Multiple sequence alignment - TraesCS5A01G318600

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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 TraesCS5A01G318600 chr5A 100.000 2384 0 0 1 2384 529303311 529300928 0 4403
1 TraesCS5A01G318600 chr5A 96.970 825 20 5 1 822 556585383 556584561 0 1380
2 TraesCS5A01G318600 chr1A 97.420 814 20 1 1 814 334512023 334511211 0 1386
3 TraesCS5A01G318600 chr7A 96.386 830 24 5 1 826 628238793 628237966 0 1362
4 TraesCS5A01G318600 chr7A 91.317 691 47 10 966 1652 292816789 292817470 0 931
5 TraesCS5A01G318600 chr7A 88.439 692 65 8 970 1652 121066106 121066791 0 821
6 TraesCS5A01G318600 chr2A 96.814 816 23 2 1 814 205006300 205007114 0 1360
7 TraesCS5A01G318600 chr2A 96.560 814 27 1 1 813 672716175 672716988 0 1347
8 TraesCS5A01G318600 chr2A 95.360 819 25 7 1 819 754576194 754576999 0 1290
9 TraesCS5A01G318600 chr3A 96.699 818 20 6 1 814 706822151 706821337 0 1354
10 TraesCS5A01G318600 chr3A 95.636 825 25 7 1 819 676759473 676760292 0 1314
11 TraesCS5A01G318600 chr4A 96.654 807 27 0 1 807 309678060 309678866 0 1341
12 TraesCS5A01G318600 chr4A 94.278 734 40 2 1652 2384 496722225 496722957 0 1122
13 TraesCS5A01G318600 chr3D 94.959 734 33 4 1653 2384 103388846 103389577 0 1147
14 TraesCS5A01G318600 chr3D 94.679 733 37 2 1653 2384 445563738 445564469 0 1136
15 TraesCS5A01G318600 chr1D 94.816 733 35 3 1653 2384 236539147 236539877 0 1140
16 TraesCS5A01G318600 chr6D 94.407 733 39 2 1653 2384 292323263 292322532 0 1125
17 TraesCS5A01G318600 chr5D 94.414 734 38 3 1653 2384 211973777 211973045 0 1125
18 TraesCS5A01G318600 chr5D 89.213 686 62 5 975 1652 565324222 565323541 0 846
19 TraesCS5A01G318600 chr2D 94.414 734 38 3 1653 2384 34810073 34810805 0 1125
20 TraesCS5A01G318600 chr2D 89.736 682 61 3 973 1650 531478051 531477375 0 863
21 TraesCS5A01G318600 chr2D 88.167 693 67 9 970 1652 291863718 291864405 0 811
22 TraesCS5A01G318600 chr4D 94.414 734 36 5 1654 2384 346544201 346543470 0 1123
23 TraesCS5A01G318600 chr4D 94.278 734 39 3 1653 2384 228225455 228226187 0 1120
24 TraesCS5A01G318600 chr4D 91.001 689 55 3 966 1651 299780923 299780239 0 922
25 TraesCS5A01G318600 chr7B 90.087 686 55 7 970 1652 64724216 64724891 0 878
26 TraesCS5A01G318600 chr7B 88.439 692 64 8 970 1652 75184760 75185444 0 821
27 TraesCS5A01G318600 chr3B 89.260 689 59 8 973 1652 254763168 254762486 0 848


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 TraesCS5A01G318600 chr5A 529300928 529303311 2383 True 4403 4403 100.000 1 2384 1 chr5A.!!$R1 2383
1 TraesCS5A01G318600 chr5A 556584561 556585383 822 True 1380 1380 96.970 1 822 1 chr5A.!!$R2 821
