Multiple sequence alignment - TraesCS5D01G399400

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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 TraesCS5D01G399400 chr5D 100.000 1839 0 0 985 2823 465012873 465011035 0.000000e+00 3397
1 TraesCS5D01G399400 chr5D 100.000 715 0 0 1 715 465013857 465013143 0.000000e+00 1321
2 TraesCS5D01G399400 chr5D 83.134 836 82 31 997 1811 465022644 465021847 0.000000e+00 708
3 TraesCS5D01G399400 chr5D 87.917 240 29 0 1390 1629 465031487 465031248 1.660000e-72 283
4 TraesCS5D01G399400 chr5D 85.830 247 26 6 1052 1295 465031852 465031612 1.300000e-63 254
5 TraesCS5D01G399400 chr5D 88.281 128 11 3 589 715 465022838 465022714 1.750000e-32 150
6 TraesCS5D01G399400 chr5D 93.000 100 7 0 1725 1824 465030237 465030138 2.270000e-31 147
7 TraesCS5D01G399400 chr5D 81.006 179 29 4 63 237 387926006 387925829 1.360000e-28 137
8 TraesCS5D01G399400 chr5B 90.256 975 70 16 1866 2822 572363681 572362714 0.000000e+00 1251
9 TraesCS5D01G399400 chr5B 88.098 899 57 24 1000 1866 572364663 572363783 0.000000e+00 1022
10 TraesCS5D01G399400 chr5B 91.870 246 20 0 1384 1629 572379171 572378926 7.490000e-91 344
11 TraesCS5D01G399400 chr5B 87.582 306 18 7 415 715 572365028 572364738 1.250000e-88 337
12 TraesCS5D01G399400 chr5B 87.866 239 29 0 1390 1628 572390525 572390287 5.950000e-72 281
13 TraesCS5D01G399400 chr5B 87.978 183 16 4 1113 1295 572390826 572390650 7.920000e-51 211
14 TraesCS5D01G399400 chr5B 96.460 113 2 2 985 1096 572379411 572379300 4.800000e-43 185
15 TraesCS5D01G399400 chr5B 93.000 100 7 0 1725 1824 572389360 572389261 2.270000e-31 147
16 TraesCS5D01G399400 chr5B 88.776 98 11 0 1726 1823 572378840 572378743 1.370000e-23 121
17 TraesCS5D01G399400 chr5A 90.055 905 47 16 1000 1878 585417373 585416486 0.000000e+00 1133
18 TraesCS5D01G399400 chr5A 91.261 595 32 7 1899 2473 585416405 585415811 0.000000e+00 793
19 TraesCS5D01G399400 chr5A 93.460 367 21 3 2459 2823 585415796 585415431 2.470000e-150 542
20 TraesCS5D01G399400 chr5A 85.684 475 47 12 1162 1625 585421584 585421120 5.470000e-132 481
21 TraesCS5D01G399400 chr5A 89.686 223 23 0 1405 1627 585430141 585429919 4.600000e-73 285
22 TraesCS5D01G399400 chr5A 84.211 304 28 10 414 710 585417731 585417441 7.700000e-71 278
23 TraesCS5D01G399400 chr5A 89.017 173 13 2 997 1169 585426653 585426487 2.850000e-50 209
24 TraesCS5D01G399400 chr5A 92.361 144 10 1 1150 1293 585430415 585430273 1.330000e-48 204
25 TraesCS5D01G399400 chr5A 96.000 100 4 0 1725 1824 585429004 585428905 2.250000e-36 163
26 TraesCS5D01G399400 chr5A 94.565 92 5 0 590 681 585426843 585426752 2.930000e-30 143
27 TraesCS5D01G399400 chr5A 89.899 99 10 0 1726 1824 585421029 585420931 8.210000e-26 128
28 TraesCS5D01G399400 chr4D 83.468 248 37 2 3 246 189210060 189210307 7.870000e-56 228
29 TraesCS5D01G399400 chr7D 84.753 223 29 1 50 267 100990656 100990434 4.730000e-53 219
30 TraesCS5D01G399400 chr4B 82.000 250 34 8 4 246 32721524 32721279 4.770000e-48 202
31 TraesCS5D01G399400 chr3D 80.228 263 44 6 3 257 269209618 269209880 1.030000e-44 191
32 TraesCS5D01G399400 chr2A 82.723 191 26 4 62 248 428663295 428663482 2.250000e-36 163
33 TraesCS5D01G399400 chr2A 78.968 252 38 4 1 246 489795638 489795880 1.050000e-34 158
34 TraesCS5D01G399400 chr3B 82.386 176 28 2 84 256 493295894 493295719 1.750000e-32 150
35 TraesCS5D01G399400 chr7B 86.861 137 13 5 105 237 535860414 535860549 6.300000e-32 148


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 TraesCS5D01G399400 chr5D 465011035 465013857 2822 True 2359.000000 3397 100.000000 1 2823 2 chr5D.!!$R2 2822
1 TraesCS5D01G399400 chr5D 465021847 465022838 991 True 429.000000 708 85.707500 589 1811 2 chr5D.!!$R3 1222
2 TraesCS5D01G399400 chr5D 465030138 465031852 1714 True 228.000000 283 88.915667 1052 1824 3 chr5D.!!$R4 772
3 TraesCS5D01G399400 chr5B 572362714 572365028 2314 True 870.000000 1251 88.645333 415 2822 3 chr5B.!!$R1 2407
4 TraesCS5D01G399400 chr5B 572378743 572379411 668 True 216.666667 344 92.368667 985 1823 3 chr5B.!!$R2 838
5 TraesCS5D01G399400 chr5B 572389261 572390826 1565 True 213.000000 281 89.614667 1113 1824 3 chr5B.!!$R3 711
6 TraesCS5D01G399400 chr5A 585415431 585421584 6153 True 559.166667 1133 89.095000 414 2823 6 chr5A.!!$R1 2409
7 TraesCS5D01G399400 chr5A 585426487 585430415 3928 True 200.800000 285 92.325800 590 1824 5 chr5A.!!$R2 1234

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
229 230 0.178906 TATCCGGATCCAGATGGGCA 60.179 55.0 23.08 0.0 36.21 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 6774 0.54341 TCCTTGAAGGGGCACTACGA 60.543 55.0 11.99 0.0 35.59 3.43 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
25 26 2.809601 CGACCGACGCCCTCTTTG 60.810 66.667 0.00 0.00 34.51 2.77
26 27 2.654877 GACCGACGCCCTCTTTGA 59.345 61.111 0.00 0.00 0.00 2.69
28 29 2.434359 CCGACGCCCTCTTTGACC 60.434 66.667 0.00 0.00 0.00 4.02
29 30 2.809601 CGACGCCCTCTTTGACCG 60.810 66.667 0.00 0.00 0.00 4.79
30 31 2.342648 GACGCCCTCTTTGACCGT 59.657 61.111 0.00 0.00 34.52 4.83
32 33 2.030562 CGCCCTCTTTGACCGTGT 59.969 61.111 0.00 0.00 0.00 4.49
33 34 1.597027 CGCCCTCTTTGACCGTGTT 60.597 57.895 0.00 0.00 0.00 3.32
34 35 1.841663 CGCCCTCTTTGACCGTGTTG 61.842 60.000 0.00 0.00 0.00 3.33
