Multiple sequence alignment - TraesCS3B01G101800

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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 TraesCS3B01G101800 chr3B 100.000 2228 0 0 1 2228 68503828 68501601 0.000000e+00 4115
1 TraesCS3B01G101800 chr3B 83.551 918 135 11 1323 2228 123127457 123128370 0.000000e+00 845
2 TraesCS3B01G101800 chr3B 92.157 408 26 4 3 408 461291537 461291134 2.480000e-159 571
3 TraesCS3B01G101800 chr5B 90.180 1446 119 7 797 2228 372999213 373000649 0.000000e+00 1862
4 TraesCS3B01G101800 chr5B 84.752 1069 147 5 1173 2228 85906071 85907136 0.000000e+00 1057
5 TraesCS3B01G101800 chr5B 92.402 408 23 3 3 408 142056130 142056531 1.920000e-160 575
6 TraesCS3B01G101800 chr5B 87.179 195 11 3 427 620 372872497 372872678 2.240000e-50 209
7 TraesCS3B01G101800 chr6B 84.561 1846 231 22 427 2228 506733813 506731978 0.000000e+00 1781
8 TraesCS3B01G101800 chr6B 90.612 980 75 6 1260 2228 51615151 51616124 0.000000e+00 1284
9 TraesCS3B01G101800 chr6B 91.727 411 27 4 3 408 415025467 415025875 4.150000e-157 564
10 TraesCS3B01G101800 chr1D 88.912 1443 142 9 797 2225 483400567 483402005 0.000000e+00 1762
11 TraesCS3B01G101800 chr3D 84.290 1795 256 16 453 2228 239599495 239597708 0.000000e+00 1729
12 TraesCS3B01G101800 chr1A 82.972 1844 266 19 427 2228 278959597 278957760 0.000000e+00 1622
13 TraesCS3B01G101800 chr2D 82.308 1820 274 30 449 2228 68910810 68912621 0.000000e+00 1533
14 TraesCS3B01G101800 chr4D 82.431 1810 251 26 464 2228 14423036 14421249 0.000000e+00 1519
15 TraesCS3B01G101800 chr4D 92.138 407 28 1 4 410 418719536 418719938 2.480000e-159 571
16 TraesCS3B01G101800 chr3A 82.099 1810 276 31 460 2228 140029564 140027762 0.000000e+00 1504
17 TraesCS3B01G101800 chr3A 84.986 1452 189 22 797 2228 267036788 267035346 0.000000e+00 1447
18 TraesCS3B01G101800 chr6D 81.528 1846 266 32 427 2228 47085669 47087483 0.000000e+00 1450
19 TraesCS3B01G101800 chr7D 82.544 1690 245 24 581 2228 388648478 388650159 0.000000e+00 1441
20 TraesCS3B01G101800 chr6A 84.535 1442 202 10 803 2228 370661692 370660256 0.000000e+00 1408
21 TraesCS3B01G101800 chr7A 84.622 1151 132 22 453 1563 374511019 374509874 0.000000e+00 1103
22 TraesCS3B01G101800 chr7B 92.629 407 24 3 3 408 439230438 439230037 4.120000e-162 580
23 TraesCS3B01G101800 chr2B 91.892 407 27 3 3 408 156709663 156710064 4.150000e-157 564
24 TraesCS3B01G101800 chr2B 91.892 407 27 3 3 408 156744468 156744869 4.150000e-157 564
25 TraesCS3B01G101800 chr1B 91.912 408 24 4 3 408 198611132 198611532 1.490000e-156 562
26 TraesCS3B01G101800 chr1B 84.483 290 43 2 500 788 328135219 328134931 3.620000e-73 285
27 TraesCS3B01G101800 chrUn 91.646 407 28 3 3 408 341624595 341624194 1.930000e-155 558
28 TraesCS3B01G101800 chr2A 78.493 730 121 18 495 1194 566604723 566604000 1.570000e-121 446
29 TraesCS3B01G101800 chr2A 78.328 646 109 14 427 1044 696069699 696070341 2.680000e-104 388
30 TraesCS3B01G101800 chr5A 76.923 546 96 18 485 1003 338206066 338206608 1.300000e-72 283


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 TraesCS3B01G101800 chr3B 68501601 68503828 2227 True 4115 4115 100.000 1 2228 1 chr3B.!!$R1 2227
1 TraesCS3B01G101800 chr3B 123127457 123128370 913 False 845 845 83.551 1323 2228 1 chr3B.!!$F1 905
2 TraesCS3B01G101800 chr5B 372999213 373000649 1436 False 1862 1862 90.180 797 2228 1 chr5B.!!$F4 1431
3 TraesCS3B01G101800 chr5B 85906071 85907136 1065 False 1057 1057 84.752 1173 2228 1 chr5B.!!$F1 1055
4 TraesCS3B01G101800 chr6B 506731978 506733813 1835 True 1781 1781 84.561 427 2228 1 chr6B.!!$R1 1801
5 TraesCS3B01G101800 chr6B 51615151 51616124 973 False 1284 1284 90.612 1260 2228 1 chr6B.!!$F1 968
6 TraesCS3B01G101800 chr1D 483400567 483402005 1438 False 1762 1762 88.912 797 2225 1 chr1D.!!$F1 1428
7 TraesCS3B01G101800 chr3D 239597708 239599495 1787 True 1729 1729 84.290 453 2228 1 chr3D.!!$R1 1775
8 TraesCS3B01G101800 chr1A 278957760 278959597 1837 True 1622 1622 82.972 427 2228 1 chr1A.!!$R1 1801
9 TraesCS3B01G101800 chr2D 68910810 68912621 1811 False 1533 1533 82.308 449 2228 1 chr2D.!!$F1 1779
10 TraesCS3B01G101800 chr4D 14421249 14423036 1787 True 1519 1519 82.431 464 2228 1 chr4D.!!$R1 1764
11 TraesCS3B01G101800 chr3A 140027762 140029564 1802 True 1504 1504 82.099 460 2228 1 chr3A.!!$R1 1768
12 TraesCS3B01G101800 chr3A 267035346 267036788 1442 True 1447 1447 84.986 797 2228 1 chr3A.!!$R2 1431
13 TraesCS3B01G101800 chr6D 47085669 47087483 1814 False 1450 1450 81.528 427 2228 1 chr6D.!!$F1 1801
14 TraesCS3B01G101800 chr7D 388648478 388650159 1681 False 1441 1441 82.544 581 2228 1 chr7D.!!$F1 1647
15 TraesCS3B01G101800 chr6A 370660256 370661692 1436 True 1408 1408 84.535 803 2228 1 chr6A.!!$R1 1425
16 TraesCS3B01G101800 chr7A 374509874 374511019 1145 True 1103 1103 84.622 453 1563 1 chr7A.!!$R1 1110
17 TraesCS3B01G101800 chr2A 566604000 566604723 723 True 446 446 78.493 495 1194 1 chr2A.!!$R1 699
18 TraesCS3B01G101800 chr2A 696069699 696070341 642 False 388 388 78.328 427 1044 1 chr2A.!!$F1 617
19 TraesCS3B01G101800 chr5A 338206066 338206608 542 False 283 283 76.923 485 1003 1 chr5A.!!$F1 518

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
