Multiple sequence alignment - TraesCS1B01G243200

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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 TraesCS1B01G243200 chr1B 100.000 2758 0 0 1 2758 432115718 432118475 0.000000e+00 5094.0
1 TraesCS1B01G243200 chr1D 92.810 1377 51 21 664 2037 319429184 319430515 0.000000e+00 1951.0
2 TraesCS1B01G243200 chr1D 88.514 592 26 16 79 663 319428597 319429153 0.000000e+00 678.0
3 TraesCS1B01G243200 chr1D 90.385 312 13 5 2448 2758 319433297 319433592 7.160000e-106 394.0
4 TraesCS1B01G243200 chr1D 100.000 33 0 0 2443 2475 319432969 319433001 8.250000e-06 62.1
5 TraesCS1B01G243200 chr1A 92.458 769 42 8 330 1094 403831865 403831109 0.000000e+00 1085.0
6 TraesCS1B01G243200 chr1A 88.255 877 59 23 1199 2061 403831074 403830228 0.000000e+00 1009.0
7 TraesCS1B01G243200 chr1A 85.938 320 30 7 2443 2758 403829971 403829663 7.360000e-86 327.0
8 TraesCS1B01G243200 chr3A 79.487 156 24 6 1366 1517 573112567 573112718 1.350000e-18 104.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G243200 chr1B 432115718 432118475 2757 False 5094.000 5094 100.000000 1 2758 1 chr1B.!!$F1 2757
1 TraesCS1B01G243200 chr1D 319428597 319433592 4995 False 771.275 1951 92.927250 79 2758 4 chr1D.!!$F1 2679
2 TraesCS1B01G243200 chr1A 403829663 403831865 2202 True 807.000 1085 88.883667 330 2758 3 chr1A.!!$R1 2428

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
76 77 0.039326 AGCGGTAGTACACCCTGAGT 59.961 55.0 2.06 0.0 45.52 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 1907 0.251787 AAAGCCCAGGAAAGCCGAAT 60.252 50.0 0.0 0.0 39.96 3.34 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
69 70 4.208074 GCTAGTTAGAGCGGTAGTACAC 57.792 50.000 2.06 0.00 31.57 2.90
70 71 3.003171 GCTAGTTAGAGCGGTAGTACACC 59.997 52.174 2.06 0.00 44.75 4.16
71 72 2.373224 AGTTAGAGCGGTAGTACACCC 58.627 52.381 2.06 0.00 45.52 4.61
72 73 2.025510 AGTTAGAGCGGTAGTACACCCT 60.026 50.000 2.06 1.11 45.52 4.34
73 74 2.048444 TAGAGCGGTAGTACACCCTG 57.952 55.000 2.06 0.00 45.52 4.45
74 75 0.330604 AGAGCGGTAGTACACCCTGA 59.669 55.000 2.06 0.00 45.52 3.86
75 76 0.739561 GAGCGGTAGTACACCCTGAG 59.260 60.000 2.06 0.00 45.52 3.35
76 77 0.039326 AGCGGTAGTACACCCTGAGT 59.961 55.000 2.06 0.00 45.52 3.41
77 78 0.893447 GCGGTAGTACACCCTGAGTT 59.107 55.000 2.06 0.00 45.52 3.01
80 81 1.621814 GGTAGTACACCCTGAGTTGCA 59.378 52.381 2.06 0.00 42.07 4.08
86 87 0.518636 CACCCTGAGTTGCATGTTCG 59.481 55.000 0.00 0.00 0.00 3.95
114 115 8.069574 TGATTGTTATCATATTGCGTGTGATTC 58.930 33.333 6.49 0.56 39.17 2.52
123 124 9.325198 TCATATTGCGTGTGATTCTTACTATTT 57.675 29.630 0.00 0.00 0.00 1.40
124 125 9.586150 CATATTGCGTGTGATTCTTACTATTTC 57.414 33.333 0.00 0.00 0.00 2.17
126 127 8.942338 ATTGCGTGTGATTCTTACTATTTCTA 57.058 30.769 0.00 0.00 0.00 2.10
184 185 7.412891 GCAAATAATGGTGTTTATGAACTTGCC 60.413 37.037 1.75 2.80 36.70 4.52
192 193 5.240844 GTGTTTATGAACTTGCCAGGTTAGT 59.759 40.000 1.75 0.00 36.70 2.24
205 207 5.222048 TGCCAGGTTAGTTAGGATTTTGTCT 60.222 40.000 0.00 0.00 0.00 3.41
222 224 5.756195 TTGTCTGACTTCTGATTGGTTTG 57.244 39.130 9.51 0.00 0.00 2.93
228 230 5.065914 TGACTTCTGATTGGTTTGAGAAGG 58.934 41.667 0.00 0.00 43.82 3.46
231 233 4.908601 TCTGATTGGTTTGAGAAGGCTA 57.091 40.909 0.00 0.00 0.00 3.93
241 243 4.511617 TTGAGAAGGCTATGAGCGATAG 57.488 45.455 0.00 2.32 43.62 2.08
242 244 3.491342 TGAGAAGGCTATGAGCGATAGT 58.509 45.455 7.41 0.00 43.62 2.12
243 245 3.254411 TGAGAAGGCTATGAGCGATAGTG 59.746 47.826 7.41 0.00 43.62 2.74
244 246 3.226777 AGAAGGCTATGAGCGATAGTGT 58.773 45.455 7.41 0.00 43.62 3.55
245 247 4.399219 AGAAGGCTATGAGCGATAGTGTA 58.601 43.478 7.41 0.00 43.62 2.90
246 248 4.216687 AGAAGGCTATGAGCGATAGTGTAC 59.783 45.833 7.41 0.00 43.62 2.90
247 249 2.820787 AGGCTATGAGCGATAGTGTACC 59.179 50.000 7.41 1.72 43.62 3.34
248 250 2.094649 GGCTATGAGCGATAGTGTACCC 60.095 54.545 7.41 0.00 43.62 3.69
249 251 2.094649 GCTATGAGCGATAGTGTACCCC 60.095 54.545 7.41 0.00 37.04 4.95
250 252 2.383442 ATGAGCGATAGTGTACCCCT 57.617 50.000 0.00 0.00 39.35 4.79
251 253 1.688772 TGAGCGATAGTGTACCCCTC 58.311 55.000 0.00 0.00 39.35 4.30
252 254 0.592148 GAGCGATAGTGTACCCCTCG 59.408 60.000 0.00 0.00 39.35 4.63
