Multiple sequence alignment - TraesCS6A01G315900

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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 TraesCS6A01G315900 chr6A 100.000 2510 0 0 1 2510 552589877 552592386 0.000000e+00 4636
1 TraesCS6A01G315900 chr6A 91.923 520 31 8 994 1509 552713026 552713538 0.000000e+00 717
2 TraesCS6A01G315900 chr6D 92.136 1297 58 17 303 1566 406167068 406168353 0.000000e+00 1790
3 TraesCS6A01G315900 chr6D 89.502 924 81 9 1590 2510 406168347 406169257 0.000000e+00 1155
4 TraesCS6A01G315900 chr6D 82.360 839 64 37 701 1509 406197542 406198326 0.000000e+00 652
5 TraesCS6A01G315900 chr6B 87.060 1507 93 47 180 1639 610064205 610065656 0.000000e+00 1609
6 TraesCS6A01G315900 chr6B 91.489 517 36 5 994 1509 610085333 610085842 0.000000e+00 704
7 TraesCS6A01G315900 chr6B 92.214 411 27 5 1697 2103 610068177 610068586 6.020000e-161 577
8 TraesCS6A01G315900 chr7D 98.507 134 2 0 1 134 101578620 101578487 1.160000e-58 237
9 TraesCS6A01G315900 chr7B 98.507 134 2 0 1 134 622432295 622432428 1.160000e-58 237
10 TraesCS6A01G315900 chr7B 98.507 134 2 0 1 134 663093751 663093884 1.160000e-58 237
11 TraesCS6A01G315900 chr5D 98.507 134 2 0 1 134 503251454 503251321 1.160000e-58 237
12 TraesCS6A01G315900 chr3D 98.507 134 2 0 1 134 213402391 213402258 1.160000e-58 237
13 TraesCS6A01G315900 chr3D 98.507 134 2 0 1 134 589254449 589254582 1.160000e-58 237
14 TraesCS6A01G315900 chr3D 98.507 134 2 0 1 134 589255315 589255182 1.160000e-58 237
15 TraesCS6A01G315900 chr2D 98.507 134 2 0 1 134 272806575 272806708 1.160000e-58 237
16 TraesCS6A01G315900 chr2D 98.507 134 2 0 1 134 591991347 591991214 1.160000e-58 237


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 TraesCS6A01G315900 chr6A 552589877 552592386 2509 False 4636.0 4636 100.000 1 2510 1 chr6A.!!$F1 2509
1 TraesCS6A01G315900 chr6A 552713026 552713538 512 False 717.0 717 91.923 994 1509 1 chr6A.!!$F2 515
2 TraesCS6A01G315900 chr6D 406167068 406169257 2189 False 1472.5 1790 90.819 303 2510 2 chr6D.!!$F2 2207
3 TraesCS6A01G315900 chr6D 406197542 406198326 784 False 652.0 652 82.360 701 1509 1 chr6D.!!$F1 808
4 TraesCS6A01G315900 chr6B 610064205 610068586 4381 False 1093.0 1609 89.637 180 2103 2 chr6B.!!$F2 1923
5 TraesCS6A01G315900 chr6B 610085333 610085842 509 False 704.0 704 91.489 994 1509 1 chr6B.!!$F1 515

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
141 142 0.038526 CCACTACGAAGACTTGGCGT 60.039 55.0 7.08 7.08 41.58 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1669 0.031585 CTGACGTCCGGTGTGAAAGA 59.968 55.0 14.12 0.0 0.0 2.52 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
25 26 8.948631 GACATCTCTTATGTCAATAAGACCAA 57.051 34.615 12.12 0.00 46.07 3.67
26 27 9.383519 GACATCTCTTATGTCAATAAGACCAAA 57.616 33.333 12.12 0.00 46.07 3.28
27 28 9.911788 ACATCTCTTATGTCAATAAGACCAAAT 57.088 29.630 4.45 0.00 46.07 2.32
29 30 8.737168 TCTCTTATGTCAATAAGACCAAATGG 57.263 34.615 4.45 0.00 46.07 3.16
30 31 8.548025 TCTCTTATGTCAATAAGACCAAATGGA 58.452 33.333 6.42 0.00 46.07 3.41
31 32 9.347240 CTCTTATGTCAATAAGACCAAATGGAT 57.653 33.333 6.42 0.00 46.07 3.41
32 33 9.123902 TCTTATGTCAATAAGACCAAATGGATG 57.876 33.333 6.42 0.00 46.07 3.51
33 34 8.355169 CTTATGTCAATAAGACCAAATGGATGG 58.645 37.037 6.42 0.00 45.62 3.51
35 36 6.966534 GTCAATAAGACCAAATGGATGGAT 57.033 37.500 6.42 0.00 43.54 3.41
37 38 8.641498 GTCAATAAGACCAAATGGATGGATAT 57.359 34.615 6.42 0.00 43.54 1.63
38 39 9.082313 GTCAATAAGACCAAATGGATGGATATT 57.918 33.333 6.42 1.72 43.54 1.28
44 45 9.659135 AAGACCAAATGGATGGATATTAAATGA 57.341 29.630 6.42 0.00 43.54 2.57
45 46 9.833179 AGACCAAATGGATGGATATTAAATGAT 57.167 29.630 6.42 0.00 43.54 2.45
53 54 9.964354 TGGATGGATATTAAATGATAGGAAGTG 57.036 33.333 0.00 0.00 0.00 3.16
54 55 8.897752 GGATGGATATTAAATGATAGGAAGTGC 58.102 37.037 0.00 0.00 0.00 4.40
55 56 9.678260 GATGGATATTAAATGATAGGAAGTGCT 57.322 33.333 0.00 0.00 0.00 4.40
58 59 9.606631 GGATATTAAATGATAGGAAGTGCTAGG 57.393 37.037 0.00 0.00 0.00 3.02
62 63 6.567602 AAATGATAGGAAGTGCTAGGAAGT 57.432 37.500 0.00 0.00 0.00 3.01
63 64 5.543507 ATGATAGGAAGTGCTAGGAAGTG 57.456 43.478 0.00 0.00 0.00 3.16
64 65 4.610333 TGATAGGAAGTGCTAGGAAGTGA 58.390 43.478 0.00 0.00 0.00 3.41
65 66 5.023452 TGATAGGAAGTGCTAGGAAGTGAA 58.977 41.667 0.00 0.00 0.00 3.18
66 67 5.483937 TGATAGGAAGTGCTAGGAAGTGAAA 59.516 40.000 0.00 0.00 0.00 2.69
