Multiple sequence alignment - TraesCS5D01G491000

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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 TraesCS5D01G491000 chr5D 100.000 2537 0 0 1 2537 525244283 525241747 0.000000e+00 4686
1 TraesCS5D01G491000 chr5D 87.260 416 44 4 1001 1407 525321862 525322277 1.370000e-127 466
2 TraesCS5D01G491000 chr5D 82.018 545 60 22 1001 1538 525086436 525085923 1.800000e-116 429
3 TraesCS5D01G491000 chr5D 81.284 545 64 21 1001 1538 525154944 525154431 8.450000e-110 407
4 TraesCS5D01G491000 chr5B 86.988 2198 165 53 250 2394 659598095 659595966 0.000000e+00 2362
5 TraesCS5D01G491000 chr5B 87.822 427 43 4 1001 1418 659743614 659744040 2.270000e-135 492
6 TraesCS5D01G491000 chr5B 86.605 433 43 8 1001 1418 659739531 659739963 4.940000e-127 464
7 TraesCS5D01G491000 chr5B 79.354 557 66 33 1001 1543 659463189 659462668 1.870000e-91 346
8 TraesCS5D01G491000 chr5A 91.907 1421 77 22 552 1957 651579782 651578385 0.000000e+00 1953
9 TraesCS5D01G491000 chr5A 88.018 434 41 8 1001 1424 651788340 651788772 1.050000e-138 503
10 TraesCS5D01G491000 chr5A 87.915 422 39 6 1001 1410 651749003 651749424 1.060000e-133 486
11 TraesCS5D01G491000 chr5A 87.441 422 41 6 1001 1410 651734296 651734717 2.280000e-130 475
12 TraesCS5D01G491000 chr5A 84.698 464 56 8 2005 2455 651578295 651577834 1.380000e-122 449
13 TraesCS5D01G491000 chr5A 88.103 311 20 13 250 555 651580234 651579936 1.120000e-93 353
14 TraesCS5D01G491000 chrUn 86.353 425 43 6 1001 1410 67240746 67241170 1.380000e-122 449
15 TraesCS5D01G491000 chr6D 96.923 195 5 1 1 195 147646677 147646484 2.430000e-85 326
16 TraesCS5D01G491000 chr6D 96.447 197 5 2 1 197 141689533 141689727 8.750000e-85 324
17 TraesCS5D01G491000 chr6D 95.500 200 8 1 1 200 126427814 126428012 4.070000e-83 318
18 TraesCS5D01G491000 chr6D 96.392 194 6 1 1 194 392794731 392794923 4.070000e-83 318
19 TraesCS5D01G491000 chr7D 96.907 194 5 1 1 194 621759104 621759296 8.750000e-85 324
20 TraesCS5D01G491000 chr4D 95.522 201 8 1 1 201 464368653 464368454 1.130000e-83 320
21 TraesCS5D01G491000 chr2D 96.392 194 5 2 1 194 160319832 160319641 4.070000e-83 318
22 TraesCS5D01G491000 chr2D 95.918 196 7 1 1 196 36546892 36546698 1.460000e-82 316
23 TraesCS5D01G491000 chr3D 95.876 194 7 1 1 194 369418633 369418825 1.890000e-81 313


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 TraesCS5D01G491000 chr5D 525241747 525244283 2536 True 4686.000000 4686 100.0000 1 2537 1 chr5D.!!$R3 2536
1 TraesCS5D01G491000 chr5D 525085923 525086436 513 True 429.000000 429 82.0180 1001 1538 1 chr5D.!!$R1 537
2 TraesCS5D01G491000 chr5D 525154431 525154944 513 True 407.000000 407 81.2840 1001 1538 1 chr5D.!!$R2 537
3 TraesCS5D01G491000 chr5B 659595966 659598095 2129 True 2362.000000 2362 86.9880 250 2394 1 chr5B.!!$R2 2144
4 TraesCS5D01G491000 chr5B 659739531 659744040 4509 False 478.000000 492 87.2135 1001 1418 2 chr5B.!!$F1 417
5 TraesCS5D01G491000 chr5B 659462668 659463189 521 True 346.000000 346 79.3540 1001 1543 1 chr5B.!!$R1 542
6 TraesCS5D01G491000 chr5A 651577834 651580234 2400 True 918.333333 1953 88.2360 250 2455 3 chr5A.!!$R1 2205

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
248 249 0.106918 TCTTTTCGCCACACACCCTT 60.107 50.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 2235 0.378257 GCATCAATTGACGCCACGAT 59.622 50.0 15.43 0.0 0.0 3.73 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
20 21 3.230743 GGAATCCAATGGTGAAAACGG 57.769 47.619 0.00 0.00 0.00 4.44
21 22 2.560981 GGAATCCAATGGTGAAAACGGT 59.439 45.455 0.00 0.00 0.00 4.83
22 23 3.006430 GGAATCCAATGGTGAAAACGGTT 59.994 43.478 0.00 0.00 0.00 4.44
23 24 4.502431 GGAATCCAATGGTGAAAACGGTTT 60.502 41.667 0.00 0.00 0.00 3.27
24 25 3.444703 TCCAATGGTGAAAACGGTTTG 57.555 42.857 1.45 0.00 0.00 2.93
25 26 3.024547 TCCAATGGTGAAAACGGTTTGA 58.975 40.909 1.45 0.00 0.00 2.69
26 27 3.067461 TCCAATGGTGAAAACGGTTTGAG 59.933 43.478 1.45 0.00 0.00 3.02
27 28 3.067461 CCAATGGTGAAAACGGTTTGAGA 59.933 43.478 1.45 0.00 0.00 3.27
28 29 4.261994 CCAATGGTGAAAACGGTTTGAGAT 60.262 41.667 1.45 0.00 0.00 2.75
29 30 5.288804 CAATGGTGAAAACGGTTTGAGATT 58.711 37.500 1.45 0.00 0.00 2.40
30 31 4.993029 TGGTGAAAACGGTTTGAGATTT 57.007 36.364 1.45 0.00 0.00 2.17
31 32 4.677584 TGGTGAAAACGGTTTGAGATTTG 58.322 39.130 1.45 0.00 0.00 2.32
32 33 4.048504 GGTGAAAACGGTTTGAGATTTGG 58.951 43.478 1.45 0.00 0.00 3.28
33 34 4.202070 GGTGAAAACGGTTTGAGATTTGGA 60.202 41.667 1.45 0.00 0.00 3.53
34 35 4.738252 GTGAAAACGGTTTGAGATTTGGAC 59.262 41.667 1.45 0.00 0.00 4.02
35 36 3.619233 AAACGGTTTGAGATTTGGACG 57.381 42.857 5.12 0.00 0.00 4.79
36 37 0.872388 ACGGTTTGAGATTTGGACGC 59.128 50.000 0.00 0.00 0.00 5.19
37 38 0.871722 CGGTTTGAGATTTGGACGCA 59.128 50.000 0.00 0.00 0.00 5.24
38 39 1.399727 CGGTTTGAGATTTGGACGCAC 60.400 52.381 0.00 0.00 0.00 5.34
39 40 1.399727 GGTTTGAGATTTGGACGCACG 60.400 52.381 0.00 0.00 0.00 5.34
40 41 0.871722 TTTGAGATTTGGACGCACGG 59.128 50.000 0.00 0.00 0.00 4.94
