Multiple sequence alignment - TraesCS1A01G219300

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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 TraesCS1A01G219300 chr1A 100.000 2640 0 0 1 2640 387994845 387997484 0.000000e+00 4876
1 TraesCS1A01G219300 chr7D 91.394 2080 167 8 1 2072 432740898 432738823 0.000000e+00 2839
2 TraesCS1A01G219300 chr4D 91.220 2073 159 9 4 2072 116524894 116522841 0.000000e+00 2798
3 TraesCS1A01G219300 chr3A 90.874 2082 165 16 1 2073 418766002 418763937 0.000000e+00 2769
4 TraesCS1A01G219300 chr5A 90.236 2079 180 13 3 2072 604232404 604230340 0.000000e+00 2693
5 TraesCS1A01G219300 chr5B 89.451 2057 181 17 1 2044 407222189 407224222 0.000000e+00 2564
6 TraesCS1A01G219300 chr5B 72.385 478 90 31 2199 2640 419301280 419300809 2.150000e-21 113
7 TraesCS1A01G219300 chr4B 88.894 2098 201 20 1 2073 551784348 551786438 0.000000e+00 2555
8 TraesCS1A01G219300 chr4B 88.132 2098 217 20 1 2073 551729740 551731830 0.000000e+00 2466
9 TraesCS1A01G219300 chr4B 74.675 462 84 30 2200 2640 72642319 72642768 9.710000e-40 174
10 TraesCS1A01G219300 chr3B 88.681 2085 202 14 1 2072 478551310 478549247 0.000000e+00 2512
11 TraesCS1A01G219300 chr2A 88.402 2078 215 18 9 2072 504065600 504067665 0.000000e+00 2479
12 TraesCS1A01G219300 chr2A 86.212 2096 233 32 4 2074 779811503 779813567 0.000000e+00 2218
13 TraesCS1A01G219300 chr2A 84.255 705 83 10 1 704 769258002 769258679 0.000000e+00 662
14 TraesCS1A01G219300 chr2A 81.366 483 55 10 1 471 456479867 456479408 6.950000e-96 361
15 TraesCS1A01G219300 chr3D 80.918 414 49 15 2251 2638 6515714 6516123 1.540000e-77 300
16 TraesCS1A01G219300 chr2B 82.927 328 42 11 2252 2571 449667967 449667646 1.550000e-72 283
17 TraesCS1A01G219300 chr7A 79.518 415 45 25 2252 2637 655945345 655945748 2.610000e-65 259
18 TraesCS1A01G219300 chr6D 77.511 458 73 24 2200 2638 368210656 368211102 5.640000e-62 248
19 TraesCS1A01G219300 chr6D 75.381 459 88 21 2199 2640 397045155 397044705 5.760000e-47 198
20 TraesCS1A01G219300 chr2D 79.666 359 54 14 2229 2571 89217045 89216690 9.440000e-60 241
21 TraesCS1A01G219300 chr2D 79.666 359 48 15 2229 2565 104875540 104875895 4.390000e-58 235
22 TraesCS1A01G219300 chr5D 80.000 340 35 14 2271 2584 43207213 43206881 1.230000e-53 220


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 TraesCS1A01G219300 chr1A 387994845 387997484 2639 False 4876 4876 100.000 1 2640 1 chr1A.!!$F1 2639
1 TraesCS1A01G219300 chr7D 432738823 432740898 2075 True 2839 2839 91.394 1 2072 1 chr7D.!!$R1 2071
2 TraesCS1A01G219300 chr4D 116522841 116524894 2053 True 2798 2798 91.220 4 2072 1 chr4D.!!$R1 2068
3 TraesCS1A01G219300 chr3A 418763937 418766002 2065 True 2769 2769 90.874 1 2073 1 chr3A.!!$R1 2072
4 TraesCS1A01G219300 chr5A 604230340 604232404 2064 True 2693 2693 90.236 3 2072 1 chr5A.!!$R1 2069
5 TraesCS1A01G219300 chr5B 407222189 407224222 2033 False 2564 2564 89.451 1 2044 1 chr5B.!!$F1 2043
6 TraesCS1A01G219300 chr4B 551784348 551786438 2090 False 2555 2555 88.894 1 2073 1 chr4B.!!$F3 2072
7 TraesCS1A01G219300 chr4B 551729740 551731830 2090 False 2466 2466 88.132 1 2073 1 chr4B.!!$F2 2072
8 TraesCS1A01G219300 chr3B 478549247 478551310 2063 True 2512 2512 88.681 1 2072 1 chr3B.!!$R1 2071
9 TraesCS1A01G219300 chr2A 504065600 504067665 2065 False 2479 2479 88.402 9 2072 1 chr2A.!!$F1 2063
10 TraesCS1A01G219300 chr2A 779811503 779813567 2064 False 2218 2218 86.212 4 2074 1 chr2A.!!$F3 2070
11 TraesCS1A01G219300 chr2A 769258002 769258679 677 False 662 662 84.255 1 704 1 chr2A.!!$F2 703

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 0.252284 AAGACCACCGGACTCCATCT 60.252 55.0 9.46 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1902 0.179032 ACACTTCGGCACAACCATGA 60.179 50.0 0.0 0.0 39.03 3.07 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
19 20 1.079256 CACTCTCCCCCACTCTCCA 59.921 63.158 0.00 0.00 0.00 3.86
76 77 0.252284 AAGACCACCGGACTCCATCT 60.252 55.000 9.46 0.00 0.00 2.90
103 104 2.745308 CGGATCATCACCTGGCCCA 61.745 63.158 0.00 0.00 0.00 5.36
141 144 3.244814 GCACGTTTTTGTTCATCATGCAA 59.755 39.130 0.00 0.00 0.00 4.08
175 178 0.387367 CGATCCGGCAGTAGATTCGG 60.387 60.000 0.00 0.00 43.42 4.30
180 183 0.389391 CGGCAGTAGATTCGGTCCAT 59.611 55.000 0.00 0.00 0.00 3.41
319 398 2.245287 GGGGATTGGGGGTACACAATAA 59.755 50.000 0.00 0.00 37.53 1.40
322 401 3.379057 GGATTGGGGGTACACAATAAACG 59.621 47.826 0.00 0.00 37.53 3.60
323 402 2.493414 TGGGGGTACACAATAAACGG 57.507 50.000 0.00 0.00 0.00 4.44
399 479 3.529533 CTTCATCTTCTTGTCCATCGCT 58.470 45.455 0.00 0.00 0.00 4.93
455 541 2.060383 CGAGGTCCATCTGCCAGGA 61.060 63.158 0.00 0.00 0.00 3.86
484 570 4.235762 GCTCCGGCGCCCTCATTA 62.236 66.667 23.46 0.00 0.00 1.90
490 576 1.968540 GGCGCCCTCATTAGCATCC 60.969 63.158 18.11 0.00 0.00 3.51
618 704 3.714798 TCTTGTACTTGGACCACCTCTTT 59.285 43.478 0.00 0.00 37.04 2.52
632 718 4.058817 CACCTCTTTCTCTGTTTAGCGTT 58.941 43.478 0.00 0.00 0.00 4.84
636 722 5.333416 CCTCTTTCTCTGTTTAGCGTTGTTC 60.333 44.000 0.00 0.00 0.00 3.18
637 723 5.113383 TCTTTCTCTGTTTAGCGTTGTTCA 58.887 37.500 0.00 0.00 0.00 3.18
676 762 1.067060 CCCAGCGAATGATGTCGACTA 59.933 52.381 17.92 3.52 43.86 2.59
