Multiple sequence alignment - TraesCS5A01G028100

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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 TraesCS5A01G028100 chr5A 100.000 1903 0 0 581 2483 23933392 23935294 0.000000e+00 3515.0
1 TraesCS5A01G028100 chr5A 86.174 745 46 19 843 1561 24182821 24182108 0.000000e+00 752.0
2 TraesCS5A01G028100 chr5A 86.910 466 41 12 998 1459 24161337 24161786 2.850000e-139 505.0
3 TraesCS5A01G028100 chr5A 83.891 478 52 11 998 1464 24177120 24177583 1.360000e-117 433.0
4 TraesCS5A01G028100 chr5A 81.104 471 60 20 998 1463 23938703 23938257 1.410000e-92 350.0
5 TraesCS5A01G028100 chr5A 100.000 183 0 0 1 183 23932812 23932994 3.060000e-89 339.0
6 TraesCS5A01G028100 chr5A 78.070 456 65 29 1020 1468 23915563 23915136 3.170000e-64 255.0
7 TraesCS5A01G028100 chr5A 89.205 176 10 4 2308 2474 24180166 24179991 6.960000e-51 211.0
8 TraesCS5A01G028100 chr5A 94.872 117 6 0 1596 1712 24182046 24181930 1.520000e-42 183.0
9 TraesCS5A01G028100 chr5D 88.687 769 36 13 862 1591 35551555 35550799 0.000000e+00 891.0
10 TraesCS5A01G028100 chr5D 87.715 757 58 19 864 1591 35305077 35305827 0.000000e+00 850.0
11 TraesCS5A01G028100 chr5D 88.781 517 24 13 843 1344 35294140 35294637 9.820000e-169 603.0
12 TraesCS5A01G028100 chr5D 86.139 505 45 16 1000 1496 35531677 35532164 2.830000e-144 521.0
13 TraesCS5A01G028100 chr5D 90.341 176 12 2 2024 2199 35547040 35546870 2.480000e-55 226.0
14 TraesCS5A01G028100 chr5D 83.710 221 21 8 1804 2024 486226173 486225968 7.010000e-46 195.0
15 TraesCS5A01G028100 chr5D 87.597 129 3 4 1597 1712 35550752 35550624 1.200000e-28 137.0
16 TraesCS5A01G028100 chrUn 83.191 934 99 40 867 1781 298147231 298146337 0.000000e+00 802.0
17 TraesCS5A01G028100 chrUn 91.392 546 41 1 998 1543 340388859 340388320 0.000000e+00 743.0
18 TraesCS5A01G028100 chrUn 85.465 516 43 14 998 1510 340491764 340491278 2.200000e-140 508.0
19 TraesCS5A01G028100 chrUn 88.076 369 21 6 1234 1580 349553679 349553312 1.370000e-112 416.0
20 TraesCS5A01G028100 chrUn 87.698 252 19 3 2241 2483 349551962 349551714 1.450000e-72 283.0
21 TraesCS5A01G028100 chrUn 86.937 222 7 5 1804 2024 83928411 83928611 1.920000e-56 230.0
22 TraesCS5A01G028100 chrUn 89.944 179 14 2 2024 2201 298146208 298146033 6.910000e-56 228.0
23 TraesCS5A01G028100 chrUn 89.385 179 15 2 2024 2201 349553072 349552897 3.210000e-54 222.0
24 TraesCS5A01G028100 chrUn 85.577 208 14 6 1817 2024 134258697 134258506 1.160000e-48 204.0
25 TraesCS5A01G028100 chrUn 93.220 118 7 1 1664 1781 349553319 349553203 3.280000e-39 172.0
26 TraesCS5A01G028100 chrUn 91.870 123 4 3 843 964 264393270 264393153 1.530000e-37 167.0
27 TraesCS5A01G028100 chrUn 98.039 51 1 0 868 918 65894850 65894800 3.400000e-14 89.8
28 TraesCS5A01G028100 chrUn 98.039 51 1 0 868 918 266223055 266223105 3.400000e-14 89.8
29 TraesCS5A01G028100 chrUn 94.737 57 3 0 1535 1591 289327669 289327613 3.400000e-14 89.8
30 TraesCS5A01G028100 chrUn 94.737 57 3 0 1535 1591 335348499 335348555 3.400000e-14 89.8
31 TraesCS5A01G028100 chrUn 90.566 53 2 2 842 891 288041100 288041048 1.590000e-07 67.6
32 TraesCS5A01G028100 chrUn 90.566 53 2 2 842 891 303001660 303001608 1.590000e-07 67.6
33 TraesCS5A01G028100 chrUn 88.462 52 6 0 895 946 316546098 316546047 2.060000e-06 63.9
34 TraesCS5A01G028100 chr1D 88.768 276 12 8 581 837 246673713 246673438 1.110000e-83 320.0
35 TraesCS5A01G028100 chr1D 96.721 183 6 0 1 183 246673991 246673809 3.100000e-79 305.0
36 TraesCS5A01G028100 chr1D 87.410 278 16 9 581 839 493973001 493973278 4.010000e-78 302.0
37 TraesCS5A01G028100 chr1D 97.024 168 5 0 1 168 493972513 493972680 1.450000e-72 283.0
