Multiple sequence alignment - TraesCS1A01G233400

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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 TraesCS1A01G233400 chr1A 100.000 6663 0 0 1 6663 407321241 407314579 0.000000e+00 12305.0
1 TraesCS1A01G233400 chr1A 95.547 247 9 2 40 285 407320959 407320714 1.740000e-105 394.0
2 TraesCS1A01G233400 chr1A 95.547 247 9 2 283 528 407321202 407320957 1.740000e-105 394.0
3 TraesCS1A01G233400 chr1A 96.154 78 1 1 3940 4017 407317185 407317110 7.010000e-25 126.0
4 TraesCS1A01G233400 chr1A 96.154 78 1 1 4057 4132 407317302 407317225 7.010000e-25 126.0
5 TraesCS1A01G233400 chr1B 93.830 3452 176 25 293 3723 442173363 442169928 0.000000e+00 5160.0
6 TraesCS1A01G233400 chr1B 93.882 2174 81 24 3703 5852 442169906 442167761 0.000000e+00 3230.0
7 TraesCS1A01G233400 chr1B 90.210 286 21 4 1 284 442173408 442173128 3.800000e-97 366.0
8 TraesCS1A01G233400 chr1B 89.431 246 18 5 5840 6080 442167731 442167489 3.020000e-78 303.0
9 TraesCS1A01G233400 chr1B 92.308 117 7 1 3940 4056 442169552 442169438 1.490000e-36 165.0
10 TraesCS1A01G233400 chr1B 96.154 78 1 1 4057 4132 442169669 442169592 7.010000e-25 126.0
11 TraesCS1A01G233400 chr1D 93.813 3459 155 31 293 3723 328080438 328077011 0.000000e+00 5147.0
12 TraesCS1A01G233400 chr1D 94.625 1079 33 5 3703 4764 328076990 328075920 0.000000e+00 1648.0
13 TraesCS1A01G233400 chr1D 92.909 959 39 14 4899 5852 328075921 328074987 0.000000e+00 1367.0
14 TraesCS1A01G233400 chr1D 90.576 573 33 8 6110 6663 375969359 375968789 0.000000e+00 739.0
15 TraesCS1A01G233400 chr1D 88.235 289 29 4 1 285 328080488 328080201 2.300000e-89 340.0
16 TraesCS1A01G233400 chr1D 95.726 117 3 1 3940 4056 328076636 328076522 3.170000e-43 187.0
17 TraesCS1A01G233400 chr1D 96.154 78 1 1 4057 4132 328076753 328076676 7.010000e-25 126.0
18 TraesCS1A01G233400 chr3D 91.637 562 37 4 6110 6663 16258624 16259183 0.000000e+00 769.0
19 TraesCS1A01G233400 chr3D 90.435 575 36 7 6107 6663 475029217 475028644 0.000000e+00 739.0
20 TraesCS1A01G233400 chr3D 88.298 564 53 6 6110 6663 545425572 545425012 0.000000e+00 664.0
21 TraesCS1A01G233400 chr3D 94.286 35 2 0 2775 2809 474998188 474998222 3.000000e-03 54.7
22 TraesCS1A01G233400 chr5A 90.543 571 36 5 6110 6663 457055682 457056251 0.000000e+00 739.0
23 TraesCS1A01G233400 chr7A 90.317 568 36 8 6113 6663 261085466 261086031 0.000000e+00 726.0
24 TraesCS1A01G233400 chr7A 96.970 33 0 1 2770 2801 512327361 512327329 3.000000e-03 54.7
25 TraesCS1A01G233400 chr5D 89.703 573 40 8 6108 6663 464040491 464039921 0.000000e+00 713.0
26 TraesCS1A01G233400 chr5D 85.417 144 14 1 6110 6246 341715795 341715652 6.970000e-30 143.0
27 TraesCS1A01G233400 chr5D 97.059 34 0 1 2770 2802 190489615 190489648 1.000000e-03 56.5
28 TraesCS1A01G233400 chr5D 94.444 36 0 2 2776 2810 444729971 444729937 3.000000e-03 54.7
29 TraesCS1A01G233400 chr2A 89.840 561 49 6 6110 6663 233218123 233217564 0.000000e+00 713.0
30 TraesCS1A01G233400 chr2D 88.713 567 50 8 6107 6663 631058424 631058986 0.000000e+00 680.0
31 TraesCS1A01G233400 chr6B 86.897 145 12 1 6106 6243 569931440 569931296 8.950000e-34 156.0
32 TraesCS1A01G233400 chr6B 96.970 33 0 1 2774 2806 456768721 456768752 3.000000e-03 54.7
33 TraesCS1A01G233400 chr3B 85.906 149 13 3 6104 6245 726127133 726127280 1.160000e-32 152.0
34 TraesCS1A01G233400 chr6D 86.331 139 12 1 6114 6245 404189220 404189082 1.940000e-30 145.0
35 TraesCS1A01G233400 chr4A 90.090 111 9 2 6105 6214 577226305 577226196 6.970000e-30 143.0
36 TraesCS1A01G233400 chr7D 85.484 62 4 3 2775 2831 501895680 501895619 7.220000e-05 60.2
37 TraesCS1A01G233400 chr7B 94.737 38 2 0 2766 2803 639916648 639916685 7.220000e-05 60.2
38 TraesCS1A01G233400 chr7B 100.000 29 0 0 2774 2802 390106794 390106822 3.000000e-03 54.7
39 TraesCS1A01G233400 chrUn 100.000 29 0 0 2774 2802 371149022 371149050 3.000000e-03 54.7


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 TraesCS1A01G233400 chr1A 407314579 407321241 6662 True 12305.000000 12305 100.000000 1 6663 1 chr1A.!!$R1 6662
1 TraesCS1A01G233400 chr1A 407317110 407321202 4092 True 260.000000 394 95.850500 40 4132 4 chr1A.!!$R2 4092
2 TraesCS1A01G233400 chr1B 442167489 442173408 5919 True 1558.333333 5160 92.635833 1 6080 6 chr1B.!!$R1 6079
3 TraesCS1A01G233400 chr1D 328074987 328080488 5501 True 1469.166667 5147 93.577000 1 5852 6 chr1D.!!$R2 5851
4 TraesCS1A01G233400 chr1D 375968789 375969359 570 True 739.000000 739 90.576000 6110 6663 1 chr1D.!!$R1 553
5 TraesCS1A01G233400 chr3D 16258624 16259183 559 False 769.000000 769 91.637000 6110 6663 1 chr3D.!!$F1 553
6 TraesCS1A01G233400 chr3D 475028644 475029217 573 True 739.000000 739 90.435000 6107 6663 1 chr3D.!!$R1 556
7 TraesCS1A01G233400 chr3D 545425012 545425572 560 True 664.000000 664 88.298000 6110 6663 1 chr3D.!!$R2 553
