34.615 19.61 19.61 43.04 2.92
2349 2410 7.581213 TCAACATAATTTATGATGACCACCC 57.419 36.000 19.61 0.00 41.24 4.61
2350 2411 7.122048 TCAACATAATTTATGATGACCACCCA 58.878 34.615 19.61 2.91 41.24 4.51
2351 2412 6.959639 ACATAATTTATGATGACCACCCAC 57.040 37.500 20.54 0.00 39.45 4.61
2352 2413 5.833131 ACATAATTTATGATGACCACCCACC 59.167 40.000 20.54 0.00 39.45 4.61
2353 2414 4.608170 AATTTATGATGACCACCCACCT 57.392 40.909 0.00 0.00 0.00 4.00
2354 2415 4.608170 ATTTATGATGACCACCCACCTT 57.392 40.909 0.00 0.00 0.00 3.50
2355 2416 3.364460 TTATGATGACCACCCACCTTG 57.636 47.619 0.00 0.00 0.00 3.61
2356 2417 0.332632 ATGATGACCACCCACCTTGG 59.667 55.000 0.00 0.00 40.32 3.61
2365 2426 2.681064 CCACCTTGGGCCCATGTG 60.681 66.667 33.23 33.23 32.67 3.21
2366 2427 2.118076 CACCTTGGGCCCATGTGT 59.882 61.111 32.39 26.20 0.00 3.72
2367 2428 1.533753 CACCTTGGGCCCATGTGTT 60.534 57.895 32.39 17.99 0.00 3.32
2368 2429 0.251564 CACCTTGGGCCCATGTGTTA 60.252 55.000 32.39 16.92 0.00 2.41
2369 2430 0.039618 ACCTTGGGCCCATGTGTTAG 59.960 55.000 29.23 19.04 0.00 2.34
2370 2431 1.322538 CCTTGGGCCCATGTGTTAGC 61.323 60.000 29.23 0.00 0.00 3.09
2371 2432 1.656818 CTTGGGCCCATGTGTTAGCG 61.657 60.000 29.23 1.75 0.00 4.26
2372 2433 2.130821 TTGGGCCCATGTGTTAGCGA 62.131 55.000 29.23 2.53 0.00 4.93
2373 2434 2.112815 GGGCCCATGTGTTAGCGAC 61.113 63.158 19.95 0.00 0.00 5.19
2374 2435 2.461110 GGCCCATGTGTTAGCGACG 61.461 63.158 0.00 0.00 0.00 5.12
2375 2436 2.461110 GCCCATGTGTTAGCGACGG 61.461 63.158 0.00 0.00 0.00 4.79
2376 2437 2.461110 CCCATGTGTTAGCGACGGC 61.461 63.158 0.00 0.00 40.37 5.68
2377 2438 2.695055 CATGTGTTAGCGACGGCG 59.305 61.111 6.12 6.12 46.35 6.46
2378 2439 2.508439 ATGTGTTAGCGACGGCGG 60.508 61.111 15.06 0.00 46.35 6.13
2380 2441 3.177249 GTGTTAGCGACGGCGGTC 61.177 66.667 23.24 6.63 46.64 4.79
2390 2451 2.048503 CGGCGGTCGTCCTCTTTT 60.049 61.111 0.00 0.00 0.00 2.27
2391 2452 1.213537 CGGCGGTCGTCCTCTTTTA 59.786 57.895 0.00 0.00 0.00 1.52
2392 2453 0.388907 CGGCGGTCGTCCTCTTTTAA 60.389 55.000 0.00 0.00 0.00 1.52
2393 2454 1.356938 GGCGGTCGTCCTCTTTTAAG 58.643 55.000 0.00 0.00 0.00 1.85
2394 2455 0.720027 GCGGTCGTCCTCTTTTAAGC 59.280 55.000 0.00 0.00 0.00 3.09
2395 2456 1.356938 CGGTCGTCCTCTTTTAAGCC 58.643 55.000 0.00 0.00 0.00 4.35
2396 2457 1.356938 GGTCGTCCTCTTTTAAGCCG 58.643 55.000 0.00 0.00 0.00 5.52
2397 2458 1.356938 GTCGTCCTCTTTTAAGCCGG 58.643 55.000 0.00 0.00 0.00 6.13
2398 2459 0.248289 TCGTCCTCTTTTAAGCCGGG 59.752 55.000 2.18 0.00 0.00 5.73
