Multiple sequence alignment - TraesCS6B01G375800

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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 TraesCS6B01G375800 chr6B 100.000 2451 0 0 1 2451 650658437 650660887 0.000000e+00 4527.0
1 TraesCS6B01G375800 chr6B 95.000 120 6 0 1866 1985 563489230 563489349 3.220000e-44 189.0
2 TraesCS6B01G375800 chr4B 94.046 991 40 7 1 981 546666786 546667767 0.000000e+00 1485.0
3 TraesCS6B01G375800 chr4B 95.069 872 37 2 997 1868 546667757 546668622 0.000000e+00 1367.0
4 TraesCS6B01G375800 chr4B 85.698 874 112 7 996 1865 248909713 248910577 0.000000e+00 909.0
5 TraesCS6B01G375800 chr3B 93.114 1002 48 9 1 990 734586687 734585695 0.000000e+00 1448.0
6 TraesCS6B01G375800 chr3B 94.424 556 31 0 1313 1868 734576821 734576266 0.000000e+00 856.0
7 TraesCS6B01G375800 chr3B 85.989 364 17 13 1981 2322 734576268 734575917 2.320000e-95 359.0
8 TraesCS6B01G375800 chr3B 93.651 126 8 0 1866 1991 725714430 725714305 3.220000e-44 189.0
9 TraesCS6B01G375800 chr3B 92.248 129 9 1 2031 2159 604755281 604755154 5.380000e-42 182.0
10 TraesCS6B01G375800 chr3B 92.126 127 10 0 1860 1986 537036719 537036845 1.940000e-41 180.0
11 TraesCS6B01G375800 chr3B 90.977 133 10 2 1867 1998 692838367 692838236 6.960000e-41 178.0
12 TraesCS6B01G375800 chr7B 93.159 994 45 11 1 981 484921235 484922218 0.000000e+00 1437.0
13 TraesCS6B01G375800 chr7B 93.058 994 46 11 1 981 484915963 484916946 0.000000e+00 1432.0
14 TraesCS6B01G375800 chr7B 95.183 872 42 0 997 1868 484922208 484923079 0.000000e+00 1378.0
15 TraesCS6B01G375800 chr7B 94.839 872 45 0 997 1868 484916936 484917807 0.000000e+00 1362.0
16 TraesCS6B01G375800 chr7B 85.034 882 112 12 996 1868 364046967 364046097 0.000000e+00 880.0
17 TraesCS6B01G375800 chr7B 84.507 355 22 12 1981 2313 484917805 484918148 1.090000e-83 320.0
18 TraesCS6B01G375800 chr7B 84.507 355 22 12 1981 2313 484923077 484923420 1.090000e-83 320.0
19 TraesCS6B01G375800 chr7B 91.729 133 9 2 1867 1998 506726791 506726660 1.500000e-42 183.0
20 TraesCS6B01G375800 chr7B 90.226 133 12 1 2029 2161 640720505 640720374 3.240000e-39 172.0
21 TraesCS6B01G375800 chr2A 93.058 994 46 11 1 981 655658684 655659667 0.000000e+00 1432.0
22 TraesCS6B01G375800 chr2A 94.610 872 47 0 997 1868 655659657 655660528 0.000000e+00 1351.0
23 TraesCS6B01G375800 chr2A 84.789 355 21 12 1981 2313 655660526 655660869 2.350000e-85 326.0
24 TraesCS6B01G375800 chr4A 83.876 1259 155 25 412 1654 225312611 225313837 0.000000e+00 1157.0
25 TraesCS6B01G375800 chr2B 86.070 883 111 6 996 1875 426777609 426778482 0.000000e+00 939.0
26 TraesCS6B01G375800 chr2B 93.548 124 7 1 1867 1989 113275275 113275152 1.500000e-42 183.0
27 TraesCS6B01G375800 chr2B 94.167 120 7 0 1867 1986 680200470 680200589 1.500000e-42 183.0
28 TraesCS6B01G375800 chr2B 92.308 39 1 2 2287 2325 27551924 27551888 1.000000e-03 54.7
29 TraesCS6B01G375800 chr1A 88.353 747 79 7 996 1735 583931615 583930870 0.000000e+00 891.0
30 TraesCS6B01G375800 chr1A 85.811 592 63 11 414 990 583932180 583931595 2.080000e-170 608.0
31 TraesCS6B01G375800 chr1B 93.609 532 33 1 995 1525 286976841 286977372 0.000000e+00 793.0
32 TraesCS6B01G375800 chr1B 90.877 570 34 5 421 981 286976293 286976853 0.000000e+00 749.0
33 TraesCS6B01G375800 chr1B 93.377 151 9 1 2163 2313 287011396 287011545 3.170000e-54 222.0
34 TraesCS6B01G375800 chr1B 90.361 166 12 4 1981 2143 286987798 286987962 5.310000e-52 215.0
35 TraesCS6B01G375800 chr1B 91.603 131 9 2 2031 2161 498976039 498976167 1.940000e-41 180.0
36 TraesCS6B01G375800 chr6D 89.365 583 59 2 1287 1868 395348972 395348392 0.000000e+00 730.0
37 TraesCS6B01G375800 chr6D 89.138 580 59 3 1291 1868 395359406 395358829 0.000000e+00 719.0
38 TraesCS6B01G375800 chr6D 88.870 584 60 4 1287 1868 395336440 395335860 0.000000e+00 713.0
39 TraesCS6B01G375800 chr6D 88.851 583 62 2 1287 1868 395338289 395337709 0.000000e+00 713.0
40 TraesCS6B01G375800 chr6D 89.895 475 31 2 1 459 395366698 395366225 1.620000e-166 595.0
41 TraesCS6B01G375800 chr6D 90.164 305 23 5 487 786 395366123 395365821 8.220000e-105 390.0
42 TraesCS6B01G375800 chr6D 91.176 204 17 1 787 990 395360044 395359842 2.400000e-70 276.0
43 TraesCS6B01G375800 chr1D 93.130 131 8 1 2031 2161 461344733 461344604 8.950000e-45 191.0
44 TraesCS6B01G375800 chr1D 87.500 48 6 0 2180 2227 8608362 8608315 3.400000e-04 56.5
45 TraesCS6B01G375800 chr5B 91.729 133 10 1 2029 2161 588876078 588875947 1.500000e-42 183.0
46 TraesCS6B01G375800 chr5B 80.180 111 19 2 2344 2451 457938003 457938113 2.020000e-11 80.5
47 TraesCS6B01G375800 chr5A 92.248 129 10 0 2031 2159 17727867 17727739 1.500000e-42 183.0
48 TraesCS6B01G375800 chr5A 92.188 128 10 0 1866 1993 684628938 684628811 5.380000e-42 182.0
49 TraesCS6B01G375800 chr5D 90.000 140 12 2 1853 1990 464292735 464292874 1.940000e-41 180.0
50 TraesCS6B01G375800 chr2D 91.603 131 10 1 2031 2161 23303518 23303647 1.940000e-41 180.0
