Multiple sequence alignment - TraesCS6B01G107200

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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 TraesCS6B01G107200 chr6B 100.000 2201 0 0 1 2201 87571396 87573596 0 4065
1 TraesCS6B01G107200 chr6B 89.625 1494 147 6 177 1668 219562561 219564048 0 1893
2 TraesCS6B01G107200 chr6B 89.290 1494 152 6 177 1668 78310847 78309360 0 1866
3 TraesCS6B01G107200 chr6B 96.442 534 17 2 1669 2201 87579908 87580440 0 880
4 TraesCS6B01G107200 chr2D 89.692 1494 146 6 177 1668 16242019 16240532 0 1899
5 TraesCS6B01G107200 chr3D 89.565 1495 145 9 177 1668 606922153 606920667 0 1886
6 TraesCS6B01G107200 chr3D 89.424 1494 147 9 177 1668 373812941 373811457 0 1873
7 TraesCS6B01G107200 chrUn 89.491 1494 149 7 177 1668 60979109 60977622 0 1882
8 TraesCS6B01G107200 chr2B 89.424 1494 150 6 177 1668 619942259 619943746 0 1877
9 TraesCS6B01G107200 chr2B 96.262 535 19 1 1668 2201 34666100 34666634 0 876
10 TraesCS6B01G107200 chr2B 96.075 535 19 2 1669 2201 559165925 559165391 0 870
11 TraesCS6B01G107200 chr2B 96.067 534 20 1 1669 2201 559159083 559158550 0 869
12 TraesCS6B01G107200 chr4B 89.502 1486 148 6 185 1668 622316122 622314643 0 1873
13 TraesCS6B01G107200 chr6A 89.365 1495 149 8 177 1668 106682815 106681328 0 1871
14 TraesCS6B01G107200 chr1B 96.584 527 18 0 1669 2195 622825080 622825606 0 874
15 TraesCS6B01G107200 chr5B 96.067 534 19 2 1669 2201 619891925 619891393 0 869
16 TraesCS6B01G107200 chr5B 96.219 529 18 2 1669 2195 553435353 553435881 0 865
17 TraesCS6B01G107200 chr5B 95.880 534 20 2 1669 2201 619898764 619898232 0 863
18 TraesCS6B01G107200 chr5B 96.038 530 21 0 1669 2198 679179324 679178795 0 863


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 TraesCS6B01G107200 chr6B 87571396 87573596 2200 False 4065 4065 100.000 1 2201 1 chr6B.!!$F1 2200
1 TraesCS6B01G107200 chr6B 219562561 219564048 1487 False 1893 1893 89.625 177 1668 1 chr6B.!!$F3 1491
2 TraesCS6B01G107200 chr6B 78309360 78310847 1487 True 1866 1866 89.290 177 1668 1 chr6B.!!$R1 1491
3 TraesCS6B01G107200 chr6B 87579908 87580440 532 False 880 880 96.442 1669 2201 1 chr6B.!!$F2 532
4 TraesCS6B01G107200 chr2D 16240532 16242019 1487 True 1899 1899 89.692 177 1668 1 chr2D.!!$R1 1491
5 TraesCS6B01G107200 chr3D 606920667 606922153 1486 True 1886 1886 89.565 177 1668 1 chr3D.!!$R2 1491
6 TraesCS6B01G107200 chr3D 373811457 373812941 1484 True 1873 1873 89.424 177 1668 1 chr3D.!!$R1 1491
7 TraesCS6B01G107200 chrUn 60977622 60979109 1487 True 1882 1882 89.491 177 1668 1 chrUn.!!$R1 1491
8 TraesCS6B01G107200 chr2B 619942259 619943746 1487 False 1877 1877 89.424 177 1668 1 chr2B.!!$F2 1491
9 TraesCS6B01G107200 chr2B 34666100 34666634 534 False 876 876 96.262 1668 2201 1 chr2B.!!$F1 533
10 TraesCS6B01G107200 chr2B 559165391 559165925 534 True 870 870 96.075 1669 2201 1 chr2B.!!$R2 532
11 TraesCS6B01G107200 chr2B 559158550 559159083 533 True 869 869 96.067 1669 2201 1 chr2B.!!$R1 532
12 TraesCS6B01G107200 chr4B 622314643 622316122 1479 True 1873 1873 89.502 185 1668 1 chr4B.!!$R1 1483
13 TraesCS6B01G107200 chr6A 106681328 106682815 1487 True 1871 1871 89.365 177 1668 1 chr6A.!!$R1 1491
14 TraesCS6B01G107200 chr1B 622825080 622825606 526 False 874 874 96.584 1669 2195 1 chr1B.!!$F1 526
15 TraesCS6B01G107200 chr5B 619891393 619891925 532 True 869 869 96.067 1669 2201 1 chr5B.!!$R1 532
16 TraesCS6B01G107200 chr5B 553435353 553435881 528 False 865 865 96.219 1669 2195 1 chr5B.!!$F1 526
17 TraesCS6B01G107200 chr5B 619898232 619898764 532 True 863 863 95.880 1669 2201 1 chr5B.!!$R2 532
18 TraesCS6B01G107200 chr5B 679178795 679179324 529 True 863 863 96.038 1669 2198 1 chr5B.!!$R3 529

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
162 163 0.179045 ACCATACGAAGAGCCATGGC 60.179 55.0 30.12 30.12 41.41 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1612 1617 0.390603 CCAAGATACCGCAACACCGA 60.391 55.0 0.0 0.0 0.0 4.69 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
24 25 6.710692 CATCAAAAGGTTGAAGCCAAATAC 57.289 37.500 0.00 0.00 46.66 1.89
25 26 5.860941 TCAAAAGGTTGAAGCCAAATACA 57.139 34.783 0.00 0.00 40.87 2.29
26 27 5.841810 TCAAAAGGTTGAAGCCAAATACAG 58.158 37.500 0.00 0.00 40.87 2.74
27 28 4.871933 AAAGGTTGAAGCCAAATACAGG 57.128 40.909 0.00 0.00 33.49 4.00
28 29 3.806949 AGGTTGAAGCCAAATACAGGA 57.193 42.857 0.00 0.00 33.49 3.86
29 30 3.690460 AGGTTGAAGCCAAATACAGGAG 58.310 45.455 0.00 0.00 33.49 3.69
30 31 2.164422 GGTTGAAGCCAAATACAGGAGC 59.836 50.000 0.00 0.00 33.49 4.70
31 32 2.819608 GTTGAAGCCAAATACAGGAGCA 59.180 45.455 0.00 0.00 33.49 4.26
32 33 3.153369 TGAAGCCAAATACAGGAGCAA 57.847 42.857 0.00 0.00 0.00 3.91
