Multiple sequence alignment - TraesCS5D01G107900

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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 TraesCS5D01G107900 chr5D 100.000 3350 0 0 1 3350 121175432 121172083 0.000000e+00 6187.0
1 TraesCS5D01G107900 chr5A 96.599 2617 71 10 213 2813 132597262 132594648 0.000000e+00 4324.0
2 TraesCS5D01G107900 chr5A 91.841 527 20 6 2827 3350 132594666 132594160 0.000000e+00 713.0
3 TraesCS5D01G107900 chr5A 82.063 223 35 5 1 220 446600196 446599976 5.710000e-43 185.0
4 TraesCS5D01G107900 chr5B 96.093 2508 74 11 315 2813 134449339 134446847 0.000000e+00 4067.0
5 TraesCS5D01G107900 chr5B 94.717 530 20 6 2827 3350 134446865 134446338 0.000000e+00 817.0
6 TraesCS5D01G107900 chr5B 86.680 488 53 8 2827 3310 215845948 215846427 6.360000e-147 531.0
7 TraesCS5D01G107900 chr5B 83.333 216 33 2 1 213 432264380 432264595 2.640000e-46 196.0
8 TraesCS5D01G107900 chr3D 89.754 1015 93 6 1316 2326 17792237 17793244 0.000000e+00 1288.0
9 TraesCS5D01G107900 chr3D 88.870 575 58 3 1752 2326 17807509 17808077 0.000000e+00 702.0
10 TraesCS5D01G107900 chr3D 86.230 610 72 6 1754 2361 17793682 17794281 0.000000e+00 651.0
11 TraesCS5D01G107900 chr3D 88.697 522 59 0 1753 2274 17796382 17796903 3.650000e-179 638.0
12 TraesCS5D01G107900 chr3D 92.287 376 29 0 1899 2274 17834713 17835088 4.920000e-148 534.0
13 TraesCS5D01G107900 chrUn 90.538 539 41 6 1826 2361 37157942 37157411 0.000000e+00 704.0
14 TraesCS5D01G107900 chrUn 88.068 528 52 7 2827 3350 244072360 244072880 1.710000e-172 616.0
15 TraesCS5D01G107900 chrUn 88.068 528 52 7 2827 3350 256066457 256065937 1.710000e-172 616.0
16 TraesCS5D01G107900 chrUn 88.068 528 52 7 2827 3350 268677015 268676495 1.710000e-172 616.0
17 TraesCS5D01G107900 chrUn 85.156 384 29 12 1415 1798 37158292 37157937 5.280000e-98 368.0
18 TraesCS5D01G107900 chr7A 87.782 532 53 7 2827 3350 727513226 727513753 2.210000e-171 612.0
19 TraesCS5D01G107900 chr2B 84.340 447 70 0 1150 1596 180558787 180559233 3.970000e-119 438.0
20 TraesCS5D01G107900 chr2B 80.962 478 62 24 1594 2055 180559327 180559791 5.320000e-93 351.0
21 TraesCS5D01G107900 chr2B 85.882 85 11 1 123 207 677343436 677343519 4.600000e-14 89.8
22 TraesCS5D01G107900 chr2D 84.116 447 71 0 1150 1596 126968383 126968829 1.850000e-117 433.0
23 TraesCS5D01G107900 chr2D 81.120 482 57 27 1594 2055 126968941 126969408 4.110000e-94 355.0
24 TraesCS5D01G107900 chr2A 83.893 447 72 0 1150 1596 133671044 133671490 8.590000e-116 427.0
25 TraesCS5D01G107900 chr2A 80.550 473 60 23 1602 2055 133671627 133672086 5.360000e-88 335.0
26 TraesCS5D01G107900 chr3B 86.730 211 28 0 1 211 578601728 578601938 5.590000e-58 235.0
27 TraesCS5D01G107900 chr1B 84.332 217 28 5 1 213 487018107 487017893 1.220000e-49 207.0
28 TraesCS5D01G107900 chr7D 82.949 217 33 4 1 214 205538160 205538375 3.410000e-45 193.0
29 TraesCS5D01G107900 chr7D 85.484 186 24 2 28 212 598310567 598310750 1.230000e-44 191.0
30 TraesCS5D01G107900 chr6D 76.104 385 72 16 1161 1535 454231330 454231704 2.050000e-42 183.0
31 TraesCS5D01G107900 chr6A 75.521 384 76 16 1161 1535 600404314 600404688 4.440000e-39 172.0
32 TraesCS5D01G107900 chr6B 75.328 381 75 15 1161 1533 690560723 690560354 7.440000e-37 165.0
33 TraesCS5D01G107900 chr1A 100.000 28 0 0 186 213 572501713 572501686 6.000000e-03 52.8


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 TraesCS5D01G107900 chr5D 121172083 121175432 3349 True 6187.0 6187 100.0000 1 3350 1 chr5D.!!$R1 3349
1 TraesCS5D01G107900 chr5A 132594160 132597262 3102 True 2518.5 4324 94.2200 213 3350 2 chr5A.!!$R2 3137
2 TraesCS5D01G107900 chr5B 134446338 134449339 3001 True 2442.0 4067 95.4050 315 3350 2 chr5B.!!$R1 3035
3 TraesCS5D01G107900 chr3D 17792237 17796903 4666 False 859.0 1288 88.2270 1316 2361 3 chr3D.!!$F3 1045
4 TraesCS5D01G107900 chr3D 17807509 17808077 568 False 702.0 702 88.8700 1752 2326 1 chr3D.!!$F1 574
