Multiple sequence alignment - TraesCS1D01G435100

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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 TraesCS1D01G435100 chr1D 100.000 2651 0 0 1 2651 483914893 483917543 0.000000e+00 4896.0
1 TraesCS1D01G435100 chr1D 97.738 2343 24 7 322 2651 254497398 254495072 0.000000e+00 4006.0
2 TraesCS1D01G435100 chr1D 96.894 1320 9 4 322 1610 19957435 19956117 0.000000e+00 2182.0
3 TraesCS1D01G435100 chr1D 99.057 318 3 0 1 318 483923365 483923048 2.960000e-159 571.0
4 TraesCS1D01G435100 chr1D 96.167 287 9 2 1 286 205714628 205714343 4.000000e-128 468.0
5 TraesCS1D01G435100 chr1D 96.154 286 11 0 1 286 214585593 214585308 4.000000e-128 468.0
6 TraesCS1D01G435100 chr1D 96.154 286 11 0 1 286 361574802 361574517 4.000000e-128 468.0
7 TraesCS1D01G435100 chr5D 98.720 2343 17 1 322 2651 240137107 240134765 0.000000e+00 4148.0
8 TraesCS1D01G435100 chr5D 97.951 2343 29 6 322 2651 6201878 6204214 0.000000e+00 4043.0
9 TraesCS1D01G435100 chr5D 96.154 286 10 1 1 286 119203703 119203987 1.440000e-127 466.0
10 TraesCS1D01G435100 chr3B 98.207 2343 28 2 322 2651 201512529 201510188 0.000000e+00 4082.0
11 TraesCS1D01G435100 chr4D 96.077 2345 72 7 322 2651 19915898 19913559 0.000000e+00 3803.0
12 TraesCS1D01G435100 chr4D 96.503 286 10 0 1 286 424253271 424252986 8.590000e-130 473.0
13 TraesCS1D01G435100 chr3D 98.154 2004 21 4 322 2311 21904027 21902026 0.000000e+00 3482.0
14 TraesCS1D01G435100 chr3D 99.099 888 7 1 1764 2651 21902036 21901150 0.000000e+00 1594.0
15 TraesCS1D01G435100 chr3D 96.154 286 11 0 1 286 349506600 349506315 4.000000e-128 468.0
16 TraesCS1D01G435100 chr2D 98.406 1568 21 3 1085 2651 334231119 334229555 0.000000e+00 2754.0
17 TraesCS1D01G435100 chr2D 96.503 286 9 1 1 286 625602041 625602325 3.090000e-129 472.0
18 TraesCS1D01G435100 chr6B 97.354 1474 25 2 322 1782 22425345 22423873 0.000000e+00 2494.0
19 TraesCS1D01G435100 chr2B 98.708 1316 15 2 1334 2649 474897223 474898536 0.000000e+00 2335.0
20 TraesCS1D01G435100 chrUn 98.087 1098 7 2 698 1782 440190305 440189209 0.000000e+00 1899.0
21 TraesCS1D01G435100 chr1A 97.665 1028 8 3 322 1334 112776632 112777658 0.000000e+00 1751.0
22 TraesCS1D01G435100 chr5B 96.154 286 11 0 1 286 631007188 631006903 4.000000e-128 468.0
23 TraesCS1D01G435100 chr4A 100.000 30 0 0 283 312 314584652 314584681 3.690000e-04 56.5


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 TraesCS1D01G435100 chr1D 483914893 483917543 2650 False 4896 4896 100.0000 1 2651 1 chr1D.!!$F1 2650
1 TraesCS1D01G435100 chr1D 254495072 254497398 2326 True 4006 4006 97.7380 322 2651 1 chr1D.!!$R4 2329
2 TraesCS1D01G435100 chr1D 19956117 19957435 1318 True 2182 2182 96.8940 322 1610 1 chr1D.!!$R1 1288
3 TraesCS1D01G435100 chr5D 240134765 240137107 2342 True 4148 4148 98.7200 322 2651 1 chr5D.!!$R1 2329
4 TraesCS1D01G435100 chr5D 6201878 6204214 2336 False 4043 4043 97.9510 322 2651 1 chr5D.!!$F1 2329
5 TraesCS1D01G435100 chr3B 201510188 201512529 2341 True 4082 4082 98.2070 322 2651 1 chr3B.!!$R1 2329
6 TraesCS1D01G435100 chr4D 19913559 19915898 2339 True 3803 3803 96.0770 322 2651 1 chr4D.!!$R1 2329
7 TraesCS1D01G435100 chr3D 21901150 21904027 2877 True 2538 3482 98.6265 322 2651 2 chr3D.!!$R2 2329
8 TraesCS1D01G435100 chr2D 334229555 334231119 1564 True 2754 2754 98.4060 1085 2651 1 chr2D.!!$R1 1566
9 TraesCS1D01G435100 chr6B 22423873 22425345 1472 True 2494 2494 97.3540 322 1782 1 chr6B.!!$R1 1460
10 TraesCS1D01G435100 chr2B 474897223 474898536 1313 False 2335 2335 98.7080 1334 2649 1 chr2B.!!$F1 1315
11 TraesCS1D01G435100 chrUn 440189209 440190305 1096 True 1899 1899 98.0870 698 1782 1 chrUn.!!$R1 1084
12 TraesCS1D01G435100 chr1A 112776632 112777658 1026 False 1751 1751 97.6650 322 1334 1 chr1A.!!$F1 1012

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
225 226 0.034059 CATCCTCGGTATGGTGGCTC 59.966 60.0 0.0 0.0 0.0 4.70 F
239 240 0.106769 TGGCTCCACTGAACTTTGCA 60.107 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1034 1050 1.753649 TCGCTTCTTCATCTCCAGGAG 59.246 52.381 10.7 10.7 0.0 3.69 R
