Multiple sequence alignment - TraesCS3D01G208900

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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 TraesCS3D01G208900 chr3D 100.000 5791 0 0 1 5791 275993913 275999703 0.000000e+00 10695.0
1 TraesCS3D01G208900 chr3D 100.000 41 0 0 5468 5508 275999340 275999380 6.220000e-10 76.8
2 TraesCS3D01G208900 chr3D 100.000 41 0 0 5428 5468 275999380 275999420 6.220000e-10 76.8
3 TraesCS3D01G208900 chr3B 96.976 3406 68 13 1826 5209 375499579 375496187 0.000000e+00 5686.0
4 TraesCS3D01G208900 chr3B 93.525 973 42 13 767 1737 375500531 375499578 0.000000e+00 1428.0
5 TraesCS3D01G208900 chr3B 96.914 324 10 0 5468 5791 375494400 375494077 1.420000e-150 544.0
6 TraesCS3D01G208900 chr3B 88.614 404 21 10 248 637 375528349 375527957 8.790000e-128 468.0
7 TraesCS3D01G208900 chr3B 96.667 270 6 1 5202 5468 375494629 375494360 4.120000e-121 446.0
8 TraesCS3D01G208900 chr3B 89.683 252 19 6 2032 2281 799775926 799776172 1.210000e-81 315.0
9 TraesCS3D01G208900 chr3B 92.891 211 14 1 1 211 375528558 375528349 7.290000e-79 305.0
10 TraesCS3D01G208900 chr3B 96.842 95 3 0 1735 1829 187150399 187150493 6.010000e-35 159.0
11 TraesCS3D01G208900 chr3B 85.906 149 21 0 1589 1737 799775767 799775915 6.010000e-35 159.0
12 TraesCS3D01G208900 chr3B 95.789 95 4 0 1736 1830 187150491 187150397 2.790000e-33 154.0
13 TraesCS3D01G208900 chr3B 80.588 170 21 9 628 787 375500708 375500541 2.830000e-23 121.0
14 TraesCS3D01G208900 chr3A 95.313 3350 108 20 1826 5143 364197519 364194187 0.000000e+00 5271.0
15 TraesCS3D01G208900 chr3A 90.735 1565 92 29 210 1737 364199066 364197518 0.000000e+00 2037.0
16 TraesCS3D01G208900 chr3A 92.400 250 14 5 2034 2281 688140713 688140959 9.230000e-93 351.0
17 TraesCS3D01G208900 chr3A 89.032 155 17 0 1583 1737 688140546 688140700 5.920000e-45 193.0
18 TraesCS3D01G208900 chr3A 81.893 243 26 7 1304 1543 688140318 688140545 7.660000e-44 189.0
19 TraesCS3D01G208900 chr3A 92.391 92 5 2 122 213 364386325 364386236 4.710000e-26 130.0
20 TraesCS3D01G208900 chr1B 91.165 249 19 3 2034 2281 248235135 248235381 9.300000e-88 335.0
21 TraesCS3D01G208900 chr1B 81.377 247 24 8 1304 1543 248234739 248234970 1.280000e-41 182.0
22 TraesCS3D01G208900 chr1B 87.692 130 12 2 1118 1247 248234594 248234719 1.300000e-31 148.0
23 TraesCS3D01G208900 chr1B 92.593 54 4 0 1194 1247 688997139 688997192 1.730000e-10 78.7
24 TraesCS3D01G208900 chr1A 91.770 243 16 4 2040 2281 9819172 9818933 9.300000e-88 335.0
25 TraesCS3D01G208900 chr1A 83.128 243 22 8 1304 1543 9819571 9819345 2.740000e-48 204.0
26 TraesCS3D01G208900 chr1A 84.211 133 17 2 1118 1250 9819716 9819588 6.090000e-25 126.0
27 TraesCS3D01G208900 chr1A 88.043 92 10 1 991 1082 591157541 591157451 2.210000e-19 108.0
28 TraesCS3D01G208900 chrUn 90.000 250 25 0 2032 2281 90339621 90339870 2.010000e-84 324.0
29 TraesCS3D01G208900 chrUn 90.000 250 25 0 2032 2281 290523846 290524095 2.010000e-84 324.0
30 TraesCS3D01G208900 chrUn 81.148 244 23 10 1304 1543 90339245 90339469 2.140000e-39 174.0
