Multiple sequence alignment - TraesCS5B01G071700

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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 TraesCS5B01G071700 chr5B 100.000 2526 0 0 1 2526 83579759 83582284 0.000000e+00 4665
1 TraesCS5B01G071700 chr5B 93.375 2249 132 11 288 2526 394186452 394184211 0.000000e+00 3312
2 TraesCS5B01G071700 chr5B 91.246 297 26 0 1 297 648950992 648951288 3.030000e-109 405
3 TraesCS5B01G071700 chr5B 88.136 295 35 0 3 297 383997937 383998231 4.000000e-93 351
4 TraesCS5B01G071700 chr4A 94.713 2251 105 9 289 2526 705684748 705686997 0.000000e+00 3485
5 TraesCS5B01G071700 chr2D 93.692 2251 129 8 288 2526 610444032 610446281 0.000000e+00 3358
6 TraesCS5B01G071700 chr2D 93.253 2253 122 22 288 2526 275220745 275222981 0.000000e+00 3291
7 TraesCS5B01G071700 chr2D 91.241 2249 165 25 288 2526 6325039 6322813 0.000000e+00 3033
8 TraesCS5B01G071700 chr2D 90.703 2248 179 24 288 2526 54650200 54652426 0.000000e+00 2966
9 TraesCS5B01G071700 chr7B 93.502 2247 127 10 288 2526 579859984 579862219 0.000000e+00 3323
10 TraesCS5B01G071700 chr7B 89.899 297 28 2 1 297 455061401 455061107 5.100000e-102 381
11 TraesCS5B01G071700 chr5A 92.089 2250 160 15 288 2526 174356675 174354433 0.000000e+00 3153
12 TraesCS5B01G071700 chr7D 91.434 2253 169 20 288 2526 195568510 195566268 0.000000e+00 3070
13 TraesCS5B01G071700 chr1B 93.266 297 20 0 1 297 469328219 469328515 2.980000e-119 438
14 TraesCS5B01G071700 chr2B 93.380 287 19 0 1 287 567312613 567312899 2.320000e-115 425
15 TraesCS5B01G071700 chr4B 92.542 295 22 0 3 297 312553759 312553465 8.350000e-115 424
16 TraesCS5B01G071700 chr3B 91.525 295 25 0 3 297 33796459 33796753 8.410000e-110 407
17 TraesCS5B01G071700 chr3B 87.879 297 36 0 1 297 162176494 162176790 1.440000e-92 350
18 TraesCS5B01G071700 chr6B 89.226 297 32 0 1 297 513727267 513726971 3.070000e-99 372
19 TraesCS5B01G071700 chr1D 87.205 297 38 0 1 297 211406227 211406523 3.110000e-89 339


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 TraesCS5B01G071700 chr5B 83579759 83582284 2525 False 4665 4665 100.000 1 2526 1 chr5B.!!$F1 2525
1 TraesCS5B01G071700 chr5B 394184211 394186452 2241 True 3312 3312 93.375 288 2526 1 chr5B.!!$R1 2238
2 TraesCS5B01G071700 chr4A 705684748 705686997 2249 False 3485 3485 94.713 289 2526 1 chr4A.!!$F1 2237
3 TraesCS5B01G071700 chr2D 610444032 610446281 2249 False 3358 3358 93.692 288 2526 1 chr2D.!!$F3 2238
4 TraesCS5B01G071700 chr2D 275220745 275222981 2236 False 3291 3291 93.253 288 2526 1 chr2D.!!$F2 2238
5 TraesCS5B01G071700 chr2D 6322813 6325039 2226 True 3033 3033 91.241 288 2526 1 chr2D.!!$R1 2238
6 TraesCS5B01G071700 chr2D 54650200 54652426 2226 False 2966 2966 90.703 288 2526 1 chr2D.!!$F1 2238
7 TraesCS5B01G071700 chr7B 579859984 579862219 2235 False 3323 3323 93.502 288 2526 1 chr7B.!!$F1 2238
8 TraesCS5B01G071700 chr5A 174354433 174356675 2242 True 3153 3153 92.089 288 2526 1 chr5A.!!$R1 2238
9 TraesCS5B01G071700 chr7D 195566268 195568510 2242 True 3070 3070 91.434 288 2526 1 chr7D.!!$R1 2238

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
195 196 0.034059 ACTTCCTCAACCTGCTCGTG 59.966 55.0 0.0 0.0 0.0 4.35 F
196 197 0.034059 CTTCCTCAACCTGCTCGTGT 59.966 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 1460 0.800631 CATTGCAGCTGTGACGACAT 59.199 50.00 16.64 0.0 0.00 3.06 R
2108 2188 3.008157 TGCCATGCAACTTCCATCAAATT 59.992 39.13 0.00 0.0 34.76 1.82 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
31 32 2.749441 GCAGGAGGCAAGACAGGC 60.749 66.667 0.00 0.00 43.97 4.85
37 38 2.747855 GGCAAGACAGGCCCGAAG 60.748 66.667 0.00 0.00 45.87 3.79
38 39 2.347490 GCAAGACAGGCCCGAAGA 59.653 61.111 0.00 0.00 0.00 2.87
39 40 1.302511 GCAAGACAGGCCCGAAGAA 60.303 57.895 0.00 0.00 0.00 2.52
40 41 0.889186 GCAAGACAGGCCCGAAGAAA 60.889 55.000 0.00 0.00 0.00 2.52
41 42 1.160137 CAAGACAGGCCCGAAGAAAG 58.840 55.000 0.00 0.00 0.00 2.62
42 43 0.765510 AAGACAGGCCCGAAGAAAGT 59.234 50.000 0.00 0.00 0.00 2.66
43 44 0.035458 AGACAGGCCCGAAGAAAGTG 59.965 55.000 0.00 0.00 0.00 3.16
44 45 0.034896 GACAGGCCCGAAGAAAGTGA 59.965 55.000 0.00 0.00 0.00 3.41
45 46 0.472471 ACAGGCCCGAAGAAAGTGAA 59.528 50.000 0.00 0.00 0.00 3.18
46 47 0.875059 CAGGCCCGAAGAAAGTGAAC 59.125 55.000 0.00 0.00 0.00 3.18
47 48 0.472471 AGGCCCGAAGAAAGTGAACA 59.528 50.000 0.00 0.00 0.00 3.18
48 49 0.591659 GGCCCGAAGAAAGTGAACAC 59.408 55.000 0.00 0.00 0.00 3.32
49 50 0.591659 GCCCGAAGAAAGTGAACACC 59.408 55.000 1.11 0.00 0.00 4.16
50 51 1.814248 GCCCGAAGAAAGTGAACACCT 60.814 52.381 1.11 0.00 0.00 4.00
51 52 1.873591 CCCGAAGAAAGTGAACACCTG 59.126 52.381 1.11 0.00 0.00 4.00
52 53 1.264288 CCGAAGAAAGTGAACACCTGC 59.736 52.381 1.11 0.00 0.00 4.85
53 54 1.264288 CGAAGAAAGTGAACACCTGCC 59.736 52.381 1.11 0.00 0.00 4.85
54 55 1.609072 GAAGAAAGTGAACACCTGCCC 59.391 52.381 1.11 0.00 0.00 5.36
55 56 0.550914 AGAAAGTGAACACCTGCCCA 59.449 50.000 1.11 0.00 0.00 5.36
56 57 1.064017 AGAAAGTGAACACCTGCCCAA 60.064 47.619 1.11 0.00 0.00 4.12
