Multiple sequence alignment - TraesCS3D01G435600

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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 TraesCS3D01G435600 chr3D 100.000 2975 0 0 1 2975 547780222 547777248 0.000000e+00 5494
1 TraesCS3D01G435600 chr3D 92.590 1363 59 16 772 2116 547632802 547634140 0.000000e+00 1919
2 TraesCS3D01G435600 chr3D 90.931 408 30 4 194 594 454744552 454744145 2.610000e-150 542
3 TraesCS3D01G435600 chr3D 95.783 166 7 0 2198 2363 547776295 547776460 4.890000e-68 268
4 TraesCS3D01G435600 chr3A 92.217 1439 59 22 772 2180 684640000 684641415 0.000000e+00 1988
5 TraesCS3D01G435600 chr3A 90.082 1462 60 24 772 2185 684698206 684696782 0.000000e+00 1818
6 TraesCS3D01G435600 chr3A 87.374 895 59 17 1236 2113 13823439 13822582 0.000000e+00 977
7 TraesCS3D01G435600 chr3A 88.620 413 30 9 194 597 675122441 675122037 1.240000e-133 486
8 TraesCS3D01G435600 chr3A 95.420 131 6 0 1 131 684698577 684698447 3.000000e-50 209
9 TraesCS3D01G435600 chr3B 90.173 1445 81 24 772 2185 725275939 725277353 0.000000e+00 1825
10 TraesCS3D01G435600 chr3B 88.596 1403 74 21 772 2116 725182031 725183405 0.000000e+00 1626
11 TraesCS3D01G435600 chr3B 90.526 475 40 1 2499 2973 819195124 819194655 9.060000e-175 623
12 TraesCS3D01G435600 chr3B 89.024 164 18 0 2200 2363 819212437 819212274 1.400000e-48 204
13 TraesCS3D01G435600 chr3B 84.868 152 10 8 624 769 725275764 725275908 1.110000e-29 141
14 TraesCS3D01G435600 chr3B 81.622 185 9 11 602 769 725181823 725181999 2.410000e-26 130
15 TraesCS3D01G435600 chr6A 98.560 486 7 0 2490 2975 610228885 610228400 0.000000e+00 859
16 TraesCS3D01G435600 chr6A 94.152 171 9 1 2193 2363 610227476 610227645 2.940000e-65 259
17 TraesCS3D01G435600 chr6A 93.373 166 11 0 2198 2363 610232552 610232387 2.290000e-61 246
18 TraesCS3D01G435600 chr6A 98.095 105 2 0 2390 2494 610231841 610231737 1.820000e-42 183
19 TraesCS3D01G435600 chr5D 98.148 486 9 0 2490 2975 386946304 386945819 0.000000e+00 848
20 TraesCS3D01G435600 chr5D 89.976 409 32 8 194 594 389749883 389749476 1.220000e-143 520
21 TraesCS3D01G435600 chr5D 96.250 160 6 0 2204 2363 386944862 386945021 2.270000e-66 263
22 TraesCS3D01G435600 chr5D 94.545 165 9 0 2199 2363 386950689 386950525 3.810000e-64 255
23 TraesCS3D01G435600 chr5D 99.074 108 1 0 2387 2494 386949982 386949875 8.410000e-46 195
24 TraesCS3D01G435600 chr6D 91.116 484 43 0 2490 2973 365443777 365444260 0.000000e+00 656
25 TraesCS3D01G435600 chr6D 88.415 164 19 0 2200 2363 365445971 365445808 6.500000e-47 198
26 TraesCS3D01G435600 chr2A 88.911 496 43 6 2490 2973 748175221 748175716 4.240000e-168 601
27 TraesCS3D01G435600 chr4D 91.463 410 25 6 194 594 507722080 507721672 3.350000e-154 555
28 TraesCS3D01G435600 chr7D 90.441 408 29 8 194 594 596879556 596879960 2.030000e-146 529
29 TraesCS3D01G435600 chr7D 88.010 417 35 9 192 594 599799619 599800034 2.070000e-131 479
30 TraesCS3D01G435600 chr7A 88.539 445 13 7 2531 2975 367014685 367014279 3.420000e-139 505
31 TraesCS3D01G435600 chr7A 93.902 164 10 0 2200 2363 367013311 367013474 6.370000e-62 248
32 TraesCS3D01G435600 chr7A 93.293 164 11 0 2200 2363 367016472 367016309 2.960000e-60 243
33 TraesCS3D01G435600 chr7A 96.296 108 4 0 2387 2494 367015771 367015664 8.470000e-41 178
34 TraesCS3D01G435600 chr5B 86.626 486 21 13 2490 2975 327191051 327191492 5.730000e-137 497
35 TraesCS3D01G435600 chr5B 93.269 104 5 2 2387 2489 327187396 327187498 5.140000e-33 152
36 TraesCS3D01G435600 chr7B 88.753 409 36 5 195 594 716975760 716976167 2.660000e-135 492
37 TraesCS3D01G435600 chr7B 88.509 409 38 5 195 594 716701459 716701051 1.240000e-133 486
38 TraesCS3D01G435600 chr1A 88.321 411 36 8 194 595 65807738 65808145 1.600000e-132 483


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 TraesCS3D01G435600 chr3D 547777248 547780222 2974 True 5494.000000 5494 100.000000 1 2975 1 chr3D.!!$R2 2974
1 TraesCS3D01G435600 chr3D 547632802 547634140 1338 False 1919.000000 1919 92.590000 772 2116 1 chr3D.!!$F1 1344
2 TraesCS3D01G435600 chr3A 684640000 684641415 1415 False 1988.000000 1988 92.217000 772 2180 1 chr3A.!!$F1 1408
3 TraesCS3D01G435600 chr3A 684696782 684698577 1795 True 1013.500000 1818 92.751000 1 2185 2 chr3A.!!$R3 2184
4 TraesCS3D01G435600 chr3A 13822582 13823439 857 True 977.000000 977 87.374000 1236 2113 1 chr3A.!!$R1 877
5 TraesCS3D01G435600 chr3B 725275764 725277353 1589 False 983.000000 1825 87.520500 624 2185 2 chr3B.!!$F2 1561
6 TraesCS3D01G435600 chr3B 725181823 725183405 1582 False 878.000000 1626 85.109000 602 2116 2 chr3B.!!$F1 1514
7 TraesCS3D01G435600 chr6A 610228400 610232552 4152 True 429.333333 859 96.676000 2198 2975 3 chr6A.!!$R1 777
8 TraesCS3D01G435600 chr5D 386945819 386950689 4870 True 432.666667 848 97.255667 2199 2975 3 chr5D.!!$R2 776
9 TraesCS3D01G435600 chr7A 367014279 367016472 2193 True 308.666667 505 92.709333 2200 2975 3 chr7A.!!$R1 775
