Multiple sequence alignment - TraesCS7A01G246700

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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 TraesCS7A01G246700 chr7A 100.000 2833 0 0 1 2833 226722892 226720060 0.000000e+00 5232.0
1 TraesCS7A01G246700 chr7A 100.000 1870 0 0 3232 5101 226719661 226717792 0.000000e+00 3454.0
2 TraesCS7A01G246700 chr7D 93.475 1364 47 13 3295 4620 214335739 214334380 0.000000e+00 1988.0
3 TraesCS7A01G246700 chr7D 95.507 1224 45 5 1612 2833 214337272 214336057 0.000000e+00 1947.0
4 TraesCS7A01G246700 chr7D 88.280 1041 56 31 619 1616 214339461 214338444 0.000000e+00 1186.0
5 TraesCS7A01G246700 chr7D 85.421 439 44 7 204 622 214340920 214340482 6.060000e-119 438.0
6 TraesCS7A01G246700 chr7D 97.581 124 2 1 4979 5101 214332920 214332797 1.440000e-50 211.0
7 TraesCS7A01G246700 chr7D 88.298 94 10 1 4832 4924 214333560 214333467 1.500000e-20 111.0
8 TraesCS7A01G246700 chr7D 81.818 121 22 0 255 375 74836951 74837071 9.040000e-18 102.0
9 TraesCS7A01G246700 chr7D 98.000 50 1 0 4922 4971 214333210 214333161 2.530000e-13 87.9
10 TraesCS7A01G246700 chr7B 95.234 1259 46 6 3232 4479 186865267 186866522 0.000000e+00 1980.0
11 TraesCS7A01G246700 chr7B 94.541 1154 58 5 1681 2833 186864052 186865201 0.000000e+00 1777.0
12 TraesCS7A01G246700 chr7B 92.691 602 36 4 871 1466 186863440 186864039 0.000000e+00 861.0
13 TraesCS7A01G246700 chr7B 85.714 476 49 11 198 661 186862684 186863152 7.680000e-133 484.0
14 TraesCS7A01G246700 chr7B 92.308 299 14 4 4478 4772 186866683 186866976 2.840000e-112 416.0
15 TraesCS7A01G246700 chr7B 92.759 290 18 2 4813 5101 186867084 186867371 2.840000e-112 416.0
16 TraesCS7A01G246700 chr7B 83.838 198 13 4 660 841 186863256 186863450 2.440000e-38 171.0
17 TraesCS7A01G246700 chr7B 92.593 54 4 0 4774 4827 127024434 127024381 1.520000e-10 78.7
18 TraesCS7A01G246700 chr2B 95.276 127 3 2 4035 4158 229995161 229995035 1.120000e-46 198.0
19 TraesCS7A01G246700 chr5B 82.883 111 19 0 265 375 400925613 400925503 3.250000e-17 100.0
20 TraesCS7A01G246700 chr5B 92.727 55 4 0 4774 4828 479726916 479726862 4.230000e-11 80.5
21 TraesCS7A01G246700 chr5B 90.909 55 5 0 4774 4828 136047731 136047785 1.970000e-09 75.0
22 TraesCS7A01G246700 chr1B 92.857 56 4 0 4773 4828 264358146 264358091 1.180000e-11 82.4
23 TraesCS7A01G246700 chr5D 92.727 55 4 0 4774 4828 399614603 399614549 4.230000e-11 80.5
24 TraesCS7A01G246700 chr5D 90.909 55 5 0 4774 4828 123085723 123085777 1.970000e-09 75.0
25 TraesCS7A01G246700 chr4B 92.453 53 4 0 4776 4828 277316600 277316652 5.480000e-10 76.8
26 TraesCS7A01G246700 chr6A 92.308 52 4 0 4777 4828 47466868 47466817 1.970000e-09 75.0
27 TraesCS7A01G246700 chr1A 90.909 55 5 0 4774 4828 520812271 520812325 1.970000e-09 75.0


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 TraesCS7A01G246700 chr7A 226717792 226722892 5100 True 4343.000000 5232 100.000000 1 5101 2 chr7A.!!$R1 5100
1 TraesCS7A01G246700 chr7D 214332797 214340920 8123 True 852.700000 1988 92.366000 204 5101 7 chr7D.!!$R1 4897
2 TraesCS7A01G246700 chr7B 186862684 186867371 4687 False 872.142857 1980 91.012143 198 5101 7 chr7B.!!$F1 4903

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
836 2002 0.110373 CGTGTTTACCGCTCAAAGCC 60.110 55.000 0.00 0.0 38.18 4.35 F
1271 2451 0.179215 GATGCGAAAAGTGGAGTGCG 60.179 55.000 0.00 0.0 0.00 5.34 F
1842 4214 1.743252 CAGTGCTTTCTCGGAGGCC 60.743 63.158 4.96 0.0 0.00 5.19 F
3613 6184 1.398692 TGCCGCACTTTCTTTTCCTT 58.601 45.000 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2683 5056 0.179056 AGGACACCAACAGGTCAACG 60.179 55.000 0.00 0.0 35.74 4.10 R
2711 5084 3.625764 TGTCAGTACCAAAAGCAGTTGTC 59.374 43.478 0.00 0.0 0.00 3.18 R
3777 6348 0.830444 ACCAGGAGCAACGGTGAGTA 60.830 55.000 3.55 0.0 0.00 2.59 R
4813 8173 0.893727 GGACGCACAAGATGGGGTTT 60.894 55.000 0.00 0.0 45.48 3.27 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
38 39 9.658799 TGTCAAAATTTACCACAGAATTTTTCA 57.341 25.926 4.56 5.15 41.16 2.69
40 41 9.883142 TCAAAATTTACCACAGAATTTTTCAGT 57.117 25.926 4.56 0.00 41.16 3.41
85 86 9.702726 ATTTTGTCGATTTTACTATTCATCACG 57.297 29.630 0.00 0.00 0.00 4.35
86 87 6.822073 TGTCGATTTTACTATTCATCACGG 57.178 37.500 0.00 0.00 0.00 4.94
87 88 6.566141 TGTCGATTTTACTATTCATCACGGA 58.434 36.000 0.00 0.00 0.00 4.69
88 89 6.695713 TGTCGATTTTACTATTCATCACGGAG 59.304 38.462 0.00 0.00 0.00 4.63
89 90 5.690409 TCGATTTTACTATTCATCACGGAGC 59.310 40.000 0.00 0.00 0.00 4.70
90 91 5.462068 CGATTTTACTATTCATCACGGAGCA 59.538 40.000 0.00 0.00 0.00 4.26
91 92 6.146184 CGATTTTACTATTCATCACGGAGCAT 59.854 38.462 0.00 0.00 0.00 3.79
92 93 7.307396 CGATTTTACTATTCATCACGGAGCATT 60.307 37.037 0.00 0.00 0.00 3.56
93 94 7.624360 TTTTACTATTCATCACGGAGCATTT 57.376 32.000 0.00 0.00 0.00 2.32
94 95 6.603237 TTACTATTCATCACGGAGCATTTG 57.397 37.500 0.00 0.00 0.00 2.32
95 96 4.769688 ACTATTCATCACGGAGCATTTGA 58.230 39.130 0.00 0.00 0.00 2.69
96 97 4.813161 ACTATTCATCACGGAGCATTTGAG 59.187 41.667 0.00 0.00 0.00 3.02
97 98 1.372582 TCATCACGGAGCATTTGAGC 58.627 50.000 0.00 0.00 0.00 4.26
107 108 3.361281 AGCATTTGAGCTCAGGATCAA 57.639 42.857 17.43 8.42 44.63 2.57