704 791 0.392595 CCCTTCGCTGGGTTAGGAAC 60.393 60.000 13.99 0.00 42.25 3.62
720 807 1.270358 GGAACCAGCGTCTTCAACTCT 60.270 52.381 0.00 0.00 0.00 3.24
932 1025 5.838955 TGGAGAGGAGAAAGGTTGATAGTA 58.161 41.667 0.00 0.00 0.00 1.82
939 1032 8.616799 AGGAGAAAGGTTGATAGTAAGAGAAT 57.383 34.615 0.00 0.00 0.00 2.40
1085 1180 3.415212 CCTGACTCCATGAATTGTGTGT 58.585 45.455 0.00 0.00 0.00 3.72
1110 1205 1.685517 CGAGGAGAGCAATGAGATGGA 59.314 52.381 0.00 0.00 0.00 3.41
1144 1239 1.228154 GGCCGTTGACAAGAAGGGT 60.228 57.895 0.00 0.00 34.05 4.34
1154 1249 0.613777 CAAGAAGGGTAAGGAGGCGT 59.386 55.000 0.00 0.00 0.00 5.68
1229 1327 1.963855 CCAACGGTTGGCGATGACA 60.964 57.895 25.60 0.00 45.17 3.58
1279 1379 0.886563 GCCACACTACGACCACTACT 59.113 55.000 0.00 0.00 0.00 2.57
1286 1386 4.197750 CACTACGACCACTACTATGAGGT 58.802 47.826 0.00 0.00 37.00 3.85
1317 1417 4.318332 CAAGTCACTTCTGCAAGGTCATA 58.682 43.478 0.00 0.00 33.37 2.15
1333 1433 2.484264 GTCATACTTGCACCGAAGCTTT 59.516 45.455 0.00 0.00 34.99 3.51
1412 1512 3.340789 GGTGAGGAACAACACCGC 58.659 61.111 0.00 0.00 44.46 5.68
1439 1539 2.047179 GAGGGTGACGGTGAAGCC 60.047 66.667 1.37 1.37 0.00 4.35
1533 1633 1.334160 TGGTGACGTTCAAGCTCCTA 58.666 50.000 0.00 0.00 0.00 2.94
1626 1726 4.760047 GAAGCCTTCGCCGCCAGA 62.760 66.667 0.00 0.00 34.57 3.86
1793 1902 3.012518 GCTCTGCTTATGATGTGTGGTT 58.987 45.455 0.00 0.00 0.00 3.67
1817 1927 1.153269 TTGTGCCGAAGTGTGCTGA 60.153 52.632 0.00 0.00 0.00 4.26
1827 1937 3.664107 GAAGTGTGCTGATAACCTCACA 58.336 45.455 0.00 0.00 37.14 3.58
1842 1952 3.391296 ACCTCACAAACTAGCCAAAGAGA 59.609 43.478 0.00 0.00 0.00 3.10
1856 1966 3.502211 CCAAAGAGATTACCACACACCAC 59.498 47.826 0.00 0.00 0.00 4.16
1888 1998 2.890311 CAACCAAACACCATGCCTTAGA 59.110 45.455 0.00 0.00 0.00 2.10
1904 2014 6.953101 TGCCTTAGATTTGTCCACTAACATA 58.047 36.000 0.00 0.00 0.00 2.29
1908 2018 8.258007 CCTTAGATTTGTCCACTAACATACAGA 58.742 37.037 0.00 0.00 0.00 3.41
1946 2056 0.918258 TATGGTTCAGCCCATGCAGA 59.082 50.000 2.99 0.00 44.93 4.26
1981 2091 1.289276 GCAACCAAACAACTTGCAGG 58.711 50.000 0.00 0.00 40.09 4.85
2044 2156 2.158711 AGAAGGCTATGCATGCAGCTAA 60.159 45.455 26.69 10.29 45.94 3.09
2068 2180 3.530265 AGACTACGACAACCAAACACA 57.470 42.857 0.00 0.00 0.00 3.72
2074 2186 1.029681 GACAACCAAACACACCCCTC 58.970 55.000 0.00 0.00 0.00 4.30
2075 2187 0.396556 ACAACCAAACACACCCCTCC 60.397 55.000 0.00 0.00 0.00 4.30
2076 2188 0.106217 CAACCAAACACACCCCTCCT 60.106 55.000 0.00 0.00 0.00 3.69
2077 2189 1.144093 CAACCAAACACACCCCTCCTA 59.856 52.381 0.00 0.00 0.00 2.94
2078 2190 1.755200 ACCAAACACACCCCTCCTAT 58.245 50.000 0.00 0.00 0.00 2.57
2079 2191 2.923908 ACCAAACACACCCCTCCTATA 58.076 47.619 0.00 0.00 0.00 1.31
2080 2192 2.574824 ACCAAACACACCCCTCCTATAC 59.425 50.000 0.00 0.00 0.00 1.47
2081 2193 2.844348 CCAAACACACCCCTCCTATACT 59.156 50.000 0.00 0.00 0.00 2.12
2082 2194 4.035112 CCAAACACACCCCTCCTATACTA 58.965 47.826 0.00 0.00 0.00 1.82
2083 2195 4.472108 CCAAACACACCCCTCCTATACTAA 59.528 45.833 0.00 0.00 0.00 2.24
2084 2196 5.396436 CCAAACACACCCCTCCTATACTAAG 60.396 48.000 0.00 0.00 0.00 2.18
2085 2197 3.924922 ACACACCCCTCCTATACTAAGG 58.075 50.000 0.00 0.00 38.06 2.69
2086 2198 3.274153 ACACACCCCTCCTATACTAAGGT 59.726 47.826 0.00 0.00 37.91 3.50
2087 2199 3.641906 CACACCCCTCCTATACTAAGGTG 59.358 52.174 4.79 4.79 46.87 4.00
2088 2200 2.633481 CACCCCTCCTATACTAAGGTGC 59.367 54.545 0.00 0.00 37.13 5.01
2089 2201 2.249214 ACCCCTCCTATACTAAGGTGCA 59.751 50.000 0.00 0.00 37.91 4.57
2090 2202 3.311103 ACCCCTCCTATACTAAGGTGCAA 60.311 47.826 0.00 0.00 37.91 4.08
2091 2203 3.071167 CCCCTCCTATACTAAGGTGCAAC 59.929 52.174 0.00 0.00 37.91 4.17
2092 2204 3.709653 CCCTCCTATACTAAGGTGCAACA 59.290 47.826 3.64 0.00 39.98 3.33
2093 2205 4.443034 CCCTCCTATACTAAGGTGCAACAC 60.443 50.000 3.64 0.00 39.98 3.32
2094 2206 4.161565 CCTCCTATACTAAGGTGCAACACA 59.838 45.833 3.64 0.00 39.98 3.72
2103 2215 3.845625 GTGCAACACACTAACCAGC 57.154 52.632 0.00 0.00 46.41 4.85
2104 2216 0.310854 GTGCAACACACTAACCAGCC 59.689 55.000 0.00 0.00 46.41 4.85
2105 2217 1.163420 TGCAACACACTAACCAGCCG 61.163 55.000 0.00 0.00 0.00 5.52
2106 2218 0.882927 GCAACACACTAACCAGCCGA 60.883 55.000 0.00 0.00 0.00 5.54
2107 2219 0.865769 CAACACACTAACCAGCCGAC 59.134 55.000 0.00 0.00 0.00 4.79
2108 2220 0.250166 AACACACTAACCAGCCGACC 60.250 55.000 0.00 0.00 0.00 4.79
2109 2221 1.369692 CACACTAACCAGCCGACCA 59.630 57.895 0.00 0.00 0.00 4.02
2110 2222 0.949105 CACACTAACCAGCCGACCAC 60.949 60.000 0.00 0.00 0.00 4.16
2111 2223 1.369692 CACTAACCAGCCGACCACA 59.630 57.895 0.00 0.00 0.00 4.17
2112 2224 0.949105 CACTAACCAGCCGACCACAC 60.949 60.000 0.00 0.00 0.00 3.82
2113 2225 1.369692 CTAACCAGCCGACCACACA 59.630 57.895 0.00 0.00 0.00 3.72
2114 2226 0.250124 CTAACCAGCCGACCACACAA 60.250 55.000 0.00 0.00 0.00 3.33
2115 2227 0.533308 TAACCAGCCGACCACACAAC 60.533 55.000 0.00 0.00 0.00 3.32
2116 2228 2.111043 CCAGCCGACCACACAACT 59.889 61.111 0.00 0.00 0.00 3.16
2117 2229 1.525995 CCAGCCGACCACACAACTT 60.526 57.895 0.00 0.00 0.00 2.66
2118 2230 1.507141 CCAGCCGACCACACAACTTC 61.507 60.000 0.00 0.00 0.00 3.01
2119 2231 0.813610 CAGCCGACCACACAACTTCA 60.814 55.000 0.00 0.00 0.00 3.02
2120 2232 0.108585 AGCCGACCACACAACTTCAT 59.891 50.000 0.00 0.00 0.00 2.57
