Multiple sequence alignment - TraesCS4D01G044600

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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 TraesCS4D01G044600 chr4D 100.000 5902 0 0 1 5902 20404623 20410524 0.000000e+00 10900
1 TraesCS4D01G044600 chr4D 92.276 3107 146 27 1886 4938 20477314 20474248 0.000000e+00 4322
2 TraesCS4D01G044600 chr4D 91.751 788 45 10 992 1779 20478152 20477385 0.000000e+00 1077
3 TraesCS4D01G044600 chr4D 84.683 457 50 13 1256 1702 20482580 20482134 7.020000e-119 438
4 TraesCS4D01G044600 chr4D 76.791 349 38 9 851 1171 20394297 20394630 7.920000e-34 156
5 TraesCS4D01G044600 chr4D 89.916 119 12 0 848 966 20478346 20478228 2.850000e-33 154
6 TraesCS4D01G044600 chr4D 91.964 112 5 3 706 813 260686693 260686582 2.850000e-33 154
7 TraesCS4D01G044600 chr4D 90.678 118 8 3 703 817 320214120 320214237 2.850000e-33 154
8 TraesCS4D01G044600 chr4D 96.610 59 2 0 1247 1305 20358230 20358288 1.350000e-16 99
9 TraesCS4D01G044600 chr4B 96.962 3292 65 8 1770 5029 32416643 32419931 0.000000e+00 5493
10 TraesCS4D01G044600 chr4B 93.134 801 34 7 976 1776 32415803 32416582 0.000000e+00 1155
11 TraesCS4D01G044600 chr4B 81.570 293 43 8 417 705 114988367 114988082 1.280000e-56 231
12 TraesCS4D01G044600 chr4B 94.286 140 2 1 845 978 32415632 32415771 5.990000e-50 209
13 TraesCS4D01G044600 chr4A 90.789 2953 181 45 2078 4968 581192950 581195873 0.000000e+00 3862
14 TraesCS4D01G044600 chr4A 86.634 621 37 18 845 1441 581191716 581192314 0.000000e+00 645
15 TraesCS4D01G044600 chr4A 81.550 813 107 23 976 1764 581188949 581189742 1.080000e-176 630
16 TraesCS4D01G044600 chr4A 86.411 287 27 10 427 705 687858760 687859042 2.670000e-78 303
17 TraesCS4D01G044600 chr4A 85.965 285 22 7 1854 2120 581192666 581192950 7.480000e-74 289
18 TraesCS4D01G044600 chr4A 92.105 114 5 3 704 813 157872408 157872521 2.200000e-34 158
19 TraesCS4D01G044600 chr3D 98.396 873 14 0 5030 5902 514675529 514674657 0.000000e+00 1535
20 TraesCS4D01G044600 chr3D 96.796 874 19 6 5030 5902 44897889 44898754 0.000000e+00 1450
21 TraesCS4D01G044600 chr3D 92.275 712 40 13 1 705 465043993 465044696 0.000000e+00 996
22 TraesCS4D01G044600 chr3D 89.252 428 17 12 304 705 74914967 74914543 5.280000e-140 508
23 TraesCS4D01G044600 chr7D 97.025 874 18 5 5030 5902 566035702 566034836 0.000000e+00 1463
24 TraesCS4D01G044600 chr7D 89.163 729 43 21 1 705 157292434 157291718 0.000000e+00 876
25 TraesCS4D01G044600 chr7D 92.174 115 5 3 703 813 554474935 554475049 6.120000e-35 159
26 TraesCS4D01G044600 chr7D 91.304 115 6 3 703 813 124837716 124837830 2.850000e-33 154
27 TraesCS4D01G044600 chr6D 96.568 874 22 5 5030 5902 162277246 162278112 0.000000e+00 1441
28 TraesCS4D01G044600 chr6D 96.246 879 25 7 5024 5902 387583817 387584687 0.000000e+00 1434
