Multiple sequence alignment - TraesCS2D01G273500

Loading Multiple Alignment...

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 TraesCS2D01G273500 chr2D 100.000 3942 0 0 1 3942 340331810 340327869 0.000000e+00 7280
1 TraesCS2D01G273500 chr4B 95.792 3850 139 13 4 3843 120262494 120258658 0.000000e+00 6191
2 TraesCS2D01G273500 chr4B 95.246 3849 162 10 1 3838 222595108 222598946 0.000000e+00 6074
3 TraesCS2D01G273500 chr4B 95.339 3583 139 13 268 3838 40493151 40496717 0.000000e+00 5666
4 TraesCS2D01G273500 chr3A 95.400 3848 151 15 1 3838 91838455 91842286 0.000000e+00 6102
5 TraesCS2D01G273500 chr6B 95.326 3851 159 14 1 3841 706416548 706412709 0.000000e+00 6095
6 TraesCS2D01G273500 chr4A 95.267 3824 157 12 1 3815 531952595 531956403 0.000000e+00 6037
7 TraesCS2D01G273500 chr4A 98.077 104 2 0 3839 3942 511978138 511978035 8.700000e-42 182
8 TraesCS2D01G273500 chr5B 95.629 3409 131 12 443 3840 10418338 10414937 0.000000e+00 5454
9 TraesCS2D01G273500 chr5A 95.339 3304 136 14 548 3839 220265038 220268335 0.000000e+00 5232
10 TraesCS2D01G273500 chr5A 97.115 104 3 0 3839 3942 334847606 334847503 4.050000e-40 176
11 TraesCS2D01G273500 chr7A 95.764 3187 119 8 1 3178 492427306 492424127 0.000000e+00 5123
12 TraesCS2D01G273500 chr2A 89.418 1805 162 17 2051 3838 724964671 724962879 0.000000e+00 2248
13 TraesCS2D01G273500 chr4D 97.115 104 3 0 3839 3942 31881407 31881510 4.050000e-40 176
14 TraesCS2D01G273500 chr4D 97.115 104 3 0 3839 3942 460425080 460425183 4.050000e-40 176
15 TraesCS2D01G273500 chr4D 96.154 104 4 0 3839 3942 256711675 256711778 1.880000e-38 171
16 TraesCS2D01G273500 chr4D 96.154 104 4 0 3839 3942 348815175 348815278 1.880000e-38 171
17 TraesCS2D01G273500 chr3D 97.115 104 3 0 3839 3942 252683103 252683206 4.050000e-40 176
18 TraesCS2D01G273500 chr1D 97.115 104 3 0 3839 3942 280181215 280181318 4.050000e-40 176
19 TraesCS2D01G273500 chrUn 96.154 104 4 0 3839 3942 246364907 246364804 1.880000e-38 171


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 TraesCS2D01G273500 chr2D 340327869 340331810 3941 True 7280 7280 100.000 1 3942 1 chr2D.!!$R1 3941
1 TraesCS2D01G273500 chr4B 120258658 120262494 3836 True 6191 6191 95.792 4 3843 1 chr4B.!!$R1 3839
2 TraesCS2D01G273500 chr4B 222595108 222598946 3838 False 6074 6074 95.246 1 3838 1 chr4B.!!$F2 3837
3 TraesCS2D01G273500 chr4B 40493151 40496717 3566 False 5666 5666 95.339 268 3838 1 chr4B.!!$F1 3570
4 TraesCS2D01G273500 chr3A 91838455 91842286 3831 False 6102 6102 95.400 1 3838 1 chr3A.!!$F1 3837
5 TraesCS2D01G273500 chr6B 706412709 706416548 3839 True 6095 6095 95.326 1 3841 1 chr6B.!!$R1 3840
6 TraesCS2D01G273500 chr4A 531952595 531956403 3808 False 6037 6037 95.267 1 3815 1 chr4A.!!$F1 3814
