Multiple sequence alignment - TraesCS1A01G426100

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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 TraesCS1A01G426100 chr1A 100.000 2794 0 0 1 2794 580924443 580927236 0.000000e+00 5160.0
1 TraesCS1A01G426100 chr1A 84.524 588 84 6 1172 1757 580893649 580894231 2.410000e-160 575.0
2 TraesCS1A01G426100 chr1A 98.760 242 3 0 1 242 593418682 593418441 5.530000e-117 431.0
3 TraesCS1A01G426100 chr1A 98.347 242 4 0 1 242 10888439 10888680 2.570000e-115 425.0
4 TraesCS1A01G426100 chr1A 98.347 242 4 0 1 242 497656773 497656532 2.570000e-115 425.0
5 TraesCS1A01G426100 chr1B 91.217 1389 73 24 814 2195 673925783 673927129 0.000000e+00 1844.0
6 TraesCS1A01G426100 chr1B 90.156 1412 86 24 814 2189 673893036 673894430 0.000000e+00 1788.0
7 TraesCS1A01G426100 chr1B 86.178 1078 125 19 864 1924 673889116 673890186 0.000000e+00 1144.0
8 TraesCS1A01G426100 chr1B 86.323 892 85 16 1303 2187 673915101 673915962 0.000000e+00 937.0
9 TraesCS1A01G426100 chr1B 90.000 560 48 3 2237 2790 673927377 673927934 0.000000e+00 717.0
10 TraesCS1A01G426100 chr1B 89.821 560 48 9 237 792 673917481 673918035 0.000000e+00 710.0
11 TraesCS1A01G426100 chr1B 82.788 825 101 27 985 1792 673855505 673856305 0.000000e+00 699.0
12 TraesCS1A01G426100 chr1B 92.020 401 32 0 2392 2792 673895155 673895555 5.220000e-157 564.0
13 TraesCS1A01G426100 chr1B 82.952 393 30 20 428 814 673892608 673892969 1.250000e-83 320.0
14 TraesCS1A01G426100 chr1B 82.952 393 30 20 428 814 673925355 673925716 1.250000e-83 320.0
15 TraesCS1A01G426100 chr1B 88.406 138 9 4 1921 2058 673890301 673890431 2.880000e-35 159.0
16 TraesCS1A01G426100 chr1B 97.436 39 1 0 2369 2407 673894684 673894722 1.800000e-07 67.6
17 TraesCS1A01G426100 chr1D 90.654 1391 93 20 814 2187 483901831 483903201 0.000000e+00 1814.0
18 TraesCS1A01G426100 chr1D 91.222 581 45 6 237 814 483901188 483901765 0.000000e+00 785.0
19 TraesCS1A01G426100 chr1D 83.496 818 99 23 985 1792 483680698 483681489 0.000000e+00 730.0
20 TraesCS1A01G426100 chr1D 81.517 936 121 35 881 1792 483865024 483865931 0.000000e+00 723.0
21 TraesCS1A01G426100 chr1D 83.210 673 93 14 1172 1841 483895754 483896409 1.430000e-167 599.0
22 TraesCS1A01G426100 chr1D 90.370 405 25 6 2392 2794 483903778 483904170 1.150000e-143 520.0
23 TraesCS1A01G426100 chr7A 99.587 242 1 0 1 242 139511000 139511241 2.550000e-120 442.0
24 TraesCS1A01G426100 chr7A 99.174 242 2 0 1 242 43328837 43329078 1.190000e-118 436.0
25 TraesCS1A01G426100 chr3A 99.174 242 2 0 1 242 63978329 63978570 1.190000e-118 436.0
26 TraesCS1A01G426100 chr6A 98.760 242 3 0 1 242 521535818 521535577 5.530000e-117 431.0
27 TraesCS1A01G426100 chr4A 98.760 242 3 0 1 242 597490831 597491072 5.530000e-117 431.0
28 TraesCS1A01G426100 chr4A 98.760 242 3 0 1 242 640951337 640951578 5.530000e-117 431.0


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 TraesCS1A01G426100 chr1A 580924443 580927236 2793 False 5160.000000 5160 100.000000 1 2794 1 chr1A.!!$F3 2793
1 TraesCS1A01G426100 chr1A 580893649 580894231 582 False 575.000000 575 84.524000 1172 1757 1 chr1A.!!$F2 585
2 TraesCS1A01G426100 chr1B 673925355 673927934 2579 False 960.333333 1844 88.056333 428 2790 3 chr1B.!!$F4 2362
3 TraesCS1A01G426100 chr1B 673915101 673918035 2934 False 823.500000 937 88.072000 237 2187 2 chr1B.!!$F3 1950
4 TraesCS1A01G426100 chr1B 673855505 673856305 800 False 699.000000 699 82.788000 985 1792 1 chr1B.!!$F1 807
5 TraesCS1A01G426100 chr1B 673889116 673895555 6439 False 673.766667 1788 89.524667 428 2792 6 chr1B.!!$F2 2364
6 TraesCS1A01G426100 chr1D 483901188 483904170 2982 False 1039.666667 1814 90.748667 237 2794 3 chr1D.!!$F4 2557
7 TraesCS1A01G426100 chr1D 483680698 483681489 791 False 730.000000 730 83.496000 985 1792 1 chr1D.!!$F1 807
8 TraesCS1A01G426100 chr1D 483865024 483865931 907 False 723.000000 723 81.517000 881 1792 1 chr1D.!!$F2 911
9 TraesCS1A01G426100 chr1D 483895754 483896409 655 False 599.000000 599 83.210000 1172 1841 1 chr1D.!!$F3 669

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
142 143 0.032678 CCTCATATCTCGCGGTGCTT 59.967 55.0 6.13 0.0 0.0 3.91 F
291 293 0.099791 CGTGTTGGTCGCTTTTTGGT 59.900 50.0 0.00 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 4368 0.846693 GCAGTGGTGGGAATAGGGAT 59.153 55.0 0.0 0.0 0.0 3.85 R
2272 5719 0.308993 GCCAGGATAACGAGCAATGC 59.691 55.0 0.0 0.0 0.0 3.56 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
