Multiple sequence alignment - TraesCS7D01G252300

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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 TraesCS7D01G252300 chr7D 100.000 2891 0 0 1 2891 227543007 227545897 0.000000e+00 5339.0
1 TraesCS7D01G252300 chr7D 94.918 669 14 6 2223 2891 564046819 564046171 0.000000e+00 1029.0
2 TraesCS7D01G252300 chr7D 94.910 668 15 8 2224 2891 206138680 206138032 0.000000e+00 1027.0
3 TraesCS7D01G252300 chr7D 92.276 246 12 5 2222 2466 374078045 374078284 2.760000e-90 342.0
4 TraesCS7D01G252300 chr7D 83.843 229 24 11 144 365 25490901 25490679 3.780000e-49 206.0
5 TraesCS7D01G252300 chr7B 93.375 1585 70 22 388 1950 199261489 199263060 0.000000e+00 2313.0
6 TraesCS7D01G252300 chr7B 94.118 136 7 1 2094 2228 199273184 199273319 3.780000e-49 206.0
7 TraesCS7D01G252300 chr7B 93.750 128 6 2 14 140 199261350 199261476 1.060000e-44 191.0
8 TraesCS7D01G252300 chr7A 92.057 1624 67 24 375 1950 239544170 239545779 0.000000e+00 2228.0
9 TraesCS7D01G252300 chr7A 92.188 256 18 2 1972 2226 239545855 239546109 7.620000e-96 361.0
10 TraesCS7D01G252300 chr7A 93.023 129 7 2 14 140 239544045 239544173 1.370000e-43 187.0
11 TraesCS7D01G252300 chr2D 95.958 668 8 5 2225 2891 580459971 580460620 0.000000e+00 1066.0
12 TraesCS7D01G252300 chr2D 95.609 501 10 5 2400 2891 580786369 580786866 0.000000e+00 793.0
13 TraesCS7D01G252300 chr2D 92.857 238 8 8 2225 2456 580786250 580786484 1.280000e-88 337.0
14 TraesCS7D01G252300 chr1D 95.224 670 14 4 2222 2891 460288942 460289593 0.000000e+00 1044.0
15 TraesCS7D01G252300 chr1D 85.845 219 25 6 144 360 268943632 268943846 8.060000e-56 228.0
16 TraesCS7D01G252300 chr3D 95.541 628 11 3 2264 2891 360036 360646 0.000000e+00 989.0
17 TraesCS7D01G252300 chr3D 95.812 573 6 4 2320 2891 554683461 554682906 0.000000e+00 909.0
18 TraesCS7D01G252300 chrUn 94.044 638 11 6 2255 2891 361663817 361664428 0.000000e+00 942.0
19 TraesCS7D01G252300 chr4D 97.154 492 11 3 2400 2891 12090571 12091059 0.000000e+00 828.0
20 TraesCS7D01G252300 chr4A 91.238 525 28 5 2222 2746 11171017 11171523 0.000000e+00 699.0
21 TraesCS7D01G252300 chr4A 81.620 321 50 9 2224 2542 678418140 678417827 1.030000e-64 257.0
22 TraesCS7D01G252300 chr2B 90.857 525 30 4 2224 2747 260623410 260622903 0.000000e+00 688.0
23 TraesCS7D01G252300 chr2B 84.483 232 31 4 135 363 105697437 105697208 1.040000e-54 224.0
24 TraesCS7D01G252300 chr6B 90.076 524 23 5 2225 2747 201909185 201909680 0.000000e+00 652.0
25 TraesCS7D01G252300 chr6B 79.389 131 25 2 1309 1438 609854828 609854699 1.100000e-14 91.6
26 TraesCS7D01G252300 chr5B 90.659 182 14 1 135 316 320410908 320411086 3.720000e-59 239.0
27 TraesCS7D01G252300 chr5B 88.360 189 20 2 129 316 19554116 19554303 2.900000e-55 226.0
28 TraesCS7D01G252300 chr6D 85.253 217 25 4 140 356 44257463 44257672 1.740000e-52 217.0
29 TraesCS7D01G252300 chr6D 83.333 228 33 5 140 365 162264041 162264265 3.780000e-49 206.0
30 TraesCS7D01G252300 chr6D 80.916 131 23 2 1309 1438 405650833 405650704 5.100000e-18 102.0
31 TraesCS7D01G252300 chr3A 84.375 224 29 3 140 363 182838846 182838629 6.270000e-52 215.0
32 TraesCS7D01G252300 chr3A 90.385 52 2 2 317 365 272767320 272767371 6.690000e-07 65.8
33 TraesCS7D01G252300 chr5D 83.550 231 29 5 140 363 7482305 7482077 1.050000e-49 207.0
34 TraesCS7D01G252300 chr3B 84.746 177 23 1 140 316 812616507 812616335 1.060000e-39 174.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G252300 chr7D 227543007 227545897 2890 False 5339.000000 5339 100.000000 1 2891 1 chr7D.!!$F1 2890
1 TraesCS7D01G252300 chr7D 564046171 564046819 648 True 1029.000000 1029 94.918000 2223 2891 1 chr7D.!!$R3 668
2 TraesCS7D01G252300 chr7D 206138032 206138680 648 True 1027.000000 1027 94.910000 2224 2891 1 chr7D.!!$R2 667
3 TraesCS7D01G252300 chr7B 199261350 199263060 1710 False 1252.000000 2313 93.562500 14 1950 2 chr7B.!!$F2 1936
4 TraesCS7D01G252300 chr7A 239544045 239546109 2064 False 925.333333 2228 92.422667 14 2226 3 chr7A.!!$F1 2212
