Multiple sequence alignment - TraesCS7B01G269700

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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 TraesCS7B01G269700 chr7B 100.000 7794 0 0 1 7794 494588688 494580895 0.000000e+00 14393
1 TraesCS7B01G269700 chr7D 95.257 6747 224 42 281 6979 470893684 470886986 0.000000e+00 10599
2 TraesCS7B01G269700 chr7D 91.466 457 14 8 7349 7794 470886675 470886233 8.650000e-169 604
3 TraesCS7B01G269700 chr7D 92.835 321 17 2 7006 7321 470886992 470886673 1.980000e-125 460
4 TraesCS7B01G269700 chr7D 90.761 184 15 2 118 300 459392088 459391906 2.170000e-60 244
5 TraesCS7B01G269700 chr7D 90.659 182 16 1 115 296 593193276 593193096 2.810000e-59 241
6 TraesCS7B01G269700 chr7D 85.593 118 17 0 1 118 470893801 470893684 2.950000e-24 124
7 TraesCS7B01G269700 chr7A 93.013 4265 200 44 281 4495 527533878 527538094 0.000000e+00 6135
8 TraesCS7B01G269700 chr7A 92.469 2908 170 27 4494 7374 527538173 527541058 0.000000e+00 4111
9 TraesCS7B01G269700 chr7A 87.166 374 29 5 7440 7794 527541069 527541442 2.620000e-109 407
10 TraesCS7B01G269700 chr6D 85.998 2364 239 46 3624 5960 91985 89687 0.000000e+00 2447
11 TraesCS7B01G269700 chr6D 90.795 1434 125 2 1777 3203 95121 93688 0.000000e+00 1910
12 TraesCS7B01G269700 chr6D 87.705 976 101 9 6081 7053 89637 88678 0.000000e+00 1120
13 TraesCS7B01G269700 chr6D 89.203 389 38 3 3204 3591 93554 93169 4.230000e-132 483
14 TraesCS7B01G269700 chr1A 92.021 188 12 3 118 302 132544058 132544245 2.160000e-65 261
15 TraesCS7B01G269700 chr1A 91.257 183 13 2 100 281 393948437 393948617 6.040000e-61 246
16 TraesCS7B01G269700 chr5A 91.573 178 15 0 104 281 290391683 290391860 6.040000e-61 246
17 TraesCS7B01G269700 chr4A 90.761 184 16 1 114 296 666921229 666921046 2.170000e-60 244
18 TraesCS7B01G269700 chr2A 91.160 181 13 3 102 281 378016091 378015913 7.810000e-60 243
19 TraesCS7B01G269700 chr2A 91.111 180 15 1 111 289 694454086 694454265 7.810000e-60 243
20 TraesCS7B01G269700 chr2B 86.916 214 20 8 111 319 651354167 651353957 4.700000e-57 233


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 TraesCS7B01G269700 chr7B 494580895 494588688 7793 True 14393.00 14393 100.000000 1 7794 1 chr7B.!!$R1 7793
1 TraesCS7B01G269700 chr7D 470886233 470893801 7568 True 2946.75 10599 91.287750 1 7794 4 chr7D.!!$R3 7793
2 TraesCS7B01G269700 chr7A 527533878 527541442 7564 False 3551.00 6135 90.882667 281 7794 3 chr7A.!!$F1 7513
3 TraesCS7B01G269700 chr6D 88678 95121 6443 True 1490.00 2447 88.425250 1777 7053 4 chr6D.!!$R1 5276

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
40 41 0.174845 TGTTCGCGAACATAGAGGGG 59.825 55.0 42.01 0.00 45.42 4.79 F
953 1015 0.322906 CAAGTGGCTTCCTTCCCTCC 60.323 60.0 0.00 0.00 0.00 4.30 F
1128 1199 0.173708 GGAGATTCTTGACGCTCCGT 59.826 55.0 0.00 0.00 45.10 4.69 F
2309 2387 0.253347 AGGGGAGGAAGAGCCATTCA 60.253 55.0 1.40 0.00 40.02 2.57 F
3837 5215 0.541863 AGGTAATGGAAGGCGGTCAG 59.458 55.0 0.00 0.00 0.00 3.51 F
4141 5519 0.179134 CGTAGAAGTCTCCAAGGGCG 60.179 60.0 0.00 0.00 0.00 6.13 F
5852 7357 0.833949 GGGAGGTGAGAACAGGATCC 59.166 60.0 2.48 2.48 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1199 1.368641 ATTAAGCGACGCTGAATGCA 58.631 45.000 27.88 5.20 38.23 3.96 R
2302 2380 0.472471 TATCTCCCCGGTTGAATGGC 59.528 55.000 0.00 0.00 0.00 4.40 R
2649 2727 2.006888 CAACCATATGAACTCGGCGTT 58.993 47.619 6.85 0.00 38.91 4.84 R
3952 5330 0.178990 ACCTGTTGCCCTTGGACTTC 60.179 55.000 0.00 0.00 0.00 3.01 R
5783 7288 1.470805 GGGTCCAAATTATTGCGCACC 60.471 52.381 11.12 3.18 35.10 5.01 R
5975 7480 7.807977 TCTGTCTTTGTTTAAGAAAGCTCAT 57.192 32.000 9.36 0.00 44.69 2.90 R
7258 8785 0.537143 GGACCACATGCACTTCCACA 60.537 55.000 0.00 0.00 0.00 4.17 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
19 20 2.649742 ATATGAGGGGTGATCCGGAT 57.350 50.000 19.21 19.21 36.01 4.18
21 22 0.400525 ATGAGGGGTGATCCGGATGT 60.401 55.000 24.82 0.00 36.01 3.06
24 25 0.914417 AGGGGTGATCCGGATGTGTT 60.914 55.000 24.82 0.00 36.01 3.32
28 29 1.518352 TGATCCGGATGTGTTCGCG 60.518 57.895 24.82 0.00 0.00 5.87
29 30 1.226859 GATCCGGATGTGTTCGCGA 60.227 57.895 24.82 3.71 0.00 5.87
39 40 3.733236 TGTTCGCGAACATAGAGGG 57.267 52.632 42.01 0.00 45.42 4.30
40 41 0.174845 TGTTCGCGAACATAGAGGGG 59.825 55.000 42.01 0.00 45.42 4.79
55 56 4.347865 GGGGGCGGATTTGCTAAA 57.652 55.556 0.00 0.00 34.52 1.85
79 80 3.054802 CCTGGTGGAAATGCTCTAAGAGT 60.055 47.826 0.00 0.00 34.57 3.24
80 81 3.937706 CTGGTGGAAATGCTCTAAGAGTG 59.062 47.826 0.00 0.00 31.39 3.51
