Multiple sequence alignment - TraesCS5B01G099300

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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 TraesCS5B01G099300 chr5B 100.000 6567 0 0 1 6567 132291307 132284741 0.000000e+00 12128.0
1 TraesCS5B01G099300 chr5B 90.323 217 16 2 1 213 9280129 9279914 5.010000e-71 279.0
2 TraesCS5B01G099300 chr5B 90.233 215 17 1 3 213 437805593 437805807 1.800000e-70 278.0
3 TraesCS5B01G099300 chr5B 89.933 149 9 2 2211 2356 132289016 132288871 3.130000e-43 187.0
4 TraesCS5B01G099300 chr5B 89.933 149 9 2 2292 2437 132289097 132288952 3.130000e-43 187.0
5 TraesCS5B01G099300 chr5B 100.000 50 0 0 5168 5217 132286085 132286036 7.010000e-15 93.5
6 TraesCS5B01G099300 chr5B 100.000 50 0 0 5223 5272 132286140 132286091 7.010000e-15 93.5
7 TraesCS5B01G099300 chr5A 96.920 5000 127 13 225 5217 129604598 129599619 0.000000e+00 8355.0
8 TraesCS5B01G099300 chr5A 95.864 1354 50 3 5220 6567 129599671 129598318 0.000000e+00 2185.0
9 TraesCS5B01G099300 chr5A 91.216 148 7 2 2212 2356 129602540 129602396 5.190000e-46 196.0
10 TraesCS5B01G099300 chr5D 93.762 5050 203 61 223 5217 119489712 119484720 0.000000e+00 7478.0
11 TraesCS5B01G099300 chr5D 94.292 1384 40 19 5220 6567 119484772 119483392 0.000000e+00 2082.0
12 TraesCS5B01G099300 chr5D 90.647 139 10 1 2292 2430 119487740 119487605 1.450000e-41 182.0
13 TraesCS5B01G099300 chr5D 96.721 61 2 0 321 381 9406644 9406704 1.160000e-17 102.0
14 TraesCS5B01G099300 chr2B 91.705 217 14 1 1 213 71584296 71584512 1.380000e-76 298.0
15 TraesCS5B01G099300 chr2B 90.323 217 15 3 1 213 162616481 162616695 5.010000e-71 279.0
16 TraesCS5B01G099300 chr6B 91.244 217 14 2 1 213 695267786 695268001 2.320000e-74 291.0
17 TraesCS5B01G099300 chr6B 90.323 217 16 2 1 213 592446744 592446529 5.010000e-71 279.0
18 TraesCS5B01G099300 chr3B 90.783 217 14 3 1 213 637055714 637055928 1.080000e-72 285.0
19 TraesCS5B01G099300 chr1B 90.783 217 15 2 1 213 101517313 101517098 1.080000e-72 285.0
20 TraesCS5B01G099300 chr4B 89.862 217 18 1 1 213 10429798 10429582 6.490000e-70 276.0
21 TraesCS5B01G099300 chr2D 84.758 269 34 6 6020 6284 500811759 500812024 5.050000e-66 263.0
22 TraesCS5B01G099300 chr3A 82.528 269 35 5 6020 6278 25032143 25031877 6.630000e-55 226.0


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 TraesCS5B01G099300 chr5B 132284741 132291307 6566 True 12128.000000 12128 100.000000 1 6567 1 chr5B.!!$R2 6566
1 TraesCS5B01G099300 chr5A 129598318 129604598 6280 True 3578.666667 8355 94.666667 225 6567 3 chr5A.!!$R1 6342
2 TraesCS5B01G099300 chr5D 119483392 119489712 6320 True 3247.333333 7478 92.900333 223 6567 3 chr5D.!!$R1 6344

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
183 184 0.035176 TTTACCCCAAACGGACGGAG 59.965 55.0 0.00 0.0 0.00 4.63 F
199 200 0.041386 GGAGCCGGATAGGATAGGGT 59.959 60.0 5.05 0.0 39.82 4.34 F
960 972 0.179020 TGTCCTTGTGCAGGGTTCTG 60.179 55.0 0.00 0.0 44.12 3.02 F
2264 2276 0.107456 ACAGAAGCTGTCACTGGTGG 59.893 55.0 12.62 0.0 41.21 4.61 F
3816 3875 0.179000 ATTGACGATGTCCCTGAGGC 59.821 55.0 0.00 0.0 0.00 4.70 F
4487 4546 0.616111 GGGCTCAGGAGTTCCTCAGA 60.616 60.0 2.95 0.0 46.65 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1428 0.038744 AGGATGCACCAGGAACAAGG 59.961 55.000 0.00 0.00 42.04 3.61 R
1611 1623 0.391661 TTGTCAAGGAGATGCGCCTC 60.392 55.000 4.18 4.25 31.02 4.70 R
2460 2472 1.480137 ACTGATTCTTCTGGCTCCTCG 59.520 52.381 0.00 0.00 0.00 4.63 R
3868 3927 0.392193 CACGGATCTGCTCAGGCTTT 60.392 55.000 0.00 0.00 39.59 3.51 R
5564 5626 0.833287 GCTGGATGTGGAAGCTCCTA 59.167 55.000 0.00 0.00 37.46 2.94 R
5683 5745 1.342496 TGGGCATCATCTCTAGCTTCG 59.658 52.381 0.00 0.00 0.00 3.79 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
69 70 4.973055 CGCGTCCGTTTCACCCCA 62.973 66.667 0.00 0.00 0.00 4.96
70 71 2.592287 GCGTCCGTTTCACCCCAA 60.592 61.111 0.00 0.00 0.00 4.12
71 72 2.188161 GCGTCCGTTTCACCCCAAA 61.188 57.895 0.00 0.00 0.00 3.28
72 73 1.650363 CGTCCGTTTCACCCCAAAC 59.350 57.895 0.00 0.00 33.57 2.93
73 74 1.788067 CGTCCGTTTCACCCCAAACC 61.788 60.000 0.00 0.00 33.37 3.27
74 75 1.526455 TCCGTTTCACCCCAAACCG 60.526 57.895 0.00 0.00 33.37 4.44
75 76 1.526455 CCGTTTCACCCCAAACCGA 60.526 57.895 0.00 0.00 33.37 4.69
