Multiple sequence alignment - TraesCS7B01G027400

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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 TraesCS7B01G027400 chr7B 100.000 2219 0 0 1 2219 26215901 26213683 0.000000e+00 4098
1 TraesCS7B01G027400 chr7B 92.105 1064 40 6 692 1746 26236693 26235665 0.000000e+00 1459
2 TraesCS7B01G027400 chr7B 89.505 505 44 4 198 693 26237444 26236940 4.020000e-177 630
3 TraesCS7B01G027400 chr7B 95.025 201 9 1 1 201 549674819 549674620 4.600000e-82 315
4 TraesCS7B01G027400 chr7D 90.008 1181 75 12 578 1746 78882973 78881824 0.000000e+00 1487
5 TraesCS7B01G027400 chr7D 90.372 914 59 7 1000 1906 78865525 78864634 0.000000e+00 1173
6 TraesCS7B01G027400 chr7D 90.145 619 46 7 1000 1616 78844340 78843735 0.000000e+00 791
7 TraesCS7B01G027400 chr7A 90.406 886 43 15 1000 1864 81949345 81948481 0.000000e+00 1127
8 TraesCS7B01G027400 chr7A 83.918 342 30 9 1878 2204 81945069 81944738 9.960000e-79 303
9 TraesCS7B01G027400 chr6D 96.429 196 7 0 1 196 178698282 178698477 7.640000e-85 324
10 TraesCS7B01G027400 chr4D 96.000 200 7 1 1 200 55439929 55439731 7.640000e-85 324
11 TraesCS7B01G027400 chr2A 96.392 194 7 0 1 194 462609867 462609674 9.890000e-84 320
12 TraesCS7B01G027400 chr5D 95.500 200 8 1 1 200 400645632 400645434 3.560000e-83 318
13 TraesCS7B01G027400 chr2D 94.660 206 9 2 1 206 132153946 132153743 3.560000e-83 318
14 TraesCS7B01G027400 chr2D 95.500 200 8 1 1 200 433771944 433772142 3.560000e-83 318
15 TraesCS7B01G027400 chr3D 94.203 207 10 2 1 207 256974226 256974022 4.600000e-82 315
16 TraesCS7B01G027400 chr3B 95.025 201 8 2 1 200 307244082 307244281 4.600000e-82 315


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 TraesCS7B01G027400 chr7B 26213683 26215901 2218 True 4098.0 4098 100.000 1 2219 1 chr7B.!!$R1 2218
1 TraesCS7B01G027400 chr7B 26235665 26237444 1779 True 1044.5 1459 90.805 198 1746 2 chr7B.!!$R3 1548
2 TraesCS7B01G027400 chr7D 78881824 78882973 1149 True 1487.0 1487 90.008 578 1746 1 chr7D.!!$R3 1168
3 TraesCS7B01G027400 chr7D 78864634 78865525 891 True 1173.0 1173 90.372 1000 1906 1 chr7D.!!$R2 906
4 TraesCS7B01G027400 chr7D 78843735 78844340 605 True 791.0 791 90.145 1000 1616 1 chr7D.!!$R1 616
5 TraesCS7B01G027400 chr7A 81944738 81949345 4607 True 715.0 1127 87.162 1000 2204 2 chr7A.!!$R1 1204

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
748 1006 0.034059 CCTGCTTGTCGAGACACCTT 59.966 55.0 5.3 0.0 41.67 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 2008 0.109723 ACAGGTTGGCGTATGGTTGT 59.89 50.0 0.0 0.0 0.0 3.32 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
29 30 8.773033 AATAAAGATTGACCAATATCCAAGCT 57.227 30.769 0.00 0.00 38.05 3.74
30 31 6.461110 AAAGATTGACCAATATCCAAGCTG 57.539 37.500 0.00 0.00 36.75 4.24
31 32 5.378230 AGATTGACCAATATCCAAGCTGA 57.622 39.130 0.00 0.00 35.53 4.26
32 33 5.759059 AGATTGACCAATATCCAAGCTGAA 58.241 37.500 0.00 0.00 35.53 3.02
33 34 6.189859 AGATTGACCAATATCCAAGCTGAAA 58.810 36.000 0.00 0.00 35.53 2.69
34 35 6.664816 AGATTGACCAATATCCAAGCTGAAAA 59.335 34.615 0.00 0.00 35.53 2.29
35 36 6.855763 TTGACCAATATCCAAGCTGAAAAT 57.144 33.333 0.00 0.00 0.00 1.82
36 37 7.953005 TTGACCAATATCCAAGCTGAAAATA 57.047 32.000 0.00 0.00 0.00 1.40
37 38 8.537728 TTGACCAATATCCAAGCTGAAAATAT 57.462 30.769 0.00 0.00 0.00 1.28
38 39 9.639563 TTGACCAATATCCAAGCTGAAAATATA 57.360 29.630 0.00 0.00 0.00 0.86
39 40 9.812347 TGACCAATATCCAAGCTGAAAATATAT 57.188 29.630 0.00 0.00 0.00 0.86
48 49 8.840321 TCCAAGCTGAAAATATATAAGTGAAGC 58.160 33.333 0.00 0.00 0.00 3.86
49 50 8.623903 CCAAGCTGAAAATATATAAGTGAAGCA 58.376 33.333 10.75 0.00 0.00 3.91
50 51 9.443283 CAAGCTGAAAATATATAAGTGAAGCAC 57.557 33.333 10.75 0.00 34.10 4.40
51 52 8.737168 AGCTGAAAATATATAAGTGAAGCACA 57.263 30.769 10.75 0.00 36.74 4.57
61 62 1.955762 GTGAAGCACACGAAGCATTC 58.044 50.000 0.00 0.00 39.78 2.67
62 63 1.532868 GTGAAGCACACGAAGCATTCT 59.467 47.619 0.00 0.00 39.89 2.40
63 64 2.736721 GTGAAGCACACGAAGCATTCTA 59.263 45.455 0.00 0.00 39.89 2.10
64 65 3.372206 GTGAAGCACACGAAGCATTCTAT 59.628 43.478 0.00 0.00 39.89 1.98
65 66 4.566759 GTGAAGCACACGAAGCATTCTATA 59.433 41.667 0.00 0.00 39.89 1.31
66 67 5.063438 GTGAAGCACACGAAGCATTCTATAA 59.937 40.000 0.00 0.00 39.89 0.98
67 68 5.641636 TGAAGCACACGAAGCATTCTATAAA 59.358 36.000 0.00 0.00 44.75 1.40
68 69 5.725110 AGCACACGAAGCATTCTATAAAG 57.275 39.130 0.00 0.00 44.75 1.85
69 70 4.034510 AGCACACGAAGCATTCTATAAAGC 59.965 41.667 0.00 0.00 44.75 3.51
70 71 4.786609 GCACACGAAGCATTCTATAAAGCC 60.787 45.833 0.00 0.00 44.75 4.35
71 72 4.332543 CACACGAAGCATTCTATAAAGCCA 59.667 41.667 0.00 0.00 44.75 4.75
