Multiple sequence alignment - TraesCS3B01G376500

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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 TraesCS3B01G376500 chr3B 100.000 2839 0 0 1 2839 592826099 592823261 0.000000e+00 5243
1 TraesCS3B01G376500 chr3D 91.193 2691 117 46 230 2839 451163414 451160763 0.000000e+00 3546
2 TraesCS3B01G376500 chr3A 89.241 1738 61 55 334 2015 594302287 594300620 0.000000e+00 2058
3 TraesCS3B01G376500 chr3A 92.042 289 20 2 2553 2839 594298129 594297842 1.220000e-108 403
4 TraesCS3B01G376500 chr3A 86.909 275 30 3 2553 2822 594300357 594300084 1.280000e-78 303
5 TraesCS3B01G376500 chr3A 92.708 96 7 0 183 278 594304264 594304169 3.810000e-29 139
6 TraesCS3B01G376500 chr1A 78.125 448 57 21 1129 1573 495332560 495332969 2.180000e-61 246
7 TraesCS3B01G376500 chr1B 77.389 429 63 19 1150 1573 533815489 533815888 1.020000e-54 224
8 TraesCS3B01G376500 chr4D 75.054 461 90 21 1128 1572 100483175 100483626 1.040000e-44 191
9 TraesCS3B01G376500 chr5B 75.878 427 69 22 1151 1572 491246065 491246462 1.340000e-43 187
10 TraesCS3B01G376500 chr5B 89.130 138 15 0 1409 1546 491280364 491280501 3.760000e-39 172
11 TraesCS3B01G376500 chr5A 87.349 166 17 4 1409 1572 520681110 520681273 1.340000e-43 187
12 TraesCS3B01G376500 chr5D 89.855 138 14 0 1409 1546 409575934 409576071 8.080000e-41 178
13 TraesCS3B01G376500 chr5D 87.681 138 17 0 1409 1546 409523595 409523732 8.140000e-36 161


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 TraesCS3B01G376500 chr3B 592823261 592826099 2838 True 5243.00 5243 100.000 1 2839 1 chr3B.!!$R1 2838
1 TraesCS3B01G376500 chr3D 451160763 451163414 2651 True 3546.00 3546 91.193 230 2839 1 chr3D.!!$R1 2609
2 TraesCS3B01G376500 chr3A 594297842 594304264 6422 True 725.75 2058 90.225 183 2839 4 chr3A.!!$R1 2656

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
140 141 0.035739 ATACCACGACGCCTTGGTTT 59.964 50.0 13.14 3.95 41.57 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 3924 0.251341 AGGGGATGCACCACAACTTC 60.251 55.0 9.77 0.0 46.31 3.01 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
22 23 5.314923 CCTGGTGAAAGTGGACATATTTG 57.685 43.478 0.00 0.00 0.00 2.32
23 24 5.009631 CCTGGTGAAAGTGGACATATTTGA 58.990 41.667 0.00 0.00 0.00 2.69
24 25 5.106157 CCTGGTGAAAGTGGACATATTTGAC 60.106 44.000 0.00 0.00 0.00 3.18
25 26 4.764823 TGGTGAAAGTGGACATATTTGACC 59.235 41.667 11.72 11.72 39.67 4.02
26 27 4.157840 GGTGAAAGTGGACATATTTGACCC 59.842 45.833 9.06 0.00 35.09 4.46
27 28 5.010282 GTGAAAGTGGACATATTTGACCCT 58.990 41.667 2.60 0.00 36.93 4.34
28 29 5.476945 GTGAAAGTGGACATATTTGACCCTT 59.523 40.000 2.60 3.39 36.93 3.95
29 30 6.015434 GTGAAAGTGGACATATTTGACCCTTT 60.015 38.462 14.83 14.83 38.95 3.11
30 31 6.553100 TGAAAGTGGACATATTTGACCCTTTT 59.447 34.615 15.48 10.40 37.78 2.27
31 32 6.994421 AAGTGGACATATTTGACCCTTTTT 57.006 33.333 2.60 0.00 36.93 1.94
32 33 8.485578 AAAGTGGACATATTTGACCCTTTTTA 57.514 30.769 11.68 0.00 36.16 1.52
33 34 7.703058 AGTGGACATATTTGACCCTTTTTAG 57.297 36.000 2.60 0.00 36.93 1.85
34 35 7.466804 AGTGGACATATTTGACCCTTTTTAGA 58.533 34.615 2.60 0.00 36.93 2.10
35 36 7.947890 AGTGGACATATTTGACCCTTTTTAGAA 59.052 33.333 2.60 0.00 36.93 2.10
36 37 8.581578 GTGGACATATTTGACCCTTTTTAGAAA 58.418 33.333 2.60 0.00 36.93 2.52