33 34 2.819608 TGAAGCCAAATACAGGAGCAAC 59.180 45.455 0.00 0.00 0.00 4.17
34 35 2.584835 AGCCAAATACAGGAGCAACA 57.415 45.000 0.00 0.00 0.00 3.33
35 36 2.162681 AGCCAAATACAGGAGCAACAC 58.837 47.619 0.00 0.00 0.00 3.32
36 37 1.885887 GCCAAATACAGGAGCAACACA 59.114 47.619 0.00 0.00 0.00 3.72
37 38 2.493278 GCCAAATACAGGAGCAACACAT 59.507 45.455 0.00 0.00 0.00 3.21
38 39 3.674138 GCCAAATACAGGAGCAACACATG 60.674 47.826 0.00 0.00 0.00 3.21
39 40 3.507233 CCAAATACAGGAGCAACACATGT 59.493 43.478 0.00 0.00 0.00 3.21
40 41 4.478699 CAAATACAGGAGCAACACATGTG 58.521 43.478 24.25 24.25 0.00 3.21
41 42 3.701205 ATACAGGAGCAACACATGTGA 57.299 42.857 31.94 5.91 0.00 3.58
42 43 2.346766 ACAGGAGCAACACATGTGAA 57.653 45.000 31.94 0.00 0.00 3.18
43 44 1.949525 ACAGGAGCAACACATGTGAAC 59.050 47.619 31.94 18.95 0.00 3.18
44 45 1.948834 CAGGAGCAACACATGTGAACA 59.051 47.619 31.94 0.00 0.00 3.18
45 46 1.949525 AGGAGCAACACATGTGAACAC 59.050 47.619 31.94 16.92 0.00 3.32
46 47 1.001378 GGAGCAACACATGTGAACACC 60.001 52.381 31.94 21.36 0.00 4.16
47 48 1.675483 GAGCAACACATGTGAACACCA 59.325 47.619 31.94 0.00 0.00 4.17
48 49 1.677576 AGCAACACATGTGAACACCAG 59.322 47.619 31.94 13.14 0.00 4.00
49 50 1.405105 GCAACACATGTGAACACCAGT 59.595 47.619 31.94 4.03 0.00 4.00
50 51 2.616376 GCAACACATGTGAACACCAGTA 59.384 45.455 31.94 0.00 0.00 2.74
51 52 3.303990 GCAACACATGTGAACACCAGTAG 60.304 47.826 31.94 9.39 0.00 2.57
52 53 4.126437 CAACACATGTGAACACCAGTAGA 58.874 43.478 31.94 0.00 0.00 2.59
53 54 4.415881 ACACATGTGAACACCAGTAGAA 57.584 40.909 31.94 0.00 0.00 2.10
54 55 4.776349 ACACATGTGAACACCAGTAGAAA 58.224 39.130 31.94 0.00 0.00 2.52
55 56 4.816385 ACACATGTGAACACCAGTAGAAAG 59.184 41.667 31.94 0.00 0.00 2.62
56 57 4.816385 CACATGTGAACACCAGTAGAAAGT 59.184 41.667 21.64 0.00 0.00 2.66
57 58 5.296780 CACATGTGAACACCAGTAGAAAGTT 59.703 40.000 21.64 0.00 0.00 2.66
58 59 5.885912 ACATGTGAACACCAGTAGAAAGTTT 59.114 36.000 0.00 0.00 0.00 2.66
59 60 6.377146 ACATGTGAACACCAGTAGAAAGTTTT 59.623 34.615 0.00 0.00 0.00 2.43
60 61 6.827586 TGTGAACACCAGTAGAAAGTTTTT 57.172 33.333 2.46 0.00 0.00 1.94
80 81 6.732896 TTTTTGGGTGGAATTTGCTAGTAA 57.267 33.333 0.00 0.00 0.00 2.24
81 82 6.926630 TTTTGGGTGGAATTTGCTAGTAAT 57.073 33.333 0.00 0.00 0.00 1.89
82 83 8.423906 TTTTTGGGTGGAATTTGCTAGTAATA 57.576 30.769 0.00 0.00 0.00 0.98
83 84 7.399245 TTTGGGTGGAATTTGCTAGTAATAC 57.601 36.000 0.00 0.00 0.00 1.89
84 85 6.068461 TGGGTGGAATTTGCTAGTAATACA 57.932 37.500 0.00 0.00 0.00 2.29
85 86 6.486056 TGGGTGGAATTTGCTAGTAATACAA 58.514 36.000 0.00 0.00 0.00 2.41
86 87 6.601613 TGGGTGGAATTTGCTAGTAATACAAG 59.398 38.462 0.00 0.00 0.00 3.16
87 88 6.459710 GGGTGGAATTTGCTAGTAATACAAGC 60.460 42.308 0.00 0.00 0.00 4.01
88 89 6.318900 GGTGGAATTTGCTAGTAATACAAGCT 59.681 38.462 0.00 0.00 0.00 3.74
89 90 7.148069 GGTGGAATTTGCTAGTAATACAAGCTT 60.148 37.037 0.00 0.00 0.00 3.74
90 91 7.698130 GTGGAATTTGCTAGTAATACAAGCTTG 59.302 37.037 24.84 24.84 0.00 4.01
91 92 7.393234 TGGAATTTGCTAGTAATACAAGCTTGT 59.607 33.333 32.97 32.97 44.86 3.16
92 93 7.698130 GGAATTTGCTAGTAATACAAGCTTGTG 59.302 37.037 36.50 21.34 42.31 3.33
93 94 7.687941 ATTTGCTAGTAATACAAGCTTGTGT 57.312 32.000 36.50 29.47 42.31 3.72
94 95 8.786826 ATTTGCTAGTAATACAAGCTTGTGTA 57.213 30.769 36.50 25.75 42.31 2.90
95 96 7.591006 TTGCTAGTAATACAAGCTTGTGTAC 57.409 36.000 36.50 32.53 42.31 2.90
96 97 6.931838 TGCTAGTAATACAAGCTTGTGTACT 58.068 36.000 35.42 35.42 42.31 2.73
97 98 7.383687 TGCTAGTAATACAAGCTTGTGTACTT 58.616 34.615 36.82 27.59 42.31 2.24
98 99 7.330946 TGCTAGTAATACAAGCTTGTGTACTTG 59.669 37.037 36.82 34.76 46.91 3.16
99 100 7.201530 GCTAGTAATACAAGCTTGTGTACTTGG 60.202 40.741 36.82 31.42 46.03 3.61
100 101 5.938125 AGTAATACAAGCTTGTGTACTTGGG 59.062 40.000 36.50 6.94 46.03 4.12
101 102 1.318576 ACAAGCTTGTGTACTTGGGC 58.681 50.000 30.66 0.00 46.03 5.36
102 103 1.317613 CAAGCTTGTGTACTTGGGCA 58.682 50.000 18.65 0.00 39.67 5.36
103 104 1.888512 CAAGCTTGTGTACTTGGGCAT 59.111 47.619 18.65 0.00 39.67 4.40
104 105 1.826385 AGCTTGTGTACTTGGGCATC 58.174 50.000 0.00 0.00 0.00 3.91
105 106 1.073763 AGCTTGTGTACTTGGGCATCA 59.926 47.619 0.00 0.00 0.00 3.07
106 107 1.200020 GCTTGTGTACTTGGGCATCAC 59.800 52.381 0.00 0.00 0.00 3.06
107 108 2.503331 CTTGTGTACTTGGGCATCACA 58.497 47.619 0.00 0.00 37.27 3.58
108 109 2.877097 TGTGTACTTGGGCATCACAT 57.123 45.000 0.00 0.00 34.74 3.21
109 110 3.153369 TGTGTACTTGGGCATCACATT 57.847 42.857 0.00 0.00 34.74 2.71
110 111 4.293662 TGTGTACTTGGGCATCACATTA 57.706 40.909 0.00 0.00 34.74 1.90
111 112 4.657013 TGTGTACTTGGGCATCACATTAA 58.343 39.130 0.00 0.00 34.74 1.40
112 113 5.073428 TGTGTACTTGGGCATCACATTAAA 58.927 37.500 0.00 0.00 34.74 1.52
