Multiple sequence alignment - TraesCS6A01G277900

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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 TraesCS6A01G277900 chr6A 100.000 2404 0 0 1 2404 505898541 505896138 0.000000e+00 4440.0
1 TraesCS6A01G277900 chr6A 76.203 1122 233 28 460 1555 441150290 441149177 1.610000e-156 562.0
2 TraesCS6A01G277900 chr6A 75.601 1123 238 28 460 1555 441084628 441083515 7.610000e-145 523.0
3 TraesCS6A01G277900 chr6A 75.623 1124 235 30 460 1555 441032965 441031853 2.740000e-144 521.0
4 TraesCS6A01G277900 chr6A 75.304 1150 243 35 418 1541 450684247 450683113 1.650000e-141 512.0
5 TraesCS6A01G277900 chr6A 81.183 186 33 2 1370 1555 444070413 444070596 5.350000e-32 148.0
6 TraesCS6A01G277900 chr6D 95.014 2126 103 3 1 2125 364438402 364436279 0.000000e+00 3336.0
7 TraesCS6A01G277900 chr6D 76.060 1132 232 34 460 1562 313795647 313794526 9.710000e-154 553.0
8 TraesCS6A01G277900 chr6D 74.747 1089 245 25 460 1523 313721346 313720263 6.060000e-126 460.0
9 TraesCS6A01G277900 chr6D 89.076 238 20 1 2124 2355 364430205 364429968 8.410000e-75 291.0
10 TraesCS6A01G277900 chr6B 92.448 2145 148 9 1 2138 549415407 549413270 0.000000e+00 3051.0
11 TraesCS6A01G277900 chr6B 89.091 220 20 2 2134 2353 549388792 549388577 1.100000e-68 270.0
12 TraesCS6A01G277900 chr6B 91.045 67 4 2 2335 2400 387345669 387345604 3.290000e-14 89.8
13 TraesCS6A01G277900 chr4A 85.349 860 101 11 628 1474 657939105 657938258 0.000000e+00 867.0
14 TraesCS6A01G277900 chr4A 84.056 853 106 18 628 1474 657978383 657977555 0.000000e+00 795.0
15 TraesCS6A01G277900 chr4A 92.188 64 3 2 2341 2404 13814468 13814529 3.290000e-14 89.8
16 TraesCS6A01G277900 chr2A 76.384 813 153 32 900 1695 704058621 704057831 3.720000e-108 401.0
17 TraesCS6A01G277900 chr2A 95.556 45 2 0 1306 1350 5404986 5404942 3.320000e-09 73.1
18 TraesCS6A01G277900 chr2D 77.519 258 44 11 1 250 425775040 425774789 2.490000e-30 143.0
19 TraesCS6A01G277900 chr2D 81.633 147 22 4 1723 1867 578872976 578873119 1.510000e-22 117.0
20 TraesCS6A01G277900 chr2D 98.182 55 0 1 2350 2404 333494456 333494403 7.080000e-16 95.3
21 TraesCS6A01G277900 chr3D 80.117 171 28 5 1700 1866 575754911 575754743 3.250000e-24 122.0
22 TraesCS6A01G277900 chr3D 98.182 55 1 0 2350 2404 96015578 96015632 1.970000e-16 97.1
23 TraesCS6A01G277900 chr3D 98.182 55 0 1 2350 2404 35079034 35079087 7.080000e-16 95.3
24 TraesCS6A01G277900 chr3D 93.651 63 1 3 2344 2404 184688374 184688313 9.150000e-15 91.6
25 TraesCS6A01G277900 chr3D 91.045 67 3 3 2340 2404 284134126 284134191 1.180000e-13 87.9
26 TraesCS6A01G277900 chr4D 98.182 55 1 0 2350 2404 405477639 405477693 1.970000e-16 97.1
27 TraesCS6A01G277900 chr3B 95.000 60 2 1 2346 2404 435253353 435253294 2.540000e-15 93.5
28 TraesCS6A01G277900 chr1D 84.884 86 10 3 45 128 442943587 442943503 1.530000e-12 84.2


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 TraesCS6A01G277900 chr6A 505896138 505898541 2403 True 4440 4440 100.000 1 2404 1 chr6A.!!$R5 2403
1 TraesCS6A01G277900 chr6A 441149177 441150290 1113 True 562 562 76.203 460 1555 1 chr6A.!!$R3 1095
2 TraesCS6A01G277900 chr6A 441083515 441084628 1113 True 523 523 75.601 460 1555 1 chr6A.!!$R2 1095
3 TraesCS6A01G277900 chr6A 441031853 441032965 1112 True 521 521 75.623 460 1555 1 chr6A.!!$R1 1095
4 TraesCS6A01G277900 chr6A 450683113 450684247 1134 True 512 512 75.304 418 1541 1 chr6A.!!$R4 1123
5 TraesCS6A01G277900 chr6D 364436279 364438402 2123 True 3336 3336 95.014 1 2125 1 chr6D.!!$R4 2124
6 TraesCS6A01G277900 chr6D 313794526 313795647 1121 True 553 553 76.060 460 1562 1 chr6D.!!$R2 1102
7 TraesCS6A01G277900 chr6D 313720263 313721346 1083 True 460 460 74.747 460 1523 1 chr6D.!!$R1 1063
8 TraesCS6A01G277900 chr6B 549413270 549415407 2137 True 3051 3051 92.448 1 2138 1 chr6B.!!$R3 2137
9 TraesCS6A01G277900 chr4A 657938258 657939105 847 True 867 867 85.349 628 1474 1 chr4A.!!$R1 846
10 TraesCS6A01G277900 chr4A 657977555 657978383 828 True 795 795 84.056 628 1474 1 chr4A.!!$R2 846
11 TraesCS6A01G277900 chr2A 704057831 704058621 790 True 401 401 76.384 900 1695 1 chr2A.!!$R2 795

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
268 270 1.551883 ACGCCCGGTTACACTCTAAAT 59.448 47.619 0.0 0.0 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2273 0.032017 AAGGTCTCCTCCCACGCTAT 60.032 55.0 0.0 0.0 30.89 2.97 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
37 38 1.764134 ACACTACACTTCCCGTTCCAA 59.236 47.619 0.00 0.00 0.00 3.53
38 39 2.140717 CACTACACTTCCCGTTCCAAC 58.859 52.381 0.00 0.00 0.00 3.77
148 149 6.047511 AGACCGTAGTGTCTTTCTACTCTA 57.952 41.667 0.00 0.00 42.92 2.43