88 89 2.820178 TGCTCTAAGAGTGGTGGATCA 58.180 47.619 0.00 0.00 31.39 2.92
127 128 8.926092 TTGATCATATAGATATACTCCCTCCG 57.074 38.462 0.00 0.00 37.00 4.63
128 129 8.046867 TGATCATATAGATATACTCCCTCCGT 57.953 38.462 0.00 0.00 37.00 4.69
129 130 8.503573 TGATCATATAGATATACTCCCTCCGTT 58.496 37.037 0.00 0.00 37.00 4.44
130 131 8.927675 ATCATATAGATATACTCCCTCCGTTC 57.072 38.462 0.00 0.00 34.43 3.95
131 132 7.288560 TCATATAGATATACTCCCTCCGTTCC 58.711 42.308 0.00 0.00 0.00 3.62
132 133 5.799978 ATAGATATACTCCCTCCGTTCCT 57.200 43.478 0.00 0.00 0.00 3.36
133 134 6.905067 ATAGATATACTCCCTCCGTTCCTA 57.095 41.667 0.00 0.00 0.00 2.94
134 135 5.595814 AGATATACTCCCTCCGTTCCTAA 57.404 43.478 0.00 0.00 0.00 2.69
135 136 5.961897 AGATATACTCCCTCCGTTCCTAAA 58.038 41.667 0.00 0.00 0.00 1.85
136 137 6.563163 AGATATACTCCCTCCGTTCCTAAAT 58.437 40.000 0.00 0.00 0.00 1.40
137 138 7.706674 AGATATACTCCCTCCGTTCCTAAATA 58.293 38.462 0.00 0.00 0.00 1.40
138 139 8.345306 AGATATACTCCCTCCGTTCCTAAATAT 58.655 37.037 0.00 0.00 0.00 1.28
139 140 8.912614 ATATACTCCCTCCGTTCCTAAATATT 57.087 34.615 0.00 0.00 0.00 1.28
140 141 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
141 142 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
142 143 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
143 144 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
144 145 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
145 146 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
146 147 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
147 148 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
148 149 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
149 150 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
150 151 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
151 152 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
164 165 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
165 166 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
166 167 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
167 168 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
168 169 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
169 170 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
170 171 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
171 172 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
172 173 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
174 175 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
175 176 8.367911 AGAGATTTCAACAAGTGACTACATACA 58.632 33.333 0.00 0.00 35.39 2.29
176 177 8.539770 AGATTTCAACAAGTGACTACATACAG 57.460 34.615 0.00 0.00 35.39 2.74
177 178 8.367911 AGATTTCAACAAGTGACTACATACAGA 58.632 33.333 0.00 0.00 35.39 3.41
178 179 8.902540 ATTTCAACAAGTGACTACATACAGAA 57.097 30.769 0.00 0.00 35.39 3.02
179 180 7.709269 TTCAACAAGTGACTACATACAGAAC 57.291 36.000 0.00 0.00 35.39 3.01
180 181 6.811954 TCAACAAGTGACTACATACAGAACA 58.188 36.000 0.00 0.00 0.00 3.18
181 182 7.269316 TCAACAAGTGACTACATACAGAACAA 58.731 34.615 0.00 0.00 0.00 2.83
182 183 7.766738 TCAACAAGTGACTACATACAGAACAAA 59.233 33.333 0.00 0.00 0.00 2.83
183 184 8.394877 CAACAAGTGACTACATACAGAACAAAA 58.605 33.333 0.00 0.00 0.00 2.44
184 185 8.677148 ACAAGTGACTACATACAGAACAAAAT 57.323 30.769 0.00 0.00 0.00 1.82
185 186 8.559536 ACAAGTGACTACATACAGAACAAAATG 58.440 33.333 0.00 0.00 0.00 2.32
186 187 8.773645 CAAGTGACTACATACAGAACAAAATGA 58.226 33.333 0.00 0.00 0.00 2.57
187 188 8.539770 AGTGACTACATACAGAACAAAATGAG 57.460 34.615 0.00 0.00 0.00 2.90
188 189 8.150945 AGTGACTACATACAGAACAAAATGAGT 58.849 33.333 0.00 0.00 0.00 3.41
189 190 8.223769 GTGACTACATACAGAACAAAATGAGTG 58.776 37.037 0.00 0.00 0.00 3.51
190 191 8.147704 TGACTACATACAGAACAAAATGAGTGA 58.852 33.333 0.00 0.00 0.00 3.41
191 192 8.902540 ACTACATACAGAACAAAATGAGTGAA 57.097 30.769 0.00 0.00 0.00 3.18
192 193 9.507329 ACTACATACAGAACAAAATGAGTGAAT 57.493 29.630 0.00 0.00 0.00 2.57
193 194 9.979270 CTACATACAGAACAAAATGAGTGAATC 57.021 33.333 0.00 0.00 0.00 2.52
194 195 8.627208 ACATACAGAACAAAATGAGTGAATCT 57.373 30.769 0.00 0.00 0.00 2.40
195 196 9.725019 ACATACAGAACAAAATGAGTGAATCTA 57.275 29.630 0.00 0.00 0.00 1.98
196 197 9.979270 CATACAGAACAAAATGAGTGAATCTAC 57.021 33.333 0.00 0.00 0.00 2.59
197 198 9.950496 ATACAGAACAAAATGAGTGAATCTACT 57.050 29.630 0.00 0.00 0.00 2.57
199 200 9.950496 ACAGAACAAAATGAGTGAATCTACTAT 57.050 29.630 0.00 0.00 0.00 2.12
241 242 9.764363 ATACATCTGTATGTGGTAGTACATTTG 57.236 33.333 2.06 0.00 45.99 2.32