76 77 1.102222 CCGTTTCACCCCAAACCGAA 61.102 55.000 0.00 0.00 33.37 4.30
77 78 0.739561 CGTTTCACCCCAAACCGAAA 59.260 50.000 0.00 0.00 33.37 3.46
78 79 1.268845 CGTTTCACCCCAAACCGAAAG 60.269 52.381 0.00 0.00 33.37 2.62
79 80 1.752498 GTTTCACCCCAAACCGAAAGT 59.248 47.619 0.00 0.00 31.10 2.66
80 81 2.146920 TTCACCCCAAACCGAAAGTT 57.853 45.000 0.00 0.00 41.81 2.66
90 91 3.663202 CGAAAGTTTGGGTCGGGG 58.337 61.111 0.00 0.00 0.00 5.73
91 92 1.071814 CGAAAGTTTGGGTCGGGGA 59.928 57.895 0.00 0.00 0.00 4.81
92 93 0.322187 CGAAAGTTTGGGTCGGGGAT 60.322 55.000 0.00 0.00 0.00 3.85
93 94 1.173913 GAAAGTTTGGGTCGGGGATG 58.826 55.000 0.00 0.00 0.00 3.51
94 95 0.251608 AAAGTTTGGGTCGGGGATGG 60.252 55.000 0.00 0.00 0.00 3.51
95 96 2.044352 GTTTGGGTCGGGGATGGG 60.044 66.667 0.00 0.00 0.00 4.00
96 97 2.533232 TTTGGGTCGGGGATGGGT 60.533 61.111 0.00 0.00 0.00 4.51
97 98 1.229886 TTTGGGTCGGGGATGGGTA 60.230 57.895 0.00 0.00 0.00 3.69
98 99 0.845543 TTTGGGTCGGGGATGGGTAA 60.846 55.000 0.00 0.00 0.00 2.85
99 100 0.845543 TTGGGTCGGGGATGGGTAAA 60.846 55.000 0.00 0.00 0.00 2.01
100 101 0.845543 TGGGTCGGGGATGGGTAAAA 60.846 55.000 0.00 0.00 0.00 1.52
101 102 0.332293 GGGTCGGGGATGGGTAAAAA 59.668 55.000 0.00 0.00 0.00 1.94
127 128 2.825086 GGAATCCGAACATTTGTCCG 57.175 50.000 0.00 0.00 0.00 4.79
128 129 2.081462 GGAATCCGAACATTTGTCCGT 58.919 47.619 0.00 0.00 0.00 4.69
129 130 2.486592 GGAATCCGAACATTTGTCCGTT 59.513 45.455 0.00 0.00 0.00 4.44
130 131 3.057806 GGAATCCGAACATTTGTCCGTTT 60.058 43.478 0.00 0.00 0.00 3.60
131 132 3.552604 ATCCGAACATTTGTCCGTTTG 57.447 42.857 0.00 0.00 0.00 2.93
132 133 2.562635 TCCGAACATTTGTCCGTTTGA 58.437 42.857 0.00 0.00 0.00 2.69
133 134 2.546368 TCCGAACATTTGTCCGTTTGAG 59.454 45.455 0.00 0.00 0.00 3.02
134 135 2.546368 CCGAACATTTGTCCGTTTGAGA 59.454 45.455 0.00 0.00 0.00 3.27
135 136 3.541711 CGAACATTTGTCCGTTTGAGAC 58.458 45.455 0.00 0.00 34.72 3.36
136 137 3.606153 CGAACATTTGTCCGTTTGAGACC 60.606 47.826 0.00 0.00 33.09 3.85
137 138 1.871039 ACATTTGTCCGTTTGAGACCG 59.129 47.619 0.00 0.00 33.09 4.79
138 139 1.871039 CATTTGTCCGTTTGAGACCGT 59.129 47.619 0.00 0.00 33.09 4.83
139 140 1.292061 TTTGTCCGTTTGAGACCGTG 58.708 50.000 0.00 0.00 33.09 4.94
140 141 1.155424 TTGTCCGTTTGAGACCGTGC 61.155 55.000 0.00 0.00 33.09 5.34
141 142 2.355363 TCCGTTTGAGACCGTGCG 60.355 61.111 0.00 0.00 0.00 5.34
142 143 4.072088 CCGTTTGAGACCGTGCGC 62.072 66.667 0.00 0.00 0.00 6.09
143 144 3.036084 CGTTTGAGACCGTGCGCT 61.036 61.111 9.73 0.00 0.00 5.92
144 145 2.551270 GTTTGAGACCGTGCGCTG 59.449 61.111 9.73 0.08 0.00 5.18
145 146 2.664851 TTTGAGACCGTGCGCTGG 60.665 61.111 16.28 16.28 0.00 4.85
146 147 3.158537 TTTGAGACCGTGCGCTGGA 62.159 57.895 23.25 0.73 0.00 3.86
147 148 3.858868 TTGAGACCGTGCGCTGGAC 62.859 63.158 23.25 17.53 0.00 4.02
157 158 2.358737 CGCTGGACCGCCTCTTTT 60.359 61.111 3.27 0.00 34.31 2.27
158 159 1.079405 CGCTGGACCGCCTCTTTTA 60.079 57.895 3.27 0.00 34.31 1.52
159 160 0.462047 CGCTGGACCGCCTCTTTTAT 60.462 55.000 3.27 0.00 34.31 1.40
160 161 1.751437 GCTGGACCGCCTCTTTTATT 58.249 50.000 0.00 0.00 34.31 1.40
161 162 2.092323 GCTGGACCGCCTCTTTTATTT 58.908 47.619 0.00 0.00 34.31 1.40
162 163 2.492088 GCTGGACCGCCTCTTTTATTTT 59.508 45.455 0.00 0.00 34.31 1.82
163 164 3.056821 GCTGGACCGCCTCTTTTATTTTT 60.057 43.478 0.00 0.00 34.31 1.94
181 182 1.316651 TTTTTACCCCAAACGGACGG 58.683 50.000 0.00 0.00 0.00 4.79
182 183 0.471617 TTTTACCCCAAACGGACGGA 59.528 50.000 0.00 0.00 0.00 4.69
183 184 0.035176 TTTACCCCAAACGGACGGAG 59.965 55.000 0.00 0.00 0.00 4.63
184 185 2.453379 TTACCCCAAACGGACGGAGC 62.453 60.000 0.00 0.00 0.00 4.70
193 194 2.203451 GGACGGAGCCGGATAGGA 60.203 66.667 5.05 0.00 45.00 2.94
194 195 1.606889 GGACGGAGCCGGATAGGAT 60.607 63.158 5.05 0.00 44.48 3.24
195 196 0.323178 GGACGGAGCCGGATAGGATA 60.323 60.000 5.05 0.00 39.82 2.59
196 197 1.096416 GACGGAGCCGGATAGGATAG 58.904 60.000 5.05 0.00 39.82 2.08
197 198 0.323542 ACGGAGCCGGATAGGATAGG 60.324 60.000 5.05 0.00 39.82 2.57
198 199 1.038130 CGGAGCCGGATAGGATAGGG 61.038 65.000 5.05 0.00 39.82 3.53
199 200 0.041386 GGAGCCGGATAGGATAGGGT 59.959 60.000 5.05 0.00 39.82 4.34
200 201 1.476477 GAGCCGGATAGGATAGGGTC 58.524 60.000 5.05 0.00 39.82 4.46
