Multiple sequence alignment - TraesCS1D01G100900

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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 TraesCS1D01G100900 chr1D 100.000 3306 0 0 1 3306 88245442 88242137 0.000000e+00 6106.0
1 TraesCS1D01G100900 chr1D 97.941 874 14 4 720 1591 88282992 88282121 0.000000e+00 1511.0
2 TraesCS1D01G100900 chr1D 92.281 868 37 14 1594 2459 88282001 88281162 0.000000e+00 1205.0
3 TraesCS1D01G100900 chr1D 94.650 729 32 5 865 1590 88208045 88208769 0.000000e+00 1123.0
4 TraesCS1D01G100900 chr1D 94.176 704 21 9 905 1590 87903421 87904122 0.000000e+00 1055.0
5 TraesCS1D01G100900 chr1D 90.452 597 37 10 1589 2179 87904237 87904819 0.000000e+00 769.0
6 TraesCS1D01G100900 chr1D 89.537 497 33 10 1688 2179 88215120 88215602 2.180000e-171 612.0
7 TraesCS1D01G100900 chr1D 88.000 225 14 9 2237 2459 88215804 88216017 1.520000e-63 254.0
8 TraesCS1D01G100900 chr1D 83.444 151 13 6 2766 2913 88216304 88216445 2.680000e-26 130.0
9 TraesCS1D01G100900 chr1D 84.444 135 6 11 2237 2369 87905022 87905143 5.800000e-23 119.0
10 TraesCS1D01G100900 chr1A 91.369 1738 83 19 1589 3306 84796119 84794429 0.000000e+00 2316.0
11 TraesCS1D01G100900 chr1A 94.697 660 23 10 934 1591 85006766 85006117 0.000000e+00 1014.0
12 TraesCS1D01G100900 chr1A 91.723 737 39 13 859 1591 84796951 84796233 0.000000e+00 1003.0
13 TraesCS1D01G100900 chr1A 87.879 792 39 11 1589 2370 85006003 85005259 0.000000e+00 878.0
14 TraesCS1D01G100900 chr1A 89.950 597 40 9 1589 2179 84621522 84622104 0.000000e+00 752.0
15 TraesCS1D01G100900 chr1A 89.782 597 41 9 1589 2179 84484325 84484907 0.000000e+00 747.0
16 TraesCS1D01G100900 chr1A 90.741 216 20 0 2244 2459 84622323 84622538 4.170000e-74 289.0
17 TraesCS1D01G100900 chr1A 90.278 216 21 0 2244 2459 84485125 84485340 1.940000e-72 283.0
18 TraesCS1D01G100900 chr1A 93.750 48 2 1 2570 2617 84485526 84485572 1.650000e-08 71.3
19 TraesCS1D01G100900 chr1A 93.750 48 2 1 2570 2617 84622727 84622773 1.650000e-08 71.3
20 TraesCS1D01G100900 chr4D 91.046 1731 95 23 1589 3306 464797412 464795729 0.000000e+00 2283.0
21 TraesCS1D01G100900 chr4D 90.450 733 32 10 859 1590 464798222 464797527 0.000000e+00 931.0
22 TraesCS1D01G100900 chr1B 98.363 733 12 0 859 1591 142134777 142134045 0.000000e+00 1288.0
23 TraesCS1D01G100900 chr1B 92.639 883 33 8 2456 3306 142133063 142132181 0.000000e+00 1242.0
24 TraesCS1D01G100900 chr1B 92.081 745 40 12 859 1590 142037219 142037957 0.000000e+00 1031.0
25 TraesCS1D01G100900 chr1B 91.935 744 43 11 860 1590 141844709 141845448 0.000000e+00 1026.0
26 TraesCS1D01G100900 chr1B 91.141 745 47 12 859 1590 142093479 142094217 0.000000e+00 992.0
27 TraesCS1D01G100900 chr1B 91.817 721 30 10 1589 2301 142133931 142133232 0.000000e+00 977.0
28 TraesCS1D01G100900 chr1B 87.093 891 48 22 1589 2459 141845563 141846406 0.000000e+00 946.0
29 TraesCS1D01G100900 chr1B 90.066 604 36 15 1589 2179 142038072 142038664 0.000000e+00 761.0
30 TraesCS1D01G100900 chr1B 94.661 487 21 2 1589 2074 142094332 142094814 0.000000e+00 750.0
31 TraesCS1D01G100900 chr1B 82.051 117 12 5 2765 2881 142103366 142103473 1.260000e-14 91.6
32 TraesCS1D01G100900 chr1B 96.000 50 2 0 861 910 142036330 142036379 7.600000e-12 82.4
33 TraesCS1D01G100900 chr3B 88.945 597 46 9 1589 2179 535705028 535704446 0.000000e+00 719.0
34 TraesCS1D01G100900 chr3B 90.244 82 7 1 2245 2325 535704347 535704266 4.510000e-19 106.0


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 TraesCS1D01G100900 chr1D 88242137 88245442 3305 True 6106.000000 6106 100.000000 1 3306 1 chr1D.!!$R1 3305
1 TraesCS1D01G100900 chr1D 88281162 88282992 1830 True 1358.000000 1511 95.111000 720 2459 2 chr1D.!!$R2 1739
2 TraesCS1D01G100900 chr1D 88208045 88208769 724 False 1123.000000 1123 94.650000 865 1590 1 chr1D.!!$F1 725
3 TraesCS1D01G100900 chr1D 87903421 87905143 1722 False 647.666667 1055 89.690667 905 2369 3 chr1D.!!$F2 1464
4 TraesCS1D01G100900 chr1D 88215120 88216445 1325 False 332.000000 612 86.993667 1688 2913 3 chr1D.!!$F3 1225
5 TraesCS1D01G100900 chr1A 84794429 84796951 2522 True 1659.500000 2316 91.546000 859 3306 2 chr1A.!!$R1 2447
6 TraesCS1D01G100900 chr1A 85005259 85006766 1507 True 946.000000 1014 91.288000 934 2370 2 chr1A.!!$R2 1436
7 TraesCS1D01G100900 chr1A 84621522 84622773 1251 False 370.766667 752 91.480333 1589 2617 3 chr1A.!!$F2 1028
8 TraesCS1D01G100900 chr1A 84484325 84485572 1247 False 367.100000 747 91.270000 1589 2617 3 chr1A.!!$F1 1028
9 TraesCS1D01G100900 chr4D 464795729 464798222 2493 True 1607.000000 2283 90.748000 859 3306 2 chr4D.!!$R1 2447
10 TraesCS1D01G100900 chr1B 142132181 142134777 2596 True 1169.000000 1288 94.273000 859 3306 3 chr1B.!!$R1 2447
11 TraesCS1D01G100900 chr1B 141844709 141846406 1697 False 986.000000 1026 89.514000 860 2459 2 chr1B.!!$F2 1599
12 TraesCS1D01G100900 chr1B 142093479 142094814 1335 False 871.000000 992 92.901000 859 2074 2 chr1B.!!$F4 1215