2 TraesCS5A01G318600 chr1A 334511211 334512023 812 True 1386 1386 97.420 1 814 1 chr1A.!!$R1 813
3 TraesCS5A01G318600 chr7A 628237966 628238793 827 True 1362 1362 96.386 1 826 1 chr7A.!!$R1 825
4 TraesCS5A01G318600 chr7A 292816789 292817470 681 False 931 931 91.317 966 1652 1 chr7A.!!$F2 686
5 TraesCS5A01G318600 chr7A 121066106 121066791 685 False 821 821 88.439 970 1652 1 chr7A.!!$F1 682
6 TraesCS5A01G318600 chr2A 205006300 205007114 814 False 1360 1360 96.814 1 814 1 chr2A.!!$F1 813
7 TraesCS5A01G318600 chr2A 672716175 672716988 813 False 1347 1347 96.560 1 813 1 chr2A.!!$F2 812
8 TraesCS5A01G318600 chr2A 754576194 754576999 805 False 1290 1290 95.360 1 819 1 chr2A.!!$F3 818
9 TraesCS5A01G318600 chr3A 706821337 706822151 814 True 1354 1354 96.699 1 814 1 chr3A.!!$R1 813
10 TraesCS5A01G318600 chr3A 676759473 676760292 819 False 1314 1314 95.636 1 819 1 chr3A.!!$F1 818
11 TraesCS5A01G318600 chr4A 309678060 309678866 806 False 1341 1341 96.654 1 807 1 chr4A.!!$F1 806
12 TraesCS5A01G318600 chr4A 496722225 496722957 732 False 1122 1122 94.278 1652 2384 1 chr4A.!!$F2 732
13 TraesCS5A01G318600 chr3D 103388846 103389577 731 False 1147 1147 94.959 1653 2384 1 chr3D.!!$F1 731
14 TraesCS5A01G318600 chr3D 445563738 445564469 731 False 1136 1136 94.679 1653 2384 1 chr3D.!!$F2 731
15 TraesCS5A01G318600 chr1D 236539147 236539877 730 False 1140 1140 94.816 1653 2384 1 chr1D.!!$F1 731
16 TraesCS5A01G318600 chr6D 292322532 292323263 731 True 1125 1125 94.407 1653 2384 1 chr6D.!!$R1 731
17 TraesCS5A01G318600 chr5D 211973045 211973777 732 True 1125 1125 94.414 1653 2384 1 chr5D.!!$R1 731
18 TraesCS5A01G318600 chr5D 565323541 565324222 681 True 846 846 89.213 975 1652 1 chr5D.!!$R2 677
19 TraesCS5A01G318600 chr2D 34810073 34810805 732 False 1125 1125 94.414 1653 2384 1 chr2D.!!$F1 731
20 TraesCS5A01G318600 chr2D 531477375 531478051 676 True 863 863 89.736 973 1650 1 chr2D.!!$R1 677
21 TraesCS5A01G318600 chr2D 291863718 291864405 687 False 811 811 88.167 970 1652 1 chr2D.!!$F2 682
22 TraesCS5A01G318600 chr4D 346543470 346544201 731 True 1123 1123 94.414 1654 2384 1 chr4D.!!$R2 730
23 TraesCS5A01G318600 chr4D 228225455 228226187 732 False 1120 1120 94.278 1653 2384 1 chr4D.!!$F1 731
24 TraesCS5A01G318600 chr4D 299780239 299780923 684 True 922 922 91.001 966 1651 1 chr4D.!!$R1 685
25 TraesCS5A01G318600 chr7B 64724216 64724891 675 False 878 878 90.087 970 1652 1 chr7B.!!$F1 682
26 TraesCS5A01G318600 chr7B 75184760 75185444 684 False 821 821 88.439 970 1652 1 chr7B.!!$F2 682
