Multiple sequence alignment - TraesCS5B01G249200

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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 TraesCS5B01G249200 chr5B 100.000 3238 0 0 1 3238 431794073 431797310 0.000000e+00 5980
1 TraesCS5B01G249200 chr5A 87.418 3052 217 83 250 3238 466981754 466984701 0.000000e+00 3354
2 TraesCS5B01G249200 chr5A 87.402 127 15 1 6 131 466981573 466981699 9.360000e-31 145
3 TraesCS5B01G249200 chr5D 89.357 1851 122 25 218 2039 365320312 365322116 0.000000e+00 2257
4 TraesCS5B01G249200 chr5D 86.577 1192 75 37 2077 3238 365322112 365323248 0.000000e+00 1236


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 TraesCS5B01G249200 chr5B 431794073 431797310 3237 False 5980.0 5980 100.000 1 3238 1 chr5B.!!$F1 3237
1 TraesCS5B01G249200 chr5A 466981573 466984701 3128 False 1749.5 3354 87.410 6 3238 2 chr5A.!!$F1 3232
2 TraesCS5B01G249200 chr5D 365320312 365323248 2936 False 1746.5 2257 87.967 218 3238 2 chr5D.!!$F1 3020

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
143 145 0.036306 CCACGGATGTATAAGGCCCC 59.964 60.0 0.00 0.0 0.0 5.80 F
155 157 0.261696 AAGGCCCCGGAATAAGCAAT 59.738 50.0 0.73 0.0 0.0 3.56 F
156 158 0.261696 AGGCCCCGGAATAAGCAATT 59.738 50.0 0.73 0.0 0.0 2.32 F
658 673 0.392595 GGAGATCGCCCGAGGTTTTT 60.393 55.0 3.71 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1512 0.105039 CTCTGGGAGTGCGGTAATCC 59.895 60.000 3.86 3.86 42.82 3.01 R
1749 1793 0.618458 TAATTGCCCTTCTCCACGCT 59.382 50.000 0.00 0.00 0.00 5.07 R
2044 2099 1.224039 GCTGCTGATCCCTTGCTCT 59.776 57.895 0.00 0.00 0.00 4.09 R
2327 2382 0.111253 ATGTGCTAGCTAATGGCCCC 59.889 55.000 17.23 0.00 43.05 5.80 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
35 36 2.094752 GCACTATTCATTGTTTGGCCGT 60.095 45.455 0.00 0.00 0.00 5.68
38 39 2.723124 ATTCATTGTTTGGCCGTGAC 57.277 45.000 0.00 0.00 0.00 3.67
80 81 8.341173 GTTTGCATGTATTTGATGTTCCAAAAA 58.659 29.630 0.00 0.00 39.20 1.94
93 95 6.723298 TGTTCCAAAAATAAGACATGTGGT 57.277 33.333 1.15 0.00 0.00 4.16
106 108 2.892852 ACATGTGGTTGGGTCATTTGAG 59.107 45.455 0.00 0.00 0.00 3.02
127 129 2.049433 CGGTCGGTCACTGTCCAC 60.049 66.667 0.54 0.00 0.00 4.02
131 133 1.605451 TCGGTCACTGTCCACGGAT 60.605 57.895 0.00 0.00 0.00 4.18
132 134 1.446099 CGGTCACTGTCCACGGATG 60.446 63.158 0.00 0.00 0.00 3.51
133 135 1.671742 GGTCACTGTCCACGGATGT 59.328 57.895 0.00 0.00 0.00 3.06
134 136 0.892755 GGTCACTGTCCACGGATGTA 59.107 55.000 0.00 0.00 0.00 2.29
137 139 3.131577 GGTCACTGTCCACGGATGTATAA 59.868 47.826 0.00 0.00 0.00 0.98
138 140 4.360563 GTCACTGTCCACGGATGTATAAG 58.639 47.826 0.00 0.00 0.00 1.73
139 141 3.383505 TCACTGTCCACGGATGTATAAGG 59.616 47.826 0.00 0.00 0.00 2.69
141 143 1.414919 TGTCCACGGATGTATAAGGCC 59.585 52.381 0.00 0.00 0.00 5.19
142 144 1.053424 TCCACGGATGTATAAGGCCC 58.947 55.000 0.00 0.00 0.00 5.80
143 145 0.036306 CCACGGATGTATAAGGCCCC 59.964 60.000 0.00 0.00 0.00 5.80
145 147 1.295423 CGGATGTATAAGGCCCCGG 59.705 63.158 0.00 0.00 33.94 5.73
146 148 1.189524 CGGATGTATAAGGCCCCGGA 61.190 60.000 0.73 0.00 33.94 5.14
147 149 1.061546 GGATGTATAAGGCCCCGGAA 58.938 55.000 0.73 0.00 0.00 4.30
149 151 2.841881 GGATGTATAAGGCCCCGGAATA 59.158 50.000 0.73 0.00 0.00 1.75
151 153 4.514401 GATGTATAAGGCCCCGGAATAAG 58.486 47.826 0.73 0.00 0.00 1.73
153 155 1.145571 ATAAGGCCCCGGAATAAGCA 58.854 50.000 0.73 0.00 0.00 3.91
154 156 0.920438 TAAGGCCCCGGAATAAGCAA 59.080 50.000 0.73 0.00 0.00 3.91
155 157 0.261696 AAGGCCCCGGAATAAGCAAT 59.738 50.000 0.73 0.00 0.00 3.56
156 158 0.261696 AGGCCCCGGAATAAGCAATT 59.738 50.000 0.73 0.00 0.00 2.32
157 159 1.119684 GGCCCCGGAATAAGCAATTT 58.880 50.000 0.73 0.00 0.00 1.82
158 160 1.068588 GGCCCCGGAATAAGCAATTTC 59.931 52.381 0.73 0.00 0.00 2.17
159 161 1.754226 GCCCCGGAATAAGCAATTTCA 59.246 47.619 0.73 0.00 0.00 2.69
160 162 2.167487 GCCCCGGAATAAGCAATTTCAA 59.833 45.455 0.73 0.00 0.00 2.69
161 163 3.181466 GCCCCGGAATAAGCAATTTCAAT 60.181 43.478 0.73 0.00 0.00 2.57
162 164 4.683129 GCCCCGGAATAAGCAATTTCAATT 60.683 41.667 0.73 0.00 0.00 2.32
