Multiple sequence alignment - TraesCS6A01G147100

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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 TraesCS6A01G147100 chr6A 100.000 2921 0 0 1 2921 126915360 126918280 0.000000e+00 5395
1 TraesCS6A01G147100 chr6A 94.858 564 25 4 2361 2921 608334664 608334102 0.000000e+00 878
2 TraesCS6A01G147100 chr6B 93.197 2102 101 25 3 2077 191199287 191201373 0.000000e+00 3051
3 TraesCS6A01G147100 chr6D 96.248 1226 37 2 859 2076 104783114 104784338 0.000000e+00 2001
4 TraesCS6A01G147100 chr6D 94.776 804 38 4 3 805 104768275 104769075 0.000000e+00 1249
5 TraesCS6A01G147100 chr2A 94.139 563 27 6 2361 2921 566599374 566599932 0.000000e+00 852
6 TraesCS6A01G147100 chr3A 94.255 557 29 3 2367 2921 27542563 27542008 0.000000e+00 848
7 TraesCS6A01G147100 chr3A 92.460 557 37 5 2367 2921 599820424 599819871 0.000000e+00 791
8 TraesCS6A01G147100 chr3A 94.565 184 9 1 2179 2361 643158430 643158613 1.710000e-72 283
9 TraesCS6A01G147100 chr7A 94.245 556 29 2 2367 2921 436896566 436897119 0.000000e+00 846
10 TraesCS6A01G147100 chr7A 91.848 184 14 1 2179 2361 686948717 686948900 3.740000e-64 255
11 TraesCS6A01G147100 chr4A 93.571 560 31 5 2363 2921 195386334 195385779 0.000000e+00 830
12 TraesCS6A01G147100 chr7D 91.562 557 41 5 2367 2921 553481258 553480706 0.000000e+00 763
13 TraesCS6A01G147100 chrUn 91.562 557 38 7 2367 2921 385731923 385731374 0.000000e+00 760
14 TraesCS6A01G147100 chr3D 91.166 566 40 9 2357 2919 603950585 603951143 0.000000e+00 760
15 TraesCS6A01G147100 chr5B 93.085 188 11 2 2176 2361 436236465 436236278 1.030000e-69 274
16 TraesCS6A01G147100 chr5B 93.478 184 11 1 2179 2361 680717640 680717823 3.710000e-69 272
17 TraesCS6A01G147100 chr5B 92.135 178 12 2 2179 2355 509463930 509464106 1.740000e-62 250
18 TraesCS6A01G147100 chr1A 92.391 184 13 1 2179 2361 264982724 264982907 8.030000e-66 261
19 TraesCS6A01G147100 chr5D 91.848 184 14 1 2179 2361 8039508 8039691 3.740000e-64 255
20 TraesCS6A01G147100 chr5A 89.560 182 17 2 2174 2353 618958160 618957979 2.260000e-56 230
21 TraesCS6A01G147100 chr1D 87.629 194 20 4 2163 2353 11356651 11356843 3.790000e-54 222


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 TraesCS6A01G147100 chr6A 126915360 126918280 2920 False 5395 5395 100.000 1 2921 1 chr6A.!!$F1 2920
1 TraesCS6A01G147100 chr6A 608334102 608334664 562 True 878 878 94.858 2361 2921 1 chr6A.!!$R1 560
2 TraesCS6A01G147100 chr6B 191199287 191201373 2086 False 3051 3051 93.197 3 2077 1 chr6B.!!$F1 2074
3 TraesCS6A01G147100 chr6D 104783114 104784338 1224 False 2001 2001 96.248 859 2076 1 chr6D.!!$F2 1217
4 TraesCS6A01G147100 chr6D 104768275 104769075 800 False 1249 1249 94.776 3 805 1 chr6D.!!$F1 802
5 TraesCS6A01G147100 chr2A 566599374 566599932 558 False 852 852 94.139 2361 2921 1 chr2A.!!$F1 560
6 TraesCS6A01G147100 chr3A 27542008 27542563 555 True 848 848 94.255 2367 2921 1 chr3A.!!$R1 554
7 TraesCS6A01G147100 chr3A 599819871 599820424 553 True 791 791 92.460 2367 2921 1 chr3A.!!$R2 554
8 TraesCS6A01G147100 chr7A 436896566 436897119 553 False 846 846 94.245 2367 2921 1 chr7A.!!$F1 554
9 TraesCS6A01G147100 chr4A 195385779 195386334 555 True 830 830 93.571 2363 2921 1 chr4A.!!$R1 558
10 TraesCS6A01G147100 chr7D 553480706 553481258 552 True 763 763 91.562 2367 2921 1 chr7D.!!$R1 554
11 TraesCS6A01G147100 chrUn 385731374 385731923 549 True 760 760 91.562 2367 2921 1 chrUn.!!$R1 554
12 TraesCS6A01G147100 chr3D 603950585 603951143 558 False 760 760 91.166 2357 2919 1 chr3D.!!$F1 562

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
208 209 0.310854 CTTCAAAGTTGCCCGTGGTC 59.689 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2130 0.767998 TCTGCCACATGGTTACCACA 59.232 50.0 6.1 0.0 35.8 4.17 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
25 26 3.715015 GAGGTTCGGGAGCTCCTT 58.285 61.111 31.36 10.89 45.14 3.36
52 53 3.677700 CGGGTAAAATCATCGGTGTCTCA 60.678 47.826 0.00 0.00 0.00 3.27
67 68 1.001764 CTCATGCAAGACCCCTGCA 60.002 57.895 0.00 0.00 43.04 4.41
202 203 0.601046 GCTTGGCTTCAAAGTTGCCC 60.601 55.000 0.00 0.00 45.56 5.36
208 209 0.310854 CTTCAAAGTTGCCCGTGGTC 59.689 55.000 0.00 0.00 0.00 4.02
258 259 1.697432 AGGTTCGGTGATGGAACTTGA 59.303 47.619 4.86 0.00 42.58 3.02
260 261 2.550208 GGTTCGGTGATGGAACTTGACT 60.550 50.000 4.86 0.00 42.58 3.41
307 308 1.059835 GTCTCTGCTTTGTTCGATCGC 59.940 52.381 11.09 0.00 0.00 4.58
350 351 4.450053 GAGAAACCTCAGATCCATCTTGG 58.550 47.826 0.00 4.58 39.43 3.61
378 379 1.017387 CGTTGCTTGGCTTAGATCCC 58.983 55.000 0.00 0.00 0.00 3.85
406 407 6.319911 AGCTAGCTTTCACTTCTCTTGTTTTT 59.680 34.615 12.68 0.00 0.00 1.94
470 471 8.782339 AATCCATCTGAAAAATTGGAAATCAC 57.218 30.769 1.38 0.00 41.36 3.06
501 503 0.455464 GCGGTGGTACGAAATTTGCC 60.455 55.000 0.00 0.00 35.47 4.52
516 518 2.799126 TTGCCTCCACGGTTTGATAT 57.201 45.000 0.00 0.00 34.25 1.63
648 650 5.486775 TCTCCATGACATCTTCCTCTCTTTT 59.513 40.000 0.00 0.00 0.00 2.27
649 651 6.013032 TCTCCATGACATCTTCCTCTCTTTTT 60.013 38.462 0.00 0.00 0.00 1.94
700 702 7.831691 TTTGACCAACATCTCTAAATTTCCA 57.168 32.000 0.00 0.00 0.00 3.53
703 705 5.640147 ACCAACATCTCTAAATTTCCACCA 58.360 37.500 0.00 0.00 0.00 4.17
