Multiple sequence alignment - TraesCS3D01G307200

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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 TraesCS3D01G307200 chr3D 100.000 2579 0 0 1 2579 421291784 421289206 0.000000e+00 4763.0
1 TraesCS3D01G307200 chr3D 93.509 570 36 1 996 1565 421314077 421313509 0.000000e+00 846.0
2 TraesCS3D01G307200 chr3D 87.406 667 66 5 1 658 421315043 421314386 0.000000e+00 750.0
3 TraesCS3D01G307200 chr3D 80.449 312 51 8 127 436 421704614 421704311 2.000000e-56 230.0
4 TraesCS3D01G307200 chr3D 79.167 312 51 10 127 436 422023175 422022876 1.210000e-48 204.0
5 TraesCS3D01G307200 chr3D 97.917 48 1 0 939 986 421314180 421314133 1.640000e-12 84.2
6 TraesCS3D01G307200 chr3B 95.254 1749 65 8 1 1737 548039994 548038252 0.000000e+00 2754.0
7 TraesCS3D01G307200 chr3B 91.270 630 52 2 939 1565 548044824 548044195 0.000000e+00 856.0
8 TraesCS3D01G307200 chr3B 87.199 664 70 11 1 658 548045685 548045031 0.000000e+00 741.0
9 TraesCS3D01G307200 chr3B 92.350 183 14 0 1751 1933 548038169 548037987 7.080000e-66 261.0
10 TraesCS3D01G307200 chr3B 79.167 312 55 7 127 436 549427794 549427491 9.350000e-50 207.0
11 TraesCS3D01G307200 chr3A 94.963 1747 64 7 1 1732 529842815 529844552 0.000000e+00 2717.0
12 TraesCS3D01G307200 chr3A 86.145 664 67 10 1 658 529776924 529777568 0.000000e+00 693.0
13 TraesCS3D01G307200 chr3A 89.734 526 43 6 957 1471 529779272 529779797 0.000000e+00 662.0
14 TraesCS3D01G307200 chr3A 86.000 200 25 1 1734 1933 529844631 529844827 7.230000e-51 211.0
15 TraesCS3D01G307200 chr3A 96.000 100 4 0 1466 1565 529840267 529840366 2.050000e-36 163.0
16 TraesCS3D01G307200 chr4A 89.270 233 25 0 1147 1379 538833455 538833223 2.510000e-75 292.0
17 TraesCS3D01G307200 chr4A 93.333 45 3 0 1473 1517 538833228 538833184 1.660000e-07 67.6
18 TraesCS3D01G307200 chr2A 80.000 340 62 6 116 453 15815213 15815548 1.980000e-61 246.0
19 TraesCS3D01G307200 chr4D 94.937 79 4 0 1202 1280 450198655 450198733 9.690000e-25 124.0


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 TraesCS3D01G307200 chr3D 421289206 421291784 2578 True 4763.000000 4763 100.0000 1 2579 1 chr3D.!!$R1 2578
1 TraesCS3D01G307200 chr3D 421313509 421315043 1534 True 560.066667 846 92.9440 1 1565 3 chr3D.!!$R4 1564
2 TraesCS3D01G307200 chr3B 548037987 548039994 2007 True 1507.500000 2754 93.8020 1 1933 2 chr3B.!!$R2 1932
3 TraesCS3D01G307200 chr3B 548044195 548045685 1490 True 798.500000 856 89.2345 1 1565 2 chr3B.!!$R3 1564
4 TraesCS3D01G307200 chr3A 529840267 529844827 4560 False 1030.333333 2717 92.3210 1 1933 3 chr3A.!!$F2 1932
5 TraesCS3D01G307200 chr3A 529776924 529779797 2873 False 677.500000 693 87.9395 1 1471 2 chr3A.!!$F1 1470

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
821 3409 0.249741 CAACCGAACTCCCTCACGTT 60.25 55.0 0.0 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 6212 0.17925 CATGTTGTAGTGCACGTCGC 60.179 55.0 12.01 3.7 42.89 5.19 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
94 2643 3.712907 GCCGAAGTAGCCCCACCA 61.713 66.667 0.00 0.00 0.00 4.17
98 2647 1.827399 CGAAGTAGCCCCACCACAGT 61.827 60.000 0.00 0.00 0.00 3.55
350 2899 1.132640 GGCGCACGTCTTGTTCATC 59.867 57.895 10.83 0.00 0.00 2.92
511 3060 2.301870 TCACTCCAACCGAAAGTAGCAT 59.698 45.455 0.00 0.00 0.00 3.79
693 3261 3.932089 GCTGTCTTCAAGCTTCTTCTAGG 59.068 47.826 0.00 0.00 0.00 3.02
796 3384 5.071384 TCCGTATCCAGCGATAGGATATCTA 59.929 44.000 12.74 0.00 46.63 1.98
812 3400 6.657541 AGGATATCTAGATCTCAACCGAACTC 59.342 42.308 17.22 0.54 0.00 3.01
821 3409 0.249741 CAACCGAACTCCCTCACGTT 60.250 55.000 0.00 0.00 0.00 3.99
876 3464 3.118738 CCTGTACCTTAATTGTCCTCGCT 60.119 47.826 0.00 0.00 0.00 4.93
986 5051 3.461773 GGCGGCCTAGTCAGCTCA 61.462 66.667 12.87 0.00 0.00 4.26
987 5052 2.105930 GCGGCCTAGTCAGCTCAG 59.894 66.667 0.00 0.00 0.00 3.35
988 5053 2.105930 CGGCCTAGTCAGCTCAGC 59.894 66.667 0.00 0.00 0.00 4.26
989 5054 2.422231 CGGCCTAGTCAGCTCAGCT 61.422 63.158 0.00 0.00 40.77 4.24
990 5055 1.441311 GGCCTAGTCAGCTCAGCTC 59.559 63.158 0.00 0.00 36.40 4.09
1091 5207 2.106938 TGCGATCCTCATGACCGC 59.893 61.111 15.69 15.69 45.28 5.68
1158 5274 1.758514 CTCCAGCTTCGAGGGCCTA 60.759 63.158 5.73 0.00 0.00 3.93
1161 5285 1.118356 CCAGCTTCGAGGGCCTAGAT 61.118 60.000 17.47 1.39 0.00 1.98
1670 5798 8.908786 ACCATGAAACGATGAACTCATATATT 57.091 30.769 0.00 0.00 36.57 1.28
1732 5861 6.564125 CGCGAGCCTTTTTCAGTATAAATAGG 60.564 42.308 0.00 0.00 39.32 2.57
