Multiple sequence alignment - TraesCS3A01G129300

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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 TraesCS3A01G129300 chr3A 100.000 2750 0 0 1 2750 106658980 106661729 0.000000e+00 5079
1 TraesCS3A01G129300 chr3A 81.159 276 47 5 1974 2247 106674408 106674680 1.660000e-52 217
2 TraesCS3A01G129300 chr3A 96.825 126 3 1 1846 1970 106660703 106660828 2.780000e-50 209
3 TraesCS3A01G129300 chr3A 96.825 126 3 1 1724 1849 106660825 106660949 2.780000e-50 209
4 TraesCS3A01G129300 chr3A 86.885 122 16 0 2629 2750 106677202 106677323 1.330000e-28 137
5 TraesCS3A01G129300 chr3D 88.184 1718 118 50 186 1849 90371075 90372761 0.000000e+00 1969
6 TraesCS3A01G129300 chr3D 92.850 937 34 8 1846 2750 90372638 90373573 0.000000e+00 1328
7 TraesCS3A01G129300 chr3D 90.164 122 12 0 2629 2750 90380072 90380193 2.830000e-35 159
8 TraesCS3A01G129300 chr3D 88.148 135 13 3 1974 2107 90379323 90379455 1.020000e-34 158
9 TraesCS3A01G129300 chr3D 92.308 78 6 0 1 78 90370955 90371032 8.050000e-21 111
10 TraesCS3A01G129300 chr3B 92.402 1066 53 14 805 1849 139777048 139778106 0.000000e+00 1495
11 TraesCS3A01G129300 chr3B 93.435 914 44 9 1846 2750 139777987 139778893 0.000000e+00 1341
12 TraesCS3A01G129300 chr3B 88.906 640 61 7 186 819 139776291 139776926 0.000000e+00 780
13 TraesCS3A01G129300 chr3B 78.081 844 113 32 1974 2750 139832097 139832935 4.150000e-128 468
14 TraesCS3A01G129300 chr4D 90.000 80 8 0 2649 2728 10835265 10835186 1.350000e-18 104
15 TraesCS3A01G129300 chr4B 89.157 83 9 0 2649 2731 20361228 20361146 1.350000e-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 TraesCS3A01G129300 chr3A 106658980 106661729 2749 False 1832.333333 5079 97.883333 1 2750 3 chr3A.!!$F1 2749
1 TraesCS3A01G129300 chr3D 90370955 90373573 2618 False 1136.000000 1969 91.114000 1 2750 3 chr3D.!!$F1 2749
2 TraesCS3A01G129300 chr3B 139776291 139778893 2602 False 1205.333333 1495 91.581000 186 2750 3 chr3B.!!$F2 2564
3 TraesCS3A01G129300 chr3B 139832097 139832935 838 False 468.000000 468 78.081000 1974 2750 1 chr3B.!!$F1 776

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
175 176 0.320374 CAGGGAACGTCAGCCAGTTA 59.68 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2319 0.179089 CTTCCGTGGCCTCTGATCAG 60.179 60.0 17.07 17.07 0.0 2.9 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
40 41 5.392767 TCGCTGTTGAGAAGAGTAAGAAT 57.607 39.130 0.00 0.00 0.00 2.40
42 43 5.184096 TCGCTGTTGAGAAGAGTAAGAATCT 59.816 40.000 0.00 0.00 0.00 2.40
53 54 8.487313 GAAGAGTAAGAATCTTCTTCTTTCCC 57.513 38.462 17.33 6.92 46.01 3.97
61 62 7.694093 AGAATCTTCTTCTTTCCCTGTAATGT 58.306 34.615 0.00 0.00 32.55 2.71
65 66 7.612677 TCTTCTTCTTTCCCTGTAATGTAGAC 58.387 38.462 0.00 0.00 0.00 2.59
78 79 8.633561 CCTGTAATGTAGACTATGTCTGATCAA 58.366 37.037 10.14 0.00 43.30 2.57
82 83 8.899427 AATGTAGACTATGTCTGATCAAATGG 57.101 34.615 10.14 0.00 43.30 3.16
83 84 7.423844 TGTAGACTATGTCTGATCAAATGGT 57.576 36.000 10.14 0.00 43.30 3.55
84 85 7.267857 TGTAGACTATGTCTGATCAAATGGTG 58.732 38.462 10.14 0.00 43.30 4.17
85 86 6.305272 AGACTATGTCTGATCAAATGGTGT 57.695 37.500 0.00 0.00 41.76 4.16
86 87 6.715280 AGACTATGTCTGATCAAATGGTGTT 58.285 36.000 0.00 0.00 41.76 3.32
87 88 6.596888 AGACTATGTCTGATCAAATGGTGTTG 59.403 38.462 0.00 0.00 41.76 3.33
88 89 6.240894 ACTATGTCTGATCAAATGGTGTTGT 58.759 36.000 0.00 0.00 0.00 3.32
89 90 6.716628 ACTATGTCTGATCAAATGGTGTTGTT 59.283 34.615 0.00 0.00 0.00 2.83
90 91 7.882791 ACTATGTCTGATCAAATGGTGTTGTTA 59.117 33.333 0.00 0.00 0.00 2.41
91 92 7.707624 ATGTCTGATCAAATGGTGTTGTTAT 57.292 32.000 0.00 0.00 0.00 1.89
92 93 6.912082 TGTCTGATCAAATGGTGTTGTTATG 58.088 36.000 0.00 0.00 0.00 1.90
93 94 5.801947 GTCTGATCAAATGGTGTTGTTATGC 59.198 40.000 0.00 0.00 0.00 3.14
94 95 4.731720 TGATCAAATGGTGTTGTTATGCG 58.268 39.130 0.00 0.00 0.00 4.73
96 97 4.837896 TCAAATGGTGTTGTTATGCGAA 57.162 36.364 0.00 0.00 0.00 4.70
97 98 5.188327 TCAAATGGTGTTGTTATGCGAAA 57.812 34.783 0.00 0.00 0.00 3.46
98 99 5.592054 TCAAATGGTGTTGTTATGCGAAAA 58.408 33.333 0.00 0.00 0.00 2.29
99 100 6.219473 TCAAATGGTGTTGTTATGCGAAAAT 58.781 32.000 0.00 0.00 0.00 1.82
103 104 3.987220 GGTGTTGTTATGCGAAAATTGCT 59.013 39.130 0.00 0.00 0.00 3.91
105 106 5.060446 GGTGTTGTTATGCGAAAATTGCTAC 59.940 40.000 0.00 0.00 0.00 3.58
107 108 4.671880 TGTTATGCGAAAATTGCTACGT 57.328 36.364 0.00 0.00 0.00 3.57
