Multiple sequence alignment - TraesCS2A01G394500

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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 TraesCS2A01G394500 chr2A 100.000 1754 0 0 715 2468 644253569 644255322 0.000000e+00 3240.0
1 TraesCS2A01G394500 chr2A 100.000 325 0 0 1 325 644252855 644253179 3.510000e-168 601.0
2 TraesCS2A01G394500 chr2A 76.087 230 45 7 1951 2179 31083471 31083691 7.210000e-21 111.0
3 TraesCS2A01G394500 chr2A 92.500 40 2 1 2367 2406 333764111 333764073 3.430000e-04 56.5
4 TraesCS2A01G394500 chr2B 88.783 1471 135 14 715 2178 587247418 587248865 0.000000e+00 1775.0
5 TraesCS2A01G394500 chr2B 95.963 322 13 0 1 322 587247090 587247411 7.820000e-145 523.0
6 TraesCS2A01G394500 chr2B 95.000 60 3 0 2408 2467 587248879 587248938 7.270000e-16 95.3
7 TraesCS2A01G394500 chr2B 83.607 61 9 1 2337 2397 737686651 737686710 3.430000e-04 56.5
8 TraesCS2A01G394500 chr2D 92.657 926 43 8 727 1634 499732218 499733136 0.000000e+00 1310.0
9 TraesCS2A01G394500 chr2D 86.061 330 23 15 1 322 499731898 499732212 1.410000e-87 333.0
10 TraesCS2A01G394500 chr2D 95.000 60 3 0 2408 2467 499735346 499735405 7.270000e-16 95.3
11 TraesCS2A01G394500 chr5A 84.713 157 22 2 1938 2093 16733123 16732968 3.290000e-34 156.0
12 TraesCS2A01G394500 chr5A 92.500 40 3 0 2364 2403 597792175 597792214 9.530000e-05 58.4
13 TraesCS2A01G394500 chr3D 75.806 310 61 7 1877 2179 87483593 87483895 7.110000e-31 145.0
14 TraesCS2A01G394500 chr7A 80.488 164 30 2 1950 2112 27883560 27883398 9.270000e-25 124.0
15 TraesCS2A01G394500 chr7A 95.000 40 2 0 2364 2403 733521583 733521622 2.050000e-06 63.9
16 TraesCS2A01G394500 chrUn 77.619 210 39 6 1946 2155 50281686 50281887 1.200000e-23 121.0
17 TraesCS2A01G394500 chrUn 97.059 34 1 0 2370 2403 144835003 144835036 9.530000e-05 58.4
18 TraesCS2A01G394500 chrUn 97.059 34 1 0 2370 2403 144878710 144878743 9.530000e-05 58.4
19 TraesCS2A01G394500 chr1D 78.947 171 29 5 1937 2102 95443774 95443606 2.590000e-20 110.0
20 TraesCS2A01G394500 chr3B 75.309 243 49 8 1942 2179 120582089 120582325 3.360000e-19 106.0
21 TraesCS2A01G394500 chr3B 78.431 153 21 9 2038 2186 775488735 775488879 3.380000e-14 89.8
22 TraesCS2A01G394500 chr6B 76.037 217 40 11 1982 2192 563086623 563086833 4.340000e-18 102.0
23 TraesCS2A01G394500 chr1A 74.180 244 52 9 1941 2179 413799687 413799450 9.400000e-15 91.6
24 TraesCS2A01G394500 chr4B 75.500 200 40 6 1941 2137 596782281 596782474 3.380000e-14 89.8
25 TraesCS2A01G394500 chr4A 74.390 246 46 12 1941 2179 621927649 621927884 3.380000e-14 89.8
26 TraesCS2A01G394500 chr7D 92.683 41 3 0 2364 2404 397528 397568 2.650000e-05 60.2
27 TraesCS2A01G394500 chr6D 92.500 40 3 0 2364 2403 464854656 464854695 9.530000e-05 58.4
28 TraesCS2A01G394500 chr5D 92.500 40 3 0 2364 2403 495621748 495621709 9.530000e-05 58.4


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 TraesCS2A01G394500 chr2A 644252855 644255322 2467 False 1920.500000 3240 100.000000 1 2468 2 chr2A.!!$F2 2467
1 TraesCS2A01G394500 chr2B 587247090 587248938 1848 False 797.766667 1775 93.248667 1 2467 3 chr2B.!!$F2 2466
2 TraesCS2A01G394500 chr2D 499731898 499735405 3507 False 579.433333 1310 91.239333 1 2467 3 chr2D.!!$F1 2466

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
149 151 0.722676 TACTCCCCTCCCACCAATCT 59.277 55.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1697 0.036732 AAGTTCCAGCATCGCAAGGA 59.963 50.0 0.0 0.0 34.24 3.36 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
93 94 4.901866 AAAAACAACAAACACGAAGCTG 57.098 36.364 0.00 0.00 0.00 4.24
133 134 3.004171 TGACACGTGCAACACTTTTACT 58.996 40.909 17.22 0.00 35.74 2.24
149 151 0.722676 TACTCCCCTCCCACCAATCT 59.277 55.000 0.00 0.00 0.00 2.40
188 196 1.135972 CCACGACAATCTCAAAAGCCG 60.136 52.381 0.00 0.00 0.00 5.52
324 332 2.506438 GCCACTCGCTCCACGTAC 60.506 66.667 0.00 0.00 44.19 3.67
809 817 1.782181 GCTCAAAAGCGAGGTCGAC 59.218 57.895 7.13 7.13 43.02 4.20
885 893 1.448013 GCTCCGTCGCCTTTTAGCT 60.448 57.895 0.00 0.00 0.00 3.32
910 918 5.048013 TGTGTATATAAGCGCTCTGTATGCT 60.048 40.000 12.06 0.00 41.60 3.79
917 925 1.734465 GCGCTCTGTATGCTGTTCTTT 59.266 47.619 0.00 0.00 0.00 2.52
949 957 1.086067 ACACCGCTGAATGCTGATCG 61.086 55.000 0.00 0.00 40.11 3.69
969 977 2.266554 GGCTGACATCGAGTTCTTGAG 58.733 52.381 0.00 0.00 0.00 3.02
