Multiple sequence alignment - TraesCS3B01G122700

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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 TraesCS3B01G122700 chr3B 100.000 2285 0 0 1 2285 92608614 92610898 0.000000e+00 4220
1 TraesCS3B01G122700 chr6B 94.000 1300 73 4 974 2269 625079603 625078305 0.000000e+00 1964
2 TraesCS3B01G122700 chr6B 93.502 1308 82 3 981 2285 472600977 472602284 0.000000e+00 1941
3 TraesCS3B01G122700 chr6B 94.624 558 23 6 415 972 625226913 625226363 0.000000e+00 857
4 TraesCS3B01G122700 chr6B 92.919 579 27 7 406 973 288471178 288471753 0.000000e+00 830
5 TraesCS3B01G122700 chr6B 92.573 579 31 5 406 973 130550459 130551036 0.000000e+00 821
6 TraesCS3B01G122700 chr6B 94.052 269 15 1 141 408 26600367 26600099 7.600000e-110 407
7 TraesCS3B01G122700 chr6B 94.309 123 7 0 1 123 144247043 144246921 3.000000e-44 189
8 TraesCS3B01G122700 chr6B 95.000 120 6 0 1 120 472597495 472597614 3.000000e-44 189
9 TraesCS3B01G122700 chr6B 83.429 175 20 7 2101 2271 625078349 625078180 1.090000e-33 154
10 TraesCS3B01G122700 chr2D 94.638 1175 55 8 981 2150 50977808 50976637 0.000000e+00 1814
11 TraesCS3B01G122700 chr2D 89.429 1173 97 17 986 2151 314479440 314478288 0.000000e+00 1454
12 TraesCS3B01G122700 chr2D 92.977 598 40 2 1690 2285 519141421 519142018 0.000000e+00 870
13 TraesCS3B01G122700 chr2D 95.833 120 4 1 1 120 591322927 591323045 2.320000e-45 193
14 TraesCS3B01G122700 chr2D 83.708 178 22 4 2098 2271 519141955 519142129 6.530000e-36 161
15 TraesCS3B01G122700 chr6D 94.669 1163 57 5 981 2139 62860309 62861470 0.000000e+00 1799
16 TraesCS3B01G122700 chr6D 94.845 1067 43 5 981 2045 59107455 59106399 0.000000e+00 1655
17 TraesCS3B01G122700 chr6D 96.667 120 4 0 1 120 364500421 364500540 1.380000e-47 200
18 TraesCS3B01G122700 chr6D 81.421 183 24 8 2094 2271 327603454 327603277 8.510000e-30 141
19 TraesCS3B01G122700 chr7B 93.463 1178 70 3 981 2151 2706138 2707315 0.000000e+00 1742
20 TraesCS3B01G122700 chr7B 92.708 576 30 5 409 973 673551444 673550870 0.000000e+00 821
21 TraesCS3B01G122700 chr7B 93.431 274 16 2 134 406 556547369 556547097 2.730000e-109 405
22 TraesCS3B01G122700 chr4A 91.633 1255 93 5 981 2233 695047722 695046478 0.000000e+00 1725
23 TraesCS3B01G122700 chr4A 96.667 120 4 0 1 120 447983126 447983245 1.380000e-47 200
24 TraesCS3B01G122700 chr2B 92.889 1111 73 4 1177 2285 82426784 82425678 0.000000e+00 1609
25 TraesCS3B01G122700 chr2B 84.492 187 20 7 2098 2279 82425741 82425559 2.330000e-40 176
26 TraesCS3B01G122700 chr3D 90.708 1173 91 11 981 2151 445803494 445804650 0.000000e+00 1546
27 TraesCS3B01G122700 chr3D 94.251 574 25 4 406 973 536281717 536282288 0.000000e+00 870
28 TraesCS3B01G122700 chr3D 95.000 120 6 0 1 120 415994825 415994944 3.000000e-44 189
29 TraesCS3B01G122700 chr1D 88.095 1176 111 17 981 2150 92055237 92056389 0.000000e+00 1369
30 TraesCS3B01G122700 chr7D 94.271 576 22 2 409 973 493558586 493558011 0.000000e+00 870
31 TraesCS3B01G122700 chr7D 95.122 123 6 0 1 123 514985978 514985856 6.440000e-46 195
32 TraesCS3B01G122700 chr7D 94.309 123 7 0 1 123 587998617 587998495 3.000000e-44 189
33 TraesCS3B01G122700 chr5B 93.892 573 29 2 406 973 551741483 551742054 0.000000e+00 859
34 TraesCS3B01G122700 chr5B 92.573 579 32 4 406 973 40986589 40987167 0.000000e+00 821
35 TraesCS3B01G122700 chr5B 93.525 278 16 2 134 410 383920893 383920617 1.630000e-111 412
36 TraesCS3B01G122700 chr1B 93.229 576 27 5 409 973 649195897 649195323 0.000000e+00 837
37 TraesCS3B01G122700 chr4D 93.841 276 15 2 134 408 444466612 444466338 4.540000e-112 414
38 TraesCS3B01G122700 chrUn 92.958 284 18 2 134 416 283498413 283498695 1.630000e-111 412
39 TraesCS3B01G122700 chrUn 92.958 284 18 2 134 416 283505064 283505346 1.630000e-111 412
40 TraesCS3B01G122700 chrUn 92.958 284 18 2 134 416 309805446 309805164 1.630000e-111 412
41 TraesCS3B01G122700 chr4B 94.030 268 15 1 143 409 511372079 511372346 2.730000e-109 405
42 TraesCS3B01G122700 chr5A 92.281 285 20 2 134 417 487399213 487398930 9.830000e-109 403
43 TraesCS3B01G122700 chr1A 96.581 117 4 0 4 120 372265836 372265952 6.440000e-46 195


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 TraesCS3B01G122700 chr3B 92608614 92610898 2284 False 4220.0 4220 100.0000 1 2285 1 chr3B.!!$F1 2284
1 TraesCS3B01G122700 chr6B 472597495 472602284 4789 False 1065.0 1941 94.2510 1 2285 2 chr6B.!!$F3 2284
2 TraesCS3B01G122700 chr6B 625078180 625079603 1423 True 1059.0 1964 88.7145 974 2271 2 chr6B.!!$R4 1297
3 TraesCS3B01G122700 chr6B 625226363 625226913 550 True 857.0 857 94.6240 415 972 1 chr6B.!!$R3 557
4 TraesCS3B01G122700 chr6B 288471178 288471753 575 False 830.0 830 92.9190 406 973 1 chr6B.!!$F2 567
5 TraesCS3B01G122700 chr6B 130550459 130551036 577 False 821.0 821 92.5730 406 973 1 chr6B.!!$F1 567
6 TraesCS3B01G122700 chr2D 50976637 50977808 1171 True 1814.0 1814 94.6380 981 2150 1 chr2D.!!$R1 1169
7 TraesCS3B01G122700 chr2D 314478288 314479440 1152 True 1454.0 1454 89.4290 986 2151 1 chr2D.!!$R2 1165
