Multiple sequence alignment - TraesCS3D01G101400

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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 TraesCS3D01G101400 chr3D 100.000 2546 0 0 1 2546 54459129 54456584 0.000000e+00 4702
1 TraesCS3D01G101400 chr3D 95.103 919 31 6 633 1547 54393742 54394650 0.000000e+00 1435
2 TraesCS3D01G101400 chr3D 93.112 421 28 1 1 421 480960387 480959968 1.290000e-172 616
3 TraesCS3D01G101400 chr3A 91.860 2150 117 18 428 2546 65402807 65400685 0.000000e+00 2948
4 TraesCS3D01G101400 chr3A 96.991 565 17 0 983 1547 65360851 65361415 0.000000e+00 950
5 TraesCS3D01G101400 chr3A 92.056 428 34 0 1 428 77489530 77489103 1.010000e-168 603
6 TraesCS3D01G101400 chr3A 92.784 194 7 2 739 932 65360666 65360852 8.970000e-70 274
7 TraesCS3D01G101400 chr3A 97.059 102 2 1 654 755 65360545 65360645 1.210000e-38 171
8 TraesCS3D01G101400 chr3B 91.540 1312 71 19 423 1715 84876629 84875339 0.000000e+00 1772
9 TraesCS3D01G101400 chr3B 93.437 899 44 6 654 1547 84763207 84764095 0.000000e+00 1319
10 TraesCS3D01G101400 chr3B 86.866 434 31 12 2114 2546 84874879 84874471 1.780000e-126 462
11 TraesCS3D01G101400 chr3B 87.404 389 39 5 1718 2102 84875305 84874923 3.010000e-119 438
12 TraesCS3D01G101400 chr4D 93.072 433 28 2 1 432 490098892 490098461 1.290000e-177 632
13 TraesCS3D01G101400 chr4D 92.453 424 31 1 1 424 380343634 380344056 2.800000e-169 604
14 TraesCS3D01G101400 chr7D 93.412 425 26 1 1 423 264984023 264984447 1.660000e-176 628
15 TraesCS3D01G101400 chr1D 93.039 431 26 4 1 427 302826453 302826023 5.980000e-176 627
16 TraesCS3D01G101400 chr1D 93.128 422 28 1 1 422 448104477 448104057 3.600000e-173 617
17 TraesCS3D01G101400 chr1D 92.453 424 31 1 1 424 18574472 18574894 2.800000e-169 604
18 TraesCS3D01G101400 chr7A 92.471 425 29 3 1 423 24469998 24469575 2.800000e-169 604


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 TraesCS3D01G101400 chr3D 54456584 54459129 2545 True 4702.000000 4702 100.000000 1 2546 1 chr3D.!!$R1 2545
1 TraesCS3D01G101400 chr3D 54393742 54394650 908 False 1435.000000 1435 95.103000 633 1547 1 chr3D.!!$F1 914
2 TraesCS3D01G101400 chr3A 65400685 65402807 2122 True 2948.000000 2948 91.860000 428 2546 1 chr3A.!!$R1 2118
3 TraesCS3D01G101400 chr3A 65360545 65361415 870 False 465.000000 950 95.611333 654 1547 3 chr3A.!!$F1 893
4 TraesCS3D01G101400 chr3B 84763207 84764095 888 False 1319.000000 1319 93.437000 654 1547 1 chr3B.!!$F1 893
5 TraesCS3D01G101400 chr3B 84874471 84876629 2158 True 890.666667 1772 88.603333 423 2546 3 chr3B.!!$R1 2123

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
193 194 0.030908 GGGAGGCGAGTTATGAGACG 59.969 60.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2183 1.024579 CCAACCAGGTATGCCACGTC 61.025 60.0 1.54 0.0 37.19 4.34 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
37 38 4.172512 AGCGCTCCTGGATGCTGG 62.173 66.667 19.24 3.55 36.09 4.85
40 41 4.166888 GCTCCTGGATGCTGGCGA 62.167 66.667 5.18 0.00 0.00 5.54
41 42 2.827423 CTCCTGGATGCTGGCGAT 59.173 61.111 5.18 0.00 0.00 4.58
42 43 1.597302 CTCCTGGATGCTGGCGATG 60.597 63.158 5.18 0.00 0.00 3.84
43 44 3.285215 CCTGGATGCTGGCGATGC 61.285 66.667 0.00 0.00 0.00 3.91
44 45 3.646976 CTGGATGCTGGCGATGCG 61.647 66.667 0.00 0.00 0.00 4.73
62 63 3.760035 CTGGTCGACGGGGGTCAG 61.760 72.222 9.92 6.17 0.00 3.51
63 64 4.289101 TGGTCGACGGGGGTCAGA 62.289 66.667 9.92 0.00 0.00 3.27
64 65 3.450115 GGTCGACGGGGGTCAGAG 61.450 72.222 9.92 0.00 0.00 3.35
65 66 3.450115 GTCGACGGGGGTCAGAGG 61.450 72.222 0.00 0.00 0.00 3.69
66 67 4.753662 TCGACGGGGGTCAGAGGG 62.754 72.222 0.00 0.00 0.00 4.30
104 105 2.519541 CGGAGCCATCGGAGGAGA 60.520 66.667 0.00 0.00 0.00 3.71
105 106 2.560119 CGGAGCCATCGGAGGAGAG 61.560 68.421 0.00 0.00 0.00 3.20
106 107 2.206536 GGAGCCATCGGAGGAGAGG 61.207 68.421 0.00 0.00 0.00 3.69
107 108 1.152652 GAGCCATCGGAGGAGAGGA 60.153 63.158 0.00 0.00 0.00 3.71
108 109 1.152567 AGCCATCGGAGGAGAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
109 110 1.152652 GCCATCGGAGGAGAGGAGA 60.153 63.158 0.00 0.00 0.00 3.71
110 111 1.178534 GCCATCGGAGGAGAGGAGAG 61.179 65.000 0.00 0.00 0.00 3.20
111 112 0.539438 CCATCGGAGGAGAGGAGAGG 60.539 65.000 0.00 0.00 0.00 3.69
112 113 0.539438 CATCGGAGGAGAGGAGAGGG 60.539 65.000 0.00 0.00 0.00 4.30
113 114 0.699577 ATCGGAGGAGAGGAGAGGGA 60.700 60.000 0.00 0.00 0.00 4.20
114 115 1.150536 CGGAGGAGAGGAGAGGGAG 59.849 68.421 0.00 0.00 0.00 4.30
115 116 1.541672 GGAGGAGAGGAGAGGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
116 117 1.541672 GAGGAGAGGAGAGGGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
117 118 2.018086 AGGAGAGGAGAGGGAGGGG 61.018 68.421 0.00 0.00 0.00 4.79
118 119 2.123033 GAGAGGAGAGGGAGGGGC 60.123 72.222 0.00 0.00 0.00 5.80
119 120 4.150454 AGAGGAGAGGGAGGGGCG 62.150 72.222 0.00 0.00 0.00 6.13
123 124 4.779733 GAGAGGGAGGGGCGGTGA 62.780 72.222 0.00 0.00 0.00 4.02
