Multiple sequence alignment - TraesCS4A01G196500

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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 TraesCS4A01G196500 chr4A 100.000 2916 0 0 1 2916 478741792 478744707 0.000000e+00 5385.0
1 TraesCS4A01G196500 chr4A 94.245 139 6 1 286 424 112769338 112769474 8.190000e-51 211.0
2 TraesCS4A01G196500 chr4D 94.576 2415 92 20 426 2825 97421503 97419113 0.000000e+00 3698.0
3 TraesCS4A01G196500 chr4D 100.000 76 0 0 2820 2895 97419083 97419008 1.090000e-29 141.0
4 TraesCS4A01G196500 chr4B 92.785 2370 108 27 471 2825 139139299 139136978 0.000000e+00 3371.0
5 TraesCS4A01G196500 chr4B 88.079 151 11 3 153 297 139139785 139139636 3.860000e-39 172.0
6 TraesCS4A01G196500 chr4B 98.734 79 1 0 2820 2898 139136951 139136873 1.090000e-29 141.0
7 TraesCS4A01G196500 chr5B 75.395 760 123 46 1080 1821 232214152 232214865 2.820000e-80 309.0
8 TraesCS4A01G196500 chr5B 96.875 128 4 0 296 423 82212300 82212173 6.330000e-52 215.0
9 TraesCS4A01G196500 chr5B 80.000 150 25 5 470 615 356715786 356715934 3.970000e-19 106.0
10 TraesCS4A01G196500 chr5D 75.421 712 116 39 1120 1815 216098706 216099374 1.020000e-74 291.0
11 TraesCS4A01G196500 chr3B 96.899 129 4 0 296 424 25395774 25395646 1.760000e-52 217.0
12 TraesCS4A01G196500 chr3B 83.036 112 15 4 468 579 752670112 752670219 6.650000e-17 99.0
13 TraesCS4A01G196500 chr6A 94.928 138 6 1 295 431 349574928 349575065 6.330000e-52 215.0
14 TraesCS4A01G196500 chr6A 94.203 138 6 2 285 422 330044988 330045123 2.940000e-50 209.0
15 TraesCS4A01G196500 chr1A 94.853 136 7 0 287 422 213289527 213289392 2.280000e-51 213.0
16 TraesCS4A01G196500 chr1A 94.853 136 5 2 287 422 12159678 12159811 8.190000e-51 211.0
17 TraesCS4A01G196500 chr5A 96.094 128 5 0 295 422 569162853 569162726 2.940000e-50 209.0
18 TraesCS4A01G196500 chr5A 76.156 411 54 30 1080 1486 285306292 285306662 2.990000e-40 176.0
19 TraesCS4A01G196500 chr3A 89.571 163 13 3 283 444 69626027 69626186 1.370000e-48 204.0
20 TraesCS4A01G196500 chr3A 82.394 142 20 4 476 614 53256305 53256166 5.100000e-23 119.0
21 TraesCS4A01G196500 chr1D 82.609 138 20 4 481 615 156123362 156123226 5.100000e-23 119.0
22 TraesCS4A01G196500 chr3D 81.119 143 22 5 476 615 39532539 39532399 3.070000e-20 110.0
23 TraesCS4A01G196500 chr7D 79.577 142 21 7 480 615 56496476 56496337 8.600000e-16 95.3
24 TraesCS4A01G196500 chr7D 78.767 146 24 6 476 615 56512823 56512679 1.110000e-14 91.6


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 TraesCS4A01G196500 chr4A 478741792 478744707 2915 False 5385.0 5385 100.000000 1 2916 1 chr4A.!!$F2 2915
1 TraesCS4A01G196500 chr4D 97419008 97421503 2495 True 1919.5 3698 97.288000 426 2895 2 chr4D.!!$R1 2469
2 TraesCS4A01G196500 chr4B 139136873 139139785 2912 True 1228.0 3371 93.199333 153 2898 3 chr4B.!!$R1 2745
3 TraesCS4A01G196500 chr5B 232214152 232214865 713 False 309.0 309 75.395000 1080 1821 1 chr5B.!!$F1 741
4 TraesCS4A01G196500 chr5D 216098706 216099374 668 False 291.0 291 75.421000 1120 1815 1 chr5D.!!$F1 695

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
65 66 0.036105 ACCTGTTGCTCATGCGATCA 60.036 50.0 0.0 0.0 43.34 2.92 F
311 318 0.038744 ACCTACTCCCTCCGTTTCGA 59.961 55.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 2072 0.179097 CACAAACCAAACCCAACCCG 60.179 55.0 0.0 0.0 0.0 5.28 R
2213 2450 1.523758 AGGACGGTGAGAAACAATGC 58.476 50.0 0.0 0.0 0.0 3.56 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
18 19 2.466867 CGTGGATTGTACCCTGTGC 58.533 57.895 0.00 0.00 0.00 4.57
19 20 1.358725 CGTGGATTGTACCCTGTGCG 61.359 60.000 0.00 0.00 0.00 5.34
20 21 0.036765 GTGGATTGTACCCTGTGCGA 60.037 55.000 0.00 0.00 0.00 5.10
21 22 0.687920 TGGATTGTACCCTGTGCGAA 59.312 50.000 0.00 0.00 0.00 4.70
22 23 1.280710 TGGATTGTACCCTGTGCGAAT 59.719 47.619 0.00 0.00 0.00 3.34
23 24 1.670811 GGATTGTACCCTGTGCGAATG 59.329 52.381 0.00 0.00 0.00 2.67
24 25 2.627945 GATTGTACCCTGTGCGAATGA 58.372 47.619 0.00 0.00 0.00 2.57
25 26 2.779755 TTGTACCCTGTGCGAATGAT 57.220 45.000 0.00 0.00 0.00 2.45
26 27 3.897141 TTGTACCCTGTGCGAATGATA 57.103 42.857 0.00 0.00 0.00 2.15
27 28 3.173668 TGTACCCTGTGCGAATGATAC 57.826 47.619 0.00 0.00 0.00 2.24
28 29 2.124903 GTACCCTGTGCGAATGATACG 58.875 52.381 0.00 0.00 0.00 3.06
29 30 0.179084 ACCCTGTGCGAATGATACGG 60.179 55.000 0.00 0.00 0.00 4.02
30 31 0.880278 CCCTGTGCGAATGATACGGG 60.880 60.000 0.00 0.00 39.93 5.28
31 32 0.179084 CCTGTGCGAATGATACGGGT 60.179 55.000 0.00 0.00 36.36 5.28
