Multiple sequence alignment - TraesCS5A01G165300

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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 TraesCS5A01G165300 chr5A 100.000 4007 0 0 1 4007 353864003 353859997 0.000000e+00 7400
1 TraesCS5A01G165300 chr5D 91.759 1808 75 37 750 2539 266747996 266749747 0.000000e+00 2446
2 TraesCS5A01G165300 chr5D 90.022 1353 79 24 2537 3859 266749828 266751154 0.000000e+00 1700
3 TraesCS5A01G165300 chr5D 91.522 519 36 6 1 514 266741767 266742282 0.000000e+00 708
4 TraesCS5A01G165300 chr5D 87.421 159 14 4 526 682 266742264 266742418 1.140000e-40 178
5 TraesCS5A01G165300 chr5D 100.000 57 0 0 680 736 266742455 266742511 5.480000e-19 106
6 TraesCS5A01G165300 chr5B 88.283 1485 90 39 2537 3998 300378138 300379561 0.000000e+00 1701
7 TraesCS5A01G165300 chr5B 93.176 806 32 16 680 1478 300376385 300377174 0.000000e+00 1162
8 TraesCS5A01G165300 chr5B 95.113 573 16 5 1522 2091 300377181 300377744 0.000000e+00 893
9 TraesCS5A01G165300 chr5B 90.751 519 40 8 1 514 300375698 300376213 0.000000e+00 686
10 TraesCS5A01G165300 chr5B 89.355 310 20 8 2232 2539 300377760 300378058 1.050000e-100 377
11 TraesCS5A01G165300 chr7A 94.400 125 7 0 2109 2233 105313727 105313851 4.090000e-45 193
12 TraesCS5A01G165300 chr7A 89.147 129 11 3 3320 3446 732094364 732094491 1.490000e-34 158
13 TraesCS5A01G165300 chr7A 88.550 131 12 3 3318 3446 723356046 723355917 5.360000e-34 156
14 TraesCS5A01G165300 chr6A 94.400 125 7 0 2109 2233 147303784 147303660 4.090000e-45 193
15 TraesCS5A01G165300 chr3A 93.023 129 9 0 2106 2234 607108055 607108183 5.290000e-44 189
16 TraesCS5A01G165300 chr3A 89.062 128 12 2 3321 3446 323103773 323103900 1.490000e-34 158
17 TraesCS5A01G165300 chr2A 95.000 120 6 0 2114 2233 78845570 78845689 5.290000e-44 189
18 TraesCS5A01G165300 chr2A 88.889 126 13 1 3321 3446 537476711 537476587 1.930000e-33 154
19 TraesCS5A01G165300 chr7B 92.424 132 9 1 2111 2242 81425110 81424980 1.900000e-43 187
20 TraesCS5A01G165300 chr2B 91.791 134 10 1 2109 2242 643184611 643184743 6.840000e-43 185
21 TraesCS5A01G165300 chr6D 94.215 121 6 1 2114 2234 17055122 17055003 2.460000e-42 183
22 TraesCS5A01G165300 chr3D 90.647 139 11 2 2106 2244 609106184 609106320 2.460000e-42 183
23 TraesCS5A01G165300 chr1D 90.141 142 12 2 2101 2242 116548470 116548331 2.460000e-42 183
24 TraesCS5A01G165300 chr1D 88.889 126 13 1 3322 3446 493673824 493673699 1.930000e-33 154
25 TraesCS5A01G165300 chrUn 88.550 131 13 2 3317 3446 30689426 30689297 1.490000e-34 158
26 TraesCS5A01G165300 chr1A 88.462 130 13 2 3319 3446 290344234 290344363 5.360000e-34 156
27 TraesCS5A01G165300 chr4B 88.095 126 12 3 3323 3446 207094040 207093916 3.230000e-31 147


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 TraesCS5A01G165300 chr5A 353859997 353864003 4006 True 7400.000000 7400 100.0000 1 4007 1 chr5A.!!$R1 4006
1 TraesCS5A01G165300 chr5D 266747996 266751154 3158 False 2073.000000 2446 90.8905 750 3859 2 chr5D.!!$F2 3109
2 TraesCS5A01G165300 chr5D 266741767 266742511 744 False 330.666667 708 92.9810 1 736 3 chr5D.!!$F1 735
3 TraesCS5A01G165300 chr5B 300375698 300379561 3863 False 963.800000 1701 91.3356 1 3998 5 chr5B.!!$F1 3997

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
208 210 0.036022 GCTTCTGGTTCACTGGCTCT 59.964 55.0 0.00 0.00 0.00 4.09 F
668 674 0.465824 TGGAGCTCGAGTAGTAGCCC 60.466 60.0 15.13 5.72 39.64 5.19 F
736 782 1.078759 GAGATGACGCTGGGTGTTCG 61.079 60.0 0.70 0.00 0.00 3.95 F
2135 2300 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.0 0.00 0.00 0.00 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1544 0.110056 GCACGGACATGCAAAGACAG 60.110 55.0 0.00 0.0 45.39 3.51 R
2117 2282 0.320697 ACTTTTTCGGACGGAGGGAG 59.679 55.0 0.00 0.0 0.00 4.30 R
2303 2468 0.401356 ACTGTGTGGCATCATGACCA 59.599 50.0 0.00 0.0 0.00 4.02 R
3928 4227 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.0 4.96 0.0 31.08 2.90 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
44 45 1.195448 GATCATATGTTTCCTGCGCCG 59.805 52.381 4.18 0.00 0.00 6.46
208 210 0.036022 GCTTCTGGTTCACTGGCTCT 59.964 55.000 0.00 0.00 0.00 4.09
213 215 0.843309 TGGTTCACTGGCTCTTTCCA 59.157 50.000 0.00 0.00 34.42 3.53
214 216 1.214175 TGGTTCACTGGCTCTTTCCAA 59.786 47.619 0.00 0.00 35.36 3.53
567 572 4.090090 AGGACGAAGGGGATAGATATGTG 58.910 47.826 0.00 0.00 0.00 3.21
575 580 7.878127 CGAAGGGGATAGATATGTGTAAAACAT 59.122 37.037 0.00 0.00 44.51 2.71
603 609 2.144482 GCATTGCCAATGGTATGCTC 57.856 50.000 24.25 6.41 38.69 4.26