169 170 7.888021 ACTCTATTCTCGTTGAGATAGATCCAT 59.112 37.037 12.28 0.00 38.56 3.41
179 180 2.440627 AGATAGATCCATGCCTTGCACA 59.559 45.455 0.00 0.00 43.04 4.57
190 191 2.005451 GCCTTGCACACTGTCTATGAG 58.995 52.381 0.00 0.00 0.00 2.90
268 270 1.551883 ACGCCCGGTTACACTCTAAAT 59.448 47.619 0.00 0.00 0.00 1.40
294 296 3.060602 GAGTATCCACAAATCTAGGCGC 58.939 50.000 0.00 0.00 0.00 6.53
346 348 2.096174 ACTCACTCTCGATCTAACACGC 59.904 50.000 0.00 0.00 0.00 5.34
384 386 1.770658 CCCATGCATCCTCCACTAAGA 59.229 52.381 0.00 0.00 0.00 2.10
387 389 3.464907 CATGCATCCTCCACTAAGAGTG 58.535 50.000 0.00 0.00 45.53 3.51
427 429 7.649306 GTGTCCTCATTTGTATTGCCATAATTC 59.351 37.037 0.00 0.00 0.00 2.17
430 432 7.014518 TCCTCATTTGTATTGCCATAATTCCAG 59.985 37.037 0.00 0.00 0.00 3.86
574 579 5.185056 GGTCAACAATTAGGTGGCAACTATT 59.815 40.000 14.01 7.15 42.90 1.73
614 621 5.097529 CCATATGCACATGTCAACAACTTC 58.902 41.667 3.92 0.00 0.00 3.01
703 711 7.204604 TCAAAACGACTACATGTAGACAAAGA 58.795 34.615 34.16 20.01 36.97 2.52
1132 1156 9.139174 CTTCCTTCGTGCAATATTTTACATTTT 57.861 29.630 0.00 0.00 0.00 1.82
1535 1574 9.366216 CAAATATTCCTTACCTTTTGGCTTAAC 57.634 33.333 0.00 0.00 45.59 2.01
1555 1594 7.919621 GCTTAACGTACAAATAGGACTACTCAT 59.080 37.037 0.00 0.00 0.00 2.90
1579 1618 2.819019 TGCAGGTACATCAAACACATGG 59.181 45.455 0.00 0.00 0.00 3.66
1583 1622 2.819608 GGTACATCAAACACATGGCACT 59.180 45.455 0.00 0.00 0.00 4.40
1661 1703 3.639561 ACCCACAAACATTTTGTCCCTAC 59.360 43.478 1.25 0.00 0.00 3.18
1665 1707 5.478679 CCACAAACATTTTGTCCCTACCATA 59.521 40.000 1.25 0.00 0.00 2.74
1689 1731 2.554893 CTCTAGCGTATGTCCTTCCCTC 59.445 54.545 0.00 0.00 0.00 4.30
1708 1750 4.082571 CCCTCTGGTGATGCTTGTTAAAAG 60.083 45.833 0.00 0.00 0.00 2.27
1713 1755 6.939730 TCTGGTGATGCTTGTTAAAAGTATGA 59.060 34.615 0.00 0.00 0.00 2.15
1864 1906 5.983333 AGATAAACACCAATCAGATCCCT 57.017 39.130 0.00 0.00 0.00 4.20
1867 1909 3.567478 AACACCAATCAGATCCCTAGC 57.433 47.619 0.00 0.00 0.00 3.42
1907 1949 1.633945 GGTACCTGTTGAACCCTCCAT 59.366 52.381 4.06 0.00 0.00 3.41
1937 1979 3.454375 CCGTGCCGACTCATTAATTACT 58.546 45.455 0.00 0.00 0.00 2.24
1954 1996 2.034532 TGGGAGTACGCCGAGACA 59.965 61.111 9.72 0.00 0.00 3.41
1974 2016 3.181451 ACATCAACAGAACCTGAAGCTCA 60.181 43.478 0.45 0.00 35.18 4.26
1989 2031 2.839228 AGCTCATACAAGACCCCTCTT 58.161 47.619 0.00 0.00 37.19 2.85
2014 2056 3.092301 GGATTCAAGTAAGGCAAGGCTT 58.908 45.455 13.55 13.55 0.00 4.35
2093 2135 2.570752 AGAGCATCAAGACATCCACACT 59.429 45.455 0.00 0.00 37.82 3.55
2100 2142 4.352893 TCAAGACATCCACACTCATCCTA 58.647 43.478 0.00 0.00 0.00 2.94
2107 2149 3.096852 TCCACACTCATCCTACGAATGT 58.903 45.455 0.00 0.00 0.00 2.71
2122 2164 2.483013 CGAATGTCCGAAGAATGGGCTA 60.483 50.000 0.00 0.00 0.00 3.93
2131 2173 0.753262 AGAATGGGCTATCGCGAAGT 59.247 50.000 15.24 0.00 36.88 3.01
2143 2185 2.261671 CGAAGTGGTCGTCCCCTG 59.738 66.667 0.00 0.00 45.09 4.45
2144 2186 2.571216 CGAAGTGGTCGTCCCCTGT 61.571 63.158 0.00 0.00 45.09 4.00
2145 2187 1.004918 GAAGTGGTCGTCCCCTGTG 60.005 63.158 0.00 0.00 0.00 3.66
2146 2188 1.458777 AAGTGGTCGTCCCCTGTGA 60.459 57.895 0.00 0.00 0.00 3.58
2147 2189 1.052124 AAGTGGTCGTCCCCTGTGAA 61.052 55.000 0.00 0.00 0.00 3.18
2148 2190 0.836400 AGTGGTCGTCCCCTGTGAAT 60.836 55.000 0.00 0.00 0.00 2.57
2149 2191 0.899720 GTGGTCGTCCCCTGTGAATA 59.100 55.000 0.00 0.00 0.00 1.75
2150 2192 1.134788 GTGGTCGTCCCCTGTGAATAG 60.135 57.143 0.00 0.00 0.00 1.73
2151 2193 0.464452 GGTCGTCCCCTGTGAATAGG 59.536 60.000 0.00 0.00 37.59 2.57
2152 2194 0.179081 GTCGTCCCCTGTGAATAGGC 60.179 60.000 0.00 0.00 36.47 3.93
2153 2195 1.227263 CGTCCCCTGTGAATAGGCG 60.227 63.158 0.00 0.00 36.47 5.52
2154 2196 1.672854 CGTCCCCTGTGAATAGGCGA 61.673 60.000 0.00 0.00 36.47 5.54
2155 2197 0.179081 GTCCCCTGTGAATAGGCGAC 60.179 60.000 0.00 0.00 38.18 5.19
2156 2198 1.227263 CCCCTGTGAATAGGCGACG 60.227 63.158 0.00 0.00 36.47 5.12
2157 2199 1.227263 CCCTGTGAATAGGCGACGG 60.227 63.158 0.00 0.00 36.47 4.79
2158 2200 1.672854 CCCTGTGAATAGGCGACGGA 61.673 60.000 0.00 0.00 36.47 4.69
2159 2201 0.389391 CCTGTGAATAGGCGACGGAT 59.611 55.000 0.00 0.00 0.00 4.18
2160 2202 1.603172 CCTGTGAATAGGCGACGGATC 60.603 57.143 0.00 0.00 0.00 3.36
2161 2203 0.387929 TGTGAATAGGCGACGGATCC 59.612 55.000 0.00 0.00 0.00 3.36
2162 2204 0.387929 GTGAATAGGCGACGGATCCA 59.612 55.000 13.41 0.00 0.00 3.41
2163 2205 0.387929 TGAATAGGCGACGGATCCAC 59.612 55.000 13.41 4.15 0.00 4.02
2164 2206 0.319641 GAATAGGCGACGGATCCACC 60.320 60.000 13.41 7.27 0.00 4.61
2165 2207 1.046472 AATAGGCGACGGATCCACCA 61.046 55.000 13.41 0.00 38.90 4.17
2166 2208 1.745320 ATAGGCGACGGATCCACCAC 61.745 60.000 13.41 0.00 38.90 4.16
2169 2211 4.508128 CGACGGATCCACCACGGG 62.508 72.222 13.41 0.00 38.90 5.28
