Multiple sequence alignment - TraesCS4A01G427300

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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 TraesCS4A01G427300 chr4A 100.000 2409 0 0 1 2409 698174294 698176702 0.000000e+00 4449.0
1 TraesCS4A01G427300 chr4A 93.951 1091 44 8 805 1880 699004182 699005265 0.000000e+00 1629.0
2 TraesCS4A01G427300 chr4A 89.162 489 49 4 100 587 698835732 698836217 7.370000e-170 606.0
3 TraesCS4A01G427300 chr4A 88.548 489 52 4 100 587 698961670 698962155 7.420000e-165 590.0
4 TraesCS4A01G427300 chr4A 84.634 410 32 11 1240 1637 699007342 699007732 1.750000e-101 379.0
5 TraesCS4A01G427300 chr7D 84.758 1673 160 48 1 1637 30242271 30240658 0.000000e+00 1589.0
6 TraesCS4A01G427300 chr7D 94.801 327 14 3 2084 2409 508339711 508339387 7.680000e-140 507.0
7 TraesCS4A01G427300 chr7D 88.053 226 16 3 1633 1852 30240630 30240410 8.540000e-65 257.0
8 TraesCS4A01G427300 chr7D 84.884 172 7 8 1936 2091 508340320 508340152 3.210000e-34 156.0
9 TraesCS4A01G427300 chr7A 84.385 1268 125 40 414 1637 30640363 30639125 0.000000e+00 1177.0
10 TraesCS4A01G427300 chr7A 90.455 220 15 3 1633 1852 30639097 30638884 3.920000e-73 285.0
11 TraesCS4A01G427300 chr6A 87.963 108 11 2 2217 2323 123511776 123511882 2.510000e-25 126.0
12 TraesCS4A01G427300 chr2D 80.682 88 17 0 507 594 448203447 448203360 4.300000e-08 69.4
13 TraesCS4A01G427300 chr2B 88.889 54 6 0 542 595 528160427 528160374 1.550000e-07 67.6


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 TraesCS4A01G427300 chr4A 698174294 698176702 2408 False 4449.0 4449 100.0000 1 2409 1 chr4A.!!$F1 2408
1 TraesCS4A01G427300 chr4A 699004182 699007732 3550 False 1004.0 1629 89.2925 805 1880 2 chr4A.!!$F4 1075
2 TraesCS4A01G427300 chr7D 30240410 30242271 1861 True 923.0 1589 86.4055 1 1852 2 chr7D.!!$R1 1851
3 TraesCS4A01G427300 chr7D 508339387 508340320 933 True 331.5 507 89.8425 1936 2409 2 chr7D.!!$R2 473
4 TraesCS4A01G427300 chr7A 30638884 30640363 1479 True 731.0 1177 87.4200 414 1852 2 chr7A.!!$R1 1438

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
428 431 0.032912 AGGCATGGTGATGGATTGCA 60.033 50.0 0.0 0.0 35.04 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 4705 0.03601 GCTGCTAGGACATGGTGTGT 60.036 55.0 0.0 0.0 45.83 3.72 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
36 38 5.526506 AAGTACGAATACGCCTCCTATTT 57.473 39.130 0.00 0.00 43.96 1.40
41 43 5.180271 ACGAATACGCCTCCTATTTCAAAA 58.820 37.500 0.00 0.00 43.96 2.44
42 44 5.064325 ACGAATACGCCTCCTATTTCAAAAC 59.936 40.000 0.00 0.00 43.96 2.43
45 47 1.749063 CGCCTCCTATTTCAAAACCCC 59.251 52.381 0.00 0.00 0.00 4.95
49 51 4.017126 CCTCCTATTTCAAAACCCCAGTC 58.983 47.826 0.00 0.00 0.00 3.51
53 55 1.448922 TTTCAAAACCCCAGTCGCCG 61.449 55.000 0.00 0.00 0.00 6.46
68 70 2.966309 GCCGCCAAAGGTGTTCTCG 61.966 63.158 0.00 0.00 0.00 4.04
73 75 0.878523 CCAAAGGTGTTCTCGACGCA 60.879 55.000 0.00 0.00 40.59 5.24
77 79 3.470567 GTGTTCTCGACGCAGCCG 61.471 66.667 0.00 0.00 38.64 5.52
82 84 4.492160 CTCGACGCAGCCGCCTTA 62.492 66.667 0.00 0.00 38.22 2.69
144 146 2.280103 AGAGGAGTGAGGACCTGTCTA 58.720 52.381 0.00 0.00 36.57 2.59
150 152 4.223032 GGAGTGAGGACCTGTCTATTTCAA 59.777 45.833 0.00 0.00 0.00 2.69
151 153 5.280011 GGAGTGAGGACCTGTCTATTTCAAA 60.280 44.000 0.00 0.00 0.00 2.69
