Multiple sequence alignment - TraesCS3A01G015400

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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 TraesCS3A01G015400 chr3A 100.000 3686 0 0 1 3686 10289732 10293417 0.000000e+00 6807.0
1 TraesCS3A01G015400 chr3A 90.496 242 10 7 3 233 505060981 505060742 1.290000e-79 307.0
2 TraesCS3A01G015400 chr4D 97.685 3024 65 3 664 3686 127927843 127930862 0.000000e+00 5192.0
3 TraesCS3A01G015400 chr4D 95.735 422 11 5 231 651 127927145 127927560 0.000000e+00 673.0
4 TraesCS3A01G015400 chr4D 85.668 614 85 3 3075 3686 85641400 85642012 0.000000e+00 643.0
5 TraesCS3A01G015400 chr4D 78.535 396 81 3 294 689 458156947 458156556 1.310000e-64 257.0
6 TraesCS3A01G015400 chr4B 93.072 3089 162 25 629 3686 191787977 191791044 0.000000e+00 4471.0
7 TraesCS3A01G015400 chr4B 91.928 223 16 2 398 620 191715032 191715252 9.940000e-81 311.0
8 TraesCS3A01G015400 chr4A 93.528 2395 113 14 231 2590 440255932 440253545 0.000000e+00 3526.0
9 TraesCS3A01G015400 chr4A 89.062 192 18 2 27 215 217351778 217351969 6.150000e-58 235.0
10 TraesCS3A01G015400 chr7A 89.122 763 76 6 2928 3686 8585251 8586010 0.000000e+00 942.0
11 TraesCS3A01G015400 chr7A 77.297 947 150 37 1254 2193 126919190 126918302 7.110000e-137 497.0
12 TraesCS3A01G015400 chr7A 87.500 152 17 2 86 236 599944023 599943873 1.360000e-39 174.0
13 TraesCS3A01G015400 chr7A 81.111 180 21 11 1463 1637 80143644 80143815 8.310000e-27 132.0
14 TraesCS3A01G015400 chr2D 85.033 902 119 13 2790 3686 393209604 393210494 0.000000e+00 904.0
15 TraesCS3A01G015400 chr5B 82.547 911 134 20 2795 3686 222296571 222295667 0.000000e+00 778.0
16 TraesCS3A01G015400 chr5D 81.818 902 149 12 2790 3686 350437426 350438317 0.000000e+00 743.0
17 TraesCS3A01G015400 chr7B 76.194 1466 259 52 1254 2691 86165887 86164484 0.000000e+00 691.0
18 TraesCS3A01G015400 chr7B 81.529 157 19 7 1463 1614 22463401 22463552 1.800000e-23 121.0
19 TraesCS3A01G015400 chr2A 82.949 780 117 12 2789 3557 662749845 662750619 0.000000e+00 689.0
20 TraesCS3A01G015400 chr7D 75.770 1461 265 53 1254 2691 124504984 124503590 0.000000e+00 654.0
21 TraesCS3A01G015400 chr7D 79.679 187 20 15 1463 1637 75956101 75955921 6.470000e-23 119.0
22 TraesCS3A01G015400 chr3B 79.912 911 156 22 2791 3686 446061636 446060738 0.000000e+00 643.0
23 TraesCS3A01G015400 chr2B 81.439 792 139 7 2900 3686 542954110 542953322 3.100000e-180 641.0
24 TraesCS3A01G015400 chr2B 90.295 237 9 2 1 233 780823486 780823260 7.740000e-77 298.0
25 TraesCS3A01G015400 chr1B 93.776 241 10 2 3 239 84417255 84417016 1.260000e-94 357.0
26 TraesCS3A01G015400 chr1B 79.024 410 66 16 294 697 98429050 98429445 2.820000e-66 263.0
27 TraesCS3A01G015400 chr6B 93.966 232 10 1 1 228 107875597 107875828 7.580000e-92 348.0
28 TraesCS3A01G015400 chr6B 92.340 235 14 1 1 231 664715388 664715154 7.630000e-87 331.0
29 TraesCS3A01G015400 chr6B 89.787 235 10 2 1 231 232756548 232756772 4.660000e-74 289.0
30 TraesCS3A01G015400 chr6B 88.971 136 14 1 97 232 675193191 675193057 2.280000e-37 167.0
31 TraesCS3A01G015400 chr5A 89.167 240 13 6 1 229 510986734 510986497 1.680000e-73 287.0
32 TraesCS3A01G015400 chrUn 79.024 410 66 16 294 697 397660239 397660634 2.820000e-66 263.0
33 TraesCS3A01G015400 chr1A 96.711 152 4 1 2795 2945 13822539 13822690 6.110000e-63 252.0
34 TraesCS3A01G015400 chr6A 89.062 192 18 2 27 215 321274922 321274731 6.150000e-58 235.0
35 TraesCS3A01G015400 chr6A 86.207 87 9 3 2783 2867 390575392 390575477 1.410000e-14 91.6
36 TraesCS3A01G015400 chr6D 78.613 173 27 8 2785 2948 3968337 3968166 5.030000e-19 106.0


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 TraesCS3A01G015400 chr3A 10289732 10293417 3685 False 6807.0 6807 100.000 1 3686 1 chr3A.!!$F1 3685
1 TraesCS3A01G015400 chr4D 127927145 127930862 3717 False 2932.5 5192 96.710 231 3686 2 chr4D.!!$F2 3455
2 TraesCS3A01G015400 chr4D 85641400 85642012 612 False 643.0 643 85.668 3075 3686 1 chr4D.!!$F1 611
3 TraesCS3A01G015400 chr4B 191787977 191791044 3067 False 4471.0 4471 93.072 629 3686 1 chr4B.!!$F2 3057
4 TraesCS3A01G015400 chr4A 440253545 440255932 2387 True 3526.0 3526 93.528 231 2590 1 chr4A.!!$R1 2359
5 TraesCS3A01G015400 chr7A 8585251 8586010 759 False 942.0 942 89.122 2928 3686 1 chr7A.!!$F1 758
6 TraesCS3A01G015400 chr7A 126918302 126919190 888 True 497.0 497 77.297 1254 2193 1 chr7A.!!$R1 939
