Multiple sequence alignment - TraesCS1B01G289000

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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 TraesCS1B01G289000 chr1B 100.000 2580 0 0 1 2580 503663209 503660630 0.000000e+00 4765.0
1 TraesCS1B01G289000 chr1B 100.000 32 0 0 1 32 56751944 56751913 2.770000e-05 60.2
2 TraesCS1B01G289000 chr1D 93.875 1502 71 7 326 1821 376872255 376870769 0.000000e+00 2244.0
3 TraesCS1B01G289000 chr1D 86.015 665 62 15 1941 2580 376870616 376869958 0.000000e+00 684.0
4 TraesCS1B01G289000 chr1D 93.103 87 5 1 1850 1935 376870776 376870690 2.700000e-25 126.0
5 TraesCS1B01G289000 chr1A 95.181 83 4 0 1505 1587 477408874 477408792 5.790000e-27 132.0
6 TraesCS1B01G289000 chr2B 83.908 87 11 1 1852 1935 758120706 758120620 2.130000e-11 80.5
7 TraesCS1B01G289000 chr2A 83.908 87 11 1 1852 1935 750567548 750567462 2.130000e-11 80.5
8 TraesCS1B01G289000 chr7B 100.000 32 0 0 1 32 711479387 711479418 2.770000e-05 60.2
9 TraesCS1B01G289000 chr7B 97.143 35 0 1 1 34 697548341 697548375 9.970000e-05 58.4
10 TraesCS1B01G289000 chr6D 100.000 32 0 0 1 32 31863906 31863875 2.770000e-05 60.2
11 TraesCS1B01G289000 chr6D 100.000 32 0 0 1 32 436760102 436760133 2.770000e-05 60.2
12 TraesCS1B01G289000 chr3A 100.000 32 0 0 2 33 690458135 690458166 2.770000e-05 60.2
13 TraesCS1B01G289000 chrUn 97.059 34 1 0 1 34 325895957 325895924 9.970000e-05 58.4
14 TraesCS1B01G289000 chr7A 94.737 38 0 2 1 38 706965461 706965426 9.970000e-05 58.4
15 TraesCS1B01G289000 chr5B 97.059 34 1 0 1 34 15508413 15508380 9.970000e-05 58.4


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 TraesCS1B01G289000 chr1B 503660630 503663209 2579 True 4765 4765 100.000000 1 2580 1 chr1B.!!$R2 2579
1 TraesCS1B01G289000 chr1D 376869958 376872255 2297 True 1018 2244 90.997667 326 2580 3 chr1D.!!$R1 2254


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
25 26 0.178068 TACTCAAATCCTGGCTCCGC 59.822 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1858 0.035458 GAAGGGCATATGAGGGGACG 59.965 60.0 6.97 0.0 0.0 4.79 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
20 21 3.425162 CCCCTATACTCAAATCCTGGC 57.575 52.381 0.00 0.00 0.00 4.85
21 22 2.982488 CCCCTATACTCAAATCCTGGCT 59.018 50.000 0.00 0.00 0.00 4.75
22 23 3.008485 CCCCTATACTCAAATCCTGGCTC 59.992 52.174 0.00 0.00 0.00 4.70
23 24 3.008485 CCCTATACTCAAATCCTGGCTCC 59.992 52.174 0.00 0.00 0.00 4.70
24 25 2.918712 ATACTCAAATCCTGGCTCCG 57.081 50.000 0.00 0.00 0.00 4.63
25 26 0.178068 TACTCAAATCCTGGCTCCGC 59.822 55.000 0.00 0.00 0.00 5.54
44 45 3.898509 CCTGAGCTCCGAGCCGAG 61.899 72.222 16.99 12.24 43.77 4.63
45 46 2.826287 CTGAGCTCCGAGCCGAGA 60.826 66.667 16.99 0.00 43.77 4.04
46 47 2.361230 TGAGCTCCGAGCCGAGAA 60.361 61.111 16.99 0.00 43.77 2.87
47 48 2.103340 GAGCTCCGAGCCGAGAAC 59.897 66.667 16.99 0.00 43.77 3.01
48 49 3.743091 GAGCTCCGAGCCGAGAACG 62.743 68.421 16.99 0.00 43.77 3.95
59 60 4.742201 GAGAACGGCGCCTGAGCA 62.742 66.667 26.68 0.00 39.83 4.26
70 71 4.624364 CTGAGCACCACGCCCACA 62.624 66.667 0.00 0.00 44.04 4.17
71 72 4.927782 TGAGCACCACGCCCACAC 62.928 66.667 0.00 0.00 44.04 3.82
109 110 4.390584 GACAACACGTCGACGCGC 62.391 66.667 35.92 15.78 44.43 6.86
119 120 4.124351 CGACGCGCCCTTGACCTA 62.124 66.667 5.73 0.00 0.00 3.08
120 121 2.508663 GACGCGCCCTTGACCTAC 60.509 66.667 5.73 0.00 0.00 3.18
121 122 4.078516 ACGCGCCCTTGACCTACC 62.079 66.667 5.73 0.00 0.00 3.18
122 123 4.077184 CGCGCCCTTGACCTACCA 62.077 66.667 0.00 0.00 0.00 3.25
123 124 2.436115 GCGCCCTTGACCTACCAC 60.436 66.667 0.00 0.00 0.00 4.16
124 125 2.125673 CGCCCTTGACCTACCACG 60.126 66.667 0.00 0.00 0.00 4.94
125 126 2.436115 GCCCTTGACCTACCACGC 60.436 66.667 0.00 0.00 0.00 5.34
126 127 2.267961 CCCTTGACCTACCACGCC 59.732 66.667 0.00 0.00 0.00 5.68
127 128 2.267961 CCTTGACCTACCACGCCC 59.732 66.667 0.00 0.00 0.00 6.13
128 129 2.589157 CCTTGACCTACCACGCCCA 61.589 63.158 0.00 0.00 0.00 5.36
129 130 1.375523 CTTGACCTACCACGCCCAC 60.376 63.158 0.00 0.00 0.00 4.61
130 131 2.798148 CTTGACCTACCACGCCCACC 62.798 65.000 0.00 0.00 0.00 4.61
131 132 3.315949 GACCTACCACGCCCACCA 61.316 66.667 0.00 0.00 0.00 4.17
132 133 3.310860 GACCTACCACGCCCACCAG 62.311 68.421 0.00 0.00 0.00 4.00
133 134 4.778143 CCTACCACGCCCACCAGC 62.778 72.222 0.00 0.00 0.00 4.85
134 135 4.015406 CTACCACGCCCACCAGCA 62.015 66.667 0.00 0.00 0.00 4.41
135 136 4.323477 TACCACGCCCACCAGCAC 62.323 66.667 0.00 0.00 0.00 4.40
141 142 3.595758 GCCCACCAGCACACACAC 61.596 66.667 0.00 0.00 0.00 3.82
142 143 2.124362 CCCACCAGCACACACACA 60.124 61.111 0.00 0.00 0.00 3.72
143 144 2.188829 CCCACCAGCACACACACAG 61.189 63.158 0.00 0.00 0.00 3.66
144 145 2.717485 CACCAGCACACACACAGC 59.283 61.111 0.00 0.00 0.00 4.40
145 146 2.516930 ACCAGCACACACACAGCC 60.517 61.111 0.00 0.00 0.00 4.85