201 202 0.323542 AGCCGGATAGGATAGGGTCG 60.324 60.000 5.05 0.00 45.00 4.79
202 203 1.946475 GCCGGATAGGATAGGGTCGC 61.946 65.000 5.05 0.00 45.00 5.19
203 204 1.654954 CCGGATAGGATAGGGTCGCG 61.655 65.000 0.00 0.00 45.00 5.87
204 205 1.511768 GGATAGGATAGGGTCGCGC 59.488 63.158 0.00 0.00 0.00 6.86
205 206 1.136984 GATAGGATAGGGTCGCGCG 59.863 63.158 26.76 26.76 0.00 6.86
206 207 2.267681 GATAGGATAGGGTCGCGCGG 62.268 65.000 31.69 11.75 0.00 6.46
207 208 3.779850 TAGGATAGGGTCGCGCGGT 62.780 63.158 31.69 14.72 0.00 5.68
208 209 4.944372 GGATAGGGTCGCGCGGTG 62.944 72.222 31.69 1.17 0.00 4.94
209 210 4.944372 GATAGGGTCGCGCGGTGG 62.944 72.222 31.69 0.71 0.00 4.61
218 219 4.681978 GCGCGGTGGAGTGGAGTT 62.682 66.667 8.83 0.00 0.00 3.01
219 220 2.738521 CGCGGTGGAGTGGAGTTG 60.739 66.667 0.00 0.00 0.00 3.16
220 221 2.358737 GCGGTGGAGTGGAGTTGG 60.359 66.667 0.00 0.00 0.00 3.77
221 222 2.347490 CGGTGGAGTGGAGTTGGG 59.653 66.667 0.00 0.00 0.00 4.12
249 250 0.821711 CGGAACTCAAAGGCAACCCA 60.822 55.000 0.00 0.00 37.17 4.51
358 359 2.364002 GTCTATCACCTCTGCTCCTTCC 59.636 54.545 0.00 0.00 0.00 3.46
425 426 1.938596 TCCTCCTCAGCCTCCCTCT 60.939 63.158 0.00 0.00 0.00 3.69
478 479 4.503314 CGCCCCGACGAGGTAACC 62.503 72.222 0.00 0.00 38.74 2.85
489 490 1.461849 AGGTAACCCCGTGTTCCCA 60.462 57.895 0.66 0.00 35.47 4.37
522 531 3.407657 CGTAGCTAGCTCGTCGGT 58.592 61.111 23.26 0.00 0.00 4.69
538 547 2.461110 GGTGACACTAATGCGGCCG 61.461 63.158 24.05 24.05 0.00 6.13
668 677 2.549282 CGACGGCCGTCTTGTTTG 59.451 61.111 44.83 29.74 42.54 2.93
699 708 2.598787 CCCGCTTTCCCACCCTGTA 61.599 63.158 0.00 0.00 0.00 2.74
720 732 6.934056 TGTAAAAGCGATAAGTTGTAGGGTA 58.066 36.000 0.00 0.00 0.00 3.69
766 778 4.728409 TGCTGGACAGGAAGCATG 57.272 55.556 1.01 0.00 44.26 4.06
769 781 1.251251 GCTGGACAGGAAGCATGTTT 58.749 50.000 0.00 0.00 39.31 2.83
771 783 2.819608 GCTGGACAGGAAGCATGTTTAA 59.180 45.455 0.00 0.00 39.31 1.52
778 790 5.783111 ACAGGAAGCATGTTTAAAATCCAC 58.217 37.500 0.00 0.00 0.00 4.02
813 825 1.375780 CCCAAATTTTGCTGGGCCG 60.376 57.895 0.00 0.00 45.80 6.13
851 863 2.708514 CACGTTTGCACTTCTCAACTG 58.291 47.619 0.00 0.00 0.00 3.16
852 864 2.351418 CACGTTTGCACTTCTCAACTGA 59.649 45.455 0.00 0.00 0.00 3.41
886 898 5.405797 TCGCAGCATCTCTATCATGTATTC 58.594 41.667 0.00 0.00 0.00 1.75
892 904 7.760794 CAGCATCTCTATCATGTATTCCTCTTC 59.239 40.741 0.00 0.00 0.00 2.87
960 972 0.179020 TGTCCTTGTGCAGGGTTCTG 60.179 55.000 0.00 0.00 44.12 3.02
966 978 1.067295 TGTGCAGGGTTCTGAAGGAT 58.933 50.000 0.00 0.00 43.49 3.24
995 1007 6.383726 AGATTCTGATATAGCTCCCCTGAATC 59.616 42.308 18.86 18.86 39.91 2.52
1014 1026 4.760047 AGCATGACGCCGGTGGTC 62.760 66.667 21.14 19.08 44.04 4.02
1208 1220 1.673665 GCTGGTCCTCTGCCAACAG 60.674 63.158 0.00 0.00 45.95 3.16
1293 1305 1.014564 CGGCAGGAGAAACTTCCGAC 61.015 60.000 0.00 0.00 42.29 4.79
1320 1332 1.639298 CTGCCGCTGCTGAAACTACC 61.639 60.000 0.70 0.00 38.61 3.18
1323 1335 2.740714 CGCTGCTGAAACTACCGGC 61.741 63.158 0.00 0.00 36.49 6.13
1340 1352 2.437359 CCAGGCTGTGGCTAGCAC 60.437 66.667 18.24 13.11 45.46 4.40
1416 1428 1.635663 CGCCGTTGAAGGATGGTGAC 61.636 60.000 0.00 0.00 38.25 3.67
1509 1521 1.200948 GCATTCACTGAAGGCCTTGTC 59.799 52.381 26.25 10.63 42.44 3.18
1539 1551 2.867975 CCGAGTAAGTGACGGTTTTGTT 59.132 45.455 0.00 0.00 41.47 2.83
1725 1737 1.406614 CCTAGAAGCTCACCAAGGCAG 60.407 57.143 0.00 0.00 0.00 4.85
2043 2055 1.690633 GCAGGGATGGTCCAGAGGA 60.691 63.158 0.00 0.00 38.64 3.71
2049 2061 1.566231 GGATGGTCCAGAGGAACCAAT 59.434 52.381 0.00 0.00 38.96 3.16
2118 2130 2.374170 GGACCAGAGGGAAAAGGTTACA 59.626 50.000 0.00 0.00 38.05 2.41
2178 2190 2.372172 AGTTTCGACTTCTGGGGTTGAT 59.628 45.455 0.00 0.00 0.00 2.57
2191 2203 2.552155 GGGGTTGATAGCACAGTTGACA 60.552 50.000 0.00 0.00 0.00 3.58
2243 2255 7.174080 AGTTGAAAGCAAAGAGGATAGTTCTTC 59.826 37.037 0.00 0.00 35.42 2.87
2262 2274 1.486310 TCAACAGAAGCTGTCACTGGT 59.514 47.619 0.00 5.63 44.62 4.00
2263 2275 1.600957 CAACAGAAGCTGTCACTGGTG 59.399 52.381 11.88 11.88 44.62 4.17
2264 2276 0.107456 ACAGAAGCTGTCACTGGTGG 59.893 55.000 12.62 0.00 41.21 4.61
2349 2361 2.358003 GAAGCTGTCACTGGCGCT 60.358 61.111 7.64 0.00 0.00 5.92
2400 2412 3.749226 AGTTGAAAGCAAAGAGGAGGAG 58.251 45.455 0.00 0.00 35.42 3.69
