Multiple sequence alignment - TraesCS5B01G525900

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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 TraesCS5B01G525900 chr5B 100.000 2750 0 0 1 2750 685530007 685527258 0.000000e+00 5079.0
1 TraesCS5B01G525900 chr5B 98.503 668 10 0 877 1544 685305748 685306415 0.000000e+00 1179.0
2 TraesCS5B01G525900 chr5B 93.926 675 17 7 187 846 685305084 685305749 0.000000e+00 998.0
3 TraesCS5B01G525900 chr5B 93.750 272 12 3 1546 1812 685306649 685306920 1.190000e-108 403.0
4 TraesCS5B01G525900 chr5B 88.843 242 16 5 1798 2035 685306946 685307180 1.250000e-73 287.0
5 TraesCS5B01G525900 chr5B 95.385 65 3 0 1 65 228817764 228817828 1.350000e-18 104.0
6 TraesCS5B01G525900 chr5D 93.934 1599 48 17 187 1757 543496272 543497849 0.000000e+00 2370.0
7 TraesCS5B01G525900 chr5D 84.444 720 110 2 2032 2750 240522796 240522078 0.000000e+00 708.0
8 TraesCS5B01G525900 chr5D 92.857 70 4 1 1 69 420996338 420996407 1.740000e-17 100.0
9 TraesCS5B01G525900 chr5D 91.667 72 4 2 1 70 276306891 276306820 6.270000e-17 99.0
10 TraesCS5B01G525900 chr5D 91.549 71 6 0 1 71 375170858 375170928 6.270000e-17 99.0
11 TraesCS5B01G525900 chr5D 93.750 64 1 1 1876 1936 543498393 543498456 2.920000e-15 93.5
12 TraesCS5B01G525900 chr6B 96.940 719 22 0 2032 2750 67340295 67341013 0.000000e+00 1206.0
13 TraesCS5B01G525900 chr3B 92.907 719 47 1 2032 2750 636765453 636766167 0.000000e+00 1042.0
14 TraesCS5B01G525900 chr3B 91.667 72 5 1 1 71 757960159 757960230 6.270000e-17 99.0
15 TraesCS5B01G525900 chr4B 88.750 720 80 1 2032 2750 654049728 654049009 0.000000e+00 880.0
16 TraesCS5B01G525900 chr4B 86.777 726 88 3 2032 2750 664172067 664172791 0.000000e+00 802.0
17 TraesCS5B01G525900 chr2D 84.306 720 111 2 2032 2750 650477860 650477142 0.000000e+00 702.0
18 TraesCS5B01G525900 chr2D 76.501 783 136 30 933 1709 569120442 569119702 1.550000e-102 383.0
19 TraesCS5B01G525900 chr3D 84.306 720 110 3 2032 2750 570310367 570311084 0.000000e+00 701.0
20 TraesCS5B01G525900 chr3D 84.151 713 111 2 2032 2743 406418128 406418839 0.000000e+00 689.0
21 TraesCS5B01G525900 chr3D 95.385 65 3 0 1 65 9253611 9253675 1.350000e-18 104.0
22 TraesCS5B01G525900 chr1D 84.167 720 112 2 2032 2750 431515998 431516716 0.000000e+00 697.0
23 TraesCS5B01G525900 chr7A 77.238 782 124 34 938 1710 603331048 603330312 2.550000e-110 409.0
24 TraesCS5B01G525900 chr7A 75.824 546 96 28 286 822 19960378 19959860 7.610000e-61 244.0
25 TraesCS5B01G525900 chr7D 77.081 781 127 32 938 1710 523056407 523055671 1.190000e-108 403.0
26 TraesCS5B01G525900 chr7D 76.410 780 134 34 938 1710 500774360 500775096 2.590000e-100 375.0
27 TraesCS5B01G525900 chr7B 76.923 793 125 40 933 1714 557490995 557490250 5.520000e-107 398.0