146 147 2.516695 CCAGCACACACACAGCCA 60.517 61.111 0.00 0.00 0.00 4.75
147 148 1.900016 CCAGCACACACACAGCCAT 60.900 57.895 0.00 0.00 0.00 4.40
148 149 0.606130 CCAGCACACACACAGCCATA 60.606 55.000 0.00 0.00 0.00 2.74
149 150 1.237533 CAGCACACACACAGCCATAA 58.762 50.000 0.00 0.00 0.00 1.90
150 151 1.814394 CAGCACACACACAGCCATAAT 59.186 47.619 0.00 0.00 0.00 1.28
151 152 2.086869 AGCACACACACAGCCATAATC 58.913 47.619 0.00 0.00 0.00 1.75
152 153 1.202065 GCACACACACAGCCATAATCG 60.202 52.381 0.00 0.00 0.00 3.34
153 154 1.086696 ACACACACAGCCATAATCGC 58.913 50.000 0.00 0.00 0.00 4.58
154 155 0.378257 CACACACAGCCATAATCGCC 59.622 55.000 0.00 0.00 0.00 5.54
155 156 0.748005 ACACACAGCCATAATCGCCC 60.748 55.000 0.00 0.00 0.00 6.13
156 157 1.523711 ACACAGCCATAATCGCCCG 60.524 57.895 0.00 0.00 0.00 6.13
157 158 2.591715 ACAGCCATAATCGCCCGC 60.592 61.111 0.00 0.00 0.00 6.13
158 159 3.716006 CAGCCATAATCGCCCGCG 61.716 66.667 0.00 0.00 41.35 6.46
161 162 4.012895 CCATAATCGCCCGCGCAC 62.013 66.667 8.75 0.00 39.59 5.34
162 163 4.354212 CATAATCGCCCGCGCACG 62.354 66.667 8.75 12.10 39.59 5.34
180 181 4.111016 CCACGCCGACAGACGCTA 62.111 66.667 0.00 0.00 41.07 4.26
181 182 2.577112 CACGCCGACAGACGCTAG 60.577 66.667 0.00 0.00 41.07 3.42
182 183 4.477975 ACGCCGACAGACGCTAGC 62.478 66.667 4.06 4.06 41.07 3.42
183 184 4.180946 CGCCGACAGACGCTAGCT 62.181 66.667 13.93 0.00 41.07 3.32
184 185 2.278271 GCCGACAGACGCTAGCTC 60.278 66.667 13.93 9.43 41.07 4.09
185 186 2.023461 CCGACAGACGCTAGCTCG 59.977 66.667 13.93 14.23 41.07 5.03
186 187 2.649349 CGACAGACGCTAGCTCGC 60.649 66.667 13.93 0.00 34.51 5.03
187 188 2.278271 GACAGACGCTAGCTCGCC 60.278 66.667 13.93 0.00 0.00 5.54
188 189 4.180946 ACAGACGCTAGCTCGCCG 62.181 66.667 13.93 1.86 0.00 6.46
209 210 4.722700 CGCCCCACACCTCCCTTG 62.723 72.222 0.00 0.00 0.00 3.61
210 211 4.366684 GCCCCACACCTCCCTTGG 62.367 72.222 0.00 0.00 0.00 3.61
211 212 4.366684 CCCCACACCTCCCTTGGC 62.367 72.222 0.00 0.00 0.00 4.52
212 213 4.366684 CCCACACCTCCCTTGGCC 62.367 72.222 0.00 0.00 0.00 5.36
213 214 3.260100 CCACACCTCCCTTGGCCT 61.260 66.667 3.32 0.00 0.00 5.19
214 215 1.923395 CCACACCTCCCTTGGCCTA 60.923 63.158 3.32 0.00 0.00 3.93
215 216 1.604378 CACACCTCCCTTGGCCTAG 59.396 63.158 7.29 7.29 0.00 3.02
216 217 2.301738 ACACCTCCCTTGGCCTAGC 61.302 63.158 8.91 0.00 0.00 3.42
217 218 3.083997 ACCTCCCTTGGCCTAGCG 61.084 66.667 8.91 0.00 0.00 4.26
218 219 3.866582 CCTCCCTTGGCCTAGCGG 61.867 72.222 8.91 11.44 0.00 5.52
244 245 4.697756 CACCCCAGCCTCGCGAAA 62.698 66.667 11.33 0.00 0.00 3.46
245 246 4.394712 ACCCCAGCCTCGCGAAAG 62.395 66.667 11.33 5.77 0.00 2.62
259 260 3.406728 GCGAAAGGGAAGTAATGAAGC 57.593 47.619 0.00 0.00 0.00 3.86
260 261 2.223044 GCGAAAGGGAAGTAATGAAGCG 60.223 50.000 0.00 0.00 0.00 4.68
261 262 3.000727 CGAAAGGGAAGTAATGAAGCGT 58.999 45.455 0.00 0.00 0.00 5.07
262 263 3.062234 CGAAAGGGAAGTAATGAAGCGTC 59.938 47.826 0.00 0.00 0.00 5.19
263 264 2.693267 AGGGAAGTAATGAAGCGTCC 57.307 50.000 0.00 0.00 33.49 4.79
264 265 1.664873 GGGAAGTAATGAAGCGTCCC 58.335 55.000 0.00 0.00 43.87 4.46
265 266 1.287425 GGAAGTAATGAAGCGTCCCG 58.713 55.000 0.00 0.00 0.00 5.14
307 308 4.410400 GCGAGGGTGGGAGGGTTG 62.410 72.222 0.00 0.00 0.00 3.77
308 309 3.717294 CGAGGGTGGGAGGGTTGG 61.717 72.222 0.00 0.00 0.00 3.77
309 310 2.204090 GAGGGTGGGAGGGTTGGA 60.204 66.667 0.00 0.00 0.00 3.53
310 311 2.204151 AGGGTGGGAGGGTTGGAG 60.204 66.667 0.00 0.00 0.00 3.86
311 312 2.204090 GGGTGGGAGGGTTGGAGA 60.204 66.667 0.00 0.00 0.00 3.71
312 313 2.301738 GGGTGGGAGGGTTGGAGAG 61.302 68.421 0.00 0.00 0.00 3.20
313 314 2.301738 GGTGGGAGGGTTGGAGAGG 61.302 68.421 0.00 0.00 0.00 3.69
314 315 2.124996 TGGGAGGGTTGGAGAGGG 59.875 66.667 0.00 0.00 0.00 4.30
315 316 2.692741 GGGAGGGTTGGAGAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
316 317 2.692741 GGAGGGTTGGAGAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
317 318 2.125225 GAGGGTTGGAGAGGGGGT 59.875 66.667 0.00 0.00 0.00 4.95
318 319 2.204151 AGGGTTGGAGAGGGGGTG 60.204 66.667 0.00 0.00 0.00 4.61
319 320 3.339093 GGGTTGGAGAGGGGGTGG 61.339 72.222 0.00 0.00 0.00 4.61
320 321 2.531942 GGTTGGAGAGGGGGTGGT 60.532 66.667 0.00 0.00 0.00 4.16
321 322 2.160853 GGTTGGAGAGGGGGTGGTT 61.161 63.158 0.00 0.00 0.00 3.67
322 323 1.074951 GTTGGAGAGGGGGTGGTTG 59.925 63.158 0.00 0.00 0.00 3.77
323 324 2.160171 TTGGAGAGGGGGTGGTTGG 61.160 63.158 0.00 0.00 0.00 3.77
324 325 4.048470 GGAGAGGGGGTGGTTGGC 62.048 72.222 0.00 0.00 0.00 4.52
343 344 2.244117 CTCAGCGGGCAAGGCTTCTA 62.244 60.000 0.00 0.00 39.08 2.10
349 350 2.091541 CGGGCAAGGCTTCTAATTTCA 58.908 47.619 0.00 0.00 0.00 2.69
350 351 2.689983 CGGGCAAGGCTTCTAATTTCAT 59.310 45.455 0.00 0.00 0.00 2.57
351 352 3.882888 CGGGCAAGGCTTCTAATTTCATA 59.117 43.478 0.00 0.00 0.00 2.15
352 353 4.023707 CGGGCAAGGCTTCTAATTTCATAG 60.024 45.833 0.00 0.00 0.00 2.23
