Multiple sequence alignment - TraesCS2B01G226200

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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 TraesCS2B01G226200 chr2B 100.000 4082 0 0 1 4082 216941157 216945238 0.000000e+00 7539
1 TraesCS2B01G226200 chr2B 97.561 328 8 0 3755 4082 248154825 248154498 2.750000e-156 562
2 TraesCS2B01G226200 chr2D 95.699 3767 115 21 1 3755 159851505 159855236 0.000000e+00 6015
3 TraesCS2B01G226200 chr2A 95.548 3639 142 11 125 3755 171079089 171082715 0.000000e+00 5805
4 TraesCS2B01G226200 chr2A 97.006 334 10 0 3749 4082 93984590 93984923 2.750000e-156 562
5 TraesCS2B01G226200 chr2A 91.406 256 18 3 46 300 171078921 171079173 8.400000e-92 348
6 TraesCS2B01G226200 chrUn 100.000 391 0 0 1698 2088 479827048 479827438 0.000000e+00 723
7 TraesCS2B01G226200 chrUn 97.256 328 8 1 3755 4082 332730082 332729756 4.610000e-154 555
8 TraesCS2B01G226200 chr6B 98.788 330 4 0 3753 4082 714486516 714486845 4.550000e-164 588
9 TraesCS2B01G226200 chr3B 97.879 330 7 0 3753 4082 788949407 788949078 4.580000e-159 571
10 TraesCS2B01G226200 chr1B 97.879 330 7 0 3753 4082 431181904 431182233 4.580000e-159 571
11 TraesCS2B01G226200 chr7A 97.866 328 7 0 3755 4082 260315034 260315361 5.920000e-158 568
12 TraesCS2B01G226200 chr7A 97.866 328 7 0 3755 4082 672322222 672321895 5.920000e-158 568
13 TraesCS2B01G226200 chr4A 96.165 339 12 1 3744 4082 625186199 625185862 1.660000e-153 553


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 TraesCS2B01G226200 chr2B 216941157 216945238 4081 False 7539.0 7539 100.000 1 4082 1 chr2B.!!$F1 4081
1 TraesCS2B01G226200 chr2D 159851505 159855236 3731 False 6015.0 6015 95.699 1 3755 1 chr2D.!!$F1 3754
2 TraesCS2B01G226200 chr2A 171078921 171082715 3794 False 3076.5 5805 93.477 46 3755 2 chr2A.!!$F2 3709

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
469 559 0.394352 GGCCGAATGTCTGAACCCAT 60.394 55.000 0.00 0.0 0.00 4.00 F
1629 1728 0.393132 GTTACCAGGCCAGCTCCTTC 60.393 60.000 5.01 0.0 33.25 3.46 F
2585 2684 1.153524 TCACCACTGGCAAGGCAAT 59.846 52.632 5.61 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2250 0.252558 TCCTTCCCTGTGTAGACCCC 60.253 60.0 0.0 0.0 0.00 4.95 R
2781 2880 0.677288 ACAGTCCGACGACCATCAAA 59.323 50.0 0.0 0.0 40.12 2.69 R
3755 3855 0.040246 GGCCGCTACATAGACTCGTC 60.040 60.0 0.0 0.0 0.00 4.20 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
120 121 6.639686 CACTTGATGATTTTTGTCCTGTGAAG 59.360 38.462 0.00 0.00 0.00 3.02
189 192 1.552337 AGTGTGCCTGTGTCCTCTATG 59.448 52.381 0.00 0.00 0.00 2.23
205 208 7.933577 TGTCCTCTATGCTAAGATTTGTATTGG 59.066 37.037 0.00 0.00 0.00 3.16
248 336 6.726035 ACGTGTGATAATTTTGTTTGTTCG 57.274 33.333 0.00 0.00 0.00 3.95
274 362 2.621763 CAGTGTGCCTGTGTTCTCC 58.378 57.895 0.00 0.00 36.37 3.71
281 369 3.580895 TGTGCCTGTGTTCTCCATACTAA 59.419 43.478 0.00 0.00 0.00 2.24
311 399 2.673368 CTGAGCATTCGGGTTTACTGAC 59.327 50.000 0.00 0.00 33.15 3.51
312 400 2.301870 TGAGCATTCGGGTTTACTGACT 59.698 45.455 0.00 0.00 33.15 3.41
410 500 5.536554 AACAACACGTCATGATCAAGATC 57.463 39.130 3.62 3.12 38.29 2.75
436 526 1.997606 GGGTAAACGTCATGTCGAAGG 59.002 52.381 19.02 0.00 34.70 3.46
439 529 2.536761 AAACGTCATGTCGAAGGGAA 57.463 45.000 19.02 0.00 34.70 3.97
469 559 0.394352 GGCCGAATGTCTGAACCCAT 60.394 55.000 0.00 0.00 0.00 4.00
533 627 1.466167 CCTGTTCCAATCTGCTGAACG 59.534 52.381 0.00 0.00 40.92 3.95
568 662 1.066858 GCTTCCTGTCTTCGACCATCA 60.067 52.381 0.00 0.00 0.00 3.07
703 799 4.245660 CTGTTGGAAAGCTCGACTCATTA 58.754 43.478 0.00 0.00 0.00 1.90
710 806 6.037500 TGGAAAGCTCGACTCATTATTCATTG 59.962 38.462 0.00 0.00 0.00 2.82
715 811 7.246311 AGCTCGACTCATTATTCATTGTTTTG 58.754 34.615 0.00 0.00 0.00 2.44
832 929 0.727398 GCAGTATGACAAACCCGAGC 59.273 55.000 0.00 0.00 39.69 5.03
845 944 3.730761 CGAGCACTGCAAGGCCAC 61.731 66.667 5.01 0.00 39.30 5.01
847 946 4.208403 AGCACTGCAAGGCCACCA 62.208 61.111 5.01 0.00 39.30 4.17
849 948 2.730094 CACTGCAAGGCCACCAAC 59.270 61.111 5.01 0.00 39.30 3.77
850 949 2.906897 ACTGCAAGGCCACCAACG 60.907 61.111 5.01 0.00 39.30 4.10
866 965 3.142951 CCAACGGTTGACCAAGTTGATA 58.857 45.455 21.88 0.00 44.64 2.15
869 968 2.370849 ACGGTTGACCAAGTTGATACCT 59.629 45.455 3.87 0.00 35.14 3.08
872 971 4.652822 GGTTGACCAAGTTGATACCTTCT 58.347 43.478 3.87 0.00 35.64 2.85
876 975 4.518970 TGACCAAGTTGATACCTTCTTTGC 59.481 41.667 3.87 0.00 0.00 3.68
880 979 6.206829 ACCAAGTTGATACCTTCTTTGCTTAC 59.793 38.462 3.87 0.00 0.00 2.34
883 982 7.440523 AGTTGATACCTTCTTTGCTTACTTG 57.559 36.000 0.00 0.00 0.00 3.16
954 1053 3.006967 TGTTCCTCTTCTTCCTTCCTTCG 59.993 47.826 0.00 0.00 0.00 3.79
1152 1251 2.681976 CGCAATCAAGTTCCAGGAGGAT 60.682 50.000 0.00 0.00 45.26 3.24
1234 1333 1.355916 GTAGGCCGAGCAGTCTACG 59.644 63.158 0.00 0.00 0.00 3.51
1248 1347 1.299468 CTACGCCGATCCAGTGCTC 60.299 63.158 0.00 0.00 0.00 4.26
1333 1432 1.405821 CCACAAACTTAACCGCAACCA 59.594 47.619 0.00 0.00 0.00 3.67
1336 1435 2.492484 ACAAACTTAACCGCAACCAACA 59.508 40.909 0.00 0.00 0.00 3.33
1492 1591 3.064207 GTTGAGTTCGACAGCCACAATA 58.936 45.455 0.00 0.00 0.00 1.90
1540 1639 1.233019 GGGCATCGACATCCATTCAG 58.767 55.000 0.00 0.00 0.00 3.02