28 TraesCS5B01G525900 chr7B 76.718 786 118 41 938 1710 557256816 557256083 7.190000e-101 377.0
29 TraesCS5B01G525900 chr2A 75.888 788 138 33 930 1709 708862924 708863667 3.370000e-94 355.0
30 TraesCS5B01G525900 chr6A 77.207 487 85 20 284 745 496577639 496578124 7.550000e-66 261.0
31 TraesCS5B01G525900 chr6D 74.897 486 98 17 284 745 346834313 346833828 1.670000e-47 200.0
32 TraesCS5B01G525900 chr6D 96.774 62 2 0 1 62 373052023 373051962 1.350000e-18 104.0
33 TraesCS5B01G525900 chr5A 98.305 59 1 0 1 59 672806688 672806746 1.350000e-18 104.0
34 TraesCS5B01G525900 chr3A 87.356 87 9 2 1 87 437619791 437619707 6.270000e-17 99.0


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 TraesCS5B01G525900 chr5B 685527258 685530007 2749 True 5079.00 5079 100.0000 1 2750 1 chr5B.!!$R1 2749
1 TraesCS5B01G525900 chr5B 685305084 685307180 2096 False 716.75 1179 93.7555 187 2035 4 chr5B.!!$F2 1848
2 TraesCS5B01G525900 chr5D 543496272 543498456 2184 False 1231.75 2370 93.8420 187 1936 2 chr5D.!!$F3 1749
3 TraesCS5B01G525900 chr5D 240522078 240522796 718 True 708.00 708 84.4440 2032 2750 1 chr5D.!!$R1 718
4 TraesCS5B01G525900 chr6B 67340295 67341013 718 False 1206.00 1206 96.9400 2032 2750 1 chr6B.!!$F1 718
5 TraesCS5B01G525900 chr3B 636765453 636766167 714 False 1042.00 1042 92.9070 2032 2750 1 chr3B.!!$F1 718
6 TraesCS5B01G525900 chr4B 654049009 654049728 719 True 880.00 880 88.7500 2032 2750 1 chr4B.!!$R1 718
7 TraesCS5B01G525900 chr4B 664172067 664172791 724 False 802.00 802 86.7770 2032 2750 1 chr4B.!!$F1 718
8 TraesCS5B01G525900 chr2D 650477142 650477860 718 True 702.00 702 84.3060 2032 2750 1 chr2D.!!$R2 718
9 TraesCS5B01G525900 chr2D 569119702 569120442 740 True 383.00 383 76.5010 933 1709 1 chr2D.!!$R1 776
10 TraesCS5B01G525900 chr3D 570310367 570311084 717 False 701.00 701 84.3060 2032 2750 1 chr3D.!!$F3 718
11 TraesCS5B01G525900 chr3D 406418128 406418839 711 False 689.00 689 84.1510 2032 2743 1 chr3D.!!$F2 711
12 TraesCS5B01G525900 chr1D 431515998 431516716 718 False 697.00 697 84.1670 2032 2750 1 chr1D.!!$F1 718
13 TraesCS5B01G525900 chr7A 603330312 603331048 736 True 409.00 409 77.2380 938 1710 1 chr7A.!!$R2 772
14 TraesCS5B01G525900 chr7A 19959860 19960378 518 True 244.00 244 75.8240 286 822 1 chr7A.!!$R1 536
15 TraesCS5B01G525900 chr7D 523055671 523056407 736 True 403.00 403 77.0810 938 1710 1 chr7D.!!$R1 772
16 TraesCS5B01G525900 chr7D 500774360 500775096 736 False 375.00 375 76.4100 938 1710 1 chr7D.!!$F1 772
17 TraesCS5B01G525900 chr7B 557490250 557490995 745 True 398.00 398 76.9230 933 1714 1 chr7B.!!$R2 781
18 TraesCS5B01G525900 chr7B 557256083 557256816 733 True 377.00 377 76.7180 938 1710 1 chr7B.!!$R1 772
19 TraesCS5B01G525900 chr2A 708862924 708863667 743 False 355.00 355 75.8880 930 1709 1 chr2A.!!$F1 779

