Multiple sequence alignment - TraesCS2D01G386900

Loading Multiple Alignment...

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 TraesCS2D01G386900 chr2D 100.000 3065 0 0 1 3065 492024006 492020942 0.000000e+00 5661.0
1 TraesCS2D01G386900 chr2D 100.000 33 0 0 1278 1310 183630571 183630539 9.180000e-06 62.1
2 TraesCS2D01G386900 chr2B 93.405 2335 103 20 207 2511 576746081 576743768 0.000000e+00 3411.0
3 TraesCS2D01G386900 chr2B 90.347 259 14 4 2810 3065 576743411 576743161 2.280000e-86 329.0
4 TraesCS2D01G386900 chr2B 100.000 30 0 0 1281 1310 23111457 23111428 4.270000e-04 56.5
5 TraesCS2D01G386900 chr2A 94.269 1902 73 17 616 2503 637223808 637221929 0.000000e+00 2876.0
6 TraesCS2D01G386900 chr2A 92.500 400 17 6 206 604 637224238 637223851 7.420000e-156 560.0
7 TraesCS2D01G386900 chr2A 86.022 372 39 8 2701 3065 637220185 637219820 1.330000e-103 387.0
8 TraesCS2D01G386900 chr2A 100.000 33 0 0 1278 1310 197925679 197925647 9.180000e-06 62.1
9 TraesCS2D01G386900 chr1B 95.333 300 14 0 2057 2356 482177759 482178058 7.690000e-131 477.0
10 TraesCS2D01G386900 chr6B 86.325 234 32 0 1142 1375 513135647 513135880 3.920000e-64 255.0
11 TraesCS2D01G386900 chr7B 93.750 48 3 0 1743 1790 57633389 57633342 4.240000e-09 73.1
12 TraesCS2D01G386900 chr3D 93.333 45 3 0 1736 1780 48365681 48365637 1.970000e-07 67.6
13 TraesCS2D01G386900 chr3D 89.583 48 5 0 1741 1788 516385275 516385228 9.180000e-06 62.1
14 TraesCS2D01G386900 chr5D 91.111 45 4 0 1744 1788 438361885 438361841 9.180000e-06 62.1
15 TraesCS2D01G386900 chr3B 89.583 48 5 0 1741 1788 679646141 679646094 9.180000e-06 62.1
16 TraesCS2D01G386900 chr3A 89.583 48 5 0 1741 1788 651588232 651588185 9.180000e-06 62.1
17 TraesCS2D01G386900 chr5B 88.235 51 5 1 1739 1788 532891852 532891802 3.300000e-05 60.2


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 TraesCS2D01G386900 chr2D 492020942 492024006 3064 True 5661.000000 5661 100.000000 1 3065 1 chr2D.!!$R2 3064
1 TraesCS2D01G386900 chr2B 576743161 576746081 2920 True 1870.000000 3411 91.876000 207 3065 2 chr2B.!!$R2 2858
2 TraesCS2D01G386900 chr2A 637219820 637224238 4418 True 1274.333333 2876 90.930333 206 3065 3 chr2A.!!$R2 2859

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
82 83 0.033796 CAGGTACGAGGGGTCCAGTA 60.034 60.0 0.0 0.0 0.00 2.74 F
980 1043 0.036010 CACTTGGAGAGCCGGTCATT 60.036 55.0 1.9 0.0 36.79 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 1909 1.002134 CCACGTTCCCCTTGCTGAT 60.002 57.895 0.0 0.00 0.0 2.90 R
2859 4605 0.181587 TTTCTCACCGGTGGCTTTCA 59.818 50.000 33.4 12.97 0.0 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.664062 CCTCATGTCCGCCCAAAT 57.336 55.556 0.00 0.00 0.00 2.32
18 19 2.886382 CCTCATGTCCGCCCAAATT 58.114 52.632 0.00 0.00 0.00 1.82
19 20 2.051334 CCTCATGTCCGCCCAAATTA 57.949 50.000 0.00 0.00 0.00 1.40
20 21 1.676006 CCTCATGTCCGCCCAAATTAC 59.324 52.381 0.00 0.00 0.00 1.89
21 22 2.364632 CTCATGTCCGCCCAAATTACA 58.635 47.619 0.00 0.00 0.00 2.41
22 23 2.752354 CTCATGTCCGCCCAAATTACAA 59.248 45.455 0.00 0.00 0.00 2.41
23 24 2.752354 TCATGTCCGCCCAAATTACAAG 59.248 45.455 0.00 0.00 0.00 3.16
24 25 2.279935 TGTCCGCCCAAATTACAAGT 57.720 45.000 0.00 0.00 0.00 3.16
25 26 2.588620 TGTCCGCCCAAATTACAAGTT 58.411 42.857 0.00 0.00 0.00 2.66
26 27 2.294791 TGTCCGCCCAAATTACAAGTTG 59.705 45.455 0.00 0.00 34.07 3.16
38 39 7.676004 CAAATTACAAGTTGGATTTAAGGGGT 58.324 34.615 15.02 0.00 30.93 4.95
39 40 8.808092 CAAATTACAAGTTGGATTTAAGGGGTA 58.192 33.333 15.02 0.00 30.93 3.69
40 41 7.949690 ATTACAAGTTGGATTTAAGGGGTAC 57.050 36.000 7.96 0.00 0.00 3.34
41 42 4.329392 ACAAGTTGGATTTAAGGGGTACG 58.671 43.478 7.96 0.00 0.00 3.67
42 43 4.041938 ACAAGTTGGATTTAAGGGGTACGA 59.958 41.667 7.96 0.00 0.00 3.43
43 44 4.482952 AGTTGGATTTAAGGGGTACGAG 57.517 45.455 0.00 0.00 0.00 4.18
44 45 4.098894 AGTTGGATTTAAGGGGTACGAGA 58.901 43.478 0.00 0.00 0.00 4.04
45 46 4.720273 AGTTGGATTTAAGGGGTACGAGAT 59.280 41.667 0.00 0.00 0.00 2.75
46 47 5.901276 AGTTGGATTTAAGGGGTACGAGATA 59.099 40.000 0.00 0.00 0.00 1.98
47 48 6.041751 AGTTGGATTTAAGGGGTACGAGATAG 59.958 42.308 0.00 0.00 0.00 2.08
48 49 4.282703 TGGATTTAAGGGGTACGAGATAGC 59.717 45.833 0.00 0.00 0.00 2.97
49 50 4.527427 GGATTTAAGGGGTACGAGATAGCT 59.473 45.833 0.00 0.00 0.00 3.32
50 51 5.336610 GGATTTAAGGGGTACGAGATAGCTC 60.337 48.000 0.00 0.00 37.81 4.09
66 67 2.772739 CTCGGACATTTGAGCCAGG 58.227 57.895 0.00 0.00 0.00 4.45
67 68 0.036010 CTCGGACATTTGAGCCAGGT 60.036 55.000 0.00 0.00 0.00 4.00
68 69 1.207089 CTCGGACATTTGAGCCAGGTA 59.793 52.381 0.00 0.00 0.00 3.08
69 70 1.066430 TCGGACATTTGAGCCAGGTAC 60.066 52.381 0.00 0.00 0.00 3.34
70 71 1.369625 GGACATTTGAGCCAGGTACG 58.630 55.000 0.00 0.00 0.00 3.67
71 72 1.066430 GGACATTTGAGCCAGGTACGA 60.066 52.381 0.00 0.00 0.00 3.43