29 TraesCS4D01G044600 chr6D 90.981 754 25 25 1 718 50610587 50609841 0.000000e+00 976
30 TraesCS4D01G044600 chr6D 91.304 115 6 3 703 813 426089321 426089435 2.850000e-33 154
31 TraesCS4D01G044600 chr6D 89.565 115 8 3 703 813 362301431 362301545 6.170000e-30 143
32 TraesCS4D01G044600 chr6B 95.904 879 28 4 5025 5902 65094619 65095490 0.000000e+00 1417
33 TraesCS4D01G044600 chr7B 95.757 872 31 2 5030 5901 312350203 312351068 0.000000e+00 1400
34 TraesCS4D01G044600 chr5B 95.762 873 29 6 5030 5902 629697612 629696748 0.000000e+00 1400
35 TraesCS4D01G044600 chr5B 89.641 724 48 22 1 711 701898413 701897704 0.000000e+00 896
36 TraesCS4D01G044600 chr7A 95.657 875 29 8 5030 5902 115534138 115535005 0.000000e+00 1397
37 TraesCS4D01G044600 chr5D 94.110 730 17 8 1 705 494630867 494631595 0.000000e+00 1086
38 TraesCS4D01G044600 chr5D 93.989 732 16 10 1 705 410256895 410256165 0.000000e+00 1083
39 TraesCS4D01G044600 chr5D 93.570 731 19 10 1 705 195258619 195257891 0.000000e+00 1064
40 TraesCS4D01G044600 chr5D 85.733 750 60 31 1 713 127722624 127723363 0.000000e+00 749
41 TraesCS4D01G044600 chr5D 90.435 115 7 3 703 813 449912122 449912236 1.330000e-31 148
42 TraesCS4D01G044600 chr2D 93.733 734 16 12 1 705 373241932 373242664 0.000000e+00 1074
43 TraesCS4D01G044600 chr2D 89.503 724 43 21 1 705 153665101 153665810 0.000000e+00 885
44 TraesCS4D01G044600 chr1D 89.152 719 58 18 1 705 262999876 263000588 0.000000e+00 878
45 TraesCS4D01G044600 chr1D 90.179 112 7 3 706 813 183999873 183999762 6.170000e-30 143


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 TraesCS4D01G044600 chr4D 20404623 20410524 5901 False 10900.000000 10900 100.0000 1 5902 1 chr4D.!!$F3 5901
1 TraesCS4D01G044600 chr4D 20474248 20482580 8332 True 1497.750000 4322 89.6565 848 4938 4 chr4D.!!$R2 4090
2 TraesCS4D01G044600 chr4B 32415632 32419931 4299 False 2285.666667 5493 94.7940 845 5029 3 chr4B.!!$F1 4184
3 TraesCS4D01G044600 chr4A 581188949 581195873 6924 False 1356.500000 3862 86.2345 845 4968 4 chr4A.!!$F3 4123
4 TraesCS4D01G044600 chr3D 514674657 514675529 872 True 1535.000000 1535 98.3960 5030 5902 1 chr3D.!!$R2 872
5 TraesCS4D01G044600 chr3D 44897889 44898754 865 False 1450.000000 1450 96.7960 5030 5902 1 chr3D.!!$F1 872
6 TraesCS4D01G044600 chr3D 465043993 465044696 703 False 996.000000 996 92.2750 1 705 1 chr3D.!!$F2 704
7 TraesCS4D01G044600 chr7D 566034836 566035702 866 True 1463.000000 1463 97.0250 5030 5902 1 chr7D.!!$R2 872
8 TraesCS4D01G044600 chr7D 157291718 157292434 716 True 876.000000 876 89.1630 1 705 1 chr7D.!!$R1 704
9 TraesCS4D01G044600 chr6D 162277246 162278112 866 False 1441.000000 1441 96.5680 5030 5902 1 chr6D.!!$F1 872
10 TraesCS4D01G044600 chr6D 387583817 387584687 870 False 1434.000000 1434 96.2460 5024 5902 1 chr6D.!!$F3 878