503 504 2.486955 GGGCAACAAAGGTTCCTACCG 61.487 57.143 0.00 0.00 44.87 4.02
535 536 1.532868 GGTCTGCAGCCTATTATTGCG 59.467 52.381 9.47 0.00 40.62 4.85
577 578 7.012704 ACAAATCATGGGAGAATTAAGACATCG 59.987 37.037 0.00 0.00 0.00 3.84
631 632 8.291191 AGAGGGTAGATTAGTAGTGTGTTAAC 57.709 38.462 0.00 0.00 0.00 2.01
635 636 6.755607 GGTAGATTAGTAGTGTGTTAACCTGC 59.244 42.308 2.48 0.00 0.00 4.85
641 642 2.783135 AGTGTGTTAACCTGCTGATGG 58.217 47.619 2.48 0.00 0.00 3.51
649 650 1.180029 ACCTGCTGATGGTGCATTTC 58.820 50.000 0.00 0.00 39.86 2.17
705 706 7.735326 TTTAGGAGTTACTGGCTTCTAGATT 57.265 36.000 0.00 0.00 0.00 2.40
712 713 7.686434 AGTTACTGGCTTCTAGATTTGGTTAA 58.314 34.615 0.00 0.00 0.00 2.01
713 714 8.161425 AGTTACTGGCTTCTAGATTTGGTTAAA 58.839 33.333 0.00 0.00 0.00 1.52
754 755 6.741992 TGAAGTGATAAAAAGCGTCATGAT 57.258 33.333 0.00 0.00 0.00 2.45
769 770 4.441495 CGTCATGATAGCCACTTGTAGGAA 60.441 45.833 0.00 0.00 0.00 3.36
777 778 3.452627 AGCCACTTGTAGGAAGACATAGG 59.547 47.826 0.00 0.00 0.00 2.57
792 793 8.847196 GGAAGACATAGGGGAAACATAATTTAC 58.153 37.037 0.00 0.00 0.00 2.01
796 797 4.976224 AGGGGAAACATAATTTACGCAC 57.024 40.909 2.05 0.00 0.00 5.34
811 812 2.504367 ACGCACTGCCACTTTAATTCT 58.496 42.857 0.00 0.00 0.00 2.40
814 815 2.729156 GCACTGCCACTTTAATTCTCGC 60.729 50.000 0.00 0.00 0.00 5.03
825 826 5.924825 ACTTTAATTCTCGCGTGGTATATCC 59.075 40.000 5.77 0.00 0.00 2.59
897 898 3.634397 TTCCAGCCTTACTCATTCAGG 57.366 47.619 0.00 0.00 0.00 3.86
905 906 6.146837 CAGCCTTACTCATTCAGGATTAATCG 59.853 42.308 9.32 0.00 0.00 3.34
912 913 6.870965 ACTCATTCAGGATTAATCGACTATGC 59.129 38.462 9.32 0.00 0.00 3.14
923 924 1.941294 TCGACTATGCCGAGTCTCTTC 59.059 52.381 11.95 0.00 43.18 2.87
925 926 2.032377 CGACTATGCCGAGTCTCTTCTC 60.032 54.545 11.95 0.00 43.18 2.87
939 940 4.702612 GTCTCTTCTCAGTCATGTGGTAGA 59.297 45.833 0.00 0.00 0.00 2.59
943 944 6.634805 TCTTCTCAGTCATGTGGTAGATTTC 58.365 40.000 0.00 0.00 0.00 2.17
981 982 5.939296 AGTGCCCACAAATTCCAAATATTTG 59.061 36.000 19.40 19.40 44.59 2.32
990 991 4.448537 TTCCAAATATTTGCCTCGTTGG 57.551 40.909 20.67 7.35 36.86 3.77
1084 1085 0.250295 TGACGGAGACAAGGCTTTGG 60.250 55.000 13.65 0.00 38.66 3.28
1104 1105 3.132111 TGGTAGATGCTAACGAATGCAGA 59.868 43.478 0.00 0.00 42.74 4.26
1185 1186 7.973048 ACTGAAGGTTACATAGAAGATACCA 57.027 36.000 0.00 0.00 0.00 3.25
1237 1238 6.985188 TTTCCTCTATATGAGTTTGTGTGC 57.015 37.500 0.00 0.00 41.11 4.57
1293 1294 9.223764 TATCATCAGGATTACAAGGGTGCTTGT 62.224 40.741 0.00 0.00 42.24 3.16
1297 1298 3.572255 GGATTACAAGGGTGCTTGTGAAA 59.428 43.478 0.00 0.00 45.83 2.69
1298 1299 4.321230 GGATTACAAGGGTGCTTGTGAAAG 60.321 45.833 0.00 0.00 45.83 2.62
1301 1302 2.166254 ACAAGGGTGCTTGTGAAAGTTG 59.834 45.455 0.00 0.00 44.79 3.16
1325 1326 1.676014 GGATGGACTCAAGTTGGACCG 60.676 57.143 2.34 0.00 0.00 4.79
1372 1373 1.122019 ACGGTATCCCATCTGCCTCC 61.122 60.000 0.00 0.00 0.00 4.30
1394 1395 4.023707 CCTTTTTGTTGTTTGTGGCAAACA 60.024 37.500 19.50 19.50 38.26 2.83
1429 1430 4.735578 GCATTATGCATTGTGAGGAACCAG 60.736 45.833 12.80 0.00 44.26 4.00
1496 1497 6.094061 GCTCCTAAGTGTTACTACAAGTGAG 58.906 44.000 0.00 0.00 35.69 3.51
1564 1566 1.263484 GATGCCATGCAAGATGTCTCG 59.737 52.381 0.00 0.00 43.62 4.04
1565 1567 0.249955 TGCCATGCAAGATGTCTCGA 59.750 50.000 0.00 0.00 34.76 4.04
1567 1569 1.329906 GCCATGCAAGATGTCTCGAAG 59.670 52.381 0.00 0.00 0.00 3.79
1632 1637 8.766000 TTTGTTTTCTTTAAAAGTGGGAAGAC 57.234 30.769 0.00 0.00 35.29 3.01
1637 1642 4.508861 TCTTTAAAAGTGGGAAGACGTTCG 59.491 41.667 0.00 0.00 32.92 3.95
1655 1660 1.202830 TCGGGATCTGCTCTCTAGTCC 60.203 57.143 0.00 0.00 0.00 3.85
1656 1661 1.627864 GGGATCTGCTCTCTAGTCCC 58.372 60.000 0.00 0.00 38.61 4.46
1657 1662 1.146982 GGGATCTGCTCTCTAGTCCCT 59.853 57.143 4.00 0.00 41.63 4.20
1658 1663 2.238521 GGATCTGCTCTCTAGTCCCTG 58.761 57.143 0.00 0.00 0.00 4.45
1660 1665 3.181438 GGATCTGCTCTCTAGTCCCTGTA 60.181 52.174 0.00 0.00 0.00 2.74
1661 1666 3.569194 TCTGCTCTCTAGTCCCTGTAG 57.431 52.381 0.00 0.00 0.00 2.74
1662 1667 2.847449 TCTGCTCTCTAGTCCCTGTAGT 59.153 50.000 0.00 0.00 0.00 2.73
1706 1713 7.467947 GCTTATAGGCTTTGAATTCCTGAACTC 60.468 40.741 2.27 0.00 0.00 3.01
1711 1718 4.377841 GCTTTGAATTCCTGAACTCGTCTG 60.378 45.833 2.27 0.00 0.00 3.51
1790 1797 8.634335 TCCTATCTTTTTGTGTCATTCATTCA 57.366 30.769 0.00 0.00 0.00 2.57
1797 1804 3.076621 TGTGTCATTCATTCAGGCTGTC 58.923 45.455 15.27 0.00 0.00 3.51
1798 1805 3.076621 GTGTCATTCATTCAGGCTGTCA 58.923 45.455 15.27 2.79 0.00 3.58
1799 1806 3.076621 TGTCATTCATTCAGGCTGTCAC 58.923 45.455 15.27 1.85 0.00 3.67
1818 1825 9.703892 GCTGTCACAAGATAGATTATTATCTGT 57.296 33.333 4.47 0.00 41.25 3.41
1823 1830 9.650539 CACAAGATAGATTATTATCTGTCCTGG 57.349 37.037 16.57 9.49 45.26 4.45
1824 1831 9.607333 ACAAGATAGATTATTATCTGTCCTGGA 57.393 33.333 16.57 0.00 45.26 3.86
