Multiple sequence alignment - TraesCS4D01G225600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G225600 chr4D 100.000 2312 0 0 1 2312 384271916 384269605 0.000000e+00 4270.0
1 TraesCS4D01G225600 chr4D 93.023 86 6 0 1947 2032 466837227 466837142 2.410000e-25 126.0
2 TraesCS4D01G225600 chr4B 90.456 943 40 20 735 1646 471338599 471337676 0.000000e+00 1197.0
3 TraesCS4D01G225600 chr4B 95.730 281 11 1 2033 2312 471337486 471337206 3.500000e-123 451.0
4 TraesCS4D01G225600 chr4A 86.076 1106 59 38 735 1784 66148471 66147405 0.000000e+00 1101.0
5 TraesCS4D01G225600 chr4A 94.815 270 7 4 2047 2312 66147410 66147144 4.600000e-112 414.0
6 TraesCS4D01G225600 chr4A 81.757 148 18 9 1803 1945 517032909 517032766 5.220000e-22 115.0
7 TraesCS4D01G225600 chr2A 91.457 398 31 3 348 744 16935524 16935129 5.620000e-151 544.0
8 TraesCS4D01G225600 chr2A 88.218 348 38 3 390 736 764330747 764330402 1.650000e-111 412.0
9 TraesCS4D01G225600 chr2A 95.789 95 2 1 210 304 16935700 16935608 3.980000e-33 152.0
10 TraesCS4D01G225600 chr5B 94.643 336 16 2 979 1314 535715431 535715098 9.470000e-144 520.0
11 TraesCS4D01G225600 chr5B 93.137 204 13 1 5 207 456637608 456637405 4.830000e-77 298.0
12 TraesCS4D01G225600 chr5B 89.888 89 9 0 390 478 589121431 589121519 5.220000e-22 115.0
13 TraesCS4D01G225600 chr5B 97.727 44 1 0 475 518 589121120 589121163 2.460000e-10 76.8
14 TraesCS4D01G225600 chr5D 95.312 320 15 0 995 1314 405334716 405334397 2.050000e-140 508.0
15 TraesCS4D01G225600 chr5D 93.805 339 17 4 977 1314 440375463 440375128 7.370000e-140 507.0
16 TraesCS4D01G225600 chr5D 93.093 333 21 2 983 1314 332459489 332459158 9.600000e-134 486.0
17 TraesCS4D01G225600 chr5D 93.269 208 12 2 2 207 380694820 380694613 2.890000e-79 305.0
18 TraesCS4D01G225600 chr5D 91.398 93 7 1 1945 2037 543829156 543829247 2.410000e-25 126.0
19 TraesCS4D01G225600 chr5D 89.655 87 9 0 392 478 480706711 480706797 6.750000e-21 111.0
20 TraesCS4D01G225600 chr5D 97.727 44 1 0 475 518 480706398 480706441 2.460000e-10 76.8
21 TraesCS4D01G225600 chr7B 93.994 333 19 1 982 1314 589740543 589740212 9.530000e-139 503.0
22 TraesCS4D01G225600 chr7B 93.407 273 16 2 465 736 708484610 708484881 9.950000e-109 403.0
23 TraesCS4D01G225600 chr7B 85.586 111 12 3 1945 2054 173865877 173865770 1.880000e-21 113.0
24 TraesCS4D01G225600 chr7B 79.618 157 24 8 1802 1953 557435619 557435772 3.140000e-19 106.0
25 TraesCS4D01G225600 chr5A 93.275 342 19 4 976 1315 550802051 550802390 3.430000e-138 501.0
26 TraesCS4D01G225600 chr5A 93.255 341 19 4 976 1314 551041469 551041807 1.230000e-137 499.0
27 TraesCS4D01G225600 chr5A 93.627 204 12 1 5 207 480817252 480817049 1.040000e-78 303.0
28 TraesCS4D01G225600 chr5A 89.130 92 10 0 387 478 599803881 599803972 5.220000e-22 115.0
29 TraesCS4D01G225600 chr5A 97.727 44 1 0 475 518 599803573 599803616 2.460000e-10 76.8