113 114 5.536538 TGTGTACTTGGGCATCACATTAAAA 59.463 36.000 0.00 0.00 34.74 1.52
114 115 6.092748 GTGTACTTGGGCATCACATTAAAAG 58.907 40.000 0.00 0.00 0.00 2.27
115 116 4.806640 ACTTGGGCATCACATTAAAAGG 57.193 40.909 0.00 0.00 0.00 3.11
116 117 3.515104 ACTTGGGCATCACATTAAAAGGG 59.485 43.478 0.00 0.00 0.00 3.95
117 118 3.464720 TGGGCATCACATTAAAAGGGA 57.535 42.857 0.00 0.00 0.00 4.20
118 119 3.364549 TGGGCATCACATTAAAAGGGAG 58.635 45.455 0.00 0.00 0.00 4.30
119 120 2.101415 GGGCATCACATTAAAAGGGAGC 59.899 50.000 0.00 0.00 0.00 4.70
120 121 3.026694 GGCATCACATTAAAAGGGAGCT 58.973 45.455 0.00 0.00 0.00 4.09
121 122 3.067320 GGCATCACATTAAAAGGGAGCTC 59.933 47.826 4.71 4.71 0.00 4.09
122 123 3.242870 GCATCACATTAAAAGGGAGCTCG 60.243 47.826 7.83 0.00 0.00 5.03
123 124 2.985896 TCACATTAAAAGGGAGCTCGG 58.014 47.619 7.83 0.00 0.00 4.63
124 125 2.304761 TCACATTAAAAGGGAGCTCGGT 59.695 45.455 7.83 0.00 0.00 4.69
125 126 3.081804 CACATTAAAAGGGAGCTCGGTT 58.918 45.455 7.83 0.00 0.00 4.44
126 127 4.020039 TCACATTAAAAGGGAGCTCGGTTA 60.020 41.667 7.83 0.54 0.00 2.85
127 128 4.698304 CACATTAAAAGGGAGCTCGGTTAA 59.302 41.667 7.83 9.44 0.00 2.01
128 129 5.357032 CACATTAAAAGGGAGCTCGGTTAAT 59.643 40.000 7.83 11.15 0.00 1.40
129 130 5.949952 ACATTAAAAGGGAGCTCGGTTAATT 59.050 36.000 7.83 0.80 0.00 1.40
130 131 6.436218 ACATTAAAAGGGAGCTCGGTTAATTT 59.564 34.615 7.83 5.51 0.00 1.82
131 132 6.904463 TTAAAAGGGAGCTCGGTTAATTTT 57.096 33.333 7.83 10.15 0.00 1.82
132 133 5.386958 AAAAGGGAGCTCGGTTAATTTTC 57.613 39.130 7.83 0.00 0.00 2.29
133 134 3.000684 AGGGAGCTCGGTTAATTTTCC 57.999 47.619 7.83 0.00 0.00 3.13
134 135 2.307686 AGGGAGCTCGGTTAATTTTCCA 59.692 45.455 7.83 0.00 0.00 3.53
135 136 3.053619 AGGGAGCTCGGTTAATTTTCCAT 60.054 43.478 7.83 0.00 0.00 3.41
136 137 4.165372 AGGGAGCTCGGTTAATTTTCCATA 59.835 41.667 7.83 0.00 0.00 2.74
137 138 4.515567 GGGAGCTCGGTTAATTTTCCATAG 59.484 45.833 7.83 0.00 0.00 2.23
138 139 5.123936 GGAGCTCGGTTAATTTTCCATAGT 58.876 41.667 7.83 0.00 0.00 2.12
139 140 5.007724 GGAGCTCGGTTAATTTTCCATAGTG 59.992 44.000 7.83 0.00 0.00 2.74
140 141 5.497474 AGCTCGGTTAATTTTCCATAGTGT 58.503 37.500 0.00 0.00 0.00 3.55
141 142 5.585047 AGCTCGGTTAATTTTCCATAGTGTC 59.415 40.000 0.00 0.00 0.00 3.67
142 143 5.353123 GCTCGGTTAATTTTCCATAGTGTCA 59.647 40.000 0.00 0.00 0.00 3.58
143 144 6.128117 GCTCGGTTAATTTTCCATAGTGTCAA 60.128 38.462 0.00 0.00 0.00 3.18
144 145 7.136289 TCGGTTAATTTTCCATAGTGTCAAC 57.864 36.000 0.00 0.00 0.00 3.18
145 146 6.149807 TCGGTTAATTTTCCATAGTGTCAACC 59.850 38.462 0.00 0.00 0.00 3.77
146 147 6.072397 CGGTTAATTTTCCATAGTGTCAACCA 60.072 38.462 0.00 0.00 33.00 3.67
147 148 7.362574 CGGTTAATTTTCCATAGTGTCAACCAT 60.363 37.037 0.00 0.00 33.00 3.55
148 149 8.962679 GGTTAATTTTCCATAGTGTCAACCATA 58.037 33.333 0.00 0.00 33.52 2.74
149 150 9.783256 GTTAATTTTCCATAGTGTCAACCATAC 57.217 33.333 0.00 0.00 0.00 2.39
150 151 6.677781 ATTTTCCATAGTGTCAACCATACG 57.322 37.500 0.00 0.00 0.00 3.06
151 152 5.408880 TTTCCATAGTGTCAACCATACGA 57.591 39.130 0.00 0.00 0.00 3.43
152 153 5.408880 TTCCATAGTGTCAACCATACGAA 57.591 39.130 0.00 0.00 0.00 3.85
153 154 5.006153 TCCATAGTGTCAACCATACGAAG 57.994 43.478 0.00 0.00 0.00 3.79
154 155 4.707934 TCCATAGTGTCAACCATACGAAGA 59.292 41.667 0.00 0.00 0.00 2.87
155 156 5.043903 CCATAGTGTCAACCATACGAAGAG 58.956 45.833 0.00 0.00 0.00 2.85
156 157 2.960819 AGTGTCAACCATACGAAGAGC 58.039 47.619 0.00 0.00 0.00 4.09
157 158 2.000447 GTGTCAACCATACGAAGAGCC 59.000 52.381 0.00 0.00 0.00 4.70
158 159 1.621317 TGTCAACCATACGAAGAGCCA 59.379 47.619 0.00 0.00 0.00 4.75
159 160 2.236146 TGTCAACCATACGAAGAGCCAT 59.764 45.455 0.00 0.00 0.00 4.40
160 161 2.609459 GTCAACCATACGAAGAGCCATG 59.391 50.000 0.00 0.00 0.00 3.66
161 162 1.942657 CAACCATACGAAGAGCCATGG 59.057 52.381 7.63 7.63 43.02 3.66
162 163 0.179045 ACCATACGAAGAGCCATGGC 60.179 55.000 30.12 30.12 41.41 4.40
173 174 2.123939 CCATGGCGCCAATGGGTA 60.124 61.111 36.33 8.35 36.17 3.69
174 175 2.489275 CCATGGCGCCAATGGGTAC 61.489 63.158 36.33 0.00 36.17 3.34
188 189 2.685202 GGTACCAGGCTGAGGACTT 58.315 57.895 17.94 0.00 0.00 3.01
217 218 2.403252 ATAGTTGAAAGCAGTCGGGG 57.597 50.000 0.00 0.00 0.00 5.73
225 226 1.200519 AAGCAGTCGGGGCTATACAA 58.799 50.000 0.00 0.00 41.66 2.41
237 238 4.513442 GGGCTATACAATTGTGTCTGTCA 58.487 43.478 21.42 0.00 39.30 3.58
244 245 1.059098 ATTGTGTCTGTCAGCCCAGA 58.941 50.000 0.00 0.00 39.11 3.86
253 254 7.147567 TGTGTCTGTCAGCCCAGATTATTTATA 60.148 37.037 0.00 0.00 43.03 0.98
258 259 8.995027 TGTCAGCCCAGATTATTTATAATGTT 57.005 30.769 0.00 0.00 33.37 2.71
351 352 4.584325 AGCAAGGTGTATCTGAAGCAAAAA 59.416 37.500 0.00 0.00 0.00 1.94
