Multiple sequence alignment - TraesCS2B01G435600

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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 TraesCS2B01G435600 chr2B 100.000 4775 0 0 1 4775 625916098 625920872 0.000000e+00 8818.0
1 TraesCS2B01G435600 chr2B 91.007 834 60 9 14 840 131297999 131298824 0.000000e+00 1110.0
2 TraesCS2B01G435600 chr2B 98.039 153 3 0 3887 4039 625926507 625926659 2.830000e-67 267.0
3 TraesCS2B01G435600 chr2D 97.143 2975 78 3 916 3888 528077024 528079993 0.000000e+00 5016.0
4 TraesCS2B01G435600 chr2A 92.234 2923 222 5 969 3888 672836676 672839596 0.000000e+00 4135.0
5 TraesCS2B01G435600 chr2A 87.277 841 90 16 4 836 20009093 20009924 0.000000e+00 944.0
6 TraesCS2B01G435600 chr2A 79.348 276 40 12 3887 4155 1301361 1301096 1.370000e-40 178.0
7 TraesCS2B01G435600 chr4B 96.171 888 32 1 3887 4774 60056413 60055528 0.000000e+00 1450.0
8 TraesCS2B01G435600 chr4B 98.013 151 3 0 3887 4037 60033620 60033470 3.660000e-66 263.0
9 TraesCS2B01G435600 chr6B 95.422 830 30 4 1 829 272592126 272592948 0.000000e+00 1315.0
10 TraesCS2B01G435600 chr6B 95.181 830 32 4 1 829 101272062 101272884 0.000000e+00 1304.0
11 TraesCS2B01G435600 chr1D 75.275 2819 624 64 988 3769 44651990 44649208 0.000000e+00 1277.0
12 TraesCS2B01G435600 chr7D 92.289 830 49 8 1 829 80349732 80350547 0.000000e+00 1164.0
13 TraesCS2B01G435600 chr7D 90.444 743 58 9 1 733 108286152 108286891 0.000000e+00 966.0
14 TraesCS2B01G435600 chr7D 86.591 880 95 12 3910 4770 46413434 46414309 0.000000e+00 950.0
15 TraesCS2B01G435600 chr7D 87.056 479 45 11 3887 4351 599946770 599946295 4.230000e-145 525.0
16 TraesCS2B01G435600 chr6D 89.282 905 76 11 3887 4775 24438355 24437456 0.000000e+00 1114.0
17 TraesCS2B01G435600 chr6D 89.578 806 74 8 1 804 141273581 141274378 0.000000e+00 1014.0
18 TraesCS2B01G435600 chr6D 83.377 758 98 17 3887 4622 433620294 433619543 0.000000e+00 676.0
19 TraesCS2B01G435600 chr6D 100.000 29 0 0 864 892 21995689 21995661 2.000000e-03 54.7
20 TraesCS2B01G435600 chr1A 87.956 905 91 10 3886 4775 535710519 535711420 0.000000e+00 1051.0
21 TraesCS2B01G435600 chr7A 91.768 741 45 11 1 739 198010962 198010236 0.000000e+00 1016.0
22 TraesCS2B01G435600 chr7A 85.675 726 91 5 4057 4770 680580084 680580808 0.000000e+00 752.0
23 TraesCS2B01G435600 chr7A 81.657 905 135 20 3885 4770 155491936 155492828 0.000000e+00 723.0
24 TraesCS2B01G435600 chr3D 88.612 843 78 11 1 839 598388868 598388040 0.000000e+00 1009.0
25 TraesCS2B01G435600 chr4A 86.570 901 102 10 3887 4773 703035503 703034608 0.000000e+00 976.0
26 TraesCS2B01G435600 chr4A 86.459 901 103 10 3887 4773 702970241 702969346 0.000000e+00 970.0
