Multiple sequence alignment - TraesCS2D01G204700

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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 TraesCS2D01G204700 chr2D 100.000 4124 0 0 1 4124 156706471 156710594 0.000000e+00 7616.0
1 TraesCS2D01G204700 chr2D 91.101 2742 184 35 490 3218 182576391 182573697 0.000000e+00 3657.0
2 TraesCS2D01G204700 chr2D 94.214 2264 104 7 1010 3273 156592469 156594705 0.000000e+00 3430.0
3 TraesCS2D01G204700 chr2D 84.330 351 35 11 544 879 156591711 156592056 3.980000e-85 326.0
4 TraesCS2D01G204700 chr2A 96.358 3515 114 5 613 4124 166627709 166631212 0.000000e+00 5770.0
5 TraesCS2D01G204700 chr2A 91.336 2747 198 22 492 3218 197566683 197563957 0.000000e+00 3718.0
6 TraesCS2D01G204700 chr2A 88.081 1032 92 24 702 1720 197344832 197343819 0.000000e+00 1195.0
7 TraesCS2D01G204700 chr2A 86.217 341 29 9 551 879 166254140 166254474 1.820000e-93 353.0
8 TraesCS2D01G204700 chr2A 87.850 107 11 2 492 597 197345478 197345373 1.560000e-24 124.0
9 TraesCS2D01G204700 chr2A 88.764 89 4 2 407 489 166627494 166627582 2.030000e-18 104.0
10 TraesCS2D01G204700 chr2A 77.778 180 10 14 3097 3276 166256549 166256698 2.640000e-12 84.2
11 TraesCS2D01G204700 chr2B 94.468 3760 113 41 407 4124 214312334 214316040 0.000000e+00 5703.0
12 TraesCS2D01G204700 chr2B 92.474 2551 169 11 623 3161 214280766 214283305 0.000000e+00 3626.0
13 TraesCS2D01G204700 chr2B 94.505 182 9 1 216 396 214312112 214312293 3.140000e-71 279.0
14 TraesCS2D01G204700 chr2B 90.588 170 13 3 406 574 214280578 214280745 5.370000e-54 222.0
15 TraesCS2D01G204700 chr2B 94.444 54 1 2 338 390 214280405 214280457 9.500000e-12 82.4
16 TraesCS2D01G204700 chr1B 89.935 2762 196 44 534 3276 148416732 148414034 0.000000e+00 3485.0
17 TraesCS2D01G204700 chr1D 89.458 2770 209 44 534 3276 93105628 93102915 0.000000e+00 3421.0
18 TraesCS2D01G204700 chr1A 92.492 2211 157 4 960 3166 90163538 90161333 0.000000e+00 3155.0
19 TraesCS2D01G204700 chr1A 85.818 275 26 8 610 877 90163840 90163572 3.140000e-71 279.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G204700 chr2D 156706471 156710594 4123 False 7616.000000 7616 100.0000 1 4124 1 chr2D.!!$F1 4123
1 TraesCS2D01G204700 chr2D 182573697 182576391 2694 True 3657.000000 3657 91.1010 490 3218 1 chr2D.!!$R1 2728
2 TraesCS2D01G204700 chr2D 156591711 156594705 2994 False 1878.000000 3430 89.2720 544 3273 2 chr2D.!!$F2 2729
