Multiple sequence alignment - TraesCS6D01G405300

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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 TraesCS6D01G405300 chr6D 100.000 2630 0 0 1 2630 472569969 472567340 0.000000e+00 4857.0
1 TraesCS6D01G405300 chr6A 89.603 1058 60 20 665 1682 617096851 617097898 0.000000e+00 1299.0
2 TraesCS6D01G405300 chr6A 89.484 504 17 18 2142 2630 617098455 617098937 2.900000e-169 604.0
3 TraesCS6D01G405300 chr6A 94.737 76 1 2 1709 1783 617097894 617097967 5.950000e-22 115.0
4 TraesCS6D01G405300 chr6B 88.909 1091 66 30 90 1137 114938828 114937750 0.000000e+00 1293.0
5 TraesCS6D01G405300 chr6B 89.980 978 49 18 850 1797 717597231 717596273 0.000000e+00 1218.0
6 TraesCS6D01G405300 chr6B 85.323 511 21 23 2149 2630 717595811 717595326 1.830000e-131 479.0
7 TraesCS6D01G405300 chr6B 83.988 331 27 11 522 832 717602255 717601931 7.120000e-76 294.0
8 TraesCS6D01G405300 chr6B 90.503 179 15 2 293 470 717605792 717605615 4.380000e-58 235.0
9 TraesCS6D01G405300 chr1D 82.663 323 35 12 501 804 462387798 462387478 1.550000e-67 267.0
10 TraesCS6D01G405300 chr7B 79.167 408 43 23 484 859 621456135 621455738 7.270000e-61 244.0
11 TraesCS6D01G405300 chr7B 80.576 139 27 0 1338 1476 734430598 734430736 9.950000e-20 108.0
12 TraesCS6D01G405300 chr5D 77.876 339 51 16 540 865 2502777 2503104 3.460000e-44 189.0
13 TraesCS6D01G405300 chr5A 81.538 130 24 0 1338 1467 663189908 663189779 9.950000e-20 108.0
14 TraesCS6D01G405300 chr4D 80.769 130 25 0 1338 1467 483041301 483041172 4.630000e-18 102.0
15 TraesCS6D01G405300 chr4B 85.417 96 14 0 1372 1467 612877377 612877282 1.670000e-17 100.0
16 TraesCS6D01G405300 chr4A 91.803 61 3 2 766 826 603760270 603760328 1.680000e-12 84.2
17 TraesCS6D01G405300 chr4A 91.803 61 3 2 766 826 603830868 603830926 1.680000e-12 84.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G405300 chr6D 472567340 472569969 2629 True 4857.000000 4857 100.000000 1 2630 1 chr6D.!!$R1 2629
1 TraesCS6D01G405300 chr6A 617096851 617098937 2086 False 672.666667 1299 91.274667 665 2630 3 chr6A.!!$F1 1965
2 TraesCS6D01G405300 chr6B 114937750 114938828 1078 True 1293.000000 1293 88.909000 90 1137 1 chr6B.!!$R1 1047
3 TraesCS6D01G405300 chr6B 717595326 717597231 1905 True 848.500000 1218 87.651500 850 2630 2 chr6B.!!$R2 1780
4 TraesCS6D01G405300 chr6B 717601931 717605792 3861 True 264.500000 294 87.245500 293 832 2 chr6B.!!$R3 539

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
176 177 0.393132 TGCGTGAGATCGAGAGGAGT 60.393 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 5470 0.171903 CTCAAAATGCAAGAGGGCCG 59.828 55.0 0.0 0.0 0.0 6.13 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
21 22 4.032703 GATGAAACATTTCCCATCGGTG 57.967 45.455 2.00 0.00 36.36 4.94
22 23 2.166829 TGAAACATTTCCCATCGGTGG 58.833 47.619 8.08 8.08 45.61 4.61
23 24 2.224892 TGAAACATTTCCCATCGGTGGA 60.225 45.455 18.77 0.00 45.68 4.02
24 25 3.752218 TGAAACATTTCCCATCGGTGGAA 60.752 43.478 18.77 3.25 45.68 3.53
25 26 5.056113 TGAAACATTTCCCATCGGTGGAAT 61.056 41.667 18.77 5.98 45.68 3.01
26 27 6.840479 TGAAACATTTCCCATCGGTGGAATC 61.840 44.000 18.77 3.73 45.68 2.52
32 33 3.760693 CATCGGTGGAATCGTCCTT 57.239 52.632 0.00 0.00 45.22 3.36
33 34 2.024176 CATCGGTGGAATCGTCCTTT 57.976 50.000 0.00 0.00 45.22 3.11
34 35 2.356135 CATCGGTGGAATCGTCCTTTT 58.644 47.619 0.00 0.00 45.22 2.27
35 36 2.554370 TCGGTGGAATCGTCCTTTTT 57.446 45.000 0.00 0.00 45.22 1.94
67 68 6.524101 AAAAACCTTAACAGAGCTTGTCAA 57.476 33.333 0.00 0.00 39.73 3.18
68 69 6.715347 AAAACCTTAACAGAGCTTGTCAAT 57.285 33.333 0.00 0.00 39.73 2.57
69 70 5.948992 AACCTTAACAGAGCTTGTCAATC 57.051 39.130 0.00 0.00 39.73 2.67
70 71 5.234466 ACCTTAACAGAGCTTGTCAATCT 57.766 39.130 0.00 0.00 39.73 2.40
71 72 5.625150 ACCTTAACAGAGCTTGTCAATCTT 58.375 37.500 0.00 0.00 39.73 2.40
72 73 5.703130 ACCTTAACAGAGCTTGTCAATCTTC 59.297 40.000 0.00 0.00 39.73 2.87
73 74 5.936956 CCTTAACAGAGCTTGTCAATCTTCT 59.063 40.000 0.00 0.00 39.73 2.85
74 75 6.429385 CCTTAACAGAGCTTGTCAATCTTCTT 59.571 38.462 0.00 0.00 39.73 2.52
