Multiple sequence alignment - TraesCS3B01G121100

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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 TraesCS3B01G121100 chr3B 100.000 2868 0 0 1 2868 91428817 91431684 0.000000e+00 5297
1 TraesCS3B01G121100 chr3B 100.000 2671 0 0 3116 5786 91431932 91434602 0.000000e+00 4933
2 TraesCS3B01G121100 chr3D 95.087 2707 93 10 3116 5786 58115926 58118628 0.000000e+00 4226
3 TraesCS3B01G121100 chr3D 91.781 1825 99 23 268 2069 58113470 58115266 0.000000e+00 2492
4 TraesCS3B01G121100 chr3D 96.624 622 20 1 2248 2868 58115249 58115870 0.000000e+00 1031
5 TraesCS3B01G121100 chr3D 92.157 153 4 2 72 216 58113302 58113454 5.870000e-50 209
6 TraesCS3B01G121100 chr3A 94.867 2708 92 13 3116 5786 67153902 67156599 0.000000e+00 4187
7 TraesCS3B01G121100 chr3A 92.801 1903 90 22 192 2068 67151355 67153236 0.000000e+00 2712
8 TraesCS3B01G121100 chr3A 96.469 623 20 2 2248 2868 67153220 67153842 0.000000e+00 1027
9 TraesCS3B01G121100 chr1A 96.465 198 5 2 2056 2251 82525871 82526068 5.590000e-85 326
10 TraesCS3B01G121100 chr7B 97.382 191 4 1 2067 2257 198551251 198551062 2.010000e-84 324
11 TraesCS3B01G121100 chr7B 98.370 184 3 0 2065 2248 252794266 252794449 2.010000e-84 324
12 TraesCS3B01G121100 chr7B 97.382 191 3 2 2068 2258 700410918 700410730 2.010000e-84 324
13 TraesCS3B01G121100 chr4B 98.370 184 3 0 2065 2248 588430815 588430998 2.010000e-84 324
14 TraesCS3B01G121100 chr1B 98.370 184 2 1 2065 2248 225811788 225811970 7.230000e-84 322
15 TraesCS3B01G121100 chr4A 96.875 192 5 1 2067 2258 114586279 114586469 2.600000e-83 320
16 TraesCS3B01G121100 chr5A 95.455 198 5 4 2053 2248 2668874 2669069 4.350000e-81 313
17 TraesCS3B01G121100 chr7A 96.739 184 6 0 2068 2251 596735725 596735542 2.030000e-79 307


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 TraesCS3B01G121100 chr3B 91428817 91434602 5785 False 5115.0 5297 100.000000 1 5786 2 chr3B.!!$F1 5785
1 TraesCS3B01G121100 chr3D 58113302 58118628 5326 False 1989.5 4226 93.912250 72 5786 4 chr3D.!!$F1 5714
2 TraesCS3B01G121100 chr3A 67151355 67156599 5244 False 2642.0 4187 94.712333 192 5786 3 chr3A.!!$F1 5594

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
900 936 0.253327 ATTCCTCGGCCAGAAACCTC 59.747 55.0 2.24 0.00 0.00 3.85 F
1082 1120 0.107165 GCTCCGCTCCAAACCCTAAT 60.107 55.0 0.00 0.00 0.00 1.73 F
2104 2152 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.0 12.44 8.34 40.80 4.35 F
2128 2176 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.0 0.00 0.00 0.00 2.69 F
2251 2299 0.106918 CACCGGGCTGCCCTTTATTA 60.107 55.0 33.39 0.00 42.67 0.98 F
2775 2825 0.322322 TTGTGTTAGCCCCTACACGG 59.678 55.0 0.00 0.00 36.02 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2146 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85 R
2118 2166 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94 R
3781 3834 0.882927 TAGCACAACGAACTGTGGGC 60.883 55.000 15.31 6.57 45.66 5.36 R
4094 4147 5.253330 TCCTTTCTTGGTGTCCATGAATAC 58.747 41.667 14.66 0.00 43.73 1.89 R
4557 4610 0.889186 CACCACGGCCCATATTAGCC 60.889 60.000 0.00 3.05 46.17 3.93 R
4801 4858 4.790140 GTCAAATATCGCTCTTTGCAACAG 59.210 41.667 0.00 0.00 43.06 3.16 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
22 23 4.947645 ACCAACCAACAATCAATTGACAG 58.052 39.130 11.07 8.80 40.14 3.51
23 24 4.648762 ACCAACCAACAATCAATTGACAGA 59.351 37.500 11.07 0.00 40.14 3.41
24 25 5.128499 ACCAACCAACAATCAATTGACAGAA 59.872 36.000 11.07 0.00 40.14 3.02
25 26 6.183360 ACCAACCAACAATCAATTGACAGAAT 60.183 34.615 11.07 0.00 40.14 2.40
26 27 7.015098 ACCAACCAACAATCAATTGACAGAATA 59.985 33.333 11.07 0.00 40.14 1.75
27 28 7.871973 CCAACCAACAATCAATTGACAGAATAA 59.128 33.333 11.07 0.00 40.14 1.40
28 29 9.258826 CAACCAACAATCAATTGACAGAATAAA 57.741 29.630 11.07 0.00 40.14 1.40
29 30 9.829507 AACCAACAATCAATTGACAGAATAAAA 57.170 25.926 11.07 0.00 40.14 1.52
30 31 9.829507 ACCAACAATCAATTGACAGAATAAAAA 57.170 25.926 11.07 0.00 40.14 1.94
53 54 8.779354 AAAACTTCTCTGCCTAAATAGTGTAG 57.221 34.615 0.00 0.00 0.00 2.74
54 55 7.483580 AACTTCTCTGCCTAAATAGTGTAGT 57.516 36.000 0.00 0.00 0.00 2.73
55 56 8.591114 AACTTCTCTGCCTAAATAGTGTAGTA 57.409 34.615 0.00 0.00 0.00 1.82
56 57 8.591114 ACTTCTCTGCCTAAATAGTGTAGTAA 57.409 34.615 0.00 0.00 0.00 2.24
57 58 8.468399 ACTTCTCTGCCTAAATAGTGTAGTAAC 58.532 37.037 0.00 0.00 0.00 2.50
58 59 8.591114 TTCTCTGCCTAAATAGTGTAGTAACT 57.409 34.615 0.00 0.00 0.00 2.24
59 60 9.690913 TTCTCTGCCTAAATAGTGTAGTAACTA 57.309 33.333 0.00 0.00 37.08 2.24
60 61 9.118300 TCTCTGCCTAAATAGTGTAGTAACTAC 57.882 37.037 0.00 0.00 35.53 2.73
61 62 8.812513 TCTGCCTAAATAGTGTAGTAACTACA 57.187 34.615 0.00 0.00 43.56 2.74
159 167 4.686091 TGTTCTCATTCTCGATGACACAAC 59.314 41.667 0.00 0.00 39.83 3.32
173 181 4.397420 TGACACAACCATTCTATTGCACT 58.603 39.130 0.00 0.00 0.00 4.40
210 219 9.599322 GTCAAAATCTATATGTAATTGCCTTCG 57.401 33.333 0.00 0.00 0.00 3.79