32 33 1.209128 CTGTGCGAATGATACGGGTC 58.791 55.000 0.00 0.00 0.00 4.46
33 34 0.533032 TGTGCGAATGATACGGGTCA 59.467 50.000 0.00 0.00 0.00 4.02
34 35 1.209128 GTGCGAATGATACGGGTCAG 58.791 55.000 0.00 0.00 0.00 3.51
35 36 0.104120 TGCGAATGATACGGGTCAGG 59.896 55.000 0.00 0.00 0.00 3.86
36 37 0.104304 GCGAATGATACGGGTCAGGT 59.896 55.000 0.00 0.00 0.00 4.00
37 38 1.868519 GCGAATGATACGGGTCAGGTC 60.869 57.143 0.00 0.00 0.00 3.85
38 39 1.599667 CGAATGATACGGGTCAGGTCG 60.600 57.143 11.14 11.14 35.02 4.79
39 40 1.679680 GAATGATACGGGTCAGGTCGA 59.320 52.381 0.00 0.00 0.00 4.20
40 41 1.771565 ATGATACGGGTCAGGTCGAA 58.228 50.000 0.00 0.00 0.00 3.71
41 42 1.548081 TGATACGGGTCAGGTCGAAA 58.452 50.000 0.00 0.00 0.00 3.46
42 43 1.894466 TGATACGGGTCAGGTCGAAAA 59.106 47.619 0.00 0.00 0.00 2.29
43 44 2.094390 TGATACGGGTCAGGTCGAAAAG 60.094 50.000 0.00 0.00 0.00 2.27
44 45 1.331214 TACGGGTCAGGTCGAAAAGT 58.669 50.000 0.00 0.00 0.00 2.66
45 46 0.466963 ACGGGTCAGGTCGAAAAGTT 59.533 50.000 0.00 0.00 0.00 2.66
46 47 1.688197 ACGGGTCAGGTCGAAAAGTTA 59.312 47.619 0.00 0.00 0.00 2.24
47 48 2.064014 CGGGTCAGGTCGAAAAGTTAC 58.936 52.381 0.00 0.00 0.00 2.50
48 49 2.420642 GGGTCAGGTCGAAAAGTTACC 58.579 52.381 0.00 0.00 0.00 2.85
49 50 2.038164 GGGTCAGGTCGAAAAGTTACCT 59.962 50.000 0.00 0.00 44.54 3.08
54 55 2.876550 AGGTCGAAAAGTTACCTGTTGC 59.123 45.455 0.00 0.00 42.08 4.17
55 56 2.876550 GGTCGAAAAGTTACCTGTTGCT 59.123 45.455 0.00 0.00 0.00 3.91
56 57 3.059120 GGTCGAAAAGTTACCTGTTGCTC 60.059 47.826 0.00 0.00 0.00 4.26
57 58 3.558418 GTCGAAAAGTTACCTGTTGCTCA 59.442 43.478 0.00 0.00 0.00 4.26
58 59 4.213482 GTCGAAAAGTTACCTGTTGCTCAT 59.787 41.667 0.00 0.00 0.00 2.90
59 60 4.213270 TCGAAAAGTTACCTGTTGCTCATG 59.787 41.667 0.00 0.00 0.00 3.07
60 61 3.923017 AAAGTTACCTGTTGCTCATGC 57.077 42.857 0.00 0.00 40.20 4.06
61 62 1.442769 AGTTACCTGTTGCTCATGCG 58.557 50.000 0.00 0.00 43.34 4.73
62 63 1.001974 AGTTACCTGTTGCTCATGCGA 59.998 47.619 0.00 0.00 43.34 5.10
63 64 2.009774 GTTACCTGTTGCTCATGCGAT 58.990 47.619 0.00 0.00 43.34 4.58
64 65 1.939974 TACCTGTTGCTCATGCGATC 58.060 50.000 0.00 0.00 43.34 3.69
65 66 0.036105 ACCTGTTGCTCATGCGATCA 60.036 50.000 0.00 0.00 43.34 2.92
66 67 0.376152 CCTGTTGCTCATGCGATCAC 59.624 55.000 0.00 0.00 43.34 3.06
67 68 1.081094 CTGTTGCTCATGCGATCACA 58.919 50.000 0.00 0.00 43.34 3.58
68 69 1.669265 CTGTTGCTCATGCGATCACAT 59.331 47.619 0.00 0.00 43.34 3.21
70 71 0.379316 TTGCTCATGCGATCACATGC 59.621 50.000 17.19 8.61 45.75 4.06
71 72 1.082951 GCTCATGCGATCACATGCG 60.083 57.895 17.19 13.03 45.75 4.73
72 73 1.769098 GCTCATGCGATCACATGCGT 61.769 55.000 17.19 0.00 45.75 5.24
73 74 0.654160 CTCATGCGATCACATGCGTT 59.346 50.000 17.19 0.00 45.75 4.84
74 75 1.063027 CTCATGCGATCACATGCGTTT 59.937 47.619 17.19 0.00 45.75 3.60
75 76 1.185189 CATGCGATCACATGCGTTTG 58.815 50.000 10.61 0.00 40.89 2.93
76 77 0.804364 ATGCGATCACATGCGTTTGT 59.196 45.000 0.00 0.00 0.00 2.83
77 78 0.110283 TGCGATCACATGCGTTTGTG 60.110 50.000 12.04 12.04 46.70 3.33
78 79 0.794229 GCGATCACATGCGTTTGTGG 60.794 55.000 16.41 5.54 45.63 4.17
79 80 0.516877 CGATCACATGCGTTTGTGGT 59.483 50.000 16.41 11.48 45.63 4.16
80 81 1.069296 CGATCACATGCGTTTGTGGTT 60.069 47.619 16.41 7.59 45.63 3.67
81 82 2.158645 CGATCACATGCGTTTGTGGTTA 59.841 45.455 16.41 2.37 45.63 2.85
82 83 3.181511 CGATCACATGCGTTTGTGGTTAT 60.182 43.478 16.41 6.26 45.63 1.89
83 84 3.822594 TCACATGCGTTTGTGGTTATC 57.177 42.857 16.41 0.00 45.63 1.75
84 85 2.486203 TCACATGCGTTTGTGGTTATCC 59.514 45.455 16.41 0.00 45.63 2.59
85 86 1.816224 ACATGCGTTTGTGGTTATCCC 59.184 47.619 0.00 0.00 0.00 3.85
86 87 1.815613 CATGCGTTTGTGGTTATCCCA 59.184 47.619 0.00 0.00 42.51 4.37
87 88 1.529226 TGCGTTTGTGGTTATCCCAG 58.471 50.000 0.00 0.00 46.45 4.45
88 89 0.808755 GCGTTTGTGGTTATCCCAGG 59.191 55.000 0.00 0.00 46.45 4.45
89 90 0.808755 CGTTTGTGGTTATCCCAGGC 59.191 55.000 0.00 0.00 46.45 4.85
90 91 0.808755 GTTTGTGGTTATCCCAGGCG 59.191 55.000 0.00 0.00 46.45 5.52
91 92 0.963355 TTTGTGGTTATCCCAGGCGC 60.963 55.000 0.00 0.00 46.45 6.53
92 93 2.895372 GTGGTTATCCCAGGCGCG 60.895 66.667 0.00 0.00 46.45 6.86
93 94 3.395702 TGGTTATCCCAGGCGCGT 61.396 61.111 8.43 0.00 38.72 6.01
94 95 2.124860 GGTTATCCCAGGCGCGTT 60.125 61.111 8.43 0.00 0.00 4.84
95 96 1.747745 GGTTATCCCAGGCGCGTTT 60.748 57.895 8.43 0.00 0.00 3.60
96 97 1.427819 GTTATCCCAGGCGCGTTTG 59.572 57.895 8.43 6.48 0.00 2.93
97 98 2.403378 TTATCCCAGGCGCGTTTGC 61.403 57.895 8.43 0.00 37.91 3.68
98 99 2.813226 TTATCCCAGGCGCGTTTGCT 62.813 55.000 8.43 0.00 39.65 3.91