41 42 0.250124 TTGAGATTTGGACGCACGGT 60.250 50.000 0.00 0.00 0.00 4.83
42 43 0.250124 TGAGATTTGGACGCACGGTT 60.250 50.000 0.00 0.00 0.00 4.44
43 44 0.872388 GAGATTTGGACGCACGGTTT 59.128 50.000 0.00 0.00 0.00 3.27
44 45 2.070783 GAGATTTGGACGCACGGTTTA 58.929 47.619 0.00 0.00 0.00 2.01
45 46 2.481185 GAGATTTGGACGCACGGTTTAA 59.519 45.455 0.00 0.00 0.00 1.52
46 47 2.482721 AGATTTGGACGCACGGTTTAAG 59.517 45.455 0.00 0.00 0.00 1.85
47 48 1.950828 TTTGGACGCACGGTTTAAGA 58.049 45.000 0.00 0.00 0.00 2.10
48 49 1.504359 TTGGACGCACGGTTTAAGAG 58.496 50.000 0.00 0.00 0.00 2.85
49 50 0.675083 TGGACGCACGGTTTAAGAGA 59.325 50.000 0.00 0.00 0.00 3.10
50 51 1.274167 TGGACGCACGGTTTAAGAGAT 59.726 47.619 0.00 0.00 0.00 2.75
51 52 2.492881 TGGACGCACGGTTTAAGAGATA 59.507 45.455 0.00 0.00 0.00 1.98
52 53 3.056678 TGGACGCACGGTTTAAGAGATAA 60.057 43.478 0.00 0.00 0.00 1.75
53 54 3.928375 GGACGCACGGTTTAAGAGATAAA 59.072 43.478 0.00 0.00 0.00 1.40
54 55 4.389687 GGACGCACGGTTTAAGAGATAAAA 59.610 41.667 0.00 0.00 35.33 1.52
55 56 5.273523 ACGCACGGTTTAAGAGATAAAAC 57.726 39.130 0.00 0.00 37.75 2.43
101 102 4.736126 AAAAGGGAAAACTCACAGGTTG 57.264 40.909 0.00 0.00 0.00 3.77
102 103 1.692411 AGGGAAAACTCACAGGTTGC 58.308 50.000 0.00 0.00 0.00 4.17
103 104 0.310854 GGGAAAACTCACAGGTTGCG 59.689 55.000 0.00 0.00 0.00 4.85
104 105 1.305201 GGAAAACTCACAGGTTGCGA 58.695 50.000 0.00 0.00 0.00 5.10
105 106 1.002792 GGAAAACTCACAGGTTGCGAC 60.003 52.381 0.00 0.00 0.00 5.19
106 107 1.668751 GAAAACTCACAGGTTGCGACA 59.331 47.619 6.39 0.00 0.00 4.35
107 108 1.745232 AAACTCACAGGTTGCGACAA 58.255 45.000 6.39 0.00 0.00 3.18
108 109 1.299541 AACTCACAGGTTGCGACAAG 58.700 50.000 6.39 0.00 0.00 3.16
109 110 0.178068 ACTCACAGGTTGCGACAAGT 59.822 50.000 6.39 0.32 0.00 3.16
110 111 0.583438 CTCACAGGTTGCGACAAGTG 59.417 55.000 17.54 17.54 35.00 3.16
111 112 0.176910 TCACAGGTTGCGACAAGTGA 59.823 50.000 20.66 20.66 38.17 3.41
112 113 0.304705 CACAGGTTGCGACAAGTGAC 59.695 55.000 18.40 0.00 35.41 3.67
113 114 1.151777 ACAGGTTGCGACAAGTGACG 61.152 55.000 6.39 0.00 36.38 4.35
119 120 4.415501 CGACAAGTGACGCGCTGC 62.416 66.667 5.73 0.00 0.00 5.25
120 121 3.337889 GACAAGTGACGCGCTGCA 61.338 61.111 5.73 0.00 0.00 4.41
121 122 3.287121 GACAAGTGACGCGCTGCAG 62.287 63.158 10.11 10.11 0.00 4.41
122 123 4.081030 CAAGTGACGCGCTGCAGG 62.081 66.667 17.12 6.85 0.00 4.85
123 124 4.609018 AAGTGACGCGCTGCAGGT 62.609 61.111 17.12 4.61 0.00 4.00
139 140 4.994201 GTGCGCCACTCGTCGTGA 62.994 66.667 4.18 0.00 46.81 4.35
140 141 4.994201 TGCGCCACTCGTCGTGAC 62.994 66.667 4.18 0.00 46.81 3.67
142 143 4.039357 CGCCACTCGTCGTGACCT 62.039 66.667 0.56 0.00 46.81 3.85
143 144 2.430921 GCCACTCGTCGTGACCTG 60.431 66.667 0.56 0.00 46.81 4.00
144 145 2.258591 CCACTCGTCGTGACCTGG 59.741 66.667 0.56 0.00 46.81 4.45
145 146 2.258591 CACTCGTCGTGACCTGGG 59.741 66.667 0.00 0.00 46.81 4.45
146 147 2.114625 ACTCGTCGTGACCTGGGA 59.885 61.111 0.00 0.00 0.00 4.37
147 148 1.529948 ACTCGTCGTGACCTGGGAA 60.530 57.895 0.00 0.00 0.00 3.97
148 149 1.213013 CTCGTCGTGACCTGGGAAG 59.787 63.158 0.00 0.00 0.00 3.46
149 150 1.228337 TCGTCGTGACCTGGGAAGA 60.228 57.895 0.00 0.00 0.00 2.87
150 151 0.611062 TCGTCGTGACCTGGGAAGAT 60.611 55.000 0.00 0.00 0.00 2.40
151 152 0.458543 CGTCGTGACCTGGGAAGATG 60.459 60.000 0.00 0.00 0.00 2.90
152 153 0.108138 GTCGTGACCTGGGAAGATGG 60.108 60.000 0.00 0.00 0.00 3.51
153 154 0.252057 TCGTGACCTGGGAAGATGGA 60.252 55.000 0.00 0.00 0.00 3.41
154 155 0.176680 CGTGACCTGGGAAGATGGAG 59.823 60.000 0.00 0.00 0.00 3.86
155 156 1.280457 GTGACCTGGGAAGATGGAGT 58.720 55.000 0.00 0.00 0.00 3.85
156 157 1.065854 GTGACCTGGGAAGATGGAGTG 60.066 57.143 0.00 0.00 0.00 3.51
157 158 1.280457 GACCTGGGAAGATGGAGTGT 58.720 55.000 0.00 0.00 0.00 3.55
158 159 1.630878 GACCTGGGAAGATGGAGTGTT 59.369 52.381 0.00 0.00 0.00 3.32
159 160 1.630878 ACCTGGGAAGATGGAGTGTTC 59.369 52.381 0.00 0.00 0.00 3.18
160 161 1.912043 CCTGGGAAGATGGAGTGTTCT 59.088 52.381 0.00 0.00 31.12 3.01
161 162 2.307098 CCTGGGAAGATGGAGTGTTCTT 59.693 50.000 0.00 0.00 34.95 2.52
162 163 3.245052 CCTGGGAAGATGGAGTGTTCTTT 60.245 47.826 0.00 0.00 32.46 2.52
163 164 3.754965 TGGGAAGATGGAGTGTTCTTTG 58.245 45.455 0.00 0.00 32.46 2.77
164 165 2.489722 GGGAAGATGGAGTGTTCTTTGC 59.510 50.000 0.00 0.00 32.46 3.68
165 166 3.149196 GGAAGATGGAGTGTTCTTTGCA 58.851 45.455 0.00 0.00 32.46 4.08
166 167 3.569701 GGAAGATGGAGTGTTCTTTGCAA 59.430 43.478 0.00 0.00 32.46 4.08
167 168 4.540824 GAAGATGGAGTGTTCTTTGCAAC 58.459 43.478 0.00 0.00 32.46 4.17
168 169 2.549754 AGATGGAGTGTTCTTTGCAACG 59.450 45.455 0.00 0.00 0.00 4.10
169 170 2.031258 TGGAGTGTTCTTTGCAACGA 57.969 45.000 0.00 0.00 0.00 3.85
170 171 1.939934 TGGAGTGTTCTTTGCAACGAG 59.060 47.619 0.00 0.00 0.00 4.18
171 172 1.940613 GGAGTGTTCTTTGCAACGAGT 59.059 47.619 0.00 0.00 0.00 4.18
172 173 3.128349 GGAGTGTTCTTTGCAACGAGTA 58.872 45.455 0.00 0.00 0.00 2.59
173 174 3.059800 GGAGTGTTCTTTGCAACGAGTAC 60.060 47.826 0.00 6.11 0.00 2.73