972 980 3.430098 GCTGACATCGAGTTCTTGAGGAT 60.430 47.826 8.43 0.00 0.00 3.24
1181 1204 1.406341 GCCTGAGCAATGGGTACGTTA 60.406 52.381 0.00 0.00 39.53 3.18
1182 1205 2.550978 CCTGAGCAATGGGTACGTTAG 58.449 52.381 0.00 0.00 0.00 2.34
1401 1427 1.296715 CGCCTCCAAGCACTACCTT 59.703 57.895 0.00 0.00 0.00 3.50
1510 1536 1.312815 GTTTTGTCTCAGTGCCTGCT 58.687 50.000 0.00 0.00 0.00 4.24
1511 1537 1.002033 GTTTTGTCTCAGTGCCTGCTG 60.002 52.381 0.00 0.00 37.81 4.41
1512 1538 0.535780 TTTGTCTCAGTGCCTGCTGG 60.536 55.000 5.03 5.03 37.12 4.85
1558 1584 1.585267 TTGCACTGCAGTAATGGCCG 61.585 55.000 21.20 6.37 40.61 6.13
1621 1647 7.413475 ACATATCGAATAAATGTGCTCTGTC 57.587 36.000 0.00 0.00 32.74 3.51
1626 1652 4.666237 GAATAAATGTGCTCTGTCCTTGC 58.334 43.478 0.00 0.00 0.00 4.01
1637 1663 3.157087 TCTGTCCTTGCCTTTTGGAATC 58.843 45.455 0.00 0.00 44.07 2.52
1671 1697 5.815581 TCTGTAATCTGTAGGTTGGCAAAT 58.184 37.500 0.00 0.00 0.00 2.32
1685 1711 3.635433 CAAATCCTTGCGATGCTGG 57.365 52.632 0.00 0.00 0.00 4.85
1686 1712 1.097232 CAAATCCTTGCGATGCTGGA 58.903 50.000 6.57 6.57 36.68 3.86
1687 1713 1.473677 CAAATCCTTGCGATGCTGGAA 59.526 47.619 7.83 0.00 36.14 3.53
1688 1714 1.098050 AATCCTTGCGATGCTGGAAC 58.902 50.000 7.83 0.00 36.14 3.62
1689 1715 0.254178 ATCCTTGCGATGCTGGAACT 59.746 50.000 7.83 0.00 36.14 3.01
1690 1716 0.036732 TCCTTGCGATGCTGGAACTT 59.963 50.000 0.00 0.00 31.73 2.66
1693 1719 2.288395 CCTTGCGATGCTGGAACTTTTT 60.288 45.455 0.00 0.00 0.00 1.94
1748 1776 7.171508 CGTATCATGGCAGTATAAAGAACACAT 59.828 37.037 0.00 0.00 0.00 3.21
1753 1781 9.454585 CATGGCAGTATAAAGAACACATAAATG 57.545 33.333 0.00 0.00 0.00 2.32
1792 3500 4.569943 TGCTCTTAGACCACTTAGCAAAG 58.430 43.478 0.00 0.00 34.61 2.77
1798 3506 7.511268 TCTTAGACCACTTAGCAAAGGTTTTA 58.489 34.615 0.00 0.00 37.01 1.52
1799 3507 7.994334 TCTTAGACCACTTAGCAAAGGTTTTAA 59.006 33.333 0.00 0.00 37.01 1.52
1800 3508 8.522542 TTAGACCACTTAGCAAAGGTTTTAAA 57.477 30.769 0.00 0.00 37.01 1.52
1801 3509 7.412853 AGACCACTTAGCAAAGGTTTTAAAA 57.587 32.000 0.00 0.00 37.01 1.52
1802 3510 8.018537 AGACCACTTAGCAAAGGTTTTAAAAT 57.981 30.769 3.52 0.00 37.01 1.82
1803 3511 9.138596 AGACCACTTAGCAAAGGTTTTAAAATA 57.861 29.630 3.52 0.00 37.01 1.40
1804 3512 9.923143 GACCACTTAGCAAAGGTTTTAAAATAT 57.077 29.630 3.52 0.00 37.01 1.28
1836 3544 1.922570 ACTGTATTCCACATCGACGC 58.077 50.000 0.00 0.00 36.29 5.19
1914 3622 4.339814 TGGTTAAGTTCATTGTGGTGGAAC 59.660 41.667 0.00 0.00 40.84 3.62
1940 3650 2.550208 CCACAGGGTTTGTCCTAGACAC 60.550 54.545 0.00 0.00 42.60 3.67
1941 3651 2.368875 CACAGGGTTTGTCCTAGACACT 59.631 50.000 0.00 0.00 42.60 3.55
1988 3698 3.266510 TCAGTCCTATTGGTGATGTGC 57.733 47.619 0.00 0.00 34.23 4.57
1989 3699 2.571202 TCAGTCCTATTGGTGATGTGCA 59.429 45.455 0.00 0.00 34.23 4.57
1994 3704 4.036027 GTCCTATTGGTGATGTGCATTCAG 59.964 45.833 2.81 0.00 34.23 3.02
1998 3708 0.813184 GGTGATGTGCATTCAGTGGG 59.187 55.000 2.81 0.00 0.00 4.61
2001 3711 1.340308 TGATGTGCATTCAGTGGGAGG 60.340 52.381 0.00 0.00 0.00 4.30
2009 3719 1.420430 TTCAGTGGGAGGAGACGTTT 58.580 50.000 0.00 0.00 0.00 3.60
2010 3720 0.966920 TCAGTGGGAGGAGACGTTTC 59.033 55.000 0.00 0.00 0.00 2.78
2042 3752 0.670546 AGGCGTTCATGACCACTTCG 60.671 55.000 0.00 0.00 0.00 3.79
2043 3753 0.669318 GGCGTTCATGACCACTTCGA 60.669 55.000 0.00 0.00 0.00 3.71
2049 3759 3.961480 TCATGACCACTTCGACAATCT 57.039 42.857 0.00 0.00 0.00 2.40
2058 3768 4.692625 CCACTTCGACAATCTCAAGATGTT 59.307 41.667 0.00 0.00 34.49 2.71
2081 3791 2.945008 TGCCGGCTCAATATCTTGAAAG 59.055 45.455 29.70 0.00 40.78 2.62
2093 3803 9.671279 TCAATATCTTGAAAGTGCTCATAAAGA 57.329 29.630 0.00 0.00 38.43 2.52
2103 3813 1.801178 GCTCATAAAGATAGGGTGCGC 59.199 52.381 0.00 0.00 0.00 6.09
2106 3816 3.466836 TCATAAAGATAGGGTGCGCTTG 58.533 45.455 9.73 0.00 0.00 4.01
2109 3819 2.511600 GATAGGGTGCGCTTGCGT 60.512 61.111 16.38 0.00 43.34 5.24
2134 3844 5.630539 GCATGGGTTCATAGGGTTAAGTGTA 60.631 44.000 0.00 0.00 31.33 2.90
2135 3845 6.601332 CATGGGTTCATAGGGTTAAGTGTAT 58.399 40.000 0.00 0.00 31.33 2.29
2142 3852 7.011499 TCATAGGGTTAAGTGTATGTGTGTT 57.989 36.000 0.00 0.00 0.00 3.32
2145 3855 8.879759 CATAGGGTTAAGTGTATGTGTGTTTAG 58.120 37.037 0.00 0.00 0.00 1.85
2196 3906 2.850695 AAGGTACTCCCTCCTACAGG 57.149 55.000 0.00 0.00 45.47 4.00
2197 3907 0.262285 AGGTACTCCCTCCTACAGGC 59.738 60.000 0.00 0.00 40.71 4.85
2198 3908 0.032416 GGTACTCCCTCCTACAGGCA 60.032 60.000 0.00 0.00 41.80 4.75