7 TraesCS2D01G273500 chr5B 10414937 10418338 3401 True 5454 5454 95.629 443 3840 1 chr5B.!!$R1 3397
8 TraesCS2D01G273500 chr5A 220265038 220268335 3297 False 5232 5232 95.339 548 3839 1 chr5A.!!$F1 3291
9 TraesCS2D01G273500 chr7A 492424127 492427306 3179 True 5123 5123 95.764 1 3178 1 chr7A.!!$R1 3177
10 TraesCS2D01G273500 chr2A 724962879 724964671 1792 True 2248 2248 89.418 2051 3838 1 chr2A.!!$R1 1787

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
974 981 2.287188 GGATTCACATAATGCTGGCACG 60.287 50.000 0.0 0.0 0.0 5.34 F
2188 2202 2.092914 GGTAGGTGATGGAAACCAGGAG 60.093 54.545 0.0 0.0 40.4 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2272 0.877743 GCCTTCTTTTTGAGCGAGCT 59.122 50.0 0.0 0.0 0.0 4.09 R
3905 3957 0.036388 GGTCCTCGAAACTCCATGCA 60.036 55.0 0.0 0.0 0.0 3.96 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
204 209 6.961554 GGCGTCATTTCATTAGTACTTTTCTG 59.038 38.462 0.00 0.00 0.00 3.02
205 210 7.360946 GGCGTCATTTCATTAGTACTTTTCTGT 60.361 37.037 0.00 0.00 0.00 3.41
298 303 4.770010 CCAAAGGGGCAAAGAATAGTTGTA 59.230 41.667 0.00 0.00 0.00 2.41
410 415 5.719085 TGCCCACTAAACATAAATGATTGGT 59.281 36.000 0.00 0.00 35.32 3.67
415 420 8.303156 CCACTAAACATAAATGATTGGTGTCAA 58.697 33.333 20.20 0.00 44.55 3.18
421 426 8.125978 ACATAAATGATTGGTGTCAAGTCAAT 57.874 30.769 0.00 0.00 36.19 2.57
427 432 7.202016 TGATTGGTGTCAAGTCAATAAGAAC 57.798 36.000 0.00 0.00 36.19 3.01
454 459 4.218417 GGTGAGGAAACAATATTGCAGTGT 59.782 41.667 15.48 0.00 36.93 3.55
974 981 2.287188 GGATTCACATAATGCTGGCACG 60.287 50.000 0.00 0.00 0.00 5.34
981 990 3.623060 ACATAATGCTGGCACGAAGTTAG 59.377 43.478 0.00 0.00 41.61 2.34
1050 1059 6.524586 GTGTTTTTCTGTGTCTCTTTTGTCAG 59.475 38.462 0.00 0.00 0.00 3.51
1438 1447 3.163467 ACTCCTAAGCAAGTCTACGGTT 58.837 45.455 0.00 0.00 0.00 4.44
1473 1482 8.926710 CGGTATCTAAAGAACATCAATATGACC 58.073 37.037 0.00 0.00 36.54 4.02
1626 1635 5.250774 TGGCATAGAAGAGGTAAAGGACTTT 59.749 40.000 2.57 2.57 36.63 2.66
1947 1960 8.589338 AGTTACTCTTACTCATGTCACAAAGAT 58.411 33.333 0.00 0.00 0.00 2.40
1948 1961 9.856488 GTTACTCTTACTCATGTCACAAAGATA 57.144 33.333 0.00 0.00 0.00 1.98
2183 2197 5.445964 ACATATTGGTAGGTGATGGAAACC 58.554 41.667 0.00 0.00 38.03 3.27
2188 2202 2.092914 GGTAGGTGATGGAAACCAGGAG 60.093 54.545 0.00 0.00 40.40 3.69
2198 2212 3.461831 TGGAAACCAGGAGTATAATGGGG 59.538 47.826 0.00 0.00 38.48 4.96
2251 2271 0.182775 AGAACTGAACACCCACACCC 59.817 55.000 0.00 0.00 0.00 4.61
2252 2272 0.106918 GAACTGAACACCCACACCCA 60.107 55.000 0.00 0.00 0.00 4.51
2253 2273 0.106719 AACTGAACACCCACACCCAG 60.107 55.000 0.00 0.00 0.00 4.45
2254 2274 1.898574 CTGAACACCCACACCCAGC 60.899 63.158 0.00 0.00 0.00 4.85
2255 2275 2.343475 CTGAACACCCACACCCAGCT 62.343 60.000 0.00 0.00 0.00 4.24
2256 2276 1.600916 GAACACCCACACCCAGCTC 60.601 63.158 0.00 0.00 0.00 4.09
