Multiple sequence alignment - TraesCS7B01G242300

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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 TraesCS7B01G242300 chr7B 100.000 7792 0 0 1 7792 450562850 450570641 0.000000e+00 14390
1 TraesCS7B01G242300 chr7B 98.876 89 0 1 1 89 744290700 744290787 2.910000e-34 158
2 TraesCS7B01G242300 chr7B 97.727 88 1 1 3 90 8922486 8922572 4.870000e-32 150
3 TraesCS7B01G242300 chr7D 96.322 4405 124 19 2169 6552 431934954 431930567 0.000000e+00 7203
4 TraesCS7B01G242300 chr7D 93.524 2023 70 27 107 2089 431936954 431934953 0.000000e+00 2953
5 TraesCS7B01G242300 chr7D 92.645 1210 66 12 6563 7756 431930527 431929325 0.000000e+00 1720
6 TraesCS7B01G242300 chr7A 96.406 3005 73 17 3233 6216 501058988 501061978 0.000000e+00 4918
7 TraesCS7B01G242300 chr7A 93.054 2030 89 29 83 2089 501056010 501058010 0.000000e+00 2920
8 TraesCS7B01G242300 chr7A 96.757 740 24 0 2169 2908 501058009 501058748 0.000000e+00 1234
9 TraesCS7B01G242300 chr7A 90.256 780 45 12 6560 7336 501062097 501062848 0.000000e+00 990
10 TraesCS7B01G242300 chr7A 89.928 139 11 1 4797 4935 686805271 686805136 8.040000e-40 176
11 TraesCS7B01G242300 chr7A 98.936 94 1 0 6470 6563 501061972 501062065 1.340000e-37 169
12 TraesCS7B01G242300 chr7A 95.918 98 2 1 2079 2174 129877032 129876935 2.910000e-34 158
13 TraesCS7B01G242300 chr7A 91.566 83 6 1 2983 3065 501058745 501058826 6.390000e-21 113
14 TraesCS7B01G242300 chr1D 91.506 777 48 8 4161 4935 468887229 468887989 0.000000e+00 1053
15 TraesCS7B01G242300 chr1D 90.886 779 50 9 4161 4935 49519585 49520346 0.000000e+00 1026
16 TraesCS7B01G242300 chr4D 91.014 779 49 11 4161 4935 500521908 500521147 0.000000e+00 1031
17 TraesCS7B01G242300 chr1B 88.757 507 32 10 4440 4935 46149830 46150322 1.450000e-166 597
18 TraesCS7B01G242300 chr1B 94.419 215 12 0 4161 4375 46139499 46139713 1.620000e-86 331
19 TraesCS7B01G242300 chr1B 100.000 84 0 0 1 84 334446153 334446236 1.050000e-33 156
20 TraesCS7B01G242300 chr5D 89.826 344 24 5 4272 4613 445653645 445653979 1.550000e-116 431
21 TraesCS7B01G242300 chr5D 89.535 344 25 5 4272 4613 445651784 445652118 7.230000e-115 425
22 TraesCS7B01G242300 chr5A 100.000 85 0 0 1 85 541842052 541842136 2.910000e-34 158
23 TraesCS7B01G242300 chr6A 100.000 84 0 0 1 84 457402410 457402327 1.050000e-33 156
24 TraesCS7B01G242300 chr6A 97.701 87 2 0 1 87 600701765 600701851 4.870000e-32 150
25 TraesCS7B01G242300 chr5B 100.000 84 0 0 1 84 543932643 543932726 1.050000e-33 156
26 TraesCS7B01G242300 chr5B 93.204 103 3 3 2073 2172 711237867 711237968 1.750000e-31 148
27 TraesCS7B01G242300 chrUn 96.774 93 1 1 2085 2175 23900850 23900942 3.770000e-33 154
28 TraesCS7B01G242300 chr2B 96.774 93 1 1 2085 2175 799161052 799161144 3.770000e-33 154
29 TraesCS7B01G242300 chr2B 96.774 93 1 1 2085 2175 799214208 799214300 3.770000e-33 154
30 TraesCS7B01G242300 chr2B 88.793 116 8 3 2088 2201 798196761 798196649 3.790000e-28 137
31 TraesCS7B01G242300 chr4B 98.824 85 1 0 1 85 216815011 216815095 1.350000e-32 152
32 TraesCS7B01G242300 chr3B 90.000 120 7 4 2081 2195 427633827 427633708 4.870000e-32 150
33 TraesCS7B01G242300 chr3A 95.699 93 2 1 2081 2171 629669318 629669410 1.750000e-31 148
34 TraesCS7B01G242300 chr3A 97.647 85 2 0 1 85 581268702 581268786 6.300000e-31 147
35 TraesCS7B01G242300 chr2D 90.909 110 3 6 2085 2191 422331552 422331657 2.930000e-29 141


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 TraesCS7B01G242300 chr7B 450562850 450570641 7791 False 14390.000000 14390 100.000000 1 7792 1 chr7B.!!$F2 7791
1 TraesCS7B01G242300 chr7D 431929325 431936954 7629 True 3958.666667 7203 94.163667 107 7756 3 chr7D.!!$R1 7649
2 TraesCS7B01G242300 chr7A 501056010 501062848 6838 False 1724.000000 4918 94.495833 83 7336 6 chr7A.!!$F1 7253
3 TraesCS7B01G242300 chr1D 468887229 468887989 760 False 1053.000000 1053 91.506000 4161 4935 1 chr1D.!!$F2 774
4 TraesCS7B01G242300 chr1D 49519585 49520346 761 False 1026.000000 1026 90.886000 4161 4935 1 chr1D.!!$F1 774
5 TraesCS7B01G242300 chr4D 500521147 500521908 761 True 1031.000000 1031 91.014000 4161 4935 1 chr4D.!!$R1 774
6 TraesCS7B01G242300 chr5D 445651784 445653979 2195 False 428.000000 431 89.680500 4272 4613 2 chr5D.!!$F1 341


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
663 671 0.178891 TCAGCTCTTCCTCCACCCTT 60.179 55.0 0.00 0.00 0.00 3.95 F
667 675 0.322906 CTCTTCCTCCACCCTTTGCC 60.323 60.0 0.00 0.00 0.00 4.52 F
2101 2165 0.324091 TCAACTACTCCCTCCGTCCC 60.324 60.0 0.00 0.00 0.00 4.46 F
2103 2167 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.0 0.00 0.00 0.00 4.00 F