31 TraesCS3D01G208900 chrUn 81.148 244 23 10 1304 1543 290523470 290523694 2.140000e-39 174.0
32 TraesCS3D01G208900 chr6B 89.286 252 21 5 2032 2281 337884740 337884987 1.570000e-80 311.0
33 TraesCS3D01G208900 chr6B 81.609 174 16 6 1359 1531 337884423 337884581 4.710000e-26 130.0
34 TraesCS3D01G208900 chr6B 86.022 93 11 2 1283 1373 337876249 337876341 1.330000e-16 99.0
35 TraesCS3D01G208900 chr4B 82.661 248 23 10 1292 1536 97560312 97560082 9.840000e-48 202.0
36 TraesCS3D01G208900 chr7A 95.000 100 5 0 1736 1835 125149693 125149792 2.160000e-34 158.0
37 TraesCS3D01G208900 chr7A 92.593 54 4 0 1194 1247 37300361 37300308 1.730000e-10 78.7
38 TraesCS3D01G208900 chr7D 94.175 103 3 2 1734 1833 635688981 635688879 2.790000e-33 154.0
39 TraesCS3D01G208900 chr7D 94.175 103 3 2 1734 1833 636310156 636310258 2.790000e-33 154.0
40 TraesCS3D01G208900 chr7D 100.000 32 0 0 288 319 59616718 59616687 6.270000e-05 60.2
41 TraesCS3D01G208900 chr2B 95.833 96 2 1 1736 1829 206371277 206371182 2.790000e-33 154.0
42 TraesCS3D01G208900 chr6D 94.845 97 4 1 1735 1831 431311851 431311756 3.610000e-32 150.0
43 TraesCS3D01G208900 chr6D 91.150 113 4 3 1736 1843 428262041 428262152 1.300000e-31 148.0
44 TraesCS3D01G208900 chr5A 89.565 115 8 2 1729 1839 230755588 230755702 6.050000e-30 143.0
45 TraesCS3D01G208900 chr1D 92.593 54 4 0 1194 1247 492650295 492650242 1.730000e-10 78.7
46 TraesCS3D01G208900 chr7B 88.889 54 6 0 1194 1247 689887697 689887644 3.740000e-07 67.6
47 TraesCS3D01G208900 chr5D 94.737 38 2 0 288 325 444710131 444710094 6.270000e-05 60.2
48 TraesCS3D01G208900 chr2D 100.000 32 0 0 288 319 569433464 569433433 6.270000e-05 60.2


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 TraesCS3D01G208900 chr3D 275993913 275999703 5790 False 3616.200000 10695 100.000000 1 5791 3 chr3D.!!$F1 5790
1 TraesCS3D01G208900 chr3B 375494077 375500708 6631 True 1645.000000 5686 92.934000 628 5791 5 chr3B.!!$R2 5163
2 TraesCS3D01G208900 chr3B 375527957 375528558 601 True 386.500000 468 90.752500 1 637 2 chr3B.!!$R3 636
3 TraesCS3D01G208900 chr3A 364194187 364199066 4879 True 3654.000000 5271 93.024000 210 5143 2 chr3A.!!$R2 4933
4 TraesCS3D01G208900 chr3A 688140318 688140959 641 False 244.333333 351 87.775000 1304 2281 3 chr3A.!!$F1 977
5 TraesCS3D01G208900 chr1B 248234594 248235381 787 False 221.666667 335 86.744667 1118 2281 3 chr1B.!!$F2 1163
6 TraesCS3D01G208900 chr1A 9818933 9819716 783 True 221.666667 335 86.369667 1118 2281 3 chr1A.!!$R2 1163
7 TraesCS3D01G208900 chrUn 90339245 90339870 625 False 249.000000 324 85.574000 1304 2281 2 chrUn.!!$F1 977
8 TraesCS3D01G208900 chrUn 290523470 290524095 625 False 249.000000 324 85.574000 1304 2281 2 chrUn.!!$F2 977
9 TraesCS3D01G208900 chr6B 337884423 337884987 564 False 220.500000 311 85.447500 1359 2281 2 chr6B.!!$F2 922

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
414 420 1.439679 GGGTGTGAACTCGGATGAAC 58.560 55.000 0.0 0.0 0.00 3.18 F
