Multiple sequence alignment - TraesCS5A01G262400

Loading Multiple Alignment...

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 TraesCS5A01G262400 chr5A 100.000 2616 0 0 1 2616 475631764 475634379 0.000000e+00 4831
1 TraesCS5A01G262400 chr5D 93.181 2361 119 12 278 2613 373773326 373775669 0.000000e+00 3430
2 TraesCS5A01G262400 chr5B 93.716 2021 93 12 607 2616 445193509 445195506 0.000000e+00 2998
3 TraesCS5A01G262400 chr2D 90.464 388 33 2 1885 2268 626672600 626672987 2.320000e-140 508


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 TraesCS5A01G262400 chr5A 475631764 475634379 2615 False 4831 4831 100.000 1 2616 1 chr5A.!!$F1 2615
1 TraesCS5A01G262400 chr5D 373773326 373775669 2343 False 3430 3430 93.181 278 2613 1 chr5D.!!$F1 2335
2 TraesCS5A01G262400 chr5B 445193509 445195506 1997 False 2998 2998 93.716 607 2616 1 chr5B.!!$F1 2009

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
25 26 0.183492 AGCTGAGCTTGTGAACCCAA 59.817 50.0 0.0 0.0 33.89 4.12 F
26 27 0.595095 GCTGAGCTTGTGAACCCAAG 59.405 55.0 0.0 0.0 43.76 3.61 F
1043 1066 0.549950 CCACATTCCCTCAGAGCCAT 59.450 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1047 0.549950 ATGGCTCTGAGGGAATGTGG 59.450 55.000 6.83 0.0 0.00 4.17 R
1316 1339 0.599204 GGTCGAACCTCGCAAACAGA 60.599 55.000 0.00 0.0 40.21 3.41 R
2412 2444 1.134175 GGTGAGCTCGAGGAGAAGAAG 59.866 57.143 15.58 0.0 0.00 2.85 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
20 21 3.893326 TGCTATAGCTGAGCTTGTGAA 57.107 42.857 24.61 0.00 40.44 3.18
21 22 3.525537 TGCTATAGCTGAGCTTGTGAAC 58.474 45.455 24.61 0.00 40.44 3.18
22 23 2.869192 GCTATAGCTGAGCTTGTGAACC 59.131 50.000 14.14 0.00 40.44 3.62
23 24 2.409948 ATAGCTGAGCTTGTGAACCC 57.590 50.000 14.14 0.00 40.44 4.11
24 25 1.055849 TAGCTGAGCTTGTGAACCCA 58.944 50.000 14.14 0.00 40.44 4.51
25 26 0.183492 AGCTGAGCTTGTGAACCCAA 59.817 50.000 0.00 0.00 33.89 4.12
26 27 0.595095 GCTGAGCTTGTGAACCCAAG 59.405 55.000 0.00 0.00 43.76 3.61
35 36 4.696455 CTTGTGAACCCAAGCAAATTTCT 58.304 39.130 0.00 0.00 35.80 2.52
36 37 4.320608 TGTGAACCCAAGCAAATTTCTC 57.679 40.909 0.00 0.00 0.00 2.87
37 38 3.960102 TGTGAACCCAAGCAAATTTCTCT 59.040 39.130 0.00 0.00 0.00 3.10
38 39 4.037923 TGTGAACCCAAGCAAATTTCTCTC 59.962 41.667 0.00 0.00 0.00 3.20
39 40 3.573967 TGAACCCAAGCAAATTTCTCTCC 59.426 43.478 0.00 0.00 0.00 3.71
40 41 3.243359 ACCCAAGCAAATTTCTCTCCA 57.757 42.857 0.00 0.00 0.00 3.86
41 42 3.575805 ACCCAAGCAAATTTCTCTCCAA 58.424 40.909 0.00 0.00 0.00 3.53
42 43 3.966665 ACCCAAGCAAATTTCTCTCCAAA 59.033 39.130 0.00 0.00 0.00 3.28
43 44 4.408596 ACCCAAGCAAATTTCTCTCCAAAA 59.591 37.500 0.00 0.00 0.00 2.44
44 45 5.072193 ACCCAAGCAAATTTCTCTCCAAAAT 59.928 36.000 0.00 0.00 0.00 1.82
45 46 5.410439 CCCAAGCAAATTTCTCTCCAAAATG 59.590 40.000 0.00 0.00 0.00 2.32
46 47 5.106830 CCAAGCAAATTTCTCTCCAAAATGC 60.107 40.000 0.00 0.00 34.64 3.56
47 48 5.217978 AGCAAATTTCTCTCCAAAATGCA 57.782 34.783 0.00 0.00 35.86 3.96
48 49 5.235516 AGCAAATTTCTCTCCAAAATGCAG 58.764 37.500 0.00 0.00 35.86 4.41
49 50 4.142966 GCAAATTTCTCTCCAAAATGCAGC 60.143 41.667 0.00 0.00 34.60 5.25
50 51 4.877378 AATTTCTCTCCAAAATGCAGCA 57.123 36.364 0.00 0.00 0.00 4.41
51 52 5.416271 AATTTCTCTCCAAAATGCAGCAT 57.584 34.783 0.52 0.52 0.00 3.79
52 53 4.877378 TTTCTCTCCAAAATGCAGCATT 57.123 36.364 15.33 15.33 35.39 3.56
53 54 4.877378 TTCTCTCCAAAATGCAGCATTT 57.123 36.364 25.07 25.07 44.62 2.32
54 55 4.445452 TCTCTCCAAAATGCAGCATTTC 57.555 40.909 29.42 0.00 42.32 2.17
55 56 4.084287 TCTCTCCAAAATGCAGCATTTCT 58.916 39.130 29.42 18.14 42.32 2.52
56 57 5.255687 TCTCTCCAAAATGCAGCATTTCTA 58.744 37.500 29.42 17.90 42.32 2.10
57 58 5.711506 TCTCTCCAAAATGCAGCATTTCTAA 59.288 36.000 29.42 17.59 42.32 2.10
58 59 5.713025 TCTCCAAAATGCAGCATTTCTAAC 58.287 37.500 29.42 0.00 42.32 2.34
59 60 5.243507 TCTCCAAAATGCAGCATTTCTAACA 59.756 36.000 29.42 13.81 42.32 2.41
60 61 6.040209 TCCAAAATGCAGCATTTCTAACAT 57.960 33.333 29.42 13.21 42.32 2.71
61 62 6.465948 TCCAAAATGCAGCATTTCTAACATT 58.534 32.000 29.42 12.54 42.32 2.71
62 63 6.369340 TCCAAAATGCAGCATTTCTAACATTG 59.631 34.615 29.42 21.57 42.32 2.82
63 64 6.148150 CCAAAATGCAGCATTTCTAACATTGT 59.852 34.615 29.42 11.20 42.32 2.71
64 65 6.956299 AAATGCAGCATTTCTAACATTGTC 57.044 33.333 25.07 0.00 39.50 3.18
65 66 5.909621 ATGCAGCATTTCTAACATTGTCT 57.090 34.783 0.52 0.00 0.00 3.41
66 67 7.395190 AATGCAGCATTTCTAACATTGTCTA 57.605 32.000 15.33 0.00 32.61 2.59
67 68 7.578310 ATGCAGCATTTCTAACATTGTCTAT 57.422 32.000 0.52 0.00 0.00 1.98
