Multiple sequence alignment - TraesCS3A01G362700

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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 TraesCS3A01G362700 chr3A 100.000 2210 0 0 1 2210 611154762 611156971 0.000000e+00 4082
1 TraesCS3A01G362700 chr3A 85.967 1019 110 16 1194 2210 135531468 135530481 0.000000e+00 1059
2 TraesCS3A01G362700 chr3A 86.762 491 58 3 485 975 135532068 135531585 6.940000e-150 540
3 TraesCS3A01G362700 chr3A 92.199 141 11 0 1 141 35392400 35392540 1.340000e-47 200
4 TraesCS3A01G362700 chr3A 88.652 141 16 0 1 141 615096890 615097030 2.920000e-39 172
5 TraesCS3A01G362700 chr3A 90.833 120 10 1 1 120 93995739 93995857 2.270000e-35 159
6 TraesCS3A01G362700 chr7A 97.370 1749 46 0 462 2210 303967882 303969630 0.000000e+00 2976
7 TraesCS3A01G362700 chr2A 96.716 1279 42 0 521 1799 35658763 35657485 0.000000e+00 2130
8 TraesCS3A01G362700 chr2A 98.045 358 6 1 1854 2210 35656978 35656621 2.410000e-174 621
9 TraesCS3A01G362700 chr2A 90.000 140 14 0 1 140 41980528 41980389 4.850000e-42 182
10 TraesCS3A01G362700 chr2A 100.000 74 0 0 1681 1754 35656974 35657047 1.060000e-28 137
11 TraesCS3A01G362700 chr4B 86.569 1020 105 15 1192 2210 574062628 574061640 0.000000e+00 1096
12 TraesCS3A01G362700 chr4B 83.848 421 41 11 547 964 574063150 574062754 2.070000e-100 375
13 TraesCS3A01G362700 chr3B 86.368 1027 105 17 1186 2210 828435941 828436934 0.000000e+00 1088
14 TraesCS3A01G362700 chr3B 82.826 460 78 1 1749 2208 805978500 805978958 5.680000e-111 411
15 TraesCS3A01G362700 chr6B 84.382 461 68 4 1749 2207 615291093 615291551 1.200000e-122 449
16 TraesCS3A01G362700 chr5B 84.052 464 66 5 1749 2208 611863690 611864149 7.240000e-120 440
17 TraesCS3A01G362700 chr5B 83.117 462 74 4 1749 2208 653435375 653434916 3.390000e-113 418
18 TraesCS3A01G362700 chr2D 83.333 270 40 1 1430 1699 587006671 587006407 6.100000e-61 244
19 TraesCS3A01G362700 chr2D 90.071 141 14 0 1 141 293118227 293118367 1.350000e-42 183
20 TraesCS3A01G362700 chr4A 87.333 150 18 1 1 149 201636743 201636892 1.050000e-38 171
21 TraesCS3A01G362700 chr5A 94.340 106 6 0 1 106 398058110 398058005 1.760000e-36 163


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 TraesCS3A01G362700 chr3A 611154762 611156971 2209 False 4082.0 4082 100.0000 1 2210 1 chr3A.!!$F3 2209
1 TraesCS3A01G362700 chr3A 135530481 135532068 1587 True 799.5 1059 86.3645 485 2210 2 chr3A.!!$R1 1725
2 TraesCS3A01G362700 chr7A 303967882 303969630 1748 False 2976.0 2976 97.3700 462 2210 1 chr7A.!!$F1 1748
3 TraesCS3A01G362700 chr2A 35656621 35658763 2142 True 1375.5 2130 97.3805 521 2210 2 chr2A.!!$R2 1689
4 TraesCS3A01G362700 chr4B 574061640 574063150 1510 True 735.5 1096 85.2085 547 2210 2 chr4B.!!$R1 1663
5 TraesCS3A01G362700 chr3B 828435941 828436934 993 False 1088.0 1088 86.3680 1186 2210 1 chr3B.!!$F2 1024

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
217 218 0.466124 AGTCTAGCAGAAATCCGCCC 59.534 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2463 0.53065 CGATAGGCAACAGCGATGGT 60.531 55.0 5.32 0.0 41.41 3.55 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
22 23 5.843019 ATGGAGGAGTAAGAAACCAGAAA 57.157 39.130 0.00 0.00 0.00 2.52
23 24 5.640158 TGGAGGAGTAAGAAACCAGAAAA 57.360 39.130 0.00 0.00 0.00 2.29
24 25 6.008696 TGGAGGAGTAAGAAACCAGAAAAA 57.991 37.500 0.00 0.00 0.00 1.94
41 42 1.612676 AAAACCTTACAACGAGGCCC 58.387 50.000 0.00 0.00 37.84 5.80
42 43 0.604511 AAACCTTACAACGAGGCCCG 60.605 55.000 11.48 11.48 45.44 6.13
43 44 2.818274 CCTTACAACGAGGCCCGC 60.818 66.667 12.78 0.00 43.32 6.13
44 45 3.186047 CTTACAACGAGGCCCGCG 61.186 66.667 4.98 4.98 43.32 6.46
45 46 4.745751 TTACAACGAGGCCCGCGG 62.746 66.667 21.04 21.04 43.32 6.46
108 109 9.288124 TGAGCATTGTTTACATATTCATTTTCG 57.712 29.630 0.00 0.00 0.00 3.46
109 110 8.633075 AGCATTGTTTACATATTCATTTTCGG 57.367 30.769 0.00 0.00 0.00 4.30
110 111 7.222611 AGCATTGTTTACATATTCATTTTCGGC 59.777 33.333 0.00 0.00 0.00 5.54
111 112 7.009999 GCATTGTTTACATATTCATTTTCGGCA 59.990 33.333 0.00 0.00 0.00 5.69
112 113 9.033481 CATTGTTTACATATTCATTTTCGGCAT 57.967 29.630 0.00 0.00 0.00 4.40
113 114 7.984002 TGTTTACATATTCATTTTCGGCATG 57.016 32.000 0.00 0.00 0.00 4.06
114 115 7.542890 TGTTTACATATTCATTTTCGGCATGT 58.457 30.769 0.00 0.00 0.00 3.21
115 116 7.487509 TGTTTACATATTCATTTTCGGCATGTG 59.512 33.333 0.00 0.00 0.00 3.21
116 117 4.935702 ACATATTCATTTTCGGCATGTGG 58.064 39.130 0.00 0.00 0.00 4.17
117 118 2.298411 ATTCATTTTCGGCATGTGGC 57.702 45.000 0.00 0.00 43.74 5.01
129 130 2.594536 TGTGGCAACTCACAGGCA 59.405 55.556 0.00 0.00 42.05 4.75
130 131 1.077140 TGTGGCAACTCACAGGCAA 60.077 52.632 0.00 0.00 42.05 4.52
131 132 0.467844 TGTGGCAACTCACAGGCAAT 60.468 50.000 0.00 0.00 42.05 3.56
132 133 0.675633 GTGGCAACTCACAGGCAATT 59.324 50.000 0.00 0.00 42.20 2.32
133 134 1.069049 GTGGCAACTCACAGGCAATTT 59.931 47.619 0.00 0.00 42.20 1.82
134 135 1.068895 TGGCAACTCACAGGCAATTTG 59.931 47.619 0.00 0.00 37.37 2.32
135 136 1.142474 GCAACTCACAGGCAATTTGC 58.858 50.000 13.04 13.04 44.08 3.68
136 137 1.269936 GCAACTCACAGGCAATTTGCT 60.270 47.619 20.06 4.63 44.28 3.91