30 TraesCS4D01G225600 chr3B 86.235 494 30 20 249 739 805272002 805271544 3.430000e-138 501.0
31 TraesCS4D01G225600 chr3B 94.677 263 12 2 4 264 805272282 805272020 7.690000e-110 407.0
32 TraesCS4D01G225600 chr6D 88.716 257 24 3 484 736 43049967 43050222 2.230000e-80 309.0
33 TraesCS4D01G225600 chr6D 91.146 192 14 3 546 736 424723556 424723745 8.200000e-65 257.0
34 TraesCS4D01G225600 chr6D 93.182 88 6 0 1945 2032 131945924 131945837 1.860000e-26 130.0
35 TraesCS4D01G225600 chr6D 85.714 98 11 3 1842 1936 111432790 111432693 1.460000e-17 100.0
36 TraesCS4D01G225600 chr2D 89.640 222 20 3 515 736 352709616 352709398 1.750000e-71 279.0
37 TraesCS4D01G225600 chr3A 90.732 205 17 2 533 736 17272164 17272367 2.930000e-69 272.0
38 TraesCS4D01G225600 chr3A 86.667 120 16 0 357 476 17272045 17272164 1.440000e-27 134.0
39 TraesCS4D01G225600 chr2B 87.603 242 20 6 357 598 28170240 28170471 2.930000e-69 272.0
40 TraesCS4D01G225600 chr2B 94.382 89 5 0 1943 2031 751183375 751183287 1.110000e-28 137.0
41 TraesCS4D01G225600 chr2B 89.691 97 10 0 1946 2042 165512949 165513045 8.670000e-25 124.0
42 TraesCS4D01G225600 chr2B 78.626 131 24 4 1813 1940 463862160 463862031 1.470000e-12 84.2
43 TraesCS4D01G225600 chr1D 88.288 222 18 6 515 736 307206116 307205903 2.280000e-65 259.0
44 TraesCS4D01G225600 chr1A 88.462 208 19 4 533 736 543639202 543639408 1.770000e-61 246.0
45 TraesCS4D01G225600 chr1A 86.598 97 10 2 381 476 543639108 543639202 1.130000e-18 104.0
46 TraesCS4D01G225600 chr6A 94.318 88 5 0 1945 2032 170907906 170907819 4.010000e-28 135.0
47 TraesCS4D01G225600 chr6A 80.537 149 21 8 1802 1946 499460237 499460381 8.730000e-20 108.0
48 TraesCS4D01G225600 chr7D 93.333 90 6 0 1942 2031 10855098 10855009 1.440000e-27 134.0
49 TraesCS4D01G225600 chr7D 92.135 89 7 0 1944 2032 575228024 575227936 2.410000e-25 126.0
50 TraesCS4D01G225600 chrUn 79.661 177 24 11 1779 1949 60297899 60297729 1.450000e-22 117.0
51 TraesCS4D01G225600 chrUn 80.519 154 20 9 1802 1949 375800024 375799875 2.430000e-20 110.0
52 TraesCS4D01G225600 chrUn 80.795 151 19 9 1802 1946 391468745 391468891 2.430000e-20 110.0
53 TraesCS4D01G225600 chrUn 82.171 129 15 7 1802 1924 365985088 365985214 1.130000e-18 104.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G225600 chr4D 384269605 384271916 2311 True 4270.0 4270 100.0000 1 2312 1 chr4D.!!$R1 2311
1 TraesCS4D01G225600 chr4B 471337206 471338599 1393 True 824.0 1197 93.0930 735 2312 2 chr4B.!!$R1 1577
2 TraesCS4D01G225600 chr4A 66147144 66148471 1327 True 757.5 1101 90.4455 735 2312 2 chr4A.!!$R2 1577
3 TraesCS4D01G225600 chr2A 16935129 16935700 571 True 348.0 544 93.6230 210 744 2 chr2A.!!$R2 534
4 TraesCS4D01G225600 chr3B 805271544 805272282 738 True 454.0 501 90.4560 4 739 2 chr3B.!!$R1 735

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
