Multiple sequence alignment - TraesCS6B01G346200

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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 TraesCS6B01G346200 chr6B 100.000 2761 0 0 1 2761 609924167 609926927 0.000000e+00 5099.0
1 TraesCS6B01G346200 chr6B 96.891 386 12 0 2004 2389 567613309 567613694 0.000000e+00 647.0
2 TraesCS6B01G346200 chr6A 90.360 2054 87 45 1 2003 552483658 552485651 0.000000e+00 2593.0
3 TraesCS6B01G346200 chr6D 93.290 1073 47 12 944 2003 406105153 406106213 0.000000e+00 1559.0
4 TraesCS6B01G346200 chr6D 90.279 967 39 26 2 930 406104219 406105168 0.000000e+00 1214.0
5 TraesCS6B01G346200 chr6D 88.859 377 38 3 2388 2761 406106205 406106580 6.970000e-126 460.0
6 TraesCS6B01G346200 chr6D 94.406 143 8 0 111 253 406001659 406001801 1.290000e-53 220.0
7 TraesCS6B01G346200 chr2B 96.891 386 12 0 2005 2390 790240797 790240412 0.000000e+00 647.0
8 TraesCS6B01G346200 chr2B 96.373 386 14 0 2004 2389 759258460 759258845 1.080000e-178 636.0
9 TraesCS6B01G346200 chr2B 96.104 385 15 0 2005 2389 588362431 588362047 1.800000e-176 628.0
10 TraesCS6B01G346200 chr5A 96.632 386 13 0 2004 2389 295308422 295308037 2.320000e-180 641.0
11 TraesCS6B01G346200 chr7A 96.124 387 15 0 2004 2390 536141602 536141988 1.400000e-177 632.0
12 TraesCS6B01G346200 chr3B 96.114 386 15 0 2004 2389 79089626 79089241 5.020000e-177 630.0
13 TraesCS6B01G346200 chr3A 96.104 385 15 0 2005 2389 192412507 192412123 1.800000e-176 628.0
14 TraesCS6B01G346200 chr5B 95.596 386 17 0 2005 2390 140974932 140975317 1.090000e-173 619.0
15 TraesCS6B01G346200 chr2D 84.397 141 21 1 2622 2761 301532660 301532800 1.330000e-28 137.0
16 TraesCS6B01G346200 chr4D 88.679 53 6 0 2703 2755 496281731 496281783 6.380000e-07 65.8
17 TraesCS6B01G346200 chr7D 77.885 104 18 5 2567 2669 79267099 79267198 2.970000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G346200 chr6B 609924167 609926927 2760 False 5099.000000 5099 100.000000 1 2761 1 chr6B.!!$F2 2760
1 TraesCS6B01G346200 chr6A 552483658 552485651 1993 False 2593.000000 2593 90.360000 1 2003 1 chr6A.!!$F1 2002
2 TraesCS6B01G346200 chr6D 406104219 406106580 2361 False 1077.666667 1559 90.809333 2 2761 3 chr6D.!!$F2 2759

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
936 995 0.037232 GCTAGCACCTGAGTCCGTTT 60.037 55.0 10.63 0.0 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2472 0.032267 GTCCGATTTAGGAGCGAGGG 59.968 60.0 0.0 0.0 41.68 4.3 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
61 63 3.014604 ACAAACTGTGTCTACTCTCGC 57.985 47.619 0.00 0.00 34.38 5.03
446 468 3.890147 ACCACCCGCAAATTTTAACTACA 59.110 39.130 0.00 0.00 0.00 2.74
563 590 5.155278 TCGAGCTAGGTGGTTCAAATTAA 57.845 39.130 0.00 0.00 0.00 1.40
593 620 8.408601 AGCTGATCACCAAATGTTTATGAATAC 58.591 33.333 0.00 0.00 0.00 1.89
594 621 8.190122 GCTGATCACCAAATGTTTATGAATACA 58.810 33.333 0.00 0.00 0.00 2.29
595 622 9.507280 CTGATCACCAAATGTTTATGAATACAC 57.493 33.333 0.00 0.00 0.00 2.90
596 623 8.180920 TGATCACCAAATGTTTATGAATACACG 58.819 33.333 0.00 0.00 0.00 4.49
597 624 6.847400 TCACCAAATGTTTATGAATACACGG 58.153 36.000 0.00 0.00 0.00 4.94
683 731 0.039256 CGGTTGTTGGCATGAACAGG 60.039 55.000 0.00 0.00 37.16 4.00
704 752 2.287608 GGCCAGCCGTTCAATAATTAGC 60.288 50.000 0.00 0.00 0.00 3.09
710 758 7.201732 GCCAGCCGTTCAATAATTAGCATATAT 60.202 37.037 0.00 0.00 0.00 0.86
711 759 9.325198 CCAGCCGTTCAATAATTAGCATATATA 57.675 33.333 0.00 0.00 0.00 0.86
874 933 1.133216 CGCGTCTCTTCTTCTCATCCA 59.867 52.381 0.00 0.00 0.00 3.41
889 948 1.859427 ATCCAAGTGCAACGCAGCAG 61.859 55.000 2.27 0.00 46.69 4.24
895 954 0.590732 GTGCAACGCAGCAGCATATC 60.591 55.000 0.82 0.00 46.69 1.63
896 955 1.025647 TGCAACGCAGCAGCATATCA 61.026 50.000 0.82 0.00 40.11 2.15
897 956 0.309922 GCAACGCAGCAGCATATCAT 59.690 50.000 0.82 0.00 42.27 2.45
898 957 1.532437 GCAACGCAGCAGCATATCATA 59.468 47.619 0.82 0.00 42.27 2.15
899 958 2.161012 GCAACGCAGCAGCATATCATAT 59.839 45.455 0.82 0.00 42.27 1.78
900 959 3.727079 GCAACGCAGCAGCATATCATATC 60.727 47.826 0.82 0.00 42.27 1.63
909 968 5.484644 AGCAGCATATCATATCTCCTCTGTT 59.515 40.000 0.00 0.00 0.00 3.16
913 972 7.487509 CAGCATATCATATCTCCTCTGTTAACG 59.512 40.741 0.26 0.00 0.00 3.18
915 974 8.029522 GCATATCATATCTCCTCTGTTAACGAA 58.970 37.037 0.26 0.00 0.00 3.85
916 975 9.914131 CATATCATATCTCCTCTGTTAACGAAA 57.086 33.333 0.26 0.00 0.00 3.46
918 977 6.273825 TCATATCTCCTCTGTTAACGAAAGC 58.726 40.000 0.26 0.00 0.00 3.51
919 978 4.810191 ATCTCCTCTGTTAACGAAAGCT 57.190 40.909 0.26 0.00 0.00 3.74
920 979 5.916661 ATCTCCTCTGTTAACGAAAGCTA 57.083 39.130 0.26 0.00 0.00 3.32
921 980 5.312120 TCTCCTCTGTTAACGAAAGCTAG 57.688 43.478 0.26 0.00 0.00 3.42
922 981 3.846360 TCCTCTGTTAACGAAAGCTAGC 58.154 45.455 6.62 6.62 0.00 3.42
923 982 3.257375 TCCTCTGTTAACGAAAGCTAGCA 59.743 43.478 18.83 0.00 0.00 3.49
924 983 3.368236 CCTCTGTTAACGAAAGCTAGCAC 59.632 47.826 18.83 6.99 0.00 4.40
925 984 3.323243 TCTGTTAACGAAAGCTAGCACC 58.677 45.455 18.83 4.21 0.00 5.01
926 985 3.006537 TCTGTTAACGAAAGCTAGCACCT 59.993 43.478 18.83 0.00 0.00 4.00