137 138 2.030007 GCAACTCACAGGCAATTTGCTA 60.030 45.455 20.06 1.96 44.28 3.49
138 139 3.829948 CAACTCACAGGCAATTTGCTAG 58.170 45.455 20.06 14.78 44.28 3.42
139 140 3.146104 ACTCACAGGCAATTTGCTAGT 57.854 42.857 20.06 15.36 44.28 2.57
140 141 3.490348 ACTCACAGGCAATTTGCTAGTT 58.510 40.909 20.06 3.21 44.28 2.24
141 142 4.651778 ACTCACAGGCAATTTGCTAGTTA 58.348 39.130 20.06 9.95 44.28 2.24
142 143 5.070001 ACTCACAGGCAATTTGCTAGTTAA 58.930 37.500 20.06 8.99 44.28 2.01
143 144 5.711976 ACTCACAGGCAATTTGCTAGTTAAT 59.288 36.000 20.06 0.00 44.28 1.40
144 145 6.209391 ACTCACAGGCAATTTGCTAGTTAATT 59.791 34.615 20.06 0.00 44.28 1.40
145 146 6.991938 TCACAGGCAATTTGCTAGTTAATTT 58.008 32.000 20.06 0.00 44.28 1.82
146 147 8.116651 TCACAGGCAATTTGCTAGTTAATTTA 57.883 30.769 20.06 0.19 44.28 1.40
147 148 8.580720 TCACAGGCAATTTGCTAGTTAATTTAA 58.419 29.630 20.06 0.00 44.28 1.52
148 149 9.202273 CACAGGCAATTTGCTAGTTAATTTAAA 57.798 29.630 20.06 0.00 44.28 1.52
149 150 9.203421 ACAGGCAATTTGCTAGTTAATTTAAAC 57.797 29.630 20.06 0.00 44.28 2.01
150 151 9.423061 CAGGCAATTTGCTAGTTAATTTAAACT 57.577 29.630 20.06 1.81 44.28 2.66
151 152 9.996554 AGGCAATTTGCTAGTTAATTTAAACTT 57.003 25.926 20.06 0.00 44.28 2.66
158 159 9.872757 TTGCTAGTTAATTTAAACTTTGACGAG 57.127 29.630 0.00 0.00 40.20 4.18
159 160 9.263538 TGCTAGTTAATTTAAACTTTGACGAGA 57.736 29.630 9.33 0.00 40.20 4.04
163 164 9.117183 AGTTAATTTAAACTTTGACGAGAAGGT 57.883 29.630 0.00 0.00 36.26 3.50
167 168 9.893305 AATTTAAACTTTGACGAGAAGGTATTG 57.107 29.630 0.00 0.00 0.00 1.90
168 169 8.441312 TTTAAACTTTGACGAGAAGGTATTGT 57.559 30.769 0.00 0.00 0.00 2.71
169 170 6.937436 AAACTTTGACGAGAAGGTATTGTT 57.063 33.333 0.00 0.00 0.00 2.83
170 171 6.937436 AACTTTGACGAGAAGGTATTGTTT 57.063 33.333 0.00 0.00 0.00 2.83
171 172 6.937436 ACTTTGACGAGAAGGTATTGTTTT 57.063 33.333 0.00 0.00 0.00 2.43
172 173 6.725246 ACTTTGACGAGAAGGTATTGTTTTG 58.275 36.000 0.00 0.00 0.00 2.44
173 174 6.317893 ACTTTGACGAGAAGGTATTGTTTTGT 59.682 34.615 0.00 0.00 0.00 2.83
174 175 6.687081 TTGACGAGAAGGTATTGTTTTGTT 57.313 33.333 0.00 0.00 0.00 2.83
175 176 6.055231 TGACGAGAAGGTATTGTTTTGTTG 57.945 37.500 0.00 0.00 0.00 3.33
176 177 5.008217 TGACGAGAAGGTATTGTTTTGTTGG 59.992 40.000 0.00 0.00 0.00 3.77
177 178 4.885325 ACGAGAAGGTATTGTTTTGTTGGT 59.115 37.500 0.00 0.00 0.00 3.67
178 179 5.358725 ACGAGAAGGTATTGTTTTGTTGGTT 59.641 36.000 0.00 0.00 0.00 3.67
179 180 6.127563 ACGAGAAGGTATTGTTTTGTTGGTTT 60.128 34.615 0.00 0.00 0.00 3.27
180 181 6.416750 CGAGAAGGTATTGTTTTGTTGGTTTC 59.583 38.462 0.00 0.00 0.00 2.78
181 182 7.418337 AGAAGGTATTGTTTTGTTGGTTTCT 57.582 32.000 0.00 0.00 0.00 2.52
182 183 7.489160 AGAAGGTATTGTTTTGTTGGTTTCTC 58.511 34.615 0.00 0.00 0.00 2.87
183 184 7.342026 AGAAGGTATTGTTTTGTTGGTTTCTCT 59.658 33.333 0.00 0.00 0.00 3.10
184 185 7.039313 AGGTATTGTTTTGTTGGTTTCTCTC 57.961 36.000 0.00 0.00 0.00 3.20
185 186 6.605594 AGGTATTGTTTTGTTGGTTTCTCTCA 59.394 34.615 0.00 0.00 0.00 3.27
186 187 7.123547 AGGTATTGTTTTGTTGGTTTCTCTCAA 59.876 33.333 0.00 0.00 0.00 3.02
187 188 7.435192 GGTATTGTTTTGTTGGTTTCTCTCAAG 59.565 37.037 0.00 0.00 0.00 3.02
188 189 6.582677 TTGTTTTGTTGGTTTCTCTCAAGA 57.417 33.333 0.00 0.00 0.00 3.02
189 190 6.194796 TGTTTTGTTGGTTTCTCTCAAGAG 57.805 37.500 0.33 0.33 43.36 2.85
190 191 5.125417 TGTTTTGTTGGTTTCTCTCAAGAGG 59.875 40.000 7.17 0.00 42.30 3.69
191 192 4.771114 TTGTTGGTTTCTCTCAAGAGGA 57.229 40.909 7.17 0.00 42.30 3.71
192 193 4.342862 TGTTGGTTTCTCTCAAGAGGAG 57.657 45.455 7.17 0.00 45.49 3.69
216 217 3.019933 CTAGTCTAGCAGAAATCCGCC 57.980 52.381 0.00 0.00 0.00 6.13
217 218 0.466124 AGTCTAGCAGAAATCCGCCC 59.534 55.000 0.00 0.00 0.00 6.13
218 219 0.533085 GTCTAGCAGAAATCCGCCCC 60.533 60.000 0.00 0.00 0.00 5.80
219 220 0.691078 TCTAGCAGAAATCCGCCCCT 60.691 55.000 0.00 0.00 0.00 4.79
220 221 0.533755 CTAGCAGAAATCCGCCCCTG 60.534 60.000 0.00 0.00 0.00 4.45
221 222 0.980754 TAGCAGAAATCCGCCCCTGA 60.981 55.000 0.00 0.00 0.00 3.86
222 223 1.152881 GCAGAAATCCGCCCCTGAT 60.153 57.895 0.00 0.00 0.00 2.90
223 224 0.753111 GCAGAAATCCGCCCCTGATT 60.753 55.000 0.00 0.00 33.97 2.57
224 225 1.476833 GCAGAAATCCGCCCCTGATTA 60.477 52.381 0.00 0.00 32.31 1.75
225 226 2.222027 CAGAAATCCGCCCCTGATTAC 58.778 52.381 0.00 0.00 32.31 1.89
226 227 1.202651 AGAAATCCGCCCCTGATTACG 60.203 52.381 0.00 0.00 32.31 3.18
227 228 0.834612 AAATCCGCCCCTGATTACGA 59.165 50.000 0.00 0.00 32.31 3.43
228 229 0.834612 AATCCGCCCCTGATTACGAA 59.165 50.000 0.00 0.00 30.85 3.85
229 230 1.056660 ATCCGCCCCTGATTACGAAT 58.943 50.000 0.00 0.00 0.00 3.34
230 231 0.834612 TCCGCCCCTGATTACGAATT 59.165 50.000 0.00 0.00 0.00 2.17
231 232 1.202604 TCCGCCCCTGATTACGAATTC 60.203 52.381 0.00 0.00 0.00 2.17
232 233 1.474320 CCGCCCCTGATTACGAATTCA 60.474 52.381 6.22 0.00 0.00 2.57
233 234 2.494059 CGCCCCTGATTACGAATTCAT 58.506 47.619 6.22 0.00 0.00 2.57
234 235 3.556213 CCGCCCCTGATTACGAATTCATA 60.556 47.826 6.22 0.00 0.00 2.15
235 236 4.253685 CGCCCCTGATTACGAATTCATAT 58.746 43.478 6.22 0.00 0.00 1.78
236 237 4.093408 CGCCCCTGATTACGAATTCATATG 59.907 45.833 6.22 0.00 0.00 1.78
237 238 4.142600 GCCCCTGATTACGAATTCATATGC 60.143 45.833 6.22 0.00 0.00 3.14