8 TraesCS1A01G233400 chr5A 457055682 457056251 569 False 739.000000 739 90.543000 6110 6663 1 chr5A.!!$F1 553
9 TraesCS1A01G233400 chr7A 261085466 261086031 565 False 726.000000 726 90.317000 6113 6663 1 chr7A.!!$F1 550
10 TraesCS1A01G233400 chr5D 464039921 464040491 570 True 713.000000 713 89.703000 6108 6663 1 chr5D.!!$R3 555
11 TraesCS1A01G233400 chr2A 233217564 233218123 559 True 713.000000 713 89.840000 6110 6663 1 chr2A.!!$R1 553
12 TraesCS1A01G233400 chr2D 631058424 631058986 562 False 680.000000 680 88.713000 6107 6663 1 chr2D.!!$F1 556

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
317 319 0.032815 TTGGACATGTCGCTCGTTCA 59.967 50.000 19.33 7.15 0.00 3.18 F
318 320 0.246360 TGGACATGTCGCTCGTTCAT 59.754 50.000 19.33 0.00 0.00 2.57 F
319 321 1.474879 TGGACATGTCGCTCGTTCATA 59.525 47.619 19.33 0.00 0.00 2.15 F
320 322 2.100749 TGGACATGTCGCTCGTTCATAT 59.899 45.455 19.33 0.00 0.00 1.78 F
4484 4853 0.512952 GCACACTCTGTAAACAGGCG 59.487 55.000 10.11 4.86 43.91 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4268 4636 0.833287 GCTGCTTCCAGATGGAGGTA 59.167 55.000 12.08 7.16 46.36 3.08 R
4475 4844 6.416415 TCCCAAAGTATTAATCGCCTGTTTA 58.584 36.000 0.00 0.00 0.00 2.01 R
4484 4853 7.259290 TGCTTCGAATCCCAAAGTATTAATC 57.741 36.000 0.00 0.00 0.00 1.75 R
4520 4890 5.535753 AAAATGTTAGTGCCTTGCTCTTT 57.464 34.783 0.00 0.00 34.22 2.52 R
6087 6510 0.324943 CGGAGGAAAGGGAGAAAGCA 59.675 55.000 0.00 0.00 0.00 3.91 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
89 91 5.778345 CGCTCGTTCATATTTTTGTTTTTGC 59.222 36.000 0.00 0.00 0.00 3.68
90 92 6.561166 CGCTCGTTCATATTTTTGTTTTTGCA 60.561 34.615 0.00 0.00 0.00 4.08
91 93 7.122550 GCTCGTTCATATTTTTGTTTTTGCAA 58.877 30.769 0.00 0.00 0.00 4.08
92 94 7.110079 GCTCGTTCATATTTTTGTTTTTGCAAC 59.890 33.333 0.00 0.00 0.00 4.17
93 95 8.190888 TCGTTCATATTTTTGTTTTTGCAACT 57.809 26.923 0.00 0.00 0.00 3.16
94 96 8.660373 TCGTTCATATTTTTGTTTTTGCAACTT 58.340 25.926 0.00 0.00 0.00 2.66
95 97 8.932963 CGTTCATATTTTTGTTTTTGCAACTTC 58.067 29.630 0.00 0.00 0.00 3.01
96 98 9.986833 GTTCATATTTTTGTTTTTGCAACTTCT 57.013 25.926 0.00 0.00 0.00 2.85
98 100 9.598517 TCATATTTTTGTTTTTGCAACTTCTCT 57.401 25.926 0.00 0.00 0.00 3.10
103 105 9.871299 TTTTTGTTTTTGCAACTTCTCTAAAAC 57.129 25.926 0.00 5.40 37.93 2.43
104 106 8.825667 TTTGTTTTTGCAACTTCTCTAAAACT 57.174 26.923 16.00 0.00 38.11 2.66
105 107 9.915629 TTTGTTTTTGCAACTTCTCTAAAACTA 57.084 25.926 16.00 8.93 38.11 2.24
174 176 7.840342 GAGAATCTAAGTGCTTGAATGAGAA 57.160 36.000 0.00 0.00 0.00 2.87
175 177 8.261492 GAGAATCTAAGTGCTTGAATGAGAAA 57.739 34.615 0.00 0.00 0.00 2.52
176 178 8.627208 AGAATCTAAGTGCTTGAATGAGAAAA 57.373 30.769 0.00 0.00 0.00 2.29
177 179 8.510505 AGAATCTAAGTGCTTGAATGAGAAAAC 58.489 33.333 0.00 0.00 0.00 2.43
178 180 6.228273 TCTAAGTGCTTGAATGAGAAAACG 57.772 37.500 0.00 0.00 0.00 3.60
179 181 3.904136 AGTGCTTGAATGAGAAAACGG 57.096 42.857 0.00 0.00 0.00 4.44
180 182 2.554032 AGTGCTTGAATGAGAAAACGGG 59.446 45.455 0.00 0.00 0.00 5.28
181 183 1.885887 TGCTTGAATGAGAAAACGGGG 59.114 47.619 0.00 0.00 0.00 5.73
182 184 2.159382 GCTTGAATGAGAAAACGGGGA 58.841 47.619 0.00 0.00 0.00 4.81
183 185 2.556622 GCTTGAATGAGAAAACGGGGAA 59.443 45.455 0.00 0.00 0.00 3.97
184 186 3.005367 GCTTGAATGAGAAAACGGGGAAA 59.995 43.478 0.00 0.00 0.00 3.13
185 187 4.798574 CTTGAATGAGAAAACGGGGAAAG 58.201 43.478 0.00 0.00 0.00 2.62
186 188 3.827722 TGAATGAGAAAACGGGGAAAGT 58.172 40.909 0.00 0.00 0.00 2.66
187 189 4.975631 TGAATGAGAAAACGGGGAAAGTA 58.024 39.130 0.00 0.00 0.00 2.24
188 190 5.566469 TGAATGAGAAAACGGGGAAAGTAT 58.434 37.500 0.00 0.00 0.00 2.12
189 191 5.414454 TGAATGAGAAAACGGGGAAAGTATG 59.586 40.000 0.00 0.00 0.00 2.39
190 192 3.681593 TGAGAAAACGGGGAAAGTATGG 58.318 45.455 0.00 0.00 0.00 2.74
191 193 3.328343 TGAGAAAACGGGGAAAGTATGGA 59.672 43.478 0.00 0.00 0.00 3.41
192 194 3.939592 GAGAAAACGGGGAAAGTATGGAG 59.060 47.826 0.00 0.00 0.00 3.86
193 195 2.801077 AAACGGGGAAAGTATGGAGG 57.199 50.000 0.00 0.00 0.00 4.30
194 196 1.665137 AACGGGGAAAGTATGGAGGT 58.335 50.000 0.00 0.00 0.00 3.85
195 197 1.665137 ACGGGGAAAGTATGGAGGTT 58.335 50.000 0.00 0.00 0.00 3.50
196 198 1.280998 ACGGGGAAAGTATGGAGGTTG 59.719 52.381 0.00 0.00 0.00 3.77
197 199 1.557832 CGGGGAAAGTATGGAGGTTGA 59.442 52.381 0.00 0.00 0.00 3.18
198 200 2.420129 CGGGGAAAGTATGGAGGTTGAG 60.420 54.545 0.00 0.00 0.00 3.02
199 201 2.844348 GGGGAAAGTATGGAGGTTGAGA 59.156 50.000 0.00 0.00 0.00 3.27
200 202 3.459969 GGGGAAAGTATGGAGGTTGAGAT 59.540 47.826 0.00 0.00 0.00 2.75
201 203 4.658901 GGGGAAAGTATGGAGGTTGAGATA 59.341 45.833 0.00 0.00 0.00 1.98
202 204 5.310857 GGGGAAAGTATGGAGGTTGAGATAT 59.689 44.000 0.00 0.00 0.00 1.63
203 205 6.234177 GGGAAAGTATGGAGGTTGAGATATG 58.766 44.000 0.00 0.00 0.00 1.78
