Multiple sequence alignment - TraesCS1A01G312500

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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 TraesCS1A01G312500 chr1A 100.000 3468 0 0 1 3468 504396252 504399719 0.000000e+00 6405.0
1 TraesCS1A01G312500 chr1A 90.461 1279 95 6 1 1255 504412630 504413905 0.000000e+00 1661.0
2 TraesCS1A01G312500 chr1A 93.643 645 32 4 2830 3467 525143437 525142795 0.000000e+00 955.0
3 TraesCS1A01G312500 chr1A 93.730 622 32 3 2851 3467 522974832 522975451 0.000000e+00 926.0
4 TraesCS1A01G312500 chr1A 94.810 578 29 1 2056 2633 525144012 525143436 0.000000e+00 900.0
5 TraesCS1A01G312500 chr1A 95.114 307 15 0 2327 2633 523369591 523369285 5.200000e-133 484.0
6 TraesCS1A01G312500 chr1A 92.419 277 20 1 2056 2332 523378462 523378187 9.020000e-106 394.0
7 TraesCS1A01G312500 chr1A 91.753 97 8 0 1832 1928 381310364 381310268 6.040000e-28 135.0
8 TraesCS1A01G312500 chr1A 81.548 168 13 1 2942 3109 539593416 539593267 4.700000e-24 122.0
9 TraesCS1A01G312500 chr1A 100.000 30 0 0 2830 2859 523369286 523369257 4.840000e-04 56.5
10 TraesCS1A01G312500 chr7A 96.907 1552 37 5 1928 3468 655418535 655416984 0.000000e+00 2590.0
11 TraesCS1A01G312500 chr7A 88.356 146 17 0 2165 2310 41465881 41465736 3.560000e-40 176.0
12 TraesCS1A01G312500 chr7A 88.356 146 17 0 2165 2310 617597403 617597548 3.560000e-40 176.0
13 TraesCS1A01G312500 chr7A 85.714 168 21 2 2942 3109 21874627 21874791 1.280000e-39 174.0
14 TraesCS1A01G312500 chr1B 89.915 1656 146 8 1 1639 549618046 549619697 0.000000e+00 2113.0
15 TraesCS1A01G312500 chr1B 88.855 1624 143 17 1 1603 549675060 549676666 0.000000e+00 1962.0
16 TraesCS1A01G312500 chr1B 89.622 925 94 2 820 1742 549594855 549595779 0.000000e+00 1175.0
17 TraesCS1A01G312500 chr1B 91.016 768 49 5 1 748 549580520 549581287 0.000000e+00 1018.0
18 TraesCS1A01G312500 chr1B 76.953 512 110 8 1243 1751 550288483 550288989 5.670000e-73 285.0
19 TraesCS1A01G312500 chr1B 88.679 53 4 2 1932 1983 456159673 456159622 2.890000e-06 63.9
20 TraesCS1A01G312500 chr5B 89.168 1394 107 19 2080 3467 275021148 275019793 0.000000e+00 1698.0
21 TraesCS1A01G312500 chr5B 91.919 99 8 0 1830 1928 217612607 217612705 4.670000e-29 139.0
22 TraesCS1A01G312500 chr5B 91.919 99 8 0 1830 1928 327082777 327082875 4.670000e-29 139.0
23 TraesCS1A01G312500 chr5B 86.441 59 6 2 1933 1990 660791023 660791080 2.890000e-06 63.9
24 TraesCS1A01G312500 chr4A 98.111 953 17 1 2082 3034 312733045 312732094 0.000000e+00 1659.0
25 TraesCS1A01G312500 chr4A 97.572 453 5 2 3020 3468 312732045 312731595 0.000000e+00 771.0
26 TraesCS1A01G312500 chr4A 92.593 162 10 2 1932 2092 304840009 304839849 7.490000e-57 231.0
27 TraesCS1A01G312500 chr4A 82.143 168 12 5 2942 3109 102386717 102386568 1.010000e-25 128.0
28 TraesCS1A01G312500 chr3D 95.874 1018 32 5 2023 3034 43583841 43582828 0.000000e+00 1639.0
29 TraesCS1A01G312500 chr3D 86.357 667 74 12 2362 3015 381985036 381985698 0.000000e+00 712.0
30 TraesCS1A01G312500 chr3D 95.652 437 15 1 3035 3467 43582760 43582324 0.000000e+00 699.0
31 TraesCS1A01G312500 chr3D 91.139 237 18 2 3141 3377 422642934 422642701 5.590000e-83 318.0
32 TraesCS1A01G312500 chr3D 74.573 586 125 20 1244 1816 603089691 603090265 5.790000e-58 235.0
33 TraesCS1A01G312500 chr1D 89.325 1096 98 6 1 1082 408451720 408452810 0.000000e+00 1358.0
34 TraesCS1A01G312500 chr1D 89.912 684 63 5 1149 1827 408453036 408453718 0.000000e+00 876.0