1817 1856 2.413796 CGTATTGGCTGTCTTGCGTTTA 59.586 45.455 0.0 0.0 0.0 2.01 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
25 26 6.624352 TGCATACAATTTCTAGGATCAAGC 57.376 37.500 0.00 0.00 0.00 4.01
26 27 5.532406 TGCATACAATTTCTAGGATCAAGCC 59.468 40.000 0.00 0.00 0.00 4.35
27 28 5.532406 GCATACAATTTCTAGGATCAAGCCA 59.468 40.000 0.00 0.00 0.00 4.75
28 29 6.039717 GCATACAATTTCTAGGATCAAGCCAA 59.960 38.462 0.00 0.00 0.00 4.52
29 30 7.416664 GCATACAATTTCTAGGATCAAGCCAAA 60.417 37.037 0.00 0.00 0.00 3.28
30 31 6.916360 ACAATTTCTAGGATCAAGCCAAAA 57.084 33.333 0.00 0.00 0.00 2.44
31 32 7.486407 ACAATTTCTAGGATCAAGCCAAAAT 57.514 32.000 0.00 0.00 0.00 1.82
32 33 7.325694 ACAATTTCTAGGATCAAGCCAAAATG 58.674 34.615 0.00 0.00 0.00 2.32
33 34 4.989279 TTCTAGGATCAAGCCAAAATGC 57.011 40.909 0.00 0.00 0.00 3.56
34 35 3.966979 TCTAGGATCAAGCCAAAATGCA 58.033 40.909 0.00 0.00 0.00 3.96
35 36 4.343231 TCTAGGATCAAGCCAAAATGCAA 58.657 39.130 0.00 0.00 0.00 4.08
36 37 4.957954 TCTAGGATCAAGCCAAAATGCAAT 59.042 37.500 0.00 0.00 0.00 3.56
37 38 6.128486 TCTAGGATCAAGCCAAAATGCAATA 58.872 36.000 0.00 0.00 0.00 1.90
38 39 5.680594 AGGATCAAGCCAAAATGCAATAA 57.319 34.783 0.00 0.00 0.00 1.40
39 40 6.052405 AGGATCAAGCCAAAATGCAATAAA 57.948 33.333 0.00 0.00 0.00 1.40
40 41 6.474630 AGGATCAAGCCAAAATGCAATAAAA 58.525 32.000 0.00 0.00 0.00 1.52
41 42 6.941436 AGGATCAAGCCAAAATGCAATAAAAA 59.059 30.769 0.00 0.00 0.00 1.94
42 43 7.612633 AGGATCAAGCCAAAATGCAATAAAAAT 59.387 29.630 0.00 0.00 0.00 1.82
43 44 8.891720 GGATCAAGCCAAAATGCAATAAAAATA 58.108 29.630 0.00 0.00 0.00 1.40
46 47 9.445878 TCAAGCCAAAATGCAATAAAAATATGA 57.554 25.926 0.00 0.00 0.00 2.15
68 69 7.931578 TGATATGCAATGATGATCTAATGCA 57.068 32.000 17.65 17.65 46.43 3.96
106 107 9.639563 ATTGAAAATTTGGGATTTTACAAACCT 57.360 25.926 0.00 0.00 39.15 3.50
108 109 9.549078 TGAAAATTTGGGATTTTACAAACCTAC 57.451 29.630 0.00 0.00 39.15 3.18
109 110 8.911918 AAAATTTGGGATTTTACAAACCTACC 57.088 30.769 0.00 0.00 39.15 3.18
110 111 6.614694 ATTTGGGATTTTACAAACCTACCC 57.385 37.500 0.00 0.00 39.15 3.69
111 112 4.050315 TGGGATTTTACAAACCTACCCC 57.950 45.455 0.00 0.00 35.69 4.95
112 113 3.245694 TGGGATTTTACAAACCTACCCCC 60.246 47.826 0.00 0.00 35.69 5.40
129 130 2.772287 CCCCCTTAAGATGAATCTCGC 58.228 52.381 3.36 0.00 35.76 5.03
130 131 2.551071 CCCCCTTAAGATGAATCTCGCC 60.551 54.545 3.36 0.00 35.76 5.54
131 132 2.551071 CCCCTTAAGATGAATCTCGCCC 60.551 54.545 3.36 0.00 35.76 6.13
132 133 2.370189 CCCTTAAGATGAATCTCGCCCT 59.630 50.000 3.36 0.00 35.76 5.19
133 134 3.556004 CCCTTAAGATGAATCTCGCCCTC 60.556 52.174 3.36 0.00 35.76 4.30
134 135 3.312828 CTTAAGATGAATCTCGCCCTCG 58.687 50.000 0.00 0.00 35.76 4.63
135 136 1.403814 AAGATGAATCTCGCCCTCGA 58.596 50.000 0.00 0.00 43.28 4.04
143 144 3.217017 TCGCCCTCGAGATTCGGG 61.217 66.667 15.71 8.33 40.73 5.14
144 145 3.528370 CGCCCTCGAGATTCGGGT 61.528 66.667 15.71 0.00 39.06 5.28
145 146 2.901042 GCCCTCGAGATTCGGGTT 59.099 61.111 15.71 0.00 39.06 4.11
146 147 1.521681 GCCCTCGAGATTCGGGTTG 60.522 63.158 15.71 0.00 39.06 3.77
147 148 1.144057 CCCTCGAGATTCGGGTTGG 59.856 63.158 15.71 0.00 39.06 3.77
148 149 1.521681 CCTCGAGATTCGGGTTGGC 60.522 63.158 15.71 0.00 39.06 4.52
149 150 1.517832 CTCGAGATTCGGGTTGGCT 59.482 57.895 6.58 0.00 40.88 4.75
150 151 0.744874 CTCGAGATTCGGGTTGGCTA 59.255 55.000 6.58 0.00 40.88 3.93
151 152 0.744874 TCGAGATTCGGGTTGGCTAG 59.255 55.000 0.00 0.00 40.88 3.42
152 153 0.744874 CGAGATTCGGGTTGGCTAGA 59.255 55.000 0.00 0.00 36.00 2.43
153 154 1.136305 CGAGATTCGGGTTGGCTAGAA 59.864 52.381 0.00 0.00 36.00 2.10
154 155 2.418197 CGAGATTCGGGTTGGCTAGAAA 60.418 50.000 0.00 0.00 36.00 2.52
155 156 3.606687 GAGATTCGGGTTGGCTAGAAAA 58.393 45.455 0.00 0.00 0.00 2.29
156 157 4.200092 GAGATTCGGGTTGGCTAGAAAAT 58.800 43.478 0.00 0.00 0.00 1.82
157 158 5.365619 GAGATTCGGGTTGGCTAGAAAATA 58.634 41.667 0.00 0.00 0.00 1.40
158 159 5.368989 AGATTCGGGTTGGCTAGAAAATAG 58.631 41.667 0.00 0.00 0.00 1.73
159 160 3.553828 TCGGGTTGGCTAGAAAATAGG 57.446 47.619 0.00 0.00 0.00 2.57