216 225 7.450074 TCTATATGTAATTGCCTTCGACCAAT 58.550 34.615 0.00 0.00 33.35 3.16
218 227 5.659440 ATGTAATTGCCTTCGACCAATTT 57.341 34.783 17.66 3.91 40.81 1.82
219 228 5.461032 TGTAATTGCCTTCGACCAATTTT 57.539 34.783 17.66 4.42 40.81 1.82
247 261 1.970114 ACTGACAGCATGCTGCCAC 60.970 57.895 40.65 31.17 46.52 5.01
259 273 3.933048 CTGCCACAGCTTCAGGGGG 62.933 68.421 0.00 0.00 40.80 5.40
273 287 3.306379 GGGGGTAGAACGTGGAGG 58.694 66.667 0.00 0.00 0.00 4.30
427 441 2.524148 GGGCTGGCTTGGGTTTGT 60.524 61.111 0.00 0.00 0.00 2.83
671 703 2.693762 CCTGGCAGTGCGGTCATTG 61.694 63.158 14.43 0.00 33.59 2.82
683 715 0.878416 GGTCATTGCCAGTTTACGCA 59.122 50.000 0.00 0.00 0.00 5.24
685 717 2.094752 GGTCATTGCCAGTTTACGCATT 60.095 45.455 0.00 0.00 34.35 3.56
713 745 6.481954 AGACATGGAAAGACGTTTCATAAC 57.518 37.500 0.00 0.00 43.52 1.89
722 754 3.062042 GACGTTTCATAACTCGGGTTGT 58.938 45.455 11.94 0.00 36.92 3.32
728 760 6.540205 GTTTCATAACTCGGGTTGTGTATTC 58.460 40.000 22.27 9.65 42.54 1.75
729 761 4.761975 TCATAACTCGGGTTGTGTATTCC 58.238 43.478 22.27 0.00 42.54 3.01
732 764 2.253610 ACTCGGGTTGTGTATTCCTGA 58.746 47.619 0.00 0.00 35.62 3.86
746 778 3.814005 TTCCTGAGAAATACGCCTACC 57.186 47.619 0.00 0.00 0.00 3.18
814 847 2.048127 GTTGAACTCGCCGCCTCT 60.048 61.111 0.00 0.00 0.00 3.69
876 912 3.924686 CCATTAGCTTTGCTTGCTTCTTG 59.075 43.478 0.00 1.71 40.44 3.02
892 928 2.184533 TCTTGTAGAATTCCTCGGCCA 58.815 47.619 2.24 0.00 0.00 5.36
893 929 2.168521 TCTTGTAGAATTCCTCGGCCAG 59.831 50.000 2.24 0.00 0.00 4.85
894 930 1.860641 TGTAGAATTCCTCGGCCAGA 58.139 50.000 2.24 0.00 0.00 3.86
895 931 2.184533 TGTAGAATTCCTCGGCCAGAA 58.815 47.619 2.24 2.46 0.00 3.02
896 932 2.569853 TGTAGAATTCCTCGGCCAGAAA 59.430 45.455 2.24 0.00 0.00 2.52
897 933 2.115343 AGAATTCCTCGGCCAGAAAC 57.885 50.000 2.24 2.05 0.00 2.78
898 934 1.095600 GAATTCCTCGGCCAGAAACC 58.904 55.000 2.24 0.00 0.00 3.27
899 935 0.698818 AATTCCTCGGCCAGAAACCT 59.301 50.000 2.24 0.00 0.00 3.50
900 936 0.253327 ATTCCTCGGCCAGAAACCTC 59.747 55.000 2.24 0.00 0.00 3.85
901 937 2.125512 CCTCGGCCAGAAACCTCG 60.126 66.667 2.24 0.00 0.00 4.63
902 938 2.815647 CTCGGCCAGAAACCTCGC 60.816 66.667 2.24 0.00 0.00 5.03
903 939 3.302347 CTCGGCCAGAAACCTCGCT 62.302 63.158 2.24 0.00 0.00 4.93
904 940 2.815647 CGGCCAGAAACCTCGCTC 60.816 66.667 2.24 0.00 0.00 5.03
919 955 2.585247 CTCGCCGAATCGAACCCC 60.585 66.667 3.36 0.00 38.08 4.95
1082 1120 0.107165 GCTCCGCTCCAAACCCTAAT 60.107 55.000 0.00 0.00 0.00 1.73
1089 1127 3.203716 GCTCCAAACCCTAATCCTAACG 58.796 50.000 0.00 0.00 0.00 3.18
1091 1129 3.183801 TCCAAACCCTAATCCTAACGGT 58.816 45.455 0.00 0.00 0.00 4.83
1129 1167 2.564504 GTTCTAGGTCCGGTTGGTTACT 59.435 50.000 0.00 0.00 36.30 2.24
1157 1195 3.357079 CGTGTTGGCAGTGAGGGC 61.357 66.667 0.00 0.00 0.00 5.19
1310 1348 2.683933 ATGACGGCGGAGGAGGTT 60.684 61.111 13.24 0.00 0.00 3.50
1411 1449 0.849094 TTCCCAGGTTAGGCCATGGT 60.849 55.000 14.67 0.00 40.61 3.55
1444 1486 3.997064 CTTCTCTCCCCGTGCGCTG 62.997 68.421 9.73 0.08 0.00 5.18
1504 1546 4.415596 AGAATCAGCAGGGAGTAGGATAG 58.584 47.826 0.00 0.00 0.00 2.08
1521 1563 4.521256 AGGATAGGTTCTCGTTAGCATCTC 59.479 45.833 0.00 0.00 0.00 2.75
1578 1620 3.492102 TCATTTAGCTATGTGCCTCCC 57.508 47.619 0.00 0.00 44.23 4.30
1605 1647 8.641541 TGTATCACATGATGCTCTGTTTCTATA 58.358 33.333 10.70 0.00 37.90 1.31
1788 1830 7.638444 TCTCCCATTTTTCCTACATATGTGAA 58.362 34.615 18.81 11.16 0.00 3.18
1863 1906 2.554032 GTGCCAGTCACTGCACTTATTT 59.446 45.455 19.28 0.00 42.38 1.40
1875 1919 7.041372 TCACTGCACTTATTTCCAGAAGTTTAC 60.041 37.037 0.00 0.00 33.60 2.01
2042 2090 4.279145 AGCTCATGCATCTGGAGAAATTT 58.721 39.130 14.88 0.00 42.74 1.82
2069 2117 7.526041 AGCACCATATTATGATACCCTTTGAA 58.474 34.615 5.21 0.00 0.00 2.69
2071 2119 7.094205 GCACCATATTATGATACCCTTTGAAGG 60.094 40.741 5.21 2.69 46.06 3.46
2080 2128 2.967270 CCTTTGAAGGGGAGCCTTG 58.033 57.895 1.68 0.00 42.66 3.61
2081 2129 0.405585 CCTTTGAAGGGGAGCCTTGA 59.594 55.000 1.68 0.00 42.66 3.02
2082 2130 1.539157 CTTTGAAGGGGAGCCTTGAC 58.461 55.000 0.00 0.00 0.00 3.18
2083 2131 0.250727 TTTGAAGGGGAGCCTTGACG 60.251 55.000 0.00 0.00 0.00 4.35
2084 2132 2.436824 GAAGGGGAGCCTTGACGC 60.437 66.667 0.00 0.00 0.00 5.19
2085 2133 3.249189 AAGGGGAGCCTTGACGCA 61.249 61.111 0.00 0.00 0.00 5.24
2086 2134 3.259633 AAGGGGAGCCTTGACGCAG 62.260 63.158 0.00 0.00 0.00 5.18
