Multiple sequence alignment - TraesCS2A01G352900

Loading Multiple Alignment...

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 TraesCS2A01G352900 chr2A 100.000 2456 0 0 1 2456 593489072 593486617 0.000000e+00 4536
1 TraesCS2A01G352900 chr2A 98.347 242 4 0 114 355 722380324 722380565 2.260000e-115 425
2 TraesCS2A01G352900 chr2B 88.546 1362 72 25 353 1673 528968526 528967208 0.000000e+00 1574
3 TraesCS2A01G352900 chr2B 90.517 116 10 1 1 115 528968640 528968525 4.230000e-33 152
4 TraesCS2A01G352900 chr2D 89.483 1179 65 16 507 1662 449524481 449525623 0.000000e+00 1435
5 TraesCS2A01G352900 chr2D 93.590 156 10 0 353 508 449524222 449524377 1.470000e-57 233
6 TraesCS2A01G352900 chr2D 90.265 113 11 0 3 115 449524111 449524223 5.470000e-32 148
7 TraesCS2A01G352900 chr6B 99.178 730 6 0 1727 2456 166618945 166618216 0.000000e+00 1315
8 TraesCS2A01G352900 chr6B 99.045 733 7 0 1724 2456 226650568 226651300 0.000000e+00 1315
9 TraesCS2A01G352900 chr4B 99.042 731 7 0 1726 2456 135905985 135905255 0.000000e+00 1312
10 TraesCS2A01G352900 chr4A 99.041 730 7 0 1727 2456 618643118 618643847 0.000000e+00 1310
11 TraesCS2A01G352900 chr4A 97.942 243 5 0 112 354 37605313 37605555 2.920000e-114 422
12 TraesCS2A01G352900 chr4A 97.942 243 5 0 112 354 560038704 560038946 2.920000e-114 422
13 TraesCS2A01G352900 chr4A 95.420 262 9 3 113 372 597929283 597929543 4.890000e-112 414
14 TraesCS2A01G352900 chr1A 98.909 733 8 0 1724 2456 101094913 101094181 0.000000e+00 1310
15 TraesCS2A01G352900 chr1A 99.040 729 7 0 1728 2456 19701095 19700367 0.000000e+00 1308
16 TraesCS2A01G352900 chr1A 99.040 729 7 0 1728 2456 591504818 591504090 0.000000e+00 1308
17 TraesCS2A01G352900 chr1A 97.942 243 5 0 112 354 412001838 412002080 2.920000e-114 422
18 TraesCS2A01G352900 chr6A 99.040 729 7 0 1728 2456 317335965 317335237 0.000000e+00 1308
19 TraesCS2A01G352900 chr5B 99.040 729 7 0 1728 2456 271029165 271029893 0.000000e+00 1308
20 TraesCS2A01G352900 chr1B 99.588 243 1 0 112 354 97920905 97920663 6.230000e-121 444
21 TraesCS2A01G352900 chr7A 98.354 243 4 0 112 354 528574578 528574820 6.280000e-116 427
22 TraesCS2A01G352900 chr7A 97.211 251 6 1 105 355 23347031 23346782 8.120000e-115 424
23 TraesCS2A01G352900 chr6D 97.177 248 7 0 110 357 149882402 149882155 1.050000e-113 420


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 TraesCS2A01G352900 chr2A 593486617 593489072 2455 True 4536.000000 4536 100.000000 1 2456 1 chr2A.!!$R1 2455
1 TraesCS2A01G352900 chr2B 528967208 528968640 1432 True 863.000000 1574 89.531500 1 1673 2 chr2B.!!$R1 1672
2 TraesCS2A01G352900 chr2D 449524111 449525623 1512 False 605.333333 1435 91.112667 3 1662 3 chr2D.!!$F1 1659
3 TraesCS2A01G352900 chr6B 166618216 166618945 729 True 1315.000000 1315 99.178000 1727 2456 1 chr6B.!!$R1 729
4 TraesCS2A01G352900 chr6B 226650568 226651300 732 False 1315.000000 1315 99.045000 1724 2456 1 chr6B.!!$F1 732
5 TraesCS2A01G352900 chr4B 135905255 135905985 730 True 1312.000000 1312 99.042000 1726 2456 1 chr4B.!!$R1 730
6 TraesCS2A01G352900 chr4A 618643118 618643847 729 False 1310.000000 1310 99.041000 1727 2456 1 chr4A.!!$F4 729
7 TraesCS2A01G352900 chr1A 101094181 101094913 732 True 1310.000000 1310 98.909000 1724 2456 1 chr1A.!!$R2 732
8 TraesCS2A01G352900 chr1A 19700367 19701095 728 True 1308.000000 1308 99.040000 1728 2456 1 chr1A.!!$R1 728
9 TraesCS2A01G352900 chr1A 591504090 591504818 728 True 1308.000000 1308 99.040000 1728 2456 1 chr1A.!!$R3 728
10 TraesCS2A01G352900 chr6A 317335237 317335965 728 True 1308.000000 1308 99.040000 1728 2456 1 chr6A.!!$R1 728
11 TraesCS2A01G352900 chr5B 271029165 271029893 728 False 1308.000000 1308 99.040000 1728 2456 1 chr5B.!!$F1 728

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
969 1088 0.10852 ATACCACGCACTAACACCGG 60.109 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2472 2.401568 TCTCTGATGCAGATTGGGCTA 58.598 47.619 0.0 0.0 39.92 3.93 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 1.908483 GCGAATTGTCCCTCTCCCT 59.092 57.895 0.00 0.00 0.00 4.20
22 24 1.486211 GAATTGTCCCTCTCCCTCGA 58.514 55.000 0.00 0.00 0.00 4.04
27 29 1.033202 GTCCCTCTCCCTCGACAGTC 61.033 65.000 0.00 0.00 0.00 3.51
113 115 8.224389 TGATCATCCACATTCGATTTTTGTAT 57.776 30.769 0.00 0.00 0.00 2.29
114 116 9.336171 TGATCATCCACATTCGATTTTTGTATA 57.664 29.630 0.00 0.00 0.00 1.47
115 117 9.599322 GATCATCCACATTCGATTTTTGTATAC 57.401 33.333 0.00 0.00 0.00 1.47
116 118 8.731275 TCATCCACATTCGATTTTTGTATACT 57.269 30.769 4.17 0.00 0.00 2.12
117 119 8.826710 TCATCCACATTCGATTTTTGTATACTC 58.173 33.333 4.17 0.00 0.00 2.59
