Multiple sequence alignment - TraesCS2B01G410200

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 TraesCS2B01G410200 chr2B 100.000 5435 0 0 1 5435 583683721 583678287 0.000000e+00 10037
1 TraesCS2B01G410200 chr2B 79.032 496 98 3 2991 3481 794502341 794501847 8.720000e-88 335
2 TraesCS2B01G410200 chr2A 95.969 3250 83 17 1806 5028 641960608 641957380 0.000000e+00 5232
3 TraesCS2B01G410200 chr2A 89.202 1880 111 41 2 1806 641962514 641960652 0.000000e+00 2263
4 TraesCS2B01G410200 chr2A 85.903 227 16 6 5190 5405 641957249 641957028 1.520000e-55 228
5 TraesCS2B01G410200 chr2D 96.119 3221 93 18 1806 5019 497370434 497367239 0.000000e+00 5227
6 TraesCS2B01G410200 chr2D 89.417 1871 106 45 4 1806 497372325 497370479 0.000000e+00 2274
7 TraesCS2B01G410200 chr2D 76.141 482 95 16 3214 3689 637092092 637092559 9.100000e-58 235
8 TraesCS2B01G410200 chr3D 78.412 403 49 25 5065 5435 460939538 460939934 1.520000e-55 228
9 TraesCS2B01G410200 chr3B 76.371 474 68 29 4994 5435 611179221 611179682 1.190000e-51 215
10 TraesCS2B01G410200 chr3A 76.181 487 70 28 4983 5435 603267967 603268441 1.190000e-51 215


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 TraesCS2B01G410200 chr2B 583678287 583683721 5434 True 10037.000000 10037 100.000 1 5435 1 chr2B.!!$R1 5434
1 TraesCS2B01G410200 chr2A 641957028 641962514 5486 True 2574.333333 5232 90.358 2 5405 3 chr2A.!!$R1 5403
2 TraesCS2B01G410200 chr2D 497367239 497372325 5086 True 3750.500000 5227 92.768 4 5019 2 chr2D.!!$R1 5015

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
179 187 1.001378 GTGCATGGGTGAACAGAACAC 60.001 52.381 0.0 0.0 33.74 3.32 F
1237 1300 0.032267 CTCCGGTTCCTAATCTCGCC 59.968 60.000 0.0 0.0 0.00 5.54 F
1504 1596 0.249676 AGATGCAGCTCACACTCCTG 59.750 55.000 0.0 0.0 0.00 3.86 F
3115 3273 0.596577 TCACTCGGACCAAGTCTTCG 59.403 55.000 0.0 0.0 32.47 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1374 0.960861 GGCCCGGAACTCTTTTCCAG 60.961 60.0 0.73 0.0 38.49 3.86 R
3115 3273 2.309528 TGACAAGCATATCCACGGAC 57.690 50.0 0.00 0.0 0.00 4.79 R
3415 3573 0.538287 ACCACTTTGGCTTCTCAGGC 60.538 55.0 0.00 0.0 42.67 4.85 R
4668 4830 0.899717 TCTCCAAAAGCCCACATGCC 60.900 55.0 0.00 0.0 0.00 4.40 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
69 72 7.843490 CTTGGAAGCATCATTTCAATCAATT 57.157 32.000 0.00 0.00 0.00 2.32
99 102 5.120830 CGATCTCCTTTTAATTCCTATGCCG 59.879 44.000 0.00 0.00 0.00 5.69
131 139 6.269769 ACTTAAAAATGACCCATTGGATGTGT 59.730 34.615 3.62 0.00 34.04 3.72
134 142 4.806640 AATGACCCATTGGATGTGTTTC 57.193 40.909 3.62 0.00 32.39 2.78
165 173 2.543641 TCATTGCTCTAGACGTGCATG 58.456 47.619 3.82 3.82 41.29 4.06
179 187 1.001378 GTGCATGGGTGAACAGAACAC 60.001 52.381 0.00 0.00 33.74 3.32
281 290 9.271828 CTTTAAAGGTAAGCAAATTGACCAATT 57.728 29.630 7.37 2.38 42.35 2.32
282 291 8.600449 TTAAAGGTAAGCAAATTGACCAATTG 57.400 30.769 8.55 0.00 40.57 2.32
303 312 6.544327 TTGGTTCATCAAATATCCCCCTAT 57.456 37.500 0.00 0.00 0.00 2.57
305 314 6.552008 TGGTTCATCAAATATCCCCCTATTC 58.448 40.000 0.00 0.00 0.00 1.75
314 323 1.815757 TCCCCCTATTCCCACTTAGC 58.184 55.000 0.00 0.00 0.00 3.09
319 328 1.202651 CCTATTCCCACTTAGCCCACG 60.203 57.143 0.00 0.00 0.00 4.94
335 345 3.623060 GCCCACGCCACATGATTATATAG 59.377 47.826 0.00 0.00 0.00 1.31
336 346 4.832248 CCCACGCCACATGATTATATAGT 58.168 43.478 0.00 0.00 0.00 2.12
337 347 5.625886 GCCCACGCCACATGATTATATAGTA 60.626 44.000 0.00 0.00 0.00 1.82
422 433 2.889678 AGAAAAGAAGCTTTGGCCTCTG 59.110 45.455 3.32 0.00 38.19 3.35
436 447 1.417145 GCCTCTGCCATCTCTCAATCT 59.583 52.381 0.00 0.00 0.00 2.40
444 455 3.894427 GCCATCTCTCAATCTCTACCTCA 59.106 47.826 0.00 0.00 0.00 3.86
499 535 8.082242 AGTTGCTTGGCTTTTTAAACTATACTG 58.918 33.333 0.00 0.00 0.00 2.74
531 568 3.078918 TCTTTTGGATTCCTCCCCCAAAT 59.921 43.478 3.95 0.00 45.83 2.32
755 806 1.153549 CACCTACCGAGCAAGCCTC 60.154 63.158 0.00 0.00 37.22 4.70
756 807 2.359967 ACCTACCGAGCAAGCCTCC 61.360 63.158 0.00 0.00 37.27 4.30
757 808 2.105128 CTACCGAGCAAGCCTCCG 59.895 66.667 0.00 0.00 37.27 4.63
758 809 2.678934 TACCGAGCAAGCCTCCGT 60.679 61.111 0.00 0.00 37.27 4.69