51 TraesCS6B01G375800 chrUn 90.226 133 12 1 2029 2161 358260647 358260778 3.240000e-39 172.0
52 TraesCS6B01G375800 chr3D 90.226 133 12 1 2029 2161 380180044 380179913 3.240000e-39 172.0
53 TraesCS6B01G375800 chr3D 97.059 34 1 0 2281 2314 350134262 350134295 9.470000e-05 58.4
54 TraesCS6B01G375800 chr7D 92.857 42 1 2 2273 2313 543214554 543214594 2.630000e-05 60.2
55 TraesCS6B01G375800 chr7D 90.476 42 1 3 2287 2328 573966120 573966158 4.000000e-03 52.8


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 TraesCS6B01G375800 chr6B 650658437 650660887 2450 False 4527.000000 4527 100.0000 1 2451 1 chr6B.!!$F2 2450
1 TraesCS6B01G375800 chr4B 546666786 546668622 1836 False 1426.000000 1485 94.5575 1 1868 2 chr4B.!!$F2 1867
2 TraesCS6B01G375800 chr4B 248909713 248910577 864 False 909.000000 909 85.6980 996 1865 1 chr4B.!!$F1 869
3 TraesCS6B01G375800 chr3B 734585695 734586687 992 True 1448.000000 1448 93.1140 1 990 1 chr3B.!!$R4 989
4 TraesCS6B01G375800 chr3B 734575917 734576821 904 True 607.500000 856 90.2065 1313 2322 2 chr3B.!!$R5 1009
5 TraesCS6B01G375800 chr7B 484915963 484923420 7457 False 1041.500000 1437 90.8755 1 2313 6 chr7B.!!$F1 2312
6 TraesCS6B01G375800 chr7B 364046097 364046967 870 True 880.000000 880 85.0340 996 1868 1 chr7B.!!$R1 872
7 TraesCS6B01G375800 chr2A 655658684 655660869 2185 False 1036.333333 1432 90.8190 1 2313 3 chr2A.!!$F1 2312
8 TraesCS6B01G375800 chr4A 225312611 225313837 1226 False 1157.000000 1157 83.8760 412 1654 1 chr4A.!!$F1 1242
9 TraesCS6B01G375800 chr2B 426777609 426778482 873 False 939.000000 939 86.0700 996 1875 1 chr2B.!!$F1 879
10 TraesCS6B01G375800 chr1A 583930870 583932180 1310 True 749.500000 891 87.0820 414 1735 2 chr1A.!!$R1 1321
11 TraesCS6B01G375800 chr1B 286976293 286977372 1079 False 771.000000 793 92.2430 421 1525 2 chr1B.!!$F4 1104
12 TraesCS6B01G375800 chr6D 395348392 395348972 580 True 730.000000 730 89.3650 1287 1868 1 chr6D.!!$R1 581
13 TraesCS6B01G375800 chr6D 395335860 395338289 2429 True 713.000000 713 88.8605 1287 1868 2 chr6D.!!$R2 581
14 TraesCS6B01G375800 chr6D 395358829 395360044 1215 True 497.500000 719 90.1570 787 1868 2 chr6D.!!$R3 1081
15 TraesCS6B01G375800 chr6D 395365821 395366698 877 True 492.500000 595 90.0295 1 786 2 chr6D.!!$R4 785

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
981 6366 0.313672 GGCGCCAAAAACATGTCAGA 59.686 50.0 24.8 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 9817 0.036164 ACGCCACTTGTTGCATCCTA 59.964 50.0 0.0 0.0 0.0 2.94 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
25 26 2.649816 AGGCCCCTTCTAATGTTGAAGT 59.350 45.455 0.00 0.00 39.24 3.01
81 82 7.596248 TGCTTCAACATTTATTTCTTCAAGCTC 59.404 33.333 0.00 0.00 34.83 4.09
96 97 3.646162 TCAAGCTCTAACAAGAGTTCCCA 59.354 43.478 4.46 0.00 39.15 4.37
97 98 4.287067 TCAAGCTCTAACAAGAGTTCCCAT 59.713 41.667 4.46 0.00 39.15 4.00
331 348 4.082625 ACATCGCATGCAGAAATCTTCAAA 60.083 37.500 19.57 0.00 0.00 2.69
433 5722 5.182950 TGACAAACGTAGGTCCGATTAAGTA 59.817 40.000 14.66 0.00 33.09 2.24
683 6051 2.295253 ATCTCCGACGACAACCAATC 57.705 50.000 0.00 0.00 0.00 2.67
693 6061 2.031157 CGACAACCAATCCTGTGAAACC 60.031 50.000 0.00 0.00 34.36 3.27
827 6197 4.380550 CCTCGAGCAACAGATGTAGTGTTA 60.381 45.833 6.99 0.00 35.93 2.41
852 6222 4.931601 CAGTCTCTGAAAATGTGAATCCGA 59.068 41.667 0.00 0.00 32.44 4.55
970 6355 4.418401 GCATCAAGCGGCGCCAAA 62.418 61.111 30.40 14.54 0.00 3.28
971 6356 2.257980 CATCAAGCGGCGCCAAAA 59.742 55.556 30.40 12.50 0.00 2.44
972 6357 1.372748 CATCAAGCGGCGCCAAAAA 60.373 52.632 30.40 10.49 0.00 1.94
973 6358 1.372872 ATCAAGCGGCGCCAAAAAC 60.373 52.632 30.40 9.84 0.00 2.43
974 6359 2.081425 ATCAAGCGGCGCCAAAAACA 62.081 50.000 30.40 5.22 0.00 2.83
975 6360 1.664333 CAAGCGGCGCCAAAAACAT 60.664 52.632 30.40 3.74 0.00 2.71
976 6361 1.664333 AAGCGGCGCCAAAAACATG 60.664 52.632 30.40 8.44 0.00 3.21
977 6362 2.355718 GCGGCGCCAAAAACATGT 60.356 55.556 28.98 0.00 0.00 3.21
978 6363 2.371923 GCGGCGCCAAAAACATGTC 61.372 57.895 28.98 0.00 0.00 3.06
979 6364 1.007964 CGGCGCCAAAAACATGTCA 60.008 52.632 28.98 0.00 0.00 3.58
980 6365 1.003262 CGGCGCCAAAAACATGTCAG 61.003 55.000 28.98 0.12 0.00 3.51
981 6366 0.313672 GGCGCCAAAAACATGTCAGA 59.686 50.000 24.80 0.00 0.00 3.27
982 6367 1.067635 GGCGCCAAAAACATGTCAGAT 60.068 47.619 24.80 0.00 0.00 2.90
983 6368 2.610232 GGCGCCAAAAACATGTCAGATT 60.610 45.455 24.80 0.00 0.00 2.40
984 6369 2.663119 GCGCCAAAAACATGTCAGATTC 59.337 45.455 0.00 0.00 0.00 2.52
985 6370 3.612479 GCGCCAAAAACATGTCAGATTCT 60.612 43.478 0.00 0.00 0.00 2.40
986 6371 3.916172 CGCCAAAAACATGTCAGATTCTG 59.084 43.478 7.38 7.38 0.00 3.02
987 6372 4.557296 CGCCAAAAACATGTCAGATTCTGT 60.557 41.667 13.23 0.00 32.61 3.41
988 6373 4.919754 GCCAAAAACATGTCAGATTCTGTC 59.080 41.667 13.23 8.60 32.61 3.51
989 6374 5.507817 GCCAAAAACATGTCAGATTCTGTCA 60.508 40.000 14.50 14.50 34.54 3.58