2102 2150 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2103 2151 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2104 2152 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2105 2153 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2106 2154 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2107 2155 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2108 2156 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2109 2157 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2110 2158 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2111 2159 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2112 2160 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2113 2161 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2114 2162 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2115 2163 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2116 2164 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2126 2174 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2127 2175 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2128 2176 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2129 2177 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2130 2178 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2131 2179 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2132 2180 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2133 2181 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2134 2182 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2135 2183 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2136 2184 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2137 2185 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2138 2186 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2139 2187 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2140 2188 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2154 2202 4.431416 TGGAAACAGCCTCTTACTGAAA 57.569 40.909 0.00 0.00 38.55 2.69
2155 2203 4.985538 TGGAAACAGCCTCTTACTGAAAT 58.014 39.130 0.00 0.00 38.55 2.17
2156 2204 4.761739 TGGAAACAGCCTCTTACTGAAATG 59.238 41.667 0.00 0.00 38.55 2.32
2157 2205 4.762251 GGAAACAGCCTCTTACTGAAATGT 59.238 41.667 0.00 0.00 38.55 2.71
2158 2206 5.938125 GGAAACAGCCTCTTACTGAAATGTA 59.062 40.000 0.00 0.00 38.55 2.29
2159 2207 6.092807 GGAAACAGCCTCTTACTGAAATGTAG 59.907 42.308 0.00 0.00 38.55 2.74
2160 2208 5.091261 ACAGCCTCTTACTGAAATGTAGG 57.909 43.478 0.00 0.00 38.55 3.18
2161 2209 4.080863 ACAGCCTCTTACTGAAATGTAGGG 60.081 45.833 0.00 0.00 38.55 3.53
2162 2210 4.162320 CAGCCTCTTACTGAAATGTAGGGA 59.838 45.833 0.00 0.00 37.32 4.20
2163 2211 4.783227 AGCCTCTTACTGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2164 2212 5.250774 AGCCTCTTACTGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2165 2213 5.586643 GCCTCTTACTGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2166 2214 6.116126 CCTCTTACTGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2167 2215 5.497474 TCTTACTGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2168 2216 5.250774 TCTTACTGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2169 2217 3.690460 ACTGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2170 2218 2.424956 CTGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2171 2219 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2172 2220 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2173 2221 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2174 2222 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2175 2223 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2176 2224 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2177 2225 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2178 2226 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2179 2227 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2180 2228 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2181 2229 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2182 2230 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2183 2231 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2184 2232 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2185 2233 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2186 2234 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2187 2235 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2188 2236 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2189 2237 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2190 2238 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2191 2239 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2196 2244 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2197 2245 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2198 2246 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2199 2247 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2200 2248 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2201 2249 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2202 2250 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2203 2251 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2204 2252 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
2211 2259 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
2238 2286 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
2239 2287 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
2240 2288 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
2241 2289 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