174 175 3.793559 AGTGTTCTTTGCAACGAGTACT 58.206 40.909 14.37 14.37 0.00 2.73
175 176 3.802685 AGTGTTCTTTGCAACGAGTACTC 59.197 43.478 13.18 13.18 0.00 2.59
176 177 3.059800 GTGTTCTTTGCAACGAGTACTCC 60.060 47.826 17.23 3.69 0.00 3.85
177 178 3.181469 TGTTCTTTGCAACGAGTACTCCT 60.181 43.478 17.23 2.73 0.00 3.69
178 179 3.746045 TCTTTGCAACGAGTACTCCTT 57.254 42.857 17.23 9.18 0.00 3.36
179 180 4.067972 TCTTTGCAACGAGTACTCCTTT 57.932 40.909 17.23 7.84 0.00 3.11
180 181 5.204409 TCTTTGCAACGAGTACTCCTTTA 57.796 39.130 17.23 1.50 0.00 1.85
181 182 5.603596 TCTTTGCAACGAGTACTCCTTTAA 58.396 37.500 17.23 7.03 0.00 1.52
182 183 6.228258 TCTTTGCAACGAGTACTCCTTTAAT 58.772 36.000 17.23 0.00 0.00 1.40
183 184 6.708949 TCTTTGCAACGAGTACTCCTTTAATT 59.291 34.615 17.23 0.07 0.00 1.40
184 185 7.874016 TCTTTGCAACGAGTACTCCTTTAATTA 59.126 33.333 17.23 0.00 0.00 1.40
185 186 7.591006 TTGCAACGAGTACTCCTTTAATTAG 57.409 36.000 17.23 2.42 0.00 1.73
186 187 6.694447 TGCAACGAGTACTCCTTTAATTAGT 58.306 36.000 17.23 3.06 0.00 2.24
187 188 6.588756 TGCAACGAGTACTCCTTTAATTAGTG 59.411 38.462 17.23 1.20 0.00 2.74
188 189 6.455246 GCAACGAGTACTCCTTTAATTAGTGC 60.455 42.308 17.23 6.29 0.00 4.40
189 190 6.527057 ACGAGTACTCCTTTAATTAGTGCT 57.473 37.500 17.23 0.00 38.64 4.40
190 191 6.932947 ACGAGTACTCCTTTAATTAGTGCTT 58.067 36.000 17.23 0.00 36.49 3.91
191 192 7.384477 ACGAGTACTCCTTTAATTAGTGCTTT 58.616 34.615 17.23 0.00 36.49 3.51
192 193 7.544915 ACGAGTACTCCTTTAATTAGTGCTTTC 59.455 37.037 17.23 0.00 36.49 2.62
193 194 7.253684 CGAGTACTCCTTTAATTAGTGCTTTCG 60.254 40.741 17.23 0.00 36.49 3.46
194 195 5.547181 ACTCCTTTAATTAGTGCTTTCGC 57.453 39.130 0.00 0.00 0.00 4.70
195 196 5.246307 ACTCCTTTAATTAGTGCTTTCGCT 58.754 37.500 0.00 0.00 36.97 4.93
196 197 6.403878 ACTCCTTTAATTAGTGCTTTCGCTA 58.596 36.000 0.00 0.00 36.97 4.26
197 198 6.877322 ACTCCTTTAATTAGTGCTTTCGCTAA 59.123 34.615 1.48 1.48 45.88 3.09
198 199 7.389607 ACTCCTTTAATTAGTGCTTTCGCTAAA 59.610 33.333 2.94 0.00 45.23 1.85
199 200 8.101654 TCCTTTAATTAGTGCTTTCGCTAAAA 57.898 30.769 2.94 0.00 45.23 1.52
200 201 8.234546 TCCTTTAATTAGTGCTTTCGCTAAAAG 58.765 33.333 2.94 4.54 45.23 2.27
201 202 8.021396 CCTTTAATTAGTGCTTTCGCTAAAAGT 58.979 33.333 9.38 0.00 45.23 2.66
202 203 8.944212 TTTAATTAGTGCTTTCGCTAAAAGTC 57.056 30.769 9.38 4.18 45.23 3.01
203 204 6.554334 AATTAGTGCTTTCGCTAAAAGTCA 57.446 33.333 9.38 6.11 45.23 3.41
204 205 3.879932 AGTGCTTTCGCTAAAAGTCAC 57.120 42.857 17.79 17.79 45.23 3.67
205 206 2.548480 AGTGCTTTCGCTAAAAGTCACC 59.452 45.455 19.71 10.76 44.37 4.02
206 207 2.548480 GTGCTTTCGCTAAAAGTCACCT 59.452 45.455 16.24 0.00 45.23 4.00
207 208 2.548057 TGCTTTCGCTAAAAGTCACCTG 59.452 45.455 9.38 0.00 45.23 4.00
208 209 2.806244 GCTTTCGCTAAAAGTCACCTGA 59.194 45.455 9.38 0.00 45.23 3.86
209 210 3.364068 GCTTTCGCTAAAAGTCACCTGAC 60.364 47.826 9.38 0.00 45.23 3.51
218 219 3.842869 GTCACCTGACATCCACTCC 57.157 57.895 0.31 0.00 44.18 3.85
219 220 0.976641 GTCACCTGACATCCACTCCA 59.023 55.000 0.31 0.00 44.18 3.86
220 221 1.556911 GTCACCTGACATCCACTCCAT 59.443 52.381 0.31 0.00 44.18 3.41
221 222 1.556451 TCACCTGACATCCACTCCATG 59.444 52.381 0.00 0.00 0.00 3.66
222 223 1.280133 CACCTGACATCCACTCCATGT 59.720 52.381 0.00 0.00 37.18 3.21
223 224 2.501316 CACCTGACATCCACTCCATGTA 59.499 50.000 0.00 0.00 34.49 2.29
224 225 2.768527 ACCTGACATCCACTCCATGTAG 59.231 50.000 0.00 0.00 34.49 2.74
225 226 2.103771 CCTGACATCCACTCCATGTAGG 59.896 54.545 0.00 0.00 34.49 3.18
226 227 3.033909 CTGACATCCACTCCATGTAGGA 58.966 50.000 0.00 0.00 46.75 2.94
237 238 4.060038 TCCATGTAGGAGATCTTTTCGC 57.940 45.455 0.00 0.00 43.07 4.70
238 239 3.134458 CCATGTAGGAGATCTTTTCGCC 58.866 50.000 0.00 0.00 44.17 5.54
239 240 3.432186 CCATGTAGGAGATCTTTTCGCCA 60.432 47.826 0.00 0.00 46.11 5.69
240 241 3.247006 TGTAGGAGATCTTTTCGCCAC 57.753 47.619 0.00 0.00 46.11 5.01
241 242 2.565391 TGTAGGAGATCTTTTCGCCACA 59.435 45.455 0.00 0.00 46.11 4.17
242 243 2.100605 AGGAGATCTTTTCGCCACAC 57.899 50.000 0.00 0.00 46.11 3.82
243 244 1.347707 AGGAGATCTTTTCGCCACACA 59.652 47.619 0.00 0.00 46.11 3.72
244 245 1.464997 GGAGATCTTTTCGCCACACAC 59.535 52.381 0.00 0.00 43.37 3.82
245 246 1.464997 GAGATCTTTTCGCCACACACC 59.535 52.381 0.00 0.00 0.00 4.16
246 247 0.521735 GATCTTTTCGCCACACACCC 59.478 55.000 0.00 0.00 0.00 4.61
247 248 0.110486 ATCTTTTCGCCACACACCCT 59.890 50.000 0.00 0.00 0.00 4.34
248 249 0.106918 TCTTTTCGCCACACACCCTT 60.107 50.000 0.00 0.00 0.00 3.95
260 261 5.474189 GCCACACACCCTTAATTAACTGTTA 59.526 40.000 0.00 0.00 0.00 2.41
267 268 7.285172 ACACCCTTAATTAACTGTTAACGGTTT 59.715 33.333 31.94 19.60 42.39 3.27
274 275 1.314730 CTGTTAACGGTTTGGCAGGT 58.685 50.000 6.25 0.00 0.00 4.00
472 481 2.405172 GTCGACCTTGGACAGAAAGAC 58.595 52.381 3.51 0.00 34.56 3.01
489 498 3.409026 AGACACTCCAGAACATTCCAC 57.591 47.619 0.00 0.00 0.00 4.02
514 537 2.512515 GCTCGATCCAGTGTGCCC 60.513 66.667 0.00 0.00 0.00 5.36
559 743 7.448777 CAGCCTGGACTATTCTACTACTGATAA 59.551 40.741 0.00 0.00 0.00 1.75