101 102 3.434319 CCAGGCGCGTTTGCTCAT 61.434 61.111 8.43 0.00 39.65 2.90
102 103 2.202388 CAGGCGCGTTTGCTCATG 60.202 61.111 8.43 0.00 39.65 3.07
103 104 2.358615 AGGCGCGTTTGCTCATGA 60.359 55.556 8.43 0.00 39.65 3.07
104 105 2.099062 GGCGCGTTTGCTCATGAG 59.901 61.111 18.84 18.84 39.65 2.90
105 106 2.680913 GGCGCGTTTGCTCATGAGT 61.681 57.895 23.38 0.00 39.65 3.41
106 107 1.207593 GCGCGTTTGCTCATGAGTT 59.792 52.632 23.38 0.00 39.65 3.01
107 108 1.061799 GCGCGTTTGCTCATGAGTTG 61.062 55.000 23.38 10.28 39.65 3.16
108 109 0.453282 CGCGTTTGCTCATGAGTTGG 60.453 55.000 23.38 10.10 39.65 3.77
109 110 0.109597 GCGTTTGCTCATGAGTTGGG 60.110 55.000 23.38 10.75 38.39 4.12
113 114 2.437359 GCTCATGAGTTGGGCGCT 60.437 61.111 23.38 0.00 43.28 5.92
114 115 2.042831 GCTCATGAGTTGGGCGCTT 61.043 57.895 23.38 0.00 43.28 4.68
115 116 1.798735 CTCATGAGTTGGGCGCTTG 59.201 57.895 14.95 0.00 0.00 4.01
116 117 1.651240 CTCATGAGTTGGGCGCTTGG 61.651 60.000 14.95 0.00 0.00 3.61
117 118 1.675310 CATGAGTTGGGCGCTTGGA 60.675 57.895 7.64 0.00 0.00 3.53
118 119 1.675641 ATGAGTTGGGCGCTTGGAC 60.676 57.895 7.64 1.22 0.00 4.02
119 120 2.032681 GAGTTGGGCGCTTGGACT 59.967 61.111 7.64 6.66 0.00 3.85
120 121 2.281761 AGTTGGGCGCTTGGACTG 60.282 61.111 7.64 0.00 0.00 3.51
121 122 2.594592 GTTGGGCGCTTGGACTGT 60.595 61.111 7.64 0.00 0.00 3.55
122 123 2.594303 TTGGGCGCTTGGACTGTG 60.594 61.111 7.64 0.00 0.00 3.66
123 124 3.113514 TTGGGCGCTTGGACTGTGA 62.114 57.895 7.64 0.00 0.00 3.58
124 125 2.045926 GGGCGCTTGGACTGTGAT 60.046 61.111 7.64 0.00 0.00 3.06
125 126 2.401766 GGGCGCTTGGACTGTGATG 61.402 63.158 7.64 0.00 0.00 3.07
126 127 1.672356 GGCGCTTGGACTGTGATGT 60.672 57.895 7.64 0.00 0.00 3.06
127 128 1.499056 GCGCTTGGACTGTGATGTG 59.501 57.895 0.00 0.00 0.00 3.21
128 129 1.915614 GCGCTTGGACTGTGATGTGG 61.916 60.000 0.00 0.00 0.00 4.17
129 130 0.320683 CGCTTGGACTGTGATGTGGA 60.321 55.000 0.00 0.00 0.00 4.02
130 131 1.676916 CGCTTGGACTGTGATGTGGAT 60.677 52.381 0.00 0.00 0.00 3.41
131 132 2.418609 CGCTTGGACTGTGATGTGGATA 60.419 50.000 0.00 0.00 0.00 2.59
132 133 3.742327 CGCTTGGACTGTGATGTGGATAT 60.742 47.826 0.00 0.00 0.00 1.63
133 134 3.812053 GCTTGGACTGTGATGTGGATATC 59.188 47.826 0.00 0.00 0.00 1.63
134 135 3.733443 TGGACTGTGATGTGGATATCG 57.267 47.619 0.00 0.00 0.00 2.92
135 136 2.365293 TGGACTGTGATGTGGATATCGG 59.635 50.000 0.00 0.00 0.00 4.18
136 137 2.289072 GGACTGTGATGTGGATATCGGG 60.289 54.545 0.00 0.00 0.00 5.14
137 138 1.694150 ACTGTGATGTGGATATCGGGG 59.306 52.381 0.00 0.00 0.00 5.73
138 139 1.002430 CTGTGATGTGGATATCGGGGG 59.998 57.143 0.00 0.00 0.00 5.40
139 140 1.348064 GTGATGTGGATATCGGGGGA 58.652 55.000 0.00 0.00 0.00 4.81
140 141 1.909302 GTGATGTGGATATCGGGGGAT 59.091 52.381 0.00 0.00 0.00 3.85
141 142 3.104512 GTGATGTGGATATCGGGGGATA 58.895 50.000 0.00 0.00 0.00 2.59
142 143 3.711704 GTGATGTGGATATCGGGGGATAT 59.288 47.826 0.00 0.00 0.00 1.63
143 144 3.967326 TGATGTGGATATCGGGGGATATC 59.033 47.826 13.23 13.23 41.46 1.63
144 145 2.384828 TGTGGATATCGGGGGATATCG 58.615 52.381 14.54 0.00 42.51 2.92
145 146 1.068741 GTGGATATCGGGGGATATCGC 59.931 57.143 11.21 11.21 42.51 4.58
146 147 1.342574 TGGATATCGGGGGATATCGCA 60.343 52.381 20.16 11.73 42.51 5.10
147 148 1.068741 GGATATCGGGGGATATCGCAC 59.931 57.143 20.16 16.29 42.51 5.34
148 149 2.032620 GATATCGGGGGATATCGCACT 58.967 52.381 18.78 4.90 35.60 4.40
149 150 2.812836 TATCGGGGGATATCGCACTA 57.187 50.000 18.78 9.44 0.00 2.74
150 151 1.475403 ATCGGGGGATATCGCACTAG 58.525 55.000 18.78 5.63 0.00 2.57
151 152 0.611062 TCGGGGGATATCGCACTAGG 60.611 60.000 18.78 4.96 0.00 3.02
169 170 5.824624 CACTAGGTATTTCCATGCTCACAAT 59.175 40.000 0.00 0.00 39.02 2.71
170 171 6.992123 CACTAGGTATTTCCATGCTCACAATA 59.008 38.462 0.00 0.00 39.02 1.90
249 254 5.816682 ACGATCCCTTCTTTGGTTTAGAAT 58.183 37.500 0.00 0.00 31.66 2.40
302 309 7.515166 TCTTTTTCCTACTAAAACCTACTCCCT 59.485 37.037 0.00 0.00 0.00 4.20
304 311 4.876580 TCCTACTAAAACCTACTCCCTCC 58.123 47.826 0.00 0.00 0.00 4.30
305 312 3.635836 CCTACTAAAACCTACTCCCTCCG 59.364 52.174 0.00 0.00 0.00 4.63
307 314 3.514539 ACTAAAACCTACTCCCTCCGTT 58.485 45.455 0.00 0.00 0.00 4.44
308 315 3.906218 ACTAAAACCTACTCCCTCCGTTT 59.094 43.478 0.00 0.00 0.00 3.60
309 316 3.413846 AAAACCTACTCCCTCCGTTTC 57.586 47.619 0.00 0.00 0.00 2.78
310 317 0.893447 AACCTACTCCCTCCGTTTCG 59.107 55.000 0.00 0.00 0.00 3.46
311 318 0.038744 ACCTACTCCCTCCGTTTCGA 59.961 55.000 0.00 0.00 0.00 3.71
312 319 1.180029 CCTACTCCCTCCGTTTCGAA 58.820 55.000 0.00 0.00 0.00 3.71
313 320 1.755380 CCTACTCCCTCCGTTTCGAAT 59.245 52.381 0.00 0.00 0.00 3.34