191 193 3.499737 GTTCCCGTGGCAGCATCG 61.500 66.667 0.00 0.00 0.00 3.84
208 210 2.390599 CGATGAGGTGGTGGCAACG 61.391 63.158 0.00 0.00 42.51 4.10
211 213 0.908910 ATGAGGTGGTGGCAACGATA 59.091 50.000 0.00 0.00 42.51 2.92
231 233 5.390673 CGATATCGTGCTAGAATAAGGTCGT 60.391 44.000 17.06 0.00 34.11 4.34
233 235 3.766151 TCGTGCTAGAATAAGGTCGTTG 58.234 45.455 0.00 0.00 0.00 4.10
243 245 1.407656 AAGGTCGTTGTGGCCTCTCA 61.408 55.000 3.32 0.00 0.00 3.27
247 249 0.601558 TCGTTGTGGCCTCTCACTAC 59.398 55.000 3.32 0.00 39.04 2.73
260 262 0.037882 TCACTACCTCGACGACGTCT 60.038 55.000 24.36 9.36 40.69 4.18
267 269 0.446616 CTCGACGACGTCTCATCCAA 59.553 55.000 24.36 2.13 40.69 3.53
275 277 0.392863 CGTCTCATCCAATGGCACCA 60.393 55.000 0.00 0.00 0.00 4.17
361 363 6.968131 TGTTCCTATCGAGAAGAACAATTG 57.032 37.500 19.11 3.24 44.04 2.32
363 365 5.677319 TCCTATCGAGAAGAACAATTGGT 57.323 39.130 10.83 1.89 0.00 3.67
375 377 3.643199 ACAATTGGTTGGCTTTGGTTT 57.357 38.095 10.83 0.00 39.70 3.27
377 379 4.702831 ACAATTGGTTGGCTTTGGTTTAG 58.297 39.130 10.83 0.00 39.70 1.85
378 380 2.900716 TTGGTTGGCTTTGGTTTAGC 57.099 45.000 0.00 0.00 37.91 3.09
379 381 2.080654 TGGTTGGCTTTGGTTTAGCT 57.919 45.000 0.00 0.00 38.67 3.32
397 399 4.264460 AGCTGACTTCGACATCTTCTTT 57.736 40.909 0.00 0.00 0.00 2.52
409 412 5.411361 CGACATCTTCTTTATGTTGTTCCCA 59.589 40.000 0.00 0.00 37.69 4.37
427 430 0.387929 CAGGCATGGTGATGGATTGC 59.612 55.000 0.00 0.00 0.00 3.56
428 431 0.032912 AGGCATGGTGATGGATTGCA 60.033 50.000 0.00 0.00 35.04 4.08
429 432 0.825410 GGCATGGTGATGGATTGCAA 59.175 50.000 0.00 0.00 35.04 4.08
430 433 1.202486 GGCATGGTGATGGATTGCAAG 60.202 52.381 4.94 0.00 35.04 4.01
431 434 1.805120 GCATGGTGATGGATTGCAAGC 60.805 52.381 6.04 6.04 33.58 4.01
433 436 2.804986 TGGTGATGGATTGCAAGCTA 57.195 45.000 15.27 9.30 0.00 3.32
434 437 3.301794 TGGTGATGGATTGCAAGCTAT 57.698 42.857 13.76 13.76 0.00 2.97
435 438 4.436113 TGGTGATGGATTGCAAGCTATA 57.564 40.909 13.85 1.52 0.00 1.31
436 439 4.136796 TGGTGATGGATTGCAAGCTATAC 58.863 43.478 13.85 11.55 0.00 1.47
437 440 4.141413 TGGTGATGGATTGCAAGCTATACT 60.141 41.667 13.85 0.00 0.00 2.12
438 441 5.071653 TGGTGATGGATTGCAAGCTATACTA 59.928 40.000 13.85 7.80 0.00 1.82
439 442 5.409826 GGTGATGGATTGCAAGCTATACTAC 59.590 44.000 13.85 12.42 0.00 2.73
440 443 5.991606 GTGATGGATTGCAAGCTATACTACA 59.008 40.000 13.85 4.89 0.00 2.74
441 444 6.483307 GTGATGGATTGCAAGCTATACTACAA 59.517 38.462 13.85 0.00 0.00 2.41
442 445 6.707608 TGATGGATTGCAAGCTATACTACAAG 59.292 38.462 13.85 0.00 30.54 3.16
443 446 5.368145 TGGATTGCAAGCTATACTACAAGG 58.632 41.667 15.27 0.00 30.54 3.61
444 447 4.757149 GGATTGCAAGCTATACTACAAGGG 59.243 45.833 15.27 0.00 30.54 3.95
445 448 3.838244 TGCAAGCTATACTACAAGGGG 57.162 47.619 0.00 0.00 0.00 4.79
446 449 3.112263 TGCAAGCTATACTACAAGGGGT 58.888 45.455 0.00 0.00 0.00 4.95
447 450 3.118408 TGCAAGCTATACTACAAGGGGTG 60.118 47.826 0.00 0.00 0.00 4.61
448 451 3.134081 GCAAGCTATACTACAAGGGGTGA 59.866 47.826 0.00 0.00 0.00 4.02
449 452 4.202367 GCAAGCTATACTACAAGGGGTGAT 60.202 45.833 0.00 0.00 0.00 3.06
450 453 5.300752 CAAGCTATACTACAAGGGGTGATG 58.699 45.833 0.00 0.00 0.00 3.07
451 454 3.325135 AGCTATACTACAAGGGGTGATGC 59.675 47.826 0.00 0.00 0.00 3.91
452 455 3.325135 GCTATACTACAAGGGGTGATGCT 59.675 47.826 0.00 0.00 0.00 3.79
453 456 4.561734 GCTATACTACAAGGGGTGATGCTC 60.562 50.000 0.00 0.00 0.00 4.26