615 640 0.034616 GTAGCCCTGCTCTGCCTATG 59.965 60.0 0.0 0.0 40.44 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 2116 0.322187 AAACGCCAATACGCCTCCTT 60.322 50.0 0.0 0.0 36.19 3.36 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 6.996180 CCCTGATGTTTCTAGGGTATAAGA 57.004 41.667 0.00 0.00 45.00 2.10
26 27 6.998802 CCCTGATGTTTCTAGGGTATAAGAG 58.001 44.000 0.00 0.00 45.00 2.85
27 28 6.555360 CCCTGATGTTTCTAGGGTATAAGAGT 59.445 42.308 0.00 0.00 45.00 3.24
28 29 7.728981 CCCTGATGTTTCTAGGGTATAAGAGTA 59.271 40.741 0.00 0.00 45.00 2.59
29 30 9.315363 CCTGATGTTTCTAGGGTATAAGAGTAT 57.685 37.037 0.00 0.00 0.00 2.12
49 50 8.881743 AGAGTATATATAGGCGAAAGAAGTACG 58.118 37.037 0.00 0.00 0.00 3.67
50 51 8.558973 AGTATATATAGGCGAAAGAAGTACGT 57.441 34.615 0.00 0.00 0.00 3.57
51 52 8.663911 AGTATATATAGGCGAAAGAAGTACGTC 58.336 37.037 0.00 0.00 0.00 4.34
52 53 2.532531 TAGGCGAAAGAAGTACGTCG 57.467 50.000 3.05 2.94 36.74 5.12
53 54 0.109412 AGGCGAAAGAAGTACGTCGG 60.109 55.000 3.05 0.00 36.74 4.79
54 55 0.387750 GGCGAAAGAAGTACGTCGGT 60.388 55.000 3.05 0.00 33.68 4.69
55 56 0.706729 GCGAAAGAAGTACGTCGGTG 59.293 55.000 3.05 0.00 33.68 4.94
56 57 1.334054 CGAAAGAAGTACGTCGGTGG 58.666 55.000 3.05 0.00 0.00 4.61
57 58 1.069022 CGAAAGAAGTACGTCGGTGGA 60.069 52.381 3.05 0.00 0.00 4.02
58 59 2.593257 GAAAGAAGTACGTCGGTGGAG 58.407 52.381 3.05 0.00 0.00 3.86
59 60 0.243095 AAGAAGTACGTCGGTGGAGC 59.757 55.000 3.05 0.00 0.00 4.70
60 61 0.608582 AGAAGTACGTCGGTGGAGCT 60.609 55.000 3.05 0.00 0.00 4.09
61 62 1.089920 GAAGTACGTCGGTGGAGCTA 58.910 55.000 0.00 0.00 0.00 3.32
62 63 0.807496 AAGTACGTCGGTGGAGCTAC 59.193 55.000 0.00 0.00 0.00 3.58
63 64 0.321919 AGTACGTCGGTGGAGCTACA 60.322 55.000 0.00 0.00 0.00 2.74
64 65 0.523072 GTACGTCGGTGGAGCTACAA 59.477 55.000 0.00 0.00 0.00 2.41
65 66 0.806868 TACGTCGGTGGAGCTACAAG 59.193 55.000 0.00 0.00 0.00 3.16
66 67 1.153823 CGTCGGTGGAGCTACAAGG 60.154 63.158 0.00 0.00 0.00 3.61
67 68 1.218316 GTCGGTGGAGCTACAAGGG 59.782 63.158 0.00 0.00 0.00 3.95
68 69 1.987855 TCGGTGGAGCTACAAGGGG 60.988 63.158 0.00 0.00 0.00 4.79
69 70 2.272471 GGTGGAGCTACAAGGGGC 59.728 66.667 0.00 0.00 0.00 5.80
70 71 2.272471 GTGGAGCTACAAGGGGCC 59.728 66.667 0.00 0.00 0.00 5.80
71 72 3.015145 TGGAGCTACAAGGGGCCC 61.015 66.667 17.12 17.12 0.00 5.80
72 73 3.015145 GGAGCTACAAGGGGCCCA 61.015 66.667 27.72 1.89 0.00 5.36
73 74 2.272471 GAGCTACAAGGGGCCCAC 59.728 66.667 27.72 13.61 0.00 4.61
74 75 3.682292 GAGCTACAAGGGGCCCACG 62.682 68.421 27.72 17.86 0.00 4.94
75 76 3.712907 GCTACAAGGGGCCCACGA 61.713 66.667 27.72 5.77 0.00 4.35
76 77 2.584608 CTACAAGGGGCCCACGAG 59.415 66.667 27.72 13.62 0.00 4.18
77 78 3.006728 TACAAGGGGCCCACGAGG 61.007 66.667 27.72 11.32 39.47 4.63
119 120 3.854669 CCTAGGCGTGCCCTCCTG 61.855 72.222 7.39 0.00 44.96 3.86
120 121 4.537433 CTAGGCGTGCCCTCCTGC 62.537 72.222 7.39 0.00 44.96 4.85
126 127 4.767255 GTGCCCTCCTGCCTCGTG 62.767 72.222 0.00 0.00 0.00 4.35
137 138 3.065306 CCTCGTGGCCACCTTGTA 58.935 61.111 29.95 9.57 0.00 2.41
138 139 1.079127 CCTCGTGGCCACCTTGTAG 60.079 63.158 29.95 17.78 0.00 2.74
139 140 1.541310 CCTCGTGGCCACCTTGTAGA 61.541 60.000 29.95 18.27 0.00 2.59
140 141 0.108615 CTCGTGGCCACCTTGTAGAG 60.109 60.000 29.95 23.20 0.00 2.43
141 142 0.830444 TCGTGGCCACCTTGTAGAGT 60.830 55.000 29.95 0.00 0.00 3.24
142 143 0.389948 CGTGGCCACCTTGTAGAGTC 60.390 60.000 29.95 0.40 0.00 3.36
143 144 0.036294 GTGGCCACCTTGTAGAGTCC 60.036 60.000 26.31 0.00 0.00 3.85
144 145 1.198759 TGGCCACCTTGTAGAGTCCC 61.199 60.000 0.00 0.00 0.00 4.46
145 146 1.198759 GGCCACCTTGTAGAGTCCCA 61.199 60.000 0.00 0.00 0.00 4.37
146 147 0.250513 GCCACCTTGTAGAGTCCCAG 59.749 60.000 0.00 0.00 0.00 4.45
147 148 1.938585 CCACCTTGTAGAGTCCCAGA 58.061 55.000 0.00 0.00 0.00 3.86
148 149 1.550976 CCACCTTGTAGAGTCCCAGAC 59.449 57.143 0.00 0.00 0.00 3.51
149 150 2.530701 CACCTTGTAGAGTCCCAGACT 58.469 52.381 0.00 0.00 46.42 3.24
150 151 2.900546 CACCTTGTAGAGTCCCAGACTT 59.099 50.000 0.00 0.00 43.53 3.01
151 152 2.900546 ACCTTGTAGAGTCCCAGACTTG 59.099 50.000 0.00 0.00 43.53 3.16
152 153 3.165875 CCTTGTAGAGTCCCAGACTTGA 58.834 50.000 0.00 0.00 43.53 3.02
153 154 3.578716 CCTTGTAGAGTCCCAGACTTGAA 59.421 47.826 0.00 0.00 43.53 2.69
154 155 4.561105 CTTGTAGAGTCCCAGACTTGAAC 58.439 47.826 0.00 0.00 43.53 3.18
155 156 3.845860 TGTAGAGTCCCAGACTTGAACT 58.154 45.455 0.00 0.00 43.53 3.01
156 157 3.827302 TGTAGAGTCCCAGACTTGAACTC 59.173 47.826 0.00 0.00 43.53 3.01
157 158 2.252714 AGAGTCCCAGACTTGAACTCC 58.747 52.381 0.00 0.00 43.53 3.85
158 159 1.971357 GAGTCCCAGACTTGAACTCCA 59.029 52.381 0.00 0.00 43.53 3.86
159 160 2.368875 GAGTCCCAGACTTGAACTCCAA 59.631 50.000 0.00 0.00 43.53 3.53
169 170 4.342862 CTTGAACTCCAAGTCTTCTGGA 57.657 45.455 0.00 0.00 45.52 3.86
170 171 4.904241 CTTGAACTCCAAGTCTTCTGGAT 58.096 43.478 0.00 0.00 45.52 3.41
171 172 4.982241 TGAACTCCAAGTCTTCTGGATT 57.018 40.909 0.00 0.00 0.00 3.01
172 173 4.645535 TGAACTCCAAGTCTTCTGGATTG 58.354 43.478 0.00 0.00 0.00 2.67
173 174 4.347876 TGAACTCCAAGTCTTCTGGATTGA 59.652 41.667 0.00 0.00 0.00 2.57
174 175 5.013495 TGAACTCCAAGTCTTCTGGATTGAT 59.987 40.000 0.00 0.00 0.00 2.57
175 176 5.511386 ACTCCAAGTCTTCTGGATTGATT 57.489 39.130 0.00 0.00 0.00 2.57
176 177 5.885465 ACTCCAAGTCTTCTGGATTGATTT 58.115 37.500 0.00 0.00 0.00 2.17
177 178 6.310149 ACTCCAAGTCTTCTGGATTGATTTT 58.690 36.000 0.00 0.00 0.00 1.82