68 69 6.788243 TGCAGCATTTCTAACATTGTCTATG 58.212 36.000 0.00 0.00 40.26 2.23
69 70 5.684626 GCAGCATTTCTAACATTGTCTATGC 59.315 40.000 0.00 0.00 37.81 3.14
70 71 6.459298 GCAGCATTTCTAACATTGTCTATGCT 60.459 38.462 13.57 13.57 45.87 3.79
71 72 7.254898 GCAGCATTTCTAACATTGTCTATGCTA 60.255 37.037 16.57 0.00 43.87 3.49
72 73 8.066595 CAGCATTTCTAACATTGTCTATGCTAC 58.933 37.037 16.57 0.00 43.87 3.58
73 74 7.989741 AGCATTTCTAACATTGTCTATGCTACT 59.010 33.333 15.95 0.00 43.87 2.57
74 75 8.279103 GCATTTCTAACATTGTCTATGCTACTC 58.721 37.037 0.00 0.00 37.81 2.59
75 76 9.539825 CATTTCTAACATTGTCTATGCTACTCT 57.460 33.333 0.00 0.00 37.81 3.24
77 78 9.944376 TTTCTAACATTGTCTATGCTACTCTTT 57.056 29.630 0.00 0.00 37.81 2.52
78 79 9.944376 TTCTAACATTGTCTATGCTACTCTTTT 57.056 29.630 0.00 0.00 37.81 2.27
79 80 9.587772 TCTAACATTGTCTATGCTACTCTTTTC 57.412 33.333 0.00 0.00 37.81 2.29
80 81 9.593134 CTAACATTGTCTATGCTACTCTTTTCT 57.407 33.333 0.00 0.00 37.81 2.52
81 82 7.840342 ACATTGTCTATGCTACTCTTTTCTG 57.160 36.000 0.00 0.00 37.81 3.02
82 83 6.314896 ACATTGTCTATGCTACTCTTTTCTGC 59.685 38.462 0.00 0.00 37.81 4.26
83 84 4.424626 TGTCTATGCTACTCTTTTCTGCG 58.575 43.478 0.00 0.00 0.00 5.18
84 85 3.799420 GTCTATGCTACTCTTTTCTGCGG 59.201 47.826 0.00 0.00 0.00 5.69
85 86 3.699538 TCTATGCTACTCTTTTCTGCGGA 59.300 43.478 0.00 0.00 0.00 5.54
86 87 3.550437 ATGCTACTCTTTTCTGCGGAT 57.450 42.857 0.00 0.00 0.00 4.18
87 88 4.672587 ATGCTACTCTTTTCTGCGGATA 57.327 40.909 0.00 0.00 0.00 2.59
88 89 4.046938 TGCTACTCTTTTCTGCGGATAG 57.953 45.455 0.00 0.00 0.00 2.08
89 90 3.447586 TGCTACTCTTTTCTGCGGATAGT 59.552 43.478 0.00 0.93 0.00 2.12
90 91 4.081642 TGCTACTCTTTTCTGCGGATAGTT 60.082 41.667 0.00 0.00 0.00 2.24
91 92 4.268884 GCTACTCTTTTCTGCGGATAGTTG 59.731 45.833 0.00 1.04 0.00 3.16
92 93 4.273148 ACTCTTTTCTGCGGATAGTTGT 57.727 40.909 0.00 0.00 0.00 3.32
93 94 4.246458 ACTCTTTTCTGCGGATAGTTGTC 58.754 43.478 0.00 0.00 0.00 3.18
94 95 4.021016 ACTCTTTTCTGCGGATAGTTGTCT 60.021 41.667 0.00 0.00 0.00 3.41
95 96 5.185249 ACTCTTTTCTGCGGATAGTTGTCTA 59.815 40.000 0.00 0.00 0.00 2.59
96 97 6.127310 ACTCTTTTCTGCGGATAGTTGTCTAT 60.127 38.462 0.00 0.00 39.31 1.98
97 98 7.068348 ACTCTTTTCTGCGGATAGTTGTCTATA 59.932 37.037 0.00 0.00 37.05 1.31
98 99 7.201145 TCTTTTCTGCGGATAGTTGTCTATAC 58.799 38.462 0.00 0.00 37.05 1.47
99 100 6.710597 TTTCTGCGGATAGTTGTCTATACT 57.289 37.500 0.00 0.00 37.05 2.12
100 101 7.812690 TTTCTGCGGATAGTTGTCTATACTA 57.187 36.000 0.00 0.00 37.05 1.82
101 102 6.798315 TCTGCGGATAGTTGTCTATACTAC 57.202 41.667 0.00 0.00 37.05 2.73
102 103 6.531923 TCTGCGGATAGTTGTCTATACTACT 58.468 40.000 0.00 1.42 42.98 2.57
103 104 6.427242 TCTGCGGATAGTTGTCTATACTACTG 59.573 42.308 5.77 0.00 41.04 2.74
104 105 6.293698 TGCGGATAGTTGTCTATACTACTGA 58.706 40.000 5.77 0.00 41.04 3.41
105 106 6.204301 TGCGGATAGTTGTCTATACTACTGAC 59.796 42.308 5.77 0.00 41.04 3.51
106 107 6.427547 GCGGATAGTTGTCTATACTACTGACT 59.572 42.308 5.77 0.00 41.04 3.41
107 108 7.360269 GCGGATAGTTGTCTATACTACTGACTC 60.360 44.444 5.77 1.50 41.04 3.36
108 109 7.656542 CGGATAGTTGTCTATACTACTGACTCA 59.343 40.741 5.77 0.00 41.04 3.41
109 110 9.339850 GGATAGTTGTCTATACTACTGACTCAA 57.660 37.037 5.77 0.00 41.04 3.02
113 114 9.862371 AGTTGTCTATACTACTGACTCAAATTG 57.138 33.333 0.00 0.00 39.72 2.32
114 115 9.088512 GTTGTCTATACTACTGACTCAAATTGG 57.911 37.037 0.00 0.00 0.00 3.16
115 116 7.265673 TGTCTATACTACTGACTCAAATTGGC 58.734 38.462 0.00 0.00 0.00 4.52
116 117 7.124298 TGTCTATACTACTGACTCAAATTGGCT 59.876 37.037 0.00 0.00 0.00 4.75
117 118 8.630917 GTCTATACTACTGACTCAAATTGGCTA 58.369 37.037 0.00 0.00 0.00 3.93
118 119 9.197306 TCTATACTACTGACTCAAATTGGCTAA 57.803 33.333 0.00 0.00 0.00 3.09
119 120 9.988815 CTATACTACTGACTCAAATTGGCTAAT 57.011 33.333 0.00 0.00 0.00 1.73
121 122 9.686683 ATACTACTGACTCAAATTGGCTAATTT 57.313 29.630 14.39 14.39 45.01 1.82
122 123 8.409358 ACTACTGACTCAAATTGGCTAATTTT 57.591 30.769 17.17 4.50 42.33 1.82
123 124 8.299570 ACTACTGACTCAAATTGGCTAATTTTG 58.700 33.333 17.17 14.76 42.33 2.44
124 125 7.288810 ACTGACTCAAATTGGCTAATTTTGA 57.711 32.000 17.17 15.67 42.33 2.69
125 126 7.147976 ACTGACTCAAATTGGCTAATTTTGAC 58.852 34.615 17.17 13.27 42.33 3.18
126 127 7.014615 ACTGACTCAAATTGGCTAATTTTGACT 59.985 33.333 17.17 8.21 42.33 3.41
127 128 7.147312 TGACTCAAATTGGCTAATTTTGACTG 58.853 34.615 17.17 7.76 42.33 3.51
128 129 7.014134 TGACTCAAATTGGCTAATTTTGACTGA 59.986 33.333 17.17 11.32 42.33 3.41
129 130 7.899973 ACTCAAATTGGCTAATTTTGACTGAT 58.100 30.769 17.17 2.07 42.33 2.90