454 457 1.958288 ACTACAAGGGGTGATGCTCT 58.042 50.000 0.00 0.00 0.00 4.09
467 470 5.163513 GGTGATGCTCTAACAAATGTTTGG 58.836 41.667 3.85 0.00 42.34 3.28
469 472 6.215845 GTGATGCTCTAACAAATGTTTGGTT 58.784 36.000 3.85 5.00 42.34 3.67
473 476 4.739137 GCTCTAACAAATGTTTGGTTGGCA 60.739 41.667 3.85 0.00 42.34 4.92
478 481 5.246145 ACAAATGTTTGGTTGGCAATTTG 57.754 34.783 15.06 15.06 42.34 2.32
481 484 6.545298 ACAAATGTTTGGTTGGCAATTTGTAT 59.455 30.769 18.86 3.06 42.34 2.29
492 495 6.043327 TGGCAATTTGTATATCTCGTTTCG 57.957 37.500 0.00 0.00 0.00 3.46
527 530 8.087982 CAACTATTGCAGTCTTTAAAGTCTGA 57.912 34.615 32.90 20.19 42.33 3.27
530 533 9.593134 ACTATTGCAGTCTTTAAAGTCTGATAG 57.407 33.333 32.90 29.60 42.33 2.08
544 547 6.011122 AGTCTGATAGAATGAGGGCATTTT 57.989 37.500 0.00 0.00 44.47 1.82
595 598 7.337689 GGTTAGGTGTAATTTTTAATCTCCGGT 59.662 37.037 0.00 0.00 0.00 5.28
692 697 7.645058 ATGTATCTGGTTGTCTTTTTATGGG 57.355 36.000 0.00 0.00 0.00 4.00
697 702 4.148838 TGGTTGTCTTTTTATGGGACTGG 58.851 43.478 0.00 0.00 0.00 4.00
699 704 5.163077 TGGTTGTCTTTTTATGGGACTGGTA 60.163 40.000 0.00 0.00 0.00 3.25
771 778 6.432403 AGAATCCCAATTTGTTTTTAGGCA 57.568 33.333 0.00 0.00 0.00 4.75
790 797 5.459536 GGCAACTTCCTCTGATTTTTCTT 57.540 39.130 0.00 0.00 0.00 2.52
791 798 5.847304 GGCAACTTCCTCTGATTTTTCTTT 58.153 37.500 0.00 0.00 0.00 2.52
792 799 5.923114 GGCAACTTCCTCTGATTTTTCTTTC 59.077 40.000 0.00 0.00 0.00 2.62
793 800 6.461509 GGCAACTTCCTCTGATTTTTCTTTCA 60.462 38.462 0.00 0.00 0.00 2.69
794 801 6.640092 GCAACTTCCTCTGATTTTTCTTTCAG 59.360 38.462 0.00 0.00 40.58 3.02
797 804 8.525290 ACTTCCTCTGATTTTTCTTTCAGAAA 57.475 30.769 4.40 0.00 45.64 2.52
870 878 0.745845 AAGCAGAGCAATAGCCACCG 60.746 55.000 0.00 0.00 43.56 4.94
885 893 2.360980 CCGACCTCCTCCTCACCT 59.639 66.667 0.00 0.00 0.00 4.00
900 913 1.007336 CACCTTCTTCCGTCCGTTCG 61.007 60.000 0.00 0.00 0.00 3.95
902 915 1.372499 CTTCTTCCGTCCGTTCGCA 60.372 57.895 0.00 0.00 0.00 5.10
1173 1218 0.542938 CCCGCCCATCTCCTCATCTA 60.543 60.000 0.00 0.00 0.00 1.98
1180 1225 4.718774 GCCCATCTCCTCATCTATCCATTA 59.281 45.833 0.00 0.00 0.00 1.90
1415 1460 2.564504 TCGGGGATATCTTGATCTGCTG 59.435 50.000 2.05 0.00 0.00 4.41
1455 1500 0.879765 AGAACCTCATTCGTCGTCGT 59.120 50.000 1.33 0.00 42.69 4.34
1518 1567 4.125703 GGCTCGTTCAGAATCAGAATCAT 58.874 43.478 0.00 0.00 0.00 2.45
1573 1622 7.886629 AACATGCCAGATTTTGTACATAGAT 57.113 32.000 0.00 0.00 0.00 1.98
1639 1720 6.237755 CGGTGTTATCTTCGTTCTACATTTCC 60.238 42.308 0.00 0.00 0.00 3.13
1662 1743 3.517602 TCGGTTGATCGTAACATTCAGG 58.482 45.455 0.00 0.00 32.22 3.86
1663 1744 3.056393 TCGGTTGATCGTAACATTCAGGT 60.056 43.478 0.00 0.00 32.22 4.00
1728 1814 2.539688 CCTCGATCGCGATTCAAATCAA 59.460 45.455 24.55 0.00 46.80 2.57
1755 1847 1.271102 TGGTTGCCGCTGTATTTTTCC 59.729 47.619 0.00 0.00 0.00 3.13
1756 1848 1.271102 GGTTGCCGCTGTATTTTTCCA 59.729 47.619 0.00 0.00 0.00 3.53
1757 1849 2.288518 GGTTGCCGCTGTATTTTTCCAA 60.289 45.455 0.00 0.00 0.00 3.53
1758 1850 3.584834 GTTGCCGCTGTATTTTTCCAAT 58.415 40.909 0.00 0.00 0.00 3.16
1759 1851 3.229276 TGCCGCTGTATTTTTCCAATG 57.771 42.857 0.00 0.00 0.00 2.82
1797 1893 5.119588 TCCGTCGTTTCTGATAAATGTTCAC 59.880 40.000 0.00 0.00 0.00 3.18
1852 1948 1.296715 GATTCCCCACGTCTGCACT 59.703 57.895 0.00 0.00 0.00 4.40