178 179 6.208204 ACTCCAAGTCTTCTGGATTGATTTTG 59.792 38.462 0.00 0.00 0.00 2.44
179 180 5.477984 TCCAAGTCTTCTGGATTGATTTTGG 59.522 40.000 0.00 0.00 33.04 3.28
180 181 5.244626 CCAAGTCTTCTGGATTGATTTTGGT 59.755 40.000 0.00 0.00 0.00 3.67
181 182 6.385033 CAAGTCTTCTGGATTGATTTTGGTC 58.615 40.000 0.00 0.00 0.00 4.02
182 183 5.012893 AGTCTTCTGGATTGATTTTGGTCC 58.987 41.667 0.00 0.00 0.00 4.46
183 184 4.766891 GTCTTCTGGATTGATTTTGGTCCA 59.233 41.667 0.00 0.00 38.37 4.02
184 185 5.243730 GTCTTCTGGATTGATTTTGGTCCAA 59.756 40.000 0.00 0.00 40.03 3.53
185 186 6.018469 TCTTCTGGATTGATTTTGGTCCAAT 58.982 36.000 4.80 0.00 40.03 3.16
186 187 7.122650 GTCTTCTGGATTGATTTTGGTCCAATA 59.877 37.037 4.80 0.39 40.03 1.90
187 188 7.673504 TCTTCTGGATTGATTTTGGTCCAATAA 59.326 33.333 4.80 3.61 40.03 1.40
188 189 7.789202 TCTGGATTGATTTTGGTCCAATAAA 57.211 32.000 4.80 0.00 40.03 1.40
189 190 7.839907 TCTGGATTGATTTTGGTCCAATAAAG 58.160 34.615 4.80 0.00 40.03 1.85
190 191 7.673504 TCTGGATTGATTTTGGTCCAATAAAGA 59.326 33.333 4.80 0.00 40.03 2.52
191 192 8.378115 TGGATTGATTTTGGTCCAATAAAGAT 57.622 30.769 4.80 0.00 37.78 2.40
192 193 8.477256 TGGATTGATTTTGGTCCAATAAAGATC 58.523 33.333 4.80 7.10 37.78 2.75
193 194 7.928167 GGATTGATTTTGGTCCAATAAAGATCC 59.072 37.037 4.80 11.90 31.40 3.36
194 195 8.613922 ATTGATTTTGGTCCAATAAAGATCCT 57.386 30.769 4.80 0.00 0.00 3.24
195 196 7.645058 TGATTTTGGTCCAATAAAGATCCTC 57.355 36.000 4.80 0.00 0.00 3.71
196 197 6.318648 TGATTTTGGTCCAATAAAGATCCTCG 59.681 38.462 4.80 0.00 0.00 4.63
197 198 3.194005 TGGTCCAATAAAGATCCTCGC 57.806 47.619 0.00 0.00 0.00 5.03
198 199 2.503765 TGGTCCAATAAAGATCCTCGCA 59.496 45.455 0.00 0.00 0.00 5.10
199 200 3.054728 TGGTCCAATAAAGATCCTCGCAA 60.055 43.478 0.00 0.00 0.00 4.85
200 201 3.945285 GGTCCAATAAAGATCCTCGCAAA 59.055 43.478 0.00 0.00 0.00 3.68
201 202 4.035675 GGTCCAATAAAGATCCTCGCAAAG 59.964 45.833 0.00 0.00 0.00 2.77
203 204 3.947834 CCAATAAAGATCCTCGCAAAGGT 59.052 43.478 2.27 0.00 46.32 3.50
204 205 4.399303 CCAATAAAGATCCTCGCAAAGGTT 59.601 41.667 2.27 0.00 46.32 3.50
205 206 5.105756 CCAATAAAGATCCTCGCAAAGGTTT 60.106 40.000 2.27 0.00 46.32 3.27
206 207 5.819825 ATAAAGATCCTCGCAAAGGTTTC 57.180 39.130 2.27 2.07 46.32 2.78
207 208 2.859165 AGATCCTCGCAAAGGTTTCA 57.141 45.000 2.27 0.00 46.32 2.69
208 209 3.356529 AGATCCTCGCAAAGGTTTCAT 57.643 42.857 2.27 0.00 46.32 2.57
209 210 3.690460 AGATCCTCGCAAAGGTTTCATT 58.310 40.909 2.27 0.00 46.32 2.57
210 211 3.691609 AGATCCTCGCAAAGGTTTCATTC 59.308 43.478 2.27 0.00 46.32 2.67
211 212 2.159382 TCCTCGCAAAGGTTTCATTCC 58.841 47.619 2.27 0.00 46.32 3.01
212 213 1.135689 CCTCGCAAAGGTTTCATTCCG 60.136 52.381 0.00 0.00 40.67 4.30
213 214 1.535462 CTCGCAAAGGTTTCATTCCGT 59.465 47.619 0.00 0.00 0.00 4.69
214 215 1.950909 TCGCAAAGGTTTCATTCCGTT 59.049 42.857 0.00 0.00 0.00 4.44
215 216 2.359531 TCGCAAAGGTTTCATTCCGTTT 59.640 40.909 0.00 0.00 0.00 3.60
216 217 2.470999 CGCAAAGGTTTCATTCCGTTTG 59.529 45.455 0.00 0.00 0.00 2.93
217 218 2.799978 GCAAAGGTTTCATTCCGTTTGG 59.200 45.455 0.00 0.00 0.00 3.28
218 219 3.739830 GCAAAGGTTTCATTCCGTTTGGT 60.740 43.478 0.00 0.00 36.30 3.67
219 220 4.048504 CAAAGGTTTCATTCCGTTTGGTC 58.951 43.478 0.00 0.00 36.30 4.02
220 221 3.223674 AGGTTTCATTCCGTTTGGTCT 57.776 42.857 0.00 0.00 36.30 3.85
221 222 3.146847 AGGTTTCATTCCGTTTGGTCTC 58.853 45.455 0.00 0.00 36.30 3.36
222 223 2.228103 GGTTTCATTCCGTTTGGTCTCC 59.772 50.000 0.00 0.00 36.30 3.71
223 224 2.882137 GTTTCATTCCGTTTGGTCTCCA 59.118 45.455 0.00 0.00 36.30 3.86
224 225 3.433306 TTCATTCCGTTTGGTCTCCAT 57.567 42.857 0.00 0.00 36.30 3.41
225 226 3.433306 TCATTCCGTTTGGTCTCCATT 57.567 42.857 0.00 0.00 36.30 3.16
226 227 3.761897 TCATTCCGTTTGGTCTCCATTT 58.238 40.909 0.00 0.00 36.30 2.32
227 228 3.505680 TCATTCCGTTTGGTCTCCATTTG 59.494 43.478 0.00 0.00 36.30 2.32
228 229 2.940994 TCCGTTTGGTCTCCATTTGA 57.059 45.000 0.00 0.00 36.30 2.69
229 230 3.433306 TCCGTTTGGTCTCCATTTGAT 57.567 42.857 0.00 0.00 36.30 2.57
230 231 4.561500 TCCGTTTGGTCTCCATTTGATA 57.438 40.909 0.00 0.00 36.30 2.15
231 232 5.110814 TCCGTTTGGTCTCCATTTGATAT 57.889 39.130 0.00 0.00 36.30 1.63
232 233 5.505780 TCCGTTTGGTCTCCATTTGATATT 58.494 37.500 0.00 0.00 36.30 1.28
233 234 5.588648 TCCGTTTGGTCTCCATTTGATATTC 59.411 40.000 0.00 0.00 36.30 1.75
234 235 5.221048 CCGTTTGGTCTCCATTTGATATTCC 60.221 44.000 0.00 0.00 31.53 3.01
235 236 5.590259 CGTTTGGTCTCCATTTGATATTCCT 59.410 40.000 0.00 0.00 31.53 3.36
236 237 6.095440 CGTTTGGTCTCCATTTGATATTCCTT 59.905 38.462 0.00 0.00 31.53 3.36
237 238 7.362920 CGTTTGGTCTCCATTTGATATTCCTTT 60.363 37.037 0.00 0.00 31.53 3.11
238 239 8.314021 GTTTGGTCTCCATTTGATATTCCTTTT 58.686 33.333 0.00 0.00 31.53 2.27
239 240 7.645058 TGGTCTCCATTTGATATTCCTTTTC 57.355 36.000 0.00 0.00 0.00 2.29
240 241 7.413446 TGGTCTCCATTTGATATTCCTTTTCT 58.587 34.615 0.00 0.00 0.00 2.52
241 242 7.340232 TGGTCTCCATTTGATATTCCTTTTCTG 59.660 37.037 0.00 0.00 0.00 3.02
242 243 7.340487 GGTCTCCATTTGATATTCCTTTTCTGT 59.660 37.037 0.00 0.00 0.00 3.41
243 244 9.396022 GTCTCCATTTGATATTCCTTTTCTGTA 57.604 33.333 0.00 0.00 0.00 2.74
244 245 9.973661 TCTCCATTTGATATTCCTTTTCTGTAA 57.026 29.630 0.00 0.00 0.00 2.41
258 259 9.333724 TCCTTTTCTGTAAAACACTAAAGTAGG 57.666 33.333 0.00 0.00 31.37 3.18
