Multiple sequence alignment - TraesCS3A01G246700

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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 TraesCS3A01G246700 chr3A 100.000 1703 0 0 1 1703 464798078 464796376 0.000000e+00 3145.0
1 TraesCS3A01G246700 chr3A 100.000 616 0 0 2085 2700 464795994 464795379 0.000000e+00 1138.0
2 TraesCS3A01G246700 chr3B 88.268 1432 98 41 306 1702 438929821 438931217 0.000000e+00 1650.0
3 TraesCS3A01G246700 chr3B 98.305 236 4 0 2085 2320 26835758 26835523 5.380000e-112 414.0
4 TraesCS3A01G246700 chr3B 97.881 236 5 0 2085 2320 120567745 120567980 2.500000e-110 409.0
5 TraesCS3A01G246700 chr3B 87.379 309 27 2 1 308 438923130 438923427 7.160000e-91 344.0
6 TraesCS3A01G246700 chr3B 86.164 318 17 6 2383 2697 438931304 438931597 4.340000e-83 318.0
7 TraesCS3A01G246700 chr3B 83.420 193 25 4 226 413 711347750 711347940 3.570000e-39 172.0
8 TraesCS3A01G246700 chr3D 92.884 1068 34 5 637 1703 340069229 340070255 0.000000e+00 1513.0
9 TraesCS3A01G246700 chr3D 92.857 350 24 1 1 350 340068534 340068882 8.630000e-140 507.0
10 TraesCS3A01G246700 chr3D 86.553 409 53 2 5 413 182165036 182165442 1.470000e-122 449.0
11 TraesCS3A01G246700 chr3D 93.069 303 19 2 340 642 340068899 340069199 2.470000e-120 442.0
12 TraesCS3A01G246700 chr3D 89.720 321 22 8 2383 2697 340070341 340070656 1.510000e-107 399.0
13 TraesCS3A01G246700 chr2B 100.000 236 0 0 2085 2320 225398358 225398593 1.150000e-118 436.0
14 TraesCS3A01G246700 chr2B 97.881 236 5 0 2085 2320 659017663 659017898 2.500000e-110 409.0
15 TraesCS3A01G246700 chr1A 100.000 236 0 0 2085 2320 40891108 40891343 1.150000e-118 436.0
16 TraesCS3A01G246700 chr1A 87.119 295 29 5 1232 1517 562902607 562902901 2.590000e-85 326.0
17 TraesCS3A01G246700 chr1A 86.689 293 29 6 1227 1515 562923320 562923034 1.560000e-82 316.0
18 TraesCS3A01G246700 chr5B 99.153 236 2 0 2085 2320 548556927 548557162 2.480000e-115 425.0
19 TraesCS3A01G246700 chr7A 98.729 236 3 0 2085 2320 727375871 727376106 1.160000e-113 420.0
20 TraesCS3A01G246700 chr4A 98.729 236 3 0 2085 2320 21229741 21229506 1.160000e-113 420.0
21 TraesCS3A01G246700 chr4A 97.479 238 6 0 2085 2322 708433871 708433634 9.000000e-110 407.0
22 TraesCS3A01G246700 chr1D 87.372 293 28 7 1232 1515 469795672 469795964 7.210000e-86 327.0
23 TraesCS3A01G246700 chr1B 86.897 290 32 4 1232 1515 649670329 649670618 1.210000e-83 320.0
24 TraesCS3A01G246700 chr7B 84.444 315 37 10 1213 1515 722094452 722094766 1.570000e-77 300.0
25 TraesCS3A01G246700 chr7D 84.983 293 35 6 1232 1515 561875576 561875868 3.400000e-74 289.0
26 TraesCS3A01G246700 chr7D 72.508 331 69 20 80 400 75579893 75579575 1.330000e-13 87.9
27 TraesCS3A01G246700 chr5A 82.540 315 43 10 1213 1515 69536252 69536566 1.590000e-67 267.0
28 TraesCS3A01G246700 chr2A 92.857 42 2 1 586 627 100816209 100816169 2.900000e-05 60.2


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 TraesCS3A01G246700 chr3A 464795379 464798078 2699 True 2141.50 3145 100.0000 1 2700 2 chr3A.!!$R1 2699
1 TraesCS3A01G246700 chr3B 438929821 438931597 1776 False 984.00 1650 87.2160 306 2697 2 chr3B.!!$F4 2391
2 TraesCS3A01G246700 chr3D 340068534 340070656 2122 False 715.25 1513 92.1325 1 2697 4 chr3D.!!$F2 2696

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
41 42 0.540597 AAGCCCTTGCCAGGAGTTTC 60.541 55.0 5.14 0.0 44.19 2.78 F
1010 1092 0.679002 CTCCCCAAGCCATCACACAG 60.679 60.0 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1687 0.643820 GCGGTGTAAACTTCGATCCG 59.356 55.0 0.00 0.0 39.52 4.18 R
2267 2370 0.108774 GTCCTATGGGGCCTTAGCAC 59.891 60.0 0.84 0.0 43.97 4.40 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
32 33 1.948721 GCATGGTGTAAGCCCTTGCC 61.949 60.000 6.14 0.00 43.64 4.52
41 42 0.540597 AAGCCCTTGCCAGGAGTTTC 60.541 55.000 5.14 0.00 44.19 2.78
63 64 3.713936 CACATTCGTGGTCGAGCTA 57.286 52.632 16.64 0.00 46.81 3.32
147 148 2.508526 GTTGACTGCCTGGATCTTGTT 58.491 47.619 0.00 0.00 0.00 2.83
150 151 4.365514 TGACTGCCTGGATCTTGTTAAA 57.634 40.909 0.00 0.00 0.00 1.52
154 155 6.067217 ACTGCCTGGATCTTGTTAAACTAT 57.933 37.500 0.00 0.00 0.00 2.12
175 176 8.585471 ACTATGGAACTCACATCAAAATTCAT 57.415 30.769 0.00 0.00 0.00 2.57
179 180 7.499292 TGGAACTCACATCAAAATTCATGTTT 58.501 30.769 0.00 0.00 30.48 2.83
181 182 7.652909 GGAACTCACATCAAAATTCATGTTTGA 59.347 33.333 11.15 11.15 46.12 2.69
196 197 3.899981 TTGATTGCGGCGCCTGTCT 62.900 57.895 30.82 9.02 0.00 3.41
279 280 2.052104 CCTGAATTTCCCGGCCCAC 61.052 63.158 0.00 0.00 0.00 4.61
281 282 2.036572 GAATTTCCCGGCCCACCA 59.963 61.111 0.00 0.00 34.57 4.17
291 292 1.907807 GGCCCACCAATGTGCTCAA 60.908 57.895 0.00 0.00 41.35 3.02
