Multiple sequence alignment - TraesCS1D01G275100

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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 TraesCS1D01G275100 chr1D 100.000 2690 0 0 1 2690 370883876 370886565 0.000000e+00 4968
1 TraesCS1D01G275100 chr1D 92.857 518 29 4 2180 2690 377406576 377407092 0.000000e+00 745
2 TraesCS1D01G275100 chr1A 91.264 1923 80 40 127 2018 469643759 469645624 0.000000e+00 2540
3 TraesCS1D01G275100 chr1A 95.683 139 4 2 3 139 469639797 469639935 3.490000e-54 222
4 TraesCS1D01G275100 chr1B 91.701 1205 43 30 844 2018 494222141 494223318 0.000000e+00 1618
5 TraesCS1D01G275100 chr1B 89.815 648 30 18 3 642 494221074 494221693 0.000000e+00 798
6 TraesCS1D01G275100 chr1B 85.629 167 7 9 640 789 494221967 494222133 2.770000e-35 159
7 TraesCS1D01G275100 chr7D 93.256 519 27 3 2180 2690 458911576 458912094 0.000000e+00 758
8 TraesCS1D01G275100 chr7D 92.678 519 30 3 2180 2690 458920123 458920641 0.000000e+00 741
9 TraesCS1D01G275100 chr2D 93.191 514 27 3 2185 2690 470938231 470938744 0.000000e+00 749
10 TraesCS1D01G275100 chr5D 92.871 519 29 5 2180 2690 424345380 424345898 0.000000e+00 747
11 TraesCS1D01G275100 chr5D 92.293 519 32 3 2180 2690 424323391 424323909 0.000000e+00 730
12 TraesCS1D01G275100 chr4D 92.293 519 32 3 2180 2690 347122223 347122741 0.000000e+00 730
13 TraesCS1D01G275100 chr4D 92.293 519 32 3 2180 2690 366595959 366595441 0.000000e+00 730
14 TraesCS1D01G275100 chr6D 92.100 519 33 3 2180 2690 323129500 323128982 0.000000e+00 725
15 TraesCS1D01G275100 chr3D 87.273 220 25 2 1460 1679 481739896 481739680 5.750000e-62 248
16 TraesCS1D01G275100 chr3A 87.273 220 25 2 1460 1679 624942401 624942185 5.750000e-62 248
17 TraesCS1D01G275100 chr3B 86.818 220 26 2 1460 1679 643857290 643857074 2.680000e-60 243
18 TraesCS1D01G275100 chr3B 94.286 105 4 2 2018 2121 6030083 6029980 2.770000e-35 159
19 TraesCS1D01G275100 chrUn 95.098 102 3 2 2018 2118 251414993 251415093 2.770000e-35 159
20 TraesCS1D01G275100 chrUn 95.098 102 3 2 2018 2118 260205537 260205637 2.770000e-35 159
21 TraesCS1D01G275100 chrUn 95.098 102 3 2 2018 2118 264055490 264055590 2.770000e-35 159
22 TraesCS1D01G275100 chrUn 95.098 102 3 2 2018 2118 266525420 266525520 2.770000e-35 159
23 TraesCS1D01G275100 chrUn 95.098 102 3 2 2018 2118 270911032 270911132 2.770000e-35 159
24 TraesCS1D01G275100 chrUn 95.098 102 3 2 2018 2118 282366517 282366617 2.770000e-35 159
25 TraesCS1D01G275100 chrUn 94.286 105 4 2 2018 2121 314444101 314443998 2.770000e-35 159
26 TraesCS1D01G275100 chr7B 94.286 105 4 2 2018 2121 742914896 742914793 2.770000e-35 159
27 TraesCS1D01G275100 chr4B 94.118 68 4 0 2118 2185 209042412 209042345 1.320000e-18 104


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 TraesCS1D01G275100 chr1D 370883876 370886565 2689 False 4968.000000 4968 100.000000 1 2690 1 chr1D.!!$F1 2689
1 TraesCS1D01G275100 chr1D 377406576 377407092 516 False 745.000000 745 92.857000 2180 2690 1 chr1D.!!$F2 510
2 TraesCS1D01G275100 chr1A 469639797 469645624 5827 False 1381.000000 2540 93.473500 3 2018 2 chr1A.!!$F1 2015
3 TraesCS1D01G275100 chr1B 494221074 494223318 2244 False 858.333333 1618 89.048333 3 2018 3 chr1B.!!$F1 2015
4 TraesCS1D01G275100 chr7D 458911576 458912094 518 False 758.000000 758 93.256000 2180 2690 1 chr7D.!!$F1 510
5 TraesCS1D01G275100 chr7D 458920123 458920641 518 False 741.000000 741 92.678000 2180 2690 1 chr7D.!!$F2 510
6 TraesCS1D01G275100 chr2D 470938231 470938744 513 False 749.000000 749 93.191000 2185 2690 1 chr2D.!!$F1 505
7 TraesCS1D01G275100 chr5D 424345380 424345898 518 False 747.000000 747 92.871000 2180 2690 1 chr5D.!!$F2 510
8 TraesCS1D01G275100 chr5D 424323391 424323909 518 False 730.000000 730 92.293000 2180 2690 1 chr5D.!!$F1 510
9 TraesCS1D01G275100 chr4D 347122223 347122741 518 False 730.000000 730 92.293000 2180 2690 1 chr4D.!!$F1 510
10 TraesCS1D01G275100 chr4D 366595441 366595959 518 True 730.000000 730 92.293000 2180 2690 1 chr4D.!!$R1 510
11 TraesCS1D01G275100 chr6D 323128982 323129500 518 True 725.000000 725 92.100000 2180 2690 1 chr6D.!!$R1 510

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
384 4223 0.103572 ACGCAGTAACGTTCCACACT 59.896 50.0 2.82 0.0 45.75 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 6035 0.028242 CGGAGTAGCAGAGTAGCACG 59.972 60.0 0.0 0.0 36.85 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.997932 AGAGTACTCGAGTGCGTACG 59.002 55.000 28.12 11.84 40.41 3.67
28 29 1.656095 AGTACTCGAGTGCGTACGTAC 59.344 52.381 28.12 26.29 40.41 3.67
287 4125 2.035961 GCTGCTGCATTGGATCATCATT 59.964 45.455 11.11 0.00 39.41 2.57
313 4151 6.968131 TCATAAAAAGTCGGACAATCTCAG 57.032 37.500 11.27 0.00 0.00 3.35
340 4179 0.320683 TCATGAGTTGCACGTCCTGG 60.321 55.000 0.00 0.00 0.00 4.45
341 4180 0.603707 CATGAGTTGCACGTCCTGGT 60.604 55.000 0.00 0.00 0.00 4.00
342 4181 0.320771 ATGAGTTGCACGTCCTGGTC 60.321 55.000 0.00 0.00 0.00 4.02
381 4220 1.203313 GCACGCAGTAACGTTCCAC 59.797 57.895 2.82 0.00 45.75 4.02
