Multiple sequence alignment - TraesCS5B01G406100

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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 TraesCS5B01G406100 chr5B 100.000 3227 0 0 1 3227 582150083 582153309 0.000000e+00 5960.0
1 TraesCS5B01G406100 chr5B 96.063 127 5 0 2860 2986 354511533 354511659 1.170000e-49 207.0
2 TraesCS5B01G406100 chr5B 95.349 129 6 0 2858 2986 345346729 345346857 4.220000e-49 206.0
3 TraesCS5B01G406100 chr5B 91.729 133 10 1 3079 3211 139169318 139169187 1.980000e-42 183.0
4 TraesCS5B01G406100 chr5B 89.189 148 15 1 3079 3226 582157851 582157997 1.980000e-42 183.0
5 TraesCS5B01G406100 chr5D 87.899 1504 104 38 1305 2753 475000926 475002406 0.000000e+00 1698.0
6 TraesCS5B01G406100 chr5D 90.356 674 33 12 537 1204 475000145 475000792 0.000000e+00 856.0
7 TraesCS5B01G406100 chr5D 88.528 523 29 13 1 515 474996416 474996915 3.560000e-169 604.0
8 TraesCS5B01G406100 chr5D 85.308 211 19 4 3027 3227 475004934 475005142 1.170000e-49 207.0
9 TraesCS5B01G406100 chr5D 90.226 133 12 1 3079 3211 126268769 126268638 4.280000e-39 172.0
10 TraesCS5B01G406100 chr5D 91.304 69 3 3 2792 2860 475004744 475004809 1.230000e-14 91.6
11 TraesCS5B01G406100 chr5A 84.595 1493 122 50 1305 2719 594132981 594134443 0.000000e+00 1384.0
12 TraesCS5B01G406100 chr5A 86.949 613 36 13 603 1204 594132265 594132844 0.000000e+00 649.0
13 TraesCS5B01G406100 chr5A 88.000 375 21 5 236 607 594131560 594131913 3.850000e-114 422.0
14 TraesCS5B01G406100 chr5A 95.699 186 7 1 1 186 594131371 594131555 6.770000e-77 298.0
15 TraesCS5B01G406100 chr5A 89.055 201 17 4 3027 3227 594134748 594134943 8.940000e-61 244.0
16 TraesCS5B01G406100 chr5A 86.667 150 16 4 3079 3227 594138067 594138213 2.580000e-36 163.0
17 TraesCS5B01G406100 chr2B 96.094 128 5 0 2859 2986 436038193 436038066 3.260000e-50 209.0
18 TraesCS5B01G406100 chr2B 84.667 150 22 1 3078 3227 796674565 796674417 7.210000e-32 148.0
19 TraesCS5B01G406100 chr2B 84.932 146 20 1 3079 3224 150531106 150531249 2.590000e-31 147.0
20 TraesCS5B01G406100 chr7B 96.063 127 5 0 2860 2986 46905866 46905992 1.170000e-49 207.0
21 TraesCS5B01G406100 chr7B 92.806 139 8 2 2851 2987 395246361 395246223 1.960000e-47 200.0
22 TraesCS5B01G406100 chr3A 95.385 130 6 0 2857 2986 644820390 644820519 1.170000e-49 207.0
23 TraesCS5B01G406100 chr6B 93.431 137 8 1 2860 2996 172239631 172239766 5.460000e-48 202.0
24 TraesCS5B01G406100 chr7A 91.608 143 10 2 2845 2986 65974511 65974370 2.540000e-46 196.0
25 TraesCS5B01G406100 chr4B 91.608 143 10 2 2851 2992 548610801 548610660 2.540000e-46 196.0
26 TraesCS5B01G406100 chr2A 85.882 170 21 3 2859 3028 669632485 669632319 9.200000e-41 178.0
27 TraesCS5B01G406100 chr1D 84.722 144 21 1 3081 3224 33593880 33594022 3.360000e-30 143.0


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 TraesCS5B01G406100 chr5B 582150083 582153309 3226 False 5960.000000 5960 100.000000 1 3227 1 chr5B.!!$F3 3226
1 TraesCS5B01G406100 chr5D 474996416 475005142 8726 False 691.320000 1698 88.679000 1 3227 5 chr5D.!!$F1 3226
2 TraesCS5B01G406100 chr5A 594131371 594138213 6842 False 526.666667 1384 88.494167 1 3227 6 chr5A.!!$F1 3226

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
885 4472 0.177141 TTGCGTACATGCTCCCTACC 59.823 55.0 0.0 0.0 35.36 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2853 8983 0.335361 AGACGGAGGGAGTACACCAT 59.665 55.0 11.69 3.58 0.0 3.55 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
49 50 0.664761 GCAGCTTGCAAGACTGTCAA 59.335 50.000 32.36 1.58 44.26 3.18
135 136 4.021102 AGCTACACTGGCACTTAACAAT 57.979 40.909 0.00 0.00 0.00 2.71
189 190 4.978580 GCTGCTAAAACTTTCACAAGGAAG 59.021 41.667 0.00 0.00 36.72 3.46
191 192 6.680378 GCTGCTAAAACTTTCACAAGGAAGAA 60.680 38.462 0.00 0.00 36.72 2.52
199 200 5.869344 ACTTTCACAAGGAAGAAAAACAAGC 59.131 36.000 0.00 0.00 36.72 4.01
203 204 3.181490 ACAAGGAAGAAAAACAAGCGGAC 60.181 43.478 0.00 0.00 0.00 4.79
207 208 3.304458 GGAAGAAAAACAAGCGGACGAAT 60.304 43.478 0.00 0.00 0.00 3.34
212 213 0.591170 AACAAGCGGACGAATTGTGG 59.409 50.000 13.75 0.00 37.24 4.17
217 218 1.696832 GCGGACGAATTGTGGAGCTC 61.697 60.000 4.71 4.71 0.00 4.09
246 247 3.753272 TGTCTAATTGCACCTCAAAGCTC 59.247 43.478 0.00 0.00 38.34 4.09
254 255 3.009473 TGCACCTCAAAGCTCTCCTTTAT 59.991 43.478 0.00 0.00 41.75 1.40
255 256 4.225042 TGCACCTCAAAGCTCTCCTTTATA 59.775 41.667 0.00 0.00 41.75 0.98
256 257 4.572795 GCACCTCAAAGCTCTCCTTTATAC 59.427 45.833 0.00 0.00 41.75 1.47
257 258 5.734720 CACCTCAAAGCTCTCCTTTATACA 58.265 41.667 0.00 0.00 41.75 2.29
258 259 5.814705 CACCTCAAAGCTCTCCTTTATACAG 59.185 44.000 0.00 0.00 41.75 2.74
330 336 7.278203 TCGTTAGCACATTGTTAATTCGGATTA 59.722 33.333 0.00 0.00 0.00 1.75
362 371 5.952347 TGTATCACTTTAGAGAGGCTCAAGA 59.048 40.000 18.26 0.00 32.06 3.02
