Multiple sequence alignment - TraesCS5A01G435100

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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 TraesCS5A01G435100 chr5A 100.000 2462 0 0 1 2462 618306873 618309334 0.000000e+00 4547
1 TraesCS5A01G435100 chr5A 83.600 939 128 18 536 1464 618188729 618189651 0.000000e+00 857
2 TraesCS5A01G435100 chr5A 76.987 1447 228 61 202 1620 618273093 618274462 0.000000e+00 730
3 TraesCS5A01G435100 chr5A 81.366 805 120 15 297 1096 618158728 618159507 1.610000e-176 628
4 TraesCS5A01G435100 chr5A 77.883 737 143 11 365 1096 618125876 618126597 8.080000e-120 440
5 TraesCS5A01G435100 chr5A 80.576 556 77 11 1833 2373 618432752 618433291 1.370000e-107 399
6 TraesCS5A01G435100 chr5A 84.661 339 50 2 1127 1464 618430888 618431225 1.090000e-88 337
7 TraesCS5A01G435100 chr5B 96.134 1371 39 8 230 1593 611129272 611130635 0.000000e+00 2226
8 TraesCS5A01G435100 chr5B 79.741 1160 197 26 317 1464 610880387 610881520 0.000000e+00 806
9 TraesCS5A01G435100 chr5B 80.126 1107 192 24 366 1464 610882882 610883968 0.000000e+00 800
10 TraesCS5A01G435100 chr5B 79.838 739 123 18 365 1096 610867407 610868126 1.310000e-142 516
11 TraesCS5A01G435100 chr5B 78.700 831 136 22 271 1089 611077184 611077985 1.310000e-142 516
12 TraesCS5A01G435100 chr5B 81.250 528 82 7 576 1096 610876840 610877357 6.340000e-111 411
13 TraesCS5A01G435100 chr5B 76.716 743 147 17 366 1086 611327365 611328103 8.250000e-105 390
14 TraesCS5A01G435100 chr5B 80.739 514 60 15 1749 2251 611131312 611131797 5.000000e-97 364
15 TraesCS5A01G435100 chr5B 86.061 330 45 1 1130 1458 610923693 610924022 1.080000e-93 353
16 TraesCS5A01G435100 chr5B 85.251 339 48 2 1127 1464 610966310 610966647 5.040000e-92 348
17 TraesCS5A01G435100 chr5B 85.759 323 46 0 1136 1458 610877367 610877689 2.340000e-90 342
18 TraesCS5A01G435100 chr5B 96.721 183 6 0 1 183 611129088 611129270 3.080000e-79 305
19 TraesCS5A01G435100 chr5B 80.511 313 44 4 1833 2145 610968003 610968298 8.860000e-55 224
20 TraesCS5A01G435100 chr5B 95.833 96 4 0 2367 2462 712439351 712439256 3.280000e-34 156
21 TraesCS5A01G435100 chr5D 79.352 1419 227 41 74 1464 494657034 494658414 0.000000e+00 937
22 TraesCS5A01G435100 chr5D 80.146 821 133 15 281 1096 494651418 494652213 9.810000e-164 586
23 TraesCS5A01G435100 chr5D 78.290 737 127 21 365 1096 494645936 494646644 6.250000e-121 444
24 TraesCS5A01G435100 chr5D 78.049 656 134 8 437 1087 494783312 494783962 2.950000e-109 405
25 TraesCS5A01G435100 chr5D 87.616 323 40 0 1136 1458 494655134 494655456 2.310000e-100 375
26 TraesCS5A01G435100 chr5D 84.756 328 46 4 1136 1461 494765442 494765767 2.360000e-85 326
27 TraesCS5A01G435100 chr5D 95.833 96 4 0 2367 2462 70640596 70640501 3.280000e-34 156
28 TraesCS5A01G435100 chr7D 95.192 104 3 1 2359 2462 621738229 621738330 1.960000e-36 163
29 TraesCS5A01G435100 chr7A 97.872 94 2 0 2369 2462 267276162 267276069 1.960000e-36 163
30 TraesCS5A01G435100 chr4A 96.875 96 3 0 2367 2462 681900750 681900845 7.050000e-36 161
31 TraesCS5A01G435100 chr2D 97.826 92 2 0 2371 2462 542514672 542514763 2.530000e-35 159
32 TraesCS5A01G435100 chr6A 95.876 97 4 0 2366 2462 479885243 479885339 9.110000e-35 158
33 TraesCS5A01G435100 chr2B 97.802 91 2 0 2372 2462 783405623 783405533 9.110000e-35 158
34 TraesCS5A01G435100 chr2A 96.809 94 3 0 2369 2462 180979265 180979172 9.110000e-35 158


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 TraesCS5A01G435100 chr5A 618306873 618309334 2461 False 4547.000000 4547 100.000000 1 2462 1 chr5A.!!$F5 2461
1 TraesCS5A01G435100 chr5A 618188729 618189651 922 False 857.000000 857 83.600000 536 1464 1 chr5A.!!$F3 928
2 TraesCS5A01G435100 chr5A 618273093 618274462 1369 False 730.000000 730 76.987000 202 1620 1 chr5A.!!$F4 1418
3 TraesCS5A01G435100 chr5A 618158728 618159507 779 False 628.000000 628 81.366000 297 1096 1 chr5A.!!$F2 799
4 TraesCS5A01G435100 chr5A 618125876 618126597 721 False 440.000000 440 77.883000 365 1096 1 chr5A.!!$F1 731
5 TraesCS5A01G435100 chr5A 618430888 618433291 2403 False 368.000000 399 82.618500 1127 2373 2 chr5A.!!$F6 1246
6 TraesCS5A01G435100 chr5B 611129088 611131797 2709 False 965.000000 2226 91.198000 1 2251 3 chr5B.!!$F7 2250
7 TraesCS5A01G435100 chr5B 610876840 610883968 7128 False 589.750000 806 81.719000 317 1464 4 chr5B.!!$F5 1147
