Multiple sequence alignment - TraesCS2A01G300900

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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 TraesCS2A01G300900 chr2A 100.000 2929 0 0 1 2929 516297248 516294320 0.000000e+00 5409.0
1 TraesCS2A01G300900 chr2B 95.352 2345 85 10 77 2402 452774741 452772402 0.000000e+00 3705.0
2 TraesCS2A01G300900 chr2B 93.039 431 29 1 2398 2828 452660307 452659878 1.920000e-176 628.0
3 TraesCS2A01G300900 chr2D 96.396 2109 66 6 25 2129 381885855 381883753 0.000000e+00 3465.0
4 TraesCS2A01G300900 chr2D 94.349 637 23 8 2204 2828 381883750 381883115 0.000000e+00 965.0
5 TraesCS2A01G300900 chr6B 92.784 97 7 0 2833 2929 611508805 611508901 1.090000e-29 141.0
6 TraesCS2A01G300900 chr4D 77.990 209 26 15 2398 2598 10100687 10100883 2.390000e-21 113.0
7 TraesCS2A01G300900 chr4B 77.358 106 15 7 2519 2617 582161883 582161780 1.000000e-03 54.7


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 TraesCS2A01G300900 chr2A 516294320 516297248 2928 True 5409 5409 100.0000 1 2929 1 chr2A.!!$R1 2928
1 TraesCS2A01G300900 chr2B 452772402 452774741 2339 True 3705 3705 95.3520 77 2402 1 chr2B.!!$R2 2325
2 TraesCS2A01G300900 chr2D 381883115 381885855 2740 True 2215 3465 95.3725 25 2828 2 chr2D.!!$R1 2803

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
255 256 0.323629 TTGATCTTTCGTCGGGCCTT 59.676 50.000 0.84 0.00 0.0 4.35 F
380 382 1.343465 CGGGACCAAAGTACTGTGAGT 59.657 52.381 15.05 10.39 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1393 0.235926 GTTGTCCGCTTCTCTTGCAC 59.764 55.0 0.0 0.0 0.00 4.57 R
1953 1959 0.733150 TGTGAGTCCGCATCTACGAG 59.267 55.0 0.0 0.0 34.06 4.18 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
22 23 4.849111 TGGTGAAAACACGAAAATTTGC 57.151 36.364 0.00 0.00 0.00 3.68
23 24 3.619038 TGGTGAAAACACGAAAATTTGCC 59.381 39.130 0.00 0.00 0.00 4.52
31 32 4.546570 ACACGAAAATTTGCCTAAAGCTC 58.453 39.130 0.00 0.00 44.23 4.09
66 67 4.379243 CTTCGCGTGCCCCTGTCT 62.379 66.667 5.77 0.00 0.00 3.41
67 68 4.373116 TTCGCGTGCCCCTGTCTC 62.373 66.667 5.77 0.00 0.00 3.36
72 73 1.856265 GCGTGCCCCTGTCTCTTTTG 61.856 60.000 0.00 0.00 0.00 2.44
167 168 2.125753 CCTCTGCTGACAGTCCGC 60.126 66.667 9.92 9.92 44.77 5.54
255 256 0.323629 TTGATCTTTCGTCGGGCCTT 59.676 50.000 0.84 0.00 0.00 4.35
342 343 3.574445 GCTCTGCTCAGCGCCATG 61.574 66.667 2.29 0.00 38.05 3.66
380 382 1.343465 CGGGACCAAAGTACTGTGAGT 59.657 52.381 15.05 10.39 0.00 3.41
529 532 3.759618 GCATACTACTCCTACCTGCTAGG 59.240 52.174 0.00 1.16 43.54 3.02
547 550 5.307196 TGCTAGGGGTATGAGTTTATTCCTC 59.693 44.000 0.00 0.00 0.00 3.71
