Multiple sequence alignment - TraesCS1D01G408400

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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 TraesCS1D01G408400 chr1D 100.000 2954 0 0 1 2954 470734490 470731537 0.000000e+00 5456.0
1 TraesCS1D01G408400 chr1A 90.571 2153 127 30 73 2194 564397750 564395643 0.000000e+00 2782.0
2 TraesCS1D01G408400 chr1A 90.712 646 37 8 2309 2953 564395653 564395030 0.000000e+00 839.0
3 TraesCS1D01G408400 chr1B 89.486 2102 118 45 1 2061 654032245 654030206 0.000000e+00 2562.0
4 TraesCS1D01G408400 chr1B 89.773 528 34 8 2277 2799 654030090 654029578 0.000000e+00 658.0
5 TraesCS1D01G408400 chr3B 87.919 149 18 0 2778 2926 763531062 763530914 3.030000e-40 176.0
6 TraesCS1D01G408400 chrUn 92.593 54 4 0 2778 2831 287140620 287140567 8.780000e-11 78.7
7 TraesCS1D01G408400 chrUn 92.593 54 4 0 2778 2831 287146788 287146735 8.780000e-11 78.7
8 TraesCS1D01G408400 chrUn 94.118 51 3 0 2778 2828 293606177 293606227 8.780000e-11 78.7


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 TraesCS1D01G408400 chr1D 470731537 470734490 2953 True 5456.0 5456 100.0000 1 2954 1 chr1D.!!$R1 2953
1 TraesCS1D01G408400 chr1A 564395030 564397750 2720 True 1810.5 2782 90.6415 73 2953 2 chr1A.!!$R1 2880
2 TraesCS1D01G408400 chr1B 654029578 654032245 2667 True 1610.0 2562 89.6295 1 2799 2 chr1B.!!$R1 2798

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
195 199 0.187361 CCCACCCAAAAGACTTCCCA 59.813 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 2185 1.08992 GCATCCACAAATCAGCGAGT 58.91 50.0 0.0 0.0 0.0 4.18 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
33 34 1.663702 CACCGCTCGAAAACGACCT 60.664 57.895 3.94 0.00 0.00 3.85
55 58 2.276430 GCGCGTGTTATCGTTGCC 60.276 61.111 8.43 0.00 0.00 4.52
67 70 0.250295 TCGTTGCCCTGTCTTCCTTG 60.250 55.000 0.00 0.00 0.00 3.61
68 71 0.535102 CGTTGCCCTGTCTTCCTTGT 60.535 55.000 0.00 0.00 0.00 3.16
69 72 1.270625 CGTTGCCCTGTCTTCCTTGTA 60.271 52.381 0.00 0.00 0.00 2.41
70 73 2.152016 GTTGCCCTGTCTTCCTTGTAC 58.848 52.381 0.00 0.00 0.00 2.90
71 74 1.429930 TGCCCTGTCTTCCTTGTACA 58.570 50.000 0.00 0.00 0.00 2.90
75 78 2.609737 CCCTGTCTTCCTTGTACACGAC 60.610 54.545 0.00 1.89 0.00 4.34
168 171 2.631428 CATAAATCACGCCGCCCG 59.369 61.111 0.00 0.00 44.21 6.13
191 195 2.748465 CGAAGACCCACCCAAAAGACTT 60.748 50.000 0.00 0.00 0.00 3.01
192 196 2.658807 AGACCCACCCAAAAGACTTC 57.341 50.000 0.00 0.00 0.00 3.01
193 197 1.145119 AGACCCACCCAAAAGACTTCC 59.855 52.381 0.00 0.00 0.00 3.46
195 199 0.187361 CCCACCCAAAAGACTTCCCA 59.813 55.000 0.00 0.00 0.00 4.37
199 203 1.063266 ACCCAAAAGACTTCCCAAGCA 60.063 47.619 0.00 0.00 0.00 3.91
201 205 2.031120 CCAAAAGACTTCCCAAGCACA 58.969 47.619 0.00 0.00 0.00 4.57
202 206 2.035066 CCAAAAGACTTCCCAAGCACAG 59.965 50.000 0.00 0.00 0.00 3.66