2199 3909 1.112950 GTACTCCCTCCTACAGGCAC 58.887 60.000 0.00 0.00 41.80 5.01
2200 3910 0.708209 TACTCCCTCCTACAGGCACA 59.292 55.000 0.00 0.00 41.80 4.57
2201 3911 0.178903 ACTCCCTCCTACAGGCACAA 60.179 55.000 0.00 0.00 41.80 3.33
2202 3912 0.250513 CTCCCTCCTACAGGCACAAC 59.749 60.000 0.00 0.00 41.80 3.32
2203 3913 0.178903 TCCCTCCTACAGGCACAACT 60.179 55.000 0.00 0.00 41.80 3.16
2204 3914 0.250513 CCCTCCTACAGGCACAACTC 59.749 60.000 0.00 0.00 41.80 3.01
2205 3915 1.270907 CCTCCTACAGGCACAACTCT 58.729 55.000 0.00 0.00 34.56 3.24
2206 3916 1.066573 CCTCCTACAGGCACAACTCTG 60.067 57.143 0.00 0.00 34.56 3.35
2207 3917 0.976641 TCCTACAGGCACAACTCTGG 59.023 55.000 0.00 0.00 35.47 3.86
2208 3918 0.976641 CCTACAGGCACAACTCTGGA 59.023 55.000 0.00 0.00 35.47 3.86
2209 3919 1.338200 CCTACAGGCACAACTCTGGAC 60.338 57.143 0.00 0.00 35.47 4.02
2210 3920 0.317160 TACAGGCACAACTCTGGACG 59.683 55.000 0.00 0.00 35.47 4.79
2211 3921 1.669115 CAGGCACAACTCTGGACGG 60.669 63.158 0.00 0.00 0.00 4.79
2212 3922 2.358737 GGCACAACTCTGGACGGG 60.359 66.667 0.00 0.00 0.00 5.28
2213 3923 3.050275 GCACAACTCTGGACGGGC 61.050 66.667 0.00 0.00 0.00 6.13
2214 3924 2.358737 CACAACTCTGGACGGGCC 60.359 66.667 0.00 0.00 37.10 5.80
2215 3925 2.847234 ACAACTCTGGACGGGCCA 60.847 61.111 4.39 0.77 46.96 5.36
2222 3932 2.989639 TGGACGGGCCAGATCAAG 59.010 61.111 10.86 0.00 43.33 3.02
2223 3933 1.612146 TGGACGGGCCAGATCAAGA 60.612 57.895 10.86 0.00 43.33 3.02
2224 3934 1.198094 TGGACGGGCCAGATCAAGAA 61.198 55.000 10.86 0.00 43.33 2.52
2225 3935 0.035439 GGACGGGCCAGATCAAGAAA 60.035 55.000 10.86 0.00 36.34 2.52
2226 3936 1.408822 GGACGGGCCAGATCAAGAAAT 60.409 52.381 10.86 0.00 36.34 2.17
2227 3937 2.369394 GACGGGCCAGATCAAGAAATT 58.631 47.619 10.86 0.00 0.00 1.82
2228 3938 2.356069 GACGGGCCAGATCAAGAAATTC 59.644 50.000 10.86 0.00 0.00 2.17
2229 3939 1.678101 CGGGCCAGATCAAGAAATTCC 59.322 52.381 4.39 0.00 0.00 3.01
2230 3940 1.678101 GGGCCAGATCAAGAAATTCCG 59.322 52.381 4.39 0.00 0.00 4.30
2231 3941 1.066152 GGCCAGATCAAGAAATTCCGC 59.934 52.381 0.00 0.00 0.00 5.54
2232 3942 2.019984 GCCAGATCAAGAAATTCCGCT 58.980 47.619 0.00 0.00 0.00 5.52
2233 3943 3.206150 GCCAGATCAAGAAATTCCGCTA 58.794 45.455 0.00 0.00 0.00 4.26
2234 3944 3.627577 GCCAGATCAAGAAATTCCGCTAA 59.372 43.478 0.00 0.00 0.00 3.09
2235 3945 4.096382 GCCAGATCAAGAAATTCCGCTAAA 59.904 41.667 0.00 0.00 0.00 1.85
2236 3946 5.393027 GCCAGATCAAGAAATTCCGCTAAAA 60.393 40.000 0.00 0.00 0.00 1.52
2237 3947 6.681368 GCCAGATCAAGAAATTCCGCTAAAAT 60.681 38.462 0.00 0.00 0.00 1.82
2238 3948 7.260603 CCAGATCAAGAAATTCCGCTAAAATT 58.739 34.615 0.00 0.00 0.00 1.82
2239 3949 7.761249 CCAGATCAAGAAATTCCGCTAAAATTT 59.239 33.333 0.00 0.00 38.64 1.82
2240 3950 8.801913 CAGATCAAGAAATTCCGCTAAAATTTC 58.198 33.333 14.97 14.97 46.37 2.17
2244 3954 5.926894 GAAATTCCGCTAAAATTTCGTCC 57.073 39.130 10.37 0.00 40.97 4.79
2245 3955 5.637809 GAAATTCCGCTAAAATTTCGTCCT 58.362 37.500 10.37 0.00 40.97 3.85
2246 3956 4.877323 ATTCCGCTAAAATTTCGTCCTC 57.123 40.909 0.00 0.00 0.00 3.71
2247 3957 3.322211 TCCGCTAAAATTTCGTCCTCA 57.678 42.857 0.00 0.00 0.00 3.86
2248 3958 3.259064 TCCGCTAAAATTTCGTCCTCAG 58.741 45.455 0.00 0.00 0.00 3.35
2249 3959 2.351726 CCGCTAAAATTTCGTCCTCAGG 59.648 50.000 0.00 0.00 0.00 3.86
2250 3960 2.223044 CGCTAAAATTTCGTCCTCAGGC 60.223 50.000 0.00 0.00 0.00 4.85
2251 3961 3.010420 GCTAAAATTTCGTCCTCAGGCT 58.990 45.455 0.00 0.00 0.00 4.58
2252 3962 3.064134 GCTAAAATTTCGTCCTCAGGCTC 59.936 47.826 0.00 0.00 0.00 4.70
2253 3963 2.859165 AAATTTCGTCCTCAGGCTCA 57.141 45.000 0.00 0.00 0.00 4.26
2254 3964 2.859165 AATTTCGTCCTCAGGCTCAA 57.141 45.000 0.00 0.00 0.00 3.02
2255 3965 2.859165 ATTTCGTCCTCAGGCTCAAA 57.141 45.000 0.00 0.00 0.00 2.69
2256 3966 2.169832 TTTCGTCCTCAGGCTCAAAG 57.830 50.000 0.00 0.00 0.00 2.77
2257 3967 1.048601 TTCGTCCTCAGGCTCAAAGT 58.951 50.000 0.00 0.00 0.00 2.66
2258 3968 1.048601 TCGTCCTCAGGCTCAAAGTT 58.951 50.000 0.00 0.00 0.00 2.66
2259 3969 2.244695 TCGTCCTCAGGCTCAAAGTTA 58.755 47.619 0.00 0.00 0.00 2.24
2260 3970 2.231478 TCGTCCTCAGGCTCAAAGTTAG 59.769 50.000 0.00 0.00 0.00 2.34
2261 3971 2.351455 GTCCTCAGGCTCAAAGTTAGC 58.649 52.381 0.00 0.00 39.33 3.09
2262 3972 2.027653 GTCCTCAGGCTCAAAGTTAGCT 60.028 50.000 0.00 0.00 39.97 3.32
2263 3973 2.234908 TCCTCAGGCTCAAAGTTAGCTC 59.765 50.000 0.00 0.00 39.97 4.09