314 315 3.244284 TGTGCTTGTACGTTTGAGGGTAT 60.244 43.478 0.00 0.00 0.00 2.73
356 384 4.088634 AGCCCAGATTTTGTCATTAGCAA 58.911 39.130 0.00 0.00 0.00 3.91
377 405 1.208535 CCTACGGGCAGATTGTAACCA 59.791 52.381 0.00 0.00 0.00 3.67
416 452 6.833416 TGAATAAAGTCCCAATTCGATGGAAT 59.167 34.615 6.63 0.00 44.69 3.01
481 519 4.772624 TGTGCCTCTCAACTCTAATGTACT 59.227 41.667 0.00 0.00 0.00 2.73
598 636 1.521450 TTCAGGACACGAGACCGGAC 61.521 60.000 9.46 0.10 40.78 4.79
627 665 1.271597 CCTCCAGAAAGGACCTTGGTG 60.272 57.143 7.72 8.23 43.07 4.17
676 749 2.265182 AACATCCACCGGCCAAACG 61.265 57.895 0.00 0.00 0.00 3.60
761 835 1.683365 GCTGCCCACACCCATGATT 60.683 57.895 0.00 0.00 0.00 2.57
767 841 2.094675 CCCACACCCATGATTTGACTC 58.905 52.381 0.00 0.00 0.00 3.36
873 954 3.403057 CCCGCGACAACTCGTGTG 61.403 66.667 8.23 0.00 46.93 3.82
874 955 4.059459 CCGCGACAACTCGTGTGC 62.059 66.667 8.23 0.00 46.93 4.57
875 956 3.030308 CGCGACAACTCGTGTGCT 61.030 61.111 0.00 0.00 43.97 4.40
876 957 2.546321 GCGACAACTCGTGTGCTG 59.454 61.111 0.00 0.00 41.96 4.41
877 958 2.237751 GCGACAACTCGTGTGCTGT 61.238 57.895 0.00 0.00 41.96 4.40
967 1048 1.687493 CACCTCACCTCCCTCCTCC 60.687 68.421 0.00 0.00 0.00 4.30
989 1071 2.100916 CTGTATATATCGGGCCCCTTCG 59.899 54.545 18.66 4.09 0.00 3.79
1010 1092 0.679002 CTCCCCAAGCCATCACACAG 60.679 60.000 0.00 0.00 0.00 3.66
1018 1100 1.742880 CCATCACACAGACGCCCAG 60.743 63.158 0.00 0.00 0.00 4.45
1020 1102 3.612247 ATCACACAGACGCCCAGCC 62.612 63.158 0.00 0.00 0.00 4.85
1025 1107 4.457496 CAGACGCCCAGCCATCGT 62.457 66.667 0.00 0.00 39.33 3.73
1026 1108 4.457496 AGACGCCCAGCCATCGTG 62.457 66.667 0.00 0.00 36.50 4.35
1044 1126 3.010767 CACACGAACCACACACCG 58.989 61.111 0.00 0.00 0.00 4.94
1071 1153 1.705745 GACAGGGAAAAGAGGGAAGGT 59.294 52.381 0.00 0.00 0.00 3.50
1109 1212 1.578926 GTGCGCAATGTACCAAGCA 59.421 52.632 14.00 0.00 0.00 3.91
1584 1687 1.712018 GCGGTTTAATCCTGGCCGTC 61.712 60.000 0.00 0.21 43.78 4.79
1593 1696 2.278857 CTGGCCGTCGGATCGAAG 60.279 66.667 17.49 0.00 37.72 3.79
1649 1752 5.777732 TGGGTTTCTTTAATGGTGTGCTAAT 59.222 36.000 0.00 0.00 0.00 1.73
2109 2212 7.882179 CAATCTATTCATCTTCAATCATGGCA 58.118 34.615 0.00 0.00 0.00 4.92
2110 2213 7.689446 ATCTATTCATCTTCAATCATGGCAG 57.311 36.000 0.00 0.00 0.00 4.85
2111 2214 6.598503 TCTATTCATCTTCAATCATGGCAGT 58.401 36.000 0.00 0.00 0.00 4.40
2112 2215 7.738847 TCTATTCATCTTCAATCATGGCAGTA 58.261 34.615 0.00 0.00 0.00 2.74
2113 2216 6.630444 ATTCATCTTCAATCATGGCAGTAC 57.370 37.500 0.00 0.00 0.00 2.73
2114 2217 5.101648 TCATCTTCAATCATGGCAGTACA 57.898 39.130 0.00 0.00 0.00 2.90
2115 2218 5.499313 TCATCTTCAATCATGGCAGTACAA 58.501 37.500 0.00 0.00 0.00 2.41
2116 2219 5.355071 TCATCTTCAATCATGGCAGTACAAC 59.645 40.000 0.00 0.00 0.00 3.32
2117 2220 3.684305 TCTTCAATCATGGCAGTACAACG 59.316 43.478 0.00 0.00 0.00 4.10
2118 2221 3.326836 TCAATCATGGCAGTACAACGA 57.673 42.857 0.00 0.00 0.00 3.85
2119 2222 3.669536 TCAATCATGGCAGTACAACGAA 58.330 40.909 0.00 0.00 0.00 3.85
2120 2223 4.260985 TCAATCATGGCAGTACAACGAAT 58.739 39.130 0.00 0.00 0.00 3.34
2121 2224 5.423886 TCAATCATGGCAGTACAACGAATA 58.576 37.500 0.00 0.00 0.00 1.75
2122 2225 5.293324 TCAATCATGGCAGTACAACGAATAC 59.707 40.000 0.00 0.00 0.00 1.89
2123 2226 3.527533 TCATGGCAGTACAACGAATACC 58.472 45.455 0.00 0.00 0.00 2.73
2124 2227 3.055747 TCATGGCAGTACAACGAATACCA 60.056 43.478 0.00 0.00 0.00 3.25
2125 2228 2.967362 TGGCAGTACAACGAATACCAG 58.033 47.619 0.00 0.00 0.00 4.00
2126 2229 2.563620 TGGCAGTACAACGAATACCAGA 59.436 45.455 0.00 0.00 0.00 3.86
2127 2230 3.007074 TGGCAGTACAACGAATACCAGAA 59.993 43.478 0.00 0.00 0.00 3.02
2128 2231 3.998341 GGCAGTACAACGAATACCAGAAA 59.002 43.478 0.00 0.00 0.00 2.52
2129 2232 4.634443 GGCAGTACAACGAATACCAGAAAT 59.366 41.667 0.00 0.00 0.00 2.17
2130 2233 5.813672 GGCAGTACAACGAATACCAGAAATA 59.186 40.000 0.00 0.00 0.00 1.40
2131 2234 6.314400 GGCAGTACAACGAATACCAGAAATAA 59.686 38.462 0.00 0.00 0.00 1.40
2132 2235 7.148373 GGCAGTACAACGAATACCAGAAATAAA 60.148 37.037 0.00 0.00 0.00 1.40
2133 2236 8.231837 GCAGTACAACGAATACCAGAAATAAAA 58.768 33.333 0.00 0.00 0.00 1.52
2157 2260 9.705290 AAAATTACAACCAGAATCATAAACCAC 57.295 29.630 0.00 0.00 0.00 4.16
2158 2261 6.827586 TTACAACCAGAATCATAAACCACC 57.172 37.500 0.00 0.00 0.00 4.61
2159 2262 4.998051 ACAACCAGAATCATAAACCACCT 58.002 39.130 0.00 0.00 0.00 4.00
2160 2263 6.134535 ACAACCAGAATCATAAACCACCTA 57.865 37.500 0.00 0.00 0.00 3.08
2161 2264 6.180472 ACAACCAGAATCATAAACCACCTAG 58.820 40.000 0.00 0.00 0.00 3.02
2162 2265 4.781934 ACCAGAATCATAAACCACCTAGC 58.218 43.478 0.00 0.00 0.00 3.42
2163 2266 3.809832 CCAGAATCATAAACCACCTAGCG 59.190 47.826 0.00 0.00 0.00 4.26