7 TraesCS3A01G015400 chr2D 393209604 393210494 890 False 904.0 904 85.033 2790 3686 1 chr2D.!!$F1 896
8 TraesCS3A01G015400 chr5B 222295667 222296571 904 True 778.0 778 82.547 2795 3686 1 chr5B.!!$R1 891
9 TraesCS3A01G015400 chr5D 350437426 350438317 891 False 743.0 743 81.818 2790 3686 1 chr5D.!!$F1 896
10 TraesCS3A01G015400 chr7B 86164484 86165887 1403 True 691.0 691 76.194 1254 2691 1 chr7B.!!$R1 1437
11 TraesCS3A01G015400 chr2A 662749845 662750619 774 False 689.0 689 82.949 2789 3557 1 chr2A.!!$F1 768
12 TraesCS3A01G015400 chr7D 124503590 124504984 1394 True 654.0 654 75.770 1254 2691 1 chr7D.!!$R2 1437
13 TraesCS3A01G015400 chr3B 446060738 446061636 898 True 643.0 643 79.912 2791 3686 1 chr3B.!!$R1 895
14 TraesCS3A01G015400 chr2B 542953322 542954110 788 True 641.0 641 81.439 2900 3686 1 chr2B.!!$R1 786

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
228 229 0.179094 CGCACGGGCATCTTTACCTA 60.179 55.000 11.77 0.0 41.24 3.08 F
229 230 1.583054 GCACGGGCATCTTTACCTAG 58.417 55.000 3.77 0.0 40.72 3.02 F
2125 2455 1.143838 CCGCCCGAGATCATGTTCA 59.856 57.895 6.55 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1320 0.108138 CATCCCGGCGTTTCTCTCTT 60.108 55.000 6.01 0.0 0.0 2.85 R
2204 2534 1.336887 CGACGGCCTTCTTCTTCTTCA 60.337 52.381 7.75 0.0 0.0 3.02 R
3634 4015 0.970937 CCCCGTGCTCTTGGAGACTA 60.971 60.000 0.00 0.0 0.0 2.59 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
22 23 2.584064 TCGTAGACGTCCGGGCTA 59.416 61.111 13.01 0.00 40.80 3.93
23 24 1.146930 TCGTAGACGTCCGGGCTAT 59.853 57.895 13.01 0.00 40.80 2.97
24 25 0.882042 TCGTAGACGTCCGGGCTATC 60.882 60.000 13.01 0.97 40.80 2.08
25 26 1.573436 GTAGACGTCCGGGCTATCG 59.427 63.158 13.01 3.49 0.00 2.92
32 33 4.394712 CCGGGCTATCGGGCATCC 62.395 72.222 0.00 0.00 45.78 3.51
33 34 4.394712 CGGGCTATCGGGCATCCC 62.395 72.222 0.00 0.00 42.84 3.85
34 35 2.930562 GGGCTATCGGGCATCCCT 60.931 66.667 0.00 0.00 42.67 4.20
35 36 2.348998 GGCTATCGGGCATCCCTG 59.651 66.667 0.00 0.00 42.67 4.45
40 41 2.674754 TCGGGCATCCCTGAAACC 59.325 61.111 0.00 0.00 43.59 3.27
41 42 2.440247 CGGGCATCCCTGAAACCC 60.440 66.667 0.00 0.00 42.67 4.11
42 43 2.770130 GGGCATCCCTGAAACCCA 59.230 61.111 0.00 0.00 41.34 4.51
43 44 1.380380 GGGCATCCCTGAAACCCAG 60.380 63.158 0.00 0.00 41.34 4.45
44 45 2.054453 GGCATCCCTGAAACCCAGC 61.054 63.158 0.00 0.00 41.57 4.85
45 46 2.054453 GCATCCCTGAAACCCAGCC 61.054 63.158 0.00 0.00 41.57 4.85
46 47 1.380380 CATCCCTGAAACCCAGCCC 60.380 63.158 0.00 0.00 41.57 5.19
47 48 1.856873 ATCCCTGAAACCCAGCCCA 60.857 57.895 0.00 0.00 41.57 5.36
48 49 1.442886 ATCCCTGAAACCCAGCCCAA 61.443 55.000 0.00 0.00 41.57 4.12
49 50 1.152355 CCCTGAAACCCAGCCCAAA 60.152 57.895 0.00 0.00 41.57 3.28
50 51 0.545071 CCCTGAAACCCAGCCCAAAT 60.545 55.000 0.00 0.00 41.57 2.32
51 52 0.897621 CCTGAAACCCAGCCCAAATC 59.102 55.000 0.00 0.00 41.57 2.17
52 53 0.897621 CTGAAACCCAGCCCAAATCC 59.102 55.000 0.00 0.00 35.89 3.01
53 54 0.189574 TGAAACCCAGCCCAAATCCA 59.810 50.000 0.00 0.00 0.00 3.41
54 55 1.203288 TGAAACCCAGCCCAAATCCAT 60.203 47.619 0.00 0.00 0.00 3.41
55 56 2.043664 TGAAACCCAGCCCAAATCCATA 59.956 45.455 0.00 0.00 0.00 2.74
56 57 3.308401 GAAACCCAGCCCAAATCCATAT 58.692 45.455 0.00 0.00 0.00 1.78
57 58 4.078922 TGAAACCCAGCCCAAATCCATATA 60.079 41.667 0.00 0.00 0.00 0.86
58 59 4.551215 AACCCAGCCCAAATCCATATAA 57.449 40.909 0.00 0.00 0.00 0.98
59 60 3.844640 ACCCAGCCCAAATCCATATAAC 58.155 45.455 0.00 0.00 0.00 1.89
60 61 3.165071 CCCAGCCCAAATCCATATAACC 58.835 50.000 0.00 0.00 0.00 2.85
61 62 3.181418 CCCAGCCCAAATCCATATAACCT 60.181 47.826 0.00 0.00 0.00 3.50
62 63 4.082125 CCAGCCCAAATCCATATAACCTC 58.918 47.826 0.00 0.00 0.00 3.85
63 64 4.447616 CCAGCCCAAATCCATATAACCTCA 60.448 45.833 0.00 0.00 0.00 3.86
64 65 4.520492 CAGCCCAAATCCATATAACCTCAC 59.480 45.833 0.00 0.00 0.00 3.51
65 66 4.416848 AGCCCAAATCCATATAACCTCACT 59.583 41.667 0.00 0.00 0.00 3.41
66 67 5.103515 AGCCCAAATCCATATAACCTCACTT 60.104 40.000 0.00 0.00 0.00 3.16
67 68 5.241728 GCCCAAATCCATATAACCTCACTTC 59.758 44.000 0.00 0.00 0.00 3.01
68 69 5.470098 CCCAAATCCATATAACCTCACTTCG 59.530 44.000 0.00 0.00 0.00 3.79
69 70 5.470098 CCAAATCCATATAACCTCACTTCGG 59.530 44.000 0.00 0.00 0.00 4.30
70 71 6.288294 CAAATCCATATAACCTCACTTCGGA 58.712 40.000 0.00 0.00 0.00 4.55
71 72 6.688073 AATCCATATAACCTCACTTCGGAT 57.312 37.500 0.00 0.00 32.15 4.18