383 384 0.620556 GAAGATGCAGGAGGGGTCAA 59.379 55.000 0.00 0.00 0.00 3.18
412 413 5.813672 TGTGGAGTATATGAACGCCTTTAAC 59.186 40.000 0.86 0.00 39.79 2.01
419 420 2.920524 TGAACGCCTTTAACCAAGTCA 58.079 42.857 0.00 0.00 0.00 3.41
444 445 2.347490 CCTAGCACGCTTGGGTGT 59.653 61.111 16.95 8.31 40.08 4.16
454 455 2.027192 ACGCTTGGGTGTGATAGTTGAT 60.027 45.455 0.00 0.00 34.60 2.57
468 469 3.314307 AGTTGATGACGAGGATAGGGA 57.686 47.619 0.00 0.00 0.00 4.20
491 492 6.703165 GGAAATTCTGCTTCTTTGTTCATTGT 59.297 34.615 0.00 0.00 0.00 2.71
496 497 4.786507 TGCTTCTTTGTTCATTGTCATCG 58.213 39.130 0.00 0.00 0.00 3.84
504 505 4.441792 TGTTCATTGTCATCGTCCTATGG 58.558 43.478 0.00 0.00 0.00 2.74
563 564 9.647918 AGACTGTCAAGAATGAGGATATTACTA 57.352 33.333 10.88 0.00 35.88 1.82
565 566 9.427821 ACTGTCAAGAATGAGGATATTACTACT 57.572 33.333 0.00 0.00 35.88 2.57
574 575 6.830912 TGAGGATATTACTACTGCATTGCTT 58.169 36.000 10.49 0.00 0.00 3.91
650 651 0.191064 AGTCAAGGGTGAGGAGTGGA 59.809 55.000 0.00 0.00 33.27 4.02
666 667 2.251338 AGTGGAGGAAGGGATATGAGGT 59.749 50.000 0.00 0.00 0.00 3.85
679 680 5.132144 GGGATATGAGGTAGGGAAGAACAAA 59.868 44.000 0.00 0.00 0.00 2.83
723 724 1.765904 TCACAAGTGTAAGCAGTGGGA 59.234 47.619 0.00 0.00 0.00 4.37
778 779 0.593128 GGGCAAGTGCTAATATGGCG 59.407 55.000 2.85 0.00 41.70 5.69
794 795 1.148157 GGCGACTCATGGTGATGACG 61.148 60.000 0.00 0.00 34.71 4.35
804 805 1.225855 GGTGATGACGCAGACAACAA 58.774 50.000 0.00 0.00 36.75 2.83
853 854 1.398692 GGTCAACCAAAGGTGAAGCA 58.601 50.000 0.00 0.00 35.34 3.91
858 859 2.364970 CAACCAAAGGTGAAGCATGGAA 59.635 45.455 10.24 0.00 35.34 3.53
880 881 1.909700 TGGATTCGGCTTGCTCTTTT 58.090 45.000 0.00 0.00 0.00 2.27
881 882 1.812571 TGGATTCGGCTTGCTCTTTTC 59.187 47.619 0.00 0.00 0.00 2.29
900 901 2.046292 TCTCATGTGACACCCAACAGA 58.954 47.619 2.45 0.00 0.00 3.41
923 924 2.963782 AGTGGTTCTCTTCGTACAGGTT 59.036 45.455 0.00 0.00 0.00 3.50
935 936 3.118702 TCGTACAGGTTTGGTGAGTTTGA 60.119 43.478 0.00 0.00 0.00 2.69
958 959 1.447643 GCCTATGTGGGCGATGACT 59.552 57.895 0.00 0.00 42.82 3.41
961 962 1.345741 CCTATGTGGGCGATGACTCAT 59.654 52.381 0.00 0.00 0.00 2.90
967 968 3.206150 GTGGGCGATGACTCATGTTATT 58.794 45.455 0.00 0.00 0.00 1.40
974 975 5.390885 GCGATGACTCATGTTATTGTGTTGT 60.391 40.000 0.00 0.00 0.00 3.32
987 988 4.431416 TTGTGTTGTTGGAGTAGGTGAT 57.569 40.909 0.00 0.00 0.00 3.06
990 991 6.860790 TGTGTTGTTGGAGTAGGTGATATA 57.139 37.500 0.00 0.00 0.00 0.86
1035 1036 2.584608 CGGATGCTTCGGGGAGTT 59.415 61.111 0.00 0.00 0.00 3.01
1115 1116 4.162509 TGGTATGGTATTCCGTTGTGATCA 59.837 41.667 0.00 0.00 36.30 2.92
1122 1123 6.053005 GGTATTCCGTTGTGATCAGGATAAA 58.947 40.000 0.00 0.00 32.19 1.40
1127 1128 6.234920 TCCGTTGTGATCAGGATAAAAAGAA 58.765 36.000 0.00 0.00 0.00 2.52
1155 1156 5.163322 GAGAATCATGGAAGATGAGGTGACT 60.163 44.000 0.00 0.00 38.48 3.41
1168 1169 3.327464 TGAGGTGACTGTGATGATTGGAA 59.673 43.478 0.00 0.00 44.43 3.53
1181 1182 0.698818 ATTGGAAGGAGGACGGCTTT 59.301 50.000 0.00 0.00 0.00 3.51
1198 1199 4.620982 GGCTTTGCATCTTTACAAGTTGT 58.379 39.130 14.05 14.05 32.17 3.32
1267 1268 0.760567 TAGCAGCGGGATCTCATGGT 60.761 55.000 5.01 5.01 0.00 3.55
1356 1357 4.346709 TCTGGAGTACATGGAAGTTTGACA 59.653 41.667 0.00 0.00 0.00 3.58
1359 1360 4.819630 GGAGTACATGGAAGTTTGACACAA 59.180 41.667 0.00 0.00 0.00 3.33
1361 1362 6.183360 GGAGTACATGGAAGTTTGACACAAAA 60.183 38.462 0.00 0.00 0.00 2.44
1371 1372 8.450180 GGAAGTTTGACACAAAAACAAATTCAT 58.550 29.630 0.00 0.00 39.49 2.57
1373 1374 8.545229 AGTTTGACACAAAAACAAATTCATGA 57.455 26.923 0.00 0.00 39.49 3.07
1376 1377 6.946165 TGACACAAAAACAAATTCATGATGC 58.054 32.000 0.00 0.00 0.00 3.91
1407 1408 2.993937 TCGTCAAGGTGGAGTTTGTTT 58.006 42.857 0.00 0.00 0.00 2.83
1408 1409 2.680841 TCGTCAAGGTGGAGTTTGTTTG 59.319 45.455 0.00 0.00 0.00 2.93
1409 1410 2.680841 CGTCAAGGTGGAGTTTGTTTGA 59.319 45.455 0.00 0.00 0.00 2.69
1419 1420 4.520874 TGGAGTTTGTTTGAGTTTGTGTCA 59.479 37.500 0.00 0.00 0.00 3.58
1432 1433 8.775220 TGAGTTTGTGTCAAATATTTTGTACG 57.225 30.769 0.00 0.00 0.00 3.67
1449 1450 0.939419 ACGAGTTGGGTTACGTTTGC 59.061 50.000 0.00 0.00 35.47 3.68
1471 1472 1.946768 CTTGGTGTTGTAGTGTGGGTG 59.053 52.381 0.00 0.00 0.00 4.61
1478 1479 2.303600 GTTGTAGTGTGGGTGGGATACA 59.696 50.000 0.00 0.00 39.74 2.29
1483 1484 2.504175 AGTGTGGGTGGGATACATGTAC 59.496 50.000 7.96 2.44 39.74 2.90
1496 1497 1.819288 ACATGTACTGTCAGAGTCGGG 59.181 52.381 6.91 0.00 35.96 5.14
1509 1512 0.899717 AGTCGGGCGTTGTACCCTTA 60.900 55.000 0.00 0.00 46.04 2.69
1554 1558 1.742831 CCATGTTGTAACCCATGACGG 59.257 52.381 0.00 0.00 40.70 4.79
1581 1586 2.356278 GACAGGCATGCAAGGGGA 59.644 61.111 21.36 0.00 0.00 4.81
1582 1587 1.304381 GACAGGCATGCAAGGGGAA 60.304 57.895 21.36 0.00 0.00 3.97
