Multiple sequence alignment - TraesCS7B01G108600

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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 TraesCS7B01G108600 chr7B 100.000 2703 0 0 1 2703 124691102 124693804 0.000000e+00 4992
1 TraesCS7B01G108600 chr7A 90.011 1872 110 36 736 2578 163379978 163381801 0.000000e+00 2350
2 TraesCS7B01G108600 chr7A 93.714 175 11 0 1 175 120613177 120613003 2.060000e-66 263
3 TraesCS7B01G108600 chr7A 93.258 178 12 0 1 178 646092307 646092484 2.060000e-66 263
4 TraesCS7B01G108600 chr7A 93.069 101 5 2 2599 2699 163381785 163381883 2.170000e-31 147
5 TraesCS7B01G108600 chr7D 92.088 1087 55 17 855 1929 162673734 162674801 0.000000e+00 1502
6 TraesCS7B01G108600 chr7D 89.868 681 57 8 176 850 162669104 162669778 0.000000e+00 865
7 TraesCS7B01G108600 chr7D 86.107 655 57 21 1937 2578 162674838 162675471 0.000000e+00 675
8 TraesCS7B01G108600 chr7D 91.919 99 6 2 2599 2697 162675455 162675551 1.310000e-28 137
9 TraesCS7B01G108600 chr5A 94.857 175 9 0 1 175 522024842 522025016 9.530000e-70 274
10 TraesCS7B01G108600 chr5A 93.889 180 11 0 1 180 666870211 666870390 3.430000e-69 272
11 TraesCS7B01G108600 chr4B 94.828 174 9 0 1 174 74947883 74947710 3.430000e-69 272
12 TraesCS7B01G108600 chr1A 93.820 178 11 0 1 178 20098326 20098503 4.440000e-68 268
13 TraesCS7B01G108600 chr1A 92.350 183 14 0 1 183 114799300 114799118 7.420000e-66 261
14 TraesCS7B01G108600 chr6B 93.785 177 11 0 1 177 139506386 139506210 1.600000e-67 267
15 TraesCS7B01G108600 chr3A 93.750 176 11 0 1 176 431171134 431171309 5.740000e-67 265


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 TraesCS7B01G108600 chr7B 124691102 124693804 2702 False 4992.00 4992 100.0000 1 2703 1 chr7B.!!$F1 2702
1 TraesCS7B01G108600 chr7A 163379978 163381883 1905 False 1248.50 2350 91.5400 736 2699 2 chr7A.!!$F2 1963
2 TraesCS7B01G108600 chr7D 162669104 162675551 6447 False 794.75 1502 89.9955 176 2697 4 chr7D.!!$F1 2521

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
435 440 0.173708 GTCACCCGGAACTAGAGCAG 59.826 60.0 0.73 0.00 0.0 4.24 F
960 4918 0.179134 AGAACGTACGAGCAGGCATC 60.179 55.0 24.41 6.62 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 5537 0.179032 ACACGGTGAATCCTGCAACA 60.179 50.0 16.29 0.0 0.0 3.33 R
2149 6176 0.249955 TGCACGATGGAGCTGAATCA 59.750 50.0 0.00 0.0 0.0 2.57 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
17 18 3.793060 ACTGGTAGCTGCTCGGTT 58.207 55.556 4.91 0.00 0.00 4.44
18 19 2.058675 ACTGGTAGCTGCTCGGTTT 58.941 52.632 4.91 0.00 0.00 3.27
19 20 0.320771 ACTGGTAGCTGCTCGGTTTG 60.321 55.000 4.91 0.00 0.00 2.93
20 21 1.639298 CTGGTAGCTGCTCGGTTTGC 61.639 60.000 4.91 0.00 0.00 3.68
21 22 1.376037 GGTAGCTGCTCGGTTTGCT 60.376 57.895 4.91 0.00 39.30 3.91
22 23 1.639298 GGTAGCTGCTCGGTTTGCTG 61.639 60.000 4.91 0.00 37.02 4.41
23 24 1.375908 TAGCTGCTCGGTTTGCTGG 60.376 57.895 4.91 0.00 37.02 4.85
24 25 4.410743 GCTGCTCGGTTTGCTGGC 62.411 66.667 0.00 0.00 0.00 4.85
25 26 4.093952 CTGCTCGGTTTGCTGGCG 62.094 66.667 0.00 0.00 0.00 5.69
26 27 4.617520 TGCTCGGTTTGCTGGCGA 62.618 61.111 0.00 0.00 0.00 5.54
27 28 3.793144 GCTCGGTTTGCTGGCGAG 61.793 66.667 0.00 0.00 0.00 5.03
28 29 2.357517 CTCGGTTTGCTGGCGAGT 60.358 61.111 0.00 0.00 0.00 4.18
29 30 1.080093 CTCGGTTTGCTGGCGAGTA 60.080 57.895 0.00 0.00 0.00 2.59
30 31 1.078759 CTCGGTTTGCTGGCGAGTAG 61.079 60.000 0.00 0.00 0.00 2.57
31 32 2.100631 CGGTTTGCTGGCGAGTAGG 61.101 63.158 0.00 0.00 0.00 3.18
32 33 1.745489 GGTTTGCTGGCGAGTAGGG 60.745 63.158 0.00 0.00 0.00 3.53
33 34 1.745489 GTTTGCTGGCGAGTAGGGG 60.745 63.158 0.00 0.00 0.00 4.79
34 35 1.916273 TTTGCTGGCGAGTAGGGGA 60.916 57.895 0.00 0.00 0.00 4.81
35 36 1.271840 TTTGCTGGCGAGTAGGGGAT 61.272 55.000 0.00 0.00 0.00 3.85
36 37 1.271840 TTGCTGGCGAGTAGGGGATT 61.272 55.000 0.00 0.00 0.00 3.01
37 38 0.397957 TGCTGGCGAGTAGGGGATTA 60.398 55.000 0.00 0.00 0.00 1.75
38 39 0.756903 GCTGGCGAGTAGGGGATTAA 59.243 55.000 0.00 0.00 0.00 1.40
39 40 1.348036 GCTGGCGAGTAGGGGATTAAT 59.652 52.381 0.00 0.00 0.00 1.40
40 41 2.565834 GCTGGCGAGTAGGGGATTAATA 59.434 50.000 0.00 0.00 0.00 0.98
41 42 3.197983 GCTGGCGAGTAGGGGATTAATAT 59.802 47.826 0.00 0.00 0.00 1.28
42 43 4.759782 CTGGCGAGTAGGGGATTAATATG 58.240 47.826 0.00 0.00 0.00 1.78
43 44 3.055385 TGGCGAGTAGGGGATTAATATGC 60.055 47.826 0.00 0.00 0.00 3.14
44 45 3.197983 GGCGAGTAGGGGATTAATATGCT 59.802 47.826 0.00 0.00 0.00 3.79
45 46 4.404715 GGCGAGTAGGGGATTAATATGCTA 59.595 45.833 0.00 0.00 0.00 3.49
46 47 5.105064 GGCGAGTAGGGGATTAATATGCTAA 60.105 44.000 0.00 0.00 0.00 3.09
47 48 6.408206 GGCGAGTAGGGGATTAATATGCTAAT 60.408 42.308 0.00 0.00 0.00 1.73
48 49 6.702282 GCGAGTAGGGGATTAATATGCTAATC 59.298 42.308 0.00 0.27 37.50 1.75
49 50 6.918569 CGAGTAGGGGATTAATATGCTAATCG 59.081 42.308 0.00 0.00 38.61 3.34
50 51 7.125792 AGTAGGGGATTAATATGCTAATCGG 57.874 40.000 0.00 0.00 38.61 4.18
51 52 6.901300 AGTAGGGGATTAATATGCTAATCGGA 59.099 38.462 0.00 0.00 38.61 4.55
52 53 6.636454 AGGGGATTAATATGCTAATCGGAA 57.364 37.500 0.00 0.00 38.61 4.30
53 54 7.027874 AGGGGATTAATATGCTAATCGGAAA 57.972 36.000 0.00 0.00 38.61 3.13
54 55 7.112779 AGGGGATTAATATGCTAATCGGAAAG 58.887 38.462 0.00 0.00 38.61 2.62