11 TraesCS4D01G044600 chr6D 50609841 50610587 746 True 976.000000 976 90.9810 1 718 1 chr6D.!!$R1 717
12 TraesCS4D01G044600 chr6B 65094619 65095490 871 False 1417.000000 1417 95.9040 5025 5902 1 chr6B.!!$F1 877
13 TraesCS4D01G044600 chr7B 312350203 312351068 865 False 1400.000000 1400 95.7570 5030 5901 1 chr7B.!!$F1 871
14 TraesCS4D01G044600 chr5B 629696748 629697612 864 True 1400.000000 1400 95.7620 5030 5902 1 chr5B.!!$R1 872
15 TraesCS4D01G044600 chr5B 701897704 701898413 709 True 896.000000 896 89.6410 1 711 1 chr5B.!!$R2 710
16 TraesCS4D01G044600 chr7A 115534138 115535005 867 False 1397.000000 1397 95.6570 5030 5902 1 chr7A.!!$F1 872
17 TraesCS4D01G044600 chr5D 494630867 494631595 728 False 1086.000000 1086 94.1100 1 705 1 chr5D.!!$F3 704
18 TraesCS4D01G044600 chr5D 410256165 410256895 730 True 1083.000000 1083 93.9890 1 705 1 chr5D.!!$R2 704
19 TraesCS4D01G044600 chr5D 195257891 195258619 728 True 1064.000000 1064 93.5700 1 705 1 chr5D.!!$R1 704
20 TraesCS4D01G044600 chr5D 127722624 127723363 739 False 749.000000 749 85.7330 1 713 1 chr5D.!!$F1 712
21 TraesCS4D01G044600 chr2D 373241932 373242664 732 False 1074.000000 1074 93.7330 1 705 1 chr2D.!!$F2 704
22 TraesCS4D01G044600 chr2D 153665101 153665810 709 False 885.000000 885 89.5030 1 705 1 chr2D.!!$F1 704
23 TraesCS4D01G044600 chr1D 262999876 263000588 712 False 878.000000 878 89.1520 1 705 1 chr1D.!!$F1 704

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
796 860 0.037447 TCGGGTGATGGATGTTTGCA 59.963 50.000 0.00 0.0 0.00 4.08 F
843 907 0.167470 CTGTCGGCGTACTCTCGAAA 59.833 55.000 6.85 0.0 34.62 3.46 F
844 908 0.592637 TGTCGGCGTACTCTCGAAAA 59.407 50.000 6.85 0.0 34.62 2.29 F
2502 6531 0.771127 TTCAGAAGGAACACCAGGGG 59.229 55.000 0.00 0.0 0.00 4.79 F
3800 7834 1.817447 ACTGCTGTAAGGACGTACTCC 59.183 52.381 0.00 0.0 39.81 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 6531 1.952296 CTATCATGGAAAGGCACAGGC 59.048 52.381 0.00 0.00 40.13 4.85 R
2769 6800 3.331591 CCATTGATCACCAGATATCCCCA 59.668 47.826 0.00 0.00 33.72 4.96 R
2848 6880 6.959639 AATGGTAAGTGAACAATCAACTGT 57.040 33.333 0.00 0.00 37.30 3.55 R
4104 8160 1.727335 GTAGAAGCGGCTCACAAGAAC 59.273 52.381 1.45 0.00 0.00 3.01 R
5422 9523 0.036875 ACTTAGGGACTTGCAGGTGC 59.963 55.000 12.24 12.24 41.75 5.01 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
611 673 5.509927 GCTTCTGCTTTCGGTCTACGAGA 62.510 52.174 0.00 0.00 43.96 4.04
621 683 1.012841 GTCTACGAGAGGTACGTGGG 58.987 60.000 0.00 0.00 43.73 4.61
643 705 0.178958 ACACTCTCCCCTCTCGTTGT 60.179 55.000 0.00 0.00 0.00 3.32
718 782 4.579384 CCAAGTGTGGGTGCGGGT 62.579 66.667 0.00 0.00 41.77 5.28
719 783 3.286751 CAAGTGTGGGTGCGGGTG 61.287 66.667 0.00 0.00 0.00 4.61
720 784 4.579384 AAGTGTGGGTGCGGGTGG 62.579 66.667 0.00 0.00 0.00 4.61
722 786 4.344865 GTGTGGGTGCGGGTGGAT 62.345 66.667 0.00 0.00 0.00 3.41