8 TraesCS5A01G435100 chr5B 610867407 610868126 719 False 516.000000 516 79.838000 365 1096 1 chr5B.!!$F1 731
9 TraesCS5A01G435100 chr5B 611077184 611077985 801 False 516.000000 516 78.700000 271 1089 1 chr5B.!!$F3 818
10 TraesCS5A01G435100 chr5B 611327365 611328103 738 False 390.000000 390 76.716000 366 1086 1 chr5B.!!$F4 720
11 TraesCS5A01G435100 chr5B 610966310 610968298 1988 False 286.000000 348 82.881000 1127 2145 2 chr5B.!!$F6 1018
12 TraesCS5A01G435100 chr5D 494651418 494658414 6996 False 632.666667 937 82.371333 74 1464 3 chr5D.!!$F4 1390
13 TraesCS5A01G435100 chr5D 494645936 494646644 708 False 444.000000 444 78.290000 365 1096 1 chr5D.!!$F1 731
14 TraesCS5A01G435100 chr5D 494783312 494783962 650 False 405.000000 405 78.049000 437 1087 1 chr5D.!!$F3 650

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
368 4798 0.029681 AGCCCACCTCCATAGTCCAT 60.03 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 13292 0.179045 GATGTCCTTGGGGTGGATCG 60.179 60.0 0.0 0.0 35.87 3.69 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
23 24 2.347452 CGTATTTTCTGGTCGCACGAAT 59.653 45.455 0.00 0.00 0.00 3.34
35 36 1.165270 GCACGAATAGCAACCTTGGT 58.835 50.000 0.00 0.00 42.29 3.67
36 37 1.539827 GCACGAATAGCAACCTTGGTT 59.460 47.619 0.00 0.00 39.88 3.67
78 79 6.088016 TCATTATTAATCACAGCCAATGCC 57.912 37.500 0.00 0.00 38.69 4.40
183 184 0.594540 TGACATGCAGCAACGCAAAC 60.595 50.000 0.00 0.00 46.87 2.93
184 185 0.594540 GACATGCAGCAACGCAAACA 60.595 50.000 0.00 0.00 46.87 2.83
185 186 0.032403 ACATGCAGCAACGCAAACAT 59.968 45.000 0.00 0.00 46.87 2.71
186 187 0.711670 CATGCAGCAACGCAAACATC 59.288 50.000 0.00 0.00 46.87 3.06
187 188 0.599558 ATGCAGCAACGCAAACATCT 59.400 45.000 0.00 0.00 46.87 2.90
188 189 1.233919 TGCAGCAACGCAAACATCTA 58.766 45.000 0.00 0.00 39.45 1.98
189 190 1.197492 TGCAGCAACGCAAACATCTAG 59.803 47.619 0.00 0.00 39.45 2.43
190 191 1.197721 GCAGCAACGCAAACATCTAGT 59.802 47.619 0.00 0.00 0.00 2.57
191 192 2.415168 GCAGCAACGCAAACATCTAGTA 59.585 45.455 0.00 0.00 0.00 1.82
192 193 3.484229 GCAGCAACGCAAACATCTAGTAG 60.484 47.826 0.00 0.00 0.00 2.57
193 194 3.926527 CAGCAACGCAAACATCTAGTAGA 59.073 43.478 1.45 1.45 0.00 2.59
194 195 4.568359 CAGCAACGCAAACATCTAGTAGAT 59.432 41.667 6.86 6.86 34.74 1.98
195 196 4.806247 AGCAACGCAAACATCTAGTAGATC 59.194 41.667 9.84 0.00 31.32 2.75
196 197 4.317418 GCAACGCAAACATCTAGTAGATCG 60.317 45.833 9.84 12.13 31.32 3.69
197 198 4.895224 ACGCAAACATCTAGTAGATCGA 57.105 40.909 19.39 0.00 31.32 3.59
198 199 5.244785 ACGCAAACATCTAGTAGATCGAA 57.755 39.130 19.39 0.00 31.32 3.71
199 200 5.647589 ACGCAAACATCTAGTAGATCGAAA 58.352 37.500 19.39 0.00 31.32 3.46
200 201 5.744345 ACGCAAACATCTAGTAGATCGAAAG 59.256 40.000 19.39 8.45 31.32 2.62
203 204 6.531948 GCAAACATCTAGTAGATCGAAAGTGT 59.468 38.462 9.84 2.32 31.32 3.55
211 212 3.753294 AGATCGAAAGTGTGAACAGGT 57.247 42.857 0.00 0.00 0.00 4.00
226 227 1.609208 CAGGTCACTGTTTCCCCTTG 58.391 55.000 0.00 0.00 39.92 3.61
227 228 1.142870 CAGGTCACTGTTTCCCCTTGA 59.857 52.381 0.00 0.00 39.92 3.02
228 229 1.143073 AGGTCACTGTTTCCCCTTGAC 59.857 52.381 0.00 0.00 36.63 3.18
259 260 3.840124 ACGAATGGATCTAACTTCCCC 57.160 47.619 0.00 0.00 31.87 4.81
260 261 2.102588 ACGAATGGATCTAACTTCCCCG 59.897 50.000 0.00 0.00 31.87 5.73
262 267 3.553096 CGAATGGATCTAACTTCCCCGAG 60.553 52.174 0.00 0.00 31.87 4.63
265 270 3.294214 TGGATCTAACTTCCCCGAGTAC 58.706 50.000 0.00 0.00 31.87 2.73
267 272 3.959449 GGATCTAACTTCCCCGAGTACTT 59.041 47.826 0.00 0.00 0.00 2.24
283 288 7.663081 CCCGAGTACTTGTACACCTCTATATAA 59.337 40.741 9.32 0.00 0.00 0.98
360 365 1.920325 CTCTCCAAGCCCACCTCCA 60.920 63.158 0.00 0.00 0.00 3.86
361 366 1.229951 TCTCCAAGCCCACCTCCAT 60.230 57.895 0.00 0.00 0.00 3.41
363 368 0.471617 CTCCAAGCCCACCTCCATAG 59.528 60.000 0.00 0.00 0.00 2.23
368 4798 0.029681 AGCCCACCTCCATAGTCCAT 60.030 55.000 0.00 0.00 0.00 3.41
527 4986 1.562008 TGTTGGAGGTCACAACTGGAA 59.438 47.619 9.36 0.00 46.28 3.53
667 7571 1.271379 ACAAGAATGGAGAACCGGTGG 60.271 52.381 8.52 0.00 39.42 4.61
674 7578 1.026718 GGAGAACCGGTGGCTTCATG 61.027 60.000 8.52 0.00 0.00 3.07
677 7581 1.523154 GAACCGGTGGCTTCATGCAA 61.523 55.000 8.52 0.00 45.15 4.08
732 7643 5.064325 GGAGGTTTCATATTGTGGTTACGAC 59.936 44.000 0.00 0.00 0.00 4.34
1113 10969 0.322277 CTGTGCTTCAGATGGCCAGT 60.322 55.000 13.05 0.00 46.27 4.00
1187 11043 2.872245 CGGCTGACAGGTACAATATTGG 59.128 50.000 19.37 3.97 0.00 3.16