1629 1728 0.393132 GTTACCAGGCCAGCTCCTTC 60.393 60.000 5.01 0.00 33.25 3.46
2585 2684 1.153524 TCACCACTGGCAAGGCAAT 59.846 52.632 5.61 0.00 0.00 3.56
2610 2709 7.164122 TCAAAGAATCTGATGTCTACAGCTTT 58.836 34.615 0.00 0.00 35.61 3.51
2655 2754 1.290955 CGGAAGGCGACCAGTTGTA 59.709 57.895 0.00 0.00 0.00 2.41
2755 2854 2.437449 ACAGCAGGCTTGATGGCA 59.563 55.556 18.80 0.00 44.84 4.92
2778 2877 2.879002 TTGAAGATAGAGAGGCAGCG 57.121 50.000 0.00 0.00 0.00 5.18
2781 2880 1.407258 GAAGATAGAGAGGCAGCGTGT 59.593 52.381 0.00 0.00 0.00 4.49
2790 2889 1.210155 GGCAGCGTGTTTGATGGTC 59.790 57.895 0.00 0.00 0.00 4.02
2799 2898 1.068474 GTTTGATGGTCGTCGGACTG 58.932 55.000 6.57 0.31 42.97 3.51
3061 3160 1.407656 TTCACCTCCTTCTGTGCGGT 61.408 55.000 0.00 0.00 32.51 5.68
3113 3212 7.912250 GCAGTTCCTTTCTATATGTTCAACATG 59.088 37.037 13.65 0.00 39.53 3.21
3204 3303 5.435686 TGTTATTAACTCTGGCTGGATGT 57.564 39.130 7.99 0.00 0.00 3.06
3267 3366 4.571176 GGCTACCTGTAGAACATAAGCAAC 59.429 45.833 8.48 0.00 35.21 4.17
3328 3427 7.350110 ACAGTTGTTGTCTTGTTCATTTTTG 57.650 32.000 0.00 0.00 33.87 2.44
3338 3437 6.311200 GTCTTGTTCATTTTTGTTCAGCAAGT 59.689 34.615 0.00 0.00 38.47 3.16
3339 3438 6.873076 TCTTGTTCATTTTTGTTCAGCAAGTT 59.127 30.769 0.00 0.00 38.47 2.66
3365 3464 6.825284 TTGCGCATTTGTATTTGGATATTG 57.175 33.333 12.75 0.00 0.00 1.90
3369 3468 6.073657 GCGCATTTGTATTTGGATATTGCATT 60.074 34.615 0.30 0.00 0.00 3.56
3464 3564 5.464057 CGTAGATACAGTGAACAAACACCAA 59.536 40.000 0.00 0.00 41.12 3.67
3760 3860 9.915629 AATAGTAGCTATAGAATTTTGGACGAG 57.084 33.333 3.21 0.00 0.00 4.18
3761 3861 7.349412 AGTAGCTATAGAATTTTGGACGAGT 57.651 36.000 3.21 0.00 0.00 4.18
3762 3862 7.427214 AGTAGCTATAGAATTTTGGACGAGTC 58.573 38.462 3.21 0.00 0.00 3.36
3763 3863 6.472686 AGCTATAGAATTTTGGACGAGTCT 57.527 37.500 3.21 0.00 0.00 3.24
3764 3864 7.584122 AGCTATAGAATTTTGGACGAGTCTA 57.416 36.000 3.21 0.00 0.00 2.59
3765 3865 8.184304 AGCTATAGAATTTTGGACGAGTCTAT 57.816 34.615 3.21 0.00 33.86 1.98
3766 3866 8.085296 AGCTATAGAATTTTGGACGAGTCTATG 58.915 37.037 3.21 0.00 32.17 2.23
3767 3867 7.868415 GCTATAGAATTTTGGACGAGTCTATGT 59.132 37.037 3.21 0.00 32.17 2.29
3770 3870 6.043411 AGAATTTTGGACGAGTCTATGTAGC 58.957 40.000 3.09 0.00 0.00 3.58
3771 3871 3.416119 TTTGGACGAGTCTATGTAGCG 57.584 47.619 3.09 0.00 0.00 4.26
3772 3872 1.306148 TGGACGAGTCTATGTAGCGG 58.694 55.000 3.09 0.00 0.00 5.52
3773 3873 0.040246 GGACGAGTCTATGTAGCGGC 60.040 60.000 3.09 0.00 0.00 6.53
3774 3874 0.040246 GACGAGTCTATGTAGCGGCC 60.040 60.000 0.00 0.00 0.00 6.13
3775 3875 1.082038 CGAGTCTATGTAGCGGCCG 60.082 63.158 24.05 24.05 0.00 6.13
3776 3876 1.286260 GAGTCTATGTAGCGGCCGG 59.714 63.158 29.38 8.29 0.00 6.13
3777 3877 2.355956 GTCTATGTAGCGGCCGGC 60.356 66.667 29.38 21.18 44.05 6.13
3812 3912 2.516225 GAGCGGCCGGCCTAAAAT 60.516 61.111 41.01 22.65 45.17 1.82
3813 3913 1.227734 GAGCGGCCGGCCTAAAATA 60.228 57.895 41.01 0.00 45.17 1.40
3814 3914 1.227853 AGCGGCCGGCCTAAAATAG 60.228 57.895 41.01 25.35 45.17 1.73
3815 3915 1.227734 GCGGCCGGCCTAAAATAGA 60.228 57.895 41.01 0.00 34.80 1.98
3816 3916 0.816421 GCGGCCGGCCTAAAATAGAA 60.816 55.000 41.01 0.00 34.80 2.10
3817 3917 1.670791 CGGCCGGCCTAAAATAGAAA 58.329 50.000 41.01 0.00 0.00 2.52
3818 3918 2.227194 CGGCCGGCCTAAAATAGAAAT 58.773 47.619 41.01 0.00 0.00 2.17
3819 3919 2.621526 CGGCCGGCCTAAAATAGAAATT 59.378 45.455 41.01 0.00 0.00 1.82
3820 3920 3.304458 CGGCCGGCCTAAAATAGAAATTC 60.304 47.826 41.01 11.00 0.00 2.17
3821 3921 3.889538 GGCCGGCCTAAAATAGAAATTCT 59.110 43.478 38.76 0.00 0.00 2.40
3822 3922 4.341235 GGCCGGCCTAAAATAGAAATTCTT 59.659 41.667 38.76 0.00 0.00 2.52
3823 3923 5.163447 GGCCGGCCTAAAATAGAAATTCTTT 60.163 40.000 38.76 0.00 0.00 2.52
3824 3924 6.338146 GCCGGCCTAAAATAGAAATTCTTTT 58.662 36.000 18.11 0.00 0.00 2.27
3825 3925 7.417003 GGCCGGCCTAAAATAGAAATTCTTTTA 60.417 37.037 38.76 0.53 0.00 1.52
3826 3926 8.141909 GCCGGCCTAAAATAGAAATTCTTTTAT 58.858 33.333 18.11 0.00 0.00 1.40
3827 3927 9.678941 CCGGCCTAAAATAGAAATTCTTTTATC 57.321 33.333 0.00 0.00 0.00 1.75
3828 3928 9.678941 CGGCCTAAAATAGAAATTCTTTTATCC 57.321 33.333 0.00 5.12 0.00 2.59
3829 3929 9.678941 GGCCTAAAATAGAAATTCTTTTATCCG 57.321 33.333 0.00 0.00 0.00 4.18
3830 3930 9.181805 GCCTAAAATAGAAATTCTTTTATCCGC 57.818 33.333 0.00 0.89 0.00 5.54
3834 3934 9.952188 AAAATAGAAATTCTTTTATCCGCTAGC 57.048 29.630 4.06 4.06 0.00 3.42
3835 3935 5.659048 AGAAATTCTTTTATCCGCTAGCG 57.341 39.130 29.93 29.93 39.44 4.26
3836 3936 5.116882 AGAAATTCTTTTATCCGCTAGCGT 58.883 37.500 33.18 19.86 37.81 5.07
3837 3937 5.234543 AGAAATTCTTTTATCCGCTAGCGTC 59.765 40.000 33.18 19.50 37.81 5.19
3838 3938 3.795623 TTCTTTTATCCGCTAGCGTCT 57.204 42.857 33.18 22.33 37.81 4.18
3839 3939 3.079960 TCTTTTATCCGCTAGCGTCTG 57.920 47.619 33.18 19.61 37.81 3.51
3840 3940 1.523095 CTTTTATCCGCTAGCGTCTGC 59.477 52.381 33.18 0.00 43.24 4.26
3851 3951 2.587574 GCGTCTGCTCTGCATAGAC 58.412 57.895 2.78 6.85 38.13 2.59
3852 3952 0.179127 GCGTCTGCTCTGCATAGACA 60.179 55.000 15.97 8.07 38.13 3.41
3853 3953 1.537776 GCGTCTGCTCTGCATAGACAT 60.538 52.381 15.97 0.00 38.13 3.06
3854 3954 2.287849 GCGTCTGCTCTGCATAGACATA 60.288 50.000 15.97 1.50 38.13 2.29
