Multiple sequence alignment - TraesCS1B01G019600

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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 TraesCS1B01G019600 chr1B 100.000 3182 0 0 1 3182 9262405 9259224 0.000000e+00 5877.0
1 TraesCS1B01G019600 chr1B 92.872 2918 139 33 297 3182 8916976 8919856 0.000000e+00 4172.0
2 TraesCS1B01G019600 chr1B 85.455 220 22 8 81 296 177471373 177471586 1.490000e-53 220.0
3 TraesCS1B01G019600 chr1B 95.946 74 3 0 1 74 8916903 8916976 1.550000e-23 121.0
4 TraesCS1B01G019600 chr1D 87.934 1384 94 33 919 2260 6787756 6786404 0.000000e+00 1563.0
5 TraesCS1B01G019600 chr1D 79.487 585 112 4 1589 2172 6732260 6731683 2.950000e-110 409.0
6 TraesCS1B01G019600 chr1D 77.547 579 122 5 1589 2166 6865375 6865946 3.040000e-90 342.0
7 TraesCS1B01G019600 chr1D 86.555 238 22 8 79 309 451426647 451426881 1.460000e-63 254.0
8 TraesCS1B01G019600 chr1D 85.656 244 17 3 72 297 157542963 157542720 1.140000e-59 241.0
9 TraesCS1B01G019600 chr1D 84.454 238 27 9 79 309 274195276 274195042 3.190000e-55 226.0
10 TraesCS1B01G019600 chr1D 88.421 190 10 4 565 747 6788179 6787995 5.340000e-53 219.0
11 TraesCS1B01G019600 chr1D 86.131 137 5 3 425 549 6788301 6788167 5.540000e-28 135.0
12 TraesCS1B01G019600 chr1A 87.762 1381 104 30 919 2260 8292782 8291428 0.000000e+00 1554.0
13 TraesCS1B01G019600 chr1A 85.878 262 21 6 425 679 8294584 8294332 6.770000e-67 265.0
14 TraesCS1B01G019600 chr1A 95.238 63 2 1 3121 3182 8283746 8283684 7.260000e-17 99.0
15 TraesCS1B01G019600 chr2D 80.513 585 106 4 1590 2173 11775326 11775903 2.910000e-120 442.0
16 TraesCS1B01G019600 chr2D 77.282 515 77 21 929 1414 11774722 11775225 1.880000e-67 267.0
17 TraesCS1B01G019600 chr2D 85.532 235 24 9 80 309 570676762 570676991 1.480000e-58 237.0
18 TraesCS1B01G019600 chr2B 79.829 585 110 4 1590 2173 18177928 18177351 1.360000e-113 420.0
19 TraesCS1B01G019600 chr2B 77.265 585 126 5 1590 2173 18174028 18173450 1.410000e-88 337.0
20 TraesCS1B01G019600 chr2B 77.087 515 76 21 929 1413 18178544 18178042 3.150000e-65 259.0
21 TraesCS1B01G019600 chr2A 79.487 585 112 4 1590 2173 12288365 12288942 2.950000e-110 409.0
22 TraesCS1B01G019600 chr2A 76.893 515 79 22 929 1414 12287755 12288258 4.070000e-64 255.0
23 TraesCS1B01G019600 chr6D 86.957 230 24 5 72 298 252427434 252427660 1.460000e-63 254.0
24 TraesCS1B01G019600 chr3D 85.246 244 19 2 73 299 25248976 25249219 5.310000e-58 235.0
25 TraesCS1B01G019600 chr7B 84.977 213 30 2 88 298 131273374 131273162 6.910000e-52 215.0
26 TraesCS1B01G019600 chr7B 96.970 33 1 0 977 1009 557057601 557057633 4.430000e-04 56.5
27 TraesCS1B01G019600 chr4A 84.977 213 22 7 100 309 519251357 519251152 1.160000e-49 207.0
28 TraesCS1B01G019600 chr4A 100.000 29 0 0 2609 2637 349488551 349488579 2.000000e-03 54.7
29 TraesCS1B01G019600 chr6B 86.022 186 22 4 116 298 659061677 659061493 2.500000e-46 196.0
30 TraesCS1B01G019600 chr3B 100.000 31 0 0 2267 2297 804855795 804855825 1.230000e-04 58.4
31 TraesCS1B01G019600 chr7D 100.000 28 0 0 982 1009 523045747 523045774 6.000000e-03 52.8
32 TraesCS1B01G019600 chr7A 100.000 28 0 0 982 1009 603291900 603291927 6.000000e-03 52.8


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 TraesCS1B01G019600 chr1B 9259224 9262405 3181 True 5877.000000 5877 100.000000 1 3182 1 chr1B.!!$R1 3181
1 TraesCS1B01G019600 chr1B 8916903 8919856 2953 False 2146.500000 4172 94.409000 1 3182 2 chr1B.!!$F2 3181
2 TraesCS1B01G019600 chr1D 6786404 6788301 1897 True 639.000000 1563 87.495333 425 2260 3 chr1D.!!$R4 1835
3 TraesCS1B01G019600 chr1D 6731683 6732260 577 True 409.000000 409 79.487000 1589 2172 1 chr1D.!!$R1 583
4 TraesCS1B01G019600 chr1D 6865375 6865946 571 False 342.000000 342 77.547000 1589 2166 1 chr1D.!!$F1 577
5 TraesCS1B01G019600 chr1A 8291428 8294584 3156 True 909.500000 1554 86.820000 425 2260 2 chr1A.!!$R2 1835
6 TraesCS1B01G019600 chr2D 11774722 11775903 1181 False 354.500000 442 78.897500 929 2173 2 chr2D.!!$F2 1244
7 TraesCS1B01G019600 chr2B 18173450 18178544 5094 True 338.666667 420 78.060333 929 2173 3 chr2B.!!$R1 1244
8 TraesCS1B01G019600 chr2A 12287755 12288942 1187 False 332.000000 409 78.190000 929 2173 2 chr2A.!!$F1 1244

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
123 124 0.178998 GATGATGTGCCTGCCATCCT 60.179 55.000 14.08 7.63 38.32 3.24 F
130 131 0.186630 TGCCTGCCATCCTGCAATAT 59.813 50.000 0.00 0.00 41.51 1.28 F
209 210 0.687354 ACCCGCAACTCTCTTCACAT 59.313 50.000 0.00 0.00 0.00 3.21 F
