Multiple sequence alignment - TraesCS6D01G365800

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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 TraesCS6D01G365800 chr6D 100.000 2738 0 0 1 2738 454685316 454688053 0.000000e+00 5057.0
1 TraesCS6D01G365800 chr6D 93.873 1322 66 7 432 1741 454801194 454799876 0.000000e+00 1978.0
2 TraesCS6D01G365800 chr6D 89.085 852 76 12 893 1738 162125767 162126607 0.000000e+00 1042.0
3 TraesCS6D01G365800 chr6D 96.899 258 8 0 1849 2106 16637716 16637459 1.510000e-117 433.0
4 TraesCS6D01G365800 chr6A 92.922 1427 78 11 334 1747 601134912 601133496 0.000000e+00 2054.0
5 TraesCS6D01G365800 chr6A 88.495 1269 81 27 516 1741 601006545 601005299 0.000000e+00 1474.0
6 TraesCS6D01G365800 chr6A 89.202 852 78 10 893 1738 221554039 221554882 0.000000e+00 1051.0
7 TraesCS6D01G365800 chr6A 89.583 432 29 10 2316 2738 601132928 601132504 4.010000e-148 534.0
8 TraesCS6D01G365800 chr6A 90.794 315 19 9 2430 2738 601004232 601003922 1.960000e-111 412.0
9 TraesCS6D01G365800 chr6A 88.070 285 32 1 1 283 601136068 601135784 1.210000e-88 337.0
10 TraesCS6D01G365800 chr6A 94.340 106 5 1 2102 2206 601005131 601005026 7.850000e-36 161.0
11 TraesCS6D01G365800 chr6A 93.750 96 6 0 1747 1842 601133263 601133168 7.900000e-31 145.0
12 TraesCS6D01G365800 chr6A 85.859 99 10 4 1747 1842 601005222 601005125 4.820000e-18 102.0
13 TraesCS6D01G365800 chr6A 96.364 55 2 0 334 388 601006672 601006618 1.040000e-14 91.6
14 TraesCS6D01G365800 chr6B 93.036 1321 74 4 432 1740 691750099 691748785 0.000000e+00 1914.0
15 TraesCS6D01G365800 chr6B 88.784 847 83 9 896 1738 300242604 300241766 0.000000e+00 1027.0
16 TraesCS6D01G365800 chr6B 83.796 216 19 10 2102 2309 691748521 691748314 1.000000e-44 191.0
17 TraesCS6D01G365800 chr6B 93.069 101 6 1 334 434 691754974 691754875 2.200000e-31 147.0
18 TraesCS6D01G365800 chr6B 100.000 29 0 0 1814 1842 691748543 691748515 1.000000e-03 54.7
19 TraesCS6D01G365800 chr7D 98.062 258 5 0 1849 2106 505595077 505594820 1.500000e-122 449.0
20 TraesCS6D01G365800 chr5D 96.241 266 9 1 1849 2113 456603472 456603207 4.190000e-118 435.0
21 TraesCS6D01G365800 chr5D 80.263 456 71 14 980 1431 410444128 410444568 2.630000e-85 326.0
22 TraesCS6D01G365800 chr2D 97.266 256 7 0 1849 2104 138290967 138290712 4.190000e-118 435.0
23 TraesCS6D01G365800 chr3D 96.875 256 8 0 1849 2104 96588461 96588716 1.950000e-116 429.0
24 TraesCS6D01G365800 chr3D 95.833 264 9 1 1849 2112 596656929 596656668 2.520000e-115 425.0
25 TraesCS6D01G365800 chr1D 96.875 256 8 0 1849 2104 442407070 442406815 1.950000e-116 429.0
26 TraesCS6D01G365800 chrUn 95.833 264 9 1 1849 2112 45825114 45824853 2.520000e-115 425.0
27 TraesCS6D01G365800 chrUn 95.833 264 9 1 1849 2112 314873974 314873713 2.520000e-115 425.0
28 TraesCS6D01G365800 chr4B 83.871 341 44 9 1 333 471068095 471067758 5.690000e-82 315.0
29 TraesCS6D01G365800 chr4B 83.529 340 45 8 1 333 6050373 6050708 9.520000e-80 307.0
30 TraesCS6D01G365800 chr3B 83.578 341 45 9 1 333 116016242 116015905 2.650000e-80 309.0
31 TraesCS6D01G365800 chr1A 83.626 342 42 12 1 333 403705316 403704980 2.650000e-80 309.0
32 TraesCS6D01G365800 chr4A 83.529 340 45 9 1 333 704792181 704791846 9.520000e-80 307.0
33 TraesCS6D01G365800 chr4D 83.235 340 47 8 1 333 496811345 496811009 1.230000e-78 303.0
34 TraesCS6D01G365800 chr4D 83.235 340 47 8 1 333 496843431 496843095 1.230000e-78 303.0
35 TraesCS6D01G365800 chr1B 83.284 341 46 9 1 333 489797503 489797166 1.230000e-78 303.0
36 TraesCS6D01G365800 chr5B 83.333 336 44 11 1078 1407 492619514 492619843 1.590000e-77 300.0


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 TraesCS6D01G365800 chr6D 454685316 454688053 2737 False 5057.00 5057 100.000000 1 2738 1 chr6D.!!$F2 2737
1 TraesCS6D01G365800 chr6D 454799876 454801194 1318 True 1978.00 1978 93.873000 432 1741 1 chr6D.!!$R2 1309
2 TraesCS6D01G365800 chr6D 162125767 162126607 840 False 1042.00 1042 89.085000 893 1738 1 chr6D.!!$F1 845
3 TraesCS6D01G365800 chr6A 221554039 221554882 843 False 1051.00 1051 89.202000 893 1738 1 chr6A.!!$F1 845
4 TraesCS6D01G365800 chr6A 601132504 601136068 3564 True 767.50 2054 91.081250 1 2738 4 chr6A.!!$R2 2737
5 TraesCS6D01G365800 chr6A 601003922 601006672 2750 True 448.12 1474 91.170400 334 2738 5 chr6A.!!$R1 2404
6 TraesCS6D01G365800 chr6B 300241766 300242604 838 True 1027.00 1027 88.784000 896 1738 1 chr6B.!!$R1 842
7 TraesCS6D01G365800 chr6B 691748314 691750099 1785 True 719.90 1914 92.277333 432 2309 3 chr6B.!!$R3 1877

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
121 124 0.107214 ATACGGTCAGCCATTGTGGG 60.107 55.0 0.00 0.00 38.19 4.61 F
910 1748 0.300491 CACGTATAAATGCGCGCACT 59.700 50.0 39.05 26.35 39.55 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 2319 1.458777 TGGACGTGACTTCCTGGGT 60.459 57.895 9.63 0.0 33.84 4.51 R
2206 3358 1.383456 GGGCAGACACACACAGCAAA 61.383 55.000 0.00 0.0 0.00 3.68 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
21 22 1.204231 GTAACCGTCCTCAAGGGTCTC 59.796 57.143 0.00 0.00 45.41 3.36
22 23 0.471211 AACCGTCCTCAAGGGTCTCA 60.471 55.000 0.00 0.00 45.41 3.27