27 TraesCS2B01G435600 chr5A 85.333 900 111 12 3887 4770 642657887 642658781 0.000000e+00 911.0
28 TraesCS2B01G435600 chr5B 94.727 550 29 0 4226 4775 123014402 123014951 0.000000e+00 856.0
29 TraesCS2B01G435600 chr5B 92.977 299 20 1 3886 4184 123014109 123014406 7.340000e-118 435.0


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 TraesCS2B01G435600 chr2B 625916098 625920872 4774 False 8818.0 8818 100.000 1 4775 1 chr2B.!!$F2 4774
1 TraesCS2B01G435600 chr2B 131297999 131298824 825 False 1110.0 1110 91.007 14 840 1 chr2B.!!$F1 826
2 TraesCS2B01G435600 chr2D 528077024 528079993 2969 False 5016.0 5016 97.143 916 3888 1 chr2D.!!$F1 2972
3 TraesCS2B01G435600 chr2A 672836676 672839596 2920 False 4135.0 4135 92.234 969 3888 1 chr2A.!!$F2 2919
4 TraesCS2B01G435600 chr2A 20009093 20009924 831 False 944.0 944 87.277 4 836 1 chr2A.!!$F1 832
5 TraesCS2B01G435600 chr4B 60055528 60056413 885 True 1450.0 1450 96.171 3887 4774 1 chr4B.!!$R2 887
6 TraesCS2B01G435600 chr6B 272592126 272592948 822 False 1315.0 1315 95.422 1 829 1 chr6B.!!$F2 828
7 TraesCS2B01G435600 chr6B 101272062 101272884 822 False 1304.0 1304 95.181 1 829 1 chr6B.!!$F1 828
8 TraesCS2B01G435600 chr1D 44649208 44651990 2782 True 1277.0 1277 75.275 988 3769 1 chr1D.!!$R1 2781
9 TraesCS2B01G435600 chr7D 80349732 80350547 815 False 1164.0 1164 92.289 1 829 1 chr7D.!!$F2 828
10 TraesCS2B01G435600 chr7D 108286152 108286891 739 False 966.0 966 90.444 1 733 1 chr7D.!!$F3 732
11 TraesCS2B01G435600 chr7D 46413434 46414309 875 False 950.0 950 86.591 3910 4770 1 chr7D.!!$F1 860
12 TraesCS2B01G435600 chr6D 24437456 24438355 899 True 1114.0 1114 89.282 3887 4775 1 chr6D.!!$R2 888
13 TraesCS2B01G435600 chr6D 141273581 141274378 797 False 1014.0 1014 89.578 1 804 1 chr6D.!!$F1 803
14 TraesCS2B01G435600 chr6D 433619543 433620294 751 True 676.0 676 83.377 3887 4622 1 chr6D.!!$R3 735
15 TraesCS2B01G435600 chr1A 535710519 535711420 901 False 1051.0 1051 87.956 3886 4775 1 chr1A.!!$F1 889
16 TraesCS2B01G435600 chr7A 198010236 198010962 726 True 1016.0 1016 91.768 1 739 1 chr7A.!!$R1 738
17 TraesCS2B01G435600 chr7A 680580084 680580808 724 False 752.0 752 85.675 4057 4770 1 chr7A.!!$F2 713
18 TraesCS2B01G435600 chr7A 155491936 155492828 892 False 723.0 723 81.657 3885 4770 1 chr7A.!!$F1 885
19 TraesCS2B01G435600 chr3D 598388040 598388868 828 True 1009.0 1009 88.612 1 839 1 chr3D.!!$R1 838
20 TraesCS2B01G435600 chr4A 703034608 703035503 895 True 976.0 976 86.570 3887 4773 1 chr4A.!!$R2 886
21 TraesCS2B01G435600 chr4A 702969346 702970241 895 True 970.0 970 86.459 3887 4773 1 chr4A.!!$R1 886