759 810 2.227089 CTACCGAGCAAGCCTCCGTT 62.227 60.000 0.00 0.00 37.27 4.44
760 811 2.501223 TACCGAGCAAGCCTCCGTTG 62.501 60.000 0.00 0.00 37.27 4.10
761 812 3.121030 CGAGCAAGCCTCCGTTGG 61.121 66.667 0.00 0.00 37.27 3.77
762 813 2.747855 GAGCAAGCCTCCGTTGGG 60.748 66.667 0.00 0.00 34.35 4.12
829 880 2.224621 CCGGGCCTGAACAGATTCATAT 60.225 50.000 15.09 0.00 43.92 1.78
830 881 3.480470 CGGGCCTGAACAGATTCATATT 58.520 45.455 5.28 0.00 43.92 1.28
903 958 5.680229 CGAATTACTTGCTAGTACTACCACG 59.320 44.000 7.56 0.00 36.61 4.94
904 959 2.935481 ACTTGCTAGTACTACCACGC 57.065 50.000 0.00 1.65 31.21 5.34
975 1035 1.529865 CGGTTCTTCCTCGTTTGTTCC 59.470 52.381 0.00 0.00 0.00 3.62
1014 1075 1.000866 AGGCATGGGAAAGGAAGGC 59.999 57.895 0.00 0.00 0.00 4.35
1237 1300 0.032267 CTCCGGTTCCTAATCTCGCC 59.968 60.000 0.00 0.00 0.00 5.54
1266 1329 2.098934 TGTTGATTGCTGTTCGTTTGCT 59.901 40.909 0.00 0.00 0.00 3.91
1290 1353 5.476599 TGTTTGGTAGATGTTAGCTGCAATT 59.523 36.000 1.02 0.00 0.00 2.32
1295 1358 5.123820 GGTAGATGTTAGCTGCAATTTGTCA 59.876 40.000 1.02 0.00 0.00 3.58
1297 1360 5.706916 AGATGTTAGCTGCAATTTGTCAAG 58.293 37.500 1.02 0.00 0.00 3.02
1322 1385 2.370189 CCTGAGGTGTCTGGAAAAGAGT 59.630 50.000 0.00 0.00 43.06 3.24
1325 1388 3.181454 TGAGGTGTCTGGAAAAGAGTTCC 60.181 47.826 0.00 0.00 34.84 3.62
1358 1422 2.314071 TTGGGTTAAGGTCTCGGAGA 57.686 50.000 2.97 2.97 0.00 3.71
1483 1575 1.816835 CCTGTGCAGACAATGAGCAAT 59.183 47.619 0.02 0.00 40.35 3.56
1504 1596 0.249676 AGATGCAGCTCACACTCCTG 59.750 55.000 0.00 0.00 0.00 3.86
1517 1609 6.037786 TCACACTCCTGTTATACAAGAAGG 57.962 41.667 0.00 0.00 0.00 3.46
1518 1610 5.778241 TCACACTCCTGTTATACAAGAAGGA 59.222 40.000 0.00 0.00 0.00 3.36
1560 1652 6.127196 TGCCAAACAAACATTTAGAGTTCCTT 60.127 34.615 0.00 0.00 0.00 3.36
1568 1660 5.810095 ACATTTAGAGTTCCTTAGCTGCTT 58.190 37.500 7.79 0.00 0.00 3.91
1625 1717 6.573664 TTTGCTGCTTTGTGTAATCTATGT 57.426 33.333 0.00 0.00 0.00 2.29
1668 1760 2.717639 AACCTCTGTGGCATCATACC 57.282 50.000 0.00 0.00 40.22 2.73
1702 1794 4.543590 TTAGCTCTTACTGAAGCAAGCT 57.456 40.909 0.00 0.00 42.51 3.74
1751 1843 2.558359 GGTATGCCTCATTTGGTATGGC 59.442 50.000 0.00 0.00 43.49 4.40
1755 1847 1.766494 CCTCATTTGGTATGGCAGCA 58.234 50.000 0.00 0.00 0.00 4.41
1771 1863 7.956420 ATGGCAGCAAATGAATAATTACATG 57.044 32.000 0.00 0.00 0.00 3.21
1869 2007 1.496060 TGCATTCCTCGATACCACCT 58.504 50.000 0.00 0.00 0.00 4.00
1891 2029 5.121454 CCTTCTCTTGTGATAGCAAAGACAC 59.879 44.000 0.00 0.00 0.00 3.67
1892 2030 5.213891 TCTCTTGTGATAGCAAAGACACA 57.786 39.130 0.00 0.00 40.66 3.72
1938 2076 3.406361 GTGACGGACACGCTGCTG 61.406 66.667 0.00 0.00 46.04 4.41
2625 2767 5.484290 AGTTCTTGTAGTACTACCCTTGCAT 59.516 40.000 26.41 7.90 35.26 3.96
2725 2875 1.529244 AGCAACCCCACTTCACTGC 60.529 57.895 0.00 0.00 0.00 4.40
2814 2972 8.343168 TGTATTCAAATGACGACCCTAAAATT 57.657 30.769 0.00 0.00 0.00 1.82
2880 3038 6.035650 ACCACACATGAACTCGATTAAATACG 59.964 38.462 0.00 0.00 0.00 3.06
3115 3273 0.596577 TCACTCGGACCAAGTCTTCG 59.403 55.000 0.00 0.00 32.47 3.79
3285 3443 7.554118 TCTGAGAAGTTCAAACTCAAAATCAGT 59.446 33.333 5.50 0.00 39.60 3.41
3415 3573 3.859386 GGGCAAGTAATTCAAATGCTTCG 59.141 43.478 0.00 0.00 37.20 3.79
3666 3825 4.675063 ACCCTGGAAAATGTAGGTTCAT 57.325 40.909 0.00 0.00 0.00 2.57
3728 3888 0.106819 CTCATTGCCCCCTCCTTCTG 60.107 60.000 0.00 0.00 0.00 3.02
3741 3901 4.013050 CCTCCTTCTGTCCATTTTTCCTC 58.987 47.826 0.00 0.00 0.00 3.71
3775 3936 3.209410 CTTGGTGCTTTCTCTTCACTGT 58.791 45.455 0.00 0.00 0.00 3.55
3782 3943 5.348997 GTGCTTTCTCTTCACTGTATACACC 59.651 44.000 0.08 0.00 0.00 4.16
3783 3944 5.011635 TGCTTTCTCTTCACTGTATACACCA 59.988 40.000 0.08 0.00 0.00 4.17
3791 3952 9.770097 CTCTTCACTGTATACACCATTATGAAT 57.230 33.333 0.08 0.00 0.00 2.57
3853 4015 5.104485 TCTCTTATTTTAGGGAGAAGGCACC 60.104 44.000 0.00 0.00 32.76 5.01
3914 4076 3.023832 GACCTTACCAAATCCACCATGG 58.976 50.000 11.19 11.19 39.43 3.66
4183 4345 3.347216 GCTATGGCTCCTCAGTTCAAAA 58.653 45.455 0.00 0.00 35.22 2.44
4496 4658 4.977739 TCCCTTAGTTTCCTGGATCATCAT 59.022 41.667 0.00 0.00 0.00 2.45
4596 4758 0.817229 TTGACAATGTGCGTCTGCCA 60.817 50.000 0.00 0.00 41.78 4.92
