Multiple sequence alignment - TraesCS6A01G328500

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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 TraesCS6A01G328500 chr6A 100.000 1714 0 0 1 1714 561851524 561849811 0.000000e+00 3166.0
1 TraesCS6A01G328500 chr6A 100.000 418 0 0 1793 2210 561849732 561849315 0.000000e+00 773.0
2 TraesCS6A01G328500 chr6A 97.778 225 4 1 1490 1714 97376911 97376688 9.570000e-104 387.0
3 TraesCS6A01G328500 chr6A 88.119 101 8 3 411 509 270780096 270780194 1.390000e-22 117.0
4 TraesCS6A01G328500 chr5A 94.767 1051 51 3 419 1467 523743108 523744156 0.000000e+00 1633.0
5 TraesCS6A01G328500 chr5A 92.417 422 22 6 1795 2210 668374808 668375225 5.250000e-166 593.0
6 TraesCS6A01G328500 chr5A 91.059 425 26 8 1795 2210 647318433 647318012 4.120000e-157 564.0
7 TraesCS6A01G328500 chr5A 94.862 253 7 6 1464 1711 547562993 547563244 7.400000e-105 390.0
8 TraesCS6A01G328500 chr5A 93.927 247 10 2 1468 1714 659038619 659038378 3.470000e-98 368.0
9 TraesCS6A01G328500 chr2A 98.054 411 6 2 1 411 555100285 555099877 0.000000e+00 713.0
10 TraesCS6A01G328500 chr2A 95.134 411 18 2 1 411 177102355 177102763 0.000000e+00 647.0
11 TraesCS6A01G328500 chr2A 98.643 221 3 0 1490 1710 26097462 26097682 2.060000e-105 392.0
12 TraesCS6A01G328500 chr2A 97.357 227 4 2 1489 1714 92042753 92042528 3.440000e-103 385.0
13 TraesCS6A01G328500 chr2A 89.855 207 17 4 60 264 395702750 395702954 1.680000e-66 263.0
14 TraesCS6A01G328500 chr2A 89.202 213 19 4 60 270 405477823 405477613 1.680000e-66 263.0
15 TraesCS6A01G328500 chr5B 95.620 411 16 2 1 410 614839640 614839231 0.000000e+00 658.0
16 TraesCS6A01G328500 chr5B 88.889 207 19 4 60 264 166657550 166657754 3.640000e-63 252.0
17 TraesCS6A01G328500 chr5B 87.059 85 7 3 431 513 495429834 495429916 2.340000e-15 93.5
18 TraesCS6A01G328500 chr6B 95.377 411 17 2 1 411 543015085 543014677 0.000000e+00 652.0
19 TraesCS6A01G328500 chr3A 93.412 425 18 4 1795 2210 593022560 593022983 2.410000e-174 621.0
20 TraesCS6A01G328500 chr3A 92.326 430 17 7 1795 2210 655757822 655758249 4.060000e-167 597.0
21 TraesCS6A01G328500 chr3A 91.667 432 17 6 1796 2210 704199965 704200394 4.090000e-162 580.0
22 TraesCS6A01G328500 chr3A 97.778 225 5 0 1490 1714 701325883 701325659 2.660000e-104 388.0
23 TraesCS6A01G328500 chr3A 95.161 248 6 6 1468 1711 655757667 655757912 9.570000e-104 387.0
24 TraesCS6A01G328500 chr7B 93.571 420 18 8 1795 2210 5968333 5968747 3.120000e-173 617.0
25 TraesCS6A01G328500 chr7B 85.294 68 6 3 27 93 65354369 65354305 1.420000e-07 67.6
26 TraesCS6A01G328500 chr7A 93.571 420 18 8 1795 2210 581727623 581727209 3.120000e-173 617.0
27 TraesCS6A01G328500 chr7A 91.784 426 18 7 1795 2210 23127545 23127963 5.290000e-161 577.0
28 TraesCS6A01G328500 chr7A 91.262 309 25 2 1 308 130193800 130194107 9.440000e-114 420.0
29 TraesCS6A01G328500 chr7A 95.378 238 8 3 1477 1711 647480251 647480488 2.070000e-100 375.0
30 TraesCS6A01G328500 chr7A 90.090 111 5 2 306 410 130194154 130194264 2.960000e-29 139.0
31 TraesCS6A01G328500 chr7A 87.805 82 8 1 431 510 59837362 59837443 6.500000e-16 95.3
32 TraesCS6A01G328500 chrUn 91.745 424 26 6 1795 2210 306553861 306553439 4.090000e-162 580.0
33 TraesCS6A01G328500 chrUn 97.872 47 1 0 431 477 327756218 327756264 5.060000e-12 82.4
34 TraesCS6A01G328500 chrUn 97.059 34 1 0 480 513 13787136 13787169 8.520000e-05 58.4
35 TraesCS6A01G328500 chr7D 87.474 479 38 7 564 1032 7881043 7881509 1.160000e-147 532.0
36 TraesCS6A01G328500 chr7D 89.269 438 26 12 1030 1467 7881638 7882054 1.500000e-146 529.0
37 TraesCS6A01G328500 chr7D 86.170 94 7 5 421 509 7880874 7880966 1.810000e-16 97.1
38 TraesCS6A01G328500 chr3B 91.262 309 25 2 1 308 614900750 614901057 9.440000e-114 420.0
39 TraesCS6A01G328500 chr3B 90.090 111 5 2 306 410 614901104 614901214 2.960000e-29 139.0
40 TraesCS6A01G328500 chr4A 98.222 225 3 1 1490 1714 20625616 20625393 2.060000e-105 392.0
41 TraesCS6A01G328500 chr4A 84.158 101 8 5 428 525 377612303 377612208 8.400000e-15 91.6
42 TraesCS6A01G328500 chr6D 83.636 330 24 11 9 311 463265771 463265445 1.290000e-72 283.0
43 TraesCS6A01G328500 chr6D 87.059 85 9 1 431 513 291658163 291658247 6.500000e-16 95.3
44 TraesCS6A01G328500 chr6D 85.714 84 9 2 428 509 369423975 369424057 3.910000e-13 86.1
45 TraesCS6A01G328500 chr5D 90.217 92 6 2 431 520 448746803 448746713 1.390000e-22 117.0
46 TraesCS6A01G328500 chr4D 90.698 86 4 2 431 513 215197329 215197245 6.450000e-21 111.0
47 TraesCS6A01G328500 chr4D 89.024 82 6 3 428 507 24108025 24108105 5.020000e-17 99.0
48 TraesCS6A01G328500 chr1D 88.889 81 6 2 431 509 209986909 209986988 1.810000e-16 97.1
49 TraesCS6A01G328500 chr3D 87.342 79 7 2 431 507 351926132 351926055 1.090000e-13 87.9


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 TraesCS6A01G328500 chr6A 561849315 561851524 2209 True 1969.500000 3166 100.000000 1 2210 2 chr6A.!!$R2 2209
1 TraesCS6A01G328500 chr5A 523743108 523744156 1048 False 1633.000000 1633 94.767000 419 1467 1 chr5A.!!$F1 1048
2 TraesCS6A01G328500 chr3A 655757667 655758249 582 False 492.000000 597 93.743500 1468 2210 2 chr3A.!!$F3 742
3 TraesCS6A01G328500 chr7D 7880874 7882054 1180 False 386.033333 532 87.637667 421 1467 3 chr7D.!!$F1 1046

