Multiple sequence alignment - TraesCS3B01G123900

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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 TraesCS3B01G123900 chr3B 100.000 2213 0 0 1 2213 96849462 96851674 0.000000e+00 4087
1 TraesCS3B01G123900 chr3B 99.760 835 2 0 1379 2213 46273742 46272908 0.000000e+00 1531
2 TraesCS3B01G123900 chr4A 100.000 835 0 0 1379 2213 659643706 659642872 0.000000e+00 1543
3 TraesCS3B01G123900 chr4A 99.641 835 3 0 1379 2213 624491146 624490312 0.000000e+00 1526
4 TraesCS3B01G123900 chr7B 99.880 835 1 0 1379 2213 68322561 68321727 0.000000e+00 1537
5 TraesCS3B01G123900 chr7B 83.565 359 27 15 601 953 610752220 610751888 7.680000e-80 307
6 TraesCS3B01G123900 chr7B 82.645 363 37 12 594 953 611044850 611044511 4.620000e-77 298
7 TraesCS3B01G123900 chr7B 98.551 69 0 1 1020 1087 611044480 611044412 1.070000e-23 121
8 TraesCS3B01G123900 chr7B 85.593 118 6 5 1001 1111 610751890 610751777 1.800000e-21 113
9 TraesCS3B01G123900 chrUn 99.641 835 3 0 1379 2213 2354456 2355290 0.000000e+00 1526
10 TraesCS3B01G123900 chr5A 99.641 835 3 0 1379 2213 555226774 555225940 0.000000e+00 1526
11 TraesCS3B01G123900 chr4B 99.641 835 3 0 1379 2213 509297326 509296492 0.000000e+00 1526
12 TraesCS3B01G123900 chr1B 99.641 835 3 0 1379 2213 2774626 2773792 0.000000e+00 1526
13 TraesCS3B01G123900 chr1A 99.641 835 3 0 1379 2213 9098461 9099295 0.000000e+00 1526
14 TraesCS3B01G123900 chr3D 89.140 1151 64 30 243 1371 61223845 61224956 0.000000e+00 1376
15 TraesCS3B01G123900 chr3A 88.215 1171 75 33 243 1380 69310546 69311686 0.000000e+00 1339
16 TraesCS3B01G123900 chr6B 84.483 232 7 12 316 519 716372834 716373064 3.730000e-48 202
17 TraesCS3B01G123900 chr6B 85.593 118 11 4 1253 1366 716373199 716373314 3.860000e-23 119


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 TraesCS3B01G123900 chr3B 96849462 96851674 2212 False 4087 4087 100.000 1 2213 1 chr3B.!!$F1 2212
1 TraesCS3B01G123900 chr3B 46272908 46273742 834 True 1531 1531 99.760 1379 2213 1 chr3B.!!$R1 834
2 TraesCS3B01G123900 chr4A 659642872 659643706 834 True 1543 1543 100.000 1379 2213 1 chr4A.!!$R2 834
3 TraesCS3B01G123900 chr4A 624490312 624491146 834 True 1526 1526 99.641 1379 2213 1 chr4A.!!$R1 834
4 TraesCS3B01G123900 chr7B 68321727 68322561 834 True 1537 1537 99.880 1379 2213 1 chr7B.!!$R1 834
5 TraesCS3B01G123900 chrUn 2354456 2355290 834 False 1526 1526 99.641 1379 2213 1 chrUn.!!$F1 834
6 TraesCS3B01G123900 chr5A 555225940 555226774 834 True 1526 1526 99.641 1379 2213 1 chr5A.!!$R1 834
7 TraesCS3B01G123900 chr4B 509296492 509297326 834 True 1526 1526 99.641 1379 2213 1 chr4B.!!$R1 834
8 TraesCS3B01G123900 chr1B 2773792 2774626 834 True 1526 1526 99.641 1379 2213 1 chr1B.!!$R1 834
9 TraesCS3B01G123900 chr1A 9098461 9099295 834 False 1526 1526 99.641 1379 2213 1 chr1A.!!$F1 834
10 TraesCS3B01G123900 chr3D 61223845 61224956 1111 False 1376 1376 89.140 243 1371 1 chr3D.!!$F1 1128
11 TraesCS3B01G123900 chr3A 69310546 69311686 1140 False 1339 1339 88.215 243 1380 1 chr3A.!!$F1 1137

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
221 222 0.03659 TTTACCCTGTTACCGGCACC 59.963 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 1417 1.656652 CTGCCGCAGCTTGTATTACT 58.343 50.0 7.61 0.0 40.8 2.24 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
55 56 7.845617 TTTATTTTCCGTGTTTTCTTGATCG 57.154 32.000 0.00 0.00 0.00 3.69
56 57 5.682943 ATTTTCCGTGTTTTCTTGATCGA 57.317 34.783 0.00 0.00 0.00 3.59
57 58 5.487153 TTTTCCGTGTTTTCTTGATCGAA 57.513 34.783 0.00 0.00 0.00 3.71
58 59 5.682943 TTTCCGTGTTTTCTTGATCGAAT 57.317 34.783 0.00 0.00 0.00 3.34
59 60 6.788684 TTTCCGTGTTTTCTTGATCGAATA 57.211 33.333 0.00 0.00 0.00 1.75
60 61 6.788684 TTCCGTGTTTTCTTGATCGAATAA 57.211 33.333 0.00 0.00 0.00 1.40
61 62 6.403333 TCCGTGTTTTCTTGATCGAATAAG 57.597 37.500 5.85 5.85 0.00 1.73
62 63 5.022021 CCGTGTTTTCTTGATCGAATAAGC 58.978 41.667 7.05 0.00 0.00 3.09
63 64 5.163854 CCGTGTTTTCTTGATCGAATAAGCT 60.164 40.000 7.05 0.00 0.00 3.74
64 65 5.954349 CGTGTTTTCTTGATCGAATAAGCTC 59.046 40.000 7.05 0.00 0.00 4.09
65 66 6.183360 CGTGTTTTCTTGATCGAATAAGCTCT 60.183 38.462 7.05 0.00 0.00 4.09
66 67 7.176741 GTGTTTTCTTGATCGAATAAGCTCTC 58.823 38.462 7.05 0.00 0.00 3.20
67 68 6.313905 TGTTTTCTTGATCGAATAAGCTCTCC 59.686 38.462 7.05 0.00 0.00 3.71
68 69 5.598416 TTCTTGATCGAATAAGCTCTCCA 57.402 39.130 7.05 0.00 0.00 3.86