108 109 4.399112 TGTTATGCGAAAATTGCTACGTG 58.601 39.130 0.00 0.00 0.00 4.49
109 110 4.083749 TGTTATGCGAAAATTGCTACGTGT 60.084 37.500 0.00 0.00 0.00 4.49
110 111 2.308347 TGCGAAAATTGCTACGTGTG 57.692 45.000 0.00 0.00 0.00 3.82
111 112 1.867865 TGCGAAAATTGCTACGTGTGA 59.132 42.857 0.00 0.00 0.00 3.58
114 115 3.424302 GCGAAAATTGCTACGTGTGATCA 60.424 43.478 0.00 0.00 0.00 2.92
115 116 4.727734 GCGAAAATTGCTACGTGTGATCAT 60.728 41.667 0.00 0.00 0.00 2.45
116 117 4.725280 CGAAAATTGCTACGTGTGATCATG 59.275 41.667 0.00 0.00 36.71 3.07
118 119 6.441093 AAAATTGCTACGTGTGATCATGAT 57.559 33.333 8.25 8.25 34.90 2.45
119 120 5.663795 AATTGCTACGTGTGATCATGATC 57.336 39.130 25.91 25.91 38.29 2.92
120 121 3.799281 TGCTACGTGTGATCATGATCA 57.201 42.857 30.27 30.27 44.83 2.92
129 130 2.989909 TGATCATGATCAAACGGCTGT 58.010 42.857 31.46 0.00 44.14 4.40
130 131 2.679336 TGATCATGATCAAACGGCTGTG 59.321 45.455 31.46 0.00 44.14 3.66
131 132 0.804364 TCATGATCAAACGGCTGTGC 59.196 50.000 0.00 0.00 0.00 4.57
132 133 0.521867 CATGATCAAACGGCTGTGCG 60.522 55.000 0.00 0.00 0.00 5.34
133 134 1.647545 ATGATCAAACGGCTGTGCGG 61.648 55.000 0.00 0.00 35.02 5.69
134 135 3.039202 GATCAAACGGCTGTGCGGG 62.039 63.158 0.00 0.00 33.14 6.13
168 169 2.982130 CCTCCCAGGGAACGTCAG 59.018 66.667 10.32 0.00 0.00 3.51
169 170 2.266055 CTCCCAGGGAACGTCAGC 59.734 66.667 10.32 0.00 0.00 4.26
170 171 3.316573 CTCCCAGGGAACGTCAGCC 62.317 68.421 10.32 0.00 0.00 4.85
171 172 3.636231 CCCAGGGAACGTCAGCCA 61.636 66.667 0.00 0.00 0.00 4.75
172 173 2.046892 CCAGGGAACGTCAGCCAG 60.047 66.667 0.00 0.00 0.00 4.85
173 174 2.743718 CAGGGAACGTCAGCCAGT 59.256 61.111 0.00 0.00 0.00 4.00
174 175 1.071471 CAGGGAACGTCAGCCAGTT 59.929 57.895 0.00 0.00 0.00 3.16
175 176 0.320374 CAGGGAACGTCAGCCAGTTA 59.680 55.000 0.00 0.00 0.00 2.24
176 177 1.053424 AGGGAACGTCAGCCAGTTAA 58.947 50.000 0.00 0.00 0.00 2.01
177 178 1.154197 GGGAACGTCAGCCAGTTAAC 58.846 55.000 0.00 0.00 0.00 2.01
178 179 1.541670 GGGAACGTCAGCCAGTTAACA 60.542 52.381 8.61 0.00 0.00 2.41
179 180 2.423577 GGAACGTCAGCCAGTTAACAT 58.576 47.619 8.61 0.00 0.00 2.71
180 181 2.812011 GGAACGTCAGCCAGTTAACATT 59.188 45.455 8.61 0.00 0.00 2.71
181 182 3.998341 GGAACGTCAGCCAGTTAACATTA 59.002 43.478 8.61 0.00 0.00 1.90
182 183 4.142966 GGAACGTCAGCCAGTTAACATTAC 60.143 45.833 8.61 0.00 0.00 1.89
183 184 3.332034 ACGTCAGCCAGTTAACATTACC 58.668 45.455 8.61 0.00 0.00 2.85
184 185 2.347452 CGTCAGCCAGTTAACATTACCG 59.653 50.000 8.61 0.00 0.00 4.02
225 226 7.343357 TCTGAACTTTCCTCTTTTAACCTTGA 58.657 34.615 0.00 0.00 0.00 3.02
251 252 5.127194 GTGTGTAGAGATTAGGACATCCACA 59.873 44.000 0.00 0.00 38.89 4.17
272 273 6.094048 CCACAGTGGAAATAAATGACGAATCT 59.906 38.462 15.35 0.00 40.96 2.40
302 303 1.276138 CCATTCCAAAAGGCCAAGGTC 59.724 52.381 5.01 0.00 0.00 3.85
308 309 2.586425 CAAAAGGCCAAGGTCAGAGAA 58.414 47.619 5.01 0.00 0.00 2.87
309 327 2.555757 CAAAAGGCCAAGGTCAGAGAAG 59.444 50.000 5.01 0.00 0.00 2.85
326 344 4.096984 AGAGAAGAACAACAGTTTGGCTTG 59.903 41.667 0.00 0.00 37.00 4.01
335 353 2.689983 ACAGTTTGGCTTGTCTCTTTGG 59.310 45.455 0.00 0.00 0.00 3.28
339 357 1.032014 TGGCTTGTCTCTTTGGTTGC 58.968 50.000 0.00 0.00 0.00 4.17
342 360 1.000938 GCTTGTCTCTTTGGTTGCCAG 60.001 52.381 0.00 0.00 33.81 4.85
347 367 1.064758 TCTCTTTGGTTGCCAGTGTGT 60.065 47.619 0.00 0.00 33.81 3.72
350 370 1.682854 CTTTGGTTGCCAGTGTGTCAT 59.317 47.619 0.00 0.00 33.81 3.06
357 377 2.497138 TGCCAGTGTGTCATTTCTCTG 58.503 47.619 0.00 0.00 0.00 3.35
367 387 7.879677 AGTGTGTCATTTCTCTGATGTATGAAA 59.120 33.333 0.00 0.00 33.74 2.69
371 391 8.606602 TGTCATTTCTCTGATGTATGAAATTCG 58.393 33.333 0.00 0.00 37.12 3.34
376 396 9.869757 TTTCTCTGATGTATGAAATTCGACTTA 57.130 29.630 0.00 0.00 0.00 2.24
381 404 9.478019 CTGATGTATGAAATTCGACTTAACAAC 57.522 33.333 0.00 0.00 0.00 3.32
392 415 7.830940 TTCGACTTAACAACTAAAACTGACA 57.169 32.000 0.00 0.00 0.00 3.58
396 419 7.042321 CGACTTAACAACTAAAACTGACATGGA 60.042 37.037 0.00 0.00 0.00 3.41
429 452 3.737850 GCAGATTGAGATAGAGTTGGGG 58.262 50.000 0.00 0.00 0.00 4.96
533 556 4.944372 CCGTAGCGACCGCATCCC 62.944 72.222 16.97 0.51 44.88 3.85
550 573 3.202829 TCCCGTTGCTCTACTTTGTTT 57.797 42.857 0.00 0.00 0.00 2.83
551 574 3.135994 TCCCGTTGCTCTACTTTGTTTC 58.864 45.455 0.00 0.00 0.00 2.78
572 596 4.915704 TCCGCTGTTGTTTAAAACTTCAG 58.084 39.130 0.00 0.00 36.59 3.02
583 607 7.271511 TGTTTAAAACTTCAGAACCAATGCAT 58.728 30.769 0.00 0.00 0.00 3.96