2320 2340 2.009774 CGAAGGAGCATGGTTTACTGG 58.990 52.381 0.00 0.00 0.00 4.00
2328 2348 2.029380 GCATGGTTTACTGGACCCAAAC 60.029 50.000 0.00 5.35 36.30 2.93
2434 2455 6.885735 AACGATAAATTTAACCAAGCATGC 57.114 33.333 10.51 10.51 0.00 4.06
2620 2655 8.392612 TCCAAAGTAGTTTTAAAGACTTCAACG 58.607 33.333 10.76 0.00 30.98 4.10
2729 2764 0.037419 TGCTCTTGTGCGCATAGACA 60.037 50.000 15.91 16.10 35.36 3.41
2783 2818 4.540824 GGAAGTTTCTGATTGCAAGACAC 58.459 43.478 4.94 0.00 0.00 3.67
2828 2863 2.171003 ACTTAATTGCCTGGCCTTCAC 58.829 47.619 17.53 0.00 0.00 3.18
2876 2912 8.689061 CCTTCCACATTCTCAAATCATATTTGA 58.311 33.333 12.97 12.97 36.98 2.69
3340 3387 7.488322 CCATAAAATGGGTATCGAATTTGTGT 58.512 34.615 0.00 0.00 46.86 3.72
3507 3556 4.483476 AGTTGTGTTCCGATGCTAAAAC 57.517 40.909 0.00 0.00 0.00 2.43
3631 3681 0.584876 GTGTTACTGGTGTGTTCGGC 59.415 55.000 0.00 0.00 0.00 5.54
3788 3840 2.228103 GGCCTAGTAACACACTTTTGGC 59.772 50.000 0.00 0.00 41.86 4.52
3842 3894 3.131400 GTCTGTCCTCTTGTAGTGATCCC 59.869 52.174 0.00 0.00 0.00 3.85
3843 3895 3.099905 CTGTCCTCTTGTAGTGATCCCA 58.900 50.000 0.00 0.00 0.00 4.37
3844 3896 3.099905 TGTCCTCTTGTAGTGATCCCAG 58.900 50.000 0.00 0.00 0.00 4.45
3845 3897 3.100671 GTCCTCTTGTAGTGATCCCAGT 58.899 50.000 0.00 0.00 0.00 4.00
3846 3898 3.099905 TCCTCTTGTAGTGATCCCAGTG 58.900 50.000 0.00 0.00 0.00 3.66
3847 3899 3.099905 CCTCTTGTAGTGATCCCAGTGA 58.900 50.000 0.00 0.00 0.00 3.41
3848 3900 3.515502 CCTCTTGTAGTGATCCCAGTGAA 59.484 47.826 0.00 0.00 0.00 3.18
3849 3901 4.020218 CCTCTTGTAGTGATCCCAGTGAAA 60.020 45.833 0.00 0.00 0.00 2.69
3850 3902 5.513094 CCTCTTGTAGTGATCCCAGTGAAAA 60.513 44.000 0.00 0.00 0.00 2.29
3851 3903 5.305585 TCTTGTAGTGATCCCAGTGAAAAC 58.694 41.667 0.00 0.00 0.00 2.43
3852 3904 4.015872 TGTAGTGATCCCAGTGAAAACC 57.984 45.455 0.00 0.00 0.00 3.27
3853 3905 3.392947 TGTAGTGATCCCAGTGAAAACCA 59.607 43.478 0.00 0.00 0.00 3.67
3854 3906 2.863809 AGTGATCCCAGTGAAAACCAC 58.136 47.619 0.00 0.00 46.03 4.16
3867 3919 5.144359 GTGAAAACCACTTATACAAGCACG 58.856 41.667 0.00 0.00 42.44 5.34
3868 3920 5.049954 GTGAAAACCACTTATACAAGCACGA 60.050 40.000 0.00 0.00 42.44 4.35
3869 3921 5.527951 TGAAAACCACTTATACAAGCACGAA 59.472 36.000 0.00 0.00 34.94 3.85
3870 3922 5.607119 AAACCACTTATACAAGCACGAAG 57.393 39.130 0.00 0.00 34.94 3.79
3871 3923 4.267349 ACCACTTATACAAGCACGAAGT 57.733 40.909 0.00 0.00 36.69 3.01
3872 3924 4.638304 ACCACTTATACAAGCACGAAGTT 58.362 39.130 0.00 0.00 33.13 2.66
3873 3925 4.451096 ACCACTTATACAAGCACGAAGTTG 59.549 41.667 0.00 0.00 33.13 3.16
3874 3926 4.142902 CCACTTATACAAGCACGAAGTTGG 60.143 45.833 0.00 0.00 33.13 3.77
3875 3927 3.435671 ACTTATACAAGCACGAAGTTGGC 59.564 43.478 0.00 0.00 33.13 4.52
3876 3928 1.165270 ATACAAGCACGAAGTTGGCC 58.835 50.000 0.00 0.00 41.61 5.36