4668 4830 1.688197 AGGCTTGTGTTGGTTTCCATG 59.312 47.619 0.00 0.00 31.53 3.66
4707 4869 8.547481 TGGAGAAAGTATAACTCATATCACCA 57.453 34.615 0.00 0.00 33.00 4.17
4726 4891 8.655935 ATCACCATGGAAAATAGAACTCTTTT 57.344 30.769 21.47 0.00 0.00 2.27
4736 4901 9.201989 GAAAATAGAACTCTTTTATGGGGGAAT 57.798 33.333 0.00 0.00 0.00 3.01
4746 4911 5.707066 TTTATGGGGGAATTGGAAAATGG 57.293 39.130 0.00 0.00 0.00 3.16
4752 4917 4.525996 GGGGAATTGGAAAATGGAAATGG 58.474 43.478 0.00 0.00 0.00 3.16
4753 4918 4.227073 GGGGAATTGGAAAATGGAAATGGA 59.773 41.667 0.00 0.00 0.00 3.41
4754 4919 5.103982 GGGGAATTGGAAAATGGAAATGGAT 60.104 40.000 0.00 0.00 0.00 3.41
4755 4920 6.101005 GGGGAATTGGAAAATGGAAATGGATA 59.899 38.462 0.00 0.00 0.00 2.59
4756 4921 7.202214 GGGGAATTGGAAAATGGAAATGGATAT 60.202 37.037 0.00 0.00 0.00 1.63
4757 4922 7.662669 GGGAATTGGAAAATGGAAATGGATATG 59.337 37.037 0.00 0.00 0.00 1.78
4758 4923 8.431222 GGAATTGGAAAATGGAAATGGATATGA 58.569 33.333 0.00 0.00 0.00 2.15
4760 4925 8.786710 ATTGGAAAATGGAAATGGATATGAGA 57.213 30.769 0.00 0.00 0.00 3.27
4761 4926 7.828508 TGGAAAATGGAAATGGATATGAGAG 57.171 36.000 0.00 0.00 0.00 3.20
4762 4927 7.585440 TGGAAAATGGAAATGGATATGAGAGA 58.415 34.615 0.00 0.00 0.00 3.10
4763 4928 8.229605 TGGAAAATGGAAATGGATATGAGAGAT 58.770 33.333 0.00 0.00 0.00 2.75
4770 4935 8.054572 TGGAAATGGATATGAGAGATTTCAACA 58.945 33.333 0.00 0.00 35.59 3.33
4783 4948 8.038492 AGAGATTTCAACAAGTTGCTTATCTC 57.962 34.615 24.65 24.65 41.73 2.75
4798 4963 5.880332 TGCTTATCTCGGCTCACTTATTTTT 59.120 36.000 0.00 0.00 0.00 1.94
4800 4965 6.258947 GCTTATCTCGGCTCACTTATTTTTCT 59.741 38.462 0.00 0.00 0.00 2.52
4802 4967 8.873215 TTATCTCGGCTCACTTATTTTTCTAG 57.127 34.615 0.00 0.00 0.00 2.43
4869 5035 3.071312 GGCAGGTCATCTTGATCTCAGAT 59.929 47.826 0.00 0.00 35.21 2.90
4874 5040 6.014413 CAGGTCATCTTGATCTCAGATGGTAT 60.014 42.308 24.14 13.66 35.21 2.73
4875 5041 6.014413 AGGTCATCTTGATCTCAGATGGTATG 60.014 42.308 24.14 9.63 30.67 2.39
4876 5042 5.638657 GTCATCTTGATCTCAGATGGTATGC 59.361 44.000 24.14 12.68 39.69 3.14
4877 5043 4.613925 TCTTGATCTCAGATGGTATGCC 57.386 45.455 0.00 0.00 0.00 4.40
4895 5061 4.224991 TGCCTGTCTGAATGATTGATGA 57.775 40.909 0.00 0.00 0.00 2.92
4946 5112 6.432581 ACAGGTGTACATTATCTCTAGGTGA 58.567 40.000 0.00 0.00 0.00 4.02
4982 5148 7.014326 GTGTACATGATCTTCAGGTGACCTATA 59.986 40.741 2.59 0.00 41.84 1.31
4983 5149 7.730332 TGTACATGATCTTCAGGTGACCTATAT 59.270 37.037 2.59 0.00 41.84 0.86
4992 5158 8.807118 TCTTCAGGTGACCTATATGATATCAAC 58.193 37.037 9.99 0.37 29.64 3.18
4996 5162 9.467796 CAGGTGACCTATATGATATCAACTCTA 57.532 37.037 9.99 0.00 35.13 2.43
5015 5181 5.869888 ACTCTACTTAAATCACAAAGCTCCG 59.130 40.000 0.00 0.00 0.00 4.63
5019 5185 2.163818 AAATCACAAAGCTCCGACGA 57.836 45.000 0.00 0.00 0.00 4.20
5021 5187 2.163818 ATCACAAAGCTCCGACGAAA 57.836 45.000 0.00 0.00 0.00 3.46
5023 5189 2.489971 TCACAAAGCTCCGACGAAATT 58.510 42.857 0.00 0.00 0.00 1.82
5028 5194 3.982576 AAGCTCCGACGAAATTTGTTT 57.017 38.095 0.00 0.00 0.00 2.83
5029 5195 3.982576 AGCTCCGACGAAATTTGTTTT 57.017 38.095 0.00 0.00 0.00 2.43
5030 5196 5.427036 AAGCTCCGACGAAATTTGTTTTA 57.573 34.783 0.00 0.00 0.00 1.52
5031 5197 5.427036 AGCTCCGACGAAATTTGTTTTAA 57.573 34.783 0.00 0.00 0.00 1.52
5032 5198 6.009115 AGCTCCGACGAAATTTGTTTTAAT 57.991 33.333 0.00 0.00 0.00 1.40
5033 5199 6.443792 AGCTCCGACGAAATTTGTTTTAATT 58.556 32.000 0.00 0.00 0.00 1.40
5034 5200 6.921307 AGCTCCGACGAAATTTGTTTTAATTT 59.079 30.769 0.00 0.00 39.68 1.82
5035 5201 7.001347 GCTCCGACGAAATTTGTTTTAATTTG 58.999 34.615 0.00 0.00 37.72 2.32
5036 5202 7.096394 GCTCCGACGAAATTTGTTTTAATTTGA 60.096 33.333 0.00 0.00 37.72 2.69
5037 5203 8.052313 TCCGACGAAATTTGTTTTAATTTGAC 57.948 30.769 0.00 0.00 37.72 3.18
5038 5204 7.167801 TCCGACGAAATTTGTTTTAATTTGACC 59.832 33.333 0.00 0.00 37.72 4.02
5039 5205 7.277917 CGACGAAATTTGTTTTAATTTGACCC 58.722 34.615 0.00 0.00 37.72 4.46
5040 5206 7.167831 ACGAAATTTGTTTTAATTTGACCCG 57.832 32.000 0.00 0.00 37.72 5.28
5041 5207 6.979238 ACGAAATTTGTTTTAATTTGACCCGA 59.021 30.769 0.00 0.00 37.72 5.14
5042 5208 7.654116 ACGAAATTTGTTTTAATTTGACCCGAT 59.346 29.630 0.00 0.00 37.72 4.18