203 207 1.322442 AAAGACTTCCCAAGCACAGC 58.678 50.000 0.00 0.00 0.00 4.40
204 208 0.538287 AAGACTTCCCAAGCACAGCC 60.538 55.000 0.00 0.00 0.00 4.85
205 209 2.281761 ACTTCCCAAGCACAGCCG 60.282 61.111 0.00 0.00 0.00 5.52
639 652 0.248843 CGCTCTCCTGCTTCTTCCTT 59.751 55.000 0.00 0.00 0.00 3.36
748 769 5.585500 TTTTTCGTTTTCATCGATCGTCT 57.415 34.783 15.94 0.69 37.18 4.18
749 770 6.693761 TTTTTCGTTTTCATCGATCGTCTA 57.306 33.333 15.94 0.00 37.18 2.59
750 771 5.675778 TTTCGTTTTCATCGATCGTCTAC 57.324 39.130 15.94 5.43 37.18 2.59
751 772 4.611310 TCGTTTTCATCGATCGTCTACT 57.389 40.909 15.94 0.00 32.30 2.57
821 847 4.885907 TCCCAATCTGCTCAAGATGATTTC 59.114 41.667 0.00 0.00 45.37 2.17
868 909 5.327616 TGGATGGTGTGATGCAATTTTAG 57.672 39.130 0.00 0.00 0.00 1.85
926 968 1.959747 CTGTCTCGTGCAAATGCTTG 58.040 50.000 6.97 0.00 42.66 4.01
935 977 2.699910 CAAATGCTTGCACGACGAC 58.300 52.632 0.00 0.00 0.00 4.34
936 978 1.054348 CAAATGCTTGCACGACGACG 61.054 55.000 5.58 5.58 45.75 5.12
988 1030 1.194781 TGGGAGTGAAGGAGGACTGC 61.195 60.000 0.00 0.00 0.00 4.40
1821 1872 2.444895 GACGGCCAGGAGGAGGAT 60.445 66.667 2.24 0.00 36.89 3.24
1982 2044 0.309612 GGTGTTCGTCAAAATGCGGT 59.690 50.000 0.00 0.00 0.00 5.68
2027 2090 8.723365 TGGTCATGTATTATTAGATTTCCTGGT 58.277 33.333 0.00 0.00 0.00 4.00
2050 2113 9.904198 TGGTCAAAATTCAATCTCTATGTCATA 57.096 29.630 0.00 0.00 0.00 2.15
2071 2134 8.643752 GTCATATTTTTAACCAACGATTTGTGG 58.356 33.333 0.00 0.00 0.00 4.17
2073 2136 9.364989 CATATTTTTAACCAACGATTTGTGGAT 57.635 29.630 0.00 0.00 0.00 3.41
2074 2137 7.650834 ATTTTTAACCAACGATTTGTGGATG 57.349 32.000 0.00 0.00 0.00 3.51
2082 2145 5.446709 CAACGATTTGTGGATGCTATCATC 58.553 41.667 0.00 0.00 46.46 2.92
2105 2185 9.143631 CATCGATCATACTGTTATCATGCTTTA 57.856 33.333 0.00 0.00 0.00 1.85
2124 2204 1.089920 ACTCGCTGATTTGTGGATGC 58.910 50.000 0.00 0.00 0.00 3.91
2129 2209 3.561310 TCGCTGATTTGTGGATGCTATTC 59.439 43.478 0.00 0.00 0.00 1.75
2133 2213 5.163581 GCTGATTTGTGGATGCTATTCTTGT 60.164 40.000 0.00 0.00 0.00 3.16
2135 2215 7.230849 TGATTTGTGGATGCTATTCTTGTTT 57.769 32.000 0.00 0.00 0.00 2.83
2136 2216 8.347004 TGATTTGTGGATGCTATTCTTGTTTA 57.653 30.769 0.00 0.00 0.00 2.01
2139 2219 8.984891 TTTGTGGATGCTATTCTTGTTTATTG 57.015 30.769 0.00 0.00 0.00 1.90
2140 2220 7.701539 TGTGGATGCTATTCTTGTTTATTGT 57.298 32.000 0.00 0.00 0.00 2.71
2142 2222 8.028354 TGTGGATGCTATTCTTGTTTATTGTTG 58.972 33.333 0.00 0.00 0.00 3.33
2143 2223 8.243426 GTGGATGCTATTCTTGTTTATTGTTGA 58.757 33.333 0.00 0.00 0.00 3.18
2145 2225 9.241317 GGATGCTATTCTTGTTTATTGTTGATG 57.759 33.333 0.00 0.00 0.00 3.07
2146 2226 9.793252 GATGCTATTCTTGTTTATTGTTGATGT 57.207 29.630 0.00 0.00 0.00 3.06
2148 2228 9.624697 TGCTATTCTTGTTTATTGTTGATGTTC 57.375 29.630 0.00 0.00 0.00 3.18