10 TraesCS3D01G435600 chr5B 327187396 327191492 4096 False 324.500000 497 89.947500 2387 2975 2 chr5B.!!$F1 588

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
148 149 0.032912 TCCATACTACCTGTCCCGCA 60.033 55.0 0.0 0.0 0.0 5.69 F
161 162 0.036388 TCCCGCACAAATCTCTCCAC 60.036 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1887 0.384309 TTAGGGCTCGTGCGATAGTG 59.616 55.0 3.02 0.0 40.82 2.74 R
2086 2280 0.396811 ACCACTTGGCACTGAGTACC 59.603 55.0 0.00 0.0 39.32 3.34 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
32 33 4.409570 CAGTTCCTTCATTCAATGCGAAG 58.590 43.478 0.00 0.00 36.95 3.79
52 53 2.171448 AGGTACATTGATCACTGCCCTC 59.829 50.000 12.62 1.56 0.00 4.30
115 116 3.593442 TTTCACCTGGTGATTTGACCT 57.407 42.857 28.76 0.00 42.40 3.85
136 137 9.997172 TGACCTATCATATACATTCTCCATACT 57.003 33.333 0.00 0.00 0.00 2.12
142 143 9.775539 ATCATATACATTCTCCATACTACCTGT 57.224 33.333 0.00 0.00 0.00 4.00
143 144 9.244292 TCATATACATTCTCCATACTACCTGTC 57.756 37.037 0.00 0.00 0.00 3.51
144 145 6.919775 ATACATTCTCCATACTACCTGTCC 57.080 41.667 0.00 0.00 0.00 4.02
145 146 3.967987 ACATTCTCCATACTACCTGTCCC 59.032 47.826 0.00 0.00 0.00 4.46
146 147 2.359981 TCTCCATACTACCTGTCCCG 57.640 55.000 0.00 0.00 0.00 5.14
147 148 0.674534 CTCCATACTACCTGTCCCGC 59.325 60.000 0.00 0.00 0.00 6.13
148 149 0.032912 TCCATACTACCTGTCCCGCA 60.033 55.000 0.00 0.00 0.00 5.69
149 150 0.104304 CCATACTACCTGTCCCGCAC 59.896 60.000 0.00 0.00 0.00 5.34
150 151 0.821517 CATACTACCTGTCCCGCACA 59.178 55.000 0.00 0.00 0.00 4.57
151 152 1.206132 CATACTACCTGTCCCGCACAA 59.794 52.381 0.00 0.00 33.31 3.33
161 162 0.036388 TCCCGCACAAATCTCTCCAC 60.036 55.000 0.00 0.00 0.00 4.02
177 178 1.554836 CCACACCATGGGCACATTTA 58.445 50.000 18.09 0.00 45.95 1.40
178 179 2.109774 CCACACCATGGGCACATTTAT 58.890 47.619 18.09 0.00 45.95 1.40
180 181 3.055240 CCACACCATGGGCACATTTATTT 60.055 43.478 18.09 0.00 45.95 1.40
181 182 4.565236 CCACACCATGGGCACATTTATTTT 60.565 41.667 18.09 0.00 45.95 1.82
182 183 4.392445 CACACCATGGGCACATTTATTTTG 59.608 41.667 18.09 2.50 34.35 2.44
183 184 4.041444 ACACCATGGGCACATTTATTTTGT 59.959 37.500 18.09 3.20 34.35 2.83
184 185 5.247110 ACACCATGGGCACATTTATTTTGTA 59.753 36.000 18.09 0.00 34.35 2.41
186 187 6.091986 CACCATGGGCACATTTATTTTGTAAC 59.908 38.462 18.09 0.00 34.35 2.50
187 188 6.169094 CCATGGGCACATTTATTTTGTAACA 58.831 36.000 0.00 0.00 34.35 2.41
188 189 6.652481 CCATGGGCACATTTATTTTGTAACAA 59.348 34.615 0.00 0.00 34.35 2.83
189 190 7.360776 CCATGGGCACATTTATTTTGTAACAAC 60.361 37.037 0.00 0.00 34.35 3.32
191 192 7.275920 TGGGCACATTTATTTTGTAACAACTT 58.724 30.769 0.00 0.00 0.00 2.66
192 193 7.225538 TGGGCACATTTATTTTGTAACAACTTG 59.774 33.333 0.00 0.00 0.00 3.16
193 194 7.307692 GGGCACATTTATTTTGTAACAACTTGG 60.308 37.037 0.00 0.00 0.00 3.61
194 195 7.307692 GGCACATTTATTTTGTAACAACTTGGG 60.308 37.037 0.00 0.00 0.00 4.12
195 196 7.439655 GCACATTTATTTTGTAACAACTTGGGA 59.560 33.333 0.00 0.00 0.00 4.37
196 197 8.977505 CACATTTATTTTGTAACAACTTGGGAG 58.022 33.333 0.00 0.00 0.00 4.30
197 198 8.147704 ACATTTATTTTGTAACAACTTGGGAGG 58.852 33.333 0.00 0.00 0.00 4.30
198 199 6.658188 TTATTTTGTAACAACTTGGGAGGG 57.342 37.500 0.00 0.00 0.00 4.30
199 200 2.668144 TTGTAACAACTTGGGAGGGG 57.332 50.000 0.00 0.00 0.00 4.79
200 201 1.822425 TGTAACAACTTGGGAGGGGA 58.178 50.000 0.00 0.00 0.00 4.81
201 202 2.136863 TGTAACAACTTGGGAGGGGAA 58.863 47.619 0.00 0.00 0.00 3.97
202 203 2.158579 TGTAACAACTTGGGAGGGGAAC 60.159 50.000 0.00 0.00 0.00 3.62
203 204 1.231963 AACAACTTGGGAGGGGAACT 58.768 50.000 0.00 0.00 0.00 3.01
204 205 1.231963 ACAACTTGGGAGGGGAACTT 58.768 50.000 0.00 0.00 0.00 2.66
205 206 1.573857 ACAACTTGGGAGGGGAACTTT 59.426 47.619 0.00 0.00 0.00 2.66
206 207 2.023404 ACAACTTGGGAGGGGAACTTTT 60.023 45.455 0.00 0.00 0.00 2.27
207 208 2.365293 CAACTTGGGAGGGGAACTTTTG 59.635 50.000 0.00 0.00 0.00 2.44
208 209 1.133167 ACTTGGGAGGGGAACTTTTGG 60.133 52.381 0.00 0.00 0.00 3.28
209 210 0.938192 TTGGGAGGGGAACTTTTGGT 59.062 50.000 0.00 0.00 0.00 3.67
210 211 0.481128 TGGGAGGGGAACTTTTGGTC 59.519 55.000 0.00 0.00 34.82 4.02
211 212 0.778083 GGGAGGGGAACTTTTGGTCT 59.222 55.000 0.00 0.00 36.15 3.85
212 213 1.990327 GGGAGGGGAACTTTTGGTCTA 59.010 52.381 0.00 0.00 36.15 2.59
213 214 2.581246 GGGAGGGGAACTTTTGGTCTAT 59.419 50.000 0.00 0.00 36.15 1.98
214 215 3.621558 GGAGGGGAACTTTTGGTCTATG 58.378 50.000 0.00 0.00 36.15 2.23
215 216 3.621558 GAGGGGAACTTTTGGTCTATGG 58.378 50.000 0.00 0.00 36.15 2.74
216 217 2.311841 AGGGGAACTTTTGGTCTATGGG 59.688 50.000 0.00 0.00 36.15 4.00
217 218 2.623239 GGGGAACTTTTGGTCTATGGGG 60.623 54.545 0.00 0.00 36.15 4.96
218 219 2.310647 GGGAACTTTTGGTCTATGGGGA 59.689 50.000 0.00 0.00 36.15 4.81
219 220 3.353557 GGAACTTTTGGTCTATGGGGAC 58.646 50.000 0.00 0.00 36.15 4.46
220 221 3.245122 GGAACTTTTGGTCTATGGGGACA 60.245 47.826 0.00 0.00 39.95 4.02
221 222 4.569865 GGAACTTTTGGTCTATGGGGACAT 60.570 45.833 0.00 0.00 43.22 3.06
