Multiple sequence alignment - TraesCS2A01G408700

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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 TraesCS2A01G408700 chr2A 100.000 3028 0 0 1 3028 666024828 666027855 0.000000e+00 5592.0
1 TraesCS2A01G408700 chr2A 90.526 95 7 1 9 101 68018363 68018269 1.140000e-24 124.0
2 TraesCS2A01G408700 chr2D 91.989 1885 82 31 390 2210 521534823 521532944 0.000000e+00 2580.0
3 TraesCS2A01G408700 chr2D 89.904 832 53 18 2219 3027 521532863 521532040 0.000000e+00 1042.0
4 TraesCS2A01G408700 chr2D 84.672 137 17 4 48 180 521564090 521563954 1.890000e-27 134.0
5 TraesCS2A01G408700 chr2D 96.429 56 2 0 341 396 521536412 521536357 3.210000e-15 93.5
6 TraesCS2A01G408700 chr7B 85.420 1406 176 18 371 1761 329515159 329516550 0.000000e+00 1434.0
7 TraesCS2A01G408700 chr7B 74.750 1398 268 58 370 1748 557490261 557491592 5.710000e-152 547.0
8 TraesCS2A01G408700 chr7B 86.239 109 13 1 1 107 34048069 34047961 1.910000e-22 117.0
9 TraesCS2A01G408700 chr7D 85.340 1412 173 19 371 1761 186427062 186428460 0.000000e+00 1430.0
10 TraesCS2A01G408700 chr7D 75.139 1078 216 39 372 1433 523126813 523127854 2.750000e-125 459.0
11 TraesCS2A01G408700 chr2B 90.345 1129 53 16 1134 2216 614329473 614330591 0.000000e+00 1430.0
12 TraesCS2A01G408700 chr2B 90.168 1129 55 16 1134 2216 614432845 614433963 0.000000e+00 1419.0
13 TraesCS2A01G408700 chr2B 93.588 811 49 2 330 1139 614313705 614314513 0.000000e+00 1206.0
14 TraesCS2A01G408700 chr2B 93.095 811 53 2 330 1139 614418776 614419584 0.000000e+00 1184.0
15 TraesCS2A01G408700 chr2B 93.571 560 33 1 2469 3028 614330840 614331396 0.000000e+00 832.0
16 TraesCS2A01G408700 chr2B 93.571 560 33 1 2469 3028 614434247 614434803 0.000000e+00 832.0
17 TraesCS2A01G408700 chr6A 82.739 1431 201 36 370 1773 496579034 496577623 0.000000e+00 1232.0
18 TraesCS2A01G408700 chr7A 87.061 1082 126 11 374 1449 198512371 198511298 0.000000e+00 1210.0
19 TraesCS2A01G408700 chr6D 82.135 1405 212 24 370 1748 346832918 346834309 0.000000e+00 1168.0
20 TraesCS2A01G408700 chr6B 82.064 1405 213 23 370 1748 534236767 534235376 0.000000e+00 1162.0
21 TraesCS2A01G408700 chr5D 90.426 94 7 1 1 92 312116246 312116339 4.100000e-24 122.0
22 TraesCS2A01G408700 chr5B 88.660 97 9 1 1 95 241673221 241673125 1.910000e-22 117.0
23 TraesCS2A01G408700 chr3D 90.805 87 8 0 1 87 582014840 582014754 1.910000e-22 117.0
24 TraesCS2A01G408700 chr3B 87.255 102 11 1 2 101 816225879 816225778 6.860000e-22 115.0
25 TraesCS2A01G408700 chr3B 84.545 110 15 1 1 108 784924725 784924834 1.150000e-19 108.0
26 TraesCS2A01G408700 chr1B 87.629 97 10 1 1 95 517901698 517901602 8.870000e-21 111.0


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 TraesCS2A01G408700 chr2A 666024828 666027855 3027 False 5592.0 5592 100.0000 1 3028 1 chr2A.!!$F1 3027
1 TraesCS2A01G408700 chr2D 521532040 521536412 4372 True 1238.5 2580 92.7740 341 3027 3 chr2D.!!$R2 2686
2 TraesCS2A01G408700 chr7B 329515159 329516550 1391 False 1434.0 1434 85.4200 371 1761 1 chr7B.!!$F1 1390
3 TraesCS2A01G408700 chr7B 557490261 557491592 1331 False 547.0 547 74.7500 370 1748 1 chr7B.!!$F2 1378
4 TraesCS2A01G408700 chr7D 186427062 186428460 1398 False 1430.0 1430 85.3400 371 1761 1 chr7D.!!$F1 1390
5 TraesCS2A01G408700 chr7D 523126813 523127854 1041 False 459.0 459 75.1390 372 1433 1 chr7D.!!$F2 1061
6 TraesCS2A01G408700 chr2B 614313705 614314513 808 False 1206.0 1206 93.5880 330 1139 1 chr2B.!!$F1 809
7 TraesCS2A01G408700 chr2B 614418776 614419584 808 False 1184.0 1184 93.0950 330 1139 1 chr2B.!!$F2 809
8 TraesCS2A01G408700 chr2B 614329473 614331396 1923 False 1131.0 1430 91.9580 1134 3028 2 chr2B.!!$F3 1894
9 TraesCS2A01G408700 chr2B 614432845 614434803 1958 False 1125.5 1419 91.8695 1134 3028 2 chr2B.!!$F4 1894
10 TraesCS2A01G408700 chr6A 496577623 496579034 1411 True 1232.0 1232 82.7390 370 1773 1 chr6A.!!$R1 1403
11 TraesCS2A01G408700 chr7A 198511298 198512371 1073 True 1210.0 1210 87.0610 374 1449 1 chr7A.!!$R1 1075
12 TraesCS2A01G408700 chr6D 346832918 346834309 1391 False 1168.0 1168 82.1350 370 1748 1 chr6D.!!$F1 1378
13 TraesCS2A01G408700 chr6B 534235376 534236767 1391 True 1162.0 1162 82.0640 370 1748 1 chr6B.!!$R1 1378