3 TraesCS2D01G204700 chr2A 197563957 197566683 2726 True 3718.000000 3718 91.3360 492 3218 1 chr2A.!!$R1 2726
4 TraesCS2D01G204700 chr2A 166627494 166631212 3718 False 2937.000000 5770 92.5610 407 4124 2 chr2A.!!$F2 3717
5 TraesCS2D01G204700 chr2A 197343819 197345478 1659 True 659.500000 1195 87.9655 492 1720 2 chr2A.!!$R2 1228
6 TraesCS2D01G204700 chr2A 166254140 166256698 2558 False 218.600000 353 81.9975 551 3276 2 chr2A.!!$F1 2725
7 TraesCS2D01G204700 chr2B 214312112 214316040 3928 False 2991.000000 5703 94.4865 216 4124 2 chr2B.!!$F2 3908
8 TraesCS2D01G204700 chr2B 214280405 214283305 2900 False 1310.133333 3626 92.5020 338 3161 3 chr2B.!!$F1 2823
9 TraesCS2D01G204700 chr1B 148414034 148416732 2698 True 3485.000000 3485 89.9350 534 3276 1 chr1B.!!$R1 2742
10 TraesCS2D01G204700 chr1D 93102915 93105628 2713 True 3421.000000 3421 89.4580 534 3276 1 chr1D.!!$R1 2742
11 TraesCS2D01G204700 chr1A 90161333 90163840 2507 True 1717.000000 3155 89.1550 610 3166 2 chr1A.!!$R1 2556

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
192 193 0.106519 AGCCACCAGACAAAGCACTT 60.107 50.0 0.0 0.0 0.0 3.16 F
193 194 0.312102 GCCACCAGACAAAGCACTTC 59.688 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1050 2092 4.760047 CCCCAGTTGAGCGGGTCG 62.760 72.222 2.41 0.0 41.3 4.79 R
3228 4298 4.000988 GCATCAACGTTTTAGAAGAGGGA 58.999 43.478 0.00 0.0 0.0 4.20 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
24 25 7.602517 TTCCCCGCAATAAAAATATGTTTTG 57.397 32.000 0.51 0.00 37.59 2.44
25 26 6.702329 TCCCCGCAATAAAAATATGTTTTGT 58.298 32.000 0.51 0.00 37.59 2.83
26 27 7.837863 TCCCCGCAATAAAAATATGTTTTGTA 58.162 30.769 0.51 0.00 37.59 2.41
27 28 8.311836 TCCCCGCAATAAAAATATGTTTTGTAA 58.688 29.630 0.51 0.00 37.59 2.41
28 29 9.103861 CCCCGCAATAAAAATATGTTTTGTAAT 57.896 29.630 0.51 0.00 37.59 1.89
71 72 9.851686 ATTCTACCTAATATCATTTTGCAGTCA 57.148 29.630 0.00 0.00 0.00 3.41
72 73 8.893219 TCTACCTAATATCATTTTGCAGTCAG 57.107 34.615 0.00 0.00 0.00 3.51
73 74 6.382869 ACCTAATATCATTTTGCAGTCAGC 57.617 37.500 0.00 0.00 45.96 4.26
83 84 3.963622 GCAGTCAGCATCTTTCGTG 57.036 52.632 0.00 0.00 44.79 4.35
84 85 0.179205 GCAGTCAGCATCTTTCGTGC 60.179 55.000 0.00 0.00 44.79 5.34
85 86 1.150827 CAGTCAGCATCTTTCGTGCA 58.849 50.000 0.69 0.00 44.87 4.57
86 87 1.532437 CAGTCAGCATCTTTCGTGCAA 59.468 47.619 0.00 0.00 44.87 4.08