55 56 6.884836 GGGGATTAATATGCTAATCGGAAAGT 59.115 38.462 0.00 0.00 38.61 2.66
56 57 7.393515 GGGGATTAATATGCTAATCGGAAAGTT 59.606 37.037 0.00 0.00 38.61 2.66
57 58 9.444600 GGGATTAATATGCTAATCGGAAAGTTA 57.555 33.333 0.00 0.00 38.61 2.24
62 63 5.924475 ATGCTAATCGGAAAGTTAATCGG 57.076 39.130 0.00 0.00 0.00 4.18
63 64 3.558418 TGCTAATCGGAAAGTTAATCGGC 59.442 43.478 0.00 0.00 0.00 5.54
64 65 3.059120 GCTAATCGGAAAGTTAATCGGCC 60.059 47.826 0.00 0.00 0.00 6.13
65 66 2.702592 ATCGGAAAGTTAATCGGCCA 57.297 45.000 2.24 0.00 0.00 5.36
66 67 2.702592 TCGGAAAGTTAATCGGCCAT 57.297 45.000 2.24 0.00 0.00 4.40
67 68 2.993937 TCGGAAAGTTAATCGGCCATT 58.006 42.857 2.24 4.55 0.00 3.16
68 69 3.349022 TCGGAAAGTTAATCGGCCATTT 58.651 40.909 2.24 0.00 0.00 2.32
69 70 4.515361 TCGGAAAGTTAATCGGCCATTTA 58.485 39.130 2.24 0.00 0.00 1.40
70 71 4.942483 TCGGAAAGTTAATCGGCCATTTAA 59.058 37.500 2.24 3.07 0.00 1.52
71 72 5.591067 TCGGAAAGTTAATCGGCCATTTAAT 59.409 36.000 2.24 0.00 0.00 1.40
72 73 5.912955 CGGAAAGTTAATCGGCCATTTAATC 59.087 40.000 2.24 1.28 0.00 1.75
73 74 6.459024 CGGAAAGTTAATCGGCCATTTAATCA 60.459 38.462 2.24 0.00 0.00 2.57
74 75 7.262048 GGAAAGTTAATCGGCCATTTAATCAA 58.738 34.615 2.24 0.00 0.00 2.57
75 76 7.926018 GGAAAGTTAATCGGCCATTTAATCAAT 59.074 33.333 2.24 0.00 0.00 2.57
76 77 9.313118 GAAAGTTAATCGGCCATTTAATCAATT 57.687 29.630 2.24 1.13 0.00 2.32
81 82 9.619316 TTAATCGGCCATTTAATCAATTAATCG 57.381 29.630 2.24 0.00 32.78 3.34
82 83 6.007936 TCGGCCATTTAATCAATTAATCGG 57.992 37.500 2.24 2.40 32.78 4.18
83 84 5.765677 TCGGCCATTTAATCAATTAATCGGA 59.234 36.000 2.24 0.00 32.78 4.55
84 85 5.856455 CGGCCATTTAATCAATTAATCGGAC 59.144 40.000 2.24 9.25 32.60 4.79
85 86 5.856455 GGCCATTTAATCAATTAATCGGACG 59.144 40.000 0.00 0.00 32.78 4.79
86 87 6.293735 GGCCATTTAATCAATTAATCGGACGA 60.294 38.462 0.00 0.00 32.78 4.20
87 88 7.305474 GCCATTTAATCAATTAATCGGACGAT 58.695 34.615 0.65 0.65 32.78 3.73
88 89 7.807907 GCCATTTAATCAATTAATCGGACGATT 59.192 33.333 21.60 21.60 45.58 3.34
89 90 9.677567 CCATTTAATCAATTAATCGGACGATTT 57.322 29.630 22.82 5.63 41.55 2.17
108 109 7.183116 CGATTTATCGCTTTATCGTCTACTC 57.817 40.000 0.00 0.00 43.84 2.59
109 110 6.023180 CGATTTATCGCTTTATCGTCTACTCG 60.023 42.308 0.00 0.00 43.84 4.18
110 111 3.539431 ATCGCTTTATCGTCTACTCGG 57.461 47.619 0.00 0.00 0.00 4.63
111 112 2.283298 TCGCTTTATCGTCTACTCGGT 58.717 47.619 0.00 0.00 0.00 4.69
112 113 2.031314 TCGCTTTATCGTCTACTCGGTG 59.969 50.000 0.00 0.00 0.00 4.94
113 114 2.031314 CGCTTTATCGTCTACTCGGTGA 59.969 50.000 0.00 0.00 0.00 4.02
114 115 3.361414 GCTTTATCGTCTACTCGGTGAC 58.639 50.000 0.00 0.00 0.00 3.67
115 116 3.065095 GCTTTATCGTCTACTCGGTGACT 59.935 47.826 0.00 0.00 0.00 3.41
116 117 4.785975 GCTTTATCGTCTACTCGGTGACTC 60.786 50.000 0.00 0.00 0.00 3.36
117 118 2.398252 ATCGTCTACTCGGTGACTCA 57.602 50.000 0.00 0.00 0.00 3.41
118 119 2.174363 TCGTCTACTCGGTGACTCAA 57.826 50.000 0.00 0.00 0.00 3.02
119 120 2.708051 TCGTCTACTCGGTGACTCAAT 58.292 47.619 0.00 0.00 0.00 2.57
120 121 2.418976 TCGTCTACTCGGTGACTCAATG 59.581 50.000 0.00 0.00 0.00 2.82
121 122 2.418976 CGTCTACTCGGTGACTCAATGA 59.581 50.000 0.00 0.00 0.00 2.57
122 123 3.486043 CGTCTACTCGGTGACTCAATGAG 60.486 52.174 8.98 8.98 35.52 2.90
123 124 3.440872 GTCTACTCGGTGACTCAATGAGT 59.559 47.826 16.70 16.70 46.42 3.41
124 125 4.634883 GTCTACTCGGTGACTCAATGAGTA 59.365 45.833 16.71 15.69 43.53 2.59
126 127 2.755655 ACTCGGTGACTCAATGAGTAGG 59.244 50.000 16.71 6.06 43.53 3.18
127 128 1.476891 TCGGTGACTCAATGAGTAGGC 59.523 52.381 16.71 9.03 43.53 3.93
128 129 1.204704 CGGTGACTCAATGAGTAGGCA 59.795 52.381 16.71 7.52 43.53 4.75
129 130 2.159043 CGGTGACTCAATGAGTAGGCAT 60.159 50.000 16.71 0.00 43.53 4.40
130 131 3.679917 CGGTGACTCAATGAGTAGGCATT 60.680 47.826 16.71 0.00 43.53 3.56
131 132 4.441495 CGGTGACTCAATGAGTAGGCATTA 60.441 45.833 16.71 0.00 43.53 1.90
132 133 5.428253 GGTGACTCAATGAGTAGGCATTAA 58.572 41.667 16.71 0.00 43.53 1.40
133 134 6.058183 GGTGACTCAATGAGTAGGCATTAAT 58.942 40.000 16.71 0.00 43.53 1.40
134 135 6.203723 GGTGACTCAATGAGTAGGCATTAATC 59.796 42.308 16.71 0.28 43.53 1.75
135 136 5.985530 TGACTCAATGAGTAGGCATTAATCG 59.014 40.000 16.71 0.00 43.53 3.34
136 137 5.300752 ACTCAATGAGTAGGCATTAATCGG 58.699 41.667 15.09 0.00 41.51 4.18
137 138 4.065088 TCAATGAGTAGGCATTAATCGGC 58.935 43.478 0.00 4.11 36.39 5.54
138 139 3.769739 ATGAGTAGGCATTAATCGGCA 57.230 42.857 11.87 0.00 0.00 5.69
139 140 3.552132 TGAGTAGGCATTAATCGGCAA 57.448 42.857 11.87 0.00 0.00 4.52
140 141 3.466836 TGAGTAGGCATTAATCGGCAAG 58.533 45.455 11.87 0.00 0.00 4.01
141 142 3.118408 TGAGTAGGCATTAATCGGCAAGT 60.118 43.478 11.87 0.00 0.00 3.16
142 143 3.877508 GAGTAGGCATTAATCGGCAAGTT 59.122 43.478 11.87 0.00 0.00 2.66
143 144 5.031066 AGTAGGCATTAATCGGCAAGTTA 57.969 39.130 11.87 0.00 0.00 2.24
144 145 5.433526 AGTAGGCATTAATCGGCAAGTTAA 58.566 37.500 11.87 0.00 0.00 2.01
145 146 4.632538 AGGCATTAATCGGCAAGTTAAC 57.367 40.909 0.00 0.00 0.00 2.01
146 147 4.270008 AGGCATTAATCGGCAAGTTAACT 58.730 39.130 1.12 1.12 0.00 2.24
147 148 4.096382 AGGCATTAATCGGCAAGTTAACTG 59.904 41.667 9.34 4.88 0.00 3.16
148 149 4.351192 GCATTAATCGGCAAGTTAACTGG 58.649 43.478 9.34 7.35 0.00 4.00
149 150 4.142469 GCATTAATCGGCAAGTTAACTGGT 60.142 41.667 9.34 0.00 0.00 4.00