67 68 4.917906 AGGAAGTGCTAGGAAGTGAAAT 57.082 40.909 0.00 0.00 0.00 2.17
68 69 7.344612 TGATAGGAAGTGCTAGGAAGTGAAATA 59.655 37.037 0.00 0.00 0.00 1.40
69 70 5.983540 AGGAAGTGCTAGGAAGTGAAATAG 58.016 41.667 0.00 0.00 0.00 1.73
70 71 5.721960 AGGAAGTGCTAGGAAGTGAAATAGA 59.278 40.000 0.00 0.00 0.00 1.98
71 72 6.213600 AGGAAGTGCTAGGAAGTGAAATAGAA 59.786 38.462 0.00 0.00 0.00 2.10
72 73 7.051000 GGAAGTGCTAGGAAGTGAAATAGAAT 58.949 38.462 0.00 0.00 0.00 2.40
73 74 7.011857 GGAAGTGCTAGGAAGTGAAATAGAATG 59.988 40.741 0.00 0.00 0.00 2.67
74 75 7.187824 AGTGCTAGGAAGTGAAATAGAATGA 57.812 36.000 0.00 0.00 0.00 2.57
75 76 7.624549 AGTGCTAGGAAGTGAAATAGAATGAA 58.375 34.615 0.00 0.00 0.00 2.57
76 77 8.103305 AGTGCTAGGAAGTGAAATAGAATGAAA 58.897 33.333 0.00 0.00 0.00 2.69
77 78 8.897752 GTGCTAGGAAGTGAAATAGAATGAAAT 58.102 33.333 0.00 0.00 0.00 2.17
82 83 9.336171 AGGAAGTGAAATAGAATGAAATAGAGC 57.664 33.333 0.00 0.00 0.00 4.09
83 84 9.113838 GGAAGTGAAATAGAATGAAATAGAGCA 57.886 33.333 0.00 0.00 0.00 4.26
86 87 9.678260 AGTGAAATAGAATGAAATAGAGCAACT 57.322 29.630 0.00 0.00 0.00 3.16
91 92 6.521151 AGAATGAAATAGAGCAACTTTGGG 57.479 37.500 0.00 0.00 0.00 4.12
92 93 4.725790 ATGAAATAGAGCAACTTTGGGC 57.274 40.909 0.00 0.00 0.00 5.36
93 94 3.766545 TGAAATAGAGCAACTTTGGGCT 58.233 40.909 0.00 0.00 44.48 5.19
94 95 4.151883 TGAAATAGAGCAACTTTGGGCTT 58.848 39.130 0.00 0.00 41.22 4.35
95 96 4.218417 TGAAATAGAGCAACTTTGGGCTTC 59.782 41.667 0.00 0.00 41.22 3.86
96 97 2.200373 TAGAGCAACTTTGGGCTTCC 57.800 50.000 0.00 0.00 41.22 3.46
97 98 0.540597 AGAGCAACTTTGGGCTTCCC 60.541 55.000 0.00 0.00 45.71 3.97
98 99 0.540597 GAGCAACTTTGGGCTTCCCT 60.541 55.000 3.27 0.00 45.70 4.20
99 100 0.777446 AGCAACTTTGGGCTTCCCTA 59.223 50.000 3.27 0.00 45.70 3.53
100 101 1.359130 AGCAACTTTGGGCTTCCCTAT 59.641 47.619 3.27 0.00 45.70 2.57
101 102 1.478105 GCAACTTTGGGCTTCCCTATG 59.522 52.381 3.27 1.06 45.70 2.23
102 103 2.883888 GCAACTTTGGGCTTCCCTATGA 60.884 50.000 3.27 0.00 45.70 2.15
103 104 3.430453 CAACTTTGGGCTTCCCTATGAA 58.570 45.455 3.27 0.00 45.70 2.57
104 105 3.825908 ACTTTGGGCTTCCCTATGAAA 57.174 42.857 3.27 0.00 45.70 2.69
105 106 4.337264 ACTTTGGGCTTCCCTATGAAAT 57.663 40.909 3.27 0.00 45.70 2.17
106 107 4.026052 ACTTTGGGCTTCCCTATGAAATG 58.974 43.478 3.27 0.00 45.70 2.32
107 108 4.264352 ACTTTGGGCTTCCCTATGAAATGA 60.264 41.667 3.27 0.00 45.70 2.57
108 109 3.582998 TGGGCTTCCCTATGAAATGAG 57.417 47.619 3.27 0.00 45.70 2.90
109 110 2.175499 TGGGCTTCCCTATGAAATGAGG 59.825 50.000 3.27 0.00 45.70 3.86
110 111 2.234143 GGCTTCCCTATGAAATGAGGC 58.766 52.381 0.00 0.00 31.06 4.70
111 112 2.423373 GGCTTCCCTATGAAATGAGGCA 60.423 50.000 0.00 0.00 31.06 4.75
112 113 3.494332 GCTTCCCTATGAAATGAGGCAT 58.506 45.455 0.00 0.00 31.06 4.40
113 114 3.255149 GCTTCCCTATGAAATGAGGCATG 59.745 47.826 0.00 0.00 31.06 4.06
114 115 3.513909 TCCCTATGAAATGAGGCATGG 57.486 47.619 0.00 0.00 0.00 3.66
115 116 3.055328 TCCCTATGAAATGAGGCATGGA 58.945 45.455 0.00 0.00 0.00 3.41
116 117 3.462954 TCCCTATGAAATGAGGCATGGAA 59.537 43.478 0.00 0.00 0.00 3.53
117 118 3.571401 CCCTATGAAATGAGGCATGGAAC 59.429 47.826 0.00 0.00 0.00 3.62
118 119 3.251729 CCTATGAAATGAGGCATGGAACG 59.748 47.826 0.00 0.00 0.00 3.95
119 120 1.462616 TGAAATGAGGCATGGAACGG 58.537 50.000 0.00 0.00 0.00 4.44
120 121 1.004161 TGAAATGAGGCATGGAACGGA 59.996 47.619 0.00 0.00 0.00 4.69
121 122 1.672881 GAAATGAGGCATGGAACGGAG 59.327 52.381 0.00 0.00 0.00 4.63
122 123 0.749454 AATGAGGCATGGAACGGAGC 60.749 55.000 0.00 0.00 0.00 4.70
125 126 3.134127 GGCATGGAACGGAGCCAC 61.134 66.667 0.00 0.00 46.26 5.01
126 127 2.045926 GCATGGAACGGAGCCACT 60.046 61.111 0.00 0.00 38.44 4.00
127 128 1.220749 GCATGGAACGGAGCCACTA 59.779 57.895 0.00 0.00 38.44 2.74
128 129 1.090052 GCATGGAACGGAGCCACTAC 61.090 60.000 0.00 0.00 38.44 2.73
129 130 0.806102 CATGGAACGGAGCCACTACG 60.806 60.000 0.00 0.00 44.37 3.51
130 131 0.968901 ATGGAACGGAGCCACTACGA 60.969 55.000 6.17 0.00 40.79 3.43
131 132 1.180456 TGGAACGGAGCCACTACGAA 61.180 55.000 6.17 0.00 40.79 3.85
132 133 0.458025 GGAACGGAGCCACTACGAAG 60.458 60.000 6.17 0.00 40.79 3.79
133 134 0.524862 GAACGGAGCCACTACGAAGA 59.475 55.000 6.17 0.00 40.79 2.87
134 135 0.243095 AACGGAGCCACTACGAAGAC 59.757 55.000 6.17 0.00 40.79 3.01
135 136 0.608582 ACGGAGCCACTACGAAGACT 60.609 55.000 6.17 0.00 40.79 3.24
136 137 0.526662 CGGAGCCACTACGAAGACTT 59.473 55.000 0.00 0.00 40.79 3.01