314 321 2.167900 CCTACTCCCTCCGTTTCGAATT 59.832 50.000 0.00 0.00 0.00 2.17
316 325 3.242549 ACTCCCTCCGTTTCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
319 328 3.592059 TCCCTCCGTTTCGAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
321 330 3.370061 CCCTCCGTTTCGAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
323 332 4.689345 CCTCCGTTTCGAATTACTTGTCTT 59.311 41.667 0.00 0.00 0.00 3.01
327 336 5.121768 CCGTTTCGAATTACTTGTCTTGGAT 59.878 40.000 0.00 0.00 0.00 3.41
330 339 7.059488 CGTTTCGAATTACTTGTCTTGGATTTG 59.941 37.037 0.00 0.00 0.00 2.32
331 340 7.504924 TTCGAATTACTTGTCTTGGATTTGT 57.495 32.000 0.00 0.00 0.00 2.83
332 341 7.129109 TCGAATTACTTGTCTTGGATTTGTC 57.871 36.000 0.00 0.00 0.00 3.18
336 345 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
337 346 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
339 348 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
344 353 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
346 355 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
363 372 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
364 373 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
365 374 8.353684 CGGATGTATCTAGACTCATTTTAGTGT 58.646 37.037 11.25 0.00 0.00 3.55
377 458 9.522804 GACTCATTTTAGTGTTAGATACCTCTG 57.477 37.037 0.00 0.00 32.66 3.35
378 459 9.036980 ACTCATTTTAGTGTTAGATACCTCTGT 57.963 33.333 0.00 0.00 32.66 3.41
397 478 9.127277 ACCTCTGTATCTAGACAAATCTAAGAC 57.873 37.037 0.00 0.00 36.98 3.01
413 494 9.855021 AAATCTAAGACAAATAATTTGGAACGG 57.145 29.630 0.00 0.00 44.81 4.44
415 496 8.263940 TCTAAGACAAATAATTTGGAACGGAG 57.736 34.615 0.00 0.00 44.81 4.63
416 497 5.897377 AGACAAATAATTTGGAACGGAGG 57.103 39.130 0.00 0.00 44.81 4.30
417 498 4.705023 AGACAAATAATTTGGAACGGAGGG 59.295 41.667 0.00 0.00 44.81 4.30
424 617 4.684484 ATTTGGAACGGAGGGAGTATAC 57.316 45.455 0.00 0.00 0.00 1.47
624 827 9.639601 CTATACATACTCAAATCGGCAATTAGA 57.360 33.333 0.00 0.00 0.00 2.10
637 841 9.520204 AATCGGCAATTAGATTGTTAATTCAAG 57.480 29.630 2.97 0.00 42.20 3.02
677 884 5.689383 TCAACACAAGATTCTTTACTGGC 57.311 39.130 0.00 0.00 0.00 4.85
678 885 4.518970 TCAACACAAGATTCTTTACTGGCC 59.481 41.667 0.00 0.00 0.00 5.36
679 886 4.373156 ACACAAGATTCTTTACTGGCCT 57.627 40.909 3.32 0.00 0.00 5.19
721 928 2.508439 ACGGGTAGCATCGCAACG 60.508 61.111 0.00 0.00 0.00 4.10
746 953 3.456280 GTGCTTCTAGAATCTGGAGCAG 58.544 50.000 13.51 6.12 30.94 4.24
772 980 2.692368 TGGAGCCATCCTGACCCC 60.692 66.667 0.00 0.00 46.80 4.95
837 1045 7.818930 TCCGACTTTTGATAAACCGTTTACTAT 59.181 33.333 5.86 0.00 0.00 2.12
1026 1239 3.707189 TTCCTCCCCTCCCCTCCC 61.707 72.222 0.00 0.00 0.00 4.30
1072 1288 1.657751 CCTCTCTCATGGCGACGTCA 61.658 60.000 17.16 3.85 0.00 4.35
1207 1423 2.198426 ACCAACCCCAAGTGCCTG 59.802 61.111 0.00 0.00 0.00 4.85
1838 2072 5.451103 GGGCAGGAGATTTAATTTTGCTCTC 60.451 44.000 0.00 0.00 33.24 3.20
1858 2092 0.906066 GGGTTGGGTTTGGTTTGTGT 59.094 50.000 0.00 0.00 0.00 3.72
1859 2093 1.134640 GGGTTGGGTTTGGTTTGTGTC 60.135 52.381 0.00 0.00 0.00 3.67
1902 2136 3.445857 CCGTGCTCTAGGCTTAGTAAAC 58.554 50.000 2.43 0.00 42.39 2.01
1903 2137 3.130693 CCGTGCTCTAGGCTTAGTAAACT 59.869 47.826 2.43 0.00 42.39 2.66
1904 2138 4.381718 CCGTGCTCTAGGCTTAGTAAACTT 60.382 45.833 2.43 0.00 42.39 2.66
1907 2141 5.932883 GTGCTCTAGGCTTAGTAAACTTGTT 59.067 40.000 2.43 0.00 42.39 2.83
1909 2143 6.649557 TGCTCTAGGCTTAGTAAACTTGTTTC 59.350 38.462 2.43 0.00 42.39 2.78
1917 2151 7.431376 GGCTTAGTAAACTTGTTTCTGTTTGTC 59.569 37.037 1.72 0.00 37.06 3.18
2013 2248 3.988976 TTGCTAGTTTCCTCATCTGCT 57.011 42.857 0.00 0.00 0.00 4.24
2040 2275 3.983344 GCTCGTTTCTGAATTGTTGCAAT 59.017 39.130 0.59 0.00 0.00 3.56
2061 2297 6.586751 CAATTTCACATGTTCTTGACAATGC 58.413 36.000 0.00 0.00 42.62 3.56
2071 2307 2.104622 TCTTGACAATGCAGTCCTGACA 59.895 45.455 3.85 0.00 37.73 3.58
2074 2310 2.012673 GACAATGCAGTCCTGACATCC 58.987 52.381 0.00 0.00 32.36 3.51
2155 2391 1.002773 TCTTGCAGAAGATCAGCAGCA 59.997 47.619 0.00 0.00 39.99 4.41
2178 2414 1.467713 GCTTGAGAGGTAGAACGTCGG 60.468 57.143 0.00 0.00 37.99 4.79
2184 2420 2.101770 GTAGAACGTCGGCCCTCG 59.898 66.667 11.81 11.81 40.90 4.63
2213 2450 0.665670 CCTCAGCTGTCGTGTCACTG 60.666 60.000 14.67 0.00 0.00 3.66
2228 2465 1.872952 TCACTGCATTGTTTCTCACCG 59.127 47.619 3.77 0.00 0.00 4.94
2230 2467 1.873591 ACTGCATTGTTTCTCACCGTC 59.126 47.619 0.00 0.00 0.00 4.79
2319 2556 4.536765 TCCAAAGGCATTCCTCTTATTCC 58.463 43.478 0.00 0.00 43.40 3.01
2335 2572 7.497249 CCTCTTATTCCAGTGAGTTTAATCCAG 59.503 40.741 0.00 0.00 0.00 3.86
