Multiple sequence alignment - TraesCS4B01G255700

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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 TraesCS4B01G255700 chr4B 100.000 2354 0 0 1 2354 520418156 520420509 0.000000e+00 4348
1 TraesCS4B01G255700 chr4B 90.625 96 5 3 274 367 520418204 520418297 8.830000e-25 124
2 TraesCS4B01G255700 chr4B 90.625 96 5 3 49 142 520418429 520418522 8.830000e-25 124
3 TraesCS4B01G255700 chr4A 87.896 1545 77 29 660 2176 40237504 40236042 0.000000e+00 1716
4 TraesCS4B01G255700 chr4A 91.696 289 20 2 274 559 40238026 40237739 4.710000e-107 398
5 TraesCS4B01G255700 chr4A 95.652 184 4 3 2173 2354 40235709 40235528 2.290000e-75 292
6 TraesCS4B01G255700 chr4A 83.333 156 13 7 505 648 40237739 40237585 5.280000e-27 132
7 TraesCS4B01G255700 chr4D 91.143 1129 49 18 660 1742 424572782 424573905 0.000000e+00 1483
8 TraesCS4B01G255700 chr4D 87.269 432 23 12 1750 2167 424573879 424574292 4.580000e-127 464
9 TraesCS4B01G255700 chr4D 89.199 287 21 4 274 559 424572104 424572381 1.340000e-92 350
10 TraesCS4B01G255700 chr4D 95.055 182 3 2 2173 2354 424574853 424575028 4.950000e-72 281
11 TraesCS4B01G255700 chr4D 86.822 129 11 5 526 648 424572558 424572686 3.150000e-29 139
12 TraesCS4B01G255700 chr4D 84.615 143 17 4 3 142 424572057 424572197 1.130000e-28 137


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 TraesCS4B01G255700 chr4B 520418156 520420509 2353 False 1532.000000 4348 93.750000 1 2354 3 chr4B.!!$F1 2353
1 TraesCS4B01G255700 chr4A 40235528 40238026 2498 True 634.500000 1716 89.644250 274 2354 4 chr4A.!!$R1 2080
2 TraesCS4B01G255700 chr4D 424572057 424575028 2971 False 475.666667 1483 89.017167 3 2354 6 chr4D.!!$F1 2351

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
53 54 0.238289 CAAAGACATCACGCACCACC 59.762 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 2082 0.106519 AGGCTGCAGAACACAAAGGT 60.107 50.0 20.43 0.0 0.0 3.5 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
34 35 7.017055 GGTATGTGATTGTACCGTGTTAAAAC 58.983 38.462 0.00 0.00 31.83 2.43
38 39 6.967767 TGTGATTGTACCGTGTTAAAACAAAG 59.032 34.615 0.00 0.00 41.21 2.77
39 40 7.148289 TGTGATTGTACCGTGTTAAAACAAAGA 60.148 33.333 0.00 0.00 41.21 2.52
43 44 6.717413 TGTACCGTGTTAAAACAAAGACATC 58.283 36.000 0.00 0.00 41.21 3.06
48 49 5.031578 GTGTTAAAACAAAGACATCACGCA 58.968 37.500 0.00 0.00 41.21 5.24
49 50 5.031578 TGTTAAAACAAAGACATCACGCAC 58.968 37.500 0.00 0.00 35.67 5.34
50 51 2.774439 AAACAAAGACATCACGCACC 57.226 45.000 0.00 0.00 0.00 5.01
51 52 1.674359 AACAAAGACATCACGCACCA 58.326 45.000 0.00 0.00 0.00 4.17
52 53 0.944386 ACAAAGACATCACGCACCAC 59.056 50.000 0.00 0.00 0.00 4.16
53 54 0.238289 CAAAGACATCACGCACCACC 59.762 55.000 0.00 0.00 0.00 4.61
54 55 0.889186 AAAGACATCACGCACCACCC 60.889 55.000 0.00 0.00 0.00 4.61
55 56 3.118454 GACATCACGCACCACCCG 61.118 66.667 0.00 0.00 0.00 5.28
56 57 4.697756 ACATCACGCACCACCCGG 62.698 66.667 0.00 0.00 38.77 5.73
57 58 4.386951 CATCACGCACCACCCGGA 62.387 66.667 0.73 0.00 35.59 5.14
58 59 4.082523 ATCACGCACCACCCGGAG 62.083 66.667 0.73 0.00 35.59 4.63
73 74 4.329545 GAGGCCAAGGCACGGTCA 62.330 66.667 13.87 0.00 44.11 4.02
74 75 4.335647 AGGCCAAGGCACGGTCAG 62.336 66.667 13.87 0.00 44.11 3.51
77 78 4.641645 CCAAGGCACGGTCAGGCA 62.642 66.667 0.00 0.00 0.00 4.75
78 79 2.360350 CAAGGCACGGTCAGGCAT 60.360 61.111 0.00 0.00 0.00 4.40
79 80 1.973281 CAAGGCACGGTCAGGCATT 60.973 57.895 0.00 0.00 33.88 3.56
80 81 1.228552 AAGGCACGGTCAGGCATTT 60.229 52.632 0.00 0.00 28.42 2.32
81 82 1.526575 AAGGCACGGTCAGGCATTTG 61.527 55.000 0.00 0.00 28.42 2.32
82 83 2.568090 GCACGGTCAGGCATTTGG 59.432 61.111 0.00 0.00 0.00 3.28
83 84 2.268076 GCACGGTCAGGCATTTGGT 61.268 57.895 0.00 0.00 0.00 3.67
84 85 1.805428 GCACGGTCAGGCATTTGGTT 61.805 55.000 0.00 0.00 0.00 3.67
85 86 1.529226 CACGGTCAGGCATTTGGTTA 58.471 50.000 0.00 0.00 0.00 2.85
86 87 1.468520 CACGGTCAGGCATTTGGTTAG 59.531 52.381 0.00 0.00 0.00 2.34
87 88 0.451783 CGGTCAGGCATTTGGTTAGC 59.548 55.000 0.00 0.00 0.00 3.09
88 89 1.544724 GGTCAGGCATTTGGTTAGCA 58.455 50.000 0.00 0.00 0.00 3.49
89 90 1.474077 GGTCAGGCATTTGGTTAGCAG 59.526 52.381 0.00 0.00 0.00 4.24
90 91 2.436417 GTCAGGCATTTGGTTAGCAGA 58.564 47.619 0.00 0.00 0.00 4.26
91 92 2.819608 GTCAGGCATTTGGTTAGCAGAA 59.180 45.455 0.00 0.00 0.00 3.02
92 93 3.255642 GTCAGGCATTTGGTTAGCAGAAA 59.744 43.478 0.00 0.00 0.00 2.52
