Multiple sequence alignment - TraesCS4A01G084700

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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 TraesCS4A01G084700 chr4A 100.000 2276 0 0 1 2276 89443696 89445971 0.000000e+00 4204
1 TraesCS4A01G084700 chr4A 96.875 192 6 0 1981 2172 136618023 136617832 2.820000e-84 322
2 TraesCS4A01G084700 chr4A 95.337 193 9 0 1980 2172 564144968 564145160 7.900000e-80 307
3 TraesCS4A01G084700 chr4B 91.004 2012 138 23 1 1980 462216971 462214971 0.000000e+00 2673
4 TraesCS4A01G084700 chr4B 90.426 94 5 2 2172 2262 462214978 462214886 1.100000e-23 121
5 TraesCS4A01G084700 chr4D 92.946 1616 88 12 383 1980 375123935 375122328 0.000000e+00 2329
6 TraesCS4A01G084700 chr4D 88.798 366 36 5 1 363 375124483 375124120 5.770000e-121 444
7 TraesCS4A01G084700 chr4D 90.588 85 4 2 2172 2253 375122335 375122252 2.390000e-20 110
8 TraesCS4A01G084700 chr3D 96.859 191 6 0 1981 2171 337532240 337532050 1.010000e-83 320
9 TraesCS4A01G084700 chr5D 96.373 193 7 0 1981 2173 420901066 420900874 3.650000e-83 318
10 TraesCS4A01G084700 chr6D 96.335 191 7 0 1981 2171 418875183 418875373 4.720000e-82 315
11 TraesCS4A01G084700 chr7D 95.385 195 8 1 1978 2171 565658871 565658677 2.200000e-80 309
12 TraesCS4A01G084700 chr2A 95.312 192 9 0 1981 2172 722564094 722564285 2.840000e-79 305
13 TraesCS4A01G084700 chr6A 95.288 191 9 0 1981 2171 4914226 4914416 1.020000e-78 303
14 TraesCS4A01G084700 chr2D 95.288 191 9 0 1978 2168 526613971 526614161 1.020000e-78 303


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 TraesCS4A01G084700 chr4A 89443696 89445971 2275 False 4204 4204 100.000000 1 2276 1 chr4A.!!$F1 2275
1 TraesCS4A01G084700 chr4B 462214886 462216971 2085 True 1397 2673 90.715000 1 2262 2 chr4B.!!$R1 2261
2 TraesCS4A01G084700 chr4D 375122252 375124483 2231 True 961 2329 90.777333 1 2253 3 chr4D.!!$R1 2252

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
771 942 0.442699 CGAAAGCGGAAAGTAGTGGC 59.557 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2201 0.044855 AGCCTACCCTCCAATGTCCT 59.955 55.0 0.0 0.0 0.0 3.85 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
29 30 8.450964 TCGCTTACATGATAGAAAAGAAAAAGG 58.549 33.333 0.00 0.00 0.00 3.11
51 52 5.054477 GGACACGGCAATATAAGCTAAAGA 58.946 41.667 0.00 0.00 0.00 2.52
99 100 8.738645 AGACAAAAGAGTAAAGACAAAGATGT 57.261 30.769 0.00 0.00 44.25 3.06
123 125 4.211794 CCACAATTGCAAAAGACAATGGAC 59.788 41.667 1.71 0.00 37.78 4.02
125 127 2.791383 TTGCAAAAGACAATGGACGG 57.209 45.000 0.00 0.00 0.00 4.79
129 131 1.265635 CAAAAGACAATGGACGGCGAA 59.734 47.619 16.62 0.00 0.00 4.70
140 142 1.571919 GACGGCGAATAGAAGCACAT 58.428 50.000 16.62 0.00 34.54 3.21
148 150 6.566564 CGGCGAATAGAAGCACATAAATTCAT 60.567 38.462 0.00 0.00 34.54 2.57
149 151 6.798959 GGCGAATAGAAGCACATAAATTCATC 59.201 38.462 0.00 0.00 34.54 2.92
150 152 7.308229 GGCGAATAGAAGCACATAAATTCATCT 60.308 37.037 0.00 0.00 34.54 2.90
160 162 9.793252 AGCACATAAATTCATCTTTGTACAATC 57.207 29.630 9.56 0.00 0.00 2.67
201 204 7.387122 TCAACTATGCATCATTCTTCAGATAGC 59.613 37.037 0.19 0.00 0.00 2.97
202 205 6.766429 ACTATGCATCATTCTTCAGATAGCA 58.234 36.000 0.19 0.00 34.92 3.49
203 206 5.943706 ATGCATCATTCTTCAGATAGCAC 57.056 39.130 0.00 0.00 34.02 4.40
208 213 6.205076 GCATCATTCTTCAGATAGCACAAGAT 59.795 38.462 0.00 0.00 0.00 2.40
223 228 5.122396 AGCACAAGATCAAAAATACCGACTC 59.878 40.000 0.00 0.00 0.00 3.36
238 243 2.483188 CCGACTCCCTAATGTAACAGGC 60.483 54.545 0.00 0.00 0.00 4.85
305 310 4.825546 AGCAGAACTCACAATTCAGTTG 57.174 40.909 0.00 0.00 43.64 3.16
406 576 1.786579 GGCAACACAAACGATTCAAGC 59.213 47.619 0.00 0.00 0.00 4.01
445 615 4.101790 CCACACAATGCCCGCGTC 62.102 66.667 4.92 0.00 0.00 5.19
464 634 5.508489 CGCGTCTAGAAATTAGGGGTCAATA 60.508 44.000 0.00 0.00 0.00 1.90
478 648 7.750947 AGGGGTCAATAGATAAACAAGTAGT 57.249 36.000 0.00 0.00 0.00 2.73
480 650 8.702819 AGGGGTCAATAGATAAACAAGTAGTAC 58.297 37.037 0.00 0.00 0.00 2.73
490 660 8.603304 AGATAAACAAGTAGTACAAGGGTGAAT 58.397 33.333 2.52 0.00 0.00 2.57
744 915 2.571757 CAAGAGCCAGTACGCCGA 59.428 61.111 0.00 0.00 0.00 5.54
771 942 0.442699 CGAAAGCGGAAAGTAGTGGC 59.557 55.000 0.00 0.00 0.00 5.01
773 944 2.152016 GAAAGCGGAAAGTAGTGGCTT 58.848 47.619 0.00 0.00 45.11 4.35