253 255 0.106819 AGCGATAGTGTACCCCTCGT 60.107 55.000 0.00 0.00 39.35 4.18
254 256 0.743097 GCGATAGTGTACCCCTCGTT 59.257 55.000 0.00 0.00 39.35 3.85
255 257 1.949525 GCGATAGTGTACCCCTCGTTA 59.050 52.381 0.00 0.00 39.35 3.18
256 258 2.358898 GCGATAGTGTACCCCTCGTTAA 59.641 50.000 0.00 0.00 39.35 2.01
257 259 3.181487 GCGATAGTGTACCCCTCGTTAAA 60.181 47.826 0.00 0.00 39.35 1.52
258 260 4.354587 CGATAGTGTACCCCTCGTTAAAC 58.645 47.826 0.00 0.00 0.00 2.01
259 261 4.142403 CGATAGTGTACCCCTCGTTAAACA 60.142 45.833 0.00 0.00 0.00 2.83
260 262 5.622007 CGATAGTGTACCCCTCGTTAAACAA 60.622 44.000 0.00 0.00 0.00 2.83
261 263 4.628963 AGTGTACCCCTCGTTAAACAAT 57.371 40.909 0.00 0.00 0.00 2.71
262 264 4.320870 AGTGTACCCCTCGTTAAACAATG 58.679 43.478 0.00 0.00 0.00 2.82
263 265 4.067192 GTGTACCCCTCGTTAAACAATGT 58.933 43.478 0.00 0.00 0.00 2.71
264 266 5.011943 AGTGTACCCCTCGTTAAACAATGTA 59.988 40.000 0.00 0.00 0.00 2.29
265 267 5.700373 GTGTACCCCTCGTTAAACAATGTAA 59.300 40.000 0.00 0.00 0.00 2.41
266 268 5.700373 TGTACCCCTCGTTAAACAATGTAAC 59.300 40.000 0.00 0.00 0.00 2.50
288 290 7.928307 AACTGCTATGTGTGATGAATAAAGT 57.072 32.000 0.00 0.00 0.00 2.66
300 302 8.613482 TGTGATGAATAAAGTGTTTCGTGTTTA 58.387 29.630 0.00 0.00 0.00 2.01
333 335 7.711339 ACAGAACGTGACTCTCTTCTTTAAAAT 59.289 33.333 0.00 0.00 0.00 1.82
338 340 7.114529 ACGTGACTCTCTTCTTTAAAATACACG 59.885 37.037 0.00 0.00 46.03 4.49
353 355 3.374402 ACGAGACTCGGGGTGCAG 61.374 66.667 27.39 0.00 45.59 4.41
574 582 0.244994 GTCCACAGTGACTCAGCGAT 59.755 55.000 0.62 0.00 32.39 4.58
583 591 0.867753 GACTCAGCGATACACTGCGG 60.868 60.000 0.00 0.00 35.04 5.69
968 1012 1.891150 AGCTGCCAATTCCAAAGACTG 59.109 47.619 0.00 0.00 0.00 3.51
1041 1085 4.011517 GACTTTGTCCCGGCCGGA 62.012 66.667 45.44 27.72 38.83 5.14
1217 1261 7.010552 CAGATTCTTTTGTAATGTAGCTAGCGT 59.989 37.037 9.55 0.21 0.00 5.07
1218 1262 7.549488 AGATTCTTTTGTAATGTAGCTAGCGTT 59.451 33.333 9.55 6.05 0.00 4.84
1219 1263 7.429636 TTCTTTTGTAATGTAGCTAGCGTTT 57.570 32.000 9.55 4.54 0.00 3.60
1220 1264 6.827641 TCTTTTGTAATGTAGCTAGCGTTTG 58.172 36.000 9.55 0.00 0.00 2.93
1221 1265 4.593597 TTGTAATGTAGCTAGCGTTTGC 57.406 40.909 9.55 6.16 43.24 3.68
1263 1307 3.087031 ACACTGAGCTTGCATGCTAATT 58.913 40.909 25.39 11.22 44.17 1.40
1266 1310 2.858344 CTGAGCTTGCATGCTAATTTGC 59.142 45.455 25.39 13.23 44.17 3.68
1283 1327 6.854496 AATTTGCTCTGTACTGTTCGTTTA 57.146 33.333 0.00 0.00 0.00 2.01
1295 1339 9.531942 TGTACTGTTCGTTTATGTTTCTCTTTA 57.468 29.630 0.00 0.00 0.00 1.85
1320 1364 1.550976 GTGAGGAGGTGACGGAGAAAT 59.449 52.381 0.00 0.00 0.00 2.17
1517 1561 1.228552 GGCCAAGCTCAACTTCCCA 60.229 57.895 0.00 0.00 36.04 4.37
1586 1630 3.093278 CCCAAGAAGCGTCGCATC 58.907 61.111 21.09 17.56 0.00 3.91
1632 1676 4.097361 GGTCTCCACTTCCGGCCC 62.097 72.222 0.00 0.00 0.00 5.80
1749 1793 0.465705 GGAGGCCGTCAATCTCATCA 59.534 55.000 0.00 0.00 0.00 3.07
1849 1897 7.118390 CAGATTGGTCGAAGTCTTTTGATTAGT 59.882 37.037 0.00 0.00 0.00 2.24
1924 1972 8.800370 TTTGTAGTGGAATGCTATGTAATTCA 57.200 30.769 0.00 0.00 35.00 2.57
1962 2015 1.620822 AATGTGGAGAACTTGCACCC 58.379 50.000 0.00 0.00 46.57 4.61
1968 2021 2.031870 GGAGAACTTGCACCCACTTTT 58.968 47.619 0.00 0.00 0.00 2.27
1981 2035 5.634859 GCACCCACTTTTCTGACATAAAATG 59.365 40.000 0.00 2.10 0.00 2.32
2006 2060 6.348540 GGAACTTTTCACGCTCTCATTTGTAT 60.349 38.462 0.00 0.00 0.00 2.29
2033 2087 0.865769 ACGAAACAGTTCATGTCCGC 59.134 50.000 0.00 0.00 43.00 5.54
2039 2093 1.673920 ACAGTTCATGTCCGCGTTTTT 59.326 42.857 4.92 0.00 37.75 1.94
2040 2094 2.286772 ACAGTTCATGTCCGCGTTTTTC 60.287 45.455 4.92 0.00 37.75 2.29
2041 2095 1.944024 AGTTCATGTCCGCGTTTTTCA 59.056 42.857 4.92 0.00 0.00 2.69
2042 2096 2.356382 AGTTCATGTCCGCGTTTTTCAA 59.644 40.909 4.92 0.00 0.00 2.69
2043 2097 2.392933 TCATGTCCGCGTTTTTCAAC 57.607 45.000 4.92 0.00 0.00 3.18
2072 2127 9.639601 TTTTACGCACATCTATCTATAGATTGG 57.360 33.333 20.13 13.26 45.32 3.16
2073 2128 8.575649 TTACGCACATCTATCTATAGATTGGA 57.424 34.615 20.13 17.44 45.32 3.53
2075 2130 7.316640 ACGCACATCTATCTATAGATTGGAAC 58.683 38.462 20.13 6.36 45.32 3.62
2076 2131 7.039714 ACGCACATCTATCTATAGATTGGAACA 60.040 37.037 20.13 3.52 45.32 3.18