382 4221 1.492319 GCACGCAGTAACGTTCCACA 61.492 55.000 2.82 0.00 45.75 4.17
383 4222 0.231279 CACGCAGTAACGTTCCACAC 59.769 55.000 2.82 0.00 45.75 3.82
384 4223 0.103572 ACGCAGTAACGTTCCACACT 59.896 50.000 2.82 0.00 45.75 3.55
385 4224 0.782384 CGCAGTAACGTTCCACACTC 59.218 55.000 2.82 0.00 0.00 3.51
386 4225 1.602165 CGCAGTAACGTTCCACACTCT 60.602 52.381 2.82 0.00 0.00 3.24
387 4226 2.480845 GCAGTAACGTTCCACACTCTT 58.519 47.619 2.82 0.00 0.00 2.85
388 4227 2.870411 GCAGTAACGTTCCACACTCTTT 59.130 45.455 2.82 0.00 0.00 2.52
389 4228 3.311596 GCAGTAACGTTCCACACTCTTTT 59.688 43.478 2.82 0.00 0.00 2.27
390 4229 4.785341 GCAGTAACGTTCCACACTCTTTTG 60.785 45.833 2.82 0.00 0.00 2.44
391 4230 3.875134 AGTAACGTTCCACACTCTTTTGG 59.125 43.478 2.82 0.00 0.00 3.28
392 4231 1.675552 ACGTTCCACACTCTTTTGGG 58.324 50.000 0.00 0.00 33.25 4.12
393 4232 1.064979 ACGTTCCACACTCTTTTGGGT 60.065 47.619 0.00 0.00 33.25 4.51
394 4233 2.021457 CGTTCCACACTCTTTTGGGTT 58.979 47.619 0.00 0.00 33.25 4.11
395 4234 2.032924 CGTTCCACACTCTTTTGGGTTC 59.967 50.000 0.00 0.00 33.25 3.62
396 4235 2.358322 TCCACACTCTTTTGGGTTCC 57.642 50.000 0.00 0.00 33.25 3.62
397 4236 1.850345 TCCACACTCTTTTGGGTTCCT 59.150 47.619 0.00 0.00 33.25 3.36
398 4237 2.243736 TCCACACTCTTTTGGGTTCCTT 59.756 45.455 0.00 0.00 33.25 3.36
399 4238 2.362077 CCACACTCTTTTGGGTTCCTTG 59.638 50.000 0.00 0.00 0.00 3.61
400 4239 2.031870 ACACTCTTTTGGGTTCCTTGC 58.968 47.619 0.00 0.00 0.00 4.01
401 4240 1.001378 CACTCTTTTGGGTTCCTTGCG 60.001 52.381 0.00 0.00 0.00 4.85
402 4241 1.133915 ACTCTTTTGGGTTCCTTGCGA 60.134 47.619 0.00 0.00 0.00 5.10
403 4242 1.953686 CTCTTTTGGGTTCCTTGCGAA 59.046 47.619 0.00 0.00 0.00 4.70
419 4260 1.823828 CGAACAGCGCGTAGTAAGAT 58.176 50.000 8.43 0.00 0.00 2.40
425 4274 0.997726 GCGCGTAGTAAGATCTCGCC 60.998 60.000 17.09 8.61 43.18 5.54
458 4307 8.080083 ACAAATGTTTTCTTGAATGCATTCTC 57.920 30.769 33.23 15.22 37.67 2.87
481 4330 3.648339 TTTTGAGAGGCTTGAATGCAC 57.352 42.857 0.00 0.00 34.04 4.57
487 4336 0.813184 AGGCTTGAATGCACGATTGG 59.187 50.000 0.00 0.00 34.04 3.16
497 4346 1.337728 TGCACGATTGGAGGTACTGTG 60.338 52.381 0.00 0.00 41.55 3.66
498 4347 1.359848 CACGATTGGAGGTACTGTGC 58.640 55.000 0.00 0.00 41.55 4.57
500 4349 0.249120 CGATTGGAGGTACTGTGCCA 59.751 55.000 17.35 3.81 41.55 4.92
501 4350 1.740380 CGATTGGAGGTACTGTGCCAG 60.740 57.143 17.35 1.16 41.55 4.85
503 4352 0.396435 TTGGAGGTACTGTGCCAGTG 59.604 55.000 17.35 0.00 45.01 3.66
609 4465 2.626780 CCCTCGTCTGCTCGTCACA 61.627 63.158 0.00 0.00 0.00 3.58
728 4877 2.807895 CACACGTACCGCCCGAAG 60.808 66.667 0.00 0.00 0.00 3.79
815 4964 7.023197 GCTAGCTAGCCTATGATCTTACTAC 57.977 44.000 31.67 1.13 43.39 2.73
829 4978 5.230746 TCTTACTACCCCCATTTACCTCT 57.769 43.478 0.00 0.00 0.00 3.69
905 5054 0.250770 CCCCCTATTTAAGCCGCTCC 60.251 60.000 0.00 0.00 0.00 4.70
997 5162 2.353607 GTAGCCGAGCCACGATCG 60.354 66.667 14.88 14.88 45.77 3.69
998 5163 2.515290 TAGCCGAGCCACGATCGA 60.515 61.111 24.34 0.00 44.55 3.59
1047 5212 0.669625 GTAGCGGCGACAGTTTCCTT 60.670 55.000 12.98 0.00 0.00 3.36
1137 5302 3.052620 CTCGTCGCTCATGTCCCGT 62.053 63.158 0.00 0.00 0.00 5.28
1159 5324 2.043248 GTGGAGGAGGAGGCCGTA 60.043 66.667 0.00 0.00 0.00 4.02
1317 5482 2.479750 GCTCTACGAGGACGACCCC 61.480 68.421 0.00 0.00 42.66 4.95
1446 5614 1.456705 CGGGGAGAAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1447 5615 1.074850 GGGGAGAAGGAGGAGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
1448 5616 1.595058 GGGGAGAAGGAGGAGGAGGA 61.595 65.000 0.00 0.00 0.00 3.71
1693 5861 1.324383 GTGCCTAGGCCTCTAGAGTC 58.676 60.000 30.81 5.52 44.35 3.36
1696 5864 1.477195 GCCTAGGCCTCTAGAGTCGAA 60.477 57.143 24.19 1.00 44.35 3.71
1698 5866 1.877443 CTAGGCCTCTAGAGTCGAAGC 59.123 57.143 9.68 13.26 44.35 3.86
1699 5867 0.257616 AGGCCTCTAGAGTCGAAGCT 59.742 55.000 18.42 0.00 0.00 3.74
1700 5868 0.383949 GGCCTCTAGAGTCGAAGCTG 59.616 60.000 18.42 1.78 0.00 4.24
1701 5869 0.248866 GCCTCTAGAGTCGAAGCTGC 60.249 60.000 18.42 8.15 0.00 5.25
1702 5870 1.098869 CCTCTAGAGTCGAAGCTGCA 58.901 55.000 18.42 0.00 0.00 4.41
1703 5871 1.202245 CCTCTAGAGTCGAAGCTGCAC 60.202 57.143 18.42 0.00 0.00 4.57
1735 5903 2.028337 GCGCCACCTAGCTAGCTC 59.972 66.667 23.26 4.46 0.00 4.09
1739 5907 0.963225 GCCACCTAGCTAGCTCTACC 59.037 60.000 23.26 2.36 0.00 3.18
1796 5978 2.552093 AGGCTGGGTCATACTACTGT 57.448 50.000 0.00 0.00 0.00 3.55
1797 5979 2.111384 AGGCTGGGTCATACTACTGTG 58.889 52.381 0.00 0.00 0.00 3.66
1799 5981 3.028850 GGCTGGGTCATACTACTGTGTA 58.971 50.000 0.00 0.00 0.00 2.90
1800 5982 3.181478 GGCTGGGTCATACTACTGTGTAC 60.181 52.174 0.00 0.00 0.00 2.90
1801 5983 3.488721 GCTGGGTCATACTACTGTGTACG 60.489 52.174 0.00 0.00 0.00 3.67
1803 5985 4.842574 TGGGTCATACTACTGTGTACGTA 58.157 43.478 0.00 0.00 0.00 3.57
1804 5986 4.635765 TGGGTCATACTACTGTGTACGTAC 59.364 45.833 18.90 18.90 0.00 3.67
1805 5987 4.260375 GGGTCATACTACTGTGTACGTACG 60.260 50.000 20.18 15.01 0.00 3.67
1834 6016 1.331756 ACTGTAGTTGTCGTCGTCGTT 59.668 47.619 1.33 0.00 38.33 3.85
1850 6032 2.975851 GTCGTTCTCGTCGTTGTTGTAT 59.024 45.455 0.00 0.00 38.33 2.29
