Multiple sequence alignment - TraesCS7D01G418200

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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 TraesCS7D01G418200 chr7D 100.000 6854 0 0 1 6854 537678550 537671697 0.000000e+00 12658.0
1 TraesCS7D01G418200 chr7D 74.157 1068 250 22 5047 6102 591009203 591008150 2.960000e-113 420.0
2 TraesCS7D01G418200 chr7D 92.169 166 13 0 3885 4050 397554916 397555081 1.150000e-57 235.0
3 TraesCS7D01G418200 chr7B 96.761 3118 83 12 774 3884 580163670 580160564 0.000000e+00 5182.0
4 TraesCS7D01G418200 chr7B 98.398 1997 26 3 4048 6043 580160563 580158572 0.000000e+00 3506.0
5 TraesCS7D01G418200 chr7B 89.303 402 16 5 2443 2837 489143618 489143999 4.810000e-131 479.0
6 TraesCS7D01G418200 chr7B 94.805 308 12 1 6040 6347 580156159 580155856 1.730000e-130 477.0
7 TraesCS7D01G418200 chr7B 96.071 280 6 3 6341 6619 580155834 580155559 1.050000e-122 451.0
8 TraesCS7D01G418200 chr7B 93.357 286 15 2 491 776 580164170 580163889 2.960000e-113 420.0
9 TraesCS7D01G418200 chr7B 73.460 1055 260 17 5047 6092 666511738 666510695 5.020000e-101 379.0
10 TraesCS7D01G418200 chr7B 88.000 175 21 0 2836 3010 489144160 489144334 2.510000e-49 207.0
11 TraesCS7D01G418200 chr7B 93.525 139 5 2 1 135 580164479 580164341 3.240000e-48 204.0
12 TraesCS7D01G418200 chr7A 96.840 2911 80 9 2443 5347 619034931 619032027 0.000000e+00 4855.0
13 TraesCS7D01G418200 chr7A 97.493 1675 38 3 774 2446 619036725 619035053 0.000000e+00 2857.0
14 TraesCS7D01G418200 chr7A 89.394 2112 211 10 4199 6307 618683077 618680976 0.000000e+00 2647.0
15 TraesCS7D01G418200 chr7A 93.613 1503 54 24 5383 6854 619032024 619030533 0.000000e+00 2206.0
16 TraesCS7D01G418200 chr7A 86.927 436 39 8 6420 6845 618680885 618680458 2.240000e-129 473.0
17 TraesCS7D01G418200 chr7A 93.133 233 15 1 491 723 619037254 619037023 2.370000e-89 340.0
18 TraesCS7D01G418200 chr7A 92.771 166 12 0 3885 4050 451519972 451519807 2.470000e-59 241.0
19 TraesCS7D01G418200 chr7A 91.667 168 13 1 294 460 619037422 619037255 1.490000e-56 231.0
20 TraesCS7D01G418200 chr7A 96.825 63 1 1 18 79 619037517 619037455 3.380000e-18 104.0
21 TraesCS7D01G418200 chr7A 100.000 42 0 0 623 664 619037030 619036989 2.050000e-10 78.7
22 TraesCS7D01G418200 chr1D 94.662 562 25 1 2449 3010 478349291 478348735 0.000000e+00 867.0
23 TraesCS7D01G418200 chr1D 94.330 388 18 3 2432 2819 129681098 129681481 5.920000e-165 592.0
24 TraesCS7D01G418200 chr1D 90.449 356 24 5 2435 2784 416746948 416746597 1.740000e-125 460.0
25 TraesCS7D01G418200 chr1D 73.411 944 228 20 5158 6089 439928689 439927757 1.420000e-86 331.0
26 TraesCS7D01G418200 chr1D 94.675 169 6 2 133 298 360358224 360358392 6.820000e-65 259.0
27 TraesCS7D01G418200 chr1D 97.778 90 2 0 2865 2954 129681478 129681567 9.200000e-34 156.0
28 TraesCS7D01G418200 chr1D 95.349 86 4 0 2878 2963 416731485 416731400 3.330000e-28 137.0
29 TraesCS7D01G418200 chr1D 98.649 74 1 0 2864 2937 416731619 416731546 1.550000e-26 132.0
30 TraesCS7D01G418200 chr5D 93.380 574 29 2 2436 3009 520967530 520968094 0.000000e+00 841.0
31 TraesCS7D01G418200 chr5D 74.277 968 232 15 5122 6080 500132720 500131761 6.440000e-105 392.0
32 TraesCS7D01G418200 chr4D 91.111 360 17 5 2604 2963 347513452 347513108 2.240000e-129 473.0
33 TraesCS7D01G418200 chr4D 93.642 173 8 1 132 301 75782052 75782224 8.820000e-64 255.0
34 TraesCS7D01G418200 chr4D 91.848 184 8 5 132 310 6588593 6588412 4.100000e-62 250.0
35 TraesCS7D01G418200 chr4D 88.525 183 20 1 3864 4046 334164371 334164552 3.220000e-53 220.0
36 TraesCS7D01G418200 chr4D 77.333 150 32 2 5300 5448 2999756 2999904 3.410000e-13 87.9
37 TraesCS7D01G418200 chr5B 74.327 966 235 11 5122 6080 621468906 621467947 1.390000e-106 398.0
38 TraesCS7D01G418200 chr5B 93.678 174 8 1 127 297 427931196 427931369 2.450000e-64 257.0
39 TraesCS7D01G418200 chr2D 94.220 173 7 1 133 302 560959485 560959657 1.900000e-65 261.0
40 TraesCS7D01G418200 chr3A 94.152 171 7 1 131 298 611185139 611185309 2.450000e-64 257.0
41 TraesCS7D01G418200 chr3A 92.121 165 13 0 3882 4046 600921019 600920855 4.130000e-57 233.0
42 TraesCS7D01G418200 chr3A 90.588 170 16 0 3885 4054 238686371 238686202 6.920000e-55 226.0
43 TraesCS7D01G418200 chr4B 93.182 176 9 1 126 298 86060293 86060468 8.820000e-64 255.0
44 TraesCS7D01G418200 chr1A 93.605 172 9 1 133 302 34971277 34971448 8.820000e-64 255.0
45 TraesCS7D01G418200 chr3B 90.256 195 11 6 108 298 225180149 225179959 1.480000e-61 248.0
46 TraesCS7D01G418200 chr2A 93.865 163 9 1 3885 4046 703708263 703708425 1.910000e-60 244.0
47 TraesCS7D01G418200 chr2A 77.778 207 44 2 2432 2637 770388538 770388743 7.220000e-25 126.0
48 TraesCS7D01G418200 chr5A 90.857 175 14 2 3879 4051 320214236 320214410 4.130000e-57 233.0
