Multiple sequence alignment - TraesCS1D01G164000

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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 TraesCS1D01G164000 chr1D 100.000 1865 0 0 424 2288 234655810 234657674 0.000000e+00 3445.0
1 TraesCS1D01G164000 chr1D 100.000 91 0 0 1 91 234655387 234655477 3.910000e-38 169.0
2 TraesCS1D01G164000 chr1A 92.958 923 35 12 654 1559 313007423 313006514 0.000000e+00 1317.0
3 TraesCS1D01G164000 chr1A 94.872 78 4 0 1652 1729 313006462 313006385 3.090000e-24 122.0
4 TraesCS1D01G164000 chr1A 86.813 91 11 1 2196 2285 490780223 490780313 1.450000e-17 100.0
5 TraesCS1D01G164000 chr1B 95.455 638 24 1 822 1459 340367044 340367676 0.000000e+00 1013.0
6 TraesCS1D01G164000 chr1B 91.345 751 30 13 681 1406 338430826 338430086 0.000000e+00 994.0
7 TraesCS1D01G164000 chr1B 86.871 457 35 12 1639 2087 338428629 338428190 2.640000e-134 488.0
8 TraesCS1D01G164000 chr1B 84.116 277 22 10 424 687 338431193 338430926 4.880000e-62 248.0
9 TraesCS1D01G164000 chr1B 83.577 274 22 12 424 684 340365396 340365659 3.800000e-58 235.0
10 TraesCS1D01G164000 chr1B 89.071 183 13 4 1865 2041 340369446 340369627 1.060000e-53 220.0
11 TraesCS1D01G164000 chr1B 92.466 146 6 3 681 826 340365762 340365902 1.070000e-48 204.0
12 TraesCS1D01G164000 chr1B 83.505 97 4 2 1505 1589 340367703 340367799 1.880000e-11 80.5
13 TraesCS1D01G164000 chr5A 89.011 91 8 2 2196 2285 442695114 442695025 6.680000e-21 111.0
14 TraesCS1D01G164000 chr2D 88.889 90 5 3 2198 2287 603661443 603661359 3.110000e-19 106.0
15 TraesCS1D01G164000 chr2D 88.372 86 9 1 2197 2281 81810599 81810684 4.020000e-18 102.0
16 TraesCS1D01G164000 chr7A 87.500 80 9 1 2047 2125 563257904 563257983 8.700000e-15 91.6
17 TraesCS1D01G164000 chr7D 87.179 78 8 2 2046 2121 497338398 497338475 1.130000e-13 87.9


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 TraesCS1D01G164000 chr1D 234655387 234657674 2287 False 1807.000000 3445 100.0000 1 2288 2 chr1D.!!$F1 2287
1 TraesCS1D01G164000 chr1A 313006385 313007423 1038 True 719.500000 1317 93.9150 654 1729 2 chr1A.!!$R1 1075
2 TraesCS1D01G164000 chr1B 338428190 338431193 3003 True 576.666667 994 87.4440 424 2087 3 chr1B.!!$R1 1663
3 TraesCS1D01G164000 chr1B 340365396 340369627 4231 False 350.500000 1013 88.8148 424 2041 5 chr1B.!!$F1 1617

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
643 657 0.035739 GACTGCCCGGTTCCACTTAA 59.964 55.0 0.0 0.0 0.0 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 6162 0.03831 GCTGGCTAGGGTTTCTTGGT 59.962 55.0 0.0 0.0 0.0 3.67 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
28 29 3.833304 GCCCACTGCATAGGCTTC 58.167 61.111 13.09 0.00 43.62 3.86
29 30 2.182842 GCCCACTGCATAGGCTTCG 61.183 63.158 13.09 0.00 43.62 3.79
30 31 2.182842 CCCACTGCATAGGCTTCGC 61.183 63.158 0.00 0.00 41.91 4.70
40 41 4.778143 GGCTTCGCCCGGTGTGAT 62.778 66.667 0.00 0.00 44.06 3.06
41 42 3.195698 GCTTCGCCCGGTGTGATC 61.196 66.667 0.00 0.00 32.45 2.92
42 43 2.579201 CTTCGCCCGGTGTGATCT 59.421 61.111 0.00 0.00 32.45 2.75
43 44 1.519455 CTTCGCCCGGTGTGATCTC 60.519 63.158 0.00 0.00 32.45 2.75
44 45 2.907897 CTTCGCCCGGTGTGATCTCC 62.908 65.000 0.00 0.00 32.45 3.71
45 46 4.873129 CGCCCGGTGTGATCTCCG 62.873 72.222 0.00 14.33 46.28 4.63
50 51 2.202756 GGTGTGATCTCCGACGGC 60.203 66.667 9.66 0.00 0.00 5.68
51 52 2.579787 GTGTGATCTCCGACGGCG 60.580 66.667 9.66 1.94 37.24 6.46
71 72 4.862823 GGGAGGGAGGGGTCGAGG 62.863 77.778 0.00 0.00 0.00 4.63
72 73 3.752167 GGAGGGAGGGGTCGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
73 74 2.363361 GAGGGAGGGGTCGAGGAA 59.637 66.667 0.00 0.00 0.00 3.36
74 75 1.305887 GAGGGAGGGGTCGAGGAAA 60.306 63.158 0.00 0.00 0.00 3.13
75 76 1.306226 AGGGAGGGGTCGAGGAAAG 60.306 63.158 0.00 0.00 0.00 2.62
76 77 2.368011 GGGAGGGGTCGAGGAAAGG 61.368 68.421 0.00 0.00 0.00 3.11
77 78 1.305887 GGAGGGGTCGAGGAAAGGA 60.306 63.158 0.00 0.00 0.00 3.36
78 79 1.331399 GGAGGGGTCGAGGAAAGGAG 61.331 65.000 0.00 0.00 0.00 3.69
79 80 0.615261 GAGGGGTCGAGGAAAGGAGT 60.615 60.000 0.00 0.00 0.00 3.85
80 81 0.615261 AGGGGTCGAGGAAAGGAGTC 60.615 60.000 0.00 0.00 0.00 3.36
81 82 1.615165 GGGGTCGAGGAAAGGAGTCC 61.615 65.000 0.00 0.00 38.03 3.85
87 88 3.325994 AGGAAAGGAGTCCTAGGGC 57.674 57.895 13.43 4.79 46.69 5.19
88 89 0.719623 AGGAAAGGAGTCCTAGGGCT 59.280 55.000 18.01 18.01 46.69 5.19
89 90 1.938069 AGGAAAGGAGTCCTAGGGCTA 59.062 52.381 17.98 0.00 46.69 3.93
90 91 2.090999 AGGAAAGGAGTCCTAGGGCTAG 60.091 54.545 17.98 0.00 46.69 3.42
449 452 3.182967 GAGTTGGCACATAGAGAGTTCG 58.817 50.000 0.00 0.00 39.30 3.95