2121 2233 0.517316 GCCGACCACACAACTTCATC 59.483 55.000 0.00 0.00 0.00 2.92
2122 2234 0.790207 CCGACCACACAACTTCATCG 59.210 55.000 0.00 0.00 0.00 3.84
2123 2235 0.790207 CGACCACACAACTTCATCGG 59.210 55.000 0.00 0.00 0.00 4.18
2124 2236 1.604438 CGACCACACAACTTCATCGGA 60.604 52.381 0.00 0.00 0.00 4.55
2125 2237 1.798813 GACCACACAACTTCATCGGAC 59.201 52.381 0.00 0.00 0.00 4.79
2126 2238 1.140052 ACCACACAACTTCATCGGACA 59.860 47.619 0.00 0.00 0.00 4.02
2127 2239 2.224523 ACCACACAACTTCATCGGACAT 60.225 45.455 0.00 0.00 0.00 3.06
2128 2240 2.813754 CCACACAACTTCATCGGACATT 59.186 45.455 0.00 0.00 0.00 2.71
2129 2241 3.365264 CCACACAACTTCATCGGACATTG 60.365 47.826 0.00 0.00 0.00 2.82
2130 2242 3.250762 CACACAACTTCATCGGACATTGT 59.749 43.478 0.00 0.00 33.66 2.71
2131 2243 3.882888 ACACAACTTCATCGGACATTGTT 59.117 39.130 0.00 0.00 31.97 2.83
2132 2244 4.024048 ACACAACTTCATCGGACATTGTTC 60.024 41.667 0.00 0.00 31.97 3.18
2133 2245 4.024133 CACAACTTCATCGGACATTGTTCA 60.024 41.667 0.00 0.00 31.97 3.18
2134 2246 4.761739 ACAACTTCATCGGACATTGTTCAT 59.238 37.500 0.00 0.00 30.79 2.57
2135 2247 5.106555 ACAACTTCATCGGACATTGTTCATC 60.107 40.000 0.00 0.00 30.79 2.92
2136 2248 4.836825 ACTTCATCGGACATTGTTCATCT 58.163 39.130 0.00 0.00 0.00 2.90
2137 2249 5.248640 ACTTCATCGGACATTGTTCATCTT 58.751 37.500 0.00 0.00 0.00 2.40
2138 2250 5.707298 ACTTCATCGGACATTGTTCATCTTT 59.293 36.000 0.00 0.00 0.00 2.52
2139 2251 6.207417 ACTTCATCGGACATTGTTCATCTTTT 59.793 34.615 0.00 0.00 0.00 2.27
2140 2252 6.182039 TCATCGGACATTGTTCATCTTTTC 57.818 37.500 0.00 0.00 0.00 2.29
2141 2253 4.661993 TCGGACATTGTTCATCTTTTCG 57.338 40.909 0.00 0.00 0.00 3.46
2142 2254 4.311606 TCGGACATTGTTCATCTTTTCGA 58.688 39.130 0.00 0.00 0.00 3.71
2143 2255 4.752604 TCGGACATTGTTCATCTTTTCGAA 59.247 37.500 0.00 0.00 0.00 3.71
2144 2256 4.846137 CGGACATTGTTCATCTTTTCGAAC 59.154 41.667 0.00 0.00 41.53 3.95
2145 2257 5.334105 CGGACATTGTTCATCTTTTCGAACT 60.334 40.000 0.00 0.00 41.67 3.01
2146 2258 6.080406 GGACATTGTTCATCTTTTCGAACTC 58.920 40.000 0.00 0.00 41.67 3.01
2147 2259 6.073003 GGACATTGTTCATCTTTTCGAACTCT 60.073 38.462 0.00 0.00 41.67 3.24
2148 2260 7.264373 ACATTGTTCATCTTTTCGAACTCTT 57.736 32.000 0.00 0.00 41.67 2.85
2149 2261 7.707104 ACATTGTTCATCTTTTCGAACTCTTT 58.293 30.769 0.00 0.00 41.67 2.52
2150 2262 8.190784 ACATTGTTCATCTTTTCGAACTCTTTT 58.809 29.630 0.00 0.00 41.67 2.27
2151 2263 9.663904 CATTGTTCATCTTTTCGAACTCTTTTA 57.336 29.630 0.00 0.00 41.67 1.52
2166 2278 9.503427 CGAACTCTTTTATTAATTCCACATTCC 57.497 33.333 0.00 0.00 0.00 3.01
2167 2279 9.503427 GAACTCTTTTATTAATTCCACATTCCG 57.497 33.333 0.00 0.00 0.00 4.30
2168 2280 8.575649 ACTCTTTTATTAATTCCACATTCCGT 57.424 30.769 0.00 0.00 0.00 4.69
2169 2281 9.020731 ACTCTTTTATTAATTCCACATTCCGTT 57.979 29.630 0.00 0.00 0.00 4.44
2170 2282 9.503427 CTCTTTTATTAATTCCACATTCCGTTC 57.497 33.333 0.00 0.00 0.00 3.95
2171 2283 8.463607 TCTTTTATTAATTCCACATTCCGTTCC 58.536 33.333 0.00 0.00 0.00 3.62
2172 2284 6.702716 TTATTAATTCCACATTCCGTTCCC 57.297 37.500 0.00 0.00 0.00 3.97
2173 2285 2.899303 AATTCCACATTCCGTTCCCT 57.101 45.000 0.00 0.00 0.00 4.20
2174 2286 2.899303 ATTCCACATTCCGTTCCCTT 57.101 45.000 0.00 0.00 0.00 3.95
2175 2287 2.668144 TTCCACATTCCGTTCCCTTT 57.332 45.000 0.00 0.00 0.00 3.11
2176 2288 2.668144 TCCACATTCCGTTCCCTTTT 57.332 45.000 0.00 0.00 0.00 2.27
2177 2289 2.952116 TCCACATTCCGTTCCCTTTTT 58.048 42.857 0.00 0.00 0.00 1.94
2178 2290 2.888414 TCCACATTCCGTTCCCTTTTTC 59.112 45.455 0.00 0.00 0.00 2.29
2179 2291 2.625790 CCACATTCCGTTCCCTTTTTCA 59.374 45.455 0.00 0.00 0.00 2.69
2180 2292 3.258123 CCACATTCCGTTCCCTTTTTCAT 59.742 43.478 0.00 0.00 0.00 2.57
2181 2293 4.262420 CCACATTCCGTTCCCTTTTTCATT 60.262 41.667 0.00 0.00 0.00 2.57
2182 2294 5.296748 CACATTCCGTTCCCTTTTTCATTT 58.703 37.500 0.00 0.00 0.00 2.32
2183 2295 5.757808 CACATTCCGTTCCCTTTTTCATTTT 59.242 36.000 0.00 0.00 0.00 1.82
2184 2296 6.259829 CACATTCCGTTCCCTTTTTCATTTTT 59.740 34.615 0.00 0.00 0.00 1.94
2243 2355 6.703857 TCGTAAAAATCGACGAACTTTTTCA 58.296 32.000 19.68 7.78 44.56 2.69
2244 2356 7.346695 TCGTAAAAATCGACGAACTTTTTCAT 58.653 30.769 19.68 5.35 44.56 2.57
2245 2357 8.486383 TCGTAAAAATCGACGAACTTTTTCATA 58.514 29.630 19.68 5.97 44.56 2.15
2246 2358 9.257865 CGTAAAAATCGACGAACTTTTTCATAT 57.742 29.630 19.68 4.79 41.60 1.78
2322 2434 8.848474 TTTTTCAAAACCCATGAACTTTGTAA 57.152 26.923 0.00 0.00 36.57 2.41
2323 2435 8.848474 TTTTCAAAACCCATGAACTTTGTAAA 57.152 26.923 0.00 4.53 36.57 2.01
2324 2436 8.848474 TTTCAAAACCCATGAACTTTGTAAAA 57.152 26.923 0.00 0.00 36.57 1.52
2325 2437 7.835634 TCAAAACCCATGAACTTTGTAAAAC 57.164 32.000 0.00 0.00 32.00 2.43
2326 2438 7.386851 TCAAAACCCATGAACTTTGTAAAACA 58.613 30.769 0.00 0.00 32.00 2.83
2327 2439 7.878127 TCAAAACCCATGAACTTTGTAAAACAA 59.122 29.630 0.00 0.00 36.11 2.83
2328 2440 8.672815 CAAAACCCATGAACTTTGTAAAACAAT 58.327 29.630 0.00 0.00 38.00 2.71
2329 2441 7.784633 AACCCATGAACTTTGTAAAACAATG 57.215 32.000 0.00 4.63 38.00 2.82
2330 2442 7.118496 ACCCATGAACTTTGTAAAACAATGA 57.882 32.000 11.31 0.00 38.00 2.57
2331 2443 7.560368 ACCCATGAACTTTGTAAAACAATGAA 58.440 30.769 11.31 0.25 38.00 2.57
2332 2444 7.494298 ACCCATGAACTTTGTAAAACAATGAAC 59.506 33.333 11.31 6.40 38.00 3.18