1851 6033 3.423206 GTCGTTCTCGTCGTTGTTGTATT 59.577 43.478 0.00 0.00 38.33 1.89
1852 6034 4.612614 GTCGTTCTCGTCGTTGTTGTATTA 59.387 41.667 0.00 0.00 38.33 0.98
1853 6035 4.612614 TCGTTCTCGTCGTTGTTGTATTAC 59.387 41.667 0.00 0.00 38.33 1.89
1854 6036 4.486069 CGTTCTCGTCGTTGTTGTATTACG 60.486 45.833 0.00 0.00 36.67 3.18
1856 6038 3.907788 TCTCGTCGTTGTTGTATTACGTG 59.092 43.478 0.00 0.00 36.70 4.49
1919 6101 3.546670 CGGACTGCGTACTAATCTTTGTC 59.453 47.826 0.00 0.00 0.00 3.18
1920 6102 3.864003 GGACTGCGTACTAATCTTTGTCC 59.136 47.826 0.00 0.00 35.39 4.02
1921 6103 3.508762 ACTGCGTACTAATCTTTGTCCG 58.491 45.455 0.00 0.00 0.00 4.79
1922 6104 3.057033 ACTGCGTACTAATCTTTGTCCGT 60.057 43.478 0.00 0.00 0.00 4.69
1923 6105 3.247442 TGCGTACTAATCTTTGTCCGTG 58.753 45.455 0.00 0.00 0.00 4.94
1924 6106 3.248266 GCGTACTAATCTTTGTCCGTGT 58.752 45.455 0.00 0.00 0.00 4.49
1925 6107 3.302699 GCGTACTAATCTTTGTCCGTGTC 59.697 47.826 0.00 0.00 0.00 3.67
1926 6108 3.855950 CGTACTAATCTTTGTCCGTGTCC 59.144 47.826 0.00 0.00 0.00 4.02
1928 6110 2.298163 ACTAATCTTTGTCCGTGTCCGT 59.702 45.455 0.00 0.00 0.00 4.69
1929 6111 1.508632 AATCTTTGTCCGTGTCCGTG 58.491 50.000 0.00 0.00 0.00 4.94
1930 6112 0.391597 ATCTTTGTCCGTGTCCGTGT 59.608 50.000 0.00 0.00 0.00 4.49
1931 6113 0.528901 TCTTTGTCCGTGTCCGTGTG 60.529 55.000 0.00 0.00 0.00 3.82
1932 6114 0.808453 CTTTGTCCGTGTCCGTGTGT 60.808 55.000 0.00 0.00 0.00 3.72
1933 6115 0.806884 TTTGTCCGTGTCCGTGTGTC 60.807 55.000 0.00 0.00 0.00 3.67
1934 6116 2.728383 GTCCGTGTCCGTGTGTCG 60.728 66.667 0.00 0.00 39.52 4.35
2018 6200 6.701145 TGAGCTCTGTTCGTTTCTATAGAT 57.299 37.500 16.19 0.00 0.00 1.98
2019 6201 7.101652 TGAGCTCTGTTCGTTTCTATAGATT 57.898 36.000 16.19 0.00 0.00 2.40
2020 6202 6.975197 TGAGCTCTGTTCGTTTCTATAGATTG 59.025 38.462 16.19 0.00 0.00 2.67
2021 6203 6.868622 AGCTCTGTTCGTTTCTATAGATTGT 58.131 36.000 2.58 0.00 0.00 2.71
2022 6204 7.324178 AGCTCTGTTCGTTTCTATAGATTGTT 58.676 34.615 2.58 0.00 0.00 2.83
2023 6205 7.489757 AGCTCTGTTCGTTTCTATAGATTGTTC 59.510 37.037 2.58 0.00 0.00 3.18
2024 6206 7.513814 GCTCTGTTCGTTTCTATAGATTGTTCG 60.514 40.741 2.58 5.04 0.00 3.95
2025 6207 7.310664 TCTGTTCGTTTCTATAGATTGTTCGT 58.689 34.615 2.58 0.00 0.00 3.85
2026 6208 7.811236 TCTGTTCGTTTCTATAGATTGTTCGTT 59.189 33.333 2.58 0.00 0.00 3.85
2027 6209 7.946043 TGTTCGTTTCTATAGATTGTTCGTTC 58.054 34.615 2.58 4.11 0.00 3.95
2028 6210 7.811236 TGTTCGTTTCTATAGATTGTTCGTTCT 59.189 33.333 2.58 0.00 0.00 3.01
2029 6211 7.736031 TCGTTTCTATAGATTGTTCGTTCTG 57.264 36.000 2.58 0.00 0.00 3.02
2030 6212 7.532571 TCGTTTCTATAGATTGTTCGTTCTGA 58.467 34.615 2.58 0.00 0.00 3.27
2031 6213 7.696872 TCGTTTCTATAGATTGTTCGTTCTGAG 59.303 37.037 2.58 0.00 0.00 3.35
2032 6214 7.043986 CGTTTCTATAGATTGTTCGTTCTGAGG 60.044 40.741 2.58 0.00 0.00 3.86
2033 6215 7.406031 TTCTATAGATTGTTCGTTCTGAGGT 57.594 36.000 2.58 0.00 0.00 3.85
2034 6216 6.796426 TCTATAGATTGTTCGTTCTGAGGTG 58.204 40.000 0.00 0.00 0.00 4.00
2035 6217 3.045601 AGATTGTTCGTTCTGAGGTGG 57.954 47.619 0.00 0.00 0.00 4.61
2036 6218 2.632996 AGATTGTTCGTTCTGAGGTGGA 59.367 45.455 0.00 0.00 0.00 4.02
2037 6219 3.261897 AGATTGTTCGTTCTGAGGTGGAT 59.738 43.478 0.00 0.00 0.00 3.41
2038 6220 3.485463 TTGTTCGTTCTGAGGTGGATT 57.515 42.857 0.00 0.00 0.00 3.01
2039 6221 3.040147 TGTTCGTTCTGAGGTGGATTC 57.960 47.619 0.00 0.00 0.00 2.52
2040 6222 1.993370 GTTCGTTCTGAGGTGGATTCG 59.007 52.381 0.00 0.00 0.00 3.34
2041 6223 1.541379 TCGTTCTGAGGTGGATTCGA 58.459 50.000 0.00 0.00 0.00 3.71
2042 6224 1.890489 TCGTTCTGAGGTGGATTCGAA 59.110 47.619 0.00 0.00 0.00 3.71
2043 6225 1.993370 CGTTCTGAGGTGGATTCGAAC 59.007 52.381 0.00 0.00 0.00 3.95
2044 6226 2.347731 GTTCTGAGGTGGATTCGAACC 58.652 52.381 0.00 4.86 36.66 3.62
2045 6227 1.639722 TCTGAGGTGGATTCGAACCA 58.360 50.000 13.34 13.34 39.05 3.67
2051 6233 3.082619 TGGATTCGAACCACTCCCT 57.917 52.632 11.96 0.00 32.03 4.20
2052 6234 0.902531 TGGATTCGAACCACTCCCTC 59.097 55.000 11.96 0.00 32.03 4.30
2053 6235 0.178301 GGATTCGAACCACTCCCTCC 59.822 60.000 0.00 0.00 0.00 4.30
2054 6236 0.179108 GATTCGAACCACTCCCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
2055 6237 0.903454 ATTCGAACCACTCCCTCCGT 60.903 55.000 0.00 0.00 0.00 4.69
2056 6238 1.117142 TTCGAACCACTCCCTCCGTT 61.117 55.000 0.00 0.00 0.00 4.44
2057 6239 1.117142 TCGAACCACTCCCTCCGTTT 61.117 55.000 0.00 0.00 0.00 3.60
2058 6240 0.949105 CGAACCACTCCCTCCGTTTG 60.949 60.000 0.00 0.00 0.00 2.93
2059 6241 0.108019 GAACCACTCCCTCCGTTTGT 59.892 55.000 0.00 0.00 0.00 2.83
2060 6242 1.345415 GAACCACTCCCTCCGTTTGTA 59.655 52.381 0.00 0.00 0.00 2.41
2061 6243 1.652947 ACCACTCCCTCCGTTTGTAT 58.347 50.000 0.00 0.00 0.00 2.29
2062 6244 1.982958 ACCACTCCCTCCGTTTGTATT 59.017 47.619 0.00 0.00 0.00 1.89
2063 6245 2.374170 ACCACTCCCTCCGTTTGTATTT 59.626 45.455 0.00 0.00 0.00 1.40
2064 6246 3.007635 CCACTCCCTCCGTTTGTATTTC 58.992 50.000 0.00 0.00 0.00 2.17
2065 6247 2.671396 CACTCCCTCCGTTTGTATTTCG 59.329 50.000 0.00 0.00 0.00 3.46
2066 6248 2.564062 ACTCCCTCCGTTTGTATTTCGA 59.436 45.455 0.00 0.00 0.00 3.71