707 710 2.850695 AGTACTCCCTCCGGAAAGAT 57.149 50.000 5.23 0.00 37.86 2.40
716 719 7.246763 ACTCCCTCCGGAAAGATATATAAGAA 58.753 38.462 5.23 0.00 37.86 2.52
722 725 8.583810 TCCGGAAAGATATATAAGAACGTTTG 57.416 34.615 0.00 0.00 0.00 2.93
813 816 4.202451 TGCGAGATCATAATTCCCCAATCA 60.202 41.667 0.00 0.00 0.00 2.57
841 844 9.607333 AGATGATCTACTTATGGTCCTCATTAA 57.393 33.333 0.00 0.00 37.30 1.40
868 871 1.840635 GGCTAGACCAAAGAGGGATGT 59.159 52.381 0.00 0.00 43.89 3.06
878 881 1.843368 AGAGGGATGTCGTTTACCGA 58.157 50.000 0.00 0.00 45.00 4.69
979 982 5.770663 AGATAAGTTCTAGCTCGCCAAGATA 59.229 40.000 0.00 0.00 30.96 1.98
1126 1129 6.853362 GCAAGTATCAATTCCTTTATTCGCTC 59.147 38.462 0.00 0.00 0.00 5.03
1188 1194 8.772705 TCATTTGATTGCAAAATGGTTTACTTC 58.227 29.630 17.91 2.69 46.19 3.01
1189 1195 8.776470 CATTTGATTGCAAAATGGTTTACTTCT 58.224 29.630 1.71 0.00 46.19 2.85
1190 1196 8.729805 TTTGATTGCAAAATGGTTTACTTCTT 57.270 26.923 1.71 0.00 40.82 2.52
1203 1209 6.039382 TGGTTTACTTCTTGCCTCTTTTCTTC 59.961 38.462 0.00 0.00 0.00 2.87
1273 1279 2.874648 GATGTGCCTGGTCATCCGCA 62.875 60.000 17.10 5.23 35.71 5.69
1387 1393 4.899239 GGCCGAGGTGCTGATCCG 62.899 72.222 0.00 0.00 0.00 4.18
1452 1458 1.008538 CACGGCACAAACAAGGAGC 60.009 57.895 0.00 0.00 0.00 4.70
1608 1614 1.616187 CGAAGGACAGTCCCTCTACCA 60.616 57.143 16.72 0.00 37.19 3.25
1841 1847 4.933064 GATGTCGCGCGCCTAGCT 62.933 66.667 27.95 6.52 45.59 3.32
1875 1881 1.000274 GTGTCCCTGTTCAACAATGCC 60.000 52.381 0.00 0.00 0.00 4.40
1880 1886 1.619827 CCTGTTCAACAATGCCACCAT 59.380 47.619 0.00 0.00 0.00 3.55
1886 1892 0.538118 AACAATGCCACCATGGATGC 59.462 50.000 21.47 20.04 40.96 3.91
1888 1894 1.001888 AATGCCACCATGGATGCCA 59.998 52.632 21.47 9.57 40.96 4.92
1891 1897 0.467844 TGCCACCATGGATGCCATAC 60.468 55.000 21.47 0.00 43.15 2.39
1893 1899 2.028472 GCCACCATGGATGCCATACAA 61.028 52.381 21.47 0.00 43.15 2.41
1894 1900 2.600790 CCACCATGGATGCCATACAAT 58.399 47.619 21.47 0.00 43.15 2.71
1916 1922 2.081161 AGATCACTGGGGGCCATCC 61.081 63.158 4.39 6.20 30.82 3.51
1930 1936 0.036952 CCATCCCATGGCTACTAGCG 60.037 60.000 6.09 0.00 44.70 4.26
1948 1954 3.822940 AGCGGAGTATGCTCTACTAAGT 58.177 45.455 10.82 0.00 38.62 2.24
1953 1959 6.128580 GCGGAGTATGCTCTACTAAGTAGTAC 60.129 46.154 10.82 0.00 41.38 2.73
1954 1960 7.153985 CGGAGTATGCTCTACTAAGTAGTACT 58.846 42.308 10.82 0.00 41.38 2.73
1955 1961 7.329226 CGGAGTATGCTCTACTAAGTAGTACTC 59.671 44.444 10.82 12.26 38.65 2.59
1963 1972 7.148755 GCTCTACTAAGTAGTACTCGTAGATGC 60.149 44.444 26.43 25.33 38.87 3.91
2065 2074 2.182516 AAGTAGATAGGGCTGGTGCT 57.817 50.000 0.00 0.00 39.59 4.40