3877 3929 0.179043 TACAAGCACGAAGTTGGCCA 60.179 50.000 0.00 0.00 41.61 5.36
3878 3930 1.283793 CAAGCACGAAGTTGGCCAG 59.716 57.895 5.11 0.00 41.61 4.85
3879 3931 1.898574 AAGCACGAAGTTGGCCAGG 60.899 57.895 5.11 0.00 41.61 4.45
3880 3932 2.281484 GCACGAAGTTGGCCAGGA 60.281 61.111 5.11 0.00 41.61 3.86
3881 3933 1.675641 GCACGAAGTTGGCCAGGAT 60.676 57.895 5.11 0.00 41.61 3.24
3882 3934 0.392461 GCACGAAGTTGGCCAGGATA 60.392 55.000 5.11 0.00 41.61 2.59
3883 3935 1.747206 GCACGAAGTTGGCCAGGATAT 60.747 52.381 5.11 0.00 41.61 1.63
3884 3936 2.484770 GCACGAAGTTGGCCAGGATATA 60.485 50.000 5.11 0.00 41.61 0.86
3885 3937 3.807209 GCACGAAGTTGGCCAGGATATAT 60.807 47.826 5.11 0.00 41.61 0.86
3886 3938 4.562757 GCACGAAGTTGGCCAGGATATATA 60.563 45.833 5.11 0.00 41.61 0.86
3887 3939 5.734720 CACGAAGTTGGCCAGGATATATAT 58.265 41.667 5.11 0.00 41.61 0.86
3888 3940 5.582269 CACGAAGTTGGCCAGGATATATATG 59.418 44.000 5.11 0.00 41.61 1.78
3889 3941 5.483937 ACGAAGTTGGCCAGGATATATATGA 59.516 40.000 5.11 0.00 37.78 2.15
3890 3942 5.812642 CGAAGTTGGCCAGGATATATATGAC 59.187 44.000 5.11 0.00 0.00 3.06
3891 3943 5.700402 AGTTGGCCAGGATATATATGACC 57.300 43.478 5.11 0.00 0.00 4.02
3892 3944 5.100811 AGTTGGCCAGGATATATATGACCA 58.899 41.667 5.11 2.41 0.00 4.02
3893 3945 5.190528 AGTTGGCCAGGATATATATGACCAG 59.809 44.000 5.11 0.00 0.00 4.00
3894 3946 4.040047 TGGCCAGGATATATATGACCAGG 58.960 47.826 0.00 13.33 33.21 4.45
3895 3947 4.265261 TGGCCAGGATATATATGACCAGGA 60.265 45.833 18.56 3.66 32.01 3.86
3896 3948 4.910304 GGCCAGGATATATATGACCAGGAT 59.090 45.833 18.56 0.00 32.01 3.24
3897 3949 5.012561 GGCCAGGATATATATGACCAGGATC 59.987 48.000 18.56 10.15 32.01 3.36
3898 3950 5.279206 GCCAGGATATATATGACCAGGATCG 60.279 48.000 18.56 0.00 32.01 3.69
3899 3951 5.835819 CCAGGATATATATGACCAGGATCGT 59.164 44.000 12.72 0.00 32.01 3.73
3900 3952 7.004691 CCAGGATATATATGACCAGGATCGTA 58.995 42.308 12.72 0.00 32.01 3.43
3901 3953 7.671819 CCAGGATATATATGACCAGGATCGTAT 59.328 40.741 12.72 1.50 35.44 3.06
3902 3954 8.518702 CAGGATATATATGACCAGGATCGTATG 58.481 40.741 0.00 0.00 33.68 2.39
3903 3955 8.228206 AGGATATATATGACCAGGATCGTATGT 58.772 37.037 0.00 0.23 33.68 2.29
3904 3956 8.516234 GGATATATATGACCAGGATCGTATGTC 58.484 40.741 0.00 9.25 33.68 3.06
3905 3957 9.290988 GATATATATGACCAGGATCGTATGTCT 57.709 37.037 14.59 6.62 33.68 3.41
3906 3958 5.651387 ATATGACCAGGATCGTATGTCTG 57.349 43.478 14.59 3.90 30.99 3.51
3907 3959 1.409064 TGACCAGGATCGTATGTCTGC 59.591 52.381 14.59 0.00 0.00 4.26
3908 3960 1.409064 GACCAGGATCGTATGTCTGCA 59.591 52.381 0.00 0.00 0.00 4.41
3909 3961 2.036475 GACCAGGATCGTATGTCTGCAT 59.964 50.000 0.00 0.00 39.03 3.96
3910 3962 2.224137 ACCAGGATCGTATGTCTGCATG 60.224 50.000 0.00 0.00 36.58 4.06
3911 3963 2.410939 CAGGATCGTATGTCTGCATGG 58.589 52.381 0.00 0.00 36.58 3.66