38 TraesCS5A01G028100 chr4B 86.182 275 16 7 581 833 553508488 553508214 6.760000e-71 278.0
39 TraesCS5A01G028100 chr4B 84.141 227 21 8 1801 2024 73615863 73616077 3.240000e-49 206.0
40 TraesCS5A01G028100 chr4B 96.491 114 4 0 1 114 553508879 553508766 3.260000e-44 189.0
41 TraesCS5A01G028100 chr7D 87.826 230 11 6 1797 2024 586785417 586785203 1.140000e-63 254.0
42 TraesCS5A01G028100 chr7D 86.222 225 8 12 1801 2024 11043435 11043637 3.210000e-54 222.0
43 TraesCS5A01G028100 chr7D 83.007 153 8 8 1802 1954 83871344 83871478 3.350000e-24 122.0
44 TraesCS5A01G028100 chr2B 87.615 218 9 7 1808 2024 684870861 684871061 1.150000e-58 237.0
45 TraesCS5A01G028100 chr2B 85.276 163 23 1 674 836 671753852 671753691 1.530000e-37 167.0
46 TraesCS5A01G028100 chr2B 93.590 78 4 1 1803 1880 579684126 579684202 5.610000e-22 115.0
47 TraesCS5A01G028100 chr2B 85.714 84 10 2 755 837 703798868 703798950 1.220000e-13 87.9
48 TraesCS5A01G028100 chr2D 86.878 221 13 4 1802 2022 68920678 68920474 1.480000e-57 233.0
49 TraesCS5A01G028100 chr2D 86.036 222 15 4 1804 2024 492033929 492033723 8.940000e-55 224.0
50 TraesCS5A01G028100 chr2D 86.473 207 8 4 1819 2024 398778388 398778201 2.500000e-50 209.0
51 TraesCS5A01G028100 chr3D 86.607 224 10 3 1801 2024 5039877 5040080 1.920000e-56 230.0
52 TraesCS5A01G028100 chr3D 89.655 58 4 2 784 840 31057938 31057882 3.430000e-09 73.1
53 TraesCS5A01G028100 chr4A 86.636 217 10 7 1808 2024 724732359 724732162 3.210000e-54 222.0
54 TraesCS5A01G028100 chr7A 84.513 226 27 8 1801 2024 732510391 732510172 1.500000e-52 217.0
55 TraesCS5A01G028100 chr7A 85.586 222 13 9 1804 2024 141017039 141016836 5.380000e-52 215.0
56 TraesCS5A01G028100 chr1B 86.036 222 8 6 1804 2024 570289845 570289646 1.500000e-52 217.0
57 TraesCS5A01G028100 chr6D 80.841 214 25 8 1804 2016 446533055 446532857 1.190000e-33 154.0
58 TraesCS5A01G028100 chr5B 91.667 96 2 2 864 959 26611550 26611639 7.210000e-26 128.0
59 TraesCS5A01G028100 chr2A 85.366 82 7 4 755 833 44072970 44073049 2.050000e-11 80.5
60 TraesCS5A01G028100 chr4D 91.228 57 3 2 784 839 497692883 497692828 2.650000e-10 76.8
61 TraesCS5A01G028100 chr4D 81.395 86 13 3 755 838 464674934 464674850 1.590000e-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 TraesCS5A01G028100 chr5A 23932812 23935294 2482 False 1927.00 3515 100.000000 1 2483 2 chr5A.!!$F3 2482
1 TraesCS5A01G028100 chr5A 24179991 24182821 2830 True 382.00 752 90.083667 843 2474 3 chr5A.!!$R3 1631
2 TraesCS5A01G028100 chr5D 35305077 35305827 750 False 850.00 850 87.715000 864 1591 1 chr5D.!!$F2 727
3 TraesCS5A01G028100 chr5D 35546870 35551555 4685 True 418.00 891 88.875000 862 2199 3 chr5D.!!$R2 1337
4 TraesCS5A01G028100 chrUn 340388320 340388859 539 True 743.00 743 91.392000 998 1543 1 chrUn.!!$R8 545
5 TraesCS5A01G028100 chrUn 298146033 298147231 1198 True 515.00 802 86.567500 867 2201 2 chrUn.!!$R10 1334
6 TraesCS5A01G028100 chrUn 349551714 349553679 1965 True 273.25 416 89.594750 1234 2483 4 chrUn.!!$R11 1249
7 TraesCS5A01G028100 chr1D 246673438 246673991 553 True 312.50 320 92.744500 1 837 2 chr1D.!!$R1 836
8 TraesCS5A01G028100 chr1D 493972513 493973278 765 False 292.50 302 92.217000 1 839 2 chr1D.!!$F1 838
9 TraesCS5A01G028100 chr4B 553508214 553508879 665 True 233.50 278 91.336500 1 833 2 chr4B.!!$R1 832

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
633 637 0.8003 CGACAGAGAGAGCGGCTTTC 60.8 60.0 12.27 12.27 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 6721 0.17668 TTTTGGGCGCATTGTTGTGT 59.823 45.0 10.83 0.0 35.72 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
83 84 1.599047 CCCTAGCACACCTCACAGG 59.401 63.158 0.00 0.00 42.49 4.00
