Multiple sequence alignment - TraesCS7D01G040500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G040500 chr7D 100.000 4502 0 0 1 4502 20420257 20424758 0.000000e+00 8314.0
1 TraesCS7D01G040500 chr7D 83.489 2780 434 21 731 3496 20404307 20407075 0.000000e+00 2567.0
2 TraesCS7D01G040500 chr7D 83.195 2779 455 11 740 3510 89533029 89530255 0.000000e+00 2534.0
3 TraesCS7D01G040500 chr7D 80.952 3003 528 35 534 3509 20460216 20463201 0.000000e+00 2337.0
4 TraesCS7D01G040500 chr7A 97.238 3367 82 3 276 3641 20613220 20616576 0.000000e+00 5692.0
5 TraesCS7D01G040500 chr7A 81.395 2940 512 28 587 3509 20779391 20782312 0.000000e+00 2366.0
6 TraesCS7D01G040500 chr7A 81.407 2899 487 40 566 3440 20980440 20983310 0.000000e+00 2320.0
7 TraesCS7D01G040500 chr7A 94.876 683 33 2 3625 4306 287486620 287485939 0.000000e+00 1066.0
8 TraesCS7D01G040500 chr7A 98.039 204 4 0 1 204 20613013 20613216 5.540000e-94 355.0
9 TraesCS7D01G040500 chr7A 90.566 106 10 0 4327 4432 20633316 20633421 1.690000e-29 141.0
10 TraesCS7D01G040500 chr7A 90.566 53 3 1 4450 4502 20604359 20604409 8.080000e-08 69.4
11 TraesCS7D01G040500 chr7A 95.000 40 0 2 8 46 707687322 707687284 1.350000e-05 62.1
12 TraesCS7D01G040500 chr2A 81.009 3291 552 57 319 3570 733087372 733090628 0.000000e+00 2547.0
13 TraesCS7D01G040500 chr2D 81.944 2974 497 32 676 3632 598814028 598816978 0.000000e+00 2481.0
14 TraesCS7D01G040500 chr2D 95.704 675 27 2 3634 4306 644242771 644243445 0.000000e+00 1085.0
15 TraesCS7D01G040500 chr2D 95.075 670 28 3 3638 4306 3772636 3771971 0.000000e+00 1050.0
16 TraesCS7D01G040500 chr2B 82.536 2800 465 21 744 3530 727686048 727688836 0.000000e+00 2440.0
17 TraesCS7D01G040500 chr2B 95.000 680 33 1 3628 4306 461519225 461519904 0.000000e+00 1066.0
18 TraesCS7D01G040500 chr2B 95.217 669 29 3 3634 4301 734840103 734839437 0.000000e+00 1055.0
19 TraesCS7D01G040500 chr6D 96.707 668 18 3 3634 4300 101207417 101208081 0.000000e+00 1109.0
20 TraesCS7D01G040500 chr6D 97.561 41 0 1 6 45 132027399 132027359 8.080000e-08 69.4
21 TraesCS7D01G040500 chr6D 92.857 42 3 0 6 47 121815109 121815150 1.350000e-05 62.1
22 TraesCS7D01G040500 chr3D 96.131 672 25 1 3634 4304 23630194 23629523 0.000000e+00 1096.0
23 TraesCS7D01G040500 chr7B 94.412 680 36 2 3628 4306 186867944 186868622 0.000000e+00 1044.0
24 TraesCS7D01G040500 chr5B 93.979 681 40 1 3628 4307 711051767 711052447 0.000000e+00 1029.0
25 TraesCS7D01G040500 chr3A 93.333 45 2 1 2 46 457465198 457465241 1.050000e-06 65.8
26 TraesCS7D01G040500 chr4B 95.122 41 0 2 6 45 665004465 665004504 3.760000e-06 63.9
27 TraesCS7D01G040500 chr4B 95.122 41 0 2 6 45 665058951 665058990 3.760000e-06 63.9
28 TraesCS7D01G040500 chr4B 95.122 41 0 2 6 45 665112014 665112053 3.760000e-06 63.9
29 TraesCS7D01G040500 chr5D 92.857 42 1 2 4 45 242117132 242117171 4.860000e-05 60.2


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 TraesCS7D01G040500 chr7D 20420257 20424758 4501 False 8314.0 8314 100.0000 1 4502 1 chr7D.!!$F2 4501
1 TraesCS7D01G040500 chr7D 20404307 20407075 2768 False 2567.0 2567 83.4890 731 3496 1 chr7D.!!$F1 2765
2 TraesCS7D01G040500 chr7D 89530255 89533029 2774 True 2534.0 2534 83.1950 740 3510 1 chr7D.!!$R1 2770
3 TraesCS7D01G040500 chr7D 20460216 20463201 2985 False 2337.0 2337 80.9520 534 3509 1 chr7D.!!$F3 2975
4 TraesCS7D01G040500 chr7A 20613013 20616576 3563 False 3023.5 5692 97.6385 1 3641 2 chr7A.!!$F5 3640
5 TraesCS7D01G040500 chr7A 20779391 20782312 2921 False 2366.0 2366 81.3950 587 3509 1 chr7A.!!$F3 2922
6 TraesCS7D01G040500 chr7A 20980440 20983310 2870 False 2320.0 2320 81.4070 566 3440 1 chr7A.!!$F4 2874
7 TraesCS7D01G040500 chr7A 287485939 287486620 681 True 1066.0 1066 94.8760 3625 4306 1 chr7A.!!$R1 681
8 TraesCS7D01G040500 chr2A 733087372 733090628 3256 False 2547.0 2547 81.0090 319 3570 1 chr2A.!!$F1 3251
9 TraesCS7D01G040500 chr2D 598814028 598816978 2950 False 2481.0 2481 81.9440 676 3632 1 chr2D.!!$F1 2956
10 TraesCS7D01G040500 chr2D 644242771 644243445 674 False 1085.0 1085 95.7040 3634 4306 1 chr2D.!!$F2 672
11 TraesCS7D01G040500 chr2D 3771971 3772636 665 True 1050.0 1050 95.0750 3638 4306 1 chr2D.!!$R1 668
12 TraesCS7D01G040500 chr2B 727686048 727688836 2788 False 2440.0 2440 82.5360 744 3530 1 chr2B.!!$F2 2786
13 TraesCS7D01G040500 chr2B 461519225 461519904 679 False 1066.0 1066 95.0000 3628 4306 1 chr2B.!!$F1 678
14 TraesCS7D01G040500 chr2B 734839437 734840103 666 True 1055.0 1055 95.2170 3634 4301 1 chr2B.!!$R1 667
15 TraesCS7D01G040500 chr6D 101207417 101208081 664 False 1109.0 1109 96.7070 3634 4300 1 chr6D.!!$F1 666
16 TraesCS7D01G040500 chr3D 23629523 23630194 671 True 1096.0 1096 96.1310 3634 4304 1 chr3D.!!$R1 670
17 TraesCS7D01G040500 chr7B 186867944 186868622 678 False 1044.0 1044 94.4120 3628 4306 1 chr7B.!!$F1 678
18 TraesCS7D01G040500 chr5B 711051767 711052447 680 False 1029.0 1029 93.9790 3628 4307 1 chr5B.!!$F1 679

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
209 210 0.038021 TGAGCTGGCAGGCATGTTTA 59.962 50.000 17.64 0.00 34.17 2.01 F