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
154 155 1.00243 AGAGCTCTTTTCGATGCCACA 59.998 47.619 11.45 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1452 0.248743 TATCTTGCCGCGTAAGGTCG 60.249 55.0 16.98 0.0 38.28 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
83 84 9.491675 AATAATGATGCAAAACATTCAACTTGA 57.508 25.926 16.37 0.00 39.84 3.02
84 85 6.774354 ATGATGCAAAACATTCAACTTGAC 57.226 33.333 0.00 0.00 39.84 3.18
85 86 5.658468 TGATGCAAAACATTCAACTTGACA 58.342 33.333 0.00 0.00 39.84 3.58
86 87 6.282167 TGATGCAAAACATTCAACTTGACAT 58.718 32.000 0.00 0.00 39.84 3.06
87 88 7.432059 TGATGCAAAACATTCAACTTGACATA 58.568 30.769 0.00 0.00 39.84 2.29
88 89 7.924947 TGATGCAAAACATTCAACTTGACATAA 59.075 29.630 0.00 0.00 39.84 1.90
89 90 7.462109 TGCAAAACATTCAACTTGACATAAC 57.538 32.000 0.00 0.00 0.00 1.89
90 91 7.038048 TGCAAAACATTCAACTTGACATAACA 58.962 30.769 0.00 0.00 0.00 2.41
91 92 7.222417 TGCAAAACATTCAACTTGACATAACAG 59.778 33.333 0.00 0.00 0.00 3.16
92 93 7.222611 GCAAAACATTCAACTTGACATAACAGT 59.777 33.333 0.00 0.00 0.00 3.55
93 94 9.086336 CAAAACATTCAACTTGACATAACAGTT 57.914 29.630 0.00 0.00 0.00 3.16
94 95 8.633075 AAACATTCAACTTGACATAACAGTTG 57.367 30.769 10.30 10.30 40.59 3.16
95 96 7.333528 ACATTCAACTTGACATAACAGTTGT 57.666 32.000 14.42 0.00 40.26 3.32
96 97 7.417612 ACATTCAACTTGACATAACAGTTGTC 58.582 34.615 14.42 0.00 43.04 3.18
106 107 7.426929 GACATAACAGTTGTCAAACATCTCT 57.573 36.000 0.00 0.00 42.43 3.10
107 108 7.807977 ACATAACAGTTGTCAAACATCTCTT 57.192 32.000 0.00 0.00 38.88 2.85
108 109 8.902540 ACATAACAGTTGTCAAACATCTCTTA 57.097 30.769 0.00 0.00 38.88 2.10
109 110 9.337396 ACATAACAGTTGTCAAACATCTCTTAA 57.663 29.630 0.00 0.00 38.88 1.85
113 114 8.450578 ACAGTTGTCAAACATCTCTTAAATCA 57.549 30.769 0.00 0.00 38.88 2.57
114 115 9.071276 ACAGTTGTCAAACATCTCTTAAATCAT 57.929 29.630 0.00 0.00 38.88 2.45
115 116 9.903682 CAGTTGTCAAACATCTCTTAAATCATT 57.096 29.630 0.00 0.00 38.88 2.57
136 137 9.713684 ATCATTAAATTAACAGGAAATGGGAGA 57.286 29.630 0.00 0.00 0.00 3.71
137 138 9.189156 TCATTAAATTAACAGGAAATGGGAGAG 57.811 33.333 0.00 0.00 0.00 3.20
138 139 5.921962 AAATTAACAGGAAATGGGAGAGC 57.078 39.130 0.00 0.00 0.00 4.09
139 140 4.870021 ATTAACAGGAAATGGGAGAGCT 57.130 40.909 0.00 0.00 0.00 4.09
140 141 2.797177 AACAGGAAATGGGAGAGCTC 57.203 50.000 5.27 5.27 0.00 4.09
141 142 1.963985 ACAGGAAATGGGAGAGCTCT 58.036 50.000 18.28 18.28 0.00 4.09
142 143 2.273619 ACAGGAAATGGGAGAGCTCTT 58.726 47.619 19.36 0.00 0.00 2.85
143 144 2.646798 ACAGGAAATGGGAGAGCTCTTT 59.353 45.455 19.36 7.58 0.00 2.52
144 145 3.075134 ACAGGAAATGGGAGAGCTCTTTT 59.925 43.478 19.36 14.14 0.00 2.27
145 146 3.693578 CAGGAAATGGGAGAGCTCTTTTC 59.306 47.826 22.31 22.31 0.00 2.29
146 147 2.680339 GGAAATGGGAGAGCTCTTTTCG 59.320 50.000 22.99 0.00 30.89 3.46
147 148 3.600388 GAAATGGGAGAGCTCTTTTCGA 58.400 45.455 19.36 8.60 0.00 3.71
148 149 3.922171 AATGGGAGAGCTCTTTTCGAT 57.078 42.857 19.36 10.49 0.00 3.59
149 150 2.680312 TGGGAGAGCTCTTTTCGATG 57.320 50.000 19.36 0.00 0.00 3.84
150 151 1.294857 GGGAGAGCTCTTTTCGATGC 58.705 55.000 19.36 1.62 0.00 3.91
151 152 1.294857 GGAGAGCTCTTTTCGATGCC 58.705 55.000 19.36 7.92 0.00 4.40
152 153 1.406069 GGAGAGCTCTTTTCGATGCCA 60.406 52.381 19.36 0.00 0.00 4.92
153 154 1.663135 GAGAGCTCTTTTCGATGCCAC 59.337 52.381 19.36 0.00 0.00 5.01
154 155 1.002430 AGAGCTCTTTTCGATGCCACA 59.998 47.619 11.45 0.00 0.00 4.17
155 156 1.806542 GAGCTCTTTTCGATGCCACAA 59.193 47.619 6.43 0.00 0.00 3.33
156 157 2.421424 GAGCTCTTTTCGATGCCACAAT 59.579 45.455 6.43 0.00 0.00 2.71
157 158 2.163010 AGCTCTTTTCGATGCCACAATG 59.837 45.455 0.00 0.00 0.00 2.82
158 159 2.095059 GCTCTTTTCGATGCCACAATGT 60.095 45.455 0.00 0.00 0.00 2.71
159 160 3.126858 GCTCTTTTCGATGCCACAATGTA 59.873 43.478 0.00 0.00 0.00 2.29
160 161 4.201950 GCTCTTTTCGATGCCACAATGTAT 60.202 41.667 0.00 0.00 0.00 2.29
161 162 5.233957 TCTTTTCGATGCCACAATGTATG 57.766 39.130 0.00 0.00 0.00 2.39
162 163 4.940654 TCTTTTCGATGCCACAATGTATGA 59.059 37.500 0.00 0.00 0.00 2.15
163 164 5.589855 TCTTTTCGATGCCACAATGTATGAT 59.410 36.000 0.00 0.00 0.00 2.45
164 165 4.816786 TTCGATGCCACAATGTATGATG 57.183 40.909 0.00 0.00 0.00 3.07
165 166 3.140623 TCGATGCCACAATGTATGATGG 58.859 45.455 0.00 0.00 34.94 3.51
166 167 3.140623 CGATGCCACAATGTATGATGGA 58.859 45.455 0.00 0.00 34.19 3.41
167 168 3.565063 CGATGCCACAATGTATGATGGAA 59.435 43.478 0.00 0.00 34.19 3.53
168 169 4.036616 CGATGCCACAATGTATGATGGAAA 59.963 41.667 0.00 0.00 34.19 3.13
169 170 5.450274 CGATGCCACAATGTATGATGGAAAA 60.450 40.000 0.00 0.00 34.19 2.29
170 171 5.735285 TGCCACAATGTATGATGGAAAAA 57.265 34.783 0.00 0.00 34.19 1.94
171 172 6.297080 TGCCACAATGTATGATGGAAAAAT 57.703 33.333 0.00 0.00 34.19 1.82
172 173 6.339730 TGCCACAATGTATGATGGAAAAATC 58.660 36.000 0.00 0.00 34.19 2.17
173 174 6.070938 TGCCACAATGTATGATGGAAAAATCA 60.071 34.615 0.00 0.00 40.73 2.57
174 175 6.987992 GCCACAATGTATGATGGAAAAATCAT 59.012 34.615 5.14 5.14 46.55 2.45
175 176 7.496591 GCCACAATGTATGATGGAAAAATCATT 59.503 33.333 5.10 0.00 43.28 2.57
176 177 9.386010 CCACAATGTATGATGGAAAAATCATTT 57.614 29.630 5.10 0.00 43.28 2.32
186 187 9.844257 TGATGGAAAAATCATTTTGTAAAGGTT 57.156 25.926 0.00 0.00 38.83 3.50
189 190 8.401709 TGGAAAAATCATTTTGTAAAGGTTTGC 58.598 29.630 0.00 0.00 38.83 3.68