204 206 6.043243 GGGAAAGTATGGAGGTTGAGATATGA 59.957 42.308 0.00 0.00 0.00 2.15
205 207 7.256835 GGGAAAGTATGGAGGTTGAGATATGAT 60.257 40.741 0.00 0.00 0.00 2.45
206 208 8.816894 GGAAAGTATGGAGGTTGAGATATGATA 58.183 37.037 0.00 0.00 0.00 2.15
209 211 8.727100 AGTATGGAGGTTGAGATATGATAACA 57.273 34.615 0.00 0.00 0.00 2.41
210 212 8.589338 AGTATGGAGGTTGAGATATGATAACAC 58.411 37.037 0.00 0.00 0.00 3.32
211 213 7.623999 ATGGAGGTTGAGATATGATAACACT 57.376 36.000 0.00 0.00 0.00 3.55
212 214 6.820335 TGGAGGTTGAGATATGATAACACTG 58.180 40.000 0.00 0.00 0.00 3.66
213 215 6.384015 TGGAGGTTGAGATATGATAACACTGT 59.616 38.462 0.00 0.00 0.00 3.55
214 216 7.563556 TGGAGGTTGAGATATGATAACACTGTA 59.436 37.037 0.00 0.00 0.00 2.74
215 217 8.589338 GGAGGTTGAGATATGATAACACTGTAT 58.411 37.037 0.00 0.00 0.00 2.29
216 218 9.988815 GAGGTTGAGATATGATAACACTGTATT 57.011 33.333 0.00 0.00 0.00 1.89
227 229 8.851960 TGATAACACTGTATTTAGATGTCGTC 57.148 34.615 0.00 0.00 0.00 4.20
228 230 8.683615 TGATAACACTGTATTTAGATGTCGTCT 58.316 33.333 0.00 0.00 41.11 4.18
229 231 9.171701 GATAACACTGTATTTAGATGTCGTCTC 57.828 37.037 0.00 0.00 38.42 3.36
230 232 5.570344 ACACTGTATTTAGATGTCGTCTCG 58.430 41.667 0.00 0.00 38.42 4.04
231 233 5.353400 ACACTGTATTTAGATGTCGTCTCGA 59.647 40.000 0.00 0.00 38.42 4.04
245 247 4.063689 TCGTCTCGACAACCTCTATATCC 58.936 47.826 0.00 0.00 0.00 2.59
246 248 3.120615 CGTCTCGACAACCTCTATATCCG 60.121 52.174 0.00 0.00 0.00 4.18
247 249 3.814283 GTCTCGACAACCTCTATATCCGT 59.186 47.826 0.00 0.00 0.00 4.69
248 250 4.993584 GTCTCGACAACCTCTATATCCGTA 59.006 45.833 0.00 0.00 0.00 4.02
249 251 5.642919 GTCTCGACAACCTCTATATCCGTAT 59.357 44.000 0.00 0.00 0.00 3.06
250 252 5.642491 TCTCGACAACCTCTATATCCGTATG 59.358 44.000 0.00 0.00 0.00 2.39
251 253 5.554070 TCGACAACCTCTATATCCGTATGA 58.446 41.667 0.00 0.00 0.00 2.15
252 254 5.999600 TCGACAACCTCTATATCCGTATGAA 59.000 40.000 0.00 0.00 0.00 2.57
253 255 6.487668 TCGACAACCTCTATATCCGTATGAAA 59.512 38.462 0.00 0.00 0.00 2.69
254 256 6.581542 CGACAACCTCTATATCCGTATGAAAC 59.418 42.308 0.00 0.00 0.00 2.78
273 275 6.115452 GAAACGCGTTTCATATGCATTATG 57.885 37.500 43.68 7.13 46.03 1.90
274 276 5.416862 AACGCGTTTCATATGCATTATGA 57.583 34.783 20.79 9.42 43.95 2.15
275 277 4.772434 ACGCGTTTCATATGCATTATGAC 58.228 39.130 5.58 1.99 45.02 3.06
276 278 3.834702 CGCGTTTCATATGCATTATGACG 59.165 43.478 3.54 13.29 45.02 4.35
277 279 4.375908 CGCGTTTCATATGCATTATGACGA 60.376 41.667 21.01 11.78 45.02 4.20
278 280 5.621422 GCGTTTCATATGCATTATGACGAT 58.379 37.500 21.01 3.43 45.02 3.73
279 281 5.729883 GCGTTTCATATGCATTATGACGATC 59.270 40.000 21.01 11.82 45.02 3.69
280 282 5.948085 CGTTTCATATGCATTATGACGATCG 59.052 40.000 14.88 14.88 45.02 3.69
281 283 6.399986 CGTTTCATATGCATTATGACGATCGT 60.400 38.462 22.97 22.97 45.02 3.73
282 284 6.632171 TTCATATGCATTATGACGATCGTC 57.368 37.500 35.46 35.46 45.02 4.20
290 292 3.374330 GACGATCGTCAACGCCAG 58.626 61.111 36.61 0.00 44.02 4.85
291 293 1.154093 GACGATCGTCAACGCCAGA 60.154 57.895 36.61 0.00 44.02 3.86
292 294 0.525668 GACGATCGTCAACGCCAGAT 60.526 55.000 36.61 4.72 44.02 2.90
293 295 0.802222 ACGATCGTCAACGCCAGATG 60.802 55.000 16.60 0.00 39.60 2.90
294 296 0.802222 CGATCGTCAACGCCAGATGT 60.802 55.000 7.03 0.00 39.60 3.06
295 297 0.647410 GATCGTCAACGCCAGATGTG 59.353 55.000 0.00 0.00 39.60 3.21
296 298 0.246360 ATCGTCAACGCCAGATGTGA 59.754 50.000 0.00 0.00 39.60 3.58
297 299 0.246360 TCGTCAACGCCAGATGTGAT 59.754 50.000 0.00 0.00 39.60 3.06
298 300 1.078709 CGTCAACGCCAGATGTGATT 58.921 50.000 0.00 0.00 0.00 2.57
299 301 1.464608 CGTCAACGCCAGATGTGATTT 59.535 47.619 0.00 0.00 0.00 2.17
300 302 2.725759 CGTCAACGCCAGATGTGATTTG 60.726 50.000 0.00 0.00 0.00 2.32
301 303 1.811965 TCAACGCCAGATGTGATTTGG 59.188 47.619 0.00 0.00 35.06 3.28
302 304 1.811965 CAACGCCAGATGTGATTTGGA 59.188 47.619 0.00 0.00 33.76 3.53
303 305 1.453155 ACGCCAGATGTGATTTGGAC 58.547 50.000 0.00 0.00 33.76 4.02
304 306 1.271325 ACGCCAGATGTGATTTGGACA 60.271 47.619 0.00 0.00 33.76 4.02
305 307 2.019249 CGCCAGATGTGATTTGGACAT 58.981 47.619 0.00 0.00 36.73 3.06
306 308 2.223409 CGCCAGATGTGATTTGGACATG 60.223 50.000 0.00 0.00 34.10 3.21
307 309 2.756760 GCCAGATGTGATTTGGACATGT 59.243 45.455 0.00 0.00 34.10 3.21
308 310 3.181493 GCCAGATGTGATTTGGACATGTC 60.181 47.826 17.91 17.91 34.10 3.06
309 311 3.064408 CCAGATGTGATTTGGACATGTCG 59.936 47.826 19.33 1.01 34.10 4.35
310 312 2.679837 AGATGTGATTTGGACATGTCGC 59.320 45.455 19.33 12.69 34.10 5.19
311 313 2.183478 TGTGATTTGGACATGTCGCT 57.817 45.000 19.33 3.94 0.00 4.93
312 314 2.076100 TGTGATTTGGACATGTCGCTC 58.924 47.619 19.33 12.74 0.00 5.03
313 315 1.061131 GTGATTTGGACATGTCGCTCG 59.939 52.381 19.33 0.00 0.00 5.03
314 316 1.337728 TGATTTGGACATGTCGCTCGT 60.338 47.619 19.33 4.58 0.00 4.18
315 317 1.732259 GATTTGGACATGTCGCTCGTT 59.268 47.619 19.33 2.34 0.00 3.85