72 73 5.468540 TCCATATAACCTCACTTCGGATG 57.531 43.478 0.00 0.00 0.00 3.51
73 74 5.144832 TCCATATAACCTCACTTCGGATGA 58.855 41.667 0.00 0.00 0.00 2.92
74 75 5.600898 TCCATATAACCTCACTTCGGATGAA 59.399 40.000 0.00 0.00 0.00 2.57
75 76 5.696724 CCATATAACCTCACTTCGGATGAAC 59.303 44.000 0.00 0.00 0.00 3.18
76 77 4.819105 ATAACCTCACTTCGGATGAACA 57.181 40.909 0.00 0.00 0.00 3.18
77 78 2.457366 ACCTCACTTCGGATGAACAC 57.543 50.000 0.00 0.00 0.00 3.32
78 79 1.971357 ACCTCACTTCGGATGAACACT 59.029 47.619 0.00 0.00 0.00 3.55
79 80 3.162666 ACCTCACTTCGGATGAACACTA 58.837 45.455 0.00 0.00 0.00 2.74
80 81 3.193691 ACCTCACTTCGGATGAACACTAG 59.806 47.826 0.00 0.00 0.00 2.57
81 82 3.444034 CCTCACTTCGGATGAACACTAGA 59.556 47.826 0.00 0.00 0.00 2.43
82 83 4.416620 CTCACTTCGGATGAACACTAGAC 58.583 47.826 0.00 0.00 0.00 2.59
83 84 4.079970 TCACTTCGGATGAACACTAGACT 58.920 43.478 0.00 0.00 0.00 3.24
84 85 4.523173 TCACTTCGGATGAACACTAGACTT 59.477 41.667 0.00 0.00 0.00 3.01
85 86 5.708697 TCACTTCGGATGAACACTAGACTTA 59.291 40.000 0.00 0.00 0.00 2.24
86 87 6.208007 TCACTTCGGATGAACACTAGACTTAA 59.792 38.462 0.00 0.00 0.00 1.85
87 88 6.866770 CACTTCGGATGAACACTAGACTTAAA 59.133 38.462 0.00 0.00 0.00 1.52
88 89 7.545965 CACTTCGGATGAACACTAGACTTAAAT 59.454 37.037 0.00 0.00 0.00 1.40
89 90 7.760340 ACTTCGGATGAACACTAGACTTAAATC 59.240 37.037 0.00 0.00 0.00 2.17
90 91 7.406031 TCGGATGAACACTAGACTTAAATCT 57.594 36.000 0.00 0.00 0.00 2.40
91 92 8.515695 TCGGATGAACACTAGACTTAAATCTA 57.484 34.615 0.00 0.00 0.00 1.98
92 93 8.963725 TCGGATGAACACTAGACTTAAATCTAA 58.036 33.333 0.00 0.00 30.76 2.10
93 94 9.239002 CGGATGAACACTAGACTTAAATCTAAG 57.761 37.037 0.00 0.00 40.46 2.18
100 101 9.372369 ACACTAGACTTAAATCTAAGACAATGC 57.628 33.333 0.00 0.00 38.35 3.56
101 102 8.821894 CACTAGACTTAAATCTAAGACAATGCC 58.178 37.037 0.00 0.00 38.35 4.40
102 103 8.540388 ACTAGACTTAAATCTAAGACAATGCCA 58.460 33.333 0.00 0.00 38.35 4.92
103 104 9.553064 CTAGACTTAAATCTAAGACAATGCCAT 57.447 33.333 0.00 0.00 38.35 4.40
104 105 8.218338 AGACTTAAATCTAAGACAATGCCATG 57.782 34.615 0.00 0.00 38.35 3.66
105 106 7.831193 AGACTTAAATCTAAGACAATGCCATGT 59.169 33.333 0.00 0.00 38.35 3.21
106 107 8.353423 ACTTAAATCTAAGACAATGCCATGTT 57.647 30.769 0.00 0.00 38.35 2.71
107 108 8.246180 ACTTAAATCTAAGACAATGCCATGTTG 58.754 33.333 0.00 0.00 38.35 3.33
108 109 6.839124 AAATCTAAGACAATGCCATGTTGA 57.161 33.333 1.85 0.00 32.57 3.18
109 110 6.839124 AATCTAAGACAATGCCATGTTGAA 57.161 33.333 1.85 0.00 32.57 2.69
110 111 6.839124 ATCTAAGACAATGCCATGTTGAAA 57.161 33.333 1.85 0.00 32.57 2.69
111 112 6.258230 TCTAAGACAATGCCATGTTGAAAG 57.742 37.500 1.85 0.00 32.57 2.62
112 113 6.003326 TCTAAGACAATGCCATGTTGAAAGA 58.997 36.000 1.85 0.00 32.57 2.52
113 114 5.733620 AAGACAATGCCATGTTGAAAGAT 57.266 34.783 1.85 0.00 32.57 2.40
114 115 5.068234 AGACAATGCCATGTTGAAAGATG 57.932 39.130 1.85 0.00 32.57 2.90
116 117 3.055675 ACAATGCCATGTTGAAAGATGGG 60.056 43.478 18.01 6.52 46.76 4.00
117 118 0.896923 TGCCATGTTGAAAGATGGGC 59.103 50.000 18.01 11.88 46.76 5.36
118 119 1.188863 GCCATGTTGAAAGATGGGCT 58.811 50.000 18.01 0.00 46.76 5.19
119 120 1.551883 GCCATGTTGAAAGATGGGCTT 59.448 47.619 18.01 0.00 46.76 4.35
120 121 2.675889 GCCATGTTGAAAGATGGGCTTG 60.676 50.000 18.01 0.00 46.76 4.01
121 122 2.613691 CATGTTGAAAGATGGGCTTGC 58.386 47.619 0.00 0.00 36.80 4.01
122 123 0.597568 TGTTGAAAGATGGGCTTGCG 59.402 50.000 0.00 0.00 34.60 4.85
123 124 0.881118 GTTGAAAGATGGGCTTGCGA 59.119 50.000 0.00 0.00 34.60 5.10
124 125 1.269448 GTTGAAAGATGGGCTTGCGAA 59.731 47.619 0.00 0.00 34.60 4.70
125 126 1.167851 TGAAAGATGGGCTTGCGAAG 58.832 50.000 0.00 0.00 34.60 3.79
126 127 1.271325 TGAAAGATGGGCTTGCGAAGA 60.271 47.619 0.00 0.00 34.60 2.87
127 128 2.019984 GAAAGATGGGCTTGCGAAGAT 58.980 47.619 0.00 0.00 36.80 2.40
128 129 2.134789 AAGATGGGCTTGCGAAGATT 57.865 45.000 0.00 0.00 34.93 2.40
129 130 1.673168 AGATGGGCTTGCGAAGATTC 58.327 50.000 0.00 0.00 0.00 2.52
130 131 1.065199 AGATGGGCTTGCGAAGATTCA 60.065 47.619 0.00 0.00 0.00 2.57
131 132 1.952296 GATGGGCTTGCGAAGATTCAT 59.048 47.619 0.00 0.00 0.00 2.57
132 133 1.382522 TGGGCTTGCGAAGATTCATC 58.617 50.000 0.00 0.00 0.00 2.92
133 134 1.065199 TGGGCTTGCGAAGATTCATCT 60.065 47.619 0.00 0.00 39.22 2.90
134 135 1.601430 GGGCTTGCGAAGATTCATCTC 59.399 52.381 0.00 0.00 35.76 2.75
135 136 2.283298 GGCTTGCGAAGATTCATCTCA 58.717 47.619 0.00 0.00 35.76 3.27