118 120 7.548196 TCCACATTCGATTTTTGTATACTCC 57.452 36.000 4.17 0.00 0.00 3.85
119 121 6.540914 TCCACATTCGATTTTTGTATACTCCC 59.459 38.462 4.17 0.00 0.00 4.30
120 122 6.542370 CCACATTCGATTTTTGTATACTCCCT 59.458 38.462 4.17 0.00 0.00 4.20
121 123 7.254795 CCACATTCGATTTTTGTATACTCCCTC 60.255 40.741 4.17 0.00 0.00 4.30
122 124 6.766467 ACATTCGATTTTTGTATACTCCCTCC 59.234 38.462 4.17 0.00 0.00 4.30
123 125 6.555463 TTCGATTTTTGTATACTCCCTCCT 57.445 37.500 4.17 0.00 0.00 3.69
124 126 6.555463 TCGATTTTTGTATACTCCCTCCTT 57.445 37.500 4.17 0.00 0.00 3.36
125 127 6.579865 TCGATTTTTGTATACTCCCTCCTTC 58.420 40.000 4.17 0.00 0.00 3.46
126 128 5.758784 CGATTTTTGTATACTCCCTCCTTCC 59.241 44.000 4.17 0.00 0.00 3.46
127 129 6.631766 CGATTTTTGTATACTCCCTCCTTCCA 60.632 42.308 4.17 0.00 0.00 3.53
128 130 6.652205 TTTTTGTATACTCCCTCCTTCCAT 57.348 37.500 4.17 0.00 0.00 3.41
129 131 5.888982 TTTGTATACTCCCTCCTTCCATC 57.111 43.478 4.17 0.00 0.00 3.51
130 132 4.834406 TGTATACTCCCTCCTTCCATCT 57.166 45.455 4.17 0.00 0.00 2.90
131 133 5.942977 TGTATACTCCCTCCTTCCATCTA 57.057 43.478 4.17 0.00 0.00 1.98
132 134 6.485388 TGTATACTCCCTCCTTCCATCTAT 57.515 41.667 4.17 0.00 0.00 1.98
133 135 7.599353 TGTATACTCCCTCCTTCCATCTATA 57.401 40.000 4.17 0.00 0.00 1.31
134 136 8.188501 TGTATACTCCCTCCTTCCATCTATAT 57.811 38.462 4.17 0.00 0.00 0.86
135 137 9.305169 TGTATACTCCCTCCTTCCATCTATATA 57.695 37.037 4.17 0.00 0.00 0.86
136 138 9.802039 GTATACTCCCTCCTTCCATCTATATAG 57.198 40.741 3.10 3.10 0.00 1.31
137 139 6.098716 ACTCCCTCCTTCCATCTATATAGG 57.901 45.833 9.89 0.00 0.00 2.57
138 140 5.042979 ACTCCCTCCTTCCATCTATATAGGG 60.043 48.000 9.89 4.49 43.23 3.53
139 141 3.970640 CCCTCCTTCCATCTATATAGGGC 59.029 52.174 9.89 0.00 36.30 5.19
140 142 3.970640 CCTCCTTCCATCTATATAGGGCC 59.029 52.174 9.89 0.00 0.00 5.80
141 143 4.327332 CCTCCTTCCATCTATATAGGGCCT 60.327 50.000 12.58 12.58 0.00 5.19
142 144 5.103043 CCTCCTTCCATCTATATAGGGCCTA 60.103 48.000 17.16 17.16 0.00 3.93
143 145 6.432190 TCCTTCCATCTATATAGGGCCTAA 57.568 41.667 18.91 7.61 0.00 2.69
144 146 7.009960 TCCTTCCATCTATATAGGGCCTAAT 57.990 40.000 18.91 14.19 0.00 1.73
145 147 6.846505 TCCTTCCATCTATATAGGGCCTAATG 59.153 42.308 18.91 15.42 0.00 1.90
146 148 6.465035 CCTTCCATCTATATAGGGCCTAATGC 60.465 46.154 18.91 0.00 40.16 3.56
147 149 4.588951 TCCATCTATATAGGGCCTAATGCG 59.411 45.833 18.91 10.04 42.61 4.73
148 150 4.345257 CCATCTATATAGGGCCTAATGCGT 59.655 45.833 18.91 2.76 42.61 5.24
149 151 5.163301 CCATCTATATAGGGCCTAATGCGTT 60.163 44.000 18.91 1.94 42.61 4.84
150 152 6.349300 CATCTATATAGGGCCTAATGCGTTT 58.651 40.000 18.91 1.12 42.61 3.60
151 153 6.368779 TCTATATAGGGCCTAATGCGTTTT 57.631 37.500 18.91 0.30 42.61 2.43
152 154 6.775708 TCTATATAGGGCCTAATGCGTTTTT 58.224 36.000 18.91 0.00 42.61 1.94
174 176 7.769272 TTTTGAAGCTAACTTTGACCAAATG 57.231 32.000 0.00 0.00 35.82 2.32
175 177 6.463995 TTGAAGCTAACTTTGACCAAATGT 57.536 33.333 0.00 0.00 35.82 2.71
176 178 6.463995 TGAAGCTAACTTTGACCAAATGTT 57.536 33.333 0.00 11.80 35.82 2.71
177 179 7.575414 TGAAGCTAACTTTGACCAAATGTTA 57.425 32.000 0.00 12.42 35.82 2.41
178 180 7.648142 TGAAGCTAACTTTGACCAAATGTTAG 58.352 34.615 22.72 22.72 40.29 2.34
179 181 7.500892 TGAAGCTAACTTTGACCAAATGTTAGA 59.499 33.333 26.48 15.32 40.08 2.10
180 182 7.440523 AGCTAACTTTGACCAAATGTTAGAG 57.559 36.000 26.48 16.32 40.08 2.43
181 183 6.072452 AGCTAACTTTGACCAAATGTTAGAGC 60.072 38.462 26.48 20.97 40.08 4.09
182 184 6.293955 GCTAACTTTGACCAAATGTTAGAGCA 60.294 38.462 26.48 10.01 40.08 4.26
183 185 6.463995 AACTTTGACCAAATGTTAGAGCAA 57.536 33.333 0.00 0.00 0.00 3.91
184 186 6.655078 ACTTTGACCAAATGTTAGAGCAAT 57.345 33.333 0.00 0.00 0.00 3.56
185 187 7.759489 ACTTTGACCAAATGTTAGAGCAATA 57.241 32.000 0.00 0.00 0.00 1.90
186 188 8.177119 ACTTTGACCAAATGTTAGAGCAATAA 57.823 30.769 0.00 0.00 0.00 1.40
187 189 8.806146 ACTTTGACCAAATGTTAGAGCAATAAT 58.194 29.630 0.00 0.00 0.00 1.28
199 201 9.723601 TGTTAGAGCAATAATATATGACATGCA 57.276 29.630 10.78 0.00 34.89 3.96
202 204 8.859236 AGAGCAATAATATATGACATGCAACT 57.141 30.769 10.78 7.52 34.89 3.16
203 205 9.293404 AGAGCAATAATATATGACATGCAACTT 57.707 29.630 10.78 0.00 34.89 2.66
212 214 3.963665 TGACATGCAACTTACACAAAGC 58.036 40.909 0.00 0.00 38.93 3.51
213 215 3.379688 TGACATGCAACTTACACAAAGCA 59.620 39.130 0.00 0.00 38.93 3.91
214 216 3.705604 ACATGCAACTTACACAAAGCAC 58.294 40.909 0.00 0.00 38.93 4.40
215 217 3.130164 ACATGCAACTTACACAAAGCACA 59.870 39.130 0.00 0.00 38.93 4.57
216 218 4.202141 ACATGCAACTTACACAAAGCACAT 60.202 37.500 0.00 0.00 38.93 3.21
217 219 3.963665 TGCAACTTACACAAAGCACATC 58.036 40.909 0.00 0.00 38.93 3.06
