Multiple sequence alignment - TraesCS1A01G415100

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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 TraesCS1A01G415100 chr1A 100.000 2504 0 0 1 2504 574333076 574330573 0.000000e+00 4625
1 TraesCS1A01G415100 chr1A 96.175 549 18 1 1 546 321881696 321882244 0.000000e+00 894
2 TraesCS1A01G415100 chr1A 83.951 162 15 4 2224 2382 313323703 313323856 7.220000e-31 145
3 TraesCS1A01G415100 chr1A 93.407 91 6 0 2224 2314 231291087 231290997 4.340000e-28 135
4 TraesCS1A01G415100 chr1A 81.875 160 24 3 2224 2382 49144905 49144750 2.020000e-26 130
5 TraesCS1A01G415100 chr1A 92.308 91 7 0 2224 2314 557736581 557736671 2.020000e-26 130
6 TraesCS1A01G415100 chr1D 90.210 1573 56 32 551 2072 478117503 478115978 0.000000e+00 1962
7 TraesCS1A01G415100 chr1D 95.971 546 20 1 1 546 402299311 402298768 0.000000e+00 885
8 TraesCS1A01G415100 chr1D 90.291 103 3 2 2104 2206 478115979 478115884 7.270000e-26 128
9 TraesCS1A01G415100 chr1B 89.753 1298 56 36 551 1804 665292771 665291507 0.000000e+00 1589
10 TraesCS1A01G415100 chr1B 94.000 50 1 1 2100 2147 665291238 665291189 9.610000e-10 75
11 TraesCS1A01G415100 chr3D 96.520 546 18 1 1 546 351946474 351945930 0.000000e+00 902
12 TraesCS1A01G415100 chr5B 94.333 547 31 0 1 547 373223814 373224360 0.000000e+00 839
13 TraesCS1A01G415100 chr5A 85.974 385 30 7 993 1368 41880136 41879767 8.400000e-105 390
14 TraesCS1A01G415100 chr4B 89.423 312 29 3 243 550 536121532 536121843 8.400000e-105 390
15 TraesCS1A01G415100 chr4B 91.209 91 8 0 2224 2314 10868590 10868500 9.400000e-25 124
16 TraesCS1A01G415100 chr7D 89.172 314 24 4 995 1304 23669343 23669650 1.410000e-102 383
17 TraesCS1A01G415100 chr7D 92.513 187 12 1 363 547 159740247 159740061 1.480000e-67 267
18 TraesCS1A01G415100 chr4A 86.875 320 20 11 995 1303 707843164 707842856 3.090000e-89 339
19 TraesCS1A01G415100 chr5D 90.909 187 15 1 363 547 333057253 333057067 1.490000e-62 250
20 TraesCS1A01G415100 chr6A 82.716 162 17 4 2224 2382 371704318 371704471 1.560000e-27 134
21 TraesCS1A01G415100 chr3A 82.716 162 17 4 2224 2382 552492583 552492430 1.560000e-27 134
22 TraesCS1A01G415100 chr2A 82.716 162 17 4 2224 2382 291781660 291781813 1.560000e-27 134
23 TraesCS1A01G415100 chr2A 82.716 162 17 4 2224 2382 436071831 436071678 1.560000e-27 134
24 TraesCS1A01G415100 chr7A 84.685 111 13 4 2383 2491 579266615 579266507 9.470000e-20 108


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 TraesCS1A01G415100 chr1A 574330573 574333076 2503 True 4625 4625 100.0000 1 2504 1 chr1A.!!$R3 2503
1 TraesCS1A01G415100 chr1A 321881696 321882244 548 False 894 894 96.1750 1 546 1 chr1A.!!$F2 545
2 TraesCS1A01G415100 chr1D 478115884 478117503 1619 True 1045 1962 90.2505 551 2206 2 chr1D.!!$R2 1655
3 TraesCS1A01G415100 chr1D 402298768 402299311 543 True 885 885 95.9710 1 546 1 chr1D.!!$R1 545
4 TraesCS1A01G415100 chr1B 665291189 665292771 1582 True 832 1589 91.8765 551 2147 2 chr1B.!!$R1 1596
5 TraesCS1A01G415100 chr3D 351945930 351946474 544 True 902 902 96.5200 1 546 1 chr3D.!!$R1 545
6 TraesCS1A01G415100 chr5B 373223814 373224360 546 False 839 839 94.3330 1 547 1 chr5B.!!$F1 546

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
975 1030 0.105709 CTTCCTCCTCCTCCTCCTCC 60.106 65.0 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
2435 2558 0.045469 AAGGGAGGGAGAGATGCCTT 59.955 55.0 0.0 0.0 41.86 4.35 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
108 109 2.068821 GGAGGATGAGGAGCCAGCA 61.069 63.158 0.00 0.00 0.00 4.41
171 172 3.592814 CGCCGTCTCTCCGCCATA 61.593 66.667 0.00 0.00 0.00 2.74
349 350 2.894257 TTGTCCGGCTCCAGTGCAT 61.894 57.895 0.00 0.00 34.04 3.96
610 614 1.438651 ACGACAAAGCATGTACGCAT 58.561 45.000 0.00 0.00 44.12 4.73
618 622 2.516930 ATGTACGCATGCCTGCCC 60.517 61.111 13.15 0.00 46.07 5.36
957 1012 2.664081 GCCTAGCTGCCACCACTCT 61.664 63.158 0.00 0.00 0.00 3.24
960 1015 0.107945 CTAGCTGCCACCACTCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
974 1029 0.930726 TCTTCCTCCTCCTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
975 1030 0.105709 CTTCCTCCTCCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
976 1031 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
977 1032 0.350904 TCCTCCTCCTCCTCCTCCTA 59.649 60.000 0.00 0.00 0.00 2.94
978 1033 0.777446 CCTCCTCCTCCTCCTCCTAG 59.223 65.000 0.00 0.00 0.00 3.02
979 1034 1.529744 CTCCTCCTCCTCCTCCTAGT 58.470 60.000 0.00 0.00 0.00 2.57
980 1035 1.423921 CTCCTCCTCCTCCTCCTAGTC 59.576 61.905 0.00 0.00 0.00 2.59
982 1037 0.481128 CTCCTCCTCCTCCTAGTCCC 59.519 65.000 0.00 0.00 0.00 4.46
983 1038 1.151908 CCTCCTCCTCCTAGTCCCG 59.848 68.421 0.00 0.00 0.00 5.14
984 1039 1.151908 CTCCTCCTCCTAGTCCCGG 59.848 68.421 0.00 0.00 0.00 5.73
985 1040 1.621822 TCCTCCTCCTAGTCCCGGT 60.622 63.158 0.00 0.00 0.00 5.28
986 1041 1.152715 CCTCCTCCTAGTCCCGGTC 60.153 68.421 0.00 0.00 0.00 4.79
987 1042 1.613610 CTCCTCCTAGTCCCGGTCA 59.386 63.158 0.00 0.00 0.00 4.02
989 1044 1.000019 CCTCCTAGTCCCGGTCACA 60.000 63.158 0.00 0.00 0.00 3.58