1833 6039 7.144722 TCCAAATGATAAGTGTCACATGTTC 57.855 36.000 5.62 0.00 0.00 3.18
1848 6054 3.053291 TTCGGTGCGTGGCATTCC 61.053 61.111 0.00 0.00 41.91 3.01
1868 6074 1.539388 CAGCCCTGACGTTTTGCAATA 59.461 47.619 0.00 0.00 0.00 1.90
1893 6099 2.885135 TTCAGTCATGCAAGGATGGT 57.115 45.000 0.00 0.00 0.00 3.55
1954 6160 9.088512 AGTAACAATTTAGCTATTCTTCAGTCG 57.911 33.333 0.00 0.00 0.00 4.18
1955 6161 6.351327 ACAATTTAGCTATTCTTCAGTCGC 57.649 37.500 0.00 0.00 0.00 5.19
1956 6162 5.294552 ACAATTTAGCTATTCTTCAGTCGCC 59.705 40.000 0.00 0.00 0.00 5.54
1957 6163 4.737855 TTTAGCTATTCTTCAGTCGCCT 57.262 40.909 0.00 0.00 0.00 5.52
1958 6164 2.593346 AGCTATTCTTCAGTCGCCTG 57.407 50.000 0.00 0.00 40.25 4.85
1959 6165 2.103373 AGCTATTCTTCAGTCGCCTGA 58.897 47.619 0.00 0.00 45.95 3.86
1974 6180 9.725019 TCAGTCGCCTGAAAATATATTTATGAT 57.275 29.630 11.07 0.00 44.67 2.45
1975 6181 9.979270 CAGTCGCCTGAAAATATATTTATGATC 57.021 33.333 11.07 5.99 41.50 2.92
1976 6182 9.725019 AGTCGCCTGAAAATATATTTATGATCA 57.275 29.630 11.07 9.89 0.00 2.92
1977 6183 9.979270 GTCGCCTGAAAATATATTTATGATCAG 57.021 33.333 20.94 20.94 34.34 2.90
1978 6184 9.725019 TCGCCTGAAAATATATTTATGATCAGT 57.275 29.630 23.53 5.92 33.55 3.41
1979 6185 9.979270 CGCCTGAAAATATATTTATGATCAGTC 57.021 33.333 23.53 16.36 33.55 3.51
1980 6186 9.979270 GCCTGAAAATATATTTATGATCAGTCG 57.021 33.333 23.53 15.92 33.55 4.18
1988 6194 7.745620 ATATTTATGATCAGTCGGTTTTCCC 57.254 36.000 0.09 0.00 36.42 3.97
1989 6195 2.420058 ATGATCAGTCGGTTTTCCCC 57.580 50.000 0.09 0.00 36.42 4.81
1990 6196 0.326927 TGATCAGTCGGTTTTCCCCC 59.673 55.000 0.00 0.00 36.42 5.40
2004 6210 4.425099 CCCCCACCGTTTTATGCA 57.575 55.556 0.00 0.00 0.00 3.96
2005 6211 1.887301 CCCCCACCGTTTTATGCAC 59.113 57.895 0.00 0.00 0.00 4.57
2006 6212 1.504446 CCCCACCGTTTTATGCACG 59.496 57.895 0.00 0.00 37.39 5.34
2007 6213 1.154112 CCCACCGTTTTATGCACGC 60.154 57.895 0.00 0.00 36.27 5.34
2008 6214 1.511043 CCACCGTTTTATGCACGCG 60.511 57.895 3.53 3.53 36.27 6.01
2009 6215 1.493750 CACCGTTTTATGCACGCGA 59.506 52.632 15.93 0.00 36.27 5.87
2010 6216 0.787908 CACCGTTTTATGCACGCGAC 60.788 55.000 15.93 4.74 36.27 5.19
2011 6217 1.576618 CCGTTTTATGCACGCGACG 60.577 57.895 15.93 9.72 36.27 5.12
2012 6218 1.129009 CGTTTTATGCACGCGACGT 59.871 52.632 15.93 8.63 42.36 4.34
2021 6227 2.026445 ACGCGACGTGCACTACAA 59.974 55.556 15.93 0.00 46.97 2.41
2022 6228 2.297912 ACGCGACGTGCACTACAAC 61.298 57.895 15.93 0.00 46.97 3.32
2023 6229 2.297195 CGCGACGTGCACTACAACA 61.297 57.895 16.19 0.00 46.97 3.33
2024 6230 1.614227 CGCGACGTGCACTACAACAT 61.614 55.000 16.19 0.00 46.97 2.71
2025 6231 0.179250 GCGACGTGCACTACAACATG 60.179 55.000 16.19 0.00 45.45 3.21
2026 6232 0.179250 CGACGTGCACTACAACATGC 60.179 55.000 16.19 0.00 42.40 4.06
2031 6237 1.245732 TGCACTACAACATGCATGCA 58.754 45.000 26.53 25.04 46.63 3.96
2032 6238 1.612463 TGCACTACAACATGCATGCAA 59.388 42.857 26.68 8.49 46.63 4.08
2033 6239 2.256174 GCACTACAACATGCATGCAAG 58.744 47.619 26.68 23.45 41.65 4.01
2034 6240 2.256174 CACTACAACATGCATGCAAGC 58.744 47.619 26.68 7.04 0.00 4.01
2035 6241 2.094906 CACTACAACATGCATGCAAGCT 60.095 45.455 26.68 9.07 34.99 3.74
2036 6242 2.094906 ACTACAACATGCATGCAAGCTG 60.095 45.455 26.68 23.49 34.99 4.24
2037 6243 0.669318 ACAACATGCATGCAAGCTGC 60.669 50.000 26.68 9.73 45.29 5.25
2073 6279 2.588731 CAGCCGATGCATGCAAATG 58.411 52.632 26.68 16.65 41.13 2.32
2095 6301 0.039708 AGCTTGCTTGCTTTCTTCGC 60.040 50.000 0.00 0.00 40.93 4.70
2096 6302 0.318107 GCTTGCTTGCTTTCTTCGCA 60.318 50.000 0.00 0.00 35.22 5.10
2097 6303 1.865248 GCTTGCTTGCTTTCTTCGCAA 60.865 47.619 0.00 0.00 44.36 4.85
2098 6304 2.462889 CTTGCTTGCTTTCTTCGCAAA 58.537 42.857 0.00 0.00 45.64 3.68
2099 6305 2.575694 TGCTTGCTTTCTTCGCAAAA 57.424 40.000 0.00 0.00 45.64 2.44
2100 6306 2.886081 TGCTTGCTTTCTTCGCAAAAA 58.114 38.095 0.00 0.00 45.64 1.94
2131 6337 2.352503 CAAGCTTGCTTAATTGGCGT 57.647 45.000 14.65 0.00 0.00 5.68
2132 6338 1.987770 CAAGCTTGCTTAATTGGCGTG 59.012 47.619 14.65 0.00 0.00 5.34
2133 6339 1.533625 AGCTTGCTTAATTGGCGTGA 58.466 45.000 0.00 0.00 0.00 4.35
2134 6340 1.470098 AGCTTGCTTAATTGGCGTGAG 59.530 47.619 0.00 0.00 0.00 3.51
2135 6341 1.200020 GCTTGCTTAATTGGCGTGAGT 59.800 47.619 0.00 0.00 0.00 3.41
2136 6342 2.855180 CTTGCTTAATTGGCGTGAGTG 58.145 47.619 0.00 0.00 0.00 3.51
2137 6343 1.890876 TGCTTAATTGGCGTGAGTGT 58.109 45.000 0.00 0.00 0.00 3.55
2138 6344 1.804151 TGCTTAATTGGCGTGAGTGTC 59.196 47.619 0.00 0.00 0.00 3.67