150 151 5.621329 GCATTAATCGGCAAGTTAACTGGTT 60.621 40.000 9.34 1.66 0.00 3.67
151 152 6.403855 GCATTAATCGGCAAGTTAACTGGTTA 60.404 38.462 9.34 0.65 0.00 2.85
152 153 7.531716 CATTAATCGGCAAGTTAACTGGTTAA 58.468 34.615 9.34 9.79 33.48 2.01
153 154 7.690952 TTAATCGGCAAGTTAACTGGTTAAT 57.309 32.000 9.34 0.00 37.37 1.40
154 155 5.813080 ATCGGCAAGTTAACTGGTTAATC 57.187 39.130 9.34 0.00 37.37 1.75
155 156 3.680937 TCGGCAAGTTAACTGGTTAATCG 59.319 43.478 9.34 7.09 37.37 3.34
156 157 3.181514 CGGCAAGTTAACTGGTTAATCGG 60.182 47.826 9.34 0.00 37.37 4.18
157 158 4.004982 GGCAAGTTAACTGGTTAATCGGA 58.995 43.478 9.34 0.00 37.37 4.55
158 159 4.638865 GGCAAGTTAACTGGTTAATCGGAT 59.361 41.667 9.34 0.00 37.37 4.18
159 160 5.448632 GGCAAGTTAACTGGTTAATCGGATG 60.449 44.000 9.34 0.03 37.37 3.51
160 161 5.353123 GCAAGTTAACTGGTTAATCGGATGA 59.647 40.000 9.34 0.00 37.37 2.92
161 162 6.128117 GCAAGTTAACTGGTTAATCGGATGAA 60.128 38.462 9.34 0.00 37.37 2.57
162 163 7.415206 GCAAGTTAACTGGTTAATCGGATGAAT 60.415 37.037 9.34 0.00 37.37 2.57
163 164 8.458843 CAAGTTAACTGGTTAATCGGATGAATT 58.541 33.333 9.34 0.00 37.37 2.17
164 165 8.209917 AGTTAACTGGTTAATCGGATGAATTC 57.790 34.615 7.48 0.00 37.37 2.17
165 166 8.047310 AGTTAACTGGTTAATCGGATGAATTCT 58.953 33.333 7.48 0.00 37.37 2.40
166 167 8.674607 GTTAACTGGTTAATCGGATGAATTCTT 58.325 33.333 7.05 0.00 37.37 2.52
167 168 9.893634 TTAACTGGTTAATCGGATGAATTCTTA 57.106 29.630 7.05 0.00 30.78 2.10
168 169 8.801882 AACTGGTTAATCGGATGAATTCTTAA 57.198 30.769 7.05 0.00 0.00 1.85
169 170 8.801882 ACTGGTTAATCGGATGAATTCTTAAA 57.198 30.769 7.05 0.00 0.00 1.52
170 171 8.674607 ACTGGTTAATCGGATGAATTCTTAAAC 58.325 33.333 7.05 5.52 0.00 2.01
171 172 8.568676 TGGTTAATCGGATGAATTCTTAAACA 57.431 30.769 7.05 7.93 0.00 2.83
172 173 8.673711 TGGTTAATCGGATGAATTCTTAAACAG 58.326 33.333 7.05 0.00 0.00 3.16
173 174 8.129211 GGTTAATCGGATGAATTCTTAAACAGG 58.871 37.037 7.05 0.00 0.00 4.00
174 175 6.699575 AATCGGATGAATTCTTAAACAGGG 57.300 37.500 7.05 0.00 0.00 4.45
186 187 6.256643 TCTTAAACAGGGGTCAAAACTAGT 57.743 37.500 0.00 0.00 0.00 2.57
204 209 4.500887 ACTAGTTAAGTTCGCTCACAAGCA 60.501 41.667 0.00 0.00 41.65 3.91
267 272 2.414029 CCGAATTTGGGATGTGACAACG 60.414 50.000 3.45 0.00 0.00 4.10
323 328 6.826668 TCTGTGGAGAAGAAAACAATACAGA 58.173 36.000 0.00 0.00 39.50 3.41
325 330 5.997746 TGTGGAGAAGAAAACAATACAGAGG 59.002 40.000 0.00 0.00 0.00 3.69
326 331 5.412904 GTGGAGAAGAAAACAATACAGAGGG 59.587 44.000 0.00 0.00 0.00 4.30
327 332 5.073144 TGGAGAAGAAAACAATACAGAGGGT 59.927 40.000 0.00 0.00 0.00 4.34
328 333 6.271391 TGGAGAAGAAAACAATACAGAGGGTA 59.729 38.462 0.00 0.00 36.16 3.69
329 334 7.037586 TGGAGAAGAAAACAATACAGAGGGTAT 60.038 37.037 0.00 0.00 44.62 2.73
376 381 4.481368 AAGGAGTTGGGAAACAAAAACC 57.519 40.909 0.00 0.00 41.58 3.27
378 383 3.704566 AGGAGTTGGGAAACAAAAACCTC 59.295 43.478 0.00 0.00 41.58 3.85
379 384 3.449377 GGAGTTGGGAAACAAAAACCTCA 59.551 43.478 0.00 0.00 41.58 3.86
413 418 3.322466 CCCGAGACTGGCCAACCT 61.322 66.667 7.01 6.57 36.63 3.50
429 434 0.540365 ACCTTCGTCACCCGGAACTA 60.540 55.000 0.73 0.00 37.11 2.24
434 439 1.592400 CGTCACCCGGAACTAGAGCA 61.592 60.000 0.73 0.00 0.00 4.26
435 440 0.173708 GTCACCCGGAACTAGAGCAG 59.826 60.000 0.73 0.00 0.00 4.24
445 450 1.270907 ACTAGAGCAGGTGGACCAAG 58.729 55.000 0.00 0.00 38.89 3.61
447 452 2.114616 CTAGAGCAGGTGGACCAAGAT 58.885 52.381 0.00 0.00 38.89 2.40
464 469 4.275689 CCAAGATGTTTTGTCTACACTGCA 59.724 41.667 0.00 0.00 0.00 4.41
478 483 1.221466 ACTGCATGACAACACGGACG 61.221 55.000 0.00 0.00 0.00 4.79
506 511 6.775629 AGTTCCACACAAACCTTATTACACAT 59.224 34.615 0.00 0.00 0.00 3.21
513 518 5.346822 ACAAACCTTATTACACATCGACGAC 59.653 40.000 0.00 0.00 0.00 4.34
514 519 4.707030 ACCTTATTACACATCGACGACA 57.293 40.909 0.00 0.00 0.00 4.35
547 552 2.732016 CACCACCGAACGGAGACA 59.268 61.111 20.14 0.00 38.96 3.41
566 571 3.474600 ACATATCTCATGCCACAAGAGC 58.525 45.455 0.00 0.00 30.47 4.09
595 600 3.862600 ATGGCTCCCACCTATAGATCT 57.137 47.619 0.00 0.00 35.80 2.75
597 602 2.180086 TGGCTCCCACCTATAGATCTGT 59.820 50.000 5.18 0.16 0.00 3.41
614 619 2.694616 TGGCCTCCCACATACCCC 60.695 66.667 3.32 0.00 35.79 4.95
620 625 1.151565 TCCCACATACCCCCACCAA 60.152 57.895 0.00 0.00 0.00 3.67
625 630 0.917333 ACATACCCCCACCAACGGAT 60.917 55.000 0.00 0.00 0.00 4.18
628 633 2.767424 TACCCCCACCAACGGATCCA 62.767 60.000 13.41 0.00 0.00 3.41
632 637 2.264480 CACCAACGGATCCAGCGA 59.736 61.111 13.41 0.00 0.00 4.93
633 638 1.375396 CACCAACGGATCCAGCGAA 60.375 57.895 13.41 0.00 0.00 4.70
634 639 0.953471 CACCAACGGATCCAGCGAAA 60.953 55.000 13.41 0.00 0.00 3.46
647 652 2.184579 CGAAAGAGGACGAGGCCC 59.815 66.667 0.00 0.00 0.00 5.80
662 667 4.514577 CCCGCGGTCTACTGGCAG 62.515 72.222 26.12 14.16 0.00 4.85
674 679 0.980231 ACTGGCAGAGGAGGATGACC 60.980 60.000 23.66 0.00 0.00 4.02
675 680 2.025767 CTGGCAGAGGAGGATGACCG 62.026 65.000 9.42 0.00 41.83 4.79
688 693 0.893727 ATGACCGTGCAGGAAAACCC 60.894 55.000 8.24 0.00 45.00 4.11
696 701 3.686016 GTGCAGGAAAACCCTAGATCAA 58.314 45.455 0.00 0.00 45.60 2.57
701 706 5.181748 CAGGAAAACCCTAGATCAACTCTG 58.818 45.833 0.00 0.00 45.60 3.35
706 711 6.783708 AAACCCTAGATCAACTCTGACTAG 57.216 41.667 0.00 0.00 35.38 2.57