992 1047 2.722201 CCTAGTCCCGGTCACAGCC 61.722 68.421 0.00 0.00 0.00 4.85
993 1048 1.682684 CTAGTCCCGGTCACAGCCT 60.683 63.158 0.00 0.00 0.00 4.58
1070 1141 2.989824 CACGGACCTGGACGACCT 60.990 66.667 18.96 0.00 37.04 3.85
1275 1346 1.517475 GTTCTCCTTCGCGCTCCTC 60.517 63.158 5.56 0.00 0.00 3.71
1588 1672 1.384525 CGTCTCTGTACTCTCCCAGG 58.615 60.000 0.00 0.00 0.00 4.45
1600 1684 0.692476 CTCCCAGGTGTTGGTGATCA 59.308 55.000 0.00 0.00 46.25 2.92
1621 1705 2.782163 CGTCGTCTTCACGTGTATGAT 58.218 47.619 16.51 0.00 46.76 2.45
1655 1743 3.676540 TCGTTTGTTCGTTCTTTCTTGC 58.323 40.909 0.00 0.00 0.00 4.01
1660 1748 0.865769 TTCGTTCTTTCTTGCCTCGC 59.134 50.000 0.00 0.00 0.00 5.03
1700 1788 1.877443 TCGATCGACGATCATAAGGCA 59.123 47.619 31.15 8.22 46.45 4.75
1701 1789 1.979469 CGATCGACGATCATAAGGCAC 59.021 52.381 31.15 7.79 45.77 5.01
1708 1796 1.470805 CGATCATAAGGCACACGTCCA 60.471 52.381 0.00 0.00 0.00 4.02
1709 1797 2.627945 GATCATAAGGCACACGTCCAA 58.372 47.619 0.00 0.00 0.00 3.53
1745 1833 2.829043 TTCCGGCGATGAACTGGTCG 62.829 60.000 9.30 0.00 40.62 4.79
1806 1894 1.746615 CTTGGCCACGCACTAGCAT 60.747 57.895 3.88 0.00 42.27 3.79
1862 1950 3.699538 ACACACTTATACTCGGATGCAGA 59.300 43.478 0.00 0.00 0.00 4.26
1863 1951 4.202060 ACACACTTATACTCGGATGCAGAG 60.202 45.833 0.00 0.00 41.27 3.35
1865 1953 4.402793 ACACTTATACTCGGATGCAGAGTT 59.597 41.667 11.84 4.19 45.74 3.01
1866 1954 4.979197 CACTTATACTCGGATGCAGAGTTC 59.021 45.833 11.84 0.00 45.74 3.01
1867 1955 4.890581 ACTTATACTCGGATGCAGAGTTCT 59.109 41.667 11.84 4.16 45.74 3.01
1868 1956 5.361285 ACTTATACTCGGATGCAGAGTTCTT 59.639 40.000 11.84 2.23 45.74 2.52
1869 1957 2.663826 ACTCGGATGCAGAGTTCTTC 57.336 50.000 1.42 0.00 45.74 2.87
1870 1958 1.895798 ACTCGGATGCAGAGTTCTTCA 59.104 47.619 1.42 0.00 45.74 3.02
1871 1959 2.094286 ACTCGGATGCAGAGTTCTTCAG 60.094 50.000 1.42 0.00 45.74 3.02
1872 1960 2.165234 CTCGGATGCAGAGTTCTTCAGA 59.835 50.000 0.00 0.00 0.00 3.27
1873 1961 2.762887 TCGGATGCAGAGTTCTTCAGAT 59.237 45.455 0.00 0.00 0.00 2.90
1874 1962 3.196469 TCGGATGCAGAGTTCTTCAGATT 59.804 43.478 0.00 0.00 0.00 2.40
1875 1963 4.402474 TCGGATGCAGAGTTCTTCAGATTA 59.598 41.667 0.00 0.00 0.00 1.75
1876 1964 4.505922 CGGATGCAGAGTTCTTCAGATTAC 59.494 45.833 0.00 0.00 0.00 1.89
1877 1965 5.423015 GGATGCAGAGTTCTTCAGATTACA 58.577 41.667 0.00 0.00 0.00 2.41
1878 1966 5.293079 GGATGCAGAGTTCTTCAGATTACAC 59.707 44.000 0.00 0.00 0.00 2.90
1879 1967 5.474578 TGCAGAGTTCTTCAGATTACACT 57.525 39.130 0.00 0.00 0.00 3.55
1880 1968 5.858381 TGCAGAGTTCTTCAGATTACACTT 58.142 37.500 0.00 0.00 0.00 3.16
1921 2009 1.067283 ACACTCGGATGCAGAGTTCTG 60.067 52.381 4.44 4.77 45.74 3.02
2019 2108 1.658717 GACCGATCGATGCCTCACG 60.659 63.158 18.66 0.00 0.00 4.35
2079 2173 6.089016 GTGGTATACATCCGTCGTCATAAATG 59.911 42.308 5.01 0.00 0.00 2.32
2090 2211 4.565564 GTCGTCATAAATGTAGTGTGGACC 59.434 45.833 0.00 0.00 0.00 4.46
2091 2212 3.869246 CGTCATAAATGTAGTGTGGACCC 59.131 47.826 0.00 0.00 0.00 4.46
2093 2214 3.201266 TCATAAATGTAGTGTGGACCCCC 59.799 47.826 0.00 0.00 0.00 5.40
2095 2216 2.653543 AATGTAGTGTGGACCCCCTA 57.346 50.000 0.00 0.00 0.00 3.53
2098 2219 2.703947 TGTAGTGTGGACCCCCTAAAA 58.296 47.619 0.00 0.00 0.00 1.52
2235 2358 9.796120 GCTAAATAGCCAATAAAACATAACACA 57.204 29.630 0.82 0.00 43.39 3.72
2238 2361 8.647143 AATAGCCAATAAAACATAACACATGC 57.353 30.769 0.00 0.00 0.00 4.06
2239 2362 6.284891 AGCCAATAAAACATAACACATGCT 57.715 33.333 0.00 0.00 0.00 3.79
2240 2363 6.332630 AGCCAATAAAACATAACACATGCTC 58.667 36.000 0.00 0.00 0.00 4.26
2241 2364 6.153340 AGCCAATAAAACATAACACATGCTCT 59.847 34.615 0.00 0.00 0.00 4.09
2242 2365 6.813152 GCCAATAAAACATAACACATGCTCTT 59.187 34.615 0.00 0.00 0.00 2.85
2243 2366 7.973388 GCCAATAAAACATAACACATGCTCTTA 59.027 33.333 0.00 0.00 0.00 2.10
2244 2367 9.853555 CCAATAAAACATAACACATGCTCTTAA 57.146 29.630 0.00 0.00 0.00 1.85
2248 2371 7.744087 AAACATAACACATGCTCTTAACTCA 57.256 32.000 0.00 0.00 0.00 3.41
2249 2372 7.744087 AACATAACACATGCTCTTAACTCAA 57.256 32.000 0.00 0.00 0.00 3.02
2250 2373 7.133891 ACATAACACATGCTCTTAACTCAAC 57.866 36.000 0.00 0.00 0.00 3.18
2251 2374 6.710295 ACATAACACATGCTCTTAACTCAACA 59.290 34.615 0.00 0.00 0.00 3.33
2252 2375 7.228507 ACATAACACATGCTCTTAACTCAACAA 59.771 33.333 0.00 0.00 0.00 2.83
2253 2376 5.424121 ACACATGCTCTTAACTCAACAAC 57.576 39.130 0.00 0.00 0.00 3.32
2254 2377 4.275936 ACACATGCTCTTAACTCAACAACC 59.724 41.667 0.00 0.00 0.00 3.77
2255 2378 4.275689 CACATGCTCTTAACTCAACAACCA 59.724 41.667 0.00 0.00 0.00 3.67
2256 2379 5.048504 CACATGCTCTTAACTCAACAACCAT 60.049 40.000 0.00 0.00 0.00 3.55
2257 2380 5.182001 ACATGCTCTTAACTCAACAACCATC 59.818 40.000 0.00 0.00 0.00 3.51
2258 2381 4.713553 TGCTCTTAACTCAACAACCATCA 58.286 39.130 0.00 0.00 0.00 3.07
2259 2382 4.515191 TGCTCTTAACTCAACAACCATCAC 59.485 41.667 0.00 0.00 0.00 3.06
2260 2383 4.757149 GCTCTTAACTCAACAACCATCACT 59.243 41.667 0.00 0.00 0.00 3.41
2261 2384 5.106908 GCTCTTAACTCAACAACCATCACTC 60.107 44.000 0.00 0.00 0.00 3.51