274 275 0.804364 TGCATCTTGATGTTCCGTGC 59.196 50.000 11.61 0.00 0.00 5.34 F
275 276 0.804364 GCATCTTGATGTTCCGTGCA 59.196 50.000 11.61 0.00 0.00 4.57 F
276 277 1.199789 GCATCTTGATGTTCCGTGCAA 59.800 47.619 11.61 0.00 0.00 4.08 F
1684 3196 1.226575 CGCGAAGATGAGTACGGCA 60.227 57.895 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 2730 0.245539 CCTCCTCGAAGCCGTTGTTA 59.754 55.000 0.00 0.0 37.05 2.41 R
1520 2984 0.376852 GCAGAGCACAACGAACACAA 59.623 50.000 0.00 0.0 0.00 3.33 R
1521 2985 0.461870 AGCAGAGCACAACGAACACA 60.462 50.000 0.00 0.0 0.00 3.72 R
1522 2986 0.657840 AAGCAGAGCACAACGAACAC 59.342 50.000 0.00 0.0 0.00 3.32 R
1671 3183 1.142748 GCTGCTGCCGTACTCATCT 59.857 57.895 3.85 0.0 0.00 2.90 R
1979 3491 1.613928 TCCCTGTCATACCCGCCAA 60.614 57.895 0.00 0.0 0.00 4.52 R
2652 8066 0.108585 ACAGGCCGATGTCAGTTTGT 59.891 50.000 0.00 0.0 0.00 2.83 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
69 70 7.594758 CACCTCACAATTGTAAATCGAAAACAT 59.405 33.333 11.53 0.00 0.00 2.71
113 114 4.445452 AAAGTTGGTGATGATGATGTGC 57.555 40.909 0.00 0.00 0.00 4.57
114 115 2.372264 AGTTGGTGATGATGATGTGCC 58.628 47.619 0.00 0.00 0.00 5.01
115 116 2.025605 AGTTGGTGATGATGATGTGCCT 60.026 45.455 0.00 0.00 0.00 4.75
116 117 2.047002 TGGTGATGATGATGTGCCTG 57.953 50.000 0.00 0.00 0.00 4.85
117 118 0.666913 GGTGATGATGATGTGCCTGC 59.333 55.000 0.00 0.00 0.00 4.85
118 119 0.666913 GTGATGATGATGTGCCTGCC 59.333 55.000 0.00 0.00 0.00 4.85
119 120 0.256464 TGATGATGATGTGCCTGCCA 59.744 50.000 0.00 0.00 0.00 4.92
120 121 1.133606 TGATGATGATGTGCCTGCCAT 60.134 47.619 0.00 0.00 0.00 4.40
121 122 1.540267 GATGATGATGTGCCTGCCATC 59.460 52.381 11.37 11.37 39.32 3.51
122 123 0.466739 TGATGATGTGCCTGCCATCC 60.467 55.000 14.08 4.95 38.32 3.51
123 124 0.178998 GATGATGTGCCTGCCATCCT 60.179 55.000 14.08 7.63 38.32 3.24
124 125 0.467474 ATGATGTGCCTGCCATCCTG 60.467 55.000 14.08 0.00 38.32 3.86
125 126 2.441532 ATGTGCCTGCCATCCTGC 60.442 61.111 0.00 0.00 0.00 4.85
126 127 3.291031 ATGTGCCTGCCATCCTGCA 62.291 57.895 0.00 0.00 39.37 4.41
127 128 2.677524 GTGCCTGCCATCCTGCAA 60.678 61.111 0.00 0.00 41.51 4.08
128 129 2.056223 GTGCCTGCCATCCTGCAAT 61.056 57.895 0.00 0.00 41.51 3.56
129 130 0.752743 GTGCCTGCCATCCTGCAATA 60.753 55.000 0.00 0.00 41.51 1.90
130 131 0.186630 TGCCTGCCATCCTGCAATAT 59.813 50.000 0.00 0.00 41.51 1.28
131 132 1.424684 TGCCTGCCATCCTGCAATATA 59.575 47.619 0.00 0.00 41.51 0.86
132 133 2.089980 GCCTGCCATCCTGCAATATAG 58.910 52.381 0.00 0.00 41.51 1.31
133 134 2.719739 CCTGCCATCCTGCAATATAGG 58.280 52.381 0.00 0.00 41.51 2.57
134 135 2.089980 CTGCCATCCTGCAATATAGGC 58.910 52.381 9.23 9.23 41.51 3.93
135 136 1.272092 TGCCATCCTGCAATATAGGCC 60.272 52.381 12.50 0.00 38.56 5.19
136 137 1.742761 CCATCCTGCAATATAGGCCG 58.257 55.000 0.00 0.00 35.23 6.13
137 138 1.089920 CATCCTGCAATATAGGCCGC 58.910 55.000 0.00 0.00 35.23 6.53
138 139 0.987294 ATCCTGCAATATAGGCCGCT 59.013 50.000 0.00 0.00 35.23 5.52
139 140 0.764890 TCCTGCAATATAGGCCGCTT 59.235 50.000 0.00 0.00 35.23 4.68
140 141 0.877071 CCTGCAATATAGGCCGCTTG 59.123 55.000 0.00 0.97 0.00 4.01
141 142 1.543208 CCTGCAATATAGGCCGCTTGA 60.543 52.381 12.03 0.00 0.00 3.02
142 143 2.430465 CTGCAATATAGGCCGCTTGAT 58.570 47.619 12.03 0.00 0.00 2.57
143 144 2.417933 CTGCAATATAGGCCGCTTGATC 59.582 50.000 12.03 0.00 0.00 2.92
144 145 2.038952 TGCAATATAGGCCGCTTGATCT 59.961 45.455 12.03 0.00 0.00 2.75
145 146 3.260632 TGCAATATAGGCCGCTTGATCTA 59.739 43.478 12.03 0.00 0.00 1.98
146 147 4.080919 TGCAATATAGGCCGCTTGATCTAT 60.081 41.667 12.03 0.00 0.00 1.98
147 148 5.128663 TGCAATATAGGCCGCTTGATCTATA 59.871 40.000 12.03 1.25 0.00 1.31
148 149 6.183361 TGCAATATAGGCCGCTTGATCTATAT 60.183 38.462 12.03 3.29 37.13 0.86
149 150 6.367422 GCAATATAGGCCGCTTGATCTATATC 59.633 42.308 12.03 0.00 35.53 1.63
150 151 7.665690 CAATATAGGCCGCTTGATCTATATCT 58.334 38.462 0.00 0.00 35.53 1.98
151 152 3.883830 AGGCCGCTTGATCTATATCTG 57.116 47.619 0.00 0.00 32.93 2.90
152 153 3.435275 AGGCCGCTTGATCTATATCTGA 58.565 45.455 0.00 0.00 32.93 3.27
153 154 3.194542 AGGCCGCTTGATCTATATCTGAC 59.805 47.826 0.00 0.00 32.93 3.51
154 155 3.175152 GCCGCTTGATCTATATCTGACG 58.825 50.000 0.00 0.00 32.93 4.35
155 156 3.763902 CCGCTTGATCTATATCTGACGG 58.236 50.000 0.00 0.00 32.93 4.79
156 157 3.440522 CCGCTTGATCTATATCTGACGGA 59.559 47.826 9.20 0.00 39.22 4.69
157 158 4.097135 CCGCTTGATCTATATCTGACGGAT 59.903 45.833 1.60 1.60 39.22 4.18