2170 2212 3.387947 GACGGATCCACCACGGGT 61.388 66.667 13.41 0.00 38.90 5.28
2171 2213 3.366739 GACGGATCCACCACGGGTC 62.367 68.421 13.41 5.25 45.30 4.46
2174 2216 2.494918 GATCCACCACGGGTCGAG 59.505 66.667 0.00 0.00 34.35 4.04
2175 2217 3.718210 GATCCACCACGGGTCGAGC 62.718 68.421 5.93 5.93 34.35 5.03
2198 2240 3.016971 CCATGGGTGGGAGGAGCA 61.017 66.667 2.85 0.00 42.11 4.26
2199 2241 2.593978 CATGGGTGGGAGGAGCAG 59.406 66.667 0.00 0.00 0.00 4.24
2200 2242 3.415087 ATGGGTGGGAGGAGCAGC 61.415 66.667 0.00 0.00 0.00 5.25
2208 2250 4.475135 GAGGAGCAGCCCCCGAAC 62.475 72.222 0.00 0.00 37.37 3.95
2210 2252 4.785453 GGAGCAGCCCCCGAACAG 62.785 72.222 0.00 0.00 0.00 3.16
2211 2253 4.021925 GAGCAGCCCCCGAACAGT 62.022 66.667 0.00 0.00 0.00 3.55
2212 2254 2.606519 AGCAGCCCCCGAACAGTA 60.607 61.111 0.00 0.00 0.00 2.74
2213 2255 2.436115 GCAGCCCCCGAACAGTAC 60.436 66.667 0.00 0.00 0.00 2.73
2214 2256 3.065306 CAGCCCCCGAACAGTACA 58.935 61.111 0.00 0.00 0.00 2.90
2215 2257 1.602237 CAGCCCCCGAACAGTACAT 59.398 57.895 0.00 0.00 0.00 2.29
2216 2258 0.035439 CAGCCCCCGAACAGTACATT 60.035 55.000 0.00 0.00 0.00 2.71
2217 2259 0.035439 AGCCCCCGAACAGTACATTG 60.035 55.000 0.00 0.00 0.00 2.82
2218 2260 1.029947 GCCCCCGAACAGTACATTGG 61.030 60.000 0.00 0.00 0.00 3.16
2219 2261 1.029947 CCCCCGAACAGTACATTGGC 61.030 60.000 0.00 0.00 0.00 4.52
2220 2262 1.029947 CCCCGAACAGTACATTGGCC 61.030 60.000 0.00 0.00 0.00 5.36
2221 2263 0.035439 CCCGAACAGTACATTGGCCT 60.035 55.000 3.32 0.00 0.00 5.19
2222 2264 1.208535 CCCGAACAGTACATTGGCCTA 59.791 52.381 3.32 0.00 0.00 3.93
2223 2265 2.550978 CCGAACAGTACATTGGCCTAG 58.449 52.381 3.32 0.00 0.00 3.02
2224 2266 2.550978 CGAACAGTACATTGGCCTAGG 58.449 52.381 3.67 3.67 0.00 3.02
2225 2267 2.289565 GAACAGTACATTGGCCTAGGC 58.710 52.381 26.55 26.55 41.06 3.93
2236 2278 2.846371 GCCTAGGCCAATGATAGCG 58.154 57.895 24.19 0.00 34.56 4.26
2237 2279 0.035458 GCCTAGGCCAATGATAGCGT 59.965 55.000 24.19 0.00 34.56 5.07
2238 2280 1.800805 CCTAGGCCAATGATAGCGTG 58.199 55.000 5.01 0.00 0.00 5.34
2239 2281 1.609061 CCTAGGCCAATGATAGCGTGG 60.609 57.143 5.01 0.00 35.39 4.94
2240 2282 0.396435 TAGGCCAATGATAGCGTGGG 59.604 55.000 5.01 0.00 32.71 4.61
2241 2283 1.148273 GGCCAATGATAGCGTGGGA 59.852 57.895 0.00 0.00 32.71 4.37
2242 2284 0.886490 GGCCAATGATAGCGTGGGAG 60.886 60.000 0.00 0.00 32.71 4.30
2243 2285 0.886490 GCCAATGATAGCGTGGGAGG 60.886 60.000 0.00 0.00 32.71 4.30
2244 2286 0.758734 CCAATGATAGCGTGGGAGGA 59.241 55.000 0.00 0.00 0.00 3.71
2245 2287 1.270518 CCAATGATAGCGTGGGAGGAG 60.271 57.143 0.00 0.00 0.00 3.69
2246 2288 1.688735 CAATGATAGCGTGGGAGGAGA 59.311 52.381 0.00 0.00 0.00 3.71
2247 2289 1.333177 ATGATAGCGTGGGAGGAGAC 58.667 55.000 0.00 0.00 0.00 3.36
2248 2290 0.755698 TGATAGCGTGGGAGGAGACC 60.756 60.000 0.00 0.00 0.00 3.85
2249 2291 0.468400 GATAGCGTGGGAGGAGACCT 60.468 60.000 0.00 0.00 36.03 3.85
2250 2292 0.032017 ATAGCGTGGGAGGAGACCTT 60.032 55.000 0.00 0.00 31.76 3.50
2251 2293 0.252103 TAGCGTGGGAGGAGACCTTT 60.252 55.000 0.00 0.00 31.76 3.11
2252 2294 1.376037 GCGTGGGAGGAGACCTTTG 60.376 63.158 0.00 0.00 31.76 2.77
2253 2295 1.827399 GCGTGGGAGGAGACCTTTGA 61.827 60.000 0.00 0.00 31.76 2.69
2254 2296 0.037232 CGTGGGAGGAGACCTTTGAC 60.037 60.000 0.00 0.00 31.76 3.18
2255 2297 0.037232 GTGGGAGGAGACCTTTGACG 60.037 60.000 0.00 0.00 31.76 4.35
2256 2298 0.178944 TGGGAGGAGACCTTTGACGA 60.179 55.000 0.00 0.00 31.76 4.20
2257 2299 1.196012 GGGAGGAGACCTTTGACGAT 58.804 55.000 0.00 0.00 31.76 3.73
2258 2300 1.134670 GGGAGGAGACCTTTGACGATG 60.135 57.143 0.00 0.00 31.76 3.84
2259 2301 1.550976 GGAGGAGACCTTTGACGATGT 59.449 52.381 0.00 0.00 31.76 3.06
2260 2302 2.611518 GAGGAGACCTTTGACGATGTG 58.388 52.381 0.00 0.00 31.76 3.21
2261 2303 1.971357 AGGAGACCTTTGACGATGTGT 59.029 47.619 0.00 0.00 0.00 3.72
2262 2304 2.368875 AGGAGACCTTTGACGATGTGTT 59.631 45.455 0.00 0.00 0.00 3.32
2263 2305 3.139077 GGAGACCTTTGACGATGTGTTT 58.861 45.455 0.00 0.00 0.00 2.83
2264 2306 3.186613 GGAGACCTTTGACGATGTGTTTC 59.813 47.826 0.00 0.00 0.00 2.78
2265 2307 4.058817 GAGACCTTTGACGATGTGTTTCT 58.941 43.478 0.00 0.00 0.00 2.52
2266 2308 4.058817 AGACCTTTGACGATGTGTTTCTC 58.941 43.478 0.00 0.00 0.00 2.87
2267 2309 3.804036 ACCTTTGACGATGTGTTTCTCA 58.196 40.909 0.00 0.00 0.00 3.27
2268 2310 3.560068 ACCTTTGACGATGTGTTTCTCAC 59.440 43.478 0.00 0.00 46.31 3.51
2269 2311 3.809832 CCTTTGACGATGTGTTTCTCACT 59.190 43.478 0.00 0.00 46.27 3.41
2270 2312 4.319046 CCTTTGACGATGTGTTTCTCACTG 60.319 45.833 0.00 0.00 46.27 3.66
2271 2313 2.754472 TGACGATGTGTTTCTCACTGG 58.246 47.619 0.00 0.00 46.27 4.00
2272 2314 2.364002 TGACGATGTGTTTCTCACTGGA 59.636 45.455 0.00 0.00 46.27 3.86
2273 2315 2.989840 GACGATGTGTTTCTCACTGGAG 59.010 50.000 0.00 0.00 46.27 3.86
