Multiple sequence alignment - TraesCS2A01G169300

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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 TraesCS2A01G169300 chr2A 100.000 3657 0 0 1 3657 124214547 124210891 0.000000e+00 6754
1 TraesCS2A01G169300 chr2D 91.922 3194 153 40 265 3399 120257156 120254009 0.000000e+00 4372
2 TraesCS2A01G169300 chr2D 96.907 291 8 1 3343 3633 120254013 120253724 1.530000e-133 486
3 TraesCS2A01G169300 chr2B 89.177 1737 105 36 243 1936 173206698 173205002 0.000000e+00 2089
4 TraesCS2A01G169300 chr2B 93.943 908 42 9 2755 3654 173204270 173203368 0.000000e+00 1360
5 TraesCS2A01G169300 chr2B 95.168 745 27 6 1971 2715 173205000 173204265 0.000000e+00 1168


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 TraesCS2A01G169300 chr2A 124210891 124214547 3656 True 6754 6754 100.000000 1 3657 1 chr2A.!!$R1 3656
1 TraesCS2A01G169300 chr2D 120253724 120257156 3432 True 2429 4372 94.414500 265 3633 2 chr2D.!!$R1 3368
2 TraesCS2A01G169300 chr2B 173203368 173206698 3330 True 1539 2089 92.762667 243 3654 3 chr2B.!!$R1 3411

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
782 835 0.037046 GAAACCGCGTCCTTCCCTTA 60.037 55.0 4.92 0.0 0.0 2.69 F
982 1043 0.175989 GGTTCGGAGGTGGAGCTTAG 59.824 60.0 0.00 0.0 0.0 2.18 F
1132 1194 0.251787 AATCAACAAGGGTGAGGGGC 60.252 55.0 0.00 0.0 0.0 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 2338 0.603569 ATTCGGACGAGCAGACTTGT 59.396 50.0 0.0 0.0 43.65 3.16 R
2250 2339 0.994995 CATTCGGACGAGCAGACTTG 59.005 55.0 0.0 0.0 0.00 3.16 R
3107 3201 1.014564 CGCCTCGACAAAACTCCCTC 61.015 60.0 0.0 0.0 0.00 4.30 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
50 51 9.797642 ATTAAAGGAAATTGGAAGAGCAAAATT 57.202 25.926 0.00 0.00 0.00 1.82
51 52 9.625747 TTAAAGGAAATTGGAAGAGCAAAATTT 57.374 25.926 0.00 0.00 35.50 1.82
52 53 7.734924 AAGGAAATTGGAAGAGCAAAATTTC 57.265 32.000 9.97 9.97 43.46 2.17
53 54 7.071069 AGGAAATTGGAAGAGCAAAATTTCT 57.929 32.000 15.42 0.00 43.59 2.52
54 55 8.193953 AGGAAATTGGAAGAGCAAAATTTCTA 57.806 30.769 15.42 0.00 43.59 2.10
55 56 8.090831 AGGAAATTGGAAGAGCAAAATTTCTAC 58.909 33.333 15.42 4.66 43.59 2.59
56 57 8.090831 GGAAATTGGAAGAGCAAAATTTCTACT 58.909 33.333 15.42 0.00 43.59 2.57
57 58 8.822652 AAATTGGAAGAGCAAAATTTCTACTG 57.177 30.769 0.00 0.00 28.57 2.74
58 59 5.376854 TGGAAGAGCAAAATTTCTACTGC 57.623 39.130 4.71 4.71 34.96 4.40
65 66 6.743575 AGCAAAATTTCTACTGCTCGTTAT 57.256 33.333 8.89 0.00 41.18 1.89
66 67 7.843490 AGCAAAATTTCTACTGCTCGTTATA 57.157 32.000 8.89 0.00 41.18 0.98
67 68 7.910304 AGCAAAATTTCTACTGCTCGTTATAG 58.090 34.615 8.89 0.00 41.18 1.31
68 69 7.549488 AGCAAAATTTCTACTGCTCGTTATAGT 59.451 33.333 8.89 0.00 41.18 2.12
69 70 8.814235 GCAAAATTTCTACTGCTCGTTATAGTA 58.186 33.333 5.51 0.00 0.00 1.82
82 83 9.674824 TGCTCGTTATAGTAGAAATAACTTAGC 57.325 33.333 15.75 15.75 41.26 3.09
83 84 9.896263 GCTCGTTATAGTAGAAATAACTTAGCT 57.104 33.333 15.54 0.00 39.83 3.32
97 98 9.912634 AAATAACTTAGCTAGTAACGTAACACA 57.087 29.630 0.00 0.00 35.54 3.72
98 99 8.902040 ATAACTTAGCTAGTAACGTAACACAC 57.098 34.615 0.00 0.00 35.54 3.82
99 100 5.703876 ACTTAGCTAGTAACGTAACACACC 58.296 41.667 0.00 0.00 34.56 4.16
100 101 3.582714 AGCTAGTAACGTAACACACCC 57.417 47.619 0.00 0.00 0.00 4.61
101 102 2.892852 AGCTAGTAACGTAACACACCCA 59.107 45.455 0.00 0.00 0.00 4.51
102 103 3.057033 AGCTAGTAACGTAACACACCCAG 60.057 47.826 0.00 0.00 0.00 4.45
103 104 2.159327 AGTAACGTAACACACCCAGC 57.841 50.000 0.00 0.00 0.00 4.85
104 105 1.413445 AGTAACGTAACACACCCAGCA 59.587 47.619 0.00 0.00 0.00 4.41
105 106 2.038033 AGTAACGTAACACACCCAGCAT 59.962 45.455 0.00 0.00 0.00 3.79
106 107 2.843401 AACGTAACACACCCAGCATA 57.157 45.000 0.00 0.00 0.00 3.14
107 108 3.343941 AACGTAACACACCCAGCATAT 57.656 42.857 0.00 0.00 0.00 1.78
108 109 2.627945 ACGTAACACACCCAGCATATG 58.372 47.619 0.00 0.00 0.00 1.78
109 110 2.027561 ACGTAACACACCCAGCATATGT 60.028 45.455 4.29 0.00 0.00 2.29
110 111 3.006940 CGTAACACACCCAGCATATGTT 58.993 45.455 4.29 0.00 37.30 2.71
111 112 3.438781 CGTAACACACCCAGCATATGTTT 59.561 43.478 4.29 0.00 35.26 2.83
112 113 3.940209 AACACACCCAGCATATGTTTG 57.060 42.857 4.29 3.68 29.30 2.93
113 114 2.875296 ACACACCCAGCATATGTTTGT 58.125 42.857 4.29 0.00 0.00 2.83
114 115 3.230134 ACACACCCAGCATATGTTTGTT 58.770 40.909 4.29 0.00 0.00 2.83
115 116 3.640967 ACACACCCAGCATATGTTTGTTT 59.359 39.130 4.29 0.00 0.00 2.83
116 117 4.830046 ACACACCCAGCATATGTTTGTTTA 59.170 37.500 4.29 0.00 0.00 2.01
117 118 5.480073 ACACACCCAGCATATGTTTGTTTAT 59.520 36.000 4.29 0.00 0.00 1.40
118 119 6.661377 ACACACCCAGCATATGTTTGTTTATA 59.339 34.615 4.29 0.00 0.00 0.98
119 120 6.972328 CACACCCAGCATATGTTTGTTTATAC 59.028 38.462 4.29 0.00 0.00 1.47