316 318 1.144969 TTTGGACATGTCGCTCGTTC 58.855 50.000 19.33 4.53 0.00 3.95
317 319 0.032815 TTGGACATGTCGCTCGTTCA 59.967 50.000 19.33 7.15 0.00 3.18
318 320 0.246360 TGGACATGTCGCTCGTTCAT 59.754 50.000 19.33 0.00 0.00 2.57
319 321 1.474879 TGGACATGTCGCTCGTTCATA 59.525 47.619 19.33 0.00 0.00 2.15
320 322 2.100749 TGGACATGTCGCTCGTTCATAT 59.899 45.455 19.33 0.00 0.00 1.78
321 323 3.123804 GGACATGTCGCTCGTTCATATT 58.876 45.455 19.33 0.00 0.00 1.28
322 324 3.555956 GGACATGTCGCTCGTTCATATTT 59.444 43.478 19.33 0.00 0.00 1.40
323 325 4.034048 GGACATGTCGCTCGTTCATATTTT 59.966 41.667 19.33 0.00 0.00 1.82
324 326 5.447279 GGACATGTCGCTCGTTCATATTTTT 60.447 40.000 19.33 0.00 0.00 1.94
325 327 5.323900 ACATGTCGCTCGTTCATATTTTTG 58.676 37.500 0.00 0.00 0.00 2.44
326 328 5.106712 ACATGTCGCTCGTTCATATTTTTGT 60.107 36.000 0.00 0.00 0.00 2.83
327 329 5.351233 TGTCGCTCGTTCATATTTTTGTT 57.649 34.783 0.00 0.00 0.00 2.83
328 330 5.753744 TGTCGCTCGTTCATATTTTTGTTT 58.246 33.333 0.00 0.00 0.00 2.83
329 331 6.202937 TGTCGCTCGTTCATATTTTTGTTTT 58.797 32.000 0.00 0.00 0.00 2.43
330 332 6.693545 TGTCGCTCGTTCATATTTTTGTTTTT 59.306 30.769 0.00 0.00 0.00 1.94
331 333 6.995633 GTCGCTCGTTCATATTTTTGTTTTTG 59.004 34.615 0.00 0.00 0.00 2.44
4267 4635 4.397730 CCCGTCTCTATCTCTATCATGGTG 59.602 50.000 0.00 0.00 0.00 4.17
4268 4636 5.007034 CCGTCTCTATCTCTATCATGGTGT 58.993 45.833 0.00 0.00 0.00 4.16
4475 4844 2.566833 TTGGCAATAGCACACTCTGT 57.433 45.000 0.00 0.00 44.61 3.41
4484 4853 0.512952 GCACACTCTGTAAACAGGCG 59.487 55.000 10.11 4.86 43.91 5.52
4605 4975 0.109723 TAGGTGGCCACGAAAGCTTT 59.890 50.000 29.08 12.53 0.00 3.51
4624 4994 4.301628 CTTTTGAAGTGCAGGAATGAACC 58.698 43.478 0.00 0.00 0.00 3.62
4726 5096 3.312697 GGATAATGTTCCAGAAAGACCGC 59.687 47.826 0.00 0.00 35.72 5.68
4766 5136 1.064389 GGGCTTGTTCCTGAGGCTTAT 60.064 52.381 0.00 0.00 38.40 1.73
4771 5141 4.335416 CTTGTTCCTGAGGCTTATTGGAA 58.665 43.478 0.00 7.16 34.81 3.53
4781 5151 5.473504 TGAGGCTTATTGGAACTTCTGTTTC 59.526 40.000 0.00 0.00 36.39 2.78
4794 5164 7.920682 GGAACTTCTGTTTCTTAATTGCTTGAA 59.079 33.333 0.00 0.00 36.39 2.69
4795 5165 8.634475 AACTTCTGTTTCTTAATTGCTTGAAC 57.366 30.769 0.00 0.00 31.37 3.18
4864 5234 8.306761 GGTCCACAATTTCTAGTTCAATTCAAT 58.693 33.333 0.00 0.00 0.00 2.57
4924 5294 4.273480 CAGTCCCAAGTTGTCTTTAGTGTG 59.727 45.833 1.45 0.00 0.00 3.82
4962 5332 0.764369 TGGCCTGTCTGACCAGTTCT 60.764 55.000 3.32 0.00 0.00 3.01
5023 5393 5.235850 TGTTGGCATTTAACTAGGACTCA 57.764 39.130 0.00 0.00 0.00 3.41
5044 5414 1.209621 GCACCCACTGGACCCTAATA 58.790 55.000 0.00 0.00 34.81 0.98
5045 5415 1.562475 GCACCCACTGGACCCTAATAA 59.438 52.381 0.00 0.00 34.81 1.40
5046 5416 2.174854 GCACCCACTGGACCCTAATAAT 59.825 50.000 0.00 0.00 34.81 1.28
5052 5422 6.218938 ACCCACTGGACCCTAATAATTACTTT 59.781 38.462 0.00 0.00 34.81 2.66
5129 5499 8.154203 TGTCCTCAACATTCATTTTGTACTAGA 58.846 33.333 0.00 0.00 31.20 2.43
5130 5500 9.167311 GTCCTCAACATTCATTTTGTACTAGAT 57.833 33.333 0.00 0.00 0.00 1.98
5216 5587 3.990092 AGCAATTAGATAATCCGCGTGA 58.010 40.909 4.92 1.95 32.44 4.35
5217 5588 4.569943 AGCAATTAGATAATCCGCGTGAT 58.430 39.130 4.92 4.67 32.44 3.06
5314 5686 2.420022 CGAAGCTTATGTTCACCCCTTG 59.580 50.000 0.00 0.00 0.00 3.61
5422 5794 0.030908 ATCAAGTAGAGCTACGGCGC 59.969 55.000 6.90 0.00 44.37 6.53
5454 5826 6.735130 ACCACTTCATTTGTAAGTAGCAAAC 58.265 36.000 0.00 0.00 38.44 2.93
5482 5854 7.500559 ACCTGTTTATAATGGCTCTGATTCTTC 59.499 37.037 0.00 0.00 0.00 2.87
5556 5930 2.463876 GTTGCTTGTTTCTGCTGGTTC 58.536 47.619 0.00 0.00 0.00 3.62
5579 5953 1.771565 TACAATCGAGTCCACCGGAT 58.228 50.000 9.46 0.00 32.73 4.18
5685 6059 7.332557 TGAGCCCGATATAAAGTTTTCAGTAA 58.667 34.615 0.00 0.00 0.00 2.24
5706 6080 7.325338 CAGTAATGTTCTGATGCAGTTTTTCTG 59.675 37.037 0.00 0.00 39.67 3.02
5709 6083 6.691754 TGTTCTGATGCAGTTTTTCTGTTA 57.308 33.333 0.00 0.00 45.23 2.41
5712 6086 6.304356 TCTGATGCAGTTTTTCTGTTACTG 57.696 37.500 0.00 0.00 45.23 2.74
5713 6087 5.822519 TCTGATGCAGTTTTTCTGTTACTGT 59.177 36.000 0.00 0.00 45.23 3.55
5714 6088 5.820131 TGATGCAGTTTTTCTGTTACTGTG 58.180 37.500 0.00 0.00 45.23 3.66
5715 6089 5.356751 TGATGCAGTTTTTCTGTTACTGTGT 59.643 36.000 0.00 0.00 45.23 3.72
5716 6090 5.637006 TGCAGTTTTTCTGTTACTGTGTT 57.363 34.783 0.00 0.00 45.23 3.32
5717 6091 5.398169 TGCAGTTTTTCTGTTACTGTGTTG 58.602 37.500 0.00 0.00 45.23 3.33
5718 6092 5.048364 TGCAGTTTTTCTGTTACTGTGTTGT 60.048 36.000 0.00 0.00 45.23 3.32
5719 6093 5.286082 GCAGTTTTTCTGTTACTGTGTTGTG 59.714 40.000 0.00 0.00 45.23 3.33
5720 6094 6.378582 CAGTTTTTCTGTTACTGTGTTGTGT 58.621 36.000 0.00 0.00 39.17 3.72
5721 6095 6.861055 CAGTTTTTCTGTTACTGTGTTGTGTT 59.139 34.615 0.00 0.00 39.17 3.32
5722 6096 6.861055 AGTTTTTCTGTTACTGTGTTGTGTTG 59.139 34.615 0.00 0.00 0.00 3.33
5723 6097 6.561737 TTTTCTGTTACTGTGTTGTGTTGA 57.438 33.333 0.00 0.00 0.00 3.18