2077 2132 7.814587 CGCACATCTATCTATAGATTGGAACAA 59.185 37.037 20.13 3.17 45.32 2.83
2078 2133 9.149225 GCACATCTATCTATAGATTGGAACAAG 57.851 37.037 20.13 9.83 45.32 3.16
2079 2134 9.650539 CACATCTATCTATAGATTGGAACAAGG 57.349 37.037 20.13 6.72 45.32 3.61
2094 2149 7.883391 TGGAACAAGGTTACAAACTTAATCA 57.117 32.000 0.00 0.00 31.92 2.57
2095 2150 8.472007 TGGAACAAGGTTACAAACTTAATCAT 57.528 30.769 0.00 0.00 31.92 2.45
2096 2151 8.356657 TGGAACAAGGTTACAAACTTAATCATG 58.643 33.333 0.00 0.00 31.92 3.07
2097 2152 8.357402 GGAACAAGGTTACAAACTTAATCATGT 58.643 33.333 0.00 0.00 27.71 3.21
2098 2153 9.394477 GAACAAGGTTACAAACTTAATCATGTC 57.606 33.333 0.00 0.00 26.80 3.06
2099 2154 8.691661 ACAAGGTTACAAACTTAATCATGTCT 57.308 30.769 0.00 0.00 0.00 3.41
2100 2155 9.131791 ACAAGGTTACAAACTTAATCATGTCTT 57.868 29.630 0.00 0.00 0.00 3.01
2164 2219 6.875926 AAAGAAAATGCACGAAATCTATGC 57.124 33.333 0.00 0.00 39.88 3.14
2170 2225 4.801147 TGCACGAAATCTATGCAAGATC 57.199 40.909 10.52 0.00 45.96 2.75
2171 2226 4.445453 TGCACGAAATCTATGCAAGATCT 58.555 39.130 10.52 0.00 45.96 2.75
2172 2227 5.600696 TGCACGAAATCTATGCAAGATCTA 58.399 37.500 10.52 0.00 45.96 1.98
2173 2228 5.693555 TGCACGAAATCTATGCAAGATCTAG 59.306 40.000 10.52 0.00 45.96 2.43
2174 2229 5.923114 GCACGAAATCTATGCAAGATCTAGA 59.077 40.000 10.52 0.00 44.56 2.43
2175 2230 6.128956 GCACGAAATCTATGCAAGATCTAGAC 60.129 42.308 10.52 0.00 44.56 2.59
2176 2231 7.144661 CACGAAATCTATGCAAGATCTAGACT 58.855 38.462 10.52 0.00 44.56 3.24
2177 2232 7.114670 CACGAAATCTATGCAAGATCTAGACTG 59.885 40.741 10.52 0.00 44.56 3.51
2178 2233 7.013750 ACGAAATCTATGCAAGATCTAGACTGA 59.986 37.037 10.52 0.00 44.56 3.41
2179 2234 7.538334 CGAAATCTATGCAAGATCTAGACTGAG 59.462 40.741 10.52 0.00 44.56 3.35
2180 2235 8.476064 AAATCTATGCAAGATCTAGACTGAGA 57.524 34.615 10.52 0.00 44.56 3.27
2181 2236 8.654485 AATCTATGCAAGATCTAGACTGAGAT 57.346 34.615 10.52 0.00 44.56 2.75
2182 2237 8.654485 ATCTATGCAAGATCTAGACTGAGATT 57.346 34.615 0.00 0.00 41.32 2.40
2183 2238 8.476064 TCTATGCAAGATCTAGACTGAGATTT 57.524 34.615 0.00 0.00 36.27 2.17
2184 2239 9.579932 TCTATGCAAGATCTAGACTGAGATTTA 57.420 33.333 0.00 0.00 36.27 1.40
2185 2240 9.844790 CTATGCAAGATCTAGACTGAGATTTAG 57.155 37.037 0.00 0.00 36.27 1.85
2186 2241 6.511416 TGCAAGATCTAGACTGAGATTTAGC 58.489 40.000 0.00 0.00 36.27 3.09
2187 2242 5.629020 GCAAGATCTAGACTGAGATTTAGCG 59.371 44.000 0.00 0.00 36.27 4.26
2188 2243 6.514212 GCAAGATCTAGACTGAGATTTAGCGA 60.514 42.308 0.00 0.00 36.27 4.93
2189 2244 7.592938 CAAGATCTAGACTGAGATTTAGCGAT 58.407 38.462 0.00 0.00 36.27 4.58
2190 2245 7.377766 AGATCTAGACTGAGATTTAGCGATC 57.622 40.000 0.00 0.00 36.27 3.69
2191 2246 5.950758 TCTAGACTGAGATTTAGCGATCC 57.049 43.478 0.00 0.00 0.00 3.36
2192 2247 3.634568 AGACTGAGATTTAGCGATCCG 57.365 47.619 0.00 0.00 0.00 4.18
2193 2248 2.294791 AGACTGAGATTTAGCGATCCGG 59.705 50.000 0.00 0.00 0.00 5.14
2206 2261 4.761975 AGCGATCCGGTTAGAACAAATTA 58.238 39.130 0.00 0.00 32.22 1.40
2209 2264 5.235616 GCGATCCGGTTAGAACAAATTATCA 59.764 40.000 0.00 0.00 0.00 2.15
2213 2268 9.849166 GATCCGGTTAGAACAAATTATCAAAAA 57.151 29.630 0.00 0.00 0.00 1.94
2236 2538 9.952030 AAAAATTCCTTTCCTTTTTGTGTCTAA 57.048 25.926 0.00 0.00 32.46 2.10
2255 2557 9.408731 GTGTCTAAAATTTTCTTTTCTTTTGCG 57.591 29.630 6.72 0.00 0.00 4.85
2256 2558 8.599774 TGTCTAAAATTTTCTTTTCTTTTGCGG 58.400 29.630 6.72 0.00 0.00 5.69
2257 2559 8.061857 GTCTAAAATTTTCTTTTCTTTTGCGGG 58.938 33.333 6.72 0.00 0.00 6.13
2259 2561 1.846541 TTTCTTTTCTTTTGCGGGCG 58.153 45.000 0.00 0.00 0.00 6.13
2260 2562 1.025812 TTCTTTTCTTTTGCGGGCGA 58.974 45.000 0.00 0.00 0.00 5.54
2261 2563 1.243902 TCTTTTCTTTTGCGGGCGAT 58.756 45.000 0.00 0.00 0.00 4.58
2268 3746 4.181309 TCTTTTGCGGGCGATAAAATTT 57.819 36.364 0.00 0.00 0.00 1.82
2269 3747 4.170256 TCTTTTGCGGGCGATAAAATTTC 58.830 39.130 0.00 0.00 0.00 2.17
2270 3748 3.859411 TTTGCGGGCGATAAAATTTCT 57.141 38.095 0.00 0.00 0.00 2.52
2272 3750 2.639065 TGCGGGCGATAAAATTTCTCT 58.361 42.857 0.00 0.00 0.00 3.10
2274 3752 3.442273 TGCGGGCGATAAAATTTCTCTTT 59.558 39.130 0.00 0.00 0.00 2.52
2276 3754 4.499399 GCGGGCGATAAAATTTCTCTTTTC 59.501 41.667 0.00 0.00 31.15 2.29
2282 3760 9.797473 GGCGATAAAATTTCTCTTTTCTTTTTG 57.203 29.630 0.00 0.00 31.15 2.44