2164 2267 4.442893 CCAGAATCATAAACCACCTAGCGA 60.443 45.833 0.00 0.00 0.00 4.93
2165 2268 4.508124 CAGAATCATAAACCACCTAGCGAC 59.492 45.833 0.00 0.00 0.00 5.19
2166 2269 2.572191 TCATAAACCACCTAGCGACG 57.428 50.000 0.00 0.00 0.00 5.12
2167 2270 2.093890 TCATAAACCACCTAGCGACGA 58.906 47.619 0.00 0.00 0.00 4.20
2168 2271 2.159338 TCATAAACCACCTAGCGACGAC 60.159 50.000 0.00 0.00 0.00 4.34
2169 2272 1.538047 TAAACCACCTAGCGACGACT 58.462 50.000 0.00 0.00 0.00 4.18
2170 2273 1.538047 AAACCACCTAGCGACGACTA 58.462 50.000 0.00 0.00 0.00 2.59
2171 2274 0.807496 AACCACCTAGCGACGACTAC 59.193 55.000 0.00 0.00 0.00 2.73
2172 2275 0.321919 ACCACCTAGCGACGACTACA 60.322 55.000 0.00 0.00 0.00 2.74
2173 2276 0.806868 CCACCTAGCGACGACTACAA 59.193 55.000 0.00 0.00 0.00 2.41
2174 2277 1.202154 CCACCTAGCGACGACTACAAG 60.202 57.143 0.00 0.00 0.00 3.16
2175 2278 0.450983 ACCTAGCGACGACTACAAGC 59.549 55.000 0.00 0.00 0.00 4.01
2176 2279 0.450583 CCTAGCGACGACTACAAGCA 59.549 55.000 0.00 0.00 0.00 3.91
2177 2280 1.536149 CTAGCGACGACTACAAGCAC 58.464 55.000 0.00 0.00 0.00 4.40
2178 2281 0.169672 TAGCGACGACTACAAGCACC 59.830 55.000 0.00 0.00 0.00 5.01
2179 2282 2.434134 GCGACGACTACAAGCACCG 61.434 63.158 0.00 0.00 0.00 4.94
2180 2283 1.208358 CGACGACTACAAGCACCGA 59.792 57.895 0.00 0.00 0.00 4.69
2181 2284 0.386352 CGACGACTACAAGCACCGAA 60.386 55.000 0.00 0.00 0.00 4.30
2182 2285 1.337821 GACGACTACAAGCACCGAAG 58.662 55.000 0.00 0.00 0.00 3.79
2183 2286 0.666577 ACGACTACAAGCACCGAAGC 60.667 55.000 0.00 0.00 0.00 3.86
2184 2287 1.674611 CGACTACAAGCACCGAAGCG 61.675 60.000 0.00 0.00 40.15 4.68
2185 2288 0.388134 GACTACAAGCACCGAAGCGA 60.388 55.000 0.00 0.00 40.15 4.93
2186 2289 0.388649 ACTACAAGCACCGAAGCGAG 60.389 55.000 0.00 0.00 40.15 5.03
2187 2290 1.687494 CTACAAGCACCGAAGCGAGC 61.687 60.000 0.00 0.00 40.15 5.03
2188 2291 3.793144 CAAGCACCGAAGCGAGCC 61.793 66.667 0.00 0.00 40.15 4.70
2192 2295 3.181967 CACCGAAGCGAGCCGAAG 61.182 66.667 0.00 0.00 0.00 3.79
2218 2321 3.550431 CCGTCATCGCCCCTCCAT 61.550 66.667 0.00 0.00 35.54 3.41
2219 2322 2.029666 CGTCATCGCCCCTCCATC 59.970 66.667 0.00 0.00 0.00 3.51
2220 2323 2.029666 GTCATCGCCCCTCCATCG 59.970 66.667 0.00 0.00 0.00 3.84
2221 2324 3.928779 TCATCGCCCCTCCATCGC 61.929 66.667 0.00 0.00 0.00 4.58
2222 2325 4.996434 CATCGCCCCTCCATCGCC 62.996 72.222 0.00 0.00 0.00 5.54
2240 2343 3.365265 GGAGCCGGGCACAACTTG 61.365 66.667 23.09 0.00 0.00 3.16
2241 2344 2.594592 GAGCCGGGCACAACTTGT 60.595 61.111 23.09 0.00 0.00 3.16
2242 2345 2.123897 AGCCGGGCACAACTTGTT 60.124 55.556 23.09 0.00 0.00 2.83
2243 2346 2.027460 GCCGGGCACAACTTGTTG 59.973 61.111 15.62 11.44 0.00 3.33
2244 2347 2.781158 GCCGGGCACAACTTGTTGT 61.781 57.895 15.62 12.73 35.14 3.32
2245 2348 1.448922 GCCGGGCACAACTTGTTGTA 61.449 55.000 15.62 0.00 33.17 2.41
2246 2349 0.591170 CCGGGCACAACTTGTTGTAG 59.409 55.000 17.26 12.96 33.17 2.74
2247 2350 1.305201 CGGGCACAACTTGTTGTAGT 58.695 50.000 17.26 0.00 33.17 2.73
2248 2351 2.485903 CGGGCACAACTTGTTGTAGTA 58.514 47.619 17.26 0.00 33.17 1.82
2249 2352 2.478894 CGGGCACAACTTGTTGTAGTAG 59.521 50.000 17.26 7.80 33.17 2.57
2250 2353 3.735591 GGGCACAACTTGTTGTAGTAGA 58.264 45.455 17.26 0.00 33.17 2.59
2251 2354 3.497262 GGGCACAACTTGTTGTAGTAGAC 59.503 47.826 17.26 8.51 33.17 2.59
2252 2355 4.124238 GGCACAACTTGTTGTAGTAGACA 58.876 43.478 17.26 0.00 35.78 3.41
2253 2356 4.211374 GGCACAACTTGTTGTAGTAGACAG 59.789 45.833 17.26 5.63 39.88 3.51
2254 2357 4.809426 GCACAACTTGTTGTAGTAGACAGT 59.191 41.667 17.26 0.00 39.88 3.55
2255 2358 5.050972 GCACAACTTGTTGTAGTAGACAGTC 60.051 44.000 17.26 0.00 39.88 3.51
2256 2359 5.173312 CACAACTTGTTGTAGTAGACAGTCG 59.827 44.000 17.26 0.00 39.88 4.18
2257 2360 4.500603 ACTTGTTGTAGTAGACAGTCGG 57.499 45.455 0.00 0.00 39.88 4.79
2258 2361 3.255149 ACTTGTTGTAGTAGACAGTCGGG 59.745 47.826 0.00 0.00 39.88 5.14
2259 2362 3.144657 TGTTGTAGTAGACAGTCGGGA 57.855 47.619 0.00 0.00 39.88 5.14
2260 2363 3.489355 TGTTGTAGTAGACAGTCGGGAA 58.511 45.455 0.00 0.00 39.88 3.97
2261 2364 3.504906 TGTTGTAGTAGACAGTCGGGAAG 59.495 47.826 0.00 0.00 39.88 3.46
2262 2365 3.430042 TGTAGTAGACAGTCGGGAAGT 57.570 47.619 0.00 0.00 32.86 3.01
2263 2366 3.341823 TGTAGTAGACAGTCGGGAAGTC 58.658 50.000 0.00 0.00 32.86 3.01
2264 2367 1.451067 AGTAGACAGTCGGGAAGTCG 58.549 55.000 0.00 0.00 37.36 4.18
2265 2368 1.163554 GTAGACAGTCGGGAAGTCGT 58.836 55.000 0.00 0.00 37.36 4.34
2266 2369 1.130186 GTAGACAGTCGGGAAGTCGTC 59.870 57.143 0.00 0.00 37.36 4.20
2267 2370 1.154263 GACAGTCGGGAAGTCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
2268 2371 1.849976 GACAGTCGGGAAGTCGTCGT 61.850 60.000 0.00 0.00 0.00 4.34