709 714 5.055265 CCTAGATCAACTCTGACTAGGGA 57.945 47.826 0.00 0.00 42.48 4.20
710 715 5.640147 CCTAGATCAACTCTGACTAGGGAT 58.360 45.833 0.00 0.00 42.48 3.85
711 716 5.710099 CCTAGATCAACTCTGACTAGGGATC 59.290 48.000 0.00 0.00 42.48 3.36
713 718 2.656002 TCAACTCTGACTAGGGATCCG 58.344 52.381 5.45 0.00 0.00 4.18
714 719 2.025226 TCAACTCTGACTAGGGATCCGT 60.025 50.000 12.41 12.41 0.00 4.69
715 720 2.351706 ACTCTGACTAGGGATCCGTC 57.648 55.000 10.94 10.64 0.00 4.79
729 734 2.019807 TCCGTCCCATACCCCTATTC 57.980 55.000 0.00 0.00 0.00 1.75
792 798 8.813643 ATAAAATCGTCTTAATTCTACCCTCG 57.186 34.615 0.00 0.00 0.00 4.63
940 4898 3.711704 TCACCTGCTTCCCTTCTTATAGG 59.288 47.826 0.00 0.00 34.92 2.57
945 4903 5.454045 CCTGCTTCCCTTCTTATAGGAGAAC 60.454 48.000 0.00 0.00 37.50 3.01
946 4904 4.099573 TGCTTCCCTTCTTATAGGAGAACG 59.900 45.833 0.00 0.00 37.50 3.95
947 4905 4.099727 GCTTCCCTTCTTATAGGAGAACGT 59.900 45.833 0.00 0.00 37.50 3.99
948 4906 5.301298 GCTTCCCTTCTTATAGGAGAACGTA 59.699 44.000 0.00 0.00 37.50 3.57
960 4918 0.179134 AGAACGTACGAGCAGGCATC 60.179 55.000 24.41 6.62 0.00 3.91
1289 5247 2.072298 GCAGCAAGAAGACGATCAGTT 58.928 47.619 0.00 0.00 0.00 3.16
1302 5260 2.854777 CGATCAGTTCCAAGAACGCTAG 59.145 50.000 2.04 0.00 0.00 3.42
1308 5266 0.896940 TCCAAGAACGCTAGACCCGT 60.897 55.000 0.00 0.00 41.24 5.28
1342 5312 4.947147 CCACCACCACCACCACCG 62.947 72.222 0.00 0.00 0.00 4.94
1394 5364 1.675310 CATCTGGGGAAGCACGCAA 60.675 57.895 0.00 0.00 32.65 4.85
1442 5412 2.668185 TTCCTCCGCCGCTGAAAACA 62.668 55.000 0.00 0.00 0.00 2.83
1563 5537 5.957842 TGTGGAATTCAAATACGAAAGCT 57.042 34.783 7.93 0.00 0.00 3.74
1591 5565 3.689649 AGGATTCACCGTGTAATTTGAGC 59.310 43.478 0.00 0.00 44.74 4.26
1599 5573 7.269316 TCACCGTGTAATTTGAGCATCTATTA 58.731 34.615 0.00 0.00 34.92 0.98
1600 5574 7.931407 TCACCGTGTAATTTGAGCATCTATTAT 59.069 33.333 0.00 0.00 34.92 1.28
1601 5575 9.203421 CACCGTGTAATTTGAGCATCTATTATA 57.797 33.333 0.00 0.00 34.92 0.98
1660 5642 2.278026 TGTGAGTGATCGGTCGATTG 57.722 50.000 7.32 0.00 34.60 2.67
1707 5689 8.016801 CAGATAAATTTTGTTCAATGGTTTGGC 58.983 33.333 0.00 0.00 33.44 4.52
1709 5691 3.526931 TTTTGTTCAATGGTTTGGCGA 57.473 38.095 0.00 0.00 33.44 5.54
1720 5702 4.223556 TGGTTTGGCGAGGATTTACATA 57.776 40.909 0.00 0.00 0.00 2.29
1728 5710 5.057149 GGCGAGGATTTACATATTCTGTGT 58.943 41.667 0.00 0.00 38.92 3.72
1791 5773 4.343239 AGCTGCTCTTTTGGAGTTTTTGAT 59.657 37.500 0.00 0.00 43.62 2.57
1795 5781 4.561530 GCTCTTTTGGAGTTTTTGATCCCC 60.562 45.833 0.00 0.00 43.62 4.81
1799 5785 4.469469 TTGGAGTTTTTGATCCCCTCTT 57.531 40.909 0.00 0.00 34.47 2.85
1807 5793 2.988010 TGATCCCCTCTTGTTGATCG 57.012 50.000 0.00 0.00 37.11 3.69
1934 5920 0.937231 ATTTTCAAACGGCGGCGTTG 60.937 50.000 43.67 34.56 31.96 4.10
1940 5926 0.100146 AAACGGCGGCGTTGTAAAAA 59.900 45.000 43.67 0.00 31.96 1.94
1975 5990 7.924103 CGGTTAGCAAAAGACATTTAAGTTT 57.076 32.000 0.00 0.00 0.00 2.66
2015 6034 9.503427 GTATTTTAATTATGTGCTTGTGACTCC 57.497 33.333 0.00 0.00 0.00 3.85
2096 6118 4.615588 TTGCGGGAAGAAATTCCATTTT 57.384 36.364 9.13 0.00 42.89 1.82
2101 6123 7.488322 TGCGGGAAGAAATTCCATTTTATTAG 58.512 34.615 9.13 0.00 42.89 1.73
2142 6169 3.993920 ACTTGAAAATTTCAGCGGCAAT 58.006 36.364 8.51 0.00 41.38 3.56
2143 6170 5.132897 ACTTGAAAATTTCAGCGGCAATA 57.867 34.783 8.51 0.00 41.38 1.90
2146 6173 6.650390 ACTTGAAAATTTCAGCGGCAATATTT 59.350 30.769 8.51 0.77 41.38 1.40
2147 6174 7.816995 ACTTGAAAATTTCAGCGGCAATATTTA 59.183 29.630 8.51 0.00 41.38 1.40
2148 6175 7.518731 TGAAAATTTCAGCGGCAATATTTAC 57.481 32.000 4.03 0.00 34.08 2.01
2149 6176 7.319646 TGAAAATTTCAGCGGCAATATTTACT 58.680 30.769 4.03 0.00 34.08 2.24
2154 6192 5.673337 TCAGCGGCAATATTTACTGATTC 57.327 39.130 1.45 0.00 0.00 2.52
2161 6199 5.532406 GGCAATATTTACTGATTCAGCTCCA 59.468 40.000 13.64 0.00 34.37 3.86
2229 6267 3.733337 TCTTTTGCTGGAAGTCTGAGAC 58.267 45.455 3.98 3.98 35.30 3.36
2314 6356 1.441729 GATGCGACGGAGATGGGAA 59.558 57.895 0.00 0.00 0.00 3.97
2360 6402 2.097825 GAAGGTGGCATTGAATGAGCT 58.902 47.619 9.76 0.95 0.00 4.09
2397 6439 1.712018 CTCAGGTGTCCGTATCGCGA 61.712 60.000 13.09 13.09 44.77 5.87
2423 6465 2.786512 ATTTGGGAGCCATGCACGGT 62.787 55.000 0.00 0.00 31.53 4.83
2440 6482 3.066190 TTCGGCCGGTCGATCTGT 61.066 61.111 34.25 0.00 39.03 3.41
2442 6484 4.570663 CGGCCGGTCGATCTGTCC 62.571 72.222 27.65 0.00 0.00 4.02
2451 6493 0.614697 TCGATCTGTCCCAGCCTTCA 60.615 55.000 0.00 0.00 0.00 3.02
2519 6561 1.726865 CAACGTTCCAGCAAGCACA 59.273 52.632 0.00 0.00 0.00 4.57
2520 6562 0.592247 CAACGTTCCAGCAAGCACAC 60.592 55.000 0.00 0.00 0.00 3.82
2530 6572 2.281761 AAGCACACGGGCCAGAAG 60.282 61.111 10.86 4.09 0.00 2.85
2543 6585 1.429463 CCAGAAGTGCCGTGAACTAC 58.571 55.000 0.00 0.00 0.00 2.73
2560 6604 2.227388 ACTACGTAAGGGAAGTCGTGTG 59.773 50.000 0.00 0.00 46.39 3.82
2561 6605 1.321474 ACGTAAGGGAAGTCGTGTGA 58.679 50.000 0.00 0.00 46.39 3.58
2562 6606 1.891150 ACGTAAGGGAAGTCGTGTGAT 59.109 47.619 0.00 0.00 46.39 3.06
2563 6607 2.298163 ACGTAAGGGAAGTCGTGTGATT 59.702 45.455 0.00 0.00 46.39 2.57
2564 6608 3.243975 ACGTAAGGGAAGTCGTGTGATTT 60.244 43.478 0.00 0.00 46.39 2.17
2565 6609 3.744426 CGTAAGGGAAGTCGTGTGATTTT 59.256 43.478 0.00 0.00 0.00 1.82