2404 2416 1.655372 AAGCAAAGAGGAGGAGAGCT 58.345 50.000 0.00 0.00 0.00 4.09
2430 2442 2.358003 GAAGCTGTCACTGGCGCT 60.358 61.111 7.64 0.00 0.00 5.92
2433 2445 3.418068 GCTGTCACTGGCGCTGTC 61.418 66.667 7.64 0.00 0.00 3.51
2460 2472 4.429854 AATCACTCCTCTTGATAAGGCC 57.570 45.455 0.00 0.00 32.29 5.19
2921 2963 6.784473 TGTACAATCCAGATATCACCTCATCT 59.216 38.462 5.32 0.00 31.58 2.90
3816 3875 0.179000 ATTGACGATGTCCCTGAGGC 59.821 55.000 0.00 0.00 0.00 4.70
4232 4291 6.909357 GCTCATATGTGCTGTTTATGTTTCTC 59.091 38.462 19.89 0.00 0.00 2.87
4275 4334 6.544197 TGCACCAGAATGTTTTTACTGTCTTA 59.456 34.615 0.00 0.00 0.00 2.10
4327 4386 4.351874 TTCCCCTAAAGTCAACACTCAG 57.648 45.455 0.00 0.00 29.93 3.35
4415 4474 1.741401 CCGAGATGAAACTGGCGCA 60.741 57.895 10.83 0.00 0.00 6.09
4487 4546 0.616111 GGGCTCAGGAGTTCCTCAGA 60.616 60.000 2.95 0.00 46.65 3.27
4529 4588 1.467734 GACAAGAAGTCGTCTCGCCTA 59.532 52.381 0.00 0.00 37.53 3.93
5093 5152 8.532977 AATTTTGTATCACTTGTTACCATTGC 57.467 30.769 0.00 0.00 0.00 3.56
5213 5274 7.881142 TGGTATCTTGTTCCATGTTTTACTTG 58.119 34.615 0.00 0.00 0.00 3.16
5214 5275 7.721842 TGGTATCTTGTTCCATGTTTTACTTGA 59.278 33.333 0.00 0.00 0.00 3.02
5215 5276 8.237267 GGTATCTTGTTCCATGTTTTACTTGAG 58.763 37.037 0.00 0.00 0.00 3.02
5216 5277 8.999431 GTATCTTGTTCCATGTTTTACTTGAGA 58.001 33.333 0.00 0.00 0.00 3.27
5217 5278 8.641498 ATCTTGTTCCATGTTTTACTTGAGAT 57.359 30.769 0.00 0.00 0.00 2.75
5218 5279 8.099364 TCTTGTTCCATGTTTTACTTGAGATC 57.901 34.615 0.00 0.00 0.00 2.75
5219 5280 7.939039 TCTTGTTCCATGTTTTACTTGAGATCT 59.061 33.333 0.00 0.00 0.00 2.75
5220 5281 7.439157 TGTTCCATGTTTTACTTGAGATCTG 57.561 36.000 0.00 0.00 0.00 2.90
5221 5282 7.223584 TGTTCCATGTTTTACTTGAGATCTGA 58.776 34.615 0.00 0.00 0.00 3.27
5222 5283 7.719193 TGTTCCATGTTTTACTTGAGATCTGAA 59.281 33.333 0.00 0.00 0.00 3.02
5223 5284 8.567948 GTTCCATGTTTTACTTGAGATCTGAAA 58.432 33.333 0.00 0.00 0.00 2.69
5224 5285 8.327941 TCCATGTTTTACTTGAGATCTGAAAG 57.672 34.615 0.00 6.58 0.00 2.62
5225 5286 7.391554 TCCATGTTTTACTTGAGATCTGAAAGG 59.608 37.037 15.74 0.79 0.00 3.11
5226 5287 7.391554 CCATGTTTTACTTGAGATCTGAAAGGA 59.608 37.037 15.74 7.42 0.00 3.36
5227 5288 8.954350 CATGTTTTACTTGAGATCTGAAAGGAT 58.046 33.333 15.74 2.85 0.00 3.24
5228 5289 8.924511 TGTTTTACTTGAGATCTGAAAGGATT 57.075 30.769 15.74 2.31 0.00 3.01
5231 5292 8.703604 TTTACTTGAGATCTGAAAGGATTACG 57.296 34.615 15.74 0.00 0.00 3.18
5232 5293 5.665459 ACTTGAGATCTGAAAGGATTACGG 58.335 41.667 15.74 0.00 0.00 4.02
5233 5294 4.060038 TGAGATCTGAAAGGATTACGGC 57.940 45.455 0.00 0.00 0.00 5.68
5234 5295 3.450817 TGAGATCTGAAAGGATTACGGCA 59.549 43.478 0.00 0.00 0.00 5.69
5235 5296 4.081142 TGAGATCTGAAAGGATTACGGCAA 60.081 41.667 0.00 0.00 0.00 4.52
5236 5297 4.843728 AGATCTGAAAGGATTACGGCAAA 58.156 39.130 0.00 0.00 0.00 3.68
5237 5298 5.440610 AGATCTGAAAGGATTACGGCAAAT 58.559 37.500 0.00 0.00 0.00 2.32
5238 5299 5.888161 AGATCTGAAAGGATTACGGCAAATT 59.112 36.000 0.00 0.00 0.00 1.82
5239 5300 7.054124 AGATCTGAAAGGATTACGGCAAATTA 58.946 34.615 0.00 0.00 0.00 1.40
5240 5301 7.556275 AGATCTGAAAGGATTACGGCAAATTAA 59.444 33.333 0.00 0.00 0.00 1.40
5241 5302 7.455641 TCTGAAAGGATTACGGCAAATTAAA 57.544 32.000 0.00 0.00 0.00 1.52
5242 5303 8.062065 TCTGAAAGGATTACGGCAAATTAAAT 57.938 30.769 0.00 0.00 0.00 1.40
5243 5304 8.527810 TCTGAAAGGATTACGGCAAATTAAATT 58.472 29.630 0.00 0.00 0.00 1.82
5244 5305 8.472683 TGAAAGGATTACGGCAAATTAAATTG 57.527 30.769 0.00 0.00 0.00 2.32
5245 5306 7.547370 TGAAAGGATTACGGCAAATTAAATTGG 59.453 33.333 5.45 0.00 0.00 3.16
5246 5307 6.538945 AGGATTACGGCAAATTAAATTGGT 57.461 33.333 5.45 0.00 0.00 3.67
5247 5308 7.648039 AGGATTACGGCAAATTAAATTGGTA 57.352 32.000 5.45 0.00 0.00 3.25
5248 5309 8.245195 AGGATTACGGCAAATTAAATTGGTAT 57.755 30.769 5.45 0.00 0.00 2.73
5249 5310 8.357402 AGGATTACGGCAAATTAAATTGGTATC 58.643 33.333 5.45 1.72 0.00 2.24
5250 5311 8.357402 GGATTACGGCAAATTAAATTGGTATCT 58.643 33.333 5.45 0.00 0.00 1.98
5251 5312 9.744468 GATTACGGCAAATTAAATTGGTATCTT 57.256 29.630 5.45 0.00 0.00 2.40
5252 5313 8.918961 TTACGGCAAATTAAATTGGTATCTTG 57.081 30.769 5.45 0.00 0.00 3.02
5253 5314 6.930731 ACGGCAAATTAAATTGGTATCTTGT 58.069 32.000 5.45 0.00 0.00 3.16
5254 5315 7.382898 ACGGCAAATTAAATTGGTATCTTGTT 58.617 30.769 5.45 0.00 0.00 2.83