1826 1833 8.305046 AGATAGATTATTATCTGTCCTGGAGC 57.695 38.462 13.02 0.00 45.26 4.70
1827 1834 7.898100 AGATAGATTATTATCTGTCCTGGAGCA 59.102 37.037 13.02 0.00 45.26 4.26
1828 1835 6.949117 AGATTATTATCTGTCCTGGAGCAT 57.051 37.500 0.00 0.00 39.66 3.79
1829 1836 6.945218 AGATTATTATCTGTCCTGGAGCATC 58.055 40.000 0.00 0.00 39.66 3.91
1830 1837 6.730038 AGATTATTATCTGTCCTGGAGCATCT 59.270 38.462 0.00 0.00 39.66 2.90
1831 1838 7.898100 AGATTATTATCTGTCCTGGAGCATCTA 59.102 37.037 0.00 0.00 39.66 1.98
1832 1839 5.736951 ATTATCTGTCCTGGAGCATCTAC 57.263 43.478 0.00 0.00 33.73 2.59
1833 1840 2.532250 TCTGTCCTGGAGCATCTACA 57.468 50.000 0.00 0.00 33.73 2.74
1834 1841 2.820178 TCTGTCCTGGAGCATCTACAA 58.180 47.619 0.00 0.00 33.73 2.41
1835 1842 2.497675 TCTGTCCTGGAGCATCTACAAC 59.502 50.000 0.00 0.00 33.73 3.32
1836 1843 1.555075 TGTCCTGGAGCATCTACAACC 59.445 52.381 0.00 0.00 33.73 3.77
1837 1844 1.555075 GTCCTGGAGCATCTACAACCA 59.445 52.381 0.00 0.00 33.73 3.67
1838 1845 1.555075 TCCTGGAGCATCTACAACCAC 59.445 52.381 0.00 0.00 33.73 4.16
1839 1846 1.278985 CCTGGAGCATCTACAACCACA 59.721 52.381 0.00 0.00 33.73 4.17
1840 1847 2.350522 CTGGAGCATCTACAACCACAC 58.649 52.381 0.00 0.00 33.73 3.82
1841 1848 1.977854 TGGAGCATCTACAACCACACT 59.022 47.619 0.00 0.00 33.73 3.55
1842 1849 2.371841 TGGAGCATCTACAACCACACTT 59.628 45.455 0.00 0.00 33.73 3.16
1843 1850 3.580895 TGGAGCATCTACAACCACACTTA 59.419 43.478 0.00 0.00 33.73 2.24
1844 1851 4.184629 GGAGCATCTACAACCACACTTAG 58.815 47.826 0.00 0.00 33.73 2.18
1845 1852 4.184629 GAGCATCTACAACCACACTTAGG 58.815 47.826 0.00 0.00 0.00 2.69
1846 1853 2.678336 GCATCTACAACCACACTTAGGC 59.322 50.000 0.00 0.00 0.00 3.93
1847 1854 3.868369 GCATCTACAACCACACTTAGGCA 60.868 47.826 0.00 0.00 0.00 4.75
1848 1855 4.323417 CATCTACAACCACACTTAGGCAA 58.677 43.478 0.00 0.00 0.00 4.52
1849 1856 4.425180 TCTACAACCACACTTAGGCAAA 57.575 40.909 0.00 0.00 0.00 3.68
1850 1857 4.980573 TCTACAACCACACTTAGGCAAAT 58.019 39.130 0.00 0.00 0.00 2.32
1851 1858 5.001232 TCTACAACCACACTTAGGCAAATC 58.999 41.667 0.00 0.00 0.00 2.17
1852 1859 2.552315 ACAACCACACTTAGGCAAATCG 59.448 45.455 0.00 0.00 0.00 3.34
1893 1900 9.622004 CTTCAAATCCATATAATCTCATGCAAC 57.378 33.333 0.00 0.00 0.00 4.17
1894 1901 8.694581 TCAAATCCATATAATCTCATGCAACA 57.305 30.769 0.00 0.00 0.00 3.33
1908 1915 7.477494 TCTCATGCAACATAGATCAAACAATG 58.523 34.615 0.00 0.00 0.00 2.82
1956 2031 8.920665 CATAGAATTAACGAGCTATGGAGAAAG 58.079 37.037 0.00 0.00 37.57 2.62
1996 2071 4.481368 TGCACTTGTCCGGTTTATAGAT 57.519 40.909 0.00 0.00 0.00 1.98
2003 2078 9.537192 CACTTGTCCGGTTTATAGATATTGTAA 57.463 33.333 0.00 0.00 0.00 2.41
2017 2092 9.935241 ATAGATATTGTAACGCTTGAAGATGAT 57.065 29.630 0.00 0.00 0.00 2.45
2027 2102 5.092105 CGCTTGAAGATGATATAGAGACCG 58.908 45.833 0.00 0.00 0.00 4.79
2047 2122 2.202479 GCGGATCTGTTTTGCGCC 60.202 61.111 4.18 0.00 46.47 6.53
2064 2139 1.811266 CCTGGAGGTGTCGAATGCG 60.811 63.158 0.00 0.00 39.35 4.73
2077 2152 1.429463 GAATGCGACACCGTTCTTCT 58.571 50.000 0.00 0.00 38.24 2.85
2078 2153 1.390463 GAATGCGACACCGTTCTTCTC 59.610 52.381 0.00 0.00 38.24 2.87
2079 2154 0.603569 ATGCGACACCGTTCTTCTCT 59.396 50.000 0.00 0.00 38.24 3.10
2080 2155 0.387929 TGCGACACCGTTCTTCTCTT 59.612 50.000 0.00 0.00 38.24 2.85
2129 2204 0.470766 GGGCATGGACAATACGGGTA 59.529 55.000 0.00 0.00 0.00 3.69
2141 2216 4.155733 CGGGTATGCTCCACCGCA 62.156 66.667 0.00 0.00 45.10 5.69
2143 2218 1.819632 GGGTATGCTCCACCGCAAG 60.820 63.158 0.00 0.00 44.06 4.01
2186 2261 1.912371 GCTCGCCAGGTTACAAGCAC 61.912 60.000 0.00 0.00 0.00 4.40
2188 2263 1.666553 CGCCAGGTTACAAGCACGA 60.667 57.895 0.00 0.00 0.00 4.35
2208 2284 3.481453 GAATATCCTTCTGGCCTTGTCC 58.519 50.000 3.32 0.00 0.00 4.02
2211 2287 1.376037 CCTTCTGGCCTTGTCCGAC 60.376 63.158 3.32 0.00 0.00 4.79
2302 2378 2.031157 CCAAACTTGAAGCCTAACACCG 60.031 50.000 0.00 0.00 0.00 4.94
2304 2380 1.878953 ACTTGAAGCCTAACACCGTG 58.121 50.000 0.00 0.00 0.00 4.94
2308 2384 1.833787 GAAGCCTAACACCGTGGGGA 61.834 60.000 3.03 0.00 36.97 4.81
2309 2385 2.046604 GCCTAACACCGTGGGGAC 60.047 66.667 3.03 0.00 36.97 4.46
2324 2400 2.353610 GGACAAGGGCCCAATGCAG 61.354 63.158 27.56 9.09 43.89 4.41
2356 2459 1.003355 ACACACCTCAAGCCATCGG 60.003 57.895 0.00 0.00 0.00 4.18
2383 2486 1.062525 GCATCACCGCCGTTCAATC 59.937 57.895 0.00 0.00 0.00 2.67
2436 2539 2.746472 GCCATGTGGTTGAGTATCCTCC 60.746 54.545 0.35 0.00 35.68 4.30
2440 2543 1.486726 GTGGTTGAGTATCCTCCTGGG 59.513 57.143 0.00 0.00 36.86 4.45
2454 2557 0.539051 CCTGGGATCGACAGAAAGCT 59.461 55.000 15.34 0.00 38.20 3.74
2457 2560 1.137086 TGGGATCGACAGAAAGCTAGC 59.863 52.381 6.62 6.62 0.00 3.42
2460 2563 2.418746 GGATCGACAGAAAGCTAGCCAA 60.419 50.000 12.13 0.00 0.00 4.52
2478 2581 3.120304 GCCAAATCCAAGTTGACGTACTC 60.120 47.826 3.87 0.00 0.00 2.59