37 38 9.320295 TGGACATATTTGACCCTTTTTAGAAAT 57.680 29.630 2.60 0.00 36.93 2.17
43 44 8.607441 ATTTGACCCTTTTTAGAAATTTCAGC 57.393 30.769 19.99 0.00 0.00 4.26
44 45 6.723298 TGACCCTTTTTAGAAATTTCAGCA 57.277 33.333 19.99 2.27 0.00 4.41
45 46 6.512297 TGACCCTTTTTAGAAATTTCAGCAC 58.488 36.000 19.99 0.00 0.00 4.40
46 47 6.097554 TGACCCTTTTTAGAAATTTCAGCACA 59.902 34.615 19.99 5.91 0.00 4.57
47 48 6.883744 ACCCTTTTTAGAAATTTCAGCACAA 58.116 32.000 19.99 5.53 0.00 3.33
48 49 7.508687 ACCCTTTTTAGAAATTTCAGCACAAT 58.491 30.769 19.99 0.27 0.00 2.71
49 50 8.646900 ACCCTTTTTAGAAATTTCAGCACAATA 58.353 29.630 19.99 0.00 0.00 1.90
50 51 9.657419 CCCTTTTTAGAAATTTCAGCACAATAT 57.343 29.630 19.99 0.00 0.00 1.28
56 57 9.781834 TTAGAAATTTCAGCACAATATAAACCG 57.218 29.630 19.99 0.00 0.00 4.44
57 58 7.257722 AGAAATTTCAGCACAATATAAACCGG 58.742 34.615 19.99 0.00 0.00 5.28
58 59 6.767524 AATTTCAGCACAATATAAACCGGA 57.232 33.333 9.46 0.00 0.00 5.14
59 60 6.959639 ATTTCAGCACAATATAAACCGGAT 57.040 33.333 9.46 0.00 0.00 4.18
60 61 6.371809 TTTCAGCACAATATAAACCGGATC 57.628 37.500 9.46 0.00 0.00 3.36
61 62 5.290493 TCAGCACAATATAAACCGGATCT 57.710 39.130 9.46 0.00 0.00 2.75
62 63 6.413783 TCAGCACAATATAAACCGGATCTA 57.586 37.500 9.46 0.00 0.00 1.98
63 64 6.822442 TCAGCACAATATAAACCGGATCTAA 58.178 36.000 9.46 0.00 0.00 2.10
64 65 7.276658 TCAGCACAATATAAACCGGATCTAAA 58.723 34.615 9.46 0.00 0.00 1.85
65 66 7.771361 TCAGCACAATATAAACCGGATCTAAAA 59.229 33.333 9.46 0.00 0.00 1.52
66 67 8.402472 CAGCACAATATAAACCGGATCTAAAAA 58.598 33.333 9.46 0.00 0.00 1.94
67 68 9.131791 AGCACAATATAAACCGGATCTAAAAAT 57.868 29.630 9.46 0.00 0.00 1.82
108 109 5.811399 TTTTTATGATGCCAGACGTTAGG 57.189 39.130 3.07 3.07 0.00 2.69
109 110 3.469008 TTATGATGCCAGACGTTAGGG 57.531 47.619 8.98 3.40 0.00 3.53
114 115 4.077184 CCAGACGTTAGGGCGCCA 62.077 66.667 30.85 5.28 34.88 5.69
115 116 2.813908 CAGACGTTAGGGCGCCAC 60.814 66.667 30.85 17.46 34.88 5.01
116 117 2.995574 AGACGTTAGGGCGCCACT 60.996 61.111 30.85 24.19 34.88 4.00
117 118 2.813908 GACGTTAGGGCGCCACTG 60.814 66.667 30.85 15.09 34.88 3.66
118 119 3.584868 GACGTTAGGGCGCCACTGT 62.585 63.158 30.85 18.42 34.88 3.55
119 120 2.216750 GACGTTAGGGCGCCACTGTA 62.217 60.000 30.85 10.94 34.88 2.74
120 121 1.518572 CGTTAGGGCGCCACTGTAG 60.519 63.158 30.85 10.79 0.00 2.74
121 122 1.895238 GTTAGGGCGCCACTGTAGA 59.105 57.895 30.85 4.88 0.00 2.59
122 123 0.464452 GTTAGGGCGCCACTGTAGAT 59.536 55.000 30.85 5.35 0.00 1.98
123 124 1.684983 GTTAGGGCGCCACTGTAGATA 59.315 52.381 30.85 3.73 0.00 1.98
124 125 1.325355 TAGGGCGCCACTGTAGATAC 58.675 55.000 30.85 6.30 0.00 2.24
125 126 1.069258 GGGCGCCACTGTAGATACC 59.931 63.158 30.85 1.22 0.00 2.73
126 127 1.682451 GGGCGCCACTGTAGATACCA 61.682 60.000 30.85 0.00 0.00 3.25
127 128 0.529992 GGCGCCACTGTAGATACCAC 60.530 60.000 24.80 0.00 0.00 4.16
128 129 0.870307 GCGCCACTGTAGATACCACG 60.870 60.000 0.00 0.00 0.00 4.94
129 130 0.736636 CGCCACTGTAGATACCACGA 59.263 55.000 0.00 0.00 0.00 4.35
130 131 1.533338 CGCCACTGTAGATACCACGAC 60.533 57.143 0.00 0.00 0.00 4.34
131 132 1.533338 GCCACTGTAGATACCACGACG 60.533 57.143 0.00 0.00 0.00 5.12
132 133 1.533338 CCACTGTAGATACCACGACGC 60.533 57.143 0.00 0.00 0.00 5.19
133 134 0.737219 ACTGTAGATACCACGACGCC 59.263 55.000 0.00 0.00 0.00 5.68
134 135 1.022735 CTGTAGATACCACGACGCCT 58.977 55.000 0.00 0.00 0.00 5.52