1864 1960 3.495670 GTCTGCACTAGACGATTCTGT 57.504 47.619 0.00 0.00 45.77 3.41
1871 1967 2.100197 CTAGACGATTCTGTGACCCCA 58.900 52.381 0.00 0.00 32.75 4.96
1882 1978 3.479979 GACCCCAAGTCGGACCTT 58.520 61.111 4.14 0.00 35.30 3.50
1884 1980 1.460689 ACCCCAAGTCGGACCTTCA 60.461 57.895 4.14 0.00 36.56 3.02
1886 1982 0.109723 CCCCAAGTCGGACCTTCAAA 59.890 55.000 4.14 0.00 36.56 2.69
1889 1985 3.270877 CCCAAGTCGGACCTTCAAATAG 58.729 50.000 4.14 0.00 36.56 1.73
1890 1986 3.055385 CCCAAGTCGGACCTTCAAATAGA 60.055 47.826 4.14 0.00 36.56 1.98
1891 1987 4.184629 CCAAGTCGGACCTTCAAATAGAG 58.815 47.826 4.14 0.00 36.56 2.43
1892 1988 3.528597 AGTCGGACCTTCAAATAGAGC 57.471 47.619 4.14 0.00 0.00 4.09
1893 1989 2.168728 AGTCGGACCTTCAAATAGAGCC 59.831 50.000 4.14 0.00 0.00 4.70
1894 1990 1.136305 TCGGACCTTCAAATAGAGCCG 59.864 52.381 0.00 0.00 38.89 5.52
1895 1991 1.136305 CGGACCTTCAAATAGAGCCGA 59.864 52.381 0.00 0.00 39.85 5.54
1896 1992 2.799917 CGGACCTTCAAATAGAGCCGAG 60.800 54.545 0.00 0.00 39.85 4.63
1897 1993 2.431057 GGACCTTCAAATAGAGCCGAGA 59.569 50.000 0.00 0.00 0.00 4.04
1898 1994 3.118738 GGACCTTCAAATAGAGCCGAGAA 60.119 47.826 0.00 0.00 0.00 2.87
1899 1995 4.504858 GACCTTCAAATAGAGCCGAGAAA 58.495 43.478 0.00 0.00 0.00 2.52
1900 1996 4.906618 ACCTTCAAATAGAGCCGAGAAAA 58.093 39.130 0.00 0.00 0.00 2.29
1901 1997 4.938226 ACCTTCAAATAGAGCCGAGAAAAG 59.062 41.667 0.00 0.00 0.00 2.27
1902 1998 5.178797 CCTTCAAATAGAGCCGAGAAAAGA 58.821 41.667 0.00 0.00 0.00 2.52
1903 1999 5.064071 CCTTCAAATAGAGCCGAGAAAAGAC 59.936 44.000 0.00 0.00 0.00 3.01
1904 2000 5.147330 TCAAATAGAGCCGAGAAAAGACA 57.853 39.130 0.00 0.00 0.00 3.41
1905 2001 5.547465 TCAAATAGAGCCGAGAAAAGACAA 58.453 37.500 0.00 0.00 0.00 3.18
1906 2002 5.408604 TCAAATAGAGCCGAGAAAAGACAAC 59.591 40.000 0.00 0.00 0.00 3.32
1907 2003 4.810191 ATAGAGCCGAGAAAAGACAACT 57.190 40.909 0.00 0.00 0.00 3.16
1908 2004 3.033368 AGAGCCGAGAAAAGACAACTC 57.967 47.619 0.00 0.00 0.00 3.01
1909 2005 2.365617 AGAGCCGAGAAAAGACAACTCA 59.634 45.455 0.00 0.00 0.00 3.41
1910 2006 2.476997 GAGCCGAGAAAAGACAACTCAC 59.523 50.000 0.00 0.00 0.00 3.51
1911 2007 1.531578 GCCGAGAAAAGACAACTCACC 59.468 52.381 0.00 0.00 0.00 4.02
1912 2008 2.807108 GCCGAGAAAAGACAACTCACCT 60.807 50.000 0.00 0.00 0.00 4.00
1913 2009 3.554337 GCCGAGAAAAGACAACTCACCTA 60.554 47.826 0.00 0.00 0.00 3.08
1914 2010 4.822026 CCGAGAAAAGACAACTCACCTAT 58.178 43.478 0.00 0.00 0.00 2.57
1915 2011 5.623824 GCCGAGAAAAGACAACTCACCTATA 60.624 44.000 0.00 0.00 0.00 1.31
1916 2012 6.574350 CCGAGAAAAGACAACTCACCTATAT 58.426 40.000 0.00 0.00 0.00 0.86
1917 2013 7.683704 GCCGAGAAAAGACAACTCACCTATATA 60.684 40.741 0.00 0.00 0.00 0.86
1918 2014 7.863375 CCGAGAAAAGACAACTCACCTATATAG 59.137 40.741 2.46 2.46 0.00 1.31
1919 2015 8.622157 CGAGAAAAGACAACTCACCTATATAGA 58.378 37.037 11.53 0.00 0.00 1.98
1924 2020 9.838339 AAAGACAACTCACCTATATAGAAATGG 57.162 33.333 11.53 0.00 0.00 3.16
1925 2021 8.783660 AGACAACTCACCTATATAGAAATGGA 57.216 34.615 11.53 1.02 0.00 3.41
1926 2022 8.643324 AGACAACTCACCTATATAGAAATGGAC 58.357 37.037 11.53 2.10 0.00 4.02
1927 2023 7.434492 ACAACTCACCTATATAGAAATGGACG 58.566 38.462 11.53 0.00 0.00 4.79
1928 2024 6.026947 ACTCACCTATATAGAAATGGACGC 57.973 41.667 11.53 0.00 0.00 5.19
1929 2025 5.775701 ACTCACCTATATAGAAATGGACGCT 59.224 40.000 11.53 0.00 0.00 5.07