2242 2290 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
2243 2291 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
2248 2296 4.733542 GCACCGGGCTGCCCTTTA 62.734 66.667 33.39 0.00 42.67 1.85
2249 2297 2.275418 CACCGGGCTGCCCTTTAT 59.725 61.111 33.39 14.39 42.67 1.40
2250 2298 1.379843 CACCGGGCTGCCCTTTATT 60.380 57.895 33.39 11.43 42.67 1.40
2251 2299 0.106918 CACCGGGCTGCCCTTTATTA 60.107 55.000 33.39 0.00 42.67 0.98
2252 2300 0.850784 ACCGGGCTGCCCTTTATTAT 59.149 50.000 33.39 9.44 42.67 1.28
2253 2301 1.247567 CCGGGCTGCCCTTTATTATG 58.752 55.000 33.39 16.14 42.67 1.90
2254 2302 1.202879 CCGGGCTGCCCTTTATTATGA 60.203 52.381 33.39 0.00 42.67 2.15
2255 2303 2.555227 CCGGGCTGCCCTTTATTATGAT 60.555 50.000 33.39 0.00 42.67 2.45
2256 2304 3.308117 CCGGGCTGCCCTTTATTATGATA 60.308 47.826 33.39 0.00 42.67 2.15
2257 2305 3.689649 CGGGCTGCCCTTTATTATGATAC 59.310 47.826 33.39 3.99 42.67 2.24
2258 2306 4.017126 GGGCTGCCCTTTATTATGATACC 58.983 47.826 30.42 0.00 41.34 2.73
2259 2307 4.017126 GGCTGCCCTTTATTATGATACCC 58.983 47.826 7.66 0.00 0.00 3.69
2260 2308 4.263949 GGCTGCCCTTTATTATGATACCCT 60.264 45.833 7.66 0.00 0.00 4.34
2261 2309 5.325239 GCTGCCCTTTATTATGATACCCTT 58.675 41.667 0.00 0.00 0.00 3.95
2262 2310 5.775195 GCTGCCCTTTATTATGATACCCTTT 59.225 40.000 0.00 0.00 0.00 3.11
2263 2311 6.294731 GCTGCCCTTTATTATGATACCCTTTG 60.295 42.308 0.00 0.00 0.00 2.77
2264 2312 6.916909 TGCCCTTTATTATGATACCCTTTGA 58.083 36.000 0.00 0.00 0.00 2.69
2269 2317 7.095774 CCTTTATTATGATACCCTTTGACGTCG 60.096 40.741 11.62 0.00 0.00 5.12
2270 2318 4.987408 TTATGATACCCTTTGACGTCGA 57.013 40.909 11.62 6.16 0.00 4.20
2281 2329 4.034279 CCTTTGACGTCGACCTTTGTTTTA 59.966 41.667 10.58 0.00 0.00 1.52
2304 2352 9.810545 TTTACTCCACCTTTGTTCTTAAATTTG 57.189 29.630 0.00 0.00 0.00 2.32
2345 2394 9.605955 AAAATTGTGCTGTTTGTTTAAGAAAAC 57.394 25.926 7.70 7.70 44.40 2.43
2429 2479 6.016276 CACAGCCTTTGTTTCCACTTACTTAT 60.016 38.462 0.00 0.00 38.16 1.73
2430 2480 6.016276 ACAGCCTTTGTTTCCACTTACTTATG 60.016 38.462 0.00 0.00 36.31 1.90
2654 2704 1.303309 AGGTGCGAATATGCTGCTTC 58.697 50.000 0.00 0.00 35.36 3.86
2775 2825 0.322322 TTGTGTTAGCCCCTACACGG 59.678 55.000 0.00 0.00 36.02 4.94
2862 2912 1.071542 TGCATATATGGTGGTGTCCCG 59.928 52.381 14.51 0.00 0.00 5.14
3154 3204 7.009540 GTGTCTGTTTGAAAGGATTTTCTGTTG 59.990 37.037 2.21 0.00 39.27 3.33
3172 3222 8.722480 TTCTGTTGGTCTATACTCAATTGATG 57.278 34.615 8.96 6.02 0.00 3.07
3217 3267 9.535878 GTTGGTTTTTATTGGTTCTTTACATGA 57.464 29.630 0.00 0.00 0.00 3.07
3416 3466 2.233305 TCTCAGGTACACCTCTTCCC 57.767 55.000 0.00 0.00 46.65 3.97
3422 3472 1.281287 GGTACACCTCTTCCCTTTCCC 59.719 57.143 0.00 0.00 0.00 3.97
3430 3480 1.566703 TCTTCCCTTTCCCACAACACA 59.433 47.619 0.00 0.00 0.00 3.72
3468 3520 4.468510 AGGGTAAATCCTGAATGTACGTGA 59.531 41.667 0.00 0.00 35.47 4.35
3499 3551 9.117183 CAATGTTCTGATCTTCTCCATTTGATA 57.883 33.333 0.00 0.00 0.00 2.15
3508 3560 5.824624 TCTTCTCCATTTGATATGTGCCTTC 59.175 40.000 0.00 0.00 0.00 3.46
3531 3583 6.339730 TCTTGACTTGCACATTGTCATTTTT 58.660 32.000 10.46 0.00 39.92 1.94
3622 3675 7.494922 ACCCATCAAAATTAGTATTGGCTTT 57.505 32.000 0.00 0.00 0.00 3.51
3697 3750 2.804697 TTCGTCCAGATCGACAAACA 57.195 45.000 0.00 0.00 37.05 2.83
3703 3756 4.625742 CGTCCAGATCGACAAACACTTTAT 59.374 41.667 0.00 0.00 32.74 1.40
3736 3789 0.884514 GGCCAAAGGAAGTTGAGCTC 59.115 55.000 6.82 6.82 0.00 4.09
4094 4147 2.023673 TGGATGGCAGCCGAATTTTAG 58.976 47.619 18.16 0.00 0.00 1.85
4133 4186 0.683973 AGGATGCGATCAGATCACCC 59.316 55.000 11.12 5.45 0.00 4.61
4557 4610 2.629617 ACAAAAGGTCAGCCCTGAATTG 59.370 45.455 0.00 6.28 45.47 2.32
4678 4735 4.224147 GCACCCATTATTTTGTTTACCCCT 59.776 41.667 0.00 0.00 0.00 4.79
5049 5107 6.458751 CGAAACTCATATTTTGGTCCCATCAG 60.459 42.308 0.00 0.00 0.00 2.90
5139 5197 9.251792 TGAATATCAATGCATCATTAGTTTTGC 57.748 29.630 0.00 0.00 32.35 3.68
5175 5244 5.123820 TCTGTTTGTTTTCCTCTTGTCACTG 59.876 40.000 0.00 0.00 0.00 3.66
5186 5255 7.244886 TCCTCTTGTCACTGATGAGAAATAA 57.755 36.000 7.72 0.00 37.63 1.40
5229 5298 3.265489 ACCTAGAATGGGGTTTCTTCCA 58.735 45.455 0.00 0.00 43.69 3.53
5232 5301 5.222547 ACCTAGAATGGGGTTTCTTCCAATT 60.223 40.000 0.00 0.00 43.69 2.32
5248 5317 4.340617 TCCAATTGGTACAGTGGGATTTC 58.659 43.478 23.76 0.00 43.66 2.17
5307 5377 2.092968 TGGTATGGATGGTCACAGCTTC 60.093 50.000 0.00 0.00 32.48 3.86
5348 5418 6.237861 GGTCATAAGCATTGTTCGAACTAGAC 60.238 42.308 27.32 19.33 0.00 2.59
5511 5608 2.026641 CAAGTCAATGCCCCTACATGG 58.973 52.381 0.00 0.00 0.00 3.66
5568 5665 0.615850 GCTTCCCTCTAGTGGTTGCT 59.384 55.000 9.90 0.00 0.00 3.91
5601 5698 6.620877 TCCACATCTTTGTTAGTACCATCT 57.379 37.500 0.00 0.00 32.34 2.90
5636 5733 1.266989 GCTTTTGCTGTACTGGTCCAC 59.733 52.381 1.65 0.00 43.35 4.02
5712 5815 5.580691 TGCTGTTGCATGTCTAATACTACAC 59.419 40.000 0.00 0.00 45.31 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.648762 TCTGTCAATTGATTGTTGGTTGGT 59.351 37.500 12.12 0.00 38.84 3.67