621 645 7.558444 TGTGTCCCTGTTTAACTTGTATTTTCT 59.442 33.333 0.00 0.00 0.00 2.52
657 681 3.754850 TGTGAACTCTTTGGCAGATGATG 59.245 43.478 0.00 0.00 0.00 3.07
678 702 0.881118 ATCTGTTCCGCGTGCATTTT 59.119 45.000 4.92 0.00 0.00 1.82
679 703 0.665835 TCTGTTCCGCGTGCATTTTT 59.334 45.000 4.92 0.00 0.00 1.94
725 762 1.512926 ATCTTTTTCGCGTGTGCTCT 58.487 45.000 5.77 0.00 39.65 4.09
727 764 0.993746 CTTTTTCGCGTGTGCTCTGC 60.994 55.000 5.77 0.00 39.65 4.26
735 772 1.968540 GTGTGCTCTGCTTGGTCCC 60.969 63.158 0.00 0.00 0.00 4.46
761 802 5.597806 TCTGGTGGCTCTACGTTTATAATG 58.402 41.667 0.00 0.00 0.00 1.90
770 811 7.850982 GGCTCTACGTTTATAATGTTGTTGATG 59.149 37.037 0.00 0.00 0.00 3.07
802 843 3.455685 GCAAATGCAAGCGCTGTC 58.544 55.556 12.58 6.43 41.59 3.51
841 1018 3.891366 AGTTTGGAATGTGAAAGTCTGGG 59.109 43.478 0.00 0.00 0.00 4.45
982 1161 4.596311 TGCACAGCAGATACACGG 57.404 55.556 0.00 0.00 33.32 4.94
989 1168 2.271800 CAGCAGATACACGGGAGAAAC 58.728 52.381 0.00 0.00 0.00 2.78
1430 1625 3.181467 CCTCTAGCTGCTCTGCTATTGTT 60.181 47.826 4.91 0.00 43.54 2.83
1456 1653 1.915489 ACATCAGCCATGGACCAAGTA 59.085 47.619 18.40 0.00 36.72 2.24
1458 1655 3.144506 CATCAGCCATGGACCAAGTATC 58.855 50.000 18.40 0.00 0.00 2.24
1468 1665 6.405065 CCATGGACCAAGTATCAGAAATGTTG 60.405 42.308 5.56 0.00 0.00 3.33
1471 1668 6.016360 TGGACCAAGTATCAGAAATGTTGTTG 60.016 38.462 0.00 0.00 0.00 3.33
1472 1669 5.772521 ACCAAGTATCAGAAATGTTGTTGC 58.227 37.500 0.00 0.00 0.00 4.17
1473 1670 5.536161 ACCAAGTATCAGAAATGTTGTTGCT 59.464 36.000 0.00 0.00 0.00 3.91
1483 1682 1.360192 GTTGTTGCTGTGCAGGTCC 59.640 57.895 1.11 0.00 40.61 4.46
1498 1697 3.055819 GCAGGTCCTACATCAAGTCTGAA 60.056 47.826 0.00 0.00 34.49 3.02
1501 1700 3.196685 GGTCCTACATCAAGTCTGAAGCT 59.803 47.826 0.00 0.00 34.49 3.74
1525 1724 3.898123 TGCTGAGGATAATGGAGTACCTC 59.102 47.826 0.00 0.00 44.90 3.85
1596 1795 1.599071 AGCTCAATTCACACACACACG 59.401 47.619 0.00 0.00 0.00 4.49
1646 1852 3.438781 TGCAAACTACTAATTCTTGGCGG 59.561 43.478 0.00 0.00 0.00 6.13
1754 1960 4.625028 TCATGCGAGATACTCTGAATTGG 58.375 43.478 0.00 0.00 0.00 3.16
1759 1965 3.126831 GAGATACTCTGAATTGGTGCCG 58.873 50.000 0.00 0.00 0.00 5.69
1765 1971 1.209261 TCTGAATTGGTGCCGCAGATA 59.791 47.619 0.00 0.00 31.24 1.98
1766 1972 2.016318 CTGAATTGGTGCCGCAGATAA 58.984 47.619 0.00 0.00 0.00 1.75
1767 1973 2.016318 TGAATTGGTGCCGCAGATAAG 58.984 47.619 0.00 0.00 0.00 1.73
1768 1974 0.740737 AATTGGTGCCGCAGATAAGC 59.259 50.000 0.00 0.00 0.00 3.09
1769 1975 0.394216 ATTGGTGCCGCAGATAAGCA 60.394 50.000 0.00 0.00 0.00 3.91
1772 1978 2.989639 TGCCGCAGATAAGCACCT 59.010 55.556 0.00 0.00 0.00 4.00
1773 1979 1.153369 TGCCGCAGATAAGCACCTC 60.153 57.895 0.00 0.00 0.00 3.85
1774 1980 1.153369 GCCGCAGATAAGCACCTCA 60.153 57.895 0.00 0.00 0.00 3.86
1775 1981 1.156645 GCCGCAGATAAGCACCTCAG 61.157 60.000 0.00 0.00 0.00 3.35
1776 1982 0.176680 CCGCAGATAAGCACCTCAGT 59.823 55.000 0.00 0.00 0.00 3.41
1786 1992 3.319135 CACCTCAGTGCTCTTGCTT 57.681 52.632 0.00 0.00 37.14 3.91
1787 1993 2.462456 CACCTCAGTGCTCTTGCTTA 57.538 50.000 0.00 0.00 37.14 3.09
1788 1994 2.983229 CACCTCAGTGCTCTTGCTTAT 58.017 47.619 0.00 0.00 37.14 1.73
1789 1995 4.128925 CACCTCAGTGCTCTTGCTTATA 57.871 45.455 0.00 0.00 37.14 0.98
1790 1996 4.118410 CACCTCAGTGCTCTTGCTTATAG 58.882 47.826 0.00 0.00 37.14 1.31
1791 1997 3.772025 ACCTCAGTGCTCTTGCTTATAGT 59.228 43.478 0.00 0.00 40.48 2.12
1792 1998 4.956700 ACCTCAGTGCTCTTGCTTATAGTA 59.043 41.667 0.00 0.00 40.48 1.82
1793 1999 5.600484 ACCTCAGTGCTCTTGCTTATAGTAT 59.400 40.000 0.00 0.00 40.48 2.12
1794 2000 6.098982 ACCTCAGTGCTCTTGCTTATAGTATT 59.901 38.462 0.00 0.00 40.48 1.89
1795 2001 7.287927 ACCTCAGTGCTCTTGCTTATAGTATTA 59.712 37.037 0.00 0.00 40.48 0.98
1796 2002 8.310382 CCTCAGTGCTCTTGCTTATAGTATTAT 58.690 37.037 0.00 0.00 40.48 1.28
1821 2027 7.083062 AGATAGAAGAATGGCCATACATTGA 57.917 36.000 21.15 4.08 40.92 2.57
1822 2028 7.166851 AGATAGAAGAATGGCCATACATTGAG 58.833 38.462 21.15 0.00 40.92 3.02
1823 2029 5.378230 AGAAGAATGGCCATACATTGAGA 57.622 39.130 21.15 0.00 40.92 3.27
1824 2030 5.759059 AGAAGAATGGCCATACATTGAGAA 58.241 37.500 21.15 0.00 40.92 2.87
1825 2031 5.826737 AGAAGAATGGCCATACATTGAGAAG 59.173 40.000 21.15 0.00 40.92 2.85
1826 2032 5.121380 AGAATGGCCATACATTGAGAAGT 57.879 39.130 21.15 0.00 40.92 3.01
1827 2033 5.513233 AGAATGGCCATACATTGAGAAGTT 58.487 37.500 21.15 0.00 40.92 2.66