259 260 8.074370 CCTTTTCTGTAAAACACTAAAGTAGGC 58.926 37.037 0.00 0.00 31.37 3.93
260 261 8.508883 TTTTCTGTAAAACACTAAAGTAGGCA 57.491 30.769 0.00 0.00 29.59 4.75
261 262 8.508883 TTTCTGTAAAACACTAAAGTAGGCAA 57.491 30.769 0.00 0.00 0.00 4.52
262 263 8.508883 TTCTGTAAAACACTAAAGTAGGCAAA 57.491 30.769 0.00 0.00 0.00 3.68
263 264 8.508883 TCTGTAAAACACTAAAGTAGGCAAAA 57.491 30.769 0.00 0.00 0.00 2.44
264 265 8.958506 TCTGTAAAACACTAAAGTAGGCAAAAA 58.041 29.630 0.00 0.00 0.00 1.94
265 266 9.744468 CTGTAAAACACTAAAGTAGGCAAAAAT 57.256 29.630 0.00 0.00 0.00 1.82
271 272 9.961265 AACACTAAAGTAGGCAAAAATAGAAAC 57.039 29.630 0.00 0.00 0.00 2.78
272 273 9.350951 ACACTAAAGTAGGCAAAAATAGAAACT 57.649 29.630 0.00 0.00 0.00 2.66
273 274 9.612620 CACTAAAGTAGGCAAAAATAGAAACTG 57.387 33.333 0.00 0.00 0.00 3.16
274 275 9.569122 ACTAAAGTAGGCAAAAATAGAAACTGA 57.431 29.630 0.00 0.00 0.00 3.41
275 276 9.827411 CTAAAGTAGGCAAAAATAGAAACTGAC 57.173 33.333 0.00 0.00 0.00 3.51
276 277 6.481954 AGTAGGCAAAAATAGAAACTGACG 57.518 37.500 0.00 0.00 0.00 4.35
277 278 4.160736 AGGCAAAAATAGAAACTGACGC 57.839 40.909 0.00 0.00 0.00 5.19
278 279 3.821033 AGGCAAAAATAGAAACTGACGCT 59.179 39.130 0.00 0.00 0.00 5.07
279 280 5.001232 AGGCAAAAATAGAAACTGACGCTA 58.999 37.500 0.00 0.00 0.00 4.26
280 281 5.122396 AGGCAAAAATAGAAACTGACGCTAG 59.878 40.000 0.00 0.00 0.00 3.42
281 282 5.324697 GCAAAAATAGAAACTGACGCTAGG 58.675 41.667 0.00 0.00 0.00 3.02
282 283 5.324697 CAAAAATAGAAACTGACGCTAGGC 58.675 41.667 0.00 0.00 0.00 3.93
283 284 2.892784 ATAGAAACTGACGCTAGGCC 57.107 50.000 0.00 0.00 0.00 5.19
284 285 1.848652 TAGAAACTGACGCTAGGCCT 58.151 50.000 11.78 11.78 0.00 5.19
285 286 0.533032 AGAAACTGACGCTAGGCCTC 59.467 55.000 9.68 0.00 0.00 4.70
286 287 0.533032 GAAACTGACGCTAGGCCTCT 59.467 55.000 9.68 0.00 0.00 3.69
287 288 0.247736 AAACTGACGCTAGGCCTCTG 59.752 55.000 9.68 4.61 0.00 3.35
288 289 1.608717 AACTGACGCTAGGCCTCTGG 61.609 60.000 9.68 1.00 0.00 3.86
289 290 2.037367 TGACGCTAGGCCTCTGGT 59.963 61.111 9.68 5.13 0.00 4.00
290 291 1.608717 CTGACGCTAGGCCTCTGGTT 61.609 60.000 9.68 0.00 0.00 3.67
291 292 0.323999 TGACGCTAGGCCTCTGGTTA 60.324 55.000 9.68 0.00 0.00 2.85
292 293 0.822164 GACGCTAGGCCTCTGGTTAA 59.178 55.000 9.68 0.00 0.00 2.01
293 294 1.413077 GACGCTAGGCCTCTGGTTAAT 59.587 52.381 9.68 0.00 0.00 1.40
294 295 2.626743 GACGCTAGGCCTCTGGTTAATA 59.373 50.000 9.68 0.00 0.00 0.98
295 296 2.628657 ACGCTAGGCCTCTGGTTAATAG 59.371 50.000 9.68 0.00 0.00 1.73
296 297 2.628657 CGCTAGGCCTCTGGTTAATAGT 59.371 50.000 9.68 0.00 0.00 2.12
297 298 3.069729 CGCTAGGCCTCTGGTTAATAGTT 59.930 47.826 9.68 0.00 0.00 2.24
298 299 4.443034 CGCTAGGCCTCTGGTTAATAGTTT 60.443 45.833 9.68 0.00 0.00 2.66
299 300 5.437946 GCTAGGCCTCTGGTTAATAGTTTT 58.562 41.667 9.68 0.00 0.00 2.43
300 301 5.297029 GCTAGGCCTCTGGTTAATAGTTTTG 59.703 44.000 9.68 0.00 0.00 2.44
301 302 5.256806 AGGCCTCTGGTTAATAGTTTTGT 57.743 39.130 0.00 0.00 0.00 2.83
302 303 5.254115 AGGCCTCTGGTTAATAGTTTTGTC 58.746 41.667 0.00 0.00 0.00 3.18
303 304 4.398358 GGCCTCTGGTTAATAGTTTTGTCC 59.602 45.833 0.00 0.00 0.00 4.02
304 305 4.398358 GCCTCTGGTTAATAGTTTTGTCCC 59.602 45.833 0.00 0.00 0.00 4.46
305 306 5.566469 CCTCTGGTTAATAGTTTTGTCCCA 58.434 41.667 0.00 0.00 0.00 4.37
306 307 5.414765 CCTCTGGTTAATAGTTTTGTCCCAC 59.585 44.000 0.00 0.00 0.00 4.61
307 308 5.942961 TCTGGTTAATAGTTTTGTCCCACA 58.057 37.500 0.00 0.00 0.00 4.17
308 309 6.366340 TCTGGTTAATAGTTTTGTCCCACAA 58.634 36.000 0.00 0.00 36.11 3.33
309 310 6.834451 TCTGGTTAATAGTTTTGTCCCACAAA 59.166 34.615 0.00 0.00 45.37 2.83
310 311 7.507616 TCTGGTTAATAGTTTTGTCCCACAAAT 59.492 33.333 2.76 0.00 46.17 2.32
311 312 8.707796 TGGTTAATAGTTTTGTCCCACAAATA 57.292 30.769 2.76 0.00 46.17 1.40
312 313 9.144298 TGGTTAATAGTTTTGTCCCACAAATAA 57.856 29.630 2.76 0.00 46.17 1.40
324 325 8.815565 TGTCCCACAAATAATATAAAAGAGCA 57.184 30.769 0.00 0.00 0.00 4.26
325 326 9.420118 TGTCCCACAAATAATATAAAAGAGCAT 57.580 29.630 0.00 0.00 0.00 3.79
341 342 8.766994 AAAAGAGCATATTAAAGCCCATTAGA 57.233 30.769 0.00 0.00 0.00 2.10
342 343 7.751768 AAGAGCATATTAAAGCCCATTAGAC 57.248 36.000 0.00 0.00 0.00 2.59
343 344 6.841601 AGAGCATATTAAAGCCCATTAGACA 58.158 36.000 0.00 0.00 0.00 3.41
344 345 7.465116 AGAGCATATTAAAGCCCATTAGACAT 58.535 34.615 0.00 0.00 0.00 3.06
345 346 7.609532 AGAGCATATTAAAGCCCATTAGACATC 59.390 37.037 0.00 0.00 0.00 3.06
346 347 6.660949 AGCATATTAAAGCCCATTAGACATCC 59.339 38.462 0.00 0.00 0.00 3.51
347 348 6.434028 GCATATTAAAGCCCATTAGACATCCA 59.566 38.462 0.00 0.00 0.00 3.41
348 349 7.039784 GCATATTAAAGCCCATTAGACATCCAA 60.040 37.037 0.00 0.00 0.00 3.53
349 350 8.859090 CATATTAAAGCCCATTAGACATCCAAA 58.141 33.333 0.00 0.00 0.00 3.28
350 351 7.732222 ATTAAAGCCCATTAGACATCCAAAA 57.268 32.000 0.00 0.00 0.00 2.44
351 352 5.405935 AAAGCCCATTAGACATCCAAAAC 57.594 39.130 0.00 0.00 0.00 2.43
352 353 4.046286 AGCCCATTAGACATCCAAAACA 57.954 40.909 0.00 0.00 0.00 2.83
353 354 4.019174 AGCCCATTAGACATCCAAAACAG 58.981 43.478 0.00 0.00 0.00 3.16
354 355 4.016444 GCCCATTAGACATCCAAAACAGA 58.984 43.478 0.00 0.00 0.00 3.41
355 356 4.646492 GCCCATTAGACATCCAAAACAGAT 59.354 41.667 0.00 0.00 0.00 2.90
356 357 5.827797 GCCCATTAGACATCCAAAACAGATA 59.172 40.000 0.00 0.00 0.00 1.98
357 358 6.321181 GCCCATTAGACATCCAAAACAGATAA 59.679 38.462 0.00 0.00 0.00 1.75
