Multiple sequence alignment - TraesCS2D01G020900

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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 TraesCS2D01G020900 chr2D 100.000 2111 0 0 1 2111 9784879 9786989 0.000000e+00 3899
1 TraesCS2D01G020900 chr2D 96.407 167 6 0 1 167 628010427 628010261 2.060000e-70 276
2 TraesCS2D01G020900 chr5D 97.762 1966 20 9 166 2111 503287200 503289161 0.000000e+00 3365
3 TraesCS2D01G020900 chr5D 97.296 1960 25 11 166 2111 6181046 6179101 0.000000e+00 3301
4 TraesCS2D01G020900 chr5D 96.786 1960 32 13 166 2111 120799771 120801713 0.000000e+00 3241
5 TraesCS2D01G020900 chr5D 95.763 1959 50 16 166 2111 167071834 167073772 0.000000e+00 3127
6 TraesCS2D01G020900 chr6D 97.706 1962 16 15 166 2111 45511671 45509723 0.000000e+00 3347
7 TraesCS2D01G020900 chr1D 97.651 1958 18 9 166 2111 254416965 254418906 0.000000e+00 3336
8 TraesCS2D01G020900 chr1D 97.194 1960 32 11 166 2111 51878173 51876223 0.000000e+00 3293
9 TraesCS2D01G020900 chr1D 92.814 167 12 0 1 167 306623583 306623417 2.090000e-60 243
10 TraesCS2D01G020900 chr1A 97.252 1965 21 11 166 2111 554458367 554460317 0.000000e+00 3299
11 TraesCS2D01G020900 chr2B 97.039 1959 24 12 166 2111 474900242 474902179 0.000000e+00 3265
12 TraesCS2D01G020900 chr2B 94.012 167 10 0 1 167 771153659 771153493 9.670000e-64 254
13 TraesCS2D01G020900 chr2B 96.721 61 2 0 1 61 575183049 575183109 3.710000e-18 102
14 TraesCS2D01G020900 chr5A 96.170 1958 39 17 166 2111 607200190 607198257 0.000000e+00 3168
15 TraesCS2D01G020900 chr4A 95.148 1958 58 13 166 2111 309507234 309505302 0.000000e+00 3055
16 TraesCS2D01G020900 chr4A 95.486 997 32 3 166 1152 310730700 310729707 0.000000e+00 1580
17 TraesCS2D01G020900 chr2A 97.082 891 12 5 166 1045 335830728 335829841 0.000000e+00 1489
18 TraesCS2D01G020900 chr2A 95.210 167 8 0 1 167 758520752 758520586 4.470000e-67 265


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 TraesCS2D01G020900 chr2D 9784879 9786989 2110 False 3899 3899 100.000 1 2111 1 chr2D.!!$F1 2110
1 TraesCS2D01G020900 chr5D 503287200 503289161 1961 False 3365 3365 97.762 166 2111 1 chr5D.!!$F3 1945
2 TraesCS2D01G020900 chr5D 6179101 6181046 1945 True 3301 3301 97.296 166 2111 1 chr5D.!!$R1 1945
3 TraesCS2D01G020900 chr5D 120799771 120801713 1942 False 3241 3241 96.786 166 2111 1 chr5D.!!$F1 1945
4 TraesCS2D01G020900 chr5D 167071834 167073772 1938 False 3127 3127 95.763 166 2111 1 chr5D.!!$F2 1945
5 TraesCS2D01G020900 chr6D 45509723 45511671 1948 True 3347 3347 97.706 166 2111 1 chr6D.!!$R1 1945
6 TraesCS2D01G020900 chr1D 254416965 254418906 1941 False 3336 3336 97.651 166 2111 1 chr1D.!!$F1 1945
7 TraesCS2D01G020900 chr1D 51876223 51878173 1950 True 3293 3293 97.194 166 2111 1 chr1D.!!$R1 1945
8 TraesCS2D01G020900 chr1A 554458367 554460317 1950 False 3299 3299 97.252 166 2111 1 chr1A.!!$F1 1945
9 TraesCS2D01G020900 chr2B 474900242 474902179 1937 False 3265 3265 97.039 166 2111 1 chr2B.!!$F1 1945