2068 2077 2.178106 AGTAGATAGGGCTGGTGCTAGT 59.822 50.000 0.00 0.00 39.59 2.57
2331 2353 7.962964 TTTAGAGTGGAGTTGATGTTTGTAG 57.037 36.000 0.00 0.00 0.00 2.74
2417 2439 8.573035 TCTTTGGAAACCATGTTCTACATTAAC 58.427 33.333 0.00 0.00 36.53 2.01
2461 2483 7.870509 AACATGTCATGCATTAACTCAGTAT 57.129 32.000 12.91 0.00 35.19 2.12
2463 2485 9.565090 AACATGTCATGCATTAACTCAGTATAT 57.435 29.630 12.91 0.00 35.19 0.86
2540 2562 7.310609 CCTTCCACTACCCAAATCAAATCAAAT 60.311 37.037 0.00 0.00 0.00 2.32
2730 2753 4.859304 TTCACACACGACAAGTACCTAT 57.141 40.909 0.00 0.00 0.00 2.57
2769 2792 5.302568 TCATTTCTTTGATCTGTGTGGCTTT 59.697 36.000 0.00 0.00 0.00 3.51
2822 2845 0.588252 ATCGTGTGTGCTGCAGTTTC 59.412 50.000 16.64 6.77 0.00 2.78
2828 2851 2.032117 TGTGTGCTGCAGTTTCGTATTG 60.032 45.455 16.64 0.00 0.00 1.90
2829 2852 2.223144 GTGTGCTGCAGTTTCGTATTGA 59.777 45.455 16.64 0.00 0.00 2.57
2830 2853 3.073678 TGTGCTGCAGTTTCGTATTGAT 58.926 40.909 16.64 0.00 0.00 2.57
2831 2854 3.501828 TGTGCTGCAGTTTCGTATTGATT 59.498 39.130 16.64 0.00 0.00 2.57
2832 2855 3.848019 GTGCTGCAGTTTCGTATTGATTG 59.152 43.478 16.64 0.00 0.00 2.67
2833 2856 2.848302 GCTGCAGTTTCGTATTGATTGC 59.152 45.455 16.64 0.00 32.53 3.56
2834 2857 3.670359 GCTGCAGTTTCGTATTGATTGCA 60.670 43.478 16.64 0.00 36.83 4.08
2835 2858 4.665212 CTGCAGTTTCGTATTGATTGCAT 58.335 39.130 5.25 0.00 37.82 3.96
2836 2859 4.413969 TGCAGTTTCGTATTGATTGCATG 58.586 39.130 0.00 0.00 35.32 4.06
2837 2860 3.792956 GCAGTTTCGTATTGATTGCATGG 59.207 43.478 0.00 0.00 32.32 3.66
2838 2861 4.438608 GCAGTTTCGTATTGATTGCATGGA 60.439 41.667 0.00 0.00 32.32 3.41
2839 2862 5.030295 CAGTTTCGTATTGATTGCATGGAC 58.970 41.667 0.00 0.00 0.00 4.02
2840 2863 4.096382 AGTTTCGTATTGATTGCATGGACC 59.904 41.667 0.00 0.00 0.00 4.46
2841 2864 3.274095 TCGTATTGATTGCATGGACCA 57.726 42.857 0.00 0.00 0.00 4.02
2842 2865 3.615155 TCGTATTGATTGCATGGACCAA 58.385 40.909 0.00 0.00 0.00 3.67
2843 2866 3.627123 TCGTATTGATTGCATGGACCAAG 59.373 43.478 0.00 0.00 0.00 3.61
2844 2867 3.627123 CGTATTGATTGCATGGACCAAGA 59.373 43.478 0.00 0.91 0.00 3.02
2845 2868 4.096231 CGTATTGATTGCATGGACCAAGAA 59.904 41.667 0.00 0.00 0.00 2.52
2846 2869 5.221106 CGTATTGATTGCATGGACCAAGAAT 60.221 40.000 0.00 0.00 0.00 2.40
2847 2870 6.017192 CGTATTGATTGCATGGACCAAGAATA 60.017 38.462 0.00 0.00 0.00 1.75
2848 2871 5.581126 TTGATTGCATGGACCAAGAATAC 57.419 39.130 0.00 0.00 0.00 1.89
2849 2872 3.627123 TGATTGCATGGACCAAGAATACG 59.373 43.478 0.00 0.00 0.00 3.06
2850 2873 2.036958 TGCATGGACCAAGAATACGG 57.963 50.000 0.00 0.00 0.00 4.02