130 131 8.031277 ACTCAAATTGGCTAATTTTGACTGATC 58.969 33.333 17.17 0.00 42.33 2.92
131 132 7.894708 TCAAATTGGCTAATTTTGACTGATCA 58.105 30.769 17.17 0.00 42.33 2.92
132 133 8.030692 TCAAATTGGCTAATTTTGACTGATCAG 58.969 33.333 21.37 21.37 42.33 2.90
133 134 7.472334 AATTGGCTAATTTTGACTGATCAGT 57.528 32.000 28.23 28.23 37.52 3.41
134 135 6.899393 TTGGCTAATTTTGACTGATCAGTT 57.101 33.333 28.46 14.50 42.66 3.16
135 136 6.258230 TGGCTAATTTTGACTGATCAGTTG 57.742 37.500 28.46 12.40 42.66 3.16
136 137 5.098211 GGCTAATTTTGACTGATCAGTTGC 58.902 41.667 28.46 17.40 42.66 4.17
137 138 5.335897 GGCTAATTTTGACTGATCAGTTGCA 60.336 40.000 28.46 19.74 42.66 4.08
138 139 6.151691 GCTAATTTTGACTGATCAGTTGCAA 58.848 36.000 28.46 23.89 42.66 4.08
139 140 6.642131 GCTAATTTTGACTGATCAGTTGCAAA 59.358 34.615 28.46 27.43 42.66 3.68
140 141 7.169645 GCTAATTTTGACTGATCAGTTGCAAAA 59.830 33.333 34.36 34.36 43.19 2.44
141 142 9.199982 CTAATTTTGACTGATCAGTTGCAAAAT 57.800 29.630 35.05 35.05 46.38 1.82
142 143 7.647907 ATTTTGACTGATCAGTTGCAAAATC 57.352 32.000 35.05 22.12 44.05 2.17
143 144 4.771590 TGACTGATCAGTTGCAAAATCC 57.228 40.909 28.46 13.23 42.66 3.01
144 145 4.401022 TGACTGATCAGTTGCAAAATCCT 58.599 39.130 28.46 1.61 42.66 3.24
145 146 4.828939 TGACTGATCAGTTGCAAAATCCTT 59.171 37.500 28.46 1.39 42.66 3.36
146 147 5.302568 TGACTGATCAGTTGCAAAATCCTTT 59.697 36.000 28.46 0.92 42.66 3.11
147 148 5.535333 ACTGATCAGTTGCAAAATCCTTTG 58.465 37.500 22.89 0.00 40.84 2.77
148 149 5.302568 ACTGATCAGTTGCAAAATCCTTTGA 59.697 36.000 22.89 0.00 40.58 2.69
149 150 5.775686 TGATCAGTTGCAAAATCCTTTGAG 58.224 37.500 0.00 0.00 44.03 3.02
150 151 5.302568 TGATCAGTTGCAAAATCCTTTGAGT 59.697 36.000 0.00 0.00 44.03 3.41
151 152 5.596836 TCAGTTGCAAAATCCTTTGAGTT 57.403 34.783 0.00 0.00 44.03 3.01
152 153 5.976458 TCAGTTGCAAAATCCTTTGAGTTT 58.024 33.333 0.00 0.00 44.03 2.66
162 163 8.881743 CAAAATCCTTTGAGTTTGTTTGATTCA 58.118 29.630 7.18 0.00 46.27 2.57
163 164 9.617523 AAAATCCTTTGAGTTTGTTTGATTCAT 57.382 25.926 0.00 0.00 37.39 2.57
164 165 8.822652 AATCCTTTGAGTTTGTTTGATTCATC 57.177 30.769 0.00 0.00 0.00 2.92
165 166 7.587037 TCCTTTGAGTTTGTTTGATTCATCT 57.413 32.000 0.00 0.00 0.00 2.90
166 167 7.651808 TCCTTTGAGTTTGTTTGATTCATCTC 58.348 34.615 0.00 0.00 0.00 2.75
167 168 7.503566 TCCTTTGAGTTTGTTTGATTCATCTCT 59.496 33.333 0.00 0.00 0.00 3.10
168 169 7.594015 CCTTTGAGTTTGTTTGATTCATCTCTG 59.406 37.037 0.00 0.00 0.00 3.35
169 170 7.806409 TTGAGTTTGTTTGATTCATCTCTGA 57.194 32.000 0.00 0.00 0.00 3.27
170 171 7.806409 TGAGTTTGTTTGATTCATCTCTGAA 57.194 32.000 0.00 0.00 45.15 3.02
171 172 8.224389 TGAGTTTGTTTGATTCATCTCTGAAA 57.776 30.769 0.00 0.00 44.29 2.69
172 173 8.853126 TGAGTTTGTTTGATTCATCTCTGAAAT 58.147 29.630 0.00 0.00 44.29 2.17
233 234 8.706322 ATTCCTTATTTTGTTCCAACTACACT 57.294 30.769 0.00 0.00 0.00 3.55
234 235 8.528044 TTCCTTATTTTGTTCCAACTACACTT 57.472 30.769 0.00 0.00 0.00 3.16
235 236 7.936584 TCCTTATTTTGTTCCAACTACACTTG 58.063 34.615 0.00 0.00 0.00 3.16
236 237 7.558444 TCCTTATTTTGTTCCAACTACACTTGT 59.442 33.333 0.00 0.00 0.00 3.16
237 238 7.647715 CCTTATTTTGTTCCAACTACACTTGTG 59.352 37.037 0.00 0.00 0.00 3.33
238 239 5.968528 TTTTGTTCCAACTACACTTGTGT 57.031 34.783 11.30 11.30 0.00 3.72
239 240 5.968528 TTTGTTCCAACTACACTTGTGTT 57.031 34.783 11.80 0.14 0.00 3.32
240 241 5.968528 TTGTTCCAACTACACTTGTGTTT 57.031 34.783 11.80 0.00 0.00 2.83
241 242 7.450124 TTTGTTCCAACTACACTTGTGTTTA 57.550 32.000 11.80 0.00 0.00 2.01
242 243 6.425577 TGTTCCAACTACACTTGTGTTTAC 57.574 37.500 11.80 0.00 0.00 2.01
243 244 5.938710 TGTTCCAACTACACTTGTGTTTACA 59.061 36.000 11.80 1.15 34.31 2.41
244 245 6.430308 TGTTCCAACTACACTTGTGTTTACAA 59.570 34.615 11.80 0.00 44.17 2.41
245 246 7.040617 TGTTCCAACTACACTTGTGTTTACAAA 60.041 33.333 11.80 0.00 45.53 2.83
246 247 7.450124 TCCAACTACACTTGTGTTTACAAAA 57.550 32.000 11.80 0.00 45.53 2.44
247 248 8.057536 TCCAACTACACTTGTGTTTACAAAAT 57.942 30.769 11.80 0.00 45.53 1.82
248 249 7.971168 TCCAACTACACTTGTGTTTACAAAATG 59.029 33.333 11.80 0.00 45.53 2.32
249 250 7.971168 CCAACTACACTTGTGTTTACAAAATGA 59.029 33.333 11.80 0.00 45.53 2.57
250 251 8.794406 CAACTACACTTGTGTTTACAAAATGAC 58.206 33.333 11.80 0.00 45.53 3.06
251 252 8.276252 ACTACACTTGTGTTTACAAAATGACT 57.724 30.769 11.80 0.00 45.53 3.41
252 253 8.181573 ACTACACTTGTGTTTACAAAATGACTG 58.818 33.333 11.80 4.24 45.53 3.51
253 254 7.151999 ACACTTGTGTTTACAAAATGACTGA 57.848 32.000 0.00 0.00 45.53 3.41
254 255 7.598278 ACACTTGTGTTTACAAAATGACTGAA 58.402 30.769 0.00 0.00 45.53 3.02