990 6375 6.506147 CCAAAAACATGTCAGATTCTGTCAA 58.494 36.000 15.79 3.56 33.86 3.18
991 6376 6.979817 CCAAAAACATGTCAGATTCTGTCAAA 59.020 34.615 15.79 1.38 33.86 2.69
992 6377 7.492020 CCAAAAACATGTCAGATTCTGTCAAAA 59.508 33.333 15.79 0.00 33.86 2.44
993 6378 8.871862 CAAAAACATGTCAGATTCTGTCAAAAA 58.128 29.630 15.79 0.00 33.86 1.94
1054 6439 3.262420 CTTATTGGTGGACTTCCTCACG 58.738 50.000 0.00 0.00 36.82 4.35
1178 6564 8.812513 ATCATTTTCTTGTGGATAACAGATCA 57.187 30.769 0.00 0.00 40.74 2.92
1219 6607 3.254060 AGTCATGAACGAGGACAAATCG 58.746 45.455 0.00 0.00 45.54 3.34
1499 7050 2.550830 ACCATCGTTGTGAGCTTCTT 57.449 45.000 0.00 0.00 0.00 2.52
1509 7060 1.066858 GTGAGCTTCTTCGGGATGTCA 60.067 52.381 0.00 0.00 0.00 3.58
1543 7094 4.036971 GTGTACTGATCACGAGGCTTCTAT 59.963 45.833 0.00 0.00 0.00 1.98
1579 8980 0.392998 GATCAAGGTGGTGCATCGGT 60.393 55.000 0.00 0.00 0.00 4.69
1599 9000 0.911045 TCCTCATGCTTCTCCAGGCA 60.911 55.000 0.00 0.00 42.80 4.75
1728 9134 5.469421 AGTTGAAGAGAAAGTGCATGAAGAG 59.531 40.000 0.00 0.00 0.00 2.85
1735 9141 6.154192 AGAGAAAGTGCATGAAGAGACATCTA 59.846 38.462 0.00 0.00 33.45 1.98
1739 9145 9.102757 GAAAGTGCATGAAGAGACATCTAAATA 57.897 33.333 0.00 0.00 33.45 1.40
1752 9158 9.508567 GAGACATCTAAATATTTTTGAGTTGCC 57.491 33.333 5.91 0.00 0.00 4.52
1776 9182 7.378181 CCACCTGCTATTTTGTTGTAATTCTT 58.622 34.615 0.00 0.00 0.00 2.52
1827 9233 3.317711 TGTCAAAATGTGCGATCTTGGTT 59.682 39.130 0.00 0.00 0.00 3.67
1831 9237 5.240623 TCAAAATGTGCGATCTTGGTTACTT 59.759 36.000 0.00 0.00 0.00 2.24
1875 9281 5.728937 TGTTACTATCAGGTACTCCCTCT 57.271 43.478 0.00 0.00 43.86 3.69
1876 9282 5.446860 TGTTACTATCAGGTACTCCCTCTG 58.553 45.833 0.00 0.00 43.86 3.35
1877 9283 5.044328 TGTTACTATCAGGTACTCCCTCTGT 60.044 44.000 0.00 0.00 43.86 3.41
1878 9284 4.173290 ACTATCAGGTACTCCCTCTGTC 57.827 50.000 0.00 0.00 43.86 3.51
1879 9285 3.789274 ACTATCAGGTACTCCCTCTGTCT 59.211 47.826 0.00 0.00 43.86 3.41
1880 9286 4.976442 ACTATCAGGTACTCCCTCTGTCTA 59.024 45.833 0.00 0.00 43.86 2.59
1881 9287 3.935818 TCAGGTACTCCCTCTGTCTAG 57.064 52.381 0.00 0.00 43.86 2.43
1882 9288 3.461824 TCAGGTACTCCCTCTGTCTAGA 58.538 50.000 0.00 0.00 43.86 2.43
1883 9289 3.850774 TCAGGTACTCCCTCTGTCTAGAA 59.149 47.826 0.00 0.00 43.86 2.10
1884 9290 4.291513 TCAGGTACTCCCTCTGTCTAGAAA 59.708 45.833 0.00 0.00 43.86 2.52
1885 9291 5.044030 TCAGGTACTCCCTCTGTCTAGAAAT 60.044 44.000 0.00 0.00 43.86 2.17
1886 9292 6.159928 TCAGGTACTCCCTCTGTCTAGAAATA 59.840 42.308 0.00 0.00 43.86 1.40
1887 9293 6.263617 CAGGTACTCCCTCTGTCTAGAAATAC 59.736 46.154 0.00 0.00 43.86 1.89
1888 9294 6.160814 AGGTACTCCCTCTGTCTAGAAATACT 59.839 42.308 0.00 0.00 40.71 2.12
1889 9295 6.487668 GGTACTCCCTCTGTCTAGAAATACTC 59.512 46.154 0.00 0.00 31.21 2.59
1890 9296 5.127491 ACTCCCTCTGTCTAGAAATACTCG 58.873 45.833 0.00 0.00 31.21 4.18
1891 9297 5.113446 TCCCTCTGTCTAGAAATACTCGT 57.887 43.478 0.00 0.00 31.21 4.18
1892 9298 5.124645 TCCCTCTGTCTAGAAATACTCGTC 58.875 45.833 0.00 0.00 31.21 4.20
1893 9299 4.024725 CCCTCTGTCTAGAAATACTCGTCG 60.025 50.000 0.00 0.00 31.21 5.12
1894 9300 4.809958 CCTCTGTCTAGAAATACTCGTCGA 59.190 45.833 0.00 0.00 31.21 4.20
1895 9301 5.293814 CCTCTGTCTAGAAATACTCGTCGAA 59.706 44.000 0.00 0.00 31.21 3.71
1896 9302 6.347270 TCTGTCTAGAAATACTCGTCGAAG 57.653 41.667 0.00 0.00 0.00 3.79
1897 9303 6.104665 TCTGTCTAGAAATACTCGTCGAAGA 58.895 40.000 0.03 0.03 0.00 2.87
1898 9304 6.592994 TCTGTCTAGAAATACTCGTCGAAGAA 59.407 38.462 1.95 0.00 39.69 2.52
1899 9305 7.118825 TCTGTCTAGAAATACTCGTCGAAGAAA 59.881 37.037 1.95 0.00 39.69 2.52
1900 9306 7.759465 TGTCTAGAAATACTCGTCGAAGAAAT 58.241 34.615 1.95 0.00 39.69 2.17
1901 9307 7.696872 TGTCTAGAAATACTCGTCGAAGAAATG 59.303 37.037 1.95 0.00 39.69 2.32
1902 9308 5.704217 AGAAATACTCGTCGAAGAAATGC 57.296 39.130 1.95 0.00 39.69 3.56
1903 9309 5.168569 AGAAATACTCGTCGAAGAAATGCA 58.831 37.500 1.95 0.00 39.69 3.96
1904 9310 5.812642 AGAAATACTCGTCGAAGAAATGCAT 59.187 36.000 1.95 0.00 39.69 3.96
1905 9311 6.978659 AGAAATACTCGTCGAAGAAATGCATA 59.021 34.615 0.00 0.00 39.69 3.14
1906 9312 7.491372 AGAAATACTCGTCGAAGAAATGCATAA 59.509 33.333 0.00 0.00 39.69 1.90
1907 9313 7.534085 AATACTCGTCGAAGAAATGCATAAA 57.466 32.000 0.00 0.00 39.69 1.40
1908 9314 5.856126 ACTCGTCGAAGAAATGCATAAAA 57.144 34.783 0.00 0.00 39.69 1.52
1909 9315 6.236017 ACTCGTCGAAGAAATGCATAAAAA 57.764 33.333 0.00 0.00 39.69 1.94
1910 9316 6.842163 ACTCGTCGAAGAAATGCATAAAAAT 58.158 32.000 0.00 0.00 39.69 1.82
1911 9317 6.742718 ACTCGTCGAAGAAATGCATAAAAATG 59.257 34.615 0.00 0.00 39.69 2.32
1912 9318 6.836953 TCGTCGAAGAAATGCATAAAAATGA 58.163 32.000 0.00 0.00 39.69 2.57
1913 9319 7.301789 TCGTCGAAGAAATGCATAAAAATGAA 58.698 30.769 0.00 0.00 39.69 2.57
1914 9320 7.967854 TCGTCGAAGAAATGCATAAAAATGAAT 59.032 29.630 0.00 0.00 39.69 2.57
1915 9321 8.046132 CGTCGAAGAAATGCATAAAAATGAATG 58.954 33.333 0.00 0.00 39.69 2.67
1916 9322 8.863049 GTCGAAGAAATGCATAAAAATGAATGT 58.137 29.630 0.00 0.00 39.69 2.71
