Multiple sequence alignment - TraesCS7B01G381400

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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 TraesCS7B01G381400 chr7B 100.000 3218 0 0 1 3218 646211514 646208297 0.000000e+00 5943.0
1 TraesCS7B01G381400 chr7B 97.500 80 2 0 1 80 438379450 438379371 1.560000e-28 137.0
2 TraesCS7B01G381400 chr7B 90.164 61 5 1 3067 3127 113308632 113308691 9.570000e-11 78.7
3 TraesCS7B01G381400 chr7D 91.896 1456 76 27 328 1767 579962643 579961214 0.000000e+00 1997.0
4 TraesCS7B01G381400 chr7D 87.679 349 13 12 1777 2097 579961167 579960821 2.340000e-101 379.0
5 TraesCS7B01G381400 chr7D 90.361 249 17 4 2306 2553 579958815 579958573 1.440000e-83 320.0
6 TraesCS7B01G381400 chr7D 86.792 159 15 2 2089 2247 579958968 579958816 4.270000e-39 172.0
7 TraesCS7B01G381400 chr7D 92.188 64 3 2 3065 3127 119058659 119058597 4.420000e-14 89.8
8 TraesCS7B01G381400 chr7D 84.211 95 12 2 234 325 579962781 579962687 4.420000e-14 89.8
9 TraesCS7B01G381400 chr7D 87.692 65 6 2 3065 3128 31577386 31577449 1.240000e-09 75.0
10 TraesCS7B01G381400 chr7A 91.202 1489 78 29 325 1767 671484655 671483174 0.000000e+00 1975.0
11 TraesCS7B01G381400 chr7A 87.408 1493 92 42 1777 3217 671483127 671481679 0.000000e+00 1628.0
12 TraesCS7B01G381400 chr6B 79.121 273 32 19 1234 1492 207155633 207155372 7.140000e-37 165.0
13 TraesCS7B01G381400 chr6A 78.521 284 37 19 1232 1502 145134357 145134085 7.140000e-37 165.0
14 TraesCS7B01G381400 chr6A 79.365 126 22 4 2715 2838 414861129 414861252 5.720000e-13 86.1
15 TraesCS7B01G381400 chr6D 78.014 282 42 16 1232 1502 116953093 116952821 3.320000e-35 159.0
16 TraesCS7B01G381400 chr6D 90.323 62 3 3 3068 3127 357785025 357785085 9.570000e-11 78.7
17 TraesCS7B01G381400 chr6D 100.000 32 0 0 2805 2836 38855459 38855490 3.470000e-05 60.2
18 TraesCS7B01G381400 chr1A 84.906 159 20 3 2706 2862 513837123 513837279 1.200000e-34 158.0
19 TraesCS7B01G381400 chr1A 75.969 129 27 4 2712 2838 436229510 436229636 2.680000e-06 63.9
20 TraesCS7B01G381400 chr5D 92.553 94 7 0 1 94 557596788 557596695 5.600000e-28 135.0
21 TraesCS7B01G381400 chr2D 95.294 85 4 0 1 85 593274263 593274347 5.600000e-28 135.0
22 TraesCS7B01G381400 chr2D 91.935 62 3 2 3067 3127 314902611 314902671 5.720000e-13 86.1
23 TraesCS7B01G381400 chr2D 90.000 60 6 0 3068 3127 154827211 154827152 9.570000e-11 78.7
24 TraesCS7B01G381400 chrUn 94.186 86 4 1 1 85 305213152 305213237 2.610000e-26 130.0
25 TraesCS7B01G381400 chr3A 96.203 79 3 0 2 80 64055730 64055652 2.610000e-26 130.0
26 TraesCS7B01G381400 chr3D 95.062 81 4 0 1 81 462197490 462197410 9.370000e-26 128.0
27 TraesCS7B01G381400 chr2B 95.062 81 4 0 1 81 214828133 214828213 9.370000e-26 128.0
28 TraesCS7B01G381400 chr2B 90.476 63 4 2 3065 3126 137262291 137262230 7.400000e-12 82.4
29 TraesCS7B01G381400 chr1D 96.154 78 3 0 1 78 174151194 174151271 9.370000e-26 128.0
30 TraesCS7B01G381400 chr4B 94.048 84 3 2 1 82 569768614 569768697 3.370000e-25 126.0
31 TraesCS7B01G381400 chr4B 76.724 116 25 2 2724 2838 658555105 658554991 2.680000e-06 63.9
32 TraesCS7B01G381400 chr1B 82.456 114 16 4 2755 2865 563118327 563118439 2.640000e-16 97.1
33 TraesCS7B01G381400 chr4D 89.062 64 5 2 3065 3127 439880905 439880843 9.570000e-11 78.7


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 TraesCS7B01G381400 chr7B 646208297 646211514 3217 True 5943.00 5943 100.0000 1 3218 1 chr7B.!!$R2 3217
1 TraesCS7B01G381400 chr7D 579958573 579962781 4208 True 591.56 1997 88.1878 234 2553 5 chr7D.!!$R2 2319
2 TraesCS7B01G381400 chr7A 671481679 671484655 2976 True 1801.50 1975 89.3050 325 3217 2 chr7A.!!$R1 2892

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
285 286 0.031585 GTGCGTAGATGTATGCGGGA 59.968 55.0 9.32 0.0 43.25 5.14 F
1878 2034 0.109597 GCCTGTGATTTTGCCACTCG 60.110 55.0 0.00 0.0 35.66 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2126 0.253820 ATCCATCCTTCCACCCACCT 60.254 55.0 0.0 0.0 0.00 4.00 R
2846 4881 0.107945 GTCAGCTCCTCCAAAGCGAT 60.108 55.0 0.0 0.0 44.59 4.58 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
52 53 9.716531 AGTACAAAGTTAGTATAAAGTTGGGTC 57.283 33.333 0.00 0.00 0.00 4.46
53 54 9.492973 GTACAAAGTTAGTATAAAGTTGGGTCA 57.507 33.333 0.00 0.00 0.00 4.02
55 56 9.227777 ACAAAGTTAGTATAAAGTTGGGTCATC 57.772 33.333 0.00 0.00 0.00 2.92
56 57 9.449719 CAAAGTTAGTATAAAGTTGGGTCATCT 57.550 33.333 0.00 0.00 0.00 2.90
67 68 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
68 69 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
69 70 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
70 71 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
71 72 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
72 73 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
73 74 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
74 75 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
75 76 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
76 77 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
77 78 5.727434 TCTATTTTGAAACGGAGGGAGTAC 58.273 41.667 0.00 0.00 0.00 2.73
78 79 4.635699 ATTTTGAAACGGAGGGAGTACT 57.364 40.909 0.00 0.00 0.00 2.73