368 372 0.102481 GGAAGCTGAGCATGCATTGG 59.898 55.000 21.98 7.98 0.00 3.16 F
839 864 1.203262 TCCAGCCAGTACCCAGTTAGT 60.203 52.381 0.00 0.00 0.00 2.24 F
2357 2383 1.048601 TGTGGGGTGTCTCTTGAGAC 58.951 55.000 20.32 20.32 39.15 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 1255 2.432510 CGCTAGATCTTGGGACCTCTTT 59.567 50.0 14.60 0.00 0.00 2.52 R
2357 2383 0.382873 TACCAATCGACGTCCATCCG 59.617 55.0 10.58 0.00 0.00 4.18 R
2823 2852 0.038892 CTTGCGCTTCCAATGCTTGT 60.039 50.0 9.73 0.00 0.00 3.16 R
3963 4008 0.779997 AAGAAGGAATGGTGGCACCT 59.220 50.0 34.69 18.24 39.58 4.00 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
114 115 2.153645 CTGATGTTGGCAAGCACAGTA 58.846 47.619 0.00 0.00 0.00 2.74
204 205 4.043100 TGCTGAGCTGGCAGGCAT 62.043 61.111 17.64 0.00 36.41 4.40
206 207 2.045242 CTGAGCTGGCAGGCATGT 60.045 61.111 17.64 0.00 32.26 3.21
207 208 1.677966 CTGAGCTGGCAGGCATGTT 60.678 57.895 17.64 0.00 32.26 2.71
208 209 1.228644 TGAGCTGGCAGGCATGTTT 60.229 52.632 17.64 0.00 34.17 2.83
209 210 0.038021 TGAGCTGGCAGGCATGTTTA 59.962 50.000 17.64 0.00 34.17 2.01
210 211 0.737219 GAGCTGGCAGGCATGTTTAG 59.263 55.000 17.64 0.00 34.17 1.85
211 212 0.682209 AGCTGGCAGGCATGTTTAGG 60.682 55.000 17.64 0.00 34.17 2.69
212 213 0.967380 GCTGGCAGGCATGTTTAGGT 60.967 55.000 17.64 0.00 0.00 3.08
213 214 1.549203 CTGGCAGGCATGTTTAGGTT 58.451 50.000 6.61 0.00 0.00 3.50
214 215 1.895131 CTGGCAGGCATGTTTAGGTTT 59.105 47.619 6.61 0.00 0.00 3.27
215 216 2.299867 CTGGCAGGCATGTTTAGGTTTT 59.700 45.455 6.61 0.00 0.00 2.43
216 217 3.501349 TGGCAGGCATGTTTAGGTTTTA 58.499 40.909 0.00 0.00 0.00 1.52
217 218 3.509575 TGGCAGGCATGTTTAGGTTTTAG 59.490 43.478 0.00 0.00 0.00 1.85
218 219 3.509967 GGCAGGCATGTTTAGGTTTTAGT 59.490 43.478 0.00 0.00 0.00 2.24
219 220 4.021456 GGCAGGCATGTTTAGGTTTTAGTT 60.021 41.667 0.00 0.00 0.00 2.24
220 221 4.923281 GCAGGCATGTTTAGGTTTTAGTTG 59.077 41.667 0.00 0.00 0.00 3.16
221 222 4.923281 CAGGCATGTTTAGGTTTTAGTTGC 59.077 41.667 0.00 0.00 0.00 4.17
222 223 4.021456 AGGCATGTTTAGGTTTTAGTTGCC 60.021 41.667 0.00 0.00 45.74 4.52
223 224 4.262249 GGCATGTTTAGGTTTTAGTTGCCA 60.262 41.667 5.30 0.00 44.96 4.92
224 225 5.478407 GCATGTTTAGGTTTTAGTTGCCAT 58.522 37.500 0.00 0.00 0.00 4.40
225 226 5.576774 GCATGTTTAGGTTTTAGTTGCCATC 59.423 40.000 0.00 0.00 0.00 3.51
226 227 5.715434 TGTTTAGGTTTTAGTTGCCATCC 57.285 39.130 0.00 0.00 0.00 3.51
227 228 5.141182 TGTTTAGGTTTTAGTTGCCATCCA 58.859 37.500 0.00 0.00 0.00 3.41
228 229 5.777732 TGTTTAGGTTTTAGTTGCCATCCAT 59.222 36.000 0.00 0.00 0.00 3.41
229 230 6.268847 TGTTTAGGTTTTAGTTGCCATCCATT 59.731 34.615 0.00 0.00 0.00 3.16
230 231 6.926630 TTAGGTTTTAGTTGCCATCCATTT 57.073 33.333 0.00 0.00 0.00 2.32
231 232 8.308207 GTTTAGGTTTTAGTTGCCATCCATTTA 58.692 33.333 0.00 0.00 0.00 1.40
232 233 8.602472 TTAGGTTTTAGTTGCCATCCATTTAT 57.398 30.769 0.00 0.00 0.00 1.40
233 234 7.494922 AGGTTTTAGTTGCCATCCATTTATT 57.505 32.000 0.00 0.00 0.00 1.40
234 235 7.917003 AGGTTTTAGTTGCCATCCATTTATTT 58.083 30.769 0.00 0.00 0.00 1.40
235 236 8.040727 AGGTTTTAGTTGCCATCCATTTATTTC 58.959 33.333 0.00 0.00 0.00 2.17
236 237 7.279981 GGTTTTAGTTGCCATCCATTTATTTCC 59.720 37.037 0.00 0.00 0.00 3.13
237 238 7.732222 TTTAGTTGCCATCCATTTATTTCCT 57.268 32.000 0.00 0.00 0.00 3.36
238 239 5.603170 AGTTGCCATCCATTTATTTCCTG 57.397 39.130 0.00 0.00 0.00 3.86
239 240 4.406649 AGTTGCCATCCATTTATTTCCTGG 59.593 41.667 0.00 0.00 0.00 4.45
240 241 3.307506 TGCCATCCATTTATTTCCTGGG 58.692 45.455 0.00 0.00 0.00 4.45
241 242 3.052262 TGCCATCCATTTATTTCCTGGGA 60.052 43.478 0.00 0.00 0.00 4.37
242 243 4.162651 GCCATCCATTTATTTCCTGGGAT 58.837 43.478 0.00 0.00 35.60 3.85
243 244 4.594491 GCCATCCATTTATTTCCTGGGATT 59.406 41.667 0.00 0.00 33.04 3.01
244 245 5.779771 GCCATCCATTTATTTCCTGGGATTA 59.220 40.000 0.00 0.00 33.04 1.75
245 246 6.269769 GCCATCCATTTATTTCCTGGGATTAA 59.730 38.462 0.00 0.00 33.04 1.40
246 247 7.202084 GCCATCCATTTATTTCCTGGGATTAAA 60.202 37.037 4.90 4.90 33.04 1.52
247 248 8.883302 CCATCCATTTATTTCCTGGGATTAAAT 58.117 33.333 8.44 8.44 33.04 1.40
250 251 9.944079 TCCATTTATTTCCTGGGATTAAATACA 57.056 29.630 12.35 2.19 29.59 2.29
257 258 8.630054 TTTCCTGGGATTAAATACAATATCCG 57.370 34.615 0.00 0.00 37.92 4.18
258 259 6.717289 TCCTGGGATTAAATACAATATCCGG 58.283 40.000 0.00 0.00 37.92 5.14
259 260 6.502510 TCCTGGGATTAAATACAATATCCGGA 59.497 38.462 6.61 6.61 37.92 5.14
260 261 7.017750 TCCTGGGATTAAATACAATATCCGGAA 59.982 37.037 9.01 0.00 37.92 4.30
261 262 7.834181 CCTGGGATTAAATACAATATCCGGAAT 59.166 37.037 9.01 0.00 37.92 3.01
262 263 8.801882 TGGGATTAAATACAATATCCGGAATC 57.198 34.615 9.01 1.56 37.92 2.52
263 264 8.387039 TGGGATTAAATACAATATCCGGAATCA 58.613 33.333 9.01 0.00 37.92 2.57
264 265 9.238368 GGGATTAAATACAATATCCGGAATCAA 57.762 33.333 9.01 0.00 37.92 2.57
272 273 7.730364 ACAATATCCGGAATCAATCTACAAC 57.270 36.000 9.01 0.00 0.00 3.32
273 274 6.423905 ACAATATCCGGAATCAATCTACAACG 59.576 38.462 9.01 0.00 0.00 4.10
274 275 3.880047 TCCGGAATCAATCTACAACGT 57.120 42.857 0.00 0.00 0.00 3.99
300 301 7.739295 TGTTGTTGATAATTCTTCTTAGTCGC 58.261 34.615 0.00 0.00 0.00 5.19