2262 2385 5.924356 TCTTAACTCAACAACCATCACTCA 58.076 37.500 0.00 0.00 0.00 3.41
2263 2386 6.353323 TCTTAACTCAACAACCATCACTCAA 58.647 36.000 0.00 0.00 0.00 3.02
2264 2387 6.483307 TCTTAACTCAACAACCATCACTCAAG 59.517 38.462 0.00 0.00 0.00 3.02
2265 2388 4.422073 ACTCAACAACCATCACTCAAGA 57.578 40.909 0.00 0.00 0.00 3.02
2266 2389 4.978099 ACTCAACAACCATCACTCAAGAT 58.022 39.130 0.00 0.00 0.00 2.40
2267 2390 4.999950 ACTCAACAACCATCACTCAAGATC 59.000 41.667 0.00 0.00 0.00 2.75
2268 2391 4.971939 TCAACAACCATCACTCAAGATCA 58.028 39.130 0.00 0.00 0.00 2.92
2269 2392 4.756642 TCAACAACCATCACTCAAGATCAC 59.243 41.667 0.00 0.00 0.00 3.06
2270 2393 4.356405 ACAACCATCACTCAAGATCACA 57.644 40.909 0.00 0.00 0.00 3.58
2271 2394 4.717877 ACAACCATCACTCAAGATCACAA 58.282 39.130 0.00 0.00 0.00 3.33
2272 2395 5.319453 ACAACCATCACTCAAGATCACAAT 58.681 37.500 0.00 0.00 0.00 2.71
2273 2396 6.475504 ACAACCATCACTCAAGATCACAATA 58.524 36.000 0.00 0.00 0.00 1.90
2274 2397 6.596888 ACAACCATCACTCAAGATCACAATAG 59.403 38.462 0.00 0.00 0.00 1.73
2275 2398 6.550938 ACCATCACTCAAGATCACAATAGA 57.449 37.500 0.00 0.00 0.00 1.98
2276 2399 7.134362 ACCATCACTCAAGATCACAATAGAT 57.866 36.000 0.00 0.00 0.00 1.98
2277 2400 7.571919 ACCATCACTCAAGATCACAATAGATT 58.428 34.615 0.00 0.00 0.00 2.40
2278 2401 7.714377 ACCATCACTCAAGATCACAATAGATTC 59.286 37.037 0.00 0.00 0.00 2.52
2279 2402 7.095732 CCATCACTCAAGATCACAATAGATTCG 60.096 40.741 0.00 0.00 0.00 3.34
2280 2403 6.867550 TCACTCAAGATCACAATAGATTCGT 58.132 36.000 0.00 0.00 0.00 3.85
2281 2404 6.975197 TCACTCAAGATCACAATAGATTCGTC 59.025 38.462 0.00 0.00 0.00 4.20
2282 2405 6.753744 CACTCAAGATCACAATAGATTCGTCA 59.246 38.462 0.00 0.00 0.00 4.35
2283 2406 6.754209 ACTCAAGATCACAATAGATTCGTCAC 59.246 38.462 0.00 0.00 0.00 3.67
2284 2407 6.867550 TCAAGATCACAATAGATTCGTCACT 58.132 36.000 0.00 0.00 0.00 3.41
2285 2408 7.323420 TCAAGATCACAATAGATTCGTCACTT 58.677 34.615 0.00 0.00 0.00 3.16
2286 2409 7.819415 TCAAGATCACAATAGATTCGTCACTTT 59.181 33.333 0.00 0.00 0.00 2.66
2287 2410 8.446273 CAAGATCACAATAGATTCGTCACTTTT 58.554 33.333 0.00 0.00 0.00 2.27
2288 2411 9.653287 AAGATCACAATAGATTCGTCACTTTTA 57.347 29.630 0.00 0.00 0.00 1.52
2289 2412 9.823647 AGATCACAATAGATTCGTCACTTTTAT 57.176 29.630 0.00 0.00 0.00 1.40
2296 2419 6.911484 AGATTCGTCACTTTTATTTTTGCG 57.089 33.333 0.00 0.00 0.00 4.85
2297 2420 6.664515 AGATTCGTCACTTTTATTTTTGCGA 58.335 32.000 0.00 0.00 0.00 5.10
2298 2421 6.797033 AGATTCGTCACTTTTATTTTTGCGAG 59.203 34.615 0.00 0.00 0.00 5.03
2299 2422 5.660629 TCGTCACTTTTATTTTTGCGAGA 57.339 34.783 0.00 0.00 0.00 4.04
2300 2423 5.437263 TCGTCACTTTTATTTTTGCGAGAC 58.563 37.500 0.00 0.00 0.00 3.36
2301 2424 5.006844 TCGTCACTTTTATTTTTGCGAGACA 59.993 36.000 0.00 0.00 0.00 3.41
2302 2425 5.851177 CGTCACTTTTATTTTTGCGAGACAT 59.149 36.000 0.00 0.00 0.00 3.06
2303 2426 6.359617 CGTCACTTTTATTTTTGCGAGACATT 59.640 34.615 0.00 0.00 0.00 2.71
2304 2427 7.532546 CGTCACTTTTATTTTTGCGAGACATTA 59.467 33.333 0.00 0.00 0.00 1.90
2305 2428 9.341899 GTCACTTTTATTTTTGCGAGACATTAT 57.658 29.630 0.00 0.00 0.00 1.28
2318 2441 9.715123 TTGCGAGACATTATATTTGTGTATTTG 57.285 29.630 0.00 0.00 0.00 2.32
2319 2442 8.888716 TGCGAGACATTATATTTGTGTATTTGT 58.111 29.630 0.00 0.00 0.00 2.83
2320 2443 9.158364 GCGAGACATTATATTTGTGTATTTGTG 57.842 33.333 0.00 0.00 0.00 3.33
2325 2448 9.364989 ACATTATATTTGTGTATTTGTGTTGGC 57.635 29.630 0.00 0.00 0.00 4.52
2326 2449 8.530720 CATTATATTTGTGTATTTGTGTTGGCG 58.469 33.333 0.00 0.00 0.00 5.69
2327 2450 2.126914 TTGTGTATTTGTGTTGGCGC 57.873 45.000 0.00 0.00 0.00 6.53
2328 2451 1.313772 TGTGTATTTGTGTTGGCGCT 58.686 45.000 7.64 0.00 0.00 5.92
2329 2452 1.678627 TGTGTATTTGTGTTGGCGCTT 59.321 42.857 7.64 0.00 0.00 4.68
2330 2453 2.879026 TGTGTATTTGTGTTGGCGCTTA 59.121 40.909 7.64 0.00 0.00 3.09
2331 2454 3.504134 TGTGTATTTGTGTTGGCGCTTAT 59.496 39.130 7.64 0.00 0.00 1.73
2332 2455 4.095610 GTGTATTTGTGTTGGCGCTTATC 58.904 43.478 7.64 0.00 0.00 1.75
2333 2456 2.939460 ATTTGTGTTGGCGCTTATCC 57.061 45.000 7.64 0.00 0.00 2.59
2334 2457 1.904287 TTTGTGTTGGCGCTTATCCT 58.096 45.000 7.64 0.00 0.00 3.24
2335 2458 1.904287 TTGTGTTGGCGCTTATCCTT 58.096 45.000 7.64 0.00 0.00 3.36
2336 2459 1.448985 TGTGTTGGCGCTTATCCTTC 58.551 50.000 7.64 0.00 0.00 3.46
2337 2460 1.003118 TGTGTTGGCGCTTATCCTTCT 59.997 47.619 7.64 0.00 0.00 2.85
2338 2461 1.666189 GTGTTGGCGCTTATCCTTCTC 59.334 52.381 7.64 0.00 0.00 2.87
2339 2462 1.277842 TGTTGGCGCTTATCCTTCTCA 59.722 47.619 7.64 0.00 0.00 3.27
2340 2463 2.092968 TGTTGGCGCTTATCCTTCTCAT 60.093 45.455 7.64 0.00 0.00 2.90
2341 2464 2.533266 TGGCGCTTATCCTTCTCATC 57.467 50.000 7.64 0.00 0.00 2.92
2342 2465 1.070758 TGGCGCTTATCCTTCTCATCC 59.929 52.381 7.64 0.00 0.00 3.51
2343 2466 1.346068 GGCGCTTATCCTTCTCATCCT 59.654 52.381 7.64 0.00 0.00 3.24
2344 2467 2.224402 GGCGCTTATCCTTCTCATCCTT 60.224 50.000 7.64 0.00 0.00 3.36
2345 2468 2.805099 GCGCTTATCCTTCTCATCCTTG 59.195 50.000 0.00 0.00 0.00 3.61
2346 2469 3.742640 GCGCTTATCCTTCTCATCCTTGT 60.743 47.826 0.00 0.00 0.00 3.16
2347 2470 4.446371 CGCTTATCCTTCTCATCCTTGTT 58.554 43.478 0.00 0.00 0.00 2.83