79 80 4.426736 TTTTGAAACGGAGGGAGTACTT 57.573 40.909 0.00 0.00 0.00 2.24
80 81 4.426736 TTTGAAACGGAGGGAGTACTTT 57.573 40.909 0.00 0.00 0.00 2.66
81 82 3.396260 TGAAACGGAGGGAGTACTTTG 57.604 47.619 0.00 0.00 0.00 2.77
82 83 2.701951 TGAAACGGAGGGAGTACTTTGT 59.298 45.455 0.00 0.00 0.00 2.83
83 84 3.896888 TGAAACGGAGGGAGTACTTTGTA 59.103 43.478 0.00 0.00 0.00 2.41
84 85 4.344679 TGAAACGGAGGGAGTACTTTGTAA 59.655 41.667 0.00 0.00 0.00 2.41
85 86 4.532314 AACGGAGGGAGTACTTTGTAAG 57.468 45.455 0.00 0.00 0.00 2.34
86 87 3.504375 ACGGAGGGAGTACTTTGTAAGT 58.496 45.455 0.00 0.00 45.40 2.24
87 88 3.257624 ACGGAGGGAGTACTTTGTAAGTG 59.742 47.826 0.00 0.00 42.84 3.16
88 89 3.257624 CGGAGGGAGTACTTTGTAAGTGT 59.742 47.826 0.00 0.00 42.84 3.55
89 90 4.460382 CGGAGGGAGTACTTTGTAAGTGTA 59.540 45.833 0.00 0.00 42.84 2.90
90 91 5.126707 CGGAGGGAGTACTTTGTAAGTGTAT 59.873 44.000 0.00 0.00 42.84 2.29
91 92 6.350780 CGGAGGGAGTACTTTGTAAGTGTATT 60.351 42.308 0.00 0.00 42.84 1.89
92 93 7.392418 GGAGGGAGTACTTTGTAAGTGTATTT 58.608 38.462 0.00 0.00 42.84 1.40
93 94 7.548427 GGAGGGAGTACTTTGTAAGTGTATTTC 59.452 40.741 0.00 0.00 42.84 2.17
94 95 7.095270 AGGGAGTACTTTGTAAGTGTATTTCG 58.905 38.462 0.00 0.00 42.84 3.46
95 96 7.039504 AGGGAGTACTTTGTAAGTGTATTTCGA 60.040 37.037 0.00 0.00 42.84 3.71
96 97 7.275123 GGGAGTACTTTGTAAGTGTATTTCGAG 59.725 40.741 0.00 0.00 42.84 4.04
97 98 7.275123 GGAGTACTTTGTAAGTGTATTTCGAGG 59.725 40.741 0.00 0.00 42.84 4.63
98 99 7.889469 AGTACTTTGTAAGTGTATTTCGAGGA 58.111 34.615 2.45 0.00 42.84 3.71
99 100 7.811713 AGTACTTTGTAAGTGTATTTCGAGGAC 59.188 37.037 2.45 0.00 42.84 3.85
100 101 6.518493 ACTTTGTAAGTGTATTTCGAGGACA 58.482 36.000 0.00 0.00 41.01 4.02
101 102 6.645415 ACTTTGTAAGTGTATTTCGAGGACAG 59.355 38.462 0.00 0.00 41.01 3.51
102 103 5.970317 TGTAAGTGTATTTCGAGGACAGA 57.030 39.130 0.00 0.00 0.00 3.41
103 104 6.525578 TGTAAGTGTATTTCGAGGACAGAT 57.474 37.500 0.00 0.00 0.00 2.90
104 105 7.634671 TGTAAGTGTATTTCGAGGACAGATA 57.365 36.000 0.00 0.00 0.00 1.98
105 106 8.234136 TGTAAGTGTATTTCGAGGACAGATAT 57.766 34.615 0.00 0.00 0.00 1.63
106 107 9.346005 TGTAAGTGTATTTCGAGGACAGATATA 57.654 33.333 0.00 0.00 0.00 0.86
109 110 8.234136 AGTGTATTTCGAGGACAGATATAACA 57.766 34.615 0.00 0.00 0.00 2.41
110 111 8.692710 AGTGTATTTCGAGGACAGATATAACAA 58.307 33.333 0.00 0.00 0.00 2.83
111 112 9.477484 GTGTATTTCGAGGACAGATATAACAAT 57.523 33.333 0.00 0.00 0.00 2.71
112 113 9.692749 TGTATTTCGAGGACAGATATAACAATC 57.307 33.333 0.00 0.00 0.00 2.67
113 114 9.692749 GTATTTCGAGGACAGATATAACAATCA 57.307 33.333 0.00 0.00 0.00 2.57
115 116 9.784531 ATTTCGAGGACAGATATAACAATCAAT 57.215 29.630 0.00 0.00 0.00 2.57
116 117 9.613428 TTTCGAGGACAGATATAACAATCAATT 57.387 29.630 0.00 0.00 0.00 2.32
155 156 8.592105 ACTTTGTTGATAAATTTCACCACATG 57.408 30.769 0.00 0.00 0.00 3.21
156 157 7.171337 ACTTTGTTGATAAATTTCACCACATGC 59.829 33.333 0.00 0.00 0.00 4.06
157 158 5.159925 TGTTGATAAATTTCACCACATGCG 58.840 37.500 0.00 0.00 0.00 4.73
158 159 5.160641 GTTGATAAATTTCACCACATGCGT 58.839 37.500 0.00 0.00 0.00 5.24
159 160 4.731720 TGATAAATTTCACCACATGCGTG 58.268 39.130 3.82 3.82 43.21 5.34
160 161 1.782044 AAATTTCACCACATGCGTGC 58.218 45.000 5.64 0.00 42.17 5.34
161 162 0.672889 AATTTCACCACATGCGTGCA 59.327 45.000 5.64 0.00 42.17 4.57
162 163 0.672889 ATTTCACCACATGCGTGCAA 59.327 45.000 5.64 5.14 42.17 4.08
163 164 0.457443 TTTCACCACATGCGTGCAAA 59.543 45.000 5.64 7.47 42.17 3.68
164 165 0.672889 TTCACCACATGCGTGCAAAT 59.327 45.000 5.64 0.00 42.17 2.32
165 166 0.039346 TCACCACATGCGTGCAAATG 60.039 50.000 5.64 0.02 42.17 2.32
166 167 0.318869 CACCACATGCGTGCAAATGT 60.319 50.000 5.64 5.36 42.17 2.71
167 168 0.388659 ACCACATGCGTGCAAATGTT 59.611 45.000 5.64 0.00 42.17 2.71
168 169 0.785378 CCACATGCGTGCAAATGTTG 59.215 50.000 5.64 2.66 42.17 3.33
169 170 1.489574 CACATGCGTGCAAATGTTGT 58.510 45.000 5.64 0.00 34.81 3.32
170 171 1.859703 CACATGCGTGCAAATGTTGTT 59.140 42.857 5.64 0.00 34.81 2.83
171 172 2.284684 CACATGCGTGCAAATGTTGTTT 59.715 40.909 5.64 0.00 34.81 2.83
172 173 2.935201 ACATGCGTGCAAATGTTGTTTT 59.065 36.364 5.64 0.00 33.19 2.43
173 174 3.373439 ACATGCGTGCAAATGTTGTTTTT 59.627 34.783 5.64 0.00 33.19 1.94
174 175 3.380486 TGCGTGCAAATGTTGTTTTTG 57.620 38.095 0.00 0.00 37.18 2.44
175 176 2.738846 TGCGTGCAAATGTTGTTTTTGT 59.261 36.364 0.00 0.00 36.63 2.83
176 177 3.089982 GCGTGCAAATGTTGTTTTTGTG 58.910 40.909 0.00 0.00 36.63 3.33
177 178 3.424170 GCGTGCAAATGTTGTTTTTGTGT 60.424 39.130 0.00 0.00 36.63 3.72
178 179 4.201628 GCGTGCAAATGTTGTTTTTGTGTA 60.202 37.500 0.00 0.00 36.63 2.90
179 180 5.501574 GCGTGCAAATGTTGTTTTTGTGTAT 60.502 36.000 0.00 0.00 36.63 2.29
180 181 6.119502 CGTGCAAATGTTGTTTTTGTGTATC 58.880 36.000 0.00 0.00 36.63 2.24
181 182 6.237675 CGTGCAAATGTTGTTTTTGTGTATCA 60.238 34.615 0.00 0.00 36.63 2.15
182 183 7.459486 GTGCAAATGTTGTTTTTGTGTATCAA 58.541 30.769 0.00 0.00 36.63 2.57
183 184 8.121708 GTGCAAATGTTGTTTTTGTGTATCAAT 58.878 29.630 0.00 0.00 36.63 2.57
184 185 8.671921 TGCAAATGTTGTTTTTGTGTATCAATT 58.328 25.926 0.00 0.00 36.63 2.32
185 186 8.945930 GCAAATGTTGTTTTTGTGTATCAATTG 58.054 29.630 0.00 0.00 36.63 2.32
186 187 9.435802 CAAATGTTGTTTTTGTGTATCAATTGG 57.564 29.630 5.42 0.00 35.84 3.16