87 88 2.161012 CAGTCAGCATCTTTCGTGCAAT 59.839 45.455 0.00 0.00 44.87 3.56
88 89 2.161012 AGTCAGCATCTTTCGTGCAATG 59.839 45.455 0.00 0.00 44.87 2.82
89 90 2.160219 GTCAGCATCTTTCGTGCAATGA 59.840 45.455 0.00 0.00 44.87 2.57
90 91 2.813172 TCAGCATCTTTCGTGCAATGAA 59.187 40.909 0.00 0.00 44.87 2.57
139 140 8.057812 GTGTATTACATGTACACGATTACTGG 57.942 38.462 13.16 0.00 41.53 4.00
140 141 7.703621 GTGTATTACATGTACACGATTACTGGT 59.296 37.037 13.16 0.00 41.53 4.00
141 142 8.252417 TGTATTACATGTACACGATTACTGGTT 58.748 33.333 4.68 0.00 0.00 3.67
142 143 9.734620 GTATTACATGTACACGATTACTGGTTA 57.265 33.333 4.68 0.00 0.00 2.85
145 146 9.955208 TTACATGTACACGATTACTGGTTATAG 57.045 33.333 4.68 0.00 0.00 1.31
146 147 8.229253 ACATGTACACGATTACTGGTTATAGA 57.771 34.615 0.00 0.00 0.00 1.98
147 148 8.689061 ACATGTACACGATTACTGGTTATAGAA 58.311 33.333 0.00 0.00 0.00 2.10
148 149 9.181805 CATGTACACGATTACTGGTTATAGAAG 57.818 37.037 0.00 0.00 0.00 2.85
149 150 7.709947 TGTACACGATTACTGGTTATAGAAGG 58.290 38.462 0.00 0.00 0.00 3.46
150 151 6.786967 ACACGATTACTGGTTATAGAAGGT 57.213 37.500 0.00 0.00 0.00 3.50
151 152 7.179076 ACACGATTACTGGTTATAGAAGGTT 57.821 36.000 0.00 0.00 0.00 3.50
152 153 7.263496 ACACGATTACTGGTTATAGAAGGTTC 58.737 38.462 0.00 0.00 0.00 3.62
153 154 7.093640 ACACGATTACTGGTTATAGAAGGTTCA 60.094 37.037 0.00 0.00 0.00 3.18
154 155 7.926555 CACGATTACTGGTTATAGAAGGTTCAT 59.073 37.037 0.00 0.00 0.00 2.57
155 156 9.139734 ACGATTACTGGTTATAGAAGGTTCATA 57.860 33.333 0.00 0.00 0.00 2.15
156 157 9.627395 CGATTACTGGTTATAGAAGGTTCATAG 57.373 37.037 0.00 0.00 0.00 2.23
157 158 9.425577 GATTACTGGTTATAGAAGGTTCATAGC 57.574 37.037 0.00 0.00 0.00 2.97
158 159 5.844004 ACTGGTTATAGAAGGTTCATAGCG 58.156 41.667 0.00 0.00 0.00 4.26
159 160 4.628074 TGGTTATAGAAGGTTCATAGCGC 58.372 43.478 0.00 0.00 0.00 5.92
160 161 4.344102 TGGTTATAGAAGGTTCATAGCGCT 59.656 41.667 17.26 17.26 0.00 5.92
161 162 4.924462 GGTTATAGAAGGTTCATAGCGCTC 59.076 45.833 16.34 0.00 0.00 5.03
162 163 5.509163 GGTTATAGAAGGTTCATAGCGCTCA 60.509 44.000 16.34 0.02 0.00 4.26
163 164 4.881019 ATAGAAGGTTCATAGCGCTCAT 57.119 40.909 16.34 2.98 0.00 2.90
164 165 2.831333 AGAAGGTTCATAGCGCTCATG 58.169 47.619 16.34 16.22 0.00 3.07
165 166 2.169352 AGAAGGTTCATAGCGCTCATGT 59.831 45.455 16.34 0.00 0.00 3.21
166 167 1.945387 AGGTTCATAGCGCTCATGTG 58.055 50.000 16.34 9.54 0.00 3.21