2149 2229 9.624697 GCTATTCTTGTTTATTGTTGATGTTCA 57.375 29.630 0.00 0.00 0.00 3.18
2152 2232 8.627487 TTCTTGTTTATTGTTGATGTTCACAC 57.373 30.769 0.00 0.00 0.00 3.82
2157 2240 7.283354 TGTTTATTGTTGATGTTCACACCAGTA 59.717 33.333 0.00 0.00 0.00 2.74
2158 2241 7.809546 TTATTGTTGATGTTCACACCAGTAA 57.190 32.000 0.00 0.00 0.00 2.24
2166 2249 6.204688 TGATGTTCACACCAGTAATTCAGTTC 59.795 38.462 0.00 0.00 0.00 3.01
2172 2255 8.740123 TCACACCAGTAATTCAGTTCTTTTTA 57.260 30.769 0.00 0.00 0.00 1.52
2180 2263 9.403583 AGTAATTCAGTTCTTTTTACCAAGTGA 57.596 29.630 0.00 0.00 0.00 3.41
2185 2268 6.764560 TCAGTTCTTTTTACCAAGTGAGGTAC 59.235 38.462 0.00 0.00 43.57 3.34
2203 2286 5.990668 AGGTACTCTGATGAATTACCAACC 58.009 41.667 0.00 0.00 35.16 3.77
2204 2287 5.104485 AGGTACTCTGATGAATTACCAACCC 60.104 44.000 0.00 0.00 35.16 4.11
2205 2288 4.927267 ACTCTGATGAATTACCAACCCA 57.073 40.909 0.00 0.00 0.00 4.51
2206 2289 5.255397 ACTCTGATGAATTACCAACCCAA 57.745 39.130 0.00 0.00 0.00 4.12
2207 2290 5.256474 ACTCTGATGAATTACCAACCCAAG 58.744 41.667 0.00 0.00 0.00 3.61
2208 2291 5.014123 ACTCTGATGAATTACCAACCCAAGA 59.986 40.000 0.00 0.00 0.00 3.02
2209 2292 6.078456 TCTGATGAATTACCAACCCAAGAT 57.922 37.500 0.00 0.00 0.00 2.40
2210 2293 7.092444 ACTCTGATGAATTACCAACCCAAGATA 60.092 37.037 0.00 0.00 0.00 1.98
2211 2294 7.054124 TCTGATGAATTACCAACCCAAGATAC 58.946 38.462 0.00 0.00 0.00 2.24
2212 2295 6.726379 TGATGAATTACCAACCCAAGATACA 58.274 36.000 0.00 0.00 0.00 2.29
2213 2296 6.828273 TGATGAATTACCAACCCAAGATACAG 59.172 38.462 0.00 0.00 0.00 2.74
2214 2297 6.381498 TGAATTACCAACCCAAGATACAGA 57.619 37.500 0.00 0.00 0.00 3.41
2215 2298 6.969043 TGAATTACCAACCCAAGATACAGAT 58.031 36.000 0.00 0.00 0.00 2.90
2216 2299 7.410174 TGAATTACCAACCCAAGATACAGATT 58.590 34.615 0.00 0.00 0.00 2.40
2217 2300 7.556275 TGAATTACCAACCCAAGATACAGATTC 59.444 37.037 0.00 0.00 0.00 2.52
2218 2301 4.927267 ACCAACCCAAGATACAGATTCA 57.073 40.909 0.00 0.00 0.00 2.57
2219 2302 5.456921 ACCAACCCAAGATACAGATTCAT 57.543 39.130 0.00 0.00 0.00 2.57
2220 2303 6.575244 ACCAACCCAAGATACAGATTCATA 57.425 37.500 0.00 0.00 0.00 2.15
2221 2304 7.154191 ACCAACCCAAGATACAGATTCATAT 57.846 36.000 0.00 0.00 0.00 1.78
2250 2333 7.571798 GCCTTTTTACATTTGCATCTCCAAAAG 60.572 37.037 0.00 0.00 38.12 2.27
2252 2335 8.954950 TTTTTACATTTGCATCTCCAAAAGAA 57.045 26.923 0.00 0.00 38.12 2.52
2253 2336 8.954950 TTTTACATTTGCATCTCCAAAAGAAA 57.045 26.923 0.00 0.00 38.12 2.52
2254 2337 8.954950 TTTACATTTGCATCTCCAAAAGAAAA 57.045 26.923 0.00 0.00 38.12 2.29
2255 2338 6.849588 ACATTTGCATCTCCAAAAGAAAAC 57.150 33.333 0.00 0.00 38.12 2.43
2258 2341 5.350504 TTGCATCTCCAAAAGAAAACCAA 57.649 34.783 0.00 0.00 37.61 3.67
2260 2343 4.202243 TGCATCTCCAAAAGAAAACCAAGG 60.202 41.667 0.00 0.00 37.61 3.61