218 220 3.379688 TGCAACTTACACAAAGCACATCA 59.620 39.130 0.00 0.00 38.93 3.07
219 221 4.037803 TGCAACTTACACAAAGCACATCAT 59.962 37.500 0.00 0.00 38.93 2.45
220 222 4.618489 GCAACTTACACAAAGCACATCATC 59.382 41.667 0.00 0.00 38.93 2.92
221 223 5.761003 CAACTTACACAAAGCACATCATCA 58.239 37.500 0.00 0.00 38.93 3.07
222 224 6.207928 CAACTTACACAAAGCACATCATCAA 58.792 36.000 0.00 0.00 38.93 2.57
223 225 6.389830 ACTTACACAAAGCACATCATCAAA 57.610 33.333 0.00 0.00 38.93 2.69
224 226 6.985117 ACTTACACAAAGCACATCATCAAAT 58.015 32.000 0.00 0.00 38.93 2.32
225 227 7.436118 ACTTACACAAAGCACATCATCAAATT 58.564 30.769 0.00 0.00 38.93 1.82
226 228 7.596248 ACTTACACAAAGCACATCATCAAATTC 59.404 33.333 0.00 0.00 38.93 2.17
227 229 4.919168 ACACAAAGCACATCATCAAATTCG 59.081 37.500 0.00 0.00 0.00 3.34
228 230 4.919168 CACAAAGCACATCATCAAATTCGT 59.081 37.500 0.00 0.00 0.00 3.85
229 231 6.085573 CACAAAGCACATCATCAAATTCGTA 58.914 36.000 0.00 0.00 0.00 3.43
230 232 6.748658 CACAAAGCACATCATCAAATTCGTAT 59.251 34.615 0.00 0.00 0.00 3.06
231 233 6.748658 ACAAAGCACATCATCAAATTCGTATG 59.251 34.615 0.00 0.00 0.00 2.39
232 234 6.441093 AAGCACATCATCAAATTCGTATGT 57.559 33.333 0.00 0.00 0.00 2.29
233 235 5.813717 AGCACATCATCAAATTCGTATGTG 58.186 37.500 8.50 8.50 44.34 3.21
234 236 5.585844 AGCACATCATCAAATTCGTATGTGA 59.414 36.000 15.34 0.00 44.30 3.58
235 237 6.093909 AGCACATCATCAAATTCGTATGTGAA 59.906 34.615 15.34 0.00 44.30 3.18
236 238 6.746822 GCACATCATCAAATTCGTATGTGAAA 59.253 34.615 15.34 0.00 44.30 2.69
237 239 7.044510 GCACATCATCAAATTCGTATGTGAAAG 60.045 37.037 15.34 0.00 44.30 2.62
238 240 7.430211 CACATCATCAAATTCGTATGTGAAAGG 59.570 37.037 7.32 0.00 44.30 3.11
239 241 7.336679 ACATCATCAAATTCGTATGTGAAAGGA 59.663 33.333 0.00 0.00 31.82 3.36
240 242 7.307493 TCATCAAATTCGTATGTGAAAGGAG 57.693 36.000 0.00 0.00 31.82 3.69
241 243 5.545658 TCAAATTCGTATGTGAAAGGAGC 57.454 39.130 0.00 0.00 0.00 4.70
242 244 5.245531 TCAAATTCGTATGTGAAAGGAGCT 58.754 37.500 0.00 0.00 0.00 4.09
243 245 5.705441 TCAAATTCGTATGTGAAAGGAGCTT 59.295 36.000 0.00 0.00 0.00 3.74
244 246 6.206634 TCAAATTCGTATGTGAAAGGAGCTTT 59.793 34.615 0.00 0.00 36.29 3.51
245 247 5.803020 ATTCGTATGTGAAAGGAGCTTTC 57.197 39.130 0.00 0.00 46.88 2.62
280 282 9.524106 AATTTTCACATTATGCATGTCATGTAG 57.476 29.630 10.16 9.56 43.17 2.74
281 283 7.628769 TTTCACATTATGCATGTCATGTAGT 57.371 32.000 10.16 1.63 43.17 2.73
282 284 8.729805 TTTCACATTATGCATGTCATGTAGTA 57.270 30.769 10.16 2.89 43.17 1.82
283 285 8.907222 TTCACATTATGCATGTCATGTAGTAT 57.093 30.769 10.16 4.99 43.17 2.12
284 286 8.907222 TCACATTATGCATGTCATGTAGTATT 57.093 30.769 10.16 0.00 43.17 1.89
285 287 9.995003 TCACATTATGCATGTCATGTAGTATTA 57.005 29.630 10.16 0.00 43.17 0.98
314 316 9.816354 TTTATCAATAGTCAATGACGATCTTGA 57.184 29.630 17.87 17.87 37.67 3.02
315 317 9.816354 TTATCAATAGTCAATGACGATCTTGAA 57.184 29.630 18.78 7.77 37.67 2.69
316 318 8.722480 ATCAATAGTCAATGACGATCTTGAAA 57.278 30.769 18.78 5.97 37.67 2.69
317 319 8.546597 TCAATAGTCAATGACGATCTTGAAAA 57.453 30.769 9.34 0.00 37.67 2.29
318 320 8.998377 TCAATAGTCAATGACGATCTTGAAAAA 58.002 29.630 9.34 0.00 37.67 1.94
319 321 9.055248 CAATAGTCAATGACGATCTTGAAAAAC 57.945 33.333 9.34 0.00 37.67 2.43
320 322 5.679906 AGTCAATGACGATCTTGAAAAACG 58.320 37.500 7.83 0.00 37.67 3.60
321 323 4.318332 GTCAATGACGATCTTGAAAAACGC 59.682 41.667 0.00 0.00 33.45 4.84
322 324 4.024472 TCAATGACGATCTTGAAAAACGCA 60.024 37.500 0.00 0.00 0.00 5.24
323 325 4.685169 ATGACGATCTTGAAAAACGCAT 57.315 36.364 0.00 0.00 0.00 4.73
324 326 4.481930 TGACGATCTTGAAAAACGCATT 57.518 36.364 0.00 0.00 0.00 3.56
325 327 5.599359 TGACGATCTTGAAAAACGCATTA 57.401 34.783 0.00 0.00 0.00 1.90
326 328 5.617609 TGACGATCTTGAAAAACGCATTAG 58.382 37.500 0.00 0.00 0.00 1.73
327 329 4.969816 ACGATCTTGAAAAACGCATTAGG 58.030 39.130 0.00 0.00 0.00 2.69
328 330 3.786048 CGATCTTGAAAAACGCATTAGGC 59.214 43.478 0.00 0.00 39.90 3.93
329 331 3.569250 TCTTGAAAAACGCATTAGGCC 57.431 42.857 0.00 0.00 40.31 5.19
330 332 2.230266 TCTTGAAAAACGCATTAGGCCC 59.770 45.455 0.00 0.00 40.31 5.80
331 333 1.917872 TGAAAAACGCATTAGGCCCT 58.082 45.000 0.00 0.00 40.31 5.19
332 334 3.074675 TGAAAAACGCATTAGGCCCTA 57.925 42.857 0.00 0.00 40.31 3.53
333 335 3.626930 TGAAAAACGCATTAGGCCCTAT 58.373 40.909 0.00 0.00 40.31 2.57
334 336 4.783055 TGAAAAACGCATTAGGCCCTATA 58.217 39.130 0.00 0.00 40.31 1.31
335 337 5.381757 TGAAAAACGCATTAGGCCCTATAT 58.618 37.500 0.00 0.00 40.31 0.86
336 338 6.535540 TGAAAAACGCATTAGGCCCTATATA 58.464 36.000 0.00 0.00 40.31 0.86
337 339 6.653320 TGAAAAACGCATTAGGCCCTATATAG 59.347 38.462 0.00 2.46 40.31 1.31