1828 2034 5.359009 AGAATGGCCATACATTGAGAAGTTG 59.641 40.000 21.15 0.00 40.92 3.16
1829 2035 4.032960 TGGCCATACATTGAGAAGTTGT 57.967 40.909 0.00 0.00 0.00 3.32
1830 2036 5.172687 TGGCCATACATTGAGAAGTTGTA 57.827 39.130 0.00 0.00 0.00 2.41
1831 2037 5.185454 TGGCCATACATTGAGAAGTTGTAG 58.815 41.667 0.00 0.00 30.03 2.74
1832 2038 4.576463 GGCCATACATTGAGAAGTTGTAGG 59.424 45.833 0.00 0.00 30.03 3.18
1833 2039 4.035675 GCCATACATTGAGAAGTTGTAGGC 59.964 45.833 0.00 0.00 35.28 3.93
1834 2040 5.185454 CCATACATTGAGAAGTTGTAGGCA 58.815 41.667 0.00 0.00 30.03 4.75
1835 2041 5.824624 CCATACATTGAGAAGTTGTAGGCAT 59.175 40.000 0.00 0.00 30.03 4.40
1836 2042 6.238566 CCATACATTGAGAAGTTGTAGGCATG 60.239 42.308 0.00 0.00 30.03 4.06
1837 2043 4.910195 ACATTGAGAAGTTGTAGGCATGA 58.090 39.130 0.00 0.00 0.00 3.07
1838 2044 4.697352 ACATTGAGAAGTTGTAGGCATGAC 59.303 41.667 0.00 0.00 0.00 3.06
1839 2045 4.350368 TTGAGAAGTTGTAGGCATGACA 57.650 40.909 0.00 0.00 0.00 3.58
1840 2046 3.930336 TGAGAAGTTGTAGGCATGACAG 58.070 45.455 0.00 0.00 0.00 3.51
1841 2047 3.578282 TGAGAAGTTGTAGGCATGACAGA 59.422 43.478 0.00 0.00 0.00 3.41
1842 2048 4.223700 TGAGAAGTTGTAGGCATGACAGAT 59.776 41.667 0.00 0.00 0.00 2.90
1843 2049 5.422012 TGAGAAGTTGTAGGCATGACAGATA 59.578 40.000 0.00 0.00 0.00 1.98
1844 2050 6.098838 TGAGAAGTTGTAGGCATGACAGATAT 59.901 38.462 0.00 0.00 0.00 1.63
1845 2051 6.286758 AGAAGTTGTAGGCATGACAGATATG 58.713 40.000 0.00 0.00 0.00 1.78
1846 2052 5.876651 AGTTGTAGGCATGACAGATATGA 57.123 39.130 0.00 0.00 0.00 2.15
1847 2053 5.851720 AGTTGTAGGCATGACAGATATGAG 58.148 41.667 0.00 0.00 0.00 2.90
1848 2054 5.600069 AGTTGTAGGCATGACAGATATGAGA 59.400 40.000 0.00 0.00 0.00 3.27
1849 2055 5.459536 TGTAGGCATGACAGATATGAGAC 57.540 43.478 0.00 0.00 0.00 3.36
1850 2056 4.895297 TGTAGGCATGACAGATATGAGACA 59.105 41.667 0.00 0.00 0.00 3.41
1851 2057 4.603989 AGGCATGACAGATATGAGACAG 57.396 45.455 0.00 0.00 0.00 3.51
1852 2058 4.221530 AGGCATGACAGATATGAGACAGA 58.778 43.478 0.00 0.00 0.00 3.41
1853 2059 4.652881 AGGCATGACAGATATGAGACAGAA 59.347 41.667 0.00 0.00 0.00 3.02
1854 2060 5.307456 AGGCATGACAGATATGAGACAGAAT 59.693 40.000 0.00 0.00 0.00 2.40
1855 2061 5.638657 GGCATGACAGATATGAGACAGAATC 59.361 44.000 0.00 0.00 0.00 2.52
1856 2062 6.221659 GCATGACAGATATGAGACAGAATCA 58.778 40.000 0.00 0.00 0.00 2.57
1857 2063 6.874664 GCATGACAGATATGAGACAGAATCAT 59.125 38.462 0.00 0.00 40.45 2.45
1858 2064 7.148557 GCATGACAGATATGAGACAGAATCATG 60.149 40.741 0.00 8.24 41.56 3.07
1859 2065 6.221659 TGACAGATATGAGACAGAATCATGC 58.778 40.000 0.00 0.00 37.91 4.06
1860 2066 5.228665 ACAGATATGAGACAGAATCATGCG 58.771 41.667 0.00 0.00 37.91 4.73
1861 2067 5.010415 ACAGATATGAGACAGAATCATGCGA 59.990 40.000 0.00 0.00 37.91 5.10
1862 2068 5.573669 CAGATATGAGACAGAATCATGCGAG 59.426 44.000 0.00 0.00 37.91 5.03
1863 2069 5.476254 AGATATGAGACAGAATCATGCGAGA 59.524 40.000 0.00 0.00 37.91 4.04
1864 2070 4.603989 ATGAGACAGAATCATGCGAGAT 57.396 40.909 0.00 0.00 36.07 2.75
1865 2071 5.718724 ATGAGACAGAATCATGCGAGATA 57.281 39.130 0.00 0.00 36.07 1.98
1866 2072 4.864633 TGAGACAGAATCATGCGAGATAC 58.135 43.478 0.00 0.00 0.00 2.24
1867 2073 4.582240 TGAGACAGAATCATGCGAGATACT 59.418 41.667 0.00 0.00 0.00 2.12
1868 2074 5.119931 AGACAGAATCATGCGAGATACTC 57.880 43.478 0.00 0.00 0.00 2.59
1869 2075 4.826733 AGACAGAATCATGCGAGATACTCT 59.173 41.667 0.00 0.00 0.00 3.24
1870 2076 4.869215 ACAGAATCATGCGAGATACTCTG 58.131 43.478 13.88 13.88 38.19 3.35
1871 2077 4.582240 ACAGAATCATGCGAGATACTCTGA 59.418 41.667 18.92 0.00 36.00 3.27
1872 2078 5.068329 ACAGAATCATGCGAGATACTCTGAA 59.932 40.000 18.92 0.00 36.00 3.02
1873 2079 6.157904 CAGAATCATGCGAGATACTCTGAAT 58.842 40.000 11.56 0.00 36.00 2.57
1874 2080 6.645827 CAGAATCATGCGAGATACTCTGAATT 59.354 38.462 11.56 0.00 36.00 2.17
1875 2081 6.645827 AGAATCATGCGAGATACTCTGAATTG 59.354 38.462 0.00 0.00 0.00 2.32
1876 2082 5.520376 TCATGCGAGATACTCTGAATTGA 57.480 39.130 0.00 0.00 0.00 2.57
1877 2083 6.094193 TCATGCGAGATACTCTGAATTGAT 57.906 37.500 0.00 0.00 0.00 2.57
1878 2084 5.924825 TCATGCGAGATACTCTGAATTGATG 59.075 40.000 0.00 0.00 0.00 3.07
1879 2085 4.053983 TGCGAGATACTCTGAATTGATGC 58.946 43.478 0.00 0.00 0.00 3.91
1880 2086 3.431572 GCGAGATACTCTGAATTGATGCC 59.568 47.826 0.00 0.00 0.00 4.40
1881 2087 3.672397 CGAGATACTCTGAATTGATGCCG 59.328 47.826 0.00 0.00 0.00 5.69
1882 2088 3.397482 AGATACTCTGAATTGATGCCGC 58.603 45.455 0.00 0.00 0.00 6.53