242 243 7.847096 ACATCTGTATGTGGTAGTACATTTGA 58.153 34.615 2.06 0.00 44.79 2.69
243 244 8.318412 ACATCTGTATGTGGTAGTACATTTGAA 58.682 33.333 2.06 0.00 44.79 2.69
244 245 9.161629 CATCTGTATGTGGTAGTACATTTGAAA 57.838 33.333 2.06 0.00 41.31 2.69
245 246 9.905713 ATCTGTATGTGGTAGTACATTTGAAAT 57.094 29.630 2.06 0.00 41.31 2.17
246 247 9.378551 TCTGTATGTGGTAGTACATTTGAAATC 57.621 33.333 2.06 0.00 41.31 2.17
247 248 9.383519 CTGTATGTGGTAGTACATTTGAAATCT 57.616 33.333 2.06 0.00 41.31 2.40
248 249 9.733556 TGTATGTGGTAGTACATTTGAAATCTT 57.266 29.630 2.06 0.00 41.31 2.40
251 252 7.802738 TGTGGTAGTACATTTGAAATCTTTCG 58.197 34.615 2.06 0.00 40.01 3.46
252 253 7.658167 TGTGGTAGTACATTTGAAATCTTTCGA 59.342 33.333 2.06 0.00 40.01 3.71
253 254 8.500773 GTGGTAGTACATTTGAAATCTTTCGAA 58.499 33.333 7.59 7.59 42.85 3.71
254 255 9.058174 TGGTAGTACATTTGAAATCTTTCGAAA 57.942 29.630 10.71 10.71 42.19 3.46
255 256 9.543018 GGTAGTACATTTGAAATCTTTCGAAAG 57.457 33.333 28.26 28.26 42.19 2.62
258 259 8.836413 AGTACATTTGAAATCTTTCGAAAGACA 58.164 29.630 36.05 27.39 46.80 3.41
259 260 9.445786 GTACATTTGAAATCTTTCGAAAGACAA 57.554 29.630 36.05 30.45 46.80 3.18
260 261 8.925161 ACATTTGAAATCTTTCGAAAGACAAA 57.075 26.923 33.79 33.79 46.80 2.83
261 262 9.533253 ACATTTGAAATCTTTCGAAAGACAAAT 57.467 25.926 34.50 34.50 46.80 2.32
269 270 9.720769 AATCTTTCGAAAGACAAATACTTAGGA 57.279 29.630 36.05 14.47 46.80 2.94
270 271 9.720769 ATCTTTCGAAAGACAAATACTTAGGAA 57.279 29.630 36.05 13.68 46.80 3.36
271 272 8.985805 TCTTTCGAAAGACAAATACTTAGGAAC 58.014 33.333 31.62 0.00 39.95 3.62
272 273 8.665643 TTTCGAAAGACAAATACTTAGGAACA 57.334 30.769 6.47 0.00 41.84 3.18
273 274 7.884816 TCGAAAGACAAATACTTAGGAACAG 57.115 36.000 0.00 0.00 33.31 3.16
274 275 7.663827 TCGAAAGACAAATACTTAGGAACAGA 58.336 34.615 0.00 0.00 33.31 3.41
275 276 7.813148 TCGAAAGACAAATACTTAGGAACAGAG 59.187 37.037 0.00 0.00 33.31 3.35
276 277 7.063544 CGAAAGACAAATACTTAGGAACAGAGG 59.936 40.741 0.00 0.00 0.00 3.69
277 278 6.301169 AGACAAATACTTAGGAACAGAGGG 57.699 41.667 0.00 0.00 0.00 4.30
278 279 6.023603 AGACAAATACTTAGGAACAGAGGGA 58.976 40.000 0.00 0.00 0.00 4.20
279 280 6.155393 AGACAAATACTTAGGAACAGAGGGAG 59.845 42.308 0.00 0.00 0.00 4.30
343 344 1.439644 GTGATCTCACCTCCCGAGC 59.560 63.158 0.00 0.00 40.85 5.03
449 454 1.048601 CGTCCATACTAGCCCCACAT 58.951 55.000 0.00 0.00 0.00 3.21
463 468 1.672363 CCCACATGATCATGGACAACG 59.328 52.381 33.31 16.83 42.91 4.10
484 490 5.069516 AACGTCTTACTCCACAAGAGGTAAA 59.930 40.000 9.92 0.00 45.47 2.01
485 491 6.737899 AACGTCTTACTCCACAAGAGGTAAAG 60.738 42.308 9.92 0.00 45.47 1.85
486 492 8.822484 AACGTCTTACTCCACAAGAGGTAAAGA 61.822 40.741 9.92 0.00 45.47 2.52
708 737 1.373497 CGTGCGACCTGCTCTTCTT 60.373 57.895 0.00 0.00 46.63 2.52
709 738 1.347817 CGTGCGACCTGCTCTTCTTC 61.348 60.000 0.00 0.00 46.63 2.87
711 740 1.202582 GTGCGACCTGCTCTTCTTCTA 59.797 52.381 0.00 0.00 46.63 2.10
803 856 4.954118 TCCTCCGGCCACCACAGT 62.954 66.667 2.24 0.00 0.00 3.55
823 876 1.203013 TCCGGAGTGGTCTTCTCTTCA 60.203 52.381 0.00 0.00 39.52 3.02
824 877 1.067495 CCGGAGTGGTCTTCTCTTCAC 60.067 57.143 0.00 0.00 33.06 3.18
825 878 1.889829 CGGAGTGGTCTTCTCTTCACT 59.110 52.381 0.00 0.00 42.37 3.41
826 879 2.297597 CGGAGTGGTCTTCTCTTCACTT 59.702 50.000 0.00 0.00 40.13 3.16
827 880 3.612955 CGGAGTGGTCTTCTCTTCACTTC 60.613 52.174 0.00 0.00 40.13 3.01
860 913 2.478831 GATCTCAGACAAATCCTCCGC 58.521 52.381 0.00 0.00 0.00 5.54
897 950 1.584761 GCGAATATACGTGAACGCACA 59.415 47.619 17.16 0.00 45.41 4.57
910 963 4.380628 GCACACGCTGCTGCACTC 62.381 66.667 16.29 0.00 43.33 3.51
911 964 3.720193 CACACGCTGCTGCACTCC 61.720 66.667 16.29 0.00 39.64 3.85
927 989 2.307768 ACTCCGCTAGTGCTGCTATAA 58.692 47.619 0.00 0.00 36.93 0.98
946 1008 8.217799 TGCTATAATATAAACAAGTGGCTTCCT 58.782 33.333 0.00 0.00 0.00 3.36
950 1012 1.704641 AAACAAGTGGCTTCCTTCCC 58.295 50.000 0.00 0.00 0.00 3.97
951 1013 0.853530 AACAAGTGGCTTCCTTCCCT 59.146 50.000 0.00 0.00 0.00 4.20
952 1014 0.402121 ACAAGTGGCTTCCTTCCCTC 59.598 55.000 0.00 0.00 0.00 4.30
953 1015 0.322906 CAAGTGGCTTCCTTCCCTCC 60.323 60.000 0.00 0.00 0.00 4.30
1121 1192 1.555533 ACCCTTCCGGAGATTCTTGAC 59.444 52.381 3.34 0.00 34.64 3.18
1128 1199 0.173708 GGAGATTCTTGACGCTCCGT 59.826 55.000 0.00 0.00 45.10 4.69
1150 1221 3.935450 GCATTCAGCGTCGCTTAATTAA 58.065 40.909 21.01 10.15 36.40 1.40
1181 1253 1.055040 TGCTTGGGTTGGAATTTGGG 58.945 50.000 0.00 0.00 0.00 4.12
1293 1371 1.135489 GTCTGGTCGACTGCGTCAATA 60.135 52.381 16.46 0.00 39.61 1.90
1838 1916 1.371183 CTTCTCGTGGCTGAACCCA 59.629 57.895 0.00 0.00 37.83 4.51