158 159 5.297029 CCGCTTGATCTATATCTGACGGATA 59.703 44.000 6.45 6.45 40.69 2.59
159 160 6.426327 CGCTTGATCTATATCTGACGGATAG 58.574 44.000 9.78 0.00 39.89 2.08
160 161 6.512578 CGCTTGATCTATATCTGACGGATAGG 60.513 46.154 9.78 5.66 39.89 2.57
161 162 6.544197 GCTTGATCTATATCTGACGGATAGGA 59.456 42.308 9.78 10.10 39.89 2.94
162 163 7.067615 GCTTGATCTATATCTGACGGATAGGAA 59.932 40.741 9.78 0.00 39.89 3.36
163 164 8.512966 TTGATCTATATCTGACGGATAGGAAG 57.487 38.462 9.78 7.25 39.89 3.46
164 165 7.862675 TGATCTATATCTGACGGATAGGAAGA 58.137 38.462 9.78 11.46 39.89 2.87
165 166 8.329502 TGATCTATATCTGACGGATAGGAAGAA 58.670 37.037 9.78 0.00 39.89 2.52
166 167 9.179909 GATCTATATCTGACGGATAGGAAGAAA 57.820 37.037 9.78 0.00 39.89 2.52
167 168 8.338072 TCTATATCTGACGGATAGGAAGAAAC 57.662 38.462 9.78 0.00 39.89 2.78
168 169 8.164733 TCTATATCTGACGGATAGGAAGAAACT 58.835 37.037 9.78 0.00 39.89 2.66
169 170 9.451002 CTATATCTGACGGATAGGAAGAAACTA 57.549 37.037 9.78 0.00 39.89 2.24
170 171 8.887264 ATATCTGACGGATAGGAAGAAACTAT 57.113 34.615 9.78 0.00 39.89 2.12
171 172 6.392625 TCTGACGGATAGGAAGAAACTATG 57.607 41.667 0.00 0.00 31.58 2.23
172 173 6.127101 TCTGACGGATAGGAAGAAACTATGA 58.873 40.000 0.00 0.00 31.58 2.15
173 174 6.778069 TCTGACGGATAGGAAGAAACTATGAT 59.222 38.462 0.00 0.00 31.58 2.45
174 175 7.942894 TCTGACGGATAGGAAGAAACTATGATA 59.057 37.037 0.00 0.00 31.58 2.15
175 176 8.473358 TGACGGATAGGAAGAAACTATGATAA 57.527 34.615 0.00 0.00 31.58 1.75
176 177 9.090103 TGACGGATAGGAAGAAACTATGATAAT 57.910 33.333 0.00 0.00 31.58 1.28
177 178 9.930693 GACGGATAGGAAGAAACTATGATAATT 57.069 33.333 0.00 0.00 31.58 1.40
195 196 8.359060 TGATAATTTTGCAAAAATATACCCGC 57.641 30.769 27.10 15.77 27.30 6.13
196 197 7.981789 TGATAATTTTGCAAAAATATACCCGCA 59.018 29.630 27.10 17.78 27.30 5.69
197 198 8.723942 ATAATTTTGCAAAAATATACCCGCAA 57.276 26.923 27.10 2.48 37.57 4.85
198 199 5.847670 TTTTGCAAAAATATACCCGCAAC 57.152 34.783 21.94 0.00 38.94 4.17
199 200 4.792521 TTGCAAAAATATACCCGCAACT 57.207 36.364 0.00 0.00 34.66 3.16
200 201 4.364415 TGCAAAAATATACCCGCAACTC 57.636 40.909 0.00 0.00 0.00 3.01
201 202 4.013728 TGCAAAAATATACCCGCAACTCT 58.986 39.130 0.00 0.00 0.00 3.24
202 203 4.095782 TGCAAAAATATACCCGCAACTCTC 59.904 41.667 0.00 0.00 0.00 3.20
203 204 4.335594 GCAAAAATATACCCGCAACTCTCT 59.664 41.667 0.00 0.00 0.00 3.10
204 205 5.163652 GCAAAAATATACCCGCAACTCTCTT 60.164 40.000 0.00 0.00 0.00 2.85
205 206 6.487103 CAAAAATATACCCGCAACTCTCTTC 58.513 40.000 0.00 0.00 0.00 2.87
206 207 5.353394 AAATATACCCGCAACTCTCTTCA 57.647 39.130 0.00 0.00 0.00 3.02
207 208 2.674796 ATACCCGCAACTCTCTTCAC 57.325 50.000 0.00 0.00 0.00 3.18
208 209 1.334160 TACCCGCAACTCTCTTCACA 58.666 50.000 0.00 0.00 0.00 3.58
209 210 0.687354 ACCCGCAACTCTCTTCACAT 59.313 50.000 0.00 0.00 0.00 3.21
210 211 1.072331 ACCCGCAACTCTCTTCACATT 59.928 47.619 0.00 0.00 0.00 2.71
211 212 2.154462 CCCGCAACTCTCTTCACATTT 58.846 47.619 0.00 0.00 0.00 2.32
212 213 3.244422 ACCCGCAACTCTCTTCACATTTA 60.244 43.478 0.00 0.00 0.00 1.40
213 214 3.125316 CCCGCAACTCTCTTCACATTTAC 59.875 47.826 0.00 0.00 0.00 2.01
214 215 3.745975 CCGCAACTCTCTTCACATTTACA 59.254 43.478 0.00 0.00 0.00 2.41
215 216 4.143030 CCGCAACTCTCTTCACATTTACAG 60.143 45.833 0.00 0.00 0.00 2.74
216 217 4.686091 CGCAACTCTCTTCACATTTACAGA 59.314 41.667 0.00 0.00 0.00 3.41
217 218 5.349817 CGCAACTCTCTTCACATTTACAGAT 59.650 40.000 0.00 0.00 0.00 2.90
218 219 6.531594 CGCAACTCTCTTCACATTTACAGATA 59.468 38.462 0.00 0.00 0.00 1.98
219 220 7.063426 CGCAACTCTCTTCACATTTACAGATAA 59.937 37.037 0.00 0.00 0.00 1.75
220 221 8.887717 GCAACTCTCTTCACATTTACAGATAAT 58.112 33.333 0.00 0.00 0.00 1.28
222 223 9.606631 AACTCTCTTCACATTTACAGATAATCC 57.393 33.333 0.00 0.00 0.00 3.01
223 224 8.986991 ACTCTCTTCACATTTACAGATAATCCT 58.013 33.333 0.00 0.00 0.00 3.24
224 225 9.829507 CTCTCTTCACATTTACAGATAATCCTT 57.170 33.333 0.00 0.00 0.00 3.36
243 244 7.698163 ATCCTTATCTCCCACAAGATAAACT 57.302 36.000 7.52 0.00 43.92 2.66
244 245 8.798975 ATCCTTATCTCCCACAAGATAAACTA 57.201 34.615 7.52 0.00 43.92 2.24
245 246 8.019656 TCCTTATCTCCCACAAGATAAACTAC 57.980 38.462 7.52 0.00 43.92 2.73
246 247 7.844779 TCCTTATCTCCCACAAGATAAACTACT 59.155 37.037 7.52 0.00 43.92 2.57
247 248 8.145122 CCTTATCTCCCACAAGATAAACTACTC 58.855 40.741 7.52 0.00 43.92 2.59
248 249 8.603898 TTATCTCCCACAAGATAAACTACTCA 57.396 34.615 4.33 0.00 42.47 3.41
249 250 7.682787 ATCTCCCACAAGATAAACTACTCAT 57.317 36.000 0.00 0.00 34.21 2.90
250 251 8.783660 ATCTCCCACAAGATAAACTACTCATA 57.216 34.615 0.00 0.00 34.21 2.15