72 73 2.271800 GACATTTGAGCCAGGTACGAG 58.728 52.381 0.00 0.00 0.00 4.18
73 74 1.066143 ACATTTGAGCCAGGTACGAGG 60.066 52.381 0.00 0.00 0.00 4.63
74 75 0.541863 ATTTGAGCCAGGTACGAGGG 59.458 55.000 4.61 0.00 0.00 4.30
75 76 1.550130 TTTGAGCCAGGTACGAGGGG 61.550 60.000 4.61 0.00 0.00 4.79
76 77 2.363925 GAGCCAGGTACGAGGGGT 60.364 66.667 4.61 2.85 34.59 4.95
77 78 2.363925 AGCCAGGTACGAGGGGTC 60.364 66.667 4.61 0.00 0.00 4.46
78 79 3.468140 GCCAGGTACGAGGGGTCC 61.468 72.222 4.61 0.00 0.00 4.46
79 80 2.038329 CCAGGTACGAGGGGTCCA 59.962 66.667 0.00 0.00 0.00 4.02
80 81 2.058595 CCAGGTACGAGGGGTCCAG 61.059 68.421 0.00 0.00 0.00 3.86
81 82 1.305046 CAGGTACGAGGGGTCCAGT 60.305 63.158 0.00 0.00 0.00 4.00
82 83 0.033796 CAGGTACGAGGGGTCCAGTA 60.034 60.000 0.00 0.00 0.00 2.74
83 84 0.258194 AGGTACGAGGGGTCCAGTAG 59.742 60.000 0.00 0.00 0.00 2.57
84 85 0.754587 GGTACGAGGGGTCCAGTAGG 60.755 65.000 0.00 0.00 0.00 3.18
85 86 0.257039 GTACGAGGGGTCCAGTAGGA 59.743 60.000 0.00 0.00 43.21 2.94
93 94 4.349682 TCCAGTAGGACGCGGATT 57.650 55.556 12.47 0.00 39.61 3.01
94 95 2.587080 TCCAGTAGGACGCGGATTT 58.413 52.632 12.47 0.00 39.61 2.17
95 96 0.899720 TCCAGTAGGACGCGGATTTT 59.100 50.000 12.47 0.00 39.61 1.82
96 97 1.276989 TCCAGTAGGACGCGGATTTTT 59.723 47.619 12.47 0.00 39.61 1.94
97 98 1.396996 CCAGTAGGACGCGGATTTTTG 59.603 52.381 12.47 1.74 36.89 2.44
98 99 1.396996 CAGTAGGACGCGGATTTTTGG 59.603 52.381 12.47 0.00 0.00 3.28
99 100 1.002773 AGTAGGACGCGGATTTTTGGT 59.997 47.619 12.47 0.00 0.00 3.67
100 101 1.395954 GTAGGACGCGGATTTTTGGTC 59.604 52.381 12.47 0.00 0.00 4.02
101 102 0.250553 AGGACGCGGATTTTTGGTCA 60.251 50.000 12.47 0.00 0.00 4.02
102 103 0.168128 GGACGCGGATTTTTGGTCAG 59.832 55.000 12.47 0.00 0.00 3.51
103 104 0.168128 GACGCGGATTTTTGGTCAGG 59.832 55.000 12.47 0.00 0.00 3.86
104 105 1.241315 ACGCGGATTTTTGGTCAGGG 61.241 55.000 12.47 0.00 0.00 4.45
105 106 1.215382 GCGGATTTTTGGTCAGGGC 59.785 57.895 0.00 0.00 0.00 5.19
106 107 1.531739 GCGGATTTTTGGTCAGGGCA 61.532 55.000 0.00 0.00 0.00 5.36
107 108 0.527565 CGGATTTTTGGTCAGGGCAG 59.472 55.000 0.00 0.00 0.00 4.85
108 109 0.247460 GGATTTTTGGTCAGGGCAGC 59.753 55.000 0.00 0.00 0.00 5.25
109 110 0.109132 GATTTTTGGTCAGGGCAGCG 60.109 55.000 0.00 0.00 0.00 5.18
110 111 0.827507 ATTTTTGGTCAGGGCAGCGT 60.828 50.000 0.00 0.00 0.00 5.07
111 112 1.452145 TTTTTGGTCAGGGCAGCGTC 61.452 55.000 0.00 0.00 0.00 5.19
112 113 3.842925 TTTGGTCAGGGCAGCGTCC 62.843 63.158 0.00 0.00 0.00 4.79
140 141 2.183409 CGCAGGAACAAATGAGGGG 58.817 57.895 0.00 0.00 0.00 4.79
141 142 0.609131 CGCAGGAACAAATGAGGGGT 60.609 55.000 0.00 0.00 0.00 4.95
142 143 1.339631 CGCAGGAACAAATGAGGGGTA 60.340 52.381 0.00 0.00 0.00 3.69
143 144 2.369394 GCAGGAACAAATGAGGGGTAG 58.631 52.381 0.00 0.00 0.00 3.18
144 145 2.290960 GCAGGAACAAATGAGGGGTAGT 60.291 50.000 0.00 0.00 0.00 2.73
145 146 3.347216 CAGGAACAAATGAGGGGTAGTG 58.653 50.000 0.00 0.00 0.00 2.74
146 147 2.308866 AGGAACAAATGAGGGGTAGTGG 59.691 50.000 0.00 0.00 0.00 4.00
147 148 2.620627 GGAACAAATGAGGGGTAGTGGG 60.621 54.545 0.00 0.00 0.00 4.61
148 149 1.755200 ACAAATGAGGGGTAGTGGGT 58.245 50.000 0.00 0.00 0.00 4.51
149 150 1.633945 ACAAATGAGGGGTAGTGGGTC 59.366 52.381 0.00 0.00 0.00 4.46
150 151 1.064685 CAAATGAGGGGTAGTGGGTCC 60.065 57.143 0.00 0.00 0.00 4.46
151 152 0.981277 AATGAGGGGTAGTGGGTCCG 60.981 60.000 0.00 0.00 0.00 4.79
152 153 2.762875 GAGGGGTAGTGGGTCCGG 60.763 72.222 0.00 0.00 0.00 5.14
153 154 3.608357 AGGGGTAGTGGGTCCGGT 61.608 66.667 0.00 0.00 0.00 5.28
154 155 2.608678 GGGGTAGTGGGTCCGGTT 60.609 66.667 0.00 0.00 0.00 4.44
155 156 2.666812 GGGTAGTGGGTCCGGTTG 59.333 66.667 0.00 0.00 0.00 3.77
156 157 2.219164 GGGTAGTGGGTCCGGTTGT 61.219 63.158 0.00 0.00 0.00 3.32
157 158 0.904394 GGGTAGTGGGTCCGGTTGTA 60.904 60.000 0.00 0.00 0.00 2.41
158 159 0.533951 GGTAGTGGGTCCGGTTGTAG 59.466 60.000 0.00 0.00 0.00 2.74
159 160 1.549203 GTAGTGGGTCCGGTTGTAGA 58.451 55.000 0.00 0.00 0.00 2.59
160 161 2.105766 GTAGTGGGTCCGGTTGTAGAT 58.894 52.381 0.00 0.00 0.00 1.98
161 162 2.537633 AGTGGGTCCGGTTGTAGATA 57.462 50.000 0.00 0.00 0.00 1.98
162 163 2.105766 AGTGGGTCCGGTTGTAGATAC 58.894 52.381 0.00 0.00 0.00 2.24
163 164 2.105766 GTGGGTCCGGTTGTAGATACT 58.894 52.381 0.00 0.00 0.00 2.12
164 165 2.100418 GTGGGTCCGGTTGTAGATACTC 59.900 54.545 0.00 0.00 0.00 2.59
165 166 2.291735 TGGGTCCGGTTGTAGATACTCA 60.292 50.000 0.00 0.00 0.00 3.41
166 167 2.963782 GGGTCCGGTTGTAGATACTCAT 59.036 50.000 0.00 0.00 0.00 2.90
167 168 4.147321 GGGTCCGGTTGTAGATACTCATA 58.853 47.826 0.00 0.00 0.00 2.15
168 169 4.771054 GGGTCCGGTTGTAGATACTCATAT 59.229 45.833 0.00 0.00 0.00 1.78
169 170 5.948162 GGGTCCGGTTGTAGATACTCATATA 59.052 44.000 0.00 0.00 0.00 0.86
170 171 6.127786 GGGTCCGGTTGTAGATACTCATATAC 60.128 46.154 0.00 0.00 30.87 1.47