2566 6610 4.377022 CGTAAGGGAAGTCGTGTGATTTTG 60.377 45.833 0.00 0.00 0.00 2.44
2567 6611 2.504367 AGGGAAGTCGTGTGATTTTGG 58.496 47.619 0.00 0.00 0.00 3.28
2568 6612 1.068541 GGGAAGTCGTGTGATTTTGGC 60.069 52.381 0.00 0.00 0.00 4.52
2569 6613 1.606668 GGAAGTCGTGTGATTTTGGCA 59.393 47.619 0.00 0.00 0.00 4.92
2570 6614 2.228822 GGAAGTCGTGTGATTTTGGCAT 59.771 45.455 0.00 0.00 0.00 4.40
2571 6615 3.492313 GAAGTCGTGTGATTTTGGCATC 58.508 45.455 0.00 0.00 0.00 3.91
2572 6616 1.812571 AGTCGTGTGATTTTGGCATCC 59.187 47.619 0.00 0.00 0.00 3.51
2573 6617 0.801872 TCGTGTGATTTTGGCATCCG 59.198 50.000 0.00 0.00 0.00 4.18
2574 6618 0.801872 CGTGTGATTTTGGCATCCGA 59.198 50.000 0.00 0.00 0.00 4.55
2575 6619 1.401552 CGTGTGATTTTGGCATCCGAT 59.598 47.619 0.00 0.00 0.00 4.18
2576 6620 2.159393 CGTGTGATTTTGGCATCCGATT 60.159 45.455 0.00 0.00 0.00 3.34
2577 6621 3.673052 CGTGTGATTTTGGCATCCGATTT 60.673 43.478 0.00 0.00 0.00 2.17
2578 6622 4.244862 GTGTGATTTTGGCATCCGATTTT 58.755 39.130 0.00 0.00 0.00 1.82
2579 6623 4.690280 GTGTGATTTTGGCATCCGATTTTT 59.310 37.500 0.00 0.00 0.00 1.94
2686 6730 6.369890 AGCCTTAGTAAAACTAAAGGTTACGC 59.630 38.462 12.65 0.00 39.89 4.42
2699 6743 4.720530 AGGTTACGCTAAACTGTTTTCG 57.279 40.909 11.48 16.23 33.67 3.46
2700 6744 4.370917 AGGTTACGCTAAACTGTTTTCGA 58.629 39.130 24.10 11.83 33.67 3.71
2701 6745 4.209911 AGGTTACGCTAAACTGTTTTCGAC 59.790 41.667 24.10 16.28 33.67 4.20
2702 6746 4.025813 GGTTACGCTAAACTGTTTTCGACA 60.026 41.667 24.10 13.86 36.65 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.320771 CAAACCGAGCAGCTACCAGT 60.321 55.000 0.00 0.00 0.00 4.00
1 2 1.639298 GCAAACCGAGCAGCTACCAG 61.639 60.000 0.00 0.00 0.00 4.00
2 3 1.671054 GCAAACCGAGCAGCTACCA 60.671 57.895 0.00 0.00 0.00 3.25
3 4 1.376037 AGCAAACCGAGCAGCTACC 60.376 57.895 0.00 0.00 35.19 3.18
4 5 1.639298 CCAGCAAACCGAGCAGCTAC 61.639 60.000 0.00 0.00 35.19 3.58
5 6 1.375908 CCAGCAAACCGAGCAGCTA 60.376 57.895 0.00 0.00 35.19 3.32
6 7 2.670934 CCAGCAAACCGAGCAGCT 60.671 61.111 0.00 0.00 37.95 4.24
7 8 4.410743 GCCAGCAAACCGAGCAGC 62.411 66.667 0.00 0.00 0.00 5.25
8 9 4.093952 CGCCAGCAAACCGAGCAG 62.094 66.667 0.00 0.00 0.00 4.24
9 10 4.617520 TCGCCAGCAAACCGAGCA 62.618 61.111 0.00 0.00 0.00 4.26
10 11 3.793144 CTCGCCAGCAAACCGAGC 61.793 66.667 0.00 0.00 41.41 5.03
12 13 1.080093 CTACTCGCCAGCAAACCGA 60.080 57.895 0.00 0.00 0.00 4.69
13 14 2.100631 CCTACTCGCCAGCAAACCG 61.101 63.158 0.00 0.00 0.00 4.44
14 15 1.745489 CCCTACTCGCCAGCAAACC 60.745 63.158 0.00 0.00 0.00 3.27
15 16 1.745489 CCCCTACTCGCCAGCAAAC 60.745 63.158 0.00 0.00 0.00 2.93
16 17 1.271840 ATCCCCTACTCGCCAGCAAA 61.272 55.000 0.00 0.00 0.00 3.68
17 18 1.271840 AATCCCCTACTCGCCAGCAA 61.272 55.000 0.00 0.00 0.00 3.91
18 19 0.397957 TAATCCCCTACTCGCCAGCA 60.398 55.000 0.00 0.00 0.00 4.41
19 20 0.756903 TTAATCCCCTACTCGCCAGC 59.243 55.000 0.00 0.00 0.00 4.85
20 21 4.759782 CATATTAATCCCCTACTCGCCAG 58.240 47.826 0.00 0.00 0.00 4.85
21 22 3.055385 GCATATTAATCCCCTACTCGCCA 60.055 47.826 0.00 0.00 0.00 5.69
22 23 3.197983 AGCATATTAATCCCCTACTCGCC 59.802 47.826 0.00 0.00 0.00 5.54
23 24 4.473477 AGCATATTAATCCCCTACTCGC 57.527 45.455 0.00 0.00 0.00 5.03
24 25 6.918569 CGATTAGCATATTAATCCCCTACTCG 59.081 42.308 0.00 3.50 36.93 4.18
25 26 7.069578 TCCGATTAGCATATTAATCCCCTACTC 59.930 40.741 0.00 0.00 36.93 2.59
26 27 6.901300 TCCGATTAGCATATTAATCCCCTACT 59.099 38.462 0.00 0.00 36.93 2.57
27 28 7.120923 TCCGATTAGCATATTAATCCCCTAC 57.879 40.000 0.00 0.00 36.93 3.18
28 29 7.743116 TTCCGATTAGCATATTAATCCCCTA 57.257 36.000 0.00 0.00 36.93 3.53
29 30 6.636454 TTCCGATTAGCATATTAATCCCCT 57.364 37.500 0.00 0.00 36.93 4.79
30 31 6.884836 ACTTTCCGATTAGCATATTAATCCCC 59.115 38.462 0.00 0.00 36.93 4.81
31 32 7.923414 ACTTTCCGATTAGCATATTAATCCC 57.077 36.000 0.00 0.00 36.93 3.85
36 37 9.146984 CCGATTAACTTTCCGATTAGCATATTA 57.853 33.333 0.00 0.00 0.00 0.98
37 38 7.360946 GCCGATTAACTTTCCGATTAGCATATT 60.361 37.037 0.00 0.00 0.00 1.28
38 39 6.092259 GCCGATTAACTTTCCGATTAGCATAT 59.908 38.462 0.00 0.00 0.00 1.78
39 40 5.407387 GCCGATTAACTTTCCGATTAGCATA 59.593 40.000 0.00 0.00 0.00 3.14
40 41 4.213482 GCCGATTAACTTTCCGATTAGCAT 59.787 41.667 0.00 0.00 0.00 3.79
41 42 3.558418 GCCGATTAACTTTCCGATTAGCA 59.442 43.478 0.00 0.00 0.00 3.49
42 43 3.059120 GGCCGATTAACTTTCCGATTAGC 60.059 47.826 0.00 0.00 0.00 3.09
43 44 4.124238 TGGCCGATTAACTTTCCGATTAG 58.876 43.478 0.00 0.00 0.00 1.73
44 45 4.139859 TGGCCGATTAACTTTCCGATTA 57.860 40.909 0.00 0.00 0.00 1.75
45 46 2.993937 TGGCCGATTAACTTTCCGATT 58.006 42.857 0.00 0.00 0.00 3.34
46 47 2.702592 TGGCCGATTAACTTTCCGAT 57.297 45.000 0.00 0.00 0.00 4.18
47 48 2.702592 ATGGCCGATTAACTTTCCGA 57.297 45.000 0.00 0.00 0.00 4.55
48 49 3.775661 AAATGGCCGATTAACTTTCCG 57.224 42.857 0.00 0.00 0.00 4.30
49 50 6.801575 TGATTAAATGGCCGATTAACTTTCC 58.198 36.000 13.26 4.25 0.00 3.13
50 51 8.871686 ATTGATTAAATGGCCGATTAACTTTC 57.128 30.769 13.26 9.07 0.00 2.62
55 56 9.619316 CGATTAATTGATTAAATGGCCGATTAA 57.381 29.630 13.33 13.33 36.02 1.40
56 57 8.240682 CCGATTAATTGATTAAATGGCCGATTA 58.759 33.333 4.10 0.00 36.02 1.75
57 58 7.040062 TCCGATTAATTGATTAAATGGCCGATT 60.040 33.333 4.10 0.00 36.02 3.34
58 59 6.432783 TCCGATTAATTGATTAAATGGCCGAT 59.567 34.615 4.10 0.00 36.02 4.18