72 73 5.008019 CACACGAAGCATTCTATAAAGCCAT 59.992 40.000 0.00 0.00 44.75 4.40
73 74 6.202762 CACACGAAGCATTCTATAAAGCCATA 59.797 38.462 0.00 0.00 44.75 2.74
74 75 6.202954 ACACGAAGCATTCTATAAAGCCATAC 59.797 38.462 0.00 0.00 44.75 2.39
75 76 6.425114 CACGAAGCATTCTATAAAGCCATACT 59.575 38.462 0.00 0.00 44.75 2.12
76 77 6.647067 ACGAAGCATTCTATAAAGCCATACTC 59.353 38.462 0.00 0.00 44.75 2.59
77 78 6.646653 CGAAGCATTCTATAAAGCCATACTCA 59.353 38.462 0.00 0.00 44.75 3.41
78 79 7.171508 CGAAGCATTCTATAAAGCCATACTCAA 59.828 37.037 0.00 0.00 44.75 3.02
79 80 8.752005 AAGCATTCTATAAAGCCATACTCAAA 57.248 30.769 0.00 0.00 29.49 2.69
80 81 8.752005 AGCATTCTATAAAGCCATACTCAAAA 57.248 30.769 0.00 0.00 29.49 2.44
81 82 8.844244 AGCATTCTATAAAGCCATACTCAAAAG 58.156 33.333 0.00 0.00 29.49 2.27
82 83 8.840321 GCATTCTATAAAGCCATACTCAAAAGA 58.160 33.333 0.00 0.00 0.00 2.52
91 92 8.635765 AAGCCATACTCAAAAGATTTAAGTGA 57.364 30.769 4.41 0.00 0.00 3.41
92 93 8.635765 AGCCATACTCAAAAGATTTAAGTGAA 57.364 30.769 4.41 0.00 0.00 3.18
93 94 8.734386 AGCCATACTCAAAAGATTTAAGTGAAG 58.266 33.333 4.41 0.00 0.00 3.02
94 95 7.486232 GCCATACTCAAAAGATTTAAGTGAAGC 59.514 37.037 4.41 0.00 0.00 3.86
95 96 8.514594 CCATACTCAAAAGATTTAAGTGAAGCA 58.485 33.333 0.00 0.00 0.00 3.91
96 97 9.334693 CATACTCAAAAGATTTAAGTGAAGCAC 57.665 33.333 0.00 0.00 34.10 4.40
97 98 7.333528 ACTCAAAAGATTTAAGTGAAGCACA 57.666 32.000 0.00 0.00 36.74 4.57
98 99 7.771183 ACTCAAAAGATTTAAGTGAAGCACAA 58.229 30.769 0.00 0.00 36.74 3.33
99 100 8.250332 ACTCAAAAGATTTAAGTGAAGCACAAA 58.750 29.630 0.00 0.00 36.74 2.83
100 101 8.633075 TCAAAAGATTTAAGTGAAGCACAAAG 57.367 30.769 0.00 0.00 36.74 2.77
101 102 8.465999 TCAAAAGATTTAAGTGAAGCACAAAGA 58.534 29.630 0.00 0.00 36.74 2.52
102 103 8.749499 CAAAAGATTTAAGTGAAGCACAAAGAG 58.251 33.333 0.00 0.00 36.74 2.85
103 104 6.006759 AGATTTAAGTGAAGCACAAAGAGC 57.993 37.500 0.00 0.00 36.74 4.09
104 105 5.532406 AGATTTAAGTGAAGCACAAAGAGCA 59.468 36.000 0.00 0.00 36.74 4.26
105 106 5.772825 TTTAAGTGAAGCACAAAGAGCAT 57.227 34.783 0.00 0.00 36.74 3.79
106 107 5.772825 TTAAGTGAAGCACAAAGAGCATT 57.227 34.783 0.00 0.00 36.74 3.56
107 108 3.911661 AGTGAAGCACAAAGAGCATTC 57.088 42.857 0.00 0.00 36.74 2.67
108 109 3.484407 AGTGAAGCACAAAGAGCATTCT 58.516 40.909 0.00 0.00 36.74 2.40
109 110 4.645535 AGTGAAGCACAAAGAGCATTCTA 58.354 39.130 0.00 0.00 36.74 2.10
110 111 5.251764 AGTGAAGCACAAAGAGCATTCTAT 58.748 37.500 0.00 0.00 36.74 1.98
111 112 6.409704 AGTGAAGCACAAAGAGCATTCTATA 58.590 36.000 0.00 0.00 36.74 1.31
112 113 6.881065 AGTGAAGCACAAAGAGCATTCTATAA 59.119 34.615 0.00 0.00 36.74 0.98
113 114 7.391554 AGTGAAGCACAAAGAGCATTCTATAAA 59.608 33.333 0.00 0.00 36.74 1.40
114 115 7.695618 GTGAAGCACAAAGAGCATTCTATAAAG 59.304 37.037 0.00 0.00 34.08 1.85
115 116 6.129053 AGCACAAAGAGCATTCTATAAAGC 57.871 37.500 0.00 0.00 31.96 3.51
116 117 5.067023 AGCACAAAGAGCATTCTATAAAGCC 59.933 40.000 0.00 0.00 31.96 4.35
117 118 5.163622 GCACAAAGAGCATTCTATAAAGCCA 60.164 40.000 0.00 0.00 31.96 4.75
118 119 6.460676 GCACAAAGAGCATTCTATAAAGCCAT 60.461 38.462 0.00 0.00 31.96 4.40
119 120 7.255242 GCACAAAGAGCATTCTATAAAGCCATA 60.255 37.037 0.00 0.00 31.96 2.74
120 121 8.072567 CACAAAGAGCATTCTATAAAGCCATAC 58.927 37.037 0.00 0.00 31.96 2.39
121 122 7.995488 ACAAAGAGCATTCTATAAAGCCATACT 59.005 33.333 0.00 0.00 31.96 2.12
122 123 8.502387 CAAAGAGCATTCTATAAAGCCATACTC 58.498 37.037 0.00 0.00 31.96 2.59
123 124 7.308450 AGAGCATTCTATAAAGCCATACTCA 57.692 36.000 0.00 0.00 29.49 3.41
124 125 7.739825 AGAGCATTCTATAAAGCCATACTCAA 58.260 34.615 0.00 0.00 29.49 3.02
125 126 8.213679 AGAGCATTCTATAAAGCCATACTCAAA 58.786 33.333 0.00 0.00 29.49 2.69
126 127 8.752005 AGCATTCTATAAAGCCATACTCAAAA 57.248 30.769 0.00 0.00 29.49 2.44
127 128 8.844244 AGCATTCTATAAAGCCATACTCAAAAG 58.156 33.333 0.00 0.00 29.49 2.27
128 129 8.840321 GCATTCTATAAAGCCATACTCAAAAGA 58.160 33.333 0.00 0.00 0.00 2.52
137 138 8.635765 AAGCCATACTCAAAAGATTTAAGTGA 57.364 30.769 4.41 0.00 0.00 3.41
138 139 8.635765 AGCCATACTCAAAAGATTTAAGTGAA 57.364 30.769 4.41 0.00 0.00 3.18
139 140 8.734386 AGCCATACTCAAAAGATTTAAGTGAAG 58.266 33.333 4.41 0.00 0.00 3.02
140 141 7.486232 GCCATACTCAAAAGATTTAAGTGAAGC 59.514 37.037 4.41 0.00 0.00 3.86
141 142 8.514594 CCATACTCAAAAGATTTAAGTGAAGCA 58.485 33.333 0.00 0.00 0.00 3.91
142 143 9.334693 CATACTCAAAAGATTTAAGTGAAGCAC 57.665 33.333 0.00 0.00 34.10 4.40
143 144 7.333528 ACTCAAAAGATTTAAGTGAAGCACA 57.666 32.000 0.00 0.00 36.74 4.57
144 145 7.945134 ACTCAAAAGATTTAAGTGAAGCACAT 58.055 30.769 0.00 0.00 36.74 3.21
145 146 7.864379 ACTCAAAAGATTTAAGTGAAGCACATG 59.136 33.333 0.00 0.00 36.74 3.21
146 147 7.939782 TCAAAAGATTTAAGTGAAGCACATGA 58.060 30.769 0.00 0.00 36.74 3.07