35 TraesCS1A01G312500 chr1D 75.116 430 86 18 1373 1792 121307893 121307475 7.650000e-42 182.0
36 TraesCS1A01G312500 chr1D 90.984 122 11 0 2165 2286 62893259 62893380 7.700000e-37 165.0
37 TraesCS1A01G312500 chr1D 90.909 99 9 0 1830 1928 321675164 321675066 2.170000e-27 134.0
38 TraesCS1A01G312500 chr3A 83.058 667 83 17 2362 3015 505216112 505216761 2.320000e-161 579.0
39 TraesCS1A01G312500 chr3B 82.759 667 76 21 2362 3015 497704523 497705163 3.020000e-155 558.0
40 TraesCS1A01G312500 chr3B 81.548 168 11 3 2942 3109 104696115 104695968 1.690000e-23 121.0
41 TraesCS1A01G312500 chr3B 100.000 34 0 0 1932 1965 740854958 740854991 2.890000e-06 63.9
42 TraesCS1A01G312500 chr6D 79.606 559 105 7 1270 1821 472276180 472275624 3.240000e-105 392.0
43 TraesCS1A01G312500 chr4B 79.592 539 100 9 1159 1690 10383727 10384262 9.090000e-101 377.0
44 TraesCS1A01G312500 chr4D 76.616 526 115 8 1241 1764 400168186 400168705 2.040000e-72 283.0
45 TraesCS1A01G312500 chr4D 90.909 99 9 0 1830 1928 505534505 505534407 2.170000e-27 134.0
46 TraesCS1A01G312500 chr4D 88.889 81 5 4 1929 2006 313880042 313879963 2.850000e-16 97.1
47 TraesCS1A01G312500 chr2D 76.445 467 98 11 1242 1703 70019449 70019908 3.460000e-60 243.0
48 TraesCS1A01G312500 chr2D 91.919 99 8 0 1830 1928 136979428 136979526 4.670000e-29 139.0
49 TraesCS1A01G312500 chr7D 78.316 392 69 11 1432 1820 29257727 29257349 4.470000e-59 239.0
50 TraesCS1A01G312500 chr6A 74.199 593 128 20 1242 1817 94188755 94189339 1.250000e-54 224.0
51 TraesCS1A01G312500 chr2A 88.356 146 17 0 2165 2310 756523370 756523515 3.560000e-40 176.0
52 TraesCS1A01G312500 chr2A 91.919 99 8 0 1830 1928 214289200 214289298 4.670000e-29 139.0
53 TraesCS1A01G312500 chr2A 88.235 51 4 2 1931 1980 197554133 197554182 3.740000e-05 60.2
54 TraesCS1A01G312500 chr5A 91.919 99 8 0 1830 1928 12412832 12412734 4.670000e-29 139.0
55 TraesCS1A01G312500 chr2B 91.837 98 8 0 1830 1927 481879415 481879512 1.680000e-28 137.0
56 TraesCS1A01G312500 chr2B 90.323 62 5 1 3048 3109 144064158 144064098 2.870000e-11 80.5
57 TraesCS1A01G312500 chr2B 92.308 52 4 0 1932 1983 706847714 706847663 1.330000e-09 75.0
58 TraesCS1A01G312500 chr7B 94.915 59 3 0 1932 1990 113915431 113915489 3.690000e-15 93.5


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 TraesCS1A01G312500 chr1A 504396252 504399719 3467 False 6405.0 6405 100.0000 1 3468 1 chr1A.!!$F1 3467
1 TraesCS1A01G312500 chr1A 504412630 504413905 1275 False 1661.0 1661 90.4610 1 1255 1 chr1A.!!$F2 1254
2 TraesCS1A01G312500 chr1A 525142795 525144012 1217 True 927.5 955 94.2265 2056 3467 2 chr1A.!!$R5 1411
3 TraesCS1A01G312500 chr1A 522974832 522975451 619 False 926.0 926 93.7300 2851 3467 1 chr1A.!!$F3 616
4 TraesCS1A01G312500 chr7A 655416984 655418535 1551 True 2590.0 2590 96.9070 1928 3468 1 chr7A.!!$R2 1540
5 TraesCS1A01G312500 chr1B 549618046 549619697 1651 False 2113.0 2113 89.9150 1 1639 1 chr1B.!!$F3 1638
6 TraesCS1A01G312500 chr1B 549675060 549676666 1606 False 1962.0 1962 88.8550 1 1603 1 chr1B.!!$F4 1602
7 TraesCS1A01G312500 chr1B 549594855 549595779 924 False 1175.0 1175 89.6220 820 1742 1 chr1B.!!$F2 922
8 TraesCS1A01G312500 chr1B 549580520 549581287 767 False 1018.0 1018 91.0160 1 748 1 chr1B.!!$F1 747
9 TraesCS1A01G312500 chr1B 550288483 550288989 506 False 285.0 285 76.9530 1243 1751 1 chr1B.!!$F5 508
10 TraesCS1A01G312500 chr5B 275019793 275021148 1355 True 1698.0 1698 89.1680 2080 3467 1 chr5B.!!$R1 1387