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
158 159 0.250684 TTCATTGCAGCGAACCTCCA 60.251 50.0 0.0 0.0 0.0 3.86 F
188 189 0.468029 CAAGGAGCAAGGGTGTGGTT 60.468 55.0 0.0 0.0 0.0 3.67 F
191 192 0.690762 GGAGCAAGGGTGTGGTTAGA 59.309 55.0 0.0 0.0 0.0 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 3531 0.035152 AATGCGATGCTCCCACTTGA 60.035 50.00 0.00 0.00 0.00 3.02 R
1990 3623 0.609406 AAGAAAAAGGAGGAGCCGGC 60.609 55.00 21.89 21.89 43.43 6.13 R
2110 3767 3.375610 TCAGCAAAGTTAGCAAAACGTGA 59.624 39.13 0.00 3.24 0.00 4.35 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
46 47 6.803154 AGACTGTAGGTTAACTCATTTTGC 57.197 37.500 5.42 0.00 0.00 3.68
47 48 6.534634 AGACTGTAGGTTAACTCATTTTGCT 58.465 36.000 5.42 0.00 0.00 3.91
48 49 6.651225 AGACTGTAGGTTAACTCATTTTGCTC 59.349 38.462 5.42 0.00 0.00 4.26
49 50 5.705905 ACTGTAGGTTAACTCATTTTGCTCC 59.294 40.000 5.42 0.00 0.00 4.70
50 51 4.693566 TGTAGGTTAACTCATTTTGCTCCG 59.306 41.667 5.42 0.00 0.00 4.63
51 52 3.751518 AGGTTAACTCATTTTGCTCCGT 58.248 40.909 5.42 0.00 0.00 4.69
52 53 4.901868 AGGTTAACTCATTTTGCTCCGTA 58.098 39.130 5.42 0.00 0.00 4.02
53 54 5.497474 AGGTTAACTCATTTTGCTCCGTAT 58.503 37.500 5.42 0.00 0.00 3.06
54 55 5.354234 AGGTTAACTCATTTTGCTCCGTATG 59.646 40.000 5.42 0.00 0.00 2.39
55 56 5.123344 GGTTAACTCATTTTGCTCCGTATGT 59.877 40.000 5.42 0.00 0.00 2.29
56 57 6.314400 GGTTAACTCATTTTGCTCCGTATGTA 59.686 38.462 5.42 0.00 0.00 2.29
57 58 7.399523 GTTAACTCATTTTGCTCCGTATGTAG 58.600 38.462 0.00 0.00 0.00 2.74
58 59 5.086104 ACTCATTTTGCTCCGTATGTAGT 57.914 39.130 0.00 0.00 0.00 2.73
59 60 5.109903 ACTCATTTTGCTCCGTATGTAGTC 58.890 41.667 0.00 0.00 0.00 2.59
60 61 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
61 62 5.730550 TCATTTTGCTCCGTATGTAGTCTT 58.269 37.500 0.00 0.00 0.00 3.01
62 63 6.869695 TCATTTTGCTCCGTATGTAGTCTTA 58.130 36.000 0.00 0.00 0.00 2.10
63 64 7.497595 TCATTTTGCTCCGTATGTAGTCTTAT 58.502 34.615 0.00 0.00 0.00 1.73
64 65 7.985184 TCATTTTGCTCCGTATGTAGTCTTATT 59.015 33.333 0.00 0.00 0.00 1.40
65 66 7.534085 TTTTGCTCCGTATGTAGTCTTATTG 57.466 36.000 0.00 0.00 0.00 1.90
66 67 6.459670 TTGCTCCGTATGTAGTCTTATTGA 57.540 37.500 0.00 0.00 0.00 2.57
67 68 6.459670 TGCTCCGTATGTAGTCTTATTGAA 57.540 37.500 0.00 0.00 0.00 2.69
68 69 6.869695 TGCTCCGTATGTAGTCTTATTGAAA 58.130 36.000 0.00 0.00 0.00 2.69
69 70 7.497595 TGCTCCGTATGTAGTCTTATTGAAAT 58.502 34.615 0.00 0.00 0.00 2.17
70 71 7.652105 TGCTCCGTATGTAGTCTTATTGAAATC 59.348 37.037 0.00 0.00 0.00 2.17
71 72 7.868415 GCTCCGTATGTAGTCTTATTGAAATCT 59.132 37.037 0.00 0.00 0.00 2.40
72 73 9.751542 CTCCGTATGTAGTCTTATTGAAATCTT 57.248 33.333 0.00 0.00 0.00 2.40
116 117 9.866655 AGGAATGAAGGAACTATAATTTATGCA 57.133 29.630 0.00 0.00 38.49 3.96
117 118 9.899226 GGAATGAAGGAACTATAATTTATGCAC 57.101 33.333 0.00 0.00 38.49 4.57
137 138 8.876275 ATGCACATAATGTTCAATATTTGTCC 57.124 30.769 0.00 0.00 25.52 4.02
138 139 7.834803 TGCACATAATGTTCAATATTTGTCCA 58.165 30.769 0.00 0.00 0.00 4.02
139 140 8.476447 TGCACATAATGTTCAATATTTGTCCAT 58.524 29.630 0.00 0.00 0.00 3.41
140 141 9.316730 GCACATAATGTTCAATATTTGTCCATT 57.683 29.630 0.00 9.96 36.64 3.16
146 147 7.830940 TGTTCAATATTTGTCCATTCATTGC 57.169 32.000 0.00 0.00 0.00 3.56
147 148 7.384477 TGTTCAATATTTGTCCATTCATTGCA 58.616 30.769 0.00 0.00 0.00 4.08
148 149 7.546316 TGTTCAATATTTGTCCATTCATTGCAG 59.454 33.333 0.00 0.00 0.00 4.41
149 150 6.044046 TCAATATTTGTCCATTCATTGCAGC 58.956 36.000 0.00 0.00 0.00 5.25
150 151 2.350899 TTTGTCCATTCATTGCAGCG 57.649 45.000 0.00 0.00 0.00 5.18
151 152 1.532523 TTGTCCATTCATTGCAGCGA 58.467 45.000 0.00 0.00 0.00 4.93
152 153 1.532523 TGTCCATTCATTGCAGCGAA 58.467 45.000 2.74 2.74 0.00 4.70
153 154 1.199789 TGTCCATTCATTGCAGCGAAC 59.800 47.619 2.33 0.00 0.00 3.95
154 155 0.810648 TCCATTCATTGCAGCGAACC 59.189 50.000 2.33 0.00 0.00 3.62
155 156 0.813184 CCATTCATTGCAGCGAACCT 59.187 50.000 2.33 0.00 0.00 3.50
156 157 1.202222 CCATTCATTGCAGCGAACCTC 60.202 52.381 2.33 0.00 0.00 3.85
157 158 1.098050 ATTCATTGCAGCGAACCTCC 58.902 50.000 2.33 0.00 0.00 4.30
158 159 0.250684 TTCATTGCAGCGAACCTCCA 60.251 50.000 0.00 0.00 0.00 3.86
159 160 0.674581 TCATTGCAGCGAACCTCCAG 60.675 55.000 0.00 0.00 0.00 3.86