137 138 1.732732 CGGAGCCACTACGAAGACTTG 60.733 57.143 0.00 0.00 40.79 3.16
138 139 1.404315 GGAGCCACTACGAAGACTTGG 60.404 57.143 0.00 0.00 0.00 3.61
139 140 2.457080 GCCACTACGAAGACTTGGC 58.543 57.895 0.00 0.00 45.64 4.52
140 141 1.352156 GCCACTACGAAGACTTGGCG 61.352 60.000 0.00 0.00 43.18 5.69
141 142 0.038526 CCACTACGAAGACTTGGCGT 60.039 55.000 7.08 7.08 41.58 5.68
142 143 1.337821 CACTACGAAGACTTGGCGTC 58.662 55.000 5.32 0.00 43.17 5.19
150 151 3.580658 GACTTGGCGTCGTATTTGC 57.419 52.632 0.00 0.00 32.04 3.68
151 152 0.247145 GACTTGGCGTCGTATTTGCG 60.247 55.000 0.00 0.00 32.04 4.85
152 153 0.947180 ACTTGGCGTCGTATTTGCGT 60.947 50.000 0.00 0.00 0.00 5.24
153 154 0.247145 CTTGGCGTCGTATTTGCGTC 60.247 55.000 0.00 0.00 0.00 5.19
154 155 0.944788 TTGGCGTCGTATTTGCGTCA 60.945 50.000 0.00 0.00 38.50 4.35
155 156 1.343821 GGCGTCGTATTTGCGTCAG 59.656 57.895 0.00 0.00 0.00 3.51
156 157 1.349259 GGCGTCGTATTTGCGTCAGT 61.349 55.000 0.00 0.00 0.00 3.41
157 158 0.246757 GCGTCGTATTTGCGTCAGTG 60.247 55.000 0.00 0.00 0.00 3.66
158 159 1.057636 CGTCGTATTTGCGTCAGTGT 58.942 50.000 0.00 0.00 0.00 3.55
159 160 1.057285 CGTCGTATTTGCGTCAGTGTC 59.943 52.381 0.00 0.00 0.00 3.67
160 161 2.325761 GTCGTATTTGCGTCAGTGTCT 58.674 47.619 0.00 0.00 0.00 3.41
161 162 3.495193 GTCGTATTTGCGTCAGTGTCTA 58.505 45.455 0.00 0.00 0.00 2.59
162 163 3.300066 GTCGTATTTGCGTCAGTGTCTAC 59.700 47.826 0.00 0.00 0.00 2.59
163 164 2.597305 CGTATTTGCGTCAGTGTCTACC 59.403 50.000 0.00 0.00 0.00 3.18
164 165 2.094762 ATTTGCGTCAGTGTCTACCC 57.905 50.000 0.00 0.00 0.00 3.69
165 166 0.319211 TTTGCGTCAGTGTCTACCCG 60.319 55.000 0.00 0.00 0.00 5.28
166 167 2.506438 GCGTCAGTGTCTACCCGC 60.506 66.667 0.00 0.00 33.78 6.13
167 168 2.959372 CGTCAGTGTCTACCCGCA 59.041 61.111 0.00 0.00 0.00 5.69
168 169 1.287815 CGTCAGTGTCTACCCGCAA 59.712 57.895 0.00 0.00 0.00 4.85
169 170 0.319211 CGTCAGTGTCTACCCGCAAA 60.319 55.000 0.00 0.00 0.00 3.68
170 171 1.870580 CGTCAGTGTCTACCCGCAAAA 60.871 52.381 0.00 0.00 0.00 2.44
171 172 2.215196 GTCAGTGTCTACCCGCAAAAA 58.785 47.619 0.00 0.00 0.00 1.94
197 198 5.409643 AGTATTTGCGTCAATATCTGTGC 57.590 39.130 0.00 0.00 0.00 4.57
208 209 2.904697 TATCTGTGCAGCCAGATCAG 57.095 50.000 22.50 7.40 46.70 2.90
210 211 1.201424 TCTGTGCAGCCAGATCAGAT 58.799 50.000 8.95 0.00 36.57 2.90
218 219 1.454976 CCAGATCAGATGGCAGGGG 59.545 63.158 0.00 0.00 0.00 4.79
220 221 1.005289 AGATCAGATGGCAGGGGGT 59.995 57.895 0.00 0.00 0.00 4.95
222 223 1.140312 GATCAGATGGCAGGGGGTAA 58.860 55.000 0.00 0.00 0.00 2.85
223 224 1.072965 GATCAGATGGCAGGGGGTAAG 59.927 57.143 0.00 0.00 0.00 2.34
224 225 0.988145 TCAGATGGCAGGGGGTAAGG 60.988 60.000 0.00 0.00 0.00 2.69
225 226 1.697754 AGATGGCAGGGGGTAAGGG 60.698 63.158 0.00 0.00 0.00 3.95
226 227 1.696314 GATGGCAGGGGGTAAGGGA 60.696 63.158 0.00 0.00 0.00 4.20
227 228 1.697754 ATGGCAGGGGGTAAGGGAG 60.698 63.158 0.00 0.00 0.00 4.30
228 229 3.097162 GGCAGGGGGTAAGGGAGG 61.097 72.222 0.00 0.00 0.00 4.30
229 230 2.042261 GCAGGGGGTAAGGGAGGA 59.958 66.667 0.00 0.00 0.00 3.71
230 231 2.073101 GCAGGGGGTAAGGGAGGAG 61.073 68.421 0.00 0.00 0.00 3.69
244 245 2.514824 GGAGGTTCGCCAGCATCC 60.515 66.667 0.00 0.00 40.60 3.51
246 247 4.473520 AGGTTCGCCAGCATCCGG 62.474 66.667 0.00 0.00 40.60 5.14
258 259 1.153168 CATCCGGCTCCCAACGAAT 60.153 57.895 0.00 0.00 0.00 3.34
259 260 1.153168 ATCCGGCTCCCAACGAATG 60.153 57.895 0.00 0.00 0.00 2.67
275 276 3.291585 CGAATGTTCGCCAAATAGCATC 58.708 45.455 1.90 0.00 44.26 3.91
276 277 3.632189 GAATGTTCGCCAAATAGCATCC 58.368 45.455 0.00 0.00 0.00 3.51
277 278 1.013596 TGTTCGCCAAATAGCATCCG 58.986 50.000 0.00 0.00 0.00 4.18
279 280 0.746204 TTCGCCAAATAGCATCCGCA 60.746 50.000 0.00 0.00 42.27 5.69
285 287 3.737663 GCCAAATAGCATCCGCAAAATCA 60.738 43.478 0.00 0.00 42.27 2.57
298 300 3.656266 CGCAAAATCAATCATCGACATCG 59.344 43.478 0.00 0.00 41.45 3.84
329 331 3.198635 CCATATATTCCTCGATGGGCACT 59.801 47.826 0.00 0.00 36.06 4.40
335 337 1.293179 CTCGATGGGCACTGTCACA 59.707 57.895 0.00 0.00 0.00 3.58
355 357 2.953284 TCCCCGTCATTTAACCAACA 57.047 45.000 0.00 0.00 0.00 3.33
356 358 2.506444 TCCCCGTCATTTAACCAACAC 58.494 47.619 0.00 0.00 0.00 3.32
357 359 1.198178 CCCCGTCATTTAACCAACACG 59.802 52.381 0.00 0.00 0.00 4.49
358 360 1.198178 CCCGTCATTTAACCAACACGG 59.802 52.381 1.27 1.27 41.25 4.94
379 381 1.915769 AGCAGTTTCTCCGGCTCCT 60.916 57.895 0.00 0.00 28.71 3.69