35 36 0.534203 GCCCTCTTTGACCGTGTTGA 60.534 55.000 0.00 0.00 0.00 3.18
36 37 1.961793 CCCTCTTTGACCGTGTTGAA 58.038 50.000 0.00 0.00 0.00 2.69
37 38 1.873591 CCCTCTTTGACCGTGTTGAAG 59.126 52.381 0.00 0.00 0.00 3.02
38 39 1.264288 CCTCTTTGACCGTGTTGAAGC 59.736 52.381 0.00 0.00 0.00 3.86
46 47 2.081526 CGTGTTGAAGCGGAGATGG 58.918 57.895 0.00 0.00 0.00 3.51
47 48 0.389817 CGTGTTGAAGCGGAGATGGA 60.390 55.000 0.00 0.00 0.00 3.41
48 49 1.740380 CGTGTTGAAGCGGAGATGGAT 60.740 52.381 0.00 0.00 0.00 3.41
49 50 1.667724 GTGTTGAAGCGGAGATGGATG 59.332 52.381 0.00 0.00 0.00 3.51
52 53 1.958205 GAAGCGGAGATGGATGCGG 60.958 63.158 0.00 0.00 34.24 5.69
53 54 2.369257 GAAGCGGAGATGGATGCGGA 62.369 60.000 0.00 0.00 34.24 5.54
54 55 1.971505 AAGCGGAGATGGATGCGGAA 61.972 55.000 0.00 0.00 34.24 4.30
56 57 1.742146 CGGAGATGGATGCGGAAGA 59.258 57.895 0.00 0.00 0.00 2.87
58 59 1.043816 GGAGATGGATGCGGAAGAGA 58.956 55.000 0.00 0.00 0.00 3.10
59 60 1.270041 GGAGATGGATGCGGAAGAGAC 60.270 57.143 0.00 0.00 0.00 3.36
61 62 0.465705 GATGGATGCGGAAGAGACCA 59.534 55.000 0.00 0.00 33.92 4.02
63 64 0.250234 TGGATGCGGAAGAGACCAAG 59.750 55.000 0.00 0.00 0.00 3.61
64 65 0.462759 GGATGCGGAAGAGACCAAGG 60.463 60.000 0.00 0.00 0.00 3.61
66 67 0.539051 ATGCGGAAGAGACCAAGGAG 59.461 55.000 0.00 0.00 0.00 3.69
67 68 1.448717 GCGGAAGAGACCAAGGAGC 60.449 63.158 0.00 0.00 0.00 4.70
68 69 1.219393 CGGAAGAGACCAAGGAGCC 59.781 63.158 0.00 0.00 0.00 4.70
69 70 1.219393 GGAAGAGACCAAGGAGCCG 59.781 63.158 0.00 0.00 0.00 5.52
71 72 1.229209 AAGAGACCAAGGAGCCGGA 60.229 57.895 5.05 0.00 0.00 5.14
72 73 1.261238 AAGAGACCAAGGAGCCGGAG 61.261 60.000 5.05 0.00 0.00 4.63
73 74 1.985116 GAGACCAAGGAGCCGGAGT 60.985 63.158 5.05 0.00 0.00 3.85
74 75 1.536662 AGACCAAGGAGCCGGAGTT 60.537 57.895 5.05 0.00 0.00 3.01
77 78 3.121030 CAAGGAGCCGGAGTTGCG 61.121 66.667 5.05 0.00 0.00 4.85
78 79 4.394712 AAGGAGCCGGAGTTGCGG 62.395 66.667 5.05 7.78 0.00 5.69
112 113 4.059304 TGGCGTTGGGCATGGGAT 62.059 61.111 0.00 0.00 44.78 3.85
115 116 1.152963 GCGTTGGGCATGGGATAGT 60.153 57.895 0.00 0.00 42.87 2.12
116 117 1.447317 GCGTTGGGCATGGGATAGTG 61.447 60.000 0.00 0.00 42.87 2.74
117 118 0.819259 CGTTGGGCATGGGATAGTGG 60.819 60.000 0.00 0.00 0.00 4.00
118 119 0.550914 GTTGGGCATGGGATAGTGGA 59.449 55.000 0.00 0.00 0.00 4.02
119 120 0.550914 TTGGGCATGGGATAGTGGAC 59.449 55.000 0.00 0.00 0.00 4.02
120 121 0.623031 TGGGCATGGGATAGTGGACA 60.623 55.000 0.00 0.00 0.00 4.02
121 122 0.773644 GGGCATGGGATAGTGGACAT 59.226 55.000 0.00 0.00 0.00 3.06
122 123 1.271597 GGGCATGGGATAGTGGACATC 60.272 57.143 0.00 0.00 0.00 3.06
123 124 1.701847 GGCATGGGATAGTGGACATCT 59.298 52.381 0.00 0.00 0.00 2.90
124 125 2.107204 GGCATGGGATAGTGGACATCTT 59.893 50.000 0.00 0.00 0.00 2.40
125 126 3.435601 GGCATGGGATAGTGGACATCTTT 60.436 47.826 0.00 0.00 0.00 2.52
126 127 4.202461 GGCATGGGATAGTGGACATCTTTA 60.202 45.833 0.00 0.00 0.00 1.85
127 128 5.376625 GCATGGGATAGTGGACATCTTTAA 58.623 41.667 0.00 0.00 0.00 1.52
128 129 5.239525 GCATGGGATAGTGGACATCTTTAAC 59.760 44.000 0.00 0.00 0.00 2.01
129 130 5.018539 TGGGATAGTGGACATCTTTAACG 57.981 43.478 0.00 0.00 0.00 3.18
130 131 4.712829 TGGGATAGTGGACATCTTTAACGA 59.287 41.667 0.00 0.00 0.00 3.85
131 132 5.163447 TGGGATAGTGGACATCTTTAACGAG 60.163 44.000 0.00 0.00 0.00 4.18
132 133 5.290386 GGATAGTGGACATCTTTAACGAGG 58.710 45.833 0.00 0.00 0.00 4.63
133 134 5.068723 GGATAGTGGACATCTTTAACGAGGA 59.931 44.000 0.21 0.00 0.00 3.71
135 136 3.833070 AGTGGACATCTTTAACGAGGACT 59.167 43.478 0.21 0.00 0.00 3.85
136 137 5.014858 AGTGGACATCTTTAACGAGGACTA 58.985 41.667 0.21 0.00 0.00 2.59
138 139 5.805994 GTGGACATCTTTAACGAGGACTAAG 59.194 44.000 0.21 0.00 0.00 2.18
139 140 4.804665 GGACATCTTTAACGAGGACTAAGC 59.195 45.833 0.21 0.00 0.00 3.09
140 141 5.394333 GGACATCTTTAACGAGGACTAAGCT 60.394 44.000 0.21 0.00 0.00 3.74
141 142 6.183360 GGACATCTTTAACGAGGACTAAGCTA 60.183 42.308 0.21 0.00 0.00 3.32
142 143 6.797454 ACATCTTTAACGAGGACTAAGCTAG 58.203 40.000 0.21 0.00 0.00 3.42
143 144 6.377712 ACATCTTTAACGAGGACTAAGCTAGT 59.622 38.462 0.21 0.00 42.86 2.57
144 145 6.830873 TCTTTAACGAGGACTAAGCTAGTT 57.169 37.500 0.00 0.00 39.59 2.24
145 146 6.618811 TCTTTAACGAGGACTAAGCTAGTTG 58.381 40.000 0.00 0.00 39.59 3.16
147 148 6.770746 TTAACGAGGACTAAGCTAGTTGAT 57.229 37.500 0.00 0.00 39.59 2.57
149 150 4.528920 ACGAGGACTAAGCTAGTTGATCT 58.471 43.478 0.00 0.00 39.59 2.75
151 152 6.300703 ACGAGGACTAAGCTAGTTGATCTAT 58.699 40.000 0.00 0.00 39.59 1.98
152 153 6.205853 ACGAGGACTAAGCTAGTTGATCTATG 59.794 42.308 0.00 0.00 39.59 2.23
153 154 6.205853 CGAGGACTAAGCTAGTTGATCTATGT 59.794 42.308 0.00 0.00 39.59 2.29
154 155 7.388224 CGAGGACTAAGCTAGTTGATCTATGTA 59.612 40.741 0.00 0.00 39.59 2.29
155 156 8.630054 AGGACTAAGCTAGTTGATCTATGTAG 57.370 38.462 0.00 0.00 39.59 2.74
157 158 9.504708 GGACTAAGCTAGTTGATCTATGTAGTA 57.495 37.037 0.00 0.00 39.59 1.82
159 160 9.287373 ACTAAGCTAGTTGATCTATGTAGTACC 57.713 37.037 0.00 0.00 34.86 3.34
160 161 9.509956 CTAAGCTAGTTGATCTATGTAGTACCT 57.490 37.037 0.00 0.00 0.00 3.08
162 163 9.509956 AAGCTAGTTGATCTATGTAGTACCTAG 57.490 37.037 6.33 6.33 0.00 3.02
164 165 8.102047 GCTAGTTGATCTATGTAGTACCTAGGA 58.898 40.741 17.98 0.00 0.00 2.94
167 168 9.884814 AGTTGATCTATGTAGTACCTAGGATTT 57.115 33.333 17.98 2.20 0.00 2.17