120 121 6.183360 ACACCCAGCATATGTTTGTTTATACG 60.183 38.462 4.29 0.00 0.00 3.06
121 122 6.037720 CACCCAGCATATGTTTGTTTATACGA 59.962 38.462 4.29 0.00 0.00 3.43
122 123 6.037830 ACCCAGCATATGTTTGTTTATACGAC 59.962 38.462 4.29 0.00 0.00 4.34
123 124 6.037720 CCCAGCATATGTTTGTTTATACGACA 59.962 38.462 4.29 0.00 0.00 4.35
124 125 7.414651 CCCAGCATATGTTTGTTTATACGACAA 60.415 37.037 4.29 0.00 35.36 3.18
125 126 7.639850 CCAGCATATGTTTGTTTATACGACAAG 59.360 37.037 4.29 0.00 38.17 3.16
126 127 8.175069 CAGCATATGTTTGTTTATACGACAAGT 58.825 33.333 4.29 0.00 38.17 3.16
127 128 9.373603 AGCATATGTTTGTTTATACGACAAGTA 57.626 29.630 4.29 0.00 38.17 2.24
128 129 9.632969 GCATATGTTTGTTTATACGACAAGTAG 57.367 33.333 4.29 0.00 38.94 2.57
143 144 8.064336 ACGACAAGTAGTTAATGATAAGAGGT 57.936 34.615 0.00 0.00 0.00 3.85
144 145 9.182214 ACGACAAGTAGTTAATGATAAGAGGTA 57.818 33.333 0.00 0.00 0.00 3.08
175 176 9.502091 AATACATTATCATAACATAACGCACCT 57.498 29.630 0.00 0.00 0.00 4.00
176 177 7.421530 ACATTATCATAACATAACGCACCTC 57.578 36.000 0.00 0.00 0.00 3.85
177 178 6.145534 ACATTATCATAACATAACGCACCTCG 59.854 38.462 0.00 0.00 45.38 4.63
178 179 3.786516 TCATAACATAACGCACCTCGA 57.213 42.857 0.00 0.00 41.67 4.04
179 180 4.112716 TCATAACATAACGCACCTCGAA 57.887 40.909 0.00 0.00 41.67 3.71
180 181 4.689071 TCATAACATAACGCACCTCGAAT 58.311 39.130 0.00 0.00 41.67 3.34
181 182 4.743151 TCATAACATAACGCACCTCGAATC 59.257 41.667 0.00 0.00 41.67 2.52
182 183 2.665649 ACATAACGCACCTCGAATCA 57.334 45.000 0.00 0.00 41.67 2.57
183 184 2.967362 ACATAACGCACCTCGAATCAA 58.033 42.857 0.00 0.00 41.67 2.57
184 185 3.331150 ACATAACGCACCTCGAATCAAA 58.669 40.909 0.00 0.00 41.67 2.69
185 186 3.749088 ACATAACGCACCTCGAATCAAAA 59.251 39.130 0.00 0.00 41.67 2.44
186 187 4.394920 ACATAACGCACCTCGAATCAAAAT 59.605 37.500 0.00 0.00 41.67 1.82
187 188 2.900122 ACGCACCTCGAATCAAAATG 57.100 45.000 0.00 0.00 41.67 2.32
188 189 2.422597 ACGCACCTCGAATCAAAATGA 58.577 42.857 0.00 0.00 41.67 2.57
189 190 2.416547 ACGCACCTCGAATCAAAATGAG 59.583 45.455 0.00 0.00 41.67 2.90
190 191 2.789092 CGCACCTCGAATCAAAATGAGC 60.789 50.000 0.00 0.00 41.67 4.26
191 192 2.478539 GCACCTCGAATCAAAATGAGCC 60.479 50.000 0.00 0.00 0.00 4.70
192 193 3.012518 CACCTCGAATCAAAATGAGCCT 58.987 45.455 0.00 0.00 0.00 4.58
193 194 4.191544 CACCTCGAATCAAAATGAGCCTA 58.808 43.478 0.00 0.00 0.00 3.93
194 195 4.034510 CACCTCGAATCAAAATGAGCCTAC 59.965 45.833 0.00 0.00 0.00 3.18
195 196 4.191544 CCTCGAATCAAAATGAGCCTACA 58.808 43.478 0.00 0.00 0.00 2.74
196 197 4.818546 CCTCGAATCAAAATGAGCCTACAT 59.181 41.667 0.00 0.00 0.00 2.29
197 198 5.277683 CCTCGAATCAAAATGAGCCTACATG 60.278 44.000 0.00 0.00 0.00 3.21
198 199 5.185454 TCGAATCAAAATGAGCCTACATGT 58.815 37.500 2.69 2.69 0.00 3.21
199 200 6.345298 TCGAATCAAAATGAGCCTACATGTA 58.655 36.000 5.25 5.25 0.00 2.29
200 201 6.257849 TCGAATCAAAATGAGCCTACATGTAC 59.742 38.462 0.08 0.00 0.00 2.90
201 202 6.037062 CGAATCAAAATGAGCCTACATGTACA 59.963 38.462 0.08 0.00 0.00 2.90
202 203 7.254898 CGAATCAAAATGAGCCTACATGTACAT 60.255 37.037 1.41 1.41 0.00 2.29
203 204 6.682423 TCAAAATGAGCCTACATGTACATG 57.318 37.500 29.97 29.97 44.15 3.21
204 205 6.413892 TCAAAATGAGCCTACATGTACATGA 58.586 36.000 36.36 20.94 41.20 3.07
205 206 6.883756 TCAAAATGAGCCTACATGTACATGAA 59.116 34.615 36.36 15.68 41.20 2.57
206 207 6.683974 AAATGAGCCTACATGTACATGAAC 57.316 37.500 36.36 22.58 41.20 3.18
207 208 5.620738 ATGAGCCTACATGTACATGAACT 57.379 39.130 36.36 25.97 41.20 3.01
208 209 6.731292 ATGAGCCTACATGTACATGAACTA 57.269 37.500 36.36 20.11 41.20 2.24
209 210 6.538945 TGAGCCTACATGTACATGAACTAA 57.461 37.500 36.36 19.42 41.20 2.24
210 211 6.573434 TGAGCCTACATGTACATGAACTAAG 58.427 40.000 36.36 23.40 41.20 2.18
211 212 6.379988 TGAGCCTACATGTACATGAACTAAGA 59.620 38.462 36.36 15.70 41.20 2.10
212 213 6.574350 AGCCTACATGTACATGAACTAAGAC 58.426 40.000 36.36 18.82 41.20 3.01
213 214 6.381420 AGCCTACATGTACATGAACTAAGACT 59.619 38.462 36.36 20.31 41.20 3.24
214 215 7.042335 GCCTACATGTACATGAACTAAGACTT 58.958 38.462 36.36 16.12 41.20 3.01
215 216 7.010552 GCCTACATGTACATGAACTAAGACTTG 59.989 40.741 36.36 14.92 41.20 3.16
216 217 6.727824 ACATGTACATGAACTAAGACTTGC 57.272 37.500 36.36 0.00 41.20 4.01
217 218 6.230472 ACATGTACATGAACTAAGACTTGCA 58.770 36.000 36.36 0.00 41.20 4.08
218 219 6.881065 ACATGTACATGAACTAAGACTTGCAT 59.119 34.615 36.36 10.24 41.20 3.96
219 220 6.726258 TGTACATGAACTAAGACTTGCATG 57.274 37.500 0.00 14.94 39.09 4.06
220 221 6.463360 TGTACATGAACTAAGACTTGCATGA 58.537 36.000 19.76 8.37 37.24 3.07
221 222 7.105588 TGTACATGAACTAAGACTTGCATGAT 58.894 34.615 19.76 11.64 37.24 2.45