8 TraesCS3B01G122700 chr2D 519141421 519142129 708 False 515.5 870 88.3425 1690 2285 2 chr2D.!!$F2 595
9 TraesCS3B01G122700 chr6D 62860309 62861470 1161 False 1799.0 1799 94.6690 981 2139 1 chr6D.!!$F1 1158
10 TraesCS3B01G122700 chr6D 59106399 59107455 1056 True 1655.0 1655 94.8450 981 2045 1 chr6D.!!$R1 1064
11 TraesCS3B01G122700 chr7B 2706138 2707315 1177 False 1742.0 1742 93.4630 981 2151 1 chr7B.!!$F1 1170
12 TraesCS3B01G122700 chr7B 673550870 673551444 574 True 821.0 821 92.7080 409 973 1 chr7B.!!$R2 564
13 TraesCS3B01G122700 chr4A 695046478 695047722 1244 True 1725.0 1725 91.6330 981 2233 1 chr4A.!!$R1 1252
14 TraesCS3B01G122700 chr2B 82425559 82426784 1225 True 892.5 1609 88.6905 1177 2285 2 chr2B.!!$R1 1108
15 TraesCS3B01G122700 chr3D 445803494 445804650 1156 False 1546.0 1546 90.7080 981 2151 1 chr3D.!!$F2 1170
16 TraesCS3B01G122700 chr3D 536281717 536282288 571 False 870.0 870 94.2510 406 973 1 chr3D.!!$F3 567
17 TraesCS3B01G122700 chr1D 92055237 92056389 1152 False 1369.0 1369 88.0950 981 2150 1 chr1D.!!$F1 1169
18 TraesCS3B01G122700 chr7D 493558011 493558586 575 True 870.0 870 94.2710 409 973 1 chr7D.!!$R1 564
19 TraesCS3B01G122700 chr5B 551741483 551742054 571 False 859.0 859 93.8920 406 973 1 chr5B.!!$F2 567
20 TraesCS3B01G122700 chr5B 40986589 40987167 578 False 821.0 821 92.5730 406 973 1 chr5B.!!$F1 567
21 TraesCS3B01G122700 chr1B 649195323 649195897 574 True 837.0 837 93.2290 409 973 1 chr1B.!!$R1 564

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
140 141 0.104487 CTCTCTCCATGCATGCGAGT 59.896 55.0 28.94 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 4792 0.527565 AATTGCTTACTGCCAAGGCG 59.472 50.0 6.6 4.13 45.51 5.52 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
26 27 1.411651 GCACCCACTAGATCCCCCTC 61.412 65.000 0.00 0.00 0.00 4.30
72 73 4.870069 AGGCCATTTGCATCACCA 57.130 50.000 5.01 0.00 43.89 4.17
78 79 3.188846 GCCATTTGCATCACCAAAGGTG 61.189 50.000 9.87 9.87 46.83 4.00
119 120 8.096414 CCTTTATTTGGTTGGTTCAAATCATCT 58.904 33.333 5.47 0.00 41.97 2.90
120 121 8.830201 TTTATTTGGTTGGTTCAAATCATCTG 57.170 30.769 5.47 0.00 41.97 2.90
121 122 3.940209 TGGTTGGTTCAAATCATCTGC 57.060 42.857 0.00 0.00 0.00 4.26
122 123 3.499338 TGGTTGGTTCAAATCATCTGCT 58.501 40.909 0.00 0.00 0.00 4.24
123 124 3.507233 TGGTTGGTTCAAATCATCTGCTC 59.493 43.478 0.00 0.00 0.00 4.26
124 125 3.760684 GGTTGGTTCAAATCATCTGCTCT 59.239 43.478 0.00 0.00 0.00 4.09
125 126 4.142513 GGTTGGTTCAAATCATCTGCTCTC 60.143 45.833 0.00 0.00 0.00 3.20
126 127 4.564782 TGGTTCAAATCATCTGCTCTCT 57.435 40.909 0.00 0.00 0.00 3.10
127 128 4.511527 TGGTTCAAATCATCTGCTCTCTC 58.488 43.478 0.00 0.00 0.00 3.20
128 129 3.876320 GGTTCAAATCATCTGCTCTCTCC 59.124 47.826 0.00 0.00 0.00 3.71
129 130 4.511527 GTTCAAATCATCTGCTCTCTCCA 58.488 43.478 0.00 0.00 0.00 3.86
130 131 5.124645 GTTCAAATCATCTGCTCTCTCCAT 58.875 41.667 0.00 0.00 0.00 3.41
131 132 4.704965 TCAAATCATCTGCTCTCTCCATG 58.295 43.478 0.00 0.00 0.00 3.66
132 133 2.843401 ATCATCTGCTCTCTCCATGC 57.157 50.000 0.00 0.00 0.00 4.06
133 134 1.492764 TCATCTGCTCTCTCCATGCA 58.507 50.000 0.00 0.00 35.30 3.96
134 135 2.047830 TCATCTGCTCTCTCCATGCAT 58.952 47.619 0.00 0.00 36.07 3.96
135 136 2.147150 CATCTGCTCTCTCCATGCATG 58.853 52.381 20.19 20.19 36.07 4.06
136 137 0.179054 TCTGCTCTCTCCATGCATGC 60.179 55.000 21.69 11.82 36.07 4.06
137 138 1.499688 CTGCTCTCTCCATGCATGCG 61.500 60.000 21.69 14.24 36.07 4.73
138 139 1.227468 GCTCTCTCCATGCATGCGA 60.227 57.895 21.69 17.51 0.00 5.10
139 140 1.222766 GCTCTCTCCATGCATGCGAG 61.223 60.000 26.62 26.62 0.00 5.03
140 141 0.104487 CTCTCTCCATGCATGCGAGT 59.896 55.000 28.94 0.00 0.00 4.18
141 142 1.339291 CTCTCTCCATGCATGCGAGTA 59.661 52.381 28.94 21.68 0.00 2.59
142 143 1.966354 TCTCTCCATGCATGCGAGTAT 59.034 47.619 28.94 0.00 0.00 2.12
143 144 3.157087 TCTCTCCATGCATGCGAGTATA 58.843 45.455 28.94 19.22 0.00 1.47
144 145 3.057245 TCTCTCCATGCATGCGAGTATAC 60.057 47.826 28.94 0.00 0.00 1.47
145 146 2.627699 TCTCCATGCATGCGAGTATACA 59.372 45.455 28.94 16.32 0.00 2.29
146 147 3.259123 TCTCCATGCATGCGAGTATACAT 59.741 43.478 28.94 0.00 0.00 2.29
147 148 3.999001 CTCCATGCATGCGAGTATACATT 59.001 43.478 25.27 0.00 0.00 2.71
148 149 4.388485 TCCATGCATGCGAGTATACATTT 58.612 39.130 21.69 0.00 0.00 2.32
149 150 4.821260 TCCATGCATGCGAGTATACATTTT 59.179 37.500 21.69 0.00 0.00 1.82
150 151 4.913345 CCATGCATGCGAGTATACATTTTG 59.087 41.667 21.69 0.00 0.00 2.44
151 152 3.951306 TGCATGCGAGTATACATTTTGC 58.049 40.909 14.09 8.02 0.00 3.68
152 153 3.376546 TGCATGCGAGTATACATTTTGCA 59.623 39.130 14.09 10.35 35.10 4.08
153 154 4.036616 TGCATGCGAGTATACATTTTGCAT 59.963 37.500 14.09 10.94 41.83 3.96
154 155 4.614284 GCATGCGAGTATACATTTTGCATC 59.386 41.667 12.98 7.14 39.36 3.91
155 156 5.561532 GCATGCGAGTATACATTTTGCATCT 60.562 40.000 12.98 0.00 39.36 2.90
156 157 6.347644 GCATGCGAGTATACATTTTGCATCTA 60.348 38.462 12.98 0.00 39.36 1.98
157 158 7.624974 GCATGCGAGTATACATTTTGCATCTAT 60.625 37.037 12.98 0.00 39.36 1.98