447 455 0.739462 TCATCCATCAACGTCACGGC 60.739 55.000 0.35 0.00 0.00 5.68
468 476 2.030562 GCGGTGACCCATATCCCG 59.969 66.667 0.00 0.00 41.50 5.14
492 501 1.336125 GCTATTGGCACATCTCCTTGC 59.664 52.381 0.00 0.00 39.30 4.01
668 710 8.707938 ATTCTCAAAAGTGAAAAGGAACAAAG 57.292 30.769 0.00 0.00 31.88 2.77
768 810 4.421515 CAGCCAGGACCCAGCCAG 62.422 72.222 0.00 0.00 0.00 4.85
930 1010 1.179332 CGCACAAACAACAACGACAG 58.821 50.000 0.00 0.00 0.00 3.51
977 1057 3.771160 GACCGGCCGTGACATCCT 61.771 66.667 26.12 0.00 0.00 3.24
1364 1467 2.316067 TGATGAGAAGGAGGAGGGAGAA 59.684 50.000 0.00 0.00 0.00 2.87
1461 1564 1.209275 CGCATTCCAGGACGATCGAC 61.209 60.000 24.34 16.38 0.00 4.20
1520 1623 5.048643 GGATCGTATTCTAGCTAGTTCTGCA 60.049 44.000 20.10 3.03 0.00 4.41
1521 1624 5.171147 TCGTATTCTAGCTAGTTCTGCAC 57.829 43.478 20.10 9.74 0.00 4.57
1569 1672 4.027755 CGCTGTTCGGTGTGTCTT 57.972 55.556 0.00 0.00 33.78 3.01
1570 1673 2.307363 CGCTGTTCGGTGTGTCTTT 58.693 52.632 0.00 0.00 33.78 2.52
1571 1674 0.232303 CGCTGTTCGGTGTGTCTTTC 59.768 55.000 0.00 0.00 33.78 2.62
1572 1675 1.295792 GCTGTTCGGTGTGTCTTTCA 58.704 50.000 0.00 0.00 0.00 2.69
1573 1676 1.003866 GCTGTTCGGTGTGTCTTTCAC 60.004 52.381 0.00 0.00 46.31 3.18
1581 1684 4.742274 TGTCTTTCACACCGGACG 57.258 55.556 9.46 0.00 0.00 4.79
1582 1685 1.817881 TGTCTTTCACACCGGACGT 59.182 52.632 9.46 0.78 0.00 4.34
1583 1686 0.249155 TGTCTTTCACACCGGACGTC 60.249 55.000 9.46 7.13 0.00 4.34
1584 1687 0.249155 GTCTTTCACACCGGACGTCA 60.249 55.000 18.91 0.00 0.00 4.35
1585 1688 0.031585 TCTTTCACACCGGACGTCAG 59.968 55.000 18.91 13.87 0.00 3.51
1586 1689 0.031585 CTTTCACACCGGACGTCAGA 59.968 55.000 18.91 2.11 0.00 3.27
1587 1690 0.031585 TTTCACACCGGACGTCAGAG 59.968 55.000 18.91 11.74 0.00 3.35
1588 1691 2.416244 TTCACACCGGACGTCAGAGC 62.416 60.000 18.91 0.00 0.00 4.09
1589 1692 3.681835 ACACCGGACGTCAGAGCC 61.682 66.667 18.91 0.00 0.00 4.70
1590 1693 4.778415 CACCGGACGTCAGAGCCG 62.778 72.222 18.91 11.87 44.42 5.52
1593 1696 4.180946 CGGACGTCAGAGCCGGAG 62.181 72.222 18.91 0.00 41.29 4.63
1594 1697 2.750637 GGACGTCAGAGCCGGAGA 60.751 66.667 18.91 0.00 0.00 3.71
1599 1733 1.791103 CGTCAGAGCCGGAGAGATCC 61.791 65.000 5.05 0.00 0.00 3.36
1619 1753 6.939163 AGATCCACAGTTAATTAGATCCATGC 59.061 38.462 6.54 0.00 32.38 4.06
1687 1846 6.578023 ACTACTATTTGCCAAAGTTTTGCAA 58.422 32.000 19.92 19.92 36.86 4.08
1724 4321 1.523758 ACACAAATTCCAGAGACGCC 58.476 50.000 0.00 0.00 0.00 5.68
1736 4333 4.699522 GACGCCCGGTCCTTTGCT 62.700 66.667 0.00 0.00 39.90 3.91
2092 4693 9.874215 TTAATCTTGACGTATATAGACGAACTG 57.126 33.333 25.38 12.53 45.82 3.16
2111 4712 0.037326 GAGTGTTGCTCGGATGGTCA 60.037 55.000 0.00 0.00 34.13 4.02
2142 4743 0.037605 GTGGAAGTGACGTACCAGGG 60.038 60.000 0.00 0.00 32.89 4.45
2143 4744 0.470456 TGGAAGTGACGTACCAGGGT 60.470 55.000 0.00 0.00 0.00 4.34
2145 4746 1.337541 GGAAGTGACGTACCAGGGTTC 60.338 57.143 0.00 0.00 0.00 3.62
2203 4804 7.897575 TTTGGATTTATTTCATGTTTTCCGG 57.102 32.000 0.00 0.00 0.00 5.14
2204 4805 6.597832 TGGATTTATTTCATGTTTTCCGGT 57.402 33.333 0.00 0.00 0.00 5.28
2210 4811 4.927978 TTTCATGTTTTCCGGTGATGTT 57.072 36.364 0.00 0.00 0.00 2.71
2211 4812 4.927978 TTCATGTTTTCCGGTGATGTTT 57.072 36.364 0.00 0.00 0.00 2.83
2221 4822 2.570169 CGGTGATGTTTGTTTAGTGCG 58.430 47.619 0.00 0.00 0.00 5.34
2223 4824 3.120338 CGGTGATGTTTGTTTAGTGCGAT 60.120 43.478 0.00 0.00 0.00 4.58
2232 4833 3.386486 TGTTTAGTGCGATGAGACGTTT 58.614 40.909 0.00 0.00 35.59 3.60
2233 4834 3.805422 TGTTTAGTGCGATGAGACGTTTT 59.195 39.130 0.00 0.00 35.59 2.43
2235 4836 2.148916 AGTGCGATGAGACGTTTTCA 57.851 45.000 6.22 6.22 35.59 2.69
2244 4845 3.057019 TGAGACGTTTTCATCGACCAAG 58.943 45.455 0.00 0.00 0.00 3.61
2249 4850 1.128692 GTTTTCATCGACCAAGAGGCG 59.871 52.381 0.00 0.00 39.06 5.52
2257 4858 3.818787 CCAAGAGGCGCATGTGGC 61.819 66.667 24.15 24.15 39.90 5.01
2273 4874 1.936547 GTGGCGACTTCATGAATCTCC 59.063 52.381 8.96 12.78 0.00 3.71
2287 4888 0.249120 ATCTCCGAATGTTGTGCCGA 59.751 50.000 0.00 0.00 0.00 5.54
2296 4897 4.550831 CGAATGTTGTGCCGACTCAATATC 60.551 45.833 0.00 0.00 32.18 1.63
2301 4902 3.023832 TGTGCCGACTCAATATCTCAGA 58.976 45.455 0.00 0.00 0.00 3.27
2307 4908 4.484236 CGACTCAATATCTCAGAGATGCC 58.516 47.826 21.58 0.00 35.37 4.40
2319 4920 1.983691 AGAGATGCCCATGGACATAGG 59.016 52.381 14.17 0.00 0.00 2.57
2346 4947 6.713792 TGCGCGTATGCATTTATAAAGATA 57.286 33.333 3.54 0.00 40.62 1.98