10 TraesCS2D01G020900 chr5A 607198257 607200190 1933 True 3168 3168 96.170 166 2111 1 chr5A.!!$R1 1945
11 TraesCS2D01G020900 chr4A 309505302 309507234 1932 True 3055 3055 95.148 166 2111 1 chr4A.!!$R1 1945
12 TraesCS2D01G020900 chr4A 310729707 310730700 993 True 1580 1580 95.486 166 1152 1 chr4A.!!$R2 986
13 TraesCS2D01G020900 chr2A 335829841 335830728 887 True 1489 1489 97.082 166 1045 1 chr2A.!!$R1 879

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
31 32 0.034059 ACACTCTCACAAAGCCCTCG 59.966 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1256 3.687125 GGGTTCGAATCCCTTTCTTTCT 58.313 45.455 17.16 0.0 41.58 2.52 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
21 22 4.782019 ATCAGAGAAGTCACACTCTCAC 57.218 45.455 9.06 0.00 40.85 3.51
22 23 3.555966 TCAGAGAAGTCACACTCTCACA 58.444 45.455 9.06 0.00 40.85 3.58
23 24 3.954258 TCAGAGAAGTCACACTCTCACAA 59.046 43.478 9.06 0.00 40.85 3.33
24 25 4.402474 TCAGAGAAGTCACACTCTCACAAA 59.598 41.667 9.06 0.00 40.85 2.83
25 26 4.744137 CAGAGAAGTCACACTCTCACAAAG 59.256 45.833 9.06 0.00 40.85 2.77
26 27 3.462021 AGAAGTCACACTCTCACAAAGC 58.538 45.455 0.00 0.00 0.00 3.51
27 28 2.246719 AGTCACACTCTCACAAAGCC 57.753 50.000 0.00 0.00 0.00 4.35
28 29 1.202698 AGTCACACTCTCACAAAGCCC 60.203 52.381 0.00 0.00 0.00 5.19
29 30 1.131638 TCACACTCTCACAAAGCCCT 58.868 50.000 0.00 0.00 0.00 5.19
30 31 1.070758 TCACACTCTCACAAAGCCCTC 59.929 52.381 0.00 0.00 0.00 4.30
31 32 0.034059 ACACTCTCACAAAGCCCTCG 59.966 55.000 0.00 0.00 0.00 4.63
32 33 0.318441 CACTCTCACAAAGCCCTCGA 59.682 55.000 0.00 0.00 0.00 4.04
33 34 0.605589 ACTCTCACAAAGCCCTCGAG 59.394 55.000 5.13 5.13 0.00 4.04
34 35 0.108424 CTCTCACAAAGCCCTCGAGG 60.108 60.000 25.36 25.36 39.47 4.63
47 48 3.211288 CGAGGGAGTCGGAAGCAT 58.789 61.111 0.00 0.00 45.58 3.79
48 49 1.227089 CGAGGGAGTCGGAAGCATG 60.227 63.158 0.00 0.00 45.58 4.06
49 50 1.667154 CGAGGGAGTCGGAAGCATGA 61.667 60.000 0.00 0.00 45.58 3.07
50 51 0.179097 GAGGGAGTCGGAAGCATGAC 60.179 60.000 0.00 0.00 35.33 3.06
51 52 0.904865 AGGGAGTCGGAAGCATGACA 60.905 55.000 0.00 0.00 37.58 3.58
52 53 0.179000 GGGAGTCGGAAGCATGACAT 59.821 55.000 0.00 0.00 37.58 3.06
53 54 1.293924 GGAGTCGGAAGCATGACATG 58.706 55.000 11.27 11.27 37.58 3.21
54 55 1.293924 GAGTCGGAAGCATGACATGG 58.706 55.000 17.03 0.18 37.58 3.66
55 56 0.904649 AGTCGGAAGCATGACATGGA 59.095 50.000 17.03 2.64 37.58 3.41
56 57 1.134580 AGTCGGAAGCATGACATGGAG 60.135 52.381 17.03 0.00 37.58 3.86
57 58 0.904649 TCGGAAGCATGACATGGAGT 59.095 50.000 17.03 0.00 0.00 3.85
58 59 2.107366 TCGGAAGCATGACATGGAGTA 58.893 47.619 17.03 0.00 0.00 2.59
59 60 2.159099 TCGGAAGCATGACATGGAGTAC 60.159 50.000 17.03 0.00 0.00 2.73
60 61 2.418609 CGGAAGCATGACATGGAGTACA 60.419 50.000 17.03 0.00 0.00 2.90
61 62 2.939103 GGAAGCATGACATGGAGTACAC 59.061 50.000 17.03 0.00 0.00 2.90
62 63 2.698855 AGCATGACATGGAGTACACC 57.301 50.000 17.03 1.82 0.00 4.16