1953 9359 8.423906 AAATACGTCTAGATACATCCATTCCT 57.576 34.615 0.00 0.00 0.00 3.36
1954 9360 5.968528 ACGTCTAGATACATCCATTCCTC 57.031 43.478 0.00 0.00 0.00 3.71
1955 9361 4.767928 ACGTCTAGATACATCCATTCCTCC 59.232 45.833 0.00 0.00 0.00 4.30
1956 9362 5.013547 CGTCTAGATACATCCATTCCTCCT 58.986 45.833 0.00 0.00 0.00 3.69
1957 9363 6.181190 CGTCTAGATACATCCATTCCTCCTA 58.819 44.000 0.00 0.00 0.00 2.94
1958 9364 6.094325 CGTCTAGATACATCCATTCCTCCTAC 59.906 46.154 0.00 0.00 0.00 3.18
1959 9365 6.948886 GTCTAGATACATCCATTCCTCCTACA 59.051 42.308 0.00 0.00 0.00 2.74
1960 9366 7.451877 GTCTAGATACATCCATTCCTCCTACAA 59.548 40.741 0.00 0.00 0.00 2.41
1961 9367 6.678568 AGATACATCCATTCCTCCTACAAG 57.321 41.667 0.00 0.00 0.00 3.16
1962 9368 6.146760 AGATACATCCATTCCTCCTACAAGT 58.853 40.000 0.00 0.00 0.00 3.16
1963 9369 7.306013 AGATACATCCATTCCTCCTACAAGTA 58.694 38.462 0.00 0.00 0.00 2.24
1964 9370 7.958583 AGATACATCCATTCCTCCTACAAGTAT 59.041 37.037 0.00 0.00 0.00 2.12
1965 9371 6.831664 ACATCCATTCCTCCTACAAGTATT 57.168 37.500 0.00 0.00 0.00 1.89
1966 9372 7.213178 ACATCCATTCCTCCTACAAGTATTT 57.787 36.000 0.00 0.00 0.00 1.40
1967 9373 7.283329 ACATCCATTCCTCCTACAAGTATTTC 58.717 38.462 0.00 0.00 0.00 2.17
1968 9374 6.884472 TCCATTCCTCCTACAAGTATTTCA 57.116 37.500 0.00 0.00 0.00 2.69
1969 9375 6.889198 TCCATTCCTCCTACAAGTATTTCAG 58.111 40.000 0.00 0.00 0.00 3.02
1970 9376 6.058183 CCATTCCTCCTACAAGTATTTCAGG 58.942 44.000 0.00 0.00 0.00 3.86
1971 9377 6.126768 CCATTCCTCCTACAAGTATTTCAGGA 60.127 42.308 0.00 0.00 34.30 3.86
1972 9378 5.934402 TCCTCCTACAAGTATTTCAGGAC 57.066 43.478 0.00 0.00 32.09 3.85
1973 9379 4.401519 TCCTCCTACAAGTATTTCAGGACG 59.598 45.833 0.00 0.00 32.09 4.79
1974 9380 4.441634 CCTCCTACAAGTATTTCAGGACGG 60.442 50.000 0.00 0.00 32.09 4.79
1975 9381 4.346730 TCCTACAAGTATTTCAGGACGGA 58.653 43.478 0.00 0.00 30.43 4.69
1976 9382 4.401519 TCCTACAAGTATTTCAGGACGGAG 59.598 45.833 0.00 0.00 30.43 4.63
1977 9383 3.611766 ACAAGTATTTCAGGACGGAGG 57.388 47.619 0.00 0.00 0.00 4.30
1978 9384 2.236395 ACAAGTATTTCAGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
1979 9385 2.500098 CAAGTATTTCAGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
1980 9386 2.389715 AGTATTTCAGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
1981 9387 2.108970 GTATTTCAGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
1982 9388 2.544844 ATTTCAGGACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
1990 9396 5.427481 TCAGGACGGAGGGAGTATTTTATTT 59.573 40.000 0.00 0.00 0.00 1.40
2016 9423 5.591877 AGCAGAAAAACAACAAGATCAGTCT 59.408 36.000 0.00 0.00 35.82 3.24
2017 9424 6.096001 AGCAGAAAAACAACAAGATCAGTCTT 59.904 34.615 0.00 0.00 45.46 3.01
2018 9425 6.753744 GCAGAAAAACAACAAGATCAGTCTTT 59.246 34.615 0.00 0.00 41.92 2.52
2019 9426 7.043788 GCAGAAAAACAACAAGATCAGTCTTTC 60.044 37.037 0.00 2.37 41.92 2.62
2024 9431 5.684704 ACAACAAGATCAGTCTTTCCTTCA 58.315 37.500 0.00 0.00 41.92 3.02
2042 9449 5.470098 TCCTTCATTTTCTGTCTCCTTTTCG 59.530 40.000 0.00 0.00 0.00 3.46
2046 9453 4.893424 TTTTCTGTCTCCTTTTCGTTGG 57.107 40.909 0.00 0.00 0.00 3.77
2058 9465 0.761323 TTCGTTGGTGGAGAGGGACA 60.761 55.000 0.00 0.00 0.00 4.02
2059 9466 0.544357 TCGTTGGTGGAGAGGGACAT 60.544 55.000 0.00 0.00 0.00 3.06
2060 9467 0.391661 CGTTGGTGGAGAGGGACATG 60.392 60.000 0.00 0.00 0.00 3.21
2061 9468 0.678048 GTTGGTGGAGAGGGACATGC 60.678 60.000 0.00 0.00 0.00 4.06
2062 9469 2.184020 TTGGTGGAGAGGGACATGCG 62.184 60.000 0.00 0.00 0.00 4.73
2063 9470 2.512515 GTGGAGAGGGACATGCGC 60.513 66.667 0.00 0.00 0.00 6.09
2066 9473 2.202987 GAGAGGGACATGCGCTGG 60.203 66.667 9.73 2.61 40.28 4.85
2069 9476 1.220749 GAGGGACATGCGCTGGTTA 59.779 57.895 9.73 0.00 40.28 2.85
2224 9652 0.536006 ATTTAGCGGCATCCTGCTCC 60.536 55.000 1.45 0.00 44.28 4.70
2229 9657 2.679716 GGCATCCTGCTCCAACCT 59.320 61.111 0.00 0.00 44.28 3.50
2247 9675 7.705700 TCCAACCTGTATAGTAGGCTATATCA 58.294 38.462 0.00 0.00 40.90 2.15
2265 9693 8.584157 GCTATATCAGTGCTATAGATGGCTATT 58.416 37.037 20.31 0.00 38.30 1.73
2314 9742 3.187700 GCACGTGCAAGCTTACTAGTAT 58.812 45.455 34.52 0.00 41.59 2.12
2316 9744 3.797256 CACGTGCAAGCTTACTAGTATCC 59.203 47.826 0.82 0.00 0.00 2.59
2317 9745 3.043586 CGTGCAAGCTTACTAGTATCCG 58.956 50.000 2.79 0.00 0.00 4.18
2320 9748 5.562307 CGTGCAAGCTTACTAGTATCCGTAT 60.562 44.000 2.79 0.00 0.00 3.06
2321 9749 6.347969 CGTGCAAGCTTACTAGTATCCGTATA 60.348 42.308 2.79 0.00 0.00 1.47
2322 9750 7.536855 GTGCAAGCTTACTAGTATCCGTATAT 58.463 38.462 2.79 0.00 0.00 0.86
2323 9751 8.671921 GTGCAAGCTTACTAGTATCCGTATATA 58.328 37.037 2.79 0.00 0.00 0.86
2324 9752 9.234827 TGCAAGCTTACTAGTATCCGTATATAA 57.765 33.333 2.79 0.00 0.00 0.98
2349 9777 9.883142 AATTTTGTTAGGTTCAAACTGAAATCA 57.117 25.926 0.00 0.00 38.22 2.57
2350 9778 8.696410 TTTTGTTAGGTTCAAACTGAAATCAC 57.304 30.769 0.00 0.00 38.22 3.06
2351 9779 7.639113 TTGTTAGGTTCAAACTGAAATCACT 57.361 32.000 0.00 0.00 38.22 3.41