222 223 8.257306 TGTACATGAACTAAGACTTGCATGATA 58.743 33.333 19.76 11.04 37.24 2.15
223 224 7.545362 ACATGAACTAAGACTTGCATGATAC 57.455 36.000 19.76 0.00 37.24 2.24
224 225 6.540189 ACATGAACTAAGACTTGCATGATACC 59.460 38.462 19.76 0.00 37.24 2.73
225 226 6.048732 TGAACTAAGACTTGCATGATACCA 57.951 37.500 6.60 0.00 0.00 3.25
226 227 5.874810 TGAACTAAGACTTGCATGATACCAC 59.125 40.000 6.60 0.00 0.00 4.16
227 228 5.420725 ACTAAGACTTGCATGATACCACA 57.579 39.130 6.60 0.00 0.00 4.17
228 229 5.423015 ACTAAGACTTGCATGATACCACAG 58.577 41.667 6.60 0.00 0.00 3.66
229 230 4.558226 AAGACTTGCATGATACCACAGA 57.442 40.909 6.60 0.00 0.00 3.41
230 231 3.866651 AGACTTGCATGATACCACAGAC 58.133 45.455 6.60 0.00 0.00 3.51
231 232 3.261643 AGACTTGCATGATACCACAGACA 59.738 43.478 6.60 0.00 0.00 3.41
232 233 3.603532 ACTTGCATGATACCACAGACAG 58.396 45.455 6.60 0.00 0.00 3.51
233 234 3.261643 ACTTGCATGATACCACAGACAGA 59.738 43.478 6.60 0.00 0.00 3.41
234 235 4.080695 ACTTGCATGATACCACAGACAGAT 60.081 41.667 6.60 0.00 0.00 2.90
235 236 5.129320 ACTTGCATGATACCACAGACAGATA 59.871 40.000 6.60 0.00 0.00 1.98
236 237 5.813513 TGCATGATACCACAGACAGATAT 57.186 39.130 0.00 0.00 0.00 1.63
237 238 5.544650 TGCATGATACCACAGACAGATATG 58.455 41.667 0.00 0.00 0.00 1.78
238 239 5.070847 TGCATGATACCACAGACAGATATGT 59.929 40.000 0.00 0.00 0.00 2.29
239 240 5.994054 GCATGATACCACAGACAGATATGTT 59.006 40.000 0.00 0.00 0.00 2.71
240 241 7.154656 GCATGATACCACAGACAGATATGTTA 58.845 38.462 0.00 0.00 0.00 2.41
241 242 7.821359 GCATGATACCACAGACAGATATGTTAT 59.179 37.037 0.00 0.00 0.00 1.89
242 243 9.148104 CATGATACCACAGACAGATATGTTATG 57.852 37.037 0.00 0.00 0.00 1.90
243 244 8.477419 TGATACCACAGACAGATATGTTATGA 57.523 34.615 12.06 0.00 0.00 2.15
244 245 8.923270 TGATACCACAGACAGATATGTTATGAA 58.077 33.333 12.06 0.00 0.00 2.57
245 246 9.416794 GATACCACAGACAGATATGTTATGAAG 57.583 37.037 12.06 6.45 0.00 3.02
246 247 7.187824 ACCACAGACAGATATGTTATGAAGT 57.812 36.000 12.06 6.92 0.00 3.01
247 248 7.624549 ACCACAGACAGATATGTTATGAAGTT 58.375 34.615 12.06 0.00 0.00 2.66
330 340 4.581309 ATTTGAGGGAGAGCAAGATTGA 57.419 40.909 0.00 0.00 0.00 2.57
339 352 4.035441 GGAGAGCAAGATTGAGAGAAATGC 59.965 45.833 0.00 0.00 0.00 3.56
342 355 5.816777 AGAGCAAGATTGAGAGAAATGCTAC 59.183 40.000 0.00 0.00 42.24 3.58
343 356 5.743117 AGCAAGATTGAGAGAAATGCTACT 58.257 37.500 0.00 0.00 40.56 2.57
344 357 5.816777 AGCAAGATTGAGAGAAATGCTACTC 59.183 40.000 0.00 0.00 40.56 2.59
413 426 1.815003 GGATCTGACCAAACAGGCAAG 59.185 52.381 0.00 0.00 43.14 4.01
629 670 1.681825 GAACCACGTGCGAAATTTCC 58.318 50.000 10.91 6.21 0.00 3.13
691 744 4.209288 CGCTAAACTAATCCAACCATCGAG 59.791 45.833 0.00 0.00 0.00 4.04
713 766 2.507102 CACCCACGCTCGCACTAG 60.507 66.667 0.00 0.00 0.00 2.57
753 806 1.554617 CGGGGGCTGGATTTCAATTTT 59.445 47.619 0.00 0.00 0.00 1.82
754 807 2.677613 CGGGGGCTGGATTTCAATTTTG 60.678 50.000 0.00 0.00 0.00 2.44
756 809 2.026915 GGGGCTGGATTTCAATTTTGCT 60.027 45.455 0.00 0.00 0.00 3.91
757 810 3.559811 GGGGCTGGATTTCAATTTTGCTT 60.560 43.478 0.00 0.00 0.00 3.91
776 829 1.823169 TAGCCAGAAACCGCGTCCTT 61.823 55.000 4.92 0.00 0.00 3.36
779 832 2.033194 CAGAAACCGCGTCCTTCCC 61.033 63.158 4.92 0.00 0.00 3.97
781 834 1.302271 GAAACCGCGTCCTTCCCTT 60.302 57.895 4.92 0.00 0.00 3.95
782 835 0.037046 GAAACCGCGTCCTTCCCTTA 60.037 55.000 4.92 0.00 0.00 2.69
783 836 0.616891 AAACCGCGTCCTTCCCTTAT 59.383 50.000 4.92 0.00 0.00 1.73
786 839 1.411612 ACCGCGTCCTTCCCTTATAAG 59.588 52.381 4.92 5.43 0.00 1.73
813 874 1.302112 CACACGGCACACCACCATA 60.302 57.895 0.00 0.00 34.57 2.74
937 998 0.504384 CGATTCCGTCTGCGCTATTG 59.496 55.000 9.73 0.00 36.67 1.90
950 1011 2.671070 GCGCTATTGAGGTTTGTTTGGG 60.671 50.000 0.00 0.00 0.00 4.12
962 1023 3.272847 TTTGGGGGAAGGGGAGGC 61.273 66.667 0.00 0.00 0.00 4.70
980 1041 2.943978 CGGTTCGGAGGTGGAGCTT 61.944 63.158 0.00 0.00 0.00 3.74
981 1042 1.601419 CGGTTCGGAGGTGGAGCTTA 61.601 60.000 0.00 0.00 0.00 3.09
982 1043 0.175989 GGTTCGGAGGTGGAGCTTAG 59.824 60.000 0.00 0.00 0.00 2.18
983 1044 0.175989 GTTCGGAGGTGGAGCTTAGG 59.824 60.000 0.00 0.00 0.00 2.69
1129 1191 1.003118 TCGGAATCAACAAGGGTGAGG 59.997 52.381 0.00 0.00 0.00 3.86
1132 1194 0.251787 AATCAACAAGGGTGAGGGGC 60.252 55.000 0.00 0.00 0.00 5.80
1189 1251 8.907685 GCTGTTCGCTGTTTGTTTATTTATTTA 58.092 29.630 0.00 0.00 35.14 1.40
1229 1295 2.412325 CGTTCCGATTCGTGGGAAAAAG 60.412 50.000 5.20 0.00 43.52 2.27
1230 1296 2.551032 GTTCCGATTCGTGGGAAAAAGT 59.449 45.455 5.20 0.00 43.52 2.66
1268 1336 2.324332 TTCCGCGCGAGATCTGAGTC 62.324 60.000 34.63 0.00 0.00 3.36
1311 1381 2.350985 GTCCTCGTCGCGTCGATC 60.351 66.667 27.02 16.70 38.42 3.69
1426 1496 4.717629 CGGCGGACACGAAGAGCA 62.718 66.667 0.00 0.00 44.60 4.26