776 947 3.412237 AGCGGAAAGTAGTGGCTTTTA 57.588 42.857 0.00 0.00 38.64 1.52
801 972 1.560866 ATAACCCCCGCCAACCGTAA 61.561 55.000 0.00 0.00 34.38 3.18
813 984 2.486592 CCAACCGTAATTTTCTTCGGCT 59.513 45.455 0.00 0.00 45.76 5.52
822 993 1.573108 TTTCTTCGGCTCAGATCCCT 58.427 50.000 0.00 0.00 0.00 4.20
831 1002 2.612760 TCAGATCCCTGAGGCCTTG 58.387 57.895 6.77 2.72 44.01 3.61
833 1004 2.203126 GATCCCTGAGGCCTTGCG 60.203 66.667 6.77 0.00 0.00 4.85
851 1022 1.405272 CGGGGCTAAGGGGTATCGTT 61.405 60.000 0.00 0.00 0.00 3.85
866 1037 5.006746 GGGTATCGTTCACAATAAGCTTCAG 59.993 44.000 0.00 0.00 0.00 3.02
953 1136 4.778143 CAAAGCCCTCGTCCCCCG 62.778 72.222 0.00 0.00 38.13 5.73
1221 1405 1.673665 CAAGAGGCAGGTGCTGGTC 60.674 63.158 1.26 0.00 41.70 4.02
1301 1485 0.318441 CCAGAGAGAGGTTTCACGCA 59.682 55.000 0.00 0.00 0.00 5.24
1318 1511 2.158579 ACGCACTCCTTTTTCCCCTTTA 60.159 45.455 0.00 0.00 0.00 1.85
1466 1664 9.669353 GTTCGCAAATTAATGATCATGATACTT 57.331 29.630 9.46 7.73 0.00 2.24
1479 1677 8.238631 TGATCATGATACTTTGTGTTTCACATG 58.761 33.333 8.54 0.00 44.16 3.21
1482 1680 4.582240 TGATACTTTGTGTTTCACATGCCA 59.418 37.500 3.43 0.00 44.16 4.92
1486 1684 4.571580 ACTTTGTGTTTCACATGCCAATTG 59.428 37.500 0.00 0.00 44.16 2.32
1487 1685 2.481854 TGTGTTTCACATGCCAATTGC 58.518 42.857 0.00 0.00 39.62 3.56
1538 1740 5.746990 AGAATTATCGTATAGCCTTGCCT 57.253 39.130 0.00 0.00 0.00 4.75
1597 1799 1.406539 CATCCCACTAGCATTTGTGCC 59.593 52.381 0.00 0.00 34.90 5.01
1725 1927 3.342377 TCATGCATCCTCGGTTACAAA 57.658 42.857 0.00 0.00 0.00 2.83
1814 2016 3.617263 CCGAGTAGTGTTTACCAGAATGC 59.383 47.826 0.00 0.00 31.97 3.56
1839 2041 5.753921 CCTGATCCGTACAAGAAAAGGATAC 59.246 44.000 7.82 0.00 41.34 2.24
1969 2174 4.842948 TGGATCTATTCTTGGCTAGCTGAT 59.157 41.667 15.72 5.85 0.00 2.90
1972 2177 5.207110 TCTATTCTTGGCTAGCTGATGAC 57.793 43.478 15.72 0.00 0.00 3.06
1973 2178 3.920231 ATTCTTGGCTAGCTGATGACA 57.080 42.857 15.72 0.00 0.00 3.58
1974 2179 3.701205 TTCTTGGCTAGCTGATGACAA 57.299 42.857 15.72 8.10 0.00 3.18
1975 2180 3.257469 TCTTGGCTAGCTGATGACAAG 57.743 47.619 15.72 19.39 37.31 3.16
1976 2181 1.669779 CTTGGCTAGCTGATGACAAGC 59.330 52.381 15.72 6.39 0.00 4.01
1977 2182 0.614812 TGGCTAGCTGATGACAAGCA 59.385 50.000 15.72 0.00 34.85 3.91
1978 2183 1.003464 TGGCTAGCTGATGACAAGCAA 59.997 47.619 15.72 0.00 34.85 3.91
1979 2184 1.669779 GGCTAGCTGATGACAAGCAAG 59.330 52.381 15.72 0.00 34.85 4.01
1980 2185 1.063764 GCTAGCTGATGACAAGCAAGC 59.936 52.381 7.70 0.00 33.38 4.01
1981 2186 2.353323 CTAGCTGATGACAAGCAAGCA 58.647 47.619 0.00 0.00 0.00 3.91
1982 2187 1.166129 AGCTGATGACAAGCAAGCAG 58.834 50.000 2.12 0.00 36.57 4.24
1983 2188 0.879765 GCTGATGACAAGCAAGCAGT 59.120 50.000 0.00 0.00 36.16 4.40
1984 2189 1.401148 GCTGATGACAAGCAAGCAGTG 60.401 52.381 0.00 0.00 36.16 3.66
1985 2190 1.199327 CTGATGACAAGCAAGCAGTGG 59.801 52.381 0.00 0.00 31.89 4.00
1986 2191 0.109412 GATGACAAGCAAGCAGTGGC 60.109 55.000 0.00 0.00 41.61 5.01
1996 2201 4.521075 GCAGTGGCGAATCTAGCA 57.479 55.556 0.00 0.00 36.08 3.49
1997 2202 2.305405 GCAGTGGCGAATCTAGCAG 58.695 57.895 0.00 0.00 36.08 4.24
1998 2203 1.156645 GCAGTGGCGAATCTAGCAGG 61.157 60.000 0.00 0.00 36.08 4.85
1999 2204 0.461548 CAGTGGCGAATCTAGCAGGA 59.538 55.000 0.00 0.00 36.08 3.86
2000 2205 0.461961 AGTGGCGAATCTAGCAGGAC 59.538 55.000 0.00 0.00 36.08 3.85
2001 2206 0.175760 GTGGCGAATCTAGCAGGACA 59.824 55.000 0.00 0.00 36.08 4.02
2002 2207 1.123077 TGGCGAATCTAGCAGGACAT 58.877 50.000 0.00 0.00 36.08 3.06
2003 2208 1.486310 TGGCGAATCTAGCAGGACATT 59.514 47.619 0.00 0.00 36.08 2.71
2004 2209 1.869767 GGCGAATCTAGCAGGACATTG 59.130 52.381 0.00 0.00 36.08 2.82
2005 2210 1.869767 GCGAATCTAGCAGGACATTGG 59.130 52.381 0.00 0.00 34.19 3.16
2006 2211 2.483714 GCGAATCTAGCAGGACATTGGA 60.484 50.000 0.00 0.00 34.19 3.53
2007 2212 3.388308 CGAATCTAGCAGGACATTGGAG 58.612 50.000 0.00 0.00 0.00 3.86
2008 2213 3.737850 GAATCTAGCAGGACATTGGAGG 58.262 50.000 0.00 0.00 0.00 4.30
2009 2214 1.500474 TCTAGCAGGACATTGGAGGG 58.500 55.000 0.00 0.00 0.00 4.30
2010 2215 1.207791 CTAGCAGGACATTGGAGGGT 58.792 55.000 0.00 0.00 0.00 4.34
2011 2216 2.023404 TCTAGCAGGACATTGGAGGGTA 60.023 50.000 0.00 0.00 0.00 3.69
2012 2217 1.207791 AGCAGGACATTGGAGGGTAG 58.792 55.000 0.00 0.00 0.00 3.18
2013 2218 0.181350 GCAGGACATTGGAGGGTAGG 59.819 60.000 0.00 0.00 0.00 3.18