124 125 4.787280 AGAGGGAGGGGCGGTGAG 62.787 72.222 0.00 0.00 0.00 3.51
129 130 4.779733 GAGGGGCGGTGAGGGAGA 62.780 72.222 0.00 0.00 0.00 3.71
130 131 4.787280 AGGGGCGGTGAGGGAGAG 62.787 72.222 0.00 0.00 0.00 3.20
131 132 4.779733 GGGGCGGTGAGGGAGAGA 62.780 72.222 0.00 0.00 0.00 3.10
132 133 3.151022 GGGCGGTGAGGGAGAGAG 61.151 72.222 0.00 0.00 0.00 3.20
133 134 3.151022 GGCGGTGAGGGAGAGAGG 61.151 72.222 0.00 0.00 0.00 3.69
134 135 2.043852 GCGGTGAGGGAGAGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
135 136 1.682684 GCGGTGAGGGAGAGAGGAA 60.683 63.158 0.00 0.00 0.00 3.36
136 137 1.671901 GCGGTGAGGGAGAGAGGAAG 61.672 65.000 0.00 0.00 0.00 3.46
137 138 1.671901 CGGTGAGGGAGAGAGGAAGC 61.672 65.000 0.00 0.00 0.00 3.86
138 139 1.671901 GGTGAGGGAGAGAGGAAGCG 61.672 65.000 0.00 0.00 0.00 4.68
139 140 1.380515 TGAGGGAGAGAGGAAGCGG 60.381 63.158 0.00 0.00 0.00 5.52
140 141 1.380650 GAGGGAGAGAGGAAGCGGT 60.381 63.158 0.00 0.00 0.00 5.68
141 142 1.671901 GAGGGAGAGAGGAAGCGGTG 61.672 65.000 0.00 0.00 0.00 4.94
142 143 2.726351 GGGAGAGAGGAAGCGGTGG 61.726 68.421 0.00 0.00 0.00 4.61
143 144 2.726351 GGAGAGAGGAAGCGGTGGG 61.726 68.421 0.00 0.00 0.00 4.61
144 145 1.682684 GAGAGAGGAAGCGGTGGGA 60.683 63.158 0.00 0.00 0.00 4.37
145 146 1.229209 AGAGAGGAAGCGGTGGGAA 60.229 57.895 0.00 0.00 0.00 3.97
146 147 1.079057 GAGAGGAAGCGGTGGGAAC 60.079 63.158 0.00 0.00 0.00 3.62
147 148 1.827399 GAGAGGAAGCGGTGGGAACA 61.827 60.000 0.00 0.00 38.70 3.18
148 149 1.376037 GAGGAAGCGGTGGGAACAG 60.376 63.158 0.00 0.00 44.46 3.16
149 150 2.113243 GAGGAAGCGGTGGGAACAGT 62.113 60.000 0.00 0.00 44.46 3.55
150 151 1.966451 GGAAGCGGTGGGAACAGTG 60.966 63.158 0.00 0.00 44.46 3.66
151 152 2.594592 AAGCGGTGGGAACAGTGC 60.595 61.111 0.00 0.00 44.46 4.40
152 153 4.988598 AGCGGTGGGAACAGTGCG 62.989 66.667 0.00 0.00 44.19 5.34
153 154 4.980805 GCGGTGGGAACAGTGCGA 62.981 66.667 0.00 0.00 44.46 5.10
154 155 3.041940 CGGTGGGAACAGTGCGAC 61.042 66.667 0.00 0.00 44.46 5.19
155 156 2.426023 GGTGGGAACAGTGCGACT 59.574 61.111 0.00 0.00 44.46 4.18
168 169 4.742201 CGACTGGGCGGTGACAGG 62.742 72.222 0.00 0.00 39.00 4.00
169 170 3.311110 GACTGGGCGGTGACAGGA 61.311 66.667 0.00 0.00 39.00 3.86
170 171 3.302347 GACTGGGCGGTGACAGGAG 62.302 68.421 0.00 0.00 39.00 3.69
171 172 2.997315 CTGGGCGGTGACAGGAGA 60.997 66.667 0.00 0.00 0.00 3.71
172 173 2.997315 TGGGCGGTGACAGGAGAG 60.997 66.667 0.00 0.00 0.00 3.20
173 174 2.997897 GGGCGGTGACAGGAGAGT 60.998 66.667 0.00 0.00 0.00 3.24
174 175 2.262915 GGCGGTGACAGGAGAGTG 59.737 66.667 0.00 0.00 0.00 3.51
175 176 2.262915 GCGGTGACAGGAGAGTGG 59.737 66.667 0.00 0.00 0.00 4.00
176 177 2.973899 CGGTGACAGGAGAGTGGG 59.026 66.667 0.00 0.00 0.00 4.61
177 178 1.606601 CGGTGACAGGAGAGTGGGA 60.607 63.158 0.00 0.00 0.00 4.37
178 179 1.599606 CGGTGACAGGAGAGTGGGAG 61.600 65.000 0.00 0.00 0.00 4.30
179 180 1.261238 GGTGACAGGAGAGTGGGAGG 61.261 65.000 0.00 0.00 0.00 4.30
180 181 1.610673 TGACAGGAGAGTGGGAGGC 60.611 63.158 0.00 0.00 0.00 4.70
181 182 2.681778 ACAGGAGAGTGGGAGGCG 60.682 66.667 0.00 0.00 0.00 5.52
182 183 2.363018 CAGGAGAGTGGGAGGCGA 60.363 66.667 0.00 0.00 0.00 5.54
183 184 2.043450 AGGAGAGTGGGAGGCGAG 60.043 66.667 0.00 0.00 0.00 5.03
184 185 2.363147 GGAGAGTGGGAGGCGAGT 60.363 66.667 0.00 0.00 0.00 4.18
185 186 1.985116 GGAGAGTGGGAGGCGAGTT 60.985 63.158 0.00 0.00 0.00 3.01
186 187 0.683504 GGAGAGTGGGAGGCGAGTTA 60.684 60.000 0.00 0.00 0.00 2.24
187 188 1.404843 GAGAGTGGGAGGCGAGTTAT 58.595 55.000 0.00 0.00 0.00 1.89
188 189 1.067821 GAGAGTGGGAGGCGAGTTATG 59.932 57.143 0.00 0.00 0.00 1.90
189 190 1.112113 GAGTGGGAGGCGAGTTATGA 58.888 55.000 0.00 0.00 0.00 2.15
190 191 1.067821 GAGTGGGAGGCGAGTTATGAG 59.932 57.143 0.00 0.00 0.00 2.90
191 192 1.112113 GTGGGAGGCGAGTTATGAGA 58.888 55.000 0.00 0.00 0.00 3.27
192 193 1.112113 TGGGAGGCGAGTTATGAGAC 58.888 55.000 0.00 0.00 0.00 3.36
193 194 0.030908 GGGAGGCGAGTTATGAGACG 59.969 60.000 0.00 0.00 0.00 4.18
194 195 0.739561 GGAGGCGAGTTATGAGACGT 59.260 55.000 0.00 0.00 0.00 4.34
195 196 1.268640 GGAGGCGAGTTATGAGACGTC 60.269 57.143 7.70 7.70 0.00 4.34
196 197 0.377554 AGGCGAGTTATGAGACGTCG 59.622 55.000 10.46 0.00 35.52 5.12
198 199 3.899836 CGAGTTATGAGACGTCGCT 57.100 52.632 20.11 8.43 0.00 4.93
199 200 2.175530 CGAGTTATGAGACGTCGCTT 57.824 50.000 20.11 15.92 0.00 4.68
200 201 2.102633 CGAGTTATGAGACGTCGCTTC 58.897 52.381 20.11 8.52 0.00 3.86
201 202 2.452105 GAGTTATGAGACGTCGCTTCC 58.548 52.381 20.11 8.40 0.00 3.46
202 203 1.189403 GTTATGAGACGTCGCTTCCG 58.811 55.000 20.11 0.00 0.00 4.30
203 204 0.806868 TTATGAGACGTCGCTTCCGT 59.193 50.000 20.11 7.65 42.06 4.69
208 209 3.745803 ACGTCGCTTCCGTCTCCC 61.746 66.667 0.00 0.00 31.97 4.30
209 210 4.831307 CGTCGCTTCCGTCTCCCG 62.831 72.222 0.00 0.00 35.54 5.14
232 233 3.818787 CCCGAGGCATGCAACTGC 61.819 66.667 21.36 3.60 41.53 4.40
238 239 3.740397 GCATGCAACTGCCTCGCA 61.740 61.111 14.21 0.00 41.18 5.10