190 191 7.860373 GGAAAAATCATTTTGTAAAGGTTTGCC 59.140 33.333 0.00 0.00 38.83 4.52
191 192 7.872113 AAAATCATTTTGTAAAGGTTTGCCA 57.128 28.000 0.00 0.00 37.19 4.92
192 193 7.872113 AAATCATTTTGTAAAGGTTTGCCAA 57.128 28.000 0.00 0.00 37.19 4.52
193 194 7.872113 AATCATTTTGTAAAGGTTTGCCAAA 57.128 28.000 0.00 0.00 37.19 3.28
194 195 6.670077 TCATTTTGTAAAGGTTTGCCAAAC 57.330 33.333 11.88 11.88 40.65 2.93
207 208 3.810310 TGCCAAACCACAAACTAAAGG 57.190 42.857 0.00 0.00 0.00 3.11
208 209 3.366396 TGCCAAACCACAAACTAAAGGA 58.634 40.909 0.00 0.00 0.00 3.36
209 210 3.769844 TGCCAAACCACAAACTAAAGGAA 59.230 39.130 0.00 0.00 0.00 3.36
210 211 4.116961 GCCAAACCACAAACTAAAGGAAC 58.883 43.478 0.00 0.00 0.00 3.62
211 212 4.382147 GCCAAACCACAAACTAAAGGAACA 60.382 41.667 0.00 0.00 0.00 3.18
212 213 5.725362 CCAAACCACAAACTAAAGGAACAA 58.275 37.500 0.00 0.00 0.00 2.83
213 214 6.166982 CCAAACCACAAACTAAAGGAACAAA 58.833 36.000 0.00 0.00 0.00 2.83
214 215 6.821160 CCAAACCACAAACTAAAGGAACAAAT 59.179 34.615 0.00 0.00 0.00 2.32
215 216 7.982354 CCAAACCACAAACTAAAGGAACAAATA 59.018 33.333 0.00 0.00 0.00 1.40
216 217 9.372369 CAAACCACAAACTAAAGGAACAAATAA 57.628 29.630 0.00 0.00 0.00 1.40
218 219 9.541143 AACCACAAACTAAAGGAACAAATAATG 57.459 29.630 0.00 0.00 0.00 1.90
219 220 8.700973 ACCACAAACTAAAGGAACAAATAATGT 58.299 29.630 0.00 0.00 46.82 2.71
227 228 9.716507 CTAAAGGAACAAATAATGTATTCACCG 57.283 33.333 0.00 0.00 42.99 4.94
228 229 7.696992 AAGGAACAAATAATGTATTCACCGT 57.303 32.000 0.00 0.00 42.99 4.83
229 230 8.795842 AAGGAACAAATAATGTATTCACCGTA 57.204 30.769 0.00 0.00 42.99 4.02
230 231 8.795842 AGGAACAAATAATGTATTCACCGTAA 57.204 30.769 0.00 0.00 42.99 3.18
231 232 9.403583 AGGAACAAATAATGTATTCACCGTAAT 57.596 29.630 0.00 0.00 42.99 1.89
232 233 9.445786 GGAACAAATAATGTATTCACCGTAATG 57.554 33.333 0.00 0.00 42.99 1.90
239 240 9.719355 ATAATGTATTCACCGTAATGATAAGCA 57.281 29.630 0.00 0.00 0.00 3.91
240 241 7.658179 ATGTATTCACCGTAATGATAAGCAG 57.342 36.000 0.00 0.00 0.00 4.24
241 242 5.989168 TGTATTCACCGTAATGATAAGCAGG 59.011 40.000 0.00 0.00 0.00 4.85
242 243 3.469008 TCACCGTAATGATAAGCAGGG 57.531 47.619 0.00 0.00 0.00 4.45
243 244 2.769663 TCACCGTAATGATAAGCAGGGT 59.230 45.455 0.00 0.00 0.00 4.34
244 245 3.962063 TCACCGTAATGATAAGCAGGGTA 59.038 43.478 0.00 0.00 0.00 3.69
245 246 4.591498 TCACCGTAATGATAAGCAGGGTAT 59.409 41.667 0.00 0.00 0.00 2.73
246 247 4.929808 CACCGTAATGATAAGCAGGGTATC 59.070 45.833 0.00 0.00 0.00 2.24
247 248 4.020485 ACCGTAATGATAAGCAGGGTATCC 60.020 45.833 0.00 0.00 0.00 2.59
248 249 4.223032 CCGTAATGATAAGCAGGGTATCCT 59.777 45.833 0.00 0.00 46.26 3.24
249 250 5.421056 CCGTAATGATAAGCAGGGTATCCTA 59.579 44.000 0.00 0.00 42.67 2.94
250 251 6.405953 CCGTAATGATAAGCAGGGTATCCTAG 60.406 46.154 0.00 0.00 42.67 3.02
251 252 5.428184 AATGATAAGCAGGGTATCCTAGC 57.572 43.478 0.00 0.79 42.67 3.42
252 253 3.856900 TGATAAGCAGGGTATCCTAGCA 58.143 45.455 15.89 0.00 42.67 3.49
253 254 4.429505 TGATAAGCAGGGTATCCTAGCAT 58.570 43.478 15.89 8.68 42.67 3.79
254 255 4.846367 TGATAAGCAGGGTATCCTAGCATT 59.154 41.667 15.89 10.62 42.67 3.56
255 256 3.778954 AAGCAGGGTATCCTAGCATTC 57.221 47.619 15.89 0.00 42.67 2.67
256 257 2.983296 AGCAGGGTATCCTAGCATTCT 58.017 47.619 15.89 0.00 42.67 2.40
257 258 3.321950 AGCAGGGTATCCTAGCATTCTT 58.678 45.455 15.89 0.00 42.67 2.52
258 259 3.072184 AGCAGGGTATCCTAGCATTCTTG 59.928 47.826 15.89 0.00 42.67 3.02
259 260 3.181450 GCAGGGTATCCTAGCATTCTTGT 60.181 47.826 10.51 0.00 42.67 3.16
260 261 4.687219 GCAGGGTATCCTAGCATTCTTGTT 60.687 45.833 10.51 0.00 42.67 2.83
261 262 5.440610 CAGGGTATCCTAGCATTCTTGTTT 58.559 41.667 0.00 0.00 42.67 2.83
262 263 5.888161 CAGGGTATCCTAGCATTCTTGTTTT 59.112 40.000 0.00 0.00 42.67 2.43
263 264 6.378280 CAGGGTATCCTAGCATTCTTGTTTTT 59.622 38.462 0.00 0.00 42.67 1.94
264 265 6.378280 AGGGTATCCTAGCATTCTTGTTTTTG 59.622 38.462 0.00 0.00 42.75 2.44
265 266 6.152831 GGGTATCCTAGCATTCTTGTTTTTGT 59.847 38.462 0.00 0.00 0.00 2.83
266 267 7.309805 GGGTATCCTAGCATTCTTGTTTTTGTT 60.310 37.037 0.00 0.00 0.00 2.83
267 268 8.736244 GGTATCCTAGCATTCTTGTTTTTGTTA 58.264 33.333 0.00 0.00 0.00 2.41
270 271 8.865590 TCCTAGCATTCTTGTTTTTGTTAAAC 57.134 30.769 0.00 0.00 0.00 2.01
271 272 7.923878 TCCTAGCATTCTTGTTTTTGTTAAACC 59.076 33.333 0.00 0.00 0.00 3.27
272 273 6.582437 AGCATTCTTGTTTTTGTTAAACCG 57.418 33.333 0.00 0.00 0.00 4.44
273 274 5.522097 AGCATTCTTGTTTTTGTTAAACCGG 59.478 36.000 0.00 0.00 0.00 5.28
274 275 5.733299 CATTCTTGTTTTTGTTAAACCGGC 58.267 37.500 0.00 0.00 0.00 6.13
275 276 4.451629 TCTTGTTTTTGTTAAACCGGCA 57.548 36.364 0.00 0.00 0.00 5.69
276 277 5.012328 TCTTGTTTTTGTTAAACCGGCAT 57.988 34.783 0.00 0.00 0.00 4.40
277 278 5.420409 TCTTGTTTTTGTTAAACCGGCATT 58.580 33.333 0.00 0.00 0.00 3.56
278 279 6.570692 TCTTGTTTTTGTTAAACCGGCATTA 58.429 32.000 0.00 0.00 0.00 1.90
279 280 6.476053 TCTTGTTTTTGTTAAACCGGCATTAC 59.524 34.615 0.00 0.00 0.00 1.89
280 281 5.048507 TGTTTTTGTTAAACCGGCATTACC 58.951 37.500 0.00 0.00 0.00 2.85
281 282 4.931661 TTTTGTTAAACCGGCATTACCA 57.068 36.364 0.00 0.00 39.03 3.25
282 283 5.470047 TTTTGTTAAACCGGCATTACCAT 57.530 34.783 0.00 0.00 39.03 3.55
283 284 5.470047 TTTGTTAAACCGGCATTACCATT 57.530 34.783 0.00 0.00 39.03 3.16
284 285 6.585695 TTTGTTAAACCGGCATTACCATTA 57.414 33.333 0.00 0.00 39.03 1.90