5 TraesCS7D01G252300 chr2D 580459971 580460620 649 False 1066.000000 1066 95.958000 2225 2891 1 chr2D.!!$F1 666
6 TraesCS7D01G252300 chr2D 580786250 580786866 616 False 565.000000 793 94.233000 2225 2891 2 chr2D.!!$F2 666
7 TraesCS7D01G252300 chr1D 460288942 460289593 651 False 1044.000000 1044 95.224000 2222 2891 1 chr1D.!!$F2 669
8 TraesCS7D01G252300 chr3D 360036 360646 610 False 989.000000 989 95.541000 2264 2891 1 chr3D.!!$F1 627
9 TraesCS7D01G252300 chr3D 554682906 554683461 555 True 909.000000 909 95.812000 2320 2891 1 chr3D.!!$R1 571
10 TraesCS7D01G252300 chrUn 361663817 361664428 611 False 942.000000 942 94.044000 2255 2891 1 chrUn.!!$F1 636
11 TraesCS7D01G252300 chr4A 11171017 11171523 506 False 699.000000 699 91.238000 2222 2746 1 chr4A.!!$F1 524
12 TraesCS7D01G252300 chr2B 260622903 260623410 507 True 688.000000 688 90.857000 2224 2747 1 chr2B.!!$R2 523

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
376 380 0.396811 GTGACACTGTACCTGCCCTT 59.603 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2196 0.389426 AGTGGGTGCTAAAGTACGCG 60.389 55.0 3.53 3.53 44.2 6.01 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
97 100 1.680989 TCGACTCCCGAGCAATCCA 60.681 57.895 0.00 0.00 43.23 3.41
98 101 1.519455 CGACTCCCGAGCAATCCAC 60.519 63.158 0.00 0.00 41.76 4.02
103 106 1.046472 TCCCGAGCAATCCACGGTAT 61.046 55.000 0.00 0.00 44.34 2.73
140 144 3.521937 TGGGTGGGTTGGAATACTCTTAG 59.478 47.826 0.00 0.00 0.00 2.18
141 145 3.118000 GGGTGGGTTGGAATACTCTTAGG 60.118 52.174 0.00 0.00 0.00 2.69
142 146 3.522343 GGTGGGTTGGAATACTCTTAGGT 59.478 47.826 0.00 0.00 0.00 3.08
145 149 5.036916 TGGGTTGGAATACTCTTAGGTCAT 58.963 41.667 0.00 0.00 0.00 3.06
146 150 5.104527 TGGGTTGGAATACTCTTAGGTCATG 60.105 44.000 0.00 0.00 0.00 3.07
147 151 5.104485 GGGTTGGAATACTCTTAGGTCATGT 60.104 44.000 0.00 0.00 0.00 3.21
148 152 6.099269 GGGTTGGAATACTCTTAGGTCATGTA 59.901 42.308 0.00 0.00 0.00 2.29
149 153 6.985059 GGTTGGAATACTCTTAGGTCATGTAC 59.015 42.308 0.00 0.00 0.00 2.90
150 154 7.364408 GGTTGGAATACTCTTAGGTCATGTACA 60.364 40.741 0.00 0.00 0.00 2.90
151 155 7.727578 TGGAATACTCTTAGGTCATGTACAA 57.272 36.000 0.00 0.00 0.00 2.41
152 156 8.319057 TGGAATACTCTTAGGTCATGTACAAT 57.681 34.615 0.00 0.00 0.00 2.71
153 157 8.204160 TGGAATACTCTTAGGTCATGTACAATG 58.796 37.037 0.00 0.00 0.00 2.82
154 158 8.421784 GGAATACTCTTAGGTCATGTACAATGA 58.578 37.037 0.00 1.68 0.00 2.57
155 159 9.988815 GAATACTCTTAGGTCATGTACAATGAT 57.011 33.333 0.00 0.00 0.00 2.45
157 161 9.770097 ATACTCTTAGGTCATGTACAATGATTG 57.230 33.333 3.16 3.16 0.00 2.67
158 162 7.851228 ACTCTTAGGTCATGTACAATGATTGA 58.149 34.615 12.80 0.00 0.00 2.57
159 163 8.489489 ACTCTTAGGTCATGTACAATGATTGAT 58.511 33.333 12.80 0.00 0.00 2.57
160 164 9.987272 CTCTTAGGTCATGTACAATGATTGATA 57.013 33.333 12.80 0.00 0.00 2.15
198 202 9.733556 TCTTAAACCTTGCATGTAATTTAGAGA 57.266 29.630 0.00 4.37 0.00 3.10
201 205 8.579850 AAACCTTGCATGTAATTTAGAGATGA 57.420 30.769 0.00 0.00 0.00 2.92
202 206 7.559590 ACCTTGCATGTAATTTAGAGATGAC 57.440 36.000 0.00 0.00 0.00 3.06
203 207 7.112122 ACCTTGCATGTAATTTAGAGATGACA 58.888 34.615 0.00 0.00 0.00 3.58
204 208 7.611467 ACCTTGCATGTAATTTAGAGATGACAA 59.389 33.333 0.00 0.00 0.00 3.18
205 209 8.461222 CCTTGCATGTAATTTAGAGATGACAAA 58.539 33.333 0.00 0.00 0.00 2.83
206 210 9.844790 CTTGCATGTAATTTAGAGATGACAAAA 57.155 29.630 0.00 0.00 0.00 2.44
230 234 7.881775 AAAAAGGTATCTACAATGGGTCATC 57.118 36.000 0.00 0.00 0.00 2.92
231 235 6.831664 AAAGGTATCTACAATGGGTCATCT 57.168 37.500 0.00 0.00 0.00 2.90
232 236 6.426646 AAGGTATCTACAATGGGTCATCTC 57.573 41.667 0.00 0.00 0.00 2.75
233 237 5.721225 AGGTATCTACAATGGGTCATCTCT 58.279 41.667 0.00 0.00 0.00 3.10
234 238 6.146760 AGGTATCTACAATGGGTCATCTCTT 58.853 40.000 0.00 0.00 0.00 2.85
235 239 7.306013 AGGTATCTACAATGGGTCATCTCTTA 58.694 38.462 0.00 0.00 0.00 2.10
236 240 7.453126 AGGTATCTACAATGGGTCATCTCTTAG 59.547 40.741 0.00 0.00 0.00 2.18
237 241 5.537300 TCTACAATGGGTCATCTCTTAGC 57.463 43.478 0.00 0.00 0.00 3.09
238 242 3.567478 ACAATGGGTCATCTCTTAGCC 57.433 47.619 0.00 0.00 0.00 3.93