1151 1222 0.961019 TTGTGCTGATTCTGTTGGGC 59.039 50.000 0.0 0.0 0.00 5.36 F
1752 1851 1.286849 TGATACTCCCTCCGTTCCAGA 59.713 52.381 0.0 0.0 0.00 3.86 F
1757 1856 2.024273 ACTCCCTCCGTTCCAGAATAGA 60.024 50.000 0.0 0.0 0.00 1.98 F
1831 1930 2.108168 TGGAACGGAGGAAGTAGATGG 58.892 52.381 0.0 0.0 0.00 3.51 F
3777 3885 1.663702 GACCAGTGTTCCACGACGG 60.664 63.158 0.0 0.0 39.64 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1929 0.107165 GAGGTGGATGGGCTGTTACC 60.107 60.000 0.00 0.0 0.00 2.85 R
2009 2108 2.295349 CTGAACAGAACAAAGCCTGCAT 59.705 45.455 0.00 0.0 33.90 3.96 R
3374 3477 0.106918 AAGTGGCAACCTTCCGTTCA 60.107 50.000 0.00 0.0 29.93 3.18 R
3384 3487 2.622942 TCACCTCAATTGAAGTGGCAAC 59.377 45.455 28.49 0.0 37.17 4.17 R
3808 3916 0.179234 TCCACGGACAAGTGCAGAAA 59.821 50.000 0.00 0.0 40.59 2.52 R
5270 6977 0.173708 TTTTGGCAACCAACACGTCC 59.826 50.000 0.00 0.0 43.82 4.79 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
56 57 5.712152 AAAGACTAAAACAGATTGGCCAG 57.288 39.130 5.11 0.00 0.00 4.85
127 128 6.069963 ACCTAGATTAAGCCACTCAATCACTT 60.070 38.462 0.00 0.00 32.27 3.16
129 130 7.337942 CCTAGATTAAGCCACTCAATCACTTTT 59.662 37.037 0.00 0.00 32.27 2.27
148 149 6.366332 CACTTTTTGAGCCAGTACTACACTAG 59.634 42.308 0.00 0.00 34.98 2.57
166 167 9.429359 CTACACTAGTCAATCACTTTTCTGATT 57.571 33.333 0.00 0.00 40.81 2.57
224 225 6.570692 AGTACTACACTAAATCGGTCATTGG 58.429 40.000 0.00 0.00 34.98 3.16
227 228 6.938507 ACTACACTAAATCGGTCATTGGTAA 58.061 36.000 0.00 0.00 0.00 2.85
228 229 6.815142 ACTACACTAAATCGGTCATTGGTAAC 59.185 38.462 0.00 0.00 0.00 2.50
235 236 6.557291 AATCGGTCATTGGTAACGTAAAAA 57.443 33.333 0.00 0.00 42.51 1.94
325 331 5.957842 TTGAGCGACAACTAATTTGGATT 57.042 34.783 0.00 0.00 39.84 3.01
367 373 8.713708 TTGGGTAACATAAAAAGAAATCTCCA 57.286 30.769 0.00 0.00 39.74 3.86
414 420 1.439679 GGGTGTGAACTCGGATGAAC 58.560 55.000 0.00 0.00 0.00 3.18
477 486 8.707796 TGACTTTTTATAAACATTGGTGGGTA 57.292 30.769 0.00 0.00 0.00 3.69
486 495 4.470334 ACATTGGTGGGTATTTCATTGC 57.530 40.909 0.00 0.00 0.00 3.56
487 496 3.119173 ACATTGGTGGGTATTTCATTGCG 60.119 43.478 0.00 0.00 0.00 4.85
490 499 2.294074 GGTGGGTATTTCATTGCGCTA 58.706 47.619 9.73 0.00 0.00 4.26
491 500 2.685897 GGTGGGTATTTCATTGCGCTAA 59.314 45.455 9.73 1.22 0.00 3.09
606 627 5.065602 CACATCCACGAATGTCATTTCATCT 59.934 40.000 0.00 0.00 37.78 2.90
693 715 8.722342 TTGTTTCTTCTTATTTTTCCGATTCG 57.278 30.769 0.00 0.00 0.00 3.34
723 745 5.600696 AGAATGGCATTTTCGTCACTTTTT 58.399 33.333 14.93 0.00 0.00 1.94
733 771 2.798283 TCGTCACTTTTTCTAGTTGCGG 59.202 45.455 0.00 0.00 0.00 5.69
923 993 3.738481 CCCCGCAATTCCTCCCCA 61.738 66.667 0.00 0.00 0.00 4.96
1116 1186 3.013921 GCCTGAACAAACCATTCGGATA 58.986 45.455 0.00 0.00 34.85 2.59
1150 1221 2.029649 CCTTTGTGCTGATTCTGTTGGG 60.030 50.000 0.00 0.00 0.00 4.12
1151 1222 0.961019 TTGTGCTGATTCTGTTGGGC 59.039 50.000 0.00 0.00 0.00 5.36
1171 1242 3.419915 GCTGCTGATTAAATCGTGTGTG 58.580 45.455 0.00 0.00 0.00 3.82
1482 1581 2.092699 GCTCCTTGGCTATTCCTTCAGT 60.093 50.000 0.00 0.00 35.26 3.41