611 795 2.819550 CCCACGCGGCTAAGGTAT 59.180 61.111 12.47 0.00 0.00 2.73
613 797 2.244651 CCACGCGGCTAAGGTATGC 61.245 63.158 12.47 0.00 0.00 3.14
614 798 1.520564 CACGCGGCTAAGGTATGCA 60.521 57.895 12.47 0.00 0.00 3.96
615 799 0.880278 CACGCGGCTAAGGTATGCAT 60.880 55.000 12.47 3.79 0.00 3.96
773 962 2.753701 CGATTGGTCCACCCACCA 59.246 61.111 0.00 0.00 45.19 4.17
942 1143 7.400439 TCCATCAACTCATTCATCTTCTTTCT 58.600 34.615 0.00 0.00 0.00 2.52
943 1144 7.886970 TCCATCAACTCATTCATCTTCTTTCTT 59.113 33.333 0.00 0.00 0.00 2.52
944 1145 8.182881 CCATCAACTCATTCATCTTCTTTCTTC 58.817 37.037 0.00 0.00 0.00 2.87
952 1153 1.878953 TCTTCTTTCTTCGCCACACC 58.121 50.000 0.00 0.00 0.00 4.16
959 1160 4.651008 TTCGCCACACCGACGGAC 62.651 66.667 23.38 3.28 36.90 4.79
980 1181 3.999663 ACCGATCAAGAAGAGCAGAAAAG 59.000 43.478 0.00 0.00 31.47 2.27
1074 1297 4.436998 CTCACCACGGACTCGGCC 62.437 72.222 0.00 0.00 41.39 6.13
1543 1790 1.746220 AGCTGTTCGTCTAGGTAGCTG 59.254 52.381 4.27 0.00 39.77 4.24
1545 1792 2.366533 CTGTTCGTCTAGGTAGCTGGA 58.633 52.381 3.59 3.59 0.00 3.86
1578 1832 7.824779 AGTAGTTACAATTTCTTGATGGAGGAC 59.175 37.037 0.00 0.00 36.20 3.85
1650 1904 7.009723 GGTTAATTGTTGGGCATTGTAATTACG 59.990 37.037 10.92 0.00 0.00 3.18
1652 1906 4.955925 TGTTGGGCATTGTAATTACGAG 57.044 40.909 11.20 4.86 0.00 4.18
1703 1959 2.270352 TGGCGTTTCTGTTCTTGGAT 57.730 45.000 0.00 0.00 0.00 3.41
1715 1971 4.450053 TGTTCTTGGATTTTTGCTTTGGG 58.550 39.130 0.00 0.00 0.00 4.12
1725 1982 2.685106 TTGCTTTGGGTTGGTCCATA 57.315 45.000 0.00 0.00 36.58 2.74
1828 2182 3.134458 CAGTCCACTTCAGAACCTCAAC 58.866 50.000 0.00 0.00 0.00 3.18
1844 2198 6.076981 ACCTCAACTTGTAAAATTCTGCAG 57.923 37.500 7.63 7.63 0.00 4.41
1881 2235 9.667107 TTCTAGAAAAGAAAGACAAACTCTCAA 57.333 29.630 1.68 0.00 41.35 3.02
1886 2240 5.914085 AGAAAGACAAACTCTCAATCGTG 57.086 39.130 0.00 0.00 0.00 4.35
1912 2267 4.971830 GTCAATTGATGCAACACGATATGG 59.028 41.667 12.12 0.00 0.00 2.74
1927 2282 7.556844 ACACGATATGGAAGAAGATAAACACT 58.443 34.615 0.00 0.00 0.00 3.55
1928 2283 7.492669 ACACGATATGGAAGAAGATAAACACTG 59.507 37.037 0.00 0.00 0.00 3.66
1931 2286 9.265901 CGATATGGAAGAAGATAAACACTGAAT 57.734 33.333 0.00 0.00 0.00 2.57
1942 2297 4.685169 AAACACTGAATAGTTGCATCGG 57.315 40.909 0.00 0.00 34.07 4.18
1957 2312 2.222729 GCATCGGTTGATACAACACGAC 60.223 50.000 20.53 11.66 32.18 4.34
1990 2381 5.541101 TGGCAGTATACCGGATAACTATTGT 59.459 40.000 9.46 0.00 0.00 2.71
1992 2383 6.098017 GCAGTATACCGGATAACTATTGTCC 58.902 44.000 9.46 0.00 37.56 4.02
2064 2483 0.618458 TGAGTTTTAGGAGCCGCCAT 59.382 50.000 0.00 0.00 40.02 4.40
2101 2522 5.281727 TCATCCGTGATCTGATTCTAAACG 58.718 41.667 0.00 0.00 0.00 3.60
2112 3313 5.411361 TCTGATTCTAAACGACATGGTTTGG 59.589 40.000 9.54 7.28 40.18 3.28
2135 3336 3.915437 AATTGACTTGCAACCTAACCG 57.085 42.857 0.00 0.00 39.78 4.44
2146 3347 2.109126 CCTAACCGAAGCAGCTGGC 61.109 63.158 17.12 7.98 45.30 4.85
2169 3370 3.253432 GGTTCAGGATTTCACAACTGGTC 59.747 47.826 0.00 0.00 0.00 4.02
2184 3642 6.811170 CACAACTGGTCAACACAATAACTTTT 59.189 34.615 0.00 0.00 0.00 2.27
2185 3643 7.330700 CACAACTGGTCAACACAATAACTTTTT 59.669 33.333 0.00 0.00 0.00 1.94
2186 3644 7.544217 ACAACTGGTCAACACAATAACTTTTTC 59.456 33.333 0.00 0.00 0.00 2.29
2255 3995 9.809096 TGAACTACTTGAGCTTAGATCAAATAG 57.191 33.333 21.80 21.80 40.53 1.73
2303 4045 8.898761 ACATCACAAAATGTTGTCAGTTTAGTA 58.101 29.630 0.00 0.00 45.00 1.82
2307 4049 8.957028 CACAAAATGTTGTCAGTTTAGTATGTG 58.043 33.333 0.00 0.00 45.00 3.21
2318 4060 6.266786 TCAGTTTAGTATGTGTCAGGTCTTCA 59.733 38.462 0.00 0.00 0.00 3.02
2323 4065 8.918202 TTAGTATGTGTCAGGTCTTCAATTTT 57.082 30.769 0.00 0.00 0.00 1.82
2345 4087 1.672881 GGTTTCTTGGCTGGATCATCG 59.327 52.381 0.00 0.00 0.00 3.84
2362 4104 5.119931 TCATCGATTTGGTCTGGTTTTTG 57.880 39.130 0.00 0.00 0.00 2.44
2373 4115 4.321230 GGTCTGGTTTTTGGAACTATGCTG 60.321 45.833 0.00 0.00 0.00 4.41
2384 4126 4.223700 TGGAACTATGCTGAACAGATGTCT 59.776 41.667 5.97 0.00 0.00 3.41
2395 4137 5.052481 TGAACAGATGTCTGAAGTTCACAG 58.948 41.667 16.41 0.00 46.59 3.66
2396 4138 4.944619 ACAGATGTCTGAAGTTCACAGA 57.055 40.909 16.41 0.00 46.59 3.41
2400 4142 6.870965 ACAGATGTCTGAAGTTCACAGAATAC 59.129 38.462 16.41 0.00 46.59 1.89
2406 4148 6.743627 GTCTGAAGTTCACAGAATACGAGTAG 59.256 42.308 0.08 0.00 44.29 2.57
2418 4160 1.726853 ACGAGTAGATTGCCAAGTGC 58.273 50.000 0.00 0.00 41.77 4.40
2435 4177 0.037326 TGCCGACTACCAAGAAGCAG 60.037 55.000 0.00 0.00 0.00 4.24
2458 4200 9.301153 GCAGAAAAGAAATCTAAACTGTGAAAA 57.699 29.630 0.00 0.00 0.00 2.29
2467 4209 8.614994 AATCTAAACTGTGAAAACTTTGAACG 57.385 30.769 0.00 0.00 0.00 3.95
2471 4213 4.729595 ACTGTGAAAACTTTGAACGAACC 58.270 39.130 0.00 0.00 0.00 3.62
2473 4215 2.528688 GTGAAAACTTTGAACGAACCGC 59.471 45.455 0.00 0.00 0.00 5.68
2474 4216 2.420722 TGAAAACTTTGAACGAACCGCT 59.579 40.909 0.00 0.00 0.00 5.52
2476 4218 4.273969 TGAAAACTTTGAACGAACCGCTAT 59.726 37.500 0.00 0.00 0.00 2.97
2477 4219 5.466058 TGAAAACTTTGAACGAACCGCTATA 59.534 36.000 0.00 0.00 0.00 1.31