371 380 2.808315 GGCTCAAGAGGCGATCGA 59.192 61.111 21.57 0.00 44.15 3.59
372 381 1.299773 GGCTCAAGAGGCGATCGAG 60.300 63.158 21.57 6.31 44.15 4.04
373 382 1.299773 GCTCAAGAGGCGATCGAGG 60.300 63.158 21.57 0.48 0.00 4.63
374 383 1.361993 CTCAAGAGGCGATCGAGGG 59.638 63.158 21.57 1.24 0.00 4.30
375 384 2.081425 CTCAAGAGGCGATCGAGGGG 62.081 65.000 21.57 2.38 0.00 4.79
376 385 2.840102 AAGAGGCGATCGAGGGGG 60.840 66.667 21.57 0.00 0.00 5.40
451 460 3.299020 CGCTTTGAAGATTTCATCGCAAC 59.701 43.478 11.00 0.00 39.84 4.17
453 462 4.681025 GCTTTGAAGATTTCATCGCAACAA 59.319 37.500 0.00 0.00 39.84 2.83
462 471 2.736978 TCATCGCAACAACGCATTTTT 58.263 38.095 0.00 0.00 0.00 1.94
498 507 7.829211 TCTTGGACAGGATAAATCAAAAGGTAG 59.171 37.037 0.00 0.00 0.00 3.18
554 3771 0.436913 TGCACGAATTAACTGACGCG 59.563 50.000 3.53 3.53 0.00 6.01
560 3777 0.713883 AATTAACTGACGCGCACTCG 59.286 50.000 5.73 0.00 39.07 4.18
631 4204 4.068599 TCTGTGTTGTCAGTTGTCACAAA 58.931 39.130 0.00 0.00 38.30 2.83
683 4256 4.141711 CCCATTTTCCTCTTCGAGATGGTA 60.142 45.833 7.90 0.00 32.61 3.25
684 4257 4.811557 CCATTTTCCTCTTCGAGATGGTAC 59.188 45.833 0.00 0.00 0.00 3.34
727 4300 8.697292 ACTACTAGTGTTCTTTCTTGAGACTTT 58.303 33.333 5.39 0.00 0.00 2.66
749 4322 6.855763 TTTGATATTTTGCTGACCCAATCT 57.144 33.333 0.00 0.00 0.00 2.40
785 4366 2.227036 ACCCAGCACTAGCAGCCTT 61.227 57.895 4.30 0.00 45.49 4.35
812 4393 3.492011 GTGCAAGGAACAATTTTGAGCTG 59.508 43.478 0.00 0.00 0.00 4.24
813 4394 2.477754 GCAAGGAACAATTTTGAGCTGC 59.522 45.455 0.00 0.00 0.00 5.25
814 4395 3.801293 GCAAGGAACAATTTTGAGCTGCT 60.801 43.478 0.00 0.00 0.00 4.24
819 4400 3.863142 ACAATTTTGAGCTGCTCATCC 57.137 42.857 30.80 6.14 40.39 3.51
828 4415 4.776322 TGCTCATCCCAACGGCCG 62.776 66.667 26.86 26.86 0.00 6.13
830 4417 2.511600 CTCATCCCAACGGCCGTC 60.512 66.667 34.29 0.00 0.00 4.79
831 4418 4.090588 TCATCCCAACGGCCGTCC 62.091 66.667 34.29 0.00 0.00 4.79
835 4422 1.415672 ATCCCAACGGCCGTCCATAT 61.416 55.000 34.29 19.80 0.00 1.78
837 4424 0.323629 CCCAACGGCCGTCCATATAT 59.676 55.000 34.29 11.63 0.00 0.86
838 4425 1.551430 CCCAACGGCCGTCCATATATA 59.449 52.381 34.29 0.00 0.00 0.86
884 4471 1.134788 ACTTGCGTACATGCTCCCTAC 60.135 52.381 0.00 0.00 35.36 3.18
885 4472 0.177141 TTGCGTACATGCTCCCTACC 59.823 55.000 0.00 0.00 35.36 3.18
886 4473 0.686441 TGCGTACATGCTCCCTACCT 60.686 55.000 0.00 0.00 35.36 3.08
887 4474 1.325355 GCGTACATGCTCCCTACCTA 58.675 55.000 0.00 0.00 0.00 3.08
888 4475 1.000496 GCGTACATGCTCCCTACCTAC 60.000 57.143 0.00 0.00 0.00 3.18
889 4476 1.612463 CGTACATGCTCCCTACCTACC 59.388 57.143 0.00 0.00 0.00 3.18
890 4477 2.752154 CGTACATGCTCCCTACCTACCT 60.752 54.545 0.00 0.00 0.00 3.08
891 4478 3.497405 CGTACATGCTCCCTACCTACCTA 60.497 52.174 0.00 0.00 0.00 3.08
892 4479 3.246416 ACATGCTCCCTACCTACCTAG 57.754 52.381 0.00 0.00 0.00 3.02
893 4480 2.518834 ACATGCTCCCTACCTACCTAGT 59.481 50.000 0.00 0.00 0.00 2.57
894 4481 3.158676 CATGCTCCCTACCTACCTAGTC 58.841 54.545 0.00 0.00 0.00 2.59
895 4482 1.498145 TGCTCCCTACCTACCTAGTCC 59.502 57.143 0.00 0.00 0.00 3.85
908 4499 2.513317 ACCTAGTCCCTACTCCCTACAC 59.487 54.545 0.00 0.00 37.15 2.90
937 4528 2.432628 GCAGCTAGCGTCCGTTGT 60.433 61.111 9.55 0.00 0.00 3.32
991 4582 2.864968 CTTGGACAGCAGTACGTACTC 58.135 52.381 25.10 18.48 33.46 2.59
998 4589 0.525668 GCAGTACGTACTCGCTGCAT 60.526 55.000 27.92 8.05 45.41 3.96
1032 4623 4.057428 GCGGCTGTCGTCAGGTCT 62.057 66.667 11.61 0.00 41.57 3.85
1204 4795 3.826754 CGCTCTCCTACTGCGGCA 61.827 66.667 1.29 1.29 45.07 5.69
1205 4796 2.105930 GCTCTCCTACTGCGGCAG 59.894 66.667 27.43 27.43 37.52 4.85
1206 4797 2.105930 CTCTCCTACTGCGGCAGC 59.894 66.667 28.80 0.31 45.41 5.25
1243 4834 0.101399 CATCGACCTCAACCTCTCCG 59.899 60.000 0.00 0.00 0.00 4.63
1246 4837 2.284699 ACCTCAACCTCTCCGGGG 60.285 66.667 0.00 0.00 36.97 5.73
1257 4848 3.430497 TCCGGGGAGGAGGAGGAG 61.430 72.222 0.00 0.00 45.98 3.69
1261 4852 2.015726 GGGGAGGAGGAGGAGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1264 4855 0.856982 GGAGGAGGAGGAGAGGATCA 59.143 60.000 0.00 0.00 37.82 2.92
1277 4889 1.153628 GGATCAGTAAGCGTGCCGT 60.154 57.895 0.00 0.00 0.00 5.68
1383 5043 1.907936 CATGATCAGGGAGGGGATCTC 59.092 57.143 0.09 0.00 40.41 2.75
1407 5067 0.603975 GGCACAAGAAGAAGGCTCGT 60.604 55.000 0.00 0.00 0.00 4.18
1413 5073 2.734673 GAAGAAGGCTCGTGCTGCG 61.735 63.158 9.61 0.00 43.01 5.18
1428 5088 1.002257 TGCGGATCACAAGGCATGT 60.002 52.632 0.00 0.00 45.34 3.21
1442 5102 2.772568 GCATGTGGCATAATAACGCA 57.227 45.000 0.00 0.00 43.97 5.24
1444 5104 2.653890 CATGTGGCATAATAACGCAGC 58.346 47.619 0.00 0.00 0.00 5.25
1445 5105 0.655208 TGTGGCATAATAACGCAGCG 59.345 50.000 14.82 14.82 0.00 5.18
1446 5106 0.655733 GTGGCATAATAACGCAGCGT 59.344 50.000 16.61 16.61 43.97 5.07
1447 5107 1.862201 GTGGCATAATAACGCAGCGTA 59.138 47.619 23.30 5.57 39.99 4.42