502 505 6.316890 AGTTTAAAACAGACTTTACTCGGCAA 59.683 34.615 0.00 0.00 0.00 4.52
503 506 6.680874 TTAAAACAGACTTTACTCGGCAAA 57.319 33.333 0.00 0.00 0.00 3.68
504 507 5.767816 AAAACAGACTTTACTCGGCAAAT 57.232 34.783 0.00 0.00 0.00 2.32
511 514 7.224753 ACAGACTTTACTCGGCAAATATACATG 59.775 37.037 0.00 0.00 0.00 3.21
543 546 3.319122 ACTTTTGTTCCTCACAAGGCATC 59.681 43.478 0.00 0.00 46.37 3.91
547 550 2.290260 TGTTCCTCACAAGGCATCGAAT 60.290 45.455 0.00 0.00 43.02 3.34
569 572 7.412563 CGAATTAAAATCATCCCGTACGCATAT 60.413 37.037 10.49 0.00 0.00 1.78
574 577 7.499321 AAATCATCCCGTACGCATATAAAAA 57.501 32.000 10.49 0.00 0.00 1.94
634 648 3.760035 CGTAGCAGACTGCCCGGT 61.760 66.667 23.74 7.98 46.52 5.28
635 649 2.663196 GTAGCAGACTGCCCGGTT 59.337 61.111 23.74 7.59 46.52 4.44
636 650 1.448013 GTAGCAGACTGCCCGGTTC 60.448 63.158 23.74 0.00 46.52 3.62
640 654 2.526873 AGACTGCCCGGTTCCACT 60.527 61.111 0.00 0.00 0.00 4.00
641 655 2.147387 AGACTGCCCGGTTCCACTT 61.147 57.895 0.00 0.00 0.00 3.16
642 656 0.834687 AGACTGCCCGGTTCCACTTA 60.835 55.000 0.00 0.00 0.00 2.24
643 657 0.035739 GACTGCCCGGTTCCACTTAA 59.964 55.000 0.00 0.00 0.00 1.85
645 659 1.094785 CTGCCCGGTTCCACTTAATG 58.905 55.000 0.00 0.00 0.00 1.90
646 660 0.693622 TGCCCGGTTCCACTTAATGA 59.306 50.000 0.00 0.00 0.00 2.57
647 661 1.074084 TGCCCGGTTCCACTTAATGAA 59.926 47.619 0.00 0.00 0.00 2.57
648 662 2.291282 TGCCCGGTTCCACTTAATGAAT 60.291 45.455 0.00 0.00 0.00 2.57
649 663 2.099098 GCCCGGTTCCACTTAATGAATG 59.901 50.000 0.00 0.00 0.00 2.67
650 664 2.099098 CCCGGTTCCACTTAATGAATGC 59.901 50.000 0.00 0.00 0.00 3.56
651 665 2.099098 CCGGTTCCACTTAATGAATGCC 59.901 50.000 0.00 0.00 0.00 4.40
652 666 3.016736 CGGTTCCACTTAATGAATGCCT 58.983 45.455 0.00 0.00 0.00 4.75
727 847 9.933723 AGGTTTATATGTACGGTAATAATGTCC 57.066 33.333 0.00 0.00 0.00 4.02
865 2137 2.223572 CGCATTGCCTACCAAATTCCTC 60.224 50.000 2.41 0.00 36.92 3.71
913 2186 4.368391 AGCAACGCTCCTCTTGTG 57.632 55.556 0.00 0.00 30.62 3.33
914 2187 1.302033 AGCAACGCTCCTCTTGTGG 60.302 57.895 0.00 0.00 30.62 4.17
915 2188 1.598130 GCAACGCTCCTCTTGTGGT 60.598 57.895 0.00 0.00 0.00 4.16
980 2253 0.935196 AACGTCGTGTTTGGAGAAGC 59.065 50.000 0.00 0.00 37.59 3.86
1298 2577 0.447801 CCGCAGTAGAAACATGGTGC 59.552 55.000 0.00 0.00 0.00 5.01
1477 3337 0.780596 GTTCTTTTCGACGACCGGAC 59.219 55.000 9.46 0.00 39.14 4.79
1486 3346 1.356938 GACGACCGGACAAGGATTTC 58.643 55.000 9.46 0.00 34.73 2.17
1504 3364 5.392057 GGATTTCGGGATGAGAACTTCAAAC 60.392 44.000 0.00 0.00 39.77 2.93
1535 3405 3.696051 TCCAACGTATACAGGTACCTGAC 59.304 47.826 41.87 29.30 46.30 3.51
1589 3482 4.487714 TGATTCGAATTACAAGGCCTCT 57.512 40.909 12.81 0.00 0.00 3.69
1590 3483 4.191544 TGATTCGAATTACAAGGCCTCTG 58.808 43.478 12.81 9.66 0.00 3.35
1594 3487 2.678336 CGAATTACAAGGCCTCTGGTTC 59.322 50.000 5.23 11.44 0.00 3.62
1625 3620 6.478512 AAAATTTACAAGGCCTCAAACTGA 57.521 33.333 5.23 0.00 0.00 3.41
1626 3621 5.453567 AATTTACAAGGCCTCAAACTGAC 57.546 39.130 5.23 0.00 0.00 3.51
1627 3622 2.561478 TACAAGGCCTCAAACTGACC 57.439 50.000 5.23 0.00 0.00 4.02
1629 3624 0.250295 CAAGGCCTCAAACTGACCGA 60.250 55.000 5.23 0.00 0.00 4.69
1630 3625 0.693049 AAGGCCTCAAACTGACCGAT 59.307 50.000 5.23 0.00 0.00 4.18
1631 3626 1.568504 AGGCCTCAAACTGACCGATA 58.431 50.000 0.00 0.00 0.00 2.92
1632 3627 1.482593 AGGCCTCAAACTGACCGATAG 59.517 52.381 0.00 0.00 0.00 2.08
1650 4178 2.820728 AGGTTTATAGGTTGTGGGGC 57.179 50.000 0.00 0.00 0.00 5.80
1690 5615 6.403866 AAGCTAAAATTCCACACACATGAA 57.596 33.333 0.00 0.00 0.00 2.57
1692 5617 5.536161 AGCTAAAATTCCACACACATGAACT 59.464 36.000 0.00 0.00 0.00 3.01
1793 5722 3.285484 TCCTACCGAGGTTAGTGATGAC 58.715 50.000 0.00 0.00 44.19 3.06
1794 5723 3.053842 TCCTACCGAGGTTAGTGATGACT 60.054 47.826 0.00 0.00 44.19 3.41
1795 5724 3.066900 CCTACCGAGGTTAGTGATGACTG 59.933 52.174 0.00 0.00 38.16 3.51
1796 5725 1.825474 ACCGAGGTTAGTGATGACTGG 59.175 52.381 0.00 0.00 33.21 4.00
1797 5726 1.825474 CCGAGGTTAGTGATGACTGGT 59.175 52.381 0.00 0.00 33.21 4.00
1798 5727 2.417379 CCGAGGTTAGTGATGACTGGTG 60.417 54.545 0.00 0.00 33.21 4.17
1799 5728 2.492088 CGAGGTTAGTGATGACTGGTGA 59.508 50.000 0.00 0.00 33.21 4.02
1800 5729 3.428180 CGAGGTTAGTGATGACTGGTGAG 60.428 52.174 0.00 0.00 33.21 3.51
1801 5730 3.764434 GAGGTTAGTGATGACTGGTGAGA 59.236 47.826 0.00 0.00 33.21 3.27
1802 5731 4.357325 AGGTTAGTGATGACTGGTGAGAT 58.643 43.478 0.00 0.00 33.21 2.75
1803 5732 4.780021 AGGTTAGTGATGACTGGTGAGATT 59.220 41.667 0.00 0.00 33.21 2.40
1804 5733 5.958380 AGGTTAGTGATGACTGGTGAGATTA 59.042 40.000 0.00 0.00 33.21 1.75