2326 4532 4.520492 ACTAAAACAATGGGTCTGCTTCAG 59.480 41.667 0.00 0.00 0.00 3.02
2352 4562 5.775195 ACACCCCCTCTCAAAAATAAGAAAG 59.225 40.000 0.00 0.00 0.00 2.62
2353 4563 6.010219 CACCCCCTCTCAAAAATAAGAAAGA 58.990 40.000 0.00 0.00 0.00 2.52
2356 4566 6.151817 CCCCCTCTCAAAAATAAGAAAGAGTG 59.848 42.308 0.00 0.00 0.00 3.51
2361 4571 8.324163 TCTCAAAAATAAGAAAGAGTGGCTAC 57.676 34.615 0.00 0.00 0.00 3.58
2371 4581 0.796927 GAGTGGCTACGTTTGCTTCC 59.203 55.000 11.91 2.60 0.00 3.46
2380 4590 4.442472 GCTACGTTTGCTTCCCTAGGAATA 60.442 45.833 11.48 0.00 41.23 1.75
2384 4594 6.838382 ACGTTTGCTTCCCTAGGAATATATT 58.162 36.000 11.48 0.00 41.23 1.28
2385 4595 7.970102 ACGTTTGCTTCCCTAGGAATATATTA 58.030 34.615 11.48 0.00 41.23 0.98
2386 4596 8.603304 ACGTTTGCTTCCCTAGGAATATATTAT 58.397 33.333 11.48 0.00 41.23 1.28
2387 4597 8.883731 CGTTTGCTTCCCTAGGAATATATTATG 58.116 37.037 11.48 0.00 41.23 1.90
2388 4598 9.740710 GTTTGCTTCCCTAGGAATATATTATGT 57.259 33.333 11.48 0.00 41.23 2.29
2412 4622 7.876068 TGTATACACTCTTTCCTTTTCACGAAT 59.124 33.333 0.08 0.00 0.00 3.34
2413 4623 7.745620 ATACACTCTTTCCTTTTCACGAATT 57.254 32.000 0.00 0.00 0.00 2.17
2416 4633 7.415229 ACACTCTTTCCTTTTCACGAATTAAC 58.585 34.615 0.00 0.00 0.00 2.01
2432 4649 6.531240 ACGAATTAACGTATGTACATTCCGTT 59.469 34.615 31.11 31.11 44.72 4.44
2436 4653 8.700722 ATTAACGTATGTACATTCCGTTTGTA 57.299 30.769 32.40 23.59 37.85 2.41
2437 4654 8.526218 TTAACGTATGTACATTCCGTTTGTAA 57.474 30.769 32.40 23.83 37.85 2.41
2438 4655 7.418840 AACGTATGTACATTCCGTTTGTAAA 57.581 32.000 26.93 2.27 35.27 2.01
2440 4657 7.859598 ACGTATGTACATTCCGTTTGTAAAAA 58.140 30.769 20.89 0.00 31.72 1.94
2475 4721 5.527951 TCAAAGTGTACCAAATTCATGTGC 58.472 37.500 0.00 0.00 0.00 4.57
2484 5051 7.714377 TGTACCAAATTCATGTGCATTTTTCTT 59.286 29.630 0.00 0.00 0.00 2.52
2492 5059 5.927689 TCATGTGCATTTTTCTTGTCCATTC 59.072 36.000 0.00 0.00 0.00 2.67
2502 5069 8.477419 TTTTTCTTGTCCATTCTTGTCCTATT 57.523 30.769 0.00 0.00 0.00 1.73
2560 5134 4.280174 GTGCCATGATTAAATGCCTCTGAT 59.720 41.667 0.00 0.00 0.00 2.90
2561 5135 4.897076 TGCCATGATTAAATGCCTCTGATT 59.103 37.500 0.00 0.00 0.00 2.57
2562 5136 5.010314 TGCCATGATTAAATGCCTCTGATTC 59.990 40.000 0.00 0.00 0.00 2.52
2563 5137 5.243283 GCCATGATTAAATGCCTCTGATTCT 59.757 40.000 0.00 0.00 0.00 2.40
2564 5138 6.678878 CCATGATTAAATGCCTCTGATTCTG 58.321 40.000 0.00 0.00 0.00 3.02
2565 5139 6.489022 CCATGATTAAATGCCTCTGATTCTGA 59.511 38.462 0.00 0.00 0.00 3.27
2609 5183 4.342951 TGTGATCCTACCAAACCCTATACG 59.657 45.833 0.00 0.00 0.00 3.06
2610 5184 4.343239 GTGATCCTACCAAACCCTATACGT 59.657 45.833 0.00 0.00 0.00 3.57
2611 5185 4.342951 TGATCCTACCAAACCCTATACGTG 59.657 45.833 0.00 0.00 0.00 4.49
2612 5186 3.711863 TCCTACCAAACCCTATACGTGT 58.288 45.455 0.00 0.00 0.00 4.49
2613 5187 4.865905 TCCTACCAAACCCTATACGTGTA 58.134 43.478 0.00 0.00 0.00 2.90
2614 5188 4.644685 TCCTACCAAACCCTATACGTGTAC 59.355 45.833 0.00 0.00 0.00 2.90
2615 5189 4.646492 CCTACCAAACCCTATACGTGTACT 59.354 45.833 0.00 0.00 0.00 2.73
2690 5265 6.872920 TGCACTCTTTTGACAACCTTTTATT 58.127 32.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.860881 CTAGCTCCCGCTCCCCCA 62.861 72.222 0.00 0.00 45.15 4.96
36 37 2.941563 TAACTAGCTCCCGCTCCCCC 62.942 65.000 0.00 0.00 45.15 5.40
37 38 1.457079 TAACTAGCTCCCGCTCCCC 60.457 63.158 0.00 0.00 45.15 4.81
38 39 0.467659 TCTAACTAGCTCCCGCTCCC 60.468 60.000 0.00 0.00 45.15 4.30
39 40 0.955905 CTCTAACTAGCTCCCGCTCC 59.044 60.000 0.00 0.00 45.15 4.70
40 41 0.312729 GCTCTAACTAGCTCCCGCTC 59.687 60.000 0.00 0.00 45.15 5.03
42 43 1.008309 CGCTCTAACTAGCTCCCGC 60.008 63.158 0.00 0.00 40.49 6.13
43 44 1.102222 ACCGCTCTAACTAGCTCCCG 61.102 60.000 0.00 0.00 40.49 5.14
44 45 1.881324 CTACCGCTCTAACTAGCTCCC 59.119 57.143 0.00 0.00 40.49 4.30
45 46 2.574450 ACTACCGCTCTAACTAGCTCC 58.426 52.381 0.00 0.00 40.49 4.70
46 47 4.024977 GTGTACTACCGCTCTAACTAGCTC 60.025 50.000 0.00 0.00 40.49 4.09
47 48 3.876320 GTGTACTACCGCTCTAACTAGCT 59.124 47.826 0.00 0.00 40.49 3.32
48 49 3.003171 GGTGTACTACCGCTCTAACTAGC 59.997 52.174 0.00 0.00 40.26 3.42
49 50 4.809815 GGTGTACTACCGCTCTAACTAG 57.190 50.000 0.00 0.00 40.26 2.57