41 42 3.787001 CGCACCCTCCTCCCCTTC 61.787 72.222 0.00 0.00 0.00 3.46
42 43 3.412408 GCACCCTCCTCCCCTTCC 61.412 72.222 0.00 0.00 0.00 3.46
44 45 4.040198 ACCCTCCTCCCCTTCCCC 62.040 72.222 0.00 0.00 0.00 4.81
45 46 3.711782 CCCTCCTCCCCTTCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
47 48 1.690148 CCCTCCTCCCCTTCCCCTAT 61.690 65.000 0.00 0.00 0.00 2.57
48 49 1.177104 CCTCCTCCCCTTCCCCTATA 58.823 60.000 0.00 0.00 0.00 1.31
49 50 1.731062 CCTCCTCCCCTTCCCCTATAT 59.269 57.143 0.00 0.00 0.00 0.86
50 51 2.940728 CCTCCTCCCCTTCCCCTATATA 59.059 54.545 0.00 0.00 0.00 0.86
51 52 3.542402 CCTCCTCCCCTTCCCCTATATAT 59.458 52.174 0.00 0.00 0.00 0.86
52 53 4.742838 CCTCCTCCCCTTCCCCTATATATA 59.257 50.000 0.00 0.00 0.00 0.86
53 54 5.383282 CCTCCTCCCCTTCCCCTATATATAT 59.617 48.000 0.00 0.00 0.00 0.86
54 55 6.309050 TCCTCCCCTTCCCCTATATATATG 57.691 45.833 5.44 0.00 0.00 1.78
56 57 6.106343 TCCTCCCCTTCCCCTATATATATGAG 59.894 46.154 5.44 0.00 0.00 2.90
57 58 6.309050 TCCCCTTCCCCTATATATATGAGG 57.691 45.833 5.44 5.80 0.00 3.86
58 59 4.846940 CCCCTTCCCCTATATATATGAGGC 59.153 50.000 5.44 0.00 0.00 4.70
59 60 4.846940 CCCTTCCCCTATATATATGAGGCC 59.153 50.000 5.44 0.00 0.00 5.19
60 61 5.403121 CCCTTCCCCTATATATATGAGGCCT 60.403 48.000 3.86 3.86 0.00 5.19
61 62 6.183361 CCCTTCCCCTATATATATGAGGCCTA 60.183 46.154 4.42 0.00 0.00 3.93
64 65 5.318889 TCCCCTATATATATGAGGCCTAGGG 59.681 48.000 20.56 20.56 42.34 3.53
83 84 2.434884 CTGCCCAAGACACGCGAT 60.435 61.111 15.93 0.00 0.00 4.58
84 85 2.434185 TGCCCAAGACACGCGATC 60.434 61.111 15.93 10.41 0.00 3.69
86 87 2.456119 GCCCAAGACACGCGATCTG 61.456 63.158 15.93 2.56 0.00 2.90
87 88 1.215382 CCCAAGACACGCGATCTGA 59.785 57.895 15.93 0.00 0.00 3.27
92 93 1.674359 AGACACGCGATCTGATCTCT 58.326 50.000 15.93 8.06 0.00 3.10
93 94 1.333308 AGACACGCGATCTGATCTCTG 59.667 52.381 15.93 9.80 0.00 3.35
94 95 0.248825 ACACGCGATCTGATCTCTGC 60.249 55.000 15.93 10.29 0.00 4.26
95 96 0.938637 CACGCGATCTGATCTCTGCC 60.939 60.000 15.93 0.00 0.00 4.85
97 98 0.663867 CGCGATCTGATCTCTGCCTG 60.664 60.000 15.16 0.00 0.00 4.85
98 99 0.388659 GCGATCTGATCTCTGCCTGT 59.611 55.000 15.16 0.00 0.00 4.00
100 101 2.471818 CGATCTGATCTCTGCCTGTTG 58.528 52.381 15.16 0.00 0.00 3.33
101 102 2.802415 CGATCTGATCTCTGCCTGTTGG 60.802 54.545 15.16 0.00 0.00 3.77
102 103 1.649321 TCTGATCTCTGCCTGTTGGT 58.351 50.000 0.00 0.00 35.27 3.67
103 104 1.277273 TCTGATCTCTGCCTGTTGGTG 59.723 52.381 0.00 0.00 35.27 4.17
105 106 0.321919 GATCTCTGCCTGTTGGTGCA 60.322 55.000 0.00 0.00 35.86 4.57
110 111 4.982701 GCCTGTTGGTGCAGCCCT 62.983 66.667 14.36 0.00 35.28 5.19
111 112 2.674380 CCTGTTGGTGCAGCCCTC 60.674 66.667 14.36 4.36 35.28 4.30
112 113 2.674380 CTGTTGGTGCAGCCCTCC 60.674 66.667 14.36 0.00 36.04 4.30
113 114 4.284550 TGTTGGTGCAGCCCTCCC 62.285 66.667 14.36 0.00 36.04 4.30
114 115 3.971702 GTTGGTGCAGCCCTCCCT 61.972 66.667 14.36 0.00 36.04 4.20
115 116 3.650950 TTGGTGCAGCCCTCCCTC 61.651 66.667 14.36 0.00 36.04 4.30
116 117 4.664267 TGGTGCAGCCCTCCCTCT 62.664 66.667 14.36 0.00 36.04 3.69
119 120 2.123632 TGCAGCCCTCCCTCTCTT 59.876 61.111 0.00 0.00 0.00 2.85
121 122 1.223211 GCAGCCCTCCCTCTCTTTC 59.777 63.158 0.00 0.00 0.00 2.62
122 123 1.271127 GCAGCCCTCCCTCTCTTTCT 61.271 60.000 0.00 0.00 0.00 2.52
123 124 0.829990 CAGCCCTCCCTCTCTTTCTC 59.170 60.000 0.00 0.00 0.00 2.87
124 125 0.326143 AGCCCTCCCTCTCTTTCTCC 60.326 60.000 0.00 0.00 0.00 3.71
127 128 1.007721 CCCTCCCTCTCTTTCTCCTCA 59.992 57.143 0.00 0.00 0.00 3.86
128 129 2.360209 CCCTCCCTCTCTTTCTCCTCAT 60.360 54.545 0.00 0.00 0.00 2.90
129 130 3.116939 CCCTCCCTCTCTTTCTCCTCATA 60.117 52.174 0.00 0.00 0.00 2.15
130 131 4.450563 CCCTCCCTCTCTTTCTCCTCATAT 60.451 50.000 0.00 0.00 0.00 1.78
133 134 5.640147 TCCCTCTCTTTCTCCTCATATCTC 58.360 45.833 0.00 0.00 0.00 2.75
134 135 4.458989 CCCTCTCTTTCTCCTCATATCTCG 59.541 50.000 0.00 0.00 0.00 4.04
136 137 3.500299 TCTCTTTCTCCTCATATCTCGCG 59.500 47.826 0.00 0.00 0.00 5.87
137 138 2.554462 TCTTTCTCCTCATATCTCGCGG 59.446 50.000 6.13 0.00 0.00 6.46
139 140 1.239347 TCTCCTCATATCTCGCGGTG 58.761 55.000 6.13 0.00 0.00 4.94
140 141 0.387878 CTCCTCATATCTCGCGGTGC 60.388 60.000 6.13 0.00 0.00 5.01
141 142 0.823769 TCCTCATATCTCGCGGTGCT 60.824 55.000 6.13 0.00 0.00 4.40
142 143 0.032678 CCTCATATCTCGCGGTGCTT 59.967 55.000 6.13 0.00 0.00 3.91
143 144 1.135046 CTCATATCTCGCGGTGCTTG 58.865 55.000 6.13 0.00 0.00 4.01