22 TraesCS2B01G435600 chr5A 642657887 642658781 894 False 911.0 911 85.333 3887 4770 1 chr5A.!!$F1 883
23 TraesCS2B01G435600 chr5B 123014109 123014951 842 False 645.5 856 93.852 3886 4775 2 chr5B.!!$F1 889

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
869 889 0.658829 TGAACGATTTTTGCGCCACG 60.659 50.000 4.18 4.19 0.00 4.94 F
912 932 0.753262 ACCGGATGTGGTAGAGATGC 59.247 55.000 9.46 0.00 41.55 3.91 F
966 986 0.957888 GACCAGGGCAGCACTTTCTC 60.958 60.000 0.00 0.00 0.00 2.87 F
1978 2010 1.026718 CATGTTGGAACCGCTCCCTC 61.027 60.000 0.00 0.00 44.69 4.30 F
2032 2064 1.402968 CATTCAGGGAAGATGCCAACG 59.597 52.381 0.00 0.00 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2105 0.036732 GACCACAACATCTGCCCAGA 59.963 55.000 0.0 0.0 42.37 3.86 R
2208 2240 0.447801 GTATGCTTGACACTTGCCCG 59.552 55.000 0.0 0.0 0.00 6.13 R
2595 2627 2.245159 GATGATCACTTGCCCATCGA 57.755 50.000 0.0 0.0 0.00 3.59 R
3560 3592 1.140852 TCTCGATGCCTTGGGGTATTG 59.859 52.381 0.0 0.0 38.05 1.90 R
3882 3914 2.919666 ACAACACAACTCAACAGTGC 57.080 45.000 0.0 0.0 36.76 4.40 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
309 315 1.557099 AAGCCTACACATCCACGAGA 58.443 50.000 0.00 0.00 0.00 4.04
619 636 0.739462 ATCTGAAATCCGACGCGCAA 60.739 50.000 5.73 0.00 0.00 4.85
699 718 6.219302 TGTTTCTTTCGAATCGAACTAACC 57.781 37.500 18.30 8.29 45.64 2.85
744 763 8.588472 ACTAATAATGACATGCACTAGCTGATA 58.412 33.333 0.00 0.00 42.74 2.15
745 764 7.664082 AATAATGACATGCACTAGCTGATAC 57.336 36.000 0.00 0.00 42.74 2.24
746 765 4.952071 ATGACATGCACTAGCTGATACT 57.048 40.909 0.00 0.00 42.74 2.12
747 766 4.050852 TGACATGCACTAGCTGATACTG 57.949 45.455 0.00 0.00 42.74 2.74
748 767 3.448660 TGACATGCACTAGCTGATACTGT 59.551 43.478 0.00 0.00 42.74 3.55
804 824 4.801516 GCCGCTTGTTTTCTTCAAAAAGTA 59.198 37.500 0.00 0.00 33.17 2.24
806 826 5.802956 CCGCTTGTTTTCTTCAAAAAGTACA 59.197 36.000 0.00 0.00 33.17 2.90
813 833 5.493133 TTCTTCAAAAAGTACACGTGCAT 57.507 34.783 17.22 0.00 33.95 3.96
843 863 6.472016 AGAATTTGGGAAAATATTTTGCGGT 58.528 32.000 21.57 8.39 39.09 5.68
844 864 7.616313 AGAATTTGGGAAAATATTTTGCGGTA 58.384 30.769 21.57 11.92 39.09 4.02
845 865 8.264347 AGAATTTGGGAAAATATTTTGCGGTAT 58.736 29.630 21.57 13.29 39.09 2.73
846 866 8.432110 AATTTGGGAAAATATTTTGCGGTATC 57.568 30.769 21.57 11.03 39.09 2.24
847 867 5.523438 TGGGAAAATATTTTGCGGTATCC 57.477 39.130 21.57 13.29 39.09 2.59
848 868 5.205056 TGGGAAAATATTTTGCGGTATCCT 58.795 37.500 21.57 0.00 39.09 3.24
849 869 5.659079 TGGGAAAATATTTTGCGGTATCCTT 59.341 36.000 21.57 0.00 39.09 3.36
850 870 6.155393 TGGGAAAATATTTTGCGGTATCCTTT 59.845 34.615 21.57 0.00 39.09 3.11
851 871 6.478673 GGGAAAATATTTTGCGGTATCCTTTG 59.521 38.462 21.57 0.00 39.09 2.77