2139 6345 1.804151 GCTTAATTGGCGTGAGTGTCA 59.196 47.619 0.00 0.00 0.00 3.58
2140 6346 2.225491 GCTTAATTGGCGTGAGTGTCAA 59.775 45.455 0.00 0.00 0.00 3.18
2141 6347 3.119849 GCTTAATTGGCGTGAGTGTCAAT 60.120 43.478 0.00 0.00 32.80 2.57
2142 6348 4.651994 CTTAATTGGCGTGAGTGTCAATC 58.348 43.478 0.00 0.00 31.74 2.67
2143 6349 2.183478 ATTGGCGTGAGTGTCAATCA 57.817 45.000 0.00 0.00 0.00 2.57
2144 6350 1.225855 TTGGCGTGAGTGTCAATCAC 58.774 50.000 20.77 20.77 46.46 3.06
2154 6360 3.914555 GTGTCAATCACTAGACGCATG 57.085 47.619 0.00 0.00 43.00 4.06
2155 6361 2.604914 GTGTCAATCACTAGACGCATGG 59.395 50.000 0.00 0.00 43.00 3.66
2156 6362 1.594862 GTCAATCACTAGACGCATGGC 59.405 52.381 0.00 0.00 0.00 4.40
2168 6374 3.369400 CATGGCGGGCGGACAAAA 61.369 61.111 4.14 0.00 37.08 2.44
2169 6375 2.598985 ATGGCGGGCGGACAAAAA 60.599 55.556 4.14 0.00 37.08 1.94
2193 6399 9.702726 AAAATATTAATCGACGTGTTTCTCATG 57.297 29.630 0.00 0.00 38.86 3.07
2194 6400 4.577687 TTAATCGACGTGTTTCTCATGC 57.422 40.909 0.00 0.00 36.60 4.06
2195 6401 2.078849 ATCGACGTGTTTCTCATGCA 57.921 45.000 0.00 0.00 36.60 3.96
2196 6402 1.418373 TCGACGTGTTTCTCATGCAG 58.582 50.000 0.00 0.00 36.60 4.41
2197 6403 1.139989 CGACGTGTTTCTCATGCAGT 58.860 50.000 0.00 0.00 36.60 4.40
2198 6404 1.136529 CGACGTGTTTCTCATGCAGTG 60.137 52.381 0.00 0.00 36.60 3.66
2199 6405 1.867233 GACGTGTTTCTCATGCAGTGT 59.133 47.619 0.00 0.00 36.60 3.55
2200 6406 2.287915 GACGTGTTTCTCATGCAGTGTT 59.712 45.455 0.00 0.00 36.60 3.32
2201 6407 3.462982 ACGTGTTTCTCATGCAGTGTTA 58.537 40.909 0.00 0.00 36.60 2.41
2202 6408 3.494626 ACGTGTTTCTCATGCAGTGTTAG 59.505 43.478 0.00 0.00 36.60 2.34
2203 6409 3.494626 CGTGTTTCTCATGCAGTGTTAGT 59.505 43.478 0.00 0.00 0.00 2.24
2204 6410 4.024893 CGTGTTTCTCATGCAGTGTTAGTT 60.025 41.667 0.00 0.00 0.00 2.24
2205 6411 5.504010 CGTGTTTCTCATGCAGTGTTAGTTT 60.504 40.000 0.00 0.00 0.00 2.66
2206 6412 6.292649 CGTGTTTCTCATGCAGTGTTAGTTTA 60.293 38.462 0.00 0.00 0.00 2.01
2207 6413 7.414436 GTGTTTCTCATGCAGTGTTAGTTTAA 58.586 34.615 0.00 0.00 0.00 1.52
2208 6414 7.587757 GTGTTTCTCATGCAGTGTTAGTTTAAG 59.412 37.037 0.00 0.00 0.00 1.85
2209 6415 7.282224 TGTTTCTCATGCAGTGTTAGTTTAAGT 59.718 33.333 0.00 0.00 0.00 2.24
2210 6416 7.801716 TTCTCATGCAGTGTTAGTTTAAGTT 57.198 32.000 0.00 0.00 0.00 2.66
2211 6417 7.801716 TCTCATGCAGTGTTAGTTTAAGTTT 57.198 32.000 0.00 0.00 0.00 2.66
2212 6418 8.896320 TCTCATGCAGTGTTAGTTTAAGTTTA 57.104 30.769 0.00 0.00 0.00 2.01
2213 6419 9.332502 TCTCATGCAGTGTTAGTTTAAGTTTAA 57.667 29.630 0.00 0.00 0.00 1.52
2214 6420 9.944663 CTCATGCAGTGTTAGTTTAAGTTTAAA 57.055 29.630 0.00 0.00 0.00 1.52
2215 6421 9.944663 TCATGCAGTGTTAGTTTAAGTTTAAAG 57.055 29.630 0.00 0.00 33.66 1.85
2216 6422 9.944663 CATGCAGTGTTAGTTTAAGTTTAAAGA 57.055 29.630 0.00 0.00 33.66 2.52
2217 6423 9.946165 ATGCAGTGTTAGTTTAAGTTTAAAGAC 57.054 29.630 0.00 0.00 33.66 3.01
2218 6424 8.948145 TGCAGTGTTAGTTTAAGTTTAAAGACA 58.052 29.630 0.00 2.14 33.66 3.41
2219 6425 9.777575 GCAGTGTTAGTTTAAGTTTAAAGACAA 57.222 29.630 0.00 0.00 33.66 3.18
2254 6460 7.731556 GCTTTTGCTATTTGATTGACAGTAG 57.268 36.000 0.00 0.00 43.35 2.57
2255 6461 7.308435 GCTTTTGCTATTTGATTGACAGTAGT 58.692 34.615 0.00 0.00 43.35 2.73
2256 6462 7.483059 GCTTTTGCTATTTGATTGACAGTAGTC 59.517 37.037 0.00 0.00 42.94 2.59
2257 6463 8.621532 TTTTGCTATTTGATTGACAGTAGTCT 57.378 30.769 0.00 0.00 45.20 3.24
2258 6464 7.601073 TTGCTATTTGATTGACAGTAGTCTG 57.399 36.000 0.00 0.00 45.20 3.51
2259 6465 6.935167 TGCTATTTGATTGACAGTAGTCTGA 58.065 36.000 2.17 0.00 45.20 3.27
2260 6466 7.386059 TGCTATTTGATTGACAGTAGTCTGAA 58.614 34.615 2.17 0.00 45.20 3.02
2261 6467 8.043113 TGCTATTTGATTGACAGTAGTCTGAAT 58.957 33.333 2.17 0.00 45.20 2.57
2262 6468 8.547069 GCTATTTGATTGACAGTAGTCTGAATC 58.453 37.037 2.17 3.30 45.20 2.52
2263 6469 6.951256 TTTGATTGACAGTAGTCTGAATCG 57.049 37.500 2.17 0.00 45.20 3.34
2264 6470 4.998788 TGATTGACAGTAGTCTGAATCGG 58.001 43.478 2.17 0.00 45.20 4.18
2265 6471 4.462834 TGATTGACAGTAGTCTGAATCGGT 59.537 41.667 2.17 0.00 45.20 4.69
2266 6472 4.866508 TTGACAGTAGTCTGAATCGGTT 57.133 40.909 2.17 0.00 45.20 4.44
2267 6473 5.970317 TTGACAGTAGTCTGAATCGGTTA 57.030 39.130 2.17 0.00 45.20 2.85
2268 6474 5.970317 TGACAGTAGTCTGAATCGGTTAA 57.030 39.130 2.17 0.00 45.20 2.01
2269 6475 6.525578 TGACAGTAGTCTGAATCGGTTAAT 57.474 37.500 2.17 0.00 45.20 1.40
2270 6476 6.330278 TGACAGTAGTCTGAATCGGTTAATG 58.670 40.000 2.17 0.00 45.20 1.90
2271 6477 5.109903 ACAGTAGTCTGAATCGGTTAATGC 58.890 41.667 2.17 0.00 43.76 3.56