255 256 7.540745 ACACTTGTGTTTACAAAATGACTGAAC 59.459 33.333 0.00 0.00 45.53 3.18
256 257 7.754924 CACTTGTGTTTACAAAATGACTGAACT 59.245 33.333 0.00 0.00 45.53 3.01
257 258 8.952278 ACTTGTGTTTACAAAATGACTGAACTA 58.048 29.630 0.00 0.00 45.53 2.24
258 259 9.950680 CTTGTGTTTACAAAATGACTGAACTAT 57.049 29.630 0.00 0.00 45.53 2.12
273 274 8.846211 TGACTGAACTATTTACAAGAAAAAGGG 58.154 33.333 0.00 0.00 0.00 3.95
274 275 8.178313 ACTGAACTATTTACAAGAAAAAGGGG 57.822 34.615 0.00 0.00 0.00 4.79
275 276 6.988522 TGAACTATTTACAAGAAAAAGGGGC 58.011 36.000 0.00 0.00 0.00 5.80
276 277 6.551601 TGAACTATTTACAAGAAAAAGGGGCA 59.448 34.615 0.00 0.00 0.00 5.36
304 305 6.455647 TGCCTATATCCGTGAATCTAACAAG 58.544 40.000 0.00 0.00 0.00 3.16
325 326 4.273318 AGATATTCTTGGAACCAACAGGC 58.727 43.478 1.83 0.00 0.00 4.85
331 332 3.010027 TCTTGGAACCAACAGGCATATCA 59.990 43.478 1.83 0.00 0.00 2.15
344 345 7.502120 ACAGGCATATCAAGATCAATGTTAC 57.498 36.000 0.00 0.00 0.00 2.50
357 358 8.114331 AGATCAATGTTACTGAATTCAAGCAA 57.886 30.769 9.88 1.06 0.00 3.91
422 423 9.965824 GAATGAAACTTCCACTAAAAATCTTCA 57.034 29.630 0.00 0.00 0.00 3.02
450 461 7.561021 TGTGTTACTATGCTTTGAAAACTCA 57.439 32.000 0.00 0.00 0.00 3.41
464 475 8.795842 TTTGAAAACTCACTCAAACCTAAGTA 57.204 30.769 0.00 0.00 36.79 2.24
471 482 4.217118 TCACTCAAACCTAAGTAGACCGTC 59.783 45.833 0.00 0.00 0.00 4.79
476 487 4.516365 AACCTAAGTAGACCGTCTGTTG 57.484 45.455 11.52 0.00 0.00 3.33
523 534 4.746611 CCTTTTTCAAACAAGGATCACTGC 59.253 41.667 2.13 0.00 42.11 4.40
535 546 6.820656 ACAAGGATCACTGCATAAAAGTAGAG 59.179 38.462 0.00 0.00 0.00 2.43
556 567 2.799562 GCGGGGCAAGCTATGAATTTTC 60.800 50.000 0.00 0.00 0.00 2.29
562 573 6.183360 GGGGCAAGCTATGAATTTTCAGTATT 60.183 38.462 0.00 0.00 41.08 1.89
591 602 7.439157 TCCATAATGATTTAGCAAGATTCCG 57.561 36.000 0.00 0.00 0.00 4.30
610 621 1.678728 CGTAACATGCACCACCAGGAT 60.679 52.381 0.00 0.00 38.69 3.24
635 646 2.514803 AGTTAGAGCGGGTGCATTTTT 58.485 42.857 0.00 0.00 46.23 1.94
640 651 3.616219 AGAGCGGGTGCATTTTTGTATA 58.384 40.909 0.00 0.00 46.23 1.47
641 652 4.207165 AGAGCGGGTGCATTTTTGTATAT 58.793 39.130 0.00 0.00 46.23 0.86
644 655 3.380142 CGGGTGCATTTTTGTATATGCC 58.620 45.455 0.00 0.00 45.03 4.40
733 750 3.403968 GGTGGACCAGAGACTTTTCTTC 58.596 50.000 0.00 0.00 35.64 2.87
734 751 3.071747 GGTGGACCAGAGACTTTTCTTCT 59.928 47.826 0.00 0.00 35.64 2.85
735 752 4.283722 GGTGGACCAGAGACTTTTCTTCTA 59.716 45.833 0.00 0.00 35.64 2.10
750 767 7.809806 ACTTTTCTTCTAAGATTTCGCAAATGG 59.190 33.333 0.00 0.00 34.49 3.16
849 872 4.379243 ACAGGCCGCTTCTCACCG 62.379 66.667 0.00 0.00 0.00 4.94
932 955 1.556911 CCACAGGCTACTTCTGACCAT 59.443 52.381 0.00 0.00 36.22 3.55
1020 1043 3.506067 GCCTATTTAAACAGCACACACCT 59.494 43.478 0.00 0.00 0.00 4.00
1024 1047 1.593196 TAAACAGCACACACCTGCTC 58.407 50.000 0.00 0.00 44.58 4.26
1043 1066 0.549950 CCACATTCCCTCAGAGCCAT 59.450 55.000 0.00 0.00 0.00 4.40
1157 1180 1.021390 AAGGCGCCTTCAACTCATCG 61.021 55.000 35.84 0.00 0.00 3.84
1163 1186 1.407437 GCCTTCAACTCATCGGTGGAT 60.407 52.381 0.00 0.00 0.00 3.41
1208 1231 1.077285 CCATGATGGCCTGCTGTCA 60.077 57.895 3.32 0.88 0.00 3.58
1232 1255 2.509916 GAGATGGCCCAGGAGCTG 59.490 66.667 0.00 0.00 0.00 4.24
1271 1294 0.663153 AGAAGCACTTTGGCGTTGAC 59.337 50.000 0.00 0.00 39.27 3.18
1288 1311 4.147449 CGAGTCCGCCATGAGCCA 62.147 66.667 0.00 0.00 38.78 4.75
1316 1339 0.390124 TTGTCGAGCTTTACCGTGGT 59.610 50.000 0.00 0.00 0.00 4.16
1451 1474 0.041238 AGATGGTGGTCGAGGAAGGA 59.959 55.000 0.00 0.00 0.00 3.36
1564 1587 9.549509 GCATGTTCACGAATTGTAACTTTTATA 57.450 29.630 0.00 0.00 0.00 0.98
1637 1660 5.695851 AATAAGTGAAACAGAAGCCACAG 57.304 39.130 0.00 0.00 41.43 3.66
1651 1674 4.445452 AGCCACAGCATCAGTTTAATTG 57.555 40.909 0.00 0.00 43.56 2.32
1668 1691 9.683069 AGTTTAATTGACAAAATGACAAGCTAG 57.317 29.630 0.00 0.00 35.72 3.42
1690 1713 7.968405 GCTAGTTATGTAAAGGGAAATGTTGTG 59.032 37.037 0.00 0.00 0.00 3.33
1759 1782 8.387354 CAGTTTTAGAATTTGGGTGTTTTGTTC 58.613 33.333 0.00 0.00 0.00 3.18
1764 1787 5.186797 AGAATTTGGGTGTTTTGTTCTCACA 59.813 36.000 0.00 0.00 34.27 3.58
1850 1873 8.352942 ACCAAGAAGAATCAGATTAACACAAAC 58.647 33.333 0.00 0.00 0.00 2.93
1870 1893 3.305964 ACTGAATCAACCGCGTATATCG 58.694 45.455 4.92 0.00 43.12 2.92
1926 1950 7.873505 ACCTCATGTTAGTACAAAGAGAAGTTC 59.126 37.037 0.00 0.00 40.28 3.01
2085 2110 4.124970 TGATTCATCTGCTACTCACATGC 58.875 43.478 0.00 0.00 0.00 4.06
2176 2201 1.136305 CCATGCTGCCCTTTCTGAATG 59.864 52.381 0.00 0.00 0.00 2.67