144 145 0.249447 TCATATCTCGCGGTGCTTGG 60.249 55.000 6.13 0.00 0.00 3.61
145 146 1.595382 ATATCTCGCGGTGCTTGGC 60.595 57.895 6.13 0.00 0.00 4.52
151 152 4.090057 GCGGTGCTTGGCGAAGTC 62.090 66.667 10.35 3.45 0.00 3.01
152 153 3.423154 CGGTGCTTGGCGAAGTCC 61.423 66.667 10.35 11.45 0.00 3.85
153 154 2.032681 GGTGCTTGGCGAAGTCCT 59.967 61.111 10.35 0.00 0.00 3.85
156 157 2.669569 GCTTGGCGAAGTCCTGCA 60.670 61.111 10.35 0.00 0.00 4.41
158 159 2.032528 TTGGCGAAGTCCTGCAGG 59.967 61.111 27.87 27.87 0.00 4.85
171 172 3.512516 GCAGGATTGCCACGCTCC 61.513 66.667 0.00 0.00 44.74 4.70
172 173 2.270205 CAGGATTGCCACGCTCCT 59.730 61.111 0.00 0.00 40.05 3.69
173 174 1.817099 CAGGATTGCCACGCTCCTC 60.817 63.158 0.00 0.00 37.30 3.71
175 176 2.268920 GATTGCCACGCTCCTCCA 59.731 61.111 0.00 0.00 0.00 3.86
176 177 1.153086 GATTGCCACGCTCCTCCAT 60.153 57.895 0.00 0.00 0.00 3.41
177 178 1.153086 ATTGCCACGCTCCTCCATC 60.153 57.895 0.00 0.00 0.00 3.51
178 179 1.913951 ATTGCCACGCTCCTCCATCA 61.914 55.000 0.00 0.00 0.00 3.07
179 180 2.512515 GCCACGCTCCTCCATCAC 60.513 66.667 0.00 0.00 0.00 3.06
180 181 2.187946 CCACGCTCCTCCATCACC 59.812 66.667 0.00 0.00 0.00 4.02
181 182 2.659063 CCACGCTCCTCCATCACCA 61.659 63.158 0.00 0.00 0.00 4.17
182 183 1.448540 CACGCTCCTCCATCACCAC 60.449 63.158 0.00 0.00 0.00 4.16
183 184 2.187946 CGCTCCTCCATCACCACC 59.812 66.667 0.00 0.00 0.00 4.61
184 185 2.659063 CGCTCCTCCATCACCACCA 61.659 63.158 0.00 0.00 0.00 4.17
185 186 1.078143 GCTCCTCCATCACCACCAC 60.078 63.158 0.00 0.00 0.00 4.16
186 187 1.219124 CTCCTCCATCACCACCACG 59.781 63.158 0.00 0.00 0.00 4.94
189 190 4.386951 TCCATCACCACCACGCCG 62.387 66.667 0.00 0.00 0.00 6.46
190 191 4.697756 CCATCACCACCACGCCGT 62.698 66.667 0.00 0.00 0.00 5.68
191 192 2.668212 CATCACCACCACGCCGTT 60.668 61.111 0.00 0.00 0.00 4.44
192 193 2.668212 ATCACCACCACGCCGTTG 60.668 61.111 0.00 0.00 0.00 4.10
193 194 3.469863 ATCACCACCACGCCGTTGT 62.470 57.895 0.00 0.00 0.00 3.32
194 195 3.947841 CACCACCACGCCGTTGTG 61.948 66.667 13.93 13.93 39.60 3.33
197 198 4.312231 CACCACGCCGTTGTGCTG 62.312 66.667 8.58 0.00 38.55 4.41
204 205 4.034258 CCGTTGTGCTGCTGCTGG 62.034 66.667 17.00 7.00 40.48 4.85
205 206 2.974148 CGTTGTGCTGCTGCTGGA 60.974 61.111 17.00 2.36 40.48 3.86
206 207 2.330372 CGTTGTGCTGCTGCTGGAT 61.330 57.895 17.00 0.00 40.48 3.41
207 208 1.211969 GTTGTGCTGCTGCTGGATG 59.788 57.895 17.00 0.00 40.48 3.51
209 210 2.045634 GTGCTGCTGCTGGATGGA 60.046 61.111 17.00 0.00 40.48 3.41
210 211 2.113433 GTGCTGCTGCTGGATGGAG 61.113 63.158 17.00 0.00 40.48 3.86
211 212 2.271497 GCTGCTGCTGGATGGAGT 59.729 61.111 8.53 0.00 36.43 3.85
213 214 1.906253 CTGCTGCTGGATGGAGTCT 59.094 57.895 0.00 0.00 36.43 3.24
214 215 0.252479 CTGCTGCTGGATGGAGTCTT 59.748 55.000 0.00 0.00 36.43 3.01
217 218 1.202330 CTGCTGGATGGAGTCTTCCT 58.798 55.000 12.12 0.00 44.36 3.36
218 219 1.138661 CTGCTGGATGGAGTCTTCCTC 59.861 57.143 12.12 6.46 44.36 3.71
219 220 1.198713 GCTGGATGGAGTCTTCCTCA 58.801 55.000 12.12 0.00 44.36 3.86
220 221 1.556911 GCTGGATGGAGTCTTCCTCAA 59.443 52.381 12.12 0.00 44.36 3.02
221 222 2.679349 GCTGGATGGAGTCTTCCTCAAC 60.679 54.545 12.12 0.00 44.36 3.18
222 223 1.909302 TGGATGGAGTCTTCCTCAACC 59.091 52.381 12.12 1.27 44.36 3.77
223 224 2.192263 GGATGGAGTCTTCCTCAACCT 58.808 52.381 5.66 0.00 44.36 3.50
224 225 2.169561 GGATGGAGTCTTCCTCAACCTC 59.830 54.545 5.66 0.00 44.36 3.85
225 226 2.704190 TGGAGTCTTCCTCAACCTCT 57.296 50.000 0.00 0.00 44.36 3.69
226 227 2.530701 TGGAGTCTTCCTCAACCTCTC 58.469 52.381 0.00 0.00 44.36 3.20
227 228 1.828595 GGAGTCTTCCTCAACCTCTCC 59.171 57.143 0.00 0.00 42.40 3.71
228 229 1.828595 GAGTCTTCCTCAACCTCTCCC 59.171 57.143 0.00 0.00 40.17 4.30
229 230 1.435168 AGTCTTCCTCAACCTCTCCCT 59.565 52.381 0.00 0.00 0.00 4.20
230 231 1.828595 GTCTTCCTCAACCTCTCCCTC 59.171 57.143 0.00 0.00 0.00 4.30
232 233 2.107366 CTTCCTCAACCTCTCCCTCTC 58.893 57.143 0.00 0.00 0.00 3.20
233 234 1.388174 TCCTCAACCTCTCCCTCTCT 58.612 55.000 0.00 0.00 0.00 3.10
234 235 1.286553 TCCTCAACCTCTCCCTCTCTC 59.713 57.143 0.00 0.00 0.00 3.20
235 236 1.687996 CCTCAACCTCTCCCTCTCTCC 60.688 61.905 0.00 0.00 0.00 3.71
263 265 3.243907 GCCTGAACGTAGCCTAGATTCAT 60.244 47.826 0.00 0.00 0.00 2.57
291 293 0.099791 CGTGTTGGTCGCTTTTTGGT 59.900 50.000 0.00 0.00 0.00 3.67
355 357 6.414694 GCGCGAGATCAATGAAATGATTTTTA 59.585 34.615 12.10 0.00 40.08 1.52
357 359 7.852454 CGCGAGATCAATGAAATGATTTTTAGA 59.148 33.333 0.00 0.00 40.08 2.10