2480 2583 4.152402 CCAAATCCAAGTTGACGTACTCAG 59.848 45.833 3.87 0.00 0.00 3.35
2492 2595 1.333931 CGTACTCAGATTCGCTGCCTA 59.666 52.381 0.00 0.00 44.52 3.93
2499 2602 2.679837 CAGATTCGCTGCCTACAATGTT 59.320 45.455 0.00 0.00 37.90 2.71
2510 2613 4.021544 TGCCTACAATGTTGAAAATGACCC 60.022 41.667 0.00 0.00 0.00 4.46
2523 2626 5.365025 TGAAAATGACCCAAGATCACCAAAA 59.635 36.000 0.00 0.00 0.00 2.44
2539 2642 0.394192 AAAAAGGAGCTGGGCAAAGC 59.606 50.000 0.00 3.39 43.88 3.51
2546 2649 2.032528 CTGGGCAAAGCGGACTGA 59.967 61.111 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.982488 AGCCAGGATTTGAGTATAGGGG 59.018 50.000 0.00 0.00 0.00 4.79
1 2 3.008485 GGAGCCAGGATTTGAGTATAGGG 59.992 52.174 0.00 0.00 0.00 3.53
2 3 3.306364 CGGAGCCAGGATTTGAGTATAGG 60.306 52.174 0.00 0.00 0.00 2.57
3 4 3.919216 CGGAGCCAGGATTTGAGTATAG 58.081 50.000 0.00 0.00 0.00 1.31
5 6 2.918712 CGGAGCCAGGATTTGAGTAT 57.081 50.000 0.00 0.00 0.00 2.12
27 28 3.898509 CTCGGCTCGGAGCTCAGG 61.899 72.222 27.47 15.16 41.99 3.86
28 29 2.410687 TTCTCGGCTCGGAGCTCAG 61.411 63.158 27.47 21.85 41.99 3.35
29 30 2.361230 TTCTCGGCTCGGAGCTCA 60.361 61.111 27.47 14.28 41.99 4.26
30 31 2.103340 GTTCTCGGCTCGGAGCTC 59.897 66.667 27.47 17.07 41.99 4.09
31 32 3.816524 CGTTCTCGGCTCGGAGCT 61.817 66.667 27.47 0.00 41.99 4.09
42 43 4.742201 TGCTCAGGCGCCGTTCTC 62.742 66.667 23.20 11.19 42.25 2.87
102 103 4.124351 TAGGTCAAGGGCGCGTCG 62.124 66.667 8.43 0.00 0.00 5.12
103 104 2.508663 GTAGGTCAAGGGCGCGTC 60.509 66.667 8.43 4.38 0.00 5.19
104 105 4.078516 GGTAGGTCAAGGGCGCGT 62.079 66.667 8.43 0.00 0.00 6.01
105 106 4.077184 TGGTAGGTCAAGGGCGCG 62.077 66.667 0.00 0.00 0.00 6.86
106 107 2.436115 GTGGTAGGTCAAGGGCGC 60.436 66.667 0.00 0.00 0.00 6.53
107 108 2.125673 CGTGGTAGGTCAAGGGCG 60.126 66.667 0.00 0.00 0.00 6.13
108 109 2.436115 GCGTGGTAGGTCAAGGGC 60.436 66.667 0.00 0.00 0.00 5.19
109 110 2.267961 GGCGTGGTAGGTCAAGGG 59.732 66.667 0.00 0.00 0.00 3.95
110 111 2.267961 GGGCGTGGTAGGTCAAGG 59.732 66.667 0.00 0.00 0.00 3.61
111 112 1.375523 GTGGGCGTGGTAGGTCAAG 60.376 63.158 0.00 0.00 0.00 3.02
112 113 2.745037 GTGGGCGTGGTAGGTCAA 59.255 61.111 0.00 0.00 0.00 3.18
113 114 3.315949 GGTGGGCGTGGTAGGTCA 61.316 66.667 0.00 0.00 0.00 4.02
114 115 3.310860 CTGGTGGGCGTGGTAGGTC 62.311 68.421 0.00 0.00 0.00 3.85
115 116 3.319198 CTGGTGGGCGTGGTAGGT 61.319 66.667 0.00 0.00 0.00 3.08
116 117 4.778143 GCTGGTGGGCGTGGTAGG 62.778 72.222 0.00 0.00 0.00 3.18
117 118 4.015406 TGCTGGTGGGCGTGGTAG 62.015 66.667 0.00 0.00 34.52 3.18
118 119 4.323477 GTGCTGGTGGGCGTGGTA 62.323 66.667 0.00 0.00 34.52 3.25
124 125 3.595758 GTGTGTGTGCTGGTGGGC 61.596 66.667 0.00 0.00 0.00 5.36
125 126 2.124362 TGTGTGTGTGCTGGTGGG 60.124 61.111 0.00 0.00 0.00 4.61
126 127 2.837883 GCTGTGTGTGTGCTGGTGG 61.838 63.158 0.00 0.00 0.00 4.61
127 128 2.717485 GCTGTGTGTGTGCTGGTG 59.283 61.111 0.00 0.00 0.00 4.17
128 129 2.516930 GGCTGTGTGTGTGCTGGT 60.517 61.111 0.00 0.00 0.00 4.00
129 130 0.606130 TATGGCTGTGTGTGTGCTGG 60.606 55.000 0.00 0.00 0.00 4.85
130 131 1.237533 TTATGGCTGTGTGTGTGCTG 58.762 50.000 0.00 0.00 0.00 4.41
131 132 2.086869 GATTATGGCTGTGTGTGTGCT 58.913 47.619 0.00 0.00 0.00 4.40
132 133 1.202065 CGATTATGGCTGTGTGTGTGC 60.202 52.381 0.00 0.00 0.00 4.57
133 134 1.202065 GCGATTATGGCTGTGTGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
134 135 1.086696 GCGATTATGGCTGTGTGTGT 58.913 50.000 0.00 0.00 0.00 3.72
135 136 0.378257 GGCGATTATGGCTGTGTGTG 59.622 55.000 0.00 0.00 0.00 3.82
136 137 0.748005 GGGCGATTATGGCTGTGTGT 60.748 55.000 0.00 0.00 34.31 3.72
137 138 1.775039 CGGGCGATTATGGCTGTGTG 61.775 60.000 0.00 0.00 36.14 3.82
138 139 1.523711 CGGGCGATTATGGCTGTGT 60.524 57.895 0.00 0.00 36.14 3.72
139 140 2.896801 GCGGGCGATTATGGCTGTG 61.897 63.158 0.00 0.00 42.45 3.66
140 141 2.591715 GCGGGCGATTATGGCTGT 60.592 61.111 0.00 0.00 42.45 4.40
141 142 3.716006 CGCGGGCGATTATGGCTG 61.716 66.667 7.38 0.00 42.83 4.85
144 145 4.012895 GTGCGCGGGCGATTATGG 62.013 66.667 20.22 0.00 44.10 2.74
145 146 4.354212 CGTGCGCGGGCGATTATG 62.354 66.667 20.22 3.61 44.10 1.90
163 164 4.111016 TAGCGTCTGTCGGCGTGG 62.111 66.667 6.85 0.00 40.26 4.94
164 165 2.577112 CTAGCGTCTGTCGGCGTG 60.577 66.667 6.85 0.00 40.26 5.34
165 166 4.477975 GCTAGCGTCTGTCGGCGT 62.478 66.667 6.85 0.00 40.26 5.68
166 167 4.180946 AGCTAGCGTCTGTCGGCG 62.181 66.667 9.55 0.00 40.26 6.46
167 168 2.278271 GAGCTAGCGTCTGTCGGC 60.278 66.667 9.55 0.00 40.26 5.54
168 169 2.023461 CGAGCTAGCGTCTGTCGG 59.977 66.667 9.55 0.00 40.26 4.79
169 170 2.649349 GCGAGCTAGCGTCTGTCG 60.649 66.667 16.47 16.47 43.12 4.35
170 171 2.278271 GGCGAGCTAGCGTCTGTC 60.278 66.667 12.91 0.00 38.18 3.51
171 172 4.180946 CGGCGAGCTAGCGTCTGT 62.181 66.667 12.91 0.00 38.18 3.41
192 193 4.722700 CAAGGGAGGTGTGGGGCG 62.723 72.222 0.00 0.00 0.00 6.13