61 62 3.262420 CATGCAACTCAGGGTGTACTAC 58.738 50.000 0.00 0.00 0.00 2.73
62 63 2.903784 ACATGCAACTCAGGGTGTACTA 59.096 45.455 0.00 0.00 0.00 1.82
63 64 1.699634 ACATGCAACTCAGGGTGTACT 59.300 47.619 0.00 0.00 0.00 2.73
64 65 2.185004 ACATGCAACTCAGGGTGTAC 57.815 50.000 0.00 0.00 0.00 2.90
65 66 2.778299 GAACATGCAACTCAGGGTGTA 58.222 47.619 0.00 0.00 0.00 2.90
66 67 1.609208 GAACATGCAACTCAGGGTGT 58.391 50.000 0.00 0.00 0.00 4.16
67 68 0.518636 CGAACATGCAACTCAGGGTG 59.481 55.000 0.00 0.00 0.00 4.61
68 69 0.396435 TCGAACATGCAACTCAGGGT 59.604 50.000 0.00 0.00 0.00 4.34
69 70 1.399440 CATCGAACATGCAACTCAGGG 59.601 52.381 0.00 0.00 0.00 4.45
70 71 2.349590 TCATCGAACATGCAACTCAGG 58.650 47.619 0.00 0.00 0.00 3.86
71 72 4.142752 ACAATCATCGAACATGCAACTCAG 60.143 41.667 0.00 0.00 0.00 3.35
72 73 3.752747 ACAATCATCGAACATGCAACTCA 59.247 39.130 0.00 0.00 0.00 3.41
73 74 4.346734 ACAATCATCGAACATGCAACTC 57.653 40.909 0.00 0.00 0.00 3.01
74 75 4.771590 AACAATCATCGAACATGCAACT 57.228 36.364 0.00 0.00 0.00 3.16
75 76 6.257423 TGATAACAATCATCGAACATGCAAC 58.743 36.000 0.00 0.00 0.00 4.17
76 77 6.434018 TGATAACAATCATCGAACATGCAA 57.566 33.333 0.00 0.00 0.00 4.08
77 78 6.622833 ATGATAACAATCATCGAACATGCA 57.377 33.333 0.00 0.00 36.63 3.96
80 81 7.959109 CGCAATATGATAACAATCATCGAACAT 59.041 33.333 4.21 0.00 41.20 2.71
86 87 7.575365 TCACACGCAATATGATAACAATCATC 58.425 34.615 4.21 0.00 41.20 2.92
105 106 8.928270 AACCTAGAAATAGTAAGAATCACACG 57.072 34.615 0.00 0.00 0.00 4.49
144 145 9.643693 CACCATTATTTGCTTCTCTAAAACAAT 57.356 29.630 0.00 0.00 0.00 2.71
145 146 8.637986 ACACCATTATTTGCTTCTCTAAAACAA 58.362 29.630 0.00 0.00 0.00 2.83
146 147 8.177119 ACACCATTATTTGCTTCTCTAAAACA 57.823 30.769 0.00 0.00 0.00 2.83
147 148 9.476202 AAACACCATTATTTGCTTCTCTAAAAC 57.524 29.630 0.00 0.00 0.00 2.43
151 152 9.679661 TCATAAACACCATTATTTGCTTCTCTA 57.320 29.630 0.00 0.00 0.00 2.43
168 169 4.584327 AACCTGGCAAGTTCATAAACAC 57.416 40.909 0.00 0.00 37.88 3.32
169 170 5.381757 ACTAACCTGGCAAGTTCATAAACA 58.618 37.500 4.45 0.00 37.88 2.83
184 185 7.162082 AGTCAGACAAAATCCTAACTAACCTG 58.838 38.462 2.66 0.00 0.00 4.00
192 193 7.391554 CCAATCAGAAGTCAGACAAAATCCTAA 59.608 37.037 2.66 0.00 0.00 2.69
205 207 5.065914 CCTTCTCAAACCAATCAGAAGTCA 58.934 41.667 6.75 0.00 40.14 3.41
222 224 3.254657 ACACTATCGCTCATAGCCTTCTC 59.745 47.826 0.00 0.00 38.54 2.87
228 230 2.094649 GGGGTACACTATCGCTCATAGC 60.095 54.545 0.00 0.00 38.54 2.97
231 233 2.240279 GAGGGGTACACTATCGCTCAT 58.760 52.381 0.00 0.00 45.26 2.90
241 243 4.067192 ACATTGTTTAACGAGGGGTACAC 58.933 43.478 2.02 0.00 0.00 2.90
242 244 4.354893 ACATTGTTTAACGAGGGGTACA 57.645 40.909 2.02 0.00 0.00 2.90
243 245 5.934043 AGTTACATTGTTTAACGAGGGGTAC 59.066 40.000 2.02 0.00 35.05 3.34
244 246 5.933463 CAGTTACATTGTTTAACGAGGGGTA 59.067 40.000 2.02 0.00 35.05 3.69
245 247 4.758165 CAGTTACATTGTTTAACGAGGGGT 59.242 41.667 2.02 0.00 35.05 4.95
246 248 4.379082 GCAGTTACATTGTTTAACGAGGGG 60.379 45.833 2.02 0.00 35.05 4.79
247 249 4.454504 AGCAGTTACATTGTTTAACGAGGG 59.545 41.667 2.02 0.00 35.05 4.30
248 250 5.607119 AGCAGTTACATTGTTTAACGAGG 57.393 39.130 0.00 0.00 35.05 4.63
249 251 7.688167 CACATAGCAGTTACATTGTTTAACGAG 59.312 37.037 0.00 0.00 35.05 4.18
250 252 7.171848 ACACATAGCAGTTACATTGTTTAACGA 59.828 33.333 0.00 0.00 35.05 3.85
251 253 7.268235 CACACATAGCAGTTACATTGTTTAACG 59.732 37.037 0.00 0.00 35.05 3.18
252 254 8.286800 TCACACATAGCAGTTACATTGTTTAAC 58.713 33.333 0.00 0.00 0.00 2.01
253 255 8.384607 TCACACATAGCAGTTACATTGTTTAA 57.615 30.769 0.00 0.00 0.00 1.52
254 256 7.971183 TCACACATAGCAGTTACATTGTTTA 57.029 32.000 0.00 0.00 0.00 2.01
255 257 6.875948 TCACACATAGCAGTTACATTGTTT 57.124 33.333 0.00 0.00 0.00 2.83
256 258 6.654582 TCATCACACATAGCAGTTACATTGTT 59.345 34.615 0.00 0.00 0.00 2.83
257 259 6.172630 TCATCACACATAGCAGTTACATTGT 58.827 36.000 0.00 0.00 0.00 2.71
258 260 6.667007 TCATCACACATAGCAGTTACATTG 57.333 37.500 0.00 0.00 0.00 2.82
259 261 7.870509 ATTCATCACACATAGCAGTTACATT 57.129 32.000 0.00 0.00 0.00 2.71
260 262 8.962884 TTATTCATCACACATAGCAGTTACAT 57.037 30.769 0.00 0.00 0.00 2.29
261 263 8.785329 TTTATTCATCACACATAGCAGTTACA 57.215 30.769 0.00 0.00 0.00 2.41