75 76 5.938438 AACAGAGCTTGTCAATCTTCTTC 57.062 39.130 0.00 0.00 39.73 2.87
76 77 4.322567 ACAGAGCTTGTCAATCTTCTTCC 58.677 43.478 0.00 0.00 33.87 3.46
77 78 3.688673 CAGAGCTTGTCAATCTTCTTCCC 59.311 47.826 0.00 0.00 0.00 3.97
78 79 3.328931 AGAGCTTGTCAATCTTCTTCCCA 59.671 43.478 0.00 0.00 0.00 4.37
79 80 4.074970 GAGCTTGTCAATCTTCTTCCCAA 58.925 43.478 0.00 0.00 0.00 4.12
80 81 3.823304 AGCTTGTCAATCTTCTTCCCAAC 59.177 43.478 0.00 0.00 0.00 3.77
81 82 3.057245 GCTTGTCAATCTTCTTCCCAACC 60.057 47.826 0.00 0.00 0.00 3.77
82 83 2.778299 TGTCAATCTTCTTCCCAACCG 58.222 47.619 0.00 0.00 0.00 4.44
83 84 2.370519 TGTCAATCTTCTTCCCAACCGA 59.629 45.455 0.00 0.00 0.00 4.69
84 85 3.003480 GTCAATCTTCTTCCCAACCGAG 58.997 50.000 0.00 0.00 0.00 4.63
85 86 2.027192 TCAATCTTCTTCCCAACCGAGG 60.027 50.000 0.00 0.00 0.00 4.63
86 87 1.952621 ATCTTCTTCCCAACCGAGGA 58.047 50.000 0.00 0.00 0.00 3.71
87 88 1.724545 TCTTCTTCCCAACCGAGGAA 58.275 50.000 0.00 0.00 41.14 3.36
96 97 1.918800 AACCGAGGAAGGGGGTCAG 60.919 63.158 0.00 0.00 32.47 3.51
176 177 0.393132 TGCGTGAGATCGAGAGGAGT 60.393 55.000 0.00 0.00 0.00 3.85
182 183 1.680735 GAGATCGAGAGGAGTGTGCAT 59.319 52.381 0.00 0.00 0.00 3.96
240 241 1.810030 CGAGCGGGCAAACTAGACC 60.810 63.158 0.00 0.00 0.00 3.85
289 295 1.585521 CGAGAAATCCCCGTCGACG 60.586 63.158 30.33 30.33 34.28 5.12
290 296 1.877165 GAGAAATCCCCGTCGACGC 60.877 63.158 31.73 16.23 38.18 5.19
375 381 7.617723 ACAAGGGTAAAATGTGGCAGAATTATA 59.382 33.333 0.00 0.00 0.00 0.98
448 458 7.507829 TCAAAATAGGGGCAAATAATGGAATG 58.492 34.615 0.00 0.00 0.00 2.67
480 490 5.054477 AGTTAATATACACCCATCACGTGC 58.946 41.667 11.67 0.00 34.45 5.34
482 492 0.528901 TATACACCCATCACGTGCGC 60.529 55.000 11.67 0.00 34.45 6.09
492 502 2.048033 ACGTGCGCGAAATACCCA 60.048 55.556 28.73 0.00 42.00 4.51
499 509 1.135228 GCGCGAAATACCCATTGGTTT 60.135 47.619 12.10 0.00 44.75 3.27
512 522 4.584325 CCCATTGGTTTCTGGGTGTATATG 59.416 45.833 1.20 0.00 46.01 1.78
644 3984 3.013921 AGAAAACCAGCGTTGACTTCAA 58.986 40.909 0.00 0.00 30.72 2.69
646 3986 2.325583 AACCAGCGTTGACTTCAAGA 57.674 45.000 0.00 0.00 36.39 3.02
647 3987 1.871080 ACCAGCGTTGACTTCAAGAG 58.129 50.000 0.00 0.00 36.39 2.85
650 3997 2.872245 CCAGCGTTGACTTCAAGAGAAA 59.128 45.455 0.00 0.00 36.39 2.52
772 4136 8.197988 CCAGTACAATGGTAGATCAAGTTTAC 57.802 38.462 0.00 0.00 35.47 2.01
867 4241 0.894835 CCAAAATTTCCCCTCCCACG 59.105 55.000 0.00 0.00 0.00 4.94
868 4242 1.627864 CAAAATTTCCCCTCCCACGT 58.372 50.000 0.00 0.00 0.00 4.49
869 4243 1.272212 CAAAATTTCCCCTCCCACGTG 59.728 52.381 9.08 9.08 0.00 4.49
872 4246 0.548197 ATTTCCCCTCCCACGTGGTA 60.548 55.000 31.80 17.41 34.77 3.25
880 4254 2.358247 CCACGTGGTAGGGTGTGC 60.358 66.667 26.95 0.00 32.30 4.57
961 4335 3.638484 GTGGTACTCATTTGTTGCCAAC 58.362 45.455 0.00 0.00 0.00 3.77
982 4370 0.463116 AAACAACCGCCTCGTCACTT 60.463 50.000 0.00 0.00 0.00 3.16
987 4375 2.564975 CGCCTCGTCACTTACCGT 59.435 61.111 0.00 0.00 0.00 4.83
988 4376 1.647545 CCGCCTCGTCACTTACCGTA 61.648 60.000 0.00 0.00 0.00 4.02
993 4381 0.438445 TCGTCACTTACCGTACGTCG 59.562 55.000 15.21 1.90 36.73 5.12
1005 4393 3.975083 TACGTCGACCACCATGCGC 62.975 63.158 10.58 0.00 0.00 6.09
1042 4434 1.285078 TCCACTCTAGCTCTAGCACCA 59.715 52.381 4.54 0.00 45.16 4.17
1080 4472 0.179051 CAGCTGCCTCCTCATCTTCC 60.179 60.000 0.00 0.00 0.00 3.46
1138 4530 1.620589 ATGGTGGTCATCCTGGCCT 60.621 57.895 3.32 0.00 44.07 5.19
1489 4881 1.535226 CCGCCATTATCGACTCGTCAA 60.535 52.381 0.00 0.00 0.00 3.18
1511 4903 3.137459 CTCCTCGTCCTGCTCGCT 61.137 66.667 0.00 0.00 0.00 4.93
1633 5025 1.743252 AGCTTCTTGCCGTAGCTGC 60.743 57.895 0.00 0.00 43.66 5.25
1681 5082 5.640218 CAAACTTGCAATGGTTGTTAGTG 57.360 39.130 14.71 3.35 34.31 2.74
1682 5083 3.369546 ACTTGCAATGGTTGTTAGTGC 57.630 42.857 0.00 0.00 39.38 4.40
1683 5084 2.692557 ACTTGCAATGGTTGTTAGTGCA 59.307 40.909 0.00 0.00 45.87 4.57
1686 5087 4.333913 TGCAATGGTTGTTAGTGCAATT 57.666 36.364 0.00 0.00 44.78 2.32
1687 5088 4.305769 TGCAATGGTTGTTAGTGCAATTC 58.694 39.130 0.00 0.00 44.78 2.17