5 TraesCS5D01G107900 chrUn 244072360 244072880 520 False 616.0 616 88.0680 2827 3350 1 chrUn.!!$F1 523
6 TraesCS5D01G107900 chrUn 256065937 256066457 520 True 616.0 616 88.0680 2827 3350 1 chrUn.!!$R1 523
7 TraesCS5D01G107900 chrUn 268676495 268677015 520 True 616.0 616 88.0680 2827 3350 1 chrUn.!!$R2 523
8 TraesCS5D01G107900 chrUn 37157411 37158292 881 True 536.0 704 87.8470 1415 2361 2 chrUn.!!$R3 946
9 TraesCS5D01G107900 chr7A 727513226 727513753 527 False 612.0 612 87.7820 2827 3350 1 chr7A.!!$F1 523
10 TraesCS5D01G107900 chr2B 180558787 180559791 1004 False 394.5 438 82.6510 1150 2055 2 chr2B.!!$F2 905
11 TraesCS5D01G107900 chr2D 126968383 126969408 1025 False 394.0 433 82.6180 1150 2055 2 chr2D.!!$F1 905
12 TraesCS5D01G107900 chr2A 133671044 133672086 1042 False 381.0 427 82.2215 1150 2055 2 chr2A.!!$F1 905

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
77 78 0.103208 CATAGGCGTGTGAGAGGGAC 59.897 60.0 0.0 0.0 0.0 4.46 F
899 906 0.108186 GCCCTTTAATTGCCTGCCAC 60.108 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1068 1075 0.538977 TCGGGTCGAGGGGATCATAC 60.539 60.0 0.0 0.0 0.0 2.39 R
2795 4403 0.322975 GGGTGCATCTGTCAGTGAGT 59.677 55.0 0.0 0.0 0.0 3.41 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 3.369381 CCATGAGGTACGAAGCCTG 57.631 57.895 0.00 0.00 36.29 4.85
21 22 0.824109 CCATGAGGTACGAAGCCTGA 59.176 55.000 0.00 0.00 36.29 3.86
22 23 1.471676 CCATGAGGTACGAAGCCTGAC 60.472 57.143 0.00 0.00 36.29 3.51
23 24 0.456221 ATGAGGTACGAAGCCTGACG 59.544 55.000 0.00 0.00 36.29 4.35
24 25 0.892358 TGAGGTACGAAGCCTGACGT 60.892 55.000 0.00 0.00 44.72 4.34
25 26 1.089920 GAGGTACGAAGCCTGACGTA 58.910 55.000 0.00 0.00 42.61 3.57
26 27 1.674962 GAGGTACGAAGCCTGACGTAT 59.325 52.381 0.00 0.00 44.50 3.06
27 28 1.404391 AGGTACGAAGCCTGACGTATG 59.596 52.381 0.00 0.00 44.50 2.39
28 29 1.535437 GGTACGAAGCCTGACGTATGG 60.535 57.143 0.00 0.00 44.50 2.74
33 34 2.890474 GCCTGACGTATGGCCGTG 60.890 66.667 17.54 0.00 41.98 4.94
34 35 2.577059 CCTGACGTATGGCCGTGT 59.423 61.111 8.05 0.00 41.98 4.49
35 36 1.809619 CCTGACGTATGGCCGTGTG 60.810 63.158 8.05 1.79 41.98 3.82
36 37 1.809619 CTGACGTATGGCCGTGTGG 60.810 63.158 8.05 0.00 41.98 4.17
37 38 2.510691 GACGTATGGCCGTGTGGG 60.511 66.667 8.05 0.00 41.98 4.61
47 48 3.980583 CCGTGTGGGCGTTATCTAT 57.019 52.632 0.00 0.00 0.00 1.98
48 49 2.234300 CCGTGTGGGCGTTATCTATT 57.766 50.000 0.00 0.00 0.00 1.73
49 50 2.557317 CCGTGTGGGCGTTATCTATTT 58.443 47.619 0.00 0.00 0.00 1.40
50 51 2.940410 CCGTGTGGGCGTTATCTATTTT 59.060 45.455 0.00 0.00 0.00 1.82
51 52 3.242608 CCGTGTGGGCGTTATCTATTTTG 60.243 47.826 0.00 0.00 0.00 2.44
52 53 3.372822 CGTGTGGGCGTTATCTATTTTGT 59.627 43.478 0.00 0.00 0.00 2.83
53 54 4.493545 CGTGTGGGCGTTATCTATTTTGTC 60.494 45.833 0.00 0.00 0.00 3.18
54 55 3.942748 TGTGGGCGTTATCTATTTTGTCC 59.057 43.478 0.00 0.00 0.00 4.02
55 56 3.942748 GTGGGCGTTATCTATTTTGTCCA 59.057 43.478 0.00 0.00 0.00 4.02
56 57 4.578928 GTGGGCGTTATCTATTTTGTCCAT 59.421 41.667 0.00 0.00 0.00 3.41
57 58 5.761234 GTGGGCGTTATCTATTTTGTCCATA 59.239 40.000 0.00 0.00 0.00 2.74
58 59 5.761234 TGGGCGTTATCTATTTTGTCCATAC 59.239 40.000 0.00 0.00 0.00 2.39
59 60 5.761234 GGGCGTTATCTATTTTGTCCATACA 59.239 40.000 0.00 0.00 0.00 2.29
60 61 6.430000 GGGCGTTATCTATTTTGTCCATACAT 59.570 38.462 0.00 0.00 34.97 2.29
61 62 7.604927 GGGCGTTATCTATTTTGTCCATACATA 59.395 37.037 0.00 0.00 34.97 2.29
62 63 8.656849 GGCGTTATCTATTTTGTCCATACATAG 58.343 37.037 0.00 0.00 34.97 2.23
63 64 8.656849 GCGTTATCTATTTTGTCCATACATAGG 58.343 37.037 0.00 0.00 34.97 2.57
64 65 8.656849 CGTTATCTATTTTGTCCATACATAGGC 58.343 37.037 0.00 0.00 34.97 3.93
65 66 8.656849 GTTATCTATTTTGTCCATACATAGGCG 58.343 37.037 0.00 0.00 34.97 5.52
66 67 6.169557 TCTATTTTGTCCATACATAGGCGT 57.830 37.500 0.00 0.00 34.97 5.68
67 68 5.989168 TCTATTTTGTCCATACATAGGCGTG 59.011 40.000 0.00 0.00 34.97 5.34
68 69 3.620427 TTTGTCCATACATAGGCGTGT 57.380 42.857 4.13 4.13 34.97 4.49