114 115 5.698741 TTGAGCTCAGGATCAAAATAGGA 57.301 39.130 17.43 0.00 43.58 2.94
115 116 5.028549 TGAGCTCAGGATCAAAATAGGAC 57.971 43.478 13.74 0.00 34.74 3.85
116 117 4.718774 TGAGCTCAGGATCAAAATAGGACT 59.281 41.667 13.74 0.00 34.74 3.85
117 118 5.190528 TGAGCTCAGGATCAAAATAGGACTT 59.809 40.000 13.74 0.00 34.74 3.01
118 119 6.072199 AGCTCAGGATCAAAATAGGACTTT 57.928 37.500 0.00 0.00 0.00 2.66
119 120 6.488715 AGCTCAGGATCAAAATAGGACTTTT 58.511 36.000 0.00 0.00 0.00 2.27
120 121 6.376581 AGCTCAGGATCAAAATAGGACTTTTG 59.623 38.462 0.00 3.49 44.02 2.44
130 131 9.965824 TCAAAATAGGACTTTTGAGTCAAAATC 57.034 29.630 26.87 23.24 45.45 2.17
131 132 8.905702 CAAAATAGGACTTTTGAGTCAAAATCG 58.094 33.333 26.87 19.64 44.97 3.34
132 133 7.979444 AATAGGACTTTTGAGTCAAAATCGA 57.021 32.000 26.87 17.01 41.53 3.59
133 134 7.979444 ATAGGACTTTTGAGTCAAAATCGAA 57.021 32.000 26.87 17.41 41.53 3.71
134 135 6.884280 AGGACTTTTGAGTCAAAATCGAAT 57.116 33.333 26.87 13.07 41.53 3.34
135 136 7.277174 AGGACTTTTGAGTCAAAATCGAATT 57.723 32.000 26.87 11.33 41.53 2.17
136 137 7.716612 AGGACTTTTGAGTCAAAATCGAATTT 58.283 30.769 26.87 10.04 41.53 1.82
137 138 7.862873 AGGACTTTTGAGTCAAAATCGAATTTC 59.137 33.333 26.87 15.31 41.53 2.17
138 139 7.862873 GGACTTTTGAGTCAAAATCGAATTTCT 59.137 33.333 26.87 4.24 41.53 2.52
139 140 9.237846 GACTTTTGAGTCAAAATCGAATTTCTT 57.762 29.630 26.87 3.64 41.53 2.52
140 141 9.586435 ACTTTTGAGTCAAAATCGAATTTCTTT 57.414 25.926 26.87 0.78 41.53 2.52
142 143 8.574196 TTTGAGTCAAAATCGAATTTCTTTCC 57.426 30.769 15.92 0.00 29.89 3.13
143 144 7.270757 TGAGTCAAAATCGAATTTCTTTCCA 57.729 32.000 0.00 0.00 0.00 3.53
144 145 7.138736 TGAGTCAAAATCGAATTTCTTTCCAC 58.861 34.615 0.00 0.00 0.00 4.02
145 146 7.013274 TGAGTCAAAATCGAATTTCTTTCCACT 59.987 33.333 0.00 0.00 0.00 4.00
146 147 7.363431 AGTCAAAATCGAATTTCTTTCCACTC 58.637 34.615 0.00 0.00 0.00 3.51
147 148 7.229506 AGTCAAAATCGAATTTCTTTCCACTCT 59.770 33.333 0.00 0.00 0.00 3.24
148 149 7.535599 GTCAAAATCGAATTTCTTTCCACTCTC 59.464 37.037 0.00 0.00 0.00 3.20
149 150 7.228507 TCAAAATCGAATTTCTTTCCACTCTCA 59.771 33.333 0.00 0.00 0.00 3.27
150 151 6.487689 AATCGAATTTCTTTCCACTCTCAC 57.512 37.500 0.00 0.00 0.00 3.51
151 152 3.987868 TCGAATTTCTTTCCACTCTCACG 59.012 43.478 0.00 0.00 0.00 4.35
152 153 3.423645 CGAATTTCTTTCCACTCTCACGC 60.424 47.826 0.00 0.00 0.00 5.34
153 154 2.613026 TTTCTTTCCACTCTCACGCA 57.387 45.000 0.00 0.00 0.00 5.24
154 155 2.613026 TTCTTTCCACTCTCACGCAA 57.387 45.000 0.00 0.00 0.00 4.85
155 156 2.613026 TCTTTCCACTCTCACGCAAA 57.387 45.000 0.00 0.00 0.00 3.68
156 157 2.483876 TCTTTCCACTCTCACGCAAAG 58.516 47.619 0.00 0.00 0.00 2.77
157 158 0.944386 TTTCCACTCTCACGCAAAGC 59.056 50.000 0.00 0.00 0.00 3.51
158 159 0.884704 TTCCACTCTCACGCAAAGCC 60.885 55.000 0.00 0.00 0.00 4.35
159 160 1.302033 CCACTCTCACGCAAAGCCT 60.302 57.895 0.00 0.00 0.00 4.58
160 161 0.886490 CCACTCTCACGCAAAGCCTT 60.886 55.000 0.00 0.00 0.00 4.35
161 162 0.514691 CACTCTCACGCAAAGCCTTC 59.485 55.000 0.00 0.00 0.00 3.46
162 163 0.603975 ACTCTCACGCAAAGCCTTCC 60.604 55.000 0.00 0.00 0.00 3.46
163 164 0.321122 CTCTCACGCAAAGCCTTCCT 60.321 55.000 0.00 0.00 0.00 3.36
164 165 0.320771 TCTCACGCAAAGCCTTCCTC 60.321 55.000 0.00 0.00 0.00 3.71
165 166 1.301677 CTCACGCAAAGCCTTCCTCC 61.302 60.000 0.00 0.00 0.00 4.30
166 167 1.302832 CACGCAAAGCCTTCCTCCT 60.303 57.895 0.00 0.00 0.00 3.69
167 168 1.003233 ACGCAAAGCCTTCCTCCTC 60.003 57.895 0.00 0.00 0.00 3.71
168 169 1.298014 CGCAAAGCCTTCCTCCTCT 59.702 57.895 0.00 0.00 0.00 3.69
169 170 0.742635 CGCAAAGCCTTCCTCCTCTC 60.743 60.000 0.00 0.00 0.00 3.20
170 171 0.742635 GCAAAGCCTTCCTCCTCTCG 60.743 60.000 0.00 0.00 0.00 4.04
171 172 0.898320 CAAAGCCTTCCTCCTCTCGA 59.102 55.000 0.00 0.00 0.00 4.04
172 173 1.484240 CAAAGCCTTCCTCCTCTCGAT 59.516 52.381 0.00 0.00 0.00 3.59
173 174 1.408969 AAGCCTTCCTCCTCTCGATC 58.591 55.000 0.00 0.00 0.00 3.69
174 175 0.555769 AGCCTTCCTCCTCTCGATCT 59.444 55.000 0.00 0.00 0.00 2.75
175 176 1.063266 AGCCTTCCTCCTCTCGATCTT 60.063 52.381 0.00 0.00 0.00 2.40
176 177 1.339929 GCCTTCCTCCTCTCGATCTTC 59.660 57.143 0.00 0.00 0.00 2.87
177 178 1.606668 CCTTCCTCCTCTCGATCTTCG 59.393 57.143 0.00 0.00 42.10 3.79
178 179 2.294074 CTTCCTCCTCTCGATCTTCGT 58.706 52.381 0.00 0.00 41.35 3.85
179 180 1.956297 TCCTCCTCTCGATCTTCGTC 58.044 55.000 0.00 0.00 41.35 4.20
180 181 1.209747 TCCTCCTCTCGATCTTCGTCA 59.790 52.381 0.00 0.00 41.35 4.35
181 182 1.601903 CCTCCTCTCGATCTTCGTCAG 59.398 57.143 0.00 0.00 41.35 3.51
182 183 1.002900 CTCCTCTCGATCTTCGTCAGC 60.003 57.143 0.00 0.00 41.35 4.26
183 184 0.735471 CCTCTCGATCTTCGTCAGCA 59.265 55.000 0.00 0.00 41.35 4.41
184 185 1.133216 CCTCTCGATCTTCGTCAGCAA 59.867 52.381 0.00 0.00 41.35 3.91
185 186 2.416027 CCTCTCGATCTTCGTCAGCAAA 60.416 50.000 0.00 0.00 41.35 3.68
186 187 2.596419 CTCTCGATCTTCGTCAGCAAAC 59.404 50.000 0.00 0.00 41.35 2.93
187 188 1.656095 CTCGATCTTCGTCAGCAAACC 59.344 52.381 0.00 0.00 41.35 3.27
188 189 1.000394 TCGATCTTCGTCAGCAAACCA 60.000 47.619 0.00 0.00 41.35 3.67
189 190 1.798223 CGATCTTCGTCAGCAAACCAA 59.202 47.619 0.00 0.00 34.72 3.67
190 191 2.416547 CGATCTTCGTCAGCAAACCAAT 59.583 45.455 0.00 0.00 34.72 3.16
191 192 3.725895 CGATCTTCGTCAGCAAACCAATG 60.726 47.826 0.00 0.00 34.72 2.82