345 346 4.440112 GGGCATTTTAACTTGAGATTCCCG 60.440 45.833 0.00 0.00 0.00 5.14
368 372 0.102481 GGAAGCTGAGCATGCATTGG 59.898 55.000 21.98 7.98 0.00 3.16
406 410 5.864986 AGTGTCACTTGTTTTTGTTCTACG 58.135 37.500 0.00 0.00 0.00 3.51
416 420 2.961526 TTGTTCTACGGGAGCATCTC 57.038 50.000 0.00 0.00 35.21 2.75
531 537 6.403878 TGGAGCAAGATAGGTTTAACTGTAC 58.596 40.000 0.00 0.00 0.00 2.90
711 736 2.819984 AATGTACAGCCAGGCCACCG 62.820 60.000 8.22 0.00 0.00 4.94
723 748 3.896317 GCCACCGCCAAACAATTAA 57.104 47.368 0.00 0.00 0.00 1.40
839 864 1.203262 TCCAGCCAGTACCCAGTTAGT 60.203 52.381 0.00 0.00 0.00 2.24
890 915 2.802792 CAGCATGGGTCGCATTGG 59.197 61.111 0.00 0.00 0.00 3.16
914 939 1.331756 GGAGCTTCGTGTAATGCATGG 59.668 52.381 0.00 0.00 34.91 3.66
937 962 4.744631 GCGTTCTTTGTGAAATGGACATTT 59.255 37.500 9.84 9.84 43.14 2.32
961 986 8.669946 TTGAAACCGCAATGATCAAGTATATA 57.330 30.769 0.00 0.00 0.00 0.86
978 1003 1.912862 ATAAGGGCTGGTTGGAGGAT 58.087 50.000 0.00 0.00 0.00 3.24
1230 1255 5.068591 TCCTAGCAGCTCGAATTACATTGTA 59.931 40.000 0.00 0.00 0.00 2.41
1588 1613 7.726216 TGAAGAGACACTGAAGACATTTCTAA 58.274 34.615 0.00 0.00 0.00 2.10
1646 1671 2.101917 GGAATCCACAGGCATTTGATGG 59.898 50.000 0.00 0.00 0.00 3.51
2357 2383 1.048601 TGTGGGGTGTCTCTTGAGAC 58.951 55.000 20.32 20.32 39.15 3.36
2409 2435 4.205587 CAAAGAAGGATATTCAGCTGCCT 58.794 43.478 9.47 6.41 0.00 4.75
2819 2848 9.052759 TCTTGGAAATCTAACAAACTTACAGAC 57.947 33.333 0.00 0.00 0.00 3.51
2820 2849 8.740123 TTGGAAATCTAACAAACTTACAGACA 57.260 30.769 0.00 0.00 0.00 3.41
2821 2850 8.149973 TGGAAATCTAACAAACTTACAGACAC 57.850 34.615 0.00 0.00 0.00 3.67
2822 2851 7.990886 TGGAAATCTAACAAACTTACAGACACT 59.009 33.333 0.00 0.00 0.00 3.55
2823 2852 9.485206 GGAAATCTAACAAACTTACAGACACTA 57.515 33.333 0.00 0.00 0.00 2.74
2825 2854 9.826574 AAATCTAACAAACTTACAGACACTACA 57.173 29.630 0.00 0.00 0.00 2.74
2826 2855 9.826574 AATCTAACAAACTTACAGACACTACAA 57.173 29.630 0.00 0.00 0.00 2.41
2827 2856 8.867112 TCTAACAAACTTACAGACACTACAAG 57.133 34.615 0.00 0.00 0.00 3.16
2880 2918 4.222145 CAGTTAGGGGAGCTAACACAACTA 59.778 45.833 0.00 0.00 39.13 2.24
3157 3195 1.821088 ACTGACAGAAGACCCCCTTT 58.179 50.000 10.08 0.00 34.68 3.11
3450 3488 4.154918 GGTTACTTCTTGATGTTGCTCCAG 59.845 45.833 0.00 0.00 0.00 3.86
3587 3631 2.564062 ACCATCTTTTCGTCGTCCCTAA 59.436 45.455 0.00 0.00 0.00 2.69
3839 3883 2.431683 GAGACAGCTTGGGTGGCA 59.568 61.111 5.38 0.00 42.14 4.92
3914 3958 3.956314 GGCGGTGGGGTTGGTGTA 61.956 66.667 0.00 0.00 0.00 2.90
4053 4098 4.835891 CCTAGGACTCGCCCGGGT 62.836 72.222 24.63 0.09 37.37 5.28
4266 4311 4.320023 TGCTATGTGTATGGTGTTCGTTT 58.680 39.130 0.00 0.00 0.00 3.60
4308 4353 4.929819 GGAAACCCTTTTTCTGTAAGCA 57.070 40.909 0.00 0.00 0.00 3.91
4309 4354 5.468540 GGAAACCCTTTTTCTGTAAGCAT 57.531 39.130 0.00 0.00 0.00 3.79
4310 4355 5.230182 GGAAACCCTTTTTCTGTAAGCATG 58.770 41.667 0.00 0.00 0.00 4.06
4311 4356 4.871933 AACCCTTTTTCTGTAAGCATGG 57.128 40.909 0.00 0.00 0.00 3.66
4312 4357 3.165071 ACCCTTTTTCTGTAAGCATGGG 58.835 45.455 0.00 0.00 38.13 4.00
4313 4358 3.165071 CCCTTTTTCTGTAAGCATGGGT 58.835 45.455 0.00 0.00 0.00 4.51
4314 4359 3.578282 CCCTTTTTCTGTAAGCATGGGTT 59.422 43.478 0.00 0.00 0.00 4.11
4315 4360 4.559153 CCTTTTTCTGTAAGCATGGGTTG 58.441 43.478 0.00 0.00 0.00 3.77
4316 4361 4.039124 CCTTTTTCTGTAAGCATGGGTTGT 59.961 41.667 0.00 0.00 0.00 3.32
4317 4362 4.582701 TTTTCTGTAAGCATGGGTTGTG 57.417 40.909 0.00 0.00 0.00 3.33
4318 4363 2.949177 TCTGTAAGCATGGGTTGTGT 57.051 45.000 0.00 0.00 0.00 3.72
4319 4364 2.503331 TCTGTAAGCATGGGTTGTGTG 58.497 47.619 0.00 0.00 0.00 3.82
4320 4365 2.105649 TCTGTAAGCATGGGTTGTGTGA 59.894 45.455 0.00 0.00 0.00 3.58
4321 4366 2.884012 CTGTAAGCATGGGTTGTGTGAA 59.116 45.455 0.00 0.00 0.00 3.18
4322 4367 2.621055 TGTAAGCATGGGTTGTGTGAAC 59.379 45.455 0.00 0.00 0.00 3.18
4323 4368 1.774110 AAGCATGGGTTGTGTGAACA 58.226 45.000 0.00 0.00 0.00 3.18
4324 4369 1.032014 AGCATGGGTTGTGTGAACAC 58.968 50.000 6.63 6.63 46.59 3.32
4325 4370 0.031994 GCATGGGTTGTGTGAACACC 59.968 55.000 10.92 0.00 45.88 4.16
4326 4371 1.691196 CATGGGTTGTGTGAACACCT 58.309 50.000 10.92 0.00 45.88 4.00
4327 4372 1.608590 CATGGGTTGTGTGAACACCTC 59.391 52.381 10.92 4.26 45.88 3.85
4328 4373 0.621082 TGGGTTGTGTGAACACCTCA 59.379 50.000 10.92 0.12 45.88 3.86
4329 4374 1.004862 TGGGTTGTGTGAACACCTCAA 59.995 47.619 10.92 7.35 45.88 3.02
4330 4375 1.676006 GGGTTGTGTGAACACCTCAAG 59.324 52.381 10.92 0.00 45.88 3.02
4331 4376 2.639065 GGTTGTGTGAACACCTCAAGA 58.361 47.619 10.92 0.00 45.88 3.02
4332 4377 3.013921 GGTTGTGTGAACACCTCAAGAA 58.986 45.455 10.92 0.00 45.88 2.52
4333 4378 3.632145 GGTTGTGTGAACACCTCAAGAAT 59.368 43.478 10.92 0.00 45.88 2.40
4334 4379 4.819630 GGTTGTGTGAACACCTCAAGAATA 59.180 41.667 10.92 0.00 45.88 1.75
4335 4380 5.298276 GGTTGTGTGAACACCTCAAGAATAA 59.702 40.000 10.92 0.00 45.88 1.40
4336 4381 6.183360 GGTTGTGTGAACACCTCAAGAATAAA 60.183 38.462 10.92 0.00 45.88 1.40
4337 4382 7.254852 GTTGTGTGAACACCTCAAGAATAAAA 58.745 34.615 10.92 0.00 45.88 1.52
4338 4383 7.581213 TGTGTGAACACCTCAAGAATAAAAT 57.419 32.000 10.92 0.00 45.88 1.82