238 239 5.248640 CCCCTGATTACGAATTCATATGCT 58.751 41.667 6.22 0.00 0.00 3.79
239 240 5.352569 CCCCTGATTACGAATTCATATGCTC 59.647 44.000 6.22 0.00 0.00 4.26
240 241 5.062683 CCCTGATTACGAATTCATATGCTCG 59.937 44.000 15.69 15.69 37.33 5.03
241 242 5.635280 CCTGATTACGAATTCATATGCTCGT 59.365 40.000 22.32 22.32 45.71 4.18
242 243 6.400409 CCTGATTACGAATTCATATGCTCGTG 60.400 42.308 25.02 14.48 43.81 4.35
243 244 5.405269 TGATTACGAATTCATATGCTCGTGG 59.595 40.000 25.02 7.43 43.81 4.94
244 245 3.452755 ACGAATTCATATGCTCGTGGA 57.547 42.857 19.78 0.00 42.54 4.02
245 246 3.995199 ACGAATTCATATGCTCGTGGAT 58.005 40.909 19.78 0.00 42.54 3.41
246 247 3.742882 ACGAATTCATATGCTCGTGGATG 59.257 43.478 19.78 0.00 42.54 3.51
247 248 3.989817 CGAATTCATATGCTCGTGGATGA 59.010 43.478 6.22 0.00 0.00 2.92
248 249 4.448732 CGAATTCATATGCTCGTGGATGAA 59.551 41.667 6.22 0.00 41.27 2.57
249 250 5.613360 CGAATTCATATGCTCGTGGATGAAC 60.613 44.000 6.22 0.00 40.19 3.18
250 251 3.817709 TCATATGCTCGTGGATGAACA 57.182 42.857 1.40 0.00 0.00 3.18
251 252 3.721035 TCATATGCTCGTGGATGAACAG 58.279 45.455 1.40 0.00 0.00 3.16
252 253 3.132824 TCATATGCTCGTGGATGAACAGT 59.867 43.478 1.40 0.00 0.00 3.55
253 254 4.340950 TCATATGCTCGTGGATGAACAGTA 59.659 41.667 1.40 0.00 0.00 2.74
254 255 3.610040 ATGCTCGTGGATGAACAGTAA 57.390 42.857 0.00 0.00 0.00 2.24
255 256 3.394674 TGCTCGTGGATGAACAGTAAA 57.605 42.857 0.00 0.00 0.00 2.01
256 257 3.734463 TGCTCGTGGATGAACAGTAAAA 58.266 40.909 0.00 0.00 0.00 1.52
257 258 4.323417 TGCTCGTGGATGAACAGTAAAAT 58.677 39.130 0.00 0.00 0.00 1.82
258 259 4.759693 TGCTCGTGGATGAACAGTAAAATT 59.240 37.500 0.00 0.00 0.00 1.82
259 260 5.935206 TGCTCGTGGATGAACAGTAAAATTA 59.065 36.000 0.00 0.00 0.00 1.40
260 261 6.428465 TGCTCGTGGATGAACAGTAAAATTAA 59.572 34.615 0.00 0.00 0.00 1.40
261 262 7.041030 TGCTCGTGGATGAACAGTAAAATTAAA 60.041 33.333 0.00 0.00 0.00 1.52
262 263 7.806014 GCTCGTGGATGAACAGTAAAATTAAAA 59.194 33.333 0.00 0.00 0.00 1.52
263 264 9.672086 CTCGTGGATGAACAGTAAAATTAAAAA 57.328 29.630 0.00 0.00 0.00 1.94
264 265 9.453325 TCGTGGATGAACAGTAAAATTAAAAAC 57.547 29.630 0.00 0.00 0.00 2.43
265 266 9.239002 CGTGGATGAACAGTAAAATTAAAAACA 57.761 29.630 0.00 0.00 0.00 2.83
303 304 9.705290 AAAGATTAAAATGATTACAGCCGTTTT 57.295 25.926 0.00 0.00 36.07 2.43
304 305 9.705290 AAGATTAAAATGATTACAGCCGTTTTT 57.295 25.926 0.00 0.00 34.49 1.94
307 308 9.915629 ATTAAAATGATTACAGCCGTTTTTACA 57.084 25.926 0.00 0.00 34.49 2.41
308 309 9.915629 TTAAAATGATTACAGCCGTTTTTACAT 57.084 25.926 0.00 0.00 34.49 2.29
309 310 7.810766 AAATGATTACAGCCGTTTTTACATG 57.189 32.000 0.00 0.00 0.00 3.21
310 311 6.751514 ATGATTACAGCCGTTTTTACATGA 57.248 33.333 0.00 0.00 0.00 3.07
311 312 6.561737 TGATTACAGCCGTTTTTACATGAA 57.438 33.333 0.00 0.00 0.00 2.57
312 313 6.971602 TGATTACAGCCGTTTTTACATGAAA 58.028 32.000 0.00 0.00 0.00 2.69
313 314 7.081349 TGATTACAGCCGTTTTTACATGAAAG 58.919 34.615 0.00 0.00 0.00 2.62
314 315 6.621316 TTACAGCCGTTTTTACATGAAAGA 57.379 33.333 0.00 0.00 0.00 2.52
315 316 5.705609 ACAGCCGTTTTTACATGAAAGAT 57.294 34.783 0.00 0.00 0.00 2.40
316 317 5.460646 ACAGCCGTTTTTACATGAAAGATG 58.539 37.500 0.00 0.00 0.00 2.90
317 318 5.240623 ACAGCCGTTTTTACATGAAAGATGA 59.759 36.000 0.00 0.00 0.00 2.92
318 319 6.148948 CAGCCGTTTTTACATGAAAGATGAA 58.851 36.000 0.00 0.00 0.00 2.57
319 320 6.088085 CAGCCGTTTTTACATGAAAGATGAAC 59.912 38.462 0.00 0.00 0.00 3.18
320 321 5.918011 GCCGTTTTTACATGAAAGATGAACA 59.082 36.000 0.00 0.00 0.00 3.18
321 322 6.088085 GCCGTTTTTACATGAAAGATGAACAG 59.912 38.462 0.00 0.00 0.00 3.16
322 323 7.359595 CCGTTTTTACATGAAAGATGAACAGA 58.640 34.615 0.00 0.00 0.00 3.41
323 324 7.323656 CCGTTTTTACATGAAAGATGAACAGAC 59.676 37.037 0.00 0.00 0.00 3.51
324 325 7.855409 CGTTTTTACATGAAAGATGAACAGACA 59.145 33.333 0.00 0.00 0.00 3.41
325 326 9.515020 GTTTTTACATGAAAGATGAACAGACAA 57.485 29.630 0.00 0.00 0.00 3.18
326 327 9.515020 TTTTTACATGAAAGATGAACAGACAAC 57.485 29.630 0.00 0.00 0.00 3.32
327 328 8.450578 TTTACATGAAAGATGAACAGACAACT 57.549 30.769 0.00 0.00 0.00 3.16
328 329 9.554395 TTTACATGAAAGATGAACAGACAACTA 57.446 29.630 0.00 0.00 0.00 2.24
329 330 7.426929 ACATGAAAGATGAACAGACAACTAC 57.573 36.000 0.00 0.00 0.00 2.73
330 331 6.146184 ACATGAAAGATGAACAGACAACTACG 59.854 38.462 0.00 0.00 0.00 3.51
331 332 5.597806 TGAAAGATGAACAGACAACTACGT 58.402 37.500 0.00 0.00 0.00 3.57
332 333 5.462068 TGAAAGATGAACAGACAACTACGTG 59.538 40.000 0.00 0.00 0.00 4.49
333 334 3.318017 AGATGAACAGACAACTACGTGC 58.682 45.455 0.00 0.00 0.00 5.34
334 335 1.860676 TGAACAGACAACTACGTGCC 58.139 50.000 0.00 0.00 0.00 5.01
335 336 1.411246 TGAACAGACAACTACGTGCCT 59.589 47.619 0.00 0.00 0.00 4.75
336 337 2.624364 TGAACAGACAACTACGTGCCTA 59.376 45.455 0.00 0.00 0.00 3.93
337 338 3.257375 TGAACAGACAACTACGTGCCTAT 59.743 43.478 0.00 0.00 0.00 2.57
338 339 4.460034 TGAACAGACAACTACGTGCCTATA 59.540 41.667 0.00 0.00 0.00 1.31
339 340 5.047872 TGAACAGACAACTACGTGCCTATAA 60.048 40.000 0.00 0.00 0.00 0.98
340 341 5.395682 ACAGACAACTACGTGCCTATAAA 57.604 39.130 0.00 0.00 0.00 1.40
341 342 5.408356 ACAGACAACTACGTGCCTATAAAG 58.592 41.667 0.00 0.00 0.00 1.85