2333 2445 7.493971 CCCATGAACTTTGTAAAACAATGAACA 59.506 33.333 11.31 10.32 38.00 3.18
2334 2446 9.044150 CCATGAACTTTGTAAAACAATGAACAT 57.956 29.630 11.31 11.60 38.00 2.71
2363 2475 8.783833 TTTGGAAATTCATGAACTGTTTTTCA 57.216 26.923 23.14 16.64 39.79 2.69
2364 2476 8.783833 TTGGAAATTCATGAACTGTTTTTCAA 57.216 26.923 23.14 20.06 38.95 2.69
2365 2477 8.961294 TGGAAATTCATGAACTGTTTTTCAAT 57.039 26.923 23.14 0.29 38.95 2.57
2366 2478 9.393512 TGGAAATTCATGAACTGTTTTTCAATT 57.606 25.926 23.14 5.58 38.95 2.32
2367 2479 9.868389 GGAAATTCATGAACTGTTTTTCAATTC 57.132 29.630 23.14 9.87 38.95 2.17
2368 2480 9.571804 GAAATTCATGAACTGTTTTTCAATTCG 57.428 29.630 19.48 0.00 38.95 3.34
2369 2481 8.870160 AATTCATGAACTGTTTTTCAATTCGA 57.130 26.923 11.07 0.00 38.95 3.71
2370 2482 9.480053 AATTCATGAACTGTTTTTCAATTCGAT 57.520 25.926 11.07 0.00 38.95 3.59
2371 2483 7.856492 TCATGAACTGTTTTTCAATTCGATG 57.144 32.000 0.00 0.00 38.95 3.84
2372 2484 7.647228 TCATGAACTGTTTTTCAATTCGATGA 58.353 30.769 0.00 0.00 38.95 2.92
2373 2485 8.134261 TCATGAACTGTTTTTCAATTCGATGAA 58.866 29.630 0.00 0.00 38.95 2.57
2374 2486 7.678194 TGAACTGTTTTTCAATTCGATGAAC 57.322 32.000 0.95 0.00 38.95 3.18
2375 2487 7.254137 TGAACTGTTTTTCAATTCGATGAACA 58.746 30.769 0.95 0.00 38.95 3.18
2376 2488 7.920151 TGAACTGTTTTTCAATTCGATGAACAT 59.080 29.630 0.95 0.00 38.95 2.71
2377 2489 8.647143 AACTGTTTTTCAATTCGATGAACATT 57.353 26.923 0.95 0.00 38.95 2.71
2378 2490 8.647143 ACTGTTTTTCAATTCGATGAACATTT 57.353 26.923 0.95 0.00 38.95 2.32
2379 2491 9.097257 ACTGTTTTTCAATTCGATGAACATTTT 57.903 25.926 0.95 0.00 38.95 1.82
2380 2492 9.919348 CTGTTTTTCAATTCGATGAACATTTTT 57.081 25.926 0.95 0.00 38.95 1.94
2381 2493 9.913451 TGTTTTTCAATTCGATGAACATTTTTC 57.087 25.926 0.95 0.00 38.95 2.29
2382 2494 9.368921 GTTTTTCAATTCGATGAACATTTTTCC 57.631 29.630 0.95 0.00 38.95 3.13
2383 2495 8.654230 TTTTCAATTCGATGAACATTTTTCCA 57.346 26.923 0.95 0.00 38.95 3.53
2384 2496 8.654230 TTTCAATTCGATGAACATTTTTCCAA 57.346 26.923 0.95 0.00 38.95 3.53
2385 2497 8.654230 TTCAATTCGATGAACATTTTTCCAAA 57.346 26.923 0.00 0.00 34.50 3.28
2386 2498 8.654230 TCAATTCGATGAACATTTTTCCAAAA 57.346 26.923 0.00 0.00 0.00 2.44
2387 2499 9.270640 TCAATTCGATGAACATTTTTCCAAAAT 57.729 25.926 0.00 0.00 0.00 1.82
2388 2500 9.881529 CAATTCGATGAACATTTTTCCAAAATT 57.118 25.926 0.00 0.00 0.00 1.82
2389 2501 9.881529 AATTCGATGAACATTTTTCCAAAATTG 57.118 25.926 0.00 5.51 36.10 2.32
2390 2502 8.654230 TTCGATGAACATTTTTCCAAAATTGA 57.346 26.923 11.70 0.00 34.84 2.57
2391 2503 8.830201 TCGATGAACATTTTTCCAAAATTGAT 57.170 26.923 11.70 2.65 34.84 2.57
2392 2504 8.710551 TCGATGAACATTTTTCCAAAATTGATG 58.289 29.630 11.70 4.33 34.84 3.07
2393 2505 8.710551 CGATGAACATTTTTCCAAAATTGATGA 58.289 29.630 11.70 0.00 34.84 2.92
2396 2508 9.393512 TGAACATTTTTCCAAAATTGATGAACT 57.606 25.926 11.70 0.00 34.84 3.01
2429 2541 8.925161 AAAAATTGAACTTTCTGTGAAATCGA 57.075 26.923 0.00 0.00 0.00 3.59
2430 2542 9.533253 AAAAATTGAACTTTCTGTGAAATCGAT 57.467 25.926 0.00 0.00 0.00 3.59
2431 2543 9.533253 AAAATTGAACTTTCTGTGAAATCGATT 57.467 25.926 4.39 4.39 0.00 3.34
2434 2546 9.612620 ATTGAACTTTCTGTGAAATCGATTAAC 57.387 29.630 11.83 13.24 0.00 2.01
2435 2547 8.378172 TGAACTTTCTGTGAAATCGATTAACT 57.622 30.769 11.83 0.00 0.00 2.24
2436 2548 8.836413 TGAACTTTCTGTGAAATCGATTAACTT 58.164 29.630 11.83 0.00 0.00 2.66
2437 2549 9.665264 GAACTTTCTGTGAAATCGATTAACTTT 57.335 29.630 11.83 0.00 0.00 2.66
2512 2624 8.870160 ACGATGAACTTTTTCAAAATTGATGA 57.130 26.923 0.00 0.00 45.01 2.92
2513 2625 9.311916 ACGATGAACTTTTTCAAAATTGATGAA 57.688 25.926 0.00 3.48 45.01 2.57
2514 2626 9.571804 CGATGAACTTTTTCAAAATTGATGAAC 57.428 29.630 6.46 0.00 45.01 3.18
2517 2629 9.434420 TGAACTTTTTCAAAATTGATGAACTGT 57.566 25.926 6.46 4.31 38.87 3.55
2523 2635 9.650539 TTTTCAAAATTGATGAACTGTTTCTCA 57.349 25.926 6.46 0.00 36.57 3.27
2524 2636 9.650539 TTTCAAAATTGATGAACTGTTTCTCAA 57.349 25.926 16.10 16.10 36.57 3.02
2525 2637 9.650539 TTCAAAATTGATGAACTGTTTCTCAAA 57.349 25.926 17.10 4.22 37.00 2.69
2526 2638 9.650539 TCAAAATTGATGAACTGTTTCTCAAAA 57.349 25.926 17.10 3.61 34.94 2.44
2530 2642 9.820725 AATTGATGAACTGTTTCTCAAAATTGA 57.179 25.926 17.10 0.00 34.94 2.57
2531 2643 9.991906 ATTGATGAACTGTTTCTCAAAATTGAT 57.008 25.926 17.10 3.72 34.94 2.57
2532 2644 8.806177 TGATGAACTGTTTCTCAAAATTGATG 57.194 30.769 0.00 0.00 36.46 3.07
2533 2645 8.631797 TGATGAACTGTTTCTCAAAATTGATGA 58.368 29.630 0.00 0.00 36.46 2.92
2534 2646 9.467258 GATGAACTGTTTCTCAAAATTGATGAA 57.533 29.630 0.00 1.16 36.46 2.57
2535 2647 8.633075 TGAACTGTTTCTCAAAATTGATGAAC 57.367 30.769 0.00 11.66 36.46 3.18
2536 2648 8.469200 TGAACTGTTTCTCAAAATTGATGAACT 58.531 29.630 16.14 4.10 36.46 3.01
2537 2649 9.305925 GAACTGTTTCTCAAAATTGATGAACTT 57.694 29.630 16.14 8.38 36.46 2.66
2538 2650 9.657419 AACTGTTTCTCAAAATTGATGAACTTT 57.343 25.926 16.14 10.30 36.46 2.66
2539 2651 9.657419 ACTGTTTCTCAAAATTGATGAACTTTT 57.343 25.926 16.14 0.00 36.46 2.27
2542 2654 9.920826 GTTTCTCAAAATTGATGAACTTTTTCC 57.079 29.630 11.44 0.00 36.46 3.13
2543 2655 9.664332 TTTCTCAAAATTGATGAACTTTTTCCA 57.336 25.926 0.00 0.00 36.46 3.53
2544 2656 9.664332 TTCTCAAAATTGATGAACTTTTTCCAA 57.336 25.926 0.00 0.00 36.46 3.53