2348 4949 7.233689 TGCGCGTATGCATTTATAAAGATAAG 58.766 34.615 3.54 4.34 40.62 1.73
2349 4950 7.095397 TGCGCGTATGCATTTATAAAGATAAGT 60.095 33.333 3.54 0.00 40.62 2.24
2350 4951 7.214449 GCGCGTATGCATTTATAAAGATAAGTG 59.786 37.037 3.54 9.32 42.97 3.16
2351 4952 8.221100 CGCGTATGCATTTATAAAGATAAGTGT 58.779 33.333 3.54 0.00 42.97 3.55
2381 4982 9.022915 TGTGTATGTAAGTATATGCGTTTGTAC 57.977 33.333 0.00 0.00 0.00 2.90
2385 4986 6.100668 TGTAAGTATATGCGTTTGTACTGCA 58.899 36.000 0.00 0.00 37.87 4.41
2491 5092 2.143925 GCCCGATAGCACAGTATTTCC 58.856 52.381 0.00 0.00 0.00 3.13
2500 5101 2.352715 GCACAGTATTTCCCAAAGGCAC 60.353 50.000 0.00 0.00 0.00 5.01
2503 5104 2.420022 CAGTATTTCCCAAAGGCACGAG 59.580 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.123902 CATCCATTTGGTCTTATTGACATAAGA 57.876 33.333 1.29 1.29 45.90 2.10
12 13 6.966534 ATCCATCCATTTGGTCTTATTGAC 57.033 37.500 0.00 0.00 44.63 3.18
18 19 9.659135 TCATTTAATATCCATCCATTTGGTCTT 57.341 29.630 0.00 0.00 38.01 3.01
19 20 9.833179 ATCATTTAATATCCATCCATTTGGTCT 57.167 29.630 0.00 0.00 38.01 3.85
27 28 9.964354 CACTTCCTATCATTTAATATCCATCCA 57.036 33.333 0.00 0.00 0.00 3.41
28 29 8.897752 GCACTTCCTATCATTTAATATCCATCC 58.102 37.037 0.00 0.00 0.00 3.51
29 30 9.678260 AGCACTTCCTATCATTTAATATCCATC 57.322 33.333 0.00 0.00 0.00 3.51
32 33 9.606631 CCTAGCACTTCCTATCATTTAATATCC 57.393 37.037 0.00 0.00 0.00 2.59
36 37 8.718656 ACTTCCTAGCACTTCCTATCATTTAAT 58.281 33.333 0.00 0.00 0.00 1.40
37 38 7.987458 CACTTCCTAGCACTTCCTATCATTTAA 59.013 37.037 0.00 0.00 0.00 1.52
38 39 7.344612 TCACTTCCTAGCACTTCCTATCATTTA 59.655 37.037 0.00 0.00 0.00 1.40
39 40 6.156949 TCACTTCCTAGCACTTCCTATCATTT 59.843 38.462 0.00 0.00 0.00 2.32
40 41 5.663106 TCACTTCCTAGCACTTCCTATCATT 59.337 40.000 0.00 0.00 0.00 2.57
41 42 5.211973 TCACTTCCTAGCACTTCCTATCAT 58.788 41.667 0.00 0.00 0.00 2.45
42 43 4.610333 TCACTTCCTAGCACTTCCTATCA 58.390 43.478 0.00 0.00 0.00 2.15
43 44 5.599999 TTCACTTCCTAGCACTTCCTATC 57.400 43.478 0.00 0.00 0.00 2.08
44 45 6.567602 ATTTCACTTCCTAGCACTTCCTAT 57.432 37.500 0.00 0.00 0.00 2.57
45 46 6.895756 TCTATTTCACTTCCTAGCACTTCCTA 59.104 38.462 0.00 0.00 0.00 2.94
46 47 4.917906 ATTTCACTTCCTAGCACTTCCT 57.082 40.909 0.00 0.00 0.00 3.36
47 48 5.978814 TCTATTTCACTTCCTAGCACTTCC 58.021 41.667 0.00 0.00 0.00 3.46
48 49 7.766278 TCATTCTATTTCACTTCCTAGCACTTC 59.234 37.037 0.00 0.00 0.00 3.01
49 50 7.624549 TCATTCTATTTCACTTCCTAGCACTT 58.375 34.615 0.00 0.00 0.00 3.16
50 51 7.187824 TCATTCTATTTCACTTCCTAGCACT 57.812 36.000 0.00 0.00 0.00 4.40
51 52 7.849804 TTCATTCTATTTCACTTCCTAGCAC 57.150 36.000 0.00 0.00 0.00 4.40
56 57 9.336171 GCTCTATTTCATTCTATTTCACTTCCT 57.664 33.333 0.00 0.00 0.00 3.36
57 58 9.113838 TGCTCTATTTCATTCTATTTCACTTCC 57.886 33.333 0.00 0.00 0.00 3.46
60 61 9.678260 AGTTGCTCTATTTCATTCTATTTCACT 57.322 29.630 0.00 0.00 0.00 3.41
65 66 8.689972 CCCAAAGTTGCTCTATTTCATTCTATT 58.310 33.333 0.00 0.00 0.00 1.73
66 67 7.201857 GCCCAAAGTTGCTCTATTTCATTCTAT 60.202 37.037 0.00 0.00 0.00 1.98
67 68 6.095440 GCCCAAAGTTGCTCTATTTCATTCTA 59.905 38.462 0.00 0.00 0.00 2.10
68 69 5.105595 GCCCAAAGTTGCTCTATTTCATTCT 60.106 40.000 0.00 0.00 0.00 2.40
69 70 5.105063 GCCCAAAGTTGCTCTATTTCATTC 58.895 41.667 0.00 0.00 0.00 2.67
70 71 4.774200 AGCCCAAAGTTGCTCTATTTCATT 59.226 37.500 0.00 0.00 30.33 2.57
71 72 4.347607 AGCCCAAAGTTGCTCTATTTCAT 58.652 39.130 0.00 0.00 30.33 2.57
72 73 3.766545 AGCCCAAAGTTGCTCTATTTCA 58.233 40.909 0.00 0.00 30.33 2.69
73 74 4.380973 GGAAGCCCAAAGTTGCTCTATTTC 60.381 45.833 0.00 0.00 36.66 2.17
74 75 3.511540 GGAAGCCCAAAGTTGCTCTATTT 59.488 43.478 0.00 0.00 36.66 1.40
75 76 3.092301 GGAAGCCCAAAGTTGCTCTATT 58.908 45.455 0.00 0.00 36.66 1.73
76 77 2.621668 GGGAAGCCCAAAGTTGCTCTAT 60.622 50.000 0.00 0.00 44.65 1.98
77 78 1.271926 GGGAAGCCCAAAGTTGCTCTA 60.272 52.381 0.00 0.00 44.65 2.43
78 79 0.540597 GGGAAGCCCAAAGTTGCTCT 60.541 55.000 0.00 0.00 44.65 4.09
79 80 1.967535 GGGAAGCCCAAAGTTGCTC 59.032 57.895 0.00 0.00 44.65 4.26
80 81 4.198087 GGGAAGCCCAAAGTTGCT 57.802 55.556 0.00 0.00 44.65 3.91
89 90 2.868899 CCTCATTTCATAGGGAAGCCC 58.131 52.381 0.00 0.00 45.90 5.19
90 91 2.234143 GCCTCATTTCATAGGGAAGCC 58.766 52.381 0.00 0.00 36.72 4.35
91 92 2.936202 TGCCTCATTTCATAGGGAAGC 58.064 47.619 0.00 0.00 36.72 3.86
92 93 3.825014 CCATGCCTCATTTCATAGGGAAG 59.175 47.826 0.00 0.00 36.74 3.46
93 94 3.462954 TCCATGCCTCATTTCATAGGGAA 59.537 43.478 0.00 0.00 36.74 3.97