31 32 4.349636 TCCTCAAGGGTCTCAATTTGTACA 59.650 41.667 0.00 0.00 36.25 2.90
32 33 5.070001 CCTCAAGGGTCTCAATTTGTACAA 58.930 41.667 3.59 3.59 0.00 2.41
36 37 6.605594 TCAAGGGTCTCAATTTGTACAAGTTT 59.394 34.615 13.15 6.80 0.00 2.66
42 43 7.254852 GTCTCAATTTGTACAAGTTTGGTGAA 58.745 34.615 22.75 10.51 0.00 3.18
43 44 7.920682 GTCTCAATTTGTACAAGTTTGGTGAAT 59.079 33.333 22.75 5.89 0.00 2.57
44 45 7.920151 TCTCAATTTGTACAAGTTTGGTGAATG 59.080 33.333 22.75 9.78 0.00 2.67
72 73 4.953478 AAGGGTCCCTTAGTGGATTCACG 61.953 52.174 22.57 0.00 42.74 4.35
81 82 0.517316 GTGGATTCACGACACCTTGC 59.483 55.000 0.00 0.00 33.87 4.01
105 108 2.094700 TGTGTGAGCGTGAGGAGAATAC 60.095 50.000 0.00 0.00 0.00 1.89
106 109 1.132453 TGTGAGCGTGAGGAGAATACG 59.868 52.381 0.00 0.00 40.52 3.06
109 112 0.739561 AGCGTGAGGAGAATACGGTC 59.260 55.000 0.00 0.00 43.97 4.79
121 124 0.107214 ATACGGTCAGCCATTGTGGG 60.107 55.000 0.00 0.00 38.19 4.61
134 137 0.690762 TTGTGGGTCTTAGGGAGCAC 59.309 55.000 0.00 0.00 43.58 4.40
140 143 0.391793 GTCTTAGGGAGCACTGTGCC 60.392 60.000 27.74 18.73 46.52 5.01
150 153 4.626081 ACTGTGCCTCCACACCGC 62.626 66.667 0.00 0.00 46.51 5.68
172 175 3.906998 TCTAGCGAAGATTAGCATCTGC 58.093 45.455 0.57 0.00 39.00 4.26
184 187 1.188863 GCATCTGCAAAGGGGTGAAT 58.811 50.000 0.00 0.00 41.59 2.57
185 188 1.551883 GCATCTGCAAAGGGGTGAATT 59.448 47.619 0.00 0.00 41.59 2.17
201 204 4.116961 GTGAATTTCGGGATACATCGTCA 58.883 43.478 0.00 0.00 39.74 4.35
206 209 3.141767 TCGGGATACATCGTCATCTCT 57.858 47.619 0.00 0.00 39.74 3.10
210 213 3.056250 GGGATACATCGTCATCTCTGCAT 60.056 47.826 0.00 0.00 39.74 3.96
294 971 7.720957 TGTGCTTCAGGTTATATATCTTGCAAT 59.279 33.333 0.00 0.00 0.00 3.56
299 976 8.607441 TCAGGTTATATATCTTGCAATCACAC 57.393 34.615 0.00 0.00 0.00 3.82
300 977 7.661437 TCAGGTTATATATCTTGCAATCACACC 59.339 37.037 0.00 0.00 0.00 4.16
306 983 2.020720 TCTTGCAATCACACCGTTGTT 58.979 42.857 0.00 0.00 31.66 2.83
313 990 4.083537 GCAATCACACCGTTGTTTATCTGA 60.084 41.667 0.00 0.00 31.66 3.27
324 1001 6.742718 CCGTTGTTTATCTGATTTAGCACAAG 59.257 38.462 0.00 0.00 0.00 3.16
329 1006 8.629158 TGTTTATCTGATTTAGCACAAGTTGTT 58.371 29.630 5.57 0.00 0.00 2.83
352 1176 4.018506 TGGTTAGATTTGCCCTGAGATTCA 60.019 41.667 0.00 0.00 0.00 2.57
406 1231 5.511571 GTTTTGAGGTGCTAAAACTCTGAC 58.488 41.667 0.00 0.00 41.30 3.51
422 1247 7.907214 AACTCTGACGTTAGCTTTATTCATT 57.093 32.000 1.76 0.00 0.00 2.57
467 1293 0.402504 TACATGGAACCCAAACGCCT 59.597 50.000 0.00 0.00 36.95 5.52
514 1340 2.387757 TCAGTTTCAGCAAAGCCCTTT 58.612 42.857 0.00 0.00 0.00 3.11
555 1381 2.023461 CGCTAGGCTCACGAGTCG 59.977 66.667 11.85 11.85 38.27 4.18
595 1421 2.035961 TGACCTGACCTGACTTTCTTCG 59.964 50.000 0.00 0.00 0.00 3.79
701 1536 1.735018 CCATGCCACAAATCGACGTTA 59.265 47.619 0.00 0.00 0.00 3.18
706 1541 2.092211 GCCACAAATCGACGTTACAGAG 59.908 50.000 0.00 0.00 0.00 3.35
734 1569 1.732941 AACAACACGTGAACTCAGCA 58.267 45.000 25.01 0.00 0.00 4.41
795 1633 1.595109 CGCTGGAGTGCACACAGAA 60.595 57.895 32.73 12.72 34.21 3.02
906 1744 3.556288 TGTTACACGTATAAATGCGCG 57.444 42.857 0.00 0.00 39.55 6.86
910 1748 0.300491 CACGTATAAATGCGCGCACT 59.700 50.000 39.05 26.35 39.55 4.40
1371 2252 2.418910 CCTCTCTGATGTCCGGCGT 61.419 63.158 6.01 0.00 0.00 5.68
1543 2424 1.999648 TGCCACTTTTGAAGAGCCAT 58.000 45.000 0.00 0.00 32.76 4.40
1614 2495 3.462021 GGACTCGGACACGTACTACTAT 58.538 50.000 0.00 0.00 41.85 2.12
1668 2549 3.407967 CCTACCATGGCCACCGGT 61.408 66.667 27.29 27.29 36.79 5.28
1671 2552 2.191786 CTACCATGGCCACCGGTCAA 62.192 60.000 27.84 13.71 42.14 3.18
1741 2622 1.331138 CGCTCTGGAGTTACTAGGACG 59.669 57.143 0.00 0.00 0.00 4.79
1745 2626 4.734917 CTCTGGAGTTACTAGGACGTTTG 58.265 47.826 0.00 0.00 0.00 2.93
1777 2928 3.305720 CAAGTGGTAGCCTGGTAGGATA 58.694 50.000 0.00 0.00 37.67 2.59
1783 2934 2.405618 AGCCTGGTAGGATAGATGCA 57.594 50.000 0.00 0.00 37.67 3.96
1790 2941 5.338626 CCTGGTAGGATAGATGCAATGCATA 60.339 44.000 21.70 6.94 43.46 3.14
1791 2942 7.129539 CCTGGTAGGATAGATGCAATGCATAG 61.130 46.154 21.70 10.19 43.46 2.23
1842 2993 4.705991 ACTAACACAGTAGCCCTCTTAGAC 59.294 45.833 0.00 0.00 34.98 2.59
1843 2994 3.459710 ACACAGTAGCCCTCTTAGACT 57.540 47.619 0.00 0.00 0.00 3.24
1844 2995 4.587976 ACACAGTAGCCCTCTTAGACTA 57.412 45.455 0.00 0.00 0.00 2.59
1845 2996 4.528920 ACACAGTAGCCCTCTTAGACTAG 58.471 47.826 0.00 0.00 0.00 2.57
1846 2997 3.316868 CACAGTAGCCCTCTTAGACTAGC 59.683 52.174 0.00 0.00 0.00 3.42
1847 2998 2.888414 CAGTAGCCCTCTTAGACTAGCC 59.112 54.545 0.00 0.00 0.00 3.93
1848 2999 2.787035 AGTAGCCCTCTTAGACTAGCCT 59.213 50.000 0.00 0.00 0.00 4.58
1849 3000 3.982052 AGTAGCCCTCTTAGACTAGCCTA 59.018 47.826 0.00 0.00 0.00 3.93
1850 3001 3.975479 AGCCCTCTTAGACTAGCCTAA 57.025 47.619 0.00 0.00 0.00 2.69
1851 3002 3.568443 AGCCCTCTTAGACTAGCCTAAC 58.432 50.000 0.00 0.00 0.00 2.34
1852 3003 3.205733 AGCCCTCTTAGACTAGCCTAACT 59.794 47.826 0.00 0.00 0.00 2.24
1853 3004 3.962063 GCCCTCTTAGACTAGCCTAACTT 59.038 47.826 0.00 0.00 0.00 2.66
1854 3005 4.038282 GCCCTCTTAGACTAGCCTAACTTC 59.962 50.000 0.00 0.00 0.00 3.01
1855 3006 5.202004 CCCTCTTAGACTAGCCTAACTTCA 58.798 45.833 0.00 0.00 0.00 3.02
1856 3007 5.300792 CCCTCTTAGACTAGCCTAACTTCAG 59.699 48.000 0.00 0.00 0.00 3.02