49 TraesCS7D01G418200 chr3D 90.643 171 16 0 3885 4055 187836308 187836478 1.920000e-55 228.0
50 TraesCS7D01G418200 chr3D 76.733 202 45 2 2434 2634 466382448 466382648 2.020000e-20 111.0
51 TraesCS7D01G418200 chr2B 94.737 38 1 1 2429 2466 425793026 425792990 2.670000e-04 58.4


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 TraesCS7D01G418200 chr7D 537671697 537678550 6853 True 12658.000000 12658 100.000000 1 6854 1 chr7D.!!$R1 6853
1 TraesCS7D01G418200 chr7D 591008150 591009203 1053 True 420.000000 420 74.157000 5047 6102 1 chr7D.!!$R2 1055
2 TraesCS7D01G418200 chr7B 580155559 580164479 8920 True 1706.666667 5182 95.486167 1 6619 6 chr7B.!!$R2 6618
3 TraesCS7D01G418200 chr7B 666510695 666511738 1043 True 379.000000 379 73.460000 5047 6092 1 chr7B.!!$R1 1045
4 TraesCS7D01G418200 chr7B 489143618 489144334 716 False 343.000000 479 88.651500 2443 3010 2 chr7B.!!$F1 567
5 TraesCS7D01G418200 chr7A 618680458 618683077 2619 True 1560.000000 2647 88.160500 4199 6845 2 chr7A.!!$R2 2646
6 TraesCS7D01G418200 chr7A 619030533 619037517 6984 True 1524.528571 4855 95.653000 18 6854 7 chr7A.!!$R3 6836
7 TraesCS7D01G418200 chr1D 478348735 478349291 556 True 867.000000 867 94.662000 2449 3010 1 chr1D.!!$R3 561
8 TraesCS7D01G418200 chr1D 439927757 439928689 932 True 331.000000 331 73.411000 5158 6089 1 chr1D.!!$R2 931
9 TraesCS7D01G418200 chr5D 520967530 520968094 564 False 841.000000 841 93.380000 2436 3009 1 chr5D.!!$F1 573
10 TraesCS7D01G418200 chr5D 500131761 500132720 959 True 392.000000 392 74.277000 5122 6080 1 chr5D.!!$R1 958
11 TraesCS7D01G418200 chr5B 621467947 621468906 959 True 398.000000 398 74.327000 5122 6080 1 chr5B.!!$R1 958


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
386 397 0.179034 TGCCCACACCAAAAATTGCC 60.179 50.000 0.00 0.0 0.00 4.52 F
1044 1302 0.984961 TGCTAGGGATGGCTGAAGCT 60.985 55.000 1.74 0.0 41.70 3.74 F
2597 2984 0.729690 GTTTCCTGGATTCGCTCTGC 59.270 55.000 0.00 0.0 0.00 4.26 F
2649 3043 1.069765 CTGGAACACTCACGGCACT 59.930 57.895 0.00 0.0 0.00 4.40 F
3131 3693 1.456544 GTTGCCACACATTCATTTGCG 59.543 47.619 0.00 0.0 0.00 4.85 F
4834 5401 0.531974 GAGTGCAAACGGACACCAGA 60.532 55.000 0.00 0.0 37.51 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1328 1586 2.555325 CACAAGTTCACTGACATGCCAT 59.445 45.455 0.0 0.0 0.00 4.40 R
2649 3043 1.141858 TGTGGTGTGTGGTAGCATTCA 59.858 47.619 0.0 0.0 0.00 2.57 R
4430 4997 5.043903 ACACTCGACTCATATTTGATTCCG 58.956 41.667 0.0 0.0 29.96 4.30 R
4649 5216 3.945285 CACACCTGTATCCAACATAACCC 59.055 47.826 0.0 0.0 37.50 4.11 R
4984 5551 0.984230 TCTTTTGAGGGGACGAGCAT 59.016 50.000 0.0 0.0 0.00 3.79 R
6785 9810 0.617413 ACACCTCAGGGATGCTTCTG 59.383 55.000 0.0 0.0 36.25 3.02 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
76 78 8.674263 ACTGTGAAAATTGGAAAATGCATTAA 57.326 26.923 13.39 3.40 0.00 1.40
124 129 5.749588 TGTGAACAATGAAGCATTTTCTGTG 59.250 36.000 0.00 0.00 31.05 3.66
132 137 9.577110 CAATGAAGCATTTTCTGTGTAATGTAT 57.423 29.630 0.00 0.00 34.88 2.29
135 140 9.448438 TGAAGCATTTTCTGTGTAATGTATACT 57.552 29.630 4.17 0.00 34.88 2.12
138 143 8.893727 AGCATTTTCTGTGTAATGTATACTTCC 58.106 33.333 4.17 0.00 34.88 3.46
139 144 8.893727 GCATTTTCTGTGTAATGTATACTTCCT 58.106 33.333 4.17 0.00 34.88 3.36
141 146 9.614792 ATTTTCTGTGTAATGTATACTTCCTCC 57.385 33.333 4.17 0.00 0.00 4.30
142 147 6.387041 TCTGTGTAATGTATACTTCCTCCG 57.613 41.667 4.17 0.00 0.00 4.63
143 148 5.889853 TCTGTGTAATGTATACTTCCTCCGT 59.110 40.000 4.17 0.00 0.00 4.69
144 149 6.379133 TCTGTGTAATGTATACTTCCTCCGTT 59.621 38.462 4.17 0.00 0.00 4.44
145 150 6.567050 TGTGTAATGTATACTTCCTCCGTTC 58.433 40.000 4.17 0.00 0.00 3.95
146 151 5.981915 GTGTAATGTATACTTCCTCCGTTCC 59.018 44.000 4.17 0.00 0.00 3.62
147 152 5.895534 TGTAATGTATACTTCCTCCGTTCCT 59.104 40.000 4.17 0.00 0.00 3.36
148 153 7.013655 GTGTAATGTATACTTCCTCCGTTCCTA 59.986 40.741 4.17 0.00 0.00 2.94
149 154 7.560991 TGTAATGTATACTTCCTCCGTTCCTAA 59.439 37.037 4.17 0.00 0.00 2.69
150 155 7.427989 AATGTATACTTCCTCCGTTCCTAAA 57.572 36.000 4.17 0.00 0.00 1.85
151 156 7.613551 ATGTATACTTCCTCCGTTCCTAAAT 57.386 36.000 4.17 0.00 0.00 1.40
152 157 8.716674 ATGTATACTTCCTCCGTTCCTAAATA 57.283 34.615 4.17 0.00 0.00 1.40
153 158 8.716674 TGTATACTTCCTCCGTTCCTAAATAT 57.283 34.615 4.17 0.00 0.00 1.28
154 159 9.151177 TGTATACTTCCTCCGTTCCTAAATATT 57.849 33.333 4.17 0.00 0.00 1.28
155 160 9.993454 GTATACTTCCTCCGTTCCTAAATATTT 57.007 33.333 5.89 5.89 0.00 1.40
156 161 8.904099 ATACTTCCTCCGTTCCTAAATATTTG 57.096 34.615 11.05 1.40 0.00 2.32
157 162 5.589050 ACTTCCTCCGTTCCTAAATATTTGC 59.411 40.000 11.05 0.00 0.00 3.68
158 163 5.105567 TCCTCCGTTCCTAAATATTTGCA 57.894 39.130 11.05 0.00 0.00 4.08
