Multiple sequence alignment - TraesCS3B01G087700

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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 TraesCS3B01G087700 chr3B 100.000 2558 0 0 1 2558 55773577 55771020 0.000000e+00 4724.0
1 TraesCS3B01G087700 chr3D 91.111 900 47 16 928 1800 33206540 33205647 0.000000e+00 1188.0
2 TraesCS3B01G087700 chr3D 89.032 310 8 8 639 943 33206891 33206603 6.730000e-96 361.0
3 TraesCS3B01G087700 chr3A 89.321 899 45 26 3 877 45709937 45709066 0.000000e+00 1081.0
4 TraesCS3B01G087700 chr3A 93.617 658 27 8 924 1569 45709068 45708414 0.000000e+00 968.0
5 TraesCS3B01G087700 chr7D 83.957 561 47 15 1897 2447 616528388 616527861 4.920000e-137 497.0
6 TraesCS3B01G087700 chr7D 93.578 109 7 0 2443 2551 511116444 511116552 2.040000e-36 163.0
7 TraesCS3B01G087700 chr4D 82.056 496 86 3 1038 1531 2770205 2769711 1.090000e-113 420.0
8 TraesCS3B01G087700 chr4B 81.452 496 89 3 1038 1531 2380134 2379640 1.100000e-108 403.0
9 TraesCS3B01G087700 chr1A 95.495 111 5 0 2441 2551 22292684 22292574 7.270000e-41 178.0
10 TraesCS3B01G087700 chr1A 90.566 106 10 0 2446 2551 471571534 471571429 9.540000e-30 141.0
11 TraesCS3B01G087700 chr6D 92.661 109 7 1 2444 2551 28160626 28160734 3.410000e-34 156.0
12 TraesCS3B01G087700 chr6D 91.509 106 9 0 2450 2555 430305768 430305663 2.050000e-31 147.0
13 TraesCS3B01G087700 chr6D 85.606 132 17 2 2312 2441 319356008 319356139 1.230000e-28 137.0
14 TraesCS3B01G087700 chr6D 95.349 43 2 0 66 108 148801791 148801833 4.570000e-08 69.4
15 TraesCS3B01G087700 chr2B 91.667 108 5 3 2446 2551 419289887 419289782 2.050000e-31 147.0
16 TraesCS3B01G087700 chr2B 100.000 31 0 0 2377 2407 188253600 188253570 9.890000e-05 58.4
17 TraesCS3B01G087700 chr7A 90.090 111 11 0 2441 2551 128048419 128048309 7.380000e-31 145.0
18 TraesCS3B01G087700 chr7A 80.531 113 17 4 1 108 287222789 287222677 5.870000e-12 82.4
19 TraesCS3B01G087700 chr5A 90.179 112 10 1 2441 2551 708124571 708124682 7.380000e-31 145.0
20 TraesCS3B01G087700 chr4A 92.000 100 8 0 2442 2541 596981497 596981398 9.540000e-30 141.0
21 TraesCS3B01G087700 chr2A 81.111 90 14 1 22 108 751011492 751011581 4.570000e-08 69.4
22 TraesCS3B01G087700 chr2A 78.505 107 18 5 20 123 721803129 721803025 5.910000e-07 65.8
23 TraesCS3B01G087700 chr2A 97.059 34 1 0 66 99 575691194 575691161 9.890000e-05 58.4
24 TraesCS3B01G087700 chr6B 94.737 38 2 0 66 103 261656820 261656857 2.750000e-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 TraesCS3B01G087700 chr3B 55771020 55773577 2557 True 4724.0 4724 100.0000 1 2558 1 chr3B.!!$R1 2557
1 TraesCS3B01G087700 chr3D 33205647 33206891 1244 True 774.5 1188 90.0715 639 1800 2 chr3D.!!$R1 1161
2 TraesCS3B01G087700 chr3A 45708414 45709937 1523 True 1024.5 1081 91.4690 3 1569 2 chr3A.!!$R1 1566
3 TraesCS3B01G087700 chr7D 616527861 616528388 527 True 497.0 497 83.9570 1897 2447 1 chr7D.!!$R1 550

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
904 931 0.179029 CTCCCGTCAACCAACCAACT 60.179 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2252 0.248907 CGGGTCGCAGATTCGTATGT 60.249 55.0 0.0 0.0 40.67 2.29 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
264 267 5.408299 CAGAACATATTCTTGGAACGTGTGA 59.592 40.000 0.00 0.00 42.91 3.58
266 269 6.485313 AGAACATATTCTTGGAACGTGTGAAA 59.515 34.615 0.00 0.00 42.91 2.69
267 270 6.817765 ACATATTCTTGGAACGTGTGAAAT 57.182 33.333 0.00 0.00 0.00 2.17
271 274 6.826893 ATTCTTGGAACGTGTGAAATTTTG 57.173 33.333 0.00 0.00 0.00 2.44
278 281 6.423905 TGGAACGTGTGAAATTTTGTTTTGAA 59.576 30.769 0.00 0.00 0.00 2.69
279 282 7.118390 TGGAACGTGTGAAATTTTGTTTTGAAT 59.882 29.630 0.00 0.00 0.00 2.57
280 283 7.960195 GGAACGTGTGAAATTTTGTTTTGAATT 59.040 29.630 0.00 0.00 0.00 2.17
348 351 6.100792 ACACAAGCGGTTTTTAAAAATGTG 57.899 33.333 27.17 27.17 38.68 3.21
354 357 7.172654 AGCGGTTTTTAAAAATGTGATGAAC 57.827 32.000 16.02 1.40 0.00 3.18
357 360 7.043059 GCGGTTTTTAAAAATGTGATGAACTCA 60.043 33.333 16.02 0.00 0.00 3.41
551 563 7.425577 TGACACTTCATGAACATTCTGTAAG 57.574 36.000 3.38 0.00 0.00 2.34
570 582 5.760743 TGTAAGTTCACGATGGACATTTTCA 59.239 36.000 0.00 0.00 0.00 2.69
575 587 7.209475 AGTTCACGATGGACATTTTCAAAAAT 58.791 30.769 0.00 0.00 39.07 1.82
586 598 8.016801 GGACATTTTCAAAAATTGGCTAATGTG 58.983 33.333 15.86 0.00 36.52 3.21