2851 2874 0.663153 GCATGGACCAAGAATACGGC 59.337 55.000 0.00 0.00 0.00 5.68
2852 2875 2.016604 GCATGGACCAAGAATACGGCA 61.017 52.381 0.00 0.00 0.00 5.69
2853 2876 1.942657 CATGGACCAAGAATACGGCAG 59.057 52.381 0.00 0.00 0.00 4.85
2854 2877 0.392461 TGGACCAAGAATACGGCAGC 60.392 55.000 0.00 0.00 0.00 5.25
2855 2878 0.392461 GGACCAAGAATACGGCAGCA 60.392 55.000 0.00 0.00 0.00 4.41
2856 2879 1.009829 GACCAAGAATACGGCAGCAG 58.990 55.000 0.00 0.00 0.00 4.24
2857 2880 0.613260 ACCAAGAATACGGCAGCAGA 59.387 50.000 0.00 0.00 0.00 4.26
2858 2881 1.003118 ACCAAGAATACGGCAGCAGAA 59.997 47.619 0.00 0.00 0.00 3.02
2859 2882 1.398390 CCAAGAATACGGCAGCAGAAC 59.602 52.381 0.00 0.00 0.00 3.01
2860 2883 2.350522 CAAGAATACGGCAGCAGAACT 58.649 47.619 0.00 0.00 0.00 3.01
2861 2884 3.521560 CAAGAATACGGCAGCAGAACTA 58.478 45.455 0.00 0.00 0.00 2.24
2862 2885 3.166489 AGAATACGGCAGCAGAACTAC 57.834 47.619 0.00 0.00 0.00 2.73
2863 2886 2.761208 AGAATACGGCAGCAGAACTACT 59.239 45.455 0.00 0.00 0.00 2.57
2864 2887 2.873133 ATACGGCAGCAGAACTACTC 57.127 50.000 0.00 0.00 0.00 2.59
2865 2888 0.450583 TACGGCAGCAGAACTACTCG 59.549 55.000 0.00 0.00 0.00 4.18
2866 2889 1.517257 CGGCAGCAGAACTACTCGG 60.517 63.158 0.00 0.00 0.00 4.63
2867 2890 1.811679 GGCAGCAGAACTACTCGGC 60.812 63.158 0.00 0.00 44.77 5.54
2868 2891 1.079819 GCAGCAGAACTACTCGGCA 60.080 57.895 0.00 0.00 46.63 5.69
2869 2892 1.080995 GCAGCAGAACTACTCGGCAG 61.081 60.000 0.00 0.00 46.63 4.85
2870 2893 1.080995 CAGCAGAACTACTCGGCAGC 61.081 60.000 0.00 0.00 46.63 5.25
2871 2894 1.216710 GCAGAACTACTCGGCAGCT 59.783 57.895 0.00 0.00 43.95 4.24
2872 2895 0.804156 GCAGAACTACTCGGCAGCTC 60.804 60.000 0.00 0.00 43.95 4.09
2873 2896 0.179124 CAGAACTACTCGGCAGCTCC 60.179 60.000 0.00 0.00 0.00 4.70
2874 2897 0.323908 AGAACTACTCGGCAGCTCCT 60.324 55.000 0.00 0.00 0.00 3.69
2875 2898 0.179124 GAACTACTCGGCAGCTCCTG 60.179 60.000 0.00 0.00 34.12 3.86
2884 2907 2.898738 CAGCTCCTGCCTGATCGT 59.101 61.111 0.00 0.00 40.80 3.73
2885 2908 1.227205 CAGCTCCTGCCTGATCGTC 60.227 63.158 0.00 0.00 40.80 4.20
2886 2909 1.683707 AGCTCCTGCCTGATCGTCA 60.684 57.895 0.00 0.00 40.80 4.35
2887 2910 1.227205 GCTCCTGCCTGATCGTCAG 60.227 63.158 7.72 7.72 43.91 3.51
2888 2911 1.227205 CTCCTGCCTGATCGTCAGC 60.227 63.158 8.85 6.18 42.98 4.26
2889 2912 2.202987 CCTGCCTGATCGTCAGCC 60.203 66.667 8.85 0.56 42.98 4.85
2890 2913 2.729479 CCTGCCTGATCGTCAGCCT 61.729 63.158 8.85 0.00 42.98 4.58
2891 2914 1.220206 CTGCCTGATCGTCAGCCTT 59.780 57.895 8.85 0.00 42.98 4.35
2892 2915 1.078918 TGCCTGATCGTCAGCCTTG 60.079 57.895 8.85 0.00 42.98 3.61
2893 2916 2.467826 GCCTGATCGTCAGCCTTGC 61.468 63.158 8.85 4.62 42.98 4.01