163 165 4.810491 CCCCGGAATAAGCAATTTCAATTG 59.190 41.667 0.73 7.76 46.55 2.32
164 166 5.418676 CCCGGAATAAGCAATTTCAATTGT 58.581 37.500 0.73 0.00 45.77 2.71
165 167 6.406400 CCCCGGAATAAGCAATTTCAATTGTA 60.406 38.462 0.73 0.00 45.77 2.41
166 168 6.697019 CCCGGAATAAGCAATTTCAATTGTAG 59.303 38.462 0.73 0.00 45.77 2.74
167 169 7.416213 CCCGGAATAAGCAATTTCAATTGTAGA 60.416 37.037 0.73 0.91 45.77 2.59
168 170 8.137437 CCGGAATAAGCAATTTCAATTGTAGAT 58.863 33.333 12.71 2.85 45.77 1.98
169 171 8.961092 CGGAATAAGCAATTTCAATTGTAGATG 58.039 33.333 12.71 2.92 45.77 2.90
170 172 8.758715 GGAATAAGCAATTTCAATTGTAGATGC 58.241 33.333 12.71 15.93 45.77 3.91
171 173 9.525409 GAATAAGCAATTTCAATTGTAGATGCT 57.475 29.630 18.74 18.74 45.77 3.79
172 174 9.525409 AATAAGCAATTTCAATTGTAGATGCTC 57.475 29.630 22.14 3.81 45.77 4.26
173 175 6.770746 AGCAATTTCAATTGTAGATGCTCT 57.229 33.333 18.74 5.77 45.77 4.09
174 176 7.870509 AGCAATTTCAATTGTAGATGCTCTA 57.129 32.000 18.74 0.00 45.77 2.43
175 177 8.284945 AGCAATTTCAATTGTAGATGCTCTAA 57.715 30.769 18.74 0.00 45.77 2.10
176 178 8.186821 AGCAATTTCAATTGTAGATGCTCTAAC 58.813 33.333 18.74 0.00 45.77 2.34
177 179 8.186821 GCAATTTCAATTGTAGATGCTCTAACT 58.813 33.333 12.71 0.00 45.77 2.24
180 182 9.678260 ATTTCAATTGTAGATGCTCTAACTTCT 57.322 29.630 5.13 0.00 29.58 2.85
181 183 8.484641 TTCAATTGTAGATGCTCTAACTTCTG 57.515 34.615 5.13 0.00 29.58 3.02
182 184 6.536582 TCAATTGTAGATGCTCTAACTTCTGC 59.463 38.462 5.13 0.00 29.58 4.26
183 185 5.667539 TTGTAGATGCTCTAACTTCTGCT 57.332 39.130 0.00 0.00 29.58 4.24
184 186 5.255710 TGTAGATGCTCTAACTTCTGCTC 57.744 43.478 0.00 0.00 29.58 4.26
185 187 3.817709 AGATGCTCTAACTTCTGCTCC 57.182 47.619 0.00 0.00 0.00 4.70
186 188 2.433970 AGATGCTCTAACTTCTGCTCCC 59.566 50.000 0.00 0.00 0.00 4.30
187 189 1.944177 TGCTCTAACTTCTGCTCCCT 58.056 50.000 0.00 0.00 0.00 4.20
188 190 1.827969 TGCTCTAACTTCTGCTCCCTC 59.172 52.381 0.00 0.00 0.00 4.30
189 191 1.202359 GCTCTAACTTCTGCTCCCTCG 60.202 57.143 0.00 0.00 0.00 4.63
190 192 2.370349 CTCTAACTTCTGCTCCCTCGA 58.630 52.381 0.00 0.00 0.00 4.04
191 193 2.955660 CTCTAACTTCTGCTCCCTCGAT 59.044 50.000 0.00 0.00 0.00 3.59
192 194 4.138290 CTCTAACTTCTGCTCCCTCGATA 58.862 47.826 0.00 0.00 0.00 2.92
193 195 4.533815 TCTAACTTCTGCTCCCTCGATAA 58.466 43.478 0.00 0.00 0.00 1.75
194 196 4.954202 TCTAACTTCTGCTCCCTCGATAAA 59.046 41.667 0.00 0.00 0.00 1.40
195 197 3.810310 ACTTCTGCTCCCTCGATAAAG 57.190 47.619 0.00 0.00 0.00 1.85
196 198 3.100671 ACTTCTGCTCCCTCGATAAAGT 58.899 45.455 0.00 0.00 0.00 2.66
197 199 4.279145 ACTTCTGCTCCCTCGATAAAGTA 58.721 43.478 0.00 0.00 0.00 2.24
230 232 5.886960 ACATTTCATCAGGCTGAAACTAC 57.113 39.130 22.84 0.00 45.21 2.73
231 233 5.564550 ACATTTCATCAGGCTGAAACTACT 58.435 37.500 22.84 0.00 45.21 2.57
233 235 4.890158 TTCATCAGGCTGAAACTACTCA 57.110 40.909 22.84 0.00 32.35 3.41
234 236 4.462508 TCATCAGGCTGAAACTACTCAG 57.537 45.455 22.84 3.50 44.82 3.35
244 246 7.478520 GCTGAAACTACTCAGACAACTAAAA 57.521 36.000 4.81 0.00 44.82 1.52
281 283 1.293267 AATGCGAACGTACGTTGGGG 61.293 55.000 36.11 24.23 38.60 4.96
284 286 2.030862 GAACGTACGTTGGGGGCA 59.969 61.111 36.11 0.00 38.60 5.36
288 290 1.885850 CGTACGTTGGGGGCATAGC 60.886 63.158 7.22 0.00 0.00 2.97
289 291 1.222387 GTACGTTGGGGGCATAGCA 59.778 57.895 0.00 0.00 0.00 3.49
291 293 2.602746 TACGTTGGGGGCATAGCAGC 62.603 60.000 0.00 0.00 0.00 5.25
337 342 1.038130 AATCCGAGACCGCAGCTAGT 61.038 55.000 0.00 0.00 0.00 2.57
346 351 1.365633 CGCAGCTAGTGATCTCCCC 59.634 63.158 0.00 0.00 0.00 4.81
352 357 2.111384 GCTAGTGATCTCCCCACAAGA 58.889 52.381 0.00 0.00 37.01 3.02
585 600 3.450115 GCGGAGGAGGCACGTACT 61.450 66.667 0.00 0.00 0.00 2.73
586 601 2.799371 CGGAGGAGGCACGTACTC 59.201 66.667 10.15 10.15 0.00 2.59
658 673 0.392595 GGAGATCGCCCGAGGTTTTT 60.393 55.000 3.71 0.00 0.00 1.94
668 687 3.555586 GCCCGAGGTTTTTCTGTACTACA 60.556 47.826 0.00 0.00 0.00 2.74
817 839 2.348998 CGGCAGCTCCCTTTGACT 59.651 61.111 0.00 0.00 0.00 3.41
902 924 8.311395 TCTAATCTGCCTCCTTGGTATATATG 57.689 38.462 0.00 0.00 38.35 1.78