5724 6098 5.794687 TTCTGTTACTGTGTTGTGTTGAG 57.205 39.130 0.00 0.00 0.00 3.02
5725 6099 4.188462 TCTGTTACTGTGTTGTGTTGAGG 58.812 43.478 0.00 0.00 0.00 3.86
5726 6100 2.680841 TGTTACTGTGTTGTGTTGAGGC 59.319 45.455 0.00 0.00 0.00 4.70
5745 6119 1.261619 GCTGTTGTGTTGAGGACGAAG 59.738 52.381 0.00 0.00 0.00 3.79
5784 6158 9.924650 AGTATAGGTTACTGTAAAACTTCTGTG 57.075 33.333 1.10 0.00 0.00 3.66
5819 6193 7.712639 TCTGGAGTCACATTCAGCTAATTTATC 59.287 37.037 0.00 0.00 0.00 1.75
5849 6267 4.645535 TGGTATATGCAGCTCCTTTCATC 58.354 43.478 0.00 0.00 0.00 2.92
5872 6290 3.060602 GAGGAACTTGGAAACTCAGACG 58.939 50.000 0.00 0.00 41.55 4.18
5895 6313 1.818674 GCCGTTGGATCTGGAATTTGT 59.181 47.619 0.00 0.00 0.00 2.83
5912 6330 3.842732 TTGTGCTGCTGATTGAATCTG 57.157 42.857 6.73 7.19 0.00 2.90
5913 6331 2.786777 TGTGCTGCTGATTGAATCTGT 58.213 42.857 12.61 0.00 0.00 3.41
5914 6332 2.486592 TGTGCTGCTGATTGAATCTGTG 59.513 45.455 12.61 7.92 0.00 3.66
5955 6376 6.125949 ACCCTAGGGCTAGTTATTGTAGTACT 60.126 42.308 28.88 0.00 39.32 2.73
5956 6377 7.074237 ACCCTAGGGCTAGTTATTGTAGTACTA 59.926 40.741 28.88 0.00 39.32 1.82
5957 6378 7.392953 CCCTAGGGCTAGTTATTGTAGTACTAC 59.607 44.444 23.58 23.58 36.63 2.73
5967 6388 3.581024 TGTAGTACTACACAAAGCCCG 57.419 47.619 27.99 0.00 40.77 6.13
5971 6392 2.892852 AGTACTACACAAAGCCCGTGTA 59.107 45.455 0.00 9.48 45.55 2.90
6010 6433 2.027561 CACGGAATGGTAGGTGGAAGAA 60.028 50.000 0.00 0.00 0.00 2.52
6015 6438 4.325030 GGAATGGTAGGTGGAAGAATTGGA 60.325 45.833 0.00 0.00 0.00 3.53
6038 6461 5.452255 ACATTAGATTGCAGATCCAATGGT 58.548 37.500 21.46 12.11 35.67 3.55
6063 6486 7.218614 TCCGTATTGGAGTTTCTAAGTTTTCA 58.781 34.615 0.00 0.00 43.74 2.69
6088 6511 2.618053 GTGGTAGGTTTCCACGAGATG 58.382 52.381 0.00 0.00 44.34 2.90
6089 6512 1.066430 TGGTAGGTTTCCACGAGATGC 60.066 52.381 0.00 0.00 0.00 3.91
6090 6513 1.207329 GGTAGGTTTCCACGAGATGCT 59.793 52.381 0.00 0.00 0.00 3.79
6091 6514 2.354805 GGTAGGTTTCCACGAGATGCTT 60.355 50.000 0.00 0.00 0.00 3.91
6092 6515 2.568623 AGGTTTCCACGAGATGCTTT 57.431 45.000 0.00 0.00 0.00 3.51
6093 6516 2.427506 AGGTTTCCACGAGATGCTTTC 58.572 47.619 0.00 0.00 0.00 2.62
6094 6517 2.039084 AGGTTTCCACGAGATGCTTTCT 59.961 45.455 0.00 0.00 37.41 2.52
6095 6518 2.416893 GGTTTCCACGAGATGCTTTCTC 59.583 50.000 7.06 7.06 46.36 2.87
6103 6526 3.643199 GAGATGCTTTCTCCCTTTCCT 57.357 47.619 6.09 0.00 44.46 3.36
6104 6527 3.540617 GAGATGCTTTCTCCCTTTCCTC 58.459 50.000 6.09 0.00 44.46 3.71
6105 6528 2.240921 AGATGCTTTCTCCCTTTCCTCC 59.759 50.000 0.00 0.00 0.00 4.30
6159 6583 3.489568 GGACGTTTGATTTGTCCGGTTTT 60.490 43.478 0.00 0.00 42.42 2.43
6165 6589 2.362717 TGATTTGTCCGGTTTTTGTCCC 59.637 45.455 0.00 0.00 0.00 4.46
6246 6689 0.178975 TTTGCCCCATCTTGTCCGTT 60.179 50.000 0.00 0.00 0.00 4.44
6251 6694 1.200519 CCCATCTTGTCCGTTAGGGA 58.799 55.000 0.00 0.00 44.68 4.20
6445 6890 0.320771 GATCCCACACGTGCTCAACT 60.321 55.000 17.22 0.00 0.00 3.16
6465 6910 9.604626 CTCAACTAAGTCATTTTGAAGATTCAC 57.395 33.333 0.00 0.00 36.83 3.18
6514 6959 1.339610 TGGAATTGGGCAAACTGTTCG 59.660 47.619 0.00 0.00 0.00 3.95
6532 6977 1.002624 GAATGTGGCCGGGTCTTGA 60.003 57.895 2.18 0.00 0.00 3.02
6537 6982 2.361104 GGCCGGGTCTTGATGCAA 60.361 61.111 2.18 0.00 0.00 4.08
6583 7028 5.824904 AATCAAATCCTTGGTCGAAGATG 57.175 39.130 0.00 0.00 40.67 2.90
6591 7036 3.529533 CTTGGTCGAAGATGCTCTCATT 58.470 45.455 0.00 0.00 40.67 2.57
6595 7040 3.489398 GGTCGAAGATGCTCTCATTACGT 60.489 47.826 0.00 0.00 40.67 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 144 6.998074 TCAAGCACTTAGATTCTCTCCAAAAA 59.002 34.615 0.00 0.00 0.00 1.94
143 145 6.533730 TCAAGCACTTAGATTCTCTCCAAAA 58.466 36.000 0.00 0.00 0.00 2.44
144 146 6.114187 TCAAGCACTTAGATTCTCTCCAAA 57.886 37.500 0.00 0.00 0.00 3.28
145 147 5.745312 TCAAGCACTTAGATTCTCTCCAA 57.255 39.130 0.00 0.00 0.00 3.53
146 148 5.745312 TTCAAGCACTTAGATTCTCTCCA 57.255 39.130 0.00 0.00 0.00 3.86
147 149 6.344500 TCATTCAAGCACTTAGATTCTCTCC 58.656 40.000 0.00 0.00 0.00 3.71
148 150 7.264221 TCTCATTCAAGCACTTAGATTCTCTC 58.736 38.462 0.00 0.00 0.00 3.20
149 151 7.180322 TCTCATTCAAGCACTTAGATTCTCT 57.820 36.000 0.00 0.00 0.00 3.10
150 152 7.840342 TTCTCATTCAAGCACTTAGATTCTC 57.160 36.000 0.00 0.00 0.00 2.87
151 153 8.510505 GTTTTCTCATTCAAGCACTTAGATTCT 58.489 33.333 0.00 0.00 0.00 2.40
152 154 7.479916 CGTTTTCTCATTCAAGCACTTAGATTC 59.520 37.037 0.00 0.00 0.00 2.52
153 155 7.301054 CGTTTTCTCATTCAAGCACTTAGATT 58.699 34.615 0.00 0.00 0.00 2.40
154 156 6.128172 CCGTTTTCTCATTCAAGCACTTAGAT 60.128 38.462 0.00 0.00 0.00 1.98
155 157 5.179368 CCGTTTTCTCATTCAAGCACTTAGA 59.821 40.000 0.00 0.00 0.00 2.10
156 158 5.385617 CCGTTTTCTCATTCAAGCACTTAG 58.614 41.667 0.00 0.00 0.00 2.18
157 159 4.215399 CCCGTTTTCTCATTCAAGCACTTA 59.785 41.667 0.00 0.00 0.00 2.24