338 340 6.368779 AAAACGCATTAGGCCCTATATAGA 57.631 37.500 11.53 0.00 40.31 1.98
339 341 6.561519 AAACGCATTAGGCCCTATATAGAT 57.438 37.500 11.53 0.00 40.31 1.98
340 342 5.537300 ACGCATTAGGCCCTATATAGATG 57.463 43.478 11.53 6.87 40.31 2.90
341 343 4.345257 ACGCATTAGGCCCTATATAGATGG 59.655 45.833 11.53 6.04 40.31 3.51
342 344 4.588951 CGCATTAGGCCCTATATAGATGGA 59.411 45.833 11.53 0.00 40.31 3.41
343 345 5.070446 CGCATTAGGCCCTATATAGATGGAA 59.930 44.000 11.53 0.00 40.31 3.53
344 346 6.529220 GCATTAGGCCCTATATAGATGGAAG 58.471 44.000 11.53 0.00 36.11 3.46
345 347 6.465035 GCATTAGGCCCTATATAGATGGAAGG 60.465 46.154 11.53 3.94 36.11 3.46
346 348 4.994411 AGGCCCTATATAGATGGAAGGA 57.006 45.455 11.53 0.00 0.00 3.36
347 349 4.889780 AGGCCCTATATAGATGGAAGGAG 58.110 47.826 11.53 0.00 0.00 3.69
348 350 3.970640 GGCCCTATATAGATGGAAGGAGG 59.029 52.174 11.53 1.87 0.00 4.30
349 351 3.970640 GCCCTATATAGATGGAAGGAGGG 59.029 52.174 11.53 3.52 44.52 4.30
350 352 4.327010 GCCCTATATAGATGGAAGGAGGGA 60.327 50.000 11.53 0.00 44.48 4.20
351 353 5.463154 CCCTATATAGATGGAAGGAGGGAG 58.537 50.000 11.53 0.00 44.48 4.30
364 366 1.282157 GGAGGGAGTAGGTGTTTGCAT 59.718 52.381 0.00 0.00 0.00 3.96
366 368 1.066143 AGGGAGTAGGTGTTTGCATCG 60.066 52.381 0.00 0.00 0.00 3.84
462 465 7.600065 TGTAGTAGTAACACTCAGTTTCATCC 58.400 38.462 0.00 0.00 41.64 3.51
490 493 2.025636 ATCCCTACCCCTAATCACCG 57.974 55.000 0.00 0.00 0.00 4.94
602 711 3.947612 ATTGAGACCTCATCATTGGCT 57.052 42.857 0.01 0.00 39.64 4.75
603 712 2.996249 TGAGACCTCATCATTGGCTC 57.004 50.000 0.00 0.00 34.14 4.70
604 713 2.190538 TGAGACCTCATCATTGGCTCA 58.809 47.619 0.00 0.00 35.65 4.26
605 714 2.775960 TGAGACCTCATCATTGGCTCAT 59.224 45.455 0.00 0.00 34.28 2.90
606 715 3.181457 TGAGACCTCATCATTGGCTCATC 60.181 47.826 0.00 0.00 34.28 2.92
607 716 2.141517 GACCTCATCATTGGCTCATCG 58.858 52.381 0.00 0.00 0.00 3.84
608 717 0.873054 CCTCATCATTGGCTCATCGC 59.127 55.000 0.00 0.00 38.13 4.58
609 718 1.589803 CTCATCATTGGCTCATCGCA 58.410 50.000 0.00 0.00 41.67 5.10
610 719 1.944709 CTCATCATTGGCTCATCGCAA 59.055 47.619 0.00 0.00 41.67 4.85
611 720 2.356695 CTCATCATTGGCTCATCGCAAA 59.643 45.455 0.00 0.00 41.67 3.68
612 721 2.754002 TCATCATTGGCTCATCGCAAAA 59.246 40.909 0.00 0.00 41.67 2.44
613 722 3.193056 TCATCATTGGCTCATCGCAAAAA 59.807 39.130 0.00 0.00 41.67 1.94
736 853 1.133025 CTGGTTTGGCTCGCTTAATGG 59.867 52.381 0.00 0.00 0.00 3.16
737 854 0.179137 GGTTTGGCTCGCTTAATGGC 60.179 55.000 0.00 0.00 0.00 4.40
738 855 0.525761 GTTTGGCTCGCTTAATGGCA 59.474 50.000 0.00 0.00 34.48 4.92
739 856 1.067915 GTTTGGCTCGCTTAATGGCAA 60.068 47.619 0.00 0.00 42.90 4.52
762 879 9.987272 GCAAATATATCCCTTTCTTTAAGCATT 57.013 29.630 0.00 0.00 32.19 3.56
821 938 2.564721 GGCTTGCTTTCGGTTGCCT 61.565 57.895 0.00 0.00 37.58 4.75
822 939 1.372128 GCTTGCTTTCGGTTGCCTG 60.372 57.895 0.00 0.00 0.00 4.85
823 940 1.795170 GCTTGCTTTCGGTTGCCTGA 61.795 55.000 0.00 0.00 0.00 3.86
969 1088 0.108520 ATACCACGCACTAACACCGG 60.109 55.000 0.00 0.00 0.00 5.28
1105 1225 4.479993 AGCCTGAGGATGCCACGC 62.480 66.667 0.65 0.00 0.00 5.34
1463 1607 1.620822 GTGGCATTGTGAGGAAGGTT 58.379 50.000 0.00 0.00 0.00 3.50
1469 1613 3.629398 GCATTGTGAGGAAGGTTATCTGG 59.371 47.826 0.00 0.00 0.00 3.86
1505 1649 2.034685 GTGAAACCAAAGTGGAAGGAGC 59.965 50.000 0.18 0.00 40.96 4.70
1517 1661 1.668237 GGAAGGAGCGCTTCAAGATTC 59.332 52.381 20.11 12.53 32.84 2.52
1518 1662 1.325943 GAAGGAGCGCTTCAAGATTCG 59.674 52.381 20.11 0.00 0.00 3.34
1519 1663 1.086634 AGGAGCGCTTCAAGATTCGC 61.087 55.000 20.11 0.06 46.95 4.70
1522 1666 3.139794 GCGCTTCAAGATTCGCATC 57.860 52.632 0.00 0.00 45.99 3.91
1526 1671 2.012673 GCTTCAAGATTCGCATCACCT 58.987 47.619 0.00 0.00 0.00 4.00
1531 1676 1.098050 AGATTCGCATCACCTTTGGC 58.902 50.000 0.00 0.00 0.00 4.52
1549 1694 1.021390 GCTGAGTGTGTGGAATCGGG 61.021 60.000 0.00 0.00 0.00 5.14
1562 1707 5.946972 TGTGGAATCGGGTTTATATGTGTTT 59.053 36.000 0.00 0.00 0.00 2.83
1563 1708 7.066043 GTGTGGAATCGGGTTTATATGTGTTTA 59.934 37.037 0.00 0.00 0.00 2.01
1614 1767 2.605030 GCAAAATGCTTGCGGACATTA 58.395 42.857 0.00 0.00 40.96 1.90
1615 1768 3.189285 GCAAAATGCTTGCGGACATTAT 58.811 40.909 0.00 0.00 40.96 1.28
1616 1769 3.243643 GCAAAATGCTTGCGGACATTATC 59.756 43.478 0.00 0.00 40.96 1.75
1618 1771 3.976793 AATGCTTGCGGACATTATCTG 57.023 42.857 0.00 0.00 34.80 2.90
1619 1772 2.689553 TGCTTGCGGACATTATCTGA 57.310 45.000 0.00 0.00 35.44 3.27
1620 1773 3.198409 TGCTTGCGGACATTATCTGAT 57.802 42.857 0.00 0.00 35.44 2.90
1621 1774 4.335400 TGCTTGCGGACATTATCTGATA 57.665 40.909 0.00 0.00 35.44 2.15