2067 6249 3.187700 CTCCCTCCGTTTGTATTTCGAG 58.812 50.000 0.00 0.00 0.00 4.04
2068 6250 2.564062 TCCCTCCGTTTGTATTTCGAGT 59.436 45.455 0.00 0.00 0.00 4.18
2069 6251 2.928116 CCCTCCGTTTGTATTTCGAGTC 59.072 50.000 0.00 0.00 0.00 3.36
2070 6252 2.928116 CCTCCGTTTGTATTTCGAGTCC 59.072 50.000 0.00 0.00 0.00 3.85
2071 6253 3.581755 CTCCGTTTGTATTTCGAGTCCA 58.418 45.455 0.00 0.00 0.00 4.02
2072 6254 3.991773 CTCCGTTTGTATTTCGAGTCCAA 59.008 43.478 0.00 0.00 0.00 3.53
2073 6255 4.378774 TCCGTTTGTATTTCGAGTCCAAA 58.621 39.130 0.00 0.00 0.00 3.28
2074 6256 4.815308 TCCGTTTGTATTTCGAGTCCAAAA 59.185 37.500 4.05 0.00 0.00 2.44
2075 6257 5.049954 TCCGTTTGTATTTCGAGTCCAAAAG 60.050 40.000 4.05 5.88 0.00 2.27
2076 6258 5.144359 CGTTTGTATTTCGAGTCCAAAAGG 58.856 41.667 4.05 0.00 0.00 3.11
2077 6259 4.759516 TTGTATTTCGAGTCCAAAAGGC 57.240 40.909 0.00 0.00 0.00 4.35
2078 6260 3.078837 TGTATTTCGAGTCCAAAAGGCC 58.921 45.455 0.00 0.00 0.00 5.19
2079 6261 1.165270 ATTTCGAGTCCAAAAGGCCG 58.835 50.000 0.00 0.00 0.00 6.13
2080 6262 0.887387 TTTCGAGTCCAAAAGGCCGG 60.887 55.000 0.00 0.00 0.00 6.13
2081 6263 3.431725 CGAGTCCAAAAGGCCGGC 61.432 66.667 21.18 21.18 0.00 6.13
2082 6264 2.034221 GAGTCCAAAAGGCCGGCT 59.966 61.111 28.56 9.77 0.00 5.52
2083 6265 2.282462 AGTCCAAAAGGCCGGCTG 60.282 61.111 28.56 16.81 0.00 4.85
2084 6266 2.282180 GTCCAAAAGGCCGGCTGA 60.282 61.111 28.56 10.58 0.00 4.26
2085 6267 1.901464 GTCCAAAAGGCCGGCTGAA 60.901 57.895 28.56 0.00 0.00 3.02
2086 6268 1.152652 TCCAAAAGGCCGGCTGAAA 60.153 52.632 28.56 5.40 0.00 2.69
2087 6269 1.178534 TCCAAAAGGCCGGCTGAAAG 61.179 55.000 28.56 13.79 0.00 2.62
2088 6270 1.178534 CCAAAAGGCCGGCTGAAAGA 61.179 55.000 28.56 0.00 34.07 2.52
2089 6271 0.242017 CAAAAGGCCGGCTGAAAGAG 59.758 55.000 28.56 6.93 34.07 2.85
2090 6272 0.895559 AAAAGGCCGGCTGAAAGAGG 60.896 55.000 28.56 0.00 34.07 3.69
2091 6273 1.779061 AAAGGCCGGCTGAAAGAGGA 61.779 55.000 28.56 0.00 35.65 3.71
2092 6274 1.566298 AAGGCCGGCTGAAAGAGGAT 61.566 55.000 28.56 0.00 35.65 3.24
2093 6275 1.077429 GGCCGGCTGAAAGAGGATT 60.077 57.895 28.56 0.00 35.65 3.01
2094 6276 0.681243 GGCCGGCTGAAAGAGGATTT 60.681 55.000 28.56 0.00 35.65 2.17
2095 6277 1.177401 GCCGGCTGAAAGAGGATTTT 58.823 50.000 22.15 0.00 35.65 1.82
2096 6278 1.133216 GCCGGCTGAAAGAGGATTTTC 59.867 52.381 22.15 0.00 35.65 2.29
2097 6279 2.436417 CCGGCTGAAAGAGGATTTTCA 58.564 47.619 0.00 1.76 42.93 2.69
2106 6288 7.020827 TGAAAGAGGATTTTCAGTCCTATGT 57.979 36.000 0.00 0.00 45.93 2.29
2107 6289 7.106239 TGAAAGAGGATTTTCAGTCCTATGTC 58.894 38.462 1.02 1.02 45.93 3.06
2108 6290 5.622346 AGAGGATTTTCAGTCCTATGTCC 57.378 43.478 0.00 0.00 45.93 4.02
2109 6291 4.100189 AGAGGATTTTCAGTCCTATGTCCG 59.900 45.833 0.00 0.00 45.93 4.79
2110 6292 2.872858 GGATTTTCAGTCCTATGTCCGC 59.127 50.000 0.00 0.00 32.85 5.54
2111 6293 3.432326 GGATTTTCAGTCCTATGTCCGCT 60.432 47.826 0.00 0.00 32.85 5.52
2112 6294 2.672961 TTTCAGTCCTATGTCCGCTG 57.327 50.000 0.00 0.00 0.00 5.18
2113 6295 0.175760 TTCAGTCCTATGTCCGCTGC 59.824 55.000 0.00 0.00 0.00 5.25
2114 6296 1.227380 CAGTCCTATGTCCGCTGCC 60.227 63.158 0.00 0.00 0.00 4.85
2115 6297 1.685765 AGTCCTATGTCCGCTGCCA 60.686 57.895 0.00 0.00 0.00 4.92
2116 6298 1.227380 GTCCTATGTCCGCTGCCAG 60.227 63.158 0.00 0.00 0.00 4.85
2117 6299 2.590007 CCTATGTCCGCTGCCAGC 60.590 66.667 6.63 6.63 38.02 4.85
2118 6300 2.187685 CTATGTCCGCTGCCAGCA 59.812 61.111 18.21 0.00 42.58 4.41
2119 6301 1.450134 CTATGTCCGCTGCCAGCAA 60.450 57.895 18.21 0.44 42.58 3.91
2120 6302 0.816825 CTATGTCCGCTGCCAGCAAT 60.817 55.000 18.21 6.93 42.58 3.56
2121 6303 1.096967 TATGTCCGCTGCCAGCAATG 61.097 55.000 18.21 4.48 42.58 2.82
2122 6304 3.818787 GTCCGCTGCCAGCAATGG 61.819 66.667 18.21 10.15 42.58 3.16
2123 6305 4.032452 TCCGCTGCCAGCAATGGA 62.032 61.111 18.21 12.49 42.58 3.41
2124 6306 3.063704 CCGCTGCCAGCAATGGAA 61.064 61.111 18.21 0.00 42.58 3.53
2125 6307 2.638354 CCGCTGCCAGCAATGGAAA 61.638 57.895 18.21 0.00 42.58 3.13
2126 6308 1.289694 CGCTGCCAGCAATGGAAAA 59.710 52.632 18.21 0.00 42.58 2.29
2127 6309 0.108520 CGCTGCCAGCAATGGAAAAT 60.109 50.000 18.21 0.00 42.58 1.82
2128 6310 1.365699 GCTGCCAGCAATGGAAAATG 58.634 50.000 12.82 0.00 41.89 2.32
2129 6311 2.010043 GCTGCCAGCAATGGAAAATGG 61.010 52.381 12.82 0.00 41.89 3.16
2130 6312 1.551430 CTGCCAGCAATGGAAAATGGA 59.449 47.619 0.00 0.00 32.55 3.41
2131 6313 1.976404 TGCCAGCAATGGAAAATGGAA 59.024 42.857 0.00 0.00 32.55 3.53
2132 6314 2.027929 TGCCAGCAATGGAAAATGGAAG 60.028 45.455 0.00 0.00 32.55 3.46
2133 6315 2.027837 GCCAGCAATGGAAAATGGAAGT 60.028 45.455 0.00 0.00 32.55 3.01
2134 6316 3.557686 GCCAGCAATGGAAAATGGAAGTT 60.558 43.478 0.00 0.00 32.55 2.66
2135 6317 4.644498 CCAGCAATGGAAAATGGAAGTTT 58.356 39.130 0.00 0.00 36.50 2.66
2146 6328 7.163001 GAAAATGGAAGTTTCTAGGATTGCT 57.837 36.000 0.00 0.00 46.45 3.91
2147 6329 6.521151 AAATGGAAGTTTCTAGGATTGCTG 57.479 37.500 0.00 0.00 0.00 4.41
2148 6330 3.347216 TGGAAGTTTCTAGGATTGCTGC 58.653 45.455 0.00 0.00 0.00 5.25
2149 6331 3.009473 TGGAAGTTTCTAGGATTGCTGCT 59.991 43.478 0.00 0.00 0.00 4.24