159 164 5.690865 TCCTCCGTTCCTAAATATTTGCAT 58.309 37.500 11.05 0.00 0.00 3.96
160 165 6.126409 TCCTCCGTTCCTAAATATTTGCATT 58.874 36.000 11.05 0.00 0.00 3.56
161 166 6.605594 TCCTCCGTTCCTAAATATTTGCATTT 59.394 34.615 11.05 0.00 32.91 2.32
162 167 7.123547 TCCTCCGTTCCTAAATATTTGCATTTT 59.876 33.333 11.05 0.00 30.84 1.82
163 168 7.763985 CCTCCGTTCCTAAATATTTGCATTTTT 59.236 33.333 11.05 0.00 30.84 1.94
164 169 9.796120 CTCCGTTCCTAAATATTTGCATTTTTA 57.204 29.630 11.05 0.00 30.84 1.52
165 170 9.796120 TCCGTTCCTAAATATTTGCATTTTTAG 57.204 29.630 11.05 0.00 35.36 1.85
166 171 9.796120 CCGTTCCTAAATATTTGCATTTTTAGA 57.204 29.630 11.05 0.00 36.64 2.10
181 186 9.638239 TGCATTTTTAGAGATTTCAAATGTACC 57.362 29.630 8.43 0.00 37.23 3.34
182 187 9.638239 GCATTTTTAGAGATTTCAAATGTACCA 57.362 29.630 8.43 0.00 37.23 3.25
188 193 7.539712 AGAGATTTCAAATGTACCACATACG 57.460 36.000 0.00 0.00 37.97 3.06
189 194 6.538742 AGAGATTTCAAATGTACCACATACGG 59.461 38.462 0.00 0.00 37.97 4.02
190 195 6.411376 AGATTTCAAATGTACCACATACGGA 58.589 36.000 0.00 0.00 37.97 4.69
191 196 7.054124 AGATTTCAAATGTACCACATACGGAT 58.946 34.615 0.00 0.00 37.97 4.18
192 197 6.429791 TTTCAAATGTACCACATACGGATG 57.570 37.500 5.94 5.94 37.97 3.51
193 198 3.874543 TCAAATGTACCACATACGGATGC 59.125 43.478 7.78 0.00 37.97 3.91
194 199 3.552132 AATGTACCACATACGGATGCA 57.448 42.857 7.78 0.00 37.97 3.96
195 200 3.769739 ATGTACCACATACGGATGCAT 57.230 42.857 7.78 0.00 36.99 3.96
196 201 4.882842 ATGTACCACATACGGATGCATA 57.117 40.909 7.78 0.00 36.99 3.14
197 202 4.882842 TGTACCACATACGGATGCATAT 57.117 40.909 7.78 0.00 36.43 1.78
198 203 5.986501 TGTACCACATACGGATGCATATA 57.013 39.130 7.78 0.00 36.43 0.86
199 204 5.961272 TGTACCACATACGGATGCATATAG 58.039 41.667 7.78 0.00 36.43 1.31
200 205 5.712917 TGTACCACATACGGATGCATATAGA 59.287 40.000 7.78 0.00 36.43 1.98
201 206 5.073311 ACCACATACGGATGCATATAGAC 57.927 43.478 7.78 0.00 36.43 2.59
202 207 4.526650 ACCACATACGGATGCATATAGACA 59.473 41.667 7.78 0.00 36.43 3.41
203 208 5.187772 ACCACATACGGATGCATATAGACAT 59.812 40.000 7.78 0.00 36.43 3.06
204 209 6.379988 ACCACATACGGATGCATATAGACATA 59.620 38.462 7.78 0.00 36.43 2.29
205 210 7.069950 ACCACATACGGATGCATATAGACATAT 59.930 37.037 7.78 0.00 36.43 1.78
206 211 7.928167 CCACATACGGATGCATATAGACATATT 59.072 37.037 7.78 0.00 36.43 1.28
207 212 9.317936 CACATACGGATGCATATAGACATATTT 57.682 33.333 7.78 0.00 36.43 1.40
208 213 9.890629 ACATACGGATGCATATAGACATATTTT 57.109 29.630 7.78 0.00 36.43 1.82
212 217 9.809096 ACGGATGCATATAGACATATTTTAGAG 57.191 33.333 0.00 0.00 0.00 2.43
213 218 8.759641 CGGATGCATATAGACATATTTTAGAGC 58.240 37.037 0.00 0.00 0.00 4.09
214 219 8.759641 GGATGCATATAGACATATTTTAGAGCG 58.240 37.037 0.00 0.00 0.00 5.03
215 220 9.307121 GATGCATATAGACATATTTTAGAGCGT 57.693 33.333 0.00 0.00 0.00 5.07
217 222 9.788960 TGCATATAGACATATTTTAGAGCGTAG 57.211 33.333 0.00 0.00 0.00 3.51
223 228 8.804688 AGACATATTTTAGAGCGTAGATTCAC 57.195 34.615 0.00 0.00 0.00 3.18
224 229 8.634444 AGACATATTTTAGAGCGTAGATTCACT 58.366 33.333 0.00 0.00 0.00 3.41
225 230 8.804688 ACATATTTTAGAGCGTAGATTCACTC 57.195 34.615 0.00 0.00 0.00 3.51
226 231 8.414003 ACATATTTTAGAGCGTAGATTCACTCA 58.586 33.333 0.00 0.00 0.00 3.41
227 232 9.416794 CATATTTTAGAGCGTAGATTCACTCAT 57.583 33.333 0.00 0.00 0.00 2.90
228 233 9.988815 ATATTTTAGAGCGTAGATTCACTCATT 57.011 29.630 0.00 0.00 0.00 2.57
229 234 8.723942 ATTTTAGAGCGTAGATTCACTCATTT 57.276 30.769 0.00 0.00 0.00 2.32
230 235 8.547967 TTTTAGAGCGTAGATTCACTCATTTT 57.452 30.769 0.00 0.00 0.00 1.82
231 236 7.525688 TTAGAGCGTAGATTCACTCATTTTG 57.474 36.000 0.00 0.00 0.00 2.44
232 237 4.331168 AGAGCGTAGATTCACTCATTTTGC 59.669 41.667 0.00 0.00 0.00 3.68
233 238 4.256920 AGCGTAGATTCACTCATTTTGCT 58.743 39.130 0.00 0.00 0.00 3.91
234 239 4.331168 AGCGTAGATTCACTCATTTTGCTC 59.669 41.667 0.00 0.00 0.00 4.26
235 240 4.494855 GCGTAGATTCACTCATTTTGCTCC 60.495 45.833 0.00 0.00 0.00 4.70
236 241 4.259970 CGTAGATTCACTCATTTTGCTCCG 60.260 45.833 0.00 0.00 0.00 4.63
237 242 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
238 243 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
239 244 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
240 245 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
241 246 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
242 247 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
243 248 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
244 249 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
245 250 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
246 251 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
247 252 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
248 253 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