942 964 1.373536 AAACCTCTCCTTTCCCCTCC 58.626 55.000 0.00 0.00 0.00 4.30
1080 1102 1.470805 GCCGAAGCAAACAACAAGGTT 60.471 47.619 0.00 0.00 39.53 3.50
1086 1108 3.793797 GCAAACAACAAGGTTGGTACT 57.206 42.857 13.09 0.00 45.28 2.73
1087 1109 4.118093 GCAAACAACAAGGTTGGTACTT 57.882 40.909 13.09 0.00 45.28 2.24
1088 1110 4.109766 GCAAACAACAAGGTTGGTACTTC 58.890 43.478 13.09 0.00 45.28 3.01
1089 1111 4.347813 CAAACAACAAGGTTGGTACTTCG 58.652 43.478 13.09 0.00 41.35 3.79
1090 1112 1.944709 ACAACAAGGTTGGTACTTCGC 59.055 47.619 13.09 0.00 0.00 4.70
1091 1113 1.944024 CAACAAGGTTGGTACTTCGCA 59.056 47.619 1.23 0.00 0.00 5.10
1092 1114 1.878953 ACAAGGTTGGTACTTCGCAG 58.121 50.000 0.00 0.00 0.00 5.18
1093 1115 1.140252 ACAAGGTTGGTACTTCGCAGT 59.860 47.619 0.00 0.00 36.99 4.40
1096 1118 3.036075 AGGTTGGTACTTCGCAGTAAC 57.964 47.619 3.08 3.08 42.89 2.50
1103 1125 1.860676 ACTTCGCAGTAACTTCGCAA 58.139 45.000 0.00 0.00 0.00 4.85
1195 1225 2.094957 GGCGGAGTAGTGCTGATATCTC 60.095 54.545 3.98 0.00 0.00 2.75
1205 1235 2.031595 TGCTGATATCTCGCTTCTCGAC 60.032 50.000 15.34 0.00 43.16 4.20
1282 1312 1.304547 CACCTGAGAGGACGGAGGT 60.305 63.158 0.00 0.00 37.67 3.85
1293 1323 4.473520 CGGAGGTCAATGGCGGCT 62.474 66.667 11.43 0.00 0.00 5.52
1307 1337 4.247380 GGCTCGAGGGCATGGAGG 62.247 72.222 15.58 0.00 40.53 4.30
1317 1347 2.765807 CATGGAGGAGCGGGGAGT 60.766 66.667 0.00 0.00 0.00 3.85
1482 1512 2.753966 CCAAGTGCCGCTCCATTCG 61.754 63.158 0.00 0.00 0.00 3.34
1594 1637 6.599356 TGATTACTGCTAAGTGGTAGTTCA 57.401 37.500 0.00 0.00 37.19 3.18
1602 1646 7.502561 ACTGCTAAGTGGTAGTTCAATTTTTCT 59.497 33.333 0.00 0.00 34.48 2.52
1607 1651 6.004574 AGTGGTAGTTCAATTTTTCTCTCCC 58.995 40.000 0.00 0.00 0.00 4.30
1617 1661 7.871853 TCAATTTTTCTCTCCCGAAGTAAAAG 58.128 34.615 0.00 0.00 0.00 2.27
1619 1663 6.613755 TTTTTCTCTCCCGAAGTAAAAGTG 57.386 37.500 0.00 0.00 0.00 3.16
1620 1664 3.314541 TCTCTCCCGAAGTAAAAGTGC 57.685 47.619 0.00 0.00 0.00 4.40
1643 1687 2.360726 TAGTGCGGTGCTCCTCGA 60.361 61.111 2.85 0.00 0.00 4.04
1646 1690 3.611674 TGCGGTGCTCCTCGACAA 61.612 61.111 2.85 0.00 0.00 3.18
1698 1742 9.646427 GTACTGTAGAGATTCTTGTCAAATCTT 57.354 33.333 0.00 0.00 42.17 2.40
1709 1753 2.017049 GTCAAATCTTCCACCCCATCG 58.983 52.381 0.00 0.00 0.00 3.84
1749 1793 7.395617 TGTAATTAGTGTACTGCAAATGGGTA 58.604 34.615 0.00 0.00 0.00 3.69
1754 1798 1.396996 GTACTGCAAATGGGTAGCGTG 59.603 52.381 0.00 0.00 0.00 5.34
1830 1878 5.396772 GGACCCTGAATGATGAACTGATACA 60.397 44.000 0.00 0.00 0.00 2.29
1833 1881 6.060136 CCCTGAATGATGAACTGATACATGT 58.940 40.000 2.69 2.69 0.00 3.21
1874 1922 5.530171 GGAGCAAATGAAGAAGCAGATCATA 59.470 40.000 0.00 0.00 33.60 2.15
1910 1958 2.139323 ACATGATGAGGCAAGTGCAT 57.861 45.000 0.00 0.00 44.36 3.96
1931 1979 1.499949 GCCGCACGCTTTACATGAA 59.500 52.632 0.00 0.00 0.00 2.57
1934 1982 2.862512 CCGCACGCTTTACATGAATTT 58.137 42.857 0.00 0.00 0.00 1.82
1936 1984 4.597079 CCGCACGCTTTACATGAATTTAT 58.403 39.130 0.00 0.00 0.00 1.40
1991 2046 1.126662 CCACATCACAATCGACACACG 59.873 52.381 0.00 0.00 44.09 4.49
2023 2078 3.051479 CATGTGCTGACGGCTGCA 61.051 61.111 19.96 19.96 45.14 4.41
2044 2099 4.038642 GCAGTTTCATTTCCAGGGTAAACA 59.961 41.667 0.00 0.00 31.02 2.83
2052 2107 1.351017 TCCAGGGTAAACAGAGCAAGG 59.649 52.381 0.00 0.00 0.00 3.61
2054 2109 1.351017 CAGGGTAAACAGAGCAAGGGA 59.649 52.381 0.00 0.00 0.00 4.20
2055 2110 2.025887 CAGGGTAAACAGAGCAAGGGAT 60.026 50.000 0.00 0.00 0.00 3.85
2060 2115 0.694771 AACAGAGCAAGGGATCAGCA 59.305 50.000 0.00 0.00 0.00 4.41
2108 2163 0.530650 GCCATCGTCATCGTCACCAT 60.531 55.000 0.00 0.00 38.33 3.55
2238 2293 0.173708 CGCGGAGAAGAAGCCTTAGT 59.826 55.000 0.00 0.00 31.62 2.24
2251 2306 0.527817 CCTTAGTTAGCTGCCGGTCG 60.528 60.000 1.90 0.00 0.00 4.79
2280 2335 1.606668 GAGAAGATGCGACTCGATCCT 59.393 52.381 1.63 0.00 0.00 3.24
2283 2338 3.823873 AGAAGATGCGACTCGATCCTATT 59.176 43.478 1.63 0.00 0.00 1.73
2284 2339 3.567576 AGATGCGACTCGATCCTATTG 57.432 47.619 1.63 0.00 0.00 1.90
2285 2340 1.989165 GATGCGACTCGATCCTATTGC 59.011 52.381 1.63 0.00 0.00 3.56
2286 2341 0.744281 TGCGACTCGATCCTATTGCA 59.256 50.000 1.63 0.00 0.00 4.08