3855 3955 3.304257 CGTCTGCTCTGCATAGACATAC 58.696 50.000 15.97 9.81 38.13 2.39
3856 3956 3.243201 CGTCTGCTCTGCATAGACATACA 60.243 47.826 15.97 0.67 38.13 2.29
3857 3957 4.558296 CGTCTGCTCTGCATAGACATACAT 60.558 45.833 15.97 0.00 38.13 2.29
3858 3958 4.685165 GTCTGCTCTGCATAGACATACATG 59.315 45.833 2.78 0.00 38.13 3.21
3859 3959 4.343239 TCTGCTCTGCATAGACATACATGT 59.657 41.667 2.69 2.69 40.14 3.21
3860 3960 4.374399 TGCTCTGCATAGACATACATGTG 58.626 43.478 9.11 0.00 35.67 3.21
3861 3961 4.141869 TGCTCTGCATAGACATACATGTGT 60.142 41.667 9.11 0.00 35.67 3.72
3862 3962 4.210746 GCTCTGCATAGACATACATGTGTG 59.789 45.833 19.81 19.81 41.95 3.82
3863 3963 5.343307 TCTGCATAGACATACATGTGTGT 57.657 39.130 26.02 26.02 41.95 3.72
3864 3964 6.463995 TCTGCATAGACATACATGTGTGTA 57.536 37.500 25.81 13.59 44.43 2.90
3865 3965 6.872920 TCTGCATAGACATACATGTGTGTAA 58.127 36.000 25.81 17.83 43.60 2.41
3866 3966 7.500141 TCTGCATAGACATACATGTGTGTAAT 58.500 34.615 25.81 19.08 43.60 1.89
3867 3967 7.986889 TCTGCATAGACATACATGTGTGTAATT 59.013 33.333 25.81 16.98 43.60 1.40
3868 3968 8.504812 TGCATAGACATACATGTGTGTAATTT 57.495 30.769 25.81 14.87 43.60 1.82
3869 3969 8.955388 TGCATAGACATACATGTGTGTAATTTT 58.045 29.630 25.81 12.79 43.60 1.82
3870 3970 9.787532 GCATAGACATACATGTGTGTAATTTTT 57.212 29.630 25.81 11.32 43.60 1.94
3874 3974 8.296713 AGACATACATGTGTGTAATTTTTGTCC 58.703 33.333 25.81 11.00 41.90 4.02
3875 3975 7.081349 ACATACATGTGTGTAATTTTTGTCCG 58.919 34.615 24.77 0.00 43.60 4.79
3876 3976 4.295051 ACATGTGTGTAATTTTTGTCCGC 58.705 39.130 0.00 0.00 36.63 5.54
3877 3977 4.037446 ACATGTGTGTAATTTTTGTCCGCT 59.963 37.500 0.00 0.00 36.63 5.52
3878 3978 5.239744 ACATGTGTGTAATTTTTGTCCGCTA 59.760 36.000 0.00 0.00 36.63 4.26
3879 3979 5.351233 TGTGTGTAATTTTTGTCCGCTAG 57.649 39.130 0.00 0.00 0.00 3.42
3880 3980 4.156182 GTGTGTAATTTTTGTCCGCTAGC 58.844 43.478 4.06 4.06 0.00 3.42
3881 3981 3.120477 TGTGTAATTTTTGTCCGCTAGCG 60.120 43.478 29.93 29.93 39.44 4.26
3882 3982 2.159626 TGTAATTTTTGTCCGCTAGCGC 60.160 45.455 31.35 18.99 38.24 5.92
3883 3983 0.878416 AATTTTTGTCCGCTAGCGCA 59.122 45.000 31.35 21.45 38.24 6.09
3884 3984 1.094785 ATTTTTGTCCGCTAGCGCAT 58.905 45.000 31.35 7.15 38.24 4.73
3885 3985 0.167908 TTTTTGTCCGCTAGCGCATG 59.832 50.000 31.35 18.02 38.24 4.06
3886 3986 0.953471 TTTTGTCCGCTAGCGCATGT 60.953 50.000 31.35 0.00 38.24 3.21
3887 3987 0.108567 TTTGTCCGCTAGCGCATGTA 60.109 50.000 31.35 12.98 38.24 2.29
3888 3988 0.104120 TTGTCCGCTAGCGCATGTAT 59.896 50.000 31.35 0.00 38.24 2.29
3889 3989 0.318699 TGTCCGCTAGCGCATGTATC 60.319 55.000 31.35 14.60 38.24 2.24
3890 3990 0.039074 GTCCGCTAGCGCATGTATCT 60.039 55.000 31.35 0.00 38.24 1.98
3891 3991 0.673985 TCCGCTAGCGCATGTATCTT 59.326 50.000 31.35 0.00 38.24 2.40
3892 3992 1.068588 TCCGCTAGCGCATGTATCTTT 59.931 47.619 31.35 0.00 38.24 2.52
3893 3993 1.867233 CCGCTAGCGCATGTATCTTTT 59.133 47.619 31.35 0.00 38.24 2.27
3894 3994 3.057019 CCGCTAGCGCATGTATCTTTTA 58.943 45.455 31.35 0.00 38.24 1.52
3895 3995 3.121944 CCGCTAGCGCATGTATCTTTTAG 59.878 47.826 31.35 8.68 38.24 1.85
3896 3996 3.422343 CGCTAGCGCATGTATCTTTTAGC 60.422 47.826 26.07 9.05 35.30 3.09
3897 3997 3.494626 GCTAGCGCATGTATCTTTTAGCA 59.505 43.478 11.47 0.00 34.09 3.49
3898 3998 4.153117 GCTAGCGCATGTATCTTTTAGCAT 59.847 41.667 11.47 0.00 34.09 3.79
3899 3999 5.334414 GCTAGCGCATGTATCTTTTAGCATT 60.334 40.000 11.47 0.00 34.09 3.56
3900 4000 5.505173 AGCGCATGTATCTTTTAGCATTT 57.495 34.783 11.47 0.00 0.00 2.32
3901 4001 6.618287 AGCGCATGTATCTTTTAGCATTTA 57.382 33.333 11.47 0.00 0.00 1.40
3902 4002 7.026631 AGCGCATGTATCTTTTAGCATTTAA 57.973 32.000 11.47 0.00 0.00 1.52
3903 4003 7.651808 AGCGCATGTATCTTTTAGCATTTAAT 58.348 30.769 11.47 0.00 0.00 1.40
3904 4004 8.783093 AGCGCATGTATCTTTTAGCATTTAATA 58.217 29.630 11.47 0.00 0.00 0.98
3905 4005 8.840867 GCGCATGTATCTTTTAGCATTTAATAC 58.159 33.333 0.30 0.00 0.00 1.89
3906 4006 9.877137 CGCATGTATCTTTTAGCATTTAATACA 57.123 29.630 0.00 0.00 33.94 2.29
3916 4016 9.729023 TTTTAGCATTTAATACATTCACATCGG 57.271 29.630 0.00 0.00 0.00 4.18
3917 4017 6.942532 AGCATTTAATACATTCACATCGGT 57.057 33.333 0.00 0.00 0.00 4.69
3918 4018 6.959361 AGCATTTAATACATTCACATCGGTC 58.041 36.000 0.00 0.00 0.00 4.79
3919 4019 6.542005 AGCATTTAATACATTCACATCGGTCA 59.458 34.615 0.00 0.00 0.00 4.02
3920 4020 6.632834 GCATTTAATACATTCACATCGGTCAC 59.367 38.462 0.00 0.00 0.00 3.67
3921 4021 7.678454 GCATTTAATACATTCACATCGGTCACA 60.678 37.037 0.00 0.00 0.00 3.58
3922 4022 7.674471 TTTAATACATTCACATCGGTCACAA 57.326 32.000 0.00 0.00 0.00 3.33
3923 4023 7.857734 TTAATACATTCACATCGGTCACAAT 57.142 32.000 0.00 0.00 0.00 2.71
3924 4024 5.991328 ATACATTCACATCGGTCACAATC 57.009 39.130 0.00 0.00 0.00 2.67
3925 4025 3.673902 ACATTCACATCGGTCACAATCA 58.326 40.909 0.00 0.00 0.00 2.57
3926 4026 3.686241 ACATTCACATCGGTCACAATCAG 59.314 43.478 0.00 0.00 0.00 2.90
3927 4027 3.401033 TTCACATCGGTCACAATCAGT 57.599 42.857 0.00 0.00 0.00 3.41
3928 4028 3.401033 TCACATCGGTCACAATCAGTT 57.599 42.857 0.00 0.00 0.00 3.16
3929 4029 3.066380 TCACATCGGTCACAATCAGTTG 58.934 45.455 0.00 0.00 41.20 3.16