708 710 9.740239 CAACATCTCTAAATTTCCACCAATATG 57.260 33.333 0.00 0.00 0.00 1.78
710 712 9.699410 ACATCTCTAAATTTCCACCAATATGAA 57.301 29.630 0.00 0.00 0.00 2.57
723 725 5.754890 CACCAATATGAACGATCTGATGACA 59.245 40.000 0.00 0.00 0.00 3.58
737 739 4.633175 CTGATGACAGAATCCATCTCTGG 58.367 47.826 4.96 0.00 46.03 3.86
762 764 1.000060 GCAACTTGAAGCATTGCCAGA 60.000 47.619 4.70 0.00 42.32 3.86
764 766 2.283145 ACTTGAAGCATTGCCAGACT 57.717 45.000 4.70 0.00 0.00 3.24
765 767 3.423539 ACTTGAAGCATTGCCAGACTA 57.576 42.857 4.70 0.00 0.00 2.59
767 769 4.338879 ACTTGAAGCATTGCCAGACTAAT 58.661 39.130 4.70 0.00 0.00 1.73
769 771 5.244626 ACTTGAAGCATTGCCAGACTAATTT 59.755 36.000 4.70 0.00 0.00 1.82
771 773 5.472148 TGAAGCATTGCCAGACTAATTTTG 58.528 37.500 4.70 0.00 0.00 2.44
787 794 9.651718 GACTAATTTTGTTTCTGAAGTGTACTG 57.348 33.333 0.00 0.00 0.00 2.74
817 824 2.346766 AGTAAATGGCCGATGATGCA 57.653 45.000 0.00 0.00 0.00 3.96
818 825 2.224606 AGTAAATGGCCGATGATGCAG 58.775 47.619 0.00 0.00 0.00 4.41
819 826 0.953727 TAAATGGCCGATGATGCAGC 59.046 50.000 0.00 0.00 0.00 5.25
820 827 0.754217 AAATGGCCGATGATGCAGCT 60.754 50.000 2.53 0.00 0.00 4.24
821 828 1.452953 AATGGCCGATGATGCAGCTG 61.453 55.000 10.11 10.11 0.00 4.24
822 829 3.285215 GGCCGATGATGCAGCTGG 61.285 66.667 17.12 3.67 0.00 4.85
840 847 2.554032 CTGGAGCTGGTTGTTAAGTTGG 59.446 50.000 0.00 0.00 0.00 3.77
895 928 3.350219 AAGTTCTGGTATCGCCACATT 57.650 42.857 0.00 0.00 43.61 2.71
956 990 1.906333 ATTTGACAACACCCCCGCC 60.906 57.895 0.00 0.00 0.00 6.13
961 995 4.676951 CAACACCCCCGCCACCAT 62.677 66.667 0.00 0.00 0.00 3.55
1122 1156 3.793144 GCGTTCTTGGCAGAGGCG 61.793 66.667 0.00 0.00 42.47 5.52
1473 1507 2.997897 ACCGAGGACCAGCTGGAC 60.998 66.667 39.19 31.70 38.94 4.02
1474 1508 2.997315 CCGAGGACCAGCTGGACA 60.997 66.667 39.19 0.00 38.94 4.02
1641 1675 4.479993 CAGGGCCCGCTCTTGGAG 62.480 72.222 18.44 0.00 0.00 3.86
1980 2022 5.335348 CCGGCCTTTCGATCTTTTAAGAAAA 60.335 40.000 0.00 0.00 38.77 2.29
2004 2046 3.311596 CCGGTCTGAAATTATTTCGGTCC 59.688 47.826 23.47 23.47 45.12 4.46
2009 2051 4.473559 TCTGAAATTATTTCGGTCCCCTCT 59.526 41.667 21.51 0.00 44.52 3.69
2044 2087 3.463944 TGGTCTTCGGTCTCTTTTGAAC 58.536 45.455 0.00 0.00 0.00 3.18
2078 2121 4.871557 CCGGACCAAACATACTAATTTCGA 59.128 41.667 0.00 0.00 0.00 3.71
2079 2122 5.352016 CCGGACCAAACATACTAATTTCGAA 59.648 40.000 0.00 0.00 0.00 3.71
2080 2123 6.128227 CCGGACCAAACATACTAATTTCGAAA 60.128 38.462 13.91 13.91 0.00 3.46
2081 2124 7.414762 CCGGACCAAACATACTAATTTCGAAAT 60.415 37.037 17.60 17.60 0.00 2.17
2082 2125 8.605746 CGGACCAAACATACTAATTTCGAAATA 58.394 33.333 22.99 8.59 0.00 1.40
2096 2139 8.751302 AATTTCGAAATATGTTTGTGGTAACC 57.249 30.769 22.99 0.00 0.00 2.85
2097 2140 6.879276 TTCGAAATATGTTTGTGGTAACCA 57.121 33.333 0.00 0.00 0.00 3.67
2098 2141 7.455641 TTCGAAATATGTTTGTGGTAACCAT 57.544 32.000 0.00 0.00 35.28 3.55
2099 2142 6.847400 TCGAAATATGTTTGTGGTAACCATG 58.153 36.000 0.00 0.00 35.28 3.66
2100 2143 6.431543 TCGAAATATGTTTGTGGTAACCATGT 59.568 34.615 0.00 0.00 35.28 3.21
2101 2144 6.526325 CGAAATATGTTTGTGGTAACCATGTG 59.474 38.462 0.00 0.00 35.28 3.21
2102 2145 5.913137 ATATGTTTGTGGTAACCATGTGG 57.087 39.130 0.00 0.00 35.28 4.17
2103 2146 1.683917 TGTTTGTGGTAACCATGTGGC 59.316 47.619 0.00 0.00 39.32 5.01
2104 2147 1.683917 GTTTGTGGTAACCATGTGGCA 59.316 47.619 0.00 0.00 39.32 4.92
2105 2148 1.614996 TTGTGGTAACCATGTGGCAG 58.385 50.000 0.00 0.00 39.32 4.85
2106 2149 0.767998 TGTGGTAACCATGTGGCAGA 59.232 50.000 0.00 0.00 39.32 4.26
2107 2150 1.354031 TGTGGTAACCATGTGGCAGAT 59.646 47.619 0.00 0.00 39.32 2.90
2108 2151 2.224992 TGTGGTAACCATGTGGCAGATT 60.225 45.455 0.00 0.00 39.32 2.40
2109 2152 3.009584 TGTGGTAACCATGTGGCAGATTA 59.990 43.478 0.00 0.00 39.32 1.75
2110 2153 3.377172 GTGGTAACCATGTGGCAGATTAC 59.623 47.826 0.00 0.00 39.32 1.89
2111 2154 3.009584 TGGTAACCATGTGGCAGATTACA 59.990 43.478 8.35 0.00 39.32 2.41
2112 2155 4.013728 GGTAACCATGTGGCAGATTACAA 58.986 43.478 8.35 0.00 39.32 2.41
2113 2156 4.461081 GGTAACCATGTGGCAGATTACAAA 59.539 41.667 8.35 0.00 39.32 2.83
2114 2157 5.047660 GGTAACCATGTGGCAGATTACAAAA 60.048 40.000 8.35 0.00 39.32 2.44
2115 2158 4.519540 ACCATGTGGCAGATTACAAAAC 57.480 40.909 0.00 0.00 39.32 2.43
2116 2159 4.151883 ACCATGTGGCAGATTACAAAACT 58.848 39.130 0.00 0.00 39.32 2.66
2117 2160 4.022068 ACCATGTGGCAGATTACAAAACTG 60.022 41.667 0.00 0.00 39.32 3.16
2118 2161 4.022068 CCATGTGGCAGATTACAAAACTGT 60.022 41.667 0.00 0.00 34.60 3.55
2119 2162 4.829064 TGTGGCAGATTACAAAACTGTC 57.171 40.909 0.00 0.00 36.88 3.51
2120 2163 4.203226 TGTGGCAGATTACAAAACTGTCA 58.797 39.130 0.00 0.00 42.60 3.58
2121 2164 4.826733 TGTGGCAGATTACAAAACTGTCAT 59.173 37.500 7.36 0.00 45.51 3.06
2122 2165 6.000840 TGTGGCAGATTACAAAACTGTCATA 58.999 36.000 7.36 2.89 45.51 2.15
2123 2166 6.658816 TGTGGCAGATTACAAAACTGTCATAT 59.341 34.615 7.36 0.00 45.51 1.78
2124 2167 7.148255 TGTGGCAGATTACAAAACTGTCATATC 60.148 37.037 7.36 0.00 45.51 1.63
2125 2168 6.883756 TGGCAGATTACAAAACTGTCATATCA 59.116 34.615 0.00 0.00 40.52 2.15
2126 2169 7.392953 TGGCAGATTACAAAACTGTCATATCAA 59.607 33.333 0.00 0.00 40.52 2.57
2127 2170 8.243426 GGCAGATTACAAAACTGTCATATCAAA 58.757 33.333 0.00 0.00 36.45 2.69