1622 1775 4.309933 TGCTTGCGGACATTATCTGATAG 58.690 43.478 0.00 0.00 35.44 2.08
1683 1850 9.990360 TTTTTCAAATAAAAATGTACTCCCCTC 57.010 29.630 0.00 0.00 0.00 4.30
1684 1851 8.950007 TTTCAAATAAAAATGTACTCCCCTCT 57.050 30.769 0.00 0.00 0.00 3.69
1689 1856 8.502105 AATAAAAATGTACTCCCCTCTAAACG 57.498 34.615 0.00 0.00 0.00 3.60
1690 1857 3.538634 AATGTACTCCCCTCTAAACGC 57.461 47.619 0.00 0.00 0.00 4.84
1691 1858 2.226962 TGTACTCCCCTCTAAACGCT 57.773 50.000 0.00 0.00 0.00 5.07
1692 1859 2.097825 TGTACTCCCCTCTAAACGCTC 58.902 52.381 0.00 0.00 0.00 5.03
1693 1860 2.291411 TGTACTCCCCTCTAAACGCTCT 60.291 50.000 0.00 0.00 0.00 4.09
1694 1861 1.939980 ACTCCCCTCTAAACGCTCTT 58.060 50.000 0.00 0.00 0.00 2.85
1695 1862 3.097342 ACTCCCCTCTAAACGCTCTTA 57.903 47.619 0.00 0.00 0.00 2.10
1696 1863 3.644335 ACTCCCCTCTAAACGCTCTTAT 58.356 45.455 0.00 0.00 0.00 1.73
1697 1864 4.801164 ACTCCCCTCTAAACGCTCTTATA 58.199 43.478 0.00 0.00 0.00 0.98
1698 1865 5.395611 ACTCCCCTCTAAACGCTCTTATAT 58.604 41.667 0.00 0.00 0.00 0.86
1699 1866 5.839606 ACTCCCCTCTAAACGCTCTTATATT 59.160 40.000 0.00 0.00 0.00 1.28
1700 1867 6.015265 ACTCCCCTCTAAACGCTCTTATATTC 60.015 42.308 0.00 0.00 0.00 1.75
1701 1868 5.245526 TCCCCTCTAAACGCTCTTATATTCC 59.754 44.000 0.00 0.00 0.00 3.01
1702 1869 5.246429 CCCCTCTAAACGCTCTTATATTCCT 59.754 44.000 0.00 0.00 0.00 3.36
1703 1870 6.239629 CCCCTCTAAACGCTCTTATATTCCTT 60.240 42.308 0.00 0.00 0.00 3.36
1704 1871 7.217906 CCCTCTAAACGCTCTTATATTCCTTT 58.782 38.462 0.00 0.00 0.00 3.11
1705 1872 8.365647 CCCTCTAAACGCTCTTATATTCCTTTA 58.634 37.037 0.00 0.00 0.00 1.85
1706 1873 9.930693 CCTCTAAACGCTCTTATATTCCTTTAT 57.069 33.333 0.00 0.00 0.00 1.40
1955 2122 6.887013 AGTGAAGATATCTGCAAGTTGATCT 58.113 36.000 15.37 3.60 32.26 2.75
2296 2463 1.739667 CCGTGGATCGCCTGTCATA 59.260 57.895 0.00 0.00 38.35 2.15
2305 2472 0.681733 CGCCTGTCATATGGGCTACT 59.318 55.000 16.45 0.00 43.29 2.57
2380 2547 1.544724 TGCATACCAAAAGTCAGGGC 58.455 50.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.612174 CTGTCGAGGGAGAGGGACAA 60.612 60.000 0.00 0.00 38.77 3.18
10 11 1.755008 GGACTGTCGAGGGAGAGGG 60.755 68.421 1.07 0.00 37.86 4.30
19 20 3.437213 TCTCCTATTTTGGGACTGTCGA 58.563 45.455 1.07 0.00 0.00 4.20
22 24 4.111577 TGGATCTCCTATTTTGGGACTGT 58.888 43.478 0.00 0.00 36.82 3.55
27 29 6.830873 GATCAATGGATCTCCTATTTTGGG 57.169 41.667 2.52 0.00 45.32 4.12
113 115 6.162420 CCCTATATAGATGGAAGGAGGGAGTA 59.838 46.154 11.53 0.00 44.48 2.59
114 116 5.042979 CCCTATATAGATGGAAGGAGGGAGT 60.043 48.000 11.53 0.00 44.48 3.85
115 117 5.463154 CCCTATATAGATGGAAGGAGGGAG 58.537 50.000 11.53 0.00 44.48 4.30
116 118 4.327010 GCCCTATATAGATGGAAGGAGGGA 60.327 50.000 11.53 0.00 44.48 4.20
117 119 3.970640 GCCCTATATAGATGGAAGGAGGG 59.029 52.174 11.53 3.52 44.52 4.30
118 120 3.970640 GGCCCTATATAGATGGAAGGAGG 59.029 52.174 11.53 1.87 0.00 4.30
119 121 4.889780 AGGCCCTATATAGATGGAAGGAG 58.110 47.826 11.53 0.00 0.00 3.69
120 122 4.994411 AGGCCCTATATAGATGGAAGGA 57.006 45.455 11.53 0.00 0.00 3.36
121 123 6.465035 GCATTAGGCCCTATATAGATGGAAGG 60.465 46.154 11.53 3.94 36.11 3.46
122 124 6.529220 GCATTAGGCCCTATATAGATGGAAG 58.471 44.000 11.53 0.00 36.11 3.46
123 125 5.070446 CGCATTAGGCCCTATATAGATGGAA 59.930 44.000 11.53 0.00 40.31 3.53
124 126 4.588951 CGCATTAGGCCCTATATAGATGGA 59.411 45.833 11.53 0.00 40.31 3.41
125 127 4.345257 ACGCATTAGGCCCTATATAGATGG 59.655 45.833 11.53 6.04 40.31 3.51
126 128 5.537300 ACGCATTAGGCCCTATATAGATG 57.463 43.478 11.53 6.87 40.31 2.90
127 129 6.561519 AAACGCATTAGGCCCTATATAGAT 57.438 37.500 11.53 0.00 40.31 1.98
128 130 6.368779 AAAACGCATTAGGCCCTATATAGA 57.631 37.500 11.53 0.00 40.31 1.98
149 151 7.821846 ACATTTGGTCAAAGTTAGCTTCAAAAA 59.178 29.630 0.00 0.46 32.36 1.94
150 152 7.327214 ACATTTGGTCAAAGTTAGCTTCAAAA 58.673 30.769 0.00 0.00 32.36 2.44
151 153 6.872920 ACATTTGGTCAAAGTTAGCTTCAAA 58.127 32.000 0.00 6.44 32.81 2.69
152 154 6.463995 ACATTTGGTCAAAGTTAGCTTCAA 57.536 33.333 0.00 0.00 33.01 2.69
153 155 6.463995 AACATTTGGTCAAAGTTAGCTTCA 57.536 33.333 0.00 0.00 33.01 3.02
154 156 7.871853 TCTAACATTTGGTCAAAGTTAGCTTC 58.128 34.615 22.83 0.00 39.10 3.86
155 157 7.522236 GCTCTAACATTTGGTCAAAGTTAGCTT 60.522 37.037 22.83 0.00 39.10 3.74
156 158 6.072452 GCTCTAACATTTGGTCAAAGTTAGCT 60.072 38.462 22.83 0.00 39.10 3.32
157 159 6.086871 GCTCTAACATTTGGTCAAAGTTAGC 58.913 40.000 22.83 17.67 39.10 3.09
158 160 7.202016 TGCTCTAACATTTGGTCAAAGTTAG 57.798 36.000 22.30 22.30 39.68 2.34
159 161 7.575414 TTGCTCTAACATTTGGTCAAAGTTA 57.425 32.000 2.55 9.12 33.32 2.24
160 162 6.463995 TTGCTCTAACATTTGGTCAAAGTT 57.536 33.333 2.55 8.59 33.32 2.66