2373 2610 6.927936 CCATCTAGTCATTCCTACTCACAATG 59.072 42.308 0.00 0.00 0.00 2.82
2509 2746 0.543749 AGTACTCTGCCCAGCATTCC 59.456 55.000 0.00 0.00 38.13 3.01
2530 2767 1.432514 TGCTCAAGTGCGACTTCATC 58.567 50.000 0.00 0.00 36.03 2.92
2541 2778 3.447229 TGCGACTTCATCCAGATTAGTGA 59.553 43.478 0.00 0.00 0.00 3.41
2570 2807 6.496144 AATAAACCTAAGCCTTCGGTAGAT 57.504 37.500 0.46 0.00 0.00 1.98
2631 2868 1.022451 TCGTGGTTAGATTTGGGCGC 61.022 55.000 0.00 0.00 0.00 6.53
2642 2879 3.835790 TTGGGCGCGCCACTTACTT 62.836 57.895 46.88 0.00 37.98 2.24
2679 2916 6.140737 CGCCTTAAATTATTCTTTCATCGCAC 59.859 38.462 0.00 0.00 0.00 5.34
2895 3169 3.898123 TGCTAGTATCCTTGATCCTCCAC 59.102 47.826 0.00 0.00 0.00 4.02
2898 3172 4.970860 AGTATCCTTGATCCTCCACATG 57.029 45.455 0.00 0.00 0.00 3.21
2899 3173 3.649981 AGTATCCTTGATCCTCCACATGG 59.350 47.826 0.00 0.00 34.17 3.66
2900 3174 1.971149 TCCTTGATCCTCCACATGGT 58.029 50.000 0.00 0.00 36.34 3.55
2901 3175 2.278245 TCCTTGATCCTCCACATGGTT 58.722 47.619 0.00 0.00 36.34 3.67
2902 3176 2.649312 TCCTTGATCCTCCACATGGTTT 59.351 45.455 0.00 0.00 36.34 3.27
2903 3177 3.075882 TCCTTGATCCTCCACATGGTTTT 59.924 43.478 0.00 0.00 36.34 2.43
2904 3178 3.445096 CCTTGATCCTCCACATGGTTTTC 59.555 47.826 0.00 0.00 36.34 2.29
2905 3179 3.805066 TGATCCTCCACATGGTTTTCA 57.195 42.857 0.00 0.00 36.34 2.69
2906 3180 3.420893 TGATCCTCCACATGGTTTTCAC 58.579 45.455 0.00 0.00 36.34 3.18
2907 3181 3.074390 TGATCCTCCACATGGTTTTCACT 59.926 43.478 0.00 0.00 36.34 3.41
2908 3182 3.593442 TCCTCCACATGGTTTTCACTT 57.407 42.857 0.00 0.00 36.34 3.16
2909 3183 3.909732 TCCTCCACATGGTTTTCACTTT 58.090 40.909 0.00 0.00 36.34 2.66
2910 3184 3.888930 TCCTCCACATGGTTTTCACTTTC 59.111 43.478 0.00 0.00 36.34 2.62
2911 3185 3.304659 CCTCCACATGGTTTTCACTTTCG 60.305 47.826 0.00 0.00 36.34 3.46
2912 3186 2.621055 TCCACATGGTTTTCACTTTCGG 59.379 45.455 0.00 0.00 36.34 4.30
2913 3187 2.360801 CCACATGGTTTTCACTTTCGGT 59.639 45.455 0.00 0.00 0.00 4.69
2914 3188 3.371168 CACATGGTTTTCACTTTCGGTG 58.629 45.455 0.00 0.00 46.60 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.358725 CGCACAGGGTACAATCCACG 61.359 60.000 0.00 0.00 0.00 4.94
1 2 0.036765 TCGCACAGGGTACAATCCAC 60.037 55.000 0.00 0.00 0.00 4.02
2 3 0.687920 TTCGCACAGGGTACAATCCA 59.312 50.000 0.00 0.00 0.00 3.41
3 4 1.670811 CATTCGCACAGGGTACAATCC 59.329 52.381 0.00 0.00 0.00 3.01
4 5 2.627945 TCATTCGCACAGGGTACAATC 58.372 47.619 0.00 0.00 0.00 2.67
5 6 2.779755 TCATTCGCACAGGGTACAAT 57.220 45.000 0.00 0.00 0.00 2.71
6 7 2.779755 ATCATTCGCACAGGGTACAA 57.220 45.000 0.00 0.00 0.00 2.41
7 8 2.480587 CGTATCATTCGCACAGGGTACA 60.481 50.000 0.00 0.00 0.00 2.90
8 9 2.124903 CGTATCATTCGCACAGGGTAC 58.875 52.381 0.00 0.00 0.00 3.34
9 10 1.067974 CCGTATCATTCGCACAGGGTA 59.932 52.381 0.00 0.00 0.00 3.69
10 11 0.179084 CCGTATCATTCGCACAGGGT 60.179 55.000 0.00 0.00 0.00 4.34
11 12 0.880278 CCCGTATCATTCGCACAGGG 60.880 60.000 0.00 0.00 0.00 4.45
12 13 0.179084 ACCCGTATCATTCGCACAGG 60.179 55.000 0.00 0.00 0.00 4.00
13 14 1.209128 GACCCGTATCATTCGCACAG 58.791 55.000 0.00 0.00 0.00 3.66
14 15 0.533032 TGACCCGTATCATTCGCACA 59.467 50.000 0.00 0.00 0.00 4.57
15 16 1.209128 CTGACCCGTATCATTCGCAC 58.791 55.000 0.00 0.00 0.00 5.34
16 17 0.104120 CCTGACCCGTATCATTCGCA 59.896 55.000 0.00 0.00 0.00 5.10
17 18 0.104304 ACCTGACCCGTATCATTCGC 59.896 55.000 0.00 0.00 0.00 4.70
18 19 1.599667 CGACCTGACCCGTATCATTCG 60.600 57.143 4.13 4.13 31.52 3.34
19 20 1.679680 TCGACCTGACCCGTATCATTC 59.320 52.381 0.00 0.00 0.00 2.67
20 21 1.771565 TCGACCTGACCCGTATCATT 58.228 50.000 0.00 0.00 0.00 2.57
21 22 1.771565 TTCGACCTGACCCGTATCAT 58.228 50.000 0.00 0.00 0.00 2.45
22 23 1.548081 TTTCGACCTGACCCGTATCA 58.452 50.000 0.00 0.00 0.00 2.15
23 24 2.094338 ACTTTTCGACCTGACCCGTATC 60.094 50.000 0.00 0.00 0.00 2.24
24 25 1.897802 ACTTTTCGACCTGACCCGTAT 59.102 47.619 0.00 0.00 0.00 3.06
25 26 1.331214 ACTTTTCGACCTGACCCGTA 58.669 50.000 0.00 0.00 0.00 4.02
26 27 0.466963 AACTTTTCGACCTGACCCGT 59.533 50.000 0.00 0.00 0.00 5.28
27 28 2.064014 GTAACTTTTCGACCTGACCCG 58.936 52.381 0.00 0.00 0.00 5.28
28 29 2.420642 GGTAACTTTTCGACCTGACCC 58.579 52.381 0.00 0.00 0.00 4.46
36 37 7.264817 GCATGAGCAACAGGTAACTTTTCGA 62.265 44.000 0.00 0.00 44.06 3.71
37 38 5.135562 GCATGAGCAACAGGTAACTTTTCG 61.136 45.833 0.00 0.00 44.06 3.46
38 39 4.229876 GCATGAGCAACAGGTAACTTTTC 58.770 43.478 0.00 0.00 44.06 2.29
39 40 3.304659 CGCATGAGCAACAGGTAACTTTT 60.305 43.478 0.00 0.00 44.24 2.27