1811 5778 7.071698 AGTGATGACTGGTGAGATTATTACCAT 59.928 37.037 0.00 0.00 43.05 3.55
1824 5791 9.289782 GAGATTATTACCATTAGTTTGGAGCAT 57.710 33.333 0.00 0.00 39.25 3.79
1825 5792 9.289782 AGATTATTACCATTAGTTTGGAGCATC 57.710 33.333 0.00 0.00 39.25 3.91
1826 5793 9.289782 GATTATTACCATTAGTTTGGAGCATCT 57.710 33.333 0.00 0.00 39.25 2.90
1827 5794 6.949352 ATTACCATTAGTTTGGAGCATCTG 57.051 37.500 0.00 0.00 39.25 2.90
1828 5795 3.624777 ACCATTAGTTTGGAGCATCTGG 58.375 45.455 0.00 0.00 39.25 3.86
1829 5796 3.266772 ACCATTAGTTTGGAGCATCTGGA 59.733 43.478 0.00 0.00 39.25 3.86
1830 5797 3.629398 CCATTAGTTTGGAGCATCTGGAC 59.371 47.826 0.00 0.00 39.25 4.02
1834 5801 0.955428 TTTGGAGCATCTGGACGCAC 60.955 55.000 0.00 0.00 33.73 5.34
1854 5821 1.918253 CCAAGGGGTCTCATCCAGG 59.082 63.158 0.00 0.00 0.00 4.45
1855 5822 1.639635 CCAAGGGGTCTCATCCAGGG 61.640 65.000 0.00 0.00 0.00 4.45
1856 5823 2.003548 AAGGGGTCTCATCCAGGGC 61.004 63.158 0.00 0.00 0.00 5.19
1858 5825 3.083997 GGGTCTCATCCAGGGCGT 61.084 66.667 0.00 0.00 0.00 5.68
1859 5826 2.670148 GGGTCTCATCCAGGGCGTT 61.670 63.158 0.00 0.00 0.00 4.84
1860 5827 1.450312 GGTCTCATCCAGGGCGTTG 60.450 63.158 0.00 0.00 0.00 4.10
1924 5894 3.181487 GCACCATTACCCTGCAATTACAG 60.181 47.826 0.00 0.00 37.42 2.74
1937 5911 4.186159 GCAATTACAGCAAAGCCATCAAT 58.814 39.130 0.00 0.00 0.00 2.57
1938 5912 4.033587 GCAATTACAGCAAAGCCATCAATG 59.966 41.667 0.00 0.00 0.00 2.82
2003 5977 8.879759 CGACATTAACTATTTCATAACACACCT 58.120 33.333 0.00 0.00 0.00 4.00
2028 6004 3.481112 GTTGTAAACCTGGGCAATACG 57.519 47.619 0.00 0.00 42.21 3.06
2030 6006 2.702261 TGTAAACCTGGGCAATACGAC 58.298 47.619 0.00 0.00 0.00 4.34
2041 6017 5.034200 TGGGCAATACGACCCCTATATAAT 58.966 41.667 0.00 0.00 45.87 1.28
2046 6022 6.420008 GCAATACGACCCCTATATAATTAGCG 59.580 42.308 0.00 0.00 0.00 4.26
2055 6031 5.607171 CCCTATATAATTAGCGGGGGATCTT 59.393 44.000 9.46 0.00 34.94 2.40
2068 6044 0.247854 GGATCTTCTCTTTTGCGCGC 60.248 55.000 27.26 27.26 0.00 6.86
2083 6059 0.095245 CGCGCGAACTCAATCACATT 59.905 50.000 28.94 0.00 0.00 2.71
2084 6060 1.802839 GCGCGAACTCAATCACATTC 58.197 50.000 12.10 0.00 0.00 2.67
2086 6062 2.159653 GCGCGAACTCAATCACATTCTT 60.160 45.455 12.10 0.00 0.00 2.52
2087 6063 3.667960 GCGCGAACTCAATCACATTCTTT 60.668 43.478 12.10 0.00 0.00 2.52
2088 6064 3.842428 CGCGAACTCAATCACATTCTTTG 59.158 43.478 0.00 0.00 0.00 2.77
2089 6065 4.611355 CGCGAACTCAATCACATTCTTTGT 60.611 41.667 0.00 0.00 39.91 2.83
2090 6066 5.389411 CGCGAACTCAATCACATTCTTTGTA 60.389 40.000 0.00 0.00 36.57 2.41
2091 6067 6.370593 GCGAACTCAATCACATTCTTTGTAA 58.629 36.000 0.00 0.00 36.57 2.41
2092 6068 7.023575 GCGAACTCAATCACATTCTTTGTAAT 58.976 34.615 0.00 0.00 36.57 1.89
2093 6069 7.217070 GCGAACTCAATCACATTCTTTGTAATC 59.783 37.037 0.00 0.00 36.57 1.75
2094 6070 7.693951 CGAACTCAATCACATTCTTTGTAATCC 59.306 37.037 0.00 0.00 36.57 3.01
2095 6071 7.396540 ACTCAATCACATTCTTTGTAATCCC 57.603 36.000 0.00 0.00 36.57 3.85
2096 6072 7.177878 ACTCAATCACATTCTTTGTAATCCCT 58.822 34.615 0.00 0.00 36.57 4.20
2097 6073 8.328758 ACTCAATCACATTCTTTGTAATCCCTA 58.671 33.333 0.00 0.00 36.57 3.53
2098 6074 9.347240 CTCAATCACATTCTTTGTAATCCCTAT 57.653 33.333 0.00 0.00 36.57 2.57
2102 6078 8.958119 TCACATTCTTTGTAATCCCTATACAC 57.042 34.615 0.00 0.00 36.57 2.90
2103 6079 8.544622 TCACATTCTTTGTAATCCCTATACACA 58.455 33.333 0.00 0.00 36.57 3.72
2104 6080 9.173021 CACATTCTTTGTAATCCCTATACACAA 57.827 33.333 0.00 0.00 36.57 3.33
2105 6081 9.920946 ACATTCTTTGTAATCCCTATACACAAT 57.079 29.630 0.00 0.00 36.57 2.71
2112 6088 8.991243 TGTAATCCCTATACACAATTATACGC 57.009 34.615 0.00 0.00 0.00 4.42
2113 6089 8.586744 TGTAATCCCTATACACAATTATACGCA 58.413 33.333 0.00 0.00 0.00 5.24
2114 6090 9.426837 GTAATCCCTATACACAATTATACGCAA 57.573 33.333 0.00 0.00 0.00 4.85
2116 6092 7.292713 TCCCTATACACAATTATACGCAAGA 57.707 36.000 0.00 0.00 43.62 3.02
2117 6093 7.728148 TCCCTATACACAATTATACGCAAGAA 58.272 34.615 0.00 0.00 43.62 2.52
2118 6094 7.654520 TCCCTATACACAATTATACGCAAGAAC 59.345 37.037 0.00 0.00 43.62 3.01
2119 6095 7.439955 CCCTATACACAATTATACGCAAGAACA 59.560 37.037 0.00 0.00 43.62 3.18
2120 6096 8.273557 CCTATACACAATTATACGCAAGAACAC 58.726 37.037 0.00 0.00 43.62 3.32
2121 6097 5.291293 ACACAATTATACGCAAGAACACC 57.709 39.130 0.00 0.00 43.62 4.16
2122 6098 4.155280 ACACAATTATACGCAAGAACACCC 59.845 41.667 0.00 0.00 43.62 4.61
2123 6099 4.155099 CACAATTATACGCAAGAACACCCA 59.845 41.667 0.00 0.00 43.62 4.51
2124 6100 4.155280 ACAATTATACGCAAGAACACCCAC 59.845 41.667 0.00 0.00 43.62 4.61
2125 6101 3.404224 TTATACGCAAGAACACCCACA 57.596 42.857 0.00 0.00 43.62 4.17