167 168 1.208052 AGGTTCATAGCGCTCATGTGT 59.792 47.619 16.34 0.00 0.00 3.72
168 169 2.430694 AGGTTCATAGCGCTCATGTGTA 59.569 45.455 16.34 0.00 0.00 2.90
169 170 3.118775 AGGTTCATAGCGCTCATGTGTAA 60.119 43.478 16.34 4.50 0.00 2.41
170 171 3.621268 GGTTCATAGCGCTCATGTGTAAA 59.379 43.478 16.34 4.16 0.00 2.01
171 172 4.494199 GGTTCATAGCGCTCATGTGTAAAC 60.494 45.833 16.34 14.66 0.00 2.01
172 173 4.123497 TCATAGCGCTCATGTGTAAACT 57.877 40.909 16.34 0.00 0.00 2.66
173 174 5.257082 TCATAGCGCTCATGTGTAAACTA 57.743 39.130 16.34 0.00 0.00 2.24
174 175 5.281727 TCATAGCGCTCATGTGTAAACTAG 58.718 41.667 16.34 0.00 0.00 2.57
175 176 2.271800 AGCGCTCATGTGTAAACTAGC 58.728 47.619 2.64 0.00 0.00 3.42
176 177 1.327764 GCGCTCATGTGTAAACTAGCC 59.672 52.381 0.00 0.00 0.00 3.93
177 178 2.616960 CGCTCATGTGTAAACTAGCCA 58.383 47.619 0.00 0.00 0.00 4.75
178 179 2.348666 CGCTCATGTGTAAACTAGCCAC 59.651 50.000 0.00 0.00 0.00 5.01
179 180 2.678336 GCTCATGTGTAAACTAGCCACC 59.322 50.000 0.00 0.00 0.00 4.61
180 181 3.868369 GCTCATGTGTAAACTAGCCACCA 60.868 47.826 0.00 0.00 0.00 4.17
181 182 3.935203 CTCATGTGTAAACTAGCCACCAG 59.065 47.826 0.00 0.00 0.00 4.00
182 183 3.580895 TCATGTGTAAACTAGCCACCAGA 59.419 43.478 0.00 0.00 0.00 3.86
183 184 3.396260 TGTGTAAACTAGCCACCAGAC 57.604 47.619 0.00 0.00 0.00 3.51
184 185 2.701423 TGTGTAAACTAGCCACCAGACA 59.299 45.455 0.00 0.00 0.00 3.41
185 186 3.134985 TGTGTAAACTAGCCACCAGACAA 59.865 43.478 0.00 0.00 0.00 3.18
186 187 4.131596 GTGTAAACTAGCCACCAGACAAA 58.868 43.478 0.00 0.00 0.00 2.83
187 188 4.213482 GTGTAAACTAGCCACCAGACAAAG 59.787 45.833 0.00 0.00 0.00 2.77
188 189 1.897560 AACTAGCCACCAGACAAAGC 58.102 50.000 0.00 0.00 0.00 3.51
189 190 0.764890 ACTAGCCACCAGACAAAGCA 59.235 50.000 0.00 0.00 0.00 3.91
190 191 1.160137 CTAGCCACCAGACAAAGCAC 58.840 55.000 0.00 0.00 0.00 4.40
191 192 0.764890 TAGCCACCAGACAAAGCACT 59.235 50.000 0.00 0.00 0.00 4.40
192 193 0.106519 AGCCACCAGACAAAGCACTT 60.107 50.000 0.00 0.00 0.00 3.16
193 194 0.312102 GCCACCAGACAAAGCACTTC 59.688 55.000 0.00 0.00 0.00 3.01
194 195 1.972872 CCACCAGACAAAGCACTTCT 58.027 50.000 0.00 0.00 0.00 2.85
195 196 2.810400 GCCACCAGACAAAGCACTTCTA 60.810 50.000 0.00 0.00 0.00 2.10
196 197 3.476552 CCACCAGACAAAGCACTTCTAA 58.523 45.455 0.00 0.00 0.00 2.10
197 198 4.074970 CCACCAGACAAAGCACTTCTAAT 58.925 43.478 0.00 0.00 0.00 1.73