285 286 6.585695 TTGTTAAACCGGCATTACCATTAA 57.414 33.333 0.00 0.00 39.03 1.40
286 287 6.777213 TGTTAAACCGGCATTACCATTAAT 57.223 33.333 0.00 0.00 39.03 1.40
287 288 6.565234 TGTTAAACCGGCATTACCATTAATG 58.435 36.000 8.58 8.58 45.25 1.90
304 305 9.030452 ACCATTAATGCAACCTACAATTAAAGA 57.970 29.630 10.11 0.00 0.00 2.52
305 306 9.868277 CCATTAATGCAACCTACAATTAAAGAA 57.132 29.630 10.11 0.00 0.00 2.52
310 311 8.761575 ATGCAACCTACAATTAAAGAACAATG 57.238 30.769 0.00 0.00 0.00 2.82
311 312 7.151308 TGCAACCTACAATTAAAGAACAATGG 58.849 34.615 0.00 0.00 0.00 3.16
312 313 6.090763 GCAACCTACAATTAAAGAACAATGGC 59.909 38.462 0.00 0.00 0.00 4.40
313 314 6.280855 ACCTACAATTAAAGAACAATGGCC 57.719 37.500 0.00 0.00 0.00 5.36
314 315 6.016555 ACCTACAATTAAAGAACAATGGCCT 58.983 36.000 3.32 0.00 0.00 5.19
315 316 6.071391 ACCTACAATTAAAGAACAATGGCCTG 60.071 38.462 3.32 0.00 0.00 4.85
316 317 4.568956 ACAATTAAAGAACAATGGCCTGC 58.431 39.130 3.32 0.00 0.00 4.85
317 318 4.040217 ACAATTAAAGAACAATGGCCTGCA 59.960 37.500 3.32 0.00 0.00 4.41
318 319 4.888326 ATTAAAGAACAATGGCCTGCAA 57.112 36.364 3.32 0.00 0.00 4.08
319 320 2.531522 AAAGAACAATGGCCTGCAAC 57.468 45.000 3.32 0.00 0.00 4.17
320 321 1.708341 AAGAACAATGGCCTGCAACT 58.292 45.000 3.32 0.00 0.00 3.16
321 322 1.708341 AGAACAATGGCCTGCAACTT 58.292 45.000 3.32 0.00 0.00 2.66
322 323 2.041701 AGAACAATGGCCTGCAACTTT 58.958 42.857 3.32 0.00 0.00 2.66
323 324 2.137523 GAACAATGGCCTGCAACTTTG 58.862 47.619 3.32 0.00 0.00 2.77
324 325 1.412079 ACAATGGCCTGCAACTTTGA 58.588 45.000 3.32 0.00 0.00 2.69
325 326 1.972795 ACAATGGCCTGCAACTTTGAT 59.027 42.857 3.32 0.00 0.00 2.57
326 327 2.369532 ACAATGGCCTGCAACTTTGATT 59.630 40.909 3.32 0.00 0.00 2.57
327 328 3.181452 ACAATGGCCTGCAACTTTGATTT 60.181 39.130 3.32 0.00 0.00 2.17
328 329 3.775261 ATGGCCTGCAACTTTGATTTT 57.225 38.095 3.32 0.00 0.00 1.82
329 330 4.888326 ATGGCCTGCAACTTTGATTTTA 57.112 36.364 3.32 0.00 0.00 1.52
330 331 4.888326 TGGCCTGCAACTTTGATTTTAT 57.112 36.364 3.32 0.00 0.00 1.40
331 332 4.819769 TGGCCTGCAACTTTGATTTTATC 58.180 39.130 3.32 0.00 0.00 1.75
332 333 4.282957 TGGCCTGCAACTTTGATTTTATCA 59.717 37.500 3.32 0.00 37.55 2.15
333 334 4.866486 GGCCTGCAACTTTGATTTTATCAG 59.134 41.667 0.00 0.00 40.94 2.90
334 335 5.336690 GGCCTGCAACTTTGATTTTATCAGA 60.337 40.000 0.00 0.00 40.94 3.27
335 336 5.574443 GCCTGCAACTTTGATTTTATCAGAC 59.426 40.000 0.00 0.00 40.94 3.51
336 337 6.571150 GCCTGCAACTTTGATTTTATCAGACT 60.571 38.462 0.00 0.00 40.94 3.24
337 338 6.805271 CCTGCAACTTTGATTTTATCAGACTG 59.195 38.462 0.00 0.00 40.94 3.51
338 339 7.308770 CCTGCAACTTTGATTTTATCAGACTGA 60.309 37.037 7.80 7.80 40.94 3.41
339 340 7.587629 TGCAACTTTGATTTTATCAGACTGAG 58.412 34.615 11.52 0.00 40.94 3.35
340 341 7.025963 GCAACTTTGATTTTATCAGACTGAGG 58.974 38.462 11.52 0.00 40.94 3.86
341 342 7.094634 GCAACTTTGATTTTATCAGACTGAGGA 60.095 37.037 11.52 0.00 40.94 3.71
342 343 8.786898 CAACTTTGATTTTATCAGACTGAGGAA 58.213 33.333 11.52 4.99 40.94 3.36
343 344 8.558973 ACTTTGATTTTATCAGACTGAGGAAG 57.441 34.615 11.52 7.92 40.94 3.46
344 345 8.160106 ACTTTGATTTTATCAGACTGAGGAAGT 58.840 33.333 11.52 5.01 40.94 3.01
345 346 9.658799 CTTTGATTTTATCAGACTGAGGAAGTA 57.341 33.333 11.52 0.00 40.94 2.24
346 347 9.658799 TTTGATTTTATCAGACTGAGGAAGTAG 57.341 33.333 11.52 0.00 40.94 2.57
347 348 8.367660 TGATTTTATCAGACTGAGGAAGTAGT 57.632 34.615 11.52 0.00 34.91 2.73
348 349 9.475620 TGATTTTATCAGACTGAGGAAGTAGTA 57.524 33.333 11.52 0.00 34.91 1.82
352 353 9.529823 TTTATCAGACTGAGGAAGTAGTAAAGA 57.470 33.333 11.52 0.00 40.07 2.52
353 354 9.529823 TTATCAGACTGAGGAAGTAGTAAAGAA 57.470 33.333 11.52 0.00 40.07 2.52
354 355 8.602472 ATCAGACTGAGGAAGTAGTAAAGAAT 57.398 34.615 11.52 0.00 40.07 2.40
355 356 7.831753 TCAGACTGAGGAAGTAGTAAAGAATG 58.168 38.462 0.00 0.00 40.07 2.67
356 357 7.451877 TCAGACTGAGGAAGTAGTAAAGAATGT 59.548 37.037 0.00 0.00 40.07 2.71
357 358 8.091449 CAGACTGAGGAAGTAGTAAAGAATGTT 58.909 37.037 0.00 0.00 40.07 2.71
358 359 8.652290 AGACTGAGGAAGTAGTAAAGAATGTTT 58.348 33.333 0.00 0.00 40.07 2.83
359 360 9.924650 GACTGAGGAAGTAGTAAAGAATGTTTA 57.075 33.333 0.00 0.00 40.07 2.01
360 361 9.708092 ACTGAGGAAGTAGTAAAGAATGTTTAC 57.292 33.333 5.04 5.04 37.36 2.01
361 362 9.706691 CTGAGGAAGTAGTAAAGAATGTTTACA 57.293 33.333 14.17 0.00 0.00 2.41
379 380 8.614469 TGTTTACATATGTTGTCTCATTGTCA 57.386 30.769 14.77 0.00 39.87 3.58
380 381 9.230122 TGTTTACATATGTTGTCTCATTGTCAT 57.770 29.630 14.77 0.00 39.87 3.06
383 384 9.671279 TTACATATGTTGTCTCATTGTCATTCT 57.329 29.630 14.77 0.00 39.87 2.40
384 385 7.982224 ACATATGTTGTCTCATTGTCATTCTG 58.018 34.615 1.41 0.00 30.89 3.02
385 386 7.825761 ACATATGTTGTCTCATTGTCATTCTGA 59.174 33.333 1.41 0.00 30.89 3.27
386 387 8.671028 CATATGTTGTCTCATTGTCATTCTGAA 58.329 33.333 0.00 0.00 0.00 3.02
387 388 6.549912 TGTTGTCTCATTGTCATTCTGAAG 57.450 37.500 0.00 0.00 0.00 3.02
388 389 6.057533 TGTTGTCTCATTGTCATTCTGAAGT 58.942 36.000 0.00 0.00 0.00 3.01
389 390 7.216494 TGTTGTCTCATTGTCATTCTGAAGTA 58.784 34.615 0.00 0.00 0.00 2.24
390 391 7.879677 TGTTGTCTCATTGTCATTCTGAAGTAT 59.120 33.333 0.00 0.00 0.00 2.12
391 392 8.725148 GTTGTCTCATTGTCATTCTGAAGTATT 58.275 33.333 0.00 0.00 0.00 1.89
392 393 8.853077 TGTCTCATTGTCATTCTGAAGTATTT 57.147 30.769 0.00 0.00 0.00 1.40