2478 4220 5.927954 AAACTTTGAACGAACCGCTATAA 57.072 34.783 0.00 0.00 0.00 0.98
2479 4221 4.916099 ACTTTGAACGAACCGCTATAAC 57.084 40.909 0.00 0.00 0.00 1.89
2481 4223 5.713025 ACTTTGAACGAACCGCTATAACTA 58.287 37.500 0.00 0.00 0.00 2.24
2482 4224 6.335777 ACTTTGAACGAACCGCTATAACTAT 58.664 36.000 0.00 0.00 0.00 2.12
2484 4226 5.762825 TGAACGAACCGCTATAACTATCT 57.237 39.130 0.00 0.00 0.00 1.98
2485 4227 6.866010 TGAACGAACCGCTATAACTATCTA 57.134 37.500 0.00 0.00 0.00 1.98
2486 4228 6.662616 TGAACGAACCGCTATAACTATCTAC 58.337 40.000 0.00 0.00 0.00 2.59
2487 4229 5.619625 ACGAACCGCTATAACTATCTACC 57.380 43.478 0.00 0.00 0.00 3.18
2488 4230 4.457257 ACGAACCGCTATAACTATCTACCC 59.543 45.833 0.00 0.00 0.00 3.69
2492 4234 3.760684 CCGCTATAACTATCTACCCCGTT 59.239 47.826 0.00 0.00 0.00 4.44
2494 4236 4.142513 CGCTATAACTATCTACCCCGTTCC 60.143 50.000 0.00 0.00 0.00 3.62
2495 4237 4.768968 GCTATAACTATCTACCCCGTTCCA 59.231 45.833 0.00 0.00 0.00 3.53
2496 4238 5.244626 GCTATAACTATCTACCCCGTTCCAA 59.755 44.000 0.00 0.00 0.00 3.53
2497 4239 6.239402 GCTATAACTATCTACCCCGTTCCAAA 60.239 42.308 0.00 0.00 0.00 3.28
2498 4240 4.914177 AACTATCTACCCCGTTCCAAAA 57.086 40.909 0.00 0.00 0.00 2.44
2499 4241 5.446260 AACTATCTACCCCGTTCCAAAAT 57.554 39.130 0.00 0.00 0.00 1.82
2500 4242 6.564557 AACTATCTACCCCGTTCCAAAATA 57.435 37.500 0.00 0.00 0.00 1.40
2502 4244 5.664457 ACTATCTACCCCGTTCCAAAATAGT 59.336 40.000 0.00 0.00 0.00 2.12
2504 4246 4.581868 TCTACCCCGTTCCAAAATAGTTG 58.418 43.478 0.00 0.00 0.00 3.16
2505 4247 3.512219 ACCCCGTTCCAAAATAGTTGA 57.488 42.857 0.00 0.00 0.00 3.18
2506 4248 3.834938 ACCCCGTTCCAAAATAGTTGAA 58.165 40.909 0.00 0.00 0.00 2.69
2508 4250 3.824443 CCCCGTTCCAAAATAGTTGAAGT 59.176 43.478 0.00 0.00 0.00 3.01
2510 4252 5.106436 CCCCGTTCCAAAATAGTTGAAGTAC 60.106 44.000 0.00 0.00 0.00 2.73
2511 4253 5.704053 CCCGTTCCAAAATAGTTGAAGTACT 59.296 40.000 0.00 0.00 0.00 2.73
2512 4254 6.875195 CCCGTTCCAAAATAGTTGAAGTACTA 59.125 38.462 0.00 0.00 35.25 1.82
2514 4256 7.816031 CCGTTCCAAAATAGTTGAAGTACTAGA 59.184 37.037 0.00 0.00 34.32 2.43
2515 4257 9.199982 CGTTCCAAAATAGTTGAAGTACTAGAA 57.800 33.333 0.00 0.00 34.32 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.560981 ACCGTTTTCACCATTGGATTCC 59.439 45.455 10.37 0.00 0.00 3.01
1 2 3.934457 ACCGTTTTCACCATTGGATTC 57.066 42.857 10.37 0.00 0.00 2.52
2 3 4.100189 TCAAACCGTTTTCACCATTGGATT 59.900 37.500 10.37 0.00 0.00 3.01
3 4 3.639094 TCAAACCGTTTTCACCATTGGAT 59.361 39.130 10.37 0.00 0.00 3.41
4 5 3.024547 TCAAACCGTTTTCACCATTGGA 58.975 40.909 10.37 0.00 0.00 3.53
5 6 3.067461 TCTCAAACCGTTTTCACCATTGG 59.933 43.478 0.00 0.00 0.00 3.16
6 7 4.300189 TCTCAAACCGTTTTCACCATTG 57.700 40.909 0.00 0.00 0.00 2.82
7 8 5.529581 AATCTCAAACCGTTTTCACCATT 57.470 34.783 0.00 0.00 0.00 3.16
8 9 5.288804 CAAATCTCAAACCGTTTTCACCAT 58.711 37.500 0.00 0.00 0.00 3.55
9 10 4.440802 CCAAATCTCAAACCGTTTTCACCA 60.441 41.667 0.00 0.00 0.00 4.17
10 11 4.048504 CCAAATCTCAAACCGTTTTCACC 58.951 43.478 0.00 0.00 0.00 4.02
11 12 4.738252 GTCCAAATCTCAAACCGTTTTCAC 59.262 41.667 0.00 0.00 0.00 3.18
12 13 4.496673 CGTCCAAATCTCAAACCGTTTTCA 60.497 41.667 0.00 0.00 0.00 2.69
13 14 3.972502 CGTCCAAATCTCAAACCGTTTTC 59.027 43.478 0.00 0.00 0.00 2.29
14 15 3.794138 GCGTCCAAATCTCAAACCGTTTT 60.794 43.478 0.00 0.00 0.00 2.43
15 16 2.287368 GCGTCCAAATCTCAAACCGTTT 60.287 45.455 0.00 0.00 0.00 3.60
16 17 1.265905 GCGTCCAAATCTCAAACCGTT 59.734 47.619 0.00 0.00 0.00 4.44
17 18 0.872388 GCGTCCAAATCTCAAACCGT 59.128 50.000 0.00 0.00 0.00 4.83
18 19 0.871722 TGCGTCCAAATCTCAAACCG 59.128 50.000 0.00 0.00 0.00 4.44
19 20 1.399727 CGTGCGTCCAAATCTCAAACC 60.400 52.381 0.00 0.00 0.00 3.27
20 21 1.399727 CCGTGCGTCCAAATCTCAAAC 60.400 52.381 0.00 0.00 0.00 2.93
21 22 0.871722 CCGTGCGTCCAAATCTCAAA 59.128 50.000 0.00 0.00 0.00 2.69
22 23 0.250124 ACCGTGCGTCCAAATCTCAA 60.250 50.000 0.00 0.00 0.00 3.02
23 24 0.250124 AACCGTGCGTCCAAATCTCA 60.250 50.000 0.00 0.00 0.00 3.27
24 25 0.872388 AAACCGTGCGTCCAAATCTC 59.128 50.000 0.00 0.00 0.00 2.75
25 26 2.172851 TAAACCGTGCGTCCAAATCT 57.827 45.000 0.00 0.00 0.00 2.40
26 27 2.481185 TCTTAAACCGTGCGTCCAAATC 59.519 45.455 0.00 0.00 0.00 2.17
27 28 2.482721 CTCTTAAACCGTGCGTCCAAAT 59.517 45.455 0.00 0.00 0.00 2.32
28 29 1.868498 CTCTTAAACCGTGCGTCCAAA 59.132 47.619 0.00 0.00 0.00 3.28
29 30 1.068895 TCTCTTAAACCGTGCGTCCAA 59.931 47.619 0.00 0.00 0.00 3.53
30 31 0.675083 TCTCTTAAACCGTGCGTCCA 59.325 50.000 0.00 0.00 0.00 4.02
31 32 2.005971 ATCTCTTAAACCGTGCGTCC 57.994 50.000 0.00 0.00 0.00 4.79
32 33 5.311271 GTTTTATCTCTTAAACCGTGCGTC 58.689 41.667 0.00 0.00 29.47 5.19
33 34 4.143263 CGTTTTATCTCTTAAACCGTGCGT 60.143 41.667 0.00 0.00 32.79 5.24
34 35 4.143263 ACGTTTTATCTCTTAAACCGTGCG 60.143 41.667 0.86 0.00 44.18 5.34
35 36 5.273523 ACGTTTTATCTCTTAAACCGTGC 57.726 39.130 0.86 0.00 44.18 5.34
36 37 7.851963 TCAAAACGTTTTATCTCTTAAACCGTG 59.148 33.333 24.79 8.65 44.82 4.94
37 38 7.918643 TCAAAACGTTTTATCTCTTAAACCGT 58.081 30.769 24.79 0.00 46.69 4.83