2545 2657 9.664332 TCTCAAAATTGATGAACTTTTTCCAAA 57.336 25.926 0.00 0.00 36.46 3.28
2552 2664 7.966246 TGATGAACTTTTTCCAAATTCATGG 57.034 32.000 2.68 0.00 39.49 3.66
2566 2678 9.796180 TCCAAATTCATGGAAATTCTTTGAAAT 57.204 25.926 12.47 4.92 46.36 2.17
2568 2680 9.749490 CAAATTCATGGAAATTCTTTGAAATCG 57.251 29.630 12.47 4.08 30.81 3.34
2569 2681 9.492973 AAATTCATGGAAATTCTTTGAAATCGT 57.507 25.926 12.47 0.00 30.81 3.73
2570 2682 7.872163 TTCATGGAAATTCTTTGAAATCGTG 57.128 32.000 8.08 0.00 0.00 4.35
2571 2683 7.213216 TCATGGAAATTCTTTGAAATCGTGA 57.787 32.000 0.00 0.00 0.00 4.35
2572 2684 7.656412 TCATGGAAATTCTTTGAAATCGTGAA 58.344 30.769 0.00 0.00 0.00 3.18
2573 2685 7.594758 TCATGGAAATTCTTTGAAATCGTGAAC 59.405 33.333 0.00 0.00 0.00 3.18
2574 2686 7.038154 TGGAAATTCTTTGAAATCGTGAACT 57.962 32.000 0.00 0.00 0.00 3.01
2575 2687 7.138736 TGGAAATTCTTTGAAATCGTGAACTC 58.861 34.615 0.00 0.00 0.00 3.01
2576 2688 7.013274 TGGAAATTCTTTGAAATCGTGAACTCT 59.987 33.333 0.00 0.00 0.00 3.24
2577 2689 7.862873 GGAAATTCTTTGAAATCGTGAACTCTT 59.137 33.333 0.00 0.00 0.00 2.85
2578 2690 9.237846 GAAATTCTTTGAAATCGTGAACTCTTT 57.762 29.630 0.00 0.00 0.00 2.52
2579 2691 9.586435 AAATTCTTTGAAATCGTGAACTCTTTT 57.414 25.926 0.00 0.00 0.00 2.27
2580 2692 9.586435 AATTCTTTGAAATCGTGAACTCTTTTT 57.414 25.926 0.00 0.00 0.00 1.94
2604 2716 9.974750 TTTTAATTCGTGGTTTGTTTTGAAATC 57.025 25.926 0.00 0.00 0.00 2.17
2605 2717 8.934507 TTAATTCGTGGTTTGTTTTGAAATCT 57.065 26.923 0.00 0.00 0.00 2.40
2606 2718 6.826893 ATTCGTGGTTTGTTTTGAAATCTG 57.173 33.333 0.00 0.00 0.00 2.90
2607 2719 5.317733 TCGTGGTTTGTTTTGAAATCTGT 57.682 34.783 0.00 0.00 0.00 3.41
2608 2720 5.098893 TCGTGGTTTGTTTTGAAATCTGTG 58.901 37.500 0.00 0.00 0.00 3.66
2609 2721 5.098893 CGTGGTTTGTTTTGAAATCTGTGA 58.901 37.500 0.00 0.00 0.00 3.58
2610 2722 5.574830 CGTGGTTTGTTTTGAAATCTGTGAA 59.425 36.000 0.00 0.00 0.00 3.18
2611 2723 6.453659 CGTGGTTTGTTTTGAAATCTGTGAAC 60.454 38.462 0.00 0.00 0.00 3.18
2612 2724 6.589907 GTGGTTTGTTTTGAAATCTGTGAACT 59.410 34.615 0.00 0.00 0.00 3.01
2613 2725 7.117667 GTGGTTTGTTTTGAAATCTGTGAACTT 59.882 33.333 0.00 0.00 0.00 2.66
2614 2726 7.659390 TGGTTTGTTTTGAAATCTGTGAACTTT 59.341 29.630 0.00 0.00 0.00 2.66
2615 2727 8.168626 GGTTTGTTTTGAAATCTGTGAACTTTC 58.831 33.333 0.00 0.00 0.00 2.62
2616 2728 8.707839 GTTTGTTTTGAAATCTGTGAACTTTCA 58.292 29.630 0.00 0.00 37.17 2.69
2617 2729 8.824159 TTGTTTTGAAATCTGTGAACTTTCAA 57.176 26.923 5.77 5.77 43.43 2.69
2624 2736 9.874205 TGAAATCTGTGAACTTTCAAATTTTCT 57.126 25.926 13.54 0.00 39.21 2.52
2627 2739 9.874205 AATCTGTGAACTTTCAAATTTTCTTCA 57.126 25.926 0.00 0.00 39.21 3.02
2628 2740 8.687824 TCTGTGAACTTTCAAATTTTCTTCAC 57.312 30.769 12.21 12.21 39.21 3.18
2629 2741 8.303156 TCTGTGAACTTTCAAATTTTCTTCACA 58.697 29.630 16.91 16.91 42.14 3.58
2630 2742 9.090692 CTGTGAACTTTCAAATTTTCTTCACAT 57.909 29.630 17.58 0.00 42.93 3.21
2631 2743 9.434420 TGTGAACTTTCAAATTTTCTTCACATT 57.566 25.926 15.31 0.00 40.47 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.031120 CTTCTTGCTCTCCTCCGATCT 58.969 52.381 0.00 0.00 0.00 2.75
103 104 3.131478 GCTTACCGCCATTGCCGT 61.131 61.111 0.00 0.00 33.45 5.68
123 124 9.934190 AAAAAGTATTGCATGATGAACAAAAAC 57.066 25.926 0.00 0.00 0.00 2.43
150 153 0.313987 CTACTGCCGGATCGTATGCA 59.686 55.000 5.05 0.00 0.00 3.96
153 156 2.161808 CGAATCTACTGCCGGATCGTAT 59.838 50.000 5.05 0.00 0.00 3.06
155 158 0.311165 CGAATCTACTGCCGGATCGT 59.689 55.000 5.05 0.00 0.00 3.73
175 178 3.866582 CCCCTCTCCGCCATGGAC 61.867 72.222 18.40 5.97 43.74 4.02
180 183 3.089874 CCATTCCCCTCTCCGCCA 61.090 66.667 0.00 0.00 0.00 5.69
233 241 9.516314 CATGAACTAGTATGAACTCGTATGAAA 57.484 33.333 0.00 0.00 37.15 2.69
408 488 2.779033 GGACGACGATAACCCGCCT 61.779 63.158 0.00 0.00 0.00 5.52
444 530 2.699073 CCGTCATTCCTGGCAGATG 58.301 57.895 17.94 12.88 0.00 2.90
455 541 4.473520 CGGAGCCAGGCCGTCATT 62.474 66.667 8.22 0.00 43.66 2.57
490 576 2.434359 GGAGGAAGAACCGGTGCG 60.434 66.667 8.52 0.00 44.74 5.34
618 704 4.506654 GTCTTGAACAACGCTAAACAGAGA 59.493 41.667 0.00 0.00 0.00 3.10
632 718 1.071542 TGAATCAGGCCGTCTTGAACA 59.928 47.619 0.00 0.00 0.00 3.18
636 722 1.019673 CCATGAATCAGGCCGTCTTG 58.980 55.000 0.00 2.64 0.00 3.02
637 723 0.749454 GCCATGAATCAGGCCGTCTT 60.749 55.000 11.11 0.00 45.18 3.01
704 791 2.032549 CACAAAGAGTTGAAGACGCTGG 60.033 50.000 0.00 0.00 38.49 4.85
720 807 1.153524 ATGAGGGCCACTGCACAAA 59.846 52.632 6.18 0.00 46.13 2.83
784 871 0.321564 CCATGGAGGTGTGCTCGAAA 60.322 55.000 5.56 0.00 0.00 3.46
907 1000 5.728741 ACTATCAACCTTTCTCCTCTCCATT 59.271 40.000 0.00 0.00 0.00 3.16
932 1025 1.369983 ACCCACCCCCTCTATTCTCTT 59.630 52.381 0.00 0.00 0.00 2.85
939 1032 2.023695 CACTACTTACCCACCCCCTCTA 60.024 54.545 0.00 0.00 0.00 2.43
1085 1180 4.092116 TCTCATTGCTCTCCTCGATCTA 57.908 45.455 0.00 0.00 0.00 1.98
1144 1239 3.278574 CATTGGATGAAACGCCTCCTTA 58.721 45.455 0.00 0.00 0.00 2.69
1154 1249 0.331278 ACCTCGGGCATTGGATGAAA 59.669 50.000 0.00 0.00 0.00 2.69
1229 1327 4.496336 GGGCTCCTCCATGCGCTT 62.496 66.667 9.73 0.00 38.77 4.68
1255 1354 1.213537 GGTCGTAGTGTGGCGCTTA 59.786 57.895 7.64 0.00 0.00 3.09
1298 1398 3.931578 AGTATGACCTTGCAGAAGTGAC 58.068 45.455 0.00 0.00 0.00 3.67