358 360 9.507280 GCGAGATCAATGAAATGATTTTTAGAA 57.493 29.630 0.00 0.00 40.08 2.10
512 3578 0.476771 TTTTCCAAGAACTCCGGCCT 59.523 50.000 0.00 0.00 0.00 5.19
545 3615 0.322008 TCAACGTGGGCATGCATGTA 60.322 50.000 26.79 11.84 0.00 2.29
569 3639 3.469899 TTTGCAATTCAACTCCGATCG 57.530 42.857 8.51 8.51 33.73 3.69
577 3647 1.471287 TCAACTCCGATCGATGTCGTT 59.529 47.619 18.66 8.90 39.89 3.85
587 3657 1.388768 TCGATGTCGTTCGATTTGTGC 59.611 47.619 2.04 0.00 42.81 4.57
598 3668 4.209452 TCGATTTGTGCTGTCTTTGTTC 57.791 40.909 0.00 0.00 0.00 3.18
634 3705 7.745620 ATTATATCCCGTGAGTTCCAAATTC 57.254 36.000 0.00 0.00 0.00 2.17
646 3717 9.097257 GTGAGTTCCAAATTCAAAAAGAAATGA 57.903 29.630 0.00 0.00 40.22 2.57
755 3827 0.677288 TCCACCTCAACGTGTGTAGG 59.323 55.000 0.00 0.00 33.26 3.18
769 3841 3.758554 GTGTGTAGGATGCAAATGGTCTT 59.241 43.478 0.00 0.00 27.52 3.01
822 3961 2.323059 GACGTCGTACAGAAGGAAACC 58.677 52.381 0.00 0.00 32.45 3.27
823 3962 1.959282 ACGTCGTACAGAAGGAAACCT 59.041 47.619 0.00 0.00 33.87 3.50
824 3963 2.288030 ACGTCGTACAGAAGGAAACCTG 60.288 50.000 0.00 0.00 32.13 4.00
861 4000 8.383175 ACAGACCTCAATCTAGTTGGATAAAAA 58.617 33.333 5.57 0.00 38.39 1.94
907 4046 6.946229 TTCAAACTTGTCTATCTCTAACGC 57.054 37.500 0.00 0.00 0.00 4.84
952 4094 6.607198 AGCAGTATAAATAGTTGGGCAAACAT 59.393 34.615 7.64 0.00 41.61 2.71
967 4114 3.694734 CAAACATACGAATGCCATCCAC 58.305 45.455 0.00 0.00 36.50 4.02
970 4117 0.843309 ATACGAATGCCATCCACCCA 59.157 50.000 0.00 0.00 0.00 4.51
971 4118 0.843309 TACGAATGCCATCCACCCAT 59.157 50.000 0.00 0.00 0.00 4.00
975 4122 2.552809 CGAATGCCATCCACCCATATCA 60.553 50.000 0.00 0.00 0.00 2.15
1190 4346 4.240103 TCAGATCCCCGGCATGCG 62.240 66.667 12.44 7.08 0.00 4.73
1212 4368 0.963962 GCCTACCACCGATATTCCGA 59.036 55.000 0.00 0.00 0.00 4.55
1218 4374 2.225192 ACCACCGATATTCCGATCCCTA 60.225 50.000 0.00 0.00 0.00 3.53
1242 4398 4.181010 CCACTGCCCCAGATCCCG 62.181 72.222 0.00 0.00 35.18 5.14
1374 4530 2.747855 CCGCCAAAGGAGTGCCTC 60.748 66.667 0.00 0.00 46.28 4.70
1659 4835 5.709966 ACCTTGTTCTGTGTGTTTTTCTTC 58.290 37.500 0.00 0.00 0.00 2.87
1668 4844 6.039159 TCTGTGTGTTTTTCTTCATATGTGCA 59.961 34.615 1.90 0.00 0.00 4.57
1704 4887 6.438425 AGGAGATTGATTAACTTGCATTGGTT 59.562 34.615 0.00 0.00 0.00 3.67
1705 4888 7.038799 AGGAGATTGATTAACTTGCATTGGTTT 60.039 33.333 5.74 0.00 0.00 3.27
1713 4896 7.856145 TTAACTTGCATTGGTTTTGATTTGT 57.144 28.000 5.74 0.00 0.00 2.83
1738 4921 3.860930 AACCCTTGCCGCCGTTGAT 62.861 57.895 0.00 0.00 0.00 2.57
1829 5021 2.095059 GCAGATCACCGATGCTTTTGTT 60.095 45.455 0.00 0.00 37.00 2.83
1882 5076 8.915036 TGTTTAGGTAGGATCAGAGAAAGATAC 58.085 37.037 0.00 0.00 0.00 2.24
1889 5083 6.322126 AGGATCAGAGAAAGATACCAGCTAT 58.678 40.000 0.00 0.00 0.00 2.97
1923 5136 6.262720 GGTTTAGGACGTCTCTCATATGTAGT 59.737 42.308 16.46 0.00 0.00 2.73
1938 5151 8.534954 TCATATGTAGTTCCTAGTGCTACTTT 57.465 34.615 1.90 6.85 36.84 2.66
1939 5152 9.636789 TCATATGTAGTTCCTAGTGCTACTTTA 57.363 33.333 1.90 8.14 36.84 1.85
1940 5153 9.900710 CATATGTAGTTCCTAGTGCTACTTTAG 57.099 37.037 13.25 0.00 36.84 1.85
1942 5155 7.771927 TGTAGTTCCTAGTGCTACTTTAGTT 57.228 36.000 13.25 0.00 36.84 2.24
1943 5156 8.868522 TGTAGTTCCTAGTGCTACTTTAGTTA 57.131 34.615 13.25 0.00 36.84 2.24
1945 5158 7.167924 AGTTCCTAGTGCTACTTTAGTTACC 57.832 40.000 0.00 0.00 0.00 2.85
1946 5159 6.723052 AGTTCCTAGTGCTACTTTAGTTACCA 59.277 38.462 0.00 0.00 0.00 3.25
1947 5160 7.399478 AGTTCCTAGTGCTACTTTAGTTACCAT 59.601 37.037 0.00 0.00 0.00 3.55
1984 5197 3.068165 TCATGTAAGATCTCCGTCGCATT 59.932 43.478 0.00 0.00 0.00 3.56
1987 5200 5.196341 TGTAAGATCTCCGTCGCATTATT 57.804 39.130 0.00 0.00 0.00 1.40
1992 5205 9.350357 GTAAGATCTCCGTCGCATTATTTAATA 57.650 33.333 0.00 0.00 0.00 0.98
2041 5259 2.540973 CGATGCATGCTTGGTGATTCAG 60.541 50.000 20.33 0.00 0.00 3.02
2109 5334 3.111838 CGATCTGATCTATATGCGTGCC 58.888 50.000 15.16 0.00 0.00 5.01
2144 5378 5.314529 TCCGTTGGTATTGGTACATGAAAA 58.685 37.500 0.00 0.00 39.30 2.29
2195 5430 3.798202 ACCTCTGTTATCCTGCGAAATC 58.202 45.455 0.00 0.00 0.00 2.17
2196 5431 3.197766 ACCTCTGTTATCCTGCGAAATCA 59.802 43.478 0.00 0.00 0.00 2.57
2199 5434 4.433615 TCTGTTATCCTGCGAAATCAGAC 58.566 43.478 0.00 0.00 36.19 3.51
2200 5435 3.186909 TGTTATCCTGCGAAATCAGACG 58.813 45.455 0.00 0.00 36.19 4.18
2201 5436 2.509052 TATCCTGCGAAATCAGACGG 57.491 50.000 0.00 0.00 36.19 4.79
2202 5437 0.179073 ATCCTGCGAAATCAGACGGG 60.179 55.000 0.00 0.00 36.19 5.28
2203 5438 2.464459 CCTGCGAAATCAGACGGGC 61.464 63.158 0.00 0.00 36.19 6.13