393 394 8.939929 TGTCTCATTGTCATTCTGAAGTATTTC 58.060 33.333 0.00 0.00 0.00 2.17
394 395 8.939929 GTCTCATTGTCATTCTGAAGTATTTCA 58.060 33.333 0.34 0.34 40.92 2.69
395 396 9.676861 TCTCATTGTCATTCTGAAGTATTTCAT 57.323 29.630 0.64 0.00 42.19 2.57
400 401 9.897744 TTGTCATTCTGAAGTATTTCATTGAAC 57.102 29.630 0.64 0.00 42.19 3.18
401 402 9.065798 TGTCATTCTGAAGTATTTCATTGAACA 57.934 29.630 0.64 1.34 42.19 3.18
402 403 9.897744 GTCATTCTGAAGTATTTCATTGAACAA 57.102 29.630 0.64 0.00 42.19 2.83
417 418 8.964476 TCATTGAACAAAATAGTATCTCTCCC 57.036 34.615 0.00 0.00 0.00 4.30
457 458 9.846248 AATAATAAAGCACAGATTGAGTTTGTC 57.154 29.630 0.00 0.00 0.00 3.18
463 464 3.315191 CACAGATTGAGTTTGTCGGGTTT 59.685 43.478 0.00 0.00 0.00 3.27
569 594 4.082733 GCGCTTAGGGAAAAAGATTCTTGT 60.083 41.667 0.00 0.00 0.00 3.16
578 603 9.367160 AGGGAAAAAGATTCTTGTCTTATTTGA 57.633 29.630 0.00 0.00 37.46 2.69
587 612 8.970691 ATTCTTGTCTTATTTGATTTTCCGTG 57.029 30.769 0.00 0.00 0.00 4.94
610 635 1.048160 TCCATCCAGGCTATGCGTGA 61.048 55.000 12.88 1.52 45.68 4.35
763 789 2.622436 CTCCTCAAATCGAACCAGGAC 58.378 52.381 0.00 0.00 0.00 3.85
766 792 2.484264 CCTCAAATCGAACCAGGACAAC 59.516 50.000 0.00 0.00 0.00 3.32
801 828 4.819761 GACGCATCCTCAGCCGCA 62.820 66.667 0.00 0.00 0.00 5.69
979 1014 1.672356 AGATGACAGGTGCGGCAAC 60.672 57.895 10.72 10.72 0.00 4.17
1050 1216 1.218047 CCACATCCGACCACGTCAT 59.782 57.895 0.00 0.00 37.88 3.06
1051 1217 0.391130 CCACATCCGACCACGTCATT 60.391 55.000 0.00 0.00 37.88 2.57
1086 1252 0.768221 ACCTCCTTGCCTCCTTCACA 60.768 55.000 0.00 0.00 0.00 3.58
1102 1268 0.321653 CACAGGCTACCCACTCAACC 60.322 60.000 0.00 0.00 0.00 3.77
1116 1282 1.003355 CAACCAGGTGCTCGGATGT 60.003 57.895 0.00 0.00 0.00 3.06
1121 1287 1.359848 CAGGTGCTCGGATGTAACAC 58.640 55.000 0.00 0.00 0.00 3.32
1274 1440 1.204941 CCTCTGGAGGTTAACTGGACG 59.795 57.143 5.42 0.00 43.61 4.79
1286 1452 0.033090 ACTGGACGACTTTCCGAACC 59.967 55.000 0.00 0.00 38.69 3.62
1471 1637 3.253188 TGGTTGCACAAGCTAGCTAAAAG 59.747 43.478 19.70 10.99 42.95 2.27
1474 1640 5.335976 GGTTGCACAAGCTAGCTAAAAGAAT 60.336 40.000 19.70 0.00 40.13 2.40
1844 2014 9.906660 TCTAAAACTAATGGCATTAACACAAAG 57.093 29.630 19.68 11.12 0.00 2.77
1845 2015 9.691362 CTAAAACTAATGGCATTAACACAAAGT 57.309 29.630 19.68 11.73 0.00 2.66
1846 2016 8.956533 AAAACTAATGGCATTAACACAAAGTT 57.043 26.923 19.68 16.39 44.27 2.66
1847 2017 8.956533 AAACTAATGGCATTAACACAAAGTTT 57.043 26.923 20.89 20.89 41.64 2.66
1862 2032 8.587952 ACACAAAGTTTATAATTTTGCTGACC 57.412 30.769 16.73 0.00 35.71 4.02
1863 2033 8.421002 ACACAAAGTTTATAATTTTGCTGACCT 58.579 29.630 16.73 1.81 35.71 3.85
1864 2034 9.906660 CACAAAGTTTATAATTTTGCTGACCTA 57.093 29.630 16.73 0.00 35.71 3.08
1869 2039 9.639601 AGTTTATAATTTTGCTGACCTAAAAGC 57.360 29.630 0.00 0.00 39.96 3.51
2039 2211 8.001881 TGAAAACTAATGGCACTAACAGAAAA 57.998 30.769 0.00 0.00 0.00 2.29
2192 2370 6.400568 CCTAAATACGACTAGAAACCCAACA 58.599 40.000 0.00 0.00 0.00 3.33
2205 2383 2.204748 CCAACATGGGCCAGGATTG 58.795 57.895 27.05 22.37 32.67 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 9.491675 TCAAGTTGAATGTTTTGCATCATTATT 57.508 25.926 2.20 0.00 36.67 1.40
58 59 8.928733 GTCAAGTTGAATGTTTTGCATCATTAT 58.071 29.630 7.25 0.00 36.67 1.28
59 60 7.924947 TGTCAAGTTGAATGTTTTGCATCATTA 59.075 29.630 7.25 0.00 36.67 1.90
60 61 6.762187 TGTCAAGTTGAATGTTTTGCATCATT 59.238 30.769 7.25 10.56 36.67 2.57
61 62 6.282167 TGTCAAGTTGAATGTTTTGCATCAT 58.718 32.000 7.25 0.00 36.67 2.45
62 63 5.658468 TGTCAAGTTGAATGTTTTGCATCA 58.342 33.333 7.25 0.00 36.67 3.07
63 64 6.774354 ATGTCAAGTTGAATGTTTTGCATC 57.226 33.333 7.25 0.00 36.67 3.91
64 65 7.710044 TGTTATGTCAAGTTGAATGTTTTGCAT 59.290 29.630 7.25 6.83 40.03 3.96
65 66 7.038048 TGTTATGTCAAGTTGAATGTTTTGCA 58.962 30.769 7.25 0.00 0.00 4.08
66 67 7.222611 ACTGTTATGTCAAGTTGAATGTTTTGC 59.777 33.333 7.25 0.00 0.00 3.68
67 68 8.633075 ACTGTTATGTCAAGTTGAATGTTTTG 57.367 30.769 7.25 0.00 0.00 2.44
68 69 9.086336 CAACTGTTATGTCAAGTTGAATGTTTT 57.914 29.630 7.25 0.00 41.42 2.43
69 70 8.250332 ACAACTGTTATGTCAAGTTGAATGTTT 58.750 29.630 17.91 0.00 41.42 2.83
70 71 7.771183 ACAACTGTTATGTCAAGTTGAATGTT 58.229 30.769 17.91 2.99 41.42 2.71
71 72 7.333528 ACAACTGTTATGTCAAGTTGAATGT 57.666 32.000 17.91 0.00 41.42 2.71
72 73 7.842525 GACAACTGTTATGTCAAGTTGAATG 57.157 36.000 17.91 0.00 45.13 2.67
82 83 7.426929 AGAGATGTTTGACAACTGTTATGTC 57.573 36.000 5.82 5.82 45.82 3.06
83 84 7.807977 AAGAGATGTTTGACAACTGTTATGT 57.192 32.000 0.00 0.00 33.81 2.29
87 88 8.902806 TGATTTAAGAGATGTTTGACAACTGTT 58.097 29.630 6.13 6.13 37.96 3.16
88 89 8.450578 TGATTTAAGAGATGTTTGACAACTGT 57.549 30.769 0.00 0.00 31.03 3.55
89 90 9.903682 AATGATTTAAGAGATGTTTGACAACTG 57.096 29.630 0.00 0.00 31.03 3.16
110 111 9.713684 TCTCCCATTTCCTGTTAATTTAATGAT 57.286 29.630 0.00 0.00 0.00 2.45
111 112 9.189156 CTCTCCCATTTCCTGTTAATTTAATGA 57.811 33.333 0.00 0.00 0.00 2.57
112 113 7.922811 GCTCTCCCATTTCCTGTTAATTTAATG 59.077 37.037 0.00 0.00 0.00 1.90
113 114 7.841222 AGCTCTCCCATTTCCTGTTAATTTAAT 59.159 33.333 0.00 0.00 0.00 1.40
114 115 7.182060 AGCTCTCCCATTTCCTGTTAATTTAA 58.818 34.615 0.00 0.00 0.00 1.52
115 116 6.731467 AGCTCTCCCATTTCCTGTTAATTTA 58.269 36.000 0.00 0.00 0.00 1.40
116 117 5.583932 AGCTCTCCCATTTCCTGTTAATTT 58.416 37.500 0.00 0.00 0.00 1.82