2272 6478 5.105310 ACAGTAGTCTGAATCGGTTAATGCT 60.105 40.000 2.17 0.00 43.76 3.79
2273 6479 6.096423 ACAGTAGTCTGAATCGGTTAATGCTA 59.904 38.462 2.17 0.00 43.76 3.49
2274 6480 7.148641 CAGTAGTCTGAATCGGTTAATGCTAT 58.851 38.462 0.00 0.00 43.76 2.97
2275 6481 7.653713 CAGTAGTCTGAATCGGTTAATGCTATT 59.346 37.037 0.00 0.00 43.76 1.73
2276 6482 7.868415 AGTAGTCTGAATCGGTTAATGCTATTC 59.132 37.037 0.00 0.00 0.00 1.75
2277 6483 6.821388 AGTCTGAATCGGTTAATGCTATTCT 58.179 36.000 0.00 0.00 0.00 2.40
2278 6484 7.952671 AGTCTGAATCGGTTAATGCTATTCTA 58.047 34.615 0.00 0.00 0.00 2.10
2279 6485 8.589338 AGTCTGAATCGGTTAATGCTATTCTAT 58.411 33.333 0.00 0.00 0.00 1.98
2280 6486 9.209175 GTCTGAATCGGTTAATGCTATTCTATT 57.791 33.333 0.00 0.00 0.00 1.73
2281 6487 9.778741 TCTGAATCGGTTAATGCTATTCTATTT 57.221 29.630 0.00 0.00 0.00 1.40
2353 6559 9.688091 TTATGTGTATGTGTAAATATTGGGTGT 57.312 29.630 0.00 0.00 0.00 4.16
2355 6561 9.860650 ATGTGTATGTGTAAATATTGGGTGTAT 57.139 29.630 0.00 0.00 0.00 2.29
2356 6562 9.114952 TGTGTATGTGTAAATATTGGGTGTATG 57.885 33.333 0.00 0.00 0.00 2.39
2357 6563 9.116067 GTGTATGTGTAAATATTGGGTGTATGT 57.884 33.333 0.00 0.00 0.00 2.29
2358 6564 9.332502 TGTATGTGTAAATATTGGGTGTATGTC 57.667 33.333 0.00 0.00 0.00 3.06
2359 6565 9.332502 GTATGTGTAAATATTGGGTGTATGTCA 57.667 33.333 0.00 0.00 0.00 3.58
2360 6566 7.857734 TGTGTAAATATTGGGTGTATGTCAG 57.142 36.000 0.00 0.00 0.00 3.51
2361 6567 7.398829 TGTGTAAATATTGGGTGTATGTCAGT 58.601 34.615 0.00 0.00 0.00 3.41
2362 6568 7.335673 TGTGTAAATATTGGGTGTATGTCAGTG 59.664 37.037 0.00 0.00 0.00 3.66
2363 6569 7.335924 GTGTAAATATTGGGTGTATGTCAGTGT 59.664 37.037 0.00 0.00 0.00 3.55
2364 6570 8.541234 TGTAAATATTGGGTGTATGTCAGTGTA 58.459 33.333 0.00 0.00 0.00 2.90
2365 6571 9.555727 GTAAATATTGGGTGTATGTCAGTGTAT 57.444 33.333 0.00 0.00 0.00 2.29
2367 6573 9.555727 AAATATTGGGTGTATGTCAGTGTATAC 57.444 33.333 11.09 11.09 0.00 1.47
2368 6574 5.347620 TTGGGTGTATGTCAGTGTATACC 57.652 43.478 13.77 7.05 32.98 2.73
2369 6575 4.616553 TGGGTGTATGTCAGTGTATACCT 58.383 43.478 13.77 0.00 33.90 3.08
2370 6576 5.768752 TGGGTGTATGTCAGTGTATACCTA 58.231 41.667 13.77 3.59 33.90 3.08
2371 6577 6.378745 TGGGTGTATGTCAGTGTATACCTAT 58.621 40.000 13.77 0.00 33.90 2.57
2372 6578 6.266786 TGGGTGTATGTCAGTGTATACCTATG 59.733 42.308 13.77 0.00 33.90 2.23
2373 6579 6.267014 GGGTGTATGTCAGTGTATACCTATGT 59.733 42.308 13.77 0.00 33.90 2.29
2374 6580 7.449395 GGGTGTATGTCAGTGTATACCTATGTA 59.551 40.741 13.77 0.00 33.90 2.29
2375 6581 9.021807 GGTGTATGTCAGTGTATACCTATGTAT 57.978 37.037 13.77 0.00 40.72 2.29
2410 6616 8.275015 TGTGTGTAAATTATATTGGGAGTGTG 57.725 34.615 0.00 0.00 0.00 3.82
2411 6617 8.103935 TGTGTGTAAATTATATTGGGAGTGTGA 58.896 33.333 0.00 0.00 0.00 3.58
2412 6618 8.952278 GTGTGTAAATTATATTGGGAGTGTGAA 58.048 33.333 0.00 0.00 0.00 3.18
2413 6619 9.521841 TGTGTAAATTATATTGGGAGTGTGAAA 57.478 29.630 0.00 0.00 0.00 2.69
2497 6703 5.618056 TTTTTCAGCAAATTGTGTGCAAA 57.382 30.435 3.58 0.00 44.74 3.68
2498 6704 5.618056 TTTTCAGCAAATTGTGTGCAAAA 57.382 30.435 3.58 0.47 44.74 2.44
2499 6705 5.618056 TTTCAGCAAATTGTGTGCAAAAA 57.382 30.435 3.58 1.19 44.74 1.94
2500 6706 5.814764 TTCAGCAAATTGTGTGCAAAAAT 57.185 30.435 3.58 0.00 44.74 1.82
2501 6707 5.814764 TCAGCAAATTGTGTGCAAAAATT 57.185 30.435 3.58 0.00 44.74 1.82
2502 6708 5.808403 TCAGCAAATTGTGTGCAAAAATTC 58.192 33.333 3.58 0.00 44.74 2.17
2503 6709 5.585445 TCAGCAAATTGTGTGCAAAAATTCT 59.415 32.000 3.58 0.00 44.74 2.40
2504 6710 6.760298 TCAGCAAATTGTGTGCAAAAATTCTA 59.240 30.769 3.58 0.00 44.74 2.10
2505 6711 7.279536 TCAGCAAATTGTGTGCAAAAATTCTAA 59.720 29.630 3.58 0.00 44.74 2.10
2506 6712 8.071368 CAGCAAATTGTGTGCAAAAATTCTAAT 58.929 29.630 3.58 0.00 44.74 1.73
2507 6713 9.270640 AGCAAATTGTGTGCAAAAATTCTAATA 57.729 25.926 3.58 0.00 44.74 0.98
2508 6714 9.875675 GCAAATTGTGTGCAAAAATTCTAATAA 57.124 25.926 0.00 0.00 41.80 1.40
2547 6753 9.981114 TTTTATTTTCAATCTTCTTCAAGGACC 57.019 29.630 0.00 0.00 0.00 4.46
2548 6754 8.704849 TTATTTTCAATCTTCTTCAAGGACCA 57.295 30.769 0.00 0.00 0.00 4.02
2549 6755 7.601705 ATTTTCAATCTTCTTCAAGGACCAA 57.398 32.000 0.00 0.00 0.00 3.67
2550 6756 7.601705 TTTTCAATCTTCTTCAAGGACCAAT 57.398 32.000 0.00 0.00 0.00 3.16
2551 6757 6.579666 TTCAATCTTCTTCAAGGACCAATG 57.420 37.500 0.00 0.00 0.00 2.82
2552 6758 5.634118 TCAATCTTCTTCAAGGACCAATGT 58.366 37.500 0.00 0.00 0.00 2.71
2553 6759 5.707298 TCAATCTTCTTCAAGGACCAATGTC 59.293 40.000 0.00 0.00 40.98 3.06