775 792 0.387929 CGCTTCTACGCCCTGGAATA 59.612 55.000 0.00 0.00 0.00 1.75
886 913 0.900647 CCTAAGATCGATCCCGGCCT 60.901 60.000 21.66 0.00 36.24 5.19
903 930 1.170290 CCTCCCGTCAACCAACCAAC 61.170 60.000 0.00 0.00 0.00 3.77
904 931 0.179029 CTCCCGTCAACCAACCAACT 60.179 55.000 0.00 0.00 0.00 3.16
905 932 1.071071 CTCCCGTCAACCAACCAACTA 59.929 52.381 0.00 0.00 0.00 2.24
919 946 3.644335 ACCAACTACTACTCCATCCCTC 58.356 50.000 0.00 0.00 0.00 4.30
923 950 2.241685 ACTACTACTCCATCCCTCACGT 59.758 50.000 0.00 0.00 0.00 4.49
924 951 1.765230 ACTACTCCATCCCTCACGTC 58.235 55.000 0.00 0.00 0.00 4.34
925 952 0.663688 CTACTCCATCCCTCACGTCG 59.336 60.000 0.00 0.00 0.00 5.12
926 953 1.381928 TACTCCATCCCTCACGTCGC 61.382 60.000 0.00 0.00 0.00 5.19
967 1075 2.162681 GCATATGTTGGGCTACATCCC 58.837 52.381 4.29 0.00 46.73 3.85
968 1076 2.224867 GCATATGTTGGGCTACATCCCT 60.225 50.000 4.29 0.00 46.67 4.20
970 1078 1.595311 ATGTTGGGCTACATCCCTCA 58.405 50.000 0.12 0.92 46.67 3.86
971 1079 0.618458 TGTTGGGCTACATCCCTCAC 59.382 55.000 0.12 0.00 46.67 3.51
992 1114 1.529865 GTCAAGTGGTTAGTTGGCGAC 59.470 52.381 0.00 0.00 37.73 5.19
994 1116 0.601841 AAGTGGTTAGTTGGCGACCG 60.602 55.000 0.00 0.00 36.22 4.79
1036 1158 1.658114 CAACAGCAGCAGCACATGT 59.342 52.632 3.17 0.00 45.49 3.21
1118 1240 0.520404 ATCAAGTCGACGTGCGTAGT 59.480 50.000 24.25 6.91 41.80 2.73
1267 1389 1.370172 GTCTCGTCGACGTTGCACT 60.370 57.895 34.40 0.00 40.80 4.40
1396 1518 2.048222 CGTCGCCCAAGCTCAAGA 60.048 61.111 0.00 0.00 36.60 3.02
1413 1535 4.393155 AGCGCATCGTTCCAGCCA 62.393 61.111 11.47 0.00 0.00 4.75
1450 1572 1.556451 CCATGATGGAGAGTGACACCA 59.444 52.381 5.27 0.00 40.96 4.17
1492 1614 3.191371 GGAGAACAATGCTAACCAGTTGG 59.809 47.826 0.00 0.00 42.17 3.77
1525 1647 0.638746 GTACAACATCGCGGAACTCG 59.361 55.000 6.13 0.00 42.76 4.18
1643 1765 9.729023 TTTCATTACTTTGTCACAGTTATGTTG 57.271 29.630 14.55 0.00 37.65 3.33
1644 1766 8.445275 TCATTACTTTGTCACAGTTATGTTGT 57.555 30.769 14.55 0.00 37.65 3.32
1657 1790 7.955324 CACAGTTATGTTGTAACGGATTTACTG 59.045 37.037 0.00 0.00 38.33 2.74
1693 1826 6.834959 ATCTCAGTCAACGCTATAAACATG 57.165 37.500 0.00 0.00 0.00 3.21
1697 1830 7.979537 TCTCAGTCAACGCTATAAACATGTAAT 59.020 33.333 0.00 0.00 0.00 1.89
1762 1896 3.731652 TGTTCCTTGGCACATCTTTTG 57.268 42.857 0.00 0.00 39.30 2.44
1816 1950 2.228545 TTTTATGTGCCCATCAGCCA 57.771 45.000 0.00 0.00 32.29 4.75
1817 1951 1.473258 TTTATGTGCCCATCAGCCAC 58.527 50.000 0.00 0.00 32.29 5.01
1818 1952 0.330941 TTATGTGCCCATCAGCCACA 59.669 50.000 0.00 0.00 32.29 4.17
1819 1953 0.394216 TATGTGCCCATCAGCCACAC 60.394 55.000 0.00 0.00 32.29 3.82
1820 1954 2.282391 GTGCCCATCAGCCACACA 60.282 61.111 0.00 0.00 0.00 3.72
1821 1955 1.902918 GTGCCCATCAGCCACACAA 60.903 57.895 0.00 0.00 0.00 3.33
1822 1956 1.902918 TGCCCATCAGCCACACAAC 60.903 57.895 0.00 0.00 0.00 3.32
1823 1957 2.639327 GCCCATCAGCCACACAACC 61.639 63.158 0.00 0.00 0.00 3.77
1824 1958 1.228521 CCCATCAGCCACACAACCA 60.229 57.895 0.00 0.00 0.00 3.67
1825 1959 1.246056 CCCATCAGCCACACAACCAG 61.246 60.000 0.00 0.00 0.00 4.00
1826 1960 1.246056 CCATCAGCCACACAACCAGG 61.246 60.000 0.00 0.00 0.00 4.45
1827 1961 1.075482 ATCAGCCACACAACCAGGG 59.925 57.895 0.00 0.00 0.00 4.45
1828 1962 2.430704 ATCAGCCACACAACCAGGGG 62.431 60.000 0.00 0.00 0.00 4.79
1829 1963 4.603535 AGCCACACAACCAGGGGC 62.604 66.667 0.00 0.00 44.92 5.80
1832 1966 4.263572 CACACAACCAGGGGCGGA 62.264 66.667 0.00 0.00 0.00 5.54
1833 1967 3.953775 ACACAACCAGGGGCGGAG 61.954 66.667 0.00 0.00 0.00 4.63
1847 1981 2.192605 CGGAGCCCTGGAATTTTGG 58.807 57.895 0.00 0.00 0.00 3.28
1848 1982 0.323360 CGGAGCCCTGGAATTTTGGA 60.323 55.000 0.00 0.00 0.00 3.53
1849 1983 1.186200 GGAGCCCTGGAATTTTGGAC 58.814 55.000 0.00 0.00 0.00 4.02
1850 1984 1.186200 GAGCCCTGGAATTTTGGACC 58.814 55.000 0.00 0.00 0.00 4.46
1851 1985 0.611896 AGCCCTGGAATTTTGGACCG 60.612 55.000 0.00 0.00 0.00 4.79
1852 1986 1.604147 GCCCTGGAATTTTGGACCGG 61.604 60.000 0.00 0.00 0.00 5.28
1853 1987 1.604147 CCCTGGAATTTTGGACCGGC 61.604 60.000 0.00 0.00 0.00 6.13
1854 1988 1.604147 CCTGGAATTTTGGACCGGCC 61.604 60.000 0.00 4.32 37.10 6.13
1855 1989 1.604147 CTGGAATTTTGGACCGGCCC 61.604 60.000 0.00 0.00 34.97 5.80
1856 1990 1.608046 GGAATTTTGGACCGGCCCA 60.608 57.895 4.87 4.87 34.97 5.36
1857 1991 0.975556 GGAATTTTGGACCGGCCCAT 60.976 55.000 11.52 0.00 35.87 4.00