117 118 5.044550 AGAGCTCTCCCATTTCCTGTTAATT 60.045 40.000 11.45 0.00 0.00 1.40
118 119 4.476479 AGAGCTCTCCCATTTCCTGTTAAT 59.524 41.667 11.45 0.00 0.00 1.40
119 120 3.846588 AGAGCTCTCCCATTTCCTGTTAA 59.153 43.478 11.45 0.00 0.00 2.01
120 121 3.454858 AGAGCTCTCCCATTTCCTGTTA 58.545 45.455 11.45 0.00 0.00 2.41
121 122 2.273619 AGAGCTCTCCCATTTCCTGTT 58.726 47.619 11.45 0.00 0.00 3.16
122 123 1.963985 AGAGCTCTCCCATTTCCTGT 58.036 50.000 11.45 0.00 0.00 4.00
123 124 3.362870 AAAGAGCTCTCCCATTTCCTG 57.637 47.619 18.55 0.00 0.00 3.86
124 125 3.620966 CGAAAAGAGCTCTCCCATTTCCT 60.621 47.826 23.49 3.54 30.25 3.36
125 126 2.680339 CGAAAAGAGCTCTCCCATTTCC 59.320 50.000 23.49 12.22 30.25 3.13
126 127 3.600388 TCGAAAAGAGCTCTCCCATTTC 58.400 45.455 18.55 20.25 0.00 2.17
127 128 3.703001 TCGAAAAGAGCTCTCCCATTT 57.297 42.857 18.55 13.74 0.00 2.32
128 129 3.539604 CATCGAAAAGAGCTCTCCCATT 58.460 45.455 18.55 10.04 0.00 3.16
129 130 2.744494 GCATCGAAAAGAGCTCTCCCAT 60.744 50.000 18.55 3.32 0.00 4.00
130 131 1.406069 GCATCGAAAAGAGCTCTCCCA 60.406 52.381 18.55 0.00 0.00 4.37
131 132 1.294857 GCATCGAAAAGAGCTCTCCC 58.705 55.000 18.55 8.23 0.00 4.30
132 133 1.294857 GGCATCGAAAAGAGCTCTCC 58.705 55.000 18.55 7.42 0.00 3.71
133 134 1.663135 GTGGCATCGAAAAGAGCTCTC 59.337 52.381 18.55 3.81 0.00 3.20
134 135 1.002430 TGTGGCATCGAAAAGAGCTCT 59.998 47.619 11.45 11.45 0.00 4.09
135 136 1.442769 TGTGGCATCGAAAAGAGCTC 58.557 50.000 5.27 5.27 0.00 4.09
136 137 1.896220 TTGTGGCATCGAAAAGAGCT 58.104 45.000 0.00 0.00 0.00 4.09
137 138 2.095059 ACATTGTGGCATCGAAAAGAGC 60.095 45.455 0.00 0.00 0.00 4.09
138 139 3.837213 ACATTGTGGCATCGAAAAGAG 57.163 42.857 0.00 0.00 0.00 2.85
139 140 4.940654 TCATACATTGTGGCATCGAAAAGA 59.059 37.500 0.00 0.00 0.00 2.52
140 141 5.233957 TCATACATTGTGGCATCGAAAAG 57.766 39.130 0.00 0.00 0.00 2.27
141 142 5.450274 CCATCATACATTGTGGCATCGAAAA 60.450 40.000 0.00 0.00 0.00 2.29
142 143 4.036616 CCATCATACATTGTGGCATCGAAA 59.963 41.667 0.00 0.00 0.00 3.46
143 144 3.565063 CCATCATACATTGTGGCATCGAA 59.435 43.478 0.00 0.00 0.00 3.71
144 145 3.140623 CCATCATACATTGTGGCATCGA 58.859 45.455 0.00 0.00 0.00 3.59
145 146 3.140623 TCCATCATACATTGTGGCATCG 58.859 45.455 0.00 0.00 0.00 3.84
146 147 5.518848 TTTCCATCATACATTGTGGCATC 57.481 39.130 0.00 0.00 0.00 3.91
147 148 5.936187 TTTTCCATCATACATTGTGGCAT 57.064 34.783 0.00 0.00 0.00 4.40
148 149 5.735285 TTTTTCCATCATACATTGTGGCA 57.265 34.783 0.00 0.00 0.00 4.92
149 150 6.339730 TGATTTTTCCATCATACATTGTGGC 58.660 36.000 0.00 0.00 0.00 5.01
150 151 8.951787 AATGATTTTTCCATCATACATTGTGG 57.048 30.769 0.00 0.00 42.12 4.17
160 161 9.844257 AACCTTTACAAAATGATTTTTCCATCA 57.156 25.926 0.00 0.00 37.58 3.07
163 164 8.401709 GCAAACCTTTACAAAATGATTTTTCCA 58.598 29.630 0.00 0.00 32.72 3.53
164 165 7.860373 GGCAAACCTTTACAAAATGATTTTTCC 59.140 33.333 0.00 0.00 32.72 3.13
165 166 8.401709 TGGCAAACCTTTACAAAATGATTTTTC 58.598 29.630 0.00 0.00 32.83 2.29
166 167 8.286191 TGGCAAACCTTTACAAAATGATTTTT 57.714 26.923 0.00 0.00 34.37 1.94
167 168 7.872113 TGGCAAACCTTTACAAAATGATTTT 57.128 28.000 0.00 0.00 36.63 1.82
168 169 7.872113 TTGGCAAACCTTTACAAAATGATTT 57.128 28.000 0.00 0.00 36.63 2.17
169 170 7.702386 GTTTGGCAAACCTTTACAAAATGATT 58.298 30.769 28.40 0.00 35.35 2.57
170 171 7.258022 GTTTGGCAAACCTTTACAAAATGAT 57.742 32.000 28.40 0.00 35.35 2.45
171 172 6.670077 GTTTGGCAAACCTTTACAAAATGA 57.330 33.333 28.40 0.00 35.35 2.57
185 186 4.223032 TCCTTTAGTTTGTGGTTTGGCAAA 59.777 37.500 8.93 8.93 32.89 3.68
186 187 3.769844 TCCTTTAGTTTGTGGTTTGGCAA 59.230 39.130 0.00 0.00 0.00 4.52
187 188 3.366396 TCCTTTAGTTTGTGGTTTGGCA 58.634 40.909 0.00 0.00 0.00 4.92
188 189 4.116961 GTTCCTTTAGTTTGTGGTTTGGC 58.883 43.478 0.00 0.00 0.00 4.52
189 190 5.331876 TGTTCCTTTAGTTTGTGGTTTGG 57.668 39.130 0.00 0.00 0.00 3.28
190 191 7.841915 ATTTGTTCCTTTAGTTTGTGGTTTG 57.158 32.000 0.00 0.00 0.00 2.93
192 193 9.541143 CATTATTTGTTCCTTTAGTTTGTGGTT 57.459 29.630 0.00 0.00 0.00 3.67
193 194 8.700973 ACATTATTTGTTCCTTTAGTTTGTGGT 58.299 29.630 0.00 0.00 33.74 4.16
201 202 9.716507 CGGTGAATACATTATTTGTTCCTTTAG 57.283 33.333 0.00 0.00 39.87 1.85
202 203 9.233649 ACGGTGAATACATTATTTGTTCCTTTA 57.766 29.630 0.00 0.00 39.87 1.85
203 204 8.117813 ACGGTGAATACATTATTTGTTCCTTT 57.882 30.769 0.00 0.00 39.87 3.11
204 205 7.696992 ACGGTGAATACATTATTTGTTCCTT 57.303 32.000 0.00 0.00 39.87 3.36
205 206 8.795842 TTACGGTGAATACATTATTTGTTCCT 57.204 30.769 0.00 0.00 39.87 3.36
206 207 9.445786 CATTACGGTGAATACATTATTTGTTCC 57.554 33.333 0.00 0.00 39.87 3.62
213 214 9.719355 TGCTTATCATTACGGTGAATACATTAT 57.281 29.630 0.00 0.00 0.00 1.28
214 215 9.203421 CTGCTTATCATTACGGTGAATACATTA 57.797 33.333 0.00 0.00 0.00 1.90
215 216 7.173218 CCTGCTTATCATTACGGTGAATACATT 59.827 37.037 0.00 0.00 0.00 2.71
216 217 6.650807 CCTGCTTATCATTACGGTGAATACAT 59.349 38.462 0.00 0.00 0.00 2.29
217 218 5.989168 CCTGCTTATCATTACGGTGAATACA 59.011 40.000 0.00 0.00 0.00 2.29
218 219 5.408604 CCCTGCTTATCATTACGGTGAATAC 59.591 44.000 0.00 0.00 0.00 1.89
219 220 5.071250 ACCCTGCTTATCATTACGGTGAATA 59.929 40.000 0.00 0.00 0.00 1.75
220 221 4.141482 ACCCTGCTTATCATTACGGTGAAT 60.141 41.667 0.00 0.00 0.00 2.57
221 222 3.199071 ACCCTGCTTATCATTACGGTGAA 59.801 43.478 0.00 0.00 0.00 3.18