1857 3008 5.221165 CCTCTTAGACTAGCCTAACTTCAGC 60.221 48.000 0.00 0.00 0.00 4.26
1858 3009 5.262009 TCTTAGACTAGCCTAACTTCAGCA 58.738 41.667 0.00 0.00 0.00 4.41
1859 3010 5.358442 TCTTAGACTAGCCTAACTTCAGCAG 59.642 44.000 0.00 0.00 0.00 4.24
1860 3011 3.436243 AGACTAGCCTAACTTCAGCAGT 58.564 45.455 0.00 0.00 37.30 4.40
1861 3012 4.601084 AGACTAGCCTAACTTCAGCAGTA 58.399 43.478 0.00 0.00 32.94 2.74
1862 3013 5.017490 AGACTAGCCTAACTTCAGCAGTAA 58.983 41.667 0.00 0.00 32.94 2.24
1863 3014 5.074584 ACTAGCCTAACTTCAGCAGTAAC 57.925 43.478 0.00 0.00 32.94 2.50
1864 3015 4.773149 ACTAGCCTAACTTCAGCAGTAACT 59.227 41.667 0.00 0.00 32.94 2.24
1865 3016 4.625607 AGCCTAACTTCAGCAGTAACTT 57.374 40.909 0.00 0.00 32.94 2.66
1866 3017 4.570930 AGCCTAACTTCAGCAGTAACTTC 58.429 43.478 0.00 0.00 32.94 3.01
1867 3018 4.040461 AGCCTAACTTCAGCAGTAACTTCA 59.960 41.667 0.00 0.00 32.94 3.02
1868 3019 4.755123 GCCTAACTTCAGCAGTAACTTCAA 59.245 41.667 0.00 0.00 32.94 2.69
1869 3020 5.106908 GCCTAACTTCAGCAGTAACTTCAAG 60.107 44.000 0.00 0.00 32.94 3.02
1870 3021 5.992217 CCTAACTTCAGCAGTAACTTCAAGT 59.008 40.000 0.00 0.00 32.94 3.16
1871 3022 5.993106 AACTTCAGCAGTAACTTCAAGTC 57.007 39.130 0.00 0.00 32.94 3.01
1872 3023 4.381411 ACTTCAGCAGTAACTTCAAGTCC 58.619 43.478 0.00 0.00 31.97 3.85
1873 3024 4.141711 ACTTCAGCAGTAACTTCAAGTCCA 60.142 41.667 0.00 0.00 31.97 4.02
1874 3025 4.415881 TCAGCAGTAACTTCAAGTCCAA 57.584 40.909 0.00 0.00 0.00 3.53
1875 3026 4.127171 TCAGCAGTAACTTCAAGTCCAAC 58.873 43.478 0.00 0.00 0.00 3.77
1876 3027 4.130118 CAGCAGTAACTTCAAGTCCAACT 58.870 43.478 0.00 0.00 0.00 3.16
1877 3028 4.212214 CAGCAGTAACTTCAAGTCCAACTC 59.788 45.833 0.00 0.00 0.00 3.01
1878 3029 4.127171 GCAGTAACTTCAAGTCCAACTCA 58.873 43.478 0.00 0.00 0.00 3.41
1879 3030 4.212214 GCAGTAACTTCAAGTCCAACTCAG 59.788 45.833 0.00 0.00 0.00 3.35
1880 3031 4.212214 CAGTAACTTCAAGTCCAACTCAGC 59.788 45.833 0.00 0.00 0.00 4.26
1881 3032 3.281727 AACTTCAAGTCCAACTCAGCA 57.718 42.857 0.00 0.00 0.00 4.41
1882 3033 3.281727 ACTTCAAGTCCAACTCAGCAA 57.718 42.857 0.00 0.00 0.00 3.91
1883 3034 3.620488 ACTTCAAGTCCAACTCAGCAAA 58.380 40.909 0.00 0.00 0.00 3.68
1884 3035 4.210331 ACTTCAAGTCCAACTCAGCAAAT 58.790 39.130 0.00 0.00 0.00 2.32
1885 3036 4.646492 ACTTCAAGTCCAACTCAGCAAATT 59.354 37.500 0.00 0.00 0.00 1.82
1886 3037 5.127682 ACTTCAAGTCCAACTCAGCAAATTT 59.872 36.000 0.00 0.00 0.00 1.82
1887 3038 4.935702 TCAAGTCCAACTCAGCAAATTTG 58.064 39.130 14.03 14.03 0.00 2.32
1888 3039 4.402155 TCAAGTCCAACTCAGCAAATTTGT 59.598 37.500 19.03 3.98 0.00 2.83
1889 3040 4.574599 AGTCCAACTCAGCAAATTTGTC 57.425 40.909 19.03 11.45 0.00 3.18
1890 3041 4.210331 AGTCCAACTCAGCAAATTTGTCT 58.790 39.130 19.03 13.38 0.00 3.41
1891 3042 5.376625 AGTCCAACTCAGCAAATTTGTCTA 58.623 37.500 19.03 4.50 0.00 2.59
1892 3043 6.006449 AGTCCAACTCAGCAAATTTGTCTAT 58.994 36.000 19.03 1.31 0.00 1.98
1893 3044 6.072286 AGTCCAACTCAGCAAATTTGTCTATG 60.072 38.462 19.03 12.62 0.00 2.23
1894 3045 5.769662 TCCAACTCAGCAAATTTGTCTATGT 59.230 36.000 19.03 13.81 0.00 2.29
1895 3046 5.860182 CCAACTCAGCAAATTTGTCTATGTG 59.140 40.000 19.03 14.49 0.00 3.21
1896 3047 5.633830 ACTCAGCAAATTTGTCTATGTGG 57.366 39.130 19.03 11.82 0.00 4.17
1897 3048 4.082571 ACTCAGCAAATTTGTCTATGTGGC 60.083 41.667 19.03 1.86 0.00 5.01
1898 3049 3.825585 TCAGCAAATTTGTCTATGTGGCA 59.174 39.130 19.03 0.00 0.00 4.92
1899 3050 4.280425 TCAGCAAATTTGTCTATGTGGCAA 59.720 37.500 19.03 0.00 38.67 4.52
1900 3051 5.047164 TCAGCAAATTTGTCTATGTGGCAAT 60.047 36.000 19.03 0.00 40.27 3.56
1901 3052 5.062934 CAGCAAATTTGTCTATGTGGCAATG 59.937 40.000 19.03 0.10 40.27 2.82
1902 3053 5.047164 AGCAAATTTGTCTATGTGGCAATGA 60.047 36.000 19.03 0.00 40.27 2.57
1903 3054 5.290158 GCAAATTTGTCTATGTGGCAATGAG 59.710 40.000 19.03 0.00 40.27 2.90
1904 3055 6.392354 CAAATTTGTCTATGTGGCAATGAGT 58.608 36.000 10.15 0.00 40.27 3.41
1905 3056 6.594788 AATTTGTCTATGTGGCAATGAGTT 57.405 33.333 0.00 0.00 40.27 3.01
1906 3057 7.701539 AATTTGTCTATGTGGCAATGAGTTA 57.298 32.000 0.00 0.00 40.27 2.24
1907 3058 7.701539 ATTTGTCTATGTGGCAATGAGTTAA 57.298 32.000 0.00 0.00 40.27 2.01
1908 3059 7.701539 TTTGTCTATGTGGCAATGAGTTAAT 57.298 32.000 0.00 0.00 40.27 1.40
1909 3060 6.682423 TGTCTATGTGGCAATGAGTTAATG 57.318 37.500 0.00 0.00 0.00 1.90
1910 3061 6.413892 TGTCTATGTGGCAATGAGTTAATGA 58.586 36.000 0.00 0.00 0.00 2.57
1911 3062 6.883756 TGTCTATGTGGCAATGAGTTAATGAA 59.116 34.615 0.00 0.00 0.00 2.57
1912 3063 7.066163 TGTCTATGTGGCAATGAGTTAATGAAG 59.934 37.037 0.00 0.00 0.00 3.02
1913 3064 7.280876 GTCTATGTGGCAATGAGTTAATGAAGA 59.719 37.037 0.00 0.00 0.00 2.87
1914 3065 5.885230 TGTGGCAATGAGTTAATGAAGAG 57.115 39.130 0.00 0.00 0.00 2.85
1915 3066 5.559770 TGTGGCAATGAGTTAATGAAGAGA 58.440 37.500 0.00 0.00 0.00 3.10
1916 3067 6.003326 TGTGGCAATGAGTTAATGAAGAGAA 58.997 36.000 0.00 0.00 0.00 2.87
1917 3068 6.489700 TGTGGCAATGAGTTAATGAAGAGAAA 59.510 34.615 0.00 0.00 0.00 2.52
1918 3069 7.025963 GTGGCAATGAGTTAATGAAGAGAAAG 58.974 38.462 0.00 0.00 0.00 2.62
1919 3070 6.151648 TGGCAATGAGTTAATGAAGAGAAAGG 59.848 38.462 0.00 0.00 0.00 3.11
1920 3071 6.151817 GGCAATGAGTTAATGAAGAGAAAGGT 59.848 38.462 0.00 0.00 0.00 3.50