57 58 1.963515 GAAAGTGAACACCTGCCCAAT 59.036 47.619 1.11 0.00 0.00 3.16
58 59 2.969821 AAGTGAACACCTGCCCAATA 57.030 45.000 1.11 0.00 0.00 1.90
59 60 3.456380 AAGTGAACACCTGCCCAATAT 57.544 42.857 1.11 0.00 0.00 1.28
60 61 2.726821 AGTGAACACCTGCCCAATATG 58.273 47.619 1.11 0.00 0.00 1.78
61 62 1.134946 GTGAACACCTGCCCAATATGC 59.865 52.381 0.00 0.00 0.00 3.14
62 63 1.272369 TGAACACCTGCCCAATATGCA 60.272 47.619 0.00 0.00 37.17 3.96
63 64 1.824230 GAACACCTGCCCAATATGCAA 59.176 47.619 0.00 0.00 38.46 4.08
64 65 1.935799 ACACCTGCCCAATATGCAAA 58.064 45.000 0.00 0.00 38.46 3.68
65 66 1.826720 ACACCTGCCCAATATGCAAAG 59.173 47.619 0.00 0.00 38.46 2.77
66 67 1.137479 CACCTGCCCAATATGCAAAGG 59.863 52.381 0.00 0.00 38.46 3.11
67 68 1.006998 ACCTGCCCAATATGCAAAGGA 59.993 47.619 0.00 0.00 38.46 3.36
68 69 1.684983 CCTGCCCAATATGCAAAGGAG 59.315 52.381 0.00 0.00 38.46 3.69
69 70 1.684983 CTGCCCAATATGCAAAGGAGG 59.315 52.381 0.00 0.00 38.46 4.30
70 71 0.390492 GCCCAATATGCAAAGGAGGC 59.610 55.000 4.89 4.89 0.00 4.70
71 72 2.031097 GCCCAATATGCAAAGGAGGCT 61.031 52.381 11.86 0.00 36.22 4.58
72 73 1.684983 CCCAATATGCAAAGGAGGCTG 59.315 52.381 0.00 0.00 0.00 4.85
73 74 1.068127 CCAATATGCAAAGGAGGCTGC 59.932 52.381 0.00 0.00 39.09 5.25
74 75 2.029623 CAATATGCAAAGGAGGCTGCT 58.970 47.619 1.28 1.28 39.38 4.24
75 76 2.429610 CAATATGCAAAGGAGGCTGCTT 59.570 45.455 16.16 16.16 39.38 3.91
76 77 2.220653 TATGCAAAGGAGGCTGCTTT 57.779 45.000 25.88 25.88 38.60 3.51
80 81 3.042481 AAAGGAGGCTGCTTTGGTC 57.958 52.632 29.74 0.00 36.65 4.02
81 82 0.540597 AAAGGAGGCTGCTTTGGTCC 60.541 55.000 29.74 5.10 36.65 4.46
82 83 2.361737 GGAGGCTGCTTTGGTCCC 60.362 66.667 0.00 0.00 0.00 4.46
83 84 2.436109 GAGGCTGCTTTGGTCCCA 59.564 61.111 0.00 0.00 0.00 4.37
84 85 1.000396 GAGGCTGCTTTGGTCCCAT 60.000 57.895 0.00 0.00 0.00 4.00
85 86 0.613012 GAGGCTGCTTTGGTCCCATT 60.613 55.000 0.00 0.00 0.00 3.16
86 87 0.901580 AGGCTGCTTTGGTCCCATTG 60.902 55.000 0.00 0.00 0.00 2.82
87 88 1.593265 GCTGCTTTGGTCCCATTGG 59.407 57.895 0.00 0.00 0.00 3.16
88 89 1.891722 GCTGCTTTGGTCCCATTGGG 61.892 60.000 16.26 16.26 46.11 4.12
99 100 3.633137 CCATTGGGGGCTGGTAAAT 57.367 52.632 0.00 0.00 0.00 1.40
100 101 1.878211 CCATTGGGGGCTGGTAAATT 58.122 50.000 0.00 0.00 0.00 1.82
101 102 3.039252 CCATTGGGGGCTGGTAAATTA 57.961 47.619 0.00 0.00 0.00 1.40
102 103 2.698274 CCATTGGGGGCTGGTAAATTAC 59.302 50.000 0.00 0.00 0.00 1.89
114 115 3.334272 GTAAATTACCACATCCGCAGC 57.666 47.619 0.00 0.00 0.00 5.25
115 116 1.832883 AAATTACCACATCCGCAGCA 58.167 45.000 0.00 0.00 0.00 4.41
116 117 2.057137 AATTACCACATCCGCAGCAT 57.943 45.000 0.00 0.00 0.00 3.79
117 118 1.597742 ATTACCACATCCGCAGCATC 58.402 50.000 0.00 0.00 0.00 3.91
118 119 0.251634 TTACCACATCCGCAGCATCA 59.748 50.000 0.00 0.00 0.00 3.07
119 120 0.179076 TACCACATCCGCAGCATCAG 60.179 55.000 0.00 0.00 0.00 2.90
120 121 2.184830 CCACATCCGCAGCATCAGG 61.185 63.158 0.00 0.00 0.00 3.86
121 122 2.184830 CACATCCGCAGCATCAGGG 61.185 63.158 0.00 0.00 0.00 4.45
122 123 2.369633 ACATCCGCAGCATCAGGGA 61.370 57.895 0.00 0.00 0.00 4.20
123 124 1.890979 CATCCGCAGCATCAGGGAC 60.891 63.158 0.00 0.00 0.00 4.46
124 125 2.369633 ATCCGCAGCATCAGGGACA 61.370 57.895 0.00 0.00 0.00 4.02
125 126 1.703014 ATCCGCAGCATCAGGGACAT 61.703 55.000 0.00 0.00 0.00 3.06
126 127 1.452651 CCGCAGCATCAGGGACATT 60.453 57.895 0.00 0.00 0.00 2.71
127 128 1.721664 CCGCAGCATCAGGGACATTG 61.722 60.000 0.00 0.00 0.00 2.82
128 129 1.028330 CGCAGCATCAGGGACATTGT 61.028 55.000 0.00 0.00 0.00 2.71
129 130 1.180029 GCAGCATCAGGGACATTGTT 58.820 50.000 0.00 0.00 0.00 2.83
130 131 2.368439 GCAGCATCAGGGACATTGTTA 58.632 47.619 0.00 0.00 0.00 2.41
131 132 2.754552 GCAGCATCAGGGACATTGTTAA 59.245 45.455 0.00 0.00 0.00 2.01
132 133 3.428045 GCAGCATCAGGGACATTGTTAAC 60.428 47.826 0.00 0.00 0.00 2.01
133 134 4.012374 CAGCATCAGGGACATTGTTAACT 58.988 43.478 7.22 0.00 0.00 2.24
134 135 4.012374 AGCATCAGGGACATTGTTAACTG 58.988 43.478 7.22 0.01 0.00 3.16
135 136 4.009675 GCATCAGGGACATTGTTAACTGA 58.990 43.478 16.21 16.21 39.05 3.41
136 137 4.458989 GCATCAGGGACATTGTTAACTGAA 59.541 41.667 17.20 0.00 38.32 3.02
137 138 5.126061 GCATCAGGGACATTGTTAACTGAAT 59.874 40.000 17.20 0.00 38.32 2.57
138 139 6.678900 GCATCAGGGACATTGTTAACTGAATC 60.679 42.308 17.20 11.14 38.32 2.52
139 140 5.875224 TCAGGGACATTGTTAACTGAATCA 58.125 37.500 7.22 0.00 32.60 2.57
140 141 6.484288 TCAGGGACATTGTTAACTGAATCAT 58.516 36.000 7.22 0.00 32.60 2.45
141 142 6.947733 TCAGGGACATTGTTAACTGAATCATT 59.052 34.615 7.22 0.00 32.60 2.57
142 143 8.106462 TCAGGGACATTGTTAACTGAATCATTA 58.894 33.333 7.22 0.00 32.60 1.90
143 144 8.400947 CAGGGACATTGTTAACTGAATCATTAG 58.599 37.037 7.22 0.00 0.00 1.73
144 145 8.328758 AGGGACATTGTTAACTGAATCATTAGA 58.671 33.333 7.22 0.00 0.00 2.10
145 146 8.956426 GGGACATTGTTAACTGAATCATTAGAA 58.044 33.333 7.22 0.00 0.00 2.10
151 152 9.677567 TTGTTAACTGAATCATTAGAAACTTGC 57.322 29.630 7.22 0.00 0.00 4.01
152 153 8.845227 TGTTAACTGAATCATTAGAAACTTGCA 58.155 29.630 7.22 0.00 0.00 4.08
