Multiple sequence alignment - TraesCS2A01G351900

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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 TraesCS2A01G351900 chr2A 100.000 2600 0 0 1 2600 592453115 592455714 0.000000e+00 4802.0
1 TraesCS2A01G351900 chr2D 91.676 1718 82 20 913 2599 447839873 447841560 0.000000e+00 2324.0
2 TraesCS2A01G351900 chr2B 92.831 1102 44 7 1007 2101 527587063 527588136 0.000000e+00 1565.0
3 TraesCS2A01G351900 chr2B 86.412 471 34 7 2138 2595 527588140 527588593 3.010000e-134 488.0
4 TraesCS2A01G351900 chr1D 84.414 879 115 17 1 864 249746582 249745711 0.000000e+00 845.0
5 TraesCS2A01G351900 chr1D 81.187 893 133 24 1 872 470919060 470919938 0.000000e+00 686.0
6 TraesCS2A01G351900 chr3D 84.181 885 108 27 3 872 89632459 89631592 0.000000e+00 830.0
7 TraesCS2A01G351900 chr3D 82.511 892 119 30 1 872 413623310 413622436 0.000000e+00 749.0
8 TraesCS2A01G351900 chr3D 81.195 904 118 35 1 876 566072567 566073446 0.000000e+00 680.0
9 TraesCS2A01G351900 chr6D 82.751 887 123 22 1 872 347714696 347713825 0.000000e+00 763.0
10 TraesCS2A01G351900 chr6D 82.091 899 121 23 1 872 428602132 428603017 0.000000e+00 732.0
11 TraesCS2A01G351900 chr6D 100.000 30 0 0 870 899 359557806 359557777 3.610000e-04 56.5
12 TraesCS2A01G351900 chr6D 100.000 29 0 0 872 900 384434431 384434403 1.000000e-03 54.7
13 TraesCS2A01G351900 chr7D 81.889 900 123 30 1 872 434162814 434163701 0.000000e+00 723.0
14 TraesCS2A01G351900 chr4D 81.556 900 120 32 1 872 49799137 49800018 0.000000e+00 701.0
15 TraesCS2A01G351900 chr4D 100.000 32 0 0 870 901 44834481 44834450 2.790000e-05 60.2
16 TraesCS2A01G351900 chr4D 96.875 32 1 0 870 901 379346898 379346867 1.000000e-03 54.7
17 TraesCS2A01G351900 chr1A 85.354 198 25 4 1135 1329 560372712 560372908 4.390000e-48 202.0
18 TraesCS2A01G351900 chr7B 92.771 83 6 0 1162 1244 738151604 738151522 1.260000e-23 121.0
19 TraesCS2A01G351900 chr7B 100.000 30 0 0 870 899 658280320 658280291 3.610000e-04 56.5
20 TraesCS2A01G351900 chr5D 100.000 31 0 0 870 900 480965374 480965404 1.000000e-04 58.4
21 TraesCS2A01G351900 chr7A 100.000 30 0 0 870 899 79229765 79229736 3.610000e-04 56.5


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 TraesCS2A01G351900 chr2A 592453115 592455714 2599 False 4802.0 4802 100.0000 1 2600 1 chr2A.!!$F1 2599
1 TraesCS2A01G351900 chr2D 447839873 447841560 1687 False 2324.0 2324 91.6760 913 2599 1 chr2D.!!$F1 1686
2 TraesCS2A01G351900 chr2B 527587063 527588593 1530 False 1026.5 1565 89.6215 1007 2595 2 chr2B.!!$F1 1588
3 TraesCS2A01G351900 chr1D 249745711 249746582 871 True 845.0 845 84.4140 1 864 1 chr1D.!!$R1 863