160 161 0.957395 CATTGCAGCGAACCTCCAGT 60.957 55.000 0.00 0.00 0.00 4.00
161 162 0.957395 ATTGCAGCGAACCTCCAGTG 60.957 55.000 0.00 0.00 0.00 3.66
162 163 2.743928 GCAGCGAACCTCCAGTGG 60.744 66.667 1.40 1.40 0.00 4.00
163 164 3.059982 CAGCGAACCTCCAGTGGA 58.940 61.111 12.40 12.40 0.00 4.02
164 165 1.374758 CAGCGAACCTCCAGTGGAC 60.375 63.158 8.12 0.00 0.00 4.02
165 166 1.837051 AGCGAACCTCCAGTGGACA 60.837 57.895 8.12 0.00 0.00 4.02
166 167 1.668151 GCGAACCTCCAGTGGACAC 60.668 63.158 8.12 0.00 0.00 3.67
167 168 1.372997 CGAACCTCCAGTGGACACG 60.373 63.158 8.12 7.85 36.20 4.49
168 169 1.004918 GAACCTCCAGTGGACACGG 60.005 63.158 8.12 11.20 36.20 4.94
169 170 3.178540 AACCTCCAGTGGACACGGC 62.179 63.158 8.12 0.00 36.20 5.68
170 171 3.625897 CCTCCAGTGGACACGGCA 61.626 66.667 8.12 0.00 36.20 5.69
171 172 2.425592 CTCCAGTGGACACGGCAA 59.574 61.111 8.12 0.00 36.20 4.52
172 173 1.669115 CTCCAGTGGACACGGCAAG 60.669 63.158 8.12 0.00 36.20 4.01
173 174 2.669569 CCAGTGGACACGGCAAGG 60.670 66.667 1.68 0.00 36.20 3.61
174 175 2.425592 CAGTGGACACGGCAAGGA 59.574 61.111 0.00 0.00 36.20 3.36
175 176 1.669115 CAGTGGACACGGCAAGGAG 60.669 63.158 0.00 0.00 36.20 3.69
176 177 3.050275 GTGGACACGGCAAGGAGC 61.050 66.667 0.00 0.00 44.65 4.70
185 186 3.359002 GCAAGGAGCAAGGGTGTG 58.641 61.111 0.00 0.00 44.79 3.82
186 187 2.270986 GCAAGGAGCAAGGGTGTGG 61.271 63.158 0.00 0.00 44.79 4.17
187 188 1.151450 CAAGGAGCAAGGGTGTGGT 59.849 57.895 0.00 0.00 0.00 4.16
188 189 0.468029 CAAGGAGCAAGGGTGTGGTT 60.468 55.000 0.00 0.00 0.00 3.67
189 190 1.145571 AAGGAGCAAGGGTGTGGTTA 58.854 50.000 0.00 0.00 0.00 2.85
190 191 0.693049 AGGAGCAAGGGTGTGGTTAG 59.307 55.000 0.00 0.00 0.00 2.34
191 192 0.690762 GGAGCAAGGGTGTGGTTAGA 59.309 55.000 0.00 0.00 0.00 2.10
192 193 1.282157 GGAGCAAGGGTGTGGTTAGAT 59.718 52.381 0.00 0.00 0.00 1.98
193 194 2.633488 GAGCAAGGGTGTGGTTAGATC 58.367 52.381 0.00 0.00 0.00 2.75
194 195 1.066143 AGCAAGGGTGTGGTTAGATCG 60.066 52.381 0.00 0.00 0.00 3.69
195 196 1.066430 GCAAGGGTGTGGTTAGATCGA 60.066 52.381 0.00 0.00 0.00 3.59
196 197 2.618053 CAAGGGTGTGGTTAGATCGAC 58.382 52.381 0.00 0.00 0.00 4.20
197 198 2.233305 AGGGTGTGGTTAGATCGACT 57.767 50.000 0.00 0.00 0.00 4.18
198 199 2.537143 AGGGTGTGGTTAGATCGACTT 58.463 47.619 0.00 0.00 0.00 3.01
199 200 2.233922 AGGGTGTGGTTAGATCGACTTG 59.766 50.000 0.00 0.00 0.00 3.16
200 201 2.232941 GGGTGTGGTTAGATCGACTTGA 59.767 50.000 0.00 0.00 0.00 3.02
201 202 3.251571 GGTGTGGTTAGATCGACTTGAC 58.748 50.000 0.00 0.00 0.00 3.18
202 203 2.915463 GTGTGGTTAGATCGACTTGACG 59.085 50.000 0.00 0.00 0.00 4.35
203 204 2.815503 TGTGGTTAGATCGACTTGACGA 59.184 45.455 0.00 0.00 46.04 4.20
204 205 3.253921 TGTGGTTAGATCGACTTGACGAA 59.746 43.478 0.00 0.00 45.16 3.85
205 206 3.852536 GTGGTTAGATCGACTTGACGAAG 59.147 47.826 0.00 0.00 45.16 3.79
222 223 5.303747 ACGAAGTCTCAGTCAAGTGATAG 57.696 43.478 0.00 0.00 29.74 2.08
223 224 5.004448 ACGAAGTCTCAGTCAAGTGATAGA 58.996 41.667 0.00 0.00 29.74 1.98
224 225 5.473846 ACGAAGTCTCAGTCAAGTGATAGAA 59.526 40.000 0.00 0.00 29.74 2.10
225 226 6.151985 ACGAAGTCTCAGTCAAGTGATAGAAT 59.848 38.462 0.00 0.00 29.74 2.40
226 227 7.337184 ACGAAGTCTCAGTCAAGTGATAGAATA 59.663 37.037 0.00 0.00 29.74 1.75
227 228 8.349245 CGAAGTCTCAGTCAAGTGATAGAATAT 58.651 37.037 0.00 0.00 0.00 1.28
295 296 8.484641 AATGTAATGAATATAGCATCGACTGG 57.515 34.615 0.00 0.00 0.00 4.00
296 297 6.398095 TGTAATGAATATAGCATCGACTGGG 58.602 40.000 0.00 0.00 0.00 4.45
297 298 5.489792 AATGAATATAGCATCGACTGGGT 57.510 39.130 0.00 0.00 0.00 4.51
298 299 4.521130 TGAATATAGCATCGACTGGGTC 57.479 45.455 0.00 0.00 0.00 4.46
299 300 3.895041 TGAATATAGCATCGACTGGGTCA 59.105 43.478 0.00 0.00 32.09 4.02
300 301 4.343814 TGAATATAGCATCGACTGGGTCAA 59.656 41.667 0.00 0.00 32.09 3.18
301 302 5.012046 TGAATATAGCATCGACTGGGTCAAT 59.988 40.000 0.00 0.00 32.09 2.57
302 303 3.845781 ATAGCATCGACTGGGTCAATT 57.154 42.857 0.00 0.00 32.09 2.32
303 304 4.955811 ATAGCATCGACTGGGTCAATTA 57.044 40.909 0.00 0.00 32.09 1.40
304 305 3.627395 AGCATCGACTGGGTCAATTAA 57.373 42.857 0.00 0.00 32.09 1.40
305 306 3.535561 AGCATCGACTGGGTCAATTAAG 58.464 45.455 0.00 0.00 32.09 1.85
306 307 3.197766 AGCATCGACTGGGTCAATTAAGA 59.802 43.478 0.00 0.00 32.09 2.10