2554 6760 4.705110 TCTTCTTCAAGGACCAATGTCA 57.295 40.909 0.00 0.00 43.65 3.58
2555 6761 5.246981 TCTTCTTCAAGGACCAATGTCAT 57.753 39.130 0.00 0.00 43.65 3.06
2556 6762 5.005740 TCTTCTTCAAGGACCAATGTCATG 58.994 41.667 0.00 0.00 43.65 3.07
2557 6763 4.639078 TCTTCAAGGACCAATGTCATGA 57.361 40.909 0.00 0.00 43.65 3.07
2558 6764 4.984295 TCTTCAAGGACCAATGTCATGAA 58.016 39.130 0.00 10.63 43.65 2.57
2559 6765 5.573219 TCTTCAAGGACCAATGTCATGAAT 58.427 37.500 0.00 0.00 42.70 2.57
2560 6766 6.012113 TCTTCAAGGACCAATGTCATGAATT 58.988 36.000 0.00 0.00 42.70 2.17
2561 6767 6.494491 TCTTCAAGGACCAATGTCATGAATTT 59.506 34.615 0.00 0.00 42.70 1.82
2562 6768 7.669304 TCTTCAAGGACCAATGTCATGAATTTA 59.331 33.333 0.00 0.00 42.70 1.40
2563 6769 7.959658 TCAAGGACCAATGTCATGAATTTAT 57.040 32.000 0.00 0.00 43.65 1.40
2564 6770 9.473007 TTCAAGGACCAATGTCATGAATTTATA 57.527 29.630 0.00 0.00 43.65 0.98
2565 6771 9.645128 TCAAGGACCAATGTCATGAATTTATAT 57.355 29.630 0.00 0.00 43.65 0.86
2569 6775 9.696917 GGACCAATGTCATGAATTTATATTTCC 57.303 33.333 0.00 0.00 43.65 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
350 2899 2.664851 TTCAACCTCACGCTGCGG 60.665 61.111 26.95 15.00 0.00 5.69
425 2974 3.745803 GCGTCCTTCTCCGTCGGT 61.746 66.667 11.88 0.00 0.00 4.69
511 3060 3.055385 CGGACCCACCTTTCTAATCTTGA 60.055 47.826 0.00 0.00 36.31 3.02
693 3261 3.879892 GGCATCTCCAACAAATACTCCTC 59.120 47.826 0.00 0.00 34.01 3.71
796 3384 2.104170 GAGGGAGTTCGGTTGAGATCT 58.896 52.381 0.00 0.00 0.00 2.75
838 3426 2.463752 ACAGGCCGTTCCTAACAGATA 58.536 47.619 0.00 0.00 45.52 1.98
876 3464 6.288941 TCCTCCAGAAAATACACGTATGAA 57.711 37.500 0.00 0.00 0.00 2.57
986 5051 1.340399 TTCCATGGATGCTCCGAGCT 61.340 55.000 17.06 6.97 42.97 4.09
987 5052 0.883814 CTTCCATGGATGCTCCGAGC 60.884 60.000 17.06 13.81 40.17 5.03
988 5053 0.755079 TCTTCCATGGATGCTCCGAG 59.245 55.000 17.06 8.20 40.17 4.63
989 5054 1.134401 GTTCTTCCATGGATGCTCCGA 60.134 52.381 17.06 0.00 40.17 4.55
990 5055 1.303309 GTTCTTCCATGGATGCTCCG 58.697 55.000 17.06 0.52 40.17 4.63
1196 5320 2.809601 CGTTCTTGACGCGGAGGG 60.810 66.667 12.47 0.00 45.86 4.30
1732 5861 6.251376 CACCGCAAGTCATAAAATTCTAAAGC 59.749 38.462 0.00 0.00 0.00 3.51
1737 5866 3.505680 TGCACCGCAAGTCATAAAATTCT 59.494 39.130 0.00 0.00 34.76 2.40
1738 5867 3.832276 TGCACCGCAAGTCATAAAATTC 58.168 40.909 0.00 0.00 34.76 2.17
1739 5868 3.932545 TGCACCGCAAGTCATAAAATT 57.067 38.095 0.00 0.00 34.76 1.82
1740 5869 3.932545 TTGCACCGCAAGTCATAAAAT 57.067 38.095 0.00 0.00 43.99 1.82
1785 5991 3.181488 TGAACGAACAAGGTCTAACGACA 60.181 43.478 0.00 0.00 42.05 4.35
1833 6039 3.803082 CTGGAATGCCACGCACCG 61.803 66.667 0.00 0.00 43.04 4.94
1848 6054 0.314935 ATTGCAAAACGTCAGGGCTG 59.685 50.000 1.71 0.00 0.00 4.85
1868 6074 3.159472 TCCTTGCATGACTGAAATTGCT 58.841 40.909 0.00 0.00 36.10 3.91
1893 6099 5.234757 ACTTGTCGCGTGTCACTTAAAATTA 59.765 36.000 5.77 0.00 0.00 1.40
1929 6135 7.846592 GCGACTGAAGAATAGCTAAATTGTTAC 59.153 37.037 0.00 0.00 0.00 2.50
1933 6139 5.525378 AGGCGACTGAAGAATAGCTAAATTG 59.475 40.000 0.00 0.00 41.13 2.32
1934 6140 5.675538 AGGCGACTGAAGAATAGCTAAATT 58.324 37.500 0.00 0.00 41.13 1.82
1935 6141 5.283457 AGGCGACTGAAGAATAGCTAAAT 57.717 39.130 0.00 0.00 41.13 1.40
1936 6142 4.737855 AGGCGACTGAAGAATAGCTAAA 57.262 40.909 0.00 0.00 41.13 1.85
1950 6156 9.725019 TGATCATAAATATATTTTCAGGCGACT 57.275 29.630 15.64 0.00 46.44 4.18
1951 6157 9.979270 CTGATCATAAATATATTTTCAGGCGAC 57.021 33.333 20.49 0.00 30.87 5.19
1952 6158 9.725019 ACTGATCATAAATATATTTTCAGGCGA 57.275 29.630 26.48 13.44 34.83 5.54
1953 6159 9.979270 GACTGATCATAAATATATTTTCAGGCG 57.021 33.333 26.48 13.47 34.83 5.52
1954 6160 9.979270 CGACTGATCATAAATATATTTTCAGGC 57.021 33.333 26.48 24.70 34.98 4.85
1962 6168 9.449719 GGGAAAACCGACTGATCATAAATATAT 57.550 33.333 0.00 0.00 0.00 0.86
1963 6169 7.881232 GGGGAAAACCGACTGATCATAAATATA 59.119 37.037 0.00 0.00 41.60 0.86
1964 6170 6.715264 GGGGAAAACCGACTGATCATAAATAT 59.285 38.462 0.00 0.00 41.60 1.28
1965 6171 6.059484 GGGGAAAACCGACTGATCATAAATA 58.941 40.000 0.00 0.00 41.60 1.40
1966 6172 4.887655 GGGGAAAACCGACTGATCATAAAT 59.112 41.667 0.00 0.00 41.60 1.40
1967 6173 4.266714 GGGGAAAACCGACTGATCATAAA 58.733 43.478 0.00 0.00 41.60 1.40
1968 6174 3.371166 GGGGGAAAACCGACTGATCATAA 60.371 47.826 0.00 0.00 41.60 1.90
1969 6175 2.171870 GGGGGAAAACCGACTGATCATA 59.828 50.000 0.00 0.00 41.60 2.15
1970 6176 1.064685 GGGGGAAAACCGACTGATCAT 60.065 52.381 0.00 0.00 41.60 2.45