5043 5209 8.159709 CGAAATTTGTTTTAATTTGACCCGATC 58.840 33.333 0.00 0.00 37.72 3.69
5044 5210 7.575332 AATTTGTTTTAATTTGACCCGATCG 57.425 32.000 8.51 8.51 0.00 3.69
5045 5211 5.692613 TTGTTTTAATTTGACCCGATCGT 57.307 34.783 15.09 0.00 0.00 3.73
5046 5212 5.692613 TGTTTTAATTTGACCCGATCGTT 57.307 34.783 15.09 0.00 0.00 3.85
5047 5213 6.798315 TGTTTTAATTTGACCCGATCGTTA 57.202 33.333 15.09 1.12 0.00 3.18
5048 5214 6.833839 TGTTTTAATTTGACCCGATCGTTAG 58.166 36.000 15.09 4.92 0.00 2.34
5049 5215 6.427547 TGTTTTAATTTGACCCGATCGTTAGT 59.572 34.615 15.09 8.38 0.00 2.24
5050 5216 7.041235 TGTTTTAATTTGACCCGATCGTTAGTT 60.041 33.333 15.09 2.43 0.00 2.24
5051 5217 6.651755 TTAATTTGACCCGATCGTTAGTTC 57.348 37.500 15.09 3.30 0.00 3.01
5052 5218 3.663995 TTTGACCCGATCGTTAGTTCA 57.336 42.857 15.09 5.88 0.00 3.18
5053 5219 3.663995 TTGACCCGATCGTTAGTTCAA 57.336 42.857 15.09 11.31 0.00 2.69
5054 5220 3.880047 TGACCCGATCGTTAGTTCAAT 57.120 42.857 15.09 0.00 0.00 2.57
5055 5221 3.777478 TGACCCGATCGTTAGTTCAATC 58.223 45.455 15.09 0.00 0.00 2.67
5056 5222 2.787680 GACCCGATCGTTAGTTCAATCG 59.212 50.000 15.09 0.00 40.41 3.34
5057 5223 2.165030 ACCCGATCGTTAGTTCAATCGT 59.835 45.455 15.09 0.00 39.39 3.73
5058 5224 3.184541 CCCGATCGTTAGTTCAATCGTT 58.815 45.455 15.09 0.00 39.39 3.85
5059 5225 3.615496 CCCGATCGTTAGTTCAATCGTTT 59.385 43.478 15.09 0.00 39.39 3.60
5060 5226 4.491924 CCCGATCGTTAGTTCAATCGTTTG 60.492 45.833 15.09 0.00 39.39 2.93
5061 5227 4.013397 CGATCGTTAGTTCAATCGTTTGC 58.987 43.478 7.03 0.00 36.99 3.68
5062 5228 3.427516 TCGTTAGTTCAATCGTTTGCG 57.572 42.857 1.18 0.00 39.92 4.85
5063 5229 1.896193 CGTTAGTTCAATCGTTTGCGC 59.104 47.619 0.00 0.00 38.14 6.09
5064 5230 2.411031 CGTTAGTTCAATCGTTTGCGCT 60.411 45.455 9.73 4.88 38.14 5.92
5065 5231 3.181538 CGTTAGTTCAATCGTTTGCGCTA 60.182 43.478 9.73 0.00 38.14 4.26
5066 5232 4.664640 CGTTAGTTCAATCGTTTGCGCTAA 60.665 41.667 9.73 3.97 38.14 3.09
5067 5233 5.321516 GTTAGTTCAATCGTTTGCGCTAAT 58.678 37.500 9.73 0.00 34.50 1.73
5068 5234 4.419522 AGTTCAATCGTTTGCGCTAATT 57.580 36.364 9.73 0.00 38.14 1.40
5069 5235 4.794169 AGTTCAATCGTTTGCGCTAATTT 58.206 34.783 9.73 0.25 38.14 1.82
5070 5236 4.851558 AGTTCAATCGTTTGCGCTAATTTC 59.148 37.500 9.73 0.00 38.14 2.17
5071 5237 4.678509 TCAATCGTTTGCGCTAATTTCT 57.321 36.364 9.73 0.00 38.14 2.52
5072 5238 5.041951 TCAATCGTTTGCGCTAATTTCTT 57.958 34.783 9.73 0.00 38.14 2.52
5073 5239 5.457140 TCAATCGTTTGCGCTAATTTCTTT 58.543 33.333 9.73 0.00 38.14 2.52
5074 5240 5.918011 TCAATCGTTTGCGCTAATTTCTTTT 59.082 32.000 9.73 0.00 38.14 2.27
5075 5241 5.992489 ATCGTTTGCGCTAATTTCTTTTC 57.008 34.783 9.73 0.00 38.14 2.29
5116 5282 4.552166 TTTGTGCTTCTCTTGTTAGTGC 57.448 40.909 0.00 0.00 0.00 4.40
5117 5283 3.475566 TGTGCTTCTCTTGTTAGTGCT 57.524 42.857 0.00 0.00 0.00 4.40
5118 5284 4.600692 TGTGCTTCTCTTGTTAGTGCTA 57.399 40.909 0.00 0.00 0.00 3.49
5119 5285 5.152623 TGTGCTTCTCTTGTTAGTGCTAT 57.847 39.130 0.00 0.00 0.00 2.97
5120 5286 5.551233 TGTGCTTCTCTTGTTAGTGCTATT 58.449 37.500 0.00 0.00 0.00 1.73
5121 5287 5.639506 TGTGCTTCTCTTGTTAGTGCTATTC 59.360 40.000 0.00 0.00 0.00 1.75
5122 5288 5.639506 GTGCTTCTCTTGTTAGTGCTATTCA 59.360 40.000 0.00 0.00 0.00 2.57
5123 5289 6.147821 GTGCTTCTCTTGTTAGTGCTATTCAA 59.852 38.462 0.00 0.00 0.00 2.69
5124 5290 6.710295 TGCTTCTCTTGTTAGTGCTATTCAAA 59.290 34.615 0.00 0.00 0.00 2.69
5125 5291 7.228507 TGCTTCTCTTGTTAGTGCTATTCAAAA 59.771 33.333 0.00 0.00 0.00 2.44
5126 5292 7.748241 GCTTCTCTTGTTAGTGCTATTCAAAAG 59.252 37.037 0.00 0.00 0.00 2.27
5127 5293 7.133891 TCTCTTGTTAGTGCTATTCAAAAGC 57.866 36.000 0.00 0.00 40.50 3.51
5134 5300 3.872511 TGCTATTCAAAAGCACCATGG 57.127 42.857 11.19 11.19 44.78 3.66
5135 5301 3.429492 TGCTATTCAAAAGCACCATGGA 58.571 40.909 21.47 0.00 44.78 3.41
5136 5302 3.444742 TGCTATTCAAAAGCACCATGGAG 59.555 43.478 21.47 12.70 44.78 3.86
5137 5303 3.696051 GCTATTCAAAAGCACCATGGAGA 59.304 43.478 21.47 1.45 39.83 3.71
5138 5304 4.201990 GCTATTCAAAAGCACCATGGAGAG 60.202 45.833 21.47 9.02 39.83 3.20
5139 5305 2.957402 TCAAAAGCACCATGGAGAGT 57.043 45.000 21.47 0.00 0.00 3.24
5140 5306 4.365514 TTCAAAAGCACCATGGAGAGTA 57.634 40.909 21.47 0.00 0.00 2.59