2150 6332 3.625313 GGAAGTTTCTAGGATTGCTGCTC 59.375 47.826 0.00 0.00 0.00 4.26
2151 6333 4.512484 GAAGTTTCTAGGATTGCTGCTCT 58.488 43.478 0.00 0.00 0.00 4.09
2152 6334 4.566426 AGTTTCTAGGATTGCTGCTCTT 57.434 40.909 0.00 0.00 0.00 2.85
2153 6335 4.916183 AGTTTCTAGGATTGCTGCTCTTT 58.084 39.130 0.00 0.00 0.00 2.52
2154 6336 5.320277 AGTTTCTAGGATTGCTGCTCTTTT 58.680 37.500 0.00 0.00 0.00 2.27
2155 6337 5.414144 AGTTTCTAGGATTGCTGCTCTTTTC 59.586 40.000 0.00 0.00 0.00 2.29
2156 6338 4.833478 TCTAGGATTGCTGCTCTTTTCT 57.167 40.909 0.00 0.00 0.00 2.52
2157 6339 4.511527 TCTAGGATTGCTGCTCTTTTCTG 58.488 43.478 0.00 0.00 0.00 3.02
2158 6340 3.151912 AGGATTGCTGCTCTTTTCTGT 57.848 42.857 0.00 0.00 0.00 3.41
2159 6341 3.494332 AGGATTGCTGCTCTTTTCTGTT 58.506 40.909 0.00 0.00 0.00 3.16
2160 6342 3.505293 AGGATTGCTGCTCTTTTCTGTTC 59.495 43.478 0.00 0.00 0.00 3.18
2161 6343 3.254166 GGATTGCTGCTCTTTTCTGTTCA 59.746 43.478 0.00 0.00 0.00 3.18
2162 6344 4.261741 GGATTGCTGCTCTTTTCTGTTCAA 60.262 41.667 0.00 0.00 0.00 2.69
2163 6345 3.976793 TGCTGCTCTTTTCTGTTCAAG 57.023 42.857 0.00 0.00 0.00 3.02
2164 6346 3.544684 TGCTGCTCTTTTCTGTTCAAGA 58.455 40.909 0.00 0.00 0.00 3.02
2165 6347 3.947196 TGCTGCTCTTTTCTGTTCAAGAA 59.053 39.130 0.00 0.00 43.37 2.52
2166 6348 4.036027 TGCTGCTCTTTTCTGTTCAAGAAG 59.964 41.667 0.00 0.00 45.64 2.85
2167 6349 4.036144 GCTGCTCTTTTCTGTTCAAGAAGT 59.964 41.667 0.00 0.00 45.64 3.01
2168 6350 5.741388 TGCTCTTTTCTGTTCAAGAAGTC 57.259 39.130 0.00 0.00 45.64 3.01
2169 6351 5.431765 TGCTCTTTTCTGTTCAAGAAGTCT 58.568 37.500 0.00 0.00 45.64 3.24
2170 6352 5.882557 TGCTCTTTTCTGTTCAAGAAGTCTT 59.117 36.000 0.00 0.00 45.64 3.01
2171 6353 6.375455 TGCTCTTTTCTGTTCAAGAAGTCTTT 59.625 34.615 0.00 0.00 45.64 2.52
2172 6354 6.909895 GCTCTTTTCTGTTCAAGAAGTCTTTC 59.090 38.462 0.00 0.00 45.64 2.62
2173 6355 7.201688 GCTCTTTTCTGTTCAAGAAGTCTTTCT 60.202 37.037 0.00 0.00 45.64 2.52
2174 6356 8.202745 TCTTTTCTGTTCAAGAAGTCTTTCTC 57.797 34.615 0.00 0.00 45.64 2.87
2175 6357 6.927294 TTTCTGTTCAAGAAGTCTTTCTCC 57.073 37.500 0.00 0.00 45.64 3.71
2176 6358 5.614324 TCTGTTCAAGAAGTCTTTCTCCA 57.386 39.130 0.00 0.00 42.80 3.86
2177 6359 5.605534 TCTGTTCAAGAAGTCTTTCTCCAG 58.394 41.667 0.00 0.00 42.80 3.86
2178 6360 4.708177 TGTTCAAGAAGTCTTTCTCCAGG 58.292 43.478 0.00 0.00 42.80 4.45
2192 6374 2.338620 CAGGTGTCGGCGTTCTGA 59.661 61.111 6.85 0.00 0.00 3.27
2193 6375 1.300620 CAGGTGTCGGCGTTCTGAA 60.301 57.895 6.85 0.00 0.00 3.02
2204 6387 0.250166 CGTTCTGAAAACGGGGTCCT 60.250 55.000 2.53 0.00 39.73 3.85
2222 6405 0.887836 CTCAGACTTGCCTGCTTGCA 60.888 55.000 0.00 0.00 40.07 4.08
2224 6407 1.150081 AGACTTGCCTGCTTGCAGT 59.850 52.632 19.49 3.27 43.21 4.40
2225 6408 0.466922 AGACTTGCCTGCTTGCAGTT 60.467 50.000 19.49 0.76 43.21 3.16
2295 6478 1.303398 ACTCAAGACCCTCGCGAGA 60.303 57.895 36.59 14.57 39.12 4.04
2337 6521 1.971357 GACACAAGACCTCCTCAGGAA 59.029 52.381 0.00 0.00 43.65 3.36
2407 6591 1.227089 CCTCGCGAGGTTCTCATGG 60.227 63.158 40.77 18.18 43.61 3.66
2494 6678 2.527951 CTAAGGAGGCAAGCGCAGGT 62.528 60.000 11.47 0.00 41.24 4.00
2500 6684 2.669569 GCAAGCGCAGGTGAGGAA 60.670 61.111 11.47 0.00 39.47 3.36
2631 6821 3.790212 GGCGAAGACTACTTTTGTCAC 57.210 47.619 0.00 0.00 36.39 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.415857 CGCACTCGAGTACTCTACTGTT 59.584 50.000 19.57 0.00 39.59 3.16
25 26 1.405821 CTGTGAGACGGGAGATGGTAC 59.594 57.143 0.00 0.00 0.00 3.34
28 29 1.142748 GCTGTGAGACGGGAGATGG 59.857 63.158 0.00 0.00 0.00 3.51
287 4125 6.708502 TGAGATTGTCCGACTTTTTATGAACA 59.291 34.615 0.00 0.00 0.00 3.18
313 4151 2.730090 CGTGCAACTCATGATCAAAGGC 60.730 50.000 0.00 1.53 33.49 4.35
340 4179 2.933495 TGCATAGTGTACCGTGAGAC 57.067 50.000 0.00 0.00 0.00 3.36
341 4180 2.481276 GCATGCATAGTGTACCGTGAGA 60.481 50.000 14.21 0.00 0.00 3.27
342 4181 1.860950 GCATGCATAGTGTACCGTGAG 59.139 52.381 14.21 0.00 0.00 3.51
381 4220 1.001378 CGCAAGGAACCCAAAAGAGTG 60.001 52.381 0.00 0.00 0.00 3.51
382 4221 1.133915 TCGCAAGGAACCCAAAAGAGT 60.134 47.619 0.00 0.00 38.47 3.24
383 4222 1.604604 TCGCAAGGAACCCAAAAGAG 58.395 50.000 0.00 0.00 38.47 2.85
384 4223 2.060050 TTCGCAAGGAACCCAAAAGA 57.940 45.000 0.00 0.00 38.47 2.52
400 4239 1.774085 GATCTTACTACGCGCTGTTCG 59.226 52.381 5.73 3.17 42.12 3.95
401 4240 3.037324 GAGATCTTACTACGCGCTGTTC 58.963 50.000 5.73 0.00 0.00 3.18
402 4241 2.539142 CGAGATCTTACTACGCGCTGTT 60.539 50.000 5.73 0.00 0.00 3.16
403 4242 1.003759 CGAGATCTTACTACGCGCTGT 60.004 52.381 5.73 8.07 0.00 4.40
404 4243 1.664629 CGAGATCTTACTACGCGCTG 58.335 55.000 5.73 0.62 0.00 5.18
405 4244 0.041135 GCGAGATCTTACTACGCGCT 60.041 55.000 5.73 0.00 45.72 5.92
406 4245 2.411877 GCGAGATCTTACTACGCGC 58.588 57.895 5.73 8.25 43.76 6.86
419 4260 2.875933 ACATTTGTTTTTCTCGGCGAGA 59.124 40.909 33.80 33.80 36.86 4.04
464 4313 0.321346 TCGTGCATTCAAGCCTCTCA 59.679 50.000 0.00 0.00 0.00 3.27
465 4314 1.661341 ATCGTGCATTCAAGCCTCTC 58.339 50.000 0.00 0.00 0.00 3.20
466 4315 1.741706 CAATCGTGCATTCAAGCCTCT 59.258 47.619 0.00 0.00 0.00 3.69