249 254 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
250 255 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
251 256 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
252 257 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
253 258 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
254 259 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
255 260 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
256 261 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
257 262 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
258 263 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
259 264 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
260 265 7.117812 CCGTATGTAGTCACTTGTTGAAATCTT 59.882 37.037 0.00 0.00 35.39 2.40
261 266 8.495949 CGTATGTAGTCACTTGTTGAAATCTTT 58.504 33.333 0.00 0.00 35.39 2.52
264 269 9.778741 ATGTAGTCACTTGTTGAAATCTTTAGA 57.221 29.630 0.00 0.00 35.39 2.10
265 270 9.607988 TGTAGTCACTTGTTGAAATCTTTAGAA 57.392 29.630 0.00 0.00 35.39 2.10
268 273 9.396022 AGTCACTTGTTGAAATCTTTAGAAAGA 57.604 29.630 7.15 7.15 41.72 2.52
269 274 9.439537 GTCACTTGTTGAAATCTTTAGAAAGAC 57.560 33.333 6.85 0.00 40.95 3.01
270 275 9.173021 TCACTTGTTGAAATCTTTAGAAAGACA 57.827 29.630 6.85 0.00 46.80 3.41
271 276 9.787532 CACTTGTTGAAATCTTTAGAAAGACAA 57.212 29.630 6.85 4.98 46.80 3.18
286 291 9.947433 TTAGAAAGACAAATATTTAGGAACGGA 57.053 29.630 0.00 0.00 0.00 4.69
287 292 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
288 293 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
289 294 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
290 295 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
291 296 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
292 297 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
317 322 4.806342 TTGTAGGTGTCGAAAAAGAAGC 57.194 40.909 0.00 0.00 0.00 3.86
339 344 5.774690 AGCAAGGTGGTTGAAATCTTTATCA 59.225 36.000 0.00 0.00 38.60 2.15
349 354 7.807907 GGTTGAAATCTTTATCATGAAACACGT 59.192 33.333 0.00 0.00 0.00 4.49
357 362 9.123709 TCTTTATCATGAAACACGTAAAATTGC 57.876 29.630 0.00 0.00 0.00 3.56
386 397 0.179034 TGCCCACACCAAAAATTGCC 60.179 50.000 0.00 0.00 0.00 4.52
387 398 0.179034 GCCCACACCAAAAATTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
404 415 3.815809 TGCCACTCCCCTAAATAAATCG 58.184 45.455 0.00 0.00 0.00 3.34
428 439 6.524933 CGAAGAAACATTACACAACAACACAA 59.475 34.615 0.00 0.00 0.00 3.33
460 471 5.822519 CAGATGGAAAATAAACGGAGATCCA 59.177 40.000 0.00 0.00 39.59 3.41
461 472 6.488006 CAGATGGAAAATAAACGGAGATCCAT 59.512 38.462 4.18 4.18 46.07 3.41
462 473 6.884280 ATGGAAAATAAACGGAGATCCATC 57.116 37.500 0.00 0.00 41.14 3.51
463 474 5.750524 TGGAAAATAAACGGAGATCCATCA 58.249 37.500 0.00 0.00 35.14 3.07
464 475 6.184068 TGGAAAATAAACGGAGATCCATCAA 58.816 36.000 0.00 0.00 35.14 2.57
465 476 6.094881 TGGAAAATAAACGGAGATCCATCAAC 59.905 38.462 0.00 0.00 35.14 3.18
466 477 5.734855 AAATAAACGGAGATCCATCAACG 57.265 39.130 0.00 2.53 35.14 4.10
467 478 4.665833 ATAAACGGAGATCCATCAACGA 57.334 40.909 9.12 0.00 35.14 3.85
468 479 2.295253 AACGGAGATCCATCAACGAC 57.705 50.000 9.12 0.00 35.14 4.34
469 480 1.475403 ACGGAGATCCATCAACGACT 58.525 50.000 9.12 0.00 35.14 4.18
470 481 1.135139 ACGGAGATCCATCAACGACTG 59.865 52.381 9.12 0.00 35.14 3.51
471 482 1.405463 CGGAGATCCATCAACGACTGA 59.595 52.381 0.00 0.00 38.81 3.41
472 483 2.796383 CGGAGATCCATCAACGACTGAC 60.796 54.545 0.00 0.00 36.69 3.51
473 484 2.428890 GGAGATCCATCAACGACTGACT 59.571 50.000 0.00 0.00 36.69 3.41
474 485 3.118956 GGAGATCCATCAACGACTGACTT 60.119 47.826 0.00 0.00 36.69 3.01
475 486 4.499183 GAGATCCATCAACGACTGACTTT 58.501 43.478 0.00 0.00 36.69 2.66
476 487 4.499183 AGATCCATCAACGACTGACTTTC 58.501 43.478 0.00 0.00 36.69 2.62
477 488 3.744238 TCCATCAACGACTGACTTTCA 57.256 42.857 0.00 0.00 36.69 2.69
502 513 8.443937 CAGTCCAAAAATTGTAGCTTCTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
552 563 2.154567 ATGTGCCTGCTTGGATTGAT 57.845 45.000 0.49 0.00 38.35 2.57
558 569 2.223340 GCCTGCTTGGATTGATTGTACG 60.223 50.000 0.49 0.00 38.35 3.67
571 582 3.435327 TGATTGTACGCAGTTCCATCAAC 59.565 43.478 0.00 0.00 37.78 3.18
714 725 6.126863 TCATGGGTTAGAATGTTTCTGTCT 57.873 37.500 0.00 0.00 40.94 3.41
735 772 2.590821 AGTGACTGCCATTGCTTCTTT 58.409 42.857 0.00 0.00 38.71 2.52
744 781 4.219507 TGCCATTGCTTCTTTTCCGATTAA 59.780 37.500 0.00 0.00 38.71 1.40
1044 1302 0.984961 TGCTAGGGATGGCTGAAGCT 60.985 55.000 1.74 0.00 41.70 3.74
1051 1309 1.427592 GATGGCTGAAGCTCGAGCAC 61.428 60.000 36.87 28.52 45.16 4.40
1108 1366 1.900351 CCTCTGAACCGCCTGATCA 59.100 57.895 0.00 0.00 0.00 2.92
1251 1509 1.603802 AGTCTCATTTGCAACCACACG 59.396 47.619 0.00 0.00 0.00 4.49