2261 2344 4.039124 GCATCTCCAAAAGAAAACCAAGGA 59.961 41.667 0.00 0.00 37.61 3.36
2262 2345 5.453198 GCATCTCCAAAAGAAAACCAAGGAA 60.453 40.000 0.00 0.00 37.61 3.36
2263 2346 5.852282 TCTCCAAAAGAAAACCAAGGAAG 57.148 39.130 0.00 0.00 0.00 3.46
2264 2347 5.269189 TCTCCAAAAGAAAACCAAGGAAGT 58.731 37.500 0.00 0.00 0.00 3.01
2265 2348 6.428295 TCTCCAAAAGAAAACCAAGGAAGTA 58.572 36.000 0.00 0.00 0.00 2.24
2266 2349 6.546034 TCTCCAAAAGAAAACCAAGGAAGTAG 59.454 38.462 0.00 0.00 0.00 2.57
2267 2350 5.068591 TCCAAAAGAAAACCAAGGAAGTAGC 59.931 40.000 0.00 0.00 0.00 3.58
2268 2351 5.163457 CCAAAAGAAAACCAAGGAAGTAGCA 60.163 40.000 0.00 0.00 0.00 3.49
2269 2352 5.774498 AAAGAAAACCAAGGAAGTAGCAG 57.226 39.130 0.00 0.00 0.00 4.24
2270 2353 4.439253 AGAAAACCAAGGAAGTAGCAGT 57.561 40.909 0.00 0.00 0.00 4.40
2271 2354 4.137543 AGAAAACCAAGGAAGTAGCAGTG 58.862 43.478 0.00 0.00 0.00 3.66
2272 2355 3.857157 AAACCAAGGAAGTAGCAGTGA 57.143 42.857 0.00 0.00 0.00 3.41
2273 2356 3.409026 AACCAAGGAAGTAGCAGTGAG 57.591 47.619 0.00 0.00 0.00 3.51
2274 2357 1.002544 ACCAAGGAAGTAGCAGTGAGC 59.997 52.381 0.00 0.00 46.19 4.26
2291 2374 3.605486 GTGAGCAAAAATTGAGACGATGC 59.395 43.478 0.00 0.00 0.00 3.91
2328 2412 6.556116 TCTTCTATTCAGATGATGGGATGTGA 59.444 38.462 0.00 0.00 31.78 3.58
2384 2468 4.890158 CTTGTAAAATTCCAAGGGCCTT 57.110 40.909 14.48 14.48 35.51 4.35
2386 2470 4.882842 TGTAAAATTCCAAGGGCCTTTC 57.117 40.909 18.16 0.00 0.00 2.62
2397 2481 2.338620 GCCTTTCGCCCAACCAAC 59.661 61.111 0.00 0.00 0.00 3.77
2398 2482 3.047735 CCTTTCGCCCAACCAACC 58.952 61.111 0.00 0.00 0.00 3.77
2399 2483 1.830408 CCTTTCGCCCAACCAACCA 60.830 57.895 0.00 0.00 0.00 3.67
2400 2484 1.184970 CCTTTCGCCCAACCAACCAT 61.185 55.000 0.00 0.00 0.00 3.55
2401 2485 0.038343 CTTTCGCCCAACCAACCATG 60.038 55.000 0.00 0.00 0.00 3.66
2402 2486 0.757188 TTTCGCCCAACCAACCATGT 60.757 50.000 0.00 0.00 0.00 3.21
2403 2487 1.459455 TTCGCCCAACCAACCATGTG 61.459 55.000 0.00 0.00 0.00 3.21
2404 2488 1.900981 CGCCCAACCAACCATGTGA 60.901 57.895 0.00 0.00 0.00 3.58
2405 2489 1.865788 CGCCCAACCAACCATGTGAG 61.866 60.000 0.00 0.00 0.00 3.51
2406 2490 0.539438 GCCCAACCAACCATGTGAGA 60.539 55.000 0.00 0.00 0.00 3.27
2407 2491 1.892329 GCCCAACCAACCATGTGAGAT 60.892 52.381 0.00 0.00 0.00 2.75
2514 2600 4.712337 TCTCCTTATCTCTTTCACTCCCAC 59.288 45.833 0.00 0.00 0.00 4.61
2602 2690 4.308458 CCAAGTGCCGTCCGGTGA 62.308 66.667 7.66 0.00 37.65 4.02
2737 2825 3.381272 GGTCTCACTCTCTCCATCTTGAG 59.619 52.174 0.00 0.00 33.26 3.02
2804 2892 9.847224 TCTGATGATAGATGTAGTAGTGTGTTA 57.153 33.333 0.00 0.00 0.00 2.41
2830 2918 9.806448 ATATCTGTCACTAGTTCTGATAGATGT 57.194 33.333 21.46 15.97 42.98 3.06
2861 2949 3.706389 TCCCTTCAGACTGGATGGATA 57.294 47.619 3.70 0.00 34.82 2.59
2871 2959 3.110705 ACTGGATGGATAGTGCAAGTCT 58.889 45.455 0.00 0.00 0.00 3.24