609 615 1.136891 GCCAATGGTATGCTCCAAACC 59.863 52.381 0.00 0.00 41.09 3.27
611 617 3.897239 CCAATGGTATGCTCCAAACCTA 58.103 45.455 0.00 0.00 41.09 3.08
633 639 1.274184 TGCCCCACTATCCAACTAGGT 60.274 52.381 0.00 0.00 39.02 3.08
634 640 1.141053 GCCCCACTATCCAACTAGGTG 59.859 57.143 0.00 0.00 39.02 4.00
635 641 1.768870 CCCCACTATCCAACTAGGTGG 59.231 57.143 21.74 21.74 44.77 4.61
636 642 1.141053 CCCACTATCCAACTAGGTGGC 59.859 57.143 22.94 0.00 44.09 5.01
637 643 2.119495 CCACTATCCAACTAGGTGGCT 58.881 52.381 22.94 15.68 40.44 4.75
638 644 2.103263 CCACTATCCAACTAGGTGGCTC 59.897 54.545 22.94 0.00 40.44 4.70
644 650 1.971357 CCAACTAGGTGGCTCGGATAT 59.029 52.381 15.42 0.00 0.00 1.63
668 674 0.465824 TGGAGCTCGAGTAGTAGCCC 60.466 60.000 15.13 5.72 39.64 5.19
736 782 1.078759 GAGATGACGCTGGGTGTTCG 61.079 60.000 0.70 0.00 0.00 3.95
745 791 4.340246 GGGTGTTCGGGTGGGGAC 62.340 72.222 0.00 0.00 0.00 4.46
768 814 7.016153 ACCTAAAAATATGACACAGGTGAGA 57.984 36.000 6.40 0.00 33.73 3.27
803 849 3.046374 AGCCTCAATTTAGGGTATCGGT 58.954 45.455 8.63 0.00 45.47 4.69
806 857 4.632153 CCTCAATTTAGGGTATCGGTGAG 58.368 47.826 0.00 0.00 32.55 3.51
840 891 9.603921 CAAACCAATGCCTCATTATTTTTCTAT 57.396 29.630 0.00 0.00 32.35 1.98
989 1048 1.316651 GTCCTCCTAATCGTACGGCT 58.683 55.000 16.52 5.32 0.00 5.52
1215 1274 2.726351 GCGCACCCTAGCCTCTCTT 61.726 63.158 0.30 0.00 0.00 2.85
1290 1349 2.203938 TCCTGGTCCCTCGCCTTT 60.204 61.111 0.00 0.00 0.00 3.11
1402 1461 1.372997 AACTATGCCGCGCTATCCG 60.373 57.895 5.56 0.00 40.75 4.18
1482 1543 4.435651 CCTGCCTTCGTTTCGTTATCTTTC 60.436 45.833 0.00 0.00 0.00 2.62
1483 1544 3.434299 TGCCTTCGTTTCGTTATCTTTCC 59.566 43.478 0.00 0.00 0.00 3.13
1517 1578 2.165301 GTGCGTGCGGATGGAGTAC 61.165 63.158 0.00 0.00 0.00 2.73
1524 1588 1.828595 TGCGGATGGAGTACTAAAGCA 59.171 47.619 0.00 0.00 0.00 3.91
1923 1993 2.624364 TGAACAGAGCAACGTACAGGTA 59.376 45.455 0.00 0.00 0.00 3.08
1924 1994 3.068448 TGAACAGAGCAACGTACAGGTAA 59.932 43.478 0.00 0.00 0.00 2.85
1927 1997 3.257375 ACAGAGCAACGTACAGGTAATGA 59.743 43.478 0.00 0.00 0.00 2.57
1935 2005 6.293244 GCAACGTACAGGTAATGAAAGACTTT 60.293 38.462 0.00 0.00 0.00 2.66
1982 2052 4.275662 TGACGTGTTTGCTTCGTTAATTG 58.724 39.130 0.00 0.00 37.92 2.32
1989 2059 4.560136 TTGCTTCGTTAATTGTTCAGCA 57.440 36.364 0.00 0.00 34.04 4.41
2117 2282 9.769093 GTTGTTCAACTTGGTCATAATGTATAC 57.231 33.333 8.23 0.00 0.00 1.47
2119 2284 9.378551 TGTTCAACTTGGTCATAATGTATACTC 57.621 33.333 4.17 0.00 0.00 2.59
2120 2285 8.827677 GTTCAACTTGGTCATAATGTATACTCC 58.172 37.037 4.17 0.00 0.00 3.85
2121 2286 7.506114 TCAACTTGGTCATAATGTATACTCCC 58.494 38.462 4.17 0.00 0.00 4.30
2122 2287 7.347222 TCAACTTGGTCATAATGTATACTCCCT 59.653 37.037 4.17 0.00 0.00 4.20
2123 2288 7.304497 ACTTGGTCATAATGTATACTCCCTC 57.696 40.000 4.17 0.00 0.00 4.30
2124 2289 6.270231 ACTTGGTCATAATGTATACTCCCTCC 59.730 42.308 4.17 0.00 0.00 4.30
2125 2290 4.770531 TGGTCATAATGTATACTCCCTCCG 59.229 45.833 4.17 0.00 0.00 4.63
2126 2291 4.771054 GGTCATAATGTATACTCCCTCCGT 59.229 45.833 4.17 0.00 0.00 4.69
2127 2292 5.105837 GGTCATAATGTATACTCCCTCCGTC 60.106 48.000 4.17 0.00 0.00 4.79
2128 2293 5.014858 TCATAATGTATACTCCCTCCGTCC 58.985 45.833 4.17 0.00 0.00 4.79
2129 2294 1.906990 ATGTATACTCCCTCCGTCCG 58.093 55.000 4.17 0.00 0.00 4.79
2130 2295 0.839277 TGTATACTCCCTCCGTCCGA 59.161 55.000 4.17 0.00 0.00 4.55
2131 2296 1.212688 TGTATACTCCCTCCGTCCGAA 59.787 52.381 4.17 0.00 0.00 4.30
2132 2297 2.301346 GTATACTCCCTCCGTCCGAAA 58.699 52.381 0.00 0.00 0.00 3.46
2133 2298 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2134 2299 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
2135 2300 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
2136 2301 0.320697 CTCCCTCCGTCCGAAAAAGT 59.679 55.000 0.00 0.00 0.00 2.66
2137 2302 0.760572 TCCCTCCGTCCGAAAAAGTT 59.239 50.000 0.00 0.00 0.00 2.66
2138 2303 1.141455 TCCCTCCGTCCGAAAAAGTTT 59.859 47.619 0.00 0.00 0.00 2.66
2139 2304 1.265905 CCCTCCGTCCGAAAAAGTTTG 59.734 52.381 0.00 0.00 0.00 2.93
2140 2305 1.944709 CCTCCGTCCGAAAAAGTTTGT 59.055 47.619 0.00 0.00 0.00 2.83
2141 2306 2.032290 CCTCCGTCCGAAAAAGTTTGTC 60.032 50.000 0.00 0.00 0.00 3.18
2142 2307 1.941975 TCCGTCCGAAAAAGTTTGTCC 59.058 47.619 0.00 0.00 0.00 4.02
2143 2308 1.002142 CCGTCCGAAAAAGTTTGTCCC 60.002 52.381 0.00 0.00 0.00 4.46
2144 2309 1.944709 CGTCCGAAAAAGTTTGTCCCT 59.055 47.619 0.00 0.00 0.00 4.20
2145 2310 2.032290 CGTCCGAAAAAGTTTGTCCCTC 60.032 50.000 0.00 0.00 0.00 4.30
2146 2311 2.946990 GTCCGAAAAAGTTTGTCCCTCA 59.053 45.455 0.00 0.00 0.00 3.86
2147 2312 3.379057 GTCCGAAAAAGTTTGTCCCTCAA 59.621 43.478 0.00 0.00 0.00 3.02
