Multiple sequence alignment - TraesCS1A01G375700

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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 TraesCS1A01G375700 chr1A 100.000 2393 0 0 1 2393 550337523 550339915 0.000000e+00 4420.0
1 TraesCS1A01G375700 chr1D 92.975 1395 59 21 694 2071 457875458 457876830 0.000000e+00 1997.0
2 TraesCS1A01G375700 chr1D 97.126 696 18 2 1 695 457874607 457875301 0.000000e+00 1173.0
3 TraesCS1A01G375700 chr1B 95.036 967 38 3 694 1650 627943237 627944203 0.000000e+00 1511.0
4 TraesCS1A01G375700 chr1B 96.691 695 21 2 1 694 627942382 627943075 0.000000e+00 1155.0
5 TraesCS1A01G375700 chr1B 89.444 180 15 2 1892 2067 627944240 627944419 8.610000e-55 224.0
6 TraesCS1A01G375700 chr5A 81.555 553 65 17 1418 1958 447369645 447369118 2.840000e-114 422.0
7 TraesCS1A01G375700 chr2A 94.030 67 2 2 2311 2375 283947840 283947774 1.510000e-17 100.0
8 TraesCS1A01G375700 chr2D 92.537 67 3 2 2311 2375 243662874 243662808 7.040000e-16 95.3
9 TraesCS1A01G375700 chr2D 90.000 70 4 3 2311 2378 599615419 599615351 1.180000e-13 87.9
10 TraesCS1A01G375700 chr4D 89.041 73 6 2 2311 2381 21682354 21682282 3.280000e-14 89.8
11 TraesCS1A01G375700 chr2B 90.000 70 5 2 2308 2375 337075104 337075173 3.280000e-14 89.8
12 TraesCS1A01G375700 chr3A 100.000 28 0 0 2354 2381 594649951 594649978 4.000000e-03 52.8


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 TraesCS1A01G375700 chr1A 550337523 550339915 2392 False 4420.000000 4420 100.000000 1 2393 1 chr1A.!!$F1 2392
1 TraesCS1A01G375700 chr1D 457874607 457876830 2223 False 1585.000000 1997 95.050500 1 2071 2 chr1D.!!$F1 2070
2 TraesCS1A01G375700 chr1B 627942382 627944419 2037 False 963.333333 1511 93.723667 1 2067 3 chr1B.!!$F1 2066
3 TraesCS1A01G375700 chr5A 447369118 447369645 527 True 422.000000 422 81.555000 1418 1958 1 chr5A.!!$R1 540

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
113 114 1.071228 TCTGAGGGCATGATGATTCCG 59.929 52.381 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1901 0.613777 CCCGAGGCTATACCCATTCC 59.386 60.0 0.0 0.0 40.58 3.01 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
113 114 1.071228 TCTGAGGGCATGATGATTCCG 59.929 52.381 0.00 0.00 0.00 4.30
225 226 5.540719 AGCTTACTAATCCAGACAGGGATAC 59.459 44.000 0.00 0.00 46.96 2.24
387 388 2.922740 TCCCCGGTGCAATAAGATAC 57.077 50.000 0.00 0.00 0.00 2.24
469 470 7.220030 ACAGTATAACTAAGATTGCCCTCATG 58.780 38.462 0.00 0.00 0.00 3.07
526 527 4.839668 AGTATCTTGCTCTGATCCGTAC 57.160 45.455 0.00 0.00 0.00 3.67
740 904 8.712285 TGTAACACTATACTTGGATAGTTTGC 57.288 34.615 2.93 6.13 40.03 3.68
745 909 8.705594 ACACTATACTTGGATAGTTTGCAGTAT 58.294 33.333 2.93 0.00 40.03 2.12
882 1052 1.679898 GGTGAGGTGAGGAAGGTGG 59.320 63.158 0.00 0.00 0.00 4.61
953 1123 5.144359 GTTTTGTGTGGTTCTAGTAATGCG 58.856 41.667 0.00 0.00 0.00 4.73
974 1144 5.406477 TGCGAGCATATCTCACATGTAAATC 59.594 40.000 0.00 0.00 41.98 2.17
984 1154 6.542821 TCTCACATGTAAATCCCTTTCTTGT 58.457 36.000 0.00 0.00 0.00 3.16
1405 1575 5.567037 TCTTTCCTGAGAATTGAAGGTCA 57.433 39.130 0.00 0.00 32.59 4.02
1427 1597 1.226717 GAGCCTACAGAAGCGTCGG 60.227 63.158 0.00 0.00 0.00 4.79
1690 1869 9.288576 AGTGTGTTCTCATTAATTTCTGAATGA 57.711 29.630 2.28 2.28 39.24 2.57
1770 1949 6.457257 CCAGATTTGGTTTGCTTTTCTGTTTG 60.457 38.462 0.00 0.00 39.79 2.93
1779 1958 4.636249 TGCTTTTCTGTTTGTTGGTGTTT 58.364 34.783 0.00 0.00 0.00 2.83
1780 1959 4.450419 TGCTTTTCTGTTTGTTGGTGTTTG 59.550 37.500 0.00 0.00 0.00 2.93
1786 1970 6.532365 TCTGTTTGTTGGTGTTTGTTTTTC 57.468 33.333 0.00 0.00 0.00 2.29
1788 1972 6.538742 TCTGTTTGTTGGTGTTTGTTTTTCAA 59.461 30.769 0.00 0.00 0.00 2.69
1791 1975 7.227512 TGTTTGTTGGTGTTTGTTTTTCAAGAT 59.772 29.630 0.00 0.00 37.35 2.40
1793 1977 7.736447 TGTTGGTGTTTGTTTTTCAAGATTT 57.264 28.000 0.00 0.00 37.35 2.17
1794 1978 8.833231 TGTTGGTGTTTGTTTTTCAAGATTTA 57.167 26.923 0.00 0.00 37.35 1.40
1815 1999 9.269415 GATTTATTATTTGCGAGTGTTTTACGT 57.731 29.630 0.00 0.00 0.00 3.57
1816 2000 7.996465 TTATTATTTGCGAGTGTTTTACGTG 57.004 32.000 0.00 0.00 0.00 4.49
1817 2001 2.093972 TTTGCGAGTGTTTTACGTGC 57.906 45.000 0.00 0.00 35.65 5.34
1818 2002 1.007580 TTGCGAGTGTTTTACGTGCA 58.992 45.000 0.00 0.00 40.74 4.57
1819 2003 0.579630 TGCGAGTGTTTTACGTGCAG 59.420 50.000 0.00 0.00 38.68 4.41
1821 2005 1.459592 GCGAGTGTTTTACGTGCAGAT 59.540 47.619 0.00 0.00 35.33 2.90
1822 2006 2.096417 GCGAGTGTTTTACGTGCAGATT 60.096 45.455 0.00 0.00 35.33 2.40
1847 2034 5.419542 TGGATTAGAAATGACGGAGACAAG 58.580 41.667 0.00 0.00 35.03 3.16
1849 2036 6.127054 TGGATTAGAAATGACGGAGACAAGAT 60.127 38.462 0.00 0.00 35.03 2.40
1862 2049 1.320344 ACAAGATGCCATGCTGCCAG 61.320 55.000 0.00 0.00 0.00 4.85
1863 2050 1.000019 AAGATGCCATGCTGCCAGT 60.000 52.632 0.00 0.00 0.00 4.00
1864 2051 1.320344 AAGATGCCATGCTGCCAGTG 61.320 55.000 0.00 0.00 0.00 3.66
1865 2052 3.426117 GATGCCATGCTGCCAGTGC 62.426 63.158 0.00 0.00 38.26 4.40
1887 2074 1.819632 CGCTGCCCTGGATGGTAAC 60.820 63.158 0.00 0.00 0.00 2.50