11 TraesCS1A01G312500 chr4A 312731595 312733045 1450 True 1215.0 1659 97.8415 2082 3468 2 chr4A.!!$R3 1386
12 TraesCS1A01G312500 chr3D 43582324 43583841 1517 True 1169.0 1639 95.7630 2023 3467 2 chr3D.!!$R2 1444
13 TraesCS1A01G312500 chr3D 381985036 381985698 662 False 712.0 712 86.3570 2362 3015 1 chr3D.!!$F1 653
14 TraesCS1A01G312500 chr3D 603089691 603090265 574 False 235.0 235 74.5730 1244 1816 1 chr3D.!!$F2 572
15 TraesCS1A01G312500 chr1D 408451720 408453718 1998 False 1117.0 1358 89.6185 1 1827 2 chr1D.!!$F2 1826
16 TraesCS1A01G312500 chr3A 505216112 505216761 649 False 579.0 579 83.0580 2362 3015 1 chr3A.!!$F1 653
17 TraesCS1A01G312500 chr3B 497704523 497705163 640 False 558.0 558 82.7590 2362 3015 1 chr3B.!!$F1 653
18 TraesCS1A01G312500 chr6D 472275624 472276180 556 True 392.0 392 79.6060 1270 1821 1 chr6D.!!$R1 551
19 TraesCS1A01G312500 chr4B 10383727 10384262 535 False 377.0 377 79.5920 1159 1690 1 chr4B.!!$F1 531
20 TraesCS1A01G312500 chr4D 400168186 400168705 519 False 283.0 283 76.6160 1241 1764 1 chr4D.!!$F1 523
21 TraesCS1A01G312500 chr6A 94188755 94189339 584 False 224.0 224 74.1990 1242 1817 1 chr6A.!!$F1 575

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
773 797 0.757188 CCATAGTCCGCCACTCCTCT 60.757 60.0 0.00 0.00 36.43 3.69 F
1007 1039 0.251922 AGTCTTGTTGCCATGGCCAT 60.252 50.0 33.44 14.09 41.09 4.40 F
1645 1862 0.320771 TTGAGCGCCACTCTCTTTCC 60.321 55.0 2.29 0.00 46.41 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2075 0.026803 CATTCTCCGCACGCTTTAGC 59.973 55.0 0.0 0.0 37.78 3.09 R
1858 2081 0.237235 TTTTGACATTCTCCGCACGC 59.763 50.0 0.0 0.0 0.00 5.34 R
2545 2779 0.624500 AGGCACACCCTATGGATGGT 60.625 55.0 0.0 0.0 44.08 3.55 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
214 230 6.819397 AGTGTGGTCTAAAATAAAAGGAGC 57.181 37.500 0.00 0.00 0.00 4.70
233 249 2.088423 GCGTCCACCAATTATTGTCCA 58.912 47.619 4.15 0.00 0.00 4.02
258 278 9.887629 CAGATGCTATAATCCTATCATGAACTT 57.112 33.333 0.00 0.00 0.00 2.66
342 362 8.915871 AATTTGCATCATTACACATACTTGTC 57.084 30.769 0.00 0.00 32.34 3.18
365 385 7.613022 TGTCAAGCTCCAATCAAATAAGAAGAT 59.387 33.333 0.00 0.00 0.00 2.40
427 449 5.751243 AGTGTAGTGTGGTGTTTTTGATC 57.249 39.130 0.00 0.00 0.00 2.92
743 767 3.766691 GGCGTCCCAAGGCGTAGA 61.767 66.667 0.00 0.00 37.15 2.59
773 797 0.757188 CCATAGTCCGCCACTCCTCT 60.757 60.000 0.00 0.00 36.43 3.69
775 799 1.115467 ATAGTCCGCCACTCCTCTTG 58.885 55.000 0.00 0.00 36.43 3.02
776 800 1.605058 TAGTCCGCCACTCCTCTTGC 61.605 60.000 0.00 0.00 36.43 4.01
844 868 7.548427 CCTAGATCATATAGAAACACATGCCAG 59.452 40.741 0.00 0.00 0.00 4.85
951 983 2.280797 GGTTGTCTGCGGCAGTCA 60.281 61.111 27.63 25.10 32.61 3.41
982 1014 2.501723 GGACTAGTGATTCCTTGCCTCA 59.498 50.000 0.00 0.00 0.00 3.86
986 1018 3.278668 AGTGATTCCTTGCCTCATCTG 57.721 47.619 0.00 0.00 0.00 2.90
995 1027 1.649321 TGCCTCATCTGGAGTCTTGT 58.351 50.000 0.00 0.00 42.40 3.16
1007 1039 0.251922 AGTCTTGTTGCCATGGCCAT 60.252 50.000 33.44 14.09 41.09 4.40
1032 1064 2.616376 CGATCTGGAGTCTTCGATCTGT 59.384 50.000 9.73 0.00 33.59 3.41
1039 1071 0.532573 GTCTTCGATCTGTCCTGGCA 59.467 55.000 0.00 0.00 0.00 4.92
1062 1094 1.668294 CACCTCGTGCTTCCTCACT 59.332 57.895 0.00 0.00 34.92 3.41
1106 1138 0.991920 CCTAATGGTGGTGTGGAGGT 59.008 55.000 0.00 0.00 0.00 3.85
1281 1473 2.986019 TCATGAGGGTTTCTCCTTCCAA 59.014 45.455 0.00 0.00 41.01 3.53
1322 1515 3.181458 GCGGGGAGATACAAACTATGGAA 60.181 47.826 0.00 0.00 0.00 3.53