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
22 23 0.045623 ACACTGGTGGGATGGGGATA 59.954 55.0 5.7 0.0 34.19 2.59 F
67 68 0.261696 ACAGGTTGGTTTGCTCCCTT 59.738 50.0 0.0 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 1180 1.140589 CTGCTCGCTGGAGACGATT 59.859 57.895 0.00 0.00 43.27 3.34 R
1786 2251 2.408880 TACTGGTGGCTGCATGCACA 62.409 55.000 18.46 11.97 45.15 4.57 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
18 19 1.767036 TGAACACTGGTGGGATGGG 59.233 57.895 5.70 0.00 34.19 4.00
19 20 1.000896 GAACACTGGTGGGATGGGG 60.001 63.158 5.70 0.00 34.19 4.96
20 21 1.465188 AACACTGGTGGGATGGGGA 60.465 57.895 5.70 0.00 34.19 4.81
21 22 0.850883 AACACTGGTGGGATGGGGAT 60.851 55.000 5.70 0.00 34.19 3.85
22 23 0.045623 ACACTGGTGGGATGGGGATA 59.954 55.000 5.70 0.00 34.19 2.59
23 24 0.474184 CACTGGTGGGATGGGGATAC 59.526 60.000 0.00 0.00 0.00 2.24
39 40 2.699321 GGATACCACAGTCCCTCTAACC 59.301 54.545 0.00 0.00 0.00 2.85
40 41 3.371965 GATACCACAGTCCCTCTAACCA 58.628 50.000 0.00 0.00 0.00 3.67
41 42 2.344093 ACCACAGTCCCTCTAACCAT 57.656 50.000 0.00 0.00 0.00 3.55
42 43 2.188817 ACCACAGTCCCTCTAACCATC 58.811 52.381 0.00 0.00 0.00 3.51
43 44 1.486726 CCACAGTCCCTCTAACCATCC 59.513 57.143 0.00 0.00 0.00 3.51
44 45 2.187958 CACAGTCCCTCTAACCATCCA 58.812 52.381 0.00 0.00 0.00 3.41
45 46 2.571653 CACAGTCCCTCTAACCATCCAA 59.428 50.000 0.00 0.00 0.00 3.53
46 47 2.572104 ACAGTCCCTCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
47 48 2.092914 CAGTCCCTCTAACCATCCAACC 60.093 54.545 0.00 0.00 0.00 3.77
48 49 1.913419 GTCCCTCTAACCATCCAACCA 59.087 52.381 0.00 0.00 0.00 3.67
49 50 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
50 51 1.633432 CCCTCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
51 52 2.356125 CCCTCTAACCATCCAACCACAG 60.356 54.545 0.00 0.00 0.00 3.66
52 53 2.356125 CCTCTAACCATCCAACCACAGG 60.356 54.545 0.00 0.00 0.00 4.00
53 54 2.305927 CTCTAACCATCCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
64 65 2.041153 CCACAGGTTGGTTTGCTCC 58.959 57.895 0.00 0.00 41.10 4.70
65 66 1.463553 CCACAGGTTGGTTTGCTCCC 61.464 60.000 0.00 0.00 41.10 4.30
66 67 0.468029 CACAGGTTGGTTTGCTCCCT 60.468 55.000 0.00 0.00 0.00 4.20
67 68 0.261696 ACAGGTTGGTTTGCTCCCTT 59.738 50.000 0.00 0.00 0.00 3.95
68 69 1.342975 ACAGGTTGGTTTGCTCCCTTT 60.343 47.619 0.00 0.00 0.00 3.11
69 70 2.091555 ACAGGTTGGTTTGCTCCCTTTA 60.092 45.455 0.00 0.00 0.00 1.85
70 71 2.962421 CAGGTTGGTTTGCTCCCTTTAA 59.038 45.455 0.00 0.00 0.00 1.52
71 72 3.386402 CAGGTTGGTTTGCTCCCTTTAAA 59.614 43.478 0.00 0.00 0.00 1.52
72 73 4.034410 AGGTTGGTTTGCTCCCTTTAAAA 58.966 39.130 0.00 0.00 0.00 1.52
73 74 4.100963 AGGTTGGTTTGCTCCCTTTAAAAG 59.899 41.667 0.00 0.00 0.00 2.27
74 75 3.744238 TGGTTTGCTCCCTTTAAAAGC 57.256 42.857 3.82 3.82 36.56 3.51