927 986 3.064207 TGTTAACGAAAGCTAGCACCTG 58.936 45.455 18.83 6.50 0.00 4.00
928 987 3.243941 TGTTAACGAAAGCTAGCACCTGA 60.244 43.478 18.83 0.00 0.00 3.86
929 988 2.086054 AACGAAAGCTAGCACCTGAG 57.914 50.000 18.83 5.49 0.00 3.35
930 989 0.969894 ACGAAAGCTAGCACCTGAGT 59.030 50.000 18.83 6.14 0.00 3.41
931 990 1.067495 ACGAAAGCTAGCACCTGAGTC 60.067 52.381 18.83 2.20 0.00 3.36
932 991 1.737363 CGAAAGCTAGCACCTGAGTCC 60.737 57.143 18.83 0.00 0.00 3.85
933 992 0.247736 AAAGCTAGCACCTGAGTCCG 59.752 55.000 18.83 0.00 0.00 4.79
934 993 0.900647 AAGCTAGCACCTGAGTCCGT 60.901 55.000 18.83 0.00 0.00 4.69
935 994 0.900647 AGCTAGCACCTGAGTCCGTT 60.901 55.000 18.83 0.00 0.00 4.44
936 995 0.037232 GCTAGCACCTGAGTCCGTTT 60.037 55.000 10.63 0.00 0.00 3.60
937 996 1.997669 CTAGCACCTGAGTCCGTTTC 58.002 55.000 0.00 0.00 0.00 2.78
938 997 1.272490 CTAGCACCTGAGTCCGTTTCA 59.728 52.381 0.00 0.00 0.00 2.69
939 998 0.468226 AGCACCTGAGTCCGTTTCAA 59.532 50.000 0.00 0.00 0.00 2.69
940 999 1.134220 AGCACCTGAGTCCGTTTCAAA 60.134 47.619 0.00 0.00 0.00 2.69
941 1000 1.673920 GCACCTGAGTCCGTTTCAAAA 59.326 47.619 0.00 0.00 0.00 2.44
965 1024 3.030873 AGCTAGCACCTGAGAGAAGAT 57.969 47.619 18.83 0.00 0.00 2.40
1092 1151 3.231736 ACCAGCTTCACCGTCGGT 61.232 61.111 12.23 12.23 35.62 4.69
1140 1199 2.122144 TACACCACCTGGGCCAGT 60.122 61.111 30.68 16.76 42.05 4.00
1195 1259 6.418819 CGGTAAGACTTTTAGTTTCTTCGTGA 59.581 38.462 0.00 0.00 31.93 4.35
1196 1260 7.358187 CGGTAAGACTTTTAGTTTCTTCGTGAG 60.358 40.741 0.00 0.00 31.93 3.51
1204 1268 7.786305 TTTAGTTTCTTCGTGAGTACATACG 57.214 36.000 13.65 13.65 41.38 3.06
1228 1297 3.936453 GCCGTTAATCATGTGACTGGTTA 59.064 43.478 0.00 0.00 0.00 2.85
1229 1298 4.574828 GCCGTTAATCATGTGACTGGTTAT 59.425 41.667 0.00 0.00 0.00 1.89
1230 1299 5.504010 GCCGTTAATCATGTGACTGGTTATG 60.504 44.000 0.00 0.00 0.00 1.90
1231 1300 5.007626 CCGTTAATCATGTGACTGGTTATGG 59.992 44.000 0.00 0.00 0.00 2.74
1232 1301 5.584649 CGTTAATCATGTGACTGGTTATGGT 59.415 40.000 0.00 0.00 0.00 3.55
1233 1302 6.093495 CGTTAATCATGTGACTGGTTATGGTT 59.907 38.462 0.00 0.00 0.00 3.67
1234 1303 7.361713 CGTTAATCATGTGACTGGTTATGGTTT 60.362 37.037 0.00 0.00 0.00 3.27
1235 1304 8.952278 GTTAATCATGTGACTGGTTATGGTTTA 58.048 33.333 0.00 0.00 0.00 2.01
1277 1346 0.887387 TGTTCAACTACGCCAAGGGC 60.887 55.000 0.00 0.00 46.75 5.19
1413 1482 3.246226 GCACTACTTTATCTGCACCATCG 59.754 47.826 0.00 0.00 0.00 3.84
1454 1523 0.607217 TGAAGCTCGAGGTGACCGTA 60.607 55.000 19.39 0.00 0.00 4.02
1672 1747 2.384203 GCACCATGCCGTTCTACTC 58.616 57.895 0.00 0.00 37.42 2.59
1673 1748 1.421410 GCACCATGCCGTTCTACTCG 61.421 60.000 0.00 0.00 37.42 4.18
1762 1837 2.289382 TGCAGCTCGGACTGTTATGAAA 60.289 45.455 7.32 0.00 39.96 2.69
1763 1838 2.939103 GCAGCTCGGACTGTTATGAAAT 59.061 45.455 7.32 0.00 39.96 2.17
1764 1839 4.119862 GCAGCTCGGACTGTTATGAAATA 58.880 43.478 7.32 0.00 39.96 1.40
1765 1840 4.570772 GCAGCTCGGACTGTTATGAAATAA 59.429 41.667 7.32 0.00 39.96 1.40
1766 1841 5.277058 GCAGCTCGGACTGTTATGAAATAAG 60.277 44.000 7.32 0.00 39.94 1.73
1767 1842 5.812642 CAGCTCGGACTGTTATGAAATAAGT 59.187 40.000 0.00 0.00 39.94 2.24
1768 1843 6.978659 CAGCTCGGACTGTTATGAAATAAGTA 59.021 38.462 0.00 0.00 39.94 2.24
1769 1844 7.653713 CAGCTCGGACTGTTATGAAATAAGTAT 59.346 37.037 0.00 0.00 39.94 2.12
1770 1845 7.653713 AGCTCGGACTGTTATGAAATAAGTATG 59.346 37.037 0.00 0.00 39.94 2.39
1771 1846 7.652105 GCTCGGACTGTTATGAAATAAGTATGA 59.348 37.037 0.00 0.00 39.94 2.15
1772 1847 9.529325 CTCGGACTGTTATGAAATAAGTATGAA 57.471 33.333 0.00 0.00 39.94 2.57
1902 1978 1.388547 TCCATTAATTGCCGTCTGCC 58.611 50.000 0.00 0.00 40.16 4.85
1994 2070 2.907910 CAATGCTTGCAGACACCTAC 57.092 50.000 0.87 0.00 0.00 3.18
2003 2079 0.179000 CAGACACCTACAGGGCATCC 59.821 60.000 0.00 0.00 40.27 3.51
2004 2080 0.043334 AGACACCTACAGGGCATCCT 59.957 55.000 0.00 0.00 46.26 3.24
2005 2081 1.291033 AGACACCTACAGGGCATCCTA 59.709 52.381 0.00 0.00 42.67 2.94
2006 2082 2.116238 GACACCTACAGGGCATCCTAA 58.884 52.381 0.00 0.00 42.67 2.69
2007 2083 2.504175 GACACCTACAGGGCATCCTAAA 59.496 50.000 0.00 0.00 42.67 1.85
2008 2084 2.238898 ACACCTACAGGGCATCCTAAAC 59.761 50.000 0.00 0.00 42.67 2.01
2009 2085 1.844497 ACCTACAGGGCATCCTAAACC 59.156 52.381 0.00 0.00 42.67 3.27
2010 2086 2.127708 CCTACAGGGCATCCTAAACCT 58.872 52.381 0.00 0.00 42.67 3.50
2012 2088 3.502164 CAGGGCATCCTAAACCTGG 57.498 57.895 0.00 0.00 45.21 4.45
2013 2089 0.106519 CAGGGCATCCTAAACCTGGG 60.107 60.000 0.00 0.00 45.21 4.45
2014 2090 1.455773 GGGCATCCTAAACCTGGGC 60.456 63.158 0.00 0.00 0.00 5.36
2015 2091 1.306296 GGCATCCTAAACCTGGGCA 59.694 57.895 0.00 0.00 0.00 5.36
2016 2092 0.106015 GGCATCCTAAACCTGGGCAT 60.106 55.000 0.00 0.00 0.00 4.40
2017 2093 1.035139 GCATCCTAAACCTGGGCATG 58.965 55.000 0.00 0.00 0.00 4.06
2018 2094 1.696063 CATCCTAAACCTGGGCATGG 58.304 55.000 0.00 0.00 0.00 3.66
2019 2095 0.557729 ATCCTAAACCTGGGCATGGG 59.442 55.000 0.00 0.00 0.00 4.00
2020 2096 1.758122 CCTAAACCTGGGCATGGGC 60.758 63.158 0.00 0.00 40.13 5.36
2021 2097 1.000233 CTAAACCTGGGCATGGGCA 60.000 57.895 0.00 0.00 43.71 5.36