1419 1677 3.373438 CCATCCCCATGAAATCTGGTCTT 60.373 47.826 0.00 0.00 30.57 3.01
1628 1886 1.675219 GCCCTGGGTCGTGTTCTTA 59.325 57.895 15.56 0.00 0.00 2.10
1656 1914 7.174772 ACATATTCTGCATTAACAGTTCACACA 59.825 33.333 0.00 0.00 38.84 3.72
1687 1945 3.636300 TCAATTTGTTCCCCACAAGACAG 59.364 43.478 0.00 0.00 46.37 3.51
1876 2134 5.222079 TGCCGATAAAGGTTATATCTGCA 57.778 39.130 8.07 8.07 43.28 4.41
2097 2356 5.484734 ACTATCTCACTAAGTACCCCCTT 57.515 43.478 0.00 0.00 0.00 3.95
2129 2388 7.287005 TGAAATATAAGGCTTCTTCGGTCTCTA 59.713 37.037 1.30 0.00 32.23 2.43
2171 2432 8.032451 ACCAACAATTGCTTTAATATGTGGTAC 58.968 33.333 5.05 0.00 30.86 3.34
2501 2888 3.949754 TCCATCAAGATTCATGAGCAACC 59.050 43.478 0.00 0.00 0.00 3.77
2597 2984 0.729690 GTTTCCTGGATTCGCTCTGC 59.270 55.000 0.00 0.00 0.00 4.26
2615 3002 2.647784 CACAAACACGTGCCAACAC 58.352 52.632 17.22 0.00 43.76 3.32
2649 3043 1.069765 CTGGAACACTCACGGCACT 59.930 57.895 0.00 0.00 0.00 4.40
2789 3187 6.653320 ACAAAGACTCACTGAACAACTAACAA 59.347 34.615 0.00 0.00 0.00 2.83
3131 3693 1.456544 GTTGCCACACATTCATTTGCG 59.543 47.619 0.00 0.00 0.00 4.85
3353 3918 4.631131 TGGTCATATGATTGCTACTTCCG 58.369 43.478 9.02 0.00 0.00 4.30
3354 3919 4.343814 TGGTCATATGATTGCTACTTCCGA 59.656 41.667 9.02 0.00 0.00 4.55
3613 4179 2.866762 GTGTTGAGAACAAGAGCGACTT 59.133 45.455 0.00 0.00 44.16 3.01
3892 4458 8.747471 ACAACTACAAGTATAAACTACTCCCTC 58.253 37.037 0.00 0.00 33.75 4.30
3893 4459 7.894753 ACTACAAGTATAAACTACTCCCTCC 57.105 40.000 0.00 0.00 33.75 4.30
3894 4460 5.848833 ACAAGTATAAACTACTCCCTCCG 57.151 43.478 0.00 0.00 33.75 4.63
4017 4583 8.547967 TGTAGTCCACATTGAAATCTCTAAAC 57.452 34.615 0.00 0.00 30.04 2.01
4045 4611 9.364653 GACTTATATTTAGGAACAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
4367 4934 1.878656 GCTCAGACACTACACCGCCT 61.879 60.000 0.00 0.00 0.00 5.52
4649 5216 1.474677 GGTGTCATCAGCTCCATGGAG 60.475 57.143 33.73 33.73 44.56 3.86
4710 5277 5.464588 TGAAGGAAATCCATACATCCCAA 57.535 39.130 1.67 0.00 38.89 4.12
4834 5401 0.531974 GAGTGCAAACGGACACCAGA 60.532 55.000 0.00 0.00 37.51 3.86
4932 5499 7.377398 TGATATAACAAAAATGCAGTGCACTT 58.623 30.769 22.44 14.14 43.04 3.16
4984 5551 5.302059 GTGAGCCCATCTCTACTGTATGTTA 59.698 44.000 0.00 0.00 42.38 2.41
4987 5554 4.932200 GCCCATCTCTACTGTATGTTATGC 59.068 45.833 0.00 0.00 0.00 3.14
5508 6077 3.660865 AGTGTACGACTTCATTCCCAAC 58.339 45.455 0.00 0.00 0.00 3.77
5722 6291 0.375106 GGATTTCGGCGCTTCAAGAG 59.625 55.000 7.64 0.00 0.00 2.85
6130 9116 6.896613 CGTACAAATTCATCTCAAGTTGATCG 59.103 38.462 5.91 0.00 35.41 3.69
6175 9161 4.573210 CCAGTCCATGGCCATGAG 57.427 61.111 41.32 30.62 43.83 2.90
6288 9274 2.224281 CCCCGCTAGATATGCTTGTCAA 60.224 50.000 0.00 0.00 0.00 3.18
6294 9280 4.987912 GCTAGATATGCTTGTCAACTCTCC 59.012 45.833 0.00 0.00 0.00 3.71
6334 9320 4.067896 TGTTCTTTCTAAGCTGAGGCAAG 58.932 43.478 0.00 1.62 41.70 4.01
6363 9377 2.092968 TCTTGTAAGGCCCTACATGCAG 60.093 50.000 14.99 9.78 31.96 4.41
6403 9418 8.848474 AAATGTACTATTATGCAGTACCATCC 57.152 34.615 9.85 0.00 45.10 3.51
6630 9648 9.313118 TCTTTTTATTCTTTGAACTTTCCAAGC 57.687 29.630 0.00 0.00 31.91 4.01
6667 9685 5.365403 TTTAGTCAAAAGGTTACATGCGG 57.635 39.130 0.00 0.00 0.00 5.69
6714 9732 1.108776 TACGGTGTAGGGTCTCATGC 58.891 55.000 0.00 0.00 0.00 4.06
6785 9810 7.484324 GCTTTCAGCTCTTCAATCTTCATAAAC 59.516 37.037 0.00 0.00 38.45 2.01
6786 9811 7.984422 TTCAGCTCTTCAATCTTCATAAACA 57.016 32.000 0.00 0.00 0.00 2.83
6806 9831 2.114616 AGAAGCATCCCTGAGGTGTAG 58.885 52.381 0.00 0.00 0.00 2.74
6819 9844 0.820871 GGTGTAGAGAGCCCACTGAG 59.179 60.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 7.330208 ACACGTTCAAAGCTTCGTATATTTAGT 59.670 33.333 10.18 1.20 35.13 2.24
97 102 3.988379 AATGCTTCATTGTTCACACGT 57.012 38.095 0.00 0.00 32.39 4.49
124 129 6.402456 AGGAACGGAGGAAGTATACATTAC 57.598 41.667 5.50 0.00 0.00 1.89
132 137 6.764560 GCAAATATTTAGGAACGGAGGAAGTA 59.235 38.462 0.00 0.00 0.00 2.24
133 138 5.589050 GCAAATATTTAGGAACGGAGGAAGT 59.411 40.000 0.00 0.00 0.00 3.01
134 139 5.588648 TGCAAATATTTAGGAACGGAGGAAG 59.411 40.000 0.00 0.00 0.00 3.46
135 140 5.502079 TGCAAATATTTAGGAACGGAGGAA 58.498 37.500 0.00 0.00 0.00 3.36
136 141 5.105567 TGCAAATATTTAGGAACGGAGGA 57.894 39.130 0.00 0.00 0.00 3.71
137 142 6.391227 AATGCAAATATTTAGGAACGGAGG 57.609 37.500 0.00 0.00 0.00 4.30
138 143 8.702163 AAAAATGCAAATATTTAGGAACGGAG 57.298 30.769 0.00 0.00 30.47 4.63
139 144 9.796120 CTAAAAATGCAAATATTTAGGAACGGA 57.204 29.630 0.00 0.00 33.69 4.69
140 145 9.796120 TCTAAAAATGCAAATATTTAGGAACGG 57.204 29.630 16.87 0.00 36.48 4.44
155 160 9.638239 GGTACATTTGAAATCTCTAAAAATGCA 57.362 29.630 6.39 0.00 40.32 3.96
156 161 9.638239 TGGTACATTTGAAATCTCTAAAAATGC 57.362 29.630 6.39 0.00 40.32 3.56
162 167 9.093970 CGTATGTGGTACATTTGAAATCTCTAA 57.906 33.333 0.00 0.00 44.52 2.10