1584 1589 1.304713 CAGGCATGCAAGGGGAAGT 60.305 57.895 21.36 0.00 0.00 3.01
1585 1590 0.034186 CAGGCATGCAAGGGGAAGTA 60.034 55.000 21.36 0.00 0.00 2.24
1588 1593 0.034089 GCATGCAAGGGGAAGTAGGT 60.034 55.000 14.21 0.00 0.00 3.08
1629 1634 0.390735 GGTCGGTGTTGCGGTATCTT 60.391 55.000 0.00 0.00 0.00 2.40
2005 2011 1.751552 CCTAAACTCCGCGACGATAC 58.248 55.000 8.23 0.00 0.00 2.24
2030 2036 2.408565 GAGGTGGAATATGGTGGAGGA 58.591 52.381 0.00 0.00 0.00 3.71
2087 2095 2.955660 CAACTTGTGTGTTATGGGGTGT 59.044 45.455 0.00 0.00 0.00 4.16
2116 2124 3.581332 CCCCCGTATATAAAGGAGCAAGA 59.419 47.826 7.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.222389 TGTATTTGGCTTCAACCTTTTGATG 58.778 36.000 0.00 0.00 41.50 3.07
2 3 6.418057 TGTATTTGGCTTCAACCTTTTGAT 57.582 33.333 0.00 0.00 41.50 2.57
3 4 5.221422 CCTGTATTTGGCTTCAACCTTTTGA 60.221 40.000 0.00 0.00 40.14 2.69
4 5 4.990426 CCTGTATTTGGCTTCAACCTTTTG 59.010 41.667 0.00 0.00 0.00 2.44
5 6 4.898861 TCCTGTATTTGGCTTCAACCTTTT 59.101 37.500 0.00 0.00 0.00 2.27
6 7 4.479158 TCCTGTATTTGGCTTCAACCTTT 58.521 39.130 0.00 0.00 0.00 3.11
7 8 4.082125 CTCCTGTATTTGGCTTCAACCTT 58.918 43.478 0.00 0.00 0.00 3.50
8 9 3.690460 CTCCTGTATTTGGCTTCAACCT 58.310 45.455 0.00 0.00 0.00 3.50
9 10 2.164422 GCTCCTGTATTTGGCTTCAACC 59.836 50.000 0.00 0.00 0.00 3.77
10 11 2.819608 TGCTCCTGTATTTGGCTTCAAC 59.180 45.455 0.00 0.00 0.00 3.18
11 12 3.153369 TGCTCCTGTATTTGGCTTCAA 57.847 42.857 0.00 0.00 0.00 2.69
12 13 2.819608 GTTGCTCCTGTATTTGGCTTCA 59.180 45.455 0.00 0.00 0.00 3.02
13 14 2.819608 TGTTGCTCCTGTATTTGGCTTC 59.180 45.455 0.00 0.00 0.00 3.86
14 15 2.558359 GTGTTGCTCCTGTATTTGGCTT 59.442 45.455 0.00 0.00 0.00 4.35
15 16 2.162681 GTGTTGCTCCTGTATTTGGCT 58.837 47.619 0.00 0.00 0.00 4.75
16 17 1.885887 TGTGTTGCTCCTGTATTTGGC 59.114 47.619 0.00 0.00 0.00 4.52
17 18 3.507233 ACATGTGTTGCTCCTGTATTTGG 59.493 43.478 0.00 0.00 0.00 3.28
18 19 4.216042 TCACATGTGTTGCTCCTGTATTTG 59.784 41.667 24.63 0.00 0.00 2.32
19 20 4.397420 TCACATGTGTTGCTCCTGTATTT 58.603 39.130 24.63 0.00 0.00 1.40
20 21 4.019792 TCACATGTGTTGCTCCTGTATT 57.980 40.909 24.63 0.00 0.00 1.89
21 22 3.701205 TCACATGTGTTGCTCCTGTAT 57.299 42.857 24.63 0.00 0.00 2.29
22 23 3.138304 GTTCACATGTGTTGCTCCTGTA 58.862 45.455 24.63 0.00 0.00 2.74
23 24 1.949525 GTTCACATGTGTTGCTCCTGT 59.050 47.619 24.63 0.00 0.00 4.00
24 25 1.948834 TGTTCACATGTGTTGCTCCTG 59.051 47.619 24.63 0.00 0.00 3.86
25 26 1.949525 GTGTTCACATGTGTTGCTCCT 59.050 47.619 24.63 0.00 0.00 3.69
26 27 1.001378 GGTGTTCACATGTGTTGCTCC 60.001 52.381 24.63 19.34 0.00 4.70
27 28 1.675483 TGGTGTTCACATGTGTTGCTC 59.325 47.619 24.63 15.28 0.00 4.26
28 29 1.677576 CTGGTGTTCACATGTGTTGCT 59.322 47.619 24.63 0.00 0.00 3.91
29 30 1.405105 ACTGGTGTTCACATGTGTTGC 59.595 47.619 24.63 15.75 0.00 4.17
30 31 4.126437 TCTACTGGTGTTCACATGTGTTG 58.874 43.478 24.63 10.67 0.00 3.33
31 32 4.415881 TCTACTGGTGTTCACATGTGTT 57.584 40.909 24.63 4.02 0.00 3.32
32 33 4.415881 TTCTACTGGTGTTCACATGTGT 57.584 40.909 24.63 6.17 0.00 3.72
33 34 4.816385 ACTTTCTACTGGTGTTCACATGTG 59.184 41.667 20.18 20.18 0.00 3.21
34 35 5.036117 ACTTTCTACTGGTGTTCACATGT 57.964 39.130 0.00 0.00 0.00 3.21
35 36 6.377327 AAACTTTCTACTGGTGTTCACATG 57.623 37.500 5.32 0.00 0.00 3.21
36 37 7.404671 AAAAACTTTCTACTGGTGTTCACAT 57.595 32.000 5.32 0.00 0.00 3.21
37 38 6.827586 AAAAACTTTCTACTGGTGTTCACA 57.172 33.333 5.32 0.00 0.00 3.58
57 58 6.732896 TTACTAGCAAATTCCACCCAAAAA 57.267 33.333 0.00 0.00 0.00 1.94
58 59 6.926630 ATTACTAGCAAATTCCACCCAAAA 57.073 33.333 0.00 0.00 0.00 2.44
59 60 6.948886 TGTATTACTAGCAAATTCCACCCAAA 59.051 34.615 0.00 0.00 0.00 3.28
60 61 6.486056 TGTATTACTAGCAAATTCCACCCAA 58.514 36.000 0.00 0.00 0.00 4.12
61 62 6.068461 TGTATTACTAGCAAATTCCACCCA 57.932 37.500 0.00 0.00 0.00 4.51
62 63 6.459710 GCTTGTATTACTAGCAAATTCCACCC 60.460 42.308 20.61 0.00 44.40 4.61
63 64 6.318900 AGCTTGTATTACTAGCAAATTCCACC 59.681 38.462 25.14 0.48 46.76 4.61
64 65 7.321745 AGCTTGTATTACTAGCAAATTCCAC 57.678 36.000 25.14 1.05 46.76 4.02
65 66 7.393234 ACAAGCTTGTATTACTAGCAAATTCCA 59.607 33.333 30.25 0.00 46.76 3.53
66 67 7.698130 CACAAGCTTGTATTACTAGCAAATTCC 59.302 37.037 30.67 2.20 46.76 3.01
67 68 8.237267 ACACAAGCTTGTATTACTAGCAAATTC 58.763 33.333 30.67 2.78 46.76 2.17
68 69 8.110860 ACACAAGCTTGTATTACTAGCAAATT 57.889 30.769 30.67 12.78 46.76 1.82
69 70 7.687941 ACACAAGCTTGTATTACTAGCAAAT 57.312 32.000 30.67 12.66 46.76 2.32
70 71 7.876068 AGTACACAAGCTTGTATTACTAGCAAA 59.124 33.333 32.37 8.63 46.76 3.68
71 72 7.383687 AGTACACAAGCTTGTATTACTAGCAA 58.616 34.615 32.37 9.23 46.76 3.91
72 73 6.931838 AGTACACAAGCTTGTATTACTAGCA 58.068 36.000 32.37 13.05 46.76 3.49