239 243 3.118531 ACAATGGGTCATCTCTTAGCCT 58.881 45.455 0.00 0.00 34.30 4.58
240 244 3.525199 ACAATGGGTCATCTCTTAGCCTT 59.475 43.478 0.00 0.00 34.30 4.35
241 245 4.721776 ACAATGGGTCATCTCTTAGCCTTA 59.278 41.667 0.00 0.00 34.30 2.69
242 246 5.370880 ACAATGGGTCATCTCTTAGCCTTAT 59.629 40.000 0.00 0.00 34.30 1.73
243 247 5.753721 ATGGGTCATCTCTTAGCCTTATC 57.246 43.478 0.00 0.00 34.30 1.75
244 248 4.820775 TGGGTCATCTCTTAGCCTTATCT 58.179 43.478 0.00 0.00 34.30 1.98
245 249 5.219739 TGGGTCATCTCTTAGCCTTATCTT 58.780 41.667 0.00 0.00 34.30 2.40
246 250 5.305644 TGGGTCATCTCTTAGCCTTATCTTC 59.694 44.000 0.00 0.00 34.30 2.87
247 251 5.305644 GGGTCATCTCTTAGCCTTATCTTCA 59.694 44.000 0.00 0.00 0.00 3.02
248 252 6.183361 GGGTCATCTCTTAGCCTTATCTTCAA 60.183 42.308 0.00 0.00 0.00 2.69
249 253 7.449247 GGTCATCTCTTAGCCTTATCTTCAAT 58.551 38.462 0.00 0.00 0.00 2.57
250 254 8.589338 GGTCATCTCTTAGCCTTATCTTCAATA 58.411 37.037 0.00 0.00 0.00 1.90
251 255 9.988815 GTCATCTCTTAGCCTTATCTTCAATAA 57.011 33.333 0.00 0.00 0.00 1.40
252 256 9.988815 TCATCTCTTAGCCTTATCTTCAATAAC 57.011 33.333 0.00 0.00 0.00 1.89
253 257 9.995003 CATCTCTTAGCCTTATCTTCAATAACT 57.005 33.333 0.00 0.00 0.00 2.24
276 280 9.701098 AACTAACTATTCTTACAAACATGACGA 57.299 29.630 0.00 0.00 0.00 4.20
277 281 9.355215 ACTAACTATTCTTACAAACATGACGAG 57.645 33.333 0.00 0.00 0.00 4.18
278 282 7.596749 AACTATTCTTACAAACATGACGAGG 57.403 36.000 0.00 0.00 0.00 4.63
279 283 4.946784 ATTCTTACAAACATGACGAGGC 57.053 40.909 0.00 0.00 0.00 4.70
280 284 3.394674 TCTTACAAACATGACGAGGCA 57.605 42.857 0.00 0.00 0.00 4.75
281 285 3.937814 TCTTACAAACATGACGAGGCAT 58.062 40.909 0.00 0.00 0.00 4.40
282 286 5.079689 TCTTACAAACATGACGAGGCATA 57.920 39.130 0.00 0.00 0.00 3.14
283 287 5.670485 TCTTACAAACATGACGAGGCATAT 58.330 37.500 0.00 0.00 0.00 1.78
284 288 6.112734 TCTTACAAACATGACGAGGCATATT 58.887 36.000 0.00 0.00 0.00 1.28
285 289 4.621068 ACAAACATGACGAGGCATATTG 57.379 40.909 0.00 12.34 33.75 1.90
286 290 4.009675 ACAAACATGACGAGGCATATTGT 58.990 39.130 13.30 13.30 34.95 2.71
287 291 4.142622 ACAAACATGACGAGGCATATTGTG 60.143 41.667 16.52 5.35 36.73 3.33
341 345 6.591750 TTTTACGAGTTCTCTCCTTCATCT 57.408 37.500 0.00 0.00 37.40 2.90
342 346 5.821516 TTACGAGTTCTCTCCTTCATCTC 57.178 43.478 0.00 0.00 37.40 2.75
343 347 3.691575 ACGAGTTCTCTCCTTCATCTCA 58.308 45.455 0.00 0.00 37.40 3.27
344 348 4.277476 ACGAGTTCTCTCCTTCATCTCAT 58.723 43.478 0.00 0.00 37.40 2.90
345 349 4.338118 ACGAGTTCTCTCCTTCATCTCATC 59.662 45.833 0.00 0.00 37.40 2.92
346 350 4.337836 CGAGTTCTCTCCTTCATCTCATCA 59.662 45.833 0.00 0.00 37.40 3.07
347 351 5.009911 CGAGTTCTCTCCTTCATCTCATCAT 59.990 44.000 0.00 0.00 37.40 2.45
348 352 6.461370 CGAGTTCTCTCCTTCATCTCATCATT 60.461 42.308 0.00 0.00 37.40 2.57
349 353 7.197901 AGTTCTCTCCTTCATCTCATCATTT 57.802 36.000 0.00 0.00 0.00 2.32
350 354 8.316497 AGTTCTCTCCTTCATCTCATCATTTA 57.684 34.615 0.00 0.00 0.00 1.40
351 355 8.936787 AGTTCTCTCCTTCATCTCATCATTTAT 58.063 33.333 0.00 0.00 0.00 1.40
352 356 9.206870 GTTCTCTCCTTCATCTCATCATTTATC 57.793 37.037 0.00 0.00 0.00 1.75
353 357 7.905265 TCTCTCCTTCATCTCATCATTTATCC 58.095 38.462 0.00 0.00 0.00 2.59
354 358 7.733955 TCTCTCCTTCATCTCATCATTTATCCT 59.266 37.037 0.00 0.00 0.00 3.24
355 359 8.962912 TCTCCTTCATCTCATCATTTATCCTA 57.037 34.615 0.00 0.00 0.00 2.94
356 360 8.811017 TCTCCTTCATCTCATCATTTATCCTAC 58.189 37.037 0.00 0.00 0.00 3.18
357 361 7.606349 TCCTTCATCTCATCATTTATCCTACG 58.394 38.462 0.00 0.00 0.00 3.51
358 362 7.233553 TCCTTCATCTCATCATTTATCCTACGT 59.766 37.037 0.00 0.00 0.00 3.57
359 363 7.330454 CCTTCATCTCATCATTTATCCTACGTG 59.670 40.741 0.00 0.00 0.00 4.49
360 364 7.524717 TCATCTCATCATTTATCCTACGTGA 57.475 36.000 0.00 0.00 0.00 4.35
361 365 7.371159 TCATCTCATCATTTATCCTACGTGAC 58.629 38.462 0.00 0.00 0.00 3.67
362 366 6.709018 TCTCATCATTTATCCTACGTGACA 57.291 37.500 0.00 0.00 0.00 3.58
363 367 6.504398 TCTCATCATTTATCCTACGTGACAC 58.496 40.000 0.00 0.00 0.00 3.67
364 368 6.321435 TCTCATCATTTATCCTACGTGACACT 59.679 38.462 0.00 0.00 0.00 3.55
365 369 6.273071 TCATCATTTATCCTACGTGACACTG 58.727 40.000 0.00 0.06 0.00 3.66