187 188 8.729805 AATGTTGTTTTTGTGTATCAATTGGT 57.270 26.923 5.42 0.00 35.84 3.67
188 189 8.729805 ATGTTGTTTTTGTGTATCAATTGGTT 57.270 26.923 5.42 0.00 35.84 3.67
189 190 7.968246 TGTTGTTTTTGTGTATCAATTGGTTG 58.032 30.769 5.42 0.00 35.84 3.77
190 191 6.595772 TGTTTTTGTGTATCAATTGGTTGC 57.404 33.333 5.42 0.00 35.84 4.17
191 192 6.108687 TGTTTTTGTGTATCAATTGGTTGCA 58.891 32.000 5.42 0.96 35.84 4.08
192 193 6.595326 TGTTTTTGTGTATCAATTGGTTGCAA 59.405 30.769 5.42 0.00 35.84 4.08
193 194 7.119699 TGTTTTTGTGTATCAATTGGTTGCAAA 59.880 29.630 0.00 8.01 35.84 3.68
194 195 6.595772 TTTGTGTATCAATTGGTTGCAAAC 57.404 33.333 7.78 7.78 40.06 2.93
195 196 5.233050 TTTGTGTATCAATTGGTTGCAAACG 59.767 36.000 10.47 0.00 41.01 3.60
196 197 8.141265 TTTGTGTATCAATTGGTTGCAAACGC 62.141 38.462 10.47 4.44 41.01 4.84
205 206 0.581053 GTTGCAAACGCACAAATGGG 59.419 50.000 0.00 0.00 39.71 4.00
206 207 1.156645 TTGCAAACGCACAAATGGGC 61.157 50.000 0.00 0.00 42.46 5.36
207 208 1.593750 GCAAACGCACAAATGGGCA 60.594 52.632 8.56 0.00 46.93 5.36
208 209 1.156645 GCAAACGCACAAATGGGCAA 61.157 50.000 8.56 0.00 46.93 4.52
209 210 1.293924 CAAACGCACAAATGGGCAAA 58.706 45.000 8.56 0.00 46.93 3.68
210 211 1.667724 CAAACGCACAAATGGGCAAAA 59.332 42.857 8.56 0.00 46.93 2.44
211 212 1.294857 AACGCACAAATGGGCAAAAC 58.705 45.000 8.56 0.00 46.93 2.43
212 213 0.176680 ACGCACAAATGGGCAAAACA 59.823 45.000 8.56 0.00 46.93 2.83
213 214 0.581053 CGCACAAATGGGCAAAACAC 59.419 50.000 8.56 0.00 46.93 3.32
214 215 0.581053 GCACAAATGGGCAAAACACG 59.419 50.000 2.06 0.00 45.57 4.49
215 216 1.804372 GCACAAATGGGCAAAACACGA 60.804 47.619 2.06 0.00 45.57 4.35
216 217 2.126467 CACAAATGGGCAAAACACGAG 58.874 47.619 0.00 0.00 0.00 4.18
217 218 1.068434 ACAAATGGGCAAAACACGAGG 59.932 47.619 0.00 0.00 0.00 4.63
218 219 1.339610 CAAATGGGCAAAACACGAGGA 59.660 47.619 0.00 0.00 0.00 3.71
219 220 1.247567 AATGGGCAAAACACGAGGAG 58.752 50.000 0.00 0.00 0.00 3.69
220 221 1.244019 ATGGGCAAAACACGAGGAGC 61.244 55.000 0.00 0.00 0.00 4.70
221 222 2.626780 GGGCAAAACACGAGGAGCC 61.627 63.158 0.00 0.00 41.29 4.70
222 223 2.556287 GCAAAACACGAGGAGCCG 59.444 61.111 0.00 0.00 0.00 5.52
223 224 1.959226 GCAAAACACGAGGAGCCGA 60.959 57.895 0.00 0.00 0.00 5.54
224 225 1.298859 GCAAAACACGAGGAGCCGAT 61.299 55.000 0.00 0.00 0.00 4.18
225 226 0.443869 CAAAACACGAGGAGCCGATG 59.556 55.000 0.00 0.00 0.00 3.84
226 227 0.673644 AAAACACGAGGAGCCGATGG 60.674 55.000 0.00 0.00 0.00 3.51
227 228 1.541310 AAACACGAGGAGCCGATGGA 61.541 55.000 0.00 0.00 0.00 3.41
228 229 1.949847 AACACGAGGAGCCGATGGAG 61.950 60.000 0.00 0.00 0.00 3.86
229 230 2.043852 ACGAGGAGCCGATGGAGT 60.044 61.111 0.00 0.00 0.00 3.85
230 231 1.682684 ACGAGGAGCCGATGGAGTT 60.683 57.895 0.00 0.00 0.00 3.01
231 232 0.395311 ACGAGGAGCCGATGGAGTTA 60.395 55.000 0.00 0.00 0.00 2.24
232 233 0.962489 CGAGGAGCCGATGGAGTTAT 59.038 55.000 0.00 0.00 0.00 1.89
242 243 6.779860 AGCCGATGGAGTTATTACCATAAAT 58.220 36.000 0.00 0.00 45.41 1.40
245 246 8.357402 GCCGATGGAGTTATTACCATAAATTTT 58.643 33.333 0.00 0.00 45.41 1.82
270 271 0.452987 CCTGGTTTGGATGATGTGCG 59.547 55.000 0.00 0.00 0.00 5.34
272 273 2.355197 CTGGTTTGGATGATGTGCGTA 58.645 47.619 0.00 0.00 0.00 4.42
273 274 2.352651 CTGGTTTGGATGATGTGCGTAG 59.647 50.000 0.00 0.00 0.00 3.51
275 276 3.206150 GGTTTGGATGATGTGCGTAGAT 58.794 45.455 0.00 0.00 0.00 1.98
276 277 3.002656 GGTTTGGATGATGTGCGTAGATG 59.997 47.826 0.00 0.00 0.00 2.90
277 278 3.541996 TTGGATGATGTGCGTAGATGT 57.458 42.857 0.00 0.00 0.00 3.06
278 279 4.664150 TTGGATGATGTGCGTAGATGTA 57.336 40.909 0.00 0.00 0.00 2.29
279 280 4.871933 TGGATGATGTGCGTAGATGTAT 57.128 40.909 0.00 0.00 0.00 2.29
280 281 4.559153 TGGATGATGTGCGTAGATGTATG 58.441 43.478 0.00 0.00 0.00 2.39
281 282 3.369147 GGATGATGTGCGTAGATGTATGC 59.631 47.826 7.12 7.12 41.04 3.14
284 285 0.249280 TGTGCGTAGATGTATGCGGG 60.249 55.000 9.32 0.00 43.25 6.13
285 286 0.031585 GTGCGTAGATGTATGCGGGA 59.968 55.000 9.32 0.00 43.25 5.14
343 388 9.636879 AATCATATATATGCGTCAGATCATAGC 57.363 33.333 16.59 0.00 33.76 2.97
354 399 4.222145 GTCAGATCATAGCGGGGGTAATAA 59.778 45.833 0.00 0.00 0.00 1.40
358 403 3.746940 TCATAGCGGGGGTAATAAAAGC 58.253 45.455 0.00 0.00 0.00 3.51
417 462 8.245195 AGTGATTTTGTAGTGGGTTGTTATTT 57.755 30.769 0.00 0.00 0.00 1.40
418 463 9.357161 AGTGATTTTGTAGTGGGTTGTTATTTA 57.643 29.630 0.00 0.00 0.00 1.40
516 561 2.746277 GCCCAACCTGAACGCGAT 60.746 61.111 15.93 0.00 0.00 4.58
546 591 5.049928 CGGTCTCCAAGGTGGATACTGAG 62.050 56.522 13.69 3.63 46.88 3.35
597 644 1.134487 CGCACGTGCCGAAATTCAT 59.866 52.632 33.23 0.00 37.91 2.57
632 684 1.074248 ACCCAAAACGGATTCGCCT 59.926 52.632 0.00 0.00 40.63 5.52
633 685 0.958876 ACCCAAAACGGATTCGCCTC 60.959 55.000 0.00 0.00 40.63 4.70
634 686 1.423845 CCAAAACGGATTCGCCTCG 59.576 57.895 0.00 0.00 40.63 4.63
635 687 1.226018 CAAAACGGATTCGCCTCGC 60.226 57.895 0.00 0.00 40.63 5.03
636 688 2.396157 AAAACGGATTCGCCTCGCC 61.396 57.895 0.00 0.00 40.63 5.54
910 968 2.262915 CGGTCAGACAGCCACCTC 59.737 66.667 2.17 0.00 0.00 3.85
1043 1101 0.666374 GGTCTCGAGCTCTTCCTAGC 59.334 60.000 12.85 0.00 43.11 3.42
1050 1108 1.439644 GCTCTTCCTAGCTCCCACG 59.560 63.158 0.00 0.00 39.50 4.94