73 74 7.201530 CCAAGTACACAAGCTTGTATTACTAGC 60.202 40.741 32.94 18.70 45.15 3.42
74 75 7.277981 CCCAAGTACACAAGCTTGTATTACTAG 59.722 40.741 32.94 28.22 39.91 2.57
75 76 7.101054 CCCAAGTACACAAGCTTGTATTACTA 58.899 38.462 32.94 18.04 39.91 1.82
76 77 5.938125 CCCAAGTACACAAGCTTGTATTACT 59.062 40.000 30.14 30.14 39.91 2.24
77 78 5.391629 GCCCAAGTACACAAGCTTGTATTAC 60.392 44.000 30.67 28.93 39.91 1.89
78 79 4.698304 GCCCAAGTACACAAGCTTGTATTA 59.302 41.667 30.67 21.05 39.91 0.98
79 80 3.506067 GCCCAAGTACACAAGCTTGTATT 59.494 43.478 30.67 22.04 39.91 1.89
80 81 3.081804 GCCCAAGTACACAAGCTTGTAT 58.918 45.455 30.67 23.48 39.91 2.29
81 82 2.158740 TGCCCAAGTACACAAGCTTGTA 60.159 45.455 30.67 14.83 39.91 2.41
82 83 1.318576 GCCCAAGTACACAAGCTTGT 58.681 50.000 26.36 26.36 43.36 3.16
83 84 1.317613 TGCCCAAGTACACAAGCTTG 58.682 50.000 24.84 24.84 41.08 4.01
84 85 2.162681 GATGCCCAAGTACACAAGCTT 58.837 47.619 0.00 0.00 0.00 3.74
85 86 1.073763 TGATGCCCAAGTACACAAGCT 59.926 47.619 0.00 0.00 0.00 3.74
86 87 1.200020 GTGATGCCCAAGTACACAAGC 59.800 52.381 0.00 0.00 0.00 4.01
87 88 2.503331 TGTGATGCCCAAGTACACAAG 58.497 47.619 0.00 0.00 38.28 3.16
88 89 2.647683 TGTGATGCCCAAGTACACAA 57.352 45.000 0.00 0.00 38.28 3.33
89 90 2.877097 ATGTGATGCCCAAGTACACA 57.123 45.000 0.00 0.00 43.70 3.72
90 91 5.637006 TTTAATGTGATGCCCAAGTACAC 57.363 39.130 0.00 0.00 0.00 2.90
91 92 5.184864 CCTTTTAATGTGATGCCCAAGTACA 59.815 40.000 0.00 0.00 0.00 2.90
92 93 5.394115 CCCTTTTAATGTGATGCCCAAGTAC 60.394 44.000 0.00 0.00 0.00 2.73
93 94 4.709397 CCCTTTTAATGTGATGCCCAAGTA 59.291 41.667 0.00 0.00 0.00 2.24
94 95 3.515104 CCCTTTTAATGTGATGCCCAAGT 59.485 43.478 0.00 0.00 0.00 3.16
95 96 3.768757 TCCCTTTTAATGTGATGCCCAAG 59.231 43.478 0.00 0.00 0.00 3.61
96 97 3.768757 CTCCCTTTTAATGTGATGCCCAA 59.231 43.478 0.00 0.00 0.00 4.12
97 98 3.364549 CTCCCTTTTAATGTGATGCCCA 58.635 45.455 0.00 0.00 0.00 5.36
98 99 2.101415 GCTCCCTTTTAATGTGATGCCC 59.899 50.000 0.00 0.00 0.00 5.36
99 100 3.026694 AGCTCCCTTTTAATGTGATGCC 58.973 45.455 0.00 0.00 0.00 4.40
100 101 3.242870 CGAGCTCCCTTTTAATGTGATGC 60.243 47.826 8.47 0.00 0.00 3.91
101 102 3.313526 CCGAGCTCCCTTTTAATGTGATG 59.686 47.826 8.47 0.00 0.00 3.07
102 103 3.054361 ACCGAGCTCCCTTTTAATGTGAT 60.054 43.478 8.47 0.00 0.00 3.06
103 104 2.304761 ACCGAGCTCCCTTTTAATGTGA 59.695 45.455 8.47 0.00 0.00 3.58
104 105 2.711542 ACCGAGCTCCCTTTTAATGTG 58.288 47.619 8.47 0.00 0.00 3.21
105 106 3.434940 AACCGAGCTCCCTTTTAATGT 57.565 42.857 8.47 0.00 0.00 2.71
106 107 6.451064 AATTAACCGAGCTCCCTTTTAATG 57.549 37.500 8.47 0.00 0.00 1.90
107 108 7.363530 GGAAAATTAACCGAGCTCCCTTTTAAT 60.364 37.037 8.47 8.97 0.00 1.40
108 109 6.071784 GGAAAATTAACCGAGCTCCCTTTTAA 60.072 38.462 8.47 7.09 0.00 1.52
109 110 5.416639 GGAAAATTAACCGAGCTCCCTTTTA 59.583 40.000 8.47 0.00 0.00 1.52
110 111 4.219944 GGAAAATTAACCGAGCTCCCTTTT 59.780 41.667 8.47 5.38 0.00 2.27
111 112 3.762288 GGAAAATTAACCGAGCTCCCTTT 59.238 43.478 8.47 1.17 0.00 3.11
112 113 3.245122 TGGAAAATTAACCGAGCTCCCTT 60.245 43.478 8.47 1.81 0.00 3.95
113 114 2.307686 TGGAAAATTAACCGAGCTCCCT 59.692 45.455 8.47 0.00 0.00 4.20
114 115 2.718563 TGGAAAATTAACCGAGCTCCC 58.281 47.619 8.47 0.00 0.00 4.30
115 116 5.007724 CACTATGGAAAATTAACCGAGCTCC 59.992 44.000 8.47 0.00 0.00 4.70
116 117 5.585047 ACACTATGGAAAATTAACCGAGCTC 59.415 40.000 2.73 2.73 0.00 4.09
117 118 5.497474 ACACTATGGAAAATTAACCGAGCT 58.503 37.500 0.00 0.00 0.00 4.09
118 119 5.353123 TGACACTATGGAAAATTAACCGAGC 59.647 40.000 0.00 0.00 0.00 5.03
119 120 6.978343 TGACACTATGGAAAATTAACCGAG 57.022 37.500 0.00 0.00 0.00 4.63
120 121 6.149807 GGTTGACACTATGGAAAATTAACCGA 59.850 38.462 0.00 0.00 0.00 4.69
121 122 6.072397 TGGTTGACACTATGGAAAATTAACCG 60.072 38.462 0.00 0.00 37.30 4.44
122 123 7.222000 TGGTTGACACTATGGAAAATTAACC 57.778 36.000 0.00 0.00 35.59 2.85
123 124 9.783256 GTATGGTTGACACTATGGAAAATTAAC 57.217 33.333 0.00 0.00 0.00 2.01
124 125 8.670135 CGTATGGTTGACACTATGGAAAATTAA 58.330 33.333 0.00 0.00 0.00 1.40
125 126 8.041919 TCGTATGGTTGACACTATGGAAAATTA 58.958 33.333 0.00 0.00 0.00 1.40
126 127 6.882140 TCGTATGGTTGACACTATGGAAAATT 59.118 34.615 0.00 0.00 0.00 1.82
127 128 6.411376 TCGTATGGTTGACACTATGGAAAAT 58.589 36.000 0.00 0.00 0.00 1.82
128 129 5.795972 TCGTATGGTTGACACTATGGAAAA 58.204 37.500 0.00 0.00 0.00 2.29
129 130 5.408880 TCGTATGGTTGACACTATGGAAA 57.591 39.130 0.00 0.00 0.00 3.13
130 131 5.186215 TCTTCGTATGGTTGACACTATGGAA 59.814 40.000 0.00 0.00 0.00 3.53
131 132 4.707934 TCTTCGTATGGTTGACACTATGGA 59.292 41.667 0.00 0.00 0.00 3.41
132 133 5.006153 TCTTCGTATGGTTGACACTATGG 57.994 43.478 0.00 0.00 0.00 2.74
133 134 4.504461 GCTCTTCGTATGGTTGACACTATG 59.496 45.833 0.00 0.00 0.00 2.23
