Multiple sequence alignment - TraesCS5A01G546100

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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 TraesCS5A01G546100 chr5A 100.000 3179 0 0 1 3179 700450987 700447809 0.000000e+00 5871.0
1 TraesCS5A01G546100 chr5A 92.507 347 17 4 1 347 496614819 496615156 3.690000e-134 488.0
2 TraesCS5A01G546100 chr5A 92.000 350 20 6 1 348 378278081 378278424 4.770000e-133 484.0
3 TraesCS5A01G546100 chr5A 91.714 350 24 5 1 349 512462035 512461690 6.170000e-132 481.0
4 TraesCS5A01G546100 chr5A 98.824 85 1 0 2901 2985 11183489 11183405 5.490000e-33 152.0
5 TraesCS5A01G546100 chrUn 91.860 2420 139 26 793 3179 110527762 110525368 0.000000e+00 3325.0
6 TraesCS5A01G546100 chrUn 80.603 464 55 16 344 804 110528214 110527783 3.060000e-85 326.0
7 TraesCS5A01G546100 chr4B 89.925 2541 132 55 485 2985 660596079 660593623 0.000000e+00 3160.0
8 TraesCS5A01G546100 chr2A 89.933 596 46 7 928 1520 510441935 510442519 0.000000e+00 756.0
9 TraesCS5A01G546100 chr2A 92.068 353 24 3 1 352 764494908 764494559 7.920000e-136 494.0
10 TraesCS5A01G546100 chr2A 91.931 347 21 4 1 347 430362569 430362230 2.220000e-131 479.0
11 TraesCS5A01G546100 chr7A 96.552 348 9 2 1 347 664118932 664118587 9.890000e-160 573.0
12 TraesCS5A01G546100 chr7A 92.464 345 15 6 1 345 79740667 79741000 1.710000e-132 483.0
13 TraesCS5A01G546100 chr4A 92.286 350 22 4 1 350 605130917 605130573 2.850000e-135 492.0
14 TraesCS5A01G546100 chr3A 92.464 345 18 5 1 345 669179490 669179826 1.330000e-133 486.0
15 TraesCS5A01G546100 chr3A 98.824 85 1 0 2901 2985 722603943 722604027 5.490000e-33 152.0
16 TraesCS5A01G546100 chr7B 83.871 434 44 13 985 1414 679845021 679844610 1.070000e-104 390.0
17 TraesCS5A01G546100 chr5B 98.824 85 1 0 2901 2985 34369770 34369854 5.490000e-33 152.0
18 TraesCS5A01G546100 chr2B 98.824 85 1 0 2901 2985 755118683 755118599 5.490000e-33 152.0
19 TraesCS5A01G546100 chr2B 97.647 85 2 0 2901 2985 535432836 535432920 2.560000e-31 147.0
20 TraesCS5A01G546100 chr2B 87.952 83 7 1 1182 1261 254695647 254695729 9.390000e-16 95.3
21 TraesCS5A01G546100 chr2B 87.952 83 7 1 1182 1261 411514036 411513954 9.390000e-16 95.3
22 TraesCS5A01G546100 chr4D 96.386 83 3 0 1143 1225 494358747 494358829 1.540000e-28 137.0
23 TraesCS5A01G546100 chr2D 84.043 94 4 3 955 1048 5919341 5919259 2.630000e-11 80.5


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 TraesCS5A01G546100 chr5A 700447809 700450987 3178 True 5871.0 5871 100.0000 1 3179 1 chr5A.!!$R3 3178
1 TraesCS5A01G546100 chrUn 110525368 110528214 2846 True 1825.5 3325 86.2315 344 3179 2 chrUn.!!$R1 2835
2 TraesCS5A01G546100 chr4B 660593623 660596079 2456 True 3160.0 3160 89.9250 485 2985 1 chr4B.!!$R1 2500
3 TraesCS5A01G546100 chr2A 510441935 510442519 584 False 756.0 756 89.9330 928 1520 1 chr2A.!!$F1 592

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
199 200 0.034896 ACTTCGCCGAATGGTTCTGT 59.965 50.0 0.0 0.0 37.67 3.41 F
807 849 0.038892 GCCGTTCTCTCCGTGTGTTA 60.039 55.0 0.0 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1046 1106 1.203523 CGAGGTCTGGTGGAGAGAAAG 59.796 57.143 0.0 0.0 0.00 2.62 R
2663 2765 0.179004 TCCTGCCACAACATTCGGTT 60.179 50.000 0.0 0.0 41.47 4.44 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
47 48 4.821589 GCCCGCGTCAAGGAGGAG 62.822 72.222 4.92 0.00 0.00 3.69
48 49 3.068691 CCCGCGTCAAGGAGGAGA 61.069 66.667 4.92 0.00 0.00 3.71
49 50 2.646175 CCCGCGTCAAGGAGGAGAA 61.646 63.158 4.92 0.00 0.00 2.87
50 51 1.153745 CCGCGTCAAGGAGGAGAAG 60.154 63.158 4.92 0.00 0.00 2.85
51 52 1.153745 CGCGTCAAGGAGGAGAAGG 60.154 63.158 0.00 0.00 0.00 3.46
52 53 1.448717 GCGTCAAGGAGGAGAAGGC 60.449 63.158 0.00 0.00 0.00 4.35
53 54 1.219393 CGTCAAGGAGGAGAAGGCC 59.781 63.158 0.00 0.00 0.00 5.19
54 55 1.219393 GTCAAGGAGGAGAAGGCCG 59.781 63.158 0.00 0.00 0.00 6.13
55 56 1.078528 TCAAGGAGGAGAAGGCCGA 59.921 57.895 0.00 0.00 0.00 5.54
56 57 1.219393 CAAGGAGGAGAAGGCCGAC 59.781 63.158 0.00 0.00 0.00 4.79
57 58 2.352032 AAGGAGGAGAAGGCCGACG 61.352 63.158 0.00 0.00 0.00 5.12
58 59 2.754658 GGAGGAGAAGGCCGACGA 60.755 66.667 0.00 0.00 0.00 4.20
59 60 2.490685 GAGGAGAAGGCCGACGAC 59.509 66.667 0.00 0.00 0.00 4.34
60 61 3.398353 GAGGAGAAGGCCGACGACG 62.398 68.421 0.00 0.00 39.43 5.12
61 62 3.437795 GGAGAAGGCCGACGACGA 61.438 66.667 9.28 0.00 42.66 4.20
62 63 2.202453 GAGAAGGCCGACGACGAC 60.202 66.667 9.28 0.00 42.66 4.34
63 64 3.996744 GAGAAGGCCGACGACGACG 62.997 68.421 12.66 12.66 42.66 5.12
64 65 4.093952 GAAGGCCGACGACGACGA 62.094 66.667 20.63 0.00 42.66 4.20
65 66 3.392595 GAAGGCCGACGACGACGAT 62.393 63.158 20.63 4.00 42.66 3.73
66 67 3.678717 AAGGCCGACGACGACGATG 62.679 63.158 20.63 6.46 42.66 3.84
87 88 4.070552 GCGACGACTTCAGCCCCT 62.071 66.667 0.00 0.00 0.00 4.79
88 89 2.657237 CGACGACTTCAGCCCCTT 59.343 61.111 0.00 0.00 0.00 3.95