723 787 3.575247 TGTGGGTGCGGGTGGATT 61.575 61.111 0.00 0.00 0.00 3.01
725 789 1.451387 GTGGGTGCGGGTGGATTAG 60.451 63.158 0.00 0.00 0.00 1.73
726 790 1.613928 TGGGTGCGGGTGGATTAGA 60.614 57.895 0.00 0.00 0.00 2.10
727 791 1.153229 GGGTGCGGGTGGATTAGAC 60.153 63.158 0.00 0.00 0.00 2.59
728 792 1.153229 GGTGCGGGTGGATTAGACC 60.153 63.158 0.00 0.00 0.00 3.85
735 799 2.786777 GGGTGGATTAGACCGTTTTGT 58.213 47.619 0.00 0.00 33.89 2.83
736 800 2.486592 GGGTGGATTAGACCGTTTTGTG 59.513 50.000 0.00 0.00 33.89 3.33
737 801 3.404899 GGTGGATTAGACCGTTTTGTGA 58.595 45.455 0.00 0.00 0.00 3.58
738 802 3.435671 GGTGGATTAGACCGTTTTGTGAG 59.564 47.826 0.00 0.00 0.00 3.51
740 804 4.389077 GTGGATTAGACCGTTTTGTGAGAG 59.611 45.833 0.00 0.00 0.00 3.20
741 805 4.282449 TGGATTAGACCGTTTTGTGAGAGA 59.718 41.667 0.00 0.00 0.00 3.10
742 806 5.046591 TGGATTAGACCGTTTTGTGAGAGAT 60.047 40.000 0.00 0.00 0.00 2.75
778 842 4.672587 TTATAGGTGTGAGTGGATGCTC 57.327 45.455 0.00 0.00 36.12 4.26
779 843 0.817654 TAGGTGTGAGTGGATGCTCG 59.182 55.000 0.00 0.00 38.28 5.03
780 844 1.448540 GGTGTGAGTGGATGCTCGG 60.449 63.158 0.00 0.00 38.28 4.63
783 847 1.448540 GTGAGTGGATGCTCGGGTG 60.449 63.158 0.00 0.00 38.28 4.61
784 848 1.609210 TGAGTGGATGCTCGGGTGA 60.609 57.895 0.00 0.00 38.28 4.02
785 849 0.977627 TGAGTGGATGCTCGGGTGAT 60.978 55.000 0.00 0.00 38.28 3.06
786 850 0.531532 GAGTGGATGCTCGGGTGATG 60.532 60.000 0.00 0.00 0.00 3.07
787 851 1.524621 GTGGATGCTCGGGTGATGG 60.525 63.158 0.00 0.00 0.00 3.51
790 854 0.604780 GGATGCTCGGGTGATGGATG 60.605 60.000 0.00 0.00 0.00 3.51
794 858 0.734889 GCTCGGGTGATGGATGTTTG 59.265 55.000 0.00 0.00 0.00 2.93
795 859 0.734889 CTCGGGTGATGGATGTTTGC 59.265 55.000 0.00 0.00 0.00 3.68
796 860 0.037447 TCGGGTGATGGATGTTTGCA 59.963 50.000 0.00 0.00 0.00 4.08
797 861 1.105457 CGGGTGATGGATGTTTGCAT 58.895 50.000 0.00 0.00 36.50 3.96
806 870 2.675767 GATGTTTGCATCGATCGCAT 57.324 45.000 18.73 6.02 41.60 4.73
807 871 2.304413 GATGTTTGCATCGATCGCATG 58.696 47.619 18.73 15.37 41.60 4.06
808 872 1.367659 TGTTTGCATCGATCGCATGA 58.632 45.000 23.05 10.83 39.58 3.07
809 873 1.736681 TGTTTGCATCGATCGCATGAA 59.263 42.857 23.05 14.70 39.58 2.57
812 876 2.159327 TGCATCGATCGCATGAATCT 57.841 45.000 23.05 0.00 33.55 2.40
813 877 3.302365 TGCATCGATCGCATGAATCTA 57.698 42.857 23.05 1.51 33.55 1.98
815 879 4.248058 TGCATCGATCGCATGAATCTAAT 58.752 39.130 23.05 3.00 33.55 1.73
816 880 5.410067 TGCATCGATCGCATGAATCTAATA 58.590 37.500 23.05 0.20 33.55 0.98
818 882 5.553396 GCATCGATCGCATGAATCTAATACG 60.553 44.000 23.05 0.00 0.00 3.06
819 883 4.412207 TCGATCGCATGAATCTAATACGG 58.588 43.478 11.09 0.00 0.00 4.02
820 884 4.082949 TCGATCGCATGAATCTAATACGGT 60.083 41.667 11.09 0.00 0.00 4.83
821 885 5.122711 TCGATCGCATGAATCTAATACGGTA 59.877 40.000 11.09 0.00 0.00 4.02