1858 1992 1.686741 GGAATTTTGGACCGGCCCATA 60.687 52.381 11.52 2.11 35.87 2.74
1859 1993 2.316108 GAATTTTGGACCGGCCCATAT 58.684 47.619 11.52 4.58 35.87 1.78
1860 1994 3.492337 GAATTTTGGACCGGCCCATATA 58.508 45.455 11.52 0.00 35.87 0.86
1861 1995 2.351706 TTTTGGACCGGCCCATATAC 57.648 50.000 11.52 0.00 35.87 1.47
1862 1996 0.475044 TTTGGACCGGCCCATATACC 59.525 55.000 11.52 0.00 35.87 2.73
1863 1997 0.694783 TTGGACCGGCCCATATACCA 60.695 55.000 11.52 0.00 35.87 3.25
1864 1998 0.474854 TGGACCGGCCCATATACCAT 60.475 55.000 4.87 0.00 34.97 3.55
1865 1999 1.203326 TGGACCGGCCCATATACCATA 60.203 52.381 4.87 0.00 34.97 2.74
1866 2000 2.124411 GGACCGGCCCATATACCATAT 58.876 52.381 0.00 0.00 0.00 1.78
1867 2001 3.310731 TGGACCGGCCCATATACCATATA 60.311 47.826 4.87 0.00 34.97 0.86
1868 2002 3.323979 GGACCGGCCCATATACCATATAG 59.676 52.174 0.00 0.00 0.00 1.31
1869 2003 3.314693 ACCGGCCCATATACCATATAGG 58.685 50.000 0.00 0.00 45.67 2.57
1883 2017 5.825593 CCATATAGGTGGGCTAGAGAAAA 57.174 43.478 0.00 0.00 35.55 2.29
1884 2018 5.799213 CCATATAGGTGGGCTAGAGAAAAG 58.201 45.833 0.00 0.00 35.55 2.27
1885 2019 5.544176 CCATATAGGTGGGCTAGAGAAAAGA 59.456 44.000 0.00 0.00 35.55 2.52
1886 2020 6.043243 CCATATAGGTGGGCTAGAGAAAAGAA 59.957 42.308 0.00 0.00 35.55 2.52
1887 2021 7.420214 CCATATAGGTGGGCTAGAGAAAAGAAA 60.420 40.741 0.00 0.00 35.55 2.52
1888 2022 4.724279 AGGTGGGCTAGAGAAAAGAAAA 57.276 40.909 0.00 0.00 0.00 2.29
1889 2023 5.061721 AGGTGGGCTAGAGAAAAGAAAAA 57.938 39.130 0.00 0.00 0.00 1.94
1941 2075 0.941463 CAGCAGACGCGAGAAACAGT 60.941 55.000 15.93 0.00 45.49 3.55
1948 2082 1.775962 GCGAGAAACAGTGAGACGC 59.224 57.895 0.00 0.00 38.03 5.19
1949 2083 1.935065 GCGAGAAACAGTGAGACGCG 61.935 60.000 3.53 3.53 35.78 6.01
1963 2097 3.439129 TGAGACGCGACTGAATCTTCTAA 59.561 43.478 17.32 0.00 0.00 2.10
1967 2101 2.416836 CGCGACTGAATCTTCTAACCCA 60.417 50.000 0.00 0.00 0.00 4.51
1971 2105 5.452077 GCGACTGAATCTTCTAACCCACTAT 60.452 44.000 0.00 0.00 0.00 2.12
1980 2114 1.978455 TAACCCACTATGCCCAGCCG 61.978 60.000 0.00 0.00 0.00 5.52
2064 2206 0.912006 GGCTCCTCCACTCCTTCCTT 60.912 60.000 0.00 0.00 34.01 3.36
2068 2210 1.985895 TCCTCCACTCCTTCCTTTTCC 59.014 52.381 0.00 0.00 0.00 3.13
2077 2219 0.108329 CTTCCTTTTCCTCGCGCCTA 60.108 55.000 0.00 0.00 0.00 3.93
2118 2260 1.739929 CAGCCGCACCACATACGAA 60.740 57.895 0.00 0.00 0.00 3.85
2119 2261 1.089481 CAGCCGCACCACATACGAAT 61.089 55.000 0.00 0.00 0.00 3.34
2127 2269 1.209128 CCACATACGAATCTGCGACC 58.791 55.000 0.00 0.00 34.83 4.79
2181 2323 3.781307 AGGTGCAAGCCGGCGATA 61.781 61.111 23.20 6.17 36.28 2.92
2182 2324 3.272334 GGTGCAAGCCGGCGATAG 61.272 66.667 23.20 13.38 36.28 2.08
2195 2337 4.221422 GATAGCCGTCCTGCCGCA 62.221 66.667 0.00 0.00 0.00 5.69
2196 2338 3.521529 GATAGCCGTCCTGCCGCAT 62.522 63.158 0.00 0.00 0.00 4.73
2197 2339 2.996168 GATAGCCGTCCTGCCGCATT 62.996 60.000 0.00 0.00 0.00 3.56
2198 2340 2.996168 ATAGCCGTCCTGCCGCATTC 62.996 60.000 0.00 0.00 0.00 2.67
2200 2342 3.197790 CCGTCCTGCCGCATTCTG 61.198 66.667 0.00 0.00 0.00 3.02
2201 2343 3.197790 CGTCCTGCCGCATTCTGG 61.198 66.667 0.00 0.00 0.00 3.86
2237 2379 3.118261 TGATTTGAGGTACCATCTCCAGC 60.118 47.826 15.94 0.00 0.00 4.85
2251 2393 3.515286 CAGCAGCTCGCCAATGGG 61.515 66.667 0.00 0.00 44.04 4.00
2272 2414 3.947196 GGCCATTCCCCAATTTTCAATTC 59.053 43.478 0.00 0.00 0.00 2.17
2273 2415 4.567327 GGCCATTCCCCAATTTTCAATTCA 60.567 41.667 0.00 0.00 0.00 2.57
2274 2416 4.637091 GCCATTCCCCAATTTTCAATTCAG 59.363 41.667 0.00 0.00 0.00 3.02
2275 2417 5.187687 CCATTCCCCAATTTTCAATTCAGG 58.812 41.667 0.00 0.00 0.00 3.86
2276 2418 4.906747 TTCCCCAATTTTCAATTCAGGG 57.093 40.909 7.24 7.24 34.41 4.45
2277 2419 3.868062 TCCCCAATTTTCAATTCAGGGT 58.132 40.909 11.26 0.00 34.74 4.34
2278 2420 4.238669 TCCCCAATTTTCAATTCAGGGTT 58.761 39.130 11.26 0.00 34.74 4.11
2279 2421 4.662650 TCCCCAATTTTCAATTCAGGGTTT 59.337 37.500 11.26 0.00 34.74 3.27
2280 2422 5.133491 TCCCCAATTTTCAATTCAGGGTTTT 59.867 36.000 11.26 0.00 34.74 2.43
2281 2423 5.473162 CCCCAATTTTCAATTCAGGGTTTTC 59.527 40.000 0.00 0.00 32.90 2.29
2288 2430 7.961325 TTTCAATTCAGGGTTTTCTATTTGC 57.039 32.000 0.00 0.00 0.00 3.68
2297 2439 5.034797 GGGTTTTCTATTTGCTTATCGTGC 58.965 41.667 0.00 0.00 0.00 5.34
2300 2442 5.871465 TTTCTATTTGCTTATCGTGCACA 57.129 34.783 18.64 4.45 40.40 4.57
2301 2443 5.469373 TTCTATTTGCTTATCGTGCACAG 57.531 39.130 18.64 7.64 40.40 3.66