59 60 5.765677 TCCGATTAATTGATTAAATGGCCGA 59.234 36.000 4.10 0.00 36.02 5.54
60 61 5.856455 GTCCGATTAATTGATTAAATGGCCG 59.144 40.000 4.10 0.00 36.02 6.13
61 62 5.856455 CGTCCGATTAATTGATTAAATGGCC 59.144 40.000 4.10 0.00 36.02 5.36
62 63 6.664515 TCGTCCGATTAATTGATTAAATGGC 58.335 36.000 4.10 2.85 36.02 4.40
63 64 9.677567 AAATCGTCCGATTAATTGATTAAATGG 57.322 29.630 14.61 5.88 43.26 3.16
84 85 6.023180 CGAGTAGACGATAAAGCGATAAATCG 60.023 42.308 13.89 13.89 45.06 3.34
85 86 6.248839 CCGAGTAGACGATAAAGCGATAAATC 59.751 42.308 0.00 0.00 35.09 2.17
86 87 6.084925 CCGAGTAGACGATAAAGCGATAAAT 58.915 40.000 0.00 0.00 35.09 1.40
87 88 5.008019 ACCGAGTAGACGATAAAGCGATAAA 59.992 40.000 0.00 0.00 35.09 1.40
88 89 4.512944 ACCGAGTAGACGATAAAGCGATAA 59.487 41.667 0.00 0.00 35.09 1.75
89 90 4.060900 ACCGAGTAGACGATAAAGCGATA 58.939 43.478 0.00 0.00 35.09 2.92
90 91 2.877168 ACCGAGTAGACGATAAAGCGAT 59.123 45.455 0.00 0.00 35.09 4.58
91 92 2.031314 CACCGAGTAGACGATAAAGCGA 59.969 50.000 0.00 0.00 35.09 4.93
92 93 2.031314 TCACCGAGTAGACGATAAAGCG 59.969 50.000 0.00 0.00 35.09 4.68
93 94 3.065095 AGTCACCGAGTAGACGATAAAGC 59.935 47.826 0.00 0.00 39.67 3.51
94 95 4.331992 TGAGTCACCGAGTAGACGATAAAG 59.668 45.833 0.00 0.00 39.67 1.85
95 96 4.256110 TGAGTCACCGAGTAGACGATAAA 58.744 43.478 0.00 0.00 39.67 1.40
96 97 3.865446 TGAGTCACCGAGTAGACGATAA 58.135 45.455 0.00 0.00 39.67 1.75
97 98 3.531934 TGAGTCACCGAGTAGACGATA 57.468 47.619 0.00 0.00 39.67 2.92
98 99 2.398252 TGAGTCACCGAGTAGACGAT 57.602 50.000 0.00 0.00 39.67 3.73
99 100 2.174363 TTGAGTCACCGAGTAGACGA 57.826 50.000 0.00 0.00 39.67 4.20
100 101 2.418976 TCATTGAGTCACCGAGTAGACG 59.581 50.000 0.00 0.00 39.67 4.18
101 102 3.440872 ACTCATTGAGTCACCGAGTAGAC 59.559 47.826 17.96 0.00 38.71 2.59
102 103 3.687125 ACTCATTGAGTCACCGAGTAGA 58.313 45.455 17.96 0.00 38.71 2.59
103 104 5.163302 CTACTCATTGAGTCACCGAGTAG 57.837 47.826 27.68 27.68 45.63 2.57
104 105 3.945921 CCTACTCATTGAGTCACCGAGTA 59.054 47.826 22.16 21.36 42.40 2.59
105 106 2.755655 CCTACTCATTGAGTCACCGAGT 59.244 50.000 22.16 21.40 42.40 4.18
106 107 2.480416 GCCTACTCATTGAGTCACCGAG 60.480 54.545 22.16 13.42 42.40 4.63
107 108 1.476891 GCCTACTCATTGAGTCACCGA 59.523 52.381 22.16 4.43 42.40 4.69
108 109 1.204704 TGCCTACTCATTGAGTCACCG 59.795 52.381 22.16 9.64 42.40 4.94
109 110 3.550437 ATGCCTACTCATTGAGTCACC 57.450 47.619 22.16 11.88 42.40 4.02
110 111 6.074088 CGATTAATGCCTACTCATTGAGTCAC 60.074 42.308 22.16 13.24 42.40 3.67
111 112 5.985530 CGATTAATGCCTACTCATTGAGTCA 59.014 40.000 22.16 14.64 42.40 3.41
112 113 5.406780 CCGATTAATGCCTACTCATTGAGTC 59.593 44.000 22.16 9.50 42.40 3.36
113 114 5.300752 CCGATTAATGCCTACTCATTGAGT 58.699 41.667 22.16 22.16 45.54 3.41
114 115 4.153117 GCCGATTAATGCCTACTCATTGAG 59.847 45.833 12.17 12.17 37.27 3.02
115 116 4.065088 GCCGATTAATGCCTACTCATTGA 58.935 43.478 0.00 0.00 37.27 2.57
116 117 3.814842 TGCCGATTAATGCCTACTCATTG 59.185 43.478 0.00 0.00 37.27 2.82
117 118 4.085357 TGCCGATTAATGCCTACTCATT 57.915 40.909 0.00 0.00 39.70 2.57
118 119 3.769739 TGCCGATTAATGCCTACTCAT 57.230 42.857 0.00 0.00 0.00 2.90
119 120 3.118408 ACTTGCCGATTAATGCCTACTCA 60.118 43.478 0.00 0.00 0.00 3.41
120 121 3.467803 ACTTGCCGATTAATGCCTACTC 58.532 45.455 0.00 0.00 0.00 2.59
121 122 3.560636 ACTTGCCGATTAATGCCTACT 57.439 42.857 0.00 0.00 0.00 2.57
122 123 5.296035 AGTTAACTTGCCGATTAATGCCTAC 59.704 40.000 1.12 0.00 0.00 3.18
123 124 5.295787 CAGTTAACTTGCCGATTAATGCCTA 59.704 40.000 5.07 0.00 0.00 3.93
124 125 4.096382 CAGTTAACTTGCCGATTAATGCCT 59.904 41.667 5.07 0.00 0.00 4.75
125 126 4.351192 CAGTTAACTTGCCGATTAATGCC 58.649 43.478 5.07 0.00 0.00 4.40
126 127 4.142469 ACCAGTTAACTTGCCGATTAATGC 60.142 41.667 5.07 0.00 0.00 3.56
127 128 5.560966 ACCAGTTAACTTGCCGATTAATG 57.439 39.130 5.07 0.00 0.00 1.90
128 129 7.690952 TTAACCAGTTAACTTGCCGATTAAT 57.309 32.000 5.07 0.00 30.78 1.40
129 130 7.413219 CGATTAACCAGTTAACTTGCCGATTAA 60.413 37.037 5.07 4.36 37.80 1.40
130 131 6.036300 CGATTAACCAGTTAACTTGCCGATTA 59.964 38.462 5.07 0.00 37.80 1.75
131 132 5.163794 CGATTAACCAGTTAACTTGCCGATT 60.164 40.000 5.07 0.00 37.80 3.34
132 133 4.331717 CGATTAACCAGTTAACTTGCCGAT 59.668 41.667 5.07 0.00 37.80 4.18
133 134 3.680937 CGATTAACCAGTTAACTTGCCGA 59.319 43.478 5.07 0.00 37.80 5.54
134 135 3.181514 CCGATTAACCAGTTAACTTGCCG 60.182 47.826 5.07 3.31 37.80 5.69
135 136 4.004982 TCCGATTAACCAGTTAACTTGCC 58.995 43.478 5.07 0.00 37.80 4.52
136 137 5.353123 TCATCCGATTAACCAGTTAACTTGC 59.647 40.000 5.07 0.00 37.80 4.01
137 138 6.978343 TCATCCGATTAACCAGTTAACTTG 57.022 37.500 5.07 5.14 37.80 3.16
138 139 8.575649 AATTCATCCGATTAACCAGTTAACTT 57.424 30.769 5.07 0.00 37.80 2.66
139 140 8.047310 AGAATTCATCCGATTAACCAGTTAACT 58.953 33.333 8.44 1.12 37.80 2.24
140 141 8.209917 AGAATTCATCCGATTAACCAGTTAAC 57.790 34.615 8.44 0.00 37.80 2.01
141 142 8.801882 AAGAATTCATCCGATTAACCAGTTAA 57.198 30.769 8.44 5.51 39.12 2.01
142 143 9.893634 TTAAGAATTCATCCGATTAACCAGTTA 57.106 29.630 8.44 0.00 0.00 2.24
143 144 8.801882 TTAAGAATTCATCCGATTAACCAGTT 57.198 30.769 8.44 0.00 0.00 3.16
144 145 8.674607 GTTTAAGAATTCATCCGATTAACCAGT 58.325 33.333 8.44 0.00 0.00 4.00