2348 2471 4.272018 CGCTTATCCTTCTCATCCTTGTTG 59.728 45.833 0.00 0.00 0.00 3.33
2349 2472 4.578105 GCTTATCCTTCTCATCCTTGTTGG 59.422 45.833 0.00 0.00 37.10 3.77
2350 2473 2.496899 TCCTTCTCATCCTTGTTGGC 57.503 50.000 0.00 0.00 35.26 4.52
2351 2474 1.089920 CCTTCTCATCCTTGTTGGCG 58.910 55.000 0.00 0.00 35.26 5.69
2352 2475 1.339055 CCTTCTCATCCTTGTTGGCGA 60.339 52.381 0.00 0.00 35.26 5.54
2353 2476 2.636830 CTTCTCATCCTTGTTGGCGAT 58.363 47.619 0.00 0.00 35.26 4.58
2354 2477 2.028420 TCTCATCCTTGTTGGCGATG 57.972 50.000 0.00 0.00 35.71 3.84
2355 2478 1.019673 CTCATCCTTGTTGGCGATGG 58.980 55.000 0.00 0.00 35.22 3.51
2356 2479 1.031571 TCATCCTTGTTGGCGATGGC 61.032 55.000 0.00 0.00 35.22 4.40
2366 2489 3.365535 GCGATGGCCTTGGTGTTT 58.634 55.556 3.32 0.00 0.00 2.83
2367 2490 2.562125 GCGATGGCCTTGGTGTTTA 58.438 52.632 3.32 0.00 0.00 2.01
2368 2491 1.102978 GCGATGGCCTTGGTGTTTAT 58.897 50.000 3.32 0.00 0.00 1.40
2369 2492 2.294074 GCGATGGCCTTGGTGTTTATA 58.706 47.619 3.32 0.00 0.00 0.98
2370 2493 2.032924 GCGATGGCCTTGGTGTTTATAC 59.967 50.000 3.32 0.00 0.00 1.47
2371 2494 3.275143 CGATGGCCTTGGTGTTTATACA 58.725 45.455 3.32 0.00 0.00 2.29
2372 2495 3.692101 CGATGGCCTTGGTGTTTATACAA 59.308 43.478 3.32 0.00 35.69 2.41
2373 2496 4.156922 CGATGGCCTTGGTGTTTATACAAA 59.843 41.667 3.32 0.00 35.69 2.83
2374 2497 5.336055 CGATGGCCTTGGTGTTTATACAAAA 60.336 40.000 3.32 0.00 35.69 2.44
2375 2498 6.619329 ATGGCCTTGGTGTTTATACAAAAT 57.381 33.333 3.32 0.00 35.69 1.82
2376 2499 7.415765 CGATGGCCTTGGTGTTTATACAAAATA 60.416 37.037 3.32 0.00 35.69 1.40
2377 2500 7.540474 TGGCCTTGGTGTTTATACAAAATAA 57.460 32.000 3.32 0.00 35.69 1.40
2378 2501 8.140112 TGGCCTTGGTGTTTATACAAAATAAT 57.860 30.769 3.32 0.00 35.69 1.28
2379 2502 9.256228 TGGCCTTGGTGTTTATACAAAATAATA 57.744 29.630 3.32 0.00 35.69 0.98
2438 2561 9.173021 TGTGTGTTGAATATGGTTATTCTAAGG 57.827 33.333 7.13 0.00 42.79 2.69
2439 2562 8.129211 GTGTGTTGAATATGGTTATTCTAAGGC 58.871 37.037 7.13 0.00 42.79 4.35
2440 2563 7.831690 TGTGTTGAATATGGTTATTCTAAGGCA 59.168 33.333 7.13 0.00 42.79 4.75
2441 2564 8.850156 GTGTTGAATATGGTTATTCTAAGGCAT 58.150 33.333 7.13 0.00 42.79 4.40
2442 2565 9.066892 TGTTGAATATGGTTATTCTAAGGCATC 57.933 33.333 7.13 0.00 42.79 3.91
2443 2566 9.289782 GTTGAATATGGTTATTCTAAGGCATCT 57.710 33.333 7.13 0.00 42.79 2.90
2444 2567 9.507329 TTGAATATGGTTATTCTAAGGCATCTC 57.493 33.333 7.13 0.00 42.79 2.75
2445 2568 8.884323 TGAATATGGTTATTCTAAGGCATCTCT 58.116 33.333 7.13 0.00 42.79 3.10
2446 2569 9.377312 GAATATGGTTATTCTAAGGCATCTCTC 57.623 37.037 0.00 0.00 40.32 3.20
2447 2570 5.552870 TGGTTATTCTAAGGCATCTCTCC 57.447 43.478 0.00 0.00 0.00 3.71
2448 2571 4.348168 TGGTTATTCTAAGGCATCTCTCCC 59.652 45.833 0.00 0.00 0.00 4.30
2449 2572 4.595350 GGTTATTCTAAGGCATCTCTCCCT 59.405 45.833 0.00 0.00 0.00 4.20
2450 2573 5.279758 GGTTATTCTAAGGCATCTCTCCCTC 60.280 48.000 0.00 0.00 0.00 4.30
2451 2574 2.390225 TCTAAGGCATCTCTCCCTCC 57.610 55.000 0.00 0.00 0.00 4.30
2452 2575 1.133009 TCTAAGGCATCTCTCCCTCCC 60.133 57.143 0.00 0.00 0.00 4.30
2453 2576 0.944999 TAAGGCATCTCTCCCTCCCT 59.055 55.000 0.00 0.00 0.00 4.20
2454 2577 0.045469 AAGGCATCTCTCCCTCCCTT 59.955 55.000 0.00 0.00 0.00 3.95
2455 2578 0.399806 AGGCATCTCTCCCTCCCTTC 60.400 60.000 0.00 0.00 0.00 3.46
2456 2579 0.399806 GGCATCTCTCCCTCCCTTCT 60.400 60.000 0.00 0.00 0.00 2.85
2457 2580 1.047801 GCATCTCTCCCTCCCTTCTC 58.952 60.000 0.00 0.00 0.00 2.87
2458 2581 1.715785 CATCTCTCCCTCCCTTCTCC 58.284 60.000 0.00 0.00 0.00 3.71
2459 2582 0.565674 ATCTCTCCCTCCCTTCTCCC 59.434 60.000 0.00 0.00 0.00 4.30
2460 2583 0.556380 TCTCTCCCTCCCTTCTCCCT 60.556 60.000 0.00 0.00 0.00 4.20
2461 2584 0.105709 CTCTCCCTCCCTTCTCCCTC 60.106 65.000 0.00 0.00 0.00 4.30
2462 2585 0.556380 TCTCCCTCCCTTCTCCCTCT 60.556 60.000 0.00 0.00 0.00 3.69
2463 2586 0.341609 CTCCCTCCCTTCTCCCTCTT 59.658 60.000 0.00 0.00 0.00 2.85
2464 2587 0.800239 TCCCTCCCTTCTCCCTCTTT 59.200 55.000 0.00 0.00 0.00 2.52
2465 2588 1.208706 CCCTCCCTTCTCCCTCTTTC 58.791 60.000 0.00 0.00 0.00 2.62
2466 2589 1.274126 CCCTCCCTTCTCCCTCTTTCT 60.274 57.143 0.00 0.00 0.00 2.52
2467 2590 2.556766 CCTCCCTTCTCCCTCTTTCTT 58.443 52.381 0.00 0.00 0.00 2.52
2468 2591 2.503765 CCTCCCTTCTCCCTCTTTCTTC 59.496 54.545 0.00 0.00 0.00 2.87
2469 2592 2.503765 CTCCCTTCTCCCTCTTTCTTCC 59.496 54.545 0.00 0.00 0.00 3.46
2470 2593 2.114506 TCCCTTCTCCCTCTTTCTTCCT 59.885 50.000 0.00 0.00 0.00 3.36
2471 2594 2.503765 CCCTTCTCCCTCTTTCTTCCTC 59.496 54.545 0.00 0.00 0.00 3.71
2472 2595 3.449918 CCTTCTCCCTCTTTCTTCCTCT 58.550 50.000 0.00 0.00 0.00 3.69
2473 2596 3.450817 CCTTCTCCCTCTTTCTTCCTCTC 59.549 52.174 0.00 0.00 0.00 3.20
2474 2597 4.352893 CTTCTCCCTCTTTCTTCCTCTCT 58.647 47.826 0.00 0.00 0.00 3.10
2475 2598 3.707316 TCTCCCTCTTTCTTCCTCTCTG 58.293 50.000 0.00 0.00 0.00 3.35
2476 2599 2.168313 CTCCCTCTTTCTTCCTCTCTGC 59.832 54.545 0.00 0.00 0.00 4.26
2477 2600 2.187100 CCCTCTTTCTTCCTCTCTGCT 58.813 52.381 0.00 0.00 0.00 4.24
2478 2601 2.571202 CCCTCTTTCTTCCTCTCTGCTT 59.429 50.000 0.00 0.00 0.00 3.91