27 TraesCS5A01G318600 chr3B 254762486 254763168 682 True 848 848 89.260 973 1652 1 chr3B.!!$R1 679

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
906 918 0.387565 GGCACCATGGTGTCGTTTTT 59.612 50.0 38.41 3.15 46.9 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2201 1.20258 AGCGCTATCATGTTCCTCACC 60.203 52.381 8.99 0.0 0.0 4.02 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
55 60 6.761099 TGTATAAAACGGCAATGGTTGTAT 57.239 33.333 0.00 0.00 33.51 2.29
72 77 5.883673 GGTTGTATAGGATTTACAAGGCACA 59.116 40.000 0.00 0.00 39.52 4.57
619 629 1.535860 CCAACTGTTGGCCGAAAAGTG 60.536 52.381 25.21 0.00 45.17 3.16
632 642 2.284952 CGAAAAGTGCTTTTTGGCCAAG 59.715 45.455 19.48 8.58 42.26 3.61
835 847 9.528018 AAAAACAAATATCGTTGTGTCTCATTT 57.472 25.926 0.00 0.00 40.86 2.32
836 848 9.528018 AAAACAAATATCGTTGTGTCTCATTTT 57.472 25.926 0.00 0.00 40.86 1.82
837 849 8.728088 AACAAATATCGTTGTGTCTCATTTTC 57.272 30.769 0.00 0.00 40.86 2.29
838 850 7.305474 ACAAATATCGTTGTGTCTCATTTTCC 58.695 34.615 0.00 0.00 40.22 3.13
839 851 7.174946 ACAAATATCGTTGTGTCTCATTTTCCT 59.825 33.333 0.00 0.00 40.22 3.36
840 852 7.687941 AATATCGTTGTGTCTCATTTTCCTT 57.312 32.000 0.00 0.00 0.00 3.36
841 853 7.687941 ATATCGTTGTGTCTCATTTTCCTTT 57.312 32.000 0.00 0.00 0.00 3.11
842 854 5.828299 TCGTTGTGTCTCATTTTCCTTTT 57.172 34.783 0.00 0.00 0.00 2.27
843 855 6.202516 TCGTTGTGTCTCATTTTCCTTTTT 57.797 33.333 0.00 0.00 0.00 1.94
877 889 3.658351 CGAAAGACGGGAAATTGCTAG 57.342 47.619 0.00 0.00 38.46 3.42
878 890 3.259064 CGAAAGACGGGAAATTGCTAGA 58.741 45.455 0.00 0.00 38.46 2.43
879 891 3.871594 CGAAAGACGGGAAATTGCTAGAT 59.128 43.478 0.00 0.00 38.46 1.98
880 892 4.260375 CGAAAGACGGGAAATTGCTAGATG 60.260 45.833 0.00 0.00 38.46 2.90
881 893 3.914426 AGACGGGAAATTGCTAGATGT 57.086 42.857 0.00 0.00 0.00 3.06
882 894 3.535561 AGACGGGAAATTGCTAGATGTG 58.464 45.455 0.00 0.00 0.00 3.21
883 895 3.055094 AGACGGGAAATTGCTAGATGTGT 60.055 43.478 0.00 0.00 0.00 3.72
884 896 4.161565 AGACGGGAAATTGCTAGATGTGTA 59.838 41.667 0.00 0.00 0.00 2.90
885 897 4.442706 ACGGGAAATTGCTAGATGTGTAG 58.557 43.478 0.00 0.00 0.00 2.74
886 898 3.809832 CGGGAAATTGCTAGATGTGTAGG 59.190 47.826 0.00 0.00 0.00 3.18
887 899 4.137543 GGGAAATTGCTAGATGTGTAGGG 58.862 47.826 0.00 0.00 0.00 3.53
888 900 4.137543 GGAAATTGCTAGATGTGTAGGGG 58.862 47.826 0.00 0.00 0.00 4.79
889 901 2.938956 ATTGCTAGATGTGTAGGGGC 57.061 50.000 0.00 0.00 0.00 5.80
890 902 1.578897 TTGCTAGATGTGTAGGGGCA 58.421 50.000 0.00 0.00 0.00 5.36
891 903 0.830648 TGCTAGATGTGTAGGGGCAC 59.169 55.000 0.00 0.00 39.65 5.01
904 916 3.758172 GGCACCATGGTGTCGTTT 58.242 55.556 38.41 4.74 46.90 3.60