1686 1785 7.222872 TGCATTAGTTCATTTTTGTTCCCAAT 58.777 30.769 0.00 0.00 0.00 3.16
1738 1837 9.890915 AGATATAGGAGAGGAAAAGTTGATACT 57.109 33.333 0.00 0.00 35.68 2.12
1741 1840 4.471747 AGGAGAGGAAAAGTTGATACTCCC 59.528 45.833 0.00 6.64 42.20 4.30
1743 1842 5.395879 GGAGAGGAAAAGTTGATACTCCCTC 60.396 48.000 0.00 0.00 39.26 4.30
1744 1843 4.471747 AGAGGAAAAGTTGATACTCCCTCC 59.528 45.833 0.00 5.52 39.67 4.30
1747 1846 4.565028 GGAAAAGTTGATACTCCCTCCGTT 60.565 45.833 0.00 0.00 31.99 4.44
1748 1847 3.889520 AAGTTGATACTCCCTCCGTTC 57.110 47.619 0.00 0.00 31.99 3.95
1749 1848 2.108970 AGTTGATACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
1750 1849 1.829222 GTTGATACTCCCTCCGTTCCA 59.171 52.381 0.00 0.00 0.00 3.53
1751 1850 1.776662 TGATACTCCCTCCGTTCCAG 58.223 55.000 0.00 0.00 0.00 3.86
1752 1851 1.286849 TGATACTCCCTCCGTTCCAGA 59.713 52.381 0.00 0.00 0.00 3.86
1753 1852 2.291996 TGATACTCCCTCCGTTCCAGAA 60.292 50.000 0.00 0.00 0.00 3.02
1754 1853 2.544844 TACTCCCTCCGTTCCAGAAT 57.455 50.000 0.00 0.00 0.00 2.40
1755 1854 2.544844 ACTCCCTCCGTTCCAGAATA 57.455 50.000 0.00 0.00 0.00 1.75
1756 1855 2.389715 ACTCCCTCCGTTCCAGAATAG 58.610 52.381 0.00 0.00 0.00 1.73
1757 1856 2.024273 ACTCCCTCCGTTCCAGAATAGA 60.024 50.000 0.00 0.00 0.00 1.98
1758 1857 3.235200 CTCCCTCCGTTCCAGAATAGAT 58.765 50.000 0.00 0.00 0.00 1.98
1759 1858 2.965831 TCCCTCCGTTCCAGAATAGATG 59.034 50.000 0.00 0.00 0.00 2.90
1760 1859 2.965831 CCCTCCGTTCCAGAATAGATGA 59.034 50.000 0.00 0.00 0.00 2.92
1761 1860 3.243907 CCCTCCGTTCCAGAATAGATGAC 60.244 52.174 0.00 0.00 0.00 3.06
1762 1861 3.639094 CCTCCGTTCCAGAATAGATGACT 59.361 47.826 0.00 0.00 0.00 3.41
1763 1862 4.261825 CCTCCGTTCCAGAATAGATGACTC 60.262 50.000 0.00 0.00 0.00 3.36
1764 1863 4.278310 TCCGTTCCAGAATAGATGACTCA 58.722 43.478 0.00 0.00 0.00 3.41
1765 1864 4.709886 TCCGTTCCAGAATAGATGACTCAA 59.290 41.667 0.00 0.00 0.00 3.02
1766 1865 4.806247 CCGTTCCAGAATAGATGACTCAAC 59.194 45.833 0.00 0.00 0.00 3.18
1767 1866 5.394663 CCGTTCCAGAATAGATGACTCAACT 60.395 44.000 0.00 0.00 0.00 3.16
1768 1867 6.102663 CGTTCCAGAATAGATGACTCAACTT 58.897 40.000 0.00 0.00 0.00 2.66
1769 1868 6.591834 CGTTCCAGAATAGATGACTCAACTTT 59.408 38.462 0.00 0.00 0.00 2.66
1770 1869 7.412346 CGTTCCAGAATAGATGACTCAACTTTG 60.412 40.741 0.00 0.00 0.00 2.77
1771 1870 7.009179 TCCAGAATAGATGACTCAACTTTGT 57.991 36.000 0.00 0.00 0.00 2.83
1772 1871 8.134202 TCCAGAATAGATGACTCAACTTTGTA 57.866 34.615 0.00 0.00 0.00 2.41
1773 1872 8.035394 TCCAGAATAGATGACTCAACTTTGTAC 58.965 37.037 0.00 0.00 0.00 2.90
1774 1873 8.037758 CCAGAATAGATGACTCAACTTTGTACT 58.962 37.037 0.00 0.00 0.00 2.73
1813 1912 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1814 1913 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1815 1914 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1816 1915 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
1817 1916 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1818 1917 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