135 136 1.404391 CTGTAGATACCACGACGCCTT 59.596 52.381 0.00 0.00 0.00 4.35
136 137 1.133598 TGTAGATACCACGACGCCTTG 59.866 52.381 0.00 0.00 0.00 3.61
137 138 0.742505 TAGATACCACGACGCCTTGG 59.257 55.000 0.00 0.00 37.68 3.61
138 139 1.217244 GATACCACGACGCCTTGGT 59.783 57.895 12.60 12.60 45.55 3.67
139 140 0.390735 GATACCACGACGCCTTGGTT 60.391 55.000 13.14 3.07 41.57 3.67
140 141 0.035739 ATACCACGACGCCTTGGTTT 59.964 50.000 13.14 3.95 41.57 3.27
141 142 0.881159 TACCACGACGCCTTGGTTTG 60.881 55.000 13.14 0.00 41.57 2.93
142 143 2.637025 CACGACGCCTTGGTTTGG 59.363 61.111 0.00 0.00 0.00 3.28
143 144 1.890041 CACGACGCCTTGGTTTGGA 60.890 57.895 0.00 0.00 0.00 3.53
144 145 1.597027 ACGACGCCTTGGTTTGGAG 60.597 57.895 0.00 0.00 0.00 3.86
145 146 1.301401 CGACGCCTTGGTTTGGAGA 60.301 57.895 0.00 0.00 0.00 3.71
146 147 1.291877 CGACGCCTTGGTTTGGAGAG 61.292 60.000 0.00 0.00 0.00 3.20
147 148 0.250338 GACGCCTTGGTTTGGAGAGT 60.250 55.000 0.00 0.00 0.00 3.24
148 149 0.250338 ACGCCTTGGTTTGGAGAGTC 60.250 55.000 0.00 0.00 0.00 3.36
149 150 0.250295 CGCCTTGGTTTGGAGAGTCA 60.250 55.000 0.00 0.00 0.00 3.41
150 151 1.611673 CGCCTTGGTTTGGAGAGTCAT 60.612 52.381 0.00 0.00 0.00 3.06
151 152 1.815003 GCCTTGGTTTGGAGAGTCATG 59.185 52.381 0.00 0.00 0.00 3.07
152 153 1.815003 CCTTGGTTTGGAGAGTCATGC 59.185 52.381 0.00 0.00 0.00 4.06
153 154 2.553904 CCTTGGTTTGGAGAGTCATGCT 60.554 50.000 0.00 0.00 0.00 3.79
154 155 3.307691 CCTTGGTTTGGAGAGTCATGCTA 60.308 47.826 0.00 0.00 0.00 3.49
155 156 3.616956 TGGTTTGGAGAGTCATGCTAG 57.383 47.619 0.00 0.00 0.00 3.42
156 157 3.173151 TGGTTTGGAGAGTCATGCTAGA 58.827 45.455 0.00 0.00 0.00 2.43
157 158 3.055819 TGGTTTGGAGAGTCATGCTAGAC 60.056 47.826 0.00 1.49 38.81 2.59
158 159 3.055819 GGTTTGGAGAGTCATGCTAGACA 60.056 47.826 10.88 0.00 40.98 3.41
159 160 4.563580 GGTTTGGAGAGTCATGCTAGACAA 60.564 45.833 10.88 0.00 40.98 3.18
160 161 3.876274 TGGAGAGTCATGCTAGACAAC 57.124 47.619 10.88 5.46 40.98 3.32
161 162 3.165071 TGGAGAGTCATGCTAGACAACA 58.835 45.455 10.88 2.78 40.98 3.33
162 163 3.771479 TGGAGAGTCATGCTAGACAACAT 59.229 43.478 10.88 0.00 40.98 2.71
163 164 4.118410 GGAGAGTCATGCTAGACAACATG 58.882 47.826 10.88 0.00 44.05 3.21
168 169 3.599343 TCATGCTAGACAACATGACACC 58.401 45.455 0.00 0.00 45.79 4.16
169 170 2.472695 TGCTAGACAACATGACACCC 57.527 50.000 0.00 0.00 0.00 4.61
170 171 1.977854 TGCTAGACAACATGACACCCT 59.022 47.619 0.00 0.00 0.00 4.34
171 172 2.028112 TGCTAGACAACATGACACCCTC 60.028 50.000 0.00 0.00 0.00 4.30
172 173 2.028112 GCTAGACAACATGACACCCTCA 60.028 50.000 0.00 0.00 0.00 3.86
173 174 3.557054 GCTAGACAACATGACACCCTCAA 60.557 47.826 0.00 0.00 30.60 3.02
174 175 3.795688 AGACAACATGACACCCTCAAT 57.204 42.857 0.00 0.00 30.60 2.57
175 176 4.908601 AGACAACATGACACCCTCAATA 57.091 40.909 0.00 0.00 30.60 1.90
176 177 4.579869 AGACAACATGACACCCTCAATAC 58.420 43.478 0.00 0.00 30.60 1.89
177 178 4.041567 AGACAACATGACACCCTCAATACA 59.958 41.667 0.00 0.00 30.60 2.29
178 179 4.072131 ACAACATGACACCCTCAATACAC 58.928 43.478 0.00 0.00 30.60 2.90
179 180 4.071423 CAACATGACACCCTCAATACACA 58.929 43.478 0.00 0.00 30.60 3.72
180 181 4.574674 ACATGACACCCTCAATACACAT 57.425 40.909 0.00 0.00 30.60 3.21
181 182 4.517285 ACATGACACCCTCAATACACATC 58.483 43.478 0.00 0.00 30.60 3.06
196 197 7.869429 TCAATACACATCACATAGCTATCACAG 59.131 37.037 2.34 0.00 0.00 3.66