1450 5110 3.185594 TGGCATAATAACGCAGCGTAATC 59.814 43.478 23.30 6.31 39.99 1.75
1451 5111 3.424433 GGCATAATAACGCAGCGTAATCC 60.424 47.826 23.30 11.63 39.99 3.01
1452 5112 3.432252 GCATAATAACGCAGCGTAATCCT 59.568 43.478 23.30 7.70 39.99 3.24
1460 5120 2.533266 CAGCGTAATCCTGCCATAGT 57.467 50.000 0.00 0.00 0.00 2.12
1461 5121 2.408050 CAGCGTAATCCTGCCATAGTC 58.592 52.381 0.00 0.00 0.00 2.59
1472 5132 1.488812 TGCCATAGTCGCAGGGTTTAT 59.511 47.619 0.00 0.00 0.00 1.40
1477 5137 1.173913 AGTCGCAGGGTTTATTTGCC 58.826 50.000 0.00 0.00 34.42 4.52
1478 5138 0.885196 GTCGCAGGGTTTATTTGCCA 59.115 50.000 0.00 0.00 34.42 4.92
1512 5184 1.197721 CTGATTCAGTTTGGCCGTGAC 59.802 52.381 5.46 0.00 0.00 3.67
1523 5195 3.716195 CCGTGACCATGCAGGGGA 61.716 66.667 23.35 4.62 43.89 4.81
1524 5196 2.591753 CGTGACCATGCAGGGGAT 59.408 61.111 23.35 0.05 43.89 3.85
1525 5197 1.524621 CGTGACCATGCAGGGGATC 60.525 63.158 23.35 11.76 43.89 3.36
1539 5211 4.194640 CAGGGGATCAAGTCTGTAACATG 58.805 47.826 0.00 0.00 0.00 3.21
1778 5459 3.594232 TGGGTGGGTGTATACAAGGATTT 59.406 43.478 7.25 0.00 0.00 2.17
1820 5501 3.533547 CAATGCAGAGAAGAAGGGAGAG 58.466 50.000 0.00 0.00 0.00 3.20
1821 5502 2.612285 TGCAGAGAAGAAGGGAGAGA 57.388 50.000 0.00 0.00 0.00 3.10
1876 5557 0.879090 GCCCAACGGAACCAAAGTAG 59.121 55.000 0.00 0.00 0.00 2.57
1877 5558 1.816572 GCCCAACGGAACCAAAGTAGT 60.817 52.381 0.00 0.00 0.00 2.73
1878 5559 2.550639 GCCCAACGGAACCAAAGTAGTA 60.551 50.000 0.00 0.00 0.00 1.82
1879 5560 3.742385 CCCAACGGAACCAAAGTAGTAA 58.258 45.455 0.00 0.00 0.00 2.24
1880 5561 4.136051 CCCAACGGAACCAAAGTAGTAAA 58.864 43.478 0.00 0.00 0.00 2.01
1881 5562 4.763279 CCCAACGGAACCAAAGTAGTAAAT 59.237 41.667 0.00 0.00 0.00 1.40
1882 5563 5.106436 CCCAACGGAACCAAAGTAGTAAATC 60.106 44.000 0.00 0.00 0.00 2.17
1883 5564 5.390145 CCAACGGAACCAAAGTAGTAAATCG 60.390 44.000 0.00 0.00 0.00 3.34
1884 5565 5.138125 ACGGAACCAAAGTAGTAAATCGA 57.862 39.130 0.00 0.00 0.00 3.59
1886 5567 6.168389 ACGGAACCAAAGTAGTAAATCGATT 58.832 36.000 4.39 4.39 0.00 3.34
1888 5569 6.534079 CGGAACCAAAGTAGTAAATCGATTCT 59.466 38.462 11.83 7.82 0.00 2.40
1889 5570 7.254017 CGGAACCAAAGTAGTAAATCGATTCTC 60.254 40.741 11.83 7.68 0.00 2.87
1890 5571 7.764901 GGAACCAAAGTAGTAAATCGATTCTCT 59.235 37.037 11.83 14.30 0.00 3.10
1891 5572 9.152595 GAACCAAAGTAGTAAATCGATTCTCTT 57.847 33.333 11.83 8.79 0.00 2.85
1892 5573 9.503399 AACCAAAGTAGTAAATCGATTCTCTTT 57.497 29.630 11.83 13.47 0.00 2.52
1894 5575 9.760660 CCAAAGTAGTAAATCGATTCTCTTTTG 57.239 33.333 11.83 17.13 0.00 2.44
1899 5580 7.365840 AGTAAATCGATTCTCTTTTGTCCAC 57.634 36.000 11.83 0.00 0.00 4.02
1905 5586 5.007626 TCGATTCTCTTTTGTCCACTTTGTG 59.992 40.000 0.00 0.00 0.00 3.33
1908 5589 5.818136 TCTCTTTTGTCCACTTTGTGAAG 57.182 39.130 0.00 0.00 35.23 3.02
1909 5590 4.096382 TCTCTTTTGTCCACTTTGTGAAGC 59.904 41.667 0.00 0.00 36.29 3.86
1913 5594 3.502191 TGTCCACTTTGTGAAGCAAAC 57.498 42.857 0.00 0.00 41.68 2.93
1915 5596 3.119531 TGTCCACTTTGTGAAGCAAACTG 60.120 43.478 0.00 0.00 41.68 3.16
1920 5601 4.560035 CACTTTGTGAAGCAAACTGAACTG 59.440 41.667 0.00 0.00 41.68 3.16
1921 5602 2.849880 TGTGAAGCAAACTGAACTGC 57.150 45.000 0.00 0.00 38.91 4.40
1922 5603 1.063912 TGTGAAGCAAACTGAACTGCG 59.936 47.619 0.00 0.00 43.51 5.18
1928 5609 1.001378 GCAAACTGAACTGCGGATTGT 60.001 47.619 0.00 0.00 37.80 2.71
1929 5610 2.653890 CAAACTGAACTGCGGATTGTG 58.346 47.619 0.00 0.00 32.65 3.33
1930 5611 0.593128 AACTGAACTGCGGATTGTGC 59.407 50.000 0.00 0.00 0.00 4.57
1932 5613 1.001974 ACTGAACTGCGGATTGTGCTA 59.998 47.619 0.00 0.00 0.00 3.49
1937 5618 3.543680 ACTGCGGATTGTGCTAGTTAT 57.456 42.857 0.00 0.00 0.00 1.89
1940 5621 5.050490 ACTGCGGATTGTGCTAGTTATTAG 58.950 41.667 0.00 0.00 0.00 1.73
1971 5667 8.687824 TTTTCTGACTGTTGTGAAATTTCTTC 57.312 30.769 18.64 12.06 0.00 2.87
2044 5740 2.680312 TGCAGCTACAGATCAAGGTC 57.320 50.000 0.00 0.00 0.00 3.85
2054 5750 4.458397 ACAGATCAAGGTCAGCATAATGG 58.542 43.478 0.00 0.00 0.00 3.16
2084 5780 8.098912 TGGTTGTATTAGACCTTTCTTTCCTAC 58.901 37.037 0.00 0.00 36.86 3.18
2102 5798 3.364023 CCTACGAACTTTGTGTGATCGTC 59.636 47.826 2.12 0.00 40.14 4.20
2142 5838 1.746470 TGCTTCATGATCAGGTGCTG 58.254 50.000 21.17 7.95 0.00 4.41
2234 5930 1.270414 ACCCCTCAGTGATGAGCCTG 61.270 60.000 0.00 0.00 34.74 4.85
2244 5944 6.061441 TCAGTGATGAGCCTGTTCTTTTAAA 58.939 36.000 0.00 0.00 0.00 1.52
2300 6000 1.207089 TCCATCTCAACGAGGCGAAAT 59.793 47.619 0.00 0.00 0.00 2.17
2349 6049 5.730550 TGTTAAGAACGATCCATGCTTACT 58.269 37.500 0.00 0.00 0.00 2.24
2398 6101 3.569194 TCTGTACCCAAGAGTTTGCAA 57.431 42.857 0.00 0.00 32.79 4.08
2447 6153 0.170561 AATCTTCCGGTCACTCGACG 59.829 55.000 0.00 0.00 43.61 5.12
2459 6178 0.109086 ACTCGACGGCATGTCTTCAG 60.109 55.000 4.56 3.67 45.87 3.02
2476 6195 5.403466 GTCTTCAGAATCACAAATGCAAACC 59.597 40.000 0.00 0.00 0.00 3.27