1971 6177 0.326927 GGGGGAAAACCGACTGATCA 59.673 55.000 0.00 0.00 41.60 2.92
1972 6178 3.170360 GGGGGAAAACCGACTGATC 57.830 57.895 0.00 0.00 41.60 2.92
1987 6193 1.887301 GTGCATAAAACGGTGGGGG 59.113 57.895 0.00 0.00 0.00 5.40
1988 6194 1.504446 CGTGCATAAAACGGTGGGG 59.496 57.895 0.00 0.00 37.39 4.96
1989 6195 1.154112 GCGTGCATAAAACGGTGGG 60.154 57.895 0.00 0.00 41.31 4.61
1990 6196 1.511043 CGCGTGCATAAAACGGTGG 60.511 57.895 0.00 0.00 41.31 4.61
1991 6197 0.787908 GTCGCGTGCATAAAACGGTG 60.788 55.000 5.77 0.00 41.31 4.94
1992 6198 1.494189 GTCGCGTGCATAAAACGGT 59.506 52.632 5.77 0.00 41.31 4.83
1993 6199 1.576618 CGTCGCGTGCATAAAACGG 60.577 57.895 5.77 0.00 41.31 4.44
1994 6200 1.129009 ACGTCGCGTGCATAAAACG 59.871 52.632 5.77 8.72 39.18 3.60
2004 6210 2.026445 TTGTAGTGCACGTCGCGT 59.974 55.556 12.01 0.00 46.97 6.01
2005 6211 1.614227 ATGTTGTAGTGCACGTCGCG 61.614 55.000 12.01 0.00 46.97 5.87
2006 6212 0.179250 CATGTTGTAGTGCACGTCGC 60.179 55.000 12.01 3.70 42.89 5.19
2007 6213 0.179250 GCATGTTGTAGTGCACGTCG 60.179 55.000 12.01 0.00 40.94 5.12
2008 6214 0.865111 TGCATGTTGTAGTGCACGTC 59.135 50.000 12.01 9.21 45.60 4.34
2009 6215 2.999356 TGCATGTTGTAGTGCACGT 58.001 47.368 12.01 2.47 45.60 4.49
2013 6219 2.256174 CTTGCATGCATGTTGTAGTGC 58.744 47.619 26.79 12.85 41.61 4.40
2014 6220 2.094906 AGCTTGCATGCATGTTGTAGTG 60.095 45.455 28.20 11.75 34.99 2.74
2015 6221 2.094906 CAGCTTGCATGCATGTTGTAGT 60.095 45.455 30.10 11.28 34.99 2.73
2016 6222 2.526077 CAGCTTGCATGCATGTTGTAG 58.474 47.619 30.10 21.35 34.99 2.74
2017 6223 1.403116 GCAGCTTGCATGCATGTTGTA 60.403 47.619 34.53 16.97 44.26 2.41
2018 6224 0.669318 GCAGCTTGCATGCATGTTGT 60.669 50.000 34.53 19.62 44.26 3.32
2019 6225 2.078226 GCAGCTTGCATGCATGTTG 58.922 52.632 32.48 32.48 44.26 3.33
2020 6226 4.590487 GCAGCTTGCATGCATGTT 57.410 50.000 28.20 22.43 44.26 2.71
2029 6235 2.339418 TGCATGTTAATTGCAGCTTGC 58.661 42.857 10.88 1.70 44.73 4.01
2055 6261 2.588731 CATTTGCATGCATCGGCTG 58.411 52.632 23.37 10.72 41.91 4.85
2077 6283 0.318107 TGCGAAGAAAGCAAGCAAGC 60.318 50.000 0.00 0.00 42.18 4.01
2078 6284 3.851620 TGCGAAGAAAGCAAGCAAG 57.148 47.368 0.00 0.00 42.18 4.01
2112 6318 1.987770 CACGCCAATTAAGCAAGCTTG 59.012 47.619 22.44 22.44 37.47 4.01
2113 6319 1.885887 TCACGCCAATTAAGCAAGCTT 59.114 42.857 12.42 12.42 39.83 3.74
2114 6320 1.470098 CTCACGCCAATTAAGCAAGCT 59.530 47.619 0.00 0.00 0.00 3.74
2115 6321 1.200020 ACTCACGCCAATTAAGCAAGC 59.800 47.619 1.09 0.00 0.00 4.01
2116 6322 2.226437 ACACTCACGCCAATTAAGCAAG 59.774 45.455 1.09 0.00 0.00 4.01
2117 6323 2.225491 GACACTCACGCCAATTAAGCAA 59.775 45.455 1.09 0.00 0.00 3.91
2118 6324 1.804151 GACACTCACGCCAATTAAGCA 59.196 47.619 1.09 0.00 0.00 3.91
2119 6325 1.804151 TGACACTCACGCCAATTAAGC 59.196 47.619 0.00 0.00 0.00 3.09
2120 6326 4.154015 TGATTGACACTCACGCCAATTAAG 59.846 41.667 0.00 0.00 30.29 1.85
2121 6327 4.068599 TGATTGACACTCACGCCAATTAA 58.931 39.130 0.00 0.00 30.29 1.40
2122 6328 3.435327 GTGATTGACACTCACGCCAATTA 59.565 43.478 9.84 0.00 45.13 1.40
2123 6329 2.226437 GTGATTGACACTCACGCCAATT 59.774 45.455 9.84 0.00 45.13 2.32
2124 6330 1.806542 GTGATTGACACTCACGCCAAT 59.193 47.619 9.84 0.00 45.13 3.16
2125 6331 1.225855 GTGATTGACACTCACGCCAA 58.774 50.000 9.84 0.00 45.13 4.52
2126 6332 2.912986 GTGATTGACACTCACGCCA 58.087 52.632 9.84 0.00 45.13 5.69
2135 6341 2.892374 CCATGCGTCTAGTGATTGACA 58.108 47.619 0.00 0.00 33.18 3.58
2136 6342 1.594862 GCCATGCGTCTAGTGATTGAC 59.405 52.381 0.00 0.00 0.00 3.18
2137 6343 1.939974 GCCATGCGTCTAGTGATTGA 58.060 50.000 0.00 0.00 0.00 2.57
2151 6357 2.925262 TTTTTGTCCGCCCGCCATG 61.925 57.895 0.00 0.00 0.00 3.66
2152 6358 2.598985 TTTTTGTCCGCCCGCCAT 60.599 55.556 0.00 0.00 0.00 4.40
2167 6373 9.702726 CATGAGAAACACGTCGATTAATATTTT 57.297 29.630 0.00 0.00 0.00 1.82
2168 6374 7.850982 GCATGAGAAACACGTCGATTAATATTT 59.149 33.333 0.00 0.00 0.00 1.40
2169 6375 7.011016 TGCATGAGAAACACGTCGATTAATATT 59.989 33.333 0.00 0.00 0.00 1.28
2170 6376 6.478673 TGCATGAGAAACACGTCGATTAATAT 59.521 34.615 0.00 0.00 0.00 1.28
2171 6377 5.808030 TGCATGAGAAACACGTCGATTAATA 59.192 36.000 0.00 0.00 0.00 0.98
2172 6378 4.629634 TGCATGAGAAACACGTCGATTAAT 59.370 37.500 0.00 0.00 0.00 1.40
2173 6379 3.991121 TGCATGAGAAACACGTCGATTAA 59.009 39.130 0.00 0.00 0.00 1.40
2174 6380 3.580731 TGCATGAGAAACACGTCGATTA 58.419 40.909 0.00 0.00 0.00 1.75
2175 6381 2.412870 TGCATGAGAAACACGTCGATT 58.587 42.857 0.00 0.00 0.00 3.34
2176 6382 1.995484 CTGCATGAGAAACACGTCGAT 59.005 47.619 0.00 0.00 0.00 3.59