3752 3922 0.172803 GGTGTGTAGGCGACCAGTAG 59.827 60.0 0.00 0.00 0.00 2.57 F
3835 4005 1.067295 AGGCCATGAGTCACTTTCCA 58.933 50.0 5.01 0.00 0.00 3.53 F
3972 4150 1.821216 TCCTTTCAGATGGAAACGCC 58.179 50.0 0.00 0.00 40.51 5.68 F
5353 5539 0.530744 ATTCCGTTAGCGAGCACTCA 59.469 50.0 0.00 0.00 41.33 3.41 F
6456 6657 1.011451 GGTGAGCTCTTGTCGAGTGC 61.011 60.0 16.19 6.08 43.51 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2217 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.0 0.00 4.00 R
2155 2219 1.272037 CCTATCTACTCCCTCCGTCCC 60.272 61.905 0.00 0.0 0.00 4.46 R
3730 3900 0.034896 CTGGTCGCCTACACACCTTT 59.965 55.000 0.00 0.0 0.00 3.11 R
4002 4180 2.301346 GATTCCGGTTCAGGCATCAAT 58.699 47.619 0.00 0.0 34.68 2.57 R
4767 4953 2.289002 AGAAGAAGCAACTTGTGAAGCG 59.711 45.455 0.34 0.0 0.00 4.68 R
5131 5317 3.313526 GCACGAAAGAGGCATCAATGTAT 59.686 43.478 0.00 0.0 35.60 2.29 R
5445 5643 3.697166 AGGTGCCAGGTTTGGTTATAAG 58.303 45.455 0.00 0.0 46.80 1.73 R
6614 6860 0.250234 CTTCTGTCATCCCGGCTGAA 59.750 55.000 6.53 3.0 0.00 3.02 R
7577 7828 0.031585 TGCAGGACGCGTATATGGTC 59.968 55.000 13.97 0.0 46.97 4.02 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
56 57 8.801715 TTAGTACAAAGTTAGTACGAAGTTGG 57.198 34.615 9.24 8.92 44.92 3.77
57 58 6.218746 AGTACAAAGTTAGTACGAAGTTGGG 58.781 40.000 13.37 9.80 44.92 4.12
58 59 5.027293 ACAAAGTTAGTACGAAGTTGGGT 57.973 39.130 13.37 10.29 37.78 4.51
59 60 5.052481 ACAAAGTTAGTACGAAGTTGGGTC 58.948 41.667 13.37 0.00 37.78 4.46
61 62 5.479124 AAGTTAGTACGAAGTTGGGTCAT 57.521 39.130 7.86 0.00 37.78 3.06
62 63 5.069501 AGTTAGTACGAAGTTGGGTCATC 57.930 43.478 0.00 0.00 37.78 2.92
63 64 4.771054 AGTTAGTACGAAGTTGGGTCATCT 59.229 41.667 0.00 0.00 37.78 2.90
64 65 5.948162 AGTTAGTACGAAGTTGGGTCATCTA 59.052 40.000 0.00 0.00 37.78 1.98
66 67 5.934402 AGTACGAAGTTGGGTCATCTATT 57.066 39.130 0.00 0.00 37.78 1.73
68 69 6.708285 AGTACGAAGTTGGGTCATCTATTTT 58.292 36.000 0.00 0.00 37.78 1.82
69 70 5.880054 ACGAAGTTGGGTCATCTATTTTG 57.120 39.130 0.00 0.00 37.78 2.44
70 71 4.700213 ACGAAGTTGGGTCATCTATTTTGG 59.300 41.667 0.00 0.00 37.78 3.28
71 72 4.941263 CGAAGTTGGGTCATCTATTTTGGA 59.059 41.667 0.00 0.00 0.00 3.53
72 73 5.414454 CGAAGTTGGGTCATCTATTTTGGAA 59.586 40.000 0.00 0.00 0.00 3.53
73 74 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
74 75 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
75 76 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
76 77 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
78 79 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
79 80 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
80 81 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
92 93 1.108132 CGGAGGGAGTAGGTAGGTGC 61.108 65.000 0.00 0.00 0.00 5.01
96 97 1.076485 GGAGTAGGTAGGTGCGGGA 60.076 63.158 0.00 0.00 0.00 5.14
312 319 5.864474 GCCAAGATCCATATACTACAACGAG 59.136 44.000 0.00 0.00 0.00 4.18
367 374 7.898309 GGCAATATCAAAACTAAGCGTATATCG 59.102 37.037 0.00 0.00 43.12 2.92
368 375 7.898309 GCAATATCAAAACTAAGCGTATATCGG 59.102 37.037 0.00 0.00 40.26 4.18
471 478 9.935682 ATAAATTTACAGCTGACAATTCATACG 57.064 29.630 23.35 0.00 0.00 3.06
532 540 4.510571 ACCCGCTGGTATAGTAAAAACAG 58.489 43.478 0.00 0.00 45.45 3.16
632 640 0.322008 CAAACAGACCTCCTCCTGCC 60.322 60.000 0.00 0.00 33.90 4.85
660 668 0.179936 CCATCAGCTCTTCCTCCACC 59.820 60.000 0.00 0.00 0.00 4.61
663 671 0.178891 TCAGCTCTTCCTCCACCCTT 60.179 55.000 0.00 0.00 0.00 3.95
664 672 0.695347 CAGCTCTTCCTCCACCCTTT 59.305 55.000 0.00 0.00 0.00 3.11
665 673 0.695347 AGCTCTTCCTCCACCCTTTG 59.305 55.000 0.00 0.00 0.00 2.77
667 675 0.322906 CTCTTCCTCCACCCTTTGCC 60.323 60.000 0.00 0.00 0.00 4.52
1216 1241 3.730061 GCATGAAGAACTTGGCTCGATTG 60.730 47.826 0.00 0.00 0.00 2.67
1322 1361 8.990163 TGAGGTTAGAGAAATTTTGGTAGTTT 57.010 30.769 0.00 0.00 0.00 2.66
1385 1424 4.141801 TGGCCTGTAGTATATTGGACACAC 60.142 45.833 3.32 0.00 30.61 3.82
1458 1497 9.051679 AGGGTTTGAATTTAAGTACAAAAATGC 57.948 29.630 0.00 0.00 34.76 3.56
1459 1498 9.051679 GGGTTTGAATTTAAGTACAAAAATGCT 57.948 29.630 10.58 0.00 34.76 3.79
1581 1635 2.479566 AGAAGCGCTGATGGAAAGAA 57.520 45.000 12.58 0.00 0.00 2.52
1621 1676 5.872963 TGTTATAGTAGAGCCATCTCCGTA 58.127 41.667 0.00 0.00 40.22 4.02
1765 1821 9.226345 GCACAATACTGCATCTATAAAAAGTTC 57.774 33.333 0.00 0.00 37.11 3.01
1809 1865 5.712152 ACTTGTATTTTCCAGAAAGCCAG 57.288 39.130 0.00 0.00 0.00 4.85
1814 1870 2.452600 TTTCCAGAAAGCCAGTGGTT 57.547 45.000 11.74 0.44 32.73 3.67
1877 1933 3.969981 GCAATTGCAAAAATTCACACTGC 59.030 39.130 25.36 0.00 41.59 4.40
1914 1973 8.034058 AGTTTTCTAGCACATGAGTATTTGTC 57.966 34.615 0.00 0.00 0.00 3.18
2004 2064 7.414222 ACATTCTATTGTCATGCAAGGAAAT 57.586 32.000 16.42 0.00 40.86 2.17