69 70 5.798125 TCTTGATCGAATAAGCTCTCCAT 57.202 39.130 7.05 0.00 0.00 3.41
70 71 5.777802 TCTTGATCGAATAAGCTCTCCATC 58.222 41.667 7.05 0.00 0.00 3.51
71 72 5.538053 TCTTGATCGAATAAGCTCTCCATCT 59.462 40.000 7.05 0.00 0.00 2.90
72 73 5.384063 TGATCGAATAAGCTCTCCATCTC 57.616 43.478 0.00 0.00 0.00 2.75
73 74 4.219507 TGATCGAATAAGCTCTCCATCTCC 59.780 45.833 0.00 0.00 0.00 3.71
74 75 3.566351 TCGAATAAGCTCTCCATCTCCA 58.434 45.455 0.00 0.00 0.00 3.86
75 76 4.155709 TCGAATAAGCTCTCCATCTCCAT 58.844 43.478 0.00 0.00 0.00 3.41
76 77 4.021632 TCGAATAAGCTCTCCATCTCCATG 60.022 45.833 0.00 0.00 0.00 3.66
77 78 4.262377 CGAATAAGCTCTCCATCTCCATGT 60.262 45.833 0.00 0.00 0.00 3.21
78 79 5.047731 CGAATAAGCTCTCCATCTCCATGTA 60.048 44.000 0.00 0.00 0.00 2.29
79 80 5.999205 ATAAGCTCTCCATCTCCATGTAG 57.001 43.478 0.00 0.00 0.00 2.74
80 81 3.326946 AGCTCTCCATCTCCATGTAGT 57.673 47.619 0.00 0.00 0.00 2.73
81 82 4.461450 AGCTCTCCATCTCCATGTAGTA 57.539 45.455 0.00 0.00 0.00 1.82
82 83 4.148838 AGCTCTCCATCTCCATGTAGTAC 58.851 47.826 0.00 0.00 0.00 2.73
83 84 4.141041 AGCTCTCCATCTCCATGTAGTACT 60.141 45.833 0.00 0.00 0.00 2.73
84 85 5.073827 AGCTCTCCATCTCCATGTAGTACTA 59.926 44.000 0.00 0.00 0.00 1.82
85 86 5.414454 GCTCTCCATCTCCATGTAGTACTAG 59.586 48.000 1.87 0.00 0.00 2.57
86 87 5.317808 TCTCCATCTCCATGTAGTACTAGC 58.682 45.833 1.87 0.00 0.00 3.42
87 88 5.061721 TCCATCTCCATGTAGTACTAGCA 57.938 43.478 1.87 5.33 0.00 3.49
88 89 5.073428 TCCATCTCCATGTAGTACTAGCAG 58.927 45.833 1.87 0.00 0.00 4.24
89 90 4.830046 CCATCTCCATGTAGTACTAGCAGT 59.170 45.833 1.87 0.00 0.00 4.40
90 91 6.004574 CCATCTCCATGTAGTACTAGCAGTA 58.995 44.000 1.87 0.00 0.00 2.74
91 92 6.661377 CCATCTCCATGTAGTACTAGCAGTAT 59.339 42.308 1.87 0.00 32.65 2.12
92 93 7.148154 CCATCTCCATGTAGTACTAGCAGTATC 60.148 44.444 1.87 0.00 32.65 2.24
93 94 6.838382 TCTCCATGTAGTACTAGCAGTATCA 58.162 40.000 1.87 0.00 32.65 2.15
94 95 6.937465 TCTCCATGTAGTACTAGCAGTATCAG 59.063 42.308 1.87 0.00 32.65 2.90
95 96 6.602278 TCCATGTAGTACTAGCAGTATCAGT 58.398 40.000 1.87 0.00 32.65 3.41
96 97 7.061054 TCCATGTAGTACTAGCAGTATCAGTT 58.939 38.462 1.87 0.00 32.65 3.16
97 98 7.228906 TCCATGTAGTACTAGCAGTATCAGTTC 59.771 40.741 1.87 0.00 32.65 3.01
98 99 6.939132 TGTAGTACTAGCAGTATCAGTTCC 57.061 41.667 1.87 0.00 32.65 3.62
99 100 5.526479 TGTAGTACTAGCAGTATCAGTTCCG 59.474 44.000 1.87 0.00 32.65 4.30
100 101 3.884091 AGTACTAGCAGTATCAGTTCCGG 59.116 47.826 0.00 0.00 32.65 5.14
101 102 2.032620 ACTAGCAGTATCAGTTCCGGG 58.967 52.381 0.00 0.00 0.00 5.73
102 103 2.307768 CTAGCAGTATCAGTTCCGGGA 58.692 52.381 0.00 0.00 0.00 5.14
103 104 1.794714 AGCAGTATCAGTTCCGGGAT 58.205 50.000 0.00 0.00 0.00 3.85
104 105 2.119495 AGCAGTATCAGTTCCGGGATT 58.881 47.619 0.00 0.00 0.00 3.01
105 106 2.103263 AGCAGTATCAGTTCCGGGATTC 59.897 50.000 0.00 0.00 0.00 2.52
106 107 2.103263 GCAGTATCAGTTCCGGGATTCT 59.897 50.000 0.00 0.00 0.00 2.40
107 108 3.321111 GCAGTATCAGTTCCGGGATTCTA 59.679 47.826 0.00 0.00 0.00 2.10
108 109 4.202223 GCAGTATCAGTTCCGGGATTCTAA 60.202 45.833 0.00 0.00 0.00 2.10
109 110 5.290386 CAGTATCAGTTCCGGGATTCTAAC 58.710 45.833 0.00 0.00 0.00 2.34
110 111 5.069251 CAGTATCAGTTCCGGGATTCTAACT 59.931 44.000 0.00 0.00 32.52 2.24
111 112 5.661759 AGTATCAGTTCCGGGATTCTAACTT 59.338 40.000 0.00 0.00 29.93 2.66
112 113 4.903045 TCAGTTCCGGGATTCTAACTTT 57.097 40.909 0.00 0.00 29.93 2.66
113 114 4.575885 TCAGTTCCGGGATTCTAACTTTG 58.424 43.478 0.00 0.00 29.93 2.77
114 115 4.285003 TCAGTTCCGGGATTCTAACTTTGA 59.715 41.667 0.00 0.00 29.93 2.69
115 116 5.045869 TCAGTTCCGGGATTCTAACTTTGAT 60.046 40.000 0.00 0.00 29.93 2.57
116 117 5.065218 CAGTTCCGGGATTCTAACTTTGATG 59.935 44.000 0.00 0.00 29.93 3.07
117 118 5.045869 AGTTCCGGGATTCTAACTTTGATGA 60.046 40.000 0.00 0.00 0.00 2.92
118 119 5.429681 TCCGGGATTCTAACTTTGATGAA 57.570 39.130 0.00 0.00 0.00 2.57
119 120 6.001449 TCCGGGATTCTAACTTTGATGAAT 57.999 37.500 0.00 0.00 32.59 2.57
120 121 6.423182 TCCGGGATTCTAACTTTGATGAATT 58.577 36.000 0.00 0.00 30.41 2.17
121 122 6.889722 TCCGGGATTCTAACTTTGATGAATTT 59.110 34.615 0.00 0.00 30.41 1.82
122 123 7.067008 TCCGGGATTCTAACTTTGATGAATTTC 59.933 37.037 0.00 0.00 30.41 2.17
123 124 7.067494 CCGGGATTCTAACTTTGATGAATTTCT 59.933 37.037 0.00 0.00 30.41 2.52
124 125 8.462016 CGGGATTCTAACTTTGATGAATTTCTT 58.538 33.333 0.00 0.00 30.41 2.52