2894 2917 2.169789 CCTGATCGTCAGCCTTGCG 61.170 63.158 8.85 0.00 42.98 4.85
2895 2918 2.806856 CTGATCGTCAGCCTTGCGC 61.807 63.158 0.00 0.00 37.72 6.09
2896 2919 3.567797 GATCGTCAGCCTTGCGCC 61.568 66.667 4.18 0.00 38.78 6.53
2915 2938 3.928343 GGAGACGGAGAATCACGAG 57.072 57.895 4.50 0.00 36.25 4.18
2916 2939 0.382515 GGAGACGGAGAATCACGAGG 59.617 60.000 4.50 0.00 36.25 4.63
2917 2940 1.380524 GAGACGGAGAATCACGAGGA 58.619 55.000 4.50 0.00 36.25 3.71
2918 2941 1.950909 GAGACGGAGAATCACGAGGAT 59.049 52.381 4.50 0.00 36.25 3.24
2919 2942 1.950909 AGACGGAGAATCACGAGGATC 59.049 52.381 4.50 0.00 36.25 3.36
2920 2943 1.950909 GACGGAGAATCACGAGGATCT 59.049 52.381 4.50 0.00 36.25 2.75
2921 2944 1.950909 ACGGAGAATCACGAGGATCTC 59.049 52.381 4.50 0.00 36.25 2.75
2922 2945 2.226330 CGGAGAATCACGAGGATCTCT 58.774 52.381 12.66 9.36 36.25 3.10
2923 2946 2.225491 CGGAGAATCACGAGGATCTCTC 59.775 54.545 12.66 14.57 38.30 3.20
2924 2947 2.556622 GGAGAATCACGAGGATCTCTCC 59.443 54.545 21.31 21.31 44.12 3.71
2925 2948 2.556622 GAGAATCACGAGGATCTCTCCC 59.443 54.545 0.00 0.00 37.38 4.30
2926 2949 2.176798 AGAATCACGAGGATCTCTCCCT 59.823 50.000 0.00 0.00 43.21 4.20
2927 2950 2.286365 ATCACGAGGATCTCTCCCTC 57.714 55.000 0.00 0.00 43.21 4.30
2928 2951 1.217916 TCACGAGGATCTCTCCCTCT 58.782 55.000 0.00 0.00 46.15 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.576551 TTAGGCAAATTTTCGTGTTTTCAC 57.423 33.333 0.00 0.00 46.33 3.18
4 5 6.237969 GCTTTAGGCAAATTTTCGTGTTTTCA 60.238 34.615 0.00 0.00 41.35 2.69
5 6 6.019075 AGCTTTAGGCAAATTTTCGTGTTTTC 60.019 34.615 0.00 0.00 44.79 2.29
6 7 5.815222 AGCTTTAGGCAAATTTTCGTGTTTT 59.185 32.000 0.00 0.00 44.79 2.43
7 8 5.356426 AGCTTTAGGCAAATTTTCGTGTTT 58.644 33.333 0.00 0.00 44.79 2.83
8 9 4.944048 AGCTTTAGGCAAATTTTCGTGTT 58.056 34.783 0.00 0.00 44.79 3.32
9 10 4.037446 TGAGCTTTAGGCAAATTTTCGTGT 59.963 37.500 0.00 0.00 44.79 4.49
10 11 4.545610 TGAGCTTTAGGCAAATTTTCGTG 58.454 39.130 0.00 0.00 44.79 4.35
11 12 4.846779 TGAGCTTTAGGCAAATTTTCGT 57.153 36.364 0.00 0.00 44.79 3.85
12 13 4.563976 CCATGAGCTTTAGGCAAATTTTCG 59.436 41.667 0.00 0.00 44.79 3.46
13 14 4.330894 GCCATGAGCTTTAGGCAAATTTTC 59.669 41.667 16.48 0.00 46.26 2.29
14 15 4.256110 GCCATGAGCTTTAGGCAAATTTT 58.744 39.130 16.48 0.00 46.26 1.82
15 16 3.865446 GCCATGAGCTTTAGGCAAATTT 58.135 40.909 16.48 0.00 46.26 1.82
16 17 3.531934 GCCATGAGCTTTAGGCAAATT 57.468 42.857 16.48 0.00 46.26 1.82
31 32 0.037303 AGGTGTGAGTTGGAGCCATG 59.963 55.000 0.00 0.00 0.00 3.66
72 73 8.017946 ACATGCGAGATAAGAAAAGAGAAAAAC 58.982 33.333 0.00 0.00 0.00 2.43