307 308 4.130118 GCATCGACTGGGTCAATTAAGAT 58.870 43.478 0.00 0.00 32.09 2.40
308 309 4.576463 GCATCGACTGGGTCAATTAAGATT 59.424 41.667 0.00 0.00 32.09 2.40
309 310 5.066505 GCATCGACTGGGTCAATTAAGATTT 59.933 40.000 0.00 0.00 32.09 2.17
310 311 6.260050 GCATCGACTGGGTCAATTAAGATTTA 59.740 38.462 0.00 0.00 32.09 1.40
311 312 7.519008 GCATCGACTGGGTCAATTAAGATTTAG 60.519 40.741 0.00 0.00 32.09 1.85
312 313 5.815740 TCGACTGGGTCAATTAAGATTTAGC 59.184 40.000 0.00 0.00 32.09 3.09
313 314 5.584649 CGACTGGGTCAATTAAGATTTAGCA 59.415 40.000 0.00 0.00 32.09 3.49
314 315 6.093495 CGACTGGGTCAATTAAGATTTAGCAA 59.907 38.462 0.00 0.00 32.09 3.91
315 316 7.201732 CGACTGGGTCAATTAAGATTTAGCAAT 60.202 37.037 0.00 0.00 32.09 3.56
316 317 8.000780 ACTGGGTCAATTAAGATTTAGCAATC 57.999 34.615 0.00 0.00 39.45 2.67
317 318 7.068716 ACTGGGTCAATTAAGATTTAGCAATCC 59.931 37.037 0.00 0.00 39.95 3.01
318 319 6.323739 TGGGTCAATTAAGATTTAGCAATCCC 59.676 38.462 0.00 0.00 39.95 3.85
319 320 6.438763 GGTCAATTAAGATTTAGCAATCCCG 58.561 40.000 0.00 0.00 39.95 5.14
320 321 6.039382 GGTCAATTAAGATTTAGCAATCCCGT 59.961 38.462 0.00 0.00 39.95 5.28
321 322 7.416326 GGTCAATTAAGATTTAGCAATCCCGTT 60.416 37.037 0.00 0.00 39.95 4.44
322 323 7.973944 GTCAATTAAGATTTAGCAATCCCGTTT 59.026 33.333 0.00 0.00 39.95 3.60
323 324 8.188139 TCAATTAAGATTTAGCAATCCCGTTTC 58.812 33.333 0.00 0.00 39.95 2.78
324 325 4.983671 AAGATTTAGCAATCCCGTTTCC 57.016 40.909 0.00 0.00 39.95 3.13
325 326 2.943033 AGATTTAGCAATCCCGTTTCCG 59.057 45.455 0.00 0.00 39.95 4.30
388 1929 2.092699 GGTGAGCTCCTTGATAAAGCCT 60.093 50.000 12.15 0.00 36.69 4.58
555 2096 2.825836 CTTCATGTCCAGCCCCGC 60.826 66.667 0.00 0.00 0.00 6.13
673 2214 4.652131 TTCCACCCGGCATGCGTT 62.652 61.111 12.44 0.00 0.00 4.84
833 2374 1.740296 GCCCACATGAACGCGTAGT 60.740 57.895 14.46 6.45 0.00 2.73
883 2425 1.078426 AACTCCTCCCGCGAAATGG 60.078 57.895 8.23 0.00 0.00 3.16
885 2427 1.078426 CTCCTCCCGCGAAATGGTT 60.078 57.895 8.23 0.00 0.00 3.67
944 2486 4.760047 GTGCCCATCGAGCCACGT 62.760 66.667 0.00 0.00 43.13 4.49
1158 2700 4.783621 TGCAGCATGGGGTCGAGC 62.784 66.667 5.93 5.93 35.86 5.03
1275 2827 3.224324 TCGGCGCCTACAGGGATC 61.224 66.667 26.68 0.00 37.23 3.36
1780 3359 3.934962 GCCTCTCCTCCATCGCCC 61.935 72.222 0.00 0.00 0.00 6.13
1822 3401 3.335534 GCGTCAAGTGCGTTCCGT 61.336 61.111 0.00 0.00 0.00 4.69
1828 3407 1.529438 TCAAGTGCGTTCCGTCAAATC 59.471 47.619 0.00 0.00 0.00 2.17
1838 3417 1.071542 TCCGTCAAATCCAACTCAGCA 59.928 47.619 0.00 0.00 0.00 4.41
1847 3426 4.314440 AACTCAGCAAGCGCCGGA 62.314 61.111 5.05 0.00 39.83 5.14
1885 3489 9.944663 TTCATGTTGATAAAGTATTTAATCGGC 57.055 29.630 0.00 0.00 44.76 5.54
1915 3519 2.466846 CTGTGCCTGCTCTTTTGTTTG 58.533 47.619 0.00 0.00 0.00 2.93
1918 3522 2.099756 GTGCCTGCTCTTTTGTTTGTCT 59.900 45.455 0.00 0.00 0.00 3.41
1959 3568 2.760634 TCGCATTCCAGTTTCTGCTA 57.239 45.000 0.00 0.00 32.48 3.49
1961 3570 4.400529 TCGCATTCCAGTTTCTGCTATA 57.599 40.909 0.00 0.00 32.48 1.31
1969 3580 8.821894 CATTCCAGTTTCTGCTATACTTTACTC 58.178 37.037 0.00 0.00 0.00 2.59
1988 3621 2.467826 GCTGAAGGGCGAGCATGAC 61.468 63.158 0.00 0.00 35.15 3.06
1989 3622 1.817099 CTGAAGGGCGAGCATGACC 60.817 63.158 0.00 0.00 37.26 4.02
1990 3623 2.892425 GAAGGGCGAGCATGACCG 60.892 66.667 0.00 0.00 44.11 4.79
2048 3688 2.912690 AGAGGCCGGCTAAGAATTAC 57.087 50.000 28.56 5.83 0.00 1.89
2056 3700 4.624015 CCGGCTAAGAATTACATACGGAA 58.376 43.478 0.00 0.00 41.13 4.30
2057 3701 5.235516 CCGGCTAAGAATTACATACGGAAT 58.764 41.667 0.00 0.00 41.13 3.01
2079 3723 9.307121 GGAATATATACTGATCAATTGACGGAG 57.693 37.037 11.07 9.23 0.00 4.63
2182 3840 7.116376 TCTCTAAAACAGTGCTCAAAACTATCG 59.884 37.037 0.00 0.00 0.00 2.92
2216 3874 1.257743 GCGATATGGTAGCCAGGAGA 58.742 55.000 0.00 0.00 36.75 3.71
2217 3875 1.618837 GCGATATGGTAGCCAGGAGAA 59.381 52.381 0.00 0.00 36.75 2.87
2250 3984 0.459934 TGTTGCAACCAGCTGTTTGC 60.460 50.000 34.37 34.37 45.94 3.68
2299 4033 1.091771 TGCTTCAGCCATTAGAGCGC 61.092 55.000 0.00 0.00 41.18 5.92
2319 4053 3.374988 CGCTTGCACTCCAATCAATCTTA 59.625 43.478 0.00 0.00 31.91 2.10
2320 4054 4.036027 CGCTTGCACTCCAATCAATCTTAT 59.964 41.667 0.00 0.00 31.91 1.73
2365 4103 6.406692 AAACAGAGTTTCTCAGTACAGCTA 57.593 37.500 0.00 0.00 30.25 3.32