4339 4384 8.006298 TGTGTGAACACCTCAAGAATAAAATT 57.994 30.769 10.92 0.00 45.88 1.82
4340 4385 8.474025 TGTGTGAACACCTCAAGAATAAAATTT 58.526 29.630 10.92 0.00 45.88 1.82
4341 4386 8.755018 GTGTGAACACCTCAAGAATAAAATTTG 58.245 33.333 1.99 0.00 40.85 2.32
4342 4387 8.474025 TGTGAACACCTCAAGAATAAAATTTGT 58.526 29.630 2.46 0.00 35.22 2.83
4343 4388 9.313118 GTGAACACCTCAAGAATAAAATTTGTT 57.687 29.630 0.00 0.00 35.22 2.83
4347 4392 9.965824 ACACCTCAAGAATAAAATTTGTTAGTG 57.034 29.630 0.00 0.00 0.00 2.74
4363 4408 7.558161 TTGTTAGTGATTCATAATGCTCAGG 57.442 36.000 0.00 0.00 0.00 3.86
4364 4409 6.653020 TGTTAGTGATTCATAATGCTCAGGT 58.347 36.000 0.00 0.00 0.00 4.00
4365 4410 7.791029 TGTTAGTGATTCATAATGCTCAGGTA 58.209 34.615 0.00 0.00 0.00 3.08
4366 4411 8.432013 TGTTAGTGATTCATAATGCTCAGGTAT 58.568 33.333 0.00 0.00 0.00 2.73
4367 4412 9.277783 GTTAGTGATTCATAATGCTCAGGTATT 57.722 33.333 0.00 0.00 0.00 1.89
4368 4413 7.741027 AGTGATTCATAATGCTCAGGTATTG 57.259 36.000 0.00 0.00 0.00 1.90
4369 4414 6.713903 AGTGATTCATAATGCTCAGGTATTGG 59.286 38.462 0.00 0.00 0.00 3.16
4370 4415 6.488006 GTGATTCATAATGCTCAGGTATTGGT 59.512 38.462 0.00 0.00 0.00 3.67
4371 4416 7.013655 GTGATTCATAATGCTCAGGTATTGGTT 59.986 37.037 0.00 0.00 0.00 3.67
4372 4417 7.560991 TGATTCATAATGCTCAGGTATTGGTTT 59.439 33.333 0.00 0.00 0.00 3.27
4373 4418 6.698008 TCATAATGCTCAGGTATTGGTTTG 57.302 37.500 0.00 0.00 0.00 2.93
4374 4419 6.186957 TCATAATGCTCAGGTATTGGTTTGT 58.813 36.000 0.00 0.00 0.00 2.83
4375 4420 4.789012 AATGCTCAGGTATTGGTTTGTG 57.211 40.909 0.00 0.00 0.00 3.33
4376 4421 1.885887 TGCTCAGGTATTGGTTTGTGC 59.114 47.619 0.00 0.00 0.00 4.57
4377 4422 2.162681 GCTCAGGTATTGGTTTGTGCT 58.837 47.619 0.00 0.00 0.00 4.40
4378 4423 2.162408 GCTCAGGTATTGGTTTGTGCTC 59.838 50.000 0.00 0.00 0.00 4.26
4379 4424 3.411446 CTCAGGTATTGGTTTGTGCTCA 58.589 45.455 0.00 0.00 0.00 4.26
4380 4425 3.146066 TCAGGTATTGGTTTGTGCTCAC 58.854 45.455 0.00 0.00 0.00 3.51
4381 4426 2.228822 CAGGTATTGGTTTGTGCTCACC 59.771 50.000 0.00 0.00 0.00 4.02
4382 4427 2.108250 AGGTATTGGTTTGTGCTCACCT 59.892 45.455 0.00 0.00 33.76 4.00
4383 4428 3.329520 AGGTATTGGTTTGTGCTCACCTA 59.670 43.478 0.00 0.00 33.46 3.08
4384 4429 4.076394 GGTATTGGTTTGTGCTCACCTAA 58.924 43.478 0.00 0.00 33.76 2.69
4385 4430 4.521256 GGTATTGGTTTGTGCTCACCTAAA 59.479 41.667 0.00 0.00 33.76 1.85
4386 4431 5.010213 GGTATTGGTTTGTGCTCACCTAAAA 59.990 40.000 0.00 0.00 33.76 1.52
4387 4432 5.606348 ATTGGTTTGTGCTCACCTAAAAA 57.394 34.783 0.00 0.00 33.76 1.94
4414 4459 9.715121 AGCAAAAATGATTTGTGATTCATTACT 57.285 25.926 12.11 0.00 40.70 2.24
4415 4460 9.749490 GCAAAAATGATTTGTGATTCATTACTG 57.251 29.630 12.11 0.00 40.70 2.74
4416 4461 9.749490 CAAAAATGATTTGTGATTCATTACTGC 57.251 29.630 1.80 0.00 40.70 4.40
4417 4462 9.715121 AAAAATGATTTGTGATTCATTACTGCT 57.285 25.926 0.00 0.00 40.70 4.24
4418 4463 8.697846 AAATGATTTGTGATTCATTACTGCTG 57.302 30.769 0.00 0.00 40.70 4.41
4419 4464 7.634671 ATGATTTGTGATTCATTACTGCTGA 57.365 32.000 0.00 0.00 0.00 4.26
4420 4465 7.080353 TGATTTGTGATTCATTACTGCTGAG 57.920 36.000 0.00 0.00 0.00 3.35
4421 4466 5.885230 TTTGTGATTCATTACTGCTGAGG 57.115 39.130 0.00 0.00 0.00 3.86
4422 4467 4.558226 TGTGATTCATTACTGCTGAGGT 57.442 40.909 0.00 0.00 0.00 3.85
4423 4468 5.675684 TGTGATTCATTACTGCTGAGGTA 57.324 39.130 0.00 0.00 0.00 3.08
4424 4469 6.239217 TGTGATTCATTACTGCTGAGGTAT 57.761 37.500 0.00 0.00 0.00 2.73
4425 4470 6.653020 TGTGATTCATTACTGCTGAGGTATT 58.347 36.000 0.00 0.00 0.00 1.89
4426 4471 6.763135 TGTGATTCATTACTGCTGAGGTATTC 59.237 38.462 0.00 0.00 0.00 1.75
4427 4472 6.763135 GTGATTCATTACTGCTGAGGTATTCA 59.237 38.462 0.00 0.00 0.00 2.57
4428 4473 7.443575 GTGATTCATTACTGCTGAGGTATTCAT 59.556 37.037 0.00 0.00 34.68 2.57
4429 4474 7.994911 TGATTCATTACTGCTGAGGTATTCATT 59.005 33.333 0.00 0.00 34.68 2.57
4430 4475 7.792374 TTCATTACTGCTGAGGTATTCATTC 57.208 36.000 0.00 0.00 34.68 2.67
4431 4476 7.129457 TCATTACTGCTGAGGTATTCATTCT 57.871 36.000 0.00 0.00 34.68 2.40
4432 4477 7.212976 TCATTACTGCTGAGGTATTCATTCTC 58.787 38.462 0.00 0.00 34.68 2.87
4433 4478 6.798427 TTACTGCTGAGGTATTCATTCTCT 57.202 37.500 0.00 0.00 34.68 3.10
4434 4479 5.275067 ACTGCTGAGGTATTCATTCTCTC 57.725 43.478 0.00 0.00 34.68 3.20
4435 4480 4.961730 ACTGCTGAGGTATTCATTCTCTCT 59.038 41.667 0.00 0.00 34.68 3.10
4436 4481 5.068987 ACTGCTGAGGTATTCATTCTCTCTC 59.931 44.000 0.00 0.00 34.68 3.20
4437 4482 4.958581 TGCTGAGGTATTCATTCTCTCTCA 59.041 41.667 0.00 0.00 34.68 3.27
4438 4483 5.601729 TGCTGAGGTATTCATTCTCTCTCAT 59.398 40.000 0.00 0.00 34.68 2.90
4439 4484 6.779539 TGCTGAGGTATTCATTCTCTCTCATA 59.220 38.462 0.00 0.00 34.68 2.15
4440 4485 7.288621 TGCTGAGGTATTCATTCTCTCTCATAA 59.711 37.037 0.00 0.00 34.68 1.90
4441 4486 7.598493 GCTGAGGTATTCATTCTCTCTCATAAC 59.402 40.741 0.00 0.00 34.68 1.89
4442 4487 8.774546 TGAGGTATTCATTCTCTCTCATAACT 57.225 34.615 0.00 0.00 0.00 2.24
4443 4488 8.637099 TGAGGTATTCATTCTCTCTCATAACTG 58.363 37.037 0.00 0.00 0.00 3.16
4444 4489 8.774546 AGGTATTCATTCTCTCTCATAACTGA 57.225 34.615 0.00 0.00 0.00 3.41
4445 4490 9.378504 AGGTATTCATTCTCTCTCATAACTGAT 57.621 33.333 0.00 0.00 0.00 2.90