822 886 5.227391 CGATCGCATGAATCTAATACGGTAC 59.773 44.000 0.26 0.00 0.00 3.34
840 904 2.277373 GCTGTCGGCGTACTCTCG 60.277 66.667 6.85 0.00 0.00 4.04
841 905 2.747822 GCTGTCGGCGTACTCTCGA 61.748 63.158 6.85 0.00 0.00 4.04
843 907 0.167470 CTGTCGGCGTACTCTCGAAA 59.833 55.000 6.85 0.00 34.62 3.46
844 908 0.592637 TGTCGGCGTACTCTCGAAAA 59.407 50.000 6.85 0.00 34.62 2.29
845 909 1.001487 TGTCGGCGTACTCTCGAAAAA 60.001 47.619 6.85 0.00 34.62 1.94
1114 4994 2.486966 GCCAGAAGCGTTGCCATC 59.513 61.111 0.00 0.00 0.00 3.51
1115 4995 2.334946 GCCAGAAGCGTTGCCATCA 61.335 57.895 0.00 0.00 0.00 3.07
1116 4996 1.503542 CCAGAAGCGTTGCCATCAC 59.496 57.895 0.00 0.00 0.00 3.06
1117 4997 1.503542 CAGAAGCGTTGCCATCACC 59.496 57.895 0.00 0.00 0.00 4.02
1135 5024 4.722700 GCCATCACCACCGCCACT 62.723 66.667 0.00 0.00 0.00 4.00
1231 5120 1.465200 GGGCGAGGTAGAGGATGGTC 61.465 65.000 0.00 0.00 0.00 4.02
1433 5328 6.676950 TGCTGATTTATCGTGTGAATTTTGT 58.323 32.000 0.00 0.00 0.00 2.83
1454 5349 4.646945 TGTTGGAGCTTGGTGTGATTTTTA 59.353 37.500 0.00 0.00 0.00 1.52
1455 5350 5.127845 TGTTGGAGCTTGGTGTGATTTTTAA 59.872 36.000 0.00 0.00 0.00 1.52
1456 5351 5.860941 TGGAGCTTGGTGTGATTTTTAAA 57.139 34.783 0.00 0.00 0.00 1.52
1457 5352 6.227298 TGGAGCTTGGTGTGATTTTTAAAA 57.773 33.333 0.00 0.00 0.00 1.52
1458 5353 6.644347 TGGAGCTTGGTGTGATTTTTAAAAA 58.356 32.000 15.38 15.38 0.00 1.94
1667 5563 5.708948 TGAAGCACATTTATTAACCACTGC 58.291 37.500 0.00 0.00 0.00 4.40
1711 5607 8.660373 GTTGTTTAGTTTCCTCTGTGATGATAG 58.340 37.037 0.00 0.00 0.00 2.08
1722 5618 6.183360 CCTCTGTGATGATAGATCAAGGACAA 60.183 42.308 0.00 0.00 40.69 3.18
1736 5632 5.601662 TCAAGGACAACTTACTCTGTTCTG 58.398 41.667 0.00 0.00 37.29 3.02
2130 6153 6.628919 TTGTAGGAAAAGGCTTTTAGTCAC 57.371 37.500 24.15 18.27 31.94 3.67
2502 6531 0.771127 TTCAGAAGGAACACCAGGGG 59.229 55.000 0.00 0.00 0.00 4.79
2769 6800 7.775053 TCCAGCCTAACATTTCAATAAACTT 57.225 32.000 0.00 0.00 0.00 2.66
2930 6963 7.496346 TTTTACAGGGTGATAGATCTTCAGT 57.504 36.000 0.00 2.38 0.00 3.41
3213 7246 5.068855 TGCATGTCAGGAAAAATTCACTTCA 59.931 36.000 0.00 0.00 0.00 3.02
3220 7253 6.039270 TCAGGAAAAATTCACTTCACGACAAT 59.961 34.615 0.00 0.00 0.00 2.71
3272 7305 5.689835 AGCTCTATCAATCTTTCCTTTCCC 58.310 41.667 0.00 0.00 0.00 3.97
3800 7834 1.817447 ACTGCTGTAAGGACGTACTCC 59.183 52.381 0.00 0.00 39.81 3.85
3890 7924 7.197017 CAGATAATATACTGGTATGTCCGCTC 58.803 42.308 3.76 0.00 39.52 5.03
4093 8149 1.846007 TTGCCTGCCGGAATAAATGT 58.154 45.000 5.05 0.00 0.00 2.71
4104 8160 5.505654 GCCGGAATAAATGTTATCACACCAG 60.506 44.000 5.05 0.00 35.03 4.00
4547 8640 7.280356 TGTTTCTAATTATACAGGGAGCCTTC 58.720 38.462 0.00 0.00 0.00 3.46
4797 8892 0.541863 AGGCGAGGATCCGAAAATGT 59.458 50.000 5.98 0.00 0.00 2.71
4920 9015 7.640240 GCAAGTGAAATAAAGACGATCAATACC 59.360 37.037 0.00 0.00 0.00 2.73