192 193 2.844946 TCTTCGTCAGCAAACCAATGA 58.155 42.857 0.00 0.00 0.00 2.57
193 194 3.210227 TCTTCGTCAGCAAACCAATGAA 58.790 40.909 0.00 0.00 0.00 2.57
194 195 3.820467 TCTTCGTCAGCAAACCAATGAAT 59.180 39.130 0.00 0.00 0.00 2.57
195 196 4.278170 TCTTCGTCAGCAAACCAATGAATT 59.722 37.500 0.00 0.00 0.00 2.17
196 197 4.159377 TCGTCAGCAAACCAATGAATTC 57.841 40.909 0.00 0.00 0.00 2.17
197 198 2.910482 CGTCAGCAAACCAATGAATTCG 59.090 45.455 0.04 0.00 0.00 3.34
198 199 2.663119 GTCAGCAAACCAATGAATTCGC 59.337 45.455 0.04 0.00 0.00 4.70
199 200 1.994779 CAGCAAACCAATGAATTCGCC 59.005 47.619 0.04 0.00 0.00 5.54
200 201 1.617850 AGCAAACCAATGAATTCGCCA 59.382 42.857 0.04 0.00 0.00 5.69
221 222 1.733360 CGGCTCCGTCTAGTAGATAGC 59.267 57.143 17.45 17.45 34.35 2.97
280 288 4.495422 GTGGCTCTTCTTATTCGAGTCAA 58.505 43.478 0.00 0.00 40.62 3.18
312 320 4.764172 CTCCGATCCTTCTCAAGTTCATT 58.236 43.478 0.00 0.00 0.00 2.57
316 324 6.605995 TCCGATCCTTCTCAAGTTCATTAGTA 59.394 38.462 0.00 0.00 0.00 1.82
321 329 8.830915 TCCTTCTCAAGTTCATTAGTAGAGAT 57.169 34.615 0.00 0.00 31.53 2.75
340 348 0.747255 TGGATTAGACGGAGCTCTGC 59.253 55.000 22.80 14.77 0.00 4.26
366 374 1.617018 TTCATGTCAGCTCCTCGGGG 61.617 60.000 0.00 0.00 0.00 5.73
384 392 3.515286 CGGCGAGGCGAGGTTAGA 61.515 66.667 13.92 0.00 0.00 2.10
398 406 5.049818 GCGAGGTTAGATTTTCTCATCATGG 60.050 44.000 0.00 0.00 0.00 3.66
411 419 1.134367 CATCATGGGTACGTGACGACT 59.866 52.381 13.70 0.00 44.85 4.18
422 430 3.179830 ACGTGACGACTAGATTTGATGC 58.820 45.455 13.70 0.00 0.00 3.91
426 434 3.195610 TGACGACTAGATTTGATGCCAGT 59.804 43.478 0.00 0.00 0.00 4.00
450 458 9.219603 AGTTTCTTCAGATCGATTCAATTGTTA 57.780 29.630 5.13 0.00 0.00 2.41
470 478 1.698165 AACGACGACGACTACGACTA 58.302 50.000 15.32 0.00 42.66 2.59
474 482 0.718343 ACGACGACTACGACTACAGC 59.282 55.000 0.00 0.00 42.66 4.40
475 483 0.997932 CGACGACTACGACTACAGCT 59.002 55.000 0.00 0.00 42.66 4.24
476 484 1.006183 CGACGACTACGACTACAGCTC 60.006 57.143 0.00 0.00 42.66 4.09
477 485 1.998315 GACGACTACGACTACAGCTCA 59.002 52.381 0.00 0.00 42.66 4.26
478 486 2.414481 GACGACTACGACTACAGCTCAA 59.586 50.000 0.00 0.00 42.66 3.02
479 487 2.810274 ACGACTACGACTACAGCTCAAA 59.190 45.455 0.00 0.00 42.66 2.69
502 522 1.670811 CGTGCACAAAGACTTTCCTGT 59.329 47.619 18.64 0.00 0.00 4.00
522 542 5.590259 CCTGTTATCATCAACAAGGTTAGGG 59.410 44.000 0.00 0.00 37.93 3.53
526 546 0.696501 ATCAACAAGGTTAGGGCGGT 59.303 50.000 0.00 0.00 0.00 5.68
528 548 1.133730 TCAACAAGGTTAGGGCGGTTT 60.134 47.619 0.00 0.00 0.00 3.27
529 549 1.268625 CAACAAGGTTAGGGCGGTTTC 59.731 52.381 0.00 0.00 0.00 2.78
573 593 2.786495 ATCGGCGGCTCGTTCTGAT 61.786 57.895 7.21 0.00 0.00 2.90
579 600 1.227380 GGCTCGTTCTGATGGCGAT 60.227 57.895 0.00 0.00 34.04 4.58
602 623 1.073603 TGGTCATTCTGTGGTGCATGA 59.926 47.619 0.00 0.00 0.00 3.07
616 637 5.068198 GTGGTGCATGATCCTCATTGTAATT 59.932 40.000 0.00 0.00 34.28 1.40
617 638 6.262944 GTGGTGCATGATCCTCATTGTAATTA 59.737 38.462 0.00 0.00 34.28 1.40
642 1688 7.789341 TTATCATGTTTGAAATGCGTTGTAC 57.211 32.000 0.00 0.00 34.96 2.90
706 1858 2.550830 TGAGGAAAGAACAGACAGGC 57.449 50.000 0.00 0.00 0.00 4.85
794 1960 7.962995 ACAACCTCTCACTAATCTGATTCTA 57.037 36.000 6.10 0.00 0.00 2.10
806 1972 3.369175 TCTGATTCTAGAGCTGGCTTGA 58.631 45.455 0.00 0.00 0.00 3.02
836 2002 0.110373 CGTGTTTACCGCTCAAAGCC 60.110 55.000 0.00 0.00 38.18 4.35
844 2010 2.551270 GCTCAAAGCCACGACGTG 59.449 61.111 21.02 21.02 34.48 4.49
903 2070 1.420532 AACAACGCCAACCCTCCCTA 61.421 55.000 0.00 0.00 0.00 3.53
915 2083 1.143889 CCCTCCCTATTCTTTCTGCCC 59.856 57.143 0.00 0.00 0.00 5.36
923 2091 0.323629 TTCTTTCTGCCCACCTACCG 59.676 55.000 0.00 0.00 0.00 4.02
930 2098 3.327404 CCCACCTACCGCCACCTT 61.327 66.667 0.00 0.00 0.00 3.50
942 2110 4.148825 CACCTTCCCCTCGCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
985 2162 1.425066 TCACAAGTGAAGGGGCAGATT 59.575 47.619 0.00 0.00 36.53 2.40
986 2163 2.158475 TCACAAGTGAAGGGGCAGATTT 60.158 45.455 0.00 0.00 36.53 2.17
1020 2197 3.787001 CCAAGTCGCCTCCTCCCC 61.787 72.222 0.00 0.00 0.00 4.81
1088 2265 7.656948 CAGAATCCTCTCCATCTTCTTTCATAC 59.343 40.741 0.00 0.00 0.00 2.39
1191 2371 2.035626 CTTTGGGGACGGCATGGT 59.964 61.111 0.00 0.00 0.00 3.55
1210 2390 1.541588 GTTGGGTGATGCAAGAACTCC 59.458 52.381 0.00 0.00 0.00 3.85
1216 2396 1.078143 ATGCAAGAACTCCGCCTCC 60.078 57.895 0.00 0.00 0.00 4.30
1246 2426 3.305110 CGCAATTCCTGGTTGTTGTTAC 58.695 45.455 0.00 0.00 0.00 2.50
1271 2451 0.179215 GATGCGAAAAGTGGAGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
1391 2586 5.666969 TTCAATAAGTGAAACGAGTGTGG 57.333 39.130 0.00 0.00 43.43 4.17
1410 2605 3.641436 GTGGTGATAAATCCCCATTTCCC 59.359 47.826 0.00 0.00 36.72 3.97
1418 2613 3.618120 ATCCCCATTTCCCATTCGATT 57.382 42.857 0.00 0.00 0.00 3.34
1423 2618 2.366266 CCATTTCCCATTCGATTGCCAT 59.634 45.455 1.71 0.00 0.00 4.40
1469 2664 9.162764 TCGTAGAATGGAAATCTTAAAAGAAGG 57.837 33.333 0.00 0.00 38.77 3.46
1470 2665 9.162764 CGTAGAATGGAAATCTTAAAAGAAGGA 57.837 33.333 0.00 0.00 38.77 3.36
1491 2686 9.315525 GAAGGAGTATTAGTTTTAAGTGGCTAG 57.684 37.037 0.00 0.00 0.00 3.42
1502 2697 3.971032 AAGTGGCTAGCGAAAATATGC 57.029 42.857 9.00 0.00 0.00 3.14