63 64 1.134699 AGCATGACATGGAGTACACCG 60.135 52.381 17.03 0.00 0.00 4.94
64 65 1.939974 CATGACATGGAGTACACCGG 58.060 55.000 7.60 0.00 0.00 5.28
65 66 1.207089 CATGACATGGAGTACACCGGT 59.793 52.381 0.00 0.00 0.00 5.28
66 67 2.219080 TGACATGGAGTACACCGGTA 57.781 50.000 6.87 0.00 0.00 4.02
67 68 2.742348 TGACATGGAGTACACCGGTAT 58.258 47.619 6.87 0.00 0.00 2.73
68 69 3.101437 TGACATGGAGTACACCGGTATT 58.899 45.455 6.87 0.00 0.00 1.89
69 70 3.118920 TGACATGGAGTACACCGGTATTG 60.119 47.826 6.87 0.00 0.00 1.90
70 71 2.210116 CATGGAGTACACCGGTATTGC 58.790 52.381 6.87 0.08 0.00 3.56
71 72 0.538118 TGGAGTACACCGGTATTGCC 59.462 55.000 6.87 6.24 28.40 4.52
72 73 0.828677 GGAGTACACCGGTATTGCCT 59.171 55.000 6.87 0.00 34.25 4.75
73 74 1.472728 GGAGTACACCGGTATTGCCTG 60.473 57.143 6.87 0.00 34.25 4.85
74 75 0.107848 AGTACACCGGTATTGCCTGC 60.108 55.000 6.87 0.00 34.25 4.85
75 76 1.153529 TACACCGGTATTGCCTGCG 60.154 57.895 6.87 0.00 34.25 5.18
76 77 3.876198 CACCGGTATTGCCTGCGC 61.876 66.667 6.87 0.00 34.25 6.09
77 78 4.096003 ACCGGTATTGCCTGCGCT 62.096 61.111 4.49 0.00 35.36 5.92
78 79 2.108157 CCGGTATTGCCTGCGCTA 59.892 61.111 9.73 0.00 35.36 4.26
79 80 2.244651 CCGGTATTGCCTGCGCTAC 61.245 63.158 9.73 0.66 35.36 3.58
80 81 1.520564 CGGTATTGCCTGCGCTACA 60.521 57.895 9.73 0.36 35.36 2.74
81 82 1.490693 CGGTATTGCCTGCGCTACAG 61.491 60.000 9.73 0.00 46.77 2.74
94 95 5.657470 TGCGCTACAGATTTGATCAATAC 57.343 39.130 9.40 6.63 0.00 1.89
95 96 4.511454 TGCGCTACAGATTTGATCAATACC 59.489 41.667 9.40 1.75 0.00 2.73
96 97 4.752101 GCGCTACAGATTTGATCAATACCT 59.248 41.667 9.40 4.11 0.00 3.08
97 98 5.107298 GCGCTACAGATTTGATCAATACCTC 60.107 44.000 9.40 4.58 0.00 3.85
98 99 5.406780 CGCTACAGATTTGATCAATACCTCC 59.593 44.000 9.40 0.00 0.00 4.30
99 100 6.529220 GCTACAGATTTGATCAATACCTCCT 58.471 40.000 9.40 0.00 0.00 3.69
100 101 6.995091 GCTACAGATTTGATCAATACCTCCTT 59.005 38.462 9.40 0.00 0.00 3.36
101 102 7.500559 GCTACAGATTTGATCAATACCTCCTTT 59.499 37.037 9.40 0.00 0.00 3.11
102 103 9.401058 CTACAGATTTGATCAATACCTCCTTTT 57.599 33.333 9.40 0.00 0.00 2.27
103 104 8.286191 ACAGATTTGATCAATACCTCCTTTTC 57.714 34.615 9.40 0.00 0.00 2.29
104 105 8.112183 ACAGATTTGATCAATACCTCCTTTTCT 58.888 33.333 9.40 0.00 0.00 2.52
105 106 8.404000 CAGATTTGATCAATACCTCCTTTTCTG 58.596 37.037 9.40 5.78 0.00 3.02
106 107 6.515272 TTTGATCAATACCTCCTTTTCTGC 57.485 37.500 9.40 0.00 0.00 4.26
107 108 5.178096 TGATCAATACCTCCTTTTCTGCA 57.822 39.130 0.00 0.00 0.00 4.41
108 109 5.188434 TGATCAATACCTCCTTTTCTGCAG 58.812 41.667 7.63 7.63 0.00 4.41
109 110 3.347216 TCAATACCTCCTTTTCTGCAGC 58.653 45.455 9.47 0.00 0.00 5.25
110 111 3.084039 CAATACCTCCTTTTCTGCAGCA 58.916 45.455 9.47 0.00 0.00 4.41
111 112 2.479566 TACCTCCTTTTCTGCAGCAG 57.520 50.000 17.10 17.10 0.00 4.24
112 113 0.767375 ACCTCCTTTTCTGCAGCAGA 59.233 50.000 21.85 21.85 38.87 4.26
113 114 1.353694 ACCTCCTTTTCTGCAGCAGAT 59.646 47.619 25.94 5.47 40.39 2.90