1921 3072 7.336931 GGCAATGAGTTAATGAAGAGAAAGGTA 59.663 37.037 0.00 0.00 0.00 3.08
1922 3073 8.394121 GCAATGAGTTAATGAAGAGAAAGGTAG 58.606 37.037 0.00 0.00 0.00 3.18
1923 3074 9.442047 CAATGAGTTAATGAAGAGAAAGGTAGT 57.558 33.333 0.00 0.00 0.00 2.73
1925 3076 9.660180 ATGAGTTAATGAAGAGAAAGGTAGTTC 57.340 33.333 0.00 0.00 0.00 3.01
1926 3077 8.871125 TGAGTTAATGAAGAGAAAGGTAGTTCT 58.129 33.333 0.00 0.00 40.62 3.01
1933 3084 8.937207 TGAAGAGAAAGGTAGTTCTAGTAACT 57.063 34.615 10.91 10.91 37.98 2.24
1934 3085 9.364653 TGAAGAGAAAGGTAGTTCTAGTAACTT 57.635 33.333 11.25 0.00 37.98 2.66
1937 3088 8.959548 AGAGAAAGGTAGTTCTAGTAACTTAGC 58.040 37.037 11.25 8.22 37.98 3.09
1938 3089 8.882557 AGAAAGGTAGTTCTAGTAACTTAGCT 57.117 34.615 11.25 0.00 36.06 3.32
1939 3090 9.972106 AGAAAGGTAGTTCTAGTAACTTAGCTA 57.028 33.333 11.25 0.00 36.06 3.32
1941 3092 9.752228 AAAGGTAGTTCTAGTAACTTAGCTAGT 57.248 33.333 11.25 0.00 39.32 2.57
1967 3118 7.969536 ACTGTAATATCACACATATCAAGGC 57.030 36.000 0.00 0.00 0.00 4.35
1968 3119 7.508687 ACTGTAATATCACACATATCAAGGCA 58.491 34.615 0.00 0.00 0.00 4.75
1969 3120 7.992608 ACTGTAATATCACACATATCAAGGCAA 59.007 33.333 0.00 0.00 0.00 4.52
1970 3121 8.382030 TGTAATATCACACATATCAAGGCAAG 57.618 34.615 0.00 0.00 0.00 4.01
1971 3122 8.210265 TGTAATATCACACATATCAAGGCAAGA 58.790 33.333 0.00 0.00 0.00 3.02
1972 3123 9.224267 GTAATATCACACATATCAAGGCAAGAT 57.776 33.333 0.00 0.00 0.00 2.40
1973 3124 7.683437 ATATCACACATATCAAGGCAAGATG 57.317 36.000 2.43 0.00 0.00 2.90
1974 3125 5.101648 TCACACATATCAAGGCAAGATGA 57.898 39.130 2.43 0.00 0.00 2.92
1975 3126 5.121105 TCACACATATCAAGGCAAGATGAG 58.879 41.667 2.43 0.00 0.00 2.90
1976 3127 4.880120 CACACATATCAAGGCAAGATGAGT 59.120 41.667 2.43 0.00 0.00 3.41
1977 3128 5.007430 CACACATATCAAGGCAAGATGAGTC 59.993 44.000 2.43 0.00 0.00 3.36
1978 3129 5.104610 ACACATATCAAGGCAAGATGAGTCT 60.105 40.000 2.43 0.00 35.82 3.24
1979 3130 6.098838 ACACATATCAAGGCAAGATGAGTCTA 59.901 38.462 2.43 0.00 33.30 2.59
1980 3131 7.160049 CACATATCAAGGCAAGATGAGTCTAT 58.840 38.462 2.43 0.00 33.30 1.98
1981 3132 8.309656 CACATATCAAGGCAAGATGAGTCTATA 58.690 37.037 2.43 0.00 33.30 1.31
1982 3133 8.530311 ACATATCAAGGCAAGATGAGTCTATAG 58.470 37.037 0.00 0.00 33.30 1.31
1983 3134 5.207110 TCAAGGCAAGATGAGTCTATAGC 57.793 43.478 0.00 0.00 33.30 2.97
1984 3135 4.651045 TCAAGGCAAGATGAGTCTATAGCA 59.349 41.667 0.00 0.00 33.30 3.49
1985 3136 5.306419 TCAAGGCAAGATGAGTCTATAGCAT 59.694 40.000 0.00 0.00 33.30 3.79
1986 3137 6.494835 TCAAGGCAAGATGAGTCTATAGCATA 59.505 38.462 0.00 0.00 33.30 3.14
1987 3138 6.924913 AGGCAAGATGAGTCTATAGCATAA 57.075 37.500 0.00 0.00 33.30 1.90
1988 3139 7.493499 AGGCAAGATGAGTCTATAGCATAAT 57.507 36.000 0.00 0.00 33.30 1.28
1989 3140 8.601047 AGGCAAGATGAGTCTATAGCATAATA 57.399 34.615 0.00 0.00 33.30 0.98
1990 3141 9.040259 AGGCAAGATGAGTCTATAGCATAATAA 57.960 33.333 0.00 0.00 33.30 1.40
1991 3142 9.658799 GGCAAGATGAGTCTATAGCATAATAAA 57.341 33.333 0.00 0.00 33.30 1.40
2005 3156 7.997107 AGCATAATAAATGAAGTGTTGCATG 57.003 32.000 0.00 0.00 0.00 4.06
2006 3157 7.549839 AGCATAATAAATGAAGTGTTGCATGT 58.450 30.769 0.00 0.00 0.00 3.21
2007 3158 8.036575 AGCATAATAAATGAAGTGTTGCATGTT 58.963 29.630 0.00 0.00 0.00 2.71
2008 3159 9.299963 GCATAATAAATGAAGTGTTGCATGTTA 57.700 29.630 0.00 0.00 0.00 2.41
2012 3163 9.840427 AATAAATGAAGTGTTGCATGTTACTAC 57.160 29.630 0.00 0.00 0.00 2.73
2013 3164 6.875948 AATGAAGTGTTGCATGTTACTACA 57.124 33.333 0.00 0.00 38.95 2.74
2014 3165 5.666969 TGAAGTGTTGCATGTTACTACAC 57.333 39.130 7.36 7.36 41.91 2.90
2015 3166 5.119694 TGAAGTGTTGCATGTTACTACACA 58.880 37.500 15.74 0.00 43.34 3.72
2016 3167 5.762711 TGAAGTGTTGCATGTTACTACACAT 59.237 36.000 15.74 5.81 43.34 3.21
2017 3168 6.931840 TGAAGTGTTGCATGTTACTACACATA 59.068 34.615 15.74 1.77 43.34 2.29
2018 3169 7.606073 TGAAGTGTTGCATGTTACTACACATAT 59.394 33.333 15.74 4.04 43.34 1.78
2019 3170 7.307493 AGTGTTGCATGTTACTACACATATG 57.693 36.000 15.74 0.00 43.34 1.78
2020 3171 6.878923 AGTGTTGCATGTTACTACACATATGT 59.121 34.615 15.74 1.41 43.34 2.29
2021 3172 7.390440 AGTGTTGCATGTTACTACACATATGTT 59.610 33.333 15.74 0.84 43.34 2.71
2022 3173 8.661257 GTGTTGCATGTTACTACACATATGTTA 58.339 33.333 5.37 2.01 41.45 2.41
2023 3174 8.661257 TGTTGCATGTTACTACACATATGTTAC 58.339 33.333 5.37 0.00 40.48 2.50
2024 3175 8.879759 GTTGCATGTTACTACACATATGTTACT 58.120 33.333 5.37 0.00 40.48 2.24
2025 3176 9.443323 TTGCATGTTACTACACATATGTTACTT 57.557 29.630 5.37 0.00 40.48 2.24
2026 3177 9.443323 TGCATGTTACTACACATATGTTACTTT 57.557 29.630 5.37 0.00 40.48 2.66
2027 3178 9.916397 GCATGTTACTACACATATGTTACTTTC 57.084 33.333 5.37 0.00 40.48 2.62
2030 3181 9.426837 TGTTACTACACATATGTTACTTTCCAC 57.573 33.333 5.37 0.00 40.48 4.02
2031 3182 9.649167 GTTACTACACATATGTTACTTTCCACT 57.351 33.333 5.37 0.00 40.48 4.00
2038 3189 9.698309 CACATATGTTACTTTCCACTATAGAGG 57.302 37.037 5.37 9.79 0.00 3.69
2039 3190 9.435570 ACATATGTTACTTTCCACTATAGAGGT 57.564 33.333 14.95 0.00 0.00 3.85
2044 3195 9.979897 TGTTACTTTCCACTATAGAGGTAGTAA 57.020 33.333 24.68 24.68 34.91 2.24
2046 3197 9.979897 TTACTTTCCACTATAGAGGTAGTAACA 57.020 33.333 24.68 14.84 33.82 2.41
