Multiple sequence alignment - TraesCS7A01G348000

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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 TraesCS7A01G348000 chr7A 100.000 2549 0 0 1 2549 510731532 510734080 0.000000e+00 4708
1 TraesCS7A01G348000 chr7A 85.793 908 74 26 763 1657 510552001 510552866 0.000000e+00 911
2 TraesCS7A01G348000 chr7A 93.510 339 19 3 1 338 404007702 404008038 3.790000e-138 501
3 TraesCS7A01G348000 chr7A 84.935 385 38 8 338 716 510551478 510551848 3.100000e-99 372
4 TraesCS7A01G348000 chr7A 86.061 165 19 4 1525 1686 510629507 510629670 9.370000e-40 174
5 TraesCS7A01G348000 chr2A 96.248 773 26 3 1778 2549 733656330 733655560 0.000000e+00 1264
6 TraesCS7A01G348000 chr2A 92.515 334 25 0 1 334 674342011 674342344 1.770000e-131 479
7 TraesCS7A01G348000 chr5A 95.501 778 30 5 1774 2549 546134329 546133555 0.000000e+00 1238
8 TraesCS7A01G348000 chr1A 95.602 773 31 3 1778 2549 534171188 534171958 0.000000e+00 1236
9 TraesCS7A01G348000 chr1A 95.084 773 36 2 1778 2549 472139620 472138849 0.000000e+00 1216
10 TraesCS7A01G348000 chr1A 89.157 83 9 0 427 509 505103977 505104059 1.250000e-18 104
11 TraesCS7A01G348000 chr3D 95.343 773 34 2 1778 2549 426434086 426433315 0.000000e+00 1227
12 TraesCS7A01G348000 chr5B 95.128 780 32 3 1775 2549 38109898 38110676 0.000000e+00 1225
13 TraesCS7A01G348000 chr3A 95.343 773 33 3 1778 2549 8177182 8177952 0.000000e+00 1225
14 TraesCS7A01G348000 chr3A 95.220 774 33 4 1778 2549 14861267 14862038 0.000000e+00 1221
15 TraesCS7A01G348000 chr5D 95.220 774 30 4 1777 2549 437909785 437910552 0.000000e+00 1218
16 TraesCS7A01G348000 chr5D 92.330 339 25 1 1 338 287288669 287289007 4.930000e-132 481
17 TraesCS7A01G348000 chr7D 85.533 1023 95 23 784 1781 422571974 422570980 0.000000e+00 1020
18 TraesCS7A01G348000 chr7D 87.132 917 87 16 763 1665 422618500 422617601 0.000000e+00 1011
19 TraesCS7A01G348000 chr7D 92.035 339 26 1 1 338 231098038 231097700 2.290000e-130 475
20 TraesCS7A01G348000 chr7D 86.682 443 30 9 338 767 422619008 422618582 4.970000e-127 464
21 TraesCS7A01G348000 chr7B 87.118 916 75 21 764 1665 439604221 439603335 0.000000e+00 998
22 TraesCS7A01G348000 chr7B 87.442 430 48 4 1138 1566 439589903 439589479 8.200000e-135 490
23 TraesCS7A01G348000 chr7B 86.131 411 32 8 369 767 439604706 439604309 1.090000e-113 420
24 TraesCS7A01G348000 chr1D 84.780 841 86 25 763 1572 408960346 408961175 0.000000e+00 806
25 TraesCS7A01G348000 chr1D 92.920 339 23 1 1 338 101434002 101433664 2.280000e-135 492
26 TraesCS7A01G348000 chr1D 92.353 340 22 3 1 338 280199867 280199530 4.930000e-132 481
27 TraesCS7A01G348000 chr1D 92.035 339 26 1 1 338 27171710 27171372 2.290000e-130 475
28 TraesCS7A01G348000 chr1D 82.732 388 34 13 338 711 408940853 408941221 5.290000e-82 315
29 TraesCS7A01G348000 chr1B 85.714 497 55 9 883 1369 550501726 550502216 6.290000e-141 510
30 TraesCS7A01G348000 chr1B 81.503 346 24 13 448 765 550759669 550760002 5.450000e-62 248
31 TraesCS7A01G348000 chr1B 83.913 230 19 7 1418 1646 550502225 550502437 1.200000e-48 204
32 TraesCS7A01G348000 chr1B 79.899 199 28 8 891 1085 550765235 550765425 4.420000e-28 135
33 TraesCS7A01G348000 chr6D 93.215 339 22 1 1 338 353006341 353006003 4.900000e-137 497
34 TraesCS7A01G348000 chr2D 92.035 339 26 1 1 338 191278225 191278563 2.290000e-130 475


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 TraesCS7A01G348000 chr7A 510731532 510734080 2548 False 4708.0 4708 100.0000 1 2549 1 chr7A.!!$F3 2548
1 TraesCS7A01G348000 chr7A 510551478 510552866 1388 False 641.5 911 85.3640 338 1657 2 chr7A.!!$F4 1319
2 TraesCS7A01G348000 chr2A 733655560 733656330 770 True 1264.0 1264 96.2480 1778 2549 1 chr2A.!!$R1 771
3 TraesCS7A01G348000 chr5A 546133555 546134329 774 True 1238.0 1238 95.5010 1774 2549 1 chr5A.!!$R1 775
4 TraesCS7A01G348000 chr1A 534171188 534171958 770 False 1236.0 1236 95.6020 1778 2549 1 chr1A.!!$F2 771
5 TraesCS7A01G348000 chr1A 472138849 472139620 771 True 1216.0 1216 95.0840 1778 2549 1 chr1A.!!$R1 771
6 TraesCS7A01G348000 chr3D 426433315 426434086 771 True 1227.0 1227 95.3430 1778 2549 1 chr3D.!!$R1 771
7 TraesCS7A01G348000 chr5B 38109898 38110676 778 False 1225.0 1225 95.1280 1775 2549 1 chr5B.!!$F1 774
8 TraesCS7A01G348000 chr3A 8177182 8177952 770 False 1225.0 1225 95.3430 1778 2549 1 chr3A.!!$F1 771
9 TraesCS7A01G348000 chr3A 14861267 14862038 771 False 1221.0 1221 95.2200 1778 2549 1 chr3A.!!$F2 771
10 TraesCS7A01G348000 chr5D 437909785 437910552 767 False 1218.0 1218 95.2200 1777 2549 1 chr5D.!!$F2 772
11 TraesCS7A01G348000 chr7D 422570980 422571974 994 True 1020.0 1020 85.5330 784 1781 1 chr7D.!!$R2 997
12 TraesCS7A01G348000 chr7D 422617601 422619008 1407 True 737.5 1011 86.9070 338 1665 2 chr7D.!!$R3 1327
13 TraesCS7A01G348000 chr7B 439603335 439604706 1371 True 709.0 998 86.6245 369 1665 2 chr7B.!!$R2 1296
14 TraesCS7A01G348000 chr1D 408960346 408961175 829 False 806.0 806 84.7800 763 1572 1 chr1D.!!$F2 809