2399 2460 1.366854 CGTCCTCTTTTAAGCCGGGC 61.367 60.000 12.11 12.11 0.00 6.13
2400 2461 1.078708 TCCTCTTTTAAGCCGGGCG 60.079 57.895 14.39 0.00 0.00 6.13
2401 2462 1.376812 CCTCTTTTAAGCCGGGCGT 60.377 57.895 14.39 13.69 0.00 5.68
2402 2463 1.644786 CCTCTTTTAAGCCGGGCGTG 61.645 60.000 18.00 0.50 0.00 5.34
2403 2464 0.672401 CTCTTTTAAGCCGGGCGTGA 60.672 55.000 18.00 6.51 0.00 4.35
2404 2465 0.672401 TCTTTTAAGCCGGGCGTGAG 60.672 55.000 18.00 12.07 0.00 3.51
2405 2466 1.644786 CTTTTAAGCCGGGCGTGAGG 61.645 60.000 18.00 3.06 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 176 1.272313 TGGCGTTGTAGGAGGTCTAGT 60.272 52.381 0.00 0.00 0.00 2.57
880 885 4.760204 GGCACTTCCTTTGTGTGTATAACT 59.240 41.667 0.00 0.00 37.70 2.24
936 941 1.214305 ATTGAGCTTAGCCCACCCCA 61.214 55.000 0.00 0.00 0.00 4.96
1138 1146 2.668457 CACAGTCGAGCTCAACCATAAC 59.332 50.000 15.40 0.00 0.00 1.89
1437 1453 0.040958 CACTGCAGCAACCTTCGTTC 60.041 55.000 15.27 0.00 0.00 3.95
1440 1456 2.253452 GCACTGCAGCAACCTTCG 59.747 61.111 15.27 0.00 0.00 3.79
1471 1487 2.694760 GCGGAAAGAAGCAGCAGGG 61.695 63.158 0.00 0.00 0.00 4.45
1480 1496 0.944311 GCTGACAGTCGCGGAAAGAA 60.944 55.000 6.13 0.00 0.00 2.52
1500 1516 2.355956 GGCCGCCGATACTGTAGC 60.356 66.667 0.00 0.00 0.00 3.58
1501 1517 1.745320 AAGGGCCGCCGATACTGTAG 61.745 60.000 2.55 0.00 0.00 2.74
1502 1518 1.332144 AAAGGGCCGCCGATACTGTA 61.332 55.000 2.55 0.00 0.00 2.74
1504 1520 1.029947 AAAAAGGGCCGCCGATACTG 61.030 55.000 2.55 0.00 0.00 2.74
1505 1521 0.746923 GAAAAAGGGCCGCCGATACT 60.747 55.000 2.55 0.00 0.00 2.12
1506 1522 0.746923 AGAAAAAGGGCCGCCGATAC 60.747 55.000 2.55 0.00 0.00 2.24
1507 1523 0.746563 CAGAAAAAGGGCCGCCGATA 60.747 55.000 2.55 0.00 0.00 2.92
1508 1524 2.046285 CAGAAAAAGGGCCGCCGAT 61.046 57.895 2.55 0.00 0.00 4.18
1509 1525 2.671619 CAGAAAAAGGGCCGCCGA 60.672 61.111 2.55 0.00 0.00 5.54
1510 1526 2.265182 TTCAGAAAAAGGGCCGCCG 61.265 57.895 2.55 0.00 0.00 6.46
1511 1527 1.289066 GTTCAGAAAAAGGGCCGCC 59.711 57.895 0.00 0.00 0.00 6.13
1512 1528 1.289066 GGTTCAGAAAAAGGGCCGC 59.711 57.895 0.00 0.00 0.00 6.53
1524 1540 0.390472 GAGTCTGGAAGCGGGTTCAG 60.390 60.000 20.23 14.95 36.82 3.02
1525 1541 0.832135 AGAGTCTGGAAGCGGGTTCA 60.832 55.000 20.23 7.00 36.82 3.18
1553 1569 3.103091 GCTTGCGGGGTAGGGTAGG 62.103 68.421 0.00 0.00 0.00 3.18
1554 1570 1.623542 AAGCTTGCGGGGTAGGGTAG 61.624 60.000 0.00 0.00 0.00 3.18
1555 1571 1.202769 AAAGCTTGCGGGGTAGGGTA 61.203 55.000 0.00 0.00 0.00 3.69
1556 1572 2.479820 GAAAGCTTGCGGGGTAGGGT 62.480 60.000 0.00 0.00 0.00 4.34
