Multiple sequence alignment - TraesCS2A01G217800

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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 TraesCS2A01G217800 chr2A 100.000 2669 0 0 1 2669 204931775 204934443 0.000000e+00 4929
1 TraesCS2A01G217800 chr6A 96.548 1709 55 4 962 2669 496587902 496589607 0.000000e+00 2826
2 TraesCS2A01G217800 chr7A 81.951 1712 274 22 962 2666 491320547 491322230 0.000000e+00 1417
3 TraesCS2A01G217800 chr7A 95.661 484 17 1 481 964 506720156 506719677 0.000000e+00 774
4 TraesCS2A01G217800 chr7A 95.287 488 19 1 477 964 506722421 506721938 0.000000e+00 771
5 TraesCS2A01G217800 chr1A 95.277 487 18 2 478 964 209622073 209622554 0.000000e+00 767
6 TraesCS2A01G217800 chr2D 95.248 484 17 2 481 964 42879862 42879385 0.000000e+00 761
7 TraesCS2A01G217800 chr7D 94.867 487 21 1 478 964 18896937 18897419 0.000000e+00 758
8 TraesCS2A01G217800 chr5D 94.661 487 22 2 478 964 185244819 185245301 0.000000e+00 752
9 TraesCS2A01G217800 chr5D 93.890 491 26 1 474 964 185242562 185243048 0.000000e+00 737
10 TraesCS2A01G217800 chr6D 81.763 817 144 5 980 1793 37736992 37737806 0.000000e+00 678
11 TraesCS2A01G217800 chr5A 89.938 487 45 3 478 964 171917614 171918096 2.260000e-175 625
12 TraesCS2A01G217800 chr5A 89.117 487 49 3 478 964 171915368 171915850 1.060000e-168 603
13 TraesCS2A01G217800 chr3A 81.840 424 72 4 2248 2669 17359060 17359480 4.230000e-93 351
14 TraesCS2A01G217800 chr1D 74.311 689 170 7 1073 1757 365283572 365284257 4.350000e-73 285


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 TraesCS2A01G217800 chr2A 204931775 204934443 2668 False 4929.0 4929 100.0000 1 2669 1 chr2A.!!$F1 2668
1 TraesCS2A01G217800 chr6A 496587902 496589607 1705 False 2826.0 2826 96.5480 962 2669 1 chr6A.!!$F1 1707
2 TraesCS2A01G217800 chr7A 491320547 491322230 1683 False 1417.0 1417 81.9510 962 2666 1 chr7A.!!$F1 1704
3 TraesCS2A01G217800 chr7A 506719677 506722421 2744 True 772.5 774 95.4740 477 964 2 chr7A.!!$R1 487
4 TraesCS2A01G217800 chr5D 185242562 185245301 2739 False 744.5 752 94.2755 474 964 2 chr5D.!!$F1 490
5 TraesCS2A01G217800 chr6D 37736992 37737806 814 False 678.0 678 81.7630 980 1793 1 chr6D.!!$F1 813
6 TraesCS2A01G217800 chr5A 171915368 171918096 2728 False 614.0 625 89.5275 478 964 2 chr5A.!!$F1 486
7 TraesCS2A01G217800 chr1D 365283572 365284257 685 False 285.0 285 74.3110 1073 1757 1 chr1D.!!$F1 684

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
827 3086 0.108585 AAAGGAGTCCATGCACGTGT 59.891 50.0 18.38 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 4648 1.066143 GGCAATTTGGTCTCCGAGAGA 60.066 52.381 0.0 0.11 36.22 3.1 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
22 23 5.050644 TGAAGCTTGTTACTCATTGCATG 57.949 39.130 2.10 0.00 0.00 4.06
23 24 4.520111 TGAAGCTTGTTACTCATTGCATGT 59.480 37.500 2.10 0.00 0.00 3.21
24 25 5.009911 TGAAGCTTGTTACTCATTGCATGTT 59.990 36.000 2.10 0.00 0.00 2.71
25 26 5.458041 AGCTTGTTACTCATTGCATGTTT 57.542 34.783 0.00 0.00 0.00 2.83
26 27 5.846203 AGCTTGTTACTCATTGCATGTTTT 58.154 33.333 0.00 0.00 0.00 2.43
27 28 5.922544 AGCTTGTTACTCATTGCATGTTTTC 59.077 36.000 0.00 0.00 0.00 2.29
28 29 5.922544 GCTTGTTACTCATTGCATGTTTTCT 59.077 36.000 0.00 0.00 0.00 2.52
29 30 6.421801 GCTTGTTACTCATTGCATGTTTTCTT 59.578 34.615 0.00 0.00 0.00 2.52
30 31 7.594758 GCTTGTTACTCATTGCATGTTTTCTTA 59.405 33.333 0.00 0.00 0.00 2.10
31 32 9.630098 CTTGTTACTCATTGCATGTTTTCTTAT 57.370 29.630 0.00 0.00 0.00 1.73
32 33 9.979578 TTGTTACTCATTGCATGTTTTCTTATT 57.020 25.926 0.00 0.00 0.00 1.40
33 34 9.979578 TGTTACTCATTGCATGTTTTCTTATTT 57.020 25.926 0.00 0.00 0.00 1.40
35 36 9.979578 TTACTCATTGCATGTTTTCTTATTTGT 57.020 25.926 0.00 0.00 0.00 2.83
37 38 9.630098 ACTCATTGCATGTTTTCTTATTTGTAG 57.370 29.630 0.00 0.00 0.00 2.74
38 39 8.984891 TCATTGCATGTTTTCTTATTTGTAGG 57.015 30.769 0.00 0.00 0.00 3.18
39 40 8.584157 TCATTGCATGTTTTCTTATTTGTAGGT 58.416 29.630 0.00 0.00 0.00 3.08
40 41 8.649841 CATTGCATGTTTTCTTATTTGTAGGTG 58.350 33.333 0.00 0.00 0.00 4.00
41 42 7.283625 TGCATGTTTTCTTATTTGTAGGTGT 57.716 32.000 0.00 0.00 0.00 4.16
42 43 7.721402 TGCATGTTTTCTTATTTGTAGGTGTT 58.279 30.769 0.00 0.00 0.00 3.32
43 44 8.200792 TGCATGTTTTCTTATTTGTAGGTGTTT 58.799 29.630 0.00 0.00 0.00 2.83
44 45 8.699749 GCATGTTTTCTTATTTGTAGGTGTTTC 58.300 33.333 0.00 0.00 0.00 2.78
45 46 9.965824 CATGTTTTCTTATTTGTAGGTGTTTCT 57.034 29.630 0.00 0.00 0.00 2.52
46 47 9.965824 ATGTTTTCTTATTTGTAGGTGTTTCTG 57.034 29.630 0.00 0.00 0.00 3.02
47 48 7.918562 TGTTTTCTTATTTGTAGGTGTTTCTGC 59.081 33.333 0.00 0.00 0.00 4.26
48 49 7.817418 TTTCTTATTTGTAGGTGTTTCTGCT 57.183 32.000 0.00 0.00 0.00 4.24
49 50 7.817418 TTCTTATTTGTAGGTGTTTCTGCTT 57.183 32.000 0.00 0.00 0.00 3.91
50 51 7.817418 TCTTATTTGTAGGTGTTTCTGCTTT 57.183 32.000 0.00 0.00 0.00 3.51
51 52 8.232913 TCTTATTTGTAGGTGTTTCTGCTTTT 57.767 30.769 0.00 0.00 0.00 2.27
52 53 8.134895 TCTTATTTGTAGGTGTTTCTGCTTTTG 58.865 33.333 0.00 0.00 0.00 2.44
96 97 7.639945 AGTCGAGTTTTCTTTCTTTACATTGG 58.360 34.615 0.00 0.00 0.00 3.16