2269 2372 1.442184 CAGTCGGGAAGTCGTCGTG 60.442 63.158 0.00 0.00 0.00 4.35
2270 2373 2.804090 GTCGGGAAGTCGTCGTGC 60.804 66.667 0.00 0.00 0.00 5.34
2271 2374 2.981909 TCGGGAAGTCGTCGTGCT 60.982 61.111 0.00 0.00 0.00 4.40
2272 2375 1.672030 TCGGGAAGTCGTCGTGCTA 60.672 57.895 0.00 0.00 0.00 3.49
2273 2376 1.210931 CGGGAAGTCGTCGTGCTAA 59.789 57.895 0.00 0.00 0.00 3.09
2274 2377 0.797249 CGGGAAGTCGTCGTGCTAAG 60.797 60.000 0.00 0.00 0.00 2.18
2275 2378 0.458025 GGGAAGTCGTCGTGCTAAGG 60.458 60.000 0.00 0.00 0.00 2.69
2276 2379 1.077089 GGAAGTCGTCGTGCTAAGGC 61.077 60.000 0.00 0.00 39.26 4.35
2277 2380 1.077089 GAAGTCGTCGTGCTAAGGCC 61.077 60.000 0.00 0.00 37.74 5.19
2278 2381 2.502692 AAGTCGTCGTGCTAAGGCCC 62.503 60.000 0.00 0.00 37.74 5.80
2279 2382 3.766691 TCGTCGTGCTAAGGCCCC 61.767 66.667 0.00 0.00 37.74 5.80
2280 2383 4.077184 CGTCGTGCTAAGGCCCCA 62.077 66.667 0.00 0.00 37.74 4.96
2281 2384 2.590092 GTCGTGCTAAGGCCCCAT 59.410 61.111 0.00 0.00 37.74 4.00
2282 2385 1.827394 GTCGTGCTAAGGCCCCATA 59.173 57.895 0.00 0.00 37.74 2.74
2283 2386 0.249911 GTCGTGCTAAGGCCCCATAG 60.250 60.000 0.00 0.67 37.74 2.23
2284 2387 1.071471 CGTGCTAAGGCCCCATAGG 59.929 63.158 0.00 0.00 37.74 2.57
2285 2388 1.407656 CGTGCTAAGGCCCCATAGGA 61.408 60.000 0.00 0.00 38.24 2.94
2291 2394 3.096495 GGCCCCATAGGACCAGCA 61.096 66.667 0.00 0.00 37.96 4.41
2292 2395 2.193248 GCCCCATAGGACCAGCAC 59.807 66.667 0.00 0.00 38.24 4.40
2293 2396 2.919043 CCCCATAGGACCAGCACC 59.081 66.667 0.00 0.00 38.24 5.01
2294 2397 2.757124 CCCCATAGGACCAGCACCC 61.757 68.421 0.00 0.00 38.24 4.61
2295 2398 2.757124 CCCATAGGACCAGCACCCC 61.757 68.421 0.00 0.00 33.47 4.95
2296 2399 2.000701 CCATAGGACCAGCACCCCA 61.001 63.158 0.00 0.00 0.00 4.96
2297 2400 1.528824 CATAGGACCAGCACCCCAG 59.471 63.158 0.00 0.00 0.00 4.45
2298 2401 0.982852 CATAGGACCAGCACCCCAGA 60.983 60.000 0.00 0.00 0.00 3.86
2299 2402 0.253160 ATAGGACCAGCACCCCAGAA 60.253 55.000 0.00 0.00 0.00 3.02
2300 2403 1.198759 TAGGACCAGCACCCCAGAAC 61.199 60.000 0.00 0.00 0.00 3.01
2301 2404 2.829384 GGACCAGCACCCCAGAACA 61.829 63.158 0.00 0.00 0.00 3.18
2302 2405 1.302832 GACCAGCACCCCAGAACAG 60.303 63.158 0.00 0.00 0.00 3.16
2303 2406 2.056906 GACCAGCACCCCAGAACAGT 62.057 60.000 0.00 0.00 0.00 3.55
2304 2407 0.766674 ACCAGCACCCCAGAACAGTA 60.767 55.000 0.00 0.00 0.00 2.74
2305 2408 0.400213 CCAGCACCCCAGAACAGTAA 59.600 55.000 0.00 0.00 0.00 2.24
2306 2409 1.523758 CAGCACCCCAGAACAGTAAC 58.476 55.000 0.00 0.00 0.00 2.50
2307 2410 0.400594 AGCACCCCAGAACAGTAACC 59.599 55.000 0.00 0.00 0.00 2.85
2308 2411 0.953960 GCACCCCAGAACAGTAACCG 60.954 60.000 0.00 0.00 0.00 4.44
2309 2412 0.953960 CACCCCAGAACAGTAACCGC 60.954 60.000 0.00 0.00 0.00 5.68
2310 2413 1.376812 CCCCAGAACAGTAACCGCC 60.377 63.158 0.00 0.00 0.00 6.13
2311 2414 1.740296 CCCAGAACAGTAACCGCCG 60.740 63.158 0.00 0.00 0.00 6.46
2312 2415 2.388232 CCAGAACAGTAACCGCCGC 61.388 63.158 0.00 0.00 0.00 6.53
2313 2416 2.047560 AGAACAGTAACCGCCGCC 60.048 61.111 0.00 0.00 0.00 6.13
2314 2417 3.484547 GAACAGTAACCGCCGCCG 61.485 66.667 0.00 0.00 0.00 6.46
2315 2418 3.919973 GAACAGTAACCGCCGCCGA 62.920 63.158 0.00 0.00 36.29 5.54
2316 2419 3.305177 AACAGTAACCGCCGCCGAT 62.305 57.895 0.00 0.00 36.29 4.18
2317 2420 3.261951 CAGTAACCGCCGCCGATG 61.262 66.667 0.00 0.00 36.29 3.84
2318 2421 3.454573 AGTAACCGCCGCCGATGA 61.455 61.111 0.00 0.00 36.29 2.92
2319 2422 2.509786 GTAACCGCCGCCGATGAA 60.510 61.111 0.00 0.00 36.29 2.57
2320 2423 2.202824 TAACCGCCGCCGATGAAG 60.203 61.111 0.00 0.00 36.29 3.02
2321 2424 2.712944 TAACCGCCGCCGATGAAGA 61.713 57.895 0.00 0.00 36.29 2.87
2322 2425 2.023414 TAACCGCCGCCGATGAAGAT 62.023 55.000 0.00 0.00 36.29 2.40
2323 2426 2.588877 CCGCCGCCGATGAAGATT 60.589 61.111 0.00 0.00 36.29 2.40
2324 2427 2.180204 CCGCCGCCGATGAAGATTT 61.180 57.895 0.00 0.00 36.29 2.17
2325 2428 1.714899 CCGCCGCCGATGAAGATTTT 61.715 55.000 0.00 0.00 36.29 1.82
2326 2429 0.589729 CGCCGCCGATGAAGATTTTG 60.590 55.000 0.00 0.00 36.29 2.44
2327 2430 0.248621 GCCGCCGATGAAGATTTTGG 60.249 55.000 0.00 0.00 0.00 3.28
2328 2431 1.094785 CCGCCGATGAAGATTTTGGT 58.905 50.000 0.00 0.00 0.00 3.67
2329 2432 2.285083 CCGCCGATGAAGATTTTGGTA 58.715 47.619 0.00 0.00 0.00 3.25
2330 2433 2.680841 CCGCCGATGAAGATTTTGGTAA 59.319 45.455 0.00 0.00 0.00 2.85
2354 2457 7.553881 AGTAATTTATTTCGTCTGGTCATGG 57.446 36.000 0.00 0.00 0.00 3.66
2365 2468 1.407618 CTGGTCATGGGCATGTGAATG 59.592 52.381 0.00 0.00 39.72 2.67
2366 2469 1.005687 TGGTCATGGGCATGTGAATGA 59.994 47.619 0.00 0.00 39.72 2.57
2367 2470 1.679680 GGTCATGGGCATGTGAATGAG 59.320 52.381 6.59 0.00 39.72 2.90
2368 2471 2.372264 GTCATGGGCATGTGAATGAGT 58.628 47.619 6.59 0.00 39.72 3.41