5161 5327 9.810545 AGAGTAAGAGTAGTAATTGAAGAATGC 57.189 33.333 0.00 0.00 0.00 3.56
5162 5328 9.587772 GAGTAAGAGTAGTAATTGAAGAATGCA 57.412 33.333 0.00 0.00 0.00 3.96
5163 5329 9.372369 AGTAAGAGTAGTAATTGAAGAATGCAC 57.628 33.333 0.00 0.00 0.00 4.57
5168 5334 5.886960 AGTAATTGAAGAATGCACCAGTC 57.113 39.130 0.00 0.00 0.00 3.51
5172 5338 7.776969 AGTAATTGAAGAATGCACCAGTCATAT 59.223 33.333 0.00 0.00 30.35 1.78
5175 5341 5.255687 TGAAGAATGCACCAGTCATATTGT 58.744 37.500 0.00 0.00 30.35 2.71
5185 5351 8.210265 TGCACCAGTCATATTGTATTAAGATGA 58.790 33.333 0.00 0.00 0.00 2.92
5216 5423 8.506168 ACTGGTCGAATGAATTATAAACATGT 57.494 30.769 0.00 0.00 0.00 3.21
5223 5430 7.862372 CGAATGAATTATAAACATGTTCCCCTG 59.138 37.037 12.39 0.00 0.00 4.45
5228 5435 9.936759 GAATTATAAACATGTTCCCCTGAAAAA 57.063 29.630 12.39 0.00 30.79 1.94
5252 5459 8.491331 AAAGAATTACATGTTGCAACAAAACT 57.509 26.923 34.06 21.91 43.03 2.66
5253 5460 7.698836 AGAATTACATGTTGCAACAAAACTC 57.301 32.000 34.06 24.77 43.03 3.01
5272 5479 1.968017 ACCAATGAGGCTGCACACG 60.968 57.895 0.50 0.00 43.14 4.49
5340 5555 8.903820 GCAGTAAACCATAAGATAAAACCTGAT 58.096 33.333 0.00 0.00 0.00 2.90
5357 5572 6.672266 ACCTGATAACAAGACAAGAAGAGA 57.328 37.500 0.00 0.00 0.00 3.10
5398 5616 1.544825 TAGCAAGCGAGCCACTCCTT 61.545 55.000 0.00 0.00 34.23 3.36
5401 5619 3.317571 AGCGAGCCACTCCTTGCT 61.318 61.111 0.00 0.00 45.52 3.91
5405 5623 1.018226 CGAGCCACTCCTTGCTGAAG 61.018 60.000 0.00 0.00 38.11 3.02
5406 5624 1.303155 AGCCACTCCTTGCTGAAGC 60.303 57.895 0.00 0.00 36.23 3.86
5432 5650 9.722056 CATACACTTATGCAGGAAAAAGTAATC 57.278 33.333 0.00 0.00 31.20 1.75
5433 5651 7.759489 ACACTTATGCAGGAAAAAGTAATCA 57.241 32.000 0.00 0.00 31.20 2.57
5434 5652 8.353423 ACACTTATGCAGGAAAAAGTAATCAT 57.647 30.769 0.00 0.00 31.20 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.633500 TGCTAGAAAAACACAGCATAACTT 57.367 33.333 0.00 0.00 39.03 2.66
75 78 5.120830 CGGCATAGGAATTAAAAGGAGATCG 59.879 44.000 0.00 0.00 0.00 3.69
83 86 6.378848 AGTTAAAGCCGGCATAGGAATTAAAA 59.621 34.615 31.54 7.50 30.32 1.52
88 91 3.577805 AGTTAAAGCCGGCATAGGAAT 57.422 42.857 31.54 1.71 0.00 3.01
99 102 7.119116 CCAATGGGTCATTTTTAAGTTAAAGCC 59.881 37.037 8.04 6.81 31.05 4.35
131 139 3.023119 AGCAATGAATACGCCATGGAAA 58.977 40.909 18.40 0.00 0.00 3.13
134 142 2.224606 AGAGCAATGAATACGCCATGG 58.775 47.619 7.63 7.63 0.00 3.66
165 173 1.375551 AACACGTGTTCTGTTCACCC 58.624 50.000 27.70 0.00 31.64 4.61
179 187 3.869065 TGCCCCTTTAAGAGATAACACG 58.131 45.455 0.00 0.00 0.00 4.49
281 290 6.468651 GGAATAGGGGGATATTTGATGAACCA 60.469 42.308 0.00 0.00 0.00 3.67
282 291 5.952347 GGAATAGGGGGATATTTGATGAACC 59.048 44.000 0.00 0.00 0.00 3.62
287 296 5.180927 AGTGGGAATAGGGGGATATTTGAT 58.819 41.667 0.00 0.00 0.00 2.57
303 312 2.349755 GCGTGGGCTAAGTGGGAA 59.650 61.111 0.00 0.00 35.83 3.97
305 314 4.028490 TGGCGTGGGCTAAGTGGG 62.028 66.667 0.00 0.00 39.81 4.61
314 323 4.832248 ACTATATAATCATGTGGCGTGGG 58.168 43.478 0.00 0.00 0.00 4.61
319 328 9.448438 TTCATTGGTACTATATAATCATGTGGC 57.552 33.333 0.00 0.00 0.00 5.01
357 367 6.658188 TTGGGGTTTTCTTTGTTACTATGG 57.342 37.500 0.00 0.00 0.00 2.74
422 433 3.894427 TGAGGTAGAGATTGAGAGATGGC 59.106 47.826 0.00 0.00 0.00 4.40
432 443 4.898861 GGACAAGGAGATGAGGTAGAGATT 59.101 45.833 0.00 0.00 0.00 2.40
434 445 3.269643 TGGACAAGGAGATGAGGTAGAGA 59.730 47.826 0.00 0.00 0.00 3.10
436 447 3.757947 TGGACAAGGAGATGAGGTAGA 57.242 47.619 0.00 0.00 0.00 2.59
444 455 2.519013 GGCAAAGTTGGACAAGGAGAT 58.481 47.619 0.00 0.00 0.00 2.75
635 686 0.923358 GTGAGGAGAGAGAGAGGGGA 59.077 60.000 0.00 0.00 0.00 4.81
638 689 0.926293 AGGGTGAGGAGAGAGAGAGG 59.074 60.000 0.00 0.00 0.00 3.69
639 690 1.846439 AGAGGGTGAGGAGAGAGAGAG 59.154 57.143 0.00 0.00 0.00 3.20
640 691 1.843851 GAGAGGGTGAGGAGAGAGAGA 59.156 57.143 0.00 0.00 0.00 3.10
829 880 2.031465 GGCGGTTCTTCGGTGGAA 59.969 61.111 0.00 0.00 0.00 3.53
830 881 4.011517 GGGCGGTTCTTCGGTGGA 62.012 66.667 0.00 0.00 0.00 4.02
904 959 3.399440 AACAGAGAGGAGCAGTTCTTG 57.601 47.619 0.00 0.00 0.00 3.02
1014 1075 2.879907 CCGCAATGACAGCAAGGG 59.120 61.111 0.00 0.00 0.00 3.95
1023 1084 2.809174 CTCGTGACGCCGCAATGA 60.809 61.111 0.00 0.00 0.00 2.57