239 240 2.177531 CATGCAACTGCCTCGCAC 59.822 61.111 0.00 0.00 38.73 5.34
240 241 3.425713 ATGCAACTGCCTCGCACG 61.426 61.111 0.00 0.00 38.73 5.34
271 272 4.760047 GGCCAGGCTCGCGAGAAA 62.760 66.667 38.74 1.86 41.32 2.52
272 273 3.491652 GCCAGGCTCGCGAGAAAC 61.492 66.667 38.74 25.78 41.32 2.78
273 274 2.262915 CCAGGCTCGCGAGAAACT 59.737 61.111 38.74 27.47 41.32 2.66
274 275 2.097038 CCAGGCTCGCGAGAAACTG 61.097 63.158 38.74 34.30 41.13 3.16
275 276 1.080501 CAGGCTCGCGAGAAACTGA 60.081 57.895 38.74 0.00 42.91 3.41
276 277 1.080434 AGGCTCGCGAGAAACTGAC 60.080 57.895 38.74 18.82 41.32 3.51
277 278 2.437343 GGCTCGCGAGAAACTGACG 61.437 63.158 38.74 11.21 41.32 4.35
278 279 1.442184 GCTCGCGAGAAACTGACGA 60.442 57.895 38.74 0.00 41.32 4.20
279 280 0.798771 GCTCGCGAGAAACTGACGAT 60.799 55.000 38.74 0.00 41.32 3.73
280 281 1.618861 CTCGCGAGAAACTGACGATT 58.381 50.000 32.06 0.00 41.32 3.34
281 282 1.579808 CTCGCGAGAAACTGACGATTC 59.420 52.381 32.06 0.00 41.32 2.52
282 283 0.291989 CGCGAGAAACTGACGATTCG 59.708 55.000 0.00 4.14 0.00 3.34
283 284 0.640768 GCGAGAAACTGACGATTCGG 59.359 55.000 11.29 0.00 0.00 4.30
284 285 0.640768 CGAGAAACTGACGATTCGGC 59.359 55.000 11.29 8.19 34.27 5.54
285 286 1.710013 GAGAAACTGACGATTCGGCA 58.290 50.000 14.95 14.95 45.13 5.69
292 293 0.787787 TGACGATTCGGCAGTTTTCG 59.212 50.000 11.32 0.00 41.22 3.46
293 294 0.518559 GACGATTCGGCAGTTTTCGC 60.519 55.000 7.13 0.00 33.63 4.70
294 295 0.949105 ACGATTCGGCAGTTTTCGCT 60.949 50.000 11.29 0.00 33.30 4.93
295 296 0.519175 CGATTCGGCAGTTTTCGCTG 60.519 55.000 0.00 0.00 39.37 5.18
296 297 0.179189 GATTCGGCAGTTTTCGCTGG 60.179 55.000 0.00 0.00 37.00 4.85
297 298 1.586154 ATTCGGCAGTTTTCGCTGGG 61.586 55.000 0.00 0.00 37.00 4.45
298 299 4.404654 CGGCAGTTTTCGCTGGGC 62.405 66.667 0.00 0.00 37.00 5.36
299 300 4.056125 GGCAGTTTTCGCTGGGCC 62.056 66.667 0.00 0.00 37.00 5.80
300 301 3.294493 GCAGTTTTCGCTGGGCCA 61.294 61.111 5.85 5.85 37.00 5.36
301 302 2.956987 CAGTTTTCGCTGGGCCAG 59.043 61.111 29.44 29.44 33.11 4.85
302 303 2.282462 AGTTTTCGCTGGGCCAGG 60.282 61.111 33.43 22.98 31.21 4.45
303 304 4.056125 GTTTTCGCTGGGCCAGGC 62.056 66.667 33.43 23.59 31.21 4.85
304 305 4.284550 TTTTCGCTGGGCCAGGCT 62.285 61.111 33.43 0.00 31.21 4.58
316 317 3.297620 CAGGCTGCGGGTTGCTTT 61.298 61.111 0.00 0.00 46.63 3.51
317 318 1.971167 CAGGCTGCGGGTTGCTTTA 60.971 57.895 0.00 0.00 46.63 1.85
318 319 1.228429 AGGCTGCGGGTTGCTTTAA 60.228 52.632 0.00 0.00 46.63 1.52
319 320 1.212751 GGCTGCGGGTTGCTTTAAG 59.787 57.895 0.00 0.00 46.63 1.85
320 321 1.524008 GGCTGCGGGTTGCTTTAAGT 61.524 55.000 0.00 0.00 46.63 2.24
321 322 0.313987 GCTGCGGGTTGCTTTAAGTT 59.686 50.000 0.00 0.00 46.63 2.66
322 323 1.666023 GCTGCGGGTTGCTTTAAGTTC 60.666 52.381 0.00 0.00 46.63 3.01
323 324 0.955905 TGCGGGTTGCTTTAAGTTCC 59.044 50.000 0.00 0.00 46.63 3.62
324 325 0.109919 GCGGGTTGCTTTAAGTTCCG 60.110 55.000 10.87 10.87 41.73 4.30
325 326 1.232119 CGGGTTGCTTTAAGTTCCGT 58.768 50.000 0.00 0.00 0.00 4.69
326 327 1.069500 CGGGTTGCTTTAAGTTCCGTG 60.069 52.381 0.00 0.00 0.00 4.94
327 328 1.335597 GGGTTGCTTTAAGTTCCGTGC 60.336 52.381 0.00 0.00 0.00 5.34
328 329 1.662026 GGTTGCTTTAAGTTCCGTGCG 60.662 52.381 0.00 0.00 0.00 5.34
329 330 0.589223 TTGCTTTAAGTTCCGTGCGG 59.411 50.000 3.94 3.94 0.00 5.69
330 331 1.231958 TGCTTTAAGTTCCGTGCGGG 61.232 55.000 10.94 0.00 35.59 6.13
331 332 1.500396 CTTTAAGTTCCGTGCGGGC 59.500 57.895 10.94 4.59 34.94 6.13
332 333 1.918868 CTTTAAGTTCCGTGCGGGCC 61.919 60.000 10.94 0.00 34.94 5.80
333 334 2.677765 TTTAAGTTCCGTGCGGGCCA 62.678 55.000 4.39 0.00 34.94 5.36
334 335 3.887335 TAAGTTCCGTGCGGGCCAC 62.887 63.158 4.39 0.00 41.15 5.01
337 338 4.877619 TTCCGTGCGGGCCACAAA 62.878 61.111 4.39 0.00 44.91 2.83
344 345 4.418401 CGGGCCACAAACCGCATG 62.418 66.667 4.39 0.00 43.96 4.06
345 346 4.740431 GGGCCACAAACCGCATGC 62.740 66.667 7.91 7.91 0.00 4.06
346 347 3.988525 GGCCACAAACCGCATGCA 61.989 61.111 19.57 0.00 0.00 3.96
347 348 2.431260 GCCACAAACCGCATGCAG 60.431 61.111 19.57 9.32 0.00 4.41
348 349 2.431260 CCACAAACCGCATGCAGC 60.431 61.111 19.57 0.00 40.87 5.25
349 350 2.431260 CACAAACCGCATGCAGCC 60.431 61.111 19.57 0.00 41.38 4.85
350 351 3.683937 ACAAACCGCATGCAGCCC 61.684 61.111 19.57 0.00 41.38 5.19
351 352 3.682885 CAAACCGCATGCAGCCCA 61.683 61.111 19.57 0.00 41.38 5.36
352 353 3.376078 AAACCGCATGCAGCCCAG 61.376 61.111 19.57 0.00 41.38 4.45
357 358 4.446413 GCATGCAGCCCAGCCAAC 62.446 66.667 14.21 0.00 37.23 3.77
358 359 3.766691 CATGCAGCCCAGCCAACC 61.767 66.667 0.00 0.00 0.00 3.77
359 360 4.304413 ATGCAGCCCAGCCAACCA 62.304 61.111 0.00 0.00 0.00 3.67
360 361 3.831727 ATGCAGCCCAGCCAACCAA 62.832 57.895 0.00 0.00 0.00 3.67
361 362 3.233231 GCAGCCCAGCCAACCAAA 61.233 61.111 0.00 0.00 0.00 3.28
362 363 2.736531 CAGCCCAGCCAACCAAAC 59.263 61.111 0.00 0.00 0.00 2.93
363 364 2.132996 CAGCCCAGCCAACCAAACA 61.133 57.895 0.00 0.00 0.00 2.83
364 365 1.833934 AGCCCAGCCAACCAAACAG 60.834 57.895 0.00 0.00 0.00 3.16