1930 2026 6.025749 TCACCTATATAGAAATGGACGCTG 57.974 41.667 11.53 0.00 0.00 5.18
1931 2027 4.627467 CACCTATATAGAAATGGACGCTGC 59.373 45.833 11.53 0.00 0.00 5.25
1932 2028 3.859961 CCTATATAGAAATGGACGCTGCG 59.140 47.826 21.91 21.91 0.00 5.18
1933 2029 2.882927 TATAGAAATGGACGCTGCGT 57.117 45.000 29.37 29.37 45.10 5.24
1934 2030 2.882927 ATAGAAATGGACGCTGCGTA 57.117 45.000 29.03 14.39 41.37 4.42
1968 2064 3.148279 GAGGATCTCGTGGCCGGT 61.148 66.667 1.90 0.00 33.95 5.28
2009 3255 2.522436 TCGGTCCCACCAAGTCGT 60.522 61.111 0.00 0.00 38.47 4.34
2036 3297 3.530910 AAAGGTGCCCACGTCTCCG 62.531 63.158 0.00 0.00 40.83 4.63
2108 4655 1.307517 GTGATCCCCCACTACCCCA 60.308 63.158 0.00 0.00 34.38 4.96
2117 4664 2.768344 ACTACCCCATCGCCCCAG 60.768 66.667 0.00 0.00 0.00 4.45
2137 4684 3.093057 AGATAACTCACGGCAACTCTCT 58.907 45.455 0.00 0.00 0.00 3.10
2236 4783 8.889717 AGTAAAGTTGAAAAGATCGTGAAGAAA 58.110 29.630 0.00 0.00 0.00 2.52
2241 4788 8.026607 AGTTGAAAAGATCGTGAAGAAAACAAA 58.973 29.630 0.00 0.00 0.00 2.83
2261 4808 2.474816 ACTCGTCTGCAACTCTTTGTC 58.525 47.619 0.00 0.00 34.90 3.18
2289 4836 3.976942 CAGGCAACAATCTGAAGAAAACG 59.023 43.478 0.00 0.00 41.41 3.60
2290 4837 3.632145 AGGCAACAATCTGAAGAAAACGT 59.368 39.130 0.00 0.00 41.41 3.99
2354 4902 7.014905 GGGGAAGAACAACAAAAGGTAATAACT 59.985 37.037 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.006358 GGCGTATTCGTACTTTTGATGACAT 59.994 40.000 0.00 0.00 39.49 3.06
10 11 3.194116 AGGAGGCGTATTCGTACTTTTGA 59.806 43.478 0.00 0.00 39.49 2.69
36 38 2.281208 CGGCGACTGGGGTTTTGA 60.281 61.111 0.00 0.00 0.00 2.69
45 47 3.726517 CACCTTTGGCGGCGACTG 61.727 66.667 16.45 0.00 0.00 3.51
49 51 2.966309 GAGAACACCTTTGGCGGCG 61.966 63.158 0.51 0.51 0.00 6.46
53 55 1.860078 CGTCGAGAACACCTTTGGC 59.140 57.895 0.00 0.00 0.00 4.52
77 79 4.243008 GAGGAGGGCGGCTAAGGC 62.243 72.222 9.56 0.00 37.82 4.35
81 83 4.541648 GGGAGAGGAGGGCGGCTA 62.542 72.222 9.56 0.00 0.00 3.93
116 118 2.922503 TCACTCCTCTTGCCGCCA 60.923 61.111 0.00 0.00 0.00 5.69
121 123 0.248843 CAGGTCCTCACTCCTCTTGC 59.751 60.000 0.00 0.00 30.91 4.01
158 160 4.139038 CGGGAACAAAACCTAGGAAAAGA 58.861 43.478 17.98 0.00 0.00 2.52
165 167 0.879090 GCCACGGGAACAAAACCTAG 59.121 55.000 0.00 0.00 0.00 3.02
169 171 1.299850 GCTGCCACGGGAACAAAAC 60.300 57.895 0.00 0.00 0.00 2.43
170 172 1.112315 ATGCTGCCACGGGAACAAAA 61.112 50.000 0.00 0.00 0.00 2.44
191 193 0.392998 ATCGTTGCCACCACCTCATC 60.393 55.000 0.00 0.00 0.00 2.92
208 210 5.940595 ACGACCTTATTCTAGCACGATATC 58.059 41.667 0.00 0.00 0.00 1.63
211 213 4.142227 ACAACGACCTTATTCTAGCACGAT 60.142 41.667 0.00 0.00 0.00 3.73
217 219 3.118738 AGGCCACAACGACCTTATTCTAG 60.119 47.826 5.01 0.00 0.00 2.43
231 233 1.267121 GAGGTAGTGAGAGGCCACAA 58.733 55.000 5.01 0.00 39.42 3.33
233 235 0.680280 TCGAGGTAGTGAGAGGCCAC 60.680 60.000 5.01 0.00 37.32 5.01
243 245 0.037882 TGAGACGTCGTCGAGGTAGT 60.038 55.000 19.61 10.76 37.67 2.73
247 249 1.352404 GGATGAGACGTCGTCGAGG 59.648 63.158 19.11 13.12 39.36 4.63
260 262 1.559368 CCTTTGGTGCCATTGGATGA 58.441 50.000 6.95 0.00 0.00 2.92
267 269 1.229272 ACATGCCCTTTGGTGCCAT 60.229 52.632 0.00 0.00 0.00 4.40
275 277 1.341080 CAAACTCCCACATGCCCTTT 58.659 50.000 0.00 0.00 0.00 3.11
307 309 6.039941 TGTTAAGATCCGAAGAAAGCCAAAAA 59.960 34.615 0.00 0.00 0.00 1.94
341 343 5.677319 ACCAATTGTTCTTCTCGATAGGA 57.323 39.130 4.43 0.00 0.00 2.94