125 126 9.578439 GGGATTCTAACTTTGATGAATTTCTTG 57.422 33.333 0.00 0.00 30.41 3.02
131 132 9.918630 CTAACTTTGATGAATTTCTTGAATGGT 57.081 29.630 0.00 0.00 0.00 3.55
132 133 8.597662 AACTTTGATGAATTTCTTGAATGGTG 57.402 30.769 0.00 0.00 0.00 4.17
133 134 7.954835 ACTTTGATGAATTTCTTGAATGGTGA 58.045 30.769 0.00 0.00 0.00 4.02
134 135 7.869429 ACTTTGATGAATTTCTTGAATGGTGAC 59.131 33.333 0.00 0.00 0.00 3.67
135 136 7.528996 TTGATGAATTTCTTGAATGGTGACT 57.471 32.000 0.00 0.00 0.00 3.41
136 137 7.528996 TGATGAATTTCTTGAATGGTGACTT 57.471 32.000 0.00 0.00 0.00 3.01
137 138 8.634335 TGATGAATTTCTTGAATGGTGACTTA 57.366 30.769 0.00 0.00 0.00 2.24
138 139 8.733458 TGATGAATTTCTTGAATGGTGACTTAG 58.267 33.333 0.00 0.00 0.00 2.18
139 140 8.868522 ATGAATTTCTTGAATGGTGACTTAGA 57.131 30.769 0.00 0.00 0.00 2.10
140 141 8.868522 TGAATTTCTTGAATGGTGACTTAGAT 57.131 30.769 0.00 0.00 0.00 1.98
141 142 8.733458 TGAATTTCTTGAATGGTGACTTAGATG 58.267 33.333 0.00 0.00 0.00 2.90
142 143 8.868522 AATTTCTTGAATGGTGACTTAGATGA 57.131 30.769 0.00 0.00 0.00 2.92
143 144 9.471702 AATTTCTTGAATGGTGACTTAGATGAT 57.528 29.630 0.00 0.00 0.00 2.45
144 145 8.868522 TTTCTTGAATGGTGACTTAGATGATT 57.131 30.769 0.00 0.00 0.00 2.57
145 146 7.854557 TCTTGAATGGTGACTTAGATGATTG 57.145 36.000 0.00 0.00 0.00 2.67
146 147 7.623630 TCTTGAATGGTGACTTAGATGATTGA 58.376 34.615 0.00 0.00 0.00 2.57
147 148 8.270030 TCTTGAATGGTGACTTAGATGATTGAT 58.730 33.333 0.00 0.00 0.00 2.57
148 149 7.797038 TGAATGGTGACTTAGATGATTGATG 57.203 36.000 0.00 0.00 0.00 3.07
149 150 7.341030 TGAATGGTGACTTAGATGATTGATGT 58.659 34.615 0.00 0.00 0.00 3.06
150 151 7.496920 TGAATGGTGACTTAGATGATTGATGTC 59.503 37.037 0.00 0.00 0.00 3.06
151 152 6.298441 TGGTGACTTAGATGATTGATGTCA 57.702 37.500 0.00 0.00 0.00 3.58
152 153 6.892485 TGGTGACTTAGATGATTGATGTCAT 58.108 36.000 0.00 0.00 41.36 3.06
153 154 7.341030 TGGTGACTTAGATGATTGATGTCATT 58.659 34.615 0.00 0.00 38.88 2.57
154 155 7.281549 TGGTGACTTAGATGATTGATGTCATTG 59.718 37.037 0.00 0.00 38.88 2.82
155 156 7.281774 GGTGACTTAGATGATTGATGTCATTGT 59.718 37.037 0.00 0.00 38.88 2.71
156 157 9.317936 GTGACTTAGATGATTGATGTCATTGTA 57.682 33.333 0.00 0.00 38.88 2.41
163 164 9.227777 AGATGATTGATGTCATTGTATACATGG 57.772 33.333 6.36 2.22 38.88 3.66
164 165 7.205737 TGATTGATGTCATTGTATACATGGC 57.794 36.000 6.36 9.26 36.48 4.40
165 166 6.999871 TGATTGATGTCATTGTATACATGGCT 59.000 34.615 6.36 0.37 36.48 4.75
166 167 6.622833 TTGATGTCATTGTATACATGGCTG 57.377 37.500 6.36 3.06 36.48 4.85
167 168 5.065235 TGATGTCATTGTATACATGGCTGG 58.935 41.667 6.36 0.00 36.48 4.85
168 169 3.213506 TGTCATTGTATACATGGCTGGC 58.786 45.455 6.36 4.89 0.00 4.85
169 170 2.224079 GTCATTGTATACATGGCTGGCG 59.776 50.000 6.36 0.00 0.00 5.69
170 171 2.103941 TCATTGTATACATGGCTGGCGA 59.896 45.455 6.36 0.00 0.00 5.54
171 172 2.238942 TTGTATACATGGCTGGCGAG 57.761 50.000 6.36 0.00 0.00 5.03
172 173 1.408969 TGTATACATGGCTGGCGAGA 58.591 50.000 0.08 0.00 0.00 4.04
173 174 1.970640 TGTATACATGGCTGGCGAGAT 59.029 47.619 0.08 0.00 0.00 2.75
174 175 2.289010 TGTATACATGGCTGGCGAGATG 60.289 50.000 0.08 0.00 0.00 2.90
175 176 0.761187 ATACATGGCTGGCGAGATGT 59.239 50.000 0.00 4.11 33.64 3.06
176 177 1.408969 TACATGGCTGGCGAGATGTA 58.591 50.000 0.00 3.08 31.56 2.29
177 178 0.541392 ACATGGCTGGCGAGATGTAA 59.459 50.000 0.00 0.00 0.00 2.41
178 179 1.065491 ACATGGCTGGCGAGATGTAAA 60.065 47.619 0.00 0.00 0.00 2.01
179 180 1.331756 CATGGCTGGCGAGATGTAAAC 59.668 52.381 0.00 0.00 0.00 2.01
180 181 0.739462 TGGCTGGCGAGATGTAAACG 60.739 55.000 0.00 0.00 0.00 3.60
181 182 0.459585 GGCTGGCGAGATGTAAACGA 60.460 55.000 0.00 0.00 0.00 3.85
182 183 0.924090 GCTGGCGAGATGTAAACGAG 59.076 55.000 0.00 0.00 0.00 4.18
183 184 1.736032 GCTGGCGAGATGTAAACGAGT 60.736 52.381 0.00 0.00 0.00 4.18
184 185 1.920574 CTGGCGAGATGTAAACGAGTG 59.079 52.381 0.00 0.00 0.00 3.51
185 186 1.271379 TGGCGAGATGTAAACGAGTGT 59.729 47.619 0.00 0.00 0.00 3.55
186 187 2.488937 TGGCGAGATGTAAACGAGTGTA 59.511 45.455 0.00 0.00 0.00 2.90
187 188 3.106672 GGCGAGATGTAAACGAGTGTAG 58.893 50.000 0.00 0.00 0.00 2.74
188 189 3.427233 GGCGAGATGTAAACGAGTGTAGT 60.427 47.826 0.00 0.00 0.00 2.73
189 190 3.542704 GCGAGATGTAAACGAGTGTAGTG 59.457 47.826 0.00 0.00 0.00 2.74
190 191 3.542704 CGAGATGTAAACGAGTGTAGTGC 59.457 47.826 0.00 0.00 0.00 4.40
191 192 3.846360 AGATGTAAACGAGTGTAGTGCC 58.154 45.455 0.00 0.00 0.00 5.01
192 193 2.054687 TGTAAACGAGTGTAGTGCCG 57.945 50.000 0.00 0.00 0.00 5.69