4 TraesCS2A01G351900 chr1D 470919060 470919938 878 False 686.0 686 81.1870 1 872 1 chr1D.!!$F1 871
5 TraesCS2A01G351900 chr3D 89631592 89632459 867 True 830.0 830 84.1810 3 872 1 chr3D.!!$R1 869
6 TraesCS2A01G351900 chr3D 413622436 413623310 874 True 749.0 749 82.5110 1 872 1 chr3D.!!$R2 871
7 TraesCS2A01G351900 chr3D 566072567 566073446 879 False 680.0 680 81.1950 1 876 1 chr3D.!!$F1 875
8 TraesCS2A01G351900 chr6D 347713825 347714696 871 True 763.0 763 82.7510 1 872 1 chr6D.!!$R1 871
9 TraesCS2A01G351900 chr6D 428602132 428603017 885 False 732.0 732 82.0910 1 872 1 chr6D.!!$F1 871
10 TraesCS2A01G351900 chr7D 434162814 434163701 887 False 723.0 723 81.8890 1 872 1 chr7D.!!$F1 871
11 TraesCS2A01G351900 chr4D 49799137 49800018 881 False 701.0 701 81.5560 1 872 1 chr4D.!!$F1 871

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
758 814 0.108207 TGCTCCCGGTTCGGTTTTTA 59.892 50.0 0.0 0.0 46.8 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 1984 0.536006 GGTATGCAGGAGTGATGGCC 60.536 60.0 0.0 0.0 0.0 5.36 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 2.046892 ACGCGCTCTCAGCCATTT 60.047 55.556 5.73 0.00 38.18 2.32
33 34 1.528076 AGCCATTTGCCACGTGTCA 60.528 52.632 15.65 4.57 42.71 3.58
36 37 1.502990 CCATTTGCCACGTGTCACGA 61.503 55.000 30.95 8.53 46.05 4.35
43 44 1.289066 CACGTGTCACGATCTGGGT 59.711 57.895 30.95 4.40 46.05 4.51
61 70 1.064979 GGTGCTCCCTCCGGATTTTTA 60.065 52.381 3.57 0.00 37.60 1.52
66 76 5.358725 GTGCTCCCTCCGGATTTTTATTTTA 59.641 40.000 3.57 0.00 37.60 1.52
134 149 8.670804 TTTTTCGACGTTTTAGTTTTTCATCA 57.329 26.923 0.00 0.00 0.00 3.07
259 282 0.668535 AGAGGCACGGTTTTGCTTTC 59.331 50.000 0.00 0.00 42.56 2.62
264 287 0.382515 CACGGTTTTGCTTTCCCGAA 59.617 50.000 11.41 0.00 43.01 4.30
278 302 2.030562 CGAAAGTCAGGGCCGTGT 59.969 61.111 24.03 5.63 0.00 4.49
347 373 1.880027 GAGTCATGGTTTTGCTTCCGT 59.120 47.619 0.00 0.00 0.00 4.69
350 376 2.034053 GTCATGGTTTTGCTTCCGTGAA 59.966 45.455 7.54 0.00 46.79 3.18
352 378 3.131223 TCATGGTTTTGCTTCCGTGAAAA 59.869 39.130 3.98 0.00 43.84 2.29
433 471 5.815964 TTTAATTTTTCTTCCTTTCGCGC 57.184 34.783 0.00 0.00 0.00 6.86
441 479 3.479269 CCTTTCGCGCGAGTCACC 61.479 66.667 32.74 0.00 0.00 4.02
452 490 1.217882 CGAGTCACCGTTTTGCTTCT 58.782 50.000 0.00 0.00 0.00 2.85
487 525 0.664767 GTGCTTTCGCGAGAGTCACT 60.665 55.000 29.26 0.00 43.69 3.41
549 594 2.814280 TTCTTTCTTCCGCGAGAGTT 57.186 45.000 8.23 0.00 0.00 3.01
551 596 4.451629 TTCTTTCTTCCGCGAGAGTTAT 57.548 40.909 8.23 0.00 0.00 1.89
599 644 1.442184 GCTTTCGCGAGAGTCACGA 60.442 57.895 25.34 6.50 43.69 4.35
661 714 3.861276 TTTTCTTCCGCGAGAGTCATA 57.139 42.857 8.23 0.00 0.00 2.15