171 172 6.658391 GGTCCGGTTGTAGATACTCATATACT 59.342 42.308 0.00 0.00 31.41 2.12
172 173 7.361885 GGTCCGGTTGTAGATACTCATATACTG 60.362 44.444 0.00 0.00 31.41 2.74
173 174 7.389884 GTCCGGTTGTAGATACTCATATACTGA 59.610 40.741 0.00 0.00 31.41 3.41
174 175 7.389884 TCCGGTTGTAGATACTCATATACTGAC 59.610 40.741 0.00 0.00 31.41 3.51
175 176 7.174426 CCGGTTGTAGATACTCATATACTGACA 59.826 40.741 0.00 0.00 31.41 3.58
176 177 8.731605 CGGTTGTAGATACTCATATACTGACAT 58.268 37.037 0.00 0.00 31.41 3.06
177 178 9.847706 GGTTGTAGATACTCATATACTGACATG 57.152 37.037 0.00 0.00 31.41 3.21
185 186 6.947903 CTCATATACTGACATGAGTGATGC 57.052 41.667 0.00 0.00 42.06 3.91
186 187 6.661304 TCATATACTGACATGAGTGATGCT 57.339 37.500 0.00 0.00 35.15 3.79
187 188 7.059202 TCATATACTGACATGAGTGATGCTT 57.941 36.000 0.00 0.00 35.15 3.91
188 189 8.181904 TCATATACTGACATGAGTGATGCTTA 57.818 34.615 0.00 0.00 35.15 3.09
189 190 8.302438 TCATATACTGACATGAGTGATGCTTAG 58.698 37.037 0.00 0.00 35.15 2.18
190 191 3.529533 ACTGACATGAGTGATGCTTAGC 58.470 45.455 0.00 0.00 35.15 3.09
191 192 3.197333 ACTGACATGAGTGATGCTTAGCT 59.803 43.478 5.60 0.00 35.15 3.32
192 193 4.190001 CTGACATGAGTGATGCTTAGCTT 58.810 43.478 5.60 0.00 35.15 3.74
193 194 4.582869 TGACATGAGTGATGCTTAGCTTT 58.417 39.130 5.60 0.00 35.15 3.51
194 195 5.005740 TGACATGAGTGATGCTTAGCTTTT 58.994 37.500 5.60 0.00 35.15 2.27
195 196 5.122869 TGACATGAGTGATGCTTAGCTTTTC 59.877 40.000 5.60 0.75 35.15 2.29
196 197 5.251764 ACATGAGTGATGCTTAGCTTTTCT 58.748 37.500 5.60 2.09 35.15 2.52
197 198 5.709164 ACATGAGTGATGCTTAGCTTTTCTT 59.291 36.000 5.60 0.00 35.15 2.52
198 199 6.208204 ACATGAGTGATGCTTAGCTTTTCTTT 59.792 34.615 5.60 0.00 35.15 2.52
199 200 6.639632 TGAGTGATGCTTAGCTTTTCTTTT 57.360 33.333 5.60 0.00 0.00 2.27
200 201 7.042797 TGAGTGATGCTTAGCTTTTCTTTTT 57.957 32.000 5.60 0.00 0.00 1.94
201 202 8.165239 TGAGTGATGCTTAGCTTTTCTTTTTA 57.835 30.769 5.60 0.00 0.00 1.52
202 203 8.292448 TGAGTGATGCTTAGCTTTTCTTTTTAG 58.708 33.333 5.60 0.00 0.00 1.85
203 204 7.597386 AGTGATGCTTAGCTTTTCTTTTTAGG 58.403 34.615 5.60 0.00 0.00 2.69
204 205 6.808704 GTGATGCTTAGCTTTTCTTTTTAGGG 59.191 38.462 5.60 0.00 0.00 3.53
205 206 5.722021 TGCTTAGCTTTTCTTTTTAGGGG 57.278 39.130 5.60 0.00 0.00 4.79
206 207 5.144832 TGCTTAGCTTTTCTTTTTAGGGGT 58.855 37.500 5.60 0.00 0.00 4.95
207 208 6.308566 TGCTTAGCTTTTCTTTTTAGGGGTA 58.691 36.000 5.60 0.00 0.00 3.69
208 209 6.951778 TGCTTAGCTTTTCTTTTTAGGGGTAT 59.048 34.615 5.60 0.00 0.00 2.73
209 210 7.093945 TGCTTAGCTTTTCTTTTTAGGGGTATG 60.094 37.037 5.60 0.00 0.00 2.39
210 211 7.122204 GCTTAGCTTTTCTTTTTAGGGGTATGA 59.878 37.037 0.00 0.00 0.00 2.15
233 234 2.164827 TGATGCTTTGCTTGCCATGTAG 59.835 45.455 0.00 0.00 0.00 2.74
269 270 5.280945 GTGCAACTGAAGTCTGCAATAAAA 58.719 37.500 16.48 0.00 40.68 1.52
270 271 5.922544 GTGCAACTGAAGTCTGCAATAAAAT 59.077 36.000 16.48 0.00 40.68 1.82
271 272 6.088616 GTGCAACTGAAGTCTGCAATAAAATC 59.911 38.462 16.48 5.04 40.68 2.17
272 273 5.284660 GCAACTGAAGTCTGCAATAAAATCG 59.715 40.000 10.67 0.00 34.53 3.34
304 305 2.565834 AGTCAACACGGGCAATAGTAGT 59.434 45.455 0.00 0.00 0.00 2.73
311 312 3.031736 ACGGGCAATAGTAGTCTGACAT 58.968 45.455 10.88 0.00 0.00 3.06
312 313 3.451178 ACGGGCAATAGTAGTCTGACATT 59.549 43.478 10.88 0.00 0.00 2.71
365 366 0.461548 CCTGACTCCGCTAGCATTGA 59.538 55.000 16.45 6.97 0.00 2.57
458 459 6.747280 CCGTCGAAAAAGCTTGAATATCAAAT 59.253 34.615 0.00 0.00 35.73 2.32
459 460 7.908082 CCGTCGAAAAAGCTTGAATATCAAATA 59.092 33.333 0.00 0.00 35.73 1.40
462 463 9.272901 TCGAAAAAGCTTGAATATCAAATAACG 57.727 29.630 0.00 0.00 35.73 3.18
463 464 9.061610 CGAAAAAGCTTGAATATCAAATAACGT 57.938 29.630 0.00 0.00 35.73 3.99
546 547 1.203994 CATTTCCAGCCCTCAAGCAAG 59.796 52.381 0.00 0.00 34.23 4.01
599 600 9.901172 ACTGTAGGAAGGAAAACGAAATATATT 57.099 29.630 0.00 0.00 0.00 1.28
632 664 4.537135 ACCAAGATGTTGATGACGTAGT 57.463 40.909 3.74 0.00 39.09 2.73
664 698 0.541863 TGAAAGAATCGGCTCTCCCC 59.458 55.000 0.00 0.00 0.00 4.81
739 792 2.309613 AGAACACAAGATGCAAGGCAA 58.690 42.857 0.00 0.00 43.62 4.52
740 793 2.295349 AGAACACAAGATGCAAGGCAAG 59.705 45.455 0.00 0.00 43.62 4.01
741 794 0.316204 ACACAAGATGCAAGGCAAGC 59.684 50.000 0.00 0.00 43.62 4.01
742 795 0.731514 CACAAGATGCAAGGCAAGCG 60.732 55.000 0.00 0.00 43.62 4.68
743 796 1.153901 CAAGATGCAAGGCAAGCGG 60.154 57.895 0.00 0.00 43.62 5.52
744 797 2.998279 AAGATGCAAGGCAAGCGGC 61.998 57.895 0.00 0.00 43.62 6.53
842 895 1.728490 GCCGGTGCCCATTGATTCTC 61.728 60.000 1.90 0.00 0.00 2.87
843 896 1.103398 CCGGTGCCCATTGATTCTCC 61.103 60.000 0.00 0.00 0.00 3.71
907 960 1.756538 AGAACCAGCAACAAAACCCAG 59.243 47.619 0.00 0.00 0.00 4.45
916 969 1.007387 CAAAACCCAGGCAAGCGTC 60.007 57.895 0.00 0.00 0.00 5.19
977 1040 3.377656 TCACTTGGAGAGCCGGTC 58.622 61.111 1.90 0.00 36.79 4.79