2485 6204 2.170187 ACAAATGCAAACCAGGCTTTGA 59.830 40.909 15.05 4.81 35.41 2.69
2510 6233 1.873591 CACAGGTCCTGCACTTTGTAC 59.126 52.381 19.40 0.00 34.37 2.90
2522 6245 3.365364 GCACTTTGTACATCAGCAGAACC 60.365 47.826 0.00 0.00 0.00 3.62
2534 6260 1.966451 CAGAACCTGTGCCGGGAAC 60.966 63.158 2.18 0.00 33.36 3.62
2640 6371 2.889852 AGACTTCGTATTTTCTCCGGC 58.110 47.619 0.00 0.00 0.00 6.13
2653 6384 2.917933 TCTCCGGCTGATTATTGTTGG 58.082 47.619 0.00 0.00 0.00 3.77
2660 6391 3.429410 GGCTGATTATTGTTGGTGGAAGC 60.429 47.826 0.00 0.00 0.00 3.86
2761 8887 1.478510 GGTGATTCTCTTCCTCGCTGA 59.521 52.381 0.00 0.00 0.00 4.26
2762 8888 2.535331 GTGATTCTCTTCCTCGCTGAC 58.465 52.381 0.00 0.00 0.00 3.51
2763 8889 2.094494 GTGATTCTCTTCCTCGCTGACA 60.094 50.000 0.00 0.00 0.00 3.58
2764 8890 2.562738 TGATTCTCTTCCTCGCTGACAA 59.437 45.455 0.00 0.00 0.00 3.18
2765 8891 3.196469 TGATTCTCTTCCTCGCTGACAAT 59.804 43.478 0.00 0.00 0.00 2.71
2766 8892 2.662006 TCTCTTCCTCGCTGACAATG 57.338 50.000 0.00 0.00 0.00 2.82
2767 8893 1.005340 CTCTTCCTCGCTGACAATGC 58.995 55.000 0.00 0.00 0.00 3.56
2768 8894 0.610174 TCTTCCTCGCTGACAATGCT 59.390 50.000 0.00 0.00 0.00 3.79
2769 8895 1.824852 TCTTCCTCGCTGACAATGCTA 59.175 47.619 0.00 0.00 0.00 3.49
2770 8896 1.929836 CTTCCTCGCTGACAATGCTAC 59.070 52.381 0.00 0.00 0.00 3.58
2771 8897 0.175760 TCCTCGCTGACAATGCTACC 59.824 55.000 0.00 0.00 0.00 3.18
2772 8898 0.176680 CCTCGCTGACAATGCTACCT 59.823 55.000 0.00 0.00 0.00 3.08
2773 8899 1.565305 CTCGCTGACAATGCTACCTC 58.435 55.000 0.00 0.00 0.00 3.85
2774 8900 0.179137 TCGCTGACAATGCTACCTCG 60.179 55.000 0.00 0.00 0.00 4.63
2775 8901 1.756375 CGCTGACAATGCTACCTCGC 61.756 60.000 0.00 0.00 0.00 5.03
2776 8902 1.432270 GCTGACAATGCTACCTCGCC 61.432 60.000 0.00 0.00 0.00 5.54
2777 8903 0.176680 CTGACAATGCTACCTCGCCT 59.823 55.000 0.00 0.00 0.00 5.52
2778 8904 1.409064 CTGACAATGCTACCTCGCCTA 59.591 52.381 0.00 0.00 0.00 3.93
2779 8905 1.136305 TGACAATGCTACCTCGCCTAC 59.864 52.381 0.00 0.00 0.00 3.18
2780 8906 0.464452 ACAATGCTACCTCGCCTACC 59.536 55.000 0.00 0.00 0.00 3.18
2781 8907 0.464036 CAATGCTACCTCGCCTACCA 59.536 55.000 0.00 0.00 0.00 3.25
2782 8908 1.134521 CAATGCTACCTCGCCTACCAA 60.135 52.381 0.00 0.00 0.00 3.67
2783 8909 1.200519 ATGCTACCTCGCCTACCAAA 58.799 50.000 0.00 0.00 0.00 3.28
2784 8910 0.978151 TGCTACCTCGCCTACCAAAA 59.022 50.000 0.00 0.00 0.00 2.44
2785 8911 1.348366 TGCTACCTCGCCTACCAAAAA 59.652 47.619 0.00 0.00 0.00 1.94
2838 8964 7.691213 TCAGGGGTATATGAACTTAACACAAA 58.309 34.615 0.00 0.00 0.00 2.83
2839 8965 8.333235 TCAGGGGTATATGAACTTAACACAAAT 58.667 33.333 0.00 0.00 0.00 2.32
2840 8966 8.966868 CAGGGGTATATGAACTTAACACAAATT 58.033 33.333 0.00 0.00 0.00 1.82
2869 8999 4.417426 AAATTATGGTGTACTCCCTCCG 57.583 45.455 11.36 0.00 0.00 4.63
2870 9000 2.537633 TTATGGTGTACTCCCTCCGT 57.462 50.000 11.36 2.45 0.00 4.69
2871 9001 2.062971 TATGGTGTACTCCCTCCGTC 57.937 55.000 11.36 0.00 0.00 4.79
2872 9002 0.335361 ATGGTGTACTCCCTCCGTCT 59.665 55.000 11.36 0.00 0.00 4.18
2873 9003 0.611062 TGGTGTACTCCCTCCGTCTG 60.611 60.000 11.36 0.00 0.00 3.51
2874 9004 0.323178 GGTGTACTCCCTCCGTCTGA 60.323 60.000 2.33 0.00 0.00 3.27
2875 9005 1.542492 GTGTACTCCCTCCGTCTGAA 58.458 55.000 0.00 0.00 0.00 3.02
2876 9006 1.891150 GTGTACTCCCTCCGTCTGAAA 59.109 52.381 0.00 0.00 0.00 2.69
2877 9007 2.298163 GTGTACTCCCTCCGTCTGAAAA 59.702 50.000 0.00 0.00 0.00 2.29
2878 9008 3.056035 GTGTACTCCCTCCGTCTGAAAAT 60.056 47.826 0.00 0.00 0.00 1.82
2879 9009 4.159135 GTGTACTCCCTCCGTCTGAAAATA 59.841 45.833 0.00 0.00 0.00 1.40
2880 9010 3.889520 ACTCCCTCCGTCTGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
2881 9011 3.442076 ACTCCCTCCGTCTGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
2882 9012 3.838903 ACTCCCTCCGTCTGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
2883 9013 4.184629 CTCCCTCCGTCTGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2884 9014 3.581332 TCCCTCCGTCTGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2885 9015 4.041198 TCCCTCCGTCTGAAAATACTTGTT 59.959 41.667 0.00 0.00 0.00 2.83
2886 9016 5.246656 TCCCTCCGTCTGAAAATACTTGTTA 59.753 40.000 0.00 0.00 0.00 2.41
2887 9017 6.070424 TCCCTCCGTCTGAAAATACTTGTTAT 60.070 38.462 0.00 0.00 0.00 1.89
2888 9018 6.258068 CCCTCCGTCTGAAAATACTTGTTATC 59.742 42.308 0.00 0.00 0.00 1.75
2889 9019 6.816640 CCTCCGTCTGAAAATACTTGTTATCA 59.183 38.462 0.00 0.00 0.00 2.15
2890 9020 7.333423 CCTCCGTCTGAAAATACTTGTTATCAA 59.667 37.037 0.00 0.00 0.00 2.57
2891 9021 8.610248 TCCGTCTGAAAATACTTGTTATCAAA 57.390 30.769 0.00 0.00 32.87 2.69
2892 9022 9.058174 TCCGTCTGAAAATACTTGTTATCAAAA 57.942 29.630 0.00 0.00 32.87 2.44
2893 9023 9.840427 CCGTCTGAAAATACTTGTTATCAAAAT 57.160 29.630 0.00 0.00 32.87 1.82
2905 9035 9.942850 ACTTGTTATCAAAATGAATAAAAGGGG 57.057 29.630 0.00 0.00 32.87 4.79
2913 9043 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