97 98 7.282450 AGTCGAGTTTTCTTTCTTTACATTGGT 59.718 33.333 0.00 0.00 0.00 3.67
98 99 8.553696 GTCGAGTTTTCTTTCTTTACATTGGTA 58.446 33.333 0.00 0.00 0.00 3.25
99 100 9.280174 TCGAGTTTTCTTTCTTTACATTGGTAT 57.720 29.630 0.00 0.00 0.00 2.73
100 101 9.893305 CGAGTTTTCTTTCTTTACATTGGTATT 57.107 29.630 0.00 0.00 0.00 1.89
106 107 8.825667 TCTTTCTTTACATTGGTATTTTTGCC 57.174 30.769 0.00 0.00 0.00 4.52
107 108 8.424918 TCTTTCTTTACATTGGTATTTTTGCCA 58.575 29.630 0.00 0.00 0.00 4.92
108 109 9.218440 CTTTCTTTACATTGGTATTTTTGCCAT 57.782 29.630 0.00 0.00 34.37 4.40
109 110 8.545229 TTCTTTACATTGGTATTTTTGCCATG 57.455 30.769 0.00 0.00 34.37 3.66
110 111 6.593382 TCTTTACATTGGTATTTTTGCCATGC 59.407 34.615 0.00 0.00 34.37 4.06
111 112 4.283363 ACATTGGTATTTTTGCCATGCA 57.717 36.364 0.00 0.00 36.47 3.96
112 113 4.002316 ACATTGGTATTTTTGCCATGCAC 58.998 39.130 0.00 0.00 38.71 4.57
113 114 3.758755 TTGGTATTTTTGCCATGCACA 57.241 38.095 0.00 0.00 38.71 4.57
114 115 3.977134 TGGTATTTTTGCCATGCACAT 57.023 38.095 0.00 0.00 38.71 3.21
115 116 4.283363 TGGTATTTTTGCCATGCACATT 57.717 36.364 0.00 0.00 38.71 2.71
116 117 4.649692 TGGTATTTTTGCCATGCACATTT 58.350 34.783 0.00 0.00 38.71 2.32
117 118 5.068636 TGGTATTTTTGCCATGCACATTTT 58.931 33.333 0.00 0.00 38.71 1.82
118 119 5.533903 TGGTATTTTTGCCATGCACATTTTT 59.466 32.000 0.00 0.00 38.71 1.94
119 120 5.857517 GGTATTTTTGCCATGCACATTTTTG 59.142 36.000 0.00 0.00 38.71 2.44
120 121 3.984508 TTTTGCCATGCACATTTTTGG 57.015 38.095 0.00 0.00 38.71 3.28
125 126 2.701107 CCATGCACATTTTTGGCATCA 58.299 42.857 0.00 0.00 45.81 3.07
126 127 2.417239 CCATGCACATTTTTGGCATCAC 59.583 45.455 0.00 0.00 45.81 3.06
127 128 3.331150 CATGCACATTTTTGGCATCACT 58.669 40.909 0.00 0.00 45.81 3.41
128 129 3.472283 TGCACATTTTTGGCATCACTT 57.528 38.095 0.00 0.00 31.58 3.16
129 130 3.806380 TGCACATTTTTGGCATCACTTT 58.194 36.364 0.00 0.00 31.58 2.66
130 131 4.953667 TGCACATTTTTGGCATCACTTTA 58.046 34.783 0.00 0.00 31.58 1.85
131 132 4.989797 TGCACATTTTTGGCATCACTTTAG 59.010 37.500 0.00 0.00 31.58 1.85
132 133 4.143052 GCACATTTTTGGCATCACTTTAGC 60.143 41.667 0.00 0.00 0.00 3.09
133 134 5.232463 CACATTTTTGGCATCACTTTAGCT 58.768 37.500 0.00 0.00 0.00 3.32
134 135 6.389091 CACATTTTTGGCATCACTTTAGCTA 58.611 36.000 0.00 0.00 0.00 3.32
135 136 6.308766 CACATTTTTGGCATCACTTTAGCTAC 59.691 38.462 0.00 0.00 0.00 3.58
136 137 5.385509 TTTTTGGCATCACTTTAGCTACC 57.614 39.130 0.00 0.00 0.00 3.18
137 138 3.712016 TTGGCATCACTTTAGCTACCA 57.288 42.857 0.00 0.00 0.00 3.25
138 139 3.266510 TGGCATCACTTTAGCTACCAG 57.733 47.619 0.00 0.00 0.00 4.00
139 140 2.571653 TGGCATCACTTTAGCTACCAGT 59.428 45.455 0.00 0.00 0.00 4.00
140 141 2.939103 GGCATCACTTTAGCTACCAGTG 59.061 50.000 19.94 19.94 39.51 3.66
141 142 2.939103 GCATCACTTTAGCTACCAGTGG 59.061 50.000 23.33 7.91 38.80 4.00
142 143 2.762535 TCACTTTAGCTACCAGTGGC 57.237 50.000 23.33 0.00 38.80 5.01
143 144 1.278127 TCACTTTAGCTACCAGTGGCC 59.722 52.381 23.33 0.00 38.80 5.36
144 145 1.279271 CACTTTAGCTACCAGTGGCCT 59.721 52.381 18.85 5.94 37.85 5.19
145 146 2.500098 CACTTTAGCTACCAGTGGCCTA 59.500 50.000 18.85 4.89 37.85 3.93
146 147 3.055385 CACTTTAGCTACCAGTGGCCTAA 60.055 47.826 18.85 10.86 37.85 2.69
147 148 3.585732 ACTTTAGCTACCAGTGGCCTAAA 59.414 43.478 20.33 20.33 37.85 1.85
148 149 4.042435 ACTTTAGCTACCAGTGGCCTAAAA 59.958 41.667 21.20 11.73 37.85 1.52
149 150 4.644163 TTAGCTACCAGTGGCCTAAAAA 57.356 40.909 9.78 0.00 37.85 1.94
150 151 3.073274 AGCTACCAGTGGCCTAAAAAG 57.927 47.619 9.78 0.00 37.85 2.27
151 152 2.375509 AGCTACCAGTGGCCTAAAAAGT 59.624 45.455 9.78 0.00 37.85 2.66
152 153 3.154710 GCTACCAGTGGCCTAAAAAGTT 58.845 45.455 9.78 0.00 0.00 2.66
153 154 4.042435 AGCTACCAGTGGCCTAAAAAGTTA 59.958 41.667 9.78 0.00 37.85 2.24
154 155 4.948004 GCTACCAGTGGCCTAAAAAGTTAT 59.052 41.667 9.78 0.00 0.00 1.89
155 156 5.417894 GCTACCAGTGGCCTAAAAAGTTATT 59.582 40.000 9.78 0.00 0.00 1.40
156 157 6.071560 GCTACCAGTGGCCTAAAAAGTTATTT 60.072 38.462 9.78 0.00 0.00 1.40
157 158 6.740944 ACCAGTGGCCTAAAAAGTTATTTT 57.259 33.333 9.78 0.00 40.37 1.82
158 159 6.755206 ACCAGTGGCCTAAAAAGTTATTTTC 58.245 36.000 9.78 0.00 37.65 2.29
159 160 5.861787 CCAGTGGCCTAAAAAGTTATTTTCG 59.138 40.000 3.32 0.00 37.65 3.46
160 161 5.861787 CAGTGGCCTAAAAAGTTATTTTCGG 59.138 40.000 3.32 1.16 37.65 4.30
161 162 5.771165 AGTGGCCTAAAAAGTTATTTTCGGA 59.229 36.000 3.32 0.00 37.65 4.55
162 163 5.860182 GTGGCCTAAAAAGTTATTTTCGGAC 59.140 40.000 3.32 5.93 37.65 4.79
163 164 5.535406 TGGCCTAAAAAGTTATTTTCGGACA 59.465 36.000 3.32 8.26 41.20 4.02
164 165 6.090783 GGCCTAAAAAGTTATTTTCGGACAG 58.909 40.000 0.00 0.00 37.65 3.51
165 166 6.294342 GGCCTAAAAAGTTATTTTCGGACAGT 60.294 38.462 0.00 0.00 37.65 3.55
166 167 6.800408 GCCTAAAAAGTTATTTTCGGACAGTC 59.200 38.462 8.02 0.00 37.65 3.51
167 168 7.013529 CCTAAAAAGTTATTTTCGGACAGTCG 58.986 38.462 0.00 0.00 37.65 4.18
168 169 6.607735 AAAAAGTTATTTTCGGACAGTCGA 57.392 33.333 0.00 0.00 37.65 4.20
169 170 6.796705 AAAAGTTATTTTCGGACAGTCGAT 57.203 33.333 0.00 0.00 39.03 3.59