978 1041 1.533033 TCACTTGGAGAGCCGGTCA 60.533 57.895 1.90 0.00 36.79 4.02
980 1043 0.036010 CACTTGGAGAGCCGGTCATT 60.036 55.000 1.90 0.00 36.79 2.57
981 1044 0.250513 ACTTGGAGAGCCGGTCATTC 59.749 55.000 1.90 0.00 36.79 2.67
982 1045 0.462759 CTTGGAGAGCCGGTCATTCC 60.463 60.000 1.90 6.40 36.79 3.01
986 1049 0.250081 GAGAGCCGGTCATTCCATCC 60.250 60.000 1.90 0.00 35.57 3.51
994 1057 1.597854 TCATTCCATCCATCCGCGC 60.598 57.895 0.00 0.00 0.00 6.86
1023 1086 2.912025 CAAGGGTGCGGCCTGTTT 60.912 61.111 0.00 0.00 37.43 2.83
1410 1473 1.516603 GCTGGTCTTCGAGTACGCC 60.517 63.158 0.00 0.00 39.58 5.68
1608 1671 1.406341 GGTAACATGGACGCCAAGCTA 60.406 52.381 0.00 0.00 36.95 3.32
1852 1915 3.635191 TGTGCCCCACGATCAGCA 61.635 61.111 0.00 0.00 37.14 4.41
2035 2098 3.060020 TTGATCTCGGCCGTCGGAC 62.060 63.158 27.15 12.55 39.77 4.79
2112 2175 7.061441 GCTGTTGATTGTGATTTGTGAATAGTG 59.939 37.037 0.00 0.00 0.00 2.74
2149 2214 3.557595 GGCAGGTAGAAGAATGAATGTCG 59.442 47.826 0.00 0.00 0.00 4.35
2323 2391 9.458374 GTCCAATGAACGGGTAATTTTATATTG 57.542 33.333 0.00 0.00 0.00 1.90
2334 2402 7.147897 GGGTAATTTTATATTGGGCCTATCTGC 60.148 40.741 4.53 0.00 0.00 4.26
2351 2419 2.760092 TCTGCTTTTTGAGGCACTTTGT 59.240 40.909 0.00 0.00 41.55 2.83
2408 2478 1.005347 CGCCGTGCCGTAGAAAATTAG 60.005 52.381 0.00 0.00 0.00 1.73
2412 2482 2.606272 CGTGCCGTAGAAAATTAGTCCC 59.394 50.000 0.00 0.00 0.00 4.46
2414 2484 2.841881 TGCCGTAGAAAATTAGTCCCCT 59.158 45.455 0.00 0.00 0.00 4.79
2437 2507 1.843992 GCCATCAACGATTGAATGGC 58.156 50.000 22.07 22.07 46.56 4.40
2461 2542 3.935315 TCTGTACAGACGTACTACAGCT 58.065 45.455 21.74 0.00 46.88 4.24
2474 2555 2.903784 ACTACAGCTCCAACCATGTACA 59.096 45.455 0.00 0.00 0.00 2.90
2495 2576 5.702865 ACATTAACATGCATGTGAACAGAC 58.297 37.500 31.98 0.00 41.61 3.51
2514 2595 2.577449 CGCAAGTGGGTTTCAACTTT 57.423 45.000 0.00 0.00 0.00 2.66
2515 2596 2.459934 CGCAAGTGGGTTTCAACTTTC 58.540 47.619 0.00 0.00 0.00 2.62
2516 2597 2.159310 CGCAAGTGGGTTTCAACTTTCA 60.159 45.455 0.00 0.00 0.00 2.69
2518 2599 4.249661 GCAAGTGGGTTTCAACTTTCAAA 58.750 39.130 0.00 0.00 0.00 2.69
2519 2600 4.092821 GCAAGTGGGTTTCAACTTTCAAAC 59.907 41.667 0.00 0.00 0.00 2.93
2520 2601 4.104696 AGTGGGTTTCAACTTTCAAACG 57.895 40.909 0.00 0.00 33.94 3.60
2521 2602 3.759618 AGTGGGTTTCAACTTTCAAACGA 59.240 39.130 0.00 0.00 33.94 3.85
2522 2603 4.401202 AGTGGGTTTCAACTTTCAAACGAT 59.599 37.500 0.00 0.00 33.94 3.73
2523 2604 4.738252 GTGGGTTTCAACTTTCAAACGATC 59.262 41.667 0.00 0.00 33.94 3.69
2524 2605 4.642885 TGGGTTTCAACTTTCAAACGATCT 59.357 37.500 0.00 0.00 33.94 2.75
2525 2606 4.976116 GGGTTTCAACTTTCAAACGATCTG 59.024 41.667 0.00 0.00 33.94 2.90
2526 2607 5.449999 GGGTTTCAACTTTCAAACGATCTGT 60.450 40.000 0.00 0.00 33.94 3.41
2527 2608 6.033966 GGTTTCAACTTTCAAACGATCTGTT 58.966 36.000 0.00 0.00 44.59 3.16
2528 2609 7.190871 GGTTTCAACTTTCAAACGATCTGTTA 58.809 34.615 0.00 0.00 40.84 2.41
2529 2610 7.165318 GGTTTCAACTTTCAAACGATCTGTTAC 59.835 37.037 0.00 0.00 40.84 2.50
2538 2619 6.741109 TCAAACGATCTGTTACTACTGTGAA 58.259 36.000 0.00 0.00 40.84 3.18
2564 4233 7.573968 AAAATCGGCAGCTCTTATTTTATCT 57.426 32.000 0.00 0.00 30.22 1.98
2565 4234 6.551385 AATCGGCAGCTCTTATTTTATCTG 57.449 37.500 0.00 0.00 0.00 2.90
2566 4235 5.276461 TCGGCAGCTCTTATTTTATCTGA 57.724 39.130 0.00 0.00 0.00 3.27
2573 4242 8.840321 GCAGCTCTTATTTTATCTGACCATTTA 58.160 33.333 0.00 0.00 0.00 1.40
2593 4262 8.400186 CCATTTAAAAGCCATTTTGATCATTCC 58.600 33.333 0.00 0.00 39.01 3.01
2597 4266 5.943349 AAGCCATTTTGATCATTCCATCA 57.057 34.783 0.00 0.00 0.00 3.07
2598 4267 6.494666 AAGCCATTTTGATCATTCCATCAT 57.505 33.333 0.00 0.00 32.69 2.45
2603 4308 7.384115 GCCATTTTGATCATTCCATCATACAAG 59.616 37.037 0.00 0.00 32.69 3.16
2610 4315 9.457436 TGATCATTCCATCATACAAGATATTGG 57.543 33.333 4.88 0.00 0.00 3.16
2627 4332 3.949586 TTGGGAGGCATGACATATGAA 57.050 42.857 10.38 0.00 0.00 2.57
2634 4339 5.449107 AGGCATGACATATGAATTCTTGC 57.551 39.130 10.38 15.09 38.86 4.01
2639 4347 7.364970 GCATGACATATGAATTCTTGCACATA 58.635 34.615 19.43 0.00 39.20 2.29
2678 4386 4.979943 TTTGACAACTTGATGCTTGTGA 57.020 36.364 0.00 0.00 30.59 3.58
2716 4424 5.912360 TCAGATTTCTTGTATGCGCATAG 57.088 39.130 29.66 20.22 0.00 2.23
2724 4432 6.435430 TCTTGTATGCGCATAGAATGTTTT 57.565 33.333 32.35 9.08 0.00 2.43
2728 4436 3.763097 TGCGCATAGAATGTTTTCTGG 57.237 42.857 5.66 0.00 42.25 3.86
2736 4444 7.483307 GCATAGAATGTTTTCTGGAATGCTTA 58.517 34.615 11.79 0.00 42.71 3.09
2741 4449 8.587608 AGAATGTTTTCTGGAATGCTTATGAAA 58.412 29.630 0.00 0.00 40.74 2.69
2745 4453 7.168972 TGTTTTCTGGAATGCTTATGAAAAACG 59.831 33.333 0.00 0.00 35.91 3.60
2782 4497 0.169009 GCTTCGGCTGCACCTTTAAG 59.831 55.000 0.50 5.96 38.08 1.85
2789 4504 1.198637 GCTGCACCTTTAAGCTCACAG 59.801 52.381 0.00 0.00 34.05 3.66
2790 4505 1.198637 CTGCACCTTTAAGCTCACAGC 59.801 52.381 0.00 0.00 42.84 4.40