94 95 3.055328 TCCATGCCTCATTTCATAGGGA 58.945 45.455 0.00 0.00 37.64 4.20
95 96 3.513909 TCCATGCCTCATTTCATAGGG 57.486 47.619 0.00 0.00 33.17 3.53
96 97 3.251729 CGTTCCATGCCTCATTTCATAGG 59.748 47.826 0.00 0.00 35.86 2.57
97 98 3.251729 CCGTTCCATGCCTCATTTCATAG 59.748 47.826 0.00 0.00 0.00 2.23
98 99 3.118075 TCCGTTCCATGCCTCATTTCATA 60.118 43.478 0.00 0.00 0.00 2.15
99 100 2.026641 CCGTTCCATGCCTCATTTCAT 58.973 47.619 0.00 0.00 0.00 2.57
100 101 1.004161 TCCGTTCCATGCCTCATTTCA 59.996 47.619 0.00 0.00 0.00 2.69
101 102 1.672881 CTCCGTTCCATGCCTCATTTC 59.327 52.381 0.00 0.00 0.00 2.17
102 103 1.755179 CTCCGTTCCATGCCTCATTT 58.245 50.000 0.00 0.00 0.00 2.32
103 104 0.749454 GCTCCGTTCCATGCCTCATT 60.749 55.000 0.00 0.00 0.00 2.57
104 105 1.153086 GCTCCGTTCCATGCCTCAT 60.153 57.895 0.00 0.00 0.00 2.90
105 106 2.268920 GCTCCGTTCCATGCCTCA 59.731 61.111 0.00 0.00 0.00 3.86
106 107 2.514824 GGCTCCGTTCCATGCCTC 60.515 66.667 0.00 0.00 41.92 4.70
107 108 3.329889 TGGCTCCGTTCCATGCCT 61.330 61.111 0.00 0.00 45.11 4.75
108 109 2.252072 TAGTGGCTCCGTTCCATGCC 62.252 60.000 0.00 0.00 45.10 4.40
109 110 1.090052 GTAGTGGCTCCGTTCCATGC 61.090 60.000 0.00 0.00 35.81 4.06
110 111 0.806102 CGTAGTGGCTCCGTTCCATG 60.806 60.000 0.00 0.00 35.81 3.66
111 112 0.968901 TCGTAGTGGCTCCGTTCCAT 60.969 55.000 0.00 0.00 35.81 3.41
112 113 1.180456 TTCGTAGTGGCTCCGTTCCA 61.180 55.000 0.00 0.00 0.00 3.53
113 114 0.458025 CTTCGTAGTGGCTCCGTTCC 60.458 60.000 0.00 0.00 0.00 3.62
114 115 0.524862 TCTTCGTAGTGGCTCCGTTC 59.475 55.000 0.00 0.00 0.00 3.95
115 116 0.243095 GTCTTCGTAGTGGCTCCGTT 59.757 55.000 0.00 0.00 0.00 4.44
116 117 0.608582 AGTCTTCGTAGTGGCTCCGT 60.609 55.000 0.00 0.00 0.00 4.69
117 118 0.526662 AAGTCTTCGTAGTGGCTCCG 59.473 55.000 0.00 0.00 0.00 4.63
118 119 1.404315 CCAAGTCTTCGTAGTGGCTCC 60.404 57.143 0.00 0.00 0.00 4.70
119 120 1.997669 CCAAGTCTTCGTAGTGGCTC 58.002 55.000 0.00 0.00 0.00 4.70
122 123 0.038526 ACGCCAAGTCTTCGTAGTGG 60.039 55.000 0.00 0.00 34.41 4.00
123 124 1.337821 GACGCCAAGTCTTCGTAGTG 58.662 55.000 0.00 0.00 46.13 2.74
124 125 3.788775 GACGCCAAGTCTTCGTAGT 57.211 52.632 0.00 0.00 46.13 2.73
132 133 0.247145 CGCAAATACGACGCCAAGTC 60.247 55.000 0.00 0.00 46.16 3.01
133 134 0.947180 ACGCAAATACGACGCCAAGT 60.947 50.000 0.00 0.00 36.70 3.16
134 135 0.247145 GACGCAAATACGACGCCAAG 60.247 55.000 0.00 0.00 36.70 3.61
135 136 0.944788 TGACGCAAATACGACGCCAA 60.945 50.000 0.00 0.00 36.70 4.52
136 137 1.348538 CTGACGCAAATACGACGCCA 61.349 55.000 0.00 0.00 36.70 5.69
137 138 1.343821 CTGACGCAAATACGACGCC 59.656 57.895 0.00 0.00 36.70 5.68
138 139 0.246757 CACTGACGCAAATACGACGC 60.247 55.000 0.00 0.00 36.70 5.19
139 140 1.057285 GACACTGACGCAAATACGACG 59.943 52.381 0.00 0.00 36.70 5.12
140 141 2.325761 AGACACTGACGCAAATACGAC 58.674 47.619 0.00 0.00 36.70 4.34
141 142 2.717580 AGACACTGACGCAAATACGA 57.282 45.000 0.00 0.00 36.70 3.43
142 143 2.597305 GGTAGACACTGACGCAAATACG 59.403 50.000 0.00 0.00 39.50 3.06
143 144 2.928116 GGGTAGACACTGACGCAAATAC 59.072 50.000 0.00 0.00 0.00 1.89
144 145 2.416296 CGGGTAGACACTGACGCAAATA 60.416 50.000 0.00 0.00 0.00 1.40
145 146 1.671850 CGGGTAGACACTGACGCAAAT 60.672 52.381 0.00 0.00 0.00 2.32
146 147 0.319211 CGGGTAGACACTGACGCAAA 60.319 55.000 0.00 0.00 0.00 3.68
147 148 1.287815 CGGGTAGACACTGACGCAA 59.712 57.895 0.00 0.00 0.00 4.85
148 149 2.959372 CGGGTAGACACTGACGCA 59.041 61.111 0.00 0.00 0.00 5.24
149 150 2.506438 GCGGGTAGACACTGACGC 60.506 66.667 0.00 0.00 36.03 5.19
150 151 0.319211 TTTGCGGGTAGACACTGACG 60.319 55.000 0.00 0.00 0.00 4.35
151 152 1.873698 TTTTGCGGGTAGACACTGAC 58.126 50.000 0.00 0.00 0.00 3.51
152 153 2.623878 TTTTTGCGGGTAGACACTGA 57.376 45.000 0.00 0.00 0.00 3.41
171 172 7.273381 GCACAGATATTGACGCAAATACTTTTT 59.727 33.333 0.00 0.00 0.00 1.94
172 173 6.747280 GCACAGATATTGACGCAAATACTTTT 59.253 34.615 0.00 0.00 0.00 2.27
173 174 6.128035 TGCACAGATATTGACGCAAATACTTT 60.128 34.615 0.00 0.00 36.37 2.66
174 175 5.353956 TGCACAGATATTGACGCAAATACTT 59.646 36.000 0.00 0.00 36.37 2.24
175 176 4.875536 TGCACAGATATTGACGCAAATACT 59.124 37.500 0.00 0.00 36.37 2.12
176 177 5.155509 TGCACAGATATTGACGCAAATAC 57.844 39.130 0.00 0.00 36.37 1.89
177 178 4.260743 GCTGCACAGATATTGACGCAAATA 60.261 41.667 0.81 0.00 37.94 1.40
178 179 3.488047 GCTGCACAGATATTGACGCAAAT 60.488 43.478 0.81 0.00 37.94 2.32