198 199 5.245531 CCACCAGACAAAGCACTTCTAATA 58.754 41.667 0.00 0.00 0.00 0.98
199 200 5.122396 CCACCAGACAAAGCACTTCTAATAC 59.878 44.000 0.00 0.00 0.00 1.89
200 201 5.122396 CACCAGACAAAGCACTTCTAATACC 59.878 44.000 0.00 0.00 0.00 2.73
201 202 4.330074 CCAGACAAAGCACTTCTAATACCG 59.670 45.833 0.00 0.00 0.00 4.02
202 203 3.933332 AGACAAAGCACTTCTAATACCGC 59.067 43.478 0.00 0.00 0.00 5.68
203 204 3.670625 ACAAAGCACTTCTAATACCGCA 58.329 40.909 0.00 0.00 0.00 5.69
204 205 4.069304 ACAAAGCACTTCTAATACCGCAA 58.931 39.130 0.00 0.00 0.00 4.85
205 206 4.083484 ACAAAGCACTTCTAATACCGCAAC 60.083 41.667 0.00 0.00 0.00 4.17
206 207 3.328382 AGCACTTCTAATACCGCAACA 57.672 42.857 0.00 0.00 0.00 3.33
207 208 3.000727 AGCACTTCTAATACCGCAACAC 58.999 45.455 0.00 0.00 0.00 3.32
208 209 2.739913 GCACTTCTAATACCGCAACACA 59.260 45.455 0.00 0.00 0.00 3.72
209 210 3.424433 GCACTTCTAATACCGCAACACAC 60.424 47.826 0.00 0.00 0.00 3.82
210 211 3.743911 CACTTCTAATACCGCAACACACA 59.256 43.478 0.00 0.00 0.00 3.72
211 212 4.212425 CACTTCTAATACCGCAACACACAA 59.788 41.667 0.00 0.00 0.00 3.33
212 213 4.817464 ACTTCTAATACCGCAACACACAAA 59.183 37.500 0.00 0.00 0.00 2.83
213 214 4.735662 TCTAATACCGCAACACACAAAC 57.264 40.909 0.00 0.00 0.00 2.93
214 215 4.127907 TCTAATACCGCAACACACAAACA 58.872 39.130 0.00 0.00 0.00 2.83
225 226 6.346999 CGCAACACACAAACATAGTACATACA 60.347 38.462 0.00 0.00 0.00 2.29
236 237 9.903682 AAACATAGTACATACATATACACGACC 57.096 33.333 0.00 0.00 0.00 4.79
240 241 9.964354 ATAGTACATACATATACACGACCCTTA 57.036 33.333 0.00 0.00 0.00 2.69
286 287 3.242543 GCACGCATTAGTGAGAATCCTTG 60.243 47.826 0.88 0.00 44.43 3.61
291 292 4.455606 CATTAGTGAGAATCCTTGGGACC 58.544 47.826 0.00 0.00 32.98 4.46
302 303 1.358152 CTTGGGACCTAACCTGGACA 58.642 55.000 0.00 0.00 0.00 4.02
305 306 1.080498 TGGGACCTAACCTGGACAGAT 59.920 52.381 0.00 0.00 0.00 2.90
320 321 9.588096 ACCTGGACAGATTATTAAGAAAACTTT 57.412 29.630 0.00 0.00 0.00 2.66
386 388 1.079503 GCCGTCTTCAAGTCATGGTC 58.920 55.000 0.00 0.00 0.00 4.02
387 389 1.608025 GCCGTCTTCAAGTCATGGTCA 60.608 52.381 0.00 0.00 0.00 4.02
388 390 2.766313 CCGTCTTCAAGTCATGGTCAA 58.234 47.619 0.00 0.00 0.00 3.18
389 391 3.138304 CCGTCTTCAAGTCATGGTCAAA 58.862 45.455 0.00 0.00 0.00 2.69
390 392 3.563808 CCGTCTTCAAGTCATGGTCAAAA 59.436 43.478 0.00 0.00 0.00 2.44
391 393 4.527564 CGTCTTCAAGTCATGGTCAAAAC 58.472 43.478 0.00 0.00 0.00 2.43