40 41 2.226437 CGCATGAGCAACAGGTAACTTT 59.774 45.455 0.00 0.00 44.24 2.66
41 42 1.806542 CGCATGAGCAACAGGTAACTT 59.193 47.619 0.00 0.00 44.24 2.66
42 43 6.660310 TGATCGCATGAGCAACAGGTAACT 62.660 45.833 0.00 0.00 43.58 2.24
43 44 1.438651 TCGCATGAGCAACAGGTAAC 58.561 50.000 0.00 0.00 42.27 2.50
44 45 2.279741 GATCGCATGAGCAACAGGTAA 58.720 47.619 0.00 0.00 42.27 2.85
45 46 1.206849 TGATCGCATGAGCAACAGGTA 59.793 47.619 0.00 0.00 37.63 3.08
46 47 0.036105 TGATCGCATGAGCAACAGGT 60.036 50.000 0.00 0.00 37.63 4.00
47 48 0.376152 GTGATCGCATGAGCAACAGG 59.624 55.000 0.16 0.00 43.13 4.00
48 49 1.081094 TGTGATCGCATGAGCAACAG 58.919 50.000 4.45 0.00 43.13 3.16
49 50 1.399089 CATGTGATCGCATGAGCAACA 59.601 47.619 35.43 10.88 46.65 3.33
50 51 1.858798 GCATGTGATCGCATGAGCAAC 60.859 52.381 40.16 24.26 46.65 4.17
51 52 0.379316 GCATGTGATCGCATGAGCAA 59.621 50.000 40.16 7.97 46.65 3.91
52 53 1.768112 CGCATGTGATCGCATGAGCA 61.768 55.000 40.16 8.69 46.65 4.26
53 54 1.082951 CGCATGTGATCGCATGAGC 60.083 57.895 40.16 28.80 46.65 4.26
54 55 0.654160 AACGCATGTGATCGCATGAG 59.346 50.000 40.16 38.10 46.65 2.90
55 56 1.085893 AAACGCATGTGATCGCATGA 58.914 45.000 40.16 10.15 46.65 3.07
56 57 1.185189 CAAACGCATGTGATCGCATG 58.815 50.000 34.70 34.70 46.50 4.06
57 58 0.804364 ACAAACGCATGTGATCGCAT 59.196 45.000 16.05 16.05 30.82 4.73
58 59 2.243056 ACAAACGCATGTGATCGCA 58.757 47.368 14.43 12.12 30.82 5.10
64 65 4.917911 TGGGATAACCACAAACGCATGTG 61.918 47.826 12.81 12.81 46.80 3.21
65 66 1.816224 GGGATAACCACAAACGCATGT 59.184 47.619 0.00 0.00 39.85 3.21
66 67 1.815613 TGGGATAACCACAAACGCATG 59.184 47.619 0.00 0.00 46.80 4.06
67 68 2.091541 CTGGGATAACCACAAACGCAT 58.908 47.619 0.00 0.00 46.80 4.73
68 69 1.529226 CTGGGATAACCACAAACGCA 58.471 50.000 0.00 0.00 46.80 5.24
69 70 0.808755 CCTGGGATAACCACAAACGC 59.191 55.000 0.00 0.00 46.80 4.84
70 71 0.808755 GCCTGGGATAACCACAAACG 59.191 55.000 0.00 0.00 46.80 3.60
71 72 0.808755 CGCCTGGGATAACCACAAAC 59.191 55.000 0.00 0.00 46.80 2.93
72 73 0.963355 GCGCCTGGGATAACCACAAA 60.963 55.000 0.00 0.00 46.80 2.83
73 74 1.377987 GCGCCTGGGATAACCACAA 60.378 57.895 0.00 0.00 46.80 3.33
74 75 2.270850 GCGCCTGGGATAACCACA 59.729 61.111 0.00 0.00 46.80 4.17
75 76 2.895372 CGCGCCTGGGATAACCAC 60.895 66.667 0.00 0.00 46.80 4.16
77 78 1.747745 AAACGCGCCTGGGATAACC 60.748 57.895 5.73 0.00 40.81 2.85
78 79 1.427819 CAAACGCGCCTGGGATAAC 59.572 57.895 5.73 0.00 0.00 1.89
79 80 2.403378 GCAAACGCGCCTGGGATAA 61.403 57.895 5.73 0.00 0.00 1.75
80 81 2.822255 GCAAACGCGCCTGGGATA 60.822 61.111 5.73 0.00 0.00 2.59
81 82 4.722700 AGCAAACGCGCCTGGGAT 62.723 61.111 5.73 0.00 0.00 3.85
84 85 3.434319 ATGAGCAAACGCGCCTGG 61.434 61.111 5.73 0.00 0.00 4.45
85 86 2.202388 CATGAGCAAACGCGCCTG 60.202 61.111 5.73 4.53 0.00 4.85
86 87 2.358615 TCATGAGCAAACGCGCCT 60.359 55.556 5.73 0.00 0.00 5.52
87 88 2.099062 CTCATGAGCAAACGCGCC 59.901 61.111 10.38 0.00 0.00 6.53
88 89 1.061799 CAACTCATGAGCAAACGCGC 61.062 55.000 22.83 0.00 0.00 6.86
89 90 0.453282 CCAACTCATGAGCAAACGCG 60.453 55.000 22.83 3.53 0.00 6.01
90 91 0.109597 CCCAACTCATGAGCAAACGC 60.110 55.000 22.83 0.00 0.00 4.84
91 92 0.109597 GCCCAACTCATGAGCAAACG 60.110 55.000 22.83 7.73 0.00 3.60
92 93 0.109597 CGCCCAACTCATGAGCAAAC 60.110 55.000 22.83 7.83 0.00 2.93
93 94 1.865788 GCGCCCAACTCATGAGCAAA 61.866 55.000 22.83 0.00 0.00 3.68
94 95 2.334946 GCGCCCAACTCATGAGCAA 61.335 57.895 22.83 0.00 0.00 3.91
95 96 2.747460 GCGCCCAACTCATGAGCA 60.747 61.111 22.83 0.00 0.00 4.26
96 97 2.042831 AAGCGCCCAACTCATGAGC 61.043 57.895 22.83 8.23 0.00 4.26
97 98 1.651240 CCAAGCGCCCAACTCATGAG 61.651 60.000 21.37 21.37 0.00 2.90
98 99 1.675310 CCAAGCGCCCAACTCATGA 60.675 57.895 2.29 0.00 0.00 3.07
99 100 1.675310 TCCAAGCGCCCAACTCATG 60.675 57.895 2.29 0.00 0.00 3.07
100 101 1.675641 GTCCAAGCGCCCAACTCAT 60.676 57.895 2.29 0.00 0.00 2.90
101 102 2.281484 GTCCAAGCGCCCAACTCA 60.281 61.111 2.29 0.00 0.00 3.41
102 103 2.032681 AGTCCAAGCGCCCAACTC 59.967 61.111 2.29 0.00 0.00 3.01
103 104 2.281761 CAGTCCAAGCGCCCAACT 60.282 61.111 2.29 0.00 0.00 3.16
104 105 2.594592 ACAGTCCAAGCGCCCAAC 60.595 61.111 2.29 0.00 0.00 3.77
105 106 2.410322 ATCACAGTCCAAGCGCCCAA 62.410 55.000 2.29 0.00 0.00 4.12
106 107 2.894257 ATCACAGTCCAAGCGCCCA 61.894 57.895 2.29 0.00 0.00 5.36
107 108 2.045926 ATCACAGTCCAAGCGCCC 60.046 61.111 2.29 0.00 0.00 6.13
108 109 1.672356 ACATCACAGTCCAAGCGCC 60.672 57.895 2.29 0.00 0.00 6.53
109 110 1.499056 CACATCACAGTCCAAGCGC 59.501 57.895 0.00 0.00 0.00 5.92
110 111 0.320683 TCCACATCACAGTCCAAGCG 60.321 55.000 0.00 0.00 0.00 4.68