193 194 4.366684 CCAAGGGAGGTGTGGGGC 62.367 72.222 0.00 0.00 0.00 5.80
194 195 4.366684 GCCAAGGGAGGTGTGGGG 62.367 72.222 0.00 0.00 32.71 4.96
195 196 4.366684 GGCCAAGGGAGGTGTGGG 62.367 72.222 0.00 0.00 32.71 4.61
196 197 1.915078 CTAGGCCAAGGGAGGTGTGG 61.915 65.000 5.01 0.00 35.39 4.17
197 198 1.604378 CTAGGCCAAGGGAGGTGTG 59.396 63.158 5.01 0.00 0.00 3.82
198 199 2.301738 GCTAGGCCAAGGGAGGTGT 61.302 63.158 5.01 0.00 0.00 4.16
199 200 2.592308 GCTAGGCCAAGGGAGGTG 59.408 66.667 5.01 0.00 0.00 4.00
200 201 3.083997 CGCTAGGCCAAGGGAGGT 61.084 66.667 5.01 0.00 0.00 3.85
201 202 3.866582 CCGCTAGGCCAAGGGAGG 61.867 72.222 5.01 0.00 0.00 4.30
227 228 4.697756 TTTCGCGAGGCTGGGGTG 62.698 66.667 9.59 0.00 0.00 4.61
228 229 4.394712 CTTTCGCGAGGCTGGGGT 62.395 66.667 9.59 0.00 0.00 4.95
231 232 3.605749 TTCCCTTTCGCGAGGCTGG 62.606 63.158 9.59 9.26 35.37 4.85
232 233 2.047274 TTCCCTTTCGCGAGGCTG 60.047 61.111 9.59 0.00 35.37 4.85
233 234 1.255667 TACTTCCCTTTCGCGAGGCT 61.256 55.000 9.59 0.00 35.37 4.58
234 235 0.390735 TTACTTCCCTTTCGCGAGGC 60.391 55.000 9.59 0.00 35.37 4.70
235 236 1.933853 CATTACTTCCCTTTCGCGAGG 59.066 52.381 9.59 8.34 36.52 4.63
236 237 2.888594 TCATTACTTCCCTTTCGCGAG 58.111 47.619 9.59 0.00 0.00 5.03
237 238 3.259064 CTTCATTACTTCCCTTTCGCGA 58.741 45.455 3.71 3.71 0.00 5.87
238 239 2.223044 GCTTCATTACTTCCCTTTCGCG 60.223 50.000 0.00 0.00 0.00 5.87
239 240 2.223044 CGCTTCATTACTTCCCTTTCGC 60.223 50.000 0.00 0.00 0.00 4.70
240 241 3.000727 ACGCTTCATTACTTCCCTTTCG 58.999 45.455 0.00 0.00 0.00 3.46
241 242 3.374367 GGACGCTTCATTACTTCCCTTTC 59.626 47.826 0.00 0.00 0.00 2.62
242 243 3.344515 GGACGCTTCATTACTTCCCTTT 58.655 45.455 0.00 0.00 0.00 3.11
243 244 2.355818 GGGACGCTTCATTACTTCCCTT 60.356 50.000 0.00 0.00 40.40 3.95
244 245 1.209747 GGGACGCTTCATTACTTCCCT 59.790 52.381 0.00 0.00 40.40 4.20
245 246 1.664873 GGGACGCTTCATTACTTCCC 58.335 55.000 0.00 0.00 37.23 3.97
290 291 4.410400 CAACCCTCCCACCCTCGC 62.410 72.222 0.00 0.00 0.00 5.03
291 292 3.717294 CCAACCCTCCCACCCTCG 61.717 72.222 0.00 0.00 0.00 4.63
292 293 2.204090 TCCAACCCTCCCACCCTC 60.204 66.667 0.00 0.00 0.00 4.30
293 294 2.204151 CTCCAACCCTCCCACCCT 60.204 66.667 0.00 0.00 0.00 4.34
294 295 2.204090 TCTCCAACCCTCCCACCC 60.204 66.667 0.00 0.00 0.00 4.61
295 296 2.301738 CCTCTCCAACCCTCCCACC 61.302 68.421 0.00 0.00 0.00 4.61
296 297 2.301738 CCCTCTCCAACCCTCCCAC 61.302 68.421 0.00 0.00 0.00 4.61
297 298 2.124996 CCCTCTCCAACCCTCCCA 59.875 66.667 0.00 0.00 0.00 4.37
298 299 2.692741 CCCCTCTCCAACCCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
299 300 2.692741 CCCCCTCTCCAACCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
300 301 2.125225 ACCCCCTCTCCAACCCTC 59.875 66.667 0.00 0.00 0.00 4.30
301 302 2.204151 CACCCCCTCTCCAACCCT 60.204 66.667 0.00 0.00 0.00 4.34
302 303 3.339093 CCACCCCCTCTCCAACCC 61.339 72.222 0.00 0.00 0.00 4.11
303 304 2.160853 AACCACCCCCTCTCCAACC 61.161 63.158 0.00 0.00 0.00 3.77
304 305 1.074951 CAACCACCCCCTCTCCAAC 59.925 63.158 0.00 0.00 0.00 3.77
305 306 2.160171 CCAACCACCCCCTCTCCAA 61.160 63.158 0.00 0.00 0.00 3.53
306 307 2.531685 CCAACCACCCCCTCTCCA 60.532 66.667 0.00 0.00 0.00 3.86
307 308 4.048470 GCCAACCACCCCCTCTCC 62.048 72.222 0.00 0.00 0.00 3.71
308 309 2.936032 AGCCAACCACCCCCTCTC 60.936 66.667 0.00 0.00 0.00 3.20
309 310 2.936032 GAGCCAACCACCCCCTCT 60.936 66.667 0.00 0.00 0.00 3.69
310 311 3.256960 TGAGCCAACCACCCCCTC 61.257 66.667 0.00 0.00 0.00 4.30
311 312 3.260100 CTGAGCCAACCACCCCCT 61.260 66.667 0.00 0.00 0.00 4.79
319 320 3.741476 CTTGCCCGCTGAGCCAAC 61.741 66.667 0.00 0.00 0.00 3.77
324 325 2.244117 TAGAAGCCTTGCCCGCTGAG 62.244 60.000 0.00 0.00 36.47 3.35
440 441 3.882131 CCCCCAACTCGATGTGAAT 57.118 52.632 0.00 0.00 0.00 2.57
473 474 2.419436 CCTTTGTTGCCCCGTTCTTTTT 60.419 45.455 0.00 0.00 0.00 1.94
474 475 1.138069 CCTTTGTTGCCCCGTTCTTTT 59.862 47.619 0.00 0.00 0.00 2.27
488 489 1.331214 TCGTCGGTAGGAACCTTTGT 58.669 50.000 0.00 0.00 44.35 2.83
503 504 2.103042 GCAGACCTGTGGCATCGTC 61.103 63.158 0.00 0.00 0.00 4.20
507 508 2.360852 GCTGCAGACCTGTGGCAT 60.361 61.111 20.43 0.00 36.87 4.40
535 536 4.038642 TGATTTGTAACAAAACCAGCTCCC 59.961 41.667 0.00 0.00 0.00 4.30
631 632 1.471119 AGAAATGCACCATCAGCAGG 58.529 50.000 0.00 0.00 46.36 4.85
635 636 5.381174 TTCTCAAAGAAATGCACCATCAG 57.619 39.130 0.00 0.00 29.99 2.90
670 671 9.043079 GCCAGTAACTCCTAAAATATTACAGTC 57.957 37.037 0.00 0.00 0.00 3.51
686 687 5.735766 ACCAAATCTAGAAGCCAGTAACTC 58.264 41.667 0.00 0.00 0.00 3.01
701 702 9.646522 ATTATCCACTATGCTTTAACCAAATCT 57.353 29.630 0.00 0.00 0.00 2.40
705 706 8.815565 TTCATTATCCACTATGCTTTAACCAA 57.184 30.769 0.00 0.00 0.00 3.67
712 713 7.994911 TCACTTCATTCATTATCCACTATGCTT 59.005 33.333 0.00 0.00 0.00 3.91
713 714 7.512130 TCACTTCATTCATTATCCACTATGCT 58.488 34.615 0.00 0.00 0.00 3.79