134 135 4.441634 GGCTCTTCGTATGGTTGACACTAT 60.442 45.833 0.00 0.00 0.00 2.12
135 136 3.119245 GGCTCTTCGTATGGTTGACACTA 60.119 47.826 0.00 0.00 0.00 2.74
136 137 2.353803 GGCTCTTCGTATGGTTGACACT 60.354 50.000 0.00 0.00 0.00 3.55
137 138 2.000447 GGCTCTTCGTATGGTTGACAC 59.000 52.381 0.00 0.00 0.00 3.67
138 139 1.621317 TGGCTCTTCGTATGGTTGACA 59.379 47.619 0.00 0.00 0.00 3.58
139 140 2.380084 TGGCTCTTCGTATGGTTGAC 57.620 50.000 0.00 0.00 0.00 3.18
140 141 2.419990 CCATGGCTCTTCGTATGGTTGA 60.420 50.000 0.00 0.00 36.25 3.18
141 142 1.942657 CCATGGCTCTTCGTATGGTTG 59.057 52.381 0.00 0.00 36.25 3.77
142 143 1.747206 GCCATGGCTCTTCGTATGGTT 60.747 52.381 29.98 0.00 41.62 3.67
143 144 0.179045 GCCATGGCTCTTCGTATGGT 60.179 55.000 29.98 0.00 41.62 3.55
144 145 1.224069 CGCCATGGCTCTTCGTATGG 61.224 60.000 33.07 10.74 42.30 2.74
145 146 1.835483 GCGCCATGGCTCTTCGTATG 61.835 60.000 33.07 15.86 39.32 2.39
146 147 1.595382 GCGCCATGGCTCTTCGTAT 60.595 57.895 33.07 0.00 39.32 3.06
147 148 2.202878 GCGCCATGGCTCTTCGTA 60.203 61.111 33.07 0.00 39.32 3.43
150 151 2.123428 ATTGGCGCCATGGCTCTTC 61.123 57.895 33.25 19.23 45.14 2.87
151 152 2.043652 ATTGGCGCCATGGCTCTT 60.044 55.556 33.25 12.69 45.14 2.85
152 153 2.831742 CATTGGCGCCATGGCTCT 60.832 61.111 33.25 8.21 45.14 4.09
153 154 3.908081 CCATTGGCGCCATGGCTC 61.908 66.667 31.50 26.32 45.14 4.70
156 157 2.123939 TACCCATTGGCGCCATGG 60.124 61.111 33.52 33.52 33.59 3.66
157 158 2.489275 GGTACCCATTGGCGCCATG 61.489 63.158 33.25 27.31 33.59 3.66
158 159 2.123897 GGTACCCATTGGCGCCAT 60.124 61.111 33.25 18.23 33.59 4.40
159 160 3.636929 CTGGTACCCATTGGCGCCA 62.637 63.158 29.03 29.03 36.67 5.69
160 161 2.828549 CTGGTACCCATTGGCGCC 60.829 66.667 22.73 22.73 30.82 6.53
161 162 2.828549 CCTGGTACCCATTGGCGC 60.829 66.667 10.07 0.00 30.82 6.53
162 163 2.828549 GCCTGGTACCCATTGGCG 60.829 66.667 10.07 0.00 35.63 5.69
163 164 1.754234 CAGCCTGGTACCCATTGGC 60.754 63.158 20.71 20.71 42.85 4.52
164 165 0.107017 CTCAGCCTGGTACCCATTGG 60.107 60.000 10.07 7.66 30.82 3.16
165 166 0.107017 CCTCAGCCTGGTACCCATTG 60.107 60.000 10.07 3.01 30.82 2.82
166 167 0.253160 TCCTCAGCCTGGTACCCATT 60.253 55.000 10.07 0.00 30.82 3.16
167 168 0.983378 GTCCTCAGCCTGGTACCCAT 60.983 60.000 10.07 0.00 30.82 4.00
168 169 1.612442 GTCCTCAGCCTGGTACCCA 60.612 63.158 10.07 0.00 0.00 4.51
169 170 0.910088 AAGTCCTCAGCCTGGTACCC 60.910 60.000 10.07 0.00 0.00 3.69
170 171 0.250513 CAAGTCCTCAGCCTGGTACC 59.749 60.000 4.43 4.43 0.00 3.34
171 172 0.250513 CCAAGTCCTCAGCCTGGTAC 59.749 60.000 0.00 0.00 0.00 3.34
172 173 0.116342 TCCAAGTCCTCAGCCTGGTA 59.884 55.000 0.00 0.00 0.00 3.25
173 174 1.152030 TCCAAGTCCTCAGCCTGGT 60.152 57.895 0.00 0.00 0.00 4.00
174 175 1.601171 CTCCAAGTCCTCAGCCTGG 59.399 63.158 0.00 0.00 0.00 4.45
175 176 0.906756 TCCTCCAAGTCCTCAGCCTG 60.907 60.000 0.00 0.00 0.00 4.85
180 181 5.208294 ACTATAACTCCTCCAAGTCCTCA 57.792 43.478 0.00 0.00 0.00 3.86
183 184 5.934402 TCAACTATAACTCCTCCAAGTCC 57.066 43.478 0.00 0.00 0.00 3.85
188 189 5.248477 ACTGCTTTCAACTATAACTCCTCCA 59.752 40.000 0.00 0.00 0.00 3.86
217 218 4.034510 GGCTGACAGACACAATTGTATAGC 59.965 45.833 11.53 5.38 35.47 2.97
225 226 1.059098 TCTGGGCTGACAGACACAAT 58.941 50.000 11.27 0.00 42.26 2.71
253 254 7.864108 TCGGTGAATTCTCATCAATAACATT 57.136 32.000 7.05 0.00 31.50 2.71
258 259 6.098266 TCTCCTTCGGTGAATTCTCATCAATA 59.902 38.462 7.05 0.00 31.50 1.90
261 262 3.769300 TCTCCTTCGGTGAATTCTCATCA 59.231 43.478 7.05 0.00 31.50 3.07
273 274 0.631753 TCTCCCAGATCTCCTTCGGT 59.368 55.000 0.00 0.00 0.00 4.69
280 281 3.902881 TTTCAGCTTCTCCCAGATCTC 57.097 47.619 0.00 0.00 0.00 2.75
329 330 4.503741 TTTTGCTTCAGATACACCTTGC 57.496 40.909 0.00 0.00 0.00 4.01
351 352 5.068636 CCTGCATCTTCAGCCTATACAATT 58.931 41.667 0.00 0.00 32.87 2.32
352 353 4.349048 TCCTGCATCTTCAGCCTATACAAT 59.651 41.667 0.00 0.00 32.87 2.71
359 360 1.633915 CCCTCCTGCATCTTCAGCCT 61.634 60.000 0.00 0.00 32.87 4.58
362 363 0.179936 GACCCCTCCTGCATCTTCAG 59.820 60.000 0.00 0.00 0.00 3.02
366 367 1.213926 GATTTGACCCCTCCTGCATCT 59.786 52.381 0.00 0.00 0.00 2.90
383 384 5.057149 GGCGTTCATATACTCCACAAGATT 58.943 41.667 0.00 0.00 0.00 2.40
412 413 2.234661 TGCTAGGTCTGTCATGACTTGG 59.765 50.000 25.55 15.49 37.16 3.61
419 420 0.898320 AAGCGTGCTAGGTCTGTCAT 59.102 50.000 0.00 0.00 0.00 3.06
444 445 4.767409 CCCTATCCTCGTCATCAACTATCA 59.233 45.833 0.00 0.00 0.00 2.15
448 449 3.314307 TCCCTATCCTCGTCATCAACT 57.686 47.619 0.00 0.00 0.00 3.16
454 455 3.181465 GCAGAATTTCCCTATCCTCGTCA 60.181 47.826 0.00 0.00 0.00 4.35
468 469 7.267128 TGACAATGAACAAAGAAGCAGAATTT 58.733 30.769 0.00 0.00 0.00 1.82