1553 1623 2.295070 GGTATTTGACCGTGCCACTTTT 59.705 45.455 0.00 0.00 38.87 2.27
1558 1628 0.868406 GACCGTGCCACTTTTCTCTG 59.132 55.000 0.00 0.00 0.00 3.35
1575 1645 5.435686 TCTCTGCTCCATTTTTAGCCTTA 57.564 39.130 0.00 0.00 37.97 2.69
1602 1680 5.108187 AGTGCAAGTCAGAATCCATACAT 57.892 39.130 0.00 0.00 0.00 2.29
1603 1681 6.239217 AGTGCAAGTCAGAATCCATACATA 57.761 37.500 0.00 0.00 0.00 2.29
1604 1682 6.051717 AGTGCAAGTCAGAATCCATACATAC 58.948 40.000 0.00 0.00 0.00 2.39
1605 1683 5.817296 GTGCAAGTCAGAATCCATACATACA 59.183 40.000 0.00 0.00 0.00 2.29
1626 1704 4.081420 ACAGATAAAAGTCAGATGGCGAGT 60.081 41.667 0.00 0.00 0.00 4.18
1627 1705 4.269603 CAGATAAAAGTCAGATGGCGAGTG 59.730 45.833 0.00 0.00 0.00 3.51
1628 1706 1.813513 AAAAGTCAGATGGCGAGTGG 58.186 50.000 0.00 0.00 0.00 4.00
1630 1708 0.534412 AAGTCAGATGGCGAGTGGAG 59.466 55.000 0.00 0.00 0.00 3.86
1631 1709 0.323816 AGTCAGATGGCGAGTGGAGA 60.324 55.000 0.00 0.00 0.00 3.71
1632 1710 0.532573 GTCAGATGGCGAGTGGAGAA 59.467 55.000 0.00 0.00 0.00 2.87
1645 1734 5.105752 CGAGTGGAGAAACCTTTCTATCTG 58.894 45.833 0.14 0.00 46.84 2.90
1649 1738 5.348997 GTGGAGAAACCTTTCTATCTGTTCG 59.651 44.000 0.14 0.00 46.84 3.95
1673 1762 6.576185 GGTTTATCTGAACCGTACTGGATTA 58.424 40.000 10.17 0.00 39.68 1.75
1782 1871 2.726821 TCTTGGGATGGAGCAATCAAC 58.273 47.619 0.00 0.00 0.00 3.18
1863 1952 6.469782 TTCGACCTTAAACCGTATCCTTAT 57.530 37.500 0.00 0.00 0.00 1.73
1908 1997 7.095397 CGAGGTGAGTTTGTTTGTACATGAATA 60.095 37.037 0.00 0.00 33.44 1.75
1932 2021 4.360951 AAATACGGTTTCCCAGAGAACA 57.639 40.909 0.00 0.00 32.95 3.18
1937 2026 2.488153 CGGTTTCCCAGAGAACATTTCC 59.512 50.000 0.00 0.00 32.95 3.13
1939 2028 2.826128 GTTTCCCAGAGAACATTTCCCC 59.174 50.000 0.00 0.00 32.95 4.81
1945 2034 3.160269 CAGAGAACATTTCCCCTTGCTT 58.840 45.455 0.00 0.00 0.00 3.91
1968 2057 4.458989 TGTGAAAATTGGTTAGGCAGCTAG 59.541 41.667 0.00 0.00 0.00 3.42
1969 2058 4.459337 GTGAAAATTGGTTAGGCAGCTAGT 59.541 41.667 0.00 0.00 0.00 2.57
2007 2096 5.613358 AGTCTGCAAGTGTACTTAATTGC 57.387 39.130 10.43 10.43 46.36 3.56
2016 2105 5.505654 AAGTGTACTTAATTGCTGTGTGCAC 60.506 40.000 10.75 10.75 42.34 4.57
2242 2331 2.835764 AGTTTGCCTAGTGATCCGGTTA 59.164 45.455 0.00 0.00 0.00 2.85
2249 2338 3.069586 CCTAGTGATCCGGTTAATGCTCA 59.930 47.826 0.00 0.00 0.00 4.26
2250 2339 2.906354 AGTGATCCGGTTAATGCTCAC 58.094 47.619 0.00 4.93 34.61 3.51
2311 2400 7.433131 CAGTGATTTGTTGTACATATCCATTGC 59.567 37.037 0.00 0.00 36.25 3.56
2330 2419 2.352034 TGCGTTGTTTGACATGTACGTT 59.648 40.909 15.68 0.00 33.74 3.99
2347 2436 4.893424 ACGTTGCTTGTTCTTATTGTGT 57.107 36.364 0.00 0.00 0.00 3.72
2466 2555 3.968649 GCTTTTGCTGTCAATGAACTCA 58.031 40.909 0.00 0.00 43.35 3.41
2470 2559 5.970317 TTTGCTGTCAATGAACTCATGAT 57.030 34.783 0.00 0.00 36.56 2.45
2496 2585 4.639078 TGATCATCTTTTCTCACCACCA 57.361 40.909 0.00 0.00 0.00 4.17
2497 2586 4.326826 TGATCATCTTTTCTCACCACCAC 58.673 43.478 0.00 0.00 0.00 4.16
2501 2590 3.644966 TCTTTTCTCACCACCACAGTT 57.355 42.857 0.00 0.00 0.00 3.16
2667 2756 1.846007 AACCAATAAGGCGGCATGAA 58.154 45.000 13.08 0.00 43.14 2.57
2670 2759 2.023673 CCAATAAGGCGGCATGAAAGA 58.976 47.619 13.08 0.00 0.00 2.52
2696 2787 5.183904 GCCTTATGCCCTTACCAGAAATATG 59.816 44.000 0.00 0.00 0.00 1.78
2719 2810 5.239306 TGTGAAATGTGCTTTGTCCTTAGAG 59.761 40.000 0.00 0.00 0.00 2.43
2720 2811 5.239525 GTGAAATGTGCTTTGTCCTTAGAGT 59.760 40.000 0.00 0.00 0.00 3.24
2721 2812 6.426937 GTGAAATGTGCTTTGTCCTTAGAGTA 59.573 38.462 0.00 0.00 0.00 2.59
2722 2813 7.119846 GTGAAATGTGCTTTGTCCTTAGAGTAT 59.880 37.037 0.00 0.00 0.00 2.12
2723 2814 7.334421 TGAAATGTGCTTTGTCCTTAGAGTATC 59.666 37.037 0.00 0.00 0.00 2.24
2724 2815 5.738619 TGTGCTTTGTCCTTAGAGTATCA 57.261 39.130 0.00 0.00 37.82 2.15
2725 2816 6.109156 TGTGCTTTGTCCTTAGAGTATCAA 57.891 37.500 0.00 0.00 37.82 2.57
2769 2860 5.296780 CCCATATCATGTTCTAGCGTTTTGT 59.703 40.000 0.00 0.00 0.00 2.83
2951 3042 9.935241 AAGAAACATAGCTGTATCCTATATGTG 57.065 33.333 0.00 0.00 37.20 3.21
3042 3133 9.008965 TGGATTCATATTATGTTTGTATTCCCG 57.991 33.333 3.67 0.00 0.00 5.14
3048 3139 1.529226 TGTTTGTATTCCCGTGGCTG 58.471 50.000 0.00 0.00 0.00 4.85
3069 3163 6.192360 GCTGTATGTTTACATGATTCGGTTC 58.808 40.000 0.00 0.00 37.68 3.62
3078 3172 5.350504 ACATGATTCGGTTCTCAGATCTT 57.649 39.130 0.00 0.00 0.00 2.40
3090 3184 8.191446 CGGTTCTCAGATCTTTATGAGTTCTTA 58.809 37.037 8.95 0.00 42.86 2.10
3107 3201 7.040478 TGAGTTCTTATTCTGTTTGTTCATGGG 60.040 37.037 0.00 0.00 0.00 4.00
3126 3226 1.004918 AGGGAGTTTTGTCGAGGCG 60.005 57.895 0.00 0.00 0.00 5.52
3141 3241 4.452455 GTCGAGGCGATGGATAATGATTTT 59.548 41.667 0.00 0.00 38.42 1.82
3152 3252 5.834742 TGGATAATGATTTTCCATGGACAGG 59.165 40.000 15.91 0.00 34.65 4.00