1237 1300 4.438797 CGAACAGCAATCAACAAAGAACAG 59.561 41.667 0.00 0.00 0.00 3.16
1266 1329 4.014569 TGCAGCTAACATCTACCAAACA 57.985 40.909 0.00 0.00 0.00 2.83
1290 1353 2.230664 ACCTCAGGTGGCTTGACAA 58.769 52.632 0.00 0.00 32.98 3.18
1311 1374 0.960861 GGCCCGGAACTCTTTTCCAG 60.961 60.000 0.73 0.00 38.49 3.86
1315 1378 1.603739 GCAGGCCCGGAACTCTTTT 60.604 57.895 0.73 0.00 0.00 2.27
1317 1380 2.529744 AAGCAGGCCCGGAACTCTT 61.530 57.895 0.73 3.90 0.00 2.85
1322 1385 2.917897 AATCCAAGCAGGCCCGGAA 61.918 57.895 0.73 0.00 37.29 4.30
1325 1388 3.142838 CCAATCCAAGCAGGCCCG 61.143 66.667 0.00 0.00 37.29 6.13
1358 1422 5.163322 TGTTCAGAATTTTGCATCCAAAGGT 60.163 36.000 0.00 0.00 41.58 3.50
1398 1462 7.507733 AATTCTGAATATCTGCCAAGATGAC 57.492 36.000 2.85 0.00 43.27 3.06
1434 1498 2.698797 ACAAGTATCCCCTACACCATCG 59.301 50.000 0.00 0.00 32.34 3.84
1483 1575 2.093816 CAGGAGTGTGAGCTGCATCTAA 60.094 50.000 1.02 0.00 0.00 2.10
1504 1596 7.011857 CAGATGGCTCTTTCCTTCTTGTATAAC 59.988 40.741 0.00 0.00 38.22 1.89
1533 1625 6.200854 GGAACTCTAAATGTTTGTTTGGCAAG 59.799 38.462 0.00 0.00 38.47 4.01
1560 1652 6.115446 AGCATTTATGTAGTTGAAGCAGCTA 58.885 36.000 0.00 0.00 0.00 3.32
1620 1712 9.160496 AGCAAAAGAAAGAACTGATCTACATAG 57.840 33.333 0.00 0.00 37.42 2.23
1623 1715 7.807977 AAGCAAAAGAAAGAACTGATCTACA 57.192 32.000 0.00 0.00 37.42 2.74
1637 1729 4.202111 GCCACAGAGGTTAAAGCAAAAGAA 60.202 41.667 0.00 0.00 40.61 2.52
1726 1818 5.305128 CCATACCAAATGAGGCATACCAAAT 59.695 40.000 0.00 0.00 39.06 2.32
1771 1863 7.603024 AGATTTGTTTCAGTGGTTAGTACTAGC 59.397 37.037 8.15 8.15 0.00 3.42
1841 1979 3.616956 TCGAGGAATGCAACTCAGAAT 57.383 42.857 14.30 0.00 0.00 2.40
1847 1985 2.420129 GGTGGTATCGAGGAATGCAACT 60.420 50.000 0.00 0.00 0.00 3.16
1849 1987 1.837439 AGGTGGTATCGAGGAATGCAA 59.163 47.619 0.00 0.00 0.00 4.08
1869 2007 5.610398 TGTGTCTTTGCTATCACAAGAGAA 58.390 37.500 0.00 0.00 37.77 2.87
1938 2076 1.264288 GCGGTATTGCAGGTGCTTATC 59.736 52.381 3.18 0.00 42.66 1.75
2104 2242 4.022416 TGCATTGGTGTGTAATTCTCCAAC 60.022 41.667 0.00 0.00 40.26 3.77
2480 2621 9.491675 TCAAGTTCCATGTTTCTACGTTAATTA 57.508 29.630 0.00 0.00 0.00 1.40
2625 2767 3.889538 ACACAGTTACTAGCACAGACTCA 59.110 43.478 0.00 0.00 0.00 3.41
2725 2875 5.355071 TGATGCAGGATTACAAAGTAAGCAG 59.645 40.000 7.37 1.32 32.59 4.24
2912 3070 8.677148 AATGTAAATTGAGCTTACGGTATCAT 57.323 30.769 0.00 0.00 32.87 2.45
3115 3273 2.309528 TGACAAGCATATCCACGGAC 57.690 50.000 0.00 0.00 0.00 4.79
3285 3443 4.074970 GTTTGCTTCTGAATCTTCCTCCA 58.925 43.478 0.00 0.00 0.00 3.86
3415 3573 0.538287 ACCACTTTGGCTTCTCAGGC 60.538 55.000 0.00 0.00 42.67 4.85
3666 3825 8.191534 ACCTCTAAAGCTACTGAAACTAAAGA 57.808 34.615 0.00 0.00 0.00 2.52
3728 3888 4.221482 AGAATTGGCTGAGGAAAAATGGAC 59.779 41.667 0.00 0.00 0.00 4.02
3775 3936 9.707957 AAGGTTGGAAATTCATAATGGTGTATA 57.292 29.630 0.00 0.00 0.00 1.47
3820 3981 9.635404 TCTCCCTAAAATAAGAGAAACAAACAA 57.365 29.630 0.00 0.00 32.58 2.83
3853 4015 5.789643 TTTCATTTCCTCCTGTTTCCTTG 57.210 39.130 0.00 0.00 0.00 3.61
4183 4345 4.347583 TCCAGATTTGGGCAAAAATGAACT 59.652 37.500 1.81 0.00 45.10 3.01
4496 4658 5.673514 GGTGATCGGTAAATAAAGGTACCA 58.326 41.667 15.94 0.00 39.92 3.25
4668 4830 0.899717 TCTCCAAAAGCCCACATGCC 60.900 55.000 0.00 0.00 0.00 4.40
4707 4869 7.565029 CCCCCATAAAAGAGTTCTATTTTCCAT 59.435 37.037 8.16 0.00 31.41 3.41
4726 4891 4.633830 TCCATTTTCCAATTCCCCCATA 57.366 40.909 0.00 0.00 0.00 2.74
4736 4901 8.060689 TCTCTCATATCCATTTCCATTTTCCAA 58.939 33.333 0.00 0.00 0.00 3.53
4746 4911 9.947669 CTTGTTGAAATCTCTCATATCCATTTC 57.052 33.333 0.00 0.00 35.09 2.17
4752 4917 7.983307 AGCAACTTGTTGAAATCTCTCATATC 58.017 34.615 16.57 0.00 0.00 1.63
4753 4918 7.934855 AGCAACTTGTTGAAATCTCTCATAT 57.065 32.000 16.57 0.00 0.00 1.78
4754 4919 7.750229 AAGCAACTTGTTGAAATCTCTCATA 57.250 32.000 16.57 0.00 0.00 2.15
4755 4920 6.645790 AAGCAACTTGTTGAAATCTCTCAT 57.354 33.333 16.57 0.00 0.00 2.90
4756 4921 7.663081 AGATAAGCAACTTGTTGAAATCTCTCA 59.337 33.333 16.57 0.00 0.00 3.27
4757 4922 8.038492 AGATAAGCAACTTGTTGAAATCTCTC 57.962 34.615 16.57 5.81 0.00 3.20
4758 4923 7.148507 CGAGATAAGCAACTTGTTGAAATCTCT 60.149 37.037 26.99 18.23 34.47 3.10