69 70 2.595124 TGTCCATACATAGGCGTGTG 57.405 50.000 8.52 1.24 33.62 3.82
70 71 2.104170 TGTCCATACATAGGCGTGTGA 58.896 47.619 10.28 0.00 33.62 3.58
71 72 2.100749 TGTCCATACATAGGCGTGTGAG 59.899 50.000 10.28 0.00 33.62 3.51
72 73 2.361119 GTCCATACATAGGCGTGTGAGA 59.639 50.000 10.28 0.00 33.62 3.27
73 74 2.623416 TCCATACATAGGCGTGTGAGAG 59.377 50.000 10.28 0.00 33.62 3.20
74 75 2.288457 CCATACATAGGCGTGTGAGAGG 60.288 54.545 10.28 4.49 33.62 3.69
75 76 1.399714 TACATAGGCGTGTGAGAGGG 58.600 55.000 10.28 0.00 33.62 4.30
76 77 0.324368 ACATAGGCGTGTGAGAGGGA 60.324 55.000 10.28 0.00 0.00 4.20
77 78 0.103208 CATAGGCGTGTGAGAGGGAC 59.897 60.000 0.00 0.00 0.00 4.46
78 79 1.043673 ATAGGCGTGTGAGAGGGACC 61.044 60.000 0.00 0.00 0.00 4.46
79 80 4.436998 GGCGTGTGAGAGGGACCG 62.437 72.222 0.00 0.00 0.00 4.79
81 82 4.778415 CGTGTGAGAGGGACCGCG 62.778 72.222 0.00 0.00 0.00 6.46
82 83 4.436998 GTGTGAGAGGGACCGCGG 62.437 72.222 26.86 26.86 0.00 6.46
88 89 4.024545 GAGGGACCGCGGGGAAAA 62.025 66.667 31.76 0.00 36.97 2.29
89 90 3.556298 GAGGGACCGCGGGGAAAAA 62.556 63.158 31.76 0.00 36.97 1.94
113 114 9.642327 AAAAAGGTACGTGAAAATTACTTGTTT 57.358 25.926 0.00 0.00 0.00 2.83
114 115 9.642327 AAAAGGTACGTGAAAATTACTTGTTTT 57.358 25.926 0.00 0.00 0.00 2.43
115 116 8.623310 AAGGTACGTGAAAATTACTTGTTTTG 57.377 30.769 0.00 0.00 0.00 2.44
116 117 6.693978 AGGTACGTGAAAATTACTTGTTTTGC 59.306 34.615 0.00 0.00 0.00 3.68
117 118 5.959652 ACGTGAAAATTACTTGTTTTGCC 57.040 34.783 0.00 0.00 0.00 4.52
118 119 5.656480 ACGTGAAAATTACTTGTTTTGCCT 58.344 33.333 0.00 0.00 0.00 4.75
119 120 6.797454 ACGTGAAAATTACTTGTTTTGCCTA 58.203 32.000 0.00 0.00 0.00 3.93
120 121 6.693978 ACGTGAAAATTACTTGTTTTGCCTAC 59.306 34.615 0.00 0.00 0.00 3.18
121 122 6.693545 CGTGAAAATTACTTGTTTTGCCTACA 59.306 34.615 0.00 0.00 0.00 2.74
122 123 7.305763 CGTGAAAATTACTTGTTTTGCCTACAC 60.306 37.037 0.00 0.00 0.00 2.90
123 124 6.693545 TGAAAATTACTTGTTTTGCCTACACG 59.306 34.615 0.00 0.00 0.00 4.49
124 125 5.761165 AATTACTTGTTTTGCCTACACGT 57.239 34.783 0.00 0.00 33.33 4.49
125 126 6.864360 AATTACTTGTTTTGCCTACACGTA 57.136 33.333 0.00 0.00 31.50 3.57
126 127 5.910637 TTACTTGTTTTGCCTACACGTAG 57.089 39.130 0.00 0.00 33.55 3.51
127 128 4.062677 ACTTGTTTTGCCTACACGTAGA 57.937 40.909 5.77 0.00 35.21 2.59
128 129 3.805971 ACTTGTTTTGCCTACACGTAGAC 59.194 43.478 5.77 0.00 35.21 2.59
129 130 2.396601 TGTTTTGCCTACACGTAGACG 58.603 47.619 5.77 0.00 46.33 4.18
140 141 3.998924 CGTAGACGTGTGAGCTGAT 57.001 52.632 0.00 0.00 34.11 2.90
141 142 1.816370 CGTAGACGTGTGAGCTGATC 58.184 55.000 0.00 0.00 34.11 2.92
142 143 1.532090 CGTAGACGTGTGAGCTGATCC 60.532 57.143 0.00 0.00 34.11 3.36
143 144 1.746220 GTAGACGTGTGAGCTGATCCT 59.254 52.381 0.00 0.00 0.00 3.24
144 145 0.814457 AGACGTGTGAGCTGATCCTC 59.186 55.000 0.00 0.00 0.00 3.71
145 146 0.814457 GACGTGTGAGCTGATCCTCT 59.186 55.000 0.00 0.00 33.02 3.69
146 147 1.203523 GACGTGTGAGCTGATCCTCTT 59.796 52.381 0.00 0.00 33.02 2.85
147 148 2.423892 GACGTGTGAGCTGATCCTCTTA 59.576 50.000 0.00 0.00 33.02 2.10
148 149 2.425312 ACGTGTGAGCTGATCCTCTTAG 59.575 50.000 0.00 0.00 33.02 2.18
149 150 2.685388 CGTGTGAGCTGATCCTCTTAGA 59.315 50.000 0.00 0.00 33.02 2.10
150 151 3.488384 CGTGTGAGCTGATCCTCTTAGAC 60.488 52.174 0.00 0.00 33.02 2.59
151 152 2.685388 TGTGAGCTGATCCTCTTAGACG 59.315 50.000 0.00 0.00 33.02 4.18
152 153 1.678627 TGAGCTGATCCTCTTAGACGC 59.321 52.381 0.00 0.00 33.02 5.19
153 154 1.000717 GAGCTGATCCTCTTAGACGCC 60.001 57.143 0.00 0.00 0.00 5.68
154 155 0.747255 GCTGATCCTCTTAGACGCCA 59.253 55.000 0.00 0.00 0.00 5.69
155 156 1.537135 GCTGATCCTCTTAGACGCCAC 60.537 57.143 0.00 0.00 0.00 5.01
156 157 1.751351 CTGATCCTCTTAGACGCCACA 59.249 52.381 0.00 0.00 0.00 4.17
157 158 1.476891 TGATCCTCTTAGACGCCACAC 59.523 52.381 0.00 0.00 0.00 3.82
158 159 1.476891 GATCCTCTTAGACGCCACACA 59.523 52.381 0.00 0.00 0.00 3.72
159 160 1.334160 TCCTCTTAGACGCCACACAA 58.666 50.000 0.00 0.00 0.00 3.33