4446 4491 9.421806 GGTATTCATTCTCTCTCATAACTGATG 57.578 37.037 0.00 0.00 36.82 3.07
4447 4492 9.979578 GTATTCATTCTCTCTCATAACTGATGT 57.020 33.333 0.00 0.00 36.84 3.06
4452 4497 9.978044 CATTCTCTCTCATAACTGATGTATTCA 57.022 33.333 0.00 0.00 36.84 2.57
4458 4503 9.978044 CTCTCATAACTGATGTATTCAATCTCA 57.022 33.333 0.00 0.00 36.84 3.27
4464 4509 8.797350 AACTGATGTATTCAATCTCATTGTCA 57.203 30.769 0.00 0.00 41.02 3.58
4465 4510 8.975663 ACTGATGTATTCAATCTCATTGTCAT 57.024 30.769 0.00 0.00 41.02 3.06
4468 4513 8.981647 TGATGTATTCAATCTCATTGTCATACG 58.018 33.333 12.06 0.00 38.67 3.06
4469 4514 7.713764 TGTATTCAATCTCATTGTCATACGG 57.286 36.000 12.06 0.00 38.67 4.02
4470 4515 7.272244 TGTATTCAATCTCATTGTCATACGGT 58.728 34.615 12.06 0.00 38.67 4.83
4471 4516 7.768582 TGTATTCAATCTCATTGTCATACGGTT 59.231 33.333 12.06 0.00 38.67 4.44
4472 4517 9.256477 GTATTCAATCTCATTGTCATACGGTTA 57.744 33.333 0.00 0.00 41.02 2.85
4473 4518 7.770801 TTCAATCTCATTGTCATACGGTTAG 57.229 36.000 0.00 0.00 41.02 2.34
4474 4519 6.873997 TCAATCTCATTGTCATACGGTTAGT 58.126 36.000 0.00 0.00 41.02 2.24
4475 4520 6.756542 TCAATCTCATTGTCATACGGTTAGTG 59.243 38.462 0.00 0.00 41.02 2.74
4476 4521 5.654603 TCTCATTGTCATACGGTTAGTGT 57.345 39.130 0.00 0.00 0.00 3.55
4477 4522 5.647589 TCTCATTGTCATACGGTTAGTGTC 58.352 41.667 0.00 0.00 0.00 3.67
4478 4523 5.417894 TCTCATTGTCATACGGTTAGTGTCT 59.582 40.000 0.00 0.00 0.00 3.41
4479 4524 6.032956 TCATTGTCATACGGTTAGTGTCTT 57.967 37.500 0.00 0.00 0.00 3.01
4480 4525 6.097356 TCATTGTCATACGGTTAGTGTCTTC 58.903 40.000 0.00 0.00 0.00 2.87
4481 4526 5.456548 TTGTCATACGGTTAGTGTCTTCA 57.543 39.130 0.00 0.00 0.00 3.02
4482 4527 5.055642 TGTCATACGGTTAGTGTCTTCAG 57.944 43.478 0.00 0.00 0.00 3.02
4483 4528 4.521639 TGTCATACGGTTAGTGTCTTCAGT 59.478 41.667 0.00 0.00 0.00 3.41
4484 4529 5.010314 TGTCATACGGTTAGTGTCTTCAGTT 59.990 40.000 0.00 0.00 0.00 3.16
4485 4530 5.345202 GTCATACGGTTAGTGTCTTCAGTTG 59.655 44.000 0.00 0.00 0.00 3.16
4486 4531 3.814005 ACGGTTAGTGTCTTCAGTTGT 57.186 42.857 0.00 0.00 0.00 3.32
4487 4532 4.133013 ACGGTTAGTGTCTTCAGTTGTT 57.867 40.909 0.00 0.00 0.00 2.83
4488 4533 3.869246 ACGGTTAGTGTCTTCAGTTGTTG 59.131 43.478 0.00 0.00 0.00 3.33
4489 4534 3.303132 CGGTTAGTGTCTTCAGTTGTTGC 60.303 47.826 0.00 0.00 0.00 4.17
4490 4535 3.877508 GGTTAGTGTCTTCAGTTGTTGCT 59.122 43.478 0.00 0.00 0.00 3.91
4491 4536 4.260784 GGTTAGTGTCTTCAGTTGTTGCTG 60.261 45.833 0.00 0.00 37.81 4.41
4492 4537 2.991250 AGTGTCTTCAGTTGTTGCTGT 58.009 42.857 0.00 0.00 37.70 4.40
4493 4538 3.347216 AGTGTCTTCAGTTGTTGCTGTT 58.653 40.909 0.00 0.00 37.70 3.16
4494 4539 3.127548 AGTGTCTTCAGTTGTTGCTGTTG 59.872 43.478 0.00 0.00 37.70 3.33
4495 4540 3.081061 TGTCTTCAGTTGTTGCTGTTGT 58.919 40.909 0.00 0.00 37.70 3.32
4496 4541 4.094294 GTGTCTTCAGTTGTTGCTGTTGTA 59.906 41.667 0.00 0.00 37.70 2.41
4497 4542 4.697828 TGTCTTCAGTTGTTGCTGTTGTAA 59.302 37.500 0.00 0.00 37.70 2.41
4498 4543 5.028375 GTCTTCAGTTGTTGCTGTTGTAAC 58.972 41.667 0.00 0.00 38.89 2.50
4499 4544 4.941263 TCTTCAGTTGTTGCTGTTGTAACT 59.059 37.500 0.00 0.00 39.12 2.24
4500 4545 4.875544 TCAGTTGTTGCTGTTGTAACTC 57.124 40.909 0.00 0.00 39.12 3.01
4501 4546 4.257731 TCAGTTGTTGCTGTTGTAACTCA 58.742 39.130 0.00 0.00 39.12 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.562182 TGTCCAGGAAAAGGAGGAAAAC 58.438 45.455 0.00 0.00 35.42 2.43
114 115 4.978083 CAAGGCATTGCTCAGAAAGTAT 57.022 40.909 8.82 0.00 0.00 2.12
171 172 2.149578 CAGCAGACCTTTGTCCAGAAG 58.850 52.381 0.00 0.00 42.81 2.85
199 200 4.021456 GGCAACTAAAACCTAAACATGCCT 60.021 41.667 5.75 0.00 45.55 4.75
204 205 5.141182 TGGATGGCAACTAAAACCTAAACA 58.859 37.500 0.00 0.00 37.61 2.83
206 207 6.926630 AATGGATGGCAACTAAAACCTAAA 57.073 33.333 0.00 0.00 37.61 1.85
207 208 6.926630 AAATGGATGGCAACTAAAACCTAA 57.073 33.333 0.00 0.00 37.61 2.69
208 209 8.602472 AATAAATGGATGGCAACTAAAACCTA 57.398 30.769 0.00 0.00 37.61 3.08
209 210 7.494922 AATAAATGGATGGCAACTAAAACCT 57.505 32.000 0.00 0.00 37.61 3.50
210 211 7.279981 GGAAATAAATGGATGGCAACTAAAACC 59.720 37.037 0.00 0.00 37.61 3.27
211 212 8.040727 AGGAAATAAATGGATGGCAACTAAAAC 58.959 33.333 0.00 0.00 37.61 2.43
212 213 8.040132 CAGGAAATAAATGGATGGCAACTAAAA 58.960 33.333 0.00 0.00 37.61 1.52
213 214 7.364585 CCAGGAAATAAATGGATGGCAACTAAA 60.365 37.037 0.00 0.00 36.09 1.85
214 215 6.098124 CCAGGAAATAAATGGATGGCAACTAA 59.902 38.462 0.00 0.00 36.09 2.24
215 216 5.598005 CCAGGAAATAAATGGATGGCAACTA 59.402 40.000 0.00 0.00 36.09 2.24
216 217 4.406649 CCAGGAAATAAATGGATGGCAACT 59.593 41.667 0.00 0.00 36.09 3.16
217 218 4.443315 CCCAGGAAATAAATGGATGGCAAC 60.443 45.833 0.00 0.00 36.09 4.17
218 219 3.710677 CCCAGGAAATAAATGGATGGCAA 59.289 43.478 0.00 0.00 36.09 4.52
219 220 3.052262 TCCCAGGAAATAAATGGATGGCA 60.052 43.478 0.00 0.00 36.09 4.92
220 221 3.575805 TCCCAGGAAATAAATGGATGGC 58.424 45.455 0.00 0.00 36.09 4.40
221 222 7.854166 TTAATCCCAGGAAATAAATGGATGG 57.146 36.000 0.00 0.00 36.09 3.51
224 225 9.944079 TGTATTTAATCCCAGGAAATAAATGGA 57.056 29.630 20.40 10.79 36.09 3.41
231 232 9.243105 CGGATATTGTATTTAATCCCAGGAAAT 57.757 33.333 0.00 0.00 35.47 2.17