1317 1417 1.873591 CACTAAAGCTTCGGTGCAAGT 59.126 47.619 15.48 3.03 34.99 3.16
1333 1433 2.926250 GGGCATGGGGATGCACTA 59.074 61.111 9.13 0.00 46.85 2.74
1353 1453 1.871080 CGAAGTGCTTGGTGAAGTCT 58.129 50.000 0.00 0.00 0.00 3.24
1396 1496 1.227853 AGGCGGTGTTGTTCCTCAC 60.228 57.895 0.00 0.00 0.00 3.51
1412 1512 2.284921 TCACCCTCCAGGAGCAGG 60.285 66.667 11.57 10.49 39.89 4.85
1439 1539 0.459237 GGTCACTCTGCCACTCATCG 60.459 60.000 0.00 0.00 0.00 3.84
1445 1545 1.557269 ATCCAGGGTCACTCTGCCAC 61.557 60.000 0.00 0.00 0.00 5.01
1533 1633 1.481056 CCTTGAGGGTGTCGGGAGTT 61.481 60.000 0.00 0.00 0.00 3.01
1739 1848 6.102897 ACAGAGCATCAACTACTTAACAGT 57.897 37.500 0.00 0.00 37.82 3.55
1793 1902 0.179032 ACACTTCGGCACAACCATGA 60.179 50.000 0.00 0.00 39.03 3.07
1817 1927 5.876357 TCTTTGGCTAGTTTGTGAGGTTAT 58.124 37.500 0.00 0.00 0.00 1.89
1827 1937 5.705905 GTGTGGTAATCTCTTTGGCTAGTTT 59.294 40.000 0.00 0.00 0.00 2.66
1842 1952 0.533308 AACGCGTGGTGTGTGGTAAT 60.533 50.000 14.98 0.00 41.44 1.89
1888 1998 6.430000 GGTTGTCTGTATGTTAGTGGACAAAT 59.570 38.462 7.70 0.00 42.56 2.32
1904 2014 6.420913 ACTATCTAGTGTTTGGTTGTCTGT 57.579 37.500 0.00 0.00 34.72 3.41
1908 2018 7.253905 ACCATACTATCTAGTGTTTGGTTGT 57.746 36.000 15.95 0.00 39.87 3.32
1946 2056 2.362120 GCCTGCATGCCCTCTTGT 60.362 61.111 16.68 0.00 0.00 3.16
2044 2156 4.986659 GTGTTTGGTTGTCGTAGTCTACAT 59.013 41.667 10.59 0.00 0.00 2.29
2068 2180 2.249214 TGCACCTTAGTATAGGAGGGGT 59.751 50.000 0.00 0.00 36.33 4.95
2086 2198 1.163420 CGGCTGGTTAGTGTGTTGCA 61.163 55.000 0.00 0.00 0.00 4.08
2087 2199 0.882927 TCGGCTGGTTAGTGTGTTGC 60.883 55.000 0.00 0.00 0.00 4.17
2088 2200 0.865769 GTCGGCTGGTTAGTGTGTTG 59.134 55.000 0.00 0.00 0.00 3.33
2089 2201 0.250166 GGTCGGCTGGTTAGTGTGTT 60.250 55.000 0.00 0.00 0.00 3.32
2090 2202 1.370064 GGTCGGCTGGTTAGTGTGT 59.630 57.895 0.00 0.00 0.00 3.72
2091 2203 0.949105 GTGGTCGGCTGGTTAGTGTG 60.949 60.000 0.00 0.00 0.00 3.82
2092 2204 1.370064 GTGGTCGGCTGGTTAGTGT 59.630 57.895 0.00 0.00 0.00 3.55
2093 2205 0.949105 GTGTGGTCGGCTGGTTAGTG 60.949 60.000 0.00 0.00 0.00 2.74
2094 2206 1.370064 GTGTGGTCGGCTGGTTAGT 59.630 57.895 0.00 0.00 0.00 2.24
2095 2207 0.250124 TTGTGTGGTCGGCTGGTTAG 60.250 55.000 0.00 0.00 0.00 2.34
2096 2208 0.533308 GTTGTGTGGTCGGCTGGTTA 60.533 55.000 0.00 0.00 0.00 2.85
2097 2209 1.822186 GTTGTGTGGTCGGCTGGTT 60.822 57.895 0.00 0.00 0.00 3.67
2098 2210 2.203153 GTTGTGTGGTCGGCTGGT 60.203 61.111 0.00 0.00 0.00 4.00
2099 2211 1.507141 GAAGTTGTGTGGTCGGCTGG 61.507 60.000 0.00 0.00 0.00 4.85
2100 2212 0.813610 TGAAGTTGTGTGGTCGGCTG 60.814 55.000 0.00 0.00 0.00 4.85
2101 2213 0.108585 ATGAAGTTGTGTGGTCGGCT 59.891 50.000 0.00 0.00 0.00 5.52
2102 2214 0.517316 GATGAAGTTGTGTGGTCGGC 59.483 55.000 0.00 0.00 0.00 5.54
2103 2215 0.790207 CGATGAAGTTGTGTGGTCGG 59.210 55.000 0.00 0.00 0.00 4.79
2104 2216 0.790207 CCGATGAAGTTGTGTGGTCG 59.210 55.000 0.00 0.00 0.00 4.79
2105 2217 1.798813 GTCCGATGAAGTTGTGTGGTC 59.201 52.381 0.00 0.00 0.00 4.02
2106 2218 1.140052 TGTCCGATGAAGTTGTGTGGT 59.860 47.619 0.00 0.00 0.00 4.16
2107 2219 1.877637 TGTCCGATGAAGTTGTGTGG 58.122 50.000 0.00 0.00 0.00 4.17
2108 2220 3.250762 ACAATGTCCGATGAAGTTGTGTG 59.749 43.478 0.00 0.00 32.35 3.82
2109 2221 3.476552 ACAATGTCCGATGAAGTTGTGT 58.523 40.909 0.00 0.00 32.35 3.72
2110 2222 4.024133 TGAACAATGTCCGATGAAGTTGTG 60.024 41.667 0.00 0.00 33.28 3.33
2111 2223 4.133820 TGAACAATGTCCGATGAAGTTGT 58.866 39.130 0.00 0.00 33.96 3.32
2112 2224 4.747540 TGAACAATGTCCGATGAAGTTG 57.252 40.909 0.00 0.00 0.00 3.16
2113 2225 5.248640 AGATGAACAATGTCCGATGAAGTT 58.751 37.500 0.00 0.00 0.00 2.66
2114 2226 4.836825 AGATGAACAATGTCCGATGAAGT 58.163 39.130 0.00 0.00 0.00 3.01
2115 2227 5.808042 AAGATGAACAATGTCCGATGAAG 57.192 39.130 0.00 0.00 0.00 3.02
2116 2228 6.573664 AAAAGATGAACAATGTCCGATGAA 57.426 33.333 0.00 0.00 0.00 2.57
2117 2229 5.163864 CGAAAAGATGAACAATGTCCGATGA 60.164 40.000 0.00 0.00 0.00 2.92
2118 2230 5.023920 CGAAAAGATGAACAATGTCCGATG 58.976 41.667 0.00 0.00 0.00 3.84
2119 2231 4.935205 TCGAAAAGATGAACAATGTCCGAT 59.065 37.500 0.00 0.00 0.00 4.18
2120 2232 4.311606 TCGAAAAGATGAACAATGTCCGA 58.688 39.130 0.00 0.00 0.00 4.55
2121 2233 4.661993 TCGAAAAGATGAACAATGTCCG 57.338 40.909 0.00 0.00 0.00 4.79
2122 2234 6.002062 AGTTCGAAAAGATGAACAATGTCC 57.998 37.500 0.00 0.00 45.34 4.02
2123 2235 6.892691 AGAGTTCGAAAAGATGAACAATGTC 58.107 36.000 0.00 0.00 45.34 3.06
2124 2236 6.867662 AGAGTTCGAAAAGATGAACAATGT 57.132 33.333 0.00 0.00 45.34 2.71
2125 2237 8.566008 AAAAGAGTTCGAAAAGATGAACAATG 57.434 30.769 0.00 0.00 45.34 2.82
2140 2252 9.503427 GGAATGTGGAATTAATAAAAGAGTTCG 57.497 33.333 0.00 0.00 0.00 3.95
2141 2253 9.503427 CGGAATGTGGAATTAATAAAAGAGTTC 57.497 33.333 0.00 0.00 0.00 3.01
2142 2254 9.020731 ACGGAATGTGGAATTAATAAAAGAGTT 57.979 29.630 0.00 0.00 0.00 3.01
2143 2255 8.575649 ACGGAATGTGGAATTAATAAAAGAGT 57.424 30.769 0.00 0.00 0.00 3.24
2144 2256 9.503427 GAACGGAATGTGGAATTAATAAAAGAG 57.497 33.333 0.00 0.00 0.00 2.85
2145 2257 8.463607 GGAACGGAATGTGGAATTAATAAAAGA 58.536 33.333 0.00 0.00 0.00 2.52
2146 2258 7.704899 GGGAACGGAATGTGGAATTAATAAAAG 59.295 37.037 0.00 0.00 0.00 2.27
2147 2259 7.397761 AGGGAACGGAATGTGGAATTAATAAAA 59.602 33.333 0.00 0.00 0.00 1.52