2006 2066 8.970020 ACATTCTATTGTCATGCAAGGAAATTA 58.030 29.630 16.42 0.00 40.86 1.40
2007 2067 9.459640 CATTCTATTGTCATGCAAGGAAATTAG 57.540 33.333 16.42 0.00 40.86 1.73
2008 2068 7.031226 TCTATTGTCATGCAAGGAAATTAGC 57.969 36.000 0.00 0.00 40.86 3.09
2087 2151 7.980099 CGTCCTGTACCTTTTAAGATATCAACT 59.020 37.037 5.32 0.00 0.00 3.16
2093 2157 9.761504 GTACCTTTTAAGATATCAACTACTCCC 57.238 37.037 5.32 0.00 0.00 4.30
2094 2158 8.625467 ACCTTTTAAGATATCAACTACTCCCT 57.375 34.615 5.32 0.00 0.00 4.20
2095 2159 8.706521 ACCTTTTAAGATATCAACTACTCCCTC 58.293 37.037 5.32 0.00 0.00 4.30
2096 2160 8.151596 CCTTTTAAGATATCAACTACTCCCTCC 58.848 40.741 5.32 0.00 0.00 4.30
2097 2161 6.896021 TTAAGATATCAACTACTCCCTCCG 57.104 41.667 5.32 0.00 0.00 4.63
2098 2162 4.456662 AGATATCAACTACTCCCTCCGT 57.543 45.455 5.32 0.00 0.00 4.69
2099 2163 4.400120 AGATATCAACTACTCCCTCCGTC 58.600 47.826 5.32 0.00 0.00 4.79
2100 2164 1.777941 ATCAACTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
2101 2165 0.324091 TCAACTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
2102 2166 0.613853 CAACTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
2103 2167 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2104 2168 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2105 2169 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2106 2170 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2107 2171 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2108 2172 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2109 2173 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2110 2174 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2111 2175 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2112 2176 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2113 2177 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2115 2179 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2116 2180 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2117 2181 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2118 2182 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2119 2183 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2162 2226 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2163 2227 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2164 2228 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2165 2229 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2166 2230 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2167 2231 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2216 2280 6.116126 ACAGTAACATAGCTTCCTCCATTTC 58.884 40.000 0.00 0.00 0.00 2.17
2309 2373 4.340950 TCCTTTTGGTCCAAAGTGATGTTC 59.659 41.667 16.47 0.00 41.38 3.18
2383 2447 9.573133 AGTAAGATCAGTTTGTTTTGAAAACAG 57.427 29.630 20.98 11.46 39.49 3.16
2397 2461 6.928979 TTGAAAACAGATTCGTAGGTTCAA 57.071 33.333 0.00 0.00 32.83 2.69
2617 2681 4.833478 ATAGAAGGTGCAATCACTGACT 57.167 40.909 0.00 0.00 42.72 3.41
2671 2735 1.672881 GCAGCAGGACTTTATTGCGAT 59.327 47.619 0.00 0.00 42.47 4.58
2779 2843 5.476945 TCCAAAGGCTTTTCAACCTAAGATC 59.523 40.000 10.36 0.00 34.31 2.75
2795 2859 5.865552 CCTAAGATCGAAAACGTTCCAAGTA 59.134 40.000 0.00 0.00 0.00 2.24
2809 2873 4.778534 TCCAAGTACTCTTAGTGTTCGG 57.221 45.455 0.00 0.00 32.07 4.30
2837 2901 7.404980 AGGTACATTCTTTCCCCTTGTAGAATA 59.595 37.037 0.00 0.00 35.70 1.75
2927 2991 4.712476 AGAAACATCAGTTCTGCACTTCT 58.288 39.130 0.00 0.00 36.84 2.85
2931 2995 3.324846 ACATCAGTTCTGCACTTCTACCA 59.675 43.478 0.00 0.00 30.92 3.25
2954 3018 7.148306 ACCATCGTTTTTATGATGTTCCTACAC 60.148 37.037 0.00 0.00 40.25 2.90
2993 3058 7.041644 TGTGTTACAACTTACAAGGTATGCTTC 60.042 37.037 0.00 0.00 0.00 3.86
3016 3081 1.308998 ACACGCCTATTAAGCATGCC 58.691 50.000 15.66 0.00 0.00 4.40
3049 3114 7.848128 TGTAAGTTCGAAGGAATCCTAGAATT 58.152 34.615 18.51 13.65 34.63 2.17
3102 3167 8.148999 ACTTAAAGAACCTATTCAAGAACGAGT 58.851 33.333 0.00 0.00 37.29 4.18
3103 3168 9.635520 CTTAAAGAACCTATTCAAGAACGAGTA 57.364 33.333 0.00 0.00 37.29 2.59
3105 3170 7.886405 AAGAACCTATTCAAGAACGAGTAAC 57.114 36.000 0.00 0.00 37.29 2.50
3106 3171 6.989659 AGAACCTATTCAAGAACGAGTAACA 58.010 36.000 0.00 0.00 37.29 2.41
3107 3172 7.612677 AGAACCTATTCAAGAACGAGTAACAT 58.387 34.615 0.00 0.00 37.29 2.71
3108 3173 7.545965 AGAACCTATTCAAGAACGAGTAACATG 59.454 37.037 0.00 0.00 37.29 3.21
3109 3174 6.931838 ACCTATTCAAGAACGAGTAACATGA 58.068 36.000 0.00 0.00 0.00 3.07
3110 3175 7.036220 ACCTATTCAAGAACGAGTAACATGAG 58.964 38.462 0.00 0.00 0.00 2.90
3111 3176 7.093902 ACCTATTCAAGAACGAGTAACATGAGA 60.094 37.037 0.00 0.00 0.00 3.27
3112 3177 7.923344 CCTATTCAAGAACGAGTAACATGAGAT 59.077 37.037 0.00 0.00 0.00 2.75