136 137 2.679837 GGCTTGCGAAGATTCATCTCAA 59.320 45.455 0.00 0.00 35.76 3.02
137 138 3.242673 GGCTTGCGAAGATTCATCTCAAG 60.243 47.826 14.26 14.26 38.38 3.02
138 139 3.620374 GCTTGCGAAGATTCATCTCAAGA 59.380 43.478 20.09 0.00 37.96 3.02
139 140 4.093998 GCTTGCGAAGATTCATCTCAAGAA 59.906 41.667 20.09 0.00 37.96 2.52
140 141 5.220815 GCTTGCGAAGATTCATCTCAAGAAT 60.221 40.000 20.09 0.00 37.96 2.40
141 142 6.677431 GCTTGCGAAGATTCATCTCAAGAATT 60.677 38.462 20.09 0.00 37.96 2.17
142 143 6.355397 TGCGAAGATTCATCTCAAGAATTC 57.645 37.500 0.00 0.00 35.93 2.17
143 144 5.295292 TGCGAAGATTCATCTCAAGAATTCC 59.705 40.000 0.65 0.00 35.93 3.01
144 145 5.277731 GCGAAGATTCATCTCAAGAATTCCC 60.278 44.000 0.65 0.00 35.93 3.97
145 146 5.050499 CGAAGATTCATCTCAAGAATTCCCG 60.050 44.000 0.65 0.00 35.93 5.14
146 147 5.620738 AGATTCATCTCAAGAATTCCCGA 57.379 39.130 0.65 0.00 35.93 5.14
147 148 5.609423 AGATTCATCTCAAGAATTCCCGAG 58.391 41.667 13.22 13.22 35.93 4.63
148 149 3.827008 TCATCTCAAGAATTCCCGAGG 57.173 47.619 17.34 5.82 0.00 4.63
149 150 2.435805 TCATCTCAAGAATTCCCGAGGG 59.564 50.000 17.34 0.65 0.00 4.30
150 151 1.952621 TCTCAAGAATTCCCGAGGGT 58.047 50.000 17.34 0.00 36.47 4.34
151 152 3.110293 TCTCAAGAATTCCCGAGGGTA 57.890 47.619 17.34 0.00 36.47 3.69
152 153 2.764572 TCTCAAGAATTCCCGAGGGTAC 59.235 50.000 17.34 0.00 36.47 3.34
153 154 2.766828 CTCAAGAATTCCCGAGGGTACT 59.233 50.000 8.20 1.38 36.47 2.73
154 155 3.178865 TCAAGAATTCCCGAGGGTACTT 58.821 45.455 8.20 6.99 36.47 2.24
155 156 3.197116 TCAAGAATTCCCGAGGGTACTTC 59.803 47.826 8.20 9.41 36.47 3.01
156 157 2.117051 AGAATTCCCGAGGGTACTTCC 58.883 52.381 8.20 0.00 36.47 3.46
157 158 0.828677 AATTCCCGAGGGTACTTCCG 59.171 55.000 8.20 0.00 37.00 4.30
158 159 0.325016 ATTCCCGAGGGTACTTCCGT 60.325 55.000 8.20 0.00 37.00 4.69
159 160 1.252904 TTCCCGAGGGTACTTCCGTG 61.253 60.000 8.20 0.00 37.00 4.94
160 161 1.980772 CCCGAGGGTACTTCCGTGT 60.981 63.158 0.00 0.00 37.00 4.49
161 162 1.538687 CCCGAGGGTACTTCCGTGTT 61.539 60.000 0.00 0.00 37.00 3.32
162 163 0.319405 CCGAGGGTACTTCCGTGTTT 59.681 55.000 0.00 0.00 37.00 2.83
163 164 1.545582 CCGAGGGTACTTCCGTGTTTA 59.454 52.381 0.00 0.00 37.00 2.01
164 165 2.167075 CCGAGGGTACTTCCGTGTTTAT 59.833 50.000 0.00 0.00 37.00 1.40
165 166 3.442100 CGAGGGTACTTCCGTGTTTATC 58.558 50.000 0.00 0.00 37.00 1.75
166 167 3.119388 CGAGGGTACTTCCGTGTTTATCA 60.119 47.826 0.00 0.00 37.00 2.15
167 168 4.441079 CGAGGGTACTTCCGTGTTTATCAT 60.441 45.833 0.00 0.00 37.00 2.45
168 169 5.221106 CGAGGGTACTTCCGTGTTTATCATA 60.221 44.000 0.00 0.00 37.00 2.15
169 170 6.516194 CGAGGGTACTTCCGTGTTTATCATAT 60.516 42.308 0.00 0.00 37.00 1.78
170 171 7.133133 AGGGTACTTCCGTGTTTATCATATT 57.867 36.000 0.00 0.00 37.00 1.28
171 172 7.571025 AGGGTACTTCCGTGTTTATCATATTT 58.429 34.615 0.00 0.00 37.00 1.40
172 173 7.497909 AGGGTACTTCCGTGTTTATCATATTTG 59.502 37.037 0.00 0.00 37.00 2.32
173 174 7.281549 GGGTACTTCCGTGTTTATCATATTTGT 59.718 37.037 0.00 0.00 37.00 2.83
174 175 8.671028 GGTACTTCCGTGTTTATCATATTTGTT 58.329 33.333 0.00 0.00 0.00 2.83
177 178 9.620660 ACTTCCGTGTTTATCATATTTGTTTTC 57.379 29.630 0.00 0.00 0.00 2.29
178 179 9.619316 CTTCCGTGTTTATCATATTTGTTTTCA 57.381 29.630 0.00 0.00 0.00 2.69
179 180 8.958175 TCCGTGTTTATCATATTTGTTTTCAC 57.042 30.769 0.00 0.00 0.00 3.18
180 181 8.568794 TCCGTGTTTATCATATTTGTTTTCACA 58.431 29.630 0.00 0.00 0.00 3.58
181 182 8.635124 CCGTGTTTATCATATTTGTTTTCACAC 58.365 33.333 0.00 0.00 30.32 3.82
182 183 8.635124 CGTGTTTATCATATTTGTTTTCACACC 58.365 33.333 0.00 0.00 30.32 4.16
183 184 9.691362 GTGTTTATCATATTTGTTTTCACACCT 57.309 29.630 0.00 0.00 30.32 4.00
186 187 9.703892 TTTATCATATTTGTTTTCACACCTTGG 57.296 29.630 0.00 0.00 30.32 3.61
187 188 6.968263 TCATATTTGTTTTCACACCTTGGA 57.032 33.333 0.00 0.00 30.32 3.53
188 189 6.744112 TCATATTTGTTTTCACACCTTGGAC 58.256 36.000 0.00 0.00 30.32 4.02
189 190 6.322456 TCATATTTGTTTTCACACCTTGGACA 59.678 34.615 0.00 0.00 30.32 4.02
190 191 5.612725 ATTTGTTTTCACACCTTGGACAT 57.387 34.783 0.00 0.00 30.32 3.06
191 192 5.413309 TTTGTTTTCACACCTTGGACATT 57.587 34.783 0.00 0.00 30.32 2.71
192 193 4.383850 TGTTTTCACACCTTGGACATTG 57.616 40.909 0.00 0.00 0.00 2.82
193 194 3.766591 TGTTTTCACACCTTGGACATTGT 59.233 39.130 0.00 0.00 0.00 2.71
194 195 4.111916 GTTTTCACACCTTGGACATTGTG 58.888 43.478 0.00 0.00 40.64 3.33
195 196 2.727123 TCACACCTTGGACATTGTGT 57.273 45.000 0.00 0.00 42.34 3.72