1409 1619 1.890174 CGGAAAATTGGTGGAGGCC 59.110 57.895 0.00 0.00 0.00 5.19
1420 1632 2.158385 TGGTGGAGGCCAAACATAAGTT 60.158 45.455 5.01 0.00 40.40 2.66
1461 1677 1.072965 CAAGGACCCAGTCTCAAGCTT 59.927 52.381 0.00 0.00 32.47 3.74
1509 1725 7.260603 ACTACGTTGGTTATACCTGACAATAC 58.739 38.462 0.00 0.00 39.58 1.89
1556 1773 5.951148 TGTTGAAGGCATTTCTTGGATATGA 59.049 36.000 0.00 0.00 36.71 2.15
1645 1862 0.320771 TTGAGCGCCACTCTCTTTCC 60.321 55.000 2.29 0.00 46.41 3.13
1703 1923 5.068855 TGTGTTGTCATCAAATGATTGGTGT 59.931 36.000 2.13 0.00 45.91 4.16
1793 2016 2.864343 CACCTACGCATAGCTTTGGTAC 59.136 50.000 6.29 0.00 34.35 3.34
1799 2022 4.369182 ACGCATAGCTTTGGTACTACATC 58.631 43.478 6.29 0.00 0.00 3.06
1827 2050 4.124238 GCTATTTGCCGGTGTACTCATTA 58.876 43.478 1.90 0.00 35.15 1.90
1828 2051 4.755123 GCTATTTGCCGGTGTACTCATTAT 59.245 41.667 1.90 0.00 35.15 1.28
1829 2052 5.334105 GCTATTTGCCGGTGTACTCATTATG 60.334 44.000 1.90 0.00 35.15 1.90
1830 2053 3.897141 TTGCCGGTGTACTCATTATGA 57.103 42.857 1.90 0.00 0.00 2.15
1831 2054 3.897141 TGCCGGTGTACTCATTATGAA 57.103 42.857 1.90 0.00 0.00 2.57
1832 2055 3.792401 TGCCGGTGTACTCATTATGAAG 58.208 45.455 1.90 0.00 0.00 3.02
1833 2056 2.544267 GCCGGTGTACTCATTATGAAGC 59.456 50.000 1.90 0.00 0.00 3.86
1834 2057 3.741388 GCCGGTGTACTCATTATGAAGCT 60.741 47.826 1.90 0.00 0.00 3.74
1835 2058 4.051922 CCGGTGTACTCATTATGAAGCTC 58.948 47.826 0.00 0.00 0.00 4.09
1836 2059 4.051922 CGGTGTACTCATTATGAAGCTCC 58.948 47.826 0.00 0.06 0.00 4.70
1837 2060 4.381411 GGTGTACTCATTATGAAGCTCCC 58.619 47.826 0.00 0.00 0.00 4.30
1838 2061 4.051922 GTGTACTCATTATGAAGCTCCCG 58.948 47.826 0.00 0.00 0.00 5.14
1839 2062 3.704566 TGTACTCATTATGAAGCTCCCGT 59.295 43.478 0.00 0.00 0.00 5.28
1840 2063 3.185246 ACTCATTATGAAGCTCCCGTG 57.815 47.619 0.00 0.00 0.00 4.94
1841 2064 1.869767 CTCATTATGAAGCTCCCGTGC 59.130 52.381 0.00 0.00 0.00 5.34
1842 2065 1.209261 TCATTATGAAGCTCCCGTGCA 59.791 47.619 0.00 0.00 34.99 4.57
1843 2066 2.158769 TCATTATGAAGCTCCCGTGCAT 60.159 45.455 0.00 0.00 34.99 3.96
1844 2067 3.070878 TCATTATGAAGCTCCCGTGCATA 59.929 43.478 0.00 0.00 34.99 3.14
1845 2068 2.820059 TATGAAGCTCCCGTGCATAG 57.180 50.000 0.00 0.00 34.99 2.23
1846 2069 0.533755 ATGAAGCTCCCGTGCATAGC 60.534 55.000 0.00 0.00 36.48 2.97
1847 2070 1.153369 GAAGCTCCCGTGCATAGCA 60.153 57.895 13.50 0.00 38.75 3.49
1848 2071 1.153289 AAGCTCCCGTGCATAGCAG 60.153 57.895 13.50 0.00 40.08 4.24
1849 2072 1.617018 AAGCTCCCGTGCATAGCAGA 61.617 55.000 13.50 1.26 40.08 4.26
1850 2073 1.884926 GCTCCCGTGCATAGCAGAC 60.885 63.158 8.03 0.00 40.08 3.51
1851 2074 1.589993 CTCCCGTGCATAGCAGACG 60.590 63.158 0.00 0.00 40.08 4.18
1852 2075 2.586079 CCCGTGCATAGCAGACGG 60.586 66.667 12.41 12.41 44.24 4.79
1853 2076 3.264897 CCGTGCATAGCAGACGGC 61.265 66.667 7.88 0.00 40.25 5.68
1862 2085 2.778679 GCAGACGGCTAAAGCGTG 59.221 61.111 0.00 0.00 43.26 5.34
1863 2086 2.778679 CAGACGGCTAAAGCGTGC 59.221 61.111 0.00 0.00 43.26 5.34
1864 2087 2.809601 AGACGGCTAAAGCGTGCG 60.810 61.111 0.00 1.74 43.26 5.34
1865 2088 3.849953 GACGGCTAAAGCGTGCGG 61.850 66.667 0.00 0.00 43.26 5.69
1866 2089 4.367023 ACGGCTAAAGCGTGCGGA 62.367 61.111 0.00 0.00 43.26 5.54
1867 2090 3.554692 CGGCTAAAGCGTGCGGAG 61.555 66.667 0.00 0.00 43.26 4.63
1868 2091 2.125673 GGCTAAAGCGTGCGGAGA 60.126 61.111 0.00 0.00 43.26 3.71
1869 2092 1.740296 GGCTAAAGCGTGCGGAGAA 60.740 57.895 0.00 0.00 43.26 2.87
1870 2093 1.090052 GGCTAAAGCGTGCGGAGAAT 61.090 55.000 0.00 0.00 43.26 2.40