2377 4115 0.976641 TACAGCTACAGTTGCAGCCT 59.023 50.000 9.75 0.00 38.61 4.58
2379 4117 0.604780 CAGCTACAGTTGCAGCCTGT 60.605 55.000 20.60 20.60 44.90 4.00
2380 4118 0.976641 AGCTACAGTTGCAGCCTGTA 59.023 50.000 20.62 20.62 42.83 2.74
2381 4119 1.556911 AGCTACAGTTGCAGCCTGTAT 59.443 47.619 21.58 10.60 42.73 2.29
2395 4133 8.827177 TGCAGCCTGTATTATAAAGTACATAC 57.173 34.615 0.00 0.00 31.06 2.39
2439 4177 0.685458 ACCATCATGCCCTTCAAGCC 60.685 55.000 0.00 0.00 0.00 4.35
2441 4179 0.749091 CATCATGCCCTTCAAGCCGA 60.749 55.000 0.00 0.00 0.00 5.54
2442 4180 0.034186 ATCATGCCCTTCAAGCCGAA 60.034 50.000 0.00 0.00 0.00 4.30
2449 4187 3.077907 TTCAAGCCGAAGAGGGGG 58.922 61.111 0.00 0.00 41.48 5.40
2464 4370 2.214920 GGGGGACTCAGACACCGTT 61.215 63.158 0.00 0.00 0.00 4.44
2467 4373 0.608640 GGGACTCAGACACCGTTCAT 59.391 55.000 0.00 0.00 0.00 2.57
2493 4403 1.473258 AACAGGCAGACAAGCAAACA 58.527 45.000 0.00 0.00 35.83 2.83
2527 4437 4.041740 GACTATGCAGTCGAATGTACCA 57.958 45.455 15.06 4.41 41.79 3.25
2543 4453 7.441157 CGAATGTACCATCCATTACATTGTACT 59.559 37.037 10.83 0.00 44.99 2.73
2544 4454 9.772973 GAATGTACCATCCATTACATTGTACTA 57.227 33.333 10.83 0.00 44.99 1.82
2545 4455 9.555727 AATGTACCATCCATTACATTGTACTAC 57.444 33.333 6.25 0.00 43.89 2.73
2559 4469 4.924305 TGTACTACGACCAACTCAAACT 57.076 40.909 0.00 0.00 0.00 2.66
2562 4472 6.985117 TGTACTACGACCAACTCAAACTTAT 58.015 36.000 0.00 0.00 0.00 1.73
2565 4475 9.410556 GTACTACGACCAACTCAAACTTATTTA 57.589 33.333 0.00 0.00 0.00 1.40
2566 4476 8.530269 ACTACGACCAACTCAAACTTATTTAG 57.470 34.615 0.00 0.00 0.00 1.85
2622 4533 1.134280 AGAGACTACACATGCATGCCC 60.134 52.381 26.53 9.16 0.00 5.36
2690 4601 4.260985 TGTTATCCATGGTGCACTTACAG 58.739 43.478 17.98 2.49 0.00 2.74
2732 4643 4.305989 GTGTTCTCCACAATTTGAGCAA 57.694 40.909 2.79 0.00 43.92 3.91
2759 4670 1.230324 ACTCGCCAAGCTCAAACTTC 58.770 50.000 0.00 0.00 0.00 3.01
2996 4907 4.453819 ACATAGAGAGCAAACACTTTCAGC 59.546 41.667 0.00 0.00 0.00 4.26
3005 4916 4.677779 GCAAACACTTTCAGCTCCAGAAAA 60.678 41.667 0.09 0.00 34.84 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.780249 GCAAAATGAGTTAACCTACAGTCTAAA 58.220 33.333 0.88 0.00 0.00 1.85
21 22 8.154856 AGCAAAATGAGTTAACCTACAGTCTAA 58.845 33.333 0.88 0.00 0.00 2.10
22 23 7.676947 AGCAAAATGAGTTAACCTACAGTCTA 58.323 34.615 0.88 0.00 0.00 2.59
23 24 6.534634 AGCAAAATGAGTTAACCTACAGTCT 58.465 36.000 0.88 0.00 0.00 3.24
24 25 6.128254 GGAGCAAAATGAGTTAACCTACAGTC 60.128 42.308 0.88 0.00 0.00 3.51
25 26 5.705905 GGAGCAAAATGAGTTAACCTACAGT 59.294 40.000 0.88 0.00 0.00 3.55
26 27 5.163854 CGGAGCAAAATGAGTTAACCTACAG 60.164 44.000 0.88 0.00 0.00 2.74
27 28 4.693566 CGGAGCAAAATGAGTTAACCTACA 59.306 41.667 0.88 1.18 0.00 2.74
28 29 4.694037 ACGGAGCAAAATGAGTTAACCTAC 59.306 41.667 0.88 0.00 0.00 3.18
29 30 4.901868 ACGGAGCAAAATGAGTTAACCTA 58.098 39.130 0.88 0.00 0.00 3.08
30 31 3.751518 ACGGAGCAAAATGAGTTAACCT 58.248 40.909 0.88 0.00 0.00 3.50
31 32 5.123344 ACATACGGAGCAAAATGAGTTAACC 59.877 40.000 0.88 0.00 0.00 2.85
32 33 6.178239 ACATACGGAGCAAAATGAGTTAAC 57.822 37.500 0.00 0.00 0.00 2.01
33 34 7.101054 ACTACATACGGAGCAAAATGAGTTAA 58.899 34.615 0.00 0.00 0.00 2.01
34 35 6.636705 ACTACATACGGAGCAAAATGAGTTA 58.363 36.000 0.00 0.00 0.00 2.24
35 36 5.488341 ACTACATACGGAGCAAAATGAGTT 58.512 37.500 0.00 0.00 0.00 3.01
36 37 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
37 38 5.352284 AGACTACATACGGAGCAAAATGAG 58.648 41.667 0.00 0.00 0.00 2.90
38 39 5.339008 AGACTACATACGGAGCAAAATGA 57.661 39.130 0.00 0.00 0.00 2.57
39 40 7.715265 ATAAGACTACATACGGAGCAAAATG 57.285 36.000 0.00 0.00 0.00 2.32
40 41 7.985184 TCAATAAGACTACATACGGAGCAAAAT 59.015 33.333 0.00 0.00 0.00 1.82
41 42 7.324935 TCAATAAGACTACATACGGAGCAAAA 58.675 34.615 0.00 0.00 0.00 2.44
42 43 6.869695 TCAATAAGACTACATACGGAGCAAA 58.130 36.000 0.00 0.00 0.00 3.68
43 44 6.459670 TCAATAAGACTACATACGGAGCAA 57.540 37.500 0.00 0.00 0.00 3.91
44 45 6.459670 TTCAATAAGACTACATACGGAGCA 57.540 37.500 0.00 0.00 0.00 4.26
45 46 7.868415 AGATTTCAATAAGACTACATACGGAGC 59.132 37.037 0.00 0.00 0.00 4.70
46 47 9.751542 AAGATTTCAATAAGACTACATACGGAG 57.248 33.333 0.00 0.00 0.00 4.63
90 91 9.866655 TGCATAAATTATAGTTCCTTCATTCCT 57.133 29.630 0.00 0.00 0.00 3.36