342 343 5.047519 ACAGACAACTACGTGCCTATAAAGT 60.048 40.000 0.00 0.00 0.00 2.66
343 344 5.867716 CAGACAACTACGTGCCTATAAAGTT 59.132 40.000 0.00 0.00 0.00 2.66
344 345 6.367969 CAGACAACTACGTGCCTATAAAGTTT 59.632 38.462 0.00 0.00 0.00 2.66
345 346 6.589139 AGACAACTACGTGCCTATAAAGTTTC 59.411 38.462 0.00 0.00 0.00 2.78
346 347 6.225318 ACAACTACGTGCCTATAAAGTTTCA 58.775 36.000 0.00 0.00 0.00 2.69
347 348 6.877322 ACAACTACGTGCCTATAAAGTTTCAT 59.123 34.615 0.00 0.00 0.00 2.57
348 349 6.903883 ACTACGTGCCTATAAAGTTTCATG 57.096 37.500 0.00 0.00 0.00 3.07
349 350 6.636705 ACTACGTGCCTATAAAGTTTCATGA 58.363 36.000 0.00 0.00 0.00 3.07
350 351 5.796350 ACGTGCCTATAAAGTTTCATGAC 57.204 39.130 0.00 0.00 0.00 3.06
351 352 4.634443 ACGTGCCTATAAAGTTTCATGACC 59.366 41.667 0.00 0.00 0.00 4.02
352 353 4.634004 CGTGCCTATAAAGTTTCATGACCA 59.366 41.667 0.00 0.00 0.00 4.02
353 354 5.296780 CGTGCCTATAAAGTTTCATGACCAT 59.703 40.000 0.00 0.00 0.00 3.55
354 355 6.481976 CGTGCCTATAAAGTTTCATGACCATA 59.518 38.462 0.00 0.00 0.00 2.74
355 356 7.173218 CGTGCCTATAAAGTTTCATGACCATAT 59.827 37.037 0.00 0.00 0.00 1.78
356 357 8.292448 GTGCCTATAAAGTTTCATGACCATATG 58.708 37.037 0.00 0.00 0.00 1.78
357 358 8.217111 TGCCTATAAAGTTTCATGACCATATGA 58.783 33.333 3.65 0.00 35.38 2.15
358 359 8.507249 GCCTATAAAGTTTCATGACCATATGAC 58.493 37.037 3.65 0.00 36.84 3.06
359 360 9.559732 CCTATAAAGTTTCATGACCATATGACA 57.440 33.333 3.65 4.70 36.84 3.58
362 363 7.943079 AAAGTTTCATGACCATATGACATCA 57.057 32.000 3.65 5.57 36.84 3.07
363 364 7.563888 AAGTTTCATGACCATATGACATCAG 57.436 36.000 3.65 0.16 36.84 2.90
364 365 6.060136 AGTTTCATGACCATATGACATCAGG 58.940 40.000 3.65 7.05 36.84 3.86
365 366 4.628963 TCATGACCATATGACATCAGGG 57.371 45.455 3.65 5.10 32.39 4.45
366 367 4.233729 TCATGACCATATGACATCAGGGA 58.766 43.478 3.65 4.87 32.39 4.20
367 368 4.659835 TCATGACCATATGACATCAGGGAA 59.340 41.667 3.65 0.21 32.39 3.97
368 369 4.694760 TGACCATATGACATCAGGGAAG 57.305 45.455 3.65 0.00 0.00 3.46
369 370 3.392285 TGACCATATGACATCAGGGAAGG 59.608 47.826 3.65 0.00 0.00 3.46
370 371 3.392616 GACCATATGACATCAGGGAAGGT 59.607 47.826 3.65 0.00 0.00 3.50
371 372 3.392616 ACCATATGACATCAGGGAAGGTC 59.607 47.826 3.65 0.00 0.00 3.85
372 373 3.392285 CCATATGACATCAGGGAAGGTCA 59.608 47.826 3.65 0.00 43.61 4.02
374 375 3.572632 ATGACATCAGGGAAGGTCATG 57.427 47.619 12.93 0.00 46.15 3.07
375 376 1.561076 TGACATCAGGGAAGGTCATGG 59.439 52.381 0.00 0.00 35.51 3.66
376 377 1.561542 GACATCAGGGAAGGTCATGGT 59.438 52.381 0.00 0.00 0.00 3.55
377 378 2.771943 GACATCAGGGAAGGTCATGGTA 59.228 50.000 0.00 0.00 0.00 3.25
378 379 2.774234 ACATCAGGGAAGGTCATGGTAG 59.226 50.000 0.00 0.00 0.00 3.18
379 380 2.940514 TCAGGGAAGGTCATGGTAGA 57.059 50.000 0.00 0.00 0.00 2.59
380 381 3.199442 TCAGGGAAGGTCATGGTAGAA 57.801 47.619 0.00 0.00 0.00 2.10
381 382 3.526899 TCAGGGAAGGTCATGGTAGAAA 58.473 45.455 0.00 0.00 0.00 2.52
382 383 3.913799 TCAGGGAAGGTCATGGTAGAAAA 59.086 43.478 0.00 0.00 0.00 2.29
383 384 4.352595 TCAGGGAAGGTCATGGTAGAAAAA 59.647 41.667 0.00 0.00 0.00 1.94
403 404 4.599047 AAAAATGAAATCGGTGCTCCAA 57.401 36.364 5.52 0.00 0.00 3.53
404 405 4.599047 AAAATGAAATCGGTGCTCCAAA 57.401 36.364 5.52 0.00 0.00 3.28
405 406 4.599047 AAATGAAATCGGTGCTCCAAAA 57.401 36.364 5.52 0.00 0.00 2.44
406 407 4.806640 AATGAAATCGGTGCTCCAAAAT 57.193 36.364 5.52 0.00 0.00 1.82
407 408 5.913137 AATGAAATCGGTGCTCCAAAATA 57.087 34.783 5.52 0.00 0.00 1.40
408 409 5.913137 ATGAAATCGGTGCTCCAAAATAA 57.087 34.783 5.52 0.00 0.00 1.40
409 410 5.713792 TGAAATCGGTGCTCCAAAATAAA 57.286 34.783 5.52 0.00 0.00 1.40
410 411 6.279513 TGAAATCGGTGCTCCAAAATAAAT 57.720 33.333 5.52 0.00 0.00 1.40
411 412 7.397892 TGAAATCGGTGCTCCAAAATAAATA 57.602 32.000 5.52 0.00 0.00 1.40
412 413 7.831753 TGAAATCGGTGCTCCAAAATAAATAA 58.168 30.769 5.52 0.00 0.00 1.40
413 414 8.307483 TGAAATCGGTGCTCCAAAATAAATAAA 58.693 29.630 5.52 0.00 0.00 1.40
414 415 9.145865 GAAATCGGTGCTCCAAAATAAATAAAA 57.854 29.630 5.52 0.00 0.00 1.52
415 416 9.495572 AAATCGGTGCTCCAAAATAAATAAAAA 57.504 25.926 5.52 0.00 0.00 1.94
416 417 9.665719 AATCGGTGCTCCAAAATAAATAAAAAT 57.334 25.926 5.52 0.00 0.00 1.82
417 418 9.665719 ATCGGTGCTCCAAAATAAATAAAAATT 57.334 25.926 5.52 0.00 0.00 1.82
418 419 9.495572 TCGGTGCTCCAAAATAAATAAAAATTT 57.504 25.926 5.52 0.00 0.00 1.82
443 444 7.631717 AACCTGACTGAAAATAAATAGAGCC 57.368 36.000 0.00 0.00 0.00 4.70
444 445 6.721318 ACCTGACTGAAAATAAATAGAGCCA 58.279 36.000 0.00 0.00 0.00 4.75
445 446 7.175104 ACCTGACTGAAAATAAATAGAGCCAA 58.825 34.615 0.00 0.00 0.00 4.52
446 447 7.669722 ACCTGACTGAAAATAAATAGAGCCAAA 59.330 33.333 0.00 0.00 0.00 3.28
447 448 7.970614 CCTGACTGAAAATAAATAGAGCCAAAC 59.029 37.037 0.00 0.00 0.00 2.93
448 449 8.635765 TGACTGAAAATAAATAGAGCCAAACT 57.364 30.769 0.00 0.00 0.00 2.66
449 450 8.730680 TGACTGAAAATAAATAGAGCCAAACTC 58.269 33.333 0.00 0.00 46.66 3.01
459 460 3.914426 GAGCCAAACTCTAGATTGGGA 57.086 47.619 21.40 0.00 44.95 4.37
460 461 3.536570 GAGCCAAACTCTAGATTGGGAC 58.463 50.000 21.40 9.76 44.95 4.46
516 517 4.388499 GCCCACACCGACACCGAT 62.388 66.667 0.00 0.00 38.22 4.18
559 563 4.204028 ACCAAACCGCAGCCCTGT 62.204 61.111 0.00 0.00 0.00 4.00