1051 1109 1.439644 CTCTTCCTAGCTCCCACGC 59.560 63.158 0.00 0.00 0.00 5.34
1053 1111 1.142748 CTTCCTAGCTCCCACGCAG 59.857 63.158 0.00 0.00 0.00 5.18
1054 1112 2.914777 CTTCCTAGCTCCCACGCAGC 62.915 65.000 0.00 0.00 37.12 5.25
1065 1137 3.352222 ACGCAGCAAGCAGAGCAC 61.352 61.111 0.00 0.00 46.13 4.40
1077 1149 0.237761 CAGAGCACAGCAAAGCAGAC 59.762 55.000 0.00 0.00 0.00 3.51
1080 1155 0.179037 AGCACAGCAAAGCAGACAGA 60.179 50.000 0.00 0.00 0.00 3.41
1086 1161 1.072015 AGCAAAGCAGACAGAGCTCTT 59.928 47.619 15.27 5.77 42.53 2.85
1151 1226 1.004440 GAGCTTCGCCAACTGGACT 60.004 57.895 0.00 0.00 37.39 3.85
1605 1701 2.031516 CACCTGCAGCACTTCCTCG 61.032 63.158 8.66 0.00 0.00 4.63
1745 1841 1.828832 ACTTCGCTTGATCGATCGAC 58.171 50.000 22.06 14.65 38.37 4.20
1814 1947 6.347696 TGAATTTCTTGGCTTGTTTGTTCAT 58.652 32.000 0.00 0.00 0.00 2.57
1818 1958 2.886862 TGGCTTGTTTGTTCATGGTG 57.113 45.000 0.00 0.00 0.00 4.17
1851 1995 6.866010 TCACCTGCAGCTATGTAAATATTG 57.134 37.500 8.66 0.00 0.00 1.90
1854 1998 6.432162 CACCTGCAGCTATGTAAATATTGGAT 59.568 38.462 8.66 0.00 0.00 3.41
1872 2028 3.814283 TGGATTTTTGCCTGTGATTTTGC 59.186 39.130 0.00 0.00 0.00 3.68
1878 2034 0.109597 GCCTGTGATTTTGCCACTCG 60.110 55.000 0.00 0.00 35.66 4.18
1942 2114 4.343814 TCGGGTGCATCTATCAAAGTGATA 59.656 41.667 0.00 0.00 38.26 2.15
1943 2115 5.012046 TCGGGTGCATCTATCAAAGTGATAT 59.988 40.000 0.00 0.00 38.54 1.63
1944 2116 6.210584 TCGGGTGCATCTATCAAAGTGATATA 59.789 38.462 0.00 0.00 38.54 0.86
2118 4151 0.746923 ACGAGATGGTGACGATCGGA 60.747 55.000 20.98 2.07 36.74 4.55
2121 4154 0.106669 AGATGGTGACGATCGGAGGA 60.107 55.000 20.98 0.00 0.00 3.71
2161 4194 3.560503 GCTGCGTGCAAAACAAAGTATA 58.439 40.909 0.00 0.00 42.31 1.47
2162 4195 3.360758 GCTGCGTGCAAAACAAAGTATAC 59.639 43.478 0.00 0.00 42.31 1.47
2163 4196 4.783242 CTGCGTGCAAAACAAAGTATACT 58.217 39.130 0.00 0.00 0.00 2.12
2164 4197 5.176407 TGCGTGCAAAACAAAGTATACTT 57.824 34.783 12.50 12.50 37.91 2.24
2170 4203 4.615541 GCAAAACAAAGTATACTTCGTGCC 59.384 41.667 18.28 0.50 34.61 5.01
2204 4237 3.084579 CTCGCATGCTCCAACGAC 58.915 61.111 17.13 0.00 0.00 4.34
2210 4243 1.666888 GCATGCTCCAACGACCAAAAG 60.667 52.381 11.37 0.00 0.00 2.27
2215 4248 1.532868 CTCCAACGACCAAAAGCTCAG 59.467 52.381 0.00 0.00 0.00 3.35
2217 4250 1.946768 CCAACGACCAAAAGCTCAGAA 59.053 47.619 0.00 0.00 0.00 3.02
2227 4260 7.148918 CGACCAAAAGCTCAGAATTAAATGTTG 60.149 37.037 0.00 0.00 0.00 3.33
2230 4263 7.041916 CCAAAAGCTCAGAATTAAATGTTGCAA 60.042 33.333 0.00 0.00 0.00 4.08
2266 4299 3.814504 AACTGTGGATGTTCCCAAGAT 57.185 42.857 0.00 0.00 38.06 2.40
2272 4305 4.018506 TGTGGATGTTCCCAAGATATGTGT 60.019 41.667 0.00 0.00 38.06 3.72
2285 4318 4.533815 AGATATGTGTCCACGTCCTCTAA 58.466 43.478 0.00 0.00 0.00 2.10
2296 4329 6.017357 GTCCACGTCCTCTAAAAAGTTCAAAT 60.017 38.462 0.00 0.00 0.00 2.32
2297 4330 6.017440 TCCACGTCCTCTAAAAAGTTCAAATG 60.017 38.462 0.00 0.00 0.00 2.32
2307 4340 8.751335 TCTAAAAAGTTCAAATGCAAATTCGAC 58.249 29.630 0.00 0.00 0.00 4.20
2321 4354 6.074409 TGCAAATTCGACATGAACAATTGAAC 60.074 34.615 13.59 6.09 40.00 3.18
2322 4355 6.507361 CAAATTCGACATGAACAATTGAACG 58.493 36.000 13.59 6.83 40.00 3.95
2323 4356 4.804608 TTCGACATGAACAATTGAACGT 57.195 36.364 13.59 4.11 0.00 3.99
2324 4357 5.908916 TTCGACATGAACAATTGAACGTA 57.091 34.783 13.59 0.00 0.00 3.57
2325 4358 5.509605 TCGACATGAACAATTGAACGTAG 57.490 39.130 13.59 2.78 0.00 3.51
2326 4359 5.224135 TCGACATGAACAATTGAACGTAGA 58.776 37.500 13.59 4.97 0.00 2.59
2327 4360 5.344933 TCGACATGAACAATTGAACGTAGAG 59.655 40.000 13.59 0.00 0.00 2.43
2328 4361 5.344933 CGACATGAACAATTGAACGTAGAGA 59.655 40.000 13.59 0.00 0.00 3.10
2331 4364 7.352739 ACATGAACAATTGAACGTAGAGAAAC 58.647 34.615 13.59 0.00 0.00 2.78
2332 4365 6.912203 TGAACAATTGAACGTAGAGAAACA 57.088 33.333 13.59 0.00 0.00 2.83
2397 4430 2.167487 AGCAAAAACACCACGGTTTCAT 59.833 40.909 0.00 0.00 39.93 2.57
2430 4463 8.464770 TTTGTCTTTTTCTTTCTCAATGTGTG 57.535 30.769 0.00 0.00 0.00 3.82
2441 4474 9.434420 TCTTTCTCAATGTGTGTTTTGATTTTT 57.566 25.926 0.00 0.00 31.83 1.94
2641 4676 7.491372 CGAAAGAAGATACTGCTACCAATTGTA 59.509 37.037 4.43 0.00 0.00 2.41
2642 4677 9.331282 GAAAGAAGATACTGCTACCAATTGTAT 57.669 33.333 4.43 0.00 0.00 2.29
2683 4718 1.609072 GGCTTTAATTCGGGATGAGGC 59.391 52.381 0.00 0.00 0.00 4.70
2707 4742 2.666272 TAATTGCACAAGGACCACCA 57.334 45.000 0.00 0.00 38.94 4.17
2715 4750 3.476386 AGGACCACCAGTGCTCTG 58.524 61.111 8.84 8.84 45.33 3.35
2734 4769 1.456705 TTGGGCACTTTGGACCACC 60.457 57.895 0.00 0.00 31.65 4.61
2800 4835 6.425577 ACTGACTGCTTGTTTAAAACGTTA 57.574 33.333 0.00 0.00 0.00 3.18
2813 4848 9.654417 TGTTTAAAACGTTAATCTTTCTACAGC 57.346 29.630 0.00 0.00 0.00 4.40
2817 4852 6.467723 AACGTTAATCTTTCTACAGCAGTG 57.532 37.500 0.00 0.00 0.00 3.66
2831 4866 7.847096 TCTACAGCAGTGGAAATTATTGACTA 58.153 34.615 0.00 0.00 31.77 2.59
2843 4878 9.190317 GGAAATTATTGACTAAGGAGGTTGATT 57.810 33.333 0.00 0.00 0.00 2.57
2873 4908 0.463620 GGAGGAGCTGACATCCAGAC 59.536 60.000 0.00 0.00 45.78 3.51
2874 4909 1.189752 GAGGAGCTGACATCCAGACA 58.810 55.000 0.00 0.00 45.78 3.41
2875 4910 1.136695 GAGGAGCTGACATCCAGACAG 59.863 57.143 0.00 0.00 45.78 3.51
2876 4911 1.189752 GGAGCTGACATCCAGACAGA 58.810 55.000 0.00 0.00 45.78 3.41