3113 3178 9.307121 CTATTCAAGAACGAGTAACATGAGATT 57.693 33.333 0.00 0.00 0.00 2.40
3153 3218 7.585210 CGAACATGAGCATATTTGTATGAACTG 59.415 37.037 0.00 0.00 0.00 3.16
3203 3268 7.016694 TTGATCAACAAAGCACATTGCATGAT 61.017 34.615 3.38 13.58 40.21 2.45
3405 3575 6.560253 ACTATTAACCAAGTGCAGAAACTG 57.440 37.500 0.00 0.00 34.12 3.16
3650 3820 0.536460 TGAAAACCGGCTCCACTTCC 60.536 55.000 0.00 0.00 0.00 3.46
3679 3849 4.681421 CACATCTGTGCCAGACGT 57.319 55.556 7.00 3.01 43.63 4.34
3692 3862 4.092968 GTGCCAGACGTTTTATTCCTAGTG 59.907 45.833 0.00 0.00 0.00 2.74
3730 3900 0.179020 GATGATCATTCCCGTGCCCA 60.179 55.000 10.14 0.00 0.00 5.36
3752 3922 0.172803 GGTGTGTAGGCGACCAGTAG 59.827 60.000 0.00 0.00 0.00 2.57
3835 4005 1.067295 AGGCCATGAGTCACTTTCCA 58.933 50.000 5.01 0.00 0.00 3.53
3892 4070 6.303839 TGGGGCATTATACTCTACCAATTTC 58.696 40.000 0.00 0.00 0.00 2.17
3906 4084 5.310720 ACCAATTTCTTCATTACCGAAGC 57.689 39.130 0.00 0.00 41.84 3.86
3931 4109 5.163622 CCAACATTATCAGTTCCGCTTCATT 60.164 40.000 0.00 0.00 0.00 2.57
3933 4111 4.336433 ACATTATCAGTTCCGCTTCATTGG 59.664 41.667 0.00 0.00 0.00 3.16
3966 4144 4.305539 TGATTGCTTCCTTTCAGATGGA 57.694 40.909 0.00 0.00 0.00 3.41
3972 4150 1.821216 TCCTTTCAGATGGAAACGCC 58.179 50.000 0.00 0.00 40.51 5.68
4549 4729 5.825151 AGAGGTAATTTCAAGATTAGCTGGC 59.175 40.000 12.43 2.25 45.37 4.85
4645 4825 6.486993 GGTAGTATCCTTTTATTTCTGCCTGG 59.513 42.308 0.00 0.00 0.00 4.45
4767 4953 3.007614 TGTTCTAGGCTAACCACTTGGAC 59.992 47.826 1.14 0.00 39.06 4.02
4873 5059 3.874392 ATGCTGGACTGGTTAATTTGC 57.126 42.857 0.00 0.00 0.00 3.68
5131 5317 6.347644 CGAAAGAACAGATGTCAATGCAGTTA 60.348 38.462 0.00 0.00 0.00 2.24
5167 5353 7.639039 CCTCTTTCGTGCATTGCTTATTAATA 58.361 34.615 10.49 0.00 0.00 0.98
5353 5539 0.530744 ATTCCGTTAGCGAGCACTCA 59.469 50.000 0.00 0.00 41.33 3.41
5373 5559 7.182761 CACTCAAATTAGGCGAACTATTCAAG 58.817 38.462 0.00 0.00 0.00 3.02
5408 5594 9.797556 GTGAAAAGATAAAACTACCTTTGTGTT 57.202 29.630 0.00 0.00 0.00 3.32
5435 5621 6.540914 AGGAACAGAACATCTTTTCGTTTGTA 59.459 34.615 1.46 0.00 34.81 2.41
5583 5781 8.749026 AGAACTTCTGAGATATCATTTGCATT 57.251 30.769 5.32 0.00 0.00 3.56
5655 5853 8.846943 TGTAGAAGAATAACTTTGCTTCATCA 57.153 30.769 0.00 0.00 39.27 3.07
5696 5894 5.888412 ACGATCACTTTGTTGCAAATTTC 57.112 34.783 0.00 0.00 0.00 2.17
5701 5899 6.419980 TCACTTTGTTGCAAATTTCAAAGG 57.580 33.333 29.07 21.83 45.97 3.11
5769 5970 7.933577 TGTCGATCCAGATTTATTTTGAGCTAT 59.066 33.333 0.00 0.00 0.00 2.97
6043 6244 5.122869 CACCGCATTTGGATCAGATTATAGG 59.877 44.000 0.00 0.00 0.00 2.57
6065 6266 5.482878 AGGACTTCATTTCCATCAGCATTTT 59.517 36.000 0.00 0.00 35.33 1.82
6223 6424 6.037940 CCTTCCATATTGATGACTTGACACTG 59.962 42.308 0.00 0.00 34.73 3.66
6238 6439 6.040729 ACTTGACACTGATCTGAGATATCCAG 59.959 42.308 6.60 12.51 0.00 3.86
6256 6457 2.812011 CCAGCTTGTTACAGTTGGGTAC 59.188 50.000 8.81 0.00 40.59 3.34
6263 6464 4.207955 TGTTACAGTTGGGTACATTGCAA 58.792 39.130 0.00 0.00 0.00 4.08
6310 6511 4.821260 ACTTGGTTTTCAAATTGGCCATTC 59.179 37.500 6.09 0.00 34.56 2.67
6315 6516 7.056635 TGGTTTTCAAATTGGCCATTCTAAAA 58.943 30.769 6.09 7.80 0.00 1.52
6395 6596 7.054855 GATGAAATCAGAACTACACACAGTC 57.945 40.000 0.00 0.00 44.70 3.51
6397 6598 6.216569 TGAAATCAGAACTACACACAGTCTC 58.783 40.000 0.00 0.00 0.00 3.36
6442 6643 1.269958 TCATGACTCCAGGTGGTGAG 58.730 55.000 5.09 0.00 36.34 3.51
6456 6657 1.011451 GGTGAGCTCTTGTCGAGTGC 61.011 60.000 16.19 6.08 43.51 4.40
6552 6753 1.133790 GCATGATGTTTCAGCCCAGAC 59.866 52.381 0.00 0.00 34.73 3.51
6580 6816 8.367156 AGATACACTGTAAACCCTAACGTTTTA 58.633 33.333 5.91 0.00 37.20 1.52
6614 6860 4.949238 TCACATGTACTTGCAGCCAATAAT 59.051 37.500 8.58 0.00 0.00 1.28
6644 6890 2.636647 TGACAGAAGCCAACACATCA 57.363 45.000 0.00 0.00 0.00 3.07
6714 6960 4.717313 GCCCCGGTGTGAGTTCCC 62.717 72.222 0.00 0.00 0.00 3.97
6785 7031 0.969894 CGAGAACAAGTGACCCCTCT 59.030 55.000 0.00 0.00 0.00 3.69
6832 7079 0.440371 GTCAGCGTGACTGCTAAAGC 59.560 55.000 9.86 0.00 45.23 3.51
6981 7229 7.862675 AGGTGTAAAAGTAGGCAAAGATAGAT 58.137 34.615 0.00 0.00 0.00 1.98
7084 7332 0.257328 TTTGGAGTTGGTGGTGAGCA 59.743 50.000 0.00 0.00 0.00 4.26
7087 7335 1.961277 GAGTTGGTGGTGAGCACGG 60.961 63.158 8.82 0.00 0.00 4.94
7170 7418 7.396339 TGTTCTTATACCTGTTTCTCTGCTAGA 59.604 37.037 0.00 0.00 0.00 2.43
7254 7502 8.893727 AGCTGTTTCGCAAATTAAGTTATCTAT 58.106 29.630 0.00 0.00 0.00 1.98
7341 7591 1.080366 TCGGCGTGAACGTTAGCAT 60.080 52.632 19.70 0.00 42.22 3.79
7380 7630 1.597854 CTCCAAGCCTCGCACAACA 60.598 57.895 0.00 0.00 0.00 3.33
7418 7668 2.097825 GGCAACATGAGAGCCTGAATT 58.902 47.619 16.71 0.00 44.92 2.17
7425 7675 1.134699 TGAGAGCCTGAATTACGCTGG 60.135 52.381 0.00 0.00 31.61 4.85