93 94 3.507233 TCAGGCATTTGGTTAGCAGAAAG 59.493 43.478 0.00 0.00 0.00 2.62
94 95 3.256631 CAGGCATTTGGTTAGCAGAAAGT 59.743 43.478 0.00 0.00 0.00 2.66
95 96 3.897505 AGGCATTTGGTTAGCAGAAAGTT 59.102 39.130 0.00 0.00 0.00 2.66
96 97 5.048083 CAGGCATTTGGTTAGCAGAAAGTTA 60.048 40.000 0.00 0.00 0.00 2.24
97 98 5.716703 AGGCATTTGGTTAGCAGAAAGTTAT 59.283 36.000 0.00 0.00 0.00 1.89
98 99 6.036470 GGCATTTGGTTAGCAGAAAGTTATC 58.964 40.000 0.00 0.00 0.00 1.75
99 100 6.127619 GGCATTTGGTTAGCAGAAAGTTATCT 60.128 38.462 0.00 0.00 0.00 1.98
100 101 7.067008 GGCATTTGGTTAGCAGAAAGTTATCTA 59.933 37.037 0.00 0.00 0.00 1.98
101 102 8.458843 GCATTTGGTTAGCAGAAAGTTATCTAA 58.541 33.333 0.00 0.00 0.00 2.10
102 103 9.774742 CATTTGGTTAGCAGAAAGTTATCTAAC 57.225 33.333 0.00 0.00 38.70 2.34
103 104 8.911918 TTTGGTTAGCAGAAAGTTATCTAACA 57.088 30.769 11.12 0.00 40.25 2.41
104 105 9.515226 TTTGGTTAGCAGAAAGTTATCTAACAT 57.485 29.630 11.12 0.00 40.25 2.71
105 106 9.515226 TTGGTTAGCAGAAAGTTATCTAACATT 57.485 29.630 11.12 0.00 40.25 2.71
106 107 9.515226 TGGTTAGCAGAAAGTTATCTAACATTT 57.485 29.630 11.12 1.51 40.25 2.32
107 108 9.774742 GGTTAGCAGAAAGTTATCTAACATTTG 57.225 33.333 11.12 0.00 40.25 2.32
108 109 9.278734 GTTAGCAGAAAGTTATCTAACATTTGC 57.721 33.333 10.66 10.66 39.04 3.68
109 110 7.452880 AGCAGAAAGTTATCTAACATTTGCA 57.547 32.000 16.41 0.00 38.62 4.08
110 111 7.533426 AGCAGAAAGTTATCTAACATTTGCAG 58.467 34.615 16.41 0.00 38.62 4.41
111 112 7.175641 AGCAGAAAGTTATCTAACATTTGCAGT 59.824 33.333 16.41 0.00 38.62 4.40
112 113 7.483059 GCAGAAAGTTATCTAACATTTGCAGTC 59.517 37.037 12.42 0.00 38.62 3.51
113 114 7.689812 CAGAAAGTTATCTAACATTTGCAGTCG 59.310 37.037 3.15 0.00 38.62 4.18
114 115 7.602644 AGAAAGTTATCTAACATTTGCAGTCGA 59.397 33.333 3.15 0.00 38.62 4.20
115 116 7.667043 AAGTTATCTAACATTTGCAGTCGAA 57.333 32.000 3.15 0.00 38.62 3.71
116 117 7.667043 AGTTATCTAACATTTGCAGTCGAAA 57.333 32.000 3.15 0.00 38.62 3.46
117 118 7.743104 AGTTATCTAACATTTGCAGTCGAAAG 58.257 34.615 3.15 0.00 38.62 2.62
118 119 7.602644 AGTTATCTAACATTTGCAGTCGAAAGA 59.397 33.333 3.15 0.00 38.62 2.52
119 120 7.688578 GTTATCTAACATTTGCAGTCGAAAGAC 59.311 37.037 0.00 0.00 46.85 3.01
133 134 5.932619 TCGAAAGACCTAGATTCATCCAA 57.067 39.130 0.00 0.00 33.31 3.53
134 135 5.661458 TCGAAAGACCTAGATTCATCCAAC 58.339 41.667 0.00 0.00 33.31 3.77
135 136 5.186992 TCGAAAGACCTAGATTCATCCAACA 59.813 40.000 0.00 0.00 33.31 3.33
136 137 5.521735 CGAAAGACCTAGATTCATCCAACAG 59.478 44.000 0.00 0.00 0.00 3.16
137 138 6.380079 AAAGACCTAGATTCATCCAACAGT 57.620 37.500 0.00 0.00 0.00 3.55
138 139 5.350504 AGACCTAGATTCATCCAACAGTG 57.649 43.478 0.00 0.00 0.00 3.66
139 140 5.026121 AGACCTAGATTCATCCAACAGTGA 58.974 41.667 0.00 0.00 0.00 3.41
140 141 5.664908 AGACCTAGATTCATCCAACAGTGAT 59.335 40.000 0.00 0.00 0.00 3.06
141 142 5.678583 ACCTAGATTCATCCAACAGTGATG 58.321 41.667 0.00 0.00 40.77 3.07
142 143 5.190528 ACCTAGATTCATCCAACAGTGATGT 59.809 40.000 0.00 0.00 40.38 3.06
143 144 6.384015 ACCTAGATTCATCCAACAGTGATGTA 59.616 38.462 0.00 0.00 40.38 2.29
144 145 7.071698 ACCTAGATTCATCCAACAGTGATGTAT 59.928 37.037 0.00 0.00 40.38 2.29
145 146 7.935755 CCTAGATTCATCCAACAGTGATGTATT 59.064 37.037 0.00 0.00 40.38 1.89
146 147 7.563888 AGATTCATCCAACAGTGATGTATTG 57.436 36.000 0.00 0.00 40.38 1.90
147 148 6.544931 AGATTCATCCAACAGTGATGTATTGG 59.455 38.462 0.00 0.00 42.55 3.16
148 149 3.947196 TCATCCAACAGTGATGTATTGGC 59.053 43.478 0.00 0.00 41.22 4.52
149 150 3.431673 TCCAACAGTGATGTATTGGCA 57.568 42.857 0.00 0.00 41.22 4.92
150 151 3.081061 TCCAACAGTGATGTATTGGCAC 58.919 45.455 0.00 0.00 41.22 5.01
151 152 2.159531 CCAACAGTGATGTATTGGCACG 60.160 50.000 0.00 0.00 35.52 5.34
152 153 2.741517 CAACAGTGATGTATTGGCACGA 59.258 45.455 0.00 0.00 37.60 4.35
153 154 3.266510 ACAGTGATGTATTGGCACGAT 57.733 42.857 0.00 0.00 37.60 3.73
154 155 3.609853 ACAGTGATGTATTGGCACGATT 58.390 40.909 0.00 0.00 37.60 3.34
155 156 4.009675 ACAGTGATGTATTGGCACGATTT 58.990 39.130 0.00 0.00 37.60 2.17
156 157 4.458989 ACAGTGATGTATTGGCACGATTTT 59.541 37.500 0.00 0.00 37.60 1.82
157 158 5.645929 ACAGTGATGTATTGGCACGATTTTA 59.354 36.000 0.00 0.00 37.60 1.52
158 159 6.150307 ACAGTGATGTATTGGCACGATTTTAA 59.850 34.615 0.00 0.00 37.60 1.52
159 160 7.026562 CAGTGATGTATTGGCACGATTTTAAA 58.973 34.615 0.00 0.00 37.60 1.52
160 161 7.540400 CAGTGATGTATTGGCACGATTTTAAAA 59.460 33.333 2.51 2.51 37.60 1.52
161 162 8.250332 AGTGATGTATTGGCACGATTTTAAAAT 58.750 29.630 13.24 13.24 37.60 1.82