2204 5439 2.802667 CTGCGAAATCAGACGGGCG 61.803 63.158 0.00 0.00 36.19 6.13
2205 5440 3.564027 GCGAAATCAGACGGGCGG 61.564 66.667 0.00 0.00 0.00 6.13
2207 5442 1.740296 CGAAATCAGACGGGCGGTT 60.740 57.895 0.00 0.00 0.00 4.44
2209 5444 1.729284 GAAATCAGACGGGCGGTTTA 58.271 50.000 0.00 0.00 0.00 2.01
2210 5445 1.395954 GAAATCAGACGGGCGGTTTAC 59.604 52.381 0.00 0.00 0.00 2.01
2211 5446 0.322322 AATCAGACGGGCGGTTTACA 59.678 50.000 0.00 0.00 0.00 2.41
2212 5447 0.108329 ATCAGACGGGCGGTTTACAG 60.108 55.000 0.00 0.00 0.00 2.74
2214 5449 0.736325 CAGACGGGCGGTTTACAGAG 60.736 60.000 0.00 0.00 0.00 3.35
2217 5452 1.449601 CGGGCGGTTTACAGAGCAT 60.450 57.895 0.00 0.00 0.00 3.79
2218 5453 1.024579 CGGGCGGTTTACAGAGCATT 61.025 55.000 0.00 0.00 0.00 3.56
2219 5454 1.741055 CGGGCGGTTTACAGAGCATTA 60.741 52.381 0.00 0.00 0.00 1.90
2220 5455 1.669265 GGGCGGTTTACAGAGCATTAC 59.331 52.381 0.00 0.00 0.00 1.89
2221 5456 1.326548 GGCGGTTTACAGAGCATTACG 59.673 52.381 0.00 0.00 0.00 3.18
2222 5457 1.326548 GCGGTTTACAGAGCATTACGG 59.673 52.381 0.00 0.00 0.00 4.02
2223 5458 1.931172 CGGTTTACAGAGCATTACGGG 59.069 52.381 0.00 0.00 0.00 5.28
2225 5460 2.629051 GTTTACAGAGCATTACGGGCT 58.371 47.619 0.00 0.00 46.07 5.19
2226 5461 2.309528 TTACAGAGCATTACGGGCTG 57.690 50.000 0.00 0.00 42.78 4.85
2227 5462 1.191535 TACAGAGCATTACGGGCTGT 58.808 50.000 3.57 3.57 42.78 4.40
2229 5464 1.271379 ACAGAGCATTACGGGCTGTTT 60.271 47.619 3.31 0.00 42.78 2.83
2230 5465 2.027561 ACAGAGCATTACGGGCTGTTTA 60.028 45.455 3.31 0.00 42.78 2.01
2231 5466 3.006940 CAGAGCATTACGGGCTGTTTAA 58.993 45.455 3.31 0.00 42.78 1.52
2232 5467 3.438781 CAGAGCATTACGGGCTGTTTAAA 59.561 43.478 3.31 0.00 42.78 1.52
2233 5468 3.439129 AGAGCATTACGGGCTGTTTAAAC 59.561 43.478 11.54 11.54 42.78 2.01
2234 5469 2.490509 AGCATTACGGGCTGTTTAAACC 59.509 45.455 15.59 0.30 40.80 3.27
2235 5470 2.229302 GCATTACGGGCTGTTTAAACCA 59.771 45.455 15.59 3.48 0.00 3.67
2263 5710 8.099537 TCCGTAATACCCTGTAAAAATGTTACA 58.900 33.333 0.00 0.00 34.17 2.41
2272 5719 6.740905 CCTGTAAAAATGTTACATGCGTGTAG 59.259 38.462 17.81 4.71 41.56 2.74
2307 5754 2.200067 CTGGCAGCTCTAAATCTGTCG 58.800 52.381 0.00 0.00 37.72 4.35
2443 7527 2.755686 TGATCATGAGAGCAGAGGGAA 58.244 47.619 0.09 0.00 34.77 3.97
2471 7555 2.566724 CAGAGCAAGAGAGGGAAAGAGT 59.433 50.000 0.00 0.00 0.00 3.24
2496 7580 1.840635 GGACCCAAAGCAGAGTAGGAT 59.159 52.381 0.00 0.00 0.00 3.24
2501 7585 3.041946 CCAAAGCAGAGTAGGATAGGGT 58.958 50.000 0.00 0.00 0.00 4.34
2511 7596 7.273712 CAGAGTAGGATAGGGTAAGGAAAAAC 58.726 42.308 0.00 0.00 0.00 2.43
2565 7650 0.179081 CCTCCCTAACCTAGCAACGC 60.179 60.000 0.00 0.00 0.00 4.84
2666 7751 6.996282 TCCAAAAGAAAACGAGGAACTAGAAT 59.004 34.615 0.00 0.00 41.55 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.412408 GGAAGGGGAGGAGGGTGC 61.412 72.222 0.00 0.00 0.00 5.01
26 27 2.692741 GGGAAGGGGAGGAGGGTG 60.693 72.222 0.00 0.00 0.00 4.61
29 30 1.177104 TATAGGGGAAGGGGAGGAGG 58.823 60.000 0.00 0.00 0.00 4.30
30 31 4.928445 ATATATAGGGGAAGGGGAGGAG 57.072 50.000 0.00 0.00 0.00 3.69
32 33 6.309050 TCATATATATAGGGGAAGGGGAGG 57.691 45.833 4.66 0.00 0.00 4.30
35 36 4.846940 GCCTCATATATATAGGGGAAGGGG 59.153 50.000 5.84 2.94 0.00 4.79
36 37 4.846940 GGCCTCATATATATAGGGGAAGGG 59.153 50.000 5.84 2.58 0.00 3.95
39 40 6.183361 CCCTAGGCCTCATATATATAGGGGAA 60.183 46.154 19.97 0.00 42.83 3.97
40 41 5.318889 CCCTAGGCCTCATATATATAGGGGA 59.681 48.000 19.97 0.00 42.83 4.81
41 42 5.594777 CCCTAGGCCTCATATATATAGGGG 58.405 50.000 19.97 10.18 42.83 4.79
42 43 5.594777 CCCCTAGGCCTCATATATATAGGG 58.405 50.000 20.56 20.56 45.08 3.53
68 69 2.125512 AGATCGCGTGTCTTGGGC 60.126 61.111 5.77 0.00 0.00 5.36
69 70 0.179100 ATCAGATCGCGTGTCTTGGG 60.179 55.000 5.77 0.21 0.00 4.12
70 71 1.202348 AGATCAGATCGCGTGTCTTGG 60.202 52.381 5.77 0.92 0.00 3.61
71 72 2.115595 GAGATCAGATCGCGTGTCTTG 58.884 52.381 5.77 6.68 0.00 3.02
73 74 1.333308 CAGAGATCAGATCGCGTGTCT 59.667 52.381 5.77 8.55 34.06 3.41
74 75 1.752753 CAGAGATCAGATCGCGTGTC 58.247 55.000 5.77 6.04 34.06 3.67
75 76 0.248825 GCAGAGATCAGATCGCGTGT 60.249 55.000 5.77 0.00 34.06 4.49
76 77 0.938637 GGCAGAGATCAGATCGCGTG 60.939 60.000 5.77 8.35 34.06 5.34
77 78 1.106351 AGGCAGAGATCAGATCGCGT 61.106 55.000 5.77 3.78 34.06 6.01
79 80 0.388659 ACAGGCAGAGATCAGATCGC 59.611 55.000 6.04 6.04 0.00 4.58
80 81 2.471818 CAACAGGCAGAGATCAGATCG 58.528 52.381 4.67 0.00 0.00 3.69
82 83 2.093075 CACCAACAGGCAGAGATCAGAT 60.093 50.000 0.00 0.00 0.00 2.90