2215 2240 8.522830 TCCCAAAATGTTCTTTTGCTAATAGAG 58.477 33.333 5.18 0.00 37.89 2.43
2271 2296 2.140717 GGTATAACATACACCGCCAGC 58.859 52.381 0.00 0.00 0.00 4.85
2334 2365 6.608610 ACTGTTAGATAATGGCAACGAAAAC 58.391 36.000 0.00 0.00 42.51 2.43
2362 2393 5.247110 AGCCATATACTGCTAATACTGCTGT 59.753 40.000 0.66 0.66 43.23 4.40
2412 2444 0.743097 GCAACCCATGAGCTCAATCC 59.257 55.000 22.50 1.47 0.00 3.01
2489 2521 3.259374 TCTTTGATCTCCAGTGACCTCAC 59.741 47.826 0.00 0.00 46.77 3.51
2505 2537 2.921754 CCTCACGAAGTTAAAGTAGGCG 59.078 50.000 0.00 0.00 41.61 5.52
2551 2583 1.071699 ACCAGTAGTTGACGGCAATGT 59.928 47.619 7.13 0.00 36.22 2.71
2557 2589 0.593128 GTTGACGGCAATGTTGAGCT 59.407 50.000 7.13 0.00 36.22 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.525537 GTTCACAAGCTCAGCTATAGCA 58.474 45.455 26.07 6.04 45.16 3.49
1 2 2.869192 GGTTCACAAGCTCAGCTATAGC 59.131 50.000 17.33 17.33 38.25 2.97
2 3 3.118629 TGGGTTCACAAGCTCAGCTATAG 60.119 47.826 0.00 0.00 38.25 1.31
3 4 2.837591 TGGGTTCACAAGCTCAGCTATA 59.162 45.455 0.00 0.00 38.25 1.31
4 5 1.630369 TGGGTTCACAAGCTCAGCTAT 59.370 47.619 0.00 0.00 38.25 2.97
5 6 1.055849 TGGGTTCACAAGCTCAGCTA 58.944 50.000 0.00 0.00 38.25 3.32
6 7 0.183492 TTGGGTTCACAAGCTCAGCT 59.817 50.000 0.00 0.00 42.56 4.24
7 8 0.595095 CTTGGGTTCACAAGCTCAGC 59.405 55.000 1.79 0.00 41.09 4.26
14 15 4.405358 AGAGAAATTTGCTTGGGTTCACAA 59.595 37.500 0.00 0.00 0.00 3.33
15 16 3.960102 AGAGAAATTTGCTTGGGTTCACA 59.040 39.130 0.00 0.00 0.00 3.58
16 17 4.550422 GAGAGAAATTTGCTTGGGTTCAC 58.450 43.478 0.00 0.00 0.00 3.18
17 18 3.573967 GGAGAGAAATTTGCTTGGGTTCA 59.426 43.478 0.00 0.00 0.00 3.18
18 19 3.573967 TGGAGAGAAATTTGCTTGGGTTC 59.426 43.478 0.00 0.00 0.00 3.62
19 20 3.575805 TGGAGAGAAATTTGCTTGGGTT 58.424 40.909 0.00 0.00 0.00 4.11
20 21 3.243359 TGGAGAGAAATTTGCTTGGGT 57.757 42.857 0.00 0.00 0.00 4.51
21 22 4.605640 TTTGGAGAGAAATTTGCTTGGG 57.394 40.909 0.00 0.00 0.00 4.12
22 23 5.106830 GCATTTTGGAGAGAAATTTGCTTGG 60.107 40.000 0.00 0.00 0.00 3.61
23 24 5.467399 TGCATTTTGGAGAGAAATTTGCTTG 59.533 36.000 0.00 0.00 30.95 4.01
24 25 5.613329 TGCATTTTGGAGAGAAATTTGCTT 58.387 33.333 0.00 0.00 30.95 3.91
25 26 5.217978 TGCATTTTGGAGAGAAATTTGCT 57.782 34.783 0.00 0.00 30.95 3.91
26 27 4.142966 GCTGCATTTTGGAGAGAAATTTGC 60.143 41.667 0.00 0.00 38.14 3.68
27 28 4.992319 TGCTGCATTTTGGAGAGAAATTTG 59.008 37.500 0.00 0.00 38.14 2.32
28 29 5.217978 TGCTGCATTTTGGAGAGAAATTT 57.782 34.783 0.00 0.00 38.14 1.82
29 30 4.877378 TGCTGCATTTTGGAGAGAAATT 57.123 36.364 0.00 0.00 38.14 1.82
30 31 5.416271 AATGCTGCATTTTGGAGAGAAAT 57.584 34.783 21.48 0.00 38.14 2.17
31 32 4.877378 AATGCTGCATTTTGGAGAGAAA 57.123 36.364 21.48 0.00 38.14 2.52
32 33 4.525487 AGAAATGCTGCATTTTGGAGAGAA 59.475 37.500 33.57 0.00 43.05 2.87
33 34 4.084287 AGAAATGCTGCATTTTGGAGAGA 58.916 39.130 33.57 0.00 43.05 3.10
34 35 4.451629 AGAAATGCTGCATTTTGGAGAG 57.548 40.909 33.57 0.00 43.05 3.20
35 36 5.243507 TGTTAGAAATGCTGCATTTTGGAGA 59.756 36.000 33.57 20.47 43.05 3.71
36 37 5.472148 TGTTAGAAATGCTGCATTTTGGAG 58.528 37.500 33.57 0.00 43.05 3.86
37 38 5.465532 TGTTAGAAATGCTGCATTTTGGA 57.534 34.783 33.57 21.75 43.05 3.53
38 39 6.148150 ACAATGTTAGAAATGCTGCATTTTGG 59.852 34.615 33.57 20.29 43.05 3.28
39 40 7.117236 AGACAATGTTAGAAATGCTGCATTTTG 59.883 33.333 33.57 27.37 43.05 2.44
40 41 7.156673 AGACAATGTTAGAAATGCTGCATTTT 58.843 30.769 33.57 25.44 43.05 1.82
41 42 6.694447 AGACAATGTTAGAAATGCTGCATTT 58.306 32.000 33.67 33.67 45.25 2.32
42 43 6.276832 AGACAATGTTAGAAATGCTGCATT 57.723 33.333 21.48 21.48 35.39 3.56
43 44 5.909621 AGACAATGTTAGAAATGCTGCAT 57.090 34.783 9.81 9.81 0.00 3.96
44 45 6.678655 GCATAGACAATGTTAGAAATGCTGCA 60.679 38.462 4.13 4.13 37.93 4.41
45 46 5.684626 GCATAGACAATGTTAGAAATGCTGC 59.315 40.000 10.11 0.00 37.93 5.25
46 47 7.024340 AGCATAGACAATGTTAGAAATGCTG 57.976 36.000 15.67 0.00 45.11 4.41
48 49 8.147642 AGTAGCATAGACAATGTTAGAAATGC 57.852 34.615 9.64 9.64 37.93 3.56
49 50 9.539825 AGAGTAGCATAGACAATGTTAGAAATG 57.460 33.333 0.00 0.00 37.93 2.32
51 52 9.944376 AAAGAGTAGCATAGACAATGTTAGAAA 57.056 29.630 0.00 0.00 37.93 2.52
52 53 9.944376 AAAAGAGTAGCATAGACAATGTTAGAA 57.056 29.630 0.00 0.00 37.93 2.10
53 54 9.587772 GAAAAGAGTAGCATAGACAATGTTAGA 57.412 33.333 0.00 0.00 37.93 2.10
54 55 9.593134 AGAAAAGAGTAGCATAGACAATGTTAG 57.407 33.333 0.00 0.00 37.93 2.34
55 56 9.371136 CAGAAAAGAGTAGCATAGACAATGTTA 57.629 33.333 0.00 0.00 37.93 2.41
56 57 7.148340 GCAGAAAAGAGTAGCATAGACAATGTT 60.148 37.037 0.00 0.00 37.93 2.71