170 171 6.796705 AAAGTTATTTTCGGACAGTCGATT 57.203 33.333 0.00 0.00 39.03 3.34
171 172 6.796705 AAGTTATTTTCGGACAGTCGATTT 57.203 33.333 0.00 0.00 39.03 2.17
172 173 6.796705 AGTTATTTTCGGACAGTCGATTTT 57.203 33.333 0.00 0.00 39.03 1.82
173 174 7.198306 AGTTATTTTCGGACAGTCGATTTTT 57.802 32.000 0.00 0.00 39.03 1.94
195 196 7.737972 TTTTCCGTTGATTTCTGTTATGAGA 57.262 32.000 0.00 0.00 0.00 3.27
196 197 7.921786 TTTCCGTTGATTTCTGTTATGAGAT 57.078 32.000 0.00 0.00 0.00 2.75
197 198 6.908870 TCCGTTGATTTCTGTTATGAGATG 57.091 37.500 0.00 0.00 0.00 2.90
198 199 6.406370 TCCGTTGATTTCTGTTATGAGATGT 58.594 36.000 0.00 0.00 0.00 3.06
199 200 6.878923 TCCGTTGATTTCTGTTATGAGATGTT 59.121 34.615 0.00 0.00 0.00 2.71
200 201 7.390440 TCCGTTGATTTCTGTTATGAGATGTTT 59.610 33.333 0.00 0.00 0.00 2.83
201 202 7.482743 CCGTTGATTTCTGTTATGAGATGTTTG 59.517 37.037 0.00 0.00 0.00 2.93
202 203 7.007725 CGTTGATTTCTGTTATGAGATGTTTGC 59.992 37.037 0.00 0.00 0.00 3.68
203 204 7.692460 TGATTTCTGTTATGAGATGTTTGCT 57.308 32.000 0.00 0.00 0.00 3.91
204 205 7.755591 TGATTTCTGTTATGAGATGTTTGCTC 58.244 34.615 0.00 0.00 0.00 4.26
205 206 7.609146 TGATTTCTGTTATGAGATGTTTGCTCT 59.391 33.333 0.00 0.00 33.57 4.09
206 207 7.750229 TTTCTGTTATGAGATGTTTGCTCTT 57.250 32.000 0.00 0.00 33.57 2.85
207 208 7.750229 TTCTGTTATGAGATGTTTGCTCTTT 57.250 32.000 0.00 0.00 33.57 2.52
208 209 7.750229 TCTGTTATGAGATGTTTGCTCTTTT 57.250 32.000 0.00 0.00 33.57 2.27
209 210 8.169977 TCTGTTATGAGATGTTTGCTCTTTTT 57.830 30.769 0.00 0.00 33.57 1.94
231 232 7.566760 TTTTCTGTTCTGTTATGTGATGTGT 57.433 32.000 0.00 0.00 0.00 3.72
232 233 7.566760 TTTCTGTTCTGTTATGTGATGTGTT 57.433 32.000 0.00 0.00 0.00 3.32
233 234 7.566760 TTCTGTTCTGTTATGTGATGTGTTT 57.433 32.000 0.00 0.00 0.00 2.83
234 235 7.566760 TCTGTTCTGTTATGTGATGTGTTTT 57.433 32.000 0.00 0.00 0.00 2.43
235 236 7.416817 TCTGTTCTGTTATGTGATGTGTTTTG 58.583 34.615 0.00 0.00 0.00 2.44
236 237 6.502652 TGTTCTGTTATGTGATGTGTTTTGG 58.497 36.000 0.00 0.00 0.00 3.28
237 238 5.703978 TCTGTTATGTGATGTGTTTTGGG 57.296 39.130 0.00 0.00 0.00 4.12
238 239 4.022416 TCTGTTATGTGATGTGTTTTGGGC 60.022 41.667 0.00 0.00 0.00 5.36
239 240 3.894427 TGTTATGTGATGTGTTTTGGGCT 59.106 39.130 0.00 0.00 0.00 5.19
240 241 4.236935 GTTATGTGATGTGTTTTGGGCTG 58.763 43.478 0.00 0.00 0.00 4.85
241 242 2.064434 TGTGATGTGTTTTGGGCTGA 57.936 45.000 0.00 0.00 0.00 4.26
242 243 1.955778 TGTGATGTGTTTTGGGCTGAG 59.044 47.619 0.00 0.00 0.00 3.35
243 244 1.956477 GTGATGTGTTTTGGGCTGAGT 59.044 47.619 0.00 0.00 0.00 3.41
244 245 2.362077 GTGATGTGTTTTGGGCTGAGTT 59.638 45.455 0.00 0.00 0.00 3.01
245 246 3.030291 TGATGTGTTTTGGGCTGAGTTT 58.970 40.909 0.00 0.00 0.00 2.66
246 247 3.450457 TGATGTGTTTTGGGCTGAGTTTT 59.550 39.130 0.00 0.00 0.00 2.43
247 248 3.971245 TGTGTTTTGGGCTGAGTTTTT 57.029 38.095 0.00 0.00 0.00 1.94
272 273 8.887264 TTTAATGACCACATATTTGGGTTAGT 57.113 30.769 12.50 0.90 41.49 2.24
273 274 8.887264 TTAATGACCACATATTTGGGTTAGTT 57.113 30.769 12.50 3.08 41.49 2.24
274 275 9.976776 TTAATGACCACATATTTGGGTTAGTTA 57.023 29.630 12.50 2.27 41.49 2.24
275 276 8.887264 AATGACCACATATTTGGGTTAGTTAA 57.113 30.769 12.50 0.00 41.49 2.01
276 277 9.487442 AATGACCACATATTTGGGTTAGTTAAT 57.513 29.630 12.50 0.00 41.49 1.40
277 278 8.887264 TGACCACATATTTGGGTTAGTTAATT 57.113 30.769 12.50 0.00 41.49 1.40
278 279 8.962679 TGACCACATATTTGGGTTAGTTAATTC 58.037 33.333 12.50 0.00 41.49 2.17
279 280 8.301252 ACCACATATTTGGGTTAGTTAATTCC 57.699 34.615 12.50 0.00 41.49 3.01
280 281 8.119891 ACCACATATTTGGGTTAGTTAATTCCT 58.880 33.333 12.50 0.00 41.49 3.36
281 282 8.413229 CCACATATTTGGGTTAGTTAATTCCTG 58.587 37.037 0.00 0.00 32.35 3.86
282 283 8.966868 CACATATTTGGGTTAGTTAATTCCTGT 58.033 33.333 0.00 0.00 0.00 4.00
283 284 8.966868 ACATATTTGGGTTAGTTAATTCCTGTG 58.033 33.333 0.00 0.00 0.00 3.66
284 285 5.715434 TTTGGGTTAGTTAATTCCTGTGC 57.285 39.130 0.00 0.00 0.00 4.57
285 286 3.340034 TGGGTTAGTTAATTCCTGTGCG 58.660 45.455 0.00 0.00 0.00 5.34
286 287 3.008157 TGGGTTAGTTAATTCCTGTGCGA 59.992 43.478 0.00 0.00 0.00 5.10
287 288 3.373130 GGGTTAGTTAATTCCTGTGCGAC 59.627 47.826 0.00 0.00 0.00 5.19
288 289 3.373130 GGTTAGTTAATTCCTGTGCGACC 59.627 47.826 0.00 0.00 0.00 4.79
289 290 2.851263 AGTTAATTCCTGTGCGACCA 57.149 45.000 0.00 0.00 0.00 4.02
290 291 3.134574 AGTTAATTCCTGTGCGACCAA 57.865 42.857 0.00 0.00 0.00 3.67
291 292 3.482436 AGTTAATTCCTGTGCGACCAAA 58.518 40.909 0.00 0.00 0.00 3.28
292 293 3.252458 AGTTAATTCCTGTGCGACCAAAC 59.748 43.478 0.00 0.00 0.00 2.93
293 294 0.958822 AATTCCTGTGCGACCAAACC 59.041 50.000 0.00 0.00 0.00 3.27
294 295 0.893727 ATTCCTGTGCGACCAAACCC 60.894 55.000 0.00 0.00 0.00 4.11
295 296 1.990160 TTCCTGTGCGACCAAACCCT 61.990 55.000 0.00 0.00 0.00 4.34
296 297 1.966451 CCTGTGCGACCAAACCCTC 60.966 63.158 0.00 0.00 0.00 4.30
297 298 1.966451 CTGTGCGACCAAACCCTCC 60.966 63.158 0.00 0.00 0.00 4.30
298 299 2.671963 GTGCGACCAAACCCTCCC 60.672 66.667 0.00 0.00 0.00 4.30
299 300 2.852075 TGCGACCAAACCCTCCCT 60.852 61.111 0.00 0.00 0.00 4.20