2919 9049 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
2927 9057 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
2968 9098 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
2969 9099 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
2970 9100 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
2971 9101 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
2972 9102 8.637099 TGTCCATTTTGATGACAAGTATTTTCA 58.363 29.630 0.00 0.00 37.32 2.69
2973 9103 9.474920 GTCCATTTTGATGACAAGTATTTTCAA 57.525 29.630 0.00 0.00 37.32 2.69
2976 9106 9.782028 CATTTTGATGACAAGTATTTTCAAACG 57.218 29.630 0.00 0.00 37.32 3.60
2977 9107 7.922505 TTTGATGACAAGTATTTTCAAACGG 57.077 32.000 0.00 0.00 37.32 4.44
2978 9108 6.869315 TGATGACAAGTATTTTCAAACGGA 57.131 33.333 0.00 0.00 0.00 4.69
2979 9109 6.898041 TGATGACAAGTATTTTCAAACGGAG 58.102 36.000 0.00 0.00 0.00 4.63
2980 9110 5.682943 TGACAAGTATTTTCAAACGGAGG 57.317 39.130 0.00 0.00 0.00 4.30
2981 9111 4.517453 TGACAAGTATTTTCAAACGGAGGG 59.483 41.667 0.00 0.00 0.00 4.30
2982 9112 4.721132 ACAAGTATTTTCAAACGGAGGGA 58.279 39.130 0.00 0.00 0.00 4.20
2983 9113 4.760204 ACAAGTATTTTCAAACGGAGGGAG 59.240 41.667 0.00 0.00 0.00 4.30
2984 9114 4.635699 AGTATTTTCAAACGGAGGGAGT 57.364 40.909 0.00 0.00 0.00 3.85
3025 9155 6.309436 GTCACATGTGTATGACAATTGACAG 58.691 40.000 24.63 1.14 43.58 3.51
3044 9263 6.878317 TGACAGGTAGACAAGAAATATCTGG 58.122 40.000 0.00 0.00 35.59 3.86
3056 9275 8.543774 ACAAGAAATATCTGGATGTGAGTACTT 58.456 33.333 0.00 0.00 35.59 2.24
3060 9279 8.783660 AAATATCTGGATGTGAGTACTTCCTA 57.216 34.615 11.68 2.30 46.23 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.444119 AACAAAGCGCGTCCACATGT 61.444 50.000 8.43 0.00 0.00 3.21
135 136 3.120580 CGCGTTATGCATGATATTCAGCA 60.121 43.478 10.16 0.00 46.97 4.41
189 190 3.179599 CACAATTCGTCCGCTTGTTTTTC 59.820 43.478 5.21 0.00 30.99 2.29
191 192 2.542824 CCACAATTCGTCCGCTTGTTTT 60.543 45.455 5.21 0.00 30.99 2.43
199 200 1.084370 GGAGCTCCACAATTCGTCCG 61.084 60.000 28.43 0.00 35.64 4.79
212 213 3.001736 GCAATTAGACAATCGTGGAGCTC 59.998 47.826 4.71 4.71 0.00 4.09
217 218 3.009723 AGGTGCAATTAGACAATCGTGG 58.990 45.455 0.00 0.00 0.00 4.94
221 222 5.098211 GCTTTGAGGTGCAATTAGACAATC 58.902 41.667 0.00 0.00 36.15 2.67
225 226 4.006319 AGAGCTTTGAGGTGCAATTAGAC 58.994 43.478 0.00 0.00 36.15 2.59
226 227 4.256920 GAGAGCTTTGAGGTGCAATTAGA 58.743 43.478 0.00 0.00 36.15 2.10
246 247 6.935208 GGGGTGCTAAATACTGTATAAAGGAG 59.065 42.308 0.00 0.00 0.00 3.69
254 255 4.781087 AGACTTGGGGTGCTAAATACTGTA 59.219 41.667 0.00 0.00 0.00 2.74
255 256 3.587506 AGACTTGGGGTGCTAAATACTGT 59.412 43.478 0.00 0.00 0.00 3.55
256 257 4.222124 AGACTTGGGGTGCTAAATACTG 57.778 45.455 0.00 0.00 0.00 2.74
257 258 4.589908 CAAGACTTGGGGTGCTAAATACT 58.410 43.478 7.35 0.00 0.00 2.12
258 259 3.128764 GCAAGACTTGGGGTGCTAAATAC 59.871 47.826 16.80 0.00 34.13 1.89
300 301 6.740905 CGAATTAACAATGTGCTAACGAATGT 59.259 34.615 0.00 0.00 0.00 2.71
307 308 9.729023 CAATAATCCGAATTAACAATGTGCTAA 57.271 29.630 0.00 0.00 31.28 3.09
310 316 8.801715 ATCAATAATCCGAATTAACAATGTGC 57.198 30.769 0.00 0.00 31.28 4.57
330 336 8.364142 GCCTCTCTAAAGTGATACACTATCAAT 58.636 37.037 4.84 0.00 44.62 2.57
498 507 4.036734 CACCATTTACATGACCTGTATGGC 59.963 45.833 0.00 0.00 43.52 4.40
560 3777 3.254014 AATTCGTGTGCGCCTGTGC 62.254 57.895 4.18 0.00 38.14 4.57
631 4204 9.911788 ATGATTGGTAAGATACTGAGAACATTT 57.088 29.630 0.00 0.00 0.00 2.32
727 4300 5.394443 GCAGATTGGGTCAGCAAAATATCAA 60.394 40.000 0.00 0.00 39.03 2.57
785 4366 4.340666 TCAAAATTGTTCCTTGCACAGCTA 59.659 37.500 0.00 0.00 0.00 3.32
797 4378 4.171754 GGATGAGCAGCTCAAAATTGTTC 58.828 43.478 28.78 18.51 44.04 3.18
812 4393 4.778143 ACGGCCGTTGGGATGAGC 62.778 66.667 28.70 0.00 34.06 4.26
813 4394 2.511600 GACGGCCGTTGGGATGAG 60.512 66.667 34.65 0.00 34.06 2.90
814 4395 4.090588 GGACGGCCGTTGGGATGA 62.091 66.667 34.65 0.00 34.06 2.92
819 4400 3.259064 CTTATATATGGACGGCCGTTGG 58.741 50.000 34.65 2.16 36.79 3.77
828 4415 6.521133 GTGTACGTACGTGCTTATATATGGAC 59.479 42.308 31.45 17.46 0.00 4.02
830 4417 6.372981 TGTGTACGTACGTGCTTATATATGG 58.627 40.000 31.45 0.00 0.00 2.74
831 4418 7.045804 CGATGTGTACGTACGTGCTTATATATG 60.046 40.741 31.45 13.67 0.00 1.78
835 4422 4.033932 ACGATGTGTACGTACGTGCTTATA 59.966 41.667 31.45 15.14 42.17 0.98
837 4424 2.159430 ACGATGTGTACGTACGTGCTTA 59.841 45.455 31.45 22.03 42.17 3.09
838 4425 1.069022 ACGATGTGTACGTACGTGCTT 60.069 47.619 31.45 18.99 42.17 3.91
872 4459 2.518834 ACTAGGTAGGTAGGGAGCATGT 59.481 50.000 0.00 0.00 0.00 3.21
884 4471 2.430963 AGGGAGTAGGGACTAGGTAGG 58.569 57.143 0.00 0.00 44.14 3.18
885 4472 3.979347 TGTAGGGAGTAGGGACTAGGTAG 59.021 52.174 0.00 0.00 44.14 3.18
886 4473 3.718956 GTGTAGGGAGTAGGGACTAGGTA 59.281 52.174 0.00 0.00 44.14 3.08