743 747 1.685820 GTGCCCAAGACCTTAGCCT 59.314 57.895 0.00 0.00 0.00 4.58
1020 1024 1.147600 GTGGTTGTCCAACTCCGGT 59.852 57.895 0.00 0.00 46.15 5.28
1061 1065 2.097825 GCACTCTGCCCATTCAAGATT 58.902 47.619 0.00 0.00 37.42 2.40
1230 1288 1.466025 TACACTGCTCCCCGAACGTT 61.466 55.000 0.00 0.00 0.00 3.99
1440 1499 1.406539 GCGCCATCATTCACCATCTTT 59.593 47.619 0.00 0.00 0.00 2.52
1901 2413 3.476552 GAGATCCATGTTAATTCGGCCA 58.523 45.455 2.24 0.00 0.00 5.36
1951 2463 2.580815 CCTCGCAGTGCATCCTGA 59.419 61.111 16.83 2.55 34.23 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.843019 TTTCTGGTTTCTTACTCCTCCAT 57.157 39.130 0.00 0.00 0.00 3.41
1 2 5.640158 TTTTCTGGTTTCTTACTCCTCCA 57.360 39.130 0.00 0.00 0.00 3.86
21 22 1.958579 GGGCCTCGTTGTAAGGTTTTT 59.041 47.619 0.84 0.00 36.21 1.94
22 23 1.612676 GGGCCTCGTTGTAAGGTTTT 58.387 50.000 0.84 0.00 36.21 2.43
23 24 0.604511 CGGGCCTCGTTGTAAGGTTT 60.605 55.000 0.84 0.00 36.21 3.27
24 25 1.004200 CGGGCCTCGTTGTAAGGTT 60.004 57.895 0.84 0.00 36.21 3.50
25 26 2.660802 CGGGCCTCGTTGTAAGGT 59.339 61.111 0.84 0.00 36.21 3.50
26 27 2.818274 GCGGGCCTCGTTGTAAGG 60.818 66.667 13.97 0.00 41.72 2.69
27 28 3.186047 CGCGGGCCTCGTTGTAAG 61.186 66.667 7.96 0.00 41.72 2.34
28 29 4.745751 CCGCGGGCCTCGTTGTAA 62.746 66.667 20.10 0.00 41.72 2.41
39 40 2.894565 TTGTAAACGTTGCCGCGGG 61.895 57.895 29.38 12.94 37.70 6.13
40 41 1.723197 GTTGTAAACGTTGCCGCGG 60.723 57.895 24.05 24.05 36.92 6.46
41 42 3.804656 GTTGTAAACGTTGCCGCG 58.195 55.556 0.00 0.00 36.92 6.46
82 83 9.288124 CGAAAATGAATATGTAAACAATGCTCA 57.712 29.630 0.00 0.00 0.00 4.26
83 84 8.745837 CCGAAAATGAATATGTAAACAATGCTC 58.254 33.333 0.00 0.00 0.00 4.26
84 85 7.222611 GCCGAAAATGAATATGTAAACAATGCT 59.777 33.333 0.00 0.00 0.00 3.79
85 86 7.009999 TGCCGAAAATGAATATGTAAACAATGC 59.990 33.333 0.00 0.00 0.00 3.56
86 87 8.404889 TGCCGAAAATGAATATGTAAACAATG 57.595 30.769 0.00 0.00 0.00 2.82
87 88 9.033481 CATGCCGAAAATGAATATGTAAACAAT 57.967 29.630 0.00 0.00 0.00 2.71
88 89 8.031864 ACATGCCGAAAATGAATATGTAAACAA 58.968 29.630 0.00 0.00 0.00 2.83
89 90 7.487509 CACATGCCGAAAATGAATATGTAAACA 59.512 33.333 0.00 0.00 0.00 2.83
90 91 7.043458 CCACATGCCGAAAATGAATATGTAAAC 60.043 37.037 0.00 0.00 0.00 2.01
91 92 6.977502 CCACATGCCGAAAATGAATATGTAAA 59.022 34.615 0.00 0.00 0.00 2.01
92 93 6.502652 CCACATGCCGAAAATGAATATGTAA 58.497 36.000 0.00 0.00 0.00 2.41
93 94 5.507149 GCCACATGCCGAAAATGAATATGTA 60.507 40.000 0.00 0.00 0.00 2.29
94 95 4.737352 GCCACATGCCGAAAATGAATATGT 60.737 41.667 0.00 0.00 0.00 2.29
95 96 3.737266 GCCACATGCCGAAAATGAATATG 59.263 43.478 0.00 0.00 0.00 1.78
96 97 3.384146 TGCCACATGCCGAAAATGAATAT 59.616 39.130 0.00 0.00 40.16 1.28
97 98 2.757314 TGCCACATGCCGAAAATGAATA 59.243 40.909 0.00 0.00 40.16 1.75
98 99 1.549620 TGCCACATGCCGAAAATGAAT 59.450 42.857 0.00 0.00 40.16 2.57
99 100 0.964700 TGCCACATGCCGAAAATGAA 59.035 45.000 0.00 0.00 40.16 2.57
100 101 0.964700 TTGCCACATGCCGAAAATGA 59.035 45.000 0.00 0.00 40.16 2.57
101 102 1.070038 GTTGCCACATGCCGAAAATG 58.930 50.000 0.00 0.00 40.16 2.32
102 103 0.968405 AGTTGCCACATGCCGAAAAT 59.032 45.000 0.00 0.00 40.16 1.82
103 104 0.313672 GAGTTGCCACATGCCGAAAA 59.686 50.000 0.00 0.00 40.16 2.29
104 105 0.821301 TGAGTTGCCACATGCCGAAA 60.821 50.000 0.00 0.00 40.16 3.46
105 106 1.228094 TGAGTTGCCACATGCCGAA 60.228 52.632 0.00 0.00 40.16 4.30
106 107 1.965930 GTGAGTTGCCACATGCCGA 60.966 57.895 0.00 0.00 40.16 5.54
107 108 2.191354 CTGTGAGTTGCCACATGCCG 62.191 60.000 0.00 0.00 44.93 5.69
108 109 1.582968 CTGTGAGTTGCCACATGCC 59.417 57.895 0.00 0.00 44.93 4.40
109 110 1.582968 CCTGTGAGTTGCCACATGC 59.417 57.895 0.00 0.00 44.93 4.06
110 111 1.174078 TGCCTGTGAGTTGCCACATG 61.174 55.000 0.00 0.00 44.93 3.21
111 112 0.467844 TTGCCTGTGAGTTGCCACAT 60.468 50.000 0.00 0.00 44.93 3.21
112 113 0.467844 ATTGCCTGTGAGTTGCCACA 60.468 50.000 0.00 0.00 43.98 4.17
113 114 0.675633 AATTGCCTGTGAGTTGCCAC 59.324 50.000 0.00 0.00 37.55 5.01
114 115 1.068895 CAAATTGCCTGTGAGTTGCCA 59.931 47.619 0.00 0.00 0.00 4.92
115 116 1.787012 CAAATTGCCTGTGAGTTGCC 58.213 50.000 0.00 0.00 0.00 4.52
116 117 1.142474 GCAAATTGCCTGTGAGTTGC 58.858 50.000 6.72 0.00 37.42 4.17
117 118 2.806608 AGCAAATTGCCTGTGAGTTG 57.193 45.000 15.04 0.00 46.52 3.16
118 119 3.490348 ACTAGCAAATTGCCTGTGAGTT 58.510 40.909 15.04 0.00 46.52 3.01
119 120 3.146104 ACTAGCAAATTGCCTGTGAGT 57.854 42.857 15.04 7.66 46.52 3.41
120 121 5.627499 TTAACTAGCAAATTGCCTGTGAG 57.373 39.130 15.04 7.06 46.52 3.51
121 122 6.588719 AATTAACTAGCAAATTGCCTGTGA 57.411 33.333 15.04 4.19 46.52 3.58
122 123 8.755696 TTAAATTAACTAGCAAATTGCCTGTG 57.244 30.769 15.04 5.08 46.52 3.66
123 124 9.203421 GTTTAAATTAACTAGCAAATTGCCTGT 57.797 29.630 15.04 10.74 46.52 4.00
124 125 9.423061 AGTTTAAATTAACTAGCAAATTGCCTG 57.577 29.630 15.04 10.08 36.08 4.85
125 126 9.996554 AAGTTTAAATTAACTAGCAAATTGCCT 57.003 25.926 15.04 4.83 39.74 4.75
132 133 9.872757 CTCGTCAAAGTTTAAATTAACTAGCAA 57.127 29.630 0.00 0.00 37.37 3.91
133 134 9.263538 TCTCGTCAAAGTTTAAATTAACTAGCA 57.736 29.630 0.00 0.00 37.37 3.49
137 138 9.117183 ACCTTCTCGTCAAAGTTTAAATTAACT 57.883 29.630 0.00 0.00 39.97 2.24