633 637 0.800300 CGACAGAGAGAGCGGCTTTC 60.800 60.000 12.27 12.27 0.00 2.62
776 799 7.592533 CAGAACGAATCACAGAACAAAATCAAT 59.407 33.333 0.00 0.00 0.00 2.57
796 819 3.485463 TGGGTGAAAAATCGACTGACT 57.515 42.857 0.00 0.00 0.00 3.41
801 824 5.444122 GGTGAAAAATCGACTGACTCAAAG 58.556 41.667 0.00 0.00 0.00 2.77
804 827 7.012358 GTGAAAAATCGACTGACTCAAAGATC 58.988 38.462 0.00 0.00 0.00 2.75
839 862 7.119262 GCTGACTGAAAAGTAGCTAAATTGGTA 59.881 37.037 0.00 0.00 0.00 3.25
840 863 8.319143 TGACTGAAAAGTAGCTAAATTGGTAC 57.681 34.615 0.00 0.00 40.14 3.34
960 988 7.643764 GGACAAATCACAAACCAATCATATACG 59.356 37.037 0.00 0.00 0.00 3.06
961 989 8.050778 ACAAATCACAAACCAATCATATACGT 57.949 30.769 0.00 0.00 0.00 3.57
962 990 9.168451 ACAAATCACAAACCAATCATATACGTA 57.832 29.630 0.00 0.00 0.00 3.57
963 991 9.650371 CAAATCACAAACCAATCATATACGTAG 57.350 33.333 0.08 0.00 0.00 3.51
994 1025 3.431725 GCACGGCCAGGTTGTAGC 61.432 66.667 2.24 0.00 0.00 3.58
1223 1273 3.834799 GGTGTACTCCTCGGCGGG 61.835 72.222 7.21 1.99 0.00 6.13
1391 1444 4.389576 CTGCAAGCACGCGTTCCC 62.390 66.667 10.22 0.09 33.35 3.97
1522 1629 0.389025 CATGTCGATCGGGACCATGA 59.611 55.000 22.14 0.00 36.07 3.07
1591 1703 0.599060 TGGCATGTCTCGTACGAACA 59.401 50.000 24.84 24.84 0.00 3.18
1592 1704 1.000052 TGGCATGTCTCGTACGAACAA 60.000 47.619 25.75 13.99 0.00 2.83
1593 1705 2.268298 GGCATGTCTCGTACGAACAAT 58.732 47.619 25.75 15.28 0.00 2.71
1594 1706 2.671396 GGCATGTCTCGTACGAACAATT 59.329 45.455 25.75 14.66 0.00 2.32
1627 1780 0.107897 TACGAAGCCGCCATGAATGT 60.108 50.000 0.00 0.00 39.95 2.71
1629 1782 0.523968 CGAAGCCGCCATGAATGTTG 60.524 55.000 0.00 0.00 0.00 3.33
1663 1816 0.908910 TGGGTAGGTCGTCATGCATT 59.091 50.000 0.00 0.00 0.00 3.56
1702 1868 0.179073 CCATGTCCCGGTCAGCTAAG 60.179 60.000 0.00 0.00 0.00 2.18
1847 5140 9.690913 AACTTCCAATCTATTCATCTTCAATCA 57.309 29.630 0.00 0.00 0.00 2.57
1848 5141 9.863650 ACTTCCAATCTATTCATCTTCAATCAT 57.136 29.630 0.00 0.00 0.00 2.45
1850 5143 9.856162 TTCCAATCTATTCATCTTCAATCATGA 57.144 29.630 0.00 0.00 0.00 3.07
1860 5153 8.579682 TCATCTTCAATCATGATAGTACAACG 57.420 34.615 9.04 0.00 34.96 4.10
1861 5154 8.413229 TCATCTTCAATCATGATAGTACAACGA 58.587 33.333 9.04 0.00 34.96 3.85
1862 5155 9.034544 CATCTTCAATCATGATAGTACAACGAA 57.965 33.333 9.04 2.03 34.96 3.85
1863 5156 8.407457 TCTTCAATCATGATAGTACAACGAAC 57.593 34.615 9.04 0.00 34.96 3.95
1864 5157 8.032451 TCTTCAATCATGATAGTACAACGAACA 58.968 33.333 9.04 0.00 34.96 3.18
1865 5158 7.520119 TCAATCATGATAGTACAACGAACAC 57.480 36.000 9.04 0.00 0.00 3.32
1866 5159 6.533723 TCAATCATGATAGTACAACGAACACC 59.466 38.462 9.04 0.00 0.00 4.16
1868 5161 5.407502 TCATGATAGTACAACGAACACCAG 58.592 41.667 0.00 0.00 0.00 4.00
1870 5163 5.456548 TGATAGTACAACGAACACCAGAA 57.543 39.130 0.00 0.00 0.00 3.02
1877 5170 8.836268 AGTACAACGAACACCAGAAATAATAA 57.164 30.769 0.00 0.00 0.00 1.40
1881 5174 8.073768 ACAACGAACACCAGAAATAATAAACAG 58.926 33.333 0.00 0.00 0.00 3.16
1884 5177 8.287503 ACGAACACCAGAAATAATAAACAGTTC 58.712 33.333 0.00 0.00 0.00 3.01
1914 5207 6.978674 AAAATCTACATCCAGATCCGTAGA 57.021 37.500 9.17 9.17 43.18 2.59
1915 5208 5.968528 AATCTACATCCAGATCCGTAGAC 57.031 43.478 9.01 0.00 42.17 2.59
1918 5211 2.964209 ACATCCAGATCCGTAGACCAT 58.036 47.619 0.00 0.00 0.00 3.55
1919 5212 2.894126 ACATCCAGATCCGTAGACCATC 59.106 50.000 0.00 0.00 0.00 3.51
1920 5213 3.161067 CATCCAGATCCGTAGACCATCT 58.839 50.000 0.00 0.00 0.00 2.90
1921 5214 4.202577 ACATCCAGATCCGTAGACCATCTA 60.203 45.833 0.00 0.00 0.00 1.98
1922 5215 4.022413 TCCAGATCCGTAGACCATCTAG 57.978 50.000 0.00 0.00 28.01 2.43
1923 5216 2.490115 CCAGATCCGTAGACCATCTAGC 59.510 54.545 0.00 0.00 28.01 3.42