2287 2342 1.136110 TGCGACTCGATCCTATTGCAA 59.864 47.619 0.00 0.00 0.00 4.08
2288 2343 2.224042 TGCGACTCGATCCTATTGCAAT 60.224 45.455 17.56 17.56 0.00 3.56
2289 2344 3.005367 TGCGACTCGATCCTATTGCAATA 59.995 43.478 17.94 17.94 0.00 1.90
2316 2371 9.290988 AGATACAGATAGTGACATAGTGTTAGG 57.709 37.037 0.00 0.00 0.00 2.69
2317 2372 6.150396 ACAGATAGTGACATAGTGTTAGGC 57.850 41.667 0.00 0.00 0.00 3.93
2318 2373 5.894393 ACAGATAGTGACATAGTGTTAGGCT 59.106 40.000 0.00 0.00 0.00 4.58
2319 2374 7.061054 ACAGATAGTGACATAGTGTTAGGCTA 58.939 38.462 0.00 0.00 0.00 3.93
2320 2375 7.229707 ACAGATAGTGACATAGTGTTAGGCTAG 59.770 40.741 0.00 0.00 0.00 3.42
2321 2376 4.657436 AGTGACATAGTGTTAGGCTAGC 57.343 45.455 6.04 6.04 0.00 3.42
2322 2377 4.282496 AGTGACATAGTGTTAGGCTAGCT 58.718 43.478 15.72 3.22 0.00 3.32
2323 2378 5.446860 AGTGACATAGTGTTAGGCTAGCTA 58.553 41.667 15.72 7.32 0.00 3.32
2324 2379 5.533154 AGTGACATAGTGTTAGGCTAGCTAG 59.467 44.000 16.84 16.84 0.00 3.42
2325 2380 5.299782 GTGACATAGTGTTAGGCTAGCTAGT 59.700 44.000 21.62 5.88 0.00 2.57
2326 2381 6.485984 GTGACATAGTGTTAGGCTAGCTAGTA 59.514 42.308 21.62 4.85 0.00 1.82
2327 2382 6.711194 TGACATAGTGTTAGGCTAGCTAGTAG 59.289 42.308 21.62 0.00 0.00 2.57
2328 2383 6.005198 ACATAGTGTTAGGCTAGCTAGTAGG 58.995 44.000 21.62 8.01 0.00 3.18
2329 2384 3.834938 AGTGTTAGGCTAGCTAGTAGGG 58.165 50.000 21.62 0.00 0.00 3.53
2330 2385 2.892215 GTGTTAGGCTAGCTAGTAGGGG 59.108 54.545 21.62 0.00 0.00 4.79
2331 2386 1.894466 GTTAGGCTAGCTAGTAGGGGC 59.106 57.143 21.62 8.87 0.00 5.80
2332 2387 0.408700 TAGGCTAGCTAGTAGGGGCC 59.591 60.000 21.62 15.89 39.82 5.80
2333 2388 1.152312 GGCTAGCTAGTAGGGGCCA 60.152 63.158 21.62 0.00 39.38 5.36
2334 2389 0.545548 GGCTAGCTAGTAGGGGCCAT 60.546 60.000 21.62 0.00 39.38 4.40
2366 2421 6.204882 GCACATGGTTAGCTTATTAGTTAGGG 59.795 42.308 0.00 0.00 0.00 3.53
2402 2457 2.586079 CCGCACGTAGAGCCCATG 60.586 66.667 0.00 0.00 42.29 3.66
2403 2458 3.264897 CGCACGTAGAGCCCATGC 61.265 66.667 0.00 0.00 42.29 4.06
2405 2460 2.203070 CACGTAGAGCCCATGCCC 60.203 66.667 0.00 0.00 38.69 5.36
2408 2463 2.109181 GTAGAGCCCATGCCCGAC 59.891 66.667 0.00 0.00 38.69 4.79
2420 2475 2.645567 CCCGACCCTCGATCGATG 59.354 66.667 19.78 15.94 43.74 3.84
2421 2476 2.645567 CCGACCCTCGATCGATGG 59.354 66.667 30.56 30.56 43.74 3.51
2423 2478 1.576920 CGACCCTCGATCGATGGAG 59.423 63.158 36.36 26.62 43.74 3.86
2424 2479 1.287503 GACCCTCGATCGATGGAGC 59.712 63.158 36.36 25.50 34.61 4.70
2425 2480 1.455773 ACCCTCGATCGATGGAGCA 60.456 57.895 36.36 8.23 34.61 4.26
2468 2531 3.477224 TTTTGGTTGCGCCGTGCTC 62.477 57.895 4.18 0.00 46.63 4.26
2504 2571 3.329386 GTCTGTAATCTGTCAGCAGCAA 58.671 45.455 0.00 0.00 42.29 3.91
2532 2599 2.995939 TGAAGCTGCAGAGAATGTAACG 59.004 45.455 20.43 0.00 0.00 3.18
2539 2606 4.692228 TGCAGAGAATGTAACGCATGATA 58.308 39.130 0.00 0.00 37.96 2.15
2575 2649 1.814394 CATGTGGCAAGCAGTATGTGT 59.186 47.619 0.00 0.00 39.31 3.72
2576 2650 1.522668 TGTGGCAAGCAGTATGTGTC 58.477 50.000 0.00 0.00 39.31 3.67
2577 2651 1.072173 TGTGGCAAGCAGTATGTGTCT 59.928 47.619 0.00 0.00 39.31 3.41
2578 2652 1.734465 GTGGCAAGCAGTATGTGTCTC 59.266 52.381 0.00 0.00 39.31 3.36
2579 2653 1.002366 GGCAAGCAGTATGTGTCTCG 58.998 55.000 0.00 0.00 39.31 4.04
2580 2654 1.002366 GCAAGCAGTATGTGTCTCGG 58.998 55.000 0.00 0.00 39.31 4.63
2581 2655 1.002366 CAAGCAGTATGTGTCTCGGC 58.998 55.000 0.00 0.00 39.31 5.54
2582 2656 0.458543 AAGCAGTATGTGTCTCGGCG 60.459 55.000 0.00 0.00 39.31 6.46
2583 2657 1.153823 GCAGTATGTGTCTCGGCGT 60.154 57.895 6.85 0.00 39.31 5.68
2584 2658 0.099968 GCAGTATGTGTCTCGGCGTA 59.900 55.000 6.85 0.00 39.31 4.42
2585 2659 1.823828 CAGTATGTGTCTCGGCGTAC 58.176 55.000 6.85 7.51 0.00 3.67
2586 2660 0.376152 AGTATGTGTCTCGGCGTACG 59.624 55.000 11.84 11.84 46.11 3.67
2598 2685 1.499949 GCGTACGAAATGCCTTGCA 59.500 52.632 21.65 0.00 44.86 4.08
2610 2697 0.877743 GCCTTGCAGGTTCAGAGTTC 59.122 55.000 0.00 0.00 37.80 3.01
2614 2701 2.827800 TGCAGGTTCAGAGTTCAGAG 57.172 50.000 0.00 0.00 0.00 3.35