2052 3203 9.168553 TCCACTATAGAGGTAGTAACATAGAGT 57.831 37.037 14.95 0.00 33.29 3.24
2062 3213 8.848182 AGGTAGTAACATAGAGTAGTAACATGC 58.152 37.037 0.00 0.00 0.00 4.06
2063 3214 8.848182 GGTAGTAACATAGAGTAGTAACATGCT 58.152 37.037 0.00 0.00 0.00 3.79
2064 3215 9.881529 GTAGTAACATAGAGTAGTAACATGCTC 57.118 37.037 0.00 0.00 32.62 4.26
2065 3216 8.521170 AGTAACATAGAGTAGTAACATGCTCA 57.479 34.615 0.00 0.00 34.67 4.26
2066 3217 9.137459 AGTAACATAGAGTAGTAACATGCTCAT 57.863 33.333 0.00 0.00 34.67 2.90
2067 3218 9.186323 GTAACATAGAGTAGTAACATGCTCATG 57.814 37.037 8.21 8.21 44.15 3.07
2084 3235 9.186323 CATGCTCATGTTACTACTCTATGTTAC 57.814 37.037 1.84 0.00 34.23 2.50
2085 3236 8.521170 TGCTCATGTTACTACTCTATGTTACT 57.479 34.615 0.00 0.00 0.00 2.24
2086 3237 9.623000 TGCTCATGTTACTACTCTATGTTACTA 57.377 33.333 0.00 0.00 0.00 1.82
2087 3238 9.881529 GCTCATGTTACTACTCTATGTTACTAC 57.118 37.037 0.00 0.00 0.00 2.73
2089 3240 9.347240 TCATGTTACTACTCTATGTTACTACCC 57.653 37.037 0.00 0.00 0.00 3.69
2090 3241 9.128404 CATGTTACTACTCTATGTTACTACCCA 57.872 37.037 0.00 0.00 0.00 4.51
2091 3242 9.878737 ATGTTACTACTCTATGTTACTACCCAT 57.121 33.333 0.00 0.00 0.00 4.00
2092 3243 9.705103 TGTTACTACTCTATGTTACTACCCATT 57.295 33.333 0.00 0.00 0.00 3.16
2093 3244 9.962783 GTTACTACTCTATGTTACTACCCATTG 57.037 37.037 0.00 0.00 0.00 2.82
2094 3245 9.705103 TTACTACTCTATGTTACTACCCATTGT 57.295 33.333 0.00 0.00 0.00 2.71
2095 3246 8.008513 ACTACTCTATGTTACTACCCATTGTG 57.991 38.462 0.00 0.00 0.00 3.33
2096 3247 6.235231 ACTCTATGTTACTACCCATTGTGG 57.765 41.667 0.00 0.00 37.25 4.17
2097 3248 5.031066 TCTATGTTACTACCCATTGTGGC 57.969 43.478 0.00 0.00 35.79 5.01
2098 3249 4.719773 TCTATGTTACTACCCATTGTGGCT 59.280 41.667 0.00 0.00 35.79 4.75
2099 3250 5.900699 TCTATGTTACTACCCATTGTGGCTA 59.099 40.000 0.00 0.00 35.79 3.93
2100 3251 4.481368 TGTTACTACCCATTGTGGCTAG 57.519 45.455 0.00 0.00 35.79 3.42
2101 3252 3.841845 TGTTACTACCCATTGTGGCTAGT 59.158 43.478 8.55 8.55 35.79 2.57
2102 3253 4.081309 TGTTACTACCCATTGTGGCTAGTC 60.081 45.833 7.13 0.00 35.79 2.59
2103 3254 2.834113 ACTACCCATTGTGGCTAGTCT 58.166 47.619 0.00 0.00 35.79 3.24
2104 3255 3.182152 ACTACCCATTGTGGCTAGTCTT 58.818 45.455 0.00 0.00 35.79 3.01
2105 3256 4.359105 ACTACCCATTGTGGCTAGTCTTA 58.641 43.478 0.00 0.00 35.79 2.10
2106 3257 3.914426 ACCCATTGTGGCTAGTCTTAG 57.086 47.619 0.00 0.00 35.79 2.18
2107 3258 3.450904 ACCCATTGTGGCTAGTCTTAGA 58.549 45.455 0.00 0.00 35.79 2.10
2220 3536 6.639671 TTTGTTAAATTTGCTGTGTGTGTC 57.360 33.333 0.00 0.00 0.00 3.67
2224 3540 0.670162 ATTTGCTGTGTGTGTCTGCC 59.330 50.000 0.00 0.00 0.00 4.85
2267 3593 7.920682 ACAGTGCCTAAGTTTAGAAAACATTTG 59.079 33.333 5.42 0.00 32.47 2.32
2280 3606 7.145932 AGAAAACATTTGTATTCCTCTTCCG 57.854 36.000 0.00 0.00 0.00 4.30
2281 3607 6.940298 AGAAAACATTTGTATTCCTCTTCCGA 59.060 34.615 0.00 0.00 0.00 4.55
2328 3684 8.608844 ATTACTTCTAATCAATCCGATCCAAC 57.391 34.615 0.00 0.00 31.11 3.77
2343 3699 6.204688 TCCGATCCAACAGAATGCATATAAAC 59.795 38.462 0.00 0.00 42.53 2.01
2570 4363 8.060090 CGCGGAGAATTTTAAAACGAGTATAAT 58.940 33.333 1.97 0.00 0.00 1.28
2573 4366 9.946165 GGAGAATTTTAAAACGAGTATAATGGG 57.054 33.333 1.97 0.00 0.00 4.00
2574 4367 9.946165 GAGAATTTTAAAACGAGTATAATGGGG 57.054 33.333 1.97 0.00 0.00 4.96
2575 4368 9.689501 AGAATTTTAAAACGAGTATAATGGGGA 57.310 29.630 1.97 0.00 0.00 4.81
2681 4482 7.172532 TCAAACTACACTTTATGCTTCGAATGT 59.827 33.333 0.00 0.00 0.00 2.71
2704 4505 9.816354 ATGTAATGAGTATTAAAAATTGGCCAC 57.184 29.630 3.88 0.00 30.92 5.01
2705 4506 9.030452 TGTAATGAGTATTAAAAATTGGCCACT 57.970 29.630 3.88 0.00 30.92 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.349636 TGTACAAATTGAGACCCTTGAGGA 59.650 41.667 0.00 0.00 39.89 3.71
12 13 6.391227 AACTTGTACAAATTGAGACCCTTG 57.609 37.500 10.03 0.00 0.00 3.61
21 22 6.292811 GGCATTCACCAAACTTGTACAAATTG 60.293 38.462 19.58 19.58 0.00 2.32
22 23 5.757808 GGCATTCACCAAACTTGTACAAATT 59.242 36.000 10.03 2.62 0.00 1.82
31 32 2.380064 TGAGGGCATTCACCAAACTT 57.620 45.000 0.00 0.00 0.00 2.66
32 33 2.242043 CTTGAGGGCATTCACCAAACT 58.758 47.619 0.00 0.00 0.00 2.66
54 55 2.232941 TGTCGTGAATCCACTAAGGGAC 59.767 50.000 0.00 0.00 40.44 4.46
57 58 2.233922 AGGTGTCGTGAATCCACTAAGG 59.766 50.000 0.00 0.00 41.06 2.69
64 65 1.453155 ATGCAAGGTGTCGTGAATCC 58.547 50.000 0.00 0.00 0.00 3.01
72 73 1.335324 GCTCACACAATGCAAGGTGTC 60.335 52.381 20.08 8.98 45.86 3.67
81 82 1.073964 CTCCTCACGCTCACACAATG 58.926 55.000 0.00 0.00 0.00 2.82
105 108 2.034066 ACCCACAATGGCTGACCG 59.966 61.111 0.00 0.00 39.70 4.79
106 109 0.251341 AAGACCCACAATGGCTGACC 60.251 55.000 0.00 0.00 35.79 4.02
109 112 1.683011 CCCTAAGACCCACAATGGCTG 60.683 57.143 0.00 0.00 35.79 4.85
121 124 0.391793 GGCACAGTGCTCCCTAAGAC 60.392 60.000 24.75 1.14 44.28 3.01
134 137 4.320456 AGCGGTGTGGAGGCACAG 62.320 66.667 0.00 0.00 40.89 3.66
150 153 3.919804 GCAGATGCTAATCTTCGCTAGAG 59.080 47.826 0.00 0.00 41.43 2.43
172 175 1.917872 TCCCGAAATTCACCCCTTTG 58.082 50.000 0.00 0.00 0.00 2.77
184 187 3.889538 AGAGATGACGATGTATCCCGAAA 59.110 43.478 0.00 0.00 0.00 3.46
185 188 3.253432 CAGAGATGACGATGTATCCCGAA 59.747 47.826 0.00 0.00 0.00 4.30