2302 2380 2.373707 CCAGCCAGGGGAGGAAGAG 61.374 68.421 0.00 0.00 0.00 2.85
2309 2387 0.253347 AGGGGAGGAAGAGCCATTCA 60.253 55.000 1.40 0.00 40.02 2.57
2411 2489 4.767255 CCGCTCCAGCTCGCCTTT 62.767 66.667 0.00 0.00 39.32 3.11
2429 2507 4.285851 GCAGTAGGCACGCTCTTT 57.714 55.556 0.00 0.00 43.97 2.52
2649 2727 1.186200 CATGGTCGAGTCCCTCAGAA 58.814 55.000 0.00 0.00 0.00 3.02
2936 3014 2.238395 AGAAGAGATCAAAGAGGGTGCC 59.762 50.000 0.00 0.00 0.00 5.01
2957 3035 1.451936 GAGGGCGCCTCCACATAAT 59.548 57.895 28.56 0.74 44.36 1.28
3218 3436 4.400251 TCATGCTCATTTCTCCATTTCCAC 59.600 41.667 0.00 0.00 0.00 4.02
3286 3505 6.343716 TCACTGGCATATGTTTCACAAAAT 57.656 33.333 4.29 0.00 0.00 1.82
3421 3640 6.683974 AATTTCAATCATGGAGACCTTACG 57.316 37.500 0.00 0.00 0.00 3.18
3457 3676 2.475666 GCTCAACATGAGTGGAGGC 58.524 57.895 0.00 0.16 44.57 4.70
3475 3694 1.895131 GGCCAGAAGCAAAGGATTCAA 59.105 47.619 0.00 0.00 46.50 2.69
3574 3793 5.412594 TGCTGCAGTTCTTTTCTATGTAAGG 59.587 40.000 16.64 0.00 0.00 2.69
3575 3794 5.643777 GCTGCAGTTCTTTTCTATGTAAGGA 59.356 40.000 16.64 0.00 0.00 3.36
3576 3795 6.183360 GCTGCAGTTCTTTTCTATGTAAGGAG 60.183 42.308 16.64 0.00 0.00 3.69
3577 3796 6.173339 TGCAGTTCTTTTCTATGTAAGGAGG 58.827 40.000 0.00 0.00 0.00 4.30
3591 3810 2.110753 AGGAGGGGGCTCTTAATCTC 57.889 55.000 0.00 0.00 0.00 2.75
3635 5005 1.721389 CCACACGAAGTTCTGATGTCG 59.279 52.381 0.56 4.29 41.61 4.35
3662 5032 1.825090 TGCAGGATTGTGTGATGACC 58.175 50.000 0.00 0.00 0.00 4.02
3672 5042 1.511850 TGTGATGACCGCACTTTCAG 58.488 50.000 0.00 0.00 37.18 3.02
3741 5111 5.836024 AACCAACAGGATTCTGGTAAGTA 57.164 39.130 5.84 0.00 42.72 2.24
3757 5127 7.615757 TCTGGTAAGTAGATCTTCTGAACATGA 59.384 37.037 4.98 3.24 37.56 3.07
3765 5135 3.807553 TCTTCTGAACATGACTGCACAA 58.192 40.909 0.00 0.00 0.00 3.33
3776 5146 6.446318 ACATGACTGCACAAAATTTCGTAAT 58.554 32.000 0.00 0.00 0.00 1.89
3789 5159 9.746711 CAAAATTTCGTAATATCGATGATCCTC 57.253 33.333 8.54 0.00 39.57 3.71
3805 5178 5.133941 TGATCCTCCTATATCATACTCGGC 58.866 45.833 0.00 0.00 0.00 5.54
3837 5215 0.541863 AGGTAATGGAAGGCGGTCAG 59.458 55.000 0.00 0.00 0.00 3.51
3867 5245 2.419574 GCAAGGGAAATACGCAGACCTA 60.420 50.000 0.00 0.00 0.00 3.08
3882 5260 0.690077 ACCTACTGGAATCCGGGACC 60.690 60.000 13.43 3.36 37.04 4.46
3888 5266 1.892391 GGAATCCGGGACCGCATTC 60.892 63.158 16.94 16.94 43.52 2.67
3906 5284 0.885879 TCGAGAAGCTAGTTTCGGCA 59.114 50.000 12.94 0.00 34.08 5.69
3909 5287 2.622436 GAGAAGCTAGTTTCGGCACAT 58.378 47.619 12.94 0.00 32.33 3.21
3948 5326 0.911769 TGGATACCACCAGCCAAGAG 59.088 55.000 0.00 0.00 34.77 2.85
3952 5330 0.320374 TACCACCAGCCAAGAGAACG 59.680 55.000 0.00 0.00 0.00 3.95
4141 5519 0.179134 CGTAGAAGTCTCCAAGGGCG 60.179 60.000 0.00 0.00 0.00 6.13
4439 5817 9.573166 CATTGGAAGAATATTGACAAGGGTATA 57.427 33.333 0.00 0.00 0.00 1.47
4456 5834 6.986250 AGGGTATATACGGTTACTTTACTGC 58.014 40.000 6.79 0.00 0.00 4.40
4459 5837 7.543520 GGGTATATACGGTTACTTTACTGCATC 59.456 40.741 6.79 0.00 0.00 3.91
4460 5838 8.302438 GGTATATACGGTTACTTTACTGCATCT 58.698 37.037 6.79 0.00 0.00 2.90
4466 5844 4.081087 GGTTACTTTACTGCATCTCTCCCA 60.081 45.833 0.00 0.00 0.00 4.37
4471 5849 6.012745 ACTTTACTGCATCTCTCCCAAAAAT 58.987 36.000 0.00 0.00 0.00 1.82
4473 5851 7.669722 ACTTTACTGCATCTCTCCCAAAAATAA 59.330 33.333 0.00 0.00 0.00 1.40
4474 5852 8.593945 TTTACTGCATCTCTCCCAAAAATAAT 57.406 30.769 0.00 0.00 0.00 1.28
4476 5854 7.814264 ACTGCATCTCTCCCAAAAATAATAG 57.186 36.000 0.00 0.00 0.00 1.73
4477 5855 7.349598 ACTGCATCTCTCCCAAAAATAATAGT 58.650 34.615 0.00 0.00 0.00 2.12
4478 5856 8.494433 ACTGCATCTCTCCCAAAAATAATAGTA 58.506 33.333 0.00 0.00 0.00 1.82
4646 6131 1.081376 CGAGGTGGTCACGACAGTC 60.081 63.158 0.00 0.00 0.00 3.51
4958 6449 1.074775 TGTGGTGACAATCAGGGCC 59.925 57.895 0.00 0.00 46.06 5.80
5296 6798 1.668751 GCACAAGTTTTCCTGACACGA 59.331 47.619 0.00 0.00 0.00 4.35
5627 7132 4.115270 GTCGGGAGGACAGGAAGT 57.885 61.111 0.00 0.00 45.36 3.01
5666 7171 1.004277 GCTCACTGTTCCGTCTCGTG 61.004 60.000 0.00 0.00 0.00 4.35
5783 7288 3.991367 ACCTACACTTTTCAGAGGAACG 58.009 45.455 0.00 0.00 31.35 3.95
5851 7356 1.573108 TGGGAGGTGAGAACAGGATC 58.427 55.000 0.00 0.00 0.00 3.36
5852 7357 0.833949 GGGAGGTGAGAACAGGATCC 59.166 60.000 2.48 2.48 0.00 3.36
5889 7394 4.067972 TGCAAAGTAGTTCGAGAAAGGT 57.932 40.909 0.00 0.00 0.00 3.50
5891 7396 3.364068 GCAAAGTAGTTCGAGAAAGGTGC 60.364 47.826 0.00 0.00 0.00 5.01
6165 7675 2.493675 TGCTGCTCTTCTCGATACAGTT 59.506 45.455 0.00 0.00 31.64 3.16