273 309 1.0076 TCCTTGAGAGCTGGAGATCCA 59.992 52.381 0.79 0.79 45.3 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1782 0.041312 GTGCGAACATGTTGAAGCGT 60.041 50.0 17.58 0.0 0.0 5.07 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
148 150 1.271054 GCACCCTCTTCACTGTCATGT 60.271 52.381 0.00 0.00 0.00 3.21
225 227 1.144936 GTGCCCAAGATCCTCTCCG 59.855 63.158 0.00 0.00 0.00 4.63
273 309 1.007600 TCCTTGAGAGCTGGAGATCCA 59.992 52.381 0.79 0.79 45.30 3.41
562 667 4.447989 GCTCTGCGGCTCTGCTCA 62.448 66.667 0.00 0.00 35.36 4.26
760 865 3.771479 GCCCTTCTTCCTGATTTCCATTT 59.229 43.478 0.00 0.00 0.00 2.32
761 866 4.382362 GCCCTTCTTCCTGATTTCCATTTG 60.382 45.833 0.00 0.00 0.00 2.32
764 874 3.099141 TCTTCCTGATTTCCATTTGGCC 58.901 45.455 0.00 0.00 34.44 5.36
816 927 1.152963 CCAATAGGAACCAGCCCCG 60.153 63.158 0.00 0.00 36.89 5.73
919 1050 5.485353 TCCAGCTCTATATATCCCAAACCAG 59.515 44.000 0.00 0.00 0.00 4.00
925 1056 7.583416 GCTCTATATATCCCAAACCAGCCAATA 60.583 40.741 0.00 0.00 0.00 1.90
977 1108 1.218316 CTTCGTCCCCGGGAAAGAG 59.782 63.158 26.32 9.32 31.38 2.85
1227 1358 1.511305 CGTCACCTACACGGAGCAT 59.489 57.895 0.00 0.00 36.31 3.79
1260 1391 3.118454 GTCACCGCCATGGACGTG 61.118 66.667 18.40 19.60 42.00 4.49
1340 1471 0.669318 TCCTCGTAGCGGCTTGTTTG 60.669 55.000 8.26 0.00 28.70 2.93
1342 1473 1.291877 CTCGTAGCGGCTTGTTTGCT 61.292 55.000 8.26 0.00 42.58 3.91
1344 1475 1.210155 GTAGCGGCTTGTTTGCTGG 59.790 57.895 8.26 0.00 39.73 4.85
1345 1476 2.519302 AGCGGCTTGTTTGCTGGT 60.519 55.556 0.00 0.00 44.09 4.00
1348 1479 2.489275 CGGCTTGTTTGCTGGTGGT 61.489 57.895 0.00 0.00 35.80 4.16
1352 1483 0.102844 CTTGTTTGCTGGTGGTGTGG 59.897 55.000 0.00 0.00 0.00 4.17
1353 1484 0.613292 TTGTTTGCTGGTGGTGTGGT 60.613 50.000 0.00 0.00 0.00 4.16
1354 1485 1.318886 TGTTTGCTGGTGGTGTGGTG 61.319 55.000 0.00 0.00 0.00 4.17
1400 1548 0.035820 TTCCTGATGTAACCGTGCCC 60.036 55.000 0.00 0.00 0.00 5.36
1471 1619 3.515562 TGTGCCCCTTTTAATCCAATGT 58.484 40.909 0.00 0.00 0.00 2.71
1476 1624 4.651045 GCCCCTTTTAATCCAATGTCAGAT 59.349 41.667 0.00 0.00 0.00 2.90
1502 1653 1.576421 CGCTTCTCTTTTGCGGCTT 59.424 52.632 0.00 0.00 45.07 4.35
1536 1687 5.260424 TGGATAATTGCTTTGCTCTGGTTA 58.740 37.500 0.00 0.00 0.00 2.85
1570 1721 0.318955 GCATGCCAGTGGTGTTGTTC 60.319 55.000 11.74 0.00 0.00 3.18
1575 1726 2.143925 GCCAGTGGTGTTGTTCTAGAC 58.856 52.381 11.74 0.00 0.00 2.59
1631 1782 3.640498 TGAAACTGCCAAATTGGTGATGA 59.360 39.130 14.17 0.00 40.46 2.92
1650 1801 0.041312 ACGCTTCAACATGTTCGCAC 60.041 50.000 8.48 0.00 0.00 5.34
1654 1805 2.541588 GCTTCAACATGTTCGCACAAGT 60.542 45.455 8.48 0.00 36.37 3.16
1661 1812 7.240674 TCAACATGTTCGCACAAGTAAATATC 58.759 34.615 8.48 0.00 33.66 1.63
1662 1813 5.795766 ACATGTTCGCACAAGTAAATATCG 58.204 37.500 0.00 0.00 33.01 2.92
1675 1826 2.559998 AATATCGGCGGTGCTTTTTG 57.440 45.000 7.21 0.00 0.00 2.44