2148 2260 6.893005 AGGGAACGGAATGTGGAATTAATAAA 59.107 34.615 0.00 0.00 0.00 1.40
2149 2261 6.428295 AGGGAACGGAATGTGGAATTAATAA 58.572 36.000 0.00 0.00 0.00 1.40
2150 2262 6.008696 AGGGAACGGAATGTGGAATTAATA 57.991 37.500 0.00 0.00 0.00 0.98
2151 2263 4.867086 AGGGAACGGAATGTGGAATTAAT 58.133 39.130 0.00 0.00 0.00 1.40
2152 2264 4.310022 AGGGAACGGAATGTGGAATTAA 57.690 40.909 0.00 0.00 0.00 1.40
2153 2265 4.310022 AAGGGAACGGAATGTGGAATTA 57.690 40.909 0.00 0.00 0.00 1.40
2154 2266 2.899303 AGGGAACGGAATGTGGAATT 57.101 45.000 0.00 0.00 0.00 2.17
2155 2267 2.899303 AAGGGAACGGAATGTGGAAT 57.101 45.000 0.00 0.00 0.00 3.01
2156 2268 2.668144 AAAGGGAACGGAATGTGGAA 57.332 45.000 0.00 0.00 0.00 3.53
2157 2269 2.668144 AAAAGGGAACGGAATGTGGA 57.332 45.000 0.00 0.00 0.00 4.02
2158 2270 2.625790 TGAAAAAGGGAACGGAATGTGG 59.374 45.455 0.00 0.00 0.00 4.17
2159 2271 4.519540 ATGAAAAAGGGAACGGAATGTG 57.480 40.909 0.00 0.00 0.00 3.21
2160 2272 5.545063 AAATGAAAAAGGGAACGGAATGT 57.455 34.783 0.00 0.00 0.00 2.71
2161 2273 6.859420 AAAAATGAAAAAGGGAACGGAATG 57.141 33.333 0.00 0.00 0.00 2.67
2219 2331 6.703857 TGAAAAAGTTCGTCGATTTTTACGA 58.296 32.000 15.62 0.00 45.64 3.43
2220 2332 6.939953 TGAAAAAGTTCGTCGATTTTTACG 57.060 33.333 15.62 0.00 36.53 3.18
2297 2409 8.848474 TTACAAAGTTCATGGGTTTTGAAAAA 57.152 26.923 17.57 9.61 35.03 1.94
2298 2410 8.848474 TTTACAAAGTTCATGGGTTTTGAAAA 57.152 26.923 17.57 11.18 35.03 2.29
2299 2411 8.722394 GTTTTACAAAGTTCATGGGTTTTGAAA 58.278 29.630 17.57 12.41 35.03 2.69
2300 2412 7.878127 TGTTTTACAAAGTTCATGGGTTTTGAA 59.122 29.630 17.57 8.98 35.21 2.69
2301 2413 7.386851 TGTTTTACAAAGTTCATGGGTTTTGA 58.613 30.769 17.57 5.13 35.21 2.69
2302 2414 7.602517 TGTTTTACAAAGTTCATGGGTTTTG 57.397 32.000 12.21 12.21 36.77 2.44
2303 2415 8.672815 CATTGTTTTACAAAGTTCATGGGTTTT 58.327 29.630 0.00 0.00 41.96 2.43
2304 2416 8.043710 TCATTGTTTTACAAAGTTCATGGGTTT 58.956 29.630 0.00 0.00 41.96 3.27
2305 2417 7.560368 TCATTGTTTTACAAAGTTCATGGGTT 58.440 30.769 0.00 0.00 41.96 4.11
2306 2418 7.118496 TCATTGTTTTACAAAGTTCATGGGT 57.882 32.000 0.00 0.00 41.96 4.51
2307 2419 7.493971 TGTTCATTGTTTTACAAAGTTCATGGG 59.506 33.333 0.00 0.00 41.96 4.00
2308 2420 8.417780 TGTTCATTGTTTTACAAAGTTCATGG 57.582 30.769 0.00 0.00 41.96 3.66
2337 2449 9.224267 TGAAAAACAGTTCATGAATTTCCAAAA 57.776 25.926 20.68 6.92 36.78 2.44
2338 2450 8.783833 TGAAAAACAGTTCATGAATTTCCAAA 57.216 26.923 20.68 7.17 36.78 3.28
2339 2451 8.783833 TTGAAAAACAGTTCATGAATTTCCAA 57.216 26.923 20.68 12.07 37.36 3.53
2340 2452 8.961294 ATTGAAAAACAGTTCATGAATTTCCA 57.039 26.923 20.68 14.32 37.36 3.53
2341 2453 9.868389 GAATTGAAAAACAGTTCATGAATTTCC 57.132 29.630 20.68 7.18 42.30 3.13
2342 2454 9.571804 CGAATTGAAAAACAGTTCATGAATTTC 57.428 29.630 18.32 18.32 42.68 2.17
2343 2455 9.311916 TCGAATTGAAAAACAGTTCATGAATTT 57.688 25.926 12.12 7.53 42.68 1.82
2344 2456 8.870160 TCGAATTGAAAAACAGTTCATGAATT 57.130 26.923 12.12 4.21 42.68 2.17
2345 2457 8.918658 CATCGAATTGAAAAACAGTTCATGAAT 58.081 29.630 12.12 0.00 42.68 2.57
2346 2458 8.134261 TCATCGAATTGAAAAACAGTTCATGAA 58.866 29.630 3.38 3.38 42.68 2.57
2347 2459 7.647228 TCATCGAATTGAAAAACAGTTCATGA 58.353 30.769 0.00 0.00 42.68 3.07
2348 2460 7.856492 TCATCGAATTGAAAAACAGTTCATG 57.144 32.000 0.00 0.00 42.68 3.07
2349 2461 7.920151 TGTTCATCGAATTGAAAAACAGTTCAT 59.080 29.630 3.10 0.00 42.68 2.57
2350 2462 7.254137 TGTTCATCGAATTGAAAAACAGTTCA 58.746 30.769 3.10 0.00 42.68 3.18
2351 2463 7.678194 TGTTCATCGAATTGAAAAACAGTTC 57.322 32.000 3.10 0.00 40.33 3.01
2352 2464 8.647143 AATGTTCATCGAATTGAAAAACAGTT 57.353 26.923 3.10 0.00 38.02 3.16
2353 2465 8.647143 AAATGTTCATCGAATTGAAAAACAGT 57.353 26.923 3.10 0.00 38.02 3.55
2354 2466 9.919348 AAAAATGTTCATCGAATTGAAAAACAG 57.081 25.926 3.10 0.00 38.02 3.16
2355 2467 9.913451 GAAAAATGTTCATCGAATTGAAAAACA 57.087 25.926 3.10 0.00 37.36 2.83
2356 2468 9.368921 GGAAAAATGTTCATCGAATTGAAAAAC 57.631 29.630 3.10 0.00 37.36 2.43
2357 2469 9.102757 TGGAAAAATGTTCATCGAATTGAAAAA 57.897 25.926 3.10 0.00 37.36 1.94
2358 2470 8.654230 TGGAAAAATGTTCATCGAATTGAAAA 57.346 26.923 3.10 0.00 37.36 2.29
2359 2471 8.654230 TTGGAAAAATGTTCATCGAATTGAAA 57.346 26.923 3.10 0.00 37.36 2.69
2360 2472 8.654230 TTTGGAAAAATGTTCATCGAATTGAA 57.346 26.923 0.00 0.00 33.32 2.69
2361 2473 8.654230 TTTTGGAAAAATGTTCATCGAATTGA 57.346 26.923 0.00 0.00 0.00 2.57
2362 2474 9.881529 AATTTTGGAAAAATGTTCATCGAATTG 57.118 25.926 0.00 0.00 0.00 2.32
2363 2475 9.881529 CAATTTTGGAAAAATGTTCATCGAATT 57.118 25.926 0.00 0.00 0.00 2.17
2364 2476 9.270640 TCAATTTTGGAAAAATGTTCATCGAAT 57.729 25.926 0.00 0.00 32.17 3.34
2365 2477 8.654230 TCAATTTTGGAAAAATGTTCATCGAA 57.346 26.923 0.00 0.00 32.17 3.71
2366 2478 8.710551 CATCAATTTTGGAAAAATGTTCATCGA 58.289 29.630 0.00 0.00 32.17 3.59
2367 2479 8.710551 TCATCAATTTTGGAAAAATGTTCATCG 58.289 29.630 0.00 0.00 32.17 3.84
2370 2482 9.393512 AGTTCATCAATTTTGGAAAAATGTTCA 57.606 25.926 0.00 0.00 32.17 3.18
2404 2516 8.925161 TCGATTTCACAGAAAGTTCAATTTTT 57.075 26.923 0.00 0.00 0.00 1.94
2405 2517 9.533253 AATCGATTTCACAGAAAGTTCAATTTT 57.467 25.926 4.39 0.00 0.00 1.82
2408 2520 9.612620 GTTAATCGATTTCACAGAAAGTTCAAT 57.387 29.630 17.19 0.00 0.00 2.57
2409 2521 8.836413 AGTTAATCGATTTCACAGAAAGTTCAA 58.164 29.630 17.19 0.00 0.00 2.69