3165 3268 7.865530 TCCATGGACAGGCTAATATAACTAA 57.134 36.000 11.44 0.00 0.00 2.24
3198 3301 2.612972 CCGCCTGTAGTCAACAAGTGAT 60.613 50.000 0.00 0.00 38.90 3.06
3203 3306 4.572389 CCTGTAGTCAACAAGTGATATGGC 59.428 45.833 0.00 0.00 38.90 4.40
3301 3404 4.097437 ACCAATCATGCAAATACAGAGCAG 59.903 41.667 0.00 0.00 42.14 4.24
3452 3611 2.159421 GCAGGAGCACATGTGAGAATTG 60.159 50.000 29.80 18.70 41.58 2.32
3466 3625 3.311327 TGAGAATTGGGGAGGTGATAGGA 60.311 47.826 0.00 0.00 0.00 2.94
3540 3699 3.865164 GGAAGTTGTTTGGAAGTTGCAAG 59.135 43.478 9.87 0.00 0.00 4.01
3591 3750 5.499139 TTGCCTTTCTACTTCAACTTGTG 57.501 39.130 0.00 0.00 0.00 3.33
3651 3810 1.153208 GCAGAGGGATGCTGGTGAG 60.153 63.158 0.00 0.00 43.07 3.51
3652 3811 1.620739 GCAGAGGGATGCTGGTGAGA 61.621 60.000 0.00 0.00 43.07 3.27
3653 3812 1.129917 CAGAGGGATGCTGGTGAGAT 58.870 55.000 0.00 0.00 0.00 2.75
3655 3814 1.489649 AGAGGGATGCTGGTGAGATTG 59.510 52.381 0.00 0.00 0.00 2.67
3656 3815 1.487976 GAGGGATGCTGGTGAGATTGA 59.512 52.381 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.797642 AATTTTGCTCTTCCAATTTCCTTTAAT 57.202 25.926 0.00 0.00 0.00 1.40
25 26 9.625747 AAATTTTGCTCTTCCAATTTCCTTTAA 57.374 25.926 0.00 0.00 0.00 1.52
26 27 9.271828 GAAATTTTGCTCTTCCAATTTCCTTTA 57.728 29.630 0.00 0.00 38.71 1.85
27 28 7.994911 AGAAATTTTGCTCTTCCAATTTCCTTT 59.005 29.630 10.97 0.00 42.70 3.11
28 29 7.512130 AGAAATTTTGCTCTTCCAATTTCCTT 58.488 30.769 10.97 0.00 42.70 3.36
29 30 7.071069 AGAAATTTTGCTCTTCCAATTTCCT 57.929 32.000 10.97 0.15 42.70 3.36
30 31 8.090831 AGTAGAAATTTTGCTCTTCCAATTTCC 58.909 33.333 10.97 0.73 42.70 3.13
31 32 8.919661 CAGTAGAAATTTTGCTCTTCCAATTTC 58.080 33.333 7.75 7.75 42.31 2.17
32 33 7.386025 GCAGTAGAAATTTTGCTCTTCCAATTT 59.614 33.333 5.51 0.00 32.69 1.82
33 34 6.870439 GCAGTAGAAATTTTGCTCTTCCAATT 59.130 34.615 5.51 0.00 33.88 2.32
34 35 6.210185 AGCAGTAGAAATTTTGCTCTTCCAAT 59.790 34.615 8.89 0.00 42.89 3.16
35 36 5.536161 AGCAGTAGAAATTTTGCTCTTCCAA 59.464 36.000 8.89 0.00 42.89 3.53
36 37 5.072741 AGCAGTAGAAATTTTGCTCTTCCA 58.927 37.500 8.89 0.00 42.89 3.53
37 38 5.635417 AGCAGTAGAAATTTTGCTCTTCC 57.365 39.130 8.89 0.00 42.89 3.46
43 44 7.685594 ACTATAACGAGCAGTAGAAATTTTGC 58.314 34.615 4.71 4.71 36.83 3.68
56 57 9.674824 GCTAAGTTATTTCTACTATAACGAGCA 57.325 33.333 19.41 3.34 43.13 4.26
57 58 9.896263 AGCTAAGTTATTTCTACTATAACGAGC 57.104 33.333 18.03 18.03 43.47 5.03
71 72 9.912634 TGTGTTACGTTACTAGCTAAGTTATTT 57.087 29.630 6.24 0.00 39.80 1.40
72 73 9.346725 GTGTGTTACGTTACTAGCTAAGTTATT 57.653 33.333 6.24 0.00 39.80 1.40
73 74 7.970614 GGTGTGTTACGTTACTAGCTAAGTTAT 59.029 37.037 6.24 0.00 39.80 1.89
74 75 7.305474 GGTGTGTTACGTTACTAGCTAAGTTA 58.695 38.462 6.24 0.00 39.80 2.24
75 76 6.152379 GGTGTGTTACGTTACTAGCTAAGTT 58.848 40.000 6.24 0.00 39.80 2.66
76 77 5.335976 GGGTGTGTTACGTTACTAGCTAAGT 60.336 44.000 6.24 0.00 42.62 2.24
77 78 5.098211 GGGTGTGTTACGTTACTAGCTAAG 58.902 45.833 6.24 0.00 0.00 2.18
78 79 4.522405 TGGGTGTGTTACGTTACTAGCTAA 59.478 41.667 6.24 0.00 0.00 3.09
79 80 4.078537 TGGGTGTGTTACGTTACTAGCTA 58.921 43.478 6.24 0.00 0.00 3.32
80 81 2.892852 TGGGTGTGTTACGTTACTAGCT 59.107 45.455 6.24 0.00 0.00 3.32
81 82 3.248266 CTGGGTGTGTTACGTTACTAGC 58.752 50.000 6.24 4.98 0.00 3.42
82 83 3.248266 GCTGGGTGTGTTACGTTACTAG 58.752 50.000 6.24 0.00 0.00 2.57
83 84 2.627221 TGCTGGGTGTGTTACGTTACTA 59.373 45.455 6.24 0.00 0.00 1.82
84 85 1.413445 TGCTGGGTGTGTTACGTTACT 59.587 47.619 6.24 0.00 0.00 2.24
85 86 1.868469 TGCTGGGTGTGTTACGTTAC 58.132 50.000 0.00 0.00 0.00 2.50
86 87 2.843401 ATGCTGGGTGTGTTACGTTA 57.157 45.000 0.00 0.00 0.00 3.18
87 88 2.843401 TATGCTGGGTGTGTTACGTT 57.157 45.000 0.00 0.00 0.00 3.99
88 89 2.027561 ACATATGCTGGGTGTGTTACGT 60.028 45.455 1.58 0.00 0.00 3.57
89 90 2.627945 ACATATGCTGGGTGTGTTACG 58.372 47.619 1.58 0.00 0.00 3.18
90 91 4.217550 ACAAACATATGCTGGGTGTGTTAC 59.782 41.667 1.58 0.00 31.83 2.50
91 92 4.402829 ACAAACATATGCTGGGTGTGTTA 58.597 39.130 1.58 0.00 31.83 2.41
92 93 3.230134 ACAAACATATGCTGGGTGTGTT 58.770 40.909 1.58 0.00 33.18 3.32
93 94 2.875296 ACAAACATATGCTGGGTGTGT 58.125 42.857 1.58 0.00 0.00 3.72
94 95 3.940209 AACAAACATATGCTGGGTGTG 57.060 42.857 1.58 0.00 0.00 3.82
95 96 6.183360 CGTATAAACAAACATATGCTGGGTGT 60.183 38.462 1.58 0.00 0.00 4.16
96 97 6.037720 TCGTATAAACAAACATATGCTGGGTG 59.962 38.462 1.58 0.00 0.00 4.61
97 98 6.037830 GTCGTATAAACAAACATATGCTGGGT 59.962 38.462 1.58 0.00 0.00 4.51
98 99 6.037720 TGTCGTATAAACAAACATATGCTGGG 59.962 38.462 1.58 0.00 0.00 4.45
99 100 7.010697 TGTCGTATAAACAAACATATGCTGG 57.989 36.000 1.58 0.00 0.00 4.85
100 101 8.175069 ACTTGTCGTATAAACAAACATATGCTG 58.825 33.333 1.58 3.20 36.27 4.41