852 872 7.262048 GGAAAATATTTTGCGGTATCCTTTGA 58.738 34.615 17.98 0.00 0.00 2.69
853 873 7.762159 GGAAAATATTTTGCGGTATCCTTTGAA 59.238 33.333 17.98 0.00 0.00 2.69
854 874 8.474006 AAAATATTTTGCGGTATCCTTTGAAC 57.526 30.769 12.62 0.00 0.00 3.18
855 875 3.546002 TTTTGCGGTATCCTTTGAACG 57.454 42.857 0.00 0.00 0.00 3.95
856 876 2.459060 TTGCGGTATCCTTTGAACGA 57.541 45.000 0.00 0.00 0.00 3.85
857 877 2.684001 TGCGGTATCCTTTGAACGAT 57.316 45.000 0.00 0.00 0.00 3.73
858 878 2.980568 TGCGGTATCCTTTGAACGATT 58.019 42.857 0.00 0.00 0.00 3.34
859 879 3.340034 TGCGGTATCCTTTGAACGATTT 58.660 40.909 0.00 0.00 0.00 2.17
860 880 3.754323 TGCGGTATCCTTTGAACGATTTT 59.246 39.130 0.00 0.00 0.00 1.82
861 881 4.216687 TGCGGTATCCTTTGAACGATTTTT 59.783 37.500 0.00 0.00 0.00 1.94
862 882 4.557301 GCGGTATCCTTTGAACGATTTTTG 59.443 41.667 0.00 0.00 0.00 2.44
863 883 4.557301 CGGTATCCTTTGAACGATTTTTGC 59.443 41.667 0.00 0.00 0.00 3.68
864 884 4.557301 GGTATCCTTTGAACGATTTTTGCG 59.443 41.667 0.00 0.00 0.00 4.85
865 885 2.389998 TCCTTTGAACGATTTTTGCGC 58.610 42.857 0.00 0.00 0.00 6.09
866 886 1.455408 CCTTTGAACGATTTTTGCGCC 59.545 47.619 4.18 0.00 0.00 6.53
867 887 2.123342 CTTTGAACGATTTTTGCGCCA 58.877 42.857 4.18 0.00 0.00 5.69
868 888 1.482278 TTGAACGATTTTTGCGCCAC 58.518 45.000 4.18 0.00 0.00 5.01
869 889 0.658829 TGAACGATTTTTGCGCCACG 60.659 50.000 4.18 4.19 0.00 4.94
870 890 1.334288 GAACGATTTTTGCGCCACGG 61.334 55.000 4.18 0.00 0.00 4.94
871 891 3.171911 CGATTTTTGCGCCACGGC 61.172 61.111 4.18 0.00 37.85 5.68
872 892 2.049618 GATTTTTGCGCCACGGCA 60.050 55.556 4.18 0.00 42.06 5.69
873 893 2.355718 ATTTTTGCGCCACGGCAC 60.356 55.556 4.18 0.00 43.82 5.01
896 916 4.977126 GCGATCCGCGTCCTACCG 62.977 72.222 4.92 0.66 44.55 4.02
897 917 4.323843 CGATCCGCGTCCTACCGG 62.324 72.222 4.92 0.00 45.64 5.28
902 922 2.278596 CGCGTCCTACCGGATGTG 60.279 66.667 9.46 0.00 46.92 3.21
903 923 2.106332 GCGTCCTACCGGATGTGG 59.894 66.667 9.46 4.29 46.22 4.17
904 924 2.718073 GCGTCCTACCGGATGTGGT 61.718 63.158 9.46 0.00 46.22 4.16
905 925 1.386525 GCGTCCTACCGGATGTGGTA 61.387 60.000 9.46 0.00 46.22 3.25
912 932 0.753262 ACCGGATGTGGTAGAGATGC 59.247 55.000 9.46 0.00 41.55 3.91
913 933 1.043816 CCGGATGTGGTAGAGATGCT 58.956 55.000 0.00 0.00 0.00 3.79
914 934 1.000283 CCGGATGTGGTAGAGATGCTC 60.000 57.143 0.00 0.00 0.00 4.26
921 941 2.032799 GTGGTAGAGATGCTCTCAGTCG 59.967 54.545 13.42 0.00 45.73 4.18
922 942 2.294074 GGTAGAGATGCTCTCAGTCGT 58.706 52.381 13.42 0.00 45.73 4.34
942 962 4.156190 TCGTAGAGAATCGCTGACTTTCTT 59.844 41.667 0.00 0.00 42.67 2.52
943 963 4.859798 CGTAGAGAATCGCTGACTTTCTTT 59.140 41.667 0.00 0.00 42.67 2.52