1 2 5.199024 TCTGTCAATTGATTGTTGGTTGG 57.801 39.130 12.12 0.00 38.84 3.77
2 3 8.815141 TTATTCTGTCAATTGATTGTTGGTTG 57.185 30.769 12.12 0.00 38.84 3.77
3 4 9.829507 TTTTATTCTGTCAATTGATTGTTGGTT 57.170 25.926 12.12 0.00 38.84 3.67
4 5 9.829507 TTTTTATTCTGTCAATTGATTGTTGGT 57.170 25.926 12.12 0.00 38.84 3.67
27 28 9.220767 CTACACTATTTAGGCAGAGAAGTTTTT 57.779 33.333 0.00 0.00 0.00 1.94
28 29 8.376270 ACTACACTATTTAGGCAGAGAAGTTTT 58.624 33.333 0.00 0.00 0.00 2.43
29 30 7.908453 ACTACACTATTTAGGCAGAGAAGTTT 58.092 34.615 0.00 0.00 0.00 2.66
30 31 7.483580 ACTACACTATTTAGGCAGAGAAGTT 57.516 36.000 0.00 0.00 0.00 2.66
31 32 8.468399 GTTACTACACTATTTAGGCAGAGAAGT 58.532 37.037 0.00 0.00 0.00 3.01
32 33 8.688151 AGTTACTACACTATTTAGGCAGAGAAG 58.312 37.037 0.00 0.00 0.00 2.85
33 34 8.591114 AGTTACTACACTATTTAGGCAGAGAA 57.409 34.615 0.00 0.00 0.00 2.87
34 35 9.118300 GTAGTTACTACACTATTTAGGCAGAGA 57.882 37.037 16.71 0.00 36.98 3.10
35 36 8.900781 TGTAGTTACTACACTATTTAGGCAGAG 58.099 37.037 19.89 0.00 41.33 3.35
36 37 8.812513 TGTAGTTACTACACTATTTAGGCAGA 57.187 34.615 19.89 0.00 41.33 4.26
49 50 5.181245 GTGTTAGGACCGTGTAGTTACTACA 59.819 44.000 19.89 19.89 43.56 2.74
50 51 5.412904 AGTGTTAGGACCGTGTAGTTACTAC 59.587 44.000 14.99 14.99 37.46 2.73
51 52 5.412594 CAGTGTTAGGACCGTGTAGTTACTA 59.587 44.000 0.00 0.00 0.00 1.82
52 53 4.217118 CAGTGTTAGGACCGTGTAGTTACT 59.783 45.833 0.00 0.00 0.00 2.24
53 54 4.216257 TCAGTGTTAGGACCGTGTAGTTAC 59.784 45.833 0.00 0.00 0.00 2.50
54 55 4.397420 TCAGTGTTAGGACCGTGTAGTTA 58.603 43.478 0.00 0.00 0.00 2.24
55 56 3.225104 TCAGTGTTAGGACCGTGTAGTT 58.775 45.455 0.00 0.00 0.00 2.24
56 57 2.867624 TCAGTGTTAGGACCGTGTAGT 58.132 47.619 0.00 0.00 0.00 2.73
57 58 3.005050 TGTTCAGTGTTAGGACCGTGTAG 59.995 47.826 0.00 0.00 0.00 2.74
58 59 2.957680 TGTTCAGTGTTAGGACCGTGTA 59.042 45.455 0.00 0.00 0.00 2.90
59 60 1.758280 TGTTCAGTGTTAGGACCGTGT 59.242 47.619 0.00 0.00 0.00 4.49
60 61 2.132762 GTGTTCAGTGTTAGGACCGTG 58.867 52.381 0.00 0.00 0.00 4.94
61 62 2.037144 AGTGTTCAGTGTTAGGACCGT 58.963 47.619 0.00 0.00 0.00 4.83
62 63 2.814280 AGTGTTCAGTGTTAGGACCG 57.186 50.000 0.00 0.00 0.00 4.79
63 64 4.618693 GCTCTAGTGTTCAGTGTTAGGACC 60.619 50.000 0.00 0.00 0.00 4.46
64 65 4.022242 TGCTCTAGTGTTCAGTGTTAGGAC 60.022 45.833 0.00 0.00 0.00 3.85
65 66 4.149598 TGCTCTAGTGTTCAGTGTTAGGA 58.850 43.478 0.00 0.00 0.00 2.94
66 67 4.489810 CTGCTCTAGTGTTCAGTGTTAGG 58.510 47.826 0.00 0.00 0.00 2.69
67 68 4.489810 CCTGCTCTAGTGTTCAGTGTTAG 58.510 47.826 0.00 0.00 0.00 2.34
68 69 3.306088 GCCTGCTCTAGTGTTCAGTGTTA 60.306 47.826 0.00 0.00 0.00 2.41
69 70 2.548920 GCCTGCTCTAGTGTTCAGTGTT 60.549 50.000 0.00 0.00 0.00 3.32
70 71 1.001406 GCCTGCTCTAGTGTTCAGTGT 59.999 52.381 0.00 0.00 0.00 3.55
148 156 4.094739 TGCAATAGAATGGTTGTGTCATCG 59.905 41.667 0.00 0.00 0.00 3.84
159 167 7.599998 ACTTTAAAAGCAAGTGCAATAGAATGG 59.400 33.333 6.00 0.00 45.16 3.16
259 273 2.629051 CCATTTCCTCCACGTTCTACC 58.371 52.381 0.00 0.00 0.00 3.18
260 274 2.007608 GCCATTTCCTCCACGTTCTAC 58.992 52.381 0.00 0.00 0.00 2.59
414 428 1.118838 CAAAGGACAAACCCAAGCCA 58.881 50.000 0.00 0.00 40.05 4.75
423 437 1.028905 CCAAGCCGTCAAAGGACAAA 58.971 50.000 0.00 0.00 44.54 2.83
427 441 2.282180 GCCCAAGCCGTCAAAGGA 60.282 61.111 0.00 0.00 0.00 3.36
551 571 1.766143 GCGAGAGTTATTGCCTGCGG 61.766 60.000 0.00 0.00 0.00 5.69
554 574 1.638467 GCGCGAGAGTTATTGCCTG 59.362 57.895 12.10 0.00 0.00 4.85
555 575 1.521681 GGCGCGAGAGTTATTGCCT 60.522 57.895 12.10 0.00 39.38 4.75
556 576 2.871427 CGGCGCGAGAGTTATTGCC 61.871 63.158 12.10 0.00 39.10 4.52
560 580 2.024305 CGACGGCGCGAGAGTTAT 59.976 61.111 12.10 0.00 0.00 1.89
561 581 3.120385 TCGACGGCGCGAGAGTTA 61.120 61.111 12.10 0.00 35.01 2.24
664 696 0.878416 TGCGTAAACTGGCAATGACC 59.122 50.000 0.00 0.00 35.98 4.02
683 715 4.817517 ACGTCTTTCCATGTCTAACGAAT 58.182 39.130 10.53 0.00 33.25 3.34
685 717 3.928727 ACGTCTTTCCATGTCTAACGA 57.071 42.857 10.53 0.00 33.25 3.85
698 730 3.999046 ACCCGAGTTATGAAACGTCTTT 58.001 40.909 0.00 0.00 40.73 2.52
713 745 2.496070 TCTCAGGAATACACAACCCGAG 59.504 50.000 0.00 0.00 0.00 4.63
722 754 5.221382 GGTAGGCGTATTTCTCAGGAATACA 60.221 44.000 15.11 0.00 0.00 2.29
728 760 2.224066 CCTGGTAGGCGTATTTCTCAGG 60.224 54.545 0.00 0.00 35.27 3.86
729 761 2.224066 CCCTGGTAGGCGTATTTCTCAG 60.224 54.545 0.00 0.00 32.73 3.35
732 764 0.468648 GCCCTGGTAGGCGTATTTCT 59.531 55.000 0.00 0.00 44.57 2.52
746 778 2.511145 GCTCGAGCTTCTGCCCTG 60.511 66.667 29.88 0.00 40.80 4.45
751 783 1.202245 GGTAGAGTGCTCGAGCTTCTG 60.202 57.143 34.87 8.63 42.66 3.02
753 785 0.101579 GGGTAGAGTGCTCGAGCTTC 59.898 60.000 35.27 29.64 42.66 3.86
756 788 1.654954 TTCGGGTAGAGTGCTCGAGC 61.655 60.000 30.42 30.42 42.50 5.03
763 795 1.883084 GCGGCATTCGGGTAGAGTG 60.883 63.158 0.00 0.00 39.31 3.51
764 796 2.355986 TGCGGCATTCGGGTAGAGT 61.356 57.895 0.00 0.00 39.69 3.24
814 847 3.125146 CGATTCGAATTGGAAGTGAAGCA 59.875 43.478 16.45 0.00 0.00 3.91
858 894 4.641396 TCTACAAGAAGCAAGCAAAGCTA 58.359 39.130 0.00 0.00 42.53 3.32