351 353 3.199727 ACCAAAGCCAACCAATTGTTCTT 59.800 39.130 4.43 0.00 34.00 2.52
361 363 1.960689 TCAGCTAAACCAAAGCCAACC 59.039 47.619 0.00 0.00 41.02 3.77
363 365 2.944129 AGTCAGCTAAACCAAAGCCAA 58.056 42.857 0.00 0.00 41.02 4.52
375 377 5.392767 AAAGAAGATGTCGAAGTCAGCTA 57.607 39.130 0.00 0.00 41.98 3.32
377 379 5.578727 ACATAAAGAAGATGTCGAAGTCAGC 59.421 40.000 0.00 0.00 31.84 4.26
378 380 7.116948 ACAACATAAAGAAGATGTCGAAGTCAG 59.883 37.037 0.00 0.00 36.50 3.51
379 381 6.929049 ACAACATAAAGAAGATGTCGAAGTCA 59.071 34.615 0.00 0.00 36.50 3.41
397 399 2.142356 CCATGCCTGGGAACAACATA 57.858 50.000 0.00 0.00 42.06 2.29
409 412 0.032912 TGCAATCCATCACCATGCCT 60.033 50.000 0.00 0.00 36.20 4.75
427 430 5.300752 CATCACCCCTTGTAGTATAGCTTG 58.699 45.833 0.00 0.00 0.00 4.01
428 431 4.202367 GCATCACCCCTTGTAGTATAGCTT 60.202 45.833 0.00 0.00 0.00 3.74
429 432 3.325135 GCATCACCCCTTGTAGTATAGCT 59.675 47.826 0.00 0.00 0.00 3.32
430 433 3.325135 AGCATCACCCCTTGTAGTATAGC 59.675 47.826 0.00 0.00 0.00 2.97
431 434 4.835615 AGAGCATCACCCCTTGTAGTATAG 59.164 45.833 0.00 0.00 37.82 1.31
433 436 3.658725 AGAGCATCACCCCTTGTAGTAT 58.341 45.455 0.00 0.00 37.82 2.12
434 437 3.116096 AGAGCATCACCCCTTGTAGTA 57.884 47.619 0.00 0.00 37.82 1.82
435 438 1.958288 AGAGCATCACCCCTTGTAGT 58.042 50.000 0.00 0.00 37.82 2.73
436 439 3.197766 TGTTAGAGCATCACCCCTTGTAG 59.802 47.826 0.00 0.00 37.82 2.74
437 440 3.178046 TGTTAGAGCATCACCCCTTGTA 58.822 45.455 0.00 0.00 37.82 2.41
438 441 1.985159 TGTTAGAGCATCACCCCTTGT 59.015 47.619 0.00 0.00 37.82 3.16
439 442 2.787473 TGTTAGAGCATCACCCCTTG 57.213 50.000 0.00 0.00 37.82 3.61
440 443 3.806949 TTTGTTAGAGCATCACCCCTT 57.193 42.857 0.00 0.00 37.82 3.95
441 444 3.010584 ACATTTGTTAGAGCATCACCCCT 59.989 43.478 0.00 0.00 37.82 4.79
442 445 3.356290 ACATTTGTTAGAGCATCACCCC 58.644 45.455 0.00 0.00 37.82 4.95
443 446 5.163513 CAAACATTTGTTAGAGCATCACCC 58.836 41.667 0.00 0.00 37.25 4.61
444 447 5.163513 CCAAACATTTGTTAGAGCATCACC 58.836 41.667 3.79 0.00 37.25 4.02
445 448 5.772521 ACCAAACATTTGTTAGAGCATCAC 58.227 37.500 3.79 0.00 37.25 3.06
446 449 6.215121 CAACCAAACATTTGTTAGAGCATCA 58.785 36.000 3.79 0.00 37.25 3.07
447 450 5.634859 CCAACCAAACATTTGTTAGAGCATC 59.365 40.000 3.79 0.00 37.25 3.91
448 451 5.540911 CCAACCAAACATTTGTTAGAGCAT 58.459 37.500 3.79 0.00 37.25 3.79
449 452 4.739137 GCCAACCAAACATTTGTTAGAGCA 60.739 41.667 3.79 0.00 37.25 4.26
450 453 3.740832 GCCAACCAAACATTTGTTAGAGC 59.259 43.478 3.79 0.00 37.25 4.09
451 454 4.942852 TGCCAACCAAACATTTGTTAGAG 58.057 39.130 3.79 0.00 37.25 2.43
452 455 5.344743 TTGCCAACCAAACATTTGTTAGA 57.655 34.783 3.79 0.00 37.25 2.10
453 456 6.616774 AATTGCCAACCAAACATTTGTTAG 57.383 33.333 3.79 0.00 37.25 2.34
454 457 6.375455 ACAAATTGCCAACCAAACATTTGTTA 59.625 30.769 3.79 0.00 39.37 2.41
467 470 6.410914 CGAAACGAGATATACAAATTGCCAAC 59.589 38.462 0.00 0.00 0.00 3.77
469 472 5.813157 TCGAAACGAGATATACAAATTGCCA 59.187 36.000 0.00 0.00 0.00 4.92
492 495 3.611433 CAATAGTTGCTTGCCGCTC 57.389 52.632 0.00 0.00 40.11 5.03
525 528 6.547141 CACCTAAAAATGCCCTCATTCTATCA 59.453 38.462 0.00 0.00 41.77 2.15
527 530 6.435164 ACACCTAAAAATGCCCTCATTCTAT 58.565 36.000 0.00 0.00 41.77 1.98
530 533 4.142160 GGACACCTAAAAATGCCCTCATTC 60.142 45.833 0.00 0.00 41.77 2.67
544 547 6.195600 ACAGTAAAGGAAATGGACACCTAA 57.804 37.500 0.00 0.00 33.34 2.69