161 163 6.655078 ATTGCTCTAACATTTGGTCAAAGT 57.345 33.333 2.55 0.00 33.32 2.66
173 175 9.723601 TGCATGTCATATATTATTGCTCTAACA 57.276 29.630 0.00 0.00 0.00 2.41
176 178 9.948964 AGTTGCATGTCATATATTATTGCTCTA 57.051 29.630 0.00 0.00 0.00 2.43
177 179 8.859236 AGTTGCATGTCATATATTATTGCTCT 57.141 30.769 0.00 0.00 0.00 4.09
186 188 8.131100 GCTTTGTGTAAGTTGCATGTCATATAT 58.869 33.333 0.00 0.00 36.19 0.86
187 189 7.120432 TGCTTTGTGTAAGTTGCATGTCATATA 59.880 33.333 0.00 0.00 36.19 0.86
188 190 6.072008 TGCTTTGTGTAAGTTGCATGTCATAT 60.072 34.615 0.00 0.00 36.19 1.78
189 191 5.240403 TGCTTTGTGTAAGTTGCATGTCATA 59.760 36.000 0.00 0.00 36.19 2.15
190 192 4.037803 TGCTTTGTGTAAGTTGCATGTCAT 59.962 37.500 0.00 0.00 36.19 3.06
191 193 3.379688 TGCTTTGTGTAAGTTGCATGTCA 59.620 39.130 0.00 0.00 36.19 3.58
192 194 3.730715 GTGCTTTGTGTAAGTTGCATGTC 59.269 43.478 0.00 0.00 36.19 3.06
193 195 3.130164 TGTGCTTTGTGTAAGTTGCATGT 59.870 39.130 0.00 0.00 36.19 3.21
194 196 3.704512 TGTGCTTTGTGTAAGTTGCATG 58.295 40.909 0.00 0.00 36.19 4.06
195 197 4.037803 TGATGTGCTTTGTGTAAGTTGCAT 59.962 37.500 0.00 0.00 36.19 3.96
196 198 3.379688 TGATGTGCTTTGTGTAAGTTGCA 59.620 39.130 0.00 0.00 36.19 4.08
197 199 3.963665 TGATGTGCTTTGTGTAAGTTGC 58.036 40.909 0.00 0.00 36.19 4.17
198 200 5.761003 TGATGATGTGCTTTGTGTAAGTTG 58.239 37.500 0.00 0.00 36.19 3.16
199 201 6.389830 TTGATGATGTGCTTTGTGTAAGTT 57.610 33.333 0.00 0.00 36.19 2.66
200 202 6.389830 TTTGATGATGTGCTTTGTGTAAGT 57.610 33.333 0.00 0.00 36.19 2.24
201 203 7.201291 CGAATTTGATGATGTGCTTTGTGTAAG 60.201 37.037 0.00 0.00 36.90 2.34
202 204 6.581919 CGAATTTGATGATGTGCTTTGTGTAA 59.418 34.615 0.00 0.00 0.00 2.41
203 205 6.085573 CGAATTTGATGATGTGCTTTGTGTA 58.914 36.000 0.00 0.00 0.00 2.90
204 206 4.919168 CGAATTTGATGATGTGCTTTGTGT 59.081 37.500 0.00 0.00 0.00 3.72
205 207 4.919168 ACGAATTTGATGATGTGCTTTGTG 59.081 37.500 0.00 0.00 0.00 3.33
206 208 5.125100 ACGAATTTGATGATGTGCTTTGT 57.875 34.783 0.00 0.00 0.00 2.83
207 209 6.748658 ACATACGAATTTGATGATGTGCTTTG 59.251 34.615 0.00 0.00 0.00 2.77
208 210 6.748658 CACATACGAATTTGATGATGTGCTTT 59.251 34.615 18.49 0.00 38.17 3.51
209 211 6.093909 TCACATACGAATTTGATGATGTGCTT 59.906 34.615 22.13 1.56 42.39 3.91
210 212 5.585844 TCACATACGAATTTGATGATGTGCT 59.414 36.000 22.13 1.79 42.39 4.40
211 213 5.809464 TCACATACGAATTTGATGATGTGC 58.191 37.500 22.13 0.00 42.39 4.57
212 214 7.430211 CCTTTCACATACGAATTTGATGATGTG 59.570 37.037 21.52 21.52 43.46 3.21
213 215 7.336679 TCCTTTCACATACGAATTTGATGATGT 59.663 33.333 0.00 3.64 0.00 3.06
214 216 7.696755 TCCTTTCACATACGAATTTGATGATG 58.303 34.615 0.00 3.05 0.00 3.07
215 217 7.467811 GCTCCTTTCACATACGAATTTGATGAT 60.468 37.037 0.00 0.00 0.00 2.45
216 218 6.183360 GCTCCTTTCACATACGAATTTGATGA 60.183 38.462 0.00 0.00 0.00 2.92
217 219 5.967674 GCTCCTTTCACATACGAATTTGATG 59.032 40.000 0.00 2.13 0.00 3.07
218 220 5.882557 AGCTCCTTTCACATACGAATTTGAT 59.117 36.000 0.00 0.00 0.00 2.57
219 221 5.245531 AGCTCCTTTCACATACGAATTTGA 58.754 37.500 0.00 0.00 0.00 2.69
220 222 5.551760 AGCTCCTTTCACATACGAATTTG 57.448 39.130 0.00 0.00 0.00 2.32
221 223 6.575162 AAAGCTCCTTTCACATACGAATTT 57.425 33.333 0.00 0.00 0.00 1.82
222 224 6.183309 GAAAGCTCCTTTCACATACGAATT 57.817 37.500 11.65 0.00 46.23 2.17
223 225 5.803020 GAAAGCTCCTTTCACATACGAAT 57.197 39.130 11.65 0.00 46.23 3.34
288 290 9.816354 TCAAGATCGTCATTGACTATTGATAAA 57.184 29.630 14.54 0.00 30.67 1.40
289 291 9.816354 TTCAAGATCGTCATTGACTATTGATAA 57.184 29.630 14.54 0.86 35.25 1.75
290 292 9.816354 TTTCAAGATCGTCATTGACTATTGATA 57.184 29.630 14.54 8.31 35.25 2.15
291 293 8.722480 TTTCAAGATCGTCATTGACTATTGAT 57.278 30.769 14.54 9.41 35.25 2.57
292 294 8.546597 TTTTCAAGATCGTCATTGACTATTGA 57.453 30.769 14.54 12.18 35.25 2.57
293 295 9.055248 GTTTTTCAAGATCGTCATTGACTATTG 57.945 33.333 14.54 10.28 35.25 1.90
294 296 7.957484 CGTTTTTCAAGATCGTCATTGACTATT 59.043 33.333 14.54 0.00 35.25 1.73
295 297 7.456253 CGTTTTTCAAGATCGTCATTGACTAT 58.544 34.615 14.54 9.21 35.25 2.12
296 298 6.617741 GCGTTTTTCAAGATCGTCATTGACTA 60.618 38.462 14.54 4.36 35.25 2.59
297 299 5.679906 CGTTTTTCAAGATCGTCATTGACT 58.320 37.500 14.54 0.00 35.25 3.41
298 300 4.318332 GCGTTTTTCAAGATCGTCATTGAC 59.682 41.667 6.73 6.73 35.25 3.18
299 301 4.024472 TGCGTTTTTCAAGATCGTCATTGA 60.024 37.500 0.00 0.00 33.73 2.57
300 302 4.218265 TGCGTTTTTCAAGATCGTCATTG 58.782 39.130 0.00 0.00 0.00 2.82
301 303 4.481930 TGCGTTTTTCAAGATCGTCATT 57.518 36.364 0.00 0.00 0.00 2.57
302 304 4.685169 ATGCGTTTTTCAAGATCGTCAT 57.315 36.364 0.00 0.00 0.00 3.06
303 305 4.481930 AATGCGTTTTTCAAGATCGTCA 57.518 36.364 0.00 0.00 0.00 4.35