2926 3014 9.328721 GCAATAAAAATTTCATTGCTTTGGTAC 57.671 29.630 27.23 9.52 46.97 3.34
2938 3026 3.190327 TGCTTTGGTACGATGGAATGTTG 59.810 43.478 0.00 0.00 0.00 3.33
2946 3034 0.458669 GATGGAATGTTGCTGCTGGG 59.541 55.000 0.00 0.00 0.00 4.45
2953 3041 2.033141 TTGCTGCTGGGCTCTGAC 59.967 61.111 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 58 2.673833 GTCGTGTACAAGGAAGACAGG 58.326 52.381 8.98 0.00 0.00 4.00
67 70 0.782384 CTTGACTTGGCGTCGTGTAC 59.218 55.000 0.00 0.00 45.87 2.90
68 71 0.942410 GCTTGACTTGGCGTCGTGTA 60.942 55.000 0.00 0.00 45.87 2.90
69 72 2.244651 GCTTGACTTGGCGTCGTGT 61.245 57.895 0.00 0.00 45.87 4.49
70 73 2.551270 GCTTGACTTGGCGTCGTG 59.449 61.111 0.00 0.00 45.87 4.35
71 74 2.665185 GGCTTGACTTGGCGTCGT 60.665 61.111 0.00 0.00 45.87 4.34
139 142 2.023673 TGATTTATGGGGCGAGCAAAG 58.976 47.619 0.00 0.00 0.00 2.77
140 143 1.748493 GTGATTTATGGGGCGAGCAAA 59.252 47.619 0.00 0.00 0.00 3.68
141 144 1.388547 GTGATTTATGGGGCGAGCAA 58.611 50.000 0.00 0.00 0.00 3.91
168 171 1.524008 CTTTTGGGTGGGTCTTCGCC 61.524 60.000 0.00 0.00 36.62 5.54
171 174 2.658807 AGTCTTTTGGGTGGGTCTTC 57.341 50.000 0.00 0.00 0.00 2.87
195 199 4.087892 ATCTCGGCGGCTGTGCTT 62.088 61.111 7.21 0.00 34.52 3.91
378 391 3.766691 GTCTTCCACCGGCGGCTA 61.767 66.667 28.71 8.86 0.00 3.93
737 758 4.212425 AGCAGAGTAAGTAGACGATCGATG 59.788 45.833 24.34 0.00 0.00 3.84
746 767 8.372459 TGGAAAATTTACAGCAGAGTAAGTAGA 58.628 33.333 0.00 0.00 35.57 2.59
748 769 7.389607 GGTGGAAAATTTACAGCAGAGTAAGTA 59.610 37.037 14.59 0.00 35.57 2.24
749 770 6.206829 GGTGGAAAATTTACAGCAGAGTAAGT 59.793 38.462 14.59 0.00 35.57 2.24
750 771 6.612306 GGTGGAAAATTTACAGCAGAGTAAG 58.388 40.000 14.59 0.00 35.57 2.34
751 772 5.180492 CGGTGGAAAATTTACAGCAGAGTAA 59.820 40.000 18.71 0.00 33.18 2.24
821 847 2.168054 GTTCATCCCCAAACGACGG 58.832 57.895 0.00 0.00 0.00 4.79
868 909 0.313987 CAACTCCCGGCTCCAAAAAC 59.686 55.000 0.00 0.00 0.00 2.43
945 987 3.850173 TCCCCAACTAACCAAAGCTAGAT 59.150 43.478 0.00 0.00 0.00 1.98
957 999 2.638325 TCACTCCCAATCCCCAACTAA 58.362 47.619 0.00 0.00 0.00 2.24
988 1030 2.022195 CATGGCCATGACCTCTTCTTG 58.978 52.381 37.84 10.15 41.20 3.02
1560 1608 2.523507 CGCGATCTTGCTGCTCTGG 61.524 63.158 0.00 0.00 0.00 3.86
1650 1698 3.991536 GAGGAACAGCCGCTCGTCC 62.992 68.421 9.95 9.95 43.43 4.79
1821 1872 2.280797 GGCAGCACGTTGACCTCA 60.281 61.111 0.00 0.00 0.00 3.86
1947 1998 2.360852 CCTGCCCTGCCTCACTTG 60.361 66.667 0.00 0.00 0.00 3.16
1952 2003 2.360475 GAACACCTGCCCTGCCTC 60.360 66.667 0.00 0.00 0.00 4.70
1982 2044 4.610333 ACCATGAGATACATATCCCGCTA 58.390 43.478 0.00 0.00 37.46 4.26
1986 2048 6.305272 ACATGACCATGAGATACATATCCC 57.695 41.667 16.07 0.00 41.20 3.85
2018 2080 7.787623 AGAGATTGAATTTTGACCAGGAAAT 57.212 32.000 0.00 0.00 0.00 2.17