2148 2313 4.017808 TCCGAAAAAGTTTGTCCCTCAAA 58.982 39.130 0.00 0.00 42.79 2.69
2149 2314 4.647399 TCCGAAAAAGTTTGTCCCTCAAAT 59.353 37.500 0.00 0.00 45.88 2.32
2150 2315 4.744631 CCGAAAAAGTTTGTCCCTCAAATG 59.255 41.667 0.00 0.00 45.88 2.32
2151 2316 4.744631 CGAAAAAGTTTGTCCCTCAAATGG 59.255 41.667 0.00 0.00 45.88 3.16
2152 2317 5.451242 CGAAAAAGTTTGTCCCTCAAATGGA 60.451 40.000 0.00 0.00 45.88 3.41
2153 2318 6.499106 AAAAAGTTTGTCCCTCAAATGGAT 57.501 33.333 0.00 0.00 45.88 3.41
2154 2319 5.473066 AAAGTTTGTCCCTCAAATGGATG 57.527 39.130 0.00 0.00 45.88 3.51
2155 2320 4.118168 AGTTTGTCCCTCAAATGGATGT 57.882 40.909 0.00 0.00 45.88 3.06
2156 2321 5.255397 AGTTTGTCCCTCAAATGGATGTA 57.745 39.130 0.00 0.00 45.88 2.29
2157 2322 5.831103 AGTTTGTCCCTCAAATGGATGTAT 58.169 37.500 0.00 0.00 45.88 2.29
2158 2323 5.888161 AGTTTGTCCCTCAAATGGATGTATC 59.112 40.000 0.00 0.00 45.88 2.24
2159 2324 5.715439 TTGTCCCTCAAATGGATGTATCT 57.285 39.130 0.00 0.00 33.65 1.98
2160 2325 6.823286 TTGTCCCTCAAATGGATGTATCTA 57.177 37.500 0.00 0.00 33.65 1.98
2161 2326 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
2162 2327 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
2163 2328 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
2164 2329 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
2165 2330 4.999950 CCTCAAATGGATGTATCTAGCACC 59.000 45.833 0.00 0.00 0.00 5.01
2166 2331 5.455183 CCTCAAATGGATGTATCTAGCACCA 60.455 44.000 0.00 0.00 0.00 4.17
2167 2332 6.000246 TCAAATGGATGTATCTAGCACCAA 58.000 37.500 0.00 0.00 0.00 3.67
2168 2333 6.057533 TCAAATGGATGTATCTAGCACCAAG 58.942 40.000 0.00 0.00 0.00 3.61
2169 2334 5.636903 AATGGATGTATCTAGCACCAAGT 57.363 39.130 0.00 0.00 0.00 3.16
2170 2335 5.636903 ATGGATGTATCTAGCACCAAGTT 57.363 39.130 0.00 0.00 0.00 2.66
2171 2336 6.747414 ATGGATGTATCTAGCACCAAGTTA 57.253 37.500 0.00 0.00 0.00 2.24
2172 2337 6.161855 TGGATGTATCTAGCACCAAGTTAG 57.838 41.667 0.00 0.00 32.79 2.34
2173 2338 5.661312 TGGATGTATCTAGCACCAAGTTAGT 59.339 40.000 0.00 0.00 33.25 2.24
2174 2339 5.986135 GGATGTATCTAGCACCAAGTTAGTG 59.014 44.000 0.00 0.00 38.30 2.74
2175 2340 5.339008 TGTATCTAGCACCAAGTTAGTGG 57.661 43.478 3.58 0.00 44.92 4.00
2187 2352 6.479972 CCAAGTTAGTGGTAGATACATCCA 57.520 41.667 0.00 0.00 33.63 3.41
2188 2353 7.067496 CCAAGTTAGTGGTAGATACATCCAT 57.933 40.000 0.00 0.00 33.63 3.41
2189 2354 7.509546 CCAAGTTAGTGGTAGATACATCCATT 58.490 38.462 0.00 0.00 33.63 3.16
2190 2355 7.993183 CCAAGTTAGTGGTAGATACATCCATTT 59.007 37.037 0.00 0.00 33.63 2.32
2191 2356 8.830580 CAAGTTAGTGGTAGATACATCCATTTG 58.169 37.037 0.00 0.00 33.68 2.32
2192 2357 8.319057 AGTTAGTGGTAGATACATCCATTTGA 57.681 34.615 0.00 0.00 33.68 2.69
2193 2358 8.424918 AGTTAGTGGTAGATACATCCATTTGAG 58.575 37.037 0.00 0.00 33.68 3.02
2194 2359 6.179906 AGTGGTAGATACATCCATTTGAGG 57.820 41.667 0.00 0.00 33.68 3.86
2195 2360 5.072329 AGTGGTAGATACATCCATTTGAGGG 59.928 44.000 0.00 0.00 33.68 4.30
2196 2361 5.071788 GTGGTAGATACATCCATTTGAGGGA 59.928 44.000 0.00 0.00 39.14 4.20
2197 2362 5.071788 TGGTAGATACATCCATTTGAGGGAC 59.928 44.000 0.00 0.00 37.23 4.46
2198 2363 5.071788 GGTAGATACATCCATTTGAGGGACA 59.928 44.000 0.00 0.00 37.23 4.02
2199 2364 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
2200 2365 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
2201 2366 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
2202 2367 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
2203 2368 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
2204 2369 2.517959 TCCATTTGAGGGACAAGCTTG 58.482 47.619 24.84 24.84 39.77 4.01
2205 2370 1.547372 CCATTTGAGGGACAAGCTTGG 59.453 52.381 29.18 12.28 39.77 3.61
2206 2371 1.547372 CATTTGAGGGACAAGCTTGGG 59.453 52.381 29.18 6.83 39.77 4.12
2207 2372 0.850100 TTTGAGGGACAAGCTTGGGA 59.150 50.000 29.18 4.51 39.77 4.37
2208 2373 1.075601 TTGAGGGACAAGCTTGGGAT 58.924 50.000 29.18 9.67 34.20 3.85
2209 2374 1.965414 TGAGGGACAAGCTTGGGATA 58.035 50.000 29.18 8.61 0.00 2.59
2210 2375 2.274542 TGAGGGACAAGCTTGGGATAA 58.725 47.619 29.18 8.47 0.00 1.75
2211 2376 2.239654 TGAGGGACAAGCTTGGGATAAG 59.760 50.000 29.18 3.71 0.00 1.73
2212 2377 2.239907 GAGGGACAAGCTTGGGATAAGT 59.760 50.000 29.18 7.31 0.00 2.24
2213 2378 2.649816 AGGGACAAGCTTGGGATAAGTT 59.350 45.455 29.18 6.52 0.00 2.66
2214 2379 3.076032 AGGGACAAGCTTGGGATAAGTTT 59.924 43.478 29.18 5.75 0.00 2.66
2215 2380 3.832490 GGGACAAGCTTGGGATAAGTTTT 59.168 43.478 29.18 4.98 0.00 2.43
2216 2381 4.283467 GGGACAAGCTTGGGATAAGTTTTT 59.717 41.667 29.18 4.43 0.00 1.94