83 84 1.277273 CACCAACAGGCAGAGATCAGA 59.723 52.381 0.00 0.00 0.00 3.27
84 85 1.735386 CACCAACAGGCAGAGATCAG 58.265 55.000 0.00 0.00 0.00 2.90
86 87 0.321919 TGCACCAACAGGCAGAGATC 60.322 55.000 0.00 0.00 34.58 2.75
87 88 1.763120 TGCACCAACAGGCAGAGAT 59.237 52.632 0.00 0.00 34.58 2.75
94 95 2.674380 GAGGGCTGCACCAACAGG 60.674 66.667 0.00 0.00 42.05 4.00
95 96 2.674380 GGAGGGCTGCACCAACAG 60.674 66.667 0.00 0.00 42.05 3.16
97 98 3.927481 GAGGGAGGGCTGCACCAAC 62.927 68.421 0.00 0.00 42.05 3.77
98 99 3.650950 GAGGGAGGGCTGCACCAA 61.651 66.667 0.00 0.00 42.05 3.67
100 101 3.791586 GAGAGGGAGGGCTGCACC 61.792 72.222 0.00 0.00 37.93 5.01
101 102 1.846712 AAAGAGAGGGAGGGCTGCAC 61.847 60.000 0.50 0.00 0.00 4.57
102 103 1.539869 AAAGAGAGGGAGGGCTGCA 60.540 57.895 0.50 0.00 0.00 4.41
103 104 1.223211 GAAAGAGAGGGAGGGCTGC 59.777 63.158 0.00 0.00 0.00 5.25
105 106 0.326143 GGAGAAAGAGAGGGAGGGCT 60.326 60.000 0.00 0.00 0.00 5.19
106 107 0.326143 AGGAGAAAGAGAGGGAGGGC 60.326 60.000 0.00 0.00 0.00 5.19
107 108 1.007721 TGAGGAGAAAGAGAGGGAGGG 59.992 57.143 0.00 0.00 0.00 4.30
109 110 5.644188 AGATATGAGGAGAAAGAGAGGGAG 58.356 45.833 0.00 0.00 0.00 4.30
110 111 5.640147 GAGATATGAGGAGAAAGAGAGGGA 58.360 45.833 0.00 0.00 0.00 4.20
111 112 4.458989 CGAGATATGAGGAGAAAGAGAGGG 59.541 50.000 0.00 0.00 0.00 4.30
112 113 4.082787 GCGAGATATGAGGAGAAAGAGAGG 60.083 50.000 0.00 0.00 0.00 3.69
113 114 4.378356 CGCGAGATATGAGGAGAAAGAGAG 60.378 50.000 0.00 0.00 0.00 3.20
114 115 3.500299 CGCGAGATATGAGGAGAAAGAGA 59.500 47.826 0.00 0.00 0.00 3.10
115 116 3.365868 CCGCGAGATATGAGGAGAAAGAG 60.366 52.174 8.23 0.00 0.00 2.85
116 117 2.554462 CCGCGAGATATGAGGAGAAAGA 59.446 50.000 8.23 0.00 0.00 2.52
119 120 1.609072 CACCGCGAGATATGAGGAGAA 59.391 52.381 8.23 0.00 0.00 2.87
121 122 0.387878 GCACCGCGAGATATGAGGAG 60.388 60.000 8.23 0.00 0.00 3.69
122 123 0.823769 AGCACCGCGAGATATGAGGA 60.824 55.000 8.23 0.00 0.00 3.71
123 124 0.032678 AAGCACCGCGAGATATGAGG 59.967 55.000 8.23 0.00 0.00 3.86
124 125 1.135046 CAAGCACCGCGAGATATGAG 58.865 55.000 8.23 0.00 0.00 2.90
127 128 1.595382 GCCAAGCACCGCGAGATAT 60.595 57.895 8.23 0.00 0.00 1.63
128 129 2.202878 GCCAAGCACCGCGAGATA 60.203 61.111 8.23 0.00 0.00 1.98
134 135 4.090057 GACTTCGCCAAGCACCGC 62.090 66.667 0.00 0.00 32.09 5.68
136 137 2.032681 AGGACTTCGCCAAGCACC 59.967 61.111 0.00 0.00 32.09 5.01
137 138 2.970974 GCAGGACTTCGCCAAGCAC 61.971 63.158 0.00 0.00 32.09 4.40
139 140 2.669569 TGCAGGACTTCGCCAAGC 60.670 61.111 0.00 0.00 32.09 4.01
140 141 2.037136 CCTGCAGGACTTCGCCAAG 61.037 63.158 29.88 0.00 37.39 3.61
141 142 2.032528 CCTGCAGGACTTCGCCAA 59.967 61.111 29.88 0.00 37.39 4.52
142 143 2.922503 TCCTGCAGGACTTCGCCA 60.923 61.111 32.00 6.91 39.78 5.69
156 157 2.586792 GAGGAGCGTGGCAATCCT 59.413 61.111 14.98 14.98 46.22 3.24
158 159 1.153086 ATGGAGGAGCGTGGCAATC 60.153 57.895 0.00 0.00 0.00 2.67
160 161 2.268920 GATGGAGGAGCGTGGCAA 59.731 61.111 0.00 0.00 0.00 4.52
161 162 3.002583 TGATGGAGGAGCGTGGCA 61.003 61.111 0.00 0.00 0.00 4.92
162 163 2.512515 GTGATGGAGGAGCGTGGC 60.513 66.667 0.00 0.00 0.00 5.01
163 164 2.187946 GGTGATGGAGGAGCGTGG 59.812 66.667 0.00 0.00 0.00 4.94
164 165 1.448540 GTGGTGATGGAGGAGCGTG 60.449 63.158 0.00 0.00 0.00 5.34
167 168 1.078143 GTGGTGGTGATGGAGGAGC 60.078 63.158 0.00 0.00 0.00 4.70
169 170 2.954684 GCGTGGTGGTGATGGAGGA 61.955 63.158 0.00 0.00 0.00 3.71
170 171 2.436646 GCGTGGTGGTGATGGAGG 60.437 66.667 0.00 0.00 0.00 4.30
171 172 2.436646 GGCGTGGTGGTGATGGAG 60.437 66.667 0.00 0.00 0.00 3.86
172 173 4.386951 CGGCGTGGTGGTGATGGA 62.387 66.667 0.00 0.00 0.00 3.41
173 174 4.697756 ACGGCGTGGTGGTGATGG 62.698 66.667 13.76 0.00 0.00 3.51
175 176 2.668212 CAACGGCGTGGTGGTGAT 60.668 61.111 15.70 0.00 0.00 3.06
176 177 4.164087 ACAACGGCGTGGTGGTGA 62.164 61.111 21.06 0.00 0.00 4.02
177 178 3.947841 CACAACGGCGTGGTGGTG 61.948 66.667 34.23 24.43 34.13 4.17
183 184 4.671549 CAGCAGCACAACGGCGTG 62.672 66.667 15.70 10.75 45.09 5.34
186 187 4.695231 CAGCAGCAGCACAACGGC 62.695 66.667 3.17 0.00 45.49 5.68
189 190 1.211969 CATCCAGCAGCAGCACAAC 59.788 57.895 3.17 0.00 45.49 3.32
190 191 1.974875 CCATCCAGCAGCAGCACAA 60.975 57.895 3.17 0.00 45.49 3.33
191 192 2.360726 CCATCCAGCAGCAGCACA 60.361 61.111 3.17 0.00 45.49 4.57
192 193 2.045634 TCCATCCAGCAGCAGCAC 60.046 61.111 3.17 0.00 45.49 4.40
193 194 2.271173 CTCCATCCAGCAGCAGCA 59.729 61.111 3.17 0.00 45.49 4.41