7429 7679 1.663695 GCCTGAATTACGCTGGCTTA 58.336 50.000 0.00 0.00 44.20 3.09
7445 7695 2.738314 GGCTTAGCACAAAAATTGCCTG 59.262 45.455 6.53 0.00 41.18 4.85
7475 7725 3.057245 TGCACATCCTATACTCGAGATGC 60.057 47.826 21.68 13.33 39.79 3.91
7484 7734 4.640789 ATACTCGAGATGCGTTTTCTCT 57.359 40.909 21.68 0.00 41.80 3.10
7489 7739 2.923655 CGAGATGCGTTTTCTCTGCTTA 59.076 45.455 8.90 0.00 37.96 3.09
7490 7740 3.367932 CGAGATGCGTTTTCTCTGCTTAA 59.632 43.478 8.90 0.00 37.96 1.85
7491 7741 4.491602 CGAGATGCGTTTTCTCTGCTTAAG 60.492 45.833 0.00 0.00 37.96 1.85
7586 7837 9.762933 ATTTGGTGCAAAAATATGACCATATAC 57.237 29.630 6.80 0.00 36.90 1.47
7587 7838 6.964908 TGGTGCAAAAATATGACCATATACG 58.035 36.000 3.22 0.00 33.86 3.06
7624 7875 3.110358 GCCAAGTTGTTACGGTTTGAAC 58.890 45.455 1.45 0.00 0.00 3.18
7662 7913 3.383620 TTCATGCTGCACCGAATTTTT 57.616 38.095 3.57 0.00 0.00 1.94
7713 7965 7.254137 GGTTGTATTTTTGCACCAAATTTTGT 58.746 30.769 8.26 0.00 33.19 2.83
7726 7978 8.647226 GCACCAAATTTTGTATGAATAGTTGTC 58.353 33.333 8.26 0.00 0.00 3.18
7745 7997 4.383173 TGTCATAGCAGCATGATGTTAGG 58.617 43.478 13.32 12.84 39.69 2.69
7760 8012 5.906113 ATGTTAGGCATCTCGAGTATAGG 57.094 43.478 13.13 0.00 30.67 2.57
7761 8013 4.079970 TGTTAGGCATCTCGAGTATAGGG 58.920 47.826 13.13 0.00 0.00 3.53
7762 8014 1.551452 AGGCATCTCGAGTATAGGGC 58.449 55.000 13.13 7.53 0.00 5.19
7763 8015 0.171455 GGCATCTCGAGTATAGGGCG 59.829 60.000 13.13 0.00 0.00 6.13
7764 8016 1.166129 GCATCTCGAGTATAGGGCGA 58.834 55.000 13.13 0.00 0.00 5.54
7769 8021 1.880271 TCGAGTATAGGGCGAGAGTG 58.120 55.000 0.00 0.00 0.00 3.51
7770 8022 0.875728 CGAGTATAGGGCGAGAGTGG 59.124 60.000 0.00 0.00 0.00 4.00
7771 8023 1.542767 CGAGTATAGGGCGAGAGTGGA 60.543 57.143 0.00 0.00 0.00 4.02
7772 8024 1.881324 GAGTATAGGGCGAGAGTGGAC 59.119 57.143 0.00 0.00 0.00 4.02
7773 8025 1.495574 AGTATAGGGCGAGAGTGGACT 59.504 52.381 0.00 0.00 0.00 3.85
7774 8026 1.881324 GTATAGGGCGAGAGTGGACTC 59.119 57.143 0.00 0.00 43.17 3.36
7783 8035 1.304217 GAGTGGACTCGGGTGGAGA 60.304 63.158 0.00 0.00 46.23 3.71
7784 8036 0.898789 GAGTGGACTCGGGTGGAGAA 60.899 60.000 0.00 0.00 46.23 2.87
7785 8037 0.252284 AGTGGACTCGGGTGGAGAAT 60.252 55.000 0.00 0.00 46.23 2.40
7786 8038 1.006758 AGTGGACTCGGGTGGAGAATA 59.993 52.381 0.00 0.00 46.23 1.75
7787 8039 2.040178 GTGGACTCGGGTGGAGAATAT 58.960 52.381 0.00 0.00 46.23 1.28
7788 8040 2.036089 GTGGACTCGGGTGGAGAATATC 59.964 54.545 0.00 0.00 46.23 1.63
7789 8041 2.091278 TGGACTCGGGTGGAGAATATCT 60.091 50.000 0.00 0.00 46.23 1.98
7790 8042 2.297597 GGACTCGGGTGGAGAATATCTG 59.702 54.545 0.00 0.00 46.23 2.90
7791 8043 1.689273 ACTCGGGTGGAGAATATCTGC 59.311 52.381 0.00 0.00 46.23 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.867403 CCCAACTTCGTACTAACTTTGTACTAA 59.133 37.037 10.52 6.27 38.39 2.24
32 33 7.014230 ACCCAACTTCGTACTAACTTTGTACTA 59.986 37.037 10.52 0.00 38.39 1.82
33 34 6.183360 ACCCAACTTCGTACTAACTTTGTACT 60.183 38.462 10.52 0.00 38.39 2.73
34 35 5.985530 ACCCAACTTCGTACTAACTTTGTAC 59.014 40.000 4.07 4.07 37.50 2.90
36 37 5.027293 ACCCAACTTCGTACTAACTTTGT 57.973 39.130 0.00 0.00 0.00 2.83
37 38 5.051816 TGACCCAACTTCGTACTAACTTTG 58.948 41.667 0.00 0.00 0.00 2.77
38 39 5.280654 TGACCCAACTTCGTACTAACTTT 57.719 39.130 0.00 0.00 0.00 2.66
40 41 4.771054 AGATGACCCAACTTCGTACTAACT 59.229 41.667 0.00 0.00 0.00 2.24
41 42 5.069501 AGATGACCCAACTTCGTACTAAC 57.930 43.478 0.00 0.00 0.00 2.34
42 43 7.414222 AATAGATGACCCAACTTCGTACTAA 57.586 36.000 0.00 0.00 0.00 2.24
43 44 7.414222 AAATAGATGACCCAACTTCGTACTA 57.586 36.000 0.00 0.00 0.00 1.82
44 45 5.934402 AATAGATGACCCAACTTCGTACT 57.066 39.130 0.00 0.00 0.00 2.73
45 46 6.183360 CCAAAATAGATGACCCAACTTCGTAC 60.183 42.308 0.00 0.00 0.00 3.67
47 48 4.700213 CCAAAATAGATGACCCAACTTCGT 59.300 41.667 0.00 0.00 0.00 3.85
49 50 6.621613 GTTCCAAAATAGATGACCCAACTTC 58.378 40.000 0.00 0.00 0.00 3.01
50 51 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
51 52 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
52 53 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
54 55 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
55 56 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
56 57 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
57 58 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
58 59 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
59 60 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
61 62 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
62 63 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
63 64 3.453353 CCTACTCCCTCCGTTCCAAAATA 59.547 47.826 0.00 0.00 0.00 1.40
64 65 2.238898 CCTACTCCCTCCGTTCCAAAAT 59.761 50.000 0.00 0.00 0.00 1.82