2128 2171 9.793252 GCAGATTACAAAACTGTCATATCAAAT 57.207 29.630 0.00 0.00 34.60 2.32
2214 2257 5.813513 AAAAAGCAAACATGAATCCTCCT 57.186 34.783 0.00 0.00 0.00 3.69
2215 2258 6.916360 AAAAAGCAAACATGAATCCTCCTA 57.084 33.333 0.00 0.00 0.00 2.94
2216 2259 6.916360 AAAAGCAAACATGAATCCTCCTAA 57.084 33.333 0.00 0.00 0.00 2.69
2217 2260 6.916360 AAAGCAAACATGAATCCTCCTAAA 57.084 33.333 0.00 0.00 0.00 1.85
2218 2261 6.521151 AAGCAAACATGAATCCTCCTAAAG 57.479 37.500 0.00 0.00 0.00 1.85
2219 2262 5.574188 AGCAAACATGAATCCTCCTAAAGT 58.426 37.500 0.00 0.00 0.00 2.66
2220 2263 5.649831 AGCAAACATGAATCCTCCTAAAGTC 59.350 40.000 0.00 0.00 0.00 3.01
2221 2264 5.415701 GCAAACATGAATCCTCCTAAAGTCA 59.584 40.000 0.00 0.00 0.00 3.41
2222 2265 6.623767 GCAAACATGAATCCTCCTAAAGTCAC 60.624 42.308 0.00 0.00 0.00 3.67
2223 2266 5.762179 ACATGAATCCTCCTAAAGTCACA 57.238 39.130 0.00 0.00 0.00 3.58
2224 2267 5.491982 ACATGAATCCTCCTAAAGTCACAC 58.508 41.667 0.00 0.00 0.00 3.82
2225 2268 4.553330 TGAATCCTCCTAAAGTCACACC 57.447 45.455 0.00 0.00 0.00 4.16
2226 2269 3.907474 TGAATCCTCCTAAAGTCACACCA 59.093 43.478 0.00 0.00 0.00 4.17
2227 2270 4.349636 TGAATCCTCCTAAAGTCACACCAA 59.650 41.667 0.00 0.00 0.00 3.67
2228 2271 4.993705 ATCCTCCTAAAGTCACACCAAA 57.006 40.909 0.00 0.00 0.00 3.28
2229 2272 4.781775 TCCTCCTAAAGTCACACCAAAA 57.218 40.909 0.00 0.00 0.00 2.44
2230 2273 5.118729 TCCTCCTAAAGTCACACCAAAAA 57.881 39.130 0.00 0.00 0.00 1.94
2231 2274 5.701224 TCCTCCTAAAGTCACACCAAAAAT 58.299 37.500 0.00 0.00 0.00 1.82
2232 2275 5.534654 TCCTCCTAAAGTCACACCAAAAATG 59.465 40.000 0.00 0.00 0.00 2.32
2233 2276 5.301805 CCTCCTAAAGTCACACCAAAAATGT 59.698 40.000 0.00 0.00 0.00 2.71
2234 2277 6.488683 CCTCCTAAAGTCACACCAAAAATGTA 59.511 38.462 0.00 0.00 0.00 2.29
2235 2278 7.266922 TCCTAAAGTCACACCAAAAATGTAC 57.733 36.000 0.00 0.00 0.00 2.90
2236 2279 6.829298 TCCTAAAGTCACACCAAAAATGTACA 59.171 34.615 0.00 0.00 0.00 2.90
2237 2280 6.915843 CCTAAAGTCACACCAAAAATGTACAC 59.084 38.462 0.00 0.00 0.00 2.90
2238 2281 5.906113 AAGTCACACCAAAAATGTACACA 57.094 34.783 0.00 0.00 0.00 3.72
2239 2282 5.499139 AGTCACACCAAAAATGTACACAG 57.501 39.130 0.00 0.00 0.00 3.66
2240 2283 5.189928 AGTCACACCAAAAATGTACACAGA 58.810 37.500 0.00 0.00 0.00 3.41
2241 2284 5.650266 AGTCACACCAAAAATGTACACAGAA 59.350 36.000 0.00 0.00 0.00 3.02
2242 2285 5.971202 GTCACACCAAAAATGTACACAGAAG 59.029 40.000 0.00 0.00 0.00 2.85
2243 2286 5.650266 TCACACCAAAAATGTACACAGAAGT 59.350 36.000 0.00 0.00 0.00 3.01
2244 2287 6.824196 TCACACCAAAAATGTACACAGAAGTA 59.176 34.615 0.00 0.00 0.00 2.24
2245 2288 6.910433 CACACCAAAAATGTACACAGAAGTAC 59.090 38.462 0.00 0.00 43.58 2.73
2246 2289 6.038936 ACACCAAAAATGTACACAGAAGTACC 59.961 38.462 0.00 0.00 42.84 3.34
2247 2290 6.038825 CACCAAAAATGTACACAGAAGTACCA 59.961 38.462 0.00 0.00 42.84 3.25
2248 2291 6.262273 ACCAAAAATGTACACAGAAGTACCAG 59.738 38.462 0.00 0.00 42.84 4.00
2249 2292 6.485313 CCAAAAATGTACACAGAAGTACCAGA 59.515 38.462 0.00 0.00 42.84 3.86
2250 2293 7.307989 CCAAAAATGTACACAGAAGTACCAGAG 60.308 40.741 0.00 0.00 42.84 3.35
2251 2294 6.665992 AAATGTACACAGAAGTACCAGAGA 57.334 37.500 0.00 0.00 42.84 3.10
2252 2295 5.646577 ATGTACACAGAAGTACCAGAGAC 57.353 43.478 0.00 0.00 42.84 3.36
2253 2296 3.501062 TGTACACAGAAGTACCAGAGACG 59.499 47.826 0.00 0.00 42.84 4.18
2254 2297 2.584236 ACACAGAAGTACCAGAGACGT 58.416 47.619 0.00 0.00 0.00 4.34
2255 2298 2.957006 ACACAGAAGTACCAGAGACGTT 59.043 45.455 0.00 0.00 0.00 3.99
2256 2299 3.383825 ACACAGAAGTACCAGAGACGTTT 59.616 43.478 0.00 0.00 0.00 3.60
2257 2300 3.736252 CACAGAAGTACCAGAGACGTTTG 59.264 47.826 0.00 0.00 0.00 2.93
2258 2301 3.635373 ACAGAAGTACCAGAGACGTTTGA 59.365 43.478 0.00 0.00 0.00 2.69
2259 2302 4.281182 ACAGAAGTACCAGAGACGTTTGAT 59.719 41.667 0.00 0.00 0.00 2.57
2260 2303 4.859798 CAGAAGTACCAGAGACGTTTGATC 59.140 45.833 0.00 0.00 0.00 2.92
2261 2304 4.523173 AGAAGTACCAGAGACGTTTGATCA 59.477 41.667 0.00 0.00 0.00 2.92
2262 2305 4.866508 AGTACCAGAGACGTTTGATCAA 57.133 40.909 3.38 3.38 0.00 2.57
2263 2306 5.407407 AGTACCAGAGACGTTTGATCAAT 57.593 39.130 9.40 0.00 0.00 2.57
2264 2307 5.411781 AGTACCAGAGACGTTTGATCAATC 58.588 41.667 9.40 7.73 0.00 2.67
2265 2308 3.600388 ACCAGAGACGTTTGATCAATCC 58.400 45.455 9.40 2.32 0.00 3.01
2266 2309 2.939103 CCAGAGACGTTTGATCAATCCC 59.061 50.000 9.40 2.64 0.00 3.85
2267 2310 3.599343 CAGAGACGTTTGATCAATCCCA 58.401 45.455 9.40 0.00 0.00 4.37
2268 2311 3.372206 CAGAGACGTTTGATCAATCCCAC 59.628 47.826 9.40 3.41 0.00 4.61
2269 2312 3.261897 AGAGACGTTTGATCAATCCCACT 59.738 43.478 9.40 5.78 0.00 4.00
2270 2313 4.466370 AGAGACGTTTGATCAATCCCACTA 59.534 41.667 9.40 0.00 0.00 2.74
2271 2314 5.046591 AGAGACGTTTGATCAATCCCACTAA 60.047 40.000 9.40 0.00 0.00 2.24
2272 2315 5.556915 AGACGTTTGATCAATCCCACTAAA 58.443 37.500 9.40 0.00 0.00 1.85
2273 2316 6.180472 AGACGTTTGATCAATCCCACTAAAT 58.820 36.000 9.40 0.00 0.00 1.40
2274 2317 6.316390 AGACGTTTGATCAATCCCACTAAATC 59.684 38.462 9.40 0.84 0.00 2.17
2275 2318 5.943416 ACGTTTGATCAATCCCACTAAATCA 59.057 36.000 9.40 0.00 0.00 2.57
2276 2319 6.128007 ACGTTTGATCAATCCCACTAAATCAC 60.128 38.462 9.40 0.00 0.00 3.06
2277 2320 6.128035 CGTTTGATCAATCCCACTAAATCACA 60.128 38.462 9.40 0.00 0.00 3.58