2022 2098 1.000233 TAAACCTGGGCATGGGCAG 60.000 57.895 0.00 0.00 43.71 4.85
2061 2137 3.744719 GAGCCCGGCCCGAAAAAC 61.745 66.667 3.71 0.00 0.00 2.43
2087 2163 4.754667 GGACGGGTCGGGCTTGAC 62.755 72.222 2.43 2.43 38.17 3.18
2090 2166 4.675029 CGGGTCGGGCTTGACGTT 62.675 66.667 0.00 0.00 39.83 3.99
2091 2167 2.741211 GGGTCGGGCTTGACGTTC 60.741 66.667 0.00 0.00 39.83 3.95
2092 2168 3.110178 GGTCGGGCTTGACGTTCG 61.110 66.667 0.00 0.00 39.83 3.95
2093 2169 3.110178 GTCGGGCTTGACGTTCGG 61.110 66.667 0.00 0.00 0.00 4.30
2094 2170 4.367023 TCGGGCTTGACGTTCGGG 62.367 66.667 0.00 0.00 0.00 5.14
2116 2192 4.043200 GCTCGGGCCTTGTGTTGC 62.043 66.667 0.84 0.00 0.00 4.17
2117 2193 2.594303 CTCGGGCCTTGTGTTGCA 60.594 61.111 0.84 0.00 0.00 4.08
2118 2194 2.594303 TCGGGCCTTGTGTTGCAG 60.594 61.111 0.84 0.00 0.00 4.41
2119 2195 4.347453 CGGGCCTTGTGTTGCAGC 62.347 66.667 0.84 0.00 0.00 5.25
2120 2196 3.994853 GGGCCTTGTGTTGCAGCC 61.995 66.667 0.84 2.37 37.61 4.85
2121 2197 3.994853 GGCCTTGTGTTGCAGCCC 61.995 66.667 0.00 0.00 33.67 5.19
2122 2198 4.347453 GCCTTGTGTTGCAGCCCG 62.347 66.667 0.00 0.00 0.00 6.13
2123 2199 3.673484 CCTTGTGTTGCAGCCCGG 61.673 66.667 0.00 0.00 0.00 5.73
2124 2200 2.594303 CTTGTGTTGCAGCCCGGA 60.594 61.111 0.73 0.00 0.00 5.14
2125 2201 2.124109 TTGTGTTGCAGCCCGGAA 60.124 55.556 0.73 0.00 0.00 4.30
2126 2202 2.133742 CTTGTGTTGCAGCCCGGAAG 62.134 60.000 0.73 0.00 0.00 3.46
2127 2203 2.281484 GTGTTGCAGCCCGGAAGA 60.281 61.111 0.73 0.00 0.00 2.87
2128 2204 1.675641 GTGTTGCAGCCCGGAAGAT 60.676 57.895 0.73 0.00 0.00 2.40
2129 2205 0.392461 GTGTTGCAGCCCGGAAGATA 60.392 55.000 0.73 0.00 0.00 1.98
2130 2206 0.107703 TGTTGCAGCCCGGAAGATAG 60.108 55.000 0.73 0.00 0.00 2.08
2131 2207 0.107654 GTTGCAGCCCGGAAGATAGT 60.108 55.000 0.73 0.00 0.00 2.12
2132 2208 0.618458 TTGCAGCCCGGAAGATAGTT 59.382 50.000 0.73 0.00 0.00 2.24
2133 2209 0.178068 TGCAGCCCGGAAGATAGTTC 59.822 55.000 0.73 0.00 0.00 3.01
2134 2210 0.876342 GCAGCCCGGAAGATAGTTCG 60.876 60.000 0.73 0.00 0.00 3.95
2135 2211 0.249489 CAGCCCGGAAGATAGTTCGG 60.249 60.000 0.73 0.00 41.90 4.30
2137 2213 4.752514 CCGGAAGATAGTTCGGGC 57.247 61.111 0.00 0.00 38.93 6.13
2138 2214 1.069258 CCGGAAGATAGTTCGGGCC 59.931 63.158 0.00 0.00 38.93 5.80
2139 2215 1.299926 CGGAAGATAGTTCGGGCCG 60.300 63.158 22.51 22.51 0.00 6.13
2140 2216 1.069258 GGAAGATAGTTCGGGCCGG 59.931 63.158 27.98 7.65 0.00 6.13
2141 2217 1.069258 GAAGATAGTTCGGGCCGGG 59.931 63.158 27.98 0.00 0.00 5.73
2142 2218 2.990830 GAAGATAGTTCGGGCCGGGC 62.991 65.000 27.98 22.00 0.00 6.13
2143 2219 3.547513 GATAGTTCGGGCCGGGCT 61.548 66.667 28.80 24.51 0.00 5.19
2144 2220 3.516866 GATAGTTCGGGCCGGGCTC 62.517 68.421 28.80 15.19 0.00 4.70
2155 2231 2.438434 CGGGCTCGGGCTTCATTT 60.438 61.111 7.48 0.00 38.73 2.32
2156 2232 2.046285 CGGGCTCGGGCTTCATTTT 61.046 57.895 7.48 0.00 38.73 1.82
2157 2233 1.595093 CGGGCTCGGGCTTCATTTTT 61.595 55.000 7.48 0.00 38.73 1.94
2175 2251 1.970092 TTTATGTATTTCGGGCCGGG 58.030 50.000 27.98 0.00 0.00 5.73
2176 2252 0.535553 TTATGTATTTCGGGCCGGGC 60.536 55.000 27.98 22.00 0.00 6.13
2177 2253 1.412453 TATGTATTTCGGGCCGGGCT 61.412 55.000 28.80 12.99 0.00 5.19
2178 2254 2.124445 GTATTTCGGGCCGGGCTT 60.124 61.111 28.80 11.28 0.00 4.35
2179 2255 1.751544 GTATTTCGGGCCGGGCTTT 60.752 57.895 28.80 9.42 0.00 3.51
2180 2256 1.452470 TATTTCGGGCCGGGCTTTC 60.452 57.895 28.80 10.53 0.00 2.62
2191 2267 4.717313 GGCTTTCGGGCTTCGGGT 62.717 66.667 0.75 0.00 39.77 5.28
2192 2268 3.125573 GCTTTCGGGCTTCGGGTC 61.126 66.667 0.75 0.00 39.77 4.46
2193 2269 2.813908 CTTTCGGGCTTCGGGTCG 60.814 66.667 0.75 0.00 39.77 4.79
2194 2270 4.382320 TTTCGGGCTTCGGGTCGG 62.382 66.667 0.75 0.00 39.77 4.79
2201 2277 4.697756 CTTCGGGTCGGGCTTGCA 62.698 66.667 0.00 0.00 0.00 4.08
2210 2286 4.084888 GGGCTTGCACGTGCGTAC 62.085 66.667 33.22 23.87 45.83 3.67
2211 2287 3.342627 GGCTTGCACGTGCGTACA 61.343 61.111 33.22 15.19 45.83 2.90
2212 2288 2.127758 GCTTGCACGTGCGTACAC 60.128 61.111 33.22 17.90 45.83 2.90
2213 2289 2.594962 GCTTGCACGTGCGTACACT 61.595 57.895 33.22 0.00 45.10 3.55
2214 2290 1.279527 GCTTGCACGTGCGTACACTA 61.280 55.000 33.22 13.22 45.10 2.74
2215 2291 1.133407 CTTGCACGTGCGTACACTAA 58.867 50.000 33.22 19.59 45.10 2.24
2216 2292 1.523515 CTTGCACGTGCGTACACTAAA 59.476 47.619 33.22 18.89 45.10 1.85
2217 2293 1.568606 TGCACGTGCGTACACTAAAA 58.431 45.000 33.22 10.88 45.10 1.52
2218 2294 1.931841 TGCACGTGCGTACACTAAAAA 59.068 42.857 33.22 10.34 45.10 1.94
2233 2309 1.731093 AAAAACAGTGTTCGGGCCG 59.269 52.632 22.51 22.51 0.00 6.13
2234 2310 1.730451 AAAAACAGTGTTCGGGCCGG 61.730 55.000 27.98 11.36 0.00 6.13
2235 2311 4.636435 AACAGTGTTCGGGCCGGG 62.636 66.667 27.98 11.20 0.00 5.73
2253 2329 2.359975 CTTTCGGGCTTCGGGCTT 60.360 61.111 1.83 0.00 41.46 4.35
2254 2330 2.671619 TTTCGGGCTTCGGGCTTG 60.672 61.111 1.83 0.00 41.46 4.01
2255 2331 3.185299 TTTCGGGCTTCGGGCTTGA 62.185 57.895 1.83 0.00 41.46 3.02
2256 2332 2.478335 TTTCGGGCTTCGGGCTTGAT 62.478 55.000 1.83 0.00 41.46 2.57
2257 2333 2.438434 CGGGCTTCGGGCTTGATT 60.438 61.111 1.83 0.00 41.46 2.57