2014 2219 0.181350 CAGGACATTGGAGGGTAGGC 59.819 60.000 0.00 0.00 0.00 3.93
2015 2220 0.044855 AGGACATTGGAGGGTAGGCT 59.955 55.000 0.00 0.00 0.00 4.58
2016 2221 0.919710 GGACATTGGAGGGTAGGCTT 59.080 55.000 0.00 0.00 0.00 4.35
2017 2222 2.124411 GGACATTGGAGGGTAGGCTTA 58.876 52.381 0.00 0.00 0.00 3.09
2018 2223 2.508300 GGACATTGGAGGGTAGGCTTAA 59.492 50.000 0.00 0.00 0.00 1.85
2019 2224 3.053917 GGACATTGGAGGGTAGGCTTAAA 60.054 47.826 0.00 0.00 0.00 1.52
2020 2225 4.569015 GGACATTGGAGGGTAGGCTTAAAA 60.569 45.833 0.00 0.00 0.00 1.52
2021 2226 4.341487 ACATTGGAGGGTAGGCTTAAAAC 58.659 43.478 0.00 0.00 0.00 2.43
2022 2227 4.202631 ACATTGGAGGGTAGGCTTAAAACA 60.203 41.667 0.00 0.00 0.00 2.83
2023 2228 4.668138 TTGGAGGGTAGGCTTAAAACAT 57.332 40.909 0.00 0.00 0.00 2.71
2024 2229 5.782677 TTGGAGGGTAGGCTTAAAACATA 57.217 39.130 0.00 0.00 0.00 2.29
2025 2230 5.367945 TGGAGGGTAGGCTTAAAACATAG 57.632 43.478 0.00 0.00 0.00 2.23
2026 2231 5.034200 TGGAGGGTAGGCTTAAAACATAGA 58.966 41.667 0.00 0.00 0.00 1.98
2027 2232 5.670361 TGGAGGGTAGGCTTAAAACATAGAT 59.330 40.000 0.00 0.00 0.00 1.98
2028 2233 6.159751 TGGAGGGTAGGCTTAAAACATAGATT 59.840 38.462 0.00 0.00 0.00 2.40
2029 2234 7.061054 GGAGGGTAGGCTTAAAACATAGATTT 58.939 38.462 0.00 0.00 0.00 2.17
2030 2235 7.228906 GGAGGGTAGGCTTAAAACATAGATTTC 59.771 40.741 0.00 0.00 0.00 2.17
2031 2236 7.061054 AGGGTAGGCTTAAAACATAGATTTCC 58.939 38.462 0.00 0.00 0.00 3.13
2032 2237 7.061054 GGGTAGGCTTAAAACATAGATTTCCT 58.939 38.462 0.00 0.00 0.00 3.36
2033 2238 8.215736 GGGTAGGCTTAAAACATAGATTTCCTA 58.784 37.037 0.00 0.00 0.00 2.94
2034 2239 9.623000 GGTAGGCTTAAAACATAGATTTCCTAA 57.377 33.333 0.00 0.00 0.00 2.69
2037 2242 9.397280 AGGCTTAAAACATAGATTTCCTAAGTC 57.603 33.333 0.00 0.00 29.81 3.01
2038 2243 9.397280 GGCTTAAAACATAGATTTCCTAAGTCT 57.603 33.333 0.00 0.00 29.81 3.24
2046 2251 9.915629 ACATAGATTTCCTAAGTCTAATTAGCG 57.084 33.333 7.67 0.00 32.42 4.26
2050 2255 9.482627 AGATTTCCTAAGTCTAATTAGCGAATG 57.517 33.333 7.67 0.00 32.42 2.67
2051 2256 7.478520 TTTCCTAAGTCTAATTAGCGAATGC 57.521 36.000 7.67 0.00 43.24 3.56
2052 2257 6.156748 TCCTAAGTCTAATTAGCGAATGCA 57.843 37.500 7.67 0.00 46.23 3.96
2053 2258 6.759272 TCCTAAGTCTAATTAGCGAATGCAT 58.241 36.000 7.67 0.00 46.23 3.96
2054 2259 7.217200 TCCTAAGTCTAATTAGCGAATGCATT 58.783 34.615 12.83 12.83 46.23 3.56
2055 2260 7.171508 TCCTAAGTCTAATTAGCGAATGCATTG 59.828 37.037 18.59 10.36 46.23 2.82
2056 2261 5.100751 AGTCTAATTAGCGAATGCATTGC 57.899 39.130 18.59 19.32 46.23 3.56
2057 2262 4.576053 AGTCTAATTAGCGAATGCATTGCA 59.424 37.500 25.39 14.72 46.23 4.08
2058 2263 5.066375 AGTCTAATTAGCGAATGCATTGCAA 59.934 36.000 25.39 19.43 43.62 4.08
2059 2264 5.916883 GTCTAATTAGCGAATGCATTGCAAT 59.083 36.000 25.39 20.28 43.62 3.56
2060 2265 6.418819 GTCTAATTAGCGAATGCATTGCAATT 59.581 34.615 25.39 25.04 43.62 2.32
2061 2266 5.398176 AATTAGCGAATGCATTGCAATTG 57.602 34.783 25.39 12.44 43.62 2.32
2062 2267 2.373540 AGCGAATGCATTGCAATTGT 57.626 40.000 25.39 1.24 43.62 2.71
2063 2268 2.690786 AGCGAATGCATTGCAATTGTT 58.309 38.095 25.39 6.44 43.62 2.83
2064 2269 2.413796 AGCGAATGCATTGCAATTGTTG 59.586 40.909 25.39 0.62 43.62 3.33
2077 2282 4.650545 CAATTGTTGCATGTAAAGCACC 57.349 40.909 0.00 0.00 42.54 5.01
2078 2283 4.056740 CAATTGTTGCATGTAAAGCACCA 58.943 39.130 0.00 0.00 42.54 4.17
2079 2284 3.367992 TTGTTGCATGTAAAGCACCAG 57.632 42.857 0.00 0.00 42.54 4.00
2080 2285 2.580962 TGTTGCATGTAAAGCACCAGA 58.419 42.857 0.00 0.00 42.54 3.86
2081 2286 2.954989 TGTTGCATGTAAAGCACCAGAA 59.045 40.909 0.00 0.00 42.54 3.02
2082 2287 3.573538 TGTTGCATGTAAAGCACCAGAAT 59.426 39.130 0.00 0.00 42.54 2.40
2083 2288 4.764308 TGTTGCATGTAAAGCACCAGAATA 59.236 37.500 0.00 0.00 42.54 1.75
2084 2289 5.418524 TGTTGCATGTAAAGCACCAGAATAT 59.581 36.000 0.00 0.00 42.54 1.28
2085 2290 6.601217 TGTTGCATGTAAAGCACCAGAATATA 59.399 34.615 0.00 0.00 42.54 0.86
2086 2291 7.285172 TGTTGCATGTAAAGCACCAGAATATAT 59.715 33.333 0.00 0.00 42.54 0.86
2087 2292 7.822161 TGCATGTAAAGCACCAGAATATATT 57.178 32.000 0.00 0.00 37.02 1.28
2088 2293 8.236585 TGCATGTAAAGCACCAGAATATATTT 57.763 30.769 0.00 0.00 37.02 1.40
2089 2294 8.136800 TGCATGTAAAGCACCAGAATATATTTG 58.863 33.333 0.00 0.85 37.02 2.32
2090 2295 8.137437 GCATGTAAAGCACCAGAATATATTTGT 58.863 33.333 0.00 0.00 0.00 2.83