300 301 2.046217 GCGACCAAACCCTCCCTC 60.046 66.667 0.00 0.00 0.00 4.30
301 302 2.593956 GCGACCAAACCCTCCCTCT 61.594 63.158 0.00 0.00 0.00 3.69
302 303 1.597461 CGACCAAACCCTCCCTCTC 59.403 63.158 0.00 0.00 0.00 3.20
303 304 1.900545 CGACCAAACCCTCCCTCTCC 61.901 65.000 0.00 0.00 0.00 3.71
304 305 1.541620 ACCAAACCCTCCCTCTCCC 60.542 63.158 0.00 0.00 0.00 4.30
305 306 2.309504 CCAAACCCTCCCTCTCCCC 61.310 68.421 0.00 0.00 0.00 4.81
306 307 2.127528 AAACCCTCCCTCTCCCCC 59.872 66.667 0.00 0.00 0.00 5.40
307 308 2.511458 AAACCCTCCCTCTCCCCCT 61.511 63.158 0.00 0.00 0.00 4.79
308 309 2.075278 AAACCCTCCCTCTCCCCCTT 62.075 60.000 0.00 0.00 0.00 3.95
309 310 2.075278 AACCCTCCCTCTCCCCCTTT 62.075 60.000 0.00 0.00 0.00 3.11
310 311 2.003548 CCCTCCCTCTCCCCCTTTG 61.004 68.421 0.00 0.00 0.00 2.77
311 312 2.684499 CCTCCCTCTCCCCCTTTGC 61.684 68.421 0.00 0.00 0.00 3.68
312 313 1.617839 CTCCCTCTCCCCCTTTGCT 60.618 63.158 0.00 0.00 0.00 3.91
313 314 1.616628 TCCCTCTCCCCCTTTGCTC 60.617 63.158 0.00 0.00 0.00 4.26
314 315 1.617839 CCCTCTCCCCCTTTGCTCT 60.618 63.158 0.00 0.00 0.00 4.09
315 316 1.210885 CCCTCTCCCCCTTTGCTCTT 61.211 60.000 0.00 0.00 0.00 2.85
316 317 0.701147 CCTCTCCCCCTTTGCTCTTT 59.299 55.000 0.00 0.00 0.00 2.52
317 318 1.076187 CCTCTCCCCCTTTGCTCTTTT 59.924 52.381 0.00 0.00 0.00 2.27
318 319 2.441410 CTCTCCCCCTTTGCTCTTTTC 58.559 52.381 0.00 0.00 0.00 2.29
319 320 1.168714 CTCCCCCTTTGCTCTTTTCG 58.831 55.000 0.00 0.00 0.00 3.46
320 321 0.251165 TCCCCCTTTGCTCTTTTCGG 60.251 55.000 0.00 0.00 0.00 4.30
321 322 0.539669 CCCCCTTTGCTCTTTTCGGT 60.540 55.000 0.00 0.00 0.00 4.69
322 323 1.328279 CCCCTTTGCTCTTTTCGGTT 58.672 50.000 0.00 0.00 0.00 4.44
323 324 1.686587 CCCCTTTGCTCTTTTCGGTTT 59.313 47.619 0.00 0.00 0.00 3.27
324 325 2.288213 CCCCTTTGCTCTTTTCGGTTTC 60.288 50.000 0.00 0.00 0.00 2.78
325 326 2.360801 CCCTTTGCTCTTTTCGGTTTCA 59.639 45.455 0.00 0.00 0.00 2.69
326 327 3.550842 CCCTTTGCTCTTTTCGGTTTCAG 60.551 47.826 0.00 0.00 0.00 3.02
327 328 2.774439 TTGCTCTTTTCGGTTTCAGC 57.226 45.000 0.00 0.00 0.00 4.26
328 329 1.967319 TGCTCTTTTCGGTTTCAGCT 58.033 45.000 0.00 0.00 0.00 4.24
329 330 2.297701 TGCTCTTTTCGGTTTCAGCTT 58.702 42.857 0.00 0.00 0.00 3.74
330 331 2.687935 TGCTCTTTTCGGTTTCAGCTTT 59.312 40.909 0.00 0.00 0.00 3.51
331 332 3.130340 TGCTCTTTTCGGTTTCAGCTTTT 59.870 39.130 0.00 0.00 0.00 2.27
332 333 4.112634 GCTCTTTTCGGTTTCAGCTTTTT 58.887 39.130 0.00 0.00 0.00 1.94
398 399 6.968263 TTTTTGGATGTTGGATGAGTGTAA 57.032 33.333 0.00 0.00 0.00 2.41
399 400 6.968263 TTTTGGATGTTGGATGAGTGTAAA 57.032 33.333 0.00 0.00 0.00 2.01
400 401 7.537596 TTTTGGATGTTGGATGAGTGTAAAT 57.462 32.000 0.00 0.00 0.00 1.40
401 402 6.513806 TTGGATGTTGGATGAGTGTAAATG 57.486 37.500 0.00 0.00 0.00 2.32
402 403 5.569355 TGGATGTTGGATGAGTGTAAATGT 58.431 37.500 0.00 0.00 0.00 2.71
403 404 6.716284 TGGATGTTGGATGAGTGTAAATGTA 58.284 36.000 0.00 0.00 0.00 2.29
404 405 7.345691 TGGATGTTGGATGAGTGTAAATGTAT 58.654 34.615 0.00 0.00 0.00 2.29
405 406 8.490311 TGGATGTTGGATGAGTGTAAATGTATA 58.510 33.333 0.00 0.00 0.00 1.47
406 407 8.774586 GGATGTTGGATGAGTGTAAATGTATAC 58.225 37.037 0.00 0.00 0.00 1.47
407 408 9.325198 GATGTTGGATGAGTGTAAATGTATACA 57.675 33.333 8.27 8.27 33.52 2.29
501 502 2.127232 GGCATGCCCTACCGCAAAT 61.127 57.895 27.24 0.00 43.24 2.32
515 516 5.593679 ACCGCAAATATGACTAGTACACT 57.406 39.130 0.00 0.00 0.00 3.55
547 2806 2.159282 GGTGAGTACGTCGGTCAATGAT 60.159 50.000 0.00 0.00 0.00 2.45
599 2858 1.064017 ACAAAGGGGTGCAAACAGAGA 60.064 47.619 0.00 0.00 0.00 3.10
640 2899 1.107945 CAATGCATGTGGATGAGGCA 58.892 50.000 0.00 0.00 39.03 4.75
688 2947 8.960591 AGAAACGAGGATGAACAAATTATGAAT 58.039 29.630 0.00 0.00 0.00 2.57
743 3002 4.216411 ACCTTGCGTATTCTATGTGGTT 57.784 40.909 0.00 0.00 0.00 3.67
744 3003 4.585879 ACCTTGCGTATTCTATGTGGTTT 58.414 39.130 0.00 0.00 0.00 3.27
827 3086 0.108585 AAAGGAGTCCATGCACGTGT 59.891 50.000 18.38 0.00 0.00 4.49
919 3178 4.561500 TTGGAGAAATAATGGGACGTGA 57.438 40.909 0.00 0.00 0.00 4.35
1036 3296 1.003696 GTGACAGAGGGAAGGGAAAGG 59.996 57.143 0.00 0.00 0.00 3.11
1098 3358 5.043737 TGCATGAAGATGATGGAGATGAA 57.956 39.130 0.00 0.00 0.00 2.57
1117 3377 4.588899 TGAATTCGTGTGGGAAGATGATT 58.411 39.130 0.04 0.00 0.00 2.57
1235 3495 1.506262 CGTGGAATCCGGCAAAAGG 59.494 57.895 0.00 0.00 0.00 3.11
1341 3601 1.470098 CCGTGGCTTTTCAGGAATCAG 59.530 52.381 0.00 0.00 0.00 2.90
1423 3683 2.804986 TGCAGTATGGGCAAGAATCA 57.195 45.000 0.00 0.00 38.54 2.57
1459 3719 4.940046 ACAACTATCTTCATGAAGCTGTGG 59.060 41.667 27.45 22.47 38.28 4.17
1901 4162 3.281727 AACACGAGTTATGATGGCCAT 57.718 42.857 20.96 20.96 35.85 4.40
1935 4196 3.926198 TGGAATGCATCATATGGGGTTT 58.074 40.909 0.00 0.00 0.00 3.27
1999 4260 1.965414 TCATTAGGCCTGGAAGTGGA 58.035 50.000 17.99 0.00 0.00 4.02
2126 4387 5.450453 TCTAAGGTTTCCAACATGGTTGAA 58.550 37.500 10.48 0.00 39.03 2.69
2258 4519 3.818961 AATGATAATGCAAGATCGGCG 57.181 42.857 0.00 0.00 0.00 6.46
2282 4543 3.263503 CTTCGTGAGTGACCGCCGA 62.264 63.158 0.00 0.00 0.00 5.54
2313 4574 7.994425 TGAATATTTTAAGCCTGAACTGTCA 57.006 32.000 0.00 0.00 0.00 3.58