236 237 5.285401 TGGGGACATATACACCCTATATGG 58.715 45.833 10.62 0.00 43.72 2.74
237 238 5.017975 TGGGGACATATACACCCTATATGGA 59.982 44.000 0.45 0.00 43.72 3.41
238 239 6.151049 GGGGACATATACACCCTATATGGAT 58.849 44.000 0.45 0.00 42.86 3.41
239 240 6.619852 GGGGACATATACACCCTATATGGATT 59.380 42.308 0.45 0.00 42.86 3.01
240 241 7.128883 GGGGACATATACACCCTATATGGATTT 59.871 40.741 0.45 0.00 42.86 2.17
241 242 8.557450 GGGACATATACACCCTATATGGATTTT 58.443 37.037 0.45 0.00 40.43 1.82
242 243 9.975218 GGACATATACACCCTATATGGATTTTT 57.025 33.333 0.45 0.00 40.43 1.94
316 317 7.875327 AAAGTTGACCTTACATTGTACTTGT 57.125 32.000 0.00 7.12 31.48 3.16
317 318 7.492352 AAGTTGACCTTACATTGTACTTGTC 57.508 36.000 5.46 4.67 0.00 3.18
318 319 6.588204 AGTTGACCTTACATTGTACTTGTCA 58.412 36.000 13.89 13.89 0.00 3.58
319 320 6.706270 AGTTGACCTTACATTGTACTTGTCAG 59.294 38.462 15.87 4.99 33.54 3.51
320 321 6.413783 TGACCTTACATTGTACTTGTCAGA 57.586 37.500 13.89 0.08 0.00 3.27
321 322 6.822442 TGACCTTACATTGTACTTGTCAGAA 58.178 36.000 13.89 0.34 0.00 3.02
322 323 7.276658 TGACCTTACATTGTACTTGTCAGAAA 58.723 34.615 13.89 0.08 0.00 2.52
323 324 7.771361 TGACCTTACATTGTACTTGTCAGAAAA 59.229 33.333 13.89 0.00 0.00 2.29
324 325 8.514330 ACCTTACATTGTACTTGTCAGAAAAA 57.486 30.769 10.46 0.00 0.00 1.94
325 326 9.131791 ACCTTACATTGTACTTGTCAGAAAAAT 57.868 29.630 10.46 0.00 0.00 1.82
326 327 9.965824 CCTTACATTGTACTTGTCAGAAAAATT 57.034 29.630 10.46 0.00 0.00 1.82
330 331 9.301153 ACATTGTACTTGTCAGAAAAATTTCAC 57.699 29.630 8.47 0.07 39.61 3.18
331 332 9.299963 CATTGTACTTGTCAGAAAAATTTCACA 57.700 29.630 8.47 2.51 39.61 3.58
332 333 9.868277 ATTGTACTTGTCAGAAAAATTTCACAA 57.132 25.926 8.47 9.28 39.61 3.33
333 334 9.698309 TTGTACTTGTCAGAAAAATTTCACAAA 57.302 25.926 8.47 0.00 39.61 2.83
334 335 9.698309 TGTACTTGTCAGAAAAATTTCACAAAA 57.302 25.926 8.47 1.15 39.61 2.44
358 359 7.660030 AAAATCCTCCTTTGACTTCTTTTCA 57.340 32.000 0.00 0.00 0.00 2.69
359 360 7.660030 AAATCCTCCTTTGACTTCTTTTCAA 57.340 32.000 0.00 0.00 0.00 2.69
360 361 7.660030 AATCCTCCTTTGACTTCTTTTCAAA 57.340 32.000 0.00 0.00 39.99 2.69
361 362 7.660030 ATCCTCCTTTGACTTCTTTTCAAAA 57.340 32.000 0.00 0.00 41.32 2.44
362 363 7.475137 TCCTCCTTTGACTTCTTTTCAAAAA 57.525 32.000 0.00 0.00 41.32 1.94
389 390 8.504812 GACAAAATTTTGGCCAAAATAATGTG 57.495 30.769 42.61 36.36 46.76 3.21
390 391 8.230472 ACAAAATTTTGGCCAAAATAATGTGA 57.770 26.923 40.10 25.61 46.76 3.58
391 392 8.689972 ACAAAATTTTGGCCAAAATAATGTGAA 58.310 25.926 40.10 25.08 46.76 3.18
392 393 9.694137 CAAAATTTTGGCCAAAATAATGTGAAT 57.306 25.926 42.25 27.72 46.76 2.57
395 396 9.737844 AATTTTGGCCAAAATAATGTGAATAGT 57.262 25.926 42.25 26.12 46.76 2.12
396 397 8.545229 TTTTGGCCAAAATAATGTGAATAGTG 57.455 30.769 34.56 0.00 35.57 2.74
397 398 7.473735 TTGGCCAAAATAATGTGAATAGTGA 57.526 32.000 17.98 0.00 0.00 3.41
398 399 6.862209 TGGCCAAAATAATGTGAATAGTGAC 58.138 36.000 0.61 0.00 0.00 3.67
399 400 6.127479 TGGCCAAAATAATGTGAATAGTGACC 60.127 38.462 0.61 0.00 0.00 4.02
400 401 6.096846 GGCCAAAATAATGTGAATAGTGACCT 59.903 38.462 0.00 0.00 0.00 3.85
401 402 7.284489 GGCCAAAATAATGTGAATAGTGACCTA 59.716 37.037 0.00 0.00 0.00 3.08
402 403 8.850156 GCCAAAATAATGTGAATAGTGACCTAT 58.150 33.333 0.00 0.00 35.33 2.57
438 439 6.959671 TTTTTGTCTTTTTCGCTGTGAAAT 57.040 29.167 16.24 0.00 45.62 2.17
439 440 6.567769 TTTTGTCTTTTTCGCTGTGAAATC 57.432 33.333 16.24 8.74 45.62 2.17
440 441 4.891627 TGTCTTTTTCGCTGTGAAATCA 57.108 36.364 16.24 10.76 45.62 2.57
441 442 5.242069 TGTCTTTTTCGCTGTGAAATCAA 57.758 34.783 16.24 8.53 45.62 2.57
442 443 5.830912 TGTCTTTTTCGCTGTGAAATCAAT 58.169 33.333 16.24 0.00 45.62 2.57
443 444 6.964908 TGTCTTTTTCGCTGTGAAATCAATA 58.035 32.000 16.24 0.00 45.62 1.90
444 445 7.592938 TGTCTTTTTCGCTGTGAAATCAATAT 58.407 30.769 16.24 0.00 45.62 1.28
445 446 8.081633 TGTCTTTTTCGCTGTGAAATCAATATT 58.918 29.630 16.24 0.00 45.62 1.28
446 447 8.368126 GTCTTTTTCGCTGTGAAATCAATATTG 58.632 33.333 16.24 9.29 45.62 1.90
447 448 7.541783 TCTTTTTCGCTGTGAAATCAATATTGG 59.458 33.333 16.24 0.00 45.62 3.16
448 449 4.898829 TCGCTGTGAAATCAATATTGGG 57.101 40.909 15.36 0.00 0.00 4.12
449 450 4.269183 TCGCTGTGAAATCAATATTGGGT 58.731 39.130 15.36 2.30 0.00 4.51
450 451 4.704540 TCGCTGTGAAATCAATATTGGGTT 59.295 37.500 15.36 9.50 0.00 4.11
451 452 5.184864 TCGCTGTGAAATCAATATTGGGTTT 59.815 36.000 15.36 15.25 0.00 3.27
452 453 5.868801 CGCTGTGAAATCAATATTGGGTTTT 59.131 36.000 15.36 12.18 0.00 2.43
453 454 6.368516 CGCTGTGAAATCAATATTGGGTTTTT 59.631 34.615 15.36 10.03 0.00 1.94
476 477 9.602568 TTTTTCGTGGAAATATATACTAGTGCA 57.397 29.630 5.39 0.00 31.34 4.57
477 478 9.602568 TTTTCGTGGAAATATATACTAGTGCAA 57.397 29.630 5.39 0.00 31.34 4.08
478 479 9.602568 TTTCGTGGAAATATATACTAGTGCAAA 57.397 29.630 5.39 0.00 0.00 3.68
479 480 9.602568 TTCGTGGAAATATATACTAGTGCAAAA 57.397 29.630 5.39 0.00 0.00 2.44
480 481 9.256477 TCGTGGAAATATATACTAGTGCAAAAG 57.744 33.333 5.39 0.00 0.00 2.27