2091 2296 9.669353 CATGTAAAGCACCAGAATATATTTGTC 57.331 33.333 0.00 0.00 0.00 3.18
2092 2297 8.800370 TGTAAAGCACCAGAATATATTTGTCA 57.200 30.769 0.00 0.00 0.00 3.58
2093 2298 9.237187 TGTAAAGCACCAGAATATATTTGTCAA 57.763 29.630 0.00 0.00 0.00 3.18
2094 2299 9.722056 GTAAAGCACCAGAATATATTTGTCAAG 57.278 33.333 0.00 0.00 0.00 3.02
2095 2300 7.944729 AAGCACCAGAATATATTTGTCAAGT 57.055 32.000 0.00 0.00 0.00 3.16
2096 2301 7.325660 AGCACCAGAATATATTTGTCAAGTG 57.674 36.000 0.00 4.13 0.00 3.16
2097 2302 6.319658 AGCACCAGAATATATTTGTCAAGTGG 59.680 38.462 0.00 2.07 0.00 4.00
2098 2303 6.095440 GCACCAGAATATATTTGTCAAGTGGT 59.905 38.462 0.00 2.61 34.90 4.16
2099 2304 7.282224 GCACCAGAATATATTTGTCAAGTGGTA 59.718 37.037 0.00 0.00 32.81 3.25
2100 2305 9.342308 CACCAGAATATATTTGTCAAGTGGTAT 57.658 33.333 0.00 0.00 32.81 2.73
2101 2306 9.342308 ACCAGAATATATTTGTCAAGTGGTATG 57.658 33.333 0.00 0.00 32.81 2.39
2102 2307 9.342308 CCAGAATATATTTGTCAAGTGGTATGT 57.658 33.333 0.00 0.00 0.00 2.29
2108 2313 8.807948 ATATTTGTCAAGTGGTATGTTTAGCT 57.192 30.769 0.00 0.00 0.00 3.32
2109 2314 6.952773 TTTGTCAAGTGGTATGTTTAGCTT 57.047 33.333 0.00 0.00 0.00 3.74
2110 2315 8.630054 ATTTGTCAAGTGGTATGTTTAGCTTA 57.370 30.769 0.00 0.00 0.00 3.09
2111 2316 8.453238 TTTGTCAAGTGGTATGTTTAGCTTAA 57.547 30.769 0.00 0.00 0.00 1.85
2112 2317 8.453238 TTGTCAAGTGGTATGTTTAGCTTAAA 57.547 30.769 0.00 0.00 0.00 1.52
2113 2318 8.630054 TGTCAAGTGGTATGTTTAGCTTAAAT 57.370 30.769 0.00 0.00 0.00 1.40
2114 2319 9.727859 TGTCAAGTGGTATGTTTAGCTTAAATA 57.272 29.630 0.00 0.00 0.00 1.40
2116 2321 9.391006 TCAAGTGGTATGTTTAGCTTAAATAGG 57.609 33.333 0.00 0.00 0.00 2.57
2117 2322 9.391006 CAAGTGGTATGTTTAGCTTAAATAGGA 57.609 33.333 0.00 0.00 0.00 2.94
2125 2330 8.964476 TGTTTAGCTTAAATAGGATTCTGGAG 57.036 34.615 0.00 0.00 0.00 3.86
2126 2331 7.993183 TGTTTAGCTTAAATAGGATTCTGGAGG 59.007 37.037 0.00 0.00 0.00 4.30
2127 2332 5.574970 AGCTTAAATAGGATTCTGGAGGG 57.425 43.478 0.00 0.00 0.00 4.30
2128 2333 4.978388 AGCTTAAATAGGATTCTGGAGGGT 59.022 41.667 0.00 0.00 0.00 4.34
2129 2334 6.151049 AGCTTAAATAGGATTCTGGAGGGTA 58.849 40.000 0.00 0.00 0.00 3.69
2130 2335 6.271159 AGCTTAAATAGGATTCTGGAGGGTAG 59.729 42.308 0.00 0.00 0.00 3.18
2131 2336 6.520913 GCTTAAATAGGATTCTGGAGGGTAGG 60.521 46.154 0.00 0.00 0.00 3.18
2132 2337 2.400467 TAGGATTCTGGAGGGTAGGC 57.600 55.000 0.00 0.00 0.00 3.93
2133 2338 0.644937 AGGATTCTGGAGGGTAGGCT 59.355 55.000 0.00 0.00 0.00 4.58
2134 2339 1.010170 AGGATTCTGGAGGGTAGGCTT 59.990 52.381 0.00 0.00 0.00 4.35
2135 2340 2.250273 AGGATTCTGGAGGGTAGGCTTA 59.750 50.000 0.00 0.00 0.00 3.09
2136 2341 3.046374 GGATTCTGGAGGGTAGGCTTAA 58.954 50.000 0.00 0.00 0.00 1.85
2137 2342 3.071747 GGATTCTGGAGGGTAGGCTTAAG 59.928 52.174 0.00 0.00 0.00 1.85
2138 2343 1.497161 TCTGGAGGGTAGGCTTAAGC 58.503 55.000 19.53 19.53 41.14 3.09
2152 2357 4.902443 GCTTAAGCCTATTGAAACCTCC 57.098 45.455 17.00 0.00 34.31 4.30
2153 2358 3.632604 GCTTAAGCCTATTGAAACCTCCC 59.367 47.826 17.00 0.00 34.31 4.30
2154 2359 4.628959 GCTTAAGCCTATTGAAACCTCCCT 60.629 45.833 17.00 0.00 34.31 4.20
2155 2360 5.397559 GCTTAAGCCTATTGAAACCTCCCTA 60.398 44.000 17.00 0.00 34.31 3.53
2156 2361 4.779993 AAGCCTATTGAAACCTCCCTAG 57.220 45.455 0.00 0.00 0.00 3.02
2157 2362 3.737263 AGCCTATTGAAACCTCCCTAGT 58.263 45.455 0.00 0.00 0.00 2.57
2158 2363 3.456277 AGCCTATTGAAACCTCCCTAGTG 59.544 47.826 0.00 0.00 0.00 2.74
2159 2364 3.433740 GCCTATTGAAACCTCCCTAGTGG 60.434 52.174 0.00 0.00 0.00 4.00
2160 2365 4.037927 CCTATTGAAACCTCCCTAGTGGA 58.962 47.826 0.71 0.71 42.41 4.02
2161 2366 4.473559 CCTATTGAAACCTCCCTAGTGGAA 59.526 45.833 2.15 0.00 44.57 3.53
2162 2367 5.132816 CCTATTGAAACCTCCCTAGTGGAAT 59.867 44.000 2.15 0.00 44.57 3.01
2163 2368 4.569719 TTGAAACCTCCCTAGTGGAATC 57.430 45.455 2.15 1.14 44.57 2.52
2164 2369 2.500098 TGAAACCTCCCTAGTGGAATCG 59.500 50.000 2.15 0.00 44.57 3.34
2165 2370 0.831307 AACCTCCCTAGTGGAATCGC 59.169 55.000 2.15 0.00 44.57 4.58
2166 2371 1.049289 ACCTCCCTAGTGGAATCGCC 61.049 60.000 2.15 0.00 44.57 5.54
2167 2372 1.048724 CCTCCCTAGTGGAATCGCCA 61.049 60.000 2.15 0.00 44.57 5.69
2190 2395 6.095440 CCACTGCAAGCAAGGTACTATAAAAT 59.905 38.462 0.00 0.00 34.37 1.82
2210 2415 5.993106 AATTTAGTATCGAAAGCAGAGGC 57.007 39.130 0.00 0.00 41.61 4.70
2211 2416 3.454371 TTAGTATCGAAAGCAGAGGCC 57.546 47.619 0.00 0.00 42.56 5.19