158 159 8.872845 CATGCGAGTATACATTTTGCATCTATA 58.127 33.333 12.98 0.00 39.36 1.31
159 160 8.239681 TGCGAGTATACATTTTGCATCTATAC 57.760 34.615 5.50 0.00 0.00 1.47
160 161 7.870445 TGCGAGTATACATTTTGCATCTATACA 59.130 33.333 5.50 0.00 0.00 2.29
161 162 8.708742 GCGAGTATACATTTTGCATCTATACAA 58.291 33.333 5.50 0.00 0.00 2.41
164 165 9.003658 AGTATACATTTTGCATCTATACAAGGC 57.996 33.333 5.50 0.00 0.00 4.35
165 166 5.520376 ACATTTTGCATCTATACAAGGCC 57.480 39.130 0.00 0.00 0.00 5.19
166 167 4.955450 ACATTTTGCATCTATACAAGGCCA 59.045 37.500 5.01 0.00 0.00 5.36
167 168 4.981806 TTTTGCATCTATACAAGGCCAC 57.018 40.909 5.01 0.00 0.00 5.01
168 169 2.638480 TGCATCTATACAAGGCCACC 57.362 50.000 5.01 0.00 0.00 4.61
169 170 1.843206 TGCATCTATACAAGGCCACCA 59.157 47.619 5.01 0.00 0.00 4.17
170 171 2.240921 TGCATCTATACAAGGCCACCAA 59.759 45.455 5.01 0.00 0.00 3.67
171 172 2.618709 GCATCTATACAAGGCCACCAAC 59.381 50.000 5.01 0.00 0.00 3.77
172 173 3.884895 CATCTATACAAGGCCACCAACA 58.115 45.455 5.01 0.00 0.00 3.33
173 174 3.627395 TCTATACAAGGCCACCAACAG 57.373 47.619 5.01 0.00 0.00 3.16
174 175 2.910319 TCTATACAAGGCCACCAACAGT 59.090 45.455 5.01 0.00 0.00 3.55
175 176 4.098155 TCTATACAAGGCCACCAACAGTA 58.902 43.478 5.01 0.00 0.00 2.74
176 177 3.799432 ATACAAGGCCACCAACAGTAA 57.201 42.857 5.01 0.00 0.00 2.24
177 178 2.675658 ACAAGGCCACCAACAGTAAT 57.324 45.000 5.01 0.00 0.00 1.89
178 179 2.514803 ACAAGGCCACCAACAGTAATC 58.485 47.619 5.01 0.00 0.00 1.75
179 180 1.468520 CAAGGCCACCAACAGTAATCG 59.531 52.381 5.01 0.00 0.00 3.34
180 181 0.981183 AGGCCACCAACAGTAATCGA 59.019 50.000 5.01 0.00 0.00 3.59
181 182 1.066143 AGGCCACCAACAGTAATCGAG 60.066 52.381 5.01 0.00 0.00 4.04
182 183 1.369625 GCCACCAACAGTAATCGAGG 58.630 55.000 0.00 0.00 0.00 4.63
183 184 1.369625 CCACCAACAGTAATCGAGGC 58.630 55.000 0.00 0.00 0.00 4.70
184 185 1.338674 CCACCAACAGTAATCGAGGCA 60.339 52.381 0.00 0.00 0.00 4.75
185 186 2.422597 CACCAACAGTAATCGAGGCAA 58.577 47.619 0.00 0.00 0.00 4.52
186 187 2.811431 CACCAACAGTAATCGAGGCAAA 59.189 45.455 0.00 0.00 0.00 3.68
187 188 3.074412 ACCAACAGTAATCGAGGCAAAG 58.926 45.455 0.00 0.00 0.00 2.77
188 189 3.074412 CCAACAGTAATCGAGGCAAAGT 58.926 45.455 0.00 0.00 0.00 2.66
189 190 3.502211 CCAACAGTAATCGAGGCAAAGTT 59.498 43.478 0.00 0.00 0.00 2.66
190 191 4.693566 CCAACAGTAATCGAGGCAAAGTTA 59.306 41.667 0.00 0.00 0.00 2.24
191 192 5.180492 CCAACAGTAATCGAGGCAAAGTTAA 59.820 40.000 0.00 0.00 0.00 2.01
192 193 6.128007 CCAACAGTAATCGAGGCAAAGTTAAT 60.128 38.462 0.00 0.00 0.00 1.40
193 194 6.422776 ACAGTAATCGAGGCAAAGTTAATG 57.577 37.500 0.00 0.00 0.00 1.90
194 195 6.170506 ACAGTAATCGAGGCAAAGTTAATGA 58.829 36.000 7.02 0.00 0.00 2.57
195 196 6.823689 ACAGTAATCGAGGCAAAGTTAATGAT 59.176 34.615 7.02 0.00 0.00 2.45
196 197 7.985184 ACAGTAATCGAGGCAAAGTTAATGATA 59.015 33.333 7.02 0.00 0.00 2.15
197 198 8.993121 CAGTAATCGAGGCAAAGTTAATGATAT 58.007 33.333 0.00 0.00 0.00 1.63
198 199 9.561069 AGTAATCGAGGCAAAGTTAATGATATT 57.439 29.630 0.00 0.00 0.00 1.28
201 202 9.736023 AATCGAGGCAAAGTTAATGATATTTTC 57.264 29.630 0.00 0.00 0.00 2.29
202 203 8.506168 TCGAGGCAAAGTTAATGATATTTTCT 57.494 30.769 0.00 0.00 0.00 2.52
203 204 8.612619 TCGAGGCAAAGTTAATGATATTTTCTC 58.387 33.333 0.00 0.00 0.00 2.87
204 205 7.584123 CGAGGCAAAGTTAATGATATTTTCTCG 59.416 37.037 0.00 0.00 33.60 4.04
205 206 8.281212 AGGCAAAGTTAATGATATTTTCTCGT 57.719 30.769 0.00 0.00 0.00 4.18
206 207 9.391006 AGGCAAAGTTAATGATATTTTCTCGTA 57.609 29.630 0.00 0.00 0.00 3.43
207 208 9.434559 GGCAAAGTTAATGATATTTTCTCGTAC 57.565 33.333 0.00 0.00 0.00 3.67
215 216 8.942338 AATGATATTTTCTCGTACTAACAGCA 57.058 30.769 0.00 0.00 0.00 4.41
216 217 9.547753 AATGATATTTTCTCGTACTAACAGCAT 57.452 29.630 0.00 0.00 0.00 3.79
217 218 8.352752 TGATATTTTCTCGTACTAACAGCATG 57.647 34.615 0.00 0.00 46.00 4.06
263 264 7.527084 GTCATAATGACAGTCAGTTACTTCC 57.473 40.000 9.15 0.00 46.22 3.46
264 265 7.324178 GTCATAATGACAGTCAGTTACTTCCT 58.676 38.462 9.15 0.00 46.22 3.36
265 266 7.489757 GTCATAATGACAGTCAGTTACTTCCTC 59.510 40.741 9.15 0.00 46.22 3.71
266 267 4.810191 ATGACAGTCAGTTACTTCCTCC 57.190 45.455 9.64 0.00 35.76 4.30
267 268 2.557056 TGACAGTCAGTTACTTCCTCCG 59.443 50.000 0.00 0.00 35.76 4.63
268 269 1.272769 ACAGTCAGTTACTTCCTCCGC 59.727 52.381 0.00 0.00 35.76 5.54
269 270 1.546476 CAGTCAGTTACTTCCTCCGCT 59.454 52.381 0.00 0.00 35.76 5.52
270 271 1.819903 AGTCAGTTACTTCCTCCGCTC 59.180 52.381 0.00 0.00 33.35 5.03
271 272 1.544691 GTCAGTTACTTCCTCCGCTCA 59.455 52.381 0.00 0.00 0.00 4.26
272 273 1.819288 TCAGTTACTTCCTCCGCTCAG 59.181 52.381 0.00 0.00 0.00 3.35
273 274 1.546476 CAGTTACTTCCTCCGCTCAGT 59.454 52.381 0.00 0.00 0.00 3.41
274 275 2.028930 CAGTTACTTCCTCCGCTCAGTT 60.029 50.000 0.00 0.00 0.00 3.16
275 276 2.633481 AGTTACTTCCTCCGCTCAGTTT 59.367 45.455 0.00 0.00 0.00 2.66
276 277 2.994578 GTTACTTCCTCCGCTCAGTTTC 59.005 50.000 0.00 0.00 0.00 2.78
277 278 1.343069 ACTTCCTCCGCTCAGTTTCT 58.657 50.000 0.00 0.00 0.00 2.52