481 482 9.042008 CGTGGAAATATATACTAGTGCAAAAGT 57.958 33.333 5.39 7.32 0.00 2.66
491 492 8.904099 ATACTAGTGCAAAAGTAAGTCAAGTT 57.096 30.769 5.39 0.00 32.24 2.66
492 493 7.625828 ACTAGTGCAAAAGTAAGTCAAGTTT 57.374 32.000 0.00 0.00 0.00 2.66
493 494 8.726870 ACTAGTGCAAAAGTAAGTCAAGTTTA 57.273 30.769 0.00 0.00 0.00 2.01
494 495 9.338622 ACTAGTGCAAAAGTAAGTCAAGTTTAT 57.661 29.630 0.00 0.00 0.00 1.40
497 498 8.903820 AGTGCAAAAGTAAGTCAAGTTTATTCT 58.096 29.630 0.00 0.00 0.00 2.40
584 585 9.528489 AATGTATATACAACCAGAAACCAAAGT 57.472 29.630 19.11 0.00 39.99 2.66
585 586 8.330466 TGTATATACAACCAGAAACCAAAGTG 57.670 34.615 13.24 0.00 32.40 3.16
586 587 7.940137 TGTATATACAACCAGAAACCAAAGTGT 59.060 33.333 13.24 0.00 32.40 3.55
587 588 9.439500 GTATATACAACCAGAAACCAAAGTGTA 57.561 33.333 8.05 0.00 0.00 2.90
589 590 7.833285 ATACAACCAGAAACCAAAGTGTATT 57.167 32.000 0.00 0.00 0.00 1.89
590 591 6.538945 ACAACCAGAAACCAAAGTGTATTT 57.461 33.333 0.00 0.00 0.00 1.40
591 592 6.569780 ACAACCAGAAACCAAAGTGTATTTC 58.430 36.000 0.00 0.00 0.00 2.17
592 593 5.784578 ACCAGAAACCAAAGTGTATTTCC 57.215 39.130 0.00 0.00 32.56 3.13
593 594 4.587262 ACCAGAAACCAAAGTGTATTTCCC 59.413 41.667 0.00 0.00 32.56 3.97
594 595 4.832823 CCAGAAACCAAAGTGTATTTCCCT 59.167 41.667 0.00 0.00 32.56 4.20
595 596 6.007703 CCAGAAACCAAAGTGTATTTCCCTA 58.992 40.000 0.00 0.00 32.56 3.53
596 597 6.492087 CCAGAAACCAAAGTGTATTTCCCTAA 59.508 38.462 0.00 0.00 32.56 2.69
597 598 7.368059 CAGAAACCAAAGTGTATTTCCCTAAC 58.632 38.462 0.00 0.00 32.56 2.34
598 599 7.013846 CAGAAACCAAAGTGTATTTCCCTAACA 59.986 37.037 0.00 0.00 32.56 2.41
599 600 7.562088 AGAAACCAAAGTGTATTTCCCTAACAA 59.438 33.333 0.00 0.00 32.56 2.83
600 601 6.894339 ACCAAAGTGTATTTCCCTAACAAG 57.106 37.500 0.00 0.00 0.00 3.16
629 641 6.816136 TCTTTCTTAGAGATGTCACACACAA 58.184 36.000 0.00 0.00 38.97 3.33
639 651 2.170397 TGTCACACACAATGAGGTCACT 59.830 45.455 0.00 0.00 29.30 3.41
655 668 0.455464 CACTCATGCATGCAACACCG 60.455 55.000 26.68 13.61 0.00 4.94
666 679 1.654220 CAACACCGAGCCCAAACAG 59.346 57.895 0.00 0.00 0.00 3.16
667 680 1.528309 AACACCGAGCCCAAACAGG 60.528 57.895 0.00 0.00 37.03 4.00
719 736 5.440234 AAGGTGCTAGTCATATGTAGTCG 57.560 43.478 1.90 0.00 0.00 4.18
769 793 6.820335 TCGAACCTTGTCTGATGATCATAAT 58.180 36.000 8.54 0.00 0.00 1.28
770 794 6.925718 TCGAACCTTGTCTGATGATCATAATC 59.074 38.462 8.54 0.00 0.00 1.75
828 885 5.234329 ACCGCACAATATATTCTTTGTCTCG 59.766 40.000 0.00 0.00 33.93 4.04
873 933 5.120363 CGTTTAGTTGGCCTTCTCTTCTTAC 59.880 44.000 3.32 0.00 0.00 2.34
874 934 6.231951 GTTTAGTTGGCCTTCTCTTCTTACT 58.768 40.000 3.32 0.00 0.00 2.24
875 935 4.984146 AGTTGGCCTTCTCTTCTTACTT 57.016 40.909 3.32 0.00 0.00 2.24
876 936 5.311844 AGTTGGCCTTCTCTTCTTACTTT 57.688 39.130 3.32 0.00 0.00 2.66
889 949 3.404899 TCTTACTTTTAAGCACCCCACG 58.595 45.455 0.00 0.00 35.53 4.94
890 950 2.934886 TACTTTTAAGCACCCCACGT 57.065 45.000 0.00 0.00 0.00 4.49
921 984 1.207488 CCATCTCCAACCCCACCTCA 61.207 60.000 0.00 0.00 0.00 3.86
959 1035 8.854979 TCATTGTTCAAAGTTCAAACACATAG 57.145 30.769 3.25 0.00 32.94 2.23
1077 1205 2.609046 GCAGGAGCCCTTCTTCCTA 58.391 57.895 0.00 0.00 33.58 2.94
1559 1726 2.152699 CCTACGTGCAAGACTCGCG 61.153 63.158 6.65 0.00 42.46 5.87
1752 1925 4.100189 CCTAAGAACTTCCATGAGGACGAT 59.900 45.833 0.00 0.00 45.73 3.73
1757 1930 3.099905 ACTTCCATGAGGACGATGAGAA 58.900 45.455 0.00 0.00 45.73 2.87
1918 2091 1.299468 GTGAGCGCCGACATAGAGG 60.299 63.158 2.29 0.00 0.00 3.69
1919 2092 1.753078 TGAGCGCCGACATAGAGGT 60.753 57.895 2.29 0.00 0.00 3.85
1979 2152 0.179111 CTCGGTGGCTGCTAATCGAA 60.179 55.000 11.24 0.00 0.00 3.71
1980 2153 0.464036 TCGGTGGCTGCTAATCGAAT 59.536 50.000 8.40 0.00 0.00 3.34
1981 2154 1.684450 TCGGTGGCTGCTAATCGAATA 59.316 47.619 8.40 0.00 0.00 1.75
1982 2155 2.101750 TCGGTGGCTGCTAATCGAATAA 59.898 45.455 8.40 0.00 0.00 1.40
1983 2156 3.067106 CGGTGGCTGCTAATCGAATAAT 58.933 45.455 0.00 0.00 0.00 1.28
1984 2157 3.120546 CGGTGGCTGCTAATCGAATAATG 60.121 47.826 0.00 0.00 0.00 1.90
1985 2158 3.189287 GGTGGCTGCTAATCGAATAATGG 59.811 47.826 0.00 0.00 0.00 3.16
1986 2159 4.065088 GTGGCTGCTAATCGAATAATGGA 58.935 43.478 0.00 0.00 0.00 3.41
2056 2249 3.391049 ACCTCTACGTTGCTCTGTTTTC 58.609 45.455 0.00 0.00 0.00 2.29
2078 2272 4.461431 TCGTTGAGTAGTTGCTCATAGGAA 59.539 41.667 0.75 0.00 43.99 3.36
2086 2280 1.348008 TGCTCATAGGAAGGGCCCTG 61.348 60.000 29.50 13.36 37.10 4.45
2105 2299 0.396811 GGTACTCAGTGCCAAGTGGT 59.603 55.000 7.13 0.00 38.20 4.16
2188 2392 9.979578 ATTGATTTGTTCTTTATGTGTTAAGCA 57.020 25.926 0.00 0.00 0.00 3.91
2189 2393 9.462174 TTGATTTGTTCTTTATGTGTTAAGCAG 57.538 29.630 0.00 0.00 0.00 4.24
2190 2394 7.594758 TGATTTGTTCTTTATGTGTTAAGCAGC 59.405 33.333 0.00 0.00 0.00 5.25
2191 2395 5.371115 TGTTCTTTATGTGTTAAGCAGCC 57.629 39.130 0.00 0.00 0.00 4.85
2192 2396 4.083537 TGTTCTTTATGTGTTAAGCAGCCG 60.084 41.667 0.00 0.00 0.00 5.52
2193 2397 3.006940 TCTTTATGTGTTAAGCAGCCGG 58.993 45.455 0.00 0.00 0.00 6.13