2406 4667 2.386661 TCTCTCGGAGACCAAATTGC 57.613 50.000 2.97 0.00 33.35 3.56
2510 4771 5.775195 AGGCCTGGTATTATTTTGGAATAGC 59.225 40.000 3.11 0.00 37.63 2.97
2616 4877 3.495100 GCGATTCACAGGATTCTATGGGT 60.495 47.826 0.00 0.00 0.00 4.51
2647 4908 2.867109 TCAAGGAGGAAAAGGAGCTG 57.133 50.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.367156 ACACCTACAAATAAGAAAACATGCAAT 58.633 29.630 0.00 0.00 0.00 3.56
16 17 7.721402 ACACCTACAAATAAGAAAACATGCAA 58.279 30.769 0.00 0.00 0.00 4.08
17 18 7.283625 ACACCTACAAATAAGAAAACATGCA 57.716 32.000 0.00 0.00 0.00 3.96
18 19 8.587952 AAACACCTACAAATAAGAAAACATGC 57.412 30.769 0.00 0.00 0.00 4.06
19 20 9.965824 AGAAACACCTACAAATAAGAAAACATG 57.034 29.630 0.00 0.00 0.00 3.21
20 21 9.965824 CAGAAACACCTACAAATAAGAAAACAT 57.034 29.630 0.00 0.00 0.00 2.71
21 22 7.918562 GCAGAAACACCTACAAATAAGAAAACA 59.081 33.333 0.00 0.00 0.00 2.83
22 23 8.135529 AGCAGAAACACCTACAAATAAGAAAAC 58.864 33.333 0.00 0.00 0.00 2.43
23 24 8.232913 AGCAGAAACACCTACAAATAAGAAAA 57.767 30.769 0.00 0.00 0.00 2.29
24 25 7.817418 AGCAGAAACACCTACAAATAAGAAA 57.183 32.000 0.00 0.00 0.00 2.52
25 26 7.817418 AAGCAGAAACACCTACAAATAAGAA 57.183 32.000 0.00 0.00 0.00 2.52
26 27 7.817418 AAAGCAGAAACACCTACAAATAAGA 57.183 32.000 0.00 0.00 0.00 2.10
27 28 7.096065 GCAAAAGCAGAAACACCTACAAATAAG 60.096 37.037 0.00 0.00 0.00 1.73
28 29 6.699642 GCAAAAGCAGAAACACCTACAAATAA 59.300 34.615 0.00 0.00 0.00 1.40
29 30 6.040391 AGCAAAAGCAGAAACACCTACAAATA 59.960 34.615 0.00 0.00 0.00 1.40
30 31 5.049828 GCAAAAGCAGAAACACCTACAAAT 58.950 37.500 0.00 0.00 0.00 2.32
31 32 4.159506 AGCAAAAGCAGAAACACCTACAAA 59.840 37.500 0.00 0.00 0.00 2.83
32 33 3.699038 AGCAAAAGCAGAAACACCTACAA 59.301 39.130 0.00 0.00 0.00 2.41
33 34 3.287222 AGCAAAAGCAGAAACACCTACA 58.713 40.909 0.00 0.00 0.00 2.74
34 35 3.990318 AGCAAAAGCAGAAACACCTAC 57.010 42.857 0.00 0.00 0.00 3.18
35 36 5.337578 AAAAGCAAAAGCAGAAACACCTA 57.662 34.783 0.00 0.00 0.00 3.08
36 37 3.893326 AAAGCAAAAGCAGAAACACCT 57.107 38.095 0.00 0.00 0.00 4.00
37 38 3.000222 CGAAAAGCAAAAGCAGAAACACC 60.000 43.478 0.00 0.00 0.00 4.16
38 39 3.612423 ACGAAAAGCAAAAGCAGAAACAC 59.388 39.130 0.00 0.00 0.00 3.32
39 40 3.843999 ACGAAAAGCAAAAGCAGAAACA 58.156 36.364 0.00 0.00 0.00 2.83
40 41 4.840401 AACGAAAAGCAAAAGCAGAAAC 57.160 36.364 0.00 0.00 0.00 2.78
41 42 8.810652 AATATAACGAAAAGCAAAAGCAGAAA 57.189 26.923 0.00 0.00 0.00 2.52
70 71 8.770828 CCAATGTAAAGAAAGAAAACTCGACTA 58.229 33.333 0.00 0.00 0.00 2.59
71 72 7.282450 ACCAATGTAAAGAAAGAAAACTCGACT 59.718 33.333 0.00 0.00 0.00 4.18
72 73 7.415229 ACCAATGTAAAGAAAGAAAACTCGAC 58.585 34.615 0.00 0.00 0.00 4.20
73 74 7.562454 ACCAATGTAAAGAAAGAAAACTCGA 57.438 32.000 0.00 0.00 0.00 4.04
74 75 9.893305 AATACCAATGTAAAGAAAGAAAACTCG 57.107 29.630 0.00 0.00 0.00 4.18
80 81 9.267084 GGCAAAAATACCAATGTAAAGAAAGAA 57.733 29.630 0.00 0.00 0.00 2.52
81 82 8.424918 TGGCAAAAATACCAATGTAAAGAAAGA 58.575 29.630 0.00 0.00 31.46 2.52
82 83 8.600449 TGGCAAAAATACCAATGTAAAGAAAG 57.400 30.769 0.00 0.00 31.46 2.62
83 84 8.997323 CATGGCAAAAATACCAATGTAAAGAAA 58.003 29.630 0.00 0.00 39.96 2.52
84 85 7.118971 GCATGGCAAAAATACCAATGTAAAGAA 59.881 33.333 0.00 0.00 39.96 2.52
85 86 6.593382 GCATGGCAAAAATACCAATGTAAAGA 59.407 34.615 0.00 0.00 39.96 2.52
86 87 6.370994 TGCATGGCAAAAATACCAATGTAAAG 59.629 34.615 0.00 0.00 39.96 1.85
87 88 6.148480 GTGCATGGCAAAAATACCAATGTAAA 59.852 34.615 0.00 0.00 41.47 2.01
88 89 5.641209 GTGCATGGCAAAAATACCAATGTAA 59.359 36.000 0.00 0.00 41.47 2.41
89 90 5.174395 GTGCATGGCAAAAATACCAATGTA 58.826 37.500 0.00 0.00 41.47 2.29
90 91 4.002316 GTGCATGGCAAAAATACCAATGT 58.998 39.130 0.00 0.00 41.47 2.71
91 92 4.001652 TGTGCATGGCAAAAATACCAATG 58.998 39.130 0.00 0.00 41.47 2.82
92 93 4.283363 TGTGCATGGCAAAAATACCAAT 57.717 36.364 0.00 0.00 41.47 3.16
93 94 3.758755 TGTGCATGGCAAAAATACCAA 57.241 38.095 0.00 0.00 41.47 3.67
94 95 3.977134 ATGTGCATGGCAAAAATACCA 57.023 38.095 0.00 0.00 41.47 3.25
95 96 5.625921 AAAATGTGCATGGCAAAAATACC 57.374 34.783 0.00 0.00 41.47 2.73
96 97 5.857517 CCAAAAATGTGCATGGCAAAAATAC 59.142 36.000 0.00 0.00 41.47 1.89
97 98 6.010294 CCAAAAATGTGCATGGCAAAAATA 57.990 33.333 0.00 0.00 41.47 1.40
98 99 4.872664 CCAAAAATGTGCATGGCAAAAAT 58.127 34.783 0.00 0.00 41.47 1.82
99 100 4.303086 CCAAAAATGTGCATGGCAAAAA 57.697 36.364 0.00 0.00 41.47 1.94
100 101 3.984508 CCAAAAATGTGCATGGCAAAA 57.015 38.095 0.00 0.00 41.47 2.44
105 106 2.417239 GTGATGCCAAAAATGTGCATGG 59.583 45.455 0.32 0.00 45.20 3.66
106 107 3.331150 AGTGATGCCAAAAATGTGCATG 58.669 40.909 0.32 0.00 45.20 4.06
108 109 3.472283 AAGTGATGCCAAAAATGTGCA 57.528 38.095 0.00 0.00 39.68 4.57
109 110 4.143052 GCTAAAGTGATGCCAAAAATGTGC 60.143 41.667 0.00 0.00 0.00 4.57
110 111 5.232463 AGCTAAAGTGATGCCAAAAATGTG 58.768 37.500 0.00 0.00 0.00 3.21
111 112 5.473066 AGCTAAAGTGATGCCAAAAATGT 57.527 34.783 0.00 0.00 0.00 2.71
112 113 5.807011 GGTAGCTAAAGTGATGCCAAAAATG 59.193 40.000 0.00 0.00 0.00 2.32
113 114 5.480073 TGGTAGCTAAAGTGATGCCAAAAAT 59.520 36.000 0.00 0.00 0.00 1.82