147 148 8.412456 TCAAAAGATTTAAGTGAAGCACATGAA 58.588 29.630 0.00 0.00 36.74 2.57
148 149 8.697067 CAAAAGATTTAAGTGAAGCACATGAAG 58.303 33.333 0.00 0.00 36.74 3.02
149 150 5.947443 AGATTTAAGTGAAGCACATGAAGC 58.053 37.500 0.00 2.85 36.74 3.86
150 151 5.474532 AGATTTAAGTGAAGCACATGAAGCA 59.525 36.000 15.23 0.00 36.74 3.91
151 152 5.710513 TTTAAGTGAAGCACATGAAGCAT 57.289 34.783 15.23 5.23 36.74 3.79
152 153 5.710513 TTAAGTGAAGCACATGAAGCATT 57.289 34.783 15.23 7.96 36.74 3.56
153 154 3.844577 AGTGAAGCACATGAAGCATTC 57.155 42.857 15.23 14.44 40.48 2.67
154 155 2.490903 AGTGAAGCACATGAAGCATTCC 59.509 45.455 15.23 10.12 39.77 3.01
155 156 2.229543 GTGAAGCACATGAAGCATTCCA 59.770 45.455 15.23 6.22 38.16 3.53
156 157 3.093814 TGAAGCACATGAAGCATTCCAT 58.906 40.909 15.23 0.00 46.93 3.41
157 158 4.096833 GTGAAGCACATGAAGCATTCCATA 59.903 41.667 15.23 1.93 38.16 2.74
158 159 4.705991 TGAAGCACATGAAGCATTCCATAA 59.294 37.500 15.23 1.68 46.93 1.90
159 160 5.185442 TGAAGCACATGAAGCATTCCATAAA 59.815 36.000 15.23 1.42 46.93 1.40
160 161 5.864418 AGCACATGAAGCATTCCATAAAT 57.136 34.783 15.23 0.00 46.93 1.40
161 162 5.839621 AGCACATGAAGCATTCCATAAATC 58.160 37.500 15.23 0.00 46.93 2.17
162 163 5.361571 AGCACATGAAGCATTCCATAAATCA 59.638 36.000 15.23 0.00 46.93 2.57
163 164 6.044046 GCACATGAAGCATTCCATAAATCAA 58.956 36.000 0.00 0.00 46.93 2.57
164 165 6.704493 GCACATGAAGCATTCCATAAATCAAT 59.296 34.615 0.00 0.00 46.93 2.57
165 166 7.307160 GCACATGAAGCATTCCATAAATCAATG 60.307 37.037 0.00 0.00 46.93 2.82
166 167 7.923878 CACATGAAGCATTCCATAAATCAATGA 59.076 33.333 0.00 0.00 46.93 2.57
167 168 8.479689 ACATGAAGCATTCCATAAATCAATGAA 58.520 29.630 0.00 0.00 46.93 2.57
168 169 8.761497 CATGAAGCATTCCATAAATCAATGAAC 58.239 33.333 0.00 0.00 46.93 3.18
169 170 6.974048 TGAAGCATTCCATAAATCAATGAACG 59.026 34.615 0.00 0.00 46.93 3.95
170 171 6.698008 AGCATTCCATAAATCAATGAACGA 57.302 33.333 0.00 0.00 30.31 3.85
171 172 6.498304 AGCATTCCATAAATCAATGAACGAC 58.502 36.000 0.00 0.00 30.31 4.34
172 173 6.319658 AGCATTCCATAAATCAATGAACGACT 59.680 34.615 0.00 0.00 30.31 4.18
173 174 7.498900 AGCATTCCATAAATCAATGAACGACTA 59.501 33.333 0.00 0.00 30.31 2.59
174 175 8.292448 GCATTCCATAAATCAATGAACGACTAT 58.708 33.333 0.00 0.00 30.31 2.12
175 176 9.817365 CATTCCATAAATCAATGAACGACTATC 57.183 33.333 0.00 0.00 30.31 2.08
176 177 9.784531 ATTCCATAAATCAATGAACGACTATCT 57.215 29.630 0.00 0.00 0.00 1.98
177 178 8.818141 TCCATAAATCAATGAACGACTATCTC 57.182 34.615 0.00 0.00 0.00 2.75
178 179 8.421002 TCCATAAATCAATGAACGACTATCTCA 58.579 33.333 0.00 0.00 0.00 3.27
179 180 9.212641 CCATAAATCAATGAACGACTATCTCAT 57.787 33.333 0.00 0.00 0.00 2.90
185 186 7.585867 TCAATGAACGACTATCTCATACTAGC 58.414 38.462 0.00 0.00 0.00 3.42
186 187 7.228706 TCAATGAACGACTATCTCATACTAGCA 59.771 37.037 0.00 0.00 0.00 3.49
187 188 7.695480 ATGAACGACTATCTCATACTAGCAT 57.305 36.000 0.00 0.00 0.00 3.79
188 189 6.903419 TGAACGACTATCTCATACTAGCATG 58.097 40.000 0.00 0.00 0.00 4.06
189 190 6.710744 TGAACGACTATCTCATACTAGCATGA 59.289 38.462 5.52 5.52 33.88 3.07
190 191 7.391833 TGAACGACTATCTCATACTAGCATGAT 59.608 37.037 6.10 0.00 34.50 2.45
191 192 7.082700 ACGACTATCTCATACTAGCATGATG 57.917 40.000 6.10 1.94 34.50 3.07
192 193 5.970612 CGACTATCTCATACTAGCATGATGC 59.029 44.000 9.89 9.89 45.46 3.91
208 209 7.792383 GCATGATGCATATAAGTGACAATTC 57.208 36.000 13.36 0.00 44.26 2.17
218 219 9.689075 CATATAAGTGACAATTCTGTACAAACG 57.311 33.333 0.00 0.00 35.30 3.60
224 225 8.280497 AGTGACAATTCTGTACAAACGATTTAC 58.720 33.333 0.00 0.00 35.30 2.01
227 228 9.953825 GACAATTCTGTACAAACGATTTACTAG 57.046 33.333 0.00 0.00 35.30 2.57
308 311 9.784531 TCAATATTTAAACTGGGCATTTTTGAA 57.215 25.926 0.00 0.00 0.00 2.69
316 319 8.688747 AAACTGGGCATTTTTGAATTTCAATA 57.311 26.923 12.39 5.51 36.11 1.90
320 323 9.962783 CTGGGCATTTTTGAATTTCAATAAAAA 57.037 25.926 15.73 12.29 36.11 1.94
427 431 8.756486 AATCATGTGATCAACTTCCATAATGA 57.244 30.769 0.00 0.00 32.75 2.57
445 449 9.859427 CCATAATGACAGAAAGCTCAAATTTTA 57.141 29.630 0.00 0.00 0.00 1.52
453 457 9.515226 ACAGAAAGCTCAAATTTTATAGGTACA 57.485 29.630 0.00 0.00 0.00 2.90
529 533 8.996651 AAATTACTCATTTAGATTACCCCCAG 57.003 34.615 0.00 0.00 32.90 4.45
532 536 6.749036 ACTCATTTAGATTACCCCCAGTAG 57.251 41.667 0.00 0.00 30.92 2.57
546 550 4.599241 CCCCCAGTAGAAAGTATGGATCAT 59.401 45.833 0.00 0.00 34.60 2.45
555 562 6.349300 AGAAAGTATGGATCATTGCTAACGT 58.651 36.000 0.00 0.00 0.00 3.99
559 566 7.233389 AGTATGGATCATTGCTAACGTAGAT 57.767 36.000 0.00 0.00 0.00 1.98
567 574 2.883574 TGCTAACGTAGATGGTTTCCG 58.116 47.619 0.00 0.00 0.00 4.30
633 640 2.317040 GAGCCTAGCCCATGTACACTA 58.683 52.381 0.00 0.00 0.00 2.74