905 917 2.037871 GGCACCATGGTGTCGTTTT 58.962 52.632 38.41 3.94 46.90 2.43
906 918 0.387565 GGCACCATGGTGTCGTTTTT 59.612 50.000 38.41 3.15 46.90 1.94
931 943 2.410469 GGCATGAAGGCGATGTGC 59.590 61.111 0.00 0.00 45.38 4.57
957 969 2.361610 CCAGCGTGAATGGCCCTT 60.362 61.111 0.00 0.00 0.00 3.95
958 970 2.703798 CCAGCGTGAATGGCCCTTG 61.704 63.158 0.00 0.00 0.00 3.61
959 971 2.361610 AGCGTGAATGGCCCTTGG 60.362 61.111 0.00 0.00 0.00 3.61
1072 1084 2.363795 CGGAGGACTACAGGCCCA 60.364 66.667 0.00 0.00 0.00 5.36
1096 1108 3.198635 GGAAGAGGATGAGTTGGACATCA 59.801 47.826 0.00 0.00 43.84 3.07
1131 1143 1.448540 CGAGGACAAGCTCGCCAAT 60.449 57.895 0.00 0.00 36.29 3.16
1132 1144 1.699656 CGAGGACAAGCTCGCCAATG 61.700 60.000 0.00 0.00 36.29 2.82
1175 1187 2.042831 GCCAGAGCAAGCGGACAAT 61.043 57.895 0.00 0.00 39.53 2.71
1234 1246 0.413037 TTGGAGGGACATTGGGCAAT 59.587 50.000 0.00 0.00 0.00 3.56
1256 1268 2.664851 CAAGGTCAGCGCCGAACA 60.665 61.111 11.96 0.00 0.00 3.18
1365 1378 1.818060 TGGATGTCCATTTCAAAGCGG 59.182 47.619 0.00 0.00 42.01 5.52
1429 1442 1.449246 GAGAGCATCAAGGCACGCT 60.449 57.895 0.00 0.00 37.82 5.07
1511 1533 3.786516 TGCATGTCCATTTGCATACTG 57.213 42.857 0.00 0.00 43.54 2.74
1555 1577 4.380233 GCATGCTATCCATTTGTAGGCATC 60.380 45.833 11.37 0.00 36.91 3.91
1581 1603 2.586425 CTTTGGAGGCTTTCAAGGTCA 58.414 47.619 0.00 0.00 0.00 4.02
1589 1612 4.154942 AGGCTTTCAAGGTCAAACATGAT 58.845 39.130 0.00 0.00 0.00 2.45
1784 1809 6.380274 TGATATTTACAGAGAAAGTCGACCCT 59.620 38.462 13.01 7.20 0.00 4.34
1786 1811 6.600882 ATTTACAGAGAAAGTCGACCCTTA 57.399 37.500 13.01 0.00 0.00 2.69
1860 1885 8.739039 TGAAGACTTTGAAAGTGAAGAAATTGA 58.261 29.630 16.25 0.00 43.03 2.57
1861 1886 8.917415 AAGACTTTGAAAGTGAAGAAATTGAC 57.083 30.769 16.25 0.00 43.03 3.18
1868 1893 2.800544 AGTGAAGAAATTGACGTGACCG 59.199 45.455 0.00 0.00 40.83 4.79
1879 1904 3.267900 CGTGACCGTGAAGACTTGT 57.732 52.632 0.00 0.00 0.00 3.16
1889 1914 8.471609 TGACCGTGAAGACTTGTTATTCATATA 58.528 33.333 0.00 0.00 37.75 0.86
1939 1965 9.498307 TTGTTTTCGTAGTTTCATTTTCTCTTC 57.502 29.630 0.00 0.00 0.00 2.87
2059 2085 2.108075 TCCCTTTGAGTGAAGCCATTGA 59.892 45.455 0.00 0.00 0.00 2.57
2096 2123 5.008019 GCTCAGTCAATTTCTTCAGTGACAA 59.992 40.000 0.00 0.00 42.29 3.18
2173 2201 1.806623 GCCAGTGCGGATTACCTACAG 60.807 57.143 0.00 0.00 36.56 2.74
2342 2373 3.538634 CTATAAATAGCCGCCCCCTAC 57.461 52.381 0.00 0.00 0.00 3.18
2344 2375 1.053424 TAAATAGCCGCCCCCTACAG 58.947 55.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
570 579 1.550130 CCCTCTTCGGCCAACACCTA 61.550 60.000 2.24 0.00 0.00 3.08
619 629 0.534877 CCAACCCTTGGCCAAAAAGC 60.535 55.000 20.91 0.00 45.17 3.51