5255 5316 7.544217 ACGGCAAATTAAATTGGTATCTTGTTC 59.456 33.333 5.45 0.00 0.00 3.18
5256 5317 7.010091 CGGCAAATTAAATTGGTATCTTGTTCC 59.990 37.037 5.45 0.00 0.00 3.62
5257 5318 7.821846 GGCAAATTAAATTGGTATCTTGTTCCA 59.178 33.333 5.45 0.00 0.00 3.53
5258 5319 9.382275 GCAAATTAAATTGGTATCTTGTTCCAT 57.618 29.630 5.45 0.00 0.00 3.41
5265 5326 9.705290 AAATTGGTATCTTGTTCCATGTTTTAC 57.295 29.630 0.00 0.00 0.00 2.01
5266 5327 8.650143 ATTGGTATCTTGTTCCATGTTTTACT 57.350 30.769 0.00 0.00 0.00 2.24
5267 5328 8.472007 TTGGTATCTTGTTCCATGTTTTACTT 57.528 30.769 0.00 0.00 0.00 2.24
5268 5329 7.881142 TGGTATCTTGTTCCATGTTTTACTTG 58.119 34.615 0.00 0.00 0.00 3.16
5292 5353 4.279420 AGAGTTTTTGCTTTAGCCAGAAGG 59.721 41.667 0.00 0.00 41.18 3.46
5564 5626 8.721478 GTTTCACTACATGTTCATGTGAGTTAT 58.279 33.333 23.33 2.76 38.60 1.89
5683 5745 0.251341 ATTGCCCACCAAGAGACACC 60.251 55.000 0.00 0.00 36.76 4.16
5890 5952 4.127907 ACTTTGGGAAGAAGAACGAGAAC 58.872 43.478 0.00 0.00 36.69 3.01
5892 5954 3.107642 TGGGAAGAAGAACGAGAACAC 57.892 47.619 0.00 0.00 0.00 3.32
5910 5972 6.311735 AGAACACCCTTAGGCAAATAAAGAA 58.688 36.000 0.00 0.00 36.11 2.52
5937 5999 1.759459 AATGCTAGGTAGGGCTCGCC 61.759 60.000 0.00 0.00 0.00 5.54
6002 6064 1.668751 GTGTGCTTCTTTCGGTTGTGA 59.331 47.619 0.00 0.00 0.00 3.58
6089 6151 4.106197 GACAGAATAAGAGTACTGCCACG 58.894 47.826 0.00 0.00 34.25 4.94
6134 6196 9.916397 GAATTTAGTAACATTATCGAAGTGTGG 57.084 33.333 0.00 0.00 0.00 4.17
6219 6315 8.745837 GCAATTACATCTGTGCATATTTAACAC 58.254 33.333 0.00 0.00 36.97 3.32
6244 6340 9.821240 ACCCATATAATTGTATTGCCATTTCTA 57.179 29.630 0.00 0.00 0.00 2.10
6302 6398 2.580966 ACTATTCCCGTCTTTCGAGC 57.419 50.000 0.00 0.00 42.86 5.03
6377 6473 1.530013 AAACAGAGGCATGCCACAGC 61.530 55.000 37.18 22.48 38.92 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.973055 TGGGGTGAAACGGACGCG 62.973 66.667 3.53 3.53 38.12 6.01
53 54 2.188161 TTTGGGGTGAAACGGACGC 61.188 57.895 0.00 0.00 38.12 5.19
54 55 1.650363 GTTTGGGGTGAAACGGACG 59.350 57.895 0.00 0.00 38.12 4.79
55 56 1.788067 CGGTTTGGGGTGAAACGGAC 61.788 60.000 0.00 0.00 38.01 4.79
56 57 1.526455 CGGTTTGGGGTGAAACGGA 60.526 57.895 0.00 0.00 38.01 4.69
57 58 1.102222 TTCGGTTTGGGGTGAAACGG 61.102 55.000 0.00 0.00 38.12 4.44
58 59 0.739561 TTTCGGTTTGGGGTGAAACG 59.260 50.000 0.00 0.00 38.12 3.60
59 60 1.752498 ACTTTCGGTTTGGGGTGAAAC 59.248 47.619 0.00 0.00 35.45 2.78
60 61 2.146920 ACTTTCGGTTTGGGGTGAAA 57.853 45.000 0.00 0.00 0.00 2.69
61 62 2.146920 AACTTTCGGTTTGGGGTGAA 57.853 45.000 0.00 0.00 33.90 3.18
62 63 2.146920 AAACTTTCGGTTTGGGGTGA 57.853 45.000 0.00 0.00 45.29 4.02
70 71 2.710440 CCGACCCAAACTTTCGGTT 58.290 52.632 1.03 0.00 45.95 4.44
71 72 4.468007 CCGACCCAAACTTTCGGT 57.532 55.556 1.03 0.00 45.95 4.69
73 74 0.322187 ATCCCCGACCCAAACTTTCG 60.322 55.000 0.00 0.00 0.00 3.46
74 75 1.173913 CATCCCCGACCCAAACTTTC 58.826 55.000 0.00 0.00 0.00 2.62
75 76 0.251608 CCATCCCCGACCCAAACTTT 60.252 55.000 0.00 0.00 0.00 2.66
76 77 1.382629 CCATCCCCGACCCAAACTT 59.617 57.895 0.00 0.00 0.00 2.66
77 78 2.612493 CCCATCCCCGACCCAAACT 61.612 63.158 0.00 0.00 0.00 2.66
78 79 1.564483 TACCCATCCCCGACCCAAAC 61.564 60.000 0.00 0.00 0.00 2.93
79 80 0.845543 TTACCCATCCCCGACCCAAA 60.846 55.000 0.00 0.00 0.00 3.28
80 81 0.845543 TTTACCCATCCCCGACCCAA 60.846 55.000 0.00 0.00 0.00 4.12
81 82 0.845543 TTTTACCCATCCCCGACCCA 60.846 55.000 0.00 0.00 0.00 4.51
82 83 0.332293 TTTTTACCCATCCCCGACCC 59.668 55.000 0.00 0.00 0.00 4.46
83 84 3.983229 TTTTTACCCATCCCCGACC 57.017 52.632 0.00 0.00 0.00 4.79
108 109 2.825086 CGGACAAATGTTCGGATTCC 57.175 50.000 6.34 0.00 43.03 3.01
115 116 3.606153 CGGTCTCAAACGGACAAATGTTC 60.606 47.826 0.00 0.00 35.61 3.18
116 117 2.289547 CGGTCTCAAACGGACAAATGTT 59.710 45.455 0.00 0.00 35.61 2.71
117 118 1.871039 CGGTCTCAAACGGACAAATGT 59.129 47.619 0.00 0.00 35.61 2.71
118 119 1.871039 ACGGTCTCAAACGGACAAATG 59.129 47.619 0.00 0.00 35.61 2.32
119 120 1.871039 CACGGTCTCAAACGGACAAAT 59.129 47.619 0.00 0.00 35.61 2.32
120 121 1.292061 CACGGTCTCAAACGGACAAA 58.708 50.000 0.00 0.00 35.61 2.83
121 122 1.155424 GCACGGTCTCAAACGGACAA 61.155 55.000 0.00 0.00 35.61 3.18
122 123 1.593209 GCACGGTCTCAAACGGACA 60.593 57.895 0.00 0.00 35.61 4.02