1505 2700 2.614057 GTGGCTAGCGAAAATATGCACT 59.386 45.455 9.00 0.00 0.00 4.40
1506 2701 2.613595 TGGCTAGCGAAAATATGCACTG 59.386 45.455 9.00 0.00 0.00 3.66
1507 2702 2.614057 GGCTAGCGAAAATATGCACTGT 59.386 45.455 9.00 0.00 0.00 3.55
1508 2703 3.807622 GGCTAGCGAAAATATGCACTGTA 59.192 43.478 9.00 0.00 0.00 2.74
1509 2704 4.272504 GGCTAGCGAAAATATGCACTGTAA 59.727 41.667 9.00 0.00 0.00 2.41
1541 2736 7.548427 TGCATTGTTTTTCTTTTCACAAGATCA 59.452 29.630 0.00 0.00 32.80 2.92
1544 2739 9.657419 ATTGTTTTTCTTTTCACAAGATCACTT 57.343 25.926 0.00 0.00 32.80 3.16
1575 2770 6.127842 GGTTTAAAACCGAGCAATAATCCAGA 60.128 38.462 0.00 0.00 42.62 3.86
1609 2804 5.779529 AGCTGCGATCAATCCATTATTTT 57.220 34.783 0.00 0.00 0.00 1.82
1659 4031 2.755103 GGTGTTTGGATCCTAGGCAAAG 59.245 50.000 14.23 0.00 0.00 2.77
1673 4045 7.346471 TCCTAGGCAAAGTGAATTATAGCTTT 58.654 34.615 2.96 0.00 0.00 3.51
1674 4046 7.499232 TCCTAGGCAAAGTGAATTATAGCTTTC 59.501 37.037 2.96 0.00 0.00 2.62
1675 4047 7.500559 CCTAGGCAAAGTGAATTATAGCTTTCT 59.499 37.037 0.00 0.00 0.00 2.52
1676 4048 7.709149 AGGCAAAGTGAATTATAGCTTTCTT 57.291 32.000 0.00 0.00 0.00 2.52
1692 4064 4.802999 CTTTCTTCAGGAGTCAAAATGCC 58.197 43.478 0.00 0.00 0.00 4.40
1804 4176 7.797121 AATACCCCTCAAAGATTCACATTTT 57.203 32.000 0.00 0.00 0.00 1.82
1842 4214 1.743252 CAGTGCTTTCTCGGAGGCC 60.743 63.158 4.96 0.00 0.00 5.19
1861 4234 3.179048 GCCAATTACGAGCCAATTTGAC 58.821 45.455 0.00 0.00 0.00 3.18
1922 4295 3.894427 TGGCTTCAAATACTGGCAAGAAA 59.106 39.130 0.00 0.00 32.14 2.52
1937 4310 4.574013 GGCAAGAAACTCATTCAGATCGAT 59.426 41.667 0.00 0.00 40.72 3.59
2003 4376 8.641498 AAAAGAATCTTGAGAAAGCTATGGAA 57.359 30.769 0.00 0.00 0.00 3.53
2071 4444 6.867550 TCACTACCATGATCTAACTTCACAG 58.132 40.000 0.00 0.00 0.00 3.66
2075 4448 5.171476 ACCATGATCTAACTTCACAGTTCG 58.829 41.667 0.00 0.00 42.66 3.95
2085 4458 3.243737 ACTTCACAGTTCGTATCAGCACA 60.244 43.478 0.00 0.00 0.00 4.57
2090 4463 3.059884 CAGTTCGTATCAGCACAGTGTT 58.940 45.455 1.61 0.00 0.00 3.32
2139 4512 2.231235 AGGTTCGTTGGCATCCATTTTC 59.769 45.455 0.00 0.00 31.53 2.29
2269 4642 5.939883 CCTCTCATTCAACTTGACCATGTTA 59.060 40.000 0.00 0.00 0.00 2.41
2309 4682 2.920724 TGTGTACTTAGCTGTTGCCA 57.079 45.000 0.00 0.00 40.80 4.92
2391 4764 7.186021 CGTAAGTGAATTGGTTCTAAACTGT 57.814 36.000 0.00 0.00 35.33 3.55
2531 4904 8.268850 ACGATAAACAAAATGCTCTTGTAGAT 57.731 30.769 0.00 0.00 35.98 1.98
2595 4968 7.857456 TGGTGATAGGTGAGTACATGTTAAAT 58.143 34.615 2.30 0.00 0.00 1.40
2659 5032 9.609346 TTCTTACCTTAATCCTACAGTTTATGC 57.391 33.333 0.00 0.00 0.00 3.14
2711 5084 3.253188 CCTGTTGGTGTCCTTTGTGTATG 59.747 47.826 0.00 0.00 0.00 2.39
2736 5109 3.820557 ACTGCTTTTGGTACTGACACAT 58.179 40.909 0.00 0.00 0.00 3.21
2755 5128 8.522003 TGACACATTATGCATATTCTGTGTTTT 58.478 29.630 30.50 19.14 45.08 2.43
2804 5177 1.580059 AGCCCCGTTATTCCTCTGAA 58.420 50.000 0.00 0.00 34.33 3.02
3251 5624 1.896220 ACACCTTCGCATGTGACAAT 58.104 45.000 8.86 0.00 36.35 2.71
3293 5855 2.573462 ACAAGTCCTGTGCCAGATACAT 59.427 45.455 4.00 0.00 36.69 2.29
3411 5979 4.787260 TGTTACATGTGCTGCATCATTT 57.213 36.364 9.11 7.27 35.19 2.32
3418 5986 5.049954 ACATGTGCTGCATCATTTTGTTTTC 60.050 36.000 5.27 0.00 35.19 2.29
3513 6084 7.362401 GCATCTGAAAACAACAGAGGATAATGT 60.362 37.037 12.50 0.00 45.14 2.71
3517 6088 7.648142 TGAAAACAACAGAGGATAATGTGAAC 58.352 34.615 0.00 0.00 0.00 3.18
3551 6122 4.256920 CATGCTACCAGAGTAAGCTGTTT 58.743 43.478 0.00 0.00 34.06 2.83
3563 6134 5.523369 AGTAAGCTGTTTGTTGCTTCATTC 58.477 37.500 3.41 0.00 45.09 2.67
3579 6150 4.508461 TCATTCACTCGAGGAAACGTAA 57.492 40.909 18.41 0.44 34.70 3.18
3613 6184 1.398692 TGCCGCACTTTCTTTTCCTT 58.601 45.000 0.00 0.00 0.00 3.36
3654 6225 3.535561 ACCACTGTTGTCTTCAGTCTTG 58.464 45.455 0.00 0.00 43.14 3.02
3777 6348 4.712337 AGGAGTCGATGAGGTATGTTTTCT 59.288 41.667 0.00 0.00 0.00 2.52
3781 6352 6.797454 AGTCGATGAGGTATGTTTTCTACTC 58.203 40.000 0.00 0.00 0.00 2.59
3926 6497 8.210946 TCCCTCACTTTGTGGTATGAATATTAG 58.789 37.037 0.00 0.00 33.87 1.73
3927 6498 7.041098 CCCTCACTTTGTGGTATGAATATTAGC 60.041 40.741 0.00 0.00 33.87 3.09
3952 6523 6.243216 ACTTTACTGTTAGTGTCCCTTTCA 57.757 37.500 0.00 0.00 0.00 2.69
3964 6535 3.519510 TGTCCCTTTCACCTCTTATCCAG 59.480 47.826 0.00 0.00 0.00 3.86
4295 6869 9.636789 ATTCTGATGTGATGATTGGAGAAATAA 57.363 29.630 0.00 0.00 0.00 1.40
4368 6966 1.647084 GCAAGGCACGTTCGAAGTT 59.353 52.632 0.00 0.00 0.00 2.66
4380 6978 0.250295 TCGAAGTTGCAAGGAGGTGG 60.250 55.000 0.00 0.00 0.00 4.61
4435 7033 8.915871 TGTATATTTACACTCCGTTTGTAGTC 57.084 34.615 0.00 0.00 33.37 2.59
4590 7350 9.290988 TGTGGAACAGAAAATTTATACTAAGCA 57.709 29.630 0.00 0.00 45.67 3.91
4634 7938 9.426837 CACAACAAAATCAAATAATCACAGGAT 57.573 29.630 0.00 0.00 34.43 3.24
4641 7945 9.865321 AAATCAAATAATCACAGGATTGAACAG 57.135 29.630 0.41 0.00 43.47 3.16
4698 8002 2.039879 TGGAAAGGTAAAGCTCTGGGAC 59.960 50.000 0.00 0.00 0.00 4.46
4729 8033 7.253750 GCATTAAGTATTTTTCCTGTTGCGATG 60.254 37.037 0.00 0.00 0.00 3.84
4730 8034 5.705609 AAGTATTTTTCCTGTTGCGATGT 57.294 34.783 0.00 0.00 0.00 3.06
4749 8058 3.450578 TGTATCGAAATAGCCAACGACC 58.549 45.455 0.00 0.00 37.58 4.79
4772 8081 3.300934 TAGCACAGTGGCAGAGGCG 62.301 63.158 1.84 0.00 42.47 5.52