162 163 8.868916 GTGATGTATTGGCACGATTTTAAAATT 58.131 29.630 14.45 0.00 0.00 1.82
166 167 9.915629 TGTATTGGCACGATTTTAAAATTAAGT 57.084 25.926 14.45 11.88 0.00 2.24
168 169 7.876896 TTGGCACGATTTTAAAATTAAGTCC 57.123 32.000 14.45 15.44 0.00 3.85
169 170 7.222000 TGGCACGATTTTAAAATTAAGTCCT 57.778 32.000 14.45 0.00 0.00 3.85
170 171 7.309920 TGGCACGATTTTAAAATTAAGTCCTC 58.690 34.615 14.45 0.01 0.00 3.71
171 172 7.175990 TGGCACGATTTTAAAATTAAGTCCTCT 59.824 33.333 14.45 0.00 0.00 3.69
172 173 8.027189 GGCACGATTTTAAAATTAAGTCCTCTT 58.973 33.333 14.45 0.00 37.65 2.85
173 174 8.850452 GCACGATTTTAAAATTAAGTCCTCTTG 58.150 33.333 14.45 5.68 35.36 3.02
189 190 7.897575 GTCCTCTTGACACCAATATCATATC 57.102 40.000 0.00 0.00 43.85 1.63
190 191 7.445121 GTCCTCTTGACACCAATATCATATCA 58.555 38.462 0.00 0.00 43.85 2.15
191 192 8.099537 GTCCTCTTGACACCAATATCATATCAT 58.900 37.037 0.00 0.00 43.85 2.45
192 193 9.325248 TCCTCTTGACACCAATATCATATCATA 57.675 33.333 0.00 0.00 0.00 2.15
209 210 9.927668 TCATATCATATTGAGTAAATGCTTCGA 57.072 29.630 0.00 0.00 0.00 3.71
210 211 9.964253 CATATCATATTGAGTAAATGCTTCGAC 57.036 33.333 0.00 0.00 0.00 4.20
211 212 6.844696 TCATATTGAGTAAATGCTTCGACC 57.155 37.500 0.00 0.00 0.00 4.79
212 213 5.462068 TCATATTGAGTAAATGCTTCGACCG 59.538 40.000 0.00 0.00 0.00 4.79
213 214 2.004583 TGAGTAAATGCTTCGACCGG 57.995 50.000 0.00 0.00 0.00 5.28
214 215 1.274167 TGAGTAAATGCTTCGACCGGT 59.726 47.619 6.92 6.92 0.00 5.28
215 216 2.289195 TGAGTAAATGCTTCGACCGGTT 60.289 45.455 9.42 0.00 0.00 4.44
216 217 3.056678 TGAGTAAATGCTTCGACCGGTTA 60.057 43.478 9.42 0.00 0.00 2.85
217 218 3.256558 AGTAAATGCTTCGACCGGTTAC 58.743 45.455 9.42 3.60 0.00 2.50
218 219 2.467566 AAATGCTTCGACCGGTTACT 57.532 45.000 9.42 0.00 0.00 2.24
219 220 2.005971 AATGCTTCGACCGGTTACTC 57.994 50.000 9.42 0.00 0.00 2.59
220 221 0.892755 ATGCTTCGACCGGTTACTCA 59.107 50.000 9.42 4.13 0.00 3.41
221 222 0.675083 TGCTTCGACCGGTTACTCAA 59.325 50.000 9.42 0.00 0.00 3.02
222 223 1.068895 TGCTTCGACCGGTTACTCAAA 59.931 47.619 9.42 0.00 0.00 2.69
223 224 2.137523 GCTTCGACCGGTTACTCAAAA 58.862 47.619 9.42 0.00 0.00 2.44
224 225 2.545106 GCTTCGACCGGTTACTCAAAAA 59.455 45.455 9.42 0.00 0.00 1.94
243 244 2.317530 AACCAAATAGAGAGAGGCGC 57.682 50.000 0.00 0.00 0.00 6.53
244 245 1.490574 ACCAAATAGAGAGAGGCGCT 58.509 50.000 7.64 0.00 0.00 5.92
245 246 1.137872 ACCAAATAGAGAGAGGCGCTG 59.862 52.381 7.64 0.00 0.00 5.18
246 247 1.410517 CCAAATAGAGAGAGGCGCTGA 59.589 52.381 7.64 0.00 0.00 4.26
247 248 2.036992 CCAAATAGAGAGAGGCGCTGAT 59.963 50.000 7.64 0.00 0.00 2.90
248 249 3.256879 CCAAATAGAGAGAGGCGCTGATA 59.743 47.826 7.64 0.00 0.00 2.15
249 250 4.081752 CCAAATAGAGAGAGGCGCTGATAT 60.082 45.833 7.64 0.00 0.00 1.63
250 251 5.477510 CAAATAGAGAGAGGCGCTGATATT 58.522 41.667 7.64 0.40 0.00 1.28
251 252 5.736951 AATAGAGAGAGGCGCTGATATTT 57.263 39.130 7.64 0.00 0.00 1.40
252 253 5.736951 ATAGAGAGAGGCGCTGATATTTT 57.263 39.130 7.64 0.00 0.00 1.82
253 254 3.988819 AGAGAGAGGCGCTGATATTTTC 58.011 45.455 7.64 0.00 0.00 2.29
254 255 3.640967 AGAGAGAGGCGCTGATATTTTCT 59.359 43.478 7.64 0.00 0.00 2.52
255 256 4.830046 AGAGAGAGGCGCTGATATTTTCTA 59.170 41.667 7.64 0.00 0.00 2.10
256 257 5.303078 AGAGAGAGGCGCTGATATTTTCTAA 59.697 40.000 7.64 0.00 0.00 2.10
257 258 5.293560 AGAGAGGCGCTGATATTTTCTAAC 58.706 41.667 7.64 0.00 0.00 2.34
258 259 5.023533 AGAGGCGCTGATATTTTCTAACA 57.976 39.130 7.64 0.00 0.00 2.41
259 260 5.053145 AGAGGCGCTGATATTTTCTAACAG 58.947 41.667 7.64 0.00 0.00 3.16
260 261 3.561725 AGGCGCTGATATTTTCTAACAGC 59.438 43.478 7.64 0.00 46.69 4.40
264 265 5.429957 GCTGATATTTTCTAACAGCCCTG 57.570 43.478 0.00 0.00 45.19 4.45
265 266 4.261363 GCTGATATTTTCTAACAGCCCTGC 60.261 45.833 0.00 0.00 45.19 4.85
266 267 3.876914 TGATATTTTCTAACAGCCCTGCG 59.123 43.478 0.00 0.00 0.00 5.18
267 268 0.811281 ATTTTCTAACAGCCCTGCGC 59.189 50.000 0.00 0.00 37.98 6.09
300 301 1.009829 GAAGCGCCAATACAGTCAGG 58.990 55.000 2.29 0.00 0.00 3.86
362 363 4.414337 AGACCTAGATTCATCCAACAGC 57.586 45.455 0.00 0.00 0.00 4.40
413 414 3.003482 GCAGCTCATCTTTAGCCATCAAG 59.997 47.826 0.00 0.00 41.02 3.02
434 435 1.072332 TGTCACGGTGACCCCATTG 59.928 57.895 31.93 0.00 46.40 2.82
521 526 6.402226 CGATCGACGATGAGTAGGAAATATCA 60.402 42.308 16.49 0.00 45.77 2.15
522 527 5.998553 TCGACGATGAGTAGGAAATATCAC 58.001 41.667 0.00 0.00 0.00 3.06