278 279 1.694696 ACTTCCTCCGCTCAGTTTCTT 59.305 47.619 0.00 0.00 0.00 2.52
279 280 2.104963 ACTTCCTCCGCTCAGTTTCTTT 59.895 45.455 0.00 0.00 0.00 2.52
280 281 2.169832 TCCTCCGCTCAGTTTCTTTG 57.830 50.000 0.00 0.00 0.00 2.77
281 282 0.519077 CCTCCGCTCAGTTTCTTTGC 59.481 55.000 0.00 0.00 0.00 3.68
282 283 1.229428 CTCCGCTCAGTTTCTTTGCA 58.771 50.000 0.00 0.00 0.00 4.08
283 284 1.808945 CTCCGCTCAGTTTCTTTGCAT 59.191 47.619 0.00 0.00 0.00 3.96
284 285 1.536766 TCCGCTCAGTTTCTTTGCATG 59.463 47.619 0.00 0.00 0.00 4.06
285 286 1.334054 CGCTCAGTTTCTTTGCATGC 58.666 50.000 11.82 11.82 0.00 4.06
286 287 1.335233 CGCTCAGTTTCTTTGCATGCA 60.335 47.619 18.46 18.46 0.00 3.96
287 288 2.670229 CGCTCAGTTTCTTTGCATGCAT 60.670 45.455 23.37 0.58 0.00 3.96
288 289 2.666508 GCTCAGTTTCTTTGCATGCATG 59.333 45.455 23.37 22.70 0.00 4.06
301 302 4.408993 GCATGCATGCGAGTATTAATGA 57.591 40.909 33.99 0.00 44.67 2.57
302 303 4.978186 GCATGCATGCGAGTATTAATGAT 58.022 39.130 33.99 0.00 44.67 2.45
303 304 5.026462 GCATGCATGCGAGTATTAATGATC 58.974 41.667 33.99 5.03 44.67 2.92
304 305 5.566623 CATGCATGCGAGTATTAATGATCC 58.433 41.667 14.93 0.00 0.00 3.36
305 306 4.002982 TGCATGCGAGTATTAATGATCCC 58.997 43.478 14.09 0.00 0.00 3.85
306 307 3.062639 GCATGCGAGTATTAATGATCCCG 59.937 47.826 0.00 0.00 0.00 5.14
307 308 3.313012 TGCGAGTATTAATGATCCCGG 57.687 47.619 0.00 0.00 0.00 5.73
308 309 2.631062 TGCGAGTATTAATGATCCCGGT 59.369 45.455 0.00 0.00 0.00 5.28
309 310 3.827876 TGCGAGTATTAATGATCCCGGTA 59.172 43.478 0.00 0.00 0.00 4.02
310 311 4.281435 TGCGAGTATTAATGATCCCGGTAA 59.719 41.667 0.00 0.00 0.00 2.85
311 312 5.221481 TGCGAGTATTAATGATCCCGGTAAA 60.221 40.000 0.00 0.00 0.00 2.01
312 313 5.119743 GCGAGTATTAATGATCCCGGTAAAC 59.880 44.000 0.00 0.00 0.00 2.01
313 314 5.636543 CGAGTATTAATGATCCCGGTAAACC 59.363 44.000 0.00 0.00 0.00 3.27
314 315 6.503560 AGTATTAATGATCCCGGTAAACCA 57.496 37.500 0.00 0.00 35.14 3.67
315 316 6.902408 AGTATTAATGATCCCGGTAAACCAA 58.098 36.000 0.00 0.00 35.14 3.67
316 317 7.348033 AGTATTAATGATCCCGGTAAACCAAA 58.652 34.615 0.00 0.00 35.14 3.28
317 318 7.835181 AGTATTAATGATCCCGGTAAACCAAAA 59.165 33.333 0.00 0.00 35.14 2.44
318 319 6.518208 TTAATGATCCCGGTAAACCAAAAG 57.482 37.500 0.00 0.00 35.14 2.27
319 320 3.791953 TGATCCCGGTAAACCAAAAGA 57.208 42.857 0.00 0.00 35.14 2.52
320 321 4.101645 TGATCCCGGTAAACCAAAAGAA 57.898 40.909 0.00 0.00 35.14 2.52
321 322 4.471548 TGATCCCGGTAAACCAAAAGAAA 58.528 39.130 0.00 0.00 35.14 2.52
322 323 4.894114 TGATCCCGGTAAACCAAAAGAAAA 59.106 37.500 0.00 0.00 35.14 2.29
323 324 5.540719 TGATCCCGGTAAACCAAAAGAAAAT 59.459 36.000 0.00 0.00 35.14 1.82
324 325 5.873146 TCCCGGTAAACCAAAAGAAAATT 57.127 34.783 0.00 0.00 35.14 1.82
325 326 6.236558 TCCCGGTAAACCAAAAGAAAATTT 57.763 33.333 0.00 0.00 35.14 1.82
326 327 6.049790 TCCCGGTAAACCAAAAGAAAATTTG 58.950 36.000 0.00 0.00 39.47 2.32
327 328 6.049790 CCCGGTAAACCAAAAGAAAATTTGA 58.950 36.000 0.00 0.00 41.73 2.69
328 329 6.018588 CCCGGTAAACCAAAAGAAAATTTGAC 60.019 38.462 0.00 0.00 41.73 3.18
329 330 6.759356 CCGGTAAACCAAAAGAAAATTTGACT 59.241 34.615 0.00 0.00 41.73 3.41
330 331 7.279090 CCGGTAAACCAAAAGAAAATTTGACTT 59.721 33.333 0.00 0.00 41.73 3.01
331 332 8.113675 CGGTAAACCAAAAGAAAATTTGACTTG 58.886 33.333 10.31 4.42 41.73 3.16
332 333 8.941977 GGTAAACCAAAAGAAAATTTGACTTGT 58.058 29.630 10.31 4.21 41.73 3.16
337 338 8.664798 ACCAAAAGAAAATTTGACTTGTAAAGC 58.335 29.630 10.31 0.00 41.19 3.51
338 339 8.663911 CCAAAAGAAAATTTGACTTGTAAAGCA 58.336 29.630 10.31 0.00 41.19 3.91
359 360 8.620116 AAGCAAGCATTAAATTTTACATTGGT 57.380 26.923 0.00 0.00 0.00 3.67
360 361 9.717942 AAGCAAGCATTAAATTTTACATTGGTA 57.282 25.926 0.00 0.00 0.00 3.25
361 362 9.150348 AGCAAGCATTAAATTTTACATTGGTAC 57.850 29.630 0.00 0.00 0.00 3.34
362 363 8.930760 GCAAGCATTAAATTTTACATTGGTACA 58.069 29.630 0.00 0.00 0.00 2.90
374 375 8.780846 TTTACATTGGTACATGTAATTCGAGT 57.219 30.769 15.63 5.40 39.77 4.18
375 376 8.780846 TTACATTGGTACATGTAATTCGAGTT 57.219 30.769 7.25 0.00 37.38 3.01
376 377 7.681939 ACATTGGTACATGTAATTCGAGTTT 57.318 32.000 7.25 0.00 39.30 2.66
377 378 7.526608 ACATTGGTACATGTAATTCGAGTTTG 58.473 34.615 7.25 0.00 39.30 2.93
378 379 7.174253 ACATTGGTACATGTAATTCGAGTTTGT 59.826 33.333 7.25 0.11 39.30 2.83
379 380 6.474819 TGGTACATGTAATTCGAGTTTGTG 57.525 37.500 7.25 0.00 0.00 3.33
380 381 5.410132 TGGTACATGTAATTCGAGTTTGTGG 59.590 40.000 7.25 0.00 0.00 4.17
381 382 4.419522 ACATGTAATTCGAGTTTGTGGC 57.580 40.909 0.00 0.00 0.00 5.01
382 383 3.190535 ACATGTAATTCGAGTTTGTGGCC 59.809 43.478 0.00 0.00 0.00 5.36
383 384 3.134574 TGTAATTCGAGTTTGTGGCCT 57.865 42.857 3.32 0.00 0.00 5.19
384 385 3.482436 TGTAATTCGAGTTTGTGGCCTT 58.518 40.909 3.32 0.00 0.00 4.35
385 386 3.252215 TGTAATTCGAGTTTGTGGCCTTG 59.748 43.478 3.32 0.00 0.00 3.61
386 387 1.981256 ATTCGAGTTTGTGGCCTTGT 58.019 45.000 3.32 0.00 0.00 3.16
387 388 2.623878 TTCGAGTTTGTGGCCTTGTA 57.376 45.000 3.32 0.00 0.00 2.41
388 389 2.851263 TCGAGTTTGTGGCCTTGTAT 57.149 45.000 3.32 0.00 0.00 2.29
389 390 3.965379 TCGAGTTTGTGGCCTTGTATA 57.035 42.857 3.32 0.00 0.00 1.47