160 161 2.841881 TCGGGTTGGCTAGAAAATAGGT 59.158 45.455 0.00 0.00 0.00 3.08
161 162 2.943033 CGGGTTGGCTAGAAAATAGGTG 59.057 50.000 0.00 0.00 0.00 4.00
162 163 3.370103 CGGGTTGGCTAGAAAATAGGTGA 60.370 47.826 0.00 0.00 0.00 4.02
163 164 4.200092 GGGTTGGCTAGAAAATAGGTGAG 58.800 47.826 0.00 0.00 0.00 3.51
164 165 4.200092 GGTTGGCTAGAAAATAGGTGAGG 58.800 47.826 0.00 0.00 0.00 3.86
165 166 4.200092 GTTGGCTAGAAAATAGGTGAGGG 58.800 47.826 0.00 0.00 0.00 4.30
166 167 3.460825 TGGCTAGAAAATAGGTGAGGGT 58.539 45.455 0.00 0.00 0.00 4.34
167 168 3.199946 TGGCTAGAAAATAGGTGAGGGTG 59.800 47.826 0.00 0.00 0.00 4.61
168 169 3.454812 GGCTAGAAAATAGGTGAGGGTGA 59.545 47.826 0.00 0.00 0.00 4.02
169 170 4.103311 GGCTAGAAAATAGGTGAGGGTGAT 59.897 45.833 0.00 0.00 0.00 3.06
170 171 5.301555 GCTAGAAAATAGGTGAGGGTGATC 58.698 45.833 0.00 0.00 0.00 2.92
171 172 4.779993 AGAAAATAGGTGAGGGTGATCC 57.220 45.455 0.00 0.00 0.00 3.36
180 181 3.225608 AGGGTGATCCTTCCGTAGG 57.774 57.895 0.00 0.00 45.47 3.18
181 182 0.338814 AGGGTGATCCTTCCGTAGGT 59.661 55.000 1.25 0.00 45.47 3.08
182 183 1.688627 AGGGTGATCCTTCCGTAGGTC 60.689 57.143 1.25 0.46 45.47 3.85
183 184 4.042832 AGGGTGATCCTTCCGTAGGTCT 62.043 54.545 1.25 0.00 45.47 3.85
184 185 5.497559 AGGGTGATCCTTCCGTAGGTCTT 62.498 52.174 1.25 0.00 45.47 3.01
194 195 2.828874 CGTAGGTCTTCCTCTCGTTC 57.171 55.000 0.00 0.00 43.94 3.95
195 196 1.401199 CGTAGGTCTTCCTCTCGTTCC 59.599 57.143 0.00 0.00 43.94 3.62
196 197 2.725637 GTAGGTCTTCCTCTCGTTCCT 58.274 52.381 0.00 0.00 43.94 3.36
197 198 3.681034 CGTAGGTCTTCCTCTCGTTCCTA 60.681 52.174 0.00 0.00 43.94 2.94
198 199 3.007473 AGGTCTTCCTCTCGTTCCTAG 57.993 52.381 0.00 0.00 40.58 3.02
199 200 2.025898 GGTCTTCCTCTCGTTCCTAGG 58.974 57.143 0.82 0.82 0.00 3.02
200 201 2.621147 GGTCTTCCTCTCGTTCCTAGGT 60.621 54.545 9.08 0.00 0.00 3.08
201 202 2.424246 GTCTTCCTCTCGTTCCTAGGTG 59.576 54.545 9.08 0.15 0.00 4.00
202 203 1.751924 CTTCCTCTCGTTCCTAGGTGG 59.248 57.143 9.08 0.00 37.10 4.61
203 204 0.683504 TCCTCTCGTTCCTAGGTGGC 60.684 60.000 9.08 0.00 35.26 5.01
204 205 0.684805 CCTCTCGTTCCTAGGTGGCT 60.685 60.000 9.08 0.00 35.26 4.75
205 206 1.187087 CTCTCGTTCCTAGGTGGCTT 58.813 55.000 9.08 0.00 35.26 4.35
206 207 1.135333 CTCTCGTTCCTAGGTGGCTTC 59.865 57.143 9.08 0.00 35.26 3.86
207 208 0.895530 CTCGTTCCTAGGTGGCTTCA 59.104 55.000 9.08 0.00 35.26 3.02
208 209 1.482593 CTCGTTCCTAGGTGGCTTCAT 59.517 52.381 9.08 0.00 35.26 2.57
209 210 1.480954 TCGTTCCTAGGTGGCTTCATC 59.519 52.381 9.08 0.00 35.26 2.92
210 211 1.473434 CGTTCCTAGGTGGCTTCATCC 60.473 57.143 9.08 0.00 35.26 3.51
211 212 1.840635 GTTCCTAGGTGGCTTCATCCT 59.159 52.381 9.08 0.00 35.26 3.24
212 213 1.794714 TCCTAGGTGGCTTCATCCTC 58.205 55.000 9.08 0.00 35.26 3.71
213 214 0.390860 CCTAGGTGGCTTCATCCTCG 59.609 60.000 0.00 0.00 33.34 4.63
214 215 0.390860 CTAGGTGGCTTCATCCTCGG 59.609 60.000 0.00 0.00 33.34 4.63
215 216 0.325296 TAGGTGGCTTCATCCTCGGT 60.325 55.000 0.00 0.00 33.34 4.69
216 217 0.325296 AGGTGGCTTCATCCTCGGTA 60.325 55.000 0.00 0.00 0.00 4.02
217 218 0.759346 GGTGGCTTCATCCTCGGTAT 59.241 55.000 0.00 0.00 0.00 2.73
218 219 1.541233 GGTGGCTTCATCCTCGGTATG 60.541 57.143 0.00 0.00 0.00 2.39
219 220 0.758734 TGGCTTCATCCTCGGTATGG 59.241 55.000 0.00 0.00 0.00 2.74
220 221 0.759346 GGCTTCATCCTCGGTATGGT 59.241 55.000 0.00 0.00 0.00 3.55
221 222 1.541233 GGCTTCATCCTCGGTATGGTG 60.541 57.143 0.00 0.00 0.00 4.17
222 223 1.541233 GCTTCATCCTCGGTATGGTGG 60.541 57.143 0.00 0.00 0.00 4.61
223 224 0.468226 TTCATCCTCGGTATGGTGGC 59.532 55.000 0.00 0.00 0.00 5.01
224 225 0.398522 TCATCCTCGGTATGGTGGCT 60.399 55.000 0.00 0.00 0.00 4.75
225 226 0.034059 CATCCTCGGTATGGTGGCTC 59.966 60.000 0.00 0.00 0.00 4.70
226 227 1.122019 ATCCTCGGTATGGTGGCTCC 61.122 60.000 0.00 0.00 0.00 4.70
234 235 3.986054 TGGTGGCTCCACTGAACT 58.014 55.556 17.57 0.00 45.52 3.01
235 236 2.230664 TGGTGGCTCCACTGAACTT 58.769 52.632 17.57 0.00 45.52 2.66
236 237 0.550914 TGGTGGCTCCACTGAACTTT 59.449 50.000 17.57 0.00 45.52 2.66
237 238 0.954452 GGTGGCTCCACTGAACTTTG 59.046 55.000 17.57 0.00 45.52 2.77