13 TraesCS1D01G100900 chr1B 142036330 142038664 2334 False 624.800000 1031 92.715667 859 2179 3 chr1B.!!$F3 1320
14 TraesCS1D01G100900 chr3B 535704266 535705028 762 True 412.500000 719 89.594500 1589 2325 2 chr3B.!!$R1 736

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
150 151 0.246086 CTCTTGCAGTCTTCGGAGCT 59.754 55.0 0.00 0.0 0.00 4.09 F
233 234 0.320771 TTCCTCGAAGCACCTGAAGC 60.321 55.0 0.00 0.0 0.00 3.86 F
235 236 0.392193 CCTCGAAGCACCTGAAGCAT 60.392 55.0 0.00 0.0 0.00 3.79 F
240 241 0.394899 AAGCACCTGAAGCATAGCCC 60.395 55.0 0.00 0.0 0.00 5.19 F
717 718 0.470341 GGGGAAGGCTCTCACCATAC 59.530 60.0 11.58 0.0 38.91 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1972 0.332632 CTCCAAATCCAGCTTCCCCA 59.667 55.000 0.00 0.0 0.00 4.96 R
2186 2401 2.907458 ACTTGGCCTTTAGCTCCATT 57.093 45.000 3.32 0.0 43.05 3.16 R
2191 2406 3.295973 TGTTCAAACTTGGCCTTTAGCT 58.704 40.909 3.32 0.0 43.05 3.32 R
2192 2407 3.726291 TGTTCAAACTTGGCCTTTAGC 57.274 42.857 3.32 0.0 42.60 3.09 R
2418 2817 0.163146 GTGCGTTGCTCTAAACCGAC 59.837 55.000 0.00 0.0 0.00 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
22 23 4.344865 GGGGGCAGCAAGGACGAA 62.345 66.667 0.00 0.00 0.00 3.85
23 24 2.747855 GGGGCAGCAAGGACGAAG 60.748 66.667 0.00 0.00 0.00 3.79
25 26 1.078143 GGGCAGCAAGGACGAAGAT 60.078 57.895 0.00 0.00 0.00 2.40
27 28 1.092345 GGCAGCAAGGACGAAGATCC 61.092 60.000 0.00 0.00 39.28 3.36
28 29 1.092345 GCAGCAAGGACGAAGATCCC 61.092 60.000 0.00 0.00 39.91 3.85
29 30 0.462759 CAGCAAGGACGAAGATCCCC 60.463 60.000 0.00 0.00 39.91 4.81
30 31 1.153147 GCAAGGACGAAGATCCCCC 60.153 63.158 0.00 0.00 39.91 5.40
31 32 1.144057 CAAGGACGAAGATCCCCCG 59.856 63.158 0.00 0.00 39.91 5.73
33 34 4.237207 GGACGAAGATCCCCCGCC 62.237 72.222 0.00 0.00 31.94 6.13
34 35 4.237207 GACGAAGATCCCCCGCCC 62.237 72.222 0.00 0.00 0.00 6.13
70 71 3.423154 GAGGGCGCTTGGTCGTTG 61.423 66.667 7.64 0.00 0.00 4.10
82 83 4.680237 TCGTTGCGAGCCACCCTG 62.680 66.667 0.00 0.00 0.00 4.45
104 105 4.379243 CAACCTGGCGTCGGAGCT 62.379 66.667 0.00 0.00 37.29 4.09
105 106 4.070552 AACCTGGCGTCGGAGCTC 62.071 66.667 4.71 4.71 37.29 4.09
108 109 4.200283 CTGGCGTCGGAGCTCCTC 62.200 72.222 29.73 20.42 37.29 3.71
117 118 4.144727 GAGCTCCTCCTCCGGGGA 62.145 72.222 0.37 7.28 42.77 4.81
118 119 4.467107 AGCTCCTCCTCCGGGGAC 62.467 72.222 0.37 0.00 39.58 4.46
143 144 2.759795 GGGGCCTCTTGCAGTCTT 59.240 61.111 0.84 0.00 43.89 3.01
145 146 1.743252 GGGCCTCTTGCAGTCTTCG 60.743 63.158 0.84 0.00 43.89 3.79
146 147 1.743252 GGCCTCTTGCAGTCTTCGG 60.743 63.158 0.00 0.00 43.89 4.30
148 149 0.739112 GCCTCTTGCAGTCTTCGGAG 60.739 60.000 0.00 0.00 40.77 4.63
149 150 0.739112 CCTCTTGCAGTCTTCGGAGC 60.739 60.000 0.00 0.00 0.00 4.70
150 151 0.246086 CTCTTGCAGTCTTCGGAGCT 59.754 55.000 0.00 0.00 0.00 4.09
151 152 1.474478 CTCTTGCAGTCTTCGGAGCTA 59.526 52.381 0.00 0.00 0.00 3.32
153 154 2.159184 TCTTGCAGTCTTCGGAGCTATG 60.159 50.000 0.00 0.00 0.00 2.23
154 155 1.474330 TGCAGTCTTCGGAGCTATGA 58.526 50.000 0.00 0.00 0.00 2.15
155 156 1.135139 TGCAGTCTTCGGAGCTATGAC 59.865 52.381 0.00 0.00 0.00 3.06
156 157 1.537135 GCAGTCTTCGGAGCTATGACC 60.537 57.143 0.00 0.00 0.00 4.02
157 158 2.028130 CAGTCTTCGGAGCTATGACCT 58.972 52.381 0.00 0.00 0.00 3.85
158 159 2.028130 AGTCTTCGGAGCTATGACCTG 58.972 52.381 0.00 0.00 0.00 4.00
159 160 2.025155 GTCTTCGGAGCTATGACCTGA 58.975 52.381 0.00 0.00 0.00 3.86
160 161 2.025155 TCTTCGGAGCTATGACCTGAC 58.975 52.381 0.00 0.00 0.00 3.51
162 163 0.755698 TCGGAGCTATGACCTGACCC 60.756 60.000 0.00 0.00 0.00 4.46
163 164 1.742768 GGAGCTATGACCTGACCCG 59.257 63.158 0.00 0.00 0.00 5.28
166 167 2.731571 GCTATGACCTGACCCGCCA 61.732 63.158 0.00 0.00 0.00 5.69
167 168 1.144057 CTATGACCTGACCCGCCAC 59.856 63.158 0.00 0.00 0.00 5.01
168 169 1.610967 TATGACCTGACCCGCCACA 60.611 57.895 0.00 0.00 0.00 4.17
169 170 1.195442 TATGACCTGACCCGCCACAA 61.195 55.000 0.00 0.00 0.00 3.33
170 171 2.668550 GACCTGACCCGCCACAAC 60.669 66.667 0.00 0.00 0.00 3.32
171 172 4.619227 ACCTGACCCGCCACAACG 62.619 66.667 0.00 0.00 0.00 4.10
181 182 2.738521 CCACAACGGAGGCAGACG 60.739 66.667 0.00 0.00 36.56 4.18
182 183 2.338620 CACAACGGAGGCAGACGA 59.661 61.111 0.00 0.00 0.00 4.20
183 184 1.079819 CACAACGGAGGCAGACGAT 60.080 57.895 0.00 0.00 0.00 3.73
184 185 1.079819 ACAACGGAGGCAGACGATG 60.080 57.895 0.00 3.80 38.58 3.84
185 186 1.079819 CAACGGAGGCAGACGATGT 60.080 57.895 0.00 0.00 0.00 3.06
186 187 1.078759 CAACGGAGGCAGACGATGTC 61.079 60.000 0.00 0.00 0.00 3.06
187 188 2.278206 CGGAGGCAGACGATGTCG 60.278 66.667 0.11 0.11 39.07 4.35
199 200 1.882198 CGATGTCGTTTGTGCAATCC 58.118 50.000 0.00 0.00 34.11 3.01
200 201 1.465689 CGATGTCGTTTGTGCAATCCC 60.466 52.381 0.00 0.00 34.11 3.85
201 202 0.521291 ATGTCGTTTGTGCAATCCCG 59.479 50.000 0.00 0.00 0.00 5.14
202 203 1.442017 GTCGTTTGTGCAATCCCGC 60.442 57.895 0.00 0.00 0.00 6.13
203 204 2.126502 CGTTTGTGCAATCCCGCC 60.127 61.111 0.00 0.00 0.00 6.13