1871 2094 0.026803 GCTAAAGCGTGCGGAGAATG 59.973 55.000 0.00 0.00 0.00 2.67
1872 2095 1.359848 CTAAAGCGTGCGGAGAATGT 58.640 50.000 0.00 0.00 0.00 2.71
1873 2096 1.324736 CTAAAGCGTGCGGAGAATGTC 59.675 52.381 0.00 0.00 0.00 3.06
1874 2097 0.602638 AAAGCGTGCGGAGAATGTCA 60.603 50.000 0.00 0.00 0.00 3.58
1875 2098 0.602638 AAGCGTGCGGAGAATGTCAA 60.603 50.000 0.00 0.00 0.00 3.18
1876 2099 0.602638 AGCGTGCGGAGAATGTCAAA 60.603 50.000 0.00 0.00 0.00 2.69
1877 2100 0.237235 GCGTGCGGAGAATGTCAAAA 59.763 50.000 0.00 0.00 0.00 2.44
1878 2101 1.725931 GCGTGCGGAGAATGTCAAAAG 60.726 52.381 0.00 0.00 0.00 2.27
1879 2102 1.798223 CGTGCGGAGAATGTCAAAAGA 59.202 47.619 0.00 0.00 0.00 2.52
1880 2103 2.159787 CGTGCGGAGAATGTCAAAAGAG 60.160 50.000 0.00 0.00 0.00 2.85
1881 2104 2.160417 GTGCGGAGAATGTCAAAAGAGG 59.840 50.000 0.00 0.00 0.00 3.69
1882 2105 2.224523 TGCGGAGAATGTCAAAAGAGGT 60.225 45.455 0.00 0.00 0.00 3.85
1883 2106 2.416893 GCGGAGAATGTCAAAAGAGGTC 59.583 50.000 0.00 0.00 0.00 3.85
1884 2107 3.866449 GCGGAGAATGTCAAAAGAGGTCT 60.866 47.826 0.00 0.00 0.00 3.85
1885 2108 3.681897 CGGAGAATGTCAAAAGAGGTCTG 59.318 47.826 0.00 0.00 0.00 3.51
1886 2109 4.006319 GGAGAATGTCAAAAGAGGTCTGG 58.994 47.826 0.00 0.00 0.00 3.86
1887 2110 4.006319 GAGAATGTCAAAAGAGGTCTGGG 58.994 47.826 0.00 0.00 0.00 4.45
1888 2111 3.395941 AGAATGTCAAAAGAGGTCTGGGT 59.604 43.478 0.00 0.00 0.00 4.51
1889 2112 4.597507 AGAATGTCAAAAGAGGTCTGGGTA 59.402 41.667 0.00 0.00 0.00 3.69
1890 2113 4.559862 ATGTCAAAAGAGGTCTGGGTAG 57.440 45.455 0.00 0.00 0.00 3.18
1891 2114 3.583228 TGTCAAAAGAGGTCTGGGTAGA 58.417 45.455 0.00 0.00 0.00 2.59
1903 2126 4.824289 GTCTGGGTAGACCGAATTTAACA 58.176 43.478 0.00 0.00 46.14 2.41
1904 2127 5.425630 GTCTGGGTAGACCGAATTTAACAT 58.574 41.667 0.00 0.00 46.14 2.71
1905 2128 5.293569 GTCTGGGTAGACCGAATTTAACATG 59.706 44.000 0.00 0.00 46.14 3.21
1906 2129 4.519213 TGGGTAGACCGAATTTAACATGG 58.481 43.478 0.00 0.00 44.64 3.66
1907 2130 3.881089 GGGTAGACCGAATTTAACATGGG 59.119 47.826 0.00 0.00 36.71 4.00
1908 2131 4.384427 GGGTAGACCGAATTTAACATGGGA 60.384 45.833 0.00 0.00 36.71 4.37
1909 2132 4.814771 GGTAGACCGAATTTAACATGGGAG 59.185 45.833 0.00 0.00 0.00 4.30
1910 2133 4.837093 AGACCGAATTTAACATGGGAGA 57.163 40.909 0.00 0.00 0.00 3.71
1911 2134 5.174037 AGACCGAATTTAACATGGGAGAA 57.826 39.130 0.00 0.00 0.00 2.87
1912 2135 5.566469 AGACCGAATTTAACATGGGAGAAA 58.434 37.500 0.00 0.00 0.00 2.52
1913 2136 6.187682 AGACCGAATTTAACATGGGAGAAAT 58.812 36.000 0.00 0.00 0.00 2.17
1914 2137 6.318900 AGACCGAATTTAACATGGGAGAAATC 59.681 38.462 0.00 0.00 0.00 2.17
1915 2138 5.359860 ACCGAATTTAACATGGGAGAAATCC 59.640 40.000 0.00 0.00 0.00 3.01
1916 2139 5.505654 CCGAATTTAACATGGGAGAAATCCG 60.506 44.000 0.00 0.00 0.00 4.18
1917 2140 5.065988 CGAATTTAACATGGGAGAAATCCGT 59.934 40.000 0.00 0.00 0.00 4.69
1918 2141 6.259167 CGAATTTAACATGGGAGAAATCCGTA 59.741 38.462 0.00 0.00 0.00 4.02
1919 2142 7.201661 CGAATTTAACATGGGAGAAATCCGTAA 60.202 37.037 0.00 0.00 0.00 3.18
1920 2143 7.948034 ATTTAACATGGGAGAAATCCGTAAA 57.052 32.000 0.00 0.00 0.00 2.01
1921 2144 7.762588 TTTAACATGGGAGAAATCCGTAAAA 57.237 32.000 0.00 0.00 0.00 1.52
1922 2145 7.762588 TTAACATGGGAGAAATCCGTAAAAA 57.237 32.000 0.00 0.00 0.00 1.94
1923 2146 5.897377 ACATGGGAGAAATCCGTAAAAAG 57.103 39.130 0.00 0.00 0.00 2.27
1924 2147 5.566469 ACATGGGAGAAATCCGTAAAAAGA 58.434 37.500 0.00 0.00 0.00 2.52
1925 2148 5.648092 ACATGGGAGAAATCCGTAAAAAGAG 59.352 40.000 0.00 0.00 0.00 2.85