251 252 8.783660 TCTCCCACAAGATAAACTACTCATAT 57.216 34.615 0.00 0.00 0.00 1.78
252 253 9.877222 TCTCCCACAAGATAAACTACTCATATA 57.123 33.333 0.00 0.00 0.00 0.86
270 271 8.790718 ACTCATATAAATGCATCTTGATGTTCC 58.209 33.333 0.00 0.00 32.76 3.62
271 272 7.809665 TCATATAAATGCATCTTGATGTTCCG 58.190 34.615 0.00 0.00 32.76 4.30
272 273 7.445096 TCATATAAATGCATCTTGATGTTCCGT 59.555 33.333 0.00 0.00 32.76 4.69
273 274 3.770263 AATGCATCTTGATGTTCCGTG 57.230 42.857 0.00 0.00 0.00 4.94
274 275 0.804364 TGCATCTTGATGTTCCGTGC 59.196 50.000 11.61 0.00 0.00 5.34
275 276 0.804364 GCATCTTGATGTTCCGTGCA 59.196 50.000 11.61 0.00 0.00 4.57
276 277 1.199789 GCATCTTGATGTTCCGTGCAA 59.800 47.619 11.61 0.00 0.00 4.08
277 278 2.855180 CATCTTGATGTTCCGTGCAAC 58.145 47.619 0.00 0.00 0.00 4.17
290 291 3.737172 GCAACGCACGGGCATCTT 61.737 61.111 11.77 0.00 41.24 2.40
291 292 2.176546 CAACGCACGGGCATCTTG 59.823 61.111 11.77 3.62 41.24 3.02
292 293 3.737172 AACGCACGGGCATCTTGC 61.737 61.111 11.77 0.00 44.08 4.01
293 294 4.704833 ACGCACGGGCATCTTGCT 62.705 61.111 11.77 0.00 44.28 3.91
294 295 2.511373 CGCACGGGCATCTTGCTA 60.511 61.111 11.77 0.00 44.28 3.49
295 296 2.528743 CGCACGGGCATCTTGCTAG 61.529 63.158 11.77 0.00 44.28 3.42
1438 2869 2.030262 GAGCTCCGGCCTATGCTG 59.970 66.667 16.09 0.00 43.89 4.41
1458 2893 1.940613 GGCGACACTTCAAACACTCTT 59.059 47.619 0.00 0.00 0.00 2.85
1460 2895 2.866762 GCGACACTTCAAACACTCTTCT 59.133 45.455 0.00 0.00 0.00 2.85
1463 2901 5.673818 GCGACACTTCAAACACTCTTCTTTT 60.674 40.000 0.00 0.00 0.00 2.27
1478 2919 3.928727 TCTTTTCATGCTCTGCTTTGG 57.071 42.857 0.00 0.00 0.00 3.28
1519 2983 2.093973 GTGCTCTGCTTTACCTGCTCTA 60.094 50.000 0.00 0.00 0.00 2.43
1520 2984 2.768527 TGCTCTGCTTTACCTGCTCTAT 59.231 45.455 0.00 0.00 0.00 1.98
1521 2985 3.198635 TGCTCTGCTTTACCTGCTCTATT 59.801 43.478 0.00 0.00 0.00 1.73
1522 2986 3.559242 GCTCTGCTTTACCTGCTCTATTG 59.441 47.826 0.00 0.00 0.00 1.90
1523 2987 4.764172 CTCTGCTTTACCTGCTCTATTGT 58.236 43.478 0.00 0.00 0.00 2.71
1524 2988 4.507710 TCTGCTTTACCTGCTCTATTGTG 58.492 43.478 0.00 0.00 0.00 3.33
1525 2989 4.020218 TCTGCTTTACCTGCTCTATTGTGT 60.020 41.667 0.00 0.00 0.00 3.72
1527 2991 4.695455 TGCTTTACCTGCTCTATTGTGTTC 59.305 41.667 0.00 0.00 0.00 3.18
1529 3001 4.530710 TTACCTGCTCTATTGTGTTCGT 57.469 40.909 0.00 0.00 0.00 3.85
1531 3003 3.067106 ACCTGCTCTATTGTGTTCGTTG 58.933 45.455 0.00 0.00 0.00 4.10
1543 3015 1.742831 TGTTCGTTGTGCTCTGCTTTT 59.257 42.857 0.00 0.00 0.00 2.27
1544 3016 2.939756 TGTTCGTTGTGCTCTGCTTTTA 59.060 40.909 0.00 0.00 0.00 1.52
1545 3017 3.375610 TGTTCGTTGTGCTCTGCTTTTAA 59.624 39.130 0.00 0.00 0.00 1.52
1552 3024 2.810852 GTGCTCTGCTTTTAACTGCTCT 59.189 45.455 1.38 0.00 0.00 4.09
1553 3025 3.997021 GTGCTCTGCTTTTAACTGCTCTA 59.003 43.478 1.38 0.00 0.00 2.43
1555 3027 4.872691 TGCTCTGCTTTTAACTGCTCTATC 59.127 41.667 1.38 0.00 0.00 2.08
1556 3028 5.115480 GCTCTGCTTTTAACTGCTCTATCT 58.885 41.667 1.38 0.00 0.00 1.98
1557 3029 5.006552 GCTCTGCTTTTAACTGCTCTATCTG 59.993 44.000 1.38 0.00 0.00 2.90
1558 3030 6.042638 TCTGCTTTTAACTGCTCTATCTGT 57.957 37.500 1.38 0.00 0.00 3.41
1559 3031 7.170393 TCTGCTTTTAACTGCTCTATCTGTA 57.830 36.000 1.38 0.00 0.00 2.74
1562 3034 9.534565 CTGCTTTTAACTGCTCTATCTGTATTA 57.465 33.333 1.38 0.00 0.00 0.98
1674 3186 2.813908 GCCAACGACCGCGAAGAT 60.814 61.111 8.23 0.00 41.64 2.40
1684 3196 1.226575 CGCGAAGATGAGTACGGCA 60.227 57.895 0.00 0.00 0.00 5.69
1699 3211 2.264166 GCAGCAGCCTCGAGAACT 59.736 61.111 15.71 8.14 33.58 3.01
1812 3324 2.711922 GGACTGCCACGACTCCGAT 61.712 63.158 0.00 0.00 39.50 4.18
2146 7559 0.613853 CTTCTACACCTCCGACCCCA 60.614 60.000 0.00 0.00 0.00 4.96
2160 7573 1.198759 ACCCCATCGTTGGCTACACT 61.199 55.000 7.02 0.00 42.15 3.55
2246 7660 7.681679 TCCAGTACATATAGTTTCACCAAACA 58.318 34.615 0.00 0.00 43.98 2.83
2264 7678 9.284594 CACCAAACATTTAAAATATGTACTCCG 57.715 33.333 0.00 0.00 35.26 4.63
2271 7685 2.994186 AATATGTACTCCGGCCGTTT 57.006 45.000 26.12 10.15 0.00 3.60
2282 7696 5.673514 ACTCCGGCCGTTTCTAAATATAAA 58.326 37.500 26.12 0.00 0.00 1.40
2420 7834 2.615912 CAAAAGGATTGGATCGGAGCTC 59.384 50.000 4.71 4.71 0.00 4.09
2464 7878 7.624549 TGATATCTTCATTACTAGGAATGGGC 58.375 38.462 24.54 9.19 37.41 5.36
2478 7892 3.477530 GAATGGGCGGAAGTTTAGCTAT 58.522 45.455 0.00 0.00 0.00 2.97
2612 8026 2.823747 TGCATTCAATTGCTTCTGCTCT 59.176 40.909 16.66 0.00 43.18 4.09
2627 8041 1.879380 TGCTCTTCGTTGGGTTTGATG 59.121 47.619 0.00 0.00 0.00 3.07