467 4316 1.202222 CCAATCGTGCATTCAAGCCTC 60.202 52.381 0.00 0.00 0.00 4.70
481 4330 0.249120 TGGCACAGTACCTCCAATCG 59.751 55.000 0.00 0.00 0.00 3.34
497 4346 2.753296 CTAGCTGAGCTATTCACTGGC 58.247 52.381 15.42 0.00 40.54 4.85
659 4791 1.601903 GGTTGCTGTGATTTGACACGA 59.398 47.619 0.00 0.00 42.86 4.35
662 4794 2.226200 CGATGGTTGCTGTGATTTGACA 59.774 45.455 0.00 0.00 0.00 3.58
728 4877 1.062148 GTAAAGCAAGCGAATCGGTCC 59.938 52.381 8.08 2.52 36.27 4.46
731 4880 1.529826 GCAGTAAAGCAAGCGAATCGG 60.530 52.381 4.35 0.00 0.00 4.18
813 4962 5.313772 TGAAAAGAAGAGGTAAATGGGGGTA 59.686 40.000 0.00 0.00 0.00 3.69
814 4963 4.107311 TGAAAAGAAGAGGTAAATGGGGGT 59.893 41.667 0.00 0.00 0.00 4.95
815 4964 4.672899 TGAAAAGAAGAGGTAAATGGGGG 58.327 43.478 0.00 0.00 0.00 5.40
829 4978 4.645535 AGCAGCTAGTGACATGAAAAGAA 58.354 39.130 0.00 0.00 0.00 2.52
1143 5308 2.279073 CTACGGCCTCCTCCTCCA 59.721 66.667 0.00 0.00 0.00 3.86
1159 5324 2.281761 CGACTTGGGCTTGGTGCT 60.282 61.111 0.00 0.00 42.39 4.40
1344 5509 2.462782 CCTCCTCGTCCTCGTCGTC 61.463 68.421 0.00 0.00 38.33 4.20
1425 5590 4.377760 TCCTCCTTCTCCCCGCGT 62.378 66.667 4.92 0.00 0.00 6.01
1435 5603 2.023532 CCTCCTCCTCCTCCTCCTT 58.976 63.158 0.00 0.00 0.00 3.36
1701 5869 3.792047 CATGTCGGCGTGCAGGTG 61.792 66.667 6.85 1.44 0.00 4.00
1714 5882 1.443407 CTAGCTAGGTGGCGCATGT 59.557 57.895 13.32 0.00 37.29 3.21
1735 5903 1.598130 GCCAGCGCTAATGGGGTAG 60.598 63.158 10.99 0.00 38.33 3.18
1739 5907 2.401583 TATATGCCAGCGCTAATGGG 57.598 50.000 10.99 8.68 38.33 4.00
1782 5950 4.260375 CGTACGTACACAGTAGTATGACCC 60.260 50.000 24.50 0.00 35.47 4.46
1783 5951 4.330074 ACGTACGTACACAGTAGTATGACC 59.670 45.833 21.41 0.00 35.47 4.02
1784 5952 5.456192 ACGTACGTACACAGTAGTATGAC 57.544 43.478 21.41 0.00 35.47 3.06
1796 5978 6.811665 ACTACAGTACAAGATACGTACGTACA 59.188 38.462 28.99 12.00 43.24 2.90
1797 5979 7.223058 ACTACAGTACAAGATACGTACGTAC 57.777 40.000 28.99 21.22 43.24 3.67
1799 5981 6.147821 ACAACTACAGTACAAGATACGTACGT 59.852 38.462 25.98 25.98 43.24 3.57
1800 5982 6.537566 ACAACTACAGTACAAGATACGTACG 58.462 40.000 15.01 15.01 43.24 3.67
1801 5983 6.680338 CGACAACTACAGTACAAGATACGTAC 59.320 42.308 0.00 0.00 39.64 3.67
1803 5985 5.180117 ACGACAACTACAGTACAAGATACGT 59.820 40.000 0.00 0.00 0.00 3.57
1804 5986 5.625251 ACGACAACTACAGTACAAGATACG 58.375 41.667 0.00 0.00 0.00 3.06
1805 5987 5.731723 CGACGACAACTACAGTACAAGATAC 59.268 44.000 0.00 0.00 0.00 2.24
1834 6016 3.907788 CACGTAATACAACAACGACGAGA 59.092 43.478 0.00 0.00 39.80 4.04
1850 6032 2.681848 GGAGTAGCAGAGTAGCACGTAA 59.318 50.000 0.00 0.00 36.85 3.18
1851 6033 2.286872 GGAGTAGCAGAGTAGCACGTA 58.713 52.381 0.00 0.00 36.85 3.57
1852 6034 1.096416 GGAGTAGCAGAGTAGCACGT 58.904 55.000 0.00 0.00 36.85 4.49
1853 6035 0.028242 CGGAGTAGCAGAGTAGCACG 59.972 60.000 0.00 0.00 36.85 5.34
1854 6036 1.096416 ACGGAGTAGCAGAGTAGCAC 58.904 55.000 0.00 0.00 41.94 4.40
2018 6200 3.399330 GAATCCACCTCAGAACGAACAA 58.601 45.455 0.00 0.00 0.00 2.83
2019 6201 2.609491 CGAATCCACCTCAGAACGAACA 60.609 50.000 0.00 0.00 0.00 3.18
2020 6202 1.993370 CGAATCCACCTCAGAACGAAC 59.007 52.381 0.00 0.00 0.00 3.95
2021 6203 1.890489 TCGAATCCACCTCAGAACGAA 59.110 47.619 0.00 0.00 0.00 3.85
2022 6204 1.541379 TCGAATCCACCTCAGAACGA 58.459 50.000 0.00 0.00 0.00 3.85
2023 6205 1.993370 GTTCGAATCCACCTCAGAACG 59.007 52.381 0.00 0.00 0.00 3.95
2024 6206 2.289444 TGGTTCGAATCCACCTCAGAAC 60.289 50.000 5.84 0.00 37.74 3.01
2025 6207 1.974957 TGGTTCGAATCCACCTCAGAA 59.025 47.619 5.84 0.00 33.76 3.02
2026 6208 1.275291 GTGGTTCGAATCCACCTCAGA 59.725 52.381 26.41 0.00 46.63 3.27
2027 6209 1.726853 GTGGTTCGAATCCACCTCAG 58.273 55.000 26.41 0.00 46.63 3.35
2028 6210 3.927555 GTGGTTCGAATCCACCTCA 57.072 52.632 26.41 0.10 46.63 3.86
2033 6215 0.902531 GAGGGAGTGGTTCGAATCCA 59.097 55.000 15.54 14.42 33.24 3.41
2034 6216 0.178301 GGAGGGAGTGGTTCGAATCC 59.822 60.000 5.84 6.46 0.00 3.01
2035 6217 0.179108 CGGAGGGAGTGGTTCGAATC 60.179 60.000 0.00 0.00 0.00 2.52
2036 6218 0.903454 ACGGAGGGAGTGGTTCGAAT 60.903 55.000 0.00 0.00 0.00 3.34
2037 6219 1.117142 AACGGAGGGAGTGGTTCGAA 61.117 55.000 0.00 0.00 0.00 3.71
2038 6220 1.117142 AAACGGAGGGAGTGGTTCGA 61.117 55.000 0.00 0.00 0.00 3.71
2039 6221 0.949105 CAAACGGAGGGAGTGGTTCG 60.949 60.000 0.00 0.00 0.00 3.95
2040 6222 0.108019 ACAAACGGAGGGAGTGGTTC 59.892 55.000 0.00 0.00 0.00 3.62
2041 6223 1.426751 TACAAACGGAGGGAGTGGTT 58.573 50.000 0.00 0.00 0.00 3.67
2042 6224 1.652947 ATACAAACGGAGGGAGTGGT 58.347 50.000 0.00 0.00 0.00 4.16
2043 6225 2.781681 AATACAAACGGAGGGAGTGG 57.218 50.000 0.00 0.00 0.00 4.00
2044 6226 2.671396 CGAAATACAAACGGAGGGAGTG 59.329 50.000 0.00 0.00 0.00 3.51
2045 6227 2.564062 TCGAAATACAAACGGAGGGAGT 59.436 45.455 0.00 0.00 0.00 3.85
2046 6228 3.187700 CTCGAAATACAAACGGAGGGAG 58.812 50.000 0.00 0.00 0.00 4.30
2047 6229 2.564062 ACTCGAAATACAAACGGAGGGA 59.436 45.455 0.00 0.00 0.00 4.20
2048 6230 2.928116 GACTCGAAATACAAACGGAGGG 59.072 50.000 0.00 0.00 0.00 4.30