163 168 7.709182 CCGTATGTGGTACATTTGAAATCTCTA 59.291 37.037 0.00 0.00 44.52 2.43
164 169 6.538742 CCGTATGTGGTACATTTGAAATCTCT 59.461 38.462 0.00 0.00 44.52 3.10
165 170 6.537301 TCCGTATGTGGTACATTTGAAATCTC 59.463 38.462 0.00 0.00 44.52 2.75
166 171 6.411376 TCCGTATGTGGTACATTTGAAATCT 58.589 36.000 0.00 0.00 44.52 2.40
167 172 6.671614 TCCGTATGTGGTACATTTGAAATC 57.328 37.500 0.00 0.00 44.52 2.17
168 173 6.459573 GCATCCGTATGTGGTACATTTGAAAT 60.460 38.462 0.00 0.00 44.52 2.17
169 174 5.163703 GCATCCGTATGTGGTACATTTGAAA 60.164 40.000 0.00 0.00 44.52 2.69
170 175 4.334203 GCATCCGTATGTGGTACATTTGAA 59.666 41.667 0.00 0.00 44.52 2.69
171 176 3.874543 GCATCCGTATGTGGTACATTTGA 59.125 43.478 0.00 0.00 44.52 2.69
172 177 3.625313 TGCATCCGTATGTGGTACATTTG 59.375 43.478 0.00 0.00 44.52 2.32
173 178 3.879998 TGCATCCGTATGTGGTACATTT 58.120 40.909 0.00 0.00 44.52 2.32
174 179 3.552132 TGCATCCGTATGTGGTACATT 57.448 42.857 0.00 0.00 44.52 2.71
175 180 3.769739 ATGCATCCGTATGTGGTACAT 57.230 42.857 0.00 0.00 44.52 2.29
176 181 4.882842 ATATGCATCCGTATGTGGTACA 57.117 40.909 0.19 0.00 35.38 2.90
177 182 6.034591 GTCTATATGCATCCGTATGTGGTAC 58.965 44.000 0.19 0.00 35.38 3.34
178 183 5.712917 TGTCTATATGCATCCGTATGTGGTA 59.287 40.000 0.19 0.00 35.38 3.25
179 184 4.526650 TGTCTATATGCATCCGTATGTGGT 59.473 41.667 0.19 0.00 35.38 4.16
180 185 5.072040 TGTCTATATGCATCCGTATGTGG 57.928 43.478 0.19 0.00 35.38 4.17
181 186 8.877808 AATATGTCTATATGCATCCGTATGTG 57.122 34.615 0.19 0.00 35.38 3.21
182 187 9.890629 AAAATATGTCTATATGCATCCGTATGT 57.109 29.630 0.19 0.00 35.38 2.29
186 191 9.809096 CTCTAAAATATGTCTATATGCATCCGT 57.191 33.333 0.19 0.00 30.00 4.69
187 192 8.759641 GCTCTAAAATATGTCTATATGCATCCG 58.240 37.037 0.19 0.00 30.00 4.18
188 193 8.759641 CGCTCTAAAATATGTCTATATGCATCC 58.240 37.037 0.19 0.00 30.00 3.51
189 194 9.307121 ACGCTCTAAAATATGTCTATATGCATC 57.693 33.333 0.19 0.00 30.00 3.91
191 196 9.788960 CTACGCTCTAAAATATGTCTATATGCA 57.211 33.333 0.00 0.00 30.00 3.96
197 202 9.894783 GTGAATCTACGCTCTAAAATATGTCTA 57.105 33.333 0.00 0.00 0.00 2.59
198 203 8.634444 AGTGAATCTACGCTCTAAAATATGTCT 58.366 33.333 0.00 0.00 0.00 3.41
199 204 8.804688 AGTGAATCTACGCTCTAAAATATGTC 57.195 34.615 0.00 0.00 0.00 3.06
200 205 8.414003 TGAGTGAATCTACGCTCTAAAATATGT 58.586 33.333 0.00 0.00 44.58 2.29
201 206 8.803201 TGAGTGAATCTACGCTCTAAAATATG 57.197 34.615 0.00 0.00 44.58 1.78
202 207 9.988815 AATGAGTGAATCTACGCTCTAAAATAT 57.011 29.630 0.00 0.00 44.58 1.28
203 208 9.817809 AAATGAGTGAATCTACGCTCTAAAATA 57.182 29.630 0.00 0.00 44.58 1.40
204 209 8.723942 AAATGAGTGAATCTACGCTCTAAAAT 57.276 30.769 0.00 0.00 44.58 1.82
205 210 8.443160 CAAAATGAGTGAATCTACGCTCTAAAA 58.557 33.333 0.00 0.00 44.58 1.52
206 211 7.413000 GCAAAATGAGTGAATCTACGCTCTAAA 60.413 37.037 0.00 0.00 44.58 1.85
207 212 6.036083 GCAAAATGAGTGAATCTACGCTCTAA 59.964 38.462 0.00 0.00 44.58 2.10
208 213 5.520288 GCAAAATGAGTGAATCTACGCTCTA 59.480 40.000 0.00 0.00 44.58 2.43
209 214 4.331168 GCAAAATGAGTGAATCTACGCTCT 59.669 41.667 0.00 0.00 44.58 4.09
210 215 4.331168 AGCAAAATGAGTGAATCTACGCTC 59.669 41.667 0.00 0.00 44.55 5.03
211 216 4.256920 AGCAAAATGAGTGAATCTACGCT 58.743 39.130 0.00 0.00 0.00 5.07
212 217 4.494855 GGAGCAAAATGAGTGAATCTACGC 60.495 45.833 0.00 0.00 0.00 4.42
213 218 4.259970 CGGAGCAAAATGAGTGAATCTACG 60.260 45.833 0.00 0.00 0.00 3.51
214 219 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
215 220 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
216 221 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
217 222 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
218 223 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
219 224 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
220 225 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
221 226 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
222 227 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
223 228 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
224 229 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
225 230 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
226 231 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
227 232 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
228 233 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
229 234 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
230 235 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
231 236 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
232 237 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
233 238 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
234 239 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