2258 2334 2.046285 CGGGCTTCGGGCTTGATTT 61.046 57.895 1.83 0.00 41.46 2.17
2259 2335 1.809869 GGGCTTCGGGCTTGATTTC 59.190 57.895 1.83 0.00 41.46 2.17
2260 2336 1.429423 GGCTTCGGGCTTGATTTCG 59.571 57.895 1.83 0.00 41.46 3.46
2261 2337 1.429423 GCTTCGGGCTTGATTTCGG 59.571 57.895 0.00 0.00 38.06 4.30
2262 2338 1.993369 GCTTCGGGCTTGATTTCGGG 61.993 60.000 0.00 0.00 38.06 5.14
2263 2339 1.993369 CTTCGGGCTTGATTTCGGGC 61.993 60.000 0.00 0.00 0.00 6.13
2264 2340 3.518068 CGGGCTTGATTTCGGGCC 61.518 66.667 0.00 0.00 43.42 5.80
2265 2341 3.518068 GGGCTTGATTTCGGGCCG 61.518 66.667 22.51 22.51 44.91 6.13
2266 2342 3.518068 GGCTTGATTTCGGGCCGG 61.518 66.667 27.98 9.08 35.08 6.13
2267 2343 3.518068 GCTTGATTTCGGGCCGGG 61.518 66.667 27.98 8.68 0.00 5.73
2268 2344 3.518068 CTTGATTTCGGGCCGGGC 61.518 66.667 27.98 22.00 0.00 6.13
2269 2345 3.995506 CTTGATTTCGGGCCGGGCT 62.996 63.158 28.80 10.61 0.00 5.19
2270 2346 3.987954 TTGATTTCGGGCCGGGCTC 62.988 63.158 28.80 15.19 0.00 4.70
2281 2357 2.671619 CGGGCTCGGGCTTGAAAA 60.672 61.111 7.48 0.00 38.73 2.29
2282 2358 2.962569 GGGCTCGGGCTTGAAAAC 59.037 61.111 7.48 0.00 38.73 2.43
2283 2359 1.901464 GGGCTCGGGCTTGAAAACA 60.901 57.895 7.48 0.00 38.73 2.83
2284 2360 1.581447 GGCTCGGGCTTGAAAACAG 59.419 57.895 7.48 0.00 38.73 3.16
2285 2361 1.581447 GCTCGGGCTTGAAAACAGG 59.419 57.895 0.00 0.00 35.22 4.00
2286 2362 1.866853 GCTCGGGCTTGAAAACAGGG 61.867 60.000 0.00 0.00 35.22 4.45
2287 2363 0.250727 CTCGGGCTTGAAAACAGGGA 60.251 55.000 0.00 0.00 0.00 4.20
2288 2364 0.250727 TCGGGCTTGAAAACAGGGAG 60.251 55.000 0.00 0.00 0.00 4.30
2289 2365 0.537371 CGGGCTTGAAAACAGGGAGT 60.537 55.000 0.00 0.00 0.00 3.85
2290 2366 1.271163 CGGGCTTGAAAACAGGGAGTA 60.271 52.381 0.00 0.00 0.00 2.59
2291 2367 2.618045 CGGGCTTGAAAACAGGGAGTAT 60.618 50.000 0.00 0.00 0.00 2.12
2292 2368 3.431415 GGGCTTGAAAACAGGGAGTATT 58.569 45.455 0.00 0.00 0.00 1.89
2293 2369 3.832490 GGGCTTGAAAACAGGGAGTATTT 59.168 43.478 0.00 0.00 0.00 1.40
2294 2370 4.082190 GGGCTTGAAAACAGGGAGTATTTC 60.082 45.833 0.00 0.00 32.61 2.17
2295 2371 4.379499 GGCTTGAAAACAGGGAGTATTTCG 60.379 45.833 0.00 0.00 33.65 3.46
2296 2372 4.379499 GCTTGAAAACAGGGAGTATTTCGG 60.379 45.833 0.00 0.00 33.65 4.30
2297 2373 3.681593 TGAAAACAGGGAGTATTTCGGG 58.318 45.455 0.00 0.00 33.65 5.14
2298 2374 2.124277 AAACAGGGAGTATTTCGGGC 57.876 50.000 0.00 0.00 0.00 6.13
2299 2375 1.286248 AACAGGGAGTATTTCGGGCT 58.714 50.000 0.00 0.00 0.00 5.19
2300 2376 1.286248 ACAGGGAGTATTTCGGGCTT 58.714 50.000 0.00 0.00 0.00 4.35
2301 2377 1.209747 ACAGGGAGTATTTCGGGCTTC 59.790 52.381 0.00 0.00 0.00 3.86
2302 2378 0.464452 AGGGAGTATTTCGGGCTTCG 59.536 55.000 0.00 0.00 40.90 3.79
2303 2379 0.532196 GGGAGTATTTCGGGCTTCGG 60.532 60.000 0.75 0.00 39.77 4.30
2304 2380 0.532196 GGAGTATTTCGGGCTTCGGG 60.532 60.000 0.75 0.00 39.77 5.14
2305 2381 1.153229 AGTATTTCGGGCTTCGGGC 60.153 57.895 0.75 0.00 39.77 6.13
2326 2402 3.200522 GCTCGGGCTTGGGAAATG 58.799 61.111 0.00 0.00 35.22 2.32
2327 2403 1.378514 GCTCGGGCTTGGGAAATGA 60.379 57.895 0.00 0.00 35.22 2.57
2328 2404 0.965363 GCTCGGGCTTGGGAAATGAA 60.965 55.000 0.00 0.00 35.22 2.57
2329 2405 1.098050 CTCGGGCTTGGGAAATGAAG 58.902 55.000 0.00 0.00 0.00 3.02
2330 2406 0.323360 TCGGGCTTGGGAAATGAAGG 60.323 55.000 0.00 0.00 0.00 3.46
2331 2407 0.611896 CGGGCTTGGGAAATGAAGGT 60.612 55.000 0.00 0.00 0.00 3.50
2332 2408 1.186200 GGGCTTGGGAAATGAAGGTC 58.814 55.000 0.00 0.00 0.00 3.85
2333 2409 0.811281 GGCTTGGGAAATGAAGGTCG 59.189 55.000 0.00 0.00 0.00 4.79
2334 2410 0.811281 GCTTGGGAAATGAAGGTCGG 59.189 55.000 0.00 0.00 0.00 4.79
2335 2411 1.463674 CTTGGGAAATGAAGGTCGGG 58.536 55.000 0.00 0.00 0.00 5.14
2336 2412 0.610785 TTGGGAAATGAAGGTCGGGC 60.611 55.000 0.00 0.00 0.00 6.13
2337 2413 1.303282 GGGAAATGAAGGTCGGGCT 59.697 57.895 0.00 0.00 0.00 5.19
2338 2414 0.323451 GGGAAATGAAGGTCGGGCTT 60.323 55.000 0.00 0.00 0.00 4.35
2339 2415 1.545841 GGAAATGAAGGTCGGGCTTT 58.454 50.000 0.00 0.00 0.00 3.51
2340 2416 1.893137 GGAAATGAAGGTCGGGCTTTT 59.107 47.619 0.00 0.00 0.00 2.27
2341 2417 3.086282 GGAAATGAAGGTCGGGCTTTTA 58.914 45.455 0.00 0.00 0.00 1.52
2342 2418 3.119602 GGAAATGAAGGTCGGGCTTTTAC 60.120 47.826 0.00 0.00 0.00 2.01
2343 2419 2.871096 ATGAAGGTCGGGCTTTTACA 57.129 45.000 0.00 0.00 0.00 2.41
2344 2420 2.642154 TGAAGGTCGGGCTTTTACAA 57.358 45.000 0.00 0.00 0.00 2.41
2345 2421 2.500229 TGAAGGTCGGGCTTTTACAAG 58.500 47.619 0.00 0.00 0.00 3.16
2353 2429 3.284336 CTTTTACAAGCCCGGCCC 58.716 61.111 5.55 0.00 0.00 5.80
2354 2430 2.673687 TTTTACAAGCCCGGCCCG 60.674 61.111 5.55 0.00 0.00 6.13
2355 2431 3.193469 TTTTACAAGCCCGGCCCGA 62.193 57.895 3.71 0.00 0.00 5.14
2356 2432 2.693896 TTTTACAAGCCCGGCCCGAA 62.694 55.000 3.71 0.00 0.00 4.30
2357 2433 2.693896 TTTACAAGCCCGGCCCGAAA 62.694 55.000 3.71 0.00 0.00 3.46
2358 2434 3.905437 TACAAGCCCGGCCCGAAAC 62.905 63.158 3.71 0.00 0.00 2.78
2387 2463 3.281395 CGACGTTTGCCCGGGTTT 61.281 61.111 24.63 0.00 0.00 3.27
2388 2464 1.960250 CGACGTTTGCCCGGGTTTA 60.960 57.895 24.63 6.20 0.00 2.01
2389 2465 1.871077 GACGTTTGCCCGGGTTTAG 59.129 57.895 24.63 12.72 0.00 1.85