3930 4030 2.160219 CACATCGGTCACAATCAGTTGG 59.840 50.000 0.00 0.00 39.70 3.77
3931 4031 2.038426 ACATCGGTCACAATCAGTTGGA 59.962 45.455 0.00 0.00 39.70 3.53
3932 4032 2.920724 TCGGTCACAATCAGTTGGAA 57.079 45.000 0.00 0.00 39.70 3.53
3933 4033 3.201353 TCGGTCACAATCAGTTGGAAA 57.799 42.857 0.00 0.00 39.70 3.13
3934 4034 3.546724 TCGGTCACAATCAGTTGGAAAA 58.453 40.909 0.00 0.00 39.70 2.29
3935 4035 3.948473 TCGGTCACAATCAGTTGGAAAAA 59.052 39.130 0.00 0.00 39.70 1.94
3957 4057 8.836268 AAAAACAGATCACATATGCATTTGTT 57.164 26.923 18.66 14.08 29.80 2.83
3958 4058 8.836268 AAAACAGATCACATATGCATTTGTTT 57.164 26.923 18.66 20.48 35.12 2.83
3959 4059 8.470040 AAACAGATCACATATGCATTTGTTTC 57.530 30.769 18.66 17.15 32.07 2.78
3960 4060 6.260377 ACAGATCACATATGCATTTGTTTCG 58.740 36.000 18.66 15.27 0.00 3.46
3961 4061 5.684184 CAGATCACATATGCATTTGTTTCGG 59.316 40.000 18.66 14.74 0.00 4.30
3962 4062 5.357878 AGATCACATATGCATTTGTTTCGGT 59.642 36.000 18.66 5.90 0.00 4.69
3963 4063 5.384063 TCACATATGCATTTGTTTCGGTT 57.616 34.783 18.66 0.00 0.00 4.44
3964 4064 5.777802 TCACATATGCATTTGTTTCGGTTT 58.222 33.333 18.66 0.00 0.00 3.27
3965 4065 6.219473 TCACATATGCATTTGTTTCGGTTTT 58.781 32.000 18.66 0.00 0.00 2.43
3966 4066 6.364706 TCACATATGCATTTGTTTCGGTTTTC 59.635 34.615 18.66 0.00 0.00 2.29
3967 4067 6.145209 CACATATGCATTTGTTTCGGTTTTCA 59.855 34.615 18.66 0.00 0.00 2.69
3968 4068 6.703607 ACATATGCATTTGTTTCGGTTTTCAA 59.296 30.769 15.98 0.00 0.00 2.69
3969 4069 7.225538 ACATATGCATTTGTTTCGGTTTTCAAA 59.774 29.630 15.98 0.00 34.95 2.69
3970 4070 6.616774 ATGCATTTGTTTCGGTTTTCAAAT 57.383 29.167 0.00 0.00 39.87 2.32
3971 4071 6.428385 TGCATTTGTTTCGGTTTTCAAATT 57.572 29.167 0.00 0.00 38.08 1.82
3972 4072 6.846350 TGCATTTGTTTCGGTTTTCAAATTT 58.154 28.000 0.00 0.00 38.08 1.82
3973 4073 7.308435 TGCATTTGTTTCGGTTTTCAAATTTT 58.692 26.923 0.00 0.00 38.08 1.82
3974 4074 7.483059 TGCATTTGTTTCGGTTTTCAAATTTTC 59.517 29.630 0.00 0.00 38.08 2.29
3975 4075 7.483059 GCATTTGTTTCGGTTTTCAAATTTTCA 59.517 29.630 0.00 0.00 38.08 2.69
3976 4076 9.334693 CATTTGTTTCGGTTTTCAAATTTTCAA 57.665 25.926 0.00 0.00 38.08 2.69
3977 4077 9.899226 ATTTGTTTCGGTTTTCAAATTTTCAAA 57.101 22.222 0.00 0.00 37.25 2.69
3978 4078 9.730420 TTTGTTTCGGTTTTCAAATTTTCAAAA 57.270 22.222 0.00 0.00 0.00 2.44
3979 4079 9.730420 TTGTTTCGGTTTTCAAATTTTCAAAAA 57.270 22.222 6.43 3.63 0.00 1.94
3980 4080 9.387123 TGTTTCGGTTTTCAAATTTTCAAAAAG 57.613 25.926 6.43 5.19 0.00 2.27
3981 4081 8.362304 GTTTCGGTTTTCAAATTTTCAAAAAGC 58.638 29.630 15.60 15.60 36.35 3.51
3982 4082 7.371126 TCGGTTTTCAAATTTTCAAAAAGCT 57.629 28.000 19.53 0.00 37.10 3.74
3983 4083 8.480643 TCGGTTTTCAAATTTTCAAAAAGCTA 57.519 26.923 19.53 12.34 37.10 3.32
3984 4084 9.103861 TCGGTTTTCAAATTTTCAAAAAGCTAT 57.896 25.926 19.53 0.00 37.10 2.97
3996 4096 9.705290 TTTTCAAAAAGCTATATCTTCCAAACC 57.295 29.630 0.00 0.00 0.00 3.27
3997 4097 7.083875 TCAAAAAGCTATATCTTCCAAACCG 57.916 36.000 0.00 0.00 0.00 4.44
3998 4098 5.500645 AAAAGCTATATCTTCCAAACCGC 57.499 39.130 0.00 0.00 0.00 5.68
3999 4099 2.755650 AGCTATATCTTCCAAACCGCG 58.244 47.619 0.00 0.00 0.00 6.46
4000 4100 1.194772 GCTATATCTTCCAAACCGCGC 59.805 52.381 0.00 0.00 0.00 6.86
4001 4101 1.455786 CTATATCTTCCAAACCGCGCG 59.544 52.381 25.67 25.67 0.00 6.86
4002 4102 0.461339 ATATCTTCCAAACCGCGCGT 60.461 50.000 29.95 14.24 0.00 6.01
4003 4103 1.079875 TATCTTCCAAACCGCGCGTC 61.080 55.000 29.95 0.00 0.00 5.19
4004 4104 4.424430 CTTCCAAACCGCGCGTCG 62.424 66.667 29.95 17.12 38.08 5.12
4013 4113 3.683055 CGCGCGTCGGAATTAAGA 58.317 55.556 24.19 0.00 33.78 2.10
4014 4114 2.213483 CGCGCGTCGGAATTAAGAT 58.787 52.632 24.19 0.00 33.78 2.40
4015 4115 0.158928 CGCGCGTCGGAATTAAGATC 59.841 55.000 24.19 0.00 33.78 2.75
4016 4116 0.507358 GCGCGTCGGAATTAAGATCC 59.493 55.000 8.43 0.88 0.00 3.36
4026 4126 4.905269 GGAATTAAGATCCGTTTTCACCG 58.095 43.478 0.00 0.00 0.00 4.94
4027 4127 4.340263 GAATTAAGATCCGTTTTCACCGC 58.660 43.478 0.00 0.00 0.00 5.68
4028 4128 2.754946 TAAGATCCGTTTTCACCGCT 57.245 45.000 0.00 0.00 0.00 5.52
4029 4129 1.156736 AAGATCCGTTTTCACCGCTG 58.843 50.000 0.00 0.00 0.00 5.18
4030 4130 0.320374 AGATCCGTTTTCACCGCTGA 59.680 50.000 0.00 0.00 0.00 4.26
4031 4131 1.153353 GATCCGTTTTCACCGCTGAA 58.847 50.000 0.00 0.00 34.39 3.02
4032 4132 1.533731 GATCCGTTTTCACCGCTGAAA 59.466 47.619 1.72 1.72 43.37 2.69
4033 4133 1.600023 TCCGTTTTCACCGCTGAAAT 58.400 45.000 6.72 0.00 44.24 2.17
4034 4134 1.533731 TCCGTTTTCACCGCTGAAATC 59.466 47.619 6.72 5.63 44.24 2.17
4035 4135 1.401018 CCGTTTTCACCGCTGAAATCC 60.401 52.381 6.72 1.13 44.24 3.01
4036 4136 1.535462 CGTTTTCACCGCTGAAATCCT 59.465 47.619 6.72 0.00 44.24 3.24
4037 4137 2.412847 CGTTTTCACCGCTGAAATCCTC 60.413 50.000 6.72 0.00 44.24 3.71
4038 4138 1.438651 TTTCACCGCTGAAATCCTCG 58.561 50.000 1.72 0.00 40.76 4.63
4039 4139 1.019278 TTCACCGCTGAAATCCTCGC 61.019 55.000 0.00 0.00 33.20 5.03
4040 4140 1.741401 CACCGCTGAAATCCTCGCA 60.741 57.895 0.00 0.00 0.00 5.10
4041 4141 1.003839 ACCGCTGAAATCCTCGCAA 60.004 52.632 0.00 0.00 0.00 4.85
4042 4142 1.298859 ACCGCTGAAATCCTCGCAAC 61.299 55.000 0.00 0.00 0.00 4.17
4043 4143 1.059369 CGCTGAAATCCTCGCAACG 59.941 57.895 0.00 0.00 0.00 4.10