2302 2444 4.503910 TCTATTTGCTTATCGTGCACAGT 58.496 39.130 18.64 6.94 40.40 3.55
2304 2446 4.600012 ATTTGCTTATCGTGCACAGTAC 57.400 40.909 18.64 1.08 40.40 2.73
2305 2447 3.313012 TTGCTTATCGTGCACAGTACT 57.687 42.857 18.64 0.00 40.40 2.73
2306 2448 4.443913 TTGCTTATCGTGCACAGTACTA 57.556 40.909 18.64 0.00 40.40 1.82
2307 2449 4.649088 TGCTTATCGTGCACAGTACTAT 57.351 40.909 18.64 2.66 35.31 2.12
2308 2450 5.761165 TGCTTATCGTGCACAGTACTATA 57.239 39.130 18.64 1.71 35.31 1.31
2309 2451 6.327279 TGCTTATCGTGCACAGTACTATAT 57.673 37.500 18.64 1.32 35.31 0.86
2317 2459 7.708998 TCGTGCACAGTACTATATTACATGAA 58.291 34.615 18.64 0.00 0.00 2.57
2350 2492 8.306038 ACATACACATAGTTTTGCACATCATTT 58.694 29.630 0.00 0.00 0.00 2.32
2358 2500 6.392354 AGTTTTGCACATCATTTATGTCCAG 58.608 36.000 0.00 0.00 46.15 3.86
2372 2514 7.389803 TTTATGTCCAGTTATGTCATTGTGG 57.610 36.000 0.00 0.00 0.00 4.17
2375 2517 5.136828 TGTCCAGTTATGTCATTGTGGTTT 58.863 37.500 0.00 0.00 0.00 3.27
2449 2591 6.641474 ACTTTTCAGGGTATGTACTTAGAGC 58.359 40.000 0.00 0.00 0.00 4.09
2450 2592 5.609533 TTTCAGGGTATGTACTTAGAGCC 57.390 43.478 0.00 0.00 0.00 4.70
2451 2593 4.537945 TCAGGGTATGTACTTAGAGCCT 57.462 45.455 0.00 0.00 40.40 4.58
2453 2595 4.267341 AGGGTATGTACTTAGAGCCTGT 57.733 45.455 0.00 0.00 38.36 4.00
2454 2596 4.621769 AGGGTATGTACTTAGAGCCTGTT 58.378 43.478 0.00 0.00 38.36 3.16
2455 2597 4.650131 AGGGTATGTACTTAGAGCCTGTTC 59.350 45.833 0.00 0.00 38.36 3.18
2456 2598 4.499357 GGGTATGTACTTAGAGCCTGTTCG 60.499 50.000 0.00 0.00 0.00 3.95
2457 2599 3.802948 ATGTACTTAGAGCCTGTTCGG 57.197 47.619 0.00 0.00 0.00 4.30
2458 2600 2.799017 TGTACTTAGAGCCTGTTCGGA 58.201 47.619 0.00 0.00 33.16 4.55
2459 2601 2.490903 TGTACTTAGAGCCTGTTCGGAC 59.509 50.000 0.00 0.00 33.16 4.79
2460 2602 1.926108 ACTTAGAGCCTGTTCGGACT 58.074 50.000 0.00 0.00 33.16 3.85
2461 2603 1.819903 ACTTAGAGCCTGTTCGGACTC 59.180 52.381 0.00 0.00 36.67 3.36
2462 2604 2.096248 CTTAGAGCCTGTTCGGACTCT 58.904 52.381 0.00 3.28 43.78 3.24
2463 2605 1.752683 TAGAGCCTGTTCGGACTCTC 58.247 55.000 1.00 0.00 41.93 3.20
2464 2606 0.039035 AGAGCCTGTTCGGACTCTCT 59.961 55.000 7.68 7.68 40.16 3.10
2465 2607 0.454196 GAGCCTGTTCGGACTCTCTC 59.546 60.000 0.00 0.00 34.83 3.20
2466 2608 0.968393 AGCCTGTTCGGACTCTCTCC 60.968 60.000 0.00 0.00 35.33 3.71
2467 2609 1.950973 GCCTGTTCGGACTCTCTCCC 61.951 65.000 0.00 0.00 35.21 4.30
2468 2610 1.324005 CCTGTTCGGACTCTCTCCCC 61.324 65.000 0.00 0.00 35.21 4.81
2469 2611 1.658686 CTGTTCGGACTCTCTCCCCG 61.659 65.000 0.00 0.00 44.22 5.73
2470 2612 2.754658 TTCGGACTCTCTCCCCGC 60.755 66.667 0.00 0.00 42.70 6.13
2471 2613 3.283812 TTCGGACTCTCTCCCCGCT 62.284 63.158 0.00 0.00 42.70 5.52
2472 2614 3.213402 CGGACTCTCTCCCCGCTC 61.213 72.222 0.00 0.00 35.21 5.03
2473 2615 2.835895 GGACTCTCTCCCCGCTCC 60.836 72.222 0.00 0.00 31.83 4.70
2474 2616 2.043852 GACTCTCTCCCCGCTCCA 60.044 66.667 0.00 0.00 0.00 3.86
2475 2617 1.682684 GACTCTCTCCCCGCTCCAA 60.683 63.158 0.00 0.00 0.00 3.53
2476 2618 1.950973 GACTCTCTCCCCGCTCCAAC 61.951 65.000 0.00 0.00 0.00 3.77
2477 2619 1.684049 CTCTCTCCCCGCTCCAACT 60.684 63.158 0.00 0.00 0.00 3.16
2478 2620 1.671901 CTCTCTCCCCGCTCCAACTC 61.672 65.000 0.00 0.00 0.00 3.01
2479 2621 2.683933 TCTCCCCGCTCCAACTCC 60.684 66.667 0.00 0.00 0.00 3.85
2480 2622 4.148825 CTCCCCGCTCCAACTCCG 62.149 72.222 0.00 0.00 0.00 4.63
2483 2625 4.821589 CCCGCTCCAACTCCGCTC 62.822 72.222 0.00 0.00 0.00 5.03
2484 2626 3.764466 CCGCTCCAACTCCGCTCT 61.764 66.667 0.00 0.00 0.00 4.09
2485 2627 2.507992 CGCTCCAACTCCGCTCTG 60.508 66.667 0.00 0.00 0.00 3.35
2486 2628 2.125350 GCTCCAACTCCGCTCTGG 60.125 66.667 0.00 0.00 40.09 3.86
2506 2648 3.805267 CGGAGCAGCATCCAGTTC 58.195 61.111 10.44 0.00 39.53 3.01
2507 2649 1.078918 CGGAGCAGCATCCAGTTCA 60.079 57.895 10.44 0.00 39.53 3.18
2508 2650 0.674581 CGGAGCAGCATCCAGTTCAA 60.675 55.000 10.44 0.00 39.53 2.69
2509 2651 1.760192 GGAGCAGCATCCAGTTCAAT 58.240 50.000 0.00 0.00 39.34 2.57
2510 2652 2.097825 GGAGCAGCATCCAGTTCAATT 58.902 47.619 0.00 0.00 39.34 2.32
2511 2653 2.494870 GGAGCAGCATCCAGTTCAATTT 59.505 45.455 0.00 0.00 39.34 1.82
2512 2654 3.056322 GGAGCAGCATCCAGTTCAATTTT 60.056 43.478 0.00 0.00 39.34 1.82
2513 2655 4.562143 GGAGCAGCATCCAGTTCAATTTTT 60.562 41.667 0.00 0.00 39.34 1.94
2514 2656 4.563061 AGCAGCATCCAGTTCAATTTTTC 58.437 39.130 0.00 0.00 0.00 2.29