15 TraesCS7A01G348000 chr1B 550501726 550502437 711 False 357.0 510 84.8135 883 1646 2 chr1B.!!$F3 763

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
961 1123 0.036388 ACTTACCAGCATCCCACACG 60.036 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 2482 0.324943 AGCAGCACTACCGGAACAAT 59.675 50.0 9.46 0.0 0.0 2.71 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
23 24 5.407407 TCCCACTATCTTGAAAGAGTGTC 57.593 43.478 10.03 0.00 38.66 3.67
24 25 4.082190 TCCCACTATCTTGAAAGAGTGTCG 60.082 45.833 10.03 2.98 38.66 4.35
25 26 4.082190 CCCACTATCTTGAAAGAGTGTCGA 60.082 45.833 10.03 0.00 38.66 4.20
26 27 4.859798 CCACTATCTTGAAAGAGTGTCGAC 59.140 45.833 9.11 9.11 38.66 4.20
27 28 5.336055 CCACTATCTTGAAAGAGTGTCGACT 60.336 44.000 17.92 0.00 38.66 4.18
28 29 6.153067 CACTATCTTGAAAGAGTGTCGACTT 58.847 40.000 17.92 4.89 38.66 3.01
29 30 6.642950 CACTATCTTGAAAGAGTGTCGACTTT 59.357 38.462 17.92 8.68 38.66 2.66
30 31 5.914085 ATCTTGAAAGAGTGTCGACTTTG 57.086 39.130 17.92 0.00 38.66 2.77
31 32 3.555956 TCTTGAAAGAGTGTCGACTTTGC 59.444 43.478 17.92 5.54 36.63 3.68
32 33 2.899976 TGAAAGAGTGTCGACTTTGCA 58.100 42.857 17.92 8.01 36.63 4.08
33 34 3.466836 TGAAAGAGTGTCGACTTTGCAT 58.533 40.909 17.92 0.00 36.63 3.96
34 35 3.248363 TGAAAGAGTGTCGACTTTGCATG 59.752 43.478 17.92 0.00 36.63 4.06
35 36 1.151668 AGAGTGTCGACTTTGCATGC 58.848 50.000 17.92 11.82 30.16 4.06
36 37 0.867746 GAGTGTCGACTTTGCATGCA 59.132 50.000 18.46 18.46 30.16 3.96
37 38 1.466167 GAGTGTCGACTTTGCATGCAT 59.534 47.619 23.37 6.60 30.16 3.96
38 39 1.198408 AGTGTCGACTTTGCATGCATG 59.802 47.619 23.37 22.70 0.00 4.06
39 40 1.069022 GTGTCGACTTTGCATGCATGT 60.069 47.619 26.79 22.34 0.00 3.21
40 41 1.069091 TGTCGACTTTGCATGCATGTG 60.069 47.619 26.79 16.34 0.00 3.21
41 42 0.522626 TCGACTTTGCATGCATGTGG 59.477 50.000 26.79 22.20 0.00 4.17
42 43 0.522626 CGACTTTGCATGCATGTGGA 59.477 50.000 26.79 11.10 0.00 4.02
43 44 1.133598 CGACTTTGCATGCATGTGGAT 59.866 47.619 26.79 10.06 0.00 3.41
44 45 2.416296 CGACTTTGCATGCATGTGGATT 60.416 45.455 26.79 9.94 0.00 3.01
45 46 3.181498 CGACTTTGCATGCATGTGGATTA 60.181 43.478 26.79 0.00 0.00 1.75
46 47 4.498513 CGACTTTGCATGCATGTGGATTAT 60.499 41.667 26.79 7.98 0.00 1.28
47 48 4.689071 ACTTTGCATGCATGTGGATTATG 58.311 39.130 26.79 8.54 0.00 1.90
48 49 4.403113 ACTTTGCATGCATGTGGATTATGA 59.597 37.500 26.79 0.00 0.00 2.15
49 50 5.105269 ACTTTGCATGCATGTGGATTATGAA 60.105 36.000 26.79 7.03 0.00 2.57
50 51 4.577834 TGCATGCATGTGGATTATGAAG 57.422 40.909 26.79 0.00 0.00 3.02
51 52 4.208746 TGCATGCATGTGGATTATGAAGA 58.791 39.130 26.79 0.00 0.00 2.87
52 53 4.277423 TGCATGCATGTGGATTATGAAGAG 59.723 41.667 26.79 0.00 0.00 2.85
53 54 4.517832 GCATGCATGTGGATTATGAAGAGA 59.482 41.667 26.79 0.00 0.00 3.10
54 55 5.009310 GCATGCATGTGGATTATGAAGAGAA 59.991 40.000 26.79 0.00 0.00 2.87
55 56 6.294564 GCATGCATGTGGATTATGAAGAGAAT 60.295 38.462 26.79 0.00 0.00 2.40
56 57 7.094506 GCATGCATGTGGATTATGAAGAGAATA 60.095 37.037 26.79 0.00 0.00 1.75
57 58 8.957466 CATGCATGTGGATTATGAAGAGAATAT 58.043 33.333 18.91 0.00 0.00 1.28
58 59 8.929260 TGCATGTGGATTATGAAGAGAATATT 57.071 30.769 0.00 0.00 0.00 1.28
59 60 9.358406 TGCATGTGGATTATGAAGAGAATATTT 57.642 29.630 0.00 0.00 0.00 1.40
103 104 9.784531 ATTGAATTCGATTATGATCCTACAAGT 57.215 29.630 2.01 0.00 0.00 3.16
136 137 7.733773 TGAGAGAGGAAAATATGGTTGTAGA 57.266 36.000 0.00 0.00 0.00 2.59
137 138 8.146053 TGAGAGAGGAAAATATGGTTGTAGAA 57.854 34.615 0.00 0.00 0.00 2.10
138 139 8.602424 TGAGAGAGGAAAATATGGTTGTAGAAA 58.398 33.333 0.00 0.00 0.00 2.52
139 140 9.620259 GAGAGAGGAAAATATGGTTGTAGAAAT 57.380 33.333 0.00 0.00 0.00 2.17
140 141 9.981460 AGAGAGGAAAATATGGTTGTAGAAATT 57.019 29.630 0.00 0.00 0.00 1.82
165 166 9.715121 TTTTCATGTTACTAAATTACCTCTCGT 57.285 29.630 0.00 0.00 0.00 4.18
166 167 9.715121 TTTCATGTTACTAAATTACCTCTCGTT 57.285 29.630 0.00 0.00 0.00 3.85
170 171 9.760077 ATGTTACTAAATTACCTCTCGTTATGG 57.240 33.333 0.00 0.00 0.00 2.74
171 172 8.752187 TGTTACTAAATTACCTCTCGTTATGGT 58.248 33.333 0.00 0.00 37.83 3.55
172 173 9.591792 GTTACTAAATTACCTCTCGTTATGGTT 57.408 33.333 0.00 0.00 35.48 3.67
175 176 9.193806 ACTAAATTACCTCTCGTTATGGTTAGA 57.806 33.333 0.00 0.00 35.48 2.10
178 179 8.888579 AATTACCTCTCGTTATGGTTAGATTG 57.111 34.615 0.00 0.00 35.48 2.67
179 180 4.694339 ACCTCTCGTTATGGTTAGATTGC 58.306 43.478 0.00 0.00 0.00 3.56
180 181 4.406003 ACCTCTCGTTATGGTTAGATTGCT 59.594 41.667 0.00 0.00 0.00 3.91
181 182 5.597182 ACCTCTCGTTATGGTTAGATTGCTA 59.403 40.000 0.00 0.00 0.00 3.49
182 183 6.267928 ACCTCTCGTTATGGTTAGATTGCTAT 59.732 38.462 0.00 0.00 0.00 2.97
183 184 7.155328 CCTCTCGTTATGGTTAGATTGCTATT 58.845 38.462 0.00 0.00 0.00 1.73
184 185 7.116948 CCTCTCGTTATGGTTAGATTGCTATTG 59.883 40.741 0.00 0.00 0.00 1.90
185 186 7.497595 TCTCGTTATGGTTAGATTGCTATTGT 58.502 34.615 0.00 0.00 0.00 2.71
186 187 7.985184 TCTCGTTATGGTTAGATTGCTATTGTT 59.015 33.333 0.00 0.00 0.00 2.83