123 124 2.654912 CGCACGGTCTCAAACGGAC 61.655 63.158 0.00 0.00 32.76 4.79
124 125 2.355363 CGCACGGTCTCAAACGGA 60.355 61.111 0.00 0.00 32.76 4.69
125 126 4.072088 GCGCACGGTCTCAAACGG 62.072 66.667 0.30 0.00 0.00 4.44
126 127 3.036084 AGCGCACGGTCTCAAACG 61.036 61.111 11.47 0.00 0.00 3.60
127 128 2.551270 CAGCGCACGGTCTCAAAC 59.449 61.111 11.47 0.00 0.00 2.93
128 129 2.664851 CCAGCGCACGGTCTCAAA 60.665 61.111 11.47 0.00 0.00 2.69
129 130 3.611674 TCCAGCGCACGGTCTCAA 61.612 61.111 11.47 0.00 0.00 3.02
130 131 4.357947 GTCCAGCGCACGGTCTCA 62.358 66.667 11.47 0.00 0.00 3.27
140 141 0.462047 ATAAAAGAGGCGGTCCAGCG 60.462 55.000 0.00 0.00 38.18 5.18
141 142 1.751437 AATAAAAGAGGCGGTCCAGC 58.249 50.000 0.00 0.00 33.74 4.85
142 143 4.783764 AAAAATAAAAGAGGCGGTCCAG 57.216 40.909 0.00 0.00 33.74 3.86
162 163 1.133976 TCCGTCCGTTTGGGGTAAAAA 60.134 47.619 0.00 0.00 36.01 1.94
163 164 0.471617 TCCGTCCGTTTGGGGTAAAA 59.528 50.000 0.00 0.00 36.01 1.52
164 165 0.035176 CTCCGTCCGTTTGGGGTAAA 59.965 55.000 0.00 0.00 36.01 2.01
165 166 1.672898 CTCCGTCCGTTTGGGGTAA 59.327 57.895 0.00 0.00 36.01 2.85
166 167 2.946346 GCTCCGTCCGTTTGGGGTA 61.946 63.158 0.00 0.00 36.01 3.69
167 168 4.324991 GCTCCGTCCGTTTGGGGT 62.325 66.667 0.00 0.00 36.01 4.95
176 177 0.323178 TATCCTATCCGGCTCCGTCC 60.323 60.000 7.59 0.00 37.81 4.79
177 178 1.096416 CTATCCTATCCGGCTCCGTC 58.904 60.000 7.59 0.00 37.81 4.79
178 179 0.323542 CCTATCCTATCCGGCTCCGT 60.324 60.000 7.59 0.00 37.81 4.69
179 180 1.038130 CCCTATCCTATCCGGCTCCG 61.038 65.000 0.00 0.48 39.44 4.63
180 181 0.041386 ACCCTATCCTATCCGGCTCC 59.959 60.000 0.00 0.00 0.00 4.70
181 182 1.476477 GACCCTATCCTATCCGGCTC 58.524 60.000 0.00 0.00 0.00 4.70
182 183 0.323542 CGACCCTATCCTATCCGGCT 60.324 60.000 0.00 0.00 0.00 5.52
183 184 1.946475 GCGACCCTATCCTATCCGGC 61.946 65.000 0.00 0.00 0.00 6.13
184 185 1.654954 CGCGACCCTATCCTATCCGG 61.655 65.000 0.00 0.00 0.00 5.14
185 186 1.801332 CGCGACCCTATCCTATCCG 59.199 63.158 0.00 0.00 0.00 4.18
186 187 1.511768 GCGCGACCCTATCCTATCC 59.488 63.158 12.10 0.00 0.00 2.59
187 188 1.136984 CGCGCGACCCTATCCTATC 59.863 63.158 28.94 0.00 0.00 2.08
188 189 2.341101 CCGCGCGACCCTATCCTAT 61.341 63.158 34.63 0.00 0.00 2.57
189 190 2.981909 CCGCGCGACCCTATCCTA 60.982 66.667 34.63 0.00 0.00 2.94
191 192 4.944372 CACCGCGCGACCCTATCC 62.944 72.222 34.63 0.00 0.00 2.59
192 193 4.944372 CCACCGCGCGACCCTATC 62.944 72.222 34.63 0.00 0.00 2.08
201 202 4.681978 AACTCCACTCCACCGCGC 62.682 66.667 0.00 0.00 0.00 6.86
202 203 2.738521 CAACTCCACTCCACCGCG 60.739 66.667 0.00 0.00 0.00 6.46
203 204 2.358737 CCAACTCCACTCCACCGC 60.359 66.667 0.00 0.00 0.00 5.68
204 205 2.347490 CCCAACTCCACTCCACCG 59.653 66.667 0.00 0.00 0.00 4.94
205 206 2.034221 GCCCAACTCCACTCCACC 59.966 66.667 0.00 0.00 0.00 4.61
206 207 1.302832 CAGCCCAACTCCACTCCAC 60.303 63.158 0.00 0.00 0.00 4.02
207 208 1.461268 TCAGCCCAACTCCACTCCA 60.461 57.895 0.00 0.00 0.00 3.86
208 209 1.003233 GTCAGCCCAACTCCACTCC 60.003 63.158 0.00 0.00 0.00 3.85
209 210 1.003233 GGTCAGCCCAACTCCACTC 60.003 63.158 0.00 0.00 0.00 3.51
210 211 2.883828 CGGTCAGCCCAACTCCACT 61.884 63.158 0.00 0.00 0.00 4.00
211 212 2.358737 CGGTCAGCCCAACTCCAC 60.359 66.667 0.00 0.00 0.00 4.02
212 213 2.525629 TCGGTCAGCCCAACTCCA 60.526 61.111 0.00 0.00 0.00 3.86
213 214 2.047179 GTCGGTCAGCCCAACTCC 60.047 66.667 0.00 0.00 0.00 3.85
214 215 2.432628 CGTCGGTCAGCCCAACTC 60.433 66.667 0.00 0.00 0.00 3.01
215 216 4.003788 CCGTCGGTCAGCCCAACT 62.004 66.667 2.08 0.00 0.00 3.16
216 217 3.524648 TTCCGTCGGTCAGCCCAAC 62.525 63.158 11.88 0.00 0.00 3.77
217 218 3.235481 TTCCGTCGGTCAGCCCAA 61.235 61.111 11.88 0.00 0.00 4.12
218 219 3.998672 GTTCCGTCGGTCAGCCCA 61.999 66.667 11.88 0.00 0.00 5.36
219 220 3.644399 GAGTTCCGTCGGTCAGCCC 62.644 68.421 11.88 0.00 0.00 5.19
220 221 2.126031 GAGTTCCGTCGGTCAGCC 60.126 66.667 11.88 0.00 0.00 4.85
221 222 0.599204 TTTGAGTTCCGTCGGTCAGC 60.599 55.000 11.88 0.75 0.00 4.26
273 274 4.007644 CTGTGCCGCTGGACCTGA 62.008 66.667 1.91 0.00 0.00 3.86
358 359 2.676342 CCTTATCTGGAAACGAAACGGG 59.324 50.000 0.00 0.00 0.00 5.28
425 426 2.750637 GGCCGTCGTGAGGAGAGA 60.751 66.667 0.00 0.00 0.00 3.10
522 531 2.125310 CCGGCCGCATTAGTGTCA 60.125 61.111 22.85 0.00 0.00 3.58