1934 2128 8.565896 TGCTTTTGTTATCTGAATATCACACT 57.434 30.769 0.00 0.00 0.00 3.55
1976 2170 1.909781 CAGCCTTGCACACCCCATT 60.910 57.895 0.00 0.00 0.00 3.16
2007 2201 6.545504 TGCACTGTCAAGAAAATTCTACTC 57.454 37.500 0.00 0.00 36.28 2.59
2012 2206 7.655328 CACTGTCAAGAAAATTCTACTCTCTGT 59.345 37.037 0.00 0.00 36.28 3.41
2020 2214 9.742144 AGAAAATTCTACTCTCTGTCTGTAGTA 57.258 33.333 0.00 0.00 35.34 1.82
2026 2220 8.771521 TCTACTCTCTGTCTGTAGTATACTCT 57.228 38.462 9.12 0.00 43.54 3.24
2030 2227 7.985184 ACTCTCTGTCTGTAGTATACTCTCTTG 59.015 40.741 9.12 2.82 43.54 3.02
2033 2230 8.270080 TCTGTCTGTAGTATACTCTCTTGTTG 57.730 38.462 9.12 0.00 43.54 3.33
2079 2276 8.924511 ATCTCAAAGAAAATTGTTCTAGGACA 57.075 30.769 0.00 0.00 0.00 4.02
2080 2277 8.154649 TCTCAAAGAAAATTGTTCTAGGACAC 57.845 34.615 2.36 0.00 0.00 3.67
2081 2278 7.993183 TCTCAAAGAAAATTGTTCTAGGACACT 59.007 33.333 2.36 0.00 0.00 3.55
2082 2279 8.519799 TCAAAGAAAATTGTTCTAGGACACTT 57.480 30.769 2.36 1.56 0.00 3.16
2083 2280 8.405531 TCAAAGAAAATTGTTCTAGGACACTTG 58.594 33.333 2.36 0.19 0.00 3.16
2084 2281 6.884280 AGAAAATTGTTCTAGGACACTTGG 57.116 37.500 2.36 0.00 0.00 3.61
2085 2282 6.365520 AGAAAATTGTTCTAGGACACTTGGT 58.634 36.000 2.36 0.00 0.00 3.67
2086 2283 7.514721 AGAAAATTGTTCTAGGACACTTGGTA 58.485 34.615 2.36 0.00 0.00 3.25
2087 2284 7.996644 AGAAAATTGTTCTAGGACACTTGGTAA 59.003 33.333 2.36 0.00 0.00 2.85
2088 2285 8.706322 AAAATTGTTCTAGGACACTTGGTAAT 57.294 30.769 2.36 0.00 0.00 1.89
2089 2286 8.706322 AAATTGTTCTAGGACACTTGGTAATT 57.294 30.769 2.36 0.00 0.00 1.40
2090 2287 8.706322 AATTGTTCTAGGACACTTGGTAATTT 57.294 30.769 2.36 0.00 0.00 1.82
2091 2288 8.706322 ATTGTTCTAGGACACTTGGTAATTTT 57.294 30.769 2.36 0.00 0.00 1.82
2092 2289 8.528044 TTGTTCTAGGACACTTGGTAATTTTT 57.472 30.769 2.36 0.00 0.00 1.94
2093 2290 9.629878 TTGTTCTAGGACACTTGGTAATTTTTA 57.370 29.630 2.36 0.00 0.00 1.52
2094 2291 9.629878 TGTTCTAGGACACTTGGTAATTTTTAA 57.370 29.630 0.00 0.00 0.00 1.52
2114 2311 9.698309 TTTTTAAATTGTTCTATTGCGGAATCA 57.302 25.926 5.06 0.00 0.00 2.57
2115 2312 9.698309 TTTTAAATTGTTCTATTGCGGAATCAA 57.302 25.926 5.06 4.67 0.00 2.57
2116 2313 8.909708 TTAAATTGTTCTATTGCGGAATCAAG 57.090 30.769 5.06 0.00 0.00 3.02
2117 2314 4.963276 TTGTTCTATTGCGGAATCAAGG 57.037 40.909 5.06 0.00 0.00 3.61
2118 2315 4.214986 TGTTCTATTGCGGAATCAAGGA 57.785 40.909 5.06 0.00 0.00 3.36
2119 2316 4.584874 TGTTCTATTGCGGAATCAAGGAA 58.415 39.130 5.06 4.53 0.00 3.36
2120 2317 5.192927 TGTTCTATTGCGGAATCAAGGAAT 58.807 37.500 5.06 1.34 33.17 3.01
2121 2318 5.652014 TGTTCTATTGCGGAATCAAGGAATT 59.348 36.000 5.06 0.00 31.11 2.17
2122 2319 5.756195 TCTATTGCGGAATCAAGGAATTG 57.244 39.130 5.06 0.44 31.11 2.32
2123 2320 5.436175 TCTATTGCGGAATCAAGGAATTGA 58.564 37.500 5.06 2.43 35.15 2.57
2124 2321 3.848272 TTGCGGAATCAAGGAATTGAC 57.152 42.857 0.00 0.00 33.23 3.18
2125 2322 2.789213 TGCGGAATCAAGGAATTGACA 58.211 42.857 0.00 0.00 33.23 3.58
2126 2323 3.355378 TGCGGAATCAAGGAATTGACAT 58.645 40.909 0.00 0.00 33.23 3.06
2127 2324 3.763360 TGCGGAATCAAGGAATTGACATT 59.237 39.130 0.00 0.00 33.23 2.71
2128 2325 4.220382 TGCGGAATCAAGGAATTGACATTT 59.780 37.500 0.00 0.00 33.23 2.32
2129 2326 4.800471 GCGGAATCAAGGAATTGACATTTC 59.200 41.667 2.11 2.11 33.23 2.17
2130 2327 5.393461 GCGGAATCAAGGAATTGACATTTCT 60.393 40.000 9.33 0.00 33.23 2.52
2131 2328 6.624423 CGGAATCAAGGAATTGACATTTCTT 58.376 36.000 9.33 0.40 38.61 2.52
2132 2329 7.628366 GCGGAATCAAGGAATTGACATTTCTTA 60.628 37.037 9.33 0.00 36.21 2.10
2133 2330 7.912250 CGGAATCAAGGAATTGACATTTCTTAG 59.088 37.037 9.33 1.78 36.21 2.18
2134 2331 8.960591 GGAATCAAGGAATTGACATTTCTTAGA 58.039 33.333 9.33 5.97 36.21 2.10
2136 2333 7.383102 TCAAGGAATTGACATTTCTTAGAGC 57.617 36.000 9.33 0.00 36.21 4.09
2137 2334 6.092670 TCAAGGAATTGACATTTCTTAGAGCG 59.907 38.462 9.33 0.00 36.21 5.03
2138 2335 5.734720 AGGAATTGACATTTCTTAGAGCGA 58.265 37.500 9.33 0.00 0.00 4.93
2139 2336 5.814705 AGGAATTGACATTTCTTAGAGCGAG 59.185 40.000 9.33 0.00 0.00 5.03
2140 2337 5.582665 GGAATTGACATTTCTTAGAGCGAGT 59.417 40.000 9.33 0.00 0.00 4.18
2141 2338 6.092807 GGAATTGACATTTCTTAGAGCGAGTT 59.907 38.462 9.33 0.00 0.00 3.01
2142 2339 5.845985 TTGACATTTCTTAGAGCGAGTTG 57.154 39.130 0.00 0.00 0.00 3.16
2143 2340 4.245660 TGACATTTCTTAGAGCGAGTTGG 58.754 43.478 0.00 0.00 0.00 3.77
2144 2341 4.246458 GACATTTCTTAGAGCGAGTTGGT 58.754 43.478 0.00 0.00 0.00 3.67
2145 2342 4.642429 ACATTTCTTAGAGCGAGTTGGTT 58.358 39.130 0.00 0.00 0.00 3.67
2146 2343 4.452455 ACATTTCTTAGAGCGAGTTGGTTG 59.548 41.667 0.00 0.00 0.00 3.77
2147 2344 2.743636 TCTTAGAGCGAGTTGGTTGG 57.256 50.000 0.00 0.00 0.00 3.77
2148 2345 1.275291 TCTTAGAGCGAGTTGGTTGGG 59.725 52.381 0.00 0.00 0.00 4.12
2149 2346 1.002087 CTTAGAGCGAGTTGGTTGGGT 59.998 52.381 0.00 0.00 0.00 4.51
2150 2347 1.053424 TAGAGCGAGTTGGTTGGGTT 58.947 50.000 0.00 0.00 0.00 4.11
2151 2348 0.250338 AGAGCGAGTTGGTTGGGTTC 60.250 55.000 0.00 0.00 0.00 3.62