201 204 3.137913 AGATAACCAAGGCATGCAGAGAT 59.862 43.478 21.36 2.70 0.00 2.75
206 209 3.370840 AAGAGATAACCAAGGCATGCA 57.629 42.857 21.36 0.00 0.00 3.96
264 267 9.888878 CAAGATATATAACCTGAAGCACAATTG 57.111 33.333 3.24 3.24 0.00 2.32
265 268 8.571336 GCAAGATATATAACCTGAAGCACAATT 58.429 33.333 0.00 0.00 0.00 2.32
269 946 7.496529 TTGCAAGATATATAACCTGAAGCAC 57.503 36.000 0.00 0.00 0.00 4.40
294 971 6.128391 GCTAAATCAGATAAACAACGGTGTGA 60.128 38.462 6.99 0.00 38.27 3.58
299 976 6.176975 TGTGCTAAATCAGATAAACAACGG 57.823 37.500 0.00 0.00 0.00 4.44
300 977 7.298122 ACTTGTGCTAAATCAGATAAACAACG 58.702 34.615 0.00 0.00 0.00 4.10
306 983 7.230510 ACCAACAACTTGTGCTAAATCAGATAA 59.769 33.333 0.00 0.00 0.00 1.75
313 990 6.952773 TCTAACCAACAACTTGTGCTAAAT 57.047 33.333 0.00 0.00 0.00 1.40
324 1001 3.572255 TCAGGGCAAATCTAACCAACAAC 59.428 43.478 0.00 0.00 0.00 3.32
329 1006 4.018506 TGAATCTCAGGGCAAATCTAACCA 60.019 41.667 0.00 0.00 0.00 3.67
438 1263 5.575104 TTGGGTTCCATGTACACGAATGTG 61.575 45.833 0.00 0.00 42.09 3.21
443 1268 2.496111 GTTTGGGTTCCATGTACACGA 58.504 47.619 0.00 0.00 31.53 4.35
467 1293 6.037830 AGCTTGCGTTTAGTTTTAGTTTCAGA 59.962 34.615 0.00 0.00 0.00 3.27
514 1340 0.322456 GCATAGTGGTGGCAACTGGA 60.322 55.000 3.27 0.00 37.61 3.86
595 1421 1.071605 CCTGTTCGCTAAGTGAGTGC 58.928 55.000 0.00 0.00 35.48 4.40
701 1536 3.381949 GTGTTGTTAAGTCGCTCTCTGT 58.618 45.455 0.00 0.00 0.00 3.41
706 1541 2.121786 TCACGTGTTGTTAAGTCGCTC 58.878 47.619 16.51 0.00 0.00 5.03
795 1633 2.663852 AAACGCAGCTTACGCCGT 60.664 55.556 5.83 0.00 35.95 5.68
910 1748 0.386858 GCTTAGTGTCGTGCTCGTGA 60.387 55.000 8.17 0.00 38.33 4.35
1438 2319 1.458777 TGGACGTGACTTCCTGGGT 60.459 57.895 9.63 0.00 33.84 4.51
1543 2424 1.948834 CATGTCCATGCTTAATGCGGA 59.051 47.619 0.00 0.00 46.63 5.54
1668 2549 4.080919 CAGTCTCCATTGTCCCAGTATTGA 60.081 45.833 0.00 0.00 0.00 2.57
1671 2552 2.171448 GCAGTCTCCATTGTCCCAGTAT 59.829 50.000 0.00 0.00 0.00 2.12
1842 2993 5.331876 AGTTACTGCTGAAGTTAGGCTAG 57.668 43.478 0.00 0.00 40.56 3.42
1843 2994 5.245301 TGAAGTTACTGCTGAAGTTAGGCTA 59.755 40.000 0.00 0.00 40.56 3.93
1844 2995 4.040461 TGAAGTTACTGCTGAAGTTAGGCT 59.960 41.667 0.00 0.00 40.56 4.58
1845 2996 4.315803 TGAAGTTACTGCTGAAGTTAGGC 58.684 43.478 0.00 0.00 40.56 3.93
1846 2997 5.992217 ACTTGAAGTTACTGCTGAAGTTAGG 59.008 40.000 0.00 0.00 40.56 2.69
1847 2998 6.146347 GGACTTGAAGTTACTGCTGAAGTTAG 59.854 42.308 0.00 0.00 40.56 2.34
1848 2999 5.989777 GGACTTGAAGTTACTGCTGAAGTTA 59.010 40.000 0.00 0.00 40.56 2.24
1849 3000 4.816925 GGACTTGAAGTTACTGCTGAAGTT 59.183 41.667 0.00 0.00 40.56 2.66
1850 3001 4.141711 TGGACTTGAAGTTACTGCTGAAGT 60.142 41.667 0.00 0.00 43.40 3.01
1851 3002 4.380531 TGGACTTGAAGTTACTGCTGAAG 58.619 43.478 0.00 0.00 0.00 3.02
1852 3003 4.415881 TGGACTTGAAGTTACTGCTGAA 57.584 40.909 0.00 0.00 0.00 3.02
1853 3004 4.127171 GTTGGACTTGAAGTTACTGCTGA 58.873 43.478 0.00 0.00 0.00 4.26
1854 3005 4.130118 AGTTGGACTTGAAGTTACTGCTG 58.870 43.478 0.00 0.00 0.00 4.41
1855 3006 4.141711 TGAGTTGGACTTGAAGTTACTGCT 60.142 41.667 11.60 5.84 0.00 4.24
1856 3007 4.127171 TGAGTTGGACTTGAAGTTACTGC 58.873 43.478 11.60 0.00 0.00 4.40
1857 3008 4.212214 GCTGAGTTGGACTTGAAGTTACTG 59.788 45.833 11.60 2.93 0.00 2.74
1858 3009 4.141711 TGCTGAGTTGGACTTGAAGTTACT 60.142 41.667 0.00 3.96 0.00 2.24
1859 3010 4.127171 TGCTGAGTTGGACTTGAAGTTAC 58.873 43.478 0.00 0.00 0.00 2.50
1860 3011 4.415881 TGCTGAGTTGGACTTGAAGTTA 57.584 40.909 0.00 0.00 0.00 2.24
1861 3012 3.281727 TGCTGAGTTGGACTTGAAGTT 57.718 42.857 0.00 0.00 0.00 2.66
1862 3013 3.281727 TTGCTGAGTTGGACTTGAAGT 57.718 42.857 0.00 0.00 0.00 3.01
1863 3014 4.843220 ATTTGCTGAGTTGGACTTGAAG 57.157 40.909 0.00 0.00 0.00 3.02
1864 3015 5.105392 ACAAATTTGCTGAGTTGGACTTGAA 60.105 36.000 18.12 0.00 0.00 2.69
1865 3016 4.402155 ACAAATTTGCTGAGTTGGACTTGA 59.598 37.500 18.12 0.00 0.00 3.02
1866 3017 4.685924 ACAAATTTGCTGAGTTGGACTTG 58.314 39.130 18.12 0.00 0.00 3.16
1867 3018 4.646492 AGACAAATTTGCTGAGTTGGACTT 59.354 37.500 18.12 0.00 0.00 3.01
1868 3019 4.210331 AGACAAATTTGCTGAGTTGGACT 58.790 39.130 18.12 0.00 0.00 3.85
1869 3020 4.574599 AGACAAATTTGCTGAGTTGGAC 57.425 40.909 18.12 0.00 0.00 4.02
1870 3021 5.769662 ACATAGACAAATTTGCTGAGTTGGA 59.230 36.000 18.12 0.79 0.00 3.53
1871 3022 5.860182 CACATAGACAAATTTGCTGAGTTGG 59.140 40.000 18.12 3.57 0.00 3.77
1872 3023 5.860182 CCACATAGACAAATTTGCTGAGTTG 59.140 40.000 18.12 10.57 0.00 3.16
1873 3024 5.565439 GCCACATAGACAAATTTGCTGAGTT 60.565 40.000 18.12 0.00 0.00 3.01
1874 3025 4.082571 GCCACATAGACAAATTTGCTGAGT 60.083 41.667 18.12 14.11 0.00 3.41
1875 3026 4.082625 TGCCACATAGACAAATTTGCTGAG 60.083 41.667 18.12 13.60 0.00 3.35
1876 3027 3.825585 TGCCACATAGACAAATTTGCTGA 59.174 39.130 18.12 3.65 0.00 4.26
1877 3028 4.177165 TGCCACATAGACAAATTTGCTG 57.823 40.909 18.12 12.32 0.00 4.41
1878 3029 4.870123 TTGCCACATAGACAAATTTGCT 57.130 36.364 18.12 16.84 0.00 3.91
1879 3030 5.170021 TCATTGCCACATAGACAAATTTGC 58.830 37.500 18.12 10.76 0.00 3.68
1880 3031 6.392354 ACTCATTGCCACATAGACAAATTTG 58.608 36.000 16.67 16.67 0.00 2.32
1881 3032 6.594788 ACTCATTGCCACATAGACAAATTT 57.405 33.333 0.00 0.00 0.00 1.82