158 160 3.004734 CCCGTTTTCTCATTCAAGCACTT 59.995 43.478 0.00 0.00 0.00 3.16
159 161 2.554032 CCCGTTTTCTCATTCAAGCACT 59.446 45.455 0.00 0.00 0.00 4.40
160 162 2.351738 CCCCGTTTTCTCATTCAAGCAC 60.352 50.000 0.00 0.00 0.00 4.40
161 163 1.885887 CCCCGTTTTCTCATTCAAGCA 59.114 47.619 0.00 0.00 0.00 3.91
162 164 2.159382 TCCCCGTTTTCTCATTCAAGC 58.841 47.619 0.00 0.00 0.00 4.01
163 165 4.278419 ACTTTCCCCGTTTTCTCATTCAAG 59.722 41.667 0.00 0.00 0.00 3.02
164 166 4.211920 ACTTTCCCCGTTTTCTCATTCAA 58.788 39.130 0.00 0.00 0.00 2.69
165 167 3.827722 ACTTTCCCCGTTTTCTCATTCA 58.172 40.909 0.00 0.00 0.00 2.57
166 168 5.163652 CCATACTTTCCCCGTTTTCTCATTC 60.164 44.000 0.00 0.00 0.00 2.67
167 169 4.705023 CCATACTTTCCCCGTTTTCTCATT 59.295 41.667 0.00 0.00 0.00 2.57
168 170 4.018779 TCCATACTTTCCCCGTTTTCTCAT 60.019 41.667 0.00 0.00 0.00 2.90
169 171 3.328343 TCCATACTTTCCCCGTTTTCTCA 59.672 43.478 0.00 0.00 0.00 3.27
170 172 3.939592 CTCCATACTTTCCCCGTTTTCTC 59.060 47.826 0.00 0.00 0.00 2.87
171 173 3.308188 CCTCCATACTTTCCCCGTTTTCT 60.308 47.826 0.00 0.00 0.00 2.52
172 174 3.014623 CCTCCATACTTTCCCCGTTTTC 58.985 50.000 0.00 0.00 0.00 2.29
173 175 2.377531 ACCTCCATACTTTCCCCGTTTT 59.622 45.455 0.00 0.00 0.00 2.43
174 176 1.990327 ACCTCCATACTTTCCCCGTTT 59.010 47.619 0.00 0.00 0.00 3.60
175 177 1.665137 ACCTCCATACTTTCCCCGTT 58.335 50.000 0.00 0.00 0.00 4.44
176 178 1.280998 CAACCTCCATACTTTCCCCGT 59.719 52.381 0.00 0.00 0.00 5.28
177 179 1.557832 TCAACCTCCATACTTTCCCCG 59.442 52.381 0.00 0.00 0.00 5.73
178 180 2.844348 TCTCAACCTCCATACTTTCCCC 59.156 50.000 0.00 0.00 0.00 4.81
179 181 4.779993 ATCTCAACCTCCATACTTTCCC 57.220 45.455 0.00 0.00 0.00 3.97
180 182 7.067496 TCATATCTCAACCTCCATACTTTCC 57.933 40.000 0.00 0.00 0.00 3.13
183 185 9.159254 TGTTATCATATCTCAACCTCCATACTT 57.841 33.333 0.00 0.00 0.00 2.24
184 186 8.589338 GTGTTATCATATCTCAACCTCCATACT 58.411 37.037 0.00 0.00 0.00 2.12
185 187 8.589338 AGTGTTATCATATCTCAACCTCCATAC 58.411 37.037 0.00 0.00 0.00 2.39
186 188 8.588472 CAGTGTTATCATATCTCAACCTCCATA 58.412 37.037 0.00 0.00 0.00 2.74
187 189 7.071698 ACAGTGTTATCATATCTCAACCTCCAT 59.928 37.037 0.00 0.00 0.00 3.41
188 190 6.384015 ACAGTGTTATCATATCTCAACCTCCA 59.616 38.462 0.00 0.00 0.00 3.86
189 191 6.821388 ACAGTGTTATCATATCTCAACCTCC 58.179 40.000 0.00 0.00 0.00 4.30
190 192 9.988815 AATACAGTGTTATCATATCTCAACCTC 57.011 33.333 0.00 0.00 0.00 3.85
201 203 9.464714 GACGACATCTAAATACAGTGTTATCAT 57.535 33.333 0.00 0.00 0.00 2.45
202 204 8.683615 AGACGACATCTAAATACAGTGTTATCA 58.316 33.333 0.00 0.00 35.15 2.15
203 205 9.171701 GAGACGACATCTAAATACAGTGTTATC 57.828 37.037 0.00 0.00 38.00 1.75
204 206 7.856398 CGAGACGACATCTAAATACAGTGTTAT 59.144 37.037 0.00 0.00 38.00 1.89
205 207 7.064966 TCGAGACGACATCTAAATACAGTGTTA 59.935 37.037 0.00 0.00 38.00 2.41
206 208 6.028368 CGAGACGACATCTAAATACAGTGTT 58.972 40.000 0.00 0.00 38.00 3.32
207 209 5.353400 TCGAGACGACATCTAAATACAGTGT 59.647 40.000 0.00 0.00 38.00 3.55
208 210 5.807344 TCGAGACGACATCTAAATACAGTG 58.193 41.667 0.00 0.00 38.00 3.66
223 225 4.063689 GGATATAGAGGTTGTCGAGACGA 58.936 47.826 0.00 0.00 0.00 4.20
224 226 3.120615 CGGATATAGAGGTTGTCGAGACG 60.121 52.174 0.00 0.00 0.00 4.18
225 227 3.814283 ACGGATATAGAGGTTGTCGAGAC 59.186 47.826 0.00 0.00 0.00 3.36
226 228 4.082665 ACGGATATAGAGGTTGTCGAGA 57.917 45.455 0.00 0.00 0.00 4.04
227 229 5.642491 TCATACGGATATAGAGGTTGTCGAG 59.358 44.000 0.00 0.00 0.00 4.04
228 230 5.554070 TCATACGGATATAGAGGTTGTCGA 58.446 41.667 0.00 0.00 0.00 4.20
229 231 5.874895 TCATACGGATATAGAGGTTGTCG 57.125 43.478 0.00 0.00 0.00 4.35
230 232 6.581542 CGTTTCATACGGATATAGAGGTTGTC 59.418 42.308 0.00 0.00 46.42 3.18
231 233 6.444633 CGTTTCATACGGATATAGAGGTTGT 58.555 40.000 0.00 0.00 46.42 3.32
232 234 6.929587 CGTTTCATACGGATATAGAGGTTG 57.070 41.667 0.00 0.00 46.42 3.77
250 252 5.906838 TCATAATGCATATGAAACGCGTTTC 59.093 36.000 42.81 42.81 45.78 2.78
251 253 5.815850 TCATAATGCATATGAAACGCGTTT 58.184 33.333 35.28 35.28 45.78 3.60
252 254 5.416862 TCATAATGCATATGAAACGCGTT 57.583 34.783 20.79 20.79 45.78 4.84
273 275 0.525668 ATCTGGCGTTGACGATCGTC 60.526 55.000 35.46 35.46 44.77 4.20
274 276 0.802222 CATCTGGCGTTGACGATCGT 60.802 55.000 22.97 22.97 43.02 3.73
275 277 0.802222 ACATCTGGCGTTGACGATCG 60.802 55.000 14.88 14.88 43.02 3.69
276 278 0.647410 CACATCTGGCGTTGACGATC 59.353 55.000 7.85 0.00 43.02 3.69
277 279 0.246360 TCACATCTGGCGTTGACGAT 59.754 50.000 7.85 0.00 43.02 3.73
278 280 0.246360 ATCACATCTGGCGTTGACGA 59.754 50.000 7.85 0.00 43.02 4.20
279 281 1.078709 AATCACATCTGGCGTTGACG 58.921 50.000 0.00 0.00 43.27 4.35
280 282 2.414559 CCAAATCACATCTGGCGTTGAC 60.415 50.000 0.00 0.00 0.00 3.18
281 283 1.811965 CCAAATCACATCTGGCGTTGA 59.188 47.619 0.00 0.00 0.00 3.18
282 284 1.811965 TCCAAATCACATCTGGCGTTG 59.188 47.619 0.00 0.00 0.00 4.10