2618 2705 3.470709 CAGGTTCAGAGTTCAGAGCAAA 58.529 45.455 0.00 0.00 0.00 3.68
2622 2709 4.122776 GTTCAGAGTTCAGAGCAAAGTGA 58.877 43.478 0.00 0.00 0.00 3.41
2642 2729 2.989639 AGCCCATCGCAGCTGTTA 59.010 55.556 16.64 3.90 41.38 2.41
2643 2730 1.528824 AGCCCATCGCAGCTGTTAT 59.471 52.632 16.64 6.34 41.38 1.89
2644 2731 0.758734 AGCCCATCGCAGCTGTTATA 59.241 50.000 16.64 0.00 41.38 0.98
2664 2751 1.310933 TTACACGTCTCCGAGCTCCC 61.311 60.000 8.47 0.00 37.88 4.30
2683 2770 2.810274 CCCATCATCATAGTTGCTTCCG 59.190 50.000 0.00 0.00 0.00 4.30
2687 2774 4.471904 TCATCATAGTTGCTTCCGTCTT 57.528 40.909 0.00 0.00 0.00 3.01
2688 2775 4.183865 TCATCATAGTTGCTTCCGTCTTG 58.816 43.478 0.00 0.00 0.00 3.02
2695 2782 2.125512 CTTCCGTCTTGGGGCTCG 60.126 66.667 0.00 0.00 38.76 5.03
2710 2797 1.330655 GCTCGGATCCTTCCAGACCA 61.331 60.000 10.75 0.00 42.74 4.02
2718 2805 2.846193 TCCTTCCAGACCAAACGAAAG 58.154 47.619 0.00 0.00 0.00 2.62
2731 2818 1.562783 ACGAAAGGAGGAAGCTAGCT 58.437 50.000 12.68 12.68 0.00 3.32
2732 2819 2.736347 ACGAAAGGAGGAAGCTAGCTA 58.264 47.619 19.70 0.00 0.00 3.32
2733 2820 2.691011 ACGAAAGGAGGAAGCTAGCTAG 59.309 50.000 19.70 16.84 0.00 3.42
2877 2964 2.786495 CCGTGACAGCGATAGGGCT 61.786 63.158 0.00 0.00 46.13 5.19
2974 3066 2.276116 GGGTGGTCAGAGCGAGACA 61.276 63.158 8.17 0.00 37.74 3.41
2977 3069 1.228583 TGGTCAGAGCGAGACACCT 60.229 57.895 8.17 0.00 37.74 4.00
2978 3070 1.214062 GGTCAGAGCGAGACACCTG 59.786 63.158 8.17 0.00 37.74 4.00
2979 3071 1.528292 GGTCAGAGCGAGACACCTGT 61.528 60.000 8.17 0.00 37.74 4.00
3019 3113 4.148825 GCACCTGGACCGAGCGAT 62.149 66.667 0.00 0.00 0.00 4.58
3157 3254 1.078143 GCAGGAAAGCGACCTCCAT 60.078 57.895 0.00 0.00 35.35 3.41
3161 3258 1.561542 AGGAAAGCGACCTCCATTGAT 59.438 47.619 0.00 0.00 33.83 2.57
3164 3261 3.209410 GAAAGCGACCTCCATTGATGAT 58.791 45.455 0.00 0.00 0.00 2.45
3169 3266 3.736720 CGACCTCCATTGATGATGATGT 58.263 45.455 0.00 0.00 38.03 3.06
3226 3323 0.960861 CTGACGGGAAAAGAAGGGCC 60.961 60.000 0.00 0.00 0.00 5.80
3227 3324 1.379146 GACGGGAAAAGAAGGGCCT 59.621 57.895 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.507817 CGGCCAAACAATGAATAGTGCATAT 60.508 40.000 2.24 0.00 0.00 1.78
17 18 3.727673 CGTCACGGCCAAACAATGAATAG 60.728 47.826 2.24 0.00 0.00 1.73
18 19 2.160615 CGTCACGGCCAAACAATGAATA 59.839 45.455 2.24 0.00 0.00 1.75
21 22 0.533085 TCGTCACGGCCAAACAATGA 60.533 50.000 2.24 0.00 0.00 2.57
38 39 2.470140 GCAAACACTTACACGTCGATCG 60.470 50.000 9.36 9.36 46.00 3.69
46 47 7.594758 ACATCAAATACATGCAAACACTTACAC 59.405 33.333 0.00 0.00 0.00 2.90
49 50 7.812191 GGAACATCAAATACATGCAAACACTTA 59.188 33.333 0.00 0.00 0.00 2.24
80 81 4.591321 ATGACCCAACCACATGTCTTAT 57.409 40.909 0.00 0.00 0.00 1.73
85 86 2.892852 CTCAAATGACCCAACCACATGT 59.107 45.455 0.00 0.00 0.00 3.21
86 87 2.231964 CCTCAAATGACCCAACCACATG 59.768 50.000 0.00 0.00 0.00 3.21
113 115 1.605451 ATCCGTGGACAGTGACCGA 60.605 57.895 7.14 0.00 0.00 4.69
127 129 1.189524 TCCGGGGCCTTATACATCCG 61.190 60.000 0.84 3.95 37.50 4.18
131 133 2.039348 GCTTATTCCGGGGCCTTATACA 59.961 50.000 0.84 0.00 0.00 2.29
132 134 2.039348 TGCTTATTCCGGGGCCTTATAC 59.961 50.000 0.84 0.00 0.00 1.47
133 135 2.340731 TGCTTATTCCGGGGCCTTATA 58.659 47.619 0.84 0.00 0.00 0.98
134 136 1.145571 TGCTTATTCCGGGGCCTTAT 58.854 50.000 0.84 0.00 0.00 1.73
137 139 0.261696 AATTGCTTATTCCGGGGCCT 59.738 50.000 0.84 0.00 0.00 5.19
138 140 1.068588 GAAATTGCTTATTCCGGGGCC 59.931 52.381 0.00 0.00 0.00 5.80
139 141 1.754226 TGAAATTGCTTATTCCGGGGC 59.246 47.619 0.00 0.00 0.00 5.80
141 143 5.971895 CAATTGAAATTGCTTATTCCGGG 57.028 39.130 0.00 0.00 39.29 5.73
166 168 2.433970 AGGGAGCAGAAGTTAGAGCATC 59.566 50.000 0.00 0.00 0.00 3.91
167 169 2.433970 GAGGGAGCAGAAGTTAGAGCAT 59.566 50.000 0.00 0.00 0.00 3.79
168 170 1.827969 GAGGGAGCAGAAGTTAGAGCA 59.172 52.381 0.00 0.00 0.00 4.26
169 171 1.202359 CGAGGGAGCAGAAGTTAGAGC 60.202 57.143 0.00 0.00 0.00 4.09
170 172 2.370349 TCGAGGGAGCAGAAGTTAGAG 58.630 52.381 0.00 0.00 0.00 2.43
171 173 2.509166 TCGAGGGAGCAGAAGTTAGA 57.491 50.000 0.00 0.00 0.00 2.10
172 174 4.920640 TTATCGAGGGAGCAGAAGTTAG 57.079 45.455 0.00 0.00 0.00 2.34