160 161 1.689813 TCCTCTTAGACGCCACACAAA 59.310 47.619 0.00 0.00 0.00 2.83
161 162 2.103432 TCCTCTTAGACGCCACACAAAA 59.897 45.455 0.00 0.00 0.00 2.44
162 163 2.223377 CCTCTTAGACGCCACACAAAAC 59.777 50.000 0.00 0.00 0.00 2.43
163 164 2.869801 CTCTTAGACGCCACACAAAACA 59.130 45.455 0.00 0.00 0.00 2.83
164 165 3.472652 TCTTAGACGCCACACAAAACAT 58.527 40.909 0.00 0.00 0.00 2.71
165 166 3.249799 TCTTAGACGCCACACAAAACATG 59.750 43.478 0.00 0.00 0.00 3.21
166 167 1.388547 AGACGCCACACAAAACATGT 58.611 45.000 0.00 0.00 45.34 3.21
175 176 2.071778 ACAAAACATGTGGGCAGACT 57.928 45.000 0.00 0.00 41.93 3.24
176 177 1.956477 ACAAAACATGTGGGCAGACTC 59.044 47.619 0.00 0.00 41.93 3.36
177 178 2.233271 CAAAACATGTGGGCAGACTCT 58.767 47.619 0.00 0.00 0.00 3.24
178 179 2.624838 CAAAACATGTGGGCAGACTCTT 59.375 45.455 0.00 0.00 0.00 2.85
179 180 2.664402 AACATGTGGGCAGACTCTTT 57.336 45.000 0.00 0.00 0.00 2.52
180 181 3.788227 AACATGTGGGCAGACTCTTTA 57.212 42.857 0.00 0.00 0.00 1.85
181 182 3.788227 ACATGTGGGCAGACTCTTTAA 57.212 42.857 0.00 0.00 0.00 1.52
182 183 3.412386 ACATGTGGGCAGACTCTTTAAC 58.588 45.455 0.00 0.00 0.00 2.01
183 184 2.163818 TGTGGGCAGACTCTTTAACG 57.836 50.000 0.00 0.00 0.00 3.18
184 185 0.796927 GTGGGCAGACTCTTTAACGC 59.203 55.000 0.00 0.00 0.00 4.84
185 186 0.321298 TGGGCAGACTCTTTAACGCC 60.321 55.000 0.00 0.00 38.85 5.68
186 187 2.467962 GGCAGACTCTTTAACGCCC 58.532 57.895 0.00 0.00 33.31 6.13
187 188 0.321298 GGCAGACTCTTTAACGCCCA 60.321 55.000 0.00 0.00 33.31 5.36
188 189 0.796927 GCAGACTCTTTAACGCCCAC 59.203 55.000 0.00 0.00 0.00 4.61
189 190 1.876416 GCAGACTCTTTAACGCCCACA 60.876 52.381 0.00 0.00 0.00 4.17
190 191 1.798813 CAGACTCTTTAACGCCCACAC 59.201 52.381 0.00 0.00 0.00 3.82
191 192 0.788391 GACTCTTTAACGCCCACACG 59.212 55.000 0.00 0.00 39.50 4.49
207 208 3.380671 CGTGTGGACGTTATCGGC 58.619 61.111 0.00 0.00 45.48 5.54
221 222 5.858581 ACGTTATCGGCGTCCTATAATTAAC 59.141 40.000 6.85 2.46 38.23 2.01
235 236 9.052759 TCCTATAATTAACTTTGCTCGGATTTC 57.947 33.333 0.00 0.00 0.00 2.17
288 289 2.540383 TCTGCATGGTAGGAAGACAGT 58.460 47.619 0.00 0.00 0.00 3.55
310 311 1.406898 TCTCATGACCAGATCAGACGC 59.593 52.381 0.00 0.00 41.91 5.19
446 447 7.995488 TGTAGTAGGGGTTGTCTAAGATACTAC 59.005 40.741 10.69 10.69 42.06 2.73
448 449 7.289310 AGTAGGGGTTGTCTAAGATACTACTC 58.711 42.308 0.00 0.00 35.09 2.59
497 502 2.308039 GCTCCACCGTCGTTGTCAC 61.308 63.158 0.00 0.00 0.00 3.67
711 718 0.681733 AGCACAGGAACACGTGAGAT 59.318 50.000 25.01 7.83 35.02 2.75
881 888 1.487452 TATTCTTCGCCGATGCACGC 61.487 55.000 0.00 0.00 41.07 5.34
899 906 0.108186 GCCCTTTAATTGCCTGCCAC 60.108 55.000 0.00 0.00 0.00 5.01
962 969 1.033574 AGCTAGCTACCTTACTGCGG 58.966 55.000 17.69 0.00 0.00 5.69
991 998 1.986882 GCAATAGCATTAGCAGGGGT 58.013 50.000 0.00 0.00 45.49 4.95
997 1004 1.660560 GCATTAGCAGGGGTGTGCAG 61.661 60.000 0.00 0.00 46.60 4.41
1049 1056 2.037053 CTCTGATCCTCGCGGTCAT 58.963 57.895 6.13 0.00 0.00 3.06
1059 1066 2.887568 GCGGTCATCTGCTCCGTG 60.888 66.667 12.48 0.00 45.11 4.94
1167 1174 2.779755 TGGTGGCGATGAACAACTAT 57.220 45.000 0.00 0.00 0.00 2.12
1179 1186 3.257375 TGAACAACTATCAGCAGTACCGT 59.743 43.478 0.00 0.00 0.00 4.83
2368 3565 5.275630 CATGATCCATCTATCCAGGGTCTA 58.724 45.833 0.00 0.00 33.64 2.59
2395 3592 6.624423 ACTCACATGCATCTTGGTAATTTTC 58.376 36.000 0.00 0.00 0.00 2.29
2440 3637 4.674281 ACAGGTTAGAGTATTAGGCAGC 57.326 45.455 0.00 0.00 0.00 5.25
2522 3720 5.331902 CGGCAACATATTTGTTTAGGAGTG 58.668 41.667 0.00 0.00 43.57 3.51
2523 3721 5.102313 GGCAACATATTTGTTTAGGAGTGC 58.898 41.667 0.00 0.00 43.57 4.40
2628 4234 5.333645 CGCATGGCATTGTTACTTAGATCTC 60.334 44.000 0.00 0.00 0.00 2.75
2689 4295 7.502226 TCTTCATTGAGTAACATGTTTCCAAGT 59.498 33.333 17.78 0.76 0.00 3.16
2764 4372 0.242286 CTCACTAGATGATCCCCGCG 59.758 60.000 0.00 0.00 36.48 6.46
2794 4402 0.676782 GGACGTTAGCATGCCAACCT 60.677 55.000 20.94 11.25 0.00 3.50