584 593 2.709213 GCAAAGGAGATGCTTGAGAGT 58.291 47.619 0.00 0.00 40.64 3.24
657 666 0.535102 AGTGCTCCCAAACAAGACGG 60.535 55.000 0.00 0.00 0.00 4.79
699 708 6.046290 ACTACCCTACAACTTATCGCTTTT 57.954 37.500 0.00 0.00 0.00 2.27
797 809 0.390209 CTCCGGCCCAGCAAAATTTG 60.390 55.000 0.00 0.57 0.00 2.32
833 845 3.248363 TCATCAGTTGAGAAGTGCAAACG 59.752 43.478 0.00 0.00 0.00 3.60
850 862 1.012086 GCTGCGAAAGAGCATCATCA 58.988 50.000 0.00 0.00 46.97 3.07
851 863 1.012086 TGCTGCGAAAGAGCATCATC 58.988 50.000 0.00 0.00 46.97 2.92
852 864 1.676746 ATGCTGCGAAAGAGCATCAT 58.323 45.000 2.78 2.93 45.28 2.45
886 898 5.176407 AGATAATCTGACGAACGAAGAGG 57.824 43.478 0.14 0.00 0.00 3.69
892 904 4.355437 AGAGCAAGATAATCTGACGAACG 58.645 43.478 0.00 0.00 0.00 3.95
960 972 9.369904 GAGCTATATCAGAATCTTGAATCCTTC 57.630 37.037 0.00 0.00 0.00 3.46
966 978 6.013898 CAGGGGAGCTATATCAGAATCTTGAA 60.014 42.308 0.00 0.00 0.00 2.69
1014 1026 1.180456 TGGTGCCAACAGAGCAATGG 61.180 55.000 0.00 0.00 43.02 3.16
1077 1089 2.904434 ACCACGGAACCTTCTTATCTGT 59.096 45.455 0.00 0.00 33.03 3.41
1208 1220 0.324943 TGACAAGGTCCTTAGCCTGC 59.675 55.000 3.08 0.00 36.30 4.85
1323 1335 2.437359 GTGCTAGCCACAGCCTGG 60.437 66.667 13.29 0.00 44.06 4.45
1416 1428 0.038744 AGGATGCACCAGGAACAAGG 59.961 55.000 0.00 0.00 42.04 3.61
1419 1431 2.554344 GGTAAAGGATGCACCAGGAACA 60.554 50.000 0.00 0.00 42.04 3.18
1509 1521 3.058155 CGTCACTTACTCGGGAGATATGG 60.058 52.174 2.08 0.00 38.80 2.74
1611 1623 0.391661 TTGTCAAGGAGATGCGCCTC 60.392 55.000 4.18 4.25 31.02 4.70
1725 1737 7.545965 TCGTCTATCTTCTTGAAATCCTTTGTC 59.454 37.037 0.00 0.00 0.00 3.18
2043 2055 3.412386 AGCTAACTCGAAAGCATTGGTT 58.588 40.909 14.38 0.00 41.32 3.67
2049 2061 2.066262 CGGAAAGCTAACTCGAAAGCA 58.934 47.619 14.38 0.00 41.32 3.91
2118 2130 3.845781 TCTGTTTTCACTTCTGGAGCT 57.154 42.857 0.00 0.00 0.00 4.09
2163 2175 2.027192 TGTGCTATCAACCCCAGAAGTC 60.027 50.000 0.00 0.00 0.00 3.01
2178 2190 2.872245 GAGCTTGTTGTCAACTGTGCTA 59.128 45.455 21.40 0.28 34.24 3.49
2243 2255 1.600957 CACCAGTGACAGCTTCTGTTG 59.399 52.381 0.66 0.00 45.44 3.33
2264 2276 2.047274 TAGCAGGCTCAACGGTGC 60.047 61.111 0.00 0.00 36.10 5.01
2278 2290 4.561105 ACTTCAGTAGCAGAAACTGTAGC 58.439 43.478 9.04 0.00 42.72 3.58
2349 2361 2.972713 AGAAACTGTAGGAGGCTCAACA 59.027 45.455 17.69 17.66 0.00 3.33
2460 2472 1.480137 ACTGATTCTTCTGGCTCCTCG 59.520 52.381 0.00 0.00 0.00 4.63
2737 2750 5.199024 TGCTTGAACAGTTTACATGCAAT 57.801 34.783 11.16 0.00 40.06 3.56
2738 2751 4.645762 TGCTTGAACAGTTTACATGCAA 57.354 36.364 11.16 0.00 40.06 4.08
2739 2752 4.097741 AGTTGCTTGAACAGTTTACATGCA 59.902 37.500 10.04 10.04 40.81 3.96
2740 2753 4.610945 AGTTGCTTGAACAGTTTACATGC 58.389 39.130 0.00 6.10 36.98 4.06
2921 2963 3.616219 AGTTCAAAACTGTACAGTGGCA 58.384 40.909 28.55 10.75 41.58 4.92
3409 3468 2.370519 TCTGCTGCCCTAACAACAGTTA 59.629 45.455 0.00 0.00 35.66 2.24
3816 3875 1.419374 CGTCTCCTTCTTCACAACCG 58.581 55.000 0.00 0.00 0.00 4.44
3868 3927 0.392193 CACGGATCTGCTCAGGCTTT 60.392 55.000 0.00 0.00 39.59 3.51
4078 4137 2.363038 TGCAACTTCAGCAGCAAAATCT 59.637 40.909 0.00 0.00 37.02 2.40
4114 4173 2.034066 GCAGCTGGTGGTGGCTTA 59.966 61.111 17.12 0.00 41.57 3.09
4147 4206 2.184533 TCAACCGATTCCTCAGGCTTA 58.815 47.619 0.00 0.00 0.00 3.09
4232 4291 1.266718 GCACATATTATGCACACCCCG 59.733 52.381 3.52 0.00 42.88 5.73
4275 4334 9.618890 TCTATGCAATTAGAAGTTAGAAATGCT 57.381 29.630 0.00 0.00 0.00 3.79
4327 4386 8.038944 TGGAAACATAGGTATGTCAAGTTAGAC 58.961 37.037 3.12 0.00 45.55 2.59
4415 4474 4.521146 CTTTCTTGCAGTCCATCATACCT 58.479 43.478 0.00 0.00 0.00 3.08
4529 4588 0.962356 CAATCAGGCCTTCAGCGGTT 60.962 55.000 0.00 0.00 45.17 4.44
4781 4840 2.667470 CCTTCCACGATCTTCTCCCTA 58.333 52.381 0.00 0.00 0.00 3.53
5093 5152 3.541632 AGTGTGTTGTTGTAACCAGGAG 58.458 45.455 0.00 0.00 0.00 3.69
5213 5274 4.060038 TGCCGTAATCCTTTCAGATCTC 57.940 45.455 0.00 0.00 0.00 2.75
5214 5275 4.487714 TTGCCGTAATCCTTTCAGATCT 57.512 40.909 0.00 0.00 0.00 2.75
5215 5276 5.757850 ATTTGCCGTAATCCTTTCAGATC 57.242 39.130 0.00 0.00 0.00 2.75
5216 5277 7.639113 TTAATTTGCCGTAATCCTTTCAGAT 57.361 32.000 0.00 0.00 0.00 2.90
5217 5278 7.455641 TTTAATTTGCCGTAATCCTTTCAGA 57.544 32.000 0.00 0.00 0.00 3.27