91 92 9.899226 GTGCATAAATTATAGTTCCTTCATTCC 57.101 33.333 0.00 0.00 0.00 3.01
111 112 9.964303 GGACAAATATTGAACATTATGTGCATA 57.036 29.630 6.87 2.95 35.48 3.14
112 113 8.476447 TGGACAAATATTGAACATTATGTGCAT 58.524 29.630 6.87 0.82 35.48 3.96
113 114 7.834803 TGGACAAATATTGAACATTATGTGCA 58.165 30.769 1.13 1.13 33.15 4.57
114 115 8.876275 ATGGACAAATATTGAACATTATGTGC 57.124 30.769 0.00 0.00 30.65 4.57
120 121 8.885722 GCAATGAATGGACAAATATTGAACATT 58.114 29.630 12.87 12.87 40.39 2.71
121 122 8.041919 TGCAATGAATGGACAAATATTGAACAT 58.958 29.630 0.00 0.00 34.09 2.71
122 123 7.384477 TGCAATGAATGGACAAATATTGAACA 58.616 30.769 0.00 0.00 0.00 3.18
123 124 7.464977 GCTGCAATGAATGGACAAATATTGAAC 60.465 37.037 0.00 0.00 0.00 3.18
124 125 6.535865 GCTGCAATGAATGGACAAATATTGAA 59.464 34.615 0.00 0.00 0.00 2.69
125 126 6.044046 GCTGCAATGAATGGACAAATATTGA 58.956 36.000 0.00 0.00 0.00 2.57
126 127 5.051307 CGCTGCAATGAATGGACAAATATTG 60.051 40.000 0.00 0.00 0.00 1.90
127 128 5.045215 CGCTGCAATGAATGGACAAATATT 58.955 37.500 0.00 0.00 0.00 1.28
128 129 4.338964 TCGCTGCAATGAATGGACAAATAT 59.661 37.500 0.00 0.00 0.00 1.28
129 130 3.693578 TCGCTGCAATGAATGGACAAATA 59.306 39.130 0.00 0.00 0.00 1.40
130 131 2.492881 TCGCTGCAATGAATGGACAAAT 59.507 40.909 0.00 0.00 0.00 2.32
131 132 1.885233 TCGCTGCAATGAATGGACAAA 59.115 42.857 0.00 0.00 0.00 2.83
132 133 1.532523 TCGCTGCAATGAATGGACAA 58.467 45.000 0.00 0.00 0.00 3.18
133 134 1.199789 GTTCGCTGCAATGAATGGACA 59.800 47.619 0.00 0.00 0.00 4.02
134 135 1.468054 GGTTCGCTGCAATGAATGGAC 60.468 52.381 0.00 0.00 0.00 4.02
135 136 0.810648 GGTTCGCTGCAATGAATGGA 59.189 50.000 0.00 0.00 0.00 3.41
136 137 0.813184 AGGTTCGCTGCAATGAATGG 59.187 50.000 0.00 0.00 0.00 3.16
137 138 1.202222 GGAGGTTCGCTGCAATGAATG 60.202 52.381 0.00 0.00 0.00 2.67
138 139 1.098050 GGAGGTTCGCTGCAATGAAT 58.902 50.000 0.00 0.00 0.00 2.57
139 140 0.250684 TGGAGGTTCGCTGCAATGAA 60.251 50.000 0.00 0.00 0.00 2.57
140 141 0.674581 CTGGAGGTTCGCTGCAATGA 60.675 55.000 0.00 0.00 0.00 2.57
141 142 0.957395 ACTGGAGGTTCGCTGCAATG 60.957 55.000 0.00 0.00 0.00 2.82
142 143 0.957395 CACTGGAGGTTCGCTGCAAT 60.957 55.000 0.00 0.00 0.00 3.56
143 144 1.597854 CACTGGAGGTTCGCTGCAA 60.598 57.895 0.00 0.00 0.00 4.08
144 145 2.031012 CACTGGAGGTTCGCTGCA 59.969 61.111 0.00 0.00 0.00 4.41
145 146 2.743928 CCACTGGAGGTTCGCTGC 60.744 66.667 0.00 0.00 0.00 5.25
146 147 1.374758 GTCCACTGGAGGTTCGCTG 60.375 63.158 0.00 0.00 29.39 5.18
147 148 1.837051 TGTCCACTGGAGGTTCGCT 60.837 57.895 0.00 0.00 29.39 4.93
148 149 1.668151 GTGTCCACTGGAGGTTCGC 60.668 63.158 0.00 0.00 29.39 4.70
149 150 1.372997 CGTGTCCACTGGAGGTTCG 60.373 63.158 0.00 0.00 29.39 3.95
150 151 1.004918 CCGTGTCCACTGGAGGTTC 60.005 63.158 0.00 0.00 29.39 3.62
151 152 3.148084 CCGTGTCCACTGGAGGTT 58.852 61.111 0.00 0.00 29.39 3.50
152 153 3.626924 GCCGTGTCCACTGGAGGT 61.627 66.667 0.00 0.00 29.39 3.85
153 154 3.177194 TTGCCGTGTCCACTGGAGG 62.177 63.158 0.00 0.00 29.39 4.30
154 155 1.669115 CTTGCCGTGTCCACTGGAG 60.669 63.158 0.00 0.00 29.39 3.86
155 156 2.425592 CTTGCCGTGTCCACTGGA 59.574 61.111 10.93 0.00 0.00 3.86
156 157 2.669569 CCTTGCCGTGTCCACTGG 60.670 66.667 0.00 0.00 0.00 4.00
157 158 1.669115 CTCCTTGCCGTGTCCACTG 60.669 63.158 0.00 0.00 0.00 3.66
158 159 2.743718 CTCCTTGCCGTGTCCACT 59.256 61.111 0.00 0.00 0.00 4.00
159 160 3.050275 GCTCCTTGCCGTGTCCAC 61.050 66.667 0.00 0.00 35.15 4.02
160 161 3.113514 TTGCTCCTTGCCGTGTCCA 62.114 57.895 0.00 0.00 42.00 4.02
161 162 2.281484 TTGCTCCTTGCCGTGTCC 60.281 61.111 0.00 0.00 42.00 4.02
162 163 2.328099 CCTTGCTCCTTGCCGTGTC 61.328 63.158 0.00 0.00 42.00 3.67
163 164 2.281761 CCTTGCTCCTTGCCGTGT 60.282 61.111 0.00 0.00 42.00 4.49
164 165 3.058160 CCCTTGCTCCTTGCCGTG 61.058 66.667 0.00 0.00 42.00 4.94
165 166 3.570212 ACCCTTGCTCCTTGCCGT 61.570 61.111 0.00 0.00 42.00 5.68
166 167 3.058160 CACCCTTGCTCCTTGCCG 61.058 66.667 0.00 0.00 42.00 5.69
167 168 2.116125 ACACCCTTGCTCCTTGCC 59.884 61.111 0.00 0.00 42.00 4.52
168 169 2.270986 CCACACCCTTGCTCCTTGC 61.271 63.158 0.00 0.00 43.25 4.01
169 170 0.468029 AACCACACCCTTGCTCCTTG 60.468 55.000 0.00 0.00 0.00 3.61
170 171 1.073923 CTAACCACACCCTTGCTCCTT 59.926 52.381 0.00 0.00 0.00 3.36
171 172 0.693049 CTAACCACACCCTTGCTCCT 59.307 55.000 0.00 0.00 0.00 3.69