2152 2349 0.534203 GAGCGAGTTGGTTGGGTTCA 60.534 55.000 0.00 0.00 0.00 3.18
2153 2350 0.110486 AGCGAGTTGGTTGGGTTCAT 59.890 50.000 0.00 0.00 0.00 2.57
2154 2351 1.349688 AGCGAGTTGGTTGGGTTCATA 59.650 47.619 0.00 0.00 0.00 2.15
2155 2352 2.026262 AGCGAGTTGGTTGGGTTCATAT 60.026 45.455 0.00 0.00 0.00 1.78
2156 2353 2.354821 GCGAGTTGGTTGGGTTCATATC 59.645 50.000 0.00 0.00 0.00 1.63
2157 2354 3.605634 CGAGTTGGTTGGGTTCATATCA 58.394 45.455 0.00 0.00 0.00 2.15
2158 2355 3.623060 CGAGTTGGTTGGGTTCATATCAG 59.377 47.826 0.00 0.00 0.00 2.90
2159 2356 4.622933 CGAGTTGGTTGGGTTCATATCAGA 60.623 45.833 0.00 0.00 0.00 3.27
2160 2357 4.848357 AGTTGGTTGGGTTCATATCAGAG 58.152 43.478 0.00 0.00 0.00 3.35
2161 2358 4.289672 AGTTGGTTGGGTTCATATCAGAGT 59.710 41.667 0.00 0.00 0.00 3.24
2162 2359 4.487714 TGGTTGGGTTCATATCAGAGTC 57.512 45.455 0.00 0.00 0.00 3.36
2163 2360 3.843619 TGGTTGGGTTCATATCAGAGTCA 59.156 43.478 0.00 0.00 0.00 3.41
2164 2361 4.288366 TGGTTGGGTTCATATCAGAGTCAA 59.712 41.667 0.00 0.00 0.00 3.18
2165 2362 5.044919 TGGTTGGGTTCATATCAGAGTCAAT 60.045 40.000 0.00 0.00 0.00 2.57
2166 2363 5.529060 GGTTGGGTTCATATCAGAGTCAATC 59.471 44.000 0.00 0.00 0.00 2.67
2167 2364 5.955961 TGGGTTCATATCAGAGTCAATCA 57.044 39.130 0.00 0.00 0.00 2.57
2168 2365 6.505048 TGGGTTCATATCAGAGTCAATCAT 57.495 37.500 0.00 0.00 0.00 2.45
2169 2366 7.616528 TGGGTTCATATCAGAGTCAATCATA 57.383 36.000 0.00 0.00 0.00 2.15
2170 2367 8.033178 TGGGTTCATATCAGAGTCAATCATAA 57.967 34.615 0.00 0.00 0.00 1.90
2171 2368 8.663167 TGGGTTCATATCAGAGTCAATCATAAT 58.337 33.333 0.00 0.00 0.00 1.28
2172 2369 8.944029 GGGTTCATATCAGAGTCAATCATAATG 58.056 37.037 0.00 0.00 0.00 1.90
2173 2370 9.716531 GGTTCATATCAGAGTCAATCATAATGA 57.283 33.333 0.00 0.00 0.00 2.57
2190 2387 8.791327 TCATAATGAGTAAATCAACAGAAGCA 57.209 30.769 0.00 0.00 42.53 3.91
2191 2388 9.230122 TCATAATGAGTAAATCAACAGAAGCAA 57.770 29.630 0.00 0.00 42.53 3.91
2192 2389 9.282247 CATAATGAGTAAATCAACAGAAGCAAC 57.718 33.333 0.00 0.00 42.53 4.17
2193 2390 5.689383 TGAGTAAATCAACAGAAGCAACC 57.311 39.130 0.00 0.00 34.02 3.77
2194 2391 5.129634 TGAGTAAATCAACAGAAGCAACCA 58.870 37.500 0.00 0.00 34.02 3.67
2195 2392 5.769662 TGAGTAAATCAACAGAAGCAACCAT 59.230 36.000 0.00 0.00 34.02 3.55
2196 2393 6.265196 TGAGTAAATCAACAGAAGCAACCATT 59.735 34.615 0.00 0.00 34.02 3.16
2197 2394 6.681777 AGTAAATCAACAGAAGCAACCATTC 58.318 36.000 0.00 0.00 0.00 2.67
2198 2395 5.796424 AAATCAACAGAAGCAACCATTCT 57.204 34.783 0.00 0.00 37.49 2.40
2199 2396 6.899393 AAATCAACAGAAGCAACCATTCTA 57.101 33.333 0.00 0.00 35.26 2.10
2200 2397 7.472334 AAATCAACAGAAGCAACCATTCTAT 57.528 32.000 0.00 0.00 35.26 1.98
2201 2398 7.472334 AATCAACAGAAGCAACCATTCTATT 57.528 32.000 0.00 0.00 35.26 1.73
2202 2399 6.899393 TCAACAGAAGCAACCATTCTATTT 57.101 33.333 0.00 0.00 35.26 1.40
2203 2400 7.994425 TCAACAGAAGCAACCATTCTATTTA 57.006 32.000 0.00 0.00 35.26 1.40
2204 2401 8.579850 TCAACAGAAGCAACCATTCTATTTAT 57.420 30.769 0.00 0.00 35.26 1.40
2205 2402 9.023962 TCAACAGAAGCAACCATTCTATTTATT 57.976 29.630 0.00 0.00 35.26 1.40
2206 2403 9.643693 CAACAGAAGCAACCATTCTATTTATTT 57.356 29.630 0.00 0.00 35.26 1.40
2228 2425 7.945033 TTTAAGAAAATGGAAATGTGTCTGC 57.055 32.000 0.00 0.00 0.00 4.26
2229 2426 5.534207 AAGAAAATGGAAATGTGTCTGCA 57.466 34.783 0.00 0.00 0.00 4.41
2230 2427 4.874970 AGAAAATGGAAATGTGTCTGCAC 58.125 39.130 0.00 0.00 45.44 4.57
2231 2428 4.586001 AGAAAATGGAAATGTGTCTGCACT 59.414 37.500 0.00 0.00 45.44 4.40
2232 2429 4.942761 AAATGGAAATGTGTCTGCACTT 57.057 36.364 0.00 0.00 45.44 3.16
2233 2430 4.510038 AATGGAAATGTGTCTGCACTTC 57.490 40.909 0.00 0.00 45.44 3.01
2234 2431 2.229792 TGGAAATGTGTCTGCACTTCC 58.770 47.619 10.12 10.12 44.07 3.46
2235 2432 1.541588 GGAAATGTGTCTGCACTTCCC 59.458 52.381 7.23 0.90 45.44 3.97
2236 2433 2.229792 GAAATGTGTCTGCACTTCCCA 58.770 47.619 0.00 0.00 45.44 4.37
2237 2434 1.609208 AATGTGTCTGCACTTCCCAC 58.391 50.000 0.00 0.00 45.44 4.61
2238 2435 0.473755 ATGTGTCTGCACTTCCCACA 59.526 50.000 0.00 0.00 45.44 4.17
2239 2436 0.254462 TGTGTCTGCACTTCCCACAA 59.746 50.000 0.00 0.00 45.44 3.33
2240 2437 0.663153 GTGTCTGCACTTCCCACAAC 59.337 55.000 0.00 0.00 42.13 3.32
2241 2438 0.465460 TGTCTGCACTTCCCACAACC 60.465 55.000 0.00 0.00 0.00 3.77
2242 2439 0.465460 GTCTGCACTTCCCACAACCA 60.465 55.000 0.00 0.00 0.00 3.67
2243 2440 0.257328 TCTGCACTTCCCACAACCAA 59.743 50.000 0.00 0.00 0.00 3.67
2244 2441 1.110442 CTGCACTTCCCACAACCAAA 58.890 50.000 0.00 0.00 0.00 3.28
2245 2442 1.480137 CTGCACTTCCCACAACCAAAA 59.520 47.619 0.00 0.00 0.00 2.44
2246 2443 2.102925 CTGCACTTCCCACAACCAAAAT 59.897 45.455 0.00 0.00 0.00 1.82
2247 2444 3.300388 TGCACTTCCCACAACCAAAATA 58.700 40.909 0.00 0.00 0.00 1.40
2248 2445 3.320541 TGCACTTCCCACAACCAAAATAG 59.679 43.478 0.00 0.00 0.00 1.73
2249 2446 3.306019 GCACTTCCCACAACCAAAATAGG 60.306 47.826 0.00 0.00 0.00 2.57
2250 2447 4.148838 CACTTCCCACAACCAAAATAGGA 58.851 43.478 0.00 0.00 0.00 2.94
2251 2448 4.022329 CACTTCCCACAACCAAAATAGGAC 60.022 45.833 0.00 0.00 0.00 3.85