2212 2417 1.490574 AGTATCGAAAGCAGAGGCCT 58.509 50.000 3.86 3.86 42.56 5.19
2216 2421 0.247736 TCGAAAGCAGAGGCCTTCTC 59.752 55.000 6.77 0.00 38.14 2.87
2217 2422 0.036952 CGAAAGCAGAGGCCTTCTCA 60.037 55.000 6.77 0.00 44.81 3.27
2259 2466 3.689347 AGCATTGCCACATTGAGACTAA 58.311 40.909 4.70 0.00 0.00 2.24
2262 2469 5.887598 AGCATTGCCACATTGAGACTAAATA 59.112 36.000 4.70 0.00 0.00 1.40
2263 2470 6.548622 AGCATTGCCACATTGAGACTAAATAT 59.451 34.615 4.70 0.00 0.00 1.28
2264 2471 6.639686 GCATTGCCACATTGAGACTAAATATG 59.360 38.462 0.00 0.00 0.00 1.78
2265 2472 7.469043 GCATTGCCACATTGAGACTAAATATGA 60.469 37.037 0.00 0.00 0.00 2.15
2266 2473 7.936496 TTGCCACATTGAGACTAAATATGAA 57.064 32.000 0.00 0.00 0.00 2.57
2267 2474 8.523915 TTGCCACATTGAGACTAAATATGAAT 57.476 30.769 0.00 0.00 0.00 2.57
2268 2475 8.158169 TGCCACATTGAGACTAAATATGAATC 57.842 34.615 0.00 0.00 0.00 2.52
2269 2476 7.994911 TGCCACATTGAGACTAAATATGAATCT 59.005 33.333 0.00 0.00 0.00 2.40
2270 2477 8.844244 GCCACATTGAGACTAAATATGAATCTT 58.156 33.333 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.430333 TGCCGTGTCCTTTTTCTTTTC 57.570 42.857 0.00 0.00 0.00 2.29
29 30 6.787085 ATCTTTAGCTTATATTGCCGTGTC 57.213 37.500 0.00 0.00 0.00 3.67
95 96 4.619973 TGTCTTTTGCAATTGTGGACATC 58.380 39.130 7.40 0.00 0.00 3.06
99 100 4.100653 TCCATTGTCTTTTGCAATTGTGGA 59.899 37.500 7.40 5.24 34.68 4.02
100 101 4.211794 GTCCATTGTCTTTTGCAATTGTGG 59.788 41.667 7.40 2.83 34.68 4.17
101 102 4.084952 CGTCCATTGTCTTTTGCAATTGTG 60.085 41.667 7.40 0.00 34.68 3.33
102 103 4.050553 CGTCCATTGTCTTTTGCAATTGT 58.949 39.130 7.40 0.00 34.68 2.71
103 104 3.429543 CCGTCCATTGTCTTTTGCAATTG 59.570 43.478 0.00 0.00 34.68 2.32
104 105 3.652274 CCGTCCATTGTCTTTTGCAATT 58.348 40.909 0.00 0.00 34.68 2.32
123 125 4.732285 ATTTATGTGCTTCTATTCGCCG 57.268 40.909 0.00 0.00 0.00 6.46
125 127 7.579726 AGATGAATTTATGTGCTTCTATTCGC 58.420 34.615 0.00 0.00 0.00 4.70
148 150 8.862325 ATGGTATGTTCTTGATTGTACAAAGA 57.138 30.769 13.23 8.36 0.00 2.52
160 162 8.382030 TGCATAGTTGATATGGTATGTTCTTG 57.618 34.615 0.00 0.00 41.49 3.02
170 173 8.331730 TGAAGAATGATGCATAGTTGATATGG 57.668 34.615 0.00 0.00 41.49 2.74
201 204 5.163754 GGGAGTCGGTATTTTTGATCTTGTG 60.164 44.000 0.00 0.00 0.00 3.33
202 205 4.941873 GGGAGTCGGTATTTTTGATCTTGT 59.058 41.667 0.00 0.00 0.00 3.16
203 206 5.186198 AGGGAGTCGGTATTTTTGATCTTG 58.814 41.667 0.00 0.00 0.00 3.02
208 213 6.057321 ACATTAGGGAGTCGGTATTTTTGA 57.943 37.500 0.00 0.00 0.00 2.69
223 228 3.181445 TGCCATAGCCTGTTACATTAGGG 60.181 47.826 0.00 0.00 38.69 3.53
238 243 4.453478 CCAGTGCTGTGTAATATGCCATAG 59.547 45.833 0.00 0.00 0.00 2.23
350 355 3.124578 TGTTCAGCACAAGTGATAGCA 57.875 42.857 4.04 0.00 29.87 3.49
402 572 0.674581 TCCAACTGCATCTCGGCTTG 60.675 55.000 0.00 0.00 34.04 4.01
406 576 1.817099 GGCTCCAACTGCATCTCGG 60.817 63.158 0.00 0.00 0.00 4.63
464 634 7.549147 TCACCCTTGTACTACTTGTTTATCT 57.451 36.000 0.00 0.00 0.00 1.98
477 647 5.407407 TCTCTCTTCATTCACCCTTGTAC 57.593 43.478 0.00 0.00 0.00 2.90
478 648 5.485353 ACATCTCTCTTCATTCACCCTTGTA 59.515 40.000 0.00 0.00 0.00 2.41
480 650 4.634883 CACATCTCTCTTCATTCACCCTTG 59.365 45.833 0.00 0.00 0.00 3.61
490 660 2.492088 CACCCGTACACATCTCTCTTCA 59.508 50.000 0.00 0.00 0.00 3.02
592 762 3.371097 GAAGATGGAGGGCGTCGCA 62.371 63.158 20.50 0.00 0.00 5.10
744 915 0.606604 TTTCCGCTTTCGCTCCTAGT 59.393 50.000 0.00 0.00 0.00 2.57
764 935 5.449999 GGGTTATGTGCATAAAAGCCACTAC 60.450 44.000 16.57 0.68 35.30 2.73
767 938 3.430236 GGGGTTATGTGCATAAAAGCCAC 60.430 47.826 20.60 8.04 35.30 5.01
768 939 2.763448 GGGGTTATGTGCATAAAAGCCA 59.237 45.455 20.60 1.64 35.30 4.75
771 942 2.223711 GCGGGGGTTATGTGCATAAAAG 60.224 50.000 6.24 0.00 35.30 2.27
773 944 1.394618 GCGGGGGTTATGTGCATAAA 58.605 50.000 6.24 0.00 35.30 1.40
776 947 2.123897 GGCGGGGGTTATGTGCAT 60.124 61.111 0.00 0.00 0.00 3.96
801 972 2.507471 AGGGATCTGAGCCGAAGAAAAT 59.493 45.455 5.78 0.00 0.00 1.82
813 984 1.630126 GCAAGGCCTCAGGGATCTGA 61.630 60.000 5.23 0.00 46.81 3.27
828 999 1.705997 ATACCCCTTAGCCCCGCAAG 61.706 60.000 0.00 0.00 0.00 4.01
831 1002 2.748350 GATACCCCTTAGCCCCGC 59.252 66.667 0.00 0.00 0.00 6.13
833 1004 0.395686 GAACGATACCCCTTAGCCCC 59.604 60.000 0.00 0.00 0.00 5.80
851 1022 5.221925 ACCCTTTCTCTGAAGCTTATTGTGA 60.222 40.000 0.00 0.00 0.00 3.58