193 194 1.336148 TGTAAACGAGTGTAGTGCCGG 60.336 52.381 0.00 0.00 0.00 6.13
194 195 0.961019 TAAACGAGTGTAGTGCCGGT 59.039 50.000 1.90 0.00 0.00 5.28
195 196 0.105408 AAACGAGTGTAGTGCCGGTT 59.895 50.000 1.90 0.00 0.00 4.44
196 197 0.105408 AACGAGTGTAGTGCCGGTTT 59.895 50.000 1.90 0.00 0.00 3.27
197 198 0.105408 ACGAGTGTAGTGCCGGTTTT 59.895 50.000 1.90 0.00 0.00 2.43
198 199 1.223187 CGAGTGTAGTGCCGGTTTTT 58.777 50.000 1.90 0.00 0.00 1.94
219 220 2.653234 TTTTTACCCTGTTACCGGCA 57.347 45.000 0.00 0.00 0.00 5.69
220 221 1.894881 TTTTACCCTGTTACCGGCAC 58.105 50.000 0.00 0.00 0.00 5.01
221 222 0.036590 TTTACCCTGTTACCGGCACC 59.963 55.000 0.00 0.00 0.00 5.01
222 223 1.840224 TTACCCTGTTACCGGCACCC 61.840 60.000 0.00 0.00 0.00 4.61
234 235 3.357079 GCACCCGGCACAGTGAAG 61.357 66.667 12.16 0.00 43.97 3.02
235 236 2.425592 CACCCGGCACAGTGAAGA 59.574 61.111 4.15 0.00 34.62 2.87
236 237 1.227823 CACCCGGCACAGTGAAGAA 60.228 57.895 4.15 0.00 34.62 2.52
237 238 0.817634 CACCCGGCACAGTGAAGAAA 60.818 55.000 4.15 0.00 34.62 2.52
238 239 0.110486 ACCCGGCACAGTGAAGAAAT 59.890 50.000 4.15 0.00 0.00 2.17
239 240 0.804989 CCCGGCACAGTGAAGAAATC 59.195 55.000 4.15 0.00 0.00 2.17
240 241 0.804989 CCGGCACAGTGAAGAAATCC 59.195 55.000 4.15 0.00 0.00 3.01
241 242 1.522668 CGGCACAGTGAAGAAATCCA 58.477 50.000 4.15 0.00 0.00 3.41
242 243 1.197721 CGGCACAGTGAAGAAATCCAC 59.802 52.381 4.15 0.00 0.00 4.02
243 244 2.229792 GGCACAGTGAAGAAATCCACA 58.770 47.619 4.15 0.00 35.84 4.17
244 245 2.227388 GGCACAGTGAAGAAATCCACAG 59.773 50.000 4.15 0.00 35.84 3.66
245 246 2.351157 GCACAGTGAAGAAATCCACAGC 60.351 50.000 4.15 0.00 35.84 4.40
246 247 2.880268 CACAGTGAAGAAATCCACAGCA 59.120 45.455 0.00 0.00 35.84 4.41
310 314 1.082117 CCGTTAATGCGAGGCGAAGT 61.082 55.000 0.00 0.00 0.00 3.01
311 315 0.297820 CGTTAATGCGAGGCGAAGTC 59.702 55.000 0.00 0.00 0.00 3.01
312 316 0.651031 GTTAATGCGAGGCGAAGTCC 59.349 55.000 0.00 0.00 0.00 3.85
362 370 3.922640 CTAGGCAGGCCGAGGAGC 61.923 72.222 12.06 0.00 41.95 4.70
405 413 3.188873 CCTAAATCCGCTCTACTCCTACG 59.811 52.174 0.00 0.00 0.00 3.51
498 513 3.367743 CCACAGCCACGCAGCAAT 61.368 61.111 0.00 0.00 34.23 3.56
499 514 2.177531 CACAGCCACGCAGCAATC 59.822 61.111 0.00 0.00 34.23 2.67
500 515 2.033141 ACAGCCACGCAGCAATCT 59.967 55.556 0.00 0.00 34.23 2.40
501 516 2.037136 ACAGCCACGCAGCAATCTC 61.037 57.895 0.00 0.00 34.23 2.75
592 613 1.534175 GCACGCGTCTAGCTAGTCATT 60.534 52.381 20.10 0.00 45.59 2.57
593 614 2.376956 CACGCGTCTAGCTAGTCATTC 58.623 52.381 20.10 6.30 45.59 2.67
608 629 1.695597 ATTCCCTAGCCAGGCTGCT 60.696 57.895 25.59 12.49 45.38 4.24
636 657 1.589414 ATCCCAGAAACAGAGGAGGG 58.411 55.000 0.00 0.00 37.65 4.30
673 694 2.498941 CGGCCGGCTCCAGAATCTA 61.499 63.158 28.56 0.00 0.00 1.98
681 702 2.368221 GGCTCCAGAATCTATGTGCTCT 59.632 50.000 6.15 0.00 0.00 4.09
749 770 3.064324 GCCATTTCACTGCCGGCT 61.064 61.111 29.70 4.80 39.73 5.52
754 775 3.825160 TTTCACTGCCGGCTTCGCT 62.825 57.895 29.70 1.67 0.00 4.93
775 796 3.630148 CGTGATCGGGCGATGTGC 61.630 66.667 0.00 0.00 45.38 4.57
868 889 2.356313 CTTGTGCTCGCCGTGTCT 60.356 61.111 0.00 0.00 0.00 3.41
908 929 1.067060 CATCGCCGGTACATCTCTTCA 59.933 52.381 1.90 0.00 0.00 3.02
938 962 1.609072 GTCTGTTTTTCCAGCACCTCC 59.391 52.381 0.00 0.00 32.32 4.30
963 987 3.337358 CTTGATGCATGCGGGACATATA 58.663 45.455 14.09 0.00 36.64 0.86
965 989 3.272581 TGATGCATGCGGGACATATATG 58.727 45.455 14.09 11.29 36.64 1.78
966 990 2.857186 TGCATGCGGGACATATATGT 57.143 45.000 18.31 18.31 45.16 2.29
974 999 2.603110 CGGGACATATATGTACGCATGC 59.397 50.000 19.67 7.91 42.67 4.06
975 1000 3.676049 CGGGACATATATGTACGCATGCT 60.676 47.826 19.67 5.50 42.67 3.79
976 1001 3.618594 GGGACATATATGTACGCATGCTG 59.381 47.826 19.67 11.87 42.67 4.41
977 1002 3.062639 GGACATATATGTACGCATGCTGC 59.937 47.826 18.28 7.17 41.95 5.25
994 1019 2.476051 CTGCATGACGCGTTGGTC 59.524 61.111 15.53 0.00 46.97 4.02
995 1020 3.027170 CTGCATGACGCGTTGGTCC 62.027 63.158 15.53 0.00 46.97 4.46
996 1021 4.147322 GCATGACGCGTTGGTCCG 62.147 66.667 15.53 0.01 36.07 4.79
997 1022 2.736995 CATGACGCGTTGGTCCGT 60.737 61.111 15.53 0.00 40.85 4.69
998 1023 2.029964 ATGACGCGTTGGTCCGTT 59.970 55.556 15.53 0.00 37.87 4.44
999 1024 2.314647 ATGACGCGTTGGTCCGTTG 61.315 57.895 15.53 0.00 37.87 4.10
1000 1025 2.659244 GACGCGTTGGTCCGTTGA 60.659 61.111 15.53 0.00 37.87 3.18
1236 1272 7.930325 TGACTCCATGAGATAATTCAGATGAAC 59.070 37.037 0.00 0.00 33.59 3.18