89 90 1.004918 CGACGACTTCAGCCCCTTT 60.005 57.895 0.00 0.00 0.00 3.11
90 91 1.014564 CGACGACTTCAGCCCCTTTC 61.015 60.000 0.00 0.00 0.00 2.62
91 92 0.321996 GACGACTTCAGCCCCTTTCT 59.678 55.000 0.00 0.00 0.00 2.52
92 93 0.765510 ACGACTTCAGCCCCTTTCTT 59.234 50.000 0.00 0.00 0.00 2.52
93 94 1.143073 ACGACTTCAGCCCCTTTCTTT 59.857 47.619 0.00 0.00 0.00 2.52
94 95 2.230660 CGACTTCAGCCCCTTTCTTTT 58.769 47.619 0.00 0.00 0.00 2.27
95 96 2.623416 CGACTTCAGCCCCTTTCTTTTT 59.377 45.455 0.00 0.00 0.00 1.94
124 125 7.100458 AGATTAGGTTCATGTAATGTTTGGC 57.900 36.000 0.00 0.00 46.80 4.52
125 126 5.652994 TTAGGTTCATGTAATGTTTGGCC 57.347 39.130 0.00 0.00 46.80 5.36
126 127 2.491693 AGGTTCATGTAATGTTTGGCCG 59.508 45.455 0.00 0.00 46.80 6.13
127 128 2.490115 GGTTCATGTAATGTTTGGCCGA 59.510 45.455 0.00 0.00 46.80 5.54
128 129 3.057174 GGTTCATGTAATGTTTGGCCGAA 60.057 43.478 0.00 0.00 46.80 4.30
129 130 4.381505 GGTTCATGTAATGTTTGGCCGAAT 60.382 41.667 9.15 0.00 46.80 3.34
130 131 5.167845 GTTCATGTAATGTTTGGCCGAATT 58.832 37.500 9.15 2.54 46.80 2.17
131 132 5.398603 TCATGTAATGTTTGGCCGAATTT 57.601 34.783 9.15 8.73 46.80 1.82
132 133 5.406649 TCATGTAATGTTTGGCCGAATTTC 58.593 37.500 9.15 0.00 46.80 2.17
133 134 3.827625 TGTAATGTTTGGCCGAATTTCG 58.172 40.909 9.15 11.81 40.07 3.46
134 135 1.708822 AATGTTTGGCCGAATTTCGC 58.291 45.000 9.15 8.66 38.82 4.70
135 136 0.108851 ATGTTTGGCCGAATTTCGCC 60.109 50.000 9.15 19.01 38.82 5.54
136 137 1.799916 GTTTGGCCGAATTTCGCCG 60.800 57.895 9.15 2.21 38.82 6.46
137 138 1.966972 TTTGGCCGAATTTCGCCGA 60.967 52.632 13.26 13.92 38.82 5.54
138 139 1.516365 TTTGGCCGAATTTCGCCGAA 61.516 50.000 21.07 21.07 38.82 4.30
139 140 1.516365 TTGGCCGAATTTCGCCGAAA 61.516 50.000 15.36 15.36 38.82 3.46
140 141 1.309499 TGGCCGAATTTCGCCGAAAT 61.309 50.000 18.74 18.74 43.07 2.17
151 152 7.414814 AATTTCGCCGAAATTTGTAATGTTT 57.585 28.000 27.14 6.90 46.07 2.83
152 153 5.814314 TTCGCCGAAATTTGTAATGTTTG 57.186 34.783 0.00 0.00 0.00 2.93
153 154 4.230657 TCGCCGAAATTTGTAATGTTTGG 58.769 39.130 0.00 0.00 0.00 3.28
154 155 3.181535 CGCCGAAATTTGTAATGTTTGGC 60.182 43.478 0.00 3.80 35.49 4.52
155 156 3.124466 GCCGAAATTTGTAATGTTTGGCC 59.876 43.478 0.00 0.00 32.75 5.36
156 157 3.366422 CCGAAATTTGTAATGTTTGGCCG 59.634 43.478 0.00 0.00 0.00 6.13
157 158 4.230657 CGAAATTTGTAATGTTTGGCCGA 58.769 39.130 0.00 0.00 0.00 5.54
158 159 4.681942 CGAAATTTGTAATGTTTGGCCGAA 59.318 37.500 0.00 0.00 0.00 4.30
159 160 5.175856 CGAAATTTGTAATGTTTGGCCGAAA 59.824 36.000 7.10 1.29 0.00 3.46
160 161 6.128688 CGAAATTTGTAATGTTTGGCCGAAAT 60.129 34.615 7.10 0.80 0.00 2.17
161 162 7.503521 AAATTTGTAATGTTTGGCCGAAATT 57.496 28.000 7.10 11.74 0.00 1.82
162 163 7.503521 AATTTGTAATGTTTGGCCGAAATTT 57.496 28.000 7.10 6.81 0.00 1.82
163 164 8.608844 AATTTGTAATGTTTGGCCGAAATTTA 57.391 26.923 7.10 5.80 0.00 1.40
164 165 8.608844 ATTTGTAATGTTTGGCCGAAATTTAA 57.391 26.923 7.10 6.49 0.00 1.52
165 166 7.409465 TTGTAATGTTTGGCCGAAATTTAAC 57.591 32.000 7.10 6.75 0.00 2.01
166 167 6.750148 TGTAATGTTTGGCCGAAATTTAACT 58.250 32.000 7.10 0.00 0.00 2.24
167 168 7.883217 TGTAATGTTTGGCCGAAATTTAACTA 58.117 30.769 7.10 0.00 0.00 2.24
168 169 8.024285 TGTAATGTTTGGCCGAAATTTAACTAG 58.976 33.333 7.10 0.00 0.00 2.57
169 170 6.584185 ATGTTTGGCCGAAATTTAACTAGT 57.416 33.333 7.10 0.00 0.00 2.57
170 171 6.394025 TGTTTGGCCGAAATTTAACTAGTT 57.606 33.333 13.68 13.68 0.00 2.24
171 172 6.807789 TGTTTGGCCGAAATTTAACTAGTTT 58.192 32.000 14.49 0.00 0.00 2.66
172 173 7.266400 TGTTTGGCCGAAATTTAACTAGTTTT 58.734 30.769 14.49 1.26 0.00 2.43
173 174 7.764901 TGTTTGGCCGAAATTTAACTAGTTTTT 59.235 29.630 14.49 8.43 0.00 1.94
174 175 9.247126 GTTTGGCCGAAATTTAACTAGTTTTTA 57.753 29.630 14.49 0.00 0.00 1.52
175 176 9.984190 TTTGGCCGAAATTTAACTAGTTTTTAT 57.016 25.926 14.49 2.42 0.00 1.40
176 177 9.628746 TTGGCCGAAATTTAACTAGTTTTTATC 57.371 29.630 14.49 5.85 0.00 1.75
177 178 8.794553 TGGCCGAAATTTAACTAGTTTTTATCA 58.205 29.630 14.49 3.22 0.00 2.15
178 179 9.797556 GGCCGAAATTTAACTAGTTTTTATCAT 57.202 29.630 14.49 0.00 0.00 2.45
188 189 7.230466 ACTAGTTTTTATCATAACTTCGCCG 57.770 36.000 0.00 0.00 36.16 6.46
189 190 7.037438 ACTAGTTTTTATCATAACTTCGCCGA 58.963 34.615 0.00 0.00 36.16 5.54
190 191 6.730960 AGTTTTTATCATAACTTCGCCGAA 57.269 33.333 0.00 0.00 30.72 4.30
191 192 7.316544 AGTTTTTATCATAACTTCGCCGAAT 57.683 32.000 0.00 0.00 30.72 3.34
192 193 7.186804 AGTTTTTATCATAACTTCGCCGAATG 58.813 34.615 0.00 0.00 30.72 2.67
193 194 5.666969 TTTATCATAACTTCGCCGAATGG 57.333 39.130 0.00 0.00 38.77 3.16
194 195 2.684001 TCATAACTTCGCCGAATGGT 57.316 45.000 0.00 0.00 37.67 3.55
195 196 2.980568 TCATAACTTCGCCGAATGGTT 58.019 42.857 0.00 4.83 37.67 3.67
196 197 2.933906 TCATAACTTCGCCGAATGGTTC 59.066 45.455 7.61 0.00 37.67 3.62
197 198 2.754946 TAACTTCGCCGAATGGTTCT 57.245 45.000 7.61 0.00 37.67 3.01