2879 4914 2.233431 GAGCTGACATCCAGACAGAGTT 59.767 50.000 0.00 0.00 45.78 3.01
2881 4916 2.873609 CTGACATCCAGACAGAGTTCG 58.126 52.381 0.00 0.00 45.78 3.95
2882 4917 1.067565 TGACATCCAGACAGAGTTCGC 60.068 52.381 0.00 0.00 0.00 4.70
2883 4918 0.969149 ACATCCAGACAGAGTTCGCA 59.031 50.000 0.00 0.00 0.00 5.10
2884 4919 1.552337 ACATCCAGACAGAGTTCGCAT 59.448 47.619 0.00 0.00 0.00 4.73
2885 4920 1.931841 CATCCAGACAGAGTTCGCATG 59.068 52.381 0.00 0.00 0.00 4.06
2913 4948 2.631062 TCTTCCCTCGCTCAACAAACTA 59.369 45.455 0.00 0.00 0.00 2.24
2957 4992 4.502087 GCTGTCTTCTTTTGGGCTTCATTT 60.502 41.667 0.00 0.00 0.00 2.32
3065 5100 2.604614 GGCTGTTGATGTTGTTTCGGTC 60.605 50.000 0.00 0.00 0.00 4.79
3084 5119 1.160137 CTTGTGGTTGCTACTCTGCC 58.840 55.000 0.00 0.00 0.00 4.85
3121 5156 0.889186 AAGTCGGGCGCATGTCTTTT 60.889 50.000 10.83 0.00 0.00 2.27
3122 5157 1.134694 GTCGGGCGCATGTCTTTTC 59.865 57.895 10.83 0.00 0.00 2.29
3123 5158 1.003839 TCGGGCGCATGTCTTTTCT 60.004 52.632 10.83 0.00 0.00 2.52
3124 5159 1.019278 TCGGGCGCATGTCTTTTCTC 61.019 55.000 10.83 0.00 0.00 2.87
3125 5160 1.021390 CGGGCGCATGTCTTTTCTCT 61.021 55.000 10.83 0.00 0.00 3.10
3127 5162 2.565841 GGGCGCATGTCTTTTCTCTAT 58.434 47.619 10.83 0.00 0.00 1.98
3128 5163 2.289002 GGGCGCATGTCTTTTCTCTATG 59.711 50.000 10.83 0.00 0.00 2.23
3130 5165 3.623060 GGCGCATGTCTTTTCTCTATGAA 59.377 43.478 10.83 0.00 0.00 2.57
3131 5166 4.494855 GGCGCATGTCTTTTCTCTATGAAC 60.495 45.833 10.83 0.00 33.88 3.18
3159 5205 3.637432 TGGTTGTGCTCTTATTTTTGCG 58.363 40.909 0.00 0.00 0.00 4.85
3186 5232 2.014068 GCTACAGTGGAAGGGCACATC 61.014 57.143 0.00 0.00 0.00 3.06
3187 5233 1.556911 CTACAGTGGAAGGGCACATCT 59.443 52.381 0.00 0.00 0.00 2.90
3199 5245 6.094186 GGAAGGGCACATCTTTTTCTAGTTAG 59.906 42.308 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.716531 GACCCAACTTTATACTAACTTTGTACT 57.283 33.333 0.00 0.00 0.00 2.73
27 28 9.492973 TGACCCAACTTTATACTAACTTTGTAC 57.507 33.333 0.00 0.00 0.00 2.90
29 30 9.227777 GATGACCCAACTTTATACTAACTTTGT 57.772 33.333 0.00 0.00 0.00 2.83
30 31 9.449719 AGATGACCCAACTTTATACTAACTTTG 57.550 33.333 0.00 0.00 0.00 2.77
41 42 8.293867 CGTTTCAAAATAGATGACCCAACTTTA 58.706 33.333 0.00 0.00 0.00 1.85
42 43 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
43 44 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
44 45 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
45 46 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
46 47 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
47 48 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
48 49 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
49 50 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
50 51 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
51 52 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
52 53 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
53 54 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
54 55 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
55 56 5.731591 AGTACTCCCTCCGTTTCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
56 57 5.750352 AGTACTCCCTCCGTTTCAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
57 58 4.635699 AGTACTCCCTCCGTTTCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
58 59 4.426736 AAGTACTCCCTCCGTTTCAAAA 57.573 40.909 0.00 0.00 0.00 2.44
59 60 4.131596 CAAAGTACTCCCTCCGTTTCAAA 58.868 43.478 0.00 0.00 0.00 2.69
60 61 3.135167 ACAAAGTACTCCCTCCGTTTCAA 59.865 43.478 0.00 0.00 0.00 2.69
61 62 2.701951 ACAAAGTACTCCCTCCGTTTCA 59.298 45.455 0.00 0.00 0.00 2.69
62 63 3.397849 ACAAAGTACTCCCTCCGTTTC 57.602 47.619 0.00 0.00 0.00 2.78
63 64 4.346127 ACTTACAAAGTACTCCCTCCGTTT 59.654 41.667 0.00 0.00 40.69 3.60
64 65 3.899980 ACTTACAAAGTACTCCCTCCGTT 59.100 43.478 0.00 0.00 40.69 4.44
65 66 3.257624 CACTTACAAAGTACTCCCTCCGT 59.742 47.826 0.00 0.00 40.46 4.69
66 67 3.257624 ACACTTACAAAGTACTCCCTCCG 59.742 47.826 0.00 0.00 40.46 4.63
67 68 4.886496 ACACTTACAAAGTACTCCCTCC 57.114 45.455 0.00 0.00 40.46 4.30
68 69 7.275123 CGAAATACACTTACAAAGTACTCCCTC 59.725 40.741 0.00 0.00 40.46 4.30
69 70 7.039504 TCGAAATACACTTACAAAGTACTCCCT 60.040 37.037 0.00 0.00 40.46 4.20
70 71 7.092716 TCGAAATACACTTACAAAGTACTCCC 58.907 38.462 0.00 0.00 40.46 4.30
71 72 7.275123 CCTCGAAATACACTTACAAAGTACTCC 59.725 40.741 0.00 0.00 40.46 3.85
72 73 8.025445 TCCTCGAAATACACTTACAAAGTACTC 58.975 37.037 0.00 0.00 40.46 2.59
73 74 7.811713 GTCCTCGAAATACACTTACAAAGTACT 59.188 37.037 0.00 0.00 40.46 2.73
74 75 7.596248 TGTCCTCGAAATACACTTACAAAGTAC 59.404 37.037 0.00 0.00 40.46 2.73
75 76 7.660112 TGTCCTCGAAATACACTTACAAAGTA 58.340 34.615 0.00 0.00 40.46 2.24
76 77 6.518493 TGTCCTCGAAATACACTTACAAAGT 58.482 36.000 0.00 0.00 44.06 2.66
77 78 6.866770 TCTGTCCTCGAAATACACTTACAAAG 59.133 38.462 0.00 0.00 0.00 2.77
78 79 6.751157 TCTGTCCTCGAAATACACTTACAAA 58.249 36.000 0.00 0.00 0.00 2.83
79 80 6.335471 TCTGTCCTCGAAATACACTTACAA 57.665 37.500 0.00 0.00 0.00 2.41
80 81 5.970317 TCTGTCCTCGAAATACACTTACA 57.030 39.130 0.00 0.00 0.00 2.41
83 84 8.692710 TGTTATATCTGTCCTCGAAATACACTT 58.307 33.333 0.00 0.00 0.00 3.16
84 85 8.234136 TGTTATATCTGTCCTCGAAATACACT 57.766 34.615 0.00 0.00 0.00 3.55