38 39 8.770850 TTCAAAACGTTTTATCTCTTAAACCG 57.229 30.769 24.79 8.91 40.37 4.44
53 54 8.274939 TTCGTAGATTCGTTTATTCAAAACGTT 58.725 29.630 18.93 0.00 44.53 3.99
54 55 7.786114 TTCGTAGATTCGTTTATTCAAAACGT 58.214 30.769 18.93 4.76 44.53 3.99
55 56 8.630494 TTTCGTAGATTCGTTTATTCAAAACG 57.370 30.769 14.92 14.92 45.10 3.60
79 80 4.622933 GCAACCTGTGAGTTTTCCCTTTTT 60.623 41.667 0.00 0.00 0.00 1.94
80 81 3.118775 GCAACCTGTGAGTTTTCCCTTTT 60.119 43.478 0.00 0.00 0.00 2.27
81 82 2.430694 GCAACCTGTGAGTTTTCCCTTT 59.569 45.455 0.00 0.00 0.00 3.11
82 83 2.031870 GCAACCTGTGAGTTTTCCCTT 58.968 47.619 0.00 0.00 0.00 3.95
83 84 1.692411 GCAACCTGTGAGTTTTCCCT 58.308 50.000 0.00 0.00 0.00 4.20
84 85 0.310854 CGCAACCTGTGAGTTTTCCC 59.689 55.000 0.00 0.00 0.00 3.97
85 86 1.002792 GTCGCAACCTGTGAGTTTTCC 60.003 52.381 0.00 0.00 37.59 3.13
86 87 1.668751 TGTCGCAACCTGTGAGTTTTC 59.331 47.619 0.00 0.00 37.59 2.29
87 88 1.745232 TGTCGCAACCTGTGAGTTTT 58.255 45.000 0.00 0.00 37.59 2.43
88 89 1.670811 CTTGTCGCAACCTGTGAGTTT 59.329 47.619 0.00 0.00 37.59 2.66
89 90 1.299541 CTTGTCGCAACCTGTGAGTT 58.700 50.000 0.00 0.00 37.59 3.01
90 91 0.178068 ACTTGTCGCAACCTGTGAGT 59.822 50.000 0.00 0.00 37.59 3.41
91 92 0.583438 CACTTGTCGCAACCTGTGAG 59.417 55.000 0.00 0.00 37.59 3.51
92 93 0.176910 TCACTTGTCGCAACCTGTGA 59.823 50.000 8.16 8.16 35.60 3.58
93 94 0.304705 GTCACTTGTCGCAACCTGTG 59.695 55.000 0.00 0.00 0.00 3.66
94 95 1.151777 CGTCACTTGTCGCAACCTGT 61.152 55.000 0.00 0.00 0.00 4.00
95 96 1.564622 CGTCACTTGTCGCAACCTG 59.435 57.895 0.00 0.00 0.00 4.00
96 97 4.027755 CGTCACTTGTCGCAACCT 57.972 55.556 0.00 0.00 0.00 3.50
101 102 4.415501 CAGCGCGTCACTTGTCGC 62.416 66.667 8.43 10.28 46.08 5.19
102 103 4.415501 GCAGCGCGTCACTTGTCG 62.416 66.667 8.43 0.00 0.00 4.35
103 104 3.287121 CTGCAGCGCGTCACTTGTC 62.287 63.158 8.43 0.00 0.00 3.18
104 105 3.341043 CTGCAGCGCGTCACTTGT 61.341 61.111 8.43 0.00 0.00 3.16
105 106 4.081030 CCTGCAGCGCGTCACTTG 62.081 66.667 8.66 0.00 0.00 3.16
106 107 4.609018 ACCTGCAGCGCGTCACTT 62.609 61.111 8.66 0.00 0.00 3.16
129 130 1.524863 CTTCCCAGGTCACGACGAGT 61.525 60.000 0.00 0.00 0.00 4.18
130 131 1.213013 CTTCCCAGGTCACGACGAG 59.787 63.158 0.00 0.00 0.00 4.18
131 132 0.611062 ATCTTCCCAGGTCACGACGA 60.611 55.000 0.00 0.00 0.00 4.20
132 133 0.458543 CATCTTCCCAGGTCACGACG 60.459 60.000 0.00 0.00 0.00 5.12
133 134 0.108138 CCATCTTCCCAGGTCACGAC 60.108 60.000 0.00 0.00 0.00 4.34
134 135 0.252057 TCCATCTTCCCAGGTCACGA 60.252 55.000 0.00 0.00 0.00 4.35
135 136 0.176680 CTCCATCTTCCCAGGTCACG 59.823 60.000 0.00 0.00 0.00 4.35
136 137 1.065854 CACTCCATCTTCCCAGGTCAC 60.066 57.143 0.00 0.00 0.00 3.67
137 138 1.279496 CACTCCATCTTCCCAGGTCA 58.721 55.000 0.00 0.00 0.00 4.02
138 139 1.280457 ACACTCCATCTTCCCAGGTC 58.720 55.000 0.00 0.00 0.00 3.85
139 140 1.630878 GAACACTCCATCTTCCCAGGT 59.369 52.381 0.00 0.00 0.00 4.00
140 141 1.912043 AGAACACTCCATCTTCCCAGG 59.088 52.381 0.00 0.00 0.00 4.45
141 142 3.710209 AAGAACACTCCATCTTCCCAG 57.290 47.619 0.00 0.00 30.16 4.45
142 143 3.754965 CAAAGAACACTCCATCTTCCCA 58.245 45.455 0.00 0.00 34.90 4.37
143 144 2.489722 GCAAAGAACACTCCATCTTCCC 59.510 50.000 0.00 0.00 34.90 3.97
144 145 3.149196 TGCAAAGAACACTCCATCTTCC 58.851 45.455 0.00 0.00 34.90 3.46
145 146 4.540824 GTTGCAAAGAACACTCCATCTTC 58.459 43.478 0.00 0.00 34.90 2.87
146 147 3.003689 CGTTGCAAAGAACACTCCATCTT 59.996 43.478 6.52 0.00 37.49 2.40
147 148 2.549754 CGTTGCAAAGAACACTCCATCT 59.450 45.455 6.52 0.00 0.00 2.90
148 149 2.548057 TCGTTGCAAAGAACACTCCATC 59.452 45.455 12.88 0.00 0.00 3.51
149 150 2.549754 CTCGTTGCAAAGAACACTCCAT 59.450 45.455 15.91 0.00 0.00 3.41
150 151 1.939934 CTCGTTGCAAAGAACACTCCA 59.060 47.619 15.91 0.00 0.00 3.86
151 152 1.940613 ACTCGTTGCAAAGAACACTCC 59.059 47.619 15.91 0.00 0.00 3.85
152 153 3.802685 AGTACTCGTTGCAAAGAACACTC 59.197 43.478 15.91 5.78 0.00 3.51
153 154 3.793559 AGTACTCGTTGCAAAGAACACT 58.206 40.909 15.91 16.69 0.00 3.55
154 155 3.059800 GGAGTACTCGTTGCAAAGAACAC 60.060 47.826 15.91 14.96 0.00 3.32
155 156 3.128349 GGAGTACTCGTTGCAAAGAACA 58.872 45.455 15.91 4.24 0.00 3.18
156 157 3.391049 AGGAGTACTCGTTGCAAAGAAC 58.609 45.455 15.91 11.95 0.00 3.01
157 158 3.746045 AGGAGTACTCGTTGCAAAGAA 57.254 42.857 15.91 0.00 0.00 2.52
158 159 3.746045 AAGGAGTACTCGTTGCAAAGA 57.254 42.857 25.72 14.45 36.47 2.52
159 160 5.917541 TTAAAGGAGTACTCGTTGCAAAG 57.082 39.130 26.70 2.46 37.69 2.77
160 161 6.870971 AATTAAAGGAGTACTCGTTGCAAA 57.129 33.333 26.70 20.94 37.69 3.68
161 162 7.117236 CACTAATTAAAGGAGTACTCGTTGCAA 59.883 37.037 26.70 22.64 37.69 4.08
162 163 6.588756 CACTAATTAAAGGAGTACTCGTTGCA 59.411 38.462 26.70 18.06 37.69 4.08
163 164 6.455246 GCACTAATTAAAGGAGTACTCGTTGC 60.455 42.308 26.70 20.35 37.69 4.17
164 165 6.812160 AGCACTAATTAAAGGAGTACTCGTTG 59.188 38.462 26.70 17.00 37.69 4.10
165 166 6.932947 AGCACTAATTAAAGGAGTACTCGTT 58.067 36.000 22.01 22.01 39.10 3.85
166 167 6.527057 AGCACTAATTAAAGGAGTACTCGT 57.473 37.500 16.56 14.43 0.00 4.18