210 211 8.840200 TGGACTTAAGATTTCTAGTATGAGGT 57.160 34.615 10.09 0.00 0.00 3.85
211 212 9.931698 TGGACTTAAGATTTCTAGTATGAGGTA 57.068 33.333 10.09 0.00 0.00 3.08
217 218 6.791371 AGATTTCTAGTATGAGGTATCCGGA 58.209 40.000 6.61 6.61 0.00 5.14
218 219 7.415086 AGATTTCTAGTATGAGGTATCCGGAT 58.585 38.462 22.95 22.95 0.00 4.18
219 220 7.558444 AGATTTCTAGTATGAGGTATCCGGATC 59.442 40.741 23.08 12.59 0.00 3.36
221 222 3.827817 AGTATGAGGTATCCGGATCCA 57.172 47.619 23.08 14.96 0.00 3.41
222 223 3.702792 AGTATGAGGTATCCGGATCCAG 58.297 50.000 23.08 0.00 0.00 3.86
223 224 3.333980 AGTATGAGGTATCCGGATCCAGA 59.666 47.826 23.08 6.30 0.00 3.86
224 225 3.481559 ATGAGGTATCCGGATCCAGAT 57.518 47.619 23.08 14.90 0.00 2.90
225 226 2.529632 TGAGGTATCCGGATCCAGATG 58.470 52.381 23.08 0.00 0.00 2.90
226 227 1.827969 GAGGTATCCGGATCCAGATGG 59.172 57.143 23.08 8.77 0.00 3.51
227 228 0.905357 GGTATCCGGATCCAGATGGG 59.095 60.000 23.08 8.40 35.41 4.00
229 230 0.178906 TATCCGGATCCAGATGGGCA 60.179 55.000 23.08 0.00 36.21 5.36
230 231 1.061905 ATCCGGATCCAGATGGGCAA 61.062 55.000 12.38 0.00 36.21 4.52
232 233 0.178981 CCGGATCCAGATGGGCAAAT 60.179 55.000 13.41 0.00 36.21 2.32
233 234 1.696063 CGGATCCAGATGGGCAAATT 58.304 50.000 13.41 0.00 36.21 1.82
234 235 2.034124 CGGATCCAGATGGGCAAATTT 58.966 47.619 13.41 0.00 36.21 1.82
236 237 3.033184 GGATCCAGATGGGCAAATTTGA 58.967 45.455 22.31 1.15 36.21 2.69
237 238 3.451902 GGATCCAGATGGGCAAATTTGAA 59.548 43.478 22.31 6.73 36.21 2.69
238 239 4.442472 GGATCCAGATGGGCAAATTTGAAG 60.442 45.833 22.31 0.00 36.21 3.02
239 240 2.234414 TCCAGATGGGCAAATTTGAAGC 59.766 45.455 22.31 8.95 36.21 3.86
240 241 2.235402 CCAGATGGGCAAATTTGAAGCT 59.765 45.455 22.31 11.02 0.00 3.74
241 242 3.307199 CCAGATGGGCAAATTTGAAGCTT 60.307 43.478 22.31 0.00 0.00 3.74
242 243 3.682858 CAGATGGGCAAATTTGAAGCTTG 59.317 43.478 22.31 8.20 0.00 4.01
243 244 3.579586 AGATGGGCAAATTTGAAGCTTGA 59.420 39.130 22.31 0.00 0.00 3.02
244 245 3.110447 TGGGCAAATTTGAAGCTTGAC 57.890 42.857 22.31 1.16 0.00 3.18
245 246 2.224257 TGGGCAAATTTGAAGCTTGACC 60.224 45.455 22.31 10.10 46.78 4.02
246 247 2.224257 GGGCAAATTTGAAGCTTGACCA 60.224 45.455 22.31 0.00 46.01 4.02
256 257 2.743928 CTTGACCAGCCAGCGTCC 60.744 66.667 0.00 0.00 0.00 4.79
257 258 4.680237 TTGACCAGCCAGCGTCCG 62.680 66.667 0.00 0.00 0.00 4.79
262 263 4.457496 CAGCCAGCGTCCGTGGAT 62.457 66.667 10.93 3.67 37.23 3.41
263 264 4.457496 AGCCAGCGTCCGTGGATG 62.457 66.667 3.65 3.65 37.23 3.51
277 278 4.910585 GATGCGCGGGTCCGGATT 62.911 66.667 7.81 0.00 39.40 3.01
278 279 4.483243 ATGCGCGGGTCCGGATTT 62.483 61.111 7.81 0.00 35.73 2.17
282 283 4.796495 GCGGGTCCGGATTTGCCT 62.796 66.667 7.81 0.00 40.19 4.75
284 285 2.124278 GGGTCCGGATTTGCCTCC 60.124 66.667 7.81 1.00 0.00 4.30
285 286 2.680370 GGGTCCGGATTTGCCTCCT 61.680 63.158 7.81 0.00 32.77 3.69
286 287 1.153147 GGTCCGGATTTGCCTCCTC 60.153 63.158 7.81 0.00 32.77 3.71
296 297 2.442272 GCCTCCTCCGGCTGTAGA 60.442 66.667 0.00 0.00 46.63 2.59
297 298 1.834822 GCCTCCTCCGGCTGTAGAT 60.835 63.158 0.00 0.00 46.63 1.98
298 299 2.045280 CCTCCTCCGGCTGTAGATG 58.955 63.158 0.00 0.00 0.00 2.90
299 300 1.365633 CTCCTCCGGCTGTAGATGC 59.634 63.158 0.00 0.00 0.00 3.91
300 301 1.075970 TCCTCCGGCTGTAGATGCT 60.076 57.895 0.00 0.00 0.00 3.79
301 302 1.109920 TCCTCCGGCTGTAGATGCTC 61.110 60.000 0.00 0.00 0.00 4.26
302 303 1.112315 CCTCCGGCTGTAGATGCTCT 61.112 60.000 0.00 0.00 0.00 4.09
303 304 0.749649 CTCCGGCTGTAGATGCTCTT 59.250 55.000 0.00 0.00 0.00 2.85
304 305 1.957177 CTCCGGCTGTAGATGCTCTTA 59.043 52.381 0.00 0.00 0.00 2.10
305 306 1.957177 TCCGGCTGTAGATGCTCTTAG 59.043 52.381 0.00 0.00 0.00 2.18
306 307 1.604185 CCGGCTGTAGATGCTCTTAGC 60.604 57.143 0.00 10.69 42.82 3.09
307 308 1.604185 CGGCTGTAGATGCTCTTAGCC 60.604 57.143 19.56 19.56 44.89 3.93
308 309 1.604185 GGCTGTAGATGCTCTTAGCCG 60.604 57.143 17.11 0.00 41.99 5.52
310 311 0.389391 TGTAGATGCTCTTAGCCGGC 59.611 55.000 21.89 21.89 41.51 6.13
311 312 0.664767 GTAGATGCTCTTAGCCGGCG 60.665 60.000 23.20 7.22 41.51 6.46
312 313 0.822121 TAGATGCTCTTAGCCGGCGA 60.822 55.000 23.20 14.61 41.51 5.54
313 314 1.227263 GATGCTCTTAGCCGGCGAA 60.227 57.895 23.20 22.12 41.51 4.70
314 315 1.491505 GATGCTCTTAGCCGGCGAAC 61.492 60.000 23.20 11.13 41.51 3.95
315 316 3.255379 GCTCTTAGCCGGCGAACG 61.255 66.667 23.20 15.58 43.80 3.95
316 317 2.181021 CTCTTAGCCGGCGAACGT 59.819 61.111 23.20 5.39 42.24 3.99
317 318 1.445582 CTCTTAGCCGGCGAACGTT 60.446 57.895 23.20 0.00 42.24 3.99
318 319 1.411493 CTCTTAGCCGGCGAACGTTC 61.411 60.000 23.20 18.47 42.24 3.95
331 332 2.885644 CGTTCGCCGTGGAGGATG 60.886 66.667 0.00 0.00 45.00 3.51
333 334 1.810030 GTTCGCCGTGGAGGATGAC 60.810 63.158 0.00 0.00 45.00 3.06
334 335 2.279810 TTCGCCGTGGAGGATGACA 61.280 57.895 0.00 0.00 45.00 3.58
336 337 2.100631 CGCCGTGGAGGATGACAAC 61.101 63.158 0.00 0.00 45.00 3.32
337 338 1.296715 GCCGTGGAGGATGACAACT 59.703 57.895 0.00 0.00 45.00 3.16
338 339 1.021390 GCCGTGGAGGATGACAACTG 61.021 60.000 0.00 0.00 45.00 3.16
339 340 0.321671 CCGTGGAGGATGACAACTGT 59.678 55.000 0.00 0.00 45.00 3.55
340 341 1.432514 CGTGGAGGATGACAACTGTG 58.567 55.000 0.00 0.00 0.00 3.66
342 343 2.547855 CGTGGAGGATGACAACTGTGAA 60.548 50.000 0.00 0.00 0.00 3.18