944 964 5.003967 CGTAGAGAATCGCTGACTTTCTTTC 59.996 44.000 0.00 0.00 42.67 2.62
946 966 4.928615 AGAGAATCGCTGACTTTCTTTCTG 59.071 41.667 0.00 0.00 42.67 3.02
947 967 3.999663 AGAATCGCTGACTTTCTTTCTGG 59.000 43.478 0.00 0.00 0.00 3.86
948 968 3.685139 ATCGCTGACTTTCTTTCTGGA 57.315 42.857 0.00 0.00 0.00 3.86
949 969 2.755650 TCGCTGACTTTCTTTCTGGAC 58.244 47.619 0.00 0.00 0.00 4.02
950 970 1.801178 CGCTGACTTTCTTTCTGGACC 59.199 52.381 0.00 0.00 0.00 4.46
966 986 0.957888 GACCAGGGCAGCACTTTCTC 60.958 60.000 0.00 0.00 0.00 2.87
1497 1526 1.749334 ATGGGGAGATCGTCGGCTTC 61.749 60.000 0.00 0.00 0.00 3.86
1683 1712 2.036089 GTCCGTCTCCAAGAACTTCACT 59.964 50.000 0.00 0.00 0.00 3.41
1719 1748 6.981722 TCTAAGGAAAATTGCCAAAGAACTC 58.018 36.000 0.00 0.00 0.00 3.01
1840 1872 1.688772 ATTGCTGGATGATGTCTGGC 58.311 50.000 0.00 0.00 0.00 4.85
1863 1895 2.139917 GCCGATGCGTGGTATGAAATA 58.860 47.619 0.00 0.00 0.00 1.40
1889 1921 2.234143 TGCGTTGGTTGATGATGGAAA 58.766 42.857 0.00 0.00 0.00 3.13
1890 1922 2.625314 TGCGTTGGTTGATGATGGAAAA 59.375 40.909 0.00 0.00 0.00 2.29
1897 1929 3.091545 GTTGATGATGGAAAAGGGAGCA 58.908 45.455 0.00 0.00 0.00 4.26
1911 1943 3.321039 AGGGAGCAGGATAATCATCACA 58.679 45.455 0.00 0.00 32.32 3.58
1978 2010 1.026718 CATGTTGGAACCGCTCCCTC 61.027 60.000 0.00 0.00 44.69 4.30
2032 2064 1.402968 CATTCAGGGAAGATGCCAACG 59.597 52.381 0.00 0.00 0.00 4.10
2208 2240 2.548057 TGAAAGCAGTGTTCGTGGAATC 59.452 45.455 0.00 0.00 0.00 2.52
2257 2289 3.812053 GAGCATTGACGATCTGCCTTATT 59.188 43.478 0.60 0.00 36.56 1.40
3358 3390 6.069789 ACTCAGAGGAGATTCAATTGGATTGA 60.070 38.462 5.42 1.18 44.29 2.57
3480 3512 5.549347 CTGAGCTTACATGAGATGCCTAAT 58.451 41.667 0.00 0.00 0.00 1.73
3499 3531 4.974103 AATCTTTCTCACGTCGAGTTTG 57.026 40.909 0.00 0.00 42.88 2.93
3560 3592 1.394917 CCGTTGTGATGAGCTAACTGC 59.605 52.381 0.00 0.00 43.29 4.40
3595 3627 0.884514 CGAGAACCTCACAGAGCTCA 59.115 55.000 17.77 0.00 0.00 4.26
3882 3914 2.351738 GGAGGCGTCATTTTGAGGTTTG 60.352 50.000 8.91 0.00 34.95 2.93
4287 4358 1.156736 CACGCAACCCGATCTTCTTT 58.843 50.000 0.00 0.00 41.02 2.52
4320 4391 4.160252 ACAAACCACATCAAGTTCTTGCTT 59.840 37.500 7.58 0.00 0.00 3.91
4484 4555 2.125961 GGATCTACGCCACCCTCGT 61.126 63.158 0.00 0.00 43.20 4.18
4594 4666 0.171903 GCGCTTCATGGTGCTCAATT 59.828 50.000 0.00 0.00 39.35 2.32
4741 4815 2.915659 TCCACGGCCTCGACAAGT 60.916 61.111 0.00 0.00 40.11 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 284 5.240844 GGATGTGTAGGCTTTTTACAGTTGT 59.759 40.000 0.00 0.00 32.08 3.32
309 315 2.635915 TCGATGTACAACCCTTGTCCTT 59.364 45.455 0.00 0.00 44.12 3.36
758 778 3.084039 GGTCTTCTCAACCATGCATGAA 58.916 45.455 28.31 11.79 36.75 2.57