2264 3974 2.235898 CCTCAGGCTCAAAGTTAGCTCT 59.764 50.000 0.00 0.00 39.97 4.09
2265 3975 3.449018 CCTCAGGCTCAAAGTTAGCTCTA 59.551 47.826 0.00 0.00 39.97 2.43
2266 3976 4.429108 CTCAGGCTCAAAGTTAGCTCTAC 58.571 47.826 0.00 0.00 39.97 2.59
2267 3977 4.090090 TCAGGCTCAAAGTTAGCTCTACT 58.910 43.478 0.00 0.00 39.97 2.57
2268 3978 4.158764 TCAGGCTCAAAGTTAGCTCTACTC 59.841 45.833 0.00 0.00 39.97 2.59
2269 3979 4.159506 CAGGCTCAAAGTTAGCTCTACTCT 59.840 45.833 0.00 0.00 39.97 3.24
2270 3980 4.401202 AGGCTCAAAGTTAGCTCTACTCTC 59.599 45.833 0.00 0.00 39.97 3.20
2271 3981 4.440940 GGCTCAAAGTTAGCTCTACTCTCC 60.441 50.000 0.00 0.00 39.97 3.71
2272 3982 4.158764 GCTCAAAGTTAGCTCTACTCTCCA 59.841 45.833 0.00 0.00 37.01 3.86
2273 3983 5.646577 TCAAAGTTAGCTCTACTCTCCAC 57.353 43.478 0.00 0.00 0.00 4.02
2274 3984 5.326069 TCAAAGTTAGCTCTACTCTCCACT 58.674 41.667 0.00 0.00 0.00 4.00
2275 3985 5.184096 TCAAAGTTAGCTCTACTCTCCACTG 59.816 44.000 0.00 0.00 0.00 3.66
2276 3986 4.577988 AGTTAGCTCTACTCTCCACTGA 57.422 45.455 0.00 0.00 0.00 3.41
2277 3987 4.924625 AGTTAGCTCTACTCTCCACTGAA 58.075 43.478 0.00 0.00 0.00 3.02
2278 3988 5.515106 AGTTAGCTCTACTCTCCACTGAAT 58.485 41.667 0.00 0.00 0.00 2.57
2279 3989 5.955355 AGTTAGCTCTACTCTCCACTGAATT 59.045 40.000 0.00 0.00 0.00 2.17
2280 3990 6.439058 AGTTAGCTCTACTCTCCACTGAATTT 59.561 38.462 0.00 0.00 0.00 1.82
2281 3991 5.753721 AGCTCTACTCTCCACTGAATTTT 57.246 39.130 0.00 0.00 0.00 1.82
2282 3992 6.120507 AGCTCTACTCTCCACTGAATTTTT 57.879 37.500 0.00 0.00 0.00 1.94
2283 3993 5.936956 AGCTCTACTCTCCACTGAATTTTTG 59.063 40.000 0.00 0.00 0.00 2.44
2284 3994 5.703130 GCTCTACTCTCCACTGAATTTTTGT 59.297 40.000 0.00 0.00 0.00 2.83
2285 3995 6.205658 GCTCTACTCTCCACTGAATTTTTGTT 59.794 38.462 0.00 0.00 0.00 2.83
2286 3996 7.496529 TCTACTCTCCACTGAATTTTTGTTG 57.503 36.000 0.00 0.00 0.00 3.33
2287 3997 5.520376 ACTCTCCACTGAATTTTTGTTGG 57.480 39.130 0.00 0.00 0.00 3.77
2288 3998 4.342092 ACTCTCCACTGAATTTTTGTTGGG 59.658 41.667 0.00 0.00 0.00 4.12
2289 3999 3.069443 TCTCCACTGAATTTTTGTTGGGC 59.931 43.478 0.00 0.00 0.00 5.36
2290 4000 3.037549 TCCACTGAATTTTTGTTGGGCT 58.962 40.909 0.00 0.00 0.00 5.19
2291 4001 3.132925 CCACTGAATTTTTGTTGGGCTG 58.867 45.455 0.00 0.00 0.00 4.85
2292 4002 3.132925 CACTGAATTTTTGTTGGGCTGG 58.867 45.455 0.00 0.00 0.00 4.85
2293 4003 2.104622 ACTGAATTTTTGTTGGGCTGGG 59.895 45.455 0.00 0.00 0.00 4.45
2294 4004 1.202746 TGAATTTTTGTTGGGCTGGGC 60.203 47.619 0.00 0.00 0.00 5.36
2295 4005 0.250252 AATTTTTGTTGGGCTGGGCG 60.250 50.000 0.00 0.00 0.00 6.13
2296 4006 2.110757 ATTTTTGTTGGGCTGGGCGG 62.111 55.000 0.00 0.00 0.00 6.13
2302 4012 4.890306 TGGGCTGGGCGGGCTATA 62.890 66.667 0.26 0.00 0.00 1.31
2303 4013 4.021925 GGGCTGGGCGGGCTATAG 62.022 72.222 0.26 0.00 0.00 1.31
2304 4014 4.706608 GGCTGGGCGGGCTATAGC 62.707 72.222 16.78 16.78 41.14 2.97
2322 4032 2.203538 CTGGTTTGGCCCAGCTGT 60.204 61.111 13.81 0.00 45.19 4.40
2323 4033 1.074775 CTGGTTTGGCCCAGCTGTA 59.925 57.895 13.81 0.00 45.19 2.74
2324 4034 0.962356 CTGGTTTGGCCCAGCTGTAG 60.962 60.000 13.81 4.69 45.19 2.74
2325 4035 2.343426 GGTTTGGCCCAGCTGTAGC 61.343 63.158 13.81 14.90 42.49 3.58
2335 4045 4.198625 GCTGTAGCTCTGCCACTG 57.801 61.111 0.00 0.00 38.21 3.66
2336 4046 2.105466 GCTGTAGCTCTGCCACTGC 61.105 63.158 0.00 4.66 38.21 4.40
2337 4047 1.595882 CTGTAGCTCTGCCACTGCT 59.404 57.895 0.00 0.00 40.43 4.24
2338 4048 0.459934 CTGTAGCTCTGCCACTGCTC 60.460 60.000 0.00 0.00 38.15 4.26
2339 4049 1.153469 GTAGCTCTGCCACTGCTCC 60.153 63.158 0.00 0.00 38.15 4.70
2340 4050 2.362369 TAGCTCTGCCACTGCTCCC 61.362 63.158 0.00 0.00 38.15 4.30
2341 4051 2.812218 TAGCTCTGCCACTGCTCCCT 62.812 60.000 0.00 0.00 38.15 4.20
2342 4052 2.583520 CTCTGCCACTGCTCCCTC 59.416 66.667 0.00 0.00 38.71 4.30
2343 4053 1.988956 CTCTGCCACTGCTCCCTCT 60.989 63.158 0.00 0.00 38.71 3.69
2344 4054 2.241479 CTCTGCCACTGCTCCCTCTG 62.241 65.000 0.00 0.00 38.71 3.35
2345 4055 2.527624 TGCCACTGCTCCCTCTGT 60.528 61.111 0.00 0.00 38.71 3.41
2346 4056 2.267324 GCCACTGCTCCCTCTGTC 59.733 66.667 0.00 0.00 33.53 3.51
2347 4057 2.985456 CCACTGCTCCCTCTGTCC 59.015 66.667 0.00 0.00 0.00 4.02
2348 4058 2.664081 CCACTGCTCCCTCTGTCCC 61.664 68.421 0.00 0.00 0.00 4.46
2349 4059 1.915266 CACTGCTCCCTCTGTCCCA 60.915 63.158 0.00 0.00 0.00 4.37
2350 4060 1.081833 ACTGCTCCCTCTGTCCCAT 59.918 57.895 0.00 0.00 0.00 4.00