671 724 3.857665 CGCGAGAGTCATAGTTTTGCTTA 59.142 43.478 0.00 0.00 0.00 3.09
672 725 4.504461 CGCGAGAGTCATAGTTTTGCTTAT 59.496 41.667 0.00 0.00 0.00 1.73
674 727 5.292101 GCGAGAGTCATAGTTTTGCTTATGT 59.708 40.000 0.00 0.00 0.00 2.29
758 814 0.108207 TGCTCCCGGTTCGGTTTTTA 59.892 50.000 0.00 0.00 46.80 1.52
762 818 1.341531 TCCCGGTTCGGTTTTTACGTA 59.658 47.619 0.00 0.00 46.80 3.57
763 819 2.028567 TCCCGGTTCGGTTTTTACGTAT 60.029 45.455 0.00 0.00 46.80 3.06
830 889 8.548025 TGGGATCTAGTTTTGAATATCTCAACA 58.452 33.333 0.00 0.00 43.90 3.33
865 924 8.353684 TCAATTGTGAAAGCGGTTTAAGATTTA 58.646 29.630 13.36 0.00 0.00 1.40
872 931 4.330740 GCGGTTTAAGATTTAGACGCAA 57.669 40.909 0.00 0.00 44.52 4.85
873 932 4.086574 GCGGTTTAAGATTTAGACGCAAC 58.913 43.478 0.00 0.00 44.52 4.17
874 933 4.320491 CGGTTTAAGATTTAGACGCAACG 58.680 43.478 0.00 0.00 0.00 4.10
875 934 4.090354 CGGTTTAAGATTTAGACGCAACGA 59.910 41.667 0.00 0.00 0.00 3.85
876 935 5.548250 GGTTTAAGATTTAGACGCAACGAG 58.452 41.667 0.00 0.00 0.00 4.18
877 936 5.119743 GGTTTAAGATTTAGACGCAACGAGT 59.880 40.000 0.00 0.00 0.00 4.18
878 937 6.308766 GGTTTAAGATTTAGACGCAACGAGTA 59.691 38.462 0.00 0.00 0.00 2.59
879 938 7.009907 GGTTTAAGATTTAGACGCAACGAGTAT 59.990 37.037 0.00 0.00 0.00 2.12
880 939 8.378421 GTTTAAGATTTAGACGCAACGAGTATT 58.622 33.333 0.00 0.00 0.00 1.89
881 940 6.570690 AAGATTTAGACGCAACGAGTATTC 57.429 37.500 0.00 0.00 0.00 1.75
882 941 5.041940 AGATTTAGACGCAACGAGTATTCC 58.958 41.667 0.00 0.00 0.00 3.01
883 942 4.445452 TTTAGACGCAACGAGTATTCCT 57.555 40.909 0.00 0.00 0.00 3.36
884 943 2.563471 AGACGCAACGAGTATTCCTC 57.437 50.000 0.00 0.00 36.80 3.71
885 944 1.816835 AGACGCAACGAGTATTCCTCA 59.183 47.619 0.00 0.00 40.48 3.86
886 945 2.230508 AGACGCAACGAGTATTCCTCAA 59.769 45.455 0.00 0.00 40.48 3.02
887 946 2.334838 ACGCAACGAGTATTCCTCAAC 58.665 47.619 0.00 0.00 40.48 3.18
888 947 2.029290 ACGCAACGAGTATTCCTCAACT 60.029 45.455 0.00 0.00 40.48 3.16
889 948 3.192001 ACGCAACGAGTATTCCTCAACTA 59.808 43.478 0.00 0.00 40.48 2.24
890 949 3.791887 CGCAACGAGTATTCCTCAACTAG 59.208 47.826 0.00 0.00 40.48 2.57
891 950 4.674623 CGCAACGAGTATTCCTCAACTAGT 60.675 45.833 0.00 0.00 40.48 2.57
892 951 4.563184 GCAACGAGTATTCCTCAACTAGTG 59.437 45.833 0.00 0.00 40.48 2.74
893 952 5.621555 GCAACGAGTATTCCTCAACTAGTGA 60.622 44.000 0.00 0.00 40.48 3.41
894 953 6.565234 CAACGAGTATTCCTCAACTAGTGAT 58.435 40.000 0.00 0.00 40.48 3.06
895 954 6.777213 ACGAGTATTCCTCAACTAGTGATT 57.223 37.500 0.00 0.00 40.48 2.57
896 955 7.171630 ACGAGTATTCCTCAACTAGTGATTT 57.828 36.000 0.00 0.00 40.48 2.17
897 956 7.259161 ACGAGTATTCCTCAACTAGTGATTTC 58.741 38.462 0.00 0.00 40.48 2.17