2352 9780 7.639113 TGTTAGGTTCAAACTGAAATCACTT 57.361 32.000 0.00 0.00 38.22 3.16
2353 9781 8.740123 TGTTAGGTTCAAACTGAAATCACTTA 57.260 30.769 0.00 0.00 38.22 2.24
2354 9782 9.349713 TGTTAGGTTCAAACTGAAATCACTTAT 57.650 29.630 0.00 0.00 38.22 1.73
2357 9785 8.463930 AGGTTCAAACTGAAATCACTTATTGA 57.536 30.769 0.00 0.00 38.22 2.57
2358 9786 8.571336 AGGTTCAAACTGAAATCACTTATTGAG 58.429 33.333 0.00 0.00 38.22 3.02
2359 9787 7.809806 GGTTCAAACTGAAATCACTTATTGAGG 59.190 37.037 0.00 0.00 38.22 3.86
2360 9788 8.567948 GTTCAAACTGAAATCACTTATTGAGGA 58.432 33.333 0.00 0.00 38.22 3.71
2361 9789 8.327941 TCAAACTGAAATCACTTATTGAGGAG 57.672 34.615 0.00 0.00 37.77 3.69
2362 9790 7.939039 TCAAACTGAAATCACTTATTGAGGAGT 59.061 33.333 0.00 0.00 37.77 3.85
2363 9791 9.219603 CAAACTGAAATCACTTATTGAGGAGTA 57.780 33.333 0.00 0.00 37.77 2.59
2364 9792 9.965902 AAACTGAAATCACTTATTGAGGAGTAT 57.034 29.630 0.00 0.00 37.77 2.12
2365 9793 9.965902 AACTGAAATCACTTATTGAGGAGTATT 57.034 29.630 0.00 0.00 37.77 1.89
2366 9794 9.965902 ACTGAAATCACTTATTGAGGAGTATTT 57.034 29.630 0.00 0.00 37.77 1.40
2379 9807 9.745018 ATTGAGGAGTATTTCTTTCAAAGATCA 57.255 29.630 0.00 0.00 37.38 2.92
2380 9808 8.553459 TGAGGAGTATTTCTTTCAAAGATCAC 57.447 34.615 0.00 0.00 37.38 3.06
2381 9809 8.378565 TGAGGAGTATTTCTTTCAAAGATCACT 58.621 33.333 0.00 4.75 37.38 3.41
2382 9810 8.785329 AGGAGTATTTCTTTCAAAGATCACTC 57.215 34.615 19.05 19.05 38.22 3.51
2383 9811 7.826744 AGGAGTATTTCTTTCAAAGATCACTCC 59.173 37.037 28.38 28.38 46.91 3.85
2384 9812 7.066404 GGAGTATTTCTTTCAAAGATCACTCCC 59.934 40.741 26.93 17.29 44.39 4.30
2385 9813 5.886960 ATTTCTTTCAAAGATCACTCCCG 57.113 39.130 0.00 0.00 37.38 5.14
2386 9814 4.351874 TTCTTTCAAAGATCACTCCCGT 57.648 40.909 0.00 0.00 37.38 5.28
2387 9815 3.926616 TCTTTCAAAGATCACTCCCGTC 58.073 45.455 0.00 0.00 31.20 4.79
2388 9816 2.363788 TTCAAAGATCACTCCCGTCG 57.636 50.000 0.00 0.00 0.00 5.12
2389 9817 1.254026 TCAAAGATCACTCCCGTCGT 58.746 50.000 0.00 0.00 0.00 4.34
2390 9818 2.439409 TCAAAGATCACTCCCGTCGTA 58.561 47.619 0.00 0.00 0.00 3.43
2391 9819 2.422479 TCAAAGATCACTCCCGTCGTAG 59.578 50.000 0.00 0.00 0.00 3.51
2392 9820 1.390565 AAGATCACTCCCGTCGTAGG 58.609 55.000 0.00 0.00 0.00 3.18
2393 9821 0.545171 AGATCACTCCCGTCGTAGGA 59.455 55.000 0.00 0.00 0.00 2.94
2394 9822 1.143277 AGATCACTCCCGTCGTAGGAT 59.857 52.381 0.00 0.00 31.48 3.24
2395 9823 1.267261 GATCACTCCCGTCGTAGGATG 59.733 57.143 0.00 0.00 31.48 3.51
2396 9824 1.065928 CACTCCCGTCGTAGGATGC 59.934 63.158 0.00 0.00 31.48 3.91
2397 9825 1.379443 ACTCCCGTCGTAGGATGCA 60.379 57.895 0.00 0.00 31.48 3.96
2398 9826 0.968901 ACTCCCGTCGTAGGATGCAA 60.969 55.000 0.00 0.00 31.48 4.08
2399 9827 0.527817 CTCCCGTCGTAGGATGCAAC 60.528 60.000 0.00 0.00 31.48 4.17
2400 9828 1.216977 CCCGTCGTAGGATGCAACA 59.783 57.895 0.00 0.00 0.00 3.33
2401 9829 0.390603 CCCGTCGTAGGATGCAACAA 60.391 55.000 0.00 0.00 0.00 2.83
2402 9830 0.999406 CCGTCGTAGGATGCAACAAG 59.001 55.000 0.00 0.00 0.00 3.16
2403 9831 1.671850 CCGTCGTAGGATGCAACAAGT 60.672 52.381 0.00 0.00 0.00 3.16
2404 9832 1.390123 CGTCGTAGGATGCAACAAGTG 59.610 52.381 0.00 0.00 0.00 3.16
2405 9833 1.732259 GTCGTAGGATGCAACAAGTGG 59.268 52.381 0.00 0.00 0.00 4.00
2406 9834 0.447801 CGTAGGATGCAACAAGTGGC 59.552 55.000 0.00 0.00 0.00 5.01
2407 9835 0.447801 GTAGGATGCAACAAGTGGCG 59.552 55.000 0.00 0.00 0.00 5.69
2408 9836 0.036164 TAGGATGCAACAAGTGGCGT 59.964 50.000 0.00 0.00 0.00 5.68
2409 9837 0.036164 AGGATGCAACAAGTGGCGTA 59.964 50.000 0.00 0.00 0.00 4.42
2410 9838 0.168128 GGATGCAACAAGTGGCGTAC 59.832 55.000 0.00 0.00 0.00 3.67
2411 9839 1.156736 GATGCAACAAGTGGCGTACT 58.843 50.000 0.00 0.00 42.89 2.73
2412 9840 0.874390 ATGCAACAAGTGGCGTACTG 59.126 50.000 0.00 0.00 40.26 2.74
2413 9841 1.082104 GCAACAAGTGGCGTACTGC 60.082 57.895 1.72 1.72 40.26 4.40
2430 9858 4.764336 CATGCGTGCCACTTGCCG 62.764 66.667 0.00 0.00 40.16 5.69
2434 9862 4.041917 CGTGCCACTTGCCGCAAT 62.042 61.111 6.19 0.00 40.16 3.56
2435 9863 2.126346 GTGCCACTTGCCGCAATC 60.126 61.111 6.19 0.00 40.16 2.67
2436 9864 2.282391 TGCCACTTGCCGCAATCT 60.282 55.556 6.19 0.00 40.16 2.40
2437 9865 2.180017 GCCACTTGCCGCAATCTG 59.820 61.111 6.19 5.21 0.00 2.90
2438 9866 2.629656 GCCACTTGCCGCAATCTGT 61.630 57.895 6.19 0.00 0.00 3.41
2439 9867 1.210931 CCACTTGCCGCAATCTGTG 59.789 57.895 6.19 11.14 0.00 3.66
2440 9868 1.236616 CCACTTGCCGCAATCTGTGA 61.237 55.000 20.03 0.00 0.00 3.58
2441 9869 0.167470 CACTTGCCGCAATCTGTGAG 59.833 55.000 15.45 1.92 0.00 3.51
2442 9870 0.250467 ACTTGCCGCAATCTGTGAGT 60.250 50.000 6.19 0.00 0.00 3.41
2443 9871 0.877071 CTTGCCGCAATCTGTGAGTT 59.123 50.000 6.19 0.00 0.00 3.01
2444 9872 1.267806 CTTGCCGCAATCTGTGAGTTT 59.732 47.619 6.19 0.00 0.00 2.66
2445 9873 1.317613 TGCCGCAATCTGTGAGTTTT 58.682 45.000 0.00 0.00 0.00 2.43
2446 9874 1.266718 TGCCGCAATCTGTGAGTTTTC 59.733 47.619 0.00 0.00 0.00 2.29
2447 9875 1.401539 GCCGCAATCTGTGAGTTTTCC 60.402 52.381 0.00 0.00 0.00 3.13