232 233 7.668052 CCGGATATTGTATTTAATCCCAGGAAA 59.332 37.037 0.00 0.00 35.47 3.13
233 234 7.017750 TCCGGATATTGTATTTAATCCCAGGAA 59.982 37.037 0.00 0.00 35.47 3.36
234 235 6.502510 TCCGGATATTGTATTTAATCCCAGGA 59.497 38.462 0.00 0.00 35.47 3.86
235 236 6.717289 TCCGGATATTGTATTTAATCCCAGG 58.283 40.000 0.00 0.00 35.47 4.45
236 237 8.807948 ATTCCGGATATTGTATTTAATCCCAG 57.192 34.615 4.15 0.00 35.47 4.45
237 238 8.387039 TGATTCCGGATATTGTATTTAATCCCA 58.613 33.333 4.15 0.00 35.47 4.37
238 239 8.801882 TGATTCCGGATATTGTATTTAATCCC 57.198 34.615 4.15 0.00 35.47 3.85
246 247 9.436957 GTTGTAGATTGATTCCGGATATTGTAT 57.563 33.333 4.15 0.00 0.00 2.29
247 248 7.597369 CGTTGTAGATTGATTCCGGATATTGTA 59.403 37.037 4.15 0.00 0.00 2.41
248 249 6.423905 CGTTGTAGATTGATTCCGGATATTGT 59.576 38.462 4.15 0.00 0.00 2.71
249 250 6.423905 ACGTTGTAGATTGATTCCGGATATTG 59.576 38.462 4.15 0.00 0.00 1.90
250 251 6.522054 ACGTTGTAGATTGATTCCGGATATT 58.478 36.000 4.15 0.00 0.00 1.28
251 252 6.097915 ACGTTGTAGATTGATTCCGGATAT 57.902 37.500 4.15 1.27 0.00 1.63
252 253 5.524971 ACGTTGTAGATTGATTCCGGATA 57.475 39.130 4.15 0.00 0.00 2.59
253 254 4.402056 ACGTTGTAGATTGATTCCGGAT 57.598 40.909 4.15 0.00 0.00 4.18
254 255 3.880047 ACGTTGTAGATTGATTCCGGA 57.120 42.857 0.00 0.00 0.00 5.14
255 256 3.682858 ACAACGTTGTAGATTGATTCCGG 59.317 43.478 31.49 0.00 40.16 5.14
256 257 4.921470 ACAACGTTGTAGATTGATTCCG 57.079 40.909 31.49 1.36 40.16 4.30
257 258 5.997385 ACAACAACGTTGTAGATTGATTCC 58.003 37.500 32.47 0.00 41.31 3.01
258 259 7.129622 TCAACAACAACGTTGTAGATTGATTC 58.870 34.615 30.99 0.00 45.28 2.52
259 260 7.022055 TCAACAACAACGTTGTAGATTGATT 57.978 32.000 30.99 21.00 45.28 2.57
260 261 6.612247 TCAACAACAACGTTGTAGATTGAT 57.388 33.333 30.99 21.34 45.28 2.57
261 262 6.612247 ATCAACAACAACGTTGTAGATTGA 57.388 33.333 33.64 33.64 45.28 2.57
262 263 8.948853 ATTATCAACAACAACGTTGTAGATTG 57.051 30.769 32.47 30.18 45.28 2.67
263 264 9.607285 GAATTATCAACAACAACGTTGTAGATT 57.393 29.630 32.47 22.66 45.28 2.40
264 265 8.999431 AGAATTATCAACAACAACGTTGTAGAT 58.001 29.630 32.47 28.88 45.28 1.98
265 266 8.373048 AGAATTATCAACAACAACGTTGTAGA 57.627 30.769 32.47 25.36 45.28 2.59
266 267 9.103048 GAAGAATTATCAACAACAACGTTGTAG 57.897 33.333 32.47 21.61 45.28 2.74
267 268 8.832521 AGAAGAATTATCAACAACAACGTTGTA 58.167 29.630 32.47 18.05 45.28 2.41
268 269 7.703328 AGAAGAATTATCAACAACAACGTTGT 58.297 30.769 27.70 27.70 45.28 3.32
269 270 8.560576 AAGAAGAATTATCAACAACAACGTTG 57.439 30.769 26.20 26.20 46.21 4.10
270 271 9.878599 CTAAGAAGAATTATCAACAACAACGTT 57.121 29.630 0.00 0.00 0.00 3.99
271 272 9.052759 ACTAAGAAGAATTATCAACAACAACGT 57.947 29.630 0.00 0.00 0.00 3.99
272 273 9.530129 GACTAAGAAGAATTATCAACAACAACG 57.470 33.333 0.00 0.00 0.00 4.10
273 274 9.530129 CGACTAAGAAGAATTATCAACAACAAC 57.470 33.333 0.00 0.00 0.00 3.32
274 275 8.227791 GCGACTAAGAAGAATTATCAACAACAA 58.772 33.333 0.00 0.00 0.00 2.83
292 293 8.669394 TGTTGATATTGTATATCGCGACTAAG 57.331 34.615 12.93 0.00 0.00 2.18
300 301 8.296000 TGCCCAAAATGTTGATATTGTATATCG 58.704 33.333 0.00 0.00 36.83 2.92
306 307 7.999450 AAAATGCCCAAAATGTTGATATTGT 57.001 28.000 0.00 0.00 36.83 2.71
311 312 7.718753 TCAAGTTAAAATGCCCAAAATGTTGAT 59.281 29.630 0.00 0.00 36.83 2.57
345 346 1.239296 TGCATGCTCAGCTTCCACAC 61.239 55.000 20.33 0.00 0.00 3.82
368 372 4.275936 AGTGACACTTGACCTAACAATTGC 59.724 41.667 5.05 0.00 35.05 3.56
405 409 4.202161 ACTGTATAACTTGAGATGCTCCCG 60.202 45.833 0.00 0.00 0.00 5.14
406 410 5.283457 ACTGTATAACTTGAGATGCTCCC 57.717 43.478 0.00 0.00 0.00 4.30
444 448 8.465999 CAAGTCCATATGCATTTTAAACACCTA 58.534 33.333 3.54 0.00 0.00 3.08
458 462 0.940126 CGACAGGCAAGTCCATATGC 59.060 55.000 0.00 0.00 41.82 3.14
493 497 1.308998 GCTCCAACCCACATAATCCG 58.691 55.000 0.00 0.00 0.00 4.18
494 498 2.435372 TGCTCCAACCCACATAATCC 57.565 50.000 0.00 0.00 0.00 3.01
575 592 2.496899 AAAATCTCCAGCCACGATGT 57.503 45.000 0.00 0.00 0.00 3.06
660 679 7.491682 GGTATGATTACCACTGCAAAATGAAT 58.508 34.615 0.00 0.00 46.24 2.57
680 705 3.560068 GGCTGTACATTTTCCTCGGTATG 59.440 47.826 0.00 0.00 0.00 2.39
742 767 6.946340 TCACAATCTCTGCCATTACTTTCTA 58.054 36.000 0.00 0.00 0.00 2.10
839 864 8.857098 ACTCTATTAGTTGTGTCTTGTACTTCA 58.143 33.333 0.00 0.00 33.35 3.02
871 896 2.044650 AATGCGACCCATGCTGCT 60.045 55.556 0.00 0.00 33.49 4.24
890 915 1.941325 CATTACACGAAGCTCCCTCC 58.059 55.000 0.00 0.00 0.00 4.30
914 939 3.347958 TGTCCATTTCACAAAGAACGC 57.652 42.857 0.00 0.00 35.56 4.84
937 962 8.669946 TTATATACTTGATCATTGCGGTTTCA 57.330 30.769 0.00 0.00 0.00 2.69
961 986 1.142688 ACATCCTCCAACCAGCCCTT 61.143 55.000 0.00 0.00 0.00 3.95
978 1003 0.950836 CATGTGCAACCTTCCGAACA 59.049 50.000 0.00 0.00 34.36 3.18
1230 1255 2.432510 CGCTAGATCTTGGGACCTCTTT 59.567 50.000 14.60 0.00 0.00 2.52
1646 1671 4.408182 TGAATAAGGGCTCTAGACAAGC 57.592 45.455 0.00 0.00 39.09 4.01
2357 2383 0.382873 TACCAATCGACGTCCATCCG 59.617 55.000 10.58 0.00 0.00 4.18
2409 2435 4.925054 CGAAGTCGGTGTATACTGGAAAAA 59.075 41.667 4.17 0.00 33.84 1.94
2819 2848 1.466360 GCGCTTCCAATGCTTGTAGTG 60.466 52.381 0.00 0.00 0.00 2.74
2820 2849 0.804989 GCGCTTCCAATGCTTGTAGT 59.195 50.000 0.00 0.00 0.00 2.73