153 154 9.334693 GTTAACTGAATCATTAGAAACTTGCAG 57.665 33.333 0.00 0.00 0.00 4.41
154 155 7.750229 AACTGAATCATTAGAAACTTGCAGA 57.250 32.000 0.00 0.00 0.00 4.26
155 156 7.750229 ACTGAATCATTAGAAACTTGCAGAA 57.250 32.000 0.00 0.00 0.00 3.02
156 157 8.345724 ACTGAATCATTAGAAACTTGCAGAAT 57.654 30.769 0.00 0.00 0.00 2.40
157 158 8.242053 ACTGAATCATTAGAAACTTGCAGAATG 58.758 33.333 0.00 0.00 40.87 2.67
158 159 8.339344 TGAATCATTAGAAACTTGCAGAATGA 57.661 30.769 0.00 0.00 39.69 2.57
159 160 8.963725 TGAATCATTAGAAACTTGCAGAATGAT 58.036 29.630 0.00 0.00 42.77 2.45
161 162 9.582431 AATCATTAGAAACTTGCAGAATGATTG 57.418 29.630 15.98 1.78 45.42 2.67
162 163 8.339344 TCATTAGAAACTTGCAGAATGATTGA 57.661 30.769 0.00 0.00 39.69 2.57
163 164 8.963725 TCATTAGAAACTTGCAGAATGATTGAT 58.036 29.630 0.00 0.00 39.69 2.57
164 165 9.020813 CATTAGAAACTTGCAGAATGATTGATG 57.979 33.333 0.00 0.00 39.69 3.07
165 166 5.408356 AGAAACTTGCAGAATGATTGATGC 58.592 37.500 5.30 5.30 39.69 3.91
166 167 3.795623 ACTTGCAGAATGATTGATGCC 57.204 42.857 8.86 0.00 39.69 4.40
167 168 3.362706 ACTTGCAGAATGATTGATGCCT 58.637 40.909 8.86 0.00 39.69 4.75
168 169 3.130516 ACTTGCAGAATGATTGATGCCTG 59.869 43.478 8.86 0.00 39.69 4.85
169 170 2.028876 TGCAGAATGATTGATGCCTGG 58.971 47.619 8.86 0.00 39.69 4.45
170 171 1.340248 GCAGAATGATTGATGCCTGGG 59.660 52.381 0.00 0.00 39.69 4.45
171 172 2.940158 CAGAATGATTGATGCCTGGGA 58.060 47.619 0.00 0.00 39.69 4.37
172 173 2.621998 CAGAATGATTGATGCCTGGGAC 59.378 50.000 0.00 0.00 39.69 4.46
173 174 2.512896 AGAATGATTGATGCCTGGGACT 59.487 45.455 0.00 0.00 0.00 3.85
174 175 2.359981 ATGATTGATGCCTGGGACTG 57.640 50.000 0.00 0.00 0.00 3.51
175 176 1.288188 TGATTGATGCCTGGGACTGA 58.712 50.000 0.00 0.00 0.00 3.41
176 177 1.634973 TGATTGATGCCTGGGACTGAA 59.365 47.619 0.00 0.00 0.00 3.02
177 178 2.019984 GATTGATGCCTGGGACTGAAC 58.980 52.381 0.00 0.00 0.00 3.18
178 179 1.067295 TTGATGCCTGGGACTGAACT 58.933 50.000 0.00 0.00 0.00 3.01
179 180 1.067295 TGATGCCTGGGACTGAACTT 58.933 50.000 0.00 0.00 0.00 2.66
180 181 1.003580 TGATGCCTGGGACTGAACTTC 59.996 52.381 0.00 0.00 0.00 3.01
181 182 0.329596 ATGCCTGGGACTGAACTTCC 59.670 55.000 0.00 0.00 0.00 3.46
182 183 0.768221 TGCCTGGGACTGAACTTCCT 60.768 55.000 0.00 0.00 33.17 3.36
183 184 0.035915 GCCTGGGACTGAACTTCCTC 60.036 60.000 0.00 0.00 33.17 3.71
184 185 1.352083 CCTGGGACTGAACTTCCTCA 58.648 55.000 0.00 0.00 33.17 3.86
185 186 1.699634 CCTGGGACTGAACTTCCTCAA 59.300 52.381 0.00 0.00 33.17 3.02
186 187 2.551071 CCTGGGACTGAACTTCCTCAAC 60.551 54.545 0.00 0.00 33.17 3.18
187 188 1.420138 TGGGACTGAACTTCCTCAACC 59.580 52.381 0.00 0.00 33.17 3.77
188 189 1.700186 GGGACTGAACTTCCTCAACCT 59.300 52.381 0.00 0.00 33.17 3.50
189 190 2.551071 GGGACTGAACTTCCTCAACCTG 60.551 54.545 0.00 0.00 33.17 4.00
190 191 2.147150 GACTGAACTTCCTCAACCTGC 58.853 52.381 0.00 0.00 0.00 4.85
191 192 1.771255 ACTGAACTTCCTCAACCTGCT 59.229 47.619 0.00 0.00 0.00 4.24
192 193 2.224402 ACTGAACTTCCTCAACCTGCTC 60.224 50.000 0.00 0.00 0.00 4.26
193 194 1.270305 TGAACTTCCTCAACCTGCTCG 60.270 52.381 0.00 0.00 0.00 5.03
194 195 0.759346 AACTTCCTCAACCTGCTCGT 59.241 50.000 0.00 0.00 0.00 4.18
195 196 0.034059 ACTTCCTCAACCTGCTCGTG 59.966 55.000 0.00 0.00 0.00 4.35
196 197 0.034059 CTTCCTCAACCTGCTCGTGT 59.966 55.000 0.00 0.00 0.00 4.49
197 198 0.468226 TTCCTCAACCTGCTCGTGTT 59.532 50.000 0.00 0.00 0.00 3.32
198 199 0.249868 TCCTCAACCTGCTCGTGTTG 60.250 55.000 0.00 0.00 42.46 3.33
199 200 0.249868 CCTCAACCTGCTCGTGTTGA 60.250 55.000 5.13 5.13 46.23 3.18
200 201 3.770625 TCAACCTGCTCGTGTTGAA 57.229 47.368 2.82 0.00 45.64 2.69
201 202 1.295792 TCAACCTGCTCGTGTTGAAC 58.704 50.000 2.82 0.00 45.64 3.18
202 203 1.134521 TCAACCTGCTCGTGTTGAACT 60.135 47.619 2.82 0.00 45.64 3.01
203 204 1.003545 CAACCTGCTCGTGTTGAACTG 60.004 52.381 0.00 0.00 43.50 3.16
204 205 1.160329 ACCTGCTCGTGTTGAACTGC 61.160 55.000 0.00 0.00 0.00 4.40
205 206 1.159713 CCTGCTCGTGTTGAACTGCA 61.160 55.000 0.00 1.80 35.55 4.41
206 207 0.870393 CTGCTCGTGTTGAACTGCAT 59.130 50.000 0.00 0.00 36.05 3.96
207 208 0.867746 TGCTCGTGTTGAACTGCATC 59.132 50.000 0.00 0.00 33.13 3.91
208 209 0.867746 GCTCGTGTTGAACTGCATCA 59.132 50.000 0.00 0.00 0.00 3.07
209 210 1.466167 GCTCGTGTTGAACTGCATCAT 59.534 47.619 0.00 0.00 0.00 2.45
210 211 2.095567 GCTCGTGTTGAACTGCATCATT 60.096 45.455 0.00 0.00 0.00 2.57
211 212 3.740590 CTCGTGTTGAACTGCATCATTC 58.259 45.455 0.00 0.00 0.00 2.67
212 213 3.137533 TCGTGTTGAACTGCATCATTCA 58.862 40.909 0.00 4.54 33.03 2.57
213 214 3.058983 TCGTGTTGAACTGCATCATTCAC 60.059 43.478 7.49 10.25 34.61 3.18
214 215 3.058708 CGTGTTGAACTGCATCATTCACT 60.059 43.478 16.60 0.00 34.61 3.41
215 216 4.224433 GTGTTGAACTGCATCATTCACTG 58.776 43.478 13.85 0.00 34.61 3.66
216 217 3.253921 TGTTGAACTGCATCATTCACTGG 59.746 43.478 7.49 0.00 34.61 4.00
217 218 3.144657 TGAACTGCATCATTCACTGGT 57.855 42.857 4.54 0.00 29.89 4.00
218 219 3.489355 TGAACTGCATCATTCACTGGTT 58.511 40.909 4.54 0.00 29.89 3.67
219 220 3.253921 TGAACTGCATCATTCACTGGTTG 59.746 43.478 4.54 0.00 29.89 3.77