1319 1361 0.664761 ATCGCCATGCAATGTACAGC 59.335 50.000 0.33 0.30 44.81 4.40
1332 1374 7.751732 TGCAATGTACAGCAAGTAGAAATAAG 58.248 34.615 7.29 0.00 37.90 1.73
1336 1378 6.403878 TGTACAGCAAGTAGAAATAAGGTCC 58.596 40.000 0.00 0.00 32.19 4.46
1372 1415 5.597182 TGGCTGGTACTAGGAGTAAATAGTG 59.403 44.000 8.46 0.00 31.62 2.74
1373 1416 5.597594 GGCTGGTACTAGGAGTAAATAGTGT 59.402 44.000 8.46 0.00 31.62 3.55
1374 1417 6.774656 GGCTGGTACTAGGAGTAAATAGTGTA 59.225 42.308 8.46 0.00 31.62 2.90
1375 1418 7.040548 GGCTGGTACTAGGAGTAAATAGTGTAG 60.041 44.444 8.46 0.00 31.62 2.74
1376 1419 7.501892 GCTGGTACTAGGAGTAAATAGTGTAGT 59.498 40.741 8.46 0.00 31.62 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 8.911662 CGATCAAGAAAACACGGAAAATAAATT 58.088 29.630 0.00 0.00 0.00 1.82
30 31 8.293867 TCGATCAAGAAAACACGGAAAATAAAT 58.706 29.630 0.00 0.00 0.00 1.40
31 32 7.640852 TCGATCAAGAAAACACGGAAAATAAA 58.359 30.769 0.00 0.00 0.00 1.40
32 33 7.192148 TCGATCAAGAAAACACGGAAAATAA 57.808 32.000 0.00 0.00 0.00 1.40
33 34 6.788684 TCGATCAAGAAAACACGGAAAATA 57.211 33.333 0.00 0.00 0.00 1.40
34 35 5.682943 TCGATCAAGAAAACACGGAAAAT 57.317 34.783 0.00 0.00 0.00 1.82
35 36 5.487153 TTCGATCAAGAAAACACGGAAAA 57.513 34.783 0.00 0.00 0.00 2.29
36 37 5.682943 ATTCGATCAAGAAAACACGGAAA 57.317 34.783 0.00 0.00 33.43 3.13
37 38 6.619874 GCTTATTCGATCAAGAAAACACGGAA 60.620 38.462 9.95 0.00 33.43 4.30
38 39 5.163893 GCTTATTCGATCAAGAAAACACGGA 60.164 40.000 9.95 0.00 33.43 4.69
39 40 5.022021 GCTTATTCGATCAAGAAAACACGG 58.978 41.667 9.95 0.00 33.43 4.94
40 41 5.858475 AGCTTATTCGATCAAGAAAACACG 58.142 37.500 9.95 0.00 33.43 4.49
41 42 7.066374 AGAGCTTATTCGATCAAGAAAACAC 57.934 36.000 9.95 0.00 33.43 3.32
42 43 6.313905 GGAGAGCTTATTCGATCAAGAAAACA 59.686 38.462 9.95 0.00 33.43 2.83
43 44 6.313905 TGGAGAGCTTATTCGATCAAGAAAAC 59.686 38.462 9.95 0.63 33.43 2.43
44 45 6.406370 TGGAGAGCTTATTCGATCAAGAAAA 58.594 36.000 9.95 0.00 33.43 2.29
45 46 5.977635 TGGAGAGCTTATTCGATCAAGAAA 58.022 37.500 9.95 0.00 33.43 2.52
46 47 5.598416 TGGAGAGCTTATTCGATCAAGAA 57.402 39.130 9.95 0.00 34.31 2.52
47 48 5.538053 AGATGGAGAGCTTATTCGATCAAGA 59.462 40.000 15.75 0.00 32.84 3.02
48 49 5.782047 AGATGGAGAGCTTATTCGATCAAG 58.218 41.667 15.75 0.00 32.84 3.02
49 50 5.279206 GGAGATGGAGAGCTTATTCGATCAA 60.279 44.000 15.75 0.00 32.84 2.57
50 51 4.219507 GGAGATGGAGAGCTTATTCGATCA 59.780 45.833 15.75 0.37 32.84 2.92
51 52 4.219507 TGGAGATGGAGAGCTTATTCGATC 59.780 45.833 9.35 9.35 0.00 3.69
52 53 4.155709 TGGAGATGGAGAGCTTATTCGAT 58.844 43.478 0.00 0.00 0.00 3.59
53 54 3.566351 TGGAGATGGAGAGCTTATTCGA 58.434 45.455 0.00 0.00 0.00 3.71
54 55 4.244066 CATGGAGATGGAGAGCTTATTCG 58.756 47.826 0.00 0.00 0.00 3.34
55 56 5.226194 ACATGGAGATGGAGAGCTTATTC 57.774 43.478 0.00 0.00 33.39 1.75
56 57 5.843421 ACTACATGGAGATGGAGAGCTTATT 59.157 40.000 13.29 0.00 42.67 1.40
57 58 5.401750 ACTACATGGAGATGGAGAGCTTAT 58.598 41.667 13.29 0.00 42.67 1.73
58 59 4.809193 ACTACATGGAGATGGAGAGCTTA 58.191 43.478 13.29 0.00 42.67 3.09
59 60 3.652055 ACTACATGGAGATGGAGAGCTT 58.348 45.455 13.29 0.00 42.67 3.74
60 61 3.326946 ACTACATGGAGATGGAGAGCT 57.673 47.619 13.29 0.00 42.67 4.09
61 62 4.148838 AGTACTACATGGAGATGGAGAGC 58.851 47.826 13.29 0.00 42.67 4.09
62 63 5.414454 GCTAGTACTACATGGAGATGGAGAG 59.586 48.000 13.29 2.20 42.67 3.20
63 64 5.163088 TGCTAGTACTACATGGAGATGGAGA 60.163 44.000 13.29 0.00 42.67 3.71
64 65 5.073428 TGCTAGTACTACATGGAGATGGAG 58.927 45.833 13.29 4.71 45.26 3.86
65 66 5.061721 TGCTAGTACTACATGGAGATGGA 57.938 43.478 13.29 0.00 33.39 3.41
66 67 4.830046 ACTGCTAGTACTACATGGAGATGG 59.170 45.833 13.29 0.21 33.39 3.51
67 68 7.391833 TGATACTGCTAGTACTACATGGAGATG 59.608 40.741 13.29 0.00 32.84 2.90
68 69 7.462590 TGATACTGCTAGTACTACATGGAGAT 58.537 38.462 13.29 0.00 32.84 2.75
69 70 6.838382 TGATACTGCTAGTACTACATGGAGA 58.162 40.000 13.29 0.00 32.84 3.71
70 71 6.712998 ACTGATACTGCTAGTACTACATGGAG 59.287 42.308 2.41 2.41 32.84 3.86
71 72 6.602278 ACTGATACTGCTAGTACTACATGGA 58.398 40.000 0.00 0.00 32.84 3.41
72 73 6.885952 ACTGATACTGCTAGTACTACATGG 57.114 41.667 0.00 0.00 32.84 3.66
73 74 7.364200 GGAACTGATACTGCTAGTACTACATG 58.636 42.308 0.00 0.00 32.84 3.21
74 75 6.205076 CGGAACTGATACTGCTAGTACTACAT 59.795 42.308 0.00 0.00 32.84 2.29
75 76 5.526479 CGGAACTGATACTGCTAGTACTACA 59.474 44.000 0.00 2.13 32.84 2.74