2433 2563 5.734720 AGAATCAGATGCTTCTTACGGAAA 58.265 37.500 0.00 0.00 33.07 3.13
2461 2591 2.533266 CTGCGGCCTGAAATTTCATTC 58.467 47.619 20.76 14.52 36.46 2.67
2465 2595 2.223340 CGGCCTGAAATTTCATTCTCCG 60.223 50.000 20.76 22.38 36.46 4.63
2493 2626 5.710513 TCAGTTAACAAGTTAGGCGTCTA 57.289 39.130 8.61 0.00 0.00 2.59
2522 2655 0.997196 GGTACACGGACGCTTGATTC 59.003 55.000 0.00 0.00 0.00 2.52
2543 2676 3.380004 TCAAGTCATGGTTGGTTGTTGAC 59.620 43.478 8.36 0.00 37.54 3.18
2548 2681 4.037923 GTCATGGTTGGTTGTTGACAAGAT 59.962 41.667 0.00 0.00 37.30 2.40
2549 2682 4.648762 TCATGGTTGGTTGTTGACAAGATT 59.351 37.500 0.00 0.00 36.39 2.40
2557 2690 7.447374 TGGTTGTTGACAAGATTTATAGGTG 57.553 36.000 0.00 0.00 36.39 4.00
2627 2763 5.715434 TTCATGTGTGTACAGTACAGCTA 57.285 39.130 14.03 3.68 40.79 3.32
2629 2765 3.928727 TGTGTGTACAGTACAGCTACC 57.071 47.619 14.03 2.67 39.77 3.18
2655 2791 3.117701 TCCATTCCAGTCCAACTGTTTCA 60.118 43.478 6.37 0.00 44.50 2.69
2662 2798 4.638421 CCAGTCCAACTGTTTCAGTGTTTA 59.362 41.667 3.12 0.00 44.62 2.01
2671 2807 3.880490 TGTTTCAGTGTTTAGTTGCGGAT 59.120 39.130 0.00 0.00 0.00 4.18
2682 2818 9.481800 GTGTTTAGTTGCGGATTACTAATAAAC 57.518 33.333 2.57 2.73 36.89 2.01
2685 2821 8.967664 TTAGTTGCGGATTACTAATAAACCAT 57.032 30.769 0.00 0.00 33.76 3.55
2687 2823 6.485648 AGTTGCGGATTACTAATAAACCATCC 59.514 38.462 0.00 0.00 33.76 3.51
2693 2829 9.231297 CGGATTACTAATAAACCATCCATCAAT 57.769 33.333 0.00 0.00 33.76 2.57
2698 2834 8.821686 ACTAATAAACCATCCATCAATCAACA 57.178 30.769 0.00 0.00 0.00 3.33
2699 2835 9.253832 ACTAATAAACCATCCATCAATCAACAA 57.746 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.774110 ACACCATGCACCAAGAAACA 58.226 45.000 0.00 0.00 0.00 2.83
32 33 1.726791 CGAATGTGTCGGAAACTCCTG 59.273 52.381 0.00 0.00 46.45 3.86
63 64 1.008938 ACCCCTTCTCTCATAGCCAGT 59.991 52.381 0.00 0.00 0.00 4.00
71 72 2.103373 CGAAGATCACCCCTTCTCTCA 58.897 52.381 0.00 0.00 38.23 3.27
127 128 2.191128 ACAAGATCCAGGCAGTCAAC 57.809 50.000 0.00 0.00 0.00 3.18
150 151 8.464404 CATGAATTTTGATGTGAGTTCCATAGT 58.536 33.333 0.00 0.00 0.00 2.12
154 155 6.653526 ACATGAATTTTGATGTGAGTTCCA 57.346 33.333 0.00 0.00 33.73 3.53
175 176 2.983030 AGGCGCCGCAATCAAACA 60.983 55.556 23.20 0.00 0.00 2.83
179 180 2.514510 TAAGACAGGCGCCGCAATCA 62.515 55.000 23.20 3.43 0.00 2.57
181 182 2.106683 GTAAGACAGGCGCCGCAAT 61.107 57.895 23.20 7.76 0.00 3.56
196 197 6.321181 GGCATAACATCCTCCAATTCTTGTAA 59.679 38.462 0.00 0.00 0.00 2.41
230 231 5.521735 CCAACATGATGAACCGAAAACAAAA 59.478 36.000 4.25 0.00 0.00 2.44
263 264 2.036572 GGTGGGCCGGGAAATTCA 59.963 61.111 2.18 0.00 0.00 2.57
265 266 1.080170 ATTGGTGGGCCGGGAAATT 59.920 52.632 2.18 0.00 37.67 1.82
279 280 2.288579 ACAAGCACATTGAGCACATTGG 60.289 45.455 8.78 2.00 41.83 3.16
281 282 3.365264 CGTACAAGCACATTGAGCACATT 60.365 43.478 8.78 0.00 41.83 2.71
291 292 2.151202 CCCTCAAACGTACAAGCACAT 58.849 47.619 0.00 0.00 0.00 3.21
420 456 4.279671 ACAAATCACTGGTGCGGATAAAAA 59.720 37.500 0.00 0.00 0.00 1.94
421 457 3.823873 ACAAATCACTGGTGCGGATAAAA 59.176 39.130 0.00 0.00 0.00 1.52
422 458 3.190327 CACAAATCACTGGTGCGGATAAA 59.810 43.478 0.00 0.00 0.00 1.40
423 459 2.746904 CACAAATCACTGGTGCGGATAA 59.253 45.455 0.00 0.00 0.00 1.75
424 460 2.355197 CACAAATCACTGGTGCGGATA 58.645 47.619 0.00 0.00 0.00 2.59
598 636 2.104792 TCCTTTCTGGAGGACAACACTG 59.895 50.000 0.00 0.00 40.87 3.66
627 665 2.915738 CTCTGGCTTTGTTGAGCATC 57.084 50.000 0.00 0.00 44.49 3.91
676 749 1.644786 CGGAGTGTGGAATTTCGGGC 61.645 60.000 0.00 0.00 0.00 6.13
752 826 2.379907 AGTTGGGAGTCAAATCATGGGT 59.620 45.455 0.00 0.00 37.08 4.51
761 835 1.444119 GCGTTGCAGTTGGGAGTCAA 61.444 55.000 0.00 0.00 0.00 3.18
918 999 2.106332 AGCACGGCGGTAGTATGC 59.894 61.111 13.24 11.10 36.52 3.14
967 1048 2.176247 AGGGGCCCGATATATACAGG 57.824 55.000 18.95 0.00 0.00 4.00
1025 1107 2.109739 GGTGTGTGGTTCGTGTGCA 61.110 57.895 0.00 0.00 0.00 4.57
1026 1108 2.713154 GGTGTGTGGTTCGTGTGC 59.287 61.111 0.00 0.00 0.00 4.57
1044 1126 0.889186 TCTTTTCCCTGTCTTGCGCC 60.889 55.000 4.18 0.00 0.00 6.53
1071 1153 1.379443 ACTACGTGGATGCTCCCGA 60.379 57.895 5.70 4.27 35.03 5.14
1089 1192 1.861542 GCTTGGTACATTGCGCACCA 61.862 55.000 11.12 11.82 40.55 4.17
1109 1212 1.609783 GGTGCTGCTGTAGGGGATT 59.390 57.895 0.00 0.00 0.00 3.01
1409 1512 4.436998 AGCTTCCCGCCGACGAAG 62.437 66.667 8.87 8.87 43.93 3.79
1418 1521 3.532155 CCTCCGAGGAGCTTCCCG 61.532 72.222 9.01 0.00 37.67 5.14
1584 1687 0.643820 GCGGTGTAAACTTCGATCCG 59.356 55.000 0.00 0.00 39.52 4.18
1593 1696 1.914531 AAATCGGCCGCGGTGTAAAC 61.915 55.000 28.70 8.51 0.00 2.01
2084 2187 7.882179 TGCCATGATTGAAGATGAATAGATTG 58.118 34.615 0.00 0.00 0.00 2.67