238 239 0.312102 GTGGCTCCACTGAACTTTGC 59.688 55.000 11.61 0.00 43.12 3.68
239 240 0.106769 TGGCTCCACTGAACTTTGCA 60.107 50.000 0.00 0.00 0.00 4.08
240 241 0.595095 GGCTCCACTGAACTTTGCAG 59.405 55.000 0.00 0.00 39.26 4.41
241 242 1.597742 GCTCCACTGAACTTTGCAGA 58.402 50.000 0.00 0.00 36.86 4.26
242 243 1.949525 GCTCCACTGAACTTTGCAGAA 59.050 47.619 0.00 0.00 36.86 3.02
243 244 2.287248 GCTCCACTGAACTTTGCAGAAC 60.287 50.000 0.00 0.00 36.86 3.01
244 245 3.209410 CTCCACTGAACTTTGCAGAACT 58.791 45.455 0.00 0.00 36.86 3.01
245 246 3.620488 TCCACTGAACTTTGCAGAACTT 58.380 40.909 0.00 0.00 36.86 2.66
246 247 3.378112 TCCACTGAACTTTGCAGAACTTG 59.622 43.478 0.00 0.00 36.86 3.16
247 248 3.378112 CCACTGAACTTTGCAGAACTTGA 59.622 43.478 0.00 0.00 36.86 3.02
248 249 4.037208 CCACTGAACTTTGCAGAACTTGAT 59.963 41.667 0.00 0.00 36.86 2.57
249 250 5.239306 CCACTGAACTTTGCAGAACTTGATA 59.761 40.000 0.00 0.00 36.86 2.15
250 251 6.238731 CCACTGAACTTTGCAGAACTTGATAA 60.239 38.462 0.00 0.00 36.86 1.75
251 252 6.634436 CACTGAACTTTGCAGAACTTGATAAC 59.366 38.462 0.00 0.00 36.86 1.89
252 253 6.072112 TGAACTTTGCAGAACTTGATAACC 57.928 37.500 0.00 0.00 0.00 2.85
253 254 5.827797 TGAACTTTGCAGAACTTGATAACCT 59.172 36.000 0.00 0.00 0.00 3.50
254 255 6.321181 TGAACTTTGCAGAACTTGATAACCTT 59.679 34.615 0.00 0.00 0.00 3.50
255 256 6.076981 ACTTTGCAGAACTTGATAACCTTG 57.923 37.500 0.00 0.00 0.00 3.61
256 257 5.594317 ACTTTGCAGAACTTGATAACCTTGT 59.406 36.000 0.00 0.00 0.00 3.16
257 258 6.096846 ACTTTGCAGAACTTGATAACCTTGTT 59.903 34.615 0.00 0.00 0.00 2.83
258 259 5.437289 TGCAGAACTTGATAACCTTGTTG 57.563 39.130 0.00 0.00 0.00 3.33
259 260 4.229876 GCAGAACTTGATAACCTTGTTGC 58.770 43.478 0.00 0.00 0.00 4.17
260 261 4.466828 CAGAACTTGATAACCTTGTTGCG 58.533 43.478 0.00 0.00 0.00 4.85
261 262 4.024048 CAGAACTTGATAACCTTGTTGCGT 60.024 41.667 0.00 0.00 0.00 5.24
262 263 3.896648 ACTTGATAACCTTGTTGCGTG 57.103 42.857 0.00 0.00 0.00 5.34
263 264 3.211045 ACTTGATAACCTTGTTGCGTGT 58.789 40.909 0.00 0.00 0.00 4.49
264 265 4.382291 ACTTGATAACCTTGTTGCGTGTA 58.618 39.130 0.00 0.00 0.00 2.90
265 266 4.817464 ACTTGATAACCTTGTTGCGTGTAA 59.183 37.500 0.00 0.00 0.00 2.41
266 267 4.735662 TGATAACCTTGTTGCGTGTAAC 57.264 40.909 0.00 0.00 0.00 2.50
267 268 4.382291 TGATAACCTTGTTGCGTGTAACT 58.618 39.130 2.63 0.00 31.75 2.24
268 269 4.449743 TGATAACCTTGTTGCGTGTAACTC 59.550 41.667 2.63 0.00 31.75 3.01
269 270 1.214367 ACCTTGTTGCGTGTAACTCG 58.786 50.000 2.63 0.00 31.75 4.18
270 271 0.511221 CCTTGTTGCGTGTAACTCGG 59.489 55.000 2.63 0.00 31.75 4.63
271 272 0.110823 CTTGTTGCGTGTAACTCGGC 60.111 55.000 2.63 0.00 31.75 5.54
272 273 0.531090 TTGTTGCGTGTAACTCGGCT 60.531 50.000 2.63 0.00 31.75 5.52
273 274 1.218875 TGTTGCGTGTAACTCGGCTG 61.219 55.000 2.63 0.00 31.75 4.85
274 275 1.666553 TTGCGTGTAACTCGGCTGG 60.667 57.895 0.00 0.00 31.75 4.85
275 276 3.488090 GCGTGTAACTCGGCTGGC 61.488 66.667 0.00 0.00 31.75 4.85
276 277 2.048597 CGTGTAACTCGGCTGGCA 60.049 61.111 1.08 0.00 31.75 4.92
277 278 1.666553 CGTGTAACTCGGCTGGCAA 60.667 57.895 1.08 0.00 31.75 4.52
278 279 1.225376 CGTGTAACTCGGCTGGCAAA 61.225 55.000 1.08 0.00 31.75 3.68
279 280 0.237498 GTGTAACTCGGCTGGCAAAC 59.763 55.000 1.08 0.00 0.00 2.93
280 281 0.107831 TGTAACTCGGCTGGCAAACT 59.892 50.000 1.08 0.00 0.00 2.66
281 282 0.796927 GTAACTCGGCTGGCAAACTC 59.203 55.000 1.08 0.00 0.00 3.01
282 283 0.669318 TAACTCGGCTGGCAAACTCG 60.669 55.000 1.08 0.00 0.00 4.18
283 284 2.048222 CTCGGCTGGCAAACTCGA 60.048 61.111 1.08 0.00 0.00 4.04
284 285 2.048222 TCGGCTGGCAAACTCGAG 60.048 61.111 11.84 11.84 0.00 4.04
285 286 2.048222 CGGCTGGCAAACTCGAGA 60.048 61.111 21.68 0.00 0.00 4.04
286 287 1.448540 CGGCTGGCAAACTCGAGAT 60.449 57.895 21.68 3.75 0.00 2.75
287 288 0.179111 CGGCTGGCAAACTCGAGATA 60.179 55.000 21.68 0.00 0.00 1.98
288 289 1.291132 GGCTGGCAAACTCGAGATAC 58.709 55.000 21.68 3.10 0.00 2.24
289 290 1.405526 GGCTGGCAAACTCGAGATACA 60.406 52.381 21.68 9.36 0.00 2.29
290 291 1.929836 GCTGGCAAACTCGAGATACAG 59.070 52.381 21.68 18.47 0.00 2.74
291 292 2.675317 GCTGGCAAACTCGAGATACAGT 60.675 50.000 21.68 0.00 0.00 3.55