235 240 7.582435 AGATTTCAACAAGTGACTACATACG 57.418 36.000 0.00 0.00 35.39 3.06
238 243 9.778741 TCTAAAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
239 244 9.607988 TTCTAAAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
242 247 9.396022 TCTTTCTAAAGATTTCAACAAGTGACT 57.604 29.630 1.00 0.00 39.95 3.41
243 248 9.439537 GTCTTTCTAAAGATTTCAACAAGTGAC 57.560 33.333 8.31 0.00 45.83 3.67
244 249 9.173021 TGTCTTTCTAAAGATTTCAACAAGTGA 57.827 29.630 8.31 0.00 45.83 3.41
245 250 9.787532 TTGTCTTTCTAAAGATTTCAACAAGTG 57.212 29.630 8.31 0.00 45.83 3.16
260 265 9.947433 TCCGTTCCTAAATATTTGTCTTTCTAA 57.053 29.630 11.05 0.00 0.00 2.10
261 266 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
262 267 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
263 268 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
264 269 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
265 270 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
266 271 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
267 272 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
268 273 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
269 274 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
270 275 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
271 276 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
272 277 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
273 278 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
274 279 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
275 280 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
276 281 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
277 282 3.028850 CAATGTACTCCCTCCGTTCCTA 58.971 50.000 0.00 0.00 0.00 2.94
278 283 1.831736 CAATGTACTCCCTCCGTTCCT 59.168 52.381 0.00 0.00 0.00 3.36
279 284 1.553704 ACAATGTACTCCCTCCGTTCC 59.446 52.381 0.00 0.00 0.00 3.62
280 285 3.181478 CCTACAATGTACTCCCTCCGTTC 60.181 52.174 0.00 0.00 0.00 3.95
281 286 2.764572 CCTACAATGTACTCCCTCCGTT 59.235 50.000 0.00 0.00 0.00 4.44
282 287 2.292061 ACCTACAATGTACTCCCTCCGT 60.292 50.000 0.00 0.00 0.00 4.69
283 288 2.100916 CACCTACAATGTACTCCCTCCG 59.899 54.545 0.00 0.00 0.00 4.63
284 289 3.105283 ACACCTACAATGTACTCCCTCC 58.895 50.000 0.00 0.00 0.00 4.30
285 290 3.181489 CGACACCTACAATGTACTCCCTC 60.181 52.174 0.00 0.00 0.00 4.30
286 291 2.758979 CGACACCTACAATGTACTCCCT 59.241 50.000 0.00 0.00 0.00 4.20
287 292 2.756760 TCGACACCTACAATGTACTCCC 59.243 50.000 0.00 0.00 0.00 4.30
288 293 4.445452 TTCGACACCTACAATGTACTCC 57.555 45.455 0.00 0.00 0.00 3.85
289 294 6.643770 TCTTTTTCGACACCTACAATGTACTC 59.356 38.462 0.00 0.00 0.00 2.59
290 295 6.518493 TCTTTTTCGACACCTACAATGTACT 58.482 36.000 0.00 0.00 0.00 2.73
291 296 6.774354 TCTTTTTCGACACCTACAATGTAC 57.226 37.500 0.00 0.00 0.00 2.90
292 297 6.073440 GCTTCTTTTTCGACACCTACAATGTA 60.073 38.462 0.00 0.00 0.00 2.29
317 322 7.829725 TCATGATAAAGATTTCAACCACCTTG 58.170 34.615 0.00 0.00 0.00 3.61
339 344 6.075099 CGAAAGTGCAATTTTACGTGTTTCAT 60.075 34.615 14.04 0.00 0.00 2.57
357 362 1.081242 GTGTGGGCATGCGAAAGTG 60.081 57.895 12.44 0.00 0.00 3.16
386 397 7.335924 TGTTTCTTCGATTTATTTAGGGGAGTG 59.664 37.037 0.00 0.00 0.00 3.51
387 398 7.399634 TGTTTCTTCGATTTATTTAGGGGAGT 58.600 34.615 0.00 0.00 0.00 3.85
404 415 7.804614 TTGTGTTGTTGTGTAATGTTTCTTC 57.195 32.000 0.00 0.00 0.00 2.87
472 483 7.428826 AGAAGCTACAATTTTTGGACTGAAAG 58.571 34.615 0.00 0.00 35.52 2.62
473 484 7.346751 AGAAGCTACAATTTTTGGACTGAAA 57.653 32.000 0.00 0.00 34.12 2.69
474 485 6.959639 AGAAGCTACAATTTTTGGACTGAA 57.040 33.333 0.00 0.00 34.12 3.02
475 486 7.224297 ACTAGAAGCTACAATTTTTGGACTGA 58.776 34.615 0.00 0.00 34.12 3.41
476 487 7.440523 ACTAGAAGCTACAATTTTTGGACTG 57.559 36.000 0.00 0.00 34.12 3.51
477 488 8.376270 AGTACTAGAAGCTACAATTTTTGGACT 58.624 33.333 0.00 0.00 34.12 3.85
478 489 8.549338 AGTACTAGAAGCTACAATTTTTGGAC 57.451 34.615 0.00 0.00 34.12 4.02
488 499 8.684520 GGACAAAGATAAGTACTAGAAGCTACA 58.315 37.037 0.00 0.00 0.00 2.74
489 500 7.856894 CGGACAAAGATAAGTACTAGAAGCTAC 59.143 40.741 0.00 0.00 0.00 3.58
502 513 1.083489 TTGCGGCGGACAAAGATAAG 58.917 50.000 9.78 0.00 0.00 1.73
552 563 1.795872 CGTTGATGGAACTGCGTACAA 59.204 47.619 0.00 0.00 31.70 2.41
558 569 1.461127 GTCAGTCGTTGATGGAACTGC 59.539 52.381 0.00 0.00 38.29 4.40
599 610 1.375523 GCAGGTACCACTCCGTTGG 60.376 63.158 15.94 0.00 43.04 3.77
603 614 1.079127 CCAAGCAGGTACCACTCCG 60.079 63.158 15.94 6.09 0.00 4.63
714 725 3.423539 AAGAAGCAATGGCAGTCACTA 57.576 42.857 0.00 0.00 44.61 2.74
735 772 3.798337 GGAACGAGCGTAATTAATCGGAA 59.202 43.478 16.02 0.00 39.42 4.30
744 781 0.108992 TGCGAAGGAACGAGCGTAAT 60.109 50.000 0.00 0.00 35.09 1.89
795 1053 7.982354 AGTTTCTCCATTTCTCTTATTAGGACG 59.018 37.037 0.00 0.00 0.00 4.79