223 224 1.275856 GAGGAGGCCATGCTATCTCAG 59.724 57.143 5.01 0.00 0.00 3.35
224 225 1.055040 GGAGGCCATGCTATCTCAGT 58.945 55.000 5.01 0.00 0.00 3.41
268 1939 5.172205 GTTGTGCAAAAGGGTCAGTTTTTA 58.828 37.500 0.00 0.00 0.00 1.52
302 1973 4.576216 TCGGCTTTTATTTTGTGCTGAA 57.424 36.364 0.00 0.00 36.29 3.02
307 1978 7.011857 TCGGCTTTTATTTTGTGCTGAATTTTT 59.988 29.630 0.00 0.00 36.29 1.94
310 1981 9.500864 GCTTTTATTTTGTGCTGAATTTTTGAA 57.499 25.926 0.00 0.00 0.00 2.69
317 1988 6.890663 TGTGCTGAATTTTTGAAAAGAGTG 57.109 33.333 0.00 0.00 0.00 3.51
542 2384 1.025812 TGTAGTTTTGCACCAACCCG 58.974 50.000 4.62 0.00 0.00 5.28
551 2397 4.130554 ACCAACCCGGCACAACCA 62.131 61.111 0.00 0.00 39.03 3.67
679 2531 3.322466 CGAACCACCTCCCTGCCT 61.322 66.667 0.00 0.00 0.00 4.75
789 2646 2.094675 CCACGGCTTGATTTTCCATCT 58.905 47.619 0.00 0.00 0.00 2.90
792 2649 2.025887 ACGGCTTGATTTTCCATCTCCT 60.026 45.455 0.00 0.00 0.00 3.69
798 2655 3.192944 TGATTTTCCATCTCCTCCCAGT 58.807 45.455 0.00 0.00 0.00 4.00
832 2692 4.033358 CGATCGAAATCCAGACAAGAAAGG 59.967 45.833 10.26 0.00 0.00 3.11
841 2701 1.705745 AGACAAGAAAGGGGTCCTTCC 59.294 52.381 0.00 0.00 43.92 3.46
842 2702 1.705745 GACAAGAAAGGGGTCCTTCCT 59.294 52.381 0.00 0.00 43.92 3.36
870 2730 1.753649 AGCTCGCACTCACACTCATAT 59.246 47.619 0.00 0.00 0.00 1.78
988 2852 1.068472 CACGTCCTTCTACAAGCGAGT 60.068 52.381 0.00 0.00 0.00 4.18
1004 2887 1.192428 GAGTGACCCATACTTCCGGT 58.808 55.000 0.00 0.00 0.00 5.28
1068 2952 3.409201 CATGAGCTGGTACATGGGG 57.591 57.895 0.00 0.00 39.79 4.96
1371 3264 2.056223 CCCCATCGAGGTGTACGGT 61.056 63.158 0.00 0.00 34.66 4.83
1775 3687 1.278172 CCGCGTCTTGTCTGTGTGAG 61.278 60.000 4.92 0.00 0.00 3.51
1776 3688 1.278172 CGCGTCTTGTCTGTGTGAGG 61.278 60.000 0.00 0.00 0.00 3.86
1778 3690 0.673985 CGTCTTGTCTGTGTGAGGGA 59.326 55.000 0.00 0.00 0.00 4.20
1783 3695 2.612285 TGTCTGTGTGAGGGAGAGAT 57.388 50.000 0.00 0.00 0.00 2.75
1862 3779 1.746787 TCGACGGCATGTACATGTACT 59.253 47.619 31.10 16.95 40.80 2.73
1967 3885 6.906659 AGAGTTCAATTTGTGCTCTGTATTG 58.093 36.000 17.79 0.00 35.48 1.90
1979 3899 3.563390 GCTCTGTATTGGCATCCTCTTTC 59.437 47.826 0.00 0.00 0.00 2.62
2002 3924 0.104120 TACATGCGGGATCTTCCACG 59.896 55.000 0.00 0.00 38.64 4.94
2008 3930 1.359848 CGGGATCTTCCACGAAGTTG 58.640 55.000 0.00 0.00 41.61 3.16
2018 3940 0.238289 CACGAAGTTGTGGTGCATCC 59.762 55.000 0.00 0.00 41.61 3.51
2019 3941 0.889186 ACGAAGTTGTGGTGCATCCC 60.889 55.000 0.00 0.00 37.78 3.85
2030 3952 1.300963 TGCATCCCCTGAGCACTTC 59.699 57.895 0.00 0.00 32.55 3.01
2034 3956 1.115467 ATCCCCTGAGCACTTCTACG 58.885 55.000 0.00 0.00 0.00 3.51
2058 3981 6.249893 CGTGCACTTTGATAATTGATGAACAG 59.750 38.462 16.19 0.00 0.00 3.16
2226 4150 9.785982 AAGAAACTTTGCTTAGTTCTCTATCTT 57.214 29.630 4.81 6.91 37.37 2.40
2255 6172 8.283992 TGAAAATTTTCATGACATTTGTGCATC 58.716 29.630 26.01 6.89 41.88 3.91
2262 6179 1.203052 GACATTTGTGCATCTGTGGGG 59.797 52.381 0.00 0.00 0.00 4.96
2268 6185 1.133513 TGTGCATCTGTGGGGAAAAGT 60.134 47.619 0.00 0.00 0.00 2.66
2269 6186 1.541588 GTGCATCTGTGGGGAAAAGTC 59.458 52.381 0.00 0.00 0.00 3.01
2270 6187 0.804989 GCATCTGTGGGGAAAAGTCG 59.195 55.000 0.00 0.00 0.00 4.18
2297 6215 4.616953 TCCGAAATGTTTTCAAAAGGAGC 58.383 39.130 1.40 0.00 0.00 4.70