204 205 2.126502 GTTTGTGCAATCCCGCCG 60.127 61.111 0.00 0.00 0.00 6.46
205 206 3.369400 TTTGTGCAATCCCGCCGG 61.369 61.111 0.00 0.00 0.00 6.13
206 207 3.851897 TTTGTGCAATCCCGCCGGA 62.852 57.895 5.05 0.00 44.33 5.14
207 208 3.851897 TTGTGCAATCCCGCCGGAA 62.852 57.895 5.05 0.00 43.10 4.30
210 211 3.508840 GCAATCCCGCCGGAAGTG 61.509 66.667 5.05 0.00 43.10 3.16
211 212 2.824041 CAATCCCGCCGGAAGTGG 60.824 66.667 5.05 0.00 43.10 4.00
223 224 3.145228 GAAGTGGCCTTCCTCGAAG 57.855 57.895 3.32 0.00 41.09 3.79
224 225 1.003233 AAGTGGCCTTCCTCGAAGC 60.003 57.895 3.32 0.00 38.24 3.86
226 227 2.035442 GTGGCCTTCCTCGAAGCAC 61.035 63.158 3.32 0.00 38.24 4.40
227 228 2.436824 GGCCTTCCTCGAAGCACC 60.437 66.667 0.00 0.00 38.24 5.01
229 230 1.743252 GCCTTCCTCGAAGCACCTG 60.743 63.158 0.00 0.00 38.24 4.00
230 231 1.975327 CCTTCCTCGAAGCACCTGA 59.025 57.895 0.00 0.00 38.24 3.86
231 232 0.321671 CCTTCCTCGAAGCACCTGAA 59.678 55.000 0.00 0.00 38.24 3.02
232 233 1.674221 CCTTCCTCGAAGCACCTGAAG 60.674 57.143 0.00 0.00 38.24 3.02
233 234 0.320771 TTCCTCGAAGCACCTGAAGC 60.321 55.000 0.00 0.00 0.00 3.86
235 236 0.392193 CCTCGAAGCACCTGAAGCAT 60.392 55.000 0.00 0.00 0.00 3.79
237 238 2.200067 CTCGAAGCACCTGAAGCATAG 58.800 52.381 0.00 0.00 0.00 2.23
238 239 0.654683 CGAAGCACCTGAAGCATAGC 59.345 55.000 0.00 0.00 0.00 2.97
239 240 1.020437 GAAGCACCTGAAGCATAGCC 58.980 55.000 0.00 0.00 0.00 3.93
240 241 0.394899 AAGCACCTGAAGCATAGCCC 60.395 55.000 0.00 0.00 0.00 5.19
241 242 1.825622 GCACCTGAAGCATAGCCCC 60.826 63.158 0.00 0.00 0.00 5.80
242 243 1.524621 CACCTGAAGCATAGCCCCG 60.525 63.158 0.00 0.00 0.00 5.73
243 244 2.592861 CCTGAAGCATAGCCCCGC 60.593 66.667 0.00 0.00 0.00 6.13
244 245 2.592861 CTGAAGCATAGCCCCGCC 60.593 66.667 0.00 0.00 0.00 6.13
245 246 3.405093 CTGAAGCATAGCCCCGCCA 62.405 63.158 0.00 0.00 0.00 5.69
247 248 1.968540 GAAGCATAGCCCCGCCATC 60.969 63.158 0.00 0.00 0.00 3.51
248 249 2.403132 GAAGCATAGCCCCGCCATCT 62.403 60.000 0.00 0.00 0.00 2.90
249 250 2.359230 GCATAGCCCCGCCATCTC 60.359 66.667 0.00 0.00 0.00 2.75
250 251 2.348998 CATAGCCCCGCCATCTCC 59.651 66.667 0.00 0.00 0.00 3.71
251 252 3.314331 ATAGCCCCGCCATCTCCG 61.314 66.667 0.00 0.00 0.00 4.63
258 259 4.530857 CGCCATCTCCGGTGGGAC 62.531 72.222 11.30 0.00 37.43 4.46
259 260 4.176752 GCCATCTCCGGTGGGACC 62.177 72.222 11.30 0.00 37.43 4.46
261 262 2.435693 CCATCTCCGGTGGGACCTC 61.436 68.421 0.00 0.00 37.43 3.85
262 263 2.041819 ATCTCCGGTGGGACCTCC 60.042 66.667 0.00 0.00 37.43 4.30
272 273 2.122769 GGACCTCCCTCCTAGGCC 60.123 72.222 2.96 0.00 37.67 5.19
273 274 2.522193 GACCTCCCTCCTAGGCCG 60.522 72.222 2.96 0.00 37.67 6.13
274 275 4.862823 ACCTCCCTCCTAGGCCGC 62.863 72.222 2.96 0.00 37.67 6.53
276 277 3.541713 CTCCCTCCTAGGCCGCAC 61.542 72.222 2.96 0.00 32.73 5.34
280 281 3.905678 CTCCTAGGCCGCACCGAG 61.906 72.222 2.96 0.00 46.52 4.63
283 284 4.208686 CTAGGCCGCACCGAGGTC 62.209 72.222 0.00 0.00 46.52 3.85
287 288 4.500116 GCCGCACCGAGGTCTCTC 62.500 72.222 0.00 0.00 36.69 3.20
288 289 3.827898 CCGCACCGAGGTCTCTCC 61.828 72.222 0.00 0.00 36.70 3.71
290 291 2.418910 CGCACCGAGGTCTCTCCAT 61.419 63.158 0.00 0.00 39.02 3.41
291 292 1.142748 GCACCGAGGTCTCTCCATG 59.857 63.158 0.00 0.00 39.02 3.66
293 294 1.381872 ACCGAGGTCTCTCCATGGG 60.382 63.158 13.02 2.57 37.16 4.00
294 295 2.801631 CCGAGGTCTCTCCATGGGC 61.802 68.421 13.02 0.00 39.02 5.36
295 296 2.060383 CGAGGTCTCTCCATGGGCA 61.060 63.158 13.02 0.00 39.02 5.36
296 297 1.828768 GAGGTCTCTCCATGGGCAG 59.171 63.158 13.02 8.22 39.02 4.85
297 298 2.191641 GGTCTCTCCATGGGCAGC 59.808 66.667 13.02 4.63 35.97 5.25
298 299 2.202987 GTCTCTCCATGGGCAGCG 60.203 66.667 13.02 0.00 0.00 5.18
299 300 3.473647 TCTCTCCATGGGCAGCGG 61.474 66.667 13.02 0.00 0.00 5.52
300 301 3.473647 CTCTCCATGGGCAGCGGA 61.474 66.667 13.02 0.62 0.00 5.54
301 302 3.746949 CTCTCCATGGGCAGCGGAC 62.747 68.421 13.02 0.00 0.00 4.79
302 303 4.864334 CTCCATGGGCAGCGGACC 62.864 72.222 13.02 0.00 45.44 4.46
315 316 3.732849 GGACCCCCTGAGGCCAAG 61.733 72.222 5.01 1.10 0.00 3.61
316 317 2.610859 GACCCCCTGAGGCCAAGA 60.611 66.667 5.01 0.00 0.00 3.02
317 318 2.936032 ACCCCCTGAGGCCAAGAC 60.936 66.667 5.01 0.00 0.00 3.01
318 319 4.101448 CCCCCTGAGGCCAAGACG 62.101 72.222 5.01 0.00 0.00 4.18
320 321 2.266055 CCCTGAGGCCAAGACGAC 59.734 66.667 5.01 0.00 0.00 4.34
321 322 2.125912 CCTGAGGCCAAGACGACG 60.126 66.667 5.01 0.00 0.00 5.12
322 323 2.811317 CTGAGGCCAAGACGACGC 60.811 66.667 5.01 0.00 0.00 5.19
323 324 4.373116 TGAGGCCAAGACGACGCC 62.373 66.667 5.01 0.00 43.35 5.68
327 328 4.373116 GCCAAGACGACGCCTCCA 62.373 66.667 0.00 0.00 0.00 3.86
328 329 2.432628 CCAAGACGACGCCTCCAC 60.433 66.667 0.00 0.00 0.00 4.02
329 330 2.338620 CAAGACGACGCCTCCACA 59.661 61.111 0.00 0.00 0.00 4.17
330 331 1.734477 CAAGACGACGCCTCCACAG 60.734 63.158 0.00 0.00 0.00 3.66
332 333 4.057428 GACGACGCCTCCACAGCT 62.057 66.667 0.00 0.00 0.00 4.24