2085 2188 7.724506 ACTGCCATGATTGAAGATGAATAGATT 59.275 33.333 0.00 0.00 0.00 2.40
2086 2189 7.232188 ACTGCCATGATTGAAGATGAATAGAT 58.768 34.615 0.00 0.00 0.00 1.98
2087 2190 6.598503 ACTGCCATGATTGAAGATGAATAGA 58.401 36.000 0.00 0.00 0.00 1.98
2088 2191 6.879276 ACTGCCATGATTGAAGATGAATAG 57.121 37.500 0.00 0.00 0.00 1.73
2089 2192 7.281841 TGTACTGCCATGATTGAAGATGAATA 58.718 34.615 0.00 0.00 0.00 1.75
2090 2193 6.124340 TGTACTGCCATGATTGAAGATGAAT 58.876 36.000 0.00 0.00 0.00 2.57
2091 2194 5.499313 TGTACTGCCATGATTGAAGATGAA 58.501 37.500 0.00 0.00 0.00 2.57
2092 2195 5.101648 TGTACTGCCATGATTGAAGATGA 57.898 39.130 0.00 0.00 0.00 2.92
2093 2196 5.575957 GTTGTACTGCCATGATTGAAGATG 58.424 41.667 0.00 0.00 0.00 2.90
2094 2197 4.333649 CGTTGTACTGCCATGATTGAAGAT 59.666 41.667 0.00 0.00 0.00 2.40
2095 2198 3.684305 CGTTGTACTGCCATGATTGAAGA 59.316 43.478 0.00 0.00 0.00 2.87
2096 2199 3.684305 TCGTTGTACTGCCATGATTGAAG 59.316 43.478 0.00 0.00 0.00 3.02
2097 2200 3.669536 TCGTTGTACTGCCATGATTGAA 58.330 40.909 0.00 0.00 0.00 2.69
2098 2201 3.326836 TCGTTGTACTGCCATGATTGA 57.673 42.857 0.00 0.00 0.00 2.57
2099 2202 4.621068 ATTCGTTGTACTGCCATGATTG 57.379 40.909 0.00 0.00 0.00 2.67
2100 2203 4.574828 GGTATTCGTTGTACTGCCATGATT 59.425 41.667 0.00 0.00 0.00 2.57
2101 2204 4.127171 GGTATTCGTTGTACTGCCATGAT 58.873 43.478 0.00 0.00 0.00 2.45
2102 2205 3.055747 TGGTATTCGTTGTACTGCCATGA 60.056 43.478 0.00 0.00 0.00 3.07
2103 2206 3.266636 TGGTATTCGTTGTACTGCCATG 58.733 45.455 0.00 0.00 0.00 3.66
2104 2207 3.196901 TCTGGTATTCGTTGTACTGCCAT 59.803 43.478 0.00 0.00 0.00 4.40
2105 2208 2.563620 TCTGGTATTCGTTGTACTGCCA 59.436 45.455 0.00 0.00 0.00 4.92
2106 2209 3.241067 TCTGGTATTCGTTGTACTGCC 57.759 47.619 0.00 0.00 0.00 4.85
2107 2210 5.796350 ATTTCTGGTATTCGTTGTACTGC 57.204 39.130 0.00 0.00 0.00 4.40
2131 2234 9.705290 GTGGTTTATGATTCTGGTTGTAATTTT 57.295 29.630 0.00 0.00 0.00 1.82
2132 2235 8.311109 GGTGGTTTATGATTCTGGTTGTAATTT 58.689 33.333 0.00 0.00 0.00 1.82
2133 2236 7.673926 AGGTGGTTTATGATTCTGGTTGTAATT 59.326 33.333 0.00 0.00 0.00 1.40
2134 2237 7.182060 AGGTGGTTTATGATTCTGGTTGTAAT 58.818 34.615 0.00 0.00 0.00 1.89
2135 2238 6.548321 AGGTGGTTTATGATTCTGGTTGTAA 58.452 36.000 0.00 0.00 0.00 2.41
2136 2239 6.134535 AGGTGGTTTATGATTCTGGTTGTA 57.865 37.500 0.00 0.00 0.00 2.41
2137 2240 4.998051 AGGTGGTTTATGATTCTGGTTGT 58.002 39.130 0.00 0.00 0.00 3.32
2138 2241 5.066505 GCTAGGTGGTTTATGATTCTGGTTG 59.933 44.000 0.00 0.00 0.00 3.77
2139 2242 5.193679 GCTAGGTGGTTTATGATTCTGGTT 58.806 41.667 0.00 0.00 0.00 3.67
2140 2243 4.683400 CGCTAGGTGGTTTATGATTCTGGT 60.683 45.833 0.00 0.00 0.00 4.00
2141 2244 3.809832 CGCTAGGTGGTTTATGATTCTGG 59.190 47.826 0.00 0.00 0.00 3.86
2142 2245 4.508124 GTCGCTAGGTGGTTTATGATTCTG 59.492 45.833 0.00 0.00 0.00 3.02
2143 2246 4.694339 GTCGCTAGGTGGTTTATGATTCT 58.306 43.478 0.00 0.00 0.00 2.40
2144 2247 3.489785 CGTCGCTAGGTGGTTTATGATTC 59.510 47.826 0.00 0.00 0.00 2.52
2145 2248 3.131577 TCGTCGCTAGGTGGTTTATGATT 59.868 43.478 0.00 0.00 0.00 2.57
2146 2249 2.691526 TCGTCGCTAGGTGGTTTATGAT 59.308 45.455 0.00 0.00 0.00 2.45
2147 2250 2.093890 TCGTCGCTAGGTGGTTTATGA 58.906 47.619 0.00 0.00 0.00 2.15
2148 2251 2.159282 AGTCGTCGCTAGGTGGTTTATG 60.159 50.000 0.00 0.00 0.00 1.90
2149 2252 2.097825 AGTCGTCGCTAGGTGGTTTAT 58.902 47.619 0.00 0.00 0.00 1.40
2150 2253 1.538047 AGTCGTCGCTAGGTGGTTTA 58.462 50.000 0.00 0.00 0.00 2.01
2151 2254 1.200948 GTAGTCGTCGCTAGGTGGTTT 59.799 52.381 0.00 0.00 0.00 3.27
2152 2255 0.807496 GTAGTCGTCGCTAGGTGGTT 59.193 55.000 0.00 0.00 0.00 3.67
2153 2256 0.321919 TGTAGTCGTCGCTAGGTGGT 60.322 55.000 0.00 0.00 0.00 4.16
2154 2257 0.806868 TTGTAGTCGTCGCTAGGTGG 59.193 55.000 0.00 0.00 0.00 4.61
2155 2258 1.794437 GCTTGTAGTCGTCGCTAGGTG 60.794 57.143 0.00 0.00 0.00 4.00
2156 2259 0.450983 GCTTGTAGTCGTCGCTAGGT 59.549 55.000 0.00 0.00 0.00 3.08
2157 2260 0.450583 TGCTTGTAGTCGTCGCTAGG 59.549 55.000 0.00 0.00 0.00 3.02
2158 2261 1.536149 GTGCTTGTAGTCGTCGCTAG 58.464 55.000 0.00 0.00 0.00 3.42
2159 2262 0.169672 GGTGCTTGTAGTCGTCGCTA 59.830 55.000 0.00 0.00 0.00 4.26
2160 2263 1.080705 GGTGCTTGTAGTCGTCGCT 60.081 57.895 0.00 0.00 0.00 4.93
2161 2264 2.434134 CGGTGCTTGTAGTCGTCGC 61.434 63.158 0.00 0.00 0.00 5.19
2162 2265 0.386352 TTCGGTGCTTGTAGTCGTCG 60.386 55.000 0.00 0.00 0.00 5.12
2163 2266 1.337821 CTTCGGTGCTTGTAGTCGTC 58.662 55.000 0.00 0.00 0.00 4.20
2164 2267 0.666577 GCTTCGGTGCTTGTAGTCGT 60.667 55.000 0.00 0.00 0.00 4.34
2165 2268 1.674611 CGCTTCGGTGCTTGTAGTCG 61.675 60.000 0.00 0.00 0.00 4.18
2166 2269 0.388134 TCGCTTCGGTGCTTGTAGTC 60.388 55.000 0.00 0.00 0.00 2.59