66 67 1.272807 CCTACTCCCTCCGTTCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
68 69 1.002069 TACCTACTCCCTCCGTTCCA 58.998 55.000 0.00 0.00 0.00 3.53
69 70 1.689984 CTACCTACTCCCTCCGTTCC 58.310 60.000 0.00 0.00 0.00 3.62
70 71 1.064091 ACCTACCTACTCCCTCCGTTC 60.064 57.143 0.00 0.00 0.00 3.95
71 72 1.006020 ACCTACCTACTCCCTCCGTT 58.994 55.000 0.00 0.00 0.00 4.44
72 73 0.258194 CACCTACCTACTCCCTCCGT 59.742 60.000 0.00 0.00 0.00 4.69
73 74 1.108132 GCACCTACCTACTCCCTCCG 61.108 65.000 0.00 0.00 0.00 4.63
74 75 1.108132 CGCACCTACCTACTCCCTCC 61.108 65.000 0.00 0.00 0.00 4.30
75 76 1.108132 CCGCACCTACCTACTCCCTC 61.108 65.000 0.00 0.00 0.00 4.30
76 77 1.076192 CCGCACCTACCTACTCCCT 60.076 63.158 0.00 0.00 0.00 4.20
78 79 0.685458 TTCCCGCACCTACCTACTCC 60.685 60.000 0.00 0.00 0.00 3.85
79 80 1.188863 TTTCCCGCACCTACCTACTC 58.811 55.000 0.00 0.00 0.00 2.59
80 81 1.648116 TTTTCCCGCACCTACCTACT 58.352 50.000 0.00 0.00 0.00 2.57
101 102 5.538849 TGCCATTATGCATCATTGTTCAT 57.461 34.783 0.19 0.00 36.04 2.57
102 103 5.340439 TTGCCATTATGCATCATTGTTCA 57.660 34.783 0.19 0.00 41.70 3.18
138 140 4.927422 TCCCAGAAACGAACAACAAATTC 58.073 39.130 0.00 0.00 0.00 2.17
269 275 2.301009 GGCCATTGATTTCCCATCCATC 59.699 50.000 0.00 0.00 0.00 3.51
312 319 6.769608 ATTTTCCGCTGAAACTTTCAAATC 57.230 33.333 2.45 0.00 40.12 2.17
532 540 2.599848 CGTGCCGATGCTGCTTATTTAC 60.600 50.000 0.00 0.00 38.71 2.01
632 640 2.749044 AGCTGATGGGCAACGCAG 60.749 61.111 0.00 0.00 35.02 5.18
667 675 4.179599 GGGAGGAGGAGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
1012 1025 3.289834 CTGGGCGTTGTGCTGCTT 61.290 61.111 0.00 0.00 45.43 3.91
1086 1108 2.725312 GGCCGAGTGCATCAGAGGA 61.725 63.158 0.00 0.00 43.89 3.71
1087 1109 2.202987 GGCCGAGTGCATCAGAGG 60.203 66.667 0.00 0.00 43.89 3.69
1088 1110 1.521010 CTGGCCGAGTGCATCAGAG 60.521 63.158 0.00 0.00 43.89 3.35
1089 1111 2.580815 CTGGCCGAGTGCATCAGA 59.419 61.111 0.00 0.00 43.89 3.27
1090 1112 2.513204 CCTGGCCGAGTGCATCAG 60.513 66.667 0.00 0.00 43.89 2.90
1114 1139 3.707793 CTTACATAGGCGTGAAGGAGAC 58.292 50.000 0.00 0.00 0.00 3.36
1216 1241 6.077197 GGCAAAATAAAATTCAAAACGCCTC 58.923 36.000 0.00 0.00 0.00 4.70
1267 1294 2.119495 TCCTTCCTGGCTCCATAAGAC 58.881 52.381 10.85 0.00 35.26 3.01
1268 1295 2.568546 TCCTTCCTGGCTCCATAAGA 57.431 50.000 10.85 0.00 35.26 2.10
1322 1361 5.937540 ACGTCCACAAACATATCAAATCTCA 59.062 36.000 0.00 0.00 0.00 3.27
1336 1375 2.299013 AGACTAGCATCACGTCCACAAA 59.701 45.455 0.00 0.00 0.00 2.83
1385 1424 2.417924 CCACAGCCTTGTCACTAGCTAG 60.418 54.545 19.44 19.44 34.62 3.42
1458 1497 7.041721 TCAATGCATACCACTTCAAGTAGTAG 58.958 38.462 0.00 0.00 26.59 2.57
1459 1498 6.941857 TCAATGCATACCACTTCAAGTAGTA 58.058 36.000 0.00 0.00 27.62 1.82
1460 1499 5.804639 TCAATGCATACCACTTCAAGTAGT 58.195 37.500 0.00 0.00 0.00 2.73
1621 1676 8.670521 ATTTTGTTTCCCTTAAGAATGGAGAT 57.329 30.769 3.36 0.00 0.00 2.75
1650 1705 7.604927 TGGTTCTACAAGTACCAATAACATCAC 59.395 37.037 3.24 0.00 41.75 3.06
1798 1854 1.691196 TTCAACCACTGGCTTTCTGG 58.309 50.000 0.00 0.00 0.00 3.86
1809 1865 7.227910 TGGAGTAACACTCTTAATTTCAACCAC 59.772 37.037 6.30 0.00 44.46 4.16
1814 1870 6.833041 TGGTGGAGTAACACTCTTAATTTCA 58.167 36.000 6.30 0.00 44.46 2.69
1868 1924 2.638480 ACAGCTTTAGGCAGTGTGAA 57.362 45.000 0.00 0.00 44.79 3.18
1877 1933 4.997395 TGCTAGAAAACTCACAGCTTTAGG 59.003 41.667 0.00 0.00 33.38 2.69
1893 1949 9.151471 GTAAAGACAAATACTCATGTGCTAGAA 57.849 33.333 0.00 0.00 0.00 2.10
2004 2064 8.815141 TTAGTTAATCACTAACACAACGCTAA 57.185 30.769 0.00 0.00 42.19 3.09
2006 2066 7.440255 AGTTTAGTTAATCACTAACACAACGCT 59.560 33.333 0.00 0.00 45.97 5.07
2007 2067 7.529519 CAGTTTAGTTAATCACTAACACAACGC 59.470 37.037 0.00 0.00 45.97 4.84
2008 2068 8.545420 ACAGTTTAGTTAATCACTAACACAACG 58.455 33.333 0.00 0.00 45.97 4.10
2087 2151 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2088 2152 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2089 2153 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2090 2154 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2091 2155 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2092 2156 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2093 2157 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2094 2158 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2137 2201 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2138 2202 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2139 2203 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2140 2204 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2141 2205 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2143 2207 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2144 2208 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2145 2209 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2146 2210 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2147 2211 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2148 2212 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2149 2213 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2150 2214 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2151 2215 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2152 2216 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