2304 6222 6.976934 ATGTTTTCAAAAGGAGCCTTTCTA 57.023 33.333 14.43 3.95 44.50 2.10
2314 6232 3.715834 AGGAGCCTTTCTAGAGCATTGAT 59.284 43.478 5.37 0.00 0.00 2.57
2315 6233 4.165758 AGGAGCCTTTCTAGAGCATTGATT 59.834 41.667 5.37 0.00 0.00 2.57
2318 6236 6.205101 AGCCTTTCTAGAGCATTGATTTTG 57.795 37.500 5.37 0.00 0.00 2.44
2395 6317 6.089820 GCAGGTGTAACAATCATCAATGTTTG 59.910 38.462 10.72 10.72 40.14 2.93
2474 6397 2.945447 AATCCCAATGCATGTGAACG 57.055 45.000 0.00 0.00 0.00 3.95
2503 6426 3.616956 ACTCCATGTGTGTCGATCATT 57.383 42.857 0.00 0.00 0.00 2.57
2513 6436 5.637810 TGTGTGTCGATCATTTTCTTCTACC 59.362 40.000 0.00 0.00 0.00 3.18
2567 6546 4.349048 TCCCTACTAGCTGCATTGATGATT 59.651 41.667 1.02 0.00 0.00 2.57
2666 6647 6.156949 TCCTTGAATGGCTGAAATACTAGAGT 59.843 38.462 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.009631 TCAAATATGTCCACTTTCACCAGG 58.990 41.667 0.00 0.00 0.00 4.45
1 2 5.106157 GGTCAAATATGTCCACTTTCACCAG 60.106 44.000 0.00 0.00 35.17 4.00
2 3 4.764823 GGTCAAATATGTCCACTTTCACCA 59.235 41.667 0.00 0.00 35.17 4.17
3 4 4.157840 GGGTCAAATATGTCCACTTTCACC 59.842 45.833 0.00 0.00 36.59 4.02
4 5 5.010282 AGGGTCAAATATGTCCACTTTCAC 58.990 41.667 0.00 0.00 36.59 3.18
5 6 5.255397 AGGGTCAAATATGTCCACTTTCA 57.745 39.130 0.00 0.00 36.59 2.69
6 7 6.590234 AAAGGGTCAAATATGTCCACTTTC 57.410 37.500 0.00 0.00 36.59 2.62
7 8 6.994421 AAAAGGGTCAAATATGTCCACTTT 57.006 33.333 0.00 0.00 37.12 2.66
8 9 6.994421 AAAAAGGGTCAAATATGTCCACTT 57.006 33.333 0.00 0.00 36.59 3.16
9 10 7.466804 TCTAAAAAGGGTCAAATATGTCCACT 58.533 34.615 0.00 0.00 36.59 4.00
10 11 7.696992 TCTAAAAAGGGTCAAATATGTCCAC 57.303 36.000 0.00 0.00 36.59 4.02
11 12 8.713708 TTTCTAAAAAGGGTCAAATATGTCCA 57.286 30.769 0.00 0.00 36.59 4.02
17 18 9.705290 GCTGAAATTTCTAAAAAGGGTCAAATA 57.295 29.630 18.64 0.00 0.00 1.40
18 19 8.210265 TGCTGAAATTTCTAAAAAGGGTCAAAT 58.790 29.630 18.64 0.00 0.00 2.32
19 20 7.494298 GTGCTGAAATTTCTAAAAAGGGTCAAA 59.506 33.333 18.64 0.00 0.00 2.69
20 21 6.983890 GTGCTGAAATTTCTAAAAAGGGTCAA 59.016 34.615 18.64 0.00 0.00 3.18
21 22 6.097554 TGTGCTGAAATTTCTAAAAAGGGTCA 59.902 34.615 18.64 0.00 0.00 4.02
22 23 6.512297 TGTGCTGAAATTTCTAAAAAGGGTC 58.488 36.000 18.64 0.00 0.00 4.46
23 24 6.478512 TGTGCTGAAATTTCTAAAAAGGGT 57.521 33.333 18.64 0.00 0.00 4.34
24 25 7.967890 ATTGTGCTGAAATTTCTAAAAAGGG 57.032 32.000 18.64 1.58 0.00 3.95
30 31 9.781834 CGGTTTATATTGTGCTGAAATTTCTAA 57.218 29.630 18.64 7.16 0.00 2.10
31 32 8.402472 CCGGTTTATATTGTGCTGAAATTTCTA 58.598 33.333 18.64 5.16 0.00 2.10
32 33 7.122055 TCCGGTTTATATTGTGCTGAAATTTCT 59.878 33.333 18.64 0.00 0.00 2.52
33 34 7.254852 TCCGGTTTATATTGTGCTGAAATTTC 58.745 34.615 11.41 11.41 0.00 2.17
34 35 7.164230 TCCGGTTTATATTGTGCTGAAATTT 57.836 32.000 0.00 0.00 0.00 1.82
35 36 6.767524 TCCGGTTTATATTGTGCTGAAATT 57.232 33.333 0.00 0.00 0.00 1.82
36 37 6.772716 AGATCCGGTTTATATTGTGCTGAAAT 59.227 34.615 0.00 0.00 0.00 2.17
37 38 6.119536 AGATCCGGTTTATATTGTGCTGAAA 58.880 36.000 0.00 0.00 0.00 2.69
38 39 5.680619 AGATCCGGTTTATATTGTGCTGAA 58.319 37.500 0.00 0.00 0.00 3.02
39 40 5.290493 AGATCCGGTTTATATTGTGCTGA 57.710 39.130 0.00 0.00 0.00 4.26
40 41 7.490962 TTTAGATCCGGTTTATATTGTGCTG 57.509 36.000 0.00 0.00 0.00 4.41
41 42 8.514330 TTTTTAGATCCGGTTTATATTGTGCT 57.486 30.769 0.00 0.00 0.00 4.40
86 87 4.638421 CCCTAACGTCTGGCATCATAAAAA 59.362 41.667 0.00 0.00 0.00 1.94