2126 6102 1.519408 ATACGCAAGAACACCCACAC 58.481 50.000 0.00 0.00 43.62 3.82
2127 6103 0.178301 TACGCAAGAACACCCACACA 59.822 50.000 0.00 0.00 43.62 3.72
2128 6104 1.355210 CGCAAGAACACCCACACAC 59.645 57.895 0.00 0.00 43.02 3.82
2129 6105 1.372838 CGCAAGAACACCCACACACA 61.373 55.000 0.00 0.00 43.02 3.72
2130 6106 0.100503 GCAAGAACACCCACACACAC 59.899 55.000 0.00 0.00 0.00 3.82
2131 6107 1.458398 CAAGAACACCCACACACACA 58.542 50.000 0.00 0.00 0.00 3.72
2132 6108 1.815613 CAAGAACACCCACACACACAA 59.184 47.619 0.00 0.00 0.00 3.33
2133 6109 1.750193 AGAACACCCACACACACAAG 58.250 50.000 0.00 0.00 0.00 3.16
2134 6110 1.280710 AGAACACCCACACACACAAGA 59.719 47.619 0.00 0.00 0.00 3.02
2135 6111 2.092429 AGAACACCCACACACACAAGAT 60.092 45.455 0.00 0.00 0.00 2.40
2136 6112 2.435372 ACACCCACACACACAAGATT 57.565 45.000 0.00 0.00 0.00 2.40
2137 6113 3.569194 ACACCCACACACACAAGATTA 57.431 42.857 0.00 0.00 0.00 1.75
2138 6114 3.476552 ACACCCACACACACAAGATTAG 58.523 45.455 0.00 0.00 0.00 1.73
2139 6115 2.813754 CACCCACACACACAAGATTAGG 59.186 50.000 0.00 0.00 0.00 2.69
2140 6116 2.224769 ACCCACACACACAAGATTAGGG 60.225 50.000 0.00 0.00 39.66 3.53
2141 6117 2.224769 CCCACACACACAAGATTAGGGT 60.225 50.000 0.00 0.00 0.00 4.34
2142 6118 3.486383 CCACACACACAAGATTAGGGTT 58.514 45.455 0.00 0.00 0.00 4.11
2143 6119 4.505918 CCCACACACACAAGATTAGGGTTA 60.506 45.833 0.00 0.00 0.00 2.85
2144 6120 5.253330 CCACACACACAAGATTAGGGTTAT 58.747 41.667 0.00 0.00 0.00 1.89
2145 6121 5.710099 CCACACACACAAGATTAGGGTTATT 59.290 40.000 0.00 0.00 0.00 1.40
2146 6122 6.882140 CCACACACACAAGATTAGGGTTATTA 59.118 38.462 0.00 0.00 0.00 0.98
2147 6123 7.148306 CCACACACACAAGATTAGGGTTATTAC 60.148 40.741 0.00 0.00 0.00 1.89
2148 6124 6.882678 ACACACACAAGATTAGGGTTATTACC 59.117 38.462 0.00 0.00 44.22 2.85
2149 6125 7.110155 CACACACAAGATTAGGGTTATTACCT 58.890 38.462 0.11 0.00 44.38 3.08
2150 6126 7.280205 CACACACAAGATTAGGGTTATTACCTC 59.720 40.741 0.11 0.00 44.38 3.85
2151 6127 6.766467 CACACAAGATTAGGGTTATTACCTCC 59.234 42.308 0.11 0.00 44.38 4.30
2152 6128 6.445786 ACACAAGATTAGGGTTATTACCTCCA 59.554 38.462 0.11 0.00 44.38 3.86
2153 6129 6.766467 CACAAGATTAGGGTTATTACCTCCAC 59.234 42.308 0.11 0.00 44.38 4.02
2154 6130 6.126565 ACAAGATTAGGGTTATTACCTCCACC 60.127 42.308 0.11 0.00 44.38 4.61
2155 6131 5.544682 AGATTAGGGTTATTACCTCCACCA 58.455 41.667 0.11 0.00 44.38 4.17
2156 6132 5.607171 AGATTAGGGTTATTACCTCCACCAG 59.393 44.000 0.11 0.00 44.38 4.00
2185 6161 8.827832 AAAATCAATTGGAATAGATGACTCCA 57.172 30.769 5.42 0.00 37.47 3.86
2190 6166 5.512942 TTGGAATAGATGACTCCAACCAA 57.487 39.130 0.00 0.00 42.86 3.67
2191 6167 5.102953 TGGAATAGATGACTCCAACCAAG 57.897 43.478 0.00 0.00 36.30 3.61
2192 6168 4.782691 TGGAATAGATGACTCCAACCAAGA 59.217 41.667 0.00 0.00 36.30 3.02
2193 6169 5.250543 TGGAATAGATGACTCCAACCAAGAA 59.749 40.000 0.00 0.00 36.30 2.52
2194 6170 6.180472 GGAATAGATGACTCCAACCAAGAAA 58.820 40.000 0.00 0.00 0.00 2.52
2195 6171 6.094186 GGAATAGATGACTCCAACCAAGAAAC 59.906 42.308 0.00 0.00 0.00 2.78
2196 6172 3.756117 AGATGACTCCAACCAAGAAACC 58.244 45.455 0.00 0.00 0.00 3.27
2197 6173 2.358322 TGACTCCAACCAAGAAACCC 57.642 50.000 0.00 0.00 0.00 4.11
2198 6174 1.850345 TGACTCCAACCAAGAAACCCT 59.150 47.619 0.00 0.00 0.00 4.34
2199 6175 3.050089 TGACTCCAACCAAGAAACCCTA 58.950 45.455 0.00 0.00 0.00 3.53
2200 6176 3.072476 TGACTCCAACCAAGAAACCCTAG 59.928 47.826 0.00 0.00 0.00 3.02
2201 6177 2.224793 ACTCCAACCAAGAAACCCTAGC 60.225 50.000 0.00 0.00 0.00 3.42
2202 6178 1.074889 TCCAACCAAGAAACCCTAGCC 59.925 52.381 0.00 0.00 0.00 3.93
2203 6179 1.203001 CCAACCAAGAAACCCTAGCCA 60.203 52.381 0.00 0.00 0.00 4.75
2204 6180 2.162681 CAACCAAGAAACCCTAGCCAG 58.837 52.381 0.00 0.00 0.00 4.85
2205 6181 0.038310 ACCAAGAAACCCTAGCCAGC 59.962 55.000 0.00 0.00 0.00 4.85
2206 6182 0.681243 CCAAGAAACCCTAGCCAGCC 60.681 60.000 0.00 0.00 0.00 4.85
2207 6183 1.026718 CAAGAAACCCTAGCCAGCCG 61.027 60.000 0.00 0.00 0.00 5.52
2208 6184 2.821679 AAGAAACCCTAGCCAGCCGC 62.822 60.000 0.00 0.00 37.98 6.53
2209 6185 4.426313 AAACCCTAGCCAGCCGCC 62.426 66.667 0.00 0.00 38.78 6.13
2222 6198 2.673687 CCGCCGCCTACCCAAAAA 60.674 61.111 0.00 0.00 0.00 1.94
2223 6199 2.696759 CCGCCGCCTACCCAAAAAG 61.697 63.158 0.00 0.00 0.00 2.27
2224 6200 2.571757 GCCGCCTACCCAAAAAGC 59.428 61.111 0.00 0.00 0.00 3.51
2225 6201 1.977009 GCCGCCTACCCAAAAAGCT 60.977 57.895 0.00 0.00 0.00 3.74
2226 6202 0.678684 GCCGCCTACCCAAAAAGCTA 60.679 55.000 0.00 0.00 0.00 3.32
2227 6203 1.379527 CCGCCTACCCAAAAAGCTAG 58.620 55.000 0.00 0.00 0.00 3.42
2228 6204 1.379527 CGCCTACCCAAAAAGCTAGG 58.620 55.000 0.00 0.00 0.00 3.02