3912 3964 2.036346 CAGGATCGTATGTCTGCATGGA 59.964 50.000 0.00 0.00 36.58 3.41
3913 3965 2.298446 AGGATCGTATGTCTGCATGGAG 59.702 50.000 8.12 8.12 36.58 3.86
3914 3966 2.036475 GGATCGTATGTCTGCATGGAGT 59.964 50.000 14.43 0.00 36.58 3.85
3915 3967 3.493350 GGATCGTATGTCTGCATGGAGTT 60.493 47.826 14.43 3.50 36.58 3.01
3916 3968 3.610040 TCGTATGTCTGCATGGAGTTT 57.390 42.857 14.43 3.16 36.58 2.66
3917 3969 3.521560 TCGTATGTCTGCATGGAGTTTC 58.478 45.455 14.43 6.94 36.58 2.78
3918 3970 2.282555 CGTATGTCTGCATGGAGTTTCG 59.717 50.000 14.43 9.27 36.58 3.46
3919 3971 2.768253 ATGTCTGCATGGAGTTTCGA 57.232 45.000 14.43 0.00 33.37 3.71
3920 3972 2.084610 TGTCTGCATGGAGTTTCGAG 57.915 50.000 14.43 0.00 0.00 4.04
3921 3973 1.338105 TGTCTGCATGGAGTTTCGAGG 60.338 52.381 14.43 0.00 0.00 4.63
3922 3974 1.066858 GTCTGCATGGAGTTTCGAGGA 60.067 52.381 14.43 0.00 0.00 3.71
3923 3975 1.066858 TCTGCATGGAGTTTCGAGGAC 60.067 52.381 14.43 0.00 0.00 3.85
3924 3976 0.036388 TGCATGGAGTTTCGAGGACC 60.036 55.000 0.00 0.00 0.00 4.46
3925 3977 0.036388 GCATGGAGTTTCGAGGACCA 60.036 55.000 0.00 0.00 35.09 4.02
3926 3978 1.407437 GCATGGAGTTTCGAGGACCAT 60.407 52.381 8.83 8.83 41.25 3.55
3927 3979 2.555199 CATGGAGTTTCGAGGACCATC 58.445 52.381 10.85 0.00 38.99 3.51
3928 3980 0.530744 TGGAGTTTCGAGGACCATCG 59.469 55.000 6.93 6.93 44.07 3.84
3929 3981 0.531200 GGAGTTTCGAGGACCATCGT 59.469 55.000 11.47 0.00 43.20 3.73
3930 3982 1.747355 GGAGTTTCGAGGACCATCGTA 59.253 52.381 11.47 2.14 43.20 3.43
3931 3983 2.361438 GGAGTTTCGAGGACCATCGTAT 59.639 50.000 11.47 0.32 43.20 3.06
3932 3984 3.550436 GGAGTTTCGAGGACCATCGTATC 60.550 52.174 11.47 4.15 43.20 2.24
3933 3985 3.021695 AGTTTCGAGGACCATCGTATCA 58.978 45.455 11.47 0.00 43.20 2.15
3934 3986 3.066900 AGTTTCGAGGACCATCGTATCAG 59.933 47.826 11.47 0.00 43.20 2.90
3935 3987 2.632987 TCGAGGACCATCGTATCAGA 57.367 50.000 11.47 0.00 43.20 3.27
3936 3988 3.141767 TCGAGGACCATCGTATCAGAT 57.858 47.619 11.47 0.00 43.20 2.90
3937 3989 4.281898 TCGAGGACCATCGTATCAGATA 57.718 45.455 11.47 0.00 43.20 1.98
3938 3990 4.254492 TCGAGGACCATCGTATCAGATAG 58.746 47.826 11.47 0.00 43.20 2.08
3939 3991 4.020485 TCGAGGACCATCGTATCAGATAGA 60.020 45.833 11.47 0.00 43.20 1.98
3940 3992 4.331443 CGAGGACCATCGTATCAGATAGAG 59.669 50.000 0.00 0.00 37.91 2.43
3941 3993 4.594970 AGGACCATCGTATCAGATAGAGG 58.405 47.826 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.421058 CAATGCTTGTGATTCATGACCTG 58.579 43.478 0.00 0.00 0.00 4.00
82 84 3.194005 TGTGAACTTGACCCTCTTCAC 57.806 47.619 0.00 0.00 41.87 3.18
221 226 1.392168 GCGCTTGCGTACTTCATTGTA 59.608 47.619 16.38 0.00 0.00 2.41
226 231 0.598942 TCTTGCGCTTGCGTACTTCA 60.599 50.000 16.38 2.73 43.34 3.02
298 303 4.442472 GGCTGGCTATCTTCATTGCATTTT 60.442 41.667 0.00 0.00 32.84 1.82
376 381 2.122783 TTAGTGGGCAAAATCCTCCG 57.877 50.000 0.00 0.00 0.00 4.63