2278 2321 7.415541 CGTTTGATCAATCCCACTAAATCACAT 60.416 37.037 9.40 0.00 0.00 3.21
2279 2322 7.572523 TTGATCAATCCCACTAAATCACATC 57.427 36.000 3.38 0.00 0.00 3.06
2280 2323 6.064060 TGATCAATCCCACTAAATCACATCC 58.936 40.000 0.00 0.00 0.00 3.51
2281 2324 5.449297 TCAATCCCACTAAATCACATCCA 57.551 39.130 0.00 0.00 0.00 3.41
2282 2325 5.825532 TCAATCCCACTAAATCACATCCAA 58.174 37.500 0.00 0.00 0.00 3.53
2283 2326 5.652014 TCAATCCCACTAAATCACATCCAAC 59.348 40.000 0.00 0.00 0.00 3.77
2284 2327 3.605634 TCCCACTAAATCACATCCAACG 58.394 45.455 0.00 0.00 0.00 4.10
2285 2328 3.008594 TCCCACTAAATCACATCCAACGT 59.991 43.478 0.00 0.00 0.00 3.99
2286 2329 3.756434 CCCACTAAATCACATCCAACGTT 59.244 43.478 0.00 0.00 0.00 3.99
2287 2330 4.142687 CCCACTAAATCACATCCAACGTTC 60.143 45.833 0.00 0.00 0.00 3.95
2288 2331 4.695455 CCACTAAATCACATCCAACGTTCT 59.305 41.667 0.00 0.00 0.00 3.01
2289 2332 5.872617 CCACTAAATCACATCCAACGTTCTA 59.127 40.000 0.00 0.00 0.00 2.10
2290 2333 6.538742 CCACTAAATCACATCCAACGTTCTAT 59.461 38.462 0.00 0.00 0.00 1.98
2291 2334 7.709182 CCACTAAATCACATCCAACGTTCTATA 59.291 37.037 0.00 0.00 0.00 1.31
2292 2335 9.261180 CACTAAATCACATCCAACGTTCTATAT 57.739 33.333 0.00 0.00 0.00 0.86
2293 2336 9.832445 ACTAAATCACATCCAACGTTCTATATT 57.168 29.630 0.00 0.00 0.00 1.28
2296 2339 9.607988 AAATCACATCCAACGTTCTATATTACA 57.392 29.630 0.00 0.00 0.00 2.41
2297 2340 9.778741 AATCACATCCAACGTTCTATATTACAT 57.221 29.630 0.00 0.00 0.00 2.29
2298 2341 8.812147 TCACATCCAACGTTCTATATTACATC 57.188 34.615 0.00 0.00 0.00 3.06
2299 2342 8.417884 TCACATCCAACGTTCTATATTACATCA 58.582 33.333 0.00 0.00 0.00 3.07
2300 2343 9.040939 CACATCCAACGTTCTATATTACATCAA 57.959 33.333 0.00 0.00 0.00 2.57
2301 2344 9.607988 ACATCCAACGTTCTATATTACATCAAA 57.392 29.630 0.00 0.00 0.00 2.69
2303 2346 8.657074 TCCAACGTTCTATATTACATCAAAGG 57.343 34.615 0.00 0.00 0.00 3.11
2304 2347 8.262227 TCCAACGTTCTATATTACATCAAAGGT 58.738 33.333 0.00 0.00 0.00 3.50
2305 2348 8.548721 CCAACGTTCTATATTACATCAAAGGTC 58.451 37.037 0.00 0.00 0.00 3.85
2306 2349 9.314321 CAACGTTCTATATTACATCAAAGGTCT 57.686 33.333 0.00 0.00 0.00 3.85
2307 2350 8.873215 ACGTTCTATATTACATCAAAGGTCTG 57.127 34.615 0.00 0.00 0.00 3.51
2308 2351 8.475639 ACGTTCTATATTACATCAAAGGTCTGT 58.524 33.333 0.00 0.00 0.00 3.41
2309 2352 8.969267 CGTTCTATATTACATCAAAGGTCTGTC 58.031 37.037 0.00 0.00 0.00 3.51
2310 2353 9.817809 GTTCTATATTACATCAAAGGTCTGTCA 57.182 33.333 0.00 0.00 0.00 3.58
2311 2354 9.817809 TTCTATATTACATCAAAGGTCTGTCAC 57.182 33.333 0.00 0.00 0.00 3.67
2312 2355 8.977412 TCTATATTACATCAAAGGTCTGTCACA 58.023 33.333 0.00 0.00 0.00 3.58
2313 2356 7.849804 ATATTACATCAAAGGTCTGTCACAC 57.150 36.000 0.00 0.00 0.00 3.82
2314 2357 2.851195 ACATCAAAGGTCTGTCACACC 58.149 47.619 0.00 0.00 0.00 4.16
2315 2358 2.172505 ACATCAAAGGTCTGTCACACCA 59.827 45.455 0.00 0.00 36.23 4.17
2316 2359 3.213506 CATCAAAGGTCTGTCACACCAA 58.786 45.455 0.00 0.00 36.23 3.67
2317 2360 3.576078 TCAAAGGTCTGTCACACCAAT 57.424 42.857 0.00 0.00 36.23 3.16
2318 2361 3.476552 TCAAAGGTCTGTCACACCAATC 58.523 45.455 0.00 0.00 36.23 2.67
2319 2362 3.118075 TCAAAGGTCTGTCACACCAATCA 60.118 43.478 0.00 0.00 36.23 2.57
2320 2363 3.576078 AAGGTCTGTCACACCAATCAA 57.424 42.857 0.00 0.00 36.23 2.57
2321 2364 2.851195 AGGTCTGTCACACCAATCAAC 58.149 47.619 0.00 0.00 36.23 3.18
2322 2365 1.531149 GGTCTGTCACACCAATCAACG 59.469 52.381 0.00 0.00 33.63 4.10
2323 2366 1.069906 GTCTGTCACACCAATCAACGC 60.070 52.381 0.00 0.00 0.00 4.84
2324 2367 1.202639 TCTGTCACACCAATCAACGCT 60.203 47.619 0.00 0.00 0.00 5.07
2325 2368 1.195448 CTGTCACACCAATCAACGCTC 59.805 52.381 0.00 0.00 0.00 5.03
2326 2369 1.225855 GTCACACCAATCAACGCTCA 58.774 50.000 0.00 0.00 0.00 4.26
2327 2370 1.195448 GTCACACCAATCAACGCTCAG 59.805 52.381 0.00 0.00 0.00 3.35
2328 2371 0.518636 CACACCAATCAACGCTCAGG 59.481 55.000 0.00 0.00 0.00 3.86
2329 2372 0.396435 ACACCAATCAACGCTCAGGA 59.604 50.000 0.00 0.00 0.00 3.86
2330 2373 1.003580 ACACCAATCAACGCTCAGGAT 59.996 47.619 0.00 0.00 0.00 3.24
2331 2374 2.086869 CACCAATCAACGCTCAGGATT 58.913 47.619 0.00 0.00 0.00 3.01
2332 2375 3.270027 CACCAATCAACGCTCAGGATTA 58.730 45.455 0.00 0.00 30.53 1.75
2333 2376 3.689161 CACCAATCAACGCTCAGGATTAA 59.311 43.478 0.00 0.00 30.53 1.40
2334 2377 4.155826 CACCAATCAACGCTCAGGATTAAA 59.844 41.667 0.00 0.00 30.53 1.52
2335 2378 4.949856 ACCAATCAACGCTCAGGATTAAAT 59.050 37.500 0.00 0.00 30.53 1.40
2336 2379 5.163622 ACCAATCAACGCTCAGGATTAAATG 60.164 40.000 0.00 0.00 30.53 2.32
2337 2380 5.163622 CCAATCAACGCTCAGGATTAAATGT 60.164 40.000 0.00 0.00 30.53 2.71
2338 2381 6.324819 CAATCAACGCTCAGGATTAAATGTT 58.675 36.000 0.00 0.00 30.53 2.71
2339 2382 5.545658 TCAACGCTCAGGATTAAATGTTC 57.454 39.130 0.00 0.00 0.00 3.18
2340 2383 5.245531 TCAACGCTCAGGATTAAATGTTCT 58.754 37.500 0.00 0.00 0.00 3.01
2341 2384 5.122239 TCAACGCTCAGGATTAAATGTTCTG 59.878 40.000 0.00 0.00 0.00 3.02
2342 2385 3.375299 ACGCTCAGGATTAAATGTTCTGC 59.625 43.478 0.00 0.00 0.00 4.26
2343 2386 3.242870 CGCTCAGGATTAAATGTTCTGCC 60.243 47.826 0.00 0.00 0.00 4.85
2344 2387 3.696051 GCTCAGGATTAAATGTTCTGCCA 59.304 43.478 0.00 0.00 0.00 4.92
2345 2388 4.201990 GCTCAGGATTAAATGTTCTGCCAG 60.202 45.833 0.00 0.00 0.00 4.85