1926 2149 5.492855 TGGGAGAAATCCGTAAAAAGAGA 57.507 39.130 0.00 0.00 0.00 3.10
1930 2153 6.374613 GGGAGAAATCCGTAAAAAGAGACATT 59.625 38.462 0.00 0.00 0.00 2.71
1949 2172 7.260603 AGACATTATTAAAACCATTCAGCTGC 58.739 34.615 9.47 0.00 0.00 5.25
1957 2180 0.248498 CCATTCAGCTGCGCATCAAG 60.248 55.000 12.24 3.66 0.00 3.02
1990 2213 2.547211 GTGATAGCCACATCATCACAGC 59.453 50.000 8.63 0.00 45.09 4.40
1997 2220 1.805943 CACATCATCACAGCGTGGAAA 59.194 47.619 8.46 0.00 33.87 3.13
2010 2233 3.380004 AGCGTGGAAAACAAAACAGATCA 59.620 39.130 0.00 0.00 0.00 2.92
2332 2556 2.966732 TTCGGGCGCCATCTCCTTT 61.967 57.895 30.85 0.00 0.00 3.11
2545 2779 1.134936 CGTCGTGATTACCATCCCACA 60.135 52.381 0.00 0.00 0.00 4.17
2705 2945 1.827344 CAGTGGCACTCATAGGTCTCA 59.173 52.381 19.13 0.00 0.00 3.27
2937 3184 6.395629 CCTTCTCTCCTTCGTACATTGTTTA 58.604 40.000 0.00 0.00 0.00 2.01
3034 3342 3.303329 GCATCTAACACACACACACACAG 60.303 47.826 0.00 0.00 0.00 3.66
3037 3345 1.737838 AACACACACACACACAGAGG 58.262 50.000 0.00 0.00 0.00 3.69
3193 3552 7.982919 TGCGCTACTGAATTAAAATTCTACCTA 59.017 33.333 9.73 0.00 43.97 3.08
3359 3718 5.914085 ACGTAGCTAATCATTGATCTTGC 57.086 39.130 0.00 5.21 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 230 3.605634 TCTGGACAATAATTGGTGGACG 58.394 45.455 0.00 0.00 34.12 4.79
233 249 9.887629 CAAGTTCATGATAGGATTATAGCATCT 57.112 33.333 0.00 0.00 29.56 2.90
342 362 9.084164 CAAATCTTCTTATTTGATTGGAGCTTG 57.916 33.333 3.76 0.00 45.61 4.01
365 385 3.565482 GTGCCAGAGTTGTTCTCATCAAA 59.435 43.478 0.00 0.00 44.98 2.69
372 392 3.498774 ATCAAGTGCCAGAGTTGTTCT 57.501 42.857 0.00 0.00 36.50 3.01
381 401 6.932356 ATACACAATAGAATCAAGTGCCAG 57.068 37.500 0.00 0.00 33.69 4.85
427 449 3.064820 GCGGTTGTTGAGGTGGTAATATG 59.935 47.826 0.00 0.00 0.00 1.78
536 559 5.762045 ACAGTCAAACATCTTGTACATTGC 58.238 37.500 0.00 0.00 0.00 3.56
743 767 2.682494 ACTATGGGTGACGGGCGT 60.682 61.111 0.00 0.00 0.00 5.68
748 772 2.106332 GGCGGACTATGGGTGACG 59.894 66.667 0.00 0.00 0.00 4.35
804 828 3.012502 TGATCTAGGGGAGTAGGTGTTGT 59.987 47.826 0.00 0.00 0.00 3.32
807 831 5.887480 ATATGATCTAGGGGAGTAGGTGT 57.113 43.478 0.00 0.00 0.00 4.16
809 833 7.848821 TTCTATATGATCTAGGGGAGTAGGT 57.151 40.000 0.00 0.00 0.00 3.08
844 868 0.447801 GATGTCAATGTGCACCCGAC 59.552 55.000 15.69 17.40 0.00 4.79
921 945 1.834263 AGACAACCCTCACTCCTATGC 59.166 52.381 0.00 0.00 0.00 3.14
951 983 2.122056 ACTAGTCCAACCCGGCCT 59.878 61.111 0.00 0.00 33.14 5.19
995 1027 2.570774 ATCGGTGATGGCCATGGCAA 62.571 55.000 36.56 28.74 42.43 4.52
1007 1039 1.095600 CGAAGACTCCAGATCGGTGA 58.904 55.000 11.03 0.00 35.57 4.02
1032 1064 4.025858 GAGGTGCTGCTGCCAGGA 62.026 66.667 13.47 0.00 39.54 3.86
1106 1138 3.003173 CCCCTCCGAGAAGGTGCA 61.003 66.667 0.00 0.00 41.99 4.57
1281 1473 1.818674 GCCGAAATCAACCACCAGATT 59.181 47.619 0.00 0.00 36.09 2.40
1322 1515 1.550327 TCCTCTGCGTCAAGTCATCT 58.450 50.000 0.00 0.00 0.00 2.90
1420 1632 3.071747 TGAGTAGCACCACCAACAACATA 59.928 43.478 0.00 0.00 0.00 2.29
1461 1677 3.544698 AGACCTAGACTTTCACCCTGA 57.455 47.619 0.00 0.00 0.00 3.86
1509 1725 2.227556 GTAACGACGCAAAAACATCGG 58.772 47.619 0.00 0.00 38.88 4.18
1545 1762 5.429762 AGAACCAGTCCAATCATATCCAAGA 59.570 40.000 0.00 0.00 0.00 3.02
1548 1765 5.191522 TGAAGAACCAGTCCAATCATATCCA 59.808 40.000 0.00 0.00 0.00 3.41
1556 1773 3.588842 TCATCCTGAAGAACCAGTCCAAT 59.411 43.478 0.00 0.00 32.43 3.16
1583 1800 2.309755 ACCATCCAAGGCAAGAATCTCA 59.690 45.455 0.00 0.00 0.00 3.27
1584 1801 3.010200 ACCATCCAAGGCAAGAATCTC 57.990 47.619 0.00 0.00 0.00 2.75