2274 2316 2.289072 ACGATGTGTTTCTCACTGGAGG 60.289 50.000 0.00 0.00 46.27 4.30
2275 2317 2.079925 GATGTGTTTCTCACTGGAGGC 58.920 52.381 0.00 0.00 46.27 4.70
2276 2318 0.108585 TGTGTTTCTCACTGGAGGCC 59.891 55.000 0.00 0.00 46.27 5.19
2277 2319 0.108585 GTGTTTCTCACTGGAGGCCA 59.891 55.000 5.01 0.00 43.13 5.36
2278 2320 0.108585 TGTTTCTCACTGGAGGCCAC 59.891 55.000 5.01 0.00 41.69 5.01
2279 2321 0.606673 GTTTCTCACTGGAGGCCACC 60.607 60.000 13.09 13.09 41.69 4.61
2280 2322 1.779061 TTTCTCACTGGAGGCCACCC 61.779 60.000 17.45 12.02 41.69 4.61
2281 2323 3.721706 CTCACTGGAGGCCACCCC 61.722 72.222 17.45 9.31 37.51 4.95
2288 2330 3.081409 GAGGCCACCCCGCTCTTA 61.081 66.667 5.01 0.00 39.21 2.10
2289 2331 2.609610 AGGCCACCCCGCTCTTAA 60.610 61.111 5.01 0.00 39.21 1.85
2290 2332 2.124695 GGCCACCCCGCTCTTAAG 60.125 66.667 0.00 0.00 0.00 1.85
2291 2333 2.824489 GCCACCCCGCTCTTAAGC 60.824 66.667 0.00 0.00 45.56 3.09
2305 2347 5.136250 CTCTTAAGCAATCATGACGTGTC 57.864 43.478 0.00 0.00 0.00 3.67
2306 2348 3.612423 TCTTAAGCAATCATGACGTGTCG 59.388 43.478 0.00 0.00 0.00 4.35
2307 2349 2.078849 AAGCAATCATGACGTGTCGA 57.921 45.000 0.00 0.00 0.00 4.20
2308 2350 1.633561 AGCAATCATGACGTGTCGAG 58.366 50.000 0.00 0.00 0.00 4.04
2309 2351 0.025513 GCAATCATGACGTGTCGAGC 59.974 55.000 0.00 0.00 0.00 5.03
2310 2352 0.295763 CAATCATGACGTGTCGAGCG 59.704 55.000 0.00 7.64 0.00 5.03
2311 2353 0.109272 AATCATGACGTGTCGAGCGT 60.109 50.000 13.73 13.73 45.86 5.07
2312 2354 0.109272 ATCATGACGTGTCGAGCGTT 60.109 50.000 14.77 0.00 43.04 4.84
2313 2355 0.318360 TCATGACGTGTCGAGCGTTT 60.318 50.000 14.77 5.13 43.04 3.60
2314 2356 1.069091 TCATGACGTGTCGAGCGTTTA 60.069 47.619 14.77 8.87 43.04 2.01
2315 2357 1.317611 CATGACGTGTCGAGCGTTTAG 59.682 52.381 14.77 5.78 43.04 1.85
2330 2372 5.344207 GCGTTTAGCCTATCTTTACCATG 57.656 43.478 0.00 0.00 40.81 3.66
2331 2373 4.319549 GCGTTTAGCCTATCTTTACCATGC 60.320 45.833 0.00 0.00 40.81 4.06
2332 2374 4.814234 CGTTTAGCCTATCTTTACCATGCA 59.186 41.667 0.00 0.00 0.00 3.96
2333 2375 5.277345 CGTTTAGCCTATCTTTACCATGCAC 60.277 44.000 0.00 0.00 0.00 4.57
2334 2376 3.931907 AGCCTATCTTTACCATGCACA 57.068 42.857 0.00 0.00 0.00 4.57
2335 2377 4.443978 AGCCTATCTTTACCATGCACAT 57.556 40.909 0.00 0.00 0.00 3.21
2336 2378 4.139786 AGCCTATCTTTACCATGCACATG 58.860 43.478 3.56 3.56 38.51 3.21
2337 2379 4.136796 GCCTATCTTTACCATGCACATGA 58.863 43.478 12.18 0.00 41.20 3.07
2338 2380 4.023707 GCCTATCTTTACCATGCACATGAC 60.024 45.833 12.18 0.00 41.20 3.06
2339 2381 5.125356 CCTATCTTTACCATGCACATGACA 58.875 41.667 12.18 0.00 41.20 3.58
2340 2382 5.589855 CCTATCTTTACCATGCACATGACAA 59.410 40.000 12.18 2.98 41.20 3.18
2341 2383 6.263842 CCTATCTTTACCATGCACATGACAAT 59.736 38.462 12.18 0.00 41.20 2.71
2342 2384 5.981088 TCTTTACCATGCACATGACAATT 57.019 34.783 12.18 0.00 41.20 2.32
2343 2385 5.712004 TCTTTACCATGCACATGACAATTG 58.288 37.500 12.18 3.24 41.20 2.32
2344 2386 5.243507 TCTTTACCATGCACATGACAATTGT 59.756 36.000 11.78 11.78 41.20 2.71
2345 2387 5.465532 TTACCATGCACATGACAATTGTT 57.534 34.783 13.36 0.00 41.20 2.83
2346 2388 4.339872 ACCATGCACATGACAATTGTTT 57.660 36.364 13.36 0.59 41.20 2.83
2347 2389 4.706035 ACCATGCACATGACAATTGTTTT 58.294 34.783 13.36 0.20 41.20 2.43
2348 2390 4.512198 ACCATGCACATGACAATTGTTTTG 59.488 37.500 13.36 15.02 41.20 2.44
2349 2391 4.083749 CCATGCACATGACAATTGTTTTGG 60.084 41.667 13.36 5.81 41.20 3.28
2350 2392 4.134379 TGCACATGACAATTGTTTTGGT 57.866 36.364 13.36 6.44 0.00 3.67
2351 2393 5.268118 TGCACATGACAATTGTTTTGGTA 57.732 34.783 13.36 5.10 0.00 3.25
2352 2394 5.046529 TGCACATGACAATTGTTTTGGTAC 58.953 37.500 13.36 4.98 0.00 3.34
2353 2395 4.148000 GCACATGACAATTGTTTTGGTACG 59.852 41.667 13.36 5.70 0.00 3.67
2354 2396 5.277825 CACATGACAATTGTTTTGGTACGT 58.722 37.500 13.36 0.00 0.00 3.57
2355 2397 5.746245 CACATGACAATTGTTTTGGTACGTT 59.254 36.000 13.36 0.00 0.00 3.99
2356 2398 5.746245 ACATGACAATTGTTTTGGTACGTTG 59.254 36.000 13.36 3.09 0.00 4.10
2357 2399 5.562506 TGACAATTGTTTTGGTACGTTGA 57.437 34.783 13.36 0.00 0.00 3.18
2358 2400 6.137794 TGACAATTGTTTTGGTACGTTGAT 57.862 33.333 13.36 0.00 0.00 2.57
2359 2401 5.974158 TGACAATTGTTTTGGTACGTTGATG 59.026 36.000 13.36 0.00 0.00 3.07
2360 2402 5.897050 ACAATTGTTTTGGTACGTTGATGT 58.103 33.333 4.92 0.00 0.00 3.06
2361 2403 5.974751 ACAATTGTTTTGGTACGTTGATGTC 59.025 36.000 4.92 0.00 0.00 3.06
2362 2404 6.183360 ACAATTGTTTTGGTACGTTGATGTCT 60.183 34.615 4.92 0.00 0.00 3.41
2363 2405 7.012515 ACAATTGTTTTGGTACGTTGATGTCTA 59.987 33.333 4.92 0.00 0.00 2.59
2364 2406 5.910637 TGTTTTGGTACGTTGATGTCTAC 57.089 39.130 0.00 0.00 0.00 2.59
2365 2407 5.603596 TGTTTTGGTACGTTGATGTCTACT 58.396 37.500 0.00 0.00 0.00 2.57