183 184 1.596260 CTGGCTGCACAGATATTGACG 59.404 52.381 11.25 0.00 40.97 4.35
208 209 1.696314 TCCCTTACCCCCTGCCATC 60.696 63.158 0.00 0.00 0.00 3.51
210 211 2.286121 CTCCCTTACCCCCTGCCA 60.286 66.667 0.00 0.00 0.00 4.92
213 214 1.384643 CCTCCTCCCTTACCCCCTG 60.385 68.421 0.00 0.00 0.00 4.45
217 218 1.969200 GCGAACCTCCTCCCTTACCC 61.969 65.000 0.00 0.00 0.00 3.69
218 219 1.521141 GCGAACCTCCTCCCTTACC 59.479 63.158 0.00 0.00 0.00 2.85
220 221 0.976073 CTGGCGAACCTCCTCCCTTA 60.976 60.000 0.00 0.00 36.63 2.69
222 223 2.685380 CTGGCGAACCTCCTCCCT 60.685 66.667 0.00 0.00 36.63 4.20
223 224 4.475135 GCTGGCGAACCTCCTCCC 62.475 72.222 0.00 0.00 36.63 4.30
224 225 2.932130 GATGCTGGCGAACCTCCTCC 62.932 65.000 0.00 0.00 36.63 4.30
225 226 1.522580 GATGCTGGCGAACCTCCTC 60.523 63.158 0.00 0.00 36.63 3.71
226 227 2.586792 GATGCTGGCGAACCTCCT 59.413 61.111 0.00 0.00 36.63 3.69
227 228 2.514824 GGATGCTGGCGAACCTCC 60.515 66.667 0.00 0.00 36.63 4.30
228 229 2.892425 CGGATGCTGGCGAACCTC 60.892 66.667 0.00 0.00 36.63 3.85
229 230 4.473520 CCGGATGCTGGCGAACCT 62.474 66.667 0.00 0.00 36.63 3.50
244 245 1.794222 GAACATTCGTTGGGAGCCG 59.206 57.895 0.00 0.00 34.75 5.52
255 256 3.632189 GGATGCTATTTGGCGAACATTC 58.368 45.455 0.00 0.00 34.52 2.67
258 259 1.013596 CGGATGCTATTTGGCGAACA 58.986 50.000 0.00 0.00 34.52 3.18
259 260 0.317020 GCGGATGCTATTTGGCGAAC 60.317 55.000 0.00 0.00 38.39 3.95
264 265 4.044336 TGATTTTGCGGATGCTATTTGG 57.956 40.909 0.00 0.00 43.34 3.28
275 276 3.403613 TGTCGATGATTGATTTTGCGG 57.596 42.857 0.00 0.00 0.00 5.69
276 277 3.656266 CGATGTCGATGATTGATTTTGCG 59.344 43.478 0.00 0.00 43.02 4.85
277 278 4.836455 TCGATGTCGATGATTGATTTTGC 58.164 39.130 0.21 0.00 44.22 3.68
298 300 4.458295 TCGAGGAATATATGGAACGGACTC 59.542 45.833 0.00 0.00 0.00 3.36
307 309 3.198635 AGTGCCCATCGAGGAATATATGG 59.801 47.826 0.00 0.00 41.22 2.74
329 331 3.340034 GTTAAATGACGGGGATGTGACA 58.660 45.455 0.00 0.00 0.00 3.58
335 337 3.086282 GTGTTGGTTAAATGACGGGGAT 58.914 45.455 0.00 0.00 0.00 3.85
355 357 1.006102 CGGAGAAACTGCTGTCCGT 60.006 57.895 11.82 0.00 45.62 4.69
356 358 3.862124 CGGAGAAACTGCTGTCCG 58.138 61.111 7.10 7.10 45.48 4.79
357 359 2.035442 GCCGGAGAAACTGCTGTCC 61.035 63.158 5.05 0.00 0.00 4.02
358 360 1.004440 AGCCGGAGAAACTGCTGTC 60.004 57.895 5.05 0.00 31.70 3.51
421 429 2.413112 GACGTTGATGGATGAGTGTGTG 59.587 50.000 0.00 0.00 0.00 3.82
447 455 0.034059 GGATATGGGTCACCGCAGAG 59.966 60.000 0.00 0.00 40.75 3.35
458 466 3.282021 CCAATAGCAATCGGGATATGGG 58.718 50.000 0.00 0.00 0.00 4.00
505 514 0.868406 CTTGTTGGGTTGCGACTCTC 59.132 55.000 5.34 0.00 0.00 3.20
577 596 1.242076 GCCGGGGATCTTCATTCATG 58.758 55.000 2.18 0.00 0.00 3.07
799 849 3.933722 CGATCGGGATGGCTGGCT 61.934 66.667 7.38 0.00 0.00 4.75
801 851 4.996434 GGCGATCGGGATGGCTGG 62.996 72.222 18.30 0.00 41.45 4.85
802 852 4.240103 TGGCGATCGGGATGGCTG 62.240 66.667 18.30 0.00 41.45 4.85
803 853 4.241555 GTGGCGATCGGGATGGCT 62.242 66.667 18.30 0.00 41.45 4.75
930 1010 7.049754 AGTTCTTCAGGTAGAGTAGTAGTAGC 58.950 42.308 0.00 0.00 0.00 3.58
977 1057 1.663379 CGCCAGTAGGATCGACCACA 61.663 60.000 6.78 0.00 42.04 4.17
1565 1668 0.249155 TGACGTCCGGTGTGAAAGAC 60.249 55.000 14.12 0.00 0.00 3.01
1566 1669 0.031585 CTGACGTCCGGTGTGAAAGA 59.968 55.000 14.12 0.00 0.00 2.52
1567 1670 0.031585 TCTGACGTCCGGTGTGAAAG 59.968 55.000 14.12 0.00 0.00 2.62
1568 1671 0.031585 CTCTGACGTCCGGTGTGAAA 59.968 55.000 14.12 0.00 0.00 2.69
1569 1672 1.658114 CTCTGACGTCCGGTGTGAA 59.342 57.895 14.12 0.00 0.00 3.18
1570 1673 2.916052 GCTCTGACGTCCGGTGTGA 61.916 63.158 14.12 0.00 0.00 3.58
1571 1674 2.430921 GCTCTGACGTCCGGTGTG 60.431 66.667 14.12 3.26 0.00 3.82
1572 1675 3.681835 GGCTCTGACGTCCGGTGT 61.682 66.667 14.12 0.51 0.00 4.16
1573 1676 4.778415 CGGCTCTGACGTCCGGTG 62.778 72.222 14.12 8.07 39.52 4.94
1576 1679 4.180946 CTCCGGCTCTGACGTCCG 62.181 72.222 14.12 9.51 42.58 4.79
1577 1680 2.750637 TCTCCGGCTCTGACGTCC 60.751 66.667 14.12 0.00 28.54 4.79
1578 1681 1.098712 ATCTCTCCGGCTCTGACGTC 61.099 60.000 9.11 9.11 28.54 4.34
1579 1682 1.077357 ATCTCTCCGGCTCTGACGT 60.077 57.895 0.00 0.00 28.54 4.34
1580 1683 1.652012 GATCTCTCCGGCTCTGACG 59.348 63.158 0.00 0.00 0.00 4.35
1581 1684 0.753479 TGGATCTCTCCGGCTCTGAC 60.753 60.000 0.00 0.00 45.37 3.51
1582 1685 0.753479 GTGGATCTCTCCGGCTCTGA 60.753 60.000 0.00 0.00 45.37 3.27
1583 1686 1.039785 TGTGGATCTCTCCGGCTCTG 61.040 60.000 0.00 0.00 45.37 3.35