75 76 3.034635 TGGTTTGCTCCCTTTAAAAGCA 58.965 40.909 8.63 8.63 43.89 3.91
81 82 5.289083 TGCTCCCTTTAAAAGCAATTTGT 57.711 34.783 10.00 0.00 42.71 2.83
82 83 6.412362 TGCTCCCTTTAAAAGCAATTTGTA 57.588 33.333 10.00 0.00 42.71 2.41
83 84 7.003402 TGCTCCCTTTAAAAGCAATTTGTAT 57.997 32.000 10.00 0.00 42.71 2.29
84 85 6.873076 TGCTCCCTTTAAAAGCAATTTGTATG 59.127 34.615 10.00 0.00 42.71 2.39
85 86 6.873605 GCTCCCTTTAAAAGCAATTTGTATGT 59.126 34.615 5.65 0.00 36.06 2.29
86 87 8.032451 GCTCCCTTTAAAAGCAATTTGTATGTA 58.968 33.333 5.65 0.00 36.06 2.29
87 88 9.573133 CTCCCTTTAAAAGCAATTTGTATGTAG 57.427 33.333 0.00 0.00 32.27 2.74
88 89 9.303116 TCCCTTTAAAAGCAATTTGTATGTAGA 57.697 29.630 0.00 0.00 32.27 2.59
89 90 9.921637 CCCTTTAAAAGCAATTTGTATGTAGAA 57.078 29.630 0.00 0.00 32.27 2.10
97 98 9.905713 AAGCAATTTGTATGTAGAAATAGGAGA 57.094 29.630 0.00 0.00 30.18 3.71
115 116 9.726438 AATAGGAGATACTATTGTTATTGCCAC 57.274 33.333 0.00 0.00 40.98 5.01
116 117 6.223852 AGGAGATACTATTGTTATTGCCACG 58.776 40.000 0.00 0.00 0.00 4.94
117 118 5.989777 GGAGATACTATTGTTATTGCCACGT 59.010 40.000 0.00 0.00 0.00 4.49
118 119 6.145696 GGAGATACTATTGTTATTGCCACGTC 59.854 42.308 0.00 0.00 0.00 4.34
119 120 6.578944 AGATACTATTGTTATTGCCACGTCA 58.421 36.000 0.00 0.00 0.00 4.35
120 121 7.045416 AGATACTATTGTTATTGCCACGTCAA 58.955 34.615 0.00 0.00 0.00 3.18
121 122 5.950758 ACTATTGTTATTGCCACGTCAAA 57.049 34.783 0.00 0.00 0.00 2.69
122 123 6.320494 ACTATTGTTATTGCCACGTCAAAA 57.680 33.333 0.00 0.00 0.00 2.44
123 124 6.740110 ACTATTGTTATTGCCACGTCAAAAA 58.260 32.000 0.00 0.00 0.00 1.94
151 152 8.948853 TTTATATGAGAAGCTTTGACAAAACG 57.051 30.769 0.00 0.00 0.00 3.60
152 153 4.900635 ATGAGAAGCTTTGACAAAACGT 57.099 36.364 0.00 0.00 0.00 3.99
153 154 7.667043 ATATGAGAAGCTTTGACAAAACGTA 57.333 32.000 0.00 0.00 0.00 3.57
154 155 6.560253 ATGAGAAGCTTTGACAAAACGTAT 57.440 33.333 0.00 0.00 0.00 3.06
155 156 7.667043 ATGAGAAGCTTTGACAAAACGTATA 57.333 32.000 0.00 0.00 0.00 1.47
156 157 7.485418 TGAGAAGCTTTGACAAAACGTATAA 57.515 32.000 0.00 0.00 0.00 0.98
157 158 8.094798 TGAGAAGCTTTGACAAAACGTATAAT 57.905 30.769 0.00 0.00 0.00 1.28
158 159 9.210329 TGAGAAGCTTTGACAAAACGTATAATA 57.790 29.630 0.00 0.00 0.00 0.98
160 161 9.988350 AGAAGCTTTGACAAAACGTATAATATG 57.012 29.630 0.00 0.00 0.00 1.78
161 162 9.769093 GAAGCTTTGACAAAACGTATAATATGT 57.231 29.630 0.00 0.00 0.00 2.29
181 182 5.593679 TGTATAGTAGGAAGCAGACAACC 57.406 43.478 0.00 0.00 0.00 3.77
182 183 5.020795 TGTATAGTAGGAAGCAGACAACCA 58.979 41.667 0.00 0.00 0.00 3.67
183 184 5.661312 TGTATAGTAGGAAGCAGACAACCAT 59.339 40.000 0.00 0.00 0.00 3.55
184 185 6.837048 TGTATAGTAGGAAGCAGACAACCATA 59.163 38.462 0.00 0.00 0.00 2.74
185 186 7.509318 TGTATAGTAGGAAGCAGACAACCATAT 59.491 37.037 0.00 0.00 0.00 1.78
203 204 4.337060 CGTCCCGCCGCGATCATA 62.337 66.667 15.93 0.00 0.00 2.15