898 957 6.415280 CGAGTATTCCTCAACTAGTGATTTCG 59.585 42.308 0.00 0.00 40.48 3.46
899 958 6.574350 AGTATTCCTCAACTAGTGATTTCGG 58.426 40.000 0.00 0.00 35.07 4.30
900 959 5.677319 ATTCCTCAACTAGTGATTTCGGA 57.323 39.130 0.00 0.00 35.07 4.55
901 960 5.677319 TTCCTCAACTAGTGATTTCGGAT 57.323 39.130 0.00 0.00 35.07 4.18
902 961 5.011090 TCCTCAACTAGTGATTTCGGATG 57.989 43.478 0.00 0.00 35.07 3.51
903 962 4.709886 TCCTCAACTAGTGATTTCGGATGA 59.290 41.667 0.00 0.00 35.07 2.92
904 963 4.806247 CCTCAACTAGTGATTTCGGATGAC 59.194 45.833 0.00 0.00 35.07 3.06
905 964 4.755411 TCAACTAGTGATTTCGGATGACC 58.245 43.478 0.00 0.00 0.00 4.02
906 965 4.466370 TCAACTAGTGATTTCGGATGACCT 59.534 41.667 0.00 0.00 0.00 3.85
907 966 4.392921 ACTAGTGATTTCGGATGACCTG 57.607 45.455 0.00 0.00 0.00 4.00
908 967 2.029838 AGTGATTTCGGATGACCTGC 57.970 50.000 0.00 0.00 0.00 4.85
909 968 1.017387 GTGATTTCGGATGACCTGCC 58.983 55.000 0.00 0.00 0.00 4.85
910 969 0.617935 TGATTTCGGATGACCTGCCA 59.382 50.000 0.00 0.00 0.00 4.92
911 970 1.212688 TGATTTCGGATGACCTGCCAT 59.787 47.619 0.00 0.00 0.00 4.40
914 973 0.327924 TTCGGATGACCTGCCATGTT 59.672 50.000 0.00 0.00 0.00 2.71
920 979 1.536940 TGACCTGCCATGTTGATGTG 58.463 50.000 0.00 0.00 0.00 3.21
933 992 6.930164 CCATGTTGATGTGAAAGGAATTTGAA 59.070 34.615 0.00 0.00 0.00 2.69
937 996 9.393512 TGTTGATGTGAAAGGAATTTGAAAATT 57.606 25.926 0.68 0.68 41.06 1.82
957 1016 8.564509 AAAATTACTACAACGTTATGGGCTAA 57.435 30.769 0.00 0.00 0.00 3.09
1000 1059 4.479993 CAAGCGGAGGAGGCCTGG 62.480 72.222 12.00 0.00 31.76 4.45
1010 1069 1.728490 GGAGGCCTGGCAAATAAGCG 61.728 60.000 22.05 0.00 34.64 4.68
1024 1083 2.113860 TAAGCGGCTGCAAAATCTCT 57.886 45.000 21.93 0.00 46.23 3.10
1034 1093 5.124457 GGCTGCAAAATCTCTGAAGTAATCA 59.876 40.000 0.50 0.00 36.38 2.57
1035 1094 6.183360 GGCTGCAAAATCTCTGAAGTAATCAT 60.183 38.462 0.50 0.00 37.44 2.45
1076 1135 3.252215 GTCACGTCAACCAAATCCAATCA 59.748 43.478 0.00 0.00 0.00 2.57
1594 1653 6.969993 AGGCCTTTGTTAAGTTGTAAATCA 57.030 33.333 0.00 0.00 0.00 2.57
1694 1758 4.530161 AGAGAGATTAGCAACAACAGGAGT 59.470 41.667 0.00 0.00 0.00 3.85
1714 1778 1.275421 GCCTAGGCTTGAAGGGAGGT 61.275 60.000 27.17 0.00 38.26 3.85
1758 1822 4.668138 TGGTTTTCAGGTTTAGCCCTAT 57.332 40.909 0.00 0.00 38.26 2.57
1779 1843 6.553100 CCTATACTTCAGAATCTCCAGGTCTT 59.447 42.308 0.00 0.00 0.00 3.01
1821 1885 0.029300 CAACAAAGTGAGTGCCACCG 59.971 55.000 0.00 0.00 46.87 4.94
1850 1914 2.866762 GTGACGTCTGTTTCTCTGCTTT 59.133 45.455 17.92 0.00 0.00 3.51
1897 1961 3.858503 GCAACTTCTTTGAACATGGCCTC 60.859 47.826 3.32 0.00 37.39 4.70
1919 1984 1.156645 GCCAGCTTCTAGTCGCCATG 61.157 60.000 0.00 0.00 0.00 3.66