2050 2113 6.147000 GCATCCACAAATCGTTGGTTAAAAAT 59.853 34.615 0.00 0.00 39.22 1.82
2058 2121 3.627123 TGATAGCATCCACAAATCGTTGG 59.373 43.478 0.00 0.00 39.22 3.77
2063 2126 5.640783 TGATCGATGATAGCATCCACAAATC 59.359 40.000 15.07 10.43 46.55 2.17
2071 2134 9.179552 GATAACAGTATGATCGATGATAGCATC 57.820 37.037 11.01 11.01 42.86 3.91
2073 2136 8.055279 TGATAACAGTATGATCGATGATAGCA 57.945 34.615 0.54 0.00 39.69 3.49
2074 2137 8.966194 CATGATAACAGTATGATCGATGATAGC 58.034 37.037 0.54 0.00 39.69 2.97
2082 2145 8.526218 AGTAAAGCATGATAACAGTATGATCG 57.474 34.615 0.00 0.00 39.69 3.69
2086 2149 6.422100 AGCGAGTAAAGCATGATAACAGTATG 59.578 38.462 0.00 0.00 38.75 2.39
2090 2153 4.805719 TCAGCGAGTAAAGCATGATAACAG 59.194 41.667 0.00 0.00 37.01 3.16
2105 2185 1.089920 GCATCCACAAATCAGCGAGT 58.910 50.000 0.00 0.00 0.00 4.18
2129 2209 6.977502 TGGTGTGAACATCAACAATAAACAAG 59.022 34.615 0.00 0.00 33.38 3.16
2133 2213 6.707440 ACTGGTGTGAACATCAACAATAAA 57.293 33.333 0.00 0.00 36.41 1.40
2135 2215 7.994425 ATTACTGGTGTGAACATCAACAATA 57.006 32.000 0.00 0.00 36.41 1.90
2136 2216 6.899393 ATTACTGGTGTGAACATCAACAAT 57.101 33.333 0.00 0.00 36.41 2.71
2139 2219 6.017109 ACTGAATTACTGGTGTGAACATCAAC 60.017 38.462 0.00 0.00 36.41 3.18
2140 2220 6.061441 ACTGAATTACTGGTGTGAACATCAA 58.939 36.000 0.00 0.00 36.41 2.57
2142 2222 6.428159 AGAACTGAATTACTGGTGTGAACATC 59.572 38.462 0.00 0.00 0.00 3.06
2143 2223 6.299141 AGAACTGAATTACTGGTGTGAACAT 58.701 36.000 0.00 0.00 0.00 2.71
2145 2225 6.619801 AAGAACTGAATTACTGGTGTGAAC 57.380 37.500 0.00 0.00 0.00 3.18
2146 2226 7.639113 AAAAGAACTGAATTACTGGTGTGAA 57.361 32.000 0.00 0.00 0.00 3.18
2147 2227 7.639113 AAAAAGAACTGAATTACTGGTGTGA 57.361 32.000 0.00 0.00 0.00 3.58
2148 2228 7.860872 GGTAAAAAGAACTGAATTACTGGTGTG 59.139 37.037 0.00 0.00 0.00 3.82
2149 2229 7.558444 TGGTAAAAAGAACTGAATTACTGGTGT 59.442 33.333 0.00 0.00 0.00 4.16
2150 2230 7.936584 TGGTAAAAAGAACTGAATTACTGGTG 58.063 34.615 0.00 0.00 0.00 4.17
2152 2232 8.630037 ACTTGGTAAAAAGAACTGAATTACTGG 58.370 33.333 0.00 0.00 0.00 4.00
2157 2240 7.342026 ACCTCACTTGGTAAAAAGAACTGAATT 59.658 33.333 0.00 0.00 38.79 2.17
2158 2241 6.833933 ACCTCACTTGGTAAAAAGAACTGAAT 59.166 34.615 0.00 0.00 38.79 2.57
2166 2249 6.522054 TCAGAGTACCTCACTTGGTAAAAAG 58.478 40.000 0.00 0.00 43.36 2.27
2172 2255 3.779444 TCATCAGAGTACCTCACTTGGT 58.221 45.455 0.00 0.00 43.66 3.67
2180 2263 5.104485 GGGTTGGTAATTCATCAGAGTACCT 60.104 44.000 2.97 0.00 37.25 3.08
2185 2268 5.500234 TCTTGGGTTGGTAATTCATCAGAG 58.500 41.667 0.00 0.00 0.00 3.35
2188 2271 6.726379 TGTATCTTGGGTTGGTAATTCATCA 58.274 36.000 0.00 0.00 0.00 3.07
2194 2277 6.969043 TGAATCTGTATCTTGGGTTGGTAAT 58.031 36.000 0.00 0.00 0.00 1.89
2195 2278 6.381498 TGAATCTGTATCTTGGGTTGGTAA 57.619 37.500 0.00 0.00 0.00 2.85