114 115 2.573462 ACCTCCTTTTCTGCAGCAGATA 59.427 45.455 25.94 18.37 40.39 1.98
115 116 3.009473 ACCTCCTTTTCTGCAGCAGATAA 59.991 43.478 25.94 23.92 40.39 1.75
116 117 4.012374 CCTCCTTTTCTGCAGCAGATAAA 58.988 43.478 25.94 23.11 40.39 1.40
117 118 4.460382 CCTCCTTTTCTGCAGCAGATAAAA 59.540 41.667 25.94 21.05 40.39 1.52
118 119 5.392811 CCTCCTTTTCTGCAGCAGATAAAAG 60.393 44.000 28.43 28.43 40.39 2.27
119 120 4.082571 TCCTTTTCTGCAGCAGATAAAAGC 60.083 41.667 29.31 0.00 40.39 3.51
120 121 4.082354 CCTTTTCTGCAGCAGATAAAAGCT 60.082 41.667 29.31 0.00 40.39 3.74
121 122 5.458041 TTTTCTGCAGCAGATAAAAGCTT 57.542 34.783 25.94 0.00 40.39 3.74
122 123 4.691860 TTCTGCAGCAGATAAAAGCTTC 57.308 40.909 25.94 0.00 40.39 3.86
123 124 3.947868 TCTGCAGCAGATAAAAGCTTCT 58.052 40.909 21.85 0.00 39.50 2.85
124 125 3.937706 TCTGCAGCAGATAAAAGCTTCTC 59.062 43.478 21.85 0.00 39.50 2.87
125 126 3.012518 TGCAGCAGATAAAAGCTTCTCC 58.987 45.455 0.00 0.00 39.50 3.71
126 127 2.031437 GCAGCAGATAAAAGCTTCTCCG 59.969 50.000 0.00 0.00 39.50 4.63
127 128 3.265791 CAGCAGATAAAAGCTTCTCCGT 58.734 45.455 0.00 0.00 39.50 4.69
128 129 3.308323 CAGCAGATAAAAGCTTCTCCGTC 59.692 47.826 0.00 0.00 39.50 4.79
129 130 2.609916 GCAGATAAAAGCTTCTCCGTCC 59.390 50.000 0.00 0.00 0.00 4.79
130 131 3.861840 CAGATAAAAGCTTCTCCGTCCA 58.138 45.455 0.00 0.00 0.00 4.02
131 132 4.446371 CAGATAAAAGCTTCTCCGTCCAT 58.554 43.478 0.00 0.00 0.00 3.41
132 133 4.509600 CAGATAAAAGCTTCTCCGTCCATC 59.490 45.833 0.00 0.00 0.00 3.51
133 134 2.115343 AAAAGCTTCTCCGTCCATCC 57.885 50.000 0.00 0.00 0.00 3.51
134 135 0.253327 AAAGCTTCTCCGTCCATCCC 59.747 55.000 0.00 0.00 0.00 3.85
135 136 1.627297 AAGCTTCTCCGTCCATCCCC 61.627 60.000 0.00 0.00 0.00 4.81
136 137 2.066999 GCTTCTCCGTCCATCCCCT 61.067 63.158 0.00 0.00 0.00 4.79
137 138 0.759436 GCTTCTCCGTCCATCCCCTA 60.759 60.000 0.00 0.00 0.00 3.53
138 139 1.789523 CTTCTCCGTCCATCCCCTAA 58.210 55.000 0.00 0.00 0.00 2.69
139 140 1.413077 CTTCTCCGTCCATCCCCTAAC 59.587 57.143 0.00 0.00 0.00 2.34
140 141 0.398098 TCTCCGTCCATCCCCTAACC 60.398 60.000 0.00 0.00 0.00 2.85
141 142 0.398664 CTCCGTCCATCCCCTAACCT 60.399 60.000 0.00 0.00 0.00 3.50
142 143 0.043637 TCCGTCCATCCCCTAACCTT 59.956 55.000 0.00 0.00 0.00 3.50
143 144 0.468648 CCGTCCATCCCCTAACCTTC 59.531 60.000 0.00 0.00 0.00 3.46
144 145 1.497161 CGTCCATCCCCTAACCTTCT 58.503 55.000 0.00 0.00 0.00 2.85
145 146 1.413077 CGTCCATCCCCTAACCTTCTC 59.587 57.143 0.00 0.00 0.00 2.87
146 147 1.769465 GTCCATCCCCTAACCTTCTCC 59.231 57.143 0.00 0.00 0.00 3.71
147 148 1.141185 CCATCCCCTAACCTTCTCCC 58.859 60.000 0.00 0.00 0.00 4.30
148 149 1.628043 CCATCCCCTAACCTTCTCCCA 60.628 57.143 0.00 0.00 0.00 4.37
149 150 2.422746 CATCCCCTAACCTTCTCCCAT 58.577 52.381 0.00 0.00 0.00 4.00
150 151 3.598264 CATCCCCTAACCTTCTCCCATA 58.402 50.000 0.00 0.00 0.00 2.74
151 152 3.056201 TCCCCTAACCTTCTCCCATAC 57.944 52.381 0.00 0.00 0.00 2.39
152 153 2.319747 TCCCCTAACCTTCTCCCATACA 59.680 50.000 0.00 0.00 0.00 2.29