1819 1918 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1820 1919 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1821 1920 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1822 1921 4.469945 AGTCATCTATTTTGGAACGGAGGA 59.530 41.667 0.00 0.00 0.00 3.71
1823 1922 5.045869 AGTCATCTATTTTGGAACGGAGGAA 60.046 40.000 0.00 0.00 0.00 3.36
1824 1923 5.294552 GTCATCTATTTTGGAACGGAGGAAG 59.705 44.000 0.00 0.00 0.00 3.46
1825 1924 4.903045 TCTATTTTGGAACGGAGGAAGT 57.097 40.909 0.00 0.00 0.00 3.01
1826 1925 6.155565 TCATCTATTTTGGAACGGAGGAAGTA 59.844 38.462 0.00 0.00 0.00 2.24
1827 1926 5.974108 TCTATTTTGGAACGGAGGAAGTAG 58.026 41.667 0.00 0.00 0.00 2.57
1828 1927 4.903045 ATTTTGGAACGGAGGAAGTAGA 57.097 40.909 0.00 0.00 0.00 2.59
1829 1928 4.903045 TTTTGGAACGGAGGAAGTAGAT 57.097 40.909 0.00 0.00 0.00 1.98
1830 1929 3.887621 TTGGAACGGAGGAAGTAGATG 57.112 47.619 0.00 0.00 0.00 2.90
1831 1930 2.108168 TGGAACGGAGGAAGTAGATGG 58.892 52.381 0.00 0.00 0.00 3.51
1832 1931 2.108970 GGAACGGAGGAAGTAGATGGT 58.891 52.381 0.00 0.00 0.00 3.55
1833 1932 3.294214 GGAACGGAGGAAGTAGATGGTA 58.706 50.000 0.00 0.00 0.00 3.25
1834 1933 3.703052 GGAACGGAGGAAGTAGATGGTAA 59.297 47.826 0.00 0.00 0.00 2.85
1852 1951 2.142292 AACAGCCCATCCACCTCCAC 62.142 60.000 0.00 0.00 0.00 4.02
1925 2024 6.926630 AATTTTAGTCCCTTATTTGTGGCA 57.073 33.333 0.00 0.00 0.00 4.92
2009 2108 8.429641 ACACTCAGTCTATTTCTCCAAAACTAA 58.570 33.333 0.00 0.00 0.00 2.24
3303 3406 3.324846 TCATCTGGTGTGTTCTAACAGCT 59.675 43.478 7.88 0.00 46.33 4.24
3374 3477 9.566432 AAGAAACAGAAGTATGAGAAAATCAGT 57.434 29.630 0.00 0.00 42.53 3.41
3384 3487 4.065088 TGAGAAAATCAGTGAACGGAAGG 58.935 43.478 0.00 0.00 32.77 3.46
3562 3665 7.904558 TGAAGACAGTCCAGACTATCAATAT 57.095 36.000 8.68 0.00 37.33 1.28
3617 3720 6.821665 TCGAGAGGGTTGGTTTTCTATTTATG 59.178 38.462 0.00 0.00 0.00 1.90
3773 3881 1.946768 ACAAATGACCAGTGTTCCACG 59.053 47.619 0.00 0.00 39.64 4.94
3777 3885 1.663702 GACCAGTGTTCCACGACGG 60.664 63.158 0.00 0.00 39.64 4.79
3867 3975 7.698836 AATGTTCATGTTCTGTTGTTTTAGC 57.301 32.000 0.00 0.00 0.00 3.09
3875 3983 1.080772 GTTGTTTTAGCCCGCTGCC 60.081 57.895 0.00 0.00 42.71 4.85
3941 4050 8.768501 ATAGACTGTCAGGTATTCTTGTCATA 57.231 34.615 10.88 0.00 0.00 2.15
3952 4061 9.331282 AGGTATTCTTGTCATATAGCTGTTTTC 57.669 33.333 0.00 0.00 32.91 2.29
3953 4062 8.560374 GGTATTCTTGTCATATAGCTGTTTTCC 58.440 37.037 0.00 0.00 0.00 3.13
3954 4063 7.573968 ATTCTTGTCATATAGCTGTTTTCCC 57.426 36.000 0.00 0.00 0.00 3.97
4170 4279 3.930336 TCAGGTGCATGTTCAGAACTAG 58.070 45.455 14.51 7.84 0.00 2.57
4797 4909 9.044646 ACGATAGGATCCACTACTAGTATCTTA 57.955 37.037 15.82 0.25 43.77 2.10
5052 5186 0.179179 GCGTTGAGATGCTGCTTTCC 60.179 55.000 0.00 0.00 34.88 3.13
5069 5203 7.910683 GCTGCTTTCCTACTTTTCACATAATAC 59.089 37.037 0.00 0.00 0.00 1.89
5133 5275 5.132897 TGTTTACATTGGAATGCCTTGTC 57.867 39.130 2.45 0.00 40.04 3.18
5172 5314 3.270027 TCGAGCCCAGTGATAATTGTTG 58.730 45.455 0.00 0.00 0.00 3.33
5194 5336 8.575589 TGTTGAAGTGCTTGTGATTATTATTGT 58.424 29.630 0.00 0.00 0.00 2.71