365 366 2.133641 GCCCAGCCAACCAAACAGT 61.134 57.895 0.00 0.00 0.00 3.55
366 367 2.041153 CCCAGCCAACCAAACAGTC 58.959 57.895 0.00 0.00 0.00 3.51
367 368 1.463553 CCCAGCCAACCAAACAGTCC 61.464 60.000 0.00 0.00 0.00 3.85
368 369 1.654220 CAGCCAACCAAACAGTCCG 59.346 57.895 0.00 0.00 0.00 4.79
369 370 2.193536 AGCCAACCAAACAGTCCGC 61.194 57.895 0.00 0.00 0.00 5.54
370 371 2.637025 CCAACCAAACAGTCCGCG 59.363 61.111 0.00 0.00 0.00 6.46
371 372 2.051345 CAACCAAACAGTCCGCGC 60.051 61.111 0.00 0.00 0.00 6.86
372 373 2.515057 AACCAAACAGTCCGCGCA 60.515 55.556 8.75 0.00 0.00 6.09
373 374 2.830285 AACCAAACAGTCCGCGCAC 61.830 57.895 8.75 0.00 0.00 5.34
374 375 3.276091 CCAAACAGTCCGCGCACA 61.276 61.111 8.75 0.00 0.00 4.57
375 376 2.616330 CCAAACAGTCCGCGCACAT 61.616 57.895 8.75 0.00 0.00 3.21
376 377 1.154413 CAAACAGTCCGCGCACATC 60.154 57.895 8.75 0.00 0.00 3.06
377 378 2.325082 AAACAGTCCGCGCACATCC 61.325 57.895 8.75 0.00 0.00 3.51
378 379 4.760047 ACAGTCCGCGCACATCCC 62.760 66.667 8.75 0.00 0.00 3.85
400 401 4.284550 GGGTCTGGTTGGGCTGCA 62.285 66.667 0.50 0.00 0.00 4.41
401 402 2.036256 GGTCTGGTTGGGCTGCAT 59.964 61.111 0.50 0.00 0.00 3.96
402 403 2.345760 GGTCTGGTTGGGCTGCATG 61.346 63.158 0.50 0.00 0.00 4.06
403 404 2.677524 TCTGGTTGGGCTGCATGC 60.678 61.111 11.82 11.82 41.94 4.06
404 405 4.124351 CTGGTTGGGCTGCATGCG 62.124 66.667 14.09 9.16 44.05 4.73
431 432 2.290641 CCAAACACGCCCTATATTGCTC 59.709 50.000 0.00 0.00 0.00 4.26
447 448 2.762745 TGCTCGTTAAAACTGGTCCTC 58.237 47.619 0.00 0.00 0.00 3.71
470 471 6.753180 TCTATAGCATCAACTCAATCCTCAC 58.247 40.000 0.00 0.00 0.00 3.51
471 472 2.996631 AGCATCAACTCAATCCTCACC 58.003 47.619 0.00 0.00 0.00 4.02
472 473 2.575279 AGCATCAACTCAATCCTCACCT 59.425 45.455 0.00 0.00 0.00 4.00
473 474 2.941720 GCATCAACTCAATCCTCACCTC 59.058 50.000 0.00 0.00 0.00 3.85
474 475 3.620719 GCATCAACTCAATCCTCACCTCA 60.621 47.826 0.00 0.00 0.00 3.86
603 608 6.887626 ATGATTTTGTACCAACGTAACCTT 57.112 33.333 0.00 0.00 0.00 3.50
624 629 0.790207 CCATTGTTCTGACACCGACG 59.210 55.000 0.00 0.00 34.98 5.12
631 636 1.030488 TCTGACACCGACGATCTCCC 61.030 60.000 0.00 0.00 0.00 4.30
663 668 2.605837 TCGCCATTAACGCAATCCTA 57.394 45.000 0.00 0.00 0.00 2.94
791 833 0.250166 ACAAACTGGCTCCCACGTAC 60.250 55.000 0.00 0.00 0.00 3.67
792 834 0.034896 CAAACTGGCTCCCACGTACT 59.965 55.000 0.00 0.00 0.00 2.73
793 835 1.274167 CAAACTGGCTCCCACGTACTA 59.726 52.381 0.00 0.00 0.00 1.82
794 836 1.183549 AACTGGCTCCCACGTACTAG 58.816 55.000 0.00 0.00 0.00 2.57
795 837 0.683504 ACTGGCTCCCACGTACTAGG 60.684 60.000 0.00 0.00 0.00 3.02
797 839 0.682209 TGGCTCCCACGTACTAGGAC 60.682 60.000 0.00 0.00 0.00 3.85
798 840 0.682209 GGCTCCCACGTACTAGGACA 60.682 60.000 5.80 0.00 0.00 4.02
799 841 1.400737 GCTCCCACGTACTAGGACAT 58.599 55.000 5.80 0.00 0.00 3.06
800 842 1.755380 GCTCCCACGTACTAGGACATT 59.245 52.381 5.80 0.00 0.00 2.71
801 843 2.481449 GCTCCCACGTACTAGGACATTG 60.481 54.545 5.80 1.20 0.00 2.82
802 844 1.479323 TCCCACGTACTAGGACATTGC 59.521 52.381 5.80 0.00 0.00 3.56
803 845 1.472728 CCCACGTACTAGGACATTGCC 60.473 57.143 5.80 0.00 0.00 4.52
804 846 1.556564 CACGTACTAGGACATTGCCG 58.443 55.000 5.80 0.00 0.00 5.69
870 914 2.664835 ATACTCTCCCTGGCCCCTCG 62.665 65.000 0.00 0.00 0.00 4.63
956 1000 1.587613 GCTGCGAGATCGTCTCCAC 60.588 63.158 3.94 3.77 40.34 4.02
995 1048 2.225066 ACGGAGTACAGTCTTCCCTTCT 60.225 50.000 0.00 0.00 41.94 2.85
1338 1403 0.333993 AGGCCGACTACTACAAGGGA 59.666 55.000 0.00 0.00 0.00 4.20
1627 1692 3.324099 CTGCGCTGCTGCTTTGGAG 62.324 63.158 9.73 5.16 36.97 3.86
1656 1721 1.609208 TTGTGGAGCTTGAAGGCTTC 58.391 50.000 20.27 20.27 43.20 3.86
1666 1731 3.675228 GCTTGAAGGCTTCATTCATGTGG 60.675 47.826 28.98 12.99 39.84 4.17
1667 1732 1.820519 TGAAGGCTTCATTCATGTGGC 59.179 47.619 25.38 0.00 34.08 5.01
1792 1891 1.062587 CGGGTAGCGCATTCTCAAAAG 59.937 52.381 11.47 0.00 0.00 2.27
1798 1897 1.135575 GCGCATTCTCAAAAGGAGGTG 60.136 52.381 0.30 0.00 44.19 4.00
1861 1960 3.247648 GCAACGCTTGAGAGAAAGTTGTA 59.752 43.478 7.75 0.00 37.01 2.41
1873 1972 5.177696 AGAGAAAGTTGTATGCGTGTTTCTC 59.822 40.000 16.80 16.80 45.30 2.87
1884 1983 5.811399 TGCGTGTTTCTCCATATTAAAGG 57.189 39.130 0.00 0.00 0.00 3.11
1890 1989 9.855021 CGTGTTTCTCCATATTAAAGGAAAAAT 57.145 29.630 0.00 0.00 32.57 1.82
2072 2175 2.738587 TTCTTACCACAGCCAACCAA 57.261 45.000 0.00 0.00 0.00 3.67
2080 2183 4.041917 AGCCAACCAACATGCGCG 62.042 61.111 0.00 0.00 0.00 6.86
2115 2254 6.013206 ACCTGGTTGGCCGAATACAATATATA 60.013 38.462 0.00 0.00 40.22 0.86
2116 2255 7.054124 CCTGGTTGGCCGAATACAATATATAT 58.946 38.462 0.00 0.00 37.67 0.86
2117 2256 7.012327 CCTGGTTGGCCGAATACAATATATATG 59.988 40.741 0.00 0.00 37.67 1.78
2118 2257 7.398829 TGGTTGGCCGAATACAATATATATGT 58.601 34.615 0.00 0.26 37.67 2.29
2202 2342 5.435686 AACCTCAATAACTGCTATGACCA 57.564 39.130 0.00 0.00 0.00 4.02
2214 2354 7.544804 ACTGCTATGACCATCATATTAGACA 57.455 36.000 12.64 0.00 38.54 3.41