1926 5219 1.590932 TCCGTAGACCATCTAGCGAC 58.409 55.000 0.00 0.00 30.61 5.19
1928 5221 1.215244 CGTAGACCATCTAGCGACGA 58.785 55.000 0.00 0.00 29.07 4.20
1929 5222 1.070710 CGTAGACCATCTAGCGACGAC 60.071 57.143 0.00 0.00 29.07 4.34
1930 5223 2.211806 GTAGACCATCTAGCGACGACT 58.788 52.381 0.00 0.00 28.01 4.18
1931 5224 2.616634 AGACCATCTAGCGACGACTA 57.383 50.000 0.00 0.00 0.00 2.59
1933 5226 1.938577 GACCATCTAGCGACGACTACA 59.061 52.381 0.00 0.00 0.00 2.74
1935 5228 2.355132 ACCATCTAGCGACGACTACAAG 59.645 50.000 0.00 0.00 0.00 3.16
1936 5229 2.376956 CATCTAGCGACGACTACAAGC 58.623 52.381 0.00 0.00 0.00 4.01
1940 5233 0.387367 AGCGACGACTACAAGCACTG 60.387 55.000 0.00 0.00 0.00 3.66
1941 5234 0.386858 GCGACGACTACAAGCACTGA 60.387 55.000 0.00 0.00 0.00 3.41
1942 5235 1.929038 GCGACGACTACAAGCACTGAA 60.929 52.381 0.00 0.00 0.00 3.02
1943 5236 1.979469 CGACGACTACAAGCACTGAAG 59.021 52.381 0.00 0.00 0.00 3.02
1945 5238 0.710567 CGACTACAAGCACTGAAGCG 59.289 55.000 0.00 0.00 40.15 4.68
1946 5239 1.666023 CGACTACAAGCACTGAAGCGA 60.666 52.381 0.00 0.00 40.15 4.93
1947 5240 1.989165 GACTACAAGCACTGAAGCGAG 59.011 52.381 0.00 0.00 40.15 5.03
1950 5243 2.740055 AAGCACTGAAGCGAGCCG 60.740 61.111 0.00 0.00 40.15 5.52
1952 5245 2.715532 AAGCACTGAAGCGAGCCGAA 62.716 55.000 0.00 0.00 40.15 4.30
1953 5246 2.734673 GCACTGAAGCGAGCCGAAG 61.735 63.158 0.00 0.00 0.00 3.79
1976 5269 4.899239 CTGCCGTCATCGCCCCTC 62.899 72.222 0.00 0.00 35.54 4.30
1979 5272 3.550431 CCGTCATCGCCCCTCCAT 61.550 66.667 0.00 0.00 35.54 3.41
1980 5273 2.029666 CGTCATCGCCCCTCCATC 59.970 66.667 0.00 0.00 0.00 3.51
1983 5276 4.996434 CATCGCCCCTCCATCGCC 62.996 72.222 0.00 0.00 0.00 5.54
2000 5293 4.058797 CGGAGTCGGGCAAACTTT 57.941 55.556 0.00 0.00 0.00 2.66
2001 5294 1.574428 CGGAGTCGGGCAAACTTTG 59.426 57.895 0.00 0.00 0.00 2.77
2003 5296 1.029681 GGAGTCGGGCAAACTTTGTT 58.970 50.000 3.48 0.00 0.00 2.83
2005 5298 1.404035 GAGTCGGGCAAACTTTGTTGT 59.596 47.619 3.48 0.00 0.00 3.32
2007 5300 2.616842 AGTCGGGCAAACTTTGTTGTAG 59.383 45.455 3.48 0.00 0.00 2.74
2009 5302 3.560896 GTCGGGCAAACTTTGTTGTAGTA 59.439 43.478 3.48 0.00 0.00 1.82
2010 5303 3.810941 TCGGGCAAACTTTGTTGTAGTAG 59.189 43.478 3.48 0.00 0.00 2.57
2014 5307 5.277828 GGGCAAACTTTGTTGTAGTAGACAG 60.278 44.000 3.48 0.00 39.88 3.51
2015 5308 5.296035 GGCAAACTTTGTTGTAGTAGACAGT 59.704 40.000 3.48 0.00 39.88 3.55
2016 5309 6.419771 GCAAACTTTGTTGTAGTAGACAGTC 58.580 40.000 3.48 0.00 39.88 3.51
2017 5310 6.637365 CAAACTTTGTTGTAGTAGACAGTCG 58.363 40.000 0.00 0.00 39.88 4.18
2018 5311 4.868067 ACTTTGTTGTAGTAGACAGTCGG 58.132 43.478 0.00 0.00 39.88 4.79
2019 5312 3.928727 TTGTTGTAGTAGACAGTCGGG 57.071 47.619 0.00 0.00 39.88 5.14
2041 5556 7.230913 TCGGGAAGTAAATGAATAACAAACCAA 59.769 33.333 0.00 0.00 0.00 3.67
2061 5576 5.124138 ACCAACTCGAACAAATTTACACACA 59.876 36.000 0.00 0.00 0.00 3.72
2076 5591 1.069703 CACACATGACAAACCGCTGAG 60.070 52.381 0.00 0.00 0.00 3.35
2111 5626 9.624373 TCTATACCCAGAATTACCGATATACTC 57.376 37.037 0.00 0.00 0.00 2.59
2144 5660 3.049912 GCAACTTTTTCTTAACCTGGCG 58.950 45.455 0.00 0.00 0.00 5.69
2204 5720 7.812191 TGTATTTCACACTTGAATAAACATGGC 59.188 33.333 0.00 0.00 41.50 4.40
2206 5722 4.068599 TCACACTTGAATAAACATGGCGA 58.931 39.130 0.00 0.00 0.00 5.54
2207 5723 4.083537 TCACACTTGAATAAACATGGCGAC 60.084 41.667 0.00 0.00 0.00 5.19
2208 5724 7.898152 TTCACACTTGAATAAACATGGCGACA 61.898 38.462 0.00 0.00 40.16 4.35
2219 5735 1.975327 TGGCGACAAAGGAGAGGAG 59.025 57.895 0.00 0.00 37.44 3.69
2221 5737 1.448717 GCGACAAAGGAGAGGAGGC 60.449 63.158 0.00 0.00 0.00 4.70
2222 5738 1.153745 CGACAAAGGAGAGGAGGCG 60.154 63.158 0.00 0.00 0.00 5.52
2224 5740 0.108567 GACAAAGGAGAGGAGGCGAC 60.109 60.000 0.00 0.00 0.00 5.19