4799 8159 1.831736 GCAAGGGTAAGGCTGTCTAGA 59.168 52.381 0.00 0.00 0.00 2.43
4806 8166 4.080526 GGGTAAGGCTGTCTAGAAATTCCA 60.081 45.833 0.00 0.00 0.00 3.53
4807 8167 5.398012 GGGTAAGGCTGTCTAGAAATTCCAT 60.398 44.000 0.00 0.00 0.00 3.41
4808 8168 6.122964 GGTAAGGCTGTCTAGAAATTCCATT 58.877 40.000 0.00 0.00 0.00 3.16
4809 8169 6.261158 GGTAAGGCTGTCTAGAAATTCCATTC 59.739 42.308 0.00 0.00 0.00 2.67
4810 8170 4.786425 AGGCTGTCTAGAAATTCCATTCC 58.214 43.478 0.00 0.00 0.00 3.01
4811 8171 3.885901 GGCTGTCTAGAAATTCCATTCCC 59.114 47.826 0.00 0.00 0.00 3.97
4813 8173 5.163195 GGCTGTCTAGAAATTCCATTCCCTA 60.163 44.000 0.00 0.00 0.00 3.53
4814 8174 6.357367 GCTGTCTAGAAATTCCATTCCCTAA 58.643 40.000 0.00 0.00 0.00 2.69
4834 8210 2.671070 CCCATCTTGTGCGTCCCT 59.329 61.111 0.00 0.00 0.00 4.20
4856 8252 8.811994 TCCCTTTCTTTCGATAAAATCCAAATT 58.188 29.630 0.00 0.00 0.00 1.82
4863 8259 6.507958 TCGATAAAATCCAAATTGCACAGA 57.492 33.333 0.00 0.00 0.00 3.41
4864 8260 6.554419 TCGATAAAATCCAAATTGCACAGAG 58.446 36.000 0.00 0.00 0.00 3.35
4887 8283 5.299531 AGAAATGATATCGGAGTCTGAACGA 59.700 40.000 5.58 0.00 41.20 3.85
4888 8284 3.965292 TGATATCGGAGTCTGAACGAC 57.035 47.619 5.58 0.00 43.17 4.34
5094 8983 7.992754 AATCATCTAATTAGCACCCTGATTC 57.007 36.000 7.67 0.00 30.80 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.658799 TGAAAAATTCTGTGGTAAATTTTGACA 57.341 25.926 0.00 7.50 41.69 3.58
14 15 9.883142 ACTGAAAAATTCTGTGGTAAATTTTGA 57.117 25.926 0.00 0.00 41.69 2.69
59 60 9.702726 CGTGATGAATAGTAAAATCGACAAAAT 57.297 29.630 0.00 0.00 0.00 1.82
60 61 8.172484 CCGTGATGAATAGTAAAATCGACAAAA 58.828 33.333 0.00 0.00 0.00 2.44
61 62 7.546316 TCCGTGATGAATAGTAAAATCGACAAA 59.454 33.333 0.00 0.00 0.00 2.83
62 63 7.036829 TCCGTGATGAATAGTAAAATCGACAA 58.963 34.615 0.00 0.00 0.00 3.18
63 64 6.566141 TCCGTGATGAATAGTAAAATCGACA 58.434 36.000 0.00 0.00 0.00 4.35
64 65 6.345882 GCTCCGTGATGAATAGTAAAATCGAC 60.346 42.308 0.00 0.00 0.00 4.20
65 66 5.690409 GCTCCGTGATGAATAGTAAAATCGA 59.310 40.000 0.00 0.00 0.00 3.59
66 67 5.462068 TGCTCCGTGATGAATAGTAAAATCG 59.538 40.000 0.00 0.00 0.00 3.34
67 68 6.844696 TGCTCCGTGATGAATAGTAAAATC 57.155 37.500 0.00 0.00 0.00 2.17
68 69 7.807977 AATGCTCCGTGATGAATAGTAAAAT 57.192 32.000 0.00 0.00 0.00 1.82
69 70 7.335673 TCAAATGCTCCGTGATGAATAGTAAAA 59.664 33.333 0.00 0.00 0.00 1.52
70 71 6.821160 TCAAATGCTCCGTGATGAATAGTAAA 59.179 34.615 0.00 0.00 0.00 2.01
71 72 6.345298 TCAAATGCTCCGTGATGAATAGTAA 58.655 36.000 0.00 0.00 0.00 2.24
72 73 5.912892 TCAAATGCTCCGTGATGAATAGTA 58.087 37.500 0.00 0.00 0.00 1.82
73 74 4.769688 TCAAATGCTCCGTGATGAATAGT 58.230 39.130 0.00 0.00 0.00 2.12
74 75 4.319333 GCTCAAATGCTCCGTGATGAATAG 60.319 45.833 0.00 0.00 0.00 1.73
75 76 3.561310 GCTCAAATGCTCCGTGATGAATA 59.439 43.478 0.00 0.00 0.00 1.75
76 77 2.357009 GCTCAAATGCTCCGTGATGAAT 59.643 45.455 0.00 0.00 0.00 2.57
77 78 1.739466 GCTCAAATGCTCCGTGATGAA 59.261 47.619 0.00 0.00 0.00 2.57
78 79 1.065926 AGCTCAAATGCTCCGTGATGA 60.066 47.619 0.00 0.00 39.34 2.92
79 80 1.376543 AGCTCAAATGCTCCGTGATG 58.623 50.000 0.00 0.00 39.34 3.07
80 81 3.869623 AGCTCAAATGCTCCGTGAT 57.130 47.368 0.00 0.00 39.34 3.06
88 89 4.445452 TTTTGATCCTGAGCTCAAATGC 57.555 40.909 18.85 8.47 40.13 3.56
89 90 6.544931 TCCTATTTTGATCCTGAGCTCAAATG 59.455 38.462 18.85 9.42 40.13 2.32
90 91 6.545298 GTCCTATTTTGATCCTGAGCTCAAAT 59.455 38.462 18.85 14.02 40.13 2.32
91 92 5.882557 GTCCTATTTTGATCCTGAGCTCAAA 59.117 40.000 18.85 9.43 39.06 2.69
92 93 5.190528 AGTCCTATTTTGATCCTGAGCTCAA 59.809 40.000 18.85 3.88 0.00 3.02
93 94 4.718774 AGTCCTATTTTGATCCTGAGCTCA 59.281 41.667 17.19 17.19 0.00 4.26
94 95 5.289083 AGTCCTATTTTGATCCTGAGCTC 57.711 43.478 6.82 6.82 0.00 4.09
95 96 5.707066 AAGTCCTATTTTGATCCTGAGCT 57.293 39.130 0.00 0.00 0.00 4.09
96 97 6.765915 AAAAGTCCTATTTTGATCCTGAGC 57.234 37.500 0.00 0.00 31.30 4.26
111 112 7.862873 GAAATTCGATTTTGACTCAAAAGTCCT 59.137 33.333 19.22 5.65 44.72 3.85
112 113 7.862873 AGAAATTCGATTTTGACTCAAAAGTCC 59.137 33.333 19.22 11.42 44.72 3.85
113 114 8.788409 AGAAATTCGATTTTGACTCAAAAGTC 57.212 30.769 19.22 15.21 44.72 3.01
114 115 9.586435 AAAGAAATTCGATTTTGACTCAAAAGT 57.414 25.926 19.22 9.81 44.72 2.66
116 117 9.030301 GGAAAGAAATTCGATTTTGACTCAAAA 57.970 29.630 17.31 17.31 41.58 2.44
117 118 8.194104 TGGAAAGAAATTCGATTTTGACTCAAA 58.806 29.630 9.85 0.00 39.05 2.69
118 119 7.647715 GTGGAAAGAAATTCGATTTTGACTCAA 59.352 33.333 9.85 0.00 39.05 3.02
119 120 7.013274 AGTGGAAAGAAATTCGATTTTGACTCA 59.987 33.333 9.85 0.80 39.05 3.41
120 121 7.363431 AGTGGAAAGAAATTCGATTTTGACTC 58.637 34.615 9.85 3.84 39.05 3.36
121 122 7.229506 AGAGTGGAAAGAAATTCGATTTTGACT 59.770 33.333 9.85 2.45 39.05 3.41
122 123 7.363431 AGAGTGGAAAGAAATTCGATTTTGAC 58.637 34.615 9.85 0.00 39.05 3.18
123 124 7.228507 TGAGAGTGGAAAGAAATTCGATTTTGA 59.771 33.333 9.85 0.00 39.05 2.69
124 125 7.324616 GTGAGAGTGGAAAGAAATTCGATTTTG 59.675 37.037 9.85 0.00 39.05 2.44
125 126 7.363431 GTGAGAGTGGAAAGAAATTCGATTTT 58.637 34.615 5.03 5.03 39.05 1.82
126 127 6.347725 CGTGAGAGTGGAAAGAAATTCGATTT 60.348 38.462 0.00 0.00 39.05 2.17
127 128 5.120830 CGTGAGAGTGGAAAGAAATTCGATT 59.879 40.000 0.00 0.00 39.05 3.34