2000 2070 2.084844 GCACTGAGCTCACATTCGG 58.915 57.895 13.74 4.41 41.15 4.30
2094 2164 3.684693 GCCTCCTGCAGAGAAGATC 57.315 57.895 17.39 1.91 46.50 2.75
2101 2171 2.026449 CCTGCAGAGAAGATCCCTTGTT 60.026 50.000 17.39 0.00 31.62 2.83
2104 2174 5.241403 TGCAGAGAAGATCCCTTGTTTTA 57.759 39.130 0.00 0.00 31.62 1.52
2109 2179 6.372937 CAGAGAAGATCCCTTGTTTTAACTCC 59.627 42.308 0.00 0.00 31.62 3.85
2111 2181 6.794534 AGAAGATCCCTTGTTTTAACTCCAT 58.205 36.000 0.00 0.00 31.62 3.41
2165 2239 4.492570 GCTTCATCGTACACTTGGATTTCG 60.493 45.833 0.00 0.00 0.00 3.46
2185 2259 1.302511 GATGGCAGGGACGTGTGTT 60.303 57.895 0.00 0.00 0.00 3.32
2195 2269 0.661020 GACGTGTGTTGGAGGGTTTG 59.339 55.000 0.00 0.00 0.00 2.93
2212 2286 7.379059 AGGGTTTGGATTTCTGAAGAAAAAT 57.621 32.000 9.42 0.00 45.81 1.82
2229 2314 9.288124 GAAGAAAAATTTGTTGGATTTGTTTGG 57.712 29.630 0.00 0.00 0.00 3.28
2236 2321 0.894141 TGGATTTGTTTGGCATCCCG 59.106 50.000 0.37 0.00 0.00 5.14
2276 2362 4.040952 TCATCAGCCCTTAGAGGATAAAGC 59.959 45.833 0.00 0.00 37.67 3.51
2302 2398 5.525378 AGATATTGCTTAGCTTTTCGGTCAG 59.475 40.000 5.60 0.00 0.00 3.51
2331 2427 7.201992 CCTCCAGTTCTTCTCTAGCTTGAATAT 60.202 40.741 0.00 0.00 0.00 1.28
2332 2428 8.768501 TCCAGTTCTTCTCTAGCTTGAATATA 57.231 34.615 0.00 0.00 0.00 0.86
2333 2429 9.201989 TCCAGTTCTTCTCTAGCTTGAATATAA 57.798 33.333 0.00 0.00 0.00 0.98
2348 2445 7.545265 GCTTGAATATAAACAGTGGCAATTGAA 59.455 33.333 10.34 0.00 0.00 2.69
2424 2522 5.223382 TCTCTAGCAAACGAAAAGAGACAG 58.777 41.667 0.00 0.00 38.17 3.51
2428 2526 2.892613 CAAACGAAAAGAGACAGCGAC 58.107 47.619 0.00 0.00 0.00 5.19
2450 2548 4.018960 ACATGAGTCTTGCATTAGTCCCTT 60.019 41.667 0.00 0.00 0.00 3.95
2469 2567 3.009033 CCTTGGTGTCCCACAGATCTTTA 59.991 47.826 0.00 0.00 41.67 1.85
2592 2690 0.319469 GTTTTGAATGGGGTGGCGTG 60.319 55.000 0.00 0.00 0.00 5.34
2599 2697 1.852157 ATGGGGTGGCGTGTCTTCAT 61.852 55.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.372872 CAGATCGTGACACGTGGCA 60.373 57.895 23.03 23.03 43.14 4.92
72 82 8.616076 CCATTTAAAAAGCCAAAAACACATGTA 58.384 29.630 0.00 0.00 0.00 2.29
73 83 7.121907 ACCATTTAAAAAGCCAAAAACACATGT 59.878 29.630 0.00 0.00 0.00 3.21
123 138 6.538263 AGCTAAGGAAGACTGATGAAAAACT 58.462 36.000 0.00 0.00 0.00 2.66
132 147 4.866508 TCGAAAAGCTAAGGAAGACTGA 57.133 40.909 0.00 0.00 0.00 3.41
134 149 5.407407 TGATCGAAAAGCTAAGGAAGACT 57.593 39.130 0.00 0.00 0.00 3.24
160 175 6.538189 TCGGGCAATTCTTTTCAAATTTTC 57.462 33.333 0.00 0.00 0.00 2.29
207 229 0.801067 CCGTAACTCTCGCGAAAGGG 60.801 60.000 14.96 3.76 46.71 3.95
208 230 0.109412 ACCGTAACTCTCGCGAAAGG 60.109 55.000 14.96 11.10 0.00 3.11
259 282 4.016706 ACGGCCCTGACTTTCGGG 62.017 66.667 0.00 0.00 42.66 5.14