111 112 2.119801 ATCCACATCACAGTCCAAGC 57.880 50.000 0.00 0.00 0.00 4.01
112 113 4.053983 CGATATCCACATCACAGTCCAAG 58.946 47.826 0.00 0.00 0.00 3.61
113 114 3.181466 CCGATATCCACATCACAGTCCAA 60.181 47.826 0.00 0.00 0.00 3.53
114 115 2.365293 CCGATATCCACATCACAGTCCA 59.635 50.000 0.00 0.00 0.00 4.02
115 116 2.289072 CCCGATATCCACATCACAGTCC 60.289 54.545 0.00 0.00 0.00 3.85
116 117 2.289072 CCCCGATATCCACATCACAGTC 60.289 54.545 0.00 0.00 0.00 3.51
117 118 1.694150 CCCCGATATCCACATCACAGT 59.306 52.381 0.00 0.00 0.00 3.55
118 119 1.002430 CCCCCGATATCCACATCACAG 59.998 57.143 0.00 0.00 0.00 3.66
119 120 1.055849 CCCCCGATATCCACATCACA 58.944 55.000 0.00 0.00 0.00 3.58
120 121 1.348064 TCCCCCGATATCCACATCAC 58.652 55.000 0.00 0.00 0.00 3.06
121 122 2.342406 ATCCCCCGATATCCACATCA 57.658 50.000 0.00 0.00 0.00 3.07
122 123 4.608948 GATATCCCCCGATATCCACATC 57.391 50.000 8.36 0.00 46.44 3.06
129 130 2.160721 AGTGCGATATCCCCCGATAT 57.839 50.000 0.00 0.00 43.15 1.63
130 131 2.651455 CTAGTGCGATATCCCCCGATA 58.349 52.381 0.00 0.00 35.43 2.92
131 132 1.475403 CTAGTGCGATATCCCCCGAT 58.525 55.000 0.00 0.00 0.00 4.18
132 133 0.611062 CCTAGTGCGATATCCCCCGA 60.611 60.000 0.00 0.00 0.00 5.14
133 134 0.898789 ACCTAGTGCGATATCCCCCG 60.899 60.000 0.00 0.00 0.00 5.73
134 135 2.226962 TACCTAGTGCGATATCCCCC 57.773 55.000 0.00 0.00 0.00 5.40
135 136 4.382793 GGAAATACCTAGTGCGATATCCCC 60.383 50.000 0.00 0.00 35.41 4.81
136 137 4.222145 TGGAAATACCTAGTGCGATATCCC 59.778 45.833 0.00 0.00 39.86 3.85
137 138 5.401531 TGGAAATACCTAGTGCGATATCC 57.598 43.478 0.00 0.00 39.86 2.59
138 139 5.292101 GCATGGAAATACCTAGTGCGATATC 59.708 44.000 0.00 0.00 39.86 1.63
139 140 5.046304 AGCATGGAAATACCTAGTGCGATAT 60.046 40.000 0.00 0.00 42.40 1.63
140 141 4.283467 AGCATGGAAATACCTAGTGCGATA 59.717 41.667 0.00 0.00 42.40 2.92
141 142 3.071602 AGCATGGAAATACCTAGTGCGAT 59.928 43.478 0.00 0.00 42.40 4.58
142 143 2.434336 AGCATGGAAATACCTAGTGCGA 59.566 45.455 0.00 0.00 42.40 5.10
143 144 2.802816 GAGCATGGAAATACCTAGTGCG 59.197 50.000 0.00 0.00 42.40 5.34
144 145 3.561725 GTGAGCATGGAAATACCTAGTGC 59.438 47.826 0.00 0.00 40.07 4.40
145 146 4.769688 TGTGAGCATGGAAATACCTAGTG 58.230 43.478 0.00 0.00 39.86 2.74
146 147 5.435686 TTGTGAGCATGGAAATACCTAGT 57.564 39.130 0.00 0.00 39.86 2.57
147 148 8.627208 AATATTGTGAGCATGGAAATACCTAG 57.373 34.615 0.00 0.00 39.86 3.02
149 150 8.995027 TTAATATTGTGAGCATGGAAATACCT 57.005 30.769 0.00 0.00 39.86 3.08
184 189 5.191124 GGGAATGGGAGAAGGTTAGAAAGTA 59.809 44.000 0.00 0.00 0.00 2.24
263 270 8.678593 AGTAGGAAAAAGAAAAGGAAGTACTG 57.321 34.615 0.00 0.00 0.00 2.74
268 275 9.745880 GGTTTTAGTAGGAAAAAGAAAAGGAAG 57.254 33.333 0.00 0.00 30.36 3.46
278 285 7.256799 GGAGGGAGTAGGTTTTAGTAGGAAAAA 60.257 40.741 0.00 0.00 30.36 1.94
297 304 3.521947 AGTAATTCGAAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
298 305 3.007182 ACAAGTAATTCGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
302 309 4.449743 CCAAGACAAGTAATTCGAAACGGA 59.550 41.667 0.00 0.00 0.00 4.69
304 311 5.585500 TCCAAGACAAGTAATTCGAAACG 57.415 39.130 0.00 0.00 0.00 3.60
305 312 7.860872 ACAAATCCAAGACAAGTAATTCGAAAC 59.139 33.333 0.00 0.00 0.00 2.78
307 314 7.444183 AGACAAATCCAAGACAAGTAATTCGAA 59.556 33.333 0.00 0.00 0.00 3.71
308 315 6.934645 AGACAAATCCAAGACAAGTAATTCGA 59.065 34.615 0.00 0.00 0.00 3.71
309 316 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
310 317 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
311 318 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
313 320 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
314 321 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
316 325 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
319 328 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
321 330 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
323 332 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
337 346 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
338 347 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
339 348 8.353684 ACACTAAAATGAGTCTAGATACATCCG 58.646 37.037 12.66 6.68 0.00 4.18
352 361 9.036980 ACAGAGGTATCTAACACTAAAATGAGT 57.963 33.333 0.00 0.00 33.22 3.41
372 453 9.126151 TGTCTTAGATTTGTCTAGATACAGAGG 57.874 37.037 0.00 0.00 0.00 3.69
387 468 9.855021 CCGTTCCAAATTATTTGTCTTAGATTT 57.145 29.630 15.40 0.00 38.98 2.17
388 469 9.238368 TCCGTTCCAAATTATTTGTCTTAGATT 57.762 29.630 15.40 0.00 38.98 2.40
390 471 7.335924 CCTCCGTTCCAAATTATTTGTCTTAGA 59.664 37.037 15.40 3.73 38.98 2.10