772 792 2.676163 AAACAAGCGGCCGGTCTTCT 62.676 55.000 32.52 13.98 0.00 2.85
804 824 5.465056 CCCAAATTCTTTAAAATGCACGTGT 59.535 36.000 18.38 0.00 0.00 4.49
806 826 5.848406 TCCCAAATTCTTTAAAATGCACGT 58.152 33.333 0.00 0.00 0.00 4.49
839 859 4.351131 AAAATCGTTCAAAGGATACCGC 57.649 40.909 0.00 0.00 33.55 5.68
840 860 4.557301 GCAAAAATCGTTCAAAGGATACCG 59.443 41.667 0.00 0.00 33.55 4.02
841 861 4.557301 CGCAAAAATCGTTCAAAGGATACC 59.443 41.667 0.00 0.00 33.55 2.73
843 863 4.162812 GCGCAAAAATCGTTCAAAGGATA 58.837 39.130 0.30 0.00 33.55 2.59
844 864 2.986479 GCGCAAAAATCGTTCAAAGGAT 59.014 40.909 0.30 0.00 35.23 3.24
845 865 2.389998 GCGCAAAAATCGTTCAAAGGA 58.610 42.857 0.30 0.00 0.00 3.36
846 866 1.455408 GGCGCAAAAATCGTTCAAAGG 59.545 47.619 10.83 0.00 0.00 3.11
847 867 2.097444 GTGGCGCAAAAATCGTTCAAAG 60.097 45.455 10.83 0.00 0.00 2.77
848 868 1.855360 GTGGCGCAAAAATCGTTCAAA 59.145 42.857 10.83 0.00 0.00 2.69
849 869 1.482278 GTGGCGCAAAAATCGTTCAA 58.518 45.000 10.83 0.00 0.00 2.69
850 870 0.658829 CGTGGCGCAAAAATCGTTCA 60.659 50.000 10.83 0.00 0.00 3.18
851 871 1.334288 CCGTGGCGCAAAAATCGTTC 61.334 55.000 10.83 0.00 0.00 3.95
852 872 1.371145 CCGTGGCGCAAAAATCGTT 60.371 52.632 10.83 0.00 0.00 3.85
853 873 2.254051 CCGTGGCGCAAAAATCGT 59.746 55.556 10.83 0.00 0.00 3.73
854 874 3.171911 GCCGTGGCGCAAAAATCG 61.172 61.111 10.83 0.00 0.00 3.34
855 875 2.049618 TGCCGTGGCGCAAAAATC 60.050 55.556 10.83 0.00 45.51 2.17
867 887 4.796231 GATCGCCTGACGTGCCGT 62.796 66.667 0.00 0.00 45.10 5.68
880 900 4.323843 CCGGTAGGACGCGGATCG 62.324 72.222 12.47 4.54 45.38 3.69
881 901 2.903855 TCCGGTAGGACGCGGATC 60.904 66.667 12.47 0.00 42.75 3.36
892 912 1.961394 GCATCTCTACCACATCCGGTA 59.039 52.381 0.00 0.00 40.67 4.02
893 913 0.753262 GCATCTCTACCACATCCGGT 59.247 55.000 0.00 0.00 43.46 5.28
894 914 1.000283 GAGCATCTCTACCACATCCGG 60.000 57.143 0.00 0.00 0.00 5.14
895 915 2.430546 GAGCATCTCTACCACATCCG 57.569 55.000 0.00 0.00 0.00 4.18
908 928 4.610456 CGATTCTCTACGACTGAGAGCATC 60.610 50.000 0.00 0.58 40.99 3.91
909 929 3.249799 CGATTCTCTACGACTGAGAGCAT 59.750 47.826 0.00 0.00 40.99 3.79
910 930 2.609916 CGATTCTCTACGACTGAGAGCA 59.390 50.000 0.00 0.00 40.99 4.26
911 931 2.601266 GCGATTCTCTACGACTGAGAGC 60.601 54.545 0.00 0.00 40.99 4.09
912 932 2.869801 AGCGATTCTCTACGACTGAGAG 59.130 50.000 0.00 0.00 40.99 3.20
913 933 2.609916 CAGCGATTCTCTACGACTGAGA 59.390 50.000 0.00 0.00 38.62 3.27
914 934 2.609916 TCAGCGATTCTCTACGACTGAG 59.390 50.000 0.00 0.00 37.55 3.35
921 941 6.034470 CAGAAAGAAAGTCAGCGATTCTCTAC 59.966 42.308 0.00 0.00 32.45 2.59
922 942 6.096036 CAGAAAGAAAGTCAGCGATTCTCTA 58.904 40.000 0.00 0.00 32.45 2.43