204 205 2.733593 GTCCCGCCGCGATCATAC 60.734 66.667 15.93 0.88 0.00 2.39
269 270 1.364171 CGAGGCGCCATTAGCTACT 59.636 57.895 31.54 3.33 40.39 2.57
270 271 0.941463 CGAGGCGCCATTAGCTACTG 60.941 60.000 31.54 4.15 40.39 2.74
271 272 1.224722 GAGGCGCCATTAGCTACTGC 61.225 60.000 31.54 2.31 40.39 4.40
711 727 1.611592 CGTGTGGTTTCCTCGCGTAC 61.612 60.000 5.77 0.00 43.17 3.67
758 774 2.125512 CGAGAAGCCCGTCCCTTG 60.126 66.667 0.00 0.00 0.00 3.61
825 841 2.805353 CGAGACCTTCCGCGTGTG 60.805 66.667 4.92 0.00 0.00 3.82
855 877 3.047877 CCTGGACGTGGAAACGGC 61.048 66.667 0.00 0.00 41.09 5.68
856 878 3.411351 CTGGACGTGGAAACGGCG 61.411 66.667 4.80 4.80 43.10 6.46
857 879 3.851845 CTGGACGTGGAAACGGCGA 62.852 63.158 16.62 0.00 43.10 5.54
858 880 2.662527 GGACGTGGAAACGGCGAA 60.663 61.111 16.62 0.00 43.10 4.70
859 881 2.664436 GGACGTGGAAACGGCGAAG 61.664 63.158 16.62 0.00 43.10 3.79
860 882 1.662446 GACGTGGAAACGGCGAAGA 60.662 57.895 16.62 0.00 37.45 2.87
861 883 1.216941 GACGTGGAAACGGCGAAGAA 61.217 55.000 16.62 0.00 37.45 2.52
862 884 1.219522 ACGTGGAAACGGCGAAGAAG 61.220 55.000 16.62 0.68 37.45 2.85
863 885 0.942410 CGTGGAAACGGCGAAGAAGA 60.942 55.000 16.62 0.00 33.99 2.87
864 886 0.790814 GTGGAAACGGCGAAGAAGAG 59.209 55.000 16.62 0.00 0.00 2.85
865 887 0.320421 TGGAAACGGCGAAGAAGAGG 60.320 55.000 16.62 0.00 0.00 3.69
866 888 0.320508 GGAAACGGCGAAGAAGAGGT 60.321 55.000 16.62 0.00 0.00 3.85
867 889 1.069255 GAAACGGCGAAGAAGAGGTC 58.931 55.000 16.62 0.00 0.00 3.85
868 890 0.666577 AAACGGCGAAGAAGAGGTCG 60.667 55.000 16.62 0.00 40.24 4.79
869 891 1.803366 AACGGCGAAGAAGAGGTCGT 61.803 55.000 16.62 0.00 39.46 4.34
870 892 1.514443 CGGCGAAGAAGAGGTCGTC 60.514 63.158 0.00 0.00 39.46 4.20
1152 1180 0.116342 TGAACCTAGGGAGCCTCACA 59.884 55.000 14.81 0.00 34.61 3.58
1757 2208 5.541845 TCCCGCTCTCACTTGATTTATATG 58.458 41.667 0.00 0.00 0.00 1.78
1758 2209 4.153117 CCCGCTCTCACTTGATTTATATGC 59.847 45.833 0.00 0.00 0.00 3.14
1759 2210 4.993584 CCGCTCTCACTTGATTTATATGCT 59.006 41.667 0.00 0.00 0.00 3.79
1760 2211 5.107182 CCGCTCTCACTTGATTTATATGCTG 60.107 44.000 0.00 0.00 0.00 4.41
1761 2212 5.693555 CGCTCTCACTTGATTTATATGCTGA 59.306 40.000 0.00 0.00 0.00 4.26
1763 2228 7.411696 CGCTCTCACTTGATTTATATGCTGATC 60.412 40.741 0.00 0.00 0.00 2.92
1786 2251 3.054434 TGCTGTAATAAGAGGTGGTGCAT 60.054 43.478 0.00 0.00 0.00 3.96
1845 2350 4.759183 TGTATTTGATGTTGTGTGCTGCTA 59.241 37.500 0.00 0.00 0.00 3.49
1846 2351 3.624326 TTTGATGTTGTGTGCTGCTAC 57.376 42.857 0.00 0.77 0.00 3.58
1863 2372 5.806502 GCTGCTACACATAATTTGCAATTGA 59.193 36.000 10.34 0.00 0.00 2.57
1881 2390 5.762179 ATTGAAGGACTGTTGAGTGGATA 57.238 39.130 0.00 0.00 30.16 2.59
2092 2999 3.576118 ACCCTATGTTCATCGATGAGGAG 59.424 47.826 26.90 20.94 38.19 3.69