76 77 5.049543 CCGGAACTGATACTGCTAGTACTAC 60.050 48.000 0.00 0.00 32.84 2.73
77 78 5.061853 CCGGAACTGATACTGCTAGTACTA 58.938 45.833 0.00 1.89 32.84 1.82
78 79 3.884091 CCGGAACTGATACTGCTAGTACT 59.116 47.826 0.00 0.00 32.84 2.73
79 80 3.004524 CCCGGAACTGATACTGCTAGTAC 59.995 52.174 0.73 0.00 32.84 2.73
80 81 3.117776 TCCCGGAACTGATACTGCTAGTA 60.118 47.826 0.73 0.00 34.82 1.82
81 82 2.032620 CCCGGAACTGATACTGCTAGT 58.967 52.381 0.73 0.00 0.00 2.57
82 83 2.307768 TCCCGGAACTGATACTGCTAG 58.692 52.381 0.73 0.00 0.00 3.42
83 84 2.447408 TCCCGGAACTGATACTGCTA 57.553 50.000 0.73 0.00 0.00 3.49
84 85 1.794714 ATCCCGGAACTGATACTGCT 58.205 50.000 0.73 0.00 0.00 4.24
85 86 2.103263 AGAATCCCGGAACTGATACTGC 59.897 50.000 0.73 0.00 0.00 4.40
86 87 5.069251 AGTTAGAATCCCGGAACTGATACTG 59.931 44.000 0.73 0.00 31.05 2.74
87 88 5.209659 AGTTAGAATCCCGGAACTGATACT 58.790 41.667 0.73 0.00 31.05 2.12
88 89 5.532664 AGTTAGAATCCCGGAACTGATAC 57.467 43.478 0.73 0.00 31.05 2.24
89 90 6.155565 TCAAAGTTAGAATCCCGGAACTGATA 59.844 38.462 0.73 0.00 32.57 2.15
90 91 5.045869 TCAAAGTTAGAATCCCGGAACTGAT 60.046 40.000 0.73 0.00 32.57 2.90
91 92 4.285003 TCAAAGTTAGAATCCCGGAACTGA 59.715 41.667 0.73 0.00 32.57 3.41
92 93 4.575885 TCAAAGTTAGAATCCCGGAACTG 58.424 43.478 0.73 0.00 32.57 3.16
93 94 4.903045 TCAAAGTTAGAATCCCGGAACT 57.097 40.909 0.73 0.00 33.60 3.01
94 95 5.183228 TCATCAAAGTTAGAATCCCGGAAC 58.817 41.667 0.73 0.00 0.00 3.62
95 96 5.429681 TCATCAAAGTTAGAATCCCGGAA 57.570 39.130 0.73 0.00 0.00 4.30
96 97 5.429681 TTCATCAAAGTTAGAATCCCGGA 57.570 39.130 0.73 0.00 0.00 5.14
97 98 6.699575 AATTCATCAAAGTTAGAATCCCGG 57.300 37.500 0.00 0.00 30.87 5.73
98 99 7.989826 AGAAATTCATCAAAGTTAGAATCCCG 58.010 34.615 0.00 0.00 30.87 5.14
99 100 9.578439 CAAGAAATTCATCAAAGTTAGAATCCC 57.422 33.333 0.00 0.00 30.87 3.85
105 106 9.918630 ACCATTCAAGAAATTCATCAAAGTTAG 57.081 29.630 0.00 0.00 0.00 2.34
106 107 9.695526 CACCATTCAAGAAATTCATCAAAGTTA 57.304 29.630 0.00 0.00 0.00 2.24
107 108 8.423349 TCACCATTCAAGAAATTCATCAAAGTT 58.577 29.630 0.00 0.00 0.00 2.66
108 109 7.869429 GTCACCATTCAAGAAATTCATCAAAGT 59.131 33.333 0.00 0.00 0.00 2.66
109 110 8.086522 AGTCACCATTCAAGAAATTCATCAAAG 58.913 33.333 0.00 0.00 0.00 2.77
110 111 7.954835 AGTCACCATTCAAGAAATTCATCAAA 58.045 30.769 0.00 0.00 0.00 2.69
111 112 7.528996 AGTCACCATTCAAGAAATTCATCAA 57.471 32.000 0.00 0.00 0.00 2.57
112 113 7.528996 AAGTCACCATTCAAGAAATTCATCA 57.471 32.000 0.00 0.00 0.00 3.07
113 114 8.950210 TCTAAGTCACCATTCAAGAAATTCATC 58.050 33.333 0.00 0.00 0.00 2.92
114 115 8.868522 TCTAAGTCACCATTCAAGAAATTCAT 57.131 30.769 0.00 0.00 0.00 2.57
115 116 8.733458 CATCTAAGTCACCATTCAAGAAATTCA 58.267 33.333 0.00 0.00 0.00 2.57
116 117 8.950210 TCATCTAAGTCACCATTCAAGAAATTC 58.050 33.333 0.00 0.00 0.00 2.17
117 118 8.868522 TCATCTAAGTCACCATTCAAGAAATT 57.131 30.769 0.00 0.00 0.00 1.82
118 119 9.471702 AATCATCTAAGTCACCATTCAAGAAAT 57.528 29.630 0.00 0.00 0.00 2.17
119 120 8.733458 CAATCATCTAAGTCACCATTCAAGAAA 58.267 33.333 0.00 0.00 0.00 2.52
120 121 8.102676 TCAATCATCTAAGTCACCATTCAAGAA 58.897 33.333 0.00 0.00 0.00 2.52
121 122 7.623630 TCAATCATCTAAGTCACCATTCAAGA 58.376 34.615 0.00 0.00 0.00 3.02
122 123 7.854557 TCAATCATCTAAGTCACCATTCAAG 57.145 36.000 0.00 0.00 0.00 3.02
123 124 7.830697 ACATCAATCATCTAAGTCACCATTCAA 59.169 33.333 0.00 0.00 0.00 2.69
124 125 7.341030 ACATCAATCATCTAAGTCACCATTCA 58.659 34.615 0.00 0.00 0.00 2.57
125 126 7.496920 TGACATCAATCATCTAAGTCACCATTC 59.503 37.037 0.00 0.00 30.43 2.67
126 127 7.341030 TGACATCAATCATCTAAGTCACCATT 58.659 34.615 0.00 0.00 30.43 3.16
127 128 6.892485 TGACATCAATCATCTAAGTCACCAT 58.108 36.000 0.00 0.00 30.43 3.55
128 129 6.298441 TGACATCAATCATCTAAGTCACCA 57.702 37.500 0.00 0.00 30.43 4.17
129 130 7.281774 ACAATGACATCAATCATCTAAGTCACC 59.718 37.037 0.00 0.00 38.40 4.02
130 131 8.206325 ACAATGACATCAATCATCTAAGTCAC 57.794 34.615 0.00 0.00 38.40 3.67
137 138 9.227777 CCATGTATACAATGACATCAATCATCT 57.772 33.333 10.14 0.00 38.40 2.90
138 139 7.966753 GCCATGTATACAATGACATCAATCATC 59.033 37.037 10.14 0.00 38.40 2.92
139 140 7.668469 AGCCATGTATACAATGACATCAATCAT 59.332 33.333 10.14 0.00 41.20 2.45
140 141 6.999871 AGCCATGTATACAATGACATCAATCA 59.000 34.615 10.14 0.00 34.01 2.57
141 142 7.303261 CAGCCATGTATACAATGACATCAATC 58.697 38.462 10.14 0.00 34.01 2.67
142 143 6.208007 CCAGCCATGTATACAATGACATCAAT 59.792 38.462 10.14 0.00 34.01 2.57