1688 5089 4.202192 TGCAATGGTTGTTAGTGCAATTCA 60.202 37.500 0.00 0.00 44.78 2.57
1689 5090 4.386652 GCAATGGTTGTTAGTGCAATTCAG 59.613 41.667 0.00 0.00 38.83 3.02
1690 5091 5.531634 CAATGGTTGTTAGTGCAATTCAGT 58.468 37.500 0.00 0.00 0.00 3.41
1691 5092 5.789643 ATGGTTGTTAGTGCAATTCAGTT 57.210 34.783 0.00 0.00 0.00 3.16
1692 5093 6.892658 ATGGTTGTTAGTGCAATTCAGTTA 57.107 33.333 0.00 0.00 0.00 2.24
1693 5094 6.312399 TGGTTGTTAGTGCAATTCAGTTAG 57.688 37.500 0.00 0.00 0.00 2.34
1694 5095 5.154222 GGTTGTTAGTGCAATTCAGTTAGC 58.846 41.667 0.00 0.00 0.00 3.09
1695 5096 5.048713 GGTTGTTAGTGCAATTCAGTTAGCT 60.049 40.000 0.00 0.00 0.00 3.32
1696 5097 6.148811 GGTTGTTAGTGCAATTCAGTTAGCTA 59.851 38.462 0.00 0.00 0.00 3.32
1697 5098 7.148239 GGTTGTTAGTGCAATTCAGTTAGCTAT 60.148 37.037 0.00 0.00 0.00 2.97
1698 5099 7.307493 TGTTAGTGCAATTCAGTTAGCTATG 57.693 36.000 0.00 0.00 0.00 2.23
1699 5100 7.102993 TGTTAGTGCAATTCAGTTAGCTATGA 58.897 34.615 0.00 0.00 0.00 2.15
1700 5101 7.606073 TGTTAGTGCAATTCAGTTAGCTATGAA 59.394 33.333 11.25 11.25 39.59 2.57
1701 5102 8.616076 GTTAGTGCAATTCAGTTAGCTATGAAT 58.384 33.333 14.25 14.25 45.67 2.57
1756 5195 5.751028 GCTTCAGTGGTAGAGTTATCATGAC 59.249 44.000 0.00 0.00 0.00 3.06
1855 5387 6.149633 CCAGTGTTAATCGATCGATGATGTA 58.850 40.000 29.99 16.15 34.70 2.29
1857 5389 6.858478 CAGTGTTAATCGATCGATGATGTACT 59.142 38.462 29.99 24.02 34.70 2.73
1858 5390 6.858478 AGTGTTAATCGATCGATGATGTACTG 59.142 38.462 29.99 0.00 34.70 2.74
1861 5393 7.167468 TGTTAATCGATCGATGATGTACTGTTG 59.833 37.037 29.99 0.00 34.70 3.33
1863 5395 5.744666 TCGATCGATGATGTACTGTTGTA 57.255 39.130 15.15 0.00 0.00 2.41
1864 5396 5.507974 TCGATCGATGATGTACTGTTGTAC 58.492 41.667 15.15 0.00 46.74 2.90
1875 5407 1.413445 ACTGTTGTACAACTACGGGCA 59.587 47.619 32.58 14.65 41.67 5.36
1876 5408 2.158928 ACTGTTGTACAACTACGGGCAA 60.159 45.455 32.58 13.96 41.67 4.52
1877 5409 2.211806 TGTTGTACAACTACGGGCAAC 58.788 47.619 32.58 9.74 41.67 4.17
1878 5410 2.158928 TGTTGTACAACTACGGGCAACT 60.159 45.455 32.58 0.00 41.67 3.16
1888 5420 4.943822 GGGCAACTGAGCTAGACC 57.056 61.111 0.00 0.00 34.17 3.85
1890 5422 1.486211 GGGCAACTGAGCTAGACCTA 58.514 55.000 0.00 0.00 34.17 3.08
1891 5423 1.410882 GGGCAACTGAGCTAGACCTAG 59.589 57.143 0.00 0.00 36.29 3.02
1893 5425 3.288964 GGCAACTGAGCTAGACCTAGTA 58.711 50.000 0.00 0.00 35.65 1.82
1894 5426 3.700038 GGCAACTGAGCTAGACCTAGTAA 59.300 47.826 0.00 0.00 35.65 2.24
1895 5427 4.342665 GGCAACTGAGCTAGACCTAGTAAT 59.657 45.833 0.00 0.00 35.65 1.89
1896 5428 5.535406 GGCAACTGAGCTAGACCTAGTAATA 59.465 44.000 0.00 0.00 35.65 0.98
1897 5429 6.294286 GGCAACTGAGCTAGACCTAGTAATAG 60.294 46.154 0.00 0.00 35.65 1.73
1898 5430 6.294286 GCAACTGAGCTAGACCTAGTAATAGG 60.294 46.154 14.67 14.67 42.86 2.57
1913 5445 9.517868 CCTAGTAATAGGTTACATACTACTGCT 57.482 37.037 8.13 0.00 42.13 4.24
1916 5448 9.294614 AGTAATAGGTTACATACTACTGCTACC 57.705 37.037 0.00 0.00 42.13 3.18
1918 5450 7.999450 ATAGGTTACATACTACTGCTACCTC 57.001 40.000 0.00 0.00 35.79 3.85
1919 5451 5.139001 AGGTTACATACTACTGCTACCTCC 58.861 45.833 0.00 0.00 31.26 4.30
1921 5453 3.294038 ACATACTACTGCTACCTCCGT 57.706 47.619 0.00 0.00 0.00 4.69
1922 5454 3.212685 ACATACTACTGCTACCTCCGTC 58.787 50.000 0.00 0.00 0.00 4.79
1923 5455 2.338577 TACTACTGCTACCTCCGTCC 57.661 55.000 0.00 0.00 0.00 4.79
1926 5458 0.395311 TACTGCTACCTCCGTCCAGG 60.395 60.000 0.00 0.00 42.97 4.45
1928 5460 1.229082 TGCTACCTCCGTCCAGGTT 60.229 57.895 3.48 0.00 45.24 3.50
1929 5461 0.834687 TGCTACCTCCGTCCAGGTTT 60.835 55.000 3.48 0.00 45.24 3.27
1930 5462 1.188863 GCTACCTCCGTCCAGGTTTA 58.811 55.000 3.48 0.00 45.24 2.01
1931 5463 1.134877 GCTACCTCCGTCCAGGTTTAC 60.135 57.143 3.48 0.00 45.24 2.01
1932 5464 1.479730 CTACCTCCGTCCAGGTTTACC 59.520 57.143 3.48 0.00 45.24 2.85
1933 5465 1.217244 CCTCCGTCCAGGTTTACCG 59.783 63.158 0.00 0.00 42.08 4.02
1934 5466 1.217244 CTCCGTCCAGGTTTACCGG 59.783 63.158 0.00 0.00 42.08 5.28
1935 5467 1.533753 TCCGTCCAGGTTTACCGGT 60.534 57.895 13.98 13.98 42.08 5.28
1936 5468 1.079612 CCGTCCAGGTTTACCGGTC 60.080 63.158 12.40 0.00 42.08 4.79