2855 4601 4.502105 TCACCAATAAGCTAGCATTCCA 57.498 40.909 18.83 0.00 0.00 3.53
2859 4605 6.380846 TCACCAATAAGCTAGCATTCCAAAAT 59.619 34.615 18.83 0.00 0.00 1.82
2958 4704 4.215109 TCCTTTCCTCCCTTTTTGTTCTG 58.785 43.478 0.00 0.00 0.00 3.02
2996 4742 5.107109 TGTTGTATGTTAGCAGCAAAGTG 57.893 39.130 0.00 0.00 0.00 3.16
3006 4752 3.070018 AGCAGCAAAGTGTGTGATCTAC 58.930 45.455 0.00 0.00 0.00 2.59
3018 4764 4.655649 TGTGTGATCTACATCTATTGGCCT 59.344 41.667 3.32 0.00 42.24 5.19
3019 4765 5.221521 TGTGTGATCTACATCTATTGGCCTC 60.222 44.000 3.32 0.00 42.24 4.70
3020 4766 4.284490 TGTGATCTACATCTATTGGCCTCC 59.716 45.833 3.32 0.00 33.42 4.30
3021 4767 3.840666 TGATCTACATCTATTGGCCTCCC 59.159 47.826 3.32 0.00 0.00 4.30
3029 4775 0.539986 TATTGGCCTCCCACTTCGTC 59.460 55.000 3.32 0.00 41.97 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.676006 GTAATTTGGGCGGACATGAGG 59.324 52.381 0.00 0.00 0.00 3.86
1 2 2.364632 TGTAATTTGGGCGGACATGAG 58.635 47.619 0.00 0.00 0.00 2.90
3 4 2.491693 ACTTGTAATTTGGGCGGACATG 59.508 45.455 0.00 0.00 0.00 3.21
5 6 2.279935 ACTTGTAATTTGGGCGGACA 57.720 45.000 0.00 0.00 0.00 4.02
6 7 2.352323 CCAACTTGTAATTTGGGCGGAC 60.352 50.000 5.98 0.00 38.96 4.79
7 8 1.889829 CCAACTTGTAATTTGGGCGGA 59.110 47.619 5.98 0.00 38.96 5.54
8 9 1.889829 TCCAACTTGTAATTTGGGCGG 59.110 47.619 12.12 0.00 42.35 6.13
9 10 3.866883 ATCCAACTTGTAATTTGGGCG 57.133 42.857 12.12 0.00 42.35 6.13
10 11 6.593770 CCTTAAATCCAACTTGTAATTTGGGC 59.406 38.462 12.12 0.00 42.35 5.36
11 12 7.102993 CCCTTAAATCCAACTTGTAATTTGGG 58.897 38.462 12.12 7.90 42.35 4.12
12 13 7.102993 CCCCTTAAATCCAACTTGTAATTTGG 58.897 38.462 7.25 7.25 43.29 3.28
13 14 7.676004 ACCCCTTAAATCCAACTTGTAATTTG 58.324 34.615 8.56 0.00 0.00 2.32
14 15 7.865530 ACCCCTTAAATCCAACTTGTAATTT 57.134 32.000 0.00 5.28 0.00 1.82
15 16 7.121611 CGTACCCCTTAAATCCAACTTGTAATT 59.878 37.037 0.00 0.00 0.00 1.40
16 17 6.600427 CGTACCCCTTAAATCCAACTTGTAAT 59.400 38.462 0.00 0.00 0.00 1.89
17 18 5.939296 CGTACCCCTTAAATCCAACTTGTAA 59.061 40.000 0.00 0.00 0.00 2.41
18 19 5.248020 TCGTACCCCTTAAATCCAACTTGTA 59.752 40.000 0.00 0.00 0.00 2.41
19 20 4.041938 TCGTACCCCTTAAATCCAACTTGT 59.958 41.667 0.00 0.00 0.00 3.16
20 21 4.581868 TCGTACCCCTTAAATCCAACTTG 58.418 43.478 0.00 0.00 0.00 3.16
21 22 4.533311 TCTCGTACCCCTTAAATCCAACTT 59.467 41.667 0.00 0.00 0.00 2.66
22 23 4.098894 TCTCGTACCCCTTAAATCCAACT 58.901 43.478 0.00 0.00 0.00 3.16
23 24 4.476628 TCTCGTACCCCTTAAATCCAAC 57.523 45.455 0.00 0.00 0.00 3.77
24 25 5.221581 GCTATCTCGTACCCCTTAAATCCAA 60.222 44.000 0.00 0.00 0.00 3.53
25 26 4.282703 GCTATCTCGTACCCCTTAAATCCA 59.717 45.833 0.00 0.00 0.00 3.41
26 27 4.527427 AGCTATCTCGTACCCCTTAAATCC 59.473 45.833 0.00 0.00 0.00 3.01
27 28 5.712004 GAGCTATCTCGTACCCCTTAAATC 58.288 45.833 0.00 0.00 0.00 2.17
28 29 5.725325 GAGCTATCTCGTACCCCTTAAAT 57.275 43.478 0.00 0.00 0.00 1.40
48 49 0.036010 ACCTGGCTCAAATGTCCGAG 60.036 55.000 0.00 0.00 0.00 4.63
49 50 1.066430 GTACCTGGCTCAAATGTCCGA 60.066 52.381 0.00 0.00 0.00 4.55
50 51 1.369625 GTACCTGGCTCAAATGTCCG 58.630 55.000 0.00 0.00 0.00 4.79
51 52 1.066430 TCGTACCTGGCTCAAATGTCC 60.066 52.381 0.00 0.00 0.00 4.02
52 53 2.271800 CTCGTACCTGGCTCAAATGTC 58.728 52.381 0.00 0.00 0.00 3.06
53 54 1.066143 CCTCGTACCTGGCTCAAATGT 60.066 52.381 0.00 0.00 0.00 2.71
54 55 1.656652 CCTCGTACCTGGCTCAAATG 58.343 55.000 0.00 0.00 0.00 2.32
55 56 0.541863 CCCTCGTACCTGGCTCAAAT 59.458 55.000 0.00 0.00 0.00 2.32
56 57 1.550130 CCCCTCGTACCTGGCTCAAA 61.550 60.000 0.00 0.00 0.00 2.69
57 58 1.987855 CCCCTCGTACCTGGCTCAA 60.988 63.158 0.00 0.00 0.00 3.02
58 59 2.363795 CCCCTCGTACCTGGCTCA 60.364 66.667 0.00 0.00 0.00 4.26
59 60 2.363925 ACCCCTCGTACCTGGCTC 60.364 66.667 0.00 0.00 0.00 4.70
60 61 2.363925 GACCCCTCGTACCTGGCT 60.364 66.667 0.00 0.00 0.00 4.75
61 62 3.468140 GGACCCCTCGTACCTGGC 61.468 72.222 0.00 0.00 0.00 4.85
62 63 2.038329 TGGACCCCTCGTACCTGG 59.962 66.667 0.00 0.00 0.00 4.45
63 64 0.033796 TACTGGACCCCTCGTACCTG 60.034 60.000 0.00 0.00 0.00 4.00
64 65 0.258194 CTACTGGACCCCTCGTACCT 59.742 60.000 0.00 0.00 0.00 3.08
65 66 0.754587 CCTACTGGACCCCTCGTACC 60.755 65.000 0.00 0.00 34.57 3.34
66 67 0.257039 TCCTACTGGACCCCTCGTAC 59.743 60.000 0.00 0.00 37.46 3.67
67 68 2.713967 TCCTACTGGACCCCTCGTA 58.286 57.895 0.00 0.00 37.46 3.43
68 69 3.516780 TCCTACTGGACCCCTCGT 58.483 61.111 0.00 0.00 37.46 4.18
76 77 0.899720 AAAATCCGCGTCCTACTGGA 59.100 50.000 4.92 0.00 40.69 3.86
77 78 1.396996 CAAAAATCCGCGTCCTACTGG 59.603 52.381 4.92 0.00 0.00 4.00
78 79 1.396996 CCAAAAATCCGCGTCCTACTG 59.603 52.381 4.92 0.00 0.00 2.74
79 80 1.002773 ACCAAAAATCCGCGTCCTACT 59.997 47.619 4.92 0.00 0.00 2.57
80 81 1.395954 GACCAAAAATCCGCGTCCTAC 59.604 52.381 4.92 0.00 0.00 3.18