167 168 7.253684 CGAAAGCACTAATTAAAGGAGTACTCG 60.254 40.741 16.56 2.22 0.00 4.18
168 169 7.896894 CGAAAGCACTAATTAAAGGAGTACTC 58.103 38.462 14.87 14.87 0.00 2.59
169 170 7.829378 CGAAAGCACTAATTAAAGGAGTACT 57.171 36.000 0.00 0.00 0.00 2.73
189 190 3.799366 TGTCAGGTGACTTTTAGCGAAA 58.201 40.909 11.31 0.00 44.99 3.46
190 191 3.462483 TGTCAGGTGACTTTTAGCGAA 57.538 42.857 11.31 0.00 44.99 4.70
191 192 3.585862 GATGTCAGGTGACTTTTAGCGA 58.414 45.455 11.31 0.00 44.99 4.93
192 193 2.673368 GGATGTCAGGTGACTTTTAGCG 59.327 50.000 11.31 0.00 44.99 4.26
193 194 3.437049 GTGGATGTCAGGTGACTTTTAGC 59.563 47.826 11.31 0.00 44.99 3.09
194 195 4.899502 AGTGGATGTCAGGTGACTTTTAG 58.100 43.478 11.31 0.00 44.99 1.85
195 196 4.262894 GGAGTGGATGTCAGGTGACTTTTA 60.263 45.833 11.31 0.00 44.99 1.52
196 197 3.496870 GGAGTGGATGTCAGGTGACTTTT 60.497 47.826 11.31 0.00 44.99 2.27
197 198 2.039084 GGAGTGGATGTCAGGTGACTTT 59.961 50.000 11.31 0.00 44.99 2.66
198 199 1.625818 GGAGTGGATGTCAGGTGACTT 59.374 52.381 11.31 5.02 44.99 3.01
199 200 1.270907 GGAGTGGATGTCAGGTGACT 58.729 55.000 11.31 0.00 44.99 3.41
200 201 0.976641 TGGAGTGGATGTCAGGTGAC 59.023 55.000 2.99 2.99 44.97 3.67
201 202 1.556451 CATGGAGTGGATGTCAGGTGA 59.444 52.381 0.00 0.00 0.00 4.02
202 203 1.280133 ACATGGAGTGGATGTCAGGTG 59.720 52.381 0.00 0.00 27.16 4.00
203 204 1.661463 ACATGGAGTGGATGTCAGGT 58.339 50.000 0.00 0.00 27.16 4.00
204 205 2.103771 CCTACATGGAGTGGATGTCAGG 59.896 54.545 3.73 0.00 38.35 3.86
205 206 3.033909 TCCTACATGGAGTGGATGTCAG 58.966 50.000 3.73 0.00 40.56 3.51
206 207 3.114643 TCCTACATGGAGTGGATGTCA 57.885 47.619 3.73 0.00 40.56 3.58
216 217 3.181465 GGCGAAAAGATCTCCTACATGGA 60.181 47.826 0.00 0.00 43.86 3.41
217 218 3.134458 GGCGAAAAGATCTCCTACATGG 58.866 50.000 0.00 0.00 29.78 3.66
218 219 3.557595 GTGGCGAAAAGATCTCCTACATG 59.442 47.826 0.00 0.00 33.82 3.21
219 220 3.197766 TGTGGCGAAAAGATCTCCTACAT 59.802 43.478 0.00 0.00 33.82 2.29
220 221 2.565391 TGTGGCGAAAAGATCTCCTACA 59.435 45.455 0.00 0.00 33.82 2.74
221 222 2.930682 GTGTGGCGAAAAGATCTCCTAC 59.069 50.000 0.00 0.00 33.82 3.18
222 223 2.565391 TGTGTGGCGAAAAGATCTCCTA 59.435 45.455 0.00 0.00 33.82 2.94
223 224 1.347707 TGTGTGGCGAAAAGATCTCCT 59.652 47.619 0.00 0.00 33.82 3.69
224 225 1.464997 GTGTGTGGCGAAAAGATCTCC 59.535 52.381 0.00 0.00 33.25 3.71
225 226 1.464997 GGTGTGTGGCGAAAAGATCTC 59.535 52.381 0.00 0.00 0.00 2.75
226 227 1.523758 GGTGTGTGGCGAAAAGATCT 58.476 50.000 0.00 0.00 0.00 2.75
227 228 0.521735 GGGTGTGTGGCGAAAAGATC 59.478 55.000 0.00 0.00 0.00 2.75
228 229 0.110486 AGGGTGTGTGGCGAAAAGAT 59.890 50.000 0.00 0.00 0.00 2.40
229 230 0.106918 AAGGGTGTGTGGCGAAAAGA 60.107 50.000 0.00 0.00 0.00 2.52
230 231 1.600023 TAAGGGTGTGTGGCGAAAAG 58.400 50.000 0.00 0.00 0.00 2.27
231 232 2.054232 TTAAGGGTGTGTGGCGAAAA 57.946 45.000 0.00 0.00 0.00 2.29
232 233 2.279935 ATTAAGGGTGTGTGGCGAAA 57.720 45.000 0.00 0.00 0.00 3.46
233 234 2.279935 AATTAAGGGTGTGTGGCGAA 57.720 45.000 0.00 0.00 0.00 4.70
234 235 3.075884 GTTAATTAAGGGTGTGTGGCGA 58.924 45.455 0.00 0.00 0.00 5.54
235 236 3.078837 AGTTAATTAAGGGTGTGTGGCG 58.921 45.455 0.00 0.00 0.00 5.69
236 237 3.824443 ACAGTTAATTAAGGGTGTGTGGC 59.176 43.478 0.00 0.00 0.00 5.01
237 238 7.364970 GTTAACAGTTAATTAAGGGTGTGTGG 58.635 38.462 9.01 0.00 0.00 4.17
238 239 7.073265 CGTTAACAGTTAATTAAGGGTGTGTG 58.927 38.462 9.01 0.00 0.00 3.82
239 240 6.205270 CCGTTAACAGTTAATTAAGGGTGTGT 59.795 38.462 9.01 0.00 40.37 3.72
240 241 6.604930 CCGTTAACAGTTAATTAAGGGTGTG 58.395 40.000 9.01 0.00 40.37 3.82
241 242 6.806388 CCGTTAACAGTTAATTAAGGGTGT 57.194 37.500 9.01 0.46 40.37 4.16
244 245 7.085746 CCAAACCGTTAACAGTTAATTAAGGG 58.914 38.462 9.01 13.48 46.17 3.95
245 246 6.583427 GCCAAACCGTTAACAGTTAATTAAGG 59.417 38.462 9.01 11.90 0.00 2.69
246 247 7.140048 TGCCAAACCGTTAACAGTTAATTAAG 58.860 34.615 9.01 1.98 0.00 1.85
247 248 7.035840 TGCCAAACCGTTAACAGTTAATTAA 57.964 32.000 9.01 0.00 0.00 1.40
248 249 6.294065 CCTGCCAAACCGTTAACAGTTAATTA 60.294 38.462 9.01 0.00 0.00 1.40
260 261 2.131067 CCCAACCTGCCAAACCGTT 61.131 57.895 0.00 0.00 0.00 4.44
267 268 2.132996 CAAAGTGCCCAACCTGCCA 61.133 57.895 0.00 0.00 0.00 4.92
274 275 0.462225 TCGACGTTCAAAGTGCCCAA 60.462 50.000 0.00 0.00 0.00 4.12
312 317 2.263945 GCTTCTTCTTCTACGCTGGAC 58.736 52.381 0.00 0.00 0.00 4.02
360 369 3.118454 CATGACGTGCGGGGTGAC 61.118 66.667 0.00 0.00 0.00 3.67
463 472 4.696479 ATGTTCTGGAGTGTCTTTCTGT 57.304 40.909 0.00 0.00 0.00 3.41
472 481 2.154462 GGTGTGGAATGTTCTGGAGTG 58.846 52.381 0.00 0.00 0.00 3.51
489 498 3.083349 TGGATCGAGCTGGGGGTG 61.083 66.667 0.00 0.00 0.00 4.61
559 743 5.163693 GGTTCGTTGGTTAATCGGAATGAAT 60.164 40.000 0.00 0.00 0.00 2.57
942 1143 4.651008 GTCCGTCGGTGTGGCGAA 62.651 66.667 11.88 0.00 0.00 4.70
952 1153 0.450583 TCTTCTTGATCGGTCCGTCG 59.549 55.000 11.88 0.00 0.00 5.12
959 1160 3.373439 CCTTTTCTGCTCTTCTTGATCGG 59.627 47.826 0.00 0.00 0.00 4.18
980 1181 2.695359 TCGCTGGATCTTTGTTGTACC 58.305 47.619 0.00 0.00 0.00 3.34