194 195 1.818785 GACTCCATCCAGCAGCAGC 60.819 63.158 0.00 0.00 42.56 5.25
196 197 0.251354 GAAGACTCCATCCAGCAGCA 59.749 55.000 0.00 0.00 0.00 4.41
197 198 0.463474 GGAAGACTCCATCCAGCAGC 60.463 60.000 0.00 0.00 41.96 5.25
198 199 1.138661 GAGGAAGACTCCATCCAGCAG 59.861 57.143 0.00 0.00 45.24 4.24
202 203 1.909302 GGTTGAGGAAGACTCCATCCA 59.091 52.381 0.00 0.00 46.01 3.41
204 205 3.103742 AGAGGTTGAGGAAGACTCCATC 58.896 50.000 0.00 0.00 46.01 3.51
205 206 3.103742 GAGAGGTTGAGGAAGACTCCAT 58.896 50.000 0.00 0.00 46.01 3.41
206 207 2.530701 GAGAGGTTGAGGAAGACTCCA 58.469 52.381 0.00 0.00 46.01 3.86
207 208 1.828595 GGAGAGGTTGAGGAAGACTCC 59.171 57.143 0.00 0.00 46.01 3.85
209 210 1.435168 AGGGAGAGGTTGAGGAAGACT 59.565 52.381 0.00 0.00 0.00 3.24
210 211 1.828595 GAGGGAGAGGTTGAGGAAGAC 59.171 57.143 0.00 0.00 0.00 3.01
211 212 1.719378 AGAGGGAGAGGTTGAGGAAGA 59.281 52.381 0.00 0.00 0.00 2.87
213 214 1.719378 AGAGAGGGAGAGGTTGAGGAA 59.281 52.381 0.00 0.00 0.00 3.36
214 215 1.286553 GAGAGAGGGAGAGGTTGAGGA 59.713 57.143 0.00 0.00 0.00 3.71
217 218 1.388174 AGGAGAGAGGGAGAGGTTGA 58.612 55.000 0.00 0.00 0.00 3.18
218 219 1.830477 CAAGGAGAGAGGGAGAGGTTG 59.170 57.143 0.00 0.00 0.00 3.77
219 220 1.899438 GCAAGGAGAGAGGGAGAGGTT 60.899 57.143 0.00 0.00 0.00 3.50
220 221 0.325203 GCAAGGAGAGAGGGAGAGGT 60.325 60.000 0.00 0.00 0.00 3.85
221 222 0.032217 AGCAAGGAGAGAGGGAGAGG 60.032 60.000 0.00 0.00 0.00 3.69
222 223 1.113788 CAGCAAGGAGAGAGGGAGAG 58.886 60.000 0.00 0.00 0.00 3.20
223 224 0.975040 GCAGCAAGGAGAGAGGGAGA 60.975 60.000 0.00 0.00 0.00 3.71
224 225 1.521616 GCAGCAAGGAGAGAGGGAG 59.478 63.158 0.00 0.00 0.00 4.30
225 226 1.992277 GGCAGCAAGGAGAGAGGGA 60.992 63.158 0.00 0.00 0.00 4.20
226 227 1.994507 AGGCAGCAAGGAGAGAGGG 60.995 63.158 0.00 0.00 0.00 4.30
227 228 1.221293 CAGGCAGCAAGGAGAGAGG 59.779 63.158 0.00 0.00 0.00 3.69
228 229 0.612229 TTCAGGCAGCAAGGAGAGAG 59.388 55.000 0.00 0.00 0.00 3.20
229 230 0.322975 GTTCAGGCAGCAAGGAGAGA 59.677 55.000 0.00 0.00 0.00 3.10
230 231 1.018226 CGTTCAGGCAGCAAGGAGAG 61.018 60.000 0.00 0.00 0.00 3.20
232 233 0.037326 TACGTTCAGGCAGCAAGGAG 60.037 55.000 0.00 0.00 0.00 3.69
233 234 0.037326 CTACGTTCAGGCAGCAAGGA 60.037 55.000 0.00 0.00 0.00 3.36
234 235 1.639298 GCTACGTTCAGGCAGCAAGG 61.639 60.000 0.00 0.00 33.73 3.61
235 236 1.639298 GGCTACGTTCAGGCAGCAAG 61.639 60.000 7.00 0.00 40.68 4.01
288 290 1.478916 CAATGGCTTGATCATGCACCA 59.521 47.619 28.58 20.44 34.04 4.17
291 293 1.134936 GTGCAATGGCTTGATCATGCA 60.135 47.619 28.58 21.65 41.91 3.96
372 374 5.741388 ACGAAAGGACTTGCATATCATTC 57.259 39.130 0.00 0.00 0.00 2.67
380 383 4.637276 TCTTGAATACGAAAGGACTTGCA 58.363 39.130 0.00 0.00 0.00 4.08
449 3515 5.702065 TTGGATAAGTACAAGGGCATACA 57.298 39.130 0.00 0.00 0.00 2.29
489 3555 2.483106 GCCGGAGTTCTTGGAAAAGTAC 59.517 50.000 5.05 0.00 0.00 2.73
496 3562 2.291043 GGAGGCCGGAGTTCTTGGA 61.291 63.158 5.05 0.00 0.00 3.53
512 3578 2.608546 CACGTTGAAAAACAGTACCGGA 59.391 45.455 9.46 0.00 0.00 5.14
519 3585 2.126467 CATGCCCACGTTGAAAAACAG 58.874 47.619 0.00 0.00 0.00 3.16
545 3615 4.582701 TCGGAGTTGAATTGCAAATTGT 57.417 36.364 1.71 0.00 38.44 2.71
569 3639 2.157668 ACAGCACAAATCGAACGACATC 59.842 45.455 0.00 0.00 0.00 3.06
577 3647 3.876914 AGAACAAAGACAGCACAAATCGA 59.123 39.130 0.00 0.00 0.00 3.59
620 3691 9.097257 TCATTTCTTTTTGAATTTGGAACTCAC 57.903 29.630 0.00 0.00 34.24 3.51
721 3792 7.119846 CGTTGAGGTGGATAAGATTCTCTTTTT 59.880 37.037 0.00 0.00 37.89 1.94
755 3827 4.448732 GGTTCAAACAAGACCATTTGCATC 59.551 41.667 0.00 0.00 36.06 3.91
769 3841 3.840666 AGATAGAGCTGGAGGTTCAAACA 59.159 43.478 0.00 0.00 0.00 2.83
822 3961 0.385390 GGTCTGTTTGGGTTGTGCAG 59.615 55.000 0.00 0.00 0.00 4.41
823 3962 0.033601 AGGTCTGTTTGGGTTGTGCA 60.034 50.000 0.00 0.00 0.00 4.57
824 3963 0.668535 GAGGTCTGTTTGGGTTGTGC 59.331 55.000 0.00 0.00 0.00 4.57
917 4056 1.672854 TTATACTGCTCCGGCTGCGT 61.673 55.000 13.17 14.63 40.37 5.24
918 4057 0.529773 TTTATACTGCTCCGGCTGCG 60.530 55.000 13.17 10.62 40.37 5.18
919 4058 1.884235 ATTTATACTGCTCCGGCTGC 58.116 50.000 11.54 11.54 40.37 5.25
952 4094 0.843309 ATGGGTGGATGGCATTCGTA 59.157 50.000 0.00 0.00 0.00 3.43
967 4114 1.611673 GGGAGGATGCGTTGATATGGG 60.612 57.143 0.00 0.00 0.00 4.00
970 4117 1.625818 GAGGGGAGGATGCGTTGATAT 59.374 52.381 0.00 0.00 0.00 1.63
971 4118 1.048601 GAGGGGAGGATGCGTTGATA 58.951 55.000 0.00 0.00 0.00 2.15
975 4122 2.990479 GTGAGGGGAGGATGCGTT 59.010 61.111 0.00 0.00 0.00 4.84