632 642 2.046217 GGACTTCTCGGCCAACCC 60.046 66.667 2.24 0.00 0.00 4.11
814 826 7.530010 AGGAAAATGAGACACAACGATATTTG 58.470 34.615 0.00 0.00 0.00 2.32
819 831 6.391227 AAAAGGAAAATGAGACACAACGAT 57.609 33.333 0.00 0.00 0.00 3.73
820 832 5.828299 AAAAGGAAAATGAGACACAACGA 57.172 34.783 0.00 0.00 0.00 3.85
842 854 5.121142 CCGTCTTTCGTGCCTCTTATAAAAA 59.879 40.000 0.00 0.00 37.94 1.94
843 855 4.628333 CCGTCTTTCGTGCCTCTTATAAAA 59.372 41.667 0.00 0.00 37.94 1.52
844 856 4.178540 CCGTCTTTCGTGCCTCTTATAAA 58.821 43.478 0.00 0.00 37.94 1.40
845 857 3.429822 CCCGTCTTTCGTGCCTCTTATAA 60.430 47.826 0.00 0.00 37.94 0.98
846 858 2.100252 CCCGTCTTTCGTGCCTCTTATA 59.900 50.000 0.00 0.00 37.94 0.98
847 859 1.134788 CCCGTCTTTCGTGCCTCTTAT 60.135 52.381 0.00 0.00 37.94 1.73
848 860 0.245539 CCCGTCTTTCGTGCCTCTTA 59.754 55.000 0.00 0.00 37.94 2.10
849 861 1.004918 CCCGTCTTTCGTGCCTCTT 60.005 57.895 0.00 0.00 37.94 2.85
850 862 1.469335 TTCCCGTCTTTCGTGCCTCT 61.469 55.000 0.00 0.00 37.94 3.69
851 863 0.601841 TTTCCCGTCTTTCGTGCCTC 60.602 55.000 0.00 0.00 37.94 4.70
852 864 0.036306 ATTTCCCGTCTTTCGTGCCT 59.964 50.000 0.00 0.00 37.94 4.75
853 865 0.879090 AATTTCCCGTCTTTCGTGCC 59.121 50.000 0.00 0.00 37.94 5.01
854 866 1.963747 CAATTTCCCGTCTTTCGTGC 58.036 50.000 0.00 0.00 37.94 5.34
855 867 1.535462 AGCAATTTCCCGTCTTTCGTG 59.465 47.619 0.00 0.00 37.94 4.35
856 868 1.892209 AGCAATTTCCCGTCTTTCGT 58.108 45.000 0.00 0.00 37.94 3.85
857 869 3.259064 TCTAGCAATTTCCCGTCTTTCG 58.741 45.455 0.00 0.00 39.52 3.46
858 870 4.636206 ACATCTAGCAATTTCCCGTCTTTC 59.364 41.667 0.00 0.00 0.00 2.62
859 871 4.396166 CACATCTAGCAATTTCCCGTCTTT 59.604 41.667 0.00 0.00 0.00 2.52
860 872 3.941483 CACATCTAGCAATTTCCCGTCTT 59.059 43.478 0.00 0.00 0.00 3.01
861 873 3.055094 ACACATCTAGCAATTTCCCGTCT 60.055 43.478 0.00 0.00 0.00 4.18
862 874 3.270877 ACACATCTAGCAATTTCCCGTC 58.729 45.455 0.00 0.00 0.00 4.79
863 875 3.350219 ACACATCTAGCAATTTCCCGT 57.650 42.857 0.00 0.00 0.00 5.28
864 876 3.809832 CCTACACATCTAGCAATTTCCCG 59.190 47.826 0.00 0.00 0.00 5.14
865 877 4.137543 CCCTACACATCTAGCAATTTCCC 58.862 47.826 0.00 0.00 0.00 3.97
866 878 4.137543 CCCCTACACATCTAGCAATTTCC 58.862 47.826 0.00 0.00 0.00 3.13
867 879 3.565902 GCCCCTACACATCTAGCAATTTC 59.434 47.826 0.00 0.00 0.00 2.17
868 880 3.053693 TGCCCCTACACATCTAGCAATTT 60.054 43.478 0.00 0.00 0.00 1.82
869 881 2.509548 TGCCCCTACACATCTAGCAATT 59.490 45.455 0.00 0.00 0.00 2.32
870 882 2.126882 TGCCCCTACACATCTAGCAAT 58.873 47.619 0.00 0.00 0.00 3.56
871 883 1.209504 GTGCCCCTACACATCTAGCAA 59.790 52.381 0.00 0.00 40.40 3.91