2795 4403 1.406341 GGACGTTAGCATGCCAACCTA 60.406 52.381 20.94 1.50 0.00 3.08
2796 4404 1.664151 GACGTTAGCATGCCAACCTAC 59.336 52.381 20.94 10.22 0.00 3.18
2797 4405 1.278127 ACGTTAGCATGCCAACCTACT 59.722 47.619 20.94 0.28 0.00 2.57
2798 4406 1.933853 CGTTAGCATGCCAACCTACTC 59.066 52.381 20.94 0.00 0.00 2.59
2799 4407 2.676750 CGTTAGCATGCCAACCTACTCA 60.677 50.000 20.94 0.00 0.00 3.41
2800 4408 2.678336 GTTAGCATGCCAACCTACTCAC 59.322 50.000 16.99 0.00 0.00 3.51
2801 4409 0.987294 AGCATGCCAACCTACTCACT 59.013 50.000 15.66 0.00 0.00 3.41
2802 4410 1.089920 GCATGCCAACCTACTCACTG 58.910 55.000 6.36 0.00 0.00 3.66
2803 4411 1.339055 GCATGCCAACCTACTCACTGA 60.339 52.381 6.36 0.00 0.00 3.41
2804 4412 2.350522 CATGCCAACCTACTCACTGAC 58.649 52.381 0.00 0.00 0.00 3.51
2805 4413 1.419381 TGCCAACCTACTCACTGACA 58.581 50.000 0.00 0.00 0.00 3.58
2806 4414 1.344438 TGCCAACCTACTCACTGACAG 59.656 52.381 0.00 0.00 0.00 3.51
2807 4415 1.618837 GCCAACCTACTCACTGACAGA 59.381 52.381 10.08 0.00 0.00 3.41
2808 4416 2.234908 GCCAACCTACTCACTGACAGAT 59.765 50.000 10.08 0.00 0.00 2.90
2809 4417 3.854666 CCAACCTACTCACTGACAGATG 58.145 50.000 10.08 4.16 0.00 2.90
2810 4418 3.257393 CAACCTACTCACTGACAGATGC 58.743 50.000 10.08 0.00 0.00 3.91
2811 4419 2.529632 ACCTACTCACTGACAGATGCA 58.470 47.619 10.08 0.00 0.00 3.96
2812 4420 2.232452 ACCTACTCACTGACAGATGCAC 59.768 50.000 10.08 0.00 0.00 4.57
2813 4421 2.417924 CCTACTCACTGACAGATGCACC 60.418 54.545 10.08 0.00 0.00 5.01
2814 4422 0.322975 ACTCACTGACAGATGCACCC 59.677 55.000 10.08 0.00 0.00 4.61
2815 4423 0.392193 CTCACTGACAGATGCACCCC 60.392 60.000 10.08 0.00 0.00 4.95
2816 4424 1.742880 CACTGACAGATGCACCCCG 60.743 63.158 10.08 0.00 0.00 5.73
2817 4425 2.821366 CTGACAGATGCACCCCGC 60.821 66.667 0.00 0.00 42.89 6.13
2852 4460 4.020307 TCACTGACAGATGCACATTAAGGA 60.020 41.667 10.08 0.00 0.00 3.36
3217 5867 2.823984 TGCAACAAATGTGAAAGCTGG 58.176 42.857 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.824759 AGGCTTCGTACCTCATGGTC 59.175 55.000 0.00 0.00 44.78 4.02
3 4 1.799181 CGTCAGGCTTCGTACCTCATG 60.799 57.143 0.00 0.00 34.42 3.07
4 5 0.456221 CGTCAGGCTTCGTACCTCAT 59.544 55.000 0.00 0.00 34.42 2.90
5 6 0.892358 ACGTCAGGCTTCGTACCTCA 60.892 55.000 11.83 0.00 38.52 3.86
6 7 1.089920 TACGTCAGGCTTCGTACCTC 58.910 55.000 14.77 0.00 40.70 3.85
7 8 1.404391 CATACGTCAGGCTTCGTACCT 59.596 52.381 19.11 6.59 43.47 3.08
8 9 1.535437 CCATACGTCAGGCTTCGTACC 60.535 57.143 19.11 0.00 43.47 3.34
9 10 1.836383 CCATACGTCAGGCTTCGTAC 58.164 55.000 19.11 0.98 43.47 3.67
16 17 2.890474 CACGGCCATACGTCAGGC 60.890 66.667 19.77 19.77 46.75 4.85
17 18 1.809619 CACACGGCCATACGTCAGG 60.810 63.158 2.24 0.00 46.75 3.86
18 19 1.809619 CCACACGGCCATACGTCAG 60.810 63.158 2.24 0.00 46.75 3.51
19 20 2.263227 CCACACGGCCATACGTCA 59.737 61.111 2.24 0.00 46.75 4.35
20 21 2.510691 CCCACACGGCCATACGTC 60.511 66.667 2.24 0.00 46.75 4.34
29 30 2.234300 AATAGATAACGCCCACACGG 57.766 50.000 0.00 0.00 37.37 4.94
30 31 3.372822 ACAAAATAGATAACGCCCACACG 59.627 43.478 0.00 0.00 39.50 4.49
31 32 4.201881 GGACAAAATAGATAACGCCCACAC 60.202 45.833 0.00 0.00 0.00 3.82
32 33 3.942748 GGACAAAATAGATAACGCCCACA 59.057 43.478 0.00 0.00 0.00 4.17
33 34 3.942748 TGGACAAAATAGATAACGCCCAC 59.057 43.478 0.00 0.00 0.00 4.61
34 35 4.223556 TGGACAAAATAGATAACGCCCA 57.776 40.909 0.00 0.00 0.00 5.36
35 36 5.761234 TGTATGGACAAAATAGATAACGCCC 59.239 40.000 0.00 0.00 30.68 6.13
36 37 6.854496 TGTATGGACAAAATAGATAACGCC 57.146 37.500 0.00 0.00 30.68 5.68
37 38 8.656849 CCTATGTATGGACAAAATAGATAACGC 58.343 37.037 0.00 0.00 39.59 4.84
38 39 8.656849 GCCTATGTATGGACAAAATAGATAACG 58.343 37.037 0.00 0.00 39.59 3.18
39 40 8.656849 CGCCTATGTATGGACAAAATAGATAAC 58.343 37.037 0.00 0.00 39.59 1.89
40 41 8.372459 ACGCCTATGTATGGACAAAATAGATAA 58.628 33.333 0.00 0.00 39.59 1.75
41 42 7.817478 CACGCCTATGTATGGACAAAATAGATA 59.183 37.037 0.00 0.00 39.59 1.98
42 43 6.650807 CACGCCTATGTATGGACAAAATAGAT 59.349 38.462 0.00 0.00 39.59 1.98