292 293 2.926200 CTGGCAAACTCGAGATACAGTG 59.074 50.000 21.68 3.41 0.00 3.66
293 294 1.661112 GGCAAACTCGAGATACAGTGC 59.339 52.381 21.68 13.71 0.00 4.40
294 295 1.661112 GCAAACTCGAGATACAGTGCC 59.339 52.381 21.68 0.00 0.00 5.01
295 296 2.930887 GCAAACTCGAGATACAGTGCCA 60.931 50.000 21.68 0.00 0.00 4.92
296 297 2.656560 AACTCGAGATACAGTGCCAC 57.343 50.000 21.68 0.00 0.00 5.01
297 298 1.840737 ACTCGAGATACAGTGCCACT 58.159 50.000 21.68 0.00 0.00 4.00
308 309 2.898705 CAGTGCCACTGGAAGAGATAC 58.101 52.381 17.22 0.00 42.35 2.24
309 310 2.234661 CAGTGCCACTGGAAGAGATACA 59.765 50.000 17.22 0.00 42.35 2.29
310 311 2.499289 AGTGCCACTGGAAGAGATACAG 59.501 50.000 0.00 0.00 46.40 2.74
316 317 2.898705 CTGGAAGAGATACAGTGCCAC 58.101 52.381 0.00 0.00 35.02 5.01
317 318 2.499289 CTGGAAGAGATACAGTGCCACT 59.501 50.000 0.00 0.00 35.02 4.00
318 319 2.497675 TGGAAGAGATACAGTGCCACTC 59.502 50.000 0.00 0.00 0.00 3.51
319 320 2.480416 GGAAGAGATACAGTGCCACTCG 60.480 54.545 0.00 0.00 33.53 4.18
320 321 1.107114 AGAGATACAGTGCCACTCGG 58.893 55.000 0.00 0.00 33.53 4.63
510 511 4.464951 ACAGTATGAACACGATACCAAGGA 59.535 41.667 0.00 0.00 39.69 3.36
831 833 9.506018 CACCCATTCCTTTTTCTTTATTCAATT 57.494 29.630 0.00 0.00 0.00 2.32
1034 1050 3.683365 TCCAAAAGTACCTTACCGGAC 57.317 47.619 9.46 0.00 36.31 4.79
1361 1399 2.795175 CGTATAGCATTCCCTCACGT 57.205 50.000 0.00 0.00 0.00 4.49
1630 1668 2.174639 ACTGATCCAGTGTGGTTTCCAA 59.825 45.455 0.00 0.00 43.63 3.53
1817 1856 7.216973 TGCCAACGGTTAAACAACTTATTAT 57.783 32.000 0.00 0.00 0.00 1.28
2493 3072 7.147897 GGAAGGTTACTATAGCAAAAGCCATTT 60.148 37.037 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.914757 GCTTGATCCTAGAAATTGTATGCAAC 59.085 38.462 0.00 0.00 37.44 4.17
1 2 6.039717 GGCTTGATCCTAGAAATTGTATGCAA 59.960 38.462 0.00 0.00 39.16 4.08
2 3 5.532406 GGCTTGATCCTAGAAATTGTATGCA 59.468 40.000 0.00 0.00 0.00 3.96
3 4 5.532406 TGGCTTGATCCTAGAAATTGTATGC 59.468 40.000 0.00 0.00 0.00 3.14
4 5 7.572523 TTGGCTTGATCCTAGAAATTGTATG 57.427 36.000 0.00 0.00 0.00 2.39
5 6 8.593945 TTTTGGCTTGATCCTAGAAATTGTAT 57.406 30.769 0.00 0.00 0.00 2.29
6 7 8.469200 CATTTTGGCTTGATCCTAGAAATTGTA 58.531 33.333 0.00 0.00 0.00 2.41
7 8 6.916360 TTTTGGCTTGATCCTAGAAATTGT 57.084 33.333 0.00 0.00 0.00 2.71
8 9 6.257193 GCATTTTGGCTTGATCCTAGAAATTG 59.743 38.462 0.00 0.00 0.00 2.32
9 10 6.070653 TGCATTTTGGCTTGATCCTAGAAATT 60.071 34.615 0.00 0.00 34.04 1.82
10 11 5.422970 TGCATTTTGGCTTGATCCTAGAAAT 59.577 36.000 0.00 0.00 34.04 2.17
11 12 4.771577 TGCATTTTGGCTTGATCCTAGAAA 59.228 37.500 0.00 0.00 34.04 2.52
12 13 4.343231 TGCATTTTGGCTTGATCCTAGAA 58.657 39.130 0.00 0.00 34.04 2.10
13 14 3.966979 TGCATTTTGGCTTGATCCTAGA 58.033 40.909 0.00 0.00 34.04 2.43
14 15 4.724074 TTGCATTTTGGCTTGATCCTAG 57.276 40.909 0.00 0.00 34.04 3.02
15 16 6.788598 TTATTGCATTTTGGCTTGATCCTA 57.211 33.333 0.00 0.00 34.04 2.94
16 17 5.680594 TTATTGCATTTTGGCTTGATCCT 57.319 34.783 0.00 0.00 34.04 3.24
17 18 6.740411 TTTTATTGCATTTTGGCTTGATCC 57.260 33.333 0.00 0.00 34.04 3.36
20 21 9.445878 TCATATTTTTATTGCATTTTGGCTTGA 57.554 25.926 0.00 0.00 34.04 3.02
42 43 9.621629 TGCATTAGATCATCATTGCATATCATA 57.378 29.630 5.36 0.00 35.36 2.15
43 44 8.519799 TGCATTAGATCATCATTGCATATCAT 57.480 30.769 5.36 0.00 35.36 2.45
44 45 7.931578 TGCATTAGATCATCATTGCATATCA 57.068 32.000 5.36 0.00 35.36 2.15
80 81 9.639563 AGGTTTGTAAAATCCCAAATTTTCAAT 57.360 25.926 0.00 0.00 33.53 2.57
82 83 9.549078 GTAGGTTTGTAAAATCCCAAATTTTCA 57.451 29.630 0.00 0.00 33.53 2.69
83 84 8.995220 GGTAGGTTTGTAAAATCCCAAATTTTC 58.005 33.333 0.00 0.00 33.53 2.29
84 85 7.940137 GGGTAGGTTTGTAAAATCCCAAATTTT 59.060 33.333 0.00 1.83 33.53 1.82
85 86 7.455058 GGGTAGGTTTGTAAAATCCCAAATTT 58.545 34.615 0.00 0.00 33.53 1.82
86 87 6.013206 GGGGTAGGTTTGTAAAATCCCAAATT 60.013 38.462 0.00 0.00 35.77 1.82
87 88 5.486063 GGGGTAGGTTTGTAAAATCCCAAAT 59.514 40.000 0.00 0.00 35.77 2.32
88 89 4.839550 GGGGTAGGTTTGTAAAATCCCAAA 59.160 41.667 0.00 0.00 35.77 3.28
89 90 4.418359 GGGGTAGGTTTGTAAAATCCCAA 58.582 43.478 0.00 0.00 35.77 4.12