220 221 2.165167 ACTGCATCATTCACTGGTTGG 58.835 47.619 0.00 0.00 0.00 3.77
221 222 2.224843 ACTGCATCATTCACTGGTTGGA 60.225 45.455 0.00 0.00 0.00 3.53
222 223 3.021695 CTGCATCATTCACTGGTTGGAT 58.978 45.455 0.00 0.00 0.00 3.41
223 224 4.201657 CTGCATCATTCACTGGTTGGATA 58.798 43.478 0.00 0.00 0.00 2.59
224 225 4.795469 TGCATCATTCACTGGTTGGATAT 58.205 39.130 0.00 0.00 0.00 1.63
225 226 4.823442 TGCATCATTCACTGGTTGGATATC 59.177 41.667 0.00 0.00 0.00 1.63
226 227 4.217118 GCATCATTCACTGGTTGGATATCC 59.783 45.833 15.39 15.39 0.00 2.59
227 228 5.628130 CATCATTCACTGGTTGGATATCCT 58.372 41.667 22.35 0.00 36.82 3.24
228 229 5.296151 TCATTCACTGGTTGGATATCCTC 57.704 43.478 22.35 14.57 36.82 3.71
229 230 4.103153 TCATTCACTGGTTGGATATCCTCC 59.897 45.833 22.35 21.92 45.19 4.30
230 231 3.421394 TCACTGGTTGGATATCCTCCT 57.579 47.619 25.59 12.32 45.21 3.69
231 232 3.041211 TCACTGGTTGGATATCCTCCTG 58.959 50.000 25.85 25.85 45.21 3.86
232 233 2.774234 CACTGGTTGGATATCCTCCTGT 59.226 50.000 26.69 26.69 45.21 4.00
233 234 2.774234 ACTGGTTGGATATCCTCCTGTG 59.226 50.000 29.06 21.86 45.21 3.66
234 235 2.105477 CTGGTTGGATATCCTCCTGTGG 59.895 54.545 25.59 15.11 45.21 4.17
235 236 1.202818 GGTTGGATATCCTCCTGTGGC 60.203 57.143 22.35 4.14 45.21 5.01
236 237 1.771255 GTTGGATATCCTCCTGTGGCT 59.229 52.381 22.35 0.00 45.21 4.75
237 238 1.427809 TGGATATCCTCCTGTGGCTG 58.572 55.000 22.35 0.00 45.21 4.85
238 239 0.036022 GGATATCCTCCTGTGGCTGC 59.964 60.000 14.97 0.00 41.29 5.25
239 240 1.055040 GATATCCTCCTGTGGCTGCT 58.945 55.000 0.00 0.00 0.00 4.24
240 241 1.001860 GATATCCTCCTGTGGCTGCTC 59.998 57.143 0.00 0.00 0.00 4.26
241 242 0.325577 TATCCTCCTGTGGCTGCTCA 60.326 55.000 0.00 0.00 0.00 4.26
242 243 0.987081 ATCCTCCTGTGGCTGCTCAT 60.987 55.000 0.00 0.00 0.00 2.90
243 244 1.203441 TCCTCCTGTGGCTGCTCATT 61.203 55.000 0.00 0.00 0.00 2.57
244 245 1.030488 CCTCCTGTGGCTGCTCATTG 61.030 60.000 0.00 0.00 0.00 2.82
245 246 0.035725 CTCCTGTGGCTGCTCATTGA 60.036 55.000 0.00 0.00 0.00 2.57
246 247 0.321919 TCCTGTGGCTGCTCATTGAC 60.322 55.000 0.00 0.00 0.00 3.18
247 248 0.607217 CCTGTGGCTGCTCATTGACA 60.607 55.000 0.00 0.00 0.00 3.58
248 249 0.803117 CTGTGGCTGCTCATTGACAG 59.197 55.000 0.00 10.20 36.96 3.51
249 250 0.607217 TGTGGCTGCTCATTGACAGG 60.607 55.000 14.14 0.00 34.38 4.00
250 251 0.607489 GTGGCTGCTCATTGACAGGT 60.607 55.000 14.14 0.00 34.38 4.00
251 252 0.607217 TGGCTGCTCATTGACAGGTG 60.607 55.000 14.14 0.00 34.38 4.00
252 253 1.310933 GGCTGCTCATTGACAGGTGG 61.311 60.000 14.14 0.00 34.38 4.61
253 254 0.607489 GCTGCTCATTGACAGGTGGT 60.607 55.000 14.14 0.00 34.38 4.16
254 255 1.162698 CTGCTCATTGACAGGTGGTG 58.837 55.000 7.82 0.00 0.00 4.17
255 256 0.250858 TGCTCATTGACAGGTGGTGG 60.251 55.000 0.00 0.00 0.00 4.61
256 257 1.589716 GCTCATTGACAGGTGGTGGC 61.590 60.000 0.00 0.00 32.89 5.01
257 258 0.250858 CTCATTGACAGGTGGTGGCA 60.251 55.000 0.00 0.00 45.30 4.92
260 261 3.249805 TGACAGGTGGTGGCACAT 58.750 55.556 20.82 0.00 40.35 3.21
261 262 1.073025 TGACAGGTGGTGGCACATC 59.927 57.895 20.82 11.12 40.35 3.06
262 263 2.032528 ACAGGTGGTGGCACATCG 59.967 61.111 20.82 5.15 46.67 3.84
263 264 2.032528 CAGGTGGTGGCACATCGT 59.967 61.111 20.82 10.03 46.67 3.73
264 265 1.600636 CAGGTGGTGGCACATCGTT 60.601 57.895 20.82 0.00 46.67 3.85
265 266 1.302511 AGGTGGTGGCACATCGTTC 60.303 57.895 20.82 0.77 46.67 3.95
266 267 2.332654 GGTGGTGGCACATCGTTCC 61.333 63.158 20.82 7.93 46.67 3.62
267 268 1.599518 GTGGTGGCACATCGTTCCA 60.600 57.895 20.82 2.96 46.67 3.53
268 269 1.599518 TGGTGGCACATCGTTCCAC 60.600 57.895 20.82 7.32 46.67 4.02
269 270 3.263941 GTGGCACATCGTTCCACC 58.736 61.111 13.86 0.00 42.41 4.61
270 271 2.033448 TGGCACATCGTTCCACCC 59.967 61.111 0.00 0.00 0.00 4.61
271 272 2.033448 GGCACATCGTTCCACCCA 59.967 61.111 0.00 0.00 0.00 4.51
272 273 1.602323 GGCACATCGTTCCACCCAA 60.602 57.895 0.00 0.00 0.00 4.12
273 274 1.586154 GGCACATCGTTCCACCCAAG 61.586 60.000 0.00 0.00 0.00 3.61
274 275 0.605319 GCACATCGTTCCACCCAAGA 60.605 55.000 0.00 0.00 0.00 3.02
275 276 1.950484 GCACATCGTTCCACCCAAGAT 60.950 52.381 0.00 0.00 0.00 2.40
276 277 2.009774 CACATCGTTCCACCCAAGATC 58.990 52.381 0.00 0.00 0.00 2.75
277 278 1.909302 ACATCGTTCCACCCAAGATCT 59.091 47.619 0.00 0.00 0.00 2.75
278 279 2.283298 CATCGTTCCACCCAAGATCTG 58.717 52.381 0.00 0.00 0.00 2.90
279 280 0.613260 TCGTTCCACCCAAGATCTGG 59.387 55.000 0.00 0.00 45.97 3.86
294 295 1.471119 TCTGGGTACTCCGACATGAC 58.529 55.000 0.00 0.00 38.76 3.06
295 296 0.460311 CTGGGTACTCCGACATGACC 59.540 60.000 0.00 0.00 38.76 4.02
472 474 9.234827 CTTCATCAACAGGCATATGGATATTTA 57.765 33.333 4.56 0.00 0.00 1.40
475 477 9.404848 CATCAACAGGCATATGGATATTTATCT 57.595 33.333 4.56 0.00 33.28 1.98
499 501 4.115516 GACAAGACGATCATGCAGTACAT 58.884 43.478 0.00 0.00 40.66 2.29
574 576 2.540736 TTTGCCGCGCATGGTGATTC 62.541 55.000 8.75 0.00 38.76 2.52
853 868 1.203052 CATTCTCTGTGGGCGCATTTT 59.797 47.619 10.83 0.00 0.00 1.82
854 869 1.327303 TTCTCTGTGGGCGCATTTTT 58.673 45.000 10.83 0.00 0.00 1.94