1135 4291 2.041265 AGACGGGGAGCCTCCATT 59.959 61.111 13.90 0.00 38.64 3.16
1190 4346 2.094854 CGGAATATCGGTGGTAGGCTAC 60.095 54.545 16.40 16.40 0.00 3.58
1212 4368 0.846693 GCAGTGGTGGGAATAGGGAT 59.153 55.000 0.00 0.00 0.00 3.85
1218 4374 2.863484 TGGGGCAGTGGTGGGAAT 60.863 61.111 0.00 0.00 0.00 3.01
1374 4530 1.441738 TCATGCTCGTCAATGGTGTG 58.558 50.000 0.00 0.00 0.00 3.82
1506 4662 2.015627 CATGCCGCCGTTGTTGTTG 61.016 57.895 0.00 0.00 0.00 3.33
1659 4835 4.397103 TCCTTCAAAGAAGCTGCACATATG 59.603 41.667 1.02 0.00 0.00 1.78
1668 4844 7.887495 AGTTAATCAATCTCCTTCAAAGAAGCT 59.113 33.333 1.29 0.00 0.00 3.74
1704 4887 1.691434 GGGTTGGGCTGACAAATCAAA 59.309 47.619 0.00 0.00 33.30 2.69
1705 4888 1.133199 AGGGTTGGGCTGACAAATCAA 60.133 47.619 0.00 0.00 33.30 2.57
1713 4896 4.659172 CGGCAAGGGTTGGGCTGA 62.659 66.667 0.00 0.00 35.98 4.26
1775 4967 4.248842 TATGGTGATGGCGCGGGG 62.249 66.667 8.83 0.00 0.00 5.73
1882 5076 3.277142 AAACCCCTAAACGATAGCTGG 57.723 47.619 0.00 0.00 42.67 4.85
1889 5083 2.231235 GACGTCCTAAACCCCTAAACGA 59.769 50.000 3.51 0.00 33.25 3.85
1923 5136 7.729124 ATGGTAACTAAAGTAGCACTAGGAA 57.271 36.000 0.00 0.00 37.61 3.36
2041 5259 9.537848 CAAGTAAACAATACAGAAATAACGACC 57.462 33.333 0.00 0.00 0.00 4.79
2109 5334 2.670934 AACGGAGCCAGCAAGCAG 60.671 61.111 0.55 0.00 34.23 4.24
2144 5378 9.561069 AAAAGTTGAGTCATACATCTACAAAGT 57.439 29.630 0.00 0.00 0.00 2.66
2195 5430 0.736325 CTCTGTAAACCGCCCGTCTG 60.736 60.000 0.00 0.00 0.00 3.51
2196 5431 1.590147 CTCTGTAAACCGCCCGTCT 59.410 57.895 0.00 0.00 0.00 4.18
2199 5434 1.024579 AATGCTCTGTAAACCGCCCG 61.025 55.000 0.00 0.00 0.00 6.13
2200 5435 1.669265 GTAATGCTCTGTAAACCGCCC 59.331 52.381 0.00 0.00 0.00 6.13
2201 5436 1.326548 CGTAATGCTCTGTAAACCGCC 59.673 52.381 0.00 0.00 0.00 6.13
2202 5437 1.326548 CCGTAATGCTCTGTAAACCGC 59.673 52.381 0.00 0.00 0.00 5.68
2203 5438 1.931172 CCCGTAATGCTCTGTAAACCG 59.069 52.381 0.00 0.00 0.00 4.44
2204 5439 1.669265 GCCCGTAATGCTCTGTAAACC 59.331 52.381 0.00 0.00 0.00 3.27
2205 5440 2.351726 CAGCCCGTAATGCTCTGTAAAC 59.648 50.000 0.00 0.00 36.81 2.01
2207 5442 1.553248 ACAGCCCGTAATGCTCTGTAA 59.447 47.619 0.00 0.00 36.81 2.41
2209 5444 0.324943 AACAGCCCGTAATGCTCTGT 59.675 50.000 0.00 0.00 39.42 3.41
2210 5445 1.453155 AAACAGCCCGTAATGCTCTG 58.547 50.000 0.00 0.00 36.81 3.35
2211 5446 3.343941 TTAAACAGCCCGTAATGCTCT 57.656 42.857 0.00 0.00 36.81 4.09
2212 5447 3.427098 GGTTTAAACAGCCCGTAATGCTC 60.427 47.826 19.57 0.00 36.81 4.26
2214 5449 2.229302 TGGTTTAAACAGCCCGTAATGC 59.771 45.455 19.57 0.00 0.00 3.56
2217 5452 3.140623 GAGTGGTTTAAACAGCCCGTAA 58.859 45.455 19.57 0.00 0.00 3.18
2218 5453 2.550639 GGAGTGGTTTAAACAGCCCGTA 60.551 50.000 19.57 0.00 0.00 4.02
2219 5454 1.601166 GAGTGGTTTAAACAGCCCGT 58.399 50.000 19.57 0.00 0.00 5.28
2220 5455 0.879090 GGAGTGGTTTAAACAGCCCG 59.121 55.000 19.57 0.00 0.00 6.13
2221 5456 0.879090 CGGAGTGGTTTAAACAGCCC 59.121 55.000 19.57 12.75 0.00 5.19
2222 5457 1.601166 ACGGAGTGGTTTAAACAGCC 58.399 50.000 19.57 12.69 42.51 4.85
2223 5458 5.163824 GGTATTACGGAGTGGTTTAAACAGC 60.164 44.000 19.57 11.18 45.73 4.40
2225 5460 5.012975 AGGGTATTACGGAGTGGTTTAAACA 59.987 40.000 19.57 3.79 45.73 2.83
2226 5461 5.352293 CAGGGTATTACGGAGTGGTTTAAAC 59.648 44.000 9.98 9.98 45.73 2.01
2227 5462 5.012975 ACAGGGTATTACGGAGTGGTTTAAA 59.987 40.000 0.00 0.00 45.73 1.52
2229 5464 4.095946 ACAGGGTATTACGGAGTGGTTTA 58.904 43.478 0.00 0.00 45.73 2.01
2230 5465 2.908351 ACAGGGTATTACGGAGTGGTTT 59.092 45.455 0.00 0.00 45.73 3.27
2231 5466 2.543635 ACAGGGTATTACGGAGTGGTT 58.456 47.619 0.00 0.00 45.73 3.67
2232 5467 2.242882 ACAGGGTATTACGGAGTGGT 57.757 50.000 0.00 0.00 45.73 4.16
2233 5468 4.741321 TTTACAGGGTATTACGGAGTGG 57.259 45.455 0.00 0.00 45.73 4.00
2234 5469 6.596497 ACATTTTTACAGGGTATTACGGAGTG 59.404 38.462 0.00 0.00 45.73 3.51
2272 5719 0.308993 GCCAGGATAACGAGCAATGC 59.691 55.000 0.00 0.00 0.00 3.56
2443 7527 2.502295 CCTCTCTTGCTCTGCTTTGTT 58.498 47.619 0.00 0.00 0.00 2.83
2471 7555 1.203313 ACTCTGCTTTGGGTCCCTCTA 60.203 52.381 10.00 0.00 0.00 2.43
2496 7580 5.034878 CCCTCTAGGTTTTTCCTTACCCTA 58.965 45.833 0.00 0.00 45.67 3.53
2501 7585 6.793988 TCTTTACCCCTCTAGGTTTTTCCTTA 59.206 38.462 0.00 0.00 45.67 2.69
2511 7596 5.141910 CCTTACTCTCTTTACCCCTCTAGG 58.858 50.000 0.00 0.00 0.00 3.02
2565 7650 3.815401 CACTTGGTGTTGACTAAGAAGGG 59.185 47.826 5.43 0.00 41.95 3.95
2666 7751 0.530744 CGACGATGTTCCTCTTCCCA 59.469 55.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.