81 82 1.002201 TGACCAAAAATCCGCGTCCTA 59.998 47.619 4.92 0.00 0.00 2.94
82 83 0.250553 TGACCAAAAATCCGCGTCCT 60.251 50.000 4.92 0.00 0.00 3.85
83 84 0.168128 CTGACCAAAAATCCGCGTCC 59.832 55.000 4.92 0.00 0.00 4.79
84 85 0.168128 CCTGACCAAAAATCCGCGTC 59.832 55.000 4.92 0.00 0.00 5.19
85 86 1.241315 CCCTGACCAAAAATCCGCGT 61.241 55.000 4.92 0.00 0.00 6.01
86 87 1.506262 CCCTGACCAAAAATCCGCG 59.494 57.895 0.00 0.00 0.00 6.46
87 88 1.215382 GCCCTGACCAAAAATCCGC 59.785 57.895 0.00 0.00 0.00 5.54
88 89 0.527565 CTGCCCTGACCAAAAATCCG 59.472 55.000 0.00 0.00 0.00 4.18
89 90 0.247460 GCTGCCCTGACCAAAAATCC 59.753 55.000 0.00 0.00 0.00 3.01
90 91 0.109132 CGCTGCCCTGACCAAAAATC 60.109 55.000 0.00 0.00 0.00 2.17
91 92 0.827507 ACGCTGCCCTGACCAAAAAT 60.828 50.000 0.00 0.00 0.00 1.82
92 93 1.452145 GACGCTGCCCTGACCAAAAA 61.452 55.000 0.00 0.00 0.00 1.94
93 94 1.896660 GACGCTGCCCTGACCAAAA 60.897 57.895 0.00 0.00 0.00 2.44
94 95 2.281484 GACGCTGCCCTGACCAAA 60.281 61.111 0.00 0.00 0.00 3.28
95 96 4.329545 GGACGCTGCCCTGACCAA 62.330 66.667 0.00 0.00 0.00 3.67
114 115 3.842925 TTGTTCCTGCGGGACAGCC 62.843 63.158 15.79 3.17 45.78 4.85
115 116 1.244019 ATTTGTTCCTGCGGGACAGC 61.244 55.000 15.79 8.41 45.78 4.40
116 117 0.523072 CATTTGTTCCTGCGGGACAG 59.477 55.000 15.79 1.02 46.77 3.51
117 118 0.109532 TCATTTGTTCCTGCGGGACA 59.890 50.000 15.79 13.10 42.05 4.02
118 119 0.804989 CTCATTTGTTCCTGCGGGAC 59.195 55.000 15.79 10.44 42.05 4.46
119 120 0.322456 CCTCATTTGTTCCTGCGGGA 60.322 55.000 11.27 11.27 40.36 5.14
120 121 1.315257 CCCTCATTTGTTCCTGCGGG 61.315 60.000 4.71 4.71 31.45 6.13
121 122 1.315257 CCCCTCATTTGTTCCTGCGG 61.315 60.000 0.00 0.00 0.00 5.69
122 123 0.609131 ACCCCTCATTTGTTCCTGCG 60.609 55.000 0.00 0.00 0.00 5.18
123 124 2.290960 ACTACCCCTCATTTGTTCCTGC 60.291 50.000 0.00 0.00 0.00 4.85
124 125 3.347216 CACTACCCCTCATTTGTTCCTG 58.653 50.000 0.00 0.00 0.00 3.86
125 126 2.308866 CCACTACCCCTCATTTGTTCCT 59.691 50.000 0.00 0.00 0.00 3.36
126 127 2.620627 CCCACTACCCCTCATTTGTTCC 60.621 54.545 0.00 0.00 0.00 3.62
127 128 2.041216 ACCCACTACCCCTCATTTGTTC 59.959 50.000 0.00 0.00 0.00 3.18
128 129 2.041216 GACCCACTACCCCTCATTTGTT 59.959 50.000 0.00 0.00 0.00 2.83
129 130 1.633945 GACCCACTACCCCTCATTTGT 59.366 52.381 0.00 0.00 0.00 2.83
130 131 1.064685 GGACCCACTACCCCTCATTTG 60.065 57.143 0.00 0.00 0.00 2.32
131 132 1.296002 GGACCCACTACCCCTCATTT 58.704 55.000 0.00 0.00 0.00 2.32
132 133 0.981277 CGGACCCACTACCCCTCATT 60.981 60.000 0.00 0.00 0.00 2.57
133 134 1.382695 CGGACCCACTACCCCTCAT 60.383 63.158 0.00 0.00 0.00 2.90
134 135 2.038329 CGGACCCACTACCCCTCA 59.962 66.667 0.00 0.00 0.00 3.86
135 136 2.762875 CCGGACCCACTACCCCTC 60.763 72.222 0.00 0.00 0.00 4.30
136 137 3.184123 AACCGGACCCACTACCCCT 62.184 63.158 9.46 0.00 0.00 4.79
137 138 2.608678 AACCGGACCCACTACCCC 60.609 66.667 9.46 0.00 0.00 4.95
138 139 0.904394 TACAACCGGACCCACTACCC 60.904 60.000 9.46 0.00 0.00 3.69
139 140 0.533951 CTACAACCGGACCCACTACC 59.466 60.000 9.46 0.00 0.00 3.18
140 141 1.549203 TCTACAACCGGACCCACTAC 58.451 55.000 9.46 0.00 0.00 2.73
141 142 2.537633 ATCTACAACCGGACCCACTA 57.462 50.000 9.46 0.00 0.00 2.74
142 143 2.105766 GTATCTACAACCGGACCCACT 58.894 52.381 9.46 0.00 0.00 4.00
143 144 2.100418 GAGTATCTACAACCGGACCCAC 59.900 54.545 9.46 0.00 0.00 4.61
144 145 2.291735 TGAGTATCTACAACCGGACCCA 60.292 50.000 9.46 0.00 34.92 4.51
145 146 2.381911 TGAGTATCTACAACCGGACCC 58.618 52.381 9.46 0.00 34.92 4.46
146 147 5.979288 ATATGAGTATCTACAACCGGACC 57.021 43.478 9.46 0.00 34.92 4.46
147 148 7.389884 TCAGTATATGAGTATCTACAACCGGAC 59.610 40.741 9.46 0.00 34.92 4.79
148 149 7.389884 GTCAGTATATGAGTATCTACAACCGGA 59.610 40.741 9.46 0.00 39.07 5.14
149 150 7.174426 TGTCAGTATATGAGTATCTACAACCGG 59.826 40.741 0.00 0.00 39.07 5.28
150 151 8.095937 TGTCAGTATATGAGTATCTACAACCG 57.904 38.462 0.00 0.00 39.07 4.44
151 152 9.847706 CATGTCAGTATATGAGTATCTACAACC 57.152 37.037 0.00 0.00 39.07 3.77
163 164 6.661304 AGCATCACTCATGTCAGTATATGA 57.339 37.500 10.75 0.00 34.56 2.15
164 165 7.063191 GCTAAGCATCACTCATGTCAGTATATG 59.937 40.741 0.00 0.00 34.56 1.78
165 166 7.039152 AGCTAAGCATCACTCATGTCAGTATAT 60.039 37.037 0.00 0.00 34.56 0.86
166 167 6.266330 AGCTAAGCATCACTCATGTCAGTATA 59.734 38.462 0.00 0.00 34.56 1.47
167 168 5.070180 AGCTAAGCATCACTCATGTCAGTAT 59.930 40.000 0.00 0.00 34.56 2.12
168 169 4.403752 AGCTAAGCATCACTCATGTCAGTA 59.596 41.667 0.00 0.00 34.56 2.74
169 170 3.197333 AGCTAAGCATCACTCATGTCAGT 59.803 43.478 0.00 0.00 34.56 3.41
170 171 3.794717 AGCTAAGCATCACTCATGTCAG 58.205 45.455 0.00 0.00 34.56 3.51
171 172 3.900966 AGCTAAGCATCACTCATGTCA 57.099 42.857 0.00 0.00 34.56 3.58
172 173 5.353678 AGAAAAGCTAAGCATCACTCATGTC 59.646 40.000 0.00 0.00 34.56 3.06
173 174 5.251764 AGAAAAGCTAAGCATCACTCATGT 58.748 37.500 0.00 0.00 34.56 3.21