2448 9876 2.154462 CCGCAATCTGTGAGTTTTCCT 58.846 47.619 0.00 0.00 0.00 3.36
2449 9877 2.554032 CCGCAATCTGTGAGTTTTCCTT 59.446 45.455 0.00 0.00 0.00 3.36
2450 9878 3.004734 CCGCAATCTGTGAGTTTTCCTTT 59.995 43.478 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.130118 GAGTTTTTCTGACCTGAGAAGCA 58.870 43.478 0.00 0.00 33.50 3.91
81 82 5.123979 GCCTTGTTATGGGAACTCTTGTTAG 59.876 44.000 0.00 0.00 36.39 2.34
242 259 3.117888 GGATTGGCAAGTCCCTTCATAGA 60.118 47.826 5.96 0.00 0.00 1.98
331 348 6.492254 GGTTACAACTTCAATCACGTCTTTT 58.508 36.000 0.00 0.00 0.00 2.27
409 5698 4.022068 ACTTAATCGGACCTACGTTTGTCA 60.022 41.667 16.08 1.01 33.09 3.58
416 5705 4.916249 GCTGATTACTTAATCGGACCTACG 59.084 45.833 18.26 0.00 46.90 3.51
452 5741 8.792633 ACTATCAGACTGTATCTCTGAAATAGC 58.207 37.037 1.59 0.00 45.67 2.97
455 5744 9.860650 ACTACTATCAGACTGTATCTCTGAAAT 57.139 33.333 1.59 0.00 45.67 2.17
636 6004 8.845227 TGTTTGTTCAGTACATGTATGTGAAAT 58.155 29.630 24.37 0.00 41.89 2.17
645 6013 6.293407 CGGAGATTTGTTTGTTCAGTACATGT 60.293 38.462 2.69 2.69 36.44 3.21
683 6051 1.228367 AGGCAGCAGGTTTCACAGG 60.228 57.895 0.00 0.00 0.00 4.00
693 6061 2.097142 GCACAAAAGATAGAGGCAGCAG 59.903 50.000 0.00 0.00 0.00 4.24
789 6159 2.168496 TCGAGGAATCCGAGACTTTGT 58.832 47.619 0.00 0.00 0.00 2.83
827 6197 5.583854 CGGATTCACATTTTCAGAGACTGAT 59.416 40.000 2.30 0.00 40.39 2.90
852 6222 3.507411 TCTGTTGTTGCCTAGGAGTAGT 58.493 45.455 14.75 0.00 0.00 2.73
994 6379 9.520204 CAAGATGAAAGTAACTGACATGTTTTT 57.480 29.630 0.00 0.00 0.00 1.94
1052 6437 5.871539 AGTTCGTTACATTGTGAAAAACGT 58.128 33.333 17.39 0.00 0.00 3.99
1054 6439 7.908601 AGAGAAGTTCGTTACATTGTGAAAAAC 59.091 33.333 0.00 0.08 0.00 2.43
1114 6499 7.264373 AGTTTTGGATGTGAGTTTTCTGTAG 57.736 36.000 0.00 0.00 0.00 2.74
1178 6564 1.102154 CGGCTGTCTCTCAGATCAGT 58.898 55.000 0.00 0.00 46.27 3.41
1219 6607 1.218316 CAGTAGTGGCCGACCTTCC 59.782 63.158 0.00 0.00 36.63 3.46
1509 7060 3.958147 TGATCAGTACACCGGTGATGTAT 59.042 43.478 40.21 24.01 35.11 2.29
1543 7094 5.473162 CCTTGATCAATGGTGTCAAGTGTTA 59.527 40.000 8.96 0.00 44.50 2.41
1579 8980 0.254178 GCCTGGAGAAGCATGAGGAA 59.746 55.000 0.00 0.00 0.00 3.36
1599 9000 6.294176 GCACCAACTAAATGAGAGAACAACAT 60.294 38.462 0.00 0.00 0.00 2.71
1728 9134 9.076596 GTGGCAACTCAAAAATATTTAGATGTC 57.923 33.333 0.01 3.15 37.61 3.06
1735 9141 4.996758 GCAGGTGGCAACTCAAAAATATTT 59.003 37.500 0.00 0.00 43.97 1.40
1739 9145 2.531522 GCAGGTGGCAACTCAAAAAT 57.468 45.000 0.00 0.00 43.97 1.82
1752 9158 7.867403 ACAAGAATTACAACAAAATAGCAGGTG 59.133 33.333 0.00 0.00 0.00 4.00
1827 9233 4.142752 CCACGATACAGACGAACTCAAGTA 60.143 45.833 0.00 0.00 34.70 2.24
1831 9237 2.429478 TCCACGATACAGACGAACTCA 58.571 47.619 0.00 0.00 34.70 3.41
1875 9281 6.732531 TTCTTCGACGAGTATTTCTAGACA 57.267 37.500 0.00 0.00 0.00 3.41
1876 9282 7.305533 GCATTTCTTCGACGAGTATTTCTAGAC 60.306 40.741 0.00 0.00 0.00 2.59
1877 9283 6.691818 GCATTTCTTCGACGAGTATTTCTAGA 59.308 38.462 0.00 0.00 0.00 2.43
1878 9284 6.472486 TGCATTTCTTCGACGAGTATTTCTAG 59.528 38.462 0.00 0.00 0.00 2.43
1879 9285 6.327154 TGCATTTCTTCGACGAGTATTTCTA 58.673 36.000 0.00 0.00 0.00 2.10
1880 9286 5.168569 TGCATTTCTTCGACGAGTATTTCT 58.831 37.500 0.00 0.00 0.00 2.52
1881 9287 5.450376 TGCATTTCTTCGACGAGTATTTC 57.550 39.130 0.00 0.00 0.00 2.17
1882 9288 7.534085 TTATGCATTTCTTCGACGAGTATTT 57.466 32.000 3.54 0.00 0.00 1.40
1883 9289 7.534085 TTTATGCATTTCTTCGACGAGTATT 57.466 32.000 3.54 0.00 0.00 1.89
1884 9290 7.534085 TTTTATGCATTTCTTCGACGAGTAT 57.466 32.000 3.54 0.00 0.00 2.12
1885 9291 6.954616 TTTTATGCATTTCTTCGACGAGTA 57.045 33.333 3.54 0.00 0.00 2.59
1886 9292 5.856126 TTTTATGCATTTCTTCGACGAGT 57.144 34.783 3.54 0.00 0.00 4.18
1887 9293 6.960992 TCATTTTTATGCATTTCTTCGACGAG 59.039 34.615 3.54 0.00 0.00 4.18
1888 9294 6.836953 TCATTTTTATGCATTTCTTCGACGA 58.163 32.000 3.54 0.00 0.00 4.20
1889 9295 7.491254 TTCATTTTTATGCATTTCTTCGACG 57.509 32.000 3.54 0.00 0.00 5.12
1890 9296 8.863049 ACATTCATTTTTATGCATTTCTTCGAC 58.137 29.630 3.54 0.00 0.00 4.20
1891 9297 8.984891 ACATTCATTTTTATGCATTTCTTCGA 57.015 26.923 3.54 0.00 0.00 3.71
1927 9333 8.871125 AGGAATGGATGTATCTAGACGTATTTT 58.129 33.333 0.00 0.00 0.00 1.82
1928 9334 8.423906 AGGAATGGATGTATCTAGACGTATTT 57.576 34.615 0.00 0.00 0.00 1.40
1929 9335 7.122948 GGAGGAATGGATGTATCTAGACGTATT 59.877 40.741 0.00 0.00 0.00 1.89
1930 9336 6.603997 GGAGGAATGGATGTATCTAGACGTAT 59.396 42.308 0.00 0.00 0.00 3.06
1931 9337 5.944599 GGAGGAATGGATGTATCTAGACGTA 59.055 44.000 0.00 0.00 0.00 3.57
1932 9338 4.767928 GGAGGAATGGATGTATCTAGACGT 59.232 45.833 0.00 0.00 0.00 4.34
1933 9339 5.013547 AGGAGGAATGGATGTATCTAGACG 58.986 45.833 0.00 0.00 0.00 4.18
1934 9340 6.948886 TGTAGGAGGAATGGATGTATCTAGAC 59.051 42.308 0.00 0.00 0.00 2.59
1935 9341 7.103745 TGTAGGAGGAATGGATGTATCTAGA 57.896 40.000 0.00 0.00 0.00 2.43
1936 9342 7.453126 ACTTGTAGGAGGAATGGATGTATCTAG 59.547 40.741 0.00 0.00 0.00 2.43
1937 9343 7.306013 ACTTGTAGGAGGAATGGATGTATCTA 58.694 38.462 0.00 0.00 0.00 1.98