2194 2398 2.772077 TTATGTGTTAAGCAGCCGGA 57.228 45.000 5.05 0.00 0.00 5.14
2195 2399 2.772077 TATGTGTTAAGCAGCCGGAA 57.228 45.000 5.05 0.00 0.00 4.30
2196 2400 1.165270 ATGTGTTAAGCAGCCGGAAC 58.835 50.000 5.05 0.00 0.00 3.62
2210 2414 3.071167 AGCCGGAACAAGAGGTAATATCC 59.929 47.826 5.05 0.00 0.00 2.59
2230 2434 1.478654 CCTGGTGGTGCCTAAACTTGT 60.479 52.381 0.00 0.00 38.35 3.16
2235 2439 1.771854 TGGTGCCTAAACTTGTCCTGA 59.228 47.619 0.00 0.00 0.00 3.86
2248 2452 5.192927 ACTTGTCCTGAATGTTCACTTTGA 58.807 37.500 0.00 0.00 32.90 2.69
2271 2475 8.630054 TGATGCCTAAACTTGTAAAATACACT 57.370 30.769 0.00 0.00 38.63 3.55
2366 2570 4.361253 GCTTGACAGCGTGGAAGA 57.639 55.556 0.00 0.00 35.91 2.87
2367 2571 2.616969 GCTTGACAGCGTGGAAGAA 58.383 52.632 0.00 0.00 35.91 2.52
2369 2573 1.873903 GCTTGACAGCGTGGAAGAAGA 60.874 52.381 0.00 0.00 35.91 2.87
2370 2574 2.483876 CTTGACAGCGTGGAAGAAGAA 58.516 47.619 0.00 0.00 0.00 2.52
2371 2575 2.839486 TGACAGCGTGGAAGAAGAAT 57.161 45.000 0.00 0.00 0.00 2.40
2373 2577 2.300152 TGACAGCGTGGAAGAAGAATCT 59.700 45.455 0.00 0.00 37.57 2.40
2376 2580 4.894784 ACAGCGTGGAAGAAGAATCTTTA 58.105 39.130 0.00 0.00 45.91 1.85
2382 3105 6.030228 CGTGGAAGAAGAATCTTTATTTGGC 58.970 40.000 0.00 0.00 45.91 4.52
2384 3107 6.153510 GTGGAAGAAGAATCTTTATTTGGCCT 59.846 38.462 3.32 0.00 45.91 5.19
2385 3108 6.725834 TGGAAGAAGAATCTTTATTTGGCCTT 59.274 34.615 3.32 0.00 45.91 4.35
2961 7354 4.582869 TGATGTTTGGACCTGATTCAGAG 58.417 43.478 15.36 7.77 32.44 3.35
2962 7355 3.423539 TGTTTGGACCTGATTCAGAGG 57.576 47.619 15.36 2.81 32.44 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.565841 GAGGGCAGTGATCAATGTACC 58.434 52.381 22.89 22.88 0.00 3.34
42 43 3.113514 TTTGTGGCGAGGGCAGTGA 62.114 57.895 0.00 0.00 42.47 3.41
52 53 0.800300 GTTGGTGTGTGTTTGTGGCG 60.800 55.000 0.00 0.00 0.00 5.69
92 93 4.342092 AGGTCAAATCACCAGGTGAAAAAG 59.658 41.667 26.53 15.73 45.96 2.27
131 132 0.821517 TGTGCGGGACAGGTAGTATG 59.178 55.000 0.00 0.00 0.00 2.39
132 133 1.563924 TTGTGCGGGACAGGTAGTAT 58.436 50.000 1.81 0.00 35.44 2.12
133 134 1.340088 TTTGTGCGGGACAGGTAGTA 58.660 50.000 1.81 0.00 35.44 1.82
134 135 0.690762 ATTTGTGCGGGACAGGTAGT 59.309 50.000 1.81 0.00 35.44 2.73
135 136 1.066143 AGATTTGTGCGGGACAGGTAG 60.066 52.381 1.81 0.00 35.44 3.18
136 137 0.981183 AGATTTGTGCGGGACAGGTA 59.019 50.000 1.81 0.00 35.44 3.08
137 138 0.321653 GAGATTTGTGCGGGACAGGT 60.322 55.000 1.81 0.00 35.44 4.00
138 139 0.036010 AGAGATTTGTGCGGGACAGG 60.036 55.000 1.81 0.00 35.44 4.00
139 140 1.363744 GAGAGATTTGTGCGGGACAG 58.636 55.000 1.81 0.00 35.44 3.51
140 141 0.036388 GGAGAGATTTGTGCGGGACA 60.036 55.000 0.00 0.00 0.00 4.02
141 142 0.036388 TGGAGAGATTTGTGCGGGAC 60.036 55.000 0.00 0.00 0.00 4.46
142 143 0.036388 GTGGAGAGATTTGTGCGGGA 60.036 55.000 0.00 0.00 0.00 5.14
143 144 0.321564 TGTGGAGAGATTTGTGCGGG 60.322 55.000 0.00 0.00 0.00 6.13
144 145 0.798776 GTGTGGAGAGATTTGTGCGG 59.201 55.000 0.00 0.00 0.00 5.69
145 146 0.798776 GGTGTGGAGAGATTTGTGCG 59.201 55.000 0.00 0.00 0.00 5.34
146 147 1.896220 TGGTGTGGAGAGATTTGTGC 58.104 50.000 0.00 0.00 0.00 4.57
161 162 4.577875 ACAAAATAAATGTGCCCATGGTG 58.422 39.130 11.73 3.26 0.00 4.17
169 170 7.439655 TCCCAAGTTGTTACAAAATAAATGTGC 59.560 33.333 0.00 0.00 32.27 4.57
177 178 3.901222 CCCCTCCCAAGTTGTTACAAAAT 59.099 43.478 0.00 0.00 0.00 1.82
178 179 3.052793 TCCCCTCCCAAGTTGTTACAAAA 60.053 43.478 0.00 0.00 0.00 2.44
180 181 2.136863 TCCCCTCCCAAGTTGTTACAA 58.863 47.619 1.45 0.00 0.00 2.41
181 182 1.822425 TCCCCTCCCAAGTTGTTACA 58.178 50.000 1.45 0.00 0.00 2.41
182 183 2.107726 AGTTCCCCTCCCAAGTTGTTAC 59.892 50.000 1.45 0.00 0.00 2.50
183 184 2.424793 AGTTCCCCTCCCAAGTTGTTA 58.575 47.619 1.45 0.00 0.00 2.41
184 185 1.231963 AGTTCCCCTCCCAAGTTGTT 58.768 50.000 1.45 0.00 0.00 2.83
186 187 2.365293 CAAAAGTTCCCCTCCCAAGTTG 59.635 50.000 0.00 0.00 0.00 3.16
187 188 2.677914 CAAAAGTTCCCCTCCCAAGTT 58.322 47.619 0.00 0.00 0.00 2.66
188 189 1.133167 CCAAAAGTTCCCCTCCCAAGT 60.133 52.381 0.00 0.00 0.00 3.16
189 190 1.133167 ACCAAAAGTTCCCCTCCCAAG 60.133 52.381 0.00 0.00 0.00 3.61
191 192 0.481128 GACCAAAAGTTCCCCTCCCA 59.519 55.000 0.00 0.00 0.00 4.37
192 193 0.778083 AGACCAAAAGTTCCCCTCCC 59.222 55.000 0.00 0.00 0.00 4.30
193 194 3.621558 CATAGACCAAAAGTTCCCCTCC 58.378 50.000 0.00 0.00 0.00 4.30
194 195 3.621558 CCATAGACCAAAAGTTCCCCTC 58.378 50.000 0.00 0.00 0.00 4.30
195 196 2.311841 CCCATAGACCAAAAGTTCCCCT 59.688 50.000 0.00 0.00 0.00 4.79
196 197 2.623239 CCCCATAGACCAAAAGTTCCCC 60.623 54.545 0.00 0.00 0.00 4.81
197 198 2.310647 TCCCCATAGACCAAAAGTTCCC 59.689 50.000 0.00 0.00 0.00 3.97
198 199 3.245122 TGTCCCCATAGACCAAAAGTTCC 60.245 47.826 0.00 0.00 35.83 3.62
199 200 4.028993 TGTCCCCATAGACCAAAAGTTC 57.971 45.455 0.00 0.00 35.83 3.01
200 201 4.675063 ATGTCCCCATAGACCAAAAGTT 57.325 40.909 0.00 0.00 35.83 2.66
201 202 5.994416 ATATGTCCCCATAGACCAAAAGT 57.006 39.130 0.00 0.00 36.99 2.66
202 203 6.710744 GTGTATATGTCCCCATAGACCAAAAG 59.289 42.308 5.36 0.00 42.48 2.27