1686 1837 1.136891 GTGCTTTTTGCCTTGTCACCT 59.863 47.619 0.00 0.00 42.00 4.00
1688 1839 2.622942 TGCTTTTTGCCTTGTCACCTAG 59.377 45.455 0.00 0.00 42.00 3.02
1690 1841 3.486383 CTTTTTGCCTTGTCACCTAGGA 58.514 45.455 17.98 0.00 35.83 2.94
1693 1844 2.787473 TGCCTTGTCACCTAGGATTG 57.213 50.000 17.98 4.10 35.83 2.67
1694 1845 1.985159 TGCCTTGTCACCTAGGATTGT 59.015 47.619 17.98 0.00 35.83 2.71
1695 1846 3.178046 TGCCTTGTCACCTAGGATTGTA 58.822 45.455 17.98 0.00 35.83 2.41
1696 1847 3.585289 TGCCTTGTCACCTAGGATTGTAA 59.415 43.478 17.98 4.07 35.83 2.41
1697 1848 4.042311 TGCCTTGTCACCTAGGATTGTAAA 59.958 41.667 17.98 2.98 35.83 2.01
1698 1849 4.395231 GCCTTGTCACCTAGGATTGTAAAC 59.605 45.833 17.98 0.00 35.83 2.01
1699 1850 5.803470 GCCTTGTCACCTAGGATTGTAAACT 60.803 44.000 17.98 0.00 35.83 2.66
1700 1851 5.643777 CCTTGTCACCTAGGATTGTAAACTG 59.356 44.000 17.98 0.00 35.83 3.16
1701 1852 5.160607 TGTCACCTAGGATTGTAAACTGG 57.839 43.478 17.98 0.00 0.00 4.00
1702 1853 3.939592 GTCACCTAGGATTGTAAACTGGC 59.060 47.826 17.98 0.00 0.00 4.85
1703 1854 3.585289 TCACCTAGGATTGTAAACTGGCA 59.415 43.478 17.98 0.00 0.00 4.92
1705 1856 4.396166 CACCTAGGATTGTAAACTGGCAAG 59.604 45.833 17.98 0.00 0.00 4.01
1707 1858 4.636206 CCTAGGATTGTAAACTGGCAAGAC 59.364 45.833 1.05 0.00 0.00 3.01
1722 1885 3.887069 CAAGACTTTGCGTTTGTTGTG 57.113 42.857 0.00 0.00 0.00 3.33
1754 1917 5.418310 TTGTTGAGAAAGAAAACTAGGCG 57.582 39.130 0.00 0.00 0.00 5.52
1755 1918 3.250040 TGTTGAGAAAGAAAACTAGGCGC 59.750 43.478 0.00 0.00 0.00 6.53
1759 1922 2.814336 AGAAAGAAAACTAGGCGCTTGG 59.186 45.455 7.64 3.66 0.00 3.61
1786 1949 6.832520 TGCTGTTTTTGAATTGCTATAGGA 57.167 33.333 1.04 0.00 0.00 2.94
1790 1953 7.814587 GCTGTTTTTGAATTGCTATAGGACTTT 59.185 33.333 1.04 0.00 0.00 2.66
1808 1971 5.811100 GGACTTTGTACAATACTAGGTGCTC 59.189 44.000 9.56 0.00 31.90 4.26
1817 1980 7.383102 ACAATACTAGGTGCTCAGAAAAATG 57.617 36.000 0.00 0.00 0.00 2.32
1823 1986 3.441572 AGGTGCTCAGAAAAATGAATCGG 59.558 43.478 0.00 0.00 0.00 4.18
1824 1987 3.440173 GGTGCTCAGAAAAATGAATCGGA 59.560 43.478 0.00 0.00 0.00 4.55
1826 1989 5.269313 GTGCTCAGAAAAATGAATCGGATC 58.731 41.667 0.00 0.00 0.00 3.36
1839 2002 7.921786 ATGAATCGGATCTTTCTAAAACACA 57.078 32.000 0.00 0.00 0.00 3.72
1840 2003 7.364522 TGAATCGGATCTTTCTAAAACACAG 57.635 36.000 0.00 0.00 0.00 3.66
1841 2004 6.371548 TGAATCGGATCTTTCTAAAACACAGG 59.628 38.462 0.00 0.00 0.00 4.00
1843 2006 4.994852 TCGGATCTTTCTAAAACACAGGTG 59.005 41.667 0.00 0.00 0.00 4.00
1844 2007 4.378459 CGGATCTTTCTAAAACACAGGTGC 60.378 45.833 0.00 0.00 0.00 5.01
1845 2008 4.082733 GGATCTTTCTAAAACACAGGTGCC 60.083 45.833 0.00 0.00 0.00 5.01
1846 2009 4.164843 TCTTTCTAAAACACAGGTGCCT 57.835 40.909 0.00 0.00 0.00 4.75
1847 2010 5.298989 TCTTTCTAAAACACAGGTGCCTA 57.701 39.130 0.00 0.00 0.00 3.93
1848 2011 5.876357 TCTTTCTAAAACACAGGTGCCTAT 58.124 37.500 0.00 0.00 0.00 2.57