4760 4925 6.128172 CCGAGATAAGCAACTTGTTGAAATCT 60.128 38.462 16.57 17.07 0.00 2.40
4761 4926 6.024049 CCGAGATAAGCAACTTGTTGAAATC 58.976 40.000 16.57 13.58 0.00 2.17
4762 4927 5.619981 GCCGAGATAAGCAACTTGTTGAAAT 60.620 40.000 16.57 6.54 0.00 2.17
4763 4928 4.320202 GCCGAGATAAGCAACTTGTTGAAA 60.320 41.667 16.57 2.26 0.00 2.69
4770 4935 2.234908 AGTGAGCCGAGATAAGCAACTT 59.765 45.455 0.00 0.00 0.00 2.66
4783 4948 6.673316 GCTCAACTAGAAAAATAAGTGAGCCG 60.673 42.308 10.46 0.00 37.84 5.52
4798 4963 3.324846 AGACACCAACATGCTCAACTAGA 59.675 43.478 0.00 0.00 0.00 2.43
4800 4965 3.557054 GGAGACACCAACATGCTCAACTA 60.557 47.826 0.00 0.00 38.79 2.24
4802 4967 1.537202 GGAGACACCAACATGCTCAAC 59.463 52.381 0.00 0.00 38.79 3.18
4869 5035 4.080413 TCAATCATTCAGACAGGCATACCA 60.080 41.667 0.00 0.00 39.06 3.25
4874 5040 4.224991 TCATCAATCATTCAGACAGGCA 57.775 40.909 0.00 0.00 0.00 4.75
4875 5041 6.653740 TGATATCATCAATCATTCAGACAGGC 59.346 38.462 0.00 0.00 36.11 4.85
4876 5042 8.794335 ATGATATCATCAATCATTCAGACAGG 57.206 34.615 12.62 0.00 40.37 4.00
4934 5100 5.828328 CACCTGTACATGTCACCTAGAGATA 59.172 44.000 0.00 0.00 0.00 1.98
4970 5136 8.359875 AGAGTTGATATCATATAGGTCACCTG 57.640 38.462 6.61 0.00 34.61 4.00
4992 5158 6.035112 GTCGGAGCTTTGTGATTTAAGTAGAG 59.965 42.308 0.00 0.00 0.00 2.43
4996 5162 3.432252 CGTCGGAGCTTTGTGATTTAAGT 59.568 43.478 0.00 0.00 0.00 2.24
5015 5181 7.167801 TCGGGTCAAATTAAAACAAATTTCGTC 59.832 33.333 0.00 0.00 37.03 4.20
5019 5185 7.654116 ACGATCGGGTCAAATTAAAACAAATTT 59.346 29.630 20.98 0.00 39.14 1.82
5021 5187 6.683715 ACGATCGGGTCAAATTAAAACAAAT 58.316 32.000 20.98 0.00 0.00 2.32
5023 5189 5.692613 ACGATCGGGTCAAATTAAAACAA 57.307 34.783 20.98 0.00 0.00 2.83
5028 5194 6.164876 TGAACTAACGATCGGGTCAAATTAA 58.835 36.000 20.98 0.00 0.00 1.40
5029 5195 5.722263 TGAACTAACGATCGGGTCAAATTA 58.278 37.500 20.98 6.02 0.00 1.40
5030 5196 4.571919 TGAACTAACGATCGGGTCAAATT 58.428 39.130 20.98 5.08 0.00 1.82
5031 5197 4.196626 TGAACTAACGATCGGGTCAAAT 57.803 40.909 20.98 0.00 0.00 2.32
5032 5198 3.663995 TGAACTAACGATCGGGTCAAA 57.336 42.857 20.98 0.00 0.00 2.69
5033 5199 3.663995 TTGAACTAACGATCGGGTCAA 57.336 42.857 20.98 18.21 0.00 3.18
5034 5200 3.732774 CGATTGAACTAACGATCGGGTCA 60.733 47.826 20.98 13.10 45.11 4.02
5035 5201 2.787680 CGATTGAACTAACGATCGGGTC 59.212 50.000 20.98 10.45 45.11 4.46
5036 5202 2.805845 CGATTGAACTAACGATCGGGT 58.194 47.619 20.98 12.05 45.11 5.28
5040 5206 4.013397 CGCAAACGATTGAACTAACGATC 58.987 43.478 9.88 0.00 43.93 3.69
5041 5207 3.723835 GCGCAAACGATTGAACTAACGAT 60.724 43.478 9.88 0.00 43.93 3.73
5042 5208 2.410517 GCGCAAACGATTGAACTAACGA 60.411 45.455 9.88 0.00 43.93 3.85
5043 5209 1.896193 GCGCAAACGATTGAACTAACG 59.104 47.619 9.88 3.27 43.93 3.18
5044 5210 3.183237 AGCGCAAACGATTGAACTAAC 57.817 42.857 11.47 0.00 43.93 2.34
5045 5211 4.994220 TTAGCGCAAACGATTGAACTAA 57.006 36.364 11.47 11.88 43.93 2.24
5046 5212 5.539582 AATTAGCGCAAACGATTGAACTA 57.460 34.783 11.47 6.66 43.93 2.24
5047 5213 4.419522 AATTAGCGCAAACGATTGAACT 57.580 36.364 11.47 7.62 43.93 3.01
5048 5214 4.851558 AGAAATTAGCGCAAACGATTGAAC 59.148 37.500 11.47 0.00 43.93 3.18
5049 5215 5.041951 AGAAATTAGCGCAAACGATTGAA 57.958 34.783 11.47 0.00 43.93 2.69
5050 5216 4.678509 AGAAATTAGCGCAAACGATTGA 57.321 36.364 11.47 0.00 43.93 2.57
5051 5217 5.745653 AAAGAAATTAGCGCAAACGATTG 57.254 34.783 11.47 0.29 43.93 2.67
5052 5218 6.088085 CAGAAAAGAAATTAGCGCAAACGATT 59.912 34.615 11.47 0.00 43.93 3.34
5053 5219 5.569059 CAGAAAAGAAATTAGCGCAAACGAT 59.431 36.000 11.47 0.00 43.93 3.73
5054 5220 4.909305 CAGAAAAGAAATTAGCGCAAACGA 59.091 37.500 11.47 0.00 43.93 3.85
5055 5221 4.675114 ACAGAAAAGAAATTAGCGCAAACG 59.325 37.500 11.47 0.00 44.07 3.60
5056 5222 6.417930 AGAACAGAAAAGAAATTAGCGCAAAC 59.582 34.615 11.47 0.00 0.00 2.93
5057 5223 6.417635 CAGAACAGAAAAGAAATTAGCGCAAA 59.582 34.615 11.47 0.00 0.00 3.68
5058 5224 5.914635 CAGAACAGAAAAGAAATTAGCGCAA 59.085 36.000 11.47 1.85 0.00 4.85
5059 5225 5.238432 TCAGAACAGAAAAGAAATTAGCGCA 59.762 36.000 11.47 0.00 0.00 6.09
5060 5226 5.689819 TCAGAACAGAAAAGAAATTAGCGC 58.310 37.500 0.00 0.00 0.00 5.92