304 306 5.022021 CCTAATGCGTTTTTCAAGATCGTC 58.978 41.667 0.00 0.00 0.00 4.20
305 307 4.671766 GCCTAATGCGTTTTTCAAGATCGT 60.672 41.667 0.00 0.00 0.00 3.73
306 308 3.786048 GCCTAATGCGTTTTTCAAGATCG 59.214 43.478 0.00 0.00 0.00 3.69
307 309 4.105486 GGCCTAATGCGTTTTTCAAGATC 58.895 43.478 0.00 0.00 42.61 2.75
308 310 3.119137 GGGCCTAATGCGTTTTTCAAGAT 60.119 43.478 0.84 0.00 42.61 2.40
309 311 2.230266 GGGCCTAATGCGTTTTTCAAGA 59.770 45.455 0.84 0.00 42.61 3.02
310 312 2.231235 AGGGCCTAATGCGTTTTTCAAG 59.769 45.455 2.82 0.00 42.61 3.02
311 313 2.243810 AGGGCCTAATGCGTTTTTCAA 58.756 42.857 2.82 0.00 42.61 2.69
312 314 1.917872 AGGGCCTAATGCGTTTTTCA 58.082 45.000 2.82 0.00 42.61 2.69
313 315 5.959618 ATATAGGGCCTAATGCGTTTTTC 57.040 39.130 18.91 0.00 42.61 2.29
314 316 6.775708 TCTATATAGGGCCTAATGCGTTTTT 58.224 36.000 18.91 0.00 42.61 1.94
315 317 6.368779 TCTATATAGGGCCTAATGCGTTTT 57.631 37.500 18.91 0.30 42.61 2.43
316 318 6.349300 CATCTATATAGGGCCTAATGCGTTT 58.651 40.000 18.91 1.12 42.61 3.60
317 319 5.163301 CCATCTATATAGGGCCTAATGCGTT 60.163 44.000 18.91 1.94 42.61 4.84
318 320 4.345257 CCATCTATATAGGGCCTAATGCGT 59.655 45.833 18.91 2.76 42.61 5.24
319 321 4.588951 TCCATCTATATAGGGCCTAATGCG 59.411 45.833 18.91 10.04 42.61 4.73
320 322 6.465035 CCTTCCATCTATATAGGGCCTAATGC 60.465 46.154 18.91 0.00 40.16 3.56
321 323 6.846505 TCCTTCCATCTATATAGGGCCTAATG 59.153 42.308 18.91 15.42 0.00 1.90
322 324 7.009960 TCCTTCCATCTATATAGGGCCTAAT 57.990 40.000 18.91 14.19 0.00 1.73
323 325 6.432190 TCCTTCCATCTATATAGGGCCTAA 57.568 41.667 18.91 7.61 0.00 2.69
324 326 5.103043 CCTCCTTCCATCTATATAGGGCCTA 60.103 48.000 17.16 17.16 0.00 3.93
325 327 4.327332 CCTCCTTCCATCTATATAGGGCCT 60.327 50.000 12.58 12.58 0.00 5.19
326 328 3.970640 CCTCCTTCCATCTATATAGGGCC 59.029 52.174 9.89 0.00 0.00 5.80
327 329 3.970640 CCCTCCTTCCATCTATATAGGGC 59.029 52.174 9.89 0.00 36.30 5.19
328 330 5.042979 ACTCCCTCCTTCCATCTATATAGGG 60.043 48.000 9.89 4.49 43.23 3.53
329 331 6.098716 ACTCCCTCCTTCCATCTATATAGG 57.901 45.833 9.89 0.00 0.00 2.57
330 332 7.091720 ACCTACTCCCTCCTTCCATCTATATAG 60.092 44.444 3.10 3.10 0.00 1.31
331 333 6.745791 ACCTACTCCCTCCTTCCATCTATATA 59.254 42.308 0.00 0.00 0.00 0.86
332 334 5.561967 ACCTACTCCCTCCTTCCATCTATAT 59.438 44.000 0.00 0.00 0.00 0.86
333 335 4.926987 ACCTACTCCCTCCTTCCATCTATA 59.073 45.833 0.00 0.00 0.00 1.31
334 336 3.735442 ACCTACTCCCTCCTTCCATCTAT 59.265 47.826 0.00 0.00 0.00 1.98
335 337 3.117093 CACCTACTCCCTCCTTCCATCTA 60.117 52.174 0.00 0.00 0.00 1.98
336 338 1.940957 ACCTACTCCCTCCTTCCATCT 59.059 52.381 0.00 0.00 0.00 2.90
337 339 2.043227 CACCTACTCCCTCCTTCCATC 58.957 57.143 0.00 0.00 0.00 3.51
338 340 1.366435 ACACCTACTCCCTCCTTCCAT 59.634 52.381 0.00 0.00 0.00 3.41
339 341 0.790993 ACACCTACTCCCTCCTTCCA 59.209 55.000 0.00 0.00 0.00 3.53
340 342 1.954035 AACACCTACTCCCTCCTTCC 58.046 55.000 0.00 0.00 0.00 3.46
341 343 2.615747 GCAAACACCTACTCCCTCCTTC 60.616 54.545 0.00 0.00 0.00 3.46
342 344 1.351350 GCAAACACCTACTCCCTCCTT 59.649 52.381 0.00 0.00 0.00 3.36
343 345 0.984995 GCAAACACCTACTCCCTCCT 59.015 55.000 0.00 0.00 0.00 3.69
344 346 0.690762 TGCAAACACCTACTCCCTCC 59.309 55.000 0.00 0.00 0.00 4.30
345 347 2.633488 GATGCAAACACCTACTCCCTC 58.367 52.381 0.00 0.00 0.00 4.30
346 348 1.066143 CGATGCAAACACCTACTCCCT 60.066 52.381 0.00 0.00 0.00 4.20
347 349 1.338769 ACGATGCAAACACCTACTCCC 60.339 52.381 0.00 0.00 0.00 4.30
348 350 2.094762 ACGATGCAAACACCTACTCC 57.905 50.000 0.00 0.00 0.00 3.85
349 351 5.796350 AAATACGATGCAAACACCTACTC 57.204 39.130 0.00 0.00 0.00 2.59
350 352 7.859325 AATAAATACGATGCAAACACCTACT 57.141 32.000 0.00 0.00 0.00 2.57
351 353 7.642586 GGAAATAAATACGATGCAAACACCTAC 59.357 37.037 0.00 0.00 0.00 3.18
364 366 9.550406 AAGAAATATGGACGGAAATAAATACGA 57.450 29.630 0.00 0.00 0.00 3.43
432 434 9.472361 GAAACTGAGTGTTACTACTACATTTCA 57.528 33.333 0.00 0.00 38.03 2.69
469 472 3.142597 TCGGTGATTAGGGGTAGGGATAA 59.857 47.826 0.00 0.00 0.00 1.75
612 721 6.409524 TTCTGCAAATGATGAGGTCTTTTT 57.590 33.333 0.00 0.00 33.37 1.94
613 722 6.409524 TTTCTGCAAATGATGAGGTCTTTT 57.590 33.333 0.00 0.00 35.31 2.27
614 723 6.409524 TTTTCTGCAAATGATGAGGTCTTT 57.590 33.333 0.00 0.00 0.00 2.52
615 724 6.409524 TTTTTCTGCAAATGATGAGGTCTT 57.590 33.333 0.00 0.00 0.00 3.01
642 751 9.799106 ATCTCTTCTTCTTGGATTAAAAGAACA 57.201 29.630 0.00 0.00 38.43 3.18
653 766 8.601047 TCAGATCTTAATCTCTTCTTCTTGGA 57.399 34.615 0.00 0.00 40.38 3.53
654 767 9.480053 GATCAGATCTTAATCTCTTCTTCTTGG 57.520 37.037 2.81 0.00 40.38 3.61
736 853 9.987272 AATGCTTAAAGAAAGGGATATATTTGC 57.013 29.630 0.00 0.00 35.58 3.68