333 334 3.973267 GACGACGCCTCCACAGCTC 62.973 68.421 0.00 0.00 0.00 4.09
334 335 4.803426 CGACGCCTCCACAGCTCC 62.803 72.222 0.00 0.00 0.00 4.70
335 336 3.386237 GACGCCTCCACAGCTCCT 61.386 66.667 0.00 0.00 0.00 3.69
336 337 2.925170 ACGCCTCCACAGCTCCTT 60.925 61.111 0.00 0.00 0.00 3.36
337 338 2.125350 CGCCTCCACAGCTCCTTC 60.125 66.667 0.00 0.00 0.00 3.46
338 339 2.270527 GCCTCCACAGCTCCTTCC 59.729 66.667 0.00 0.00 0.00 3.46
339 340 2.297129 GCCTCCACAGCTCCTTCCT 61.297 63.158 0.00 0.00 0.00 3.36
340 341 1.904032 CCTCCACAGCTCCTTCCTC 59.096 63.158 0.00 0.00 0.00 3.71
341 342 1.515020 CTCCACAGCTCCTTCCTCG 59.485 63.158 0.00 0.00 0.00 4.63
343 344 1.216710 CCACAGCTCCTTCCTCGTC 59.783 63.158 0.00 0.00 0.00 4.20
344 345 1.153939 CACAGCTCCTTCCTCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
345 346 2.344203 ACAGCTCCTTCCTCGTCGG 61.344 63.158 0.00 0.00 0.00 4.79
346 347 3.453679 AGCTCCTTCCTCGTCGGC 61.454 66.667 0.00 0.00 0.00 5.54
347 348 4.856607 GCTCCTTCCTCGTCGGCG 62.857 72.222 1.15 1.15 39.92 6.46
348 349 4.194720 CTCCTTCCTCGTCGGCGG 62.195 72.222 10.62 0.00 38.89 6.13
392 393 4.329545 GAGCAGCGTCCCCAACCA 62.330 66.667 0.00 0.00 0.00 3.67
393 394 4.643387 AGCAGCGTCCCCAACCAC 62.643 66.667 0.00 0.00 0.00 4.16
429 430 4.570663 CGCCGGACCCATCGTCTC 62.571 72.222 5.05 0.00 41.64 3.36
430 431 4.222847 GCCGGACCCATCGTCTCC 62.223 72.222 5.05 0.00 41.64 3.71
431 432 3.900892 CCGGACCCATCGTCTCCG 61.901 72.222 0.00 0.00 45.49 4.63
442 443 3.213402 GTCTCCGAGCCCTCCGAG 61.213 72.222 7.15 7.15 36.65 4.63
448 449 3.591835 GAGCCCTCCGAGCTCGAG 61.592 72.222 36.59 27.61 46.58 4.04
451 452 2.440430 CCCTCCGAGCTCGAGGAA 60.440 66.667 35.81 21.21 43.02 3.36
453 454 1.435515 CCTCCGAGCTCGAGGAAAG 59.564 63.158 36.59 22.21 43.02 2.62
455 456 2.202810 CCGAGCTCGAGGAAAGGC 60.203 66.667 36.59 0.00 43.02 4.35
456 457 2.202810 CGAGCTCGAGGAAAGGCC 60.203 66.667 32.06 0.00 43.02 5.19
457 458 2.188207 GAGCTCGAGGAAAGGCCC 59.812 66.667 15.58 0.00 37.37 5.80
458 459 2.607750 AGCTCGAGGAAAGGCCCA 60.608 61.111 15.58 0.00 37.37 5.36
459 460 2.124942 GCTCGAGGAAAGGCCCAG 60.125 66.667 15.58 0.00 37.37 4.45
460 461 2.586792 CTCGAGGAAAGGCCCAGG 59.413 66.667 3.91 0.00 37.37 4.45
506 507 3.766691 GGCGGTAGGCGAAGGTGA 61.767 66.667 0.00 0.00 44.92 4.02
507 508 2.508663 GCGGTAGGCGAAGGTGAC 60.509 66.667 0.00 0.00 0.00 3.67
508 509 2.183555 CGGTAGGCGAAGGTGACC 59.816 66.667 0.00 0.00 0.00 4.02
509 510 2.183555 GGTAGGCGAAGGTGACCG 59.816 66.667 0.00 0.00 0.00 4.79
510 511 2.345760 GGTAGGCGAAGGTGACCGA 61.346 63.158 0.00 0.00 0.00 4.69
512 513 0.735287 GTAGGCGAAGGTGACCGAAC 60.735 60.000 0.00 0.00 0.00 3.95
513 514 2.203972 TAGGCGAAGGTGACCGAACG 62.204 60.000 12.04 12.04 0.00 3.95
514 515 2.049802 GCGAAGGTGACCGAACGA 60.050 61.111 18.23 0.00 0.00 3.85
515 516 2.087009 GCGAAGGTGACCGAACGAG 61.087 63.158 18.23 1.36 0.00 4.18
516 517 1.443872 CGAAGGTGACCGAACGAGG 60.444 63.158 11.22 0.00 37.30 4.63
517 518 1.080025 GAAGGTGACCGAACGAGGG 60.080 63.158 0.00 0.00 35.02 4.30
519 520 3.692406 GGTGACCGAACGAGGGCT 61.692 66.667 0.00 0.00 40.90 5.19
520 521 2.432628 GTGACCGAACGAGGGCTG 60.433 66.667 0.00 0.00 40.90 4.85
522 523 3.379445 GACCGAACGAGGGCTGGA 61.379 66.667 0.00 0.00 36.04 3.86
523 524 3.644399 GACCGAACGAGGGCTGGAC 62.644 68.421 0.00 0.00 36.04 4.02
524 525 4.796231 CCGAACGAGGGCTGGACG 62.796 72.222 0.00 0.00 0.00 4.79
569 570 3.866582 GGCGGGGAGACATGGGAG 61.867 72.222 0.00 0.00 0.00 4.30
570 571 2.764128 GCGGGGAGACATGGGAGA 60.764 66.667 0.00 0.00 0.00 3.71
571 572 2.801631 GCGGGGAGACATGGGAGAG 61.802 68.421 0.00 0.00 0.00 3.20
573 574 1.383803 GGGGAGACATGGGAGAGCT 60.384 63.158 0.00 0.00 0.00 4.09
574 575 1.694133 GGGGAGACATGGGAGAGCTG 61.694 65.000 0.00 0.00 0.00 4.24
575 576 1.694133 GGGAGACATGGGAGAGCTGG 61.694 65.000 0.00 0.00 0.00 4.85
576 577 1.694133 GGAGACATGGGAGAGCTGGG 61.694 65.000 0.00 0.00 0.00 4.45
577 578 1.692042 AGACATGGGAGAGCTGGGG 60.692 63.158 0.00 0.00 0.00 4.96
620 621 4.736896 GTCGTGGCCGGAGTGACC 62.737 72.222 5.05 0.00 33.95 4.02
663 664 3.112709 GTCAGAGTGGCGAACGGC 61.113 66.667 13.50 13.50 42.51 5.68
664 665 4.717629 TCAGAGTGGCGAACGGCG 62.718 66.667 4.80 4.80 44.92 6.46
681 682 3.421386 GGGGAAGGGGAAGGGCTC 61.421 72.222 0.00 0.00 0.00 4.70
682 683 2.286502 GGGAAGGGGAAGGGCTCT 60.287 66.667 0.00 0.00 0.00 4.09
683 684 1.931180 GGGAAGGGGAAGGGCTCTT 60.931 63.158 0.00 0.00 35.62 2.85
684 685 1.304617 GGAAGGGGAAGGGCTCTTG 59.695 63.158 1.79 0.00 32.52 3.02
685 686 1.379176 GAAGGGGAAGGGCTCTTGC 60.379 63.158 9.77 9.77 40.10 4.01
686 687 3.273788 AAGGGGAAGGGCTCTTGCG 62.274 63.158 12.11 0.00 41.49 4.85
693 694 2.817396 GGGCTCTTGCGCTCTCAC 60.817 66.667 9.73 0.00 46.81 3.51
694 695 3.184683 GGCTCTTGCGCTCTCACG 61.185 66.667 9.73 0.00 40.82 4.35
703 704 3.760035 GCTCTCACGCTCGGGGAA 61.760 66.667 0.00 0.00 0.00 3.97
704 705 2.492090 CTCTCACGCTCGGGGAAG 59.508 66.667 0.00 0.00 0.00 3.46
705 706 3.068691 TCTCACGCTCGGGGAAGG 61.069 66.667 0.00 0.00 0.00 3.46