866 881 1.270252 CGCATTTTTGGACCCTTGCTT 60.270 47.619 0.00 0.00 0.00 3.91
876 891 2.489722 GGACCCTTGCTTCTTTGTCATC 59.510 50.000 0.00 0.00 0.00 2.92
1138 1159 6.607600 AGCTGATGAAGACCTTACTACACATA 59.392 38.462 0.00 0.00 0.00 2.29
1153 1174 7.993821 ACTACACATACTGAATTCTTCATCG 57.006 36.000 7.05 0.00 39.30 3.84
1267 1288 6.202379 GCAAGGAAACCGGTAATTACTATCTC 59.798 42.308 8.00 6.24 0.00 2.75
1294 1317 2.495155 TGTCCTCCACACCAATCATG 57.505 50.000 0.00 0.00 0.00 3.07
1422 1451 1.691196 CTTGCAAAGTGGGAAGGTCA 58.309 50.000 0.00 0.00 39.70 4.02
1431 1460 2.522367 GGGAAGGTCAACGGGTCCA 61.522 63.158 0.00 0.00 0.00 4.02
1544 1577 5.684552 GCATGAGAGTTCATAGAGGAAGCTT 60.685 44.000 0.00 0.00 42.12 3.74
1621 1656 2.795329 ACCTTACATTTCTGTGGCTGG 58.205 47.619 0.00 0.00 36.79 4.85
1622 1657 2.108250 ACCTTACATTTCTGTGGCTGGT 59.892 45.455 0.00 0.00 36.79 4.00
1676 1711 9.884636 AAAACTATGTCTGTGTGCTATGTTATA 57.115 29.630 0.00 0.00 0.00 0.98
2091 2171 4.613925 ATCTACACGATGGCAGATTCAT 57.386 40.909 0.00 0.00 0.00 2.57
2108 2188 7.922278 GCAGATTCATTAGAAATAACATGGCAA 59.078 33.333 0.00 0.00 37.29 4.52
2173 2253 9.104965 CATGGCATTTTTAGTCATTCATTCATT 57.895 29.630 0.00 0.00 0.00 2.57
2384 2469 0.741915 TTTGGACGCCCTTTTGTGAC 59.258 50.000 0.00 0.00 0.00 3.67
2416 2501 0.467290 GTTCCTGACCTGGGTTTGCA 60.467 55.000 0.00 0.00 0.00 4.08
2455 2540 5.461327 ACCCTACCTCCGAGTTTTCATATA 58.539 41.667 0.00 0.00 0.00 0.86
2479 2564 1.603455 CCCGTGGACAAAGGCACAT 60.603 57.895 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.361992 CTTGCCTCCTGCCATGCA 60.362 61.111 0.00 0.00 40.16 3.96
9 10 2.044650 TCTTGCCTCCTGCCATGC 60.045 61.111 0.00 0.00 40.16 4.06
10 11 1.001764 TGTCTTGCCTCCTGCCATG 60.002 57.895 0.00 0.00 40.16 3.66
11 12 1.302285 CTGTCTTGCCTCCTGCCAT 59.698 57.895 0.00 0.00 40.16 4.40
12 13 2.752358 CTGTCTTGCCTCCTGCCA 59.248 61.111 0.00 0.00 40.16 4.92
13 14 2.045536 CCTGTCTTGCCTCCTGCC 60.046 66.667 0.00 0.00 40.16 4.85
14 15 2.749441 GCCTGTCTTGCCTCCTGC 60.749 66.667 0.00 0.00 41.77 4.85
15 16 2.045536 GGCCTGTCTTGCCTCCTG 60.046 66.667 0.00 0.00 45.70 3.86
21 22 0.889186 TTTCTTCGGGCCTGTCTTGC 60.889 55.000 12.43 0.00 0.00 4.01
22 23 1.160137 CTTTCTTCGGGCCTGTCTTG 58.840 55.000 12.43 0.56 0.00 3.02
23 24 0.765510 ACTTTCTTCGGGCCTGTCTT 59.234 50.000 12.43 0.00 0.00 3.01
24 25 0.035458 CACTTTCTTCGGGCCTGTCT 59.965 55.000 12.43 0.00 0.00 3.41
25 26 0.034896 TCACTTTCTTCGGGCCTGTC 59.965 55.000 12.43 0.00 0.00 3.51
26 27 0.472471 TTCACTTTCTTCGGGCCTGT 59.528 50.000 12.43 0.00 0.00 4.00
27 28 0.875059 GTTCACTTTCTTCGGGCCTG 59.125 55.000 4.71 4.71 0.00 4.85
28 29 0.472471 TGTTCACTTTCTTCGGGCCT 59.528 50.000 0.84 0.00 0.00 5.19
29 30 0.591659 GTGTTCACTTTCTTCGGGCC 59.408 55.000 0.00 0.00 0.00 5.80
30 31 0.591659 GGTGTTCACTTTCTTCGGGC 59.408 55.000 2.98 0.00 0.00 6.13
31 32 1.873591 CAGGTGTTCACTTTCTTCGGG 59.126 52.381 2.98 0.00 0.00 5.14
32 33 1.264288 GCAGGTGTTCACTTTCTTCGG 59.736 52.381 2.98 0.00 0.00 4.30
33 34 1.264288 GGCAGGTGTTCACTTTCTTCG 59.736 52.381 2.98 0.00 0.00 3.79
34 35 1.609072 GGGCAGGTGTTCACTTTCTTC 59.391 52.381 2.98 0.00 0.00 2.87
35 36 1.064017 TGGGCAGGTGTTCACTTTCTT 60.064 47.619 2.98 0.00 0.00 2.52
36 37 0.550914 TGGGCAGGTGTTCACTTTCT 59.449 50.000 2.98 0.00 0.00 2.52
37 38 1.398692 TTGGGCAGGTGTTCACTTTC 58.601 50.000 2.98 0.00 0.00 2.62
38 39 2.086610 ATTGGGCAGGTGTTCACTTT 57.913 45.000 2.98 0.00 0.00 2.66
39 40 2.969821 TATTGGGCAGGTGTTCACTT 57.030 45.000 2.98 0.00 0.00 3.16
40 41 2.726821 CATATTGGGCAGGTGTTCACT 58.273 47.619 2.98 0.00 0.00 3.41
41 42 1.134946 GCATATTGGGCAGGTGTTCAC 59.865 52.381 0.00 0.00 0.00 3.18
42 43 1.272369 TGCATATTGGGCAGGTGTTCA 60.272 47.619 0.00 0.00 36.11 3.18
43 44 1.473258 TGCATATTGGGCAGGTGTTC 58.527 50.000 0.00 0.00 36.11 3.18
44 45 1.935799 TTGCATATTGGGCAGGTGTT 58.064 45.000 0.00 0.00 43.05 3.32
45 46 1.826720 CTTTGCATATTGGGCAGGTGT 59.173 47.619 0.00 0.00 43.05 4.16
46 47 1.137479 CCTTTGCATATTGGGCAGGTG 59.863 52.381 0.00 0.00 43.05 4.00
47 48 1.006998 TCCTTTGCATATTGGGCAGGT 59.993 47.619 0.00 0.00 43.05 4.00
48 49 1.684983 CTCCTTTGCATATTGGGCAGG 59.315 52.381 0.00 0.00 43.05 4.85
49 50 1.684983 CCTCCTTTGCATATTGGGCAG 59.315 52.381 0.00 0.00 43.05 4.85
50 51 1.779221 CCTCCTTTGCATATTGGGCA 58.221 50.000 0.00 0.00 40.00 5.36
51 52 0.390492 GCCTCCTTTGCATATTGGGC 59.610 55.000 5.10 5.10 0.00 5.36
52 53 1.684983 CAGCCTCCTTTGCATATTGGG 59.315 52.381 0.00 0.00 0.00 4.12
53 54 1.068127 GCAGCCTCCTTTGCATATTGG 59.932 52.381 0.00 0.00 40.02 3.16
54 55 2.029623 AGCAGCCTCCTTTGCATATTG 58.970 47.619 0.00 0.00 42.67 1.90
55 56 2.449137 AGCAGCCTCCTTTGCATATT 57.551 45.000 0.00 0.00 42.67 1.28
56 57 2.429610 CAAAGCAGCCTCCTTTGCATAT 59.570 45.455 0.00 0.00 41.63 1.78
57 58 1.820519 CAAAGCAGCCTCCTTTGCATA 59.179 47.619 0.00 0.00 41.63 3.14
58 59 0.606604 CAAAGCAGCCTCCTTTGCAT 59.393 50.000 0.00 0.00 41.63 3.96
59 60 1.466025 CCAAAGCAGCCTCCTTTGCA 61.466 55.000 2.42 0.00 44.77 4.08
60 61 1.291272 CCAAAGCAGCCTCCTTTGC 59.709 57.895 2.42 1.20 44.77 3.68