203 204 6.409925 GGTGTATATGTCCCCATAGACCAAAA 60.410 42.308 5.36 0.00 42.48 2.44
204 205 5.072600 GGTGTATATGTCCCCATAGACCAAA 59.927 44.000 5.36 0.00 42.48 3.28
205 206 4.595781 GGTGTATATGTCCCCATAGACCAA 59.404 45.833 5.36 0.00 42.48 3.67
206 207 4.164981 GGTGTATATGTCCCCATAGACCA 58.835 47.826 5.36 0.00 42.48 4.02
207 208 3.518303 GGGTGTATATGTCCCCATAGACC 59.482 52.174 5.36 0.00 42.48 3.85
208 209 4.426704 AGGGTGTATATGTCCCCATAGAC 58.573 47.826 7.81 1.57 43.13 2.59
209 210 4.777877 AGGGTGTATATGTCCCCATAGA 57.222 45.455 7.81 0.00 41.95 1.98
210 211 7.235606 CCATATAGGGTGTATATGTCCCCATAG 59.764 44.444 9.92 1.79 41.95 2.23
211 212 7.079700 CCATATAGGGTGTATATGTCCCCATA 58.920 42.308 9.92 5.63 41.95 2.74
212 213 5.911178 CCATATAGGGTGTATATGTCCCCAT 59.089 44.000 9.92 3.97 41.95 4.00
213 214 5.017975 TCCATATAGGGTGTATATGTCCCCA 59.982 44.000 2.85 0.00 41.95 4.96
214 215 5.535029 TCCATATAGGGTGTATATGTCCCC 58.465 45.833 2.85 3.47 41.95 4.81
215 216 7.691993 AATCCATATAGGGTGTATATGTCCC 57.308 40.000 2.85 0.00 41.36 4.46
216 217 9.975218 AAAAATCCATATAGGGTGTATATGTCC 57.025 33.333 2.85 0.00 36.60 4.02
290 291 9.569122 ACAAGTACAATGTAAGGTCAACTTTAT 57.431 29.630 0.00 0.00 40.64 1.40
291 292 8.967664 ACAAGTACAATGTAAGGTCAACTTTA 57.032 30.769 0.00 0.00 40.64 1.85
292 293 7.554835 TGACAAGTACAATGTAAGGTCAACTTT 59.445 33.333 15.77 1.34 40.64 2.66
293 294 7.051623 TGACAAGTACAATGTAAGGTCAACTT 58.948 34.615 15.77 5.45 43.28 2.66
294 295 6.588204 TGACAAGTACAATGTAAGGTCAACT 58.412 36.000 15.77 0.03 31.75 3.16
295 296 6.704493 TCTGACAAGTACAATGTAAGGTCAAC 59.296 38.462 17.55 0.00 34.09 3.18
296 297 6.822442 TCTGACAAGTACAATGTAAGGTCAA 58.178 36.000 17.55 10.20 34.09 3.18
297 298 6.413783 TCTGACAAGTACAATGTAAGGTCA 57.586 37.500 16.61 16.61 31.23 4.02
298 299 7.724305 TTTCTGACAAGTACAATGTAAGGTC 57.276 36.000 13.44 11.16 31.23 3.85
299 300 8.514330 TTTTTCTGACAAGTACAATGTAAGGT 57.486 30.769 13.44 0.00 31.23 3.50
300 301 9.965824 AATTTTTCTGACAAGTACAATGTAAGG 57.034 29.630 13.44 4.90 31.23 2.69
304 305 9.301153 GTGAAATTTTTCTGACAAGTACAATGT 57.699 29.630 4.20 4.20 38.02 2.71
305 306 9.299963 TGTGAAATTTTTCTGACAAGTACAATG 57.700 29.630 0.00 0.00 38.02 2.82
306 307 9.868277 TTGTGAAATTTTTCTGACAAGTACAAT 57.132 25.926 0.00 0.00 38.02 2.71
307 308 9.698309 TTTGTGAAATTTTTCTGACAAGTACAA 57.302 25.926 0.00 0.00 35.71 2.41
308 309 9.698309 TTTTGTGAAATTTTTCTGACAAGTACA 57.302 25.926 0.00 0.00 35.71 2.90
333 334 8.078060 TGAAAAGAAGTCAAAGGAGGATTTTT 57.922 30.769 0.00 0.00 0.00 1.94
334 335 7.660030 TGAAAAGAAGTCAAAGGAGGATTTT 57.340 32.000 0.00 0.00 0.00 1.82
335 336 7.660030 TTGAAAAGAAGTCAAAGGAGGATTT 57.340 32.000 0.00 0.00 32.13 2.17
336 337 7.660030 TTTGAAAAGAAGTCAAAGGAGGATT 57.340 32.000 0.00 0.00 39.46 3.01
337 338 7.660030 TTTTGAAAAGAAGTCAAAGGAGGAT 57.340 32.000 0.47 0.00 43.76 3.24
338 339 7.475137 TTTTTGAAAAGAAGTCAAAGGAGGA 57.525 32.000 0.47 0.00 43.76 3.71
361 362 9.747293 CATTATTTTGGCCAAAATTTTGTCTTT 57.253 25.926 44.95 28.74 45.67 2.52
362 363 8.911965 ACATTATTTTGGCCAAAATTTTGTCTT 58.088 25.926 44.95 29.33 45.67 3.01
363 364 8.351461 CACATTATTTTGGCCAAAATTTTGTCT 58.649 29.630 44.95 29.93 45.67 3.41
364 365 8.348507 TCACATTATTTTGGCCAAAATTTTGTC 58.651 29.630 44.95 15.67 45.67 3.18
365 366 8.230472 TCACATTATTTTGGCCAAAATTTTGT 57.770 26.923 44.95 39.96 45.67 2.83
366 367 9.694137 ATTCACATTATTTTGGCCAAAATTTTG 57.306 25.926 44.95 39.48 45.67 2.44
369 370 9.737844 ACTATTCACATTATTTTGGCCAAAATT 57.262 25.926 44.95 32.25 45.67 1.82
371 372 8.370940 TCACTATTCACATTATTTTGGCCAAAA 58.629 29.630 38.39 38.39 43.48 2.44
372 373 7.816995 GTCACTATTCACATTATTTTGGCCAAA 59.183 33.333 27.13 27.13 0.00 3.28
373 374 7.319646 GTCACTATTCACATTATTTTGGCCAA 58.680 34.615 16.05 16.05 0.00 4.52
374 375 6.127479 GGTCACTATTCACATTATTTTGGCCA 60.127 38.462 0.00 0.00 0.00 5.36
375 376 6.096846 AGGTCACTATTCACATTATTTTGGCC 59.903 38.462 0.00 0.00 0.00 5.36
376 377 7.100458 AGGTCACTATTCACATTATTTTGGC 57.900 36.000 0.00 0.00 0.00 4.52
415 416 6.587990 TGATTTCACAGCGAAAAAGACAAAAA 59.412 30.769 0.00 0.00 46.48 1.94
416 417 6.096036 TGATTTCACAGCGAAAAAGACAAAA 58.904 32.000 0.00 0.00 46.48 2.44
417 418 5.645624 TGATTTCACAGCGAAAAAGACAAA 58.354 33.333 0.00 0.00 46.48 2.83
418 419 5.242069 TGATTTCACAGCGAAAAAGACAA 57.758 34.783 0.00 0.00 46.48 3.18
419 420 4.891627 TGATTTCACAGCGAAAAAGACA 57.108 36.364 0.00 0.00 46.48 3.41
420 421 8.368126 CAATATTGATTTCACAGCGAAAAAGAC 58.632 33.333 10.04 0.00 46.48 3.01
421 422 7.541783 CCAATATTGATTTCACAGCGAAAAAGA 59.458 33.333 17.23 0.00 46.48 2.52
422 423 7.201461 CCCAATATTGATTTCACAGCGAAAAAG 60.201 37.037 17.23 0.00 46.48 2.27
423 424 6.589523 CCCAATATTGATTTCACAGCGAAAAA 59.410 34.615 17.23 0.00 46.48 1.94
424 425 6.098679 CCCAATATTGATTTCACAGCGAAAA 58.901 36.000 17.23 0.00 46.48 2.29
426 427 4.704540 ACCCAATATTGATTTCACAGCGAA 59.295 37.500 17.23 0.00 0.00 4.70
427 428 4.269183 ACCCAATATTGATTTCACAGCGA 58.731 39.130 17.23 0.00 0.00 4.93