2229 6205 1.339727 CGCCTACCCAAAAAGCTAGGT 60.340 52.381 0.00 0.00 36.36 3.08
2230 6206 2.803956 GCCTACCCAAAAAGCTAGGTT 58.196 47.619 0.12 0.12 33.70 3.50
2231 6207 2.753452 GCCTACCCAAAAAGCTAGGTTC 59.247 50.000 7.80 0.00 33.70 3.62
2232 6208 3.353557 CCTACCCAAAAAGCTAGGTTCC 58.646 50.000 7.80 0.00 33.70 3.62
2233 6209 3.010250 CCTACCCAAAAAGCTAGGTTCCT 59.990 47.826 7.80 0.00 33.70 3.36
2234 6210 3.156288 ACCCAAAAAGCTAGGTTCCTC 57.844 47.619 7.80 0.00 0.00 3.71
2235 6211 2.716969 ACCCAAAAAGCTAGGTTCCTCT 59.283 45.455 7.80 0.00 0.00 3.69
2236 6212 3.084786 CCCAAAAAGCTAGGTTCCTCTG 58.915 50.000 7.80 3.40 0.00 3.35
2237 6213 2.489722 CCAAAAAGCTAGGTTCCTCTGC 59.510 50.000 7.80 1.91 0.00 4.26
2238 6214 2.489722 CAAAAAGCTAGGTTCCTCTGCC 59.510 50.000 7.80 0.00 0.00 4.85
2239 6215 1.662686 AAAGCTAGGTTCCTCTGCCT 58.337 50.000 7.80 0.00 38.81 4.75
2240 6216 1.199615 AAGCTAGGTTCCTCTGCCTC 58.800 55.000 0.12 0.00 36.38 4.70
2241 6217 0.689412 AGCTAGGTTCCTCTGCCTCC 60.689 60.000 11.20 0.00 36.38 4.30
2242 6218 1.691195 GCTAGGTTCCTCTGCCTCCC 61.691 65.000 0.00 0.00 36.38 4.30
2243 6219 1.381327 TAGGTTCCTCTGCCTCCCG 60.381 63.158 0.00 0.00 36.38 5.14
2244 6220 2.164332 TAGGTTCCTCTGCCTCCCGT 62.164 60.000 0.00 0.00 36.38 5.28
2245 6221 2.579738 GTTCCTCTGCCTCCCGTC 59.420 66.667 0.00 0.00 0.00 4.79
2246 6222 3.068691 TTCCTCTGCCTCCCGTCG 61.069 66.667 0.00 0.00 0.00 5.12
2282 6258 4.016706 CCCGTCTTCCGTGGCCTT 62.017 66.667 3.32 0.00 33.66 4.35
2283 6259 2.652095 CCCGTCTTCCGTGGCCTTA 61.652 63.158 3.32 0.00 33.66 2.69
2284 6260 1.153628 CCGTCTTCCGTGGCCTTAG 60.154 63.158 3.32 0.00 33.66 2.18
2285 6261 1.153628 CGTCTTCCGTGGCCTTAGG 60.154 63.158 3.32 4.67 0.00 2.69
2286 6262 1.221021 GTCTTCCGTGGCCTTAGGG 59.779 63.158 3.32 0.00 0.00 3.53
2287 6263 1.229400 TCTTCCGTGGCCTTAGGGT 60.229 57.895 3.32 0.00 34.45 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.520465 TATGCAGTGGGCTGTGACGG 62.520 60.000 0.00 0.00 44.32 4.79
4 5 1.079197 TATGCAGTGGGCTGTGACG 60.079 57.895 0.00 0.00 44.32 4.35
5 6 0.745845 CCTATGCAGTGGGCTGTGAC 60.746 60.000 0.00 0.00 44.32 3.67
6 7 1.603842 CCTATGCAGTGGGCTGTGA 59.396 57.895 0.00 0.00 44.32 3.58
7 8 4.230603 CCTATGCAGTGGGCTGTG 57.769 61.111 0.00 0.00 44.32 3.66
12 13 4.131376 CGAAGCCTATGCAGTGGG 57.869 61.111 9.43 4.28 41.13 4.61
25 26 1.519455 GAGATCACACCGGGCGAAG 60.519 63.158 6.32 0.00 0.00 3.79
26 27 2.577059 GAGATCACACCGGGCGAA 59.423 61.111 6.32 0.00 0.00 4.70
27 28 3.458163 GGAGATCACACCGGGCGA 61.458 66.667 6.32 0.00 0.00 5.54
28 29 4.873129 CGGAGATCACACCGGGCG 62.873 72.222 6.32 0.00 44.22 6.13
29 30 3.458163 TCGGAGATCACACCGGGC 61.458 66.667 20.01 0.00 46.95 6.13
30 31 2.494918 GTCGGAGATCACACCGGG 59.505 66.667 20.01 0.00 46.95 5.73
31 32 2.102357 CGTCGGAGATCACACCGG 59.898 66.667 20.01 0.00 46.95 5.28
33 34 2.202756 GCCGTCGGAGATCACACC 60.203 66.667 17.49 0.00 40.67 4.16
34 35 2.579787 CGCCGTCGGAGATCACAC 60.580 66.667 17.49 0.00 40.67 3.82
54 55 4.862823 CCTCGACCCCTCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
55 56 2.817420 TTTCCTCGACCCCTCCCTCC 62.817 65.000 0.00 0.00 0.00 4.30
56 57 1.305887 TTTCCTCGACCCCTCCCTC 60.306 63.158 0.00 0.00 0.00 4.30
57 58 1.306226 CTTTCCTCGACCCCTCCCT 60.306 63.158 0.00 0.00 0.00 4.20
58 59 2.368011 CCTTTCCTCGACCCCTCCC 61.368 68.421 0.00 0.00 0.00 4.30
59 60 1.305887 TCCTTTCCTCGACCCCTCC 60.306 63.158 0.00 0.00 0.00 4.30
60 61 0.615261 ACTCCTTTCCTCGACCCCTC 60.615 60.000 0.00 0.00 0.00 4.30
61 62 0.615261 GACTCCTTTCCTCGACCCCT 60.615 60.000 0.00 0.00 0.00 4.79
62 63 1.615165 GGACTCCTTTCCTCGACCCC 61.615 65.000 0.00 0.00 32.24 4.95
63 64 0.615261 AGGACTCCTTTCCTCGACCC 60.615 60.000 0.00 0.00 42.98 4.46
64 65 2.025898 CTAGGACTCCTTTCCTCGACC 58.974 57.143 1.94 0.00 42.98 4.79
65 66 2.025898 CCTAGGACTCCTTTCCTCGAC 58.974 57.143 1.05 0.00 42.98 4.20
66 67 1.063867 CCCTAGGACTCCTTTCCTCGA 60.064 57.143 11.48 0.00 42.98 4.04
67 68 1.404843 CCCTAGGACTCCTTTCCTCG 58.595 60.000 11.48 0.00 42.98 4.63
68 69 1.124780 GCCCTAGGACTCCTTTCCTC 58.875 60.000 11.48 0.00 42.98 3.71
70 71 2.321719 CTAGCCCTAGGACTCCTTTCC 58.678 57.143 11.48 0.00 34.61 3.13
477 480 5.818857 TGCCGAGTAAAGTCTGTTTTAAACT 59.181 36.000 9.33 0.00 0.00 2.66
511 514 8.547967 TGTGAGGAACAAAAGTATTATCTCAC 57.452 34.615 11.32 11.32 44.91 3.51
525 528 1.071542 TCGATGCCTTGTGAGGAACAA 59.928 47.619 0.00 0.00 46.74 2.83
526 529 0.684535 TCGATGCCTTGTGAGGAACA 59.315 50.000 0.00 0.00 46.74 3.18
543 546 4.025563 TGCGTACGGGATGATTTTAATTCG 60.026 41.667 18.39 0.00 0.00 3.34
547 550 8.604640 TTTATATGCGTACGGGATGATTTTAA 57.395 30.769 18.39 0.00 0.00 1.52