390 391 3.592059 TCGAGTTTGTGGCCTTGTATAC 58.408 45.455 3.32 0.00 0.00 1.47
391 392 3.007074 TCGAGTTTGTGGCCTTGTATACA 59.993 43.478 3.32 0.08 0.00 2.29
392 393 3.749088 CGAGTTTGTGGCCTTGTATACAA 59.251 43.478 17.16 17.16 0.00 2.41
393 394 4.214545 CGAGTTTGTGGCCTTGTATACAAA 59.785 41.667 18.55 11.60 39.79 2.83
394 395 5.278071 CGAGTTTGTGGCCTTGTATACAAAA 60.278 40.000 18.55 6.87 42.52 2.44
395 396 6.472686 AGTTTGTGGCCTTGTATACAAAAA 57.527 33.333 18.55 12.04 42.52 1.94
396 397 7.061566 AGTTTGTGGCCTTGTATACAAAAAT 57.938 32.000 18.55 5.58 42.52 1.82
397 398 6.928492 AGTTTGTGGCCTTGTATACAAAAATG 59.072 34.615 18.55 7.55 42.52 2.32
398 399 5.398603 TGTGGCCTTGTATACAAAAATGG 57.601 39.130 18.55 16.25 35.15 3.16
399 400 5.080337 TGTGGCCTTGTATACAAAAATGGA 58.920 37.500 20.31 3.36 35.15 3.41
400 401 5.184864 TGTGGCCTTGTATACAAAAATGGAG 59.815 40.000 20.31 8.22 35.15 3.86
401 402 4.709397 TGGCCTTGTATACAAAAATGGAGG 59.291 41.667 20.31 16.09 35.15 4.30
402 403 4.099419 GGCCTTGTATACAAAAATGGAGGG 59.901 45.833 20.31 15.39 35.15 4.30
403 404 4.953579 GCCTTGTATACAAAAATGGAGGGA 59.046 41.667 20.31 0.00 35.15 4.20
404 405 5.067805 GCCTTGTATACAAAAATGGAGGGAG 59.932 44.000 20.31 5.98 35.15 4.30
407 408 7.998964 CCTTGTATACAAAAATGGAGGGAGTAT 59.001 37.037 18.55 0.00 35.15 2.12
509 510 7.904558 TTTATGGGTCATTTATGGTGCATTA 57.095 32.000 0.00 0.00 0.00 1.90
600 612 5.877012 GGTTTAGTTAGGTTAGGGTTAGTGC 59.123 44.000 0.00 0.00 0.00 4.40
602 614 7.093333 GGTTTAGTTAGGTTAGGGTTAGTGCTA 60.093 40.741 0.00 0.00 0.00 3.49
611 623 7.289549 AGGTTAGGGTTAGTGCTAAAGGTATAG 59.710 40.741 0.00 0.00 0.00 1.31
736 748 6.455360 ACTAGTGAATGTGCATTATTTGGG 57.545 37.500 0.00 0.00 0.00 4.12
779 791 3.387947 GCCGACGAAGGGGAGGAA 61.388 66.667 0.00 0.00 0.00 3.36
843 855 1.964223 TGAAAGTGAGAAGCGTCCTCT 59.036 47.619 0.00 0.00 0.00 3.69
889 901 1.334869 GAAGCTTGTTGGGCGATATGG 59.665 52.381 2.10 0.00 34.52 2.74
973 985 6.012858 TGGGATGTGTATAAGGAGAAAGTTGT 60.013 38.462 0.00 0.00 0.00 3.32
974 986 7.181305 TGGGATGTGTATAAGGAGAAAGTTGTA 59.819 37.037 0.00 0.00 0.00 2.41
975 987 8.211629 GGGATGTGTATAAGGAGAAAGTTGTAT 58.788 37.037 0.00 0.00 0.00 2.29
976 988 9.614792 GGATGTGTATAAGGAGAAAGTTGTATT 57.385 33.333 0.00 0.00 0.00 1.89
1080 3905 0.830444 AGTGGACAGACGCCCAGTTA 60.830 55.000 0.00 0.00 32.43 2.24
1202 4027 7.750903 GGAAGGAAGAAGATATTTTGTTTGTCG 59.249 37.037 0.00 0.00 0.00 4.35
1250 4075 2.035193 CAGCTCACGCCTATGATGTACT 59.965 50.000 0.00 0.00 36.60 2.73
1251 4076 3.253432 CAGCTCACGCCTATGATGTACTA 59.747 47.826 0.00 0.00 36.60 1.82
1303 4128 6.380095 TTTAACCGTTGCTACAACTTGAAT 57.620 33.333 8.66 0.00 0.00 2.57
1520 4345 1.470979 GGATGGAGCGAAAGAAGCGTA 60.471 52.381 0.00 0.00 40.04 4.42
1539 4364 4.459089 GGAGGAGAGGGCACGCAC 62.459 72.222 0.00 0.00 0.00 5.34
1556 4381 1.714794 CACGGAGAAGATTGCTCGTT 58.285 50.000 0.00 0.00 33.19 3.85
1569 4394 3.351794 TGCTCGTTAAGAGGAGAGAGA 57.648 47.619 0.00 0.00 46.91 3.10
1956 4792 3.758931 GAAACCCCACCGCCATGC 61.759 66.667 0.00 0.00 0.00 4.06
2056 4892 1.221840 CTACCGCCAAGGCAGATGT 59.778 57.895 12.19 5.02 46.52 3.06
2089 4925 3.060615 CCAACTGCCTGCTCTGCC 61.061 66.667 0.00 0.00 0.00 4.85
2213 5050 2.745037 GTTGGCCACCCTACGACA 59.255 61.111 3.88 0.00 0.00 4.35
2233 5070 6.708949 ACGACAATTACTACTGTGACCAAATT 59.291 34.615 0.00 0.00 0.00 1.82
2235 5072 7.095397 CGACAATTACTACTGTGACCAAATTGA 60.095 37.037 10.79 0.00 36.70 2.57
2237 5074 7.500892 ACAATTACTACTGTGACCAAATTGACA 59.499 33.333 10.79 0.00 36.70 3.58
2248 5085 5.128499 TGACCAAATTGACAACATTTCCAGT 59.872 36.000 0.00 0.00 0.00 4.00
2263 5100 1.458486 CAGTGGTAGGGTTGGCCAA 59.542 57.895 16.05 16.05 36.17 4.52
2272 5109 4.486887 GTTGGCCAACCTACCGTT 57.513 55.556 34.36 0.00 35.86 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.181350 GGGGATCTAGTGGGTGCTTG 59.819 60.000 0.00 0.00 0.00 4.01
26 27 1.134610 GGGGCAAATCTCAAGCAATGG 60.135 52.381 0.00 0.00 0.00 3.16
72 73 1.575447 GGGATGGGAGAGGCACCTTT 61.575 60.000 0.00 0.00 0.00 3.11
97 98 6.211184 AGCAGATGATTTGAACCAACCAAATA 59.789 34.615 0.00 0.00 42.35 1.40
119 120 1.523032 CGCATGCATGGAGAGAGCA 60.523 57.895 27.34 0.00 43.14 4.26
120 121 1.222766 CTCGCATGCATGGAGAGAGC 61.223 60.000 27.70 13.98 34.59 4.09
121 122 0.104487 ACTCGCATGCATGGAGAGAG 59.896 55.000 33.47 24.29 35.97 3.20
122 123 1.402787 TACTCGCATGCATGGAGAGA 58.597 50.000 33.47 23.64 35.97 3.10
123 124 2.452295 ATACTCGCATGCATGGAGAG 57.548 50.000 33.47 26.93 38.05 3.20
124 125 2.627699 TGTATACTCGCATGCATGGAGA 59.372 45.455 33.47 23.28 32.77 3.71
125 126 3.030668 TGTATACTCGCATGCATGGAG 57.969 47.619 28.87 28.87 33.86 3.86
126 127 3.683365 ATGTATACTCGCATGCATGGA 57.317 42.857 27.34 20.15 31.08 3.41
127 128 4.754372 AAATGTATACTCGCATGCATGG 57.246 40.909 27.34 17.21 32.41 3.66
128 129 4.380678 GCAAAATGTATACTCGCATGCATG 59.619 41.667 22.70 22.70 32.41 4.06
129 130 4.036616 TGCAAAATGTATACTCGCATGCAT 59.963 37.500 19.57 5.96 33.29 3.96
130 131 3.376546 TGCAAAATGTATACTCGCATGCA 59.623 39.130 19.57 15.11 0.00 3.96