222 223 2.769663 ACCCTGCTTATCATTACGGTGA 59.230 45.455 0.00 0.00 0.00 4.02
223 224 3.194005 ACCCTGCTTATCATTACGGTG 57.806 47.619 0.00 0.00 0.00 4.94
224 225 4.020485 GGATACCCTGCTTATCATTACGGT 60.020 45.833 0.00 0.00 0.00 4.83
225 226 4.223032 AGGATACCCTGCTTATCATTACGG 59.777 45.833 0.00 0.00 42.42 4.02
226 227 5.407407 AGGATACCCTGCTTATCATTACG 57.593 43.478 0.00 0.00 42.42 3.18
227 228 6.070767 TGCTAGGATACCCTGCTTATCATTAC 60.071 42.308 0.00 0.00 44.15 1.89
228 229 6.022958 TGCTAGGATACCCTGCTTATCATTA 58.977 40.000 0.00 0.00 44.15 1.90
229 230 4.846367 TGCTAGGATACCCTGCTTATCATT 59.154 41.667 0.00 0.00 44.15 2.57
230 231 4.429505 TGCTAGGATACCCTGCTTATCAT 58.570 43.478 0.00 0.00 44.15 2.45
231 232 3.856900 TGCTAGGATACCCTGCTTATCA 58.143 45.455 0.00 0.00 44.15 2.15
232 233 5.188751 AGAATGCTAGGATACCCTGCTTATC 59.811 44.000 0.00 0.00 44.15 1.75
233 234 5.097234 AGAATGCTAGGATACCCTGCTTAT 58.903 41.667 0.00 0.00 44.15 1.73
234 235 4.493618 AGAATGCTAGGATACCCTGCTTA 58.506 43.478 0.00 0.00 44.15 3.09
235 236 3.321950 AGAATGCTAGGATACCCTGCTT 58.678 45.455 0.00 0.00 44.15 3.91
236 237 2.983296 AGAATGCTAGGATACCCTGCT 58.017 47.619 0.00 0.00 44.15 4.24
237 238 3.181450 ACAAGAATGCTAGGATACCCTGC 60.181 47.826 0.00 0.00 44.15 4.85
238 239 4.696479 ACAAGAATGCTAGGATACCCTG 57.304 45.455 0.00 0.00 44.15 4.45
239 240 5.717119 AAACAAGAATGCTAGGATACCCT 57.283 39.130 0.00 0.00 46.62 4.34
240 241 6.152831 ACAAAAACAAGAATGCTAGGATACCC 59.847 38.462 0.00 0.00 37.17 3.69
241 242 7.158099 ACAAAAACAAGAATGCTAGGATACC 57.842 36.000 0.00 0.00 37.17 2.73
244 245 9.476202 GTTTAACAAAAACAAGAATGCTAGGAT 57.524 29.630 0.00 0.00 0.00 3.24
245 246 7.923878 GGTTTAACAAAAACAAGAATGCTAGGA 59.076 33.333 0.00 0.00 32.04 2.94
246 247 7.096230 CGGTTTAACAAAAACAAGAATGCTAGG 60.096 37.037 0.00 0.00 32.04 3.02
247 248 7.096230 CCGGTTTAACAAAAACAAGAATGCTAG 60.096 37.037 0.00 0.00 32.04 3.42
248 249 6.697892 CCGGTTTAACAAAAACAAGAATGCTA 59.302 34.615 0.00 0.00 32.04 3.49
249 250 5.522097 CCGGTTTAACAAAAACAAGAATGCT 59.478 36.000 0.00 0.00 32.04 3.79
250 251 5.733299 CCGGTTTAACAAAAACAAGAATGC 58.267 37.500 0.00 0.00 32.04 3.56
251 252 5.292101 TGCCGGTTTAACAAAAACAAGAATG 59.708 36.000 1.90 0.00 32.04 2.67
252 253 5.420409 TGCCGGTTTAACAAAAACAAGAAT 58.580 33.333 1.90 0.00 32.04 2.40
253 254 4.817517 TGCCGGTTTAACAAAAACAAGAA 58.182 34.783 1.90 0.00 32.04 2.52
254 255 4.451629 TGCCGGTTTAACAAAAACAAGA 57.548 36.364 1.90 0.00 32.04 3.02
255 256 5.726729 AATGCCGGTTTAACAAAAACAAG 57.273 34.783 1.90 0.00 32.04 3.16
256 257 5.522824 GGTAATGCCGGTTTAACAAAAACAA 59.477 36.000 1.90 0.00 32.04 2.83
257 258 5.048507 GGTAATGCCGGTTTAACAAAAACA 58.951 37.500 1.90 0.00 32.04 2.83
258 259 5.048507 TGGTAATGCCGGTTTAACAAAAAC 58.951 37.500 12.78 0.00 41.21 2.43
259 260 5.272283 TGGTAATGCCGGTTTAACAAAAA 57.728 34.783 12.78 0.00 41.21 1.94
260 261 4.931661 TGGTAATGCCGGTTTAACAAAA 57.068 36.364 12.78 0.00 41.21 2.44
261 262 5.470047 AATGGTAATGCCGGTTTAACAAA 57.530 34.783 17.33 0.57 41.21 2.83
262 263 6.585695 TTAATGGTAATGCCGGTTTAACAA 57.414 33.333 17.33 3.74 41.21 2.83
263 264 6.565234 CATTAATGGTAATGCCGGTTTAACA 58.435 36.000 16.19 16.19 40.06 2.41
278 279 9.030452 TCTTTAATTGTAGGTTGCATTAATGGT 57.970 29.630 17.02 0.00 0.00 3.55
279 280 9.868277 TTCTTTAATTGTAGGTTGCATTAATGG 57.132 29.630 17.02 0.00 0.00 3.16
284 285 9.206870 CATTGTTCTTTAATTGTAGGTTGCATT 57.793 29.630 0.00 0.00 0.00 3.56
285 286 7.818930 CCATTGTTCTTTAATTGTAGGTTGCAT 59.181 33.333 0.00 0.00 0.00 3.96
286 287 7.151308 CCATTGTTCTTTAATTGTAGGTTGCA 58.849 34.615 0.00 0.00 0.00 4.08
287 288 6.090763 GCCATTGTTCTTTAATTGTAGGTTGC 59.909 38.462 0.00 0.00 0.00 4.17
288 289 6.589907 GGCCATTGTTCTTTAATTGTAGGTTG 59.410 38.462 0.00 0.00 0.00 3.77
289 290 6.496911 AGGCCATTGTTCTTTAATTGTAGGTT 59.503 34.615 5.01 0.00 0.00 3.50
290 291 6.016555 AGGCCATTGTTCTTTAATTGTAGGT 58.983 36.000 5.01 0.00 0.00 3.08
291 292 6.332630 CAGGCCATTGTTCTTTAATTGTAGG 58.667 40.000 5.01 0.00 0.00 3.18
292 293 5.807011 GCAGGCCATTGTTCTTTAATTGTAG 59.193 40.000 5.01 0.00 0.00 2.74
293 294 5.244851 TGCAGGCCATTGTTCTTTAATTGTA 59.755 36.000 5.01 0.00 0.00 2.41
294 295 4.040217 TGCAGGCCATTGTTCTTTAATTGT 59.960 37.500 5.01 0.00 0.00 2.71
295 296 4.567971 TGCAGGCCATTGTTCTTTAATTG 58.432 39.130 5.01 0.00 0.00 2.32
296 297 4.888326 TGCAGGCCATTGTTCTTTAATT 57.112 36.364 5.01 0.00 0.00 1.40
297 298 4.284234 AGTTGCAGGCCATTGTTCTTTAAT 59.716 37.500 5.01 0.00 0.00 1.40
298 299 3.640967 AGTTGCAGGCCATTGTTCTTTAA 59.359 39.130 5.01 0.00 0.00 1.52
299 300 3.230134 AGTTGCAGGCCATTGTTCTTTA 58.770 40.909 5.01 0.00 0.00 1.85
300 301 2.041701 AGTTGCAGGCCATTGTTCTTT 58.958 42.857 5.01 0.00 0.00 2.52
301 302 1.708341 AGTTGCAGGCCATTGTTCTT 58.292 45.000 5.01 0.00 0.00 2.52
302 303 1.708341 AAGTTGCAGGCCATTGTTCT 58.292 45.000 5.01 0.00 0.00 3.01
303 304 2.137523 CAAAGTTGCAGGCCATTGTTC 58.862 47.619 5.01 0.00 0.00 3.18
304 305 1.761784 TCAAAGTTGCAGGCCATTGTT 59.238 42.857 5.01 0.00 0.00 2.83
305 306 1.412079 TCAAAGTTGCAGGCCATTGT 58.588 45.000 5.01 0.00 0.00 2.71
306 307 2.754946 ATCAAAGTTGCAGGCCATTG 57.245 45.000 5.01 0.00 0.00 2.82
307 308 3.775261 AAATCAAAGTTGCAGGCCATT 57.225 38.095 5.01 0.00 0.00 3.16
308 309 3.775261 AAAATCAAAGTTGCAGGCCAT 57.225 38.095 5.01 0.00 0.00 4.40
309 310 4.282957 TGATAAAATCAAAGTTGCAGGCCA 59.717 37.500 5.01 0.00 36.11 5.36