358 359 7.014615 GCCCATTAGACATCCAAAACAGATAAT 59.985 37.037 0.00 0.00 0.00 1.28
359 360 9.573166 CCCATTAGACATCCAAAACAGATAATA 57.427 33.333 0.00 0.00 0.00 0.98
411 412 1.811428 CGTTGGAGACGTATCACTCG 58.189 55.000 12.92 8.84 46.49 4.18
412 413 1.531264 CGTTGGAGACGTATCACTCGG 60.531 57.143 12.92 0.00 46.49 4.63
413 414 0.454600 TTGGAGACGTATCACTCGGC 59.545 55.000 12.92 0.00 36.48 5.54
414 415 0.678684 TGGAGACGTATCACTCGGCA 60.679 55.000 12.92 0.00 38.95 5.69
415 416 0.248539 GGAGACGTATCACTCGGCAC 60.249 60.000 12.92 0.00 38.95 5.01
416 417 0.248539 GAGACGTATCACTCGGCACC 60.249 60.000 5.07 0.00 38.95 5.01
417 418 1.585521 GACGTATCACTCGGCACCG 60.586 63.158 1.73 1.73 36.24 4.94
418 419 2.954868 CGTATCACTCGGCACCGC 60.955 66.667 3.66 0.00 39.59 5.68
419 420 2.585247 GTATCACTCGGCACCGCC 60.585 66.667 3.66 0.00 46.75 6.13
443 444 2.364973 TGGCGCCTCCATACTCCA 60.365 61.111 29.70 0.00 40.72 3.86
559 584 1.157751 TCCCCGGTGACTTCCTCTT 59.842 57.895 0.00 0.00 0.00 2.85
615 640 0.034616 GTAGCCCTGCTCTGCCTATG 59.965 60.000 0.00 0.00 40.44 2.23
620 645 4.552365 TGCTCTGCCTATGCCCGC 62.552 66.667 0.00 0.00 36.33 6.13
646 671 2.284699 AGCTCCGGGTTACTGCCT 60.285 61.111 0.00 0.00 0.00 4.75
647 672 1.001248 AGCTCCGGGTTACTGCCTA 59.999 57.895 0.00 0.00 0.00 3.93
674 699 0.455005 GAGCTAGGTACACCGTCCAC 59.545 60.000 0.00 0.00 42.08 4.02
678 703 2.803593 TAGGTACACCGTCCACCCCC 62.804 65.000 0.00 0.00 42.08 5.40
699 724 1.680522 CCACCTCCGCTACATGCTCT 61.681 60.000 0.00 0.00 40.11 4.09
838 893 4.609018 AGGCTCGTGCACGCTTGT 62.609 61.111 33.63 15.59 41.91 3.16
940 997 4.457496 CTGCTCCCGCATCACCGT 62.457 66.667 0.00 0.00 46.74 4.83
1118 1177 3.242739 GCCATTCAAGAAACGATGCGTAT 60.243 43.478 0.00 0.00 39.99 3.06
1210 1269 1.991099 GAGTACGGGCCACTCGAGTC 61.991 65.000 16.96 5.28 33.62 3.36
1217 1276 2.885113 CCACTCGAGTCGCATCCA 59.115 61.111 16.96 0.00 0.00 3.41
1329 1389 4.220382 ACTTCAAATGGGAAATCATTGCGA 59.780 37.500 0.00 0.00 37.42 5.10
1422 1504 1.001633 GTGGTAGGAGGCGACTTCAAA 59.998 52.381 0.00 0.00 44.43 2.69
1443 1525 2.757868 ACTCATCTGGTCGGAAGAAGAG 59.242 50.000 9.32 9.32 45.01 2.85
1492 1574 2.032550 CGGATGCAGATGTTCAATGACC 59.967 50.000 0.00 0.00 0.00 4.02
1567 1649 2.285977 GGACAAACCGACAAGTTGAGT 58.714 47.619 10.54 0.95 0.00 3.41
1651 1733 3.393089 CCTCGCTCTAGGCAATTACAT 57.607 47.619 4.43 0.00 41.91 2.29
1667 1749 6.432936 CAATTACATGGATTGGTTCAGATCG 58.567 40.000 13.39 0.00 32.24 3.69
1835 1919 0.739462 CGGCCATCGACAACTAGCAA 60.739 55.000 2.24 0.00 42.43 3.91
1870 1954 3.670055 CGGTCACAACAATTCATGAAAGC 59.330 43.478 13.09 2.01 0.00 3.51
1892 1976 3.060000 GGGTGCAAACGTAGGCCC 61.060 66.667 0.00 8.91 0.00 5.80
2027 2111 1.410517 CCAGCTCACGGTCATCTACAT 59.589 52.381 0.00 0.00 0.00 2.29
2032 2116 3.315470 GCTCACGGTCATCTACATAGACA 59.685 47.826 0.00 0.00 34.72 3.41
2040 2124 3.570125 TCATCTACATAGACAAGGAGGCG 59.430 47.826 0.00 0.00 34.72 5.52
2058 2142 2.041686 GTATTGGCGTTTGCGGGGA 61.042 57.895 0.00 0.00 44.10 4.81
2077 2161 3.800826 ACGCATAATTGGGTCCTCC 57.199 52.632 0.00 0.00 45.01 4.30
2106 2190 2.092646 TGCCAATACCGCTTACTTCCAT 60.093 45.455 0.00 0.00 0.00 3.41
2107 2191 3.134985 TGCCAATACCGCTTACTTCCATA 59.865 43.478 0.00 0.00 0.00 2.74
2131 2215 3.044235 CATAGCTAATGGCCGACATCA 57.956 47.619 0.00 0.00 39.40 3.07
2178 2263 3.283303 GAGCGACTCTCCTGCAGT 58.717 61.111 13.81 0.00 35.77 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.604657 ACTCTTATACCCTAGAAACATCAGG 57.395 40.000 0.00 0.00 0.00 3.86
23 24 8.881743 CGTACTTCTTTCGCCTATATATACTCT 58.118 37.037 0.00 0.00 0.00 3.24
24 25 8.663911 ACGTACTTCTTTCGCCTATATATACTC 58.336 37.037 0.00 0.00 0.00 2.59
25 26 8.558973 ACGTACTTCTTTCGCCTATATATACT 57.441 34.615 0.00 0.00 0.00 2.12
26 27 7.634048 CGACGTACTTCTTTCGCCTATATATAC 59.366 40.741 0.00 0.00 0.00 1.47
27 28 7.201556 CCGACGTACTTCTTTCGCCTATATATA 60.202 40.741 0.00 0.00 0.00 0.86
28 29 6.402983 CCGACGTACTTCTTTCGCCTATATAT 60.403 42.308 0.00 0.00 0.00 0.86
29 30 5.106948 CCGACGTACTTCTTTCGCCTATATA 60.107 44.000 0.00 0.00 0.00 0.86
30 31 4.320057 CCGACGTACTTCTTTCGCCTATAT 60.320 45.833 0.00 0.00 0.00 0.86
31 32 3.002656 CCGACGTACTTCTTTCGCCTATA 59.997 47.826 0.00 0.00 0.00 1.31
32 33 2.223433 CCGACGTACTTCTTTCGCCTAT 60.223 50.000 0.00 0.00 0.00 2.57
33 34 1.131126 CCGACGTACTTCTTTCGCCTA 59.869 52.381 0.00 0.00 0.00 3.93
34 35 0.109412 CCGACGTACTTCTTTCGCCT 60.109 55.000 0.00 0.00 0.00 5.52
35 36 0.387750 ACCGACGTACTTCTTTCGCC 60.388 55.000 0.00 0.00 0.00 5.54
36 37 0.706729 CACCGACGTACTTCTTTCGC 59.293 55.000 0.00 0.00 0.00 4.70
37 38 1.069022 TCCACCGACGTACTTCTTTCG 60.069 52.381 0.00 0.00 0.00 3.46
38 39 2.593257 CTCCACCGACGTACTTCTTTC 58.407 52.381 0.00 0.00 0.00 2.62
39 40 1.336609 GCTCCACCGACGTACTTCTTT 60.337 52.381 0.00 0.00 0.00 2.52
40 41 0.243095 GCTCCACCGACGTACTTCTT 59.757 55.000 0.00 0.00 0.00 2.52
41 42 0.608582 AGCTCCACCGACGTACTTCT 60.609 55.000 0.00 0.00 0.00 2.85
42 43 1.089920 TAGCTCCACCGACGTACTTC 58.910 55.000 0.00 0.00 0.00 3.01
43 44 0.807496 GTAGCTCCACCGACGTACTT 59.193 55.000 0.00 0.00 0.00 2.24
44 45 0.321919 TGTAGCTCCACCGACGTACT 60.322 55.000 0.00 0.00 0.00 2.73
45 46 0.523072 TTGTAGCTCCACCGACGTAC 59.477 55.000 0.00 0.00 0.00 3.67
46 47 0.806868 CTTGTAGCTCCACCGACGTA 59.193 55.000 0.00 0.00 0.00 3.57