173 175 4.710375 ACTTTATCGAGGGAGCAGAAGTTA 59.290 41.667 0.00 0.00 0.00 2.24
174 176 3.515901 ACTTTATCGAGGGAGCAGAAGTT 59.484 43.478 0.00 0.00 0.00 2.66
175 177 3.100671 ACTTTATCGAGGGAGCAGAAGT 58.899 45.455 0.00 0.00 0.00 3.01
176 178 3.810310 ACTTTATCGAGGGAGCAGAAG 57.190 47.619 0.00 0.00 0.00 2.85
177 179 5.670792 TTTACTTTATCGAGGGAGCAGAA 57.329 39.130 0.00 0.00 0.00 3.02
178 180 5.670792 TTTTACTTTATCGAGGGAGCAGA 57.329 39.130 0.00 0.00 0.00 4.26
179 181 5.277538 GCATTTTACTTTATCGAGGGAGCAG 60.278 44.000 0.00 0.00 0.00 4.24
180 182 4.574828 GCATTTTACTTTATCGAGGGAGCA 59.425 41.667 0.00 0.00 0.00 4.26
181 183 4.816925 AGCATTTTACTTTATCGAGGGAGC 59.183 41.667 0.00 0.00 0.00 4.70
182 184 6.927294 AAGCATTTTACTTTATCGAGGGAG 57.073 37.500 0.00 0.00 0.00 4.30
214 216 4.180057 GTCTGAGTAGTTTCAGCCTGATG 58.820 47.826 0.00 0.00 43.39 3.07
215 217 3.834813 TGTCTGAGTAGTTTCAGCCTGAT 59.165 43.478 0.00 0.00 43.39 2.90
244 246 4.320494 CGCATTCACTAGTTTCAGCCTTTT 60.320 41.667 0.00 0.00 0.00 2.27
248 250 2.346803 TCGCATTCACTAGTTTCAGCC 58.653 47.619 0.00 0.00 0.00 4.85
291 293 3.485431 CAGAAGTCTGGCGCGCTG 61.485 66.667 32.29 23.19 40.20 5.18
295 300 0.458543 TCGAATCAGAAGTCTGGCGC 60.459 55.000 8.42 0.00 43.91 6.53
337 342 1.741028 TGGTTCTTGTGGGGAGATCA 58.259 50.000 0.00 0.00 0.00 2.92
346 351 2.094286 TGGTGCTGTTTTGGTTCTTGTG 60.094 45.455 0.00 0.00 0.00 3.33
352 357 0.673437 CCGATGGTGCTGTTTTGGTT 59.327 50.000 0.00 0.00 0.00 3.67
379 384 3.283751 AGAAAACAATCGTGTGTGGGAA 58.716 40.909 0.00 0.00 38.27 3.97
428 437 0.100861 GTGTCCTCGGATCGAAGGAC 59.899 60.000 26.76 26.76 45.24 3.85
585 600 2.540910 AGACAGGGGAGGGGAGGA 60.541 66.667 0.00 0.00 0.00 3.71
586 601 2.366167 CAGACAGGGGAGGGGAGG 60.366 72.222 0.00 0.00 0.00 4.30
587 602 3.086600 GCAGACAGGGGAGGGGAG 61.087 72.222 0.00 0.00 0.00 4.30
588 603 3.273071 ATGCAGACAGGGGAGGGGA 62.273 63.158 0.00 0.00 0.00 4.81
658 673 2.965831 GCCATGGAGGATGTAGTACAGA 59.034 50.000 18.40 0.00 41.22 3.41
668 687 3.171388 GTCCCGGCCATGGAGGAT 61.171 66.667 23.53 0.00 41.22 3.24
817 839 0.528466 GCACACAGCTAGCGATGCTA 60.528 55.000 20.97 0.00 40.44 3.49
902 924 1.172812 GGTGACAGTGCAGGGGTTTC 61.173 60.000 0.00 0.00 0.00 2.78
942 964 2.202492 CTCTGAACCGGACGAGCG 60.202 66.667 9.46 0.00 0.00 5.03
992 1014 2.202797 CGCACCTCATGGTCTCCG 60.203 66.667 0.00 0.00 46.60 4.63
1006 1028 3.612247 GAAGAAGGCTCCCTGCGCA 62.612 63.158 10.98 10.98 44.05 6.09
1080 1102 2.923605 GCGAAGTTACTGCGAAGTACCA 60.924 50.000 17.94 0.00 33.75 3.25
1085 1107 4.091509 AGTTATTGCGAAGTTACTGCGAAG 59.908 41.667 17.94 0.00 33.75 3.79
1086 1108 3.991773 AGTTATTGCGAAGTTACTGCGAA 59.008 39.130 17.94 2.16 33.75 4.70
1087 1109 3.581755 AGTTATTGCGAAGTTACTGCGA 58.418 40.909 17.94 1.71 33.75 5.10
1088 1110 3.991605 AGTTATTGCGAAGTTACTGCG 57.008 42.857 8.63 8.63 35.28 5.18
1089 1111 5.532025 AGAAGTTATTGCGAAGTTACTGC 57.468 39.130 0.00 0.00 0.00 4.40
1090 1112 6.888430 ACAAGAAGTTATTGCGAAGTTACTG 58.112 36.000 10.11 0.00 0.00 2.74
1091 1113 6.147328 GGACAAGAAGTTATTGCGAAGTTACT 59.853 38.462 10.11 0.00 0.00 2.24
1092 1114 6.073440 TGGACAAGAAGTTATTGCGAAGTTAC 60.073 38.462 10.11 0.00 0.00 2.50
1093 1115 5.992829 TGGACAAGAAGTTATTGCGAAGTTA 59.007 36.000 10.11 0.00 0.00 2.24
1096 1118 4.666655 CGTGGACAAGAAGTTATTGCGAAG 60.667 45.833 10.11 0.52 0.00 3.79
1103 1125 2.423577 GTGCCGTGGACAAGAAGTTAT 58.576 47.619 0.00 0.00 0.00 1.89
1147 1177 0.815213 GCACTCACTGCCACTGACAA 60.815 55.000 0.00 0.00 40.42 3.18
1205 1235 0.449388 GCTCTCCTGCATTTTCACGG 59.551 55.000 0.00 0.00 0.00 4.94
1258 1288 1.524482 GTCCTCTCAGGTGCCATCC 59.476 63.158 0.00 0.00 36.53 3.51
1282 1312 4.161295 CCCTCGAGCCGCCATTGA 62.161 66.667 6.99 0.00 0.00 2.57
1293 1323 3.157252 GCTCCTCCATGCCCTCGA 61.157 66.667 0.00 0.00 0.00 4.04
1307 1337 2.818132 CCTCATCACTCCCCGCTC 59.182 66.667 0.00 0.00 0.00 5.03
1482 1512 0.105039 CTCTGGGAGTGCGGTAATCC 59.895 60.000 3.86 3.86 42.82 3.01
1594 1637 7.649057 CACTTTTACTTCGGGAGAGAAAAATT 58.351 34.615 0.00 0.00 41.75 1.82
1602 1646 2.367567 ACTGCACTTTTACTTCGGGAGA 59.632 45.455 0.00 0.00 0.00 3.71