1044 1302 1.595109 CACAACTGCAGGTGCTCGA 60.595 57.895 31.50 0.00 42.66 4.04
1051 1309 1.602311 AAGCTTCTCACAACTGCAGG 58.398 50.000 19.93 3.21 0.00 4.85
1251 1509 3.523972 AGAAGAGTTTAGGGGGATTGGTC 59.476 47.826 0.00 0.00 0.00 4.02
1328 1586 2.555325 CACAAGTTCACTGACATGCCAT 59.445 45.455 0.00 0.00 0.00 4.40
1419 1677 3.054508 TCCATGACATGTTGTAGGCATCA 60.055 43.478 14.26 0.00 0.00 3.07
1628 1886 9.394767 TGTGAACTGTTAATGCAGAATATGTAT 57.605 29.630 0.00 0.00 39.62 2.29
1656 1914 3.568430 GGGGAACAAATTGAAACTCGAGT 59.432 43.478 13.58 13.58 0.00 4.18
1876 2134 3.614092 CTTCATAACCACTGATGCACCT 58.386 45.455 0.00 0.00 0.00 4.00
2006 2265 8.289939 TCGTGGACTTAGTTTCATAGAACTAT 57.710 34.615 0.00 0.00 40.66 2.12
2024 2283 7.908601 GGTATTGTTTCTTTGATTATCGTGGAC 59.091 37.037 0.00 0.00 0.00 4.02
2129 2388 4.929479 TGTTGGTCAAGGCCTTGTAATAT 58.071 39.130 37.97 5.06 41.16 1.28
2241 2502 9.308318 GTTGTCAGTTAATTTGTGGTTTATGTT 57.692 29.630 0.00 0.00 0.00 2.71
2401 2663 5.365619 CCAGTAGTGTCACAGGTAAAAACT 58.634 41.667 5.62 0.00 0.00 2.66
2402 2664 4.514066 CCCAGTAGTGTCACAGGTAAAAAC 59.486 45.833 5.62 0.00 0.00 2.43
2469 2856 7.454066 TCATGAATCTTGATGGATAGCTAGTCT 59.546 37.037 0.00 0.00 0.00 3.24
2501 2888 3.837213 AGAACAAATCAATGGCTCACG 57.163 42.857 0.00 0.00 0.00 4.35
2597 2984 2.647784 GTGTTGGCACGTGTTTGTG 58.352 52.632 18.38 0.00 42.81 3.33
2615 3002 1.472878 TCCAGAAAGATCGTGGAGTCG 59.527 52.381 5.37 0.00 35.36 4.18
2649 3043 1.141858 TGTGGTGTGTGGTAGCATTCA 59.858 47.619 0.00 0.00 0.00 2.57
2677 3071 7.814107 TCCAAAATAGCAGACTTTAATTTGCAG 59.186 33.333 0.78 0.00 38.97 4.41
2750 3148 8.317679 AGTGAGTCTTTGTTTGCTAGATATTCT 58.682 33.333 0.00 0.00 0.00 2.40
2789 3187 4.078537 TGTTCACCCATCGATTTGACAAT 58.921 39.130 0.00 0.00 0.00 2.71
2839 3399 7.741652 GTGCTTTGATTTGTAAAAGCTTAATGC 59.258 33.333 17.92 1.74 45.59 3.56
2969 3530 4.917998 TGCTATGCGCGTATTTTTCAAAAA 59.082 33.333 16.54 0.00 43.27 1.94
2970 3531 4.322274 GTGCTATGCGCGTATTTTTCAAAA 59.678 37.500 16.54 0.00 43.27 2.44
2971 3532 3.849145 GTGCTATGCGCGTATTTTTCAAA 59.151 39.130 16.54 0.00 43.27 2.69
2972 3533 3.421741 GTGCTATGCGCGTATTTTTCAA 58.578 40.909 16.54 0.00 43.27 2.69
3323 3888 1.825105 ATCATATGACCAGTGGGGCT 58.175 50.000 15.21 0.00 45.45 5.19
3701 4267 6.128172 GCTTGTACATTAACTCAATCACAGCT 60.128 38.462 0.00 0.00 0.00 4.24
3927 4493 6.748658 TCGTTTTACTCCGTATGTAGTTCATG 59.251 38.462 0.00 0.00 37.91 3.07
3940 4506 5.285607 GTGTAGATTCACTCGTTTTACTCCG 59.714 44.000 0.00 0.00 35.68 4.63
3950 4516 7.303261 TGTAGTTTACAGTGTAGATTCACTCG 58.697 38.462 2.68 0.00 45.37 4.18
4017 4583 8.251383 TCCCTCTGTTCCTAAATATAAGTCTG 57.749 38.462 0.00 0.00 0.00 3.51
4036 4602 8.734763 TCAATAGGACTAGTTTATACTCCCTCT 58.265 37.037 0.00 0.00 35.78 3.69
4367 4934 5.052693 AGCCATTATTATGCCAGAGAACA 57.947 39.130 0.00 0.00 0.00 3.18
4430 4997 5.043903 ACACTCGACTCATATTTGATTCCG 58.956 41.667 0.00 0.00 29.96 4.30
4649 5216 3.945285 CACACCTGTATCCAACATAACCC 59.055 47.826 0.00 0.00 37.50 4.11
4710 5277 2.041216 GGGGAGTACCTTCACAACCATT 59.959 50.000 0.00 0.00 40.03 3.16
4984 5551 0.984230 TCTTTTGAGGGGACGAGCAT 59.016 50.000 0.00 0.00 0.00 3.79
4987 5554 3.489398 CGAGTATCTTTTGAGGGGACGAG 60.489 52.174 0.00 0.00 0.00 4.18
5722 6291 9.353531 AACATGAGTTTGATCAATGGGGACAAC 62.354 40.741 9.40 1.69 38.39 3.32
6130 9116 2.131183 GCATCTCATACTCAACGGCTC 58.869 52.381 0.00 0.00 0.00 4.70
6175 9161 1.001068 GATAAGTTCTCCCGGCTAGGC 59.999 57.143 6.15 6.15 39.21 3.93
6221 9207 1.141455 TGCTCCAAGCTATAGCATGCA 59.859 47.619 26.07 21.74 42.97 3.96
6288 9274 2.435372 TGGCAAAAACACTGGAGAGT 57.565 45.000 0.00 0.00 0.00 3.24
6294 9280 2.903798 ACAACCATGGCAAAAACACTG 58.096 42.857 13.04 0.00 0.00 3.66
6334 9320 4.489306 AGGGCCTTACAAGATACAGTTC 57.511 45.455 0.00 0.00 0.00 3.01
6383 9398 8.934697 AGAAAAGGATGGTACTGCATAATAGTA 58.065 33.333 0.00 0.00 0.00 1.82
6384 9399 7.806180 AGAAAAGGATGGTACTGCATAATAGT 58.194 34.615 0.00 0.00 0.00 2.12
6385 9400 8.682936 AAGAAAAGGATGGTACTGCATAATAG 57.317 34.615 0.00 0.00 0.00 1.73
6403 9418 9.774742 GGTACTGTATATGCTCAAAAAGAAAAG 57.225 33.333 0.00 0.00 0.00 2.27
6630 9648 5.356882 TGACTAAAGGAAGATGCAAAACG 57.643 39.130 0.00 0.00 0.00 3.60
6684 9702 3.317430 CCCTACACCGTATGTAACCTCTC 59.683 52.174 0.00 0.00 43.35 3.20
6686 9704 3.026694 ACCCTACACCGTATGTAACCTC 58.973 50.000 0.00 0.00 43.35 3.85
6714 9732 1.380524 CTTGATTCAGCAGAGCCAGG 58.619 55.000 0.00 0.00 0.00 4.45
6785 9810 0.617413 ACACCTCAGGGATGCTTCTG 59.383 55.000 0.00 0.00 36.25 3.02
6786 9811 2.114616 CTACACCTCAGGGATGCTTCT 58.885 52.381 0.00 0.00 36.25 2.85
6806 9831 4.402155 CCTCATATATCTCAGTGGGCTCTC 59.598 50.000 0.00 0.00 0.00 3.20



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

AutoCloner maintained by Alex Coulton.