706 707 4.821589 CTCACGCTCGGGGAAGGC 62.822 72.222 0.00 0.00 0.00 4.35
708 709 4.821589 CACGCTCGGGGAAGGCTC 62.822 72.222 0.00 0.00 0.00 4.70
710 711 4.214327 CGCTCGGGGAAGGCTCTC 62.214 72.222 0.00 0.00 0.00 3.20
712 713 2.896443 CTCGGGGAAGGCTCTCAC 59.104 66.667 0.00 0.00 0.00 3.51
713 714 2.683933 TCGGGGAAGGCTCTCACC 60.684 66.667 7.63 7.63 35.31 4.02
714 715 3.003173 CGGGGAAGGCTCTCACCA 61.003 66.667 15.26 0.00 39.03 4.17
715 716 2.370445 CGGGGAAGGCTCTCACCAT 61.370 63.158 15.26 0.00 39.03 3.55
716 717 1.048724 CGGGGAAGGCTCTCACCATA 61.049 60.000 15.26 0.00 39.03 2.74
717 718 0.470341 GGGGAAGGCTCTCACCATAC 59.530 60.000 11.58 0.00 38.91 2.39
718 719 0.470341 GGGAAGGCTCTCACCATACC 59.530 60.000 0.00 0.00 0.00 2.73
725 726 1.067212 GCTCTCACCATACCGACGAAT 59.933 52.381 0.00 0.00 0.00 3.34
1269 1319 0.990374 AGCTTGAGGTGCTTGGAGAT 59.010 50.000 0.00 0.00 37.52 2.75
1462 1512 2.779951 CTTGGATGTGGCGACGGACA 62.780 60.000 0.00 0.00 0.00 4.02
1766 1933 1.675720 GAGACAGAGGAGGAGCTGCC 61.676 65.000 0.00 0.00 35.57 4.85
1805 1972 3.291584 TGCGAGACCAGATCACTTCTAT 58.708 45.455 0.00 0.00 31.77 1.98
2186 2401 9.119418 ACTGTAGCATGCAAATTACATTACATA 57.881 29.630 21.98 0.00 0.00 2.29
2191 2406 8.640651 AGCATGCAAATTACATTACATAATGGA 58.359 29.630 21.98 4.69 45.54 3.41
2192 2407 8.918658 GCATGCAAATTACATTACATAATGGAG 58.081 33.333 14.21 0.00 45.54 3.86
2193 2408 8.918658 CATGCAAATTACATTACATAATGGAGC 58.081 33.333 14.53 7.46 45.54 4.70
2194 2409 8.236585 TGCAAATTACATTACATAATGGAGCT 57.763 30.769 14.53 0.00 45.54 4.09
2195 2410 9.348476 TGCAAATTACATTACATAATGGAGCTA 57.652 29.630 14.53 0.00 45.54 3.32
2256 2655 2.489722 GGCCAAGTTTCTGAATCTGGTC 59.510 50.000 0.00 7.79 0.00 4.02
2355 2754 3.710209 AGATGTGAAGTCCAAGGAAGG 57.290 47.619 0.00 0.00 0.00 3.46
2376 2775 6.899393 AGGAAAACAAATGCTGAATGTCTA 57.101 33.333 0.00 0.00 0.00 2.59
2381 2780 6.882610 AACAAATGCTGAATGTCTAAGACA 57.117 33.333 0.00 0.00 46.90 3.41
2418 2817 6.561614 TCTACTACTAGCAACTTGGATTTCG 58.438 40.000 0.00 0.00 0.00 3.46
2425 2824 2.287368 GCAACTTGGATTTCGTCGGTTT 60.287 45.455 0.00 0.00 0.00 3.27
2518 3004 7.016072 ACAATACAATGAAAAAGGGAACATCCA 59.984 33.333 0.00 0.00 38.64 3.41
2633 3119 2.094803 TCACACAAACACAAAGTGCCTG 60.095 45.455 0.00 0.00 36.98 4.85
2667 3153 3.192422 AGATTAGGCTCGATCAATCCTCG 59.808 47.826 11.83 0.00 37.47 4.63
3044 3565 2.360475 GCAGGCGGCTTCTTCCTT 60.360 61.111 9.66 0.00 40.25 3.36
3053 3574 1.908483 CTTCTTCCTTCCTCCGGGG 59.092 63.158 0.00 0.00 0.00 5.73
3161 3691 4.498520 CTCACCGGCGACTGCGAT 62.499 66.667 9.30 0.00 44.10 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.543067 ATCTTCGTCCTTGCTGCCCC 62.543 60.000 0.00 0.00 0.00 5.80
7 8 1.078143 ATCTTCGTCCTTGCTGCCC 60.078 57.895 0.00 0.00 0.00 5.36
11 12 1.627297 GGGGGATCTTCGTCCTTGCT 61.627 60.000 0.00 0.00 38.38 3.91
12 13 1.153147 GGGGGATCTTCGTCCTTGC 60.153 63.158 0.00 0.00 38.38 4.01
13 14 1.144057 CGGGGGATCTTCGTCCTTG 59.856 63.158 0.00 0.00 38.38 3.61
14 15 2.732619 GCGGGGGATCTTCGTCCTT 61.733 63.158 0.00 0.00 38.38 3.36
15 16 3.155167 GCGGGGGATCTTCGTCCT 61.155 66.667 0.00 0.00 38.38 3.85
53 54 3.423154 CAACGACCAAGCGCCCTC 61.423 66.667 2.29 0.00 33.86 4.30
60 61 2.664851 TGGCTCGCAACGACCAAG 60.665 61.111 8.25 0.00 35.45 3.61
61 62 2.970324 GTGGCTCGCAACGACCAA 60.970 61.111 11.13 0.00 38.19 3.67
62 63 4.980805 GGTGGCTCGCAACGACCA 62.981 66.667 0.00 7.05 35.78 4.02
64 65 4.681978 AGGGTGGCTCGCAACGAC 62.682 66.667 6.40 0.00 0.00 4.34
65 66 4.680237 CAGGGTGGCTCGCAACGA 62.680 66.667 6.40 0.00 0.00 3.85
88 89 4.070552 GAGCTCCGACGCCAGGTT 62.071 66.667 0.87 0.00 0.00 3.50
91 92 4.200283 GAGGAGCTCCGACGCCAG 62.200 72.222 26.95 0.00 42.08 4.85
119 120 4.785453 CAAGAGGCCCCGCAGTCC 62.785 72.222 0.00 0.00 0.00 3.85
125 126 3.259633 AAGACTGCAAGAGGCCCCG 62.260 63.158 0.00 0.00 43.89 5.73
126 127 1.377856 GAAGACTGCAAGAGGCCCC 60.378 63.158 0.00 0.00 43.89 5.80
127 128 1.743252 CGAAGACTGCAAGAGGCCC 60.743 63.158 0.00 0.00 43.89 5.80
128 129 1.743252 CCGAAGACTGCAAGAGGCC 60.743 63.158 0.00 0.00 43.89 5.19
129 130 0.739112 CTCCGAAGACTGCAAGAGGC 60.739 60.000 0.00 0.00 45.13 4.70
130 131 0.739112 GCTCCGAAGACTGCAAGAGG 60.739 60.000 0.00 0.00 37.43 3.69
131 132 0.246086 AGCTCCGAAGACTGCAAGAG 59.754 55.000 0.00 0.00 37.43 2.85
132 133 1.545841 TAGCTCCGAAGACTGCAAGA 58.454 50.000 0.00 0.00 37.43 3.02
135 136 1.135139 GTCATAGCTCCGAAGACTGCA 59.865 52.381 0.00 0.00 0.00 4.41
137 138 2.028130 AGGTCATAGCTCCGAAGACTG 58.972 52.381 0.00 0.00 0.00 3.51
138 139 2.028130 CAGGTCATAGCTCCGAAGACT 58.972 52.381 0.00 0.00 0.00 3.24
139 140 2.025155 TCAGGTCATAGCTCCGAAGAC 58.975 52.381 0.00 0.00 0.00 3.01
140 141 2.025155 GTCAGGTCATAGCTCCGAAGA 58.975 52.381 0.00 0.00 0.00 2.87
141 142 1.067821 GGTCAGGTCATAGCTCCGAAG 59.932 57.143 0.00 0.00 0.00 3.79
143 144 0.755698 GGGTCAGGTCATAGCTCCGA 60.756 60.000 0.00 0.00 0.00 4.55
145 146 1.742768 CGGGTCAGGTCATAGCTCC 59.257 63.158 0.00 0.00 0.00 4.70