876 912 2.937149 GTTTCTGGCCGAGGAATTCTAC 59.063 50.000 5.23 0.00 0.00 2.59
892 928 2.227089 ATTCGGCGAGCGAGGTTTCT 62.227 55.000 10.46 0.00 0.00 2.52
893 929 1.753468 GATTCGGCGAGCGAGGTTTC 61.753 60.000 10.46 0.00 0.00 2.78
894 930 1.810030 GATTCGGCGAGCGAGGTTT 60.810 57.895 10.46 0.00 0.00 3.27
895 931 2.202756 GATTCGGCGAGCGAGGTT 60.203 61.111 10.46 0.00 0.00 3.50
896 932 4.554363 CGATTCGGCGAGCGAGGT 62.554 66.667 23.60 3.09 0.00 3.85
897 933 3.751401 TTCGATTCGGCGAGCGAGG 62.751 63.158 26.90 11.52 41.79 4.63
898 934 2.277949 TTCGATTCGGCGAGCGAG 60.278 61.111 26.90 14.53 41.79 5.03
899 935 2.578713 GTTCGATTCGGCGAGCGA 60.579 61.111 25.56 25.56 41.79 4.93
900 936 3.617538 GGTTCGATTCGGCGAGCG 61.618 66.667 22.48 22.48 41.53 5.03
901 937 3.262686 GGGTTCGATTCGGCGAGC 61.263 66.667 10.46 5.69 41.79 5.03
902 938 2.585247 GGGGTTCGATTCGGCGAG 60.585 66.667 10.46 0.00 41.79 5.03
903 939 4.151582 GGGGGTTCGATTCGGCGA 62.152 66.667 4.99 4.99 38.72 5.54
1026 1064 2.042843 CGGTAGGAGCTGGGGTCT 60.043 66.667 0.00 0.00 0.00 3.85
1082 1120 3.951563 TTACTAGGGCTACCGTTAGGA 57.048 47.619 0.00 0.00 43.47 2.94
1089 1127 2.973710 ACCAGGATTACTAGGGCTACC 58.026 52.381 0.00 0.00 0.00 3.18
1091 1129 4.554553 AGAACCAGGATTACTAGGGCTA 57.445 45.455 0.00 0.00 0.00 3.93
1391 1429 0.334676 CCATGGCCTAACCTGGGAAA 59.665 55.000 3.32 0.00 40.22 3.13
1411 1449 3.422796 AGAGAAGGAGCTACGAAGAACA 58.577 45.455 0.00 0.00 0.00 3.18
1444 1486 2.159254 TGAAAGCCTGAAACACAACAGC 60.159 45.455 0.00 0.00 33.40 4.40
1504 1546 3.512033 ACAGAGATGCTAACGAGAACC 57.488 47.619 0.00 0.00 0.00 3.62
1547 1589 1.134371 AGCTAAATGAAGGCGTCCCTC 60.134 52.381 0.00 0.00 41.90 4.30
1551 1593 3.303395 GCACATAGCTAAATGAAGGCGTC 60.303 47.826 10.90 0.00 41.15 5.19
1578 1620 5.816258 AGAAACAGAGCATCATGTGATACAG 59.184 40.000 0.00 0.00 37.82 2.74
1788 1830 8.179487 AGGCCCAAATATCCTATTGTTGATTAT 58.821 33.333 0.00 0.00 0.00 1.28
1808 1850 1.295020 AACCAGTGCTATTAGGCCCA 58.705 50.000 0.00 0.00 0.00 5.36
2042 2090 8.664992 TCAAAGGGTATCATAATATGGTGCTAA 58.335 33.333 1.85 0.00 0.00 3.09
2069 2117 3.710722 CTGCGTCAAGGCTCCCCT 61.711 66.667 0.00 0.00 45.77 4.79
2071 2119 2.743928 CACTGCGTCAAGGCTCCC 60.744 66.667 0.00 0.00 0.00 4.30
2072 2120 2.167398 TACCACTGCGTCAAGGCTCC 62.167 60.000 0.00 0.00 0.00 4.70
2074 2122 0.107831 TTTACCACTGCGTCAAGGCT 59.892 50.000 0.00 0.00 0.00 4.58
2075 2123 0.517316 CTTTACCACTGCGTCAAGGC 59.483 55.000 0.00 0.00 0.00 4.35
2076 2124 0.517316 GCTTTACCACTGCGTCAAGG 59.483 55.000 0.00 0.00 0.00 3.61
2077 2125 1.195448 CAGCTTTACCACTGCGTCAAG 59.805 52.381 0.00 0.00 0.00 3.02
2078 2126 1.225855 CAGCTTTACCACTGCGTCAA 58.774 50.000 0.00 0.00 0.00 3.18
2079 2127 2.912986 CAGCTTTACCACTGCGTCA 58.087 52.632 0.00 0.00 0.00 4.35
2084 2132 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2085 2133 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2086 2134 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2087 2135 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2088 2136 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2089 2137 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2090 2138 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2091 2139 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2092 2140 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2093 2141 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2094 2142 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2095 2143 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2096 2144 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2097 2145 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2098 2146 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2099 2147 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2110 2158 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2111 2159 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2112 2160 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2113 2161 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2114 2162 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2115 2163 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2116 2164 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2117 2165 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
2118 2166 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2119 2167 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2120 2168 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
2121 2169 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2122 2170 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2123 2171 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2124 2172 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2125 2173 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2126 2174 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2127 2175 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2128 2176 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2129 2177 2.303311 AGTAAGAGGCTGTTTCCAGGAC 59.697 50.000 0.90 0.00 39.22 3.85