1849 2012 6.303839 TCTTTCTAAAACACAGGTGCCTATT 58.696 36.000 0.00 0.00 0.00 1.73
1850 2013 6.775629 TCTTTCTAAAACACAGGTGCCTATTT 59.224 34.615 0.00 0.00 0.00 1.40
1851 2014 6.969993 TTCTAAAACACAGGTGCCTATTTT 57.030 33.333 0.00 2.15 0.00 1.82
1852 2015 6.969993 TCTAAAACACAGGTGCCTATTTTT 57.030 33.333 0.00 9.16 0.00 1.94
1853 2016 8.466617 TTCTAAAACACAGGTGCCTATTTTTA 57.533 30.769 0.00 9.61 0.00 1.52
1854 2017 8.106247 TCTAAAACACAGGTGCCTATTTTTAG 57.894 34.615 19.51 19.51 35.24 1.85
1855 2018 6.969993 AAAACACAGGTGCCTATTTTTAGA 57.030 33.333 0.00 0.00 0.00 2.10
1856 2019 6.575162 AAACACAGGTGCCTATTTTTAGAG 57.425 37.500 0.00 0.00 0.00 2.43
1857 2020 5.242795 ACACAGGTGCCTATTTTTAGAGT 57.757 39.130 0.00 0.00 0.00 3.24
1858 2021 6.368779 ACACAGGTGCCTATTTTTAGAGTA 57.631 37.500 0.00 0.00 0.00 2.59
1859 2022 6.775708 ACACAGGTGCCTATTTTTAGAGTAA 58.224 36.000 0.00 0.00 0.00 2.24
1864 2027 6.321435 AGGTGCCTATTTTTAGAGTAAATGCC 59.679 38.462 0.00 0.00 0.00 4.40
1897 2072 6.260936 GCATGTATCCTGTACAAATAAGCACT 59.739 38.462 0.00 0.00 0.00 4.40
1899 2074 6.941857 TGTATCCTGTACAAATAAGCACTGA 58.058 36.000 0.00 0.00 0.00 3.41
1939 2114 7.170965 TGATTTATTTCTTCAAGCACCTCTCT 58.829 34.615 0.00 0.00 0.00 3.10
1940 2115 7.335422 TGATTTATTTCTTCAAGCACCTCTCTC 59.665 37.037 0.00 0.00 0.00 3.20
1941 2116 3.409026 TTTCTTCAAGCACCTCTCTCC 57.591 47.619 0.00 0.00 0.00 3.71
1942 2117 2.317371 TCTTCAAGCACCTCTCTCCT 57.683 50.000 0.00 0.00 0.00 3.69
1944 2119 3.779444 TCTTCAAGCACCTCTCTCCTAA 58.221 45.455 0.00 0.00 0.00 2.69
1945 2120 3.766591 TCTTCAAGCACCTCTCTCCTAAG 59.233 47.826 0.00 0.00 0.00 2.18
1946 2121 3.176924 TCAAGCACCTCTCTCCTAAGT 57.823 47.619 0.00 0.00 0.00 2.24
1947 2122 4.317530 TCAAGCACCTCTCTCCTAAGTA 57.682 45.455 0.00 0.00 0.00 2.24
1948 2123 4.017808 TCAAGCACCTCTCTCCTAAGTAC 58.982 47.826 0.00 0.00 0.00 2.73
1949 2124 4.020543 CAAGCACCTCTCTCCTAAGTACT 58.979 47.826 0.00 0.00 0.00 2.73
1950 2125 3.893521 AGCACCTCTCTCCTAAGTACTC 58.106 50.000 0.00 0.00 0.00 2.59
1951 2126 2.953648 GCACCTCTCTCCTAAGTACTCC 59.046 54.545 0.00 0.00 0.00 3.85
1952 2127 3.558033 CACCTCTCTCCTAAGTACTCCC 58.442 54.545 0.00 0.00 0.00 4.30
1953 2128 3.203487 CACCTCTCTCCTAAGTACTCCCT 59.797 52.174 0.00 0.00 0.00 4.20
1954 2129 3.460712 ACCTCTCTCCTAAGTACTCCCTC 59.539 52.174 0.00 0.00 0.00 4.30
1955 2130 3.720002 CCTCTCTCCTAAGTACTCCCTCT 59.280 52.174 0.00 0.00 0.00 3.69
1956 2131 4.445735 CCTCTCTCCTAAGTACTCCCTCTG 60.446 54.167 0.00 0.00 0.00 3.35
1957 2132 4.113085 TCTCTCCTAAGTACTCCCTCTGT 58.887 47.826 0.00 0.00 0.00 3.41
1958 2133 5.287042 TCTCTCCTAAGTACTCCCTCTGTA 58.713 45.833 0.00 0.00 0.00 2.74
1959 2134 5.730207 TCTCTCCTAAGTACTCCCTCTGTAA 59.270 44.000 0.00 0.00 0.00 2.41
1960 2135 6.217074 TCTCTCCTAAGTACTCCCTCTGTAAA 59.783 42.308 0.00 0.00 0.00 2.01
1961 2136 6.982899 TCTCCTAAGTACTCCCTCTGTAAAT 58.017 40.000 0.00 0.00 0.00 1.40