57 58 6.314896 GCAGAAAAGAGTAGCATAGACAATGT 59.685 38.462 0.00 0.00 37.93 2.71
58 59 6.509199 CGCAGAAAAGAGTAGCATAGACAATG 60.509 42.308 0.00 0.00 38.74 2.82
59 60 5.521735 CGCAGAAAAGAGTAGCATAGACAAT 59.478 40.000 0.00 0.00 0.00 2.71
60 61 4.864806 CGCAGAAAAGAGTAGCATAGACAA 59.135 41.667 0.00 0.00 0.00 3.18
61 62 4.424626 CGCAGAAAAGAGTAGCATAGACA 58.575 43.478 0.00 0.00 0.00 3.41
62 63 3.799420 CCGCAGAAAAGAGTAGCATAGAC 59.201 47.826 0.00 0.00 0.00 2.59
63 64 3.699538 TCCGCAGAAAAGAGTAGCATAGA 59.300 43.478 0.00 0.00 0.00 1.98
64 65 4.046938 TCCGCAGAAAAGAGTAGCATAG 57.953 45.455 0.00 0.00 0.00 2.23
65 66 4.672587 ATCCGCAGAAAAGAGTAGCATA 57.327 40.909 0.00 0.00 0.00 3.14
66 67 3.550437 ATCCGCAGAAAAGAGTAGCAT 57.450 42.857 0.00 0.00 0.00 3.79
67 68 3.447586 ACTATCCGCAGAAAAGAGTAGCA 59.552 43.478 0.00 0.00 0.00 3.49
68 69 4.048241 ACTATCCGCAGAAAAGAGTAGC 57.952 45.455 0.00 0.00 0.00 3.58
69 70 5.411781 ACAACTATCCGCAGAAAAGAGTAG 58.588 41.667 0.00 0.00 0.00 2.57
70 71 5.185249 AGACAACTATCCGCAGAAAAGAGTA 59.815 40.000 0.00 0.00 0.00 2.59
71 72 4.021016 AGACAACTATCCGCAGAAAAGAGT 60.021 41.667 0.00 0.00 0.00 3.24
72 73 4.499183 AGACAACTATCCGCAGAAAAGAG 58.501 43.478 0.00 0.00 0.00 2.85
73 74 4.537135 AGACAACTATCCGCAGAAAAGA 57.463 40.909 0.00 0.00 0.00 2.52
74 75 7.203910 AGTATAGACAACTATCCGCAGAAAAG 58.796 38.462 0.00 0.00 39.64 2.27
75 76 7.108841 AGTATAGACAACTATCCGCAGAAAA 57.891 36.000 0.00 0.00 39.64 2.29
76 77 6.710597 AGTATAGACAACTATCCGCAGAAA 57.289 37.500 0.00 0.00 39.64 2.52
77 78 6.996879 AGTAGTATAGACAACTATCCGCAGAA 59.003 38.462 0.00 0.00 39.64 3.02
78 79 6.427242 CAGTAGTATAGACAACTATCCGCAGA 59.573 42.308 0.00 0.00 39.64 4.26
79 80 6.427242 TCAGTAGTATAGACAACTATCCGCAG 59.573 42.308 0.00 0.00 39.64 5.18
80 81 6.204301 GTCAGTAGTATAGACAACTATCCGCA 59.796 42.308 0.00 0.00 39.64 5.69
81 82 6.427547 AGTCAGTAGTATAGACAACTATCCGC 59.572 42.308 7.44 0.00 39.64 5.54
82 83 7.656542 TGAGTCAGTAGTATAGACAACTATCCG 59.343 40.741 0.00 0.00 39.64 4.18
83 84 8.905660 TGAGTCAGTAGTATAGACAACTATCC 57.094 38.462 0.00 0.00 39.64 2.59
87 88 9.862371 CAATTTGAGTCAGTAGTATAGACAACT 57.138 33.333 0.00 0.00 34.80 3.16
88 89 9.088512 CCAATTTGAGTCAGTAGTATAGACAAC 57.911 37.037 0.00 3.11 34.80 3.32
89 90 7.764443 GCCAATTTGAGTCAGTAGTATAGACAA 59.236 37.037 0.00 0.00 34.80 3.18
90 91 7.124298 AGCCAATTTGAGTCAGTAGTATAGACA 59.876 37.037 0.00 0.00 34.80 3.41
91 92 7.493367 AGCCAATTTGAGTCAGTAGTATAGAC 58.507 38.462 0.00 0.00 0.00 2.59
92 93 7.661536 AGCCAATTTGAGTCAGTAGTATAGA 57.338 36.000 0.00 0.00 0.00 1.98
93 94 9.988815 ATTAGCCAATTTGAGTCAGTAGTATAG 57.011 33.333 0.00 0.00 0.00 1.31
95 96 9.686683 AAATTAGCCAATTTGAGTCAGTAGTAT 57.313 29.630 1.85 0.00 41.70 2.12
96 97 9.515226 AAAATTAGCCAATTTGAGTCAGTAGTA 57.485 29.630 3.54 0.00 42.29 1.82
97 98 8.299570 CAAAATTAGCCAATTTGAGTCAGTAGT 58.700 33.333 3.54 0.00 42.29 2.73
98 99 8.514594 TCAAAATTAGCCAATTTGAGTCAGTAG 58.485 33.333 3.54 0.00 42.29 2.57
99 100 8.296713 GTCAAAATTAGCCAATTTGAGTCAGTA 58.703 33.333 3.54 0.00 42.29 2.74
100 101 7.014615 AGTCAAAATTAGCCAATTTGAGTCAGT 59.985 33.333 3.54 0.00 42.29 3.41
101 102 7.327761 CAGTCAAAATTAGCCAATTTGAGTCAG 59.672 37.037 3.54 0.00 42.29 3.51
102 103 7.014134 TCAGTCAAAATTAGCCAATTTGAGTCA 59.986 33.333 3.54 0.00 42.29 3.41
103 104 7.370383 TCAGTCAAAATTAGCCAATTTGAGTC 58.630 34.615 3.54 0.00 42.29 3.36
104 105 7.288810 TCAGTCAAAATTAGCCAATTTGAGT 57.711 32.000 3.54 5.27 42.29 3.41
105 106 8.030692 TGATCAGTCAAAATTAGCCAATTTGAG 58.969 33.333 3.54 0.99 42.29 3.02
106 107 7.894708 TGATCAGTCAAAATTAGCCAATTTGA 58.105 30.769 3.54 2.52 42.29 2.69
107 108 7.816031 ACTGATCAGTCAAAATTAGCCAATTTG 59.184 33.333 22.89 0.19 39.06 2.32
108 109 7.899973 ACTGATCAGTCAAAATTAGCCAATTT 58.100 30.769 22.89 0.00 40.46 1.82
109 110 7.472334 ACTGATCAGTCAAAATTAGCCAATT 57.528 32.000 22.89 0.00 36.92 2.32
110 111 7.318141 CAACTGATCAGTCAAAATTAGCCAAT 58.682 34.615 28.01 4.99 41.58 3.16
111 112 6.680810 CAACTGATCAGTCAAAATTAGCCAA 58.319 36.000 28.01 0.00 41.58 4.52
112 113 5.335897 GCAACTGATCAGTCAAAATTAGCCA 60.336 40.000 28.01 0.00 41.58 4.75
113 114 5.098211 GCAACTGATCAGTCAAAATTAGCC 58.902 41.667 28.01 4.55 41.58 3.93
114 115 5.702865 TGCAACTGATCAGTCAAAATTAGC 58.297 37.500 28.01 19.39 41.58 3.09
115 116 8.578308 TTTTGCAACTGATCAGTCAAAATTAG 57.422 30.769 31.69 17.35 41.58 1.73
116 117 9.195411 GATTTTGCAACTGATCAGTCAAAATTA 57.805 29.630 37.45 26.16 45.51 1.40
117 118 7.172019 GGATTTTGCAACTGATCAGTCAAAATT 59.828 33.333 37.45 29.33 45.51 1.82