574 577 1.674817 CCTCACGTACGGGATGCTTTT 60.675 52.381 22.44 0.00 0.00 2.27
575 578 0.108329 CCTCACGTACGGGATGCTTT 60.108 55.000 22.44 0.00 0.00 3.51
576 579 1.515954 CCTCACGTACGGGATGCTT 59.484 57.895 22.44 0.00 0.00 3.91
577 580 3.077519 GCCTCACGTACGGGATGCT 62.078 63.158 32.12 4.28 36.48 3.79
578 581 2.585247 GCCTCACGTACGGGATGC 60.585 66.667 27.75 27.75 32.55 3.91
588 602 1.298157 TTCTGCGGAATTGCCTCACG 61.298 55.000 3.13 0.00 0.00 4.35
618 632 1.448013 GAACCGGGCAGTCTGCTAC 60.448 63.158 23.68 15.72 44.28 3.58
620 634 4.021925 GGAACCGGGCAGTCTGCT 62.022 66.667 23.68 3.88 44.28 4.24
623 637 0.834687 TAAGTGGAACCGGGCAGTCT 60.835 55.000 6.32 0.00 37.80 3.24
629 643 2.099098 GCATTCATTAAGTGGAACCGGG 59.901 50.000 6.32 0.00 37.80 5.73
633 647 4.273318 AGGAGGCATTCATTAAGTGGAAC 58.727 43.478 0.00 0.00 0.00 3.62
634 648 4.591321 AGGAGGCATTCATTAAGTGGAA 57.409 40.909 0.00 0.00 0.00 3.53
635 649 5.191722 ACTTAGGAGGCATTCATTAAGTGGA 59.808 40.000 11.96 0.00 36.85 4.02
636 650 5.440610 ACTTAGGAGGCATTCATTAAGTGG 58.559 41.667 11.96 0.00 36.85 4.00
649 663 3.117888 TGGAAATGGATGACTTAGGAGGC 60.118 47.826 0.00 0.00 0.00 4.70
650 664 4.778213 TGGAAATGGATGACTTAGGAGG 57.222 45.455 0.00 0.00 0.00 4.30
651 665 8.930846 ATAATTGGAAATGGATGACTTAGGAG 57.069 34.615 0.00 0.00 0.00 3.69
652 666 8.501904 TGATAATTGGAAATGGATGACTTAGGA 58.498 33.333 0.00 0.00 0.00 2.94
727 847 3.934457 ACTTTGCCATTTTTACCTCCG 57.066 42.857 0.00 0.00 0.00 4.63
744 864 7.724951 AGAAATCCCTCGCTATTACTACTACTT 59.275 37.037 0.00 0.00 0.00 2.24
788 914 3.014304 TGGAGTATACGCTTCACCTCT 57.986 47.619 6.57 0.00 0.00 3.69
789 915 3.795623 TTGGAGTATACGCTTCACCTC 57.204 47.619 6.57 0.00 0.00 3.85
865 2137 4.200283 GGGAGAGTGAGCGCCTCG 62.200 72.222 2.29 0.00 34.08 4.63
915 2188 2.260154 CGATGCAGTTGGTGGCACA 61.260 57.895 20.82 2.61 43.75 4.57
980 2253 0.594110 GGTCTTCGATCTAGCTCCGG 59.406 60.000 0.00 0.00 0.00 5.14
1143 2422 1.446792 CAGGTTCGAGCAGCACGAT 60.447 57.895 15.96 0.00 39.45 3.73
1450 2756 3.246699 GTCGTCGAAAAGAACAACATCCA 59.753 43.478 0.00 0.00 0.00 3.41
1477 3337 3.878778 AGTTCTCATCCCGAAATCCTTG 58.121 45.455 0.00 0.00 0.00 3.61
1486 3346 1.732259 CGGTTTGAAGTTCTCATCCCG 59.268 52.381 4.17 5.25 39.71 5.14
1504 3364 2.616786 TATACGTTGGAGGCGTGCGG 62.617 60.000 0.00 0.00 42.87 5.69
1607 3602 2.808933 CGGTCAGTTTGAGGCCTTGTAA 60.809 50.000 6.77 0.00 0.00 2.41
1608 3603 1.270625 CGGTCAGTTTGAGGCCTTGTA 60.271 52.381 6.77 0.00 0.00 2.41
1609 3604 0.535102 CGGTCAGTTTGAGGCCTTGT 60.535 55.000 6.77 0.00 0.00 3.16
1610 3605 0.250295 TCGGTCAGTTTGAGGCCTTG 60.250 55.000 6.77 0.00 0.00 3.61
1611 3606 0.693049 ATCGGTCAGTTTGAGGCCTT 59.307 50.000 6.77 0.00 0.00 4.35
1612 3607 1.482593 CTATCGGTCAGTTTGAGGCCT 59.517 52.381 3.86 3.86 0.00 5.19
1613 3608 1.473434 CCTATCGGTCAGTTTGAGGCC 60.473 57.143 0.00 0.00 0.00 5.19
1614 3609 1.207329 ACCTATCGGTCAGTTTGAGGC 59.793 52.381 0.00 0.00 40.27 4.70
1615 3610 3.611766 AACCTATCGGTCAGTTTGAGG 57.388 47.619 0.00 0.00 44.73 3.86
1616 3611 6.924060 CCTATAAACCTATCGGTCAGTTTGAG 59.076 42.308 6.31 4.21 44.73 3.02
1618 3613 6.579865 ACCTATAAACCTATCGGTCAGTTTG 58.420 40.000 6.31 0.00 44.73 2.93
1619 3614 6.803366 ACCTATAAACCTATCGGTCAGTTT 57.197 37.500 2.06 2.06 44.73 2.66
1620 3615 6.155737 ACAACCTATAAACCTATCGGTCAGTT 59.844 38.462 0.00 0.00 44.73 3.16
1621 3616 5.659971 ACAACCTATAAACCTATCGGTCAGT 59.340 40.000 0.00 0.00 44.73 3.41
1624 3619 5.295152 CCACAACCTATAAACCTATCGGTC 58.705 45.833 0.00 0.00 44.73 4.79
1626 3621 4.504340 CCCCACAACCTATAAACCTATCGG 60.504 50.000 0.00 0.00 0.00 4.18
1627 3622 4.638304 CCCCACAACCTATAAACCTATCG 58.362 47.826 0.00 0.00 0.00 2.92
1629 3624 3.789274 TGCCCCACAACCTATAAACCTAT 59.211 43.478 0.00 0.00 0.00 2.57
1630 3625 3.191273 TGCCCCACAACCTATAAACCTA 58.809 45.455 0.00 0.00 0.00 3.08
1631 3626 1.997040 TGCCCCACAACCTATAAACCT 59.003 47.619 0.00 0.00 0.00 3.50
1632 3627 2.517998 TGCCCCACAACCTATAAACC 57.482 50.000 0.00 0.00 0.00 3.27
1633 3628 6.512297 CAAATATGCCCCACAACCTATAAAC 58.488 40.000 0.00 0.00 0.00 2.01
1634 3629 6.723298 CAAATATGCCCCACAACCTATAAA 57.277 37.500 0.00 0.00 0.00 1.40
1793 5722 8.840321 CCAAACTAATGGTAATAATCTCACCAG 58.160 37.037 0.00 0.00 45.15 4.00
1794 5723 8.553153 TCCAAACTAATGGTAATAATCTCACCA 58.447 33.333 0.00 0.00 45.96 4.17
1795 5724 8.974060 TCCAAACTAATGGTAATAATCTCACC 57.026 34.615 0.00 0.00 41.46 4.02
1796 5725 8.560374 GCTCCAAACTAATGGTAATAATCTCAC 58.440 37.037 0.00 0.00 41.46 3.51
1797 5726 8.271458 TGCTCCAAACTAATGGTAATAATCTCA 58.729 33.333 0.00 0.00 41.46 3.27