153 154 2.438392 CCCCTAACCTTCTCCCATACAC 59.562 54.545 0.00 0.00 0.00 2.90
154 155 2.102588 CCCTAACCTTCTCCCATACACG 59.897 54.545 0.00 0.00 0.00 4.49
155 156 3.028850 CCTAACCTTCTCCCATACACGA 58.971 50.000 0.00 0.00 0.00 4.35
156 157 3.641906 CCTAACCTTCTCCCATACACGAT 59.358 47.826 0.00 0.00 0.00 3.73
157 158 3.821421 AACCTTCTCCCATACACGATC 57.179 47.619 0.00 0.00 0.00 3.69
158 159 3.033659 ACCTTCTCCCATACACGATCT 57.966 47.619 0.00 0.00 0.00 2.75
159 160 2.959707 ACCTTCTCCCATACACGATCTC 59.040 50.000 0.00 0.00 0.00 2.75
160 161 2.030717 CCTTCTCCCATACACGATCTCG 60.031 54.545 0.00 0.00 46.33 4.04
837 855 8.931568 CCTAAAGGTACCTACACAATACCTAAT 58.068 37.037 16.67 0.00 46.48 1.73
856 874 7.935405 ACCTAATCACCTAACCCTATTTTTGA 58.065 34.615 0.00 0.00 0.00 2.69
1227 1263 2.644299 TGATCCAAGGGAGCAGAAAGAA 59.356 45.455 0.00 0.00 43.58 2.52
1249 1285 0.819582 GGATTCGAACCCTCGGTACA 59.180 55.000 0.00 0.00 45.49 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.148079 TGTGAGAGTGTGACTTCTCTGAT 58.852 43.478 13.45 0.00 40.53 2.90
1 2 3.555966 TGTGAGAGTGTGACTTCTCTGA 58.444 45.455 13.45 4.96 40.53 3.27
2 3 3.998099 TGTGAGAGTGTGACTTCTCTG 57.002 47.619 13.45 0.00 40.53 3.35
3 4 4.739137 GCTTTGTGAGAGTGTGACTTCTCT 60.739 45.833 15.15 12.62 42.72 3.10
4 5 3.492756 GCTTTGTGAGAGTGTGACTTCTC 59.507 47.826 9.66 9.66 0.00 2.87
5 6 3.462021 GCTTTGTGAGAGTGTGACTTCT 58.538 45.455 0.00 0.00 0.00 2.85
6 7 2.545946 GGCTTTGTGAGAGTGTGACTTC 59.454 50.000 0.00 0.00 0.00 3.01
7 8 2.565841 GGCTTTGTGAGAGTGTGACTT 58.434 47.619 0.00 0.00 0.00 3.01
8 9 1.202698 GGGCTTTGTGAGAGTGTGACT 60.203 52.381 0.00 0.00 0.00 3.41
9 10 1.202698 AGGGCTTTGTGAGAGTGTGAC 60.203 52.381 0.00 0.00 0.00 3.67
10 11 1.070758 GAGGGCTTTGTGAGAGTGTGA 59.929 52.381 0.00 0.00 0.00 3.58
11 12 1.517242 GAGGGCTTTGTGAGAGTGTG 58.483 55.000 0.00 0.00 0.00 3.82
12 13 0.034059 CGAGGGCTTTGTGAGAGTGT 59.966 55.000 0.00 0.00 0.00 3.55
13 14 0.318441 TCGAGGGCTTTGTGAGAGTG 59.682 55.000 0.00 0.00 0.00 3.51
14 15 0.605589 CTCGAGGGCTTTGTGAGAGT 59.394 55.000 3.91 0.00 0.00 3.24
15 16 0.108424 CCTCGAGGGCTTTGTGAGAG 60.108 60.000 24.62 0.00 0.00 3.20
16 17 1.975327 CCTCGAGGGCTTTGTGAGA 59.025 57.895 24.62 0.00 0.00 3.27
17 18 4.606071 CCTCGAGGGCTTTGTGAG 57.394 61.111 24.62 0.00 0.00 3.51
27 28 2.776913 GCTTCCGACTCCCTCGAGG 61.777 68.421 25.36 25.36 46.14 4.63
28 29 1.388065 ATGCTTCCGACTCCCTCGAG 61.388 60.000 5.13 5.13 46.14 4.04
29 30 1.379977 ATGCTTCCGACTCCCTCGA 60.380 57.895 0.00 0.00 46.14 4.04
30 31 1.227089 CATGCTTCCGACTCCCTCG 60.227 63.158 0.00 0.00 42.54 4.63
31 32 0.179097 GTCATGCTTCCGACTCCCTC 60.179 60.000 0.00 0.00 0.00 4.30
32 33 0.904865 TGTCATGCTTCCGACTCCCT 60.905 55.000 0.00 0.00 33.18 4.20
33 34 0.179000 ATGTCATGCTTCCGACTCCC 59.821 55.000 0.00 0.00 33.18 4.30
34 35 1.293924 CATGTCATGCTTCCGACTCC 58.706 55.000 0.00 0.00 33.18 3.85
35 36 1.134699 TCCATGTCATGCTTCCGACTC 60.135 52.381 7.35 0.00 33.18 3.36