366 370 5.654603 TCATTTATCCTACGTGACACTGT 57.345 39.130 0.00 6.20 0.00 3.55
367 371 6.762702 TCATTTATCCTACGTGACACTGTA 57.237 37.500 0.00 7.00 0.00 2.74
368 372 6.558009 TCATTTATCCTACGTGACACTGTAC 58.442 40.000 0.00 0.00 0.00 2.90
369 373 4.970662 TTATCCTACGTGACACTGTACC 57.029 45.455 0.00 0.00 0.00 3.34
370 374 2.574006 TCCTACGTGACACTGTACCT 57.426 50.000 0.00 0.00 0.00 3.08
371 375 2.156917 TCCTACGTGACACTGTACCTG 58.843 52.381 0.00 0.00 0.00 4.00
372 376 1.402456 CCTACGTGACACTGTACCTGC 60.402 57.143 0.00 0.00 0.00 4.85
373 377 0.599558 TACGTGACACTGTACCTGCC 59.400 55.000 0.00 0.00 0.00 4.85
374 378 1.374252 CGTGACACTGTACCTGCCC 60.374 63.158 3.68 0.00 0.00 5.36
375 379 1.816863 CGTGACACTGTACCTGCCCT 61.817 60.000 3.68 0.00 0.00 5.19
376 380 0.396811 GTGACACTGTACCTGCCCTT 59.603 55.000 0.00 0.00 0.00 3.95
377 381 1.621814 GTGACACTGTACCTGCCCTTA 59.378 52.381 0.00 0.00 0.00 2.69
378 382 2.038033 GTGACACTGTACCTGCCCTTAA 59.962 50.000 0.00 0.00 0.00 1.85
379 383 2.706723 TGACACTGTACCTGCCCTTAAA 59.293 45.455 0.00 0.00 0.00 1.52
380 384 3.244422 TGACACTGTACCTGCCCTTAAAG 60.244 47.826 0.00 0.00 0.00 1.85
381 385 2.084546 CACTGTACCTGCCCTTAAAGC 58.915 52.381 0.00 0.00 0.00 3.51
382 386 1.702957 ACTGTACCTGCCCTTAAAGCA 59.297 47.619 0.37 0.37 38.82 3.91
383 387 2.107552 ACTGTACCTGCCCTTAAAGCAA 59.892 45.455 1.87 0.00 40.35 3.91
384 388 3.245264 ACTGTACCTGCCCTTAAAGCAAT 60.245 43.478 1.87 0.00 40.35 3.56
385 389 3.088532 TGTACCTGCCCTTAAAGCAATG 58.911 45.455 1.87 0.00 40.35 2.82
386 390 2.603075 ACCTGCCCTTAAAGCAATGA 57.397 45.000 1.87 0.00 40.35 2.57
462 470 1.159713 GCGTGCAATGATCCGATGGA 61.160 55.000 0.00 0.00 35.55 3.41
508 516 4.585526 TCGGCGATGATGACCGGC 62.586 66.667 4.99 0.00 46.87 6.13
547 555 2.616842 CTGTAGTTGGTGGCGTTCTTTT 59.383 45.455 0.00 0.00 0.00 2.27
561 569 3.545426 CGTTCTTTTCCTTCACGTGGTTC 60.545 47.826 17.00 0.00 0.00 3.62
562 570 2.567985 TCTTTTCCTTCACGTGGTTCC 58.432 47.619 17.00 0.00 0.00 3.62
563 571 2.092861 TCTTTTCCTTCACGTGGTTCCA 60.093 45.455 17.00 0.00 0.00 3.53
565 573 0.834612 TTCCTTCACGTGGTTCCAGT 59.165 50.000 17.00 0.00 0.00 4.00
588 600 1.716581 CACGCTCTTTCTCTCGTTCAC 59.283 52.381 0.00 0.00 32.38 3.18
589 601 0.978385 CGCTCTTTCTCTCGTTCACG 59.022 55.000 0.00 0.00 41.45 4.35
590 602 1.663445 CGCTCTTTCTCTCGTTCACGT 60.663 52.381 0.00 0.00 40.80 4.49
593 623 1.679680 TCTTTCTCTCGTTCACGTGGT 59.320 47.619 17.00 0.00 40.80 4.16
595 625 0.742505 TTCTCTCGTTCACGTGGTGT 59.257 50.000 17.00 0.00 40.80 4.16
613 648 3.000819 CCTGGAGCGGGTGTGGTA 61.001 66.667 0.00 0.00 0.00 3.25
631 666 4.873827 GTGGTATGGATCGCTTTTTCTGTA 59.126 41.667 0.00 0.00 0.00 2.74
646 681 3.371102 TCTGTATGTTATGCTCGCTCC 57.629 47.619 0.00 0.00 0.00 4.70
666 701 2.288395 CCCTGCTCAATTTGTGTTGACC 60.288 50.000 0.00 0.00 34.58 4.02
733 768 4.685513 AGTCTACTCTCCTTCCTTCCTT 57.314 45.455 0.00 0.00 0.00 3.36
735 770 3.702548 GTCTACTCTCCTTCCTTCCTTCC 59.297 52.174 0.00 0.00 0.00 3.46
736 771 3.598782 TCTACTCTCCTTCCTTCCTTCCT 59.401 47.826 0.00 0.00 0.00 3.36
856 891 1.081892 CTCAAGCACTCGTCAATGGG 58.918 55.000 0.00 0.00 0.00 4.00
894 931 1.067250 GCTCAGTCATCCTCGCCTC 59.933 63.158 0.00 0.00 0.00 4.70
897 934 1.142748 CAGTCATCCTCGCCTCCAC 59.857 63.158 0.00 0.00 0.00 4.02
1096 1137 2.837291 CCAGCCTCCTCCTCCTCG 60.837 72.222 0.00 0.00 0.00 4.63
1528 1575 3.691342 TCCTCCAAGCCGACCACG 61.691 66.667 0.00 0.00 39.43 4.94
1529 1576 4.003788 CCTCCAAGCCGACCACGT 62.004 66.667 0.00 0.00 37.88 4.49
1672 1731 1.513158 CAGCCGATGAGAAGGTCGT 59.487 57.895 0.00 0.00 0.00 4.34
1897 1956 5.163478 GCCATCTTGCCAATCTGAAACTATT 60.163 40.000 0.00 0.00 0.00 1.73
1902 1961 5.295431 TGCCAATCTGAAACTATTGTTCG 57.705 39.130 0.00 0.00 34.96 3.95
1903 1962 4.759693 TGCCAATCTGAAACTATTGTTCGT 59.240 37.500 0.00 0.00 34.96 3.85
1904 1963 5.088739 GCCAATCTGAAACTATTGTTCGTG 58.911 41.667 0.00 0.00 34.96 4.35
1905 1964 5.631026 CCAATCTGAAACTATTGTTCGTGG 58.369 41.667 0.00 0.00 34.96 4.94
1906 1965 5.181245 CCAATCTGAAACTATTGTTCGTGGT 59.819 40.000 0.00 0.00 34.96 4.16