2479 2602 3.008923 CCCTCTTTCTTCCTCTCTGCTTT 59.991 47.826 0.00 0.00 0.00 3.51
2480 2603 4.252878 CCTCTTTCTTCCTCTCTGCTTTC 58.747 47.826 0.00 0.00 0.00 2.62
2481 2604 4.020307 CCTCTTTCTTCCTCTCTGCTTTCT 60.020 45.833 0.00 0.00 0.00 2.52
2482 2605 5.146010 TCTTTCTTCCTCTCTGCTTTCTC 57.854 43.478 0.00 0.00 0.00 2.87
2483 2606 4.837860 TCTTTCTTCCTCTCTGCTTTCTCT 59.162 41.667 0.00 0.00 0.00 3.10
2484 2607 5.306678 TCTTTCTTCCTCTCTGCTTTCTCTT 59.693 40.000 0.00 0.00 0.00 2.85
2485 2608 6.495181 TCTTTCTTCCTCTCTGCTTTCTCTTA 59.505 38.462 0.00 0.00 0.00 2.10
2486 2609 6.672266 TTCTTCCTCTCTGCTTTCTCTTAA 57.328 37.500 0.00 0.00 0.00 1.85
2487 2610 6.865834 TCTTCCTCTCTGCTTTCTCTTAAT 57.134 37.500 0.00 0.00 0.00 1.40
2488 2611 6.872920 TCTTCCTCTCTGCTTTCTCTTAATC 58.127 40.000 0.00 0.00 0.00 1.75
2489 2612 6.667414 TCTTCCTCTCTGCTTTCTCTTAATCT 59.333 38.462 0.00 0.00 0.00 2.40
2490 2613 6.463995 TCCTCTCTGCTTTCTCTTAATCTC 57.536 41.667 0.00 0.00 0.00 2.75
2491 2614 5.067153 TCCTCTCTGCTTTCTCTTAATCTCG 59.933 44.000 0.00 0.00 0.00 4.04
2492 2615 5.163561 CCTCTCTGCTTTCTCTTAATCTCGT 60.164 44.000 0.00 0.00 0.00 4.18
2493 2616 5.645624 TCTCTGCTTTCTCTTAATCTCGTG 58.354 41.667 0.00 0.00 0.00 4.35
2494 2617 5.416013 TCTCTGCTTTCTCTTAATCTCGTGA 59.584 40.000 0.00 0.00 0.00 4.35
2495 2618 6.096141 TCTCTGCTTTCTCTTAATCTCGTGAT 59.904 38.462 0.00 0.00 33.70 3.06
2496 2619 6.038985 TCTGCTTTCTCTTAATCTCGTGATG 58.961 40.000 0.00 0.00 32.44 3.07
2497 2620 5.965922 TGCTTTCTCTTAATCTCGTGATGA 58.034 37.500 0.00 0.00 32.44 2.92
2498 2621 6.038985 TGCTTTCTCTTAATCTCGTGATGAG 58.961 40.000 0.00 4.16 46.72 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 4.473520 AGCCCGCGTGCTGCTTAT 62.474 61.111 17.23 0.00 40.90 1.73
212 213 4.431131 CTCCGCCCTGCCATTGGT 62.431 66.667 4.26 0.00 0.00 3.67
328 329 1.071471 CACTGGAGCCGGACAACTT 59.929 57.895 5.05 0.00 0.00 2.66
349 350 2.221299 AGTTGAACTGCCGCCCCTA 61.221 57.895 0.00 0.00 0.00 3.53
547 551 0.465642 GGCGGTATCCTTTTGGGGAG 60.466 60.000 0.00 0.00 38.92 4.30
548 552 1.610873 GGCGGTATCCTTTTGGGGA 59.389 57.895 0.00 0.00 40.87 4.81
549 553 1.455032 GGGCGGTATCCTTTTGGGG 60.455 63.158 0.00 0.00 40.87 4.96
955 1010 0.930726 GAGGAGGAGGAGGAGGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
957 1012 0.556380 AGGAGGAGGAGGAGGAGGAA 60.556 60.000 0.00 0.00 0.00 3.36
960 1015 1.423921 GACTAGGAGGAGGAGGAGGAG 59.576 61.905 0.00 0.00 0.00 3.69
974 1029 2.722201 GGCTGTGACCGGGACTAGG 61.722 68.421 6.32 0.00 0.00 3.02
975 1030 1.668101 GAGGCTGTGACCGGGACTAG 61.668 65.000 6.32 0.00 33.69 2.57
976 1031 1.681327 GAGGCTGTGACCGGGACTA 60.681 63.158 6.32 0.00 33.69 2.59
977 1032 2.997897 GAGGCTGTGACCGGGACT 60.998 66.667 6.32 0.00 33.69 3.85
978 1033 4.083862 GGAGGCTGTGACCGGGAC 62.084 72.222 6.32 2.01 33.69 4.46
979 1034 3.846405 AAGGAGGCTGTGACCGGGA 62.846 63.158 6.32 0.00 33.69 5.14
980 1035 3.316573 GAAGGAGGCTGTGACCGGG 62.317 68.421 6.32 0.00 33.69 5.73
982 1037 1.903877 ATGGAAGGAGGCTGTGACCG 61.904 60.000 0.00 0.00 33.69 4.79
983 1038 0.393537 CATGGAAGGAGGCTGTGACC 60.394 60.000 0.00 0.00 0.00 4.02
984 1039 0.393537 CCATGGAAGGAGGCTGTGAC 60.394 60.000 5.56 0.00 0.00 3.67
985 1040 1.993653 CCATGGAAGGAGGCTGTGA 59.006 57.895 5.56 0.00 0.00 3.58
986 1041 1.751927 GCCATGGAAGGAGGCTGTG 60.752 63.158 18.40 0.00 44.92 3.66
987 1042 2.679716 GCCATGGAAGGAGGCTGT 59.320 61.111 18.40 0.00 44.92 4.40
989 1044 3.801997 CCGCCATGGAAGGAGGCT 61.802 66.667 18.40 0.00 46.14 4.58
1457 1528 4.078516 GGTTGCCGAGGTAGCCGT 62.079 66.667 0.00 0.00 0.00 5.68
1555 1639 3.057596 ACAGAGACGCAAAGAGAGAAGAG 60.058 47.826 0.00 0.00 0.00 2.85
1588 1672 0.782384 GACGACGTGATCACCAACAC 59.218 55.000 20.03 5.85 0.00 3.32
1621 1705 8.801715 AACGAACAAACGAAACTAATAGTAGA 57.198 30.769 3.83 0.00 37.03 2.59
1643 1727 0.951040 AGGCGAGGCAAGAAAGAACG 60.951 55.000 0.00 0.00 0.00 3.95
1655 1743 3.251571 GACTAAACAGTACAAGGCGAGG 58.748 50.000 0.00 0.00 0.00 4.63
1660 1748 5.950883 TCGATCTGACTAAACAGTACAAGG 58.049 41.667 0.00 0.00 38.79 3.61
1700 1788 1.798223 CAACATGATCGTTGGACGTGT 59.202 47.619 0.00 0.00 43.14 4.49
1701 1789 2.065512 TCAACATGATCGTTGGACGTG 58.934 47.619 11.94 0.00 45.16 4.49
1708 1796 5.505654 GCCGGAATTAATCAACATGATCGTT 60.506 40.000 5.05 0.00 35.76 3.85
1709 1797 4.024048 GCCGGAATTAATCAACATGATCGT 60.024 41.667 5.05 0.00 35.76 3.73
1745 1833 2.501223 TACCTACAGCGCCAGTGCAC 62.501 60.000 9.40 9.40 37.32 4.57
1821 1909 4.998033 TGTGTAACCGATACATTTCTTGCA 59.002 37.500 4.66 0.00 45.87 4.08
1826 1914 9.525409 AGTATAAGTGTGTAACCGATACATTTC 57.475 33.333 4.66 0.68 45.87 2.17
1862 1950 5.645497 GCATCCAAGTGTAATCTGAAGAACT 59.355 40.000 0.00 0.00 0.00 3.01
1863 1951 5.412594 TGCATCCAAGTGTAATCTGAAGAAC 59.587 40.000 0.00 0.00 0.00 3.01
1864 1952 5.559770 TGCATCCAAGTGTAATCTGAAGAA 58.440 37.500 0.00 0.00 0.00 2.52
1865 1953 5.046376 TCTGCATCCAAGTGTAATCTGAAGA 60.046 40.000 0.00 0.00 0.00 2.87
1866 1954 5.181009 TCTGCATCCAAGTGTAATCTGAAG 58.819 41.667 0.00 0.00 0.00 3.02
1867 1955 5.164620 TCTGCATCCAAGTGTAATCTGAA 57.835 39.130 0.00 0.00 0.00 3.02