524 529 4.547532 ACGATGAGTAGGAAATATCACGC 58.452 43.478 0.00 0.00 0.00 5.34
568 786 4.992381 AAATCAGTGTTGCGAGTTACTC 57.008 40.909 1.64 1.64 0.00 2.59
569 787 2.433868 TCAGTGTTGCGAGTTACTCC 57.566 50.000 6.80 0.63 0.00 3.85
572 790 3.762288 TCAGTGTTGCGAGTTACTCCTAT 59.238 43.478 6.80 0.00 0.00 2.57
658 973 4.970392 CGTAACCTACGTGTGGCA 57.030 55.556 0.00 0.00 46.41 4.92
870 1190 1.265568 CGCGTGTACAAATACGAGCT 58.734 50.000 7.69 0.00 42.22 4.09
873 1193 1.844357 CGTGTACAAATACGAGCTCCG 59.156 52.381 8.47 6.07 42.22 4.63
876 1196 2.117910 GTACAAATACGAGCTCCGAGC 58.882 52.381 12.80 12.80 42.84 5.03
886 1206 2.438614 CTCCGAGCAGAGGACCGA 60.439 66.667 0.00 0.00 33.58 4.69
911 1232 4.534401 GGTGTCATAACCGGGAGC 57.466 61.111 6.32 0.00 0.00 4.70
1354 1714 1.467678 CCTCTGCCGGGACATCTAGG 61.468 65.000 2.18 0.00 0.00 3.02
1413 1777 1.608025 CGGCTTACTGCTTGGTCTTGA 60.608 52.381 0.00 0.00 42.39 3.02
1459 1824 3.526899 TCTGTATTGACCTTCCCTTCCA 58.473 45.455 0.00 0.00 0.00 3.53
1463 1834 0.039618 TTGACCTTCCCTTCCATGGC 59.960 55.000 6.96 0.00 0.00 4.40
1487 1858 4.707448 TCTCGATCTTTTTCCTCTGCTACT 59.293 41.667 0.00 0.00 0.00 2.57
1491 1862 2.371841 TCTTTTTCCTCTGCTACTGCCA 59.628 45.455 0.00 0.00 38.71 4.92
1501 1876 3.960755 TCTGCTACTGCCACTGTATGTAT 59.039 43.478 0.00 0.00 38.71 2.29
1502 1877 4.053983 CTGCTACTGCCACTGTATGTATG 58.946 47.826 0.00 0.00 38.71 2.39
1503 1878 2.802816 GCTACTGCCACTGTATGTATGC 59.197 50.000 0.00 0.00 0.00 3.14
1504 1879 3.493350 GCTACTGCCACTGTATGTATGCT 60.493 47.826 0.00 0.00 0.00 3.79
1558 1933 1.170919 CCCGTGTATCCGGTCGATCT 61.171 60.000 0.00 0.00 46.66 2.75
1651 2031 2.291741 ACTCCTTTCTTCTTTGCTTGCG 59.708 45.455 0.00 0.00 0.00 4.85
1663 2043 2.975410 TGCTTGCGAACTTTGATCTG 57.025 45.000 0.00 0.00 0.00 2.90
1686 2066 6.198687 TGCTACAAATATTTAGCATGCGAAC 58.801 36.000 17.76 0.00 44.55 3.95
1688 2068 5.229921 ACAAATATTTAGCATGCGAACGT 57.770 34.783 13.14 7.68 0.00 3.99
1699 2079 3.606153 GCATGCGAACGTAAACTTCAGTT 60.606 43.478 0.00 0.00 40.50 3.16
1702 2082 5.715429 TGCGAACGTAAACTTCAGTTAAA 57.285 34.783 0.00 0.00 37.25 1.52
1746 2126 6.073058 TGTTTGTTCATGCTTCAGATAGACAC 60.073 38.462 0.00 0.00 0.00 3.67
1758 2138 2.234908 AGATAGACACACCAGCCTGTTC 59.765 50.000 0.00 0.00 0.00 3.18
1774 2154 2.414481 CTGTTCGTTCAGGCTTCAGATG 59.586 50.000 0.00 0.00 0.00 2.90
1776 2158 0.976641 TCGTTCAGGCTTCAGATGGT 59.023 50.000 0.00 0.00 0.00 3.55
1783 2165 2.095567 CAGGCTTCAGATGGTCAAAACG 60.096 50.000 0.00 0.00 0.00 3.60
1787 2169 3.496884 GCTTCAGATGGTCAAAACGTACA 59.503 43.478 0.00 0.00 0.00 2.90
1789 2171 5.412526 TTCAGATGGTCAAAACGTACAAC 57.587 39.130 0.00 0.00 0.00 3.32
1842 2227 3.181456 ATCAGGTTTGATGCTCCTAGAGC 60.181 47.826 9.65 9.65 44.32 4.09
1994 2387 2.702478 TGTGGTTTTCATTGCCCATCAA 59.298 40.909 0.00 0.00 39.32 2.57
1995 2388 3.135348 TGTGGTTTTCATTGCCCATCAAA 59.865 39.130 0.00 0.00 38.34 2.69
1996 2389 3.747529 GTGGTTTTCATTGCCCATCAAAG 59.252 43.478 0.00 0.00 38.34 2.77
1997 2390 2.743664 GGTTTTCATTGCCCATCAAAGC 59.256 45.455 0.00 0.00 38.34 3.51
1998 2391 3.401182 GTTTTCATTGCCCATCAAAGCA 58.599 40.909 0.00 0.00 38.34 3.91
2028 2424 0.531753 CGATCACCACACCACACACA 60.532 55.000 0.00 0.00 0.00 3.72
2069 2465 6.019881 GCAAAACAACCGATAATAATTGCCTC 60.020 38.462 0.00 0.00 35.76 4.70
2070 2466 7.257722 CAAAACAACCGATAATAATTGCCTCT 58.742 34.615 0.00 0.00 0.00 3.69
2071 2467 6.619801 AACAACCGATAATAATTGCCTCTC 57.380 37.500 0.00 0.00 0.00 3.20
2072 2468 5.930135 ACAACCGATAATAATTGCCTCTCT 58.070 37.500 0.00 0.00 0.00 3.10
2073 2469 6.357367 ACAACCGATAATAATTGCCTCTCTT 58.643 36.000 0.00 0.00 0.00 2.85
2074 2470 6.828785 ACAACCGATAATAATTGCCTCTCTTT 59.171 34.615 0.00 0.00 0.00 2.52
2075 2471 7.339466 ACAACCGATAATAATTGCCTCTCTTTT 59.661 33.333 0.00 0.00 0.00 2.27
2076 2472 7.497925 ACCGATAATAATTGCCTCTCTTTTC 57.502 36.000 0.00 0.00 0.00 2.29
2077 2473 7.283329 ACCGATAATAATTGCCTCTCTTTTCT 58.717 34.615 0.00 0.00 0.00 2.52
2078 2474 7.442666 ACCGATAATAATTGCCTCTCTTTTCTC 59.557 37.037 0.00 0.00 0.00 2.87
2079 2475 7.095017 CCGATAATAATTGCCTCTCTTTTCTCC 60.095 40.741 0.00 0.00 0.00 3.71
2109 2505 7.515514 ACCAATATCTATCTTGACAATCTCCCT 59.484 37.037 0.00 0.00 0.00 4.20
2124 2520 0.250295 TCCCTTGAACCGCACTTCAG 60.250 55.000 0.00 0.00 31.76 3.02
2133 2529 1.204941 ACCGCACTTCAGCTAACCTAG 59.795 52.381 0.00 0.00 0.00 3.02
2134 2530 1.204941 CCGCACTTCAGCTAACCTAGT 59.795 52.381 0.00 0.00 0.00 2.57
2135 2531 2.426024 CCGCACTTCAGCTAACCTAGTA 59.574 50.000 0.00 0.00 0.00 1.82