343 344 2.808543 GTGGAGGATGACAACTGTGAAC 59.191 50.000 0.00 0.00 0.00 3.18
344 345 2.069273 GGAGGATGACAACTGTGAACG 58.931 52.381 0.00 0.00 0.00 3.95
345 346 2.548067 GGAGGATGACAACTGTGAACGT 60.548 50.000 0.00 0.00 0.00 3.99
346 347 3.131396 GAGGATGACAACTGTGAACGTT 58.869 45.455 0.00 0.00 0.00 3.99
347 348 3.541632 AGGATGACAACTGTGAACGTTT 58.458 40.909 0.46 0.00 0.00 3.60
348 349 3.945285 AGGATGACAACTGTGAACGTTTT 59.055 39.130 0.46 0.00 0.00 2.43
349 350 4.035208 AGGATGACAACTGTGAACGTTTTC 59.965 41.667 0.46 0.00 0.00 2.29
350 351 4.201871 GGATGACAACTGTGAACGTTTTCA 60.202 41.667 0.46 4.23 39.55 2.69
351 352 4.955925 TGACAACTGTGAACGTTTTCAT 57.044 36.364 0.46 0.00 43.72 2.57
352 353 4.657055 TGACAACTGTGAACGTTTTCATG 58.343 39.130 0.46 4.29 43.72 3.07
353 354 4.027572 ACAACTGTGAACGTTTTCATGG 57.972 40.909 0.46 0.00 43.72 3.66
354 355 2.774439 ACTGTGAACGTTTTCATGGC 57.226 45.000 0.46 0.00 43.72 4.40
355 356 2.020720 ACTGTGAACGTTTTCATGGCA 58.979 42.857 0.46 0.00 43.72 4.92
356 357 2.033299 ACTGTGAACGTTTTCATGGCAG 59.967 45.455 0.46 3.70 43.72 4.85
357 358 2.020720 TGTGAACGTTTTCATGGCAGT 58.979 42.857 0.46 0.00 43.72 4.40
358 359 2.425312 TGTGAACGTTTTCATGGCAGTT 59.575 40.909 0.46 0.00 43.72 3.16
359 360 3.119316 TGTGAACGTTTTCATGGCAGTTT 60.119 39.130 0.46 0.00 43.72 2.66
360 361 3.485743 GTGAACGTTTTCATGGCAGTTTC 59.514 43.478 0.46 0.00 43.72 2.78
362 363 1.001815 ACGTTTTCATGGCAGTTTCGG 60.002 47.619 0.00 0.00 0.00 4.30
363 364 1.001815 CGTTTTCATGGCAGTTTCGGT 60.002 47.619 0.00 0.00 0.00 4.69
364 365 2.542824 CGTTTTCATGGCAGTTTCGGTT 60.543 45.455 0.00 0.00 0.00 4.44
365 366 2.791383 TTTCATGGCAGTTTCGGTTG 57.209 45.000 0.00 0.00 0.00 3.77
366 367 1.686355 TTCATGGCAGTTTCGGTTGT 58.314 45.000 0.00 0.00 0.00 3.32
367 368 2.552599 TCATGGCAGTTTCGGTTGTA 57.447 45.000 0.00 0.00 0.00 2.41
368 369 2.422597 TCATGGCAGTTTCGGTTGTAG 58.577 47.619 0.00 0.00 0.00 2.74
371 372 0.250597 GGCAGTTTCGGTTGTAGGGT 60.251 55.000 0.00 0.00 0.00 4.34
372 373 1.601166 GCAGTTTCGGTTGTAGGGTT 58.399 50.000 0.00 0.00 0.00 4.11
373 374 1.951602 GCAGTTTCGGTTGTAGGGTTT 59.048 47.619 0.00 0.00 0.00 3.27
374 375 2.287368 GCAGTTTCGGTTGTAGGGTTTG 60.287 50.000 0.00 0.00 0.00 2.93
376 377 1.677052 GTTTCGGTTGTAGGGTTTGCA 59.323 47.619 0.00 0.00 0.00 4.08
377 378 1.600023 TTCGGTTGTAGGGTTTGCAG 58.400 50.000 0.00 0.00 0.00 4.41
378 379 0.470766 TCGGTTGTAGGGTTTGCAGT 59.529 50.000 0.00 0.00 0.00 4.40
379 380 1.134037 TCGGTTGTAGGGTTTGCAGTT 60.134 47.619 0.00 0.00 0.00 3.16
380 381 1.679153 CGGTTGTAGGGTTTGCAGTTT 59.321 47.619 0.00 0.00 0.00 2.66
381 382 2.100087 CGGTTGTAGGGTTTGCAGTTTT 59.900 45.455 0.00 0.00 0.00 2.43
382 383 3.429684 CGGTTGTAGGGTTTGCAGTTTTT 60.430 43.478 0.00 0.00 0.00 1.94
383 384 4.116961 GGTTGTAGGGTTTGCAGTTTTTC 58.883 43.478 0.00 0.00 0.00 2.29
384 385 4.382147 GGTTGTAGGGTTTGCAGTTTTTCA 60.382 41.667 0.00 0.00 0.00 2.69
385 386 5.172205 GTTGTAGGGTTTGCAGTTTTTCAA 58.828 37.500 0.00 0.00 0.00 2.69
387 388 4.464597 TGTAGGGTTTGCAGTTTTTCAACT 59.535 37.500 0.00 0.00 44.72 3.16
389 390 5.262588 AGGGTTTGCAGTTTTTCAACTAG 57.737 39.130 0.00 0.00 41.69 2.57
391 392 4.429108 GGTTTGCAGTTTTTCAACTAGCA 58.571 39.130 7.63 7.63 41.69 3.49
392 393 5.049828 GGTTTGCAGTTTTTCAACTAGCAT 58.950 37.500 10.79 0.00 41.69 3.79
393 394 6.212955 GGTTTGCAGTTTTTCAACTAGCATA 58.787 36.000 10.79 6.10 41.69 3.14
394 395 6.363357 GGTTTGCAGTTTTTCAACTAGCATAG 59.637 38.462 10.79 0.00 41.69 2.23
395 396 5.046910 TGCAGTTTTTCAACTAGCATAGC 57.953 39.130 7.63 0.00 44.39 2.97
396 397 4.518590 TGCAGTTTTTCAACTAGCATAGCA 59.481 37.500 7.63 0.00 44.39 3.49
397 398 5.009510 TGCAGTTTTTCAACTAGCATAGCAA 59.990 36.000 7.63 0.00 44.39 3.91
398 399 6.095377 GCAGTTTTTCAACTAGCATAGCAAT 58.905 36.000 0.00 0.00 44.39 3.56
400 401 7.533426 CAGTTTTTCAACTAGCATAGCAATCT 58.467 34.615 0.00 0.00 44.39 2.40
401 402 7.484007 CAGTTTTTCAACTAGCATAGCAATCTG 59.516 37.037 0.00 0.00 44.39 2.90
402 403 7.175641 AGTTTTTCAACTAGCATAGCAATCTGT 59.824 33.333 0.00 0.00 44.39 3.41
404 405 4.445453 TCAACTAGCATAGCAATCTGTGG 58.555 43.478 0.00 0.00 44.39 4.17
405 406 2.843701 ACTAGCATAGCAATCTGTGGC 58.156 47.619 0.00 0.00 44.39 5.01
406 407 2.171237 ACTAGCATAGCAATCTGTGGCA 59.829 45.455 0.00 0.00 44.39 4.92
407 408 1.676746 AGCATAGCAATCTGTGGCAG 58.323 50.000 0.00 0.00 32.74 4.85
408 409 1.211212 AGCATAGCAATCTGTGGCAGA 59.789 47.619 1.06 1.06 44.99 4.26
409 410 1.602851 GCATAGCAATCTGTGGCAGAG 59.397 52.381 5.07 5.07 44.08 3.35
410 411 2.744166 GCATAGCAATCTGTGGCAGAGA 60.744 50.000 17.33 17.33 44.08 3.10
470 3911 3.120442 GCGAACGTTGGTTAGTTAGCATT 60.120 43.478 5.00 0.00 44.49 3.56
471 3912 4.634991 CGAACGTTGGTTAGTTAGCATTC 58.365 43.478 5.00 0.00 36.24 2.67
472 3913 4.150980 CGAACGTTGGTTAGTTAGCATTCA 59.849 41.667 5.00 0.00 36.24 2.57
473 3914 5.163893 CGAACGTTGGTTAGTTAGCATTCAT 60.164 40.000 5.00 0.00 36.24 2.57
474 3915 6.569179 AACGTTGGTTAGTTAGCATTCATT 57.431 33.333 0.00 0.00 33.72 2.57
479 3922 8.846607 CGTTGGTTAGTTAGCATTCATTTTTAC 58.153 33.333 0.00 0.00 33.55 2.01
524 3970 2.433446 CCTGACAAGGCTGCTGGT 59.567 61.111 0.00 0.00 36.56 4.00
525 3971 1.970114 CCTGACAAGGCTGCTGGTG 60.970 63.158 0.00 0.00 36.56 4.17
705 4161 1.134280 GCTCCCCATCCATATCCATCG 60.134 57.143 0.00 0.00 0.00 3.84
1310 4804 4.728102 CGTCGCCCACGGTAAGCA 62.728 66.667 2.97 0.00 45.46 3.91