2308 2448 3.310501 ACACGTAACTAAAGTTGCACACC 59.689 43.478 10.83 0.00 40.03 4.16
2313 2453 2.297701 ACTAAAGTTGCACACCTGTGG 58.702 47.619 7.53 0.00 45.72 4.17
2334 2474 2.610232 GGGCCTTGCACAATTACAGTTG 60.610 50.000 0.84 0.00 35.25 3.16
2355 2495 1.270094 CCTCTGGTTTGCACTACGTGA 60.270 52.381 0.00 0.00 35.23 4.35
2395 2536 6.710597 AAAGGTTCCCTCTAAAAAGTTGTC 57.289 37.500 0.00 0.00 30.89 3.18
2429 2570 4.109766 GGGCATAAAACGAAATTAGGTGC 58.890 43.478 0.00 0.00 0.00 5.01
2463 2604 8.351495 AGCAATGTTTGTGTAGTTAAATTGTG 57.649 30.769 0.00 0.00 0.00 3.33
2538 2679 7.152645 ACACGAGAGTTTAACATGATAAGTGT 58.847 34.615 0.00 5.14 46.40 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.172512 AGCATCCAGGAGCGCTGG 62.173 66.667 18.48 12.12 43.06 4.85
19 20 2.895865 CAGCATCCAGGAGCGCTG 60.896 66.667 23.04 23.04 45.17 5.18
20 21 4.172512 CCAGCATCCAGGAGCGCT 62.173 66.667 11.27 11.27 35.48 5.92
23 24 3.472943 ATCGCCAGCATCCAGGAGC 62.473 63.158 0.00 0.00 0.00 4.70
24 25 1.597302 CATCGCCAGCATCCAGGAG 60.597 63.158 0.00 0.00 0.00 3.69
25 26 2.507452 CATCGCCAGCATCCAGGA 59.493 61.111 0.00 0.00 0.00 3.86
26 27 3.285215 GCATCGCCAGCATCCAGG 61.285 66.667 0.00 0.00 0.00 4.45
27 28 3.646976 CGCATCGCCAGCATCCAG 61.647 66.667 0.00 0.00 0.00 3.86
45 46 3.760035 CTGACCCCCGTCGACCAG 61.760 72.222 10.58 6.42 42.37 4.00
46 47 4.289101 TCTGACCCCCGTCGACCA 62.289 66.667 10.58 0.00 42.37 4.02
47 48 3.450115 CTCTGACCCCCGTCGACC 61.450 72.222 10.58 0.00 42.37 4.79
48 49 3.450115 CCTCTGACCCCCGTCGAC 61.450 72.222 5.18 5.18 42.37 4.20
49 50 4.753662 CCCTCTGACCCCCGTCGA 62.754 72.222 0.00 0.00 42.37 4.20
86 87 4.292178 CTCCTCCGATGGCTCCGC 62.292 72.222 0.00 0.00 0.00 5.54
87 88 2.519541 TCTCCTCCGATGGCTCCG 60.520 66.667 0.00 0.00 0.00 4.63
88 89 2.206536 CCTCTCCTCCGATGGCTCC 61.207 68.421 0.00 0.00 0.00 4.70
89 90 1.152652 TCCTCTCCTCCGATGGCTC 60.153 63.158 0.00 0.00 0.00 4.70
90 91 1.152567 CTCCTCTCCTCCGATGGCT 60.153 63.158 0.00 0.00 0.00 4.75
91 92 1.152652 TCTCCTCTCCTCCGATGGC 60.153 63.158 0.00 0.00 0.00 4.40
92 93 0.539438 CCTCTCCTCTCCTCCGATGG 60.539 65.000 0.00 0.00 0.00 3.51
93 94 0.539438 CCCTCTCCTCTCCTCCGATG 60.539 65.000 0.00 0.00 0.00 3.84
94 95 0.699577 TCCCTCTCCTCTCCTCCGAT 60.700 60.000 0.00 0.00 0.00 4.18
95 96 1.307953 TCCCTCTCCTCTCCTCCGA 60.308 63.158 0.00 0.00 0.00 4.55
96 97 1.150536 CTCCCTCTCCTCTCCTCCG 59.849 68.421 0.00 0.00 0.00 4.63
97 98 1.541672 CCTCCCTCTCCTCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
98 99 1.541672 CCCTCCCTCTCCTCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
99 100 2.018086 CCCCTCCCTCTCCTCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
100 101 2.612251 CCCCTCCCTCTCCTCTCC 59.388 72.222 0.00 0.00 0.00 3.71
101 102 2.123033 GCCCCTCCCTCTCCTCTC 60.123 72.222 0.00 0.00 0.00 3.20
102 103 4.150454 CGCCCCTCCCTCTCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
106 107 4.779733 TCACCGCCCCTCCCTCTC 62.780 72.222 0.00 0.00 0.00 3.20
107 108 4.787280 CTCACCGCCCCTCCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
112 113 4.779733 TCTCCCTCACCGCCCCTC 62.780 72.222 0.00 0.00 0.00 4.30
113 114 4.787280 CTCTCCCTCACCGCCCCT 62.787 72.222 0.00 0.00 0.00 4.79
114 115 4.779733 TCTCTCCCTCACCGCCCC 62.780 72.222 0.00 0.00 0.00 5.80
115 116 3.151022 CTCTCTCCCTCACCGCCC 61.151 72.222 0.00 0.00 0.00 6.13
116 117 3.151022 CCTCTCTCCCTCACCGCC 61.151 72.222 0.00 0.00 0.00 6.13
117 118 1.671901 CTTCCTCTCTCCCTCACCGC 61.672 65.000 0.00 0.00 0.00 5.68
118 119 1.671901 GCTTCCTCTCTCCCTCACCG 61.672 65.000 0.00 0.00 0.00 4.94
119 120 1.671901 CGCTTCCTCTCTCCCTCACC 61.672 65.000 0.00 0.00 0.00 4.02
120 121 1.671901 CCGCTTCCTCTCTCCCTCAC 61.672 65.000 0.00 0.00 0.00 3.51
121 122 1.380515 CCGCTTCCTCTCTCCCTCA 60.381 63.158 0.00 0.00 0.00 3.86
122 123 1.380650 ACCGCTTCCTCTCTCCCTC 60.381 63.158 0.00 0.00 0.00 4.30
123 124 1.684049 CACCGCTTCCTCTCTCCCT 60.684 63.158 0.00 0.00 0.00 4.20
124 125 2.726351 CCACCGCTTCCTCTCTCCC 61.726 68.421 0.00 0.00 0.00 4.30
125 126 2.726351 CCCACCGCTTCCTCTCTCC 61.726 68.421 0.00 0.00 0.00 3.71
126 127 1.258445 TTCCCACCGCTTCCTCTCTC 61.258 60.000 0.00 0.00 0.00 3.20
127 128 1.229209 TTCCCACCGCTTCCTCTCT 60.229 57.895 0.00 0.00 0.00 3.10
128 129 1.079057 GTTCCCACCGCTTCCTCTC 60.079 63.158 0.00 0.00 0.00 3.20
129 130 1.831652 CTGTTCCCACCGCTTCCTCT 61.832 60.000 0.00 0.00 0.00 3.69
130 131 1.376037 CTGTTCCCACCGCTTCCTC 60.376 63.158 0.00 0.00 0.00 3.71
131 132 2.147387 ACTGTTCCCACCGCTTCCT 61.147 57.895 0.00 0.00 0.00 3.36
132 133 1.966451 CACTGTTCCCACCGCTTCC 60.966 63.158 0.00 0.00 0.00 3.46
133 134 2.617274 GCACTGTTCCCACCGCTTC 61.617 63.158 0.00 0.00 0.00 3.86
134 135 2.594592 GCACTGTTCCCACCGCTT 60.595 61.111 0.00 0.00 0.00 4.68
135 136 4.988598 CGCACTGTTCCCACCGCT 62.989 66.667 0.00 0.00 0.00 5.52
136 137 4.980805 TCGCACTGTTCCCACCGC 62.981 66.667 0.00 0.00 0.00 5.68
137 138 3.041940 GTCGCACTGTTCCCACCG 61.042 66.667 0.00 0.00 0.00 4.94