43 44 5.989168 CACGCCTATGTATGGACAAAATAGA 59.011 40.000 0.00 0.00 39.59 1.98
44 45 5.758296 ACACGCCTATGTATGGACAAAATAG 59.242 40.000 0.00 0.00 39.59 1.73
45 46 5.525745 CACACGCCTATGTATGGACAAAATA 59.474 40.000 0.00 0.00 39.59 1.40
46 47 4.335315 CACACGCCTATGTATGGACAAAAT 59.665 41.667 0.00 0.00 39.59 1.82
47 48 3.687212 CACACGCCTATGTATGGACAAAA 59.313 43.478 0.00 0.00 39.59 2.44
48 49 3.055747 TCACACGCCTATGTATGGACAAA 60.056 43.478 0.00 0.00 39.59 2.83
49 50 2.498078 TCACACGCCTATGTATGGACAA 59.502 45.455 0.00 0.00 39.59 3.18
50 51 2.100749 CTCACACGCCTATGTATGGACA 59.899 50.000 0.00 0.00 40.72 4.02
51 52 2.361119 TCTCACACGCCTATGTATGGAC 59.639 50.000 0.00 0.00 0.00 4.02
52 53 2.623416 CTCTCACACGCCTATGTATGGA 59.377 50.000 0.00 0.00 0.00 3.41
53 54 2.288457 CCTCTCACACGCCTATGTATGG 60.288 54.545 0.00 0.00 0.00 2.74
54 55 2.288457 CCCTCTCACACGCCTATGTATG 60.288 54.545 0.00 0.00 0.00 2.39
55 56 1.964223 CCCTCTCACACGCCTATGTAT 59.036 52.381 0.00 0.00 0.00 2.29
56 57 1.064240 TCCCTCTCACACGCCTATGTA 60.064 52.381 0.00 0.00 0.00 2.29
57 58 0.324368 TCCCTCTCACACGCCTATGT 60.324 55.000 0.00 0.00 0.00 2.29
58 59 0.103208 GTCCCTCTCACACGCCTATG 59.897 60.000 0.00 0.00 0.00 2.23
59 60 1.043673 GGTCCCTCTCACACGCCTAT 61.044 60.000 0.00 0.00 0.00 2.57
60 61 1.681327 GGTCCCTCTCACACGCCTA 60.681 63.158 0.00 0.00 0.00 3.93
61 62 2.997897 GGTCCCTCTCACACGCCT 60.998 66.667 0.00 0.00 0.00 5.52
62 63 4.436998 CGGTCCCTCTCACACGCC 62.437 72.222 0.00 0.00 0.00 5.68
64 65 4.778415 CGCGGTCCCTCTCACACG 62.778 72.222 0.00 0.00 0.00 4.49
65 66 4.436998 CCGCGGTCCCTCTCACAC 62.437 72.222 19.50 0.00 0.00 3.82
71 72 3.556298 TTTTTCCCCGCGGTCCCTC 62.556 63.158 26.12 0.00 0.00 4.30
72 73 3.572222 TTTTTCCCCGCGGTCCCT 61.572 61.111 26.12 0.00 0.00 4.20
87 88 9.642327 AAACAAGTAATTTTCACGTACCTTTTT 57.358 25.926 0.00 0.00 0.00 1.94
88 89 9.642327 AAAACAAGTAATTTTCACGTACCTTTT 57.358 25.926 0.00 0.00 0.00 2.27
89 90 9.078753 CAAAACAAGTAATTTTCACGTACCTTT 57.921 29.630 0.00 0.00 0.00 3.11
90 91 7.221259 GCAAAACAAGTAATTTTCACGTACCTT 59.779 33.333 0.00 0.00 0.00 3.50
91 92 6.693978 GCAAAACAAGTAATTTTCACGTACCT 59.306 34.615 0.00 0.00 0.00 3.08
92 93 6.074729 GGCAAAACAAGTAATTTTCACGTACC 60.075 38.462 0.00 0.00 0.00 3.34
93 94 6.693978 AGGCAAAACAAGTAATTTTCACGTAC 59.306 34.615 0.00 0.00 0.00 3.67
94 95 6.797454 AGGCAAAACAAGTAATTTTCACGTA 58.203 32.000 0.00 0.00 0.00 3.57
95 96 5.656480 AGGCAAAACAAGTAATTTTCACGT 58.344 33.333 0.00 0.00 0.00 4.49
96 97 6.693545 TGTAGGCAAAACAAGTAATTTTCACG 59.306 34.615 0.00 0.00 0.00 4.35
97 98 7.305763 CGTGTAGGCAAAACAAGTAATTTTCAC 60.306 37.037 0.00 0.00 0.00 3.18
98 99 6.693545 CGTGTAGGCAAAACAAGTAATTTTCA 59.306 34.615 0.00 0.00 0.00 2.69
99 100 6.693978 ACGTGTAGGCAAAACAAGTAATTTTC 59.306 34.615 4.88 0.00 37.71 2.29
100 101 6.566141 ACGTGTAGGCAAAACAAGTAATTTT 58.434 32.000 4.88 0.00 37.71 1.82
101 102 6.139048 ACGTGTAGGCAAAACAAGTAATTT 57.861 33.333 4.88 0.00 37.71 1.82
102 103 5.761165 ACGTGTAGGCAAAACAAGTAATT 57.239 34.783 4.88 0.00 37.71 1.40
103 104 6.146673 GTCTACGTGTAGGCAAAACAAGTAAT 59.853 38.462 6.76 0.00 39.93 1.89
104 105 5.463061 GTCTACGTGTAGGCAAAACAAGTAA 59.537 40.000 6.76 4.54 39.93 2.24
105 106 4.984161 GTCTACGTGTAGGCAAAACAAGTA 59.016 41.667 6.76 10.93 39.66 2.24
106 107 3.805971 GTCTACGTGTAGGCAAAACAAGT 59.194 43.478 6.76 10.04 41.42 3.16
107 108 3.121126 CGTCTACGTGTAGGCAAAACAAG 60.121 47.826 11.76 0.00 37.63 3.16
108 109 2.796031 CGTCTACGTGTAGGCAAAACAA 59.204 45.455 11.76 0.00 37.63 2.83
109 110 2.396601 CGTCTACGTGTAGGCAAAACA 58.603 47.619 11.76 0.00 37.63 2.83
122 123 1.532090 GGATCAGCTCACACGTCTACG 60.532 57.143 0.04 0.04 46.33 3.51
123 124 1.746220 AGGATCAGCTCACACGTCTAC 59.254 52.381 0.00 0.00 0.00 2.59
124 125 2.017782 GAGGATCAGCTCACACGTCTA 58.982 52.381 0.00 0.00 33.17 2.59
125 126 0.814457 GAGGATCAGCTCACACGTCT 59.186 55.000 0.00 0.00 33.17 4.18
126 127 0.814457 AGAGGATCAGCTCACACGTC 59.186 55.000 0.00 0.00 37.82 4.34