4044 4144 1.626654 CGCTGAAATCCTCGCAACGT 61.627 55.000 0.00 0.00 0.00 3.99
4045 4145 0.179215 GCTGAAATCCTCGCAACGTG 60.179 55.000 0.00 0.00 0.00 4.49
4046 4146 0.179215 CTGAAATCCTCGCAACGTGC 60.179 55.000 0.00 0.00 40.69 5.34
4047 4147 0.602638 TGAAATCCTCGCAACGTGCT 60.603 50.000 8.07 0.00 42.25 4.40
4048 4148 0.095417 GAAATCCTCGCAACGTGCTC 59.905 55.000 8.07 0.00 42.25 4.26
4049 4149 0.320771 AAATCCTCGCAACGTGCTCT 60.321 50.000 8.07 0.00 42.25 4.09
4050 4150 0.320771 AATCCTCGCAACGTGCTCTT 60.321 50.000 8.07 0.00 42.25 2.85
4051 4151 0.737715 ATCCTCGCAACGTGCTCTTC 60.738 55.000 8.07 0.00 42.25 2.87
4052 4152 1.664649 CCTCGCAACGTGCTCTTCA 60.665 57.895 8.07 0.00 42.25 3.02
4053 4153 1.221466 CCTCGCAACGTGCTCTTCAA 61.221 55.000 8.07 0.00 42.25 2.69
4054 4154 0.581529 CTCGCAACGTGCTCTTCAAA 59.418 50.000 8.07 0.00 42.25 2.69
4055 4155 1.003972 CTCGCAACGTGCTCTTCAAAA 60.004 47.619 8.07 0.00 42.25 2.44
4056 4156 1.112459 CGCAACGTGCTCTTCAAAAC 58.888 50.000 8.07 0.00 42.25 2.43
4057 4157 1.268032 CGCAACGTGCTCTTCAAAACT 60.268 47.619 8.07 0.00 42.25 2.66
4058 4158 2.033236 CGCAACGTGCTCTTCAAAACTA 60.033 45.455 8.07 0.00 42.25 2.24
4059 4159 3.363970 CGCAACGTGCTCTTCAAAACTAT 60.364 43.478 8.07 0.00 42.25 2.12
4060 4160 4.143200 CGCAACGTGCTCTTCAAAACTATA 60.143 41.667 8.07 0.00 42.25 1.31
4061 4161 5.445939 CGCAACGTGCTCTTCAAAACTATAT 60.446 40.000 8.07 0.00 42.25 0.86
4062 4162 5.960105 GCAACGTGCTCTTCAAAACTATATC 59.040 40.000 0.00 0.00 40.96 1.63
4063 4163 6.478588 CAACGTGCTCTTCAAAACTATATCC 58.521 40.000 0.00 0.00 0.00 2.59
4064 4164 5.116882 ACGTGCTCTTCAAAACTATATCCC 58.883 41.667 0.00 0.00 0.00 3.85
4065 4165 4.209288 CGTGCTCTTCAAAACTATATCCCG 59.791 45.833 0.00 0.00 0.00 5.14
4066 4166 4.024809 GTGCTCTTCAAAACTATATCCCGC 60.025 45.833 0.00 0.00 0.00 6.13
4067 4167 4.127171 GCTCTTCAAAACTATATCCCGCA 58.873 43.478 0.00 0.00 0.00 5.69
4068 4168 4.757149 GCTCTTCAAAACTATATCCCGCAT 59.243 41.667 0.00 0.00 0.00 4.73
4069 4169 5.334414 GCTCTTCAAAACTATATCCCGCATG 60.334 44.000 0.00 0.00 0.00 4.06
4070 4170 5.063204 TCTTCAAAACTATATCCCGCATGG 58.937 41.667 0.00 0.00 0.00 3.66
4080 4180 3.110139 CCGCATGGGGATGTTTCG 58.890 61.111 23.98 0.00 0.00 3.46
4081 4181 1.451207 CCGCATGGGGATGTTTCGA 60.451 57.895 23.98 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.481954 ACGCCGATTATCCTATTCATTTTC 57.518 37.500 0.00 0.00 0.00 2.29
53 54 3.846896 CGAGAGAATGTACGCCGATTATC 59.153 47.826 0.00 0.00 0.00 1.75
100 101 5.179368 TCGACTTCACAGGACAAAAATCATC 59.821 40.000 0.00 0.00 0.00 2.92
142 145 9.566624 GTCAAACATGAACAAACAAAATTATCG 57.433 29.630 0.00 0.00 0.00 2.92
182 185 6.150140 GCCCAATACAAATCTTAGCATAGAGG 59.850 42.308 0.00 0.00 0.00 3.69
189 192 6.147864 TGAATGCCCAATACAAATCTTAGC 57.852 37.500 0.00 0.00 0.00 3.09
248 336 3.924238 CAGGCACACTGTCAAACAC 57.076 52.632 0.00 0.00 42.42 3.32
274 362 8.483218 CGAATGCTCAGTACAAATCTTAGTATG 58.517 37.037 0.00 0.00 0.00 2.39
281 369 3.055094 ACCCGAATGCTCAGTACAAATCT 60.055 43.478 0.00 0.00 0.00 2.40
410 500 2.601763 GACATGACGTTTACCCTTAGCG 59.398 50.000 0.00 0.00 0.00 4.26
439 529 0.035056 CATTCGGCCTGAAGGAAGGT 60.035 55.000 14.13 0.00 40.79 3.50
519 613 0.095935 CGCTTCGTTCAGCAGATTGG 59.904 55.000 5.17 0.00 40.09 3.16
533 627 2.987752 AAGCTATTACGGCCGCTTC 58.012 52.632 28.58 8.73 38.21 3.86
568 662 1.923356 ATCCGCCCAAATGTTGTTCT 58.077 45.000 0.00 0.00 0.00 3.01
703 799 6.600882 ATCTGAAGCTCCAAAACAATGAAT 57.399 33.333 0.00 0.00 0.00 2.57
823 920 1.898574 CCTTGCAGTGCTCGGGTTT 60.899 57.895 17.60 0.00 0.00 3.27
832 929 2.730094 GTTGGTGGCCTTGCAGTG 59.270 61.111 3.32 0.00 0.00 3.66
845 944 1.384525 TCAACTTGGTCAACCGTTGG 58.615 50.000 11.35 0.00 37.69 3.77
847 946 3.143728 GGTATCAACTTGGTCAACCGTT 58.856 45.455 0.00 0.00 39.43 4.44
849 948 3.053831 AGGTATCAACTTGGTCAACCG 57.946 47.619 0.00 0.00 39.43 4.44
850 949 4.652822 AGAAGGTATCAACTTGGTCAACC 58.347 43.478 0.00 0.00 0.00 3.77
866 965 2.294512 GCTGCAAGTAAGCAAAGAAGGT 59.705 45.455 0.00 0.00 45.13 3.50
876 975 3.708195 GCATGGTGCTGCAAGTAAG 57.292 52.632 2.77 0.00 40.96 2.34
883 982 1.026584 TCACATATGCATGGTGCTGC 58.973 50.000 21.78 0.00 45.31 5.25
889 988 6.682423 TTAGAAGTTGTCACATATGCATGG 57.318 37.500 10.16 3.88 36.39 3.66
954 1053 4.048470 GGGGGTGGTGGAAGCCTC 62.048 72.222 0.00 0.00 37.86 4.70
979 1078 3.302347 CTGGAGAAAGAGCGGCGGT 62.302 63.158 13.08 13.08 0.00 5.68
1138 1237 1.283321 GAAGGCATCCTCCTGGAACTT 59.717 52.381 0.00 0.00 46.80 2.66
1152 1251 1.440618 TCCCCTTGTTGTAGAAGGCA 58.559 50.000 0.00 0.00 39.02 4.75
1234 1333 2.107953 GAGGAGCACTGGATCGGC 59.892 66.667 0.00 0.00 0.00 5.54
1248 1347 0.833287 CAGTGGTGGTATCCCAGAGG 59.167 60.000 0.00 0.00 42.94 3.69
1333 1432 1.408266 GCCCTCACCGTATGGATTGTT 60.408 52.381 8.33 0.00 39.21 2.83
1336 1435 0.694444 AGGCCCTCACCGTATGGATT 60.694 55.000 8.33 0.00 39.21 3.01
1492 1591 1.901833 GCCTTTTGGATCCCATGTGTT 59.098 47.619 9.90 0.00 44.07 3.32
1540 1639 4.184079 ACACCTTGTCTACGGATACAAC 57.816 45.455 0.00 0.00 32.43 3.32
1629 1728 3.496130 ACGTCAAGAAGATGCTCAAGTTG 59.504 43.478 0.00 0.00 36.70 3.16
1639 1738 2.761208 CCTCCAGGTACGTCAAGAAGAT 59.239 50.000 0.00 0.00 0.00 2.40