1579 1595 0.542938 TCTCTCCTGTCCCAGTGTGG 60.543 60.000 0.00 0.00 37.25 4.17
1588 1604 3.535561 CTGTCTCTCTCTCTCTCCTGTC 58.464 54.545 0.00 0.00 0.00 3.51
1591 1607 1.915489 TGCTGTCTCTCTCTCTCTCCT 59.085 52.381 0.00 0.00 0.00 3.69
1602 1618 3.699894 CGGCCCAGTGCTGTCTCT 61.700 66.667 0.00 0.00 41.73 3.10
1833 1881 2.548904 CCAAACAAACCGTAACGATCCA 59.451 45.455 0.00 0.00 0.00 3.41
1846 1894 2.435069 TCTGACCGGAGTACCAAACAAA 59.565 45.455 9.46 0.00 35.59 2.83
1930 1984 2.153547 GATAGAGCAGAGGGAGCGGC 62.154 65.000 0.00 0.00 37.01 6.53
1931 1985 1.531739 GGATAGAGCAGAGGGAGCGG 61.532 65.000 0.00 0.00 37.01 5.52
1932 1986 0.825425 TGGATAGAGCAGAGGGAGCG 60.825 60.000 0.00 0.00 37.01 5.03
1933 1987 0.968405 CTGGATAGAGCAGAGGGAGC 59.032 60.000 0.00 0.00 0.00 4.70
1942 1996 1.776975 ATGGCTGGGCTGGATAGAGC 61.777 60.000 0.00 0.00 38.34 4.09
1943 1997 0.324285 GATGGCTGGGCTGGATAGAG 59.676 60.000 0.00 0.00 0.00 2.43
1944 1998 1.130054 GGATGGCTGGGCTGGATAGA 61.130 60.000 0.00 0.00 0.00 1.98
1945 1999 1.377994 GGATGGCTGGGCTGGATAG 59.622 63.158 0.00 0.00 0.00 2.08
1946 2000 1.385773 TGGATGGCTGGGCTGGATA 60.386 57.895 0.00 0.00 0.00 2.59
1947 2001 2.697263 TGGATGGCTGGGCTGGAT 60.697 61.111 0.00 0.00 0.00 3.41
1948 2002 3.414193 CTGGATGGCTGGGCTGGA 61.414 66.667 0.00 0.00 0.00 3.86
1949 2003 3.414193 TCTGGATGGCTGGGCTGG 61.414 66.667 0.00 0.00 0.00 4.85
1950 2004 2.124403 GTCTGGATGGCTGGGCTG 60.124 66.667 0.00 0.00 0.00 4.85
1951 2005 2.611800 TGTCTGGATGGCTGGGCT 60.612 61.111 0.00 0.00 0.00 5.19
1952 2006 2.124403 CTGTCTGGATGGCTGGGC 60.124 66.667 0.00 0.00 0.00 5.36
1953 2007 0.982852 TACCTGTCTGGATGGCTGGG 60.983 60.000 2.23 0.00 42.74 4.45
1957 2011 1.521681 GCGTACCTGTCTGGATGGC 60.522 63.158 2.23 0.00 39.71 4.40
1976 2030 0.663153 GGATCCAACGCCAGTTATGC 59.337 55.000 6.95 0.00 38.79 3.14
1993 2048 4.760047 GCCTCCGCTGCGAAAGGA 62.760 66.667 33.08 19.04 33.58 3.36
2024 2079 6.763610 AGGCTGAATTATTTAACGGAGAAGAG 59.236 38.462 0.00 0.00 0.00 2.85
2027 2082 8.974060 AATAGGCTGAATTATTTAACGGAGAA 57.026 30.769 0.00 0.00 0.00 2.87
2036 2091 7.201947 GGAGGCAGAAAATAGGCTGAATTATTT 60.202 37.037 0.00 0.00 41.09 1.40
2048 2103 0.659957 GCAGCGGAGGCAGAAAATAG 59.340 55.000 0.00 0.00 43.41 1.73
2049 2104 0.035534 TGCAGCGGAGGCAGAAAATA 60.036 50.000 0.00 0.00 43.41 1.40
2108 2167 1.076014 TGACGTGGTAGAGGCTGGA 59.924 57.895 0.00 0.00 0.00 3.86
2137 2196 1.269621 CCGCTAAGATTGGGACGTAGG 60.270 57.143 0.00 0.00 0.00 3.18
2164 2223 3.774959 GACGCGATGCATCCTCCGT 62.775 63.158 25.22 25.22 0.00 4.69