1882 3033 6.594788 AACTCATTGCCACATAGACAAATT 57.405 33.333 0.00 0.00 0.00 1.82
1883 3034 7.701539 TTAACTCATTGCCACATAGACAAAT 57.298 32.000 0.00 0.00 0.00 2.32
1884 3035 7.392953 TCATTAACTCATTGCCACATAGACAAA 59.607 33.333 0.00 0.00 0.00 2.83
1885 3036 6.883756 TCATTAACTCATTGCCACATAGACAA 59.116 34.615 0.00 0.00 0.00 3.18
1886 3037 6.413892 TCATTAACTCATTGCCACATAGACA 58.586 36.000 0.00 0.00 0.00 3.41
1887 3038 6.925610 TCATTAACTCATTGCCACATAGAC 57.074 37.500 0.00 0.00 0.00 2.59
1888 3039 7.337938 TCTTCATTAACTCATTGCCACATAGA 58.662 34.615 0.00 0.00 0.00 1.98
1889 3040 7.496920 TCTCTTCATTAACTCATTGCCACATAG 59.503 37.037 0.00 0.00 0.00 2.23
1890 3041 7.337938 TCTCTTCATTAACTCATTGCCACATA 58.662 34.615 0.00 0.00 0.00 2.29
1891 3042 6.182627 TCTCTTCATTAACTCATTGCCACAT 58.817 36.000 0.00 0.00 0.00 3.21
1892 3043 5.559770 TCTCTTCATTAACTCATTGCCACA 58.440 37.500 0.00 0.00 0.00 4.17
1893 3044 6.500684 TTCTCTTCATTAACTCATTGCCAC 57.499 37.500 0.00 0.00 0.00 5.01
1894 3045 6.151648 CCTTTCTCTTCATTAACTCATTGCCA 59.848 38.462 0.00 0.00 0.00 4.92
1895 3046 6.151817 ACCTTTCTCTTCATTAACTCATTGCC 59.848 38.462 0.00 0.00 0.00 4.52
1896 3047 7.150783 ACCTTTCTCTTCATTAACTCATTGC 57.849 36.000 0.00 0.00 0.00 3.56
1897 3048 9.442047 ACTACCTTTCTCTTCATTAACTCATTG 57.558 33.333 0.00 0.00 0.00 2.82
1899 3050 9.660180 GAACTACCTTTCTCTTCATTAACTCAT 57.340 33.333 0.00 0.00 0.00 2.90
1900 3051 8.871125 AGAACTACCTTTCTCTTCATTAACTCA 58.129 33.333 0.00 0.00 29.24 3.41
1907 3058 9.536510 AGTTACTAGAACTACCTTTCTCTTCAT 57.463 33.333 0.00 0.00 37.09 2.57
1908 3059 8.937207 AGTTACTAGAACTACCTTTCTCTTCA 57.063 34.615 0.00 0.00 37.09 3.02
1911 3062 8.959548 GCTAAGTTACTAGAACTACCTTTCTCT 58.040 37.037 0.00 0.00 37.09 3.10
1912 3063 8.959548 AGCTAAGTTACTAGAACTACCTTTCTC 58.040 37.037 0.00 0.00 37.09 2.87
1913 3064 8.882557 AGCTAAGTTACTAGAACTACCTTTCT 57.117 34.615 0.00 0.00 39.28 2.52
1915 3066 9.752228 ACTAGCTAAGTTACTAGAACTACCTTT 57.248 33.333 18.49 0.00 38.53 3.11
1916 3067 9.752228 AACTAGCTAAGTTACTAGAACTACCTT 57.248 33.333 18.49 5.65 46.85 3.50
1941 3092 9.489084 GCCTTGATATGTGTGATATTACAGTAA 57.511 33.333 0.00 0.00 0.00 2.24
1942 3093 8.646900 TGCCTTGATATGTGTGATATTACAGTA 58.353 33.333 0.00 0.00 0.00 2.74
1943 3094 7.508687 TGCCTTGATATGTGTGATATTACAGT 58.491 34.615 0.00 0.00 0.00 3.55
1944 3095 7.967890 TGCCTTGATATGTGTGATATTACAG 57.032 36.000 0.00 0.00 0.00 2.74
1945 3096 8.210265 TCTTGCCTTGATATGTGTGATATTACA 58.790 33.333 0.00 0.00 0.00 2.41
1946 3097 8.607441 TCTTGCCTTGATATGTGTGATATTAC 57.393 34.615 0.00 0.00 0.00 1.89
1947 3098 9.223099 CATCTTGCCTTGATATGTGTGATATTA 57.777 33.333 0.00 0.00 0.00 0.98
1948 3099 7.940688 TCATCTTGCCTTGATATGTGTGATATT 59.059 33.333 0.00 0.00 0.00 1.28
1949 3100 7.455891 TCATCTTGCCTTGATATGTGTGATAT 58.544 34.615 0.00 0.00 0.00 1.63
1950 3101 6.829849 TCATCTTGCCTTGATATGTGTGATA 58.170 36.000 0.00 0.00 0.00 2.15
1951 3102 5.687780 TCATCTTGCCTTGATATGTGTGAT 58.312 37.500 0.00 0.00 0.00 3.06
1952 3103 5.101648 TCATCTTGCCTTGATATGTGTGA 57.898 39.130 0.00 0.00 0.00 3.58
1953 3104 4.880120 ACTCATCTTGCCTTGATATGTGTG 59.120 41.667 0.00 0.00 0.00 3.82
1954 3105 5.104610 AGACTCATCTTGCCTTGATATGTGT 60.105 40.000 0.00 0.00 0.00 3.72
1955 3106 5.366460 AGACTCATCTTGCCTTGATATGTG 58.634 41.667 0.00 0.00 0.00 3.21
1956 3107 5.627182 AGACTCATCTTGCCTTGATATGT 57.373 39.130 0.00 0.00 0.00 2.29
1957 3108 7.492020 GCTATAGACTCATCTTGCCTTGATATG 59.508 40.741 3.21 0.00 36.29 1.78
1958 3109 7.179872 TGCTATAGACTCATCTTGCCTTGATAT 59.820 37.037 3.21 0.00 36.29 1.63
1959 3110 6.494835 TGCTATAGACTCATCTTGCCTTGATA 59.505 38.462 3.21 0.00 36.29 2.15
1960 3111 5.306419 TGCTATAGACTCATCTTGCCTTGAT 59.694 40.000 3.21 0.00 36.29 2.57
1961 3112 4.651045 TGCTATAGACTCATCTTGCCTTGA 59.349 41.667 3.21 0.00 36.29 3.02
1962 3113 4.953667 TGCTATAGACTCATCTTGCCTTG 58.046 43.478 3.21 0.00 36.29 3.61
1963 3114 5.822132 ATGCTATAGACTCATCTTGCCTT 57.178 39.130 3.21 0.00 36.29 4.35
1964 3115 6.924913 TTATGCTATAGACTCATCTTGCCT 57.075 37.500 3.21 0.00 36.29 4.75
1965 3116 9.658799 TTTATTATGCTATAGACTCATCTTGCC 57.341 33.333 3.21 0.00 36.29 4.52
1979 3130 9.687210 CATGCAACACTTCATTTATTATGCTAT 57.313 29.630 0.00 0.00 32.74 2.97
1980 3131 8.685427 ACATGCAACACTTCATTTATTATGCTA 58.315 29.630 0.00 0.00 32.74 3.49
1981 3132 7.549839 ACATGCAACACTTCATTTATTATGCT 58.450 30.769 0.00 0.00 32.74 3.79
1982 3133 7.760131 ACATGCAACACTTCATTTATTATGC 57.240 32.000 0.00 0.00 0.00 3.14
1986 3137 9.840427 GTAGTAACATGCAACACTTCATTTATT 57.160 29.630 0.00 0.00 0.00 1.40
1987 3138 9.008965 TGTAGTAACATGCAACACTTCATTTAT 57.991 29.630 0.00 0.00 0.00 1.40
1988 3139 8.286800 GTGTAGTAACATGCAACACTTCATTTA 58.713 33.333 8.05 0.00 38.08 1.40
1989 3140 7.138736 GTGTAGTAACATGCAACACTTCATTT 58.861 34.615 8.05 0.00 38.08 2.32
1990 3141 6.262049 TGTGTAGTAACATGCAACACTTCATT 59.738 34.615 14.68 0.00 40.78 2.57
1991 3142 5.762711 TGTGTAGTAACATGCAACACTTCAT 59.237 36.000 14.68 0.00 40.78 2.57
1992 3143 5.119694 TGTGTAGTAACATGCAACACTTCA 58.880 37.500 14.68 6.42 40.78 3.02
1993 3144 5.666969 TGTGTAGTAACATGCAACACTTC 57.333 39.130 14.68 4.31 40.78 3.01
1994 3145 7.390440 ACATATGTGTAGTAACATGCAACACTT 59.610 33.333 7.78 11.45 40.93 3.16