1962 2137 8.110743 TCTCCTAAGTACTCCCTCTGTAAATA 57.889 38.462 0.00 0.00 0.00 1.40
1963 2138 8.563502 TCTCCTAAGTACTCCCTCTGTAAATAA 58.436 37.037 0.00 0.00 0.00 1.40
1964 2139 9.198475 CTCCTAAGTACTCCCTCTGTAAATAAA 57.802 37.037 0.00 0.00 0.00 1.40
1965 2140 9.725206 TCCTAAGTACTCCCTCTGTAAATAAAT 57.275 33.333 0.00 0.00 0.00 1.40
1975 2150 9.841295 TCCCTCTGTAAATAAATATAAAAGCGT 57.159 29.630 0.00 0.00 0.00 5.07
2025 2200 7.218145 ACGCTCTTATATTTGTTTACAGACG 57.782 36.000 0.00 0.00 0.00 4.18
2026 2201 6.255020 ACGCTCTTATATTTGTTTACAGACGG 59.745 38.462 0.00 0.00 0.00 4.79
2027 2202 6.474427 CGCTCTTATATTTGTTTACAGACGGA 59.526 38.462 0.00 0.00 0.00 4.69
2028 2203 7.306051 CGCTCTTATATTTGTTTACAGACGGAG 60.306 40.741 0.00 0.00 0.00 4.63
2042 2217 1.808411 ACGGAGTACCTTGCATTGTG 58.192 50.000 0.00 0.00 41.94 3.33
2055 2230 1.541147 GCATTGTGCAAGGTCTAAGCA 59.459 47.619 0.00 0.00 44.26 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 127 1.768684 GACAGTGAAGAGGGTGCCCA 61.769 60.000 10.26 0.00 38.92 5.36
141 143 2.548787 CGCGCGAACAACATGACA 59.451 55.556 28.94 0.00 0.00 3.58
169 171 1.973812 GCAAGCTCCAGGTGAACCC 60.974 63.158 0.00 0.00 36.42 4.11
225 227 2.582498 CGCGTCGAATCCCAGGTC 60.582 66.667 0.00 0.00 0.00 3.85
324 425 4.489771 CATCCTCCCGGGTGTGCC 62.490 72.222 22.86 0.00 36.62 5.01
329 430 2.365635 CTCCACATCCTCCCGGGT 60.366 66.667 22.86 0.00 36.25 5.28
552 657 2.511145 CCGAGCTTGAGCAGAGCC 60.511 66.667 1.22 0.00 45.16 4.70
680 785 2.727103 TTTTTCACCGCTTGGAGGG 58.273 52.632 0.00 0.00 36.26 4.30
774 884 4.884257 GGTAGGCGCGCGGATCAA 62.884 66.667 33.06 3.97 0.00 2.57
785 895 0.318784 CTATTGGTCGAGCGGTAGGC 60.319 60.000 10.46 0.00 44.05 3.93
919 1050 3.658757 TTTCTGTTGCTTGGTATTGGC 57.341 42.857 0.00 0.00 0.00 4.52
925 1056 4.875536 GGATTTTGTTTTCTGTTGCTTGGT 59.124 37.500 0.00 0.00 0.00 3.67
977 1108 0.940126 CGCTGCTCTCTCTCTCTCTC 59.060 60.000 0.00 0.00 0.00 3.20
1044 1175 4.314440 TTCCTGTGCCGCTTCGCT 62.314 61.111 0.00 0.00 0.00 4.93
1319 1450 0.669625 AACAAGCCGCTACGAGGAAC 60.670 55.000 0.00 0.00 0.00 3.62
1340 1471 2.906897 CACCACCACACCACCAGC 60.907 66.667 0.00 0.00 0.00 4.85
1342 1473 1.693103 TACCACCACCACACCACCA 60.693 57.895 0.00 0.00 0.00 4.17
1344 1475 0.181824 AACTACCACCACCACACCAC 59.818 55.000 0.00 0.00 0.00 4.16
1345 1476 0.920438 AAACTACCACCACCACACCA 59.080 50.000 0.00 0.00 0.00 4.17
1348 1479 0.920438 ACCAAACTACCACCACCACA 59.080 50.000 0.00 0.00 0.00 4.17
1352 1483 1.202557 TCGACACCAAACTACCACCAC 60.203 52.381 0.00 0.00 0.00 4.16
1353 1484 1.121378 TCGACACCAAACTACCACCA 58.879 50.000 0.00 0.00 0.00 4.17
1354 1485 2.243602 TTCGACACCAAACTACCACC 57.756 50.000 0.00 0.00 0.00 4.61
1400 1548 4.083110 CCAGGATTTACTTCACTGCAACAG 60.083 45.833 0.00 0.00 37.52 3.16
1471 1619 0.103026 AGAAGCGCACGCATATCTGA 59.897 50.000 18.24 0.00 44.88 3.27
1476 1624 1.128507 CAAAAGAGAAGCGCACGCATA 59.871 47.619 18.24 0.00 44.88 3.14