2479 3387 4.665451 TCCATGGTTTCTCACATGTGATT 58.335 39.130 28.00 5.62 42.15 2.57
2509 3417 2.342179 GACTGCTTGGAGCTAGTTGAC 58.658 52.381 1.29 0.00 42.97 3.18
2522 3430 1.120530 AGTTGACCTGTGGAACTCGT 58.879 50.000 0.00 0.00 38.04 4.18
2722 3637 2.032528 CTGGTTTCCAGCCTGCGA 59.967 61.111 2.77 0.00 45.13 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.767036 CCCATCCCACCAGTGTTCA 59.233 57.895 0.00 0.00 0.00 3.18
1 2 1.000896 CCCCATCCCACCAGTGTTC 60.001 63.158 0.00 0.00 0.00 3.18
2 3 0.850883 ATCCCCATCCCACCAGTGTT 60.851 55.000 0.00 0.00 0.00 3.32
3 4 0.045623 TATCCCCATCCCACCAGTGT 59.954 55.000 0.00 0.00 0.00 3.55
4 5 0.474184 GTATCCCCATCCCACCAGTG 59.526 60.000 0.00 0.00 0.00 3.66
5 6 0.697854 GGTATCCCCATCCCACCAGT 60.698 60.000 0.00 0.00 0.00 4.00
6 7 0.697511 TGGTATCCCCATCCCACCAG 60.698 60.000 0.00 0.00 38.72 4.00
7 8 1.402375 TGGTATCCCCATCCCACCA 59.598 57.895 0.00 0.00 38.72 4.17
8 9 4.430388 TGGTATCCCCATCCCACC 57.570 61.111 0.00 0.00 38.72 4.61
18 19 2.699321 GGTTAGAGGGACTGTGGTATCC 59.301 54.545 0.00 0.00 41.55 2.59
19 20 3.371965 TGGTTAGAGGGACTGTGGTATC 58.628 50.000 0.00 0.00 41.55 2.24
20 21 3.484953 TGGTTAGAGGGACTGTGGTAT 57.515 47.619 0.00 0.00 41.55 2.73
21 22 3.371965 GATGGTTAGAGGGACTGTGGTA 58.628 50.000 0.00 0.00 41.55 3.25
22 23 2.188817 GATGGTTAGAGGGACTGTGGT 58.811 52.381 0.00 0.00 41.55 4.16
23 24 1.486726 GGATGGTTAGAGGGACTGTGG 59.513 57.143 0.00 0.00 41.55 4.17
24 25 2.187958 TGGATGGTTAGAGGGACTGTG 58.812 52.381 0.00 0.00 41.55 3.66
25 26 2.572104 GTTGGATGGTTAGAGGGACTGT 59.428 50.000 0.00 0.00 41.55 3.55
26 27 2.092914 GGTTGGATGGTTAGAGGGACTG 60.093 54.545 0.00 0.00 41.55 3.51
28 29 1.913419 TGGTTGGATGGTTAGAGGGAC 59.087 52.381 0.00 0.00 0.00 4.46
29 30 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
30 31 1.633432 TGTGGTTGGATGGTTAGAGGG 59.367 52.381 0.00 0.00 0.00 4.30
31 32 2.356125 CCTGTGGTTGGATGGTTAGAGG 60.356 54.545 0.00 0.00 0.00 3.69
32 33 2.305927 ACCTGTGGTTGGATGGTTAGAG 59.694 50.000 0.00 0.00 27.29 2.43
33 34 2.344592 ACCTGTGGTTGGATGGTTAGA 58.655 47.619 0.00 0.00 27.29 2.10
34 35 2.879103 ACCTGTGGTTGGATGGTTAG 57.121 50.000 0.00 0.00 27.29 2.34
47 48 0.468029 AGGGAGCAAACCAACCTGTG 60.468 55.000 0.00 0.00 0.00 3.66
48 49 0.261696 AAGGGAGCAAACCAACCTGT 59.738 50.000 0.00 0.00 0.00 4.00
49 50 1.413118 AAAGGGAGCAAACCAACCTG 58.587 50.000 0.00 0.00 0.00 4.00
50 51 3.322191 TTAAAGGGAGCAAACCAACCT 57.678 42.857 0.00 0.00 0.00 3.50
51 52 4.377021 CTTTTAAAGGGAGCAAACCAACC 58.623 43.478 0.00 0.00 0.00 3.77
52 53 3.807622 GCTTTTAAAGGGAGCAAACCAAC 59.192 43.478 6.84 0.00 36.45 3.77
53 54 3.452627 TGCTTTTAAAGGGAGCAAACCAA 59.547 39.130 10.00 0.00 42.89 3.67
54 55 3.034635 TGCTTTTAAAGGGAGCAAACCA 58.965 40.909 10.00 0.00 42.89 3.67
55 56 3.744238 TGCTTTTAAAGGGAGCAAACC 57.256 42.857 10.00 0.00 42.89 3.27