118 119 6.647895 GGATTTTGCAACTGATCAGTCAAAAT 59.352 34.615 37.65 37.65 46.67 1.82
119 120 5.984926 GGATTTTGCAACTGATCAGTCAAAA 59.015 36.000 34.36 34.36 43.19 2.44
120 121 5.302568 AGGATTTTGCAACTGATCAGTCAAA 59.697 36.000 26.73 26.73 41.58 2.69
121 122 4.828939 AGGATTTTGCAACTGATCAGTCAA 59.171 37.500 28.01 23.65 41.58 3.18
122 123 4.401022 AGGATTTTGCAACTGATCAGTCA 58.599 39.130 28.01 19.44 41.58 3.41
123 124 5.382618 AAGGATTTTGCAACTGATCAGTC 57.617 39.130 28.01 17.07 41.58 3.51
124 125 5.302568 TCAAAGGATTTTGCAACTGATCAGT 59.697 36.000 22.89 22.89 42.71 3.41
125 126 5.775686 TCAAAGGATTTTGCAACTGATCAG 58.224 37.500 21.37 21.37 42.71 2.90
126 127 5.302568 ACTCAAAGGATTTTGCAACTGATCA 59.697 36.000 0.00 0.00 42.71 2.92
127 128 5.776744 ACTCAAAGGATTTTGCAACTGATC 58.223 37.500 0.00 3.35 42.71 2.92
128 129 5.796424 ACTCAAAGGATTTTGCAACTGAT 57.204 34.783 0.00 0.00 42.71 2.90
129 130 5.596836 AACTCAAAGGATTTTGCAACTGA 57.403 34.783 0.00 0.00 42.71 3.41
130 131 5.581874 ACAAACTCAAAGGATTTTGCAACTG 59.418 36.000 0.00 0.00 43.57 3.16
131 132 5.733676 ACAAACTCAAAGGATTTTGCAACT 58.266 33.333 0.00 0.00 43.57 3.16
132 133 6.421377 AACAAACTCAAAGGATTTTGCAAC 57.579 33.333 0.00 0.00 43.57 4.17
133 134 6.652481 TCAAACAAACTCAAAGGATTTTGCAA 59.348 30.769 0.00 0.00 43.57 4.08
134 135 6.169094 TCAAACAAACTCAAAGGATTTTGCA 58.831 32.000 7.24 0.00 43.57 4.08
135 136 6.660887 TCAAACAAACTCAAAGGATTTTGC 57.339 33.333 7.24 0.00 43.57 3.68
136 137 8.881743 TGAATCAAACAAACTCAAAGGATTTTG 58.118 29.630 6.13 6.13 44.63 2.44
137 138 9.617523 ATGAATCAAACAAACTCAAAGGATTTT 57.382 25.926 0.00 0.00 35.03 1.82
138 139 9.264719 GATGAATCAAACAAACTCAAAGGATTT 57.735 29.630 0.00 0.00 40.26 2.17
139 140 8.645110 AGATGAATCAAACAAACTCAAAGGATT 58.355 29.630 0.00 0.00 0.00 3.01
140 141 8.186709 AGATGAATCAAACAAACTCAAAGGAT 57.813 30.769 0.00 0.00 0.00 3.24
141 142 7.503566 AGAGATGAATCAAACAAACTCAAAGGA 59.496 33.333 0.00 0.00 32.18 3.36
142 143 7.594015 CAGAGATGAATCAAACAAACTCAAAGG 59.406 37.037 0.00 0.00 32.18 3.11
143 144 8.347771 TCAGAGATGAATCAAACAAACTCAAAG 58.652 33.333 0.00 0.00 32.18 2.77
144 145 8.224389 TCAGAGATGAATCAAACAAACTCAAA 57.776 30.769 0.00 0.00 32.18 2.69
145 146 7.806409 TCAGAGATGAATCAAACAAACTCAA 57.194 32.000 0.00 0.00 32.18 3.02
146 147 7.806409 TTCAGAGATGAATCAAACAAACTCA 57.194 32.000 0.00 0.00 32.18 3.41
212 213 8.188139 ACACAAGTGTAGTTGGAACAAAATAAG 58.812 33.333 3.64 0.00 43.39 1.73
213 214 8.057536 ACACAAGTGTAGTTGGAACAAAATAA 57.942 30.769 3.64 0.00 43.39 1.40
214 215 7.633193 ACACAAGTGTAGTTGGAACAAAATA 57.367 32.000 3.64 0.00 43.39 1.40
215 216 6.524101 ACACAAGTGTAGTTGGAACAAAAT 57.476 33.333 3.64 0.00 43.39 1.82
216 217 5.968528 ACACAAGTGTAGTTGGAACAAAA 57.031 34.783 3.64 0.00 43.39 2.44
217 218 5.968528 AACACAAGTGTAGTTGGAACAAA 57.031 34.783 6.24 0.00 44.15 2.83
218 219 5.968528 AAACACAAGTGTAGTTGGAACAA 57.031 34.783 6.24 0.00 44.15 2.83
219 220 5.938710 TGTAAACACAAGTGTAGTTGGAACA 59.061 36.000 6.24 0.00 44.13 3.18
220 221 6.425577 TGTAAACACAAGTGTAGTTGGAAC 57.574 37.500 6.24 0.00 44.13 3.62
221 222 7.450124 TTTGTAAACACAAGTGTAGTTGGAA 57.550 32.000 6.24 0.00 44.13 3.53
222 223 7.450124 TTTTGTAAACACAAGTGTAGTTGGA 57.550 32.000 6.24 0.00 44.13 3.53
223 224 7.971168 TCATTTTGTAAACACAAGTGTAGTTGG 59.029 33.333 6.24 0.00 44.13 3.77
224 225 8.794406 GTCATTTTGTAAACACAAGTGTAGTTG 58.206 33.333 6.24 0.00 44.13 3.16
225 226 8.736244 AGTCATTTTGTAAACACAAGTGTAGTT 58.264 29.630 6.24 1.13 44.13 2.24
226 227 8.181573 CAGTCATTTTGTAAACACAAGTGTAGT 58.818 33.333 6.24 0.82 44.13 2.73
227 228 8.394877 TCAGTCATTTTGTAAACACAAGTGTAG 58.605 33.333 6.24 0.00 44.13 2.74
228 229 8.270080 TCAGTCATTTTGTAAACACAAGTGTA 57.730 30.769 6.24 0.00 44.13 2.90
230 231 7.754924 AGTTCAGTCATTTTGTAAACACAAGTG 59.245 33.333 0.00 0.00 0.00 3.16
231 232 7.826690 AGTTCAGTCATTTTGTAAACACAAGT 58.173 30.769 0.00 0.00 0.00 3.16
232 233 9.950680 ATAGTTCAGTCATTTTGTAAACACAAG 57.049 29.630 0.00 0.00 0.00 3.16
247 248 8.846211 CCCTTTTTCTTGTAAATAGTTCAGTCA 58.154 33.333 0.00 0.00 0.00 3.41
248 249 8.297426 CCCCTTTTTCTTGTAAATAGTTCAGTC 58.703 37.037 0.00 0.00 0.00 3.51
249 250 7.255836 GCCCCTTTTTCTTGTAAATAGTTCAGT 60.256 37.037 0.00 0.00 0.00 3.41
250 251 7.090808 GCCCCTTTTTCTTGTAAATAGTTCAG 58.909 38.462 0.00 0.00 0.00 3.02
251 252 6.551601 TGCCCCTTTTTCTTGTAAATAGTTCA 59.448 34.615 0.00 0.00 0.00 3.18
252 253 6.866770 GTGCCCCTTTTTCTTGTAAATAGTTC 59.133 38.462 0.00 0.00 0.00 3.01
253 254 6.239487 GGTGCCCCTTTTTCTTGTAAATAGTT 60.239 38.462 0.00 0.00 0.00 2.24