2346 2389 4.272489 TCAGGATTAAATGTTCTGCCAGG 58.728 43.478 0.00 0.00 0.00 4.45
2347 2390 4.018506 TCAGGATTAAATGTTCTGCCAGGA 60.019 41.667 0.00 0.00 0.00 3.86
2348 2391 4.096984 CAGGATTAAATGTTCTGCCAGGAC 59.903 45.833 0.00 0.00 0.00 3.85
2349 2392 4.016444 GGATTAAATGTTCTGCCAGGACA 58.984 43.478 8.59 8.59 0.00 4.02
2350 2393 4.096984 GGATTAAATGTTCTGCCAGGACAG 59.903 45.833 12.21 0.00 39.12 3.51
2351 2394 2.957402 AAATGTTCTGCCAGGACAGA 57.043 45.000 12.21 8.95 44.84 3.41
2352 2395 2.191128 AATGTTCTGCCAGGACAGAC 57.809 50.000 12.21 8.77 46.13 3.51
2353 2396 0.036952 ATGTTCTGCCAGGACAGACG 60.037 55.000 12.21 0.00 46.13 4.18
2354 2397 2.029844 GTTCTGCCAGGACAGACGC 61.030 63.158 11.82 6.16 46.13 5.19
2355 2398 2.506957 TTCTGCCAGGACAGACGCA 61.507 57.895 11.82 0.00 46.13 5.24
2356 2399 2.715532 TTCTGCCAGGACAGACGCAC 62.716 60.000 11.82 0.00 46.13 5.34
2357 2400 3.519973 CTGCCAGGACAGACGCACA 62.520 63.158 5.22 0.00 40.25 4.57
2358 2401 3.044305 GCCAGGACAGACGCACAC 61.044 66.667 0.00 0.00 0.00 3.82
2388 2432 2.834113 TCTTCGAAAAGGGGATCTCCT 58.166 47.619 8.90 8.90 39.17 3.69
2472 2516 2.698797 AGTTTCCGAAGTCTCCAACAGA 59.301 45.455 0.00 0.00 0.00 3.41
2502 2548 0.181114 AGGACAGCAAGCTCACACAA 59.819 50.000 0.00 0.00 0.00 3.33
2629 2678 4.837093 TCCAAACCGGTTGAAGATATCT 57.163 40.909 23.08 0.00 39.87 1.98
2634 2683 3.288964 ACCGGTTGAAGATATCTCGAGT 58.711 45.455 13.13 2.46 0.00 4.18
2656 2705 1.689273 ACCATCTTCCAGCGGATAGAC 59.311 52.381 0.00 0.00 0.00 2.59
2712 2761 1.799121 GTAGCGACCACGAACGGAC 60.799 63.158 0.00 0.00 42.66 4.79
2855 2905 1.137872 CGCTAAGTCAGGCTCAATCCT 59.862 52.381 0.00 0.00 36.78 3.24
2877 2927 7.534852 TCCTATTAAGCCATGTCCCAAATAAT 58.465 34.615 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.134340 CCGATGATTTTACCCGGTCCA 60.134 52.381 0.00 0.00 35.83 4.02
52 53 0.896940 CTTGTGCAGGGGTCTTGCAT 60.897 55.000 7.89 0.00 40.84 3.96
202 203 3.430862 CCACCAATGGCGACCACG 61.431 66.667 0.00 0.00 39.82 4.94
258 259 2.447047 ACACCTTTGAGATTGGGGAAGT 59.553 45.455 0.00 0.00 0.00 3.01
260 261 2.552155 CGACACCTTTGAGATTGGGGAA 60.552 50.000 0.00 0.00 0.00 3.97
307 308 0.097150 TCTCAGACGAGACGCATTCG 59.903 55.000 0.00 2.75 43.55 3.34
350 351 2.425773 CAAGCAACGCACACTCGC 60.426 61.111 0.00 0.00 0.00 5.03
378 379 4.454728 AGAGAAGTGAAAGCTAGCTCTG 57.545 45.455 19.65 0.00 32.67 3.35
406 407 6.388619 AGTAAAAGCTTATCCTCCCTTGAA 57.611 37.500 0.00 0.00 0.00 2.69
470 471 0.742990 ACCACCGCACCATGTAATCG 60.743 55.000 0.00 0.00 0.00 3.34
501 503 3.873910 ACTTCCATATCAAACCGTGGAG 58.126 45.455 0.00 0.00 41.41 3.86
516 518 6.073276 CGGAATTTCGCATTCATATACTTCCA 60.073 38.462 0.00 0.00 0.00 3.53
695 697 5.739959 TCAGATCGTTCATATTGGTGGAAA 58.260 37.500 0.00 0.00 0.00 3.13
700 702 5.917462 TGTCATCAGATCGTTCATATTGGT 58.083 37.500 0.00 0.00 0.00 3.67
723 725 2.328319 GCCTCTCCAGAGATGGATTCT 58.672 52.381 5.08 0.00 44.74 2.40
726 728 1.767681 GTTGCCTCTCCAGAGATGGAT 59.232 52.381 5.08 0.00 44.74 3.41
734 736 1.163554 GCTTCAAGTTGCCTCTCCAG 58.836 55.000 0.00 0.00 0.00 3.86
735 737 0.473755 TGCTTCAAGTTGCCTCTCCA 59.526 50.000 0.00 0.00 0.00 3.86
736 738 1.831580 ATGCTTCAAGTTGCCTCTCC 58.168 50.000 0.00 0.00 0.00 3.71
737 739 2.670509 GCAATGCTTCAAGTTGCCTCTC 60.671 50.000 0.00 0.00 41.67 3.20
744 746 2.590821 AGTCTGGCAATGCTTCAAGTT 58.409 42.857 4.82 0.00 0.00 2.66
749 751 5.473039 ACAAAATTAGTCTGGCAATGCTTC 58.527 37.500 4.82 0.00 0.00 3.86
762 764 9.174166 ACAGTACACTTCAGAAACAAAATTAGT 57.826 29.630 0.00 0.00 0.00 2.24
764 766 9.391006 AGACAGTACACTTCAGAAACAAAATTA 57.609 29.630 0.00 0.00 0.00 1.40
765 767 8.281212 AGACAGTACACTTCAGAAACAAAATT 57.719 30.769 0.00 0.00 0.00 1.82
767 769 7.103641 AGAGACAGTACACTTCAGAAACAAAA 58.896 34.615 0.00 0.00 0.00 2.44
769 771 6.096987 AGAGAGACAGTACACTTCAGAAACAA 59.903 38.462 0.00 0.00 0.00 2.83
771 773 6.079424 AGAGAGACAGTACACTTCAGAAAC 57.921 41.667 0.00 0.00 0.00 2.78
787 794 3.619038 CGGCCATTTACTTTGAGAGAGAC 59.381 47.826 2.24 0.00 0.00 3.36
818 825 1.897560 ACTTAACAACCAGCTCCAGC 58.102 50.000 0.00 0.00 42.49 4.85
819 826 2.554032 CCAACTTAACAACCAGCTCCAG 59.446 50.000 0.00 0.00 0.00 3.86
820 827 2.582052 CCAACTTAACAACCAGCTCCA 58.418 47.619 0.00 0.00 0.00 3.86
821 828 1.269723 GCCAACTTAACAACCAGCTCC 59.730 52.381 0.00 0.00 0.00 4.70
822 829 1.953686 TGCCAACTTAACAACCAGCTC 59.046 47.619 0.00 0.00 0.00 4.09
831 838 3.748021 GCACGTCTGCCAACTTAAC 57.252 52.632 0.00 0.00 37.45 2.01
840 847 3.372554 GAGTAGGGGGCACGTCTGC 62.373 68.421 0.00 0.00 43.41 4.26
895 928 3.006752 CCTACTCCATTGCAAAAGCCAAA 59.993 43.478 1.71 0.00 0.00 3.28
956 990 2.283298 CGAAGGAGATTGGTGATGGTG 58.717 52.381 0.00 0.00 0.00 4.17
961 995 0.530744 CCGACGAAGGAGATTGGTGA 59.469 55.000 0.00 0.00 28.85 4.02
1091 1125 3.226429 AACGCCTGCAGCTTCTCGA 62.226 57.895 8.66 0.00 40.39 4.04
1122 1156 4.388499 TCGTTCTTGGCCGCCTCC 62.388 66.667 11.61 0.00 0.00 4.30
1641 1675 4.760047 ACATGCCGCTCCACGTCC 62.760 66.667 0.00 0.00 41.42 4.79
1960 2002 6.581166 CCGGTTTTTCTTAAAAGATCGAAAGG 59.419 38.462 0.00 0.00 34.08 3.11
1980 2022 4.329392 ACCGAAATAATTTCAGACCGGTT 58.671 39.130 9.42 0.00 45.43 4.44
2004 2046 3.772025 ACCAGATAGTGAAGAACAGAGGG 59.228 47.826 0.00 0.00 0.00 4.30
2009 2051 4.082190 CCGAAGACCAGATAGTGAAGAACA 60.082 45.833 0.00 0.00 0.00 3.18