128 129 4.627467 CGTGAGAGTGGAAAGAAATTCGAT 59.373 41.667 0.00 0.00 39.05 3.59
129 130 3.987868 CGTGAGAGTGGAAAGAAATTCGA 59.012 43.478 0.00 0.00 39.05 3.71
130 131 3.423645 GCGTGAGAGTGGAAAGAAATTCG 60.424 47.826 0.00 0.00 39.05 3.34
131 132 3.498397 TGCGTGAGAGTGGAAAGAAATTC 59.502 43.478 0.00 0.00 37.31 2.17
132 133 3.476552 TGCGTGAGAGTGGAAAGAAATT 58.523 40.909 0.00 0.00 0.00 1.82
133 134 3.126001 TGCGTGAGAGTGGAAAGAAAT 57.874 42.857 0.00 0.00 0.00 2.17
134 135 2.613026 TGCGTGAGAGTGGAAAGAAA 57.387 45.000 0.00 0.00 0.00 2.52
135 136 2.613026 TTGCGTGAGAGTGGAAAGAA 57.387 45.000 0.00 0.00 0.00 2.52
136 137 2.483876 CTTTGCGTGAGAGTGGAAAGA 58.516 47.619 0.64 0.00 43.61 2.52
137 138 1.069636 GCTTTGCGTGAGAGTGGAAAG 60.070 52.381 2.40 2.40 43.71 2.62
138 139 0.944386 GCTTTGCGTGAGAGTGGAAA 59.056 50.000 0.00 0.00 0.00 3.13
139 140 0.884704 GGCTTTGCGTGAGAGTGGAA 60.885 55.000 0.00 0.00 0.00 3.53
140 141 1.301716 GGCTTTGCGTGAGAGTGGA 60.302 57.895 0.00 0.00 0.00 4.02
141 142 0.886490 AAGGCTTTGCGTGAGAGTGG 60.886 55.000 0.00 0.00 0.00 4.00
142 143 0.514691 GAAGGCTTTGCGTGAGAGTG 59.485 55.000 0.00 0.00 0.00 3.51
143 144 0.603975 GGAAGGCTTTGCGTGAGAGT 60.604 55.000 0.00 0.00 0.00 3.24
144 145 0.321122 AGGAAGGCTTTGCGTGAGAG 60.321 55.000 0.00 0.00 0.00 3.20
145 146 0.320771 GAGGAAGGCTTTGCGTGAGA 60.321 55.000 0.00 0.00 0.00 3.27
146 147 1.301677 GGAGGAAGGCTTTGCGTGAG 61.302 60.000 0.00 0.00 0.00 3.51
147 148 1.302511 GGAGGAAGGCTTTGCGTGA 60.303 57.895 0.00 0.00 0.00 4.35
148 149 1.301677 GAGGAGGAAGGCTTTGCGTG 61.302 60.000 0.00 0.00 0.00 5.34
149 150 1.003233 GAGGAGGAAGGCTTTGCGT 60.003 57.895 0.00 0.00 0.00 5.24
150 151 0.742635 GAGAGGAGGAAGGCTTTGCG 60.743 60.000 0.00 0.00 0.00 4.85
151 152 0.742635 CGAGAGGAGGAAGGCTTTGC 60.743 60.000 0.00 0.00 0.00 3.68
152 153 0.898320 TCGAGAGGAGGAAGGCTTTG 59.102 55.000 0.00 0.00 0.00 2.77
153 154 1.760029 GATCGAGAGGAGGAAGGCTTT 59.240 52.381 0.00 0.00 0.00 3.51
154 155 1.063266 AGATCGAGAGGAGGAAGGCTT 60.063 52.381 0.00 0.00 0.00 4.35
155 156 0.555769 AGATCGAGAGGAGGAAGGCT 59.444 55.000 0.00 0.00 0.00 4.58
156 157 1.339929 GAAGATCGAGAGGAGGAAGGC 59.660 57.143 0.00 0.00 0.00 4.35
157 158 1.606668 CGAAGATCGAGAGGAGGAAGG 59.393 57.143 0.00 0.00 43.74 3.46
158 159 2.289547 GACGAAGATCGAGAGGAGGAAG 59.710 54.545 6.78 0.00 43.74 3.46
159 160 2.290464 GACGAAGATCGAGAGGAGGAA 58.710 52.381 6.78 0.00 43.74 3.36
160 161 1.209747 TGACGAAGATCGAGAGGAGGA 59.790 52.381 6.78 0.00 43.74 3.71
161 162 1.601903 CTGACGAAGATCGAGAGGAGG 59.398 57.143 6.78 0.00 43.74 4.30
162 163 1.002900 GCTGACGAAGATCGAGAGGAG 60.003 57.143 6.78 0.00 43.74 3.69
163 164 1.018148 GCTGACGAAGATCGAGAGGA 58.982 55.000 6.78 0.00 43.74 3.71
164 165 0.735471 TGCTGACGAAGATCGAGAGG 59.265 55.000 6.78 0.00 43.74 3.69
165 166 2.551355 TTGCTGACGAAGATCGAGAG 57.449 50.000 6.78 3.07 43.74 3.20
166 167 2.596452 GTTTGCTGACGAAGATCGAGA 58.404 47.619 6.78 0.00 43.74 4.04
167 168 1.656095 GGTTTGCTGACGAAGATCGAG 59.344 52.381 6.78 0.00 43.74 4.04
168 169 1.000394 TGGTTTGCTGACGAAGATCGA 60.000 47.619 6.78 0.00 43.74 3.59
169 170 1.428448 TGGTTTGCTGACGAAGATCG 58.572 50.000 0.00 0.00 46.93 3.69
170 171 3.436704 TCATTGGTTTGCTGACGAAGATC 59.563 43.478 0.00 0.00 0.00 2.75
171 172 3.411446 TCATTGGTTTGCTGACGAAGAT 58.589 40.909 0.00 0.00 0.00 2.40
172 173 2.844946 TCATTGGTTTGCTGACGAAGA 58.155 42.857 0.00 0.00 0.00 2.87
173 174 3.624326 TTCATTGGTTTGCTGACGAAG 57.376 42.857 0.00 0.00 0.00 3.79
174 175 4.545610 GAATTCATTGGTTTGCTGACGAA 58.454 39.130 0.00 0.00 0.00 3.85
175 176 3.364864 CGAATTCATTGGTTTGCTGACGA 60.365 43.478 6.22 0.00 0.00 4.20
176 177 2.910482 CGAATTCATTGGTTTGCTGACG 59.090 45.455 6.22 0.00 0.00 4.35
177 178 2.663119 GCGAATTCATTGGTTTGCTGAC 59.337 45.455 6.22 0.00 33.04 3.51
178 179 2.352617 GGCGAATTCATTGGTTTGCTGA 60.353 45.455 6.22 0.00 35.52 4.26
179 180 1.994779 GGCGAATTCATTGGTTTGCTG 59.005 47.619 6.22 0.00 35.52 4.41
180 181 1.617850 TGGCGAATTCATTGGTTTGCT 59.382 42.857 6.22 0.00 35.52 3.91
181 182 1.726248 GTGGCGAATTCATTGGTTTGC 59.274 47.619 6.22 0.00 34.65 3.68
182 183 1.984990 CGTGGCGAATTCATTGGTTTG 59.015 47.619 6.22 0.00 0.00 2.93
183 184 1.067915 CCGTGGCGAATTCATTGGTTT 60.068 47.619 6.22 0.00 0.00 3.27
184 185 0.525761 CCGTGGCGAATTCATTGGTT 59.474 50.000 6.22 0.00 0.00 3.67
185 186 1.933115 GCCGTGGCGAATTCATTGGT 61.933 55.000 6.22 0.00 0.00 3.67
186 187 1.226660 GCCGTGGCGAATTCATTGG 60.227 57.895 6.22 0.89 0.00 3.16
187 188 4.382728 GCCGTGGCGAATTCATTG 57.617 55.556 6.22 0.00 0.00 2.82
221 222 7.599245 CGCCTCTATGAGTATTAAAACCCTAAG 59.401 40.741 0.00 0.00 0.00 2.18
262 270 8.256611 TGGAAAATTGACTCGAATAAGAAGAG 57.743 34.615 0.00 0.00 37.96 2.85
263 271 7.334421 CCTGGAAAATTGACTCGAATAAGAAGA 59.666 37.037 0.00 0.00 0.00 2.87
280 288 1.216990 AGGATCGGAGCCTGGAAAAT 58.783 50.000 15.14 0.00 33.59 1.82
312 320 5.013287 AGCTCCGTCTAATCCATCTCTACTA 59.987 44.000 0.00 0.00 0.00 1.82
316 324 3.153919 GAGCTCCGTCTAATCCATCTCT 58.846 50.000 0.87 0.00 0.00 3.10
321 329 0.747255 GCAGAGCTCCGTCTAATCCA 59.253 55.000 10.93 0.00 0.00 3.41
340 348 5.159925 CGAGGAGCTGACATGAATATACAG 58.840 45.833 0.00 0.00 0.00 2.74
384 392 4.876107 GTCACGTACCCATGATGAGAAAAT 59.124 41.667 0.00 0.00 0.00 1.82