61 62 0.600057 GACCAAAGCAGCCTCCTTTG 59.400 55.000 0.89 0.89 45.37 2.77
62 63 0.540597 GGACCAAAGCAGCCTCCTTT 60.541 55.000 0.00 0.00 33.03 3.11
63 64 1.075659 GGACCAAAGCAGCCTCCTT 59.924 57.895 0.00 0.00 0.00 3.36
64 65 2.759795 GGACCAAAGCAGCCTCCT 59.240 61.111 0.00 0.00 0.00 3.69
65 66 2.361737 GGGACCAAAGCAGCCTCC 60.362 66.667 0.00 0.00 0.00 4.30
66 67 0.613012 AATGGGACCAAAGCAGCCTC 60.613 55.000 0.00 0.00 0.00 4.70
67 68 0.901580 CAATGGGACCAAAGCAGCCT 60.902 55.000 0.00 0.00 0.00 4.58
68 69 1.593265 CAATGGGACCAAAGCAGCC 59.407 57.895 0.00 0.00 0.00 4.85
69 70 1.593265 CCAATGGGACCAAAGCAGC 59.407 57.895 0.00 0.00 35.59 5.25
81 82 1.878211 AATTTACCAGCCCCCAATGG 58.122 50.000 0.00 0.00 42.60 3.16
94 95 2.680841 TGCTGCGGATGTGGTAATTTAC 59.319 45.455 0.00 0.00 0.00 2.01
95 96 2.992593 TGCTGCGGATGTGGTAATTTA 58.007 42.857 0.00 0.00 0.00 1.40
96 97 1.832883 TGCTGCGGATGTGGTAATTT 58.167 45.000 0.00 0.00 0.00 1.82
97 98 1.949525 GATGCTGCGGATGTGGTAATT 59.050 47.619 0.00 0.00 0.00 1.40
98 99 1.134128 TGATGCTGCGGATGTGGTAAT 60.134 47.619 0.00 0.00 0.00 1.89
99 100 0.251634 TGATGCTGCGGATGTGGTAA 59.748 50.000 0.00 0.00 0.00 2.85
100 101 0.179076 CTGATGCTGCGGATGTGGTA 60.179 55.000 0.00 0.00 0.00 3.25
101 102 1.450848 CTGATGCTGCGGATGTGGT 60.451 57.895 0.00 0.00 0.00 4.16
102 103 2.184830 CCTGATGCTGCGGATGTGG 61.185 63.158 0.00 0.00 0.00 4.17
103 104 2.184830 CCCTGATGCTGCGGATGTG 61.185 63.158 0.00 0.00 0.00 3.21
104 105 2.191375 CCCTGATGCTGCGGATGT 59.809 61.111 0.00 0.00 0.00 3.06
105 106 1.890979 GTCCCTGATGCTGCGGATG 60.891 63.158 0.00 0.00 0.00 3.51
106 107 1.703014 ATGTCCCTGATGCTGCGGAT 61.703 55.000 0.00 0.00 0.00 4.18
107 108 1.913951 AATGTCCCTGATGCTGCGGA 61.914 55.000 0.00 0.00 0.00 5.54
108 109 1.452651 AATGTCCCTGATGCTGCGG 60.453 57.895 0.00 0.00 0.00 5.69
109 110 1.028330 ACAATGTCCCTGATGCTGCG 61.028 55.000 0.00 0.00 0.00 5.18
110 111 1.180029 AACAATGTCCCTGATGCTGC 58.820 50.000 0.00 0.00 0.00 5.25
111 112 4.012374 AGTTAACAATGTCCCTGATGCTG 58.988 43.478 8.61 0.00 0.00 4.41
112 113 4.012374 CAGTTAACAATGTCCCTGATGCT 58.988 43.478 8.61 0.00 0.00 3.79
113 114 4.009675 TCAGTTAACAATGTCCCTGATGC 58.990 43.478 8.61 0.00 0.00 3.91
114 115 6.375174 TGATTCAGTTAACAATGTCCCTGATG 59.625 38.462 8.61 0.00 0.00 3.07
115 116 6.484288 TGATTCAGTTAACAATGTCCCTGAT 58.516 36.000 8.61 2.87 0.00 2.90
116 117 5.875224 TGATTCAGTTAACAATGTCCCTGA 58.125 37.500 8.61 5.77 0.00 3.86
117 118 6.764308 ATGATTCAGTTAACAATGTCCCTG 57.236 37.500 8.61 0.00 0.00 4.45
118 119 8.328758 TCTAATGATTCAGTTAACAATGTCCCT 58.671 33.333 8.61 0.00 0.00 4.20
119 120 8.506168 TCTAATGATTCAGTTAACAATGTCCC 57.494 34.615 8.61 0.00 0.00 4.46
125 126 9.677567 GCAAGTTTCTAATGATTCAGTTAACAA 57.322 29.630 8.61 0.00 0.00 2.83
126 127 8.845227 TGCAAGTTTCTAATGATTCAGTTAACA 58.155 29.630 8.61 0.00 0.00 2.41
127 128 9.334693 CTGCAAGTTTCTAATGATTCAGTTAAC 57.665 33.333 0.00 0.00 0.00 2.01
128 129 9.283768 TCTGCAAGTTTCTAATGATTCAGTTAA 57.716 29.630 0.00 0.00 33.76 2.01
129 130 8.846943 TCTGCAAGTTTCTAATGATTCAGTTA 57.153 30.769 0.00 0.00 33.76 2.24
130 131 7.750229 TCTGCAAGTTTCTAATGATTCAGTT 57.250 32.000 0.00 0.00 33.76 3.16
131 132 7.750229 TTCTGCAAGTTTCTAATGATTCAGT 57.250 32.000 0.00 0.00 33.76 3.41
132 133 8.456471 TCATTCTGCAAGTTTCTAATGATTCAG 58.544 33.333 0.00 0.00 30.59 3.02
133 134 8.339344 TCATTCTGCAAGTTTCTAATGATTCA 57.661 30.769 0.00 0.00 30.59 2.57
134 135 9.798994 AATCATTCTGCAAGTTTCTAATGATTC 57.201 29.630 16.12 0.00 44.56 2.52
135 136 9.582431 CAATCATTCTGCAAGTTTCTAATGATT 57.418 29.630 16.12 16.12 46.80 2.57
136 137 8.963725 TCAATCATTCTGCAAGTTTCTAATGAT 58.036 29.630 0.00 0.00 42.73 2.45
137 138 8.339344 TCAATCATTCTGCAAGTTTCTAATGA 57.661 30.769 0.00 0.00 37.64 2.57
138 139 9.020813 CATCAATCATTCTGCAAGTTTCTAATG 57.979 33.333 0.00 0.00 33.76 1.90
139 140 7.705325 GCATCAATCATTCTGCAAGTTTCTAAT 59.295 33.333 0.00 0.00 34.77 1.73
140 141 7.031372 GCATCAATCATTCTGCAAGTTTCTAA 58.969 34.615 0.00 0.00 34.77 2.10
141 142 6.405065 GGCATCAATCATTCTGCAAGTTTCTA 60.405 38.462 4.30 0.00 36.34 2.10
142 143 5.408356 GCATCAATCATTCTGCAAGTTTCT 58.592 37.500 0.00 0.00 34.77 2.52
143 144 4.565564 GGCATCAATCATTCTGCAAGTTTC 59.434 41.667 4.30 0.00 36.34 2.78
144 145 4.222145 AGGCATCAATCATTCTGCAAGTTT 59.778 37.500 4.30 0.00 36.34 2.66
145 146 3.767673 AGGCATCAATCATTCTGCAAGTT 59.232 39.130 4.30 0.00 36.34 2.66
146 147 3.130516 CAGGCATCAATCATTCTGCAAGT 59.869 43.478 4.30 0.00 36.34 3.16
147 148 3.490933 CCAGGCATCAATCATTCTGCAAG 60.491 47.826 4.30 0.00 36.34 4.01
148 149 2.429250 CCAGGCATCAATCATTCTGCAA 59.571 45.455 4.30 0.00 36.34 4.08
149 150 2.028876 CCAGGCATCAATCATTCTGCA 58.971 47.619 4.30 0.00 36.34 4.41
150 151 1.340248 CCCAGGCATCAATCATTCTGC 59.660 52.381 0.00 0.00 0.00 4.26
151 152 2.621998 GTCCCAGGCATCAATCATTCTG 59.378 50.000 0.00 0.00 0.00 3.02
152 153 2.512896 AGTCCCAGGCATCAATCATTCT 59.487 45.455 0.00 0.00 0.00 2.40
153 154 2.621998 CAGTCCCAGGCATCAATCATTC 59.378 50.000 0.00 0.00 0.00 2.67
154 155 2.242965 TCAGTCCCAGGCATCAATCATT 59.757 45.455 0.00 0.00 0.00 2.57