872 884 0.830648 GTGCCCCTACACATCTAGCA 59.169 55.000 0.00 0.00 40.40 3.49
873 885 0.106894 GGTGCCCCTACACATCTAGC 59.893 60.000 0.00 0.00 42.55 3.42
874 886 1.496060 TGGTGCCCCTACACATCTAG 58.504 55.000 0.00 0.00 42.55 2.43
875 887 1.768275 CATGGTGCCCCTACACATCTA 59.232 52.381 0.00 0.00 42.55 1.98
876 888 0.548031 CATGGTGCCCCTACACATCT 59.452 55.000 0.00 0.00 42.55 2.90
877 889 0.466189 CCATGGTGCCCCTACACATC 60.466 60.000 2.57 0.00 42.55 3.06
878 890 1.214305 ACCATGGTGCCCCTACACAT 61.214 55.000 18.99 0.00 42.55 3.21
879 891 1.850289 ACCATGGTGCCCCTACACA 60.850 57.895 18.99 0.00 42.55 3.72
880 892 1.378514 CACCATGGTGCCCCTACAC 60.379 63.158 31.13 0.00 39.39 2.90
881 893 3.086143 CACCATGGTGCCCCTACA 58.914 61.111 31.13 0.00 39.39 2.74
903 915 5.189928 TCGCCTTCATGCCTCTTATAAAAA 58.810 37.500 0.00 0.00 0.00 1.94
904 916 4.776349 TCGCCTTCATGCCTCTTATAAAA 58.224 39.130 0.00 0.00 0.00 1.52
905 917 4.415881 TCGCCTTCATGCCTCTTATAAA 57.584 40.909 0.00 0.00 0.00 1.40
906 918 4.202357 ACATCGCCTTCATGCCTCTTATAA 60.202 41.667 0.00 0.00 0.00 0.98
907 919 3.324846 ACATCGCCTTCATGCCTCTTATA 59.675 43.478 0.00 0.00 0.00 0.98
908 920 2.105477 ACATCGCCTTCATGCCTCTTAT 59.895 45.455 0.00 0.00 0.00 1.73
909 921 1.486310 ACATCGCCTTCATGCCTCTTA 59.514 47.619 0.00 0.00 0.00 2.10
910 922 0.254178 ACATCGCCTTCATGCCTCTT 59.746 50.000 0.00 0.00 0.00 2.85
911 923 0.463295 CACATCGCCTTCATGCCTCT 60.463 55.000 0.00 0.00 0.00 3.69
912 924 2.020131 CACATCGCCTTCATGCCTC 58.980 57.895 0.00 0.00 0.00 4.70
913 925 2.117156 GCACATCGCCTTCATGCCT 61.117 57.895 0.00 0.00 32.94 4.75
914 926 2.332362 CTGCACATCGCCTTCATGCC 62.332 60.000 0.00 0.00 41.33 4.40
915 927 1.063649 CTGCACATCGCCTTCATGC 59.936 57.895 0.00 0.00 41.33 4.06
916 928 0.656259 CTCTGCACATCGCCTTCATG 59.344 55.000 0.00 0.00 41.33 3.07
917 929 0.463295 CCTCTGCACATCGCCTTCAT 60.463 55.000 0.00 0.00 41.33 2.57
918 930 1.078918 CCTCTGCACATCGCCTTCA 60.079 57.895 0.00 0.00 41.33 3.02
919 931 2.467826 GCCTCTGCACATCGCCTTC 61.468 63.158 0.00 0.00 41.33 3.46
920 932 2.437359 GCCTCTGCACATCGCCTT 60.437 61.111 0.00 0.00 41.33 4.35
921 933 3.677284 CTGCCTCTGCACATCGCCT 62.677 63.158 0.00 0.00 44.23 5.52
922 934 3.200593 CTGCCTCTGCACATCGCC 61.201 66.667 0.00 0.00 44.23 5.54
923 935 3.873883 GCTGCCTCTGCACATCGC 61.874 66.667 0.00 0.00 44.23 4.58
924 936 3.200593 GGCTGCCTCTGCACATCG 61.201 66.667 12.43 0.00 44.23 3.84
925 937 2.045634 TGGCTGCCTCTGCACATC 60.046 61.111 21.03 0.00 44.23 3.06
926 938 2.045242 CTGGCTGCCTCTGCACAT 60.045 61.111 21.03 0.00 44.23 3.21
931 943 3.889134 TTCACGCTGGCTGCCTCTG 62.889 63.158 21.03 11.33 38.78 3.35