1868 1956 4.223700 ACTCTGCATCCAAGTGTAATCTGA 59.776 41.667 0.00 0.00 0.00 3.27
1869 1957 4.511527 ACTCTGCATCCAAGTGTAATCTG 58.488 43.478 0.00 0.00 0.00 2.90
1870 1958 4.833478 ACTCTGCATCCAAGTGTAATCT 57.167 40.909 0.00 0.00 0.00 2.40
1871 1959 5.181748 AGAACTCTGCATCCAAGTGTAATC 58.818 41.667 0.00 0.00 0.00 1.75
1872 1960 5.171339 AGAACTCTGCATCCAAGTGTAAT 57.829 39.130 0.00 0.00 0.00 1.89
1873 1961 4.623932 AGAACTCTGCATCCAAGTGTAA 57.376 40.909 0.00 0.00 0.00 2.41
1874 1962 4.040339 TGAAGAACTCTGCATCCAAGTGTA 59.960 41.667 0.00 0.00 0.00 2.90
1875 1963 3.181451 TGAAGAACTCTGCATCCAAGTGT 60.181 43.478 0.00 0.00 0.00 3.55
1876 1964 3.405831 TGAAGAACTCTGCATCCAAGTG 58.594 45.455 0.00 0.00 0.00 3.16
1877 1965 3.072184 ACTGAAGAACTCTGCATCCAAGT 59.928 43.478 0.00 0.00 29.53 3.16
1878 1966 3.672808 ACTGAAGAACTCTGCATCCAAG 58.327 45.455 0.00 0.00 29.53 3.61
1879 1967 3.777106 ACTGAAGAACTCTGCATCCAA 57.223 42.857 0.00 0.00 29.53 3.53
1880 1968 3.777106 AACTGAAGAACTCTGCATCCA 57.223 42.857 0.00 0.00 29.53 3.41
2019 2108 9.841880 TCTGTATACGATATTTATGAGCTGAAC 57.158 33.333 0.00 0.00 0.00 3.18
2079 2173 3.793819 TTTTTAGGGGGTCCACACTAC 57.206 47.619 0.00 0.00 34.83 2.73
2154 2277 1.520600 AAAAGCGCCGTCCGGATTTT 61.521 50.000 7.81 6.39 37.50 1.82
2156 2279 2.359478 AAAAGCGCCGTCCGGATT 60.359 55.556 7.81 0.00 37.50 3.01
2212 2335 9.097257 GCATGTGTTATGTTTTATTGGCTATTT 57.903 29.630 0.00 0.00 0.00 1.40
2213 2336 8.477256 AGCATGTGTTATGTTTTATTGGCTATT 58.523 29.630 0.00 0.00 0.00 1.73
2214 2337 8.010733 AGCATGTGTTATGTTTTATTGGCTAT 57.989 30.769 0.00 0.00 0.00 2.97
2215 2338 7.339212 AGAGCATGTGTTATGTTTTATTGGCTA 59.661 33.333 0.00 0.00 0.00 3.93
2216 2339 6.153340 AGAGCATGTGTTATGTTTTATTGGCT 59.847 34.615 0.00 0.00 0.00 4.75
2217 2340 6.332630 AGAGCATGTGTTATGTTTTATTGGC 58.667 36.000 0.00 0.00 0.00 4.52
2218 2341 9.853555 TTAAGAGCATGTGTTATGTTTTATTGG 57.146 29.630 0.00 0.00 0.00 3.16
2222 2345 9.278978 TGAGTTAAGAGCATGTGTTATGTTTTA 57.721 29.630 0.00 0.00 0.00 1.52
2223 2346 8.165239 TGAGTTAAGAGCATGTGTTATGTTTT 57.835 30.769 0.00 0.00 0.00 2.43
2224 2347 7.744087 TGAGTTAAGAGCATGTGTTATGTTT 57.256 32.000 0.00 0.00 0.00 2.83
2225 2348 7.228507 TGTTGAGTTAAGAGCATGTGTTATGTT 59.771 33.333 0.00 0.00 0.00 2.71
2226 2349 6.710295 TGTTGAGTTAAGAGCATGTGTTATGT 59.290 34.615 0.00 0.00 0.00 2.29
2227 2350 7.132694 TGTTGAGTTAAGAGCATGTGTTATG 57.867 36.000 0.00 0.00 0.00 1.90
2228 2351 7.308589 GGTTGTTGAGTTAAGAGCATGTGTTAT 60.309 37.037 0.00 0.00 0.00 1.89
2229 2352 6.017440 GGTTGTTGAGTTAAGAGCATGTGTTA 60.017 38.462 0.00 0.00 0.00 2.41
2230 2353 5.221048 GGTTGTTGAGTTAAGAGCATGTGTT 60.221 40.000 0.00 0.00 0.00 3.32
2231 2354 4.275936 GGTTGTTGAGTTAAGAGCATGTGT 59.724 41.667 0.00 0.00 0.00 3.72
2232 2355 4.275689 TGGTTGTTGAGTTAAGAGCATGTG 59.724 41.667 0.00 0.00 0.00 3.21
2233 2356 4.460263 TGGTTGTTGAGTTAAGAGCATGT 58.540 39.130 0.00 0.00 0.00 3.21
2234 2357 5.181811 TGATGGTTGTTGAGTTAAGAGCATG 59.818 40.000 0.00 0.00 0.00 4.06
2235 2358 5.182001 GTGATGGTTGTTGAGTTAAGAGCAT 59.818 40.000 0.00 0.00 0.00 3.79
2236 2359 4.515191 GTGATGGTTGTTGAGTTAAGAGCA 59.485 41.667 0.00 0.00 0.00 4.26
2237 2360 4.757149 AGTGATGGTTGTTGAGTTAAGAGC 59.243 41.667 0.00 0.00 0.00 4.09
2238 2361 5.991606 TGAGTGATGGTTGTTGAGTTAAGAG 59.008 40.000 0.00 0.00 0.00 2.85
2239 2362 5.924356 TGAGTGATGGTTGTTGAGTTAAGA 58.076 37.500 0.00 0.00 0.00 2.10
2240 2363 6.483307 TCTTGAGTGATGGTTGTTGAGTTAAG 59.517 38.462 0.00 0.00 0.00 1.85
2241 2364 6.353323 TCTTGAGTGATGGTTGTTGAGTTAA 58.647 36.000 0.00 0.00 0.00 2.01
2242 2365 5.924356 TCTTGAGTGATGGTTGTTGAGTTA 58.076 37.500 0.00 0.00 0.00 2.24
2243 2366 4.780815 TCTTGAGTGATGGTTGTTGAGTT 58.219 39.130 0.00 0.00 0.00 3.01
2244 2367 4.422073 TCTTGAGTGATGGTTGTTGAGT 57.578 40.909 0.00 0.00 0.00 3.41
2245 2368 4.999311 TGATCTTGAGTGATGGTTGTTGAG 59.001 41.667 0.00 0.00 0.00 3.02
2246 2369 4.756642 GTGATCTTGAGTGATGGTTGTTGA 59.243 41.667 0.00 0.00 0.00 3.18
2247 2370 4.516321 TGTGATCTTGAGTGATGGTTGTTG 59.484 41.667 0.00 0.00 0.00 3.33
2248 2371 4.717877 TGTGATCTTGAGTGATGGTTGTT 58.282 39.130 0.00 0.00 0.00 2.83
2249 2372 4.356405 TGTGATCTTGAGTGATGGTTGT 57.644 40.909 0.00 0.00 0.00 3.32
2250 2373 5.892160 ATTGTGATCTTGAGTGATGGTTG 57.108 39.130 0.00 0.00 0.00 3.77
2251 2374 6.950842 TCTATTGTGATCTTGAGTGATGGTT 58.049 36.000 0.00 0.00 0.00 3.67
2252 2375 6.550938 TCTATTGTGATCTTGAGTGATGGT 57.449 37.500 0.00 0.00 0.00 3.55
2253 2376 7.095732 CGAATCTATTGTGATCTTGAGTGATGG 60.096 40.741 0.00 0.00 0.00 3.51
2254 2377 7.437565 ACGAATCTATTGTGATCTTGAGTGATG 59.562 37.037 0.00 0.00 0.00 3.07
2255 2378 7.495901 ACGAATCTATTGTGATCTTGAGTGAT 58.504 34.615 0.00 0.00 0.00 3.06
2256 2379 6.867550 ACGAATCTATTGTGATCTTGAGTGA 58.132 36.000 0.00 0.00 0.00 3.41
2257 2380 6.753744 TGACGAATCTATTGTGATCTTGAGTG 59.246 38.462 0.00 0.00 0.00 3.51
2258 2381 6.754209 GTGACGAATCTATTGTGATCTTGAGT 59.246 38.462 0.00 0.00 0.00 3.41
2259 2382 6.977502 AGTGACGAATCTATTGTGATCTTGAG 59.022 38.462 0.00 0.00 0.00 3.02
2260 2383 6.867550 AGTGACGAATCTATTGTGATCTTGA 58.132 36.000 0.00 0.00 0.00 3.02