2245 2410 9.420551 GAACGGAGGGAGTATTTATTTATGTAG 57.579 37.037 0.00 0.00 0.00 2.74
2266 2431 8.800370 TGTAGTTTACTGATTATTCCATGCAA 57.200 30.769 0.00 0.00 0.00 4.08
2270 2435 9.407380 AGTTTACTGATTATTCCATGCAACATA 57.593 29.630 0.00 0.00 0.00 2.29
2306 2471 9.190317 TCGCTATATATATCATGAGAACTTGGT 57.810 33.333 0.09 0.00 0.00 3.67
2307 2472 9.457110 CGCTATATATATCATGAGAACTTGGTC 57.543 37.037 0.09 0.00 0.00 4.02
2424 2591 9.046296 GTAGAAGTTTAATCCATGTATCCAGTG 57.954 37.037 0.00 0.00 0.00 3.66
2432 2599 5.308976 TCCATGTATCCAGTGCATACATT 57.691 39.130 15.70 1.16 42.39 2.71
2446 2613 3.382546 GCATACATTGATGGGAGTTGCTT 59.617 43.478 0.00 0.00 0.00 3.91
2458 2625 2.035066 GGAGTTGCTTGTTGCTCATTGT 59.965 45.455 0.00 0.00 43.37 2.71
2459 2626 3.047796 GAGTTGCTTGTTGCTCATTGTG 58.952 45.455 0.00 0.00 43.37 3.33
2508 2675 0.746659 AGTGCAGCAACCTGGTTTTC 59.253 50.000 9.90 4.93 39.54 2.29
2529 2696 3.059461 TCGATGCGTAAAACACAAACCTC 60.059 43.478 0.00 0.00 0.00 3.85
2557 2807 3.788227 ACATTCTTAGGACAGTGCCAA 57.212 42.857 6.40 0.00 0.00 4.52
2594 2844 1.379044 CACCTTCATCCCACCTGCC 60.379 63.158 0.00 0.00 0.00 4.85
2597 2847 1.383799 CTTCATCCCACCTGCCCAA 59.616 57.895 0.00 0.00 0.00 4.12
2603 2853 0.033208 TCCCACCTGCCCAAATGATC 60.033 55.000 0.00 0.00 0.00 2.92
2604 2854 0.324552 CCCACCTGCCCAAATGATCA 60.325 55.000 0.00 0.00 0.00 2.92
2605 2855 0.819582 CCACCTGCCCAAATGATCAC 59.180 55.000 0.00 0.00 0.00 3.06
2606 2856 0.819582 CACCTGCCCAAATGATCACC 59.180 55.000 0.00 0.00 0.00 4.02
2641 2891 5.832595 TGGGTCATGTTCATCTTTCTTTTCA 59.167 36.000 0.00 0.00 0.00 2.69
2645 2895 8.919661 GGTCATGTTCATCTTTCTTTTCATTTC 58.080 33.333 0.00 0.00 0.00 2.17
2665 2915 3.857052 TCGAATATCACACCTGTGGTTC 58.143 45.455 5.60 7.15 45.65 3.62
2680 2930 2.093869 GTGGTTCGGTGCTATCCTGTTA 60.094 50.000 0.00 0.00 0.00 2.41
2683 2933 4.196971 GGTTCGGTGCTATCCTGTTAAAT 58.803 43.478 0.00 0.00 0.00 1.40
2725 2977 5.536916 GGTATACCTGTAGTCTGATGCTCTT 59.463 44.000 15.09 0.00 0.00 2.85
2869 3122 2.300437 ACCTCTCTCCTTCCTTTTCGTG 59.700 50.000 0.00 0.00 0.00 4.35
2894 3149 7.275779 TGTCTTCTGATTATTCTTGTAACTCGC 59.724 37.037 0.00 0.00 0.00 5.03
2956 3211 1.349357 GGAAGTTGACTCCCTCAAGCT 59.651 52.381 0.00 0.00 39.69 3.74
3077 3332 4.729918 GTGGAGCCACTGCCCTGG 62.730 72.222 12.30 0.00 43.12 4.45
3106 3361 2.426024 TCTACACCTAAGATCGTGTGCC 59.574 50.000 12.65 0.00 42.96 5.01
3122 3377 1.138247 GCCCCGACTATATACGCCG 59.862 63.158 0.00 0.00 0.00 6.46
3175 3430 0.250684 TTGGCTGCATGAGTTCGGAA 60.251 50.000 0.50 0.00 0.00 4.30
3253 3508 3.838317 TGTGTGCTTACAATCCTAGGACT 59.162 43.478 15.42 0.00 32.27 3.85
3270 3525 8.002459 TCCTAGGACTTGTAAAATCCAGTTTTT 58.998 33.333 7.62 0.00 40.40 1.94
3287 3542 0.031857 TTTGGCACCAACGCTGATTG 59.968 50.000 0.45 0.00 35.46 2.67
3310 3565 9.850198 ATTGAAGAATTTTTGGAAGGAATTTCA 57.150 25.926 0.00 0.00 37.54 2.69
3379 3635 6.226787 AGTATTGCACATCTAAGTCCTATGC 58.773 40.000 0.00 0.00 0.00 3.14
3394 3650 2.422519 CCTATGCCCTTGATCTTGCACT 60.423 50.000 0.00 0.00 36.41 4.40
3415 3671 6.411376 CACTGAGGTTTGTGTGGGTATTATA 58.589 40.000 0.00 0.00 0.00 0.98
3445 3701 9.435688 TTTCTTTTTCTTTTCCTTTTCTCCTTG 57.564 29.630 0.00 0.00 0.00 3.61
3446 3702 7.041721 TCTTTTTCTTTTCCTTTTCTCCTTGC 58.958 34.615 0.00 0.00 0.00 4.01
3447 3703 4.937201 TTCTTTTCCTTTTCTCCTTGCC 57.063 40.909 0.00 0.00 0.00 4.52
3448 3704 3.909732 TCTTTTCCTTTTCTCCTTGCCA 58.090 40.909 0.00 0.00 0.00 4.92
3450 3706 1.995376 TTCCTTTTCTCCTTGCCACC 58.005 50.000 0.00 0.00 0.00 4.61
3465 3758 1.296715 CACCGGGGTTTCCTCTCTG 59.703 63.158 6.32 0.00 0.00 3.35
3502 3795 0.472471 TTTTTCTCCTCCACGCACCT 59.528 50.000 0.00 0.00 0.00 4.00
3532 3825 8.768397 TCTTAGAAATAATGCTCCCTTGTCTTA 58.232 33.333 0.00 0.00 0.00 2.10
3589 3883 7.743116 TTCTTATCCTACTGGAAACCACATA 57.257 36.000 0.00 0.00 46.80 2.29
3675 3969 9.793252 AGTATTATGTTCTGCATTGAAATCAAC 57.207 29.630 0.00 0.00 38.86 3.18
3750 4044 8.184249 TCTACCTATACTCCAATATGATGGGTT 58.816 37.037 0.00 0.00 41.05 4.11
3756 4050 5.140454 ACTCCAATATGATGGGTTTAAGGC 58.860 41.667 0.00 0.00 41.05 4.35
3791 4087 6.964934 ACTCGATTGTTGTTTAACACTGAAAC 59.035 34.615 0.00 0.00 45.91 2.78
3800 4096 9.619316 GTTGTTTAACACTGAAACATATATGCA 57.381 29.630 12.79 2.30 44.12 3.96
3815 4111 1.175654 ATGCATCATTCCAACGCACA 58.824 45.000 0.00 0.00 35.02 4.57
3818 4114 1.402968 GCATCATTCCAACGCACAGAT 59.597 47.619 0.00 0.00 0.00 2.90
3821 4117 4.591202 CATCATTCCAACGCACAGATAAC 58.409 43.478 0.00 0.00 0.00 1.89
3827 4126 4.854399 TCCAACGCACAGATAACTTTTTG 58.146 39.130 0.00 0.00 0.00 2.44
3841 4140 9.046296 AGATAACTTTTTGAACACAGTAGACAG 57.954 33.333 0.00 0.00 0.00 3.51