145 146 8.673711 TGTTTAAGAATTCATCCGATTAACCAG 58.326 33.333 8.44 0.00 0.00 4.00
146 147 8.568676 TGTTTAAGAATTCATCCGATTAACCA 57.431 30.769 8.44 0.00 0.00 3.67
147 148 8.129211 CCTGTTTAAGAATTCATCCGATTAACC 58.871 37.037 8.44 0.00 0.00 2.85
148 149 8.129211 CCCTGTTTAAGAATTCATCCGATTAAC 58.871 37.037 8.44 1.69 0.00 2.01
149 150 7.284489 CCCCTGTTTAAGAATTCATCCGATTAA 59.716 37.037 8.44 0.02 0.00 1.40
150 151 6.770785 CCCCTGTTTAAGAATTCATCCGATTA 59.229 38.462 8.44 0.00 0.00 1.75
151 152 5.594317 CCCCTGTTTAAGAATTCATCCGATT 59.406 40.000 8.44 0.00 0.00 3.34
152 153 5.133221 CCCCTGTTTAAGAATTCATCCGAT 58.867 41.667 8.44 0.00 0.00 4.18
153 154 4.018779 ACCCCTGTTTAAGAATTCATCCGA 60.019 41.667 8.44 0.00 0.00 4.55
154 155 4.270008 ACCCCTGTTTAAGAATTCATCCG 58.730 43.478 8.44 0.00 0.00 4.18
155 156 5.261216 TGACCCCTGTTTAAGAATTCATCC 58.739 41.667 8.44 0.00 0.00 3.51
156 157 6.834168 TTGACCCCTGTTTAAGAATTCATC 57.166 37.500 8.44 0.00 0.00 2.92
157 158 7.290014 AGTTTTGACCCCTGTTTAAGAATTCAT 59.710 33.333 8.44 0.00 0.00 2.57
158 159 6.609616 AGTTTTGACCCCTGTTTAAGAATTCA 59.390 34.615 8.44 0.00 0.00 2.57
159 160 7.050970 AGTTTTGACCCCTGTTTAAGAATTC 57.949 36.000 0.00 0.00 0.00 2.17
160 161 7.783119 ACTAGTTTTGACCCCTGTTTAAGAATT 59.217 33.333 0.00 0.00 0.00 2.17
161 162 7.295340 ACTAGTTTTGACCCCTGTTTAAGAAT 58.705 34.615 0.00 0.00 0.00 2.40
162 163 6.665695 ACTAGTTTTGACCCCTGTTTAAGAA 58.334 36.000 0.00 0.00 0.00 2.52
163 164 6.256643 ACTAGTTTTGACCCCTGTTTAAGA 57.743 37.500 0.00 0.00 0.00 2.10
164 165 6.954487 AACTAGTTTTGACCCCTGTTTAAG 57.046 37.500 1.12 0.00 0.00 1.85
165 166 8.054572 ACTTAACTAGTTTTGACCCCTGTTTAA 58.945 33.333 14.49 0.00 31.29 1.52
166 167 7.576403 ACTTAACTAGTTTTGACCCCTGTTTA 58.424 34.615 14.49 0.00 31.29 2.01
167 168 6.429151 ACTTAACTAGTTTTGACCCCTGTTT 58.571 36.000 14.49 0.00 31.29 2.83
168 169 6.009908 ACTTAACTAGTTTTGACCCCTGTT 57.990 37.500 14.49 0.00 31.29 3.16
169 170 5.641789 ACTTAACTAGTTTTGACCCCTGT 57.358 39.130 14.49 0.00 31.29 4.00
170 171 5.178809 CGAACTTAACTAGTTTTGACCCCTG 59.821 44.000 14.49 0.00 47.00 4.45
171 172 5.303165 CGAACTTAACTAGTTTTGACCCCT 58.697 41.667 14.49 0.00 47.00 4.79
172 173 4.083643 GCGAACTTAACTAGTTTTGACCCC 60.084 45.833 14.49 0.00 47.00 4.95
173 174 4.753610 AGCGAACTTAACTAGTTTTGACCC 59.246 41.667 14.49 0.00 47.00 4.46
174 175 5.464389 TGAGCGAACTTAACTAGTTTTGACC 59.536 40.000 14.49 0.61 47.00 4.02
225 230 6.391537 TCGGAATGTTTAAAACAATTAGGGC 58.608 36.000 0.00 0.00 45.86 5.19
234 239 7.386573 ACATCCCAAATTCGGAATGTTTAAAAC 59.613 33.333 3.59 0.00 31.75 2.43
244 249 3.147553 TGTCACATCCCAAATTCGGAA 57.852 42.857 0.00 0.00 31.75 4.30
277 282 7.065563 ACAGAGACAATTTGCTATGAAGATCAC 59.934 37.037 16.75 0.00 0.00 3.06
318 323 5.186409 GTGGTGTTCTACAATACCCTCTGTA 59.814 44.000 0.00 0.00 41.96 2.74
319 324 4.020485 GTGGTGTTCTACAATACCCTCTGT 60.020 45.833 0.00 0.00 41.96 3.41
320 325 4.020573 TGTGGTGTTCTACAATACCCTCTG 60.021 45.833 0.00 0.00 41.96 3.35
323 328 4.986054 TTGTGGTGTTCTACAATACCCT 57.014 40.909 0.00 0.00 41.96 4.34
329 334 3.568007 GCTGGAATTGTGGTGTTCTACAA 59.432 43.478 0.00 0.00 45.99 2.41
376 381 1.932604 GCTTGTCGGAGAGTGTGTGAG 60.933 57.143 0.00 0.00 36.95 3.51
378 383 0.946221 GGCTTGTCGGAGAGTGTGTG 60.946 60.000 0.00 0.00 36.95 3.82
379 384 1.367840 GGCTTGTCGGAGAGTGTGT 59.632 57.895 0.00 0.00 36.95 3.72
429 434 0.617413 CATCTTGGTCCACCTGCTCT 59.383 55.000 0.00 0.00 36.82 4.09
434 439 3.117512 AGACAAAACATCTTGGTCCACCT 60.118 43.478 0.00 0.00 36.82 4.00
435 440 3.222603 AGACAAAACATCTTGGTCCACC 58.777 45.455 0.00 0.00 0.00 4.61
445 450 5.049474 TGTCATGCAGTGTAGACAAAACATC 60.049 40.000 10.59 0.00 37.99 3.06
447 452 4.195416 TGTCATGCAGTGTAGACAAAACA 58.805 39.130 10.59 0.00 37.99 2.83
464 469 0.959553 ACTCTCGTCCGTGTTGTCAT 59.040 50.000 0.00 0.00 0.00 3.06
478 483 6.708949 TGTAATAAGGTTTGTGTGGAACTCTC 59.291 38.462 0.00 0.00 38.04 3.20
506 511 4.544762 CGATGGTGTTGTCGTCGA 57.455 55.556 0.00 0.00 43.83 4.20
542 547 8.846033 TGCTCTTGTGGCATGAGATATGTCTC 62.846 46.154 12.27 12.27 41.68 3.36
547 552 3.390311 TCTGCTCTTGTGGCATGAGATAT 59.610 43.478 15.78 0.00 37.70 1.63
559 564 4.400567 GGAGCCATAATTTTCTGCTCTTGT 59.599 41.667 14.53 0.00 45.88 3.16
566 571 3.635591 AGGTGGGAGCCATAATTTTCTG 58.364 45.455 0.00 0.00 35.28 3.02
597 602 2.694616 GGGGTATGTGGGAGGCCA 60.695 66.667 5.01 0.00 0.00 5.36
609 614 1.996748 GGATCCGTTGGTGGGGGTA 60.997 63.158 0.00 0.00 0.00 3.69
614 619 2.796483 TTCGCTGGATCCGTTGGTGG 62.796 60.000 7.39 0.00 0.00 4.61
620 625 0.970937 TCCTCTTTCGCTGGATCCGT 60.971 55.000 7.39 0.00 0.00 4.69
625 630 1.595993 CCTCGTCCTCTTTCGCTGGA 61.596 60.000 0.00 0.00 0.00 3.86
628 633 2.574399 GCCTCGTCCTCTTTCGCT 59.426 61.111 0.00 0.00 0.00 4.93
632 637 4.083862 GCGGGCCTCGTCCTCTTT 62.084 66.667 13.97 0.00 41.72 2.52
647 652 2.103143 CTCTGCCAGTAGACCGCG 59.897 66.667 0.00 0.00 0.00 6.46
661 666 1.305297 TGCACGGTCATCCTCCTCT 60.305 57.895 0.00 0.00 0.00 3.69
662 667 1.142748 CTGCACGGTCATCCTCCTC 59.857 63.158 0.00 0.00 0.00 3.71
688 693 5.710099 GGATCCCTAGTCAGAGTTGATCTAG 59.290 48.000 0.00 0.00 36.10 2.43
696 701 1.133730 GGACGGATCCCTAGTCAGAGT 60.134 57.143 17.00 2.26 39.39 3.24
709 714 2.158066 TGAATAGGGGTATGGGACGGAT 60.158 50.000 0.00 0.00 0.00 4.18