2078 2121 6.696411 CCACATGGTTACCACAAACATATTT 58.304 36.000 6.10 0.00 35.80 1.40
2079 2122 5.337169 GCCACATGGTTACCACAAACATATT 60.337 40.000 6.10 0.00 35.80 1.28
2080 2123 4.159506 GCCACATGGTTACCACAAACATAT 59.840 41.667 6.10 0.00 35.80 1.78
2081 2124 3.508012 GCCACATGGTTACCACAAACATA 59.492 43.478 6.10 0.00 35.80 2.29
2082 2125 2.298729 GCCACATGGTTACCACAAACAT 59.701 45.455 6.10 0.00 35.80 2.71
2083 2126 1.683917 GCCACATGGTTACCACAAACA 59.316 47.619 6.10 0.00 35.80 2.83
2084 2127 1.683917 TGCCACATGGTTACCACAAAC 59.316 47.619 6.10 0.00 35.80 2.93
2085 2128 1.959985 CTGCCACATGGTTACCACAAA 59.040 47.619 6.10 0.00 35.80 2.83
2086 2129 1.143889 TCTGCCACATGGTTACCACAA 59.856 47.619 6.10 0.00 35.80 3.33
2087 2130 0.767998 TCTGCCACATGGTTACCACA 59.232 50.000 6.10 0.00 35.80 4.17
2088 2131 2.128771 ATCTGCCACATGGTTACCAC 57.871 50.000 6.10 0.00 35.80 4.16
2089 2132 2.897271 AATCTGCCACATGGTTACCA 57.103 45.000 6.53 6.53 38.19 3.25
2090 2133 3.616219 TGTAATCTGCCACATGGTTACC 58.384 45.455 0.00 0.00 37.57 2.85
2091 2134 5.637006 TTTGTAATCTGCCACATGGTTAC 57.363 39.130 0.00 1.56 37.57 2.50
2092 2135 5.772672 AGTTTTGTAATCTGCCACATGGTTA 59.227 36.000 0.00 0.00 37.57 2.85
2093 2136 4.588528 AGTTTTGTAATCTGCCACATGGTT 59.411 37.500 0.00 0.00 37.57 3.67
2094 2137 4.022068 CAGTTTTGTAATCTGCCACATGGT 60.022 41.667 0.00 0.00 37.57 3.55
2095 2138 4.022068 ACAGTTTTGTAATCTGCCACATGG 60.022 41.667 0.00 0.00 35.25 3.66
2096 2139 5.125100 ACAGTTTTGTAATCTGCCACATG 57.875 39.130 0.00 0.00 35.25 3.21
2097 2140 4.826733 TGACAGTTTTGTAATCTGCCACAT 59.173 37.500 0.00 0.00 37.76 3.21
2098 2141 4.203226 TGACAGTTTTGTAATCTGCCACA 58.797 39.130 0.00 0.00 37.76 4.17
2099 2142 4.829064 TGACAGTTTTGTAATCTGCCAC 57.171 40.909 0.00 0.00 37.76 5.01
2100 2143 6.883756 TGATATGACAGTTTTGTAATCTGCCA 59.116 34.615 0.00 0.00 37.76 4.92
2101 2144 7.320443 TGATATGACAGTTTTGTAATCTGCC 57.680 36.000 0.00 0.00 37.76 4.85
2102 2145 9.793252 ATTTGATATGACAGTTTTGTAATCTGC 57.207 29.630 0.00 0.00 37.76 4.26
2192 2235 5.813513 AGGAGGATTCATGTTTGCTTTTT 57.186 34.783 0.00 0.00 0.00 1.94
2193 2236 6.916360 TTAGGAGGATTCATGTTTGCTTTT 57.084 33.333 0.00 0.00 0.00 2.27
2194 2237 6.494835 ACTTTAGGAGGATTCATGTTTGCTTT 59.505 34.615 0.00 0.00 0.00 3.51
2195 2238 6.012745 ACTTTAGGAGGATTCATGTTTGCTT 58.987 36.000 0.00 0.00 0.00 3.91
2196 2239 5.574188 ACTTTAGGAGGATTCATGTTTGCT 58.426 37.500 0.00 0.00 0.00 3.91
2197 2240 5.415701 TGACTTTAGGAGGATTCATGTTTGC 59.584 40.000 0.00 0.00 0.00 3.68
2198 2241 6.430925 TGTGACTTTAGGAGGATTCATGTTTG 59.569 38.462 0.00 0.00 0.00 2.93
2199 2242 6.431234 GTGTGACTTTAGGAGGATTCATGTTT 59.569 38.462 0.00 0.00 0.00 2.83
2200 2243 5.940470 GTGTGACTTTAGGAGGATTCATGTT 59.060 40.000 0.00 0.00 0.00 2.71
2201 2244 5.491982 GTGTGACTTTAGGAGGATTCATGT 58.508 41.667 0.00 0.00 0.00 3.21
2202 2245 4.878397 GGTGTGACTTTAGGAGGATTCATG 59.122 45.833 0.00 0.00 0.00 3.07
2203 2246 4.536090 TGGTGTGACTTTAGGAGGATTCAT 59.464 41.667 0.00 0.00 0.00 2.57
2204 2247 3.907474 TGGTGTGACTTTAGGAGGATTCA 59.093 43.478 0.00 0.00 0.00 2.57
2205 2248 4.553330 TGGTGTGACTTTAGGAGGATTC 57.447 45.455 0.00 0.00 0.00 2.52
2206 2249 4.993705 TTGGTGTGACTTTAGGAGGATT 57.006 40.909 0.00 0.00 0.00 3.01
2207 2250 4.993705 TTTGGTGTGACTTTAGGAGGAT 57.006 40.909 0.00 0.00 0.00 3.24
2208 2251 4.781775 TTTTGGTGTGACTTTAGGAGGA 57.218 40.909 0.00 0.00 0.00 3.71
2209 2252 5.301805 ACATTTTTGGTGTGACTTTAGGAGG 59.698 40.000 0.00 0.00 0.00 4.30
2210 2253 6.391227 ACATTTTTGGTGTGACTTTAGGAG 57.609 37.500 0.00 0.00 0.00 3.69
2211 2254 6.829298 TGTACATTTTTGGTGTGACTTTAGGA 59.171 34.615 0.00 0.00 0.00 2.94
2212 2255 6.915843 GTGTACATTTTTGGTGTGACTTTAGG 59.084 38.462 0.00 0.00 0.00 2.69
2213 2256 7.476667 TGTGTACATTTTTGGTGTGACTTTAG 58.523 34.615 0.00 0.00 0.00 1.85
2214 2257 7.337184 TCTGTGTACATTTTTGGTGTGACTTTA 59.663 33.333 0.00 0.00 0.00 1.85
2215 2258 6.151985 TCTGTGTACATTTTTGGTGTGACTTT 59.848 34.615 0.00 0.00 0.00 2.66
2216 2259 5.650266 TCTGTGTACATTTTTGGTGTGACTT 59.350 36.000 0.00 0.00 0.00 3.01
2217 2260 5.189928 TCTGTGTACATTTTTGGTGTGACT 58.810 37.500 0.00 0.00 0.00 3.41
2218 2261 5.493133 TCTGTGTACATTTTTGGTGTGAC 57.507 39.130 0.00 0.00 0.00 3.67
2219 2262 5.650266 ACTTCTGTGTACATTTTTGGTGTGA 59.350 36.000 0.00 0.00 0.00 3.58
2220 2263 5.890334 ACTTCTGTGTACATTTTTGGTGTG 58.110 37.500 0.00 0.00 0.00 3.82
2221 2264 6.038936 GGTACTTCTGTGTACATTTTTGGTGT 59.961 38.462 0.00 0.00 43.17 4.16
2222 2265 6.038825 TGGTACTTCTGTGTACATTTTTGGTG 59.961 38.462 0.00 0.00 43.17 4.17
2223 2266 6.123651 TGGTACTTCTGTGTACATTTTTGGT 58.876 36.000 0.00 0.00 43.17 3.67
2224 2267 6.485313 TCTGGTACTTCTGTGTACATTTTTGG 59.515 38.462 0.00 0.00 43.17 3.28
2225 2268 7.441157 TCTCTGGTACTTCTGTGTACATTTTTG 59.559 37.037 0.00 0.00 43.17 2.44
2226 2269 7.441458 GTCTCTGGTACTTCTGTGTACATTTTT 59.559 37.037 0.00 0.00 43.17 1.94
2227 2270 6.929606 GTCTCTGGTACTTCTGTGTACATTTT 59.070 38.462 0.00 0.00 43.17 1.82
2228 2271 6.456501 GTCTCTGGTACTTCTGTGTACATTT 58.543 40.000 0.00 0.00 43.17 2.32
2229 2272 5.335740 CGTCTCTGGTACTTCTGTGTACATT 60.336 44.000 0.00 0.00 43.17 2.71
2230 2273 4.156190 CGTCTCTGGTACTTCTGTGTACAT 59.844 45.833 0.00 0.00 43.17 2.29
2231 2274 3.501062 CGTCTCTGGTACTTCTGTGTACA 59.499 47.826 0.00 0.00 43.17 2.90