1883 2089 2.689553 TACTCTGAATTGATGCCGCA 57.310 45.000 0.00 0.00 0.00 5.69
1884 2090 1.376543 ACTCTGAATTGATGCCGCAG 58.623 50.000 0.00 0.00 0.00 5.18
1885 2091 1.065926 ACTCTGAATTGATGCCGCAGA 60.066 47.619 0.00 0.00 34.71 4.26
1886 2092 2.219458 CTCTGAATTGATGCCGCAGAT 58.781 47.619 0.00 0.00 35.32 2.90
1887 2093 3.181462 ACTCTGAATTGATGCCGCAGATA 60.181 43.478 0.00 0.00 35.32 1.98
2030 2239 1.283029 ACTACTACCCTGCCTCACGTA 59.717 52.381 0.00 0.00 0.00 3.57
2042 2251 0.663688 CTCACGTAGCGCTCACCTAT 59.336 55.000 16.34 0.00 0.00 2.57
2095 2305 2.412870 TGTCCAAGCACTATGTTCACG 58.587 47.619 0.00 0.00 0.00 4.35
2108 2318 0.318784 GTTCACGACGGAGAGCACTT 60.319 55.000 0.00 0.00 0.00 3.16
2109 2319 0.039437 TTCACGACGGAGAGCACTTC 60.039 55.000 0.00 0.00 0.00 3.01
2110 2320 0.889638 TCACGACGGAGAGCACTTCT 60.890 55.000 0.00 0.00 39.43 2.85
2122 2332 0.251354 GCACTTCTGATCAGAGGCCA 59.749 55.000 29.18 13.62 37.99 5.36
2158 2368 3.883744 CTTCACCTTGCCCGCGACT 62.884 63.158 8.23 0.00 0.00 4.18
2248 2458 1.272425 TGGAGAAAAATCCCGTGGCAT 60.272 47.619 0.00 0.00 38.72 4.40
2320 2530 2.423373 CCCCCGGATGTTGATGAATCTT 60.423 50.000 0.73 0.00 0.00 2.40
2354 2564 1.331214 CACACCACCTTCCTGCAAAT 58.669 50.000 0.00 0.00 0.00 2.32
2464 2702 3.181469 GGGCAATAGAACTGGTCGATGTA 60.181 47.826 0.00 0.00 0.00 2.29
2499 2737 2.289072 ACTTCAGTCATGTTGAGGTCCG 60.289 50.000 10.36 0.00 30.07 4.79
2569 2808 9.928618 TCATAACATCATATAAGTTTGGGGAAA 57.071 29.630 0.00 0.00 0.00 3.13
2616 2881 4.394729 TGGGTTGGTATCTTTGAACTGAC 58.605 43.478 0.00 0.00 0.00 3.51
2731 3016 4.906618 ACTGTAATTCTTTCCACCATCGT 58.093 39.130 0.00 0.00 0.00 3.73
2733 3018 5.768164 ACTGTAATTCTTTCCACCATCGTTT 59.232 36.000 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 7.455008 AGTCTACATTACAGGGAAAGAAGAAGA 59.545 37.037 0.00 0.00 0.00 2.87
42 43 7.554959 AGTCTACATTACAGGGAAAGAAGAA 57.445 36.000 0.00 0.00 0.00 2.52
61 62 7.423844 ACACCATTTGATCAGACATAGTCTA 57.576 36.000 0.00 0.00 41.37 2.59
65 66 6.748333 ACAACACCATTTGATCAGACATAG 57.252 37.500 0.00 0.00 0.00 2.23
78 79 5.107143 GCAATTTTCGCATAACAACACCATT 60.107 36.000 0.00 0.00 0.00 3.16
81 82 3.987220 AGCAATTTTCGCATAACAACACC 59.013 39.130 0.00 0.00 0.00 4.16
82 83 5.219768 CGTAGCAATTTTCGCATAACAACAC 60.220 40.000 0.00 0.00 0.00 3.32
83 84 4.848841 CGTAGCAATTTTCGCATAACAACA 59.151 37.500 0.00 0.00 0.00 3.33
84 85 4.849383 ACGTAGCAATTTTCGCATAACAAC 59.151 37.500 0.00 0.00 0.00 3.32
85 86 4.848841 CACGTAGCAATTTTCGCATAACAA 59.151 37.500 0.00 0.00 0.00 2.83
86 87 4.083749 ACACGTAGCAATTTTCGCATAACA 60.084 37.500 0.00 0.00 0.00 2.41
87 88 4.259734 CACACGTAGCAATTTTCGCATAAC 59.740 41.667 0.00 0.00 0.00 1.89
88 89 4.152580 TCACACGTAGCAATTTTCGCATAA 59.847 37.500 0.00 0.00 0.00 1.90
89 90 3.680458 TCACACGTAGCAATTTTCGCATA 59.320 39.130 0.00 0.00 0.00 3.14
90 91 2.482336 TCACACGTAGCAATTTTCGCAT 59.518 40.909 0.00 0.00 0.00 4.73
91 92 1.867865 TCACACGTAGCAATTTTCGCA 59.132 42.857 0.00 0.00 0.00 5.10
92 93 2.587612 TCACACGTAGCAATTTTCGC 57.412 45.000 0.00 0.00 0.00 4.70
93 94 4.320667 TGATCACACGTAGCAATTTTCG 57.679 40.909 0.00 0.00 0.00 3.46
94 95 5.868257 TCATGATCACACGTAGCAATTTTC 58.132 37.500 0.00 0.00 0.00 2.29
96 97 5.585844 TGATCATGATCACACGTAGCAATTT 59.414 36.000 30.27 0.00 42.42 1.82
97 98 5.118286 TGATCATGATCACACGTAGCAATT 58.882 37.500 30.27 0.00 42.42 2.32
98 99 4.696455 TGATCATGATCACACGTAGCAAT 58.304 39.130 30.27 0.00 42.42 3.56
99 100 4.122143 TGATCATGATCACACGTAGCAA 57.878 40.909 30.27 7.52 42.42 3.91
107 108 2.679336 CAGCCGTTTGATCATGATCACA 59.321 45.455 33.02 25.79 46.49 3.58
108 109 2.679837 ACAGCCGTTTGATCATGATCAC 59.320 45.455 33.02 22.71 46.49 3.06
109 110 2.679336 CACAGCCGTTTGATCATGATCA 59.321 45.455 30.27 30.27 45.30 2.92
110 111 2.540361 GCACAGCCGTTTGATCATGATC 60.540 50.000 25.91 25.91 38.29 2.92
111 112 1.402968 GCACAGCCGTTTGATCATGAT 59.597 47.619 8.25 8.25 0.00 2.45
114 115 1.647545 CCGCACAGCCGTTTGATCAT 61.648 55.000 0.00 0.00 0.00 2.45
115 116 2.324330 CCGCACAGCCGTTTGATCA 61.324 57.895 0.00 0.00 0.00 2.92
116 117 2.480555 CCGCACAGCCGTTTGATC 59.519 61.111 0.00 0.00 0.00 2.92
151 152 2.982130 CTGACGTTCCCTGGGAGG 59.018 66.667 16.38 14.28 31.21 4.30
152 153 2.266055 GCTGACGTTCCCTGGGAG 59.734 66.667 16.38 8.03 31.21 4.30
153 154 3.319198 GGCTGACGTTCCCTGGGA 61.319 66.667 12.53 12.53 0.00 4.37
154 155 3.612247 CTGGCTGACGTTCCCTGGG 62.612 68.421 6.33 6.33 0.00 4.45