2366 2408 6.747125 TGTTTTGGTACGTTGATGTCTACTA 58.253 36.000 0.00 0.00 0.00 1.82
2367 2409 7.380536 TGTTTTGGTACGTTGATGTCTACTAT 58.619 34.615 0.00 0.00 0.00 2.12
2368 2410 7.329962 TGTTTTGGTACGTTGATGTCTACTATG 59.670 37.037 0.00 0.00 0.00 2.23
2369 2411 4.928601 TGGTACGTTGATGTCTACTATGC 58.071 43.478 0.00 0.00 0.00 3.14
2370 2412 4.399934 TGGTACGTTGATGTCTACTATGCA 59.600 41.667 0.00 0.00 0.00 3.96
2371 2413 5.105675 TGGTACGTTGATGTCTACTATGCAA 60.106 40.000 0.00 0.00 0.00 4.08
2372 2414 5.231568 GGTACGTTGATGTCTACTATGCAAC 59.768 44.000 0.00 0.00 34.04 4.17
2373 2415 5.073311 ACGTTGATGTCTACTATGCAACT 57.927 39.130 0.00 0.00 34.92 3.16
2374 2416 5.479306 ACGTTGATGTCTACTATGCAACTT 58.521 37.500 0.00 0.00 34.92 2.66
2375 2417 5.932303 ACGTTGATGTCTACTATGCAACTTT 59.068 36.000 0.00 0.00 34.92 2.66
2376 2418 7.094631 ACGTTGATGTCTACTATGCAACTTTA 58.905 34.615 0.00 0.00 34.92 1.85
2377 2419 7.764443 ACGTTGATGTCTACTATGCAACTTTAT 59.236 33.333 0.00 0.00 34.92 1.40
2378 2420 8.604035 CGTTGATGTCTACTATGCAACTTTATT 58.396 33.333 0.00 0.00 34.92 1.40
2379 2421 9.922305 GTTGATGTCTACTATGCAACTTTATTC 57.078 33.333 0.00 0.00 34.43 1.75
2380 2422 9.890629 TTGATGTCTACTATGCAACTTTATTCT 57.109 29.630 0.00 0.00 0.00 2.40
2381 2423 9.890629 TGATGTCTACTATGCAACTTTATTCTT 57.109 29.630 0.00 0.00 0.00 2.52
2383 2425 9.672673 ATGTCTACTATGCAACTTTATTCTTGT 57.327 29.630 0.00 0.00 0.00 3.16
2389 2431 8.936864 ACTATGCAACTTTATTCTTGTAGACAC 58.063 33.333 0.00 0.00 0.00 3.67
2390 2432 7.744087 ATGCAACTTTATTCTTGTAGACACA 57.256 32.000 0.00 0.00 0.00 3.72
2391 2433 7.744087 TGCAACTTTATTCTTGTAGACACAT 57.256 32.000 0.00 0.00 33.76 3.21
2392 2434 7.584108 TGCAACTTTATTCTTGTAGACACATG 58.416 34.615 0.00 0.00 33.76 3.21
2393 2435 7.228507 TGCAACTTTATTCTTGTAGACACATGT 59.771 33.333 0.00 0.00 33.76 3.21
2394 2436 8.076178 GCAACTTTATTCTTGTAGACACATGTT 58.924 33.333 0.00 0.00 33.76 2.71
2395 2437 9.385902 CAACTTTATTCTTGTAGACACATGTTG 57.614 33.333 0.00 0.00 33.76 3.33
2396 2438 8.099364 ACTTTATTCTTGTAGACACATGTTGG 57.901 34.615 0.00 0.00 33.76 3.77
2397 2439 7.174946 ACTTTATTCTTGTAGACACATGTTGGG 59.825 37.037 0.00 0.00 33.76 4.12
2398 2440 2.778299 TCTTGTAGACACATGTTGGGC 58.222 47.619 0.00 0.00 33.76 5.36
2399 2441 1.812571 CTTGTAGACACATGTTGGGCC 59.187 52.381 0.00 0.00 33.76 5.80
2400 2442 1.064003 TGTAGACACATGTTGGGCCT 58.936 50.000 4.53 0.00 0.00 5.19
2401 2443 1.003118 TGTAGACACATGTTGGGCCTC 59.997 52.381 4.53 0.00 0.00 4.70
2402 2444 0.618458 TAGACACATGTTGGGCCTCC 59.382 55.000 4.53 0.00 0.00 4.30
2403 2445 1.074775 GACACATGTTGGGCCTCCA 59.925 57.895 4.53 0.88 42.25 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.544595 AGAGAGCTACAAACCCCCGT 60.545 55.000 0.00 0.00 0.00 5.28
38 39 1.481871 TAGAGAGCTACAAACCCCCG 58.518 55.000 0.00 0.00 0.00 5.73
43 44 4.737855 TGGTGGATAGAGAGCTACAAAC 57.262 45.455 0.00 0.00 0.00 2.93
148 149 5.477510 GCATGGATCTATCTCAACGAGAAT 58.522 41.667 0.00 0.00 42.27 2.40
169 170 1.347378 TCATAGACAGTGTGCAAGGCA 59.653 47.619 0.00 0.00 35.60 4.75
179 180 2.755655 CCCTTGTCGACTCATAGACAGT 59.244 50.000 17.92 0.00 46.39 3.55
190 191 1.153349 GGAGGCATCCCTTGTCGAC 60.153 63.158 5.99 9.11 43.12 4.20
250 252 2.169978 AGGATTTAGAGTGTAACCGGGC 59.830 50.000 6.32 0.00 37.80 6.13
294 296 3.356529 AGCTAGGAAACAAGGACATGG 57.643 47.619 0.00 0.00 0.00 3.66
346 348 1.374252 GTGTGTGTGGGGCTAGACG 60.374 63.158 0.00 0.00 0.00 4.18
384 386 4.080526 AGGACACAACTAGTTGGTTTCACT 60.081 41.667 33.11 21.39 44.45 3.41
387 389 4.448210 TGAGGACACAACTAGTTGGTTTC 58.552 43.478 33.11 24.96 44.45 2.78
388 390 4.497291 TGAGGACACAACTAGTTGGTTT 57.503 40.909 33.11 19.72 44.45 3.27
427 429 7.936847 TGGGAAGTATAAATTGTATAGTGCTGG 59.063 37.037 0.00 0.00 0.00 4.85
574 579 6.014755 TGCATATGGATTTTCAACAACCTCAA 60.015 34.615 4.56 0.00 0.00 3.02
781 789 7.805071 GTGGTTCTAAAAGACATGAATCAACAG 59.195 37.037 0.00 0.00 32.34 3.16
1397 1434 5.801444 TCGCAGCATGATTTTTATTCAACAG 59.199 36.000 0.00 0.00 39.69 3.16
1461 1499 9.919416 TTTCCCATTCTCAATTCATCATACTAA 57.081 29.630 0.00 0.00 0.00 2.24
1535 1574 6.363626 GCATCATGAGTAGTCCTATTTGTACG 59.636 42.308 0.09 0.00 0.00 3.67
1661 1703 5.906113 AGGACATACGCTAGAGAATATGG 57.094 43.478 0.00 0.00 30.71 2.74
1665 1707 3.574826 GGGAAGGACATACGCTAGAGAAT 59.425 47.826 0.00 0.00 0.00 2.40
1689 1731 7.023575 GTCATACTTTTAACAAGCATCACCAG 58.976 38.462 0.00 0.00 0.00 4.00
1789 1831 8.786898 ACGAATCTCATATTGAATAACCATTGG 58.213 33.333 0.00 0.00 0.00 3.16
1801 1843 6.765989 TGGGTTTTCCTACGAATCTCATATTG 59.234 38.462 0.00 0.00 40.46 1.90
1864 1906 4.440112 CCATTATCTGTGACACTGACGCTA 60.440 45.833 16.37 4.15 0.00 4.26
1867 1909 3.190079 CCCATTATCTGTGACACTGACG 58.810 50.000 16.37 6.67 0.00 4.35