4943 9038 8.918202 ACCTCTCAGTTGTAATATTGTTGAAA 57.082 30.769 0.00 0.00 0.00 2.69
4989 9085 8.485578 AATTTTGGATTTAACCTGTCTAACCA 57.514 30.769 0.00 0.00 0.00 3.67
4992 9088 6.195600 TGGATTTAACCTGTCTAACCAACT 57.804 37.500 0.00 0.00 0.00 3.16
4998 9094 1.298859 CTGTCTAACCAACTGGCGGC 61.299 60.000 0.00 0.00 39.32 6.53
5293 9393 4.808414 TTATCCGGGAAGCTCTATCATG 57.192 45.455 0.00 0.00 0.00 3.07
5422 9523 0.908198 CAAGAAGAGACTCCCCCTGG 59.092 60.000 0.00 0.00 0.00 4.45
5498 9599 6.981559 GGAATGTAGAATGTGGTAGAGACTTC 59.018 42.308 0.00 0.00 0.00 3.01
5579 9681 5.422012 GCTTTTCTGAAGATTATGGGGGAAA 59.578 40.000 0.00 0.00 0.00 3.13
5705 9807 2.401583 TCGAACCCATTCCACATGAG 57.598 50.000 0.00 0.00 0.00 2.90
5809 9911 2.540383 AGATGTTGCCACCAGAGTCTA 58.460 47.619 0.00 0.00 0.00 2.59
5813 9915 4.098914 TGTTGCCACCAGAGTCTATTTT 57.901 40.909 0.00 0.00 0.00 1.82
5819 9921 5.003804 GCCACCAGAGTCTATTTTGAAGAA 58.996 41.667 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
456 494 1.009389 GGAGAGTTTCGTCAGCACGG 61.009 60.000 0.00 0.00 46.70 4.94
553 592 3.375299 GGTTGATGTAGTCGTACGTACCT 59.625 47.826 19.67 13.88 29.26 3.08
621 683 1.216710 CGAGAGGGGAGAGTGTTGC 59.783 63.158 0.00 0.00 0.00 4.17
643 705 3.251487 CGCAAGATCATGGTGATGCATAA 59.749 43.478 0.00 0.00 37.20 1.90
715 779 2.486592 CACAAAACGGTCTAATCCACCC 59.513 50.000 0.00 0.00 0.00 4.61
716 780 3.404899 TCACAAAACGGTCTAATCCACC 58.595 45.455 0.00 0.00 0.00 4.61
717 781 4.312443 TCTCACAAAACGGTCTAATCCAC 58.688 43.478 0.00 0.00 0.00 4.02
718 782 4.282449 TCTCTCACAAAACGGTCTAATCCA 59.718 41.667 0.00 0.00 0.00 3.41
719 783 4.817517 TCTCTCACAAAACGGTCTAATCC 58.182 43.478 0.00 0.00 0.00 3.01
720 784 6.100004 TGATCTCTCACAAAACGGTCTAATC 58.900 40.000 0.00 0.00 0.00 1.75
722 786 5.462530 TGATCTCTCACAAAACGGTCTAA 57.537 39.130 0.00 0.00 0.00 2.10
754 818 5.815581 AGCATCCACTCACACCTATAAAAA 58.184 37.500 0.00 0.00 0.00 1.94
755 819 5.428253 GAGCATCCACTCACACCTATAAAA 58.572 41.667 0.00 0.00 36.65 1.52
756 820 4.441495 CGAGCATCCACTCACACCTATAAA 60.441 45.833 0.00 0.00 36.42 1.40
757 821 3.068165 CGAGCATCCACTCACACCTATAA 59.932 47.826 0.00 0.00 36.42 0.98
758 822 2.623416 CGAGCATCCACTCACACCTATA 59.377 50.000 0.00 0.00 36.42 1.31
760 824 0.817654 CGAGCATCCACTCACACCTA 59.182 55.000 0.00 0.00 36.42 3.08
761 825 1.593787 CGAGCATCCACTCACACCT 59.406 57.895 0.00 0.00 36.42 4.00
762 826 1.448540 CCGAGCATCCACTCACACC 60.449 63.158 0.00 0.00 36.42 4.16
763 827 1.448540 CCCGAGCATCCACTCACAC 60.449 63.158 0.00 0.00 36.42 3.82
765 829 1.448540 CACCCGAGCATCCACTCAC 60.449 63.158 0.00 0.00 36.42 3.51
767 831 0.531532 CATCACCCGAGCATCCACTC 60.532 60.000 0.00 0.00 0.00 3.51
768 832 1.524002 CATCACCCGAGCATCCACT 59.476 57.895 0.00 0.00 0.00 4.00
769 833 1.524621 CCATCACCCGAGCATCCAC 60.525 63.158 0.00 0.00 0.00 4.02