6409 7919 0.459899 ACTCCGCGACTGATGCAATA 59.540 50.000 8.23 0.00 0.00 1.90
6457 7967 5.468540 TCACTAGTTGCACAGTGATAACT 57.531 39.130 20.72 20.72 44.70 2.24
6584 8094 3.144068 TCTCTGGTCCATTCCCCATAA 57.856 47.619 0.00 0.00 0.00 1.90
6600 8110 7.228314 TCCCCATAATCTCTAGTGATAAACG 57.772 40.000 7.69 0.00 0.00 3.60
6745 8255 2.053627 GACAAACAATCAGCCTTTGCG 58.946 47.619 0.00 0.00 44.33 4.85
6960 8474 8.469200 TCAATTACTGGAAATAAAGAAGGCATG 58.531 33.333 0.00 0.00 0.00 4.06
6968 8482 7.099120 GGAAATAAAGAAGGCATGAACAACAT 58.901 34.615 0.00 0.00 40.17 2.71
6988 8502 6.560253 ACATTGTAAAGTTGGTCAGTGATC 57.440 37.500 0.00 0.00 0.00 2.92
7001 8516 4.298332 GTCAGTGATCGCAAATTTTTGGT 58.702 39.130 9.33 0.00 38.57 3.67
7031 8546 5.482908 GTTGATGGAGAGAACTAGCTCAAA 58.517 41.667 0.00 0.00 37.37 2.69
7058 8573 2.370349 TGACTCGAGTCCTCCAAGATC 58.630 52.381 36.01 13.82 44.15 2.75
7067 8582 1.487976 TCCTCCAAGATCAGCATGTCC 59.512 52.381 0.00 0.00 37.40 4.02
7258 8785 5.012975 TCCTAAATAAGGTTGGTTGTACCGT 59.987 40.000 0.00 0.00 46.62 4.83
7273 8800 1.165907 ACCGTGTGGAAGTGCATGTG 61.166 55.000 0.00 0.00 39.21 3.21
7319 8846 7.761249 CCAAGAACCTTTTAGGATTTTATGCAG 59.239 37.037 0.00 0.00 37.67 4.41
7336 8863 5.557891 ATGCAGTGAAGTTATGCTTTCTC 57.442 39.130 0.00 0.00 40.62 2.87
7337 8864 3.433274 TGCAGTGAAGTTATGCTTTCTCG 59.567 43.478 0.00 0.00 40.62 4.04
7338 8865 3.433615 GCAGTGAAGTTATGCTTTCTCGT 59.566 43.478 0.00 0.00 37.59 4.18
7339 8866 4.667668 GCAGTGAAGTTATGCTTTCTCGTG 60.668 45.833 0.00 0.00 37.59 4.35
7345 8873 4.377021 AGTTATGCTTTCTCGTGTGTTCA 58.623 39.130 0.00 0.00 0.00 3.18
7347 8875 6.163476 AGTTATGCTTTCTCGTGTGTTCATA 58.837 36.000 0.00 0.00 0.00 2.15
7353 8881 6.073980 TGCTTTCTCGTGTGTTCATAAGTAAC 60.074 38.462 0.00 0.00 0.00 2.50
7521 9050 9.447157 TCACACAAAACATAATCACTATCATCA 57.553 29.630 0.00 0.00 0.00 3.07
7564 9093 9.135189 TGATTAATCTTTCCATACCTCAAATGG 57.865 33.333 16.24 0.00 44.51 3.16
7623 9157 5.521906 TTCAGTACCTTAGAGCATAGCAG 57.478 43.478 0.00 0.00 0.00 4.24
7631 9165 4.562963 CCTTAGAGCATAGCAGCATCATGA 60.563 45.833 0.00 0.00 36.85 3.07
7662 9196 5.575157 TGTGCCCAGATTAAAATACCAAGA 58.425 37.500 0.00 0.00 0.00 3.02
7761 9308 7.730364 ACAGGAACAAGTGACAAATAGTAAG 57.270 36.000 0.00 0.00 0.00 2.34
7765 9312 6.204882 GGAACAAGTGACAAATAGTAAGCTGT 59.795 38.462 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.082117 GTTCGCGAACACATCCGGAT 61.082 55.000 39.21 12.38 40.84 4.18
15 16 3.544728 TGTTCGCGAACACATCCG 58.455 55.556 42.01 0.00 45.42 4.18
24 25 3.533720 CCCCCTCTATGTTCGCGA 58.466 61.111 3.71 3.71 0.00 5.87
55 56 3.782523 TCTTAGAGCATTTCCACCAGGAT 59.217 43.478 0.00 0.00 45.26 3.24
59 60 3.307691 CCACTCTTAGAGCATTTCCACCA 60.308 47.826 9.44 0.00 32.04 4.17
64 65 4.207891 TCCACCACTCTTAGAGCATTTC 57.792 45.455 9.44 0.00 32.04 2.17
79 80 4.879295 ATTACCCTCAATTGATCCACCA 57.121 40.909 8.96 0.00 0.00 4.17
80 81 6.154363 TCAAAATTACCCTCAATTGATCCACC 59.846 38.462 8.96 0.00 0.00 4.61
118 119 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
119 120 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
120 121 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
121 122 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
122 123 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
123 124 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
124 125 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
125 126 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
138 139 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
139 140 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
140 141 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
141 142 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
142 143 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
143 144 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
144 145 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
145 146 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
146 147 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
147 148 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
148 149 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
149 150 8.367911 TGTATGTAGTCACTTGTTGAAATCTCT 58.632 33.333 0.00 0.00 35.39 3.10
150 151 8.534333 TGTATGTAGTCACTTGTTGAAATCTC 57.466 34.615 0.00 0.00 35.39 2.75
151 152 8.367911 TCTGTATGTAGTCACTTGTTGAAATCT 58.632 33.333 0.00 0.00 35.39 2.40
152 153 8.534333 TCTGTATGTAGTCACTTGTTGAAATC 57.466 34.615 0.00 0.00 35.39 2.17
153 154 8.774586 GTTCTGTATGTAGTCACTTGTTGAAAT 58.225 33.333 0.00 0.00 35.39 2.17