264 287 1.534235 AGAGACACGGCCCTGACTT 60.534 57.895 8.88 0.00 0.00 3.01
381 408 0.306533 TTCGTTTTTGAGAGGCACGC 59.693 50.000 0.00 0.00 0.00 5.34
405 435 7.614026 CGAAAGGAAGAAAAATTAAAAACGCA 58.386 30.769 0.00 0.00 0.00 5.24
406 436 6.568601 GCGAAAGGAAGAAAAATTAAAAACGC 59.431 34.615 0.00 0.00 0.00 4.84
415 448 1.533731 TCGCGCGAAAGGAAGAAAAAT 59.466 42.857 32.97 0.00 0.00 1.82
424 462 3.479269 GGTGACTCGCGCGAAAGG 61.479 66.667 33.99 23.99 0.00 3.11
433 471 1.070577 CAGAAGCAAAACGGTGACTCG 60.071 52.381 0.00 0.00 0.00 4.18
539 584 1.202031 GCAAAACCATAACTCTCGCGG 60.202 52.381 6.13 0.00 0.00 6.46
599 644 0.673644 CGTTTCCGAGAAGGCATGGT 60.674 55.000 0.00 0.00 40.77 3.55
661 714 4.449068 CGTGTCTCTCACATAAGCAAAACT 59.551 41.667 0.00 0.00 46.44 2.66
671 724 1.686587 TCACAACCGTGTCTCTCACAT 59.313 47.619 0.00 0.00 46.44 3.21
672 725 1.107945 TCACAACCGTGTCTCTCACA 58.892 50.000 0.00 0.00 46.44 3.58
674 727 3.181470 TGAAATCACAACCGTGTCTCTCA 60.181 43.478 0.00 0.00 44.02 3.27
773 829 6.451064 AGGTTTTGACGAACTTTTCTTCAT 57.549 33.333 0.00 0.00 37.71 2.57
830 889 5.865552 CCGCTTTCACAATTGAATTTCTCAT 59.134 36.000 13.59 0.00 41.50 2.90
839 898 5.759506 TCTTAAACCGCTTTCACAATTGA 57.240 34.783 13.59 0.00 0.00 2.57
844 903 6.347079 CGTCTAAATCTTAAACCGCTTTCACA 60.347 38.462 0.00 0.00 0.00 3.58
865 924 2.563471 GAGGAATACTCGTTGCGTCT 57.437 50.000 0.00 0.00 36.29 4.18
874 933 6.697892 CCGAAATCACTAGTTGAGGAATACTC 59.302 42.308 0.00 0.00 46.78 2.59
875 934 6.380274 TCCGAAATCACTAGTTGAGGAATACT 59.620 38.462 0.00 0.00 37.77 2.12
876 935 6.570692 TCCGAAATCACTAGTTGAGGAATAC 58.429 40.000 0.00 0.00 37.77 1.89
877 936 6.785337 TCCGAAATCACTAGTTGAGGAATA 57.215 37.500 0.00 0.00 37.77 1.75
878 937 5.677319 TCCGAAATCACTAGTTGAGGAAT 57.323 39.130 0.00 0.00 37.77 3.01
879 938 5.186992 TCATCCGAAATCACTAGTTGAGGAA 59.813 40.000 0.00 0.00 37.77 3.36
880 939 4.709886 TCATCCGAAATCACTAGTTGAGGA 59.290 41.667 0.00 0.00 37.77 3.71
881 940 4.806247 GTCATCCGAAATCACTAGTTGAGG 59.194 45.833 0.00 0.00 37.77 3.86
882 941 4.806247 GGTCATCCGAAATCACTAGTTGAG 59.194 45.833 0.00 0.00 37.77 3.02
883 942 4.466370 AGGTCATCCGAAATCACTAGTTGA 59.534 41.667 0.00 0.00 37.45 3.18
884 943 4.568359 CAGGTCATCCGAAATCACTAGTTG 59.432 45.833 0.00 0.00 39.05 3.16
885 944 4.759782 CAGGTCATCCGAAATCACTAGTT 58.240 43.478 0.00 0.00 39.05 2.24
886 945 3.430929 GCAGGTCATCCGAAATCACTAGT 60.431 47.826 0.00 0.00 39.05 2.57
887 946 3.126831 GCAGGTCATCCGAAATCACTAG 58.873 50.000 0.00 0.00 39.05 2.57
888 947 2.158957 GGCAGGTCATCCGAAATCACTA 60.159 50.000 0.00 0.00 39.05 2.74
889 948 1.407437 GGCAGGTCATCCGAAATCACT 60.407 52.381 0.00 0.00 39.05 3.41