1552 5127 0.694444 GACCCCAAGGAGGCCATCTA 60.694 60.000 5.01 0.00 36.73 1.98
1629 5204 3.006967 GGGCATGATCAAGAGGTACGTAT 59.993 47.826 0.00 0.00 0.00 3.06
1632 5207 4.620982 CATGATCAAGAGGTACGTATGCA 58.379 43.478 0.00 0.00 0.00 3.96
1676 5829 1.747709 GAGCTACCACTACTGACCGA 58.252 55.000 0.00 0.00 0.00 4.69
1683 5836 4.232188 ACCACTACTGACCGATTCTCTA 57.768 45.455 0.00 0.00 0.00 2.43
1853 6409 0.039527 CACAGGCTACGTTTTTGGGC 60.040 55.000 0.00 0.00 0.00 5.36
1854 6410 1.209127 CAGGCTACGTTTTTGGGCG 59.791 57.895 0.00 0.00 0.00 6.13
1855 6411 1.228033 AGGCTACGTTTTTGGGCGT 60.228 52.632 0.00 0.00 44.02 5.68
1856 6412 1.208358 GGCTACGTTTTTGGGCGTC 59.792 57.895 0.00 0.00 41.77 5.19
1859 6415 0.110373 CTACGTTTTTGGGCGTCTGC 60.110 55.000 0.00 0.00 41.77 4.26
1873 6532 2.479219 GCGTCTGCCAACTAGTAGTACC 60.479 54.545 2.50 0.00 33.98 3.34
1876 6535 2.758979 TCTGCCAACTAGTAGTACCAGC 59.241 50.000 2.50 5.19 0.00 4.85
1882 6541 2.100989 ACTAGTAGTACCAGCAGCACC 58.899 52.381 0.00 0.00 0.00 5.01
1917 6639 5.277058 CGACTAGTGCTTCCAATAAAGATGC 60.277 44.000 0.00 0.00 35.55 3.91
2001 6738 8.037382 TGTTCAGAAGTTCAATCTCAATCATC 57.963 34.615 5.50 0.00 0.00 2.92
2022 6759 2.040278 CAAGTTCTCCCAGGAATGTGGA 59.960 50.000 0.00 0.00 40.44 4.02
2056 6793 0.543410 TCGTAGTGCCCCTTCAAGGA 60.543 55.000 4.43 0.00 37.67 3.36
2076 6814 0.037046 CATGGGGGCTCAAAACAAGC 60.037 55.000 0.00 0.00 39.09 4.01
2119 6878 4.157289 TCTGGTTCACCTAATACGTGAGAC 59.843 45.833 0.00 0.00 41.10 3.36
2127 6892 4.096081 ACCTAATACGTGAGACTACACAGC 59.904 45.833 0.00 0.00 40.34 4.40
2130 6895 0.039074 ACGTGAGACTACACAGCTGC 60.039 55.000 15.27 0.00 40.34 5.25
2178 6943 5.924475 AATTCGTGTTTACCAGACTGAAG 57.076 39.130 3.32 0.00 0.00 3.02
2189 6954 3.139850 CCAGACTGAAGGATGCATCATC 58.860 50.000 27.25 22.85 39.87 2.92
2221 6987 2.492019 TAGGATGAACATCGCTGTCG 57.508 50.000 8.41 0.00 38.69 4.35
2242 7008 1.894466 CATTTCCACAAGCACCATGGA 59.106 47.619 21.47 0.00 40.83 3.41
2244 7010 0.539438 TTCCACAAGCACCATGGACC 60.539 55.000 21.47 8.59 42.26 4.46
2267 7033 3.525199 ACCTCATCAGAAGGCTAAATGGT 59.475 43.478 0.00 0.00 0.00 3.55
2442 7766 3.609409 CGCCTGGCAGAAGAAGTTTAAAC 60.609 47.826 20.29 10.47 0.00 2.01
2467 7791 8.246180 ACCATATGCATTAGAGAACAAACAAAG 58.754 33.333 3.54 0.00 0.00 2.77
2474 7827 8.227791 GCATTAGAGAACAAACAAAGTATTCGA 58.772 33.333 0.00 0.00 0.00 3.71
2481 7834 7.638683 AGAACAAACAAAGTATTCGAAAAGACG 59.361 33.333 0.00 0.00 31.81 4.18
2586 8423 7.019418 CACGGGTTCTTAAATTGTAAACTAGC 58.981 38.462 0.00 0.00 0.00 3.42
2731 8570 3.829948 CTGAAGTTGTGCTAAATGCCAG 58.170 45.455 0.00 0.00 42.00 4.85
2765 8604 6.102897 AGTTGCAACTACACTTGATCTACT 57.897 37.500 30.25 0.00 37.52 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.809601 CAAAGAGGGCGTCGGTCG 60.810 66.667 0.96 0.00 43.12 4.79
10 11 2.342648 GTCAAAGAGGGCGTCGGT 59.657 61.111 0.96 0.00 0.00 4.69
11 12 2.434359 GGTCAAAGAGGGCGTCGG 60.434 66.667 0.96 0.00 0.00 4.79
12 13 2.809601 CGGTCAAAGAGGGCGTCG 60.810 66.667 0.96 0.00 0.00 5.12
14 15 2.030562 CACGGTCAAAGAGGGCGT 59.969 61.111 0.00 0.00 0.00 5.68
17 18 1.873591 CTTCAACACGGTCAAAGAGGG 59.126 52.381 0.00 0.00 0.00 4.30
18 19 1.264288 GCTTCAACACGGTCAAAGAGG 59.736 52.381 0.00 0.00 0.00 3.69
19 20 1.070577 CGCTTCAACACGGTCAAAGAG 60.071 52.381 0.00 0.00 0.00 2.85
20 21 0.934496 CGCTTCAACACGGTCAAAGA 59.066 50.000 0.00 0.00 0.00 2.52
22 23 2.018544 CCGCTTCAACACGGTCAAA 58.981 52.632 0.00 0.00 44.46 2.69
23 24 3.725819 CCGCTTCAACACGGTCAA 58.274 55.556 0.00 0.00 44.46 3.18
28 29 0.389817 TCCATCTCCGCTTCAACACG 60.390 55.000 0.00 0.00 0.00 4.49
29 30 1.667724 CATCCATCTCCGCTTCAACAC 59.332 52.381 0.00 0.00 0.00 3.32
30 31 2.013563 GCATCCATCTCCGCTTCAACA 61.014 52.381 0.00 0.00 0.00 3.33
32 33 0.811219 CGCATCCATCTCCGCTTCAA 60.811 55.000 0.00 0.00 0.00 2.69
33 34 1.227350 CGCATCCATCTCCGCTTCA 60.227 57.895 0.00 0.00 0.00 3.02
34 35 1.958205 CCGCATCCATCTCCGCTTC 60.958 63.158 0.00 0.00 0.00 3.86
35 36 1.971505 TTCCGCATCCATCTCCGCTT 61.972 55.000 0.00 0.00 0.00 4.68
36 37 2.374830 CTTCCGCATCCATCTCCGCT 62.375 60.000 0.00 0.00 0.00 5.52
37 38 1.958205 CTTCCGCATCCATCTCCGC 60.958 63.158 0.00 0.00 0.00 5.54
38 39 0.319383 CTCTTCCGCATCCATCTCCG 60.319 60.000 0.00 0.00 0.00 4.63
40 41 1.270041 GGTCTCTTCCGCATCCATCTC 60.270 57.143 0.00 0.00 0.00 2.75
42 43 0.465705 TGGTCTCTTCCGCATCCATC 59.534 55.000 0.00 0.00 0.00 3.51
43 44 0.911769 TTGGTCTCTTCCGCATCCAT 59.088 50.000 0.00 0.00 0.00 3.41
44 45 0.250234 CTTGGTCTCTTCCGCATCCA 59.750 55.000 0.00 0.00 0.00 3.41
46 47 0.537188 TCCTTGGTCTCTTCCGCATC 59.463 55.000 0.00 0.00 0.00 3.91
47 48 0.539051 CTCCTTGGTCTCTTCCGCAT 59.461 55.000 0.00 0.00 0.00 4.73
48 49 1.975327 CTCCTTGGTCTCTTCCGCA 59.025 57.895 0.00 0.00 0.00 5.69
49 50 1.448717 GCTCCTTGGTCTCTTCCGC 60.449 63.158 0.00 0.00 0.00 5.54
52 53 1.219393 CCGGCTCCTTGGTCTCTTC 59.781 63.158 0.00 0.00 0.00 2.87
53 54 1.229209 TCCGGCTCCTTGGTCTCTT 60.229 57.895 0.00 0.00 0.00 2.85
54 55 1.684049 CTCCGGCTCCTTGGTCTCT 60.684 63.158 0.00 0.00 0.00 3.10
56 57 1.536662 AACTCCGGCTCCTTGGTCT 60.537 57.895 0.00 0.00 0.00 3.85
58 59 2.750350 CAACTCCGGCTCCTTGGT 59.250 61.111 0.00 0.00 0.00 3.67
59 60 2.747855 GCAACTCCGGCTCCTTGG 60.748 66.667 0.00 0.00 0.00 3.61
61 62 4.394712 CCGCAACTCCGGCTCCTT 62.395 66.667 0.00 0.00 42.03 3.36