2197 2280 4.927267 TGAATCTGTATCTTGGGTTGGT 57.073 40.909 0.00 0.00 0.00 3.67
2198 2281 7.456725 AGATATGAATCTGTATCTTGGGTTGG 58.543 38.462 3.91 0.00 41.08 3.77
2213 2296 8.758715 GCAAATGTAAAAAGGCAGATATGAATC 58.241 33.333 0.00 0.00 0.00 2.52
2214 2297 8.259411 TGCAAATGTAAAAAGGCAGATATGAAT 58.741 29.630 0.00 0.00 0.00 2.57
2215 2298 7.609960 TGCAAATGTAAAAAGGCAGATATGAA 58.390 30.769 0.00 0.00 0.00 2.57
2216 2299 7.167924 TGCAAATGTAAAAAGGCAGATATGA 57.832 32.000 0.00 0.00 0.00 2.15
2217 2300 7.924412 AGATGCAAATGTAAAAAGGCAGATATG 59.076 33.333 0.00 0.00 34.43 1.78
2218 2301 8.015185 AGATGCAAATGTAAAAAGGCAGATAT 57.985 30.769 0.00 0.00 34.43 1.63
2219 2302 7.408756 AGATGCAAATGTAAAAAGGCAGATA 57.591 32.000 0.00 0.00 34.43 1.98
2220 2303 6.290294 AGATGCAAATGTAAAAAGGCAGAT 57.710 33.333 0.00 0.00 34.43 2.90
2221 2304 5.336690 GGAGATGCAAATGTAAAAAGGCAGA 60.337 40.000 0.00 0.00 34.43 4.26
2227 2310 8.954950 TTCTTTTGGAGATGCAAATGTAAAAA 57.045 26.923 10.86 0.00 33.49 1.94
2250 2333 4.134563 TCACTGCTACTTCCTTGGTTTTC 58.865 43.478 0.00 0.00 0.00 2.29
2252 2335 3.744660 CTCACTGCTACTTCCTTGGTTT 58.255 45.455 0.00 0.00 0.00 3.27
2253 2336 2.551071 GCTCACTGCTACTTCCTTGGTT 60.551 50.000 0.00 0.00 38.95 3.67
2254 2337 1.002544 GCTCACTGCTACTTCCTTGGT 59.997 52.381 0.00 0.00 38.95 3.67
2255 2338 1.002430 TGCTCACTGCTACTTCCTTGG 59.998 52.381 0.00 0.00 43.37 3.61
2258 2341 3.492102 TTTTGCTCACTGCTACTTCCT 57.508 42.857 0.00 0.00 43.37 3.36
2260 2343 5.762045 TCAATTTTTGCTCACTGCTACTTC 58.238 37.500 0.00 0.00 43.37 3.01
2261 2344 5.532406 TCTCAATTTTTGCTCACTGCTACTT 59.468 36.000 0.00 0.00 43.37 2.24
2262 2345 5.049129 GTCTCAATTTTTGCTCACTGCTACT 60.049 40.000 0.00 0.00 43.37 2.57
2263 2346 5.149977 GTCTCAATTTTTGCTCACTGCTAC 58.850 41.667 0.00 0.00 43.37 3.58
2264 2347 4.083855 CGTCTCAATTTTTGCTCACTGCTA 60.084 41.667 0.00 0.00 43.37 3.49
2265 2348 3.304257 CGTCTCAATTTTTGCTCACTGCT 60.304 43.478 0.00 0.00 43.37 4.24
2266 2349 2.975851 CGTCTCAATTTTTGCTCACTGC 59.024 45.455 0.00 0.00 43.25 4.40
2267 2350 4.472691 TCGTCTCAATTTTTGCTCACTG 57.527 40.909 0.00 0.00 0.00 3.66
2268 2351 4.614535 GCATCGTCTCAATTTTTGCTCACT 60.615 41.667 0.00 0.00 0.00 3.41
2269 2352 3.605486 GCATCGTCTCAATTTTTGCTCAC 59.395 43.478 0.00 0.00 0.00 3.51
2270 2353 3.503363 AGCATCGTCTCAATTTTTGCTCA 59.497 39.130 0.00 0.00 34.02 4.26
2271 2354 3.850273 CAGCATCGTCTCAATTTTTGCTC 59.150 43.478 0.00 0.00 36.87 4.26
2272 2355 3.829948 CAGCATCGTCTCAATTTTTGCT 58.170 40.909 0.00 0.00 39.38 3.91
2273 2356 2.343544 GCAGCATCGTCTCAATTTTTGC 59.656 45.455 0.00 0.00 0.00 3.68
2274 2357 3.362831 GTGCAGCATCGTCTCAATTTTTG 59.637 43.478 0.00 0.00 0.00 2.44
2275 2358 3.004629 TGTGCAGCATCGTCTCAATTTTT 59.995 39.130 0.00 0.00 0.00 1.94
2291 2374 7.463485 ATCTGAATAGAAGATGCCATGTGCAG 61.463 42.308 13.20 0.00 44.88 4.41