2225 5741 0.832135 ACAAAGGAGAGGAGGCGACA 60.832 55.000 0.00 0.00 0.00 4.35
2226 5742 0.321671 CAAAGGAGAGGAGGCGACAA 59.678 55.000 0.00 0.00 0.00 3.18
2228 5744 0.543174 AAGGAGAGGAGGCGACAACT 60.543 55.000 0.00 0.00 0.00 3.16
2229 5745 0.543174 AGGAGAGGAGGCGACAACTT 60.543 55.000 0.00 0.00 0.00 2.66
2231 5747 0.603569 GAGAGGAGGCGACAACTTGA 59.396 55.000 0.00 0.00 0.00 3.02
2232 5748 1.000955 GAGAGGAGGCGACAACTTGAA 59.999 52.381 0.00 0.00 0.00 2.69
2233 5749 1.625818 AGAGGAGGCGACAACTTGAAT 59.374 47.619 0.00 0.00 0.00 2.57
2234 5750 2.832129 AGAGGAGGCGACAACTTGAATA 59.168 45.455 0.00 0.00 0.00 1.75
2235 5751 3.118956 AGAGGAGGCGACAACTTGAATAG 60.119 47.826 0.00 0.00 0.00 1.73
2238 5754 2.605366 GAGGCGACAACTTGAATAGAGC 59.395 50.000 0.00 0.00 0.00 4.09
2239 5755 1.666189 GGCGACAACTTGAATAGAGCC 59.334 52.381 0.00 0.00 35.00 4.70
2264 6709 2.503895 ATGGACCTCAAGCAAAGGAG 57.496 50.000 6.10 0.00 37.35 3.69
2272 6717 1.023513 CAAGCAAAGGAGAGGAGGCG 61.024 60.000 0.00 0.00 0.00 5.52
2276 6721 0.321671 CAAAGGAGAGGAGGCGACAA 59.678 55.000 0.00 0.00 0.00 3.18
2288 6733 1.268113 GGCGACAACACAACAATGCG 61.268 55.000 0.00 0.00 0.00 4.73
2297 6742 2.036475 ACACAACAATGCGCCCAAAATA 59.964 40.909 4.18 0.00 0.00 1.40
2303 6765 3.181480 ACAATGCGCCCAAAATATACACC 60.181 43.478 4.18 0.00 0.00 4.16
2304 6766 1.018148 TGCGCCCAAAATATACACCG 58.982 50.000 4.18 0.00 0.00 4.94
2325 6787 2.039418 TGCCTAGGCGTCATAATCACT 58.961 47.619 28.28 0.00 45.51 3.41
2335 6797 4.671766 GCGTCATAATCACTGTTTCAACCC 60.672 45.833 0.00 0.00 0.00 4.11
2339 6801 2.631160 ATCACTGTTTCAACCCGTCA 57.369 45.000 0.00 0.00 0.00 4.35
2380 6842 2.044946 GCCACATCCCAGTCCACC 60.045 66.667 0.00 0.00 0.00 4.61
2392 6854 0.253160 AGTCCACCCCATGCCTAAGA 60.253 55.000 0.00 0.00 0.00 2.10
2436 6907 2.280628 CGCCACCTTCAAACTAGATCC 58.719 52.381 0.00 0.00 0.00 3.36
2474 6945 6.071320 AGAACAAATCAGAAACCCTAGCTTT 58.929 36.000 0.00 0.00 0.00 3.51
2476 6947 6.332735 ACAAATCAGAAACCCTAGCTTTTC 57.667 37.500 0.00 0.00 32.76 2.29
2477 6948 6.071320 ACAAATCAGAAACCCTAGCTTTTCT 58.929 36.000 5.47 5.47 41.73 2.52
2478 6949 7.231467 ACAAATCAGAAACCCTAGCTTTTCTA 58.769 34.615 10.11 2.12 39.54 2.10
2479 6950 7.391833 ACAAATCAGAAACCCTAGCTTTTCTAG 59.608 37.037 10.11 6.36 39.54 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 3.751518 TGGTTAGGGTTTTCTCTGCTTC 58.248 45.455 0.00 0.00 0.00 3.86
633 637 3.854669 CAGCCCAGCCCGTAGAGG 61.855 72.222 0.00 0.00 40.63 3.69
776 799 3.181459 TGAGTCAGTCGATTTTTCACCCA 60.181 43.478 0.00 0.00 0.00 4.51
796 819 6.487668 TCAGTCAGCTGATTTTTGATCTTTGA 59.512 34.615 21.47 2.10 45.94 2.69
839 862 3.908103 AGCCCCGGACATATAAATACAGT 59.092 43.478 0.73 0.00 0.00 3.55
840 863 4.020573 TCAGCCCCGGACATATAAATACAG 60.021 45.833 0.73 0.00 0.00 2.74
841 864 3.904965 TCAGCCCCGGACATATAAATACA 59.095 43.478 0.73 0.00 0.00 2.29
960 988 3.372954 CGTGCAGCTTCTATGTACCTAC 58.627 50.000 0.00 0.00 30.46 3.18
961 989 2.361119 CCGTGCAGCTTCTATGTACCTA 59.639 50.000 0.00 0.00 30.46 3.08
962 990 1.137086 CCGTGCAGCTTCTATGTACCT 59.863 52.381 0.00 0.00 30.46 3.08
963 991 1.571919 CCGTGCAGCTTCTATGTACC 58.428 55.000 0.00 0.00 30.46 3.34
994 1025 2.281761 GGAGCCCGGCATGGTATG 60.282 66.667 13.15 0.00 35.15 2.39
1188 1238 4.712425 GTGGTCGTGTACGCGGCT 62.712 66.667 29.84 0.00 39.60 5.52
1565 1676 3.733988 CGTACGAGACATGCCATGTACTT 60.734 47.826 10.93 4.73 45.03 2.24
1591 1703 6.402875 GGCTTCGTACGGAACATTTCTAAATT 60.403 38.462 16.52 0.00 0.00 1.82
1592 1704 5.064325 GGCTTCGTACGGAACATTTCTAAAT 59.936 40.000 16.52 0.00 0.00 1.40
1593 1705 4.389687 GGCTTCGTACGGAACATTTCTAAA 59.610 41.667 16.52 0.00 0.00 1.85