392 394 4.273480 CGTCTTCAAGTCATGGTCAAAACT 59.727 41.667 0.00 0.00 0.00 2.66
442 594 6.677781 TTTGTAAAGAAACAGTCTCACCTG 57.322 37.500 0.00 0.00 34.56 4.00
597 829 2.693762 CGACTCGTGCGTTCCCCTA 61.694 63.158 0.00 0.00 0.00 3.53
606 875 4.216257 TCGTGCGTTCCCCTAATATACTAC 59.784 45.833 0.00 0.00 0.00 2.73
607 876 4.217118 CGTGCGTTCCCCTAATATACTACT 59.783 45.833 0.00 0.00 0.00 2.57
608 877 5.467705 GTGCGTTCCCCTAATATACTACTG 58.532 45.833 0.00 0.00 0.00 2.74
724 1428 1.045407 AGTCCAGCGGTCAACACTAA 58.955 50.000 0.00 0.00 0.00 2.24
841 1568 1.383803 AGCATCCCTCACCTCTCCC 60.384 63.158 0.00 0.00 0.00 4.30
884 1628 1.194781 ACGGCCACTCCACAGAATCT 61.195 55.000 2.24 0.00 34.01 2.40
890 1634 2.038952 CCACTCCACAGAATCTCCACAA 59.961 50.000 0.00 0.00 0.00 3.33
898 1642 6.550854 TCCACAGAATCTCCACAAAGAAAATT 59.449 34.615 0.00 0.00 0.00 1.82
913 1657 6.734104 AAGAAAATTCAGCTGCTACAGTAG 57.266 37.500 9.47 2.85 33.43 2.57
919 1663 2.875317 TCAGCTGCTACAGTAGAGATCG 59.125 50.000 12.15 0.00 33.43 3.69
989 1753 5.914898 TCGAGACTTCAAGATCCATTGTA 57.085 39.130 0.00 0.00 0.00 2.41
2763 3814 0.820226 AGAAGATGCGAGCAGTGCTA 59.180 50.000 19.77 2.38 39.88 3.49
3173 4243 1.661341 CAGAATTCTGAAGGCTCCCG 58.339 55.000 28.13 0.00 46.59 5.14
3396 4466 7.117285 TGATGTTCTACTACTGAATCAGCAT 57.883 36.000 10.62 2.94 34.37 3.79
3498 4569 5.043903 TCGCACTGCAATATAGAGAGAAAC 58.956 41.667 1.11 0.00 0.00 2.78
3516 4587 2.949177 ACAGCACCAGGTTGTGATTA 57.051 45.000 5.09 0.00 39.69 1.75
3714 4786 9.593134 CAGAAGAAGAATGTACAAGTATAAGCT 57.407 33.333 0.00 0.00 0.00 3.74
3776 4848 4.557605 GCACCGCCCGCATTCATG 62.558 66.667 0.00 0.00 0.00 3.07
3932 5004 1.881973 GCTTCCTCATTGAGTTGCACA 59.118 47.619 12.54 0.00 0.00 4.57
4053 5125 3.056304 GAGCAGCGAGTCAGGAAATATC 58.944 50.000 0.00 0.00 0.00 1.63
4106 5178 4.696877 AGAAATTCAGCACGACATTGATGA 59.303 37.500 0.00 0.00 40.09 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.162082 ACAAAACATATTTTTATTGCGGGGAA 58.838 30.769 0.00 0.00 35.79 3.97
1 2 6.702329 ACAAAACATATTTTTATTGCGGGGA 58.298 32.000 0.00 0.00 35.79 4.81
2 3 6.976636 ACAAAACATATTTTTATTGCGGGG 57.023 33.333 0.00 0.00 35.79 5.73
45 46 9.851686 TGACTGCAAAATGATATTAGGTAGAAT 57.148 29.630 0.00 0.00 0.00 2.40
46 47 9.330063 CTGACTGCAAAATGATATTAGGTAGAA 57.670 33.333 0.00 0.00 0.00 2.10
47 48 7.442364 GCTGACTGCAAAATGATATTAGGTAGA 59.558 37.037 0.00 0.00 42.31 2.59