410 415 5.527214 CACCACTGTTCTTATTGACTTGACA 59.473 40.000 0.00 0.00 0.00 3.58
415 420 4.593206 TCCTCACCACTGTTCTTATTGACT 59.407 41.667 0.00 0.00 0.00 3.41
421 426 4.764050 TGTTTCCTCACCACTGTTCTTA 57.236 40.909 0.00 0.00 0.00 2.10
427 432 4.218200 TGCAATATTGTTTCCTCACCACTG 59.782 41.667 16.61 0.00 0.00 3.66
454 459 8.205512 TCTTGTTAATTGTGAAGTACCTGTACA 58.794 33.333 9.90 0.00 38.48 2.90
974 981 1.886542 CACCCCAACAAGCCTAACTTC 59.113 52.381 0.00 0.00 36.04 3.01
981 990 0.467290 TGTCTTCACCCCAACAAGCC 60.467 55.000 0.00 0.00 0.00 4.35
1050 1059 4.754322 ACAAAACAGAAACAACACCCATC 58.246 39.130 0.00 0.00 0.00 3.51
1209 1218 4.770795 ACTTGATCCCGAGAACAATTAGG 58.229 43.478 0.00 0.00 34.65 2.69
1438 1447 1.135527 CTTTAGATACCGTGGCGTCCA 59.864 52.381 0.00 0.00 0.00 4.02
1626 1635 2.235898 GCATGCAAAGGGTGGGATAAAA 59.764 45.455 14.21 0.00 0.00 1.52
2068 2081 4.332819 GCACGAAAATTACCTCTAGCACAT 59.667 41.667 0.00 0.00 0.00 3.21
2160 2174 5.044476 TGGTTTCCATCACCTACCAATATGT 60.044 40.000 0.00 0.00 36.03 2.29
2164 2178 3.309121 CCTGGTTTCCATCACCTACCAAT 60.309 47.826 0.00 0.00 38.33 3.16
2183 2197 7.516450 AATAGATTCCCCCATTATACTCCTG 57.484 40.000 0.00 0.00 0.00 3.86
2188 2202 9.232473 GTCTTGAAATAGATTCCCCCATTATAC 57.768 37.037 0.00 0.00 37.22 1.47
2198 2212 5.183228 TGGTTCGGTCTTGAAATAGATTCC 58.817 41.667 0.00 0.00 37.22 3.01
2251 2271 1.400759 GCCTTCTTTTTGAGCGAGCTG 60.401 52.381 0.84 0.00 0.00 4.24
2252 2272 0.877743 GCCTTCTTTTTGAGCGAGCT 59.122 50.000 0.00 0.00 0.00 4.09
2253 2273 3.391425 GCCTTCTTTTTGAGCGAGC 57.609 52.632 0.00 0.00 0.00 5.03
2320 2340 2.363038 GTTTGGGTTGGTAGTTTGGGTC 59.637 50.000 0.00 0.00 0.00 4.46
2328 2348 2.899303 ATGAGGGTTTGGGTTGGTAG 57.101 50.000 0.00 0.00 0.00 3.18
2434 2455 1.517257 CAAGGTCACCTCGCTAGCG 60.517 63.158 30.91 30.91 41.35 4.26
2620 2655 2.365582 ACATTCCGCTTGTTGGGATAC 58.634 47.619 0.00 0.00 31.11 2.24
2729 2764 9.401058 CAACTCCTCATTATCAAGAATAGGTTT 57.599 33.333 0.00 0.00 0.00 3.27
3044 3081 8.076178 TCAATTCACGAAAGAAAAAGATCTTCC 58.924 33.333 8.78 1.54 38.69 3.46
3507 3556 6.371809 AGTAACACAACTGGTAACACATTG 57.628 37.500 0.00 0.00 46.17 2.82
3605 3655 4.957759 ACACACCAGTAACACACTTTTC 57.042 40.909 0.00 0.00 34.26 2.29
3788 3840 4.253685 CACCATCTTGTGTTACTACAGGG 58.746 47.826 0.00 0.00 34.24 4.45
3844 3896 5.049954 TCGTGCTTGTATAAGTGGTTTTCAC 60.050 40.000 0.90 0.00 46.39 3.18
3845 3897 5.057819 TCGTGCTTGTATAAGTGGTTTTCA 58.942 37.500 0.90 0.00 36.27 2.69
3846 3898 5.600908 TCGTGCTTGTATAAGTGGTTTTC 57.399 39.130 0.90 0.00 36.27 2.29
3847 3899 5.529800 ACTTCGTGCTTGTATAAGTGGTTTT 59.470 36.000 0.90 0.00 36.27 2.43
3848 3900 5.061179 ACTTCGTGCTTGTATAAGTGGTTT 58.939 37.500 0.90 0.00 36.27 3.27
3849 3901 4.638304 ACTTCGTGCTTGTATAAGTGGTT 58.362 39.130 0.90 0.00 36.27 3.67