1594 1706 3.928375 GGCTTCGTACGGAACATTTCTAA 59.072 43.478 16.52 0.00 0.00 2.10
1627 1780 0.888619 CCACGGACTCTGCTCTACAA 59.111 55.000 0.00 0.00 0.00 2.41
1629 1782 0.966370 ACCCACGGACTCTGCTCTAC 60.966 60.000 0.00 0.00 0.00 2.59
1740 1906 1.621992 ACTCGGTCGGATGCATCTAT 58.378 50.000 25.28 0.00 0.00 1.98
1752 3301 6.148150 TGAAATACACATAACCAAACTCGGTC 59.852 38.462 0.00 0.00 38.76 4.79
1821 5114 9.690913 TGATTGAAGATGAATAGATTGGAAGTT 57.309 29.630 0.00 0.00 0.00 2.66
1822 5115 9.863650 ATGATTGAAGATGAATAGATTGGAAGT 57.136 29.630 0.00 0.00 0.00 3.01
1824 5117 9.856162 TCATGATTGAAGATGAATAGATTGGAA 57.144 29.630 0.00 0.00 0.00 3.53
1834 5127 9.034544 CGTTGTACTATCATGATTGAAGATGAA 57.965 33.333 21.64 4.00 34.96 2.57
1835 5128 8.413229 TCGTTGTACTATCATGATTGAAGATGA 58.587 33.333 21.64 12.27 34.96 2.92
1836 5129 8.579682 TCGTTGTACTATCATGATTGAAGATG 57.420 34.615 21.64 10.62 34.96 2.90
1837 5130 9.035607 GTTCGTTGTACTATCATGATTGAAGAT 57.964 33.333 21.64 4.07 34.96 2.40
1838 5131 8.032451 TGTTCGTTGTACTATCATGATTGAAGA 58.968 33.333 21.64 6.21 34.96 2.87
1839 5132 8.110612 GTGTTCGTTGTACTATCATGATTGAAG 58.889 37.037 21.64 12.40 34.96 3.02
1840 5133 7.064134 GGTGTTCGTTGTACTATCATGATTGAA 59.936 37.037 21.64 5.14 34.96 2.69
1841 5134 6.533723 GGTGTTCGTTGTACTATCATGATTGA 59.466 38.462 21.64 1.13 36.00 2.57
1842 5135 6.312672 TGGTGTTCGTTGTACTATCATGATTG 59.687 38.462 14.65 14.58 0.00 2.67
1843 5136 6.403049 TGGTGTTCGTTGTACTATCATGATT 58.597 36.000 14.65 0.00 0.00 2.57
1844 5137 5.972935 TGGTGTTCGTTGTACTATCATGAT 58.027 37.500 13.81 13.81 0.00 2.45
1845 5138 5.184287 TCTGGTGTTCGTTGTACTATCATGA 59.816 40.000 0.00 0.00 0.00 3.07
1846 5139 5.407502 TCTGGTGTTCGTTGTACTATCATG 58.592 41.667 0.00 0.00 0.00 3.07
1847 5140 5.654603 TCTGGTGTTCGTTGTACTATCAT 57.345 39.130 0.00 0.00 0.00 2.45
1848 5141 5.456548 TTCTGGTGTTCGTTGTACTATCA 57.543 39.130 0.00 0.00 0.00 2.15
1849 5142 6.963049 ATTTCTGGTGTTCGTTGTACTATC 57.037 37.500 0.00 0.00 0.00 2.08
1851 5144 9.926158 TTATTATTTCTGGTGTTCGTTGTACTA 57.074 29.630 0.00 0.00 0.00 1.82
1852 5145 8.836268 TTATTATTTCTGGTGTTCGTTGTACT 57.164 30.769 0.00 0.00 0.00 2.73
1853 5146 9.321590 GTTTATTATTTCTGGTGTTCGTTGTAC 57.678 33.333 0.00 0.00 0.00 2.90
1854 5147 9.053840 TGTTTATTATTTCTGGTGTTCGTTGTA 57.946 29.630 0.00 0.00 0.00 2.41
1855 5148 7.932335 TGTTTATTATTTCTGGTGTTCGTTGT 58.068 30.769 0.00 0.00 0.00 3.32
1856 5149 8.073768 ACTGTTTATTATTTCTGGTGTTCGTTG 58.926 33.333 0.00 0.00 0.00 4.10
1857 5150 8.161699 ACTGTTTATTATTTCTGGTGTTCGTT 57.838 30.769 0.00 0.00 0.00 3.85
1858 5151 7.739498 ACTGTTTATTATTTCTGGTGTTCGT 57.261 32.000 0.00 0.00 0.00 3.85
1859 5152 8.286800 TGAACTGTTTATTATTTCTGGTGTTCG 58.713 33.333 0.00 0.00 33.78 3.95
1887 5180 9.712305 CTACGGATCTGGATGTAGATTTTATTT 57.288 33.333 6.47 0.00 37.53 1.40
1889 5182 8.524487 GTCTACGGATCTGGATGTAGATTTTAT 58.476 37.037 6.47 0.00 43.52 1.40
1895 5188 3.137728 TGGTCTACGGATCTGGATGTAGA 59.862 47.826 6.47 7.22 40.57 2.59
1896 5189 3.487372 TGGTCTACGGATCTGGATGTAG 58.513 50.000 6.47 5.16 36.49 2.74
1901 5194 3.811098 GCTAGATGGTCTACGGATCTGGA 60.811 52.174 6.47 0.00 28.72 3.86
1902 5195 2.490115 GCTAGATGGTCTACGGATCTGG 59.510 54.545 6.47 0.00 0.00 3.86
1903 5196 2.160615 CGCTAGATGGTCTACGGATCTG 59.839 54.545 0.00 0.00 0.00 2.90
1904 5197 2.038689 TCGCTAGATGGTCTACGGATCT 59.961 50.000 0.00 0.00 30.31 2.75
1905 5198 2.160022 GTCGCTAGATGGTCTACGGATC 59.840 54.545 0.00 0.00 30.31 3.36
1907 5200 1.590932 GTCGCTAGATGGTCTACGGA 58.409 55.000 0.00 0.00 30.31 4.69
1909 5202 1.070710 GTCGTCGCTAGATGGTCTACG 60.071 57.143 0.00 0.00 34.23 3.51
1910 5203 2.211806 AGTCGTCGCTAGATGGTCTAC 58.788 52.381 0.00 0.00 34.23 2.59
1914 5207 2.034104 TGTAGTCGTCGCTAGATGGT 57.966 50.000 0.00 0.00 34.23 3.55