154 155 7.766738 TGTTCTGTATGTAGTCACTTGTTGAAA 59.233 33.333 0.00 0.00 35.39 2.69
155 156 7.269316 TGTTCTGTATGTAGTCACTTGTTGAA 58.731 34.615 0.00 0.00 35.39 2.69
156 157 6.811954 TGTTCTGTATGTAGTCACTTGTTGA 58.188 36.000 0.00 0.00 0.00 3.18
157 158 7.477144 TTGTTCTGTATGTAGTCACTTGTTG 57.523 36.000 0.00 0.00 0.00 3.33
158 159 8.500753 TTTTGTTCTGTATGTAGTCACTTGTT 57.499 30.769 0.00 0.00 0.00 2.83
159 160 8.559536 CATTTTGTTCTGTATGTAGTCACTTGT 58.440 33.333 0.00 0.00 0.00 3.16
160 161 8.773645 TCATTTTGTTCTGTATGTAGTCACTTG 58.226 33.333 0.00 0.00 0.00 3.16
161 162 8.902540 TCATTTTGTTCTGTATGTAGTCACTT 57.097 30.769 0.00 0.00 0.00 3.16
162 163 8.150945 ACTCATTTTGTTCTGTATGTAGTCACT 58.849 33.333 0.00 0.00 0.00 3.41
163 164 8.223769 CACTCATTTTGTTCTGTATGTAGTCAC 58.776 37.037 0.00 0.00 0.00 3.67
164 165 8.147704 TCACTCATTTTGTTCTGTATGTAGTCA 58.852 33.333 0.00 0.00 0.00 3.41
165 166 8.534333 TCACTCATTTTGTTCTGTATGTAGTC 57.466 34.615 0.00 0.00 0.00 2.59
166 167 8.902540 TTCACTCATTTTGTTCTGTATGTAGT 57.097 30.769 0.00 0.00 0.00 2.73
167 168 9.979270 GATTCACTCATTTTGTTCTGTATGTAG 57.021 33.333 0.00 0.00 0.00 2.74
168 169 9.725019 AGATTCACTCATTTTGTTCTGTATGTA 57.275 29.630 0.00 0.00 0.00 2.29
169 170 8.627208 AGATTCACTCATTTTGTTCTGTATGT 57.373 30.769 0.00 0.00 0.00 2.29
170 171 9.979270 GTAGATTCACTCATTTTGTTCTGTATG 57.021 33.333 0.00 0.00 0.00 2.39
171 172 9.950496 AGTAGATTCACTCATTTTGTTCTGTAT 57.050 29.630 0.00 0.00 0.00 2.29
173 174 9.950496 ATAGTAGATTCACTCATTTTGTTCTGT 57.050 29.630 0.00 0.00 0.00 3.41
215 216 9.764363 CAAATGTACTACCACATACAGATGTAT 57.236 33.333 0.00 0.00 44.82 2.29
216 217 8.973182 TCAAATGTACTACCACATACAGATGTA 58.027 33.333 0.00 0.00 44.82 2.29
218 219 8.716646 TTCAAATGTACTACCACATACAGATG 57.283 34.615 0.00 0.00 38.19 2.90
219 220 9.905713 ATTTCAAATGTACTACCACATACAGAT 57.094 29.630 0.00 0.00 38.19 2.90
220 221 9.378551 GATTTCAAATGTACTACCACATACAGA 57.621 33.333 0.00 0.00 38.19 3.41
221 222 9.383519 AGATTTCAAATGTACTACCACATACAG 57.616 33.333 0.00 0.00 38.19 2.74
222 223 9.733556 AAGATTTCAAATGTACTACCACATACA 57.266 29.630 0.00 0.00 38.19 2.29
225 226 8.450964 CGAAAGATTTCAAATGTACTACCACAT 58.549 33.333 6.16 0.00 37.60 3.21
226 227 7.658167 TCGAAAGATTTCAAATGTACTACCACA 59.342 33.333 6.16 0.00 37.01 4.17
227 228 8.025243 TCGAAAGATTTCAAATGTACTACCAC 57.975 34.615 6.16 0.00 37.01 4.16
228 229 8.610248 TTCGAAAGATTTCAAATGTACTACCA 57.390 30.769 0.00 0.00 41.60 3.25
229 230 9.543018 CTTTCGAAAGATTTCAAATGTACTACC 57.457 33.333 29.89 0.00 41.60 3.18
232 233 8.836413 TGTCTTTCGAAAGATTTCAAATGTACT 58.164 29.630 35.84 0.00 45.83 2.73
233 234 9.445786 TTGTCTTTCGAAAGATTTCAAATGTAC 57.554 29.630 35.84 21.95 45.83 2.90
235 236 8.925161 TTTGTCTTTCGAAAGATTTCAAATGT 57.075 26.923 35.84 0.00 45.83 2.71
243 244 9.720769 TCCTAAGTATTTGTCTTTCGAAAGATT 57.279 29.630 35.84 26.64 45.83 2.40
244 245 9.720769 TTCCTAAGTATTTGTCTTTCGAAAGAT 57.279 29.630 35.84 24.82 45.83 2.40
245 246 8.985805 GTTCCTAAGTATTTGTCTTTCGAAAGA 58.014 33.333 31.62 31.62 42.41 2.52
246 247 8.770828 TGTTCCTAAGTATTTGTCTTTCGAAAG 58.229 33.333 28.26 28.26 37.36 2.62
247 248 8.665643 TGTTCCTAAGTATTTGTCTTTCGAAA 57.334 30.769 10.71 10.71 0.00 3.46
248 249 8.145767 TCTGTTCCTAAGTATTTGTCTTTCGAA 58.854 33.333 0.00 0.00 0.00 3.71
249 250 7.663827 TCTGTTCCTAAGTATTTGTCTTTCGA 58.336 34.615 0.00 0.00 0.00 3.71
250 251 7.063544 CCTCTGTTCCTAAGTATTTGTCTTTCG 59.936 40.741 0.00 0.00 0.00 3.46
251 252 7.334671 CCCTCTGTTCCTAAGTATTTGTCTTTC 59.665 40.741 0.00 0.00 0.00 2.62
252 253 7.017254 TCCCTCTGTTCCTAAGTATTTGTCTTT 59.983 37.037 0.00 0.00 0.00 2.52
253 254 6.500751 TCCCTCTGTTCCTAAGTATTTGTCTT 59.499 38.462 0.00 0.00 0.00 3.01
254 255 6.023603 TCCCTCTGTTCCTAAGTATTTGTCT 58.976 40.000 0.00 0.00 0.00 3.41
255 256 6.070710 ACTCCCTCTGTTCCTAAGTATTTGTC 60.071 42.308 0.00 0.00 0.00 3.18
256 257 5.785940 ACTCCCTCTGTTCCTAAGTATTTGT 59.214 40.000 0.00 0.00 0.00 2.83
257 258 6.109359 CACTCCCTCTGTTCCTAAGTATTTG 58.891 44.000 0.00 0.00 0.00 2.32
258 259 5.189934 CCACTCCCTCTGTTCCTAAGTATTT 59.810 44.000 0.00 0.00 0.00 1.40
259 260 4.717280 CCACTCCCTCTGTTCCTAAGTATT 59.283 45.833 0.00 0.00 0.00 1.89
260 261 4.264895 ACCACTCCCTCTGTTCCTAAGTAT 60.265 45.833 0.00 0.00 0.00 2.12
261 262 3.077088 ACCACTCCCTCTGTTCCTAAGTA 59.923 47.826 0.00 0.00 0.00 2.24
262 263 2.158143 ACCACTCCCTCTGTTCCTAAGT 60.158 50.000 0.00 0.00 0.00 2.24
263 264 2.541466 ACCACTCCCTCTGTTCCTAAG 58.459 52.381 0.00 0.00 0.00 2.18
264 265 2.715763 ACCACTCCCTCTGTTCCTAA 57.284 50.000 0.00 0.00 0.00 2.69