131 132 3.951306 TGCAAAATGTATACTCGCATGC 58.049 40.909 7.91 7.91 0.00 4.06
132 133 5.993891 AGATGCAAAATGTATACTCGCATG 58.006 37.500 16.89 0.00 38.64 4.06
133 134 7.912056 ATAGATGCAAAATGTATACTCGCAT 57.088 32.000 13.84 13.84 41.05 4.73
134 135 7.870445 TGTATAGATGCAAAATGTATACTCGCA 59.130 33.333 11.98 6.14 34.06 5.10
135 136 8.239681 TGTATAGATGCAAAATGTATACTCGC 57.760 34.615 11.98 0.67 34.06 5.03
138 139 9.003658 GCCTTGTATAGATGCAAAATGTATACT 57.996 33.333 11.98 0.00 34.06 2.12
139 140 8.237267 GGCCTTGTATAGATGCAAAATGTATAC 58.763 37.037 0.00 0.00 33.74 1.47
140 141 7.941790 TGGCCTTGTATAGATGCAAAATGTATA 59.058 33.333 3.32 0.00 32.12 1.47
141 142 6.777091 TGGCCTTGTATAGATGCAAAATGTAT 59.223 34.615 3.32 0.00 32.12 2.29
142 143 6.039270 GTGGCCTTGTATAGATGCAAAATGTA 59.961 38.462 3.32 0.00 32.12 2.29
143 144 4.955450 TGGCCTTGTATAGATGCAAAATGT 59.045 37.500 3.32 0.00 32.12 2.71
144 145 5.284079 GTGGCCTTGTATAGATGCAAAATG 58.716 41.667 3.32 0.00 32.12 2.32
145 146 4.342092 GGTGGCCTTGTATAGATGCAAAAT 59.658 41.667 3.32 0.00 32.12 1.82
146 147 3.699038 GGTGGCCTTGTATAGATGCAAAA 59.301 43.478 3.32 0.00 32.12 2.44
147 148 3.287222 GGTGGCCTTGTATAGATGCAAA 58.713 45.455 3.32 0.00 32.12 3.68
148 149 2.240921 TGGTGGCCTTGTATAGATGCAA 59.759 45.455 3.32 0.00 0.00 4.08
149 150 1.843206 TGGTGGCCTTGTATAGATGCA 59.157 47.619 3.32 0.00 0.00 3.96
150 151 2.618709 GTTGGTGGCCTTGTATAGATGC 59.381 50.000 3.32 0.00 0.00 3.91
151 152 3.879295 CTGTTGGTGGCCTTGTATAGATG 59.121 47.826 3.32 0.00 0.00 2.90
152 153 3.523564 ACTGTTGGTGGCCTTGTATAGAT 59.476 43.478 3.32 0.00 0.00 1.98
153 154 2.910319 ACTGTTGGTGGCCTTGTATAGA 59.090 45.455 3.32 0.00 0.00 1.98
154 155 3.350219 ACTGTTGGTGGCCTTGTATAG 57.650 47.619 3.32 0.00 0.00 1.31
155 156 4.912317 TTACTGTTGGTGGCCTTGTATA 57.088 40.909 3.32 0.00 0.00 1.47
156 157 3.799432 TTACTGTTGGTGGCCTTGTAT 57.201 42.857 3.32 0.00 0.00 2.29
157 158 3.681593 GATTACTGTTGGTGGCCTTGTA 58.318 45.455 3.32 0.00 0.00 2.41
158 159 2.514803 GATTACTGTTGGTGGCCTTGT 58.485 47.619 3.32 0.00 0.00 3.16
159 160 1.468520 CGATTACTGTTGGTGGCCTTG 59.531 52.381 3.32 0.00 0.00 3.61
160 161 1.349688 TCGATTACTGTTGGTGGCCTT 59.650 47.619 3.32 0.00 0.00 4.35
161 162 0.981183 TCGATTACTGTTGGTGGCCT 59.019 50.000 3.32 0.00 0.00 5.19
162 163 1.369625 CTCGATTACTGTTGGTGGCC 58.630 55.000 0.00 0.00 0.00 5.36
163 164 1.369625 CCTCGATTACTGTTGGTGGC 58.630 55.000 0.00 0.00 0.00 5.01
164 165 1.338674 TGCCTCGATTACTGTTGGTGG 60.339 52.381 0.00 0.00 0.00 4.61
165 166 2.093306 TGCCTCGATTACTGTTGGTG 57.907 50.000 0.00 0.00 0.00 4.17
166 167 2.851263 TTGCCTCGATTACTGTTGGT 57.149 45.000 0.00 0.00 0.00 3.67
167 168 3.074412 ACTTTGCCTCGATTACTGTTGG 58.926 45.455 0.00 0.00 0.00 3.77
168 169 4.749245 AACTTTGCCTCGATTACTGTTG 57.251 40.909 0.00 0.00 0.00 3.33
169 170 6.653320 TCATTAACTTTGCCTCGATTACTGTT 59.347 34.615 0.00 0.00 0.00 3.16
170 171 6.170506 TCATTAACTTTGCCTCGATTACTGT 58.829 36.000 0.00 0.00 0.00 3.55
171 172 6.662414 TCATTAACTTTGCCTCGATTACTG 57.338 37.500 0.00 0.00 0.00 2.74
172 173 9.561069 AATATCATTAACTTTGCCTCGATTACT 57.439 29.630 0.00 0.00 0.00 2.24
175 176 9.736023 GAAAATATCATTAACTTTGCCTCGATT 57.264 29.630 0.00 0.00 0.00 3.34
176 177 9.125026 AGAAAATATCATTAACTTTGCCTCGAT 57.875 29.630 0.00 0.00 0.00 3.59
177 178 8.506168 AGAAAATATCATTAACTTTGCCTCGA 57.494 30.769 0.00 0.00 0.00 4.04
178 179 7.584123 CGAGAAAATATCATTAACTTTGCCTCG 59.416 37.037 0.00 0.00 33.08 4.63
179 180 8.398665 ACGAGAAAATATCATTAACTTTGCCTC 58.601 33.333 0.00 0.00 0.00 4.70
180 181 8.281212 ACGAGAAAATATCATTAACTTTGCCT 57.719 30.769 0.00 0.00 0.00 4.75
181 182 9.434559 GTACGAGAAAATATCATTAACTTTGCC 57.565 33.333 0.00 0.00 0.00 4.52
190 191 8.942338 TGCTGTTAGTACGAGAAAATATCATT 57.058 30.769 0.00 0.00 0.00 2.57
191 192 8.982685 CATGCTGTTAGTACGAGAAAATATCAT 58.017 33.333 0.00 0.00 0.00 2.45
192 193 7.979537 ACATGCTGTTAGTACGAGAAAATATCA 59.020 33.333 0.00 0.00 0.00 2.15
193 194 8.354011 ACATGCTGTTAGTACGAGAAAATATC 57.646 34.615 0.00 0.00 0.00 1.63
194 195 8.718102 AACATGCTGTTAGTACGAGAAAATAT 57.282 30.769 0.00 0.00 39.09 1.28
195 196 8.542497 AAACATGCTGTTAGTACGAGAAAATA 57.458 30.769 0.00 0.00 40.14 1.40
196 197 7.435068 AAACATGCTGTTAGTACGAGAAAAT 57.565 32.000 0.00 0.00 40.14 1.82
197 198 6.854496 AAACATGCTGTTAGTACGAGAAAA 57.146 33.333 0.00 0.00 40.14 2.29
198 199 7.949903 TTAAACATGCTGTTAGTACGAGAAA 57.050 32.000 0.00 0.00 40.14 2.52
199 200 9.079833 GTATTAAACATGCTGTTAGTACGAGAA 57.920 33.333 0.00 0.00 40.14 2.87
200 201 8.464404 AGTATTAAACATGCTGTTAGTACGAGA 58.536 33.333 0.00 0.00 40.14 4.04
201 202 8.630278 AGTATTAAACATGCTGTTAGTACGAG 57.370 34.615 0.00 0.00 40.14 4.18
202 203 8.865978 CAAGTATTAAACATGCTGTTAGTACGA 58.134 33.333 0.00 0.00 40.14 3.43
203 204 7.634817 GCAAGTATTAAACATGCTGTTAGTACG 59.365 37.037 0.00 0.00 46.73 3.67
204 205 8.822105 GCAAGTATTAAACATGCTGTTAGTAC 57.178 34.615 0.00 1.34 46.73 2.73
228 229 3.305964 GTCATTATGACTGCATGCATGC 58.694 45.455 38.71 38.71 44.66 4.06
240 241 7.363880 GGAGGAAGTAACTGACTGTCATTATGA 60.364 40.741 11.45 0.00 38.87 2.15