2252 2449 3.163616 TCCCACAACCAAAATAGGACC 57.836 47.619 0.00 0.00 0.00 4.46
2253 2450 2.447429 TCCCACAACCAAAATAGGACCA 59.553 45.455 0.00 0.00 0.00 4.02
2254 2451 3.076785 TCCCACAACCAAAATAGGACCAT 59.923 43.478 0.00 0.00 0.00 3.55
2255 2452 4.292571 TCCCACAACCAAAATAGGACCATA 59.707 41.667 0.00 0.00 0.00 2.74
2256 2453 5.043732 TCCCACAACCAAAATAGGACCATAT 60.044 40.000 0.00 0.00 0.00 1.78
2257 2454 5.301805 CCCACAACCAAAATAGGACCATATC 59.698 44.000 0.00 0.00 0.00 1.63
2258 2455 6.129179 CCACAACCAAAATAGGACCATATCT 58.871 40.000 0.00 0.00 0.00 1.98
2259 2456 6.263168 CCACAACCAAAATAGGACCATATCTC 59.737 42.308 0.00 0.00 0.00 2.75
2260 2457 6.828273 CACAACCAAAATAGGACCATATCTCA 59.172 38.462 0.00 0.00 0.00 3.27
2261 2458 6.828785 ACAACCAAAATAGGACCATATCTCAC 59.171 38.462 0.00 0.00 0.00 3.51
2262 2459 6.575244 ACCAAAATAGGACCATATCTCACA 57.425 37.500 0.00 0.00 0.00 3.58
2263 2460 7.154191 ACCAAAATAGGACCATATCTCACAT 57.846 36.000 0.00 0.00 0.00 3.21
2264 2461 8.275187 ACCAAAATAGGACCATATCTCACATA 57.725 34.615 0.00 0.00 0.00 2.29
2265 2462 8.723365 ACCAAAATAGGACCATATCTCACATAA 58.277 33.333 0.00 0.00 0.00 1.90
2266 2463 9.745018 CCAAAATAGGACCATATCTCACATAAT 57.255 33.333 0.00 0.00 0.00 1.28
2273 2470 9.997172 AGGACCATATCTCACATAATAGATACA 57.003 33.333 0.00 0.00 37.49 2.29
2296 2493 7.250569 ACACATAGAAAATGGAATACTTTGCG 58.749 34.615 0.00 0.00 0.00 4.85
2297 2494 7.120579 ACACATAGAAAATGGAATACTTTGCGA 59.879 33.333 0.00 0.00 0.00 5.10
2298 2495 7.641411 CACATAGAAAATGGAATACTTTGCGAG 59.359 37.037 0.00 0.00 0.00 5.03
2299 2496 7.552687 ACATAGAAAATGGAATACTTTGCGAGA 59.447 33.333 0.00 0.00 0.00 4.04
2300 2497 8.562892 CATAGAAAATGGAATACTTTGCGAGAT 58.437 33.333 0.00 0.00 0.00 2.75
2301 2498 6.789262 AGAAAATGGAATACTTTGCGAGATG 58.211 36.000 0.00 0.00 0.00 2.90
2302 2499 6.375455 AGAAAATGGAATACTTTGCGAGATGT 59.625 34.615 0.00 0.00 0.00 3.06
2303 2500 6.515272 AAATGGAATACTTTGCGAGATGTT 57.485 33.333 0.00 0.00 0.00 2.71
2304 2501 4.944962 TGGAATACTTTGCGAGATGTTG 57.055 40.909 0.00 0.00 0.00 3.33
2305 2502 4.323417 TGGAATACTTTGCGAGATGTTGT 58.677 39.130 0.00 0.00 0.00 3.32
2306 2503 4.154015 TGGAATACTTTGCGAGATGTTGTG 59.846 41.667 0.00 0.00 0.00 3.33
2307 2504 4.154195 GGAATACTTTGCGAGATGTTGTGT 59.846 41.667 0.00 0.00 0.00 3.72
2308 2505 5.350365 GGAATACTTTGCGAGATGTTGTGTA 59.650 40.000 0.00 0.00 0.00 2.90
2309 2506 6.408858 AATACTTTGCGAGATGTTGTGTAG 57.591 37.500 0.00 0.00 0.00 2.74
2310 2507 3.728845 ACTTTGCGAGATGTTGTGTAGT 58.271 40.909 0.00 0.00 0.00 2.73
2311 2508 4.127171 ACTTTGCGAGATGTTGTGTAGTT 58.873 39.130 0.00 0.00 0.00 2.24
2312 2509 4.574828 ACTTTGCGAGATGTTGTGTAGTTT 59.425 37.500 0.00 0.00 0.00 2.66
2313 2510 4.466567 TTGCGAGATGTTGTGTAGTTTG 57.533 40.909 0.00 0.00 0.00 2.93
2314 2511 3.462982 TGCGAGATGTTGTGTAGTTTGT 58.537 40.909 0.00 0.00 0.00 2.83
2315 2512 3.874543 TGCGAGATGTTGTGTAGTTTGTT 59.125 39.130 0.00 0.00 0.00 2.83
2316 2513 4.025229 TGCGAGATGTTGTGTAGTTTGTTC 60.025 41.667 0.00 0.00 0.00 3.18
2317 2514 4.025229 GCGAGATGTTGTGTAGTTTGTTCA 60.025 41.667 0.00 0.00 0.00 3.18
2318 2515 5.503357 GCGAGATGTTGTGTAGTTTGTTCAA 60.503 40.000 0.00 0.00 0.00 2.69
2319 2516 6.658831 CGAGATGTTGTGTAGTTTGTTCAAT 58.341 36.000 0.00 0.00 0.00 2.57
2320 2517 7.570507 GCGAGATGTTGTGTAGTTTGTTCAATA 60.571 37.037 0.00 0.00 0.00 1.90
2321 2518 8.443160 CGAGATGTTGTGTAGTTTGTTCAATAT 58.557 33.333 0.00 0.00 0.00 1.28
2322 2519 9.546909 GAGATGTTGTGTAGTTTGTTCAATATG 57.453 33.333 0.00 0.00 0.00 1.78
2323 2520 8.023128 AGATGTTGTGTAGTTTGTTCAATATGC 58.977 33.333 0.00 0.00 0.00 3.14
2324 2521 7.032377 TGTTGTGTAGTTTGTTCAATATGCA 57.968 32.000 0.00 0.00 0.00 3.96
2325 2522 7.656412 TGTTGTGTAGTTTGTTCAATATGCAT 58.344 30.769 3.79 3.79 0.00 3.96
2326 2523 7.594386 TGTTGTGTAGTTTGTTCAATATGCATG 59.406 33.333 10.16 0.00 0.00 4.06
2327 2524 6.092092 TGTGTAGTTTGTTCAATATGCATGC 58.908 36.000 11.82 11.82 0.00 4.06
2328 2525 6.092092 GTGTAGTTTGTTCAATATGCATGCA 58.908 36.000 25.04 25.04 0.00 3.96
2329 2526 6.585702 GTGTAGTTTGTTCAATATGCATGCAA 59.414 34.615 26.68 14.46 0.00 4.08
2330 2527 7.276218 GTGTAGTTTGTTCAATATGCATGCAAT 59.724 33.333 26.68 16.11 0.00 3.56
2331 2528 7.818446 TGTAGTTTGTTCAATATGCATGCAATT 59.182 29.630 26.68 20.69 0.00 2.32
2332 2529 7.067532 AGTTTGTTCAATATGCATGCAATTG 57.932 32.000 29.78 29.78 32.96 2.32
2333 2530 6.651643 AGTTTGTTCAATATGCATGCAATTGT 59.348 30.769 31.65 20.00 33.35 2.71
2334 2531 6.410243 TTGTTCAATATGCATGCAATTGTG 57.590 33.333 31.65 24.45 33.35 3.33
2335 2532 4.870991 TGTTCAATATGCATGCAATTGTGG 59.129 37.500 31.65 20.07 33.35 4.17
2336 2533 4.061357 TCAATATGCATGCAATTGTGGG 57.939 40.909 31.65 18.96 33.35 4.61
2337 2534 3.135225 CAATATGCATGCAATTGTGGGG 58.865 45.455 28.56 15.22 0.00 4.96
2338 2535 2.156102 TATGCATGCAATTGTGGGGA 57.844 45.000 26.68 0.00 0.00 4.81
2339 2536 1.277579 ATGCATGCAATTGTGGGGAA 58.722 45.000 26.68 0.00 0.00 3.97
2340 2537 1.054231 TGCATGCAATTGTGGGGAAA 58.946 45.000 20.30 0.00 0.00 3.13