187 188 8.500753 TCGTTATGGTTAGATTGCTATTGTTT 57.499 30.769 0.00 0.00 0.00 2.83
188 189 8.609176 TCGTTATGGTTAGATTGCTATTGTTTC 58.391 33.333 0.00 0.00 0.00 2.78
189 190 8.612619 CGTTATGGTTAGATTGCTATTGTTTCT 58.387 33.333 0.00 0.00 0.00 2.52
193 194 8.635765 TGGTTAGATTGCTATTGTTTCTTTCT 57.364 30.769 0.00 0.00 0.00 2.52
194 195 9.077885 TGGTTAGATTGCTATTGTTTCTTTCTT 57.922 29.630 0.00 0.00 0.00 2.52
195 196 9.561270 GGTTAGATTGCTATTGTTTCTTTCTTC 57.439 33.333 0.00 0.00 0.00 2.87
199 200 9.905171 AGATTGCTATTGTTTCTTTCTTCTTTC 57.095 29.630 0.00 0.00 0.00 2.62
200 201 9.905171 GATTGCTATTGTTTCTTTCTTCTTTCT 57.095 29.630 0.00 0.00 0.00 2.52
202 203 9.520204 TTGCTATTGTTTCTTTCTTCTTTCTTG 57.480 29.630 0.00 0.00 0.00 3.02
203 204 7.649306 TGCTATTGTTTCTTTCTTCTTTCTTGC 59.351 33.333 0.00 0.00 0.00 4.01
204 205 7.649306 GCTATTGTTTCTTTCTTCTTTCTTGCA 59.351 33.333 0.00 0.00 0.00 4.08
205 206 9.688592 CTATTGTTTCTTTCTTCTTTCTTGCAT 57.311 29.630 0.00 0.00 0.00 3.96
208 209 9.467258 TTGTTTCTTTCTTCTTTCTTGCATATG 57.533 29.630 0.00 0.00 0.00 1.78
209 210 7.596248 TGTTTCTTTCTTCTTTCTTGCATATGC 59.404 33.333 21.09 21.09 42.50 3.14
210 211 7.458409 TTCTTTCTTCTTTCTTGCATATGCT 57.542 32.000 27.13 0.00 42.66 3.79
211 212 8.565896 TTCTTTCTTCTTTCTTGCATATGCTA 57.434 30.769 27.13 19.39 42.66 3.49
212 213 8.206325 TCTTTCTTCTTTCTTGCATATGCTAG 57.794 34.615 26.96 26.96 43.53 3.42
213 214 7.826252 TCTTTCTTCTTTCTTGCATATGCTAGT 59.174 33.333 29.80 0.00 42.89 2.57
214 215 7.928307 TTCTTCTTTCTTGCATATGCTAGTT 57.072 32.000 29.80 0.00 42.89 2.24
215 216 7.928307 TCTTCTTTCTTGCATATGCTAGTTT 57.072 32.000 29.80 0.00 42.89 2.66
216 217 8.340618 TCTTCTTTCTTGCATATGCTAGTTTT 57.659 30.769 29.80 0.00 42.89 2.43
217 218 8.796475 TCTTCTTTCTTGCATATGCTAGTTTTT 58.204 29.630 29.80 0.00 42.89 1.94
218 219 8.746922 TTCTTTCTTGCATATGCTAGTTTTTG 57.253 30.769 29.80 19.22 42.89 2.44
219 220 7.885297 TCTTTCTTGCATATGCTAGTTTTTGT 58.115 30.769 29.80 0.00 42.89 2.83
220 221 8.359642 TCTTTCTTGCATATGCTAGTTTTTGTT 58.640 29.630 29.80 0.00 42.89 2.83
221 222 8.885494 TTTCTTGCATATGCTAGTTTTTGTTT 57.115 26.923 29.80 0.00 42.89 2.83
222 223 7.872163 TCTTGCATATGCTAGTTTTTGTTTG 57.128 32.000 29.80 9.41 42.89 2.93
223 224 7.432869 TCTTGCATATGCTAGTTTTTGTTTGT 58.567 30.769 29.80 0.00 42.89 2.83
224 225 7.594758 TCTTGCATATGCTAGTTTTTGTTTGTC 59.405 33.333 29.80 0.00 42.89 3.18
225 226 6.980593 TGCATATGCTAGTTTTTGTTTGTCT 58.019 32.000 27.13 0.00 42.66 3.41
226 227 7.432869 TGCATATGCTAGTTTTTGTTTGTCTT 58.567 30.769 27.13 0.00 42.66 3.01
227 228 7.381948 TGCATATGCTAGTTTTTGTTTGTCTTG 59.618 33.333 27.13 0.00 42.66 3.02
228 229 7.594758 GCATATGCTAGTTTTTGTTTGTCTTGA 59.405 33.333 20.64 0.00 38.21 3.02
229 230 9.630098 CATATGCTAGTTTTTGTTTGTCTTGAT 57.370 29.630 0.00 0.00 0.00 2.57
241 242 9.883142 TTTGTTTGTCTTGATAATTTGTTTCCT 57.117 25.926 0.00 0.00 0.00 3.36
242 243 9.883142 TTGTTTGTCTTGATAATTTGTTTCCTT 57.117 25.926 0.00 0.00 0.00 3.36
257 258 9.822185 ATTTGTTTCCTTATGAAATTCCTATGC 57.178 29.630 0.00 0.00 44.44 3.14
258 259 7.953005 TGTTTCCTTATGAAATTCCTATGCA 57.047 32.000 0.00 0.00 44.44 3.96
259 260 8.537728 TGTTTCCTTATGAAATTCCTATGCAT 57.462 30.769 3.79 3.79 44.44 3.96
260 261 9.639563 TGTTTCCTTATGAAATTCCTATGCATA 57.360 29.630 6.20 6.20 44.44 3.14
262 263 9.300681 TTTCCTTATGAAATTCCTATGCATAGG 57.699 33.333 37.32 37.32 42.97 2.57
296 297 7.812309 AGACTTAAACTTGTTTTTCACTTGC 57.188 32.000 4.00 0.00 0.00 4.01
297 298 7.602753 AGACTTAAACTTGTTTTTCACTTGCT 58.397 30.769 4.00 0.00 0.00 3.91
298 299 8.088365 AGACTTAAACTTGTTTTTCACTTGCTT 58.912 29.630 4.00 0.00 0.00 3.91
299 300 8.239681 ACTTAAACTTGTTTTTCACTTGCTTC 57.760 30.769 4.00 0.00 0.00 3.86
300 301 7.870445 ACTTAAACTTGTTTTTCACTTGCTTCA 59.130 29.630 4.00 0.00 0.00 3.02
301 302 8.770438 TTAAACTTGTTTTTCACTTGCTTCAT 57.230 26.923 4.00 0.00 0.00 2.57
302 303 6.651755 AACTTGTTTTTCACTTGCTTCATG 57.348 33.333 0.00 0.00 0.00 3.07
303 304 5.964758 ACTTGTTTTTCACTTGCTTCATGA 58.035 33.333 0.00 0.00 0.00 3.07
304 305 6.576185 ACTTGTTTTTCACTTGCTTCATGAT 58.424 32.000 0.00 0.00 0.00 2.45
305 306 6.477688 ACTTGTTTTTCACTTGCTTCATGATG 59.522 34.615 0.00 0.00 0.00 3.07
306 307 4.746115 TGTTTTTCACTTGCTTCATGATGC 59.254 37.500 23.04 23.04 0.00 3.91
307 308 4.859304 TTTTCACTTGCTTCATGATGCT 57.141 36.364 27.81 10.71 33.23 3.79
308 309 4.430137 TTTCACTTGCTTCATGATGCTC 57.570 40.909 27.81 7.10 33.23 4.26
309 310 3.345508 TCACTTGCTTCATGATGCTCT 57.654 42.857 27.81 11.99 33.23 4.09
310 311 3.682696 TCACTTGCTTCATGATGCTCTT 58.317 40.909 27.81 13.15 33.23 2.85
311 312 4.077108 TCACTTGCTTCATGATGCTCTTT 58.923 39.130 27.81 11.69 33.23 2.52
312 313 4.521639 TCACTTGCTTCATGATGCTCTTTT 59.478 37.500 27.81 10.26 33.23 2.27
313 314 4.857588 CACTTGCTTCATGATGCTCTTTTC 59.142 41.667 27.81 4.62 33.23 2.29
314 315 3.752412 TGCTTCATGATGCTCTTTTCG 57.248 42.857 27.81 0.00 33.23 3.46
315 316 3.076621 TGCTTCATGATGCTCTTTTCGT 58.923 40.909 27.81 0.00 33.23 3.85
316 317 3.120095 TGCTTCATGATGCTCTTTTCGTG 60.120 43.478 27.81 0.00 33.23 4.35