141 142 9.893305 CAATACCTTCTCGTCAAAGTTTAAATT 57.107 29.630 0.00 0.00 0.00 1.82
142 143 9.063615 ACAATACCTTCTCGTCAAAGTTTAAAT 57.936 29.630 0.00 0.00 0.00 1.40
143 144 8.441312 ACAATACCTTCTCGTCAAAGTTTAAA 57.559 30.769 0.00 0.00 0.00 1.52
144 145 8.441312 AACAATACCTTCTCGTCAAAGTTTAA 57.559 30.769 0.00 0.00 0.00 1.52
145 146 8.441312 AAACAATACCTTCTCGTCAAAGTTTA 57.559 30.769 0.00 0.00 0.00 2.01
146 147 6.937436 AACAATACCTTCTCGTCAAAGTTT 57.063 33.333 0.00 0.00 0.00 2.66
147 148 6.937436 AAACAATACCTTCTCGTCAAAGTT 57.063 33.333 0.00 0.00 0.00 2.66
148 149 6.317893 ACAAAACAATACCTTCTCGTCAAAGT 59.682 34.615 0.00 0.00 0.00 2.66
149 150 6.725246 ACAAAACAATACCTTCTCGTCAAAG 58.275 36.000 0.00 0.00 0.00 2.77
150 151 6.687081 ACAAAACAATACCTTCTCGTCAAA 57.313 33.333 0.00 0.00 0.00 2.69
151 152 6.459024 CCAACAAAACAATACCTTCTCGTCAA 60.459 38.462 0.00 0.00 0.00 3.18
152 153 5.008217 CCAACAAAACAATACCTTCTCGTCA 59.992 40.000 0.00 0.00 0.00 4.35
153 154 5.008316 ACCAACAAAACAATACCTTCTCGTC 59.992 40.000 0.00 0.00 0.00 4.20
154 155 4.885325 ACCAACAAAACAATACCTTCTCGT 59.115 37.500 0.00 0.00 0.00 4.18
155 156 5.432885 ACCAACAAAACAATACCTTCTCG 57.567 39.130 0.00 0.00 0.00 4.04
156 157 7.489160 AGAAACCAACAAAACAATACCTTCTC 58.511 34.615 0.00 0.00 0.00 2.87
157 158 7.342026 AGAGAAACCAACAAAACAATACCTTCT 59.658 33.333 0.00 0.00 0.00 2.85
158 159 7.489160 AGAGAAACCAACAAAACAATACCTTC 58.511 34.615 0.00 0.00 0.00 3.46
159 160 7.123547 TGAGAGAAACCAACAAAACAATACCTT 59.876 33.333 0.00 0.00 0.00 3.50
160 161 6.605594 TGAGAGAAACCAACAAAACAATACCT 59.394 34.615 0.00 0.00 0.00 3.08
161 162 6.801575 TGAGAGAAACCAACAAAACAATACC 58.198 36.000 0.00 0.00 0.00 2.73
162 163 8.188139 TCTTGAGAGAAACCAACAAAACAATAC 58.812 33.333 0.00 0.00 0.00 1.89
163 164 8.287439 TCTTGAGAGAAACCAACAAAACAATA 57.713 30.769 0.00 0.00 0.00 1.90
164 165 7.169158 TCTTGAGAGAAACCAACAAAACAAT 57.831 32.000 0.00 0.00 0.00 2.71
165 166 6.350110 CCTCTTGAGAGAAACCAACAAAACAA 60.350 38.462 9.55 0.00 44.74 2.83
166 167 5.125417 CCTCTTGAGAGAAACCAACAAAACA 59.875 40.000 9.55 0.00 44.74 2.83
167 168 5.357032 TCCTCTTGAGAGAAACCAACAAAAC 59.643 40.000 9.55 0.00 44.74 2.43
168 169 5.505780 TCCTCTTGAGAGAAACCAACAAAA 58.494 37.500 9.55 0.00 44.74 2.44
169 170 5.104527 TCTCCTCTTGAGAGAAACCAACAAA 60.105 40.000 9.55 0.00 45.29 2.83
170 171 4.408921 TCTCCTCTTGAGAGAAACCAACAA 59.591 41.667 9.55 0.00 45.29 2.83
171 172 3.967326 TCTCCTCTTGAGAGAAACCAACA 59.033 43.478 9.55 0.00 45.29 3.33
172 173 4.608948 TCTCCTCTTGAGAGAAACCAAC 57.391 45.455 9.55 0.00 45.29 3.77
182 183 5.947228 CTAGACTAGCATCTCCTCTTGAG 57.053 47.826 0.00 0.00 42.90 3.02
205 206 2.222027 GTAATCAGGGGCGGATTTCTG 58.778 52.381 3.55 0.00 36.45 3.02
206 207 1.202651 CGTAATCAGGGGCGGATTTCT 60.203 52.381 3.55 0.00 36.45 2.52
207 208 1.202604 TCGTAATCAGGGGCGGATTTC 60.203 52.381 3.55 0.00 36.45 2.17
208 209 0.834612 TCGTAATCAGGGGCGGATTT 59.165 50.000 3.55 0.00 36.45 2.17
209 210 0.834612 TTCGTAATCAGGGGCGGATT 59.165 50.000 0.00 0.00 38.46 3.01
210 211 1.056660 ATTCGTAATCAGGGGCGGAT 58.943 50.000 0.00 0.00 0.00 4.18
211 212 0.834612 AATTCGTAATCAGGGGCGGA 59.165 50.000 0.00 0.00 0.00 5.54
212 213 1.226746 GAATTCGTAATCAGGGGCGG 58.773 55.000 0.00 0.00 0.00 6.13
213 214 1.948104 TGAATTCGTAATCAGGGGCG 58.052 50.000 0.04 0.00 0.00 6.13
214 215 4.142600 GCATATGAATTCGTAATCAGGGGC 60.143 45.833 11.33 4.10 0.00 5.80
215 216 5.248640 AGCATATGAATTCGTAATCAGGGG 58.751 41.667 11.33 0.00 0.00 4.79
216 217 5.062683 CGAGCATATGAATTCGTAATCAGGG 59.937 44.000 11.33 0.06 0.00 4.45
217 218 5.635280 ACGAGCATATGAATTCGTAATCAGG 59.365 40.000 21.16 4.64 43.64 3.86
218 219 6.400409 CCACGAGCATATGAATTCGTAATCAG 60.400 42.308 21.70 13.35 43.63 2.90
219 220 5.405269 CCACGAGCATATGAATTCGTAATCA 59.595 40.000 21.70 0.00 43.63 2.57
220 221 5.633601 TCCACGAGCATATGAATTCGTAATC 59.366 40.000 21.70 8.98 43.63 1.75
221 222 5.538118 TCCACGAGCATATGAATTCGTAAT 58.462 37.500 21.70 1.42 43.63 1.89
222 223 4.939271 TCCACGAGCATATGAATTCGTAA 58.061 39.130 21.70 14.21 43.63 3.18
223 224 4.577834 TCCACGAGCATATGAATTCGTA 57.422 40.909 21.70 9.78 43.63 3.43
224 225 3.452755 TCCACGAGCATATGAATTCGT 57.547 42.857 18.54 18.54 46.07 3.85
225 226 3.989817 TCATCCACGAGCATATGAATTCG 59.010 43.478 6.97 13.90 38.88 3.34
226 227 5.237127 TGTTCATCCACGAGCATATGAATTC 59.763 40.000 6.97 0.00 39.70 2.17
227 228 5.125356 TGTTCATCCACGAGCATATGAATT 58.875 37.500 6.97 0.00 39.70 2.17
228 229 4.707105 TGTTCATCCACGAGCATATGAAT 58.293 39.130 6.97 0.00 39.70 2.57
229 230 4.122046 CTGTTCATCCACGAGCATATGAA 58.878 43.478 6.97 0.00 36.32 2.57
230 231 3.132824 ACTGTTCATCCACGAGCATATGA 59.867 43.478 6.97 0.00 0.00 2.15
231 232 3.461061 ACTGTTCATCCACGAGCATATG 58.539 45.455 0.00 0.00 0.00 1.78
232 233 3.827008 ACTGTTCATCCACGAGCATAT 57.173 42.857 0.00 0.00 0.00 1.78
233 234 4.729227 TTACTGTTCATCCACGAGCATA 57.271 40.909 0.00 0.00 0.00 3.14
234 235 3.610040 TTACTGTTCATCCACGAGCAT 57.390 42.857 0.00 0.00 0.00 3.79
235 236 3.394674 TTTACTGTTCATCCACGAGCA 57.605 42.857 0.00 0.00 0.00 4.26
236 237 4.946784 ATTTTACTGTTCATCCACGAGC 57.053 40.909 0.00 0.00 0.00 5.03
237 238 9.672086 TTTTTAATTTTACTGTTCATCCACGAG 57.328 29.630 0.00 0.00 0.00 4.18