1531 11428 6.434028 TCTTCATGTATGTTTGAAGGGGAAAG 59.566 38.462 11.51 0.00 45.69 2.62
1569 11466 6.283694 TCATATTCAACCTACTCATGTGAGC 58.716 40.000 9.84 0.00 45.79 4.26
1620 11719 8.169977 AGATAAAAGAAAACATTGCTGAGACA 57.830 30.769 0.00 0.00 0.00 3.41
1636 11735 1.955529 GACAGCACATGCACGTACCG 61.956 60.000 6.64 0.00 45.16 4.02
1638 11737 3.418913 GCACATGCACGTACCGCA 61.419 61.111 7.05 7.05 44.94 5.69
1696 11829 0.308684 ACTTCATGCGTGCACTGTTG 59.691 50.000 16.19 9.17 0.00 3.33
1701 11959 0.029300 ATGCGTGCACTGTTGTGTTC 59.971 50.000 16.19 0.00 45.44 3.18
1726 11984 0.034186 GGATGCCCTTCATGTGGACA 60.034 55.000 8.66 4.44 35.05 4.02
1730 11988 1.075212 TGCCCTTCATGTGGACATTGA 59.925 47.619 8.66 0.00 33.61 2.57
1738 11996 2.859165 TGTGGACATTGAGACCTTCC 57.141 50.000 0.00 0.00 32.90 3.46
1739 11997 2.054021 TGTGGACATTGAGACCTTCCA 58.946 47.619 0.00 0.00 33.85 3.53
1743 12001 3.074390 TGGACATTGAGACCTTCCATTGT 59.926 43.478 0.00 0.00 31.19 2.71
1744 12002 4.288366 TGGACATTGAGACCTTCCATTGTA 59.712 41.667 0.00 0.00 31.19 2.41
1745 12003 4.636206 GGACATTGAGACCTTCCATTGTAC 59.364 45.833 0.00 0.00 30.11 2.90
1746 12004 5.241403 ACATTGAGACCTTCCATTGTACA 57.759 39.130 0.00 0.00 0.00 2.90
1747 12005 5.248640 ACATTGAGACCTTCCATTGTACAG 58.751 41.667 0.00 0.00 0.00 2.74
1771 12926 3.136763 CAGCTGTATCGGCATCAAGAAT 58.863 45.455 5.25 0.00 38.37 2.40
1797 12953 2.991250 TCAGGAGGCAATTAGAAGCAC 58.009 47.619 0.00 0.00 0.00 4.40
1823 12979 6.554334 AAAAACACATATACGAACAGCTGT 57.446 33.333 15.25 15.25 0.00 4.40
1824 12980 7.661127 AAAAACACATATACGAACAGCTGTA 57.339 32.000 22.01 4.30 0.00 2.74
1825 12981 7.843490 AAAACACATATACGAACAGCTGTAT 57.157 32.000 22.01 12.49 35.55 2.29
1828 12984 4.617223 CACATATACGAACAGCTGTATCGG 59.383 45.833 33.76 24.68 40.71 4.18
1837 13152 1.458445 CAGCTGTATCGGCATCATTCG 59.542 52.381 5.25 0.00 38.37 3.34
1855 13170 0.035458 CGTTTTCTGCCACCTCTCCT 59.965 55.000 0.00 0.00 0.00 3.69
1941 13264 3.435601 CCTGAGATTTTGGGTCATAGGGG 60.436 52.174 0.00 0.00 0.00 4.79
1957 13280 6.539103 GTCATAGGGGAGAAATTCAAGTACAC 59.461 42.308 0.00 0.00 0.00 2.90
1958 13281 4.993705 AGGGGAGAAATTCAAGTACACA 57.006 40.909 0.00 0.00 0.00 3.72
1962 13285 4.695928 GGGAGAAATTCAAGTACACAGGAC 59.304 45.833 0.00 0.00 0.00 3.85
1963 13286 4.695928 GGAGAAATTCAAGTACACAGGACC 59.304 45.833 0.00 0.00 0.00 4.46
1964 13287 4.652822 AGAAATTCAAGTACACAGGACCC 58.347 43.478 0.00 0.00 0.00 4.46
1965 13288 4.104102 AGAAATTCAAGTACACAGGACCCA 59.896 41.667 0.00 0.00 0.00 4.51
1966 13289 3.703001 ATTCAAGTACACAGGACCCAG 57.297 47.619 0.00 0.00 0.00 4.45
1967 13290 0.685097 TCAAGTACACAGGACCCAGC 59.315 55.000 0.00 0.00 0.00 4.85
1968 13291 0.687354 CAAGTACACAGGACCCAGCT 59.313 55.000 0.00 0.00 0.00 4.24
1969 13292 0.977395 AAGTACACAGGACCCAGCTC 59.023 55.000 0.00 0.00 0.00 4.09
1970 13293 1.215647 GTACACAGGACCCAGCTCG 59.784 63.158 0.00 0.00 0.00 5.03
1971 13294 1.076014 TACACAGGACCCAGCTCGA 59.924 57.895 0.00 0.00 0.00 4.04
1972 13295 0.324368 TACACAGGACCCAGCTCGAT 60.324 55.000 0.00 0.00 0.00 3.59
1973 13296 1.142748 CACAGGACCCAGCTCGATC 59.857 63.158 0.00 0.00 0.00 3.69
1974 13297 2.060980 ACAGGACCCAGCTCGATCC 61.061 63.158 0.00 0.00 0.00 3.36
1975 13298 2.060383 CAGGACCCAGCTCGATCCA 61.060 63.158 0.00 0.00 33.33 3.41
1976 13299 2.060980 AGGACCCAGCTCGATCCAC 61.061 63.158 0.00 0.00 33.33 4.02
1984 13307 2.367202 GCTCGATCCACCCCAAGGA 61.367 63.158 0.00 0.00 39.97 3.36
1993 13316 2.102578 CCACCCCAAGGACATCATTTC 58.897 52.381 0.00 0.00 36.73 2.17
1996 13319 2.292267 CCCCAAGGACATCATTTCTCG 58.708 52.381 0.00 0.00 33.47 4.04
1997 13320 2.356125 CCCCAAGGACATCATTTCTCGT 60.356 50.000 0.00 0.00 33.47 4.18
2003 13326 6.294176 CCAAGGACATCATTTCTCGTCTTTTT 60.294 38.462 0.00 0.00 0.00 1.94
2008 13331 7.206981 ACATCATTTCTCGTCTTTTTGATGT 57.793 32.000 9.23 9.23 44.28 3.06
2009 13332 7.080099 ACATCATTTCTCGTCTTTTTGATGTG 58.920 34.615 13.16 0.00 46.12 3.21
2019 13342 6.094881 TCGTCTTTTTGATGTGAAGTTCCTTT 59.905 34.615 0.00 0.00 33.55 3.11
2035 13358 5.129320 AGTTCCTTTCAAACAGATTTTGCCT 59.871 36.000 0.00 0.00 0.00 4.75
2054 13377 4.243270 GCCTGTTCACACGTAAGAAGTAT 58.757 43.478 2.44 0.00 43.62 2.12
2056 13383 5.287992 GCCTGTTCACACGTAAGAAGTATAC 59.712 44.000 2.44 0.00 43.62 1.47
2069 13396 9.248702 CGTAAGAAGTATACGTCGAATATCTTC 57.751 37.037 12.30 6.55 40.81 2.87
2073 13400 5.619513 AGTATACGTCGAATATCTTCAGCG 58.380 41.667 0.00 3.62 35.57 5.18