146 147 1.068250 GCGGGTCAGGTCATAGCTC 59.932 63.158 0.00 0.00 0.00 4.09
148 149 2.109181 GGCGGGTCAGGTCATAGC 59.891 66.667 0.00 0.00 0.00 2.97
149 150 1.144057 GTGGCGGGTCAGGTCATAG 59.856 63.158 0.00 0.00 0.00 2.23
150 151 1.195442 TTGTGGCGGGTCAGGTCATA 61.195 55.000 0.00 0.00 0.00 2.15
151 152 2.525124 TTGTGGCGGGTCAGGTCAT 61.525 57.895 0.00 0.00 0.00 3.06
153 154 2.668550 GTTGTGGCGGGTCAGGTC 60.669 66.667 0.00 0.00 0.00 3.85
154 155 4.619227 CGTTGTGGCGGGTCAGGT 62.619 66.667 0.00 0.00 0.00 4.00
166 167 1.079819 CATCGTCTGCCTCCGTTGT 60.080 57.895 0.00 0.00 0.00 3.32
167 168 1.078759 GACATCGTCTGCCTCCGTTG 61.079 60.000 0.00 0.00 0.00 4.10
168 169 1.215647 GACATCGTCTGCCTCCGTT 59.784 57.895 0.00 0.00 0.00 4.44
169 170 2.885861 GACATCGTCTGCCTCCGT 59.114 61.111 0.00 0.00 0.00 4.69
170 171 2.278206 CGACATCGTCTGCCTCCG 60.278 66.667 0.00 0.00 34.11 4.63
180 181 1.465689 GGGATTGCACAAACGACATCG 60.466 52.381 0.00 0.00 46.33 3.84
181 182 1.465689 CGGGATTGCACAAACGACATC 60.466 52.381 0.00 0.00 0.00 3.06
182 183 0.521291 CGGGATTGCACAAACGACAT 59.479 50.000 0.00 0.00 0.00 3.06
183 184 1.945522 CGGGATTGCACAAACGACA 59.054 52.632 0.00 0.00 0.00 4.35
184 185 1.442017 GCGGGATTGCACAAACGAC 60.442 57.895 8.87 0.00 34.15 4.34
185 186 2.622011 GGCGGGATTGCACAAACGA 61.622 57.895 8.87 0.00 36.28 3.85
186 187 2.126502 GGCGGGATTGCACAAACG 60.127 61.111 0.00 0.00 36.28 3.60
187 188 2.126502 CGGCGGGATTGCACAAAC 60.127 61.111 0.00 0.00 36.28 2.93
188 189 3.369400 CCGGCGGGATTGCACAAA 61.369 61.111 20.56 0.00 36.28 2.83
191 192 3.508840 CTTCCGGCGGGATTGCAC 61.509 66.667 27.98 0.00 43.41 4.57
193 194 3.508840 CACTTCCGGCGGGATTGC 61.509 66.667 27.98 0.00 43.41 3.56
206 207 1.003233 GCTTCGAGGAAGGCCACTT 60.003 57.895 5.01 0.00 39.76 3.16
207 208 2.217038 TGCTTCGAGGAAGGCCACT 61.217 57.895 5.01 0.00 39.76 4.00
210 211 2.436824 GGTGCTTCGAGGAAGGCC 60.437 66.667 0.00 0.00 39.76 5.19
211 212 1.743252 CAGGTGCTTCGAGGAAGGC 60.743 63.158 0.00 0.00 39.76 4.35
212 213 0.321671 TTCAGGTGCTTCGAGGAAGG 59.678 55.000 0.00 0.00 39.76 3.46
213 214 1.719600 CTTCAGGTGCTTCGAGGAAG 58.280 55.000 0.00 1.06 42.03 3.46
215 216 1.293498 GCTTCAGGTGCTTCGAGGA 59.707 57.895 0.00 0.00 0.00 3.71
216 217 0.392193 ATGCTTCAGGTGCTTCGAGG 60.392 55.000 0.00 0.00 0.00 4.63
217 218 2.200067 CTATGCTTCAGGTGCTTCGAG 58.800 52.381 0.00 0.00 0.00 4.04
219 220 0.654683 GCTATGCTTCAGGTGCTTCG 59.345 55.000 0.00 0.00 0.00 3.79
220 221 1.020437 GGCTATGCTTCAGGTGCTTC 58.980 55.000 0.00 0.00 0.00 3.86
221 222 0.394899 GGGCTATGCTTCAGGTGCTT 60.395 55.000 0.00 0.00 0.00 3.91
223 224 1.825622 GGGGCTATGCTTCAGGTGC 60.826 63.158 0.00 0.00 0.00 5.01
224 225 1.524621 CGGGGCTATGCTTCAGGTG 60.525 63.158 0.00 0.00 0.00 4.00
226 227 2.592861 GCGGGGCTATGCTTCAGG 60.593 66.667 0.00 0.00 0.00 3.86
227 228 2.592861 GGCGGGGCTATGCTTCAG 60.593 66.667 0.00 0.00 0.00 3.02
229 230 1.968540 GATGGCGGGGCTATGCTTC 60.969 63.158 0.00 0.00 27.76 3.86
230 231 2.113986 GATGGCGGGGCTATGCTT 59.886 61.111 0.00 0.00 27.76 3.91
231 232 2.851102 AGATGGCGGGGCTATGCT 60.851 61.111 0.00 0.00 27.76 3.79
232 233 2.359230 GAGATGGCGGGGCTATGC 60.359 66.667 0.00 0.00 27.76 3.14
233 234 2.348998 GGAGATGGCGGGGCTATG 59.651 66.667 0.00 0.00 27.76 2.23
241 242 4.530857 GTCCCACCGGAGATGGCG 62.531 72.222 9.46 0.00 39.51 5.69
242 243 4.176752 GGTCCCACCGGAGATGGC 62.177 72.222 9.46 0.00 39.51 4.40
243 244 2.365635 AGGTCCCACCGGAGATGG 60.366 66.667 9.46 5.28 44.90 3.51
244 245 2.435693 GGAGGTCCCACCGGAGATG 61.436 68.421 9.46 0.00 44.90 2.90
245 246 2.041819 GGAGGTCCCACCGGAGAT 60.042 66.667 9.46 0.00 44.90 2.75
255 256 2.122769 GGCCTAGGAGGGAGGTCC 60.123 72.222 14.75 0.00 35.37 4.46
256 257 2.522193 CGGCCTAGGAGGGAGGTC 60.522 72.222 14.75 0.00 35.37 3.85
257 258 4.862823 GCGGCCTAGGAGGGAGGT 62.863 72.222 14.75 0.00 35.37 3.85
258 259 4.860881 TGCGGCCTAGGAGGGAGG 62.861 72.222 14.75 0.00 35.37 4.30
259 260 3.541713 GTGCGGCCTAGGAGGGAG 61.542 72.222 14.75 0.00 35.37 4.30
263 264 3.905678 CTCGGTGCGGCCTAGGAG 61.906 72.222 14.75 6.64 34.25 3.69
266 267 4.208686 GACCTCGGTGCGGCCTAG 62.209 72.222 0.00 0.00 34.25 3.02
267 268 4.753662 AGACCTCGGTGCGGCCTA 62.754 66.667 0.00 0.00 34.25 3.93
271 272 3.827898 GGAGAGACCTCGGTGCGG 61.828 72.222 0.00 0.00 40.33 5.69
272 273 2.418910 ATGGAGAGACCTCGGTGCG 61.419 63.158 0.00 0.00 40.33 5.34
273 274 1.142748 CATGGAGAGACCTCGGTGC 59.857 63.158 0.00 0.00 40.33 5.01
274 275 1.680522 CCCATGGAGAGACCTCGGTG 61.681 65.000 15.22 0.00 40.33 4.94
276 277 2.801631 GCCCATGGAGAGACCTCGG 61.802 68.421 15.22 0.00 40.33 4.63
277 278 2.025767 CTGCCCATGGAGAGACCTCG 62.026 65.000 15.22 0.00 40.33 4.63
278 279 1.828768 CTGCCCATGGAGAGACCTC 59.171 63.158 15.22 0.00 39.86 3.85
280 281 2.191641 GCTGCCCATGGAGAGACC 59.808 66.667 15.22 0.00 39.54 3.85
281 282 2.202987 CGCTGCCCATGGAGAGAC 60.203 66.667 15.22 4.15 0.00 3.36
283 284 3.473647 TCCGCTGCCCATGGAGAG 61.474 66.667 15.22 9.52 0.00 3.20