2634 8048 3.071479 TCGTTGGGTTTGATGCTCTTAC 58.929 45.455 0.00 0.00 0.00 2.34
2652 8066 7.659799 TGCTCTTACTTTTGAACAGTGCTATAA 59.340 33.333 0.00 0.00 0.00 0.98
2653 8067 7.958025 GCTCTTACTTTTGAACAGTGCTATAAC 59.042 37.037 0.00 0.00 0.00 1.89
2671 8085 0.108585 ACAAACTGACATCGGCCTGT 59.891 50.000 0.00 0.00 0.00 4.00
2724 8138 2.361230 GAAAGCCGGGAAGGGGTG 60.361 66.667 2.18 0.00 41.48 4.61
2735 8149 1.625508 GGAAGGGGTGGGAGAGTACAT 60.626 57.143 0.00 0.00 0.00 2.29
2803 8217 1.632409 ACTCCAGTCATGAAGGTGCAT 59.368 47.619 13.51 0.00 0.00 3.96
2811 8225 3.881688 GTCATGAAGGTGCATAGCTTGAT 59.118 43.478 0.00 0.00 44.18 2.57
2853 8267 3.561310 CCGTAGCATGATGTTGTTAGCAT 59.439 43.478 0.00 0.00 0.00 3.79
2891 8305 5.393569 CGTCAATGTGAGTAAGATGAGGAGT 60.394 44.000 0.00 0.00 0.00 3.85
2906 8320 4.601084 TGAGGAGTAAGGTCTAGGTTCAG 58.399 47.826 0.00 0.00 0.00 3.02
2928 8342 0.250513 AAGAGGCGCTTAGAACCCTG 59.749 55.000 7.64 0.00 34.31 4.45
2966 8380 5.546499 TGTGGTGAAGAGTAGGAGGTAAAAT 59.454 40.000 0.00 0.00 0.00 1.82
2969 8383 6.958192 TGGTGAAGAGTAGGAGGTAAAATAGT 59.042 38.462 0.00 0.00 0.00 2.12
2974 8388 9.418839 GAAGAGTAGGAGGTAAAATAGTAGGAA 57.581 37.037 0.00 0.00 0.00 3.36
3002 8416 5.525745 TGTTGCAAGATTTTCAGTCGAGTTA 59.474 36.000 0.00 0.00 0.00 2.24
3037 8451 0.549169 TTCGGGAGAATTGGACCCCT 60.549 55.000 0.00 0.00 45.39 4.79
3068 8482 5.477510 TGGCATACAAACATTGGATTTCAC 58.522 37.500 0.00 0.00 29.73 3.18
3069 8483 4.562394 GGCATACAAACATTGGATTTCACG 59.438 41.667 0.00 0.00 29.73 4.35
3084 8498 2.038269 CACGGGGTGGATGGAAACG 61.038 63.158 0.00 0.00 0.00 3.60
3085 8499 2.218454 ACGGGGTGGATGGAAACGA 61.218 57.895 0.00 0.00 0.00 3.85
3093 8507 4.275936 GGGTGGATGGAAACGATCTTATTG 59.724 45.833 0.00 0.00 0.00 1.90
3144 8558 1.825191 GGCCATCGGTGATGCACAT 60.825 57.895 0.00 0.00 38.59 3.21
3178 8592 2.565391 TCGGAGTGACTTTAGAATGCCA 59.435 45.455 0.00 0.00 0.00 4.92
3179 8593 3.197766 TCGGAGTGACTTTAGAATGCCAT 59.802 43.478 0.00 0.00 0.00 4.40
3180 8594 4.404394 TCGGAGTGACTTTAGAATGCCATA 59.596 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 5.232463 GCACATCATCATCACCAACTTTTT 58.768 37.500 0.00 0.00 0.00 1.94
91 92 4.322198 GGCACATCATCATCACCAACTTTT 60.322 41.667 0.00 0.00 0.00 2.27
92 93 3.194116 GGCACATCATCATCACCAACTTT 59.806 43.478 0.00 0.00 0.00 2.66
93 94 2.756760 GGCACATCATCATCACCAACTT 59.243 45.455 0.00 0.00 0.00 2.66
94 95 2.025605 AGGCACATCATCATCACCAACT 60.026 45.455 0.00 0.00 0.00 3.16
95 96 2.098607 CAGGCACATCATCATCACCAAC 59.901 50.000 0.00 0.00 0.00 3.77
96 97 2.371306 CAGGCACATCATCATCACCAA 58.629 47.619 0.00 0.00 0.00 3.67
97 98 2.020181 GCAGGCACATCATCATCACCA 61.020 52.381 0.00 0.00 0.00 4.17
98 99 0.666913 GCAGGCACATCATCATCACC 59.333 55.000 0.00 0.00 0.00 4.02
99 100 0.666913 GGCAGGCACATCATCATCAC 59.333 55.000 0.00 0.00 0.00 3.06
100 101 0.256464 TGGCAGGCACATCATCATCA 59.744 50.000 0.00 0.00 0.00 3.07
101 102 1.540267 GATGGCAGGCACATCATCATC 59.460 52.381 0.00 4.15 43.21 2.92
102 103 1.617322 GATGGCAGGCACATCATCAT 58.383 50.000 0.00 0.00 43.21 2.45
103 104 0.466739 GGATGGCAGGCACATCATCA 60.467 55.000 18.08 0.00 45.01 3.07
104 105 0.178998 AGGATGGCAGGCACATCATC 60.179 55.000 18.08 10.61 45.01 2.92
105 106 0.467474 CAGGATGGCAGGCACATCAT 60.467 55.000 18.08 11.97 45.01 2.45
106 107 1.077285 CAGGATGGCAGGCACATCA 60.077 57.895 18.08 0.00 45.01 3.07
107 108 2.487532 GCAGGATGGCAGGCACATC 61.488 63.158 0.00 6.70 43.04 3.06
108 109 2.441532 GCAGGATGGCAGGCACAT 60.442 61.111 0.00 0.00 35.86 3.21
109 110 2.791613 ATTGCAGGATGGCAGGCACA 62.792 55.000 0.00 0.00 45.88 4.57
110 111 0.752743 TATTGCAGGATGGCAGGCAC 60.753 55.000 0.00 0.00 45.88 5.01
111 112 0.186630 ATATTGCAGGATGGCAGGCA 59.813 50.000 0.00 0.00 45.88 4.75
112 113 2.089980 CTATATTGCAGGATGGCAGGC 58.910 52.381 0.00 0.00 45.88 4.85
113 114 2.719739 CCTATATTGCAGGATGGCAGG 58.280 52.381 0.00 0.00 45.88 4.85
114 115 2.089980 GCCTATATTGCAGGATGGCAG 58.910 52.381 12.68 0.00 45.88 4.85
115 116 1.272092 GGCCTATATTGCAGGATGGCA 60.272 52.381 17.22 0.00 43.19 4.92
116 117 1.467920 GGCCTATATTGCAGGATGGC 58.532 55.000 0.00 10.13 34.91 4.40
117 118 1.742761 CGGCCTATATTGCAGGATGG 58.257 55.000 0.00 0.00 34.91 3.51
118 119 1.089920 GCGGCCTATATTGCAGGATG 58.910 55.000 0.00 0.00 34.91 3.51
119 120 0.987294 AGCGGCCTATATTGCAGGAT 59.013 50.000 0.00 0.00 34.91 3.24
120 121 0.764890 AAGCGGCCTATATTGCAGGA 59.235 50.000 0.00 0.00 34.91 3.86
121 122 0.877071 CAAGCGGCCTATATTGCAGG 59.123 55.000 0.00 0.00 36.16 4.85