241 242 6.758886 GGAGGAAGTAACTGACTGTCATTATG 59.241 42.308 11.45 2.04 38.87 1.90
242 243 6.405953 CGGAGGAAGTAACTGACTGTCATTAT 60.406 42.308 11.45 3.40 38.87 1.28
243 244 5.105877 CGGAGGAAGTAACTGACTGTCATTA 60.106 44.000 11.45 9.24 38.87 1.90
244 245 4.322049 CGGAGGAAGTAACTGACTGTCATT 60.322 45.833 11.45 2.47 38.87 2.57
245 246 3.193691 CGGAGGAAGTAACTGACTGTCAT 59.806 47.826 11.45 0.00 38.87 3.06
246 247 2.557056 CGGAGGAAGTAACTGACTGTCA 59.443 50.000 10.50 10.50 38.87 3.58
247 248 2.671632 GCGGAGGAAGTAACTGACTGTC 60.672 54.545 0.00 0.00 38.87 3.51
248 249 1.272769 GCGGAGGAAGTAACTGACTGT 59.727 52.381 0.00 0.00 38.87 3.55
249 250 1.546476 AGCGGAGGAAGTAACTGACTG 59.454 52.381 0.00 0.00 38.87 3.51
250 251 1.819903 GAGCGGAGGAAGTAACTGACT 59.180 52.381 0.00 0.00 41.56 3.41
251 252 1.544691 TGAGCGGAGGAAGTAACTGAC 59.455 52.381 0.00 0.00 0.00 3.51
252 253 1.819288 CTGAGCGGAGGAAGTAACTGA 59.181 52.381 0.00 0.00 0.00 3.41
253 254 1.546476 ACTGAGCGGAGGAAGTAACTG 59.454 52.381 0.00 0.00 0.00 3.16
254 255 1.926108 ACTGAGCGGAGGAAGTAACT 58.074 50.000 0.00 0.00 0.00 2.24
255 256 2.745515 AACTGAGCGGAGGAAGTAAC 57.254 50.000 0.00 0.00 0.00 2.50
256 257 2.897969 AGAAACTGAGCGGAGGAAGTAA 59.102 45.455 0.00 0.00 0.00 2.24
257 258 2.526432 AGAAACTGAGCGGAGGAAGTA 58.474 47.619 0.00 0.00 0.00 2.24
258 259 1.343069 AGAAACTGAGCGGAGGAAGT 58.657 50.000 0.00 0.00 0.00 3.01
259 260 2.464157 AAGAAACTGAGCGGAGGAAG 57.536 50.000 0.00 0.00 0.00 3.46
260 261 2.494059 CAAAGAAACTGAGCGGAGGAA 58.506 47.619 0.00 0.00 0.00 3.36
261 262 1.878102 GCAAAGAAACTGAGCGGAGGA 60.878 52.381 0.00 0.00 0.00 3.71
262 263 0.519077 GCAAAGAAACTGAGCGGAGG 59.481 55.000 0.00 0.00 0.00 4.30
263 264 1.229428 TGCAAAGAAACTGAGCGGAG 58.771 50.000 0.00 0.00 0.00 4.63
264 265 1.536766 CATGCAAAGAAACTGAGCGGA 59.463 47.619 0.00 0.00 0.00 5.54
265 266 1.973138 CATGCAAAGAAACTGAGCGG 58.027 50.000 0.00 0.00 0.00 5.52
266 267 1.334054 GCATGCAAAGAAACTGAGCG 58.666 50.000 14.21 0.00 0.00 5.03
267 268 2.427232 TGCATGCAAAGAAACTGAGC 57.573 45.000 20.30 0.00 0.00 4.26
281 282 5.448225 GGGATCATTAATACTCGCATGCATG 60.448 44.000 22.70 22.70 0.00 4.06
282 283 4.637534 GGGATCATTAATACTCGCATGCAT 59.362 41.667 19.57 4.84 0.00 3.96
283 284 4.002982 GGGATCATTAATACTCGCATGCA 58.997 43.478 19.57 4.02 0.00 3.96
284 285 3.062639 CGGGATCATTAATACTCGCATGC 59.937 47.826 7.91 7.91 0.00 4.06
285 286 3.618594 CCGGGATCATTAATACTCGCATG 59.381 47.826 0.00 0.00 0.00 4.06
286 287 3.260884 ACCGGGATCATTAATACTCGCAT 59.739 43.478 6.32 0.77 0.00 4.73
287 288 2.631062 ACCGGGATCATTAATACTCGCA 59.369 45.455 6.32 0.00 0.00 5.10
288 289 3.314541 ACCGGGATCATTAATACTCGC 57.685 47.619 6.32 0.00 0.00 5.03
289 290 5.636543 GGTTTACCGGGATCATTAATACTCG 59.363 44.000 6.32 0.00 0.00 4.18
290 291 6.527423 TGGTTTACCGGGATCATTAATACTC 58.473 40.000 6.32 0.00 39.43 2.59
291 292 6.503560 TGGTTTACCGGGATCATTAATACT 57.496 37.500 6.32 0.00 39.43 2.12
292 293 7.571080 TTTGGTTTACCGGGATCATTAATAC 57.429 36.000 6.32 0.00 39.43 1.89
293 294 8.053963 TCTTTTGGTTTACCGGGATCATTAATA 58.946 33.333 6.32 0.00 39.43 0.98
294 295 6.893005 TCTTTTGGTTTACCGGGATCATTAAT 59.107 34.615 6.32 0.00 39.43 1.40
295 296 6.246919 TCTTTTGGTTTACCGGGATCATTAA 58.753 36.000 6.32 0.00 39.43 1.40
296 297 5.817784 TCTTTTGGTTTACCGGGATCATTA 58.182 37.500 6.32 0.00 39.43 1.90
297 298 4.668636 TCTTTTGGTTTACCGGGATCATT 58.331 39.130 6.32 0.00 39.43 2.57
298 299 4.310022 TCTTTTGGTTTACCGGGATCAT 57.690 40.909 6.32 0.00 39.43 2.45
299 300 3.791953 TCTTTTGGTTTACCGGGATCA 57.208 42.857 6.32 0.00 39.43 2.92
300 301 5.456548 TTTTCTTTTGGTTTACCGGGATC 57.543 39.130 6.32 0.00 39.43 3.36
301 302 6.428083 AATTTTCTTTTGGTTTACCGGGAT 57.572 33.333 6.32 0.00 39.43 3.85
302 303 5.873146 AATTTTCTTTTGGTTTACCGGGA 57.127 34.783 6.32 0.00 39.43 5.14
303 304 6.018588 GTCAAATTTTCTTTTGGTTTACCGGG 60.019 38.462 6.32 0.00 37.23 5.73
304 305 6.759356 AGTCAAATTTTCTTTTGGTTTACCGG 59.241 34.615 0.00 0.00 37.23 5.28
305 306 7.764695 AGTCAAATTTTCTTTTGGTTTACCG 57.235 32.000 0.00 0.00 37.23 4.02
306 307 8.941977 ACAAGTCAAATTTTCTTTTGGTTTACC 58.058 29.630 0.00 0.00 37.23 2.85
311 312 8.664798 GCTTTACAAGTCAAATTTTCTTTTGGT 58.335 29.630 0.00 0.00 37.23 3.67
312 313 8.663911 TGCTTTACAAGTCAAATTTTCTTTTGG 58.336 29.630 0.00 0.00 37.23 3.28
333 334 9.065798 ACCAATGTAAAATTTAATGCTTGCTTT 57.934 25.926 0.00 0.00 0.00 3.51
334 335 8.620116 ACCAATGTAAAATTTAATGCTTGCTT 57.380 26.923 0.00 0.00 0.00 3.91
335 336 9.150348 GTACCAATGTAAAATTTAATGCTTGCT 57.850 29.630 0.00 0.00 0.00 3.91
336 337 8.930760 TGTACCAATGTAAAATTTAATGCTTGC 58.069 29.630 0.00 0.00 0.00 4.01
351 352 8.661257 CAAACTCGAATTACATGTACCAATGTA 58.339 33.333 4.68 2.70 41.09 2.29
352 353 7.174253 ACAAACTCGAATTACATGTACCAATGT 59.826 33.333 4.68 4.44 43.21 2.71
353 354 7.481483 CACAAACTCGAATTACATGTACCAATG 59.519 37.037 4.68 0.00 0.00 2.82
354 355 7.361713 CCACAAACTCGAATTACATGTACCAAT 60.362 37.037 4.68 0.00 0.00 3.16
355 356 6.072948 CCACAAACTCGAATTACATGTACCAA 60.073 38.462 4.68 0.00 0.00 3.67
356 357 5.410132 CCACAAACTCGAATTACATGTACCA 59.590 40.000 4.68 0.00 0.00 3.25