317 318 3.120060 GCTTCATGATGCTCTTTTCGTGT 60.120 43.478 22.66 0.00 32.04 4.49
318 319 4.614535 GCTTCATGATGCTCTTTTCGTGTT 60.615 41.667 22.66 0.00 32.04 3.32
319 320 5.437289 TTCATGATGCTCTTTTCGTGTTT 57.563 34.783 0.00 0.00 32.04 2.83
320 321 5.034554 TCATGATGCTCTTTTCGTGTTTC 57.965 39.130 0.00 0.00 32.04 2.78
321 322 4.514816 TCATGATGCTCTTTTCGTGTTTCA 59.485 37.500 0.00 0.00 32.04 2.69
322 323 4.891627 TGATGCTCTTTTCGTGTTTCAA 57.108 36.364 0.00 0.00 0.00 2.69
323 324 5.437289 TGATGCTCTTTTCGTGTTTCAAT 57.563 34.783 0.00 0.00 0.00 2.57
324 325 5.830912 TGATGCTCTTTTCGTGTTTCAATT 58.169 33.333 0.00 0.00 0.00 2.32
325 326 5.686841 TGATGCTCTTTTCGTGTTTCAATTG 59.313 36.000 0.00 0.00 0.00 2.32
326 327 3.796178 TGCTCTTTTCGTGTTTCAATTGC 59.204 39.130 0.00 0.00 0.00 3.56
327 328 4.044426 GCTCTTTTCGTGTTTCAATTGCT 58.956 39.130 0.00 0.00 0.00 3.91
328 329 5.212194 GCTCTTTTCGTGTTTCAATTGCTA 58.788 37.500 0.00 0.00 0.00 3.49
329 330 5.858581 GCTCTTTTCGTGTTTCAATTGCTAT 59.141 36.000 0.00 0.00 0.00 2.97
330 331 6.032880 GCTCTTTTCGTGTTTCAATTGCTATC 59.967 38.462 0.00 0.00 0.00 2.08
331 332 7.202016 TCTTTTCGTGTTTCAATTGCTATCT 57.798 32.000 0.00 0.00 0.00 1.98
332 333 7.648142 TCTTTTCGTGTTTCAATTGCTATCTT 58.352 30.769 0.00 0.00 0.00 2.40
333 334 8.134895 TCTTTTCGTGTTTCAATTGCTATCTTT 58.865 29.630 0.00 0.00 0.00 2.52
334 335 9.393249 CTTTTCGTGTTTCAATTGCTATCTTTA 57.607 29.630 0.00 0.00 0.00 1.85
335 336 9.906660 TTTTCGTGTTTCAATTGCTATCTTTAT 57.093 25.926 0.00 0.00 0.00 1.40
336 337 8.894409 TTCGTGTTTCAATTGCTATCTTTATG 57.106 30.769 0.00 0.00 0.00 1.90
348 349 7.076842 TGCTATCTTTATGTTTCAGTTGAGC 57.923 36.000 0.00 0.00 0.00 4.26
365 366 4.976540 TGAGCTGATCTCATTCATCCAT 57.023 40.909 0.00 0.00 46.34 3.41
366 367 4.642429 TGAGCTGATCTCATTCATCCATG 58.358 43.478 0.00 0.00 46.34 3.66
367 368 4.102681 TGAGCTGATCTCATTCATCCATGT 59.897 41.667 0.00 0.00 46.34 3.21
372 373 7.558807 AGCTGATCTCATTCATCCATGTTAAAA 59.441 33.333 0.00 0.00 0.00 1.52
403 404 4.153835 AGAAAGCTTCTCAAGATCTTTGCG 59.846 41.667 4.86 0.00 34.07 4.85
415 416 5.707242 AGATCTTTGCGAGTAATATCCGA 57.293 39.130 0.00 0.00 0.00 4.55
420 421 0.240411 GCGAGTAATATCCGAGCCGT 59.760 55.000 0.00 0.00 0.00 5.68
469 471 6.918626 TGTTTTTGAACTGACTGAAATGTCA 58.081 32.000 0.00 0.00 43.72 3.58
479 481 7.056006 ACTGACTGAAATGTCATGCCATATAA 58.944 34.615 0.00 0.00 44.66 0.98
524 526 4.971939 TCATCAGAATGCGAAATATCCCA 58.028 39.130 0.00 0.00 34.76 4.37
527 529 4.717877 TCAGAATGCGAAATATCCCACAT 58.282 39.130 0.00 0.00 34.76 3.21
533 535 6.899393 ATGCGAAATATCCCACATGTTTAT 57.101 33.333 0.00 0.00 0.00 1.40
559 561 3.532641 AGTCCTTTCATCCTTTGCCTT 57.467 42.857 0.00 0.00 0.00 4.35
571 573 2.700371 CCTTTGCCTTTTTCCTCCTTGT 59.300 45.455 0.00 0.00 0.00 3.16
583 589 2.677875 CCTTGTGAGGGCCTTGGC 60.678 66.667 7.89 2.49 39.55 4.52
619 625 1.749063 AGCGGATCACATCGAACTACA 59.251 47.619 0.00 0.00 0.00 2.74
628 634 7.921214 GGATCACATCGAACTACAGAAGAAATA 59.079 37.037 0.00 0.00 0.00 1.40
629 635 8.635877 ATCACATCGAACTACAGAAGAAATAC 57.364 34.615 0.00 0.00 0.00 1.89
630 636 7.827701 TCACATCGAACTACAGAAGAAATACT 58.172 34.615 0.00 0.00 0.00 2.12
631 637 8.304596 TCACATCGAACTACAGAAGAAATACTT 58.695 33.333 0.00 0.00 42.03 2.24
681 687 2.279851 CGTGGTGGCTCGAACACA 60.280 61.111 18.22 1.35 40.54 3.72
686 692 2.550606 GTGGTGGCTCGAACACAATAAA 59.449 45.455 18.22 0.45 40.54 1.40
689 695 3.120304 GGTGGCTCGAACACAATAAACTC 60.120 47.826 18.22 0.00 40.54 3.01
693 699 4.378459 GGCTCGAACACAATAAACTCAAGG 60.378 45.833 0.00 0.00 0.00 3.61
777 900 7.064728 GCATTTCTGTCGTCTAGGACTAAATTT 59.935 37.037 0.00 0.00 37.81 1.82
827 952 4.155826 CAGTAAATCAACTCAAATCCGCCA 59.844 41.667 0.00 0.00 0.00 5.69
832 957 1.322538 AACTCAAATCCGCCATGCCC 61.323 55.000 0.00 0.00 0.00 5.36
858 983 4.099170 GCTGCCTGCGCTGTCAAG 62.099 66.667 9.73 6.36 36.39 3.02
859 984 2.667536 CTGCCTGCGCTGTCAAGT 60.668 61.111 9.73 0.00 35.36 3.16
860 985 2.962827 CTGCCTGCGCTGTCAAGTG 61.963 63.158 9.73 0.00 36.97 3.16
861 986 2.974698 GCCTGCGCTGTCAAGTGT 60.975 61.111 9.73 0.00 36.24 3.55
862 987 2.959357 GCCTGCGCTGTCAAGTGTC 61.959 63.158 9.73 0.00 36.24 3.67
863 988 1.595109 CCTGCGCTGTCAAGTGTCA 60.595 57.895 9.73 0.00 36.24 3.58
864 989 1.159713 CCTGCGCTGTCAAGTGTCAA 61.160 55.000 9.73 0.00 36.24 3.18
865 990 0.041839 CTGCGCTGTCAAGTGTCAAC 60.042 55.000 9.73 0.00 36.24 3.18
866 991 1.083401 GCGCTGTCAAGTGTCAACG 60.083 57.895 0.00 0.00 36.24 4.10
873 998 1.003866 GTCAAGTGTCAACGAAGGCAC 60.004 52.381 8.20 8.20 0.00 5.01
879 1004 1.621317 TGTCAACGAAGGCACTATCCA 59.379 47.619 0.00 0.00 38.49 3.41
880 1005 2.236146 TGTCAACGAAGGCACTATCCAT 59.764 45.455 0.00 0.00 38.49 3.41
898 1047 2.431782 CCATTTCCCCAGCCTACAAATG 59.568 50.000 0.00 0.00 35.22 2.32
910 1059 0.724549 TACAAATGTGTCGCCGATGC 59.275 50.000 0.00 0.00 39.30 3.91
934 1096 2.805671 CCATTAACGCTCACAAGTCACA 59.194 45.455 0.00 0.00 0.00 3.58
935 1097 3.249799 CCATTAACGCTCACAAGTCACAA 59.750 43.478 0.00 0.00 0.00 3.33