1893 1935 2.794103 CACATGATGGAGGGTTCAACA 58.206 47.619 0.00 0.00 0.00 3.33
1937 1979 1.379443 ATGTCTCGGCGTACTCCCA 60.379 57.895 6.85 0.00 0.00 4.37
1954 1996 3.777106 TGAGCTTCAGGTTCTGTTGAT 57.223 42.857 0.00 0.00 32.61 2.57
1974 2016 6.389869 TGAATCCATTAAGAGGGGTCTTGTAT 59.610 38.462 0.00 0.00 0.00 2.29
1989 2031 4.644685 GCCTTGCCTTACTTGAATCCATTA 59.355 41.667 0.00 0.00 0.00 1.90
2093 2135 3.284617 TCTTCGGACATTCGTAGGATGA 58.715 45.455 0.00 0.00 0.00 2.92
2100 2142 2.012051 GCCCATTCTTCGGACATTCGT 61.012 52.381 0.00 0.00 0.00 3.85
2131 2173 1.191535 CTATTCACAGGGGACGACCA 58.808 55.000 6.20 0.00 42.91 4.02
2139 2181 1.227263 CCGTCGCCTATTCACAGGG 60.227 63.158 0.00 0.00 36.10 4.45
2140 2182 0.389391 ATCCGTCGCCTATTCACAGG 59.611 55.000 0.00 0.00 38.86 4.00
2141 2183 1.603172 GGATCCGTCGCCTATTCACAG 60.603 57.143 0.00 0.00 0.00 3.66
2142 2184 0.387929 GGATCCGTCGCCTATTCACA 59.612 55.000 0.00 0.00 0.00 3.58
2143 2185 0.387929 TGGATCCGTCGCCTATTCAC 59.612 55.000 7.39 0.00 0.00 3.18
2144 2186 0.387929 GTGGATCCGTCGCCTATTCA 59.612 55.000 7.39 0.00 0.00 2.57
2145 2187 0.319641 GGTGGATCCGTCGCCTATTC 60.320 60.000 7.39 0.00 0.00 1.75
2146 2188 1.046472 TGGTGGATCCGTCGCCTATT 61.046 55.000 7.39 0.00 39.52 1.73
2147 2189 1.456892 TGGTGGATCCGTCGCCTAT 60.457 57.895 7.39 0.00 39.52 2.57
2148 2190 2.043752 TGGTGGATCCGTCGCCTA 60.044 61.111 7.39 0.00 39.52 3.93
2149 2191 3.771160 GTGGTGGATCCGTCGCCT 61.771 66.667 7.39 0.00 39.52 5.52
2152 2194 4.508128 CCCGTGGTGGATCCGTCG 62.508 72.222 7.39 8.75 42.00 5.12
2153 2195 3.366739 GACCCGTGGTGGATCCGTC 62.367 68.421 7.39 2.54 42.00 4.79
2154 2196 3.387947 GACCCGTGGTGGATCCGT 61.388 66.667 7.39 0.00 42.00 4.69
2155 2197 4.508128 CGACCCGTGGTGGATCCG 62.508 72.222 7.39 0.00 42.00 4.18
2156 2198 3.072468 TCGACCCGTGGTGGATCC 61.072 66.667 4.20 4.20 42.00 3.36
2157 2199 2.494918 CTCGACCCGTGGTGGATC 59.505 66.667 7.92 0.00 39.55 3.36
2158 2200 3.771160 GCTCGACCCGTGGTGGAT 61.771 66.667 7.92 0.00 39.55 3.41
2181 2223 3.016971 TGCTCCTCCCACCCATGG 61.017 66.667 4.14 4.14 46.81 3.66
2182 2224 2.593978 CTGCTCCTCCCACCCATG 59.406 66.667 0.00 0.00 0.00 3.66
2183 2225 3.415087 GCTGCTCCTCCCACCCAT 61.415 66.667 0.00 0.00 0.00 4.00
2191 2233 4.475135 GTTCGGGGGCTGCTCCTC 62.475 72.222 19.75 7.75 34.39 3.71
2193 2235 4.785453 CTGTTCGGGGGCTGCTCC 62.785 72.222 10.98 10.98 0.00 4.70
2194 2236 2.656069 TACTGTTCGGGGGCTGCTC 61.656 63.158 0.00 0.00 0.00 4.26
2195 2237 2.606519 TACTGTTCGGGGGCTGCT 60.607 61.111 0.00 0.00 0.00 4.24
2196 2238 2.436115 GTACTGTTCGGGGGCTGC 60.436 66.667 0.00 0.00 0.00 5.25
2197 2239 0.035439 AATGTACTGTTCGGGGGCTG 60.035 55.000 0.00 0.00 0.00 4.85
2198 2240 0.035439 CAATGTACTGTTCGGGGGCT 60.035 55.000 0.00 0.00 0.00 5.19
2199 2241 1.029947 CCAATGTACTGTTCGGGGGC 61.030 60.000 0.00 0.00 0.00 5.80
2200 2242 1.029947 GCCAATGTACTGTTCGGGGG 61.030 60.000 0.00 0.00 0.00 5.40
2201 2243 1.029947 GGCCAATGTACTGTTCGGGG 61.030 60.000 0.00 0.00 0.00 5.73
2202 2244 0.035439 AGGCCAATGTACTGTTCGGG 60.035 55.000 5.01 0.00 0.00 5.14
2203 2245 2.550978 CTAGGCCAATGTACTGTTCGG 58.449 52.381 5.01 0.00 0.00 4.30
2204 2246 2.550978 CCTAGGCCAATGTACTGTTCG 58.449 52.381 5.01 0.00 0.00 3.95
2205 2247 2.289565 GCCTAGGCCAATGTACTGTTC 58.710 52.381 24.19 0.00 34.56 3.18
2206 2248 2.420058 GCCTAGGCCAATGTACTGTT 57.580 50.000 24.19 0.00 34.56 3.16
2218 2260 0.035458 ACGCTATCATTGGCCTAGGC 59.965 55.000 26.55 26.55 41.06 3.93
2219 2261 1.609061 CCACGCTATCATTGGCCTAGG 60.609 57.143 3.67 3.67 0.00 3.02
2220 2262 1.609061 CCCACGCTATCATTGGCCTAG 60.609 57.143 3.32 0.00 0.00 3.02
2221 2263 0.396435 CCCACGCTATCATTGGCCTA 59.604 55.000 3.32 0.00 0.00 3.93
2222 2264 1.149174 CCCACGCTATCATTGGCCT 59.851 57.895 3.32 0.00 0.00 5.19
2223 2265 0.886490 CTCCCACGCTATCATTGGCC 60.886 60.000 0.00 0.00 0.00 5.36
2224 2266 0.886490 CCTCCCACGCTATCATTGGC 60.886 60.000 0.00 0.00 0.00 4.52
2225 2267 0.758734 TCCTCCCACGCTATCATTGG 59.241 55.000 0.00 0.00 0.00 3.16
2226 2268 1.688735 TCTCCTCCCACGCTATCATTG 59.311 52.381 0.00 0.00 0.00 2.82
2227 2269 1.689273 GTCTCCTCCCACGCTATCATT 59.311 52.381 0.00 0.00 0.00 2.57
2228 2270 1.333177 GTCTCCTCCCACGCTATCAT 58.667 55.000 0.00 0.00 0.00 2.45
2229 2271 0.755698 GGTCTCCTCCCACGCTATCA 60.756 60.000 0.00 0.00 0.00 2.15
2230 2272 0.468400 AGGTCTCCTCCCACGCTATC 60.468 60.000 0.00 0.00 0.00 2.08
2231 2273 0.032017 AAGGTCTCCTCCCACGCTAT 60.032 55.000 0.00 0.00 30.89 2.97
2232 2274 0.252103 AAAGGTCTCCTCCCACGCTA 60.252 55.000 0.00 0.00 30.89 4.26
2233 2275 1.536662 AAAGGTCTCCTCCCACGCT 60.537 57.895 0.00 0.00 30.89 5.07
2234 2276 1.376037 CAAAGGTCTCCTCCCACGC 60.376 63.158 0.00 0.00 30.89 5.34
2235 2277 0.037232 GTCAAAGGTCTCCTCCCACG 60.037 60.000 0.00 0.00 30.89 4.94
2236 2278 0.037232 CGTCAAAGGTCTCCTCCCAC 60.037 60.000 0.00 0.00 30.89 4.61