1907 1966 6.370442 CCAATCTGAAACTATTGTTCGTGGTA 59.630 38.462 0.00 0.00 34.96 3.25
1908 1967 6.963049 ATCTGAAACTATTGTTCGTGGTAC 57.037 37.500 0.00 0.00 34.96 3.34
1928 1991 9.480053 GTGGTACTAAACTGTACATTTCTTGTA 57.520 33.333 0.00 0.00 43.17 2.41
1950 2013 6.712998 TGTAGCTAGACTAGATGATGAACTCC 59.287 42.308 13.91 0.00 0.00 3.85
1968 2069 4.879104 CTCCACTCGAGTAATACGACTT 57.121 45.455 19.57 0.00 35.88 3.01
1969 2070 4.835344 CTCCACTCGAGTAATACGACTTC 58.165 47.826 19.57 0.00 35.88 3.01
1970 2071 4.256110 TCCACTCGAGTAATACGACTTCA 58.744 43.478 19.57 0.00 35.88 3.02
1974 2092 6.196724 CCACTCGAGTAATACGACTTCATTTC 59.803 42.308 19.57 0.00 35.88 2.17
1977 2095 8.027771 ACTCGAGTAATACGACTTCATTTCTTT 58.972 33.333 18.46 0.00 35.88 2.52
1979 2097 7.811236 TCGAGTAATACGACTTCATTTCTTTGT 59.189 33.333 0.00 0.00 34.85 2.83
2029 2147 6.018425 CAGCTTTATGTTGCACTCTAATCGAT 60.018 38.462 0.00 0.00 0.00 3.59
2031 2149 6.603237 TTTATGTTGCACTCTAATCGATGG 57.397 37.500 0.00 0.00 0.00 3.51
2036 2154 3.261580 TGCACTCTAATCGATGGTGTTG 58.738 45.455 0.00 0.00 0.00 3.33
2039 2157 4.115516 CACTCTAATCGATGGTGTTGAGG 58.884 47.826 0.00 0.00 0.00 3.86
2040 2158 4.023980 ACTCTAATCGATGGTGTTGAGGA 58.976 43.478 0.00 0.00 0.00 3.71
2055 2173 4.921515 TGTTGAGGAAGTAAATCGAACGAG 59.078 41.667 2.94 0.00 0.00 4.18
2072 2190 3.283751 ACGAGTCTTGACTAGATGGGAG 58.716 50.000 15.75 0.00 34.79 4.30
2077 2195 5.197451 AGTCTTGACTAGATGGGAGTACAG 58.803 45.833 0.89 0.00 34.79 2.74
2078 2196 3.954904 TCTTGACTAGATGGGAGTACAGC 59.045 47.826 0.00 0.00 0.00 4.40
2081 2199 0.039978 CTAGATGGGAGTACAGCGCG 60.040 60.000 0.00 0.00 0.00 6.86
2099 2217 1.625616 CGTACTTTAGCACCCACTCG 58.374 55.000 0.00 0.00 0.00 4.18
2199 2317 2.679287 GAGGAGAACCCGACCCGT 60.679 66.667 0.00 0.00 40.87 5.28
2514 2642 4.372999 GCCTGCCTCCCCAAGCTT 62.373 66.667 0.00 0.00 0.00 3.74
2525 2653 0.405585 CCCAAGCTTCCCCTTTCTCA 59.594 55.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 36 3.680842 GTCGGATTTGACGGCCTAT 57.319 52.632 0.00 0.00 0.00 2.57
97 100 1.206371 GCCCAAGTGTGACTATACCGT 59.794 52.381 0.00 0.00 0.00 4.83
98 101 1.480954 AGCCCAAGTGTGACTATACCG 59.519 52.381 0.00 0.00 0.00 4.02
103 106 0.766674 ACCCAGCCCAAGTGTGACTA 60.767 55.000 0.00 0.00 0.00 2.59
172 176 9.733556 TCTCTAAATTACATGCAAGGTTTAAGA 57.266 29.630 0.00 0.00 28.09 2.10
175 179 9.679661 TCATCTCTAAATTACATGCAAGGTTTA 57.320 29.630 0.00 0.00 28.09 2.01
176 180 8.462016 GTCATCTCTAAATTACATGCAAGGTTT 58.538 33.333 0.00 0.00 28.09 3.27
177 181 7.611467 TGTCATCTCTAAATTACATGCAAGGTT 59.389 33.333 0.00 0.00 28.09 3.50
178 182 7.112122 TGTCATCTCTAAATTACATGCAAGGT 58.888 34.615 0.00 0.00 32.53 3.50
179 183 7.558161 TGTCATCTCTAAATTACATGCAAGG 57.442 36.000 0.00 0.00 0.00 3.61
180 184 9.844790 TTTTGTCATCTCTAAATTACATGCAAG 57.155 29.630 0.00 0.00 0.00 4.01
206 210 7.643123 AGATGACCCATTGTAGATACCTTTTT 58.357 34.615 0.00 0.00 0.00 1.94
207 211 7.127955 AGAGATGACCCATTGTAGATACCTTTT 59.872 37.037 0.00 0.00 0.00 2.27
208 212 6.617371 AGAGATGACCCATTGTAGATACCTTT 59.383 38.462 0.00 0.00 0.00 3.11
209 213 6.146760 AGAGATGACCCATTGTAGATACCTT 58.853 40.000 0.00 0.00 0.00 3.50
210 214 5.721225 AGAGATGACCCATTGTAGATACCT 58.279 41.667 0.00 0.00 0.00 3.08
211 215 6.426646 AAGAGATGACCCATTGTAGATACC 57.573 41.667 0.00 0.00 0.00 2.73
212 216 7.093992 GCTAAGAGATGACCCATTGTAGATAC 58.906 42.308 0.00 0.00 0.00 2.24
213 217 6.211584 GGCTAAGAGATGACCCATTGTAGATA 59.788 42.308 0.00 0.00 0.00 1.98
214 218 5.012561 GGCTAAGAGATGACCCATTGTAGAT 59.987 44.000 0.00 0.00 0.00 1.98
215 219 4.345257 GGCTAAGAGATGACCCATTGTAGA 59.655 45.833 0.00 0.00 0.00 2.59
216 220 4.346418 AGGCTAAGAGATGACCCATTGTAG 59.654 45.833 0.00 0.00 0.00 2.74
217 221 4.298626 AGGCTAAGAGATGACCCATTGTA 58.701 43.478 0.00 0.00 0.00 2.41
218 222 3.118531 AGGCTAAGAGATGACCCATTGT 58.881 45.455 0.00 0.00 0.00 2.71
219 223 3.853355 AGGCTAAGAGATGACCCATTG 57.147 47.619 0.00 0.00 0.00 2.82
220 224 5.848921 AGATAAGGCTAAGAGATGACCCATT 59.151 40.000 0.00 0.00 0.00 3.16
221 225 5.410602 AGATAAGGCTAAGAGATGACCCAT 58.589 41.667 0.00 0.00 0.00 4.00
222 226 4.820775 AGATAAGGCTAAGAGATGACCCA 58.179 43.478 0.00 0.00 0.00 4.51