636 643 4.489737 AGCCTAGCCCATGTACACTATTA 58.510 43.478 0.00 0.00 0.00 0.98
690 700 1.407936 ATGTGATCCTCGTCCCTCTG 58.592 55.000 0.00 0.00 0.00 3.35
714 972 2.158871 ACTCTCACTAGACGGCTCCTAG 60.159 54.545 0.00 0.00 39.49 3.02
748 1006 0.034059 CCTGCTTGTCGAGACACCTT 59.966 55.000 5.30 0.00 41.67 3.50
865 1123 3.127589 TCAATGTCGTGTTCGTGTTCAT 58.872 40.909 0.00 0.00 38.33 2.57
882 1140 5.228635 GTGTTCATGCTTTATTTGATCAGCG 59.771 40.000 0.00 0.00 34.82 5.18
986 1245 5.226194 TCATTTGTTTCCCCTCCATTTTG 57.774 39.130 0.00 0.00 0.00 2.44
1461 1745 5.989777 AGTTGGATGTTGTACAGTTACAGAC 59.010 40.000 5.22 1.79 39.44 3.51
1462 1746 5.801531 TGGATGTTGTACAGTTACAGACT 57.198 39.130 5.22 0.00 39.44 3.24
1463 1747 5.779922 TGGATGTTGTACAGTTACAGACTC 58.220 41.667 5.22 0.00 39.44 3.36
1464 1748 4.857588 GGATGTTGTACAGTTACAGACTCG 59.142 45.833 5.22 0.00 39.44 4.18
1465 1749 4.906065 TGTTGTACAGTTACAGACTCGT 57.094 40.909 0.00 0.00 39.44 4.18
1466 1750 4.603985 TGTTGTACAGTTACAGACTCGTG 58.396 43.478 0.00 0.00 39.44 4.35
1467 1751 3.909776 TGTACAGTTACAGACTCGTGG 57.090 47.619 0.00 0.00 36.10 4.94
1468 1752 3.216800 TGTACAGTTACAGACTCGTGGT 58.783 45.455 0.00 0.00 36.10 4.16
1469 1753 4.388485 TGTACAGTTACAGACTCGTGGTA 58.612 43.478 0.00 0.00 36.10 3.25
1470 1754 3.911661 ACAGTTACAGACTCGTGGTAC 57.088 47.619 0.00 0.00 36.10 3.34
1471 1755 2.555757 ACAGTTACAGACTCGTGGTACC 59.444 50.000 4.43 4.43 36.10 3.34
1472 1756 2.555325 CAGTTACAGACTCGTGGTACCA 59.445 50.000 11.60 11.60 36.10 3.25
1519 1815 8.103948 AGATCAGTTTGACAATAAGTTCCTTG 57.896 34.615 0.00 0.00 0.00 3.61
1577 1877 4.931601 GGATCTCAATGTTTTCTTTTGGGC 59.068 41.667 0.00 0.00 0.00 5.36
1579 1879 3.070878 TCTCAATGTTTTCTTTTGGGCCC 59.929 43.478 17.59 17.59 0.00 5.80
1635 1952 6.045318 TGCTTGAGTAATTGATGCTAGAGTC 58.955 40.000 0.00 0.00 0.00 3.36
1783 2102 2.286872 CAATAGCTGCAGGAACAGAGG 58.713 52.381 17.12 0.00 40.25 3.69
1815 2134 0.955428 TTTGCTCTGACGCCATGGAC 60.955 55.000 18.40 5.97 0.00 4.02
1887 5604 2.711542 AGGAGCAAATTGGGTTAGTCG 58.288 47.619 0.00 0.00 0.00 4.18
1915 5632 2.567615 CCACCCTACTACAAGACTTGCT 59.432 50.000 15.24 5.45 0.00 3.91
1918 5635 4.081420 CACCCTACTACAAGACTTGCTGAT 60.081 45.833 15.24 0.00 0.00 2.90
1920 5637 4.355437 CCTACTACAAGACTTGCTGATCG 58.645 47.826 15.24 0.29 0.00 3.69
1925 5642 1.920574 CAAGACTTGCTGATCGTACGG 59.079 52.381 16.52 0.00 0.00 4.02
1930 5647 4.097437 AGACTTGCTGATCGTACGGAATAA 59.903 41.667 16.52 0.00 0.00 1.40
1940 5657 8.515473 TGATCGTACGGAATAATTCATTGTAG 57.485 34.615 16.52 0.00 0.00 2.74
1965 5682 7.015098 AGAGGTCAAGGAGTGAGACAATATATG 59.985 40.741 0.00 0.00 36.74 1.78
1971 5688 6.845908 AGGAGTGAGACAATATATGCCAAAT 58.154 36.000 0.00 0.00 0.00 2.32
1972 5689 6.713903 AGGAGTGAGACAATATATGCCAAATG 59.286 38.462 0.00 0.00 0.00 2.32
1973 5690 6.072286 GGAGTGAGACAATATATGCCAAATGG 60.072 42.308 0.00 0.00 38.53 3.16
1974 5691 6.604171 AGTGAGACAATATATGCCAAATGGA 58.396 36.000 2.98 0.00 37.39 3.41
1975 5692 7.062322 AGTGAGACAATATATGCCAAATGGAA 58.938 34.615 2.98 0.00 37.39 3.53
1976 5693 7.013655 AGTGAGACAATATATGCCAAATGGAAC 59.986 37.037 2.98 0.00 37.39 3.62
1977 5694 6.017192 TGAGACAATATATGCCAAATGGAACG 60.017 38.462 2.98 0.00 37.39 3.95
1984 5701 3.781079 TGCCAAATGGAACGATTCATC 57.219 42.857 2.98 0.00 37.39 2.92
1989 5706 3.287867 AATGGAACGATTCATCCTGCT 57.712 42.857 0.00 0.00 36.64 4.24
1996 5713 1.202687 CGATTCATCCTGCTGGCCTAA 60.203 52.381 3.32 0.00 0.00 2.69
2037 5754 7.475771 TTCAGTTTTGCCATGTTCATTAAAC 57.524 32.000 0.00 0.00 38.43 2.01
2038 5755 6.815089 TCAGTTTTGCCATGTTCATTAAACT 58.185 32.000 8.21 8.21 38.76 2.66
2039 5756 7.271511 TCAGTTTTGCCATGTTCATTAAACTT 58.728 30.769 10.09 0.00 38.76 2.66
2040 5757 7.437862 TCAGTTTTGCCATGTTCATTAAACTTC 59.562 33.333 10.09 0.00 38.76 3.01
2107 5826 2.067013 GACTGAGGCAACCGTACTTTC 58.933 52.381 0.00 0.00 37.17 2.62
2116 5835 3.249080 GCAACCGTACTTTCTTGTGCTAA 59.751 43.478 0.00 0.00 0.00 3.09
2117 5836 4.769215 CAACCGTACTTTCTTGTGCTAAC 58.231 43.478 0.00 0.00 0.00 2.34
2118 5837 4.062677 ACCGTACTTTCTTGTGCTAACA 57.937 40.909 0.00 0.00 0.00 2.41
2201 5933 3.299340 TTGTCGAACCTAGTTCTCTGC 57.701 47.619 5.97 0.00 40.05 4.26
2204 5936 1.819288 TCGAACCTAGTTCTCTGCAGG 59.181 52.381 15.13 4.77 40.05 4.85
2205 5937 1.819288 CGAACCTAGTTCTCTGCAGGA 59.181 52.381 15.13 7.36 40.05 3.86
2206 5938 2.428890 CGAACCTAGTTCTCTGCAGGAT 59.571 50.000 15.13 0.00 40.05 3.24
2207 5939 3.118956 CGAACCTAGTTCTCTGCAGGATT 60.119 47.826 15.13 4.73 40.05 3.01
2208 5940 4.438148 GAACCTAGTTCTCTGCAGGATTC 58.562 47.826 15.13 6.13 39.23 2.52
2209 5941 3.445008 ACCTAGTTCTCTGCAGGATTCA 58.555 45.455 15.13 0.00 32.25 2.57