138 139 1.961277 CAGTCGCACTGTTCCCACC 60.961 63.158 7.80 0.00 41.19 4.61
139 140 1.961277 CCAGTCGCACTGTTCCCAC 60.961 63.158 13.06 0.00 44.50 4.61
140 141 2.425592 CCAGTCGCACTGTTCCCA 59.574 61.111 13.06 0.00 44.50 4.37
141 142 2.358737 CCCAGTCGCACTGTTCCC 60.359 66.667 13.06 0.00 44.50 3.97
142 143 3.050275 GCCCAGTCGCACTGTTCC 61.050 66.667 13.06 1.19 44.50 3.62
143 144 3.414700 CGCCCAGTCGCACTGTTC 61.415 66.667 13.06 5.69 44.50 3.18
144 145 4.988598 CCGCCCAGTCGCACTGTT 62.989 66.667 13.06 0.00 44.50 3.16
151 152 4.742201 CCTGTCACCGCCCAGTCG 62.742 72.222 0.00 0.00 0.00 4.18
152 153 3.302347 CTCCTGTCACCGCCCAGTC 62.302 68.421 0.00 0.00 0.00 3.51
153 154 3.314331 CTCCTGTCACCGCCCAGT 61.314 66.667 0.00 0.00 0.00 4.00
154 155 2.997315 TCTCCTGTCACCGCCCAG 60.997 66.667 0.00 0.00 0.00 4.45
155 156 2.997315 CTCTCCTGTCACCGCCCA 60.997 66.667 0.00 0.00 0.00 5.36
156 157 2.997897 ACTCTCCTGTCACCGCCC 60.998 66.667 0.00 0.00 0.00 6.13
157 158 2.262915 CACTCTCCTGTCACCGCC 59.737 66.667 0.00 0.00 0.00 6.13
158 159 2.262915 CCACTCTCCTGTCACCGC 59.737 66.667 0.00 0.00 0.00 5.68
159 160 1.599606 CTCCCACTCTCCTGTCACCG 61.600 65.000 0.00 0.00 0.00 4.94
160 161 1.261238 CCTCCCACTCTCCTGTCACC 61.261 65.000 0.00 0.00 0.00 4.02
161 162 1.893919 GCCTCCCACTCTCCTGTCAC 61.894 65.000 0.00 0.00 0.00 3.67
162 163 1.610673 GCCTCCCACTCTCCTGTCA 60.611 63.158 0.00 0.00 0.00 3.58
163 164 2.716017 CGCCTCCCACTCTCCTGTC 61.716 68.421 0.00 0.00 0.00 3.51
164 165 2.681778 CGCCTCCCACTCTCCTGT 60.682 66.667 0.00 0.00 0.00 4.00
165 166 2.363018 TCGCCTCCCACTCTCCTG 60.363 66.667 0.00 0.00 0.00 3.86
166 167 2.043450 CTCGCCTCCCACTCTCCT 60.043 66.667 0.00 0.00 0.00 3.69
167 168 0.683504 TAACTCGCCTCCCACTCTCC 60.684 60.000 0.00 0.00 0.00 3.71
168 169 1.067821 CATAACTCGCCTCCCACTCTC 59.932 57.143 0.00 0.00 0.00 3.20
169 170 1.115467 CATAACTCGCCTCCCACTCT 58.885 55.000 0.00 0.00 0.00 3.24
170 171 1.067821 CTCATAACTCGCCTCCCACTC 59.932 57.143 0.00 0.00 0.00 3.51
171 172 1.115467 CTCATAACTCGCCTCCCACT 58.885 55.000 0.00 0.00 0.00 4.00
172 173 1.112113 TCTCATAACTCGCCTCCCAC 58.888 55.000 0.00 0.00 0.00 4.61
173 174 1.112113 GTCTCATAACTCGCCTCCCA 58.888 55.000 0.00 0.00 0.00 4.37
174 175 0.030908 CGTCTCATAACTCGCCTCCC 59.969 60.000 0.00 0.00 0.00 4.30
175 176 0.739561 ACGTCTCATAACTCGCCTCC 59.260 55.000 0.00 0.00 0.00 4.30
176 177 1.595003 CGACGTCTCATAACTCGCCTC 60.595 57.143 14.70 0.00 0.00 4.70
177 178 0.377554 CGACGTCTCATAACTCGCCT 59.622 55.000 14.70 0.00 0.00 5.52
178 179 1.201098 GCGACGTCTCATAACTCGCC 61.201 60.000 14.70 0.00 38.59 5.54
179 180 0.248134 AGCGACGTCTCATAACTCGC 60.248 55.000 14.70 9.19 41.65 5.03
180 181 2.102633 GAAGCGACGTCTCATAACTCG 58.897 52.381 14.70 0.00 0.00 4.18
181 182 2.452105 GGAAGCGACGTCTCATAACTC 58.548 52.381 14.70 0.59 0.00 3.01
182 183 1.202154 CGGAAGCGACGTCTCATAACT 60.202 52.381 14.70 0.00 0.00 2.24
183 184 1.189403 CGGAAGCGACGTCTCATAAC 58.811 55.000 14.70 0.29 0.00 1.89
184 185 0.806868 ACGGAAGCGACGTCTCATAA 59.193 50.000 14.70 0.00 41.25 1.90
185 186 2.474561 ACGGAAGCGACGTCTCATA 58.525 52.632 14.70 0.00 41.25 2.15
186 187 3.275088 ACGGAAGCGACGTCTCAT 58.725 55.556 14.70 0.00 41.25 2.90
192 193 4.831307 CGGGAGACGGAAGCGACG 62.831 72.222 0.00 0.00 39.42 5.12
215 216 3.818787 GCAGTTGCATGCCTCGGG 61.819 66.667 16.68 7.29 40.43 5.14
221 222 3.740397 TGCGAGGCAGTTGCATGC 61.740 61.111 11.82 11.82 41.01 4.06
254 255 4.760047 TTTCTCGCGAGCCTGGCC 62.760 66.667 30.97 6.06 0.00 5.36
255 256 3.491652 GTTTCTCGCGAGCCTGGC 61.492 66.667 30.97 11.65 0.00 4.85
256 257 2.097038 CAGTTTCTCGCGAGCCTGG 61.097 63.158 30.97 14.72 0.00 4.45
257 258 1.080501 TCAGTTTCTCGCGAGCCTG 60.081 57.895 30.97 29.70 0.00 4.85
258 259 1.080434 GTCAGTTTCTCGCGAGCCT 60.080 57.895 30.97 21.60 0.00 4.58
259 260 2.437343 CGTCAGTTTCTCGCGAGCC 61.437 63.158 30.97 19.77 0.00 4.70
260 261 0.798771 ATCGTCAGTTTCTCGCGAGC 60.799 55.000 30.97 17.24 35.03 5.03
261 262 1.579808 GAATCGTCAGTTTCTCGCGAG 59.420 52.381 30.03 30.03 35.03 5.03
262 263 1.614385 GAATCGTCAGTTTCTCGCGA 58.386 50.000 9.26 9.26 36.02 5.87
263 264 0.291989 CGAATCGTCAGTTTCTCGCG 59.708 55.000 0.00 0.00 0.00 5.87
264 265 0.640768 CCGAATCGTCAGTTTCTCGC 59.359 55.000 0.82 0.00 0.00 5.03
265 266 0.640768 GCCGAATCGTCAGTTTCTCG 59.359 55.000 0.82 0.00 0.00 4.04
266 267 1.656095 CTGCCGAATCGTCAGTTTCTC 59.344 52.381 5.45 0.00 0.00 2.87
267 268 1.000955 ACTGCCGAATCGTCAGTTTCT 59.999 47.619 13.81 0.00 37.78 2.52
268 269 1.429463 ACTGCCGAATCGTCAGTTTC 58.571 50.000 13.81 0.00 37.78 2.78
269 270 1.878953 AACTGCCGAATCGTCAGTTT 58.121 45.000 23.64 10.22 45.55 2.66
270 271 3.606886 AACTGCCGAATCGTCAGTT 57.393 47.368 23.64 23.64 43.73 3.16
271 272 1.798813 GAAAACTGCCGAATCGTCAGT 59.201 47.619 13.81 13.81 42.28 3.41
272 273 1.201812 CGAAAACTGCCGAATCGTCAG 60.202 52.381 12.33 12.33 0.00 3.51
273 274 0.787787 CGAAAACTGCCGAATCGTCA 59.212 50.000 0.82 0.00 0.00 4.35
274 275 0.518559 GCGAAAACTGCCGAATCGTC 60.519 55.000 0.82 0.00 36.01 4.20