2151 2250 0.252558 TCCTTCCCTGTGTAGACCCC 60.253 60.000 0.00 0.00 0.00 4.95
2585 2684 6.291648 AGCTGTAGACATCAGATTCTTTGA 57.708 37.500 0.00 0.00 35.20 2.69
2610 2709 3.675348 ATCTCCAATGCAAGAATCCCA 57.325 42.857 0.00 0.00 0.00 4.37
2655 2754 5.723672 TCTTGTCATCGTCTTCCTTTAGT 57.276 39.130 0.00 0.00 0.00 2.24
2755 2854 4.450053 GCTGCCTCTCTATCTTCAAATGT 58.550 43.478 0.00 0.00 0.00 2.71
2778 2877 0.788391 GTCCGACGACCATCAAACAC 59.212 55.000 0.00 0.00 32.40 3.32
2781 2880 0.677288 ACAGTCCGACGACCATCAAA 59.323 50.000 0.00 0.00 40.12 2.69
2790 2889 3.036084 GCACACCACAGTCCGACG 61.036 66.667 0.00 0.00 0.00 5.12
2799 2898 1.538047 AATCTGGATGTGCACACCAC 58.462 50.000 27.00 19.08 44.90 4.16
3113 3212 5.346551 ACCAAACAAAAGCGAAAGTGTTAAC 59.653 36.000 0.00 0.00 33.18 2.01
3204 3303 7.341445 AGTAACTGAATTAAACTGTTGGCAA 57.659 32.000 0.00 0.00 33.12 4.52
3233 3332 7.343574 TGTTCTACAGGTAGCCAATCTATACAA 59.656 37.037 1.54 0.00 33.32 2.41
3267 3366 5.067936 AGGTACTCACTCAGGATACATTTCG 59.932 44.000 0.00 0.00 41.41 3.46
3317 3416 8.715191 ATTAACTTGCTGAACAAAAATGAACA 57.285 26.923 0.00 0.00 37.96 3.18
3338 3437 9.539825 AATATCCAAATACAAATGCGCAATTAA 57.460 25.926 17.11 4.31 0.00 1.40
3339 3438 8.976471 CAATATCCAAATACAAATGCGCAATTA 58.024 29.630 17.11 3.38 0.00 1.40
3464 3564 2.709934 AGCAGGAAGGACATATGCTCAT 59.290 45.455 1.58 0.00 43.46 2.90
3637 3737 8.938906 GTTTATTACTTCCTTTCGTTATGTGGA 58.061 33.333 0.00 0.00 0.00 4.02
3684 3784 8.177119 TGGTAATTTGCTCTCTTTTGTTATGT 57.823 30.769 0.00 0.00 0.00 2.29
3696 3796 9.474313 TGGTTTATCTATTTGGTAATTTGCTCT 57.526 29.630 0.00 0.00 0.00 4.09
3755 3855 0.040246 GGCCGCTACATAGACTCGTC 60.040 60.000 0.00 0.00 0.00 4.20
3756 3856 1.783031 CGGCCGCTACATAGACTCGT 61.783 60.000 14.67 0.00 0.00 4.18
3757 3857 1.082038 CGGCCGCTACATAGACTCG 60.082 63.158 14.67 0.00 0.00 4.18
3758 3858 1.286260 CCGGCCGCTACATAGACTC 59.714 63.158 22.85 0.00 0.00 3.36
3759 3859 2.857744 GCCGGCCGCTACATAGACT 61.858 63.158 22.85 0.00 0.00 3.24
3760 3860 2.355956 GCCGGCCGCTACATAGAC 60.356 66.667 22.85 0.00 0.00 2.59
3794 3894 2.981977 TATTTTAGGCCGGCCGCTCG 62.982 60.000 38.88 7.74 41.95 5.03
3795 3895 1.227734 TATTTTAGGCCGGCCGCTC 60.228 57.895 38.88 16.62 41.95 5.03
3796 3896 1.227853 CTATTTTAGGCCGGCCGCT 60.228 57.895 38.88 25.92 41.95 5.52
3797 3897 0.816421 TTCTATTTTAGGCCGGCCGC 60.816 55.000 38.88 17.88 41.95 6.53
3798 3898 1.670791 TTTCTATTTTAGGCCGGCCG 58.329 50.000 38.88 23.18 41.95 6.13
3799 3899 3.889538 AGAATTTCTATTTTAGGCCGGCC 59.110 43.478 39.29 39.29 0.00 6.13
3800 3900 5.515797 AAGAATTTCTATTTTAGGCCGGC 57.484 39.130 21.18 21.18 0.00 6.13
3801 3901 9.678941 GATAAAAGAATTTCTATTTTAGGCCGG 57.321 33.333 0.00 0.00 37.28 6.13
3802 3902 9.678941 GGATAAAAGAATTTCTATTTTAGGCCG 57.321 33.333 0.00 0.00 37.28 6.13
3803 3903 9.678941 CGGATAAAAGAATTTCTATTTTAGGCC 57.321 33.333 0.00 0.00 37.28 5.19
3804 3904 9.181805 GCGGATAAAAGAATTTCTATTTTAGGC 57.818 33.333 0.00 4.54 37.28 3.93
3808 3908 9.952188 GCTAGCGGATAAAAGAATTTCTATTTT 57.048 29.630 0.00 0.76 37.28 1.82
3809 3909 8.283291 CGCTAGCGGATAAAAGAATTTCTATTT 58.717 33.333 29.29 5.78 34.34 1.40
3810 3910 7.441458 ACGCTAGCGGATAAAAGAATTTCTATT 59.559 33.333 37.66 9.76 44.69 1.73
3811 3911 6.929606 ACGCTAGCGGATAAAAGAATTTCTAT 59.070 34.615 37.66 10.10 44.69 1.98
3812 3912 6.278363 ACGCTAGCGGATAAAAGAATTTCTA 58.722 36.000 37.66 0.00 44.69 2.10
3813 3913 5.116882 ACGCTAGCGGATAAAAGAATTTCT 58.883 37.500 37.66 10.86 44.69 2.52
3814 3914 5.234543 AGACGCTAGCGGATAAAAGAATTTC 59.765 40.000 37.66 21.77 44.69 2.17
3815 3915 5.006746 CAGACGCTAGCGGATAAAAGAATTT 59.993 40.000 37.66 14.63 44.69 1.82
3816 3916 4.508124 CAGACGCTAGCGGATAAAAGAATT 59.492 41.667 37.66 14.84 44.69 2.17
3817 3917 4.051922 CAGACGCTAGCGGATAAAAGAAT 58.948 43.478 37.66 15.38 44.69 2.40
3818 3918 3.444916 CAGACGCTAGCGGATAAAAGAA 58.555 45.455 37.66 0.00 44.69 2.52
3819 3919 2.798499 GCAGACGCTAGCGGATAAAAGA 60.798 50.000 37.66 0.00 44.69 2.52
3820 3920 1.523095 GCAGACGCTAGCGGATAAAAG 59.477 52.381 37.66 21.06 44.69 2.27
3821 3921 1.567504 GCAGACGCTAGCGGATAAAA 58.432 50.000 37.66 0.00 44.69 1.52
3822 3922 3.267900 GCAGACGCTAGCGGATAAA 57.732 52.632 37.66 0.00 44.69 1.40
3833 3933 0.179127 TGTCTATGCAGAGCAGACGC 60.179 55.000 2.68 0.00 43.65 5.19
3834 3934 2.505628 ATGTCTATGCAGAGCAGACG 57.494 50.000 2.68 0.00 43.65 4.18
3835 3935 4.313277 TGTATGTCTATGCAGAGCAGAC 57.687 45.455 17.67 17.67 43.65 3.51
3836 3936 4.343239 ACATGTATGTCTATGCAGAGCAGA 59.657 41.667 2.68 0.00 38.18 4.26
3837 3937 4.448060 CACATGTATGTCTATGCAGAGCAG 59.552 45.833 2.68 0.00 39.74 4.24
3838 3938 4.141869 ACACATGTATGTCTATGCAGAGCA 60.142 41.667 2.68 5.70 40.37 4.26
3839 3939 4.210746 CACACATGTATGTCTATGCAGAGC 59.789 45.833 2.68 0.00 39.39 4.09
3840 3940 5.354767 ACACACATGTATGTCTATGCAGAG 58.645 41.667 3.31 0.69 39.39 3.35
3841 3941 5.343307 ACACACATGTATGTCTATGCAGA 57.657 39.130 3.31 0.00 39.39 4.26
3842 3942 7.719778 ATTACACACATGTATGTCTATGCAG 57.280 36.000 14.15 0.00 41.02 4.41
3843 3943 8.504812 AAATTACACACATGTATGTCTATGCA 57.495 30.769 14.15 0.00 41.02 3.96
3844 3944 9.787532 AAAAATTACACACATGTATGTCTATGC 57.212 29.630 14.15 0.00 41.02 3.14
3848 3948 8.296713 GGACAAAAATTACACACATGTATGTCT 58.703 33.333 14.15 0.00 41.68 3.41