2351 4061 0.339859 ACTGCTCCCTCTGTCCCATA 59.660 55.000 0.00 0.00 0.00 2.74
2352 4062 1.273838 ACTGCTCCCTCTGTCCCATAA 60.274 52.381 0.00 0.00 0.00 1.90
2353 4063 2.053244 CTGCTCCCTCTGTCCCATAAT 58.947 52.381 0.00 0.00 0.00 1.28
2354 4064 3.242867 CTGCTCCCTCTGTCCCATAATA 58.757 50.000 0.00 0.00 0.00 0.98
2355 4065 3.843027 CTGCTCCCTCTGTCCCATAATAT 59.157 47.826 0.00 0.00 0.00 1.28
2356 4066 5.023514 TGCTCCCTCTGTCCCATAATATA 57.976 43.478 0.00 0.00 0.00 0.86
2357 4067 5.411493 TGCTCCCTCTGTCCCATAATATAA 58.589 41.667 0.00 0.00 0.00 0.98
2358 4068 5.849475 TGCTCCCTCTGTCCCATAATATAAA 59.151 40.000 0.00 0.00 0.00 1.40
2359 4069 6.331572 TGCTCCCTCTGTCCCATAATATAAAA 59.668 38.462 0.00 0.00 0.00 1.52
2360 4070 7.147213 TGCTCCCTCTGTCCCATAATATAAAAA 60.147 37.037 0.00 0.00 0.00 1.94
2361 4071 7.890655 GCTCCCTCTGTCCCATAATATAAAAAT 59.109 37.037 0.00 0.00 0.00 1.82
2362 4072 9.236006 CTCCCTCTGTCCCATAATATAAAAATG 57.764 37.037 0.00 0.00 0.00 2.32
2363 4073 8.954729 TCCCTCTGTCCCATAATATAAAAATGA 58.045 33.333 0.00 0.00 0.00 2.57
2364 4074 9.236006 CCCTCTGTCCCATAATATAAAAATGAG 57.764 37.037 0.00 0.00 0.00 2.90
2365 4075 8.734386 CCTCTGTCCCATAATATAAAAATGAGC 58.266 37.037 0.00 0.00 0.00 4.26
2366 4076 9.512588 CTCTGTCCCATAATATAAAAATGAGCT 57.487 33.333 0.00 0.00 0.00 4.09
2367 4077 9.866655 TCTGTCCCATAATATAAAAATGAGCTT 57.133 29.630 0.00 0.00 0.00 3.74
2368 4078 9.903682 CTGTCCCATAATATAAAAATGAGCTTG 57.096 33.333 0.00 0.00 0.00 4.01
2369 4079 9.639563 TGTCCCATAATATAAAAATGAGCTTGA 57.360 29.630 0.00 0.00 0.00 3.02
2406 4116 5.431179 TTATGGGACAAAGGAAGTACCTC 57.569 43.478 0.00 0.00 45.40 3.85
2453 4163 9.452287 TGATCAAGACATCAAGTTCATAAATCA 57.548 29.630 0.00 0.00 29.41 2.57
2467 4177 4.278170 TCATAAATCAATCGTTCATGGCCC 59.722 41.667 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.608130 TGATGACTCGTCAGTTGGGG 59.392 55.000 5.91 0.00 43.61 4.96
93 94 3.482833 GTCACGCTTAGATTCGTTCTAGC 59.517 47.826 0.00 0.00 38.19 3.42
133 134 2.308722 GCAGATTGGTGGGAGGGGA 61.309 63.158 0.00 0.00 0.00 4.81
188 196 1.359459 GCGTCGTGTTGGGAGGATTC 61.359 60.000 0.00 0.00 0.00 2.52
233 241 4.038080 GTTGTGGAAAGCGCCGGG 62.038 66.667 2.29 0.00 0.00 5.73
726 734 1.369091 CGGGTGCAAAAGAGATCGGG 61.369 60.000 0.00 0.00 0.00 5.14
729 737 2.151202 TGTTCGGGTGCAAAAGAGATC 58.849 47.619 0.00 0.00 0.00 2.75
885 893 5.633601 GCATACAGAGCGCTTATATACACAA 59.366 40.000 13.26 0.00 0.00 3.33
901 909 8.540388 AGATAAACCTAAAGAACAGCATACAGA 58.460 33.333 0.00 0.00 0.00 3.41
902 910 8.607459 CAGATAAACCTAAAGAACAGCATACAG 58.393 37.037 0.00 0.00 0.00 2.74
910 918 5.472137 GGTGTGCAGATAAACCTAAAGAACA 59.528 40.000 0.00 0.00 0.00 3.18
917 925 2.018542 GCGGTGTGCAGATAAACCTA 57.981 50.000 0.00 0.00 45.45 3.08
949 957 2.266554 CTCAAGAACTCGATGTCAGCC 58.733 52.381 0.00 0.00 0.00 4.85
1181 1204 3.744003 ATTCATGCATGGCCGCCCT 62.744 57.895 25.97 0.00 0.00 5.19
1182 1205 3.228759 ATTCATGCATGGCCGCCC 61.229 61.111 25.97 0.00 0.00 6.13
1387 1413 0.246635 GCTCGAAGGTAGTGCTTGGA 59.753 55.000 0.00 0.00 0.00 3.53
1389 1415 0.388649 ACGCTCGAAGGTAGTGCTTG 60.389 55.000 0.00 0.00 0.00 4.01
1487 1513 2.146342 AGGCACTGAGACAAAACATCG 58.854 47.619 0.00 0.00 37.18 3.84
1550 1576 1.077787 CAGCAACTCCCGGCCATTA 60.078 57.895 2.24 0.00 0.00 1.90
1558 1584 1.202891 ACCAAACTACCAGCAACTCCC 60.203 52.381 0.00 0.00 0.00 4.30
1626 1652 2.736400 GCAATCTGCCGATTCCAAAAGG 60.736 50.000 0.00 0.00 37.77 3.11
1637 1663 2.831333 AGATTACAGAGCAATCTGCCG 58.169 47.619 5.19 0.00 46.52 5.69
1647 1673 4.471904 TGCCAACCTACAGATTACAGAG 57.528 45.455 0.00 0.00 0.00 3.35
1650 1676 4.947388 GGATTTGCCAACCTACAGATTACA 59.053 41.667 0.00 0.00 36.34 2.41
1671 1697 0.036732 AAGTTCCAGCATCGCAAGGA 59.963 50.000 0.00 0.00 34.24 3.36
1709 1737 6.700352 TGCCATGATACGATGAATAGATTGA 58.300 36.000 0.00 0.00 0.00 2.57
1723 1751 7.786178 TGTGTTCTTTATACTGCCATGATAC 57.214 36.000 0.00 0.00 0.00 2.24
1725 1753 8.978874 TTATGTGTTCTTTATACTGCCATGAT 57.021 30.769 0.00 0.00 0.00 2.45
1761 1790 6.398234 AGTGGTCTAAGAGCATGTATGTAG 57.602 41.667 0.00 0.00 42.05 2.74
1767 1796 3.515502 TGCTAAGTGGTCTAAGAGCATGT 59.484 43.478 0.00 0.00 42.05 3.21
1773 1802 5.562298 AACCTTTGCTAAGTGGTCTAAGA 57.438 39.130 7.14 0.00 31.64 2.10
1775 1804 8.522542 TTTAAAACCTTTGCTAAGTGGTCTAA 57.477 30.769 7.14 0.26 31.64 2.10
1806 3514 9.458374 CGATGTGGAATACAGTTTTAAACTTTT 57.542 29.630 7.71 2.77 43.80 2.27