2177 6383 1.269569 ACTGCATGAGAAACACGTCGA 60.270 47.619 0.00 0.00 0.00 4.20
2178 6384 1.136529 CACTGCATGAGAAACACGTCG 60.137 52.381 0.00 0.00 0.00 5.12
2179 6385 1.867233 ACACTGCATGAGAAACACGTC 59.133 47.619 0.00 0.00 0.00 4.34
2180 6386 1.953559 ACACTGCATGAGAAACACGT 58.046 45.000 0.00 0.00 0.00 4.49
2181 6387 3.494626 ACTAACACTGCATGAGAAACACG 59.505 43.478 0.00 0.00 0.00 4.49
2182 6388 5.424121 AACTAACACTGCATGAGAAACAC 57.576 39.130 0.00 0.00 0.00 3.32
2183 6389 7.282224 ACTTAAACTAACACTGCATGAGAAACA 59.718 33.333 0.00 0.00 0.00 2.83
2184 6390 7.639945 ACTTAAACTAACACTGCATGAGAAAC 58.360 34.615 0.00 0.00 0.00 2.78
2185 6391 7.801716 ACTTAAACTAACACTGCATGAGAAA 57.198 32.000 0.00 0.00 0.00 2.52
2186 6392 7.801716 AACTTAAACTAACACTGCATGAGAA 57.198 32.000 0.00 0.00 0.00 2.87
2187 6393 7.801716 AAACTTAAACTAACACTGCATGAGA 57.198 32.000 0.00 0.00 0.00 3.27
2188 6394 9.944663 TTTAAACTTAAACTAACACTGCATGAG 57.055 29.630 0.00 0.00 0.00 2.90
2189 6395 9.944663 CTTTAAACTTAAACTAACACTGCATGA 57.055 29.630 0.00 0.00 0.00 3.07
2190 6396 9.944663 TCTTTAAACTTAAACTAACACTGCATG 57.055 29.630 0.00 0.00 0.00 4.06
2191 6397 9.946165 GTCTTTAAACTTAAACTAACACTGCAT 57.054 29.630 0.00 0.00 0.00 3.96
2192 6398 8.948145 TGTCTTTAAACTTAAACTAACACTGCA 58.052 29.630 0.00 0.00 0.00 4.41
2193 6399 9.777575 TTGTCTTTAAACTTAAACTAACACTGC 57.222 29.630 0.00 0.00 0.00 4.40
2211 6417 9.928236 GCAAAAGCAACATAAAATTTGTCTTTA 57.072 25.926 0.00 0.00 33.08 1.85
2212 6418 8.676401 AGCAAAAGCAACATAAAATTTGTCTTT 58.324 25.926 0.00 0.00 33.95 2.52
2213 6419 8.212317 AGCAAAAGCAACATAAAATTTGTCTT 57.788 26.923 0.00 0.00 32.03 3.01
2214 6420 7.790823 AGCAAAAGCAACATAAAATTTGTCT 57.209 28.000 0.00 0.00 32.03 3.41
2222 6428 9.486497 TCAATCAAATAGCAAAAGCAACATAAA 57.514 25.926 0.00 0.00 0.00 1.40
2223 6429 8.924691 GTCAATCAAATAGCAAAAGCAACATAA 58.075 29.630 0.00 0.00 0.00 1.90
2224 6430 8.087136 TGTCAATCAAATAGCAAAAGCAACATA 58.913 29.630 0.00 0.00 0.00 2.29
2225 6431 6.930164 TGTCAATCAAATAGCAAAAGCAACAT 59.070 30.769 0.00 0.00 0.00 2.71
2226 6432 6.279123 TGTCAATCAAATAGCAAAAGCAACA 58.721 32.000 0.00 0.00 0.00 3.33
2227 6433 6.421801 ACTGTCAATCAAATAGCAAAAGCAAC 59.578 34.615 0.00 0.00 0.00 4.17
2228 6434 6.514947 ACTGTCAATCAAATAGCAAAAGCAA 58.485 32.000 0.00 0.00 0.00 3.91
2229 6435 6.088016 ACTGTCAATCAAATAGCAAAAGCA 57.912 33.333 0.00 0.00 0.00 3.91
2230 6436 7.308435 ACTACTGTCAATCAAATAGCAAAAGC 58.692 34.615 0.00 0.00 0.00 3.51
2231 6437 8.725148 AGACTACTGTCAATCAAATAGCAAAAG 58.275 33.333 0.00 0.00 45.20 2.27
2232 6438 8.506437 CAGACTACTGTCAATCAAATAGCAAAA 58.494 33.333 0.00 0.00 45.20 2.44
2233 6439 7.877612 TCAGACTACTGTCAATCAAATAGCAAA 59.122 33.333 0.00 0.00 45.20 3.68
2234 6440 7.386059 TCAGACTACTGTCAATCAAATAGCAA 58.614 34.615 0.00 0.00 45.20 3.91
2235 6441 6.935167 TCAGACTACTGTCAATCAAATAGCA 58.065 36.000 0.00 0.00 45.20 3.49
2236 6442 7.834068 TTCAGACTACTGTCAATCAAATAGC 57.166 36.000 0.00 0.00 45.20 2.97
2237 6443 8.750416 CGATTCAGACTACTGTCAATCAAATAG 58.250 37.037 0.00 0.00 45.20 1.73
2238 6444 7.706607 CCGATTCAGACTACTGTCAATCAAATA 59.293 37.037 0.00 0.00 45.20 1.40
2239 6445 6.536582 CCGATTCAGACTACTGTCAATCAAAT 59.463 38.462 0.00 0.00 45.20 2.32
2240 6446 5.869344 CCGATTCAGACTACTGTCAATCAAA 59.131 40.000 0.00 0.00 45.20 2.69
2241 6447 5.047306 ACCGATTCAGACTACTGTCAATCAA 60.047 40.000 0.00 0.00 45.20 2.57
2242 6448 4.462834 ACCGATTCAGACTACTGTCAATCA 59.537 41.667 0.00 0.00 45.20 2.57
2243 6449 5.000012 ACCGATTCAGACTACTGTCAATC 58.000 43.478 0.00 0.00 45.20 2.67
2244 6450 5.407407 AACCGATTCAGACTACTGTCAAT 57.593 39.130 0.00 0.00 45.20 2.57
2245 6451 4.866508 AACCGATTCAGACTACTGTCAA 57.133 40.909 0.00 0.00 45.20 3.18
2246 6452 5.970317 TTAACCGATTCAGACTACTGTCA 57.030 39.130 0.00 0.00 45.20 3.58
2247 6453 5.232414 GCATTAACCGATTCAGACTACTGTC 59.768 44.000 0.00 0.00 43.81 3.51
2248 6454 5.105310 AGCATTAACCGATTCAGACTACTGT 60.105 40.000 0.00 0.00 43.81 3.55
2249 6455 5.352284 AGCATTAACCGATTCAGACTACTG 58.648 41.667 0.00 0.00 44.66 2.74
2250 6456 5.599999 AGCATTAACCGATTCAGACTACT 57.400 39.130 0.00 0.00 0.00 2.57
2251 6457 7.868415 AGAATAGCATTAACCGATTCAGACTAC 59.132 37.037 10.99 0.00 29.98 2.73
2252 6458 7.952671 AGAATAGCATTAACCGATTCAGACTA 58.047 34.615 10.99 0.00 29.98 2.59
2253 6459 6.821388 AGAATAGCATTAACCGATTCAGACT 58.179 36.000 10.99 0.00 29.98 3.24
2254 6460 8.764524 ATAGAATAGCATTAACCGATTCAGAC 57.235 34.615 10.99 0.00 29.98 3.51
2255 6461 9.778741 AAATAGAATAGCATTAACCGATTCAGA 57.221 29.630 10.99 2.92 29.98 3.27