48 49 7.579726 GCTGACTGCAAAATGATATTAGGTAG 58.420 38.462 0.00 0.00 42.31 3.18
49 50 7.496529 GCTGACTGCAAAATGATATTAGGTA 57.503 36.000 0.00 0.00 42.31 3.08
50 51 6.382869 GCTGACTGCAAAATGATATTAGGT 57.617 37.500 0.00 0.00 42.31 3.08
65 66 0.179205 GCACGAAAGATGCTGACTGC 60.179 55.000 0.00 0.00 40.08 4.40
66 67 1.150827 TGCACGAAAGATGCTGACTG 58.849 50.000 0.00 0.00 43.77 3.51
67 68 1.882912 TTGCACGAAAGATGCTGACT 58.117 45.000 0.00 0.00 43.77 3.41
68 69 2.160219 TCATTGCACGAAAGATGCTGAC 59.840 45.455 0.00 0.00 43.77 3.51
69 70 2.425539 TCATTGCACGAAAGATGCTGA 58.574 42.857 0.00 0.00 43.77 4.26
70 71 2.905959 TCATTGCACGAAAGATGCTG 57.094 45.000 0.00 0.00 43.77 4.41
71 72 3.921119 TTTCATTGCACGAAAGATGCT 57.079 38.095 6.42 0.00 43.77 3.79
72 73 6.630676 TTAATTTCATTGCACGAAAGATGC 57.369 33.333 14.06 0.00 43.68 3.91
114 115 7.703621 ACCAGTAATCGTGTACATGTAATACAC 59.296 37.037 16.96 16.96 45.92 2.90
115 116 7.774134 ACCAGTAATCGTGTACATGTAATACA 58.226 34.615 14.63 0.90 0.00 2.29
116 117 8.638685 AACCAGTAATCGTGTACATGTAATAC 57.361 34.615 14.63 14.46 0.00 1.89
119 120 9.955208 CTATAACCAGTAATCGTGTACATGTAA 57.045 33.333 14.63 0.00 0.00 2.41
120 121 9.341078 TCTATAACCAGTAATCGTGTACATGTA 57.659 33.333 14.63 0.08 0.00 2.29
121 122 8.229253 TCTATAACCAGTAATCGTGTACATGT 57.771 34.615 14.63 2.69 0.00 3.21
122 123 9.181805 CTTCTATAACCAGTAATCGTGTACATG 57.818 37.037 8.90 8.90 0.00 3.21
123 124 8.358148 CCTTCTATAACCAGTAATCGTGTACAT 58.642 37.037 0.00 0.00 0.00 2.29
124 125 7.340232 ACCTTCTATAACCAGTAATCGTGTACA 59.660 37.037 0.00 0.00 0.00 2.90
125 126 7.710896 ACCTTCTATAACCAGTAATCGTGTAC 58.289 38.462 0.00 0.00 0.00 2.90
126 127 7.886629 ACCTTCTATAACCAGTAATCGTGTA 57.113 36.000 0.00 0.00 0.00 2.90
127 128 6.786967 ACCTTCTATAACCAGTAATCGTGT 57.213 37.500 0.00 0.00 0.00 4.49
128 129 7.262772 TGAACCTTCTATAACCAGTAATCGTG 58.737 38.462 0.00 0.00 0.00 4.35
129 130 7.414222 TGAACCTTCTATAACCAGTAATCGT 57.586 36.000 0.00 0.00 0.00 3.73
130 131 9.627395 CTATGAACCTTCTATAACCAGTAATCG 57.373 37.037 0.00 0.00 0.00 3.34
131 132 9.425577 GCTATGAACCTTCTATAACCAGTAATC 57.574 37.037 0.00 0.00 0.00 1.75
132 133 8.088981 CGCTATGAACCTTCTATAACCAGTAAT 58.911 37.037 0.00 0.00 0.00 1.89
133 134 7.431249 CGCTATGAACCTTCTATAACCAGTAA 58.569 38.462 0.00 0.00 0.00 2.24
134 135 6.516194 GCGCTATGAACCTTCTATAACCAGTA 60.516 42.308 0.00 0.00 0.00 2.74
135 136 5.739358 GCGCTATGAACCTTCTATAACCAGT 60.739 44.000 0.00 0.00 0.00 4.00