36 37 0.904649 TCCATGTCATGCTTCCGACT 59.095 50.000 7.35 0.00 33.18 4.18
37 38 1.293924 CTCCATGTCATGCTTCCGAC 58.706 55.000 7.35 0.00 0.00 4.79
38 39 0.904649 ACTCCATGTCATGCTTCCGA 59.095 50.000 7.35 0.00 0.00 4.55
39 40 2.205074 GTACTCCATGTCATGCTTCCG 58.795 52.381 7.35 0.00 0.00 4.30
40 41 2.939103 GTGTACTCCATGTCATGCTTCC 59.061 50.000 7.35 0.00 0.00 3.46
41 42 2.939103 GGTGTACTCCATGTCATGCTTC 59.061 50.000 9.12 0.00 0.00 3.86
42 43 2.677902 CGGTGTACTCCATGTCATGCTT 60.678 50.000 14.09 0.00 0.00 3.91
43 44 1.134699 CGGTGTACTCCATGTCATGCT 60.135 52.381 14.09 0.00 0.00 3.79
44 45 1.290203 CGGTGTACTCCATGTCATGC 58.710 55.000 14.09 0.00 0.00 4.06
45 46 1.207089 ACCGGTGTACTCCATGTCATG 59.793 52.381 6.12 5.79 0.00 3.07
46 47 1.568504 ACCGGTGTACTCCATGTCAT 58.431 50.000 6.12 0.00 0.00 3.06
47 48 2.219080 TACCGGTGTACTCCATGTCA 57.781 50.000 19.93 0.00 0.00 3.58
48 49 3.454375 CAATACCGGTGTACTCCATGTC 58.546 50.000 19.93 0.00 0.00 3.06
49 50 2.419574 GCAATACCGGTGTACTCCATGT 60.420 50.000 19.93 11.85 0.00 3.21
50 51 2.210116 GCAATACCGGTGTACTCCATG 58.790 52.381 19.93 5.65 0.00 3.66
51 52 1.140252 GGCAATACCGGTGTACTCCAT 59.860 52.381 19.93 0.00 0.00 3.41
52 53 0.538118 GGCAATACCGGTGTACTCCA 59.462 55.000 19.93 0.00 0.00 3.86
53 54 0.828677 AGGCAATACCGGTGTACTCC 59.171 55.000 19.93 12.51 46.52 3.85
54 55 1.935933 CAGGCAATACCGGTGTACTC 58.064 55.000 19.93 4.06 46.52 2.59
55 56 0.107848 GCAGGCAATACCGGTGTACT 60.108 55.000 19.93 7.34 46.52 2.73
56 57 1.426041 CGCAGGCAATACCGGTGTAC 61.426 60.000 19.93 6.54 46.52 2.90
57 58 1.153529 CGCAGGCAATACCGGTGTA 60.154 57.895 19.93 0.00 46.52 2.90
58 59 2.435938 CGCAGGCAATACCGGTGT 60.436 61.111 19.93 8.05 46.52 4.16
59 60 2.916502 TAGCGCAGGCAATACCGGTG 62.917 60.000 19.93 0.65 45.87 4.94
60 61 2.727392 TAGCGCAGGCAATACCGGT 61.727 57.895 13.98 13.98 46.52 5.28
61 62 2.108157 TAGCGCAGGCAATACCGG 59.892 61.111 11.47 0.00 46.52 5.28
62 63 1.490693 CTGTAGCGCAGGCAATACCG 61.491 60.000 11.47 0.00 46.52 4.02
63 64 0.179084 TCTGTAGCGCAGGCAATACC 60.179 55.000 11.47 0.00 45.08 2.73
64 65 1.871080 ATCTGTAGCGCAGGCAATAC 58.129 50.000 11.47 2.25 45.08 1.89
65 66 2.613595 CAAATCTGTAGCGCAGGCAATA 59.386 45.455 11.47 0.00 45.08 1.90
66 67 1.402968 CAAATCTGTAGCGCAGGCAAT 59.597 47.619 11.47 0.00 45.08 3.56
67 68 0.804364 CAAATCTGTAGCGCAGGCAA 59.196 50.000 11.47 0.00 45.08 4.52
68 69 0.036483 TCAAATCTGTAGCGCAGGCA 60.036 50.000 11.47 4.08 45.08 4.75
69 70 1.262683 GATCAAATCTGTAGCGCAGGC 59.737 52.381 11.47 0.00 45.08 4.85
70 71 2.554142 TGATCAAATCTGTAGCGCAGG 58.446 47.619 11.47 0.00 45.08 4.85
71 72 4.808077 ATTGATCAAATCTGTAGCGCAG 57.192 40.909 13.09 0.00 46.34 5.18
72 73 4.511454 GGTATTGATCAAATCTGTAGCGCA 59.489 41.667 13.09 0.00 0.00 6.09
73 74 4.752101 AGGTATTGATCAAATCTGTAGCGC 59.248 41.667 13.09 0.00 0.00 5.92
74 75 5.406780 GGAGGTATTGATCAAATCTGTAGCG 59.593 44.000 13.09 0.00 0.00 4.26
75 76 6.529220 AGGAGGTATTGATCAAATCTGTAGC 58.471 40.000 13.09 9.40 0.00 3.58