2821 2850 0.804364 TGCGCTTCCAATGCTTGTAG 59.196 50.000 9.73 0.00 0.00 2.74
2822 2851 1.199789 CTTGCGCTTCCAATGCTTGTA 59.800 47.619 9.73 0.00 0.00 2.41
2823 2852 0.038892 CTTGCGCTTCCAATGCTTGT 60.039 50.000 9.73 0.00 0.00 3.16
2824 2853 1.349259 GCTTGCGCTTCCAATGCTTG 61.349 55.000 9.73 0.00 0.00 4.01
2825 2854 1.080298 GCTTGCGCTTCCAATGCTT 60.080 52.632 9.73 0.00 0.00 3.91
2826 2855 0.677731 TAGCTTGCGCTTCCAATGCT 60.678 50.000 9.73 9.58 46.47 3.79
2827 2856 0.524180 GTAGCTTGCGCTTCCAATGC 60.524 55.000 9.73 1.23 46.47 3.56
2880 2918 5.574188 ACATTCCATAACCTCAAGCTTCTT 58.426 37.500 0.00 0.00 0.00 2.52
3157 3195 9.123902 CAAATTGGACAATGGAGATAAGTATGA 57.876 33.333 0.00 0.00 0.00 2.15
3450 3488 1.267732 CCTCGAATCGCAGAACATTGC 60.268 52.381 0.00 0.00 43.58 3.56
3587 3631 8.896744 CATATCAACATGTTAAAGTGGTCAGAT 58.103 33.333 11.53 8.17 0.00 2.90
3914 3958 4.617875 CGCAAGGATTTCTCCCGT 57.382 55.556 0.00 0.00 43.21 5.28
3963 4008 0.779997 AAGAAGGAATGGTGGCACCT 59.220 50.000 34.69 18.24 39.58 4.00
4301 4346 2.621055 GTTCACACAACCCATGCTTACA 59.379 45.455 0.00 0.00 0.00 2.41
4315 4360 8.755018 CAAATTTTATTCTTGAGGTGTTCACAC 58.245 33.333 1.10 1.10 45.72 3.82
4316 4361 8.474025 ACAAATTTTATTCTTGAGGTGTTCACA 58.526 29.630 5.32 0.00 34.94 3.58
4317 4362 8.871686 ACAAATTTTATTCTTGAGGTGTTCAC 57.128 30.769 0.00 0.00 34.94 3.18
4321 4366 9.965824 CACTAACAAATTTTATTCTTGAGGTGT 57.034 29.630 0.00 0.00 0.00 4.16
4337 4382 8.627403 CCTGAGCATTATGAATCACTAACAAAT 58.373 33.333 0.00 0.00 0.00 2.32
4338 4383 7.611467 ACCTGAGCATTATGAATCACTAACAAA 59.389 33.333 0.00 0.00 0.00 2.83
4339 4384 7.112122 ACCTGAGCATTATGAATCACTAACAA 58.888 34.615 0.00 0.00 0.00 2.83
4340 4385 6.653020 ACCTGAGCATTATGAATCACTAACA 58.347 36.000 0.00 0.00 0.00 2.41
4341 4386 8.839310 ATACCTGAGCATTATGAATCACTAAC 57.161 34.615 0.00 0.00 0.00 2.34
4342 4387 9.276590 CAATACCTGAGCATTATGAATCACTAA 57.723 33.333 0.00 0.00 0.00 2.24
4343 4388 7.879677 CCAATACCTGAGCATTATGAATCACTA 59.120 37.037 0.00 0.00 0.00 2.74
4344 4389 6.713903 CCAATACCTGAGCATTATGAATCACT 59.286 38.462 0.00 0.00 0.00 3.41
4345 4390 6.488006 ACCAATACCTGAGCATTATGAATCAC 59.512 38.462 0.00 0.00 0.00 3.06
4346 4391 6.604171 ACCAATACCTGAGCATTATGAATCA 58.396 36.000 0.00 0.00 0.00 2.57
4347 4392 7.516198 AACCAATACCTGAGCATTATGAATC 57.484 36.000 0.00 0.00 0.00 2.52
4348 4393 7.342799 ACAAACCAATACCTGAGCATTATGAAT 59.657 33.333 0.00 0.00 0.00 2.57
4349 4394 6.663093 ACAAACCAATACCTGAGCATTATGAA 59.337 34.615 0.00 0.00 0.00 2.57
4350 4395 6.095300 CACAAACCAATACCTGAGCATTATGA 59.905 38.462 0.00 0.00 0.00 2.15
4351 4396 6.267817 CACAAACCAATACCTGAGCATTATG 58.732 40.000 0.00 0.00 0.00 1.90
4352 4397 5.163519 GCACAAACCAATACCTGAGCATTAT 60.164 40.000 0.00 0.00 0.00 1.28
4353 4398 4.157656 GCACAAACCAATACCTGAGCATTA 59.842 41.667 0.00 0.00 0.00 1.90
4354 4399 3.056607 GCACAAACCAATACCTGAGCATT 60.057 43.478 0.00 0.00 0.00 3.56
4355 4400 2.493278 GCACAAACCAATACCTGAGCAT 59.507 45.455 0.00 0.00 0.00 3.79
4356 4401 1.885887 GCACAAACCAATACCTGAGCA 59.114 47.619 0.00 0.00 0.00 4.26
4357 4402 2.162408 GAGCACAAACCAATACCTGAGC 59.838 50.000 0.00 0.00 0.00 4.26
4358 4403 3.189287 GTGAGCACAAACCAATACCTGAG 59.811 47.826 0.00 0.00 0.00 3.35
4359 4404 3.146066 GTGAGCACAAACCAATACCTGA 58.854 45.455 0.00 0.00 0.00 3.86
4360 4405 2.228822 GGTGAGCACAAACCAATACCTG 59.771 50.000 2.75 0.00 36.41 4.00
4361 4406 2.108250 AGGTGAGCACAAACCAATACCT 59.892 45.455 2.75 0.00 39.05 3.08
4362 4407 2.514803 AGGTGAGCACAAACCAATACC 58.485 47.619 2.75 0.00 39.05 2.73
4363 4408 5.699097 TTTAGGTGAGCACAAACCAATAC 57.301 39.130 2.75 0.00 39.05 1.89
4364 4409 6.716934 TTTTTAGGTGAGCACAAACCAATA 57.283 33.333 2.75 0.00 39.05 1.90
4365 4410 5.606348 TTTTTAGGTGAGCACAAACCAAT 57.394 34.783 2.75 0.00 39.05 3.16
4388 4433 9.715121 AGTAATGAATCACAAATCATTTTTGCT 57.285 25.926 6.34 0.00 42.12 3.91
4389 4434 9.749490 CAGTAATGAATCACAAATCATTTTTGC 57.251 29.630 6.34 0.00 42.12 3.68
4390 4435 9.749490 GCAGTAATGAATCACAAATCATTTTTG 57.251 29.630 6.34 6.85 42.12 2.44
4391 4436 9.715121 AGCAGTAATGAATCACAAATCATTTTT 57.285 25.926 6.34 0.00 42.12 1.94
4392 4437 9.146984 CAGCAGTAATGAATCACAAATCATTTT 57.853 29.630 6.34 0.00 42.12 1.82
4393 4438 8.525316 TCAGCAGTAATGAATCACAAATCATTT 58.475 29.630 6.34 0.00 42.12 2.32
4394 4439 8.058667 TCAGCAGTAATGAATCACAAATCATT 57.941 30.769 0.00 6.30 45.54 2.57
4395 4440 7.201794 CCTCAGCAGTAATGAATCACAAATCAT 60.202 37.037 0.00 0.00 37.88 2.45
4396 4441 6.094464 CCTCAGCAGTAATGAATCACAAATCA 59.906 38.462 0.00 0.00 0.00 2.57
4397 4442 6.094603 ACCTCAGCAGTAATGAATCACAAATC 59.905 38.462 0.00 0.00 0.00 2.17
4398 4443 5.948162 ACCTCAGCAGTAATGAATCACAAAT 59.052 36.000 0.00 0.00 0.00 2.32
4399 4444 5.316167 ACCTCAGCAGTAATGAATCACAAA 58.684 37.500 0.00 0.00 0.00 2.83
4400 4445 4.910195 ACCTCAGCAGTAATGAATCACAA 58.090 39.130 0.00 0.00 0.00 3.33
4401 4446 4.558226 ACCTCAGCAGTAATGAATCACA 57.442 40.909 0.00 0.00 0.00 3.58
4402 4447 6.763135 TGAATACCTCAGCAGTAATGAATCAC 59.237 38.462 0.00 0.00 0.00 3.06
4403 4448 6.888105 TGAATACCTCAGCAGTAATGAATCA 58.112 36.000 0.00 0.00 0.00 2.57