5360 7070 9.162764 ACACATGTTAATCAATCCTAACACTAC 57.837 33.333 0.00 0.00 39.99 2.73
5370 7080 8.410673 TCAATCCTAACACTACTAGATGATCC 57.589 38.462 0.00 0.00 0.00 3.36
5404 7114 5.938279 AGCAGACATCATCATGATAAAGGT 58.062 37.500 8.15 7.54 34.28 3.50
5418 7128 5.321927 TGATAAAGGTTTCTCCAAGAACCC 58.678 41.667 1.88 0.00 37.08 4.11
5708 7418 0.759346 AGCCTAATTAGGAGCCCACG 59.241 55.000 31.78 6.26 46.63 4.94
5709 7419 0.756903 GCCTAATTAGGAGCCCACGA 59.243 55.000 31.78 0.00 46.63 4.35
5713 7423 2.693267 AATTAGGAGCCCACGAACTC 57.307 50.000 0.00 0.00 0.00 3.01
5752 7462 0.620556 TTCCCCACCTCATCTCAAGC 59.379 55.000 0.00 0.00 0.00 4.01
5775 7485 1.405821 AGCCTTAGTCATTCGTCGAGG 59.594 52.381 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.722193 CCGTTCTGGCCAATCTGT 57.278 55.556 7.01 0.00 0.00 3.41
95 96 1.478837 GGCTTAATCTAGGTTGGGGGC 60.479 57.143 0.00 0.00 0.00 5.80
98 99 3.199946 TGAGTGGCTTAATCTAGGTTGGG 59.800 47.826 0.00 0.00 0.00 4.12
127 128 5.537295 TGACTAGTGTAGTACTGGCTCAAAA 59.463 40.000 5.39 0.00 41.24 2.44
129 130 4.659115 TGACTAGTGTAGTACTGGCTCAA 58.341 43.478 5.39 0.00 41.24 3.02
148 149 6.712241 TCGAGAATCAGAAAAGTGATTGAC 57.288 37.500 3.87 0.00 45.32 3.18
185 186 7.897864 AGTGTAGTACTAGCTCAAAAAGTGAT 58.102 34.615 1.87 0.00 38.04 3.06
187 188 9.472361 TTTAGTGTAGTACTAGCTCAAAAAGTG 57.528 33.333 1.87 0.00 42.57 3.16
287 293 5.463392 GTCGCTCAAATGAATGTATCTAGCA 59.537 40.000 0.00 0.00 0.00 3.49
325 331 9.548631 TGTTACCCAAAATTAATATTTCCTCCA 57.451 29.630 0.00 0.00 32.85 3.86
367 373 4.562143 GCAGAAACTTCATGCCTCCAAAAT 60.562 41.667 0.00 0.00 33.81 1.82
381 387 1.073199 CACCCGGGAGCAGAAACTT 59.927 57.895 32.02 0.00 0.00 2.66
448 454 9.927668 CCACCAATGTTTATAAAAAGTCAGAAT 57.072 29.630 0.00 0.00 0.00 2.40
449 455 8.364142 CCCACCAATGTTTATAAAAAGTCAGAA 58.636 33.333 0.00 0.00 0.00 3.02
450 456 7.507616 ACCCACCAATGTTTATAAAAAGTCAGA 59.492 33.333 0.00 0.00 0.00 3.27
452 458 7.604657 ACCCACCAATGTTTATAAAAAGTCA 57.395 32.000 0.00 0.00 0.00 3.41
606 627 9.654417 GTTTTCTAACTGTGCGTAAATTTTAGA 57.346 29.630 0.00 0.00 0.00 2.10
687 709 3.130633 TGCCATTCTAACATCCGAATCG 58.869 45.455 0.00 0.00 0.00 3.34
692 714 4.201910 ACGAAAATGCCATTCTAACATCCG 60.202 41.667 0.00 0.00 0.00 4.18
693 715 5.163663 TGACGAAAATGCCATTCTAACATCC 60.164 40.000 0.00 0.00 0.00 3.51
694 716 5.739161 GTGACGAAAATGCCATTCTAACATC 59.261 40.000 0.00 0.00 0.00 3.06
695 717 5.415701 AGTGACGAAAATGCCATTCTAACAT 59.584 36.000 0.00 0.00 0.00 2.71
696 718 4.759693 AGTGACGAAAATGCCATTCTAACA 59.240 37.500 0.00 0.00 0.00 2.41
697 719 5.296813 AGTGACGAAAATGCCATTCTAAC 57.703 39.130 0.00 0.00 0.00 2.34
723 745 1.134818 ACATCGCAATCCGCAACTAGA 60.135 47.619 0.00 0.00 42.60 2.43
733 771 5.555256 CGTGTGAGAGATTAACATCGCAATC 60.555 44.000 0.00 0.00 34.28 2.67
808 876 2.435938 TTTCGCGAGCATCACCCC 60.436 61.111 9.59 0.00 33.17 4.95
1150 1221 3.120199 ACACACACGATTTAATCAGCAGC 60.120 43.478 5.76 0.00 0.00 5.25
1151 1222 4.668576 ACACACACGATTTAATCAGCAG 57.331 40.909 5.76 0.00 0.00 4.24
1171 1242 0.312102 GCAACCCAGAGCAAGTGAAC 59.688 55.000 0.00 0.00 0.00 3.18