2148 2544 5.520649 GCTAACCTAGTAAGATGACTGCAAC 59.479 44.000 0.00 0.00 0.00 4.17
2167 2563 0.739462 CGGCTGTCGACCAAGCAATA 60.739 55.000 24.24 0.00 42.43 1.90
2311 3341 0.178873 AAAGTAGGGTGAGGAGGCCA 60.179 55.000 5.01 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.690409 CGGTACAATCACATACCTCATGTAC 59.310 44.000 0.00 0.00 46.47 2.90
2 3 5.361571 ACGGTACAATCACATACCTCATGTA 59.638 40.000 0.00 0.00 46.47 2.29
4 5 4.507756 CACGGTACAATCACATACCTCATG 59.492 45.833 0.00 0.00 39.03 3.07
5 6 4.161565 ACACGGTACAATCACATACCTCAT 59.838 41.667 0.00 0.00 39.03 2.90
6 7 3.512329 ACACGGTACAATCACATACCTCA 59.488 43.478 0.00 0.00 39.03 3.86
8 9 4.546829 AACACGGTACAATCACATACCT 57.453 40.909 0.00 0.00 39.03 3.08
9 10 6.724694 TTTAACACGGTACAATCACATACC 57.275 37.500 0.00 0.00 37.99 2.73
12 13 6.621316 TGTTTTAACACGGTACAATCACAT 57.379 33.333 0.00 0.00 33.17 3.21
14 15 7.164662 GTCTTTGTTTTAACACGGTACAATCAC 59.835 37.037 0.00 0.00 38.92 3.06
17 18 7.086230 TGTCTTTGTTTTAACACGGTACAAT 57.914 32.000 0.00 0.00 38.92 2.71
19 20 6.315642 TGATGTCTTTGTTTTAACACGGTACA 59.684 34.615 0.00 0.00 38.92 2.90
23 24 4.668837 CGTGATGTCTTTGTTTTAACACGG 59.331 41.667 0.00 0.00 42.64 4.94
34 35 0.238289 GGTGGTGCGTGATGTCTTTG 59.762 55.000 0.00 0.00 0.00 2.77
38 39 3.118454 CGGGTGGTGCGTGATGTC 61.118 66.667 0.00 0.00 0.00 3.06
39 40 4.697756 CCGGGTGGTGCGTGATGT 62.698 66.667 0.00 0.00 0.00 3.06
56 57 4.329545 TGACCGTGCCTTGGCCTC 62.330 66.667 3.32 1.87 0.00 4.70
57 58 4.335647 CTGACCGTGCCTTGGCCT 62.336 66.667 3.32 0.00 0.00 5.19
60 61 3.925630 ATGCCTGACCGTGCCTTGG 62.926 63.158 0.00 0.00 0.00 3.61
61 62 1.526575 AAATGCCTGACCGTGCCTTG 61.527 55.000 0.00 0.00 0.00 3.61
62 63 1.228552 AAATGCCTGACCGTGCCTT 60.229 52.632 0.00 0.00 0.00 4.35
63 64 1.973281 CAAATGCCTGACCGTGCCT 60.973 57.895 0.00 0.00 0.00 4.75
64 65 2.568090 CAAATGCCTGACCGTGCC 59.432 61.111 0.00 0.00 0.00 5.01
65 66 1.805428 AACCAAATGCCTGACCGTGC 61.805 55.000 0.00 0.00 0.00 5.34
66 67 1.468520 CTAACCAAATGCCTGACCGTG 59.531 52.381 0.00 0.00 0.00 4.94
67 68 1.821216 CTAACCAAATGCCTGACCGT 58.179 50.000 0.00 0.00 0.00 4.83
68 69 0.451783 GCTAACCAAATGCCTGACCG 59.548 55.000 0.00 0.00 0.00 4.79
69 70 1.474077 CTGCTAACCAAATGCCTGACC 59.526 52.381 0.00 0.00 0.00 4.02
70 71 2.436417 TCTGCTAACCAAATGCCTGAC 58.564 47.619 0.00 0.00 0.00 3.51
71 72 2.877097 TCTGCTAACCAAATGCCTGA 57.123 45.000 0.00 0.00 0.00 3.86
72 73 3.256631 ACTTTCTGCTAACCAAATGCCTG 59.743 43.478 0.00 0.00 0.00 4.85
73 74 3.500343 ACTTTCTGCTAACCAAATGCCT 58.500 40.909 0.00 0.00 0.00 4.75
74 75 3.942130 ACTTTCTGCTAACCAAATGCC 57.058 42.857 0.00 0.00 0.00 4.40
75 76 6.856895 AGATAACTTTCTGCTAACCAAATGC 58.143 36.000 0.00 0.00 0.00 3.56
76 77 9.774742 GTTAGATAACTTTCTGCTAACCAAATG 57.225 33.333 0.00 0.00 36.53 2.32
77 78 9.515226 TGTTAGATAACTTTCTGCTAACCAAAT 57.485 29.630 0.00 0.00 39.87 2.32
78 79 8.911918 TGTTAGATAACTTTCTGCTAACCAAA 57.088 30.769 0.00 0.00 39.87 3.28
79 80 9.515226 AATGTTAGATAACTTTCTGCTAACCAA 57.485 29.630 0.00 0.00 39.87 3.67
80 81 9.515226 AAATGTTAGATAACTTTCTGCTAACCA 57.485 29.630 0.00 0.00 39.87 3.67
81 82 9.774742 CAAATGTTAGATAACTTTCTGCTAACC 57.225 33.333 0.00 0.00 39.87 2.85
82 83 9.278734 GCAAATGTTAGATAACTTTCTGCTAAC 57.721 33.333 18.24 0.00 40.59 2.34
83 84 9.008965 TGCAAATGTTAGATAACTTTCTGCTAA 57.991 29.630 21.57 0.00 37.68 3.09
84 85 8.560355 TGCAAATGTTAGATAACTTTCTGCTA 57.440 30.769 21.57 14.07 37.68 3.49
85 86 7.175641 ACTGCAAATGTTAGATAACTTTCTGCT 59.824 33.333 21.57 11.69 37.68 4.24
86 87 7.308435 ACTGCAAATGTTAGATAACTTTCTGC 58.692 34.615 18.44 18.44 37.55 4.26
87 88 7.689812 CGACTGCAAATGTTAGATAACTTTCTG 59.310 37.037 4.50 6.69 37.12 3.02
88 89 7.602644 TCGACTGCAAATGTTAGATAACTTTCT 59.397 33.333 4.50 0.00 37.12 2.52
89 90 7.739295 TCGACTGCAAATGTTAGATAACTTTC 58.261 34.615 4.50 0.00 37.12 2.62
90 91 7.667043 TCGACTGCAAATGTTAGATAACTTT 57.333 32.000 4.50 1.92 37.12 2.66
91 92 7.667043 TTCGACTGCAAATGTTAGATAACTT 57.333 32.000 4.50 0.00 37.12 2.66
92 93 7.602644 TCTTTCGACTGCAAATGTTAGATAACT 59.397 33.333 4.50 0.00 37.12 2.24
93 94 7.688578 GTCTTTCGACTGCAAATGTTAGATAAC 59.311 37.037 0.00 0.00 37.19 1.89
94 95 7.148474 GGTCTTTCGACTGCAAATGTTAGATAA 60.148 37.037 0.00 0.00 40.10 1.75
95 96 6.312918 GGTCTTTCGACTGCAAATGTTAGATA 59.687 38.462 0.00 0.00 40.10 1.98
96 97 5.122396 GGTCTTTCGACTGCAAATGTTAGAT 59.878 40.000 0.00 0.00 40.10 1.98