155 156 1.848388 TCAGTCCCAGGCATCAATCAT 59.152 47.619 0.00 0.00 0.00 2.45
156 157 1.288188 TCAGTCCCAGGCATCAATCA 58.712 50.000 0.00 0.00 0.00 2.57
157 158 2.019984 GTTCAGTCCCAGGCATCAATC 58.980 52.381 0.00 0.00 0.00 2.67
158 159 1.637553 AGTTCAGTCCCAGGCATCAAT 59.362 47.619 0.00 0.00 0.00 2.57
159 160 1.067295 AGTTCAGTCCCAGGCATCAA 58.933 50.000 0.00 0.00 0.00 2.57
160 161 1.003580 GAAGTTCAGTCCCAGGCATCA 59.996 52.381 0.00 0.00 0.00 3.07
161 162 1.680249 GGAAGTTCAGTCCCAGGCATC 60.680 57.143 5.01 0.00 0.00 3.91
162 163 0.329596 GGAAGTTCAGTCCCAGGCAT 59.670 55.000 5.01 0.00 0.00 4.40
163 164 0.768221 AGGAAGTTCAGTCCCAGGCA 60.768 55.000 5.01 0.00 35.59 4.75
164 165 0.035915 GAGGAAGTTCAGTCCCAGGC 60.036 60.000 5.01 0.00 35.59 4.85
165 166 1.352083 TGAGGAAGTTCAGTCCCAGG 58.648 55.000 5.01 0.00 35.59 4.45
166 167 2.551071 GGTTGAGGAAGTTCAGTCCCAG 60.551 54.545 5.01 0.00 35.59 4.45
167 168 1.420138 GGTTGAGGAAGTTCAGTCCCA 59.580 52.381 5.01 0.00 35.59 4.37
168 169 1.700186 AGGTTGAGGAAGTTCAGTCCC 59.300 52.381 5.01 0.00 35.59 4.46
169 170 2.772287 CAGGTTGAGGAAGTTCAGTCC 58.228 52.381 5.01 0.11 35.17 3.85
170 171 2.147150 GCAGGTTGAGGAAGTTCAGTC 58.853 52.381 5.01 1.47 0.00 3.51
171 172 1.771255 AGCAGGTTGAGGAAGTTCAGT 59.229 47.619 5.01 0.00 0.00 3.41
172 173 2.421619 GAGCAGGTTGAGGAAGTTCAG 58.578 52.381 5.01 0.00 0.00 3.02
173 174 1.270305 CGAGCAGGTTGAGGAAGTTCA 60.270 52.381 5.01 0.00 0.00 3.18
174 175 1.270358 ACGAGCAGGTTGAGGAAGTTC 60.270 52.381 0.00 0.00 0.00 3.01
175 176 0.759346 ACGAGCAGGTTGAGGAAGTT 59.241 50.000 0.00 0.00 0.00 2.66
176 177 0.034059 CACGAGCAGGTTGAGGAAGT 59.966 55.000 0.00 0.00 0.00 3.01
177 178 0.034059 ACACGAGCAGGTTGAGGAAG 59.966 55.000 0.00 0.00 0.00 3.46
178 179 0.468226 AACACGAGCAGGTTGAGGAA 59.532 50.000 0.00 0.00 0.00 3.36
179 180 0.249868 CAACACGAGCAGGTTGAGGA 60.250 55.000 0.00 0.00 45.50 3.71
180 181 0.249868 TCAACACGAGCAGGTTGAGG 60.250 55.000 3.31 0.00 46.01 3.86
181 182 3.289128 TCAACACGAGCAGGTTGAG 57.711 52.632 3.31 0.00 46.01 3.02
183 184 1.003545 CAGTTCAACACGAGCAGGTTG 60.004 52.381 0.00 0.00 44.35 3.77
184 185 1.299541 CAGTTCAACACGAGCAGGTT 58.700 50.000 0.00 0.00 0.00 3.50
185 186 1.160329 GCAGTTCAACACGAGCAGGT 61.160 55.000 0.00 0.00 33.09 4.00
186 187 1.159713 TGCAGTTCAACACGAGCAGG 61.160 55.000 0.00 0.00 36.68 4.85
187 188 0.870393 ATGCAGTTCAACACGAGCAG 59.130 50.000 0.00 0.00 42.26 4.24
188 189 0.867746 GATGCAGTTCAACACGAGCA 59.132 50.000 0.00 0.00 42.86 4.26
189 190 0.867746 TGATGCAGTTCAACACGAGC 59.132 50.000 0.00 0.00 33.37 5.03
190 191 3.187022 TGAATGATGCAGTTCAACACGAG 59.813 43.478 8.89 0.00 31.85 4.18
191 192 3.058983 GTGAATGATGCAGTTCAACACGA 60.059 43.478 11.95 0.00 36.23 4.35
192 193 3.058708 AGTGAATGATGCAGTTCAACACG 60.059 43.478 17.23 0.00 39.58 4.49
193 194 4.224433 CAGTGAATGATGCAGTTCAACAC 58.776 43.478 16.32 16.32 36.23 3.32
194 195 3.253921 CCAGTGAATGATGCAGTTCAACA 59.746 43.478 11.95 5.39 36.23 3.33
195 196 3.254166 ACCAGTGAATGATGCAGTTCAAC 59.746 43.478 11.95 7.96 36.23 3.18
196 197 3.489355 ACCAGTGAATGATGCAGTTCAA 58.511 40.909 11.95 0.00 36.23 2.69
197 198 3.144657 ACCAGTGAATGATGCAGTTCA 57.855 42.857 7.61 7.61 32.31 3.18
198 199 3.366679 CCAACCAGTGAATGATGCAGTTC 60.367 47.826 0.00 0.00 0.00 3.01
199 200 2.559668 CCAACCAGTGAATGATGCAGTT 59.440 45.455 0.00 0.00 0.00 3.16
200 201 2.165167 CCAACCAGTGAATGATGCAGT 58.835 47.619 0.00 0.00 0.00 4.40
201 202 2.439409 TCCAACCAGTGAATGATGCAG 58.561 47.619 0.00 0.00 0.00 4.41
202 203 2.583024 TCCAACCAGTGAATGATGCA 57.417 45.000 0.00 0.00 0.00 3.96
203 204 4.217118 GGATATCCAACCAGTGAATGATGC 59.783 45.833 17.34 0.00 35.64 3.91
204 205 5.628130 AGGATATCCAACCAGTGAATGATG 58.372 41.667 23.81 0.00 38.89 3.07
205 206 5.874093 GAGGATATCCAACCAGTGAATGAT 58.126 41.667 23.81 0.00 38.89 2.45
206 207 5.296151 GAGGATATCCAACCAGTGAATGA 57.704 43.478 23.81 0.00 38.89 2.57
220 221 1.001860 GAGCAGCCACAGGAGGATATC 59.998 57.143 0.00 0.00 0.00 1.63
221 222 1.055040 GAGCAGCCACAGGAGGATAT 58.945 55.000 0.00 0.00 0.00 1.63
222 223 0.325577 TGAGCAGCCACAGGAGGATA 60.326 55.000 0.00 0.00 0.00 2.59
223 224 0.987081 ATGAGCAGCCACAGGAGGAT 60.987 55.000 0.00 0.00 0.00 3.24
224 225 1.203441 AATGAGCAGCCACAGGAGGA 61.203 55.000 0.00 0.00 0.00 3.71
225 226 1.030488 CAATGAGCAGCCACAGGAGG 61.030 60.000 0.00 0.00 0.00 4.30
226 227 0.035725 TCAATGAGCAGCCACAGGAG 60.036 55.000 0.00 0.00 0.00 3.69
227 228 0.321919 GTCAATGAGCAGCCACAGGA 60.322 55.000 0.00 0.00 0.00 3.86
228 229 0.607217 TGTCAATGAGCAGCCACAGG 60.607 55.000 0.00 0.00 0.00 4.00
229 230 0.803117 CTGTCAATGAGCAGCCACAG 59.197 55.000 0.00 0.00 0.00 3.66
230 231 0.607217 CCTGTCAATGAGCAGCCACA 60.607 55.000 7.13 0.00 0.00 4.17
231 232 0.607489 ACCTGTCAATGAGCAGCCAC 60.607 55.000 7.13 0.00 0.00 5.01
232 233 0.607217 CACCTGTCAATGAGCAGCCA 60.607 55.000 7.13 0.00 0.00 4.75
233 234 1.310933 CCACCTGTCAATGAGCAGCC 61.311 60.000 7.13 0.00 0.00 4.85
234 235 0.607489 ACCACCTGTCAATGAGCAGC 60.607 55.000 7.13 0.00 0.00 5.25