3846 4145 7.174253 ACTTTTTGAACACAGTAGACAGAAACA 59.826 33.333 0.00 0.00 0.00 2.83
3862 4161 9.587772 AGACAGAAACACTTATACATACATGTC 57.412 33.333 0.00 0.00 41.97 3.06
3863 4162 8.718102 ACAGAAACACTTATACATACATGTCC 57.282 34.615 0.00 0.00 41.97 4.02
3864 4163 8.540388 ACAGAAACACTTATACATACATGTCCT 58.460 33.333 0.00 0.00 41.97 3.85
3865 4164 8.820933 CAGAAACACTTATACATACATGTCCTG 58.179 37.037 0.00 4.02 41.97 3.86
3866 4165 7.495934 AGAAACACTTATACATACATGTCCTGC 59.504 37.037 0.00 0.00 41.97 4.85
3867 4166 6.233905 ACACTTATACATACATGTCCTGCA 57.766 37.500 0.00 0.00 41.97 4.41
3868 4167 6.830912 ACACTTATACATACATGTCCTGCAT 58.169 36.000 0.00 0.36 41.97 3.96
3869 4168 7.282585 ACACTTATACATACATGTCCTGCATT 58.717 34.615 0.00 0.00 41.97 3.56
3870 4169 8.428852 ACACTTATACATACATGTCCTGCATTA 58.571 33.333 0.00 0.00 41.97 1.90
3871 4170 9.271828 CACTTATACATACATGTCCTGCATTAA 57.728 33.333 0.00 0.92 41.97 1.40
3872 4171 9.273016 ACTTATACATACATGTCCTGCATTAAC 57.727 33.333 0.00 0.00 41.97 2.01
3873 4172 9.494271 CTTATACATACATGTCCTGCATTAACT 57.506 33.333 0.00 0.00 41.97 2.24
3874 4173 9.845740 TTATACATACATGTCCTGCATTAACTT 57.154 29.630 0.00 0.00 41.97 2.66
3876 4175 9.845740 ATACATACATGTCCTGCATTAACTTAA 57.154 29.630 0.00 0.00 41.97 1.85
3877 4176 8.752005 ACATACATGTCCTGCATTAACTTAAT 57.248 30.769 0.00 0.00 35.87 1.40
3878 4177 9.189156 ACATACATGTCCTGCATTAACTTAATT 57.811 29.630 0.00 0.00 35.87 1.40
3923 4222 0.886490 CCCTATGAACGCATGCCCTC 60.886 60.000 13.15 9.41 35.94 4.30
3927 4226 2.044946 GAACGCATGCCCTCCCTT 60.045 61.111 13.15 0.00 0.00 3.95
3928 4227 1.223487 GAACGCATGCCCTCCCTTA 59.777 57.895 13.15 0.00 0.00 2.69
3967 4266 6.599445 AGACTTGAGCTGGCATATAATCTTT 58.401 36.000 0.00 0.00 0.00 2.52
3972 4271 6.776744 TGAGCTGGCATATAATCTTTGAGAT 58.223 36.000 0.00 0.00 36.28 2.75
3991 4290 8.408043 TTGAGATTGATGAAGTTACCACAAAT 57.592 30.769 0.00 0.00 0.00 2.32
3998 4297 8.196802 TGATGAAGTTACCACAAATATCTTCG 57.803 34.615 0.00 0.00 33.71 3.79
3999 4298 8.038351 TGATGAAGTTACCACAAATATCTTCGA 58.962 33.333 0.00 0.00 33.71 3.71
4000 4299 8.786826 ATGAAGTTACCACAAATATCTTCGAA 57.213 30.769 0.00 0.00 33.71 3.71
4001 4300 8.251750 TGAAGTTACCACAAATATCTTCGAAG 57.748 34.615 19.35 19.35 33.71 3.79
4002 4301 7.876068 TGAAGTTACCACAAATATCTTCGAAGT 59.124 33.333 23.85 13.98 33.71 3.01
4003 4302 7.829378 AGTTACCACAAATATCTTCGAAGTC 57.171 36.000 23.85 0.00 0.00 3.01
4004 4303 6.530534 AGTTACCACAAATATCTTCGAAGTCG 59.469 38.462 23.85 10.05 41.45 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.547513 GACCCGGATCCTTCCCCG 61.548 72.222 10.75 0.00 44.94 5.73
76 78 3.144506 AGTGTCGTAGTTCTTTCTCCGA 58.855 45.455 0.00 0.00 0.00 4.55
84 86 4.096682 GCTGATCCTTAGTGTCGTAGTTCT 59.903 45.833 0.00 0.00 0.00 3.01
524 529 9.893305 CGTCCTAAAATGTAAGATTCTTGTTTT 57.107 29.630 9.22 13.80 0.00 2.43
525 530 9.280174 TCGTCCTAAAATGTAAGATTCTTGTTT 57.720 29.630 9.22 5.13 0.00 2.83
526 531 8.842358 TCGTCCTAAAATGTAAGATTCTTGTT 57.158 30.769 9.22 0.00 0.00 2.83
527 532 8.842358 TTCGTCCTAAAATGTAAGATTCTTGT 57.158 30.769 9.22 0.00 0.00 3.16
528 533 8.391106 CCTTCGTCCTAAAATGTAAGATTCTTG 58.609 37.037 9.22 0.00 0.00 3.02
529 534 7.553044 CCCTTCGTCCTAAAATGTAAGATTCTT 59.447 37.037 4.03 4.03 0.00 2.52
530 535 7.048512 CCCTTCGTCCTAAAATGTAAGATTCT 58.951 38.462 0.00 0.00 0.00 2.40
531 536 6.260271 CCCCTTCGTCCTAAAATGTAAGATTC 59.740 42.308 0.00 0.00 0.00 2.52
532 537 6.069847 TCCCCTTCGTCCTAAAATGTAAGATT 60.070 38.462 0.00 0.00 0.00 2.40
533 538 5.427481 TCCCCTTCGTCCTAAAATGTAAGAT 59.573 40.000 0.00 0.00 0.00 2.40
534 539 4.778958 TCCCCTTCGTCCTAAAATGTAAGA 59.221 41.667 0.00 0.00 0.00 2.10
535 540 5.093849 TCCCCTTCGTCCTAAAATGTAAG 57.906 43.478 0.00 0.00 0.00 2.34
536 541 5.703730 ATCCCCTTCGTCCTAAAATGTAA 57.296 39.130 0.00 0.00 0.00 2.41
537 542 6.138263 TCTATCCCCTTCGTCCTAAAATGTA 58.862 40.000 0.00 0.00 0.00 2.29
538 543 4.966805 TCTATCCCCTTCGTCCTAAAATGT 59.033 41.667 0.00 0.00 0.00 2.71
539 544 5.546621 TCTATCCCCTTCGTCCTAAAATG 57.453 43.478 0.00 0.00 0.00 2.32
540 545 7.458170 ACATATCTATCCCCTTCGTCCTAAAAT 59.542 37.037 0.00 0.00 0.00 1.82
541 546 6.785963 ACATATCTATCCCCTTCGTCCTAAAA 59.214 38.462 0.00 0.00 0.00 1.52
542 547 6.210784 CACATATCTATCCCCTTCGTCCTAAA 59.789 42.308 0.00 0.00 0.00 1.85
543 548 5.715279 CACATATCTATCCCCTTCGTCCTAA 59.285 44.000 0.00 0.00 0.00 2.69
544 549 5.222275 ACACATATCTATCCCCTTCGTCCTA 60.222 44.000 0.00 0.00 0.00 2.94
567 572 6.447162 GGCAATGCCCTTATAGATGTTTTAC 58.553 40.000 14.47 0.00 44.06 2.01
603 609 0.988832 TAGTGGGGCAGTAGGTTTGG 59.011 55.000 0.00 0.00 0.00 3.28