87 88 4.196193 CCCTAACGTCTGGCATCATAAAA 58.804 43.478 0.00 0.00 0.00 1.52
88 89 3.804036 CCCTAACGTCTGGCATCATAAA 58.196 45.455 0.00 0.00 0.00 1.40
89 90 2.484770 GCCCTAACGTCTGGCATCATAA 60.485 50.000 15.65 0.00 44.70 1.90
90 91 1.070134 GCCCTAACGTCTGGCATCATA 59.930 52.381 15.65 0.00 44.70 2.15
91 92 0.179045 GCCCTAACGTCTGGCATCAT 60.179 55.000 15.65 0.00 44.70 2.45
92 93 1.220749 GCCCTAACGTCTGGCATCA 59.779 57.895 15.65 0.00 44.70 3.07
93 94 1.883084 CGCCCTAACGTCTGGCATC 60.883 63.158 19.14 3.86 45.63 3.91
94 95 2.186903 CGCCCTAACGTCTGGCAT 59.813 61.111 19.14 0.00 45.63 4.40
95 96 4.752879 GCGCCCTAACGTCTGGCA 62.753 66.667 19.14 0.00 45.63 4.92
97 98 4.077184 TGGCGCCCTAACGTCTGG 62.077 66.667 26.77 0.00 38.79 3.86
98 99 2.813908 GTGGCGCCCTAACGTCTG 60.814 66.667 26.77 0.00 38.79 3.51
99 100 2.995574 AGTGGCGCCCTAACGTCT 60.996 61.111 26.77 7.79 38.79 4.18
100 101 2.216750 TACAGTGGCGCCCTAACGTC 62.217 60.000 26.77 5.48 38.39 4.34
101 102 2.221906 CTACAGTGGCGCCCTAACGT 62.222 60.000 26.77 18.53 34.88 3.99
102 103 1.518572 CTACAGTGGCGCCCTAACG 60.519 63.158 26.77 13.88 0.00 3.18
103 104 0.464452 ATCTACAGTGGCGCCCTAAC 59.536 55.000 26.77 16.33 0.00 2.34
104 105 1.684983 GTATCTACAGTGGCGCCCTAA 59.315 52.381 26.77 1.08 0.00 2.69
105 106 1.325355 GTATCTACAGTGGCGCCCTA 58.675 55.000 26.77 2.06 0.00 3.53
106 107 1.400530 GGTATCTACAGTGGCGCCCT 61.401 60.000 26.77 18.07 0.00 5.19
107 108 1.069258 GGTATCTACAGTGGCGCCC 59.931 63.158 26.77 15.80 0.00 6.13
108 109 0.529992 GTGGTATCTACAGTGGCGCC 60.530 60.000 22.73 22.73 0.00 6.53
109 110 0.870307 CGTGGTATCTACAGTGGCGC 60.870 60.000 0.00 0.00 0.00 6.53
110 111 0.736636 TCGTGGTATCTACAGTGGCG 59.263 55.000 0.00 0.00 0.00 5.69
111 112 1.533338 CGTCGTGGTATCTACAGTGGC 60.533 57.143 0.00 0.00 0.00 5.01
112 113 1.533338 GCGTCGTGGTATCTACAGTGG 60.533 57.143 0.00 0.00 0.00 4.00
113 114 1.533338 GGCGTCGTGGTATCTACAGTG 60.533 57.143 0.00 0.00 0.00 3.66
114 115 0.737219 GGCGTCGTGGTATCTACAGT 59.263 55.000 0.00 0.00 0.00 3.55
115 116 1.022735 AGGCGTCGTGGTATCTACAG 58.977 55.000 0.00 0.00 0.00 2.74
116 117 1.133598 CAAGGCGTCGTGGTATCTACA 59.866 52.381 0.00 0.00 0.00 2.74
117 118 1.535437 CCAAGGCGTCGTGGTATCTAC 60.535 57.143 14.30 0.00 37.68 2.59
118 119 0.742505 CCAAGGCGTCGTGGTATCTA 59.257 55.000 14.30 0.00 37.68 1.98
119 120 1.515954 CCAAGGCGTCGTGGTATCT 59.484 57.895 14.30 0.00 37.68 1.98
120 121 4.104143 CCAAGGCGTCGTGGTATC 57.896 61.111 14.30 0.00 37.68 2.24
124 125 2.637025 CAAACCAAGGCGTCGTGG 59.363 61.111 20.85 20.85 46.01 4.94
125 126 1.841663 CTCCAAACCAAGGCGTCGTG 61.842 60.000 0.00 0.00 0.00 4.35
126 127 1.597027 CTCCAAACCAAGGCGTCGT 60.597 57.895 0.00 0.00 0.00 4.34
127 128 1.291877 CTCTCCAAACCAAGGCGTCG 61.292 60.000 0.00 0.00 0.00 5.12
128 129 0.250338 ACTCTCCAAACCAAGGCGTC 60.250 55.000 0.00 0.00 0.00 5.19
129 130 0.250338 GACTCTCCAAACCAAGGCGT 60.250 55.000 0.00 0.00 0.00 5.68
130 131 0.250295 TGACTCTCCAAACCAAGGCG 60.250 55.000 0.00 0.00 0.00 5.52
131 132 1.815003 CATGACTCTCCAAACCAAGGC 59.185 52.381 0.00 0.00 0.00 4.35
132 133 1.815003 GCATGACTCTCCAAACCAAGG 59.185 52.381 0.00 0.00 0.00 3.61
133 134 2.787994 AGCATGACTCTCCAAACCAAG 58.212 47.619 0.00 0.00 0.00 3.61
134 135 2.957402 AGCATGACTCTCCAAACCAA 57.043 45.000 0.00 0.00 0.00 3.67
135 136 3.055819 GTCTAGCATGACTCTCCAAACCA 60.056 47.826 0.00 0.00 34.39 3.67