942 962 2.853542 TGCTGCCCTGGTCCAGAA 60.854 61.111 21.23 4.67 32.44 3.02
943 963 3.640407 GTGCTGCCCTGGTCCAGA 61.640 66.667 21.23 0.00 32.44 3.86
944 964 2.703675 AAAGTGCTGCCCTGGTCCAG 62.704 60.000 12.40 12.40 0.00 3.86
946 966 1.973812 GAAAGTGCTGCCCTGGTCC 60.974 63.158 0.00 0.00 0.00 4.46
947 967 0.957888 GAGAAAGTGCTGCCCTGGTC 60.958 60.000 0.00 0.00 0.00 4.02
948 968 1.073897 GAGAAAGTGCTGCCCTGGT 59.926 57.895 0.00 0.00 0.00 4.00
949 969 2.037136 CGAGAAAGTGCTGCCCTGG 61.037 63.158 0.00 0.00 0.00 4.45
950 970 2.037136 CCGAGAAAGTGCTGCCCTG 61.037 63.158 0.00 0.00 0.00 4.45
998 1018 4.273811 CGATCATCTCGGCCATGG 57.726 61.111 7.63 7.63 43.82 3.66
1060 1089 2.278013 GGAGATGTCGACGACCGC 60.278 66.667 24.33 15.88 38.37 5.68
1064 1093 1.803252 CGAGAGAGGAGATGTCGACGA 60.803 57.143 11.62 0.00 35.64 4.20
1464 1493 1.358787 TCCCCATCCTGCAAGAAATGT 59.641 47.619 0.00 0.00 34.07 2.71
1683 1712 6.555463 ATTTTCCTTAGAAGGTCATCCGTA 57.445 37.500 8.17 0.00 46.54 4.02
1840 1872 0.879839 TCATACCACGCATCGGCATG 60.880 55.000 0.00 0.00 41.24 4.06
1889 1921 3.718434 TGTGATGATTATCCTGCTCCCTT 59.282 43.478 0.00 0.00 32.09 3.95
1890 1922 3.321039 TGTGATGATTATCCTGCTCCCT 58.679 45.455 0.00 0.00 32.09 4.20
1897 1929 3.872696 TGCGTGTTGTGATGATTATCCT 58.127 40.909 0.00 0.00 32.09 3.24
1911 1943 1.002468 GCAACATCTTGACTGCGTGTT 60.002 47.619 0.00 0.00 33.63 3.32
1978 2010 0.323178 AGGGACCATGCTTCTTGCTG 60.323 55.000 0.00 0.00 43.37 4.41
2073 2105 0.036732 GACCACAACATCTGCCCAGA 59.963 55.000 0.00 0.00 42.37 3.86
2208 2240 0.447801 GTATGCTTGACACTTGCCCG 59.552 55.000 0.00 0.00 0.00 6.13
2257 2289 4.623932 ACAGCAAACATCTCTTCAGGTA 57.376 40.909 0.00 0.00 0.00 3.08
2595 2627 2.245159 GATGATCACTTGCCCATCGA 57.755 50.000 0.00 0.00 0.00 3.59
3185 3217 5.705905 GGCTCCAGGTCCAATATTACATTAC 59.294 44.000 0.00 0.00 0.00 1.89
3358 3390 1.489649 CAGCCTGGGAAGTGATGAGAT 59.510 52.381 0.00 0.00 0.00 2.75
3499 3531 5.167303 AGATGTACAAGACTCCCTTTTCC 57.833 43.478 0.00 0.00 31.42 3.13
3560 3592 1.140852 TCTCGATGCCTTGGGGTATTG 59.859 52.381 0.00 0.00 38.05 1.90
3595 3627 5.065090 GCATTTCAAAAAGCTCAAGGTTGTT 59.935 36.000 0.00 0.00 35.72 2.83
3882 3914 2.919666 ACAACACAACTCAACAGTGC 57.080 45.000 0.00 0.00 36.76 4.40
4287 4358 4.396522 TGATGTGGTTTGTGATGTGATCA 58.603 39.130 0.00 0.00 36.84 2.92
4320 4391 1.078988 GTTGTGGTCGGCCGGATTA 60.079 57.895 27.83 1.61 37.67 1.75
4594 4666 0.323302 TTCAGATTGCGGTACTGGCA 59.677 50.000 3.34 5.94 38.93 4.92
4658 4730 4.477975 CGAGACCGTCGGTGAGCC 62.478 72.222 24.45 7.24 45.58 4.70
4741 4815 4.451150 GCGGATGGTGTCGAGCCA 62.451 66.667 10.62 10.62 40.68 4.75


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

AutoCloner maintained by Alex Coulton.