155 156 2.046892 CTGGCTGACGTTCCCTGG 60.047 66.667 0.00 0.00 0.00 4.45
156 157 0.320374 TAACTGGCTGACGTTCCCTG 59.680 55.000 0.00 0.00 0.00 4.45
157 158 1.053424 TTAACTGGCTGACGTTCCCT 58.947 50.000 0.00 0.00 0.00 4.20
158 159 1.154197 GTTAACTGGCTGACGTTCCC 58.846 55.000 0.00 0.00 0.00 3.97
159 160 1.873698 TGTTAACTGGCTGACGTTCC 58.126 50.000 7.22 0.00 0.00 3.62
160 161 4.142966 GGTAATGTTAACTGGCTGACGTTC 60.143 45.833 7.22 0.00 0.00 3.95
161 162 3.749609 GGTAATGTTAACTGGCTGACGTT 59.250 43.478 7.22 0.00 0.00 3.99
162 163 3.332034 GGTAATGTTAACTGGCTGACGT 58.668 45.455 7.22 0.00 0.00 4.34
163 164 2.347452 CGGTAATGTTAACTGGCTGACG 59.653 50.000 7.22 0.00 0.00 4.35
164 165 3.332034 ACGGTAATGTTAACTGGCTGAC 58.668 45.455 7.22 0.00 0.00 3.51
165 166 3.688694 ACGGTAATGTTAACTGGCTGA 57.311 42.857 7.22 0.00 0.00 4.26
166 167 4.759516 AAACGGTAATGTTAACTGGCTG 57.240 40.909 7.22 2.81 0.00 4.85
167 168 6.174760 TGATAAACGGTAATGTTAACTGGCT 58.825 36.000 7.22 0.00 0.00 4.75
168 169 6.425577 TGATAAACGGTAATGTTAACTGGC 57.574 37.500 7.22 0.00 0.00 4.85
173 174 9.938670 GCACATAATGATAAACGGTAATGTTAA 57.061 29.630 0.00 0.00 0.00 2.01
174 175 9.332502 AGCACATAATGATAAACGGTAATGTTA 57.667 29.630 0.00 0.00 0.00 2.41
175 176 8.220755 AGCACATAATGATAAACGGTAATGTT 57.779 30.769 0.00 0.00 0.00 2.71
176 177 7.715249 AGAGCACATAATGATAAACGGTAATGT 59.285 33.333 0.00 0.00 0.00 2.71
177 178 8.011673 CAGAGCACATAATGATAAACGGTAATG 58.988 37.037 0.00 0.00 0.00 1.90
178 179 7.931407 TCAGAGCACATAATGATAAACGGTAAT 59.069 33.333 0.00 0.00 0.00 1.89
179 180 7.269316 TCAGAGCACATAATGATAAACGGTAA 58.731 34.615 0.00 0.00 0.00 2.85
180 181 6.811954 TCAGAGCACATAATGATAAACGGTA 58.188 36.000 0.00 0.00 0.00 4.02
181 182 5.670485 TCAGAGCACATAATGATAAACGGT 58.330 37.500 0.00 0.00 0.00 4.83
182 183 6.258727 AGTTCAGAGCACATAATGATAAACGG 59.741 38.462 0.00 0.00 0.00 4.44
183 184 7.239166 AGTTCAGAGCACATAATGATAAACG 57.761 36.000 0.00 0.00 0.00 3.60
184 185 9.495754 GAAAGTTCAGAGCACATAATGATAAAC 57.504 33.333 0.00 0.00 0.00 2.01
198 199 5.765677 AGGTTAAAAGAGGAAAGTTCAGAGC 59.234 40.000 0.00 0.00 0.00 4.09
225 226 5.899547 TGGATGTCCTAATCTCTACACACAT 59.100 40.000 0.09 0.00 36.82 3.21
251 252 7.928706 CCTCTAGATTCGTCATTTATTTCCACT 59.071 37.037 0.00 0.00 0.00 4.00
263 264 1.734137 GCGGCCTCTAGATTCGTCA 59.266 57.895 0.00 0.00 0.00 4.35
272 273 1.567208 TTTGGAATGGGCGGCCTCTA 61.567 55.000 29.87 14.48 0.00 2.43
302 303 3.629398 AGCCAAACTGTTGTTCTTCTCTG 59.371 43.478 0.00 0.00 34.96 3.35
308 309 3.356290 AGACAAGCCAAACTGTTGTTCT 58.644 40.909 0.00 0.00 34.55 3.01
309 327 3.378427 AGAGACAAGCCAAACTGTTGTTC 59.622 43.478 0.00 0.00 34.55 3.18
326 344 1.334869 CACACTGGCAACCAAAGAGAC 59.665 52.381 0.00 0.00 30.80 3.36
335 353 2.880890 AGAGAAATGACACACTGGCAAC 59.119 45.455 0.00 0.00 39.86 4.17
339 357 4.321718 ACATCAGAGAAATGACACACTGG 58.678 43.478 0.00 0.00 30.46 4.00
342 360 7.601073 TTCATACATCAGAGAAATGACACAC 57.399 36.000 0.00 0.00 30.46 3.82
347 367 8.820933 GTCGAATTTCATACATCAGAGAAATGA 58.179 33.333 0.00 0.00 39.75 2.57
350 370 8.777865 AAGTCGAATTTCATACATCAGAGAAA 57.222 30.769 0.00 0.00 34.83 2.52
367 387 8.428186 TGTCAGTTTTAGTTGTTAAGTCGAAT 57.572 30.769 0.00 0.00 0.00 3.34
371 391 8.149973 TCCATGTCAGTTTTAGTTGTTAAGTC 57.850 34.615 0.00 0.00 0.00 3.01
392 415 6.466812 TCAATCTGCGTGAACATATATCCAT 58.533 36.000 0.00 0.00 0.00 3.41
396 419 8.743714 TCTATCTCAATCTGCGTGAACATATAT 58.256 33.333 0.00 0.00 0.00 0.86
400 423 5.163468 ACTCTATCTCAATCTGCGTGAACAT 60.163 40.000 0.00 0.00 0.00 2.71
401 424 4.158579 ACTCTATCTCAATCTGCGTGAACA 59.841 41.667 0.00 0.00 0.00 3.18
402 425 4.677584 ACTCTATCTCAATCTGCGTGAAC 58.322 43.478 0.00 0.00 0.00 3.18
533 556 2.661979 GCGGAAACAAAGTAGAGCAACG 60.662 50.000 0.00 0.00 0.00 4.10
550 573 4.636648 TCTGAAGTTTTAAACAACAGCGGA 59.363 37.500 20.37 9.54 37.03 5.54
551 574 4.915704 TCTGAAGTTTTAAACAACAGCGG 58.084 39.130 20.37 7.96 37.03 5.52
572 596 2.480759 GCCATGTCTCATGCATTGGTTC 60.481 50.000 13.10 0.00 0.00 3.62
583 607 1.005037 GGACACACGCCATGTCTCA 60.005 57.895 12.41 0.00 44.88 3.27
621 645 5.730550 AGAGTTCACAAACACTGACACTAA 58.269 37.500 0.00 0.00 35.36 2.24
657 681 0.447801 AATGCACGCGGAACAGATTC 59.552 50.000 12.47 0.00 0.00 2.52
678 702 0.387565 GCCAGCGGTTTGGAGAAAAA 59.612 50.000 5.08 0.00 40.87 1.94
679 703 0.467290 AGCCAGCGGTTTGGAGAAAA 60.467 50.000 5.08 0.00 40.87 2.29
725 762 0.251297 CACCAGATTGGGACCAAGCA 60.251 55.000 20.09 0.00 43.87 3.91