609 615 2.119495 AGTTGGATAGTGGGGCAGTAG 58.881 52.381 0.00 0.00 0.00 2.57
611 617 2.119495 CTAGTTGGATAGTGGGGCAGT 58.881 52.381 0.00 0.00 0.00 4.40
633 639 2.550855 GCTCCATTTGATATCCGAGCCA 60.551 50.000 0.00 0.00 37.39 4.75
634 640 2.079925 GCTCCATTTGATATCCGAGCC 58.920 52.381 0.00 0.00 37.39 4.70
635 641 2.999355 GAGCTCCATTTGATATCCGAGC 59.001 50.000 0.87 13.62 42.37 5.03
636 642 3.057245 TCGAGCTCCATTTGATATCCGAG 60.057 47.826 8.47 0.00 0.00 4.63
637 643 2.890945 TCGAGCTCCATTTGATATCCGA 59.109 45.455 8.47 0.00 0.00 4.55
638 644 3.249091 CTCGAGCTCCATTTGATATCCG 58.751 50.000 8.47 0.00 0.00 4.18
644 650 3.066900 GCTACTACTCGAGCTCCATTTGA 59.933 47.826 13.61 0.00 35.73 2.69
668 674 2.806244 CCTTTTCTTCTACACACCACGG 59.194 50.000 0.00 0.00 0.00 4.94
736 782 4.212716 GTCATATTTTTAGGTCCCCACCC 58.787 47.826 0.00 0.00 45.12 4.61
745 791 6.316390 GGTCTCACCTGTGTCATATTTTTAGG 59.684 42.308 0.00 0.00 34.73 2.69
746 792 6.878923 TGGTCTCACCTGTGTCATATTTTTAG 59.121 38.462 0.00 0.00 39.58 1.85
768 814 7.902920 AAATTGAGGCTATCATTACAATGGT 57.097 32.000 2.26 0.00 37.89 3.55
840 891 6.437755 TCTTAGAGCAACCCAGTTAGGTATA 58.562 40.000 0.00 0.00 40.05 1.47
841 892 5.278061 TCTTAGAGCAACCCAGTTAGGTAT 58.722 41.667 0.00 0.00 40.05 2.73
842 893 4.680407 TCTTAGAGCAACCCAGTTAGGTA 58.320 43.478 0.00 0.00 40.05 3.08
843 894 3.517612 TCTTAGAGCAACCCAGTTAGGT 58.482 45.455 0.00 0.00 44.00 3.08
1215 1274 2.879233 AAAGGGGTTGAGCGCGAGA 61.879 57.895 12.10 0.00 0.00 4.04
1482 1543 0.518636 CACGGACATGCAAAGACAGG 59.481 55.000 0.00 0.00 0.00 4.00
1483 1544 0.110056 GCACGGACATGCAAAGACAG 60.110 55.000 0.00 0.00 45.39 3.51
1759 1823 4.082026 GCAAATGAAATCCACCTAGCTGTT 60.082 41.667 0.00 0.00 0.00 3.16
1804 1868 2.990740 AAACAAAGGACCCATGCCTA 57.009 45.000 0.00 0.00 33.76 3.93
1874 1944 9.883142 GATATCCTTTCTATCCCACAAGAATAG 57.117 37.037 0.00 0.00 32.05 1.73
1939 2009 9.219603 ACGTCAGAATCATCATAAAGAAAGAAA 57.780 29.630 0.00 0.00 0.00 2.52
1940 2010 8.659491 CACGTCAGAATCATCATAAAGAAAGAA 58.341 33.333 0.00 0.00 0.00 2.52
1941 2011 7.819415 ACACGTCAGAATCATCATAAAGAAAGA 59.181 33.333 0.00 0.00 0.00 2.52
1942 2012 7.968246 ACACGTCAGAATCATCATAAAGAAAG 58.032 34.615 0.00 0.00 0.00 2.62
1982 2052 6.560251 CGAAGCATTTACAAAGTTTGCTGAAC 60.560 38.462 15.59 1.74 42.50 3.18
2053 2123 8.914328 TGTGTTTTGTCATATTCAAGCATATG 57.086 30.769 0.00 0.00 38.16 1.78
2103 2173 4.771054 ACGGAGGGAGTATACATTATGACC 59.229 45.833 5.50 0.00 0.00 4.02
2117 2282 0.320697 ACTTTTTCGGACGGAGGGAG 59.679 55.000 0.00 0.00 0.00 4.30
2119 2284 1.265905 CAAACTTTTTCGGACGGAGGG 59.734 52.381 0.00 0.00 0.00 4.30
2120 2285 1.944709 ACAAACTTTTTCGGACGGAGG 59.055 47.619 0.00 0.00 0.00 4.30
2121 2286 2.032290 GGACAAACTTTTTCGGACGGAG 60.032 50.000 0.00 0.00 0.00 4.63
2122 2287 1.941975 GGACAAACTTTTTCGGACGGA 59.058 47.619 0.00 0.00 0.00 4.69
2123 2288 1.002142 GGGACAAACTTTTTCGGACGG 60.002 52.381 0.00 0.00 0.00 4.79
2124 2289 1.944709 AGGGACAAACTTTTTCGGACG 59.055 47.619 0.00 0.00 0.00 4.79
2125 2290 2.946990 TGAGGGACAAACTTTTTCGGAC 59.053 45.455 0.00 0.00 0.00 4.79
2126 2291 3.284793 TGAGGGACAAACTTTTTCGGA 57.715 42.857 0.00 0.00 0.00 4.55
2127 2292 4.379339 TTTGAGGGACAAACTTTTTCGG 57.621 40.909 0.00 0.00 42.57 4.30
2137 2302 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
2138 2303 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
2139 2304 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
2140 2305 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
2141 2306 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
2142 2307 4.999950 GGTGCTAGATACATCCATTTGAGG 59.000 45.833 0.00 0.00 0.00 3.86
2143 2308 5.614308 TGGTGCTAGATACATCCATTTGAG 58.386 41.667 0.00 0.00 0.00 3.02
2144 2309 5.628797 TGGTGCTAGATACATCCATTTGA 57.371 39.130 0.00 0.00 0.00 2.69
2145 2310 5.824624 ACTTGGTGCTAGATACATCCATTTG 59.175 40.000 0.00 0.00 0.00 2.32
2146 2311 6.006275 ACTTGGTGCTAGATACATCCATTT 57.994 37.500 0.00 0.00 0.00 2.32
2147 2312 5.636903 ACTTGGTGCTAGATACATCCATT 57.363 39.130 0.00 0.00 0.00 3.16
2148 2313 5.636903 AACTTGGTGCTAGATACATCCAT 57.363 39.130 0.00 0.00 0.00 3.41
2149 2314 5.661312 ACTAACTTGGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
2150 2315 5.986135 CACTAACTTGGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
2151 2316 5.986135 CCACTAACTTGGTGCTAGATACATC 59.014 44.000 0.00 0.00 33.78 3.06
2152 2317 5.918608 CCACTAACTTGGTGCTAGATACAT 58.081 41.667 0.00 0.00 33.78 2.29
2153 2318 5.339008 CCACTAACTTGGTGCTAGATACA 57.661 43.478 0.00 0.00 33.78 2.29
2164 2329 6.479972 TGGATGTATCTACCACTAACTTGG 57.520 41.667 0.00 0.00 43.04 3.61