283 285 1.812571 GTCCAAATCACATCTGGCGTT 59.187 47.619 0.00 0.00 0.00 4.84
284 286 1.271325 TGTCCAAATCACATCTGGCGT 60.271 47.619 0.00 0.00 0.00 5.68
285 287 1.452110 TGTCCAAATCACATCTGGCG 58.548 50.000 0.00 0.00 0.00 5.69
286 288 2.756760 ACATGTCCAAATCACATCTGGC 59.243 45.455 0.00 0.00 31.83 4.85
287 289 3.064408 CGACATGTCCAAATCACATCTGG 59.936 47.826 20.03 0.00 31.83 3.86
288 290 3.486375 GCGACATGTCCAAATCACATCTG 60.486 47.826 20.03 2.46 31.83 2.90
289 291 2.679837 GCGACATGTCCAAATCACATCT 59.320 45.455 20.03 0.00 31.83 2.90
290 292 2.679837 AGCGACATGTCCAAATCACATC 59.320 45.455 20.03 0.00 31.83 3.06
291 293 2.679837 GAGCGACATGTCCAAATCACAT 59.320 45.455 20.03 0.00 34.67 3.21
292 294 2.076100 GAGCGACATGTCCAAATCACA 58.924 47.619 20.03 0.00 0.00 3.58
293 295 1.061131 CGAGCGACATGTCCAAATCAC 59.939 52.381 20.03 4.42 0.00 3.06
294 296 1.337728 ACGAGCGACATGTCCAAATCA 60.338 47.619 20.03 0.00 0.00 2.57
295 297 1.359848 ACGAGCGACATGTCCAAATC 58.640 50.000 20.03 11.29 0.00 2.17
296 298 1.732259 GAACGAGCGACATGTCCAAAT 59.268 47.619 20.03 3.46 0.00 2.32
297 299 1.144969 GAACGAGCGACATGTCCAAA 58.855 50.000 20.03 0.00 0.00 3.28
298 300 0.032815 TGAACGAGCGACATGTCCAA 59.967 50.000 20.03 0.00 0.00 3.53
299 301 0.246360 ATGAACGAGCGACATGTCCA 59.754 50.000 20.03 10.37 0.00 4.02
300 302 2.203800 TATGAACGAGCGACATGTCC 57.796 50.000 20.03 12.53 0.00 4.02
301 303 4.778842 AAATATGAACGAGCGACATGTC 57.221 40.909 16.21 16.21 0.00 3.06
302 304 5.106712 ACAAAAATATGAACGAGCGACATGT 60.107 36.000 0.00 0.00 0.00 3.21
303 305 5.323900 ACAAAAATATGAACGAGCGACATG 58.676 37.500 13.64 0.00 0.00 3.21
304 306 5.545658 ACAAAAATATGAACGAGCGACAT 57.454 34.783 0.00 4.95 0.00 3.06
305 307 5.351233 AACAAAAATATGAACGAGCGACA 57.649 34.783 0.00 0.00 0.00 4.35
306 308 6.669485 AAAACAAAAATATGAACGAGCGAC 57.331 33.333 0.00 0.00 0.00 5.19
307 309 6.345408 GCAAAAACAAAAATATGAACGAGCGA 60.345 34.615 0.00 0.00 0.00 4.93
308 310 5.778345 GCAAAAACAAAAATATGAACGAGCG 59.222 36.000 0.00 0.00 0.00 5.03
309 311 6.644775 TGCAAAAACAAAAATATGAACGAGC 58.355 32.000 0.00 0.00 0.00 5.03
310 312 8.327429 AGTTGCAAAAACAAAAATATGAACGAG 58.673 29.630 0.00 0.00 0.00 4.18
311 313 8.190888 AGTTGCAAAAACAAAAATATGAACGA 57.809 26.923 0.00 0.00 0.00 3.85
312 314 8.819152 AAGTTGCAAAAACAAAAATATGAACG 57.181 26.923 0.00 0.00 0.00 3.95
313 315 9.986833 AGAAGTTGCAAAAACAAAAATATGAAC 57.013 25.926 0.00 0.00 0.00 3.18
315 317 9.598517 AGAGAAGTTGCAAAAACAAAAATATGA 57.401 25.926 0.00 0.00 0.00 2.15
320 322 9.871299 GTTTTAGAGAAGTTGCAAAAACAAAAA 57.129 25.926 0.00 0.33 37.00 1.94
321 323 9.267084 AGTTTTAGAGAAGTTGCAAAAACAAAA 57.733 25.926 16.94 8.68 38.59 2.44
322 324 8.825667 AGTTTTAGAGAAGTTGCAAAAACAAA 57.174 26.923 16.94 4.18 38.59 2.83
4267 4635 1.474143 GCTGCTTCCAGATGGAGGTAC 60.474 57.143 12.08 0.00 46.36 3.34
4268 4636 0.833287 GCTGCTTCCAGATGGAGGTA 59.167 55.000 12.08 7.16 46.36 3.08
4475 4844 6.416415 TCCCAAAGTATTAATCGCCTGTTTA 58.584 36.000 0.00 0.00 0.00 2.01
4484 4853 7.259290 TGCTTCGAATCCCAAAGTATTAATC 57.741 36.000 0.00 0.00 0.00 1.75
4520 4890 5.535753 AAAATGTTAGTGCCTTGCTCTTT 57.464 34.783 0.00 0.00 34.22 2.52
4605 4975 2.238521 GGGTTCATTCCTGCACTTCAA 58.761 47.619 0.00 0.00 0.00 2.69
4624 4994 4.749099 GCTCTGCAATTAGAGTACTCATGG 59.251 45.833 24.44 9.18 44.77 3.66
4688 5058 5.071653 ACATTATCCCCAATTTACCCATTGC 59.928 40.000 0.00 0.00 33.42 3.56
4689 5059 6.745794 ACATTATCCCCAATTTACCCATTG 57.254 37.500 0.00 0.00 34.39 2.82
4690 5060 6.328934 GGAACATTATCCCCAATTTACCCATT 59.671 38.462 0.00 0.00 33.05 3.16
4766 5136 7.346751 AGCAATTAAGAAACAGAAGTTCCAA 57.653 32.000 0.00 0.00 36.84 3.53
4771 5141 7.771183 TGTTCAAGCAATTAAGAAACAGAAGT 58.229 30.769 0.00 0.00 0.00 3.01
4781 5151 9.039870 TGTAACCATTTTGTTCAAGCAATTAAG 57.960 29.630 0.00 0.00 0.00 1.85
4794 5164 5.937111 AGGACTAGTGTGTAACCATTTTGT 58.063 37.500 0.00 0.00 34.36 2.83
4795 5165 6.877611 AAGGACTAGTGTGTAACCATTTTG 57.122 37.500 0.00 0.00 34.36 2.44
4864 5234 8.537858 GTTAACCTTTAGAAGATACCTCTGGAA 58.462 37.037 0.00 0.00 0.00 3.53
4924 5294 4.515567 GGCCAACAATAGCAGGAGTTATAC 59.484 45.833 0.00 0.00 0.00 1.47
4962 5332 7.120579 AGTGCTCGTAAACATCCAAATAAATCA 59.879 33.333 0.00 0.00 0.00 2.57
5023 5393 0.770557 TTAGGGTCCAGTGGGTGCTT 60.771 55.000 9.92 0.00 34.93 3.91
5129 5499 8.608185 AACCAATTTATTCCCATGTTGTCTAT 57.392 30.769 0.00 0.00 0.00 1.98
5130 5500 7.671819 TGAACCAATTTATTCCCATGTTGTCTA 59.328 33.333 0.00 0.00 0.00 2.59
5131 5501 6.496565 TGAACCAATTTATTCCCATGTTGTCT 59.503 34.615 0.00 0.00 0.00 3.41
5132 5502 6.696411 TGAACCAATTTATTCCCATGTTGTC 58.304 36.000 0.00 0.00 0.00 3.18
5133 5503 6.678568 TGAACCAATTTATTCCCATGTTGT 57.321 33.333 0.00 0.00 0.00 3.32
5216 5587 5.702670 CACTAGACACTTTCCATGTTGACAT 59.297 40.000 0.00 0.00 36.96 3.06
5217 5588 5.056480 CACTAGACACTTTCCATGTTGACA 58.944 41.667 0.00 0.00 0.00 3.58