398 406 4.346734 TCAAATCTAGTCGTCACGTACC 57.653 45.455 0.00 0.00 0.00 3.34
411 419 6.475504 TCTGAAGAAACTGGCATCAAATCTA 58.524 36.000 0.00 0.00 0.00 1.98
422 430 6.674694 ATTGAATCGATCTGAAGAAACTGG 57.325 37.500 0.00 0.00 0.00 4.00
450 458 0.861837 AGTCGTAGTCGTCGTCGTTT 59.138 50.000 1.33 0.00 38.33 3.60
470 478 1.024046 TGTGCACGTGTTTGAGCTGT 61.024 50.000 18.38 0.00 0.00 4.40
474 482 2.095853 AGTCTTTGTGCACGTGTTTGAG 59.904 45.455 18.38 9.25 0.00 3.02
475 483 2.080693 AGTCTTTGTGCACGTGTTTGA 58.919 42.857 18.38 4.74 0.00 2.69
476 484 2.542766 AGTCTTTGTGCACGTGTTTG 57.457 45.000 18.38 2.40 0.00 2.93
477 485 3.498082 GAAAGTCTTTGTGCACGTGTTT 58.502 40.909 18.38 6.06 0.00 2.83
478 486 2.159435 GGAAAGTCTTTGTGCACGTGTT 60.159 45.455 18.38 0.00 0.00 3.32
479 487 1.400494 GGAAAGTCTTTGTGCACGTGT 59.600 47.619 18.38 0.00 0.00 4.49
502 522 4.196193 CGCCCTAACCTTGTTGATGATAA 58.804 43.478 0.00 0.00 0.00 1.75
522 542 1.480219 CGCTCTCATACCGAAACCGC 61.480 60.000 0.00 0.00 0.00 5.68
526 546 0.099968 CCGTCGCTCTCATACCGAAA 59.900 55.000 0.00 0.00 32.31 3.46
528 548 2.831366 GCCGTCGCTCTCATACCGA 61.831 63.158 0.00 0.00 0.00 4.69
529 549 2.353607 GCCGTCGCTCTCATACCG 60.354 66.667 0.00 0.00 0.00 4.02
573 593 3.205338 CACAGAATGACCATTATCGCCA 58.795 45.455 0.00 0.00 39.69 5.69
579 600 3.431673 TGCACCACAGAATGACCATTA 57.568 42.857 0.00 0.00 39.69 1.90
616 637 9.497030 GTACAACGCATTTCAAACATGATAATA 57.503 29.630 0.00 0.00 0.00 0.98
617 638 8.243426 AGTACAACGCATTTCAAACATGATAAT 58.757 29.630 0.00 0.00 0.00 1.28
629 1675 5.530519 TCATCAGAAGTACAACGCATTTC 57.469 39.130 0.00 0.00 0.00 2.17
633 1679 3.064207 GGTTCATCAGAAGTACAACGCA 58.936 45.455 0.00 0.00 33.63 5.24
636 1682 9.871238 TCTATAAAGGTTCATCAGAAGTACAAC 57.129 33.333 0.00 0.00 33.63 3.32
642 1688 9.695526 CTGAGATCTATAAAGGTTCATCAGAAG 57.304 37.037 0.00 0.00 33.89 2.85
695 1846 0.514691 CTTTGCTCGCCTGTCTGTTC 59.485 55.000 0.00 0.00 0.00 3.18
703 1855 1.963515 ACCAATTTTCTTTGCTCGCCT 59.036 42.857 0.00 0.00 0.00 5.52
706 1858 5.371115 TTCCTACCAATTTTCTTTGCTCG 57.629 39.130 0.00 0.00 0.00 5.03
751 1917 7.051623 AGGTTGTTGTGAAATGTCAACTAGTA 58.948 34.615 0.00 0.00 42.71 1.82
752 1918 5.885912 AGGTTGTTGTGAAATGTCAACTAGT 59.114 36.000 8.96 0.00 42.71 2.57
753 1919 6.260936 AGAGGTTGTTGTGAAATGTCAACTAG 59.739 38.462 8.96 0.00 42.71 2.57
763 1929 6.483307 CAGATTAGTGAGAGGTTGTTGTGAAA 59.517 38.462 0.00 0.00 0.00 2.69
806 1972 1.944709 GGTAAACACGTGTTTGGCTCT 59.055 47.619 42.21 25.94 46.56 4.09
836 2002 0.663568 GAGTTCCACTCCACGTCGTG 60.664 60.000 18.54 18.54 39.28 4.35
863 2029 0.317020 GCTCGTGGACTTTTGTGTGC 60.317 55.000 0.00 0.00 0.00 4.57
866 2032 2.159448 TGTTTGCTCGTGGACTTTTGTG 60.159 45.455 0.00 0.00 0.00 3.33
903 2070 1.065418 CGGTAGGTGGGCAGAAAGAAT 60.065 52.381 0.00 0.00 0.00 2.40
915 2083 2.267961 GGAAGGTGGCGGTAGGTG 59.732 66.667 0.00 0.00 0.00 4.00
937 2105 0.459585 TTGGTATCTGTTCGCGAGGC 60.460 55.000 9.59 7.39 0.00 4.70
942 2110 3.131396 CTGGGTATTGGTATCTGTTCGC 58.869 50.000 0.00 0.00 0.00 4.70
1034 2211 3.160585 CTGTGGGCTTGGTGAGGA 58.839 61.111 0.00 0.00 0.00 3.71
1088 2265 9.967346 ACAAGTACTACTGCATACATAATACAG 57.033 33.333 0.00 0.00 35.39 2.74
1161 2339 1.804748 CCCCAAAGAAAGTACAGTCGC 59.195 52.381 0.00 0.00 0.00 5.19
1191 2371 1.881925 CGGAGTTCTTGCATCACCCAA 60.882 52.381 0.00 0.00 0.00 4.12
1246 2426 2.417933 CTCCACTTTTCGCATCCTCAAG 59.582 50.000 0.00 0.00 0.00 3.02
1271 2451 4.670221 CGAGCTACAGTTTCAAGGCAAATC 60.670 45.833 0.00 0.00 0.00 2.17
1391 2586 5.278957 CGAATGGGAAATGGGGATTTATCAC 60.279 44.000 0.00 0.00 0.00 3.06
1466 2661 7.769507 GCTAGCCACTTAAAACTAATACTCCTT 59.230 37.037 2.29 0.00 0.00 3.36
1468 2663 6.200475 CGCTAGCCACTTAAAACTAATACTCC 59.800 42.308 9.66 0.00 0.00 3.85
1469 2664 6.976925 TCGCTAGCCACTTAAAACTAATACTC 59.023 38.462 9.66 0.00 0.00 2.59
1470 2665 6.870769 TCGCTAGCCACTTAAAACTAATACT 58.129 36.000 9.66 0.00 0.00 2.12
1471 2666 7.529880 TTCGCTAGCCACTTAAAACTAATAC 57.470 36.000 9.66 0.00 0.00 1.89
1491 2686 5.856455 AGTTTGTTACAGTGCATATTTTCGC 59.144 36.000 0.00 0.00 0.00 4.70
1502 2697 6.645700 AAAACAATGCAGTTTGTTACAGTG 57.354 33.333 16.60 0.00 46.33 3.66
1505 2700 7.897575 AAGAAAAACAATGCAGTTTGTTACA 57.102 28.000 16.60 0.00 46.33 2.41
1506 2701 9.261318 GAAAAGAAAAACAATGCAGTTTGTTAC 57.739 29.630 16.60 11.84 46.33 2.50
1507 2702 8.993121 TGAAAAGAAAAACAATGCAGTTTGTTA 58.007 25.926 16.60 0.00 46.33 2.41
1509 2704 7.041508 TGTGAAAAGAAAAACAATGCAGTTTGT 60.042 29.630 4.97 2.47 40.60 2.83
1571 2766 2.286025 GCAGCTTTGCAAGTTTTTCTGG 59.714 45.455 0.00 0.00 34.41 3.86
1575 2770 2.292103 TCGCAGCTTTGCAAGTTTTT 57.708 40.000 0.00 0.00 34.41 1.94
1609 2804 5.893824 ACCAGAGACAGTCATACATATGTCA 59.106 40.000 12.68 0.00 43.55 3.58
1659 4031 7.766278 TGACTCCTGAAGAAAGCTATAATTCAC 59.234 37.037 0.00 0.00 0.00 3.18
1673 4045 3.795688 AGGCATTTTGACTCCTGAAGA 57.204 42.857 0.00 0.00 18.29 2.87
1674 4046 4.077822 AGAAGGCATTTTGACTCCTGAAG 58.922 43.478 0.00 0.00 31.94 3.02
1675 4047 4.104383 AGAAGGCATTTTGACTCCTGAA 57.896 40.909 0.00 0.00 31.94 3.02
1676 4048 3.795688 AGAAGGCATTTTGACTCCTGA 57.204 42.857 0.00 0.00 31.94 3.86
1804 4176 5.991606 CACTGACAGATTAGTCCACTTCAAA 59.008 40.000 10.08 0.00 37.73 2.69