3850 3902 4.267349 ACTTCGTGCTTGTATAAGTGGT 57.733 40.909 0.90 0.00 36.27 4.16
3851 3903 4.142902 CCAACTTCGTGCTTGTATAAGTGG 60.143 45.833 0.90 0.00 36.27 4.00
3852 3904 4.669197 GCCAACTTCGTGCTTGTATAAGTG 60.669 45.833 0.90 0.00 36.27 3.16
3853 3905 3.435671 GCCAACTTCGTGCTTGTATAAGT 59.564 43.478 0.90 0.00 36.27 2.24
3854 3906 3.181510 GGCCAACTTCGTGCTTGTATAAG 60.182 47.826 0.00 0.00 36.97 1.73
3855 3907 2.745281 GGCCAACTTCGTGCTTGTATAA 59.255 45.455 0.00 0.00 0.00 0.98
3856 3908 2.289756 TGGCCAACTTCGTGCTTGTATA 60.290 45.455 0.61 0.00 0.00 1.47
3857 3909 1.165270 GGCCAACTTCGTGCTTGTAT 58.835 50.000 0.00 0.00 0.00 2.29
3858 3910 0.179043 TGGCCAACTTCGTGCTTGTA 60.179 50.000 0.61 0.00 0.00 2.41
3859 3911 1.447317 CTGGCCAACTTCGTGCTTGT 61.447 55.000 7.01 0.00 0.00 3.16
3860 3912 1.283793 CTGGCCAACTTCGTGCTTG 59.716 57.895 7.01 0.00 0.00 4.01
3861 3913 1.898574 CCTGGCCAACTTCGTGCTT 60.899 57.895 7.01 0.00 0.00 3.91
3862 3914 2.129555 ATCCTGGCCAACTTCGTGCT 62.130 55.000 7.01 0.00 0.00 4.40
3863 3915 0.392461 TATCCTGGCCAACTTCGTGC 60.392 55.000 7.01 0.00 0.00 5.34
3864 3916 2.332063 ATATCCTGGCCAACTTCGTG 57.668 50.000 7.01 0.00 0.00 4.35
3865 3917 5.483937 TCATATATATCCTGGCCAACTTCGT 59.516 40.000 7.01 0.00 0.00 3.85
3866 3918 5.812642 GTCATATATATCCTGGCCAACTTCG 59.187 44.000 7.01 0.00 0.00 3.79
3867 3919 6.116126 GGTCATATATATCCTGGCCAACTTC 58.884 44.000 7.01 0.00 34.74 3.01
3868 3920 5.551583 TGGTCATATATATCCTGGCCAACTT 59.448 40.000 15.63 0.00 41.48 2.66
3869 3921 5.100811 TGGTCATATATATCCTGGCCAACT 58.899 41.667 15.63 0.00 41.48 3.16
3870 3922 5.431765 CTGGTCATATATATCCTGGCCAAC 58.568 45.833 17.59 0.00 43.61 3.77
3871 3923 4.474651 CCTGGTCATATATATCCTGGCCAA 59.525 45.833 17.59 0.00 43.61 4.52
3872 3924 4.040047 CCTGGTCATATATATCCTGGCCA 58.960 47.826 16.56 16.56 42.14 5.36
3873 3925 4.298626 TCCTGGTCATATATATCCTGGCC 58.701 47.826 16.06 10.53 38.42 5.36
3874 3926 5.279206 CGATCCTGGTCATATATATCCTGGC 60.279 48.000 16.06 1.07 38.42 4.85
3875 3927 5.835819 ACGATCCTGGTCATATATATCCTGG 59.164 44.000 15.25 15.25 39.40 4.45
3876 3928 6.968263 ACGATCCTGGTCATATATATCCTG 57.032 41.667 0.00 0.00 0.00 3.86
3877 3929 8.228206 ACATACGATCCTGGTCATATATATCCT 58.772 37.037 0.00 0.00 0.00 3.24
3878 3930 8.410673 ACATACGATCCTGGTCATATATATCC 57.589 38.462 0.00 0.00 0.00 2.59
3879 3931 9.290988 AGACATACGATCCTGGTCATATATATC 57.709 37.037 0.00 0.00 0.00 1.63
3880 3932 9.072375 CAGACATACGATCCTGGTCATATATAT 57.928 37.037 0.00 0.00 0.00 0.86
3881 3933 7.013369 GCAGACATACGATCCTGGTCATATATA 59.987 40.741 0.00 0.00 0.00 0.86
3882 3934 6.183360 GCAGACATACGATCCTGGTCATATAT 60.183 42.308 0.00 0.00 0.00 0.86
3883 3935 5.125578 GCAGACATACGATCCTGGTCATATA 59.874 44.000 0.00 0.00 0.00 0.86
3884 3936 4.081972 GCAGACATACGATCCTGGTCATAT 60.082 45.833 0.00 0.00 0.00 1.78