198 199 1.156736 AACTTCGCCGAATGGTTCTG 58.843 50.000 0.00 0.00 37.67 3.02
199 200 0.034896 ACTTCGCCGAATGGTTCTGT 59.965 50.000 0.00 0.00 37.67 3.41
200 201 1.156736 CTTCGCCGAATGGTTCTGTT 58.843 50.000 0.00 0.00 37.67 3.16
201 202 1.535462 CTTCGCCGAATGGTTCTGTTT 59.465 47.619 0.00 0.00 37.67 2.83
202 203 1.600023 TCGCCGAATGGTTCTGTTTT 58.400 45.000 0.00 0.00 37.67 2.43
203 204 1.950909 TCGCCGAATGGTTCTGTTTTT 59.049 42.857 0.00 0.00 37.67 1.94
224 225 1.658994 TTTTAAGATACGCGCCTGGG 58.341 50.000 5.73 0.00 0.00 4.45
225 226 0.179067 TTTAAGATACGCGCCTGGGG 60.179 55.000 5.73 6.36 0.00 4.96
226 227 2.035237 TTAAGATACGCGCCTGGGGG 62.035 60.000 5.73 5.39 0.00 5.40
266 267 4.828296 GGGACCGACTCGCCCCTA 62.828 72.222 15.89 0.00 36.07 3.53
267 268 3.217743 GGACCGACTCGCCCCTAG 61.218 72.222 0.00 0.00 0.00 3.02
268 269 2.439883 GACCGACTCGCCCCTAGT 60.440 66.667 0.00 0.00 0.00 2.57
269 270 2.754658 ACCGACTCGCCCCTAGTG 60.755 66.667 0.00 0.00 0.00 2.74
270 271 4.208686 CCGACTCGCCCCTAGTGC 62.209 72.222 0.00 0.00 0.00 4.40
271 272 4.208686 CGACTCGCCCCTAGTGCC 62.209 72.222 0.00 0.00 0.00 5.01
272 273 3.075005 GACTCGCCCCTAGTGCCA 61.075 66.667 0.00 0.00 0.00 4.92
273 274 2.365635 ACTCGCCCCTAGTGCCAT 60.366 61.111 0.00 0.00 0.00 4.40
274 275 1.972660 GACTCGCCCCTAGTGCCATT 61.973 60.000 0.00 0.00 0.00 3.16
275 276 1.224592 CTCGCCCCTAGTGCCATTT 59.775 57.895 0.00 0.00 0.00 2.32
276 277 0.394352 CTCGCCCCTAGTGCCATTTT 60.394 55.000 0.00 0.00 0.00 1.82
277 278 0.039035 TCGCCCCTAGTGCCATTTTT 59.961 50.000 0.00 0.00 0.00 1.94
292 293 2.981350 TTTTTCGCCGGCTCACCC 60.981 61.111 26.68 0.00 0.00 4.61
309 310 3.508840 CCCAGGCGGCGCTTTTAG 61.509 66.667 32.30 14.75 0.00 1.85
310 311 2.435938 CCAGGCGGCGCTTTTAGA 60.436 61.111 32.30 0.00 0.00 2.10
311 312 2.750888 CCAGGCGGCGCTTTTAGAC 61.751 63.158 32.30 13.09 0.00 2.59
312 313 2.813908 AGGCGGCGCTTTTAGACG 60.814 61.111 32.30 0.56 0.00 4.18
318 319 2.267961 CGCTTTTAGACGCCCCCT 59.732 61.111 0.00 0.00 0.00 4.79
319 320 2.106683 CGCTTTTAGACGCCCCCTG 61.107 63.158 0.00 0.00 0.00 4.45
320 321 1.298667 GCTTTTAGACGCCCCCTGA 59.701 57.895 0.00 0.00 0.00 3.86
321 322 0.744771 GCTTTTAGACGCCCCCTGAG 60.745 60.000 0.00 0.00 0.00 3.35
322 323 0.107654 CTTTTAGACGCCCCCTGAGG 60.108 60.000 0.00 0.00 0.00 3.86
333 334 3.083997 CCTGAGGGGCTAACGGCT 61.084 66.667 0.00 0.00 41.46 5.52
334 335 2.187946 CTGAGGGGCTAACGGCTG 59.812 66.667 0.00 0.00 41.46 4.85
335 336 3.391665 CTGAGGGGCTAACGGCTGG 62.392 68.421 0.00 0.00 41.46 4.85
336 337 3.081409 GAGGGGCTAACGGCTGGA 61.081 66.667 0.00 0.00 41.46 3.86
337 338 3.083997 AGGGGCTAACGGCTGGAG 61.084 66.667 0.00 0.00 41.46 3.86
338 339 3.081409 GGGGCTAACGGCTGGAGA 61.081 66.667 0.00 0.00 41.46 3.71
339 340 2.444256 GGGGCTAACGGCTGGAGAT 61.444 63.158 0.00 0.00 41.46 2.75
340 341 1.227674 GGGCTAACGGCTGGAGATG 60.228 63.158 0.00 0.00 41.46 2.90
341 342 1.889573 GGCTAACGGCTGGAGATGC 60.890 63.158 0.00 0.00 41.46 3.91
342 343 1.889573 GCTAACGGCTGGAGATGCC 60.890 63.158 0.00 0.00 46.42 4.40
353 354 3.012518 CTGGAGATGCCCTTAGTGTTTG 58.987 50.000 0.00 0.00 34.97 2.93
373 374 3.540617 TGCTTGTGTCAAGAACTTGCTA 58.459 40.909 12.77 0.00 40.24 3.49
379 380 8.066595 GCTTGTGTCAAGAACTTGCTATATATG 58.933 37.037 12.77 0.00 40.24 1.78
406 407 4.820284 CTGGAACTGGAAGAGAACAAAC 57.180 45.455 0.00 0.00 37.43 2.93
408 409 3.053991 TGGAACTGGAAGAGAACAAACCA 60.054 43.478 0.00 0.00 37.43 3.67
435 436 4.039124 CAGGTGGTGAAAAGTTAAAGGCAT 59.961 41.667 0.00 0.00 0.00 4.40
437 438 5.130311 AGGTGGTGAAAAGTTAAAGGCATTT 59.870 36.000 0.53 0.53 0.00 2.32
441 442 7.065204 GTGGTGAAAAGTTAAAGGCATTTTGAA 59.935 33.333 0.00 0.00 0.00 2.69
458 459 6.639632 TTTTGAATGCCTGGATAATCTAGC 57.360 37.500 0.00 0.00 0.00 3.42
470 471 9.388506 CCTGGATAATCTAGCTTTTATGTATGG 57.611 37.037 0.00 0.00 0.00 2.74
473 474 9.384764 GGATAATCTAGCTTTTATGTATGGACC 57.615 37.037 0.00 0.00 0.00 4.46
477 478 9.950496 AATCTAGCTTTTATGTATGGACCTATG 57.050 33.333 0.00 0.00 0.00 2.23
478 479 8.492415 TCTAGCTTTTATGTATGGACCTATGT 57.508 34.615 0.00 0.00 0.00 2.29
479 480 8.367911 TCTAGCTTTTATGTATGGACCTATGTG 58.632 37.037 0.00 0.00 0.00 3.21
480 481 6.299141 AGCTTTTATGTATGGACCTATGTGG 58.701 40.000 0.00 0.00 42.93 4.17
481 482 5.048713 GCTTTTATGTATGGACCTATGTGGC 60.049 44.000 0.00 0.00 40.22 5.01
496 497 1.026718 GTGGCTATGTCAGTGGTGGC 61.027 60.000 0.00 0.00 0.00 5.01
498 499 0.462759 GGCTATGTCAGTGGTGGCTC 60.463 60.000 0.00 0.00 0.00 4.70
500 501 1.472376 GCTATGTCAGTGGTGGCTCTC 60.472 57.143 0.00 0.00 0.00 3.20
531 532 3.125146 TCGCTTTGCTTGCAGTAAGTATG 59.875 43.478 0.00 0.00 38.70 2.39
539 540 5.046591 TGCTTGCAGTAAGTATGGTAAGACT 60.047 40.000 0.00 0.00 38.70 3.24
596 597 1.671979 TGAAGGAGCTATGCACATGC 58.328 50.000 0.00 0.00 42.50 4.06
642 643 4.856182 AGAGGGTTATAACTTTGGAGGGTT 59.144 41.667 15.05 0.00 0.00 4.11