2390 2466 1.579964 GACGTTTGCCCGGGTTTAGG 61.580 60.000 24.63 14.80 0.00 2.69
2396 2472 2.194868 CCCGGGTTTAGGGCATCC 59.805 66.667 14.18 0.00 42.77 3.51
2411 2487 1.609320 GCATCCCCTCGCTCCTAAATC 60.609 57.143 0.00 0.00 0.00 2.17
2418 2494 2.224066 CCTCGCTCCTAAATCGGACATT 60.224 50.000 0.00 0.00 0.00 2.71
2423 2499 5.242171 TCGCTCCTAAATCGGACATTGTATA 59.758 40.000 0.00 0.00 0.00 1.47
2446 2522 0.316204 CCGTGGACAGGTAAACGTCT 59.684 55.000 0.00 0.00 34.30 4.18
2455 2531 4.275810 ACAGGTAAACGTCTGCCTAGATA 58.724 43.478 0.00 0.00 34.94 1.98
2457 2533 3.635836 AGGTAAACGTCTGCCTAGATACC 59.364 47.826 0.00 0.00 36.06 2.73
2458 2534 3.382546 GGTAAACGTCTGCCTAGATACCA 59.617 47.826 0.00 0.00 35.95 3.25
2459 2535 3.802948 AAACGTCTGCCTAGATACCAG 57.197 47.619 0.00 0.00 34.94 4.00
2461 2537 1.032794 CGTCTGCCTAGATACCAGCA 58.967 55.000 0.00 0.00 34.94 4.41
2502 2578 2.428890 AGCGTCCAATCACAACCAAAAA 59.571 40.909 0.00 0.00 0.00 1.94
2510 2586 4.751767 ATCACAACCAAAAAGAGCCAAA 57.248 36.364 0.00 0.00 0.00 3.28
2511 2587 4.543590 TCACAACCAAAAAGAGCCAAAA 57.456 36.364 0.00 0.00 0.00 2.44
2521 2597 6.347888 CCAAAAAGAGCCAAAAATGCATAGTG 60.348 38.462 0.00 0.00 0.00 2.74
2524 2600 5.473066 AGAGCCAAAAATGCATAGTGTTT 57.527 34.783 0.00 0.00 0.00 2.83
2525 2601 5.232463 AGAGCCAAAAATGCATAGTGTTTG 58.768 37.500 0.00 8.62 0.00 2.93
2536 2612 4.097741 TGCATAGTGTTTGCATACCCAATC 59.902 41.667 4.77 0.00 44.73 2.67
2553 2629 5.835280 ACCCAATCACAAAAGAATCTCAGTT 59.165 36.000 0.00 0.00 0.00 3.16
2554 2630 6.324770 ACCCAATCACAAAAGAATCTCAGTTT 59.675 34.615 0.00 0.00 0.00 2.66
2576 2654 2.037641 GGCATATGGATTTTTCCCTGCC 59.962 50.000 4.56 11.95 39.72 4.85
2577 2655 2.699846 GCATATGGATTTTTCCCTGCCA 59.300 45.455 4.56 0.00 0.00 4.92
2618 2696 4.007644 CTCACTCTGCCGCCACCA 62.008 66.667 0.00 0.00 0.00 4.17
2622 2700 4.335647 CTCTGCCGCCACCACCTT 62.336 66.667 0.00 0.00 0.00 3.50
2640 2718 1.899437 TTCTCCTCGCCATCCGCTTT 61.899 55.000 0.00 0.00 36.73 3.51
2646 2724 0.821517 TCGCCATCCGCTTTCTTCTA 59.178 50.000 0.00 0.00 36.73 2.10
2675 2753 4.761058 TCTCGGCCGCCTCCTTCT 62.761 66.667 23.51 0.00 0.00 2.85
2676 2754 4.214327 CTCGGCCGCCTCCTTCTC 62.214 72.222 23.51 0.00 0.00 2.87
2689 2767 1.807573 CTTCTCCGCCGTCTTCAGC 60.808 63.158 0.00 0.00 0.00 4.26
2694 2772 1.448540 CCGCCGTCTTCAGCTGATT 60.449 57.895 19.04 0.00 0.00 2.57
2741 2819 1.649664 GTCAGCTTGCACGATCATCT 58.350 50.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 4.018141 TCCTGTGAGTGAAATGGGATCATT 60.018 41.667 0.00 0.00 44.77 2.57
55 57 0.600255 ACGTTTCAAGGTGGCGAGAG 60.600 55.000 0.00 0.00 0.00 3.20
61 63 0.938713 TTGCGTACGTTTCAAGGTGG 59.061 50.000 17.90 0.00 0.00 4.61
81 83 1.160329 AACGACTTCACACTGGCAGC 61.160 55.000 15.89 0.00 0.00 5.25
529 555 6.154021 ACCACCTAGCTCGATCTTTTTACTAA 59.846 38.462 0.00 0.00 0.00 2.24
563 590 2.783135 ACATTTGGTGATCAGCTCGTT 58.217 42.857 24.30 5.57 0.00 3.85
593 620 3.543680 AGGACTACATCAAATCCCGTG 57.456 47.619 0.00 0.00 30.99 4.94
594 621 4.019681 TGAAAGGACTACATCAAATCCCGT 60.020 41.667 0.00 0.00 30.99 5.28
595 622 4.513442 TGAAAGGACTACATCAAATCCCG 58.487 43.478 0.00 0.00 30.99 5.14
596 623 6.122277 TGATGAAAGGACTACATCAAATCCC 58.878 40.000 14.89 0.00 44.42 3.85
683 731 2.287608 GCTAATTATTGAACGGCTGGCC 60.288 50.000 0.00 0.00 0.00 5.36
710 758 7.649973 AAATGCAATGAAAATGCTTTTGCTTA 58.350 26.923 10.37 0.00 44.48 3.09
711 759 6.508777 AAATGCAATGAAAATGCTTTTGCTT 58.491 28.000 10.37 0.00 44.48 3.91
725 773 7.118723 ACTTTACCTATGAGGAAATGCAATGA 58.881 34.615 0.00 0.00 37.67 2.57
727 775 7.631377 GCAACTTTACCTATGAGGAAATGCAAT 60.631 37.037 0.00 0.00 37.67 3.56
874 933 1.236616 TATGCTGCTGCGTTGCACTT 61.237 50.000 15.92 5.51 43.34 3.16
889 948 7.539436 TCGTTAACAGAGGAGATATGATATGC 58.461 38.462 6.39 0.00 0.00 3.14
895 954 6.276847 AGCTTTCGTTAACAGAGGAGATATG 58.723 40.000 6.39 0.00 0.00 1.78
896 955 6.472686 AGCTTTCGTTAACAGAGGAGATAT 57.527 37.500 6.39 0.00 0.00 1.63
897 956 5.916661 AGCTTTCGTTAACAGAGGAGATA 57.083 39.130 6.39 0.00 0.00 1.98
898 957 4.810191 AGCTTTCGTTAACAGAGGAGAT 57.190 40.909 6.39 3.05 0.00 2.75
899 958 4.380655 GCTAGCTTTCGTTAACAGAGGAGA 60.381 45.833 7.70 0.00 0.00 3.71
900 959 3.860536 GCTAGCTTTCGTTAACAGAGGAG 59.139 47.826 7.70 7.27 0.00 3.69
909 968 2.561419 ACTCAGGTGCTAGCTTTCGTTA 59.439 45.455 17.23 0.00 0.00 3.18
913 972 1.737363 CGGACTCAGGTGCTAGCTTTC 60.737 57.143 17.23 6.44 0.00 2.62
915 974 0.900647 ACGGACTCAGGTGCTAGCTT 60.901 55.000 17.23 0.00 0.00 3.74
916 975 0.900647 AACGGACTCAGGTGCTAGCT 60.901 55.000 17.23 0.00 0.00 3.32
917 976 0.037232 AAACGGACTCAGGTGCTAGC 60.037 55.000 8.10 8.10 0.00 3.42
918 977 1.272490 TGAAACGGACTCAGGTGCTAG 59.728 52.381 0.00 0.00 0.00 3.42
919 978 1.334160 TGAAACGGACTCAGGTGCTA 58.666 50.000 0.00 0.00 0.00 3.49
920 979 0.468226 TTGAAACGGACTCAGGTGCT 59.532 50.000 0.00 0.00 0.00 4.40
921 980 1.305201 TTTGAAACGGACTCAGGTGC 58.695 50.000 0.00 0.00 0.00 5.01
941 1000 4.040952 TCTTCTCTCAGGTGCTAGCTTTTT 59.959 41.667 17.23 0.00 0.00 1.94
952 1011 4.527038 TGAACCGTAAATCTTCTCTCAGGT 59.473 41.667 0.00 0.00 0.00 4.00