2210 5942 3.840666 ACCTAGTTCTCTGCAGGATTCAA 59.159 43.478 15.13 0.00 32.25 2.69
2211 5943 4.081198 ACCTAGTTCTCTGCAGGATTCAAG 60.081 45.833 15.13 2.34 32.25 3.02
2212 5944 3.347077 AGTTCTCTGCAGGATTCAAGG 57.653 47.619 15.13 0.00 0.00 3.61
2213 5945 2.026449 AGTTCTCTGCAGGATTCAAGGG 60.026 50.000 15.13 0.00 0.00 3.95
2214 5946 0.254178 TCTCTGCAGGATTCAAGGGC 59.746 55.000 15.13 0.00 0.00 5.19
2215 5947 0.255318 CTCTGCAGGATTCAAGGGCT 59.745 55.000 15.13 0.00 0.00 5.19
2216 5948 0.254178 TCTGCAGGATTCAAGGGCTC 59.746 55.000 15.13 0.00 0.00 4.70
2217 5949 0.255318 CTGCAGGATTCAAGGGCTCT 59.745 55.000 5.57 0.00 0.00 4.09
2218 5950 0.700564 TGCAGGATTCAAGGGCTCTT 59.299 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.866655 AGCTTGGATATTGGTCAATCTTTATTA 57.133 29.630 0.00 0.00 32.50 0.98
4 5 8.636213 CAGCTTGGATATTGGTCAATCTTTATT 58.364 33.333 0.00 0.00 32.50 1.40
5 6 8.000709 TCAGCTTGGATATTGGTCAATCTTTAT 58.999 33.333 0.00 0.00 32.50 1.40
6 7 7.345691 TCAGCTTGGATATTGGTCAATCTTTA 58.654 34.615 0.00 0.00 32.50 1.85
7 8 6.189859 TCAGCTTGGATATTGGTCAATCTTT 58.810 36.000 0.00 0.00 32.50 2.52
8 9 5.759059 TCAGCTTGGATATTGGTCAATCTT 58.241 37.500 0.00 0.00 32.50 2.40
9 10 5.378230 TCAGCTTGGATATTGGTCAATCT 57.622 39.130 0.00 0.00 32.50 2.40
10 11 6.455360 TTTCAGCTTGGATATTGGTCAATC 57.545 37.500 0.00 0.00 32.50 2.67
11 12 6.855763 TTTTCAGCTTGGATATTGGTCAAT 57.144 33.333 1.65 1.65 34.93 2.57
12 13 6.855763 ATTTTCAGCTTGGATATTGGTCAA 57.144 33.333 0.00 0.00 0.00 3.18
13 14 9.812347 ATATATTTTCAGCTTGGATATTGGTCA 57.188 29.630 0.00 0.00 0.00 4.02
22 23 8.840321 GCTTCACTTATATATTTTCAGCTTGGA 58.160 33.333 0.00 0.00 0.00 3.53
23 24 8.623903 TGCTTCACTTATATATTTTCAGCTTGG 58.376 33.333 0.00 0.00 0.00 3.61
24 25 9.443283 GTGCTTCACTTATATATTTTCAGCTTG 57.557 33.333 0.00 0.00 0.00 4.01
25 26 9.177608 TGTGCTTCACTTATATATTTTCAGCTT 57.822 29.630 0.00 0.00 35.11 3.74
26 27 8.616076 GTGTGCTTCACTTATATATTTTCAGCT 58.384 33.333 0.00 0.00 43.13 4.24
27 28 7.584123 CGTGTGCTTCACTTATATATTTTCAGC 59.416 37.037 9.94 0.00 44.16 4.26
28 29 8.817100 TCGTGTGCTTCACTTATATATTTTCAG 58.183 33.333 9.94 0.00 44.16 3.02
29 30 8.710835 TCGTGTGCTTCACTTATATATTTTCA 57.289 30.769 9.94 0.00 44.16 2.69
30 31 9.638300 CTTCGTGTGCTTCACTTATATATTTTC 57.362 33.333 9.94 0.00 44.16 2.29
31 32 8.122952 GCTTCGTGTGCTTCACTTATATATTTT 58.877 33.333 9.94 0.00 44.16 1.82
32 33 7.279981 TGCTTCGTGTGCTTCACTTATATATTT 59.720 33.333 9.94 0.00 44.16 1.40
33 34 6.761242 TGCTTCGTGTGCTTCACTTATATATT 59.239 34.615 9.94 0.00 44.16 1.28
34 35 6.280643 TGCTTCGTGTGCTTCACTTATATAT 58.719 36.000 9.94 0.00 44.16 0.86
35 36 5.656480 TGCTTCGTGTGCTTCACTTATATA 58.344 37.500 9.94 0.00 44.16 0.86
36 37 4.503910 TGCTTCGTGTGCTTCACTTATAT 58.496 39.130 9.94 0.00 44.16 0.86
37 38 3.920446 TGCTTCGTGTGCTTCACTTATA 58.080 40.909 9.94 0.00 44.16 0.98
38 39 2.766313 TGCTTCGTGTGCTTCACTTAT 58.234 42.857 9.94 0.00 44.16 1.73
39 40 2.232756 TGCTTCGTGTGCTTCACTTA 57.767 45.000 9.94 0.00 44.16 2.24
40 41 1.597742 ATGCTTCGTGTGCTTCACTT 58.402 45.000 9.94 0.00 44.16 3.16
41 42 1.532868 GAATGCTTCGTGTGCTTCACT 59.467 47.619 9.94 0.00 44.16 3.41
42 43 1.532868 AGAATGCTTCGTGTGCTTCAC 59.467 47.619 3.22 3.22 43.03 3.18
43 44 1.882912 AGAATGCTTCGTGTGCTTCA 58.117 45.000 0.00 0.00 34.02 3.02
44 45 5.718649 TTATAGAATGCTTCGTGTGCTTC 57.281 39.130 0.00 0.00 34.02 3.86
45 46 5.447818 GCTTTATAGAATGCTTCGTGTGCTT 60.448 40.000 1.02 0.00 33.88 3.91
46 47 4.034510 GCTTTATAGAATGCTTCGTGTGCT 59.965 41.667 1.02 0.00 33.88 4.40
47 48 4.274865 GCTTTATAGAATGCTTCGTGTGC 58.725 43.478 1.02 0.00 33.88 4.57
48 49 4.332543 TGGCTTTATAGAATGCTTCGTGTG 59.667 41.667 7.76 0.00 36.29 3.82
49 50 4.513442 TGGCTTTATAGAATGCTTCGTGT 58.487 39.130 7.76 0.00 36.29 4.49
50 51 5.679734 ATGGCTTTATAGAATGCTTCGTG 57.320 39.130 7.76 0.00 36.29 4.35
51 52 6.525629 AGTATGGCTTTATAGAATGCTTCGT 58.474 36.000 7.76 0.00 36.29 3.85
52 53 6.646653 TGAGTATGGCTTTATAGAATGCTTCG 59.353 38.462 7.76 0.00 36.29 3.79
53 54 7.969536 TGAGTATGGCTTTATAGAATGCTTC 57.030 36.000 7.76 0.00 36.29 3.86
54 55 8.752005 TTTGAGTATGGCTTTATAGAATGCTT 57.248 30.769 7.76 0.17 36.29 3.91
55 56 8.752005 TTTTGAGTATGGCTTTATAGAATGCT 57.248 30.769 7.76 0.00 36.29 3.79
56 57 8.840321 TCTTTTGAGTATGGCTTTATAGAATGC 58.160 33.333 0.00 0.00 35.49 3.56
65 66 9.077885 TCACTTAAATCTTTTGAGTATGGCTTT 57.922 29.630 0.00 0.00 0.00 3.51
66 67 8.635765 TCACTTAAATCTTTTGAGTATGGCTT 57.364 30.769 0.00 0.00 0.00 4.35
67 68 8.635765 TTCACTTAAATCTTTTGAGTATGGCT 57.364 30.769 0.00 0.00 0.00 4.75
68 69 7.486232 GCTTCACTTAAATCTTTTGAGTATGGC 59.514 37.037 0.00 0.62 0.00 4.40
69 70 8.514594 TGCTTCACTTAAATCTTTTGAGTATGG 58.485 33.333 0.00 0.00 0.00 2.74