428 429 4.637483 ACCCAATATTGATTTCACAGCG 57.363 40.909 17.23 0.00 0.00 5.18
429 430 7.671495 AAAAACCCAATATTGATTTCACAGC 57.329 32.000 17.23 0.00 0.00 4.40
450 451 9.602568 TGCACTAGTATATATTTCCACGAAAAA 57.397 29.630 0.00 0.00 35.11 1.94
451 452 9.602568 TTGCACTAGTATATATTTCCACGAAAA 57.397 29.630 0.00 0.00 35.11 2.29
452 453 9.602568 TTTGCACTAGTATATATTTCCACGAAA 57.397 29.630 0.00 0.00 35.94 3.46
453 454 9.602568 TTTTGCACTAGTATATATTTCCACGAA 57.397 29.630 0.00 0.00 0.00 3.85
454 455 9.256477 CTTTTGCACTAGTATATATTTCCACGA 57.744 33.333 0.00 0.00 0.00 4.35
455 456 9.042008 ACTTTTGCACTAGTATATATTTCCACG 57.958 33.333 0.00 0.00 0.00 4.94
465 466 9.991906 AACTTGACTTACTTTTGCACTAGTATA 57.008 29.630 7.69 0.00 0.00 1.47
466 467 8.904099 AACTTGACTTACTTTTGCACTAGTAT 57.096 30.769 7.69 0.00 0.00 2.12
467 468 8.726870 AAACTTGACTTACTTTTGCACTAGTA 57.273 30.769 0.00 3.57 0.00 1.82
468 469 7.625828 AAACTTGACTTACTTTTGCACTAGT 57.374 32.000 5.34 5.34 0.00 2.57
471 472 8.903820 AGAATAAACTTGACTTACTTTTGCACT 58.096 29.630 0.00 0.00 0.00 4.40
558 559 9.528489 ACTTTGGTTTCTGGTTGTATATACATT 57.472 29.630 16.16 0.00 35.89 2.71
559 560 8.956426 CACTTTGGTTTCTGGTTGTATATACAT 58.044 33.333 16.16 0.00 35.89 2.29
560 561 7.940137 ACACTTTGGTTTCTGGTTGTATATACA 59.060 33.333 11.62 11.62 0.00 2.29
561 562 8.331730 ACACTTTGGTTTCTGGTTGTATATAC 57.668 34.615 5.89 5.89 0.00 1.47
563 564 9.528489 AATACACTTTGGTTTCTGGTTGTATAT 57.472 29.630 0.00 0.00 0.00 0.86
564 565 8.927675 AATACACTTTGGTTTCTGGTTGTATA 57.072 30.769 0.00 0.00 0.00 1.47
565 566 7.833285 AATACACTTTGGTTTCTGGTTGTAT 57.167 32.000 0.00 0.00 0.00 2.29
566 567 7.201839 GGAAATACACTTTGGTTTCTGGTTGTA 60.202 37.037 0.00 0.00 31.35 2.41
567 568 6.406512 GGAAATACACTTTGGTTTCTGGTTGT 60.407 38.462 0.00 0.00 31.35 3.32
568 569 5.983118 GGAAATACACTTTGGTTTCTGGTTG 59.017 40.000 0.00 0.00 31.35 3.77
569 570 5.069914 GGGAAATACACTTTGGTTTCTGGTT 59.930 40.000 0.00 0.00 31.35 3.67
570 571 4.587262 GGGAAATACACTTTGGTTTCTGGT 59.413 41.667 0.00 0.00 31.35 4.00
571 572 4.832823 AGGGAAATACACTTTGGTTTCTGG 59.167 41.667 0.00 0.00 31.35 3.86
572 573 7.013846 TGTTAGGGAAATACACTTTGGTTTCTG 59.986 37.037 0.00 0.00 32.74 3.02
573 574 7.064229 TGTTAGGGAAATACACTTTGGTTTCT 58.936 34.615 0.00 0.00 32.74 2.52
574 575 7.279750 TGTTAGGGAAATACACTTTGGTTTC 57.720 36.000 0.00 0.00 32.74 2.78
575 576 7.343574 ACTTGTTAGGGAAATACACTTTGGTTT 59.656 33.333 0.00 0.00 32.74 3.27
576 577 6.837048 ACTTGTTAGGGAAATACACTTTGGTT 59.163 34.615 0.00 0.00 32.74 3.67
577 578 6.370453 ACTTGTTAGGGAAATACACTTTGGT 58.630 36.000 0.00 0.00 32.74 3.67
578 579 6.894339 ACTTGTTAGGGAAATACACTTTGG 57.106 37.500 0.00 0.00 32.74 3.28
579 580 7.712797 ACAACTTGTTAGGGAAATACACTTTG 58.287 34.615 0.00 0.00 32.74 2.77
580 581 7.891498 ACAACTTGTTAGGGAAATACACTTT 57.109 32.000 0.00 0.00 32.74 2.66
581 582 7.778382 AGAACAACTTGTTAGGGAAATACACTT 59.222 33.333 7.15 0.00 41.28 3.16
582 583 7.287810 AGAACAACTTGTTAGGGAAATACACT 58.712 34.615 7.15 0.00 41.28 3.55
583 584 7.506328 AGAACAACTTGTTAGGGAAATACAC 57.494 36.000 7.15 0.00 41.28 2.90
584 585 8.528044 AAAGAACAACTTGTTAGGGAAATACA 57.472 30.769 7.15 0.00 41.28 2.29
585 586 8.847196 AGAAAGAACAACTTGTTAGGGAAATAC 58.153 33.333 7.15 0.00 41.28 1.89
586 587 8.990163 AGAAAGAACAACTTGTTAGGGAAATA 57.010 30.769 7.15 0.00 41.28 1.40
587 588 7.898014 AGAAAGAACAACTTGTTAGGGAAAT 57.102 32.000 7.15 0.00 41.28 2.17
588 589 7.712204 AAGAAAGAACAACTTGTTAGGGAAA 57.288 32.000 7.15 0.00 41.28 3.13
589 590 8.269317 TCTAAGAAAGAACAACTTGTTAGGGAA 58.731 33.333 7.15 0.00 41.28 3.97
590 591 7.798071 TCTAAGAAAGAACAACTTGTTAGGGA 58.202 34.615 7.15 0.00 41.28 4.20
591 592 7.931948 TCTCTAAGAAAGAACAACTTGTTAGGG 59.068 37.037 7.15 0.24 41.28 3.53
592 593 8.888579 TCTCTAAGAAAGAACAACTTGTTAGG 57.111 34.615 7.15 0.00 41.28 2.69
594 595 9.832445 ACATCTCTAAGAAAGAACAACTTGTTA 57.168 29.630 7.15 0.00 41.28 2.41
595 596 8.738645 ACATCTCTAAGAAAGAACAACTTGTT 57.261 30.769 6.87 6.87 44.37 2.83
596 597 7.987458 TGACATCTCTAAGAAAGAACAACTTGT 59.013 33.333 0.00 0.00 38.98 3.16
597 598 8.279103 GTGACATCTCTAAGAAAGAACAACTTG 58.721 37.037 0.00 0.00 38.98 3.16
598 599 7.987458 TGTGACATCTCTAAGAAAGAACAACTT 59.013 33.333 0.00 0.00 40.98 2.66
599 600 7.439655 GTGTGACATCTCTAAGAAAGAACAACT 59.560 37.037 0.00 0.00 32.46 3.16
600 601 7.224753 TGTGTGACATCTCTAAGAAAGAACAAC 59.775 37.037 0.00 0.00 32.46 3.32
639 651 1.925415 GCTCGGTGTTGCATGCATGA 61.925 55.000 30.64 12.48 0.00 3.07
666 679 4.152223 GTCATGCTATTTTTGGTGTTTGCC 59.848 41.667 0.00 0.00 0.00 4.52
667 680 4.990426 AGTCATGCTATTTTTGGTGTTTGC 59.010 37.500 0.00 0.00 0.00 3.68
668 681 7.481275 AAAGTCATGCTATTTTTGGTGTTTG 57.519 32.000 0.00 0.00 0.00 2.93
669 682 7.552330 ACAAAAGTCATGCTATTTTTGGTGTTT 59.448 29.630 15.14 0.00 42.08 2.83
670 683 7.047271 ACAAAAGTCATGCTATTTTTGGTGTT 58.953 30.769 15.14 0.00 42.08 3.32
671 684 6.581712 ACAAAAGTCATGCTATTTTTGGTGT 58.418 32.000 15.14 4.36 42.08 4.16