887 4474 2.513317 GTGTAGGGAGTAGGGACTAGGT 59.487 54.545 0.00 0.00 44.14 3.08
888 4475 2.784682 AGTGTAGGGAGTAGGGACTAGG 59.215 54.545 0.00 0.00 44.14 3.02
889 4476 4.502950 CGTAGTGTAGGGAGTAGGGACTAG 60.503 54.167 0.00 0.00 44.14 2.57
890 4477 3.389329 CGTAGTGTAGGGAGTAGGGACTA 59.611 52.174 0.00 0.00 41.75 2.59
891 4478 2.172293 CGTAGTGTAGGGAGTAGGGACT 59.828 54.545 0.00 0.00 46.37 3.85
892 4479 2.092699 ACGTAGTGTAGGGAGTAGGGAC 60.093 54.545 0.00 0.00 42.51 4.46
893 4480 2.200081 ACGTAGTGTAGGGAGTAGGGA 58.800 52.381 0.00 0.00 42.51 4.20
894 4481 2.725221 ACGTAGTGTAGGGAGTAGGG 57.275 55.000 0.00 0.00 42.51 3.53
908 4499 0.863538 CTAGCTGCACTGCGACGTAG 60.864 60.000 11.65 11.65 38.13 3.51
935 4526 3.334751 CGACGCAAGCACGGAACA 61.335 61.111 0.00 0.00 45.62 3.18
936 4527 4.719616 GCGACGCAAGCACGGAAC 62.720 66.667 16.42 0.00 45.62 3.62
954 4545 3.706668 GCGATCGAGGCGAATGGC 61.707 66.667 21.57 0.00 39.99 4.40
991 4582 2.246397 CCGCGACATTATGCAGCG 59.754 61.111 21.61 21.61 42.99 5.18
998 4589 2.499205 CCTGCTCCCGCGACATTA 59.501 61.111 8.23 0.00 39.65 1.90
1206 4797 4.767255 GTGGAGCTGCTGGACCCG 62.767 72.222 7.01 0.00 0.00 5.28
1207 4798 4.416738 GGTGGAGCTGCTGGACCC 62.417 72.222 7.01 1.89 0.00 4.46
1208 4799 2.883267 GATGGTGGAGCTGCTGGACC 62.883 65.000 7.01 13.17 0.00 4.46
1209 4800 1.451028 GATGGTGGAGCTGCTGGAC 60.451 63.158 7.01 2.68 0.00 4.02
1210 4801 2.993008 GATGGTGGAGCTGCTGGA 59.007 61.111 7.01 0.00 0.00 3.86
1211 4802 2.513204 CGATGGTGGAGCTGCTGG 60.513 66.667 7.01 0.00 0.00 4.85
1212 4803 1.812922 GTCGATGGTGGAGCTGCTG 60.813 63.158 7.01 0.00 0.00 4.41
1213 4804 2.581354 GTCGATGGTGGAGCTGCT 59.419 61.111 6.82 0.00 0.00 4.24
1214 4805 2.512515 GGTCGATGGTGGAGCTGC 60.513 66.667 0.00 0.00 0.00 5.25
1215 4806 1.142748 GAGGTCGATGGTGGAGCTG 59.857 63.158 0.00 0.00 41.91 4.24
1216 4807 0.904865 TTGAGGTCGATGGTGGAGCT 60.905 55.000 0.00 0.00 44.31 4.09
1217 4808 0.741221 GTTGAGGTCGATGGTGGAGC 60.741 60.000 0.00 0.00 0.00 4.70
1218 4809 0.108138 GGTTGAGGTCGATGGTGGAG 60.108 60.000 0.00 0.00 0.00 3.86
1219 4810 0.544357 AGGTTGAGGTCGATGGTGGA 60.544 55.000 0.00 0.00 0.00 4.02
1220 4811 0.108138 GAGGTTGAGGTCGATGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
1221 4812 0.898320 AGAGGTTGAGGTCGATGGTG 59.102 55.000 0.00 0.00 0.00 4.17
1222 4813 1.187087 GAGAGGTTGAGGTCGATGGT 58.813 55.000 0.00 0.00 0.00 3.55
1243 4834 1.376249 ATCCTCTCCTCCTCCTCCCC 61.376 65.000 0.00 0.00 0.00 4.81
1246 4837 1.499007 ACTGATCCTCTCCTCCTCCTC 59.501 57.143 0.00 0.00 0.00 3.71
1255 4846 1.537135 GGCACGCTTACTGATCCTCTC 60.537 57.143 0.00 0.00 0.00 3.20
1256 4847 0.461961 GGCACGCTTACTGATCCTCT 59.538 55.000 0.00 0.00 0.00 3.69
1257 4848 2.979130 GGCACGCTTACTGATCCTC 58.021 57.895 0.00 0.00 0.00 3.71
1290 4905 2.829003 TCGCTGAGGAGGTAGCCG 60.829 66.667 0.00 0.00 36.60 5.52
1293 4908 3.111939 CGGTCGCTGAGGAGGTAG 58.888 66.667 0.00 0.00 0.00 3.18
1383 5043 1.291877 CCTTCTTCTTGTGCCGTCCG 61.292 60.000 0.00 0.00 0.00 4.79
1407 5067 2.747460 GCCTTGTGATCCGCAGCA 60.747 61.111 0.00 0.00 0.00 4.41
1428 5088 2.226602 TACGCTGCGTTATTATGCCA 57.773 45.000 33.52 8.84 41.54 4.92
1429 5089 3.424433 GGATTACGCTGCGTTATTATGCC 60.424 47.826 33.52 20.89 41.54 4.40
1431 5091 4.666655 GCAGGATTACGCTGCGTTATTATG 60.667 45.833 33.52 26.96 41.54 1.90
1433 5093 2.798283 GCAGGATTACGCTGCGTTATTA 59.202 45.455 33.52 12.57 41.54 0.98
1434 5094 1.597663 GCAGGATTACGCTGCGTTATT 59.402 47.619 33.52 17.64 41.54 1.40
1435 5095 1.217882 GCAGGATTACGCTGCGTTAT 58.782 50.000 33.52 28.56 41.54 1.89
1436 5096 0.808453 GGCAGGATTACGCTGCGTTA 60.808 55.000 33.52 24.89 41.54 3.18
1440 5100 1.151668 CTATGGCAGGATTACGCTGC 58.848 55.000 0.00 0.00 38.57 5.25
1441 5101 2.408050 GACTATGGCAGGATTACGCTG 58.592 52.381 0.00 0.00 0.00 5.18
1442 5102 1.000163 CGACTATGGCAGGATTACGCT 60.000 52.381 0.00 0.00 0.00 5.07
1444 5104 1.269569 TGCGACTATGGCAGGATTACG 60.270 52.381 0.00 0.00 35.04 3.18
1445 5105 2.526304 TGCGACTATGGCAGGATTAC 57.474 50.000 0.00 0.00 35.04 1.89
1452 5112 0.906066 TAAACCCTGCGACTATGGCA 59.094 50.000 0.00 0.00 38.92 4.92
1455 5115 3.243068 GGCAAATAAACCCTGCGACTATG 60.243 47.826 0.00 0.00 36.93 2.23
1460 5120 1.846007 ATGGCAAATAAACCCTGCGA 58.154 45.000 0.00 0.00 36.93 5.10
1461 5121 3.443976 GTTATGGCAAATAAACCCTGCG 58.556 45.455 0.00 0.00 36.93 5.18
1477 5137 0.530650 ATCAGCCTCGCCACGTTATG 60.531 55.000 0.00 0.00 0.00 1.90
1478 5138 0.178068 AATCAGCCTCGCCACGTTAT 59.822 50.000 0.00 0.00 0.00 1.89
1512 5184 0.549950 AGACTTGATCCCCTGCATGG 59.450 55.000 0.13 0.13 0.00 3.66
1523 5195 4.389992 CGTCTTGCATGTTACAGACTTGAT 59.610 41.667 11.18 0.00 35.92 2.57
1524 5196 3.740832 CGTCTTGCATGTTACAGACTTGA 59.259 43.478 11.18 0.00 35.92 3.02
1525 5197 3.120546 CCGTCTTGCATGTTACAGACTTG 60.121 47.826 11.18 0.82 36.70 3.16
1539 5211 2.180131 CTGCTTCTGCACCGTCTTGC 62.180 60.000 0.00 0.00 45.31 4.01