595 598 0.964700 TTGCCATTGATTGTCGCCAA 59.035 45.000 0.00 0.00 34.45 4.52
690 695 6.665992 AGGAAAAAGAAAATTACCAGTCCC 57.334 37.500 0.00 0.00 0.00 4.46
749 756 6.710295 AGTTGCCTAAAAACAAATTGGGATTC 59.290 34.615 0.00 0.00 30.51 2.52
754 761 6.054941 AGGAAGTTGCCTAAAAACAAATTGG 58.945 36.000 0.00 0.00 34.55 3.16
761 768 5.966742 ATCAGAGGAAGTTGCCTAAAAAC 57.033 39.130 0.00 0.00 38.73 2.43
765 772 6.306987 AGAAAAATCAGAGGAAGTTGCCTAA 58.693 36.000 0.00 0.00 38.73 2.69
766 773 5.880901 AGAAAAATCAGAGGAAGTTGCCTA 58.119 37.500 0.00 0.00 38.73 3.93
826 834 1.530655 CCGGGTTTGCTGGAAGGTT 60.531 57.895 0.00 0.00 0.00 3.50
834 842 1.905637 CTTTTACCTCCGGGTTTGCT 58.094 50.000 0.00 0.00 44.73 3.91
870 878 1.828595 GAAGAAGGTGAGGAGGAGGTC 59.171 57.143 0.00 0.00 0.00 3.85
885 893 1.372499 CTGCGAACGGACGGAAGAA 60.372 57.895 5.76 0.00 32.77 2.52
900 913 0.106967 GTGGGGGAAGGAATCTCTGC 60.107 60.000 0.00 0.00 0.00 4.26
902 915 1.886422 GAGTGGGGGAAGGAATCTCT 58.114 55.000 0.00 0.00 0.00 3.10
1153 1197 3.543536 GATGAGGAGATGGGCGGGC 62.544 68.421 0.00 0.00 0.00 6.13
1180 1225 0.863144 CGACGACGAACCAACCAATT 59.137 50.000 0.00 0.00 42.66 2.32
1426 1471 4.020218 ACGAATGAGGTTCTTCAGGATTGA 60.020 41.667 0.00 0.00 34.56 2.57
1439 1484 1.134075 CGACGACGACGAATGAGGT 59.866 57.895 15.32 0.00 42.66 3.85
1440 1485 1.582937 CCGACGACGACGAATGAGG 60.583 63.158 20.63 5.69 42.66 3.86
1455 1500 3.884350 CGAATCCCTCGTCGCCGA 61.884 66.667 0.00 0.00 42.89 5.54
1478 1527 1.672356 CCTTGCCCTTCCACGTCTG 60.672 63.158 0.00 0.00 0.00 3.51
1518 1567 4.895889 AGCAGAGCATACAGGTATGAACTA 59.104 41.667 20.55 0.00 44.22 2.24
1573 1622 4.271661 TGCAATTTAGTGAGCATCCATGA 58.728 39.130 0.00 0.00 31.05 3.07
1639 1720 4.032900 CCTGAATGTTACGATCAACCGAAG 59.967 45.833 0.00 0.00 0.00 3.79
1662 1743 1.206115 CGGGCGCAACAAACTGAAAC 61.206 55.000 10.83 0.00 0.00 2.78
1663 1744 1.064946 CGGGCGCAACAAACTGAAA 59.935 52.632 10.83 0.00 0.00 2.69
1755 1847 5.402568 CGACGGACCTACTGATTATTCATTG 59.597 44.000 0.00 0.00 0.00 2.82
1756 1848 5.068723 ACGACGGACCTACTGATTATTCATT 59.931 40.000 0.00 0.00 0.00 2.57
1757 1849 4.583489 ACGACGGACCTACTGATTATTCAT 59.417 41.667 0.00 0.00 0.00 2.57
1758 1850 3.949754 ACGACGGACCTACTGATTATTCA 59.050 43.478 0.00 0.00 0.00 2.57
1759 1851 4.564940 ACGACGGACCTACTGATTATTC 57.435 45.455 0.00 0.00 0.00 1.75
1852 1948 2.225382 TGGGGTCACAGAATCGTCTA 57.775 50.000 0.00 0.00 30.85 2.59
1864 1960 1.460689 AAGGTCCGACTTGGGGTCA 60.461 57.895 0.00 0.00 44.70 4.02
1871 1967 3.369576 GGCTCTATTTGAAGGTCCGACTT 60.370 47.826 0.00 0.00 0.00 3.01
1876 1972 2.431057 TCTCGGCTCTATTTGAAGGTCC 59.569 50.000 0.00 0.00 0.00 4.46
1880 1976 5.639506 TGTCTTTTCTCGGCTCTATTTGAAG 59.360 40.000 0.00 0.00 0.00 3.02
1881 1977 5.547465 TGTCTTTTCTCGGCTCTATTTGAA 58.453 37.500 0.00 0.00 0.00 2.69
1882 1978 5.147330 TGTCTTTTCTCGGCTCTATTTGA 57.853 39.130 0.00 0.00 0.00 2.69
1884 1980 5.552178 AGTTGTCTTTTCTCGGCTCTATTT 58.448 37.500 0.00 0.00 0.00 1.40
1886 1982 4.220821 TGAGTTGTCTTTTCTCGGCTCTAT 59.779 41.667 0.00 0.00 0.00 1.98
1889 1985 2.476997 GTGAGTTGTCTTTTCTCGGCTC 59.523 50.000 0.00 0.00 0.00 4.70
1890 1986 2.484889 GTGAGTTGTCTTTTCTCGGCT 58.515 47.619 0.00 0.00 0.00 5.52
1891 1987 1.531578 GGTGAGTTGTCTTTTCTCGGC 59.468 52.381 0.00 0.00 0.00 5.54
1892 1988 3.113260 AGGTGAGTTGTCTTTTCTCGG 57.887 47.619 0.00 0.00 0.00 4.63