1502 1653 9.369904 GCAAAGCAATTATCCAAAGAAGAAATA 57.630 29.630 0.00 0.00 0.00 1.40
1631 1782 0.041312 GTGCGAACATGTTGAAGCGT 60.041 50.000 17.58 0.00 0.00 5.07
1650 1801 2.210116 AGCACCGCCGATATTTACTTG 58.790 47.619 0.00 0.00 0.00 3.16
1654 1805 3.732471 GCAAAAAGCACCGCCGATATTTA 60.732 43.478 0.00 0.00 44.79 1.40
1675 1826 2.789409 ACAATCCTAGGTGACAAGGC 57.211 50.000 9.08 0.00 32.55 4.35
1686 1837 5.499004 AGTCTTGCCAGTTTACAATCCTA 57.501 39.130 0.00 0.00 0.00 2.94
1688 1839 5.222631 CAAAGTCTTGCCAGTTTACAATCC 58.777 41.667 0.00 0.00 0.00 3.01
1702 1853 3.241701 ACACAACAAACGCAAAGTCTTG 58.758 40.909 0.00 0.00 35.49 3.02
1703 1854 3.569250 ACACAACAAACGCAAAGTCTT 57.431 38.095 0.00 0.00 0.00 3.01
1705 1856 4.384547 AGAAAACACAACAAACGCAAAGTC 59.615 37.500 0.00 0.00 0.00 3.01
1707 1858 4.434067 CCAGAAAACACAACAAACGCAAAG 60.434 41.667 0.00 0.00 0.00 2.77
1716 1879 5.417266 TCTCAACAATCCAGAAAACACAACA 59.583 36.000 0.00 0.00 0.00 3.33
1722 1885 8.595533 GTTTTCTTTCTCAACAATCCAGAAAAC 58.404 33.333 15.17 15.17 45.33 2.43
1754 1917 4.676849 TTCAAAAACAGCAAAACCAAGC 57.323 36.364 0.00 0.00 0.00 4.01
1755 1918 5.512434 GCAATTCAAAAACAGCAAAACCAAG 59.488 36.000 0.00 0.00 0.00 3.61
1759 1922 8.223100 CCTATAGCAATTCAAAAACAGCAAAAC 58.777 33.333 0.00 0.00 0.00 2.43
1786 1949 6.210784 TCTGAGCACCTAGTATTGTACAAAGT 59.789 38.462 13.23 7.70 0.00 2.66
1790 1953 6.599356 TTTCTGAGCACCTAGTATTGTACA 57.401 37.500 0.00 0.00 0.00 2.90
1798 1961 5.352569 CGATTCATTTTTCTGAGCACCTAGT 59.647 40.000 0.00 0.00 0.00 2.57
1817 1980 6.371825 ACCTGTGTTTTAGAAAGATCCGATTC 59.628 38.462 0.00 0.00 0.00 2.52
1823 1986 4.762251 AGGCACCTGTGTTTTAGAAAGATC 59.238 41.667 0.00 0.00 0.00 2.75
1824 1987 4.729868 AGGCACCTGTGTTTTAGAAAGAT 58.270 39.130 0.00 0.00 0.00 2.40
1826 1989 6.575162 AATAGGCACCTGTGTTTTAGAAAG 57.425 37.500 0.00 0.00 0.00 2.62
1834 1997 5.631119 ACTCTAAAAATAGGCACCTGTGTT 58.369 37.500 0.00 0.00 0.00 3.32
1839 2002 6.321435 GGCATTTACTCTAAAAATAGGCACCT 59.679 38.462 0.00 0.00 0.00 4.00
1840 2003 6.321435 AGGCATTTACTCTAAAAATAGGCACC 59.679 38.462 0.00 0.00 0.00 5.01
1841 2004 7.334844 AGGCATTTACTCTAAAAATAGGCAC 57.665 36.000 0.00 0.00 0.00 5.01
1851 2014 9.627123 ACATGCTTAATTAGGCATTTACTCTAA 57.373 29.630 27.14 2.38 45.19 2.10
1853 2016 9.799106 ATACATGCTTAATTAGGCATTTACTCT 57.201 29.630 27.14 11.74 45.19 3.24
1855 2018 9.014297 GGATACATGCTTAATTAGGCATTTACT 57.986 33.333 27.14 16.50 45.19 2.24
1856 2019 9.014297 AGGATACATGCTTAATTAGGCATTTAC 57.986 33.333 27.14 19.01 45.19 2.01
1857 2020 9.013229 CAGGATACATGCTTAATTAGGCATTTA 57.987 33.333 27.14 24.83 45.19 1.40
1858 2021 7.506938 ACAGGATACATGCTTAATTAGGCATTT 59.493 33.333 27.14 23.72 45.19 2.32
1859 2022 7.006509 ACAGGATACATGCTTAATTAGGCATT 58.993 34.615 27.14 20.62 45.19 3.56
1874 2037 7.564793 TCAGTGCTTATTTGTACAGGATACAT 58.435 34.615 0.00 0.00 41.41 2.29