114 115 4.830046 TGGTAGCTAAAGTGATGCCAAAAA 59.170 37.500 0.00 0.00 0.00 1.94
115 116 4.402829 TGGTAGCTAAAGTGATGCCAAAA 58.597 39.130 0.00 0.00 0.00 2.44
116 117 4.009675 CTGGTAGCTAAAGTGATGCCAAA 58.990 43.478 0.00 0.00 0.00 3.28
117 118 3.009033 ACTGGTAGCTAAAGTGATGCCAA 59.991 43.478 9.07 0.00 0.00 4.52
118 119 2.571653 ACTGGTAGCTAAAGTGATGCCA 59.428 45.455 9.07 2.99 0.00 4.92
119 120 2.939103 CACTGGTAGCTAAAGTGATGCC 59.061 50.000 24.10 8.48 43.22 4.40
120 121 2.939103 CCACTGGTAGCTAAAGTGATGC 59.061 50.000 27.66 2.94 43.22 3.91
121 122 2.939103 GCCACTGGTAGCTAAAGTGATG 59.061 50.000 27.66 17.91 43.22 3.07
122 123 2.092914 GGCCACTGGTAGCTAAAGTGAT 60.093 50.000 27.66 1.39 43.22 3.06
123 124 1.278127 GGCCACTGGTAGCTAAAGTGA 59.722 52.381 27.66 0.00 43.22 3.41
124 125 1.279271 AGGCCACTGGTAGCTAAAGTG 59.721 52.381 22.51 22.51 40.81 3.16
125 126 1.657804 AGGCCACTGGTAGCTAAAGT 58.342 50.000 5.01 0.00 0.00 2.66
126 127 3.906720 TTAGGCCACTGGTAGCTAAAG 57.093 47.619 5.01 0.00 0.00 1.85
127 128 4.644163 TTTTAGGCCACTGGTAGCTAAA 57.356 40.909 5.01 0.00 0.00 1.85
128 129 4.042435 ACTTTTTAGGCCACTGGTAGCTAA 59.958 41.667 5.01 0.00 0.00 3.09
129 130 3.585732 ACTTTTTAGGCCACTGGTAGCTA 59.414 43.478 5.01 0.00 0.00 3.32
130 131 2.375509 ACTTTTTAGGCCACTGGTAGCT 59.624 45.455 5.01 0.00 0.00 3.32
131 132 2.791655 ACTTTTTAGGCCACTGGTAGC 58.208 47.619 5.01 0.00 0.00 3.58
132 133 7.462571 AAATAACTTTTTAGGCCACTGGTAG 57.537 36.000 5.01 0.00 0.00 3.18
133 134 7.308710 CGAAAATAACTTTTTAGGCCACTGGTA 60.309 37.037 5.01 0.00 34.73 3.25
134 135 6.516028 CGAAAATAACTTTTTAGGCCACTGGT 60.516 38.462 5.01 0.00 34.73 4.00
135 136 5.861787 CGAAAATAACTTTTTAGGCCACTGG 59.138 40.000 5.01 0.00 34.73 4.00
136 137 5.861787 CCGAAAATAACTTTTTAGGCCACTG 59.138 40.000 5.01 0.00 34.73 3.66
137 138 5.771165 TCCGAAAATAACTTTTTAGGCCACT 59.229 36.000 5.01 0.00 34.73 4.00
138 139 5.860182 GTCCGAAAATAACTTTTTAGGCCAC 59.140 40.000 5.01 0.00 34.73 5.01
139 140 5.535406 TGTCCGAAAATAACTTTTTAGGCCA 59.465 36.000 5.01 0.00 34.73 5.36
140 141 6.016213 TGTCCGAAAATAACTTTTTAGGCC 57.984 37.500 0.00 0.00 34.73 5.19
141 142 6.675026 ACTGTCCGAAAATAACTTTTTAGGC 58.325 36.000 5.42 2.91 34.73 3.93
142 143 7.013529 CGACTGTCCGAAAATAACTTTTTAGG 58.986 38.462 1.55 4.24 34.73 2.69
143 144 7.790000 TCGACTGTCCGAAAATAACTTTTTAG 58.210 34.615 1.55 0.00 34.73 1.85
144 145 7.712264 TCGACTGTCCGAAAATAACTTTTTA 57.288 32.000 1.55 0.00 34.73 1.52
145 146 6.607735 TCGACTGTCCGAAAATAACTTTTT 57.392 33.333 1.55 0.00 34.73 1.94
146 147 6.796705 ATCGACTGTCCGAAAATAACTTTT 57.203 33.333 1.55 0.00 42.22 2.27
147 148 6.796705 AATCGACTGTCCGAAAATAACTTT 57.203 33.333 1.55 0.00 42.22 2.66
148 149 6.796705 AAATCGACTGTCCGAAAATAACTT 57.203 33.333 1.55 0.00 42.22 2.66
149 150 6.796705 AAAATCGACTGTCCGAAAATAACT 57.203 33.333 1.55 0.00 42.22 2.24
170 171 8.160521 TCTCATAACAGAAATCAACGGAAAAA 57.839 30.769 0.00 0.00 0.00 1.94
171 172 7.737972 TCTCATAACAGAAATCAACGGAAAA 57.262 32.000 0.00 0.00 0.00 2.29
172 173 7.390440 ACATCTCATAACAGAAATCAACGGAAA 59.610 33.333 0.00 0.00 0.00 3.13
173 174 6.878923 ACATCTCATAACAGAAATCAACGGAA 59.121 34.615 0.00 0.00 0.00 4.30
174 175 6.406370 ACATCTCATAACAGAAATCAACGGA 58.594 36.000 0.00 0.00 0.00 4.69
175 176 6.668541 ACATCTCATAACAGAAATCAACGG 57.331 37.500 0.00 0.00 0.00 4.44
176 177 7.007725 GCAAACATCTCATAACAGAAATCAACG 59.992 37.037 0.00 0.00 0.00 4.10
177 178 8.025445 AGCAAACATCTCATAACAGAAATCAAC 58.975 33.333 0.00 0.00 0.00 3.18
178 179 8.114331 AGCAAACATCTCATAACAGAAATCAA 57.886 30.769 0.00 0.00 0.00 2.57
179 180 7.609146 AGAGCAAACATCTCATAACAGAAATCA 59.391 33.333 0.00 0.00 33.15 2.57
180 181 7.983307 AGAGCAAACATCTCATAACAGAAATC 58.017 34.615 0.00 0.00 33.15 2.17
181 182 7.934855 AGAGCAAACATCTCATAACAGAAAT 57.065 32.000 0.00 0.00 33.15 2.17
182 183 7.750229 AAGAGCAAACATCTCATAACAGAAA 57.250 32.000 0.00 0.00 33.15 2.52
183 184 7.750229 AAAGAGCAAACATCTCATAACAGAA 57.250 32.000 0.00 0.00 33.15 3.02
184 185 7.750229 AAAAGAGCAAACATCTCATAACAGA 57.250 32.000 0.00 0.00 33.15 3.41
206 207 7.995289 ACACATCACATAACAGAACAGAAAAA 58.005 30.769 0.00 0.00 0.00 1.94
207 208 7.566760 ACACATCACATAACAGAACAGAAAA 57.433 32.000 0.00 0.00 0.00 2.29
208 209 7.566760 AACACATCACATAACAGAACAGAAA 57.433 32.000 0.00 0.00 0.00 2.52
209 210 7.566760 AAACACATCACATAACAGAACAGAA 57.433 32.000 0.00 0.00 0.00 3.02
210 211 7.416817 CAAAACACATCACATAACAGAACAGA 58.583 34.615 0.00 0.00 0.00 3.41
211 212 6.638063 CCAAAACACATCACATAACAGAACAG 59.362 38.462 0.00 0.00 0.00 3.16
212 213 6.460814 CCCAAAACACATCACATAACAGAACA 60.461 38.462 0.00 0.00 0.00 3.18
213 214 5.920273 CCCAAAACACATCACATAACAGAAC 59.080 40.000 0.00 0.00 0.00 3.01
214 215 5.508825 GCCCAAAACACATCACATAACAGAA 60.509 40.000 0.00 0.00 0.00 3.02
215 216 4.022416 GCCCAAAACACATCACATAACAGA 60.022 41.667 0.00 0.00 0.00 3.41
216 217 4.022068 AGCCCAAAACACATCACATAACAG 60.022 41.667 0.00 0.00 0.00 3.16
217 218 3.894427 AGCCCAAAACACATCACATAACA 59.106 39.130 0.00 0.00 0.00 2.41
218 219 4.022416 TCAGCCCAAAACACATCACATAAC 60.022 41.667 0.00 0.00 0.00 1.89