235 236 1.162698 CACCACCTGTCAATGAGCAG 58.837 55.000 6.05 6.05 0.00 4.24
236 237 0.250858 CCACCACCTGTCAATGAGCA 60.251 55.000 0.00 0.00 0.00 4.26
237 238 1.589716 GCCACCACCTGTCAATGAGC 61.590 60.000 0.00 0.00 0.00 4.26
238 239 0.250858 TGCCACCACCTGTCAATGAG 60.251 55.000 0.00 0.00 0.00 2.90
239 240 0.537143 GTGCCACCACCTGTCAATGA 60.537 55.000 0.00 0.00 35.92 2.57
240 241 0.822944 TGTGCCACCACCTGTCAATG 60.823 55.000 0.00 0.00 41.35 2.82
241 242 0.112995 ATGTGCCACCACCTGTCAAT 59.887 50.000 0.00 0.00 41.35 2.57
242 243 0.537143 GATGTGCCACCACCTGTCAA 60.537 55.000 0.00 0.00 41.35 3.18
243 244 1.073025 GATGTGCCACCACCTGTCA 59.927 57.895 0.00 0.00 41.35 3.58
244 245 2.034879 CGATGTGCCACCACCTGTC 61.035 63.158 0.00 0.00 41.35 3.51
245 246 2.032528 CGATGTGCCACCACCTGT 59.967 61.111 0.00 0.00 41.35 4.00
246 247 1.577328 GAACGATGTGCCACCACCTG 61.577 60.000 0.00 0.00 41.35 4.00
247 248 1.302511 GAACGATGTGCCACCACCT 60.303 57.895 0.00 0.00 41.35 4.00
248 249 2.332654 GGAACGATGTGCCACCACC 61.333 63.158 0.00 0.00 41.35 4.61
249 250 1.599518 TGGAACGATGTGCCACCAC 60.600 57.895 0.00 0.00 36.10 4.16
250 251 2.832498 TGGAACGATGTGCCACCA 59.168 55.556 0.00 0.00 36.10 4.17
253 254 2.033448 GGGTGGAACGATGTGCCA 59.967 61.111 0.00 0.00 39.27 4.92
254 255 1.586154 CTTGGGTGGAACGATGTGCC 61.586 60.000 0.00 0.00 38.12 5.01
255 256 0.605319 TCTTGGGTGGAACGATGTGC 60.605 55.000 0.00 0.00 38.12 4.57
256 257 2.009774 GATCTTGGGTGGAACGATGTG 58.990 52.381 0.00 0.00 38.12 3.21
257 258 1.909302 AGATCTTGGGTGGAACGATGT 59.091 47.619 0.00 0.00 38.12 3.06
258 259 2.283298 CAGATCTTGGGTGGAACGATG 58.717 52.381 0.00 0.00 38.12 3.84
259 260 1.210478 CCAGATCTTGGGTGGAACGAT 59.790 52.381 0.00 0.00 43.75 3.73
260 261 0.613260 CCAGATCTTGGGTGGAACGA 59.387 55.000 0.00 0.00 43.75 3.85
261 262 3.159298 CCAGATCTTGGGTGGAACG 57.841 57.895 0.00 0.00 43.75 3.95
270 271 2.100197 TGTCGGAGTACCCAGATCTTG 58.900 52.381 0.00 0.00 34.14 3.02
271 272 2.526888 TGTCGGAGTACCCAGATCTT 57.473 50.000 0.00 0.00 34.14 2.40
272 273 2.091830 TCATGTCGGAGTACCCAGATCT 60.092 50.000 0.00 0.00 34.14 2.75
273 274 2.034812 GTCATGTCGGAGTACCCAGATC 59.965 54.545 0.00 0.00 34.14 2.75
274 275 2.032620 GTCATGTCGGAGTACCCAGAT 58.967 52.381 0.00 0.00 34.14 2.90
275 276 1.471119 GTCATGTCGGAGTACCCAGA 58.529 55.000 0.00 0.00 34.14 3.86
276 277 0.460311 GGTCATGTCGGAGTACCCAG 59.540 60.000 0.00 0.00 34.14 4.45
277 278 2.587080 GGTCATGTCGGAGTACCCA 58.413 57.895 0.00 0.00 34.14 4.51
278 279 1.821258 GGGTCATGTCGGAGTACCC 59.179 63.158 1.08 1.08 42.87 3.69
279 280 1.192428 AAGGGTCATGTCGGAGTACC 58.808 55.000 0.00 0.00 0.00 3.34
280 281 2.232941 TGAAAGGGTCATGTCGGAGTAC 59.767 50.000 0.00 0.00 0.00 2.73
281 282 2.531771 TGAAAGGGTCATGTCGGAGTA 58.468 47.619 0.00 0.00 0.00 2.59
282 283 1.348064 TGAAAGGGTCATGTCGGAGT 58.652 50.000 0.00 0.00 0.00 3.85
283 284 2.698855 ATGAAAGGGTCATGTCGGAG 57.301 50.000 0.00 0.00 45.69 4.63
337 339 6.971756 CGCATCACATTGTATGATTTTGGTTA 59.028 34.615 9.18 0.00 34.49 2.85
472 474 3.865446 TGCATGATCGTCTTGTCAAGAT 58.135 40.909 18.08 2.70 40.18 2.40
475 477 3.044235 ACTGCATGATCGTCTTGTCAA 57.956 42.857 0.00 0.00 0.00 3.18
499 501 4.248174 TCCCATATTTTGCAGGTCATGA 57.752 40.909 0.00 0.00 0.00 3.07
574 576 2.945008 TGTTTCTTCAGTGTGAGCTTGG 59.055 45.455 0.00 0.00 0.00 3.61
853 868 2.306847 GACAAAGAAGCAAGGGTCCAA 58.693 47.619 0.00 0.00 0.00 3.53
854 869 1.214175 TGACAAAGAAGCAAGGGTCCA 59.786 47.619 0.00 0.00 0.00 4.02
866 881 5.762179 AAGAGGTACATGGATGACAAAGA 57.238 39.130 0.00 0.00 0.00 2.52
876 891 3.733337 GGATGCAGTAAGAGGTACATGG 58.267 50.000 0.00 0.00 34.88 3.66
987 1007 0.404040 GGAACATGGGGAACAGGACA 59.596 55.000 0.00 0.00 34.35 4.02
1153 1174 4.008074 TCCATGTCTCTTTGAGGTTGTC 57.992 45.455 0.00 0.00 0.00 3.18
1177 1198 5.019785 ACCTTTGAGTTTTCGTAGTGACT 57.980 39.130 0.00 0.00 0.00 3.41
1292 1315 3.319122 GCAGAGGTGACAAAAAGGTTCAT 59.681 43.478 0.00 0.00 0.00 2.57
1294 1317 2.687935 TGCAGAGGTGACAAAAAGGTTC 59.312 45.455 0.00 0.00 0.00 3.62
1337 1361 6.371595 AGAATCAGGTGAACTCAAGAGAAT 57.628 37.500 3.73 0.00 0.00 2.40
1422 1451 1.005394 GTGACGACATGGACCCGTT 60.005 57.895 0.00 0.00 36.60 4.44
1431 1460 0.800631 CATTGCAGCTGTGACGACAT 59.199 50.000 16.64 0.00 0.00 3.06
1621 1656 6.595716 AGAACAAGCTGATACCTTACATTCAC 59.404 38.462 0.00 0.00 0.00 3.18
1622 1657 6.711277 AGAACAAGCTGATACCTTACATTCA 58.289 36.000 0.00 0.00 0.00 2.57
1680 1715 5.793034 ATATACTAGACTACGGGGGATGT 57.207 43.478 0.00 0.00 0.00 3.06
1945 1989 4.960938 TGCTTATGAACTACCATGCTAGG 58.039 43.478 0.27 0.00 0.00 3.02
2091 2171 9.381033 CCATCAAATTTGCCATGTTATTTCTAA 57.619 29.630 13.54 0.00 0.00 2.10
2108 2188 3.008157 TGCCATGCAACTTCCATCAAATT 59.992 39.130 0.00 0.00 34.76 1.82
2173 2253 6.869913 GGACATCAGAATTTGAAGAAAATGCA 59.130 34.615 0.00 0.00 38.52 3.96
2305 2388 7.440856 AGCAAAACACAAGAAAACAAAGAAAGA 59.559 29.630 0.00 0.00 0.00 2.52
2455 2540 0.251165 CCTTTGTCCACGGGTCCATT 60.251 55.000 0.00 0.00 0.00 3.16
2479 2564 2.114411 GTTCCCCCGCACCTCAAA 59.886 61.111 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.