1810 3518 6.735063 CGTCGATGTGGAATACAGTTTTAAAC 59.265 38.462 0.00 0.00 43.80 2.01
1811 3519 6.619018 GCGTCGATGTGGAATACAGTTTTAAA 60.619 38.462 6.48 0.00 43.80 1.52
1819 3527 2.200899 CATGCGTCGATGTGGAATACA 58.799 47.619 6.48 0.00 44.87 2.29
1821 3529 1.410882 TCCATGCGTCGATGTGGAATA 59.589 47.619 13.15 0.00 37.78 1.75
1822 3530 0.177836 TCCATGCGTCGATGTGGAAT 59.822 50.000 13.15 0.00 37.78 3.01
1829 3537 5.947228 ATTTGATTAATCCATGCGTCGAT 57.053 34.783 12.90 0.00 0.00 3.59
1897 3605 2.746279 TGGTTCCACCACAATGAACT 57.254 45.000 0.00 0.00 44.79 3.01
1925 3633 3.008049 ACCATCAGTGTCTAGGACAAACC 59.992 47.826 1.77 0.00 44.49 3.27
1929 3637 2.092323 CGACCATCAGTGTCTAGGACA 58.908 52.381 0.00 0.00 40.50 4.02
1940 3650 4.424061 TTCAGAAAAATGCGACCATCAG 57.576 40.909 0.00 0.00 0.00 2.90
1941 3651 5.389859 AATTCAGAAAAATGCGACCATCA 57.610 34.783 0.00 0.00 0.00 3.07
1974 3684 4.201980 CCACTGAATGCACATCACCAATAG 60.202 45.833 0.00 0.00 0.00 1.73
1980 3690 1.741706 CTCCCACTGAATGCACATCAC 59.258 52.381 0.00 0.00 0.00 3.06
1981 3691 1.340308 CCTCCCACTGAATGCACATCA 60.340 52.381 4.16 4.16 0.00 3.07
1983 3693 0.994247 TCCTCCCACTGAATGCACAT 59.006 50.000 0.00 0.00 0.00 3.21
1988 3698 0.898320 ACGTCTCCTCCCACTGAATG 59.102 55.000 0.00 0.00 0.00 2.67
1989 3699 1.645710 AACGTCTCCTCCCACTGAAT 58.354 50.000 0.00 0.00 0.00 2.57
1994 3704 0.680061 ACAGAAACGTCTCCTCCCAC 59.320 55.000 0.00 0.00 28.78 4.61
1998 3708 3.372660 AGTTGACAGAAACGTCTCCTC 57.627 47.619 0.00 0.00 36.82 3.71
2001 3711 3.881795 TCGTAGTTGACAGAAACGTCTC 58.118 45.455 0.00 0.00 36.82 3.36
2009 3719 3.786809 CGCCTTCGTAGTTGACAGA 57.213 52.632 0.00 0.00 0.00 3.41
2034 3744 4.248859 CATCTTGAGATTGTCGAAGTGGT 58.751 43.478 0.00 0.00 31.21 4.16
2036 3746 5.178252 ACAACATCTTGAGATTGTCGAAGTG 59.822 40.000 0.00 0.00 31.21 3.16
2042 3752 3.425359 CGGCACAACATCTTGAGATTGTC 60.425 47.826 0.00 0.00 31.21 3.18
2043 3753 2.485426 CGGCACAACATCTTGAGATTGT 59.515 45.455 0.00 0.00 31.21 2.71
2049 3759 0.955428 GAGCCGGCACAACATCTTGA 60.955 55.000 31.54 0.00 0.00 3.02
2058 3768 1.209261 TCAAGATATTGAGCCGGCACA 59.791 47.619 31.54 27.37 0.00 4.57
2081 3791 2.802816 CGCACCCTATCTTTATGAGCAC 59.197 50.000 0.00 0.00 0.00 4.40
2093 3803 2.819595 CACGCAAGCGCACCCTAT 60.820 61.111 15.09 0.00 44.19 2.57
2103 3813 1.064505 CTATGAACCCATGCACGCAAG 59.935 52.381 0.00 0.00 37.54 4.01
2106 3816 1.447317 CCCTATGAACCCATGCACGC 61.447 60.000 0.00 0.00 34.31 5.34
2109 3819 3.268334 ACTTAACCCTATGAACCCATGCA 59.732 43.478 0.00 0.00 34.31 3.96
2115 3825 6.315393 CACACATACACTTAACCCTATGAACC 59.685 42.308 0.00 0.00 0.00 3.62
2134 3844 4.005650 CAGATGCTCACCTAAACACACAT 58.994 43.478 0.00 0.00 0.00 3.21
2135 3845 3.402110 CAGATGCTCACCTAAACACACA 58.598 45.455 0.00 0.00 0.00 3.72
2142 3852 2.076100 CAAACGCAGATGCTCACCTAA 58.924 47.619 2.95 0.00 39.32 2.69
2145 3855 1.128692 GTACAAACGCAGATGCTCACC 59.871 52.381 2.95 0.00 39.32 4.02
2179 3889 0.032416 TGCCTGTAGGAGGGAGTACC 60.032 60.000 1.17 0.00 43.07 3.34
2184 3894 0.178903 AGTTGTGCCTGTAGGAGGGA 60.179 55.000 1.17 0.00 43.07 4.20
2185 3895 0.250513 GAGTTGTGCCTGTAGGAGGG 59.749 60.000 1.17 0.00 43.07 4.30
2186 3896 1.066573 CAGAGTTGTGCCTGTAGGAGG 60.067 57.143 1.17 0.00 46.13 4.30
2187 3897 1.066573 CCAGAGTTGTGCCTGTAGGAG 60.067 57.143 1.17 0.00 37.39 3.69
2189 3899 0.976641 TCCAGAGTTGTGCCTGTAGG 59.023 55.000 0.00 0.00 38.53 3.18
2190 3900 1.670087 CGTCCAGAGTTGTGCCTGTAG 60.670 57.143 0.00 0.00 0.00 2.74
2191 3901 0.317160 CGTCCAGAGTTGTGCCTGTA 59.683 55.000 0.00 0.00 0.00 2.74
2192 3902 1.069765 CGTCCAGAGTTGTGCCTGT 59.930 57.895 0.00 0.00 0.00 4.00
2193 3903 1.669115 CCGTCCAGAGTTGTGCCTG 60.669 63.158 0.00 0.00 0.00 4.85
2194 3904 2.743718 CCGTCCAGAGTTGTGCCT 59.256 61.111 0.00 0.00 0.00 4.75
2195 3905 2.358737 CCCGTCCAGAGTTGTGCC 60.359 66.667 0.00 0.00 0.00 5.01
2196 3906 3.050275 GCCCGTCCAGAGTTGTGC 61.050 66.667 0.00 0.00 0.00 4.57
2197 3907 2.358737 GGCCCGTCCAGAGTTGTG 60.359 66.667 0.00 0.00 34.01 3.33
2198 3908 2.847234 TGGCCCGTCCAGAGTTGT 60.847 61.111 0.00 0.00 40.72 3.32
2205 3915 1.198094 TTCTTGATCTGGCCCGTCCA 61.198 55.000 0.00 0.00 44.18 4.02
2206 3916 0.035439 TTTCTTGATCTGGCCCGTCC 60.035 55.000 0.00 0.00 0.00 4.79
2207 3917 2.044123 ATTTCTTGATCTGGCCCGTC 57.956 50.000 0.00 0.00 0.00 4.79
2208 3918 2.369394 GAATTTCTTGATCTGGCCCGT 58.631 47.619 0.00 0.00 0.00 5.28
2209 3919 1.678101 GGAATTTCTTGATCTGGCCCG 59.322 52.381 0.00 0.00 0.00 6.13