2232 2275 3.501445 ACGTCTCTGGTACTTCTGTGTAC 59.499 47.826 0.00 0.00 41.31 2.90
2233 2276 3.748083 ACGTCTCTGGTACTTCTGTGTA 58.252 45.455 0.00 0.00 0.00 2.90
2234 2277 2.584236 ACGTCTCTGGTACTTCTGTGT 58.416 47.619 0.00 0.00 0.00 3.72
2235 2278 3.644884 AACGTCTCTGGTACTTCTGTG 57.355 47.619 0.00 0.00 0.00 3.66
2236 2279 3.635373 TCAAACGTCTCTGGTACTTCTGT 59.365 43.478 0.00 0.00 0.00 3.41
2237 2280 4.238761 TCAAACGTCTCTGGTACTTCTG 57.761 45.455 0.00 0.00 0.00 3.02
2238 2281 4.523173 TGATCAAACGTCTCTGGTACTTCT 59.477 41.667 0.00 0.00 0.00 2.85
2239 2282 4.806330 TGATCAAACGTCTCTGGTACTTC 58.194 43.478 0.00 0.00 0.00 3.01
2240 2283 4.866508 TGATCAAACGTCTCTGGTACTT 57.133 40.909 0.00 0.00 0.00 2.24
2241 2284 4.866508 TTGATCAAACGTCTCTGGTACT 57.133 40.909 5.45 0.00 0.00 2.73
2242 2285 4.567159 GGATTGATCAAACGTCTCTGGTAC 59.433 45.833 13.09 0.00 0.00 3.34
2243 2286 4.382685 GGGATTGATCAAACGTCTCTGGTA 60.383 45.833 13.09 0.00 0.00 3.25
2244 2287 3.600388 GGATTGATCAAACGTCTCTGGT 58.400 45.455 13.09 0.00 0.00 4.00
2245 2288 2.939103 GGGATTGATCAAACGTCTCTGG 59.061 50.000 13.09 0.00 0.00 3.86
2246 2289 3.372206 GTGGGATTGATCAAACGTCTCTG 59.628 47.826 13.09 0.00 0.00 3.35
2247 2290 3.261897 AGTGGGATTGATCAAACGTCTCT 59.738 43.478 13.09 8.84 0.00 3.10
2248 2291 3.600388 AGTGGGATTGATCAAACGTCTC 58.400 45.455 13.09 6.35 0.00 3.36
2249 2292 3.703001 AGTGGGATTGATCAAACGTCT 57.297 42.857 13.09 6.23 0.00 4.18
2250 2293 5.873179 TTTAGTGGGATTGATCAAACGTC 57.127 39.130 13.09 5.60 0.00 4.34
2251 2294 5.943416 TGATTTAGTGGGATTGATCAAACGT 59.057 36.000 13.09 0.00 0.00 3.99
2252 2295 6.128035 TGTGATTTAGTGGGATTGATCAAACG 60.128 38.462 13.09 0.00 0.00 3.60
2253 2296 7.156876 TGTGATTTAGTGGGATTGATCAAAC 57.843 36.000 13.09 9.88 0.00 2.93
2254 2297 7.068593 GGATGTGATTTAGTGGGATTGATCAAA 59.931 37.037 13.09 0.00 0.00 2.69
2255 2298 6.547141 GGATGTGATTTAGTGGGATTGATCAA 59.453 38.462 11.26 11.26 0.00 2.57
2256 2299 6.064060 GGATGTGATTTAGTGGGATTGATCA 58.936 40.000 0.00 0.00 0.00 2.92
2257 2300 6.064060 TGGATGTGATTTAGTGGGATTGATC 58.936 40.000 0.00 0.00 0.00 2.92
2258 2301 6.017211 TGGATGTGATTTAGTGGGATTGAT 57.983 37.500 0.00 0.00 0.00 2.57
2259 2302 5.449297 TGGATGTGATTTAGTGGGATTGA 57.551 39.130 0.00 0.00 0.00 2.57
2260 2303 5.449041 CGTTGGATGTGATTTAGTGGGATTG 60.449 44.000 0.00 0.00 0.00 2.67
2261 2304 4.640201 CGTTGGATGTGATTTAGTGGGATT 59.360 41.667 0.00 0.00 0.00 3.01
2262 2305 4.199310 CGTTGGATGTGATTTAGTGGGAT 58.801 43.478 0.00 0.00 0.00 3.85
2263 2306 3.008594 ACGTTGGATGTGATTTAGTGGGA 59.991 43.478 0.00 0.00 0.00 4.37
2264 2307 3.343617 ACGTTGGATGTGATTTAGTGGG 58.656 45.455 0.00 0.00 0.00 4.61
2265 2308 4.695455 AGAACGTTGGATGTGATTTAGTGG 59.305 41.667 5.00 0.00 0.00 4.00
2266 2309 5.862924 AGAACGTTGGATGTGATTTAGTG 57.137 39.130 5.00 0.00 0.00 2.74
2267 2310 9.832445 AATATAGAACGTTGGATGTGATTTAGT 57.168 29.630 5.00 0.00 0.00 2.24
2270 2313 9.607988 TGTAATATAGAACGTTGGATGTGATTT 57.392 29.630 5.00 0.00 0.00 2.17
2271 2314 9.778741 ATGTAATATAGAACGTTGGATGTGATT 57.221 29.630 5.00 0.00 0.00 2.57
2272 2315 9.424319 GATGTAATATAGAACGTTGGATGTGAT 57.576 33.333 5.00 0.00 0.00 3.06
2273 2316 8.417884 TGATGTAATATAGAACGTTGGATGTGA 58.582 33.333 5.00 0.00 0.00 3.58
2274 2317 8.587952 TGATGTAATATAGAACGTTGGATGTG 57.412 34.615 5.00 0.00 0.00 3.21
2275 2318 9.607988 TTTGATGTAATATAGAACGTTGGATGT 57.392 29.630 5.00 0.00 0.00 3.06
2277 2320 9.273016 CCTTTGATGTAATATAGAACGTTGGAT 57.727 33.333 5.00 0.57 0.00 3.41
2278 2321 8.262227 ACCTTTGATGTAATATAGAACGTTGGA 58.738 33.333 5.00 0.00 0.00 3.53
2279 2322 8.433421 ACCTTTGATGTAATATAGAACGTTGG 57.567 34.615 5.00 0.00 0.00 3.77
2280 2323 9.314321 AGACCTTTGATGTAATATAGAACGTTG 57.686 33.333 5.00 0.00 0.00 4.10
2281 2324 9.314321 CAGACCTTTGATGTAATATAGAACGTT 57.686 33.333 0.00 0.00 0.00 3.99
2282 2325 8.475639 ACAGACCTTTGATGTAATATAGAACGT 58.524 33.333 0.00 0.00 0.00 3.99
2283 2326 8.873215 ACAGACCTTTGATGTAATATAGAACG 57.127 34.615 0.00 0.00 0.00 3.95
2284 2327 9.817809 TGACAGACCTTTGATGTAATATAGAAC 57.182 33.333 0.00 0.00 0.00 3.01
2285 2328 9.817809 GTGACAGACCTTTGATGTAATATAGAA 57.182 33.333 0.00 0.00 0.00 2.10
2286 2329 8.977412 TGTGACAGACCTTTGATGTAATATAGA 58.023 33.333 0.00 0.00 0.00 1.98
2287 2330 9.035607 GTGTGACAGACCTTTGATGTAATATAG 57.964 37.037 0.00 0.00 0.00 1.31
2288 2331 7.985184 GGTGTGACAGACCTTTGATGTAATATA 59.015 37.037 14.41 0.00 0.00 0.86
2289 2332 6.823689 GGTGTGACAGACCTTTGATGTAATAT 59.176 38.462 14.41 0.00 0.00 1.28
2290 2333 6.170506 GGTGTGACAGACCTTTGATGTAATA 58.829 40.000 14.41 0.00 0.00 0.98
2291 2334 5.003804 GGTGTGACAGACCTTTGATGTAAT 58.996 41.667 14.41 0.00 0.00 1.89
2292 2335 4.141597 TGGTGTGACAGACCTTTGATGTAA 60.142 41.667 21.39 0.00 34.26 2.41
2293 2336 3.389656 TGGTGTGACAGACCTTTGATGTA 59.610 43.478 21.39 0.00 34.26 2.29
2294 2337 2.172505 TGGTGTGACAGACCTTTGATGT 59.827 45.455 21.39 0.00 34.26 3.06
2295 2338 2.849942 TGGTGTGACAGACCTTTGATG 58.150 47.619 21.39 0.00 34.26 3.07
2296 2339 3.576078 TTGGTGTGACAGACCTTTGAT 57.424 42.857 21.39 0.00 34.26 2.57
2297 2340 3.118075 TGATTGGTGTGACAGACCTTTGA 60.118 43.478 21.39 6.73 34.26 2.69
2298 2341 3.213506 TGATTGGTGTGACAGACCTTTG 58.786 45.455 21.39 0.00 34.26 2.77