97 98 4.451096 GGTCTTTCGACTGCAAATGTTAGA 59.549 41.667 0.00 0.00 40.10 2.10
98 99 4.452455 AGGTCTTTCGACTGCAAATGTTAG 59.548 41.667 0.00 0.00 40.10 2.34
99 100 4.385825 AGGTCTTTCGACTGCAAATGTTA 58.614 39.130 0.00 0.00 40.10 2.41
100 101 3.214328 AGGTCTTTCGACTGCAAATGTT 58.786 40.909 0.00 0.00 40.10 2.71
101 102 2.851195 AGGTCTTTCGACTGCAAATGT 58.149 42.857 0.00 0.00 40.10 2.71
102 103 4.245660 TCTAGGTCTTTCGACTGCAAATG 58.754 43.478 0.00 0.00 40.10 2.32
103 104 4.537135 TCTAGGTCTTTCGACTGCAAAT 57.463 40.909 0.00 0.00 40.10 2.32
104 105 4.537135 ATCTAGGTCTTTCGACTGCAAA 57.463 40.909 0.00 0.00 40.10 3.68
105 106 4.021456 TGAATCTAGGTCTTTCGACTGCAA 60.021 41.667 0.00 0.00 40.10 4.08
106 107 3.509967 TGAATCTAGGTCTTTCGACTGCA 59.490 43.478 0.00 0.00 40.10 4.41
107 108 4.111375 TGAATCTAGGTCTTTCGACTGC 57.889 45.455 0.00 0.00 40.10 4.40
108 109 5.163509 TGGATGAATCTAGGTCTTTCGACTG 60.164 44.000 0.00 0.00 40.10 3.51
109 110 4.956700 TGGATGAATCTAGGTCTTTCGACT 59.043 41.667 0.00 0.00 40.10 4.18
110 111 5.263968 TGGATGAATCTAGGTCTTTCGAC 57.736 43.478 0.00 0.00 39.49 4.20
111 112 5.186992 TGTTGGATGAATCTAGGTCTTTCGA 59.813 40.000 0.00 0.00 0.00 3.71
112 113 5.419542 TGTTGGATGAATCTAGGTCTTTCG 58.580 41.667 0.00 0.00 0.00 3.46
113 114 6.314896 CACTGTTGGATGAATCTAGGTCTTTC 59.685 42.308 0.00 0.00 0.00 2.62
114 115 6.013379 TCACTGTTGGATGAATCTAGGTCTTT 60.013 38.462 0.00 0.00 0.00 2.52
115 116 5.485353 TCACTGTTGGATGAATCTAGGTCTT 59.515 40.000 0.00 0.00 0.00 3.01
116 117 5.026121 TCACTGTTGGATGAATCTAGGTCT 58.974 41.667 0.00 0.00 0.00 3.85
117 118 5.344743 TCACTGTTGGATGAATCTAGGTC 57.655 43.478 0.00 0.00 0.00 3.85
118 119 5.190528 ACATCACTGTTGGATGAATCTAGGT 59.809 40.000 13.24 0.00 43.80 3.08
119 120 5.678583 ACATCACTGTTGGATGAATCTAGG 58.321 41.667 13.24 0.00 43.80 3.02
120 121 8.771766 CAATACATCACTGTTGGATGAATCTAG 58.228 37.037 13.24 0.00 43.80 2.43
121 122 7.716560 CCAATACATCACTGTTGGATGAATCTA 59.283 37.037 13.24 0.00 43.80 1.98
122 123 6.544931 CCAATACATCACTGTTGGATGAATCT 59.455 38.462 13.24 0.00 43.80 2.40
123 124 6.732154 CCAATACATCACTGTTGGATGAATC 58.268 40.000 13.24 0.00 43.80 2.52
124 125 5.068198 GCCAATACATCACTGTTGGATGAAT 59.932 40.000 13.24 0.00 43.80 2.57
125 126 4.398988 GCCAATACATCACTGTTGGATGAA 59.601 41.667 13.24 0.00 43.80 2.57
126 127 3.947196 GCCAATACATCACTGTTGGATGA 59.053 43.478 13.24 0.91 43.80 2.92
127 128 3.695556 TGCCAATACATCACTGTTGGATG 59.304 43.478 7.14 6.58 45.93 3.51
128 129 3.696051 GTGCCAATACATCACTGTTGGAT 59.304 43.478 7.14 0.00 35.94 3.41
129 130 3.081061 GTGCCAATACATCACTGTTGGA 58.919 45.455 7.14 0.00 35.94 3.53
130 131 2.159531 CGTGCCAATACATCACTGTTGG 60.160 50.000 0.00 0.00 36.66 3.77
131 132 2.741517 TCGTGCCAATACATCACTGTTG 59.258 45.455 0.00 0.00 36.79 3.33
132 133 3.052455 TCGTGCCAATACATCACTGTT 57.948 42.857 0.00 0.00 36.79 3.16
133 134 2.760634 TCGTGCCAATACATCACTGT 57.239 45.000 0.00 0.00 39.49 3.55
134 135 4.621068 AAATCGTGCCAATACATCACTG 57.379 40.909 0.00 0.00 0.00 3.66
135 136 6.751514 TTAAAATCGTGCCAATACATCACT 57.248 33.333 0.00 0.00 0.00 3.41
136 137 7.804614 TTTTAAAATCGTGCCAATACATCAC 57.195 32.000 0.00 0.00 0.00 3.06
137 138 8.994429 AATTTTAAAATCGTGCCAATACATCA 57.006 26.923 13.68 0.00 0.00 3.07
140 141 9.915629 ACTTAATTTTAAAATCGTGCCAATACA 57.084 25.926 13.68 0.00 0.00 2.29
142 143 9.575783 GGACTTAATTTTAAAATCGTGCCAATA 57.424 29.630 13.68 0.00 0.00 1.90
143 144 8.311109 AGGACTTAATTTTAAAATCGTGCCAAT 58.689 29.630 13.68 0.00 0.00 3.16
144 145 7.662897 AGGACTTAATTTTAAAATCGTGCCAA 58.337 30.769 13.68 2.18 0.00 4.52
145 146 7.175990 AGAGGACTTAATTTTAAAATCGTGCCA 59.824 33.333 13.68 0.00 0.00 4.92
146 147 7.535997 AGAGGACTTAATTTTAAAATCGTGCC 58.464 34.615 13.68 11.33 0.00 5.01
147 148 8.850452 CAAGAGGACTTAATTTTAAAATCGTGC 58.150 33.333 13.68 14.71 34.70 5.34
166 167 7.616528 TGATATGATATTGGTGTCAAGAGGA 57.383 36.000 0.00 0.00 36.19 3.71
183 184 9.927668 TCGAAGCATTTACTCAATATGATATGA 57.072 29.630 0.00 0.00 0.00 2.15
184 185 9.964253 GTCGAAGCATTTACTCAATATGATATG 57.036 33.333 0.00 0.00 0.00 1.78
185 186 9.155975 GGTCGAAGCATTTACTCAATATGATAT 57.844 33.333 0.00 0.00 0.00 1.63
186 187 7.328493 CGGTCGAAGCATTTACTCAATATGATA 59.672 37.037 0.00 0.00 0.00 2.15
187 188 6.146184 CGGTCGAAGCATTTACTCAATATGAT 59.854 38.462 0.00 0.00 0.00 2.45
188 189 5.462068 CGGTCGAAGCATTTACTCAATATGA 59.538 40.000 0.00 0.00 0.00 2.15
189 190 5.333339 CCGGTCGAAGCATTTACTCAATATG 60.333 44.000 0.00 0.00 0.00 1.78