223 227 5.305644 TGAAGATAAGGCTAAGAGATGACCC 59.694 44.000 0.00 0.00 0.00 4.46
224 228 6.412362 TGAAGATAAGGCTAAGAGATGACC 57.588 41.667 0.00 0.00 0.00 4.02
225 229 9.988815 TTATTGAAGATAAGGCTAAGAGATGAC 57.011 33.333 0.00 0.00 0.00 3.06
226 230 9.988815 GTTATTGAAGATAAGGCTAAGAGATGA 57.011 33.333 0.00 0.00 0.00 2.92
227 231 9.995003 AGTTATTGAAGATAAGGCTAAGAGATG 57.005 33.333 0.00 0.00 0.00 2.90
250 254 9.701098 TCGTCATGTTTGTAAGAATAGTTAGTT 57.299 29.630 0.00 0.00 0.00 2.24
251 255 9.355215 CTCGTCATGTTTGTAAGAATAGTTAGT 57.645 33.333 0.00 0.00 0.00 2.24
252 256 8.808529 CCTCGTCATGTTTGTAAGAATAGTTAG 58.191 37.037 0.00 0.00 0.00 2.34
253 257 7.277098 GCCTCGTCATGTTTGTAAGAATAGTTA 59.723 37.037 0.00 0.00 0.00 2.24
254 258 6.092259 GCCTCGTCATGTTTGTAAGAATAGTT 59.908 38.462 0.00 0.00 0.00 2.24
255 259 5.581085 GCCTCGTCATGTTTGTAAGAATAGT 59.419 40.000 0.00 0.00 0.00 2.12
256 260 5.580691 TGCCTCGTCATGTTTGTAAGAATAG 59.419 40.000 0.00 0.00 0.00 1.73
257 261 5.483811 TGCCTCGTCATGTTTGTAAGAATA 58.516 37.500 0.00 0.00 0.00 1.75
258 262 4.323417 TGCCTCGTCATGTTTGTAAGAAT 58.677 39.130 0.00 0.00 0.00 2.40
259 263 3.734463 TGCCTCGTCATGTTTGTAAGAA 58.266 40.909 0.00 0.00 0.00 2.52
260 264 3.394674 TGCCTCGTCATGTTTGTAAGA 57.605 42.857 0.00 0.00 0.00 2.10
261 265 5.991328 ATATGCCTCGTCATGTTTGTAAG 57.009 39.130 0.00 0.00 0.00 2.34
262 266 5.645929 ACAATATGCCTCGTCATGTTTGTAA 59.354 36.000 0.00 0.00 34.90 2.41
263 267 5.064579 CACAATATGCCTCGTCATGTTTGTA 59.935 40.000 0.00 0.00 34.90 2.41
264 268 4.009675 ACAATATGCCTCGTCATGTTTGT 58.990 39.130 0.00 0.00 33.36 2.83
265 269 4.345288 CACAATATGCCTCGTCATGTTTG 58.655 43.478 0.00 0.00 32.21 2.93
266 270 4.621068 CACAATATGCCTCGTCATGTTT 57.379 40.909 0.00 0.00 0.00 2.83
276 280 9.573716 GAGATGGTCTCTTAGCACAATATGCCT 62.574 44.444 0.00 0.00 46.72 4.75
277 281 7.508741 GAGATGGTCTCTTAGCACAATATGCC 61.509 46.154 0.00 0.00 46.72 4.40
278 282 5.407995 GAGATGGTCTCTTAGCACAATATGC 59.592 44.000 0.00 0.00 46.30 3.14
317 321 6.994221 AGATGAAGGAGAGAACTCGTAAAAA 58.006 36.000 0.00 0.00 43.44 1.94
318 322 6.208797 TGAGATGAAGGAGAGAACTCGTAAAA 59.791 38.462 0.00 0.00 43.44 1.52
319 323 5.710567 TGAGATGAAGGAGAGAACTCGTAAA 59.289 40.000 0.00 0.00 43.44 2.01
320 324 5.254115 TGAGATGAAGGAGAGAACTCGTAA 58.746 41.667 0.00 0.00 43.44 3.18
321 325 4.844884 TGAGATGAAGGAGAGAACTCGTA 58.155 43.478 0.00 0.00 43.44 3.43
322 326 3.691575 TGAGATGAAGGAGAGAACTCGT 58.308 45.455 0.00 0.00 43.44 4.18
323 327 4.337836 TGATGAGATGAAGGAGAGAACTCG 59.662 45.833 0.00 0.00 43.44 4.18
324 328 5.850557 TGATGAGATGAAGGAGAGAACTC 57.149 43.478 0.00 0.00 41.94 3.01
325 329 6.811634 AATGATGAGATGAAGGAGAGAACT 57.188 37.500 0.00 0.00 0.00 3.01
326 330 9.206870 GATAAATGATGAGATGAAGGAGAGAAC 57.793 37.037 0.00 0.00 0.00 3.01
327 331 8.373981 GGATAAATGATGAGATGAAGGAGAGAA 58.626 37.037 0.00 0.00 0.00 2.87
328 332 7.733955 AGGATAAATGATGAGATGAAGGAGAGA 59.266 37.037 0.00 0.00 0.00 3.10
329 333 7.909518 AGGATAAATGATGAGATGAAGGAGAG 58.090 38.462 0.00 0.00 0.00 3.20
330 334 7.868792 AGGATAAATGATGAGATGAAGGAGA 57.131 36.000 0.00 0.00 0.00 3.71
331 335 7.758980 CGTAGGATAAATGATGAGATGAAGGAG 59.241 40.741 0.00 0.00 0.00 3.69
332 336 7.233553 ACGTAGGATAAATGATGAGATGAAGGA 59.766 37.037 0.00 0.00 0.00 3.36
333 337 7.330454 CACGTAGGATAAATGATGAGATGAAGG 59.670 40.741 0.00 0.00 0.00 3.46
334 338 8.084684 TCACGTAGGATAAATGATGAGATGAAG 58.915 37.037 0.00 0.00 0.00 3.02
335 339 7.867909 GTCACGTAGGATAAATGATGAGATGAA 59.132 37.037 0.00 0.00 0.00 2.57
336 340 7.014230 TGTCACGTAGGATAAATGATGAGATGA 59.986 37.037 0.00 0.00 0.00 2.92
337 341 7.115520 GTGTCACGTAGGATAAATGATGAGATG 59.884 40.741 0.00 0.00 0.00 2.90
338 342 7.014711 AGTGTCACGTAGGATAAATGATGAGAT 59.985 37.037 0.00 0.00 0.00 2.75
339 343 6.321435 AGTGTCACGTAGGATAAATGATGAGA 59.679 38.462 0.00 0.00 0.00 3.27
340 344 6.419116 CAGTGTCACGTAGGATAAATGATGAG 59.581 42.308 0.00 0.00 0.00 2.90
341 345 6.127451 ACAGTGTCACGTAGGATAAATGATGA 60.127 38.462 0.00 0.00 0.00 2.92
342 346 6.042777 ACAGTGTCACGTAGGATAAATGATG 58.957 40.000 0.00 0.00 0.00 3.07