275 276 0.949105 AGCGAAAACTGCCGAATCGT 60.949 50.000 0.82 0.00 36.01 3.73
276 277 0.519175 CAGCGAAAACTGCCGAATCG 60.519 55.000 0.00 0.00 36.64 3.34
277 278 0.179189 CCAGCGAAAACTGCCGAATC 60.179 55.000 0.00 0.00 36.29 2.52
278 279 1.586154 CCCAGCGAAAACTGCCGAAT 61.586 55.000 0.00 0.00 36.29 3.34
279 280 2.258013 CCCAGCGAAAACTGCCGAA 61.258 57.895 0.00 0.00 36.29 4.30
280 281 2.668212 CCCAGCGAAAACTGCCGA 60.668 61.111 0.00 0.00 36.29 5.54
281 282 4.404654 GCCCAGCGAAAACTGCCG 62.405 66.667 0.00 0.00 36.29 5.69
282 283 4.056125 GGCCCAGCGAAAACTGCC 62.056 66.667 0.00 0.00 36.29 4.85
283 284 3.273080 CTGGCCCAGCGAAAACTGC 62.273 63.158 0.00 0.00 36.29 4.40
284 285 2.629656 CCTGGCCCAGCGAAAACTG 61.630 63.158 4.81 0.00 37.42 3.16
285 286 2.282462 CCTGGCCCAGCGAAAACT 60.282 61.111 4.81 0.00 0.00 2.66
286 287 4.056125 GCCTGGCCCAGCGAAAAC 62.056 66.667 7.66 0.00 0.00 2.43
287 288 4.284550 AGCCTGGCCCAGCGAAAA 62.285 61.111 16.57 0.00 0.00 2.29
299 300 1.523154 TTAAAGCAACCCGCAGCCTG 61.523 55.000 0.00 0.00 46.13 4.85
300 301 1.228429 TTAAAGCAACCCGCAGCCT 60.228 52.632 0.00 0.00 46.13 4.58
301 302 1.212751 CTTAAAGCAACCCGCAGCC 59.787 57.895 0.00 0.00 46.13 4.85
302 303 0.313987 AACTTAAAGCAACCCGCAGC 59.686 50.000 0.00 0.00 46.13 5.25
303 304 1.068541 GGAACTTAAAGCAACCCGCAG 60.069 52.381 0.00 0.00 46.13 5.18
304 305 0.955905 GGAACTTAAAGCAACCCGCA 59.044 50.000 0.00 0.00 46.13 5.69
305 306 0.109919 CGGAACTTAAAGCAACCCGC 60.110 55.000 0.00 0.00 42.91 6.13
306 307 1.069500 CACGGAACTTAAAGCAACCCG 60.069 52.381 0.00 0.00 41.04 5.28
307 308 1.335597 GCACGGAACTTAAAGCAACCC 60.336 52.381 0.00 0.00 0.00 4.11
308 309 1.662026 CGCACGGAACTTAAAGCAACC 60.662 52.381 0.00 0.00 0.00 3.77
309 310 1.662026 CCGCACGGAACTTAAAGCAAC 60.662 52.381 2.01 0.00 37.50 4.17
310 311 0.589223 CCGCACGGAACTTAAAGCAA 59.411 50.000 2.01 0.00 37.50 3.91
311 312 1.231958 CCCGCACGGAACTTAAAGCA 61.232 55.000 11.42 0.00 37.50 3.91
312 313 1.500396 CCCGCACGGAACTTAAAGC 59.500 57.895 11.42 0.00 37.50 3.51
313 314 1.500396 GCCCGCACGGAACTTAAAG 59.500 57.895 11.42 0.00 37.50 1.85
314 315 1.967494 GGCCCGCACGGAACTTAAA 60.967 57.895 11.42 0.00 37.50 1.52
315 316 2.358984 GGCCCGCACGGAACTTAA 60.359 61.111 11.42 0.00 37.50 1.85
316 317 3.627952 TGGCCCGCACGGAACTTA 61.628 61.111 11.42 0.00 37.50 2.24
320 321 4.877619 TTTGTGGCCCGCACGGAA 62.878 61.111 11.42 0.00 37.50 4.30
327 328 4.418401 CATGCGGTTTGTGGCCCG 62.418 66.667 0.00 0.00 46.90 6.13
328 329 4.740431 GCATGCGGTTTGTGGCCC 62.740 66.667 0.00 0.00 0.00 5.80
329 330 3.919973 CTGCATGCGGTTTGTGGCC 62.920 63.158 18.84 0.00 0.00 5.36
330 331 2.431260 CTGCATGCGGTTTGTGGC 60.431 61.111 18.84 0.00 0.00 5.01
331 332 2.431260 GCTGCATGCGGTTTGTGG 60.431 61.111 26.79 4.24 0.00 4.17
332 333 2.431260 GGCTGCATGCGGTTTGTG 60.431 61.111 26.79 5.56 44.05 3.33
333 334 3.683937 GGGCTGCATGCGGTTTGT 61.684 61.111 26.79 0.00 44.05 2.83
334 335 3.636313 CTGGGCTGCATGCGGTTTG 62.636 63.158 26.79 11.60 44.05 2.93
335 336 3.376078 CTGGGCTGCATGCGGTTT 61.376 61.111 26.79 0.00 44.05 3.27
340 341 4.446413 GTTGGCTGGGCTGCATGC 62.446 66.667 11.82 11.82 41.94 4.06
341 342 3.766691 GGTTGGCTGGGCTGCATG 61.767 66.667 0.50 0.00 34.04 4.06
342 343 3.831727 TTGGTTGGCTGGGCTGCAT 62.832 57.895 0.50 0.00 34.04 3.96
343 344 4.536526 TTGGTTGGCTGGGCTGCA 62.537 61.111 0.50 0.00 34.04 4.41
344 345 3.233231 TTTGGTTGGCTGGGCTGC 61.233 61.111 0.00 0.00 0.00 5.25
345 346 2.091102 CTGTTTGGTTGGCTGGGCTG 62.091 60.000 0.00 0.00 0.00 4.85
346 347 1.833934 CTGTTTGGTTGGCTGGGCT 60.834 57.895 0.00 0.00 0.00 5.19
347 348 2.087462 GACTGTTTGGTTGGCTGGGC 62.087 60.000 0.00 0.00 0.00 5.36
348 349 1.463553 GGACTGTTTGGTTGGCTGGG 61.464 60.000 0.00 0.00 0.00 4.45
349 350 1.795170 CGGACTGTTTGGTTGGCTGG 61.795 60.000 0.00 0.00 0.00 4.85
350 351 1.654220 CGGACTGTTTGGTTGGCTG 59.346 57.895 0.00 0.00 0.00 4.85
351 352 2.193536 GCGGACTGTTTGGTTGGCT 61.194 57.895 0.00 0.00 0.00 4.75
352 353 2.335011 GCGGACTGTTTGGTTGGC 59.665 61.111 0.00 0.00 0.00 4.52
353 354 2.637025 CGCGGACTGTTTGGTTGG 59.363 61.111 0.00 0.00 0.00 3.77
354 355 2.051345 GCGCGGACTGTTTGGTTG 60.051 61.111 8.83 0.00 0.00 3.77
355 356 2.515057 TGCGCGGACTGTTTGGTT 60.515 55.556 8.83 0.00 0.00 3.67
356 357 3.276846 GTGCGCGGACTGTTTGGT 61.277 61.111 24.37 0.00 0.00 3.67
357 358 2.513065 GATGTGCGCGGACTGTTTGG 62.513 60.000 30.67 0.00 0.00 3.28
358 359 1.154413 GATGTGCGCGGACTGTTTG 60.154 57.895 30.67 0.00 0.00 2.93
359 360 2.325082 GGATGTGCGCGGACTGTTT 61.325 57.895 30.67 13.42 0.00 2.83
360 361 2.742372 GGATGTGCGCGGACTGTT 60.742 61.111 30.67 15.95 0.00 3.16
361 362 4.760047 GGGATGTGCGCGGACTGT 62.760 66.667 30.67 19.52 0.00 3.55
383 384 3.590466 ATGCAGCCCAACCAGACCC 62.590 63.158 0.00 0.00 0.00 4.46
384 385 2.036256 ATGCAGCCCAACCAGACC 59.964 61.111 0.00 0.00 0.00 3.85
385 386 2.998279 GCATGCAGCCCAACCAGAC 61.998 63.158 14.21 0.00 37.23 3.51
386 387 2.677524 GCATGCAGCCCAACCAGA 60.678 61.111 14.21 0.00 37.23 3.86