1592 1809 0.033208 GGATCCAACCATCCAAGGCA 60.033 55.000 6.95 0.00 42.02 4.75
1645 1862 2.842208 TTTCAACAGCAACACCTTCG 57.158 45.000 0.00 0.00 0.00 3.79
1732 1953 6.679327 AAACTAAAAGTGATTAGATCCGCC 57.321 37.500 1.38 0.00 36.57 6.13
1761 1982 2.247311 GCGTAGGTGATGCAACAAAG 57.753 50.000 0.00 0.00 40.11 2.77
1768 1989 1.871080 AAGCTATGCGTAGGTGATGC 58.129 50.000 17.98 1.52 38.59 3.91
1769 1990 2.545526 CCAAAGCTATGCGTAGGTGATG 59.454 50.000 17.98 17.89 38.59 3.07
1827 2050 0.533755 GCTATGCACGGGAGCTTCAT 60.534 55.000 0.00 0.00 33.28 2.57
1828 2051 1.153369 GCTATGCACGGGAGCTTCA 60.153 57.895 0.00 0.00 33.28 3.02
1829 2052 1.153369 TGCTATGCACGGGAGCTTC 60.153 57.895 11.62 0.00 37.12 3.86
1830 2053 1.153289 CTGCTATGCACGGGAGCTT 60.153 57.895 11.62 0.00 37.12 3.74
1831 2054 2.060383 TCTGCTATGCACGGGAGCT 61.060 57.895 11.62 0.00 37.12 4.09
1832 2055 1.884926 GTCTGCTATGCACGGGAGC 60.885 63.158 0.00 0.00 33.79 4.70
1833 2056 1.589993 CGTCTGCTATGCACGGGAG 60.590 63.158 0.00 0.00 33.79 4.30
1834 2057 2.494445 CGTCTGCTATGCACGGGA 59.506 61.111 0.00 0.00 33.79 5.14
1835 2058 2.586079 CCGTCTGCTATGCACGGG 60.586 66.667 11.96 0.00 42.06 5.28
1836 2059 3.264897 GCCGTCTGCTATGCACGG 61.265 66.667 14.48 14.48 46.29 4.94
1845 2068 2.778679 CACGCTTTAGCCGTCTGC 59.221 61.111 0.00 0.00 41.71 4.26
1846 2069 2.778679 GCACGCTTTAGCCGTCTG 59.221 61.111 0.00 0.00 37.91 3.51
1847 2070 2.809601 CGCACGCTTTAGCCGTCT 60.810 61.111 0.00 0.00 37.91 4.18
1848 2071 3.849953 CCGCACGCTTTAGCCGTC 61.850 66.667 0.00 0.00 37.91 4.79
1849 2072 4.367023 TCCGCACGCTTTAGCCGT 62.367 61.111 0.00 0.00 37.91 5.68
1850 2073 3.554692 CTCCGCACGCTTTAGCCG 61.555 66.667 0.00 0.00 37.91 5.52
1851 2074 1.090052 ATTCTCCGCACGCTTTAGCC 61.090 55.000 0.00 0.00 37.91 3.93
1852 2075 0.026803 CATTCTCCGCACGCTTTAGC 59.973 55.000 0.00 0.00 37.78 3.09
1853 2076 1.324736 GACATTCTCCGCACGCTTTAG 59.675 52.381 0.00 0.00 0.00 1.85
1854 2077 1.337354 TGACATTCTCCGCACGCTTTA 60.337 47.619 0.00 0.00 0.00 1.85
1855 2078 0.602638 TGACATTCTCCGCACGCTTT 60.603 50.000 0.00 0.00 0.00 3.51
1856 2079 0.602638 TTGACATTCTCCGCACGCTT 60.603 50.000 0.00 0.00 0.00 4.68
1857 2080 0.602638 TTTGACATTCTCCGCACGCT 60.603 50.000 0.00 0.00 0.00 5.07
1858 2081 0.237235 TTTTGACATTCTCCGCACGC 59.763 50.000 0.00 0.00 0.00 5.34
1859 2082 1.798223 TCTTTTGACATTCTCCGCACG 59.202 47.619 0.00 0.00 0.00 5.34
1860 2083 2.160417 CCTCTTTTGACATTCTCCGCAC 59.840 50.000 0.00 0.00 0.00 5.34
1861 2084 2.224523 ACCTCTTTTGACATTCTCCGCA 60.225 45.455 0.00 0.00 0.00 5.69
1862 2085 2.416893 GACCTCTTTTGACATTCTCCGC 59.583 50.000 0.00 0.00 0.00 5.54
1863 2086 3.681897 CAGACCTCTTTTGACATTCTCCG 59.318 47.826 0.00 0.00 0.00 4.63
1864 2087 4.006319 CCAGACCTCTTTTGACATTCTCC 58.994 47.826 0.00 0.00 0.00 3.71
1865 2088 4.006319 CCCAGACCTCTTTTGACATTCTC 58.994 47.826 0.00 0.00 0.00 2.87
1866 2089 3.395941 ACCCAGACCTCTTTTGACATTCT 59.604 43.478 0.00 0.00 0.00 2.40
1867 2090 3.756117 ACCCAGACCTCTTTTGACATTC 58.244 45.455 0.00 0.00 0.00 2.67
1868 2091 3.884037 ACCCAGACCTCTTTTGACATT 57.116 42.857 0.00 0.00 0.00 2.71
1869 2092 4.020128 GTCTACCCAGACCTCTTTTGACAT 60.020 45.833 0.00 0.00 44.72 3.06
1870 2093 3.323979 GTCTACCCAGACCTCTTTTGACA 59.676 47.826 0.00 0.00 44.72 3.58
1871 2094 3.927854 GTCTACCCAGACCTCTTTTGAC 58.072 50.000 0.00 0.00 44.72 3.18
1882 2105 5.424757 CATGTTAAATTCGGTCTACCCAGA 58.575 41.667 0.00 0.00 0.00 3.86
1883 2106 4.574828 CCATGTTAAATTCGGTCTACCCAG 59.425 45.833 0.00 0.00 0.00 4.45