1798 5727 8.677148 TGCTCCAAACTAATGGTAATAATCTC 57.323 34.615 0.00 0.00 41.46 2.75
1799 5728 9.289782 GATGCTCCAAACTAATGGTAATAATCT 57.710 33.333 0.00 0.00 41.46 2.40
1800 5729 9.289782 AGATGCTCCAAACTAATGGTAATAATC 57.710 33.333 0.00 0.00 41.46 1.75
1801 5730 9.071276 CAGATGCTCCAAACTAATGGTAATAAT 57.929 33.333 0.00 0.00 41.46 1.28
1802 5731 7.502226 CCAGATGCTCCAAACTAATGGTAATAA 59.498 37.037 0.00 0.00 41.46 1.40
1803 5732 6.998074 CCAGATGCTCCAAACTAATGGTAATA 59.002 38.462 0.00 0.00 41.46 0.98
1804 5733 5.829924 CCAGATGCTCCAAACTAATGGTAAT 59.170 40.000 0.00 0.00 41.46 1.89
1811 5778 2.935238 GCGTCCAGATGCTCCAAACTAA 60.935 50.000 4.58 0.00 40.09 2.24
1824 5791 4.680237 CCTTGGCGTGCGTCCAGA 62.680 66.667 0.00 0.00 34.66 3.86
1834 5801 2.190578 GGATGAGACCCCTTGGCG 59.809 66.667 0.00 0.00 33.59 5.69
1843 5810 1.450312 CCAACGCCCTGGATGAGAC 60.450 63.158 0.00 0.00 38.96 3.36
1856 5823 1.049251 GTAATGTTTGCGCACCAACG 58.951 50.000 11.12 0.00 31.97 4.10
1858 5825 2.031245 CAGAGTAATGTTTGCGCACCAA 60.031 45.455 11.12 0.00 0.00 3.67
1859 5826 1.535028 CAGAGTAATGTTTGCGCACCA 59.465 47.619 11.12 11.05 0.00 4.17
1860 5827 1.729149 GCAGAGTAATGTTTGCGCACC 60.729 52.381 11.12 4.02 0.00 5.01
1924 5894 0.462789 CTCCCCATTGATGGCTTTGC 59.537 55.000 4.43 0.00 46.70 3.68
1937 5911 3.450904 ACTATGCACTAGAAACTCCCCA 58.549 45.455 0.00 0.00 0.00 4.96
1938 5912 4.489306 AACTATGCACTAGAAACTCCCC 57.511 45.455 0.00 0.00 0.00 4.81
2003 5977 1.213182 TGCCCAGGTTTACAACAGTCA 59.787 47.619 0.00 0.00 0.00 3.41
2021 5995 6.420008 CGCTAATTATATAGGGGTCGTATTGC 59.580 42.308 0.00 0.00 33.50 3.56
2041 6017 2.176247 AAGAGAAGATCCCCCGCTAA 57.824 50.000 0.00 0.00 0.00 3.09
2046 6022 1.383523 CGCAAAAGAGAAGATCCCCC 58.616 55.000 0.00 0.00 0.00 5.40
2055 6031 1.886861 GAGTTCGCGCGCAAAAGAGA 61.887 55.000 32.61 16.24 0.00 3.10
2068 6044 7.693951 GGATTACAAAGAATGTGATTGAGTTCG 59.306 37.037 0.00 0.00 43.77 3.95
2086 6062 9.426837 GCGTATAATTGTGTATAGGGATTACAA 57.573 33.333 0.00 0.00 35.93 2.41
2087 6063 8.586744 TGCGTATAATTGTGTATAGGGATTACA 58.413 33.333 0.00 0.00 0.00 2.41
2088 6064 8.991243 TGCGTATAATTGTGTATAGGGATTAC 57.009 34.615 0.00 0.00 0.00 1.89
2089 6065 9.647797 CTTGCGTATAATTGTGTATAGGGATTA 57.352 33.333 0.00 0.00 0.00 1.75
2090 6066 8.372459 TCTTGCGTATAATTGTGTATAGGGATT 58.628 33.333 0.00 0.00 0.00 3.01
2091 6067 7.903145 TCTTGCGTATAATTGTGTATAGGGAT 58.097 34.615 0.00 0.00 0.00 3.85
2092 6068 7.292713 TCTTGCGTATAATTGTGTATAGGGA 57.707 36.000 0.00 0.00 0.00 4.20
2093 6069 7.439955 TGTTCTTGCGTATAATTGTGTATAGGG 59.560 37.037 0.00 0.00 0.00 3.53
2094 6070 8.273557 GTGTTCTTGCGTATAATTGTGTATAGG 58.726 37.037 0.00 0.00 0.00 2.57
2095 6071 8.273557 GGTGTTCTTGCGTATAATTGTGTATAG 58.726 37.037 0.00 0.00 0.00 1.31
2096 6072 7.225145 GGGTGTTCTTGCGTATAATTGTGTATA 59.775 37.037 0.00 0.00 0.00 1.47
2097 6073 6.037830 GGGTGTTCTTGCGTATAATTGTGTAT 59.962 38.462 0.00 0.00 0.00 2.29
2098 6074 5.352016 GGGTGTTCTTGCGTATAATTGTGTA 59.648 40.000 0.00 0.00 0.00 2.90
2099 6075 4.155280 GGGTGTTCTTGCGTATAATTGTGT 59.845 41.667 0.00 0.00 0.00 3.72
2100 6076 4.155099 TGGGTGTTCTTGCGTATAATTGTG 59.845 41.667 0.00 0.00 0.00 3.33
2101 6077 4.155280 GTGGGTGTTCTTGCGTATAATTGT 59.845 41.667 0.00 0.00 0.00 2.71
2102 6078 4.155099 TGTGGGTGTTCTTGCGTATAATTG 59.845 41.667 0.00 0.00 0.00 2.32
2103 6079 4.155280 GTGTGGGTGTTCTTGCGTATAATT 59.845 41.667 0.00 0.00 0.00 1.40
2104 6080 3.687698 GTGTGGGTGTTCTTGCGTATAAT 59.312 43.478 0.00 0.00 0.00 1.28
2105 6081 3.068560 GTGTGGGTGTTCTTGCGTATAA 58.931 45.455 0.00 0.00 0.00 0.98
2106 6082 2.037381 TGTGTGGGTGTTCTTGCGTATA 59.963 45.455 0.00 0.00 0.00 1.47
2107 6083 1.202710 TGTGTGGGTGTTCTTGCGTAT 60.203 47.619 0.00 0.00 0.00 3.06
2108 6084 0.178301 TGTGTGGGTGTTCTTGCGTA 59.822 50.000 0.00 0.00 0.00 4.42
2109 6085 1.078072 TGTGTGGGTGTTCTTGCGT 60.078 52.632 0.00 0.00 0.00 5.24
2110 6086 1.355210 GTGTGTGGGTGTTCTTGCG 59.645 57.895 0.00 0.00 0.00 4.85
2111 6087 0.100503 GTGTGTGTGGGTGTTCTTGC 59.899 55.000 0.00 0.00 0.00 4.01
2112 6088 1.458398 TGTGTGTGTGGGTGTTCTTG 58.542 50.000 0.00 0.00 0.00 3.02
2113 6089 2.091541 CTTGTGTGTGTGGGTGTTCTT 58.908 47.619 0.00 0.00 0.00 2.52
2114 6090 1.280710 TCTTGTGTGTGTGGGTGTTCT 59.719 47.619 0.00 0.00 0.00 3.01
2115 6091 1.745232 TCTTGTGTGTGTGGGTGTTC 58.255 50.000 0.00 0.00 0.00 3.18
2116 6092 2.435372 ATCTTGTGTGTGTGGGTGTT 57.565 45.000 0.00 0.00 0.00 3.32
2117 6093 2.435372 AATCTTGTGTGTGTGGGTGT 57.565 45.000 0.00 0.00 0.00 4.16
2118 6094 2.813754 CCTAATCTTGTGTGTGTGGGTG 59.186 50.000 0.00 0.00 0.00 4.61
2119 6095 2.224769 CCCTAATCTTGTGTGTGTGGGT 60.225 50.000 0.00 0.00 0.00 4.51