2237 2279 0.178944 TCGTCAAAGGTCTCCTCCCA 60.179 55.000 0.00 0.00 30.89 4.37
2238 2280 1.134670 CATCGTCAAAGGTCTCCTCCC 60.135 57.143 0.00 0.00 30.89 4.30
2239 2281 1.550976 ACATCGTCAAAGGTCTCCTCC 59.449 52.381 0.00 0.00 30.89 4.30
2240 2282 2.028930 ACACATCGTCAAAGGTCTCCTC 60.029 50.000 0.00 0.00 30.89 3.71
2241 2283 1.971357 ACACATCGTCAAAGGTCTCCT 59.029 47.619 0.00 0.00 33.87 3.69
2242 2284 2.457366 ACACATCGTCAAAGGTCTCC 57.543 50.000 0.00 0.00 0.00 3.71
2243 2285 4.058817 AGAAACACATCGTCAAAGGTCTC 58.941 43.478 0.00 0.00 0.00 3.36
2244 2286 4.058817 GAGAAACACATCGTCAAAGGTCT 58.941 43.478 0.00 0.00 0.00 3.85
2245 2287 3.807622 TGAGAAACACATCGTCAAAGGTC 59.192 43.478 0.00 0.00 0.00 3.85
2246 2288 3.804036 TGAGAAACACATCGTCAAAGGT 58.196 40.909 0.00 0.00 0.00 3.50
2259 2301 0.108585 GTGGCCTCCAGTGAGAAACA 59.891 55.000 3.32 0.00 41.42 2.83
2260 2302 0.606673 GGTGGCCTCCAGTGAGAAAC 60.607 60.000 19.19 0.00 41.42 2.78
2261 2303 1.761174 GGTGGCCTCCAGTGAGAAA 59.239 57.895 19.19 0.00 41.42 2.52
2262 2304 2.224159 GGGTGGCCTCCAGTGAGAA 61.224 63.158 24.81 0.00 41.42 2.87
2263 2305 2.607750 GGGTGGCCTCCAGTGAGA 60.608 66.667 24.81 0.00 41.42 3.27
2264 2306 3.721706 GGGGTGGCCTCCAGTGAG 61.722 72.222 24.81 0.00 38.42 3.51
2271 2313 2.595009 CTTAAGAGCGGGGTGGCCTC 62.595 65.000 3.32 0.00 0.00 4.70
2272 2314 2.609610 TTAAGAGCGGGGTGGCCT 60.610 61.111 3.32 0.00 0.00 5.19
2273 2315 2.124695 CTTAAGAGCGGGGTGGCC 60.125 66.667 0.00 0.00 0.00 5.36
2274 2316 2.824489 GCTTAAGAGCGGGGTGGC 60.824 66.667 6.67 0.00 39.48 5.01
2283 2325 4.259570 CGACACGTCATGATTGCTTAAGAG 60.260 45.833 6.67 0.00 0.00 2.85
2284 2326 3.612423 CGACACGTCATGATTGCTTAAGA 59.388 43.478 6.67 0.00 0.00 2.10
2285 2327 3.612423 TCGACACGTCATGATTGCTTAAG 59.388 43.478 0.00 0.00 0.00 1.85
2286 2328 3.580731 TCGACACGTCATGATTGCTTAA 58.419 40.909 0.00 0.00 0.00 1.85
2287 2329 3.179048 CTCGACACGTCATGATTGCTTA 58.821 45.455 0.00 0.00 0.00 3.09
2288 2330 1.995484 CTCGACACGTCATGATTGCTT 59.005 47.619 0.00 0.00 0.00 3.91
2289 2331 1.633561 CTCGACACGTCATGATTGCT 58.366 50.000 0.00 0.00 0.00 3.91
2290 2332 0.025513 GCTCGACACGTCATGATTGC 59.974 55.000 0.00 0.00 0.00 3.56
2291 2333 0.295763 CGCTCGACACGTCATGATTG 59.704 55.000 0.00 1.92 0.00 2.67
2292 2334 0.109272 ACGCTCGACACGTCATGATT 60.109 50.000 0.00 0.00 40.28 2.57
2293 2335 0.109272 AACGCTCGACACGTCATGAT 60.109 50.000 8.99 0.00 44.30 2.45
2294 2336 0.318360 AAACGCTCGACACGTCATGA 60.318 50.000 8.99 0.00 44.30 3.07
2295 2337 1.317611 CTAAACGCTCGACACGTCATG 59.682 52.381 8.99 0.00 44.30 3.07
2296 2338 1.614385 CTAAACGCTCGACACGTCAT 58.386 50.000 8.99 4.90 44.30 3.06
2297 2339 1.000233 GCTAAACGCTCGACACGTCA 61.000 55.000 8.99 0.98 44.30 4.35
2298 2340 1.671880 GGCTAAACGCTCGACACGTC 61.672 60.000 8.99 0.00 44.30 4.34
2300 2342 0.179181 TAGGCTAAACGCTCGACACG 60.179 55.000 0.00 1.72 39.13 4.49
2301 2343 2.117910 GATAGGCTAAACGCTCGACAC 58.882 52.381 0.00 0.00 39.13 3.67
2302 2344 2.022195 AGATAGGCTAAACGCTCGACA 58.978 47.619 0.00 0.00 39.13 4.35
2303 2345 2.778187 AGATAGGCTAAACGCTCGAC 57.222 50.000 0.00 0.00 39.13 4.20
2304 2346 3.795623 AAAGATAGGCTAAACGCTCGA 57.204 42.857 0.00 0.00 39.13 4.04
2305 2347 3.734735 GGTAAAGATAGGCTAAACGCTCG 59.265 47.826 0.00 0.00 39.13 5.03
2306 2348 4.690122 TGGTAAAGATAGGCTAAACGCTC 58.310 43.478 0.00 0.00 39.13 5.03
2307 2349 4.748277 TGGTAAAGATAGGCTAAACGCT 57.252 40.909 0.00 0.00 39.13 5.07
2308 2350 4.319549 GCATGGTAAAGATAGGCTAAACGC 60.320 45.833 0.00 0.00 38.13 4.84
2309 2351 4.814234 TGCATGGTAAAGATAGGCTAAACG 59.186 41.667 0.00 0.00 0.00 3.60
2310 2352 5.588648 TGTGCATGGTAAAGATAGGCTAAAC 59.411 40.000 0.00 0.00 0.00 2.01
2311 2353 5.750524 TGTGCATGGTAAAGATAGGCTAAA 58.249 37.500 0.00 0.00 0.00 1.85
2312 2354 5.366482 TGTGCATGGTAAAGATAGGCTAA 57.634 39.130 0.00 0.00 0.00 3.09
2313 2355 5.071653 TCATGTGCATGGTAAAGATAGGCTA 59.928 40.000 11.68 0.00 39.24 3.93
2314 2356 3.931907 TGTGCATGGTAAAGATAGGCT 57.068 42.857 0.00 0.00 0.00 4.58
2315 2357 4.023707 GTCATGTGCATGGTAAAGATAGGC 60.024 45.833 11.68 0.00 39.24 3.93
2316 2358 5.125356 TGTCATGTGCATGGTAAAGATAGG 58.875 41.667 11.68 0.00 39.24 2.57
2317 2359 6.682423 TTGTCATGTGCATGGTAAAGATAG 57.318 37.500 11.68 0.00 39.24 2.08
2318 2360 7.122501 ACAATTGTCATGTGCATGGTAAAGATA 59.877 33.333 4.92 0.00 39.24 1.98
2319 2361 6.071221 ACAATTGTCATGTGCATGGTAAAGAT 60.071 34.615 4.92 0.00 39.24 2.40
2320 2362 5.243507 ACAATTGTCATGTGCATGGTAAAGA 59.756 36.000 4.92 0.00 39.24 2.52
2321 2363 5.472148 ACAATTGTCATGTGCATGGTAAAG 58.528 37.500 4.92 7.51 39.24 1.85
2322 2364 5.465532 ACAATTGTCATGTGCATGGTAAA 57.534 34.783 4.92 5.31 39.24 2.01
2323 2365 5.465532 AACAATTGTCATGTGCATGGTAA 57.534 34.783 12.39 7.99 39.24 2.85