645 646 6.728411 AGGGTTATAACTTTGGAGGGTTAAG 58.272 40.000 15.05 0.00 32.70 1.85
750 754 4.690719 TCCGGAAATGCACGCGGT 62.691 61.111 12.47 0.00 0.00 5.68
799 841 4.856607 CCGCTCGCCGTTCTCTCC 62.857 72.222 0.00 0.00 34.38 3.71
807 849 0.038892 GCCGTTCTCTCCGTGTGTTA 60.039 55.000 0.00 0.00 0.00 2.41
818 860 2.030185 TCCGTGTGTTACTCTCTCTTGC 60.030 50.000 0.00 0.00 0.00 4.01
826 870 4.217334 TGTTACTCTCTCTTGCTCTCAGTG 59.783 45.833 0.00 0.00 0.00 3.66
835 879 1.685421 GCTCTCAGTGGGAGGAGCT 60.685 63.158 21.63 0.00 44.19 4.09
849 893 4.769488 GGGAGGAGCTCAGAAAAAGAAAAT 59.231 41.667 17.19 0.00 31.08 1.82
853 897 7.824779 GGAGGAGCTCAGAAAAAGAAAATAGTA 59.175 37.037 17.19 0.00 31.08 1.82
864 908 5.975988 AAGAAAATAGTATGAGGAGCCCA 57.024 39.130 0.00 0.00 0.00 5.36
889 933 1.712018 CTGGATGTGCCGCACTCATG 61.712 60.000 23.52 10.93 40.66 3.07
890 934 2.475466 GGATGTGCCGCACTCATGG 61.475 63.158 23.52 0.00 35.11 3.66
891 935 2.438975 ATGTGCCGCACTCATGGG 60.439 61.111 23.52 0.00 38.49 4.00
894 938 4.349503 TGCCGCACTCATGGGCTT 62.350 61.111 10.70 0.00 40.76 4.35
895 939 3.512516 GCCGCACTCATGGGCTTC 61.513 66.667 0.00 0.00 38.47 3.86
896 940 3.197790 CCGCACTCATGGGCTTCG 61.198 66.667 0.00 0.00 37.45 3.79
897 941 3.869272 CGCACTCATGGGCTTCGC 61.869 66.667 0.00 0.00 31.21 4.70
902 962 0.254178 ACTCATGGGCTTCGCAATCT 59.746 50.000 0.00 0.00 0.00 2.40
945 1005 9.250246 ACGAATAAAGAAGGGGAATTAATCAAA 57.750 29.630 0.00 0.00 0.00 2.69
948 1008 9.560860 AATAAAGAAGGGGAATTAATCAAACCT 57.439 29.630 0.00 0.00 31.80 3.50
953 1013 6.408770 AGGGGAATTAATCAAACCTCTCTT 57.591 37.500 0.00 0.00 0.00 2.85
975 1035 1.735376 TTATCCAGACGGCTCGGCTC 61.735 60.000 0.00 0.00 44.38 4.70
976 1036 2.626255 TATCCAGACGGCTCGGCTCT 62.626 60.000 0.00 0.00 44.38 4.09
977 1037 4.200283 CCAGACGGCTCGGCTCTC 62.200 72.222 0.00 0.00 44.38 3.20
978 1038 3.137459 CAGACGGCTCGGCTCTCT 61.137 66.667 0.00 0.00 44.38 3.10
979 1039 2.826738 AGACGGCTCGGCTCTCTC 60.827 66.667 0.00 0.00 44.38 3.20
1046 1106 0.975040 TGCTTCTGCTCCTCCTCCTC 60.975 60.000 0.00 0.00 40.48 3.71
1047 1107 0.687427 GCTTCTGCTCCTCCTCCTCT 60.687 60.000 0.00 0.00 36.03 3.69
1048 1108 1.864669 CTTCTGCTCCTCCTCCTCTT 58.135 55.000 0.00 0.00 0.00 2.85
1059 1119 1.433199 TCCTCCTCTTTCTCTCCACCA 59.567 52.381 0.00 0.00 0.00 4.17
1089 1149 1.607071 CGTCCATTCACCCCCATCA 59.393 57.895 0.00 0.00 0.00 3.07
1090 1150 0.034574 CGTCCATTCACCCCCATCAA 60.035 55.000 0.00 0.00 0.00 2.57
1091 1151 1.767759 GTCCATTCACCCCCATCAAG 58.232 55.000 0.00 0.00 0.00 3.02
1092 1152 0.033208 TCCATTCACCCCCATCAAGC 60.033 55.000 0.00 0.00 0.00 4.01
1308 1380 4.496336 GCCTGCTACCTGGGGCTG 62.496 72.222 13.42 12.48 41.20 4.85
1656 1728 1.067582 CGGCTACTTCGACATCCCC 59.932 63.158 0.00 0.00 0.00 4.81
2267 2349 1.832167 GCAGAGGCAAAACCACCCA 60.832 57.895 0.00 0.00 43.14 4.51
2390 2477 5.276270 CGTGATTGGATTGATTGGTTGATC 58.724 41.667 0.00 0.00 0.00 2.92
2453 2544 0.607112 CTCCTTGTCTCTGCTGCTGA 59.393 55.000 8.95 8.95 0.00 4.26
2497 2588 1.902918 AGCAAGTTTGATGGCGCCA 60.903 52.632 34.80 34.80 0.00 5.69
2588 2690 5.505173 AGCTGCAATAACATAACATCCAC 57.495 39.130 1.02 0.00 0.00 4.02
2592 2694 6.238842 GCTGCAATAACATAACATCCACTGAT 60.239 38.462 0.00 0.00 0.00 2.90
2611 2713 5.104360 ACTGATTATCTTACCCATGCACACT 60.104 40.000 0.00 0.00 0.00 3.55
2615 2717 3.266510 TCTTACCCATGCACACTCATC 57.733 47.619 0.00 0.00 0.00 2.92
2616 2718 1.935873 CTTACCCATGCACACTCATCG 59.064 52.381 0.00 0.00 0.00 3.84
2618 2720 0.324614 ACCCATGCACACTCATCGAA 59.675 50.000 0.00 0.00 0.00 3.71
2619 2721 1.271325 ACCCATGCACACTCATCGAAA 60.271 47.619 0.00 0.00 0.00 3.46
2620 2722 1.811965 CCCATGCACACTCATCGAAAA 59.188 47.619 0.00 0.00 0.00 2.29
2621 2723 2.424601 CCCATGCACACTCATCGAAAAT 59.575 45.455 0.00 0.00 0.00 1.82
2622 2724 3.627123 CCCATGCACACTCATCGAAAATA 59.373 43.478 0.00 0.00 0.00 1.40
2623 2725 4.276678 CCCATGCACACTCATCGAAAATAT 59.723 41.667 0.00 0.00 0.00 1.28
2624 2726 5.221106 CCCATGCACACTCATCGAAAATATT 60.221 40.000 0.00 0.00 0.00 1.28
2625 2727 5.911280 CCATGCACACTCATCGAAAATATTC 59.089 40.000 0.00 0.00 0.00 1.75
2626 2728 6.238566 CCATGCACACTCATCGAAAATATTCT 60.239 38.462 0.00 0.00 33.17 2.40
2627 2729 6.349973 TGCACACTCATCGAAAATATTCTC 57.650 37.500 0.00 0.00 33.17 2.87
2628 2730 5.874261 TGCACACTCATCGAAAATATTCTCA 59.126 36.000 0.00 0.00 33.17 3.27
2629 2731 6.183360 TGCACACTCATCGAAAATATTCTCAC 60.183 38.462 0.00 0.00 33.17 3.51
2630 2732 6.183360 GCACACTCATCGAAAATATTCTCACA 60.183 38.462 0.00 0.00 33.17 3.58
2631 2733 7.624134 GCACACTCATCGAAAATATTCTCACAA 60.624 37.037 0.00 0.00 33.17 3.33
2632 2734 8.229811 CACACTCATCGAAAATATTCTCACAAA 58.770 33.333 0.00 0.00 33.17 2.83
2633 2735 8.783093 ACACTCATCGAAAATATTCTCACAAAA 58.217 29.630 0.00 0.00 33.17 2.44
2634 2736 9.611284 CACTCATCGAAAATATTCTCACAAAAA 57.389 29.630 0.00 0.00 33.17 1.94