85 86 8.867112 TTGTTATATCTGTCCTCGAAATACAC 57.133 34.615 0.00 0.00 0.00 2.90
86 87 9.692749 GATTGTTATATCTGTCCTCGAAATACA 57.307 33.333 0.00 0.00 0.00 2.29
87 88 9.692749 TGATTGTTATATCTGTCCTCGAAATAC 57.307 33.333 0.00 0.00 0.00 1.89
89 90 9.784531 ATTGATTGTTATATCTGTCCTCGAAAT 57.215 29.630 0.00 0.00 0.00 2.17
90 91 9.613428 AATTGATTGTTATATCTGTCCTCGAAA 57.387 29.630 0.00 0.00 0.00 3.46
134 135 5.159925 CGCATGTGGTGAAATTTATCAACA 58.840 37.500 0.00 0.00 44.48 3.33
135 136 5.060816 CACGCATGTGGTGAAATTTATCAAC 59.939 40.000 11.65 0.00 42.59 3.18
136 137 5.159925 CACGCATGTGGTGAAATTTATCAA 58.840 37.500 11.65 0.00 42.59 2.57
137 138 4.731720 CACGCATGTGGTGAAATTTATCA 58.268 39.130 11.65 0.00 42.59 2.15
138 139 3.547468 GCACGCATGTGGTGAAATTTATC 59.453 43.478 19.12 0.22 46.51 1.75
139 140 3.056962 TGCACGCATGTGGTGAAATTTAT 60.057 39.130 19.12 0.00 46.51 1.40
140 141 2.294512 TGCACGCATGTGGTGAAATTTA 59.705 40.909 19.12 0.34 46.51 1.40
141 142 1.068281 TGCACGCATGTGGTGAAATTT 59.932 42.857 19.12 0.00 46.51 1.82
142 143 0.672889 TGCACGCATGTGGTGAAATT 59.327 45.000 19.12 0.00 46.51 1.82
143 144 0.672889 TTGCACGCATGTGGTGAAAT 59.327 45.000 19.12 0.00 46.51 2.17
144 145 0.457443 TTTGCACGCATGTGGTGAAA 59.543 45.000 19.12 13.70 46.51 2.69
145 146 0.672889 ATTTGCACGCATGTGGTGAA 59.327 45.000 19.12 8.96 46.51 3.18
146 147 0.039346 CATTTGCACGCATGTGGTGA 60.039 50.000 19.12 3.22 46.51 4.02
147 148 0.318869 ACATTTGCACGCATGTGGTG 60.319 50.000 11.65 12.35 46.51 4.17
148 149 0.388659 AACATTTGCACGCATGTGGT 59.611 45.000 11.65 0.00 46.51 4.16
149 150 0.785378 CAACATTTGCACGCATGTGG 59.215 50.000 11.65 0.76 46.51 4.17
151 152 2.222007 AACAACATTTGCACGCATGT 57.778 40.000 0.00 0.00 0.00 3.21
152 153 3.589061 AAAACAACATTTGCACGCATG 57.411 38.095 0.00 0.00 0.00 4.06
153 154 3.373439 ACAAAAACAACATTTGCACGCAT 59.627 34.783 0.00 0.00 40.58 4.73
154 155 2.738846 ACAAAAACAACATTTGCACGCA 59.261 36.364 0.00 0.00 40.58 5.24
155 156 3.089982 CACAAAAACAACATTTGCACGC 58.910 40.909 0.00 0.00 40.58 5.34
156 157 4.319235 ACACAAAAACAACATTTGCACG 57.681 36.364 0.00 0.00 40.58 5.34
157 158 6.998338 TGATACACAAAAACAACATTTGCAC 58.002 32.000 0.00 0.00 40.58 4.57
158 159 7.601073 TTGATACACAAAAACAACATTTGCA 57.399 28.000 0.00 0.00 40.58 4.08
159 160 8.945930 CAATTGATACACAAAAACAACATTTGC 58.054 29.630 0.00 0.00 42.03 3.68
160 161 9.435802 CCAATTGATACACAAAAACAACATTTG 57.564 29.630 7.12 0.00 42.03 2.32
161 162 9.171877 ACCAATTGATACACAAAAACAACATTT 57.828 25.926 7.12 0.00 42.03 2.32
162 163 8.729805 ACCAATTGATACACAAAAACAACATT 57.270 26.923 7.12 0.00 42.03 2.71
163 164 8.610896 CAACCAATTGATACACAAAAACAACAT 58.389 29.630 7.12 0.00 42.03 2.71
164 165 7.413438 GCAACCAATTGATACACAAAAACAACA 60.413 33.333 7.12 0.00 42.03 3.33
165 166 6.904543 GCAACCAATTGATACACAAAAACAAC 59.095 34.615 7.12 0.00 42.03 3.32
166 167 6.595326 TGCAACCAATTGATACACAAAAACAA 59.405 30.769 7.12 0.00 42.03 2.83
167 168 6.108687 TGCAACCAATTGATACACAAAAACA 58.891 32.000 7.12 0.00 42.03 2.83
168 169 6.595772 TGCAACCAATTGATACACAAAAAC 57.404 33.333 7.12 0.00 42.03 2.43
169 170 7.467623 GTTTGCAACCAATTGATACACAAAAA 58.532 30.769 7.12 0.00 42.03 1.94
170 171 6.237942 CGTTTGCAACCAATTGATACACAAAA 60.238 34.615 7.12 0.00 42.03 2.44
171 172 5.233050 CGTTTGCAACCAATTGATACACAAA 59.767 36.000 7.12 8.04 42.03 2.83
172 173 4.742167 CGTTTGCAACCAATTGATACACAA 59.258 37.500 7.12 2.15 42.95 3.33
173 174 4.294232 CGTTTGCAACCAATTGATACACA 58.706 39.130 7.12 0.00 38.15 3.72
174 175 3.121113 GCGTTTGCAACCAATTGATACAC 59.879 43.478 7.12 0.00 42.15 2.90
175 176 3.312828 GCGTTTGCAACCAATTGATACA 58.687 40.909 7.12 0.00 42.15 2.29
176 177 3.970828 GCGTTTGCAACCAATTGATAC 57.029 42.857 7.12 0.00 42.15 2.24
189 190 1.156645 TTGCCCATTTGTGCGTTTGC 61.157 50.000 0.00 0.00 43.20 3.68
190 191 1.293924 TTTGCCCATTTGTGCGTTTG 58.706 45.000 0.00 0.00 0.00 2.93
191 192 1.668237 GTTTTGCCCATTTGTGCGTTT 59.332 42.857 0.00 0.00 0.00 3.60
192 193 1.294857 GTTTTGCCCATTTGTGCGTT 58.705 45.000 0.00 0.00 0.00 4.84
193 194 0.176680 TGTTTTGCCCATTTGTGCGT 59.823 45.000 0.00 0.00 0.00 5.24
194 195 0.581053 GTGTTTTGCCCATTTGTGCG 59.419 50.000 0.00 0.00 0.00 5.34
195 196 0.581053 CGTGTTTTGCCCATTTGTGC 59.419 50.000 0.00 0.00 0.00 4.57
196 197 2.126467 CTCGTGTTTTGCCCATTTGTG 58.874 47.619 0.00 0.00 0.00 3.33
197 198 1.068434 CCTCGTGTTTTGCCCATTTGT 59.932 47.619 0.00 0.00 0.00 2.83
198 199 1.339610 TCCTCGTGTTTTGCCCATTTG 59.660 47.619 0.00 0.00 0.00 2.32
199 200 1.613437 CTCCTCGTGTTTTGCCCATTT 59.387 47.619 0.00 0.00 0.00 2.32
200 201 1.247567 CTCCTCGTGTTTTGCCCATT 58.752 50.000 0.00 0.00 0.00 3.16
201 202 1.244019 GCTCCTCGTGTTTTGCCCAT 61.244 55.000 0.00 0.00 0.00 4.00
202 203 1.896660 GCTCCTCGTGTTTTGCCCA 60.897 57.895 0.00 0.00 0.00 5.36
203 204 2.626780 GGCTCCTCGTGTTTTGCCC 61.627 63.158 0.00 0.00 34.81 5.36
204 205 2.954611 GGCTCCTCGTGTTTTGCC 59.045 61.111 0.00 0.00 0.00 4.52
205 206 1.298859 ATCGGCTCCTCGTGTTTTGC 61.299 55.000 0.00 0.00 0.00 3.68
206 207 0.443869 CATCGGCTCCTCGTGTTTTG 59.556 55.000 0.00 0.00 0.00 2.44
207 208 0.673644 CCATCGGCTCCTCGTGTTTT 60.674 55.000 0.00 0.00 0.00 2.43
208 209 1.079127 CCATCGGCTCCTCGTGTTT 60.079 57.895 0.00 0.00 0.00 2.83