1937 5469 1.079612 CGTCCAGGTTTACCGGTCC 60.080 63.158 12.40 6.52 42.08 4.46
1938 5470 1.297689 GTCCAGGTTTACCGGTCCC 59.702 63.158 12.40 10.42 42.08 4.46
1952 5484 3.338250 TCCCGGCCCTCTTGCATT 61.338 61.111 0.00 0.00 0.00 3.56
1953 5485 2.362889 CCCGGCCCTCTTGCATTT 60.363 61.111 0.00 0.00 0.00 2.32
1954 5486 1.984026 CCCGGCCCTCTTGCATTTT 60.984 57.895 0.00 0.00 0.00 1.82
1956 5488 1.250154 CCGGCCCTCTTGCATTTTGA 61.250 55.000 0.00 0.00 0.00 2.69
1957 5489 0.171903 CGGCCCTCTTGCATTTTGAG 59.828 55.000 0.00 0.00 0.00 3.02
1959 5491 1.203287 GGCCCTCTTGCATTTTGAGTC 59.797 52.381 0.00 0.00 0.00 3.36
1960 5492 1.888512 GCCCTCTTGCATTTTGAGTCA 59.111 47.619 0.00 0.00 0.00 3.41
1961 5493 2.297033 GCCCTCTTGCATTTTGAGTCAA 59.703 45.455 0.08 0.08 0.00 3.18
1962 5494 3.243839 GCCCTCTTGCATTTTGAGTCAAA 60.244 43.478 14.35 14.35 0.00 2.69
1963 5495 4.553323 CCCTCTTGCATTTTGAGTCAAAG 58.447 43.478 17.36 9.10 34.72 2.77
1964 5496 4.038402 CCCTCTTGCATTTTGAGTCAAAGT 59.962 41.667 17.36 12.66 34.72 2.66
1966 5498 6.044682 CCTCTTGCATTTTGAGTCAAAGTTT 58.955 36.000 17.36 5.38 34.72 2.66
1968 5500 7.706179 CCTCTTGCATTTTGAGTCAAAGTTTAA 59.294 33.333 17.36 11.06 34.72 1.52
1969 5501 8.406172 TCTTGCATTTTGAGTCAAAGTTTAAC 57.594 30.769 17.36 7.15 34.72 2.01
1970 5502 8.250332 TCTTGCATTTTGAGTCAAAGTTTAACT 58.750 29.630 17.36 0.00 34.72 2.24
1971 5503 9.515020 CTTGCATTTTGAGTCAAAGTTTAACTA 57.485 29.630 17.36 1.93 34.72 2.24
2122 5704 9.403583 TCAAAATTTAGCATAAGTACTAAGGGG 57.596 33.333 0.00 0.00 30.47 4.79
2123 5705 9.403583 CAAAATTTAGCATAAGTACTAAGGGGA 57.596 33.333 0.00 0.00 30.47 4.81
2124 5706 8.975663 AAATTTAGCATAAGTACTAAGGGGAC 57.024 34.615 0.00 0.00 30.47 4.46
2126 5708 9.443365 AATTTAGCATAAGTACTAAGGGGACTA 57.557 33.333 0.00 0.00 42.68 2.59
2127 5709 8.843308 TTTAGCATAAGTACTAAGGGGACTAA 57.157 34.615 0.00 0.00 42.68 2.24
2128 5710 9.443365 TTTAGCATAAGTACTAAGGGGACTAAT 57.557 33.333 0.00 0.00 42.68 1.73
2131 5713 9.443365 AGCATAAGTACTAAGGGGACTAATAAA 57.557 33.333 0.00 0.00 42.68 1.40
2132 5714 9.486497 GCATAAGTACTAAGGGGACTAATAAAC 57.514 37.037 0.00 0.00 42.68 2.01
2133 5715 9.993454 CATAAGTACTAAGGGGACTAATAAACC 57.007 37.037 0.00 0.00 42.68 3.27
2134 5716 7.443302 AAGTACTAAGGGGACTAATAAACCC 57.557 40.000 0.00 0.00 42.68 4.11
2138 5720 2.627515 GGGGACTAATAAACCCGGAC 57.372 55.000 0.73 0.00 44.09 4.79
2139 5721 1.839354 GGGGACTAATAAACCCGGACA 59.161 52.381 0.73 0.00 44.09 4.02
2140 5722 2.158856 GGGGACTAATAAACCCGGACAG 60.159 54.545 0.73 0.00 44.09 3.51
2141 5723 2.767960 GGGACTAATAAACCCGGACAGA 59.232 50.000 0.73 0.00 34.03 3.41
2142 5724 3.390311 GGGACTAATAAACCCGGACAGAT 59.610 47.826 0.73 0.00 34.03 2.90
2146 5728 7.318893 GGACTAATAAACCCGGACAGATATAC 58.681 42.308 0.73 0.00 0.00 1.47
2147 5729 7.178097 GGACTAATAAACCCGGACAGATATACT 59.822 40.741 0.73 0.00 0.00 2.12
2154 5736 8.488308 AAACCCGGACAGATATACTAGTAATT 57.512 34.615 0.73 0.00 0.00 1.40
2219 5804 6.674694 ATTTTTGAATGGAGAGATGAGACG 57.325 37.500 0.00 0.00 0.00 4.18
2223 5808 3.891366 TGAATGGAGAGATGAGACGCATA 59.109 43.478 0.00 0.00 37.34 3.14
2345 5954 2.446435 TCAATTTGTAGCCCAAGCCTC 58.554 47.619 0.00 0.00 41.25 4.70
2449 6058 1.948508 TTGCAAGTGCGACACCATC 59.051 52.632 0.00 0.00 45.83 3.51
2461 6070 2.892374 GACACCATCGATCACATCACA 58.108 47.619 0.00 0.00 0.00 3.58
2462 6071 2.862536 GACACCATCGATCACATCACAG 59.137 50.000 0.00 0.00 0.00 3.66
2463 6072 1.596260 CACCATCGATCACATCACAGC 59.404 52.381 0.00 0.00 0.00 4.40
2464 6073 1.207811 ACCATCGATCACATCACAGCA 59.792 47.619 0.00 0.00 0.00 4.41
2465 6074 1.596260 CCATCGATCACATCACAGCAC 59.404 52.381 0.00 0.00 0.00 4.40
2466 6075 2.273557 CATCGATCACATCACAGCACA 58.726 47.619 0.00 0.00 0.00 4.57
2467 6076 2.000429 TCGATCACATCACAGCACAG 58.000 50.000 0.00 0.00 0.00 3.66
2483 6092 2.519302 AGCACAGTGCCCCAACAC 60.519 61.111 22.41 0.00 46.52 3.32
2531 6141 9.254133 CACCACTTGAGAATATTAGTCATACAG 57.746 37.037 1.74 0.47 0.00 2.74
2532 6142 9.201989 ACCACTTGAGAATATTAGTCATACAGA 57.798 33.333 1.74 0.00 0.00 3.41
2556 6166 3.317711 ACACCGCATCAAATTGACAAAGA 59.682 39.130 0.00 0.00 0.00 2.52