2081 13412 4.098044 TCGAATATCTTCAGCGTCCTTTCT 59.902 41.667 0.00 0.00 0.00 2.52
2083 13414 4.744795 ATATCTTCAGCGTCCTTTCTGT 57.255 40.909 0.00 0.00 0.00 3.41
2084 13415 2.154854 TCTTCAGCGTCCTTTCTGTG 57.845 50.000 0.00 0.00 0.00 3.66
2098 13429 4.511527 CTTTCTGTGGACATGACATAGCT 58.488 43.478 0.00 0.00 0.00 3.32
2109 13440 5.987098 ACATGACATAGCTCAGAGTTCATT 58.013 37.500 0.00 0.00 0.00 2.57
2115 13446 7.816513 TGACATAGCTCAGAGTTCATTATATGC 59.183 37.037 0.00 0.00 0.00 3.14
2121 13452 8.381636 AGCTCAGAGTTCATTATATGCCTATTT 58.618 33.333 0.00 0.00 0.00 1.40
2161 13492 1.130561 GAATTGTTCCGTGTAGGCAGC 59.869 52.381 0.00 0.00 40.77 5.25
2163 13494 3.488090 GTTCCGTGTAGGCAGCGC 61.488 66.667 0.00 0.00 40.77 5.92
2223 13556 7.173390 GTCTCTAATATTTTCCACATAGGGTGC 59.827 40.741 0.00 0.00 46.50 5.01
2224 13557 6.905736 TCTAATATTTTCCACATAGGGTGCA 58.094 36.000 0.00 0.00 46.50 4.57
2225 13558 7.350382 TCTAATATTTTCCACATAGGGTGCAA 58.650 34.615 0.00 0.00 46.50 4.08
2226 13559 6.865834 AATATTTTCCACATAGGGTGCAAA 57.134 33.333 0.00 0.00 46.50 3.68
2233 13566 2.493278 CACATAGGGTGCAAAAAGGAGG 59.507 50.000 0.00 0.00 41.36 4.30
2238 13571 1.408969 GGTGCAAAAAGGAGGTTCCA 58.591 50.000 0.00 0.00 39.61 3.53
2252 13585 1.543802 GGTTCCATGTCCATTTTGCGA 59.456 47.619 0.00 0.00 0.00 5.10
2269 13602 1.673760 CGACGCAACTTTTCACCATG 58.326 50.000 0.00 0.00 0.00 3.66
2280 13613 2.936919 TTCACCATGCTGTTGAGTCT 57.063 45.000 0.00 0.00 0.00 3.24
2283 13616 2.074576 CACCATGCTGTTGAGTCTCAG 58.925 52.381 2.12 10.19 35.12 3.35
2297 13630 5.173664 TGAGTCTCAGTCATTATGCTGTTG 58.826 41.667 13.33 9.48 34.57 3.33
2299 13632 5.798132 AGTCTCAGTCATTATGCTGTTGAA 58.202 37.500 13.33 0.00 34.57 2.69
2310 13643 2.722094 TGCTGTTGAAGGTTGTTCAGT 58.278 42.857 0.00 0.00 0.00 3.41
2311 13644 3.088532 TGCTGTTGAAGGTTGTTCAGTT 58.911 40.909 0.00 0.00 0.00 3.16
2315 13648 6.096695 GCTGTTGAAGGTTGTTCAGTTTTTA 58.903 36.000 0.00 0.00 0.00 1.52
2316 13649 6.756542 GCTGTTGAAGGTTGTTCAGTTTTTAT 59.243 34.615 0.00 0.00 0.00 1.40
2317 13650 7.277760 GCTGTTGAAGGTTGTTCAGTTTTTATT 59.722 33.333 0.00 0.00 0.00 1.40
2318 13651 9.150348 CTGTTGAAGGTTGTTCAGTTTTTATTT 57.850 29.630 0.00 0.00 0.00 1.40
2363 13697 8.635328 GTTTTAAAGAGATTGTAGGGGAAAACA 58.365 33.333 0.00 0.00 34.68 2.83
2365 13699 4.576330 AGAGATTGTAGGGGAAAACAGG 57.424 45.455 0.00 0.00 0.00 4.00
2368 13702 5.074746 AGATTGTAGGGGAAAACAGGTTT 57.925 39.130 0.00 0.00 0.00 3.27
2369 13703 6.045106 AGAGATTGTAGGGGAAAACAGGTTTA 59.955 38.462 0.00 0.00 31.63 2.01
2370 13704 6.246163 AGATTGTAGGGGAAAACAGGTTTAG 58.754 40.000 0.00 0.00 31.63 1.85
2371 13705 5.391577 TTGTAGGGGAAAACAGGTTTAGT 57.608 39.130 0.00 0.00 31.63 2.24
2372 13706 6.512514 TTGTAGGGGAAAACAGGTTTAGTA 57.487 37.500 0.00 0.00 31.63 1.82
2373 13707 5.868454 TGTAGGGGAAAACAGGTTTAGTAC 58.132 41.667 0.00 0.00 31.63 2.73
2374 13708 5.608015 TGTAGGGGAAAACAGGTTTAGTACT 59.392 40.000 0.00 0.00 31.63 2.73
2375 13709 5.238624 AGGGGAAAACAGGTTTAGTACTC 57.761 43.478 0.00 0.00 31.63 2.59
2376 13710 4.042560 AGGGGAAAACAGGTTTAGTACTCC 59.957 45.833 0.00 0.00 31.63 3.85
2377 13711 4.330250 GGGAAAACAGGTTTAGTACTCCC 58.670 47.826 13.14 13.14 37.42 4.30
2378 13712 4.042560 GGGAAAACAGGTTTAGTACTCCCT 59.957 45.833 18.12 0.18 39.66 4.20
2379 13713 5.243981 GGAAAACAGGTTTAGTACTCCCTC 58.756 45.833 0.00 0.00 31.63 4.30
2380 13714 5.012871 GGAAAACAGGTTTAGTACTCCCTCT 59.987 44.000 0.00 0.00 31.63 3.69
2381 13715 5.485209 AAACAGGTTTAGTACTCCCTCTG 57.515 43.478 0.00 6.66 0.00 3.35
2382 13716 4.129317 ACAGGTTTAGTACTCCCTCTGT 57.871 45.455 0.00 7.30 0.00 3.41
2383 13717 4.490706 ACAGGTTTAGTACTCCCTCTGTT 58.509 43.478 0.00 0.00 31.17 3.16
2384 13718 4.527427 ACAGGTTTAGTACTCCCTCTGTTC 59.473 45.833 0.00 0.00 31.17 3.18
2385 13719 4.527038 CAGGTTTAGTACTCCCTCTGTTCA 59.473 45.833 0.00 0.00 0.00 3.18
2386 13720 4.527427 AGGTTTAGTACTCCCTCTGTTCAC 59.473 45.833 0.00 0.00 0.00 3.18
2387 13721 4.527427 GGTTTAGTACTCCCTCTGTTCACT 59.473 45.833 0.00 0.00 0.00 3.41
2388 13722 5.011840 GGTTTAGTACTCCCTCTGTTCACTT 59.988 44.000 0.00 0.00 0.00 3.16
2389 13723 6.464039 GGTTTAGTACTCCCTCTGTTCACTTT 60.464 42.308 0.00 0.00 0.00 2.66
2390 13724 6.742559 TTAGTACTCCCTCTGTTCACTTTT 57.257 37.500 0.00 0.00 0.00 2.27
2391 13725 7.844493 TTAGTACTCCCTCTGTTCACTTTTA 57.156 36.000 0.00 0.00 0.00 1.52
2392 13726 6.936968 AGTACTCCCTCTGTTCACTTTTAT 57.063 37.500 0.00 0.00 0.00 1.40