2410 2522 8.378172 AGTTAATCGATTTCACAGAAAGTTCA 57.622 30.769 17.19 0.00 0.00 3.18
2411 2523 9.665264 AAAGTTAATCGATTTCACAGAAAGTTC 57.335 29.630 17.19 0.00 0.00 3.01
2486 2598 9.958234 TCATCAATTTTGAAAAAGTTCATCGTA 57.042 25.926 0.00 0.00 43.29 3.43
2487 2599 8.870160 TCATCAATTTTGAAAAAGTTCATCGT 57.130 26.923 0.00 0.00 43.29 3.73
2488 2600 9.571804 GTTCATCAATTTTGAAAAAGTTCATCG 57.428 29.630 0.00 0.00 43.29 3.84
2491 2603 9.434420 ACAGTTCATCAATTTTGAAAAAGTTCA 57.566 25.926 0.00 0.00 42.12 3.18
2497 2609 9.650539 TGAGAAACAGTTCATCAATTTTGAAAA 57.349 25.926 0.00 0.00 41.13 2.29
2498 2610 9.650539 TTGAGAAACAGTTCATCAATTTTGAAA 57.349 25.926 8.41 0.00 41.13 2.69
2499 2611 9.650539 TTTGAGAAACAGTTCATCAATTTTGAA 57.349 25.926 11.86 0.00 41.13 2.69
2500 2612 9.650539 TTTTGAGAAACAGTTCATCAATTTTGA 57.349 25.926 11.86 0.00 42.14 2.69
2504 2616 9.820725 TCAATTTTGAGAAACAGTTCATCAATT 57.179 25.926 11.86 4.61 36.09 2.32
2505 2617 9.991906 ATCAATTTTGAGAAACAGTTCATCAAT 57.008 25.926 11.86 0.00 41.08 2.57
2506 2618 9.251792 CATCAATTTTGAGAAACAGTTCATCAA 57.748 29.630 8.41 8.41 41.08 2.57
2507 2619 8.631797 TCATCAATTTTGAGAAACAGTTCATCA 58.368 29.630 0.00 0.00 41.08 3.07
2508 2620 9.467258 TTCATCAATTTTGAGAAACAGTTCATC 57.533 29.630 0.00 0.00 41.08 2.92
2509 2621 9.252962 GTTCATCAATTTTGAGAAACAGTTCAT 57.747 29.630 12.25 0.00 41.08 2.57
2510 2622 8.469200 AGTTCATCAATTTTGAGAAACAGTTCA 58.531 29.630 16.48 0.00 41.08 3.18
2511 2623 8.862550 AGTTCATCAATTTTGAGAAACAGTTC 57.137 30.769 16.48 0.00 41.08 3.01
2512 2624 9.657419 AAAGTTCATCAATTTTGAGAAACAGTT 57.343 25.926 16.48 10.53 41.08 3.16
2513 2625 9.657419 AAAAGTTCATCAATTTTGAGAAACAGT 57.343 25.926 16.48 6.94 41.08 3.55
2516 2628 9.920826 GGAAAAAGTTCATCAATTTTGAGAAAC 57.079 29.630 10.38 10.38 41.08 2.78
2517 2629 9.664332 TGGAAAAAGTTCATCAATTTTGAGAAA 57.336 25.926 0.00 0.00 41.08 2.52
2518 2630 9.664332 TTGGAAAAAGTTCATCAATTTTGAGAA 57.336 25.926 0.00 1.37 41.08 2.87
2519 2631 9.664332 TTTGGAAAAAGTTCATCAATTTTGAGA 57.336 25.926 0.00 0.00 41.08 3.27
2526 2638 9.005777 CCATGAATTTGGAAAAAGTTCATCAAT 57.994 29.630 0.00 0.00 39.25 2.57
2527 2639 8.209584 TCCATGAATTTGGAAAAAGTTCATCAA 58.790 29.630 0.00 0.00 42.82 2.57
2528 2640 7.733969 TCCATGAATTTGGAAAAAGTTCATCA 58.266 30.769 0.00 0.00 42.82 3.07
2540 2652 9.796180 ATTTCAAAGAATTTCCATGAATTTGGA 57.204 25.926 12.55 0.00 44.08 3.53
2542 2654 9.749490 CGATTTCAAAGAATTTCCATGAATTTG 57.251 29.630 12.55 7.41 35.03 2.32
2543 2655 9.492973 ACGATTTCAAAGAATTTCCATGAATTT 57.507 25.926 12.55 6.45 35.03 1.82
2544 2656 8.928733 CACGATTTCAAAGAATTTCCATGAATT 58.071 29.630 12.55 10.17 35.03 2.17
2545 2657 8.306038 TCACGATTTCAAAGAATTTCCATGAAT 58.694 29.630 12.55 6.13 35.03 2.57
2546 2658 7.656412 TCACGATTTCAAAGAATTTCCATGAA 58.344 30.769 9.28 9.28 35.03 2.57
2547 2659 7.213216 TCACGATTTCAAAGAATTTCCATGA 57.787 32.000 0.00 0.00 35.03 3.07
2548 2660 7.596248 AGTTCACGATTTCAAAGAATTTCCATG 59.404 33.333 0.00 0.00 35.03 3.66
2549 2661 7.661040 AGTTCACGATTTCAAAGAATTTCCAT 58.339 30.769 0.00 0.00 35.03 3.41
2550 2662 7.013274 AGAGTTCACGATTTCAAAGAATTTCCA 59.987 33.333 0.00 0.00 35.03 3.53
2551 2663 7.363431 AGAGTTCACGATTTCAAAGAATTTCC 58.637 34.615 0.00 0.00 35.03 3.13
2552 2664 8.788409 AAGAGTTCACGATTTCAAAGAATTTC 57.212 30.769 0.00 0.00 35.03 2.17
2553 2665 9.586435 AAAAGAGTTCACGATTTCAAAGAATTT 57.414 25.926 0.00 0.00 40.26 1.82
2554 2666 9.586435 AAAAAGAGTTCACGATTTCAAAGAATT 57.414 25.926 0.00 0.00 0.00 2.17
2578 2690 9.974750 GATTTCAAAACAAACCACGAATTAAAA 57.025 25.926 0.00 0.00 0.00 1.52
2579 2691 9.372369 AGATTTCAAAACAAACCACGAATTAAA 57.628 25.926 0.00 0.00 0.00 1.52
2580 2692 8.812329 CAGATTTCAAAACAAACCACGAATTAA 58.188 29.630 0.00 0.00 0.00 1.40
2581 2693 7.976734 ACAGATTTCAAAACAAACCACGAATTA 59.023 29.630 0.00 0.00 0.00 1.40
2582 2694 6.816140 ACAGATTTCAAAACAAACCACGAATT 59.184 30.769 0.00 0.00 0.00 2.17
2583 2695 6.255453 CACAGATTTCAAAACAAACCACGAAT 59.745 34.615 0.00 0.00 0.00 3.34
2584 2696 5.574830 CACAGATTTCAAAACAAACCACGAA 59.425 36.000 0.00 0.00 0.00 3.85
2585 2697 5.098893 CACAGATTTCAAAACAAACCACGA 58.901 37.500 0.00 0.00 0.00 4.35
2586 2698 5.098893 TCACAGATTTCAAAACAAACCACG 58.901 37.500 0.00 0.00 0.00 4.94
2587 2699 6.589907 AGTTCACAGATTTCAAAACAAACCAC 59.410 34.615 0.00 0.00 0.00 4.16
2588 2700 6.696411 AGTTCACAGATTTCAAAACAAACCA 58.304 32.000 0.00 0.00 0.00 3.67
2589 2701 7.595311 AAGTTCACAGATTTCAAAACAAACC 57.405 32.000 0.00 0.00 0.00 3.27
2590 2702 8.707839 TGAAAGTTCACAGATTTCAAAACAAAC 58.292 29.630 0.00 0.00 39.34 2.93
2591 2703 8.824159 TGAAAGTTCACAGATTTCAAAACAAA 57.176 26.923 0.00 0.00 39.34 2.83
2592 2704 8.824159 TTGAAAGTTCACAGATTTCAAAACAA 57.176 26.923 9.24 0.00 45.17 2.83
2598 2710 9.874205 AGAAAATTTGAAAGTTCACAGATTTCA 57.126 25.926 15.90 0.00 40.25 2.69
2601 2713 9.874205 TGAAGAAAATTTGAAAGTTCACAGATT 57.126 25.926 0.00 0.00 36.83 2.40
2602 2714 9.305925 GTGAAGAAAATTTGAAAGTTCACAGAT 57.694 29.630 17.67 0.00 41.16 2.90
2603 2715 8.303156 TGTGAAGAAAATTTGAAAGTTCACAGA 58.697 29.630 19.61 7.80 44.39 3.41
2604 2716 8.464770 TGTGAAGAAAATTTGAAAGTTCACAG 57.535 30.769 19.61 0.00 44.39 3.66


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

AutoCloner maintained by Alex Coulton.