2515 2657 4.039488 AGCAGCATCCAGTTCAATTTTTCA 59.961 37.500 0.00 0.00 0.00 2.69
2516 2658 4.751098 GCAGCATCCAGTTCAATTTTTCAA 59.249 37.500 0.00 0.00 0.00 2.69
2517 2659 5.236911 GCAGCATCCAGTTCAATTTTTCAAA 59.763 36.000 0.00 0.00 0.00 2.69
2518 2660 6.565247 GCAGCATCCAGTTCAATTTTTCAAAG 60.565 38.462 0.00 0.00 0.00 2.77
2519 2661 6.480981 CAGCATCCAGTTCAATTTTTCAAAGT 59.519 34.615 0.00 0.00 0.00 2.66
2520 2662 6.703165 AGCATCCAGTTCAATTTTTCAAAGTC 59.297 34.615 0.00 0.00 0.00 3.01
2521 2663 6.479660 GCATCCAGTTCAATTTTTCAAAGTCA 59.520 34.615 0.00 0.00 0.00 3.41
2522 2664 7.517259 GCATCCAGTTCAATTTTTCAAAGTCAC 60.517 37.037 0.00 0.00 0.00 3.67
2523 2665 7.169158 TCCAGTTCAATTTTTCAAAGTCACT 57.831 32.000 0.00 0.00 0.00 3.41
2524 2666 7.257722 TCCAGTTCAATTTTTCAAAGTCACTC 58.742 34.615 0.00 0.00 0.00 3.51
2525 2667 7.035004 CCAGTTCAATTTTTCAAAGTCACTCA 58.965 34.615 0.00 0.00 0.00 3.41
2526 2668 7.545265 CCAGTTCAATTTTTCAAAGTCACTCAA 59.455 33.333 0.00 0.00 0.00 3.02
2527 2669 8.589629 CAGTTCAATTTTTCAAAGTCACTCAAG 58.410 33.333 0.00 0.00 0.00 3.02
2528 2670 7.761249 AGTTCAATTTTTCAAAGTCACTCAAGG 59.239 33.333 0.00 0.00 0.00 3.61
2529 2671 6.572519 TCAATTTTTCAAAGTCACTCAAGGG 58.427 36.000 0.00 0.00 0.00 3.95
2530 2672 4.385358 TTTTTCAAAGTCACTCAAGGGC 57.615 40.909 0.00 0.00 0.00 5.19
2531 2673 1.981256 TTCAAAGTCACTCAAGGGCC 58.019 50.000 0.00 0.00 0.00 5.80
2532 2674 0.843309 TCAAAGTCACTCAAGGGCCA 59.157 50.000 6.18 0.00 0.00 5.36
2533 2675 0.954452 CAAAGTCACTCAAGGGCCAC 59.046 55.000 6.18 0.00 0.00 5.01
2534 2676 0.846693 AAAGTCACTCAAGGGCCACT 59.153 50.000 6.18 0.00 0.00 4.00
2535 2677 0.398318 AAGTCACTCAAGGGCCACTC 59.602 55.000 6.18 0.00 0.00 3.51
2536 2678 0.472734 AGTCACTCAAGGGCCACTCT 60.473 55.000 6.18 0.00 0.00 3.24
2537 2679 0.321122 GTCACTCAAGGGCCACTCTG 60.321 60.000 6.18 0.00 0.00 3.35
2538 2680 1.673665 CACTCAAGGGCCACTCTGC 60.674 63.158 6.18 0.00 0.00 4.26
2539 2681 2.435586 CTCAAGGGCCACTCTGCG 60.436 66.667 6.18 0.00 0.00 5.18
2540 2682 4.704833 TCAAGGGCCACTCTGCGC 62.705 66.667 6.18 0.00 43.89 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 9.999009 TGTTCAACGTGTATTAAATGTTAAACA 57.001 25.926 4.23 4.23 34.01 2.83
240 243 5.408299 TCACACGTTCCAAGAATATGTTCTG 59.592 40.000 5.38 0.83 43.80 3.02
253 256 5.926542 TCAAAACAAAATTTCACACGTTCCA 59.073 32.000 0.00 0.00 0.00 3.53
254 257 6.396459 TCAAAACAAAATTTCACACGTTCC 57.604 33.333 0.00 0.00 0.00 3.62
255 258 8.873242 AATTCAAAACAAAATTTCACACGTTC 57.127 26.923 0.00 0.00 0.00 3.95
256 259 9.965748 CTAATTCAAAACAAAATTTCACACGTT 57.034 25.926 0.00 0.00 0.00 3.99
328 331 7.171447 TCATCACATTTTTAAAAACCGCTTG 57.829 32.000 15.35 11.63 0.00 4.01
332 335 8.346476 TGAGTTCATCACATTTTTAAAAACCG 57.654 30.769 15.35 11.91 31.12 4.44
445 456 9.388506 TGACATTTTAAAAATGTGGATGTGTTT 57.611 25.926 14.42 0.00 40.62 2.83
513 525 8.246871 TCATGAAGTGTCAACATTTTGTTTACA 58.753 29.630 0.00 3.87 40.78 2.41
519 531 7.703298 ATGTTCATGAAGTGTCAACATTTTG 57.297 32.000 8.80 0.00 37.30 2.44
523 535 6.675026 CAGAATGTTCATGAAGTGTCAACAT 58.325 36.000 8.80 4.72 35.27 2.71
524 536 6.063640 CAGAATGTTCATGAAGTGTCAACA 57.936 37.500 8.80 2.18 37.30 3.33
551 563 6.820470 TTTTTGAAAATGTCCATCGTGAAC 57.180 33.333 0.00 0.00 0.00 3.18
570 582 8.674263 TTCAAACATCACATTAGCCAATTTTT 57.326 26.923 0.00 0.00 0.00 1.94
775 792 0.675522 CACGGCCATTTCCTACGGTT 60.676 55.000 2.24 0.00 0.00 4.44
886 913 1.129917 TAGTTGGTTGGTTGACGGGA 58.870 50.000 0.00 0.00 0.00 5.14
903 930 2.879646 GACGTGAGGGATGGAGTAGTAG 59.120 54.545 0.00 0.00 0.00 2.57
904 931 2.744166 CGACGTGAGGGATGGAGTAGTA 60.744 54.545 0.00 0.00 0.00 1.82
905 932 1.765230 GACGTGAGGGATGGAGTAGT 58.235 55.000 0.00 0.00 0.00 2.73
967 1075 2.800544 CCAACTAACCACTTGACGTGAG 59.199 50.000 0.00 0.00 46.81 3.51
968 1076 2.828877 CCAACTAACCACTTGACGTGA 58.171 47.619 0.00 0.00 46.81 4.35
970 1078 1.589803 GCCAACTAACCACTTGACGT 58.410 50.000 0.00 0.00 0.00 4.34
971 1079 0.511221 CGCCAACTAACCACTTGACG 59.489 55.000 0.00 0.00 0.00 4.35
979 1101 1.632948 GCTTCGGTCGCCAACTAACC 61.633 60.000 0.00 0.00 0.00 2.85
982 1104 2.263540 GGCTTCGGTCGCCAACTA 59.736 61.111 5.80 0.00 46.77 2.24
1020 1142 1.970114 GGACATGTGCTGCTGCTGT 60.970 57.895 17.00 12.42 40.48 4.40
1036 1158 2.541466 GAAGGTGAGGAGAAGAAGGGA 58.459 52.381 0.00 0.00 0.00 4.20
1118 1240 2.358125 CGGTGGCGTTGGTGATCA 60.358 61.111 0.00 0.00 0.00 2.92