2667 2769 8.491152 CATCAGAAATAATAAGTAGCAGAACCG 58.509 37.037 0.00 0.00 0.00 4.44
2687 2789 2.223688 CGAATGTTGTGGCAGGAAACAA 60.224 45.455 12.61 0.00 37.36 2.83
2699 2801 3.052036 CAGGAAACAACAAAGGCATTCG 58.948 45.455 0.00 0.00 0.00 3.34
2707 2809 6.334102 ACAACAAAGGCATTCGGTAAAATA 57.666 33.333 0.00 0.00 0.00 1.40
2822 2924 4.503910 TGATCACTTTTGGATACTGGTCG 58.496 43.478 0.00 0.00 37.61 4.79
2840 2942 0.857935 CGATGCGAGAATCTTCCAGC 59.142 55.000 0.00 1.69 0.00 4.85
2862 2964 0.523072 CAATTCTTCCACCTGTGCCG 59.477 55.000 0.00 0.00 0.00 5.69
2865 2967 1.407656 TTCTTCCACCTGTGCCGAGT 61.408 55.000 0.00 0.00 0.00 4.18
2868 2970 0.817634 TTCCACCTGTGCCGAGTTTG 60.818 55.000 0.00 0.00 0.00 2.93
2880 2982 3.807622 TGCCGAGTTTGAAGTTCAGTAAG 59.192 43.478 5.56 0.00 0.00 2.34
2881 2983 4.056050 GCCGAGTTTGAAGTTCAGTAAGA 58.944 43.478 5.56 0.00 0.00 2.10
2963 3066 7.440856 GGAAAAGTAAAATGAGTTTGATTGCCA 59.559 33.333 0.00 0.00 0.00 4.92
2986 3089 7.002250 CATATATGGAGAGTGTCAATGTCCT 57.998 40.000 16.44 5.99 0.00 3.85
2992 3095 4.691216 GGAGAGTGTCAATGTCCTTACAAC 59.309 45.833 9.11 0.00 39.58 3.32
3014 3117 5.430886 ACTGCTTCATATGCTCACATGTAA 58.569 37.500 0.00 0.00 37.04 2.41
3137 3240 6.576185 ACAAATCAAGGGCTGCATAATTAAG 58.424 36.000 0.50 0.00 0.00 1.85
3139 3242 7.341769 ACAAATCAAGGGCTGCATAATTAAGTA 59.658 33.333 0.50 0.00 0.00 2.24
3147 3250 7.337942 AGGGCTGCATAATTAAGTAAGATATGC 59.662 37.037 16.91 16.91 40.99 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.821589 CTCCTCCTTGACGCGGGC 62.822 72.222 12.47 1.95 0.00 6.13
31 32 2.564553 CTTCTCCTCCTTGACGCGGG 62.565 65.000 12.47 0.89 0.00 6.13
32 33 1.153745 CTTCTCCTCCTTGACGCGG 60.154 63.158 12.47 0.00 0.00 6.46
33 34 1.153745 CCTTCTCCTCCTTGACGCG 60.154 63.158 3.53 3.53 0.00 6.01
34 35 1.448717 GCCTTCTCCTCCTTGACGC 60.449 63.158 0.00 0.00 0.00 5.19
35 36 1.219393 GGCCTTCTCCTCCTTGACG 59.781 63.158 0.00 0.00 0.00 4.35
36 37 1.219393 CGGCCTTCTCCTCCTTGAC 59.781 63.158 0.00 0.00 0.00 3.18
37 38 1.078528 TCGGCCTTCTCCTCCTTGA 59.921 57.895 0.00 0.00 0.00 3.02
38 39 1.219393 GTCGGCCTTCTCCTCCTTG 59.781 63.158 0.00 0.00 0.00 3.61
39 40 2.352032 CGTCGGCCTTCTCCTCCTT 61.352 63.158 0.00 0.00 0.00 3.36
40 41 2.756283 CGTCGGCCTTCTCCTCCT 60.756 66.667 0.00 0.00 0.00 3.69
41 42 2.754658 TCGTCGGCCTTCTCCTCC 60.755 66.667 0.00 0.00 0.00 4.30
42 43 2.490685 GTCGTCGGCCTTCTCCTC 59.509 66.667 0.00 0.00 0.00 3.71
43 44 3.441290 CGTCGTCGGCCTTCTCCT 61.441 66.667 0.00 0.00 0.00 3.69
44 45 3.437795 TCGTCGTCGGCCTTCTCC 61.438 66.667 0.00 0.00 37.69 3.71
45 46 2.202453 GTCGTCGTCGGCCTTCTC 60.202 66.667 0.00 0.00 35.48 2.87
46 47 4.099170 CGTCGTCGTCGGCCTTCT 62.099 66.667 0.00 0.00 38.56 2.85
47 48 3.392595 ATCGTCGTCGTCGGCCTTC 62.393 63.158 11.74 0.00 38.56 3.46
48 49 3.437795 ATCGTCGTCGTCGGCCTT 61.438 61.111 11.74 0.00 38.56 4.35
49 50 4.175489 CATCGTCGTCGTCGGCCT 62.175 66.667 11.74 0.00 38.56 5.19
63 64 3.255379 GAAGTCGTCGCCGCCATC 61.255 66.667 0.00 0.00 0.00 3.51
64 65 3.989698 CTGAAGTCGTCGCCGCCAT 62.990 63.158 0.00 0.00 0.00 4.40
65 66 4.717629 CTGAAGTCGTCGCCGCCA 62.718 66.667 0.00 0.00 0.00 5.69
70 71 3.591254 AAGGGGCTGAAGTCGTCGC 62.591 63.158 0.00 0.00 0.00 5.19
71 72 1.004918 AAAGGGGCTGAAGTCGTCG 60.005 57.895 0.00 0.00 0.00 5.12
72 73 0.321996 AGAAAGGGGCTGAAGTCGTC 59.678 55.000 0.00 0.00 0.00 4.20
73 74 0.765510 AAGAAAGGGGCTGAAGTCGT 59.234 50.000 0.00 0.00 0.00 4.34
74 75 1.897560 AAAGAAAGGGGCTGAAGTCG 58.102 50.000 0.00 0.00 0.00 4.18
98 99 8.682710 GCCAAACATTACATGAACCTAATCTAA 58.317 33.333 0.00 0.00 0.00 2.10
99 100 7.284489 GGCCAAACATTACATGAACCTAATCTA 59.716 37.037 0.00 0.00 0.00 1.98
100 101 6.096846 GGCCAAACATTACATGAACCTAATCT 59.903 38.462 0.00 0.00 0.00 2.40
101 102 6.273071 GGCCAAACATTACATGAACCTAATC 58.727 40.000 0.00 0.00 0.00 1.75
102 103 5.163561 CGGCCAAACATTACATGAACCTAAT 60.164 40.000 2.24 0.00 0.00 1.73
103 104 4.156922 CGGCCAAACATTACATGAACCTAA 59.843 41.667 2.24 0.00 0.00 2.69
104 105 3.692101 CGGCCAAACATTACATGAACCTA 59.308 43.478 2.24 0.00 0.00 3.08
105 106 2.491693 CGGCCAAACATTACATGAACCT 59.508 45.455 2.24 0.00 0.00 3.50
106 107 2.490115 TCGGCCAAACATTACATGAACC 59.510 45.455 2.24 0.00 0.00 3.62
107 108 3.840890 TCGGCCAAACATTACATGAAC 57.159 42.857 2.24 0.00 0.00 3.18
108 109 5.398603 AATTCGGCCAAACATTACATGAA 57.601 34.783 2.24 0.00 0.00 2.57
109 110 5.398603 AAATTCGGCCAAACATTACATGA 57.601 34.783 2.24 0.00 0.00 3.07
110 111 4.265085 CGAAATTCGGCCAAACATTACATG 59.735 41.667 7.61 0.00 36.00 3.21
111 112 4.420168 CGAAATTCGGCCAAACATTACAT 58.580 39.130 7.61 0.00 36.00 2.29
112 113 3.827625 CGAAATTCGGCCAAACATTACA 58.172 40.909 7.61 0.00 36.00 2.41
113 114 2.596862 GCGAAATTCGGCCAAACATTAC 59.403 45.455 17.49 0.00 40.84 1.89
114 115 2.869897 GCGAAATTCGGCCAAACATTA 58.130 42.857 17.49 0.00 40.84 1.90
115 116 1.708822 GCGAAATTCGGCCAAACATT 58.291 45.000 17.49 0.00 40.84 2.71