174 175 5.814764 AGAAAAGCTAAGCATCACTCATG 57.185 39.130 0.00 0.00 35.29 3.07
175 176 6.830873 AAAGAAAAGCTAAGCATCACTCAT 57.169 33.333 0.00 0.00 0.00 2.90
176 177 6.639632 AAAAGAAAAGCTAAGCATCACTCA 57.360 33.333 0.00 0.00 0.00 3.41
177 178 7.752686 CCTAAAAAGAAAAGCTAAGCATCACTC 59.247 37.037 0.00 0.00 0.00 3.51
178 179 7.309438 CCCTAAAAAGAAAAGCTAAGCATCACT 60.309 37.037 0.00 0.00 0.00 3.41
179 180 6.808704 CCCTAAAAAGAAAAGCTAAGCATCAC 59.191 38.462 0.00 0.00 0.00 3.06
180 181 6.071391 CCCCTAAAAAGAAAAGCTAAGCATCA 60.071 38.462 0.00 0.00 0.00 3.07
181 182 6.071334 ACCCCTAAAAAGAAAAGCTAAGCATC 60.071 38.462 0.00 0.00 0.00 3.91
182 183 5.780282 ACCCCTAAAAAGAAAAGCTAAGCAT 59.220 36.000 0.00 0.00 0.00 3.79
183 184 5.144832 ACCCCTAAAAAGAAAAGCTAAGCA 58.855 37.500 0.00 0.00 0.00 3.91
184 185 5.723672 ACCCCTAAAAAGAAAAGCTAAGC 57.276 39.130 0.00 0.00 0.00 3.09
185 186 8.575649 TCATACCCCTAAAAAGAAAAGCTAAG 57.424 34.615 0.00 0.00 0.00 2.18
186 187 8.168058 ACTCATACCCCTAAAAAGAAAAGCTAA 58.832 33.333 0.00 0.00 0.00 3.09
187 188 7.610305 CACTCATACCCCTAAAAAGAAAAGCTA 59.390 37.037 0.00 0.00 0.00 3.32
188 189 6.434340 CACTCATACCCCTAAAAAGAAAAGCT 59.566 38.462 0.00 0.00 0.00 3.74
189 190 6.433093 TCACTCATACCCCTAAAAAGAAAAGC 59.567 38.462 0.00 0.00 0.00 3.51
190 191 7.996098 TCACTCATACCCCTAAAAAGAAAAG 57.004 36.000 0.00 0.00 0.00 2.27
191 192 7.093945 GCATCACTCATACCCCTAAAAAGAAAA 60.094 37.037 0.00 0.00 0.00 2.29
192 193 6.377146 GCATCACTCATACCCCTAAAAAGAAA 59.623 38.462 0.00 0.00 0.00 2.52
193 194 5.885912 GCATCACTCATACCCCTAAAAAGAA 59.114 40.000 0.00 0.00 0.00 2.52
194 195 5.191722 AGCATCACTCATACCCCTAAAAAGA 59.808 40.000 0.00 0.00 0.00 2.52
195 196 5.440610 AGCATCACTCATACCCCTAAAAAG 58.559 41.667 0.00 0.00 0.00 2.27
196 197 5.450818 AGCATCACTCATACCCCTAAAAA 57.549 39.130 0.00 0.00 0.00 1.94
197 198 5.450818 AAGCATCACTCATACCCCTAAAA 57.549 39.130 0.00 0.00 0.00 1.52
198 199 5.192927 CAAAGCATCACTCATACCCCTAAA 58.807 41.667 0.00 0.00 0.00 1.85
199 200 4.780815 CAAAGCATCACTCATACCCCTAA 58.219 43.478 0.00 0.00 0.00 2.69
200 201 3.433598 GCAAAGCATCACTCATACCCCTA 60.434 47.826 0.00 0.00 0.00 3.53
201 202 2.684927 GCAAAGCATCACTCATACCCCT 60.685 50.000 0.00 0.00 0.00 4.79
202 203 1.678101 GCAAAGCATCACTCATACCCC 59.322 52.381 0.00 0.00 0.00 4.95
203 204 2.648059 AGCAAAGCATCACTCATACCC 58.352 47.619 0.00 0.00 0.00 3.69
204 205 3.733077 GCAAGCAAAGCATCACTCATACC 60.733 47.826 0.00 0.00 0.00 2.73
205 206 3.432782 GCAAGCAAAGCATCACTCATAC 58.567 45.455 0.00 0.00 0.00 2.39
206 207 2.424601 GGCAAGCAAAGCATCACTCATA 59.575 45.455 0.00 0.00 0.00 2.15
207 208 1.203994 GGCAAGCAAAGCATCACTCAT 59.796 47.619 0.00 0.00 0.00 2.90
208 209 0.599558 GGCAAGCAAAGCATCACTCA 59.400 50.000 0.00 0.00 0.00 3.41
209 210 0.599558 TGGCAAGCAAAGCATCACTC 59.400 50.000 0.00 0.00 0.00 3.51
210 211 1.067142 CATGGCAAGCAAAGCATCACT 60.067 47.619 0.00 0.00 0.00 3.41
269 270 3.187227 GTGTTGACTGCAATGAGTTCGAT 59.813 43.478 0.00 0.00 36.22 3.59
270 271 2.543848 GTGTTGACTGCAATGAGTTCGA 59.456 45.455 0.00 0.00 36.22 3.71
271 272 2.660094 CGTGTTGACTGCAATGAGTTCG 60.660 50.000 0.00 0.00 36.22 3.95
272 273 2.349817 CCGTGTTGACTGCAATGAGTTC 60.350 50.000 0.00 0.00 36.22 3.01
330 331 1.458777 AGGAGTGTCGGTTCCACCA 60.459 57.895 0.00 0.00 38.47 4.17
458 459 3.571401 GCTAGCTTGGGTCCTATACGTTA 59.429 47.826 7.70 0.00 0.00 3.18
459 460 2.364647 GCTAGCTTGGGTCCTATACGTT 59.635 50.000 7.70 0.00 0.00 3.99
461 462 1.272769 GGCTAGCTTGGGTCCTATACG 59.727 57.143 15.72 0.00 0.00 3.06
462 463 1.272769 CGGCTAGCTTGGGTCCTATAC 59.727 57.143 15.72 0.00 0.00 1.47
463 464 1.629043 CGGCTAGCTTGGGTCCTATA 58.371 55.000 15.72 0.00 0.00 1.31
464 465 1.759459 GCGGCTAGCTTGGGTCCTAT 61.759 60.000 15.72 0.00 44.04 2.57
546 547 1.278637 CAACGTGTTCTTGACCCGC 59.721 57.895 0.00 0.00 31.97 6.13
604 605 6.183360 ACGTCATCAACATCTTGGTTTCTTTT 60.183 34.615 0.00 0.00 0.00 2.27
606 607 4.821805 ACGTCATCAACATCTTGGTTTCTT 59.178 37.500 0.00 0.00 0.00 2.52
608 609 4.749245 ACGTCATCAACATCTTGGTTTC 57.251 40.909 0.00 0.00 0.00 2.78
610 611 4.894784 ACTACGTCATCAACATCTTGGTT 58.105 39.130 0.00 0.00 0.00 3.67
611 612 4.537135 ACTACGTCATCAACATCTTGGT 57.463 40.909 0.00 0.00 0.00 3.67
612 613 4.499399 CGTACTACGTCATCAACATCTTGG 59.501 45.833 0.00 0.00 36.74 3.61
613 614 5.606335 CGTACTACGTCATCAACATCTTG 57.394 43.478 0.00 0.00 36.74 3.02
632 664 2.297698 TCTTTCAGAGTGGGGACGTA 57.702 50.000 0.00 0.00 0.00 3.57
744 797 0.541392 TATATATGCCAGGCCGCTGG 59.459 55.000 9.64 6.66 46.83 4.85
745 798 2.627515 ATATATATGCCAGGCCGCTG 57.372 50.000 9.64 0.00 0.00 5.18
746 799 3.038280 TGTATATATATGCCAGGCCGCT 58.962 45.455 9.64 0.00 0.00 5.52
747 800 3.131396 GTGTATATATATGCCAGGCCGC 58.869 50.000 9.64 0.00 0.00 6.53
748 801 4.371786 CTGTGTATATATATGCCAGGCCG 58.628 47.826 9.64 0.00 0.00 6.13