2261 2384 7.531280 AAGTGACGAATCTATTGTGATCTTG 57.469 36.000 0.00 0.00 0.00 3.02
2262 2385 8.553459 AAAAGTGACGAATCTATTGTGATCTT 57.447 30.769 0.00 0.00 0.00 2.40
2263 2386 9.823647 ATAAAAGTGACGAATCTATTGTGATCT 57.176 29.630 0.00 0.00 0.00 2.75
2270 2393 9.061610 CGCAAAAATAAAAGTGACGAATCTATT 57.938 29.630 0.00 0.00 0.00 1.73
2271 2394 8.447833 TCGCAAAAATAAAAGTGACGAATCTAT 58.552 29.630 0.00 0.00 0.00 1.98
2272 2395 7.798801 TCGCAAAAATAAAAGTGACGAATCTA 58.201 30.769 0.00 0.00 0.00 1.98
2273 2396 6.664515 TCGCAAAAATAAAAGTGACGAATCT 58.335 32.000 0.00 0.00 0.00 2.40
2274 2397 6.795114 TCTCGCAAAAATAAAAGTGACGAATC 59.205 34.615 0.00 0.00 0.00 2.52
2275 2398 6.577427 GTCTCGCAAAAATAAAAGTGACGAAT 59.423 34.615 0.00 0.00 0.00 3.34
2276 2399 5.905181 GTCTCGCAAAAATAAAAGTGACGAA 59.095 36.000 0.00 0.00 0.00 3.85
2277 2400 5.006844 TGTCTCGCAAAAATAAAAGTGACGA 59.993 36.000 0.00 0.00 0.00 4.20
2278 2401 5.201910 TGTCTCGCAAAAATAAAAGTGACG 58.798 37.500 0.00 0.00 0.00 4.35
2279 2402 7.623268 AATGTCTCGCAAAAATAAAAGTGAC 57.377 32.000 0.00 0.00 0.00 3.67
2292 2415 9.715123 CAAATACACAAATATAATGTCTCGCAA 57.285 29.630 0.00 0.00 0.00 4.85
2293 2416 8.888716 ACAAATACACAAATATAATGTCTCGCA 58.111 29.630 0.00 0.00 0.00 5.10
2294 2417 9.158364 CACAAATACACAAATATAATGTCTCGC 57.842 33.333 0.00 0.00 0.00 5.03
2299 2422 9.364989 GCCAACACAAATACACAAATATAATGT 57.635 29.630 0.00 0.00 0.00 2.71
2300 2423 8.530720 CGCCAACACAAATACACAAATATAATG 58.469 33.333 0.00 0.00 0.00 1.90
2301 2424 7.221838 GCGCCAACACAAATACACAAATATAAT 59.778 33.333 0.00 0.00 0.00 1.28
2302 2425 6.528423 GCGCCAACACAAATACACAAATATAA 59.472 34.615 0.00 0.00 0.00 0.98
2303 2426 6.030849 GCGCCAACACAAATACACAAATATA 58.969 36.000 0.00 0.00 0.00 0.86
2304 2427 4.862018 GCGCCAACACAAATACACAAATAT 59.138 37.500 0.00 0.00 0.00 1.28
2305 2428 4.022762 AGCGCCAACACAAATACACAAATA 60.023 37.500 2.29 0.00 0.00 1.40
2306 2429 3.056304 GCGCCAACACAAATACACAAAT 58.944 40.909 0.00 0.00 0.00 2.32
2307 2430 2.099921 AGCGCCAACACAAATACACAAA 59.900 40.909 2.29 0.00 0.00 2.83
2308 2431 1.678627 AGCGCCAACACAAATACACAA 59.321 42.857 2.29 0.00 0.00 3.33
2309 2432 1.313772 AGCGCCAACACAAATACACA 58.686 45.000 2.29 0.00 0.00 3.72
2310 2433 2.415697 AAGCGCCAACACAAATACAC 57.584 45.000 2.29 0.00 0.00 2.90
2311 2434 3.127895 GGATAAGCGCCAACACAAATACA 59.872 43.478 2.29 0.00 0.00 2.29
2312 2435 3.377172 AGGATAAGCGCCAACACAAATAC 59.623 43.478 2.29 0.00 0.00 1.89
2313 2436 3.616219 AGGATAAGCGCCAACACAAATA 58.384 40.909 2.29 0.00 0.00 1.40
2314 2437 2.446435 AGGATAAGCGCCAACACAAAT 58.554 42.857 2.29 0.00 0.00 2.32
2315 2438 1.904287 AGGATAAGCGCCAACACAAA 58.096 45.000 2.29 0.00 0.00 2.83
2316 2439 1.810151 GAAGGATAAGCGCCAACACAA 59.190 47.619 2.29 0.00 0.00 3.33
2317 2440 1.003118 AGAAGGATAAGCGCCAACACA 59.997 47.619 2.29 0.00 0.00 3.72
2318 2441 1.666189 GAGAAGGATAAGCGCCAACAC 59.334 52.381 2.29 0.00 0.00 3.32
2319 2442 1.277842 TGAGAAGGATAAGCGCCAACA 59.722 47.619 2.29 0.00 0.00 3.33
2320 2443 2.024176 TGAGAAGGATAAGCGCCAAC 57.976 50.000 2.29 0.00 0.00 3.77
2321 2444 2.485479 GGATGAGAAGGATAAGCGCCAA 60.485 50.000 2.29 0.00 0.00 4.52
2322 2445 1.070758 GGATGAGAAGGATAAGCGCCA 59.929 52.381 2.29 0.00 0.00 5.69
2323 2446 1.346068 AGGATGAGAAGGATAAGCGCC 59.654 52.381 2.29 0.00 0.00 6.53
2324 2447 2.805099 CAAGGATGAGAAGGATAAGCGC 59.195 50.000 0.00 0.00 0.00 5.92
2325 2448 4.065321 ACAAGGATGAGAAGGATAAGCG 57.935 45.455 0.00 0.00 0.00 4.68
2326 2449 4.578105 CCAACAAGGATGAGAAGGATAAGC 59.422 45.833 0.00 0.00 41.22 3.09
2327 2450 4.578105 GCCAACAAGGATGAGAAGGATAAG 59.422 45.833 0.00 0.00 41.22 1.73
2328 2451 4.526970 GCCAACAAGGATGAGAAGGATAA 58.473 43.478 0.00 0.00 41.22 1.75
2329 2452 3.432186 CGCCAACAAGGATGAGAAGGATA 60.432 47.826 0.00 0.00 41.22 2.59
2330 2453 2.681976 CGCCAACAAGGATGAGAAGGAT 60.682 50.000 0.00 0.00 41.22 3.24
2331 2454 1.339055 CGCCAACAAGGATGAGAAGGA 60.339 52.381 0.00 0.00 41.22 3.36
2332 2455 1.089920 CGCCAACAAGGATGAGAAGG 58.910 55.000 0.00 0.00 41.22 3.46
2333 2456 2.099141 TCGCCAACAAGGATGAGAAG 57.901 50.000 0.00 0.00 41.22 2.85
2334 2457 2.358957 CATCGCCAACAAGGATGAGAA 58.641 47.619 0.00 0.00 39.89 2.87
2335 2458 1.407299 CCATCGCCAACAAGGATGAGA 60.407 52.381 2.05 0.00 39.89 3.27
2336 2459 1.019673 CCATCGCCAACAAGGATGAG 58.980 55.000 2.05 0.00 39.89 2.90
2337 2460 1.031571 GCCATCGCCAACAAGGATGA 61.032 55.000 2.05 0.00 39.89 2.92
2338 2461 1.434696 GCCATCGCCAACAAGGATG 59.565 57.895 0.00 0.00 41.22 3.51
2339 2462 3.924507 GCCATCGCCAACAAGGAT 58.075 55.556 0.00 0.00 41.22 3.24
2349 2472 1.102978 ATAAACACCAAGGCCATCGC 58.897 50.000 5.01 0.00 0.00 4.58
2350 2473 3.275143 TGTATAAACACCAAGGCCATCG 58.725 45.455 5.01 0.00 0.00 3.84
2351 2474 5.652994 TTTGTATAAACACCAAGGCCATC 57.347 39.130 5.01 0.00 34.61 3.51
2352 2475 6.619329 ATTTTGTATAAACACCAAGGCCAT 57.381 33.333 5.01 0.00 34.61 4.40
2353 2476 7.540474 TTATTTTGTATAAACACCAAGGCCA 57.460 32.000 5.01 0.00 34.61 5.36
2412 2535 9.173021 CCTTAGAATAACCATATTCAACACACA 57.827 33.333 10.29 0.00 46.57 3.72
2413 2536 8.129211 GCCTTAGAATAACCATATTCAACACAC 58.871 37.037 10.29 0.00 46.57 3.82