238 239 9.453325 GTTTTTAATTTTACTGTTCATCCACGA 57.547 29.630 0.00 0.00 0.00 4.35
239 240 9.239002 TGTTTTTAATTTTACTGTTCATCCACG 57.761 29.630 0.00 0.00 0.00 4.94
277 278 9.705290 AAAACGGCTGTAATCATTTTAATCTTT 57.295 25.926 0.00 0.00 0.00 2.52
278 279 9.705290 AAAAACGGCTGTAATCATTTTAATCTT 57.295 25.926 0.00 0.00 0.00 2.40
281 282 9.915629 TGTAAAAACGGCTGTAATCATTTTAAT 57.084 25.926 11.84 0.00 0.00 1.40
282 283 9.915629 ATGTAAAAACGGCTGTAATCATTTTAA 57.084 25.926 11.84 5.79 0.00 1.52
283 284 9.347934 CATGTAAAAACGGCTGTAATCATTTTA 57.652 29.630 0.00 3.35 0.00 1.52
284 285 8.085296 TCATGTAAAAACGGCTGTAATCATTTT 58.915 29.630 0.00 4.40 0.00 1.82
285 286 7.598278 TCATGTAAAAACGGCTGTAATCATTT 58.402 30.769 0.00 0.00 0.00 2.32
286 287 7.151999 TCATGTAAAAACGGCTGTAATCATT 57.848 32.000 0.00 0.00 0.00 2.57
287 288 6.751514 TCATGTAAAAACGGCTGTAATCAT 57.248 33.333 0.00 0.00 0.00 2.45
288 289 6.561737 TTCATGTAAAAACGGCTGTAATCA 57.438 33.333 0.00 0.00 0.00 2.57
289 290 7.302524 TCTTTCATGTAAAAACGGCTGTAATC 58.697 34.615 0.00 0.00 0.00 1.75
290 291 7.209471 TCTTTCATGTAAAAACGGCTGTAAT 57.791 32.000 0.00 0.00 0.00 1.89
291 292 6.621316 TCTTTCATGTAAAAACGGCTGTAA 57.379 33.333 0.00 0.00 0.00 2.41
292 293 6.428465 TCATCTTTCATGTAAAAACGGCTGTA 59.572 34.615 0.00 0.00 0.00 2.74
293 294 5.240623 TCATCTTTCATGTAAAAACGGCTGT 59.759 36.000 0.00 0.00 0.00 4.40
294 295 5.698832 TCATCTTTCATGTAAAAACGGCTG 58.301 37.500 0.00 0.00 0.00 4.85
295 296 5.957842 TCATCTTTCATGTAAAAACGGCT 57.042 34.783 0.00 0.00 0.00 5.52
296 297 5.918011 TGTTCATCTTTCATGTAAAAACGGC 59.082 36.000 0.00 0.00 0.00 5.68
297 298 7.323656 GTCTGTTCATCTTTCATGTAAAAACGG 59.676 37.037 0.00 0.41 0.00 4.44
298 299 7.855409 TGTCTGTTCATCTTTCATGTAAAAACG 59.145 33.333 0.00 0.00 0.00 3.60
299 300 9.515020 TTGTCTGTTCATCTTTCATGTAAAAAC 57.485 29.630 0.00 0.00 0.00 2.43
300 301 9.515020 GTTGTCTGTTCATCTTTCATGTAAAAA 57.485 29.630 0.00 0.00 0.00 1.94
301 302 8.902806 AGTTGTCTGTTCATCTTTCATGTAAAA 58.097 29.630 0.00 0.00 0.00 1.52
302 303 8.450578 AGTTGTCTGTTCATCTTTCATGTAAA 57.549 30.769 0.00 0.00 0.00 2.01
303 304 8.988934 GTAGTTGTCTGTTCATCTTTCATGTAA 58.011 33.333 0.00 0.00 0.00 2.41
304 305 7.328493 CGTAGTTGTCTGTTCATCTTTCATGTA 59.672 37.037 0.00 0.00 0.00 2.29
305 306 6.146184 CGTAGTTGTCTGTTCATCTTTCATGT 59.854 38.462 0.00 0.00 0.00 3.21
306 307 6.146184 ACGTAGTTGTCTGTTCATCTTTCATG 59.854 38.462 0.00 0.00 37.78 3.07
307 308 6.146184 CACGTAGTTGTCTGTTCATCTTTCAT 59.854 38.462 0.00 0.00 41.61 2.57
308 309 5.462068 CACGTAGTTGTCTGTTCATCTTTCA 59.538 40.000 0.00 0.00 41.61 2.69
309 310 5.612709 GCACGTAGTTGTCTGTTCATCTTTC 60.613 44.000 0.00 0.00 41.61 2.62
310 311 4.211374 GCACGTAGTTGTCTGTTCATCTTT 59.789 41.667 0.00 0.00 41.61 2.52
311 312 3.741344 GCACGTAGTTGTCTGTTCATCTT 59.259 43.478 0.00 0.00 41.61 2.40
312 313 3.318017 GCACGTAGTTGTCTGTTCATCT 58.682 45.455 0.00 0.00 41.61 2.90
313 314 2.412089 GGCACGTAGTTGTCTGTTCATC 59.588 50.000 0.00 0.00 41.61 2.92
314 315 2.037251 AGGCACGTAGTTGTCTGTTCAT 59.963 45.455 0.00 0.00 41.61 2.57
315 316 1.411246 AGGCACGTAGTTGTCTGTTCA 59.589 47.619 0.00 0.00 41.61 3.18
316 317 2.150397 AGGCACGTAGTTGTCTGTTC 57.850 50.000 0.00 0.00 41.61 3.18
317 318 3.955650 ATAGGCACGTAGTTGTCTGTT 57.044 42.857 0.00 0.00 41.61 3.16
318 319 5.047519 ACTTTATAGGCACGTAGTTGTCTGT 60.048 40.000 0.00 0.00 41.61 3.41
319 320 5.408356 ACTTTATAGGCACGTAGTTGTCTG 58.592 41.667 0.00 0.00 41.61 3.51
320 321 5.656213 ACTTTATAGGCACGTAGTTGTCT 57.344 39.130 0.00 0.00 41.61 3.41
321 322 6.366877 TGAAACTTTATAGGCACGTAGTTGTC 59.633 38.462 0.00 0.00 41.61 3.18
322 323 6.225318 TGAAACTTTATAGGCACGTAGTTGT 58.775 36.000 0.00 0.00 41.61 3.32
323 324 6.715344 TGAAACTTTATAGGCACGTAGTTG 57.285 37.500 0.00 0.00 41.61 3.16
324 325 7.064253 GTCATGAAACTTTATAGGCACGTAGTT 59.936 37.037 0.00 0.00 41.61 2.24
326 327 6.018994 GGTCATGAAACTTTATAGGCACGTAG 60.019 42.308 0.00 0.00 0.00 3.51
327 328 5.813672 GGTCATGAAACTTTATAGGCACGTA 59.186 40.000 0.00 0.00 0.00 3.57
328 329 4.634443 GGTCATGAAACTTTATAGGCACGT 59.366 41.667 0.00 0.00 0.00 4.49
329 330 4.634004 TGGTCATGAAACTTTATAGGCACG 59.366 41.667 0.00 0.00 0.00 5.34
330 331 6.699575 ATGGTCATGAAACTTTATAGGCAC 57.300 37.500 0.00 0.00 0.00 5.01
331 332 8.217111 TCATATGGTCATGAAACTTTATAGGCA 58.783 33.333 0.00 0.00 32.01 4.75
332 333 8.507249 GTCATATGGTCATGAAACTTTATAGGC 58.493 37.037 0.00 0.00 36.71 3.93
333 334 9.559732 TGTCATATGGTCATGAAACTTTATAGG 57.440 33.333 0.00 0.00 36.71 2.57
336 337 9.631257 TGATGTCATATGGTCATGAAACTTTAT 57.369 29.630 15.34 0.00 36.71 1.40
337 338 9.112725 CTGATGTCATATGGTCATGAAACTTTA 57.887 33.333 15.34 0.00 36.71 1.85
338 339 7.067859 CCTGATGTCATATGGTCATGAAACTTT 59.932 37.037 15.34 0.00 36.71 2.66
339 340 6.544931 CCTGATGTCATATGGTCATGAAACTT 59.455 38.462 15.34 0.00 36.71 2.66
340 341 6.060136 CCTGATGTCATATGGTCATGAAACT 58.940 40.000 15.34 0.00 36.71 2.66
341 342 5.240183 CCCTGATGTCATATGGTCATGAAAC 59.760 44.000 15.34 0.00 36.71 2.78
342 343 5.132480 TCCCTGATGTCATATGGTCATGAAA 59.868 40.000 15.34 0.00 36.71 2.69
343 344 4.659835 TCCCTGATGTCATATGGTCATGAA 59.340 41.667 15.34 6.42 36.71 2.57