116 117 3.416955 GCGAAATTCGGCCAAACAT 57.583 47.368 17.49 0.00 40.84 2.71
117 118 4.955089 GCGAAATTCGGCCAAACA 57.045 50.000 17.49 0.00 40.84 2.83
128 129 6.128688 CCAAACATTACAAATTTCGGCGAAAT 60.129 34.615 34.92 34.92 43.07 2.17
129 130 5.175856 CCAAACATTACAAATTTCGGCGAAA 59.824 36.000 33.79 33.79 35.94 3.46
130 131 4.681942 CCAAACATTACAAATTTCGGCGAA 59.318 37.500 19.83 19.83 0.00 4.70
131 132 4.230657 CCAAACATTACAAATTTCGGCGA 58.769 39.130 4.99 4.99 0.00 5.54
132 133 3.181535 GCCAAACATTACAAATTTCGGCG 60.182 43.478 0.00 0.00 0.00 6.46
133 134 3.124466 GGCCAAACATTACAAATTTCGGC 59.876 43.478 0.00 0.00 32.96 5.54
134 135 3.366422 CGGCCAAACATTACAAATTTCGG 59.634 43.478 2.24 0.00 0.00 4.30
135 136 4.230657 TCGGCCAAACATTACAAATTTCG 58.769 39.130 2.24 0.00 0.00 3.46
136 137 6.532365 TTTCGGCCAAACATTACAAATTTC 57.468 33.333 2.24 0.00 0.00 2.17
137 138 7.503521 AATTTCGGCCAAACATTACAAATTT 57.496 28.000 2.24 0.00 0.00 1.82
138 139 7.503521 AAATTTCGGCCAAACATTACAAATT 57.496 28.000 2.24 0.00 0.00 1.82
139 140 8.499967 GTTAAATTTCGGCCAAACATTACAAAT 58.500 29.630 2.24 0.00 0.00 2.32
140 141 7.711339 AGTTAAATTTCGGCCAAACATTACAAA 59.289 29.630 2.24 0.00 0.00 2.83
141 142 7.210873 AGTTAAATTTCGGCCAAACATTACAA 58.789 30.769 2.24 0.00 0.00 2.41
142 143 6.750148 AGTTAAATTTCGGCCAAACATTACA 58.250 32.000 2.24 0.00 0.00 2.41
143 144 8.024865 ACTAGTTAAATTTCGGCCAAACATTAC 58.975 33.333 2.24 0.64 0.00 1.89
144 145 8.113173 ACTAGTTAAATTTCGGCCAAACATTA 57.887 30.769 2.24 4.07 0.00 1.90
145 146 6.988522 ACTAGTTAAATTTCGGCCAAACATT 58.011 32.000 2.24 4.95 0.00 2.71
146 147 6.584185 ACTAGTTAAATTTCGGCCAAACAT 57.416 33.333 2.24 0.00 0.00 2.71
147 148 6.394025 AACTAGTTAAATTTCGGCCAAACA 57.606 33.333 6.26 0.00 0.00 2.83
148 149 7.703298 AAAACTAGTTAAATTTCGGCCAAAC 57.297 32.000 8.92 0.00 0.00 2.93
149 150 9.984190 ATAAAAACTAGTTAAATTTCGGCCAAA 57.016 25.926 8.92 2.92 0.00 3.28
150 151 9.628746 GATAAAAACTAGTTAAATTTCGGCCAA 57.371 29.630 8.92 0.00 0.00 4.52
151 152 8.794553 TGATAAAAACTAGTTAAATTTCGGCCA 58.205 29.630 8.92 1.01 0.00 5.36
152 153 9.797556 ATGATAAAAACTAGTTAAATTTCGGCC 57.202 29.630 8.92 0.00 0.00 6.13
162 163 8.810427 CGGCGAAGTTATGATAAAAACTAGTTA 58.190 33.333 8.92 0.00 34.91 2.24
163 164 7.546667 TCGGCGAAGTTATGATAAAAACTAGTT 59.453 33.333 7.35 1.12 34.91 2.24
164 165 7.037438 TCGGCGAAGTTATGATAAAAACTAGT 58.963 34.615 7.35 0.00 34.91 2.57
165 166 7.459394 TCGGCGAAGTTATGATAAAAACTAG 57.541 36.000 7.35 0.00 34.91 2.57
166 167 7.830940 TTCGGCGAAGTTATGATAAAAACTA 57.169 32.000 19.83 0.00 34.91 2.24
167 168 6.730960 TTCGGCGAAGTTATGATAAAAACT 57.269 33.333 19.83 0.00 37.54 2.66
168 169 6.413818 CCATTCGGCGAAGTTATGATAAAAAC 59.586 38.462 27.35 0.00 0.00 2.43
169 170 6.094325 ACCATTCGGCGAAGTTATGATAAAAA 59.906 34.615 27.35 0.00 34.57 1.94
170 171 5.587043 ACCATTCGGCGAAGTTATGATAAAA 59.413 36.000 27.35 0.00 34.57 1.52
171 172 5.120399 ACCATTCGGCGAAGTTATGATAAA 58.880 37.500 27.35 0.00 34.57 1.40
172 173 4.699637 ACCATTCGGCGAAGTTATGATAA 58.300 39.130 27.35 0.15 34.57 1.75
173 174 4.330944 ACCATTCGGCGAAGTTATGATA 57.669 40.909 27.35 0.99 34.57 2.15
174 175 3.194005 ACCATTCGGCGAAGTTATGAT 57.806 42.857 27.35 5.15 34.57 2.45
175 176 2.684001 ACCATTCGGCGAAGTTATGA 57.316 45.000 27.35 2.66 34.57 2.15
176 177 2.936498 AGAACCATTCGGCGAAGTTATG 59.064 45.455 27.35 19.47 34.57 1.90
177 178 2.936498 CAGAACCATTCGGCGAAGTTAT 59.064 45.455 27.35 19.84 34.57 1.89
178 179 2.289195 ACAGAACCATTCGGCGAAGTTA 60.289 45.455 27.35 4.77 34.57 2.24
179 180 1.156736 CAGAACCATTCGGCGAAGTT 58.843 50.000 27.35 24.48 34.57 2.66
180 181 0.034896 ACAGAACCATTCGGCGAAGT 59.965 50.000 27.35 17.73 34.57 3.01
181 182 1.156736 AACAGAACCATTCGGCGAAG 58.843 50.000 27.35 17.05 34.57 3.79
182 183 1.600023 AAACAGAACCATTCGGCGAA 58.400 45.000 25.88 25.88 34.57 4.70
183 184 1.600023 AAAACAGAACCATTCGGCGA 58.400 45.000 4.99 4.99 34.57 5.54
184 185 2.415697 AAAAACAGAACCATTCGGCG 57.584 45.000 0.00 0.00 34.57 6.46
204 205 2.011222 CCCAGGCGCGTATCTTAAAAA 58.989 47.619 8.43 0.00 0.00 1.94
205 206 1.658994 CCCAGGCGCGTATCTTAAAA 58.341 50.000 8.43 0.00 0.00 1.52
206 207 0.179067 CCCCAGGCGCGTATCTTAAA 60.179 55.000 8.43 0.00 0.00 1.52
207 208 1.444250 CCCCAGGCGCGTATCTTAA 59.556 57.895 8.43 0.00 0.00 1.85
208 209 2.504274 CCCCCAGGCGCGTATCTTA 61.504 63.158 8.43 0.00 0.00 2.10
209 210 3.861797 CCCCCAGGCGCGTATCTT 61.862 66.667 8.43 0.00 0.00 2.40
250 251 3.217743 CTAGGGGCGAGTCGGTCC 61.218 72.222 15.52 7.69 0.00 4.46
251 252 2.439883 ACTAGGGGCGAGTCGGTC 60.440 66.667 15.52 0.00 0.00 4.79
252 253 2.754658 CACTAGGGGCGAGTCGGT 60.755 66.667 15.52 0.00 0.00 4.69
253 254 4.208686 GCACTAGGGGCGAGTCGG 62.209 72.222 15.52 0.00 0.00 4.79
254 255 4.208686 GGCACTAGGGGCGAGTCG 62.209 72.222 8.54 8.54 0.00 4.18
255 256 1.972660 AATGGCACTAGGGGCGAGTC 61.973 60.000 14.62 0.00 35.84 3.36