343 347 6.222038 ACAGTGTCACGTAGGATAAATGAT 57.778 37.500 0.00 0.00 0.00 2.45
344 348 5.654603 ACAGTGTCACGTAGGATAAATGA 57.345 39.130 0.00 0.00 0.00 2.57
345 349 5.747197 GGTACAGTGTCACGTAGGATAAATG 59.253 44.000 0.00 0.00 0.00 2.32
346 350 5.655532 AGGTACAGTGTCACGTAGGATAAAT 59.344 40.000 0.00 0.00 0.00 1.40
347 351 5.012239 AGGTACAGTGTCACGTAGGATAAA 58.988 41.667 0.00 0.00 0.00 1.40
348 352 4.397103 CAGGTACAGTGTCACGTAGGATAA 59.603 45.833 0.00 0.00 0.00 1.75
349 353 3.943381 CAGGTACAGTGTCACGTAGGATA 59.057 47.826 0.00 0.00 0.00 2.59
350 354 2.753452 CAGGTACAGTGTCACGTAGGAT 59.247 50.000 0.00 0.00 0.00 3.24
351 355 2.156917 CAGGTACAGTGTCACGTAGGA 58.843 52.381 0.00 0.00 0.00 2.94
352 356 1.402456 GCAGGTACAGTGTCACGTAGG 60.402 57.143 0.00 0.00 0.00 3.18
353 357 1.402456 GGCAGGTACAGTGTCACGTAG 60.402 57.143 0.00 1.04 0.00 3.51
354 358 0.599558 GGCAGGTACAGTGTCACGTA 59.400 55.000 0.00 0.83 0.00 3.57
355 359 1.366366 GGCAGGTACAGTGTCACGT 59.634 57.895 0.00 1.79 0.00 4.49
356 360 1.374252 GGGCAGGTACAGTGTCACG 60.374 63.158 0.00 0.00 0.00 4.35
357 361 0.396811 AAGGGCAGGTACAGTGTCAC 59.603 55.000 0.00 0.00 0.00 3.67
358 362 2.018355 TAAGGGCAGGTACAGTGTCA 57.982 50.000 0.00 0.00 0.00 3.58
359 363 3.335579 CTTTAAGGGCAGGTACAGTGTC 58.664 50.000 0.00 0.00 0.00 3.67
360 364 2.552373 GCTTTAAGGGCAGGTACAGTGT 60.552 50.000 0.00 0.00 0.00 3.55
361 365 2.084546 GCTTTAAGGGCAGGTACAGTG 58.915 52.381 0.00 0.00 0.00 3.66
362 366 1.702957 TGCTTTAAGGGCAGGTACAGT 59.297 47.619 0.00 0.00 34.56 3.55
363 367 2.489938 TGCTTTAAGGGCAGGTACAG 57.510 50.000 0.00 0.00 34.56 2.74
364 368 2.961531 TTGCTTTAAGGGCAGGTACA 57.038 45.000 0.00 0.00 40.90 2.90
365 369 3.352648 TCATTGCTTTAAGGGCAGGTAC 58.647 45.455 5.57 0.00 40.90 3.34
366 370 3.730215 TCATTGCTTTAAGGGCAGGTA 57.270 42.857 5.57 0.00 40.90 3.08
367 371 2.603075 TCATTGCTTTAAGGGCAGGT 57.397 45.000 5.57 0.00 40.90 4.00
368 372 2.827921 ACTTCATTGCTTTAAGGGCAGG 59.172 45.455 5.57 3.77 40.90 4.85
369 373 4.702131 AGTACTTCATTGCTTTAAGGGCAG 59.298 41.667 0.00 0.00 40.90 4.85
370 374 4.458989 CAGTACTTCATTGCTTTAAGGGCA 59.541 41.667 0.00 1.81 37.97 5.36
371 375 4.459337 ACAGTACTTCATTGCTTTAAGGGC 59.541 41.667 0.00 0.00 0.00 5.19
372 376 5.106157 CCACAGTACTTCATTGCTTTAAGGG 60.106 44.000 0.00 0.00 0.00 3.95
373 377 5.473504 ACCACAGTACTTCATTGCTTTAAGG 59.526 40.000 0.00 0.00 0.00 2.69
374 378 6.017109 ACACCACAGTACTTCATTGCTTTAAG 60.017 38.462 0.00 0.00 0.00 1.85
375 379 5.825679 ACACCACAGTACTTCATTGCTTTAA 59.174 36.000 0.00 0.00 0.00 1.52
376 380 5.238432 CACACCACAGTACTTCATTGCTTTA 59.762 40.000 0.00 0.00 0.00 1.85
377 381 4.036734 CACACCACAGTACTTCATTGCTTT 59.963 41.667 0.00 0.00 0.00 3.51
378 382 3.565482 CACACCACAGTACTTCATTGCTT 59.435 43.478 0.00 0.00 0.00 3.91
379 383 3.141398 CACACCACAGTACTTCATTGCT 58.859 45.455 0.00 0.00 0.00 3.91
380 384 2.226437 CCACACCACAGTACTTCATTGC 59.774 50.000 0.00 0.00 0.00 3.56
381 385 2.226437 GCCACACCACAGTACTTCATTG 59.774 50.000 0.00 0.00 0.00 2.82
382 386 2.504367 GCCACACCACAGTACTTCATT 58.496 47.619 0.00 0.00 0.00 2.57
383 387 1.271379 GGCCACACCACAGTACTTCAT 60.271 52.381 0.00 0.00 38.86 2.57
384 388 0.107831 GGCCACACCACAGTACTTCA 59.892 55.000 0.00 0.00 38.86 3.02
385 389 0.949105 CGGCCACACCACAGTACTTC 60.949 60.000 2.24 0.00 39.03 3.01
386 390 1.070786 CGGCCACACCACAGTACTT 59.929 57.895 2.24 0.00 39.03 2.24
462 470 3.971702 GGAGGCTGGCAAGTGGGT 61.972 66.667 3.38 0.00 0.00 4.51
547 555 0.834612 AACTGGAACCACGTGAAGGA 59.165 50.000 19.30 0.00 0.00 3.36
561 569 1.001406 AGAGAAAGAGCGTGGAACTGG 59.999 52.381 0.00 0.00 31.75 4.00
562 570 2.333014 GAGAGAAAGAGCGTGGAACTG 58.667 52.381 0.00 0.00 31.75 3.16
563 571 1.068194 CGAGAGAAAGAGCGTGGAACT 60.068 52.381 0.00 0.00 31.75 3.01
565 573 0.959553 ACGAGAGAAAGAGCGTGGAA 59.040 50.000 0.00 0.00 35.44 3.53
588 600 4.742201 CCGCTCCAGGACACCACG 62.742 72.222 0.00 0.00 0.00 4.94
589 601 4.394712 CCCGCTCCAGGACACCAC 62.395 72.222 0.00 0.00 0.00 4.16
590 602 4.954118 ACCCGCTCCAGGACACCA 62.954 66.667 0.00 0.00 0.00 4.17
593 623 3.625897 CACACCCGCTCCAGGACA 61.626 66.667 0.00 0.00 0.00 4.02