47 48 1.585006 CTTGTAGCTCCACCGACGT 59.415 57.895 0.00 0.00 0.00 4.34
48 49 1.153823 CCTTGTAGCTCCACCGACG 60.154 63.158 0.00 0.00 0.00 5.12
49 50 1.218316 CCCTTGTAGCTCCACCGAC 59.782 63.158 0.00 0.00 0.00 4.79
50 51 1.987855 CCCCTTGTAGCTCCACCGA 60.988 63.158 0.00 0.00 0.00 4.69
51 52 2.584608 CCCCTTGTAGCTCCACCG 59.415 66.667 0.00 0.00 0.00 4.94
52 53 2.272471 GCCCCTTGTAGCTCCACC 59.728 66.667 0.00 0.00 0.00 4.61
53 54 2.272471 GGCCCCTTGTAGCTCCAC 59.728 66.667 0.00 0.00 0.00 4.02
54 55 3.015145 GGGCCCCTTGTAGCTCCA 61.015 66.667 12.23 0.00 0.00 3.86
55 56 3.015145 TGGGCCCCTTGTAGCTCC 61.015 66.667 22.27 0.00 0.00 4.70
56 57 2.272471 GTGGGCCCCTTGTAGCTC 59.728 66.667 22.27 0.00 0.00 4.09
57 58 3.717294 CGTGGGCCCCTTGTAGCT 61.717 66.667 22.27 0.00 0.00 3.32
58 59 3.682292 CTCGTGGGCCCCTTGTAGC 62.682 68.421 22.27 0.00 0.00 3.58
59 60 2.584608 CTCGTGGGCCCCTTGTAG 59.415 66.667 22.27 5.78 0.00 2.74
60 61 3.006728 CCTCGTGGGCCCCTTGTA 61.007 66.667 22.27 0.00 0.00 2.41
102 103 3.854669 CAGGAGGGCACGCCTAGG 61.855 72.222 12.32 3.67 45.92 3.02
103 104 4.537433 GCAGGAGGGCACGCCTAG 62.537 72.222 12.32 7.40 45.92 3.02
109 110 4.767255 CACGAGGCAGGAGGGCAC 62.767 72.222 0.00 0.00 46.44 5.01
120 121 1.079127 CTACAAGGTGGCCACGAGG 60.079 63.158 29.08 21.43 38.23 4.63
121 122 0.108615 CTCTACAAGGTGGCCACGAG 60.109 60.000 29.08 22.87 0.00 4.18
122 123 0.830444 ACTCTACAAGGTGGCCACGA 60.830 55.000 29.08 17.96 0.00 4.35
123 124 0.389948 GACTCTACAAGGTGGCCACG 60.390 60.000 29.08 18.08 0.00 4.94
124 125 0.036294 GGACTCTACAAGGTGGCCAC 60.036 60.000 28.57 28.57 0.00 5.01
125 126 1.198759 GGGACTCTACAAGGTGGCCA 61.199 60.000 0.00 0.00 0.00 5.36
126 127 1.198759 TGGGACTCTACAAGGTGGCC 61.199 60.000 0.00 0.00 0.00 5.36
127 128 0.250513 CTGGGACTCTACAAGGTGGC 59.749 60.000 0.00 0.00 0.00 5.01
128 129 1.550976 GTCTGGGACTCTACAAGGTGG 59.449 57.143 0.00 0.00 0.00 4.61
129 130 2.530701 AGTCTGGGACTCTACAAGGTG 58.469 52.381 0.00 0.00 38.71 4.00
130 131 2.900546 CAAGTCTGGGACTCTACAAGGT 59.099 50.000 0.49 0.00 42.59 3.50
131 132 3.165875 TCAAGTCTGGGACTCTACAAGG 58.834 50.000 0.49 0.00 42.59 3.61
132 133 4.282195 AGTTCAAGTCTGGGACTCTACAAG 59.718 45.833 0.49 0.00 42.59 3.16
133 134 4.223953 AGTTCAAGTCTGGGACTCTACAA 58.776 43.478 0.49 0.00 42.59 2.41
134 135 3.827302 GAGTTCAAGTCTGGGACTCTACA 59.173 47.826 8.32 0.00 42.59 2.74
135 136 3.193903 GGAGTTCAAGTCTGGGACTCTAC 59.806 52.174 14.44 0.00 42.59 2.59
136 137 3.181422 TGGAGTTCAAGTCTGGGACTCTA 60.181 47.826 14.44 6.63 42.59 2.43
137 138 2.252714 GGAGTTCAAGTCTGGGACTCT 58.747 52.381 14.44 0.00 42.59 3.24
138 139 1.971357 TGGAGTTCAAGTCTGGGACTC 59.029 52.381 7.11 7.11 42.59 3.36
139 140 2.103153 TGGAGTTCAAGTCTGGGACT 57.897 50.000 0.00 0.00 45.64 3.85
140 141 2.772287 CTTGGAGTTCAAGTCTGGGAC 58.228 52.381 2.64 0.00 45.81 4.46
149 150 4.982241 ATCCAGAAGACTTGGAGTTCAA 57.018 40.909 2.44 0.00 34.94 2.69
150 151 4.347876 TCAATCCAGAAGACTTGGAGTTCA 59.652 41.667 2.44 0.00 34.94 3.18
151 152 4.899502 TCAATCCAGAAGACTTGGAGTTC 58.100 43.478 2.44 0.00 34.94 3.01
152 153 4.982241 TCAATCCAGAAGACTTGGAGTT 57.018 40.909 2.44 0.00 34.94 3.01
153 154 5.511386 AATCAATCCAGAAGACTTGGAGT 57.489 39.130 2.44 0.00 34.94 3.85
154 155 6.349944 CCAAAATCAATCCAGAAGACTTGGAG 60.350 42.308 2.44 0.00 34.94 3.86
155 156 5.477984 CCAAAATCAATCCAGAAGACTTGGA 59.522 40.000 0.00 0.00 32.97 3.53
156 157 5.244626 ACCAAAATCAATCCAGAAGACTTGG 59.755 40.000 0.00 0.00 35.38 3.61
157 158 6.336842 ACCAAAATCAATCCAGAAGACTTG 57.663 37.500 0.00 0.00 0.00 3.16
158 159 5.478332 GGACCAAAATCAATCCAGAAGACTT 59.522 40.000 0.00 0.00 0.00 3.01
159 160 5.012893 GGACCAAAATCAATCCAGAAGACT 58.987 41.667 0.00 0.00 0.00 3.24
160 161 4.766891 TGGACCAAAATCAATCCAGAAGAC 59.233 41.667 0.00 0.00 36.30 3.01
161 162 4.996793 TGGACCAAAATCAATCCAGAAGA 58.003 39.130 0.00 0.00 36.30 2.87
162 163 5.726980 TTGGACCAAAATCAATCCAGAAG 57.273 39.130 3.84 0.00 42.12 2.85
163 164 7.789202 TTATTGGACCAAAATCAATCCAGAA 57.211 32.000 11.82 0.00 42.12 3.02
164 165 7.673504 TCTTTATTGGACCAAAATCAATCCAGA 59.326 33.333 11.82 3.03 42.12 3.86
165 166 7.839907 TCTTTATTGGACCAAAATCAATCCAG 58.160 34.615 11.82 0.94 42.12 3.86
166 167 7.789202 TCTTTATTGGACCAAAATCAATCCA 57.211 32.000 11.82 0.00 39.50 3.41
167 168 7.928167 GGATCTTTATTGGACCAAAATCAATCC 59.072 37.037 11.82 16.00 33.72 3.01
168 169 8.699130 AGGATCTTTATTGGACCAAAATCAATC 58.301 33.333 11.82 11.40 33.72 2.67
169 170 8.613922 AGGATCTTTATTGGACCAAAATCAAT 57.386 30.769 11.82 2.88 35.57 2.57
170 171 7.148086 CGAGGATCTTTATTGGACCAAAATCAA 60.148 37.037 11.82 0.61 0.00 2.57
171 172 6.318648 CGAGGATCTTTATTGGACCAAAATCA 59.681 38.462 11.82 0.00 0.00 2.57
172 173 6.729187 CGAGGATCTTTATTGGACCAAAATC 58.271 40.000 11.82 9.15 0.00 2.17
173 174 5.067805 GCGAGGATCTTTATTGGACCAAAAT 59.932 40.000 11.82 0.00 0.00 1.82
174 175 4.398044 GCGAGGATCTTTATTGGACCAAAA 59.602 41.667 11.82 0.76 0.00 2.44
175 176 3.945285 GCGAGGATCTTTATTGGACCAAA 59.055 43.478 11.82 0.00 0.00 3.28
176 177 3.054728 TGCGAGGATCTTTATTGGACCAA 60.055 43.478 9.92 9.92 0.00 3.67
177 178 2.503765 TGCGAGGATCTTTATTGGACCA 59.496 45.455 0.00 0.00 0.00 4.02
178 179 3.194005 TGCGAGGATCTTTATTGGACC 57.806 47.619 0.00 0.00 0.00 4.46
179 180 5.162000 CTTTGCGAGGATCTTTATTGGAC 57.838 43.478 0.00 0.00 0.00 4.02
193 194 1.535462 ACGGAATGAAACCTTTGCGAG 59.465 47.619 10.70 0.00 38.72 5.03