936 1098 4.457810 CATTAACGCTCACAAGTCACAAG 58.542 43.478 0.00 0.00 0.00 3.16
937 1099 2.024176 AACGCTCACAAGTCACAAGT 57.976 45.000 0.00 0.00 0.00 3.16
938 1100 2.024176 ACGCTCACAAGTCACAAGTT 57.976 45.000 0.00 0.00 0.00 2.66
939 1101 3.173668 ACGCTCACAAGTCACAAGTTA 57.826 42.857 0.00 0.00 0.00 2.24
940 1102 2.864343 ACGCTCACAAGTCACAAGTTAC 59.136 45.455 0.00 0.00 0.00 2.50
941 1103 2.221055 CGCTCACAAGTCACAAGTTACC 59.779 50.000 0.00 0.00 0.00 2.85
942 1104 3.202906 GCTCACAAGTCACAAGTTACCA 58.797 45.455 0.00 0.00 0.00 3.25
945 1107 4.839121 TCACAAGTCACAAGTTACCACTT 58.161 39.130 0.00 0.00 44.72 3.16
948 1110 5.007332 CACAAGTCACAAGTTACCACTTACC 59.993 44.000 0.00 0.00 41.69 2.85
954 1116 4.154195 CACAAGTTACCACTTACCAGCATC 59.846 45.833 0.00 0.00 41.69 3.91
955 1117 3.629142 AGTTACCACTTACCAGCATCC 57.371 47.619 0.00 0.00 0.00 3.51
961 1123 0.036388 ACTTACCAGCATCCCACACG 60.036 55.000 0.00 0.00 0.00 4.49
1011 1191 0.433492 GACCAACAATGTCGTCGTCG 59.567 55.000 0.00 0.00 38.55 5.12
1012 1192 0.942410 ACCAACAATGTCGTCGTCGG 60.942 55.000 1.55 0.00 37.69 4.79
1013 1193 1.129809 CAACAATGTCGTCGTCGGC 59.870 57.895 0.00 0.00 42.45 5.54
1014 1194 2.369629 AACAATGTCGTCGTCGGCG 61.370 57.895 14.12 14.12 45.30 6.46
1015 1195 3.541831 CAATGTCGTCGTCGGCGG 61.542 66.667 20.32 0.00 45.30 6.13
1104 1284 0.821517 TAGTGTCATACCCGGTGCTG 59.178 55.000 0.00 0.00 0.00 4.41
1306 1486 0.038067 CATCCCGGTGTTCGTGTACA 60.038 55.000 0.00 0.00 37.11 2.90
1314 1512 1.663702 GTTCGTGTACACTGCCGCT 60.664 57.895 23.01 0.00 0.00 5.52
1457 1655 0.036732 ATGTGGTTCCACTCGCATGT 59.963 50.000 20.48 0.00 37.78 3.21
1465 1663 2.023771 CACTCGCATGTGACGTGCT 61.024 57.895 25.26 6.22 40.37 4.40
1498 1696 1.153765 CATGTCGAGCCGCAGAAGA 60.154 57.895 0.00 0.00 0.00 2.87
1499 1697 1.140589 ATGTCGAGCCGCAGAAGAG 59.859 57.895 0.00 0.00 0.00 2.85
1646 1858 1.269723 CGTCTTGGTACTCTGCTGACA 59.730 52.381 0.00 0.00 0.00 3.58
1677 1889 1.471684 GTGTACTCCGTACTCCCTGTG 59.528 57.143 5.83 0.00 39.49 3.66
1690 1902 4.398319 ACTCCCTGTGTCCAAAAATACAG 58.602 43.478 0.00 0.00 40.06 2.74
1739 1951 8.744652 TCAAAACTTTGTAAATTCTGGTCAAGA 58.255 29.630 2.30 0.00 39.18 3.02
1841 2055 4.142425 GGTATTTTTGTCCCCGCGAATTTA 60.142 41.667 8.23 0.00 0.00 1.40
1897 2112 3.577919 CCCTGTCTAGCCCTGTATAACT 58.422 50.000 0.00 0.00 0.00 2.24
1925 2140 4.377021 CGTATACGTACAGTACCCTGGTA 58.623 47.826 17.16 2.38 38.29 3.25
1986 2203 2.889045 CCTGCCGAATCCAATCATTCAT 59.111 45.455 0.00 0.00 32.99 2.57
2068 2289 3.592814 CCGGCGGCTATCTCGTCA 61.593 66.667 15.42 0.00 31.94 4.35
2188 2409 1.268999 GCAACATCAAACGAACTGCCA 60.269 47.619 0.00 0.00 0.00 4.92
2189 2410 2.607771 GCAACATCAAACGAACTGCCAT 60.608 45.455 0.00 0.00 0.00 4.40
2257 2478 3.640000 GCGGCGCATGCGATAGTT 61.640 61.111 41.98 0.00 44.10 2.24
2261 2482 1.428448 GGCGCATGCGATAGTTGATA 58.572 50.000 41.98 0.00 44.10 2.15
2309 2530 2.256461 GGGTTCACGTAGCGTCGT 59.744 61.111 3.62 3.62 45.10 4.34
2486 2708 5.324409 TCCTTGATAAGTTTGGCAGATTGT 58.676 37.500 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.082190 CGACACTCTTTCAAGATAGTGGGA 60.082 45.833 11.56 0.00 36.24 4.37
2 3 4.082190 TCGACACTCTTTCAAGATAGTGGG 60.082 45.833 11.56 5.50 36.24 4.61
3 4 4.859798 GTCGACACTCTTTCAAGATAGTGG 59.140 45.833 11.55 5.88 36.24 4.00
4 5 5.704888 AGTCGACACTCTTTCAAGATAGTG 58.295 41.667 19.50 7.18 37.29 2.74
5 6 5.968528 AGTCGACACTCTTTCAAGATAGT 57.031 39.130 19.50 0.00 33.93 2.12
6 7 6.400515 GCAAAGTCGACACTCTTTCAAGATAG 60.401 42.308 19.50 0.00 33.93 2.08
7 8 5.405571 GCAAAGTCGACACTCTTTCAAGATA 59.594 40.000 19.50 0.00 33.93 1.98
8 9 4.212214 GCAAAGTCGACACTCTTTCAAGAT 59.788 41.667 19.50 0.00 33.93 2.40
9 10 3.555956 GCAAAGTCGACACTCTTTCAAGA 59.444 43.478 19.50 0.00 32.52 3.02
10 11 3.309682 TGCAAAGTCGACACTCTTTCAAG 59.690 43.478 19.50 0.00 32.52 3.02
11 12 3.266636 TGCAAAGTCGACACTCTTTCAA 58.733 40.909 19.50 0.00 32.52 2.69
12 13 2.899976 TGCAAAGTCGACACTCTTTCA 58.100 42.857 19.50 7.08 32.52 2.69
13 14 3.803555 CATGCAAAGTCGACACTCTTTC 58.196 45.455 19.50 4.81 32.52 2.62
14 15 2.031682 GCATGCAAAGTCGACACTCTTT 60.032 45.455 19.50 6.51 34.74 2.52
15 16 1.532868 GCATGCAAAGTCGACACTCTT 59.467 47.619 19.50 0.00 29.93 2.85
16 17 1.151668 GCATGCAAAGTCGACACTCT 58.848 50.000 19.50 0.00 29.93 3.24
17 18 0.867746 TGCATGCAAAGTCGACACTC 59.132 50.000 20.30 4.31 29.93 3.51
18 19 1.198408 CATGCATGCAAAGTCGACACT 59.802 47.619 26.68 0.00 0.00 3.55
19 20 1.069022 ACATGCATGCAAAGTCGACAC 60.069 47.619 26.68 4.64 0.00 3.67
20 21 1.069091 CACATGCATGCAAAGTCGACA 60.069 47.619 26.68 0.00 0.00 4.35
21 22 1.609932 CACATGCATGCAAAGTCGAC 58.390 50.000 26.68 7.70 0.00 4.20
22 23 0.522626 CCACATGCATGCAAAGTCGA 59.477 50.000 26.68 0.00 0.00 4.20
23 24 0.522626 TCCACATGCATGCAAAGTCG 59.477 50.000 26.68 18.30 0.00 4.18
24 25 2.953466 ATCCACATGCATGCAAAGTC 57.047 45.000 26.68 0.00 0.00 3.01
25 26 4.403113 TCATAATCCACATGCATGCAAAGT 59.597 37.500 26.68 22.62 0.00 2.66
26 27 4.939271 TCATAATCCACATGCATGCAAAG 58.061 39.130 26.68 21.93 0.00 2.77