90 91 3.245694 GGGGGTAGGTTTGTAAAATCCCA 60.246 47.826 0.00 0.00 35.77 4.37
91 92 3.368248 GGGGGTAGGTTTGTAAAATCCC 58.632 50.000 0.00 0.00 0.00 3.85
109 110 2.551071 GGCGAGATTCATCTTAAGGGGG 60.551 54.545 1.85 0.00 37.25 5.40
110 111 2.551071 GGGCGAGATTCATCTTAAGGGG 60.551 54.545 1.85 0.00 37.25 4.79
111 112 2.370189 AGGGCGAGATTCATCTTAAGGG 59.630 50.000 1.85 0.00 37.25 3.95
112 113 3.658709 GAGGGCGAGATTCATCTTAAGG 58.341 50.000 1.85 0.00 37.25 2.69
113 114 3.004839 TCGAGGGCGAGATTCATCTTAAG 59.995 47.826 0.00 0.00 42.51 1.85
114 115 2.956333 TCGAGGGCGAGATTCATCTTAA 59.044 45.455 0.00 0.00 42.51 1.85
115 116 2.583143 TCGAGGGCGAGATTCATCTTA 58.417 47.619 0.00 0.00 42.51 2.10
116 117 1.403814 TCGAGGGCGAGATTCATCTT 58.596 50.000 0.00 0.00 42.51 2.40
117 118 3.117657 TCGAGGGCGAGATTCATCT 57.882 52.632 0.00 0.00 42.51 2.90
126 127 3.217017 CCCGAATCTCGAGGGCGA 61.217 66.667 13.56 0.00 43.74 5.54
130 131 1.521681 GCCAACCCGAATCTCGAGG 60.522 63.158 13.56 0.00 43.74 4.63
131 132 0.744874 TAGCCAACCCGAATCTCGAG 59.255 55.000 5.93 5.93 43.74 4.04
132 133 0.744874 CTAGCCAACCCGAATCTCGA 59.255 55.000 0.00 0.00 43.74 4.04
133 134 0.744874 TCTAGCCAACCCGAATCTCG 59.255 55.000 0.00 0.00 40.07 4.04
134 135 2.981859 TTCTAGCCAACCCGAATCTC 57.018 50.000 0.00 0.00 0.00 2.75
135 136 3.713826 TTTTCTAGCCAACCCGAATCT 57.286 42.857 0.00 0.00 0.00 2.40
136 137 4.515567 CCTATTTTCTAGCCAACCCGAATC 59.484 45.833 0.00 0.00 0.00 2.52
137 138 4.079958 ACCTATTTTCTAGCCAACCCGAAT 60.080 41.667 0.00 0.00 0.00 3.34
138 139 3.264964 ACCTATTTTCTAGCCAACCCGAA 59.735 43.478 0.00 0.00 0.00 4.30
139 140 2.841881 ACCTATTTTCTAGCCAACCCGA 59.158 45.455 0.00 0.00 0.00 5.14
140 141 2.943033 CACCTATTTTCTAGCCAACCCG 59.057 50.000 0.00 0.00 0.00 5.28
141 142 4.200092 CTCACCTATTTTCTAGCCAACCC 58.800 47.826 0.00 0.00 0.00 4.11
142 143 4.200092 CCTCACCTATTTTCTAGCCAACC 58.800 47.826 0.00 0.00 0.00 3.77
143 144 4.200092 CCCTCACCTATTTTCTAGCCAAC 58.800 47.826 0.00 0.00 0.00 3.77
144 145 3.850173 ACCCTCACCTATTTTCTAGCCAA 59.150 43.478 0.00 0.00 0.00 4.52
145 146 3.199946 CACCCTCACCTATTTTCTAGCCA 59.800 47.826 0.00 0.00 0.00 4.75
146 147 3.454812 TCACCCTCACCTATTTTCTAGCC 59.545 47.826 0.00 0.00 0.00 3.93
147 148 4.755266 TCACCCTCACCTATTTTCTAGC 57.245 45.455 0.00 0.00 0.00 3.42
148 149 5.604650 AGGATCACCCTCACCTATTTTCTAG 59.395 44.000 0.00 0.00 43.31 2.43
149 150 5.538877 AGGATCACCCTCACCTATTTTCTA 58.461 41.667 0.00 0.00 43.31 2.10
150 151 4.375313 AGGATCACCCTCACCTATTTTCT 58.625 43.478 0.00 0.00 43.31 2.52
151 152 4.779993 AGGATCACCCTCACCTATTTTC 57.220 45.455 0.00 0.00 43.31 2.29
179 180 2.025898 CCTAGGAACGAGAGGAAGACC 58.974 57.143 1.05 0.00 30.78 3.85
180 181 2.424246 CACCTAGGAACGAGAGGAAGAC 59.576 54.545 17.98 0.00 34.24 3.01
181 182 2.620886 CCACCTAGGAACGAGAGGAAGA 60.621 54.545 17.98 0.00 41.22 2.87
182 183 1.751924 CCACCTAGGAACGAGAGGAAG 59.248 57.143 17.98 0.00 41.22 3.46
183 184 1.848652 CCACCTAGGAACGAGAGGAA 58.151 55.000 17.98 0.00 41.22 3.36
184 185 0.683504 GCCACCTAGGAACGAGAGGA 60.684 60.000 17.98 0.00 41.22 3.71
185 186 0.684805 AGCCACCTAGGAACGAGAGG 60.685 60.000 17.98 6.39 41.22 3.69
186 187 1.135333 GAAGCCACCTAGGAACGAGAG 59.865 57.143 17.98 0.00 41.22 3.20
187 188 1.183549 GAAGCCACCTAGGAACGAGA 58.816 55.000 17.98 0.00 41.22 4.04
188 189 0.895530 TGAAGCCACCTAGGAACGAG 59.104 55.000 17.98 0.00 41.22 4.18
189 190 1.480954 GATGAAGCCACCTAGGAACGA 59.519 52.381 17.98 0.00 41.22 3.85
190 191 1.473434 GGATGAAGCCACCTAGGAACG 60.473 57.143 17.98 3.03 41.22 3.95
191 192 1.840635 AGGATGAAGCCACCTAGGAAC 59.159 52.381 17.98 3.91 41.22 3.62
192 193 2.119495 GAGGATGAAGCCACCTAGGAA 58.881 52.381 17.98 0.00 41.22 3.36
193 194 1.794714 GAGGATGAAGCCACCTAGGA 58.205 55.000 17.98 0.00 41.22 2.94
194 195 0.390860 CGAGGATGAAGCCACCTAGG 59.609 60.000 7.41 7.41 41.84 3.02
195 196 0.390860 CCGAGGATGAAGCCACCTAG 59.609 60.000 0.00 0.00 33.89 3.02
196 197 0.325296 ACCGAGGATGAAGCCACCTA 60.325 55.000 0.00 0.00 33.89 3.08
197 198 0.325296 TACCGAGGATGAAGCCACCT 60.325 55.000 0.00 0.00 36.68 4.00
198 199 0.759346 ATACCGAGGATGAAGCCACC 59.241 55.000 0.00 0.00 0.00 4.61