209 210 1.949847 CTCCATCGGCTCCTCGTGTT 61.950 60.000 0.00 0.00 0.00 3.32
210 211 2.362503 TCCATCGGCTCCTCGTGT 60.363 61.111 0.00 0.00 0.00 4.49
211 212 1.949847 AACTCCATCGGCTCCTCGTG 61.950 60.000 0.00 0.00 0.00 4.35
212 213 0.395311 TAACTCCATCGGCTCCTCGT 60.395 55.000 0.00 0.00 0.00 4.18
213 214 0.962489 ATAACTCCATCGGCTCCTCG 59.038 55.000 0.00 0.00 0.00 4.63
214 215 3.306156 GGTAATAACTCCATCGGCTCCTC 60.306 52.174 0.00 0.00 0.00 3.71
215 216 2.633481 GGTAATAACTCCATCGGCTCCT 59.367 50.000 0.00 0.00 0.00 3.69
216 217 2.367567 TGGTAATAACTCCATCGGCTCC 59.632 50.000 0.00 0.00 0.00 4.70
217 218 3.746045 TGGTAATAACTCCATCGGCTC 57.254 47.619 0.00 0.00 0.00 4.70
218 219 5.818678 TTATGGTAATAACTCCATCGGCT 57.181 39.130 0.00 0.00 42.56 5.52
219 220 7.448748 AATTTATGGTAATAACTCCATCGGC 57.551 36.000 0.00 0.00 42.56 5.54
220 221 9.677567 CAAAATTTATGGTAATAACTCCATCGG 57.322 33.333 0.00 0.00 42.56 4.18
231 232 9.500701 AACCAGGGATACAAAATTTATGGTAAT 57.499 29.630 0.00 0.00 37.54 1.89
232 233 8.903059 AACCAGGGATACAAAATTTATGGTAA 57.097 30.769 0.00 0.00 37.54 2.85
238 239 7.676043 TCATCCAAACCAGGGATACAAAATTTA 59.324 33.333 0.00 0.00 43.24 1.40
242 243 5.004361 TCATCCAAACCAGGGATACAAAA 57.996 39.130 0.00 0.00 43.24 2.44
245 246 3.527253 ACATCATCCAAACCAGGGATACA 59.473 43.478 0.00 0.00 43.24 2.29
254 255 2.627945 TCTACGCACATCATCCAAACC 58.372 47.619 0.00 0.00 0.00 3.27
270 271 4.574828 ACACATTTTCCCGCATACATCTAC 59.425 41.667 0.00 0.00 0.00 2.59
272 273 3.620488 ACACATTTTCCCGCATACATCT 58.380 40.909 0.00 0.00 0.00 2.90
273 274 4.370364 AACACATTTTCCCGCATACATC 57.630 40.909 0.00 0.00 0.00 3.06
275 276 3.365465 CGAAACACATTTTCCCGCATACA 60.365 43.478 0.00 0.00 0.00 2.29
276 277 3.168193 CGAAACACATTTTCCCGCATAC 58.832 45.455 0.00 0.00 0.00 2.39
277 278 2.814919 ACGAAACACATTTTCCCGCATA 59.185 40.909 0.00 0.00 0.00 3.14
278 279 1.611491 ACGAAACACATTTTCCCGCAT 59.389 42.857 0.00 0.00 0.00 4.73
279 280 1.002251 GACGAAACACATTTTCCCGCA 60.002 47.619 0.00 0.00 0.00 5.69
280 281 1.002251 TGACGAAACACATTTTCCCGC 60.002 47.619 0.00 0.00 0.00 6.13
281 282 2.289547 AGTGACGAAACACATTTTCCCG 59.710 45.455 12.49 0.00 42.45 5.14
331 376 1.629043 TACCCCCGCTATGATCTGAC 58.371 55.000 0.00 0.00 0.00 3.51
340 385 1.143481 GGGCTTTTATTACCCCCGCTA 59.857 52.381 0.00 0.00 37.70 4.26
379 424 5.942872 ACAAAATCACTCATCGTTTCATCC 58.057 37.500 0.00 0.00 0.00 3.51
427 472 6.382859 ACCCATCTGTCTGTTTTTACCTTTTT 59.617 34.615 0.00 0.00 0.00 1.94
428 473 5.897250 ACCCATCTGTCTGTTTTTACCTTTT 59.103 36.000 0.00 0.00 0.00 2.27
473 518 4.540715 TCAGCTATCTCAGAGAATGACCA 58.459 43.478 3.63 0.00 33.22 4.02
516 561 1.745890 CTTGGAGACCGTGGTCACA 59.254 57.895 20.51 15.37 46.76 3.58
546 591 1.287503 GAGGAGACGGATGGATCGC 59.712 63.158 0.00 0.00 0.00 4.58
547 592 1.528292 GGGAGGAGACGGATGGATCG 61.528 65.000 0.00 0.00 0.00 3.69
957 1015 2.885644 CAGCCGTTGGATCGTCGG 60.886 66.667 14.53 14.53 45.94 4.79
967 1025 4.988598 CAGCGTCCACCAGCCGTT 62.989 66.667 0.00 0.00 0.00 4.44
1043 1101 3.429141 CTGCTTGCTGCGTGGGAG 61.429 66.667 0.00 0.00 46.63 4.30
1044 1102 3.889134 CTCTGCTTGCTGCGTGGGA 62.889 63.158 0.00 0.00 46.63 4.37
1045 1103 3.429141 CTCTGCTTGCTGCGTGGG 61.429 66.667 0.00 0.00 46.63 4.61
1047 1105 3.351416 TGCTCTGCTTGCTGCGTG 61.351 61.111 0.00 0.00 46.63 5.34
1048 1106 3.352222 GTGCTCTGCTTGCTGCGT 61.352 61.111 0.00 0.00 46.63 5.24
1050 1108 2.561885 CTGTGCTCTGCTTGCTGC 59.438 61.111 0.00 0.00 43.25 5.25
1051 1109 1.792118 TTGCTGTGCTCTGCTTGCTG 61.792 55.000 16.89 0.00 38.91 4.41
1053 1111 0.663568 CTTTGCTGTGCTCTGCTTGC 60.664 55.000 16.89 1.52 38.91 4.01
1054 1112 0.663568 GCTTTGCTGTGCTCTGCTTG 60.664 55.000 16.89 9.07 38.91 4.01
1059 1131 0.179037 TGTCTGCTTTGCTGTGCTCT 60.179 50.000 0.00 0.00 0.00 4.09
1065 1137 0.797542 GAGCTCTGTCTGCTTTGCTG 59.202 55.000 6.43 0.00 41.30 4.41
1104 1179 0.897621 TCACTCATCGCCATGTCAGT 59.102 50.000 0.00 0.00 0.00 3.41
1108 1183 0.610174 AGTGTCACTCATCGCCATGT 59.390 50.000 0.00 0.00 0.00 3.21
1151 1226 1.086067 CGTAGCGGTAGAGGTCGTCA 61.086 60.000 0.00 0.00 0.00 4.35
1448 1526 2.746277 AAGTTGATGACGGGCGCC 60.746 61.111 21.18 21.18 0.00 6.53
1512 1605 4.452733 GTCGAAGGACAGGGCGGG 62.453 72.222 0.00 0.00 42.91 6.13
1718 1814 3.067601 TCGATCAAGCGAAGTAGCCATTA 59.932 43.478 0.00 0.00 37.35 1.90
1771 1867 4.383774 TCAAACACAAGCTCGATTAACG 57.616 40.909 0.00 0.00 44.09 3.18
1773 1869 7.648142 AGAAATTCAAACACAAGCTCGATTAA 58.352 30.769 0.00 0.00 0.00 1.40
1774 1870 7.202016 AGAAATTCAAACACAAGCTCGATTA 57.798 32.000 0.00 0.00 0.00 1.75
1775 1871 6.076981 AGAAATTCAAACACAAGCTCGATT 57.923 33.333 0.00 0.00 0.00 3.34
1818 1958 1.386533 CTGCAGGTGATGGATGAACC 58.613 55.000 5.57 0.00 39.54 3.62
1851 1995 3.189080 GGCAAAATCACAGGCAAAAATCC 59.811 43.478 0.00 0.00 0.00 3.01
1854 1998 2.941720 GTGGCAAAATCACAGGCAAAAA 59.058 40.909 0.00 0.00 39.62 1.94
1878 2034 1.882912 TGAGCATCATAATCCGCACC 58.117 50.000 0.00 0.00 42.56 5.01
1922 2094 7.615403 TCCTATATCACTTTGATAGATGCACC 58.385 38.462 0.00 0.00 42.04 5.01
1923 2095 9.149225 CTTCCTATATCACTTTGATAGATGCAC 57.851 37.037 0.00 0.00 42.04 4.57
1931 2103 9.386122 ACCTATCACTTCCTATATCACTTTGAT 57.614 33.333 0.00 0.00 40.72 2.57
1942 2114 3.051341 TCCACCCACCTATCACTTCCTAT 60.051 47.826 0.00 0.00 0.00 2.57