122 123 1.882912 TCAAGCGGCCTATATTGCAG 58.117 50.000 0.00 0.00 0.00 4.41
123 124 2.038952 AGATCAAGCGGCCTATATTGCA 59.961 45.455 0.00 0.00 0.00 4.08
124 125 2.704572 AGATCAAGCGGCCTATATTGC 58.295 47.619 0.00 0.00 0.00 3.56
125 126 7.598118 CAGATATAGATCAAGCGGCCTATATTG 59.402 40.741 13.40 0.18 35.87 1.90
126 127 7.507277 TCAGATATAGATCAAGCGGCCTATATT 59.493 37.037 13.40 5.42 35.87 1.28
127 128 7.007116 TCAGATATAGATCAAGCGGCCTATAT 58.993 38.462 12.54 12.54 37.45 0.86
128 129 6.263392 GTCAGATATAGATCAAGCGGCCTATA 59.737 42.308 0.00 0.95 34.17 1.31
129 130 5.068460 GTCAGATATAGATCAAGCGGCCTAT 59.932 44.000 0.00 0.00 34.17 2.57
130 131 4.399618 GTCAGATATAGATCAAGCGGCCTA 59.600 45.833 0.00 0.00 34.17 3.93
131 132 3.194542 GTCAGATATAGATCAAGCGGCCT 59.805 47.826 0.00 0.00 34.17 5.19
132 133 3.516615 GTCAGATATAGATCAAGCGGCC 58.483 50.000 0.00 0.00 34.17 6.13
133 134 3.175152 CGTCAGATATAGATCAAGCGGC 58.825 50.000 0.00 0.00 34.17 6.53
134 135 3.440522 TCCGTCAGATATAGATCAAGCGG 59.559 47.826 15.54 15.54 34.17 5.52
135 136 4.686839 TCCGTCAGATATAGATCAAGCG 57.313 45.455 0.00 0.98 34.17 4.68
136 137 6.544197 TCCTATCCGTCAGATATAGATCAAGC 59.456 42.308 0.00 0.00 36.84 4.01
137 138 8.512966 TTCCTATCCGTCAGATATAGATCAAG 57.487 38.462 0.00 0.00 36.84 3.02
138 139 8.329502 TCTTCCTATCCGTCAGATATAGATCAA 58.670 37.037 0.00 0.00 36.84 2.57
139 140 7.862675 TCTTCCTATCCGTCAGATATAGATCA 58.137 38.462 0.00 0.00 36.84 2.92
140 141 8.740123 TTCTTCCTATCCGTCAGATATAGATC 57.260 38.462 0.00 0.00 36.84 2.75
141 142 8.962679 GTTTCTTCCTATCCGTCAGATATAGAT 58.037 37.037 0.00 0.00 36.84 1.98
142 143 8.164733 AGTTTCTTCCTATCCGTCAGATATAGA 58.835 37.037 0.00 0.00 36.84 1.98
143 144 8.343168 AGTTTCTTCCTATCCGTCAGATATAG 57.657 38.462 0.00 0.00 36.84 1.31
144 145 9.976776 ATAGTTTCTTCCTATCCGTCAGATATA 57.023 33.333 0.00 0.00 36.84 0.86
145 146 8.744652 CATAGTTTCTTCCTATCCGTCAGATAT 58.255 37.037 0.00 0.00 36.84 1.63
146 147 7.942894 TCATAGTTTCTTCCTATCCGTCAGATA 59.057 37.037 0.00 0.00 36.33 1.98
147 148 6.778069 TCATAGTTTCTTCCTATCCGTCAGAT 59.222 38.462 0.00 0.00 39.15 2.90
148 149 6.127101 TCATAGTTTCTTCCTATCCGTCAGA 58.873 40.000 0.00 0.00 0.00 3.27
149 150 6.392625 TCATAGTTTCTTCCTATCCGTCAG 57.607 41.667 0.00 0.00 0.00 3.51
150 151 6.978674 ATCATAGTTTCTTCCTATCCGTCA 57.021 37.500 0.00 0.00 0.00 4.35
151 152 9.930693 AATTATCATAGTTTCTTCCTATCCGTC 57.069 33.333 0.00 0.00 0.00 4.79
169 170 8.987890 GCGGGTATATTTTTGCAAAATTATCAT 58.012 29.630 29.09 20.47 31.06 2.45
170 171 7.981789 TGCGGGTATATTTTTGCAAAATTATCA 59.018 29.630 29.09 21.47 31.06 2.15
171 172 8.359060 TGCGGGTATATTTTTGCAAAATTATC 57.641 30.769 29.09 22.41 31.06 1.75
172 173 8.608317 GTTGCGGGTATATTTTTGCAAAATTAT 58.392 29.630 28.58 28.58 43.09 1.28
173 174 7.819900 AGTTGCGGGTATATTTTTGCAAAATTA 59.180 29.630 24.39 23.07 43.09 1.40
174 175 6.652900 AGTTGCGGGTATATTTTTGCAAAATT 59.347 30.769 24.39 21.79 43.09 1.82
175 176 6.169800 AGTTGCGGGTATATTTTTGCAAAAT 58.830 32.000 24.39 16.25 43.09 1.82
176 177 5.542779 AGTTGCGGGTATATTTTTGCAAAA 58.457 33.333 20.46 20.46 43.09 2.44
177 178 5.047660 AGAGTTGCGGGTATATTTTTGCAAA 60.048 36.000 8.05 8.05 43.09 3.68
178 179 4.461081 AGAGTTGCGGGTATATTTTTGCAA 59.539 37.500 0.00 0.00 39.73 4.08
179 180 4.013728 AGAGTTGCGGGTATATTTTTGCA 58.986 39.130 0.00 0.00 0.00 4.08
180 181 4.335594 AGAGAGTTGCGGGTATATTTTTGC 59.664 41.667 0.00 0.00 0.00 3.68
181 182 6.093495 TGAAGAGAGTTGCGGGTATATTTTTG 59.907 38.462 0.00 0.00 0.00 2.44
182 183 6.093633 GTGAAGAGAGTTGCGGGTATATTTTT 59.906 38.462 0.00 0.00 0.00 1.94
183 184 5.585047 GTGAAGAGAGTTGCGGGTATATTTT 59.415 40.000 0.00 0.00 0.00 1.82
184 185 5.116882 GTGAAGAGAGTTGCGGGTATATTT 58.883 41.667 0.00 0.00 0.00 1.40
185 186 4.161565 TGTGAAGAGAGTTGCGGGTATATT 59.838 41.667 0.00 0.00 0.00 1.28
186 187 3.704566 TGTGAAGAGAGTTGCGGGTATAT 59.295 43.478 0.00 0.00 0.00 0.86
187 188 3.093814 TGTGAAGAGAGTTGCGGGTATA 58.906 45.455 0.00 0.00 0.00 1.47
188 189 1.899814 TGTGAAGAGAGTTGCGGGTAT 59.100 47.619 0.00 0.00 0.00 2.73
189 190 1.334160 TGTGAAGAGAGTTGCGGGTA 58.666 50.000 0.00 0.00 0.00 3.69
190 191 0.687354 ATGTGAAGAGAGTTGCGGGT 59.313 50.000 0.00 0.00 0.00 5.28
191 192 1.813513 AATGTGAAGAGAGTTGCGGG 58.186 50.000 0.00 0.00 0.00 6.13
192 193 3.745975 TGTAAATGTGAAGAGAGTTGCGG 59.254 43.478 0.00 0.00 0.00 5.69
193 194 4.686091 TCTGTAAATGTGAAGAGAGTTGCG 59.314 41.667 0.00 0.00 0.00 4.85
194 195 6.734104 ATCTGTAAATGTGAAGAGAGTTGC 57.266 37.500 0.00 0.00 0.00 4.17
196 197 9.606631 GGATTATCTGTAAATGTGAAGAGAGTT 57.393 33.333 0.00 0.00 0.00 3.01