2341 2538 1.419012 TGCATGCAATTGTGGGGAAAA 59.581 42.857 20.30 0.00 0.00 2.29
2342 2539 2.158711 TGCATGCAATTGTGGGGAAAAA 60.159 40.909 20.30 0.00 0.00 1.94
2363 2560 6.680148 AAAAACATAGTTGGTGCCCTATTT 57.320 33.333 0.00 0.00 0.00 1.40
2364 2561 6.680148 AAAACATAGTTGGTGCCCTATTTT 57.320 33.333 0.00 0.00 0.00 1.82
2365 2562 7.784470 AAAACATAGTTGGTGCCCTATTTTA 57.216 32.000 0.00 0.00 0.00 1.52
2366 2563 6.769134 AACATAGTTGGTGCCCTATTTTAC 57.231 37.500 0.00 0.00 0.00 2.01
2367 2564 5.822204 ACATAGTTGGTGCCCTATTTTACA 58.178 37.500 0.00 0.00 0.00 2.41
2368 2565 6.431722 ACATAGTTGGTGCCCTATTTTACAT 58.568 36.000 0.00 0.00 0.00 2.29
2369 2566 6.546034 ACATAGTTGGTGCCCTATTTTACATC 59.454 38.462 0.00 0.00 0.00 3.06
2370 2567 4.929479 AGTTGGTGCCCTATTTTACATCA 58.071 39.130 0.00 0.00 0.00 3.07
2371 2568 5.518865 AGTTGGTGCCCTATTTTACATCAT 58.481 37.500 0.00 0.00 0.00 2.45
2372 2569 5.594317 AGTTGGTGCCCTATTTTACATCATC 59.406 40.000 0.00 0.00 0.00 2.92
2373 2570 5.387113 TGGTGCCCTATTTTACATCATCT 57.613 39.130 0.00 0.00 0.00 2.90
2374 2571 5.132502 TGGTGCCCTATTTTACATCATCTG 58.867 41.667 0.00 0.00 0.00 2.90
2375 2572 4.022849 GGTGCCCTATTTTACATCATCTGC 60.023 45.833 0.00 0.00 0.00 4.26
2376 2573 4.823989 GTGCCCTATTTTACATCATCTGCT 59.176 41.667 0.00 0.00 0.00 4.24
2377 2574 5.997746 GTGCCCTATTTTACATCATCTGCTA 59.002 40.000 0.00 0.00 0.00 3.49
2378 2575 6.656693 GTGCCCTATTTTACATCATCTGCTAT 59.343 38.462 0.00 0.00 0.00 2.97
2379 2576 6.656270 TGCCCTATTTTACATCATCTGCTATG 59.344 38.462 0.00 0.00 0.00 2.23
2380 2577 6.881065 GCCCTATTTTACATCATCTGCTATGA 59.119 38.462 5.03 5.03 0.00 2.15
2381 2578 7.555554 GCCCTATTTTACATCATCTGCTATGAT 59.444 37.037 8.72 8.72 39.16 2.45
2382 2579 9.458727 CCCTATTTTACATCATCTGCTATGATT 57.541 33.333 11.11 7.17 36.69 2.57
2386 2583 9.788889 ATTTTACATCATCTGCTATGATTCTGA 57.211 29.630 11.11 0.00 36.69 3.27
2387 2584 9.788889 TTTTACATCATCTGCTATGATTCTGAT 57.211 29.630 11.11 0.14 36.69 2.90
2388 2585 8.773404 TTACATCATCTGCTATGATTCTGATG 57.227 34.615 11.11 11.40 36.69 3.07
2389 2586 5.644206 ACATCATCTGCTATGATTCTGATGC 59.356 40.000 11.11 0.00 36.69 3.91
2390 2587 4.576879 TCATCTGCTATGATTCTGATGCC 58.423 43.478 0.00 0.00 38.05 4.40
2391 2588 3.413846 TCTGCTATGATTCTGATGCCC 57.586 47.619 0.00 0.00 0.00 5.36
2392 2589 2.977580 TCTGCTATGATTCTGATGCCCT 59.022 45.455 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 1.003223 AGGAACAACGCGTGCTTTAAC 60.003 47.619 14.98 0.00 0.00 2.01
181 182 3.372892 GCTCCCTGTTAGTAGTAGAGGGT 60.373 52.174 17.56 0.00 43.56 4.34
261 262 6.283544 TGTTTGGCATGTGATCAAATGTAT 57.716 33.333 23.83 0.65 33.72 2.29
469 470 3.548818 GCAAGATCGGCCATGATGTAAAC 60.549 47.826 2.24 0.00 0.00 2.01
667 669 3.728600 ACATCGCGTAAACGAAAATGTC 58.271 40.909 5.77 0.00 46.59 3.06
717 881 8.537016 ACTGCAAACTATCCAAGTATAGTGTTA 58.463 33.333 0.00 0.00 40.91 2.41
726 890 9.632638 AATAATGATACTGCAAACTATCCAAGT 57.367 29.630 0.00 0.00 41.49 3.16
745 909 9.836864 AAGTGAGAGCATACATACAAATAATGA 57.163 29.630 0.00 0.00 0.00 2.57
882 1052 4.324022 TCGGAAGAAAAGGATAACCCTTCC 60.324 45.833 12.18 12.18 44.89 3.46
953 1123 6.471146 AGGGATTTACATGTGAGATATGCTC 58.529 40.000 9.11 0.00 44.21 4.26
974 1144 1.905637 AACCGCCTAACAAGAAAGGG 58.094 50.000 0.00 0.00 33.17 3.95
984 1154 3.805807 GCTCCATGCTTATAACCGCCTAA 60.806 47.826 0.00 0.00 38.95 2.69
1167 1337 2.416893 CGAGAGACAGTCAACGAGATCA 59.583 50.000 2.66 0.00 31.70 2.92
1405 1575 2.060980 CGCTTCTGTAGGCTCCCCT 61.061 63.158 0.00 0.00 45.61 4.79
1427 1597 0.801836 ACAGCGCACAAAAGCACAAC 60.802 50.000 11.47 0.00 35.48 3.32
1566 1738 3.706086 AGCAAAAGAACCACCAGAACATT 59.294 39.130 0.00 0.00 0.00 2.71
1697 1876 9.054922 CCTGACCACATTTGAACAAAAATTAAT 57.945 29.630 4.12 0.00 33.56 1.40
1705 1884 4.039004 CCATTCCTGACCACATTTGAACAA 59.961 41.667 0.00 0.00 0.00 2.83
1706 1885 3.573538 CCATTCCTGACCACATTTGAACA 59.426 43.478 0.00 0.00 0.00 3.18
1722 1901 0.613777 CCCGAGGCTATACCCATTCC 59.386 60.000 0.00 0.00 40.58 3.01
1788 1972 9.485591 CGTAAAACACTCGCAAATAATAAATCT 57.514 29.630 0.00 0.00 0.00 2.40
1791 1975 7.059716 GCACGTAAAACACTCGCAAATAATAAA 59.940 33.333 0.00 0.00 0.00 1.40
1793 1977 6.016718 GCACGTAAAACACTCGCAAATAATA 58.983 36.000 0.00 0.00 0.00 0.98
1794 1978 4.849383 GCACGTAAAACACTCGCAAATAAT 59.151 37.500 0.00 0.00 0.00 1.28
1812 1996 4.471904 TTCTAATCCAGAATCTGCACGT 57.528 40.909 4.40 0.00 38.39 4.49
1813 1997 5.525012 TCATTTCTAATCCAGAATCTGCACG 59.475 40.000 4.40 0.00 42.88 5.34
1815 1999 5.525012 CGTCATTTCTAATCCAGAATCTGCA 59.475 40.000 4.40 0.00 42.88 4.41
1816 2000 5.049818 CCGTCATTTCTAATCCAGAATCTGC 60.050 44.000 4.40 0.00 42.88 4.26
1817 2001 6.283694 TCCGTCATTTCTAATCCAGAATCTG 58.716 40.000 2.68 2.68 42.88 2.90
1818 2002 6.325028 TCTCCGTCATTTCTAATCCAGAATCT 59.675 38.462 0.00 0.00 42.88 2.40
1819 2003 6.422400 GTCTCCGTCATTTCTAATCCAGAATC 59.578 42.308 0.00 0.00 42.88 2.52
1821 2005 5.186992 TGTCTCCGTCATTTCTAATCCAGAA 59.813 40.000 0.00 0.00 41.66 3.02