4404 4449 7.976135 ATGAATACCTCAGCAGTAATGAATC 57.024 36.000 0.00 0.00 37.52 2.52
4405 4450 8.216423 AGAATGAATACCTCAGCAGTAATGAAT 58.784 33.333 0.00 0.00 37.52 2.57
4406 4451 7.568349 AGAATGAATACCTCAGCAGTAATGAA 58.432 34.615 0.00 0.00 37.52 2.57
4407 4452 7.070447 AGAGAATGAATACCTCAGCAGTAATGA 59.930 37.037 0.00 0.00 37.52 2.57
4408 4453 7.215789 AGAGAATGAATACCTCAGCAGTAATG 58.784 38.462 0.00 0.00 37.52 1.90
4409 4454 7.289782 AGAGAGAATGAATACCTCAGCAGTAAT 59.710 37.037 0.00 0.00 37.52 1.89
4410 4455 6.609212 AGAGAGAATGAATACCTCAGCAGTAA 59.391 38.462 0.00 0.00 37.52 2.24
4411 4456 6.132658 AGAGAGAATGAATACCTCAGCAGTA 58.867 40.000 0.00 0.00 37.52 2.74
4412 4457 4.961730 AGAGAGAATGAATACCTCAGCAGT 59.038 41.667 0.00 0.00 37.52 4.40
4413 4458 5.068855 TGAGAGAGAATGAATACCTCAGCAG 59.931 44.000 0.00 0.00 37.52 4.24
4414 4459 4.958581 TGAGAGAGAATGAATACCTCAGCA 59.041 41.667 0.00 0.00 37.52 4.41
4415 4460 5.528043 TGAGAGAGAATGAATACCTCAGC 57.472 43.478 0.00 0.00 37.52 4.26
4416 4461 8.859090 AGTTATGAGAGAGAATGAATACCTCAG 58.141 37.037 0.00 0.00 37.52 3.35
4417 4462 8.637099 CAGTTATGAGAGAGAATGAATACCTCA 58.363 37.037 0.00 0.00 38.81 3.86
4418 4463 8.855110 TCAGTTATGAGAGAGAATGAATACCTC 58.145 37.037 0.00 0.00 0.00 3.85
4419 4464 8.774546 TCAGTTATGAGAGAGAATGAATACCT 57.225 34.615 0.00 0.00 0.00 3.08
4420 4465 9.421806 CATCAGTTATGAGAGAGAATGAATACC 57.578 37.037 0.00 0.00 39.29 2.73
4421 4466 9.979578 ACATCAGTTATGAGAGAGAATGAATAC 57.020 33.333 0.00 0.00 39.29 1.89
4426 4471 9.978044 TGAATACATCAGTTATGAGAGAGAATG 57.022 33.333 0.00 0.00 39.29 2.67
4432 4477 9.978044 TGAGATTGAATACATCAGTTATGAGAG 57.022 33.333 0.00 0.00 39.77 3.20
4438 4483 9.889128 TGACAATGAGATTGAATACATCAGTTA 57.111 29.630 3.35 0.00 42.83 2.24
4439 4484 8.797350 TGACAATGAGATTGAATACATCAGTT 57.203 30.769 3.35 0.00 42.83 3.16
4440 4485 8.975663 ATGACAATGAGATTGAATACATCAGT 57.024 30.769 3.35 0.00 42.83 3.41
4442 4487 8.981647 CGTATGACAATGAGATTGAATACATCA 58.018 33.333 17.29 7.22 42.83 3.07
4443 4488 8.438513 CCGTATGACAATGAGATTGAATACATC 58.561 37.037 17.29 3.41 42.83 3.06
4444 4489 7.933577 ACCGTATGACAATGAGATTGAATACAT 59.066 33.333 17.29 12.58 42.83 2.29
4445 4490 7.272244 ACCGTATGACAATGAGATTGAATACA 58.728 34.615 17.29 8.65 42.83 2.29
4446 4491 7.715265 ACCGTATGACAATGAGATTGAATAC 57.285 36.000 3.35 9.04 42.83 1.89
4447 4492 9.476202 CTAACCGTATGACAATGAGATTGAATA 57.524 33.333 3.35 0.00 42.83 1.75
4448 4493 7.987458 ACTAACCGTATGACAATGAGATTGAAT 59.013 33.333 3.35 0.38 42.83 2.57
4449 4494 7.277760 CACTAACCGTATGACAATGAGATTGAA 59.722 37.037 3.35 0.00 42.83 2.69
4450 4495 6.756542 CACTAACCGTATGACAATGAGATTGA 59.243 38.462 3.35 0.00 42.83 2.57
4451 4496 6.535150 ACACTAACCGTATGACAATGAGATTG 59.465 38.462 0.00 0.00 45.59 2.67
4452 4497 6.640518 ACACTAACCGTATGACAATGAGATT 58.359 36.000 0.00 0.00 0.00 2.40
4453 4498 6.096987 AGACACTAACCGTATGACAATGAGAT 59.903 38.462 0.00 0.00 0.00 2.75
4454 4499 5.417894 AGACACTAACCGTATGACAATGAGA 59.582 40.000 0.00 0.00 0.00 3.27
4455 4500 5.651530 AGACACTAACCGTATGACAATGAG 58.348 41.667 0.00 0.00 0.00 2.90
4456 4501 5.654603 AGACACTAACCGTATGACAATGA 57.345 39.130 0.00 0.00 0.00 2.57
4457 4502 5.867174 TGAAGACACTAACCGTATGACAATG 59.133 40.000 0.00 0.00 0.00 2.82
4458 4503 6.032956 TGAAGACACTAACCGTATGACAAT 57.967 37.500 0.00 0.00 0.00 2.71
4459 4504 5.010314 ACTGAAGACACTAACCGTATGACAA 59.990 40.000 0.00 0.00 0.00 3.18
4460 4505 4.521639 ACTGAAGACACTAACCGTATGACA 59.478 41.667 0.00 0.00 0.00 3.58
4461 4506 5.056894 ACTGAAGACACTAACCGTATGAC 57.943 43.478 0.00 0.00 0.00 3.06
4462 4507 5.010314 ACAACTGAAGACACTAACCGTATGA 59.990 40.000 0.00 0.00 0.00 2.15
4463 4508 5.227908 ACAACTGAAGACACTAACCGTATG 58.772 41.667 0.00 0.00 0.00 2.39
4464 4509 5.464030 ACAACTGAAGACACTAACCGTAT 57.536 39.130 0.00 0.00 0.00 3.06
4465 4510 4.924305 ACAACTGAAGACACTAACCGTA 57.076 40.909 0.00 0.00 0.00 4.02
4466 4511 3.814005 ACAACTGAAGACACTAACCGT 57.186 42.857 0.00 0.00 0.00 4.83
4467 4512 3.303132 GCAACAACTGAAGACACTAACCG 60.303 47.826 0.00 0.00 0.00 4.44
4468 4513 3.877508 AGCAACAACTGAAGACACTAACC 59.122 43.478 0.00 0.00 0.00 2.85
4469 4514 4.332819 ACAGCAACAACTGAAGACACTAAC 59.667 41.667 0.00 0.00 40.25 2.34
4470 4515 4.513442 ACAGCAACAACTGAAGACACTAA 58.487 39.130 0.00 0.00 40.25 2.24
4471 4516 4.137116 ACAGCAACAACTGAAGACACTA 57.863 40.909 0.00 0.00 40.25 2.74
4472 4517 2.991250 ACAGCAACAACTGAAGACACT 58.009 42.857 0.00 0.00 40.25 3.55
4473 4518 3.119849 ACAACAGCAACAACTGAAGACAC 60.120 43.478 0.00 0.00 40.25 3.67
4474 4519 3.081061 ACAACAGCAACAACTGAAGACA 58.919 40.909 0.00 0.00 40.25 3.41
4475 4520 3.764885 ACAACAGCAACAACTGAAGAC 57.235 42.857 0.00 0.00 40.25 3.01
4476 4521 4.941263 AGTTACAACAGCAACAACTGAAGA 59.059 37.500 0.00 0.00 40.25 2.87
4477 4522 5.163764 TGAGTTACAACAGCAACAACTGAAG 60.164 40.000 0.00 0.00 40.25 3.02
4478 4523 4.697828 TGAGTTACAACAGCAACAACTGAA 59.302 37.500 0.00 0.00 40.25 3.02
4479 4524 4.257731 TGAGTTACAACAGCAACAACTGA 58.742 39.130 0.00 0.00 40.25 3.41
4480 4525 4.614555 TGAGTTACAACAGCAACAACTG 57.385 40.909 0.00 0.00 43.59 3.16


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

AutoCloner maintained by Alex Coulton.