3885 3937 3.255888 GCAGACATACGATCCTGGTCATA 59.744 47.826 0.00 0.00 0.00 2.15
3886 3938 2.036475 GCAGACATACGATCCTGGTCAT 59.964 50.000 0.00 0.00 0.00 3.06
3887 3939 1.409064 GCAGACATACGATCCTGGTCA 59.591 52.381 0.00 0.00 0.00 4.02
3888 3940 1.409064 TGCAGACATACGATCCTGGTC 59.591 52.381 0.00 0.00 0.00 4.02
3889 3941 1.485124 TGCAGACATACGATCCTGGT 58.515 50.000 0.00 0.00 0.00 4.00
3890 3942 2.410939 CATGCAGACATACGATCCTGG 58.589 52.381 0.00 0.00 33.67 4.45
3891 3943 2.036346 TCCATGCAGACATACGATCCTG 59.964 50.000 0.00 0.00 33.67 3.86
3892 3944 2.298446 CTCCATGCAGACATACGATCCT 59.702 50.000 0.00 0.00 33.67 3.24
3893 3945 2.036475 ACTCCATGCAGACATACGATCC 59.964 50.000 0.00 0.00 33.67 3.36
3894 3946 3.377346 ACTCCATGCAGACATACGATC 57.623 47.619 0.00 0.00 33.67 3.69
3895 3947 3.827008 AACTCCATGCAGACATACGAT 57.173 42.857 0.00 0.00 33.67 3.73
3896 3948 3.521560 GAAACTCCATGCAGACATACGA 58.478 45.455 0.00 0.00 33.67 3.43
3897 3949 2.282555 CGAAACTCCATGCAGACATACG 59.717 50.000 0.00 0.00 33.67 3.06
3898 3950 3.521560 TCGAAACTCCATGCAGACATAC 58.478 45.455 0.00 0.00 33.67 2.39
3899 3951 3.430790 CCTCGAAACTCCATGCAGACATA 60.431 47.826 0.00 0.00 33.67 2.29
3900 3952 2.625737 CTCGAAACTCCATGCAGACAT 58.374 47.619 0.00 0.00 36.79 3.06
3901 3953 1.338105 CCTCGAAACTCCATGCAGACA 60.338 52.381 0.00 0.00 0.00 3.41
3902 3954 1.066858 TCCTCGAAACTCCATGCAGAC 60.067 52.381 0.00 0.00 0.00 3.51
3903 3955 1.066858 GTCCTCGAAACTCCATGCAGA 60.067 52.381 0.00 0.00 0.00 4.26
3904 3956 1.363744 GTCCTCGAAACTCCATGCAG 58.636 55.000 0.00 0.00 0.00 4.41
3905 3957 0.036388 GGTCCTCGAAACTCCATGCA 60.036 55.000 0.00 0.00 0.00 3.96
3906 3958 0.036388 TGGTCCTCGAAACTCCATGC 60.036 55.000 0.00 0.00 0.00 4.06
3907 3959 2.555199 GATGGTCCTCGAAACTCCATG 58.445 52.381 13.29 0.00 38.74 3.66
3908 3960 1.137086 CGATGGTCCTCGAAACTCCAT 59.863 52.381 9.71 9.71 41.12 3.41
3909 3961 0.530744 CGATGGTCCTCGAAACTCCA 59.469 55.000 5.15 0.00 41.12 3.86
3910 3962 0.531200 ACGATGGTCCTCGAAACTCC 59.469 55.000 15.00 0.00 41.12 3.85
3911 3963 3.066342 TGATACGATGGTCCTCGAAACTC 59.934 47.826 15.00 7.92 41.12 3.01
3912 3964 3.021695 TGATACGATGGTCCTCGAAACT 58.978 45.455 15.00 0.00 41.12 2.66
3913 3965 3.066342 TCTGATACGATGGTCCTCGAAAC 59.934 47.826 15.00 7.70 41.12 2.78
3914 3966 3.284617 TCTGATACGATGGTCCTCGAAA 58.715 45.455 15.00 5.73 41.12 3.46
3915 3967 2.927028 TCTGATACGATGGTCCTCGAA 58.073 47.619 15.00 1.28 41.12 3.71
3916 3968 2.632987 TCTGATACGATGGTCCTCGA 57.367 50.000 15.00 0.00 41.12 4.04
3917 3969 4.254492 TCTATCTGATACGATGGTCCTCG 58.746 47.826 8.60 8.60 44.14 4.63
3918 3970 4.638421 CCTCTATCTGATACGATGGTCCTC 59.362 50.000 0.00 0.00 0.00 3.71
3919 3971 4.594970 CCTCTATCTGATACGATGGTCCT 58.405 47.826 0.00 0.00 0.00 3.85
3920 3972 4.974368 CCTCTATCTGATACGATGGTCC 57.026 50.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.