1943 2115 2.316677 TCCACCCACCTATCACTTCCTA 59.683 50.000 0.00 0.00 0.00 2.94
1944 2116 1.080498 TCCACCCACCTATCACTTCCT 59.920 52.381 0.00 0.00 0.00 3.36
1954 2126 0.253820 ATCCATCCTTCCACCCACCT 60.254 55.000 0.00 0.00 0.00 4.00
2029 2201 2.515523 CTCCTCTGCCGGCCAATG 60.516 66.667 26.77 11.77 0.00 2.82
2069 2241 1.031235 CGCATGCAATTATGTCCCCA 58.969 50.000 19.57 0.00 0.00 4.96
2118 4151 4.384056 CATGACAAGTCTGACTTTGTCCT 58.616 43.478 29.13 23.19 36.03 3.85
2121 4154 3.562973 CAGCATGACAAGTCTGACTTTGT 59.437 43.478 19.89 19.23 39.69 2.83
2162 4195 1.515521 GAGTGTTTGGGGGCACGAAG 61.516 60.000 0.00 0.00 40.26 3.79
2163 4196 1.527380 GAGTGTTTGGGGGCACGAA 60.527 57.895 0.00 0.00 40.26 3.85
2164 4197 2.112297 GAGTGTTTGGGGGCACGA 59.888 61.111 0.00 0.00 40.26 4.35
2170 4203 1.369625 GAGCATACGAGTGTTTGGGG 58.630 55.000 0.00 0.00 0.00 4.96
2204 4237 6.424509 TGCAACATTTAATTCTGAGCTTTTGG 59.575 34.615 0.00 0.00 0.00 3.28
2245 4278 3.593442 TCTTGGGAACATCCACAGTTT 57.407 42.857 0.00 0.00 42.32 2.66
2246 4279 3.814504 ATCTTGGGAACATCCACAGTT 57.185 42.857 0.00 0.00 42.32 3.16
2249 4282 4.018506 ACACATATCTTGGGAACATCCACA 60.019 41.667 0.00 0.00 42.32 4.17
2255 4288 3.618752 CGTGGACACATATCTTGGGAACA 60.619 47.826 3.12 0.00 39.83 3.18
2266 4299 5.011329 ACTTTTTAGAGGACGTGGACACATA 59.989 40.000 0.00 0.00 0.00 2.29
2272 4305 4.675976 TGAACTTTTTAGAGGACGTGGA 57.324 40.909 0.00 0.00 0.00 4.02
2285 4318 6.900568 TGTCGAATTTGCATTTGAACTTTT 57.099 29.167 0.00 0.00 34.97 2.27
2296 4329 5.527033 TCAATTGTTCATGTCGAATTTGCA 58.473 33.333 5.13 0.00 35.63 4.08
2297 4330 6.291385 GTTCAATTGTTCATGTCGAATTTGC 58.709 36.000 5.13 0.00 35.63 3.68
2307 4340 7.351981 TGTTTCTCTACGTTCAATTGTTCATG 58.648 34.615 5.13 0.00 0.00 3.07
2397 4430 8.310382 TGAGAAAGAAAAAGACAAATCCAAACA 58.690 29.630 0.00 0.00 0.00 2.83
2459 4492 8.837788 TCTCAAGACATGTGCCTATTATTATG 57.162 34.615 1.15 0.00 0.00 1.90
2545 4579 0.251297 CCCAACCTTCACATGCTCCA 60.251 55.000 0.00 0.00 0.00 3.86
2613 4647 5.401531 TGGTAGCAGTATCTTCTTTCGTT 57.598 39.130 0.00 0.00 0.00 3.85
2625 4660 6.211587 ACACGTATACAATTGGTAGCAGTA 57.788 37.500 10.83 0.00 34.92 2.74
2641 4676 4.098960 CCAACTGGGTACATCTACACGTAT 59.901 45.833 0.00 0.00 0.00 3.06
2642 4677 3.444742 CCAACTGGGTACATCTACACGTA 59.555 47.826 0.00 0.00 0.00 3.57
2683 4718 4.096382 GGTGGTCCTTGTGCAATTATACAG 59.904 45.833 0.00 0.00 0.00 2.74
2715 4750 1.739667 GTGGTCCAAAGTGCCCAAC 59.260 57.895 0.00 0.00 0.00 3.77
2765 4800 0.179020 CAGTCAGTTGGCCTGTTGGA 60.179 55.000 3.32 0.00 42.19 3.53
2767 4802 0.820891 AGCAGTCAGTTGGCCTGTTG 60.821 55.000 3.32 0.00 42.19 3.33
2776 4811 5.305139 ACGTTTTAAACAAGCAGTCAGTT 57.695 34.783 8.61 0.00 0.00 3.16
2800 4835 8.814038 ATAATTTCCACTGCTGTAGAAAGATT 57.186 30.769 18.72 13.06 37.26 2.40
2813 4848 7.112779 ACCTCCTTAGTCAATAATTTCCACTG 58.887 38.462 0.00 0.00 0.00 3.66
2817 4852 8.753497 ATCAACCTCCTTAGTCAATAATTTCC 57.247 34.615 0.00 0.00 0.00 3.13
2831 4866 3.914426 AGCGATACAATCAACCTCCTT 57.086 42.857 0.00 0.00 0.00 3.36
2843 4878 1.134699 CAGCTCCTCCAAAGCGATACA 60.135 52.381 0.00 0.00 44.59 2.29
2846 4881 0.107945 GTCAGCTCCTCCAAAGCGAT 60.108 55.000 0.00 0.00 44.59 4.58
2882 4917 1.649664 CGAGGGAAGAAGCAGACATG 58.350 55.000 0.00 0.00 0.00 3.21
2883 4918 0.107945 GCGAGGGAAGAAGCAGACAT 60.108 55.000 0.00 0.00 0.00 3.06
2884 4919 1.188219 AGCGAGGGAAGAAGCAGACA 61.188 55.000 0.00 0.00 0.00 3.41
2885 4920 0.459411 GAGCGAGGGAAGAAGCAGAC 60.459 60.000 0.00 0.00 0.00 3.51
2913 4948 1.671901 GGAGAGCCTCAAGTAGCGCT 61.672 60.000 17.26 17.26 42.12 5.92
3001 5036 0.472471 ATAATACACGGCCACCAGGG 59.528 55.000 2.24 0.00 40.85 4.45
3041 5076 3.252215 CCGAAACAACATCAACAGCCTAA 59.748 43.478 0.00 0.00 0.00 2.69
3042 5077 2.811431 CCGAAACAACATCAACAGCCTA 59.189 45.455 0.00 0.00 0.00 3.93
3043 5078 1.608590 CCGAAACAACATCAACAGCCT 59.391 47.619 0.00 0.00 0.00 4.58
3046 5081 4.201910 ACAAGACCGAAACAACATCAACAG 60.202 41.667 0.00 0.00 0.00 3.16
3047 5082 3.692101 ACAAGACCGAAACAACATCAACA 59.308 39.130 0.00 0.00 0.00 3.33
3049 5084 3.066064 CCACAAGACCGAAACAACATCAA 59.934 43.478 0.00 0.00 0.00 2.57
3061 5096 1.000955 AGAGTAGCAACCACAAGACCG 59.999 52.381 0.00 0.00 0.00 4.79
3065 5100 1.160137 GGCAGAGTAGCAACCACAAG 58.840 55.000 0.00 0.00 35.83 3.16
3110 5145 5.220548 CCTGTTCATAGAGAAAAGACATGCG 60.221 44.000 0.00 0.00 43.17 4.73
3121 5156 3.474798 ACCAGGTCCTGTTCATAGAGA 57.525 47.619 17.85 0.00 0.00 3.10
3122 5157 3.261897 ACAACCAGGTCCTGTTCATAGAG 59.738 47.826 17.85 2.24 0.00 2.43
3123 5158 3.007940 CACAACCAGGTCCTGTTCATAGA 59.992 47.826 17.85 0.00 0.00 1.98
3124 5159 3.338249 CACAACCAGGTCCTGTTCATAG 58.662 50.000 17.85 3.69 0.00 2.23
3125 5160 2.552155 GCACAACCAGGTCCTGTTCATA 60.552 50.000 17.85 0.00 0.00 2.15
3127 5162 0.465460 GCACAACCAGGTCCTGTTCA 60.465 55.000 17.85 0.00 0.00 3.18
3128 5163 0.179018 AGCACAACCAGGTCCTGTTC 60.179 55.000 17.85 0.00 0.00 3.18
3130 5165 1.056700 AGAGCACAACCAGGTCCTGT 61.057 55.000 17.85 3.27 34.17 4.00
3131 5166 0.109342 AAGAGCACAACCAGGTCCTG 59.891 55.000 12.40 12.40 34.17 3.86
3159 5205 1.134670 CCTTCCACTGTAGCTAGTGCC 60.135 57.143 10.64 0.00 45.21 5.01


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

AutoCloner maintained by Alex Coulton.