2588 6198 3.505680 TGTTTTACAGCACAGCCCAATAG 59.494 43.478 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181487 CCACCGATGGGAAATGTTTCATC 60.181 47.826 0.00 3.31 43.04 2.92
1 2 2.760092 CCACCGATGGGAAATGTTTCAT 59.240 45.455 0.00 0.00 43.04 2.57
2 3 2.166829 CCACCGATGGGAAATGTTTCA 58.833 47.619 0.00 0.00 43.04 2.69
3 4 2.939460 CCACCGATGGGAAATGTTTC 57.061 50.000 0.00 0.00 43.04 2.78
4 5 3.440127 ATTCCACCGATGGGAAATGTTT 58.560 40.909 0.00 0.00 46.76 2.83
5 6 3.023832 GATTCCACCGATGGGAAATGTT 58.976 45.455 0.00 0.00 46.76 2.71
6 7 2.654863 GATTCCACCGATGGGAAATGT 58.345 47.619 0.00 0.00 46.76 2.71
7 8 1.603802 CGATTCCACCGATGGGAAATG 59.396 52.381 0.00 0.00 46.76 2.32
8 9 1.211949 ACGATTCCACCGATGGGAAAT 59.788 47.619 0.00 0.00 46.76 2.17
9 10 0.616371 ACGATTCCACCGATGGGAAA 59.384 50.000 0.00 0.00 46.76 3.13
13 14 0.178068 AAGGACGATTCCACCGATGG 59.822 55.000 0.00 0.00 45.72 3.51
14 15 2.024176 AAAGGACGATTCCACCGATG 57.976 50.000 0.00 0.00 45.72 3.84
15 16 2.781681 AAAAGGACGATTCCACCGAT 57.218 45.000 0.00 0.00 45.72 4.18
16 17 2.554370 AAAAAGGACGATTCCACCGA 57.446 45.000 0.00 0.00 45.72 4.69
44 45 6.524101 TTGACAAGCTCTGTTAAGGTTTTT 57.476 33.333 0.00 0.00 38.84 1.94
45 46 6.547510 AGATTGACAAGCTCTGTTAAGGTTTT 59.452 34.615 0.00 0.00 38.84 2.43
46 47 6.064717 AGATTGACAAGCTCTGTTAAGGTTT 58.935 36.000 0.00 0.00 38.84 3.27
47 48 5.625150 AGATTGACAAGCTCTGTTAAGGTT 58.375 37.500 0.00 0.00 38.84 3.50
48 49 5.234466 AGATTGACAAGCTCTGTTAAGGT 57.766 39.130 0.00 0.00 38.84 3.50
49 50 5.936956 AGAAGATTGACAAGCTCTGTTAAGG 59.063 40.000 6.39 0.00 38.84 2.69
50 51 7.360776 GGAAGAAGATTGACAAGCTCTGTTAAG 60.361 40.741 6.39 0.00 38.84 1.85
51 52 6.428159 GGAAGAAGATTGACAAGCTCTGTTAA 59.572 38.462 6.39 8.08 38.84 2.01
52 53 5.934625 GGAAGAAGATTGACAAGCTCTGTTA 59.065 40.000 6.39 0.00 38.84 2.41
53 54 4.759183 GGAAGAAGATTGACAAGCTCTGTT 59.241 41.667 6.39 2.58 38.84 3.16
54 55 4.322567 GGAAGAAGATTGACAAGCTCTGT 58.677 43.478 6.39 1.82 42.61 3.41
55 56 3.688673 GGGAAGAAGATTGACAAGCTCTG 59.311 47.826 6.39 0.00 0.00 3.35
56 57 3.328931 TGGGAAGAAGATTGACAAGCTCT 59.671 43.478 6.39 3.29 0.00 4.09
57 58 3.679389 TGGGAAGAAGATTGACAAGCTC 58.321 45.455 6.39 0.98 0.00 4.09
58 59 3.795688 TGGGAAGAAGATTGACAAGCT 57.204 42.857 0.00 0.00 0.00 3.74
59 60 3.057245 GGTTGGGAAGAAGATTGACAAGC 60.057 47.826 0.00 0.00 0.00 4.01
60 61 3.189287 CGGTTGGGAAGAAGATTGACAAG 59.811 47.826 0.00 0.00 0.00 3.16
61 62 3.146066 CGGTTGGGAAGAAGATTGACAA 58.854 45.455 0.00 0.00 0.00 3.18
62 63 2.370519 TCGGTTGGGAAGAAGATTGACA 59.629 45.455 0.00 0.00 0.00 3.58
63 64 3.003480 CTCGGTTGGGAAGAAGATTGAC 58.997 50.000 0.00 0.00 0.00 3.18
64 65 2.027192 CCTCGGTTGGGAAGAAGATTGA 60.027 50.000 0.00 0.00 0.00 2.57
65 66 2.027192 TCCTCGGTTGGGAAGAAGATTG 60.027 50.000 0.00 0.00 0.00 2.67
66 67 2.266279 TCCTCGGTTGGGAAGAAGATT 58.734 47.619 0.00 0.00 0.00 2.40
67 68 1.952621 TCCTCGGTTGGGAAGAAGAT 58.047 50.000 0.00 0.00 0.00 2.40
68 69 1.724545 TTCCTCGGTTGGGAAGAAGA 58.275 50.000 0.00 0.00 37.86 2.87
73 74 2.228480 CCCCTTCCTCGGTTGGGAA 61.228 63.158 14.41 0.00 42.11 3.97
74 75 2.609610 CCCCTTCCTCGGTTGGGA 60.610 66.667 14.41 0.00 42.11 4.37
75 76 3.728373 CCCCCTTCCTCGGTTGGG 61.728 72.222 8.38 8.38 39.37 4.12
76 77 2.933834 ACCCCCTTCCTCGGTTGG 60.934 66.667 0.00 0.00 0.00 3.77
77 78 2.185310 CTGACCCCCTTCCTCGGTTG 62.185 65.000 0.00 0.00 0.00 3.77
78 79 1.918800 CTGACCCCCTTCCTCGGTT 60.919 63.158 0.00 0.00 0.00 4.44
79 80 2.284699 CTGACCCCCTTCCTCGGT 60.285 66.667 0.00 0.00 0.00 4.69
80 81 1.918800 AACTGACCCCCTTCCTCGG 60.919 63.158 0.00 0.00 0.00 4.63
81 82 1.296715 CAACTGACCCCCTTCCTCG 59.703 63.158 0.00 0.00 0.00 4.63
82 83 1.002011 GCAACTGACCCCCTTCCTC 60.002 63.158 0.00 0.00 0.00 3.71
83 84 1.068352 AAGCAACTGACCCCCTTCCT 61.068 55.000 0.00 0.00 0.00 3.36
84 85 0.696501 TAAGCAACTGACCCCCTTCC 59.303 55.000 0.00 0.00 0.00 3.46
85 86 2.579410 TTAAGCAACTGACCCCCTTC 57.421 50.000 0.00 0.00 0.00 3.46
86 87 3.542969 AATTAAGCAACTGACCCCCTT 57.457 42.857 0.00 0.00 0.00 3.95
87 88 3.165071 CAAATTAAGCAACTGACCCCCT 58.835 45.455 0.00 0.00 0.00 4.79