357 358 5.672819 GCCACAAACTCGAATTACATGTACC 60.673 44.000 4.68 0.00 0.00 3.34
358 359 5.321516 GCCACAAACTCGAATTACATGTAC 58.678 41.667 4.68 0.00 0.00 2.90
359 360 4.393680 GGCCACAAACTCGAATTACATGTA 59.606 41.667 0.08 0.08 0.00 2.29
360 361 3.190535 GGCCACAAACTCGAATTACATGT 59.809 43.478 2.69 2.69 0.00 3.21
361 362 3.440173 AGGCCACAAACTCGAATTACATG 59.560 43.478 5.01 0.00 0.00 3.21
362 363 3.686016 AGGCCACAAACTCGAATTACAT 58.314 40.909 5.01 0.00 0.00 2.29
363 364 3.134574 AGGCCACAAACTCGAATTACA 57.865 42.857 5.01 0.00 0.00 2.41
364 365 3.252458 ACAAGGCCACAAACTCGAATTAC 59.748 43.478 5.01 0.00 0.00 1.89
365 366 3.482436 ACAAGGCCACAAACTCGAATTA 58.518 40.909 5.01 0.00 0.00 1.40
366 367 2.306847 ACAAGGCCACAAACTCGAATT 58.693 42.857 5.01 0.00 0.00 2.17
367 368 1.981256 ACAAGGCCACAAACTCGAAT 58.019 45.000 5.01 0.00 0.00 3.34
368 369 2.623878 TACAAGGCCACAAACTCGAA 57.376 45.000 5.01 0.00 0.00 3.71
369 370 2.851263 ATACAAGGCCACAAACTCGA 57.149 45.000 5.01 0.00 0.00 4.04
370 371 3.331150 TGTATACAAGGCCACAAACTCG 58.669 45.455 5.01 0.00 0.00 4.18
371 372 5.699097 TTTGTATACAAGGCCACAAACTC 57.301 39.130 17.36 0.00 36.31 3.01
372 373 6.472686 TTTTTGTATACAAGGCCACAAACT 57.527 33.333 17.36 0.00 39.78 2.66
373 374 6.147000 CCATTTTTGTATACAAGGCCACAAAC 59.853 38.462 17.36 1.89 39.78 2.93
374 375 6.042093 TCCATTTTTGTATACAAGGCCACAAA 59.958 34.615 17.36 13.98 38.68 2.83
375 376 5.540337 TCCATTTTTGTATACAAGGCCACAA 59.460 36.000 17.36 2.10 37.15 3.33
376 377 5.080337 TCCATTTTTGTATACAAGGCCACA 58.920 37.500 17.36 0.00 37.15 4.17
377 378 5.394115 CCTCCATTTTTGTATACAAGGCCAC 60.394 44.000 17.36 0.00 37.15 5.01
378 379 4.709397 CCTCCATTTTTGTATACAAGGCCA 59.291 41.667 17.36 1.16 37.15 5.36
379 380 4.099419 CCCTCCATTTTTGTATACAAGGCC 59.901 45.833 17.36 0.00 37.15 5.19
380 381 4.953579 TCCCTCCATTTTTGTATACAAGGC 59.046 41.667 17.36 0.00 37.15 4.35
381 382 6.187682 ACTCCCTCCATTTTTGTATACAAGG 58.812 40.000 17.36 15.00 37.15 3.61
382 383 8.980481 ATACTCCCTCCATTTTTGTATACAAG 57.020 34.615 17.36 6.89 37.15 3.16
383 384 9.762381 AAATACTCCCTCCATTTTTGTATACAA 57.238 29.630 14.35 14.35 0.00 2.41
384 385 9.762381 AAAATACTCCCTCCATTTTTGTATACA 57.238 29.630 0.08 0.08 29.77 2.29
391 392 7.071824 TCCAACAAAAATACTCCCTCCATTTTT 59.928 33.333 0.00 0.00 40.62 1.94
392 393 6.556874 TCCAACAAAAATACTCCCTCCATTTT 59.443 34.615 0.00 0.00 34.24 1.82
393 394 6.081356 TCCAACAAAAATACTCCCTCCATTT 58.919 36.000 0.00 0.00 0.00 2.32
394 395 5.650283 TCCAACAAAAATACTCCCTCCATT 58.350 37.500 0.00 0.00 0.00 3.16
395 396 5.269554 TCCAACAAAAATACTCCCTCCAT 57.730 39.130 0.00 0.00 0.00 3.41
396 397 4.733077 TCCAACAAAAATACTCCCTCCA 57.267 40.909 0.00 0.00 0.00 3.86
397 398 5.714806 TGATTCCAACAAAAATACTCCCTCC 59.285 40.000 0.00 0.00 0.00 4.30
398 399 6.834168 TGATTCCAACAAAAATACTCCCTC 57.166 37.500 0.00 0.00 0.00 4.30
509 510 8.325787 TGACACATATTACTTAGGTCAACCATT 58.674 33.333 1.33 0.00 38.89 3.16
736 748 1.669999 ATCCATGAAAGCCGCCTTGC 61.670 55.000 0.00 0.00 0.00 4.01
779 791 2.483538 GCTTGTGTCAAAAACCATGGCT 60.484 45.455 13.04 0.00 0.00 4.75
889 901 2.943036 TTTTACTCCCACTCCCACAC 57.057 50.000 0.00 0.00 0.00 3.82
974 986 9.041354 TGCCTATAAAGACAAATTTGGGTTAAT 57.959 29.630 21.74 11.66 0.00 1.40
975 987 8.423906 TGCCTATAAAGACAAATTTGGGTTAA 57.576 30.769 21.74 5.35 0.00 2.01
976 988 8.474025 CATGCCTATAAAGACAAATTTGGGTTA 58.526 33.333 21.74 15.44 0.00 2.85
978 990 6.127083 CCATGCCTATAAAGACAAATTTGGGT 60.127 38.462 21.74 5.96 0.00 4.51
1080 3905 8.324191 TCATATCTTTGTCCTTCACCTTATCT 57.676 34.615 0.00 0.00 0.00 1.98
1159 3984 6.241882 TCCTTCCGTCCATGATTTATTGTA 57.758 37.500 0.00 0.00 0.00 2.41
1250 4075 5.021033 TGAACTTGAACAACTTACCGGTA 57.979 39.130 11.16 11.16 0.00 4.02
1251 4076 3.876341 TGAACTTGAACAACTTACCGGT 58.124 40.909 13.98 13.98 0.00 5.28
1282 4107 5.302360 AGATTCAAGTTGTAGCAACGGTTA 58.698 37.500 2.11 0.00 0.00 2.85
1520 4345 3.394836 GCGTGCCCTCTCCTCCTT 61.395 66.667 0.00 0.00 0.00 3.36
1539 4364 3.770666 TCTTAACGAGCAATCTTCTCCG 58.229 45.455 0.00 0.00 0.00 4.63
1556 4381 6.696411 CAAGCTTTCTTTCTCTCTCCTCTTA 58.304 40.000 0.00 0.00 0.00 2.10
1569 4394 1.122227 TGCCCTTGCAAGCTTTCTTT 58.878 45.000 21.43 0.00 46.66 2.52
1588 4413 1.674057 CTCCTCTTGGGCTTCACGT 59.326 57.895 0.00 0.00 34.39 4.49
1956 4792 0.527565 AATTGCTTACTGCCAAGGCG 59.472 50.000 6.60 4.13 45.51 5.52
1965 4801 6.472686 TGTTGTGGGTTTTAATTGCTTACT 57.527 33.333 0.00 0.00 0.00 2.24
1979 4815 0.923358 TCCAGGAGTTTGTTGTGGGT 59.077 50.000 0.00 0.00 0.00 4.51
2089 4925 3.198068 CGATATGGTCACAGAACAAGGG 58.802 50.000 0.00 0.00 31.09 3.95
2213 5050 8.349983 GTTGTCAATTTGGTCACAGTAGTAATT 58.650 33.333 0.00 0.00 0.00 1.40
2233 5070 3.497763 CCCTACCACTGGAAATGTTGTCA 60.498 47.826 0.71 0.00 0.00 3.58
2235 5072 2.445525 ACCCTACCACTGGAAATGTTGT 59.554 45.455 0.71 0.00 0.00 3.32
2237 5074 3.496331 CAACCCTACCACTGGAAATGTT 58.504 45.455 0.71 0.00 0.00 2.71
2263 5100 0.964358 CGAGAGGTCCAACGGTAGGT 60.964 60.000 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.