2165 2330 8.830580 CAAATGGATGTATCTACCACTAACTTG 58.169 37.037 0.00 0.00 36.49 3.16
2166 2331 8.768397 TCAAATGGATGTATCTACCACTAACTT 58.232 33.333 0.00 0.00 36.49 2.66
2167 2332 8.319057 TCAAATGGATGTATCTACCACTAACT 57.681 34.615 0.00 0.00 36.49 2.24
2168 2333 7.657761 CCTCAAATGGATGTATCTACCACTAAC 59.342 40.741 0.00 0.00 36.49 2.34
2169 2334 7.202093 CCCTCAAATGGATGTATCTACCACTAA 60.202 40.741 0.00 0.00 36.49 2.24
2170 2335 6.270000 CCCTCAAATGGATGTATCTACCACTA 59.730 42.308 0.00 0.00 36.49 2.74
2171 2336 5.072329 CCCTCAAATGGATGTATCTACCACT 59.928 44.000 0.00 0.00 36.49 4.00
2172 2337 5.071788 TCCCTCAAATGGATGTATCTACCAC 59.928 44.000 0.00 0.00 36.49 4.16
2173 2338 5.071788 GTCCCTCAAATGGATGTATCTACCA 59.928 44.000 0.00 0.00 38.09 3.25
2174 2339 5.071788 TGTCCCTCAAATGGATGTATCTACC 59.928 44.000 0.00 0.00 33.65 3.18
2175 2340 6.174720 TGTCCCTCAAATGGATGTATCTAC 57.825 41.667 0.00 0.00 33.65 2.59
2176 2341 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
2177 2342 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
2178 2343 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
2179 2344 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
2180 2345 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
2181 2346 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
2182 2347 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
2183 2348 3.094572 CAAGCTTGTCCCTCAAATGGAT 58.905 45.455 18.65 0.00 35.48 3.41
2184 2349 2.517959 CAAGCTTGTCCCTCAAATGGA 58.482 47.619 18.65 0.00 35.48 3.41
2185 2350 1.547372 CCAAGCTTGTCCCTCAAATGG 59.453 52.381 24.35 1.81 35.48 3.16
2186 2351 1.547372 CCCAAGCTTGTCCCTCAAATG 59.453 52.381 24.35 5.47 35.48 2.32
2187 2352 1.428912 TCCCAAGCTTGTCCCTCAAAT 59.571 47.619 24.35 0.00 35.48 2.32
2188 2353 0.850100 TCCCAAGCTTGTCCCTCAAA 59.150 50.000 24.35 0.00 35.48 2.69
2189 2354 1.075601 ATCCCAAGCTTGTCCCTCAA 58.924 50.000 24.35 2.85 34.61 3.02
2190 2355 1.965414 TATCCCAAGCTTGTCCCTCA 58.035 50.000 24.35 2.47 0.00 3.86
2191 2356 2.239907 ACTTATCCCAAGCTTGTCCCTC 59.760 50.000 24.35 0.00 0.00 4.30
2192 2357 2.279173 ACTTATCCCAAGCTTGTCCCT 58.721 47.619 24.35 9.12 0.00 4.20
2193 2358 2.808906 ACTTATCCCAAGCTTGTCCC 57.191 50.000 24.35 0.00 0.00 4.46
2194 2359 5.468540 AAAAACTTATCCCAAGCTTGTCC 57.531 39.130 24.35 0.00 0.00 4.02
2214 2379 8.411991 AAATAAATACTCCCTCCGTTCAAAAA 57.588 30.769 0.00 0.00 0.00 1.94
2215 2380 9.689501 ATAAATAAATACTCCCTCCGTTCAAAA 57.310 29.630 0.00 0.00 0.00 2.44
2216 2381 9.116067 CATAAATAAATACTCCCTCCGTTCAAA 57.884 33.333 0.00 0.00 0.00 2.69
2217 2382 8.269317 ACATAAATAAATACTCCCTCCGTTCAA 58.731 33.333 0.00 0.00 0.00 2.69
2218 2383 7.798071 ACATAAATAAATACTCCCTCCGTTCA 58.202 34.615 0.00 0.00 0.00 3.18
2219 2384 9.420551 CTACATAAATAAATACTCCCTCCGTTC 57.579 37.037 0.00 0.00 0.00 3.95
2220 2385 8.931568 ACTACATAAATAAATACTCCCTCCGTT 58.068 33.333 0.00 0.00 0.00 4.44
2221 2386 8.488308 ACTACATAAATAAATACTCCCTCCGT 57.512 34.615 0.00 0.00 0.00 4.69
2222 2387 9.774413 AAACTACATAAATAAATACTCCCTCCG 57.226 33.333 0.00 0.00 0.00 4.63
2299 2464 1.888512 GTGTGGCATCATGACCAAGTT 59.111 47.619 6.62 0.00 37.79 2.66
2301 2466 1.471287 CTGTGTGGCATCATGACCAAG 59.529 52.381 6.62 0.00 37.79 3.61
2302 2467 1.202915 ACTGTGTGGCATCATGACCAA 60.203 47.619 6.62 0.00 37.79 3.67
2303 2468 0.401356 ACTGTGTGGCATCATGACCA 59.599 50.000 0.00 0.00 0.00 4.02
2304 2469 2.009774 GTACTGTGTGGCATCATGACC 58.990 52.381 0.00 0.00 0.00 4.02
2305 2470 2.416547 GTGTACTGTGTGGCATCATGAC 59.583 50.000 0.00 0.00 0.00 3.06
2306 2471 2.038295 TGTGTACTGTGTGGCATCATGA 59.962 45.455 0.00 0.00 0.00 3.07
2307 2472 2.425539 TGTGTACTGTGTGGCATCATG 58.574 47.619 0.00 0.00 0.00 3.07
2308 2473 2.857186 TGTGTACTGTGTGGCATCAT 57.143 45.000 0.00 0.00 0.00 2.45
2309 2474 2.857186 ATGTGTACTGTGTGGCATCA 57.143 45.000 0.00 0.00 0.00 3.07
2310 2475 4.935205 TCTTAATGTGTACTGTGTGGCATC 59.065 41.667 0.00 0.00 0.00 3.91
2311 2476 4.905429 TCTTAATGTGTACTGTGTGGCAT 58.095 39.130 0.00 0.00 0.00 4.40
2314 2479 9.988350 GAATTATTCTTAATGTGTACTGTGTGG 57.012 33.333 0.00 0.00 0.00 4.17
2417 2584 3.138839 TCCCATCAATGTATGCACTGGAT 59.861 43.478 0.00 0.00 0.00 3.41
2418 2585 2.509131 TCCCATCAATGTATGCACTGGA 59.491 45.455 0.00 0.00 0.00 3.86
2424 2591 2.954318 AGCAACTCCCATCAATGTATGC 59.046 45.455 0.00 0.00 0.00 3.14
2432 2599 0.961019 GCAACAAGCAACTCCCATCA 59.039 50.000 0.00 0.00 44.79 3.07
2446 2613 5.826601 TTCAAGTTACACAATGAGCAACA 57.173 34.783 0.00 0.00 0.00 3.33
2458 2625 7.362315 CCATTGCATCTGAGATTTCAAGTTACA 60.362 37.037 11.08 0.00 31.69 2.41
2459 2626 6.971184 CCATTGCATCTGAGATTTCAAGTTAC 59.029 38.462 11.08 0.00 31.69 2.50