70 71 9.334693 GTGCTTCACTTAAATCTTTTGAGTATG 57.665 33.333 0.00 0.00 0.00 2.39
71 72 9.066892 TGTGCTTCACTTAAATCTTTTGAGTAT 57.933 29.630 0.00 0.00 35.11 2.12
72 73 8.445275 TGTGCTTCACTTAAATCTTTTGAGTA 57.555 30.769 0.00 0.00 35.11 2.59
73 74 7.333528 TGTGCTTCACTTAAATCTTTTGAGT 57.666 32.000 0.00 0.00 35.11 3.41
74 75 8.633075 TTTGTGCTTCACTTAAATCTTTTGAG 57.367 30.769 0.00 0.00 35.11 3.02
75 76 8.465999 TCTTTGTGCTTCACTTAAATCTTTTGA 58.534 29.630 0.00 0.00 35.11 2.69
76 77 8.633075 TCTTTGTGCTTCACTTAAATCTTTTG 57.367 30.769 0.00 0.00 35.11 2.44
77 78 7.436376 GCTCTTTGTGCTTCACTTAAATCTTTT 59.564 33.333 0.00 0.00 35.11 2.27
78 79 6.920210 GCTCTTTGTGCTTCACTTAAATCTTT 59.080 34.615 0.00 0.00 35.11 2.52
79 80 6.039717 TGCTCTTTGTGCTTCACTTAAATCTT 59.960 34.615 0.00 0.00 35.11 2.40
80 81 5.532406 TGCTCTTTGTGCTTCACTTAAATCT 59.468 36.000 0.00 0.00 35.11 2.40
81 82 5.762045 TGCTCTTTGTGCTTCACTTAAATC 58.238 37.500 0.00 0.00 35.11 2.17
82 83 5.772825 TGCTCTTTGTGCTTCACTTAAAT 57.227 34.783 0.00 0.00 35.11 1.40
83 84 5.772825 ATGCTCTTTGTGCTTCACTTAAA 57.227 34.783 0.00 0.00 35.11 1.52
84 85 5.532406 AGAATGCTCTTTGTGCTTCACTTAA 59.468 36.000 0.00 0.00 35.11 1.85
85 86 5.065914 AGAATGCTCTTTGTGCTTCACTTA 58.934 37.500 0.00 0.00 35.11 2.24
86 87 3.887716 AGAATGCTCTTTGTGCTTCACTT 59.112 39.130 0.00 0.00 35.11 3.16
87 88 3.484407 AGAATGCTCTTTGTGCTTCACT 58.516 40.909 0.00 0.00 35.11 3.41
88 89 3.911661 AGAATGCTCTTTGTGCTTCAC 57.088 42.857 0.00 0.00 34.56 3.18
89 90 7.627088 GCTTTATAGAATGCTCTTTGTGCTTCA 60.627 37.037 1.02 0.00 33.88 3.02
90 91 6.690528 GCTTTATAGAATGCTCTTTGTGCTTC 59.309 38.462 1.02 0.00 33.88 3.86
91 92 6.405176 GGCTTTATAGAATGCTCTTTGTGCTT 60.405 38.462 7.76 0.00 36.29 3.91
92 93 5.067023 GGCTTTATAGAATGCTCTTTGTGCT 59.933 40.000 7.76 0.00 36.29 4.40
93 94 5.163622 TGGCTTTATAGAATGCTCTTTGTGC 60.164 40.000 7.76 0.00 36.29 4.57
94 95 6.441093 TGGCTTTATAGAATGCTCTTTGTG 57.559 37.500 7.76 0.00 36.29 3.33
95 96 7.995488 AGTATGGCTTTATAGAATGCTCTTTGT 59.005 33.333 7.76 0.00 36.29 2.83
96 97 8.388484 AGTATGGCTTTATAGAATGCTCTTTG 57.612 34.615 7.76 0.00 36.29 2.77
97 98 8.213679 TGAGTATGGCTTTATAGAATGCTCTTT 58.786 33.333 7.76 0.00 36.29 2.52
98 99 7.739825 TGAGTATGGCTTTATAGAATGCTCTT 58.260 34.615 7.76 0.97 36.29 2.85
99 100 7.308450 TGAGTATGGCTTTATAGAATGCTCT 57.692 36.000 7.76 2.86 36.29 4.09
100 101 7.969536 TTGAGTATGGCTTTATAGAATGCTC 57.030 36.000 7.76 7.13 36.29 4.26
101 102 8.752005 TTTTGAGTATGGCTTTATAGAATGCT 57.248 30.769 7.76 0.00 36.29 3.79
102 103 8.840321 TCTTTTGAGTATGGCTTTATAGAATGC 58.160 33.333 0.00 0.00 35.49 3.56
111 112 9.077885 TCACTTAAATCTTTTGAGTATGGCTTT 57.922 29.630 0.00 0.00 0.00 3.51
112 113 8.635765 TCACTTAAATCTTTTGAGTATGGCTT 57.364 30.769 0.00 0.00 0.00 4.35
113 114 8.635765 TTCACTTAAATCTTTTGAGTATGGCT 57.364 30.769 0.00 0.00 0.00 4.75
114 115 7.486232 GCTTCACTTAAATCTTTTGAGTATGGC 59.514 37.037 0.00 0.62 0.00 4.40
115 116 8.514594 TGCTTCACTTAAATCTTTTGAGTATGG 58.485 33.333 0.00 0.00 0.00 2.74
116 117 9.334693 GTGCTTCACTTAAATCTTTTGAGTATG 57.665 33.333 0.00 0.00 0.00 2.39
117 118 9.066892 TGTGCTTCACTTAAATCTTTTGAGTAT 57.933 29.630 0.00 0.00 35.11 2.12
118 119 8.445275 TGTGCTTCACTTAAATCTTTTGAGTA 57.555 30.769 0.00 0.00 35.11 2.59
119 120 7.333528 TGTGCTTCACTTAAATCTTTTGAGT 57.666 32.000 0.00 0.00 35.11 3.41
120 121 8.077991 TCATGTGCTTCACTTAAATCTTTTGAG 58.922 33.333 0.00 0.00 35.11 3.02
121 122 7.939782 TCATGTGCTTCACTTAAATCTTTTGA 58.060 30.769 0.00 0.00 35.11 2.69
122 123 8.578308 TTCATGTGCTTCACTTAAATCTTTTG 57.422 30.769 0.00 0.00 35.11 2.44
123 124 7.383300 GCTTCATGTGCTTCACTTAAATCTTTT 59.617 33.333 6.28 0.00 35.11 2.27
124 125 6.865205 GCTTCATGTGCTTCACTTAAATCTTT 59.135 34.615 6.28 0.00 35.11 2.52
125 126 6.016024 TGCTTCATGTGCTTCACTTAAATCTT 60.016 34.615 12.86 0.00 35.11 2.40
126 127 5.474532 TGCTTCATGTGCTTCACTTAAATCT 59.525 36.000 12.86 0.00 35.11 2.40
127 128 5.702865 TGCTTCATGTGCTTCACTTAAATC 58.297 37.500 12.86 0.00 35.11 2.17
128 129 5.710513 TGCTTCATGTGCTTCACTTAAAT 57.289 34.783 12.86 0.00 35.11 1.40
129 130 5.710513 ATGCTTCATGTGCTTCACTTAAA 57.289 34.783 12.86 0.00 35.11 1.52
130 131 5.335897 GGAATGCTTCATGTGCTTCACTTAA 60.336 40.000 12.86 0.00 35.11 1.85
131 132 4.156556 GGAATGCTTCATGTGCTTCACTTA 59.843 41.667 12.86 0.00 35.11 2.24
132 133 3.057033 GGAATGCTTCATGTGCTTCACTT 60.057 43.478 12.86 0.00 35.11 3.16
133 134 2.490903 GGAATGCTTCATGTGCTTCACT 59.509 45.455 12.86 0.00 35.11 3.41
134 135 2.229543 TGGAATGCTTCATGTGCTTCAC 59.770 45.455 12.86 0.00 34.56 3.18
135 136 2.516906 TGGAATGCTTCATGTGCTTCA 58.483 42.857 12.86 5.38 0.00 3.02
136 137 3.795623 ATGGAATGCTTCATGTGCTTC 57.204 42.857 12.86 12.48 0.00 3.86