491 492 2.437651 TCAAATGGCCATAGGACGATGA 59.562 45.455 21.15 11.73 29.56 2.92
496 497 3.825328 AGTGATCAAATGGCCATAGGAC 58.175 45.455 21.15 13.61 0.00 3.85
504 505 4.651994 CGTCAAAGTAGTGATCAAATGGC 58.348 43.478 0.00 0.00 0.00 4.40
541 542 8.144478 GCAGTAGTAATATCCTCATTCTTGACA 58.856 37.037 0.00 0.00 0.00 3.58
563 564 8.742777 TCTCATTTTATAAGAAAGCAATGCAGT 58.257 29.630 8.35 0.00 0.00 4.40
565 566 9.926158 TTTCTCATTTTATAAGAAAGCAATGCA 57.074 25.926 8.35 0.00 34.87 3.96
574 575 9.436957 ACGCTCTTCTTTCTCATTTTATAAGAA 57.563 29.630 0.00 0.00 34.64 2.52
581 582 4.023707 CACCACGCTCTTCTTTCTCATTTT 60.024 41.667 0.00 0.00 0.00 1.82
583 584 3.070018 CACCACGCTCTTCTTTCTCATT 58.930 45.455 0.00 0.00 0.00 2.57
597 598 1.667724 CATGAGAGAATTCCACCACGC 59.332 52.381 0.65 0.00 0.00 5.34
650 651 3.079854 TCCCTACCTCATATCCCTTCCT 58.920 50.000 0.00 0.00 0.00 3.36
692 693 6.018262 TGCTTACACTTGTGACACTGTATTTC 60.018 38.462 7.20 1.61 0.00 2.17
694 695 5.364778 TGCTTACACTTGTGACACTGTATT 58.635 37.500 7.20 0.30 0.00 1.89
723 724 8.991783 ATCTGGACAATCATTTCTCATATGTT 57.008 30.769 1.90 0.00 0.00 2.71
778 779 1.134995 TCTGCGTCATCACCATGAGTC 60.135 52.381 0.00 0.00 39.86 3.36
794 795 4.256920 AGGACATCACTATTGTTGTCTGC 58.743 43.478 18.36 7.78 45.83 4.26
804 805 6.651643 GTCTGATACTACGAGGACATCACTAT 59.348 42.308 0.00 0.00 0.00 2.12
853 854 2.094675 CAAGCCGAATCCAACTTCCAT 58.905 47.619 0.00 0.00 0.00 3.41
858 859 0.326264 AGAGCAAGCCGAATCCAACT 59.674 50.000 0.00 0.00 0.00 3.16
880 881 2.037641 CTCTGTTGGGTGTCACATGAGA 59.962 50.000 5.12 0.00 0.00 3.27
881 882 2.037641 TCTCTGTTGGGTGTCACATGAG 59.962 50.000 5.12 0.00 0.00 2.90
920 921 4.280929 AGGCTAAATCAAACTCACCAAACC 59.719 41.667 0.00 0.00 0.00 3.27
923 924 6.150976 CACATAGGCTAAATCAAACTCACCAA 59.849 38.462 0.00 0.00 0.00 3.67
958 959 6.429692 CCTACTCCAACAACACAATAACATGA 59.570 38.462 0.00 0.00 0.00 3.07
961 962 5.529430 CACCTACTCCAACAACACAATAACA 59.471 40.000 0.00 0.00 0.00 2.41
967 968 5.755409 ATATCACCTACTCCAACAACACA 57.245 39.130 0.00 0.00 0.00 3.72
987 988 9.226606 ACTCCGTCAAACATCTTGATTTTTATA 57.773 29.630 0.00 0.00 0.00 0.98
990 991 6.391227 ACTCCGTCAAACATCTTGATTTTT 57.609 33.333 0.00 0.00 0.00 1.94
1035 1036 0.978667 TTAGCCCCGACACATGCCTA 60.979 55.000 0.00 0.00 0.00 3.93
1155 1156 2.093500 CGTCCTCCTTCCAATCATCACA 60.093 50.000 0.00 0.00 0.00 3.58
1168 1169 1.078143 GATGCAAAGCCGTCCTCCT 60.078 57.895 0.00 0.00 0.00 3.69
1226 1227 2.710902 CCGCGACTCCATGTCTCCA 61.711 63.158 8.23 0.00 43.25 3.86
1233 1234 2.491022 GCTACTCCCGCGACTCCAT 61.491 63.158 8.23 0.00 0.00 3.41
1258 1259 4.552365 CCGCCGCCACCATGAGAT 62.552 66.667 0.00 0.00 0.00 2.75
1335 1336 4.141597 TGTGTCAAACTTCCATGTACTCCA 60.142 41.667 0.00 0.00 0.00 3.86
1356 1357 6.289834 TCCAGCATCATGAATTTGTTTTTGT 58.710 32.000 0.00 0.00 0.00 2.83
1359 1360 6.349243 TCTCCAGCATCATGAATTTGTTTT 57.651 33.333 0.00 0.00 0.00 2.43
1361 1362 5.988310 TTCTCCAGCATCATGAATTTGTT 57.012 34.783 0.00 0.00 0.00 2.83
1371 1372 4.670896 TGACGAATATTCTCCAGCATCA 57.329 40.909 13.45 3.52 0.00 3.07
1373 1374 4.141620 ACCTTGACGAATATTCTCCAGCAT 60.142 41.667 13.45 1.51 0.00 3.79
1376 1377 4.122776 CCACCTTGACGAATATTCTCCAG 58.877 47.826 13.45 10.18 0.00 3.86
1407 1408 8.613482 TCGTACAAAATATTTGACACAAACTCA 58.387 29.630 9.62 0.00 0.00 3.41
1408 1409 8.996988 TCGTACAAAATATTTGACACAAACTC 57.003 30.769 9.62 0.00 0.00 3.01
1409 1410 8.617809 ACTCGTACAAAATATTTGACACAAACT 58.382 29.630 9.62 0.00 0.00 2.66
1419 1420 7.173047 ACGTAACCCAACTCGTACAAAATATTT 59.827 33.333 0.00 0.00 34.78 1.40
1432 1433 1.944709 AGTGCAAACGTAACCCAACTC 59.055 47.619 0.00 0.00 0.00 3.01
1449 1450 1.946768 CCCACACTACAACACCAAGTG 59.053 52.381 0.37 0.37 44.89 3.16
1471 1472 4.261238 CGACTCTGACAGTACATGTATCCC 60.261 50.000 9.18 0.00 44.17 3.85
1478 1479 0.818296 GCCCGACTCTGACAGTACAT 59.182 55.000 1.59 0.00 34.41 2.29
1483 1484 1.734477 CAACGCCCGACTCTGACAG 60.734 63.158 0.00 0.00 0.00 3.51
1496 1497 0.535797 AGAGGCTAAGGGTACAACGC 59.464 55.000 0.00 0.00 0.00 4.84
1537 1540 2.935505 GCCGTCATGGGTTACAACA 58.064 52.632 0.00 0.00 38.63 3.33
1554 1558 1.707632 CATGCCTGTCGCTATCTAGC 58.292 55.000 0.00 0.00 45.62 3.42
1571 1575 0.625849 CCACCTACTTCCCCTTGCAT 59.374 55.000 0.00 0.00 0.00 3.96
1572 1576 2.074967 CCACCTACTTCCCCTTGCA 58.925 57.895 0.00 0.00 0.00 4.08
1607 1612 1.823169 ATACCGCAACACCGACCACT 61.823 55.000 0.00 0.00 0.00 4.00
1612 1617 0.390603 CCAAGATACCGCAACACCGA 60.391 55.000 0.00 0.00 0.00 4.69
1629 1634 3.352748 TACGGGGGCTCCTCTCCA 61.353 66.667 0.52 0.00 0.00 3.86
2005 2011 0.750850 ACCATATTCCACCTCGGTCG 59.249 55.000 0.00 0.00 35.57 4.79
2087 2095 0.492730 TTATATACGGGGGCAGGGGA 59.507 55.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.