2210 3920 1.678101 CGGAATTTCTTGATCTGGCCC 59.322 52.381 0.00 0.00 0.00 5.80
2211 3921 1.066152 GCGGAATTTCTTGATCTGGCC 59.934 52.381 0.00 0.00 0.00 5.36
2212 3922 2.019984 AGCGGAATTTCTTGATCTGGC 58.980 47.619 0.00 0.00 0.00 4.85
2213 3923 5.818136 TTTAGCGGAATTTCTTGATCTGG 57.182 39.130 0.00 0.00 0.00 3.86
2214 3924 8.693542 AAATTTTAGCGGAATTTCTTGATCTG 57.306 30.769 0.00 0.00 32.76 2.90
2215 3925 7.698130 CGAAATTTTAGCGGAATTTCTTGATCT 59.302 33.333 21.61 0.00 45.01 2.75
2216 3926 7.484959 ACGAAATTTTAGCGGAATTTCTTGATC 59.515 33.333 21.61 0.00 45.01 2.92
2217 3927 7.312899 ACGAAATTTTAGCGGAATTTCTTGAT 58.687 30.769 21.61 10.17 45.01 2.57
2218 3928 6.674066 ACGAAATTTTAGCGGAATTTCTTGA 58.326 32.000 21.61 0.00 45.01 3.02
2219 3929 6.033513 GGACGAAATTTTAGCGGAATTTCTTG 59.966 38.462 21.61 14.65 45.01 3.02
2220 3930 6.072119 AGGACGAAATTTTAGCGGAATTTCTT 60.072 34.615 21.61 16.75 45.01 2.52
2221 3931 5.414765 AGGACGAAATTTTAGCGGAATTTCT 59.585 36.000 21.61 14.14 45.01 2.52
2222 3932 5.637809 AGGACGAAATTTTAGCGGAATTTC 58.362 37.500 17.67 17.67 44.32 2.17
2223 3933 5.182380 TGAGGACGAAATTTTAGCGGAATTT 59.818 36.000 7.22 7.22 38.89 1.82
2224 3934 4.698304 TGAGGACGAAATTTTAGCGGAATT 59.302 37.500 0.00 0.00 0.00 2.17
2225 3935 4.258543 TGAGGACGAAATTTTAGCGGAAT 58.741 39.130 0.00 0.00 0.00 3.01
2226 3936 3.666274 TGAGGACGAAATTTTAGCGGAA 58.334 40.909 0.00 0.00 0.00 4.30
2227 3937 3.259064 CTGAGGACGAAATTTTAGCGGA 58.741 45.455 0.00 0.00 0.00 5.54
2228 3938 2.351726 CCTGAGGACGAAATTTTAGCGG 59.648 50.000 0.00 0.00 0.00 5.52
2229 3939 2.223044 GCCTGAGGACGAAATTTTAGCG 60.223 50.000 0.65 0.00 0.00 4.26
2230 3940 3.010420 AGCCTGAGGACGAAATTTTAGC 58.990 45.455 0.65 0.00 0.00 3.09
2231 3941 4.253685 TGAGCCTGAGGACGAAATTTTAG 58.746 43.478 0.65 0.00 0.00 1.85
2232 3942 4.280436 TGAGCCTGAGGACGAAATTTTA 57.720 40.909 0.65 0.00 0.00 1.52
2233 3943 3.140325 TGAGCCTGAGGACGAAATTTT 57.860 42.857 0.65 0.00 0.00 1.82
2234 3944 2.859165 TGAGCCTGAGGACGAAATTT 57.141 45.000 0.65 0.00 0.00 1.82
2235 3945 2.859165 TTGAGCCTGAGGACGAAATT 57.141 45.000 0.65 0.00 0.00 1.82
2236 3946 2.039084 ACTTTGAGCCTGAGGACGAAAT 59.961 45.455 0.65 0.00 0.00 2.17
2237 3947 1.416401 ACTTTGAGCCTGAGGACGAAA 59.584 47.619 0.65 0.00 0.00 3.46
2238 3948 1.048601 ACTTTGAGCCTGAGGACGAA 58.951 50.000 0.65 0.49 0.00 3.85
2239 3949 1.048601 AACTTTGAGCCTGAGGACGA 58.951 50.000 0.65 0.00 0.00 4.20
2240 3950 2.611518 CTAACTTTGAGCCTGAGGACG 58.388 52.381 0.65 0.00 0.00 4.79
2241 3951 2.027653 AGCTAACTTTGAGCCTGAGGAC 60.028 50.000 0.65 0.00 41.06 3.85
2242 3952 2.234908 GAGCTAACTTTGAGCCTGAGGA 59.765 50.000 0.65 0.00 41.06 3.71
2243 3953 2.235898 AGAGCTAACTTTGAGCCTGAGG 59.764 50.000 0.00 0.00 41.06 3.86
2244 3954 3.608316 AGAGCTAACTTTGAGCCTGAG 57.392 47.619 0.00 0.00 41.06 3.35
2245 3955 4.090090 AGTAGAGCTAACTTTGAGCCTGA 58.910 43.478 0.00 0.00 41.06 3.86
2246 3956 4.159506 AGAGTAGAGCTAACTTTGAGCCTG 59.840 45.833 2.90 0.00 41.06 4.85
2247 3957 4.349365 AGAGTAGAGCTAACTTTGAGCCT 58.651 43.478 2.90 0.00 41.06 4.58
2248 3958 4.440940 GGAGAGTAGAGCTAACTTTGAGCC 60.441 50.000 2.90 0.00 41.06 4.70
2249 3959 4.158764 TGGAGAGTAGAGCTAACTTTGAGC 59.841 45.833 2.90 0.00 40.42 4.26
2250 3960 5.417580 AGTGGAGAGTAGAGCTAACTTTGAG 59.582 44.000 2.90 0.00 0.00 3.02
2251 3961 5.184096 CAGTGGAGAGTAGAGCTAACTTTGA 59.816 44.000 2.90 0.00 0.00 2.69
2252 3962 5.184096 TCAGTGGAGAGTAGAGCTAACTTTG 59.816 44.000 2.90 0.00 0.00 2.77
2253 3963 5.326069 TCAGTGGAGAGTAGAGCTAACTTT 58.674 41.667 2.90 0.00 0.00 2.66
2254 3964 4.924625 TCAGTGGAGAGTAGAGCTAACTT 58.075 43.478 2.90 0.00 0.00 2.66
2255 3965 4.577988 TCAGTGGAGAGTAGAGCTAACT 57.422 45.455 0.88 0.88 0.00 2.24
2256 3966 5.845391 ATTCAGTGGAGAGTAGAGCTAAC 57.155 43.478 0.00 0.00 0.00 2.34
2257 3967 6.859112 AAATTCAGTGGAGAGTAGAGCTAA 57.141 37.500 0.00 0.00 0.00 3.09
2258 3968 6.859112 AAAATTCAGTGGAGAGTAGAGCTA 57.141 37.500 0.00 0.00 0.00 3.32
2259 3969 5.753721 AAAATTCAGTGGAGAGTAGAGCT 57.246 39.130 0.00 0.00 0.00 4.09
2260 3970 5.703130 ACAAAAATTCAGTGGAGAGTAGAGC 59.297 40.000 0.00 0.00 0.00 4.09
2261 3971 7.308229 CCAACAAAAATTCAGTGGAGAGTAGAG 60.308 40.741 0.00 0.00 0.00 2.43
2262 3972 6.486657 CCAACAAAAATTCAGTGGAGAGTAGA 59.513 38.462 0.00 0.00 0.00 2.59
2263 3973 6.294176 CCCAACAAAAATTCAGTGGAGAGTAG 60.294 42.308 0.00 0.00 0.00 2.57
2264 3974 5.534654 CCCAACAAAAATTCAGTGGAGAGTA 59.465 40.000 0.00 0.00 0.00 2.59