254 255 5.245301 GGTGCCCCTTTTTCTTGTAAATAGT 59.755 40.000 0.00 0.00 0.00 2.12
255 256 5.480422 AGGTGCCCCTTTTTCTTGTAAATAG 59.520 40.000 0.00 0.00 38.13 1.73
256 257 5.399113 AGGTGCCCCTTTTTCTTGTAAATA 58.601 37.500 0.00 0.00 38.13 1.40
257 258 4.231273 AGGTGCCCCTTTTTCTTGTAAAT 58.769 39.130 0.00 0.00 38.13 1.40
258 259 3.648739 AGGTGCCCCTTTTTCTTGTAAA 58.351 40.909 0.00 0.00 38.13 2.01
259 260 3.322191 AGGTGCCCCTTTTTCTTGTAA 57.678 42.857 0.00 0.00 38.13 2.41
261 262 3.946242 AGGTGCCCCTTTTTCTTGT 57.054 47.368 0.00 0.00 38.13 3.16
274 275 1.070134 TCACGGATATAGGCAAGGTGC 59.930 52.381 0.00 0.00 44.08 5.01
275 276 3.469008 TTCACGGATATAGGCAAGGTG 57.531 47.619 0.00 0.00 0.00 4.00
276 277 3.904339 AGATTCACGGATATAGGCAAGGT 59.096 43.478 0.00 0.00 0.00 3.50
304 305 4.016444 TGCCTGTTGGTTCCAAGAATATC 58.984 43.478 4.37 0.00 35.27 1.63
331 332 8.114331 TGCTTGAATTCAGTAACATTGATCTT 57.886 30.769 8.41 0.00 0.00 2.40
372 373 6.500751 TCTTCCACCTCCATTCTTACTTAAGT 59.499 38.462 13.68 13.68 34.93 2.24
375 376 6.945636 TTCTTCCACCTCCATTCTTACTTA 57.054 37.500 0.00 0.00 0.00 2.24
450 461 4.217983 CAGACGGTCTACTTAGGTTTGAGT 59.782 45.833 10.87 0.00 0.00 3.41
464 475 2.484947 GGAAAGTTCCAACAGACGGTCT 60.485 50.000 4.45 4.45 46.76 3.85
523 534 2.325583 TGCCCCGCTCTACTTTTATG 57.674 50.000 0.00 0.00 0.00 1.90
535 546 0.746659 AAATTCATAGCTTGCCCCGC 59.253 50.000 0.00 0.00 0.00 6.13
562 573 8.945195 ATCTTGCTAAATCATTATGGAATCCA 57.055 30.769 3.67 3.67 38.19 3.41
574 585 6.458206 GCATGTTACGGAATCTTGCTAAATCA 60.458 38.462 11.15 0.00 32.24 2.57
591 602 2.128771 ATCCTGGTGGTGCATGTTAC 57.871 50.000 0.00 0.00 34.23 2.50
610 621 4.682778 ATGCACCCGCTCTAACTATTTA 57.317 40.909 0.00 0.00 39.64 1.40
635 646 8.822855 CACAAAGTACGAATTAAGGCATATACA 58.177 33.333 0.00 0.00 0.00 2.29
640 651 5.007682 ACCACAAAGTACGAATTAAGGCAT 58.992 37.500 0.00 0.00 0.00 4.40
641 652 4.391155 ACCACAAAGTACGAATTAAGGCA 58.609 39.130 0.00 0.00 0.00 4.75
750 767 7.062839 TGTGATATTTAATTTGTTTCAAGCCGC 59.937 33.333 0.00 0.00 0.00 6.53
788 805 5.510179 GCTATGGGCATGAATACTTTTGCAT 60.510 40.000 0.00 0.00 41.35 3.96
932 955 2.869801 CAACTGCTAACTGGTTTCGTCA 59.130 45.455 0.00 0.00 0.00 4.35
1020 1043 0.907486 CTCTGAGGGAATGTGGAGCA 59.093 55.000 0.00 0.00 0.00 4.26
1024 1047 0.549950 ATGGCTCTGAGGGAATGTGG 59.450 55.000 6.83 0.00 0.00 4.17
1043 1066 2.685897 GTGGCAAAGTTGTGTTCTGGTA 59.314 45.455 0.00 0.00 0.00 3.25
1157 1180 3.758931 GCAAACCGCCCATCCACC 61.759 66.667 0.00 0.00 32.94 4.61
1208 1231 0.833834 CCTGGGCCATCTCGGAGTAT 60.834 60.000 6.72 0.00 36.56 2.12
1232 1255 1.556911 TCAAGAACCCTGAGGCTCATC 59.443 52.381 19.11 12.61 36.11 2.92
1271 1294 3.451556 ATGGCTCATGGCGGACTCG 62.452 63.158 0.00 0.00 42.94 4.18
1316 1339 0.599204 GGTCGAACCTCGCAAACAGA 60.599 55.000 0.00 0.00 40.21 3.41
1451 1474 1.133668 ACAGCCACCTTCAGAAAGCTT 60.134 47.619 0.00 0.00 0.00 3.74
1564 1587 5.078411 TGTAACACAACAAAATTGGCAGT 57.922 34.783 0.00 0.00 0.00 4.40
1591 1614 5.920193 AGTACAAATAACTAGCACCGGTA 57.080 39.130 6.87 0.00 0.00 4.02
1637 1660 8.296799 TGTCATTTTGTCAATTAAACTGATGC 57.703 30.769 0.00 0.00 32.04 3.91
1668 1691 9.353999 GATTCACAACATTTCCCTTTACATAAC 57.646 33.333 0.00 0.00 0.00 1.89
1690 1713 5.822519 TGTAGGCATCCACAAACATAGATTC 59.177 40.000 0.00 0.00 0.00 2.52
1759 1782 8.771766 CATAACATAATCAGATTCTGGTGTGAG 58.228 37.037 14.64 1.37 30.35 3.51
1764 1787 7.653713 GTCGTCATAACATAATCAGATTCTGGT 59.346 37.037 13.59 3.42 31.51 4.00
1805 1828 7.676004 TCTTGGTGACTGTTCTGAACATATTA 58.324 34.615 22.28 9.04 41.26 0.98
1850 1873 3.561503 TCGATATACGCGGTTGATTCAG 58.438 45.455 12.47 0.00 42.26 3.02
2085 2110 6.639686 GCATCTTGTGTAAAATATGCATGAGG 59.360 38.462 10.16 0.00 39.53 3.86
2096 2121 5.992829 TCTAGAAACGGCATCTTGTGTAAAA 59.007 36.000 0.00 0.00 0.00 1.52
2102 2127 2.567615 AGGTCTAGAAACGGCATCTTGT 59.432 45.455 0.00 0.00 0.00 3.16
2176 2201 6.156748 ACATTTTGGGAGGTGTTAAACTTC 57.843 37.500 0.00 0.00 34.17 3.01
2215 2240 3.788937 CCAAATTGGACATCAGGATTGC 58.211 45.455 6.04 0.00 40.96 3.56
2228 2253 2.188062 ATTTGCAGGTGCCAAATTGG 57.812 45.000 7.84 7.84 41.55 3.16
2334 2365 3.895232 ATTAGCAGTATATGGCTCGGG 57.105 47.619 4.57 0.00 41.41 5.14
2412 2444 1.134175 GGTGAGCTCGAGGAGAAGAAG 59.866 57.143 15.58 0.00 0.00 2.85
2489 2521 5.156355 TCAAGTACGCCTACTTTAACTTCG 58.844 41.667 5.49 0.00 40.64 3.79
2505 2537 5.049474 TGACATGCAGTTTGACATCAAGTAC 60.049 40.000 0.00 0.00 37.15 2.73
2551 2583 2.577059 CGGGCCTAACGAGCTCAA 59.423 61.111 15.40 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.