1822 2006 4.709886 TGTCTCCGTCATTTCTAATCCAGA 59.290 41.667 0.00 0.00 0.00 3.86
1834 2021 0.904649 TGGCATCTTGTCTCCGTCAT 59.095 50.000 0.00 0.00 0.00 3.06
1870 2057 1.453928 GGTTACCATCCAGGGCAGC 60.454 63.158 0.00 0.00 43.89 5.25
1887 2074 2.821546 CATTGCTGCAGATGGATTTGG 58.178 47.619 20.43 0.00 0.00 3.28
1934 2128 5.350633 CAGAACAATTGCTTGAAGAACCAA 58.649 37.500 5.05 0.00 36.20 3.67
1971 2165 1.688197 ACAGTGCAAAGGACAAATGGG 59.312 47.619 0.00 0.00 0.00 4.00
1976 2170 2.997980 TCTTGACAGTGCAAAGGACAA 58.002 42.857 0.00 0.00 0.00 3.18
2007 2201 8.394877 CAACAAGAGAGTATACTACAGACAGAG 58.605 40.741 5.09 0.00 0.00 3.35
2012 2206 7.889073 ACTTCCAACAAGAGAGTATACTACAGA 59.111 37.037 5.09 0.00 0.00 3.41
2020 2214 8.423906 TCTTCTAACTTCCAACAAGAGAGTAT 57.576 34.615 0.00 0.00 0.00 2.12
2026 2220 8.246430 TCTAACTCTTCTAACTTCCAACAAGA 57.754 34.615 0.00 0.00 0.00 3.02
2059 2256 7.342026 ACCAAGTGTCCTAGAACAATTTTCTTT 59.658 33.333 0.00 0.00 35.45 2.52
2088 2285 9.698309 TGATTCCGCAATAGAACAATTTAAAAA 57.302 25.926 0.00 0.00 0.00 1.94
2089 2286 9.698309 TTGATTCCGCAATAGAACAATTTAAAA 57.302 25.926 0.00 0.00 0.00 1.52
2090 2287 9.352784 CTTGATTCCGCAATAGAACAATTTAAA 57.647 29.630 0.00 0.00 0.00 1.52
2091 2288 7.973388 CCTTGATTCCGCAATAGAACAATTTAA 59.027 33.333 0.00 0.00 0.00 1.52
2092 2289 7.338196 TCCTTGATTCCGCAATAGAACAATTTA 59.662 33.333 0.00 0.00 0.00 1.40
2093 2290 6.152661 TCCTTGATTCCGCAATAGAACAATTT 59.847 34.615 0.00 0.00 0.00 1.82
2094 2291 5.652014 TCCTTGATTCCGCAATAGAACAATT 59.348 36.000 0.00 0.00 0.00 2.32
2095 2292 5.192927 TCCTTGATTCCGCAATAGAACAAT 58.807 37.500 0.00 0.00 0.00 2.71
2096 2293 4.584874 TCCTTGATTCCGCAATAGAACAA 58.415 39.130 0.00 0.00 0.00 2.83
2097 2294 4.214986 TCCTTGATTCCGCAATAGAACA 57.785 40.909 0.00 0.00 0.00 3.18
2098 2295 5.757850 ATTCCTTGATTCCGCAATAGAAC 57.242 39.130 0.00 0.00 0.00 3.01
2099 2296 5.885352 TCAATTCCTTGATTCCGCAATAGAA 59.115 36.000 0.00 0.00 36.46 2.10
2100 2297 5.296780 GTCAATTCCTTGATTCCGCAATAGA 59.703 40.000 0.00 0.00 43.08 1.98
2101 2298 5.066375 TGTCAATTCCTTGATTCCGCAATAG 59.934 40.000 0.00 0.00 43.08 1.73
2102 2299 4.946772 TGTCAATTCCTTGATTCCGCAATA 59.053 37.500 0.00 0.00 43.08 1.90
2103 2300 3.763360 TGTCAATTCCTTGATTCCGCAAT 59.237 39.130 0.00 0.00 43.08 3.56
2104 2301 3.153130 TGTCAATTCCTTGATTCCGCAA 58.847 40.909 0.00 0.00 43.08 4.85
2105 2302 2.789213 TGTCAATTCCTTGATTCCGCA 58.211 42.857 0.00 0.00 43.08 5.69
2106 2303 4.376340 AATGTCAATTCCTTGATTCCGC 57.624 40.909 0.00 0.00 43.08 5.54
2107 2304 6.199937 AGAAATGTCAATTCCTTGATTCCG 57.800 37.500 0.00 0.00 43.08 4.30
2108 2305 8.960591 TCTAAGAAATGTCAATTCCTTGATTCC 58.039 33.333 0.00 0.00 43.08 3.01
2110 2307 8.465201 GCTCTAAGAAATGTCAATTCCTTGATT 58.535 33.333 0.00 0.00 43.08 2.57
2111 2308 7.201679 CGCTCTAAGAAATGTCAATTCCTTGAT 60.202 37.037 0.00 0.00 43.08 2.57
2112 2309 6.092670 CGCTCTAAGAAATGTCAATTCCTTGA 59.907 38.462 0.00 0.00 39.07 3.02
2113 2310 6.092670 TCGCTCTAAGAAATGTCAATTCCTTG 59.907 38.462 0.00 0.00 0.00 3.61
2114 2311 6.173339 TCGCTCTAAGAAATGTCAATTCCTT 58.827 36.000 0.00 0.00 0.00 3.36
2115 2312 5.734720 TCGCTCTAAGAAATGTCAATTCCT 58.265 37.500 0.00 0.00 0.00 3.36
2116 2313 5.582665 ACTCGCTCTAAGAAATGTCAATTCC 59.417 40.000 0.00 0.00 0.00 3.01
2117 2314 6.654793 ACTCGCTCTAAGAAATGTCAATTC 57.345 37.500 0.00 0.00 0.00 2.17
2118 2315 6.128172 CCAACTCGCTCTAAGAAATGTCAATT 60.128 38.462 0.00 0.00 0.00 2.32
2119 2316 5.352569 CCAACTCGCTCTAAGAAATGTCAAT 59.647 40.000 0.00 0.00 0.00 2.57
2120 2317 4.690748 CCAACTCGCTCTAAGAAATGTCAA 59.309 41.667 0.00 0.00 0.00 3.18
2121 2318 4.245660 CCAACTCGCTCTAAGAAATGTCA 58.754 43.478 0.00 0.00 0.00 3.58
2122 2319 4.246458 ACCAACTCGCTCTAAGAAATGTC 58.754 43.478 0.00 0.00 0.00 3.06
2123 2320 4.273148 ACCAACTCGCTCTAAGAAATGT 57.727 40.909 0.00 0.00 0.00 2.71
2124 2321 4.142816 CCAACCAACTCGCTCTAAGAAATG 60.143 45.833 0.00 0.00 0.00 2.32
2125 2322 4.003648 CCAACCAACTCGCTCTAAGAAAT 58.996 43.478 0.00 0.00 0.00 2.17
2126 2323 3.399330 CCAACCAACTCGCTCTAAGAAA 58.601 45.455 0.00 0.00 0.00 2.52
2127 2324 2.289444 CCCAACCAACTCGCTCTAAGAA 60.289 50.000 0.00 0.00 0.00 2.52
2128 2325 1.275291 CCCAACCAACTCGCTCTAAGA 59.725 52.381 0.00 0.00 0.00 2.10
2129 2326 1.002087 ACCCAACCAACTCGCTCTAAG 59.998 52.381 0.00 0.00 0.00 2.18
2130 2327 1.053424 ACCCAACCAACTCGCTCTAA 58.947 50.000 0.00 0.00 0.00 2.10
2131 2328 1.001633 GAACCCAACCAACTCGCTCTA 59.998 52.381 0.00 0.00 0.00 2.43
2132 2329 0.250338 GAACCCAACCAACTCGCTCT 60.250 55.000 0.00 0.00 0.00 4.09
2133 2330 0.534203 TGAACCCAACCAACTCGCTC 60.534 55.000 0.00 0.00 0.00 5.03
2134 2331 0.110486 ATGAACCCAACCAACTCGCT 59.890 50.000 0.00 0.00 0.00 4.93
2135 2332 1.816074 TATGAACCCAACCAACTCGC 58.184 50.000 0.00 0.00 0.00 5.03
2136 2333 3.605634 TGATATGAACCCAACCAACTCG 58.394 45.455 0.00 0.00 0.00 4.18
2137 2334 4.843728 TCTGATATGAACCCAACCAACTC 58.156 43.478 0.00 0.00 0.00 3.01
2138 2335 4.289672 ACTCTGATATGAACCCAACCAACT 59.710 41.667 0.00 0.00 0.00 3.16
2139 2336 4.589908 ACTCTGATATGAACCCAACCAAC 58.410 43.478 0.00 0.00 0.00 3.77