262 264 8.883731 ACTTTATTCATCACACATAGCAGTTAC 58.116 33.333 0.00 0.00 0.00 2.50
263 265 8.882736 CACTTTATTCATCACACATAGCAGTTA 58.117 33.333 0.00 0.00 0.00 2.24
264 266 7.391554 ACACTTTATTCATCACACATAGCAGTT 59.608 33.333 0.00 0.00 0.00 3.16
265 267 6.881065 ACACTTTATTCATCACACATAGCAGT 59.119 34.615 0.00 0.00 0.00 4.40
266 268 7.312657 ACACTTTATTCATCACACATAGCAG 57.687 36.000 0.00 0.00 0.00 4.24
318 320 8.973835 AGTCTCGTGTATTTTAAAGAAGAGAG 57.026 34.615 4.53 5.70 33.60 3.20
333 335 2.338015 GCACCCCGAGTCTCGTGTA 61.338 63.158 20.37 0.00 38.40 2.90
338 340 4.459089 GCCTGCACCCCGAGTCTC 62.459 72.222 0.00 0.00 0.00 3.36
353 355 2.450479 AATAGCCTATCCGTGCCGCC 62.450 60.000 0.00 0.00 0.00 6.13
369 371 0.107897 ATTCGCACCACTGCCGAATA 60.108 50.000 5.79 0.00 41.08 1.75
387 389 1.532794 TGCCCCGGTTTGCTGAAAT 60.533 52.632 0.00 0.00 0.00 2.17
388 390 2.123683 TGCCCCGGTTTGCTGAAA 60.124 55.556 0.00 0.00 0.00 2.69
968 1012 2.557490 ACCACGTTCTCCTCTTACTCAC 59.443 50.000 0.00 0.00 0.00 3.51
1019 1063 2.742372 CCGGGACAAAGTCGGCTG 60.742 66.667 0.00 0.00 37.25 4.85
1153 1197 6.903883 ACTGTGACCGTATAATTTGATGAC 57.096 37.500 0.00 0.00 0.00 3.06
1217 1261 7.171508 GTCAATCATAGATATGGAAGACGCAAA 59.828 37.037 0.19 0.00 34.50 3.68
1218 1262 6.646653 GTCAATCATAGATATGGAAGACGCAA 59.353 38.462 0.19 0.00 34.50 4.85
1219 1263 6.159293 GTCAATCATAGATATGGAAGACGCA 58.841 40.000 0.19 0.00 34.50 5.24
1220 1264 6.090088 GTGTCAATCATAGATATGGAAGACGC 59.910 42.308 12.56 12.56 34.15 5.19
1221 1265 7.328005 CAGTGTCAATCATAGATATGGAAGACG 59.672 40.741 0.19 0.00 34.15 4.18
1222 1266 8.363390 TCAGTGTCAATCATAGATATGGAAGAC 58.637 37.037 0.19 6.35 34.50 3.01
1263 1307 5.294356 ACATAAACGAACAGTACAGAGCAA 58.706 37.500 0.00 0.00 0.00 3.91
1266 1310 7.595502 AGAGAAACATAAACGAACAGTACAGAG 59.404 37.037 0.00 0.00 0.00 3.35
1283 1327 7.182930 ACCTCCTCACCTTATAAAGAGAAACAT 59.817 37.037 9.60 0.00 0.00 2.71
1295 1339 1.006758 TCCGTCACCTCCTCACCTTAT 59.993 52.381 0.00 0.00 0.00 1.73
1583 1627 4.193334 TCCTCTGCCGCGACGATG 62.193 66.667 8.23 0.00 0.00 3.84
1586 1630 4.544689 CTCTCCTCTGCCGCGACG 62.545 72.222 8.23 0.00 0.00 5.12
1716 1760 3.322466 CTCCCAGGGCTCCACGTT 61.322 66.667 0.00 0.00 0.00 3.99
1740 1784 2.968574 ACGCCTACTCCATGATGAGATT 59.031 45.455 6.04 0.00 36.22 2.40
1788 1832 4.174129 GTAACCCATGCACGCCGC 62.174 66.667 0.00 0.00 42.89 6.53
1789 1833 1.653094 AATGTAACCCATGCACGCCG 61.653 55.000 0.00 0.00 32.82 6.46
1790 1834 0.530288 AAATGTAACCCATGCACGCC 59.470 50.000 0.00 0.00 32.82 5.68
1791 1835 1.627879 CAAATGTAACCCATGCACGC 58.372 50.000 0.00 0.00 32.82 5.34
1792 1836 1.627879 GCAAATGTAACCCATGCACG 58.372 50.000 0.00 0.00 32.82 5.34
1795 1839 0.814457 TCGGCAAATGTAACCCATGC 59.186 50.000 0.00 0.00 32.82 4.06
1802 1846 7.561021 TCTGCTTATTTATCGGCAAATGTAA 57.439 32.000 5.67 0.00 34.21 2.41
1849 1897 5.453339 CCAGGAAAGCCGAATGATACTCTAA 60.453 44.000 0.00 0.00 39.96 2.10
1859 1907 0.251787 AAAGCCCAGGAAAGCCGAAT 60.252 50.000 0.00 0.00 39.96 3.34
1883 1931 1.215423 ACAAAGGACCTGGATATGCCC 59.785 52.381 0.00 0.00 34.97 5.36
1924 1972 4.940046 ACATTTCTTCTGATCGTCATGCTT 59.060 37.500 0.00 0.00 0.00 3.91
1962 2015 9.533253 AAAGTTCCATTTTATGTCAGAAAAGTG 57.467 29.630 10.82 8.90 0.00 3.16
1968 2021 7.359595 CGTGAAAAGTTCCATTTTATGTCAGA 58.640 34.615 0.00 0.00 32.62 3.27
1981 2035 4.222114 CAAATGAGAGCGTGAAAAGTTCC 58.778 43.478 0.00 0.00 0.00 3.62
2006 2060 1.210870 GAACTGTTTCGTACGTGCCA 58.789 50.000 16.05 8.98 0.00 4.92
2062 2117 9.449719 AGTTTGTAACCTTGTTCCAATCTATAG 57.550 33.333 0.00 0.00 0.00 1.31
2063 2118 9.802039 AAGTTTGTAACCTTGTTCCAATCTATA 57.198 29.630 0.00 0.00 0.00 1.31
2064 2119 8.706322 AAGTTTGTAACCTTGTTCCAATCTAT 57.294 30.769 0.00 0.00 0.00 1.98
2065 2120 9.629878 TTAAGTTTGTAACCTTGTTCCAATCTA 57.370 29.630 0.00 0.00 0.00 1.98
2067 2122 9.406828 GATTAAGTTTGTAACCTTGTTCCAATC 57.593 33.333 0.00 0.00 0.00 2.67
2068 2123 8.919145 TGATTAAGTTTGTAACCTTGTTCCAAT 58.081 29.630 0.00 0.00 0.00 3.16
2071 2126 8.357402 ACATGATTAAGTTTGTAACCTTGTTCC 58.643 33.333 0.00 0.00 0.00 3.62
2072 2127 9.394477 GACATGATTAAGTTTGTAACCTTGTTC 57.606 33.333 0.00 0.00 0.00 3.18
2073 2128 9.131791 AGACATGATTAAGTTTGTAACCTTGTT 57.868 29.630 0.00 0.00 0.00 2.83