1915 5208 2.855187 GCTTGTAGTCGTCGCTAGATGG 60.855 54.545 0.00 0.00 34.23 3.51
1918 5211 1.129998 GTGCTTGTAGTCGTCGCTAGA 59.870 52.381 0.00 0.00 0.00 2.43
1919 5212 1.130749 AGTGCTTGTAGTCGTCGCTAG 59.869 52.381 0.00 0.00 0.00 3.42
1920 5213 1.135774 CAGTGCTTGTAGTCGTCGCTA 60.136 52.381 0.00 0.00 0.00 4.26
1921 5214 0.387367 CAGTGCTTGTAGTCGTCGCT 60.387 55.000 0.00 0.00 0.00 4.93
1922 5215 0.386858 TCAGTGCTTGTAGTCGTCGC 60.387 55.000 0.00 0.00 0.00 5.19
1923 5216 1.979469 CTTCAGTGCTTGTAGTCGTCG 59.021 52.381 0.00 0.00 0.00 5.12
1926 5219 0.710567 CGCTTCAGTGCTTGTAGTCG 59.289 55.000 0.00 0.00 0.00 4.18
1928 5221 1.937108 GCTCGCTTCAGTGCTTGTAGT 60.937 52.381 0.00 0.00 0.00 2.73
1929 5222 0.718343 GCTCGCTTCAGTGCTTGTAG 59.282 55.000 0.00 0.00 0.00 2.74
1930 5223 0.670546 GGCTCGCTTCAGTGCTTGTA 60.671 55.000 0.00 0.00 0.00 2.41
1931 5224 1.963338 GGCTCGCTTCAGTGCTTGT 60.963 57.895 0.00 0.00 0.00 3.16
1933 5226 2.715532 TTCGGCTCGCTTCAGTGCTT 62.716 55.000 0.00 0.00 0.00 3.91
1935 5228 2.734673 CTTCGGCTCGCTTCAGTGC 61.735 63.158 0.00 0.00 0.00 4.40
1936 5229 2.097038 CCTTCGGCTCGCTTCAGTG 61.097 63.158 0.00 0.00 0.00 3.66
1963 5256 2.029666 GATGGAGGGGCGATGACG 59.970 66.667 0.00 0.00 42.93 4.35
1964 5257 2.029666 CGATGGAGGGGCGATGAC 59.970 66.667 0.00 0.00 0.00 3.06
1966 5259 4.996434 GGCGATGGAGGGGCGATG 62.996 72.222 0.00 0.00 0.00 3.84
1983 5276 1.164041 ACAAAGTTTGCCCGACTCCG 61.164 55.000 15.59 0.00 0.00 4.63
1984 5277 1.029681 AACAAAGTTTGCCCGACTCC 58.970 50.000 15.59 0.00 0.00 3.85
1985 5278 1.404035 ACAACAAAGTTTGCCCGACTC 59.596 47.619 15.59 0.00 0.00 3.36
1986 5279 1.470051 ACAACAAAGTTTGCCCGACT 58.530 45.000 15.59 0.00 0.00 4.18
1987 5280 2.356695 ACTACAACAAAGTTTGCCCGAC 59.643 45.455 15.59 0.00 0.00 4.79
1988 5281 2.645802 ACTACAACAAAGTTTGCCCGA 58.354 42.857 15.59 0.00 0.00 5.14
1990 5283 4.577283 TGTCTACTACAACAAAGTTTGCCC 59.423 41.667 15.59 0.00 34.29 5.36
1991 5284 5.296035 ACTGTCTACTACAACAAAGTTTGCC 59.704 40.000 15.59 0.00 37.74 4.52
1992 5285 6.359480 ACTGTCTACTACAACAAAGTTTGC 57.641 37.500 15.59 0.00 37.74 3.68
1993 5286 6.292168 CCGACTGTCTACTACAACAAAGTTTG 60.292 42.308 14.13 14.13 37.74 2.93
1994 5287 5.751990 CCGACTGTCTACTACAACAAAGTTT 59.248 40.000 6.21 0.00 37.74 2.66
1996 5289 4.261909 CCCGACTGTCTACTACAACAAAGT 60.262 45.833 6.21 0.00 37.74 2.66
1997 5290 4.022589 TCCCGACTGTCTACTACAACAAAG 60.023 45.833 6.21 0.00 37.74 2.77
1998 5291 3.890756 TCCCGACTGTCTACTACAACAAA 59.109 43.478 6.21 0.00 37.74 2.83
1999 5292 3.489355 TCCCGACTGTCTACTACAACAA 58.511 45.455 6.21 0.00 37.74 2.83
2000 5293 3.144657 TCCCGACTGTCTACTACAACA 57.855 47.619 6.21 0.00 37.74 3.33
2001 5294 3.505293 ACTTCCCGACTGTCTACTACAAC 59.495 47.826 6.21 0.00 37.74 3.32
2003 5296 3.430042 ACTTCCCGACTGTCTACTACA 57.570 47.619 6.21 0.00 36.42 2.74
2005 5298 6.182627 TCATTTACTTCCCGACTGTCTACTA 58.817 40.000 6.21 0.00 0.00 1.82
2007 5300 5.320549 TCATTTACTTCCCGACTGTCTAC 57.679 43.478 6.21 0.00 0.00 2.59
2009 5302 4.884668 TTCATTTACTTCCCGACTGTCT 57.115 40.909 6.21 0.00 0.00 3.41
2010 5303 6.592607 TGTTATTCATTTACTTCCCGACTGTC 59.407 38.462 0.00 0.00 0.00 3.51
2014 5307 7.025365 GGTTTGTTATTCATTTACTTCCCGAC 58.975 38.462 0.00 0.00 0.00 4.79
2015 5308 6.715718 TGGTTTGTTATTCATTTACTTCCCGA 59.284 34.615 0.00 0.00 0.00 5.14
2016 5309 6.915349 TGGTTTGTTATTCATTTACTTCCCG 58.085 36.000 0.00 0.00 0.00 5.14
2017 5310 8.364894 AGTTGGTTTGTTATTCATTTACTTCCC 58.635 33.333 0.00 0.00 0.00 3.97
2018 5311 9.406828 GAGTTGGTTTGTTATTCATTTACTTCC 57.593 33.333 0.00 0.00 0.00 3.46
2019 5312 9.113876 CGAGTTGGTTTGTTATTCATTTACTTC 57.886 33.333 0.00 0.00 0.00 3.01
2041 5556 6.037720 TGTCATGTGTGTAAATTTGTTCGAGT 59.962 34.615 0.00 0.00 0.00 4.18