1842 4214 7.754924 AGTTATTGTCAAATTGGCTCGTAATTG 59.245 33.333 0.00 0.00 0.00 2.32
1922 4295 3.384146 AGCTCACATCGATCTGAATGAGT 59.616 43.478 20.31 12.15 42.09 3.41
1937 4310 1.202348 CACACTGTATCCGAGCTCACA 59.798 52.381 15.40 9.43 0.00 3.58
2003 4376 2.925724 TCGAACTTGTCCATGGTTTGT 58.074 42.857 12.58 4.22 0.00 2.83
2071 4444 4.492570 GCATAACACTGTGCTGATACGAAC 60.493 45.833 7.90 0.00 36.77 3.95
2085 4458 4.524714 AGACAGTCACACTAGCATAACACT 59.475 41.667 2.66 0.00 0.00 3.55
2090 4463 3.129462 GCAGAGACAGTCACACTAGCATA 59.871 47.826 2.66 0.00 0.00 3.14
2139 4512 0.617413 AGGTGCATCAGGGTTCAGAG 59.383 55.000 0.00 0.00 0.00 3.35
2309 4682 5.192927 TCGGAACATCTGCAAAAATAGGAT 58.807 37.500 0.00 0.00 0.00 3.24
2391 4764 3.281158 CACATGATGCAGGTGTATGGAA 58.719 45.455 0.00 0.00 40.60 3.53
2531 4904 8.300286 TGGCAAAAATAACTGACGAATAATTCA 58.700 29.630 0.00 0.00 0.00 2.57
2595 4968 4.398988 GCAACAATGGTCATACTCATGGAA 59.601 41.667 0.00 0.00 32.61 3.53
2671 5044 4.072131 ACAGGTCAACGCAGATTTATTGT 58.928 39.130 0.00 0.00 0.00 2.71
2683 5056 0.179056 AGGACACCAACAGGTCAACG 60.179 55.000 0.00 0.00 35.74 4.10
2698 5071 3.815401 AGCAGTTGTCATACACAAAGGAC 59.185 43.478 0.00 0.00 46.90 3.85
2711 5084 3.625764 TGTCAGTACCAAAAGCAGTTGTC 59.374 43.478 0.00 0.00 0.00 3.18
2762 5135 9.651913 GGCTTAAAAATCATTCCAAATCTTGTA 57.348 29.630 0.00 0.00 0.00 2.41
2769 5142 4.284746 ACGGGGCTTAAAAATCATTCCAAA 59.715 37.500 0.00 0.00 0.00 3.28
2777 5150 5.593095 AGAGGAATAACGGGGCTTAAAAATC 59.407 40.000 0.00 0.00 0.00 2.17
2804 5177 9.520515 AATGTCCAGATTACAATACAGTTTCTT 57.479 29.630 0.00 0.00 0.00 2.52
3251 5624 7.230510 ACTTGTAGCACAATTTCACCTCAATAA 59.769 33.333 2.83 0.00 37.48 1.40
3293 5855 6.936279 TCAAAAACCATGTGTTAAAGGTGAA 58.064 32.000 0.00 0.00 35.67 3.18
3551 6122 2.037121 TCCTCGAGTGAATGAAGCAACA 59.963 45.455 12.31 0.00 0.00 3.33
3563 6134 2.985139 GAGGTTTACGTTTCCTCGAGTG 59.015 50.000 12.31 3.02 38.37 3.51
3579 6150 2.084546 GCGGCAAGTTGATTAGAGGTT 58.915 47.619 7.16 0.00 0.00 3.50
3613 6184 9.219603 CAGTGGTCAACATAGAAAGAAAGATTA 57.780 33.333 0.00 0.00 0.00 1.75
3777 6348 0.830444 ACCAGGAGCAACGGTGAGTA 60.830 55.000 3.55 0.00 0.00 2.59
3926 6497 5.402997 AGGGACACTAACAGTAAAGTAGC 57.597 43.478 0.00 0.00 0.00 3.58
3927 6498 7.384387 GTGAAAGGGACACTAACAGTAAAGTAG 59.616 40.741 0.00 0.00 35.66 2.57
3935 6506 3.325135 AGAGGTGAAAGGGACACTAACAG 59.675 47.826 0.00 0.00 38.20 3.16
3952 6523 8.478877 CAAGTCACTAATAACTGGATAAGAGGT 58.521 37.037 0.00 0.00 0.00 3.85
3964 6535 9.265901 AGATATCATGCACAAGTCACTAATAAC 57.734 33.333 5.32 0.00 0.00 1.89
4361 6943 0.250295 CCACCTCCTTGCAACTTCGA 60.250 55.000 0.00 0.00 0.00 3.71
4362 6944 0.250295 TCCACCTCCTTGCAACTTCG 60.250 55.000 0.00 0.00 0.00 3.79
4368 6966 7.732222 ATAAATTATTTTCCACCTCCTTGCA 57.268 32.000 0.00 0.00 0.00 4.08
4435 7033 3.978855 CACAACATGACACAATTCAGCAG 59.021 43.478 0.00 0.00 0.00 4.24
4590 7350 4.090761 TGTGCAAACCTCTGATTTCTCT 57.909 40.909 0.00 0.00 0.00 3.10
4623 7387 7.044181 GTCATCTCTGTTCAATCCTGTGATTA 58.956 38.462 0.00 0.00 39.20 1.75
4634 7938 5.658634 AGGTATAGCTGTCATCTCTGTTCAA 59.341 40.000 3.03 0.00 0.00 2.69
4640 7944 6.401537 AGGATAGGTATAGCTGTCATCTCT 57.598 41.667 24.40 12.90 0.00 3.10
4641 7945 8.050325 TCTTAGGATAGGTATAGCTGTCATCTC 58.950 40.741 24.40 11.21 0.00 2.75
4698 8002 6.924111 ACAGGAAAAATACTTAATGCTGGTG 58.076 36.000 0.00 0.00 34.25 4.17
4729 8033 2.470257 CGGTCGTTGGCTATTTCGATAC 59.530 50.000 0.00 0.00 34.93 2.24
4730 8034 2.544277 CCGGTCGTTGGCTATTTCGATA 60.544 50.000 0.00 0.00 34.93 2.92
4742 8050 2.813908 GTGCTAGGCCGGTCGTTG 60.814 66.667 1.90 0.00 0.00 4.10
4772 8081 4.461198 ACAGCCTTACCCTTGCATAATAC 58.539 43.478 0.00 0.00 0.00 1.89
4799 8159 4.427956 TGGGGTTTAGGGAATGGAATTT 57.572 40.909 0.00 0.00 36.07 1.82
4806 8166 3.881713 GCACAAGATGGGGTTTAGGGAAT 60.882 47.826 0.00 0.00 0.00 3.01
4807 8167 2.556559 GCACAAGATGGGGTTTAGGGAA 60.557 50.000 0.00 0.00 0.00 3.97
4808 8168 1.005450 GCACAAGATGGGGTTTAGGGA 59.995 52.381 0.00 0.00 0.00 4.20
4809 8169 1.474330 GCACAAGATGGGGTTTAGGG 58.526 55.000 0.00 0.00 0.00 3.53
4810 8170 1.094785 CGCACAAGATGGGGTTTAGG 58.905 55.000 0.00 0.00 37.60 2.69
4811 8171 1.737793 GACGCACAAGATGGGGTTTAG 59.262 52.381 0.00 0.00 45.48 1.85
4813 8173 0.893727 GGACGCACAAGATGGGGTTT 60.894 55.000 0.00 0.00 45.48 3.27
4814 8174 1.303317 GGACGCACAAGATGGGGTT 60.303 57.895 0.00 0.00 45.48 4.11
4856 8252 4.100035 ACTCCGATATCATTTCTCTGTGCA 59.900 41.667 3.12 0.00 0.00 4.57
4863 8259 5.299531 TCGTTCAGACTCCGATATCATTTCT 59.700 40.000 3.12 0.00 0.00 2.52
4864 8260 5.399892 GTCGTTCAGACTCCGATATCATTTC 59.600 44.000 3.12 0.00 46.13 2.17
4973 8628 9.343075 CCATGCAAACAAGGAGACACTTTATGT 62.343 40.741 0.00 0.00 39.78 2.29
4978 8633 2.624838 CCATGCAAACAAGGAGACACTT 59.375 45.455 0.00 0.00 36.75 3.16
4979 8634 2.158623 TCCATGCAAACAAGGAGACACT 60.159 45.455 0.00 0.00 38.73 3.55
4982 8637 4.320608 TTTTCCATGCAAACAAGGAGAC 57.679 40.909 0.00 0.00 44.12 3.36
4983 8638 4.021192 GGATTTTCCATGCAAACAAGGAGA 60.021 41.667 0.00 0.00 44.12 3.71
4984 8639 4.248058 GGATTTTCCATGCAAACAAGGAG 58.752 43.478 0.00 0.00 44.12 3.69


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

AutoCloner maintained by Alex Coulton.