1584 1687 0.754957 CTGTGGATCTCTCCGGCTCT 60.755 60.000 0.00 0.00 45.37 4.09
1585 1688 1.040339 ACTGTGGATCTCTCCGGCTC 61.040 60.000 0.00 0.00 45.37 4.70
1586 1689 0.616111 AACTGTGGATCTCTCCGGCT 60.616 55.000 0.00 0.00 45.37 5.52
1587 1690 1.112113 TAACTGTGGATCTCTCCGGC 58.888 55.000 0.00 0.00 45.37 6.13
1588 1691 4.408182 AATTAACTGTGGATCTCTCCGG 57.592 45.455 0.00 0.00 45.37 5.14
1589 1692 6.392625 TCTAATTAACTGTGGATCTCTCCG 57.607 41.667 0.00 0.00 45.37 4.63
1590 1693 7.015682 TGGATCTAATTAACTGTGGATCTCTCC 59.984 40.741 8.97 0.00 42.45 3.71
1591 1694 7.957002 TGGATCTAATTAACTGTGGATCTCTC 58.043 38.462 8.97 0.00 32.71 3.20
1592 1695 7.921041 TGGATCTAATTAACTGTGGATCTCT 57.079 36.000 8.97 0.00 32.71 3.10
1593 1696 7.118971 GCATGGATCTAATTAACTGTGGATCTC 59.881 40.741 0.00 2.95 32.71 2.75
1594 1697 6.939163 GCATGGATCTAATTAACTGTGGATCT 59.061 38.462 0.00 0.00 32.71 2.75
1599 1733 6.765036 ACAGAGCATGGATCTAATTAACTGTG 59.235 38.462 0.00 0.00 33.51 3.66
1687 1846 3.072944 GTGTAGTCGTATAGCCGGATCT 58.927 50.000 5.05 0.00 0.00 2.75
1724 4321 2.919494 GCCACAAGCAAAGGACCGG 61.919 63.158 0.00 0.00 42.97 5.28
2085 4686 0.597637 CCGAGCAACACTCAGTTCGT 60.598 55.000 0.00 0.00 46.63 3.85
2092 4693 0.037326 TGACCATCCGAGCAACACTC 60.037 55.000 0.00 0.00 42.47 3.51
2120 4721 0.390124 TGGTACGTCACTTCCACCAC 59.610 55.000 0.00 0.00 34.40 4.16
2129 4730 1.069668 ACTTGAACCCTGGTACGTCAC 59.930 52.381 0.00 0.00 0.00 3.67
2134 4735 2.821969 TCTACGACTTGAACCCTGGTAC 59.178 50.000 0.00 0.00 0.00 3.34
2176 4777 9.592720 CGGAAAACATGAAATAAATCCAAAAAC 57.407 29.630 0.00 0.00 0.00 2.43
2179 4780 7.386299 CACCGGAAAACATGAAATAAATCCAAA 59.614 33.333 9.46 0.00 0.00 3.28
2200 4801 2.664424 CGCACTAAACAAACATCACCGG 60.664 50.000 0.00 0.00 0.00 5.28
2203 4804 5.029650 TCATCGCACTAAACAAACATCAC 57.970 39.130 0.00 0.00 0.00 3.06
2204 4805 4.994217 TCTCATCGCACTAAACAAACATCA 59.006 37.500 0.00 0.00 0.00 3.07
2210 4811 3.021269 ACGTCTCATCGCACTAAACAA 57.979 42.857 0.00 0.00 0.00 2.83
2211 4812 2.717580 ACGTCTCATCGCACTAAACA 57.282 45.000 0.00 0.00 0.00 2.83
2221 4822 3.250744 TGGTCGATGAAAACGTCTCATC 58.749 45.455 22.04 22.04 43.82 2.92
2223 4824 2.804697 TGGTCGATGAAAACGTCTCA 57.195 45.000 3.05 3.05 32.26 3.27
2232 4833 1.447838 GCGCCTCTTGGTCGATGAA 60.448 57.895 0.00 0.00 35.80 2.57
2233 4834 1.960040 ATGCGCCTCTTGGTCGATGA 61.960 55.000 4.18 0.00 35.80 2.92
2235 4836 1.522355 CATGCGCCTCTTGGTCGAT 60.522 57.895 4.18 0.00 35.80 3.59
2249 4850 0.804364 TTCATGAAGTCGCCACATGC 59.196 50.000 3.38 0.00 40.47 4.06
2257 4858 4.115516 ACATTCGGAGATTCATGAAGTCG 58.884 43.478 14.54 13.57 35.04 4.18
2266 4867 1.062587 CGGCACAACATTCGGAGATTC 59.937 52.381 0.00 0.00 35.04 2.52
2273 4874 0.865111 TTGAGTCGGCACAACATTCG 59.135 50.000 0.00 0.00 0.00 3.34
2287 4888 4.229639 TGGGCATCTCTGAGATATTGAGT 58.770 43.478 19.16 0.00 32.12 3.41
2296 4897 0.835276 TGTCCATGGGCATCTCTGAG 59.165 55.000 17.02 0.00 0.00 3.35
2301 4902 2.123018 TCCTATGTCCATGGGCATCT 57.877 50.000 34.50 16.60 39.09 2.90
2307 4908 2.283298 GCGCATATCCTATGTCCATGG 58.717 52.381 4.97 4.97 0.00 3.66
2348 4949 8.635983 CGCATATACTTACATACACACATACAC 58.364 37.037 0.00 0.00 0.00 2.90
2349 4950 8.354426 ACGCATATACTTACATACACACATACA 58.646 33.333 0.00 0.00 0.00 2.29
2350 4951 8.738199 ACGCATATACTTACATACACACATAC 57.262 34.615 0.00 0.00 0.00 2.39
2351 4952 9.752961 AAACGCATATACTTACATACACACATA 57.247 29.630 0.00 0.00 0.00 2.29
2352 4953 8.547894 CAAACGCATATACTTACATACACACAT 58.452 33.333 0.00 0.00 0.00 3.21
2353 4954 7.546316 ACAAACGCATATACTTACATACACACA 59.454 33.333 0.00 0.00 0.00 3.72
2354 4955 7.902032 ACAAACGCATATACTTACATACACAC 58.098 34.615 0.00 0.00 0.00 3.82
2355 4956 9.022915 GTACAAACGCATATACTTACATACACA 57.977 33.333 0.00 0.00 0.00 3.72
2356 4957 9.241317 AGTACAAACGCATATACTTACATACAC 57.759 33.333 0.00 0.00 0.00 2.90
2357 4958 9.240159 CAGTACAAACGCATATACTTACATACA 57.760 33.333 0.00 0.00 0.00 2.29
2394 4995 6.746745 TTTTTGTAGACGTCAAGGTTCTTT 57.253 33.333 19.50 0.00 0.00 2.52
2436 5037 3.937814 TGTCAGCGATCAGTAATGGTTT 58.062 40.909 0.00 0.00 0.00 3.27
2439 5040 4.122046 TCATTGTCAGCGATCAGTAATGG 58.878 43.478 0.00 0.00 0.00 3.16
2445 5046 4.510340 TCATGAATCATTGTCAGCGATCAG 59.490 41.667 0.00 0.00 0.00 2.90
2448 5049 4.151867 CGATCATGAATCATTGTCAGCGAT 59.848 41.667 0.00 0.00 33.65 4.58
2491 5092 2.747855 GAGCCCTCGTGCCTTTGG 60.748 66.667 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.