890 949 1.017387 GGCAGGTCATCCGAAATCAC 58.983 55.000 0.00 0.00 39.05 3.06
891 950 0.617935 TGGCAGGTCATCCGAAATCA 59.382 50.000 0.00 0.00 39.05 2.57
892 951 1.605710 CATGGCAGGTCATCCGAAATC 59.394 52.381 0.00 0.00 39.05 2.17
893 952 1.064463 ACATGGCAGGTCATCCGAAAT 60.064 47.619 0.00 0.00 39.05 2.17
894 953 0.327924 ACATGGCAGGTCATCCGAAA 59.672 50.000 0.00 0.00 39.05 3.46
895 954 0.327924 AACATGGCAGGTCATCCGAA 59.672 50.000 4.81 0.00 39.05 4.30
896 955 0.392863 CAACATGGCAGGTCATCCGA 60.393 55.000 4.81 0.00 39.05 4.55
897 956 0.392863 TCAACATGGCAGGTCATCCG 60.393 55.000 4.81 0.00 39.05 4.18
898 957 1.679680 CATCAACATGGCAGGTCATCC 59.320 52.381 4.81 0.00 0.00 3.51
899 958 2.098607 CACATCAACATGGCAGGTCATC 59.901 50.000 4.81 0.00 33.82 2.92
900 959 2.097036 CACATCAACATGGCAGGTCAT 58.903 47.619 4.81 0.00 33.82 3.06
901 960 1.073603 TCACATCAACATGGCAGGTCA 59.926 47.619 4.81 0.00 33.82 4.02
902 961 1.825090 TCACATCAACATGGCAGGTC 58.175 50.000 4.81 0.00 33.82 3.85
903 962 2.291209 TTCACATCAACATGGCAGGT 57.709 45.000 0.00 0.00 33.82 4.00
904 963 2.094390 CCTTTCACATCAACATGGCAGG 60.094 50.000 0.00 0.00 33.82 4.85
905 964 2.821378 TCCTTTCACATCAACATGGCAG 59.179 45.455 0.00 0.00 33.82 4.85
906 965 2.874014 TCCTTTCACATCAACATGGCA 58.126 42.857 0.00 0.00 33.82 4.92
907 966 3.940209 TTCCTTTCACATCAACATGGC 57.060 42.857 0.00 0.00 33.82 4.40
908 967 6.457355 TCAAATTCCTTTCACATCAACATGG 58.543 36.000 0.00 0.00 33.82 3.66
909 968 7.949903 TTCAAATTCCTTTCACATCAACATG 57.050 32.000 0.00 0.00 35.92 3.21
910 969 8.961294 TTTTCAAATTCCTTTCACATCAACAT 57.039 26.923 0.00 0.00 0.00 2.71
911 970 8.961294 ATTTTCAAATTCCTTTCACATCAACA 57.039 26.923 0.00 0.00 0.00 3.33
933 992 8.741603 ATTAGCCCATAACGTTGTAGTAATTT 57.258 30.769 11.99 0.00 0.00 1.82
937 996 6.517194 GCCTATTAGCCCATAACGTTGTAGTA 60.517 42.308 11.99 0.00 0.00 1.82
938 997 5.741093 GCCTATTAGCCCATAACGTTGTAGT 60.741 44.000 11.99 0.00 0.00 2.73
939 998 4.689345 GCCTATTAGCCCATAACGTTGTAG 59.311 45.833 11.99 0.00 0.00 2.74
957 1016 4.102681 GGGTCAGTGTATGTAAAGGCCTAT 59.897 45.833 5.16 0.00 0.00 2.57
966 1025 2.354704 GCTTGCTGGGTCAGTGTATGTA 60.355 50.000 0.00 0.00 33.43 2.29
967 1026 1.611673 GCTTGCTGGGTCAGTGTATGT 60.612 52.381 0.00 0.00 33.43 2.29
968 1027 1.089920 GCTTGCTGGGTCAGTGTATG 58.910 55.000 0.00 0.00 33.43 2.39
969 1028 0.391661 CGCTTGCTGGGTCAGTGTAT 60.392 55.000 0.00 0.00 33.43 2.29
1000 1059 1.427435 TTTTGCAGCCGCTTATTTGC 58.573 45.000 0.00 0.00 39.64 3.68
1010 1069 5.124457 TGATTACTTCAGAGATTTTGCAGCC 59.876 40.000 0.00 0.00 0.00 4.85
1024 1083 2.682856 GGGCTTCGCAATGATTACTTCA 59.317 45.455 0.00 0.00 39.12 3.02
1034 1093 0.179018 GAGGGTATGGGCTTCGCAAT 60.179 55.000 0.00 0.00 0.00 3.56