136 137 3.055819 TGTCTAGCATGACTCTCCAAACC 60.056 47.826 0.00 0.00 37.79 3.27
137 138 4.193826 TGTCTAGCATGACTCTCCAAAC 57.806 45.455 0.00 0.00 37.79 2.93
138 139 4.040339 TGTTGTCTAGCATGACTCTCCAAA 59.960 41.667 0.00 0.00 37.79 3.28
139 140 3.578282 TGTTGTCTAGCATGACTCTCCAA 59.422 43.478 0.00 0.00 37.79 3.53
140 141 3.165071 TGTTGTCTAGCATGACTCTCCA 58.835 45.455 0.00 0.00 37.79 3.86
141 142 3.876274 TGTTGTCTAGCATGACTCTCC 57.124 47.619 0.00 0.00 37.79 3.71
142 143 5.003692 TCATGTTGTCTAGCATGACTCTC 57.996 43.478 0.00 2.81 45.71 3.20
148 149 2.679837 GGGTGTCATGTTGTCTAGCATG 59.320 50.000 0.00 2.59 44.16 4.06
149 150 2.573462 AGGGTGTCATGTTGTCTAGCAT 59.427 45.455 0.00 0.00 0.00 3.79
150 151 1.977854 AGGGTGTCATGTTGTCTAGCA 59.022 47.619 0.00 0.00 0.00 3.49
151 152 2.028112 TGAGGGTGTCATGTTGTCTAGC 60.028 50.000 0.00 0.00 0.00 3.42
152 153 3.961480 TGAGGGTGTCATGTTGTCTAG 57.039 47.619 0.00 0.00 0.00 2.43
153 154 4.908601 ATTGAGGGTGTCATGTTGTCTA 57.091 40.909 0.00 0.00 34.17 2.59
154 155 3.795688 ATTGAGGGTGTCATGTTGTCT 57.204 42.857 0.00 0.00 34.17 3.41
155 156 4.154195 GTGTATTGAGGGTGTCATGTTGTC 59.846 45.833 0.00 0.00 34.17 3.18
156 157 4.072131 GTGTATTGAGGGTGTCATGTTGT 58.928 43.478 0.00 0.00 34.17 3.32
157 158 4.071423 TGTGTATTGAGGGTGTCATGTTG 58.929 43.478 0.00 0.00 34.17 3.33
158 159 4.365514 TGTGTATTGAGGGTGTCATGTT 57.634 40.909 0.00 0.00 34.17 2.71
159 160 4.019411 TGATGTGTATTGAGGGTGTCATGT 60.019 41.667 0.00 0.00 34.17 3.21
160 161 4.333649 GTGATGTGTATTGAGGGTGTCATG 59.666 45.833 0.00 0.00 34.17 3.07
161 162 4.019411 TGTGATGTGTATTGAGGGTGTCAT 60.019 41.667 0.00 0.00 34.17 3.06
162 163 3.326297 TGTGATGTGTATTGAGGGTGTCA 59.674 43.478 0.00 0.00 0.00 3.58
163 164 3.937814 TGTGATGTGTATTGAGGGTGTC 58.062 45.455 0.00 0.00 0.00 3.67
164 165 4.574674 ATGTGATGTGTATTGAGGGTGT 57.425 40.909 0.00 0.00 0.00 4.16
165 166 4.512944 GCTATGTGATGTGTATTGAGGGTG 59.487 45.833 0.00 0.00 0.00 4.61
166 167 4.410228 AGCTATGTGATGTGTATTGAGGGT 59.590 41.667 0.00 0.00 0.00 4.34
167 168 4.965814 AGCTATGTGATGTGTATTGAGGG 58.034 43.478 0.00 0.00 0.00 4.30
168 169 7.330454 GTGATAGCTATGTGATGTGTATTGAGG 59.670 40.741 11.94 0.00 0.00 3.86
169 170 7.869429 TGTGATAGCTATGTGATGTGTATTGAG 59.131 37.037 11.94 0.00 0.00 3.02
170 171 7.725251 TGTGATAGCTATGTGATGTGTATTGA 58.275 34.615 11.94 0.00 0.00 2.57
171 172 7.951530 TGTGATAGCTATGTGATGTGTATTG 57.048 36.000 11.94 0.00 0.00 1.90
196 197 1.453762 GCATGGCCTCCTCTTGATGC 61.454 60.000 3.32 4.25 34.21 3.91
207 208 3.260380 GTCATACTGAGATAGCATGGCCT 59.740 47.826 3.32 0.00 30.05 5.19
208 209 3.594134 GTCATACTGAGATAGCATGGCC 58.406 50.000 0.00 0.00 30.05 5.36
223 224 1.113517 TCTGGGCTAGGGCGTCATAC 61.114 60.000 0.00 0.00 39.81 2.39
224 225 1.113517 GTCTGGGCTAGGGCGTCATA 61.114 60.000 0.00 0.00 39.81 2.15
268 1939 8.831715 AAATAAAAGCCGATCTGAAACAATTT 57.168 26.923 0.00 0.00 0.00 1.82
302 1973 9.874205 TGAACAGATTTCACTCTTTTCAAAAAT 57.126 25.926 1.34 0.00 38.40 1.82
307 1978 9.950680 GTAAATGAACAGATTTCACTCTTTTCA 57.049 29.630 5.45 5.45 42.79 2.69
310 1981 9.125026 AGTGTAAATGAACAGATTTCACTCTTT 57.875 29.630 0.00 0.00 33.35 2.52
317 1988 7.040409 AGGTTCCAGTGTAAATGAACAGATTTC 60.040 37.037 10.21 0.00 30.28 2.17
332 2159 0.395586 TGCTTTGCAGGTTCCAGTGT 60.396 50.000 0.00 0.00 33.32 3.55