76 77 8.970859 AAAGGAGGTATTGATCAAATCTGTAG 57.029 34.615 13.09 0.00 0.00 2.74
77 78 9.396022 GAAAAGGAGGTATTGATCAAATCTGTA 57.604 33.333 13.09 0.00 0.00 2.74
78 79 8.112183 AGAAAAGGAGGTATTGATCAAATCTGT 58.888 33.333 13.09 0.00 0.00 3.41
79 80 8.404000 CAGAAAAGGAGGTATTGATCAAATCTG 58.596 37.037 13.09 9.18 0.00 2.90
80 81 7.067981 GCAGAAAAGGAGGTATTGATCAAATCT 59.932 37.037 13.09 9.95 0.00 2.40
81 82 7.148018 TGCAGAAAAGGAGGTATTGATCAAATC 60.148 37.037 13.09 8.32 0.00 2.17
82 83 6.664816 TGCAGAAAAGGAGGTATTGATCAAAT 59.335 34.615 13.09 4.08 0.00 2.32
83 84 6.009589 TGCAGAAAAGGAGGTATTGATCAAA 58.990 36.000 13.09 0.00 0.00 2.69
84 85 5.569355 TGCAGAAAAGGAGGTATTGATCAA 58.431 37.500 11.26 11.26 0.00 2.57
85 86 5.178096 TGCAGAAAAGGAGGTATTGATCA 57.822 39.130 0.00 0.00 0.00 2.92
86 87 4.036144 GCTGCAGAAAAGGAGGTATTGATC 59.964 45.833 20.43 0.00 0.00 2.92
87 88 3.950395 GCTGCAGAAAAGGAGGTATTGAT 59.050 43.478 20.43 0.00 0.00 2.57
88 89 3.244875 TGCTGCAGAAAAGGAGGTATTGA 60.245 43.478 20.43 0.00 0.00 2.57
89 90 3.084039 TGCTGCAGAAAAGGAGGTATTG 58.916 45.455 20.43 0.00 0.00 1.90
90 91 3.009473 TCTGCTGCAGAAAAGGAGGTATT 59.991 43.478 28.72 0.00 37.57 1.89
91 92 2.573462 TCTGCTGCAGAAAAGGAGGTAT 59.427 45.455 28.72 0.00 37.57 2.73
92 93 1.977854 TCTGCTGCAGAAAAGGAGGTA 59.022 47.619 28.72 3.01 37.57 3.08
93 94 0.767375 TCTGCTGCAGAAAAGGAGGT 59.233 50.000 28.72 0.00 37.57 3.85
94 95 2.125773 ATCTGCTGCAGAAAAGGAGG 57.874 50.000 33.31 4.91 44.04 4.30
95 96 5.633830 TTTTATCTGCTGCAGAAAAGGAG 57.366 39.130 33.31 5.67 44.04 3.69
96 97 4.082571 GCTTTTATCTGCTGCAGAAAAGGA 60.083 41.667 34.84 22.24 44.04 3.36
97 98 4.082354 AGCTTTTATCTGCTGCAGAAAAGG 60.082 41.667 34.84 30.31 44.04 3.11
98 99 5.056894 AGCTTTTATCTGCTGCAGAAAAG 57.943 39.130 32.67 32.67 44.04 2.27
99 100 5.242393 AGAAGCTTTTATCTGCTGCAGAAAA 59.758 36.000 33.31 26.62 44.04 2.29
100 101 4.763793 AGAAGCTTTTATCTGCTGCAGAAA 59.236 37.500 33.31 24.07 44.04 2.52
101 102 4.330250 AGAAGCTTTTATCTGCTGCAGAA 58.670 39.130 33.31 20.27 44.04 3.02
102 103 3.937706 GAGAAGCTTTTATCTGCTGCAGA 59.062 43.478 32.07 32.07 44.99 4.26
103 104 3.065095 GGAGAAGCTTTTATCTGCTGCAG 59.935 47.826 23.31 23.31 39.71 4.41
104 105 3.012518 GGAGAAGCTTTTATCTGCTGCA 58.987 45.455 0.00 0.88 39.71 4.41
105 106 2.031437 CGGAGAAGCTTTTATCTGCTGC 59.969 50.000 0.00 0.00 39.71 5.25
106 107 3.265791 ACGGAGAAGCTTTTATCTGCTG 58.734 45.455 0.00 0.00 39.71 4.41
107 108 3.526534 GACGGAGAAGCTTTTATCTGCT 58.473 45.455 0.00 0.00 41.82 4.24
108 109 2.609916 GGACGGAGAAGCTTTTATCTGC 59.390 50.000 0.00 0.00 0.00 4.26
109 110 3.861840 TGGACGGAGAAGCTTTTATCTG 58.138 45.455 0.00 7.44 0.00 2.90
110 111 4.443598 GGATGGACGGAGAAGCTTTTATCT 60.444 45.833 0.00 0.00 0.00 1.98
111 112 3.810386 GGATGGACGGAGAAGCTTTTATC 59.190 47.826 0.00 0.00 0.00 1.75
112 113 3.433740 GGGATGGACGGAGAAGCTTTTAT 60.434 47.826 0.00 0.00 0.00 1.40
113 114 2.093128 GGGATGGACGGAGAAGCTTTTA 60.093 50.000 0.00 0.00 0.00 1.52