595 625 2.815684 ATACCACACCCGCTCCAGGA 62.816 60.000 0.00 0.00 0.00 3.86
613 648 7.642669 CATAACATACAGAAAAAGCGATCCAT 58.357 34.615 0.00 0.00 0.00 3.41
631 666 0.533755 GCAGGGAGCGAGCATAACAT 60.534 55.000 0.00 0.00 0.00 2.71
733 768 3.009115 CCTTTCTGGCGGGGAGGA 61.009 66.667 9.48 0.00 0.00 3.71
735 770 2.124507 TTGACCTTTCTGGCGGGGAG 62.125 60.000 0.00 0.00 40.22 4.30
736 771 2.124507 CTTGACCTTTCTGGCGGGGA 62.125 60.000 0.00 0.00 40.22 4.81
856 891 9.664332 ACTGAGCATCCTCATATATAAAACATC 57.336 33.333 0.00 0.00 46.44 3.06
894 931 1.135257 TGTTGTTTGTTGAAGCCGTGG 60.135 47.619 0.00 0.00 0.00 4.94
897 934 1.555477 GGTGTTGTTTGTTGAAGCCG 58.445 50.000 0.00 0.00 0.00 5.52
1096 1137 2.033372 GGTGAGGAAGAGGTAGTAGGC 58.967 57.143 0.00 0.00 0.00 3.93
1162 1203 2.738521 GTGATGCTGCGTGGTCGT 60.739 61.111 0.00 0.00 39.49 4.34
1163 1204 3.490759 GGTGATGCTGCGTGGTCG 61.491 66.667 0.00 0.00 40.37 4.79
1164 1205 2.358615 TGGTGATGCTGCGTGGTC 60.359 61.111 0.00 0.00 0.00 4.02
1165 1206 2.669569 GTGGTGATGCTGCGTGGT 60.670 61.111 0.00 0.00 0.00 4.16
1480 1521 8.123445 ACGATGTCGATTTGGTTAAGTATAAC 57.877 34.615 9.67 0.00 43.02 1.89
1528 1575 1.660614 CGAGGCGATGTCGATGACTAC 60.661 57.143 6.60 0.00 43.02 2.73
1529 1576 0.586802 CGAGGCGATGTCGATGACTA 59.413 55.000 6.60 0.00 43.02 2.59
1577 1624 2.055310 TATCGTCGCAGGTACGCCAG 62.055 60.000 0.00 0.00 40.12 4.85
1672 1731 0.770499 TTGCAGGAGTCCATGGACAA 59.230 50.000 39.38 24.30 46.76 3.18
1897 1956 5.512753 TGTACAGTTTAGTACCACGAACA 57.487 39.130 0.00 0.00 42.84 3.18
1902 1961 8.374327 ACAAGAAATGTACAGTTTAGTACCAC 57.626 34.615 10.27 0.00 42.84 4.16
1903 1962 9.701098 CTACAAGAAATGTACAGTTTAGTACCA 57.299 33.333 10.27 0.00 42.84 3.25
1904 1963 8.654215 GCTACAAGAAATGTACAGTTTAGTACC 58.346 37.037 10.27 2.50 42.84 3.34
1905 1964 9.420551 AGCTACAAGAAATGTACAGTTTAGTAC 57.579 33.333 10.27 8.25 43.63 2.73
1907 1966 9.640963 CTAGCTACAAGAAATGTACAGTTTAGT 57.359 33.333 10.27 11.13 43.63 2.24
1908 1967 9.856488 TCTAGCTACAAGAAATGTACAGTTTAG 57.144 33.333 10.27 8.75 43.63 1.85
1928 1991 5.534654 GTGGAGTTCATCATCTAGTCTAGCT 59.465 44.000 1.60 0.00 0.00 3.32
1950 2013 6.967767 AGAAATGAAGTCGTATTACTCGAGTG 59.032 38.462 28.12 10.90 40.20 3.51
1959 2060 9.450807 CAGAAAACAAAGAAATGAAGTCGTATT 57.549 29.630 0.00 0.00 0.00 1.89
1968 2069 9.650539 TCATGAAAACAGAAAACAAAGAAATGA 57.349 25.926 0.00 0.00 0.00 2.57
1974 2092 6.418819 AGCGATCATGAAAACAGAAAACAAAG 59.581 34.615 0.00 0.00 0.00 2.77
1977 2095 5.437289 AGCGATCATGAAAACAGAAAACA 57.563 34.783 0.00 0.00 0.00 2.83
1979 2097 5.830912 ACAAGCGATCATGAAAACAGAAAA 58.169 33.333 0.00 0.00 0.00 2.29
2011 2129 3.873361 CACCATCGATTAGAGTGCAACAT 59.127 43.478 0.00 0.00 41.43 2.71
2012 2130 3.261580 CACCATCGATTAGAGTGCAACA 58.738 45.455 0.00 0.00 41.43 3.33
2029 2147 4.610605 TCGATTTACTTCCTCAACACCA 57.389 40.909 0.00 0.00 0.00 4.17
2031 2149 4.682860 TCGTTCGATTTACTTCCTCAACAC 59.317 41.667 0.00 0.00 0.00 3.32
2036 2154 4.984205 AGACTCGTTCGATTTACTTCCTC 58.016 43.478 0.00 0.00 0.00 3.71
2039 2157 5.857517 AGTCAAGACTCGTTCGATTTACTTC 59.142 40.000 0.00 0.00 36.92 3.01
2040 2158 5.770417 AGTCAAGACTCGTTCGATTTACTT 58.230 37.500 0.00 0.00 36.92 2.24
2055 2173 4.202070 GCTGTACTCCCATCTAGTCAAGAC 60.202 50.000 0.00 0.00 36.93 3.01
2077 2195 1.738830 TGGGTGCTAAAGTACGCGC 60.739 57.895 5.73 0.00 44.20 6.86
2078 2196 0.389426 AGTGGGTGCTAAAGTACGCG 60.389 55.000 3.53 3.53 44.20 6.01
2081 2199 2.230750 AGTCGAGTGGGTGCTAAAGTAC 59.769 50.000 0.00 0.00 0.00 2.73
2099 2217 8.999431 TGGTGTTTTATCTTTCAGATACAAGTC 58.001 33.333 0.00 0.00 36.96 3.01
2138 2256 6.466812 TGCACTTTCTCATCTGAAGACATTA 58.533 36.000 0.00 0.00 0.00 1.90
2141 2259 4.039609 TCTGCACTTTCTCATCTGAAGACA 59.960 41.667 0.00 0.00 0.00 3.41
2199 2317 1.322442 ATCTCCGATCAGCATCACGA 58.678 50.000 0.00 0.00 0.00 4.35
2274 2393 2.043992 TGGTCTGGAAAAACGAGAGGA 58.956 47.619 0.00 0.00 34.23 3.71
2289 2408 4.699522 GGAGCGCGGGTTTGGTCT 62.700 66.667 8.83 0.00 33.30 3.85


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

AutoCloner maintained by Alex Coulton.