85 86 3.751246 CAACGCCAGGTGCATGGG 61.751 66.667 8.41 2.86 40.97 4.00
86 87 3.751246 CCAACGCCAGGTGCATGG 61.751 66.667 10.30 10.30 43.72 3.66
91 92 3.751246 CATGCCCAACGCCAGGTG 61.751 66.667 0.00 0.00 36.24 4.00
94 95 2.623094 TATCCCATGCCCAACGCCAG 62.623 60.000 0.00 0.00 36.24 4.85
96 97 1.898574 CTATCCCATGCCCAACGCC 60.899 63.158 0.00 0.00 36.24 5.68
98 99 0.819259 CCACTATCCCATGCCCAACG 60.819 60.000 0.00 0.00 0.00 4.10
99 100 0.550914 TCCACTATCCCATGCCCAAC 59.449 55.000 0.00 0.00 0.00 3.77
100 101 0.550914 GTCCACTATCCCATGCCCAA 59.449 55.000 0.00 0.00 0.00 4.12
102 103 0.773644 ATGTCCACTATCCCATGCCC 59.226 55.000 0.00 0.00 0.00 5.36
103 104 1.701847 AGATGTCCACTATCCCATGCC 59.298 52.381 0.00 0.00 0.00 4.40
104 105 3.498774 AAGATGTCCACTATCCCATGC 57.501 47.619 0.00 0.00 0.00 4.06
106 107 5.365605 TCGTTAAAGATGTCCACTATCCCAT 59.634 40.000 0.00 0.00 0.00 4.00
107 108 4.712829 TCGTTAAAGATGTCCACTATCCCA 59.287 41.667 0.00 0.00 0.00 4.37
108 109 5.272283 TCGTTAAAGATGTCCACTATCCC 57.728 43.478 0.00 0.00 0.00 3.85
110 111 5.978322 GTCCTCGTTAAAGATGTCCACTATC 59.022 44.000 0.00 0.00 0.00 2.08
111 112 5.657302 AGTCCTCGTTAAAGATGTCCACTAT 59.343 40.000 0.00 0.00 0.00 2.12
112 113 5.014858 AGTCCTCGTTAAAGATGTCCACTA 58.985 41.667 0.00 0.00 0.00 2.74
115 116 5.623824 GCTTAGTCCTCGTTAAAGATGTCCA 60.624 44.000 0.00 0.00 0.00 4.02
116 117 4.804665 GCTTAGTCCTCGTTAAAGATGTCC 59.195 45.833 0.00 0.00 0.00 4.02
117 118 5.652518 AGCTTAGTCCTCGTTAAAGATGTC 58.347 41.667 0.00 0.00 0.00 3.06
118 119 5.662674 AGCTTAGTCCTCGTTAAAGATGT 57.337 39.130 0.00 0.00 0.00 3.06
119 120 6.797454 ACTAGCTTAGTCCTCGTTAAAGATG 58.203 40.000 0.00 0.00 32.47 2.90
120 121 7.122353 TCAACTAGCTTAGTCCTCGTTAAAGAT 59.878 37.037 0.00 0.00 38.26 2.40
121 122 6.432162 TCAACTAGCTTAGTCCTCGTTAAAGA 59.568 38.462 0.00 0.00 38.26 2.52
122 123 6.618811 TCAACTAGCTTAGTCCTCGTTAAAG 58.381 40.000 0.00 0.00 38.26 1.85
123 124 6.579666 TCAACTAGCTTAGTCCTCGTTAAA 57.420 37.500 0.00 0.00 38.26 1.52
124 125 6.602406 AGATCAACTAGCTTAGTCCTCGTTAA 59.398 38.462 0.00 0.00 38.26 2.01
125 126 6.120905 AGATCAACTAGCTTAGTCCTCGTTA 58.879 40.000 0.00 0.00 38.26 3.18
126 127 4.951094 AGATCAACTAGCTTAGTCCTCGTT 59.049 41.667 0.00 0.00 38.26 3.85
127 128 4.528920 AGATCAACTAGCTTAGTCCTCGT 58.471 43.478 0.00 0.00 38.26 4.18
128 129 6.205853 ACATAGATCAACTAGCTTAGTCCTCG 59.794 42.308 0.00 0.00 38.26 4.63
129 130 7.519032 ACATAGATCAACTAGCTTAGTCCTC 57.481 40.000 0.00 0.00 38.26 3.71
130 131 8.221944 ACTACATAGATCAACTAGCTTAGTCCT 58.778 37.037 0.00 0.00 38.26 3.85
131 132 8.398878 ACTACATAGATCAACTAGCTTAGTCC 57.601 38.462 0.00 0.00 38.26 3.85
133 134 9.287373 GGTACTACATAGATCAACTAGCTTAGT 57.713 37.037 0.00 0.00 41.73 2.24
136 137 9.509956 CTAGGTACTACATAGATCAACTAGCTT 57.490 37.037 2.25 0.00 41.75 3.74
138 139 8.102047 TCCTAGGTACTACATAGATCAACTAGC 58.898 40.741 9.08 0.00 41.75 3.42
141 142 9.884814 AAATCCTAGGTACTACATAGATCAACT 57.115 33.333 9.08 0.00 41.75 3.16
168 169 9.906660 CTTAAGTCCATACAAAAGTATGCAAAA 57.093 29.630 9.52 0.00 36.32 2.44
169 170 9.290988 TCTTAAGTCCATACAAAAGTATGCAAA 57.709 29.630 9.52 0.00 36.32 3.68
170 171 8.856153 TCTTAAGTCCATACAAAAGTATGCAA 57.144 30.769 9.52 0.00 36.32 4.08
171 172 9.461312 AATCTTAAGTCCATACAAAAGTATGCA 57.539 29.630 9.52 0.00 36.32 3.96
184 185 9.440761 ACCTCATACTAGAAATCTTAAGTCCAT 57.559 33.333 1.63 0.00 0.00 3.41
185 186 8.840200 ACCTCATACTAGAAATCTTAAGTCCA 57.160 34.615 1.63 0.00 0.00 4.02
190 191 9.021807 CCGGATACCTCATACTAGAAATCTTAA 57.978 37.037 0.00 0.00 0.00 1.85
191 192 8.388589 TCCGGATACCTCATACTAGAAATCTTA 58.611 37.037 0.00 0.00 0.00 2.10
192 193 7.239438 TCCGGATACCTCATACTAGAAATCTT 58.761 38.462 0.00 0.00 0.00 2.40
193 194 6.791371 TCCGGATACCTCATACTAGAAATCT 58.209 40.000 0.00 0.00 0.00 2.40
194 195 7.201839 GGATCCGGATACCTCATACTAGAAATC 60.202 44.444 19.15 0.00 0.00 2.17
196 197 5.950549 GGATCCGGATACCTCATACTAGAAA 59.049 44.000 19.15 0.00 0.00 2.52
197 198 5.014860 TGGATCCGGATACCTCATACTAGAA 59.985 44.000 24.31 0.00 0.00 2.10
198 199 4.538891 TGGATCCGGATACCTCATACTAGA 59.461 45.833 24.31 0.00 0.00 2.43
199 200 4.856509 TGGATCCGGATACCTCATACTAG 58.143 47.826 24.31 0.00 0.00 2.57
200 201 4.538891 TCTGGATCCGGATACCTCATACTA 59.461 45.833 24.31 1.32 0.00 1.82
202 203 3.698289 TCTGGATCCGGATACCTCATAC 58.302 50.000 24.31 5.57 0.00 2.39
203 204 4.281657 CATCTGGATCCGGATACCTCATA 58.718 47.826 31.50 3.69 39.80 2.15
204 205 3.102972 CATCTGGATCCGGATACCTCAT 58.897 50.000 31.50 10.08 39.80 2.90
205 206 2.529632 CATCTGGATCCGGATACCTCA 58.470 52.381 31.50 14.97 39.80 3.86
206 207 1.827969 CCATCTGGATCCGGATACCTC 59.172 57.143 31.50 9.33 39.80 3.85
207 208 1.553417 CCCATCTGGATCCGGATACCT 60.553 57.143 31.50 11.93 39.80 3.08
208 209 0.905357 CCCATCTGGATCCGGATACC 59.095 60.000 31.50 21.82 39.80 2.73
210 211 0.178906 TGCCCATCTGGATCCGGATA 60.179 55.000 31.50 16.40 39.80 2.59
211 212 1.061905 TTGCCCATCTGGATCCGGAT 61.062 55.000 27.70 27.70 42.28 4.18
212 213 1.278302 TTTGCCCATCTGGATCCGGA 61.278 55.000 25.60 25.60 37.39 5.14
214 215 1.696063 AATTTGCCCATCTGGATCCG 58.304 50.000 7.39 2.06 37.39 4.18
215 216 3.033184 TCAAATTTGCCCATCTGGATCC 58.967 45.455 13.54 4.20 37.39 3.36
217 218 3.118519 GCTTCAAATTTGCCCATCTGGAT 60.119 43.478 13.54 0.00 37.39 3.41