137 138 5.664294 TTTATGGAATGCTTCATGTGCTT 57.336 34.783 12.86 5.78 0.00 3.91
138 139 5.361571 TGATTTATGGAATGCTTCATGTGCT 59.638 36.000 12.86 0.00 0.00 4.40
139 140 5.593968 TGATTTATGGAATGCTTCATGTGC 58.406 37.500 6.53 6.53 0.00 4.57
140 141 7.923878 TCATTGATTTATGGAATGCTTCATGTG 59.076 33.333 0.00 0.00 0.00 3.21
141 142 8.014070 TCATTGATTTATGGAATGCTTCATGT 57.986 30.769 0.00 0.00 0.00 3.21
142 143 8.761497 GTTCATTGATTTATGGAATGCTTCATG 58.239 33.333 0.00 0.00 0.00 3.07
143 144 7.650504 CGTTCATTGATTTATGGAATGCTTCAT 59.349 33.333 0.00 0.00 0.00 2.57
144 145 6.974048 CGTTCATTGATTTATGGAATGCTTCA 59.026 34.615 0.00 0.00 0.00 3.02
145 146 7.166473 GTCGTTCATTGATTTATGGAATGCTTC 59.834 37.037 0.00 0.00 0.00 3.86
146 147 6.974622 GTCGTTCATTGATTTATGGAATGCTT 59.025 34.615 0.00 0.00 0.00 3.91
147 148 6.319658 AGTCGTTCATTGATTTATGGAATGCT 59.680 34.615 0.00 0.00 0.00 3.79
148 149 6.498304 AGTCGTTCATTGATTTATGGAATGC 58.502 36.000 0.00 0.00 0.00 3.56
149 150 9.817365 GATAGTCGTTCATTGATTTATGGAATG 57.183 33.333 0.00 0.00 0.00 2.67
150 151 9.784531 AGATAGTCGTTCATTGATTTATGGAAT 57.215 29.630 0.00 0.00 0.00 3.01
151 152 9.261180 GAGATAGTCGTTCATTGATTTATGGAA 57.739 33.333 0.00 0.00 0.00 3.53
152 153 8.421002 TGAGATAGTCGTTCATTGATTTATGGA 58.579 33.333 0.00 0.00 0.00 3.41
153 154 8.593492 TGAGATAGTCGTTCATTGATTTATGG 57.407 34.615 0.00 0.00 0.00 2.74
159 160 8.240682 GCTAGTATGAGATAGTCGTTCATTGAT 58.759 37.037 0.00 0.00 33.81 2.57
160 161 7.228706 TGCTAGTATGAGATAGTCGTTCATTGA 59.771 37.037 0.00 0.00 33.81 2.57
161 162 7.363431 TGCTAGTATGAGATAGTCGTTCATTG 58.637 38.462 0.00 0.00 33.81 2.82
162 163 7.511959 TGCTAGTATGAGATAGTCGTTCATT 57.488 36.000 0.00 0.00 33.81 2.57
163 164 7.391833 TCATGCTAGTATGAGATAGTCGTTCAT 59.608 37.037 18.36 0.00 32.39 2.57
164 165 6.710744 TCATGCTAGTATGAGATAGTCGTTCA 59.289 38.462 18.36 0.00 32.39 3.18
165 166 7.135089 TCATGCTAGTATGAGATAGTCGTTC 57.865 40.000 18.36 0.00 32.39 3.95
166 167 7.534282 CATCATGCTAGTATGAGATAGTCGTT 58.466 38.462 24.82 5.93 40.16 3.85
167 168 6.404184 GCATCATGCTAGTATGAGATAGTCGT 60.404 42.308 24.82 6.57 40.16 4.34
168 169 5.970612 GCATCATGCTAGTATGAGATAGTCG 59.029 44.000 24.82 10.65 40.16 4.18
169 170 6.861144 TGCATCATGCTAGTATGAGATAGTC 58.139 40.000 24.82 12.28 45.31 2.59
170 171 6.847421 TGCATCATGCTAGTATGAGATAGT 57.153 37.500 24.82 8.53 45.31 2.12
173 174 9.984190 CTTATATGCATCATGCTAGTATGAGAT 57.016 33.333 24.82 18.50 45.31 2.75
174 175 8.975295 ACTTATATGCATCATGCTAGTATGAGA 58.025 33.333 24.82 13.83 45.31 3.27
175 176 9.032420 CACTTATATGCATCATGCTAGTATGAG 57.968 37.037 24.82 18.06 45.31 2.90
176 177 8.752187 TCACTTATATGCATCATGCTAGTATGA 58.248 33.333 23.38 23.38 45.31 2.15
177 178 8.815189 GTCACTTATATGCATCATGCTAGTATG 58.185 37.037 11.84 14.12 45.31 2.39
178 179 8.534496 TGTCACTTATATGCATCATGCTAGTAT 58.466 33.333 11.84 9.17 45.31 2.12
179 180 7.895759 TGTCACTTATATGCATCATGCTAGTA 58.104 34.615 11.84 1.90 45.31 1.82
180 181 6.762333 TGTCACTTATATGCATCATGCTAGT 58.238 36.000 11.84 3.91 45.31 2.57
181 182 7.662604 TTGTCACTTATATGCATCATGCTAG 57.337 36.000 11.84 3.30 45.31 3.42
182 183 8.625786 AATTGTCACTTATATGCATCATGCTA 57.374 30.769 11.84 1.19 45.31 3.49
183 184 7.447545 AGAATTGTCACTTATATGCATCATGCT 59.552 33.333 11.84 0.00 45.31 3.79
184 185 7.537649 CAGAATTGTCACTTATATGCATCATGC 59.462 37.037 0.19 1.35 45.29 4.06
185 186 8.565416 ACAGAATTGTCACTTATATGCATCATG 58.435 33.333 0.19 0.00 29.46 3.07
186 187 8.687292 ACAGAATTGTCACTTATATGCATCAT 57.313 30.769 0.19 0.00 29.46 2.45
187 188 9.045223 GTACAGAATTGTCACTTATATGCATCA 57.955 33.333 0.19 0.00 38.76 3.07
188 189 9.045223 TGTACAGAATTGTCACTTATATGCATC 57.955 33.333 0.19 0.00 38.76 3.91
189 190 8.962884 TGTACAGAATTGTCACTTATATGCAT 57.037 30.769 3.79 3.79 38.76 3.96
190 191 8.785329 TTGTACAGAATTGTCACTTATATGCA 57.215 30.769 0.00 0.00 38.76 3.96
191 192 9.490663 GTTTGTACAGAATTGTCACTTATATGC 57.509 33.333 0.00 0.00 38.76 3.14
192 193 9.689075 CGTTTGTACAGAATTGTCACTTATATG 57.311 33.333 0.00 0.00 38.76 1.78
193 194 9.647797 TCGTTTGTACAGAATTGTCACTTATAT 57.352 29.630 0.00 0.00 38.76 0.86
194 195 9.647797 ATCGTTTGTACAGAATTGTCACTTATA 57.352 29.630 0.00 0.00 38.76 0.98
195 196 7.956420 TCGTTTGTACAGAATTGTCACTTAT 57.044 32.000 0.00 0.00 38.76 1.73
196 197 7.956420 ATCGTTTGTACAGAATTGTCACTTA 57.044 32.000 0.00 0.00 38.76 2.24
427 431 9.515226 TGTACCTATAAAATTTGAGCTTTCTGT 57.485 29.630 0.00 0.00 0.00 3.41
505 509 8.114301 ACTGGGGGTAATCTAAATGAGTAATT 57.886 34.615 0.00 0.00 0.00 1.40
511 515 7.404980 ACTTTCTACTGGGGGTAATCTAAATGA 59.595 37.037 0.00 0.00 0.00 2.57
529 533 7.438459 ACGTTAGCAATGATCCATACTTTCTAC 59.562 37.037 0.00 0.00 0.00 2.59
532 536 6.604735 ACGTTAGCAATGATCCATACTTTC 57.395 37.500 0.00 0.00 0.00 2.62