2393 13727 9.537852 TTAGTACTCCCTCTGTTCACTTTTATA 57.462 33.333 0.00 0.00 0.00 0.98
2394 13728 8.431910 AGTACTCCCTCTGTTCACTTTTATAA 57.568 34.615 0.00 0.00 0.00 0.98
2395 13729 8.532819 AGTACTCCCTCTGTTCACTTTTATAAG 58.467 37.037 0.00 0.00 37.40 1.73
2396 13730 7.554959 ACTCCCTCTGTTCACTTTTATAAGA 57.445 36.000 0.00 0.00 35.30 2.10
2397 13731 7.387643 ACTCCCTCTGTTCACTTTTATAAGAC 58.612 38.462 0.00 0.00 35.30 3.01
2398 13732 6.708285 TCCCTCTGTTCACTTTTATAAGACC 58.292 40.000 0.00 0.00 35.30 3.85
2399 13733 6.500751 TCCCTCTGTTCACTTTTATAAGACCT 59.499 38.462 0.00 0.00 35.30 3.85
2400 13734 7.017254 TCCCTCTGTTCACTTTTATAAGACCTT 59.983 37.037 0.00 0.00 35.30 3.50
2401 13735 7.119846 CCCTCTGTTCACTTTTATAAGACCTTG 59.880 40.741 0.00 0.00 35.30 3.61
2402 13736 7.878127 CCTCTGTTCACTTTTATAAGACCTTGA 59.122 37.037 0.00 0.00 35.30 3.02
2403 13737 9.273016 CTCTGTTCACTTTTATAAGACCTTGAA 57.727 33.333 0.00 0.00 35.30 2.69
2404 13738 9.273016 TCTGTTCACTTTTATAAGACCTTGAAG 57.727 33.333 0.00 0.00 35.30 3.02
2405 13739 9.273016 CTGTTCACTTTTATAAGACCTTGAAGA 57.727 33.333 0.00 0.00 35.30 2.87
2406 13740 9.052759 TGTTCACTTTTATAAGACCTTGAAGAC 57.947 33.333 0.00 0.00 35.30 3.01
2407 13741 9.052759 GTTCACTTTTATAAGACCTTGAAGACA 57.947 33.333 0.00 0.00 35.30 3.41
2408 13742 9.793259 TTCACTTTTATAAGACCTTGAAGACAT 57.207 29.630 0.00 0.00 35.30 3.06
2409 13743 9.793259 TCACTTTTATAAGACCTTGAAGACATT 57.207 29.630 0.00 0.00 35.30 2.71
2415 13749 7.913674 ATAAGACCTTGAAGACATTTCAGAC 57.086 36.000 0.00 0.00 0.00 3.51
2416 13750 5.296151 AGACCTTGAAGACATTTCAGACA 57.704 39.130 0.00 0.00 0.00 3.41
2417 13751 5.684704 AGACCTTGAAGACATTTCAGACAA 58.315 37.500 0.00 0.00 0.00 3.18
2418 13752 6.302269 AGACCTTGAAGACATTTCAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
2419 13753 6.206243 AGACCTTGAAGACATTTCAGACAATG 59.794 38.462 0.00 0.00 39.67 2.82
2421 13755 6.147581 CCTTGAAGACATTTCAGACAATGTG 58.852 40.000 12.82 2.31 45.55 3.21
2422 13756 5.112220 TGAAGACATTTCAGACAATGTGC 57.888 39.130 12.82 7.29 45.55 4.57
2423 13757 4.579753 TGAAGACATTTCAGACAATGTGCA 59.420 37.500 12.82 0.00 45.55 4.57
2424 13758 5.067544 TGAAGACATTTCAGACAATGTGCAA 59.932 36.000 12.82 0.00 45.55 4.08
2425 13759 5.518848 AGACATTTCAGACAATGTGCAAA 57.481 34.783 12.82 0.00 45.55 3.68
2426 13760 5.904941 AGACATTTCAGACAATGTGCAAAA 58.095 33.333 12.82 0.00 45.55 2.44
2427 13761 5.750067 AGACATTTCAGACAATGTGCAAAAC 59.250 36.000 12.82 2.36 45.55 2.43
2428 13762 5.417811 ACATTTCAGACAATGTGCAAAACA 58.582 33.333 0.00 0.00 44.19 2.83
2429 13763 5.521010 ACATTTCAGACAATGTGCAAAACAG 59.479 36.000 0.00 0.00 44.19 3.16
2430 13764 4.979943 TTCAGACAATGTGCAAAACAGA 57.020 36.364 0.00 0.00 43.64 3.41
2431 13765 4.291540 TCAGACAATGTGCAAAACAGAC 57.708 40.909 0.00 0.00 43.64 3.51
2432 13766 3.947196 TCAGACAATGTGCAAAACAGACT 59.053 39.130 0.00 0.00 43.64 3.24
2433 13767 5.122519 TCAGACAATGTGCAAAACAGACTA 58.877 37.500 0.00 0.00 43.64 2.59
2434 13768 5.764686 TCAGACAATGTGCAAAACAGACTAT 59.235 36.000 0.00 0.00 43.64 2.12
2435 13769 6.262944 TCAGACAATGTGCAAAACAGACTATT 59.737 34.615 0.00 0.00 43.64 1.73
2436 13770 6.919662 CAGACAATGTGCAAAACAGACTATTT 59.080 34.615 0.00 0.00 43.64 1.40
2437 13771 7.436080 CAGACAATGTGCAAAACAGACTATTTT 59.564 33.333 0.00 0.00 43.64 1.82
2438 13772 7.436080 AGACAATGTGCAAAACAGACTATTTTG 59.564 33.333 13.49 13.49 45.68 2.44
2439 13773 7.264221 ACAATGTGCAAAACAGACTATTTTGA 58.736 30.769 20.47 2.73 45.75 2.69
2440 13774 7.436080 ACAATGTGCAAAACAGACTATTTTGAG 59.564 33.333 20.47 6.72 45.75 3.02
2441 13775 6.449635 TGTGCAAAACAGACTATTTTGAGT 57.550 33.333 20.47 0.00 45.75 3.41
2442 13776 6.862209 TGTGCAAAACAGACTATTTTGAGTT 58.138 32.000 20.47 0.00 45.75 3.01
2443 13777 6.751425 TGTGCAAAACAGACTATTTTGAGTTG 59.249 34.615 20.47 0.00 45.75 3.16
2444 13778 6.751888 GTGCAAAACAGACTATTTTGAGTTGT 59.248 34.615 20.47 0.00 45.75 3.32
2445 13779 6.972328 TGCAAAACAGACTATTTTGAGTTGTC 59.028 34.615 20.47 4.55 45.75 3.18
2446 13780 7.148086 TGCAAAACAGACTATTTTGAGTTGTCT 60.148 33.333 20.47 0.00 45.75 3.41
2453 13787 8.908786 AGACTATTTTGAGTTGTCTGAAATGA 57.091 30.769 0.00 0.00 36.74 2.57
2454 13788 8.778358 AGACTATTTTGAGTTGTCTGAAATGAC 58.222 33.333 0.00 0.00 36.74 3.06
2455 13789 8.682936 ACTATTTTGAGTTGTCTGAAATGACT 57.317 30.769 0.00 0.00 37.79 3.41
2456 13790 9.125026 ACTATTTTGAGTTGTCTGAAATGACTT 57.875 29.630 0.00 0.00 37.79 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.699634 AGCAGAGAACCAAGGTTGCTA 59.300 47.619 13.03 0.00 36.91 3.49