285 286 4.864334 GGTCCGCTGCCCATGGAG 62.864 72.222 15.22 4.42 31.04 3.86
298 299 3.732849 CTTGGCCTCAGGGGGTCC 61.733 72.222 3.32 0.00 35.12 4.46
299 300 2.610859 TCTTGGCCTCAGGGGGTC 60.611 66.667 3.32 0.00 35.12 4.46
300 301 2.936032 GTCTTGGCCTCAGGGGGT 60.936 66.667 3.32 0.00 35.12 4.95
301 302 4.101448 CGTCTTGGCCTCAGGGGG 62.101 72.222 3.32 0.00 35.12 5.40
302 303 3.003173 TCGTCTTGGCCTCAGGGG 61.003 66.667 3.32 0.00 38.36 4.79
303 304 2.266055 GTCGTCTTGGCCTCAGGG 59.734 66.667 3.32 0.00 0.00 4.45
304 305 2.125912 CGTCGTCTTGGCCTCAGG 60.126 66.667 3.32 0.00 0.00 3.86
305 306 2.811317 GCGTCGTCTTGGCCTCAG 60.811 66.667 3.32 0.00 0.00 3.35
310 311 4.373116 TGGAGGCGTCGTCTTGGC 62.373 66.667 0.00 0.00 0.00 4.52
311 312 2.432628 GTGGAGGCGTCGTCTTGG 60.433 66.667 0.00 0.00 0.00 3.61
312 313 1.734477 CTGTGGAGGCGTCGTCTTG 60.734 63.158 0.00 0.00 0.00 3.02
313 314 2.651361 CTGTGGAGGCGTCGTCTT 59.349 61.111 0.00 0.00 0.00 3.01
314 315 4.057428 GCTGTGGAGGCGTCGTCT 62.057 66.667 0.00 0.00 0.00 4.18
315 316 3.973267 GAGCTGTGGAGGCGTCGTC 62.973 68.421 0.00 0.00 34.52 4.20
316 317 4.057428 GAGCTGTGGAGGCGTCGT 62.057 66.667 0.00 0.00 34.52 4.34
317 318 4.803426 GGAGCTGTGGAGGCGTCG 62.803 72.222 0.00 0.00 34.52 5.12
318 319 2.844072 GAAGGAGCTGTGGAGGCGTC 62.844 65.000 0.00 0.00 34.52 5.19
320 321 2.125350 GAAGGAGCTGTGGAGGCG 60.125 66.667 0.00 0.00 34.52 5.52
321 322 2.250741 GAGGAAGGAGCTGTGGAGGC 62.251 65.000 0.00 0.00 0.00 4.70
322 323 1.904032 GAGGAAGGAGCTGTGGAGG 59.096 63.158 0.00 0.00 0.00 4.30
323 324 1.254284 ACGAGGAAGGAGCTGTGGAG 61.254 60.000 0.00 0.00 0.00 3.86
324 325 1.228894 ACGAGGAAGGAGCTGTGGA 60.229 57.895 0.00 0.00 0.00 4.02
325 326 1.216710 GACGAGGAAGGAGCTGTGG 59.783 63.158 0.00 0.00 0.00 4.17
326 327 1.153939 CGACGAGGAAGGAGCTGTG 60.154 63.158 0.00 0.00 0.00 3.66
327 328 2.344203 CCGACGAGGAAGGAGCTGT 61.344 63.158 0.00 0.00 45.00 4.40
328 329 2.492090 CCGACGAGGAAGGAGCTG 59.508 66.667 0.00 0.00 45.00 4.24
329 330 3.453679 GCCGACGAGGAAGGAGCT 61.454 66.667 0.00 0.00 45.00 4.09
330 331 4.856607 CGCCGACGAGGAAGGAGC 62.857 72.222 0.00 0.00 45.00 4.70
375 376 4.329545 TGGTTGGGGACGCTGCTC 62.330 66.667 0.00 0.00 0.00 4.26
376 377 4.643387 GTGGTTGGGGACGCTGCT 62.643 66.667 0.00 0.00 0.00 4.24
434 435 2.010582 CTTTCCTCGAGCTCGGAGGG 62.011 65.000 34.21 30.36 40.29 4.30
435 436 1.435515 CTTTCCTCGAGCTCGGAGG 59.564 63.158 31.86 31.86 40.29 4.30
436 437 1.435515 CCTTTCCTCGAGCTCGGAG 59.564 63.158 33.98 26.68 40.29 4.63
438 439 2.202810 GCCTTTCCTCGAGCTCGG 60.203 66.667 33.98 23.77 40.29 4.63
440 441 2.188207 GGGCCTTTCCTCGAGCTC 59.812 66.667 6.99 2.73 34.39 4.09
442 443 2.124942 CTGGGCCTTTCCTCGAGC 60.125 66.667 6.99 0.00 34.39 5.03
443 444 2.586792 CCTGGGCCTTTCCTCGAG 59.413 66.667 5.13 5.13 34.39 4.04
444 445 3.717294 GCCTGGGCCTTTCCTCGA 61.717 66.667 4.53 0.00 34.56 4.04
489 490 3.766691 TCACCTTCGCCTACCGCC 61.767 66.667 0.00 0.00 36.73 6.13
490 491 2.508663 GTCACCTTCGCCTACCGC 60.509 66.667 0.00 0.00 36.73 5.68
491 492 2.183555 GGTCACCTTCGCCTACCG 59.816 66.667 0.00 0.00 38.61 4.02
493 494 0.735287 GTTCGGTCACCTTCGCCTAC 60.735 60.000 0.00 0.00 0.00 3.18
494 495 1.588082 GTTCGGTCACCTTCGCCTA 59.412 57.895 0.00 0.00 0.00 3.93
495 496 2.342648 GTTCGGTCACCTTCGCCT 59.657 61.111 0.00 0.00 0.00 5.52
496 497 3.110178 CGTTCGGTCACCTTCGCC 61.110 66.667 0.00 0.00 0.00 5.54
497 498 2.049802 TCGTTCGGTCACCTTCGC 60.050 61.111 0.00 0.00 0.00 4.70
498 499 1.443872 CCTCGTTCGGTCACCTTCG 60.444 63.158 0.00 0.00 0.00 3.79
499 500 1.080025 CCCTCGTTCGGTCACCTTC 60.080 63.158 0.00 0.00 0.00 3.46
500 501 3.057337 CCCTCGTTCGGTCACCTT 58.943 61.111 0.00 0.00 0.00 3.50
501 502 3.692406 GCCCTCGTTCGGTCACCT 61.692 66.667 0.00 0.00 0.00 4.00
502 503 3.692406 AGCCCTCGTTCGGTCACC 61.692 66.667 0.00 0.00 0.00 4.02
503 504 2.432628 CAGCCCTCGTTCGGTCAC 60.433 66.667 0.00 0.00 0.00 3.67
505 506 3.379445 TCCAGCCCTCGTTCGGTC 61.379 66.667 0.00 0.00 0.00 4.79
506 507 3.692406 GTCCAGCCCTCGTTCGGT 61.692 66.667 0.00 0.00 0.00 4.69
507 508 4.796231 CGTCCAGCCCTCGTTCGG 62.796 72.222 0.00 0.00 0.00 4.30
552 553 3.866582 CTCCCATGTCTCCCCGCC 61.867 72.222 0.00 0.00 0.00 6.13
553 554 2.764128 TCTCCCATGTCTCCCCGC 60.764 66.667 0.00 0.00 0.00 6.13
554 555 2.801631 GCTCTCCCATGTCTCCCCG 61.802 68.421 0.00 0.00 0.00 5.73
555 556 1.383803 AGCTCTCCCATGTCTCCCC 60.384 63.158 0.00 0.00 0.00 4.81
556 557 1.694133 CCAGCTCTCCCATGTCTCCC 61.694 65.000 0.00 0.00 0.00 4.30
557 558 1.694133 CCCAGCTCTCCCATGTCTCC 61.694 65.000 0.00 0.00 0.00 3.71
558 559 1.694133 CCCCAGCTCTCCCATGTCTC 61.694 65.000 0.00 0.00 0.00 3.36
559 560 1.692042 CCCCAGCTCTCCCATGTCT 60.692 63.158 0.00 0.00 0.00 3.41
560 561 2.750657 CCCCCAGCTCTCCCATGTC 61.751 68.421 0.00 0.00 0.00 3.06
561 562 2.693864 CCCCCAGCTCTCCCATGT 60.694 66.667 0.00 0.00 0.00 3.21
603 604 4.736896 GGTCACTCCGGCCACGAC 62.737 72.222 2.24 0.05 44.60 4.34
643 644 3.112709 GTTCGCCACTCTGACGGC 61.113 66.667 3.72 3.72 45.28 5.68