2140 2337 4.288366 TGACTCTGATATGAACCCAACCAA 59.712 41.667 0.00 0.00 0.00 3.67
2141 2338 3.843619 TGACTCTGATATGAACCCAACCA 59.156 43.478 0.00 0.00 0.00 3.67
2142 2339 4.487714 TGACTCTGATATGAACCCAACC 57.512 45.455 0.00 0.00 0.00 3.77
2143 2340 6.115446 TGATTGACTCTGATATGAACCCAAC 58.885 40.000 0.00 0.00 0.00 3.77
2144 2341 6.312141 TGATTGACTCTGATATGAACCCAA 57.688 37.500 0.00 0.00 0.00 4.12
2145 2342 5.955961 TGATTGACTCTGATATGAACCCA 57.044 39.130 0.00 0.00 0.00 4.51
2146 2343 8.944029 CATTATGATTGACTCTGATATGAACCC 58.056 37.037 0.00 0.00 0.00 4.11
2147 2344 9.716531 TCATTATGATTGACTCTGATATGAACC 57.283 33.333 0.00 0.00 0.00 3.62
2164 2361 9.399797 TGCTTCTGTTGATTTACTCATTATGAT 57.600 29.630 0.00 0.00 32.72 2.45
2165 2362 8.791327 TGCTTCTGTTGATTTACTCATTATGA 57.209 30.769 0.00 0.00 32.72 2.15
2166 2363 9.282247 GTTGCTTCTGTTGATTTACTCATTATG 57.718 33.333 0.00 0.00 32.72 1.90
2167 2364 8.462016 GGTTGCTTCTGTTGATTTACTCATTAT 58.538 33.333 0.00 0.00 32.72 1.28
2168 2365 7.446931 TGGTTGCTTCTGTTGATTTACTCATTA 59.553 33.333 0.00 0.00 32.72 1.90
2169 2366 6.265196 TGGTTGCTTCTGTTGATTTACTCATT 59.735 34.615 0.00 0.00 32.72 2.57
2170 2367 5.769662 TGGTTGCTTCTGTTGATTTACTCAT 59.230 36.000 0.00 0.00 32.72 2.90
2171 2368 5.129634 TGGTTGCTTCTGTTGATTTACTCA 58.870 37.500 0.00 0.00 0.00 3.41
2172 2369 5.689383 TGGTTGCTTCTGTTGATTTACTC 57.311 39.130 0.00 0.00 0.00 2.59
2173 2370 6.491403 AGAATGGTTGCTTCTGTTGATTTACT 59.509 34.615 0.00 0.00 31.84 2.24
2174 2371 6.681777 AGAATGGTTGCTTCTGTTGATTTAC 58.318 36.000 0.00 0.00 31.84 2.01
2175 2372 6.899393 AGAATGGTTGCTTCTGTTGATTTA 57.101 33.333 0.00 0.00 31.84 1.40
2176 2373 5.796424 AGAATGGTTGCTTCTGTTGATTT 57.204 34.783 0.00 0.00 31.84 2.17
2177 2374 7.472334 AATAGAATGGTTGCTTCTGTTGATT 57.528 32.000 0.00 0.00 34.17 2.57
2178 2375 7.472334 AAATAGAATGGTTGCTTCTGTTGAT 57.528 32.000 0.00 0.00 35.20 2.57
2179 2376 6.899393 AAATAGAATGGTTGCTTCTGTTGA 57.101 33.333 0.00 0.00 35.20 3.18
2180 2377 9.643693 AAATAAATAGAATGGTTGCTTCTGTTG 57.356 29.630 0.00 0.00 35.20 3.33
2202 2399 9.638239 GCAGACACATTTCCATTTTCTTAAATA 57.362 29.630 0.00 0.00 32.75 1.40
2203 2400 8.149647 TGCAGACACATTTCCATTTTCTTAAAT 58.850 29.630 0.00 0.00 34.29 1.40
2204 2401 7.437862 GTGCAGACACATTTCCATTTTCTTAAA 59.562 33.333 0.00 0.00 46.61 1.52
2205 2402 6.922957 GTGCAGACACATTTCCATTTTCTTAA 59.077 34.615 0.00 0.00 46.61 1.85
2206 2403 6.446318 GTGCAGACACATTTCCATTTTCTTA 58.554 36.000 0.00 0.00 46.61 2.10
2207 2404 5.291971 GTGCAGACACATTTCCATTTTCTT 58.708 37.500 0.00 0.00 46.61 2.52
2208 2405 4.874970 GTGCAGACACATTTCCATTTTCT 58.125 39.130 0.00 0.00 46.61 2.52
2222 2419 0.465460 GGTTGTGGGAAGTGCAGACA 60.465 55.000 0.00 0.00 0.00 3.41
2223 2420 0.465460 TGGTTGTGGGAAGTGCAGAC 60.465 55.000 0.00 0.00 0.00 3.51
2224 2421 0.257328 TTGGTTGTGGGAAGTGCAGA 59.743 50.000 0.00 0.00 0.00 4.26
2225 2422 1.110442 TTTGGTTGTGGGAAGTGCAG 58.890 50.000 0.00 0.00 0.00 4.41
2226 2423 1.561643 TTTTGGTTGTGGGAAGTGCA 58.438 45.000 0.00 0.00 0.00 4.57
2227 2424 2.908688 ATTTTGGTTGTGGGAAGTGC 57.091 45.000 0.00 0.00 0.00 4.40
2228 2425 4.022329 GTCCTATTTTGGTTGTGGGAAGTG 60.022 45.833 0.00 0.00 0.00 3.16
2229 2426 4.149598 GTCCTATTTTGGTTGTGGGAAGT 58.850 43.478 0.00 0.00 0.00 3.01
2230 2427 3.509967 GGTCCTATTTTGGTTGTGGGAAG 59.490 47.826 0.00 0.00 0.00 3.46
2231 2428 3.117093 TGGTCCTATTTTGGTTGTGGGAA 60.117 43.478 0.00 0.00 0.00 3.97
2232 2429 2.447429 TGGTCCTATTTTGGTTGTGGGA 59.553 45.455 0.00 0.00 0.00 4.37
2233 2430 2.883026 TGGTCCTATTTTGGTTGTGGG 58.117 47.619 0.00 0.00 0.00 4.61
2234 2431 6.129179 AGATATGGTCCTATTTTGGTTGTGG 58.871 40.000 0.00 0.00 0.00 4.17
2235 2432 6.828273 TGAGATATGGTCCTATTTTGGTTGTG 59.172 38.462 0.00 0.00 0.00 3.33
2236 2433 6.828785 GTGAGATATGGTCCTATTTTGGTTGT 59.171 38.462 0.00 0.00 0.00 3.32
2237 2434 6.828273 TGTGAGATATGGTCCTATTTTGGTTG 59.172 38.462 0.00 0.00 0.00 3.77
2238 2435 6.969043 TGTGAGATATGGTCCTATTTTGGTT 58.031 36.000 0.00 0.00 0.00 3.67
2239 2436 6.575244 TGTGAGATATGGTCCTATTTTGGT 57.425 37.500 0.00 0.00 0.00 3.67
2240 2437 9.745018 ATTATGTGAGATATGGTCCTATTTTGG 57.255 33.333 0.00 0.00 0.00 3.28
2247 2444 9.997172 TGTATCTATTATGTGAGATATGGTCCT 57.003 33.333 0.00 0.00 37.10 3.85
2270 2467 8.394877 CGCAAAGTATTCCATTTTCTATGTGTA 58.605 33.333 0.00 0.00 0.00 2.90
2271 2468 7.120579 TCGCAAAGTATTCCATTTTCTATGTGT 59.879 33.333 0.00 0.00 0.00 3.72
2272 2469 7.471721 TCGCAAAGTATTCCATTTTCTATGTG 58.528 34.615 0.00 0.00 0.00 3.21
2273 2470 7.552687 TCTCGCAAAGTATTCCATTTTCTATGT 59.447 33.333 0.00 0.00 0.00 2.29
2274 2471 7.919690 TCTCGCAAAGTATTCCATTTTCTATG 58.080 34.615 0.00 0.00 0.00 2.23
2275 2472 8.562892 CATCTCGCAAAGTATTCCATTTTCTAT 58.437 33.333 0.00 0.00 0.00 1.98
2276 2473 7.552687 ACATCTCGCAAAGTATTCCATTTTCTA 59.447 33.333 0.00 0.00 0.00 2.10
2277 2474 6.375455 ACATCTCGCAAAGTATTCCATTTTCT 59.625 34.615 0.00 0.00 0.00 2.52
2278 2475 6.555315 ACATCTCGCAAAGTATTCCATTTTC 58.445 36.000 0.00 0.00 0.00 2.29