1938 9344 6.146760 ACTTGTAGGAGGAATGGATGTATCT 58.853 40.000 0.00 0.00 0.00 1.98
1939 9345 6.426646 ACTTGTAGGAGGAATGGATGTATC 57.573 41.667 0.00 0.00 0.00 2.24
1940 9346 8.511748 AATACTTGTAGGAGGAATGGATGTAT 57.488 34.615 0.00 0.00 0.00 2.29
1941 9347 7.931015 AATACTTGTAGGAGGAATGGATGTA 57.069 36.000 0.00 0.00 0.00 2.29
1942 9348 6.831664 AATACTTGTAGGAGGAATGGATGT 57.168 37.500 0.00 0.00 0.00 3.06
1943 9349 7.282585 TGAAATACTTGTAGGAGGAATGGATG 58.717 38.462 0.00 0.00 0.00 3.51
1944 9350 7.420680 CCTGAAATACTTGTAGGAGGAATGGAT 60.421 40.741 0.00 0.00 0.00 3.41
1945 9351 6.126768 CCTGAAATACTTGTAGGAGGAATGGA 60.127 42.308 0.00 0.00 0.00 3.41
1946 9352 6.058183 CCTGAAATACTTGTAGGAGGAATGG 58.942 44.000 0.00 0.00 0.00 3.16
1947 9353 6.763610 GTCCTGAAATACTTGTAGGAGGAATG 59.236 42.308 0.00 0.00 38.16 2.67
1948 9354 6.407074 CGTCCTGAAATACTTGTAGGAGGAAT 60.407 42.308 0.00 0.00 42.85 3.01
1949 9355 5.105473 CGTCCTGAAATACTTGTAGGAGGAA 60.105 44.000 0.00 0.00 42.85 3.36
1950 9356 4.401519 CGTCCTGAAATACTTGTAGGAGGA 59.598 45.833 0.00 0.00 42.85 3.71
1951 9357 4.441634 CCGTCCTGAAATACTTGTAGGAGG 60.442 50.000 0.00 0.00 40.99 4.30
1952 9358 4.401519 TCCGTCCTGAAATACTTGTAGGAG 59.598 45.833 0.00 0.00 38.16 3.69
1953 9359 4.346730 TCCGTCCTGAAATACTTGTAGGA 58.653 43.478 0.00 0.00 35.29 2.94
1954 9360 4.441634 CCTCCGTCCTGAAATACTTGTAGG 60.442 50.000 0.00 0.00 0.00 3.18
1955 9361 4.441634 CCCTCCGTCCTGAAATACTTGTAG 60.442 50.000 0.00 0.00 0.00 2.74
1956 9362 3.449737 CCCTCCGTCCTGAAATACTTGTA 59.550 47.826 0.00 0.00 0.00 2.41
1957 9363 2.236395 CCCTCCGTCCTGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
1958 9364 2.500098 TCCCTCCGTCCTGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
1959 9365 2.766828 CTCCCTCCGTCCTGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
1960 9366 2.292323 ACTCCCTCCGTCCTGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
1961 9367 2.108970 ACTCCCTCCGTCCTGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
1962 9368 2.544844 ACTCCCTCCGTCCTGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
1963 9369 2.544844 TACTCCCTCCGTCCTGAAAT 57.455 50.000 0.00 0.00 0.00 2.17
1964 9370 2.544844 ATACTCCCTCCGTCCTGAAA 57.455 50.000 0.00 0.00 0.00 2.69
1965 9371 2.544844 AATACTCCCTCCGTCCTGAA 57.455 50.000 0.00 0.00 0.00 3.02
1966 9372 2.544844 AAATACTCCCTCCGTCCTGA 57.455 50.000 0.00 0.00 0.00 3.86
1967 9373 4.957684 ATAAAATACTCCCTCCGTCCTG 57.042 45.455 0.00 0.00 0.00 3.86
1968 9374 5.427481 TCAAATAAAATACTCCCTCCGTCCT 59.573 40.000 0.00 0.00 0.00 3.85
1969 9375 5.677567 TCAAATAAAATACTCCCTCCGTCC 58.322 41.667 0.00 0.00 0.00 4.79
1970 9376 5.236695 GCTCAAATAAAATACTCCCTCCGTC 59.763 44.000 0.00 0.00 0.00 4.79
1971 9377 5.123936 GCTCAAATAAAATACTCCCTCCGT 58.876 41.667 0.00 0.00 0.00 4.69
1972 9378 5.123227 TGCTCAAATAAAATACTCCCTCCG 58.877 41.667 0.00 0.00 0.00 4.63
1973 9379 6.357367 TCTGCTCAAATAAAATACTCCCTCC 58.643 40.000 0.00 0.00 0.00 4.30
1974 9380 7.865706 TTCTGCTCAAATAAAATACTCCCTC 57.134 36.000 0.00 0.00 0.00 4.30
1975 9381 8.650143 TTTTCTGCTCAAATAAAATACTCCCT 57.350 30.769 0.00 0.00 0.00 4.20
1976 9382 9.140286 GTTTTTCTGCTCAAATAAAATACTCCC 57.860 33.333 0.00 0.00 0.00 4.30
1977 9383 9.691362 TGTTTTTCTGCTCAAATAAAATACTCC 57.309 29.630 0.00 0.00 0.00 3.85
1990 9396 5.357878 ACTGATCTTGTTGTTTTTCTGCTCA 59.642 36.000 0.00 0.00 0.00 4.26
2016 9423 7.468631 CGAAAAGGAGACAGAAAATGAAGGAAA 60.469 37.037 0.00 0.00 0.00 3.13
2017 9424 6.017109 CGAAAAGGAGACAGAAAATGAAGGAA 60.017 38.462 0.00 0.00 0.00 3.36
2018 9425 5.470098 CGAAAAGGAGACAGAAAATGAAGGA 59.530 40.000 0.00 0.00 0.00 3.36
2019 9426 5.239525 ACGAAAAGGAGACAGAAAATGAAGG 59.760 40.000 0.00 0.00 0.00 3.46
2024 9431 4.887655 ACCAACGAAAAGGAGACAGAAAAT 59.112 37.500 0.00 0.00 0.00 1.82
2042 9449 0.678048 GCATGTCCCTCTCCACCAAC 60.678 60.000 0.00 0.00 0.00 3.77
2046 9453 2.512515 GCGCATGTCCCTCTCCAC 60.513 66.667 0.30 0.00 0.00 4.02
2058 9465 3.327464 CGCAAAATAACCAGCGCAT 57.673 47.368 11.47 0.00 43.80 4.73
2059 9466 4.857689 CGCAAAATAACCAGCGCA 57.142 50.000 11.47 0.00 43.80 6.09
2061 9468 9.617366 GGATAATCCTACGCAAAATAACCAGCG 62.617 44.444 3.97 3.97 43.82 5.18
2062 9469 4.632538 AATCCTACGCAAAATAACCAGC 57.367 40.909 0.00 0.00 0.00 4.85
2063 9470 6.899114 GGATAATCCTACGCAAAATAACCAG 58.101 40.000 0.00 0.00 32.53 4.00
2101 9508 3.122278 CCACGTAAACACCGACATTACAG 59.878 47.826 0.00 0.00 31.45 2.74
2158 9572 9.227490 CACTAAAGTTATGAGATAGTCTTGACG 57.773 37.037 0.00 0.00 0.00 4.35
2195 9623 4.562757 GGATGCCGCTAAATGGTACTCATA 60.563 45.833 0.00 0.00 34.44 2.15
2200 9628 1.873591 CAGGATGCCGCTAAATGGTAC 59.126 52.381 0.00 0.00 0.00 3.34
2224 9652 8.462811 CACTGATATAGCCTACTATACAGGTTG 58.537 40.741 17.31 10.01 42.71 3.77
2247 9675 9.853177 AAGTTTTAAATAGCCATCTATAGCACT 57.147 29.630 0.00 0.00 34.53 4.40
2323 9751 9.883142 TGATTTCAGTTTGAACCTAACAAAATT 57.117 25.926 0.00 0.00 35.89 1.82