1607 1651 4.056050 ACTACCACTGCACTTTTACTTCG 58.944 43.478 0.00 0.00 0.00 3.79
1617 1661 2.030562 ACCGCACTACCACTGCAC 59.969 61.111 0.00 0.00 34.00 4.57
1619 1663 3.423154 GCACCGCACTACCACTGC 61.423 66.667 0.00 0.00 0.00 4.40
1620 1664 1.738099 GAGCACCGCACTACCACTG 60.738 63.158 0.00 0.00 0.00 3.66
1632 1676 3.071479 TGTTTAATTGTCGAGGAGCACC 58.929 45.455 0.00 0.00 0.00 5.01
1643 1687 7.435192 GCAAAGAACACTAGCTTGTTTAATTGT 59.565 33.333 16.99 4.65 39.88 2.71
1646 1690 7.277174 AGCAAAGAACACTAGCTTGTTTAAT 57.723 32.000 5.30 0.00 39.88 1.40
1698 1742 3.260888 TTTGGGCGATGGGGTGGA 61.261 61.111 0.00 0.00 0.00 4.02
1709 1753 4.600692 AATTACAGGTTCAAGTTTGGGC 57.399 40.909 0.00 0.00 0.00 5.36
1749 1793 0.618458 TAATTGCCCTTCTCCACGCT 59.382 50.000 0.00 0.00 0.00 5.07
1754 1798 3.879892 CAGCTAACTAATTGCCCTTCTCC 59.120 47.826 0.00 0.00 0.00 3.71
1830 1878 3.890756 TCCTGCAACAACAGAAATGACAT 59.109 39.130 0.00 0.00 40.25 3.06
1833 1881 2.294233 GCTCCTGCAACAACAGAAATGA 59.706 45.455 0.00 0.00 40.25 2.57
1874 1922 4.314961 TCATGTACAAATTCAGCAGACGT 58.685 39.130 0.00 0.00 0.00 4.34
1945 1993 3.466836 CCATGTACGGTGCAGATAATGT 58.533 45.455 4.97 0.00 0.00 2.71
1952 2000 2.108514 CCAGCCATGTACGGTGCAG 61.109 63.158 4.97 0.00 0.00 4.41
2023 2078 5.701224 TCTGTTTACCCTGGAAATGAAACT 58.299 37.500 0.00 0.00 0.00 2.66
2044 2099 1.224039 GCTGCTGATCCCTTGCTCT 59.776 57.895 0.00 0.00 0.00 4.09
2052 2107 4.925861 GGGCCGAGCTGCTGATCC 62.926 72.222 7.01 4.43 0.00 3.36
2124 2179 2.186644 CATGTCGGACGCCATGGA 59.813 61.111 18.40 0.00 35.82 3.41
2183 2238 1.964373 GTCGTTGTTGATGGGCCGT 60.964 57.895 0.00 0.00 0.00 5.68
2238 2293 2.260434 GTGTCGACCGGCAGCTAA 59.740 61.111 14.12 0.00 0.00 3.09
2251 2306 1.704582 GCATCTTCTCGCGTGTGTC 59.295 57.895 5.77 0.00 0.00 3.67
2304 2359 6.005198 CCTACTAGCTAGCCTAACACTATGT 58.995 44.000 20.91 0.00 0.00 2.29
2305 2360 5.416326 CCCTACTAGCTAGCCTAACACTATG 59.584 48.000 20.91 0.64 0.00 2.23
2307 2362 4.202545 CCCCTACTAGCTAGCCTAACACTA 60.203 50.000 20.91 2.22 0.00 2.74
2308 2363 3.436761 CCCCTACTAGCTAGCCTAACACT 60.437 52.174 20.91 1.02 0.00 3.55
2309 2364 2.892215 CCCCTACTAGCTAGCCTAACAC 59.108 54.545 20.91 0.00 0.00 3.32
2310 2365 2.755549 GCCCCTACTAGCTAGCCTAACA 60.756 54.545 20.91 0.00 0.00 2.41
2311 2366 1.894466 GCCCCTACTAGCTAGCCTAAC 59.106 57.143 20.91 2.77 0.00 2.34
2312 2367 1.203149 GGCCCCTACTAGCTAGCCTAA 60.203 57.143 20.91 3.30 37.42 2.69
2313 2368 0.408700 GGCCCCTACTAGCTAGCCTA 59.591 60.000 20.91 5.82 37.42 3.93
2314 2369 1.156566 GGCCCCTACTAGCTAGCCT 59.843 63.158 20.91 4.85 37.42 4.58
2315 2370 0.545548 ATGGCCCCTACTAGCTAGCC 60.546 60.000 20.91 15.74 40.87 3.93
2316 2371 1.353091 AATGGCCCCTACTAGCTAGC 58.647 55.000 20.91 6.62 0.00 3.42
2317 2372 2.498078 GCTAATGGCCCCTACTAGCTAG 59.502 54.545 19.44 19.44 33.68 3.42
2318 2373 2.111972 AGCTAATGGCCCCTACTAGCTA 59.888 50.000 15.55 0.00 42.63 3.32
2319 2374 1.132689 AGCTAATGGCCCCTACTAGCT 60.133 52.381 0.00 7.78 43.05 3.32
2320 2375 1.353091 AGCTAATGGCCCCTACTAGC 58.647 55.000 0.00 5.43 43.05 3.42
2321 2376 2.498078 GCTAGCTAATGGCCCCTACTAG 59.502 54.545 7.70 6.43 43.05 2.57
2322 2377 2.158219 TGCTAGCTAATGGCCCCTACTA 60.158 50.000 17.23 0.00 43.05 1.82
2323 2378 1.353091 GCTAGCTAATGGCCCCTACT 58.647 55.000 7.70 0.00 43.05 2.57
2324 2379 1.056660 TGCTAGCTAATGGCCCCTAC 58.943 55.000 17.23 0.00 43.05 3.18
2325 2380 1.056660 GTGCTAGCTAATGGCCCCTA 58.943 55.000 17.23 0.00 43.05 3.53
2326 2381 0.988145 TGTGCTAGCTAATGGCCCCT 60.988 55.000 17.23 0.00 43.05 4.79
2327 2382 0.111253 ATGTGCTAGCTAATGGCCCC 59.889 55.000 17.23 0.00 43.05 5.80
2328 2383 1.242076 CATGTGCTAGCTAATGGCCC 58.758 55.000 17.23 0.00 43.05 5.80
2329 2384 1.242076 CCATGTGCTAGCTAATGGCC 58.758 55.000 26.22 0.00 43.05 5.36
2330 2385 1.972872 ACCATGTGCTAGCTAATGGC 58.027 50.000 32.25 8.91 42.83 4.40
2331 2386 3.499918 GCTAACCATGTGCTAGCTAATGG 59.500 47.826 31.39 31.39 44.31 3.16
2332 2387 4.384056 AGCTAACCATGTGCTAGCTAATG 58.616 43.478 17.23 17.77 45.06 1.90
2333 2388 4.696479 AGCTAACCATGTGCTAGCTAAT 57.304 40.909 17.23 6.59 45.06 1.73