2130 2178 2.303022 CAGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 39.22 3.86
2131 2179 2.303022 TCAGTAAGAGGCTGTTTCCAGG 59.697 50.000 0.90 0.00 39.22 4.45
2132 2180 3.685139 TCAGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 0.00 41.91 3.86
2133 2181 4.431416 TTTCAGTAAGAGGCTGTTTCCA 57.569 40.909 0.90 0.00 35.60 3.53
2134 2182 4.762251 ACATTTCAGTAAGAGGCTGTTTCC 59.238 41.667 0.90 0.00 35.60 3.13
2135 2183 5.948992 ACATTTCAGTAAGAGGCTGTTTC 57.051 39.130 0.90 0.00 35.60 2.78
2136 2184 5.940470 CCTACATTTCAGTAAGAGGCTGTTT 59.060 40.000 0.90 0.00 35.60 2.83
2137 2185 5.491982 CCTACATTTCAGTAAGAGGCTGTT 58.508 41.667 1.39 1.39 35.60 3.16
2138 2186 4.080863 CCCTACATTTCAGTAAGAGGCTGT 60.081 45.833 0.00 0.00 35.60 4.40
2139 2187 4.162320 TCCCTACATTTCAGTAAGAGGCTG 59.838 45.833 0.00 0.00 35.43 4.85
2140 2188 4.362677 TCCCTACATTTCAGTAAGAGGCT 58.637 43.478 0.00 0.00 0.00 4.58
2141 2189 4.755266 TCCCTACATTTCAGTAAGAGGC 57.245 45.455 0.00 0.00 0.00 4.70
2142 2190 6.116126 CCTTTCCCTACATTTCAGTAAGAGG 58.884 44.000 0.00 0.00 0.00 3.69
2143 2191 5.586643 GCCTTTCCCTACATTTCAGTAAGAG 59.413 44.000 0.00 0.00 0.00 2.85
2144 2192 5.250774 AGCCTTTCCCTACATTTCAGTAAGA 59.749 40.000 0.00 0.00 0.00 2.10
2145 2193 5.355350 CAGCCTTTCCCTACATTTCAGTAAG 59.645 44.000 0.00 0.00 0.00 2.34
2146 2194 5.253330 CAGCCTTTCCCTACATTTCAGTAA 58.747 41.667 0.00 0.00 0.00 2.24
2147 2195 4.843728 CAGCCTTTCCCTACATTTCAGTA 58.156 43.478 0.00 0.00 0.00 2.74
2148 2196 3.690460 CAGCCTTTCCCTACATTTCAGT 58.310 45.455 0.00 0.00 0.00 3.41
2149 2197 2.424956 GCAGCCTTTCCCTACATTTCAG 59.575 50.000 0.00 0.00 0.00 3.02
2150 2198 2.446435 GCAGCCTTTCCCTACATTTCA 58.554 47.619 0.00 0.00 0.00 2.69
2151 2199 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2152 2200 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2153 2201 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2154 2202 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2155 2203 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2156 2204 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2157 2205 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2158 2206 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2159 2207 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2160 2208 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2161 2209 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2162 2210 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2163 2211 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2164 2212 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2165 2213 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2166 2214 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2167 2215 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2168 2216 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2169 2217 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2170 2218 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2180 2228 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2181 2229 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2182 2230 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2183 2231 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2184 2232 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2185 2233 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2186 2234 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2187 2235 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2194 2242 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
2210 2258 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2213 2261 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2214 2262 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2215 2263 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2216 2264 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2222 2270 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
2223 2271 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
2224 2272 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
2225 2273 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
2226 2274 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
2236 2284 4.017126 GGTATCATAATAAAGGGCAGCCC 58.983 47.826 24.90 24.90 45.90 5.19
2237 2285 4.017126 GGGTATCATAATAAAGGGCAGCC 58.983 47.826 1.26 1.26 0.00 4.85
2238 2286 4.923415 AGGGTATCATAATAAAGGGCAGC 58.077 43.478 0.00 0.00 0.00 5.25
2239 2287 7.004086 TCAAAGGGTATCATAATAAAGGGCAG 58.996 38.462 0.00 0.00 0.00 4.85
2240 2288 6.775629 GTCAAAGGGTATCATAATAAAGGGCA 59.224 38.462 0.00 0.00 0.00 5.36
2241 2289 6.072673 CGTCAAAGGGTATCATAATAAAGGGC 60.073 42.308 0.00 0.00 0.00 5.19
2242 2290 6.996282 ACGTCAAAGGGTATCATAATAAAGGG 59.004 38.462 0.00 0.00 0.00 3.95