2414 2537 7.831690 TGCCTTAGAATAACCATATTCAACACA 59.168 33.333 10.29 1.36 46.57 3.72
2415 2538 8.220755 TGCCTTAGAATAACCATATTCAACAC 57.779 34.615 10.29 0.00 46.57 3.32
2416 2539 8.995027 ATGCCTTAGAATAACCATATTCAACA 57.005 30.769 10.29 2.98 46.57 3.33
2417 2540 9.289782 AGATGCCTTAGAATAACCATATTCAAC 57.710 33.333 10.29 0.00 46.57 3.18
2418 2541 9.507329 GAGATGCCTTAGAATAACCATATTCAA 57.493 33.333 10.29 3.65 46.57 2.69
2419 2542 8.884323 AGAGATGCCTTAGAATAACCATATTCA 58.116 33.333 10.29 0.00 46.57 2.57
2420 2543 9.377312 GAGAGATGCCTTAGAATAACCATATTC 57.623 37.037 1.26 1.26 45.17 1.75
2421 2544 8.325046 GGAGAGATGCCTTAGAATAACCATATT 58.675 37.037 0.00 0.00 34.40 1.28
2422 2545 7.092668 GGGAGAGATGCCTTAGAATAACCATAT 60.093 40.741 0.00 0.00 0.00 1.78
2423 2546 6.213600 GGGAGAGATGCCTTAGAATAACCATA 59.786 42.308 0.00 0.00 0.00 2.74
2424 2547 5.013599 GGGAGAGATGCCTTAGAATAACCAT 59.986 44.000 0.00 0.00 0.00 3.55
2425 2548 4.348168 GGGAGAGATGCCTTAGAATAACCA 59.652 45.833 0.00 0.00 0.00 3.67
2426 2549 4.595350 AGGGAGAGATGCCTTAGAATAACC 59.405 45.833 0.00 0.00 0.00 2.85
2427 2550 5.279758 GGAGGGAGAGATGCCTTAGAATAAC 60.280 48.000 0.00 0.00 0.00 1.89
2428 2551 4.841246 GGAGGGAGAGATGCCTTAGAATAA 59.159 45.833 0.00 0.00 0.00 1.40
2429 2552 4.421131 GGAGGGAGAGATGCCTTAGAATA 58.579 47.826 0.00 0.00 0.00 1.75
2430 2553 3.247162 GGAGGGAGAGATGCCTTAGAAT 58.753 50.000 0.00 0.00 0.00 2.40
2431 2554 2.683768 GGAGGGAGAGATGCCTTAGAA 58.316 52.381 0.00 0.00 0.00 2.10
2432 2555 1.133009 GGGAGGGAGAGATGCCTTAGA 60.133 57.143 0.00 0.00 0.00 2.10
2433 2556 1.132881 AGGGAGGGAGAGATGCCTTAG 60.133 57.143 0.00 0.00 32.63 2.18
2434 2557 0.944999 AGGGAGGGAGAGATGCCTTA 59.055 55.000 0.00 0.00 32.63 2.69
2435 2558 0.045469 AAGGGAGGGAGAGATGCCTT 59.955 55.000 0.00 0.00 41.86 4.35
2436 2559 0.399806 GAAGGGAGGGAGAGATGCCT 60.400 60.000 0.00 0.00 39.20 4.75
2437 2560 0.399806 AGAAGGGAGGGAGAGATGCC 60.400 60.000 0.00 0.00 0.00 4.40
2438 2561 1.047801 GAGAAGGGAGGGAGAGATGC 58.952 60.000 0.00 0.00 0.00 3.91
2439 2562 1.715785 GGAGAAGGGAGGGAGAGATG 58.284 60.000 0.00 0.00 0.00 2.90
2440 2563 0.565674 GGGAGAAGGGAGGGAGAGAT 59.434 60.000 0.00 0.00 0.00 2.75
2441 2564 0.556380 AGGGAGAAGGGAGGGAGAGA 60.556 60.000 0.00 0.00 0.00 3.10
2442 2565 0.105709 GAGGGAGAAGGGAGGGAGAG 60.106 65.000 0.00 0.00 0.00 3.20
2443 2566 0.556380 AGAGGGAGAAGGGAGGGAGA 60.556 60.000 0.00 0.00 0.00 3.71
2444 2567 0.341609 AAGAGGGAGAAGGGAGGGAG 59.658 60.000 0.00 0.00 0.00 4.30
2445 2568 0.800239 AAAGAGGGAGAAGGGAGGGA 59.200 55.000 0.00 0.00 0.00 4.20
2446 2569 1.208706 GAAAGAGGGAGAAGGGAGGG 58.791 60.000 0.00 0.00 0.00 4.30
2447 2570 2.262266 AGAAAGAGGGAGAAGGGAGG 57.738 55.000 0.00 0.00 0.00 4.30
2448 2571 2.503765 GGAAGAAAGAGGGAGAAGGGAG 59.496 54.545 0.00 0.00 0.00 4.30
2449 2572 2.114506 AGGAAGAAAGAGGGAGAAGGGA 59.885 50.000 0.00 0.00 0.00 4.20
2450 2573 2.503765 GAGGAAGAAAGAGGGAGAAGGG 59.496 54.545 0.00 0.00 0.00 3.95
2451 2574 3.449918 AGAGGAAGAAAGAGGGAGAAGG 58.550 50.000 0.00 0.00 0.00 3.46
2452 2575 4.160252 CAGAGAGGAAGAAAGAGGGAGAAG 59.840 50.000 0.00 0.00 0.00 2.85
2453 2576 4.093011 CAGAGAGGAAGAAAGAGGGAGAA 58.907 47.826 0.00 0.00 0.00 2.87
2454 2577 3.707316 CAGAGAGGAAGAAAGAGGGAGA 58.293 50.000 0.00 0.00 0.00 3.71
2455 2578 2.168313 GCAGAGAGGAAGAAAGAGGGAG 59.832 54.545 0.00 0.00 0.00 4.30
2456 2579 2.183679 GCAGAGAGGAAGAAAGAGGGA 58.816 52.381 0.00 0.00 0.00 4.20
2457 2580 2.187100 AGCAGAGAGGAAGAAAGAGGG 58.813 52.381 0.00 0.00 0.00 4.30
2458 2581 3.979101 AAGCAGAGAGGAAGAAAGAGG 57.021 47.619 0.00 0.00 0.00 3.69
2459 2582 5.047092 AGAGAAAGCAGAGAGGAAGAAAGAG 60.047 44.000 0.00 0.00 0.00 2.85
2460 2583 4.837860 AGAGAAAGCAGAGAGGAAGAAAGA 59.162 41.667 0.00 0.00 0.00 2.52
2461 2584 5.151297 AGAGAAAGCAGAGAGGAAGAAAG 57.849 43.478 0.00 0.00 0.00 2.62
2462 2585 5.559148 AAGAGAAAGCAGAGAGGAAGAAA 57.441 39.130 0.00 0.00 0.00 2.52
2463 2586 6.672266 TTAAGAGAAAGCAGAGAGGAAGAA 57.328 37.500 0.00 0.00 0.00 2.52
2464 2587 6.667414 AGATTAAGAGAAAGCAGAGAGGAAGA 59.333 38.462 0.00 0.00 0.00 2.87
2465 2588 6.877236 AGATTAAGAGAAAGCAGAGAGGAAG 58.123 40.000 0.00 0.00 0.00 3.46
2466 2589 6.405286 CGAGATTAAGAGAAAGCAGAGAGGAA 60.405 42.308 0.00 0.00 0.00 3.36
2467 2590 5.067153 CGAGATTAAGAGAAAGCAGAGAGGA 59.933 44.000 0.00 0.00 0.00 3.71
2468 2591 5.163561 ACGAGATTAAGAGAAAGCAGAGAGG 60.164 44.000 0.00 0.00 0.00 3.69
2469 2592 5.743398 CACGAGATTAAGAGAAAGCAGAGAG 59.257 44.000 0.00 0.00 0.00 3.20
2470 2593 5.416013 TCACGAGATTAAGAGAAAGCAGAGA 59.584 40.000 0.00 0.00 0.00 3.10
2471 2594 5.645624 TCACGAGATTAAGAGAAAGCAGAG 58.354 41.667 0.00 0.00 0.00 3.35
2472 2595 5.644977 TCACGAGATTAAGAGAAAGCAGA 57.355 39.130 0.00 0.00 0.00 4.26
2473 2596 6.038985 TCATCACGAGATTAAGAGAAAGCAG 58.961 40.000 0.00 0.00 30.20 4.24
2474 2597 5.965922 TCATCACGAGATTAAGAGAAAGCA 58.034 37.500 0.00 0.00 30.20 3.91
2475 2598 6.269315 TCTCATCACGAGATTAAGAGAAAGC 58.731 40.000 8.31 0.00 46.18 3.51


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

AutoCloner maintained by Alex Coulton.