3849 3949 7.270365 CGGACAAAAATTACACACATGTATGTC 59.730 37.037 14.15 7.71 41.46 3.06
3850 3950 7.081349 CGGACAAAAATTACACACATGTATGT 58.919 34.615 15.18 15.18 41.02 2.29
3851 3951 6.033407 GCGGACAAAAATTACACACATGTATG 59.967 38.462 1.67 1.67 41.02 2.39
3852 3952 6.072175 AGCGGACAAAAATTACACACATGTAT 60.072 34.615 0.00 0.00 41.02 2.29
3853 3953 5.239744 AGCGGACAAAAATTACACACATGTA 59.760 36.000 0.00 0.00 40.48 2.29
3854 3954 4.037446 AGCGGACAAAAATTACACACATGT 59.963 37.500 0.00 0.00 43.30 3.21
3855 3955 4.545610 AGCGGACAAAAATTACACACATG 58.454 39.130 0.00 0.00 0.00 3.21
3856 3956 4.846779 AGCGGACAAAAATTACACACAT 57.153 36.364 0.00 0.00 0.00 3.21
3857 3957 4.319911 GCTAGCGGACAAAAATTACACACA 60.320 41.667 0.00 0.00 0.00 3.72
3858 3958 4.156182 GCTAGCGGACAAAAATTACACAC 58.844 43.478 0.00 0.00 0.00 3.82
3859 3959 3.120477 CGCTAGCGGACAAAAATTACACA 60.120 43.478 29.29 0.00 35.56 3.72
3860 3960 3.413558 CGCTAGCGGACAAAAATTACAC 58.586 45.455 29.29 0.00 35.56 2.90
3861 3961 2.159626 GCGCTAGCGGACAAAAATTACA 60.160 45.455 35.86 0.00 40.19 2.41
3862 3962 2.437626 GCGCTAGCGGACAAAAATTAC 58.562 47.619 35.86 12.78 40.19 1.89
3863 3963 2.817538 GCGCTAGCGGACAAAAATTA 57.182 45.000 35.86 0.00 40.19 1.40
3864 3964 3.694889 GCGCTAGCGGACAAAAATT 57.305 47.368 35.86 0.00 40.19 1.82
3875 3975 3.494626 TGCTAAAAGATACATGCGCTAGC 59.505 43.478 9.73 4.06 45.41 3.42
3876 3976 5.852738 ATGCTAAAAGATACATGCGCTAG 57.147 39.130 9.73 3.08 0.00 3.42
3877 3977 6.618287 AAATGCTAAAAGATACATGCGCTA 57.382 33.333 9.73 0.00 0.00 4.26
3878 3978 5.505173 AAATGCTAAAAGATACATGCGCT 57.495 34.783 9.73 0.00 0.00 5.92
3879 3979 7.858052 ATTAAATGCTAAAAGATACATGCGC 57.142 32.000 0.00 0.00 0.00 6.09
3880 3980 9.877137 TGTATTAAATGCTAAAAGATACATGCG 57.123 29.630 0.00 0.00 0.00 4.73
3890 3990 9.729023 CCGATGTGAATGTATTAAATGCTAAAA 57.271 29.630 0.00 0.00 0.00 1.52
3891 3991 8.898761 ACCGATGTGAATGTATTAAATGCTAAA 58.101 29.630 0.00 0.00 0.00 1.85
3892 3992 8.445275 ACCGATGTGAATGTATTAAATGCTAA 57.555 30.769 0.00 0.00 0.00 3.09
3893 3993 7.713073 TGACCGATGTGAATGTATTAAATGCTA 59.287 33.333 0.00 0.00 0.00 3.49
3894 3994 6.542005 TGACCGATGTGAATGTATTAAATGCT 59.458 34.615 0.00 0.00 0.00 3.79
3895 3995 6.632834 GTGACCGATGTGAATGTATTAAATGC 59.367 38.462 0.00 0.00 0.00 3.56
3896 3996 7.693020 TGTGACCGATGTGAATGTATTAAATG 58.307 34.615 0.00 0.00 0.00 2.32
3897 3997 7.857734 TGTGACCGATGTGAATGTATTAAAT 57.142 32.000 0.00 0.00 0.00 1.40
3898 3998 7.674471 TTGTGACCGATGTGAATGTATTAAA 57.326 32.000 0.00 0.00 0.00 1.52
3899 3999 7.550906 TGATTGTGACCGATGTGAATGTATTAA 59.449 33.333 0.00 0.00 0.00 1.40
3900 4000 7.044798 TGATTGTGACCGATGTGAATGTATTA 58.955 34.615 0.00 0.00 0.00 0.98
3901 4001 5.879777 TGATTGTGACCGATGTGAATGTATT 59.120 36.000 0.00 0.00 0.00 1.89
3902 4002 5.427378 TGATTGTGACCGATGTGAATGTAT 58.573 37.500 0.00 0.00 0.00 2.29
3903 4003 4.826556 TGATTGTGACCGATGTGAATGTA 58.173 39.130 0.00 0.00 0.00 2.29
3904 4004 3.673902 TGATTGTGACCGATGTGAATGT 58.326 40.909 0.00 0.00 0.00 2.71
3905 4005 3.686241 ACTGATTGTGACCGATGTGAATG 59.314 43.478 0.00 0.00 0.00 2.67
3906 4006 3.942829 ACTGATTGTGACCGATGTGAAT 58.057 40.909 0.00 0.00 0.00 2.57
3907 4007 3.401033 ACTGATTGTGACCGATGTGAA 57.599 42.857 0.00 0.00 0.00 3.18
3908 4008 3.066380 CAACTGATTGTGACCGATGTGA 58.934 45.455 0.00 0.00 0.00 3.58
3909 4009 2.160219 CCAACTGATTGTGACCGATGTG 59.840 50.000 0.00 0.00 33.60 3.21
3910 4010 2.038426 TCCAACTGATTGTGACCGATGT 59.962 45.455 0.00 0.00 33.60 3.06
3911 4011 2.698803 TCCAACTGATTGTGACCGATG 58.301 47.619 0.00 0.00 33.60 3.84
3912 4012 3.417069 TTCCAACTGATTGTGACCGAT 57.583 42.857 0.00 0.00 33.60 4.18
3913 4013 2.920724 TTCCAACTGATTGTGACCGA 57.079 45.000 0.00 0.00 33.60 4.69
3914 4014 3.980646 TTTTCCAACTGATTGTGACCG 57.019 42.857 0.00 0.00 33.60 4.79
3932 4032 8.836268 AACAAATGCATATGTGATCTGTTTTT 57.164 26.923 0.00 0.00 0.00 1.94
3933 4033 8.836268 AAACAAATGCATATGTGATCTGTTTT 57.164 26.923 0.00 0.00 32.19 2.43
3934 4034 7.274033 CGAAACAAATGCATATGTGATCTGTTT 59.726 33.333 15.51 15.51 37.23 2.83
3935 4035 6.748658 CGAAACAAATGCATATGTGATCTGTT 59.251 34.615 0.00 4.03 0.00 3.16
3936 4036 6.260377 CGAAACAAATGCATATGTGATCTGT 58.740 36.000 0.00 0.00 0.00 3.41
3937 4037 5.684184 CCGAAACAAATGCATATGTGATCTG 59.316 40.000 0.00 0.00 0.00 2.90
3938 4038 5.357878 ACCGAAACAAATGCATATGTGATCT 59.642 36.000 0.00 0.00 0.00 2.75
3939 4039 5.581605 ACCGAAACAAATGCATATGTGATC 58.418 37.500 0.00 3.18 0.00 2.92
3940 4040 5.581126 ACCGAAACAAATGCATATGTGAT 57.419 34.783 0.00 0.00 0.00 3.06
3941 4041 5.384063 AACCGAAACAAATGCATATGTGA 57.616 34.783 0.00 0.00 0.00 3.58
3942 4042 6.145209 TGAAAACCGAAACAAATGCATATGTG 59.855 34.615 0.00 1.16 0.00 3.21
3943 4043 6.219473 TGAAAACCGAAACAAATGCATATGT 58.781 32.000 0.00 0.00 0.00 2.29
3944 4044 6.702972 TGAAAACCGAAACAAATGCATATG 57.297 33.333 0.00 0.00 0.00 1.78
3945 4045 7.721286 TTTGAAAACCGAAACAAATGCATAT 57.279 28.000 0.00 0.00 0.00 1.78
3946 4046 7.721286 ATTTGAAAACCGAAACAAATGCATA 57.279 28.000 0.00 0.00 40.07 3.14
3947 4047 6.616774 ATTTGAAAACCGAAACAAATGCAT 57.383 29.167 0.00 0.00 40.07 3.96
3948 4048 6.428385 AATTTGAAAACCGAAACAAATGCA 57.572 29.167 0.00 0.00 40.95 3.96