199 200 1.541233 CCATACCGAGGATGAAGCCAC 60.541 57.143 0.00 0.00 0.00 5.01
200 201 0.758734 CCATACCGAGGATGAAGCCA 59.241 55.000 0.00 0.00 0.00 4.75
201 202 0.759346 ACCATACCGAGGATGAAGCC 59.241 55.000 0.00 0.00 0.00 4.35
202 203 1.541233 CCACCATACCGAGGATGAAGC 60.541 57.143 0.00 0.00 0.00 3.86
203 204 1.541233 GCCACCATACCGAGGATGAAG 60.541 57.143 0.00 0.00 0.00 3.02
204 205 0.468226 GCCACCATACCGAGGATGAA 59.532 55.000 0.00 0.00 0.00 2.57
205 206 0.398522 AGCCACCATACCGAGGATGA 60.399 55.000 0.00 0.00 0.00 2.92
206 207 0.034059 GAGCCACCATACCGAGGATG 59.966 60.000 0.00 0.00 0.00 3.51
207 208 1.122019 GGAGCCACCATACCGAGGAT 61.122 60.000 0.00 0.00 38.79 3.24
208 209 1.760875 GGAGCCACCATACCGAGGA 60.761 63.158 0.00 0.00 38.79 3.71
209 210 2.063979 TGGAGCCACCATACCGAGG 61.064 63.158 0.00 0.00 44.64 4.63
210 211 3.628989 TGGAGCCACCATACCGAG 58.371 61.111 0.00 0.00 44.64 4.63
219 220 0.312102 GCAAAGTTCAGTGGAGCCAC 59.688 55.000 11.67 11.67 46.50 5.01
220 221 0.106769 TGCAAAGTTCAGTGGAGCCA 60.107 50.000 0.00 0.00 0.00 4.75
221 222 0.595095 CTGCAAAGTTCAGTGGAGCC 59.405 55.000 0.00 0.00 0.00 4.70
222 223 1.597742 TCTGCAAAGTTCAGTGGAGC 58.402 50.000 0.00 0.00 33.57 4.70
223 224 3.209410 AGTTCTGCAAAGTTCAGTGGAG 58.791 45.455 0.00 0.00 34.75 3.86
224 225 3.281727 AGTTCTGCAAAGTTCAGTGGA 57.718 42.857 0.00 0.00 33.48 4.02
225 226 3.378112 TCAAGTTCTGCAAAGTTCAGTGG 59.622 43.478 0.00 0.00 33.48 4.00
226 227 4.621068 TCAAGTTCTGCAAAGTTCAGTG 57.379 40.909 0.00 0.00 33.48 3.66
227 228 6.238759 GGTTATCAAGTTCTGCAAAGTTCAGT 60.239 38.462 0.00 0.00 33.48 3.41
228 229 6.016777 AGGTTATCAAGTTCTGCAAAGTTCAG 60.017 38.462 0.00 0.00 0.00 3.02
229 230 5.827797 AGGTTATCAAGTTCTGCAAAGTTCA 59.172 36.000 0.00 0.00 0.00 3.18
230 231 6.319141 AGGTTATCAAGTTCTGCAAAGTTC 57.681 37.500 0.00 0.00 0.00 3.01
231 232 6.096846 ACAAGGTTATCAAGTTCTGCAAAGTT 59.903 34.615 0.00 0.00 0.00 2.66
232 233 5.594317 ACAAGGTTATCAAGTTCTGCAAAGT 59.406 36.000 0.00 0.00 0.00 2.66
233 234 6.076981 ACAAGGTTATCAAGTTCTGCAAAG 57.923 37.500 0.00 0.00 0.00 2.77
234 235 6.272318 CAACAAGGTTATCAAGTTCTGCAAA 58.728 36.000 0.00 0.00 0.00 3.68
235 236 5.735922 GCAACAAGGTTATCAAGTTCTGCAA 60.736 40.000 0.00 0.00 0.00 4.08
236 237 4.261572 GCAACAAGGTTATCAAGTTCTGCA 60.262 41.667 0.00 0.00 0.00 4.41
237 238 4.229876 GCAACAAGGTTATCAAGTTCTGC 58.770 43.478 0.00 0.00 0.00 4.26
238 239 4.024048 ACGCAACAAGGTTATCAAGTTCTG 60.024 41.667 0.00 0.00 0.00 3.02
239 240 4.024048 CACGCAACAAGGTTATCAAGTTCT 60.024 41.667 0.00 0.00 0.00 3.01
240 241 4.219033 CACGCAACAAGGTTATCAAGTTC 58.781 43.478 0.00 0.00 0.00 3.01
241 242 3.630312 ACACGCAACAAGGTTATCAAGTT 59.370 39.130 0.00 0.00 0.00 2.66
242 243 3.211045 ACACGCAACAAGGTTATCAAGT 58.789 40.909 0.00 0.00 0.00 3.16
243 244 3.896648 ACACGCAACAAGGTTATCAAG 57.103 42.857 0.00 0.00 0.00 3.02
244 245 4.817464 AGTTACACGCAACAAGGTTATCAA 59.183 37.500 0.00 0.00 0.00 2.57
245 246 4.382291 AGTTACACGCAACAAGGTTATCA 58.618 39.130 0.00 0.00 0.00 2.15
246 247 4.433805 CGAGTTACACGCAACAAGGTTATC 60.434 45.833 0.00 0.00 0.00 1.75
247 248 3.430895 CGAGTTACACGCAACAAGGTTAT 59.569 43.478 0.00 0.00 0.00 1.89
248 249 2.796031 CGAGTTACACGCAACAAGGTTA 59.204 45.455 0.00 0.00 0.00 2.85
249 250 1.595794 CGAGTTACACGCAACAAGGTT 59.404 47.619 0.00 0.00 0.00 3.50
250 251 1.214367 CGAGTTACACGCAACAAGGT 58.786 50.000 0.00 0.00 0.00 3.50
251 252 0.511221 CCGAGTTACACGCAACAAGG 59.489 55.000 0.00 0.00 0.00 3.61
252 253 0.110823 GCCGAGTTACACGCAACAAG 60.111 55.000 0.00 0.00 0.00 3.16
253 254 0.531090 AGCCGAGTTACACGCAACAA 60.531 50.000 0.00 0.00 0.00 2.83
254 255 1.068417 AGCCGAGTTACACGCAACA 59.932 52.632 0.00 0.00 0.00 3.33
255 256 1.491563 CAGCCGAGTTACACGCAAC 59.508 57.895 0.00 0.00 0.00 4.17
256 257 1.666553 CCAGCCGAGTTACACGCAA 60.667 57.895 0.00 0.00 0.00 4.85
257 258 2.048597 CCAGCCGAGTTACACGCA 60.049 61.111 0.00 0.00 0.00 5.24
258 259 3.488090 GCCAGCCGAGTTACACGC 61.488 66.667 0.00 0.00 0.00 5.34
259 260 1.225376 TTTGCCAGCCGAGTTACACG 61.225 55.000 0.00 0.00 0.00 4.49
260 261 0.237498 GTTTGCCAGCCGAGTTACAC 59.763 55.000 0.00 0.00 0.00 2.90