754 755 4.649674 CCTATGTCTTCCTACAAGTGGCTA 59.350 45.833 0.00 0.00 32.02 3.93
769 770 6.485648 GCGTAAATTATGTTTCCCCTATGTCT 59.514 38.462 0.00 0.00 0.00 3.41
777 778 4.102649 GCAGTGCGTAAATTATGTTTCCC 58.897 43.478 0.00 0.00 0.00 3.97
792 793 2.474526 CGAGAATTAAAGTGGCAGTGCG 60.475 50.000 9.45 0.00 0.00 5.34
796 797 1.732259 ACGCGAGAATTAAAGTGGCAG 59.268 47.619 15.93 0.00 0.00 4.85
811 812 2.025898 TGTTGAGGATATACCACGCGA 58.974 47.619 15.93 0.00 42.04 5.87
814 815 4.024893 GCACAATGTTGAGGATATACCACG 60.025 45.833 0.00 0.00 42.04 4.94
854 855 5.659440 AACAAAGCCAATTAATCCGACAT 57.341 34.783 0.00 0.00 0.00 3.06
855 856 5.461032 AAACAAAGCCAATTAATCCGACA 57.539 34.783 0.00 0.00 0.00 4.35
905 906 2.946329 TGAGAAGAGACTCGGCATAGTC 59.054 50.000 9.12 9.12 45.20 2.59
912 913 2.752354 ACATGACTGAGAAGAGACTCGG 59.248 50.000 0.00 0.00 45.56 4.63
923 924 5.350504 AGGAAATCTACCACATGACTGAG 57.649 43.478 0.00 0.00 0.00 3.35
925 926 7.060383 AGATAGGAAATCTACCACATGACTG 57.940 40.000 0.00 0.00 0.00 3.51
939 940 5.128919 GGCACTGACAATGAGATAGGAAAT 58.871 41.667 0.00 0.00 0.00 2.17
943 944 2.171237 TGGGCACTGACAATGAGATAGG 59.829 50.000 0.00 0.00 0.00 2.57
1084 1085 5.718649 TTTCTGCATTCGTTAGCATCTAC 57.281 39.130 0.00 0.00 40.42 2.59
1104 1105 3.838795 CCAATCAGGCCGCATTTTT 57.161 47.368 0.00 0.00 0.00 1.94
1143 1144 3.733344 TAACATCAGAGCCGCGCCC 62.733 63.158 0.00 0.00 0.00 6.13
1237 1238 8.213812 CACAAGTTAATAGCCAAAAACAATTCG 58.786 33.333 0.00 0.00 0.00 3.34
1298 1299 1.271597 ACTTGAGTCCATCCAGGCAAC 60.272 52.381 0.00 0.00 37.29 4.17
1301 1302 1.457346 CAACTTGAGTCCATCCAGGC 58.543 55.000 0.00 0.00 37.29 4.85
1325 1326 4.727507 TCCTCAATCTCAGTGTTAGCTC 57.272 45.455 0.00 0.00 0.00 4.09
1372 1373 4.908730 GTGTTTGCCACAAACAACAAAAAG 59.091 37.500 23.18 0.00 43.92 2.27
1447 1448 8.055986 GCAAAAGCACAACAAGAACTTAATAAC 58.944 33.333 0.00 0.00 0.00 1.89
1496 1497 2.615869 GACCATCAGAGACTGCTTCAC 58.384 52.381 0.00 0.00 0.00 3.18
1564 1566 1.807142 GTTACTCAGCCTTGGTGCTTC 59.193 52.381 0.00 0.00 40.32 3.86
1565 1567 1.421646 AGTTACTCAGCCTTGGTGCTT 59.578 47.619 0.00 0.00 40.32 3.91
1567 1569 1.160137 CAGTTACTCAGCCTTGGTGC 58.840 55.000 0.00 0.00 0.00 5.01
1632 1637 1.265635 CTAGAGAGCAGATCCCGAACG 59.734 57.143 0.00 0.00 0.00 3.95
1637 1642 1.146982 AGGGACTAGAGAGCAGATCCC 59.853 57.143 0.00 0.00 45.34 3.85
1655 1660 1.798813 GGTGAAACGCTCAACTACAGG 59.201 52.381 0.00 0.00 38.87 4.00
1661 1666 1.852280 GCAAAAGGTGAAACGCTCAAC 59.148 47.619 0.00 0.00 42.69 3.18
1662 1667 1.748493 AGCAAAAGGTGAAACGCTCAA 59.252 42.857 0.00 0.00 38.12 3.02
1706 1713 5.643777 AGTTTACTTGATTTCCCATCAGACG 59.356 40.000 0.00 0.00 0.00 4.18
1711 1718 6.183360 GCCAGTAGTTTACTTGATTTCCCATC 60.183 42.308 0.00 0.00 36.76 3.51
1779 1786 3.076621 TGTGACAGCCTGAATGAATGAC 58.923 45.455 0.00 0.00 0.00 3.06
1790 1797 9.099071 AGATAATAATCTATCTTGTGACAGCCT 57.901 33.333 0.00 0.00 40.82 4.58
1797 1804 9.650539 CCAGGACAGATAATAATCTATCTTGTG 57.349 37.037 5.44 0.00 39.76 3.33
1798 1805 9.607333 TCCAGGACAGATAATAATCTATCTTGT 57.393 33.333 5.44 0.00 39.76 3.16
1818 1825 1.555075 GTGGTTGTAGATGCTCCAGGA 59.445 52.381 0.00 0.00 0.00 3.86
1819 1826 1.278985 TGTGGTTGTAGATGCTCCAGG 59.721 52.381 0.00 0.00 0.00 4.45
1820 1827 2.027745 AGTGTGGTTGTAGATGCTCCAG 60.028 50.000 0.00 0.00 0.00 3.86
1821 1828 1.977854 AGTGTGGTTGTAGATGCTCCA 59.022 47.619 0.00 0.00 0.00 3.86
1822 1829 2.770164 AGTGTGGTTGTAGATGCTCC 57.230 50.000 0.00 0.00 0.00 4.70
1823 1830 4.184629 CCTAAGTGTGGTTGTAGATGCTC 58.815 47.826 0.00 0.00 0.00 4.26
1824 1831 3.619979 GCCTAAGTGTGGTTGTAGATGCT 60.620 47.826 0.00 0.00 0.00 3.79
1825 1832 2.678336 GCCTAAGTGTGGTTGTAGATGC 59.322 50.000 0.00 0.00 0.00 3.91
1826 1833 3.937814 TGCCTAAGTGTGGTTGTAGATG 58.062 45.455 0.00 0.00 0.00 2.90
1827 1834 4.634012 TTGCCTAAGTGTGGTTGTAGAT 57.366 40.909 0.00 0.00 0.00 1.98
1828 1835 4.425180 TTTGCCTAAGTGTGGTTGTAGA 57.575 40.909 0.00 0.00 0.00 2.59
1829 1836 4.142902 CGATTTGCCTAAGTGTGGTTGTAG 60.143 45.833 0.00 0.00 0.00 2.74
1830 1837 3.749088 CGATTTGCCTAAGTGTGGTTGTA 59.251 43.478 0.00 0.00 0.00 2.41
1831 1838 2.552315 CGATTTGCCTAAGTGTGGTTGT 59.448 45.455 0.00 0.00 0.00 3.32
1832 1839 2.552315 ACGATTTGCCTAAGTGTGGTTG 59.448 45.455 0.00 0.00 0.00 3.77
1833 1840 2.812011 GACGATTTGCCTAAGTGTGGTT 59.188 45.455 0.00 0.00 0.00 3.67
1834 1841 2.423577 GACGATTTGCCTAAGTGTGGT 58.576 47.619 0.00 0.00 0.00 4.16
1835 1842 1.737793 GGACGATTTGCCTAAGTGTGG 59.262 52.381 0.00 0.00 0.00 4.17
1836 1843 1.737793 GGGACGATTTGCCTAAGTGTG 59.262 52.381 0.00 0.00 31.27 3.82
1837 1844 1.339727 GGGGACGATTTGCCTAAGTGT 60.340 52.381 0.00 0.00 35.51 3.55
1838 1845 1.065418 AGGGGACGATTTGCCTAAGTG 60.065 52.381 0.00 0.00 35.51 3.16
1839 1846 1.209747 GAGGGGACGATTTGCCTAAGT 59.790 52.381 0.00 0.00 35.51 2.24
1840 1847 1.209504 TGAGGGGACGATTTGCCTAAG 59.790 52.381 0.00 0.00 35.51 2.18