2167 2270 0.388649 CTCGCTTCGGTGCTTGTAGT 60.389 55.000 0.00 0.00 0.00 2.73
2168 2271 1.687494 GCTCGCTTCGGTGCTTGTAG 61.687 60.000 0.00 0.00 0.00 2.74
2169 2272 1.736645 GCTCGCTTCGGTGCTTGTA 60.737 57.895 0.00 0.00 0.00 2.41
2170 2273 3.044305 GCTCGCTTCGGTGCTTGT 61.044 61.111 0.00 0.00 0.00 3.16
2171 2274 3.793144 GGCTCGCTTCGGTGCTTG 61.793 66.667 0.00 0.00 0.00 4.01
2175 2278 3.181967 CTTCGGCTCGCTTCGGTG 61.182 66.667 0.00 0.00 0.00 4.94
2176 2279 4.436998 CCTTCGGCTCGCTTCGGT 62.437 66.667 0.00 0.00 0.00 4.69
2201 2304 3.521529 GATGGAGGGGCGATGACGG 62.522 68.421 0.00 0.00 40.15 4.79
2202 2305 2.029666 GATGGAGGGGCGATGACG 59.970 66.667 0.00 0.00 42.93 4.35
2203 2306 2.029666 CGATGGAGGGGCGATGAC 59.970 66.667 0.00 0.00 0.00 3.06
2204 2307 3.928779 GCGATGGAGGGGCGATGA 61.929 66.667 0.00 0.00 0.00 2.92
2205 2308 4.996434 GGCGATGGAGGGGCGATG 62.996 72.222 0.00 0.00 0.00 3.84
2223 2326 3.365265 CAAGTTGTGCCCGGCTCC 61.365 66.667 11.61 1.66 0.00 4.70
2224 2327 2.193536 AACAAGTTGTGCCCGGCTC 61.194 57.895 9.79 7.85 0.00 4.70
2225 2328 2.123897 AACAAGTTGTGCCCGGCT 60.124 55.556 9.79 0.00 0.00 5.52
2226 2329 2.027460 CAACAAGTTGTGCCCGGC 59.973 61.111 9.79 1.04 35.92 6.13
2234 2337 4.680110 CCGACTGTCTACTACAACAAGTTG 59.320 45.833 11.16 11.16 45.58 3.16
2235 2338 4.261909 CCCGACTGTCTACTACAACAAGTT 60.262 45.833 6.21 0.00 37.74 2.66
2236 2339 3.255149 CCCGACTGTCTACTACAACAAGT 59.745 47.826 6.21 0.00 37.74 3.16
2237 2340 3.504906 TCCCGACTGTCTACTACAACAAG 59.495 47.826 6.21 0.00 37.74 3.16
2238 2341 3.489355 TCCCGACTGTCTACTACAACAA 58.511 45.455 6.21 0.00 37.74 2.83
2239 2342 3.144657 TCCCGACTGTCTACTACAACA 57.855 47.619 6.21 0.00 37.74 3.33
2240 2343 3.505293 ACTTCCCGACTGTCTACTACAAC 59.495 47.826 6.21 0.00 37.74 3.32
2241 2344 3.755378 GACTTCCCGACTGTCTACTACAA 59.245 47.826 6.21 0.00 37.74 2.41
2242 2345 3.341823 GACTTCCCGACTGTCTACTACA 58.658 50.000 6.21 0.00 36.42 2.74
2243 2346 2.351111 CGACTTCCCGACTGTCTACTAC 59.649 54.545 6.21 0.00 0.00 2.73
2244 2347 2.027745 ACGACTTCCCGACTGTCTACTA 60.028 50.000 6.21 0.00 0.00 1.82
2245 2348 1.271271 ACGACTTCCCGACTGTCTACT 60.271 52.381 6.21 0.00 0.00 2.57
2246 2349 1.130186 GACGACTTCCCGACTGTCTAC 59.870 57.143 6.21 0.00 0.00 2.59
2247 2350 1.446907 GACGACTTCCCGACTGTCTA 58.553 55.000 6.21 0.00 0.00 2.59
2248 2351 1.575576 CGACGACTTCCCGACTGTCT 61.576 60.000 6.21 0.00 0.00 3.41
2249 2352 1.154263 CGACGACTTCCCGACTGTC 60.154 63.158 0.00 0.00 0.00 3.51
2250 2353 1.895707 ACGACGACTTCCCGACTGT 60.896 57.895 0.00 0.00 0.00 3.55
2251 2354 1.442184 CACGACGACTTCCCGACTG 60.442 63.158 0.00 0.00 0.00 3.51
2252 2355 2.952245 CACGACGACTTCCCGACT 59.048 61.111 0.00 0.00 0.00 4.18
2253 2356 1.915614 TAGCACGACGACTTCCCGAC 61.916 60.000 0.00 0.00 0.00 4.79
2254 2357 1.236616 TTAGCACGACGACTTCCCGA 61.237 55.000 0.00 0.00 0.00 5.14
2255 2358 0.797249 CTTAGCACGACGACTTCCCG 60.797 60.000 0.00 0.00 0.00 5.14
2256 2359 0.458025 CCTTAGCACGACGACTTCCC 60.458 60.000 0.00 0.00 0.00 3.97
2257 2360 1.077089 GCCTTAGCACGACGACTTCC 61.077 60.000 0.00 0.00 39.53 3.46
2258 2361 1.077089 GGCCTTAGCACGACGACTTC 61.077 60.000 0.00 0.00 42.56 3.01
2259 2362 1.080025 GGCCTTAGCACGACGACTT 60.080 57.895 0.00 0.00 42.56 3.01
2260 2363 2.572284 GGCCTTAGCACGACGACT 59.428 61.111 0.00 0.59 42.56 4.18
2261 2364 2.508663 GGGCCTTAGCACGACGAC 60.509 66.667 0.84 0.00 42.56 4.34
2262 2365 3.766691 GGGGCCTTAGCACGACGA 61.767 66.667 0.84 0.00 46.55 4.20
2263 2366 2.023414 TATGGGGCCTTAGCACGACG 62.023 60.000 0.84 0.00 46.55 5.12
2264 2367 0.249911 CTATGGGGCCTTAGCACGAC 60.250 60.000 0.84 0.00 46.55 4.34
2265 2368 1.407656 CCTATGGGGCCTTAGCACGA 61.408 60.000 0.84 0.00 46.55 4.35
2266 2369 1.071471 CCTATGGGGCCTTAGCACG 59.929 63.158 0.84 0.00 46.55 5.34
2267 2370 0.108774 GTCCTATGGGGCCTTAGCAC 59.891 60.000 0.84 0.00 43.97 4.40
2268 2371 2.539983 GTCCTATGGGGCCTTAGCA 58.460 57.895 0.84 0.00 42.56 3.49
2275 2378 2.193248 GTGCTGGTCCTATGGGGC 59.807 66.667 0.00 0.00 36.26 5.80
2276 2379 2.757124 GGGTGCTGGTCCTATGGGG 61.757 68.421 0.00 0.00 0.00 4.96
2277 2380 2.757124 GGGGTGCTGGTCCTATGGG 61.757 68.421 0.00 0.00 0.00 4.00
2278 2381 1.987807 CTGGGGTGCTGGTCCTATGG 61.988 65.000 0.00 0.00 0.00 2.74
2279 2382 0.982852 TCTGGGGTGCTGGTCCTATG 60.983 60.000 0.00 0.00 0.00 2.23
2280 2383 0.253160 TTCTGGGGTGCTGGTCCTAT 60.253 55.000 0.00 0.00 0.00 2.57
2281 2384 1.159905 TTCTGGGGTGCTGGTCCTA 59.840 57.895 0.00 0.00 0.00 2.94
2282 2385 2.121963 TTCTGGGGTGCTGGTCCT 60.122 61.111 0.00 0.00 0.00 3.85
2283 2386 2.034221 GTTCTGGGGTGCTGGTCC 59.966 66.667 0.00 0.00 0.00 4.46
2284 2387 1.302832 CTGTTCTGGGGTGCTGGTC 60.303 63.158 0.00 0.00 0.00 4.02
2285 2388 0.766674 TACTGTTCTGGGGTGCTGGT 60.767 55.000 0.00 0.00 0.00 4.00