866 1037 8.188799 GGTAAATTAGCAAATACACCCTTTCTC 58.811 37.037 0.00 0.00 0.00 2.87
953 1136 2.682352 GCTGGAGAAGAAATCTGGCTTC 59.318 50.000 0.00 0.00 38.96 3.86
1212 1396 1.551452 ACAGAGAGTAGACCAGCACC 58.449 55.000 0.00 0.00 0.00 5.01
1221 1405 1.355916 GGGCGCGTACAGAGAGTAG 59.644 63.158 8.43 0.00 32.19 2.57
1318 1511 4.532521 AGTACATAAAAGAGCACAGACCCT 59.467 41.667 0.00 0.00 0.00 4.34
1479 1677 3.855689 AGTTCTACATGTGCAATTGGC 57.144 42.857 9.11 0.15 45.13 4.52
1482 1680 5.804639 TCAGGTAGTTCTACATGTGCAATT 58.195 37.500 19.23 0.35 33.89 2.32
1486 1684 5.063944 CACAATCAGGTAGTTCTACATGTGC 59.936 44.000 19.23 0.00 33.89 4.57
1487 1685 5.582269 CCACAATCAGGTAGTTCTACATGTG 59.418 44.000 19.23 14.93 33.89 3.21
1494 1692 4.373156 AAAGCCACAATCAGGTAGTTCT 57.627 40.909 0.00 0.00 0.00 3.01
1495 1693 5.488341 TCTAAAGCCACAATCAGGTAGTTC 58.512 41.667 0.00 0.00 0.00 3.01
1538 1740 1.453015 ACCGCTGCAAGAACACCAA 60.453 52.632 0.00 0.00 34.07 3.67
1561 1763 6.120220 AGTGGGATGTAGTAATAGCCAAAAC 58.880 40.000 0.00 0.00 0.00 2.43
1562 1764 6.321821 AGTGGGATGTAGTAATAGCCAAAA 57.678 37.500 0.00 0.00 0.00 2.44
1597 1799 2.427453 AGCACGACAAGTATGGAGTAGG 59.573 50.000 0.00 0.00 0.00 3.18
1701 1903 4.269183 TGTAACCGAGGATGCATGATTTT 58.731 39.130 2.46 0.00 0.00 1.82
1707 1909 2.017049 GCTTTGTAACCGAGGATGCAT 58.983 47.619 0.00 0.00 0.00 3.96
1708 1910 1.448985 GCTTTGTAACCGAGGATGCA 58.551 50.000 0.00 0.00 0.00 3.96
1749 1951 6.704050 TCATTTCTCACAACAACTTATGTCGA 59.296 34.615 0.00 0.00 42.99 4.20
1778 1980 1.257750 ACTCGGTGCATAGCCAGTCA 61.258 55.000 0.00 0.00 0.00 3.41
1814 2016 3.055385 TCCTTTTCTTGTACGGATCAGGG 60.055 47.826 0.00 0.00 0.00 4.45
1839 2041 1.511850 TGACTCGTGTCTTGCATTGG 58.488 50.000 17.64 0.00 43.29 3.16
1882 2084 4.733850 TGCAGTCTGTGTTATCGAACTAG 58.266 43.478 0.93 0.00 36.45 2.57
1889 2094 4.739046 GCCATATGCAGTCTGTGTTATC 57.261 45.455 0.93 0.00 40.77 1.75
1969 2174 2.545596 CGCCACTGCTTGCTTGTCA 61.546 57.895 0.00 0.00 34.43 3.58
1972 2177 0.455633 GATTCGCCACTGCTTGCTTG 60.456 55.000 0.00 0.00 34.43 4.01
1973 2178 0.607489 AGATTCGCCACTGCTTGCTT 60.607 50.000 0.00 0.00 34.43 3.91
1974 2179 0.250234 TAGATTCGCCACTGCTTGCT 59.750 50.000 0.00 0.00 34.43 3.91
1975 2180 0.654683 CTAGATTCGCCACTGCTTGC 59.345 55.000 0.00 0.00 34.43 4.01
1976 2181 0.654683 GCTAGATTCGCCACTGCTTG 59.345 55.000 0.00 0.00 34.43 4.01
1977 2182 0.250234 TGCTAGATTCGCCACTGCTT 59.750 50.000 0.00 0.00 34.43 3.91
1978 2183 0.179089 CTGCTAGATTCGCCACTGCT 60.179 55.000 0.00 0.00 34.43 4.24
1979 2184 1.156645 CCTGCTAGATTCGCCACTGC 61.157 60.000 0.00 0.00 0.00 4.40
1980 2185 0.461548 TCCTGCTAGATTCGCCACTG 59.538 55.000 0.00 0.00 0.00 3.66
1981 2186 0.461961 GTCCTGCTAGATTCGCCACT 59.538 55.000 0.00 0.00 0.00 4.00
1982 2187 0.175760 TGTCCTGCTAGATTCGCCAC 59.824 55.000 0.00 0.00 0.00 5.01
1983 2188 1.123077 ATGTCCTGCTAGATTCGCCA 58.877 50.000 0.00 0.00 0.00 5.69
1984 2189 1.869767 CAATGTCCTGCTAGATTCGCC 59.130 52.381 0.00 0.00 0.00 5.54
1985 2190 1.869767 CCAATGTCCTGCTAGATTCGC 59.130 52.381 0.00 0.00 0.00 4.70
1986 2191 3.388308 CTCCAATGTCCTGCTAGATTCG 58.612 50.000 0.00 0.00 0.00 3.34
1987 2192 3.495806 CCCTCCAATGTCCTGCTAGATTC 60.496 52.174 0.00 0.00 0.00 2.52
1988 2193 2.441001 CCCTCCAATGTCCTGCTAGATT 59.559 50.000 0.00 0.00 0.00 2.40
1989 2194 2.053244 CCCTCCAATGTCCTGCTAGAT 58.947 52.381 0.00 0.00 0.00 1.98
1990 2195 1.273838 ACCCTCCAATGTCCTGCTAGA 60.274 52.381 0.00 0.00 0.00 2.43
1991 2196 1.207791 ACCCTCCAATGTCCTGCTAG 58.792 55.000 0.00 0.00 0.00 3.42
1992 2197 2.398588 CTACCCTCCAATGTCCTGCTA 58.601 52.381 0.00 0.00 0.00 3.49
1993 2198 1.207791 CTACCCTCCAATGTCCTGCT 58.792 55.000 0.00 0.00 0.00 4.24
1994 2199 0.181350 CCTACCCTCCAATGTCCTGC 59.819 60.000 0.00 0.00 0.00 4.85
1995 2200 0.181350 GCCTACCCTCCAATGTCCTG 59.819 60.000 0.00 0.00 0.00 3.86
1996 2201 0.044855 AGCCTACCCTCCAATGTCCT 59.955 55.000 0.00 0.00 0.00 3.85
1997 2202 0.919710 AAGCCTACCCTCCAATGTCC 59.080 55.000 0.00 0.00 0.00 4.02
1998 2203 3.926058 TTAAGCCTACCCTCCAATGTC 57.074 47.619 0.00 0.00 0.00 3.06
1999 2204 4.202631 TGTTTTAAGCCTACCCTCCAATGT 60.203 41.667 0.00 0.00 0.00 2.71
2000 2205 4.340617 TGTTTTAAGCCTACCCTCCAATG 58.659 43.478 0.00 0.00 0.00 2.82
2001 2206 4.668138 TGTTTTAAGCCTACCCTCCAAT 57.332 40.909 0.00 0.00 0.00 3.16