739 856 9.881773 TCCAATGCTTAAAGAAAGGGATATATT 57.118 29.630 0.00 0.00 35.58 1.28
762 879 0.987294 CTCCTGCCCTTCTTTCTCCA 59.013 55.000 0.00 0.00 0.00 3.86
821 938 0.176449 CGGAGGAGCACATCACATCA 59.824 55.000 0.00 0.00 0.00 3.07
822 939 1.156645 GCGGAGGAGCACATCACATC 61.157 60.000 0.00 0.00 37.05 3.06
823 940 1.153289 GCGGAGGAGCACATCACAT 60.153 57.895 0.00 0.00 37.05 3.21
995 1115 1.726853 GGCCATAGCGATCATGGTAC 58.273 55.000 11.17 3.15 44.15 3.34
1088 1208 4.479993 GCGTGGCATCCTCAGGCT 62.480 66.667 0.00 0.00 41.21 4.58
1239 1359 3.909258 CTCGTCGTGGAACCCGTGG 62.909 68.421 0.00 0.00 0.00 4.94
1440 1572 2.751436 CCTCACAATGCCACGGGG 60.751 66.667 0.00 0.00 37.18 5.73
1463 1607 6.598503 TCACTAATCCTCGAGTAACCAGATA 58.401 40.000 12.31 0.00 0.00 1.98
1469 1613 5.717119 TGGTTTCACTAATCCTCGAGTAAC 58.283 41.667 12.31 1.82 0.00 2.50
1505 1649 1.267732 GGTGATGCGAATCTTGAAGCG 60.268 52.381 4.68 0.00 0.00 4.68
1517 1661 3.985877 TCAGCCAAAGGTGATGCG 58.014 55.556 0.00 0.00 45.34 4.73
1522 1666 0.664761 CACACACTCAGCCAAAGGTG 59.335 55.000 0.00 0.00 43.07 4.00
1526 1671 2.229792 GATTCCACACACTCAGCCAAA 58.770 47.619 0.00 0.00 0.00 3.28
1531 1676 0.321671 ACCCGATTCCACACACTCAG 59.678 55.000 0.00 0.00 0.00 3.35
1563 1708 9.643693 GAAACAAGGACAAAACAATGATGATAT 57.356 29.630 0.00 0.00 0.00 1.63
1614 1767 9.155975 GTGTGATAAAGTGACAAACTATCAGAT 57.844 33.333 3.16 0.00 38.56 2.90
1615 1768 7.328493 CGTGTGATAAAGTGACAAACTATCAGA 59.672 37.037 3.16 0.62 38.56 3.27
1616 1769 7.411912 CCGTGTGATAAAGTGACAAACTATCAG 60.412 40.741 3.16 0.00 38.56 2.90
1618 1771 6.183360 CCCGTGTGATAAAGTGACAAACTATC 60.183 42.308 0.00 0.00 38.56 2.08
1619 1772 5.642063 CCCGTGTGATAAAGTGACAAACTAT 59.358 40.000 0.00 0.00 38.56 2.12
1620 1773 4.992319 CCCGTGTGATAAAGTGACAAACTA 59.008 41.667 0.00 0.00 38.56 2.24
1621 1774 3.813166 CCCGTGTGATAAAGTGACAAACT 59.187 43.478 0.00 0.00 42.60 2.66
1622 1775 3.562557 ACCCGTGTGATAAAGTGACAAAC 59.437 43.478 0.00 0.00 0.00 2.93
1673 1840 2.377073 AGAGCGTTTAGAGGGGAGTAC 58.623 52.381 0.00 0.00 0.00 2.73
1674 1841 2.822707 AGAGCGTTTAGAGGGGAGTA 57.177 50.000 0.00 0.00 0.00 2.59
1675 1842 1.939980 AAGAGCGTTTAGAGGGGAGT 58.060 50.000 0.00 0.00 0.00 3.85
1676 1843 5.986501 ATATAAGAGCGTTTAGAGGGGAG 57.013 43.478 0.00 0.00 0.00 4.30
1677 1844 5.245526 GGAATATAAGAGCGTTTAGAGGGGA 59.754 44.000 0.00 0.00 0.00 4.81
1678 1845 5.246429 AGGAATATAAGAGCGTTTAGAGGGG 59.754 44.000 0.00 0.00 0.00 4.79
1679 1846 6.347859 AGGAATATAAGAGCGTTTAGAGGG 57.652 41.667 0.00 0.00 0.00 4.30
1680 1847 9.930693 ATAAAGGAATATAAGAGCGTTTAGAGG 57.069 33.333 0.00 0.00 0.00 3.69
1701 1868 4.781934 CCCCTTGTACTCCCTTCATAAAG 58.218 47.826 0.00 0.00 0.00 1.85
1702 1869 3.053917 GCCCCTTGTACTCCCTTCATAAA 60.054 47.826 0.00 0.00 0.00 1.40
1703 1870 2.508300 GCCCCTTGTACTCCCTTCATAA 59.492 50.000 0.00 0.00 0.00 1.90
1704 1871 2.124411 GCCCCTTGTACTCCCTTCATA 58.876 52.381 0.00 0.00 0.00 2.15
1705 1872 0.919710 GCCCCTTGTACTCCCTTCAT 59.080 55.000 0.00 0.00 0.00 2.57
1706 1873 0.474854 TGCCCCTTGTACTCCCTTCA 60.475 55.000 0.00 0.00 0.00 3.02
1707 1874 0.035343 GTGCCCCTTGTACTCCCTTC 60.035 60.000 0.00 0.00 0.00 3.46
1708 1875 0.475828 AGTGCCCCTTGTACTCCCTT 60.476 55.000 0.00 0.00 34.48 3.95
1709 1876 1.161113 AGTGCCCCTTGTACTCCCT 59.839 57.895 0.00 0.00 34.48 4.20
1710 1877 1.299976 CAGTGCCCCTTGTACTCCC 59.700 63.158 0.00 0.00 37.89 4.30
1711 1878 1.272807 TACAGTGCCCCTTGTACTCC 58.727 55.000 0.00 0.00 37.89 3.85
1712 1879 2.565834 TCTTACAGTGCCCCTTGTACTC 59.434 50.000 0.00 0.00 37.89 2.59
1713 1880 2.302157 GTCTTACAGTGCCCCTTGTACT 59.698 50.000 0.00 0.00 40.97 2.73
1714 1881 2.038033 TGTCTTACAGTGCCCCTTGTAC 59.962 50.000 0.00 0.00 30.03 2.90
1715 1882 2.331166 TGTCTTACAGTGCCCCTTGTA 58.669 47.619 0.00 0.00 0.00 2.41
1716 1883 1.136828 TGTCTTACAGTGCCCCTTGT 58.863 50.000 0.00 0.00 0.00 3.16
1717 1884 2.270352 TTGTCTTACAGTGCCCCTTG 57.730 50.000 0.00 0.00 0.00 3.61
1718 1885 4.042934 ACTTATTGTCTTACAGTGCCCCTT 59.957 41.667 0.00 0.00 0.00 3.95
1719 1886 3.587506 ACTTATTGTCTTACAGTGCCCCT 59.412 43.478 0.00 0.00 0.00 4.79
1720 1887 3.951663 ACTTATTGTCTTACAGTGCCCC 58.048 45.455 0.00 0.00 0.00 5.80
1721 1888 5.959618 AAACTTATTGTCTTACAGTGCCC 57.040 39.130 0.00 0.00 0.00 5.36
1722 1889 6.149633 CCAAAACTTATTGTCTTACAGTGCC 58.850 40.000 0.00 0.00 0.00 5.01
1759 1926 1.866943 AGATAAGCCACCCCTAGAGGA 59.133 52.381 0.00 0.00 38.24 3.71
1955 2122 9.574458 CTTCAGATCAAGTTTATCTCGTCTAAA 57.426 33.333 0.00 0.00 31.22 1.85
2305 2472 2.401568 TCTCTGATGCAGATTGGGCTA 58.598 47.619 0.00 0.00 39.92 3.93
2380 2547 5.015733 GCATTCTTCGTTATGTTCAGTTCG 58.984 41.667 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.