1995 3146 6.878923 ACATATGTGTAGTAACATGCAACACT 59.121 34.615 7.78 7.40 40.93 3.55
1996 3147 7.072177 ACATATGTGTAGTAACATGCAACAC 57.928 36.000 7.78 8.32 40.93 3.32
1997 3148 7.680442 AACATATGTGTAGTAACATGCAACA 57.320 32.000 9.63 0.00 40.93 3.33
1998 3149 8.879759 AGTAACATATGTGTAGTAACATGCAAC 58.120 33.333 9.63 0.00 40.93 4.17
1999 3150 9.443323 AAGTAACATATGTGTAGTAACATGCAA 57.557 29.630 9.63 0.00 40.93 4.08
2000 3151 9.443323 AAAGTAACATATGTGTAGTAACATGCA 57.557 29.630 9.63 0.00 40.93 3.96
2001 3152 9.916397 GAAAGTAACATATGTGTAGTAACATGC 57.084 33.333 9.63 0.00 40.93 4.06
2004 3155 9.426837 GTGGAAAGTAACATATGTGTAGTAACA 57.573 33.333 9.63 2.24 37.67 2.41
2005 3156 9.649167 AGTGGAAAGTAACATATGTGTAGTAAC 57.351 33.333 9.63 2.39 37.67 2.50
2012 3163 9.698309 CCTCTATAGTGGAAAGTAACATATGTG 57.302 37.037 14.57 0.00 0.00 3.21
2013 3164 9.435570 ACCTCTATAGTGGAAAGTAACATATGT 57.564 33.333 24.32 1.41 33.21 2.29
2018 3169 9.979897 TTACTACCTCTATAGTGGAAAGTAACA 57.020 33.333 27.34 18.04 36.71 2.41
2020 3171 9.979897 TGTTACTACCTCTATAGTGGAAAGTAA 57.020 33.333 27.34 27.34 37.77 2.24
2026 3177 9.168553 ACTCTATGTTACTACCTCTATAGTGGA 57.831 37.037 24.32 9.50 36.09 4.02
2036 3187 8.848182 GCATGTTACTACTCTATGTTACTACCT 58.152 37.037 0.00 0.00 0.00 3.08
2037 3188 8.848182 AGCATGTTACTACTCTATGTTACTACC 58.152 37.037 0.00 0.00 0.00 3.18
2038 3189 9.881529 GAGCATGTTACTACTCTATGTTACTAC 57.118 37.037 0.00 0.00 0.00 2.73
2039 3190 9.623000 TGAGCATGTTACTACTCTATGTTACTA 57.377 33.333 0.00 0.00 0.00 1.82
2040 3191 8.521170 TGAGCATGTTACTACTCTATGTTACT 57.479 34.615 0.00 0.00 0.00 2.24
2041 3192 9.186323 CATGAGCATGTTACTACTCTATGTTAC 57.814 37.037 2.34 0.00 34.23 2.50
2058 3209 9.186323 GTAACATAGAGTAGTAACATGAGCATG 57.814 37.037 8.82 8.82 44.15 4.06
2059 3210 9.137459 AGTAACATAGAGTAGTAACATGAGCAT 57.863 33.333 0.00 0.00 0.00 3.79
2060 3211 8.521170 AGTAACATAGAGTAGTAACATGAGCA 57.479 34.615 0.00 0.00 0.00 4.26
2061 3212 9.881529 GTAGTAACATAGAGTAGTAACATGAGC 57.118 37.037 0.00 0.00 0.00 4.26
2063 3214 9.347240 GGGTAGTAACATAGAGTAGTAACATGA 57.653 37.037 0.00 0.00 0.00 3.07
2064 3215 9.128404 TGGGTAGTAACATAGAGTAGTAACATG 57.872 37.037 0.00 0.00 0.00 3.21
2065 3216 9.878737 ATGGGTAGTAACATAGAGTAGTAACAT 57.121 33.333 0.00 0.00 0.00 2.71
2066 3217 9.705103 AATGGGTAGTAACATAGAGTAGTAACA 57.295 33.333 0.00 0.00 0.00 2.41
2067 3218 9.962783 CAATGGGTAGTAACATAGAGTAGTAAC 57.037 37.037 0.00 0.00 0.00 2.50
2068 3219 9.705103 ACAATGGGTAGTAACATAGAGTAGTAA 57.295 33.333 0.00 0.00 0.00 2.24
2069 3220 9.128404 CACAATGGGTAGTAACATAGAGTAGTA 57.872 37.037 0.00 0.00 0.00 1.82
2070 3221 7.069578 CCACAATGGGTAGTAACATAGAGTAGT 59.930 40.741 0.00 0.00 32.67 2.73
2071 3222 7.434492 CCACAATGGGTAGTAACATAGAGTAG 58.566 42.308 0.00 0.00 32.67 2.57
2072 3223 6.183360 GCCACAATGGGTAGTAACATAGAGTA 60.183 42.308 0.00 0.00 38.19 2.59
2073 3224 5.396436 GCCACAATGGGTAGTAACATAGAGT 60.396 44.000 0.00 0.00 38.19 3.24
2074 3225 5.057149 GCCACAATGGGTAGTAACATAGAG 58.943 45.833 0.00 0.00 38.19 2.43
2075 3226 5.031066 GCCACAATGGGTAGTAACATAGA 57.969 43.478 0.00 0.00 38.19 1.98
2087 3238 3.706594 TCTCTAAGACTAGCCACAATGGG 59.293 47.826 0.00 0.00 38.19 4.00
2088 3239 5.295950 CATCTCTAAGACTAGCCACAATGG 58.704 45.833 0.00 0.00 41.55 3.16
2089 3240 5.069648 TCCATCTCTAAGACTAGCCACAATG 59.930 44.000 0.00 0.00 0.00 2.82
2090 3241 5.211973 TCCATCTCTAAGACTAGCCACAAT 58.788 41.667 0.00 0.00 0.00 2.71
2091 3242 4.610333 TCCATCTCTAAGACTAGCCACAA 58.390 43.478 0.00 0.00 0.00 3.33
2092 3243 4.251103 TCCATCTCTAAGACTAGCCACA 57.749 45.455 0.00 0.00 0.00 4.17
2093 3244 8.760980 ATATATCCATCTCTAAGACTAGCCAC 57.239 38.462 0.00 0.00 0.00 5.01
2094 3245 9.415008 GAATATATCCATCTCTAAGACTAGCCA 57.585 37.037 0.00 0.00 0.00 4.75
2095 3246 9.415008 TGAATATATCCATCTCTAAGACTAGCC 57.585 37.037 0.00 0.00 0.00 3.93
2200 3352 4.207019 GCAGACACACACAGCAAATTTAAC 59.793 41.667 0.00 0.00 0.00 2.01
2206 3358 1.383456 GGGCAGACACACACAGCAAA 61.383 55.000 0.00 0.00 0.00 3.68
2207 3359 1.823470 GGGCAGACACACACAGCAA 60.823 57.895 0.00 0.00 0.00 3.91
2224 3540 2.184448 CTGTTTCCATATTTTGCGCGG 58.816 47.619 8.83 0.00 0.00 6.46
2309 3635 5.869649 TCTGTTGGATCGGATTGATTAGA 57.130 39.130 0.00 0.00 37.47 2.10
2310 3636 6.567321 GCATTCTGTTGGATCGGATTGATTAG 60.567 42.308 0.00 0.00 37.47 1.73
2311 3637 5.239306 GCATTCTGTTGGATCGGATTGATTA 59.761 40.000 0.00 0.00 37.47 1.75
2439 4229 4.690748 TCAAGTTGCTAGACATTGCTACAC 59.309 41.667 0.00 0.00 37.38 2.90
2545 4338 9.155053 CATTATACTCGTTTTAAAATTCTCCGC 57.845 33.333 3.52 0.00 0.00 5.54
2617 4416 9.276590 TCATGCTTTGACTATCAATGTTATAGG 57.723 33.333 6.38 0.00 36.11 2.57
2681 4482 9.249053 TGAGTGGCCAATTTTTAATACTCATTA 57.751 29.630 7.24 0.00 38.55 1.90
2696 4497 2.893424 ACCAAAGAATGAGTGGCCAAT 58.107 42.857 7.24 5.98 35.72 3.16
2698 4499 2.642311 TCTACCAAAGAATGAGTGGCCA 59.358 45.455 0.00 0.00 35.72 5.36
2700 4501 4.517285 TCATCTACCAAAGAATGAGTGGC 58.483 43.478 0.00 0.00 37.89 5.01
2702 4503 8.899427 ACATATCATCTACCAAAGAATGAGTG 57.101 34.615 0.00 0.00 37.89 3.51
2705 4506 9.494271 GCTTACATATCATCTACCAAAGAATGA 57.506 33.333 0.00 0.00 37.89 2.57


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

AutoCloner maintained by Alex Coulton.