27 28 5.127356 TCTTCATAATCCACATGCATGCAAA 59.873 36.000 26.68 11.97 0.00 3.68
28 29 4.645588 TCTTCATAATCCACATGCATGCAA 59.354 37.500 26.68 8.17 0.00 4.08
29 30 4.208746 TCTTCATAATCCACATGCATGCA 58.791 39.130 26.53 25.04 0.00 3.96
30 31 4.517832 TCTCTTCATAATCCACATGCATGC 59.482 41.667 26.53 11.82 0.00 4.06
31 32 6.628919 TTCTCTTCATAATCCACATGCATG 57.371 37.500 25.09 25.09 0.00 4.06
32 33 9.529823 AATATTCTCTTCATAATCCACATGCAT 57.470 29.630 0.00 0.00 0.00 3.96
33 34 8.929260 AATATTCTCTTCATAATCCACATGCA 57.071 30.769 0.00 0.00 0.00 3.96
77 78 9.784531 ACTTGTAGGATCATAATCGAATTCAAT 57.215 29.630 6.22 0.00 32.24 2.57
110 111 9.434275 TCTACAACCATATTTTCCTCTCTCATA 57.566 33.333 0.00 0.00 0.00 2.15
111 112 8.324191 TCTACAACCATATTTTCCTCTCTCAT 57.676 34.615 0.00 0.00 0.00 2.90
112 113 7.733773 TCTACAACCATATTTTCCTCTCTCA 57.266 36.000 0.00 0.00 0.00 3.27
113 114 9.620259 ATTTCTACAACCATATTTTCCTCTCTC 57.380 33.333 0.00 0.00 0.00 3.20
114 115 9.981460 AATTTCTACAACCATATTTTCCTCTCT 57.019 29.630 0.00 0.00 0.00 3.10
139 140 9.715121 ACGAGAGGTAATTTAGTAACATGAAAA 57.285 29.630 0.00 0.00 0.00 2.29
140 141 9.715121 AACGAGAGGTAATTTAGTAACATGAAA 57.285 29.630 0.00 0.00 0.00 2.69
144 145 9.760077 CCATAACGAGAGGTAATTTAGTAACAT 57.240 33.333 0.00 0.00 36.50 2.71
145 146 8.752187 ACCATAACGAGAGGTAATTTAGTAACA 58.248 33.333 0.00 0.00 36.50 2.41
146 147 9.591792 AACCATAACGAGAGGTAATTTAGTAAC 57.408 33.333 0.00 0.00 36.50 2.50
149 150 9.193806 TCTAACCATAACGAGAGGTAATTTAGT 57.806 33.333 0.00 0.00 36.50 2.24
152 153 9.326413 CAATCTAACCATAACGAGAGGTAATTT 57.674 33.333 0.00 0.00 36.50 1.82
153 154 7.441458 GCAATCTAACCATAACGAGAGGTAATT 59.559 37.037 0.00 0.00 36.50 1.40
154 155 6.929606 GCAATCTAACCATAACGAGAGGTAAT 59.070 38.462 0.00 0.00 36.50 1.89
155 156 6.097839 AGCAATCTAACCATAACGAGAGGTAA 59.902 38.462 0.00 0.00 36.50 2.85
156 157 5.597182 AGCAATCTAACCATAACGAGAGGTA 59.403 40.000 0.00 0.00 37.90 3.08
157 158 4.406003 AGCAATCTAACCATAACGAGAGGT 59.594 41.667 0.00 0.00 37.20 3.85
158 159 4.950050 AGCAATCTAACCATAACGAGAGG 58.050 43.478 0.00 0.00 0.00 3.69
159 160 7.653713 ACAATAGCAATCTAACCATAACGAGAG 59.346 37.037 0.00 0.00 0.00 3.20
160 161 7.497595 ACAATAGCAATCTAACCATAACGAGA 58.502 34.615 0.00 0.00 0.00 4.04
161 162 7.715265 ACAATAGCAATCTAACCATAACGAG 57.285 36.000 0.00 0.00 0.00 4.18
162 163 8.500753 AAACAATAGCAATCTAACCATAACGA 57.499 30.769 0.00 0.00 0.00 3.85
163 164 8.612619 AGAAACAATAGCAATCTAACCATAACG 58.387 33.333 0.00 0.00 0.00 3.18
167 168 9.247861 AGAAAGAAACAATAGCAATCTAACCAT 57.752 29.630 0.00 0.00 0.00 3.55
168 169 8.635765 AGAAAGAAACAATAGCAATCTAACCA 57.364 30.769 0.00 0.00 0.00 3.67
169 170 9.561270 GAAGAAAGAAACAATAGCAATCTAACC 57.439 33.333 0.00 0.00 0.00 2.85
173 174 9.905171 GAAAGAAGAAAGAAACAATAGCAATCT 57.095 29.630 0.00 0.00 0.00 2.40
174 175 9.905171 AGAAAGAAGAAAGAAACAATAGCAATC 57.095 29.630 0.00 0.00 0.00 2.67
176 177 9.520204 CAAGAAAGAAGAAAGAAACAATAGCAA 57.480 29.630 0.00 0.00 0.00 3.91
177 178 7.649306 GCAAGAAAGAAGAAAGAAACAATAGCA 59.351 33.333 0.00 0.00 0.00 3.49
178 179 7.649306 TGCAAGAAAGAAGAAAGAAACAATAGC 59.351 33.333 0.00 0.00 0.00 2.97
179 180 9.688592 ATGCAAGAAAGAAGAAAGAAACAATAG 57.311 29.630 0.00 0.00 0.00 1.73
182 183 9.467258 CATATGCAAGAAAGAAGAAAGAAACAA 57.533 29.630 0.00 0.00 0.00 2.83
183 184 7.596248 GCATATGCAAGAAAGAAGAAAGAAACA 59.404 33.333 22.84 0.00 41.59 2.83
184 185 7.811713 AGCATATGCAAGAAAGAAGAAAGAAAC 59.188 33.333 28.62 0.00 45.16 2.78
185 186 7.889469 AGCATATGCAAGAAAGAAGAAAGAAA 58.111 30.769 28.62 0.00 45.16 2.52
186 187 7.458409 AGCATATGCAAGAAAGAAGAAAGAA 57.542 32.000 28.62 0.00 45.16 2.52
187 188 7.826252 ACTAGCATATGCAAGAAAGAAGAAAGA 59.174 33.333 28.62 0.00 45.16 2.52
188 189 7.983307 ACTAGCATATGCAAGAAAGAAGAAAG 58.017 34.615 28.62 9.11 45.16 2.62
189 190 7.928307 ACTAGCATATGCAAGAAAGAAGAAA 57.072 32.000 28.62 0.00 45.16 2.52
190 191 7.928307 AACTAGCATATGCAAGAAAGAAGAA 57.072 32.000 28.62 0.00 45.16 2.52
191 192 7.928307 AAACTAGCATATGCAAGAAAGAAGA 57.072 32.000 28.62 1.04 45.16 2.87
192 193 8.857216 CAAAAACTAGCATATGCAAGAAAGAAG 58.143 33.333 28.62 13.90 45.16 2.85
193 194 8.359642 ACAAAAACTAGCATATGCAAGAAAGAA 58.640 29.630 28.62 3.65 45.16 2.52
194 195 7.885297 ACAAAAACTAGCATATGCAAGAAAGA 58.115 30.769 28.62 4.75 45.16 2.52
195 196 8.524870 AACAAAAACTAGCATATGCAAGAAAG 57.475 30.769 28.62 18.16 45.16 2.62
196 197 8.763356 CAAACAAAAACTAGCATATGCAAGAAA 58.237 29.630 28.62 8.26 45.16 2.52
197 198 7.925483 ACAAACAAAAACTAGCATATGCAAGAA 59.075 29.630 28.62 10.62 45.16 2.52
198 199 7.432869 ACAAACAAAAACTAGCATATGCAAGA 58.567 30.769 28.62 12.86 45.16 3.02
199 200 7.596248 AGACAAACAAAAACTAGCATATGCAAG 59.404 33.333 28.62 11.25 45.16 4.01
200 201 7.432869 AGACAAACAAAAACTAGCATATGCAA 58.567 30.769 28.62 0.00 45.16 4.08
201 202 6.980593 AGACAAACAAAAACTAGCATATGCA 58.019 32.000 28.62 13.96 45.16 3.96
202 203 7.594758 TCAAGACAAACAAAAACTAGCATATGC 59.405 33.333 20.36 20.36 42.49 3.14
203 204 9.630098 ATCAAGACAAACAAAAACTAGCATATG 57.370 29.630 0.00 0.00 0.00 1.78