965 1024 4.208746 ACCAAACCAAGATGAACCGTAAA 58.791 39.130 0.00 0.00 0.00 2.01
1140 1199 1.403679 CCGACTTTGAAAGTGTTGCCA 59.596 47.619 16.25 0.00 43.03 4.92
1184 1248 4.201466 GCACGTATGTACTCACGAAGAAAC 60.201 45.833 21.34 5.39 40.56 2.78
1187 1251 2.159476 GGCACGTATGTACTCACGAAGA 60.159 50.000 21.34 0.00 40.56 2.87
1188 1252 2.182825 GGCACGTATGTACTCACGAAG 58.817 52.381 21.34 15.17 40.56 3.79
1204 1268 2.095853 CCAGTCACATGATTAACGGCAC 59.904 50.000 0.00 0.00 0.00 5.01
1228 1297 2.825532 GGGCAGACACATGTTAAACCAT 59.174 45.455 0.00 0.00 0.00 3.55
1229 1298 2.158534 AGGGCAGACACATGTTAAACCA 60.159 45.455 0.00 0.00 0.00 3.67
1230 1299 2.228822 CAGGGCAGACACATGTTAAACC 59.771 50.000 0.00 0.00 0.00 3.27
1231 1300 2.884639 ACAGGGCAGACACATGTTAAAC 59.115 45.455 0.00 0.00 0.00 2.01
1232 1301 3.222173 ACAGGGCAGACACATGTTAAA 57.778 42.857 0.00 0.00 0.00 1.52
1233 1302 2.949177 ACAGGGCAGACACATGTTAA 57.051 45.000 0.00 0.00 0.00 2.01
1234 1303 2.371841 AGAACAGGGCAGACACATGTTA 59.628 45.455 0.00 0.00 34.41 2.41
1235 1304 1.143684 AGAACAGGGCAGACACATGTT 59.856 47.619 0.00 0.00 36.83 2.71
1277 1346 4.624364 TCCGCCACTGTGTGCAGG 62.624 66.667 17.31 17.24 46.62 4.85
1514 1583 3.741476 GTCGGGCTCGTGTACGGT 61.741 66.667 5.57 0.00 40.29 4.83
1670 1745 3.925238 GCGGCGCCATTGTACGAG 61.925 66.667 28.98 7.61 0.00 4.18
1778 1853 0.842635 CTTCATCCTGGGCTAGCCTT 59.157 55.000 32.18 10.39 36.10 4.35
1902 1978 9.661563 TTGTAGTTATGTTAGATTTGGGTACTG 57.338 33.333 0.00 0.00 0.00 2.74
1958 2034 3.367607 CATTGCTCTAGAGACACGCTAC 58.632 50.000 24.24 3.43 0.00 3.58
1962 2038 2.575694 AGCATTGCTCTAGAGACACG 57.424 50.000 24.24 13.92 30.62 4.49
1986 2062 1.789523 TAGGATGCCCTGTAGGTGTC 58.210 55.000 0.00 0.00 44.15 3.67
1994 2070 0.106519 CCCAGGTTTAGGATGCCCTG 60.107 60.000 0.00 0.00 44.15 4.45
2003 2079 1.000233 TGCCCATGCCCAGGTTTAG 60.000 57.895 0.00 0.00 36.33 1.85
2004 2080 1.000233 CTGCCCATGCCCAGGTTTA 60.000 57.895 3.62 0.00 36.33 2.01
2005 2081 2.284112 CTGCCCATGCCCAGGTTT 60.284 61.111 3.62 0.00 36.33 3.27
2044 2120 3.744719 GTTTTTCGGGCCGGGCTC 61.745 66.667 28.80 15.19 0.00 4.70
2070 2146 4.754667 GTCAAGCCCGACCCGTCC 62.755 72.222 0.00 0.00 0.00 4.79
2073 2149 4.675029 AACGTCAAGCCCGACCCG 62.675 66.667 0.00 0.00 31.91 5.28
2074 2150 2.741211 GAACGTCAAGCCCGACCC 60.741 66.667 0.00 0.00 31.91 4.46
2075 2151 3.110178 CGAACGTCAAGCCCGACC 61.110 66.667 0.00 0.00 31.91 4.79
2076 2152 3.110178 CCGAACGTCAAGCCCGAC 61.110 66.667 0.00 0.00 0.00 4.79
2077 2153 4.367023 CCCGAACGTCAAGCCCGA 62.367 66.667 0.00 0.00 0.00 5.14
2099 2175 4.043200 GCAACACAAGGCCCGAGC 62.043 66.667 0.00 0.00 38.76 5.03
2100 2176 2.594303 TGCAACACAAGGCCCGAG 60.594 61.111 0.00 0.00 0.00 4.63
2101 2177 2.594303 CTGCAACACAAGGCCCGA 60.594 61.111 0.00 0.00 0.00 5.14
2102 2178 4.347453 GCTGCAACACAAGGCCCG 62.347 66.667 0.00 0.00 0.00 6.13
2103 2179 3.994853 GGCTGCAACACAAGGCCC 61.995 66.667 0.00 0.00 34.30 5.80
2104 2180 3.994853 GGGCTGCAACACAAGGCC 61.995 66.667 0.50 0.00 38.58 5.19
2105 2181 4.347453 CGGGCTGCAACACAAGGC 62.347 66.667 0.50 0.00 0.00 4.35
2106 2182 3.673484 CCGGGCTGCAACACAAGG 61.673 66.667 0.50 0.00 0.00 3.61
2107 2183 2.133742 CTTCCGGGCTGCAACACAAG 62.134 60.000 0.00 0.00 0.00 3.16
2108 2184 2.124109 TTCCGGGCTGCAACACAA 60.124 55.556 0.00 0.00 0.00 3.33
2109 2185 2.410322 ATCTTCCGGGCTGCAACACA 62.410 55.000 0.00 0.00 0.00 3.72
2110 2186 0.392461 TATCTTCCGGGCTGCAACAC 60.392 55.000 0.00 0.00 0.00 3.32
2111 2187 0.107703 CTATCTTCCGGGCTGCAACA 60.108 55.000 0.00 0.00 0.00 3.33
2112 2188 0.107654 ACTATCTTCCGGGCTGCAAC 60.108 55.000 0.00 0.00 0.00 4.17
2113 2189 0.618458 AACTATCTTCCGGGCTGCAA 59.382 50.000 0.00 0.00 0.00 4.08
2114 2190 0.178068 GAACTATCTTCCGGGCTGCA 59.822 55.000 0.00 0.00 0.00 4.41
2115 2191 0.876342 CGAACTATCTTCCGGGCTGC 60.876 60.000 0.00 0.00 0.00 5.25
2116 2192 0.249489 CCGAACTATCTTCCGGGCTG 60.249 60.000 0.00 0.00 38.42 4.85
2117 2193 2.125178 CCGAACTATCTTCCGGGCT 58.875 57.895 0.00 0.00 38.42 5.19
2118 2194 4.752514 CCGAACTATCTTCCGGGC 57.247 61.111 0.00 0.00 38.42 6.13
2120 2196 1.069258 GGCCCGAACTATCTTCCGG 59.931 63.158 0.00 0.00 41.47 5.14
2121 2197 1.299926 CGGCCCGAACTATCTTCCG 60.300 63.158 0.00 0.00 0.00 4.30
2122 2198 1.069258 CCGGCCCGAACTATCTTCC 59.931 63.158 3.71 0.00 0.00 3.46
2123 2199 1.069258 CCCGGCCCGAACTATCTTC 59.931 63.158 3.71 0.00 0.00 2.87
2124 2200 3.103091 GCCCGGCCCGAACTATCTT 62.103 63.158 3.71 0.00 0.00 2.40
2125 2201 3.547513 GCCCGGCCCGAACTATCT 61.548 66.667 3.71 0.00 0.00 1.98
2126 2202 3.516866 GAGCCCGGCCCGAACTATC 62.517 68.421 3.71 0.00 0.00 2.08
2127 2203 3.547513 GAGCCCGGCCCGAACTAT 61.548 66.667 3.71 0.00 0.00 2.12
2138 2214 1.595093 AAAAATGAAGCCCGAGCCCG 61.595 55.000 0.00 0.00 41.25 6.13
2139 2215 2.276869 AAAAATGAAGCCCGAGCCC 58.723 52.632 0.00 0.00 41.25 5.19
2154 2230 2.688958 CCCGGCCCGAAATACATAAAAA 59.311 45.455 3.71 0.00 0.00 1.94
2155 2231 2.299521 CCCGGCCCGAAATACATAAAA 58.700 47.619 3.71 0.00 0.00 1.52
2156 2232 1.970092 CCCGGCCCGAAATACATAAA 58.030 50.000 3.71 0.00 0.00 1.40
2157 2233 0.535553 GCCCGGCCCGAAATACATAA 60.536 55.000 3.71 0.00 0.00 1.90