88 89 2.897326 ACAAATTAAGCAACTGACCCCC 59.103 45.455 0.00 0.00 0.00 5.40
204 205 0.865111 CGTTCAATTCCACACGCTCA 59.135 50.000 0.00 0.00 0.00 4.26
271 277 1.585521 CGTCGACGGGGATTTCTCG 60.586 63.158 29.70 0.00 35.37 4.04
289 295 1.078848 AGAACACCTGATGAGCCGC 60.079 57.895 0.00 0.00 0.00 6.53
290 296 0.247460 TGAGAACACCTGATGAGCCG 59.753 55.000 0.00 0.00 0.00 5.52
473 483 2.095847 GGGTATTTCGCGCACGTGA 61.096 57.895 22.23 1.54 41.18 4.35
492 502 4.865905 TGCATATACACCCAGAAACCAAT 58.134 39.130 0.00 0.00 0.00 3.16
499 509 6.126968 CCATATGAGATGCATATACACCCAGA 60.127 42.308 3.65 0.00 46.03 3.86
512 522 6.409524 TCAATTTTTCCCCATATGAGATGC 57.590 37.500 3.65 0.00 0.00 3.91
672 4021 6.613271 AGGGTCAAGATAGTGTGAATAGTGAT 59.387 38.462 0.00 0.00 0.00 3.06
732 4096 8.356657 CCATTGTACTGGTAAAAGAAATTCACA 58.643 33.333 0.00 0.00 0.00 3.58
827 4194 8.499288 TTTGGTCTATGGGTGTATATGTATGA 57.501 34.615 0.00 0.00 0.00 2.15
832 4199 8.576442 GGAAATTTTGGTCTATGGGTGTATATG 58.424 37.037 0.00 0.00 0.00 1.78
833 4200 7.728532 GGGAAATTTTGGTCTATGGGTGTATAT 59.271 37.037 0.00 0.00 0.00 0.86
834 4201 7.064229 GGGAAATTTTGGTCTATGGGTGTATA 58.936 38.462 0.00 0.00 0.00 1.47
837 4204 4.093743 GGGAAATTTTGGTCTATGGGTGT 58.906 43.478 0.00 0.00 0.00 4.16
838 4205 3.450817 GGGGAAATTTTGGTCTATGGGTG 59.549 47.826 0.00 0.00 0.00 4.61
867 4241 2.358247 CACGGCACACCCTACCAC 60.358 66.667 0.00 0.00 0.00 4.16
868 4242 2.845317 ACACGGCACACCCTACCA 60.845 61.111 0.00 0.00 0.00 3.25
869 4243 2.358247 CACACGGCACACCCTACC 60.358 66.667 0.00 0.00 0.00 3.18
872 4246 3.475494 TCACACACGGCACACCCT 61.475 61.111 0.00 0.00 0.00 4.34
880 4254 1.844771 TAGTCGACGGTCACACACGG 61.845 60.000 10.46 0.00 0.00 4.94
961 4335 1.890041 TGACGAGGCGGTTGTTTGG 60.890 57.895 0.00 0.00 0.00 3.28
982 4370 0.676466 ATGGTGGTCGACGTACGGTA 60.676 55.000 21.06 0.89 42.82 4.02
987 4375 2.179767 CGCATGGTGGTCGACGTA 59.820 61.111 9.92 0.00 0.00 3.57
993 4381 3.127533 GGAGTGCGCATGGTGGTC 61.128 66.667 15.91 0.00 0.00 4.02
1005 4393 1.739562 GACAAGGCTCGCTGGAGTG 60.740 63.158 0.00 0.00 42.53 3.51
1467 4859 1.299850 CGAGTCGATAATGGCGGCA 60.300 57.895 16.34 16.34 35.50 5.69
1471 4863 3.123804 ACATTGACGAGTCGATAATGGC 58.876 45.455 30.41 12.23 37.69 4.40
1476 4868 2.617308 GGAGGACATTGACGAGTCGATA 59.383 50.000 21.50 4.33 35.63 2.92
1477 4869 1.405821 GGAGGACATTGACGAGTCGAT 59.594 52.381 21.50 3.12 35.63 3.59
1489 4881 1.000993 AGCAGGACGAGGAGGACAT 59.999 57.895 0.00 0.00 0.00 3.06
1585 4977 0.516439 GTGTCAGCAGAAGCAGAAGC 59.484 55.000 0.00 0.00 45.49 3.86
1633 5025 4.580995 ACTAGGATCGATGTTGTCTAGTGG 59.419 45.833 0.54 0.00 36.89 4.00
1677 5078 8.737168 AATTCATAGCTAACTGAATTGCACTA 57.263 30.769 24.60 0.70 45.59 2.74
1678 5079 7.636150 AATTCATAGCTAACTGAATTGCACT 57.364 32.000 24.60 8.95 45.59 4.40
1684 5085 9.664332 CTATAGCCAATTCATAGCTAACTGAAT 57.336 33.333 14.25 14.25 42.07 2.57
1685 5086 8.651389 ACTATAGCCAATTCATAGCTAACTGAA 58.349 33.333 11.25 11.25 42.07 3.02
1686 5087 8.090831 CACTATAGCCAATTCATAGCTAACTGA 58.909 37.037 0.00 0.00 42.07 3.41
1687 5088 8.090831 TCACTATAGCCAATTCATAGCTAACTG 58.909 37.037 0.00 0.00 42.07 3.16
1688 5089 8.195165 TCACTATAGCCAATTCATAGCTAACT 57.805 34.615 0.00 0.00 42.07 2.24
1689 5090 8.833231 TTCACTATAGCCAATTCATAGCTAAC 57.167 34.615 0.00 0.00 42.07 2.34
1690 5091 9.494271 CTTTCACTATAGCCAATTCATAGCTAA 57.506 33.333 0.00 0.00 42.07 3.09
1691 5092 8.870116 TCTTTCACTATAGCCAATTCATAGCTA 58.130 33.333 0.00 0.00 42.88 3.32
1692 5093 7.739825 TCTTTCACTATAGCCAATTCATAGCT 58.260 34.615 0.00 0.00 40.66 3.32
1693 5094 7.969536 TCTTTCACTATAGCCAATTCATAGC 57.030 36.000 0.00 0.00 0.00 2.97
1696 5097 9.466497 TTCTTTCTTTCACTATAGCCAATTCAT 57.534 29.630 0.00 0.00 0.00 2.57
1697 5098 8.862325 TTCTTTCTTTCACTATAGCCAATTCA 57.138 30.769 0.00 0.00 0.00 2.57
1707 5108 9.899226 GCACACTAATTTTCTTTCTTTCACTAT 57.101 29.630 0.00 0.00 0.00 2.12
1816 5347 2.828520 ACACTGGTCTGAGTGGTATCTG 59.171 50.000 0.00 0.00 46.56 2.90
1819 5350 5.394224 CGATTAACACTGGTCTGAGTGGTAT 60.394 44.000 0.00 0.00 43.94 2.73
1855 5387 1.413445 TGCCCGTAGTTGTACAACAGT 59.587 47.619 33.93 20.39 43.47 3.55