59 60 5.289083 ACAAATTGCTTTTAAAGGGAGCA 57.711 34.783 8.63 8.63 44.03 4.26
60 61 6.873605 ACATACAAATTGCTTTTAAAGGGAGC 59.126 34.615 6.84 3.82 36.95 4.70
61 62 9.573133 CTACATACAAATTGCTTTTAAAGGGAG 57.427 33.333 6.84 0.00 0.00 4.30
62 63 9.303116 TCTACATACAAATTGCTTTTAAAGGGA 57.697 29.630 6.84 0.00 0.00 4.20
63 64 9.921637 TTCTACATACAAATTGCTTTTAAAGGG 57.078 29.630 6.84 0.00 0.00 3.95
71 72 9.905713 TCTCCTATTTCTACATACAAATTGCTT 57.094 29.630 0.00 0.00 0.00 3.91
89 90 9.726438 GTGGCAATAACAATAGTATCTCCTATT 57.274 33.333 0.00 0.00 37.98 1.73
90 91 8.035394 CGTGGCAATAACAATAGTATCTCCTAT 58.965 37.037 0.00 0.00 0.00 2.57
91 92 7.014905 ACGTGGCAATAACAATAGTATCTCCTA 59.985 37.037 0.00 0.00 0.00 2.94
92 93 6.183360 ACGTGGCAATAACAATAGTATCTCCT 60.183 38.462 0.00 0.00 0.00 3.69
93 94 5.989777 ACGTGGCAATAACAATAGTATCTCC 59.010 40.000 0.00 0.00 0.00 3.71
94 95 6.700081 TGACGTGGCAATAACAATAGTATCTC 59.300 38.462 0.00 0.00 0.00 2.75
95 96 6.578944 TGACGTGGCAATAACAATAGTATCT 58.421 36.000 0.00 0.00 0.00 1.98
96 97 6.838198 TGACGTGGCAATAACAATAGTATC 57.162 37.500 0.00 0.00 0.00 2.24
97 98 7.618502 TTTGACGTGGCAATAACAATAGTAT 57.381 32.000 0.00 0.00 0.00 2.12
98 99 7.436430 TTTTGACGTGGCAATAACAATAGTA 57.564 32.000 0.00 0.00 0.00 1.82
99 100 5.950758 TTTGACGTGGCAATAACAATAGT 57.049 34.783 0.00 0.00 0.00 2.12
125 126 9.393249 CGTTTTGTCAAAGCTTCTCATATAAAA 57.607 29.630 0.00 0.00 0.00 1.52
126 127 8.564574 ACGTTTTGTCAAAGCTTCTCATATAAA 58.435 29.630 0.00 0.00 0.00 1.40
127 128 8.094798 ACGTTTTGTCAAAGCTTCTCATATAA 57.905 30.769 0.00 0.00 0.00 0.98
128 129 7.667043 ACGTTTTGTCAAAGCTTCTCATATA 57.333 32.000 0.00 0.00 0.00 0.86
129 130 6.560253 ACGTTTTGTCAAAGCTTCTCATAT 57.440 33.333 0.00 0.00 0.00 1.78
130 131 7.667043 ATACGTTTTGTCAAAGCTTCTCATA 57.333 32.000 0.00 0.00 0.00 2.15
131 132 4.900635 ACGTTTTGTCAAAGCTTCTCAT 57.099 36.364 0.00 0.00 0.00 2.90
132 133 7.485418 TTATACGTTTTGTCAAAGCTTCTCA 57.515 32.000 0.00 0.00 0.00 3.27
134 135 9.988350 CATATTATACGTTTTGTCAAAGCTTCT 57.012 29.630 0.00 0.00 0.00 2.85
135 136 9.769093 ACATATTATACGTTTTGTCAAAGCTTC 57.231 29.630 0.00 0.00 0.00 3.86
155 156 8.368668 GGTTGTCTGCTTCCTACTATACATATT 58.631 37.037 0.00 0.00 0.00 1.28
156 157 7.509318 TGGTTGTCTGCTTCCTACTATACATAT 59.491 37.037 0.00 0.00 0.00 1.78
157 158 6.837048 TGGTTGTCTGCTTCCTACTATACATA 59.163 38.462 0.00 0.00 0.00 2.29
158 159 5.661312 TGGTTGTCTGCTTCCTACTATACAT 59.339 40.000 0.00 0.00 0.00 2.29
159 160 5.020795 TGGTTGTCTGCTTCCTACTATACA 58.979 41.667 0.00 0.00 0.00 2.29
160 161 5.593679 TGGTTGTCTGCTTCCTACTATAC 57.406 43.478 0.00 0.00 0.00 1.47
161 162 7.094334 CGATATGGTTGTCTGCTTCCTACTATA 60.094 40.741 0.00 0.00 0.00 1.31
162 163 6.294787 CGATATGGTTGTCTGCTTCCTACTAT 60.295 42.308 0.00 0.00 0.00 2.12
163 164 5.009710 CGATATGGTTGTCTGCTTCCTACTA 59.990 44.000 0.00 0.00 0.00 1.82