101 102 8.263940 ACTTGTCGTATAAACAAACATATGCT 57.736 30.769 1.58 0.00 36.27 3.79
102 103 9.632969 CTACTTGTCGTATAAACAAACATATGC 57.367 33.333 1.58 0.00 36.27 3.14
117 118 9.182214 ACCTCTTATCATTAACTACTTGTCGTA 57.818 33.333 0.00 0.00 0.00 3.43
118 119 8.064336 ACCTCTTATCATTAACTACTTGTCGT 57.936 34.615 0.00 0.00 0.00 4.34
149 150 9.502091 AGGTGCGTTATGTTATGATAATGTATT 57.498 29.630 0.00 0.00 30.44 1.89
150 151 9.151471 GAGGTGCGTTATGTTATGATAATGTAT 57.849 33.333 0.00 0.00 30.44 2.29
151 152 7.327518 CGAGGTGCGTTATGTTATGATAATGTA 59.672 37.037 0.00 0.00 34.64 2.29
152 153 6.145534 CGAGGTGCGTTATGTTATGATAATGT 59.854 38.462 0.00 0.00 34.64 2.71
153 154 6.364976 TCGAGGTGCGTTATGTTATGATAATG 59.635 38.462 0.00 0.00 41.80 1.90
154 155 6.452242 TCGAGGTGCGTTATGTTATGATAAT 58.548 36.000 0.00 0.00 41.80 1.28
155 156 5.834169 TCGAGGTGCGTTATGTTATGATAA 58.166 37.500 0.00 0.00 41.80 1.75
156 157 5.441709 TCGAGGTGCGTTATGTTATGATA 57.558 39.130 0.00 0.00 41.80 2.15
157 158 4.316205 TCGAGGTGCGTTATGTTATGAT 57.684 40.909 0.00 0.00 41.80 2.45
158 159 3.786516 TCGAGGTGCGTTATGTTATGA 57.213 42.857 0.00 0.00 41.80 2.15
159 160 4.506288 TGATTCGAGGTGCGTTATGTTATG 59.494 41.667 0.00 0.00 41.80 1.90
160 161 4.689071 TGATTCGAGGTGCGTTATGTTAT 58.311 39.130 0.00 0.00 41.80 1.89
161 162 4.112716 TGATTCGAGGTGCGTTATGTTA 57.887 40.909 0.00 0.00 41.80 2.41
162 163 2.967362 TGATTCGAGGTGCGTTATGTT 58.033 42.857 0.00 0.00 41.80 2.71
163 164 2.665649 TGATTCGAGGTGCGTTATGT 57.334 45.000 0.00 0.00 41.80 2.29
164 165 4.335082 TTTTGATTCGAGGTGCGTTATG 57.665 40.909 0.00 0.00 41.80 1.90
165 166 4.634004 TCATTTTGATTCGAGGTGCGTTAT 59.366 37.500 0.00 0.00 41.80 1.89
166 167 3.997681 TCATTTTGATTCGAGGTGCGTTA 59.002 39.130 0.00 0.00 41.80 3.18
167 168 2.811431 TCATTTTGATTCGAGGTGCGTT 59.189 40.909 0.00 0.00 41.80 4.84
168 169 2.416547 CTCATTTTGATTCGAGGTGCGT 59.583 45.455 0.00 0.00 41.80 5.24
169 170 2.789092 GCTCATTTTGATTCGAGGTGCG 60.789 50.000 0.00 0.00 42.69 5.34
170 171 2.478539 GGCTCATTTTGATTCGAGGTGC 60.479 50.000 0.00 0.00 0.00 5.01
171 172 3.012518 AGGCTCATTTTGATTCGAGGTG 58.987 45.455 0.00 0.00 0.00 4.00
172 173 3.356529 AGGCTCATTTTGATTCGAGGT 57.643 42.857 0.00 0.00 0.00 3.85
173 174 4.191544 TGTAGGCTCATTTTGATTCGAGG 58.808 43.478 0.00 0.00 0.00 4.63
174 175 5.295292 ACATGTAGGCTCATTTTGATTCGAG 59.705 40.000 0.00 0.00 0.00 4.04
175 176 5.185454 ACATGTAGGCTCATTTTGATTCGA 58.815 37.500 0.00 0.00 0.00 3.71
176 177 5.490139 ACATGTAGGCTCATTTTGATTCG 57.510 39.130 0.00 0.00 0.00 3.34
177 178 7.320443 TGTACATGTAGGCTCATTTTGATTC 57.680 36.000 5.62 0.00 0.00 2.52
178 179 7.557358 TCATGTACATGTAGGCTCATTTTGATT 59.443 33.333 30.03 0.00 39.72 2.57
179 180 7.056006 TCATGTACATGTAGGCTCATTTTGAT 58.944 34.615 30.03 0.00 39.72 2.57
180 181 6.413892 TCATGTACATGTAGGCTCATTTTGA 58.586 36.000 30.03 8.58 39.72 2.69
181 182 6.682423 TCATGTACATGTAGGCTCATTTTG 57.318 37.500 30.03 6.39 39.72 2.44
182 183 6.886459 AGTTCATGTACATGTAGGCTCATTTT 59.114 34.615 30.03 6.40 39.72 1.82
183 184 6.418101 AGTTCATGTACATGTAGGCTCATTT 58.582 36.000 30.03 7.48 39.72 2.32
184 185 5.994250 AGTTCATGTACATGTAGGCTCATT 58.006 37.500 30.03 8.69 39.72 2.57
185 186 5.620738 AGTTCATGTACATGTAGGCTCAT 57.379 39.130 30.03 3.35 39.72 2.90
186 187 6.379988 TCTTAGTTCATGTACATGTAGGCTCA 59.620 38.462 30.03 16.02 39.72 4.26
187 188 6.697892 GTCTTAGTTCATGTACATGTAGGCTC 59.302 42.308 30.03 12.72 39.72 4.70
188 189 6.381420 AGTCTTAGTTCATGTACATGTAGGCT 59.619 38.462 30.03 22.63 39.72 4.58
189 190 6.574350 AGTCTTAGTTCATGTACATGTAGGC 58.426 40.000 30.03 21.24 39.72 3.93
190 191 7.010552 GCAAGTCTTAGTTCATGTACATGTAGG 59.989 40.741 30.03 17.99 39.72 3.18
191 192 7.545615 TGCAAGTCTTAGTTCATGTACATGTAG 59.454 37.037 30.03 20.35 39.72 2.74
192 193 7.382898 TGCAAGTCTTAGTTCATGTACATGTA 58.617 34.615 30.03 21.12 39.72 2.29
193 194 6.230472 TGCAAGTCTTAGTTCATGTACATGT 58.770 36.000 30.03 16.99 39.72 3.21
194 195 6.726258 TGCAAGTCTTAGTTCATGTACATG 57.274 37.500 26.83 26.83 40.09 3.21
195 196 7.105588 TCATGCAAGTCTTAGTTCATGTACAT 58.894 34.615 1.41 1.41 34.56 2.29
196 197 6.463360 TCATGCAAGTCTTAGTTCATGTACA 58.537 36.000 0.00 0.00 34.56 2.90
197 198 6.968131 TCATGCAAGTCTTAGTTCATGTAC 57.032 37.500 0.00 0.00 34.56 2.90
198 199 7.710907 GGTATCATGCAAGTCTTAGTTCATGTA 59.289 37.037 0.00 0.00 34.56 2.29
199 200 6.540189 GGTATCATGCAAGTCTTAGTTCATGT 59.460 38.462 0.00 6.50 34.56 3.21
200 201 6.539826 TGGTATCATGCAAGTCTTAGTTCATG 59.460 38.462 0.00 8.70 34.32 3.07
201 202 6.540189 GTGGTATCATGCAAGTCTTAGTTCAT 59.460 38.462 0.00 0.00 0.00 2.57
202 203 5.874810 GTGGTATCATGCAAGTCTTAGTTCA 59.125 40.000 0.00 0.00 0.00 3.18
203 204 5.874810 TGTGGTATCATGCAAGTCTTAGTTC 59.125 40.000 0.00 0.00 0.00 3.01