2002 2207 4.668138 ATGTTTTAAGCCTACCCTCCAA 57.332 40.909 0.00 0.00 0.00 3.53
2003 2208 5.034200 TCTATGTTTTAAGCCTACCCTCCA 58.966 41.667 0.00 0.00 0.00 3.86
2004 2209 5.625568 TCTATGTTTTAAGCCTACCCTCC 57.374 43.478 0.00 0.00 0.00 4.30
2005 2210 7.228906 GGAAATCTATGTTTTAAGCCTACCCTC 59.771 40.741 0.00 0.00 0.00 4.30
2006 2211 7.061054 GGAAATCTATGTTTTAAGCCTACCCT 58.939 38.462 0.00 0.00 0.00 4.34
2007 2212 7.061054 AGGAAATCTATGTTTTAAGCCTACCC 58.939 38.462 0.00 0.00 0.00 3.69
2008 2213 9.623000 TTAGGAAATCTATGTTTTAAGCCTACC 57.377 33.333 0.00 0.00 0.00 3.18
2011 2216 9.397280 GACTTAGGAAATCTATGTTTTAAGCCT 57.603 33.333 0.00 0.00 36.74 4.58
2012 2217 9.397280 AGACTTAGGAAATCTATGTTTTAAGCC 57.603 33.333 0.00 0.00 36.74 4.35
2020 2225 9.915629 CGCTAATTAGACTTAGGAAATCTATGT 57.084 33.333 16.85 0.00 38.54 2.29
2024 2229 9.482627 CATTCGCTAATTAGACTTAGGAAATCT 57.517 33.333 16.85 0.00 29.67 2.40
2025 2230 8.224437 GCATTCGCTAATTAGACTTAGGAAATC 58.776 37.037 16.85 0.00 34.30 2.17
2026 2231 7.715249 TGCATTCGCTAATTAGACTTAGGAAAT 59.285 33.333 16.85 1.22 39.64 2.17
2027 2232 7.045416 TGCATTCGCTAATTAGACTTAGGAAA 58.955 34.615 16.85 0.00 39.64 3.13
2028 2233 6.578944 TGCATTCGCTAATTAGACTTAGGAA 58.421 36.000 16.85 8.74 39.64 3.36
2029 2234 6.156748 TGCATTCGCTAATTAGACTTAGGA 57.843 37.500 16.85 1.22 39.64 2.94
2030 2235 7.293745 CAATGCATTCGCTAATTAGACTTAGG 58.706 38.462 16.85 1.98 39.64 2.69
2031 2236 6.794158 GCAATGCATTCGCTAATTAGACTTAG 59.206 38.462 16.85 3.84 39.64 2.18
2032 2237 6.259829 TGCAATGCATTCGCTAATTAGACTTA 59.740 34.615 24.42 0.00 39.64 2.24
2033 2238 5.066375 TGCAATGCATTCGCTAATTAGACTT 59.934 36.000 24.42 0.00 39.64 3.01
2034 2239 4.576053 TGCAATGCATTCGCTAATTAGACT 59.424 37.500 24.42 0.00 39.64 3.24
2035 2240 4.847633 TGCAATGCATTCGCTAATTAGAC 58.152 39.130 24.42 6.74 39.64 2.59
2036 2241 5.497635 TTGCAATGCATTCGCTAATTAGA 57.502 34.783 24.42 8.58 38.76 2.10
2037 2242 6.199531 ACAATTGCAATGCATTCGCTAATTAG 59.800 34.615 24.42 20.94 38.76 1.73
2038 2243 6.041511 ACAATTGCAATGCATTCGCTAATTA 58.958 32.000 24.42 9.61 38.76 1.40
2039 2244 4.871557 ACAATTGCAATGCATTCGCTAATT 59.128 33.333 24.42 22.54 38.76 1.40
2040 2245 4.435425 ACAATTGCAATGCATTCGCTAAT 58.565 34.783 24.42 19.87 38.76 1.73
2041 2246 3.847542 ACAATTGCAATGCATTCGCTAA 58.152 36.364 24.42 19.01 38.76 3.09
2042 2247 3.507103 ACAATTGCAATGCATTCGCTA 57.493 38.095 24.42 20.15 38.76 4.26
2043 2248 2.373540 ACAATTGCAATGCATTCGCT 57.626 40.000 24.42 10.66 38.76 4.93
2044 2249 2.764768 CAACAATTGCAATGCATTCGC 58.235 42.857 13.82 20.23 38.76 4.70
2056 2261 4.650545 GGTGCTTTACATGCAACAATTG 57.349 40.909 3.24 3.24 46.39 2.32
2062 2267 7.822161 ATATATTCTGGTGCTTTACATGCAA 57.178 32.000 0.00 0.00 42.41 4.08
2063 2268 7.822161 AATATATTCTGGTGCTTTACATGCA 57.178 32.000 0.00 0.00 38.19 3.96
2064 2269 8.137437 ACAAATATATTCTGGTGCTTTACATGC 58.863 33.333 0.00 0.00 0.00 4.06
2065 2270 9.669353 GACAAATATATTCTGGTGCTTTACATG 57.331 33.333 0.00 0.00 0.00 3.21
2066 2271 9.407380 TGACAAATATATTCTGGTGCTTTACAT 57.593 29.630 0.00 0.00 0.00 2.29
2067 2272 8.800370 TGACAAATATATTCTGGTGCTTTACA 57.200 30.769 0.00 0.00 0.00 2.41
2068 2273 9.722056 CTTGACAAATATATTCTGGTGCTTTAC 57.278 33.333 0.00 0.00 0.00 2.01
2069 2274 9.461312 ACTTGACAAATATATTCTGGTGCTTTA 57.539 29.630 0.00 0.00 0.00 1.85
2070 2275 8.246180 CACTTGACAAATATATTCTGGTGCTTT 58.754 33.333 0.00 0.00 0.00 3.51
2071 2276 7.148018 CCACTTGACAAATATATTCTGGTGCTT 60.148 37.037 0.00 0.00 0.00 3.91
2072 2277 6.319658 CCACTTGACAAATATATTCTGGTGCT 59.680 38.462 0.00 0.00 0.00 4.40
2073 2278 6.095440 ACCACTTGACAAATATATTCTGGTGC 59.905 38.462 0.00 0.00 0.00 5.01
2074 2279 7.630242 ACCACTTGACAAATATATTCTGGTG 57.370 36.000 0.00 0.00 0.00 4.17
2075 2280 9.342308 CATACCACTTGACAAATATATTCTGGT 57.658 33.333 0.00 0.50 33.00 4.00
2076 2281 9.342308 ACATACCACTTGACAAATATATTCTGG 57.658 33.333 0.00 0.00 0.00 3.86
2082 2287 9.899661 AGCTAAACATACCACTTGACAAATATA 57.100 29.630 0.00 0.00 0.00 0.86
2083 2288 8.807948 AGCTAAACATACCACTTGACAAATAT 57.192 30.769 0.00 0.00 0.00 1.28
2084 2289 8.630054 AAGCTAAACATACCACTTGACAAATA 57.370 30.769 0.00 0.00 0.00 1.40
2085 2290 7.524717 AAGCTAAACATACCACTTGACAAAT 57.475 32.000 0.00 0.00 0.00 2.32
2086 2291 6.952773 AAGCTAAACATACCACTTGACAAA 57.047 33.333 0.00 0.00 0.00 2.83