190 191 4.750098 CCGGTCGAAGCATTTACTCAATAT 59.250 41.667 0.00 0.00 0.00 1.28
191 192 4.116961 CCGGTCGAAGCATTTACTCAATA 58.883 43.478 0.00 0.00 0.00 1.90
192 193 2.936498 CCGGTCGAAGCATTTACTCAAT 59.064 45.455 0.00 0.00 0.00 2.57
193 194 2.289195 ACCGGTCGAAGCATTTACTCAA 60.289 45.455 0.00 0.00 0.00 3.02
194 195 1.274167 ACCGGTCGAAGCATTTACTCA 59.726 47.619 0.00 0.00 0.00 3.41
195 196 2.005971 ACCGGTCGAAGCATTTACTC 57.994 50.000 0.00 0.00 0.00 2.59
196 197 2.467566 AACCGGTCGAAGCATTTACT 57.532 45.000 8.04 0.00 0.00 2.24
197 198 3.256558 AGTAACCGGTCGAAGCATTTAC 58.743 45.455 8.04 3.01 0.00 2.01
198 199 3.056678 TGAGTAACCGGTCGAAGCATTTA 60.057 43.478 8.04 0.00 0.00 1.40
199 200 2.289195 TGAGTAACCGGTCGAAGCATTT 60.289 45.455 8.04 0.00 0.00 2.32
200 201 1.274167 TGAGTAACCGGTCGAAGCATT 59.726 47.619 8.04 0.00 0.00 3.56
201 202 0.892755 TGAGTAACCGGTCGAAGCAT 59.107 50.000 8.04 0.00 0.00 3.79
202 203 0.675083 TTGAGTAACCGGTCGAAGCA 59.325 50.000 8.04 0.00 0.00 3.91
203 204 1.787012 TTTGAGTAACCGGTCGAAGC 58.213 50.000 8.04 0.00 0.00 3.86
221 222 3.440522 GCGCCTCTCTCTATTTGGTTTTT 59.559 43.478 0.00 0.00 0.00 1.94
222 223 3.010420 GCGCCTCTCTCTATTTGGTTTT 58.990 45.455 0.00 0.00 0.00 2.43
223 224 2.237392 AGCGCCTCTCTCTATTTGGTTT 59.763 45.455 2.29 0.00 0.00 3.27
224 225 1.834263 AGCGCCTCTCTCTATTTGGTT 59.166 47.619 2.29 0.00 0.00 3.67
225 226 1.137872 CAGCGCCTCTCTCTATTTGGT 59.862 52.381 2.29 0.00 0.00 3.67
226 227 1.410517 TCAGCGCCTCTCTCTATTTGG 59.589 52.381 2.29 0.00 0.00 3.28
227 228 2.879002 TCAGCGCCTCTCTCTATTTG 57.121 50.000 2.29 0.00 0.00 2.32
228 229 5.736951 AATATCAGCGCCTCTCTCTATTT 57.263 39.130 2.29 0.00 0.00 1.40
229 230 5.736951 AAATATCAGCGCCTCTCTCTATT 57.263 39.130 2.29 0.00 0.00 1.73
230 231 5.480073 AGAAAATATCAGCGCCTCTCTCTAT 59.520 40.000 2.29 0.00 0.00 1.98
231 232 4.830046 AGAAAATATCAGCGCCTCTCTCTA 59.170 41.667 2.29 0.00 0.00 2.43
232 233 3.640967 AGAAAATATCAGCGCCTCTCTCT 59.359 43.478 2.29 0.00 0.00 3.10
233 234 3.988819 AGAAAATATCAGCGCCTCTCTC 58.011 45.455 2.29 0.00 0.00 3.20
234 235 5.163405 TGTTAGAAAATATCAGCGCCTCTCT 60.163 40.000 2.29 0.00 0.00 3.10
235 236 5.050490 TGTTAGAAAATATCAGCGCCTCTC 58.950 41.667 2.29 0.00 0.00 3.20
236 237 5.023533 TGTTAGAAAATATCAGCGCCTCT 57.976 39.130 2.29 0.00 0.00 3.69
237 238 4.319118 GCTGTTAGAAAATATCAGCGCCTC 60.319 45.833 2.29 0.00 41.15 4.70
238 239 3.561725 GCTGTTAGAAAATATCAGCGCCT 59.438 43.478 2.29 0.00 41.15 5.52
239 240 3.878245 GCTGTTAGAAAATATCAGCGCC 58.122 45.455 2.29 0.00 41.15 6.53
242 243 4.261363 GCAGGGCTGTTAGAAAATATCAGC 60.261 45.833 6.88 6.88 47.00 4.26
243 244 4.024556 CGCAGGGCTGTTAGAAAATATCAG 60.025 45.833 0.00 0.00 0.00 2.90
244 245 3.876914 CGCAGGGCTGTTAGAAAATATCA 59.123 43.478 0.00 0.00 0.00 2.15
245 246 3.304057 GCGCAGGGCTGTTAGAAAATATC 60.304 47.826 0.30 0.00 39.11 1.63
246 247 2.618709 GCGCAGGGCTGTTAGAAAATAT 59.381 45.455 0.30 0.00 39.11 1.28
247 248 2.014128 GCGCAGGGCTGTTAGAAAATA 58.986 47.619 0.30 0.00 39.11 1.40
248 249 0.811281 GCGCAGGGCTGTTAGAAAAT 59.189 50.000 0.30 0.00 39.11 1.82
249 250 2.253513 GCGCAGGGCTGTTAGAAAA 58.746 52.632 0.30 0.00 39.11 2.29
250 251 3.981308 GCGCAGGGCTGTTAGAAA 58.019 55.556 0.30 0.00 39.11 2.52
259 260 4.704833 TGGTTCAGAGCGCAGGGC 62.705 66.667 11.47 0.00 44.05 5.19
260 261 2.743928 GTGGTTCAGAGCGCAGGG 60.744 66.667 11.47 0.00 34.07 4.45
261 262 2.743928 GGTGGTTCAGAGCGCAGG 60.744 66.667 11.47 0.00 35.54 4.85
262 263 2.743928 GGGTGGTTCAGAGCGCAG 60.744 66.667 11.47 0.00 35.54 5.18
263 264 4.329545 GGGGTGGTTCAGAGCGCA 62.330 66.667 11.47 0.00 35.54 6.09
265 266 3.234630 TTCGGGGTGGTTCAGAGCG 62.235 63.158 0.00 0.00 0.00 5.03
266 267 1.376037 CTTCGGGGTGGTTCAGAGC 60.376 63.158 0.00 0.00 0.00 4.09
267 268 1.376037 GCTTCGGGGTGGTTCAGAG 60.376 63.158 0.00 0.00 0.00 3.35
268 269 2.747686 GCTTCGGGGTGGTTCAGA 59.252 61.111 0.00 0.00 0.00 3.27
269 270 2.742372 CGCTTCGGGGTGGTTCAG 60.742 66.667 0.00 0.00 0.00 3.02
300 301 7.158099 AGATAACTTTCTGGTAACCAAATGC 57.842 36.000 0.00 0.00 30.80 3.56
362 363 1.083489 TTTAAAGCTCCCGTGCATCG 58.917 50.000 0.00 0.00 39.52 3.84
509 511 4.396790 TGGGTTTTGCGTGATATTTCCTAC 59.603 41.667 0.00 0.00 0.00 3.18
521 526 1.959985 TGTTGATGATGGGTTTTGCGT 59.040 42.857 0.00 0.00 0.00 5.24
522 527 2.721274 TGTTGATGATGGGTTTTGCG 57.279 45.000 0.00 0.00 0.00 4.85
568 786 1.139853 GGGTCCTTGTCAGCTGATAGG 59.860 57.143 28.90 28.90 32.97 2.57