2243 2291 7.095774 CGACGTCAAAGGGTATCATAATAAAGG 60.096 40.741 17.16 0.00 0.00 3.11
2244 2292 7.650504 TCGACGTCAAAGGGTATCATAATAAAG 59.349 37.037 17.16 0.00 0.00 1.85
2245 2293 7.436080 GTCGACGTCAAAGGGTATCATAATAAA 59.564 37.037 17.16 0.00 0.00 1.40
2246 2294 6.919662 GTCGACGTCAAAGGGTATCATAATAA 59.080 38.462 17.16 0.00 0.00 1.40
2247 2295 6.441274 GTCGACGTCAAAGGGTATCATAATA 58.559 40.000 17.16 0.00 0.00 0.98
2248 2296 5.287226 GTCGACGTCAAAGGGTATCATAAT 58.713 41.667 17.16 0.00 0.00 1.28
2249 2297 4.440525 GGTCGACGTCAAAGGGTATCATAA 60.441 45.833 17.16 0.00 0.00 1.90
2250 2298 3.067180 GGTCGACGTCAAAGGGTATCATA 59.933 47.826 17.16 0.00 0.00 2.15
2251 2299 2.159142 GGTCGACGTCAAAGGGTATCAT 60.159 50.000 17.16 0.00 0.00 2.45
2252 2300 1.203052 GGTCGACGTCAAAGGGTATCA 59.797 52.381 17.16 0.00 0.00 2.15
2253 2301 1.475682 AGGTCGACGTCAAAGGGTATC 59.524 52.381 17.16 0.00 0.00 2.24
2254 2302 1.553706 AGGTCGACGTCAAAGGGTAT 58.446 50.000 17.16 0.00 0.00 2.73
2255 2303 1.331214 AAGGTCGACGTCAAAGGGTA 58.669 50.000 17.16 0.00 0.00 3.69
2256 2304 0.466963 AAAGGTCGACGTCAAAGGGT 59.533 50.000 17.16 0.00 0.00 4.34
2257 2305 0.865769 CAAAGGTCGACGTCAAAGGG 59.134 55.000 17.16 0.00 0.00 3.95
2258 2306 1.578583 ACAAAGGTCGACGTCAAAGG 58.421 50.000 17.16 0.00 0.00 3.11
2259 2307 3.668596 AAACAAAGGTCGACGTCAAAG 57.331 42.857 17.16 0.00 0.00 2.77
2260 2308 4.630940 AGTAAAACAAAGGTCGACGTCAAA 59.369 37.500 17.16 0.00 0.00 2.69
2261 2309 4.183101 AGTAAAACAAAGGTCGACGTCAA 58.817 39.130 17.16 0.00 0.00 3.18
2262 2310 3.784338 AGTAAAACAAAGGTCGACGTCA 58.216 40.909 17.16 0.00 0.00 4.35
2263 2311 3.183172 GGAGTAAAACAAAGGTCGACGTC 59.817 47.826 11.73 5.18 0.00 4.34
2264 2312 3.126073 GGAGTAAAACAAAGGTCGACGT 58.874 45.455 9.92 7.31 0.00 4.34
2269 2317 5.126545 ACAAAGGTGGAGTAAAACAAAGGTC 59.873 40.000 0.00 0.00 0.00 3.85
2270 2318 5.020795 ACAAAGGTGGAGTAAAACAAAGGT 58.979 37.500 0.00 0.00 0.00 3.50
2281 2329 7.418337 ACAAATTTAAGAACAAAGGTGGAGT 57.582 32.000 0.00 0.00 0.00 3.85
2323 2371 5.921408 ACGTTTTCTTAAACAAACAGCACAA 59.079 32.000 8.95 0.00 43.05 3.33
2453 2503 7.086376 GTGATTTCTTGCAACACATATTCTGT 58.914 34.615 11.14 0.00 39.20 3.41
2461 2511 4.329528 GCTTTTGTGATTTCTTGCAACACA 59.670 37.500 13.93 13.93 39.22 3.72
2775 2825 3.265791 CTGTATCTGGACAGCAAGTTCC 58.734 50.000 0.00 0.00 40.42 3.62
2820 2870 6.809689 TGCATGTGCTTTTTATCTTTGATGAG 59.190 34.615 6.55 0.00 42.66 2.90
3131 3181 6.154363 ACCAACAGAAAATCCTTTCAAACAGA 59.846 34.615 0.86 0.00 42.99 3.41
3172 3222 7.198306 ACCAACACAAATAGCAAGTAACTAC 57.802 36.000 0.00 0.00 0.00 2.73
3217 3267 3.769844 AGAACAATCGGACTATCACCAGT 59.230 43.478 0.00 0.00 0.00 4.00
3416 3466 5.757320 TGCAATAAATTGTGTTGTGGGAAAG 59.243 36.000 4.71 0.00 39.88 2.62
3422 3472 9.033481 CCCTATAATGCAATAAATTGTGTTGTG 57.967 33.333 0.00 0.00 39.88 3.33
3468 3520 8.591114 ATGGAGAAGATCAGAACATTGATTTT 57.409 30.769 0.00 0.00 37.90 1.82
3499 3551 1.985473 TGCAAGTCAAGAAGGCACAT 58.015 45.000 0.00 0.00 0.00 3.21
3508 3560 6.415702 CAAAAATGACAATGTGCAAGTCAAG 58.584 36.000 14.03 0.00 44.47 3.02
3607 3660 8.665685 CGAGTTTCAGTAAAGCCAATACTAATT 58.334 33.333 0.00 0.00 32.47 1.40
3622 3675 4.859304 TTAGACTTGCCGAGTTTCAGTA 57.141 40.909 0.00 0.00 39.19 2.74
3668 3721 3.525537 GATCTGGACGAATCTGAAGCAA 58.474 45.455 0.00 0.00 0.00 3.91
3697 3750 3.622455 GCCAGGTAGCACTCCAATAAAGT 60.622 47.826 0.00 0.00 0.00 2.66
3703 3756 1.422977 TTGGCCAGGTAGCACTCCAA 61.423 55.000 5.11 7.42 0.00 3.53
3781 3834 0.882927 TAGCACAACGAACTGTGGGC 60.883 55.000 15.31 6.57 45.66 5.36
3827 3880 7.574496 TGCTGAAATGCAACACATAAATTTTC 58.426 30.769 0.00 0.00 38.34 2.29
3828 3881 7.493743 TGCTGAAATGCAACACATAAATTTT 57.506 28.000 0.00 0.00 38.34 1.82
3829 3882 7.493743 TTGCTGAAATGCAACACATAAATTT 57.506 28.000 0.00 0.00 46.43 1.82
4094 4147 5.253330 TCCTTTCTTGGTGTCCATGAATAC 58.747 41.667 14.66 0.00 43.73 1.89
4557 4610 0.889186 CACCACGGCCCATATTAGCC 60.889 60.000 0.00 3.05 46.17 3.93
4678 4735 5.769662 ACAAGATGGCTTTCAACAATGTCTA 59.230 36.000 0.00 0.00 30.14 2.59
4738 4795 4.918588 TGCCCTCTGTATCTATCACGATA 58.081 43.478 0.00 0.00 0.00 2.92
4801 4858 4.790140 GTCAAATATCGCTCTTTGCAACAG 59.210 41.667 0.00 0.00 43.06 3.16
5085 5143 2.101917 CGGACCCAACGTAGGTGAATAT 59.898 50.000 14.51 0.00 37.88 1.28
5086 5144 1.477700 CGGACCCAACGTAGGTGAATA 59.522 52.381 14.51 0.00 37.88 1.75
5139 5197 2.213499 ACAAACAGAAGAGGAACTGCG 58.787 47.619 0.00 0.00 41.55 5.18
5175 5244 6.970484 ACAACCACAACAGTTATTTCTCATC 58.030 36.000 0.00 0.00 0.00 2.92
5186 5255 1.382522 CAGCTGACAACCACAACAGT 58.617 50.000 8.42 0.00 33.57 3.55
5348 5418 0.381801 GCAAACACCTATCATGGCCG 59.618 55.000 0.00 0.00 0.00 6.13
5396 5492 4.632251 TCGTGTGCAGAACTTTTAACTCAA 59.368 37.500 0.00 0.00 0.00 3.02
5511 5608 6.363357 GGTCATTAACTTCACACTGCAATTTC 59.637 38.462 0.00 0.00 0.00 2.17
5568 5665 8.432013 ACTAACAAAGATGTGGATATATCAGCA 58.568 33.333 14.60 11.91 40.46 4.41
5712 5815 8.152898 TCATGATAGATAACTCCAAATGACAGG 58.847 37.037 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.