1614 5295 4.796231 CGACGTTGGCCTCCTCGG 62.796 72.222 3.32 0.00 0.00 4.63
1778 5459 4.584874 TGGACAGAACAAAACTCTGAACA 58.415 39.130 6.83 2.81 42.51 3.18
1820 5501 2.095161 ACTCGGAGTCTGTCGTTGATTC 60.095 50.000 4.45 0.00 0.00 2.52
1821 5502 1.887198 ACTCGGAGTCTGTCGTTGATT 59.113 47.619 4.45 0.00 0.00 2.57
1876 5557 7.365840 AGTGGACAAAAGAGAATCGATTTAC 57.634 36.000 12.81 9.46 42.67 2.01
1877 5558 7.979444 AAGTGGACAAAAGAGAATCGATTTA 57.021 32.000 12.81 0.00 42.67 1.40
1878 5559 6.884280 AAGTGGACAAAAGAGAATCGATTT 57.116 33.333 12.81 2.33 42.67 2.17
1879 5560 6.263168 ACAAAGTGGACAAAAGAGAATCGATT 59.737 34.615 11.20 11.20 42.67 3.34
1880 5561 5.765182 ACAAAGTGGACAAAAGAGAATCGAT 59.235 36.000 0.00 0.00 42.67 3.59
1881 5562 5.007626 CACAAAGTGGACAAAAGAGAATCGA 59.992 40.000 0.00 0.00 42.67 3.59
1882 5563 5.007626 TCACAAAGTGGACAAAAGAGAATCG 59.992 40.000 0.00 0.00 35.34 3.34
1883 5564 6.377327 TCACAAAGTGGACAAAAGAGAATC 57.623 37.500 0.00 0.00 33.87 2.52
1884 5565 6.681368 GCTTCACAAAGTGGACAAAAGAGAAT 60.681 38.462 0.00 0.00 34.79 2.40
1886 5567 4.096382 GCTTCACAAAGTGGACAAAAGAGA 59.904 41.667 0.00 0.00 34.79 3.10
1888 5569 3.761218 TGCTTCACAAAGTGGACAAAAGA 59.239 39.130 0.00 0.00 34.79 2.52
1889 5570 4.108699 TGCTTCACAAAGTGGACAAAAG 57.891 40.909 0.00 0.00 34.79 2.27
1890 5571 4.527509 TTGCTTCACAAAGTGGACAAAA 57.472 36.364 0.00 0.00 34.56 2.44
1891 5572 4.527509 TTTGCTTCACAAAGTGGACAAA 57.472 36.364 0.00 3.84 43.35 2.83
1905 5586 0.944386 TCCGCAGTTCAGTTTGCTTC 59.056 50.000 0.00 0.00 38.16 3.86
1908 5589 1.001378 ACAATCCGCAGTTCAGTTTGC 60.001 47.619 0.00 0.00 36.97 3.68
1909 5590 2.653890 CACAATCCGCAGTTCAGTTTG 58.346 47.619 0.00 0.00 0.00 2.93
1913 5594 1.662629 CTAGCACAATCCGCAGTTCAG 59.337 52.381 0.00 0.00 0.00 3.02
1915 5596 1.726853 ACTAGCACAATCCGCAGTTC 58.273 50.000 0.00 0.00 0.00 3.01
1932 5613 9.726438 AACAGTCAGAAAATACTGCTAATAACT 57.274 29.630 2.52 0.00 45.65 2.24
1937 5618 6.989759 TCACAACAGTCAGAAAATACTGCTAA 59.010 34.615 2.52 0.00 45.65 3.09
1940 5621 5.673337 TCACAACAGTCAGAAAATACTGC 57.327 39.130 2.52 0.00 45.65 4.40
1941 5622 9.520204 AAATTTCACAACAGTCAGAAAATACTG 57.480 29.630 0.00 0.00 46.84 2.74
1947 5643 7.754924 GTGAAGAAATTTCACAACAGTCAGAAA 59.245 33.333 19.99 0.00 45.89 2.52
1971 5667 0.612229 AGTGCTGAGATCCACCTGTG 59.388 55.000 0.00 0.00 32.48 3.66
2044 5740 6.395426 AATACAACCATGACCATTATGCTG 57.605 37.500 0.00 0.00 0.00 4.41
2054 5750 7.923414 AAGAAAGGTCTAATACAACCATGAC 57.077 36.000 0.00 0.00 38.06 3.06
2084 5780 3.155344 GTGACGATCACACAAAGTTCG 57.845 47.619 13.01 0.00 46.22 3.95
2125 5821 3.263489 ACTCAGCACCTGATCATGAAG 57.737 47.619 0.00 0.00 39.92 3.02
2142 5838 3.119316 ACATCCACATCTCGTCAGAACTC 60.119 47.826 0.00 0.00 30.24 3.01
2244 5944 8.645110 AGTCAAGTTCATCATGGATTTTTCTTT 58.355 29.630 0.00 0.00 0.00 2.52
2300 6000 6.340962 TCATTCTCTTTCAGAACGGTTAGA 57.659 37.500 0.00 0.00 44.28 2.10
2319 6019 6.403636 GCATGGATCGTTCTTAACAGTTCATT 60.404 38.462 0.00 0.00 0.00 2.57
2398 6101 2.880443 TGGCTTCTTGCAAAGGAAGAT 58.120 42.857 24.87 0.00 46.24 2.40
2447 6153 4.771590 TTTGTGATTCTGAAGACATGCC 57.228 40.909 6.02 0.00 0.00 4.40
2459 6178 2.738314 GCCTGGTTTGCATTTGTGATTC 59.262 45.455 0.00 0.00 0.00 2.52
2476 6195 2.746362 GACCTGTGAAGATCAAAGCCTG 59.254 50.000 0.00 0.00 30.26 4.85
2485 6204 1.356124 AGTGCAGGACCTGTGAAGAT 58.644 50.000 22.58 1.10 33.43 2.40
2510 6233 1.642037 CGGCACAGGTTCTGCTGATG 61.642 60.000 0.00 0.00 42.75 3.07
2547 6273 2.034104 ACATGCCATGTGCTCTACTG 57.966 50.000 10.06 0.00 43.01 2.74
2558 6284 3.194116 CAGCTCCTACAAAAACATGCCAT 59.806 43.478 0.00 0.00 0.00 4.40
2560 6286 2.672195 GCAGCTCCTACAAAAACATGCC 60.672 50.000 0.00 0.00 0.00 4.40
2561 6287 2.030007 TGCAGCTCCTACAAAAACATGC 60.030 45.455 0.00 0.00 0.00 4.06
2640 6371 4.701651 TCTGCTTCCACCAACAATAATCAG 59.298 41.667 0.00 0.00 0.00 2.90
2653 6384 6.926272 CAGTAGTATTATTCCTCTGCTTCCAC 59.074 42.308 0.00 0.00 0.00 4.02
2660 6391 7.147897 TGTGTCACCAGTAGTATTATTCCTCTG 60.148 40.741 0.00 0.00 0.00 3.35
2741 6537 1.478510 TCAGCGAGGAAGAGAATCACC 59.521 52.381 0.00 0.00 37.82 4.02
2761 8887 0.464452 GGTAGGCGAGGTAGCATTGT 59.536 55.000 0.00 0.00 39.27 2.71
2762 8888 0.464036 TGGTAGGCGAGGTAGCATTG 59.536 55.000 0.00 0.00 39.27 2.82
2763 8889 1.200519 TTGGTAGGCGAGGTAGCATT 58.799 50.000 0.00 0.00 39.27 3.56
2764 8890 1.200519 TTTGGTAGGCGAGGTAGCAT 58.799 50.000 0.00 0.00 39.27 3.79
2765 8891 0.978151 TTTTGGTAGGCGAGGTAGCA 59.022 50.000 0.00 0.00 39.27 3.49
2766 8892 2.103537 TTTTTGGTAGGCGAGGTAGC 57.896 50.000 0.00 0.00 0.00 3.58
2786 8912 5.790593 TCTACGAGGTAGCATTGTCTTTTT 58.209 37.500 0.00 0.00 36.22 1.94
2787 8913 5.401531 TCTACGAGGTAGCATTGTCTTTT 57.598 39.130 0.00 0.00 36.22 2.27
2788 8914 5.401531 TTCTACGAGGTAGCATTGTCTTT 57.598 39.130 0.00 0.00 36.22 2.52
2789 8915 4.678309 GCTTCTACGAGGTAGCATTGTCTT 60.678 45.833 0.00 0.00 36.22 3.01