727 764 0.967380 GCCACCAGATTGGGACCAAG 60.967 60.000 9.90 0.00 43.37 3.61
735 772 2.386661 AACGTAGAGCCACCAGATTG 57.613 50.000 0.00 0.00 0.00 2.67
787 828 0.242017 GAAGGACAGCGCTTGCATTT 59.758 50.000 7.50 0.00 42.66 2.32
794 835 1.186200 TACATGAGAAGGACAGCGCT 58.814 50.000 2.64 2.64 0.00 5.92
835 1012 1.078143 AGCGGATTTGCTCCCAGAC 60.078 57.895 0.00 0.00 42.95 3.51
982 1161 0.175989 ATCGCCTCCTTCGTTTCTCC 59.824 55.000 0.00 0.00 0.00 3.71
989 1168 4.207281 TCGCCATCGCCTCCTTCG 62.207 66.667 0.00 0.00 35.26 3.79
1094 1282 4.626402 TTCCCCGTCCTCCCGTGT 62.626 66.667 0.00 0.00 0.00 4.49
1284 1472 2.364973 TACCTGATGCTCCGGCCA 60.365 61.111 2.24 0.00 37.74 5.36
1430 1625 2.158623 GGTCCATGGCTGATGTCCATTA 60.159 50.000 6.96 0.00 42.11 1.90
1456 1653 3.068448 TGCACAGCAACAACATTTCTGAT 59.932 39.130 0.00 0.00 34.76 2.90
1458 1655 2.792674 CTGCACAGCAACAACATTTCTG 59.207 45.455 0.00 0.00 38.41 3.02
1468 1665 0.250295 TGTAGGACCTGCACAGCAAC 60.250 55.000 8.39 0.00 38.41 4.17
1471 1668 0.250234 TGATGTAGGACCTGCACAGC 59.750 55.000 15.13 9.98 0.00 4.40
1472 1669 2.027745 ACTTGATGTAGGACCTGCACAG 60.028 50.000 15.13 12.96 0.00 3.66
1473 1670 1.977854 ACTTGATGTAGGACCTGCACA 59.022 47.619 15.13 11.80 0.00 4.57
1483 1682 3.370366 GCACAGCTTCAGACTTGATGTAG 59.630 47.826 0.00 0.00 32.27 2.74
1498 1697 2.104451 CTCCATTATCCTCAGCACAGCT 59.896 50.000 0.00 0.00 40.77 4.24
1501 1700 3.388024 GGTACTCCATTATCCTCAGCACA 59.612 47.826 0.00 0.00 0.00 4.57
1596 1795 2.738314 GTGGTTCAATTGAAAGCATGCC 59.262 45.455 22.07 17.23 35.58 4.40
1646 1852 0.527565 CACAAACCTAGCCATGGCAC 59.472 55.000 37.18 10.61 44.88 5.01
1768 1974 2.462456 TAAGCAAGAGCACTGAGGTG 57.538 50.000 0.00 0.00 45.49 4.00
1769 1975 3.772025 ACTATAAGCAAGAGCACTGAGGT 59.228 43.478 0.00 0.00 45.49 3.85
1770 1976 4.399004 ACTATAAGCAAGAGCACTGAGG 57.601 45.455 0.00 0.00 45.49 3.86
1795 2001 8.829746 TCAATGTATGGCCATTCTTCTATCTAT 58.170 33.333 26.37 2.55 32.81 1.98
1796 2002 8.206126 TCAATGTATGGCCATTCTTCTATCTA 57.794 34.615 26.37 0.00 32.81 1.98
1797 2003 7.016957 TCTCAATGTATGGCCATTCTTCTATCT 59.983 37.037 26.37 0.00 32.81 1.98
1798 2004 7.164122 TCTCAATGTATGGCCATTCTTCTATC 58.836 38.462 26.37 5.39 32.81 2.08
1799 2005 7.083062 TCTCAATGTATGGCCATTCTTCTAT 57.917 36.000 26.37 5.27 32.81 1.98
1800 2006 6.499106 TCTCAATGTATGGCCATTCTTCTA 57.501 37.500 26.37 0.34 32.81 2.10
1801 2007 5.378230 TCTCAATGTATGGCCATTCTTCT 57.622 39.130 26.37 0.29 32.81 2.85
1802 2008 5.591877 ACTTCTCAATGTATGGCCATTCTTC 59.408 40.000 26.37 12.64 32.81 2.87
1803 2009 5.513233 ACTTCTCAATGTATGGCCATTCTT 58.487 37.500 26.37 14.42 32.81 2.52
1804 2010 5.121380 ACTTCTCAATGTATGGCCATTCT 57.879 39.130 26.37 2.16 32.81 2.40
1805 2011 5.126061 ACAACTTCTCAATGTATGGCCATTC 59.874 40.000 26.37 20.17 32.81 2.67
1806 2012 5.018809 ACAACTTCTCAATGTATGGCCATT 58.981 37.500 26.37 2.81 35.45 3.16
1807 2013 4.603131 ACAACTTCTCAATGTATGGCCAT 58.397 39.130 24.45 24.45 0.00 4.40
1808 2014 4.032960 ACAACTTCTCAATGTATGGCCA 57.967 40.909 8.56 8.56 0.00 5.36
1809 2015 4.576463 CCTACAACTTCTCAATGTATGGCC 59.424 45.833 0.00 0.00 0.00 5.36
1810 2016 4.035675 GCCTACAACTTCTCAATGTATGGC 59.964 45.833 0.00 0.00 37.04 4.40
1811 2017 5.185454 TGCCTACAACTTCTCAATGTATGG 58.815 41.667 0.00 0.00 0.00 2.74
1812 2018 6.539826 TCATGCCTACAACTTCTCAATGTATG 59.460 38.462 0.00 0.00 0.00 2.39
1813 2019 6.540189 GTCATGCCTACAACTTCTCAATGTAT 59.460 38.462 0.00 0.00 0.00 2.29
1814 2020 5.874810 GTCATGCCTACAACTTCTCAATGTA 59.125 40.000 0.00 0.00 0.00 2.29
1815 2021 4.697352 GTCATGCCTACAACTTCTCAATGT 59.303 41.667 0.00 0.00 0.00 2.71
1816 2022 4.696877 TGTCATGCCTACAACTTCTCAATG 59.303 41.667 0.00 0.00 0.00 2.82
1817 2023 4.910195 TGTCATGCCTACAACTTCTCAAT 58.090 39.130 0.00 0.00 0.00 2.57
1818 2024 4.040339 TCTGTCATGCCTACAACTTCTCAA 59.960 41.667 0.00 0.00 0.00 3.02
1819 2025 3.578282 TCTGTCATGCCTACAACTTCTCA 59.422 43.478 0.00 0.00 0.00 3.27
1820 2026 4.193826 TCTGTCATGCCTACAACTTCTC 57.806 45.455 0.00 0.00 0.00 2.87
1821 2027 4.833478 ATCTGTCATGCCTACAACTTCT 57.167 40.909 0.00 0.00 0.00 2.85
1822 2028 6.283694 TCATATCTGTCATGCCTACAACTTC 58.716 40.000 0.00 0.00 0.00 3.01
1823 2029 6.098838 TCTCATATCTGTCATGCCTACAACTT 59.901 38.462 0.00 0.00 0.00 2.66
1824 2030 5.600069 TCTCATATCTGTCATGCCTACAACT 59.400 40.000 0.00 0.00 0.00 3.16
1825 2031 5.694006 GTCTCATATCTGTCATGCCTACAAC 59.306 44.000 0.00 0.00 0.00 3.32