5314 5686 2.370189 CTCCCCTGGACAATGGAGATAC 59.630 54.545 9.60 0.00 45.93 2.24
5422 5794 6.645415 ACTTACAAATGAAGTGGTCTCTAACG 59.355 38.462 0.00 0.00 35.80 3.18
5454 5826 4.693283 TCAGAGCCATTATAAACAGGTCG 58.307 43.478 0.00 0.00 0.00 4.79
5491 5863 2.483889 GCTAGAAGAATCGGAACCCCTG 60.484 54.545 0.00 0.00 0.00 4.45
5492 5864 1.763545 GCTAGAAGAATCGGAACCCCT 59.236 52.381 0.00 0.00 0.00 4.79
5535 5909 0.381801 ACCAGCAGAAACAAGCAACG 59.618 50.000 0.00 0.00 0.00 4.10
5556 5930 2.259618 CGGTGGACTCGATTGTAACTG 58.740 52.381 0.00 0.00 0.00 3.16
5579 5953 2.052690 GCACCTCTGGCGGTAGAGA 61.053 63.158 11.50 0.00 45.61 3.10
5617 5991 2.690497 CTCGCACTTCTCCTCAAGGATA 59.310 50.000 0.00 0.00 44.46 2.59
5706 6080 2.943033 AGCCTCAACACAACACAGTAAC 59.057 45.455 0.00 0.00 0.00 2.50
5709 6083 1.340017 ACAGCCTCAACACAACACAGT 60.340 47.619 0.00 0.00 0.00 3.55
5712 6086 1.472480 ACAACAGCCTCAACACAACAC 59.528 47.619 0.00 0.00 0.00 3.32
5713 6087 1.472082 CACAACAGCCTCAACACAACA 59.528 47.619 0.00 0.00 0.00 3.33
5714 6088 1.472480 ACACAACAGCCTCAACACAAC 59.528 47.619 0.00 0.00 0.00 3.32
5715 6089 1.832883 ACACAACAGCCTCAACACAA 58.167 45.000 0.00 0.00 0.00 3.33
5716 6090 1.472082 CAACACAACAGCCTCAACACA 59.528 47.619 0.00 0.00 0.00 3.72
5717 6091 1.742831 TCAACACAACAGCCTCAACAC 59.257 47.619 0.00 0.00 0.00 3.32
5718 6092 2.016318 CTCAACACAACAGCCTCAACA 58.984 47.619 0.00 0.00 0.00 3.33
5719 6093 1.334869 CCTCAACACAACAGCCTCAAC 59.665 52.381 0.00 0.00 0.00 3.18
5720 6094 1.211703 TCCTCAACACAACAGCCTCAA 59.788 47.619 0.00 0.00 0.00 3.02
5721 6095 0.836606 TCCTCAACACAACAGCCTCA 59.163 50.000 0.00 0.00 0.00 3.86
5722 6096 1.230324 GTCCTCAACACAACAGCCTC 58.770 55.000 0.00 0.00 0.00 4.70
5723 6097 0.532862 CGTCCTCAACACAACAGCCT 60.533 55.000 0.00 0.00 0.00 4.58
5724 6098 0.531974 TCGTCCTCAACACAACAGCC 60.532 55.000 0.00 0.00 0.00 4.85
5725 6099 1.261619 CTTCGTCCTCAACACAACAGC 59.738 52.381 0.00 0.00 0.00 4.40
5726 6100 1.867233 CCTTCGTCCTCAACACAACAG 59.133 52.381 0.00 0.00 0.00 3.16
5745 6119 8.782144 CAGTAACCTATACTAGTACACTAAGCC 58.218 40.741 4.31 0.00 0.00 4.35
5784 6158 4.744795 ATGTGACTCCAGAGTATTGGAC 57.255 45.455 0.00 0.00 42.24 4.02
5849 6267 2.037251 TCTGAGTTTCCAAGTTCCTCCG 59.963 50.000 0.00 0.00 0.00 4.63
5872 6290 2.284515 ATTCCAGATCCAACGGCCCC 62.285 60.000 0.00 0.00 0.00 5.80
5883 6301 2.799017 TCAGCAGCACAAATTCCAGAT 58.201 42.857 0.00 0.00 0.00 2.90
5895 6313 2.786777 ACACAGATTCAATCAGCAGCA 58.213 42.857 0.00 0.00 0.00 4.41
5912 6330 1.003652 GGTGCTTGCATGCAAAAACAC 60.004 47.619 32.47 32.47 45.12 3.32
5913 6331 1.297664 GGTGCTTGCATGCAAAAACA 58.702 45.000 31.37 25.30 45.12 2.83
5914 6332 0.587768 GGGTGCTTGCATGCAAAAAC 59.412 50.000 31.37 28.29 45.12 2.43
6000 6423 5.779241 TCTAATGTCCAATTCTTCCACCT 57.221 39.130 0.00 0.00 0.00 4.00
6007 6430 6.489361 GGATCTGCAATCTAATGTCCAATTCT 59.511 38.462 8.23 0.00 0.00 2.40
6010 6433 5.698104 TGGATCTGCAATCTAATGTCCAAT 58.302 37.500 8.23 0.00 32.02 3.16
6015 6438 5.452255 ACCATTGGATCTGCAATCTAATGT 58.548 37.500 26.58 19.12 42.05 2.71
6038 6461 7.172019 GTGAAAACTTAGAAACTCCAATACGGA 59.828 37.037 0.00 0.00 43.61 4.69
6074 6497 2.416893 GAGAAAGCATCTCGTGGAAACC 59.583 50.000 4.07 0.00 44.89 3.27
6084 6507 2.240921 GGAGGAAAGGGAGAAAGCATCT 59.759 50.000 0.00 0.00 42.61 2.90
6085 6508 2.649190 GGAGGAAAGGGAGAAAGCATC 58.351 52.381 0.00 0.00 0.00 3.91
6086 6509 1.065126 CGGAGGAAAGGGAGAAAGCAT 60.065 52.381 0.00 0.00 0.00 3.79
6087 6510 0.324943 CGGAGGAAAGGGAGAAAGCA 59.675 55.000 0.00 0.00 0.00 3.91
6088 6511 0.325272 ACGGAGGAAAGGGAGAAAGC 59.675 55.000 0.00 0.00 0.00 3.51
6089 6512 2.861147 AACGGAGGAAAGGGAGAAAG 57.139 50.000 0.00 0.00 0.00 2.62
6090 6513 3.975168 CTAACGGAGGAAAGGGAGAAA 57.025 47.619 0.00 0.00 0.00 2.52
6102 6525 1.067071 GGTGGAGTTGACCTAACGGAG 60.067 57.143 0.00 0.00 44.15 4.63
6103 6526 0.971386 GGTGGAGTTGACCTAACGGA 59.029 55.000 0.00 0.00 44.15 4.69
6104 6527 0.389426 CGGTGGAGTTGACCTAACGG 60.389 60.000 0.00 0.00 44.15 4.44
6105 6528 1.012486 GCGGTGGAGTTGACCTAACG 61.012 60.000 0.00 0.00 44.15 3.18
6146 6569 2.673258 AGGGACAAAAACCGGACAAAT 58.327 42.857 9.46 0.00 0.00 2.32
6165 6589 1.361197 ACCCCAAATCCCTACCCAAAG 59.639 52.381 0.00 0.00 0.00 2.77
6181 6605 2.687566 ATCCCAGGACACGACCCC 60.688 66.667 0.00 0.00 0.00 4.95
6225 6668 0.965439 CGGACAAGATGGGGCAAAAA 59.035 50.000 0.00 0.00 0.00 1.94
6397 6842 6.186957 TGGCAACCAATAGATGTATTTGTCT 58.813 36.000 0.49 0.00 0.00 3.41
6445 6890 9.288576 ACTGATGTGAATCTTCAAAATGACTTA 57.711 29.630 0.00 0.00 39.21 2.24
6514 6959 0.394352 ATCAAGACCCGGCCACATTC 60.394 55.000 2.24 0.00 0.00 2.67
6532 6977 4.141869 GGTGAAAATATTGAGCCCTTGCAT 60.142 41.667 0.00 0.00 41.13 3.96
6537 6982 4.934356 TCAAGGTGAAAATATTGAGCCCT 58.066 39.130 0.00 0.00 0.00 5.19
6583 7028 2.452105 GAGGACGAACGTAATGAGAGC 58.548 52.381 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.