672 685 7.481275 AACAAAAGTCATGCTATTTTTGGTG 57.519 32.000 15.14 3.92 42.08 4.17
673 686 9.260002 CTTAACAAAAGTCATGCTATTTTTGGT 57.740 29.630 15.14 12.47 42.08 3.67
719 736 7.843490 TTGTTCTGCCTTGTTATATACAGAC 57.157 36.000 0.00 0.00 38.19 3.51
734 757 2.293399 ACAAGGTTCGATTTGTTCTGCC 59.707 45.455 5.06 0.00 34.00 4.85
735 758 3.251004 AGACAAGGTTCGATTTGTTCTGC 59.749 43.478 10.54 1.23 37.63 4.26
769 793 3.490933 CGCATGAAGGTTAGGAGATTCGA 60.491 47.826 0.00 0.00 0.00 3.71
770 794 2.797156 CGCATGAAGGTTAGGAGATTCG 59.203 50.000 0.00 0.00 0.00 3.34
828 885 3.422546 CGTGTTTTCTGAGAAGAGACGAC 59.577 47.826 24.49 11.25 0.00 4.34
873 933 0.879090 GGACGTGGGGTGCTTAAAAG 59.121 55.000 0.00 0.00 33.58 2.27
874 934 0.183014 TGGACGTGGGGTGCTTAAAA 59.817 50.000 0.00 0.00 37.93 1.52
875 935 0.535553 GTGGACGTGGGGTGCTTAAA 60.536 55.000 0.00 0.00 37.93 1.52
876 936 1.071814 GTGGACGTGGGGTGCTTAA 59.928 57.895 0.00 0.00 37.93 1.85
889 949 0.321653 GAGATGGGTGTGTGGTGGAC 60.322 60.000 0.00 0.00 0.00 4.02
890 950 1.488705 GGAGATGGGTGTGTGGTGGA 61.489 60.000 0.00 0.00 0.00 4.02
921 984 5.946942 TGAACAATGAGCTAGGAGAAGAT 57.053 39.130 0.00 0.00 0.00 2.40
959 1035 6.374578 GCAATGAGGAAGTAGAAACAGAAAC 58.625 40.000 0.00 0.00 0.00 2.78
967 1055 5.684704 CTTATGGGCAATGAGGAAGTAGAA 58.315 41.667 0.00 0.00 0.00 2.10
1559 1726 4.481112 CGGCCATGGCGTTCTTGC 62.481 66.667 29.90 13.42 46.33 4.01
1697 1870 3.793144 GGTAGTCGTCGTCGCCGT 61.793 66.667 0.00 0.00 36.96 5.68
1698 1871 3.792047 TGGTAGTCGTCGTCGCCG 61.792 66.667 0.00 0.00 36.96 6.46
1699 1872 1.361668 TAGTGGTAGTCGTCGTCGCC 61.362 60.000 0.00 0.00 36.96 5.54
1700 1873 0.654683 ATAGTGGTAGTCGTCGTCGC 59.345 55.000 0.00 0.00 36.96 5.19
1701 1874 1.071633 CGATAGTGGTAGTCGTCGTCG 60.072 57.143 0.00 0.00 38.55 5.12
1702 1875 1.332728 GCGATAGTGGTAGTCGTCGTC 60.333 57.143 0.00 0.00 37.66 4.20
1714 1887 0.384309 TTAGGGCTCGTGCGATAGTG 59.616 55.000 3.02 0.00 40.82 2.74
1820 1993 2.286127 GACTAGCTCGGACACCCTGC 62.286 65.000 0.00 0.00 0.00 4.85
1902 2075 1.008309 GACCTCTATGTCGGCGCTC 60.008 63.158 7.64 0.00 0.00 5.03
1979 2152 1.549203 GATTGGGCGCCATCCATTAT 58.451 50.000 30.85 8.43 33.82 1.28
1980 2153 0.539438 GGATTGGGCGCCATCCATTA 60.539 55.000 31.21 9.06 34.03 1.90
1981 2154 1.833934 GGATTGGGCGCCATCCATT 60.834 57.895 31.21 16.96 34.03 3.16
1982 2155 2.203538 GGATTGGGCGCCATCCAT 60.204 61.111 31.21 17.37 34.03 3.41
1983 2156 4.873810 CGGATTGGGCGCCATCCA 62.874 66.667 33.35 20.38 33.71 3.41
2086 2280 0.396811 ACCACTTGGCACTGAGTACC 59.603 55.000 0.00 0.00 39.32 3.34
2180 2384 1.202710 TCTTGTTCCGGCTGCTTAACA 60.203 47.619 0.00 0.00 0.00 2.41
2185 2389 1.192146 TACCTCTTGTTCCGGCTGCT 61.192 55.000 0.00 0.00 0.00 4.24
2186 2390 0.321298 TTACCTCTTGTTCCGGCTGC 60.321 55.000 0.00 0.00 0.00 5.25
2187 2391 2.403252 ATTACCTCTTGTTCCGGCTG 57.597 50.000 0.00 0.00 0.00 4.85
2188 2392 3.071167 GGATATTACCTCTTGTTCCGGCT 59.929 47.826 0.00 0.00 0.00 5.52
2189 2393 3.400255 GGATATTACCTCTTGTTCCGGC 58.600 50.000 0.00 0.00 0.00 6.13
2190 2394 3.646637 AGGGATATTACCTCTTGTTCCGG 59.353 47.826 0.00 0.00 31.01 5.14
2191 2395 4.503296 CCAGGGATATTACCTCTTGTTCCG 60.503 50.000 0.00 0.00 35.78 4.30
2192 2396 4.412528 ACCAGGGATATTACCTCTTGTTCC 59.587 45.833 0.00 0.00 35.78 3.62
2193 2397 5.368989 CACCAGGGATATTACCTCTTGTTC 58.631 45.833 0.00 0.00 35.78 3.18
2194 2398 4.166144 CCACCAGGGATATTACCTCTTGTT 59.834 45.833 0.00 0.00 40.01 2.83
2195 2399 3.716872 CCACCAGGGATATTACCTCTTGT 59.283 47.826 0.00 0.00 40.01 3.16
2196 2400 3.716872 ACCACCAGGGATATTACCTCTTG 59.283 47.826 0.00 0.00 41.15 3.02
2210 2414 1.247567 CAAGTTTAGGCACCACCAGG 58.752 55.000 0.00 0.00 43.14 4.45
2230 2434 3.507233 GGCATCAAAGTGAACATTCAGGA 59.493 43.478 0.00 0.00 37.98 3.86
2235 2439 6.655078 AGTTTAGGCATCAAAGTGAACATT 57.345 33.333 0.00 0.00 0.00 2.71
2271 2475 6.398234 TTGCCAAGTTTTAGCACTCATTAA 57.602 33.333 0.00 0.00 35.96 1.40
2363 2567 7.544804 ACAAGGCCAAATAAAGATTCTTCTT 57.455 32.000 5.01 0.00 44.20 2.52
2364 2568 7.544804 AACAAGGCCAAATAAAGATTCTTCT 57.455 32.000 5.01 0.00 0.00 2.85
2365 2569 8.739972 TCTAACAAGGCCAAATAAAGATTCTTC 58.260 33.333 5.01 0.00 0.00 2.87
2366 2570 8.650143 TCTAACAAGGCCAAATAAAGATTCTT 57.350 30.769 5.01 0.00 0.00 2.52
2367 2571 8.650143 TTCTAACAAGGCCAAATAAAGATTCT 57.350 30.769 5.01 0.00 0.00 2.40
2369 2573 8.306761 CACTTCTAACAAGGCCAAATAAAGATT 58.693 33.333 5.01 0.00 0.00 2.40
2370 2574 7.451566 ACACTTCTAACAAGGCCAAATAAAGAT 59.548 33.333 5.01 0.00 0.00 2.40
2371 2575 6.775629 ACACTTCTAACAAGGCCAAATAAAGA 59.224 34.615 5.01 0.00 0.00 2.52
2373 2577 6.775629 AGACACTTCTAACAAGGCCAAATAAA 59.224 34.615 5.01 0.00 0.00 1.40
2376 2580 4.729868 AGACACTTCTAACAAGGCCAAAT 58.270 39.130 5.01 0.00 0.00 2.32
2382 3105 7.040409 AGCCAAATAAAGACACTTCTAACAAGG 60.040 37.037 0.00 0.00 0.00 3.61
2384 3107 7.817418 AGCCAAATAAAGACACTTCTAACAA 57.183 32.000 0.00 0.00 0.00 2.83
2385 3108 8.911918 TTAGCCAAATAAAGACACTTCTAACA 57.088 30.769 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.