2265 3975 4.342092 CCCAACAAAAATTCAGTGGAGAGT 59.658 41.667 0.00 0.00 0.00 3.24
2266 3976 4.797275 GCCCAACAAAAATTCAGTGGAGAG 60.797 45.833 0.00 0.00 0.00 3.20
2267 3977 3.069443 GCCCAACAAAAATTCAGTGGAGA 59.931 43.478 0.00 0.00 0.00 3.71
2268 3978 3.070015 AGCCCAACAAAAATTCAGTGGAG 59.930 43.478 0.00 0.00 0.00 3.86
2269 3979 3.037549 AGCCCAACAAAAATTCAGTGGA 58.962 40.909 0.00 0.00 0.00 4.02
2270 3980 3.132925 CAGCCCAACAAAAATTCAGTGG 58.867 45.455 0.00 0.00 0.00 4.00
2271 3981 3.132925 CCAGCCCAACAAAAATTCAGTG 58.867 45.455 0.00 0.00 0.00 3.66
2272 3982 2.104622 CCCAGCCCAACAAAAATTCAGT 59.895 45.455 0.00 0.00 0.00 3.41
2273 3983 2.769893 CCCAGCCCAACAAAAATTCAG 58.230 47.619 0.00 0.00 0.00 3.02
2274 3984 1.202746 GCCCAGCCCAACAAAAATTCA 60.203 47.619 0.00 0.00 0.00 2.57
2275 3985 1.522668 GCCCAGCCCAACAAAAATTC 58.477 50.000 0.00 0.00 0.00 2.17
2276 3986 0.250252 CGCCCAGCCCAACAAAAATT 60.250 50.000 0.00 0.00 0.00 1.82
2277 3987 1.370810 CGCCCAGCCCAACAAAAAT 59.629 52.632 0.00 0.00 0.00 1.82
2278 3988 2.801631 CCGCCCAGCCCAACAAAAA 61.802 57.895 0.00 0.00 0.00 1.94
2279 3989 3.230245 CCGCCCAGCCCAACAAAA 61.230 61.111 0.00 0.00 0.00 2.44
2285 3995 4.890306 TATAGCCCGCCCAGCCCA 62.890 66.667 0.00 0.00 0.00 5.36
2286 3996 4.021925 CTATAGCCCGCCCAGCCC 62.022 72.222 0.00 0.00 0.00 5.19
2287 3997 4.706608 GCTATAGCCCGCCCAGCC 62.707 72.222 14.13 0.00 34.31 4.85
2306 4016 1.074775 CTACAGCTGGGCCAAACCA 59.925 57.895 19.93 0.00 42.05 3.67
2307 4017 2.343426 GCTACAGCTGGGCCAAACC 61.343 63.158 19.93 0.00 38.21 3.27
2308 4018 3.278157 GCTACAGCTGGGCCAAAC 58.722 61.111 19.93 2.27 38.21 2.93
2317 4027 2.518973 GCAGTGGCAGAGCTACAGCT 62.519 60.000 13.87 2.72 45.58 4.24
2318 4028 2.105466 GCAGTGGCAGAGCTACAGC 61.105 63.158 7.07 7.07 43.58 4.40
2319 4029 0.459934 GAGCAGTGGCAGAGCTACAG 60.460 60.000 12.95 1.10 42.47 2.74
2320 4030 1.593787 GAGCAGTGGCAGAGCTACA 59.406 57.895 12.95 0.00 42.47 2.74
2321 4031 1.153469 GGAGCAGTGGCAGAGCTAC 60.153 63.158 12.95 10.23 44.61 3.58
2322 4032 2.362369 GGGAGCAGTGGCAGAGCTA 61.362 63.158 12.95 0.00 44.61 3.32
2323 4033 3.715097 GGGAGCAGTGGCAGAGCT 61.715 66.667 12.84 12.84 44.61 4.09
2324 4034 3.678951 GAGGGAGCAGTGGCAGAGC 62.679 68.421 3.06 3.06 44.61 4.09
2325 4035 1.988956 AGAGGGAGCAGTGGCAGAG 60.989 63.158 0.00 0.00 44.61 3.35
2326 4036 2.121385 AGAGGGAGCAGTGGCAGA 59.879 61.111 0.00 0.00 44.61 4.26
2327 4037 2.268280 CAGAGGGAGCAGTGGCAG 59.732 66.667 0.00 0.00 44.61 4.85
2328 4038 2.527624 ACAGAGGGAGCAGTGGCA 60.528 61.111 0.00 0.00 44.61 4.92
2329 4039 2.267324 GACAGAGGGAGCAGTGGC 59.733 66.667 0.00 0.00 41.61 5.01
2330 4040 2.664081 GGGACAGAGGGAGCAGTGG 61.664 68.421 0.00 0.00 0.00 4.00
2331 4041 1.915266 TGGGACAGAGGGAGCAGTG 60.915 63.158 0.00 0.00 0.00 3.66
2332 4042 2.533435 TGGGACAGAGGGAGCAGT 59.467 61.111 0.00 0.00 0.00 4.40
2371 4081 9.863845 CCTTTGTCCCATAATATAAAAACGTTT 57.136 29.630 7.96 7.96 0.00 3.60
2372 4082 9.245481 TCCTTTGTCCCATAATATAAAAACGTT 57.755 29.630 0.00 0.00 0.00 3.99
2373 4083 8.810990 TCCTTTGTCCCATAATATAAAAACGT 57.189 30.769 0.00 0.00 0.00 3.99
2374 4084 9.730420 CTTCCTTTGTCCCATAATATAAAAACG 57.270 33.333 0.00 0.00 0.00 3.60
2378 4088 9.856162 GGTACTTCCTTTGTCCCATAATATAAA 57.144 33.333 0.00 0.00 0.00 1.40
2379 4089 9.232882 AGGTACTTCCTTTGTCCCATAATATAA 57.767 33.333 0.00 0.00 45.67 0.98
2380 4090 8.808240 AGGTACTTCCTTTGTCCCATAATATA 57.192 34.615 0.00 0.00 45.67 0.86
2381 4091 7.707467 AGGTACTTCCTTTGTCCCATAATAT 57.293 36.000 0.00 0.00 45.67 1.28
2396 4106 2.359531 CGGTGAGATCTGAGGTACTTCC 59.640 54.545 0.00 0.00 41.55 3.46
2397 4107 2.223618 GCGGTGAGATCTGAGGTACTTC 60.224 54.545 0.00 0.00 41.55 3.01
2398 4108 1.751924 GCGGTGAGATCTGAGGTACTT 59.248 52.381 0.00 0.00 41.55 2.24
2400 4110 0.386113 GGCGGTGAGATCTGAGGTAC 59.614 60.000 0.00 0.00 0.00 3.34
2401 4111 1.101635 CGGCGGTGAGATCTGAGGTA 61.102 60.000 0.00 0.00 0.00 3.08
2402 4112 2.418910 CGGCGGTGAGATCTGAGGT 61.419 63.158 0.00 0.00 0.00 3.85
2403 4113 1.459455 ATCGGCGGTGAGATCTGAGG 61.459 60.000 7.21 0.00 0.00 3.86
2404 4114 0.039617 GATCGGCGGTGAGATCTGAG 60.040 60.000 7.21 0.00 39.92 3.35
2405 4115 0.751643 TGATCGGCGGTGAGATCTGA 60.752 55.000 7.21 0.00 42.62 3.27
2406 4116 0.316522 ATGATCGGCGGTGAGATCTG 59.683 55.000 7.21 0.00 42.62 2.90


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

AutoCloner maintained by Alex Coulton.