569 787 1.833630 TGGGTCCTTGTCAGCTGATAG 59.166 52.381 21.47 18.99 0.00 2.08
572 790 0.397941 CTTGGGTCCTTGTCAGCTGA 59.602 55.000 13.74 13.74 0.00 4.26
702 1022 1.958579 GGTGGTGGGAGTTTGTTAACC 59.041 52.381 2.48 0.00 34.71 2.85
870 1190 2.035155 TTCGGTCCTCTGCTCGGA 59.965 61.111 0.00 0.00 0.00 4.55
873 1193 2.185608 GCCTTCGGTCCTCTGCTC 59.814 66.667 0.00 0.00 0.00 4.26
886 1206 1.301954 GTTATGACACCGGGGCCTT 59.698 57.895 1.73 0.00 0.00 4.35
911 1232 1.370609 TCTAGTCAGTCCTCTTCGCG 58.629 55.000 0.00 0.00 0.00 5.87
1284 1644 4.586235 AACCTGCTGTGGCGCCTT 62.586 61.111 29.70 7.86 42.25 4.35
1413 1777 6.721318 TCAAGAAGCTAATTAACCAGGACAT 58.279 36.000 0.00 0.00 0.00 3.06
1459 1824 3.454082 AGAGGAAAAAGATCGAGAGCCAT 59.546 43.478 0.00 0.00 0.00 4.40
1463 1834 4.122143 AGCAGAGGAAAAAGATCGAGAG 57.878 45.455 0.00 0.00 0.00 3.20
1487 1858 1.210234 AGCAGCATACATACAGTGGCA 59.790 47.619 0.00 0.00 35.19 4.92
1491 1862 2.941064 CAAGCAGCAGCATACATACAGT 59.059 45.455 3.17 0.00 45.49 3.55
1558 1933 3.317406 AGGTATCACCCATCTACATGCA 58.683 45.455 0.00 0.00 39.75 3.96
1663 2043 5.336990 CGTTCGCATGCTAAATATTTGTAGC 59.663 40.000 17.13 12.60 42.56 3.58
1686 2066 7.245604 ACACAAAGGTTTAACTGAAGTTTACG 58.754 34.615 0.21 0.00 39.31 3.18
1688 2068 9.016438 AGAACACAAAGGTTTAACTGAAGTTTA 57.984 29.630 0.21 0.00 39.31 2.01
1699 2079 2.360801 GGCTGCAGAACACAAAGGTTTA 59.639 45.455 20.43 0.00 0.00 2.01
1702 2082 0.106519 AGGCTGCAGAACACAAAGGT 60.107 50.000 20.43 0.00 0.00 3.50
1746 2126 2.238353 CTGAACGAACAGGCTGGTG 58.762 57.895 20.34 9.82 34.64 4.17
1758 2138 1.338105 TGACCATCTGAAGCCTGAACG 60.338 52.381 0.00 0.00 0.00 3.95
1774 2154 1.671845 TGCTGGTTGTACGTTTTGACC 59.328 47.619 0.00 0.00 0.00 4.02
1776 2158 1.944024 CCTGCTGGTTGTACGTTTTGA 59.056 47.619 0.00 0.00 0.00 2.69
1837 2222 6.274908 TGGGTCTAGGATATTCTAGTGCTCTA 59.725 42.308 16.31 0.00 38.25 2.43
1838 2223 5.075205 TGGGTCTAGGATATTCTAGTGCTCT 59.925 44.000 16.31 0.00 38.25 4.09
1839 2224 5.326069 TGGGTCTAGGATATTCTAGTGCTC 58.674 45.833 16.31 11.52 38.25 4.26
1840 2225 5.162925 ACTGGGTCTAGGATATTCTAGTGCT 60.163 44.000 16.31 0.00 38.25 4.40
1842 2227 6.551601 ACAACTGGGTCTAGGATATTCTAGTG 59.448 42.308 16.31 8.88 38.25 2.74
1846 2231 5.131142 CCAACAACTGGGTCTAGGATATTCT 59.869 44.000 0.00 0.00 42.17 2.40
2028 2424 1.457823 TTGCGTCCGGTACAGTGTCT 61.458 55.000 0.00 0.00 0.00 3.41
2069 2465 5.760131 AGATATTGGTTGGGGAGAAAAGAG 58.240 41.667 0.00 0.00 0.00 2.85
2070 2466 5.796502 AGATATTGGTTGGGGAGAAAAGA 57.203 39.130 0.00 0.00 0.00 2.52
2071 2467 7.521669 AGATAGATATTGGTTGGGGAGAAAAG 58.478 38.462 0.00 0.00 0.00 2.27
2072 2468 7.465900 AGATAGATATTGGTTGGGGAGAAAA 57.534 36.000 0.00 0.00 0.00 2.29
2073 2469 7.128728 TCAAGATAGATATTGGTTGGGGAGAAA 59.871 37.037 0.00 0.00 30.40 2.52
2074 2470 6.619437 TCAAGATAGATATTGGTTGGGGAGAA 59.381 38.462 0.00 0.00 30.40 2.87
2075 2471 6.043243 GTCAAGATAGATATTGGTTGGGGAGA 59.957 42.308 0.00 0.00 30.40 3.71
2076 2472 6.183361 TGTCAAGATAGATATTGGTTGGGGAG 60.183 42.308 0.00 0.00 30.40 4.30
2077 2473 5.669904 TGTCAAGATAGATATTGGTTGGGGA 59.330 40.000 0.00 0.00 30.40 4.81
2078 2474 5.940617 TGTCAAGATAGATATTGGTTGGGG 58.059 41.667 0.00 0.00 30.40 4.96
2079 2475 7.941238 AGATTGTCAAGATAGATATTGGTTGGG 59.059 37.037 0.00 0.00 30.40 4.12
2109 2505 1.871039 GTTAGCTGAAGTGCGGTTCAA 59.129 47.619 0.00 0.00 36.01 2.69
2124 2520 5.263968 TGCAGTCATCTTACTAGGTTAGC 57.736 43.478 0.00 0.00 0.00 3.09
2133 2529 1.394917 CAGCCGTTGCAGTCATCTTAC 59.605 52.381 0.00 0.00 41.13 2.34
2134 2530 1.001974 ACAGCCGTTGCAGTCATCTTA 59.998 47.619 0.00 0.00 41.13 2.10
2135 2531 0.250467 ACAGCCGTTGCAGTCATCTT 60.250 50.000 0.00 0.00 41.13 2.40
2148 2544 0.739462 TATTGCTTGGTCGACAGCCG 60.739 55.000 21.23 7.12 40.25 5.52
2167 2563 3.619038 GCTGCTTAAAGACGCTAACTCAT 59.381 43.478 0.00 0.00 0.00 2.90
2298 3322 2.003548 AGGAATGGCCTCCTCACCC 61.004 63.158 7.75 0.00 46.97 4.61
2299 3323 1.225704 CAGGAATGGCCTCCTCACC 59.774 63.158 10.62 2.62 46.97 4.02
2300 3324 1.452833 GCAGGAATGGCCTCCTCAC 60.453 63.158 10.62 3.06 46.97 3.51
2301 3325 1.210204 AAGCAGGAATGGCCTCCTCA 61.210 55.000 10.62 0.00 46.97 3.86
2311 3341 3.054582 TCAGCATCAAGAGAAGCAGGAAT 60.055 43.478 0.00 0.00 40.78 3.01
2320 3350 1.003580 GGGTGGTTCAGCATCAAGAGA 59.996 52.381 0.00 0.00 33.07 3.10
2321 3351 1.004044 AGGGTGGTTCAGCATCAAGAG 59.996 52.381 0.00 0.00 33.07 2.85


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

AutoCloner maintained by Alex Coulton.