1857 5389 2.158928 AGTTGCCCGTAGTTGTACAACA 60.159 45.455 33.93 20.21 43.47 3.33
1858 5390 2.222445 CAGTTGCCCGTAGTTGTACAAC 59.778 50.000 27.72 27.72 41.45 3.32
1861 5393 2.334838 CTCAGTTGCCCGTAGTTGTAC 58.665 52.381 0.00 0.00 0.00 2.90
1863 5395 0.602905 GCTCAGTTGCCCGTAGTTGT 60.603 55.000 0.00 0.00 0.00 3.32
1864 5396 0.320771 AGCTCAGTTGCCCGTAGTTG 60.321 55.000 0.00 0.00 0.00 3.16
1867 5399 1.103803 TCTAGCTCAGTTGCCCGTAG 58.896 55.000 0.00 0.00 0.00 3.51
1868 5400 0.815734 GTCTAGCTCAGTTGCCCGTA 59.184 55.000 0.00 0.00 0.00 4.02
1869 5401 1.592223 GTCTAGCTCAGTTGCCCGT 59.408 57.895 0.00 0.00 0.00 5.28
1870 5402 1.153549 GGTCTAGCTCAGTTGCCCG 60.154 63.158 0.00 0.00 0.00 6.13
1871 5403 1.410882 CTAGGTCTAGCTCAGTTGCCC 59.589 57.143 0.00 0.00 0.00 5.36
1872 5404 2.104170 ACTAGGTCTAGCTCAGTTGCC 58.896 52.381 5.02 0.00 36.66 4.52
1890 5422 9.294614 GGTAGCAGTAGTATGTAACCTATTACT 57.705 37.037 0.00 0.00 41.24 2.24
1891 5423 9.294614 AGGTAGCAGTAGTATGTAACCTATTAC 57.705 37.037 0.00 0.00 41.07 1.89
1893 5425 7.450944 GGAGGTAGCAGTAGTATGTAACCTATT 59.549 40.741 0.00 0.00 37.48 1.73
1894 5426 6.947158 GGAGGTAGCAGTAGTATGTAACCTAT 59.053 42.308 0.00 0.00 37.48 2.57
1895 5427 6.302269 GGAGGTAGCAGTAGTATGTAACCTA 58.698 44.000 0.00 0.00 37.48 3.08
1896 5428 5.139001 GGAGGTAGCAGTAGTATGTAACCT 58.861 45.833 0.00 0.00 39.00 3.50
1897 5429 4.023365 CGGAGGTAGCAGTAGTATGTAACC 60.023 50.000 0.00 0.00 0.00 2.85
1898 5430 4.578105 ACGGAGGTAGCAGTAGTATGTAAC 59.422 45.833 0.00 0.00 0.00 2.50
1899 5431 4.785301 ACGGAGGTAGCAGTAGTATGTAA 58.215 43.478 0.00 0.00 0.00 2.41
1901 5433 3.212685 GACGGAGGTAGCAGTAGTATGT 58.787 50.000 0.00 0.00 0.00 2.29
1902 5434 2.553172 GGACGGAGGTAGCAGTAGTATG 59.447 54.545 0.00 0.00 0.00 2.39
1903 5435 2.174210 TGGACGGAGGTAGCAGTAGTAT 59.826 50.000 0.00 0.00 0.00 2.12
1904 5436 1.561076 TGGACGGAGGTAGCAGTAGTA 59.439 52.381 0.00 0.00 0.00 1.82
1905 5437 0.330604 TGGACGGAGGTAGCAGTAGT 59.669 55.000 0.00 0.00 0.00 2.73
1906 5438 1.025812 CTGGACGGAGGTAGCAGTAG 58.974 60.000 0.00 0.00 0.00 2.57
1908 5440 1.682684 CCTGGACGGAGGTAGCAGT 60.683 63.158 0.00 0.00 33.16 4.40
1909 5441 1.258445 AACCTGGACGGAGGTAGCAG 61.258 60.000 0.00 0.00 46.29 4.24
1912 5444 1.479730 GGTAAACCTGGACGGAGGTAG 59.520 57.143 0.00 0.00 46.29 3.18
1913 5445 1.560505 GGTAAACCTGGACGGAGGTA 58.439 55.000 0.00 0.00 46.29 3.08
1916 5448 4.904466 CGGTAAACCTGGACGGAG 57.096 61.111 0.00 0.00 36.31 4.63
1919 5451 1.079612 GGACCGGTAAACCTGGACG 60.080 63.158 7.34 0.00 34.97 4.79
1921 5453 2.285024 CGGGACCGGTAAACCTGGA 61.285 63.158 7.34 0.00 34.97 3.86
1922 5454 2.266689 CGGGACCGGTAAACCTGG 59.733 66.667 7.34 8.03 36.31 4.45
1934 5466 3.645268 AATGCAAGAGGGCCGGGAC 62.645 63.158 2.18 0.00 0.00 4.46
1935 5467 2.439553 AAAATGCAAGAGGGCCGGGA 62.440 55.000 2.18 0.00 0.00 5.14
1936 5468 1.984026 AAAATGCAAGAGGGCCGGG 60.984 57.895 2.18 0.00 0.00 5.73
1937 5469 1.216178 CAAAATGCAAGAGGGCCGG 59.784 57.895 0.00 0.00 0.00 6.13
1938 5470 0.171903 CTCAAAATGCAAGAGGGCCG 59.828 55.000 0.00 0.00 0.00 6.13
1940 5472 1.888512 TGACTCAAAATGCAAGAGGGC 59.111 47.619 11.75 5.79 33.76 5.19
1941 5473 4.038402 ACTTTGACTCAAAATGCAAGAGGG 59.962 41.667 5.72 0.00 32.75 4.30
1942 5474 5.192327 ACTTTGACTCAAAATGCAAGAGG 57.808 39.130 5.72 0.00 32.75 3.69
1943 5475 8.534778 GTTAAACTTTGACTCAAAATGCAAGAG 58.465 33.333 5.72 0.00 32.75 2.85
1944 5476 8.250332 AGTTAAACTTTGACTCAAAATGCAAGA 58.750 29.630 5.72 0.00 32.75 3.02
2096 5678 9.403583 CCCCTTAGTACTTATGCTAAATTTTGA 57.596 33.333 0.00 0.00 33.25 2.69
2098 5680 9.404848 GTCCCCTTAGTACTTATGCTAAATTTT 57.595 33.333 0.00 0.00 33.25 1.82
2100 5682 8.333226 AGTCCCCTTAGTACTTATGCTAAATT 57.667 34.615 0.00 0.00 33.25 1.82
2101 5683 7.932683 AGTCCCCTTAGTACTTATGCTAAAT 57.067 36.000 0.00 0.00 33.25 1.40
2102 5684 8.843308 TTAGTCCCCTTAGTACTTATGCTAAA 57.157 34.615 0.00 0.00 33.25 1.85
2105 5687 9.443365 TTTATTAGTCCCCTTAGTACTTATGCT 57.557 33.333 0.00 0.00 0.00 3.79
2106 5688 9.486497 GTTTATTAGTCCCCTTAGTACTTATGC 57.514 37.037 0.00 0.00 0.00 3.14
2107 5689 9.993454 GGTTTATTAGTCCCCTTAGTACTTATG 57.007 37.037 0.00 0.00 0.00 1.90