2286 2389 0.400213 TTACTGTTCTGGGGTGCTGG 59.600 55.000 0.00 0.00 0.00 4.85
2287 2390 1.523758 GTTACTGTTCTGGGGTGCTG 58.476 55.000 0.00 0.00 0.00 4.41
2288 2391 0.400594 GGTTACTGTTCTGGGGTGCT 59.599 55.000 0.00 0.00 0.00 4.40
2289 2392 0.953960 CGGTTACTGTTCTGGGGTGC 60.954 60.000 0.00 0.00 0.00 5.01
2290 2393 0.953960 GCGGTTACTGTTCTGGGGTG 60.954 60.000 0.00 0.00 0.00 4.61
2291 2394 1.373812 GCGGTTACTGTTCTGGGGT 59.626 57.895 0.00 0.00 0.00 4.95
2292 2395 1.376812 GGCGGTTACTGTTCTGGGG 60.377 63.158 0.00 0.00 0.00 4.96
2293 2396 1.740296 CGGCGGTTACTGTTCTGGG 60.740 63.158 0.00 0.00 0.00 4.45
2294 2397 2.388232 GCGGCGGTTACTGTTCTGG 61.388 63.158 9.78 0.00 0.00 3.86
2295 2398 2.388232 GGCGGCGGTTACTGTTCTG 61.388 63.158 9.78 0.00 0.00 3.02
2296 2399 2.047560 GGCGGCGGTTACTGTTCT 60.048 61.111 9.78 0.00 0.00 3.01
2297 2400 3.484547 CGGCGGCGGTTACTGTTC 61.485 66.667 25.36 0.00 0.00 3.18
2298 2401 3.305177 ATCGGCGGCGGTTACTGTT 62.305 57.895 31.73 3.55 0.00 3.16
2299 2402 3.766691 ATCGGCGGCGGTTACTGT 61.767 61.111 31.73 6.14 0.00 3.55
2300 2403 3.261951 CATCGGCGGCGGTTACTG 61.262 66.667 31.73 16.32 0.00 2.74
2301 2404 2.901051 CTTCATCGGCGGCGGTTACT 62.901 60.000 31.73 8.44 0.00 2.24
2302 2405 2.509786 TTCATCGGCGGCGGTTAC 60.510 61.111 31.73 0.00 0.00 2.50
2303 2406 2.023414 ATCTTCATCGGCGGCGGTTA 62.023 55.000 31.73 14.01 0.00 2.85
2304 2407 2.869503 AATCTTCATCGGCGGCGGTT 62.870 55.000 31.73 16.58 0.00 4.44
2305 2408 2.869503 AAATCTTCATCGGCGGCGGT 62.870 55.000 31.73 23.77 0.00 5.68
2306 2409 1.714899 AAAATCTTCATCGGCGGCGG 61.715 55.000 31.73 16.54 0.00 6.13
2307 2410 0.589729 CAAAATCTTCATCGGCGGCG 60.590 55.000 27.15 27.15 0.00 6.46
2308 2411 0.248621 CCAAAATCTTCATCGGCGGC 60.249 55.000 7.21 0.00 0.00 6.53
2309 2412 1.094785 ACCAAAATCTTCATCGGCGG 58.905 50.000 7.21 0.00 0.00 6.13
2310 2413 3.374058 ACTTACCAAAATCTTCATCGGCG 59.626 43.478 0.00 0.00 0.00 6.46
2311 2414 4.965119 ACTTACCAAAATCTTCATCGGC 57.035 40.909 0.00 0.00 0.00 5.54
2323 2426 9.287373 ACCAGACGAAATAAATTACTTACCAAA 57.713 29.630 0.00 0.00 0.00 3.28
2324 2427 8.851541 ACCAGACGAAATAAATTACTTACCAA 57.148 30.769 0.00 0.00 0.00 3.67
2325 2428 8.095792 TGACCAGACGAAATAAATTACTTACCA 58.904 33.333 0.00 0.00 0.00 3.25
2326 2429 8.483307 TGACCAGACGAAATAAATTACTTACC 57.517 34.615 0.00 0.00 0.00 2.85
2327 2430 9.916397 CATGACCAGACGAAATAAATTACTTAC 57.084 33.333 0.00 0.00 0.00 2.34
2328 2431 9.104965 CCATGACCAGACGAAATAAATTACTTA 57.895 33.333 0.00 0.00 0.00 2.24
2329 2432 7.067008 CCCATGACCAGACGAAATAAATTACTT 59.933 37.037 0.00 0.00 0.00 2.24
2330 2433 6.542370 CCCATGACCAGACGAAATAAATTACT 59.458 38.462 0.00 0.00 0.00 2.24
2354 2457 2.309528 TCCGTACTCATTCACATGCC 57.690 50.000 0.00 0.00 0.00 4.40
2365 2468 2.633199 AACGCTCTTCTTCCGTACTC 57.367 50.000 0.00 0.00 34.41 2.59
2366 2469 2.035576 ACAAACGCTCTTCTTCCGTACT 59.964 45.455 0.00 0.00 34.41 2.73
2367 2470 2.401351 ACAAACGCTCTTCTTCCGTAC 58.599 47.619 0.00 0.00 34.41 3.67
2368 2471 2.669364 GACAAACGCTCTTCTTCCGTA 58.331 47.619 0.00 0.00 34.41 4.02
2472 2602 4.326548 GCTAGACGCCTAACTTGTTAACTG 59.673 45.833 7.22 2.59 0.00 3.16
2473 2603 4.220163 AGCTAGACGCCTAACTTGTTAACT 59.780 41.667 7.22 0.00 40.39 2.24
2474 2604 4.492611 AGCTAGACGCCTAACTTGTTAAC 58.507 43.478 0.00 0.00 40.39 2.01
2475 2605 4.796038 AGCTAGACGCCTAACTTGTTAA 57.204 40.909 0.00 0.00 40.39 2.01
2477 2607 3.679824 AAGCTAGACGCCTAACTTGTT 57.320 42.857 0.00 0.00 40.39 2.83
2479 2609 2.599082 CGAAAGCTAGACGCCTAACTTG 59.401 50.000 0.00 0.00 40.39 3.16
2493 2626 0.390124 TCCGTGTACCAACGAAAGCT 59.610 50.000 7.27 0.00 46.49 3.74
2495 2628 0.780002 CGTCCGTGTACCAACGAAAG 59.220 55.000 7.27 0.00 46.49 2.62
2522 2655 3.130164 TGTCAACAACCAACCATGACTTG 59.870 43.478 0.00 0.00 40.70 3.16
2543 2676 7.498900 TGCAGTAACATCCACCTATAAATCTTG 59.501 37.037 0.00 0.00 0.00 3.02
2548 2681 7.797062 TGTATGCAGTAACATCCACCTATAAA 58.203 34.615 0.00 0.00 0.00 1.40
2549 2682 7.368198 TGTATGCAGTAACATCCACCTATAA 57.632 36.000 0.00 0.00 0.00 0.98
2557 2690 3.206150 CCACCTGTATGCAGTAACATCC 58.794 50.000 10.09 0.00 41.02 3.51
2612 2745 4.349501 GAATCGGTAGCTGTACTGTACAC 58.650 47.826 16.26 12.89 36.92 2.90
2613 2746 3.379372 GGAATCGGTAGCTGTACTGTACA 59.621 47.826 18.77 18.77 36.92 2.90
2627 2763 1.285280 TGGACTGGAATGGAATCGGT 58.715 50.000 0.00 0.00 0.00 4.69
2629 2765 2.679837 CAGTTGGACTGGAATGGAATCG 59.320 50.000 0.16 0.00 42.35 3.34
2655 2791 9.439500 TTTATTAGTAATCCGCAACTAAACACT 57.561 29.630 0.00 0.00 40.53 3.55
2662 2798 6.485648 GGATGGTTTATTAGTAATCCGCAACT 59.514 38.462 0.00 0.00 33.96 3.16


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

AutoCloner maintained by Alex Coulton.