194 195 1.600023 ACGGAATGAAACCTTTGCGA 58.400 45.000 10.70 0.00 38.72 5.10
195 196 2.415697 AACGGAATGAAACCTTTGCG 57.584 45.000 0.00 0.00 41.62 4.85
196 197 2.799978 CCAAACGGAATGAAACCTTTGC 59.200 45.455 0.00 0.00 31.20 3.68
197 198 4.048504 GACCAAACGGAATGAAACCTTTG 58.951 43.478 0.00 0.00 0.00 2.77
198 199 3.958147 AGACCAAACGGAATGAAACCTTT 59.042 39.130 0.00 0.00 0.00 3.11
199 200 3.562182 AGACCAAACGGAATGAAACCTT 58.438 40.909 0.00 0.00 0.00 3.50
200 201 3.146847 GAGACCAAACGGAATGAAACCT 58.853 45.455 0.00 0.00 0.00 3.50
201 202 2.228103 GGAGACCAAACGGAATGAAACC 59.772 50.000 0.00 0.00 0.00 3.27
202 203 2.882137 TGGAGACCAAACGGAATGAAAC 59.118 45.455 0.00 0.00 0.00 2.78
203 204 3.216187 TGGAGACCAAACGGAATGAAA 57.784 42.857 0.00 0.00 0.00 2.69
204 205 2.940994 TGGAGACCAAACGGAATGAA 57.059 45.000 0.00 0.00 0.00 2.57
205 206 3.433306 AATGGAGACCAAACGGAATGA 57.567 42.857 0.00 0.00 36.95 2.57
206 207 3.505680 TCAAATGGAGACCAAACGGAATG 59.494 43.478 0.00 0.00 36.95 2.67
207 208 3.761897 TCAAATGGAGACCAAACGGAAT 58.238 40.909 0.00 0.00 36.95 3.01
208 209 3.216187 TCAAATGGAGACCAAACGGAA 57.784 42.857 0.00 0.00 36.95 4.30
209 210 2.940994 TCAAATGGAGACCAAACGGA 57.059 45.000 0.00 0.00 36.95 4.69
210 211 5.221048 GGAATATCAAATGGAGACCAAACGG 60.221 44.000 0.00 0.00 36.95 4.44
211 212 5.590259 AGGAATATCAAATGGAGACCAAACG 59.410 40.000 0.00 0.00 36.95 3.60
212 213 7.410120 AAGGAATATCAAATGGAGACCAAAC 57.590 36.000 0.00 0.00 36.95 2.93
213 214 8.434589 AAAAGGAATATCAAATGGAGACCAAA 57.565 30.769 0.00 0.00 36.95 3.28
214 215 7.895429 AGAAAAGGAATATCAAATGGAGACCAA 59.105 33.333 0.00 0.00 36.95 3.67
215 216 7.340232 CAGAAAAGGAATATCAAATGGAGACCA 59.660 37.037 0.00 0.00 38.19 4.02
216 217 7.340487 ACAGAAAAGGAATATCAAATGGAGACC 59.660 37.037 0.00 0.00 0.00 3.85
217 218 8.286191 ACAGAAAAGGAATATCAAATGGAGAC 57.714 34.615 0.00 0.00 0.00 3.36
218 219 9.973661 TTACAGAAAAGGAATATCAAATGGAGA 57.026 29.630 0.00 0.00 0.00 3.71
232 233 9.333724 CCTACTTTAGTGTTTTACAGAAAAGGA 57.666 33.333 13.78 7.90 36.28 3.36
233 234 8.074370 GCCTACTTTAGTGTTTTACAGAAAAGG 58.926 37.037 13.78 8.39 36.28 3.11
234 235 8.617809 TGCCTACTTTAGTGTTTTACAGAAAAG 58.382 33.333 10.15 10.15 37.20 2.27
235 236 8.508883 TGCCTACTTTAGTGTTTTACAGAAAA 57.491 30.769 0.00 0.00 32.00 2.29
236 237 8.508883 TTGCCTACTTTAGTGTTTTACAGAAA 57.491 30.769 0.00 0.00 0.00 2.52
237 238 8.508883 TTTGCCTACTTTAGTGTTTTACAGAA 57.491 30.769 0.00 0.00 0.00 3.02
238 239 8.508883 TTTTGCCTACTTTAGTGTTTTACAGA 57.491 30.769 0.00 0.00 0.00 3.41
239 240 9.744468 ATTTTTGCCTACTTTAGTGTTTTACAG 57.256 29.630 0.00 0.00 0.00 2.74
245 246 9.961265 GTTTCTATTTTTGCCTACTTTAGTGTT 57.039 29.630 0.00 0.00 0.00 3.32
246 247 9.350951 AGTTTCTATTTTTGCCTACTTTAGTGT 57.649 29.630 0.00 0.00 0.00 3.55
247 248 9.612620 CAGTTTCTATTTTTGCCTACTTTAGTG 57.387 33.333 0.00 0.00 0.00 2.74
248 249 9.569122 TCAGTTTCTATTTTTGCCTACTTTAGT 57.431 29.630 0.00 0.00 0.00 2.24
249 250 9.827411 GTCAGTTTCTATTTTTGCCTACTTTAG 57.173 33.333 0.00 0.00 0.00 1.85
250 251 8.500773 CGTCAGTTTCTATTTTTGCCTACTTTA 58.499 33.333 0.00 0.00 0.00 1.85
251 252 7.360361 CGTCAGTTTCTATTTTTGCCTACTTT 58.640 34.615 0.00 0.00 0.00 2.66
252 253 6.567891 GCGTCAGTTTCTATTTTTGCCTACTT 60.568 38.462 0.00 0.00 0.00 2.24
253 254 5.106673 GCGTCAGTTTCTATTTTTGCCTACT 60.107 40.000 0.00 0.00 0.00 2.57
254 255 5.086727 GCGTCAGTTTCTATTTTTGCCTAC 58.913 41.667 0.00 0.00 0.00 3.18
255 256 5.001232 AGCGTCAGTTTCTATTTTTGCCTA 58.999 37.500 0.00 0.00 0.00 3.93
256 257 3.821033 AGCGTCAGTTTCTATTTTTGCCT 59.179 39.130 0.00 0.00 0.00 4.75
257 258 4.160736 AGCGTCAGTTTCTATTTTTGCC 57.839 40.909 0.00 0.00 0.00 4.52
258 259 5.324697 CCTAGCGTCAGTTTCTATTTTTGC 58.675 41.667 0.00 0.00 0.00 3.68
259 260 5.324697 GCCTAGCGTCAGTTTCTATTTTTG 58.675 41.667 0.00 0.00 0.00 2.44
260 261 4.395231 GGCCTAGCGTCAGTTTCTATTTTT 59.605 41.667 0.00 0.00 0.00 1.94
261 262 3.939592 GGCCTAGCGTCAGTTTCTATTTT 59.060 43.478 0.00 0.00 0.00 1.82
262 263 3.197983 AGGCCTAGCGTCAGTTTCTATTT 59.802 43.478 1.29 0.00 0.00 1.40
263 264 2.766828 AGGCCTAGCGTCAGTTTCTATT 59.233 45.455 1.29 0.00 0.00 1.73
264 265 2.362717 GAGGCCTAGCGTCAGTTTCTAT 59.637 50.000 4.42 0.00 42.14 1.98
265 266 1.749634 GAGGCCTAGCGTCAGTTTCTA 59.250 52.381 4.42 0.00 42.14 2.10
266 267 0.533032 GAGGCCTAGCGTCAGTTTCT 59.467 55.000 4.42 0.00 42.14 2.52
267 268 0.533032 AGAGGCCTAGCGTCAGTTTC 59.467 55.000 4.42 0.00 44.54 2.78
268 269 0.247736 CAGAGGCCTAGCGTCAGTTT 59.752 55.000 4.42 0.00 44.54 2.66
269 270 1.608717 CCAGAGGCCTAGCGTCAGTT 61.609 60.000 4.42 0.00 44.54 3.16
270 271 2.055042 CCAGAGGCCTAGCGTCAGT 61.055 63.158 4.42 0.00 44.54 3.41
271 272 1.608717 AACCAGAGGCCTAGCGTCAG 61.609 60.000 4.42 3.71 44.54 3.51
272 273 0.323999 TAACCAGAGGCCTAGCGTCA 60.324 55.000 4.42 0.00 44.54 4.35
273 274 0.822164 TTAACCAGAGGCCTAGCGTC 59.178 55.000 4.42 0.00 42.77 5.19
274 275 1.497161 ATTAACCAGAGGCCTAGCGT 58.503 50.000 4.42 0.00 0.00 5.07
275 276 2.628657 ACTATTAACCAGAGGCCTAGCG 59.371 50.000 4.42 0.00 0.00 4.26
276 277 4.691326 AACTATTAACCAGAGGCCTAGC 57.309 45.455 4.42 0.00 0.00 3.42
277 278 6.415573 ACAAAACTATTAACCAGAGGCCTAG 58.584 40.000 4.42 0.20 0.00 3.02
278 279 6.382919 ACAAAACTATTAACCAGAGGCCTA 57.617 37.500 4.42 0.00 0.00 3.93
279 280 5.254115 GACAAAACTATTAACCAGAGGCCT 58.746 41.667 3.86 3.86 0.00 5.19