1421 1668 4.338539 ACTGGTCACCGTCGTCGC 62.339 66.667 0.00 0.00 35.54 5.19
1543 1790 8.821894 CAAGAAATTGTAACTACTAGCAGATCC 58.178 37.037 0.00 0.00 0.00 3.36
1578 1832 9.831737 CCTAATCAAAGACATTTACAAGTGAAG 57.168 33.333 0.00 0.00 0.00 3.02
1650 1904 5.193936 CGTACTCTATCGAACCGTAAACTC 58.806 45.833 0.00 0.00 0.00 3.01
1652 1906 4.898370 ACGTACTCTATCGAACCGTAAAC 58.102 43.478 0.00 0.00 0.00 2.01
1681 1937 1.403679 CCAAGAACAGAAACGCCAACA 59.596 47.619 0.00 0.00 0.00 3.33
1703 1959 1.909302 TGGACCAACCCAAAGCAAAAA 59.091 42.857 0.00 0.00 38.00 1.94
1715 1971 5.524646 TCGATCGGTTAAAATATGGACCAAC 59.475 40.000 16.41 0.00 32.41 3.77
1725 1982 4.730949 TCTCCAGTCGATCGGTTAAAAT 57.269 40.909 16.41 0.00 0.00 1.82
1803 2107 1.056660 GTTCTGAAGTGGACTGGGGA 58.943 55.000 0.00 0.00 0.00 4.81
1828 2182 6.089016 CAGATTGCACTGCAGAATTTTACAAG 59.911 38.462 23.35 0.00 40.61 3.16
1844 2198 8.345565 TCTTTCTTTTCTAGAAACAGATTGCAC 58.654 33.333 17.51 0.00 45.60 4.57
1881 2235 0.378257 GCATCAATTGACGCCACGAT 59.622 50.000 15.43 0.00 0.00 3.73
1886 2240 1.339711 GTGTTGCATCAATTGACGCC 58.660 50.000 22.53 9.61 31.37 5.68
1912 2267 8.721478 TGCAACTATTCAGTGTTTATCTTCTTC 58.279 33.333 0.00 0.00 34.36 2.87
1927 2282 5.423886 TGTATCAACCGATGCAACTATTCA 58.576 37.500 0.00 0.00 40.75 2.57
1928 2283 5.984233 TGTATCAACCGATGCAACTATTC 57.016 39.130 0.00 0.00 40.75 1.75
1942 2297 4.911053 TGTTTTGGTCGTGTTGTATCAAC 58.089 39.130 5.78 5.78 0.00 3.18
1968 2357 6.098017 GGACAATAGTTATCCGGTATACTGC 58.902 44.000 6.15 0.00 0.00 4.40
2015 2406 9.352784 CAAGTGAGACAATAGTTTTCACAAAAA 57.647 29.630 13.09 0.00 41.35 1.94
2016 2407 7.973388 CCAAGTGAGACAATAGTTTTCACAAAA 59.027 33.333 13.09 0.00 41.35 2.44
2017 2408 7.416213 CCCAAGTGAGACAATAGTTTTCACAAA 60.416 37.037 13.09 0.00 41.35 2.83
2018 2409 6.039270 CCCAAGTGAGACAATAGTTTTCACAA 59.961 38.462 13.09 0.00 41.35 3.33
2019 2410 5.530915 CCCAAGTGAGACAATAGTTTTCACA 59.469 40.000 13.09 0.00 41.35 3.58
2020 2411 5.531287 ACCCAAGTGAGACAATAGTTTTCAC 59.469 40.000 0.00 0.00 40.24 3.18
2036 2455 3.253432 GCTCCTAAAACTCAACCCAAGTG 59.747 47.826 0.00 0.00 0.00 3.16
2064 2483 4.000325 CACGGATGATGGCGGATATAAAA 59.000 43.478 0.00 0.00 0.00 1.52
2101 2522 5.050159 GCAAGTCAATTTTCCAAACCATGTC 60.050 40.000 0.00 0.00 0.00 3.06
2112 3313 4.679654 CGGTTAGGTTGCAAGTCAATTTTC 59.320 41.667 0.00 0.00 36.99 2.29
2135 3336 2.669569 TGAACCGCCAGCTGCTTC 60.670 61.111 8.66 6.47 38.05 3.86
2146 3347 2.226437 CCAGTTGTGAAATCCTGAACCG 59.774 50.000 0.00 0.00 0.00 4.44
2303 4045 4.281688 CCCAAAATTGAAGACCTGACACAT 59.718 41.667 0.00 0.00 0.00 3.21
2307 4049 4.937201 AACCCAAAATTGAAGACCTGAC 57.063 40.909 0.00 0.00 0.00 3.51
2318 4060 3.044894 TCCAGCCAAGAAACCCAAAATT 58.955 40.909 0.00 0.00 0.00 1.82
2323 4065 0.776810 TGATCCAGCCAAGAAACCCA 59.223 50.000 0.00 0.00 0.00 4.51
2345 4087 5.276461 AGTTCCAAAAACCAGACCAAATC 57.724 39.130 0.00 0.00 0.00 2.17
2362 4104 4.569966 CAGACATCTGTTCAGCATAGTTCC 59.430 45.833 0.40 0.00 39.09 3.62
2373 4115 5.292765 TCTGTGAACTTCAGACATCTGTTC 58.707 41.667 8.70 6.34 44.12 3.18
2384 4126 6.812879 TCTACTCGTATTCTGTGAACTTCA 57.187 37.500 0.00 0.00 0.00 3.02
2385 4127 7.253817 GCAATCTACTCGTATTCTGTGAACTTC 60.254 40.741 0.00 0.00 0.00 3.01
2395 4137 4.025647 GCACTTGGCAATCTACTCGTATTC 60.026 45.833 0.00 0.00 43.97 1.75
2396 4138 3.871594 GCACTTGGCAATCTACTCGTATT 59.128 43.478 0.00 0.00 43.97 1.89
2418 4160 2.743636 TTCTGCTTCTTGGTAGTCGG 57.256 50.000 0.00 0.00 0.00 4.79
2458 4200 4.563061 AGTTATAGCGGTTCGTTCAAAGT 58.437 39.130 0.00 0.00 0.00 2.66
2459 4201 6.696148 AGATAGTTATAGCGGTTCGTTCAAAG 59.304 38.462 0.00 0.00 0.00 2.77
2465 4207 4.457257 GGGTAGATAGTTATAGCGGTTCGT 59.543 45.833 0.00 0.00 0.00 3.85
2466 4208 4.142513 GGGGTAGATAGTTATAGCGGTTCG 60.143 50.000 0.00 0.00 0.00 3.95
2467 4209 4.142513 CGGGGTAGATAGTTATAGCGGTTC 60.143 50.000 0.00 0.00 0.00 3.62
2471 4213 4.142513 GGAACGGGGTAGATAGTTATAGCG 60.143 50.000 0.00 0.00 0.00 4.26
2473 4215 6.906157 TTGGAACGGGGTAGATAGTTATAG 57.094 41.667 0.00 0.00 0.00 1.31
2474 4216 7.673641 TTTTGGAACGGGGTAGATAGTTATA 57.326 36.000 0.00 0.00 0.00 0.98
2476 4218 6.564557 ATTTTGGAACGGGGTAGATAGTTA 57.435 37.500 0.00 0.00 0.00 2.24
2477 4219 4.914177 TTTTGGAACGGGGTAGATAGTT 57.086 40.909 0.00 0.00 0.00 2.24
2478 4220 5.664457 ACTATTTTGGAACGGGGTAGATAGT 59.336 40.000 0.00 0.00 0.00 2.12
2479 4221 6.170846 ACTATTTTGGAACGGGGTAGATAG 57.829 41.667 0.00 0.00 0.00 2.08
2481 4223 5.045432 TCAACTATTTTGGAACGGGGTAGAT 60.045 40.000 0.00 0.00 0.00 1.98
2482 4224 4.286549 TCAACTATTTTGGAACGGGGTAGA 59.713 41.667 0.00 0.00 0.00 2.59
2484 4226 4.637387 TCAACTATTTTGGAACGGGGTA 57.363 40.909 0.00 0.00 0.00 3.69
2485 4227 3.512219 TCAACTATTTTGGAACGGGGT 57.488 42.857 0.00 0.00 0.00 4.95
2486 4228 3.824443 ACTTCAACTATTTTGGAACGGGG 59.176 43.478 0.00 0.00 0.00 5.73
2487 4229 5.704053 AGTACTTCAACTATTTTGGAACGGG 59.296 40.000 0.00 0.00 0.00 5.28
2488 4230 6.796705 AGTACTTCAACTATTTTGGAACGG 57.203 37.500 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.