2790 8916 3.181485 GCTTCTACGAGGTAGCATTGTCT 60.181 47.826 0.00 0.00 36.22 3.41
2791 8917 3.117046 GCTTCTACGAGGTAGCATTGTC 58.883 50.000 0.00 0.00 36.22 3.18
2853 8983 0.335361 AGACGGAGGGAGTACACCAT 59.665 55.000 11.69 3.58 0.00 3.55
2860 8990 3.442076 AGTATTTTCAGACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
2861 8991 4.184629 CAAGTATTTTCAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
2862 8992 3.581332 ACAAGTATTTTCAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2863 8993 3.939066 ACAAGTATTTTCAGACGGAGGG 58.061 45.455 0.00 0.00 0.00 4.30
2864 8994 6.816640 TGATAACAAGTATTTTCAGACGGAGG 59.183 38.462 0.00 0.00 0.00 4.30
2865 8995 7.827819 TGATAACAAGTATTTTCAGACGGAG 57.172 36.000 0.00 0.00 0.00 4.63
2866 8996 8.610248 TTTGATAACAAGTATTTTCAGACGGA 57.390 30.769 0.00 0.00 37.32 4.69
2867 8997 9.840427 ATTTTGATAACAAGTATTTTCAGACGG 57.160 29.630 0.00 0.00 37.32 4.79
2879 9009 9.942850 CCCCTTTTATTCATTTTGATAACAAGT 57.057 29.630 0.00 0.00 37.32 3.16
2887 9017 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
2893 9023 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
2901 9031 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
2942 9072 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
2943 9073 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
2944 9074 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
2945 9075 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
2946 9076 8.637099 TGAAAATACTTGTCATCAAAATGGACA 58.363 29.630 0.00 0.00 33.42 4.02
2947 9077 9.474920 TTGAAAATACTTGTCATCAAAATGGAC 57.525 29.630 0.00 0.00 33.42 4.02
2950 9080 9.782028 CGTTTGAAAATACTTGTCATCAAAATG 57.218 29.630 0.00 0.00 38.19 2.32
2951 9081 8.977505 CCGTTTGAAAATACTTGTCATCAAAAT 58.022 29.630 0.00 0.00 38.19 1.82
2952 9082 8.191446 TCCGTTTGAAAATACTTGTCATCAAAA 58.809 29.630 0.00 0.00 38.19 2.44
2953 9083 7.708051 TCCGTTTGAAAATACTTGTCATCAAA 58.292 30.769 0.00 0.00 35.20 2.69
2954 9084 7.265647 TCCGTTTGAAAATACTTGTCATCAA 57.734 32.000 0.00 0.00 0.00 2.57
2955 9085 6.072728 CCTCCGTTTGAAAATACTTGTCATCA 60.073 38.462 0.00 0.00 0.00 3.07
2956 9086 6.314784 CCTCCGTTTGAAAATACTTGTCATC 58.685 40.000 0.00 0.00 0.00 2.92
2957 9087 5.183140 CCCTCCGTTTGAAAATACTTGTCAT 59.817 40.000 0.00 0.00 0.00 3.06
2958 9088 4.517453 CCCTCCGTTTGAAAATACTTGTCA 59.483 41.667 0.00 0.00 0.00 3.58
2959 9089 4.758165 TCCCTCCGTTTGAAAATACTTGTC 59.242 41.667 0.00 0.00 0.00 3.18
2960 9090 4.721132 TCCCTCCGTTTGAAAATACTTGT 58.279 39.130 0.00 0.00 0.00 3.16
2961 9091 4.760204 ACTCCCTCCGTTTGAAAATACTTG 59.240 41.667 0.00 0.00 0.00 3.16
2962 9092 4.981812 ACTCCCTCCGTTTGAAAATACTT 58.018 39.130 0.00 0.00 0.00 2.24
2963 9093 4.635699 ACTCCCTCCGTTTGAAAATACT 57.364 40.909 0.00 0.00 0.00 2.12
2964 9094 5.702209 TGTTACTCCCTCCGTTTGAAAATAC 59.298 40.000 0.00 0.00 0.00 1.89
2965 9095 5.867330 TGTTACTCCCTCCGTTTGAAAATA 58.133 37.500 0.00 0.00 0.00 1.40
2966 9096 4.721132 TGTTACTCCCTCCGTTTGAAAAT 58.279 39.130 0.00 0.00 0.00 1.82
2967 9097 4.153673 TGTTACTCCCTCCGTTTGAAAA 57.846 40.909 0.00 0.00 0.00 2.29
2968 9098 3.842007 TGTTACTCCCTCCGTTTGAAA 57.158 42.857 0.00 0.00 0.00 2.69
2969 9099 4.360951 AATGTTACTCCCTCCGTTTGAA 57.639 40.909 0.00 0.00 0.00 2.69
2970 9100 4.069304 CAAATGTTACTCCCTCCGTTTGA 58.931 43.478 0.00 0.00 36.41 2.69
2971 9101 4.069304 TCAAATGTTACTCCCTCCGTTTG 58.931 43.478 0.00 0.00 35.92 2.93
2972 9102 4.202430 ACTCAAATGTTACTCCCTCCGTTT 60.202 41.667 0.00 0.00 0.00 3.60
2973 9103 3.326880 ACTCAAATGTTACTCCCTCCGTT 59.673 43.478 0.00 0.00 0.00 4.44
2974 9104 2.904434 ACTCAAATGTTACTCCCTCCGT 59.096 45.455 0.00 0.00 0.00 4.69
2975 9105 3.056107 TGACTCAAATGTTACTCCCTCCG 60.056 47.826 0.00 0.00 0.00 4.63
2976 9106 4.508662 CTGACTCAAATGTTACTCCCTCC 58.491 47.826 0.00 0.00 0.00 4.30
2977 9107 4.020128 ACCTGACTCAAATGTTACTCCCTC 60.020 45.833 0.00 0.00 0.00 4.30
2978 9108 3.910627 ACCTGACTCAAATGTTACTCCCT 59.089 43.478 0.00 0.00 0.00 4.20
2979 9109 4.003648 CACCTGACTCAAATGTTACTCCC 58.996 47.826 0.00 0.00 0.00 4.30
2980 9110 4.642429 ACACCTGACTCAAATGTTACTCC 58.358 43.478 0.00 0.00 0.00 3.85
2981 9111 5.177696 GTGACACCTGACTCAAATGTTACTC 59.822 44.000 0.00 0.00 29.76 2.59
2982 9112 5.057149 GTGACACCTGACTCAAATGTTACT 58.943 41.667 0.00 0.00 29.76 2.24
2983 9113 4.814234 TGTGACACCTGACTCAAATGTTAC 59.186 41.667 2.45 8.99 32.19 2.50
2984 9114 5.029807 TGTGACACCTGACTCAAATGTTA 57.970 39.130 2.45 0.00 0.00 2.41
3025 9155 7.500992 TCACATCCAGATATTTCTTGTCTACC 58.499 38.462 0.00 0.00 0.00 3.18
3056 9275 8.938906 GTCAACGGAGTAAATAAAAATGTAGGA 58.061 33.333 0.00 0.00 45.00 2.94
3060 9279 8.385898 TCAGTCAACGGAGTAAATAAAAATGT 57.614 30.769 0.00 0.00 45.00 2.71
3176 9405 8.786898 ACCAAATCAATACCATTAGATTCATCG 58.213 33.333 0.00 0.00 30.87 3.84


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

AutoCloner maintained by Alex Coulton.