215 216 9.883142 AGGAAACAAATTATCAAGACAAACAAA 57.117 25.926 0.00 0.00 0.00 2.83
216 217 9.883142 AAGGAAACAAATTATCAAGACAAACAA 57.117 25.926 0.00 0.00 0.00 2.83
270 271 9.349145 GCAAGTGAAAAACAAGTTTAAGTCTAA 57.651 29.630 0.00 0.00 31.63 2.10
271 272 8.736244 AGCAAGTGAAAAACAAGTTTAAGTCTA 58.264 29.630 0.00 0.00 31.63 2.59
272 273 7.602753 AGCAAGTGAAAAACAAGTTTAAGTCT 58.397 30.769 0.00 0.00 31.63 3.24
273 274 7.812309 AGCAAGTGAAAAACAAGTTTAAGTC 57.188 32.000 0.00 0.00 31.63 3.01
274 275 7.870445 TGAAGCAAGTGAAAAACAAGTTTAAGT 59.130 29.630 0.00 0.00 31.63 2.24
275 276 8.238481 TGAAGCAAGTGAAAAACAAGTTTAAG 57.762 30.769 0.00 0.00 31.63 1.85
276 277 8.655092 CATGAAGCAAGTGAAAAACAAGTTTAA 58.345 29.630 0.00 0.00 31.63 1.52
277 278 8.031864 TCATGAAGCAAGTGAAAAACAAGTTTA 58.968 29.630 0.00 0.00 31.63 2.01
278 279 6.873076 TCATGAAGCAAGTGAAAAACAAGTTT 59.127 30.769 0.00 0.00 0.00 2.66
279 280 6.397272 TCATGAAGCAAGTGAAAAACAAGTT 58.603 32.000 0.00 0.00 0.00 2.66
280 281 5.964758 TCATGAAGCAAGTGAAAAACAAGT 58.035 33.333 0.00 0.00 0.00 3.16
281 282 6.563381 GCATCATGAAGCAAGTGAAAAACAAG 60.563 38.462 17.64 0.00 0.00 3.16
282 283 5.234757 GCATCATGAAGCAAGTGAAAAACAA 59.765 36.000 17.64 0.00 0.00 2.83
283 284 4.746115 GCATCATGAAGCAAGTGAAAAACA 59.254 37.500 17.64 0.00 0.00 2.83
284 285 4.986659 AGCATCATGAAGCAAGTGAAAAAC 59.013 37.500 23.62 0.00 0.00 2.43
285 286 5.010314 AGAGCATCATGAAGCAAGTGAAAAA 59.990 36.000 23.62 0.00 37.82 1.94
286 287 4.521639 AGAGCATCATGAAGCAAGTGAAAA 59.478 37.500 23.62 0.00 37.82 2.29
287 288 4.077108 AGAGCATCATGAAGCAAGTGAAA 58.923 39.130 23.62 0.00 37.82 2.69
288 289 3.682696 AGAGCATCATGAAGCAAGTGAA 58.317 40.909 23.62 0.00 37.82 3.18
289 290 3.345508 AGAGCATCATGAAGCAAGTGA 57.654 42.857 23.62 0.00 37.82 3.41
290 291 4.436242 AAAGAGCATCATGAAGCAAGTG 57.564 40.909 23.62 6.54 37.82 3.16
291 292 4.379186 CGAAAAGAGCATCATGAAGCAAGT 60.379 41.667 23.62 4.29 37.82 3.16
292 293 4.096311 CGAAAAGAGCATCATGAAGCAAG 58.904 43.478 23.62 4.27 37.82 4.01
293 294 3.503363 ACGAAAAGAGCATCATGAAGCAA 59.497 39.130 23.62 0.00 37.82 3.91
294 295 3.076621 ACGAAAAGAGCATCATGAAGCA 58.923 40.909 23.62 0.00 37.82 3.91
295 296 3.120060 ACACGAAAAGAGCATCATGAAGC 60.120 43.478 14.96 14.96 37.82 3.86
296 297 4.675190 ACACGAAAAGAGCATCATGAAG 57.325 40.909 0.00 0.00 37.82 3.02
297 298 5.008514 TGAAACACGAAAAGAGCATCATGAA 59.991 36.000 0.00 0.00 37.82 2.57
298 299 4.514816 TGAAACACGAAAAGAGCATCATGA 59.485 37.500 0.00 0.00 37.82 3.07
299 300 4.786507 TGAAACACGAAAAGAGCATCATG 58.213 39.130 0.00 0.00 37.82 3.07
300 301 5.437289 TTGAAACACGAAAAGAGCATCAT 57.563 34.783 0.00 0.00 37.82 2.45
301 302 4.891627 TTGAAACACGAAAAGAGCATCA 57.108 36.364 0.00 0.00 37.82 3.07
302 303 5.387752 GCAATTGAAACACGAAAAGAGCATC 60.388 40.000 10.34 0.00 0.00 3.91
303 304 4.445385 GCAATTGAAACACGAAAAGAGCAT 59.555 37.500 10.34 0.00 0.00 3.79
304 305 3.796178 GCAATTGAAACACGAAAAGAGCA 59.204 39.130 10.34 0.00 0.00 4.26
305 306 4.044426 AGCAATTGAAACACGAAAAGAGC 58.956 39.130 10.34 0.00 0.00 4.09
306 307 7.301054 AGATAGCAATTGAAACACGAAAAGAG 58.699 34.615 10.34 0.00 0.00 2.85
307 308 7.202016 AGATAGCAATTGAAACACGAAAAGA 57.798 32.000 10.34 0.00 0.00 2.52
308 309 7.858052 AAGATAGCAATTGAAACACGAAAAG 57.142 32.000 10.34 0.00 0.00 2.27
309 310 9.906660 ATAAAGATAGCAATTGAAACACGAAAA 57.093 25.926 10.34 0.00 0.00 2.29
310 311 9.340695 CATAAAGATAGCAATTGAAACACGAAA 57.659 29.630 10.34 0.00 0.00 3.46
311 312 8.511321 ACATAAAGATAGCAATTGAAACACGAA 58.489 29.630 10.34 0.00 0.00 3.85
312 313 8.039603 ACATAAAGATAGCAATTGAAACACGA 57.960 30.769 10.34 0.00 0.00 4.35
313 314 8.673626 AACATAAAGATAGCAATTGAAACACG 57.326 30.769 10.34 0.00 0.00 4.49
319 320 9.844790 CAACTGAAACATAAAGATAGCAATTGA 57.155 29.630 10.34 0.00 0.00 2.57
320 321 9.844790 TCAACTGAAACATAAAGATAGCAATTG 57.155 29.630 0.00 0.00 0.00 2.32
322 323 8.186821 GCTCAACTGAAACATAAAGATAGCAAT 58.813 33.333 0.00 0.00 0.00 3.56
323 324 7.391554 AGCTCAACTGAAACATAAAGATAGCAA 59.608 33.333 0.00 0.00 0.00 3.91
324 325 6.881065 AGCTCAACTGAAACATAAAGATAGCA 59.119 34.615 0.00 0.00 0.00 3.49
325 326 7.313951 AGCTCAACTGAAACATAAAGATAGC 57.686 36.000 0.00 0.00 0.00 2.97
348 349 9.512435 GTTTTTAACATGGATGAATGAGATCAG 57.488 33.333 0.00 0.00 31.76 2.90
356 357 8.356657 TCTTTCACGTTTTTAACATGGATGAAT 58.643 29.630 0.00 0.00 0.00 2.57
362 363 6.475402 AGCTTTCTTTCACGTTTTTAACATGG 59.525 34.615 0.00 0.00 0.00 3.66
363 364 7.449934 AGCTTTCTTTCACGTTTTTAACATG 57.550 32.000 0.00 0.00 0.00 3.21
364 365 7.973944 AGAAGCTTTCTTTCACGTTTTTAACAT 59.026 29.630 0.00 0.00 36.36 2.71
365 366 7.309920 AGAAGCTTTCTTTCACGTTTTTAACA 58.690 30.769 0.00 0.00 36.36 2.41
366 367 7.483691 TGAGAAGCTTTCTTTCACGTTTTTAAC 59.516 33.333 0.00 0.00 40.87 2.01
367 368 7.531716 TGAGAAGCTTTCTTTCACGTTTTTAA 58.468 30.769 0.00 0.00 40.87 1.52
372 373 4.876107 TCTTGAGAAGCTTTCTTTCACGTT 59.124 37.500 0.00 0.00 40.87 3.99
403 404 2.292569 TGTGACGGCTCGGATATTACTC 59.707 50.000 0.00 0.00 0.00 2.59