2049 6231 2.928116 GGACTCGAAATACAAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2050 6232 3.581755 TGGACTCGAAATACAAACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2051 6233 3.663995 TGGACTCGAAATACAAACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2052 6234 4.735662 TTTGGACTCGAAATACAAACGG 57.264 40.909 3.17 0.00 0.00 4.44
2053 6235 5.144359 CCTTTTGGACTCGAAATACAAACG 58.856 41.667 6.29 5.26 44.07 3.60
2054 6236 4.915667 GCCTTTTGGACTCGAAATACAAAC 59.084 41.667 6.29 0.00 44.07 2.93
2055 6237 4.022676 GGCCTTTTGGACTCGAAATACAAA 60.023 41.667 0.00 3.17 46.73 2.83
2056 6238 3.504520 GGCCTTTTGGACTCGAAATACAA 59.495 43.478 0.00 0.00 46.73 2.41
2057 6239 3.078837 GGCCTTTTGGACTCGAAATACA 58.921 45.455 0.00 0.00 46.73 2.29
2058 6240 3.759527 GGCCTTTTGGACTCGAAATAC 57.240 47.619 0.00 0.00 46.73 1.89
2067 6249 1.460273 TTTCAGCCGGCCTTTTGGAC 61.460 55.000 26.15 0.00 46.81 4.02
2068 6250 1.152652 TTTCAGCCGGCCTTTTGGA 60.153 52.632 26.15 6.55 44.07 3.53
2069 6251 1.178534 TCTTTCAGCCGGCCTTTTGG 61.179 55.000 26.15 9.75 44.18 3.28
2070 6252 0.242017 CTCTTTCAGCCGGCCTTTTG 59.758 55.000 26.15 15.69 0.00 2.44
2071 6253 0.895559 CCTCTTTCAGCCGGCCTTTT 60.896 55.000 26.15 0.00 0.00 2.27
2072 6254 1.303643 CCTCTTTCAGCCGGCCTTT 60.304 57.895 26.15 0.18 0.00 3.11
2073 6255 1.566298 ATCCTCTTTCAGCCGGCCTT 61.566 55.000 26.15 1.18 0.00 4.35
2074 6256 1.566298 AATCCTCTTTCAGCCGGCCT 61.566 55.000 26.15 7.86 0.00 5.19
2075 6257 0.681243 AAATCCTCTTTCAGCCGGCC 60.681 55.000 26.15 5.07 0.00 6.13
2076 6258 1.133216 GAAAATCCTCTTTCAGCCGGC 59.867 52.381 21.89 21.89 35.71 6.13
2077 6259 2.436417 TGAAAATCCTCTTTCAGCCGG 58.564 47.619 0.00 0.00 39.74 6.13
2082 6264 7.020827 ACATAGGACTGAAAATCCTCTTTCA 57.979 36.000 0.00 0.00 43.49 2.69
2083 6265 6.540551 GGACATAGGACTGAAAATCCTCTTTC 59.459 42.308 0.00 0.00 43.49 2.62
2084 6266 6.418946 GGACATAGGACTGAAAATCCTCTTT 58.581 40.000 0.00 0.00 43.49 2.52
2085 6267 5.395768 CGGACATAGGACTGAAAATCCTCTT 60.396 44.000 0.00 0.00 43.49 2.85
2086 6268 4.100189 CGGACATAGGACTGAAAATCCTCT 59.900 45.833 0.00 0.00 43.49 3.69
2087 6269 4.372656 CGGACATAGGACTGAAAATCCTC 58.627 47.826 0.00 0.00 43.49 3.71
2089 6271 2.872858 GCGGACATAGGACTGAAAATCC 59.127 50.000 0.00 0.00 36.38 3.01
2090 6272 3.557595 CAGCGGACATAGGACTGAAAATC 59.442 47.826 0.00 0.00 0.00 2.17
2091 6273 3.535561 CAGCGGACATAGGACTGAAAAT 58.464 45.455 0.00 0.00 0.00 1.82
2092 6274 2.935238 GCAGCGGACATAGGACTGAAAA 60.935 50.000 0.00 0.00 0.00 2.29
2093 6275 1.405526 GCAGCGGACATAGGACTGAAA 60.406 52.381 0.00 0.00 0.00 2.69
2094 6276 0.175760 GCAGCGGACATAGGACTGAA 59.824 55.000 0.00 0.00 0.00 3.02
2095 6277 1.676678 GGCAGCGGACATAGGACTGA 61.677 60.000 0.00 0.00 0.00 3.41
2096 6278 1.227380 GGCAGCGGACATAGGACTG 60.227 63.158 0.00 0.00 0.00 3.51
2097 6279 1.680522 CTGGCAGCGGACATAGGACT 61.681 60.000 0.00 0.00 0.00 3.85
2098 6280 1.227380 CTGGCAGCGGACATAGGAC 60.227 63.158 0.00 0.00 0.00 3.85
2099 6281 3.094062 GCTGGCAGCGGACATAGGA 62.094 63.158 25.47 0.00 0.00 2.94
2100 6282 2.590007 GCTGGCAGCGGACATAGG 60.590 66.667 25.47 0.00 0.00 2.57
2101 6283 0.816825 ATTGCTGGCAGCGGACATAG 60.817 55.000 32.12 0.00 46.26 2.23
2102 6284 1.096967 CATTGCTGGCAGCGGACATA 61.097 55.000 32.12 12.91 46.26 2.29
2103 6285 2.044650 ATTGCTGGCAGCGGACAT 60.045 55.556 32.12 18.96 46.26 3.06
2104 6286 3.057548 CATTGCTGGCAGCGGACA 61.058 61.111 32.12 17.58 46.26 4.02
2105 6287 3.818787 CCATTGCTGGCAGCGGAC 61.819 66.667 32.12 8.93 46.26 4.79
2106 6288 3.565961 TTCCATTGCTGGCAGCGGA 62.566 57.895 32.12 28.21 46.26 5.54
2107 6289 2.157305 TTTTCCATTGCTGGCAGCGG 62.157 55.000 32.12 26.52 46.26 5.52
2108 6290 0.108520 ATTTTCCATTGCTGGCAGCG 60.109 50.000 32.12 19.10 46.26 5.18
2109 6291 1.365699 CATTTTCCATTGCTGGCAGC 58.634 50.000 31.91 31.91 42.80 5.25
2110 6292 1.551430 TCCATTTTCCATTGCTGGCAG 59.449 47.619 10.94 10.94 42.80 4.85
2111 6293 1.642112 TCCATTTTCCATTGCTGGCA 58.358 45.000 0.00 0.00 42.80 4.92
2112 6294 2.027837 ACTTCCATTTTCCATTGCTGGC 60.028 45.455 0.00 0.00 42.80 4.85
2113 6295 3.967332 ACTTCCATTTTCCATTGCTGG 57.033 42.857 0.00 0.00 44.64 4.85
2114 6296 5.544650 AGAAACTTCCATTTTCCATTGCTG 58.455 37.500 0.00 0.00 34.07 4.41
2115 6297 5.813513 AGAAACTTCCATTTTCCATTGCT 57.186 34.783 0.00 0.00 34.07 3.91
2116 6298 6.071391 TCCTAGAAACTTCCATTTTCCATTGC 60.071 38.462 0.00 0.00 34.07 3.56
2117 6299 7.466746 TCCTAGAAACTTCCATTTTCCATTG 57.533 36.000 0.00 0.00 34.07 2.82
2118 6300 8.534496 CAATCCTAGAAACTTCCATTTTCCATT 58.466 33.333 0.00 0.00 34.07 3.16
2119 6301 7.364144 GCAATCCTAGAAACTTCCATTTTCCAT 60.364 37.037 0.00 0.00 34.07 3.41
2120 6302 6.071391 GCAATCCTAGAAACTTCCATTTTCCA 60.071 38.462 0.00 0.00 34.07 3.53
2121 6303 6.153510 AGCAATCCTAGAAACTTCCATTTTCC 59.846 38.462 0.00 0.00 34.07 3.13
2122 6304 7.031975 CAGCAATCCTAGAAACTTCCATTTTC 58.968 38.462 0.00 0.00 33.81 2.29
2123 6305 6.573094 GCAGCAATCCTAGAAACTTCCATTTT 60.573 38.462 0.00 0.00 0.00 1.82
2124 6306 5.105595 GCAGCAATCCTAGAAACTTCCATTT 60.106 40.000 0.00 0.00 0.00 2.32
2125 6307 4.400567 GCAGCAATCCTAGAAACTTCCATT 59.599 41.667 0.00 0.00 0.00 3.16
2126 6308 3.950395 GCAGCAATCCTAGAAACTTCCAT 59.050 43.478 0.00 0.00 0.00 3.41