2138 2193 8.859156 GCATAGATTTCGTGCATTTTCTTTTAA 58.141 29.630 0.00 0.00 38.68 1.52
2139 2194 8.026026 TGCATAGATTTCGTGCATTTTCTTTTA 58.974 29.630 8.83 0.00 43.30 1.52
2140 2195 6.867816 TGCATAGATTTCGTGCATTTTCTTTT 59.132 30.769 8.83 0.00 43.30 2.27
2141 2196 6.389091 TGCATAGATTTCGTGCATTTTCTTT 58.611 32.000 8.83 0.00 43.30 2.52
2142 2197 5.953183 TGCATAGATTTCGTGCATTTTCTT 58.047 33.333 8.83 0.00 43.30 2.52
2143 2198 5.565592 TGCATAGATTTCGTGCATTTTCT 57.434 34.783 8.83 0.00 43.30 2.52
2144 2199 6.029607 TCTTGCATAGATTTCGTGCATTTTC 58.970 36.000 12.27 0.00 46.90 2.29
2145 2200 5.953183 TCTTGCATAGATTTCGTGCATTTT 58.047 33.333 12.27 0.00 46.90 1.82
2146 2201 5.565592 TCTTGCATAGATTTCGTGCATTT 57.434 34.783 12.27 0.00 46.90 2.32
2147 2202 5.530171 AGATCTTGCATAGATTTCGTGCATT 59.470 36.000 12.27 4.12 46.90 3.56
2148 2203 5.061853 AGATCTTGCATAGATTTCGTGCAT 58.938 37.500 12.27 1.68 46.90 3.96
2149 2204 4.445453 AGATCTTGCATAGATTTCGTGCA 58.555 39.130 11.18 8.83 43.75 4.57
2150 2205 5.923114 TCTAGATCTTGCATAGATTTCGTGC 59.077 40.000 0.00 4.66 43.75 5.34
2151 2206 7.114670 CAGTCTAGATCTTGCATAGATTTCGTG 59.885 40.741 0.00 4.12 43.75 4.35
2152 2207 7.013750 TCAGTCTAGATCTTGCATAGATTTCGT 59.986 37.037 0.00 2.96 43.75 3.85
2153 2208 7.366513 TCAGTCTAGATCTTGCATAGATTTCG 58.633 38.462 0.00 4.62 43.75 3.46
2154 2209 8.575589 TCTCAGTCTAGATCTTGCATAGATTTC 58.424 37.037 0.00 3.37 43.75 2.17
2155 2210 8.476064 TCTCAGTCTAGATCTTGCATAGATTT 57.524 34.615 0.00 8.98 43.75 2.17
2156 2211 8.654485 ATCTCAGTCTAGATCTTGCATAGATT 57.346 34.615 0.00 0.00 43.75 2.40
2157 2212 8.654485 AATCTCAGTCTAGATCTTGCATAGAT 57.346 34.615 0.00 10.07 46.41 1.98
2158 2213 8.476064 AAATCTCAGTCTAGATCTTGCATAGA 57.524 34.615 0.00 0.00 35.10 1.98
2159 2214 9.844790 CTAAATCTCAGTCTAGATCTTGCATAG 57.155 37.037 0.00 0.00 35.10 2.23
2160 2215 8.303156 GCTAAATCTCAGTCTAGATCTTGCATA 58.697 37.037 0.00 0.00 35.10 3.14
2161 2216 7.153985 GCTAAATCTCAGTCTAGATCTTGCAT 58.846 38.462 0.00 0.00 35.10 3.96
2162 2217 6.511416 GCTAAATCTCAGTCTAGATCTTGCA 58.489 40.000 0.00 0.00 35.10 4.08
2163 2218 5.629020 CGCTAAATCTCAGTCTAGATCTTGC 59.371 44.000 0.00 0.00 35.10 4.01
2164 2219 6.964908 TCGCTAAATCTCAGTCTAGATCTTG 58.035 40.000 0.00 0.00 35.10 3.02
2165 2220 7.094377 GGATCGCTAAATCTCAGTCTAGATCTT 60.094 40.741 0.00 0.00 35.10 2.40
2166 2221 6.374333 GGATCGCTAAATCTCAGTCTAGATCT 59.626 42.308 0.00 0.00 35.10 2.75
2167 2222 6.551736 GGATCGCTAAATCTCAGTCTAGATC 58.448 44.000 0.00 0.00 35.10 2.75
2168 2223 5.123186 CGGATCGCTAAATCTCAGTCTAGAT 59.877 44.000 0.00 0.00 37.84 1.98
2169 2224 4.452795 CGGATCGCTAAATCTCAGTCTAGA 59.547 45.833 0.00 0.00 0.00 2.43
2170 2225 4.378978 CCGGATCGCTAAATCTCAGTCTAG 60.379 50.000 0.00 0.00 0.00 2.43
2171 2226 3.502595 CCGGATCGCTAAATCTCAGTCTA 59.497 47.826 0.00 0.00 0.00 2.59
2172 2227 2.294791 CCGGATCGCTAAATCTCAGTCT 59.705 50.000 0.00 0.00 0.00 3.24
2173 2228 2.034812 ACCGGATCGCTAAATCTCAGTC 59.965 50.000 9.46 0.00 0.00 3.51
2174 2229 2.032620 ACCGGATCGCTAAATCTCAGT 58.967 47.619 9.46 0.00 0.00 3.41
2175 2230 2.802787 ACCGGATCGCTAAATCTCAG 57.197 50.000 9.46 0.00 0.00 3.35
2176 2231 3.887110 TCTAACCGGATCGCTAAATCTCA 59.113 43.478 9.46 0.00 0.00 3.27
2177 2232 4.500603 TCTAACCGGATCGCTAAATCTC 57.499 45.455 9.46 0.00 0.00 2.75
2178 2233 4.098960 TGTTCTAACCGGATCGCTAAATCT 59.901 41.667 9.46 0.00 0.00 2.40
2179 2234 4.365723 TGTTCTAACCGGATCGCTAAATC 58.634 43.478 9.46 0.00 0.00 2.17
2180 2235 4.395959 TGTTCTAACCGGATCGCTAAAT 57.604 40.909 9.46 0.00 0.00 1.40
2181 2236 3.872511 TGTTCTAACCGGATCGCTAAA 57.127 42.857 9.46 0.00 0.00 1.85
2182 2237 3.872511 TTGTTCTAACCGGATCGCTAA 57.127 42.857 9.46 0.00 0.00 3.09
2183 2238 3.872511 TTTGTTCTAACCGGATCGCTA 57.127 42.857 9.46 0.00 0.00 4.26
2184 2239 2.754946 TTTGTTCTAACCGGATCGCT 57.245 45.000 9.46 0.00 0.00 4.93
2185 2240 5.235616 TGATAATTTGTTCTAACCGGATCGC 59.764 40.000 9.46 0.00 0.00 4.58
2186 2241 6.838198 TGATAATTTGTTCTAACCGGATCG 57.162 37.500 9.46 0.00 0.00 3.69
2187 2242 9.849166 TTTTTGATAATTTGTTCTAACCGGATC 57.151 29.630 9.46 0.00 0.00 3.36
2235 2537 5.577835 GCCCGCAAAAGAAAAGAAAATTTT 58.422 33.333 2.28 2.28 0.00 1.82
2236 2538 4.260579 CGCCCGCAAAAGAAAAGAAAATTT 60.261 37.500 0.00 0.00 0.00 1.82