280 281 4.398358 GGACAAAACTATTAACCAGAGGCC 59.602 45.833 0.00 0.00 0.00 5.19
281 282 4.398358 GGGACAAAACTATTAACCAGAGGC 59.602 45.833 0.00 0.00 0.00 4.70
282 283 5.414765 GTGGGACAAAACTATTAACCAGAGG 59.585 44.000 0.00 0.00 44.16 3.69
283 284 6.001460 TGTGGGACAAAACTATTAACCAGAG 58.999 40.000 0.00 0.00 44.16 3.35
284 285 5.942961 TGTGGGACAAAACTATTAACCAGA 58.057 37.500 0.00 0.00 44.16 3.86
285 286 6.642707 TTGTGGGACAAAACTATTAACCAG 57.357 37.500 0.00 0.00 44.16 4.00
298 299 9.249053 TGCTCTTTTATATTATTTGTGGGACAA 57.751 29.630 0.00 0.00 44.16 3.18
299 300 8.815565 TGCTCTTTTATATTATTTGTGGGACA 57.184 30.769 0.00 0.00 0.00 4.02
315 316 9.860650 TCTAATGGGCTTTAATATGCTCTTTTA 57.139 29.630 0.00 0.00 31.14 1.52
316 317 8.633561 GTCTAATGGGCTTTAATATGCTCTTTT 58.366 33.333 0.00 0.00 31.14 2.27
317 318 7.779798 TGTCTAATGGGCTTTAATATGCTCTTT 59.220 33.333 0.00 0.00 32.88 2.52
318 319 7.290061 TGTCTAATGGGCTTTAATATGCTCTT 58.710 34.615 0.00 0.00 0.00 2.85
319 320 6.841601 TGTCTAATGGGCTTTAATATGCTCT 58.158 36.000 0.00 0.00 0.00 4.09
320 321 7.148171 GGATGTCTAATGGGCTTTAATATGCTC 60.148 40.741 0.00 0.00 0.00 4.26
321 322 6.660949 GGATGTCTAATGGGCTTTAATATGCT 59.339 38.462 0.00 0.00 0.00 3.79
322 323 6.434028 TGGATGTCTAATGGGCTTTAATATGC 59.566 38.462 0.00 0.00 0.00 3.14
323 324 8.408043 TTGGATGTCTAATGGGCTTTAATATG 57.592 34.615 0.00 0.00 0.00 1.78
324 325 9.432982 TTTTGGATGTCTAATGGGCTTTAATAT 57.567 29.630 0.00 0.00 0.00 1.28
325 326 8.691797 GTTTTGGATGTCTAATGGGCTTTAATA 58.308 33.333 0.00 0.00 0.00 0.98
326 327 7.180051 TGTTTTGGATGTCTAATGGGCTTTAAT 59.820 33.333 0.00 0.00 0.00 1.40
327 328 6.495181 TGTTTTGGATGTCTAATGGGCTTTAA 59.505 34.615 0.00 0.00 0.00 1.52
328 329 6.013379 TGTTTTGGATGTCTAATGGGCTTTA 58.987 36.000 0.00 0.00 0.00 1.85
329 330 4.837860 TGTTTTGGATGTCTAATGGGCTTT 59.162 37.500 0.00 0.00 0.00 3.51
330 331 4.415596 TGTTTTGGATGTCTAATGGGCTT 58.584 39.130 0.00 0.00 0.00 4.35
331 332 4.019174 CTGTTTTGGATGTCTAATGGGCT 58.981 43.478 0.00 0.00 0.00 5.19
332 333 4.016444 TCTGTTTTGGATGTCTAATGGGC 58.984 43.478 0.00 0.00 0.00 5.36
333 334 7.880160 TTATCTGTTTTGGATGTCTAATGGG 57.120 36.000 0.00 0.00 0.00 4.00
376 377 9.027129 CGTCTCCAACGTATCTATAATTTTTGA 57.973 33.333 0.00 0.00 46.42 2.69
393 394 1.798079 GCCGAGTGATACGTCTCCAAC 60.798 57.143 0.00 0.00 0.00 3.77
394 395 0.454600 GCCGAGTGATACGTCTCCAA 59.545 55.000 0.00 0.00 0.00 3.53
395 396 0.678684 TGCCGAGTGATACGTCTCCA 60.679 55.000 0.00 0.00 0.00 3.86
396 397 0.248539 GTGCCGAGTGATACGTCTCC 60.249 60.000 0.00 0.00 0.00 3.71
397 398 0.248539 GGTGCCGAGTGATACGTCTC 60.249 60.000 0.00 0.00 0.00 3.36
398 399 1.807886 GGTGCCGAGTGATACGTCT 59.192 57.895 0.00 0.00 0.00 4.18
399 400 1.585521 CGGTGCCGAGTGATACGTC 60.586 63.158 4.35 0.00 42.83 4.34
400 401 2.488355 CGGTGCCGAGTGATACGT 59.512 61.111 4.35 0.00 42.83 3.57
401 402 2.954868 GCGGTGCCGAGTGATACG 60.955 66.667 15.45 0.00 42.83 3.06
402 403 2.585247 GGCGGTGCCGAGTGATAC 60.585 66.667 15.45 0.00 39.62 2.24
585 610 3.007323 GGGCTACCCACCGGTCTT 61.007 66.667 2.59 0.00 44.65 3.01
638 663 1.749634 GCTCGAGGTTCTAGGCAGTAA 59.250 52.381 15.58 0.00 0.00 2.24
678 703 2.586079 CATGTAGCGGAGGTGGCG 60.586 66.667 0.00 0.00 40.22 5.69
699 724 2.158813 AGCCGACTCCAAGACAGAAAAA 60.159 45.455 0.00 0.00 0.00 1.94
790 818 2.548920 GCCCATCGAGGATTTCTAGTGG 60.549 54.545 0.00 0.00 41.22 4.00
794 847 1.416401 GGTGCCCATCGAGGATTTCTA 59.584 52.381 0.00 0.00 41.22 2.10
795 848 0.181350 GGTGCCCATCGAGGATTTCT 59.819 55.000 0.00 0.00 41.22 2.52
897 954 0.877649 CCGCAGATCTCAACCGGATG 60.878 60.000 9.46 7.03 41.34 3.51
940 997 2.829003 CGCTCTAGGCACGGAGGA 60.829 66.667 4.43 0.00 41.91 3.71
1217 1276 0.253160 TGGCATCCTTCACCCTAGGT 60.253 55.000 8.29 0.00 35.62 3.08
1367 1427 1.226717 CCTACGGAGTTCAGCGAGC 60.227 63.158 0.00 0.00 37.78 5.03
1422 1504 2.757868 CTCTTCTTCCGACCAGATGAGT 59.242 50.000 10.63 0.00 37.60 3.41
1443 1525 7.329471 GGAAAGTTCACCAAATTATTGCTCTTC 59.671 37.037 0.00 0.00 35.10 2.87
1492 1574 3.274586 CCCCATGTCAGCGATGCG 61.275 66.667 0.00 0.00 0.00 4.73
1567 1649 2.359602 AAGGACGGAGCGAGTCGA 60.360 61.111 18.61 0.00 39.38 4.20
1618 1700 4.860881 CGAGGCTAGGGGGCAGGA 62.861 72.222 0.00 0.00 43.56 3.86
1651 1733 2.564771 GATGCGATCTGAACCAATCCA 58.435 47.619 0.00 0.00 0.00 3.41
1667 1749 1.841103 GAGAGGAGGAGGGGGATGC 60.841 68.421 0.00 0.00 0.00 3.91
1711 1795 2.632602 TTTGAACCAGAAGCGGGGCA 62.633 55.000 0.00 0.00 0.00 5.36
1870 1954 1.312371 CCTACGTTTGCACCCCCATG 61.312 60.000 0.00 0.00 0.00 3.66
1873 1957 3.060000 GCCTACGTTTGCACCCCC 61.060 66.667 0.00 0.00 0.00 5.40
1974 2058 3.490249 CGTACCTAAGCATCCATTCGTCA 60.490 47.826 0.00 0.00 0.00 4.35
2027 2111 1.138266 GCCAATACGCCTCCTTGTCTA 59.862 52.381 0.00 0.00 0.00 2.59
2032 2116 0.322187 AAACGCCAATACGCCTCCTT 60.322 50.000 0.00 0.00 36.19 3.36
2040 2124 1.587933 TTCCCCGCAAACGCCAATAC 61.588 55.000 0.00 0.00 38.22 1.89
2058 2142 1.283613 TGGAGGACCCAATTATGCGTT 59.716 47.619 0.00 0.00 43.29 4.84
2064 2148 0.626277 CCCCCTGGAGGACCCAATTA 60.626 60.000 0.00 0.00 46.07 1.40
2077 2161 1.228245 CGGTATTGGCATCCCCCTG 60.228 63.158 0.00 0.00 0.00 4.45
2126 2210 1.485066 GGGATGGAGTTACGGTGATGT 59.515 52.381 0.00 0.00 0.00 3.06
2131 2215 0.690077 GAGGGGGATGGAGTTACGGT 60.690 60.000 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.