2324 2366 5.465532 AAACAATTGTCATGTGCATGGTA 57.534 34.783 12.39 0.00 39.24 3.25
2325 2367 4.339872 AAACAATTGTCATGTGCATGGT 57.660 36.364 12.39 0.00 39.24 3.55
2326 2368 4.083749 CCAAAACAATTGTCATGTGCATGG 60.084 41.667 12.39 7.80 39.24 3.66
2327 2369 4.512198 ACCAAAACAATTGTCATGTGCATG 59.488 37.500 12.39 5.86 40.09 4.06
2328 2370 4.706035 ACCAAAACAATTGTCATGTGCAT 58.294 34.783 12.39 0.00 0.00 3.96
2329 2371 4.134379 ACCAAAACAATTGTCATGTGCA 57.866 36.364 12.39 0.00 0.00 4.57
2330 2372 4.148000 CGTACCAAAACAATTGTCATGTGC 59.852 41.667 12.39 9.47 0.00 4.57
2331 2373 5.277825 ACGTACCAAAACAATTGTCATGTG 58.722 37.500 12.39 2.39 0.00 3.21
2332 2374 5.508200 ACGTACCAAAACAATTGTCATGT 57.492 34.783 12.39 9.49 0.00 3.21
2333 2375 5.974158 TCAACGTACCAAAACAATTGTCATG 59.026 36.000 12.39 13.26 0.00 3.07
2334 2376 6.137794 TCAACGTACCAAAACAATTGTCAT 57.862 33.333 12.39 0.93 0.00 3.06
2335 2377 5.562506 TCAACGTACCAAAACAATTGTCA 57.437 34.783 12.39 0.00 0.00 3.58
2336 2378 5.974751 ACATCAACGTACCAAAACAATTGTC 59.025 36.000 12.39 0.00 0.00 3.18
2337 2379 5.897050 ACATCAACGTACCAAAACAATTGT 58.103 33.333 4.92 4.92 0.00 2.71
2338 2380 6.205784 AGACATCAACGTACCAAAACAATTG 58.794 36.000 3.24 3.24 0.00 2.32
2339 2381 6.385649 AGACATCAACGTACCAAAACAATT 57.614 33.333 0.00 0.00 0.00 2.32
2340 2382 6.708949 AGTAGACATCAACGTACCAAAACAAT 59.291 34.615 0.00 0.00 0.00 2.71
2341 2383 6.050432 AGTAGACATCAACGTACCAAAACAA 58.950 36.000 0.00 0.00 0.00 2.83
2342 2384 5.603596 AGTAGACATCAACGTACCAAAACA 58.396 37.500 0.00 0.00 0.00 2.83
2343 2385 7.672738 CATAGTAGACATCAACGTACCAAAAC 58.327 38.462 0.00 0.00 0.00 2.43
2344 2386 6.311935 GCATAGTAGACATCAACGTACCAAAA 59.688 38.462 0.00 0.00 0.00 2.44
2345 2387 5.808540 GCATAGTAGACATCAACGTACCAAA 59.191 40.000 0.00 0.00 0.00 3.28
2346 2388 5.105675 TGCATAGTAGACATCAACGTACCAA 60.106 40.000 0.00 0.00 0.00 3.67
2347 2389 4.399934 TGCATAGTAGACATCAACGTACCA 59.600 41.667 0.00 0.00 0.00 3.25
2348 2390 4.928601 TGCATAGTAGACATCAACGTACC 58.071 43.478 0.00 0.00 0.00 3.34
2349 2391 6.034591 AGTTGCATAGTAGACATCAACGTAC 58.965 40.000 0.00 0.00 38.87 3.67
2350 2392 6.203808 AGTTGCATAGTAGACATCAACGTA 57.796 37.500 0.00 0.00 38.87 3.57
2351 2393 5.073311 AGTTGCATAGTAGACATCAACGT 57.927 39.130 0.00 0.00 38.87 3.99
2352 2394 6.408858 AAAGTTGCATAGTAGACATCAACG 57.591 37.500 0.00 0.00 38.87 4.10
2353 2395 9.922305 GAATAAAGTTGCATAGTAGACATCAAC 57.078 33.333 0.00 0.00 35.39 3.18
2354 2396 9.890629 AGAATAAAGTTGCATAGTAGACATCAA 57.109 29.630 0.00 0.00 0.00 2.57
2355 2397 9.890629 AAGAATAAAGTTGCATAGTAGACATCA 57.109 29.630 0.00 0.00 0.00 3.07
2357 2399 9.672673 ACAAGAATAAAGTTGCATAGTAGACAT 57.327 29.630 0.00 0.00 0.00 3.06
2363 2405 8.936864 GTGTCTACAAGAATAAAGTTGCATAGT 58.063 33.333 0.00 0.00 0.00 2.12
2364 2406 8.935844 TGTGTCTACAAGAATAAAGTTGCATAG 58.064 33.333 0.00 0.00 32.88 2.23
2365 2407 8.840833 TGTGTCTACAAGAATAAAGTTGCATA 57.159 30.769 0.00 0.00 32.88 3.14
2366 2408 7.744087 TGTGTCTACAAGAATAAAGTTGCAT 57.256 32.000 0.00 0.00 32.88 3.96
2367 2409 7.228507 ACATGTGTCTACAAGAATAAAGTTGCA 59.771 33.333 0.00 0.00 40.84 4.08
2368 2410 7.584987 ACATGTGTCTACAAGAATAAAGTTGC 58.415 34.615 0.00 0.00 40.84 4.17
2369 2411 9.385902 CAACATGTGTCTACAAGAATAAAGTTG 57.614 33.333 0.00 0.00 40.84 3.16
2370 2412 8.567948 CCAACATGTGTCTACAAGAATAAAGTT 58.432 33.333 0.00 0.00 40.84 2.66
2371 2413 7.174946 CCCAACATGTGTCTACAAGAATAAAGT 59.825 37.037 0.00 0.00 40.84 2.66
2372 2414 7.530010 CCCAACATGTGTCTACAAGAATAAAG 58.470 38.462 0.00 0.00 40.84 1.85
2373 2415 6.072175 GCCCAACATGTGTCTACAAGAATAAA 60.072 38.462 0.00 0.00 40.84 1.40
2374 2416 5.414454 GCCCAACATGTGTCTACAAGAATAA 59.586 40.000 0.00 0.00 40.84 1.40
2375 2417 4.941263 GCCCAACATGTGTCTACAAGAATA 59.059 41.667 0.00 0.00 40.84 1.75
2376 2418 3.758554 GCCCAACATGTGTCTACAAGAAT 59.241 43.478 0.00 0.00 40.84 2.40
2377 2419 3.146066 GCCCAACATGTGTCTACAAGAA 58.854 45.455 0.00 0.00 40.84 2.52
2378 2420 2.552155 GGCCCAACATGTGTCTACAAGA 60.552 50.000 0.00 0.00 40.84 3.02
2379 2421 1.812571 GGCCCAACATGTGTCTACAAG 59.187 52.381 0.00 0.00 40.84 3.16
2380 2422 1.423541 AGGCCCAACATGTGTCTACAA 59.576 47.619 0.00 0.00 40.84 2.41
2381 2423 1.003118 GAGGCCCAACATGTGTCTACA 59.997 52.381 0.00 0.00 41.89 2.74
2382 2424 1.679032 GGAGGCCCAACATGTGTCTAC 60.679 57.143 0.00 0.00 0.00 2.59
2383 2425 0.618458 GGAGGCCCAACATGTGTCTA 59.382 55.000 0.00 0.00 0.00 2.59
2384 2426 1.380302 GGAGGCCCAACATGTGTCT 59.620 57.895 0.00 0.00 0.00 3.41
2385 2427 1.074775 TGGAGGCCCAACATGTGTC 59.925 57.895 0.00 0.00 40.09 3.67
2386 2428 3.260297 TGGAGGCCCAACATGTGT 58.740 55.556 0.00 0.00 40.09 3.72


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

AutoCloner maintained by Alex Coulton.