749 802 4.164221 ACCTGTGTATATATATGCCAGGCC 59.836 45.833 28.27 0.00 38.75 5.19
750 803 5.359194 ACCTGTGTATATATATGCCAGGC 57.641 43.478 28.27 3.66 38.75 4.85
751 804 6.931281 GCATACCTGTGTATATATATGCCAGG 59.069 42.308 27.52 27.52 39.19 4.45
752 805 7.500141 TGCATACCTGTGTATATATATGCCAG 58.500 38.462 15.94 15.80 42.64 4.85
753 806 7.430760 TGCATACCTGTGTATATATATGCCA 57.569 36.000 15.94 4.17 42.64 4.92
754 807 8.908786 AATGCATACCTGTGTATATATATGCC 57.091 34.615 15.94 0.00 42.64 4.40
907 960 1.807573 CTCTTCTCCGACGCTTGCC 60.808 63.158 0.00 0.00 0.00 4.52
972 1035 0.603707 CGGATGGATGGAATGACCGG 60.604 60.000 0.00 0.00 42.61 5.28
975 1038 1.845809 GCGCGGATGGATGGAATGAC 61.846 60.000 8.83 0.00 0.00 3.06
976 1039 1.597854 GCGCGGATGGATGGAATGA 60.598 57.895 8.83 0.00 0.00 2.57
977 1040 2.949106 GCGCGGATGGATGGAATG 59.051 61.111 8.83 0.00 0.00 2.67
978 1041 2.666190 CGCGCGGATGGATGGAAT 60.666 61.111 24.84 0.00 0.00 3.01
986 1049 3.665825 AACATTGTGCGCGCGGATG 62.666 57.895 33.06 28.09 0.00 3.51
994 1057 1.769733 CACCCTTGAAACATTGTGCG 58.230 50.000 0.00 0.00 0.00 5.34
1846 1909 1.002134 CCACGTTCCCCTTGCTGAT 60.002 57.895 0.00 0.00 0.00 2.90
1852 1915 3.327404 ATCGGCCACGTTCCCCTT 61.327 61.111 2.24 0.00 41.85 3.95
2035 2098 1.987807 ATCCTGCGGTCCAATCTGGG 61.988 60.000 0.00 0.00 38.32 4.45
2112 2175 7.299246 TCTACCTGCCCTAACATTACTAATC 57.701 40.000 0.00 0.00 0.00 1.75
2149 2214 1.270826 TCTGAGTACTCACACTGCAGC 59.729 52.381 21.74 0.00 35.46 5.25
2323 2391 2.027385 CCTCAAAAAGCAGATAGGCCC 58.973 52.381 0.00 0.00 0.00 5.80
2334 2402 6.959671 TGTAAAACAAAGTGCCTCAAAAAG 57.040 33.333 0.00 0.00 0.00 2.27
2351 2419 3.585289 TGTCCTCCACCAGCTATGTAAAA 59.415 43.478 0.00 0.00 0.00 1.52
2412 2482 1.019673 CAATCGTTGATGGCCAGAGG 58.980 55.000 13.05 5.74 0.00 3.69
2414 2484 2.488204 TTCAATCGTTGATGGCCAGA 57.512 45.000 13.05 2.08 39.84 3.86
2474 2555 4.672542 GCGTCTGTTCACATGCATGTTAAT 60.673 41.667 29.48 5.57 39.39 1.40
2495 2576 2.159310 TGAAAGTTGAAACCCACTTGCG 60.159 45.455 0.00 0.00 0.00 4.85
2511 2592 7.381408 TCACAGTAGTAACAGATCGTTTGAAAG 59.619 37.037 7.96 0.33 39.14 2.62
2512 2593 7.204604 TCACAGTAGTAACAGATCGTTTGAAA 58.795 34.615 7.96 0.00 39.14 2.69
2513 2594 6.741109 TCACAGTAGTAACAGATCGTTTGAA 58.259 36.000 7.96 0.00 39.14 2.69
2514 2595 6.321848 TCACAGTAGTAACAGATCGTTTGA 57.678 37.500 7.96 2.83 39.14 2.69
2515 2596 7.402811 TTTCACAGTAGTAACAGATCGTTTG 57.597 36.000 7.96 3.88 39.14 2.93
2516 2597 8.428186 TTTTTCACAGTAGTAACAGATCGTTT 57.572 30.769 7.96 0.00 39.14 3.60
2546 2627 5.126067 TGGTCAGATAAAATAAGAGCTGCC 58.874 41.667 0.00 0.00 0.00 4.85
2562 4231 7.060383 TCAAAATGGCTTTTAAATGGTCAGA 57.940 32.000 0.00 0.00 32.81 3.27
2563 4232 7.603404 TGATCAAAATGGCTTTTAAATGGTCAG 59.397 33.333 7.50 0.00 32.81 3.51
2564 4233 7.448420 TGATCAAAATGGCTTTTAAATGGTCA 58.552 30.769 7.50 7.50 32.81 4.02
2565 4234 7.903995 TGATCAAAATGGCTTTTAAATGGTC 57.096 32.000 0.00 1.42 32.81 4.02
2566 4235 8.866970 AATGATCAAAATGGCTTTTAAATGGT 57.133 26.923 0.00 0.00 32.81 3.55
2573 4242 6.713276 TGATGGAATGATCAAAATGGCTTTT 58.287 32.000 0.00 0.00 34.90 2.27
2593 4262 5.563592 TGCCTCCCAATATCTTGTATGATG 58.436 41.667 0.00 0.00 0.00 3.07
2597 4266 5.073554 TGTCATGCCTCCCAATATCTTGTAT 59.926 40.000 0.00 0.00 0.00 2.29
2598 4267 4.411869 TGTCATGCCTCCCAATATCTTGTA 59.588 41.667 0.00 0.00 0.00 2.41
2603 4308 5.748402 TCATATGTCATGCCTCCCAATATC 58.252 41.667 1.90 0.00 0.00 1.63
2610 4315 5.564259 GCAAGAATTCATATGTCATGCCTCC 60.564 44.000 8.44 0.00 0.00 4.30
2627 4332 7.452880 ACTACAACAATGTATGTGCAAGAAT 57.547 32.000 10.08 0.00 42.99 2.40
2658 4366 4.979943 TTCACAAGCATCAAGTTGTCAA 57.020 36.364 2.11 0.00 34.62 3.18
2669 4377 9.754382 GAACCATATCATAAAATTCACAAGCAT 57.246 29.630 0.00 0.00 0.00 3.79
2702 4410 6.412943 CAGAAAACATTCTATGCGCATACAAG 59.587 38.462 25.78 18.31 0.00 3.16
2705 4413 5.007626 TCCAGAAAACATTCTATGCGCATAC 59.992 40.000 25.78 12.70 0.00 2.39
2716 4424 8.761575 TTTCATAAGCATTCCAGAAAACATTC 57.238 30.769 0.00 0.00 0.00 2.67
2724 4432 6.567687 TTCGTTTTTCATAAGCATTCCAGA 57.432 33.333 0.00 0.00 0.00 3.86
2736 4444 8.710835 ACCAAAACAGTAAATTCGTTTTTCAT 57.289 26.923 0.00 0.00 40.02 2.57
2741 4449 4.736307 GCGACCAAAACAGTAAATTCGTTT 59.264 37.500 0.00 0.00 34.42 3.60
2745 4453 4.611366 CGAAGCGACCAAAACAGTAAATTC 59.389 41.667 0.00 0.00 0.00 2.17
2782 4497 7.721286 ATGTTGATAGTAATAAGCTGTGAGC 57.279 36.000 0.00 0.00 42.84 4.26
2820 4566 8.034058 GCTTATTGGTGAAGCCTATATACAAG 57.966 38.462 0.00 0.00 42.90 3.16
2855 4601 1.613437 CTCACCGGTGGCTTTCATTTT 59.387 47.619 33.40 0.00 0.00 1.82
2859 4605 0.181587 TTTCTCACCGGTGGCTTTCA 59.818 50.000 33.40 12.97 0.00 2.69
2996 4742 5.220710 AGGCCAATAGATGTAGATCACAC 57.779 43.478 5.01 0.00 40.86 3.82
3006 4752 2.808202 CGAAGTGGGAGGCCAATAGATG 60.808 54.545 5.01 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.