196 197 3.011566 TCACACCTTGGACATTGTGTT 57.988 42.857 0.00 0.00 39.78 3.32
197 198 3.360867 TCACACCTTGGACATTGTGTTT 58.639 40.909 0.00 0.00 39.78 2.83
198 199 3.766591 TCACACCTTGGACATTGTGTTTT 59.233 39.130 0.00 0.00 39.78 2.43
199 200 4.111916 CACACCTTGGACATTGTGTTTTC 58.888 43.478 0.00 0.00 39.78 2.29
200 201 3.132111 ACACCTTGGACATTGTGTTTTCC 59.868 43.478 0.00 0.00 38.74 3.13
201 202 2.698274 ACCTTGGACATTGTGTTTTCCC 59.302 45.455 0.00 0.00 0.00 3.97
202 203 2.288152 CCTTGGACATTGTGTTTTCCCG 60.288 50.000 0.00 0.00 0.00 5.14
203 204 2.060050 TGGACATTGTGTTTTCCCGT 57.940 45.000 0.00 0.00 0.00 5.28
204 205 2.379972 TGGACATTGTGTTTTCCCGTT 58.620 42.857 0.00 0.00 0.00 4.44
205 206 2.099921 TGGACATTGTGTTTTCCCGTTG 59.900 45.455 0.00 0.00 0.00 4.10
206 207 2.124122 GACATTGTGTTTTCCCGTTGC 58.876 47.619 0.00 0.00 0.00 4.17
207 208 1.478510 ACATTGTGTTTTCCCGTTGCA 59.521 42.857 0.00 0.00 0.00 4.08
208 209 2.093973 ACATTGTGTTTTCCCGTTGCAA 60.094 40.909 0.00 0.00 0.00 4.08
209 210 1.997669 TTGTGTTTTCCCGTTGCAAC 58.002 45.000 19.89 19.89 0.00 4.17
219 220 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
220 221 4.036804 TTGCAACGCACGGGCATC 62.037 61.111 11.77 0.00 38.71 3.91
222 223 3.737172 GCAACGCACGGGCATCTT 61.737 61.111 11.77 0.00 41.24 2.40
223 224 2.953821 CAACGCACGGGCATCTTT 59.046 55.556 11.77 0.00 41.24 2.52
224 225 1.917782 GCAACGCACGGGCATCTTTA 61.918 55.000 11.77 0.00 41.24 1.85
225 226 0.179200 CAACGCACGGGCATCTTTAC 60.179 55.000 11.77 0.00 41.24 2.01
226 227 1.303091 AACGCACGGGCATCTTTACC 61.303 55.000 11.77 0.00 41.24 2.85
227 228 1.449601 CGCACGGGCATCTTTACCT 60.450 57.895 11.77 0.00 41.24 3.08
228 229 0.179094 CGCACGGGCATCTTTACCTA 60.179 55.000 11.77 0.00 41.24 3.08
229 230 1.583054 GCACGGGCATCTTTACCTAG 58.417 55.000 3.77 0.00 40.72 3.02
323 324 4.647424 AATATATTGTTGCGGGTGTTGG 57.353 40.909 0.00 0.00 0.00 3.77
394 401 6.647067 CCTTTTCTCCGTCTGGAATGATATAC 59.353 42.308 0.00 0.00 45.87 1.47
399 406 6.984474 TCTCCGTCTGGAATGATATACAAAAC 59.016 38.462 0.00 0.00 45.87 2.43
499 506 8.044309 TGAATCGTTTTCCCTCATCTGTTATAA 58.956 33.333 0.00 0.00 0.00 0.98
660 668 1.818674 ACCCATTTCACGAATCTTGGC 59.181 47.619 0.00 0.00 0.00 4.52
921 1206 9.265901 AGTAACTTTGCTCTATATGTATGCAAG 57.734 33.333 0.00 7.25 43.13 4.01
956 1241 3.207669 GCCTCCATTCGGCAGCAG 61.208 66.667 0.00 0.00 46.77 4.24
1117 1405 3.439513 TTGACGCACCTGCTCGTGT 62.440 57.895 5.77 0.00 39.22 4.49
1801 2131 1.686587 TGTTTCTTCTCACCGAGAGCA 59.313 47.619 0.55 0.00 44.35 4.26
2125 2455 1.143838 CCGCCCGAGATCATGTTCA 59.856 57.895 6.55 0.00 0.00 3.18
2406 2760 1.686355 CGGAGATCTACCTGCTGAGT 58.314 55.000 0.00 0.00 0.00 3.41
2453 2807 2.319841 GGTCCACGTTTGGGTACGC 61.320 63.158 2.35 2.35 45.06 4.42
2782 3142 2.049618 TTCCGCCAAACGCAATGC 60.050 55.556 0.00 0.00 41.76 3.56
2784 3144 4.354939 CCGCCAAACGCAATGCCA 62.355 61.111 0.00 0.00 41.76 4.92
2793 3153 4.143137 CCAAACGCAATGCCATTACTTTTC 60.143 41.667 0.00 0.00 0.00 2.29
3055 3430 1.949631 CGCGATAAGGAAGACGCCC 60.950 63.158 0.00 0.00 46.69 6.13
3124 3501 5.070981 TCCATCTTAGTCAATGATCTCCACC 59.929 44.000 0.00 0.00 0.00 4.61
3198 3575 7.870445 GGAAAAACATGCTCAATGGTAAACTTA 59.130 33.333 0.00 0.00 40.94 2.24
3559 3939 3.655777 ACTGAATTTGTTAGTGGGGGAGA 59.344 43.478 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.162800 ATAGCCCGGACGTCTACGAC 61.163 60.000 16.46 2.72 43.02 4.34
6 7 1.573436 GATAGCCCGGACGTCTACG 59.427 63.158 16.46 11.34 46.33 3.51
7 8 1.573436 CGATAGCCCGGACGTCTAC 59.427 63.158 16.46 0.00 0.00 2.59
8 9 4.054085 CGATAGCCCGGACGTCTA 57.946 61.111 16.46 0.00 0.00 2.59
16 17 4.394712 GGGATGCCCGATAGCCCG 62.395 72.222 0.00 0.00 32.13 6.13
25 26 1.380380 CTGGGTTTCAGGGATGCCC 60.380 63.158 0.00 0.00 45.90 5.36
26 27 2.054453 GCTGGGTTTCAGGGATGCC 61.054 63.158 0.00 0.00 43.54 4.40
27 28 2.054453 GGCTGGGTTTCAGGGATGC 61.054 63.158 0.00 0.00 43.54 3.91
28 29 1.380380 GGGCTGGGTTTCAGGGATG 60.380 63.158 0.00 0.00 43.54 3.51
29 30 1.442886 TTGGGCTGGGTTTCAGGGAT 61.443 55.000 0.00 0.00 43.54 3.85
30 31 1.660019 TTTGGGCTGGGTTTCAGGGA 61.660 55.000 0.00 0.00 43.54 4.20
31 32 0.545071 ATTTGGGCTGGGTTTCAGGG 60.545 55.000 0.00 0.00 43.54 4.45
32 33 0.897621 GATTTGGGCTGGGTTTCAGG 59.102 55.000 0.00 0.00 43.54 3.86
33 34 0.897621 GGATTTGGGCTGGGTTTCAG 59.102 55.000 0.00 0.00 46.03 3.02
34 35 0.189574 TGGATTTGGGCTGGGTTTCA 59.810 50.000 0.00 0.00 0.00 2.69