2158 2234 1.071814 GCCCGGCCCGAAATACATA 59.928 57.895 3.71 0.00 0.00 2.29
2159 2235 2.203294 GCCCGGCCCGAAATACAT 60.203 61.111 3.71 0.00 0.00 2.29
2160 2236 2.487274 AAAGCCCGGCCCGAAATACA 62.487 55.000 3.71 0.00 0.00 2.29
2161 2237 1.721664 GAAAGCCCGGCCCGAAATAC 61.722 60.000 3.71 0.00 0.00 1.89
2162 2238 1.452470 GAAAGCCCGGCCCGAAATA 60.452 57.895 3.71 0.00 0.00 1.40
2163 2239 2.754254 GAAAGCCCGGCCCGAAAT 60.754 61.111 3.71 0.00 0.00 2.17
2174 2250 4.717313 ACCCGAAGCCCGAAAGCC 62.717 66.667 0.00 0.00 41.76 4.35
2175 2251 3.125573 GACCCGAAGCCCGAAAGC 61.126 66.667 0.00 0.00 41.76 3.51
2176 2252 2.813908 CGACCCGAAGCCCGAAAG 60.814 66.667 0.00 0.00 41.76 2.62
2177 2253 4.382320 CCGACCCGAAGCCCGAAA 62.382 66.667 0.00 0.00 41.76 3.46
2184 2260 4.697756 TGCAAGCCCGACCCGAAG 62.698 66.667 0.00 0.00 0.00 3.79
2193 2269 4.084888 GTACGCACGTGCAAGCCC 62.085 66.667 37.03 17.44 42.21 5.19
2194 2270 3.342627 TGTACGCACGTGCAAGCC 61.343 61.111 37.03 22.20 42.21 4.35
2195 2271 2.127758 GTGTACGCACGTGCAAGC 60.128 61.111 37.03 25.38 41.95 4.01
2215 2291 1.730451 CCGGCCCGAACACTGTTTTT 61.730 55.000 3.71 0.00 0.00 1.94
2216 2292 2.190841 CCGGCCCGAACACTGTTTT 61.191 57.895 3.71 0.00 0.00 2.43
2217 2293 2.593436 CCGGCCCGAACACTGTTT 60.593 61.111 3.71 0.00 0.00 2.83
2218 2294 4.636435 CCCGGCCCGAACACTGTT 62.636 66.667 3.71 0.00 0.00 3.16
2236 2312 2.359975 AAGCCCGAAGCCCGAAAG 60.360 61.111 0.00 0.00 45.47 2.62
2237 2313 2.478335 ATCAAGCCCGAAGCCCGAAA 62.478 55.000 0.00 0.00 45.47 3.46
2238 2314 2.478335 AATCAAGCCCGAAGCCCGAA 62.478 55.000 0.00 0.00 45.47 4.30
2239 2315 2.478335 AAATCAAGCCCGAAGCCCGA 62.478 55.000 0.00 0.00 45.47 5.14
2240 2316 1.993369 GAAATCAAGCCCGAAGCCCG 61.993 60.000 0.00 0.00 45.47 6.13
2241 2317 1.809869 GAAATCAAGCCCGAAGCCC 59.190 57.895 0.00 0.00 45.47 5.19
2242 2318 1.429423 CGAAATCAAGCCCGAAGCC 59.571 57.895 0.00 0.00 45.47 4.35
2243 2319 1.429423 CCGAAATCAAGCCCGAAGC 59.571 57.895 0.00 0.00 44.25 3.86
2244 2320 1.993369 GCCCGAAATCAAGCCCGAAG 61.993 60.000 0.00 0.00 0.00 3.79
2245 2321 2.043980 GCCCGAAATCAAGCCCGAA 61.044 57.895 0.00 0.00 0.00 4.30
2246 2322 2.437716 GCCCGAAATCAAGCCCGA 60.438 61.111 0.00 0.00 0.00 5.14
2247 2323 3.518068 GGCCCGAAATCAAGCCCG 61.518 66.667 0.00 0.00 39.60 6.13
2248 2324 3.518068 CGGCCCGAAATCAAGCCC 61.518 66.667 0.00 0.00 42.66 5.19
2249 2325 3.518068 CCGGCCCGAAATCAAGCC 61.518 66.667 3.71 0.00 42.18 4.35
2250 2326 3.518068 CCCGGCCCGAAATCAAGC 61.518 66.667 3.71 0.00 0.00 4.01
2251 2327 3.518068 GCCCGGCCCGAAATCAAG 61.518 66.667 3.71 0.00 0.00 3.02
2252 2328 3.987954 GAGCCCGGCCCGAAATCAA 62.988 63.158 3.71 0.00 0.00 2.57
2253 2329 4.483243 GAGCCCGGCCCGAAATCA 62.483 66.667 3.71 0.00 0.00 2.57
2264 2340 2.671619 TTTTCAAGCCCGAGCCCG 60.672 61.111 0.00 0.00 41.25 6.13
2265 2341 1.866853 CTGTTTTCAAGCCCGAGCCC 61.867 60.000 0.00 0.00 41.25 5.19
2266 2342 1.581447 CTGTTTTCAAGCCCGAGCC 59.419 57.895 0.00 0.00 41.25 4.70
2267 2343 1.581447 CCTGTTTTCAAGCCCGAGC 59.419 57.895 0.00 0.00 40.32 5.03
2268 2344 0.250727 TCCCTGTTTTCAAGCCCGAG 60.251 55.000 0.00 0.00 0.00 4.63
2269 2345 0.250727 CTCCCTGTTTTCAAGCCCGA 60.251 55.000 0.00 0.00 0.00 5.14
2270 2346 0.537371 ACTCCCTGTTTTCAAGCCCG 60.537 55.000 0.00 0.00 0.00 6.13
2271 2347 2.579410 TACTCCCTGTTTTCAAGCCC 57.421 50.000 0.00 0.00 0.00 5.19
2272 2348 4.379499 CGAAATACTCCCTGTTTTCAAGCC 60.379 45.833 0.00 0.00 31.88 4.35
2273 2349 4.379499 CCGAAATACTCCCTGTTTTCAAGC 60.379 45.833 0.00 0.00 31.88 4.01
2274 2350 4.156008 CCCGAAATACTCCCTGTTTTCAAG 59.844 45.833 0.00 0.00 31.88 3.02
2275 2351 4.076394 CCCGAAATACTCCCTGTTTTCAA 58.924 43.478 0.00 0.00 31.88 2.69
2276 2352 3.681593 CCCGAAATACTCCCTGTTTTCA 58.318 45.455 0.00 0.00 31.88 2.69
2277 2353 2.422479 GCCCGAAATACTCCCTGTTTTC 59.578 50.000 0.00 0.00 0.00 2.29
2278 2354 2.041216 AGCCCGAAATACTCCCTGTTTT 59.959 45.455 0.00 0.00 0.00 2.43
2279 2355 1.633945 AGCCCGAAATACTCCCTGTTT 59.366 47.619 0.00 0.00 0.00 2.83
2280 2356 1.286248 AGCCCGAAATACTCCCTGTT 58.714 50.000 0.00 0.00 0.00 3.16
2281 2357 1.209747 GAAGCCCGAAATACTCCCTGT 59.790 52.381 0.00 0.00 0.00 4.00
2282 2358 1.806623 CGAAGCCCGAAATACTCCCTG 60.807 57.143 0.00 0.00 41.76 4.45
2283 2359 0.464452 CGAAGCCCGAAATACTCCCT 59.536 55.000 0.00 0.00 41.76 4.20
2284 2360 0.532196 CCGAAGCCCGAAATACTCCC 60.532 60.000 0.00 0.00 41.76 4.30
2285 2361 0.532196 CCCGAAGCCCGAAATACTCC 60.532 60.000 0.00 0.00 41.76 3.85
2286 2362 1.158484 GCCCGAAGCCCGAAATACTC 61.158 60.000 0.00 0.00 41.76 2.59
2287 2363 1.153229 GCCCGAAGCCCGAAATACT 60.153 57.895 0.00 0.00 41.76 2.12
2288 2364 3.417601 GCCCGAAGCCCGAAATAC 58.582 61.111 0.00 0.00 41.76 1.89
2309 2385 0.965363 TTCATTTCCCAAGCCCGAGC 60.965 55.000 0.00 0.00 40.32 5.03
2310 2386 1.098050 CTTCATTTCCCAAGCCCGAG 58.902 55.000 0.00 0.00 0.00 4.63
2311 2387 0.323360 CCTTCATTTCCCAAGCCCGA 60.323 55.000 0.00 0.00 0.00 5.14
2312 2388 0.611896 ACCTTCATTTCCCAAGCCCG 60.612 55.000 0.00 0.00 0.00 6.13
2313 2389 1.186200 GACCTTCATTTCCCAAGCCC 58.814 55.000 0.00 0.00 0.00 5.19
2314 2390 0.811281 CGACCTTCATTTCCCAAGCC 59.189 55.000 0.00 0.00 0.00 4.35