261 262 0.107831 AGTTTGCCAGCCGAGTTACA 59.892 50.000 0.00 0.00 0.00 2.41
262 263 0.796927 GAGTTTGCCAGCCGAGTTAC 59.203 55.000 0.00 0.00 0.00 2.50
263 264 0.669318 CGAGTTTGCCAGCCGAGTTA 60.669 55.000 0.00 0.00 0.00 2.24
264 265 1.961277 CGAGTTTGCCAGCCGAGTT 60.961 57.895 0.00 0.00 0.00 3.01
265 266 2.357517 CGAGTTTGCCAGCCGAGT 60.358 61.111 0.00 0.00 0.00 4.18
266 267 2.048222 TCGAGTTTGCCAGCCGAG 60.048 61.111 0.00 0.00 0.00 4.63
267 268 1.888436 ATCTCGAGTTTGCCAGCCGA 61.888 55.000 13.13 0.00 0.00 5.54
268 269 0.179111 TATCTCGAGTTTGCCAGCCG 60.179 55.000 13.13 0.00 0.00 5.52
269 270 1.291132 GTATCTCGAGTTTGCCAGCC 58.709 55.000 13.13 0.00 0.00 4.85
270 271 1.929836 CTGTATCTCGAGTTTGCCAGC 59.070 52.381 13.13 0.00 0.00 4.85
271 272 2.926200 CACTGTATCTCGAGTTTGCCAG 59.074 50.000 13.13 13.84 0.00 4.85
272 273 2.930887 GCACTGTATCTCGAGTTTGCCA 60.931 50.000 13.13 2.95 0.00 4.92
273 274 1.661112 GCACTGTATCTCGAGTTTGCC 59.339 52.381 13.13 0.00 0.00 4.52
274 275 1.661112 GGCACTGTATCTCGAGTTTGC 59.339 52.381 13.13 10.46 0.00 3.68
275 276 2.668457 GTGGCACTGTATCTCGAGTTTG 59.332 50.000 13.13 0.46 0.00 2.93
276 277 2.563179 AGTGGCACTGTATCTCGAGTTT 59.437 45.455 21.37 4.09 0.00 2.66
277 278 2.094494 CAGTGGCACTGTATCTCGAGTT 60.094 50.000 34.00 6.80 41.19 3.01
278 279 1.474478 CAGTGGCACTGTATCTCGAGT 59.526 52.381 34.00 0.37 41.19 4.18
279 280 1.202348 CCAGTGGCACTGTATCTCGAG 60.202 57.143 37.43 20.78 44.50 4.04
280 281 0.817654 CCAGTGGCACTGTATCTCGA 59.182 55.000 37.43 0.00 44.50 4.04
281 282 0.817654 TCCAGTGGCACTGTATCTCG 59.182 55.000 37.43 24.63 44.50 4.04
282 283 2.497675 TCTTCCAGTGGCACTGTATCTC 59.502 50.000 37.43 3.05 44.50 2.75
283 284 2.499289 CTCTTCCAGTGGCACTGTATCT 59.501 50.000 37.43 7.94 44.50 1.98
284 285 2.497675 TCTCTTCCAGTGGCACTGTATC 59.502 50.000 37.43 4.60 44.50 2.24
285 286 2.540383 TCTCTTCCAGTGGCACTGTAT 58.460 47.619 37.43 9.10 44.50 2.29
286 287 2.009681 TCTCTTCCAGTGGCACTGTA 57.990 50.000 37.43 25.72 44.50 2.74
287 288 1.356124 ATCTCTTCCAGTGGCACTGT 58.644 50.000 37.43 20.24 44.50 3.55
288 289 2.234661 TGTATCTCTTCCAGTGGCACTG 59.765 50.000 35.08 35.08 45.53 3.66
289 290 2.499289 CTGTATCTCTTCCAGTGGCACT 59.501 50.000 15.88 15.88 0.00 4.40
290 291 2.234908 ACTGTATCTCTTCCAGTGGCAC 59.765 50.000 10.29 10.29 38.00 5.01
291 292 2.540383 ACTGTATCTCTTCCAGTGGCA 58.460 47.619 3.51 0.00 38.00 4.92
295 296 2.234908 GTGGCACTGTATCTCTTCCAGT 59.765 50.000 11.13 0.00 39.93 4.00
296 297 2.499289 AGTGGCACTGTATCTCTTCCAG 59.501 50.000 21.37 0.00 0.00 3.86
297 298 2.497675 GAGTGGCACTGTATCTCTTCCA 59.502 50.000 27.45 0.00 0.00 3.53
298 299 2.480416 CGAGTGGCACTGTATCTCTTCC 60.480 54.545 27.45 5.18 0.00 3.46
299 300 2.480416 CCGAGTGGCACTGTATCTCTTC 60.480 54.545 27.45 6.26 0.00 2.87
300 301 1.478510 CCGAGTGGCACTGTATCTCTT 59.521 52.381 27.45 0.00 0.00 2.85
301 302 1.107114 CCGAGTGGCACTGTATCTCT 58.893 55.000 27.45 0.00 0.00 3.10
302 303 3.650409 CCGAGTGGCACTGTATCTC 57.350 57.895 27.45 8.64 0.00 2.75
313 314 0.107017 ATTCCCTTCATGCCGAGTGG 60.107 55.000 0.00 0.00 38.77 4.00
314 315 1.755179 AATTCCCTTCATGCCGAGTG 58.245 50.000 0.00 0.00 0.00 3.51
315 316 2.741878 CGTAATTCCCTTCATGCCGAGT 60.742 50.000 0.00 0.00 0.00 4.18
316 317 1.867233 CGTAATTCCCTTCATGCCGAG 59.133 52.381 0.00 0.00 0.00 4.63
317 318 1.483004 TCGTAATTCCCTTCATGCCGA 59.517 47.619 0.00 0.00 0.00 5.54
318 319 1.948104 TCGTAATTCCCTTCATGCCG 58.052 50.000 0.00 0.00 0.00 5.69
319 320 3.013921 TGTTCGTAATTCCCTTCATGCC 58.986 45.455 0.00 0.00 0.00 4.40
320 321 4.900635 ATGTTCGTAATTCCCTTCATGC 57.099 40.909 0.00 0.00 0.00 4.06
510 511 3.864556 AGGGGTATTTCCATGGGTTTT 57.135 42.857 13.02 0.00 38.11 2.43
1034 1050 1.753649 TCGCTTCTTCATCTCCAGGAG 59.246 52.381 10.70 10.70 0.00 3.69
1361 1399 3.266772 AGGTTGGTGAAGCATAATCCTCA 59.733 43.478 0.00 0.00 31.56 3.86
1630 1668 7.308951 CGGACACTACCAATCCTTAAACATTTT 60.309 37.037 0.00 0.00 0.00 1.82
1797 1836 9.328721 GCGTTTATAATAAGTTGTTTAACCGTT 57.671 29.630 0.00 0.00 37.52 4.44
1817 1856 2.413796 CGTATTGGCTGTCTTGCGTTTA 59.586 45.455 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.