1884 2107 4.519213 CCATGTTAAATTCGGTCTACCCA 58.481 43.478 0.00 0.00 0.00 4.51
1885 2108 3.881089 CCCATGTTAAATTCGGTCTACCC 59.119 47.826 0.00 0.00 0.00 3.69
1886 2109 4.773013 TCCCATGTTAAATTCGGTCTACC 58.227 43.478 0.00 0.00 0.00 3.18
1887 2110 5.667466 TCTCCCATGTTAAATTCGGTCTAC 58.333 41.667 0.00 0.00 0.00 2.59
1888 2111 5.943349 TCTCCCATGTTAAATTCGGTCTA 57.057 39.130 0.00 0.00 0.00 2.59
1889 2112 4.837093 TCTCCCATGTTAAATTCGGTCT 57.163 40.909 0.00 0.00 0.00 3.85
1890 2113 5.890424 TTTCTCCCATGTTAAATTCGGTC 57.110 39.130 0.00 0.00 0.00 4.79
1891 2114 5.359860 GGATTTCTCCCATGTTAAATTCGGT 59.640 40.000 0.00 0.00 35.28 4.69
1892 2115 5.505654 CGGATTTCTCCCATGTTAAATTCGG 60.506 44.000 10.06 0.00 36.91 4.30
1893 2116 5.065988 ACGGATTTCTCCCATGTTAAATTCG 59.934 40.000 13.84 13.84 42.99 3.34
1894 2117 6.451064 ACGGATTTCTCCCATGTTAAATTC 57.549 37.500 0.00 0.00 38.45 2.17
1895 2118 7.948034 TTACGGATTTCTCCCATGTTAAATT 57.052 32.000 0.00 0.00 38.45 1.82
1896 2119 7.948034 TTTACGGATTTCTCCCATGTTAAAT 57.052 32.000 0.00 0.00 38.45 1.40
1897 2120 7.762588 TTTTACGGATTTCTCCCATGTTAAA 57.237 32.000 0.00 0.00 38.45 1.52
1898 2121 7.666388 TCTTTTTACGGATTTCTCCCATGTTAA 59.334 33.333 0.00 0.00 38.45 2.01
1899 2122 7.169591 TCTTTTTACGGATTTCTCCCATGTTA 58.830 34.615 0.00 0.00 38.45 2.41
1900 2123 6.007703 TCTTTTTACGGATTTCTCCCATGTT 58.992 36.000 0.00 0.00 38.45 2.71
1901 2124 5.566469 TCTTTTTACGGATTTCTCCCATGT 58.434 37.500 0.00 0.00 38.45 3.21
1902 2125 5.880332 TCTCTTTTTACGGATTTCTCCCATG 59.120 40.000 0.00 0.00 38.45 3.66
1903 2126 5.880887 GTCTCTTTTTACGGATTTCTCCCAT 59.119 40.000 0.00 0.00 38.45 4.00
1904 2127 5.221762 TGTCTCTTTTTACGGATTTCTCCCA 60.222 40.000 0.00 0.00 38.45 4.37
1905 2128 5.243207 TGTCTCTTTTTACGGATTTCTCCC 58.757 41.667 0.00 0.00 38.45 4.30
1906 2129 6.986904 ATGTCTCTTTTTACGGATTTCTCC 57.013 37.500 0.00 0.00 38.29 3.71
1920 2143 9.860898 GCTGAATGGTTTTAATAATGTCTCTTT 57.139 29.630 0.00 0.00 0.00 2.52
1921 2144 9.247861 AGCTGAATGGTTTTAATAATGTCTCTT 57.752 29.630 0.00 0.00 0.00 2.85
1922 2145 8.680903 CAGCTGAATGGTTTTAATAATGTCTCT 58.319 33.333 8.42 0.00 0.00 3.10
1923 2146 7.433425 GCAGCTGAATGGTTTTAATAATGTCTC 59.567 37.037 20.43 0.00 0.00 3.36
1924 2147 7.260603 GCAGCTGAATGGTTTTAATAATGTCT 58.739 34.615 20.43 0.00 0.00 3.41
1925 2148 6.197096 CGCAGCTGAATGGTTTTAATAATGTC 59.803 38.462 20.43 0.00 0.00 3.06
1926 2149 6.035843 CGCAGCTGAATGGTTTTAATAATGT 58.964 36.000 20.43 0.00 0.00 2.71
1980 2203 2.503331 TGTTTTCCACGCTGTGATGAT 58.497 42.857 9.75 0.00 35.23 2.45
1990 2213 4.041723 GGTGATCTGTTTTGTTTTCCACG 58.958 43.478 0.00 0.00 0.00 4.94
1997 2220 2.227194 GTCCCGGTGATCTGTTTTGTT 58.773 47.619 0.00 0.00 0.00 2.83
2010 2233 2.826725 TCTGTTTTGTTTTTGTCCCGGT 59.173 40.909 0.00 0.00 0.00 5.28
2291 2515 4.097361 GACCACCCCGAGCTTCCC 62.097 72.222 0.00 0.00 0.00 3.97
2389 2614 0.842635 GGATCTGGTCCATCTGCCTT 59.157 55.000 1.02 0.00 46.96 4.35
2545 2779 0.624500 AGGCACACCCTATGGATGGT 60.625 55.000 0.00 0.00 44.08 3.55
2937 3184 2.666317 CACTTCTCAAACCAAACCCCT 58.334 47.619 0.00 0.00 0.00 4.79
3034 3342 2.408565 TCCTCTCTCTCTCTCTCCCTC 58.591 57.143 0.00 0.00 0.00 4.30
3037 3345 6.656693 CAGAATTATCCTCTCTCTCTCTCTCC 59.343 46.154 0.00 0.00 0.00 3.71
3193 3552 3.706086 GGTAACTGGGCAATGGAATGAAT 59.294 43.478 0.00 0.00 0.00 2.57
3359 3718 2.278330 GCCAGCCTTTCACCCAAGG 61.278 63.158 0.00 0.00 45.70 3.61


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

AutoCloner maintained by Alex Coulton.