35 36 4.329392 TGATCAAAATCTGCAGCAGAGAA 58.671 39.130 28.60 13.07 44.08 2.87
36 37 3.946606 TGATCAAAATCTGCAGCAGAGA 58.053 40.909 28.60 20.42 44.08 3.10
78 79 4.060667 AAAGGGGGCCACGATGGG 62.061 66.667 4.39 0.00 38.19 4.00
125 126 1.079819 ACGAGGAGACGCCATTGTG 60.080 57.895 0.00 0.00 40.02 3.33
183 184 7.251281 TGTTCACACTTTCGATCTACTAGATG 58.749 38.462 3.11 0.00 34.53 2.90
184 185 7.392494 TGTTCACACTTTCGATCTACTAGAT 57.608 36.000 0.00 0.00 37.73 1.98
185 186 6.127980 CCTGTTCACACTTTCGATCTACTAGA 60.128 42.308 0.00 0.00 0.00 2.43
186 187 6.030849 CCTGTTCACACTTTCGATCTACTAG 58.969 44.000 0.00 0.00 0.00 2.57
187 188 5.475909 ACCTGTTCACACTTTCGATCTACTA 59.524 40.000 0.00 0.00 0.00 1.82
188 189 4.281182 ACCTGTTCACACTTTCGATCTACT 59.719 41.667 0.00 0.00 0.00 2.57
189 190 4.557205 ACCTGTTCACACTTTCGATCTAC 58.443 43.478 0.00 0.00 0.00 2.59
190 191 4.279922 TGACCTGTTCACACTTTCGATCTA 59.720 41.667 0.00 0.00 0.00 1.98
191 192 3.069586 TGACCTGTTCACACTTTCGATCT 59.930 43.478 0.00 0.00 0.00 2.75
192 193 3.390135 TGACCTGTTCACACTTTCGATC 58.610 45.455 0.00 0.00 0.00 3.69
193 194 3.469008 TGACCTGTTCACACTTTCGAT 57.531 42.857 0.00 0.00 0.00 3.59
194 195 2.971660 TGACCTGTTCACACTTTCGA 57.028 45.000 0.00 0.00 0.00 3.71
211 212 2.123589 TCAGTCAAGGGGAAACAGTGA 58.876 47.619 0.00 0.00 0.00 3.41
220 221 2.226437 CGTTTCACATTCAGTCAAGGGG 59.774 50.000 0.00 0.00 0.00 4.79
222 223 4.811555 TTCGTTTCACATTCAGTCAAGG 57.188 40.909 0.00 0.00 0.00 3.61
223 224 5.049474 TCCATTCGTTTCACATTCAGTCAAG 60.049 40.000 0.00 0.00 0.00 3.02
224 225 4.819088 TCCATTCGTTTCACATTCAGTCAA 59.181 37.500 0.00 0.00 0.00 3.18
225 226 4.384940 TCCATTCGTTTCACATTCAGTCA 58.615 39.130 0.00 0.00 0.00 3.41
226 227 5.352569 AGATCCATTCGTTTCACATTCAGTC 59.647 40.000 0.00 0.00 0.00 3.51
227 228 5.248640 AGATCCATTCGTTTCACATTCAGT 58.751 37.500 0.00 0.00 0.00 3.41
228 229 5.808042 AGATCCATTCGTTTCACATTCAG 57.192 39.130 0.00 0.00 0.00 3.02
283 288 5.002516 GCATTTGCTGCCTCTATCTATCTT 58.997 41.667 0.00 0.00 45.66 2.40
306 311 0.103937 GACTGGCGAGAGGGAAGATG 59.896 60.000 1.44 0.00 0.00 2.90
360 365 3.649981 AGTGCTCTGCCATTATGGACTAT 59.350 43.478 16.46 0.00 40.96 2.12
361 366 3.041211 AGTGCTCTGCCATTATGGACTA 58.959 45.455 16.46 0.00 40.96 2.59
363 368 1.945394 CAGTGCTCTGCCATTATGGAC 59.055 52.381 16.46 7.06 39.92 4.02
527 4986 2.420408 CCGTTGGGGTAATATTCCACGT 60.420 50.000 0.00 0.00 0.00 4.49
667 7571 0.727398 GAGGTACGGTTGCATGAAGC 59.273 55.000 0.00 0.00 45.96 3.86
674 7578 2.125793 GGTCGGAGGTACGGTTGC 60.126 66.667 0.00 0.00 0.00 4.17
677 7581 1.852157 TACAGGGTCGGAGGTACGGT 61.852 60.000 0.00 0.00 0.00 4.83
1187 11043 1.139853 CAAGTATCACCCTCAGCCTCC 59.860 57.143 0.00 0.00 0.00 4.30
1569 11466 5.689068 GCAAGAAAAGAAAGTGACCATTCTG 59.311 40.000 2.52 0.00 36.09 3.02
1636 11735 9.931210 GTAAACTAATACACAATGGATAAGTGC 57.069 33.333 0.00 0.00 36.76 4.40
1670 11772 3.125829 AGTGCACGCATGAAGTAATTGAG 59.874 43.478 12.01 0.00 0.00 3.02
1673 11775 2.813754 ACAGTGCACGCATGAAGTAATT 59.186 40.909 12.01 0.00 0.00 1.40
1676 11778 1.530720 CAACAGTGCACGCATGAAGTA 59.469 47.619 12.01 0.00 0.00 2.24
1696 11829 2.717639 AGGGCATCCATACTGAACAC 57.282 50.000 0.00 0.00 34.83 3.32
1701 11959 2.882761 CACATGAAGGGCATCCATACTG 59.117 50.000 0.00 0.00 34.15 2.74
1726 11984 5.505181 ACTGTACAATGGAAGGTCTCAAT 57.495 39.130 0.00 0.00 0.00 2.57
1730 11988 4.804261 GCTGAACTGTACAATGGAAGGTCT 60.804 45.833 0.00 0.00 0.00 3.85
1746 12004 1.482182 TGATGCCGATACAGCTGAACT 59.518 47.619 23.35 3.68 0.00 3.01
1747 12005 1.939974 TGATGCCGATACAGCTGAAC 58.060 50.000 23.35 9.91 0.00 3.18
1759 12914 3.250280 CCTGAATCAGATTCTTGATGCCG 59.750 47.826 21.44 0.00 37.83 5.69
1771 12926 5.678583 CTTCTAATTGCCTCCTGAATCAGA 58.321 41.667 12.53 0.00 32.44 3.27
1809 12965 2.619646 TGCCGATACAGCTGTTCGTATA 59.380 45.455 30.95 21.20 31.55 1.47
1810 12966 1.407618 TGCCGATACAGCTGTTCGTAT 59.592 47.619 30.95 19.92 31.55 3.06
1815 12971 2.627515 ATGATGCCGATACAGCTGTT 57.372 45.000 27.06 12.95 0.00 3.16
1818 12974 1.069204 ACGAATGATGCCGATACAGCT 59.931 47.619 0.00 0.00 0.00 4.24
1819 12975 1.502231 ACGAATGATGCCGATACAGC 58.498 50.000 0.00 0.00 0.00 4.40
1820 12976 4.271049 AGAAAACGAATGATGCCGATACAG 59.729 41.667 0.00 0.00 0.00 2.74
1822 12978 4.518217 CAGAAAACGAATGATGCCGATAC 58.482 43.478 0.00 0.00 0.00 2.24
1823 12979 3.002246 GCAGAAAACGAATGATGCCGATA 59.998 43.478 0.00 0.00 0.00 2.92