218 219 2.234414 GCTTCAAATTTGCCCATCTGGA 59.766 45.455 13.54 0.00 37.39 3.86
219 220 2.235402 AGCTTCAAATTTGCCCATCTGG 59.765 45.455 13.54 0.00 37.09 3.86
221 222 3.579586 TCAAGCTTCAAATTTGCCCATCT 59.420 39.130 13.54 3.40 0.00 2.90
222 223 3.681417 GTCAAGCTTCAAATTTGCCCATC 59.319 43.478 13.54 1.24 0.00 3.51
223 224 3.557686 GGTCAAGCTTCAAATTTGCCCAT 60.558 43.478 13.54 0.00 0.00 4.00
224 225 2.224257 GGTCAAGCTTCAAATTTGCCCA 60.224 45.455 13.54 0.00 0.00 5.36
225 226 2.224257 TGGTCAAGCTTCAAATTTGCCC 60.224 45.455 13.54 4.16 0.00 5.36
226 227 3.062042 CTGGTCAAGCTTCAAATTTGCC 58.938 45.455 13.54 6.76 0.00 4.52
239 240 2.743928 GGACGCTGGCTGGTCAAG 60.744 66.667 12.46 0.00 34.87 3.02
240 241 4.680237 CGGACGCTGGCTGGTCAA 62.680 66.667 12.46 0.00 34.87 3.18
245 246 4.457496 ATCCACGGACGCTGGCTG 62.457 66.667 7.97 0.00 0.00 4.85
246 247 4.457496 CATCCACGGACGCTGGCT 62.457 66.667 7.97 0.00 0.00 4.75
260 261 4.910585 AATCCGGACCCGCGCATC 62.911 66.667 6.12 0.74 38.24 3.91
261 262 4.483243 AAATCCGGACCCGCGCAT 62.483 61.111 6.12 0.00 38.24 4.73
266 267 2.513897 GAGGCAAATCCGGACCCG 60.514 66.667 6.12 0.66 40.77 5.28
267 268 2.124278 GGAGGCAAATCCGGACCC 60.124 66.667 6.12 5.10 40.77 4.46
269 270 1.153147 GGAGGAGGCAAATCCGGAC 60.153 63.158 6.12 0.00 44.65 4.79
270 271 3.320359 GGAGGAGGCAAATCCGGA 58.680 61.111 6.61 6.61 44.65 5.14
295 296 1.227263 TTCGCCGGCTAAGAGCATC 60.227 57.895 26.68 0.00 44.75 3.91
296 297 1.521681 GTTCGCCGGCTAAGAGCAT 60.522 57.895 26.68 0.00 44.75 3.79
297 298 2.125673 GTTCGCCGGCTAAGAGCA 60.126 61.111 26.68 0.00 44.75 4.26
298 299 3.255379 CGTTCGCCGGCTAAGAGC 61.255 66.667 26.68 15.39 41.46 4.09
299 300 1.411493 GAACGTTCGCCGGCTAAGAG 61.411 60.000 26.68 18.35 42.24 2.85
300 301 1.444895 GAACGTTCGCCGGCTAAGA 60.445 57.895 26.68 12.15 42.24 2.10
301 302 2.785105 CGAACGTTCGCCGGCTAAG 61.785 63.158 34.54 16.64 44.26 2.18
302 303 2.806198 CGAACGTTCGCCGGCTAA 60.806 61.111 34.54 18.39 44.26 3.09
315 316 1.810030 GTCATCCTCCACGGCGAAC 60.810 63.158 16.62 0.00 0.00 3.95
316 317 1.822114 TTGTCATCCTCCACGGCGAA 61.822 55.000 16.62 0.00 0.00 4.70
317 318 2.279810 TTGTCATCCTCCACGGCGA 61.280 57.895 16.62 0.00 0.00 5.54
318 319 2.100631 GTTGTCATCCTCCACGGCG 61.101 63.158 4.80 4.80 0.00 6.46
319 320 1.021390 CAGTTGTCATCCTCCACGGC 61.021 60.000 0.00 0.00 0.00 5.68
320 321 0.321671 ACAGTTGTCATCCTCCACGG 59.678 55.000 0.00 0.00 0.00 4.94
321 322 1.000843 TCACAGTTGTCATCCTCCACG 59.999 52.381 0.00 0.00 0.00 4.94
323 324 2.547855 CGTTCACAGTTGTCATCCTCCA 60.548 50.000 0.00 0.00 0.00 3.86
324 325 2.069273 CGTTCACAGTTGTCATCCTCC 58.931 52.381 0.00 0.00 0.00 4.30
326 327 2.910688 ACGTTCACAGTTGTCATCCT 57.089 45.000 0.00 0.00 0.00 3.24
328 329 4.904116 TGAAAACGTTCACAGTTGTCATC 58.096 39.130 0.00 0.00 39.95 2.92
329 330 4.955925 TGAAAACGTTCACAGTTGTCAT 57.044 36.364 0.00 0.00 39.95 3.06
330 331 4.438065 CCATGAAAACGTTCACAGTTGTCA 60.438 41.667 0.00 4.68 46.40 3.58
331 332 4.035017 CCATGAAAACGTTCACAGTTGTC 58.965 43.478 0.00 0.00 46.40 3.18
333 334 2.788786 GCCATGAAAACGTTCACAGTTG 59.211 45.455 0.00 1.75 46.40 3.16
334 335 2.425312 TGCCATGAAAACGTTCACAGTT 59.575 40.909 0.00 0.00 46.40 3.16
336 337 2.033299 ACTGCCATGAAAACGTTCACAG 59.967 45.455 0.00 3.19 46.40 3.66
337 338 2.020720 ACTGCCATGAAAACGTTCACA 58.979 42.857 0.00 5.50 46.40 3.58
338 339 2.774439 ACTGCCATGAAAACGTTCAC 57.226 45.000 0.00 0.00 46.40 3.18
340 341 2.719046 CGAAACTGCCATGAAAACGTTC 59.281 45.455 0.00 0.00 0.00 3.95
342 343 1.001815 CCGAAACTGCCATGAAAACGT 60.002 47.619 0.00 0.00 0.00 3.99
343 344 1.001815 ACCGAAACTGCCATGAAAACG 60.002 47.619 0.00 0.00 0.00 3.60
344 345 2.793278 ACCGAAACTGCCATGAAAAC 57.207 45.000 0.00 0.00 0.00 2.43
345 346 2.428890 ACAACCGAAACTGCCATGAAAA 59.571 40.909 0.00 0.00 0.00 2.29
346 347 2.028130 ACAACCGAAACTGCCATGAAA 58.972 42.857 0.00 0.00 0.00 2.69
347 348 1.686355 ACAACCGAAACTGCCATGAA 58.314 45.000 0.00 0.00 0.00 2.57
348 349 2.422597 CTACAACCGAAACTGCCATGA 58.577 47.619 0.00 0.00 0.00 3.07
349 350 1.468520 CCTACAACCGAAACTGCCATG 59.531 52.381 0.00 0.00 0.00 3.66
350 351 1.613255 CCCTACAACCGAAACTGCCAT 60.613 52.381 0.00 0.00 0.00 4.40
351 352 0.250553 CCCTACAACCGAAACTGCCA 60.251 55.000 0.00 0.00 0.00 4.92
352 353 0.250597 ACCCTACAACCGAAACTGCC 60.251 55.000 0.00 0.00 0.00 4.85
353 354 1.601166 AACCCTACAACCGAAACTGC 58.399 50.000 0.00 0.00 0.00 4.40
354 355 2.287368 GCAAACCCTACAACCGAAACTG 60.287 50.000 0.00 0.00 0.00 3.16
355 356 1.951602 GCAAACCCTACAACCGAAACT 59.048 47.619 0.00 0.00 0.00 2.66
356 357 1.677052 TGCAAACCCTACAACCGAAAC 59.323 47.619 0.00 0.00 0.00 2.78
357 358 1.950909 CTGCAAACCCTACAACCGAAA 59.049 47.619 0.00 0.00 0.00 3.46
358 359 1.134037 ACTGCAAACCCTACAACCGAA 60.134 47.619 0.00 0.00 0.00 4.30
359 360 0.470766 ACTGCAAACCCTACAACCGA 59.529 50.000 0.00 0.00 0.00 4.69
360 361 1.314730 AACTGCAAACCCTACAACCG 58.685 50.000 0.00 0.00 0.00 4.44
362 363 4.749976 TGAAAAACTGCAAACCCTACAAC 58.250 39.130 0.00 0.00 0.00 3.32
363 364 5.046950 AGTTGAAAAACTGCAAACCCTACAA 60.047 36.000 0.00 0.00 0.00 2.41
364 365 4.464597 AGTTGAAAAACTGCAAACCCTACA 59.535 37.500 0.00 0.00 0.00 2.74
365 366 5.006153 AGTTGAAAAACTGCAAACCCTAC 57.994 39.130 0.00 0.00 0.00 3.18
366 367 5.221165 GCTAGTTGAAAAACTGCAAACCCTA 60.221 40.000 1.42 0.00 34.37 3.53