204 205 5.804639 TGTGGTATCATGCAAGTCTTAGTT 58.195 37.500 0.00 0.00 0.00 2.24
205 206 5.187772 TCTGTGGTATCATGCAAGTCTTAGT 59.812 40.000 0.00 0.00 0.00 2.24
206 207 5.521735 GTCTGTGGTATCATGCAAGTCTTAG 59.478 44.000 0.00 0.00 0.00 2.18
207 208 5.046663 TGTCTGTGGTATCATGCAAGTCTTA 60.047 40.000 0.00 0.00 0.00 2.10
208 209 4.256920 GTCTGTGGTATCATGCAAGTCTT 58.743 43.478 0.00 0.00 0.00 3.01
209 210 3.261643 TGTCTGTGGTATCATGCAAGTCT 59.738 43.478 0.00 0.00 0.00 3.24
210 211 3.599343 TGTCTGTGGTATCATGCAAGTC 58.401 45.455 0.00 0.00 0.00 3.01
211 212 3.261643 TCTGTCTGTGGTATCATGCAAGT 59.738 43.478 0.00 0.00 0.00 3.16
212 213 3.865446 TCTGTCTGTGGTATCATGCAAG 58.135 45.455 0.00 0.00 0.00 4.01
213 214 3.979101 TCTGTCTGTGGTATCATGCAA 57.021 42.857 0.00 0.00 0.00 4.08
214 215 5.070847 ACATATCTGTCTGTGGTATCATGCA 59.929 40.000 0.00 0.00 0.00 3.96
215 216 5.545588 ACATATCTGTCTGTGGTATCATGC 58.454 41.667 0.00 0.00 0.00 4.06
216 217 9.148104 CATAACATATCTGTCTGTGGTATCATG 57.852 37.037 0.00 0.00 33.36 3.07
217 218 9.093458 TCATAACATATCTGTCTGTGGTATCAT 57.907 33.333 0.00 0.00 33.36 2.45
218 219 8.477419 TCATAACATATCTGTCTGTGGTATCA 57.523 34.615 0.00 0.00 33.36 2.15
219 220 9.416794 CTTCATAACATATCTGTCTGTGGTATC 57.583 37.037 0.00 0.00 33.36 2.24
220 221 8.928448 ACTTCATAACATATCTGTCTGTGGTAT 58.072 33.333 0.00 0.00 33.36 2.73
221 222 8.306313 ACTTCATAACATATCTGTCTGTGGTA 57.694 34.615 0.00 0.00 33.36 3.25
222 223 7.187824 ACTTCATAACATATCTGTCTGTGGT 57.812 36.000 0.00 0.00 33.36 4.16
223 224 8.498054 AAACTTCATAACATATCTGTCTGTGG 57.502 34.615 0.00 0.00 33.36 4.17
235 236 9.769093 GCATAACTTCGTAAAACTTCATAACAT 57.231 29.630 0.00 0.00 0.00 2.71
236 237 8.775527 TGCATAACTTCGTAAAACTTCATAACA 58.224 29.630 0.00 0.00 0.00 2.41
237 238 9.769093 ATGCATAACTTCGTAAAACTTCATAAC 57.231 29.630 0.00 0.00 0.00 1.89
238 239 9.767684 CATGCATAACTTCGTAAAACTTCATAA 57.232 29.630 0.00 0.00 0.00 1.90
239 240 8.394877 CCATGCATAACTTCGTAAAACTTCATA 58.605 33.333 0.00 0.00 0.00 2.15
240 241 7.094377 ACCATGCATAACTTCGTAAAACTTCAT 60.094 33.333 0.00 0.00 0.00 2.57
241 242 6.205853 ACCATGCATAACTTCGTAAAACTTCA 59.794 34.615 0.00 0.00 0.00 3.02
242 243 6.608610 ACCATGCATAACTTCGTAAAACTTC 58.391 36.000 0.00 0.00 0.00 3.01
243 244 6.569179 ACCATGCATAACTTCGTAAAACTT 57.431 33.333 0.00 0.00 0.00 2.66
244 245 6.651643 TGTACCATGCATAACTTCGTAAAACT 59.348 34.615 0.00 0.00 0.00 2.66
245 246 6.833839 TGTACCATGCATAACTTCGTAAAAC 58.166 36.000 0.00 0.00 0.00 2.43
246 247 6.651643 ACTGTACCATGCATAACTTCGTAAAA 59.348 34.615 0.00 0.00 0.00 1.52
247 248 6.167685 ACTGTACCATGCATAACTTCGTAAA 58.832 36.000 0.00 0.00 0.00 2.01
343 356 0.325933 TTCCCTCGTGACTCCTACGA 59.674 55.000 0.00 0.00 47.00 3.43
344 357 0.450983 GTTCCCTCGTGACTCCTACG 59.549 60.000 0.00 0.00 42.56 3.51
713 766 2.538132 CGCGGTGGAAAACGGATTAATC 60.538 50.000 6.93 6.93 0.00 1.75
753 806 2.032634 CGCGGTTTCTGGCTAAGCA 61.033 57.895 0.00 0.00 0.00 3.91
754 807 1.967597 GACGCGGTTTCTGGCTAAGC 61.968 60.000 12.47 0.00 0.00 3.09
756 809 1.375013 GGACGCGGTTTCTGGCTAA 60.375 57.895 12.47 0.00 0.00 3.09
757 810 1.823169 AAGGACGCGGTTTCTGGCTA 61.823 55.000 12.47 0.00 0.00 3.93
776 829 3.851620 CGTACGCGCTTATAAGGGA 57.148 52.632 28.29 9.12 41.06 4.20
912 973 1.225745 GCAGACGGAATCGCAAACG 60.226 57.895 0.00 0.00 40.63 3.60
913 974 1.225745 CGCAGACGGAATCGCAAAC 60.226 57.895 0.00 0.00 40.63 2.93
914 975 3.022401 GCGCAGACGGAATCGCAAA 62.022 57.895 0.30 0.00 45.99 3.68
915 976 3.487202 GCGCAGACGGAATCGCAA 61.487 61.111 0.30 0.00 45.99 4.85
917 978 1.215655 AATAGCGCAGACGGAATCGC 61.216 55.000 11.47 6.33 46.95 4.58
937 998 1.338107 CCTTCCCCCAAACAAACCTC 58.662 55.000 0.00 0.00 0.00 3.85
950 1011 4.111053 GAACCGCCTCCCCTTCCC 62.111 72.222 0.00 0.00 0.00 3.97
962 1023 1.601419 TAAGCTCCACCTCCGAACCG 61.601 60.000 0.00 0.00 0.00 4.44
980 1041 1.133363 CTCCGGTCTCTCTCTCCCTA 58.867 60.000 0.00 0.00 0.00 3.53
981 1042 0.622154 TCTCCGGTCTCTCTCTCCCT 60.622 60.000 0.00 0.00 0.00 4.20
982 1043 0.476771 ATCTCCGGTCTCTCTCTCCC 59.523 60.000 0.00 0.00 0.00 4.30
983 1044 1.604604 CATCTCCGGTCTCTCTCTCC 58.395 60.000 0.00 0.00 0.00 3.71
1175 1237 9.740710 CCCCCAACCAAATAAATAAATAAACAA 57.259 29.630 0.00 0.00 0.00 2.83
1176 1238 9.112658 TCCCCCAACCAAATAAATAAATAAACA 57.887 29.630 0.00 0.00 0.00 2.83
1177 1239 9.607988 CTCCCCCAACCAAATAAATAAATAAAC 57.392 33.333 0.00 0.00 0.00 2.01
1189 1251 0.835971 GCAACCTCCCCCAACCAAAT 60.836 55.000 0.00 0.00 0.00 2.32
1251 1319 2.352915 GACTCAGATCTCGCGCGG 60.353 66.667 31.69 20.60 0.00 6.46
1311 1381 0.890683 GCCACCAAATTCCAGACCAG 59.109 55.000 0.00 0.00 0.00 4.00
1538 1608 0.468226 AGAGAAAAGTGGCACGGTCA 59.532 50.000 12.71 0.00 0.00 4.02