1841 1848 1.281419 TGAGGGGACGATTTGCCTAA 58.719 50.000 0.00 0.00 35.51 2.69
1842 1849 1.507140 ATGAGGGGACGATTTGCCTA 58.493 50.000 0.00 0.00 35.51 3.93
1843 1850 1.507140 TATGAGGGGACGATTTGCCT 58.493 50.000 0.00 0.00 35.51 4.75
1844 1851 2.154462 CATATGAGGGGACGATTTGCC 58.846 52.381 0.00 0.00 33.96 4.52
1845 1852 1.537202 GCATATGAGGGGACGATTTGC 59.463 52.381 6.97 0.00 0.00 3.68
1846 1853 2.154462 GGCATATGAGGGGACGATTTG 58.846 52.381 6.97 0.00 0.00 2.32
1847 1854 1.073923 GGGCATATGAGGGGACGATTT 59.926 52.381 6.97 0.00 0.00 2.17
1848 1855 0.693049 GGGCATATGAGGGGACGATT 59.307 55.000 6.97 0.00 0.00 3.34
1849 1856 0.178891 AGGGCATATGAGGGGACGAT 60.179 55.000 6.97 0.00 0.00 3.73
1850 1857 0.399949 AAGGGCATATGAGGGGACGA 60.400 55.000 6.97 0.00 0.00 4.20
1851 1858 0.035458 GAAGGGCATATGAGGGGACG 59.965 60.000 6.97 0.00 0.00 4.79
1852 1859 1.140312 TGAAGGGCATATGAGGGGAC 58.860 55.000 6.97 0.00 0.00 4.46
1935 1942 7.103641 TGAACTTTCTCCATAGCTCGTTAATT 58.896 34.615 0.00 0.00 0.00 1.40
1936 1943 6.640518 TGAACTTTCTCCATAGCTCGTTAAT 58.359 36.000 0.00 0.00 0.00 1.40
1938 1945 5.654603 TGAACTTTCTCCATAGCTCGTTA 57.345 39.130 0.00 0.00 0.00 3.18
1939 1946 4.537135 TGAACTTTCTCCATAGCTCGTT 57.463 40.909 0.00 0.00 0.00 3.85
1956 2031 1.133025 CAAGGGCGACAATGGATGAAC 59.867 52.381 0.00 0.00 0.00 3.18
1968 2043 2.281484 GGACAAGTGCAAGGGCGA 60.281 61.111 0.00 0.00 45.35 5.54
2003 2078 5.335269 CGGTCTCTATATCATCTTCAAGCGT 60.335 44.000 0.00 0.00 0.00 5.07
2027 2102 1.425428 CGCAAAACAGATCCGCCTC 59.575 57.895 0.00 0.00 0.00 4.70
2034 2109 0.962356 CCTCCAGGCGCAAAACAGAT 60.962 55.000 10.83 0.00 0.00 2.90
2047 2122 1.215382 TCGCATTCGACACCTCCAG 59.785 57.895 0.00 0.00 40.21 3.86
2064 2139 3.741856 GGAAGAAAGAGAAGAACGGTGTC 59.258 47.826 0.00 0.00 0.00 3.67
2173 2248 4.442706 AGGATATTCGTGCTTGTAACCTG 58.557 43.478 0.00 0.00 0.00 4.00
2186 2261 3.134458 GACAAGGCCAGAAGGATATTCG 58.866 50.000 5.01 0.00 36.89 3.34
2188 2263 2.158755 CGGACAAGGCCAGAAGGATATT 60.159 50.000 5.01 0.00 36.89 1.28
2244 2320 3.512516 GAGATGGCCAAGGTGCGC 61.513 66.667 10.96 0.00 0.00 6.09
2248 2324 0.033796 CATGGTGAGATGGCCAAGGT 60.034 55.000 10.96 0.00 38.38 3.50
2254 2330 2.123428 GTGCCCATGGTGAGATGGC 61.123 63.158 11.73 5.43 41.59 4.40
2257 2333 0.038166 AAACGTGCCCATGGTGAGAT 59.962 50.000 11.73 0.00 0.00 2.75
2280 2356 3.219281 GGTGTTAGGCTTCAAGTTTGGA 58.781 45.455 0.00 0.00 0.00 3.53
2288 2364 1.373435 CCCACGGTGTTAGGCTTCA 59.627 57.895 7.45 0.00 0.00 3.02
2304 2380 2.364186 CATTGGGCCCTTGTCCCC 60.364 66.667 25.70 0.00 43.24 4.81
2308 2384 2.284112 CCTGCATTGGGCCCTTGT 60.284 61.111 25.70 5.74 43.89 3.16
2309 2385 3.078836 CCCTGCATTGGGCCCTTG 61.079 66.667 25.70 21.23 43.89 3.61
2324 2400 1.148273 TGTGTGTCTGAGCAACCCC 59.852 57.895 0.00 0.00 0.00 4.95
2330 2406 1.506493 CTTGAGGTGTGTGTCTGAGC 58.494 55.000 0.00 0.00 0.00 4.26
2364 2467 2.631696 GATTGAACGGCGGTGATGCG 62.632 60.000 13.24 0.00 35.06 4.73
2365 2468 1.062525 GATTGAACGGCGGTGATGC 59.937 57.895 13.24 0.00 0.00 3.91
2376 2479 2.369394 CCAGTGGGGCTTAGATTGAAC 58.631 52.381 0.00 0.00 0.00 3.18
2403 2506 4.520846 CATGGCTTCGTTCGCGCC 62.521 66.667 0.00 14.72 44.02 6.53
2404 2507 3.788766 ACATGGCTTCGTTCGCGC 61.789 61.111 0.00 0.00 41.05 6.86
2410 2513 0.108585 ACTCAACCACATGGCTTCGT 59.891 50.000 0.00 0.00 39.32 3.85
2436 2539 2.801342 GCTAGCTTTCTGTCGATCCCAG 60.801 54.545 7.70 0.00 0.00 4.45
2440 2543 2.586258 TGGCTAGCTTTCTGTCGATC 57.414 50.000 15.72 0.00 0.00 3.69
2442 2545 2.831685 TTTGGCTAGCTTTCTGTCGA 57.168 45.000 15.72 0.00 0.00 4.20
2447 2550 4.039603 ACTTGGATTTGGCTAGCTTTCT 57.960 40.909 15.72 0.00 0.00 2.52
2454 2557 3.134574 ACGTCAACTTGGATTTGGCTA 57.865 42.857 0.00 0.00 0.00 3.93
2457 2560 4.062293 TGAGTACGTCAACTTGGATTTGG 58.938 43.478 0.00 0.00 29.64 3.28
2460 2563 4.866508 TCTGAGTACGTCAACTTGGATT 57.133 40.909 0.00 0.00 33.60 3.01
2478 2581 2.283298 ACATTGTAGGCAGCGAATCTG 58.717 47.619 0.00 0.00 45.62 2.90
2480 2583 2.677836 TCAACATTGTAGGCAGCGAATC 59.322 45.455 0.00 0.00 0.00 2.52
2492 2595 5.867903 TCTTGGGTCATTTTCAACATTGT 57.132 34.783 0.00 0.00 0.00 2.71
2499 2602 4.111255 TGGTGATCTTGGGTCATTTTCA 57.889 40.909 0.00 0.00 0.00 2.69
2510 2613 3.057033 CCAGCTCCTTTTTGGTGATCTTG 60.057 47.826 0.00 0.00 37.07 3.02
2523 2626 2.674380 CGCTTTGCCCAGCTCCTT 60.674 61.111 2.98 0.00 37.68 3.36
2539 2642 1.302511 CCACCCCACTTTCAGTCCG 60.303 63.158 0.00 0.00 0.00 4.79
2543 2646 0.326264 CCTCTCCACCCCACTTTCAG 59.674 60.000 0.00 0.00 0.00 3.02
2546 2649 1.360393 TTGCCTCTCCACCCCACTTT 61.360 55.000 0.00 0.00 0.00 2.66
2550 2653 0.486879 ATTTTTGCCTCTCCACCCCA 59.513 50.000 0.00 0.00 0.00 4.96
2560 2663 1.139439 AACCCTTGCCATTTTTGCCT 58.861 45.000 0.00 0.00 0.00 4.75



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

AutoCloner maintained by Alex Coulton.