2327 6533 9.688091 ACACCCAATATTTACACATACACATAA 57.312 29.630 0.00 0.00 0.00 1.90
2329 6535 9.860650 ATACACCCAATATTTACACATACACAT 57.139 29.630 0.00 0.00 0.00 3.21
2330 6536 9.114952 CATACACCCAATATTTACACATACACA 57.885 33.333 0.00 0.00 0.00 3.72
2331 6537 9.116067 ACATACACCCAATATTTACACATACAC 57.884 33.333 0.00 0.00 0.00 2.90
2332 6538 9.332502 GACATACACCCAATATTTACACATACA 57.667 33.333 0.00 0.00 0.00 2.29
2333 6539 9.332502 TGACATACACCCAATATTTACACATAC 57.667 33.333 0.00 0.00 0.00 2.39
2334 6540 9.554395 CTGACATACACCCAATATTTACACATA 57.446 33.333 0.00 0.00 0.00 2.29
2335 6541 8.052748 ACTGACATACACCCAATATTTACACAT 58.947 33.333 0.00 0.00 0.00 3.21
2336 6542 7.335673 CACTGACATACACCCAATATTTACACA 59.664 37.037 0.00 0.00 0.00 3.72
2337 6543 7.335924 ACACTGACATACACCCAATATTTACAC 59.664 37.037 0.00 0.00 0.00 2.90
2338 6544 7.398829 ACACTGACATACACCCAATATTTACA 58.601 34.615 0.00 0.00 0.00 2.41
2339 6545 7.859325 ACACTGACATACACCCAATATTTAC 57.141 36.000 0.00 0.00 0.00 2.01
2341 6547 9.555727 GTATACACTGACATACACCCAATATTT 57.444 33.333 0.00 0.00 0.00 1.40
2342 6548 8.154856 GGTATACACTGACATACACCCAATATT 58.845 37.037 5.01 0.00 30.65 1.28
2343 6549 7.512746 AGGTATACACTGACATACACCCAATAT 59.487 37.037 5.01 0.00 30.65 1.28
2344 6550 6.842280 AGGTATACACTGACATACACCCAATA 59.158 38.462 5.01 0.00 30.65 1.90
2345 6551 5.665812 AGGTATACACTGACATACACCCAAT 59.334 40.000 5.01 0.00 30.65 3.16
2346 6552 5.027460 AGGTATACACTGACATACACCCAA 58.973 41.667 5.01 0.00 30.65 4.12
2347 6553 4.616553 AGGTATACACTGACATACACCCA 58.383 43.478 5.01 0.00 30.65 4.51
2348 6554 6.267014 ACATAGGTATACACTGACATACACCC 59.733 42.308 5.01 0.00 30.65 4.61
2349 6555 7.286215 ACATAGGTATACACTGACATACACC 57.714 40.000 5.01 0.00 30.65 4.16
2384 6590 8.902806 CACACTCCCAATATAATTTACACACAT 58.097 33.333 0.00 0.00 0.00 3.21
2385 6591 8.103935 TCACACTCCCAATATAATTTACACACA 58.896 33.333 0.00 0.00 0.00 3.72
2386 6592 8.500753 TCACACTCCCAATATAATTTACACAC 57.499 34.615 0.00 0.00 0.00 3.82
2387 6593 9.521841 TTTCACACTCCCAATATAATTTACACA 57.478 29.630 0.00 0.00 0.00 3.72
2475 6681 5.618056 TTTGCACACAATTTGCTGAAAAA 57.382 30.435 2.52 0.00 40.86 1.94
2476 6682 5.618056 TTTTGCACACAATTTGCTGAAAA 57.382 30.435 2.52 0.00 40.86 2.29
2477 6683 5.618056 TTTTTGCACACAATTTGCTGAAA 57.382 30.435 2.52 1.80 40.86 2.69
2478 6684 5.814764 ATTTTTGCACACAATTTGCTGAA 57.185 30.435 2.52 0.00 40.86 3.02
2479 6685 5.585445 AGAATTTTTGCACACAATTTGCTGA 59.415 32.000 2.52 0.00 40.86 4.26
2480 6686 5.812652 AGAATTTTTGCACACAATTTGCTG 58.187 33.333 2.52 0.00 40.86 4.41
2481 6687 7.551035 TTAGAATTTTTGCACACAATTTGCT 57.449 28.000 2.52 0.00 40.86 3.91
2482 6688 9.875675 TTATTAGAATTTTTGCACACAATTTGC 57.124 25.926 0.00 0.00 40.63 3.68
2521 6727 9.981114 GGTCCTTGAAGAAGATTGAAAATAAAA 57.019 29.630 0.00 0.00 0.00 1.52
2522 6728 9.142014 TGGTCCTTGAAGAAGATTGAAAATAAA 57.858 29.630 0.00 0.00 0.00 1.40
2523 6729 8.704849 TGGTCCTTGAAGAAGATTGAAAATAA 57.295 30.769 0.00 0.00 0.00 1.40
2524 6730 8.704849 TTGGTCCTTGAAGAAGATTGAAAATA 57.295 30.769 0.00 0.00 0.00 1.40
2525 6731 7.601705 TTGGTCCTTGAAGAAGATTGAAAAT 57.398 32.000 0.00 0.00 0.00 1.82
2526 6732 7.069826 ACATTGGTCCTTGAAGAAGATTGAAAA 59.930 33.333 0.00 0.00 0.00 2.29
2527 6733 6.550854 ACATTGGTCCTTGAAGAAGATTGAAA 59.449 34.615 0.00 0.00 0.00 2.69
2528 6734 6.070656 ACATTGGTCCTTGAAGAAGATTGAA 58.929 36.000 0.00 0.00 0.00 2.69
2529 6735 5.634118 ACATTGGTCCTTGAAGAAGATTGA 58.366 37.500 0.00 0.00 0.00 2.57
2530 6736 5.474532 TGACATTGGTCCTTGAAGAAGATTG 59.525 40.000 0.00 0.00 43.65 2.67
2531 6737 5.634118 TGACATTGGTCCTTGAAGAAGATT 58.366 37.500 0.00 0.00 43.65 2.40
2532 6738 5.246981 TGACATTGGTCCTTGAAGAAGAT 57.753 39.130 0.00 0.00 43.65 2.40
2533 6739 4.705110 TGACATTGGTCCTTGAAGAAGA 57.295 40.909 0.00 0.00 43.65 2.87
2534 6740 5.005740 TCATGACATTGGTCCTTGAAGAAG 58.994 41.667 0.00 0.00 43.65 2.85
2535 6741 4.984295 TCATGACATTGGTCCTTGAAGAA 58.016 39.130 0.00 0.00 43.65 2.52
2536 6742 4.639078 TCATGACATTGGTCCTTGAAGA 57.361 40.909 0.00 0.00 43.65 2.87
2537 6743 5.909621 ATTCATGACATTGGTCCTTGAAG 57.090 39.130 0.00 0.00 42.93 3.02
2538 6744 6.669125 AAATTCATGACATTGGTCCTTGAA 57.331 33.333 0.00 10.64 43.38 2.69
2539 6745 7.959658 ATAAATTCATGACATTGGTCCTTGA 57.040 32.000 0.00 0.00 43.65 3.02
2543 6749 9.696917 GGAAATATAAATTCATGACATTGGTCC 57.303 33.333 0.00 0.00 43.65 4.46


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

AutoCloner maintained by Alex Coulton.