143 144 5.532032 CCAGCCATGTATACAATGACATCAA 59.468 40.000 10.14 0.00 34.01 2.57
144 145 5.065235 CCAGCCATGTATACAATGACATCA 58.935 41.667 10.14 0.00 34.01 3.07
145 146 4.083110 GCCAGCCATGTATACAATGACATC 60.083 45.833 10.14 0.00 34.01 3.06
146 147 3.822735 GCCAGCCATGTATACAATGACAT 59.177 43.478 10.14 0.00 36.73 3.06
147 148 3.213506 GCCAGCCATGTATACAATGACA 58.786 45.455 10.14 0.00 0.00 3.58
148 149 2.224079 CGCCAGCCATGTATACAATGAC 59.776 50.000 10.14 2.02 0.00 3.06
149 150 2.103941 TCGCCAGCCATGTATACAATGA 59.896 45.455 10.14 0.00 0.00 2.57
150 151 2.481568 CTCGCCAGCCATGTATACAATG 59.518 50.000 10.14 8.68 0.00 2.82
151 152 2.368548 TCTCGCCAGCCATGTATACAAT 59.631 45.455 10.14 0.00 0.00 2.71
152 153 1.760029 TCTCGCCAGCCATGTATACAA 59.240 47.619 10.14 0.00 0.00 2.41
153 154 1.408969 TCTCGCCAGCCATGTATACA 58.591 50.000 8.27 8.27 0.00 2.29
154 155 2.289072 ACATCTCGCCAGCCATGTATAC 60.289 50.000 0.00 0.00 0.00 1.47
155 156 1.970640 ACATCTCGCCAGCCATGTATA 59.029 47.619 0.00 0.00 0.00 1.47
156 157 0.761187 ACATCTCGCCAGCCATGTAT 59.239 50.000 0.00 0.00 0.00 2.29
157 158 1.408969 TACATCTCGCCAGCCATGTA 58.591 50.000 0.00 0.00 31.83 2.29
158 159 0.541392 TTACATCTCGCCAGCCATGT 59.459 50.000 0.00 0.00 33.95 3.21
159 160 1.331756 GTTTACATCTCGCCAGCCATG 59.668 52.381 0.00 0.00 0.00 3.66
160 161 1.668419 GTTTACATCTCGCCAGCCAT 58.332 50.000 0.00 0.00 0.00 4.40
161 162 0.739462 CGTTTACATCTCGCCAGCCA 60.739 55.000 0.00 0.00 0.00 4.75
162 163 0.459585 TCGTTTACATCTCGCCAGCC 60.460 55.000 0.00 0.00 0.00 4.85
163 164 0.924090 CTCGTTTACATCTCGCCAGC 59.076 55.000 0.00 0.00 0.00 4.85
164 165 1.920574 CACTCGTTTACATCTCGCCAG 59.079 52.381 0.00 0.00 0.00 4.85
165 166 1.271379 ACACTCGTTTACATCTCGCCA 59.729 47.619 0.00 0.00 0.00 5.69
166 167 1.992170 ACACTCGTTTACATCTCGCC 58.008 50.000 0.00 0.00 0.00 5.54
167 168 3.542704 CACTACACTCGTTTACATCTCGC 59.457 47.826 0.00 0.00 0.00 5.03
168 169 3.542704 GCACTACACTCGTTTACATCTCG 59.457 47.826 0.00 0.00 0.00 4.04
169 170 3.858238 GGCACTACACTCGTTTACATCTC 59.142 47.826 0.00 0.00 0.00 2.75
170 171 3.672511 CGGCACTACACTCGTTTACATCT 60.673 47.826 0.00 0.00 0.00 2.90
171 172 2.597305 CGGCACTACACTCGTTTACATC 59.403 50.000 0.00 0.00 0.00 3.06
172 173 2.602878 CGGCACTACACTCGTTTACAT 58.397 47.619 0.00 0.00 0.00 2.29
173 174 1.336148 CCGGCACTACACTCGTTTACA 60.336 52.381 0.00 0.00 0.00 2.41
174 175 1.336240 ACCGGCACTACACTCGTTTAC 60.336 52.381 0.00 0.00 0.00 2.01
175 176 0.961019 ACCGGCACTACACTCGTTTA 59.039 50.000 0.00 0.00 0.00 2.01
176 177 0.105408 AACCGGCACTACACTCGTTT 59.895 50.000 0.00 0.00 0.00 3.60
177 178 0.105408 AAACCGGCACTACACTCGTT 59.895 50.000 0.00 0.00 0.00 3.85
178 179 0.105408 AAAACCGGCACTACACTCGT 59.895 50.000 0.00 0.00 0.00 4.18
179 180 1.223187 AAAAACCGGCACTACACTCG 58.777 50.000 0.00 0.00 0.00 4.18
200 201 2.228925 GTGCCGGTAACAGGGTAAAAA 58.771 47.619 1.90 0.00 0.00 1.94
201 202 1.545204 GGTGCCGGTAACAGGGTAAAA 60.545 52.381 1.28 0.00 0.00 1.52
202 203 0.036590 GGTGCCGGTAACAGGGTAAA 59.963 55.000 1.28 0.00 0.00 2.01
203 204 1.678724 GGTGCCGGTAACAGGGTAA 59.321 57.895 1.28 0.00 0.00 2.85
204 205 2.292559 GGGTGCCGGTAACAGGGTA 61.293 63.158 10.62 0.00 0.00 3.69
205 206 3.643554 GGGTGCCGGTAACAGGGT 61.644 66.667 10.62 0.00 0.00 4.34
206 207 4.770874 CGGGTGCCGGTAACAGGG 62.771 72.222 10.62 0.00 44.15 4.45
216 217 4.947147 TTCACTGTGCCGGGTGCC 62.947 66.667 2.18 0.00 40.16 5.01
217 218 3.357079 CTTCACTGTGCCGGGTGC 61.357 66.667 2.18 0.00 41.77 5.01
218 219 0.817634 TTTCTTCACTGTGCCGGGTG 60.818 55.000 2.18 2.34 35.06 4.61
219 220 0.110486 ATTTCTTCACTGTGCCGGGT 59.890 50.000 2.18 0.00 0.00 5.28
220 221 0.804989 GATTTCTTCACTGTGCCGGG 59.195 55.000 2.18 0.00 0.00 5.73
221 222 0.804989 GGATTTCTTCACTGTGCCGG 59.195 55.000 2.12 0.00 0.00 6.13
222 223 1.197721 GTGGATTTCTTCACTGTGCCG 59.802 52.381 2.12 0.00 0.00 5.69
223 224 2.227388 CTGTGGATTTCTTCACTGTGCC 59.773 50.000 2.12 0.00 35.15 5.01
224 225 2.351157 GCTGTGGATTTCTTCACTGTGC 60.351 50.000 2.12 0.00 35.95 4.57
225 226 2.880268 TGCTGTGGATTTCTTCACTGTG 59.120 45.455 0.17 0.17 35.95 3.66
226 227 3.144506 CTGCTGTGGATTTCTTCACTGT 58.855 45.455 0.00 0.00 35.95 3.55
227 228 3.405831 TCTGCTGTGGATTTCTTCACTG 58.594 45.455 0.00 0.00 36.40 3.66
228 229 3.558746 CCTCTGCTGTGGATTTCTTCACT 60.559 47.826 5.83 0.00 35.15 3.41
229 230 2.746362 CCTCTGCTGTGGATTTCTTCAC 59.254 50.000 5.83 0.00 34.71 3.18