1543 1613 0.877743 GGAGCAGAGAAAAGTGGCAC 59.122 55.000 10.29 10.29 0.00 5.01
1544 1614 0.473755 TGGAGCAGAGAAAAGTGGCA 59.526 50.000 0.00 0.00 0.00 4.92
1553 1623 4.307032 AAGGCTAAAAATGGAGCAGAGA 57.693 40.909 0.00 0.00 40.64 3.10
1558 1628 3.066369 GCGTAAGGCTAAAAATGGAGC 57.934 47.619 0.00 0.00 39.11 4.70
1575 1645 2.611518 GATTCTGACTTGCACTAGCGT 58.388 47.619 0.00 0.00 46.23 5.07
1602 1680 5.127194 ACTCGCCATCTGACTTTTATCTGTA 59.873 40.000 0.00 0.00 0.00 2.74
1603 1681 4.081420 ACTCGCCATCTGACTTTTATCTGT 60.081 41.667 0.00 0.00 0.00 3.41
1604 1682 4.269603 CACTCGCCATCTGACTTTTATCTG 59.730 45.833 0.00 0.00 0.00 2.90
1605 1683 4.437239 CACTCGCCATCTGACTTTTATCT 58.563 43.478 0.00 0.00 0.00 1.98
1626 1704 5.479306 CGAACAGATAGAAAGGTTTCTCCA 58.521 41.667 8.25 0.00 43.72 3.86
1627 1705 4.870991 CCGAACAGATAGAAAGGTTTCTCC 59.129 45.833 8.25 3.10 43.72 3.71
1628 1706 5.480205 ACCGAACAGATAGAAAGGTTTCTC 58.520 41.667 8.25 0.00 43.72 2.87
1630 1708 6.555812 AAACCGAACAGATAGAAAGGTTTC 57.444 37.500 4.12 0.00 37.45 2.78
1631 1709 8.101419 AGATAAACCGAACAGATAGAAAGGTTT 58.899 33.333 13.18 13.18 33.30 3.27
1632 1710 7.549488 CAGATAAACCGAACAGATAGAAAGGTT 59.451 37.037 0.00 0.00 33.30 3.50
1649 1738 4.460948 TCCAGTACGGTTCAGATAAACC 57.539 45.455 4.11 0.00 44.40 3.27
1662 1751 1.873591 GGCCTTGCATAATCCAGTACG 59.126 52.381 0.00 0.00 0.00 3.67
1673 1762 2.091994 AGCTAGATTTCAGGCCTTGCAT 60.092 45.455 0.00 0.00 32.55 3.96
1721 1810 3.055891 GGGAGCAGTTGGTTGCAAATATT 60.056 43.478 0.00 0.00 46.47 1.28
1782 1871 2.847327 ATAACTCGGAGCATGGATGG 57.153 50.000 4.58 0.00 0.00 3.51
1840 1929 4.806640 AAGGATACGGTTTAAGGTCGAA 57.193 40.909 0.00 0.00 46.39 3.71
1932 2021 4.980339 ATTTTCACAAGCAAGGGGAAAT 57.020 36.364 1.35 0.00 0.00 2.17
1937 2026 3.473923 ACCAATTTTCACAAGCAAGGG 57.526 42.857 0.00 0.00 0.00 3.95
1939 2028 4.448732 GCCTAACCAATTTTCACAAGCAAG 59.551 41.667 0.00 0.00 0.00 4.01
1945 2034 3.230134 AGCTGCCTAACCAATTTTCACA 58.770 40.909 0.00 0.00 0.00 3.58
1968 2057 4.319118 GCAGACTACTCTTCAGTTTTGCAC 60.319 45.833 0.00 0.00 37.11 4.57
1969 2058 3.809832 GCAGACTACTCTTCAGTTTTGCA 59.190 43.478 0.00 0.00 37.11 4.08
2007 2096 4.218200 TCCCTGAAATTTATGTGCACACAG 59.782 41.667 24.37 21.15 45.48 3.66
2016 2105 6.886459 TCTTGTCTTCCTCCCTGAAATTTATG 59.114 38.462 0.00 0.00 0.00 1.90
2242 2331 1.270518 ACGAGCAGACTTGTGAGCATT 60.271 47.619 0.00 0.00 39.20 3.56
2249 2338 0.603569 ATTCGGACGAGCAGACTTGT 59.396 50.000 0.00 0.00 43.65 3.16
2250 2339 0.994995 CATTCGGACGAGCAGACTTG 59.005 55.000 0.00 0.00 0.00 3.16
2311 2400 2.711964 GCAACGTACATGTCAAACAACG 59.288 45.455 13.51 13.51 36.33 4.10
2330 2419 9.409312 CAATAATCAACACAATAAGAACAAGCA 57.591 29.630 0.00 0.00 0.00 3.91
2470 2559 6.111382 GTGGTGAGAAAAGATGATCATGAGA 58.889 40.000 14.30 0.00 0.00 3.27
2489 2578 3.955471 AGATCCATAAACTGTGGTGGTG 58.045 45.455 6.35 0.00 37.96 4.17
2496 2585 6.476378 AGCACAAGTTAGATCCATAAACTGT 58.524 36.000 0.00 0.00 33.85 3.55
2497 2586 6.992063 AGCACAAGTTAGATCCATAAACTG 57.008 37.500 0.00 0.00 33.85 3.16
2501 2590 7.759489 ACAAAAGCACAAGTTAGATCCATAA 57.241 32.000 0.00 0.00 0.00 1.90
2667 2756 2.580783 TGGTAAGGGCATAAGGCTTCTT 59.419 45.455 1.30 3.00 44.01 2.52
2670 2759 2.205342 TCTGGTAAGGGCATAAGGCTT 58.795 47.619 4.58 4.58 44.01 4.35
2696 2787 5.239525 ACTCTAAGGACAAAGCACATTTCAC 59.760 40.000 0.00 0.00 0.00 3.18
2722 2813 9.473007 TGGGATAAAATATTCATGACTTGTTGA 57.527 29.630 0.00 0.00 0.00 3.18
2935 3026 7.220741 TCAGAGTTCACATATAGGATACAGC 57.779 40.000 0.00 0.00 41.41 4.40
2951 3042 6.042777 TGACAATACGGAATGATCAGAGTTC 58.957 40.000 0.09 0.00 0.00 3.01
3042 3133 5.501715 CGAATCATGTAAACATACAGCCAC 58.498 41.667 0.00 0.00 34.26 5.01
3048 3139 7.491372 TCTGAGAACCGAATCATGTAAACATAC 59.509 37.037 0.00 0.00 34.26 2.39
3090 3184 3.075882 TCCCTCCCATGAACAAACAGAAT 59.924 43.478 0.00 0.00 0.00 2.40
3103 3197 1.279271 CTCGACAAAACTCCCTCCCAT 59.721 52.381 0.00 0.00 0.00 4.00
3107 3201 1.014564 CGCCTCGACAAAACTCCCTC 61.015 60.000 0.00 0.00 0.00 4.30
3141 3241 7.038302 CCTTAGTTATATTAGCCTGTCCATGGA 60.038 40.741 11.44 11.44 0.00 3.41
3177 3280 1.148310 CACTTGTTGACTACAGGCGG 58.852 55.000 0.00 0.00 37.35 6.13
3181 3284 5.178061 TGCCATATCACTTGTTGACTACAG 58.822 41.667 0.00 0.00 36.92 2.74
3198 3301 8.264347 TGTGTTTGTAGAGAATTAGATGCCATA 58.736 33.333 0.00 0.00 0.00 2.74
3203 3306 8.032952 TGCTTGTGTTTGTAGAGAATTAGATG 57.967 34.615 0.00 0.00 0.00 2.90
3452 3611 1.650528 CAGGATCCTATCACCTCCCC 58.349 60.000 15.67 0.00 31.06 4.81
3466 3625 2.040278 TGCTTTAGCTGTCAACCAGGAT 59.960 45.455 0.00 0.00 41.81 3.24
3591 3750 6.420604 AGCAAGCACACAAACATAAAATACAC 59.579 34.615 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.