172 173 0.690762 TCTAACCACACCCTTGCTCC 59.309 55.000 0.00 0.00 0.00 4.70
173 174 2.633488 GATCTAACCACACCCTTGCTC 58.367 52.381 0.00 0.00 0.00 4.26
174 175 1.066143 CGATCTAACCACACCCTTGCT 60.066 52.381 0.00 0.00 0.00 3.91
175 176 1.066430 TCGATCTAACCACACCCTTGC 60.066 52.381 0.00 0.00 0.00 4.01
176 177 2.233922 AGTCGATCTAACCACACCCTTG 59.766 50.000 0.00 0.00 0.00 3.61
177 178 2.537143 AGTCGATCTAACCACACCCTT 58.463 47.619 0.00 0.00 0.00 3.95
178 179 2.233305 AGTCGATCTAACCACACCCT 57.767 50.000 0.00 0.00 0.00 4.34
179 180 2.232941 TCAAGTCGATCTAACCACACCC 59.767 50.000 0.00 0.00 0.00 4.61
180 181 3.251571 GTCAAGTCGATCTAACCACACC 58.748 50.000 0.00 0.00 0.00 4.16
181 182 2.915463 CGTCAAGTCGATCTAACCACAC 59.085 50.000 0.00 0.00 0.00 3.82
182 183 2.815503 TCGTCAAGTCGATCTAACCACA 59.184 45.455 0.00 0.00 34.85 4.17
183 184 3.482722 TCGTCAAGTCGATCTAACCAC 57.517 47.619 0.00 0.00 34.85 4.16
184 185 3.504906 ACTTCGTCAAGTCGATCTAACCA 59.495 43.478 0.00 0.00 38.62 3.67
185 186 4.094090 ACTTCGTCAAGTCGATCTAACC 57.906 45.455 0.00 0.00 38.62 2.85
195 196 3.971150 CTTGACTGAGACTTCGTCAAGT 58.029 45.455 24.98 10.12 46.05 3.16
197 198 3.380320 TCACTTGACTGAGACTTCGTCAA 59.620 43.478 15.43 15.43 40.77 3.18
198 199 2.949644 TCACTTGACTGAGACTTCGTCA 59.050 45.455 4.27 4.27 36.11 4.35
199 200 3.627732 TCACTTGACTGAGACTTCGTC 57.372 47.619 0.00 0.00 0.00 4.20
200 201 5.004448 TCTATCACTTGACTGAGACTTCGT 58.996 41.667 0.00 0.00 0.00 3.85
201 202 5.553290 TCTATCACTTGACTGAGACTTCG 57.447 43.478 0.00 0.00 0.00 3.79
269 270 8.939929 CCAGTCGATGCTATATTCATTACATTT 58.060 33.333 0.00 0.00 0.00 2.32
270 271 7.550551 CCCAGTCGATGCTATATTCATTACATT 59.449 37.037 0.00 0.00 0.00 2.71
271 272 7.044181 CCCAGTCGATGCTATATTCATTACAT 58.956 38.462 0.00 0.00 0.00 2.29
272 273 6.014584 ACCCAGTCGATGCTATATTCATTACA 60.015 38.462 0.00 0.00 0.00 2.41
273 274 6.398918 ACCCAGTCGATGCTATATTCATTAC 58.601 40.000 0.00 0.00 0.00 1.89
274 275 6.210584 TGACCCAGTCGATGCTATATTCATTA 59.789 38.462 0.00 0.00 34.95 1.90
275 276 5.012046 TGACCCAGTCGATGCTATATTCATT 59.988 40.000 0.00 0.00 34.95 2.57
276 277 4.528206 TGACCCAGTCGATGCTATATTCAT 59.472 41.667 0.00 0.00 34.95 2.57
277 278 3.895041 TGACCCAGTCGATGCTATATTCA 59.105 43.478 0.00 0.00 34.95 2.57
278 279 4.521130 TGACCCAGTCGATGCTATATTC 57.479 45.455 0.00 0.00 34.95 1.75
279 280 4.955811 TTGACCCAGTCGATGCTATATT 57.044 40.909 0.00 0.00 34.95 1.28
280 281 5.489792 AATTGACCCAGTCGATGCTATAT 57.510 39.130 0.00 0.00 36.84 0.86
281 282 4.955811 AATTGACCCAGTCGATGCTATA 57.044 40.909 0.00 0.00 36.84 1.31
282 283 3.845781 AATTGACCCAGTCGATGCTAT 57.154 42.857 0.00 0.00 36.84 2.97
283 284 4.404394 TCTTAATTGACCCAGTCGATGCTA 59.596 41.667 0.00 0.00 36.84 3.49
284 285 3.197766 TCTTAATTGACCCAGTCGATGCT 59.802 43.478 0.00 0.00 36.84 3.79
285 286 3.531538 TCTTAATTGACCCAGTCGATGC 58.468 45.455 0.00 0.00 36.84 3.91
286 287 6.683974 AAATCTTAATTGACCCAGTCGATG 57.316 37.500 0.00 0.00 36.84 3.84
287 288 6.483640 GCTAAATCTTAATTGACCCAGTCGAT 59.516 38.462 0.00 0.00 38.20 3.59
288 289 5.815740 GCTAAATCTTAATTGACCCAGTCGA 59.184 40.000 0.00 0.00 34.95 4.20
289 290 5.584649 TGCTAAATCTTAATTGACCCAGTCG 59.415 40.000 0.00 0.00 34.95 4.18
290 291 7.391148 TTGCTAAATCTTAATTGACCCAGTC 57.609 36.000 0.00 0.00 0.00 3.51
291 292 7.068716 GGATTGCTAAATCTTAATTGACCCAGT 59.931 37.037 0.00 0.00 41.74 4.00
292 293 7.428826 GGATTGCTAAATCTTAATTGACCCAG 58.571 38.462 0.00 0.00 41.74 4.45
293 294 6.323739 GGGATTGCTAAATCTTAATTGACCCA 59.676 38.462 0.00 0.00 41.74 4.51
294 295 6.515035 CGGGATTGCTAAATCTTAATTGACCC 60.515 42.308 0.00 0.00 41.74 4.46
295 296 6.039382 ACGGGATTGCTAAATCTTAATTGACC 59.961 38.462 0.00 0.00 41.74 4.02
296 297 7.027778 ACGGGATTGCTAAATCTTAATTGAC 57.972 36.000 0.00 0.00 41.74 3.18
297 298 7.639113 AACGGGATTGCTAAATCTTAATTGA 57.361 32.000 0.00 0.00 41.74 2.57
298 299 7.435192 GGAAACGGGATTGCTAAATCTTAATTG 59.565 37.037 0.00 0.00 41.74 2.32
299 300 7.489160 GGAAACGGGATTGCTAAATCTTAATT 58.511 34.615 0.00 0.00 41.74 1.40
300 301 7.039313 GGAAACGGGATTGCTAAATCTTAAT 57.961 36.000 0.00 0.00 41.74 1.40
301 302 6.445357 GGAAACGGGATTGCTAAATCTTAA 57.555 37.500 0.00 0.00 41.74 1.85
303 304 4.983671 GGAAACGGGATTGCTAAATCTT 57.016 40.909 0.00 0.00 41.74 2.40