2299 2342 3.576078 TGATTGGTGTGACAGACCTTT 57.424 42.857 21.39 9.62 34.26 3.11
2300 2343 3.214328 GTTGATTGGTGTGACAGACCTT 58.786 45.455 21.39 9.96 34.26 3.50
2301 2344 2.806745 CGTTGATTGGTGTGACAGACCT 60.807 50.000 21.39 3.27 34.26 3.85
2302 2345 1.531149 CGTTGATTGGTGTGACAGACC 59.469 52.381 14.79 14.79 0.00 3.85
2303 2346 1.069906 GCGTTGATTGGTGTGACAGAC 60.070 52.381 0.00 0.00 0.00 3.51
2304 2347 1.202639 AGCGTTGATTGGTGTGACAGA 60.203 47.619 0.00 0.00 0.00 3.41
2305 2348 1.195448 GAGCGTTGATTGGTGTGACAG 59.805 52.381 0.00 0.00 0.00 3.51
2306 2349 1.225855 GAGCGTTGATTGGTGTGACA 58.774 50.000 0.00 0.00 0.00 3.58
2307 2350 1.195448 CTGAGCGTTGATTGGTGTGAC 59.805 52.381 0.00 0.00 0.00 3.67
2308 2351 1.511850 CTGAGCGTTGATTGGTGTGA 58.488 50.000 0.00 0.00 0.00 3.58
2309 2352 0.518636 CCTGAGCGTTGATTGGTGTG 59.481 55.000 0.00 0.00 0.00 3.82
2310 2353 0.396435 TCCTGAGCGTTGATTGGTGT 59.604 50.000 0.00 0.00 0.00 4.16
2311 2354 1.742761 ATCCTGAGCGTTGATTGGTG 58.257 50.000 0.00 0.00 0.00 4.17
2312 2355 2.496899 AATCCTGAGCGTTGATTGGT 57.503 45.000 0.00 0.00 0.00 3.67
2313 2356 4.963276 TTTAATCCTGAGCGTTGATTGG 57.037 40.909 0.00 0.00 31.55 3.16
2314 2357 5.883661 ACATTTAATCCTGAGCGTTGATTG 58.116 37.500 0.00 0.00 31.55 2.67
2315 2358 6.375455 AGAACATTTAATCCTGAGCGTTGATT 59.625 34.615 0.00 0.00 33.54 2.57
2316 2359 5.882557 AGAACATTTAATCCTGAGCGTTGAT 59.117 36.000 0.00 0.00 0.00 2.57
2317 2360 5.122239 CAGAACATTTAATCCTGAGCGTTGA 59.878 40.000 0.00 0.00 0.00 3.18
2318 2361 5.327091 CAGAACATTTAATCCTGAGCGTTG 58.673 41.667 0.00 0.00 0.00 4.10
2319 2362 4.142600 GCAGAACATTTAATCCTGAGCGTT 60.143 41.667 0.00 0.00 0.00 4.84
2320 2363 3.375299 GCAGAACATTTAATCCTGAGCGT 59.625 43.478 0.00 0.00 0.00 5.07
2321 2364 3.242870 GGCAGAACATTTAATCCTGAGCG 60.243 47.826 0.00 0.00 0.00 5.03
2322 2365 3.696051 TGGCAGAACATTTAATCCTGAGC 59.304 43.478 0.00 0.00 0.00 4.26
2323 2366 4.337555 CCTGGCAGAACATTTAATCCTGAG 59.662 45.833 17.94 0.00 0.00 3.35
2324 2367 4.018506 TCCTGGCAGAACATTTAATCCTGA 60.019 41.667 17.94 0.00 0.00 3.86
2325 2368 4.096984 GTCCTGGCAGAACATTTAATCCTG 59.903 45.833 17.94 0.00 0.00 3.86
2326 2369 4.263905 TGTCCTGGCAGAACATTTAATCCT 60.264 41.667 17.94 0.00 0.00 3.24
2327 2370 4.016444 TGTCCTGGCAGAACATTTAATCC 58.984 43.478 17.94 0.00 0.00 3.01
2328 2371 4.943705 TCTGTCCTGGCAGAACATTTAATC 59.056 41.667 17.94 0.00 41.93 1.75
2329 2372 4.702131 GTCTGTCCTGGCAGAACATTTAAT 59.298 41.667 17.94 0.00 45.75 1.40
2330 2373 4.072131 GTCTGTCCTGGCAGAACATTTAA 58.928 43.478 17.94 0.00 45.75 1.52
2331 2374 3.674997 GTCTGTCCTGGCAGAACATTTA 58.325 45.455 17.94 0.00 45.75 1.40
2332 2375 2.508526 GTCTGTCCTGGCAGAACATTT 58.491 47.619 17.94 0.00 45.75 2.32
2333 2376 1.609061 CGTCTGTCCTGGCAGAACATT 60.609 52.381 17.94 0.00 45.75 2.71
2334 2377 0.036952 CGTCTGTCCTGGCAGAACAT 60.037 55.000 17.94 0.00 45.75 2.71
2335 2378 1.367471 CGTCTGTCCTGGCAGAACA 59.633 57.895 17.94 12.08 45.75 3.18
2336 2379 2.029844 GCGTCTGTCCTGGCAGAAC 61.030 63.158 17.94 6.47 45.75 3.01
2337 2380 2.343758 GCGTCTGTCCTGGCAGAA 59.656 61.111 17.94 0.00 45.75 3.02
2338 2381 2.917227 TGCGTCTGTCCTGGCAGA 60.917 61.111 17.94 14.24 42.56 4.26
2339 2382 2.740055 GTGCGTCTGTCCTGGCAG 60.740 66.667 7.75 7.75 35.85 4.85
2340 2383 3.545574 TGTGCGTCTGTCCTGGCA 61.546 61.111 0.00 0.00 0.00 4.92
2341 2384 3.044305 GTGTGCGTCTGTCCTGGC 61.044 66.667 0.00 0.00 0.00 4.85
2342 2385 2.734723 CGTGTGCGTCTGTCCTGG 60.735 66.667 0.00 0.00 0.00 4.45
2352 2395 2.458966 CGAAGAAAGAAAAACGTGTGCG 59.541 45.455 0.00 0.00 44.93 5.34
2353 2396 3.676540 TCGAAGAAAGAAAAACGTGTGC 58.323 40.909 0.00 0.00 0.00 4.57
2354 2397 6.237201 CCTTTTCGAAGAAAGAAAAACGTGTG 60.237 38.462 10.51 0.00 44.02 3.82
2355 2398 5.798434 CCTTTTCGAAGAAAGAAAAACGTGT 59.202 36.000 10.51 0.00 44.02 4.49
2356 2399 5.229260 CCCTTTTCGAAGAAAGAAAAACGTG 59.771 40.000 10.51 0.00 44.02 4.49
2357 2400 5.337554 CCCTTTTCGAAGAAAGAAAAACGT 58.662 37.500 10.51 0.00 44.02 3.99
2358 2401 4.738252 CCCCTTTTCGAAGAAAGAAAAACG 59.262 41.667 10.51 0.00 44.02 3.60
2359 2402 5.898174 TCCCCTTTTCGAAGAAAGAAAAAC 58.102 37.500 10.51 0.00 44.02 2.43
2360 2403 6.549736 AGATCCCCTTTTCGAAGAAAGAAAAA 59.450 34.615 10.51 0.00 44.02 1.94
2361 2404 6.068670 AGATCCCCTTTTCGAAGAAAGAAAA 58.931 36.000 10.51 4.41 45.90 2.29
2362 2405 5.631119 AGATCCCCTTTTCGAAGAAAGAAA 58.369 37.500 10.51 0.00 45.90 2.52
2363 2406 5.242795 AGATCCCCTTTTCGAAGAAAGAA 57.757 39.130 10.51 0.00 45.90 2.52
2364 2407 4.323562 GGAGATCCCCTTTTCGAAGAAAGA 60.324 45.833 10.51 1.18 45.90 2.52
2365 2408 3.942115 GGAGATCCCCTTTTCGAAGAAAG 59.058 47.826 0.00 0.00 45.90 2.62
2369 2412 2.482142 CGAGGAGATCCCCTTTTCGAAG 60.482 54.545 0.00 0.00 36.49 3.79
2517 2564 4.911514 TTCTTGGCTAGTTTGTGTTTCC 57.088 40.909 0.00 0.00 0.00 3.13
2584 2633 3.514309 GGCGGTCATGTAATAGGATAGGT 59.486 47.826 0.00 0.00 0.00 3.08
2629 2678 1.134367 CGCTGGAAGATGGTAACTCGA 59.866 52.381 0.00 0.00 34.07 4.04
2634 2683 3.321111 GTCTATCCGCTGGAAGATGGTAA 59.679 47.826 1.44 0.00 34.34 2.85
2656 2705 1.005924 AGGGAGCATTTGGTTACTGGG 59.994 52.381 0.00 0.00 0.00 4.45
2855 2905 6.294453 CGCATTATTTGGGACATGGCTTAATA 60.294 38.462 0.00 0.00 40.62 0.98
2877 2927 0.865111 CACCGAATTCTGTCAACGCA 59.135 50.000 3.52 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.