1824 12980 2.223340 GCAGAAAACGAATGATGCCGAT 60.223 45.455 0.00 0.00 0.00 4.18
1825 12981 1.130373 GCAGAAAACGAATGATGCCGA 59.870 47.619 0.00 0.00 0.00 5.54
1828 12984 2.253603 GTGGCAGAAAACGAATGATGC 58.746 47.619 0.00 0.00 0.00 3.91
1837 13152 2.615747 GGTAGGAGAGGTGGCAGAAAAC 60.616 54.545 0.00 0.00 0.00 2.43
1855 13170 2.166870 CAGCCTGTTGGTACATACGGTA 59.833 50.000 0.00 0.00 39.30 4.02
1923 13246 3.747852 TCTCCCCTATGACCCAAAATCT 58.252 45.455 0.00 0.00 0.00 2.40
1941 13264 4.695928 GGGTCCTGTGTACTTGAATTTCTC 59.304 45.833 0.00 0.00 0.00 2.87
1957 13280 2.060383 TGGATCGAGCTGGGTCCTG 61.060 63.158 26.22 0.00 0.00 3.86
1958 13281 2.060980 GTGGATCGAGCTGGGTCCT 61.061 63.158 26.22 0.00 0.00 3.85
1962 13285 3.866582 GGGGTGGATCGAGCTGGG 61.867 72.222 6.87 0.00 0.00 4.45
1963 13286 2.599645 CTTGGGGTGGATCGAGCTGG 62.600 65.000 6.87 0.00 0.00 4.85
1964 13287 1.153289 CTTGGGGTGGATCGAGCTG 60.153 63.158 6.87 0.00 0.00 4.24
1965 13288 2.370445 CCTTGGGGTGGATCGAGCT 61.370 63.158 6.87 0.00 0.00 4.09
1966 13289 2.190578 CCTTGGGGTGGATCGAGC 59.809 66.667 0.00 0.00 0.00 5.03
1967 13290 1.264749 TGTCCTTGGGGTGGATCGAG 61.265 60.000 0.00 0.00 35.87 4.04
1968 13291 0.620410 ATGTCCTTGGGGTGGATCGA 60.620 55.000 0.00 0.00 35.87 3.59
1969 13292 0.179045 GATGTCCTTGGGGTGGATCG 60.179 60.000 0.00 0.00 35.87 3.69
1970 13293 0.918983 TGATGTCCTTGGGGTGGATC 59.081 55.000 0.00 0.00 35.87 3.36
1971 13294 1.612035 ATGATGTCCTTGGGGTGGAT 58.388 50.000 0.00 0.00 35.87 3.41
1972 13295 1.381867 AATGATGTCCTTGGGGTGGA 58.618 50.000 0.00 0.00 0.00 4.02
1973 13296 2.102578 GAAATGATGTCCTTGGGGTGG 58.897 52.381 0.00 0.00 0.00 4.61
1974 13297 3.019564 GAGAAATGATGTCCTTGGGGTG 58.980 50.000 0.00 0.00 0.00 4.61
1975 13298 2.356125 CGAGAAATGATGTCCTTGGGGT 60.356 50.000 0.00 0.00 0.00 4.95
1976 13299 2.292267 CGAGAAATGATGTCCTTGGGG 58.708 52.381 0.00 0.00 0.00 4.96
1984 13307 7.206981 ACATCAAAAAGACGAGAAATGATGT 57.793 32.000 11.50 11.50 46.48 3.06
1993 13316 5.237344 AGGAACTTCACATCAAAAAGACGAG 59.763 40.000 0.00 0.00 27.25 4.18
2054 13377 3.303593 GGACGCTGAAGATATTCGACGTA 60.304 47.826 16.84 0.00 31.89 3.57
2056 13383 2.044860 GGACGCTGAAGATATTCGACG 58.955 52.381 11.55 11.55 0.00 5.12
2069 13396 2.533318 GTCCACAGAAAGGACGCTG 58.467 57.895 0.00 0.00 45.35 5.18
2081 13412 3.099141 TCTGAGCTATGTCATGTCCACA 58.901 45.455 0.00 0.00 0.00 4.17
2083 13414 3.369175 ACTCTGAGCTATGTCATGTCCA 58.631 45.455 4.19 0.00 0.00 4.02
2084 13415 4.142071 TGAACTCTGAGCTATGTCATGTCC 60.142 45.833 4.19 0.00 0.00 4.02
2098 13429 9.276590 CACAAATAGGCATATAATGAACTCTGA 57.723 33.333 10.09 0.00 0.00 3.27
2109 13440 7.452562 TCTGCATTCTCACAAATAGGCATATA 58.547 34.615 0.00 0.00 0.00 0.86
2115 13446 6.258230 TGTTTCTGCATTCTCACAAATAGG 57.742 37.500 0.00 0.00 0.00 2.57
2121 13452 3.753815 TCCATGTTTCTGCATTCTCACA 58.246 40.909 0.00 0.00 0.00 3.58
2161 13492 6.662616 CAAAGGTGAAGATATTTATCTGGCG 58.337 40.000 0.96 0.00 41.96 5.69
2163 13494 7.255381 CCTGCAAAGGTGAAGATATTTATCTGG 60.255 40.741 0.96 0.00 41.96 3.86
2172 13503 6.480763 TCAAATACCTGCAAAGGTGAAGATA 58.519 36.000 7.87 0.00 43.03 1.98
2223 13556 3.230134 TGGACATGGAACCTCCTTTTTG 58.770 45.455 0.00 0.00 37.46 2.44
2224 13557 3.611025 TGGACATGGAACCTCCTTTTT 57.389 42.857 0.00 0.00 37.46 1.94
2225 13558 3.833559 ATGGACATGGAACCTCCTTTT 57.166 42.857 0.00 0.00 37.46 2.27
2226 13559 3.833559 AATGGACATGGAACCTCCTTT 57.166 42.857 0.00 0.00 37.46 3.11
2233 13566 2.595386 GTCGCAAAATGGACATGGAAC 58.405 47.619 0.00 0.00 33.41 3.62
2238 13571 0.595588 TTGCGTCGCAAAATGGACAT 59.404 45.000 29.22 0.00 45.96 3.06
2252 13585 1.032014 AGCATGGTGAAAAGTTGCGT 58.968 45.000 0.00 0.00 38.32 5.24
2269 13602 4.033817 GCATAATGACTGAGACTCAACAGC 59.966 45.833 6.61 6.17 37.61 4.40
2280 13613 4.910195 ACCTTCAACAGCATAATGACTGA 58.090 39.130 6.86 0.00 37.35 3.41
2283 13616 5.376854 ACAACCTTCAACAGCATAATGAC 57.623 39.130 0.00 0.00 0.00 3.06
2336 13670 8.857098 GTTTTCCCCTACAATCTCTTTAAAACT 58.143 33.333 0.00 0.00 32.90 2.66
2351 13685 6.119240 AGTACTAAACCTGTTTTCCCCTAC 57.881 41.667 0.00 0.00 34.23 3.18
2361 13695 4.129317 ACAGAGGGAGTACTAAACCTGT 57.871 45.455 15.71 13.77 32.42 4.00
2363 13697 4.527427 GTGAACAGAGGGAGTACTAAACCT 59.473 45.833 11.82 11.82 35.67 3.50
2365 13699 5.725325 AGTGAACAGAGGGAGTACTAAAC 57.275 43.478 0.00 0.00 0.00 2.01
2368 13702 9.537852 TTATAAAAGTGAACAGAGGGAGTACTA 57.462 33.333 0.00 0.00 0.00 1.82