772 836 0.107456 ACATCCATCACCCGAGCATC 59.893 55.000 0.00 0.00 0.00 3.91
775 839 0.734889 CAAACATCCATCACCCGAGC 59.265 55.000 0.00 0.00 0.00 5.03
776 840 0.734889 GCAAACATCCATCACCCGAG 59.265 55.000 0.00 0.00 0.00 4.63
778 842 1.066002 GATGCAAACATCCATCACCCG 59.934 52.381 0.00 0.00 45.94 5.28
779 843 2.877043 GATGCAAACATCCATCACCC 57.123 50.000 0.00 0.00 45.94 4.61
780 844 6.595237 CGATCGATGCAAACATCCATCACC 62.595 50.000 10.26 0.00 45.81 4.02
787 851 2.032636 TCATGCGATCGATGCAAACATC 60.033 45.455 21.57 0.00 46.87 3.06
790 854 2.456942 TTCATGCGATCGATGCAAAC 57.543 45.000 21.57 0.00 46.87 2.93
794 858 4.854361 ATTAGATTCATGCGATCGATGC 57.146 40.909 21.57 7.79 0.00 3.91
795 859 5.052106 CCGTATTAGATTCATGCGATCGATG 60.052 44.000 21.57 18.39 32.07 3.84
796 860 5.037385 CCGTATTAGATTCATGCGATCGAT 58.963 41.667 21.57 0.00 32.07 3.59
797 861 4.082949 ACCGTATTAGATTCATGCGATCGA 60.083 41.667 21.57 4.34 32.07 3.59
798 862 4.166523 ACCGTATTAGATTCATGCGATCG 58.833 43.478 11.69 11.69 32.07 3.69
799 863 5.227391 CGTACCGTATTAGATTCATGCGATC 59.773 44.000 0.00 0.00 32.07 3.69
800 864 5.093457 CGTACCGTATTAGATTCATGCGAT 58.907 41.667 0.00 0.00 32.07 4.58
801 865 4.469552 CGTACCGTATTAGATTCATGCGA 58.530 43.478 0.00 0.00 32.07 5.10
802 866 3.059044 GCGTACCGTATTAGATTCATGCG 59.941 47.826 0.00 0.00 0.00 4.73
803 867 4.090066 CAGCGTACCGTATTAGATTCATGC 59.910 45.833 0.00 0.00 0.00 4.06
804 868 5.220381 ACAGCGTACCGTATTAGATTCATG 58.780 41.667 0.00 0.00 0.00 3.07
805 869 5.449107 ACAGCGTACCGTATTAGATTCAT 57.551 39.130 0.00 0.00 0.00 2.57
806 870 4.553351 CGACAGCGTACCGTATTAGATTCA 60.553 45.833 0.00 0.00 0.00 2.57
807 871 3.904824 CGACAGCGTACCGTATTAGATTC 59.095 47.826 0.00 0.00 0.00 2.52
808 872 3.304257 CCGACAGCGTACCGTATTAGATT 60.304 47.826 0.00 0.00 35.23 2.40
809 873 2.225019 CCGACAGCGTACCGTATTAGAT 59.775 50.000 0.00 0.00 35.23 1.98
812 876 0.029300 GCCGACAGCGTACCGTATTA 59.971 55.000 0.00 0.00 35.23 0.98
813 877 1.226773 GCCGACAGCGTACCGTATT 60.227 57.895 0.00 0.00 35.23 1.89
824 888 0.167470 TTTCGAGAGTACGCCGACAG 59.833 55.000 9.05 0.00 31.60 3.51
825 889 0.592637 TTTTCGAGAGTACGCCGACA 59.407 50.000 9.05 2.10 31.60 4.35
826 890 1.689959 TTTTTCGAGAGTACGCCGAC 58.310 50.000 9.05 0.00 31.60 4.79
843 907 3.139077 AGGCGATTCTGAACGAACTTTT 58.861 40.909 13.75 0.00 33.72 2.27
844 908 2.767505 AGGCGATTCTGAACGAACTTT 58.232 42.857 13.75 0.00 33.72 2.66
845 909 2.457366 AGGCGATTCTGAACGAACTT 57.543 45.000 13.75 0.00 33.72 2.66
846 910 2.338500 GAAGGCGATTCTGAACGAACT 58.662 47.619 13.75 9.08 34.86 3.01
847 911 1.059264 CGAAGGCGATTCTGAACGAAC 59.941 52.381 13.75 7.52 40.82 3.95
850 914 1.846782 CTACGAAGGCGATTCTGAACG 59.153 52.381 0.00 0.24 41.64 3.95
851 915 2.877335 ACTACGAAGGCGATTCTGAAC 58.123 47.619 0.00 0.00 41.64 3.18
1109 4989 3.211963 GGTGATGGCGGTGATGGC 61.212 66.667 0.00 0.00 0.00 4.40