319 320 0.881118 TGCAGCTTTGATCCGGAAAC 59.119 50.000 9.01 6.66 0.00 2.78
320 321 0.881118 GTGCAGCTTTGATCCGGAAA 59.119 50.000 9.01 0.00 0.00 3.13
321 322 0.250684 TGTGCAGCTTTGATCCGGAA 60.251 50.000 9.01 0.00 0.00 4.30
322 323 0.674581 CTGTGCAGCTTTGATCCGGA 60.675 55.000 6.61 6.61 0.00 5.14
323 324 0.957395 ACTGTGCAGCTTTGATCCGG 60.957 55.000 0.00 0.00 0.00 5.14
324 325 0.167470 CACTGTGCAGCTTTGATCCG 59.833 55.000 0.00 0.00 0.00 4.18
325 326 0.109412 GCACTGTGCAGCTTTGATCC 60.109 55.000 26.70 0.00 44.26 3.36
326 327 3.396491 GCACTGTGCAGCTTTGATC 57.604 52.632 26.70 0.00 44.26 2.92
673 2214 3.712907 GCCGTGGGGTGCTTCCTA 61.713 66.667 0.00 0.00 36.25 2.94
760 2301 2.125350 GCTCTCCAGGAAGCCGTG 60.125 66.667 10.89 0.00 0.00 4.94
883 2425 2.747855 CTTGGGGAGCCTCGCAAC 60.748 66.667 11.18 0.00 36.01 4.17
944 2486 2.359107 AGGACGACGGCTGTACGA 60.359 61.111 19.70 0.00 37.61 3.43
1003 2545 1.762460 CCATAGGCCCTCTCCACGT 60.762 63.158 0.00 0.00 0.00 4.49
1024 2566 3.545481 CCACATGCGCGACGTCTC 61.545 66.667 12.10 4.41 0.00 3.36
1822 3401 1.536766 CGCTTGCTGAGTTGGATTTGA 59.463 47.619 0.00 0.00 0.00 2.69
1838 3417 2.112297 TTGAAACCTCCGGCGCTT 59.888 55.556 7.64 0.00 0.00 4.68
1861 3440 8.279800 TCGCCGATTAAATACTTTATCAACATG 58.720 33.333 0.00 0.00 0.00 3.21
1863 3442 7.517734 GCTCGCCGATTAAATACTTTATCAACA 60.518 37.037 0.00 0.00 0.00 3.33
1864 3443 6.790825 GCTCGCCGATTAAATACTTTATCAAC 59.209 38.462 0.00 0.00 0.00 3.18
1885 3489 2.667536 AGGCACAGCAACAGCTCG 60.668 61.111 0.00 0.00 36.19 5.03
1927 3531 0.035152 AATGCGATGCTCCCACTTGA 60.035 50.000 0.00 0.00 0.00 3.02
1959 3568 3.180891 GCCCTTCAGCGAGTAAAGTAT 57.819 47.619 0.00 0.00 0.00 2.12
1961 3570 3.534721 GCCCTTCAGCGAGTAAAGT 57.465 52.632 0.00 0.00 0.00 2.66
1988 3621 3.920093 AAAAAGGAGGAGCCGGCGG 62.920 63.158 24.35 24.35 43.43 6.13
1989 3622 2.359975 AAAAAGGAGGAGCCGGCG 60.360 61.111 23.20 0.00 43.43 6.46
1990 3623 0.609406 AAGAAAAAGGAGGAGCCGGC 60.609 55.000 21.89 21.89 43.43 6.13
1998 3631 6.382608 GGATTCGAAGGAAAAGAAAAAGGAG 58.617 40.000 3.35 0.00 35.40 3.69
2110 3767 3.375610 TCAGCAAAGTTAGCAAAACGTGA 59.624 39.130 0.00 3.24 0.00 4.35
2250 3984 0.179215 GATTTGGACTGTCGCTTGCG 60.179 55.000 8.87 8.87 0.00 4.85
2345 4079 5.048364 ACTGTAGCTGTACTGAGAAACTCTG 60.048 44.000 3.61 0.00 35.91 3.35
2346 4080 5.074115 ACTGTAGCTGTACTGAGAAACTCT 58.926 41.667 3.61 0.00 33.45 3.24
2414 4152 3.025978 TGAAGGGCATGATGGTCAAATC 58.974 45.455 0.00 0.00 0.00 2.17
2446 4184 2.168666 GAACGGTGTCTGAGTCCCCC 62.169 65.000 0.00 0.00 0.00 5.40
2447 4185 1.292541 GAACGGTGTCTGAGTCCCC 59.707 63.158 0.00 0.00 0.00 4.81
2448 4186 0.608640 ATGAACGGTGTCTGAGTCCC 59.391 55.000 0.00 0.00 0.00 4.46
2449 4187 2.753452 TCTATGAACGGTGTCTGAGTCC 59.247 50.000 0.00 0.00 0.00 3.85
2450 4188 4.436242 TTCTATGAACGGTGTCTGAGTC 57.564 45.455 0.00 0.00 0.00 3.36
2476 4386 2.582728 TTTGTTTGCTTGTCTGCCTG 57.417 45.000 0.00 0.00 0.00 4.85
2482 4392 6.801377 TCGATATGACATTTTGTTTGCTTGTC 59.199 34.615 0.00 0.00 37.73 3.18
2483 4393 6.676950 TCGATATGACATTTTGTTTGCTTGT 58.323 32.000 0.00 0.00 0.00 3.16
2527 4437 6.474140 TGGTCGTAGTACAATGTAATGGAT 57.526 37.500 3.40 0.00 0.00 3.41
2543 4453 9.715121 ATTCTAAATAAGTTTGAGTTGGTCGTA 57.285 29.630 0.00 0.00 0.00 3.43
2544 4454 8.617290 ATTCTAAATAAGTTTGAGTTGGTCGT 57.383 30.769 0.00 0.00 0.00 4.34
2545 4455 9.893305 AAATTCTAAATAAGTTTGAGTTGGTCG 57.107 29.630 0.00 0.00 0.00 4.79
2590 4500 7.384115 GCATGTGTAGTCTCTGTTGTTAACTAA 59.616 37.037 7.22 0.00 0.00 2.24
2591 4501 6.866770 GCATGTGTAGTCTCTGTTGTTAACTA 59.133 38.462 7.22 0.00 0.00 2.24
2598 4508 3.181513 GCATGCATGTGTAGTCTCTGTTG 60.182 47.826 26.79 0.00 0.00 3.33
2622 4533 2.639286 GCAAACTGCCTGACACCG 59.361 61.111 0.00 0.00 37.42 4.94
2690 4601 3.217626 CAACATTAATCCTCAGGAGCCC 58.782 50.000 0.00 0.00 34.05 5.19
2732 4643 0.254178 AGCTTGGCGAGTTCATGGAT 59.746 50.000 3.19 0.00 0.00 3.41
2759 4670 2.939103 CAAGGCCTTTATCTGGAACTCG 59.061 50.000 17.61 0.00 0.00 4.18
2804 4715 2.124983 TCGGCCATCTCAAGCAGC 60.125 61.111 2.24 0.00 0.00 5.25
2944 4855 2.719531 TATGGCCTCCGTAATTTGCA 57.280 45.000 3.32 0.00 0.00 4.08
3005 4916 1.604593 GCACCAGTGTTGCCCAGAT 60.605 57.895 0.25 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.