1035 1094 1.223487 GAGGGTATGGGCTTCGCAA 59.777 57.895 0.00 0.00 0.00 4.85
1050 1109 1.459592 GATTTGGTTGACGTGACGAGG 59.540 52.381 13.70 0.00 0.00 4.63
1076 1135 0.613012 GCTGAGGCCCATCTTTGGTT 60.613 55.000 0.00 0.00 41.91 3.67
1694 1758 1.274703 CCTCCCTTCAAGCCTAGGCA 61.275 60.000 34.70 12.72 44.88 4.75
1714 1778 4.993705 ACCCTACTTGAAACCTTGATCA 57.006 40.909 0.00 0.00 0.00 2.92
1758 1822 6.954684 ACTTAAGACCTGGAGATTCTGAAGTA 59.045 38.462 10.09 0.00 38.71 2.24
1779 1843 4.936802 AGCTGGAAGAGAGGACTAACTTA 58.063 43.478 0.00 0.00 34.07 2.24
1821 1885 5.921408 AGAGAAACAGACGTCACTTTGATAC 59.079 40.000 19.50 2.86 0.00 2.24
1850 1914 1.148273 GGCGGCCTGGAACATATGA 59.852 57.895 12.87 0.00 38.20 2.15
1897 1961 1.156645 GGCGACTAGAAGCTGGCATG 61.157 60.000 12.36 0.00 0.00 4.06
1919 1984 0.536006 GGTATGCAGGAGTGATGGCC 60.536 60.000 0.00 0.00 0.00 5.36
1953 2023 5.082425 GCTGGGGGATCTTGAATATTCATT 58.918 41.667 18.61 7.29 37.00 2.57
1989 2059 4.433615 TCACTTATTCTCCGAATGTGAGC 58.566 43.478 5.95 0.00 0.00 4.26
2000 2070 9.042008 TGTTGAAACTAACACTCACTTATTCTC 57.958 33.333 0.00 0.00 35.75 2.87
2094 2164 5.016173 TCATGGATGGAGTTAAAACAAGGG 58.984 41.667 0.00 0.00 0.00 3.95
2101 2171 6.152661 GGTTGATGTTCATGGATGGAGTTAAA 59.847 38.462 0.00 0.00 0.00 1.52
2104 2174 4.019174 GGTTGATGTTCATGGATGGAGTT 58.981 43.478 0.00 0.00 0.00 3.01
2109 2179 2.100252 GCCTGGTTGATGTTCATGGATG 59.900 50.000 0.00 0.00 0.00 3.51
2111 2181 1.075212 TGCCTGGTTGATGTTCATGGA 59.925 47.619 0.00 0.00 0.00 3.41
2165 2239 1.448540 CACACGTCCCTGCCATCTC 60.449 63.158 0.00 0.00 0.00 2.75
2185 2259 3.397618 TCTTCAGAAATCCAAACCCTCCA 59.602 43.478 0.00 0.00 0.00 3.86
2195 2269 8.661352 TCCAACAAATTTTTCTTCAGAAATCC 57.339 30.769 2.83 0.00 42.83 3.01
2212 2286 4.133078 GGATGCCAAACAAATCCAACAAA 58.867 39.130 0.00 0.00 39.79 2.83
2217 2291 0.894141 CGGGATGCCAAACAAATCCA 59.106 50.000 3.39 0.00 41.48 3.41
2229 2314 1.537202 GATTATCTGTTGGCGGGATGC 59.463 52.381 0.00 0.00 45.38 3.91
2236 2321 3.876914 TGATGAACGGATTATCTGTTGGC 59.123 43.478 22.37 10.63 45.29 4.52
2276 2362 4.508124 ACCGAAAAGCTAAGCAATATCTCG 59.492 41.667 0.00 0.00 0.00 4.04
2302 2398 2.418060 GCTAGAGAAGAACTGGAGGTGC 60.418 54.545 0.00 0.00 0.00 5.01
2331 2427 7.495901 TCAGAATTTTCAATTGCCACTGTTTA 58.504 30.769 0.00 0.00 0.00 2.01
2332 2428 6.347696 TCAGAATTTTCAATTGCCACTGTTT 58.652 32.000 0.00 0.00 0.00 2.83
2333 2429 5.916318 TCAGAATTTTCAATTGCCACTGTT 58.084 33.333 0.00 0.00 0.00 3.16
2428 2526 4.148128 AGGGACTAATGCAAGACTCATG 57.852 45.455 0.00 0.00 36.02 3.07
2579 2677 1.303317 GAAGACACGCCACCCCATT 60.303 57.895 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.