185 186 2.094675 CCATTTCAGAAGAATGGCGGT 58.905 47.619 1.55 0.00 32.89 5.68
380 382 0.395724 TGATCACTGCTCGGCCTCTA 60.396 55.000 0.00 0.00 0.00 2.43
529 532 6.711194 GCTTAAGGAGGAATAAACTCATACCC 59.289 42.308 4.29 0.00 36.70 3.69
772 775 8.668510 ATCTCGCAGATCAATGTAAATTACTT 57.331 30.769 4.67 0.00 33.89 2.24
813 816 9.781425 AATGAGGACCATAAGTAGATCATCTAT 57.219 33.333 0.00 0.00 34.45 1.98
841 844 3.322254 CCTCTTTGGTCTAGCCGATGTAT 59.678 47.826 0.00 0.00 41.21 2.29
878 881 0.381801 CAGTTTGGTGCTTCGCAGTT 59.618 50.000 0.00 0.00 40.08 3.16
979 982 9.793259 CACCATACATATCCTTTGGTAACTATT 57.207 33.333 0.00 0.00 38.61 1.73
1126 1129 8.024145 AGAGGGTAAGGTAATGTAAGATCAAG 57.976 38.462 0.00 0.00 0.00 3.02
1188 1194 4.986659 CACATTTGGAAGAAAAGAGGCAAG 59.013 41.667 0.00 0.00 0.00 4.01
1189 1195 4.405358 ACACATTTGGAAGAAAAGAGGCAA 59.595 37.500 0.00 0.00 0.00 4.52
1190 1196 3.960102 ACACATTTGGAAGAAAAGAGGCA 59.040 39.130 0.00 0.00 0.00 4.75
1203 1209 4.115516 CCGAGACATCTCTACACATTTGG 58.884 47.826 7.29 0.00 40.75 3.28
1297 1303 0.883833 CATCCAGTGGAAGTTGTGGC 59.116 55.000 17.71 0.00 34.34 5.01
1387 1393 0.235926 GTTGTCCGCTTCTCTTGCAC 59.764 55.000 0.00 0.00 0.00 4.57
1452 1458 1.888018 CAGCTTGTTGGATGGCCAG 59.112 57.895 13.05 0.00 46.91 4.85
1608 1614 4.511246 CGCCTGGACCATGGCCAT 62.511 66.667 22.99 14.09 45.90 4.40
1689 1695 3.152341 CCAAGGTCTTGACAGCTTTGAT 58.848 45.455 11.87 0.00 42.93 2.57
1787 1793 4.096833 TCAATGGAAGGAATGCGAAATCTG 59.903 41.667 0.00 0.00 0.00 2.90
1870 1876 1.001888 TGGCATCCATGGTGGCATT 59.998 52.632 27.75 2.87 45.67 3.56
1875 1881 3.006110 GGAATTGTATGGCATCCATGGTG 59.994 47.826 12.58 10.59 44.84 4.17
1880 1886 3.949586 TCTGGAATTGTATGGCATCCA 57.050 42.857 1.65 3.88 34.75 3.41
1916 1922 1.617322 TACTCCGCTAGTAGCCATGG 58.383 55.000 16.51 7.63 38.18 3.66
1930 1936 7.329226 CGAGTACTACTTAGTAGAGCATACTCC 59.671 44.444 25.42 16.08 37.52 3.85
1948 1954 3.181472 TGAGTCCGCATCTACGAGTACTA 60.181 47.826 0.00 0.00 34.06 1.82
1953 1959 0.733150 TGTGAGTCCGCATCTACGAG 59.267 55.000 0.00 0.00 34.06 4.18
1954 1960 0.733150 CTGTGAGTCCGCATCTACGA 59.267 55.000 0.00 0.00 34.06 3.43
1955 1961 0.733150 TCTGTGAGTCCGCATCTACG 59.267 55.000 0.00 0.00 31.63 3.51
1963 1972 6.751514 AGCTAAGATATATCTGTGAGTCCG 57.248 41.667 16.01 1.01 37.19 4.79
2221 2232 7.832187 TCATACCCCAGACTTTATTTTTCGAAT 59.168 33.333 0.00 0.00 0.00 3.34
2235 2246 7.540474 TTATACAGATTCTCATACCCCAGAC 57.460 40.000 0.00 0.00 0.00 3.51
2267 2278 4.445448 GGTTCAGATCACCAGCCTATTCAT 60.445 45.833 0.00 0.00 34.04 2.57
2269 2280 3.135530 AGGTTCAGATCACCAGCCTATTC 59.864 47.826 3.73 0.00 36.67 1.75