35 36 1.571955 ATGGATTTGGGCTGGGTTTC 58.428 50.000 0.00 0.00 0.00 2.78
36 37 2.938428 TATGGATTTGGGCTGGGTTT 57.062 45.000 0.00 0.00 0.00 3.27
37 38 4.223144 GTTATATGGATTTGGGCTGGGTT 58.777 43.478 0.00 0.00 0.00 4.11
38 39 3.437931 GGTTATATGGATTTGGGCTGGGT 60.438 47.826 0.00 0.00 0.00 4.51
39 40 3.165071 GGTTATATGGATTTGGGCTGGG 58.835 50.000 0.00 0.00 0.00 4.45
40 41 4.082125 GAGGTTATATGGATTTGGGCTGG 58.918 47.826 0.00 0.00 0.00 4.85
41 42 4.520492 GTGAGGTTATATGGATTTGGGCTG 59.480 45.833 0.00 0.00 0.00 4.85
42 43 4.416848 AGTGAGGTTATATGGATTTGGGCT 59.583 41.667 0.00 0.00 0.00 5.19
43 44 4.729868 AGTGAGGTTATATGGATTTGGGC 58.270 43.478 0.00 0.00 0.00 5.36
44 45 5.470098 CGAAGTGAGGTTATATGGATTTGGG 59.530 44.000 0.00 0.00 0.00 4.12
45 46 5.470098 CCGAAGTGAGGTTATATGGATTTGG 59.530 44.000 0.00 0.00 0.00 3.28
46 47 6.288294 TCCGAAGTGAGGTTATATGGATTTG 58.712 40.000 0.00 0.00 0.00 2.32
47 48 6.494666 TCCGAAGTGAGGTTATATGGATTT 57.505 37.500 0.00 0.00 0.00 2.17
48 49 6.270000 TCATCCGAAGTGAGGTTATATGGATT 59.730 38.462 0.00 0.00 31.59 3.01
49 50 5.780282 TCATCCGAAGTGAGGTTATATGGAT 59.220 40.000 0.00 0.00 34.15 3.41
50 51 5.144832 TCATCCGAAGTGAGGTTATATGGA 58.855 41.667 0.00 0.00 0.00 3.41
51 52 5.468540 TCATCCGAAGTGAGGTTATATGG 57.531 43.478 0.00 0.00 0.00 2.74
52 53 6.201044 GTGTTCATCCGAAGTGAGGTTATATG 59.799 42.308 0.00 0.00 0.00 1.78
53 54 6.098409 AGTGTTCATCCGAAGTGAGGTTATAT 59.902 38.462 0.00 0.00 0.00 0.86
54 55 5.421056 AGTGTTCATCCGAAGTGAGGTTATA 59.579 40.000 0.00 0.00 0.00 0.98
55 56 4.223032 AGTGTTCATCCGAAGTGAGGTTAT 59.777 41.667 0.00 0.00 0.00 1.89
56 57 3.576982 AGTGTTCATCCGAAGTGAGGTTA 59.423 43.478 0.00 0.00 0.00 2.85
57 58 2.368875 AGTGTTCATCCGAAGTGAGGTT 59.631 45.455 0.00 0.00 0.00 3.50
58 59 1.971357 AGTGTTCATCCGAAGTGAGGT 59.029 47.619 0.00 0.00 0.00 3.85
59 60 2.751166 AGTGTTCATCCGAAGTGAGG 57.249 50.000 0.00 0.00 0.00 3.86
60 61 4.156922 AGTCTAGTGTTCATCCGAAGTGAG 59.843 45.833 0.00 0.00 0.00 3.51
61 62 4.079970 AGTCTAGTGTTCATCCGAAGTGA 58.920 43.478 0.00 0.00 0.00 3.41
62 63 4.442375 AGTCTAGTGTTCATCCGAAGTG 57.558 45.455 0.00 0.00 0.00 3.16
63 64 6.585695 TTAAGTCTAGTGTTCATCCGAAGT 57.414 37.500 0.00 0.00 0.00 3.01
64 65 7.976734 AGATTTAAGTCTAGTGTTCATCCGAAG 59.023 37.037 0.00 0.00 0.00 3.79
65 66 7.837863 AGATTTAAGTCTAGTGTTCATCCGAA 58.162 34.615 0.00 0.00 0.00 4.30
66 67 7.406031 AGATTTAAGTCTAGTGTTCATCCGA 57.594 36.000 0.00 0.00 0.00 4.55
67 68 9.239002 CTTAGATTTAAGTCTAGTGTTCATCCG 57.761 37.037 7.65 0.00 32.63 4.18
74 75 9.372369 GCATTGTCTTAGATTTAAGTCTAGTGT 57.628 33.333 7.65 0.00 37.97 3.55
75 76 8.821894 GGCATTGTCTTAGATTTAAGTCTAGTG 58.178 37.037 7.65 5.98 37.97 2.74
76 77 8.540388 TGGCATTGTCTTAGATTTAAGTCTAGT 58.460 33.333 7.65 0.00 37.97 2.57
77 78 8.948631 TGGCATTGTCTTAGATTTAAGTCTAG 57.051 34.615 7.65 3.84 37.97 2.43
78 79 9.330063 CATGGCATTGTCTTAGATTTAAGTCTA 57.670 33.333 0.00 3.72 37.97 2.59
79 80 7.831193 ACATGGCATTGTCTTAGATTTAAGTCT 59.169 33.333 5.74 5.74 37.97 3.24
80 81 7.989826 ACATGGCATTGTCTTAGATTTAAGTC 58.010 34.615 0.00 0.00 37.97 3.01
81 82 7.944729 ACATGGCATTGTCTTAGATTTAAGT 57.055 32.000 0.00 0.00 37.97 2.24
82 83 8.461222 TCAACATGGCATTGTCTTAGATTTAAG 58.539 33.333 0.00 0.00 38.09 1.85
83 84 8.347004 TCAACATGGCATTGTCTTAGATTTAA 57.653 30.769 0.00 0.00 0.00 1.52
84 85 7.936496 TCAACATGGCATTGTCTTAGATTTA 57.064 32.000 0.00 0.00 0.00 1.40
85 86 6.839124 TCAACATGGCATTGTCTTAGATTT 57.161 33.333 0.00 0.00 0.00 2.17
86 87 6.839124 TTCAACATGGCATTGTCTTAGATT 57.161 33.333 0.00 0.00 0.00 2.40
87 88 6.660521 TCTTTCAACATGGCATTGTCTTAGAT 59.339 34.615 0.00 0.00 0.00 1.98
88 89 6.003326 TCTTTCAACATGGCATTGTCTTAGA 58.997 36.000 0.00 0.00 0.00 2.10
89 90 6.258230 TCTTTCAACATGGCATTGTCTTAG 57.742 37.500 0.00 0.00 0.00 2.18
90 91 6.350361 CCATCTTTCAACATGGCATTGTCTTA 60.350 38.462 0.00 0.00 33.37 2.10
91 92 5.475719 CATCTTTCAACATGGCATTGTCTT 58.524 37.500 0.00 0.00 0.00 3.01
92 93 4.081862 CCATCTTTCAACATGGCATTGTCT 60.082 41.667 0.00 0.00 33.37 3.41
93 94 4.178540 CCATCTTTCAACATGGCATTGTC 58.821 43.478 0.00 0.00 33.37 3.18
94 95 3.055675 CCCATCTTTCAACATGGCATTGT 60.056 43.478 0.00 0.00 38.67 2.71
95 96 3.527533 CCCATCTTTCAACATGGCATTG 58.472 45.455 0.00 0.00 38.67 2.82
96 97 2.093341 GCCCATCTTTCAACATGGCATT 60.093 45.455 0.00 0.00 38.67 3.56
97 98 1.483415 GCCCATCTTTCAACATGGCAT 59.517 47.619 0.00 0.00 38.67 4.40
98 99 0.896923 GCCCATCTTTCAACATGGCA 59.103 50.000 0.00 0.00 38.67 4.92