1893 1989 8.622157 TCTATATAGGTGAGTTGTCTTTTCTCG 58.378 37.037 9.89 0.00 0.00 4.04
1898 1994 9.838339 CCATTTCTATATAGGTGAGTTGTCTTT 57.162 33.333 9.89 0.00 0.00 2.52
1899 1995 9.213777 TCCATTTCTATATAGGTGAGTTGTCTT 57.786 33.333 9.89 0.00 0.00 3.01
1900 1996 8.643324 GTCCATTTCTATATAGGTGAGTTGTCT 58.357 37.037 9.89 0.00 0.00 3.41
1901 1997 7.595502 CGTCCATTTCTATATAGGTGAGTTGTC 59.404 40.741 9.89 0.00 0.00 3.18
1902 1998 7.434492 CGTCCATTTCTATATAGGTGAGTTGT 58.566 38.462 9.89 0.00 0.00 3.32
1903 1999 6.366332 GCGTCCATTTCTATATAGGTGAGTTG 59.634 42.308 9.89 0.87 0.00 3.16
1904 2000 6.267928 AGCGTCCATTTCTATATAGGTGAGTT 59.732 38.462 9.89 0.00 0.00 3.01
1905 2001 5.775701 AGCGTCCATTTCTATATAGGTGAGT 59.224 40.000 9.89 0.00 0.00 3.41
1906 2002 6.096036 CAGCGTCCATTTCTATATAGGTGAG 58.904 44.000 9.89 0.00 0.00 3.51
1907 2003 5.566826 GCAGCGTCCATTTCTATATAGGTGA 60.567 44.000 9.89 0.00 0.00 4.02
1908 2004 4.627467 GCAGCGTCCATTTCTATATAGGTG 59.373 45.833 9.89 6.78 0.00 4.00
1909 2005 4.618460 CGCAGCGTCCATTTCTATATAGGT 60.618 45.833 6.65 0.00 0.00 3.08
1910 2006 3.859961 CGCAGCGTCCATTTCTATATAGG 59.140 47.826 6.65 0.00 0.00 2.57
1911 2007 4.486090 ACGCAGCGTCCATTTCTATATAG 58.514 43.478 16.61 3.10 33.69 1.31
1912 2008 4.514781 ACGCAGCGTCCATTTCTATATA 57.485 40.909 16.61 0.00 33.69 0.86
1913 2009 3.386768 ACGCAGCGTCCATTTCTATAT 57.613 42.857 16.61 0.00 33.69 0.86
1914 2010 2.882927 ACGCAGCGTCCATTTCTATA 57.117 45.000 16.61 0.00 33.69 1.31
1915 2011 2.470821 GTACGCAGCGTCCATTTCTAT 58.529 47.619 26.87 0.00 41.54 1.98
1916 2012 1.470285 GGTACGCAGCGTCCATTTCTA 60.470 52.381 26.87 0.01 41.54 2.10
1917 2013 0.739813 GGTACGCAGCGTCCATTTCT 60.740 55.000 26.87 0.00 41.54 2.52
1918 2014 1.702491 GGGTACGCAGCGTCCATTTC 61.702 60.000 26.87 8.87 41.54 2.17
1919 2015 1.743995 GGGTACGCAGCGTCCATTT 60.744 57.895 26.87 0.04 41.54 2.32
1920 2016 2.125269 GGGTACGCAGCGTCCATT 60.125 61.111 26.87 0.93 41.54 3.16
1921 2017 4.508128 CGGGTACGCAGCGTCCAT 62.508 66.667 26.87 1.40 41.54 3.41
1945 2041 2.502492 CCACGAGATCCTCCCGCAT 61.502 63.158 0.00 0.00 0.00 4.73
1961 2057 3.724732 ACTTTCCTAAAATACCGGCCA 57.275 42.857 0.00 0.00 0.00 5.36
2092 3662 1.481056 CGATGGGGTAGTGGGGGATC 61.481 65.000 0.00 0.00 0.00 3.36
2093 3663 1.461461 CGATGGGGTAGTGGGGGAT 60.461 63.158 0.00 0.00 0.00 3.85
2094 3664 2.041301 CGATGGGGTAGTGGGGGA 60.041 66.667 0.00 0.00 0.00 4.81
2108 4655 0.389391 CGTGAGTTATCTGGGGCGAT 59.611 55.000 0.00 0.00 0.00 4.58
2117 4664 3.512033 AGAGAGTTGCCGTGAGTTATC 57.488 47.619 0.00 0.00 0.00 1.75
2137 4684 4.360405 GGCGGCTGGGGGAAGAAA 62.360 66.667 0.00 0.00 0.00 2.52
2158 4705 0.036010 GCTGCTAGGACATGGTGTGT 60.036 55.000 0.00 0.00 45.83 3.72
2162 4709 2.735772 CCCGCTGCTAGGACATGGT 61.736 63.158 0.00 0.00 0.00 3.55
2163 4710 2.109799 CCCGCTGCTAGGACATGG 59.890 66.667 0.00 0.00 0.00 3.66
2236 4783 2.906354 AGAGTTGCAGACGAGTTTGTT 58.094 42.857 0.00 0.00 0.00 2.83
2241 4788 2.101582 AGACAAAGAGTTGCAGACGAGT 59.898 45.455 0.00 0.00 38.39 4.18
2261 4808 2.507484 TCAGATTGTTGCCTGGTCAAG 58.493 47.619 4.19 0.00 0.00 3.02
2274 4821 2.293122 TGCCCACGTTTTCTTCAGATTG 59.707 45.455 0.00 0.00 0.00 2.67
2305 4852 2.358957 GGGGAAATTTGCCAATTCTGC 58.641 47.619 27.52 7.05 40.96 4.26


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

AutoCloner maintained by Alex Coulton.