344 345 4.233729 TCCCTGATGTCATATGGTCATGA 58.766 43.478 15.34 0.00 32.50 3.07
345 346 4.628963 TCCCTGATGTCATATGGTCATG 57.371 45.455 15.34 9.21 0.00 3.07
346 347 4.042560 CCTTCCCTGATGTCATATGGTCAT 59.957 45.833 2.13 8.26 0.00 3.06
347 348 3.392285 CCTTCCCTGATGTCATATGGTCA 59.608 47.826 2.13 3.58 0.00 4.02
348 349 3.392616 ACCTTCCCTGATGTCATATGGTC 59.607 47.826 2.13 0.20 0.00 4.02
349 350 3.392616 GACCTTCCCTGATGTCATATGGT 59.607 47.826 2.13 0.00 0.00 3.55
350 351 3.392285 TGACCTTCCCTGATGTCATATGG 59.608 47.826 2.13 0.00 33.09 2.74
351 352 4.694760 TGACCTTCCCTGATGTCATATG 57.305 45.455 0.00 0.00 33.09 1.78
352 353 4.042560 CCATGACCTTCCCTGATGTCATAT 59.957 45.833 3.90 0.00 44.35 1.78
353 354 3.392285 CCATGACCTTCCCTGATGTCATA 59.608 47.826 3.90 0.00 44.35 2.15
354 355 2.174210 CCATGACCTTCCCTGATGTCAT 59.826 50.000 0.00 0.00 46.41 3.06
355 356 1.561076 CCATGACCTTCCCTGATGTCA 59.439 52.381 0.00 0.00 41.52 3.58
356 357 1.561542 ACCATGACCTTCCCTGATGTC 59.438 52.381 0.00 0.00 0.00 3.06
357 358 1.673767 ACCATGACCTTCCCTGATGT 58.326 50.000 0.00 0.00 0.00 3.06
358 359 3.041211 TCTACCATGACCTTCCCTGATG 58.959 50.000 0.00 0.00 0.00 3.07
359 360 3.421394 TCTACCATGACCTTCCCTGAT 57.579 47.619 0.00 0.00 0.00 2.90
360 361 2.940514 TCTACCATGACCTTCCCTGA 57.059 50.000 0.00 0.00 0.00 3.86
361 362 4.301072 TTTTCTACCATGACCTTCCCTG 57.699 45.455 0.00 0.00 0.00 4.45
382 383 4.599047 TTGGAGCACCGATTTCATTTTT 57.401 36.364 0.00 0.00 39.42 1.94
383 384 4.599047 TTTGGAGCACCGATTTCATTTT 57.401 36.364 0.00 0.00 39.42 1.82
384 385 4.599047 TTTTGGAGCACCGATTTCATTT 57.401 36.364 0.00 0.00 39.42 2.32
385 386 4.806640 ATTTTGGAGCACCGATTTCATT 57.193 36.364 0.00 0.00 39.42 2.57
386 387 5.913137 TTATTTTGGAGCACCGATTTCAT 57.087 34.783 0.00 0.00 39.42 2.57
387 388 5.713792 TTTATTTTGGAGCACCGATTTCA 57.286 34.783 0.00 0.00 39.42 2.69
388 389 8.696410 TTTATTTATTTTGGAGCACCGATTTC 57.304 30.769 0.00 0.00 39.42 2.17
389 390 9.495572 TTTTTATTTATTTTGGAGCACCGATTT 57.504 25.926 0.00 0.00 39.42 2.17
390 391 9.665719 ATTTTTATTTATTTTGGAGCACCGATT 57.334 25.926 0.00 0.00 39.42 3.34
391 392 9.665719 AATTTTTATTTATTTTGGAGCACCGAT 57.334 25.926 0.00 0.00 39.42 4.18
392 393 9.495572 AAATTTTTATTTATTTTGGAGCACCGA 57.504 25.926 0.00 0.00 39.42 4.69
417 418 9.174166 GGCTCTATTTATTTTCAGTCAGGTTAA 57.826 33.333 0.00 0.00 0.00 2.01
418 419 8.325787 TGGCTCTATTTATTTTCAGTCAGGTTA 58.674 33.333 0.00 0.00 0.00 2.85
419 420 7.175104 TGGCTCTATTTATTTTCAGTCAGGTT 58.825 34.615 0.00 0.00 0.00 3.50
420 421 6.721318 TGGCTCTATTTATTTTCAGTCAGGT 58.279 36.000 0.00 0.00 0.00 4.00
421 422 7.630242 TTGGCTCTATTTATTTTCAGTCAGG 57.370 36.000 0.00 0.00 0.00 3.86
422 423 8.734386 AGTTTGGCTCTATTTATTTTCAGTCAG 58.266 33.333 0.00 0.00 0.00 3.51
423 424 8.635765 AGTTTGGCTCTATTTATTTTCAGTCA 57.364 30.769 0.00 0.00 0.00 3.41
439 440 3.055094 TGTCCCAATCTAGAGTTTGGCTC 60.055 47.826 16.68 12.42 41.35 4.70
440 441 2.912956 TGTCCCAATCTAGAGTTTGGCT 59.087 45.455 16.68 0.00 41.35 4.75
441 442 3.350219 TGTCCCAATCTAGAGTTTGGC 57.650 47.619 16.68 7.42 41.35 4.52
442 443 3.684788 CGTTGTCCCAATCTAGAGTTTGG 59.315 47.826 15.56 15.56 41.99 3.28
443 444 3.125316 GCGTTGTCCCAATCTAGAGTTTG 59.875 47.826 0.00 0.00 0.00 2.93
444 445 3.008049 AGCGTTGTCCCAATCTAGAGTTT 59.992 43.478 0.00 0.00 0.00 2.66
445 446 2.567615 AGCGTTGTCCCAATCTAGAGTT 59.432 45.455 0.00 0.00 0.00 3.01
446 447 2.093973 CAGCGTTGTCCCAATCTAGAGT 60.094 50.000 0.00 0.00 0.00 3.24
447 448 2.544685 CAGCGTTGTCCCAATCTAGAG 58.455 52.381 0.00 0.00 0.00 2.43
448 449 1.207089 CCAGCGTTGTCCCAATCTAGA 59.793 52.381 0.00 0.00 0.00 2.43
449 450 1.207089 TCCAGCGTTGTCCCAATCTAG 59.793 52.381 0.00 0.00 0.00 2.43
450 451 1.271856 TCCAGCGTTGTCCCAATCTA 58.728 50.000 0.00 0.00 0.00 1.98
451 452 0.400213 TTCCAGCGTTGTCCCAATCT 59.600 50.000 0.00 0.00 0.00 2.40
452 453 0.804989 CTTCCAGCGTTGTCCCAATC 59.195 55.000 0.00 0.00 0.00 2.67
453 454 0.110486 ACTTCCAGCGTTGTCCCAAT 59.890 50.000 0.00 0.00 0.00 3.16
454 455 0.817634 CACTTCCAGCGTTGTCCCAA 60.818 55.000 0.00 0.00 0.00 4.12
455 456 1.227823 CACTTCCAGCGTTGTCCCA 60.228 57.895 0.00 0.00 0.00 4.37
456 457 2.617274 GCACTTCCAGCGTTGTCCC 61.617 63.158 0.00 0.00 0.00 4.46
457 458 1.845809 CTGCACTTCCAGCGTTGTCC 61.846 60.000 0.00 0.00 33.85 4.02
458 459 1.571460 CTGCACTTCCAGCGTTGTC 59.429 57.895 0.00 0.00 33.85 3.18
459 460 3.736483 CTGCACTTCCAGCGTTGT 58.264 55.556 0.00 0.00 33.85 3.32
622 626 1.673665 GGATGGCAGCGGGATGATC 60.674 63.158 0.00 0.00 0.00 2.92
743 747 2.327343 CCGGTGGTGTCGTCGTAGA 61.327 63.158 0.00 0.00 0.00 2.59
1020 1024 0.540454 CTGGAGAAGAGCATGAGCCA 59.460 55.000 0.00 0.00 43.56 4.75
1061 1065 1.899437 GCAGGACCACGATTCTCCCA 61.899 60.000 0.00 0.00 0.00 4.37
1425 1484 5.513233 AGCCTGTTAAAGATGGTGAATGAT 58.487 37.500 0.00 0.00 0.00 2.45
1440 1499 1.223487 GGATGCCGGAAGCCTGTTA 59.777 57.895 10.40 0.00 42.71 2.41
1862 2374 1.149174 CGGGCAGCAGGGACATAAT 59.851 57.895 0.00 0.00 0.00 1.28
1901 2413 3.220110 CATACATGCCAGCTTCCTCATT 58.780 45.455 0.00 0.00 0.00 2.57
1951 2463 0.530650 CGATAGGCAACAGCGATGGT 60.531 55.000 5.32 0.00 41.41 3.55


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

AutoCloner maintained by Alex Coulton.