1267 1389 1.597854 CCACGAGCAGGTTGAGCAA 60.598 57.895 0.00 0.00 0.00 3.91
1396 1518 4.393155 TGGCTGGAACGATGCGCT 62.393 61.111 9.73 0.00 0.00 5.92
1401 1523 2.636830 CAGAAATCTGGCTGGAACGAT 58.363 47.619 2.38 0.00 40.20 3.73
1413 1535 0.036732 TGGCCAGTTCGCAGAAATCT 59.963 50.000 0.00 0.00 45.90 2.40
1450 1572 1.295423 CCGACACGGGATCCTTGTT 59.705 57.895 17.46 6.55 44.15 2.83
1492 1614 2.585247 GTACGCCATGCCGGAGAC 60.585 66.667 5.05 0.00 38.12 3.36
1631 1753 7.955324 CAGTAAATCCGTTACAACATAACTGTG 59.045 37.037 0.00 0.00 44.03 3.66
1633 1755 8.246908 TCAGTAAATCCGTTACAACATAACTG 57.753 34.615 0.00 0.00 44.03 3.16
1634 1756 9.444600 AATCAGTAAATCCGTTACAACATAACT 57.555 29.630 0.00 0.00 44.03 2.24
1638 1760 9.221933 TGTTAATCAGTAAATCCGTTACAACAT 57.778 29.630 0.00 0.00 44.03 2.71
1657 1790 9.000018 GCGTTGACTGAGATTTAATTGTTAATC 58.000 33.333 0.00 0.00 0.00 1.75
1661 1794 6.560253 AGCGTTGACTGAGATTTAATTGTT 57.440 33.333 0.00 0.00 0.00 2.83
1670 1803 6.341316 ACATGTTTATAGCGTTGACTGAGAT 58.659 36.000 0.00 0.00 0.00 2.75
1805 1939 2.639327 GGTTGTGTGGCTGATGGGC 61.639 63.158 0.00 0.00 41.27 5.36
1806 1940 1.228521 TGGTTGTGTGGCTGATGGG 60.229 57.895 0.00 0.00 0.00 4.00
1807 1941 1.246056 CCTGGTTGTGTGGCTGATGG 61.246 60.000 0.00 0.00 0.00 3.51
1808 1942 1.246056 CCCTGGTTGTGTGGCTGATG 61.246 60.000 0.00 0.00 0.00 3.07
1809 1943 1.075482 CCCTGGTTGTGTGGCTGAT 59.925 57.895 0.00 0.00 0.00 2.90
1810 1944 2.515398 CCCTGGTTGTGTGGCTGA 59.485 61.111 0.00 0.00 0.00 4.26
1811 1945 2.598394 CCCCTGGTTGTGTGGCTG 60.598 66.667 0.00 0.00 0.00 4.85
1812 1946 4.603535 GCCCCTGGTTGTGTGGCT 62.604 66.667 2.57 0.00 39.05 4.75
1815 1949 4.263572 TCCGCCCCTGGTTGTGTG 62.264 66.667 0.00 0.00 0.00 3.82
1816 1950 3.953775 CTCCGCCCCTGGTTGTGT 61.954 66.667 0.00 0.00 0.00 3.72
1828 1962 1.512694 CAAAATTCCAGGGCTCCGC 59.487 57.895 0.00 0.00 0.00 5.54
1829 1963 0.323360 TCCAAAATTCCAGGGCTCCG 60.323 55.000 0.00 0.00 0.00 4.63
1830 1964 1.186200 GTCCAAAATTCCAGGGCTCC 58.814 55.000 0.00 0.00 0.00 4.70
1831 1965 1.186200 GGTCCAAAATTCCAGGGCTC 58.814 55.000 0.00 0.00 0.00 4.70
1832 1966 0.611896 CGGTCCAAAATTCCAGGGCT 60.612 55.000 0.00 0.00 0.00 5.19
1833 1967 1.604147 CCGGTCCAAAATTCCAGGGC 61.604 60.000 0.00 0.00 0.00 5.19
1834 1968 1.604147 GCCGGTCCAAAATTCCAGGG 61.604 60.000 1.90 0.00 0.00 4.45
1835 1969 1.604147 GGCCGGTCCAAAATTCCAGG 61.604 60.000 1.90 0.00 34.01 4.45
1836 1970 1.604147 GGGCCGGTCCAAAATTCCAG 61.604 60.000 23.50 0.00 36.21 3.86
1837 1971 1.608046 GGGCCGGTCCAAAATTCCA 60.608 57.895 23.50 0.00 36.21 3.53
1838 1972 0.975556 ATGGGCCGGTCCAAAATTCC 60.976 55.000 35.35 6.07 40.62 3.01
1839 1973 1.770294 TATGGGCCGGTCCAAAATTC 58.230 50.000 35.35 0.00 40.62 2.17
1840 1974 2.470057 ATATGGGCCGGTCCAAAATT 57.530 45.000 35.35 19.08 40.62 1.82
1841 1975 2.490168 GGTATATGGGCCGGTCCAAAAT 60.490 50.000 35.35 28.89 40.62 1.82
1842 1976 1.133730 GGTATATGGGCCGGTCCAAAA 60.134 52.381 35.35 24.19 40.62 2.44
1843 1977 0.475044 GGTATATGGGCCGGTCCAAA 59.525 55.000 35.35 18.41 40.62 3.28
1844 1978 0.694783 TGGTATATGGGCCGGTCCAA 60.695 55.000 35.35 21.76 40.62 3.53
1845 1979 0.474854 ATGGTATATGGGCCGGTCCA 60.475 55.000 33.79 33.79 41.60 4.02
1846 1980 1.575419 TATGGTATATGGGCCGGTCC 58.425 55.000 21.35 21.35 0.00 4.46
1847 1981 3.323979 CCTATATGGTATATGGGCCGGTC 59.676 52.174 1.90 0.00 0.00 4.79
1848 1982 3.314693 CCTATATGGTATATGGGCCGGT 58.685 50.000 1.90 0.00 0.00 5.28
1861 1995 5.544176 TCTTTTCTCTAGCCCACCTATATGG 59.456 44.000 0.00 0.00 42.93 2.74
1862 1996 6.672266 TCTTTTCTCTAGCCCACCTATATG 57.328 41.667 0.00 0.00 0.00 1.78
1863 1997 7.691993 TTTCTTTTCTCTAGCCCACCTATAT 57.308 36.000 0.00 0.00 0.00 0.86
1864 1998 7.504926 TTTTCTTTTCTCTAGCCCACCTATA 57.495 36.000 0.00 0.00 0.00 1.31
1865 1999 6.388619 TTTTCTTTTCTCTAGCCCACCTAT 57.611 37.500 0.00 0.00 0.00 2.57
1866 2000 5.836024 TTTTCTTTTCTCTAGCCCACCTA 57.164 39.130 0.00 0.00 0.00 3.08
1867 2001 4.724279 TTTTCTTTTCTCTAGCCCACCT 57.276 40.909 0.00 0.00 0.00 4.00
1889 2023 0.368567 GCGTGCGTTGTTTGCTTTTT 59.631 45.000 0.00 0.00 0.00 1.94
1890 2024 0.734253 TGCGTGCGTTGTTTGCTTTT 60.734 45.000 0.00 0.00 0.00 2.27
1891 2025 1.153939 TGCGTGCGTTGTTTGCTTT 60.154 47.368 0.00 0.00 0.00 3.51
1892 2026 1.871789 GTGCGTGCGTTGTTTGCTT 60.872 52.632 0.00 0.00 0.00 3.91
1893 2027 2.277884 GTGCGTGCGTTGTTTGCT 60.278 55.556 0.00 0.00 0.00 3.91