2324 9752 9.313118 GTGATTTCAGTTTGAACCTAACAAAAT 57.687 29.630 0.00 0.00 35.89 1.82
2325 9753 8.527810 AGTGATTTCAGTTTGAACCTAACAAAA 58.472 29.630 0.00 0.00 35.89 2.44
2326 9754 8.062065 AGTGATTTCAGTTTGAACCTAACAAA 57.938 30.769 0.00 0.00 35.89 2.83
2327 9755 7.639113 AGTGATTTCAGTTTGAACCTAACAA 57.361 32.000 0.00 0.00 35.89 2.83
2328 9756 7.639113 AAGTGATTTCAGTTTGAACCTAACA 57.361 32.000 0.00 0.00 35.89 2.41
2331 9759 9.567776 TCAATAAGTGATTTCAGTTTGAACCTA 57.432 29.630 5.99 0.00 39.89 3.08
2332 9760 8.463930 TCAATAAGTGATTTCAGTTTGAACCT 57.536 30.769 5.99 0.00 39.89 3.50
2333 9761 7.809806 CCTCAATAAGTGATTTCAGTTTGAACC 59.190 37.037 5.99 0.00 39.89 3.62
2334 9762 8.567948 TCCTCAATAAGTGATTTCAGTTTGAAC 58.432 33.333 5.99 0.00 39.89 3.18
2335 9763 8.690203 TCCTCAATAAGTGATTTCAGTTTGAA 57.310 30.769 5.99 0.00 39.89 2.69
2336 9764 7.939039 ACTCCTCAATAAGTGATTTCAGTTTGA 59.061 33.333 5.99 4.65 39.89 2.69
2337 9765 8.103948 ACTCCTCAATAAGTGATTTCAGTTTG 57.896 34.615 5.99 0.75 39.89 2.93
2338 9766 9.965902 ATACTCCTCAATAAGTGATTTCAGTTT 57.034 29.630 5.99 0.00 39.89 2.66
2339 9767 9.965902 AATACTCCTCAATAAGTGATTTCAGTT 57.034 29.630 5.97 5.97 41.86 3.16
2340 9768 9.965902 AAATACTCCTCAATAAGTGATTTCAGT 57.034 29.630 0.00 0.00 35.07 3.41
2353 9781 9.745018 TGATCTTTGAAAGAAATACTCCTCAAT 57.255 29.630 12.10 0.00 41.63 2.57
2354 9782 9.003658 GTGATCTTTGAAAGAAATACTCCTCAA 57.996 33.333 12.10 0.00 41.63 3.02
2355 9783 8.378565 AGTGATCTTTGAAAGAAATACTCCTCA 58.621 33.333 12.10 5.69 41.63 3.86
2356 9784 8.785329 AGTGATCTTTGAAAGAAATACTCCTC 57.215 34.615 12.10 3.10 41.63 3.71
2357 9785 8.785329 GAGTGATCTTTGAAAGAAATACTCCT 57.215 34.615 23.96 12.99 41.63 3.69
2358 9786 7.980062 GGAGTGATCTTTGAAAGAAATACTCC 58.020 38.462 30.46 30.46 46.44 3.85
2359 9787 7.201565 CGGGAGTGATCTTTGAAAGAAATACTC 60.202 40.741 25.14 25.14 41.63 2.59
2360 9788 6.595716 CGGGAGTGATCTTTGAAAGAAATACT 59.404 38.462 12.10 14.87 41.63 2.12
2361 9789 6.371825 ACGGGAGTGATCTTTGAAAGAAATAC 59.628 38.462 12.10 10.76 44.82 1.89
2362 9790 6.472887 ACGGGAGTGATCTTTGAAAGAAATA 58.527 36.000 12.10 0.00 44.82 1.40
2363 9791 5.316987 ACGGGAGTGATCTTTGAAAGAAAT 58.683 37.500 12.10 0.00 44.82 2.17
2364 9792 4.714632 ACGGGAGTGATCTTTGAAAGAAA 58.285 39.130 12.10 0.66 44.82 2.52
2365 9793 4.351874 ACGGGAGTGATCTTTGAAAGAA 57.648 40.909 12.10 0.00 44.82 2.52
2380 9808 0.527817 GTTGCATCCTACGACGGGAG 60.528 60.000 0.00 0.00 36.21 4.30
2381 9809 1.252215 TGTTGCATCCTACGACGGGA 61.252 55.000 0.00 0.00 37.26 5.14
2382 9810 0.390603 TTGTTGCATCCTACGACGGG 60.391 55.000 0.00 0.00 0.00 5.28
2383 9811 0.999406 CTTGTTGCATCCTACGACGG 59.001 55.000 0.00 0.00 0.00 4.79
2384 9812 1.390123 CACTTGTTGCATCCTACGACG 59.610 52.381 0.00 0.00 0.00 5.12
2385 9813 1.732259 CCACTTGTTGCATCCTACGAC 59.268 52.381 0.00 0.00 0.00 4.34
2386 9814 1.943968 GCCACTTGTTGCATCCTACGA 60.944 52.381 0.00 0.00 0.00 3.43
2387 9815 0.447801 GCCACTTGTTGCATCCTACG 59.552 55.000 0.00 0.00 0.00 3.51
2388 9816 0.447801 CGCCACTTGTTGCATCCTAC 59.552 55.000 0.00 0.00 0.00 3.18
2389 9817 0.036164 ACGCCACTTGTTGCATCCTA 59.964 50.000 0.00 0.00 0.00 2.94
2390 9818 0.036164 TACGCCACTTGTTGCATCCT 59.964 50.000 0.00 0.00 0.00 3.24
2391 9819 0.168128 GTACGCCACTTGTTGCATCC 59.832 55.000 0.00 0.00 0.00 3.51
2392 9820 1.135972 CAGTACGCCACTTGTTGCATC 60.136 52.381 0.00 0.00 34.26 3.91
2393 9821 0.874390 CAGTACGCCACTTGTTGCAT 59.126 50.000 0.00 0.00 34.26 3.96
2394 9822 1.781025 GCAGTACGCCACTTGTTGCA 61.781 55.000 0.00 0.00 34.26 4.08
2395 9823 1.082104 GCAGTACGCCACTTGTTGC 60.082 57.895 0.00 0.00 34.26 4.17
2396 9824 0.874390 ATGCAGTACGCCACTTGTTG 59.126 50.000 0.00 0.00 41.33 3.33
2397 9825 0.874390 CATGCAGTACGCCACTTGTT 59.126 50.000 0.00 0.00 41.33 2.83
2398 9826 1.577328 GCATGCAGTACGCCACTTGT 61.577 55.000 14.21 0.00 41.33 3.16
2399 9827 1.135315 GCATGCAGTACGCCACTTG 59.865 57.895 14.21 0.00 41.33 3.16
2400 9828 2.390599 CGCATGCAGTACGCCACTT 61.391 57.895 19.57 0.00 41.33 3.16
2401 9829 2.815211 CGCATGCAGTACGCCACT 60.815 61.111 19.57 0.00 41.33 4.00
2402 9830 3.118454 ACGCATGCAGTACGCCAC 61.118 61.111 19.57 0.00 41.33 5.01
2403 9831 3.117812 CACGCATGCAGTACGCCA 61.118 61.111 19.57 0.00 41.33 5.69
2420 9848 2.180017 CAGATTGCGGCAAGTGGC 59.820 61.111 21.11 10.02 43.74 5.01
2421 9849 1.210931 CACAGATTGCGGCAAGTGG 59.789 57.895 21.11 13.89 0.00 4.00
2422 9850 0.167470 CTCACAGATTGCGGCAAGTG 59.833 55.000 21.11 21.06 0.00 3.16
2423 9851 0.250467 ACTCACAGATTGCGGCAAGT 60.250 50.000 21.11 10.68 0.00 3.16
2424 9852 0.877071 AACTCACAGATTGCGGCAAG 59.123 50.000 21.11 10.02 0.00 4.01
2425 9853 1.317613 AAACTCACAGATTGCGGCAA 58.682 45.000 18.85 18.85 0.00 4.52
2426 9854 1.266718 GAAAACTCACAGATTGCGGCA 59.733 47.619 0.00 0.00 0.00 5.69
2427 9855 1.401539 GGAAAACTCACAGATTGCGGC 60.402 52.381 0.00 0.00 0.00 6.53
2428 9856 2.154462 AGGAAAACTCACAGATTGCGG 58.846 47.619 0.00 0.00 0.00 5.69
2429 9857 3.904136 AAGGAAAACTCACAGATTGCG 57.096 42.857 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.