197 198 8.986991 AGGATTATCTGTAAATGTGAAGAGAGT 58.013 33.333 0.00 0.00 0.00 3.24
198 199 9.829507 AAGGATTATCTGTAAATGTGAAGAGAG 57.170 33.333 0.00 0.00 0.00 3.20
217 218 9.225682 AGTTTATCTTGTGGGAGATAAGGATTA 57.774 33.333 7.23 0.00 44.82 1.75
218 219 8.107196 AGTTTATCTTGTGGGAGATAAGGATT 57.893 34.615 7.23 0.00 44.82 3.01
219 220 7.698163 AGTTTATCTTGTGGGAGATAAGGAT 57.302 36.000 7.23 0.00 44.82 3.24
220 221 7.844779 AGTAGTTTATCTTGTGGGAGATAAGGA 59.155 37.037 7.23 0.00 44.82 3.36
221 222 8.024145 AGTAGTTTATCTTGTGGGAGATAAGG 57.976 38.462 7.23 0.00 44.82 2.69
222 223 8.696374 TGAGTAGTTTATCTTGTGGGAGATAAG 58.304 37.037 7.23 0.00 44.82 1.73
223 224 8.603898 TGAGTAGTTTATCTTGTGGGAGATAA 57.396 34.615 3.83 3.83 43.38 1.75
224 225 8.783660 ATGAGTAGTTTATCTTGTGGGAGATA 57.216 34.615 0.00 0.00 37.54 1.98
225 226 7.682787 ATGAGTAGTTTATCTTGTGGGAGAT 57.317 36.000 0.00 0.00 39.59 2.75
226 227 8.783660 ATATGAGTAGTTTATCTTGTGGGAGA 57.216 34.615 0.00 0.00 0.00 3.71
244 245 8.790718 GGAACATCAAGATGCATTTATATGAGT 58.209 33.333 14.86 5.91 42.39 3.41
245 246 7.961283 CGGAACATCAAGATGCATTTATATGAG 59.039 37.037 14.86 7.08 42.39 2.90
246 247 7.445096 ACGGAACATCAAGATGCATTTATATGA 59.555 33.333 14.86 9.71 42.39 2.15
247 248 7.536281 CACGGAACATCAAGATGCATTTATATG 59.464 37.037 9.85 5.48 42.39 1.78
248 249 7.587629 CACGGAACATCAAGATGCATTTATAT 58.412 34.615 9.85 0.00 42.39 0.86
249 250 6.513230 GCACGGAACATCAAGATGCATTTATA 60.513 38.462 9.85 0.00 42.39 0.98
250 251 5.734220 GCACGGAACATCAAGATGCATTTAT 60.734 40.000 9.85 0.00 42.39 1.40
251 252 4.438608 GCACGGAACATCAAGATGCATTTA 60.439 41.667 9.85 0.00 42.39 1.40
252 253 3.674138 GCACGGAACATCAAGATGCATTT 60.674 43.478 9.85 0.00 42.39 2.32
253 254 2.159338 GCACGGAACATCAAGATGCATT 60.159 45.455 9.85 0.00 42.39 3.56
254 255 1.402968 GCACGGAACATCAAGATGCAT 59.597 47.619 9.85 0.00 42.39 3.96
255 256 0.804364 GCACGGAACATCAAGATGCA 59.196 50.000 9.85 0.00 42.39 3.96
256 257 0.804364 TGCACGGAACATCAAGATGC 59.196 50.000 9.85 0.00 42.39 3.91
257 258 2.725759 CGTTGCACGGAACATCAAGATG 60.726 50.000 8.45 8.45 40.19 2.90
258 259 1.464608 CGTTGCACGGAACATCAAGAT 59.535 47.619 2.31 0.00 38.08 2.40
259 260 0.865111 CGTTGCACGGAACATCAAGA 59.135 50.000 2.31 0.00 38.08 3.02
260 261 0.725784 GCGTTGCACGGAACATCAAG 60.726 55.000 10.02 0.00 42.82 3.02
261 262 1.281353 GCGTTGCACGGAACATCAA 59.719 52.632 10.02 0.00 42.82 2.57
262 263 1.889573 TGCGTTGCACGGAACATCA 60.890 52.632 10.02 0.00 39.47 3.07
263 264 2.942879 TGCGTTGCACGGAACATC 59.057 55.556 10.02 0.00 39.47 3.06
273 274 3.737172 AAGATGCCCGTGCGTTGC 61.737 61.111 0.00 0.00 41.78 4.17
274 275 2.176546 CAAGATGCCCGTGCGTTG 59.823 61.111 0.00 0.00 41.78 4.10
275 276 3.737172 GCAAGATGCCCGTGCGTT 61.737 61.111 0.00 0.00 40.20 4.84
278 279 1.026718 AACTAGCAAGATGCCCGTGC 61.027 55.000 6.11 6.11 46.52 5.34
279 280 2.159099 TCTAACTAGCAAGATGCCCGTG 60.159 50.000 0.00 0.00 46.52 4.94
280 281 2.108168 TCTAACTAGCAAGATGCCCGT 58.892 47.619 0.00 0.00 46.52 5.28
281 282 2.474816 GTCTAACTAGCAAGATGCCCG 58.525 52.381 0.00 0.00 46.52 6.13
282 283 2.170607 TGGTCTAACTAGCAAGATGCCC 59.829 50.000 0.00 0.00 46.52 5.36
283 284 3.543680 TGGTCTAACTAGCAAGATGCC 57.456 47.619 0.00 0.00 46.52 4.40
284 285 4.697514 TCATGGTCTAACTAGCAAGATGC 58.302 43.478 0.00 0.00 45.46 3.91
285 286 7.496920 TCATTTCATGGTCTAACTAGCAAGATG 59.503 37.037 0.00 0.00 0.00 2.90
286 287 7.568349 TCATTTCATGGTCTAACTAGCAAGAT 58.432 34.615 0.00 0.00 0.00 2.40
287 288 6.946340 TCATTTCATGGTCTAACTAGCAAGA 58.054 36.000 0.00 0.00 0.00 3.02
288 289 7.615582 TTCATTTCATGGTCTAACTAGCAAG 57.384 36.000 0.00 0.00 0.00 4.01
289 290 7.611467 ACATTCATTTCATGGTCTAACTAGCAA 59.389 33.333 0.00 0.00 0.00 3.91
290 291 7.112122 ACATTCATTTCATGGTCTAACTAGCA 58.888 34.615 0.00 0.00 0.00 3.49
291 292 7.517417 CGACATTCATTTCATGGTCTAACTAGC 60.517 40.741 0.00 0.00 0.00 3.42
292 293 7.706607 TCGACATTCATTTCATGGTCTAACTAG 59.293 37.037 0.00 0.00 0.00 2.57
293 294 7.552459 TCGACATTCATTTCATGGTCTAACTA 58.448 34.615 0.00 0.00 0.00 2.24
294 295 6.406370 TCGACATTCATTTCATGGTCTAACT 58.594 36.000 0.00 0.00 0.00 2.24
295 296 6.662414 TCGACATTCATTTCATGGTCTAAC 57.338 37.500 0.00 0.00 0.00 2.34
1000 2395 4.148825 GGACCGCTGCCTCGTCAT 62.149 66.667 10.22 0.00 0.00 3.06
1297 2728 1.725164 CTCCTCGAAGCCGTTGTTAAC 59.275 52.381 0.00 0.00 37.05 2.01
1299 2730 0.245539 CCTCCTCGAAGCCGTTGTTA 59.754 55.000 0.00 0.00 37.05 2.41
1303 2734 1.186267 AACTCCTCCTCGAAGCCGTT 61.186 55.000 0.00 0.00 37.05 4.44