1393 1482 1.771854 TCGCTCTAATATTTGGGCCCA 59.228 47.619 24.45 24.45 0.00 5.36
1482 1581 5.822519 AGCTGCCAATTCACGAAATATAAGA 59.177 36.000 0.00 0.00 0.00 2.10
1577 1676 6.024552 TGGCAGGAAATAGTTTTCAATGAC 57.975 37.500 1.38 2.41 42.55 3.06
1677 1776 7.162761 TCTCTGACGTTTAATTATTGGGAACA 58.837 34.615 0.00 0.00 39.83 3.18
1686 1785 9.445878 TTCTCTACTCTCTCTGACGTTTAATTA 57.554 33.333 0.00 0.00 0.00 1.40
1743 1842 4.655762 TGAGTCATCTATTCTGGAACGG 57.344 45.455 0.00 0.00 0.00 4.44
1744 1843 5.655488 AGTTGAGTCATCTATTCTGGAACG 58.345 41.667 1.70 0.00 0.00 3.95
1747 1846 7.009179 ACAAAGTTGAGTCATCTATTCTGGA 57.991 36.000 4.14 0.00 0.00 3.86
1748 1847 8.037758 AGTACAAAGTTGAGTCATCTATTCTGG 58.962 37.037 4.14 0.00 0.00 3.86
1749 1848 8.994429 AGTACAAAGTTGAGTCATCTATTCTG 57.006 34.615 4.14 3.46 0.00 3.02
1787 1886 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1788 1887 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1789 1888 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1790 1889 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1791 1890 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1792 1891 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1793 1892 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1794 1893 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1795 1894 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1796 1895 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1797 1896 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1798 1897 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1799 1898 4.469945 TCCTCCGTTCCAAAATAGATGACT 59.530 41.667 0.00 0.00 0.00 3.41
1800 1899 4.766375 TCCTCCGTTCCAAAATAGATGAC 58.234 43.478 0.00 0.00 0.00 3.06
1801 1900 5.045869 ACTTCCTCCGTTCCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1802 1901 5.186198 ACTTCCTCCGTTCCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
1803 1902 5.437191 ACTTCCTCCGTTCCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
1804 1903 4.903045 ACTTCCTCCGTTCCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
1805 1904 5.974108 TCTACTTCCTCCGTTCCAAAATAG 58.026 41.667 0.00 0.00 0.00 1.73
1806 1905 6.346096 CATCTACTTCCTCCGTTCCAAAATA 58.654 40.000 0.00 0.00 0.00 1.40
1807 1906 4.903045 TCTACTTCCTCCGTTCCAAAAT 57.097 40.909 0.00 0.00 0.00 1.82
1808 1907 4.564821 CCATCTACTTCCTCCGTTCCAAAA 60.565 45.833 0.00 0.00 0.00 2.44
1809 1908 3.055385 CCATCTACTTCCTCCGTTCCAAA 60.055 47.826 0.00 0.00 0.00 3.28
1810 1909 2.500098 CCATCTACTTCCTCCGTTCCAA 59.500 50.000 0.00 0.00 0.00 3.53
1811 1910 2.108168 CCATCTACTTCCTCCGTTCCA 58.892 52.381 0.00 0.00 0.00 3.53
1812 1911 2.108970 ACCATCTACTTCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
1813 1912 4.159135 TGTTACCATCTACTTCCTCCGTTC 59.841 45.833 0.00 0.00 0.00 3.95
1814 1913 4.091549 TGTTACCATCTACTTCCTCCGTT 58.908 43.478 0.00 0.00 0.00 4.44
1815 1914 3.700038 CTGTTACCATCTACTTCCTCCGT 59.300 47.826 0.00 0.00 0.00 4.69
1816 1915 3.491104 GCTGTTACCATCTACTTCCTCCG 60.491 52.174 0.00 0.00 0.00 4.63