2110 5692 6.098838 CGGGTTTATTAGTCCCCTTAGTACTT 59.901 42.308 0.00 0.00 38.09 2.24
2111 5693 5.600069 CGGGTTTATTAGTCCCCTTAGTACT 59.400 44.000 0.00 0.00 38.09 2.73
2112 5694 5.221521 CCGGGTTTATTAGTCCCCTTAGTAC 60.222 48.000 0.00 0.00 38.09 2.73
2113 5695 4.901250 CCGGGTTTATTAGTCCCCTTAGTA 59.099 45.833 0.00 0.00 38.09 1.82
2115 5697 3.969312 TCCGGGTTTATTAGTCCCCTTAG 59.031 47.826 0.00 0.00 38.09 2.18
2116 5698 3.711190 GTCCGGGTTTATTAGTCCCCTTA 59.289 47.826 0.00 0.00 38.09 2.69
2117 5699 2.507058 GTCCGGGTTTATTAGTCCCCTT 59.493 50.000 0.00 0.00 38.09 3.95
2118 5700 2.121948 GTCCGGGTTTATTAGTCCCCT 58.878 52.381 0.00 0.00 38.09 4.79
2119 5701 1.839354 TGTCCGGGTTTATTAGTCCCC 59.161 52.381 0.00 0.00 38.09 4.81
2120 5702 2.767960 TCTGTCCGGGTTTATTAGTCCC 59.232 50.000 0.00 0.00 37.98 4.46
2121 5703 4.684484 ATCTGTCCGGGTTTATTAGTCC 57.316 45.455 0.00 0.00 0.00 3.85
2122 5704 8.120140 AGTATATCTGTCCGGGTTTATTAGTC 57.880 38.462 0.00 0.00 0.00 2.59
2123 5705 9.240734 CTAGTATATCTGTCCGGGTTTATTAGT 57.759 37.037 0.00 0.00 0.00 2.24
2124 5706 9.240734 ACTAGTATATCTGTCCGGGTTTATTAG 57.759 37.037 0.00 0.00 0.00 1.73
2126 5708 9.592196 TTACTAGTATATCTGTCCGGGTTTATT 57.408 33.333 0.00 0.00 0.00 1.40
2127 5709 9.765295 ATTACTAGTATATCTGTCCGGGTTTAT 57.235 33.333 0.00 0.00 0.00 1.40
2128 5710 9.592196 AATTACTAGTATATCTGTCCGGGTTTA 57.408 33.333 0.00 0.00 0.00 2.01
2129 5711 8.488308 AATTACTAGTATATCTGTCCGGGTTT 57.512 34.615 0.00 0.00 0.00 3.27
2131 5713 9.186837 CATAATTACTAGTATATCTGTCCGGGT 57.813 37.037 0.00 0.00 0.00 5.28
2132 5714 8.136165 GCATAATTACTAGTATATCTGTCCGGG 58.864 40.741 0.00 0.00 0.00 5.73
2133 5715 8.683615 TGCATAATTACTAGTATATCTGTCCGG 58.316 37.037 2.79 0.00 0.00 5.14
2146 5728 6.223852 ACCGGAGAACATGCATAATTACTAG 58.776 40.000 9.46 0.00 0.00 2.57
2147 5729 6.169557 ACCGGAGAACATGCATAATTACTA 57.830 37.500 9.46 0.00 0.00 1.82
2154 5736 3.342377 TTTGACCGGAGAACATGCATA 57.658 42.857 9.46 0.00 0.00 3.14
2196 5781 5.065731 GCGTCTCATCTCTCCATTCAAAAAT 59.934 40.000 0.00 0.00 0.00 1.82
2202 5787 2.879002 TGCGTCTCATCTCTCCATTC 57.121 50.000 0.00 0.00 0.00 2.67
2444 6053 1.207811 TGCTGTGATGTGATCGATGGT 59.792 47.619 0.54 0.00 0.00 3.55
2449 6058 0.372679 GCTGTGCTGTGATGTGATCG 59.627 55.000 0.00 0.00 0.00 3.69
2450 6059 1.129998 GTGCTGTGCTGTGATGTGATC 59.870 52.381 0.00 0.00 0.00 2.92
2451 6060 1.162698 GTGCTGTGCTGTGATGTGAT 58.837 50.000 0.00 0.00 0.00 3.06
2452 6061 0.179051 TGTGCTGTGCTGTGATGTGA 60.179 50.000 0.00 0.00 0.00 3.58
2453 6062 0.237498 CTGTGCTGTGCTGTGATGTG 59.763 55.000 0.00 0.00 0.00 3.21
2454 6063 0.179037 ACTGTGCTGTGCTGTGATGT 60.179 50.000 0.00 0.00 0.00 3.06
2455 6064 0.237498 CACTGTGCTGTGCTGTGATG 59.763 55.000 0.00 0.00 31.28 3.07
2456 6065 2.625375 CACTGTGCTGTGCTGTGAT 58.375 52.632 0.00 0.00 31.28 3.06
2457 6066 4.129757 CACTGTGCTGTGCTGTGA 57.870 55.556 0.00 0.00 31.28 3.58
2463 6072 2.519063 TTGGGGCACTGTGCTGTG 60.519 61.111 29.54 5.08 44.28 3.66
2464 6073 2.519302 GTTGGGGCACTGTGCTGT 60.519 61.111 29.54 0.00 44.28 4.40
2465 6074 2.519063 TGTTGGGGCACTGTGCTG 60.519 61.111 29.54 0.00 44.28 4.41
2466 6075 2.519302 GTGTTGGGGCACTGTGCT 60.519 61.111 29.54 0.00 44.28 4.40
2467 6076 3.605664 GGTGTTGGGGCACTGTGC 61.606 66.667 24.02 24.02 44.08 4.57
2477 6086 4.366684 GGGGCTGGGAGGTGTTGG 62.367 72.222 0.00 0.00 0.00 3.77
2523 6133 3.977427 TGATGCGGTGTATCTGTATGAC 58.023 45.455 0.00 0.00 0.00 3.06
2531 6141 4.614555 TGTCAATTTGATGCGGTGTATC 57.385 40.909 1.78 0.00 0.00 2.24
2532 6142 5.182950 TCTTTGTCAATTTGATGCGGTGTAT 59.817 36.000 1.78 0.00 0.00 2.29
2533 6143 4.517075 TCTTTGTCAATTTGATGCGGTGTA 59.483 37.500 1.78 0.00 0.00 2.90
2534 6144 3.317711 TCTTTGTCAATTTGATGCGGTGT 59.682 39.130 1.78 0.00 0.00 4.16
2535 6145 3.899734 TCTTTGTCAATTTGATGCGGTG 58.100 40.909 1.78 0.00 0.00 4.94
2536 6146 4.022068 ACATCTTTGTCAATTTGATGCGGT 60.022 37.500 16.76 0.00 38.33 5.68
2556 6166 6.475402 GCTGTGCTGTAAAACAAAAGTTACAT 59.525 34.615 0.00 0.00 39.00 2.29


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

AutoCloner maintained by Alex Coulton.