219 220 4.148079 TCAGCCCAAAACACATCACATAA 58.852 39.130 0.00 0.00 0.00 1.90
220 221 3.758023 CTCAGCCCAAAACACATCACATA 59.242 43.478 0.00 0.00 0.00 2.29
221 222 2.559668 CTCAGCCCAAAACACATCACAT 59.440 45.455 0.00 0.00 0.00 3.21
222 223 1.955778 CTCAGCCCAAAACACATCACA 59.044 47.619 0.00 0.00 0.00 3.58
223 224 1.956477 ACTCAGCCCAAAACACATCAC 59.044 47.619 0.00 0.00 0.00 3.06
224 225 2.363306 ACTCAGCCCAAAACACATCA 57.637 45.000 0.00 0.00 0.00 3.07
225 226 3.733443 AAACTCAGCCCAAAACACATC 57.267 42.857 0.00 0.00 0.00 3.06
226 227 4.486125 AAAAACTCAGCCCAAAACACAT 57.514 36.364 0.00 0.00 0.00 3.21
227 228 3.971245 AAAAACTCAGCCCAAAACACA 57.029 38.095 0.00 0.00 0.00 3.72
246 247 9.315363 ACTAACCCAAATATGTGGTCATTAAAA 57.685 29.630 11.17 0.00 36.90 1.52
247 248 8.887264 ACTAACCCAAATATGTGGTCATTAAA 57.113 30.769 11.17 0.00 36.90 1.52
248 249 8.887264 AACTAACCCAAATATGTGGTCATTAA 57.113 30.769 11.17 0.00 36.90 1.40
249 250 9.976776 TTAACTAACCCAAATATGTGGTCATTA 57.023 29.630 11.17 5.92 36.90 1.90
250 251 8.887264 TTAACTAACCCAAATATGTGGTCATT 57.113 30.769 11.17 5.10 36.90 2.57
251 252 9.487442 AATTAACTAACCCAAATATGTGGTCAT 57.513 29.630 11.17 0.00 36.90 3.06
252 253 8.887264 AATTAACTAACCCAAATATGTGGTCA 57.113 30.769 11.17 0.00 36.90 4.02
253 254 8.410912 GGAATTAACTAACCCAAATATGTGGTC 58.589 37.037 11.17 0.00 36.90 4.02
254 255 8.119891 AGGAATTAACTAACCCAAATATGTGGT 58.880 33.333 11.17 0.00 36.90 4.16
255 256 8.413229 CAGGAATTAACTAACCCAAATATGTGG 58.587 37.037 4.74 4.74 38.51 4.17
256 257 8.966868 ACAGGAATTAACTAACCCAAATATGTG 58.033 33.333 0.00 0.00 0.00 3.21
257 258 8.966868 CACAGGAATTAACTAACCCAAATATGT 58.033 33.333 0.00 0.00 0.00 2.29
258 259 7.920682 GCACAGGAATTAACTAACCCAAATATG 59.079 37.037 0.00 0.00 0.00 1.78
259 260 7.201785 CGCACAGGAATTAACTAACCCAAATAT 60.202 37.037 0.00 0.00 0.00 1.28
260 261 6.094325 CGCACAGGAATTAACTAACCCAAATA 59.906 38.462 0.00 0.00 0.00 1.40
261 262 5.105917 CGCACAGGAATTAACTAACCCAAAT 60.106 40.000 0.00 0.00 0.00 2.32
262 263 4.216687 CGCACAGGAATTAACTAACCCAAA 59.783 41.667 0.00 0.00 0.00 3.28
263 264 3.754323 CGCACAGGAATTAACTAACCCAA 59.246 43.478 0.00 0.00 0.00 4.12
264 265 3.008157 TCGCACAGGAATTAACTAACCCA 59.992 43.478 0.00 0.00 0.00 4.51
265 266 3.373130 GTCGCACAGGAATTAACTAACCC 59.627 47.826 0.00 0.00 0.00 4.11
266 267 3.373130 GGTCGCACAGGAATTAACTAACC 59.627 47.826 0.00 0.00 0.00 2.85
267 268 3.998341 TGGTCGCACAGGAATTAACTAAC 59.002 43.478 0.00 0.00 0.00 2.34
268 269 4.274602 TGGTCGCACAGGAATTAACTAA 57.725 40.909 0.00 0.00 0.00 2.24
269 270 3.965379 TGGTCGCACAGGAATTAACTA 57.035 42.857 0.00 0.00 0.00 2.24
270 271 2.851263 TGGTCGCACAGGAATTAACT 57.149 45.000 0.00 0.00 0.00 2.24
271 272 3.561503 GTTTGGTCGCACAGGAATTAAC 58.438 45.455 0.00 0.00 0.00 2.01
272 273 2.554893 GGTTTGGTCGCACAGGAATTAA 59.445 45.455 0.00 0.00 0.00 1.40
273 274 2.156098 GGTTTGGTCGCACAGGAATTA 58.844 47.619 0.00 0.00 0.00 1.40
274 275 0.958822 GGTTTGGTCGCACAGGAATT 59.041 50.000 0.00 0.00 0.00 2.17
275 276 0.893727 GGGTTTGGTCGCACAGGAAT 60.894 55.000 0.00 0.00 0.00 3.01
276 277 1.527380 GGGTTTGGTCGCACAGGAA 60.527 57.895 0.00 0.00 0.00 3.36
277 278 2.112297 GGGTTTGGTCGCACAGGA 59.888 61.111 0.00 0.00 0.00 3.86
278 279 1.966451 GAGGGTTTGGTCGCACAGG 60.966 63.158 0.00 0.00 0.00 4.00
279 280 1.966451 GGAGGGTTTGGTCGCACAG 60.966 63.158 0.00 0.00 0.00 3.66
280 281 2.112297 GGAGGGTTTGGTCGCACA 59.888 61.111 0.00 0.00 0.00 4.57
281 282 2.671963 GGGAGGGTTTGGTCGCAC 60.672 66.667 0.00 0.00 0.00 5.34
282 283 2.852075 AGGGAGGGTTTGGTCGCA 60.852 61.111 0.00 0.00 0.00 5.10
283 284 2.046217 GAGGGAGGGTTTGGTCGC 60.046 66.667 0.00 0.00 0.00 5.19
284 285 1.597461 GAGAGGGAGGGTTTGGTCG 59.403 63.158 0.00 0.00 0.00 4.79
285 286 1.563577 GGGAGAGGGAGGGTTTGGTC 61.564 65.000 0.00 0.00 0.00 4.02
286 287 1.541620 GGGAGAGGGAGGGTTTGGT 60.542 63.158 0.00 0.00 0.00 3.67
287 288 2.309504 GGGGAGAGGGAGGGTTTGG 61.310 68.421 0.00 0.00 0.00 3.28
288 289 2.309504 GGGGGAGAGGGAGGGTTTG 61.310 68.421 0.00 0.00 0.00 2.93
289 290 2.075278 AAGGGGGAGAGGGAGGGTTT 62.075 60.000 0.00 0.00 0.00 3.27
290 291 2.075278 AAAGGGGGAGAGGGAGGGTT 62.075 60.000 0.00 0.00 0.00 4.11
291 292 2.511458 AAAGGGGGAGAGGGAGGGT 61.511 63.158 0.00 0.00 0.00 4.34
292 293 2.003548 CAAAGGGGGAGAGGGAGGG 61.004 68.421 0.00 0.00 0.00 4.30
293 294 2.684499 GCAAAGGGGGAGAGGGAGG 61.684 68.421 0.00 0.00 0.00 4.30
294 295 1.617839 AGCAAAGGGGGAGAGGGAG 60.618 63.158 0.00 0.00 0.00 4.30
295 296 1.616628 GAGCAAAGGGGGAGAGGGA 60.617 63.158 0.00 0.00 0.00 4.20
296 297 1.210885 AAGAGCAAAGGGGGAGAGGG 61.211 60.000 0.00 0.00 0.00 4.30
297 298 0.701147 AAAGAGCAAAGGGGGAGAGG 59.299 55.000 0.00 0.00 0.00 3.69
298 299 2.441410 GAAAAGAGCAAAGGGGGAGAG 58.559 52.381 0.00 0.00 0.00 3.20
299 300 1.271379 CGAAAAGAGCAAAGGGGGAGA 60.271 52.381 0.00 0.00 0.00 3.71
300 301 1.168714 CGAAAAGAGCAAAGGGGGAG 58.831 55.000 0.00 0.00 0.00 4.30
301 302 0.251165 CCGAAAAGAGCAAAGGGGGA 60.251 55.000 0.00 0.00 0.00 4.81
302 303 0.539669 ACCGAAAAGAGCAAAGGGGG 60.540 55.000 0.00 0.00 0.00 5.40