3949 4049 7.483059 TGAAAATTTGAAAACCGAAACAAATGC 59.517 29.630 0.00 0.00 40.95 3.56
3950 4050 8.886816 TGAAAATTTGAAAACCGAAACAAATG 57.113 26.923 0.00 0.00 40.95 2.32
3951 4051 9.899226 TTTGAAAATTTGAAAACCGAAACAAAT 57.101 22.222 0.00 0.00 42.25 2.32
3952 4052 9.730420 TTTTGAAAATTTGAAAACCGAAACAAA 57.270 22.222 0.00 0.00 36.82 2.83
3953 4053 9.730420 TTTTTGAAAATTTGAAAACCGAAACAA 57.270 22.222 2.72 0.00 0.00 2.83
3954 4054 9.387123 CTTTTTGAAAATTTGAAAACCGAAACA 57.613 25.926 2.72 0.00 0.00 2.83
3955 4055 8.362304 GCTTTTTGAAAATTTGAAAACCGAAAC 58.638 29.630 2.72 0.00 0.00 2.78
3956 4056 8.293157 AGCTTTTTGAAAATTTGAAAACCGAAA 58.707 25.926 2.72 0.00 0.00 3.46
3957 4057 7.811653 AGCTTTTTGAAAATTTGAAAACCGAA 58.188 26.923 2.72 0.00 0.00 4.30
3958 4058 7.371126 AGCTTTTTGAAAATTTGAAAACCGA 57.629 28.000 2.72 0.00 0.00 4.69
3970 4070 9.705290 GGTTTGGAAGATATAGCTTTTTGAAAA 57.295 29.630 4.45 0.12 0.00 2.29
3971 4071 8.026607 CGGTTTGGAAGATATAGCTTTTTGAAA 58.973 33.333 4.45 0.08 0.00 2.69
3972 4072 7.535139 CGGTTTGGAAGATATAGCTTTTTGAA 58.465 34.615 4.45 0.00 0.00 2.69
3973 4073 6.404293 GCGGTTTGGAAGATATAGCTTTTTGA 60.404 38.462 4.45 0.00 0.00 2.69
3974 4074 5.743872 GCGGTTTGGAAGATATAGCTTTTTG 59.256 40.000 4.45 0.00 0.00 2.44
3975 4075 5.448632 CGCGGTTTGGAAGATATAGCTTTTT 60.449 40.000 4.45 0.00 0.00 1.94
3976 4076 4.035208 CGCGGTTTGGAAGATATAGCTTTT 59.965 41.667 4.45 0.00 0.00 2.27
3977 4077 3.560068 CGCGGTTTGGAAGATATAGCTTT 59.440 43.478 4.45 0.00 0.00 3.51
3978 4078 3.131396 CGCGGTTTGGAAGATATAGCTT 58.869 45.455 2.14 2.14 0.00 3.74
3979 4079 2.755650 CGCGGTTTGGAAGATATAGCT 58.244 47.619 0.00 0.00 0.00 3.32
3980 4080 1.194772 GCGCGGTTTGGAAGATATAGC 59.805 52.381 8.83 0.00 0.00 2.97
3981 4081 1.455786 CGCGCGGTTTGGAAGATATAG 59.544 52.381 24.84 0.00 0.00 1.31
3982 4082 1.202440 ACGCGCGGTTTGGAAGATATA 60.202 47.619 35.22 0.00 0.00 0.86
3983 4083 0.461339 ACGCGCGGTTTGGAAGATAT 60.461 50.000 35.22 4.55 0.00 1.63
3984 4084 1.079681 ACGCGCGGTTTGGAAGATA 60.080 52.632 35.22 0.00 0.00 1.98
3985 4085 2.358247 ACGCGCGGTTTGGAAGAT 60.358 55.556 35.22 5.42 0.00 2.40
3986 4086 3.039588 GACGCGCGGTTTGGAAGA 61.040 61.111 35.22 0.00 0.00 2.87
3987 4087 4.424430 CGACGCGCGGTTTGGAAG 62.424 66.667 35.22 11.38 36.03 3.46
3996 4096 0.158928 GATCTTAATTCCGACGCGCG 59.841 55.000 30.96 30.96 40.47 6.86
3997 4097 0.507358 GGATCTTAATTCCGACGCGC 59.493 55.000 5.73 0.00 0.00 6.86
4004 4104 4.729746 GCGGTGAAAACGGATCTTAATTCC 60.730 45.833 0.00 0.00 0.00 3.01
4005 4105 4.094442 AGCGGTGAAAACGGATCTTAATTC 59.906 41.667 0.00 0.00 0.00 2.17
4006 4106 4.007659 AGCGGTGAAAACGGATCTTAATT 58.992 39.130 0.00 0.00 0.00 1.40
4007 4107 3.374058 CAGCGGTGAAAACGGATCTTAAT 59.626 43.478 9.50 0.00 0.00 1.40
4008 4108 2.739913 CAGCGGTGAAAACGGATCTTAA 59.260 45.455 9.50 0.00 0.00 1.85
4009 4109 2.028839 TCAGCGGTGAAAACGGATCTTA 60.029 45.455 16.20 0.00 0.00 2.10
4010 4110 1.156736 CAGCGGTGAAAACGGATCTT 58.843 50.000 9.50 0.00 0.00 2.40
4011 4111 0.320374 TCAGCGGTGAAAACGGATCT 59.680 50.000 16.20 0.00 0.00 2.75
4012 4112 1.153353 TTCAGCGGTGAAAACGGATC 58.847 50.000 26.54 0.00 39.85 3.36
4013 4113 3.315765 TTCAGCGGTGAAAACGGAT 57.684 47.368 26.54 0.00 39.85 4.18
4014 4114 4.859400 TTCAGCGGTGAAAACGGA 57.141 50.000 26.54 3.79 39.85 4.69
4020 4120 1.019278 GCGAGGATTTCAGCGGTGAA 61.019 55.000 25.16 25.16 41.13 3.18
4021 4121 1.447838 GCGAGGATTTCAGCGGTGA 60.448 57.895 14.39 14.39 0.00 4.02
4022 4122 1.298157 TTGCGAGGATTTCAGCGGTG 61.298 55.000 8.67 8.67 0.00 4.94
4023 4123 1.003839 TTGCGAGGATTTCAGCGGT 60.004 52.632 0.00 0.00 0.00 5.68
4024 4124 1.425428 GTTGCGAGGATTTCAGCGG 59.575 57.895 0.00 0.00 0.00 5.52
4025 4125 1.059369 CGTTGCGAGGATTTCAGCG 59.941 57.895 0.00 0.00 0.00 5.18
4026 4126 0.179215 CACGTTGCGAGGATTTCAGC 60.179 55.000 0.00 0.00 0.00 4.26
4027 4127 0.179215 GCACGTTGCGAGGATTTCAG 60.179 55.000 0.00 0.00 31.71 3.02
4028 4128 1.866237 GCACGTTGCGAGGATTTCA 59.134 52.632 0.00 0.00 31.71 2.69
4029 4129 4.745549 GCACGTTGCGAGGATTTC 57.254 55.556 0.00 0.00 31.71 2.17
4038 4138 2.475200 AGTTTTGAAGAGCACGTTGC 57.525 45.000 2.28 2.28 45.46 4.17
4039 4139 6.456988 GGGATATAGTTTTGAAGAGCACGTTG 60.457 42.308 0.00 0.00 0.00 4.10
4040 4140 5.585047 GGGATATAGTTTTGAAGAGCACGTT 59.415 40.000 0.00 0.00 0.00 3.99
4041 4141 5.116882 GGGATATAGTTTTGAAGAGCACGT 58.883 41.667 0.00 0.00 0.00 4.49
4042 4142 4.209288 CGGGATATAGTTTTGAAGAGCACG 59.791 45.833 0.00 0.00 0.00 5.34
4043 4143 4.024809 GCGGGATATAGTTTTGAAGAGCAC 60.025 45.833 0.00 0.00 0.00 4.40
4044 4144 4.127171 GCGGGATATAGTTTTGAAGAGCA 58.873 43.478 0.00 0.00 0.00 4.26
4045 4145 4.127171 TGCGGGATATAGTTTTGAAGAGC 58.873 43.478 0.00 0.00 0.00 4.09
4046 4146 5.180117 CCATGCGGGATATAGTTTTGAAGAG 59.820 44.000 0.00 0.00 40.01 2.85
4047 4147 5.063204 CCATGCGGGATATAGTTTTGAAGA 58.937 41.667 0.00 0.00 40.01 2.87
4048 4148 5.362556 CCATGCGGGATATAGTTTTGAAG 57.637 43.478 0.00 0.00 40.01 3.02
4063 4163 1.451207 TCGAAACATCCCCATGCGG 60.451 57.895 0.00 0.00 32.57 5.69
4064 4164 4.217035 TCGAAACATCCCCATGCG 57.783 55.556 0.00 0.00 32.57 4.73


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

AutoCloner maintained by Alex Coulton.