2271 2282 2.769209 AGGTTCAGATCACCAGCCTAT 58.231 47.619 3.73 0.00 36.67 2.57
2272 2283 2.254152 AGGTTCAGATCACCAGCCTA 57.746 50.000 3.73 0.00 36.67 3.93
2273 2284 2.254152 TAGGTTCAGATCACCAGCCT 57.746 50.000 3.73 2.11 36.67 4.58
2275 2286 3.118629 TCACATAGGTTCAGATCACCAGC 60.119 47.826 3.73 0.00 36.67 4.85
2276 2287 4.743057 TCACATAGGTTCAGATCACCAG 57.257 45.455 3.73 0.00 36.67 4.00
2277 2288 5.426509 AGATTCACATAGGTTCAGATCACCA 59.573 40.000 3.73 0.00 36.67 4.17
2331 2353 5.048713 GGGGACGATATCAAAATTGATGACC 60.049 44.000 16.85 10.49 46.68 4.02
2475 2497 9.061610 GTGTTGATTCGGTTGATGTTTTTATAG 57.938 33.333 0.00 0.00 0.00 1.31
2479 2501 5.901552 AGTGTTGATTCGGTTGATGTTTTT 58.098 33.333 0.00 0.00 0.00 1.94
2485 2507 6.263168 AGAAAGAAAGTGTTGATTCGGTTGAT 59.737 34.615 0.00 0.00 0.00 2.57
2499 2521 4.098501 AGTGGAAGGCAAAGAAAGAAAGTG 59.901 41.667 0.00 0.00 0.00 3.16
2695 2718 2.877786 TGTGTGAATCGTGCACAAATCT 59.122 40.909 18.64 0.00 46.63 2.40
2730 2753 4.870636 AGAAATGAGGCAATCCAATGGTA 58.129 39.130 0.00 0.00 33.74 3.25
2769 2792 3.422473 CGATTTGTGCACGACGTGATTAA 60.422 43.478 31.08 17.56 35.23 1.40
2822 2845 3.627123 TCTTGGTCCATGCAATCAATACG 59.373 43.478 0.00 0.00 0.00 3.06
2828 2851 3.003689 CCGTATTCTTGGTCCATGCAATC 59.996 47.826 0.00 0.00 0.00 2.67
2829 2852 2.951642 CCGTATTCTTGGTCCATGCAAT 59.048 45.455 0.00 0.79 0.00 3.56
2830 2853 2.364632 CCGTATTCTTGGTCCATGCAA 58.635 47.619 0.00 0.00 0.00 4.08
2831 2854 2.016604 GCCGTATTCTTGGTCCATGCA 61.017 52.381 0.00 0.00 0.00 3.96
2832 2855 0.663153 GCCGTATTCTTGGTCCATGC 59.337 55.000 0.00 0.00 0.00 4.06
2833 2856 1.942657 CTGCCGTATTCTTGGTCCATG 59.057 52.381 0.00 0.00 0.00 3.66
2834 2857 1.747206 GCTGCCGTATTCTTGGTCCAT 60.747 52.381 0.00 0.00 0.00 3.41
2835 2858 0.392461 GCTGCCGTATTCTTGGTCCA 60.392 55.000 0.00 0.00 0.00 4.02
2836 2859 0.392461 TGCTGCCGTATTCTTGGTCC 60.392 55.000 0.00 0.00 0.00 4.46
2837 2860 1.009829 CTGCTGCCGTATTCTTGGTC 58.990 55.000 0.00 0.00 0.00 4.02
2838 2861 0.613260 TCTGCTGCCGTATTCTTGGT 59.387 50.000 0.00 0.00 0.00 3.67
2839 2862 1.398390 GTTCTGCTGCCGTATTCTTGG 59.602 52.381 0.00 0.00 0.00 3.61
2840 2863 2.350522 AGTTCTGCTGCCGTATTCTTG 58.649 47.619 0.00 0.00 0.00 3.02
2841 2864 2.770164 AGTTCTGCTGCCGTATTCTT 57.230 45.000 0.00 0.00 0.00 2.52
2842 2865 2.761208 AGTAGTTCTGCTGCCGTATTCT 59.239 45.455 0.00 0.00 0.00 2.40
2843 2866 3.117046 GAGTAGTTCTGCTGCCGTATTC 58.883 50.000 0.00 0.00 0.00 1.75
2844 2867 2.479730 CGAGTAGTTCTGCTGCCGTATT 60.480 50.000 0.00 0.00 0.00 1.89
2845 2868 1.065701 CGAGTAGTTCTGCTGCCGTAT 59.934 52.381 0.00 0.00 0.00 3.06