542 2384 1.683917 TGTTGGTTGTATGGTTGTGCC 59.316 47.619 0.00 0.00 37.90 5.01
551 2397 1.606668 CCACGCACTTGTTGGTTGTAT 59.393 47.619 0.00 0.00 0.00 2.29
763 2620 2.198827 AAATCAAGCCGTGGTGATGA 57.801 45.000 0.00 0.00 34.70 2.92
789 2646 3.591977 TCGGATAGATATCACTGGGAGGA 59.408 47.826 5.32 0.00 34.40 3.71
792 2649 4.080526 TCGATCGGATAGATATCACTGGGA 60.081 45.833 16.41 0.00 40.26 4.37
798 2655 6.828785 TCTGGATTTCGATCGGATAGATATCA 59.171 38.462 22.63 13.45 40.26 2.15
832 2692 0.747852 CTAGAGCGAAGGAAGGACCC 59.252 60.000 0.00 0.00 40.05 4.46
870 2730 2.218603 GTTCGGAAAAGTTGAGGCTCA 58.781 47.619 14.43 14.43 0.00 4.26
906 2766 2.542178 CGCGCTGCACTTTATATACCAA 59.458 45.455 5.56 0.00 0.00 3.67
988 2852 1.195442 TGCACCGGAAGTATGGGTCA 61.195 55.000 9.46 0.00 29.82 4.02
1167 3051 4.654412 AGCGCGGCGAGGATGATC 62.654 66.667 28.54 5.33 0.00 2.92
1319 3212 4.416738 GCTTCTTGAGCCCGCCCT 62.417 66.667 0.00 0.00 46.01 5.19
1764 3676 2.612285 ATCTCTCCCTCACACAGACA 57.388 50.000 0.00 0.00 0.00 3.41
1882 3799 2.066262 ACGGAACAGCGACAAATAGTG 58.934 47.619 0.00 0.00 0.00 2.74
1952 3870 2.754552 GGATGCCAATACAGAGCACAAA 59.245 45.455 0.00 0.00 39.77 2.83
1967 3885 3.065925 GCATGTACAAGAAAGAGGATGCC 59.934 47.826 0.00 0.00 30.90 4.40
1979 3899 2.213499 GGAAGATCCCGCATGTACAAG 58.787 52.381 0.00 0.00 0.00 3.16
2002 3924 0.251341 AGGGGATGCACCACAACTTC 60.251 55.000 9.77 0.00 46.31 3.01
2008 3930 2.439156 GCTCAGGGGATGCACCAC 60.439 66.667 7.49 3.88 43.70 4.16
2018 3940 3.425578 CACGTAGAAGTGCTCAGGG 57.574 57.895 0.00 0.00 35.17 4.45
2030 3952 7.003939 TCATCAATTATCAAAGTGCACGTAG 57.996 36.000 12.01 5.14 30.81 3.51
2034 3956 7.307694 TCTGTTCATCAATTATCAAAGTGCAC 58.692 34.615 9.40 9.40 30.81 4.57
2082 4005 9.256477 GGAAAACTTTTGATATCGGTTCTTTTT 57.744 29.630 0.00 0.21 0.00 1.94
2085 4008 7.761038 AGGAAAACTTTTGATATCGGTTCTT 57.239 32.000 0.00 0.26 0.00 2.52
2089 4012 8.053355 AGGATTAGGAAAACTTTTGATATCGGT 58.947 33.333 0.00 0.00 0.00 4.69
2242 6157 1.203052 CCCCACAGATGCACAAATGTC 59.797 52.381 0.00 0.00 0.00 3.06
2252 6167 1.271379 ACCGACTTTTCCCCACAGATG 60.271 52.381 0.00 0.00 0.00 2.90
2255 6172 1.346722 AGTACCGACTTTTCCCCACAG 59.653 52.381 0.00 0.00 28.61 3.66
2270 6187 5.918576 CCTTTTGAAAACATTTCGGAGTACC 59.081 40.000 0.00 0.00 0.00 3.34
2278 6196 6.763135 AGAAAGGCTCCTTTTGAAAACATTTC 59.237 34.615 14.46 7.56 45.16 2.17
2284 6202 5.241728 GCTCTAGAAAGGCTCCTTTTGAAAA 59.758 40.000 14.46 0.00 45.16 2.29
2288 6206 3.679389 TGCTCTAGAAAGGCTCCTTTTG 58.321 45.455 14.46 8.80 45.16 2.44
2297 6215 8.822652 AAAACAAAATCAATGCTCTAGAAAGG 57.177 30.769 0.00 0.00 0.00 3.11
2331 6249 4.216257 GGAATGGTATTGATTGATGTCCGG 59.784 45.833 0.00 0.00 0.00 5.14
2333 6251 6.491062 TGATGGAATGGTATTGATTGATGTCC 59.509 38.462 0.00 0.00 0.00 4.02
2474 6397 3.929610 GACACACATGGAGTTTCTAGCTC 59.070 47.826 0.00 0.00 0.00 4.09
2503 6426 3.263425 AGAAATGGGCTCGGTAGAAGAAA 59.737 43.478 0.00 0.00 0.00 2.52
2513 6436 1.740025 GTCCAAAGAGAAATGGGCTCG 59.260 52.381 0.00 0.00 38.31 5.03
2546 6469 5.761726 TCAAATCATCAATGCAGCTAGTAGG 59.238 40.000 0.00 0.00 0.00 3.18
2567 6546 7.216494 TGAATTATGTTGAGGATCGCTATCAA 58.784 34.615 0.17 0.00 38.61 2.57
2709 6690 3.063045 GTGGAAATAACCATCGAACCGAC 59.937 47.826 0.00 0.00 42.17 4.79


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

AutoCloner maintained by Alex Coulton.