256 257 1.562672 AAATGGCACTAGGGGCGAGT 61.563 55.000 14.62 0.83 35.84 4.18
257 258 0.394352 AAAATGGCACTAGGGGCGAG 60.394 55.000 14.62 0.00 35.84 5.03
258 259 0.039035 AAAAATGGCACTAGGGGCGA 59.961 50.000 14.62 4.93 35.84 5.54
259 260 2.578683 AAAAATGGCACTAGGGGCG 58.421 52.632 14.62 0.00 35.84 6.13
275 276 2.981350 GGGTGAGCCGGCGAAAAA 60.981 61.111 23.20 2.78 34.97 1.94
292 293 3.508840 CTAAAAGCGCCGCCTGGG 61.509 66.667 4.98 0.00 39.58 4.45
293 294 2.435938 TCTAAAAGCGCCGCCTGG 60.436 61.111 4.98 0.00 38.77 4.45
294 295 2.785258 GTCTAAAAGCGCCGCCTG 59.215 61.111 4.98 0.00 0.00 4.85
295 296 2.813908 CGTCTAAAAGCGCCGCCT 60.814 61.111 4.98 0.00 0.00 5.52
296 297 4.516135 GCGTCTAAAAGCGCCGCC 62.516 66.667 4.98 0.00 46.93 6.13
301 302 2.106683 CAGGGGGCGTCTAAAAGCG 61.107 63.158 0.00 0.00 0.00 4.68
302 303 0.744771 CTCAGGGGGCGTCTAAAAGC 60.745 60.000 0.00 0.00 0.00 3.51
303 304 0.107654 CCTCAGGGGGCGTCTAAAAG 60.108 60.000 0.00 0.00 0.00 2.27
304 305 1.988015 CCTCAGGGGGCGTCTAAAA 59.012 57.895 0.00 0.00 0.00 1.52
305 306 3.721868 CCTCAGGGGGCGTCTAAA 58.278 61.111 0.00 0.00 0.00 1.85
316 317 3.083997 AGCCGTTAGCCCCTCAGG 61.084 66.667 0.00 0.00 45.47 3.86
317 318 2.187946 CAGCCGTTAGCCCCTCAG 59.812 66.667 0.00 0.00 45.47 3.35
318 319 3.399181 CCAGCCGTTAGCCCCTCA 61.399 66.667 0.00 0.00 45.47 3.86
319 320 3.081409 TCCAGCCGTTAGCCCCTC 61.081 66.667 0.00 0.00 45.47 4.30
320 321 2.898472 ATCTCCAGCCGTTAGCCCCT 62.898 60.000 0.00 0.00 45.47 4.79
321 322 2.444256 ATCTCCAGCCGTTAGCCCC 61.444 63.158 0.00 0.00 45.47 5.80
322 323 1.227674 CATCTCCAGCCGTTAGCCC 60.228 63.158 0.00 0.00 45.47 5.19
323 324 1.889573 GCATCTCCAGCCGTTAGCC 60.890 63.158 0.00 0.00 45.47 3.93
324 325 1.889573 GGCATCTCCAGCCGTTAGC 60.890 63.158 0.00 0.00 43.15 3.09
325 326 4.445699 GGCATCTCCAGCCGTTAG 57.554 61.111 0.00 0.00 43.15 2.34
331 332 0.543749 ACACTAAGGGCATCTCCAGC 59.456 55.000 0.00 0.00 36.21 4.85
332 333 3.012518 CAAACACTAAGGGCATCTCCAG 58.987 50.000 0.00 0.00 36.21 3.86
333 334 2.879756 GCAAACACTAAGGGCATCTCCA 60.880 50.000 0.00 0.00 36.21 3.86
334 335 1.745653 GCAAACACTAAGGGCATCTCC 59.254 52.381 0.00 0.00 0.00 3.71
335 336 2.716217 AGCAAACACTAAGGGCATCTC 58.284 47.619 0.00 0.00 0.00 2.75
336 337 2.821969 CAAGCAAACACTAAGGGCATCT 59.178 45.455 0.00 0.00 0.00 2.90
337 338 2.558359 ACAAGCAAACACTAAGGGCATC 59.442 45.455 0.00 0.00 0.00 3.91
338 339 2.297033 CACAAGCAAACACTAAGGGCAT 59.703 45.455 0.00 0.00 0.00 4.40
339 340 1.680735 CACAAGCAAACACTAAGGGCA 59.319 47.619 0.00 0.00 0.00 5.36
340 341 1.681264 ACACAAGCAAACACTAAGGGC 59.319 47.619 0.00 0.00 0.00 5.19
341 342 2.948979 TGACACAAGCAAACACTAAGGG 59.051 45.455 0.00 0.00 0.00 3.95
342 343 4.335315 TCTTGACACAAGCAAACACTAAGG 59.665 41.667 6.62 0.00 0.00 2.69
353 354 4.756084 ATAGCAAGTTCTTGACACAAGC 57.244 40.909 15.52 0.00 0.00 4.01
373 374 2.915604 CCAGTTCCAGGAGGCCATATAT 59.084 50.000 5.01 0.00 33.74 0.86
379 380 1.201429 TCTTCCAGTTCCAGGAGGCC 61.201 60.000 0.00 0.00 36.33 5.19
394 395 3.699538 ACCTGGTTTGGTTTGTTCTCTTC 59.300 43.478 0.00 0.00 36.89 2.87
435 436 6.367983 AGCTAGATTATCCAGGCATTCAAAA 58.632 36.000 0.00 0.00 0.00 2.44
437 438 5.573380 AGCTAGATTATCCAGGCATTCAA 57.427 39.130 0.00 0.00 0.00 2.69
441 442 7.465116 ACATAAAAGCTAGATTATCCAGGCAT 58.535 34.615 0.00 0.00 0.00 4.40
452 453 9.105844 ACATAGGTCCATACATAAAAGCTAGAT 57.894 33.333 0.00 0.00 0.00 1.98
458 459 6.299141 AGCCACATAGGTCCATACATAAAAG 58.701 40.000 0.00 0.00 40.61 2.27
470 471 3.493350 CCACTGACATAGCCACATAGGTC 60.493 52.174 0.00 0.00 40.61 3.85
473 474 3.461061 CACCACTGACATAGCCACATAG 58.539 50.000 0.00 0.00 0.00 2.23
477 478 1.026718 GCCACCACTGACATAGCCAC 61.027 60.000 0.00 0.00 0.00 5.01
478 479 1.200760 AGCCACCACTGACATAGCCA 61.201 55.000 0.00 0.00 0.00 4.75
479 480 0.462759 GAGCCACCACTGACATAGCC 60.463 60.000 0.00 0.00 0.00 3.93
480 481 0.539051 AGAGCCACCACTGACATAGC 59.461 55.000 0.00 0.00 0.00 2.97
481 482 2.106566 AGAGAGCCACCACTGACATAG 58.893 52.381 0.00 0.00 0.00 2.23
496 497 2.093467 GCAAAGCGAGCAAAGTAGAGAG 59.907 50.000 0.00 0.00 0.00 3.20
498 499 2.072298 AGCAAAGCGAGCAAAGTAGAG 58.928 47.619 0.00 0.00 0.00 2.43
500 501 2.578495 CAAGCAAAGCGAGCAAAGTAG 58.422 47.619 0.00 0.00 0.00 2.57
531 532 8.751242 AGTTTGATCTCCTTAACTAGTCTTACC 58.249 37.037 0.00 0.00 0.00 2.85
547 548 9.531942 CCATCTATCTATATGCAGTTTGATCTC 57.468 37.037 0.00 0.00 0.00 2.75
576 577 2.228059 GCATGTGCATAGCTCCTTCAT 58.772 47.619 0.00 0.00 41.59 2.57
610 611 9.025041 CCAAAGTTATAACCCTCTGATTTTTCT 57.975 33.333 12.05 0.00 0.00 2.52
611 612 9.020731 TCCAAAGTTATAACCCTCTGATTTTTC 57.979 33.333 12.05 0.00 0.00 2.29
627 628 6.183361 ACCTCAACTTAACCCTCCAAAGTTAT 60.183 38.462 0.00 0.00 40.52 1.89
635 636 6.717997 TCAAATTTACCTCAACTTAACCCTCC 59.282 38.462 0.00 0.00 0.00 4.30
642 643 9.823647 TGCAAATTTCAAATTTACCTCAACTTA 57.176 25.926 7.80 0.00 0.00 2.24