710 715 1.221007 TGAATAGGGGTATGGGACGGA 59.779 52.381 0.00 0.00 0.00 4.69
711 716 1.724545 TGAATAGGGGTATGGGACGG 58.275 55.000 0.00 0.00 0.00 4.79
713 718 7.523415 TCTTAAAATGAATAGGGGTATGGGAC 58.477 38.462 0.00 0.00 0.00 4.46
714 719 7.715267 TCTTAAAATGAATAGGGGTATGGGA 57.285 36.000 0.00 0.00 0.00 4.37
715 720 8.956446 ATTCTTAAAATGAATAGGGGTATGGG 57.044 34.615 0.00 0.00 32.98 4.00
792 798 5.699458 TGGAGATTTAAGACGACTTTTGGTC 59.301 40.000 5.28 0.54 41.28 4.02
940 4898 0.179134 ATGCCTGCTCGTACGTTCTC 60.179 55.000 16.05 3.74 0.00 2.87
945 4903 2.055310 TACCGATGCCTGCTCGTACG 62.055 60.000 9.53 9.53 34.36 3.67
946 4904 0.594284 GTACCGATGCCTGCTCGTAC 60.594 60.000 9.11 8.09 34.36 3.67
947 4905 1.731433 GGTACCGATGCCTGCTCGTA 61.731 60.000 0.00 2.18 34.36 3.43
948 4906 2.494918 GTACCGATGCCTGCTCGT 59.505 61.111 9.11 2.84 34.36 4.18
1129 5087 2.733593 ACCTCGAACGCGTCAAGC 60.734 61.111 14.44 1.29 43.95 4.01
1289 5247 0.896940 ACGGGTCTAGCGTTCTTGGA 60.897 55.000 0.00 0.00 0.00 3.53
1325 5283 4.947147 CGGTGGTGGTGGTGGTGG 62.947 72.222 0.00 0.00 0.00 4.61
1326 5284 4.947147 CCGGTGGTGGTGGTGGTG 62.947 72.222 0.00 0.00 0.00 4.17
1342 5312 2.124942 CCCGAGAGCTTCTTGGCC 60.125 66.667 11.90 0.00 45.03 5.36
1372 5342 0.537188 CGTGCTTCCCCAGATGTAGT 59.463 55.000 0.00 0.00 0.00 2.73
1434 5404 3.267974 GCCTCCGGCTGTTTTCAG 58.732 61.111 0.00 0.00 46.69 3.02
1563 5537 0.179032 ACACGGTGAATCCTGCAACA 60.179 50.000 16.29 0.00 0.00 3.33
1660 5642 5.629020 TCTGAAATTTATTTGCACTGTTCGC 59.371 36.000 0.00 0.00 0.00 4.70
1707 5689 6.907212 GCAAACACAGAATATGTAAATCCTCG 59.093 38.462 0.00 0.00 41.41 4.63
1709 5691 7.944729 AGCAAACACAGAATATGTAAATCCT 57.055 32.000 0.00 0.00 41.41 3.24
1720 5702 5.642919 TCAAAAGCAAAAGCAAACACAGAAT 59.357 32.000 0.00 0.00 0.00 2.40
1728 5710 5.879223 TCCAATCTTCAAAAGCAAAAGCAAA 59.121 32.000 0.00 0.00 0.00 3.68
1752 5734 2.893895 CTGCCTCGCATCGCACAT 60.894 61.111 0.00 0.00 38.13 3.21
1791 5773 0.909610 AGCCGATCAACAAGAGGGGA 60.910 55.000 0.00 0.00 0.00 4.81
1795 5781 3.181526 CGAGAAAAGCCGATCAACAAGAG 60.182 47.826 0.00 0.00 0.00 2.85
1799 5785 2.163818 ACGAGAAAAGCCGATCAACA 57.836 45.000 0.00 0.00 0.00 3.33
1807 5793 0.912528 CGCGTACTACGAGAAAAGCC 59.087 55.000 12.87 0.00 46.05 4.35
1948 5963 1.803334 ATGTCTTTTGCTAACCGCGA 58.197 45.000 8.23 0.00 43.27 5.87
1949 5964 2.611974 AATGTCTTTTGCTAACCGCG 57.388 45.000 0.00 0.00 43.27 6.46
1950 5965 5.458015 ACTTAAATGTCTTTTGCTAACCGC 58.542 37.500 0.00 0.00 39.77 5.68
1951 5966 7.924103 AAACTTAAATGTCTTTTGCTAACCG 57.076 32.000 0.00 0.00 0.00 4.44
2072 6094 5.372373 AAATGGAATTTCTTCCCGCAAAAA 58.628 33.333 2.10 0.00 44.81 1.94
2073 6095 4.967036 AAATGGAATTTCTTCCCGCAAAA 58.033 34.783 2.10 0.00 44.81 2.44
2074 6096 4.615588 AAATGGAATTTCTTCCCGCAAA 57.384 36.364 2.10 0.00 44.81 3.68
2133 6160 5.422666 TGAATCAGTAAATATTGCCGCTG 57.577 39.130 0.00 0.00 0.00 5.18
2136 6163 5.334414 GGAGCTGAATCAGTAAATATTGCCG 60.334 44.000 12.29 0.00 33.43 5.69
2142 6169 5.985530 CACGATGGAGCTGAATCAGTAAATA 59.014 40.000 12.29 0.00 33.43 1.40
2143 6170 4.813161 CACGATGGAGCTGAATCAGTAAAT 59.187 41.667 12.29 1.30 33.43 1.40
2146 6173 2.481969 GCACGATGGAGCTGAATCAGTA 60.482 50.000 12.29 0.00 33.43 2.74
2147 6174 1.741732 GCACGATGGAGCTGAATCAGT 60.742 52.381 12.29 0.00 33.43 3.41
2148 6175 0.935898 GCACGATGGAGCTGAATCAG 59.064 55.000 5.78 5.78 34.12 2.90
2149 6176 0.249955 TGCACGATGGAGCTGAATCA 59.750 50.000 0.00 0.00 0.00 2.57
2154 6192 2.163390 CGACTGCACGATGGAGCTG 61.163 63.158 0.00 2.94 39.63 4.24
2161 6199 2.268022 AGGAACTCGACTGCACGAT 58.732 52.632 0.00 0.00 41.39 3.73
2360 6402 2.916052 GCGGCGATCATACGGGAGA 61.916 63.158 12.98 0.00 0.00 3.71
2397 6439 2.027837 GCATGGCTCCCAAATTCAAACT 60.028 45.455 0.00 0.00 36.95 2.66
2423 6465 3.060020 GACAGATCGACCGGCCGAA 62.060 63.158 30.73 9.56 42.22 4.30
2440 6482 3.636231 CCGTGGTGAAGGCTGGGA 61.636 66.667 0.00 0.00 0.00 4.37
2543 6585 2.649331 ATCACACGACTTCCCTTACG 57.351 50.000 0.00 0.00 0.00 3.18
2545 6587 4.069304 CCAAAATCACACGACTTCCCTTA 58.931 43.478 0.00 0.00 0.00 2.69
2586 6630 1.270571 GCCAAAATCTCCCCGCAAAAA 60.271 47.619 0.00 0.00 0.00 1.94
2587 6631 0.320050 GCCAAAATCTCCCCGCAAAA 59.680 50.000 0.00 0.00 0.00 2.44
2588 6632 0.829602 TGCCAAAATCTCCCCGCAAA 60.830 50.000 0.00 0.00 0.00 3.68
2589 6633 0.614415 ATGCCAAAATCTCCCCGCAA 60.614 50.000 0.00 0.00 0.00 4.85
2590 6634 1.000233 ATGCCAAAATCTCCCCGCA 60.000 52.632 0.00 0.00 0.00 5.69
2591 6635 1.735973 GATGCCAAAATCTCCCCGC 59.264 57.895 0.00 0.00 0.00 6.13
2592 6636 1.447317 CGGATGCCAAAATCTCCCCG 61.447 60.000 0.00 0.00 0.00 5.73
2593 6637 0.395724 ACGGATGCCAAAATCTCCCC 60.396 55.000 0.00 0.00 0.00 4.81
2594 6638 1.474330 AACGGATGCCAAAATCTCCC 58.526 50.000 0.00 0.00 0.00 4.30
2595 6639 2.491693 TCAAACGGATGCCAAAATCTCC 59.508 45.455 0.00 0.00 0.00 3.71
2596 6640 3.848272 TCAAACGGATGCCAAAATCTC 57.152 42.857 0.00 0.00 0.00 2.75
2597 6641 5.184864 TGTTATCAAACGGATGCCAAAATCT 59.815 36.000 0.00 0.00 38.53 2.40
2650 6694 7.398024 AGTTTTACTAAGGCTCATGATGTTCT 58.602 34.615 0.00 0.00 0.00 3.01
2667 6711 8.768019 CAGTTTAGCGTAACCTTTAGTTTTACT 58.232 33.333 1.09 0.00 40.05 2.24


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

AutoCloner maintained by Alex Coulton.