2153 2217 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
2154 2218 1.424302 CTATCTACTCCCTCCGTCCCA 59.576 57.143 0.00 0.00 0.00 4.37
2155 2219 1.272037 CCTATCTACTCCCTCCGTCCC 60.272 61.905 0.00 0.00 0.00 4.46
2156 2220 1.704070 TCCTATCTACTCCCTCCGTCC 59.296 57.143 0.00 0.00 0.00 4.79
2157 2221 3.505480 TTCCTATCTACTCCCTCCGTC 57.495 52.381 0.00 0.00 0.00 4.79
2158 2222 5.312708 TCTTATTCCTATCTACTCCCTCCGT 59.687 44.000 0.00 0.00 0.00 4.69
2159 2223 5.817784 TCTTATTCCTATCTACTCCCTCCG 58.182 45.833 0.00 0.00 0.00 4.63
2160 2224 7.415086 TCATCTTATTCCTATCTACTCCCTCC 58.585 42.308 0.00 0.00 0.00 4.30
2161 2225 9.131791 GATCATCTTATTCCTATCTACTCCCTC 57.868 40.741 0.00 0.00 0.00 4.30
2162 2226 8.628281 TGATCATCTTATTCCTATCTACTCCCT 58.372 37.037 0.00 0.00 0.00 4.20
2163 2227 8.830915 TGATCATCTTATTCCTATCTACTCCC 57.169 38.462 0.00 0.00 0.00 4.30
2204 2268 2.310052 AGGACAAGGGAAATGGAGGAAG 59.690 50.000 0.00 0.00 0.00 3.46
2216 2280 4.778213 TCTCCATTAATGAGGACAAGGG 57.222 45.455 17.23 0.00 0.00 3.95
2309 2373 6.197096 GCTTCATATTTTTGCCAATGACTACG 59.803 38.462 0.00 0.00 0.00 3.51
2383 2447 5.122396 AGCATGAAAGTTGAACCTACGAATC 59.878 40.000 0.00 0.00 0.00 2.52
2397 2461 7.442062 CCCAAAATAAAACAAGAGCATGAAAGT 59.558 33.333 0.00 0.00 0.00 2.66
2671 2735 4.056740 CACATTGTTTACAATTGCAGCCA 58.943 39.130 5.05 0.00 43.48 4.75
2779 2843 5.689068 ACTAAGAGTACTTGGAACGTTTTCG 59.311 40.000 0.46 0.00 41.77 3.46
2795 2859 4.147321 TGTACCTTCCGAACACTAAGAGT 58.853 43.478 0.00 0.00 0.00 3.24
2809 2873 4.663334 ACAAGGGGAAAGAATGTACCTTC 58.337 43.478 2.91 2.91 36.25 3.46
2837 2901 9.448438 TCTACTGTTGTATGATGCATTTAAACT 57.552 29.630 0.00 0.00 0.00 2.66
2888 2952 9.681692 TGATGTTTCTTATGTGTCAAAATTCAG 57.318 29.630 0.00 0.00 0.00 3.02
2927 2991 8.041919 TGTAGGAACATCATAAAAACGATGGTA 58.958 33.333 0.00 0.00 39.65 3.25
2931 2995 6.814644 TCGTGTAGGAACATCATAAAAACGAT 59.185 34.615 0.00 0.00 38.08 3.73
2968 3033 6.796705 AGCATACCTTGTAAGTTGTAACAC 57.203 37.500 0.00 0.00 0.00 3.32
2985 3050 2.295253 AGGCGTGTACAGAAGCATAC 57.705 50.000 16.50 3.48 0.00 2.39
2993 3058 3.059597 GCATGCTTAATAGGCGTGTACAG 60.060 47.826 16.21 0.00 45.32 2.74
3016 3081 2.921754 CCTTCGAACTTACAGCCTTACG 59.078 50.000 0.00 0.00 0.00 3.18
3049 3114 0.994247 ATGGACTGTCCTTGGCATCA 59.006 50.000 26.03 5.09 37.46 3.07
3178 3243 4.056092 TGCAATGTGCTTTGTTGATCAA 57.944 36.364 3.38 3.38 45.31 2.57
3186 3251 7.297229 TCAAATAATCATGCAATGTGCTTTG 57.703 32.000 0.00 0.00 46.80 2.77
3638 3808 1.078848 CAAGGAGGAAGTGGAGCCG 60.079 63.158 0.00 0.00 0.00 5.52
3650 3820 2.030540 CACAGATGTGCCAAACAAGGAG 60.031 50.000 0.00 0.00 43.61 3.69
3679 3849 3.060736 TGCGTGGCACTAGGAATAAAA 57.939 42.857 16.72 0.00 31.71 1.52
3692 3862 2.830285 AAACAGACCGTTGCGTGGC 61.830 57.895 0.00 0.00 38.07 5.01
3730 3900 0.034896 CTGGTCGCCTACACACCTTT 59.965 55.000 0.00 0.00 0.00 3.11
3752 3922 3.248266 GACTGTTGCAATGAAATCTGCC 58.752 45.455 0.59 0.00 37.79 4.85
3892 4070 2.432444 TGTTGGGCTTCGGTAATGAAG 58.568 47.619 0.00 0.00 46.47 3.02
3906 4084 2.643551 AGCGGAACTGATAATGTTGGG 58.356 47.619 0.00 0.00 0.00 4.12
4002 4180 2.301346 GATTCCGGTTCAGGCATCAAT 58.699 47.619 0.00 0.00 34.68 2.57
4025 4203 2.789409 ACTAGATGGGCAGGACAAAC 57.211 50.000 0.00 0.00 0.00 2.93
4549 4729 2.564771 TGAAGTTGCAGAACCAGTCAG 58.435 47.619 0.00 0.00 31.81 3.51
4645 4825 3.132111 ACCCAACTGGATTTTGACACAAC 59.868 43.478 0.00 0.00 37.39 3.32
4767 4953 2.289002 AGAAGAAGCAACTTGTGAAGCG 59.711 45.455 0.34 0.00 0.00 4.68
5046 5232 3.463944 GCTATAGAGCGGGCAGTAAAAA 58.536 45.455 3.21 0.00 39.39 1.94
5131 5317 3.313526 GCACGAAAGAGGCATCAATGTAT 59.686 43.478 0.00 0.00 35.60 2.29
5167 5353 7.255139 GCGGAGACCTATAAAAGTGCATATTTT 60.255 37.037 14.60 14.60 34.40 1.82
5353 5539 9.614792 AGAATACTTGAATAGTTCGCCTAATTT 57.385 29.630 0.00 0.00 38.33 1.82
5408 5594 4.703897 ACGAAAAGATGTTCTGTTCCTGA 58.296 39.130 0.00 0.00 37.42 3.86
5435 5621 9.942850 CCAGGTTTGGTTATAAGAAAAATCAAT 57.057 29.630 0.00 0.00 39.79 2.57
5445 5643 3.697166 AGGTGCCAGGTTTGGTTATAAG 58.303 45.455 0.00 0.00 46.80 1.73