99 100 1.188863 AGCCCATCTTTCAACATGGC 58.811 50.000 0.00 0.00 38.67 4.40
100 101 2.675889 GCAAGCCCATCTTTCAACATGG 60.676 50.000 0.00 0.00 39.58 3.66
101 102 2.613691 GCAAGCCCATCTTTCAACATG 58.386 47.619 0.00 0.00 31.27 3.21
102 103 1.203052 CGCAAGCCCATCTTTCAACAT 59.797 47.619 0.00 0.00 31.27 2.71
103 104 0.597568 CGCAAGCCCATCTTTCAACA 59.402 50.000 0.00 0.00 31.27 3.33
104 105 0.881118 TCGCAAGCCCATCTTTCAAC 59.119 50.000 0.00 0.00 31.27 3.18
105 106 1.541147 CTTCGCAAGCCCATCTTTCAA 59.459 47.619 0.00 0.00 31.27 2.69
106 107 1.167851 CTTCGCAAGCCCATCTTTCA 58.832 50.000 0.00 0.00 31.27 2.69
107 108 1.453155 TCTTCGCAAGCCCATCTTTC 58.547 50.000 0.00 0.00 31.27 2.62
108 109 2.134789 ATCTTCGCAAGCCCATCTTT 57.865 45.000 0.00 0.00 31.27 2.52
109 110 2.019984 GAATCTTCGCAAGCCCATCTT 58.980 47.619 0.00 0.00 34.78 2.40
110 111 1.065199 TGAATCTTCGCAAGCCCATCT 60.065 47.619 0.00 0.00 37.18 2.90
111 112 1.382522 TGAATCTTCGCAAGCCCATC 58.617 50.000 0.00 0.00 37.18 3.51
112 113 1.952296 GATGAATCTTCGCAAGCCCAT 59.048 47.619 0.00 0.00 37.18 4.00
113 114 1.065199 AGATGAATCTTCGCAAGCCCA 60.065 47.619 0.00 0.00 31.97 5.36
114 115 1.601430 GAGATGAATCTTCGCAAGCCC 59.399 52.381 0.00 0.00 37.25 5.19
115 116 2.283298 TGAGATGAATCTTCGCAAGCC 58.717 47.619 0.47 0.00 37.25 4.35
116 117 3.620374 TCTTGAGATGAATCTTCGCAAGC 59.380 43.478 26.07 4.38 45.17 4.01
117 118 5.791367 TTCTTGAGATGAATCTTCGCAAG 57.209 39.130 25.42 25.42 46.20 4.01
118 119 6.183360 GGAATTCTTGAGATGAATCTTCGCAA 60.183 38.462 12.91 12.91 37.25 4.85
119 120 5.295292 GGAATTCTTGAGATGAATCTTCGCA 59.705 40.000 5.23 0.00 37.25 5.10
120 121 5.277731 GGGAATTCTTGAGATGAATCTTCGC 60.278 44.000 5.23 0.00 37.25 4.70
121 122 5.050499 CGGGAATTCTTGAGATGAATCTTCG 60.050 44.000 5.23 0.00 37.25 3.79
122 123 6.051717 TCGGGAATTCTTGAGATGAATCTTC 58.948 40.000 5.23 0.00 37.25 2.87
123 124 5.994250 TCGGGAATTCTTGAGATGAATCTT 58.006 37.500 5.23 0.00 37.25 2.40
124 125 5.454471 CCTCGGGAATTCTTGAGATGAATCT 60.454 44.000 21.48 0.00 40.50 2.40
125 126 4.754114 CCTCGGGAATTCTTGAGATGAATC 59.246 45.833 21.48 0.00 33.54 2.52
126 127 4.445448 CCCTCGGGAATTCTTGAGATGAAT 60.445 45.833 21.48 0.00 37.50 2.57
127 128 3.118261 CCCTCGGGAATTCTTGAGATGAA 60.118 47.826 21.48 0.00 37.50 2.57
128 129 2.435805 CCCTCGGGAATTCTTGAGATGA 59.564 50.000 21.48 4.64 37.50 2.92
129 130 2.171448 ACCCTCGGGAATTCTTGAGATG 59.829 50.000 21.48 16.05 38.96 2.90
130 131 2.482494 ACCCTCGGGAATTCTTGAGAT 58.518 47.619 21.48 11.24 38.96 2.75
131 132 1.952621 ACCCTCGGGAATTCTTGAGA 58.047 50.000 21.48 9.55 38.96 3.27
132 133 2.766828 AGTACCCTCGGGAATTCTTGAG 59.233 50.000 9.43 16.02 38.96 3.02
133 134 2.829023 AGTACCCTCGGGAATTCTTGA 58.171 47.619 9.43 2.91 38.96 3.02
134 135 3.532542 GAAGTACCCTCGGGAATTCTTG 58.467 50.000 9.43 0.00 38.96 3.02
135 136 2.504585 GGAAGTACCCTCGGGAATTCTT 59.495 50.000 9.43 7.12 38.96 2.52
136 137 2.117051 GGAAGTACCCTCGGGAATTCT 58.883 52.381 9.43 0.00 38.96 2.40
137 138 1.202498 CGGAAGTACCCTCGGGAATTC 60.202 57.143 9.43 9.08 38.96 2.17
138 139 0.828677 CGGAAGTACCCTCGGGAATT 59.171 55.000 9.43 0.00 38.96 2.17
139 140 0.325016 ACGGAAGTACCCTCGGGAAT 60.325 55.000 9.43 0.00 46.88 3.01
140 141 1.077265 ACGGAAGTACCCTCGGGAA 59.923 57.895 9.43 0.00 46.88 3.97
141 142 2.765969 ACGGAAGTACCCTCGGGA 59.234 61.111 9.43 0.00 46.88 5.14
152 153 9.619316 TGAAAACAAATATGATAAACACGGAAG 57.381 29.630 0.00 0.00 0.00 3.46
153 154 9.400638 GTGAAAACAAATATGATAAACACGGAA 57.599 29.630 0.00 0.00 0.00 4.30
154 155 8.568794 TGTGAAAACAAATATGATAAACACGGA 58.431 29.630 0.00 0.00 0.00 4.69
155 156 8.635124 GTGTGAAAACAAATATGATAAACACGG 58.365 33.333 0.00 0.00 0.00 4.94
156 157 8.635124 GGTGTGAAAACAAATATGATAAACACG 58.365 33.333 0.00 0.00 35.14 4.49
157 158 9.691362 AGGTGTGAAAACAAATATGATAAACAC 57.309 29.630 0.00 0.00 33.91 3.32
160 161 9.703892 CCAAGGTGTGAAAACAAATATGATAAA 57.296 29.630 0.00 0.00 0.00 1.40
161 162 9.083422 TCCAAGGTGTGAAAACAAATATGATAA 57.917 29.630 0.00 0.00 0.00 1.75
162 163 8.519526 GTCCAAGGTGTGAAAACAAATATGATA 58.480 33.333 0.00 0.00 0.00 2.15
163 164 7.015098 TGTCCAAGGTGTGAAAACAAATATGAT 59.985 33.333 0.00 0.00 0.00 2.45
164 165 6.322456 TGTCCAAGGTGTGAAAACAAATATGA 59.678 34.615 0.00 0.00 0.00 2.15
165 166 6.511416 TGTCCAAGGTGTGAAAACAAATATG 58.489 36.000 0.00 0.00 0.00 1.78
166 167 6.723298 TGTCCAAGGTGTGAAAACAAATAT 57.277 33.333 0.00 0.00 0.00 1.28