5218 5279 8.594687 CAATTTAATTTGCCGTAATCCTTTCAG 58.405 33.333 0.00 0.00 0.00 3.02
5219 5280 7.547370 CCAATTTAATTTGCCGTAATCCTTTCA 59.453 33.333 4.84 0.00 0.00 2.69
5220 5281 7.547722 ACCAATTTAATTTGCCGTAATCCTTTC 59.452 33.333 4.84 0.00 0.00 2.62
5221 5282 7.390823 ACCAATTTAATTTGCCGTAATCCTTT 58.609 30.769 4.84 0.00 0.00 3.11
5222 5283 6.941857 ACCAATTTAATTTGCCGTAATCCTT 58.058 32.000 4.84 0.00 0.00 3.36
5223 5284 6.538945 ACCAATTTAATTTGCCGTAATCCT 57.461 33.333 4.84 0.00 0.00 3.24
5224 5285 8.357402 AGATACCAATTTAATTTGCCGTAATCC 58.643 33.333 4.84 0.11 0.00 3.01
5225 5286 9.744468 AAGATACCAATTTAATTTGCCGTAATC 57.256 29.630 4.84 3.77 0.00 1.75
5226 5287 9.528018 CAAGATACCAATTTAATTTGCCGTAAT 57.472 29.630 4.84 0.00 0.00 1.89
5227 5288 8.524487 ACAAGATACCAATTTAATTTGCCGTAA 58.476 29.630 4.84 0.00 0.00 3.18
5228 5289 8.057536 ACAAGATACCAATTTAATTTGCCGTA 57.942 30.769 4.84 3.99 0.00 4.02
5229 5290 6.930731 ACAAGATACCAATTTAATTTGCCGT 58.069 32.000 4.84 2.20 0.00 5.68
5230 5291 7.010091 GGAACAAGATACCAATTTAATTTGCCG 59.990 37.037 4.84 0.00 0.00 5.69
5231 5292 7.821846 TGGAACAAGATACCAATTTAATTTGCC 59.178 33.333 4.84 0.00 31.92 4.52
5232 5293 8.770438 TGGAACAAGATACCAATTTAATTTGC 57.230 30.769 4.84 0.00 31.92 3.68
5247 5308 7.721399 ACTCTCAAGTAAAACATGGAACAAGAT 59.279 33.333 0.00 0.00 36.12 2.40
5248 5309 7.054124 ACTCTCAAGTAAAACATGGAACAAGA 58.946 34.615 0.00 0.00 36.12 3.02
5249 5310 7.264373 ACTCTCAAGTAAAACATGGAACAAG 57.736 36.000 0.00 0.00 36.12 3.16
5250 5311 7.639113 AACTCTCAAGTAAAACATGGAACAA 57.361 32.000 0.00 0.00 36.77 2.83
5251 5312 7.639113 AAACTCTCAAGTAAAACATGGAACA 57.361 32.000 0.00 0.00 37.54 3.18
5252 5313 8.807581 CAAAAACTCTCAAGTAAAACATGGAAC 58.192 33.333 0.00 0.00 33.48 3.62
5253 5314 7.491048 GCAAAAACTCTCAAGTAAAACATGGAA 59.509 33.333 0.00 0.00 33.48 3.53
5254 5315 6.978080 GCAAAAACTCTCAAGTAAAACATGGA 59.022 34.615 0.00 0.00 33.48 3.41
5255 5316 6.980397 AGCAAAAACTCTCAAGTAAAACATGG 59.020 34.615 0.00 0.00 33.48 3.66
5256 5317 7.992180 AGCAAAAACTCTCAAGTAAAACATG 57.008 32.000 0.00 0.00 33.48 3.21
5258 5319 9.567848 CTAAAGCAAAAACTCTCAAGTAAAACA 57.432 29.630 0.00 0.00 33.48 2.83
5259 5320 8.532341 GCTAAAGCAAAAACTCTCAAGTAAAAC 58.468 33.333 0.00 0.00 41.59 2.43
5260 5321 7.704899 GGCTAAAGCAAAAACTCTCAAGTAAAA 59.295 33.333 4.07 0.00 44.36 1.52
5261 5322 7.147983 TGGCTAAAGCAAAAACTCTCAAGTAAA 60.148 33.333 4.07 0.00 44.36 2.01
5262 5323 6.320164 TGGCTAAAGCAAAAACTCTCAAGTAA 59.680 34.615 4.07 0.00 44.36 2.24
5263 5324 5.825679 TGGCTAAAGCAAAAACTCTCAAGTA 59.174 36.000 4.07 0.00 44.36 2.24
5264 5325 4.644685 TGGCTAAAGCAAAAACTCTCAAGT 59.355 37.500 4.07 0.00 44.36 3.16
5265 5326 5.009010 TCTGGCTAAAGCAAAAACTCTCAAG 59.991 40.000 4.07 0.00 44.36 3.02
5266 5327 4.887071 TCTGGCTAAAGCAAAAACTCTCAA 59.113 37.500 4.07 0.00 44.36 3.02
5267 5328 4.460263 TCTGGCTAAAGCAAAAACTCTCA 58.540 39.130 4.07 0.00 44.36 3.27
5268 5329 5.438761 TTCTGGCTAAAGCAAAAACTCTC 57.561 39.130 4.07 0.00 44.36 3.20
5292 5353 8.674607 ACCAGGATAAAAAGTGTAAAATCGATC 58.325 33.333 0.00 0.00 0.00 3.69
5414 5476 2.102578 GGCACACATCATAAGCCCTTT 58.897 47.619 0.00 0.00 39.42 3.11
5564 5626 0.833287 GCTGGATGTGGAAGCTCCTA 59.167 55.000 0.00 0.00 37.46 2.94
5619 5681 9.617523 GATTGGATTGATGGTTTGGATTTTAAT 57.382 29.630 0.00 0.00 0.00 1.40
5683 5745 1.342496 TGGGCATCATCTCTAGCTTCG 59.658 52.381 0.00 0.00 0.00 3.79
5890 5952 6.681368 GCATCTTCTTTATTTGCCTAAGGGTG 60.681 42.308 0.00 0.00 34.45 4.61
5892 5954 5.595952 AGCATCTTCTTTATTTGCCTAAGGG 59.404 40.000 0.00 0.00 33.85 3.95
5937 5999 1.998315 CAGTCAGCGAATCAGTGAAGG 59.002 52.381 0.00 0.00 0.00 3.46
6064 6126 5.578727 GTGGCAGTACTCTTATTCTGTCTTG 59.421 44.000 0.00 0.00 34.23 3.02
6083 6145 4.901868 AGAAAAATAGGAAGTACGTGGCA 58.098 39.130 0.00 0.00 0.00 4.92
6134 6196 2.843701 ACTGCACTATCATTAGCTGGC 58.156 47.619 0.00 0.00 0.00 4.85
6244 6340 4.922206 TGGCAACAGTAATTCTCTGGATT 58.078 39.130 12.90 0.40 46.17 3.01
6245 6341 4.574674 TGGCAACAGTAATTCTCTGGAT 57.425 40.909 12.90 2.18 46.17 3.41
6370 6466 1.740043 GCAAATAATGGGTGCTGTGGC 60.740 52.381 0.00 0.00 35.36 5.01
6377 6473 8.084073 CCTTATGTGATTAGCAAATAATGGGTG 58.916 37.037 0.00 0.00 36.38 4.61


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

AutoCloner maintained by Alex Coulton.