5061 5227 7.746929 AGATCAGAACAGAAAAGAAATTAGCG 58.253 34.615 0.00 0.00 0.00 4.26
5092 5258 5.506317 GCACTAACAAGAGAAGCACAAATGT 60.506 40.000 0.00 0.00 0.00 2.71
5093 5259 4.913924 GCACTAACAAGAGAAGCACAAATG 59.086 41.667 0.00 0.00 0.00 2.32
5094 5260 4.823989 AGCACTAACAAGAGAAGCACAAAT 59.176 37.500 0.00 0.00 0.00 2.32
5116 5282 4.946157 ACTCTCCATGGTGCTTTTGAATAG 59.054 41.667 12.58 1.91 0.00 1.73
5117 5283 4.922206 ACTCTCCATGGTGCTTTTGAATA 58.078 39.130 12.58 0.00 0.00 1.75
5118 5284 3.771216 ACTCTCCATGGTGCTTTTGAAT 58.229 40.909 12.58 0.00 0.00 2.57
5119 5285 3.228188 ACTCTCCATGGTGCTTTTGAA 57.772 42.857 12.58 0.00 0.00 2.69
5120 5286 2.957402 ACTCTCCATGGTGCTTTTGA 57.043 45.000 12.58 0.00 0.00 2.69
5121 5287 4.326826 TCTTACTCTCCATGGTGCTTTTG 58.673 43.478 12.58 1.12 0.00 2.44
5122 5288 4.042187 ACTCTTACTCTCCATGGTGCTTTT 59.958 41.667 12.58 0.00 0.00 2.27
5123 5289 3.584848 ACTCTTACTCTCCATGGTGCTTT 59.415 43.478 12.58 0.00 0.00 3.51
5124 5290 3.177228 ACTCTTACTCTCCATGGTGCTT 58.823 45.455 12.58 2.01 0.00 3.91
5125 5291 2.826488 ACTCTTACTCTCCATGGTGCT 58.174 47.619 12.58 0.42 0.00 4.40
5126 5292 3.702045 ACTACTCTTACTCTCCATGGTGC 59.298 47.826 12.58 0.00 0.00 5.01
5127 5293 7.589958 ATTACTACTCTTACTCTCCATGGTG 57.410 40.000 12.58 9.91 0.00 4.17
5128 5294 7.839705 TCAATTACTACTCTTACTCTCCATGGT 59.160 37.037 12.58 0.00 0.00 3.55
5129 5295 8.239038 TCAATTACTACTCTTACTCTCCATGG 57.761 38.462 4.97 4.97 0.00 3.66
5130 5296 9.743057 CTTCAATTACTACTCTTACTCTCCATG 57.257 37.037 0.00 0.00 0.00 3.66
5131 5297 9.702253 TCTTCAATTACTACTCTTACTCTCCAT 57.298 33.333 0.00 0.00 0.00 3.41
5132 5298 9.529823 TTCTTCAATTACTACTCTTACTCTCCA 57.470 33.333 0.00 0.00 0.00 3.86
5135 5301 9.810545 GCATTCTTCAATTACTACTCTTACTCT 57.189 33.333 0.00 0.00 0.00 3.24
5136 5302 9.587772 TGCATTCTTCAATTACTACTCTTACTC 57.412 33.333 0.00 0.00 0.00 2.59
5137 5303 9.372369 GTGCATTCTTCAATTACTACTCTTACT 57.628 33.333 0.00 0.00 0.00 2.24
5138 5304 8.604890 GGTGCATTCTTCAATTACTACTCTTAC 58.395 37.037 0.00 0.00 0.00 2.34
5139 5305 8.318412 TGGTGCATTCTTCAATTACTACTCTTA 58.682 33.333 0.00 0.00 0.00 2.10
5140 5306 7.168219 TGGTGCATTCTTCAATTACTACTCTT 58.832 34.615 0.00 0.00 0.00 2.85
5172 5338 9.529325 CGACCAGTCTTAATCATCTTAATACAA 57.471 33.333 0.00 0.00 0.00 2.41
5187 5353 9.878667 TGTTTATAATTCATTCGACCAGTCTTA 57.121 29.630 0.00 0.00 0.00 2.10
5188 5354 8.786826 TGTTTATAATTCATTCGACCAGTCTT 57.213 30.769 0.00 0.00 0.00 3.01
5228 5435 7.763528 TGAGTTTTGTTGCAACATGTAATTCTT 59.236 29.630 31.48 11.30 38.95 2.52
5229 5436 7.222611 GTGAGTTTTGTTGCAACATGTAATTCT 59.777 33.333 31.48 21.13 38.95 2.40
5252 5459 0.890542 GTGTGCAGCCTCATTGGTGA 60.891 55.000 0.00 0.00 38.35 4.02
5253 5460 1.582968 GTGTGCAGCCTCATTGGTG 59.417 57.895 0.00 0.00 38.35 4.17
5272 5479 1.529865 GCTACCCGATCGGTAAAATGC 59.470 52.381 31.22 20.85 46.85 3.56
5274 5481 2.433239 ACAGCTACCCGATCGGTAAAAT 59.567 45.455 31.22 12.53 46.85 1.82
5275 5482 1.826720 ACAGCTACCCGATCGGTAAAA 59.173 47.619 31.22 13.20 46.85 1.52
5276 5483 1.477553 ACAGCTACCCGATCGGTAAA 58.522 50.000 31.22 15.63 46.85 2.01
5277 5484 1.135527 CAACAGCTACCCGATCGGTAA 59.864 52.381 31.22 18.10 46.85 2.85
5291 5498 5.120674 GCATTTTCTACCAAATTCCAACAGC 59.879 40.000 0.00 0.00 0.00 4.40
5296 5503 7.531857 TTACTGCATTTTCTACCAAATTCCA 57.468 32.000 0.00 0.00 0.00 3.53
5335 5550 7.969536 TTTCTCTTCTTGTCTTGTTATCAGG 57.030 36.000 0.00 0.00 0.00 3.86
5340 5555 8.746052 TTTGGATTTCTCTTCTTGTCTTGTTA 57.254 30.769 0.00 0.00 0.00 2.41
5347 5562 5.694995 TCCACTTTGGATTTCTCTTCTTGT 58.305 37.500 0.00 0.00 42.67 3.16
5384 5602 3.317571 AGCAAGGAGTGGCTCGCT 61.318 61.111 0.00 0.00 34.76 4.93
5387 5605 1.304509 GCTTCAGCAAGGAGTGGCTC 61.305 60.000 0.00 0.00 38.56 4.70
5406 5624 9.722056 GATTACTTTTTCCTGCATAAGTGTATG 57.278 33.333 0.00 0.00 40.23 2.39
5407 5625 9.461312 TGATTACTTTTTCCTGCATAAGTGTAT 57.539 29.630 0.00 0.00 33.28 2.29
5408 5626 8.856153 TGATTACTTTTTCCTGCATAAGTGTA 57.144 30.769 0.00 0.00 33.28 2.90
5409 5627 7.759489 TGATTACTTTTTCCTGCATAAGTGT 57.241 32.000 0.00 0.00 33.28 3.55


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

AutoCloner maintained by Alex Coulton.