2127 6309 3.009473 AGCAGCAATCCTAGAAACTTCCA 59.991 43.478 0.00 0.00 0.00 3.53
2128 6310 3.615155 AGCAGCAATCCTAGAAACTTCC 58.385 45.455 0.00 0.00 0.00 3.46
2129 6311 4.512484 AGAGCAGCAATCCTAGAAACTTC 58.488 43.478 0.00 0.00 0.00 3.01
2130 6312 4.566426 AGAGCAGCAATCCTAGAAACTT 57.434 40.909 0.00 0.00 0.00 2.66
2131 6313 4.566426 AAGAGCAGCAATCCTAGAAACT 57.434 40.909 0.00 0.00 0.00 2.66
2132 6314 5.414144 AGAAAAGAGCAGCAATCCTAGAAAC 59.586 40.000 0.00 0.00 0.00 2.78
2133 6315 5.413833 CAGAAAAGAGCAGCAATCCTAGAAA 59.586 40.000 0.00 0.00 0.00 2.52
2134 6316 4.940046 CAGAAAAGAGCAGCAATCCTAGAA 59.060 41.667 0.00 0.00 0.00 2.10
2135 6317 4.019860 ACAGAAAAGAGCAGCAATCCTAGA 60.020 41.667 0.00 0.00 0.00 2.43
2136 6318 4.260170 ACAGAAAAGAGCAGCAATCCTAG 58.740 43.478 0.00 0.00 0.00 3.02
2137 6319 4.292186 ACAGAAAAGAGCAGCAATCCTA 57.708 40.909 0.00 0.00 0.00 2.94
2138 6320 3.151912 ACAGAAAAGAGCAGCAATCCT 57.848 42.857 0.00 0.00 0.00 3.24
2139 6321 3.254166 TGAACAGAAAAGAGCAGCAATCC 59.746 43.478 0.00 0.00 0.00 3.01
2140 6322 4.494350 TGAACAGAAAAGAGCAGCAATC 57.506 40.909 0.00 0.00 0.00 2.67
2141 6323 4.581824 TCTTGAACAGAAAAGAGCAGCAAT 59.418 37.500 0.00 0.00 0.00 3.56
2142 6324 3.947196 TCTTGAACAGAAAAGAGCAGCAA 59.053 39.130 0.00 0.00 0.00 3.91
2143 6325 3.544684 TCTTGAACAGAAAAGAGCAGCA 58.455 40.909 0.00 0.00 0.00 4.41
2144 6326 4.036144 ACTTCTTGAACAGAAAAGAGCAGC 59.964 41.667 0.00 0.00 41.25 5.25
2145 6327 5.526846 AGACTTCTTGAACAGAAAAGAGCAG 59.473 40.000 0.00 0.00 41.25 4.24
2146 6328 5.431765 AGACTTCTTGAACAGAAAAGAGCA 58.568 37.500 0.00 0.00 41.25 4.26
2147 6329 6.370433 AAGACTTCTTGAACAGAAAAGAGC 57.630 37.500 0.00 0.00 41.25 4.09
2148 6330 8.207521 AGAAAGACTTCTTGAACAGAAAAGAG 57.792 34.615 0.00 0.00 41.25 2.85
2149 6331 7.281100 GGAGAAAGACTTCTTGAACAGAAAAGA 59.719 37.037 0.00 0.00 42.19 2.52
2150 6332 7.066284 TGGAGAAAGACTTCTTGAACAGAAAAG 59.934 37.037 0.00 0.00 42.19 2.27
2151 6333 6.884295 TGGAGAAAGACTTCTTGAACAGAAAA 59.116 34.615 0.00 0.00 42.19 2.29
2152 6334 6.414732 TGGAGAAAGACTTCTTGAACAGAAA 58.585 36.000 0.00 0.00 42.19 2.52
2153 6335 5.989477 TGGAGAAAGACTTCTTGAACAGAA 58.011 37.500 0.00 0.00 42.19 3.02
2154 6336 5.453903 CCTGGAGAAAGACTTCTTGAACAGA 60.454 44.000 11.66 0.00 42.19 3.41
2155 6337 4.754114 CCTGGAGAAAGACTTCTTGAACAG 59.246 45.833 0.00 0.46 42.19 3.16
2156 6338 4.164221 ACCTGGAGAAAGACTTCTTGAACA 59.836 41.667 0.00 0.00 42.19 3.18
2157 6339 4.513318 CACCTGGAGAAAGACTTCTTGAAC 59.487 45.833 0.00 0.00 42.19 3.18
2158 6340 4.164221 ACACCTGGAGAAAGACTTCTTGAA 59.836 41.667 0.00 0.00 42.19 2.69
2159 6341 3.711704 ACACCTGGAGAAAGACTTCTTGA 59.288 43.478 0.00 0.00 42.19 3.02
2160 6342 4.061596 GACACCTGGAGAAAGACTTCTTG 58.938 47.826 0.00 0.00 42.19 3.02
2161 6343 3.243907 CGACACCTGGAGAAAGACTTCTT 60.244 47.826 0.00 0.00 42.19 2.52
2162 6344 2.297597 CGACACCTGGAGAAAGACTTCT 59.702 50.000 0.00 0.00 44.93 2.85
2163 6345 2.610727 CCGACACCTGGAGAAAGACTTC 60.611 54.545 0.00 0.00 0.00 3.01
2164 6346 1.344763 CCGACACCTGGAGAAAGACTT 59.655 52.381 0.00 0.00 0.00 3.01
2165 6347 0.969894 CCGACACCTGGAGAAAGACT 59.030 55.000 0.00 0.00 0.00 3.24
2166 6348 0.670854 GCCGACACCTGGAGAAAGAC 60.671 60.000 0.00 0.00 0.00 3.01
2167 6349 1.671742 GCCGACACCTGGAGAAAGA 59.328 57.895 0.00 0.00 0.00 2.52
2168 6350 1.738099 CGCCGACACCTGGAGAAAG 60.738 63.158 0.00 0.00 0.00 2.62
2169 6351 2.035237 AACGCCGACACCTGGAGAAA 62.035 55.000 0.00 0.00 0.00 2.52
2170 6352 2.430382 GAACGCCGACACCTGGAGAA 62.430 60.000 0.00 0.00 0.00 2.87
2171 6353 2.915659 AACGCCGACACCTGGAGA 60.916 61.111 0.00 0.00 0.00 3.71
2172 6354 2.432628 GAACGCCGACACCTGGAG 60.433 66.667 0.00 0.00 0.00 3.86
2173 6355 2.915659 AGAACGCCGACACCTGGA 60.916 61.111 0.00 0.00 0.00 3.86
2174 6356 2.709125 TTCAGAACGCCGACACCTGG 62.709 60.000 0.00 0.00 0.00 4.45
2175 6357 0.878523 TTTCAGAACGCCGACACCTG 60.879 55.000 0.00 0.00 0.00 4.00
2176 6358 0.179067 TTTTCAGAACGCCGACACCT 60.179 50.000 0.00 0.00 0.00 4.00
2177 6359 0.041576 GTTTTCAGAACGCCGACACC 60.042 55.000 0.00 0.00 0.00 4.16
2178 6360 0.382636 CGTTTTCAGAACGCCGACAC 60.383 55.000 0.00 0.00 36.82 3.67
2192 6374 1.137697 AAGTCTGAGGACCCCGTTTT 58.862 50.000 0.00 0.00 43.05 2.43
2193 6375 0.396811 CAAGTCTGAGGACCCCGTTT 59.603 55.000 0.00 0.00 43.05 3.60
2204 6387 0.887836 CTGCAAGCAGGCAAGTCTGA 60.888 55.000 14.10 0.00 44.40 3.27
2222 6405 4.681978 GGAGCCACGCCGTGAACT 62.682 66.667 20.57 15.52 35.23 3.01
2224 6407 4.980805 GTGGAGCCACGCCGTGAA 62.981 66.667 20.57 0.00 37.19 3.18
2407 6591 1.083806 TTGATCGTCATGGCTCACGC 61.084 55.000 0.00 0.00 35.93 5.34
2443 6627 2.967076 CAAGGACACTGTGCGCGT 60.967 61.111 8.43 0.00 0.00 6.01
2494 6678 1.139654 CTGATGCCTCGGAATTCCTCA 59.860 52.381 22.05 15.63 0.00 3.86
2500 6684 0.034186 TTTGCCTGATGCCTCGGAAT 60.034 50.000 0.00 0.00 40.16 3.01
2525 6709 2.230992 TGGTCTTGTTGCACCAATATGC 59.769 45.455 0.00 0.00 46.32 3.14
2631 6821 4.499357 GGGGACAGCTAGTACAACTTATCG 60.499 50.000 0.00 0.00 30.17 2.92


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

AutoCloner maintained by Alex Coulton.