127 128 1.261480 AAGAGGATCAGCTCACACGT 58.739 50.000 0.00 0.00 37.82 4.49
128 129 2.685388 TCTAAGAGGATCAGCTCACACG 59.315 50.000 0.00 0.00 37.82 4.49
129 130 3.488384 CGTCTAAGAGGATCAGCTCACAC 60.488 52.174 0.00 0.00 37.82 3.82
130 131 2.685388 CGTCTAAGAGGATCAGCTCACA 59.315 50.000 0.00 0.00 37.82 3.58
131 132 2.542824 GCGTCTAAGAGGATCAGCTCAC 60.543 54.545 0.00 0.00 37.82 3.51
132 133 1.678627 GCGTCTAAGAGGATCAGCTCA 59.321 52.381 0.00 0.00 37.82 4.26
133 134 1.000717 GGCGTCTAAGAGGATCAGCTC 60.001 57.143 0.00 0.00 37.82 4.09
134 135 1.036707 GGCGTCTAAGAGGATCAGCT 58.963 55.000 0.00 0.00 37.82 4.24
135 136 0.747255 TGGCGTCTAAGAGGATCAGC 59.253 55.000 0.00 0.00 37.82 4.26
136 137 1.751351 TGTGGCGTCTAAGAGGATCAG 59.249 52.381 0.00 0.00 37.82 2.90
137 138 1.476891 GTGTGGCGTCTAAGAGGATCA 59.523 52.381 0.00 0.00 37.82 2.92
138 139 1.476891 TGTGTGGCGTCTAAGAGGATC 59.523 52.381 0.00 0.00 0.00 3.36
139 140 1.557099 TGTGTGGCGTCTAAGAGGAT 58.443 50.000 0.00 0.00 0.00 3.24
140 141 1.334160 TTGTGTGGCGTCTAAGAGGA 58.666 50.000 0.00 0.00 0.00 3.71
141 142 2.163818 TTTGTGTGGCGTCTAAGAGG 57.836 50.000 0.00 0.00 0.00 3.69
142 143 2.869801 TGTTTTGTGTGGCGTCTAAGAG 59.130 45.455 0.00 0.00 0.00 2.85
143 144 2.907634 TGTTTTGTGTGGCGTCTAAGA 58.092 42.857 0.00 0.00 0.00 2.10
144 145 3.003275 ACATGTTTTGTGTGGCGTCTAAG 59.997 43.478 0.00 0.00 37.11 2.18
145 146 2.946329 ACATGTTTTGTGTGGCGTCTAA 59.054 40.909 0.00 0.00 37.11 2.10
146 147 2.566913 ACATGTTTTGTGTGGCGTCTA 58.433 42.857 0.00 0.00 37.11 2.59
147 148 1.388547 ACATGTTTTGTGTGGCGTCT 58.611 45.000 0.00 0.00 37.11 4.18
148 149 3.936585 ACATGTTTTGTGTGGCGTC 57.063 47.368 0.00 0.00 37.11 5.19
156 157 1.956477 GAGTCTGCCCACATGTTTTGT 59.044 47.619 0.00 0.00 39.91 2.83
157 158 2.233271 AGAGTCTGCCCACATGTTTTG 58.767 47.619 0.00 0.00 0.00 2.44
158 159 2.664402 AGAGTCTGCCCACATGTTTT 57.336 45.000 0.00 0.00 0.00 2.43
159 160 2.664402 AAGAGTCTGCCCACATGTTT 57.336 45.000 0.00 0.00 0.00 2.83
160 161 2.664402 AAAGAGTCTGCCCACATGTT 57.336 45.000 0.00 0.00 0.00 2.71
161 162 3.412386 GTTAAAGAGTCTGCCCACATGT 58.588 45.455 0.00 0.00 0.00 3.21
162 163 2.416547 CGTTAAAGAGTCTGCCCACATG 59.583 50.000 0.00 0.00 0.00 3.21
163 164 2.699954 CGTTAAAGAGTCTGCCCACAT 58.300 47.619 0.00 0.00 0.00 3.21
164 165 1.876416 GCGTTAAAGAGTCTGCCCACA 60.876 52.381 0.00 0.00 0.00 4.17
165 166 0.796927 GCGTTAAAGAGTCTGCCCAC 59.203 55.000 0.00 0.00 0.00 4.61
166 167 0.321298 GGCGTTAAAGAGTCTGCCCA 60.321 55.000 7.11 0.00 36.51 5.36
167 168 2.467962 GGCGTTAAAGAGTCTGCCC 58.532 57.895 7.11 0.00 36.51 5.36
168 169 0.321298 TGGGCGTTAAAGAGTCTGCC 60.321 55.000 9.46 9.46 41.72 4.85
169 170 0.796927 GTGGGCGTTAAAGAGTCTGC 59.203 55.000 0.00 0.00 0.00 4.26
170 171 1.798813 GTGTGGGCGTTAAAGAGTCTG 59.201 52.381 0.00 0.00 0.00 3.51
171 172 1.604693 CGTGTGGGCGTTAAAGAGTCT 60.605 52.381 0.00 0.00 0.00 3.24
172 173 0.788391 CGTGTGGGCGTTAAAGAGTC 59.212 55.000 0.00 0.00 0.00 3.36
173 174 0.105408 ACGTGTGGGCGTTAAAGAGT 59.895 50.000 0.00 0.00 43.04 3.24
174 175 0.511221 CACGTGTGGGCGTTAAAGAG 59.489 55.000 7.58 0.00 43.83 2.85
175 176 0.179078 ACACGTGTGGGCGTTAAAGA 60.179 50.000 22.71 0.00 43.83 2.52
176 177 0.041663 CACACGTGTGGGCGTTAAAG 60.042 55.000 35.65 10.61 43.83 1.85
177 178 2.015382 CACACGTGTGGGCGTTAAA 58.985 52.632 35.65 0.00 43.83 1.52
178 179 3.720531 CACACGTGTGGGCGTTAA 58.279 55.556 35.65 0.00 43.83 2.01
191 192 1.444895 ACGCCGATAACGTCCACAC 60.445 57.895 0.00 0.00 40.28 3.82
192 193 2.964174 ACGCCGATAACGTCCACA 59.036 55.556 0.00 0.00 40.28 4.17
198 199 6.088824 AGTTAATTATAGGACGCCGATAACG 58.911 40.000 11.47 0.00 34.80 3.18
199 200 7.880059 AAGTTAATTATAGGACGCCGATAAC 57.120 36.000 11.47 4.79 34.80 1.89
200 201 7.095523 GCAAAGTTAATTATAGGACGCCGATAA 60.096 37.037 11.58 11.58 36.02 1.75
201 202 6.366877 GCAAAGTTAATTATAGGACGCCGATA 59.633 38.462 0.00 0.00 0.00 2.92
202 203 5.178809 GCAAAGTTAATTATAGGACGCCGAT 59.821 40.000 0.00 0.00 0.00 4.18