2488 2655 1.136891 GAAAACCAGGTTGCTGCACTT 59.863 47.619 5.30 0.00 0.00 3.16
2508 2675 3.223157 GAGGTTTGTGTTTTACGCATCG 58.777 45.455 0.00 0.00 38.53 3.84
2529 2696 4.080863 ACTGTCCTAAGAATGTAGGCCTTG 60.081 45.833 12.58 0.00 40.58 3.61
2557 2807 7.123547 TGAAGGTGTGAAAGAAAATTGGTAACT 59.876 33.333 0.00 0.00 37.61 2.24
2594 2844 6.405065 CCATGTGTCTTAAGGTGATCATTTGG 60.405 42.308 0.00 3.62 0.00 3.28
2597 2847 5.195940 CCCATGTGTCTTAAGGTGATCATT 58.804 41.667 0.00 0.00 0.00 2.57
2603 2853 3.417069 TGACCCATGTGTCTTAAGGTG 57.583 47.619 9.79 0.00 36.21 4.00
2604 2854 3.955471 CATGACCCATGTGTCTTAAGGT 58.045 45.455 9.79 0.00 37.12 3.50
2632 2882 8.792633 AGGTGTGATATTCGAAATGAAAAGAAA 58.207 29.630 0.00 0.00 40.71 2.52
2665 2915 6.436843 AGAAAATTTAACAGGATAGCACCG 57.563 37.500 0.00 0.00 34.73 4.94
2725 2977 3.272574 ACCGACGGATAGTTAGAGACA 57.727 47.619 23.38 0.00 0.00 3.41
2869 3122 7.489757 AGCGAGTTACAAGAATAATCAGAAGAC 59.510 37.037 0.00 0.00 0.00 3.01
2894 3149 3.902261 TGACTGCAAAACATAGCACAG 57.098 42.857 0.00 0.00 36.62 3.66
3077 3332 6.019479 CACGATCTTAGGTGTAGAATTGCTTC 60.019 42.308 0.00 0.00 0.00 3.86
3106 3361 1.536766 TGAACGGCGTATATAGTCGGG 59.463 52.381 15.20 0.00 41.50 5.14
3175 3430 0.250553 TTGCAATCGTCTTCCCCGTT 60.251 50.000 0.00 0.00 0.00 4.44
3209 3464 0.951558 GTTTCCACATTCCGCTGTGT 59.048 50.000 3.47 0.00 44.04 3.72
3225 3480 5.789643 AGGATTGTAAGCACACATTGTTT 57.210 34.783 0.00 0.00 33.30 2.83
3270 3525 0.821301 TTCAATCAGCGTTGGTGCCA 60.821 50.000 0.00 0.00 34.65 4.92
3277 3532 5.841810 TCCAAAAATTCTTCAATCAGCGTT 58.158 33.333 0.00 0.00 0.00 4.84
3287 3542 9.201127 CTCTGAAATTCCTTCCAAAAATTCTTC 57.799 33.333 0.00 0.00 32.53 2.87
3310 3565 8.722394 GCTTTAGCAAAACTGTATTAAGACTCT 58.278 33.333 1.39 0.00 41.59 3.24
3379 3635 1.004044 ACCTCAGTGCAAGATCAAGGG 59.996 52.381 0.00 0.00 0.00 3.95
3394 3650 8.887264 AAAATATAATACCCACACAAACCTCA 57.113 30.769 0.00 0.00 0.00 3.86
3433 3689 1.244019 CCGGTGGCAAGGAGAAAAGG 61.244 60.000 4.39 0.00 0.00 3.11
3441 3697 2.989253 GAAACCCCGGTGGCAAGG 60.989 66.667 0.00 3.48 37.83 3.61
3442 3698 2.989253 GGAAACCCCGGTGGCAAG 60.989 66.667 0.00 0.00 37.83 4.01
3443 3699 3.501040 GAGGAAACCCCGGTGGCAA 62.501 63.158 0.00 0.00 40.87 4.52
3445 3701 3.623703 GAGAGGAAACCCCGGTGGC 62.624 68.421 0.00 0.00 40.87 5.01
3446 3702 1.918800 AGAGAGGAAACCCCGGTGG 60.919 63.158 0.00 3.72 40.87 4.61
3447 3703 1.296715 CAGAGAGGAAACCCCGGTG 59.703 63.158 0.00 0.00 40.87 4.94
3448 3704 2.593956 GCAGAGAGGAAACCCCGGT 61.594 63.158 0.00 0.00 40.87 5.28
3450 3706 0.462759 GATGCAGAGAGGAAACCCCG 60.463 60.000 0.00 0.00 40.87 5.73
3465 3758 1.260544 AAACCAAAGCAGAGGGATGC 58.739 50.000 0.00 0.00 46.88 3.91
3499 3792 6.603599 GGGAGCATTATTTCTAAGACAAAGGT 59.396 38.462 0.00 0.00 0.00 3.50
3502 3795 7.669722 ACAAGGGAGCATTATTTCTAAGACAAA 59.330 33.333 0.00 0.00 0.00 2.83
3638 3932 8.615211 TGCAGAACATAATACTAGCAAGATTTG 58.385 33.333 0.00 0.00 0.00 2.32
3650 3944 9.793252 AGTTGATTTCAATGCAGAACATAATAC 57.207 29.630 0.00 0.00 38.34 1.89
3659 3953 8.665643 AAAATTTGAGTTGATTTCAATGCAGA 57.334 26.923 0.00 0.00 38.24 4.26
3750 4044 6.597672 ACAATCGAGTCAAACATATGCCTTAA 59.402 34.615 1.58 0.00 0.00 1.85
3756 4050 9.605955 TTAAACAACAATCGAGTCAAACATATG 57.394 29.630 0.00 0.00 0.00 1.78
3791 4087 5.090757 GTGCGTTGGAATGATGCATATATG 58.909 41.667 8.45 8.45 40.74 1.78
3800 4096 4.517285 AGTTATCTGTGCGTTGGAATGAT 58.483 39.130 0.00 0.00 0.00 2.45
3815 4111 8.958119 TGTCTACTGTGTTCAAAAAGTTATCT 57.042 30.769 0.00 0.00 0.00 1.98
3818 4114 8.780846 TTCTGTCTACTGTGTTCAAAAAGTTA 57.219 30.769 0.00 0.00 0.00 2.24
3821 4117 7.481798 GTGTTTCTGTCTACTGTGTTCAAAAAG 59.518 37.037 0.00 0.00 0.00 2.27
3827 4126 7.948278 ATAAGTGTTTCTGTCTACTGTGTTC 57.052 36.000 0.00 0.00 0.00 3.18
3841 4140 7.279981 TGCAGGACATGTATGTATAAGTGTTTC 59.720 37.037 0.00 0.00 41.95 2.78
3846 4145 9.273016 GTTAATGCAGGACATGTATGTATAAGT 57.727 33.333 12.50 3.32 41.95 2.24
3913 4212 0.604780 CTCATAAGGGAGGGCATGCG 60.605 60.000 12.44 0.00 0.00 4.73
3923 4222 0.390860 CTCGGAGGTGCTCATAAGGG 59.609 60.000 0.00 0.00 31.08 3.95
3927 4226 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
3928 4227 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
3967 4266 9.685276 ATATTTGTGGTAACTTCATCAATCTCA 57.315 29.630 0.00 0.00 37.61 3.27
3972 4271 8.664798 CGAAGATATTTGTGGTAACTTCATCAA 58.335 33.333 0.00 0.00 33.23 2.57
3983 4282 5.068234 TCGACTTCGAAGATATTTGTGGT 57.932 39.130 31.08 5.59 46.30 4.16


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

AutoCloner maintained by Alex Coulton.