1894 2028 3.319316 GGTGCGTGCGTTGTTTGC 61.319 61.111 0.00 0.00 0.00 3.68
1895 2029 2.101185 TGGTGCGTGCGTTGTTTG 59.899 55.556 0.00 0.00 0.00 2.93
1924 2058 0.939577 TCACTGTTTCTCGCGTCTGC 60.940 55.000 5.77 0.00 37.91 4.26
1941 2075 1.813178 AGAAGATTCAGTCGCGTCTCA 59.187 47.619 5.77 0.00 0.00 3.27
1948 2082 4.457834 AGTGGGTTAGAAGATTCAGTCG 57.542 45.455 0.00 0.00 0.00 4.18
1949 2083 5.755861 GCATAGTGGGTTAGAAGATTCAGTC 59.244 44.000 0.00 0.00 0.00 3.51
1963 2097 3.797353 CGGCTGGGCATAGTGGGT 61.797 66.667 0.00 0.00 0.00 4.51
2025 2160 4.421479 CTGAGCGGTTCGGCGTCT 62.421 66.667 6.85 0.00 38.18 4.18
2032 2167 2.185608 GAGCCTCCTGAGCGGTTC 59.814 66.667 0.00 0.00 34.64 3.62
2064 2206 4.807039 GCGGTAGGCGCGAGGAAA 62.807 66.667 12.10 0.00 0.00 3.13
2110 2252 0.248907 CGGGTCGCAGATTCGTATGT 60.249 55.000 0.00 0.00 40.67 2.29
2118 2260 3.461773 CAGGGTCGGGTCGCAGAT 61.462 66.667 0.00 0.00 40.67 2.90
2127 2269 3.782443 GTGGTAGGGCAGGGTCGG 61.782 72.222 0.00 0.00 0.00 4.79
2165 2307 3.272334 CTATCGCCGGCTTGCACC 61.272 66.667 26.68 0.00 0.00 5.01
2178 2320 2.996168 AATGCGGCAGGACGGCTATC 62.996 60.000 9.25 0.00 44.53 2.08
2179 2321 2.996168 GAATGCGGCAGGACGGCTAT 62.996 60.000 9.25 0.00 44.53 2.97
2180 2322 3.733344 GAATGCGGCAGGACGGCTA 62.733 63.158 9.25 0.00 44.53 3.93
2183 2325 3.197790 CAGAATGCGGCAGGACGG 61.198 66.667 9.25 0.00 0.00 4.79
2184 2326 3.197790 CCAGAATGCGGCAGGACG 61.198 66.667 9.25 0.00 31.97 4.79
2191 2333 3.869272 GCGAGTGCCAGAATGCGG 61.869 66.667 0.00 0.00 33.98 5.69
2201 2343 3.984193 AATCAGGCCAGGCGAGTGC 62.984 63.158 5.01 0.00 41.71 4.40
2202 2344 1.377725 AAATCAGGCCAGGCGAGTG 60.378 57.895 5.01 2.84 0.00 3.51
2203 2345 1.377725 CAAATCAGGCCAGGCGAGT 60.378 57.895 5.01 0.00 0.00 4.18
2209 2351 1.281867 TGGTACCTCAAATCAGGCCAG 59.718 52.381 14.36 0.00 36.98 4.85
2210 2352 1.367346 TGGTACCTCAAATCAGGCCA 58.633 50.000 14.36 0.00 36.98 5.36
2251 2393 4.587891 TGAATTGAAAATTGGGGAATGGC 58.412 39.130 0.00 0.00 0.00 4.40
2253 2395 5.187687 CCCTGAATTGAAAATTGGGGAATG 58.812 41.667 11.81 0.00 34.94 2.67
2272 2414 6.258160 CACGATAAGCAAATAGAAAACCCTG 58.742 40.000 0.00 0.00 0.00 4.45
2273 2415 5.163652 GCACGATAAGCAAATAGAAAACCCT 60.164 40.000 0.00 0.00 0.00 4.34
2274 2416 5.034797 GCACGATAAGCAAATAGAAAACCC 58.965 41.667 0.00 0.00 0.00 4.11
2275 2417 5.511729 GTGCACGATAAGCAAATAGAAAACC 59.488 40.000 0.00 0.00 44.64 3.27
2276 2418 6.083630 TGTGCACGATAAGCAAATAGAAAAC 58.916 36.000 13.13 0.00 44.64 2.43
2277 2419 6.072728 ACTGTGCACGATAAGCAAATAGAAAA 60.073 34.615 13.13 0.00 44.64 2.29
2278 2420 5.411361 ACTGTGCACGATAAGCAAATAGAAA 59.589 36.000 13.13 0.00 44.64 2.52
2279 2421 4.935205 ACTGTGCACGATAAGCAAATAGAA 59.065 37.500 13.13 0.00 44.64 2.10
2280 2422 4.503910 ACTGTGCACGATAAGCAAATAGA 58.496 39.130 13.13 0.00 44.64 1.98
2281 2423 4.864916 ACTGTGCACGATAAGCAAATAG 57.135 40.909 13.13 1.50 44.64 1.73
2288 2430 9.841880 ATGTAATATAGTACTGTGCACGATAAG 57.158 33.333 13.13 6.35 0.00 1.73
2297 2439 8.066000 TCGTCGTTCATGTAATATAGTACTGTG 58.934 37.037 5.39 9.92 0.00 3.66
2300 2442 8.615211 TGTTCGTCGTTCATGTAATATAGTACT 58.385 33.333 11.32 0.00 0.00 2.73
2301 2443 8.772306 TGTTCGTCGTTCATGTAATATAGTAC 57.228 34.615 3.38 3.38 0.00 2.73
2304 2446 9.389570 TGTATGTTCGTCGTTCATGTAATATAG 57.610 33.333 12.44 0.00 0.00 1.31
2305 2447 9.172820 GTGTATGTTCGTCGTTCATGTAATATA 57.827 33.333 12.44 0.00 0.00 0.86
2306 2448 7.703197 TGTGTATGTTCGTCGTTCATGTAATAT 59.297 33.333 12.44 0.00 0.00 1.28
2307 2449 7.028361 TGTGTATGTTCGTCGTTCATGTAATA 58.972 34.615 12.44 0.00 0.00 0.98
2308 2450 5.865013 TGTGTATGTTCGTCGTTCATGTAAT 59.135 36.000 12.44 0.00 0.00 1.89
2309 2451 5.221130 TGTGTATGTTCGTCGTTCATGTAA 58.779 37.500 12.44 0.00 0.00 2.41
2317 2459 5.389098 GCAAAACTATGTGTATGTTCGTCGT 60.389 40.000 0.00 0.00 0.00 4.34
2350 2492 6.061022 ACCACAATGACATAACTGGACATA 57.939 37.500 11.24 0.00 0.00 2.29
2427 2569 5.724854 AGGCTCTAAGTACATACCCTGAAAA 59.275 40.000 0.00 0.00 0.00 2.29
2444 2586 1.282447 AGAGAGTCCGAACAGGCTCTA 59.718 52.381 9.78 0.00 46.31 2.43
2445 2587 4.854587 AGAGTCCGAACAGGCTCT 57.145 55.556 5.66 5.66 43.68 4.09
2446 2588 0.454196 GAGAGAGTCCGAACAGGCTC 59.546 60.000 0.00 0.00 40.87 4.70
2447 2589 0.968393 GGAGAGAGTCCGAACAGGCT 60.968 60.000 0.00 0.00 40.77 4.58
2448 2590 1.513622 GGAGAGAGTCCGAACAGGC 59.486 63.158 0.00 0.00 40.77 4.85