387 388 4.124351 CGCATGCAGCCCAACCAG 62.124 66.667 19.57 0.00 41.38 4.00
396 397 3.223710 TTTGGTTGCCCGCATGCAG 62.224 57.895 19.57 6.15 43.21 4.41
397 398 3.229501 TTTGGTTGCCCGCATGCA 61.230 55.556 19.57 0.00 40.07 3.96
398 399 2.738139 GTTTGGTTGCCCGCATGC 60.738 61.111 7.91 7.91 0.00 4.06
399 400 1.664333 GTGTTTGGTTGCCCGCATG 60.664 57.895 0.00 0.00 0.00 4.06
400 401 2.733945 GTGTTTGGTTGCCCGCAT 59.266 55.556 0.00 0.00 0.00 4.73
401 402 3.893763 CGTGTTTGGTTGCCCGCA 61.894 61.111 0.00 0.00 0.00 5.69
403 404 4.639171 GGCGTGTTTGGTTGCCCG 62.639 66.667 0.00 0.00 41.70 6.13
405 406 1.248101 ATAGGGCGTGTTTGGTTGCC 61.248 55.000 0.00 0.00 46.82 4.52
406 407 1.455248 TATAGGGCGTGTTTGGTTGC 58.545 50.000 0.00 0.00 0.00 4.17
407 408 3.733684 GCAATATAGGGCGTGTTTGGTTG 60.734 47.826 0.00 0.00 0.00 3.77
408 409 2.425668 GCAATATAGGGCGTGTTTGGTT 59.574 45.455 0.00 0.00 0.00 3.67
409 410 2.021457 GCAATATAGGGCGTGTTTGGT 58.979 47.619 0.00 0.00 0.00 3.67
410 411 2.290641 GAGCAATATAGGGCGTGTTTGG 59.709 50.000 0.00 0.00 34.54 3.28
411 412 2.032894 CGAGCAATATAGGGCGTGTTTG 60.033 50.000 0.00 0.00 34.54 2.93
412 413 2.210116 CGAGCAATATAGGGCGTGTTT 58.790 47.619 0.00 0.00 34.54 2.83
413 414 1.138266 ACGAGCAATATAGGGCGTGTT 59.862 47.619 0.00 0.00 34.54 3.32
414 415 0.750850 ACGAGCAATATAGGGCGTGT 59.249 50.000 0.00 0.00 34.54 4.49
415 416 1.865865 AACGAGCAATATAGGGCGTG 58.134 50.000 0.00 0.00 34.54 5.34
416 417 3.738830 TTAACGAGCAATATAGGGCGT 57.261 42.857 0.00 0.00 34.54 5.68
417 418 4.510340 AGTTTTAACGAGCAATATAGGGCG 59.490 41.667 0.00 0.00 34.54 6.13
418 419 5.277828 CCAGTTTTAACGAGCAATATAGGGC 60.278 44.000 0.00 0.00 0.00 5.19
419 420 5.820947 ACCAGTTTTAACGAGCAATATAGGG 59.179 40.000 0.00 0.00 0.00 3.53
420 421 6.018180 GGACCAGTTTTAACGAGCAATATAGG 60.018 42.308 0.00 0.00 0.00 2.57
421 422 6.761714 AGGACCAGTTTTAACGAGCAATATAG 59.238 38.462 0.00 0.00 0.00 1.31
431 432 5.657474 TGCTATAGAGGACCAGTTTTAACG 58.343 41.667 3.21 0.00 0.00 3.18
447 448 5.931146 GGTGAGGATTGAGTTGATGCTATAG 59.069 44.000 0.00 0.00 0.00 1.31
470 471 1.686325 CGGTATGGGGTGAGGTGAGG 61.686 65.000 0.00 0.00 0.00 3.86
471 472 1.686325 CCGGTATGGGGTGAGGTGAG 61.686 65.000 0.00 0.00 0.00 3.51
472 473 1.687840 CCGGTATGGGGTGAGGTGA 60.688 63.158 0.00 0.00 0.00 4.02
473 474 2.908015 CCGGTATGGGGTGAGGTG 59.092 66.667 0.00 0.00 0.00 4.00
474 475 3.087906 GCCGGTATGGGGTGAGGT 61.088 66.667 1.90 0.00 38.63 3.85
515 519 9.696917 GTGGTGATCACATTTTCTTTCTTTAAT 57.303 29.630 26.47 0.00 45.39 1.40
538 542 3.870422 TGTGTGTTGCGTGCGTGG 61.870 61.111 0.00 0.00 0.00 4.94
603 608 1.052617 TCGGTGTCAGAACAATGGGA 58.947 50.000 0.00 0.00 37.08 4.37
641 646 1.937359 GATTGCGTTAATGGCGATCG 58.063 50.000 11.69 11.69 40.42 3.69
663 668 2.083774 TCGATCGGCAGCAAAGATTTT 58.916 42.857 16.41 0.00 0.00 1.82
791 833 2.588877 CGGCCGGCAATGTCCTAG 60.589 66.667 30.85 3.27 0.00 3.02
792 834 4.169696 CCGGCCGGCAATGTCCTA 62.170 66.667 34.96 0.00 0.00 2.94
956 1000 3.323136 GCGTGCGTGCTAGATCGG 61.323 66.667 0.00 0.00 0.00 4.18
995 1048 0.750850 GAGGTAGGTCGCCATTGCTA 59.249 55.000 0.00 0.00 34.43 3.49
1006 1059 4.477119 GGCGAGGGGGAGGTAGGT 62.477 72.222 0.00 0.00 0.00 3.08
1627 1692 5.186996 TCAAGCTCCACAAATTTCTCAAC 57.813 39.130 0.00 0.00 0.00 3.18
1656 1721 4.753107 AGCAAAAGAAAAGCCACATGAATG 59.247 37.500 0.00 0.00 0.00 2.67
1666 1731 7.936950 AATAGAACAGAAGCAAAAGAAAAGC 57.063 32.000 0.00 0.00 0.00 3.51
1715 1783 4.805609 GCTTGACTTGTCCAAGGAAGAGAT 60.806 45.833 18.11 0.00 42.53 2.75
1792 1891 2.415893 CGAATCAAAATGCACCACCTCC 60.416 50.000 0.00 0.00 0.00 4.30
1798 1897 4.083324 TCTCAAGACGAATCAAAATGCACC 60.083 41.667 0.00 0.00 0.00 5.01
1861 1960 6.119536 TCCTTTAATATGGAGAAACACGCAT 58.880 36.000 0.00 0.00 0.00 4.73
1924 2023 4.093850 TGATGTTCATGTGATGCGAGAAAG 59.906 41.667 0.00 0.00 0.00 2.62
2051 2153 2.582052 TGGTTGGCTGTGGTAAGAAAG 58.418 47.619 0.00 0.00 0.00 2.62
2061 2164 3.041701 CGCATGTTGGTTGGCTGT 58.958 55.556 0.00 0.00 0.00 4.40
2072 2175 3.998911 TATGCCACGTCGCGCATGT 62.999 57.895 23.51 3.34 45.13 3.21
2080 2183 1.024579 CCAACCAGGTATGCCACGTC 61.025 60.000 1.54 0.00 37.19 4.34
2091 2194 1.762708 ATTGTATTCGGCCAACCAGG 58.237 50.000 2.24 0.00 41.84 4.45
2182 2321 5.614308 TGATGGTCATAGCAGTTATTGAGG 58.386 41.667 0.00 0.00 0.00 3.86
2286 2426 3.310501 GGTGTGCAACTTTAGTTACGTGT 59.689 43.478 0.00 0.00 38.04 4.49
2308 2448 1.474332 AATTGTGCAAGGCCCCACAG 61.474 55.000 17.56 0.00 42.29 3.66
2313 2453 1.256812 ACTGTAATTGTGCAAGGCCC 58.743 50.000 0.00 0.00 0.00 5.80
2334 2474 0.602905 ACGTAGTGCAAACCAGAGGC 60.603 55.000 0.00 0.00 42.51 4.70
2395 2536 5.124776 TCGTTTTATGCCCTTTTGTATGGAG 59.875 40.000 0.00 0.00 0.00 3.86
2429 2570 3.310227 ACACAAACATTGCTTTGCATGTG 59.690 39.130 16.59 16.59 44.73 3.21
2516 2657 7.478667 GCAAACACTTATCATGTTAAACTCTCG 59.521 37.037 0.00 0.00 39.36 4.04


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

AutoCloner maintained by Alex Coulton.