2087 2292 8.453238 TTTAAGCTAAACATACCACTTGACAA 57.547 30.769 0.00 0.00 0.00 3.18
2088 2293 8.630054 ATTTAAGCTAAACATACCACTTGACA 57.370 30.769 0.00 0.00 0.00 3.58
2090 2295 9.391006 CCTATTTAAGCTAAACATACCACTTGA 57.609 33.333 0.00 0.00 0.00 3.02
2091 2296 9.391006 TCCTATTTAAGCTAAACATACCACTTG 57.609 33.333 0.00 0.00 0.00 3.16
2099 2304 9.566432 CTCCAGAATCCTATTTAAGCTAAACAT 57.434 33.333 0.00 0.00 0.00 2.71
2100 2305 7.993183 CCTCCAGAATCCTATTTAAGCTAAACA 59.007 37.037 0.00 0.00 0.00 2.83
2101 2306 7.445707 CCCTCCAGAATCCTATTTAAGCTAAAC 59.554 40.741 0.00 0.00 0.00 2.01
2102 2307 7.128883 ACCCTCCAGAATCCTATTTAAGCTAAA 59.871 37.037 0.00 0.00 0.00 1.85
2103 2308 6.619852 ACCCTCCAGAATCCTATTTAAGCTAA 59.380 38.462 0.00 0.00 0.00 3.09
2104 2309 6.151049 ACCCTCCAGAATCCTATTTAAGCTA 58.849 40.000 0.00 0.00 0.00 3.32
2105 2310 4.978388 ACCCTCCAGAATCCTATTTAAGCT 59.022 41.667 0.00 0.00 0.00 3.74
2106 2311 5.311844 ACCCTCCAGAATCCTATTTAAGC 57.688 43.478 0.00 0.00 0.00 3.09
2107 2312 6.520913 GCCTACCCTCCAGAATCCTATTTAAG 60.521 46.154 0.00 0.00 0.00 1.85
2108 2313 5.309806 GCCTACCCTCCAGAATCCTATTTAA 59.690 44.000 0.00 0.00 0.00 1.52
2109 2314 4.844655 GCCTACCCTCCAGAATCCTATTTA 59.155 45.833 0.00 0.00 0.00 1.40
2110 2315 3.653352 GCCTACCCTCCAGAATCCTATTT 59.347 47.826 0.00 0.00 0.00 1.40
2111 2316 3.116159 AGCCTACCCTCCAGAATCCTATT 60.116 47.826 0.00 0.00 0.00 1.73
2112 2317 2.456733 AGCCTACCCTCCAGAATCCTAT 59.543 50.000 0.00 0.00 0.00 2.57
2113 2318 1.866943 AGCCTACCCTCCAGAATCCTA 59.133 52.381 0.00 0.00 0.00 2.94
2114 2319 0.644937 AGCCTACCCTCCAGAATCCT 59.355 55.000 0.00 0.00 0.00 3.24
2115 2320 1.512735 AAGCCTACCCTCCAGAATCC 58.487 55.000 0.00 0.00 0.00 3.01
2116 2321 3.495276 GCTTAAGCCTACCCTCCAGAATC 60.495 52.174 17.00 0.00 34.31 2.52
2117 2322 2.439880 GCTTAAGCCTACCCTCCAGAAT 59.560 50.000 17.00 0.00 34.31 2.40
2118 2323 1.838077 GCTTAAGCCTACCCTCCAGAA 59.162 52.381 17.00 0.00 34.31 3.02
2119 2324 1.497161 GCTTAAGCCTACCCTCCAGA 58.503 55.000 17.00 0.00 34.31 3.86
2131 2336 3.632604 GGGAGGTTTCAATAGGCTTAAGC 59.367 47.826 19.53 19.53 41.14 3.09
2132 2337 5.117406 AGGGAGGTTTCAATAGGCTTAAG 57.883 43.478 0.00 0.00 0.00 1.85
2133 2338 5.729718 ACTAGGGAGGTTTCAATAGGCTTAA 59.270 40.000 0.00 0.00 0.00 1.85
2134 2339 5.130477 CACTAGGGAGGTTTCAATAGGCTTA 59.870 44.000 0.00 0.00 0.00 3.09
2135 2340 4.080299 CACTAGGGAGGTTTCAATAGGCTT 60.080 45.833 0.00 0.00 0.00 4.35
2136 2341 3.456277 CACTAGGGAGGTTTCAATAGGCT 59.544 47.826 0.00 0.00 0.00 4.58
2137 2342 3.433740 CCACTAGGGAGGTTTCAATAGGC 60.434 52.174 0.00 0.00 40.01 3.93
2138 2343 4.037927 TCCACTAGGGAGGTTTCAATAGG 58.962 47.826 0.00 0.00 42.15 2.57
2150 2355 4.798585 TGGCGATTCCACTAGGGA 57.201 55.556 0.00 0.00 46.61 4.20
2157 2362 2.334946 GCTTGCAGTGGCGATTCCA 61.335 57.895 0.00 0.00 45.35 3.53
2158 2363 1.865788 TTGCTTGCAGTGGCGATTCC 61.866 55.000 0.00 0.00 45.35 3.01
2159 2364 0.455633 CTTGCTTGCAGTGGCGATTC 60.456 55.000 0.00 0.00 45.35 2.52
2160 2365 1.582968 CTTGCTTGCAGTGGCGATT 59.417 52.632 0.00 0.00 45.35 3.34
2161 2366 2.338015 CCTTGCTTGCAGTGGCGAT 61.338 57.895 0.00 0.00 45.35 4.58
2162 2367 2.390306 TACCTTGCTTGCAGTGGCGA 62.390 55.000 13.67 0.00 45.35 5.54
2163 2368 1.965930 TACCTTGCTTGCAGTGGCG 60.966 57.895 13.67 0.00 45.35 5.69
2164 2369 0.890996 AGTACCTTGCTTGCAGTGGC 60.891 55.000 13.67 0.00 41.68 5.01
2165 2370 2.472695 TAGTACCTTGCTTGCAGTGG 57.527 50.000 12.64 12.64 0.00 4.00
2166 2371 6.494893 TTTTATAGTACCTTGCTTGCAGTG 57.505 37.500 0.00 0.00 0.00 3.66
2167 2372 7.703058 AATTTTATAGTACCTTGCTTGCAGT 57.297 32.000 0.00 0.00 0.00 4.40
2168 2373 9.722056 CTAAATTTTATAGTACCTTGCTTGCAG 57.278 33.333 0.00 0.00 0.00 4.41
2169 2374 9.238368 ACTAAATTTTATAGTACCTTGCTTGCA 57.762 29.630 0.00 0.00 31.96 4.08
2190 2395 3.451178 AGGCCTCTGCTTTCGATACTAAA 59.549 43.478 0.00 0.00 37.74 1.85
2210 2415 7.011763 CACCATATTGTGACAGTATTGAGAAGG 59.988 40.741 6.25 3.18 38.55 3.46
2211 2416 7.765819 TCACCATATTGTGACAGTATTGAGAAG 59.234 37.037 5.55 0.00 40.22 2.85
2212 2417 7.619965 TCACCATATTGTGACAGTATTGAGAA 58.380 34.615 5.55 0.00 40.22 2.87
2216 2421 6.093909 TGCTTCACCATATTGTGACAGTATTG 59.906 38.462 9.06 0.00 44.55 1.90
2217 2422 6.179756 TGCTTCACCATATTGTGACAGTATT 58.820 36.000 9.06 0.00 44.55 1.89


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

AutoCloner maintained by Alex Coulton.