546 550 3.255725 CGGAAACCATCTACGTTAGCAA 58.744 45.455 0.00 0.00 0.00 3.91
559 566 8.178964 CGAAAATTTCATCTATAACGGAAACCA 58.821 33.333 6.53 0.00 32.65 3.67
690 700 1.937899 GAGCCGTCTAGTGAGAGTCTC 59.062 57.143 13.56 13.56 30.20 3.36
714 972 0.036022 GCAGGCATGGAGGATAGGAC 59.964 60.000 0.00 0.00 0.00 3.85
865 1123 5.237127 CAGATACCGCTGATCAAATAAAGCA 59.763 40.000 0.00 0.00 38.14 3.91
882 1140 2.288666 TCCGCAAATGAAGCAGATACC 58.711 47.619 0.00 0.00 0.00 2.73
1249 1515 3.230284 TCCATGGAGCGATGGACC 58.770 61.111 11.44 0.00 45.85 4.46
1461 1745 4.695455 ACTGAAAATGAATGGTACCACGAG 59.305 41.667 19.09 5.21 0.00 4.18
1462 1746 4.647611 ACTGAAAATGAATGGTACCACGA 58.352 39.130 19.09 4.06 0.00 4.35
1463 1747 5.049060 TGAACTGAAAATGAATGGTACCACG 60.049 40.000 19.09 1.46 0.00 4.94
1464 1748 6.325919 TGAACTGAAAATGAATGGTACCAC 57.674 37.500 19.09 6.10 0.00 4.16
1465 1749 7.537596 AATGAACTGAAAATGAATGGTACCA 57.462 32.000 18.99 18.99 0.00 3.25
1466 1750 7.872483 ACAAATGAACTGAAAATGAATGGTACC 59.128 33.333 4.43 4.43 0.00 3.34
1467 1751 8.702438 CACAAATGAACTGAAAATGAATGGTAC 58.298 33.333 0.00 0.00 0.00 3.34
1468 1752 8.637099 TCACAAATGAACTGAAAATGAATGGTA 58.363 29.630 0.00 0.00 0.00 3.25
1469 1753 7.499292 TCACAAATGAACTGAAAATGAATGGT 58.501 30.769 0.00 0.00 0.00 3.55
1470 1754 7.868922 TCTCACAAATGAACTGAAAATGAATGG 59.131 33.333 0.00 0.00 33.30 3.16
1471 1755 8.806177 TCTCACAAATGAACTGAAAATGAATG 57.194 30.769 0.00 0.00 33.30 2.67
1472 1756 9.635520 GATCTCACAAATGAACTGAAAATGAAT 57.364 29.630 0.00 0.00 33.30 2.57
1519 1815 1.293924 CGGCATGAACATCTCAGTCC 58.706 55.000 0.00 0.00 37.52 3.85
1577 1877 6.048509 AGTGAATAAACAAACAGCAAAAGGG 58.951 36.000 0.00 0.00 0.00 3.95
1579 1879 7.754069 TGAGTGAATAAACAAACAGCAAAAG 57.246 32.000 0.00 0.00 0.00 2.27
1635 1952 2.847327 ACACATGGTCCAAGTGAGAG 57.153 50.000 29.22 7.40 35.44 3.20
1691 2008 0.109723 ACAGGTTGGCGTATGGTTGT 59.890 50.000 0.00 0.00 0.00 3.32
1783 2102 1.880027 AGAGCAAACCAACGGATGAAC 59.120 47.619 0.00 0.00 0.00 3.18
1787 2106 1.523758 GTCAGAGCAAACCAACGGAT 58.476 50.000 0.00 0.00 0.00 4.18
1789 2108 1.569493 CGTCAGAGCAAACCAACGG 59.431 57.895 0.00 0.00 0.00 4.44
1790 2109 1.082756 GCGTCAGAGCAAACCAACG 60.083 57.895 0.00 0.00 37.05 4.10
1815 2134 1.517257 CACGCTAGTGCCTTCTCCG 60.517 63.158 2.40 0.00 41.94 4.63
1887 5604 1.272807 TGTAGTAGGGTGGTTCAGGC 58.727 55.000 0.00 0.00 0.00 4.85
1915 5632 8.354426 TCTACAATGAATTATTCCGTACGATCA 58.646 33.333 18.76 9.25 0.00 2.92
1918 5635 7.143340 CCTCTACAATGAATTATTCCGTACGA 58.857 38.462 18.76 0.00 0.00 3.43
1920 5637 7.924412 TGACCTCTACAATGAATTATTCCGTAC 59.076 37.037 2.22 0.00 0.00 3.67
1925 5642 8.964476 TCCTTGACCTCTACAATGAATTATTC 57.036 34.615 0.00 0.00 0.00 1.75
1930 5647 5.485353 TCACTCCTTGACCTCTACAATGAAT 59.515 40.000 0.00 0.00 0.00 2.57
1940 5657 3.971245 ATTGTCTCACTCCTTGACCTC 57.029 47.619 0.00 0.00 0.00 3.85
1965 5682 2.689983 AGGATGAATCGTTCCATTTGGC 59.310 45.455 5.10 0.00 34.27 4.52
1971 5688 1.407299 CCAGCAGGATGAATCGTTCCA 60.407 52.381 5.10 0.00 39.69 3.53
1972 5689 1.303309 CCAGCAGGATGAATCGTTCC 58.697 55.000 0.00 0.00 39.69 3.62
1973 5690 0.659957 GCCAGCAGGATGAATCGTTC 59.340 55.000 0.00 0.00 39.69 3.95
1974 5691 0.749454 GGCCAGCAGGATGAATCGTT 60.749 55.000 0.00 0.00 39.69 3.85
1975 5692 1.153086 GGCCAGCAGGATGAATCGT 60.153 57.895 0.00 0.00 39.69 3.73
1976 5693 0.394192 TAGGCCAGCAGGATGAATCG 59.606 55.000 5.01 0.00 39.69 3.34
1977 5694 2.645838 TTAGGCCAGCAGGATGAATC 57.354 50.000 5.01 0.00 39.69 2.52
1996 5713 7.815398 AAACTGAAAACGGTTTACGATTTTT 57.185 28.000 6.53 0.33 45.71 1.94
2008 5725 2.820330 ACATGGCAAAACTGAAAACGG 58.180 42.857 0.00 0.00 0.00 4.44
2009 5726 3.862267 TGAACATGGCAAAACTGAAAACG 59.138 39.130 0.00 0.00 0.00 3.60
2066 5785 8.103305 TCAGTCAGTTTAGCTCTTCCATTATTT 58.897 33.333 0.00 0.00 0.00 1.40
2069 5788 6.351371 CCTCAGTCAGTTTAGCTCTTCCATTA 60.351 42.308 0.00 0.00 0.00 1.90
2081 5800 1.414919 ACGGTTGCCTCAGTCAGTTTA 59.585 47.619 0.00 0.00 0.00 2.01
2089 5808 2.457366 AGAAAGTACGGTTGCCTCAG 57.543 50.000 0.00 0.00 0.00 3.35
2125 5844 2.158726 AGGGTTGCCTTAACTCGTTCAA 60.159 45.455 0.00 0.00 44.77 2.69
2132 5851 4.448720 ACAAAGTAGGGTTGCCTTAACT 57.551 40.909 0.00 0.00 39.31 2.24
2180 5912 3.069016 TGCAGAGAACTAGGTTCGACAAA 59.931 43.478 0.00 0.00 45.96 2.83
2183 5915 2.416162 CCTGCAGAGAACTAGGTTCGAC 60.416 54.545 17.39 4.37 45.96 4.20
2185 5917 1.819288 TCCTGCAGAGAACTAGGTTCG 59.181 52.381 17.39 0.00 45.96 3.95
2186 5918 4.081420 TGAATCCTGCAGAGAACTAGGTTC 60.081 45.833 17.39 9.03 42.25 3.62
2189 5921 4.440880 CTTGAATCCTGCAGAGAACTAGG 58.559 47.826 17.39 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.