5463 5661 8.927675 TGTCCAATTAACATGTTAGTTTAGGT 57.072 30.769 20.18 0.84 33.07 3.08
5583 5781 4.141344 ACCAGAAAACAGGTAGCCAAACTA 60.141 41.667 0.00 0.00 36.07 2.24
5617 5815 6.630444 ATTCTTCTACATGCAGGCATTTAG 57.370 37.500 17.27 17.27 37.79 1.85
5681 5879 9.437045 GTTATTCCTTTGAAATTTGCAACAAAG 57.563 29.630 23.43 23.43 44.65 2.77
5769 5970 6.207221 ATTGTCTGCAAATGTGAATGACACTA 59.793 34.615 5.80 0.00 42.61 2.74
5791 5992 7.708051 TCTCTACTTCCATCTCGACTTTATTG 58.292 38.462 0.00 0.00 0.00 1.90
6043 6244 8.192774 TCATAAAATGCTGATGGAAATGAAGTC 58.807 33.333 0.00 0.00 0.00 3.01
6065 6266 2.961741 GCTCTGGAGTGTCCTGATCATA 59.038 50.000 0.00 0.00 42.46 2.15
6223 6424 6.753180 TGTAACAAGCTGGATATCTCAGATC 58.247 40.000 19.48 7.59 34.36 2.75
6238 6439 4.794169 CAATGTACCCAACTGTAACAAGC 58.206 43.478 0.00 0.00 0.00 4.01
6256 6457 5.750067 GCATAGGGTGAATTTACTTGCAATG 59.250 40.000 0.00 0.00 0.00 2.82
6263 6464 6.884280 GCAATAGCATAGGGTGAATTTACT 57.116 37.500 0.00 0.00 41.58 2.24
6393 6594 5.683743 GCTCACTATCAACTGTTATCGAGAC 59.316 44.000 0.00 0.00 0.00 3.36
6394 6595 5.357032 TGCTCACTATCAACTGTTATCGAGA 59.643 40.000 0.00 0.00 0.00 4.04
6395 6596 5.582550 TGCTCACTATCAACTGTTATCGAG 58.417 41.667 0.00 0.00 0.00 4.04
6397 6598 5.582550 TCTGCTCACTATCAACTGTTATCG 58.417 41.667 0.00 0.00 0.00 2.92
6456 6657 5.107837 CGACTAGTATTATTCTTTGCGCCTG 60.108 44.000 4.18 0.00 0.00 4.85
6552 6753 8.219875 AAACGTTAGGGTTTACAGTGTATCTGG 61.220 40.741 0.00 0.00 39.16 3.86
6580 6816 4.292186 AGTACATGTGAGGCAACAGAAT 57.708 40.909 9.11 0.00 41.41 2.40
6614 6860 0.250234 CTTCTGTCATCCCGGCTGAA 59.750 55.000 6.53 3.00 0.00 3.02
6644 6890 2.203640 TCCATAGCGGGCTCGGAT 60.204 61.111 8.71 0.00 36.79 4.18
6668 6914 1.945819 GCTCCATGGTTTCTTCGAGCA 60.946 52.381 12.58 0.00 41.80 4.26
6754 7000 1.227292 GTTCTCGGATTCTCGGGGC 60.227 63.158 0.00 0.00 0.00 5.80
6785 7031 5.532406 GGCCTTCTAATCAACAATCTATGCA 59.468 40.000 0.00 0.00 0.00 3.96
6826 7073 3.335579 GTGGGTGAACCTACTGCTTTAG 58.664 50.000 8.62 0.00 43.32 1.85
6832 7079 2.536761 TTTCGTGGGTGAACCTACTG 57.463 50.000 13.34 7.67 44.32 2.74
6981 7229 2.727123 ACACAATCACAAGGGACACA 57.273 45.000 0.00 0.00 0.00 3.72
7052 7300 5.065090 ACCAACTCCAAACGTTACAAGTAAC 59.935 40.000 0.00 12.00 41.37 2.50
7053 7301 5.064962 CACCAACTCCAAACGTTACAAGTAA 59.935 40.000 0.00 0.00 0.00 2.24
7216 7464 3.001736 GCGAAACAGCTTCATCATCTACC 59.998 47.826 0.00 0.00 33.17 3.18
7287 7536 7.010183 GCAACAGTAATCGAACAGAAGCTTATA 59.990 37.037 0.00 0.00 0.00 0.98
7341 7591 2.093341 GGCTACCGGGTCTATTTTGACA 60.093 50.000 6.32 0.00 38.61 3.58
7380 7630 2.432874 TGCCAGTATACATGTTAGGCGT 59.567 45.455 2.30 0.00 43.35 5.68
7425 7675 3.392882 ACAGGCAATTTTTGTGCTAAGC 58.607 40.909 0.00 0.00 41.88 3.09
7429 7679 3.205338 GGAAACAGGCAATTTTTGTGCT 58.795 40.909 0.00 0.00 41.88 4.40
7445 7695 4.770795 AGTATAGGATGTGCAGTGGAAAC 58.229 43.478 0.00 0.00 0.00 2.78
7475 7725 5.692204 TGTCTCTTCTTAAGCAGAGAAAACG 59.308 40.000 28.93 8.11 43.88 3.60
7512 7762 5.472148 TGATGTTCATGCATGGTTCTTTTC 58.528 37.500 25.97 13.82 0.00 2.29
7577 7828 0.031585 TGCAGGACGCGTATATGGTC 59.968 55.000 13.97 0.00 46.97 4.02
7603 7854 3.110358 GTTCAAACCGTAACAACTTGGC 58.890 45.455 0.00 0.00 0.00 4.52
7624 7875 6.868864 AGCATGAAATAAGTACTAGTATGCCG 59.131 38.462 14.72 0.15 39.21 5.69
7679 7931 3.492756 GCAAAAATACAACCGTGCATGTT 59.507 39.130 4.96 1.81 32.29 2.71
7685 7937 3.085443 TGGTGCAAAAATACAACCGTG 57.915 42.857 0.00 0.00 0.00 4.94
7713 7965 7.444299 TCATGCTGCTATGACAACTATTCATA 58.556 34.615 0.00 0.00 35.31 2.15
7726 7978 3.143728 TGCCTAACATCATGCTGCTATG 58.856 45.455 0.00 5.03 0.00 2.23
7745 7997 1.166129 TCGCCCTATACTCGAGATGC 58.834 55.000 21.68 10.47 0.00 3.91
7756 8008 3.119225 GAGTCCACTCTCGCCCTAT 57.881 57.895 0.00 0.00 39.81 2.57
7757 8009 4.659986 GAGTCCACTCTCGCCCTA 57.340 61.111 0.00 0.00 39.81 3.53
7763 8015 1.304217 TCCACCCGAGTCCACTCTC 60.304 63.158 5.21 0.00 40.75 3.20
7764 8016 1.304547 CTCCACCCGAGTCCACTCT 60.305 63.158 5.21 0.00 40.75 3.24
7765 8017 0.898789 TTCTCCACCCGAGTCCACTC 60.899 60.000 0.00 0.00 39.84 3.51
7766 8018 0.252284 ATTCTCCACCCGAGTCCACT 60.252 55.000 0.00 0.00 39.84 4.00
7767 8019 1.481871 TATTCTCCACCCGAGTCCAC 58.518 55.000 0.00 0.00 39.84 4.02
7768 8020 2.091278 AGATATTCTCCACCCGAGTCCA 60.091 50.000 0.00 0.00 39.84 4.02
7769 8021 2.297597 CAGATATTCTCCACCCGAGTCC 59.702 54.545 0.00 0.00 39.84 3.85
7770 8022 2.288518 GCAGATATTCTCCACCCGAGTC 60.289 54.545 0.00 0.00 39.84 3.36
7771 8023 1.689273 GCAGATATTCTCCACCCGAGT 59.311 52.381 0.00 0.00 39.84 4.18
7772 8024 2.447244 GCAGATATTCTCCACCCGAG 57.553 55.000 0.00 0.00 40.30 4.63



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

AutoCloner maintained by Alex Coulton.