2369 13703 6.936968 ATAAAAGTGAACAGAGGGAGTACT 57.063 37.500 0.00 0.00 0.00 2.73
2370 13704 8.529476 TCTTATAAAAGTGAACAGAGGGAGTAC 58.471 37.037 0.00 0.00 34.13 2.73
2371 13705 8.529476 GTCTTATAAAAGTGAACAGAGGGAGTA 58.471 37.037 0.00 0.00 34.13 2.59
2372 13706 7.387643 GTCTTATAAAAGTGAACAGAGGGAGT 58.612 38.462 0.00 0.00 34.13 3.85
2373 13707 6.819146 GGTCTTATAAAAGTGAACAGAGGGAG 59.181 42.308 0.00 0.00 34.13 4.30
2374 13708 6.500751 AGGTCTTATAAAAGTGAACAGAGGGA 59.499 38.462 0.00 0.00 34.13 4.20
2375 13709 6.712276 AGGTCTTATAAAAGTGAACAGAGGG 58.288 40.000 0.00 0.00 34.13 4.30
2376 13710 7.878127 TCAAGGTCTTATAAAAGTGAACAGAGG 59.122 37.037 0.00 0.00 34.13 3.69
2377 13711 8.833231 TCAAGGTCTTATAAAAGTGAACAGAG 57.167 34.615 0.00 0.00 34.13 3.35
2378 13712 9.273016 CTTCAAGGTCTTATAAAAGTGAACAGA 57.727 33.333 0.00 0.00 34.13 3.41
2379 13713 9.273016 TCTTCAAGGTCTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 34.13 3.16
2380 13714 9.052759 GTCTTCAAGGTCTTATAAAAGTGAACA 57.947 33.333 0.00 0.00 34.13 3.18
2381 13715 9.052759 TGTCTTCAAGGTCTTATAAAAGTGAAC 57.947 33.333 0.00 0.00 34.13 3.18
2382 13716 9.793259 ATGTCTTCAAGGTCTTATAAAAGTGAA 57.207 29.630 0.00 0.00 34.13 3.18
2383 13717 9.793259 AATGTCTTCAAGGTCTTATAAAAGTGA 57.207 29.630 0.00 0.00 34.13 3.41
2389 13723 9.436957 GTCTGAAATGTCTTCAAGGTCTTATAA 57.563 33.333 0.00 0.00 0.00 0.98
2390 13724 8.593679 TGTCTGAAATGTCTTCAAGGTCTTATA 58.406 33.333 0.00 0.00 0.00 0.98
2391 13725 7.453393 TGTCTGAAATGTCTTCAAGGTCTTAT 58.547 34.615 0.00 0.00 0.00 1.73
2392 13726 6.826668 TGTCTGAAATGTCTTCAAGGTCTTA 58.173 36.000 0.00 0.00 0.00 2.10
2393 13727 5.684704 TGTCTGAAATGTCTTCAAGGTCTT 58.315 37.500 0.00 0.00 0.00 3.01
2394 13728 5.296151 TGTCTGAAATGTCTTCAAGGTCT 57.704 39.130 0.00 0.00 0.00 3.85
2395 13729 6.016777 ACATTGTCTGAAATGTCTTCAAGGTC 60.017 38.462 10.41 0.00 45.47 3.85
2396 13730 5.829924 ACATTGTCTGAAATGTCTTCAAGGT 59.170 36.000 10.41 0.00 45.47 3.50
2397 13731 6.147581 CACATTGTCTGAAATGTCTTCAAGG 58.852 40.000 12.25 0.00 45.47 3.61
2398 13732 5.628193 GCACATTGTCTGAAATGTCTTCAAG 59.372 40.000 12.25 5.42 45.47 3.02
2399 13733 5.067544 TGCACATTGTCTGAAATGTCTTCAA 59.932 36.000 12.25 0.00 45.47 2.69
2400 13734 4.579753 TGCACATTGTCTGAAATGTCTTCA 59.420 37.500 12.25 9.40 45.47 3.02
2401 13735 5.112220 TGCACATTGTCTGAAATGTCTTC 57.888 39.130 12.25 7.82 45.47 2.87
2402 13736 5.518848 TTGCACATTGTCTGAAATGTCTT 57.481 34.783 12.25 0.00 45.47 3.01
2403 13737 5.518848 TTTGCACATTGTCTGAAATGTCT 57.481 34.783 12.25 0.00 45.47 3.41
2404 13738 5.519566 TGTTTTGCACATTGTCTGAAATGTC 59.480 36.000 12.25 9.51 45.47 3.06
2406 13740 5.749588 TCTGTTTTGCACATTGTCTGAAATG 59.250 36.000 0.00 9.50 42.21 2.32
2407 13741 5.750067 GTCTGTTTTGCACATTGTCTGAAAT 59.250 36.000 0.00 0.00 33.76 2.17
2408 13742 5.101628 GTCTGTTTTGCACATTGTCTGAAA 58.898 37.500 0.00 0.00 33.76 2.69
2409 13743 4.398988 AGTCTGTTTTGCACATTGTCTGAA 59.601 37.500 0.00 0.00 33.76 3.02
2410 13744 3.947196 AGTCTGTTTTGCACATTGTCTGA 59.053 39.130 0.00 0.00 33.76 3.27
2411 13745 4.297299 AGTCTGTTTTGCACATTGTCTG 57.703 40.909 0.00 0.00 33.76 3.51
2412 13746 6.639632 AATAGTCTGTTTTGCACATTGTCT 57.360 33.333 0.00 0.00 33.76 3.41
2413 13747 7.434897 TCAAAATAGTCTGTTTTGCACATTGTC 59.565 33.333 23.04 0.00 43.04 3.18
2414 13748 7.264221 TCAAAATAGTCTGTTTTGCACATTGT 58.736 30.769 23.04 0.00 43.04 2.71
2415 13749 7.436080 ACTCAAAATAGTCTGTTTTGCACATTG 59.564 33.333 23.04 13.56 43.04 2.82
2416 13750 7.491682 ACTCAAAATAGTCTGTTTTGCACATT 58.508 30.769 23.04 8.08 43.04 2.71
2417 13751 7.042797 ACTCAAAATAGTCTGTTTTGCACAT 57.957 32.000 23.04 10.27 43.04 3.21
2418 13752 6.449635 ACTCAAAATAGTCTGTTTTGCACA 57.550 33.333 23.04 10.61 43.04 4.57
2419 13753 6.751888 ACAACTCAAAATAGTCTGTTTTGCAC 59.248 34.615 23.04 0.00 43.04 4.57
2420 13754 6.862209 ACAACTCAAAATAGTCTGTTTTGCA 58.138 32.000 23.04 14.24 43.04 4.08
2421 13755 7.166473 CAGACAACTCAAAATAGTCTGTTTTGC 59.834 37.037 23.04 12.26 46.72 3.68
2422 13756 8.552469 CAGACAACTCAAAATAGTCTGTTTTG 57.448 34.615 22.26 22.26 46.72 2.44
2428 13762 8.778358 GTCATTTCAGACAACTCAAAATAGTCT 58.222 33.333 0.00 0.00 39.95 3.24
2429 13763 8.778358 AGTCATTTCAGACAACTCAAAATAGTC 58.222 33.333 0.00 0.00 40.98 2.59
2430 13764 8.682936 AGTCATTTCAGACAACTCAAAATAGT 57.317 30.769 0.00 0.00 40.98 2.12


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

AutoCloner maintained by Alex Coulton.