230 231 2.877300 GCCTCTGCTGTGGATTTCTTCA 60.877 50.000 15.09 0.00 33.53 3.02
231 232 1.742268 GCCTCTGCTGTGGATTTCTTC 59.258 52.381 15.09 0.00 33.53 2.87
232 233 1.074405 TGCCTCTGCTGTGGATTTCTT 59.926 47.619 15.09 0.00 38.71 2.52
233 234 0.694771 TGCCTCTGCTGTGGATTTCT 59.305 50.000 15.09 0.00 38.71 2.52
234 235 1.093159 CTGCCTCTGCTGTGGATTTC 58.907 55.000 15.09 0.00 38.71 2.17
235 236 0.694771 TCTGCCTCTGCTGTGGATTT 59.305 50.000 15.09 0.00 38.71 2.17
236 237 0.694771 TTCTGCCTCTGCTGTGGATT 59.305 50.000 15.09 0.00 38.71 3.01
237 238 0.252479 CTTCTGCCTCTGCTGTGGAT 59.748 55.000 15.09 0.00 38.71 3.41
238 239 1.675801 CTTCTGCCTCTGCTGTGGA 59.324 57.895 15.09 0.89 38.71 4.02
239 240 2.039405 GCTTCTGCCTCTGCTGTGG 61.039 63.158 7.29 7.29 38.71 4.17
240 241 1.299562 CTGCTTCTGCCTCTGCTGTG 61.300 60.000 0.00 0.00 38.71 3.66
241 242 1.003597 CTGCTTCTGCCTCTGCTGT 60.004 57.895 0.00 0.00 38.71 4.40
242 243 0.741574 CTCTGCTTCTGCCTCTGCTG 60.742 60.000 0.00 0.00 38.71 4.41
243 244 1.597989 CTCTGCTTCTGCCTCTGCT 59.402 57.895 0.00 0.00 38.71 4.24
244 245 2.107903 GCTCTGCTTCTGCCTCTGC 61.108 63.158 0.00 0.00 38.71 4.26
245 246 0.321387 TTGCTCTGCTTCTGCCTCTG 60.321 55.000 0.00 0.00 38.71 3.35
246 247 0.399454 TTTGCTCTGCTTCTGCCTCT 59.601 50.000 0.00 0.00 38.71 3.69
362 370 0.031178 AAAGTGCGCAGGCTTTTCTG 59.969 50.000 12.22 0.00 40.82 3.02
405 413 2.534903 GCATCGAAAGGCTACGGGC 61.535 63.158 12.59 12.45 40.90 6.13
437 450 0.944311 GCTGCCGTTTCAGAGTTCGA 60.944 55.000 0.00 0.00 36.19 3.71
498 513 1.544691 GCACGGAAACTAGTCCAGAGA 59.455 52.381 0.00 0.00 37.56 3.10
499 514 1.404315 GGCACGGAAACTAGTCCAGAG 60.404 57.143 0.00 0.00 37.56 3.35
500 515 0.606604 GGCACGGAAACTAGTCCAGA 59.393 55.000 0.00 0.00 37.56 3.86
501 516 0.391263 GGGCACGGAAACTAGTCCAG 60.391 60.000 0.00 0.00 37.56 3.86
592 613 3.085947 CAGCAGCCTGGCTAGGGA 61.086 66.667 22.90 0.00 43.68 4.20
593 614 2.202236 TTTCAGCAGCCTGGCTAGGG 62.202 60.000 22.90 13.23 43.68 3.53
600 621 2.019984 GGATAAGGTTTCAGCAGCCTG 58.980 52.381 0.00 0.00 40.54 4.85
608 629 5.514834 CCTCTGTTTCTGGGATAAGGTTTCA 60.515 44.000 0.00 0.00 0.00 2.69
636 657 2.511145 CGCTCTTCTCCTGCTGCC 60.511 66.667 0.00 0.00 0.00 4.85
659 680 1.069823 AGCACATAGATTCTGGAGCCG 59.930 52.381 0.00 0.00 0.00 5.52
660 681 2.368221 AGAGCACATAGATTCTGGAGCC 59.632 50.000 0.00 0.00 0.00 4.70
661 682 3.069300 TCAGAGCACATAGATTCTGGAGC 59.931 47.826 0.00 0.00 38.05 4.70
662 683 4.262121 CCTCAGAGCACATAGATTCTGGAG 60.262 50.000 0.00 0.00 38.05 3.86
663 684 3.640498 CCTCAGAGCACATAGATTCTGGA 59.360 47.826 0.00 0.00 38.05 3.86
664 685 3.640498 TCCTCAGAGCACATAGATTCTGG 59.360 47.826 0.00 0.00 38.05 3.86
668 689 3.492309 CGCTTCCTCAGAGCACATAGATT 60.492 47.826 0.00 0.00 40.13 2.40
673 694 0.175302 CTCGCTTCCTCAGAGCACAT 59.825 55.000 0.00 0.00 40.13 3.21
823 844 1.056660 AGGCGAGGAAGAAGAACCAA 58.943 50.000 0.00 0.00 0.00 3.67
827 848 0.036952 CAGCAGGCGAGGAAGAAGAA 60.037 55.000 0.00 0.00 0.00 2.52
868 889 3.212682 CGCGGCTCCTCTGCTCTA 61.213 66.667 0.00 0.00 44.92 2.43
908 929 3.244422 TGGAAAAACAGACGGTGAGCTAT 60.244 43.478 0.00 0.00 0.00 2.97
954 978 3.618594 CAGCATGCGTACATATATGTCCC 59.381 47.826 21.49 12.47 41.97 4.46
974 999 2.202260 CAACGCGTCATGCAGCAG 60.202 61.111 14.44 7.45 46.97 4.24
975 1000 3.725459 CCAACGCGTCATGCAGCA 61.725 61.111 14.44 0.00 46.97 4.41
976 1001 3.651480 GACCAACGCGTCATGCAGC 62.651 63.158 14.44 0.00 46.97 5.25
977 1002 2.476051 GACCAACGCGTCATGCAG 59.524 61.111 14.44 0.00 46.97 4.41
994 1019 3.073678 TCACCTGAACAATCATCAACGG 58.926 45.455 0.00 0.00 34.37 4.44
995 1020 3.425359 GCTCACCTGAACAATCATCAACG 60.425 47.826 0.00 0.00 34.37 4.10
996 1021 3.425359 CGCTCACCTGAACAATCATCAAC 60.425 47.826 0.00 0.00 34.37 3.18
997 1022 2.743664 CGCTCACCTGAACAATCATCAA 59.256 45.455 0.00 0.00 34.37 2.57
998 1023 2.349590 CGCTCACCTGAACAATCATCA 58.650 47.619 0.00 0.00 34.37 3.07
999 1024 1.667724 CCGCTCACCTGAACAATCATC 59.332 52.381 0.00 0.00 34.37 2.92
1000 1025 1.679944 CCCGCTCACCTGAACAATCAT 60.680 52.381 0.00 0.00 34.37 2.45
1319 1361 4.260784 GCATGCGGACCTTATTTCTACTTG 60.261 45.833 0.00 0.00 0.00 3.16
1372 1415 2.540101 CTGCCGCAGCTTGTATTACTAC 59.460 50.000 7.61 0.00 40.80 2.73
1373 1416 2.821546 CTGCCGCAGCTTGTATTACTA 58.178 47.619 7.61 0.00 40.80 1.82
1374 1417 1.656652 CTGCCGCAGCTTGTATTACT 58.343 50.000 7.61 0.00 40.80 2.24


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

AutoCloner maintained by Alex Coulton.