645 646 8.772705 TGATGCAAATTTCAAATTTACCTCAAC 58.227 29.630 7.80 4.44 0.00 3.18
733 737 4.690719 ACCGCGTGCATTTCCGGA 62.691 61.111 19.41 0.00 43.20 5.14
799 841 3.057876 AGAGCAAGAGAGAGTAACACACG 60.058 47.826 0.00 0.00 0.00 4.49
800 842 4.022762 TGAGAGCAAGAGAGAGTAACACAC 60.023 45.833 0.00 0.00 0.00 3.82
807 849 2.170166 CCACTGAGAGCAAGAGAGAGT 58.830 52.381 0.00 0.00 0.00 3.24
818 860 0.324183 TGAGCTCCTCCCACTGAGAG 60.324 60.000 12.15 0.00 44.42 3.20
826 870 3.425162 TTCTTTTTCTGAGCTCCTCCC 57.575 47.619 12.15 0.00 0.00 4.30
835 879 9.167311 GCTCCTCATACTATTTTCTTTTTCTGA 57.833 33.333 0.00 0.00 0.00 3.27
849 893 1.709578 CTGCTGGGCTCCTCATACTA 58.290 55.000 0.00 0.00 0.00 1.82
897 941 2.096406 CGCCACGCAACGAGATTG 59.904 61.111 0.00 0.00 41.69 2.67
921 981 9.817809 GGTTTGATTAATTCCCCTTCTTTATTC 57.182 33.333 0.00 0.00 0.00 1.75
945 1005 3.292460 CGTCTGGATAAGGAAGAGAGGT 58.708 50.000 0.00 0.00 0.00 3.85
948 1008 2.032620 GCCGTCTGGATAAGGAAGAGA 58.967 52.381 0.00 0.00 37.49 3.10
953 1013 1.107538 CCGAGCCGTCTGGATAAGGA 61.108 60.000 0.00 0.00 34.48 3.36
975 1035 1.394266 GGCAGAGCAGAGGAGGAGAG 61.394 65.000 0.00 0.00 0.00 3.20
976 1036 1.381056 GGCAGAGCAGAGGAGGAGA 60.381 63.158 0.00 0.00 0.00 3.71
977 1037 1.049855 ATGGCAGAGCAGAGGAGGAG 61.050 60.000 0.00 0.00 0.00 3.69
978 1038 1.002662 ATGGCAGAGCAGAGGAGGA 59.997 57.895 0.00 0.00 0.00 3.71
979 1039 1.146485 CATGGCAGAGCAGAGGAGG 59.854 63.158 0.00 0.00 0.00 4.30
1015 1075 2.036256 GAAGCAGGTGGCCATGGT 59.964 61.111 9.72 7.04 46.50 3.55
1046 1106 1.203523 CGAGGTCTGGTGGAGAGAAAG 59.796 57.143 0.00 0.00 0.00 2.62
1047 1107 1.257743 CGAGGTCTGGTGGAGAGAAA 58.742 55.000 0.00 0.00 0.00 2.52
1048 1108 1.251527 GCGAGGTCTGGTGGAGAGAA 61.252 60.000 0.00 0.00 0.00 2.87
1089 1149 3.775654 CGGCGAGAAGGGGAGCTT 61.776 66.667 0.00 0.00 0.00 3.74
1091 1151 4.516195 GACGGCGAGAAGGGGAGC 62.516 72.222 16.62 0.00 0.00 4.70
1092 1152 4.194720 CGACGGCGAGAAGGGGAG 62.195 72.222 16.62 0.00 40.82 4.30
1319 1391 2.270923 CGAACCGCTTGATCTTGATCA 58.729 47.619 9.02 9.02 0.00 2.92
1806 1878 1.807981 CCGCCGCTTGTCGACAATA 60.808 57.895 29.79 10.66 41.67 1.90
1887 1959 1.211743 CGATCATGTCGTCCACCATG 58.788 55.000 8.84 0.00 45.19 3.66
2031 2103 2.911484 GTGATGATCACCTCCTGGAAC 58.089 52.381 14.48 0.00 41.37 3.62
2267 2349 3.002791 AGCAATGTCGTCGATGAATGTT 58.997 40.909 9.35 4.55 0.00 2.71
2390 2477 6.506500 AGAAGCAACTAATCCTTTCATGTG 57.493 37.500 0.00 0.00 0.00 3.21
2453 2544 2.287977 ATATGTGGCAGCAGCATCAT 57.712 45.000 2.65 9.16 44.61 2.45
2588 2690 5.371526 AGTGTGCATGGGTAAGATAATCAG 58.628 41.667 0.00 0.00 0.00 2.90
2592 2694 4.835284 TGAGTGTGCATGGGTAAGATAA 57.165 40.909 0.00 0.00 0.00 1.75
2645 2747 9.046296 CATTCGGTTCTGCTACTTATTATTTCT 57.954 33.333 0.00 0.00 0.00 2.52
2646 2748 8.827677 ACATTCGGTTCTGCTACTTATTATTTC 58.172 33.333 0.00 0.00 0.00 2.17
2653 2755 4.688879 CACAACATTCGGTTCTGCTACTTA 59.311 41.667 0.00 0.00 37.72 2.24
2663 2765 0.179004 TCCTGCCACAACATTCGGTT 60.179 50.000 0.00 0.00 41.47 4.44
2665 2767 0.958091 TTTCCTGCCACAACATTCGG 59.042 50.000 0.00 0.00 0.00 4.30
2667 2769 3.451141 TTGTTTCCTGCCACAACATTC 57.549 42.857 0.00 0.00 30.64 2.67
2687 2789 4.705023 AGCTATTTTACCGAATGCCTTTGT 59.295 37.500 0.00 0.00 0.00 2.83
2699 2801 6.519382 AGTATCAACCGGTAGCTATTTTACC 58.481 40.000 8.00 0.00 37.74 2.85
2707 2809 5.010820 GGATTAGAAGTATCAACCGGTAGCT 59.989 44.000 8.00 0.00 0.00 3.32
2761 2863 3.644265 TGTCTTAGAGTGGCAAGGTACAA 59.356 43.478 0.00 0.00 0.00 2.41
2822 2924 1.865970 CTGCTGGAAGATTCTCGCATC 59.134 52.381 8.84 0.00 34.07 3.91
2840 2942 1.068055 GCACAGGTGGAAGAATTGCTG 60.068 52.381 1.10 0.00 37.31 4.41
2886 2988 7.813148 CGTATATGGTGATCGAACTAATTTCCT 59.187 37.037 0.00 0.00 0.00 3.36
2888 2990 7.811236 TCCGTATATGGTGATCGAACTAATTTC 59.189 37.037 10.85 0.00 0.00 2.17
2903 3005 3.005897 GCATGACACTCTCCGTATATGGT 59.994 47.826 10.85 0.00 0.00 3.55
2963 3066 7.623999 AAGGACATTGACACTCTCCATATAT 57.376 36.000 0.00 0.00 0.00 0.86
2986 3089 5.244755 TGTGAGCATATGAAGCAGTTGTAA 58.755 37.500 6.97 0.00 0.00 2.41
2992 3095 5.996669 TTACATGTGAGCATATGAAGCAG 57.003 39.130 9.11 0.00 34.54 4.24
3048 3151 6.539173 TGGACAGAGTTACCATTTTGTGTAT 58.461 36.000 0.00 0.00 0.00 2.29
3064 3167 7.452880 TTTAATGATGGAAAGTTGGACAGAG 57.547 36.000 0.00 0.00 0.00 3.35
3109 3212 3.712016 TGCAGCCCTTGATTTGTACTA 57.288 42.857 0.00 0.00 0.00 1.82
3114 3217 6.576185 ACTTAATTATGCAGCCCTTGATTTG 58.424 36.000 0.00 0.00 0.00 2.32
3121 3224 7.337942 GCATATCTTACTTAATTATGCAGCCCT 59.662 37.037 13.81 0.00 38.77 5.19
3122 3225 7.337942 AGCATATCTTACTTAATTATGCAGCCC 59.662 37.037 17.65 0.00 40.65 5.19
3137 3240 8.414778 AGGTACTTCTGTTACAGCATATCTTAC 58.585 37.037 7.61 2.42 27.25 2.34
3139 3242 7.425224 AGGTACTTCTGTTACAGCATATCTT 57.575 36.000 7.61 0.00 27.25 2.40


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

AutoCloner maintained by Alex Coulton.