367 368 4.441495 GCTAGTTGAAAAACTGCAAACCCT 60.441 41.667 1.42 0.00 34.37 4.34
368 369 3.802139 GCTAGTTGAAAAACTGCAAACCC 59.198 43.478 1.42 0.00 34.37 4.11
371 372 5.920273 GCTATGCTAGTTGAAAAACTGCAAA 59.080 36.000 14.86 0.69 38.89 3.68
372 373 5.009510 TGCTATGCTAGTTGAAAAACTGCAA 59.990 36.000 14.86 0.00 38.89 4.08
373 374 4.518590 TGCTATGCTAGTTGAAAAACTGCA 59.481 37.500 13.88 13.88 39.34 4.41
374 375 5.046910 TGCTATGCTAGTTGAAAAACTGC 57.953 39.130 1.42 4.32 34.37 4.40
376 377 7.175641 ACAGATTGCTATGCTAGTTGAAAAACT 59.824 33.333 0.00 0.00 36.82 2.66
377 378 7.272084 CACAGATTGCTATGCTAGTTGAAAAAC 59.728 37.037 0.00 0.00 0.00 2.43
378 379 7.307694 CACAGATTGCTATGCTAGTTGAAAAA 58.692 34.615 0.00 0.00 0.00 1.94
379 380 6.127925 CCACAGATTGCTATGCTAGTTGAAAA 60.128 38.462 0.00 0.00 0.00 2.29
380 381 5.355071 CCACAGATTGCTATGCTAGTTGAAA 59.645 40.000 0.00 0.00 0.00 2.69
381 382 4.877823 CCACAGATTGCTATGCTAGTTGAA 59.122 41.667 0.00 0.00 0.00 2.69
382 383 4.445453 CCACAGATTGCTATGCTAGTTGA 58.555 43.478 0.00 0.00 0.00 3.18
383 384 3.003068 GCCACAGATTGCTATGCTAGTTG 59.997 47.826 0.00 0.00 0.00 3.16
384 385 3.209410 GCCACAGATTGCTATGCTAGTT 58.791 45.455 0.00 0.00 0.00 2.24
385 386 2.171237 TGCCACAGATTGCTATGCTAGT 59.829 45.455 0.00 0.00 0.00 2.57
387 388 2.435437 TCTGCCACAGATTGCTATGCTA 59.565 45.455 0.00 0.00 35.39 3.49
389 390 1.602851 CTCTGCCACAGATTGCTATGC 59.397 52.381 0.00 0.00 39.92 3.14
391 392 2.485124 GCTCTCTGCCACAGATTGCTAT 60.485 50.000 11.95 0.00 39.92 2.97
392 393 1.134580 GCTCTCTGCCACAGATTGCTA 60.135 52.381 11.95 0.00 39.92 3.49
393 394 0.392729 GCTCTCTGCCACAGATTGCT 60.393 55.000 11.95 0.00 39.92 3.91
394 395 2.096596 GCTCTCTGCCACAGATTGC 58.903 57.895 0.00 2.51 39.92 3.56
404 405 4.742201 TCGCAACCGGCTCTCTGC 62.742 66.667 0.00 1.82 41.67 4.26
405 406 2.048222 TTCGCAACCGGCTCTCTG 60.048 61.111 0.00 0.00 41.67 3.35
406 407 2.048127 GTTCGCAACCGGCTCTCT 60.048 61.111 0.00 0.00 41.67 3.10
407 408 3.479269 CGTTCGCAACCGGCTCTC 61.479 66.667 0.00 0.00 41.67 3.20
408 409 4.295119 ACGTTCGCAACCGGCTCT 62.295 61.111 0.00 0.00 41.67 4.09
409 410 4.072088 CACGTTCGCAACCGGCTC 62.072 66.667 0.00 0.00 41.67 4.70
410 411 4.903010 ACACGTTCGCAACCGGCT 62.903 61.111 0.00 0.00 41.67 5.52
422 423 0.040425 GAAATTGCCAGCGAACACGT 60.040 50.000 0.00 0.00 0.00 4.49
479 3922 5.571357 CCGGAAACCGTAATGATTTTTCTTG 59.429 40.000 0.00 0.00 46.80 3.02
490 3933 1.377594 GGCCACCGGAAACCGTAAT 60.378 57.895 9.46 0.00 46.80 1.89
495 3938 2.671963 GTCAGGCCACCGGAAACC 60.672 66.667 9.46 5.77 28.12 3.27
587 4033 1.039233 ATCTTGGCTTCATTGGGCGG 61.039 55.000 0.00 0.00 0.00 6.13
588 4034 1.334869 GTATCTTGGCTTCATTGGGCG 59.665 52.381 0.00 0.00 0.00 6.13
589 4035 2.099756 GTGTATCTTGGCTTCATTGGGC 59.900 50.000 0.00 0.00 0.00 5.36
590 4036 2.689983 GGTGTATCTTGGCTTCATTGGG 59.310 50.000 0.00 0.00 0.00 4.12
1532 5107 3.023735 ATGGCCTCCTTGGGGTCC 61.024 66.667 3.32 0.00 36.00 4.46
1552 5127 3.625632 ATCTCCTCCACGGCCTGGT 62.626 63.158 17.55 0.00 41.52 4.00
1676 5829 0.818296 AGCCGCTCACGTTAGAGAAT 59.182 50.000 7.07 0.00 37.87 2.40
1683 5836 2.709125 TTAGCACAGCCGCTCACGTT 62.709 55.000 0.00 0.00 42.62 3.99
1853 6409 2.751259 TGGTACTACTAGTTGGCAGACG 59.249 50.000 0.00 0.00 0.00 4.18
1854 6410 3.429135 GCTGGTACTACTAGTTGGCAGAC 60.429 52.174 0.00 0.00 0.00 3.51
1855 6411 2.758979 GCTGGTACTACTAGTTGGCAGA 59.241 50.000 0.00 0.00 0.00 4.26
1856 6412 2.496070 TGCTGGTACTACTAGTTGGCAG 59.504 50.000 0.00 0.00 0.00 4.85
1859 6415 2.496070 TGCTGCTGGTACTACTAGTTGG 59.504 50.000 0.00 0.00 0.00 3.77
1860 6416 3.512680 GTGCTGCTGGTACTACTAGTTG 58.487 50.000 0.00 0.59 0.00 3.16
1861 6417 2.496470 GGTGCTGCTGGTACTACTAGTT 59.504 50.000 0.00 0.00 0.00 2.24
1864 6420 1.100510 CGGTGCTGCTGGTACTACTA 58.899 55.000 0.00 0.00 0.00 1.82
1882 6541 1.269166 CACTAGTCGCTAACAAGCCG 58.731 55.000 0.00 0.00 0.00 5.52
1917 6639 3.842923 ACGGGAGCTCCATCGCTG 61.843 66.667 33.29 16.99 41.08 5.18
2001 6738 2.040278 TCCACATTCCTGGGAGAACTTG 59.960 50.000 0.00 0.00 31.41 3.16
2037 6774 0.543410 TCCTTGAAGGGGCACTACGA 60.543 55.000 11.99 0.00 35.59 3.43
2056 6793 1.341080 CTTGTTTTGAGCCCCCATGT 58.659 50.000 0.00 0.00 0.00 3.21
2076 6814 5.327091 CAGATTCTTCGCAAATGTAACCTG 58.673 41.667 0.00 0.00 0.00 4.00
2119 6878 3.902261 TTGTTTGATGCAGCTGTGTAG 57.098 42.857 16.64 0.00 0.00 2.74
2178 6943 5.890717 TGGATACTCTCGGATGATGCATCC 61.891 50.000 23.67 14.89 46.86 3.51
2189 6954 4.767409 TGTTCATCCTATGGATACTCTCGG 59.233 45.833 0.00 0.00 40.98 4.63
2221 6987 1.673626 CCATGGTGCTTGTGGAAATGC 60.674 52.381 2.57 0.00 34.94 3.56
2242 7008 2.254152 TAGCCTTCTGATGAGGTGGT 57.746 50.000 0.00 0.00 0.00 4.16
2244 7010 3.881688 CCATTTAGCCTTCTGATGAGGTG 59.118 47.826 0.00 0.00 0.00 4.00
2442 7766 8.246180 ACTTTGTTTGTTCTCTAATGCATATGG 58.754 33.333 0.00 0.00 0.00 2.74
2474 7827 8.259049 TCAATATGTACCGAAATTCGTCTTTT 57.741 30.769 14.58 0.00 38.40 2.27
2586 8423 4.375272 AGCATCAGAATGTGTAATCCTCG 58.625 43.478 0.00 0.00 37.40 4.63
2643 8481 3.785486 TGTATGCGAATGGTCTCTCTTG 58.215 45.455 0.00 0.00 0.00 3.02
2682 8520 9.410556 AGTTTATTTTCATCTTTCGAAACCATG 57.589 29.630 6.47 11.88 32.27 3.66
2757 8596 7.173390 CAGTCGGTATTACATCTCAGTAGATCA 59.827 40.741 0.00 0.00 40.65 2.92
2765 8604 5.907866 TGAACAGTCGGTATTACATCTCA 57.092 39.130 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.