2315 2391 0.811281 CCGACCTTCATTTCCCAAGC 59.189 55.000 0.00 0.00 0.00 4.01
2316 2392 1.463674 CCCGACCTTCATTTCCCAAG 58.536 55.000 0.00 0.00 0.00 3.61
2317 2393 0.610785 GCCCGACCTTCATTTCCCAA 60.611 55.000 0.00 0.00 0.00 4.12
2318 2394 1.001393 GCCCGACCTTCATTTCCCA 60.001 57.895 0.00 0.00 0.00 4.37
2319 2395 0.323451 AAGCCCGACCTTCATTTCCC 60.323 55.000 0.00 0.00 0.00 3.97
2320 2396 1.545841 AAAGCCCGACCTTCATTTCC 58.454 50.000 0.00 0.00 0.00 3.13
2321 2397 3.504520 TGTAAAAGCCCGACCTTCATTTC 59.495 43.478 0.00 0.00 0.00 2.17
2322 2398 3.492337 TGTAAAAGCCCGACCTTCATTT 58.508 40.909 0.00 0.00 0.00 2.32
2323 2399 3.149005 TGTAAAAGCCCGACCTTCATT 57.851 42.857 0.00 0.00 0.00 2.57
2324 2400 2.871096 TGTAAAAGCCCGACCTTCAT 57.129 45.000 0.00 0.00 0.00 2.57
2325 2401 2.500229 CTTGTAAAAGCCCGACCTTCA 58.500 47.619 0.00 0.00 0.00 3.02
2326 2402 1.199327 GCTTGTAAAAGCCCGACCTTC 59.801 52.381 6.34 0.00 39.81 3.46
2327 2403 1.244816 GCTTGTAAAAGCCCGACCTT 58.755 50.000 6.34 0.00 39.81 3.50
2328 2404 2.942641 GCTTGTAAAAGCCCGACCT 58.057 52.632 6.34 0.00 39.81 3.85
2335 2411 2.571757 GGCCGGGCTTGTAAAAGC 59.428 61.111 22.87 9.32 44.76 3.51
2336 2412 2.696759 CGGGCCGGGCTTGTAAAAG 61.697 63.158 28.80 5.53 0.00 2.27
2337 2413 2.673687 CGGGCCGGGCTTGTAAAA 60.674 61.111 28.80 0.00 0.00 1.52
2338 2414 2.693896 TTTCGGGCCGGGCTTGTAAA 62.694 55.000 28.80 18.44 0.00 2.01
2339 2415 3.193469 TTTCGGGCCGGGCTTGTAA 62.193 57.895 28.80 16.98 0.00 2.41
2340 2416 3.638316 TTTCGGGCCGGGCTTGTA 61.638 61.111 28.80 11.81 0.00 2.41
2370 2446 1.903783 CTAAACCCGGGCAAACGTCG 61.904 60.000 24.08 0.00 0.00 5.12
2371 2447 1.579964 CCTAAACCCGGGCAAACGTC 61.580 60.000 24.08 0.00 0.00 4.34
2372 2448 1.601477 CCTAAACCCGGGCAAACGT 60.601 57.895 24.08 0.00 0.00 3.99
2373 2449 2.337246 CCCTAAACCCGGGCAAACG 61.337 63.158 24.08 5.31 34.32 3.60
2374 2450 3.689414 CCCTAAACCCGGGCAAAC 58.311 61.111 24.08 0.00 34.32 2.93
2379 2455 2.194868 GGATGCCCTAAACCCGGG 59.805 66.667 22.25 22.25 44.89 5.73
2380 2456 2.194868 GGGATGCCCTAAACCCGG 59.805 66.667 0.00 0.00 41.34 5.73
2381 2457 2.194868 GGGGATGCCCTAAACCCG 59.805 66.667 16.52 0.00 44.66 5.28
2382 2458 1.537172 GAGGGGATGCCCTAAACCC 59.463 63.158 27.06 8.66 44.66 4.11
2383 2459 1.148498 CGAGGGGATGCCCTAAACC 59.852 63.158 27.06 11.90 44.66 3.27
2384 2460 1.526225 GCGAGGGGATGCCCTAAAC 60.526 63.158 27.06 13.79 44.66 2.01
2385 2461 1.692749 AGCGAGGGGATGCCCTAAA 60.693 57.895 27.06 0.00 44.66 1.85
2386 2462 2.040884 AGCGAGGGGATGCCCTAA 60.041 61.111 27.06 0.00 44.66 2.69
2387 2463 2.524394 GAGCGAGGGGATGCCCTA 60.524 66.667 27.06 0.00 44.66 3.53
2390 2466 1.696097 TTTAGGAGCGAGGGGATGCC 61.696 60.000 0.00 0.00 0.00 4.40
2391 2467 0.398318 ATTTAGGAGCGAGGGGATGC 59.602 55.000 0.00 0.00 0.00 3.91
2392 2468 1.337260 CGATTTAGGAGCGAGGGGATG 60.337 57.143 0.00 0.00 0.00 3.51
2393 2469 0.969894 CGATTTAGGAGCGAGGGGAT 59.030 55.000 0.00 0.00 0.00 3.85
2394 2470 1.113517 CCGATTTAGGAGCGAGGGGA 61.114 60.000 0.00 0.00 0.00 4.81
2395 2471 1.113517 TCCGATTTAGGAGCGAGGGG 61.114 60.000 0.00 0.00 34.92 4.79
2396 2472 0.032267 GTCCGATTTAGGAGCGAGGG 59.968 60.000 0.00 0.00 41.68 4.30
2430 2506 0.034337 GGCAGACGTTTACCTGTCCA 59.966 55.000 4.18 0.00 35.71 4.02
2435 2511 3.635836 GGTATCTAGGCAGACGTTTACCT 59.364 47.826 3.00 3.00 32.98 3.08
2442 2518 1.032794 TGCTGGTATCTAGGCAGACG 58.967 55.000 0.00 0.00 32.25 4.18
2446 2522 4.502105 TCAAATTGCTGGTATCTAGGCA 57.498 40.909 0.00 0.00 0.00 4.75
2485 2561 3.069443 GGCTCTTTTTGGTTGTGATTGGA 59.931 43.478 0.00 0.00 0.00 3.53
2502 2578 5.232463 CAAACACTATGCATTTTTGGCTCT 58.768 37.500 3.54 0.00 0.00 4.09
2521 2597 5.537188 TCTTTTGTGATTGGGTATGCAAAC 58.463 37.500 0.00 0.00 0.00 2.93
2524 2600 5.716228 AGATTCTTTTGTGATTGGGTATGCA 59.284 36.000 0.00 0.00 0.00 3.96
2525 2601 6.127647 TGAGATTCTTTTGTGATTGGGTATGC 60.128 38.462 0.00 0.00 0.00 3.14
2529 2605 5.388654 ACTGAGATTCTTTTGTGATTGGGT 58.611 37.500 0.00 0.00 0.00 4.51
2536 2612 4.935702 TGCCAAACTGAGATTCTTTTGTG 58.064 39.130 7.98 2.91 0.00 3.33
2553 2629 3.134442 GCAGGGAAAAATCCATATGCCAA 59.866 43.478 0.00 0.00 32.58 4.52
2554 2630 2.699846 GCAGGGAAAAATCCATATGCCA 59.300 45.455 0.00 0.00 32.58 4.92
2597 2675 2.282783 TGGCGGCAGAGTGAGCTTA 61.283 57.895 7.97 0.00 0.00 3.09
2599 2677 4.385405 GTGGCGGCAGAGTGAGCT 62.385 66.667 13.91 0.00 0.00 4.09
2618 2696 2.427245 CGGATGGCGAGGAGAAGGT 61.427 63.158 0.00 0.00 0.00 3.50
2640 2718 1.285373 AGAAGGAGGCGGTCTAGAAGA 59.715 52.381 0.00 0.00 0.00 2.87
2646 2724 2.756283 CCGAGAAGGAGGCGGTCT 60.756 66.667 0.00 0.00 45.00 3.85
2681 2759 3.181522 CGCTTGAAGAATCAGCTGAAGAC 60.182 47.826 22.50 14.50 36.78 3.01
2689 2767 5.034554 TGTTAAAGCGCTTGAAGAATCAG 57.965 39.130 25.80 0.00 36.78 2.90
2694 2772 3.674997 AGGATGTTAAAGCGCTTGAAGA 58.325 40.909 25.80 21.84 0.00 2.87
2722 2800 1.649664 AGATGATCGTGCAAGCTGAC 58.350 50.000 0.00 0.00 0.00 3.51
2723 2801 2.391616 AAGATGATCGTGCAAGCTGA 57.608 45.000 0.00 0.00 0.00 4.26
2725 2803 1.131883 GCAAAGATGATCGTGCAAGCT 59.868 47.619 16.05 0.00 34.06 3.74


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

AutoCloner maintained by Alex Coulton.