114 115 1.340114 GGGATGGACGGAGAAGCTTTT 60.340 52.381 0.00 0.00 0.00 2.27
115 116 0.253327 GGGATGGACGGAGAAGCTTT 59.747 55.000 0.00 0.00 0.00 3.51
116 117 1.627297 GGGGATGGACGGAGAAGCTT 61.627 60.000 0.00 0.00 0.00 3.74
117 118 2.066999 GGGGATGGACGGAGAAGCT 61.067 63.158 0.00 0.00 0.00 3.74
118 119 0.759436 TAGGGGATGGACGGAGAAGC 60.759 60.000 0.00 0.00 0.00 3.86
119 120 1.413077 GTTAGGGGATGGACGGAGAAG 59.587 57.143 0.00 0.00 0.00 2.85
120 121 1.492764 GTTAGGGGATGGACGGAGAA 58.507 55.000 0.00 0.00 0.00 2.87
121 122 0.398098 GGTTAGGGGATGGACGGAGA 60.398 60.000 0.00 0.00 0.00 3.71
122 123 0.398664 AGGTTAGGGGATGGACGGAG 60.399 60.000 0.00 0.00 0.00 4.63
123 124 0.043637 AAGGTTAGGGGATGGACGGA 59.956 55.000 0.00 0.00 0.00 4.69
124 125 0.468648 GAAGGTTAGGGGATGGACGG 59.531 60.000 0.00 0.00 0.00 4.79
125 126 1.413077 GAGAAGGTTAGGGGATGGACG 59.587 57.143 0.00 0.00 0.00 4.79
126 127 1.769465 GGAGAAGGTTAGGGGATGGAC 59.231 57.143 0.00 0.00 0.00 4.02
127 128 1.345112 GGGAGAAGGTTAGGGGATGGA 60.345 57.143 0.00 0.00 0.00 3.41
128 129 1.141185 GGGAGAAGGTTAGGGGATGG 58.859 60.000 0.00 0.00 0.00 3.51
129 130 1.893315 TGGGAGAAGGTTAGGGGATG 58.107 55.000 0.00 0.00 0.00 3.51
130 131 2.918774 ATGGGAGAAGGTTAGGGGAT 57.081 50.000 0.00 0.00 0.00 3.85
131 132 2.319747 TGTATGGGAGAAGGTTAGGGGA 59.680 50.000 0.00 0.00 0.00 4.81
132 133 2.438392 GTGTATGGGAGAAGGTTAGGGG 59.562 54.545 0.00 0.00 0.00 4.79
133 134 2.102588 CGTGTATGGGAGAAGGTTAGGG 59.897 54.545 0.00 0.00 0.00 3.53
134 135 3.028850 TCGTGTATGGGAGAAGGTTAGG 58.971 50.000 0.00 0.00 0.00 2.69
135 136 4.585162 AGATCGTGTATGGGAGAAGGTTAG 59.415 45.833 0.00 0.00 0.00 2.34
136 137 4.543689 AGATCGTGTATGGGAGAAGGTTA 58.456 43.478 0.00 0.00 0.00 2.85
137 138 3.375699 AGATCGTGTATGGGAGAAGGTT 58.624 45.455 0.00 0.00 0.00 3.50
138 139 2.959707 GAGATCGTGTATGGGAGAAGGT 59.040 50.000 0.00 0.00 0.00 3.50
139 140 2.030717 CGAGATCGTGTATGGGAGAAGG 60.031 54.545 0.00 0.00 34.11 3.46
140 141 3.275400 CGAGATCGTGTATGGGAGAAG 57.725 52.381 0.00 0.00 34.11 2.85
153 154 4.214545 AGCAAGAGAATACCTACGAGATCG 59.785 45.833 0.00 0.00 46.33 3.69
154 155 5.699097 AGCAAGAGAATACCTACGAGATC 57.301 43.478 0.00 0.00 0.00 2.75
155 156 6.300703 ACTAGCAAGAGAATACCTACGAGAT 58.699 40.000 0.00 0.00 0.00 2.75
156 157 5.682659 ACTAGCAAGAGAATACCTACGAGA 58.317 41.667 0.00 0.00 0.00 4.04
157 158 7.675962 ATACTAGCAAGAGAATACCTACGAG 57.324 40.000 0.00 0.00 0.00 4.18
158 159 7.937942 AGAATACTAGCAAGAGAATACCTACGA 59.062 37.037 0.00 0.00 0.00 3.43
159 160 8.101654 AGAATACTAGCAAGAGAATACCTACG 57.898 38.462 0.00 0.00 0.00 3.51
162 163 8.852135 GTGTAGAATACTAGCAAGAGAATACCT 58.148 37.037 0.00 0.00 43.54 3.08
163 164 8.630917 TGTGTAGAATACTAGCAAGAGAATACC 58.369 37.037 0.00 0.00 43.54 2.73
1220 1256 3.687125 GGGTTCGAATCCCTTTCTTTCT 58.313 45.455 17.16 0.00 41.58 2.52


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

AutoCloner maintained by Alex Coulton.