391 472 7.415206 CCCTCCGTTCCAAATTATTTGTCTTAG 60.415 40.741 15.40 6.14 38.98 2.18
392 473 6.376018 CCCTCCGTTCCAAATTATTTGTCTTA 59.624 38.462 15.40 0.00 38.98 2.10
395 476 4.703093 TCCCTCCGTTCCAAATTATTTGTC 59.297 41.667 15.40 5.99 38.98 3.18
397 478 4.705023 ACTCCCTCCGTTCCAAATTATTTG 59.295 41.667 10.46 10.46 40.32 2.32
402 483 4.141551 GGTATACTCCCTCCGTTCCAAATT 60.142 45.833 2.25 0.00 0.00 1.82
403 484 3.390311 GGTATACTCCCTCCGTTCCAAAT 59.610 47.826 2.25 0.00 0.00 2.32
416 497 8.867097 TGATTGAGTAAATGTAGGGTATACTCC 58.133 37.037 0.00 0.62 40.97 3.85
530 730 4.919774 TTTGATTTGGGTACAGCTAGGA 57.080 40.909 0.00 0.00 0.00 2.94
579 779 6.767902 TGTATAGGATGAGGCAAGAACATTTC 59.232 38.462 0.00 0.00 0.00 2.17
654 858 5.009610 GGCCAGTAAAGAATCTTGTGTTGAA 59.990 40.000 0.00 0.00 0.00 2.69
660 867 5.248380 AGAAGGCCAGTAAAGAATCTTGT 57.752 39.130 5.01 0.00 0.00 3.16
677 884 2.432628 GTGCGTGGACGGAGAAGG 60.433 66.667 0.71 0.00 41.17 3.46
678 885 2.022129 GTGTGCGTGGACGGAGAAG 61.022 63.158 0.71 0.00 41.17 2.85
679 886 2.028484 GTGTGCGTGGACGGAGAA 59.972 61.111 0.71 0.00 41.17 2.87
706 913 2.511600 AGCGTTGCGATGCTACCC 60.512 61.111 19.49 0.00 46.11 3.69
721 928 2.169352 TCCAGATTCTAGAAGCACCAGC 59.831 50.000 21.97 0.00 42.56 4.85
746 953 0.684479 GGATGGCTCCAGGAAAACCC 60.684 60.000 0.00 0.00 41.64 4.11
772 980 0.309612 GCCTGGTTTACAACACACCG 59.690 55.000 0.00 0.00 32.71 4.94
837 1045 3.258872 TCGATTTGTTTTCCCTCTCGGTA 59.741 43.478 0.00 0.00 0.00 4.02
847 1055 2.981400 TTCCGCCTCGATTTGTTTTC 57.019 45.000 0.00 0.00 0.00 2.29
854 1062 2.084546 CCTTTTCTTTCCGCCTCGATT 58.915 47.619 0.00 0.00 0.00 3.34
979 1192 1.670083 CGGGTTCAGGTTCCGGTTC 60.670 63.158 0.00 0.00 40.07 3.62
990 1203 3.562779 GAAGTCGTCGGCGGGTTCA 62.563 63.158 10.62 0.00 38.89 3.18
1029 1242 2.844839 GATCGGTGGGAGGAGGGG 60.845 72.222 0.00 0.00 0.00 4.79
1030 1243 1.834822 GAGATCGGTGGGAGGAGGG 60.835 68.421 0.00 0.00 0.00 4.30
1031 1244 0.825840 GAGAGATCGGTGGGAGGAGG 60.826 65.000 0.00 0.00 0.00 4.30
1032 1245 0.825840 GGAGAGATCGGTGGGAGGAG 60.826 65.000 0.00 0.00 0.00 3.69
1033 1246 1.230497 GGAGAGATCGGTGGGAGGA 59.770 63.158 0.00 0.00 0.00 3.71
1034 1247 0.825840 GAGGAGAGATCGGTGGGAGG 60.826 65.000 0.00 0.00 0.00 4.30
1035 1248 0.825840 GGAGGAGAGATCGGTGGGAG 60.826 65.000 0.00 0.00 0.00 4.30
1043 1259 3.424703 CCATGAGAGAGGAGGAGAGATC 58.575 54.545 0.00 0.00 0.00 2.75
1207 1423 2.991540 GGGTTGTGGGCCTTGAGC 60.992 66.667 4.53 0.00 42.60 4.26
1285 1507 2.359975 GTGGGCTTCAGGTTCCCG 60.360 66.667 0.00 0.00 42.98 5.14
1564 1786 2.185350 CGCATGAGGAAGCCGAGT 59.815 61.111 0.00 0.00 0.00 4.18
1838 2072 0.179097 CACAAACCAAACCCAACCCG 60.179 55.000 0.00 0.00 0.00 5.28
1903 2137 9.990360 TCAGTATATACAGACAAACAGAAACAA 57.010 29.630 15.18 0.00 0.00 2.83
2013 2248 4.647424 ACAATTCAGAAACGAGCCAAAA 57.353 36.364 0.00 0.00 0.00 2.44
2040 2275 5.163530 ACTGCATTGTCAAGAACATGTGAAA 60.164 36.000 0.00 0.00 37.82 2.69
2101 2337 6.149474 GTGCAAGGTATGTTGTCAAGATTAGT 59.851 38.462 0.00 0.00 0.00 2.24
2113 2349 2.041620 AGATGGTGGTGCAAGGTATGTT 59.958 45.455 0.00 0.00 0.00 2.71
2119 2355 1.542915 CAAGAAGATGGTGGTGCAAGG 59.457 52.381 0.00 0.00 0.00 3.61
2155 2391 3.312973 CGACGTTCTACCTCTCAAGCTAT 59.687 47.826 0.00 0.00 0.00 2.97
2178 2414 2.680339 CTGAGGAAGAAAATTCGAGGGC 59.320 50.000 0.00 0.00 0.00 5.19
2184 2420 3.748568 ACGACAGCTGAGGAAGAAAATTC 59.251 43.478 23.35 1.25 0.00 2.17
2186 2422 3.070018 CACGACAGCTGAGGAAGAAAAT 58.930 45.455 23.35 0.00 0.00 1.82
2213 2450 1.523758 AGGACGGTGAGAAACAATGC 58.476 50.000 0.00 0.00 0.00 3.56
2228 2465 6.040504 ACAAATGGAAGGTTGTAAGAAAGGAC 59.959 38.462 0.00 0.00 36.22 3.85
2230 2467 6.265422 AGACAAATGGAAGGTTGTAAGAAAGG 59.735 38.462 0.00 0.00 38.07 3.11
2319 2556 5.335191 GGTGAAAGCTGGATTAAACTCACTG 60.335 44.000 0.00 0.00 33.94 3.66
2335 2572 2.271800 CTAGATGGACACGGTGAAAGC 58.728 52.381 16.29 2.51 0.00 3.51
2373 2610 3.006752 TGCACAATTCAAAATCTGTCCCC 59.993 43.478 0.00 0.00 0.00 4.81
2439 2676 6.600032 TGAAAAGAAGTGGTTGTACAGCTAAA 59.400 34.615 9.71 0.00 0.00 1.85
2509 2746 1.220529 TGAAGTCGCACTTGAGCAAG 58.779 50.000 8.60 8.60 38.80 4.01
2561 2798 3.407698 TGCTTTTCTGCAATCTACCGAA 58.592 40.909 0.00 0.00 40.29 4.30
2570 2807 1.608590 GTAGTGGCTGCTTTTCTGCAA 59.391 47.619 0.00 0.00 42.83 4.08
2631 2868 0.865769 GTGTCACCAAGTAAGTGGCG 59.134 55.000 0.00 0.00 42.83 5.69
2642 2879 0.178301 TTAAGGCGTGTGTGTCACCA 59.822 50.000 0.00 0.00 43.51 4.17
2662 2899 6.932356 ACTGATGTGCGATGAAAGAATAAT 57.068 33.333 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.