415 416 2.976350 TCGACGACTGTGACGGCT 60.976 61.111 0.00 0.00 36.56 5.52
440 441 7.636259 TTTCAGTCAGTTCAAAAACAAACAG 57.364 32.000 0.00 0.00 37.88 3.16
442 443 8.017587 ACATTTCAGTCAGTTCAAAAACAAAC 57.982 30.769 0.00 0.00 37.88 2.93
443 444 7.869937 TGACATTTCAGTCAGTTCAAAAACAAA 59.130 29.630 0.00 0.00 43.18 2.83
469 471 6.351371 CGAGAGGGACACTTATTATATGGCAT 60.351 42.308 4.88 4.88 0.00 4.40
524 526 9.477484 GATGAAAGGACTACGATATAAACATGT 57.523 33.333 0.00 0.00 0.00 3.21
527 529 8.246430 AGGATGAAAGGACTACGATATAAACA 57.754 34.615 0.00 0.00 0.00 2.83
533 535 5.357257 GCAAAGGATGAAAGGACTACGATA 58.643 41.667 0.00 0.00 0.00 2.92
540 542 4.607293 AAAAGGCAAAGGATGAAAGGAC 57.393 40.909 0.00 0.00 0.00 3.85
571 573 4.020617 CAGTCGCCAAGGCCCTCA 62.021 66.667 5.34 0.00 37.98 3.86
595 601 1.083806 TTCGATGTGATCCGCTGTGC 61.084 55.000 0.00 0.00 0.00 4.57
596 602 0.647410 GTTCGATGTGATCCGCTGTG 59.353 55.000 0.00 0.00 0.00 3.66
597 603 0.532573 AGTTCGATGTGATCCGCTGT 59.467 50.000 0.00 0.00 0.00 4.40
628 634 5.337330 CGGGTGAAACTAGTCCAAGATAAGT 60.337 44.000 0.00 0.00 36.74 2.24
629 635 5.109903 CGGGTGAAACTAGTCCAAGATAAG 58.890 45.833 0.00 0.00 36.74 1.73
630 636 4.081309 CCGGGTGAAACTAGTCCAAGATAA 60.081 45.833 0.00 0.00 36.74 1.75
631 637 3.449737 CCGGGTGAAACTAGTCCAAGATA 59.550 47.826 0.00 0.00 36.74 1.98
666 672 2.550606 GTTTATTGTGTTCGAGCCACCA 59.449 45.455 12.93 4.65 31.71 4.17
686 692 7.659390 GCTTCTCATATTGTATTAGCCTTGAGT 59.341 37.037 0.00 0.00 33.00 3.41
689 695 7.443575 ACAGCTTCTCATATTGTATTAGCCTTG 59.556 37.037 0.00 0.00 0.00 3.61
693 699 7.439356 TGTCACAGCTTCTCATATTGTATTAGC 59.561 37.037 0.00 0.00 0.00 3.09
791 914 4.144297 TGATTTACTGAGCAAGCAAGGTT 58.856 39.130 0.00 0.00 0.00 3.50
806 929 4.695217 TGGCGGATTTGAGTTGATTTAC 57.305 40.909 0.00 0.00 0.00 2.01
827 952 1.228184 GCAGCTGCATCTAGGGCAT 60.228 57.895 33.36 0.00 41.06 4.40
858 983 2.000447 GGATAGTGCCTTCGTTGACAC 59.000 52.381 0.00 0.00 0.00 3.67
859 984 1.621317 TGGATAGTGCCTTCGTTGACA 59.379 47.619 0.00 0.00 0.00 3.58
860 985 2.380084 TGGATAGTGCCTTCGTTGAC 57.620 50.000 0.00 0.00 0.00 3.18
861 986 3.627395 AATGGATAGTGCCTTCGTTGA 57.373 42.857 0.00 0.00 0.00 3.18
862 987 3.065371 GGAAATGGATAGTGCCTTCGTTG 59.935 47.826 0.00 0.00 0.00 4.10
863 988 3.279434 GGAAATGGATAGTGCCTTCGTT 58.721 45.455 0.00 0.00 0.00 3.85
864 989 2.421529 GGGAAATGGATAGTGCCTTCGT 60.422 50.000 0.00 0.00 0.00 3.85
865 990 2.222027 GGGAAATGGATAGTGCCTTCG 58.778 52.381 0.00 0.00 0.00 3.79
866 991 2.091885 TGGGGAAATGGATAGTGCCTTC 60.092 50.000 0.00 0.00 0.00 3.46
873 998 2.711009 TGTAGGCTGGGGAAATGGATAG 59.289 50.000 0.00 0.00 0.00 2.08
879 1004 3.099141 CACATTTGTAGGCTGGGGAAAT 58.901 45.455 0.00 0.00 0.00 2.17
880 1005 2.158385 ACACATTTGTAGGCTGGGGAAA 60.158 45.455 0.00 0.00 32.60 3.13
910 1059 0.096976 CTTGTGAGCGTTAATGGCGG 59.903 55.000 0.00 0.00 35.00 6.13
935 1097 2.238898 GGGATGCTGGTAAGTGGTAACT 59.761 50.000 0.00 0.00 38.71 2.24
936 1098 2.026636 TGGGATGCTGGTAAGTGGTAAC 60.027 50.000 0.00 0.00 0.00 2.50
937 1099 2.026636 GTGGGATGCTGGTAAGTGGTAA 60.027 50.000 0.00 0.00 0.00 2.85
938 1100 1.557832 GTGGGATGCTGGTAAGTGGTA 59.442 52.381 0.00 0.00 0.00 3.25
939 1101 0.328258 GTGGGATGCTGGTAAGTGGT 59.672 55.000 0.00 0.00 0.00 4.16
940 1102 0.327924 TGTGGGATGCTGGTAAGTGG 59.672 55.000 0.00 0.00 0.00 4.00
941 1103 1.453155 GTGTGGGATGCTGGTAAGTG 58.547 55.000 0.00 0.00 0.00 3.16
942 1104 0.036388 CGTGTGGGATGCTGGTAAGT 60.036 55.000 0.00 0.00 0.00 2.24
945 1107 0.902984 ACTCGTGTGGGATGCTGGTA 60.903 55.000 0.00 0.00 0.00 3.25
948 1110 1.807165 CGACTCGTGTGGGATGCTG 60.807 63.158 0.00 0.00 0.00 4.41
955 1117 3.971453 ATGCTCGCGACTCGTGTGG 62.971 63.158 3.71 7.43 38.57 4.17
961 1123 1.011463 CATGCAATGCTCGCGACTC 60.011 57.895 3.71 0.00 37.62 3.36
1086 1266 1.596934 CAGCACCGGGTATGACACT 59.403 57.895 6.32 0.00 0.00 3.55
1104 1284 2.757917 AGGAGGACGAGGAGCAGC 60.758 66.667 0.00 0.00 0.00 5.25
1295 1475 1.952133 GCGGCAGTGTACACGAACA 60.952 57.895 19.93 0.00 36.20 3.18
1415 1613 3.171828 ATGCACCCGACGTGGAACA 62.172 57.895 0.00 6.87 46.85 3.18
1457 1655 4.357947 GGCAGACCGAGCACGTCA 62.358 66.667 2.18 0.00 37.88 4.35
1534 1736 2.666862 CAACTACACCGGCGGCAA 60.667 61.111 28.71 10.81 0.00 4.52
1646 1858 1.801395 CGGAGTACACGGCATTCGATT 60.801 52.381 0.00 0.00 42.43 3.34
1677 1889 8.947115 AGTCTAATAAGCACTGTATTTTTGGAC 58.053 33.333 12.20 12.20 32.22 4.02
1756 1969 9.914131 GGGCTCATTTATTTGGTATTCTAAATC 57.086 33.333 0.00 0.00 36.44 2.17
1762 1975 5.302823 AGCAGGGCTCATTTATTTGGTATTC 59.697 40.000 0.00 0.00 30.62 1.75
1897 2112 4.119862 GGTACTGTACGTATACGGTCTGA 58.880 47.826 27.62 7.03 46.14 3.27
1986 2203 0.812811 GATTGATGGAGCTGCTCGCA 60.813 55.000 22.25 20.20 42.61 5.10
2254 2475 4.081087 AGCACTACCGGAACAATATCAACT 60.081 41.667 9.46 0.00 0.00 3.16
2257 2478 3.792401 CAGCACTACCGGAACAATATCA 58.208 45.455 9.46 0.00 0.00 2.15
2261 2482 0.324943 AGCAGCACTACCGGAACAAT 59.675 50.000 9.46 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.