2246 2548 3.859411 ATTTTATCGCCCGCAAAAGAA 57.141 38.095 6.32 0.00 0.00 2.52
2247 2549 3.859411 AATTTTATCGCCCGCAAAAGA 57.141 38.095 6.32 0.00 0.00 2.52
2250 2552 3.442273 AGAGAAATTTTATCGCCCGCAAA 59.558 39.130 0.00 0.00 0.00 3.68
2251 2553 3.013921 AGAGAAATTTTATCGCCCGCAA 58.986 40.909 0.00 0.00 0.00 4.85
2252 2554 2.639065 AGAGAAATTTTATCGCCCGCA 58.361 42.857 0.00 0.00 0.00 5.69
2253 2555 3.692791 AAGAGAAATTTTATCGCCCGC 57.307 42.857 0.00 0.00 0.00 6.13
2255 2557 8.534333 AAAAGAAAAGAGAAATTTTATCGCCC 57.466 30.769 0.00 0.00 32.62 6.13
2256 2558 9.797473 CAAAAAGAAAAGAGAAATTTTATCGCC 57.203 29.630 0.00 0.00 32.62 5.54
2268 3746 8.197988 GTCTACTGACACAAAAAGAAAAGAGA 57.802 34.615 0.00 0.00 42.48 3.10
2299 3777 3.320826 GCAGACCCATTGTTTTAGTGGTT 59.679 43.478 0.00 0.00 34.50 3.67
2313 4519 0.685097 GGTGTACTGAAGCAGACCCA 59.315 55.000 0.82 0.00 35.18 4.51
2326 4532 5.812286 TCTTATTTTTGAGAGGGGGTGTAC 58.188 41.667 0.00 0.00 0.00 2.90
2352 4562 0.796927 GGAAGCAAACGTAGCCACTC 59.203 55.000 9.06 4.55 0.00 3.51
2353 4563 0.605589 GGGAAGCAAACGTAGCCACT 60.606 55.000 9.06 0.00 0.00 4.00
2356 4566 1.653151 CTAGGGAAGCAAACGTAGCC 58.347 55.000 9.06 0.00 0.00 3.93
2361 4571 8.883731 CATAATATATTCCTAGGGAAGCAAACG 58.116 37.037 9.46 0.00 45.48 3.60
2384 4594 8.525316 TCGTGAAAAGGAAAGAGTGTATACATA 58.475 33.333 9.18 0.00 0.00 2.29
2385 4595 7.383687 TCGTGAAAAGGAAAGAGTGTATACAT 58.616 34.615 9.18 0.00 0.00 2.29
2386 4596 6.751157 TCGTGAAAAGGAAAGAGTGTATACA 58.249 36.000 0.08 0.08 0.00 2.29
2387 4597 7.647907 TTCGTGAAAAGGAAAGAGTGTATAC 57.352 36.000 0.00 0.00 0.00 1.47
2388 4598 8.842358 AATTCGTGAAAAGGAAAGAGTGTATA 57.158 30.769 0.00 0.00 0.00 1.47
2389 4599 7.745620 AATTCGTGAAAAGGAAAGAGTGTAT 57.254 32.000 0.00 0.00 0.00 2.29
2390 4600 8.553696 GTTAATTCGTGAAAAGGAAAGAGTGTA 58.446 33.333 0.00 0.00 0.00 2.90
2391 4601 7.415229 GTTAATTCGTGAAAAGGAAAGAGTGT 58.585 34.615 0.00 0.00 0.00 3.55
2392 4602 6.573725 CGTTAATTCGTGAAAAGGAAAGAGTG 59.426 38.462 0.00 0.00 0.00 3.51
2393 4603 6.259387 ACGTTAATTCGTGAAAAGGAAAGAGT 59.741 34.615 0.00 0.00 42.56 3.24
2394 4604 6.656003 ACGTTAATTCGTGAAAAGGAAAGAG 58.344 36.000 0.00 0.00 42.56 2.85
2397 4607 7.863666 ACATACGTTAATTCGTGAAAAGGAAA 58.136 30.769 0.00 0.00 43.93 3.13
2401 4611 9.749490 AATGTACATACGTTAATTCGTGAAAAG 57.251 29.630 9.21 0.00 43.93 2.27
2406 4616 6.020440 ACGGAATGTACATACGTTAATTCGTG 60.020 38.462 24.39 10.16 43.93 4.35
2407 4617 6.035843 ACGGAATGTACATACGTTAATTCGT 58.964 36.000 24.39 14.74 45.97 3.85
2412 4622 8.526218 TTACAAACGGAATGTACATACGTTAA 57.474 30.769 32.91 25.47 40.83 2.01
2413 4623 8.526218 TTTACAAACGGAATGTACATACGTTA 57.474 30.769 32.91 22.76 40.83 3.18
2440 4657 9.442047 TTTGGTACACTTTGATTTGATGTTTTT 57.558 25.926 0.00 0.00 39.29 1.94
2441 4658 9.612066 ATTTGGTACACTTTGATTTGATGTTTT 57.388 25.926 0.00 0.00 39.29 2.43
2475 4721 6.752168 AGGACAAGAATGGACAAGAAAAATG 58.248 36.000 0.00 0.00 0.00 2.32
2502 5069 7.067737 AGACGTCAGTTTTGAGGGAAAATAAAA 59.932 33.333 19.50 0.00 42.15 1.52
2560 5134 2.489971 CGGCAAAGTGGTTACTCAGAA 58.510 47.619 0.00 0.00 35.69 3.02
2561 5135 1.270625 CCGGCAAAGTGGTTACTCAGA 60.271 52.381 0.00 0.00 35.69 3.27
2562 5136 1.156736 CCGGCAAAGTGGTTACTCAG 58.843 55.000 0.00 0.00 35.69 3.35
2563 5137 0.470766 ACCGGCAAAGTGGTTACTCA 59.529 50.000 0.00 0.00 35.69 3.41
2564 5138 1.154197 GACCGGCAAAGTGGTTACTC 58.846 55.000 0.00 0.00 38.99 2.59
2565 5139 0.763035 AGACCGGCAAAGTGGTTACT 59.237 50.000 0.00 0.00 38.99 2.24
2609 5183 5.391736 CGGTGCCTAGCTATATACAGTACAC 60.392 48.000 0.00 0.00 0.00 2.90
2610 5184 4.698780 CGGTGCCTAGCTATATACAGTACA 59.301 45.833 0.00 0.00 0.00 2.90
2611 5185 4.096081 CCGGTGCCTAGCTATATACAGTAC 59.904 50.000 0.00 0.00 0.00 2.73
2612 5186 4.263639 ACCGGTGCCTAGCTATATACAGTA 60.264 45.833 6.12 0.00 0.00 2.74
2613 5187 3.090037 CCGGTGCCTAGCTATATACAGT 58.910 50.000 0.00 0.00 0.00 3.55
2614 5188 3.090037 ACCGGTGCCTAGCTATATACAG 58.910 50.000 6.12 0.00 0.00 2.74
2615 5189 3.087031 GACCGGTGCCTAGCTATATACA 58.913 50.000 14.63 0.00 0.00 2.29
2641 5215 1.412453 TTAGGCGGTGTCCCTTGTGT 61.412 55.000 0.00 0.00 33.88 3.72


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

AutoCloner maintained by Alex Coulton.