303 304 1.328279 AACCGAAAAGAGCAAAGGGG 58.672 50.000 0.00 0.00 0.00 4.79
304 305 2.360801 TGAAACCGAAAAGAGCAAAGGG 59.639 45.455 0.00 0.00 0.00 3.95
305 306 3.632189 CTGAAACCGAAAAGAGCAAAGG 58.368 45.455 0.00 0.00 0.00 3.11
306 307 3.045688 GCTGAAACCGAAAAGAGCAAAG 58.954 45.455 0.00 0.00 0.00 2.77
307 308 2.687935 AGCTGAAACCGAAAAGAGCAAA 59.312 40.909 0.00 0.00 0.00 3.68
308 309 2.297701 AGCTGAAACCGAAAAGAGCAA 58.702 42.857 0.00 0.00 0.00 3.91
309 310 1.967319 AGCTGAAACCGAAAAGAGCA 58.033 45.000 0.00 0.00 0.00 4.26
310 311 3.355626 AAAGCTGAAACCGAAAAGAGC 57.644 42.857 0.00 0.00 0.00 4.09
375 376 6.968263 TTACACTCATCCAACATCCAAAAA 57.032 33.333 0.00 0.00 0.00 1.94
376 377 6.968263 TTTACACTCATCCAACATCCAAAA 57.032 33.333 0.00 0.00 0.00 2.44
377 378 6.493115 ACATTTACACTCATCCAACATCCAAA 59.507 34.615 0.00 0.00 0.00 3.28
378 379 6.009589 ACATTTACACTCATCCAACATCCAA 58.990 36.000 0.00 0.00 0.00 3.53
379 380 5.569355 ACATTTACACTCATCCAACATCCA 58.431 37.500 0.00 0.00 0.00 3.41
380 381 7.807977 ATACATTTACACTCATCCAACATCC 57.192 36.000 0.00 0.00 0.00 3.51
381 382 9.325198 TGTATACATTTACACTCATCCAACATC 57.675 33.333 0.08 0.00 0.00 3.06
382 383 9.109393 GTGTATACATTTACACTCATCCAACAT 57.891 33.333 9.18 0.00 45.48 2.71
383 384 8.487313 GTGTATACATTTACACTCATCCAACA 57.513 34.615 9.18 0.00 45.48 3.33
459 460 8.034804 GCCACAACAAAGTATCCAAAGAATAAT 58.965 33.333 0.00 0.00 0.00 1.28
460 461 7.014711 TGCCACAACAAAGTATCCAAAGAATAA 59.985 33.333 0.00 0.00 0.00 1.40
461 462 6.491745 TGCCACAACAAAGTATCCAAAGAATA 59.508 34.615 0.00 0.00 0.00 1.75
462 463 5.304101 TGCCACAACAAAGTATCCAAAGAAT 59.696 36.000 0.00 0.00 0.00 2.40
463 464 4.646945 TGCCACAACAAAGTATCCAAAGAA 59.353 37.500 0.00 0.00 0.00 2.52
464 465 4.211125 TGCCACAACAAAGTATCCAAAGA 58.789 39.130 0.00 0.00 0.00 2.52
465 466 4.582701 TGCCACAACAAAGTATCCAAAG 57.417 40.909 0.00 0.00 0.00 2.77
466 467 4.798924 GCATGCCACAACAAAGTATCCAAA 60.799 41.667 6.36 0.00 0.00 3.28
467 468 3.305950 GCATGCCACAACAAAGTATCCAA 60.306 43.478 6.36 0.00 0.00 3.53
468 469 2.230992 GCATGCCACAACAAAGTATCCA 59.769 45.455 6.36 0.00 0.00 3.41
469 470 2.417243 GGCATGCCACAACAAAGTATCC 60.417 50.000 32.08 0.00 35.81 2.59
470 471 2.417243 GGGCATGCCACAACAAAGTATC 60.417 50.000 36.56 11.88 37.98 2.24
471 472 1.550072 GGGCATGCCACAACAAAGTAT 59.450 47.619 36.56 0.00 37.98 2.12
472 473 0.965439 GGGCATGCCACAACAAAGTA 59.035 50.000 36.56 0.00 37.98 2.24
473 474 0.760189 AGGGCATGCCACAACAAAGT 60.760 50.000 36.56 7.44 37.98 2.66
474 475 1.067635 GTAGGGCATGCCACAACAAAG 60.068 52.381 36.56 0.00 37.98 2.77
475 476 0.965439 GTAGGGCATGCCACAACAAA 59.035 50.000 36.56 11.44 37.98 2.83
479 480 2.045438 CGGTAGGGCATGCCACAA 60.045 61.111 36.56 19.09 37.98 3.33
501 502 6.819947 TGACCTCCTAGTGTACTAGTCATA 57.180 41.667 15.72 1.19 43.34 2.15
515 516 2.025605 ACGTACTCACCATGACCTCCTA 60.026 50.000 0.00 0.00 0.00 2.94
518 519 1.202154 CGACGTACTCACCATGACCTC 60.202 57.143 0.00 0.00 0.00 3.85
547 2806 2.357760 GTCGCGTGCAACCCCTTA 60.358 61.111 5.77 0.00 0.00 2.69
599 2858 4.225042 TGTAGCCGCCTCATCCATAATATT 59.775 41.667 0.00 0.00 0.00 1.28
640 2899 9.720769 TTTCTATAAACTTTCTTTCCGACATCT 57.279 29.630 0.00 0.00 0.00 2.90
688 2947 5.046376 TCCTTTGCTAAGATGTGTCATCTCA 60.046 40.000 9.62 4.63 32.92 3.27
720 2979 4.585879 ACCACATAGAATACGCAAGGTTT 58.414 39.130 0.00 0.00 46.39 3.27
827 3086 3.046968 TCCTACTTTTGTGCGTGCATA 57.953 42.857 0.00 0.00 0.00 3.14
919 3178 7.016296 TCTTCCTATTTTTCCTCCATGGTTTT 58.984 34.615 12.58 0.00 37.07 2.43
1036 3296 5.508200 AGATCGTCTACATCCTCAACTTC 57.492 43.478 0.00 0.00 0.00 3.01
1098 3358 3.198068 CGAATCATCTTCCCACACGAAT 58.802 45.455 0.00 0.00 0.00 3.34
1117 3377 0.252513 TGGATCTTTGGGACCTCCGA 60.253 55.000 0.00 0.00 38.76 4.55
1235 3495 1.131126 CAATCATCCTCCAACGCACAC 59.869 52.381 0.00 0.00 0.00 3.82
1341 3601 0.250513 ACTCCTTCAAGATCACCGCC 59.749 55.000 0.00 0.00 0.00 6.13
1423 3683 6.878923 TGAAGATAGTTGTCCGACAATTTCAT 59.121 34.615 16.80 4.71 40.59 2.57
1459 3719 7.336931 TCCTATCTTTCTGCACATTCCTTTTAC 59.663 37.037 0.00 0.00 0.00 2.01
1901 4162 3.308401 TGCATTCCATCTCCAGCTAGTA 58.692 45.455 0.00 0.00 0.00 1.82
1935 4196 5.698369 ATCTTATCTGTAGGTTCCCCCTA 57.302 43.478 0.00 0.00 43.87 3.53
1957 4218 1.218047 GTGTCCTGCTGCACGGATA 59.782 57.895 19.05 15.24 0.00 2.59
1958 4219 2.046892 GTGTCCTGCTGCACGGAT 60.047 61.111 19.05 0.00 0.00 4.18
1959 4220 3.233980 AGTGTCCTGCTGCACGGA 61.234 61.111 14.24 14.24 40.26 4.69
1978 4239 2.239654 TCCACTTCCAGGCCTAATGAAG 59.760 50.000 25.85 25.85 39.99 3.02
1999 4260 3.521126 ACTGTGCTCCTTCTCAACCATAT 59.479 43.478 0.00 0.00 0.00 1.78
2126 4387 3.512329 TCTCATTGCTGCCATCAAACATT 59.488 39.130 0.00 0.00 0.00 2.71
2282 4543 5.067674 TCAGGCTTAAAATATTCATTGCGCT 59.932 36.000 9.73 0.00 0.00 5.92
2387 4648 1.066143 GGCAATTTGGTCTCCGAGAGA 60.066 52.381 0.00 0.11 36.22 3.10
2421 4682 3.834813 CCCAATCGGAATCTCATCTCCTA 59.165 47.826 0.00 0.00 0.00 2.94
2616 4877 4.388577 TCCTCCTTGATCTCATCGGATA 57.611 45.455 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.