1876 2039 7.855545 CATCAGTGCTTATTTGTACAGGATAC 58.144 38.462 0.00 0.00 0.00 2.24
1926 2101 3.176924 ACTTAGGAGAGAGGTGCTTGA 57.823 47.619 0.00 0.00 0.00 3.02
1930 2105 2.953648 GGAGTACTTAGGAGAGAGGTGC 59.046 54.545 0.00 0.00 0.00 5.01
1939 2114 9.725206 ATTTATTTACAGAGGGAGTACTTAGGA 57.275 33.333 0.00 0.00 0.00 2.94
1949 2124 9.841295 ACGCTTTTATATTTATTTACAGAGGGA 57.159 29.630 0.00 0.00 0.00 4.20
1999 2174 8.166706 CGTCTGTAAACAAATATAAGAGCGTTT 58.833 33.333 0.00 0.00 0.00 3.60
2000 2175 7.201496 CCGTCTGTAAACAAATATAAGAGCGTT 60.201 37.037 0.00 0.00 0.00 4.84
2001 2176 6.255020 CCGTCTGTAAACAAATATAAGAGCGT 59.745 38.462 0.00 0.00 0.00 5.07
2002 2177 6.474427 TCCGTCTGTAAACAAATATAAGAGCG 59.526 38.462 0.00 0.00 0.00 5.03
2003 2178 7.491696 ACTCCGTCTGTAAACAAATATAAGAGC 59.508 37.037 0.00 0.00 0.00 4.09
2004 2179 8.928270 ACTCCGTCTGTAAACAAATATAAGAG 57.072 34.615 0.00 0.00 0.00 2.85
2005 2180 9.793252 GTACTCCGTCTGTAAACAAATATAAGA 57.207 33.333 0.00 0.00 0.00 2.10
2006 2181 9.028185 GGTACTCCGTCTGTAAACAAATATAAG 57.972 37.037 0.00 0.00 0.00 1.73
2007 2182 8.752187 AGGTACTCCGTCTGTAAACAAATATAA 58.248 33.333 0.00 0.00 39.05 0.98
2008 2183 8.297470 AGGTACTCCGTCTGTAAACAAATATA 57.703 34.615 0.00 0.00 39.05 0.86
2009 2184 7.179076 AGGTACTCCGTCTGTAAACAAATAT 57.821 36.000 0.00 0.00 39.05 1.28
2010 2185 6.594788 AGGTACTCCGTCTGTAAACAAATA 57.405 37.500 0.00 0.00 39.05 1.40
2011 2186 5.479124 AGGTACTCCGTCTGTAAACAAAT 57.521 39.130 0.00 0.00 39.05 2.32
2012 2187 4.942761 AGGTACTCCGTCTGTAAACAAA 57.057 40.909 0.00 0.00 39.05 2.83
2013 2188 4.624015 CAAGGTACTCCGTCTGTAAACAA 58.376 43.478 0.00 0.00 38.49 2.83
2014 2189 3.553508 GCAAGGTACTCCGTCTGTAAACA 60.554 47.826 0.00 0.00 38.49 2.83
2015 2190 2.991866 GCAAGGTACTCCGTCTGTAAAC 59.008 50.000 0.00 0.00 38.49 2.01
2016 2191 2.629137 TGCAAGGTACTCCGTCTGTAAA 59.371 45.455 0.00 0.00 38.49 2.01
2017 2192 2.241160 TGCAAGGTACTCCGTCTGTAA 58.759 47.619 0.00 0.00 38.49 2.41
2018 2193 1.913778 TGCAAGGTACTCCGTCTGTA 58.086 50.000 0.00 0.00 38.49 2.74
2019 2194 1.267121 ATGCAAGGTACTCCGTCTGT 58.733 50.000 0.00 0.00 38.49 3.41
2020 2195 2.002586 CAATGCAAGGTACTCCGTCTG 58.997 52.381 0.00 0.00 38.49 3.51
2021 2196 1.623811 ACAATGCAAGGTACTCCGTCT 59.376 47.619 0.00 0.00 38.49 4.18
2022 2197 1.732259 CACAATGCAAGGTACTCCGTC 59.268 52.381 0.00 0.00 38.49 4.79
2023 2198 1.808411 CACAATGCAAGGTACTCCGT 58.192 50.000 0.00 0.00 38.49 4.69
2024 2199 0.447801 GCACAATGCAAGGTACTCCG 59.552 55.000 0.00 0.00 44.26 4.63
2042 2217 2.289694 TGGAAGACTGCTTAGACCTTGC 60.290 50.000 0.00 0.00 33.61 4.01
2055 2230 3.177228 ACATCCTTACTGCTGGAAGACT 58.823 45.455 16.67 1.05 35.81 3.24
2152 2328 9.643693 ATCAATTTGAAGGTTATCATTGTGTTC 57.356 29.630 2.68 0.00 0.00 3.18
2174 2350 4.651778 ACAGCTAAGTTAACCTGCATCAA 58.348 39.130 14.56 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.