2846 2869 0.450583 CGAGTAGTTCTGCTGCCGTA 59.549 55.000 0.00 0.00 0.00 4.02
2847 2870 1.213013 CGAGTAGTTCTGCTGCCGT 59.787 57.895 0.00 0.00 0.00 5.68
2848 2871 1.517257 CCGAGTAGTTCTGCTGCCG 60.517 63.158 0.00 0.00 0.00 5.69
2849 2872 1.811679 GCCGAGTAGTTCTGCTGCC 60.812 63.158 0.00 0.00 33.68 4.85
2850 2873 1.079819 TGCCGAGTAGTTCTGCTGC 60.080 57.895 0.00 0.00 37.00 5.25
2851 2874 1.080995 GCTGCCGAGTAGTTCTGCTG 61.081 60.000 0.00 0.00 37.00 4.41
2852 2875 1.216710 GCTGCCGAGTAGTTCTGCT 59.783 57.895 0.00 0.00 37.00 4.24
2853 2876 0.804156 GAGCTGCCGAGTAGTTCTGC 60.804 60.000 0.00 0.00 36.65 4.26
2854 2877 0.179124 GGAGCTGCCGAGTAGTTCTG 60.179 60.000 0.00 0.00 0.00 3.02
2855 2878 0.323908 AGGAGCTGCCGAGTAGTTCT 60.324 55.000 0.00 0.00 43.43 3.01
2856 2879 0.179124 CAGGAGCTGCCGAGTAGTTC 60.179 60.000 0.00 0.00 43.43 3.01
2857 2880 1.893786 CAGGAGCTGCCGAGTAGTT 59.106 57.895 0.00 0.00 43.43 2.24
2858 2881 3.609703 CAGGAGCTGCCGAGTAGT 58.390 61.111 0.00 0.00 43.43 2.73
2867 2890 1.227205 GACGATCAGGCAGGAGCTG 60.227 63.158 0.00 0.00 41.70 4.24
2868 2891 1.683707 TGACGATCAGGCAGGAGCT 60.684 57.895 0.00 0.00 41.70 4.09
2869 2892 2.895680 TGACGATCAGGCAGGAGC 59.104 61.111 0.00 0.00 41.10 4.70
2876 2899 2.169789 CGCAAGGCTGACGATCAGG 61.170 63.158 14.19 2.48 44.43 3.86
2877 2900 2.806856 GCGCAAGGCTGACGATCAG 61.807 63.158 12.98 9.73 42.46 2.90
2878 2901 2.815211 GCGCAAGGCTGACGATCA 60.815 61.111 12.98 0.00 39.11 2.92
2896 2919 0.028242 CTCGTGATTCTCCGTCTCCG 59.972 60.000 0.00 0.00 0.00 4.63
2897 2920 0.382515 CCTCGTGATTCTCCGTCTCC 59.617 60.000 0.00 0.00 0.00 3.71
2898 2921 1.380524 TCCTCGTGATTCTCCGTCTC 58.619 55.000 0.00 0.00 0.00 3.36
2899 2922 1.950909 GATCCTCGTGATTCTCCGTCT 59.049 52.381 0.00 0.00 32.41 4.18
2900 2923 1.950909 AGATCCTCGTGATTCTCCGTC 59.049 52.381 0.00 0.00 32.41 4.79
2901 2924 1.950909 GAGATCCTCGTGATTCTCCGT 59.049 52.381 0.00 0.00 32.41 4.69
2902 2925 2.225491 GAGAGATCCTCGTGATTCTCCG 59.775 54.545 10.88 0.00 34.72 4.63
2903 2926 2.556622 GGAGAGATCCTCGTGATTCTCC 59.443 54.545 19.48 19.48 43.08 3.71
2904 2927 2.556622 GGGAGAGATCCTCGTGATTCTC 59.443 54.545 7.95 7.95 42.89 2.87
2905 2928 2.176798 AGGGAGAGATCCTCGTGATTCT 59.823 50.000 5.47 0.00 42.89 2.40
2906 2929 2.556622 GAGGGAGAGATCCTCGTGATTC 59.443 54.545 0.00 0.00 42.89 2.52
2907 2930 2.593026 GAGGGAGAGATCCTCGTGATT 58.407 52.381 0.00 0.00 42.89 2.57
2908 2931 2.286365 GAGGGAGAGATCCTCGTGAT 57.714 55.000 0.00 0.00 42.89 3.06
2909 2932 3.811031 GAGGGAGAGATCCTCGTGA 57.189 57.895 0.00 0.00 42.89 4.35


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

AutoCloner maintained by Alex Coulton.