1110 4990 2.114670 GTGGTGATGGCGGTGATGG 61.115 63.158 0.00 0.00 0.00 3.51
1111 4991 2.114670 GGTGGTGATGGCGGTGATG 61.115 63.158 0.00 0.00 0.00 3.07
1112 4992 2.272146 GGTGGTGATGGCGGTGAT 59.728 61.111 0.00 0.00 0.00 3.06
1113 4993 4.386951 CGGTGGTGATGGCGGTGA 62.387 66.667 0.00 0.00 0.00 4.02
1213 5102 0.755698 TGACCATCCTCTACCTCGCC 60.756 60.000 0.00 0.00 0.00 5.54
1231 5120 1.401670 GGCGGCATCGTCTACTATCTG 60.402 57.143 3.07 0.00 38.10 2.90
1433 5328 5.860941 TTAAAAATCACACCAAGCTCCAA 57.139 34.783 0.00 0.00 0.00 3.53
1456 5351 3.668447 TGTGTGTGCCAACAACATTTTT 58.332 36.364 0.00 0.00 38.27 1.94
1457 5352 3.325293 TGTGTGTGCCAACAACATTTT 57.675 38.095 0.00 0.00 38.27 1.82
1458 5353 2.999355 GTTGTGTGTGCCAACAACATTT 59.001 40.909 12.46 0.00 41.40 2.32
1685 5581 6.861065 TCATCACAGAGGAAACTAAACAAC 57.139 37.500 0.00 0.00 44.43 3.32
1711 5607 6.367422 CAGAACAGAGTAAGTTGTCCTTGATC 59.633 42.308 0.00 0.00 34.46 2.92
1722 5618 2.802816 CAAAGCGCAGAACAGAGTAAGT 59.197 45.455 11.47 0.00 0.00 2.24
2130 6153 4.937201 ACCAAAAGTAGAAAAGCAAGGG 57.063 40.909 0.00 0.00 0.00 3.95
2502 6531 1.952296 CTATCATGGAAAGGCACAGGC 59.048 52.381 0.00 0.00 40.13 4.85
2769 6800 3.331591 CCATTGATCACCAGATATCCCCA 59.668 47.826 0.00 0.00 33.72 4.96
2848 6880 6.959639 AATGGTAAGTGAACAATCAACTGT 57.040 33.333 0.00 0.00 37.30 3.55
3213 7246 2.292267 GCTCATCATCCCAATTGTCGT 58.708 47.619 4.43 0.00 0.00 4.34
3220 7253 4.940468 ATATCCATGCTCATCATCCCAA 57.060 40.909 0.00 0.00 31.79 4.12
3347 7381 5.422012 TCTGTAATGACCATCTAGCACTTCA 59.578 40.000 0.00 0.00 0.00 3.02
3800 7834 5.660629 TCAATGCAATGAAAAGCTGTTTG 57.339 34.783 0.85 0.00 0.00 2.93
3962 8018 8.856103 AGCATACAATTAACACAAAGGTTAACT 58.144 29.630 5.42 0.00 43.68 2.24
4104 8160 1.727335 GTAGAAGCGGCTCACAAGAAC 59.273 52.381 1.45 0.00 0.00 3.01
4444 8500 9.762062 CATACTACGCATAAGAGATAAGTACAG 57.238 37.037 0.00 0.00 0.00 2.74
4547 8640 3.181497 CCTGGTCAAAGTGTTGAGTTGTG 60.181 47.826 0.00 0.00 44.44 3.33
4797 8892 6.003950 CCAGGAGATCTTTAAAACTGGACAA 58.996 40.000 16.12 0.00 45.14 3.18
4920 9015 8.725148 AGCTTTCAACAATATTACAACTGAGAG 58.275 33.333 0.00 0.00 0.00 3.20
4989 9085 4.857251 GCTACATAGCCGCCAGTT 57.143 55.556 0.00 0.00 43.39 3.16
5293 9393 8.409371 AGAACTTTTGAAGGAGAATCTTTTGAC 58.591 33.333 0.00 0.00 33.07 3.18
5422 9523 0.036875 ACTTAGGGACTTGCAGGTGC 59.963 55.000 12.24 12.24 41.75 5.01
5498 9599 5.732647 CGACAACCTTGCTGATTTATTTACG 59.267 40.000 0.00 0.00 0.00 3.18
5579 9681 7.400052 ACCAAGCATATTTCTCCTAAATGGTTT 59.600 33.333 0.00 0.00 36.45 3.27
5705 9807 6.747280 GCAGAATGATAAACCACATACAACAC 59.253 38.462 0.00 0.00 39.69 3.32
5813 9915 6.429078 GCACTGCTATATCATGGAATTCTTCA 59.571 38.462 5.23 0.00 0.00 3.02
5819 9921 4.330250 GTGGCACTGCTATATCATGGAAT 58.670 43.478 11.13 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.