644 645 2.805353 CGTTCGCCACTCTGACGG 60.805 66.667 0.00 0.00 0.00 4.79
645 646 2.805353 CCGTTCGCCACTCTGACG 60.805 66.667 0.00 0.00 0.00 4.35
646 647 3.112709 GCCGTTCGCCACTCTGAC 61.113 66.667 0.00 0.00 0.00 3.51
664 665 3.421386 GAGCCCTTCCCCTTCCCC 61.421 72.222 0.00 0.00 0.00 4.81
665 666 1.931180 AAGAGCCCTTCCCCTTCCC 60.931 63.158 0.00 0.00 0.00 3.97
666 667 1.304617 CAAGAGCCCTTCCCCTTCC 59.695 63.158 0.00 0.00 0.00 3.46
667 668 1.379176 GCAAGAGCCCTTCCCCTTC 60.379 63.158 0.00 0.00 33.58 3.46
668 669 2.766660 GCAAGAGCCCTTCCCCTT 59.233 61.111 0.00 0.00 33.58 3.95
669 670 3.721706 CGCAAGAGCCCTTCCCCT 61.722 66.667 0.00 0.00 43.02 4.79
671 672 4.416738 AGCGCAAGAGCCCTTCCC 62.417 66.667 11.47 0.00 43.02 3.97
672 673 2.821810 GAGCGCAAGAGCCCTTCC 60.822 66.667 11.47 0.00 43.02 3.46
674 675 2.267324 GAGAGCGCAAGAGCCCTT 59.733 61.111 11.47 0.00 43.02 3.95
676 677 2.817396 GTGAGAGCGCAAGAGCCC 60.817 66.667 11.47 0.00 43.02 5.19
686 687 3.708220 CTTCCCCGAGCGTGAGAGC 62.708 68.421 0.00 0.00 37.41 4.09
687 688 2.492090 CTTCCCCGAGCGTGAGAG 59.508 66.667 0.00 0.00 0.00 3.20
688 689 3.068691 CCTTCCCCGAGCGTGAGA 61.069 66.667 0.00 0.00 0.00 3.27
689 690 4.821589 GCCTTCCCCGAGCGTGAG 62.822 72.222 0.00 0.00 0.00 3.51
691 692 4.821589 GAGCCTTCCCCGAGCGTG 62.822 72.222 0.00 0.00 0.00 5.34
693 694 4.214327 GAGAGCCTTCCCCGAGCG 62.214 72.222 0.00 0.00 0.00 5.03
694 695 3.077556 TGAGAGCCTTCCCCGAGC 61.078 66.667 0.00 0.00 0.00 5.03
695 696 2.726351 GGTGAGAGCCTTCCCCGAG 61.726 68.421 0.00 0.00 0.00 4.63
696 697 2.683933 GGTGAGAGCCTTCCCCGA 60.684 66.667 0.00 0.00 0.00 5.14
697 698 1.048724 TATGGTGAGAGCCTTCCCCG 61.049 60.000 0.00 0.00 0.00 5.73
698 699 0.470341 GTATGGTGAGAGCCTTCCCC 59.530 60.000 0.00 0.00 0.00 4.81
699 700 0.470341 GGTATGGTGAGAGCCTTCCC 59.530 60.000 0.00 0.00 0.00 3.97
700 701 0.105039 CGGTATGGTGAGAGCCTTCC 59.895 60.000 0.00 0.00 0.00 3.46
701 702 1.112113 TCGGTATGGTGAGAGCCTTC 58.888 55.000 0.00 0.00 0.00 3.46
702 703 0.824759 GTCGGTATGGTGAGAGCCTT 59.175 55.000 0.00 0.00 0.00 4.35
703 704 1.384989 CGTCGGTATGGTGAGAGCCT 61.385 60.000 0.00 0.00 0.00 4.58
704 705 1.065928 CGTCGGTATGGTGAGAGCC 59.934 63.158 0.00 0.00 0.00 4.70
705 706 0.454600 TTCGTCGGTATGGTGAGAGC 59.545 55.000 0.00 0.00 0.00 4.09
706 707 2.602456 CGATTCGTCGGTATGGTGAGAG 60.602 54.545 0.00 0.00 0.00 3.20
708 709 1.332686 TCGATTCGTCGGTATGGTGAG 59.667 52.381 5.89 0.00 0.00 3.51
710 711 2.417339 ATCGATTCGTCGGTATGGTG 57.583 50.000 5.89 0.00 0.00 4.17
712 713 3.377439 TGAAATCGATTCGTCGGTATGG 58.623 45.455 11.83 0.00 41.18 2.74
713 714 5.005394 ACTTTGAAATCGATTCGTCGGTATG 59.995 40.000 11.83 2.13 41.18 2.39
714 715 5.005394 CACTTTGAAATCGATTCGTCGGTAT 59.995 40.000 11.83 0.00 41.18 2.73
715 716 4.325204 CACTTTGAAATCGATTCGTCGGTA 59.675 41.667 11.83 0.00 41.18 4.02
716 717 3.122948 CACTTTGAAATCGATTCGTCGGT 59.877 43.478 11.83 5.75 41.18 4.69
717 718 3.366724 TCACTTTGAAATCGATTCGTCGG 59.633 43.478 11.83 5.14 41.18 4.79
718 719 4.561959 TCACTTTGAAATCGATTCGTCG 57.438 40.909 11.83 2.34 41.18 5.12
725 726 5.682943 AAATCGGTTCACTTTGAAATCGA 57.317 34.783 14.01 14.01 43.17 3.59
1141 1191 3.771160 GGCCGTCGACATGACCCT 61.771 66.667 17.16 0.00 45.23 4.34
1462 1512 1.073923 GAACACATCCCCTGTCTTGGT 59.926 52.381 0.00 0.00 35.29 3.67
1766 1933 1.141881 AGCTTGTACATCTCGGCGG 59.858 57.895 7.21 0.00 0.00 6.13
1805 1972 0.332632 CTCCAAATCCAGCTTCCCCA 59.667 55.000 0.00 0.00 0.00 4.96
2051 2223 8.684973 ACTAACACAGTAATTAAGCTAACTCG 57.315 34.615 0.00 0.00 34.98 4.18
2094 2279 4.325501 CCATAAACTAAGTTTGGGCCCCTA 60.326 45.833 22.27 3.97 36.37 3.53
2186 2401 2.907458 ACTTGGCCTTTAGCTCCATT 57.093 45.000 3.32 0.00 43.05 3.16
2191 2406 3.295973 TGTTCAAACTTGGCCTTTAGCT 58.704 40.909 3.32 0.00 43.05 3.32
2192 2407 3.726291 TGTTCAAACTTGGCCTTTAGC 57.274 42.857 3.32 0.00 42.60 3.09
2193 2408 5.415221 TGTTTGTTCAAACTTGGCCTTTAG 58.585 37.500 22.90 0.94 33.95 1.85
2194 2409 5.407407 TGTTTGTTCAAACTTGGCCTTTA 57.593 34.783 22.90 3.54 33.95 1.85
2195 2410 4.278975 TGTTTGTTCAAACTTGGCCTTT 57.721 36.364 22.90 0.00 33.95 3.11
2196 2411 3.971245 TGTTTGTTCAAACTTGGCCTT 57.029 38.095 22.90 0.00 33.95 4.35
2256 2655 2.854777 CAGACCGTTCATAGAAAGCTCG 59.145 50.000 0.00 0.00 0.00 5.03
2330 2729 6.094603 CCTTCCTTGGACTTCACATCTATTTG 59.905 42.308 0.00 0.00 0.00 2.32
2355 2754 7.862372 TGTCTTAGACATTCAGCATTTGTTTTC 59.138 33.333 11.42 0.00 37.67 2.29
2418 2817 0.163146 GTGCGTTGCTCTAAACCGAC 59.837 55.000 0.00 0.00 0.00 4.79
2425 2824 3.371898 CAGATTTCATGTGCGTTGCTCTA 59.628 43.478 0.00 0.00 0.00 2.43
2493 2950 7.331687 GTGGATGTTCCCTTTTTCATTGTATTG 59.668 37.037 0.00 0.00 35.03 1.90
2518 3004 7.323420 GCCAAGAAAGCTTAGGATTTTTATGT 58.677 34.615 0.00 0.00 30.71 2.29
2667 3153 2.169842 GCAACTGCAGAGAAGAGGC 58.830 57.895 23.35 8.78 41.59 4.70
2714 3209 5.743117 AGGAGACCTGAAATGAAGATGAAG 58.257 41.667 0.00 0.00 29.57 3.02


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

AutoCloner maintained by Alex Coulton.