2061 5576 0.250467 ACTGCTCAGCGGTTTGTCAT 60.250 50.000 4.86 0.00 46.97 3.06
2076 5591 7.603024 GGTAATTCTGGGTATAGATGTTACTGC 59.397 40.741 0.00 0.00 33.38 4.40
2109 5624 6.320672 AGAAAAAGTTGCCAGATCATATGGAG 59.679 38.462 1.21 0.00 40.51 3.86
2110 5625 6.189859 AGAAAAAGTTGCCAGATCATATGGA 58.810 36.000 1.21 0.00 40.51 3.41
2111 5626 6.461110 AGAAAAAGTTGCCAGATCATATGG 57.539 37.500 2.13 0.00 41.04 2.74
2144 5660 8.245701 TGATTAAATAAAATGGCCAACGTTTC 57.754 30.769 10.96 0.00 37.31 2.78
2192 5708 4.394920 TCTCCTTTGTCGCCATGTTTATTC 59.605 41.667 0.00 0.00 0.00 1.75
2195 5711 3.334691 CTCTCCTTTGTCGCCATGTTTA 58.665 45.455 0.00 0.00 0.00 2.01
2201 5717 1.544825 CCTCCTCTCCTTTGTCGCCA 61.545 60.000 0.00 0.00 0.00 5.69
2203 5719 1.448717 GCCTCCTCTCCTTTGTCGC 60.449 63.158 0.00 0.00 0.00 5.19
2204 5720 1.153745 CGCCTCCTCTCCTTTGTCG 60.154 63.158 0.00 0.00 0.00 4.35
2206 5722 0.832135 TGTCGCCTCCTCTCCTTTGT 60.832 55.000 0.00 0.00 0.00 2.83
2207 5723 0.321671 TTGTCGCCTCCTCTCCTTTG 59.678 55.000 0.00 0.00 0.00 2.77
2208 5724 0.321996 GTTGTCGCCTCCTCTCCTTT 59.678 55.000 0.00 0.00 0.00 3.11
2210 5726 0.543174 AAGTTGTCGCCTCCTCTCCT 60.543 55.000 0.00 0.00 0.00 3.69
2212 5728 0.603569 TCAAGTTGTCGCCTCCTCTC 59.396 55.000 2.11 0.00 0.00 3.20
2213 5729 1.048601 TTCAAGTTGTCGCCTCCTCT 58.951 50.000 2.11 0.00 0.00 3.69
2214 5730 2.100605 ATTCAAGTTGTCGCCTCCTC 57.899 50.000 2.11 0.00 0.00 3.71
2217 5733 2.605366 GCTCTATTCAAGTTGTCGCCTC 59.395 50.000 2.11 0.00 0.00 4.70
2219 5735 1.666189 GGCTCTATTCAAGTTGTCGCC 59.334 52.381 2.11 3.87 0.00 5.54
2221 5737 3.369147 CACTGGCTCTATTCAAGTTGTCG 59.631 47.826 2.11 0.00 0.00 4.35
2222 5738 4.319177 ACACTGGCTCTATTCAAGTTGTC 58.681 43.478 2.11 0.00 0.00 3.18
2224 5740 5.295292 CCATACACTGGCTCTATTCAAGTTG 59.705 44.000 0.00 0.00 38.47 3.16
2225 5741 5.189736 TCCATACACTGGCTCTATTCAAGTT 59.810 40.000 0.00 0.00 45.52 2.66
2226 5742 4.716784 TCCATACACTGGCTCTATTCAAGT 59.283 41.667 0.00 0.00 45.52 3.16
2228 5744 4.141711 GGTCCATACACTGGCTCTATTCAA 60.142 45.833 0.00 0.00 45.52 2.69
2229 5745 3.388024 GGTCCATACACTGGCTCTATTCA 59.612 47.826 0.00 0.00 45.52 2.57
2231 5747 3.643792 GAGGTCCATACACTGGCTCTATT 59.356 47.826 0.00 0.00 45.52 1.73
2232 5748 3.235200 GAGGTCCATACACTGGCTCTAT 58.765 50.000 0.00 0.00 45.52 1.98
2233 5749 2.024369 TGAGGTCCATACACTGGCTCTA 60.024 50.000 0.00 0.00 45.52 2.43
2234 5750 1.273267 TGAGGTCCATACACTGGCTCT 60.273 52.381 0.00 0.00 45.52 4.09
2235 5751 1.195115 TGAGGTCCATACACTGGCTC 58.805 55.000 0.00 0.00 45.52 4.70
2239 5755 2.768253 TGCTTGAGGTCCATACACTG 57.232 50.000 0.00 0.00 0.00 3.66
2254 6699 1.194781 TCGCCTCCTCTCCTTTGCTT 61.195 55.000 0.00 0.00 0.00 3.91
2264 6709 0.531974 TGTTGTGTTGTCGCCTCCTC 60.532 55.000 0.00 0.00 0.00 3.71
2272 6717 0.939106 GGGCGCATTGTTGTGTTGTC 60.939 55.000 10.83 0.00 35.72 3.18
2276 6721 0.176680 TTTTGGGCGCATTGTTGTGT 59.823 45.000 10.83 0.00 35.72 3.72
2288 6733 1.066454 GGCACGGTGTATATTTTGGGC 59.934 52.381 10.24 0.00 0.00 5.36
2297 6742 2.012902 GACGCCTAGGCACGGTGTAT 62.013 60.000 32.47 7.46 44.74 2.29
2303 6765 1.269569 TGATTATGACGCCTAGGCACG 60.270 52.381 32.47 19.84 43.31 5.34
2304 6766 2.135933 GTGATTATGACGCCTAGGCAC 58.864 52.381 32.47 24.40 43.31 5.01
2325 6787 3.558321 CCCTATTCTGACGGGTTGAAACA 60.558 47.826 0.00 0.00 33.16 2.83
2335 6797 4.630069 ACGAATGAAAACCCTATTCTGACG 59.370 41.667 0.00 0.00 0.00 4.35
2339 6801 5.817816 CAGCTACGAATGAAAACCCTATTCT 59.182 40.000 0.00 0.00 0.00 2.40
2380 6842 5.652014 TGTTAGTCATTTTCTTAGGCATGGG 59.348 40.000 0.00 0.00 0.00 4.00
2392 6854 5.074804 GGTAGGTGGGTTGTTAGTCATTTT 58.925 41.667 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.