1433 2864 0.593128 GTTTGAAGTGTCGCCAGCAT 59.407 50.000 0.00 0.00 0.00 3.79
1438 2869 1.583054 AGAGTGTTTGAAGTGTCGCC 58.417 50.000 0.00 0.00 0.00 5.54
1441 2872 6.842163 TGAAAAGAAGAGTGTTTGAAGTGTC 58.158 36.000 0.00 0.00 0.00 3.67
1458 2893 2.029649 GCCAAAGCAGAGCATGAAAAGA 60.030 45.455 0.00 0.00 39.53 2.52
1460 2895 1.965643 AGCCAAAGCAGAGCATGAAAA 59.034 42.857 0.00 0.00 43.56 2.29
1463 2901 1.592400 GCAGCCAAAGCAGAGCATGA 61.592 55.000 0.00 0.00 43.56 3.07
1478 2919 0.516439 GACAAGCAGAACAGAGCAGC 59.484 55.000 0.00 0.00 0.00 5.25
1519 2983 1.002468 GCAGAGCACAACGAACACAAT 60.002 47.619 0.00 0.00 0.00 2.71
1520 2984 0.376852 GCAGAGCACAACGAACACAA 59.623 50.000 0.00 0.00 0.00 3.33
1521 2985 0.461870 AGCAGAGCACAACGAACACA 60.462 50.000 0.00 0.00 0.00 3.72
1522 2986 0.657840 AAGCAGAGCACAACGAACAC 59.342 50.000 0.00 0.00 0.00 3.32
1523 2987 1.378531 AAAGCAGAGCACAACGAACA 58.621 45.000 0.00 0.00 0.00 3.18
1524 2988 2.475200 AAAAGCAGAGCACAACGAAC 57.525 45.000 0.00 0.00 0.00 3.95
1525 2989 3.625764 AGTTAAAAGCAGAGCACAACGAA 59.374 39.130 0.00 0.00 0.00 3.85
1527 2991 3.291585 CAGTTAAAAGCAGAGCACAACG 58.708 45.455 0.00 0.00 0.00 4.10
1529 3001 2.951642 AGCAGTTAAAAGCAGAGCACAA 59.048 40.909 3.57 0.00 0.00 3.33
1531 3003 2.810852 AGAGCAGTTAAAAGCAGAGCAC 59.189 45.455 3.57 0.00 0.00 4.40
1543 3015 8.706322 TGGACATAATACAGATAGAGCAGTTA 57.294 34.615 0.00 0.00 0.00 2.24
1544 3016 7.603180 TGGACATAATACAGATAGAGCAGTT 57.397 36.000 0.00 0.00 0.00 3.16
1545 3017 7.234371 ACATGGACATAATACAGATAGAGCAGT 59.766 37.037 0.00 0.00 0.00 4.40
1626 3138 2.427453 GAGGAACTGCTCGATGAGGTAA 59.573 50.000 0.00 0.00 41.55 2.85
1671 3183 1.142748 GCTGCTGCCGTACTCATCT 59.857 57.895 3.85 0.00 0.00 2.90
1684 3196 1.910772 ACCAGTTCTCGAGGCTGCT 60.911 57.895 23.42 13.26 0.00 4.24
1861 3373 2.134287 GGAGGTAGAGGATGCCGCA 61.134 63.158 0.00 0.00 39.02 5.69
1979 3491 1.613928 TCCCTGTCATACCCGCCAA 60.614 57.895 0.00 0.00 0.00 4.52
2146 7559 3.068307 GGATAGTCAGTGTAGCCAACGAT 59.932 47.826 0.00 0.00 0.00 3.73
2160 7573 4.016444 GTCAGCCCAAAAATGGATAGTCA 58.984 43.478 0.00 0.00 0.00 3.41
2246 7660 5.370679 ACGGCCGGAGTACATATTTTAAAT 58.629 37.500 31.76 0.00 0.00 1.40
2264 7678 8.991243 AAAAGGTTTTATATTTAGAAACGGCC 57.009 30.769 0.00 0.00 34.85 6.13
2420 7834 8.530311 AGATATCATACATTAAGGAGACAGCTG 58.470 37.037 13.48 13.48 0.00 4.24
2456 7870 0.738975 GCTAAACTTCCGCCCATTCC 59.261 55.000 0.00 0.00 0.00 3.01
2461 7875 2.912690 AGATAGCTAAACTTCCGCCC 57.087 50.000 0.00 0.00 0.00 6.13
2464 7878 7.698130 CCAAATTCAAAGATAGCTAAACTTCCG 59.302 37.037 14.10 10.14 0.00 4.30
2478 7892 8.477419 AGGTCAAAGTAATCCAAATTCAAAGA 57.523 30.769 0.00 0.00 0.00 2.52
2554 7968 9.868277 CTGGGAATAAGCACAAAATATTTGTAA 57.132 29.630 8.04 0.00 0.00 2.41
2561 7975 7.896383 AATAGCTGGGAATAAGCACAAAATA 57.104 32.000 0.00 0.00 43.37 1.40
2571 7985 5.268387 TGCAAGGAAAATAGCTGGGAATAA 58.732 37.500 0.00 0.00 0.00 1.40
2577 7991 4.724074 TGAATGCAAGGAAAATAGCTGG 57.276 40.909 0.00 0.00 0.00 4.85
2612 8026 2.270352 AGAGCATCAAACCCAACGAA 57.730 45.000 0.00 0.00 37.82 3.85
2627 8041 4.820284 AGCACTGTTCAAAAGTAAGAGC 57.180 40.909 0.00 0.00 0.00 4.09
2634 8048 8.128582 TCAGTTTGTTATAGCACTGTTCAAAAG 58.871 33.333 6.96 0.00 38.26 2.27
2652 8066 0.108585 ACAGGCCGATGTCAGTTTGT 59.891 50.000 0.00 0.00 0.00 2.83
2653 8067 1.732259 GTACAGGCCGATGTCAGTTTG 59.268 52.381 0.00 0.00 34.56 2.93
2724 8138 8.617290 TTTCAAAACTTTCTATGTACTCTCCC 57.383 34.615 0.00 0.00 0.00 4.30
2803 8217 3.805971 CAGATGCACGAATGATCAAGCTA 59.194 43.478 0.00 0.00 0.00 3.32
2811 8225 3.521560 GGTCTAACAGATGCACGAATGA 58.478 45.455 0.00 0.00 0.00 2.57
2853 8267 0.393448 TTGACGAACATGAACCGGGA 59.607 50.000 6.32 0.00 0.00 5.14
2891 8305 3.693807 TCTTCGCTGAACCTAGACCTTA 58.306 45.455 0.00 0.00 0.00 2.69
2928 8342 2.491152 CACACCGCCATCATTGCC 59.509 61.111 0.00 0.00 0.00 4.52
2940 8354 1.550976 CCTCCTACTCTTCACCACACC 59.449 57.143 0.00 0.00 0.00 4.16
2966 8380 9.691362 GAAAATCTTGCAACAAATTTCCTACTA 57.309 29.630 0.00 0.00 0.00 1.82
2969 8383 8.203485 ACTGAAAATCTTGCAACAAATTTCCTA 58.797 29.630 14.62 3.06 0.00 2.94
2974 8388 6.272318 TCGACTGAAAATCTTGCAACAAATT 58.728 32.000 0.00 0.00 0.00 1.82
3068 8482 0.814010 GATCGTTTCCATCCACCCCG 60.814 60.000 0.00 0.00 0.00 5.73
3069 8483 0.546598 AGATCGTTTCCATCCACCCC 59.453 55.000 0.00 0.00 0.00 4.95
3144 8558 3.819337 GTCACTCCGACTATACTGCCATA 59.181 47.826 0.00 0.00 41.81 2.74


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

AutoCloner maintained by Alex Coulton.