1826 2032 5.363580 TGTCTCATATCTGTCATGCCTACAA 59.636 40.000 0.00 0.00 0.00 2.41
1827 2033 4.895297 TGTCTCATATCTGTCATGCCTACA 59.105 41.667 0.00 0.00 0.00 2.74
1828 2034 5.242615 TCTGTCTCATATCTGTCATGCCTAC 59.757 44.000 0.00 0.00 0.00 3.18
1829 2035 5.388654 TCTGTCTCATATCTGTCATGCCTA 58.611 41.667 0.00 0.00 0.00 3.93
1830 2036 4.221530 TCTGTCTCATATCTGTCATGCCT 58.778 43.478 0.00 0.00 0.00 4.75
1831 2037 4.597404 TCTGTCTCATATCTGTCATGCC 57.403 45.455 0.00 0.00 0.00 4.40
1832 2038 6.221659 TGATTCTGTCTCATATCTGTCATGC 58.778 40.000 0.00 0.00 0.00 4.06
1833 2039 7.148557 GCATGATTCTGTCTCATATCTGTCATG 60.149 40.741 0.00 0.00 41.08 3.07
1834 2040 6.874664 GCATGATTCTGTCTCATATCTGTCAT 59.125 38.462 0.00 0.00 32.18 3.06
1835 2041 6.221659 GCATGATTCTGTCTCATATCTGTCA 58.778 40.000 0.00 0.00 32.18 3.58
1836 2042 5.345472 CGCATGATTCTGTCTCATATCTGTC 59.655 44.000 0.00 0.00 32.18 3.51
1837 2043 5.010415 TCGCATGATTCTGTCTCATATCTGT 59.990 40.000 0.00 0.00 32.18 3.41
1838 2044 5.467705 TCGCATGATTCTGTCTCATATCTG 58.532 41.667 0.00 0.00 32.18 2.90
1839 2045 5.476254 TCTCGCATGATTCTGTCTCATATCT 59.524 40.000 0.00 0.00 32.18 1.98
1840 2046 5.707931 TCTCGCATGATTCTGTCTCATATC 58.292 41.667 0.00 0.00 32.18 1.63
1841 2047 5.718724 TCTCGCATGATTCTGTCTCATAT 57.281 39.130 0.00 0.00 32.18 1.78
1842 2048 5.718724 ATCTCGCATGATTCTGTCTCATA 57.281 39.130 0.00 0.00 32.18 2.15
1843 2049 4.603989 ATCTCGCATGATTCTGTCTCAT 57.396 40.909 0.00 0.00 33.65 2.90
1844 2050 4.582240 AGTATCTCGCATGATTCTGTCTCA 59.418 41.667 0.00 0.00 0.00 3.27
1845 2051 5.119931 AGTATCTCGCATGATTCTGTCTC 57.880 43.478 0.00 0.00 0.00 3.36
1846 2052 5.119931 GAGTATCTCGCATGATTCTGTCT 57.880 43.478 0.00 0.00 0.00 3.41
1862 2068 3.133691 TGCGGCATCAATTCAGAGTATC 58.866 45.455 0.00 0.00 0.00 2.24
1863 2069 3.136763 CTGCGGCATCAATTCAGAGTAT 58.863 45.455 1.75 0.00 0.00 2.12
1864 2070 2.168313 TCTGCGGCATCAATTCAGAGTA 59.832 45.455 1.75 0.00 31.07 2.59
1865 2071 1.065926 TCTGCGGCATCAATTCAGAGT 60.066 47.619 1.75 0.00 31.07 3.24
1866 2072 1.660167 TCTGCGGCATCAATTCAGAG 58.340 50.000 1.75 0.00 31.07 3.35
1867 2073 2.336945 ATCTGCGGCATCAATTCAGA 57.663 45.000 1.75 0.00 38.05 3.27
1868 2074 3.608707 GCTTATCTGCGGCATCAATTCAG 60.609 47.826 1.75 0.01 0.00 3.02
1869 2075 2.291465 GCTTATCTGCGGCATCAATTCA 59.709 45.455 1.75 0.00 0.00 2.57
1870 2076 2.291465 TGCTTATCTGCGGCATCAATTC 59.709 45.455 1.75 0.00 35.36 2.17
1871 2077 2.033801 GTGCTTATCTGCGGCATCAATT 59.966 45.455 1.75 0.00 38.27 2.32
1872 2078 1.605710 GTGCTTATCTGCGGCATCAAT 59.394 47.619 1.75 0.38 38.27 2.57
1873 2079 1.016627 GTGCTTATCTGCGGCATCAA 58.983 50.000 1.75 0.00 38.27 2.57
1874 2080 0.815213 GGTGCTTATCTGCGGCATCA 60.815 55.000 1.75 0.00 37.10 3.07
1875 2081 0.533755 AGGTGCTTATCTGCGGCATC 60.534 55.000 1.75 0.00 38.27 3.91
1876 2082 0.533755 GAGGTGCTTATCTGCGGCAT 60.534 55.000 1.75 0.00 38.27 4.40
1877 2083 1.153369 GAGGTGCTTATCTGCGGCA 60.153 57.895 1.29 1.29 35.36 5.69
1878 2084 2.240500 CGAGGTGCTTATCTGCGGC 61.241 63.158 0.00 0.00 35.36 6.53
1879 2085 1.592669 CCGAGGTGCTTATCTGCGG 60.593 63.158 0.00 0.00 35.36 5.69
1880 2086 1.141881 ACCGAGGTGCTTATCTGCG 59.858 57.895 0.00 0.00 35.36 5.18
1881 2087 2.682893 CACCGAGGTGCTTATCTGC 58.317 57.895 9.54 0.00 39.39 4.26
2042 2251 2.030007 GCAAGTGCAGAAATGCTTACCA 60.030 45.455 0.00 0.00 41.59 3.25
2095 2305 1.474478 TGATCAGAAGTGCTCTCCGTC 59.526 52.381 0.00 0.00 29.07 4.79
2108 2318 0.614697 TTCCGTGGCCTCTGATCAGA 60.615 55.000 23.75 23.75 35.85 3.27
2109 2319 0.179089 CTTCCGTGGCCTCTGATCAG 60.179 60.000 17.07 17.07 0.00 2.90
2110 2320 1.900351 CTTCCGTGGCCTCTGATCA 59.100 57.895 3.32 0.00 0.00 2.92
2158 2368 4.608170 AATCCTAAATGCCCAAGGAAGA 57.392 40.909 0.00 0.00 42.53 2.87
2248 2458 3.525545 TGCAGCAAAAGCGTGCCA 61.526 55.556 0.00 0.00 46.14 4.92
2354 2564 2.806434 ACTGAAACCATATTGGCTGCA 58.194 42.857 0.50 0.00 42.67 4.41
2464 2702 5.938279 TGACTGAAGTACGGTATCCTATCT 58.062 41.667 0.00 0.00 38.34 1.98
2499 2737 1.329599 AGCGAACACGTTCCTTTTCAC 59.670 47.619 4.40 0.00 36.27 3.18
2569 2808 5.130350 GGTTGCATACACCATGGTAGTATT 58.870 41.667 25.14 14.72 34.97 1.89
2595 2859 3.435671 CGTCAGTTCAAAGATACCAACCC 59.564 47.826 0.00 0.00 0.00 4.11
2596 2860 3.435671 CCGTCAGTTCAAAGATACCAACC 59.564 47.826 0.00 0.00 0.00 3.77
2616 2881 0.097499 CTACATGCATGTGTGTGCCG 59.903 55.000 36.72 15.12 44.43 5.69
2731 3016 3.742983 GGTGCCGGTGAAAAACAAA 57.257 47.368 1.90 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.