932 944 2.964310 ATTCACGCTGGCTGCCTCT 61.964 57.895 21.03 0.00 38.78 3.69
933 945 2.437359 ATTCACGCTGGCTGCCTC 60.437 61.111 21.03 10.63 38.78 4.70
934 946 2.749044 CATTCACGCTGGCTGCCT 60.749 61.111 21.03 0.00 38.78 4.75
935 947 3.818787 CCATTCACGCTGGCTGCC 61.819 66.667 12.87 12.87 38.78 4.85
940 952 2.361610 AAGGGCCATTCACGCTGG 60.362 61.111 6.18 0.00 36.81 4.85
941 953 2.703798 CCAAGGGCCATTCACGCTG 61.704 63.158 6.18 0.00 0.00 5.18
942 954 2.361610 CCAAGGGCCATTCACGCT 60.362 61.111 6.18 0.00 0.00 5.07
943 955 4.133796 GCCAAGGGCCATTCACGC 62.134 66.667 6.18 0.68 44.06 5.34
960 972 1.089920 CTTGATCAAAGCCAGGACGG 58.910 55.000 9.88 0.00 38.11 4.79
971 983 0.528924 GTGCATGCCAGCTTGATCAA 59.471 50.000 16.68 8.12 34.99 2.57
1066 1078 0.253347 TCATCCTCTTCCTTGGGCCT 60.253 55.000 4.53 0.00 0.00 5.19
1070 1082 2.573462 TCCAACTCATCCTCTTCCTTGG 59.427 50.000 0.00 0.00 0.00 3.61
1072 1084 3.251484 TGTCCAACTCATCCTCTTCCTT 58.749 45.455 0.00 0.00 0.00 3.36
1096 1108 2.222027 CTCGAACAAAGGCTCCTTGTT 58.778 47.619 15.27 15.27 36.26 2.83
1131 1143 0.899717 GCTTCACCCCAATGGCTTCA 60.900 55.000 0.00 0.00 37.83 3.02
1132 1144 1.607801 GGCTTCACCCCAATGGCTTC 61.608 60.000 0.00 0.00 37.83 3.86
1159 1171 1.798735 CCATTGTCCGCTTGCTCTG 59.201 57.895 0.00 0.00 0.00 3.35
1173 1185 2.202395 GGCCGCCATGTATGCCATT 61.202 57.895 3.91 0.00 43.46 3.16
1288 1301 0.320050 TTGCGCTCATGGTACTCACA 59.680 50.000 9.73 0.00 0.00 3.58
1365 1378 3.456277 ACTCTTATTGGATCACCCTCCAC 59.544 47.826 0.00 0.00 44.97 4.02
1439 1452 2.092968 ACCATGTCTTGTATGCCGATGT 60.093 45.455 0.00 0.00 0.00 3.06
1508 1530 2.669781 CATATGGGCAAATGGGTCAGT 58.330 47.619 0.00 0.00 0.00 3.41
1509 1531 1.342174 GCATATGGGCAAATGGGTCAG 59.658 52.381 4.56 0.00 0.00 3.51
1510 1532 1.063038 AGCATATGGGCAAATGGGTCA 60.063 47.619 4.56 0.00 35.83 4.02
1511 1533 1.708341 AGCATATGGGCAAATGGGTC 58.292 50.000 4.56 0.00 35.83 4.46
1581 1603 5.279456 GGTTAAAGGACTTGCCATCATGTTT 60.279 40.000 0.00 0.00 40.02 2.83
1589 1612 3.053917 GGGATAGGTTAAAGGACTTGCCA 60.054 47.826 0.00 0.00 40.02 4.92
1675 1699 7.581213 AAGTCTTCAATACACCAAAATCACA 57.419 32.000 0.00 0.00 0.00 3.58
1879 1904 8.773645 CACGCTTCATGTTCCTTATATGAATAA 58.226 33.333 0.00 0.00 41.62 1.40
1889 1914 2.808543 GTCTTCACGCTTCATGTTCCTT 59.191 45.455 0.00 0.00 0.00 3.36
1939 1965 7.923344 CAGTATAGTGTTTCCTATGACTCAAGG 59.077 40.741 0.00 2.44 0.00 3.61
2059 2085 7.934855 AATTGACTGAGCTGTATGAGATTTT 57.065 32.000 0.00 0.00 0.00 1.82
2096 2123 3.892588 AGAGACCAGAAGAACTTCGTCTT 59.107 43.478 18.53 10.76 43.97 3.01
2173 2201 1.202580 AGCGCTATCATGTTCCTCACC 60.203 52.381 8.99 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.