203 204 4.508861 GCAAAGTTAATTATAGGACGCCGA 59.491 41.667 0.00 0.00 0.00 5.54
204 205 4.510340 AGCAAAGTTAATTATAGGACGCCG 59.490 41.667 0.00 0.00 0.00 6.46
205 206 5.333111 CGAGCAAAGTTAATTATAGGACGCC 60.333 44.000 0.00 0.00 0.00 5.68
206 207 5.333111 CCGAGCAAAGTTAATTATAGGACGC 60.333 44.000 0.00 0.00 0.00 5.19
207 208 5.981315 TCCGAGCAAAGTTAATTATAGGACG 59.019 40.000 0.00 0.00 0.00 4.79
208 209 7.964604 ATCCGAGCAAAGTTAATTATAGGAC 57.035 36.000 0.00 0.00 0.00 3.85
209 210 8.974060 AAATCCGAGCAAAGTTAATTATAGGA 57.026 30.769 0.00 0.00 0.00 2.94
210 211 8.836413 TGAAATCCGAGCAAAGTTAATTATAGG 58.164 33.333 0.00 0.00 0.00 2.57
221 222 5.051891 AGTGATTTGAAATCCGAGCAAAG 57.948 39.130 14.73 0.00 35.29 2.77
235 236 5.152097 GCACTCAATGACTCAAGTGATTTG 58.848 41.667 11.89 6.87 41.26 2.32
288 289 2.948315 CGTCTGATCTGGTCATGAGAGA 59.052 50.000 0.00 0.65 35.97 3.10
310 311 7.546667 GGATTTGCTACATTGCCCATTATTATG 59.453 37.037 0.00 0.00 0.00 1.90
446 447 6.931840 GCCATCCTTCATTTACTAAGTAGGAG 59.068 42.308 0.00 0.00 0.00 3.69
448 449 5.696724 CGCCATCCTTCATTTACTAAGTAGG 59.303 44.000 0.00 0.00 0.00 3.18
480 485 0.528901 TTGTGACAACGACGGTGGAG 60.529 55.000 18.62 0.00 0.00 3.86
497 502 4.985409 GGTATCATCTCGGCTTACTTCTTG 59.015 45.833 0.00 0.00 0.00 3.02
681 686 1.597742 TCCTGTGCTTGCTCAGAAAC 58.402 50.000 21.52 0.00 34.02 2.78
686 691 1.159713 CGTGTTCCTGTGCTTGCTCA 61.160 55.000 0.00 0.00 0.00 4.26
711 718 5.238650 AGTGATCGATCGATGTACACATACA 59.761 40.000 32.55 21.42 45.37 2.29
881 888 1.560505 AGTGGCAGGCAATTAAAGGG 58.439 50.000 0.00 0.00 0.00 3.95
899 906 2.081425 CTGATCGGCCTCGGAGGAAG 62.081 65.000 27.95 18.75 37.67 3.46
991 998 2.672908 CTCCTCCATGGCTGCACA 59.327 61.111 6.96 0.00 35.26 4.57
1059 1066 2.251642 GGGATCATACGCAACCGCC 61.252 63.158 0.00 0.00 38.22 6.13
1068 1075 0.538977 TCGGGTCGAGGGGATCATAC 60.539 60.000 0.00 0.00 0.00 2.39
1167 1174 1.834188 TGATCTGACGGTACTGCTGA 58.166 50.000 0.23 5.06 0.00 4.26
1179 1186 4.240103 CCGGGCGCCATGATCTGA 62.240 66.667 30.85 0.00 0.00 3.27
1896 2087 5.164954 CAGTAGTCCTTGTAGTTGAGCTTC 58.835 45.833 0.00 0.00 0.00 3.86
2299 3487 2.584418 CGAGGCAGCGGTGATGAG 60.584 66.667 20.69 2.36 0.00 2.90
2368 3565 7.886629 AATTACCAAGATGCATGTGAGTAAT 57.113 32.000 18.58 18.58 32.16 1.89
2440 3637 1.068610 ACATCGACAACCAAAATGCCG 60.069 47.619 0.00 0.00 0.00 5.69
2522 3720 0.450184 AACTTGACAACCACACACGC 59.550 50.000 0.00 0.00 0.00 5.34
2523 3721 3.619483 TCTTAACTTGACAACCACACACG 59.381 43.478 0.00 0.00 0.00 4.49
2582 4188 5.918011 GCGTTTGACTCATTCCATAAAAACA 59.082 36.000 0.00 0.00 0.00 2.83
2583 4189 5.918011 TGCGTTTGACTCATTCCATAAAAAC 59.082 36.000 0.00 0.00 0.00 2.43
2628 4234 8.964772 ACATCAAAAAGGATCTAAAAGAGATGG 58.035 33.333 0.00 0.00 45.48 3.51
2689 4295 5.365605 TGTCAAACTCTTCTGTTAGGGAGAA 59.634 40.000 0.00 0.00 0.00 2.87
2794 4402 1.550524 GGGTGCATCTGTCAGTGAGTA 59.449 52.381 0.00 0.00 0.00 2.59
2795 4403 0.322975 GGGTGCATCTGTCAGTGAGT 59.677 55.000 0.00 0.00 0.00 3.41
2796 4404 0.392193 GGGGTGCATCTGTCAGTGAG 60.392 60.000 0.00 0.00 0.00 3.51
2797 4405 1.679311 GGGGTGCATCTGTCAGTGA 59.321 57.895 0.00 0.00 0.00 3.41
2798 4406 1.742880 CGGGGTGCATCTGTCAGTG 60.743 63.158 0.00 0.00 0.00 3.66
2799 4407 2.665000 CGGGGTGCATCTGTCAGT 59.335 61.111 0.00 0.00 0.00 3.41
2800 4408 2.821366 GCGGGGTGCATCTGTCAG 60.821 66.667 0.00 0.00 45.45 3.51
2823 4431 3.947196 TGTGCATCTGTCAGTGAGTTTTT 59.053 39.130 0.00 0.00 0.00 1.94
2824 4432 3.544684 TGTGCATCTGTCAGTGAGTTTT 58.455 40.909 0.00 0.00 0.00 2.43
2825 4433 3.198409 TGTGCATCTGTCAGTGAGTTT 57.802 42.857 0.00 0.00 0.00 2.66
2875 4486 0.323633 TGGATGTGGGCAGATGTTGG 60.324 55.000 0.00 0.00 0.00 3.77
3049 5601 5.028375 GCACCGCATTTCTACAATAACTTC 58.972 41.667 0.00 0.00 0.00 3.01
3217 5867 5.121768 TGCAACTCCGTTTATTTTAGCTCTC 59.878 40.000 0.00 0.00 0.00 3.20
3267 6141 6.291377 TGGCCATTCTCATAGACATTAACTC 58.709 40.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.