167 168 6.723298 ATGTCCAAGGTGTGAAAACAAATA 57.277 33.333 0.00 0.00 0.00 1.40
168 169 5.612725 ATGTCCAAGGTGTGAAAACAAAT 57.387 34.783 0.00 0.00 0.00 2.32
169 170 5.174395 CAATGTCCAAGGTGTGAAAACAAA 58.826 37.500 0.00 0.00 0.00 2.83
170 171 4.221703 ACAATGTCCAAGGTGTGAAAACAA 59.778 37.500 0.00 0.00 0.00 2.83
171 172 3.766591 ACAATGTCCAAGGTGTGAAAACA 59.233 39.130 0.00 0.00 0.00 2.83
172 173 4.111916 CACAATGTCCAAGGTGTGAAAAC 58.888 43.478 2.38 0.00 43.23 2.43
173 174 3.766591 ACACAATGTCCAAGGTGTGAAAA 59.233 39.130 12.75 0.00 43.23 2.29
174 175 3.360867 ACACAATGTCCAAGGTGTGAAA 58.639 40.909 12.75 0.00 43.23 2.69
175 176 3.011566 ACACAATGTCCAAGGTGTGAA 57.988 42.857 12.75 0.00 43.23 3.18
176 177 2.727123 ACACAATGTCCAAGGTGTGA 57.273 45.000 12.75 0.00 43.23 3.58
177 178 3.799281 AAACACAATGTCCAAGGTGTG 57.201 42.857 7.73 6.15 43.16 3.82
178 179 3.132111 GGAAAACACAATGTCCAAGGTGT 59.868 43.478 0.00 0.00 45.66 4.16
179 180 3.492482 GGGAAAACACAATGTCCAAGGTG 60.492 47.826 0.00 0.00 37.29 4.00
180 181 2.698274 GGGAAAACACAATGTCCAAGGT 59.302 45.455 0.00 0.00 31.30 3.50
181 182 2.288152 CGGGAAAACACAATGTCCAAGG 60.288 50.000 0.00 0.00 31.30 3.61
182 183 2.360801 ACGGGAAAACACAATGTCCAAG 59.639 45.455 0.00 0.00 31.30 3.61
183 184 2.379972 ACGGGAAAACACAATGTCCAA 58.620 42.857 0.00 0.00 31.30 3.53
184 185 2.060050 ACGGGAAAACACAATGTCCA 57.940 45.000 0.00 0.00 31.30 4.02
185 186 2.738135 CAACGGGAAAACACAATGTCC 58.262 47.619 0.00 0.00 0.00 4.02
186 187 2.124122 GCAACGGGAAAACACAATGTC 58.876 47.619 0.00 0.00 0.00 3.06
187 188 1.478510 TGCAACGGGAAAACACAATGT 59.521 42.857 0.00 0.00 0.00 2.71
188 189 2.215907 TGCAACGGGAAAACACAATG 57.784 45.000 0.00 0.00 0.00 2.82
189 190 2.545731 GTTGCAACGGGAAAACACAAT 58.454 42.857 14.90 0.00 0.00 2.71
190 191 1.997669 GTTGCAACGGGAAAACACAA 58.002 45.000 14.90 0.00 0.00 3.33
191 192 3.723554 GTTGCAACGGGAAAACACA 57.276 47.368 14.90 0.00 0.00 3.72
202 203 4.341502 ATGCCCGTGCGTTGCAAC 62.342 61.111 19.89 19.89 41.47 4.17
203 204 4.036804 GATGCCCGTGCGTTGCAA 62.037 61.111 0.00 0.00 41.47 4.08
205 206 1.917782 TAAAGATGCCCGTGCGTTGC 61.918 55.000 0.00 0.00 41.78 4.17
206 207 0.179200 GTAAAGATGCCCGTGCGTTG 60.179 55.000 0.00 0.00 41.78 4.10
207 208 1.303091 GGTAAAGATGCCCGTGCGTT 61.303 55.000 0.00 0.00 41.78 4.84
208 209 1.743995 GGTAAAGATGCCCGTGCGT 60.744 57.895 0.00 0.00 41.78 5.24
209 210 0.179094 TAGGTAAAGATGCCCGTGCG 60.179 55.000 0.00 0.00 41.78 5.34
210 211 1.134491 ACTAGGTAAAGATGCCCGTGC 60.134 52.381 0.00 0.00 38.26 5.34
211 212 2.981859 ACTAGGTAAAGATGCCCGTG 57.018 50.000 0.00 0.00 30.28 4.94
212 213 4.028825 AGTTACTAGGTAAAGATGCCCGT 58.971 43.478 0.00 0.00 29.42 5.28
213 214 4.667519 AGTTACTAGGTAAAGATGCCCG 57.332 45.455 0.00 0.00 29.42 6.13
361 367 3.257127 CAGACGGAGAAAAGGAAGAGACT 59.743 47.826 0.00 0.00 0.00 3.24
399 406 3.364964 CGTCCCTCCAAAAAGAACATTCG 60.365 47.826 0.00 0.00 0.00 3.34
660 668 1.011242 CATGTGCCGCCGATTTACG 60.011 57.895 0.00 0.00 42.18 3.18
747 1025 3.250280 TCGAGCTAATTACTACTCCAGCG 59.750 47.826 0.00 0.00 34.26 5.18
821 1103 4.820894 AGGAACGTAACTGCTTTCCTAT 57.179 40.909 4.14 0.00 42.81 2.57
822 1104 5.012239 TCTAGGAACGTAACTGCTTTCCTA 58.988 41.667 10.83 10.83 42.81 2.94
921 1206 2.102252 AGGCGAGAGACATCATCCTTTC 59.898 50.000 0.00 0.00 46.78 2.62
1032 1317 1.667830 CCGGCGTTTCTCTCTTGCA 60.668 57.895 6.01 0.00 0.00 4.08
1035 1320 0.108138 CATCCCGGCGTTTCTCTCTT 60.108 55.000 6.01 0.00 0.00 2.85
1117 1405 4.344865 GCCGAAGTGGGAGGCCAA 62.345 66.667 5.01 0.00 44.80 4.52
1231 1519 3.670625 CCGGATTGTTGTCTTCCAAGTA 58.329 45.455 0.00 0.00 32.51 2.24
1417 1705 4.980805 GTGGTCTGCGTTGCGGGA 62.981 66.667 0.00 0.00 35.34 5.14
2204 2534 1.336887 CGACGGCCTTCTTCTTCTTCA 60.337 52.381 7.75 0.00 0.00 3.02
2406 2760 0.684535 TCACCATCCTGTCGCAGAAA 59.315 50.000 8.20 0.00 39.69 2.52
2782 3142 7.607991 TGCCTCTTCTCTAAAGAAAAGTAATGG 59.392 37.037 0.00 0.00 40.95 3.16
2784 3144 9.171877 CATGCCTCTTCTCTAAAGAAAAGTAAT 57.828 33.333 0.00 0.00 40.95 1.89
3055 3430 7.495934 TCTTCTATTCTCTAAAATTCGGGCTTG 59.504 37.037 0.00 0.00 0.00 4.01
3124 3501 1.002033 GTCTTGCTTGTTCCTGCAGTG 60.002 52.381 13.81 4.33 40.46 3.66
3198 3575 3.365472 GGCCTTGTGGAATACCAGAAAT 58.635 45.455 0.00 0.00 46.30 2.17
3559 3939 9.819267 GTCTCTTTATACTAAGCTTATTGGTGT 57.181 33.333 6.64 3.64 0.00 4.16
3634 4015 0.970937 CCCCGTGCTCTTGGAGACTA 60.971 60.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.