2456 2598 2.835895 GGAGCGGGGAGAGAGTCC 60.836 72.222 0.00 0.00 46.10 3.85
2457 2599 1.682684 TTGGAGCGGGGAGAGAGTC 60.683 63.158 0.00 0.00 0.00 3.36
2458 2600 1.985116 GTTGGAGCGGGGAGAGAGT 60.985 63.158 0.00 0.00 0.00 3.24
2459 2601 1.671901 GAGTTGGAGCGGGGAGAGAG 61.672 65.000 0.00 0.00 0.00 3.20
2460 2602 1.682684 GAGTTGGAGCGGGGAGAGA 60.683 63.158 0.00 0.00 0.00 3.10
2461 2603 2.726351 GGAGTTGGAGCGGGGAGAG 61.726 68.421 0.00 0.00 0.00 3.20
2462 2604 2.683933 GGAGTTGGAGCGGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
2463 2605 4.148825 CGGAGTTGGAGCGGGGAG 62.149 72.222 0.00 0.00 0.00 4.30
2466 2608 4.821589 GAGCGGAGTTGGAGCGGG 62.822 72.222 0.00 0.00 35.78 6.13
2467 2609 3.764466 AGAGCGGAGTTGGAGCGG 61.764 66.667 0.00 0.00 35.78 5.52
2468 2610 2.507992 CAGAGCGGAGTTGGAGCG 60.508 66.667 0.00 0.00 35.78 5.03
2469 2611 2.125350 CCAGAGCGGAGTTGGAGC 60.125 66.667 0.00 0.00 36.56 4.70
2470 2612 3.700109 TCCAGAGCGGAGTTGGAG 58.300 61.111 0.00 0.00 39.64 3.86
2481 2623 2.974935 GATGCTGCTCCGCTCCAGAG 62.975 65.000 0.00 0.00 0.00 3.35
2482 2624 3.079478 ATGCTGCTCCGCTCCAGA 61.079 61.111 0.00 0.00 0.00 3.86
2483 2625 2.588314 GATGCTGCTCCGCTCCAG 60.588 66.667 0.00 0.00 0.00 3.86
2484 2626 4.166888 GGATGCTGCTCCGCTCCA 62.167 66.667 0.00 0.00 31.65 3.86
2485 2627 4.166888 TGGATGCTGCTCCGCTCC 62.167 66.667 0.00 0.44 38.21 4.70
2486 2628 2.588314 CTGGATGCTGCTCCGCTC 60.588 66.667 0.00 0.00 38.21 5.03
2487 2629 2.866085 GAACTGGATGCTGCTCCGCT 62.866 60.000 0.00 0.00 38.21 5.52
2488 2630 2.437359 AACTGGATGCTGCTCCGC 60.437 61.111 0.00 0.00 38.21 5.54
2489 2631 0.674581 TTGAACTGGATGCTGCTCCG 60.675 55.000 0.00 5.15 38.21 4.63
2490 2632 1.760192 ATTGAACTGGATGCTGCTCC 58.240 50.000 0.00 6.21 35.74 4.70
2491 2633 3.863142 AAATTGAACTGGATGCTGCTC 57.137 42.857 0.00 0.00 0.00 4.26
2492 2634 4.039488 TGAAAAATTGAACTGGATGCTGCT 59.961 37.500 0.00 0.00 0.00 4.24
2493 2635 4.309099 TGAAAAATTGAACTGGATGCTGC 58.691 39.130 0.00 0.00 0.00 5.25
2494 2636 6.480981 ACTTTGAAAAATTGAACTGGATGCTG 59.519 34.615 0.00 0.00 0.00 4.41
2495 2637 6.585416 ACTTTGAAAAATTGAACTGGATGCT 58.415 32.000 0.00 0.00 0.00 3.79
2496 2638 6.479660 TGACTTTGAAAAATTGAACTGGATGC 59.520 34.615 0.00 0.00 0.00 3.91
2497 2639 7.707893 AGTGACTTTGAAAAATTGAACTGGATG 59.292 33.333 0.00 0.00 0.00 3.51
2498 2640 7.785033 AGTGACTTTGAAAAATTGAACTGGAT 58.215 30.769 0.00 0.00 0.00 3.41
2499 2641 7.093988 TGAGTGACTTTGAAAAATTGAACTGGA 60.094 33.333 0.00 0.00 0.00 3.86
2500 2642 7.035004 TGAGTGACTTTGAAAAATTGAACTGG 58.965 34.615 0.00 0.00 0.00 4.00
2501 2643 8.464770 TTGAGTGACTTTGAAAAATTGAACTG 57.535 30.769 0.00 0.00 0.00 3.16
2502 2644 7.761249 CCTTGAGTGACTTTGAAAAATTGAACT 59.239 33.333 0.00 0.00 0.00 3.01
2503 2645 7.010460 CCCTTGAGTGACTTTGAAAAATTGAAC 59.990 37.037 0.00 0.00 0.00 3.18
2504 2646 7.041107 CCCTTGAGTGACTTTGAAAAATTGAA 58.959 34.615 0.00 0.00 0.00 2.69
2505 2647 6.572519 CCCTTGAGTGACTTTGAAAAATTGA 58.427 36.000 0.00 0.00 0.00 2.57
2506 2648 5.234972 GCCCTTGAGTGACTTTGAAAAATTG 59.765 40.000 0.00 0.00 0.00 2.32
2507 2649 5.359756 GCCCTTGAGTGACTTTGAAAAATT 58.640 37.500 0.00 0.00 0.00 1.82
2508 2650 4.202253 GGCCCTTGAGTGACTTTGAAAAAT 60.202 41.667 0.00 0.00 0.00 1.82
2509 2651 3.132111 GGCCCTTGAGTGACTTTGAAAAA 59.868 43.478 0.00 0.00 0.00 1.94
2510 2652 2.693074 GGCCCTTGAGTGACTTTGAAAA 59.307 45.455 0.00 0.00 0.00 2.29
2511 2653 2.306847 GGCCCTTGAGTGACTTTGAAA 58.693 47.619 0.00 0.00 0.00 2.69
2512 2654 1.214175 TGGCCCTTGAGTGACTTTGAA 59.786 47.619 0.00 0.00 0.00 2.69
2513 2655 0.843309 TGGCCCTTGAGTGACTTTGA 59.157 50.000 0.00 0.00 0.00 2.69
2514 2656 0.954452 GTGGCCCTTGAGTGACTTTG 59.046 55.000 0.00 0.00 0.00 2.77
2515 2657 0.846693 AGTGGCCCTTGAGTGACTTT 59.153 50.000 0.00 0.00 0.00 2.66
2516 2658 0.398318 GAGTGGCCCTTGAGTGACTT 59.602 55.000 0.00 0.00 0.00 3.01
2517 2659 0.472734 AGAGTGGCCCTTGAGTGACT 60.473 55.000 0.00 0.00 0.00 3.41
2518 2660 0.321122 CAGAGTGGCCCTTGAGTGAC 60.321 60.000 0.00 0.00 0.00 3.67
2519 2661 2.061220 CAGAGTGGCCCTTGAGTGA 58.939 57.895 0.00 0.00 0.00 3.41
2520 2662 1.673665 GCAGAGTGGCCCTTGAGTG 60.674 63.158 0.00 0.00 0.00 3.51
2521 2663 2.753029 GCAGAGTGGCCCTTGAGT 59.247 61.111 0.00 0.00 0.00 3.41
2522 2664 2.435586 CGCAGAGTGGCCCTTGAG 60.436 66.667 0.00 0.00 0.00 3.02
2523 2665 4.704833 GCGCAGAGTGGCCCTTGA 62.705 66.667 0.30 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.