1817 1916 3.181464 GGCTGTTACCATCTACTTCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
1818 1917 3.181464 GGGCTGTTACCATCTACTTCCTC 60.181 52.174 0.00 0.00 0.00 3.71
1819 1918 2.772515 GGGCTGTTACCATCTACTTCCT 59.227 50.000 0.00 0.00 0.00 3.36
1820 1919 2.504175 TGGGCTGTTACCATCTACTTCC 59.496 50.000 0.00 0.00 31.83 3.46
1821 1920 3.906720 TGGGCTGTTACCATCTACTTC 57.093 47.619 0.00 0.00 31.83 3.01
1829 1928 0.844661 AGGTGGATGGGCTGTTACCA 60.845 55.000 0.00 0.00 43.22 3.25
1830 1929 0.107165 GAGGTGGATGGGCTGTTACC 60.107 60.000 0.00 0.00 0.00 2.85
1831 1930 0.107165 GGAGGTGGATGGGCTGTTAC 60.107 60.000 0.00 0.00 0.00 2.50
1832 1931 0.548926 TGGAGGTGGATGGGCTGTTA 60.549 55.000 0.00 0.00 0.00 2.41
1833 1932 1.852157 TGGAGGTGGATGGGCTGTT 60.852 57.895 0.00 0.00 0.00 3.16
1834 1933 2.204136 TGGAGGTGGATGGGCTGT 60.204 61.111 0.00 0.00 0.00 4.40
1842 1941 1.273267 ACTAGAGCATGTGGAGGTGGA 60.273 52.381 0.00 0.00 0.00 4.02
1925 2024 3.189702 GCAGCAACATTTTTCCAATGCAT 59.810 39.130 0.00 0.00 36.30 3.96
2009 2108 2.295349 CTGAACAGAACAAAGCCTGCAT 59.705 45.455 0.00 0.00 33.90 3.96
2381 2484 7.488322 ACAAAGACTAGCTGATCTCTGTTATC 58.512 38.462 0.00 0.00 0.00 1.75
2885 2988 7.881775 AGAAAAGGATGGTTGGTAATACATC 57.118 36.000 0.00 0.00 39.11 3.06
3055 3158 8.728337 TGCATAGCAGATAAATGGATCTAATC 57.272 34.615 0.00 0.00 34.29 1.75
3137 3240 9.143155 ACCTTTATTCTTTAAACAAGATGGTGT 57.857 29.630 0.00 0.00 0.00 4.16
3178 3281 3.190118 GTCATCCCTTCTGCTTTGTTCTG 59.810 47.826 0.00 0.00 0.00 3.02
3374 3477 0.106918 AAGTGGCAACCTTCCGTTCA 60.107 50.000 0.00 0.00 29.93 3.18
3384 3487 2.622942 TCACCTCAATTGAAGTGGCAAC 59.377 45.455 28.49 0.00 37.17 4.17
3617 3720 8.850452 GCAATGCAAAACTTTATCTAGTAACAC 58.150 33.333 0.00 0.00 0.00 3.32
3656 3759 8.974060 ATGAGAAGTGTCCAAAAAGTAGTTTA 57.026 30.769 0.00 0.00 0.00 2.01
3668 3776 7.890127 AGAAAAATATCCAATGAGAAGTGTCCA 59.110 33.333 0.00 0.00 0.00 4.02
3773 3881 2.810650 CTGTACTGACAATAGCCCGTC 58.189 52.381 0.00 0.00 34.35 4.79
3777 3885 3.526931 TGAGCTGTACTGACAATAGCC 57.473 47.619 3.61 0.00 34.35 3.93
3808 3916 0.179234 TCCACGGACAAGTGCAGAAA 59.821 50.000 0.00 0.00 40.59 2.52
3875 3983 3.121030 CCCGAGCTTTGTCCTGCG 61.121 66.667 0.00 0.00 0.00 5.18
4170 4279 8.721478 TGAAGAAATAGCAATACAACAGAAGAC 58.279 33.333 0.00 0.00 0.00 3.01
4910 5030 0.396974 TTTGGGTCAGCAAACTGCCT 60.397 50.000 0.00 0.00 46.52 4.75
5133 5275 1.079503 GAAGTTACCTGCTCAAGCCG 58.920 55.000 0.00 0.00 41.18 5.52
5172 5314 7.698130 GTCCACAATAATAATCACAAGCACTTC 59.302 37.037 0.00 0.00 0.00 3.01
5270 6977 0.173708 TTTTGGCAACCAACACGTCC 59.826 50.000 0.00 0.00 43.82 4.79
5360 7070 4.236147 CTCGCTGTCAATGGATCATCTAG 58.764 47.826 0.00 0.00 0.00 2.43
5370 7080 1.326852 GATGTCTGCTCGCTGTCAATG 59.673 52.381 0.78 0.00 0.00 2.82
5404 7114 3.537337 TCCCATAGGGTTCTTGGAGAAA 58.463 45.455 1.36 0.00 44.74 2.52
5734 7444 1.617018 CGCTTGAGATGAGGTGGGGA 61.617 60.000 0.00 0.00 0.00 4.81
5752 7462 2.031314 TCGACGAATGACTAAGGCTACG 59.969 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.