2195 2254 3.435186 GAGGCTTTGGGTGAGCGC 61.435 66.667 0.00 0.00 41.03 5.92
2204 2263 1.310933 ATTCCAGCAGCGAGGCTTTG 61.311 55.000 0.00 0.00 42.71 2.77
2303 2364 4.430765 CGTAGTTGGACGGCCGCT 62.431 66.667 28.58 16.64 39.19 5.52
2304 2365 4.424566 TCGTAGTTGGACGGCCGC 62.425 66.667 28.58 18.35 43.12 6.53
2305 2366 2.505557 GTCGTAGTTGGACGGCCG 60.506 66.667 26.86 26.86 41.55 6.13
2310 2371 1.269206 TGTTGACCGTCGTAGTTGGAC 60.269 52.381 0.00 0.00 0.00 4.02
2311 2372 1.031235 TGTTGACCGTCGTAGTTGGA 58.969 50.000 0.00 0.00 0.00 3.53
2312 2373 2.074547 ATGTTGACCGTCGTAGTTGG 57.925 50.000 0.00 0.00 0.00 3.77
2313 2374 5.773239 AATTATGTTGACCGTCGTAGTTG 57.227 39.130 0.00 0.00 0.00 3.16
2314 2375 7.760794 TCATAAATTATGTTGACCGTCGTAGTT 59.239 33.333 12.18 0.00 37.45 2.24
2315 2376 7.259882 TCATAAATTATGTTGACCGTCGTAGT 58.740 34.615 12.18 0.00 37.45 2.73
2316 2377 7.688478 TCATAAATTATGTTGACCGTCGTAG 57.312 36.000 12.18 0.00 37.45 3.51
2317 2378 7.921745 TCATCATAAATTATGTTGACCGTCGTA 59.078 33.333 17.88 0.39 38.99 3.43
2318 2379 6.759356 TCATCATAAATTATGTTGACCGTCGT 59.241 34.615 17.88 0.00 38.99 4.34
2319 2380 7.172654 TCATCATAAATTATGTTGACCGTCG 57.827 36.000 17.88 0.00 38.99 5.12
2325 2386 7.068103 GTGGGTGGTCATCATAAATTATGTTGA 59.932 37.037 17.88 17.88 40.62 3.18
2326 2387 7.202526 GTGGGTGGTCATCATAAATTATGTTG 58.797 38.462 14.65 14.65 37.27 3.33
2327 2388 6.323739 GGTGGGTGGTCATCATAAATTATGTT 59.676 38.462 12.18 2.16 37.45 2.71
2328 2389 5.833131 GGTGGGTGGTCATCATAAATTATGT 59.167 40.000 12.18 0.00 37.45 2.29
2329 2390 6.070656 AGGTGGGTGGTCATCATAAATTATG 58.929 40.000 6.65 6.65 37.52 1.90
2330 2391 6.279813 AGGTGGGTGGTCATCATAAATTAT 57.720 37.500 0.00 0.00 0.00 1.28
2331 2392 5.725551 AGGTGGGTGGTCATCATAAATTA 57.274 39.130 0.00 0.00 0.00 1.40
2332 2393 4.608170 AGGTGGGTGGTCATCATAAATT 57.392 40.909 0.00 0.00 0.00 1.82
2333 2394 4.280819 CAAGGTGGGTGGTCATCATAAAT 58.719 43.478 0.00 0.00 0.00 1.40
2334 2395 3.563261 CCAAGGTGGGTGGTCATCATAAA 60.563 47.826 0.00 0.00 32.67 1.40
2335 2396 2.025416 CCAAGGTGGGTGGTCATCATAA 60.025 50.000 0.00 0.00 32.67 1.90
2336 2397 1.563879 CCAAGGTGGGTGGTCATCATA 59.436 52.381 0.00 0.00 32.67 2.15
2337 2398 0.332632 CCAAGGTGGGTGGTCATCAT 59.667 55.000 0.00 0.00 32.67 2.45
2338 2399 1.767036 CCAAGGTGGGTGGTCATCA 59.233 57.895 0.00 0.00 32.67 3.07
2339 2400 4.743018 CCAAGGTGGGTGGTCATC 57.257 61.111 0.00 0.00 32.67 2.92
2348 2409 2.681064 CACATGGGCCCAAGGTGG 60.681 66.667 35.61 23.71 37.25 4.61