2279 2476 6.515272 ACATCTCGCAAAGTATTCCATTTT 57.485 33.333 0.00 0.00 0.00 1.82
2280 2477 6.071952 ACAACATCTCGCAAAGTATTCCATTT 60.072 34.615 0.00 0.00 0.00 2.32
2281 2478 5.415701 ACAACATCTCGCAAAGTATTCCATT 59.584 36.000 0.00 0.00 0.00 3.16
2282 2479 4.943705 ACAACATCTCGCAAAGTATTCCAT 59.056 37.500 0.00 0.00 0.00 3.41
2283 2480 4.154015 CACAACATCTCGCAAAGTATTCCA 59.846 41.667 0.00 0.00 0.00 3.53
2284 2481 4.154195 ACACAACATCTCGCAAAGTATTCC 59.846 41.667 0.00 0.00 0.00 3.01
2285 2482 5.283060 ACACAACATCTCGCAAAGTATTC 57.717 39.130 0.00 0.00 0.00 1.75
2286 2483 5.932303 ACTACACAACATCTCGCAAAGTATT 59.068 36.000 0.00 0.00 0.00 1.89
2287 2484 5.479306 ACTACACAACATCTCGCAAAGTAT 58.521 37.500 0.00 0.00 0.00 2.12
2288 2485 4.878439 ACTACACAACATCTCGCAAAGTA 58.122 39.130 0.00 0.00 0.00 2.24
2289 2486 3.728845 ACTACACAACATCTCGCAAAGT 58.271 40.909 0.00 0.00 0.00 2.66
2290 2487 4.732285 AACTACACAACATCTCGCAAAG 57.268 40.909 0.00 0.00 0.00 2.77
2291 2488 4.334203 ACAAACTACACAACATCTCGCAAA 59.666 37.500 0.00 0.00 0.00 3.68
2292 2489 3.874543 ACAAACTACACAACATCTCGCAA 59.125 39.130 0.00 0.00 0.00 4.85
2293 2490 3.462982 ACAAACTACACAACATCTCGCA 58.537 40.909 0.00 0.00 0.00 5.10
2294 2491 4.025229 TGAACAAACTACACAACATCTCGC 60.025 41.667 0.00 0.00 0.00 5.03
2295 2492 5.651172 TGAACAAACTACACAACATCTCG 57.349 39.130 0.00 0.00 0.00 4.04
2296 2493 9.546909 CATATTGAACAAACTACACAACATCTC 57.453 33.333 0.00 0.00 0.00 2.75
2297 2494 8.023128 GCATATTGAACAAACTACACAACATCT 58.977 33.333 0.00 0.00 0.00 2.90
2298 2495 7.807433 TGCATATTGAACAAACTACACAACATC 59.193 33.333 0.00 0.00 0.00 3.06
2299 2496 7.656412 TGCATATTGAACAAACTACACAACAT 58.344 30.769 0.00 0.00 0.00 2.71
2300 2497 7.032377 TGCATATTGAACAAACTACACAACA 57.968 32.000 0.00 0.00 0.00 3.33
2301 2498 7.410728 GCATGCATATTGAACAAACTACACAAC 60.411 37.037 14.21 0.00 0.00 3.32
2302 2499 6.585702 GCATGCATATTGAACAAACTACACAA 59.414 34.615 14.21 0.00 0.00 3.33
2303 2500 6.092092 GCATGCATATTGAACAAACTACACA 58.908 36.000 14.21 0.00 0.00 3.72
2304 2501 6.092092 TGCATGCATATTGAACAAACTACAC 58.908 36.000 18.46 0.00 0.00 2.90
2305 2502 6.264841 TGCATGCATATTGAACAAACTACA 57.735 33.333 18.46 0.00 0.00 2.74
2306 2503 7.760131 ATTGCATGCATATTGAACAAACTAC 57.240 32.000 23.37 0.00 0.00 2.73
2307 2504 7.818446 ACAATTGCATGCATATTGAACAAACTA 59.182 29.630 35.67 17.51 33.26 2.24
2308 2505 6.651643 ACAATTGCATGCATATTGAACAAACT 59.348 30.769 35.67 21.94 33.26 2.66
2309 2506 6.739100 CACAATTGCATGCATATTGAACAAAC 59.261 34.615 35.67 6.47 33.26 2.93
2310 2507 6.128254 CCACAATTGCATGCATATTGAACAAA 60.128 34.615 35.67 18.42 33.26 2.83
2311 2508 5.351740 CCACAATTGCATGCATATTGAACAA 59.648 36.000 35.67 18.99 33.26 2.83
2312 2509 4.870991 CCACAATTGCATGCATATTGAACA 59.129 37.500 35.67 19.55 33.26 3.18
2313 2510 4.271533 CCCACAATTGCATGCATATTGAAC 59.728 41.667 35.67 7.98 33.26 3.18
2314 2511 4.443621 CCCACAATTGCATGCATATTGAA 58.556 39.130 35.67 20.70 33.26 2.69
2315 2512 3.181464 CCCCACAATTGCATGCATATTGA 60.181 43.478 35.67 21.27 33.26 2.57
2316 2513 3.135225 CCCCACAATTGCATGCATATTG 58.865 45.455 31.67 31.67 34.17 1.90
2317 2514 3.039743 TCCCCACAATTGCATGCATATT 58.960 40.909 23.37 19.42 0.00 1.28
2318 2515 2.680251 TCCCCACAATTGCATGCATAT 58.320 42.857 23.37 14.69 0.00 1.78
2319 2516 2.156102 TCCCCACAATTGCATGCATA 57.844 45.000 23.37 12.94 0.00 3.14
2320 2517 1.277579 TTCCCCACAATTGCATGCAT 58.722 45.000 23.37 4.18 0.00 3.96
2321 2518 1.054231 TTTCCCCACAATTGCATGCA 58.946 45.000 18.46 18.46 0.00 3.96
2322 2519 2.181954 TTTTCCCCACAATTGCATGC 57.818 45.000 11.82 11.82 0.00 4.06
2353 2550 4.823989 AGCAGATGATGTAAAATAGGGCAC 59.176 41.667 0.00 0.00 0.00 5.01
2354 2551 5.052693 AGCAGATGATGTAAAATAGGGCA 57.947 39.130 0.00 0.00 0.00 5.36
2355 2552 6.881065 TCATAGCAGATGATGTAAAATAGGGC 59.119 38.462 0.00 0.00 0.00 5.19
2356 2553 9.458727 AATCATAGCAGATGATGTAAAATAGGG 57.541 33.333 13.20 0.00 38.62 3.53
2360 2557 9.788889 TCAGAATCATAGCAGATGATGTAAAAT 57.211 29.630 13.20 0.00 38.62 1.82
2361 2558 9.788889 ATCAGAATCATAGCAGATGATGTAAAA 57.211 29.630 13.20 2.32 38.62 1.52
2362 2559 9.216117 CATCAGAATCATAGCAGATGATGTAAA 57.784 33.333 13.20 3.41 38.62 2.01
2363 2560 7.333672 GCATCAGAATCATAGCAGATGATGTAA 59.666 37.037 13.20 3.13 38.62 2.41
2364 2561 6.817140 GCATCAGAATCATAGCAGATGATGTA 59.183 38.462 13.20 2.84 38.62 2.29
2365 2562 5.644206 GCATCAGAATCATAGCAGATGATGT 59.356 40.000 13.20 5.77 38.62 3.06
2366 2563 5.065346 GGCATCAGAATCATAGCAGATGATG 59.935 44.000 13.20 11.17 38.62 3.07
2367 2564 5.186942 GGCATCAGAATCATAGCAGATGAT 58.813 41.667 8.01 8.01 40.20 2.45
2368 2565 4.565028 GGGCATCAGAATCATAGCAGATGA 60.565 45.833 0.00 4.02 35.98 2.92
2369 2566 3.690139 GGGCATCAGAATCATAGCAGATG 59.310 47.826 0.00 0.00 36.76 2.90
2370 2567 3.587951 AGGGCATCAGAATCATAGCAGAT 59.412 43.478 0.00 0.00 0.00 2.90
2371 2568 2.977580 AGGGCATCAGAATCATAGCAGA 59.022 45.455 0.00 0.00 0.00 4.26
2372 2569 3.420300 AGGGCATCAGAATCATAGCAG 57.580 47.619 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.