2318 2401 6.519721 GCTGTCAGATTAGTATCACATCCCAT 60.520 42.308 3.32 0.00 32.95 4.00
2328 2412 4.202305 GCTCCTTGGCTGTCAGATTAGTAT 60.202 45.833 3.32 0.00 0.00 2.12
2367 2451 2.232696 GCGAAAGGCCCTTGGAATTTTA 59.767 45.455 0.00 0.00 34.80 1.52
2384 2468 1.152652 ACATGGTTGGTTGGGCGAA 60.153 52.632 0.00 0.00 0.00 4.70
2386 2470 1.865788 CTCACATGGTTGGTTGGGCG 61.866 60.000 0.00 0.00 0.00 6.13
2389 2473 3.056607 GGAAATCTCACATGGTTGGTTGG 60.057 47.826 0.00 0.00 0.00 3.77
2393 2477 2.756760 CCTGGAAATCTCACATGGTTGG 59.243 50.000 0.00 0.00 0.00 3.77
2394 2478 3.192001 CACCTGGAAATCTCACATGGTTG 59.808 47.826 0.00 0.00 0.00 3.77
2395 2479 3.181429 ACACCTGGAAATCTCACATGGTT 60.181 43.478 0.00 0.00 0.00 3.67
2396 2480 2.376518 ACACCTGGAAATCTCACATGGT 59.623 45.455 0.00 0.00 0.00 3.55
2397 2481 3.012518 GACACCTGGAAATCTCACATGG 58.987 50.000 0.00 0.00 0.00 3.66
2398 2482 3.688185 CAGACACCTGGAAATCTCACATG 59.312 47.826 0.00 0.00 36.77 3.21
2399 2483 3.328931 ACAGACACCTGGAAATCTCACAT 59.671 43.478 0.00 0.00 44.60 3.21
2400 2484 2.705658 ACAGACACCTGGAAATCTCACA 59.294 45.455 0.00 0.00 44.60 3.58
2401 2485 3.244215 TGACAGACACCTGGAAATCTCAC 60.244 47.826 0.00 0.00 44.60 3.51
2402 2486 2.972021 TGACAGACACCTGGAAATCTCA 59.028 45.455 0.00 0.00 44.60 3.27
2403 2487 3.594134 CTGACAGACACCTGGAAATCTC 58.406 50.000 0.00 0.00 44.60 2.75
2404 2488 2.304180 CCTGACAGACACCTGGAAATCT 59.696 50.000 3.32 0.00 44.60 2.40
2405 2489 2.039084 ACCTGACAGACACCTGGAAATC 59.961 50.000 3.32 0.00 44.60 2.17
2406 2490 2.057922 ACCTGACAGACACCTGGAAAT 58.942 47.619 3.32 0.00 44.60 2.17
2407 2491 1.507140 ACCTGACAGACACCTGGAAA 58.493 50.000 3.32 0.00 44.60 3.13
2458 2544 2.747855 GCACAGGGAAAGGCTCCG 60.748 66.667 0.00 0.00 46.51 4.63
2514 2600 3.314553 CATTCTTGCTGCTGAAGGTTTG 58.685 45.455 0.00 0.00 0.00 2.93
2550 2638 1.439644 CGCCTGGAGAAGTCCTAGC 59.560 63.158 0.00 0.00 44.30 3.42
2655 2743 4.269523 TTGGTGGCCGCAGAAGCT 62.270 61.111 19.98 0.00 39.10 3.74
2679 2767 1.536662 ACGGAAGGGCCTGAGAACT 60.537 57.895 6.92 0.00 0.00 3.01
2682 2770 1.984570 CTCACGGAAGGGCCTGAGA 60.985 63.158 6.92 0.00 40.99 3.27
2737 2825 5.813080 AATTTATTACTGCACGGAAGGTC 57.187 39.130 0.00 0.00 0.00 3.85
2775 2863 7.001073 ACACTACTACATCTATCATCAGAGCA 58.999 38.462 0.00 0.00 0.00 4.26
2804 2892 9.806448 ACATCTATCAGAACTAGTGACAGATAT 57.194 33.333 0.00 0.00 36.29 1.63
2830 2918 4.523173 CAGTCTGAAGGGAACACACTACTA 59.477 45.833 0.00 0.00 0.00 1.82
2861 2949 5.016173 AGAGATGACTTCTAGACTTGCACT 58.984 41.667 0.00 0.00 33.74 4.40
2871 2959 4.081420 GCTTCAACCCAGAGATGACTTCTA 60.081 45.833 0.00 0.00 33.74 2.10
2923 3011 2.009774 AGCAGCAACATTCCATCGTAC 58.990 47.619 0.00 0.00 0.00 3.67
2926 3014 0.099968 CCAGCAGCAACATTCCATCG 59.900 55.000 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.