2349 2410 0.251564 TAACACATGGGCCCAAGGTG 60.252 55.000 38.64 38.64 39.53 4.00
2350 2411 0.039618 CTAACACATGGGCCCAAGGT 59.960 55.000 32.58 26.98 0.00 3.50
2351 2412 1.322538 GCTAACACATGGGCCCAAGG 61.323 60.000 32.58 26.24 0.00 3.61
2352 2413 1.656818 CGCTAACACATGGGCCCAAG 61.657 60.000 32.58 28.70 0.00 3.61
2353 2414 1.677300 CGCTAACACATGGGCCCAA 60.677 57.895 32.58 13.16 0.00 4.12
2354 2415 2.045438 CGCTAACACATGGGCCCA 60.045 61.111 30.92 30.92 0.00 5.36
2355 2416 2.112815 GTCGCTAACACATGGGCCC 61.113 63.158 17.59 17.59 0.00 5.80
2356 2417 2.461110 CGTCGCTAACACATGGGCC 61.461 63.158 0.00 0.00 0.00 5.80
2357 2418 2.461110 CCGTCGCTAACACATGGGC 61.461 63.158 0.00 0.00 0.00 5.36
2358 2419 2.461110 GCCGTCGCTAACACATGGG 61.461 63.158 0.00 0.00 0.00 4.00
2359 2420 2.798501 CGCCGTCGCTAACACATGG 61.799 63.158 0.00 0.00 0.00 3.66
2360 2421 2.695055 CGCCGTCGCTAACACATG 59.305 61.111 0.00 0.00 0.00 3.21
2361 2422 2.508439 CCGCCGTCGCTAACACAT 60.508 61.111 0.00 0.00 0.00 3.21
2362 2423 3.902162 GACCGCCGTCGCTAACACA 62.902 63.158 0.00 0.00 0.00 3.72
2363 2424 3.177249 GACCGCCGTCGCTAACAC 61.177 66.667 0.00 0.00 0.00 3.32
2373 2434 0.388907 TTAAAAGAGGACGACCGCCG 60.389 55.000 3.80 0.00 45.44 6.46
2374 2435 1.356938 CTTAAAAGAGGACGACCGCC 58.643 55.000 3.80 0.00 41.83 6.13
2375 2436 0.720027 GCTTAAAAGAGGACGACCGC 59.280 55.000 0.00 0.00 41.83 5.68
2376 2437 1.356938 GGCTTAAAAGAGGACGACCG 58.643 55.000 0.00 0.00 41.83 4.79
2377 2438 1.356938 CGGCTTAAAAGAGGACGACC 58.643 55.000 0.00 0.00 0.00 4.79
2378 2439 1.356938 CCGGCTTAAAAGAGGACGAC 58.643 55.000 0.00 0.00 0.00 4.34
2379 2440 0.248289 CCCGGCTTAAAAGAGGACGA 59.752 55.000 0.00 0.00 0.00 4.20
2380 2441 1.366854 GCCCGGCTTAAAAGAGGACG 61.367 60.000 0.71 0.00 0.00 4.79
2381 2442 1.366854 CGCCCGGCTTAAAAGAGGAC 61.367 60.000 8.05 0.00 0.00 3.85
2382 2443 1.078708 CGCCCGGCTTAAAAGAGGA 60.079 57.895 8.05 0.00 0.00 3.71
2383 2444 1.376812 ACGCCCGGCTTAAAAGAGG 60.377 57.895 8.05 0.00 0.00 3.69
2384 2445 0.672401 TCACGCCCGGCTTAAAAGAG 60.672 55.000 8.05 0.00 0.00 2.85
2385 2446 0.672401 CTCACGCCCGGCTTAAAAGA 60.672 55.000 8.05 0.00 0.00 2.52
2386 2447 1.644786 CCTCACGCCCGGCTTAAAAG 61.645 60.000 8.05 0.00 0.00 2.27
2387 2448 1.673009 CCTCACGCCCGGCTTAAAA 60.673 57.895 8.05 0.00 0.00 1.52
2388 2449 2.046700 CCTCACGCCCGGCTTAAA 60.047 61.111 8.05 0.00 0.00 1.52
2389 2450 4.770874 GCCTCACGCCCGGCTTAA 62.771 66.667 8.05 0.00 42.98 1.85


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

AutoCloner maintained by Alex Coulton.