2334 2389 4.487714 AAGCTAACCATGTGCTAGCTAA 57.512 40.909 17.23 4.18 45.93 3.09
2357 2412 2.246849 GAGTCCCTCCCTCCCTAACTAA 59.753 54.545 0.00 0.00 0.00 2.24
2358 2413 1.858246 GAGTCCCTCCCTCCCTAACTA 59.142 57.143 0.00 0.00 0.00 2.24
2359 2414 0.637743 GAGTCCCTCCCTCCCTAACT 59.362 60.000 0.00 0.00 0.00 2.24
2360 2415 0.637743 AGAGTCCCTCCCTCCCTAAC 59.362 60.000 0.00 0.00 0.00 2.34
2361 2416 0.935194 GAGAGTCCCTCCCTCCCTAA 59.065 60.000 0.00 0.00 35.87 2.69
2402 2457 3.296054 ATCGATCGAGGGTCGGGC 61.296 66.667 23.84 0.00 40.88 6.13
2403 2458 2.645567 CATCGATCGAGGGTCGGG 59.354 66.667 23.84 3.10 40.88 5.14
2405 2460 1.576920 CTCCATCGATCGAGGGTCG 59.423 63.158 38.68 28.80 45.33 4.79
2408 2463 1.175347 TCTGCTCCATCGATCGAGGG 61.175 60.000 36.46 36.46 46.36 4.30
2420 2475 0.820871 AACTCACCTCGATCTGCTCC 59.179 55.000 0.00 0.00 0.00 4.70
2421 2476 1.470632 CCAACTCACCTCGATCTGCTC 60.471 57.143 0.00 0.00 0.00 4.26
2423 2478 0.532573 TCCAACTCACCTCGATCTGC 59.467 55.000 0.00 0.00 0.00 4.26
2424 2479 2.482664 CCATCCAACTCACCTCGATCTG 60.483 54.545 0.00 0.00 0.00 2.90
2425 2480 1.759445 CCATCCAACTCACCTCGATCT 59.241 52.381 0.00 0.00 0.00 2.75
2468 2531 0.938713 CAGACGCTACTACCTCTCCG 59.061 60.000 0.00 0.00 0.00 4.63
2473 2536 4.525024 ACAGATTACAGACGCTACTACCT 58.475 43.478 0.00 0.00 0.00 3.08
2480 2543 1.546029 TGCTGACAGATTACAGACGCT 59.454 47.619 6.65 0.00 36.38 5.07
2527 2594 7.223971 TGAAACCTGAAGTATATCATGCGTTAC 59.776 37.037 0.00 0.00 0.00 2.50
2528 2595 7.269316 TGAAACCTGAAGTATATCATGCGTTA 58.731 34.615 0.00 0.00 0.00 3.18
2532 2599 5.528690 TGCTGAAACCTGAAGTATATCATGC 59.471 40.000 0.00 0.00 0.00 4.06
2539 2606 4.012374 CCACATGCTGAAACCTGAAGTAT 58.988 43.478 0.00 0.00 0.00 2.12
2579 2653 1.226295 GCAAGGCATTTCGTACGCC 60.226 57.895 11.24 5.41 46.62 5.68
2580 2654 0.521242 CTGCAAGGCATTTCGTACGC 60.521 55.000 11.24 0.00 38.13 4.42
2581 2655 3.586039 CTGCAAGGCATTTCGTACG 57.414 52.632 9.53 9.53 38.13 3.67
2593 2680 3.065655 CTCTGAACTCTGAACCTGCAAG 58.934 50.000 0.00 0.00 0.00 4.01
2598 2685 3.135530 ACTTTGCTCTGAACTCTGAACCT 59.864 43.478 0.00 0.00 0.00 3.50
2610 2697 1.093159 GGGCTGATCACTTTGCTCTG 58.907 55.000 4.84 0.00 0.00 3.35
2614 2701 0.379669 CGATGGGCTGATCACTTTGC 59.620 55.000 0.00 0.00 0.00 3.68
2618 2705 1.145598 CTGCGATGGGCTGATCACT 59.854 57.895 0.00 0.00 42.69 3.41
2664 2751 4.375272 AGACGGAAGCAACTATGATGATG 58.625 43.478 0.00 0.00 0.00 3.07
2683 2770 1.627297 AAGGATCCGAGCCCCAAGAC 61.627 60.000 5.98 0.00 0.00 3.01
2687 2774 2.768344 GGAAGGATCCGAGCCCCA 60.768 66.667 5.98 0.00 35.59 4.96
2695 2782 1.278127 TCGTTTGGTCTGGAAGGATCC 59.722 52.381 2.48 2.48 46.76 3.36
2710 2797 2.303311 AGCTAGCTTCCTCCTTTCGTTT 59.697 45.455 12.68 0.00 0.00 3.60
2731 2818 2.831770 GGCAGGCAGGCATAGCTA 59.168 61.111 0.00 0.00 43.51 3.32
2877 2964 1.429930 TCCTCTATTATTGGCGGCCA 58.570 50.000 19.77 19.77 0.00 5.36
2879 2966 1.798813 CGTTCCTCTATTATTGGCGGC 59.201 52.381 0.00 0.00 0.00 6.53
2880 2967 2.413837 CCGTTCCTCTATTATTGGCGG 58.586 52.381 0.00 0.00 0.00 6.13
2881 2968 2.036733 TCCCGTTCCTCTATTATTGGCG 59.963 50.000 0.00 0.00 0.00 5.69
2921 3008 2.669569 AATGCTTCGCTGCCGTGT 60.670 55.556 0.00 0.00 35.54 4.49
2963 3055 1.080230 CCACAGGTGTCTCGCTCTG 60.080 63.158 0.00 0.00 0.00 3.35
2974 3066 1.152963 GCAACAGGTGTCCACAGGT 60.153 57.895 0.00 0.00 0.00 4.00
2977 3069 0.034574 AACAGCAACAGGTGTCCACA 60.035 50.000 0.48 0.00 42.66 4.17
2978 3070 1.961793 TAACAGCAACAGGTGTCCAC 58.038 50.000 0.48 0.00 42.66 4.02
2979 3071 2.552155 GGATAACAGCAACAGGTGTCCA 60.552 50.000 0.48 0.00 42.66 4.02
3019 3113 1.007734 GTGCAGAAGACGACGTCCA 60.008 57.895 23.76 11.68 32.18 4.02
3157 3254 5.425630 CCAGAGTGAGAACATCATCATCAA 58.574 41.667 0.00 0.00 40.92 2.57
3161 3258 2.417787 CGCCAGAGTGAGAACATCATCA 60.418 50.000 0.00 0.00 40.92 3.07
3164 3261 0.969149 ACGCCAGAGTGAGAACATCA 59.031 50.000 0.00 0.00 34.79 3.07
3169 3266 0.032130 GTCACACGCCAGAGTGAGAA 59.968 55.000 8.57 0.00 45.89 2.87


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

AutoCloner maintained by Alex Coulton.