265 266 3.077088 ACTTACCACTCCCTCTGTTCCTA 59.923 47.826 0.00 0.00 0.00 2.94
266 267 2.158143 ACTTACCACTCCCTCTGTTCCT 60.158 50.000 0.00 0.00 0.00 3.36
267 268 2.258109 ACTTACCACTCCCTCTGTTCC 58.742 52.381 0.00 0.00 0.00 3.62
268 269 5.479124 TTTACTTACCACTCCCTCTGTTC 57.521 43.478 0.00 0.00 0.00 3.18
269 270 5.131475 TGTTTTACTTACCACTCCCTCTGTT 59.869 40.000 0.00 0.00 0.00 3.16
270 271 4.657039 TGTTTTACTTACCACTCCCTCTGT 59.343 41.667 0.00 0.00 0.00 3.41
271 272 5.223449 TGTTTTACTTACCACTCCCTCTG 57.777 43.478 0.00 0.00 0.00 3.35
272 273 5.899631 TTGTTTTACTTACCACTCCCTCT 57.100 39.130 0.00 0.00 0.00 3.69
273 274 6.947644 TTTTGTTTTACTTACCACTCCCTC 57.052 37.500 0.00 0.00 0.00 4.30
274 275 8.999905 TTATTTTGTTTTACTTACCACTCCCT 57.000 30.769 0.00 0.00 0.00 4.20
333 334 2.509964 AGGAAATTTATGCTCGGGAGGT 59.490 45.455 0.00 0.00 0.00 3.85
449 454 4.381612 GGAGTAAGACGTTGTCCATGATCA 60.382 45.833 0.00 0.00 32.18 2.92
463 468 6.015265 ACTCTTTACCTCTTGTGGAGTAAGAC 60.015 42.308 0.00 0.00 40.30 3.01
708 737 0.113776 AACTCGTGTGGGGAGGTAGA 59.886 55.000 0.00 0.00 35.82 2.59
709 738 0.531200 GAACTCGTGTGGGGAGGTAG 59.469 60.000 0.00 0.00 35.82 3.18
711 740 2.571216 CGAACTCGTGTGGGGAGGT 61.571 63.158 0.00 0.00 35.82 3.85
803 856 1.203013 TGAAGAGAAGACCACTCCGGA 60.203 52.381 2.93 2.93 38.63 5.14
823 876 3.482436 AGATCGATAGCGGAAGAGAAGT 58.518 45.455 0.00 0.00 38.28 3.01
824 877 3.500299 TGAGATCGATAGCGGAAGAGAAG 59.500 47.826 0.00 0.00 38.28 2.85
825 878 3.477530 TGAGATCGATAGCGGAAGAGAA 58.522 45.455 0.00 0.00 38.28 2.87
826 879 3.070748 CTGAGATCGATAGCGGAAGAGA 58.929 50.000 0.00 0.00 38.28 3.10
827 880 3.070748 TCTGAGATCGATAGCGGAAGAG 58.929 50.000 0.00 0.00 38.28 2.85
860 913 4.789075 CACGCGGGTACGGACAGG 62.789 72.222 12.47 0.00 41.36 4.00
927 989 5.044105 AGGGAAGGAAGCCACTTGTTTATAT 60.044 40.000 0.00 0.00 0.00 0.86
946 1008 1.215679 AGGAGACGAGGAGGAGGGAA 61.216 60.000 0.00 0.00 0.00 3.97
950 1012 2.124693 GGCAGGAGACGAGGAGGAG 61.125 68.421 0.00 0.00 0.00 3.69
951 1013 2.043852 GGCAGGAGACGAGGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
952 1014 3.151022 GGGCAGGAGACGAGGAGG 61.151 72.222 0.00 0.00 0.00 4.30
953 1015 2.363018 TGGGCAGGAGACGAGGAG 60.363 66.667 0.00 0.00 0.00 3.69
1128 1199 1.368641 ATTAAGCGACGCTGAATGCA 58.631 45.000 27.88 5.20 38.23 3.96
1138 1209 2.424341 CAACGGCGTTAATTAAGCGAC 58.576 47.619 26.32 15.65 0.00 5.19
1181 1253 3.952675 CCTGCCACACACACGCAC 61.953 66.667 0.00 0.00 0.00 5.34
2076 2154 1.537202 CGCAAAGAGCAATATAGGGGC 59.463 52.381 0.00 0.00 46.13 5.80
2141 2219 4.103103 CAGCCGACGAGCGACAGA 62.103 66.667 0.00 0.00 44.57 3.41
2302 2380 0.472471 TATCTCCCCGGTTGAATGGC 59.528 55.000 0.00 0.00 0.00 4.40
2309 2387 2.249309 AGTTGACTATCTCCCCGGTT 57.751 50.000 0.00 0.00 0.00 4.44
2450 2528 2.443577 GGGACTAGACCCGGGACC 60.444 72.222 32.02 18.76 40.49 4.46
2649 2727 2.006888 CAACCATATGAACTCGGCGTT 58.993 47.619 6.85 0.00 38.91 4.84
2957 3035 4.721274 TGGACATGAACCCTGATATCAGAA 59.279 41.667 30.40 12.79 46.59 3.02
3015 3093 5.335661 GGTTGACATTCCTTAGCGTCAAATT 60.336 40.000 5.47 0.00 46.62 1.82
3237 3455 4.846779 AATACGTCAACCTGCAAAACAT 57.153 36.364 0.00 0.00 0.00 2.71
3286 3505 2.840038 AGTGCCACTCTGTATCCATGAA 59.160 45.455 0.00 0.00 0.00 2.57
3421 3640 2.206536 CCCTCTCTGGCCGATCTCC 61.207 68.421 0.00 0.00 0.00 3.71
3457 3676 4.553323 CAAGTTGAATCCTTTGCTTCTGG 58.447 43.478 0.00 0.00 0.00 3.86
3475 3694 5.441500 TCACTATAGACAGCTCTAGCAAGT 58.558 41.667 6.78 2.29 45.16 3.16
3574 3793 4.564613 GCATTAGAGATTAAGAGCCCCCTC 60.565 50.000 0.00 0.00 38.42 4.30
3575 3794 3.329225 GCATTAGAGATTAAGAGCCCCCT 59.671 47.826 0.00 0.00 0.00 4.79
3576 3795 3.329225 AGCATTAGAGATTAAGAGCCCCC 59.671 47.826 0.00 0.00 0.00 5.40
3577 3796 4.632327 AGCATTAGAGATTAAGAGCCCC 57.368 45.455 0.00 0.00 0.00 5.80
3591 3810 7.094805 TGGTAGAAAACAAGCTGTTAGCATTAG 60.095 37.037 3.43 0.00 45.56 1.73
3635 5005 3.503363 TCACACAATCCTGCAAGAACATC 59.497 43.478 0.00 0.00 34.07 3.06
3662 5032 1.063806 CGGTCTTCTCTGAAAGTGCG 58.936 55.000 0.00 0.00 33.76 5.34
3672 5042 3.245519 GTCACAAGAACAACGGTCTTCTC 59.754 47.826 0.00 0.00 0.00 2.87
3741 5111 4.252073 GTGCAGTCATGTTCAGAAGATCT 58.748 43.478 0.00 0.00 0.00 2.75
3757 5127 7.067532 TCGATATTACGAAATTTTGTGCAGT 57.932 32.000 19.51 5.01 39.34 4.40
3765 5135 8.314751 AGGAGGATCATCGATATTACGAAATTT 58.685 33.333 0.00 0.00 45.16 1.82
3776 5146 9.952030 GAGTATGATATAGGAGGATCATCGATA 57.048 37.037 0.00 2.53 40.99 2.92
3789 5159 5.250235 ACAATCGCCGAGTATGATATAGG 57.750 43.478 0.00 0.00 0.00 2.57