164 165 4.202161 CGATATGGTTGTCTGCTTCCTACT 60.202 45.833 0.00 0.00 0.00 2.57
165 166 4.051922 CGATATGGTTGTCTGCTTCCTAC 58.948 47.826 0.00 0.00 0.00 3.18
166 167 3.704566 ACGATATGGTTGTCTGCTTCCTA 59.295 43.478 0.00 0.00 0.00 2.94
167 168 2.501723 ACGATATGGTTGTCTGCTTCCT 59.498 45.455 0.00 0.00 0.00 3.36
168 169 2.866762 GACGATATGGTTGTCTGCTTCC 59.133 50.000 0.00 0.00 38.09 3.46
169 170 2.866762 GGACGATATGGTTGTCTGCTTC 59.133 50.000 0.00 0.00 40.52 3.86
170 171 2.420129 GGGACGATATGGTTGTCTGCTT 60.420 50.000 0.00 0.00 40.52 3.91
171 172 1.139058 GGGACGATATGGTTGTCTGCT 59.861 52.381 0.00 0.00 40.52 4.24
172 173 1.583054 GGGACGATATGGTTGTCTGC 58.417 55.000 0.00 0.00 40.52 4.26
269 270 3.083349 CCATCTCCCCCTCACGCA 61.083 66.667 0.00 0.00 0.00 5.24
270 271 4.554036 GCCATCTCCCCCTCACGC 62.554 72.222 0.00 0.00 0.00 5.34
271 272 4.227134 CGCCATCTCCCCCTCACG 62.227 72.222 0.00 0.00 0.00 4.35
272 273 3.866582 CCGCCATCTCCCCCTCAC 61.867 72.222 0.00 0.00 0.00 3.51
696 712 1.290955 CAGGTACGCGAGGAAACCA 59.709 57.895 15.93 0.00 35.67 3.67
845 867 0.790814 CTCTTCTTCGCCGTTTCCAC 59.209 55.000 0.00 0.00 0.00 4.02
852 874 1.514443 GACGACCTCTTCTTCGCCG 60.514 63.158 0.00 0.00 38.88 6.46
855 877 3.293303 GTCGACGACCTCTTCTTCG 57.707 57.895 17.25 0.00 45.14 3.79
927 949 2.049767 TATCAGCGCCCGTGACTCA 61.050 57.895 2.29 0.00 0.00 3.41
1152 1180 1.140589 CTGCTCGCTGGAGACGATT 59.859 57.895 0.00 0.00 43.27 3.34
1757 2208 4.749099 CACCTCTTATTACAGCAGATCAGC 59.251 45.833 1.07 1.07 0.00 4.26
1758 2209 5.163364 ACCACCTCTTATTACAGCAGATCAG 60.163 44.000 0.00 0.00 0.00 2.90
1759 2210 4.716784 ACCACCTCTTATTACAGCAGATCA 59.283 41.667 0.00 0.00 0.00 2.92
1760 2211 5.053145 CACCACCTCTTATTACAGCAGATC 58.947 45.833 0.00 0.00 0.00 2.75
1761 2212 4.684485 GCACCACCTCTTATTACAGCAGAT 60.684 45.833 0.00 0.00 0.00 2.90
1763 2228 2.939103 GCACCACCTCTTATTACAGCAG 59.061 50.000 0.00 0.00 0.00 4.24
1786 2251 2.408880 TACTGGTGGCTGCATGCACA 62.409 55.000 18.46 11.97 45.15 4.57
1845 2350 6.869913 CAGTCCTTCAATTGCAAATTATGTGT 59.130 34.615 1.71 0.00 0.00 3.72
1846 2351 6.869913 ACAGTCCTTCAATTGCAAATTATGTG 59.130 34.615 1.71 0.00 0.00 3.21
1863 2372 5.338708 CCAGATTATCCACTCAACAGTCCTT 60.339 44.000 0.00 0.00 0.00 3.36
1999 2906 4.406648 TGCATGGGTTGATGACTACTAG 57.593 45.455 0.00 0.00 0.00 2.57
2425 3333 1.521681 CATCCCGTCTCGAAAGGCC 60.522 63.158 0.00 0.00 0.00 5.19
2428 3336 3.444703 AAGATCATCCCGTCTCGAAAG 57.555 47.619 0.00 0.00 0.00 2.62
2479 3387 2.625314 CTCCAAGCAGTCGATCTCCATA 59.375 50.000 0.00 0.00 0.00 2.74
2509 3417 2.320587 GCTGCACGAGTTCCACAGG 61.321 63.158 0.00 0.00 0.00 4.00
2522 3430 0.461870 ACTGAACGAGTGTTGCTGCA 60.462 50.000 0.00 0.00 38.78 4.41
2722 3637 8.604035 CGTAAAATCATAGTGTTACAATCTGCT 58.396 33.333 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.