310 311 4.819769 TGATAAAATCAAAGTTGCAGGCC 58.180 39.130 0.00 0.00 36.11 5.19
311 312 5.574443 GTCTGATAAAATCAAAGTTGCAGGC 59.426 40.000 0.00 0.00 39.11 4.85
312 313 6.805271 CAGTCTGATAAAATCAAAGTTGCAGG 59.195 38.462 0.00 0.00 39.11 4.85
313 314 7.587629 TCAGTCTGATAAAATCAAAGTTGCAG 58.412 34.615 0.00 0.00 39.11 4.41
314 315 7.308770 CCTCAGTCTGATAAAATCAAAGTTGCA 60.309 37.037 2.22 0.00 39.11 4.08
315 316 7.025963 CCTCAGTCTGATAAAATCAAAGTTGC 58.974 38.462 2.22 0.00 39.11 4.17
316 317 8.327941 TCCTCAGTCTGATAAAATCAAAGTTG 57.672 34.615 2.22 0.00 39.11 3.16
317 318 8.924511 TTCCTCAGTCTGATAAAATCAAAGTT 57.075 30.769 2.22 0.00 39.11 2.66
318 319 8.160106 ACTTCCTCAGTCTGATAAAATCAAAGT 58.840 33.333 2.22 2.66 39.11 2.66
319 320 8.558973 ACTTCCTCAGTCTGATAAAATCAAAG 57.441 34.615 2.22 2.12 39.11 2.77
320 321 9.658799 CTACTTCCTCAGTCTGATAAAATCAAA 57.341 33.333 2.22 0.00 36.48 2.69
321 322 8.816894 ACTACTTCCTCAGTCTGATAAAATCAA 58.183 33.333 2.22 0.00 36.48 2.57
322 323 8.367660 ACTACTTCCTCAGTCTGATAAAATCA 57.632 34.615 2.22 0.00 36.88 2.57
326 327 9.529823 TCTTTACTACTTCCTCAGTCTGATAAA 57.470 33.333 2.22 2.48 36.88 1.40
327 328 9.529823 TTCTTTACTACTTCCTCAGTCTGATAA 57.470 33.333 2.22 0.61 36.88 1.75
328 329 9.702253 ATTCTTTACTACTTCCTCAGTCTGATA 57.298 33.333 2.22 0.00 36.88 2.15
329 330 8.474025 CATTCTTTACTACTTCCTCAGTCTGAT 58.526 37.037 2.22 0.00 36.88 2.90
330 331 7.451877 ACATTCTTTACTACTTCCTCAGTCTGA 59.548 37.037 1.78 1.78 36.88 3.27
331 332 7.607250 ACATTCTTTACTACTTCCTCAGTCTG 58.393 38.462 0.00 0.00 36.88 3.51
332 333 7.784470 ACATTCTTTACTACTTCCTCAGTCT 57.216 36.000 0.00 0.00 36.88 3.24
333 334 8.834749 AAACATTCTTTACTACTTCCTCAGTC 57.165 34.615 0.00 0.00 36.88 3.51
334 335 9.708092 GTAAACATTCTTTACTACTTCCTCAGT 57.292 33.333 0.00 0.00 39.87 3.41
335 336 9.706691 TGTAAACATTCTTTACTACTTCCTCAG 57.293 33.333 4.96 0.00 36.23 3.35
353 354 9.230122 TGACAATGAGACAACATATGTAAACAT 57.770 29.630 9.21 8.14 44.12 2.71
354 355 8.614469 TGACAATGAGACAACATATGTAAACA 57.386 30.769 9.21 6.24 44.12 2.83
357 358 9.671279 AGAATGACAATGAGACAACATATGTAA 57.329 29.630 9.21 0.00 44.12 2.41
358 359 9.101655 CAGAATGACAATGAGACAACATATGTA 57.898 33.333 9.21 0.00 40.29 2.29
359 360 7.825761 TCAGAATGACAATGAGACAACATATGT 59.174 33.333 1.41 1.41 42.56 2.29
360 361 8.205131 TCAGAATGACAATGAGACAACATATG 57.795 34.615 0.00 0.00 42.56 1.78
391 392 9.396022 GGGAGAGATACTATTTTGTTCAATGAA 57.604 33.333 0.00 0.00 0.00 2.57
392 393 8.772250 AGGGAGAGATACTATTTTGTTCAATGA 58.228 33.333 0.00 0.00 0.00 2.57
393 394 8.970859 AGGGAGAGATACTATTTTGTTCAATG 57.029 34.615 0.00 0.00 0.00 2.82
444 445 4.070009 GGTAAACCCGACAAACTCAATCT 58.930 43.478 0.00 0.00 0.00 2.40
463 464 3.376234 CGAGAAGGAGTATTGTGACGGTA 59.624 47.826 0.00 0.00 0.00 4.02
477 478 3.587797 AGCGTAAATTCACGAGAAGGA 57.412 42.857 5.02 0.00 44.69 3.36
509 512 4.222588 AGGGAGAGAGACATGTTGAAGAAG 59.777 45.833 0.00 0.00 0.00 2.85
520 523 4.016105 AGGGAAAGATTAGGGAGAGAGACA 60.016 45.833 0.00 0.00 0.00 3.41
569 594 5.365403 AACGCACGGAAAATCAAATAAGA 57.635 34.783 0.00 0.00 0.00 2.10
578 603 0.808755 GGATGGAACGCACGGAAAAT 59.191 50.000 0.00 0.00 0.00 1.82
587 612 1.510480 GCATAGCCTGGATGGAACGC 61.510 60.000 0.00 0.00 38.35 4.84
896 931 1.873270 CTCGTGTGGACCATCGACCA 61.873 60.000 16.87 0.00 0.00 4.02
897 932 1.153823 CTCGTGTGGACCATCGACC 60.154 63.158 16.87 0.00 0.00 4.79
958 993 2.124983 CCGCACCTGTCATCTGGG 60.125 66.667 0.00 0.00 37.05 4.45
993 1028 4.404098 GGAACGGCCATCGGGTGT 62.404 66.667 2.24 0.00 44.45 4.16
1086 1252 1.201429 CCTGGTTGAGTGGGTAGCCT 61.201 60.000 13.11 0.00 0.00 4.58
1102 1268 1.359848 GTGTTACATCCGAGCACCTG 58.640 55.000 0.00 0.00 0.00 4.00
1116 1282 1.290955 CTGGAAGACCCGCGTGTTA 59.709 57.895 4.92 0.00 37.93 2.41
1121 1287 4.148825 CTCCCTGGAAGACCCGCG 62.149 72.222 0.00 0.00 37.93 6.46
1239 1405 1.745653 CAGAGGTGTGTGATCGCTAGA 59.254 52.381 7.94 0.00 0.00 2.43
1274 1440 2.332104 GTAAGGTCGGTTCGGAAAGTC 58.668 52.381 0.00 0.00 0.00 3.01
1286 1452 0.248743 TATCTTGCCGCGTAAGGTCG 60.249 55.000 16.98 0.00 38.28 4.79
1343 1509 2.917933 TGTATACCTGCATGCCTTGTC 58.082 47.619 16.68 0.53 0.00 3.18
1381 1547 2.705658 TGCCGGAATCAATCTATGGTCT 59.294 45.455 5.05 0.00 0.00 3.85
1443 1609 2.211250 AGCTTGTGCAACCAGATCAT 57.789 45.000 0.00 0.00 42.74 2.45
1818 1988 9.906660 CTTTGTGTTAATGCCATTAGTTTTAGA 57.093 29.630 0.00 0.00 0.00 2.10
1819 1989 9.691362 ACTTTGTGTTAATGCCATTAGTTTTAG 57.309 29.630 0.00 0.00 0.00 1.85
1821 1991 8.956533 AACTTTGTGTTAATGCCATTAGTTTT 57.043 26.923 0.00 0.00 37.07 2.43
1822 1992 8.956533 AAACTTTGTGTTAATGCCATTAGTTT 57.043 26.923 6.46 6.46 38.03 2.66
1836 2006 9.040939 GGTCAGCAAAATTATAAACTTTGTGTT 57.959 29.630 17.83 0.28 41.29 3.32
1837 2007 8.421002 AGGTCAGCAAAATTATAAACTTTGTGT 58.579 29.630 17.83 8.62 33.51 3.72
1838 2008 8.816640 AGGTCAGCAAAATTATAAACTTTGTG 57.183 30.769 17.83 15.19 33.51 3.33
1843 2013 9.639601 GCTTTTAGGTCAGCAAAATTATAAACT 57.360 29.630 0.00 0.00 35.95 2.66
1844 2014 9.418045 TGCTTTTAGGTCAGCAAAATTATAAAC 57.582 29.630 0.00 0.00 43.14 2.01
2171 2349 5.646360 CCATGTTGGGTTTCTAGTCGTATTT 59.354 40.000 0.00 0.00 32.67 1.40
2192 2370 2.605299 GCCTCAATCCTGGCCCAT 59.395 61.111 0.00 0.00 43.11 4.00


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

AutoCloner maintained by Alex Coulton.