2120 6096 2.224769 ACCCTAATCTTGTGTGTGTGGG 60.225 50.000 0.00 0.00 38.13 4.61
2121 6097 3.140325 ACCCTAATCTTGTGTGTGTGG 57.860 47.619 0.00 0.00 0.00 4.17
2122 6098 6.817765 AATAACCCTAATCTTGTGTGTGTG 57.182 37.500 0.00 0.00 0.00 3.82
2123 6099 6.882678 GGTAATAACCCTAATCTTGTGTGTGT 59.117 38.462 0.00 0.00 40.21 3.72
2124 6100 7.316544 GGTAATAACCCTAATCTTGTGTGTG 57.683 40.000 0.00 0.00 40.21 3.82
2159 6135 9.258629 TGGAGTCATCTATTCCAATTGATTTTT 57.741 29.630 7.12 0.00 40.79 1.94
2160 6136 8.827832 TGGAGTCATCTATTCCAATTGATTTT 57.172 30.769 7.12 0.00 40.79 1.82
2161 6137 8.827832 TTGGAGTCATCTATTCCAATTGATTT 57.172 30.769 7.12 0.00 46.05 2.17
2169 6145 4.782691 TCTTGGTTGGAGTCATCTATTCCA 59.217 41.667 0.00 0.00 41.94 3.53
2170 6146 5.359194 TCTTGGTTGGAGTCATCTATTCC 57.641 43.478 0.00 0.00 34.56 3.01
2171 6147 6.094186 GGTTTCTTGGTTGGAGTCATCTATTC 59.906 42.308 0.00 0.00 0.00 1.75
2172 6148 5.946377 GGTTTCTTGGTTGGAGTCATCTATT 59.054 40.000 0.00 0.00 0.00 1.73
2173 6149 5.501156 GGTTTCTTGGTTGGAGTCATCTAT 58.499 41.667 0.00 0.00 0.00 1.98
2174 6150 4.263331 GGGTTTCTTGGTTGGAGTCATCTA 60.263 45.833 0.00 0.00 0.00 1.98
2175 6151 3.498661 GGGTTTCTTGGTTGGAGTCATCT 60.499 47.826 0.00 0.00 0.00 2.90
2176 6152 2.820197 GGGTTTCTTGGTTGGAGTCATC 59.180 50.000 0.00 0.00 0.00 2.92
2177 6153 2.447047 AGGGTTTCTTGGTTGGAGTCAT 59.553 45.455 0.00 0.00 0.00 3.06
2178 6154 1.850345 AGGGTTTCTTGGTTGGAGTCA 59.150 47.619 0.00 0.00 0.00 3.41
2179 6155 2.658807 AGGGTTTCTTGGTTGGAGTC 57.341 50.000 0.00 0.00 0.00 3.36
2180 6156 2.224793 GCTAGGGTTTCTTGGTTGGAGT 60.225 50.000 0.00 0.00 0.00 3.85
2181 6157 2.437413 GCTAGGGTTTCTTGGTTGGAG 58.563 52.381 0.00 0.00 0.00 3.86
2182 6158 1.074889 GGCTAGGGTTTCTTGGTTGGA 59.925 52.381 0.00 0.00 0.00 3.53
2183 6159 1.203001 TGGCTAGGGTTTCTTGGTTGG 60.203 52.381 0.00 0.00 0.00 3.77
2184 6160 2.162681 CTGGCTAGGGTTTCTTGGTTG 58.837 52.381 0.00 0.00 0.00 3.77
2185 6161 1.547901 GCTGGCTAGGGTTTCTTGGTT 60.548 52.381 0.00 0.00 0.00 3.67
2186 6162 0.038310 GCTGGCTAGGGTTTCTTGGT 59.962 55.000 0.00 0.00 0.00 3.67
2187 6163 0.681243 GGCTGGCTAGGGTTTCTTGG 60.681 60.000 0.00 0.00 0.00 3.61
2188 6164 1.026718 CGGCTGGCTAGGGTTTCTTG 61.027 60.000 0.00 0.00 0.00 3.02
2189 6165 1.299976 CGGCTGGCTAGGGTTTCTT 59.700 57.895 0.00 0.00 0.00 2.52
2190 6166 2.990479 CGGCTGGCTAGGGTTTCT 59.010 61.111 0.00 0.00 0.00 2.52
2191 6167 2.824489 GCGGCTGGCTAGGGTTTC 60.824 66.667 0.00 0.00 39.11 2.78
2192 6168 4.426313 GGCGGCTGGCTAGGGTTT 62.426 66.667 12.72 0.00 42.94 3.27
2205 6181 2.673687 TTTTTGGGTAGGCGGCGG 60.674 61.111 9.78 0.00 0.00 6.13
2206 6182 2.874751 CTTTTTGGGTAGGCGGCG 59.125 61.111 0.51 0.51 0.00 6.46
2207 6183 0.678684 TAGCTTTTTGGGTAGGCGGC 60.679 55.000 0.00 0.00 0.00 6.53
2208 6184 1.379527 CTAGCTTTTTGGGTAGGCGG 58.620 55.000 0.00 0.00 34.71 6.13
2209 6185 1.379527 CCTAGCTTTTTGGGTAGGCG 58.620 55.000 0.00 0.00 46.09 5.52
2212 6188 4.019231 AGAGGAACCTAGCTTTTTGGGTAG 60.019 45.833 0.00 0.00 37.14 3.18
2213 6189 3.914435 AGAGGAACCTAGCTTTTTGGGTA 59.086 43.478 0.00 0.00 0.00 3.69
2214 6190 2.716969 AGAGGAACCTAGCTTTTTGGGT 59.283 45.455 0.00 0.00 0.00 4.51
2215 6191 3.084786 CAGAGGAACCTAGCTTTTTGGG 58.915 50.000 0.00 0.00 0.00 4.12
2216 6192 2.489722 GCAGAGGAACCTAGCTTTTTGG 59.510 50.000 0.00 0.00 0.00 3.28
2217 6193 2.489722 GGCAGAGGAACCTAGCTTTTTG 59.510 50.000 14.32 0.00 0.00 2.44
2218 6194 2.376855 AGGCAGAGGAACCTAGCTTTTT 59.623 45.455 14.32 0.00 33.38 1.94
2219 6195 1.988846 AGGCAGAGGAACCTAGCTTTT 59.011 47.619 14.32 0.00 33.38 2.27
2220 6196 1.557371 GAGGCAGAGGAACCTAGCTTT 59.443 52.381 14.32 6.45 36.05 3.51
2221 6197 1.199615 GAGGCAGAGGAACCTAGCTT 58.800 55.000 14.32 9.07 36.05 3.74
2222 6198 0.689412 GGAGGCAGAGGAACCTAGCT 60.689 60.000 14.32 0.00 36.05 3.32
2223 6199 1.691195 GGGAGGCAGAGGAACCTAGC 61.691 65.000 8.60 8.60 36.05 3.42
2224 6200 1.395826 CGGGAGGCAGAGGAACCTAG 61.396 65.000 0.00 0.00 36.05 3.02
2225 6201 1.381327 CGGGAGGCAGAGGAACCTA 60.381 63.158 0.00 0.00 36.05 3.08
2226 6202 2.685380 CGGGAGGCAGAGGAACCT 60.685 66.667 0.00 0.00 39.65 3.50
2227 6203 3.003763 ACGGGAGGCAGAGGAACC 61.004 66.667 0.00 0.00 0.00 3.62
2228 6204 2.579738 GACGGGAGGCAGAGGAAC 59.420 66.667 0.00 0.00 38.26 3.62
2229 6205 3.068691 CGACGGGAGGCAGAGGAA 61.069 66.667 0.00 0.00 38.29 3.36
2268 6244 1.221021 CCCTAAGGCCACGGAAGAC 59.779 63.158 5.01 0.00 0.00 3.01
2269 6245 1.229400 ACCCTAAGGCCACGGAAGA 60.229 57.895 5.01 0.00 36.11 2.87
2270 6246 3.400188 ACCCTAAGGCCACGGAAG 58.600 61.111 5.01 0.00 36.11 3.46


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

AutoCloner maintained by Alex Coulton.