3805 5178 5.621197 TCCATTACCTGTTGAAACAATCG 57.379 39.130 0.00 0.00 38.66 3.34
3837 5215 4.729595 CGTATTTCCCTTGCTGTTTAACC 58.270 43.478 0.00 0.00 0.00 2.85
3867 5245 3.782443 GCGGTCCCGGATTCCAGT 61.782 66.667 0.73 0.00 40.19 4.00
3882 5260 2.035342 CGAAACTAGCTTCTCGAATGCG 60.035 50.000 4.46 0.00 39.35 4.73
3888 5266 0.992802 GTGCCGAAACTAGCTTCTCG 59.007 55.000 4.46 0.00 0.00 4.04
3906 5284 2.303890 TGCTGTGATTGAGGACTGATGT 59.696 45.455 0.00 0.00 0.00 3.06
3909 5287 1.973515 AGTGCTGTGATTGAGGACTGA 59.026 47.619 0.00 0.00 40.29 3.41
3948 5326 0.591659 GTTGCCCTTGGACTTCGTTC 59.408 55.000 0.00 0.00 0.00 3.95
3952 5330 0.178990 ACCTGTTGCCCTTGGACTTC 60.179 55.000 0.00 0.00 0.00 3.01
4439 5817 6.461231 GGAGAGATGCAGTAAAGTAACCGTAT 60.461 42.308 0.00 0.00 0.00 3.06
4440 5818 5.163581 GGAGAGATGCAGTAAAGTAACCGTA 60.164 44.000 0.00 0.00 0.00 4.02
4441 5819 4.381718 GGAGAGATGCAGTAAAGTAACCGT 60.382 45.833 0.00 0.00 0.00 4.83
4442 5820 4.113354 GGAGAGATGCAGTAAAGTAACCG 58.887 47.826 0.00 0.00 0.00 4.44
4541 6026 6.776744 TGATGAAGCCTGCATAGAGATAAAT 58.223 36.000 0.00 0.00 0.00 1.40
4542 6027 6.042437 TCTGATGAAGCCTGCATAGAGATAAA 59.958 38.462 0.00 0.00 0.00 1.40
4543 6028 5.541484 TCTGATGAAGCCTGCATAGAGATAA 59.459 40.000 0.00 0.00 0.00 1.75
4544 6029 5.082425 TCTGATGAAGCCTGCATAGAGATA 58.918 41.667 0.00 0.00 0.00 1.98
4646 6131 2.838202 AGTTACAGTACCCATGACCAGG 59.162 50.000 0.00 0.00 0.00 4.45
4958 6449 2.671177 CCTGTCTGTTGCCGCGAAG 61.671 63.158 8.23 0.00 0.00 3.79
5075 6566 5.359009 AGATGTGAATATGGTCAAGCTTTGG 59.641 40.000 0.00 0.00 0.00 3.28
5627 7132 3.084039 GCTGATGAGTGTTGATTTCCCA 58.916 45.455 0.00 0.00 0.00 4.37
5666 7171 2.378634 CCTCCCACCCACAGGATCC 61.379 68.421 2.48 2.48 36.73 3.36
5783 7288 1.470805 GGGTCCAAATTATTGCGCACC 60.471 52.381 11.12 3.18 35.10 5.01
5975 7480 7.807977 TCTGTCTTTGTTTAAGAAAGCTCAT 57.192 32.000 9.36 0.00 44.69 2.90
6213 7723 3.923017 ACTCAAACTGTTTGCTATGGC 57.077 42.857 24.62 0.00 40.43 4.40
6255 7765 3.155750 CCATAGGCCAGAGGGAGC 58.844 66.667 5.01 0.00 35.59 4.70
6397 7907 4.122776 CACCCTGTAGTATTGCATCAGTC 58.877 47.826 0.00 0.00 0.00 3.51
6409 7919 0.905357 GCCTGATGACACCCTGTAGT 59.095 55.000 0.00 0.00 0.00 2.73
6457 7967 1.004277 GTTGGGACCCTGTGAGCAATA 59.996 52.381 13.00 0.00 0.00 1.90
6531 8041 8.939929 CACTTGATACATGACTGAACTGTTTAT 58.060 33.333 0.00 0.00 0.00 1.40
6584 8094 6.810911 ACATTGCTCGTTTATCACTAGAGAT 58.189 36.000 7.83 7.83 0.00 2.75
6600 8110 4.639310 AGATCAGGTTTGATGACATTGCTC 59.361 41.667 0.00 0.00 44.01 4.26
6655 8165 2.429971 AGTCATCAGCAGTCGTCATCAT 59.570 45.455 0.00 0.00 0.00 2.45
6665 8175 3.883830 ACCTGTAGAAGTCATCAGCAG 57.116 47.619 0.00 0.00 34.12 4.24
6745 8255 1.398390 CAATACTCCGCCACAAGCTTC 59.602 52.381 0.00 0.00 40.39 3.86
6960 8474 6.472163 CACTGACCAACTTTACAATGTTGTTC 59.528 38.462 15.46 12.63 42.35 3.18
6968 8482 3.496884 GCGATCACTGACCAACTTTACAA 59.503 43.478 0.00 0.00 0.00 2.41
6988 8502 5.694006 TCAACCTTATCACCAAAAATTTGCG 59.306 36.000 0.29 0.00 36.86 4.85
7001 8516 6.183360 GCTAGTTCTCTCCATCAACCTTATCA 60.183 42.308 0.00 0.00 0.00 2.15
7031 8546 2.419297 GGAGGACTCGAGTCAATGCATT 60.419 50.000 38.52 18.87 46.47 3.56
7058 8573 2.941064 CAGTATCCTTGTGGACATGCTG 59.059 50.000 0.00 0.00 46.51 4.41
7067 8582 5.277202 CGCAATGAATCTCAGTATCCTTGTG 60.277 44.000 0.00 0.00 0.00 3.33
7077 8592 3.797039 TCCCTTACGCAATGAATCTCAG 58.203 45.455 0.00 0.00 0.00 3.35
7258 8785 0.537143 GGACCACATGCACTTCCACA 60.537 55.000 0.00 0.00 0.00 4.17
7273 8800 3.118261 TGGCACTATCTTCATTCTGGACC 60.118 47.826 0.00 0.00 0.00 4.46
7319 8846 4.211374 ACACACGAGAAAGCATAACTTCAC 59.789 41.667 0.00 0.00 37.75 3.18
7327 8854 4.997395 ACTTATGAACACACGAGAAAGCAT 59.003 37.500 0.00 0.00 0.00 3.79
7336 8863 6.442487 TTTCGAGTTACTTATGAACACACG 57.558 37.500 0.00 0.00 0.00 4.49
7353 8881 7.934457 ACCCAATGATTCTCAATAATTTCGAG 58.066 34.615 0.00 0.00 0.00 4.04
7438 8966 5.809562 CAGTAATAGTTCTTGCTGTGGAGAG 59.190 44.000 0.00 0.00 35.07 3.20
7564 9093 1.009675 CACTGCACAACCTCGCAAC 60.010 57.895 0.00 0.00 37.76 4.17
7623 9157 2.547211 GGCACATGTCTAGTCATGATGC 59.453 50.000 29.02 28.39 45.41 3.91
7631 9165 5.435686 TTTAATCTGGGCACATGTCTAGT 57.564 39.130 0.00 0.00 29.82 2.57
7662 9196 4.221924 GCCCATAATAAACTGGTTTGGTGT 59.778 41.667 8.73 0.00 34.23 4.16
7741 9275 7.190920 ACAGCTTACTATTTGTCACTTGTTC 57.809 36.000 0.00 0.00 0.00 3.18
7761 9308 5.530519 TGAAACGTGAAAGATGATACAGC 57.469 39.130 0.00 0.00 0.00 4.40
7765 9312 9.825972 GAAGAATTTGAAACGTGAAAGATGATA 57.174 29.630 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.