136 137 4.686554 GCGCTATGAACCTTCTATAACCAG 59.313 45.833 0.00 0.00 0.00 4.00
137 138 4.344102 AGCGCTATGAACCTTCTATAACCA 59.656 41.667 8.99 0.00 0.00 3.67
138 139 4.884247 AGCGCTATGAACCTTCTATAACC 58.116 43.478 8.99 0.00 0.00 2.85
139 140 5.529791 TGAGCGCTATGAACCTTCTATAAC 58.470 41.667 11.50 0.00 0.00 1.89
140 141 5.784578 TGAGCGCTATGAACCTTCTATAA 57.215 39.130 11.50 0.00 0.00 0.98
141 142 5.243954 ACATGAGCGCTATGAACCTTCTATA 59.756 40.000 24.30 0.00 0.00 1.31
142 143 4.039730 ACATGAGCGCTATGAACCTTCTAT 59.960 41.667 24.30 5.11 0.00 1.98
143 144 3.384789 ACATGAGCGCTATGAACCTTCTA 59.615 43.478 24.30 0.01 0.00 2.10
144 145 2.169352 ACATGAGCGCTATGAACCTTCT 59.831 45.455 24.30 6.16 0.00 2.85
145 146 2.286294 CACATGAGCGCTATGAACCTTC 59.714 50.000 24.30 7.11 0.00 3.46
146 147 2.283298 CACATGAGCGCTATGAACCTT 58.717 47.619 24.30 4.47 0.00 3.50
147 148 1.208052 ACACATGAGCGCTATGAACCT 59.792 47.619 24.30 7.49 0.00 3.50
148 149 1.656652 ACACATGAGCGCTATGAACC 58.343 50.000 24.30 8.80 0.00 3.62
149 150 4.330074 AGTTTACACATGAGCGCTATGAAC 59.670 41.667 24.30 18.83 0.00 3.18
150 151 4.503910 AGTTTACACATGAGCGCTATGAA 58.496 39.130 24.30 8.51 0.00 2.57
151 152 4.123497 AGTTTACACATGAGCGCTATGA 57.877 40.909 24.30 9.24 0.00 2.15
152 153 4.084849 GCTAGTTTACACATGAGCGCTATG 60.085 45.833 11.50 16.70 0.00 2.23
153 154 4.051922 GCTAGTTTACACATGAGCGCTAT 58.948 43.478 11.50 1.12 0.00 2.97
154 155 3.444916 GCTAGTTTACACATGAGCGCTA 58.555 45.455 11.50 0.00 0.00 4.26
155 156 2.271800 GCTAGTTTACACATGAGCGCT 58.728 47.619 11.27 11.27 0.00 5.92
156 157 1.327764 GGCTAGTTTACACATGAGCGC 59.672 52.381 0.00 0.00 0.00 5.92
157 158 2.348666 GTGGCTAGTTTACACATGAGCG 59.651 50.000 0.00 0.00 35.30 5.03
158 159 2.678336 GGTGGCTAGTTTACACATGAGC 59.322 50.000 0.00 0.00 36.87 4.26
159 160 3.935203 CTGGTGGCTAGTTTACACATGAG 59.065 47.826 0.00 0.00 36.87 2.90
160 161 3.580895 TCTGGTGGCTAGTTTACACATGA 59.419 43.478 0.00 5.72 36.87 3.07
161 162 3.684788 GTCTGGTGGCTAGTTTACACATG 59.315 47.826 0.00 0.00 36.87 3.21
162 163 3.326588 TGTCTGGTGGCTAGTTTACACAT 59.673 43.478 9.87 0.00 36.87 3.21
163 164 2.701423 TGTCTGGTGGCTAGTTTACACA 59.299 45.455 9.87 0.00 36.87 3.72
164 165 3.396260 TGTCTGGTGGCTAGTTTACAC 57.604 47.619 0.00 0.00 0.00 2.90
165 166 4.385825 CTTTGTCTGGTGGCTAGTTTACA 58.614 43.478 0.00 0.00 0.00 2.41
166 167 3.188667 GCTTTGTCTGGTGGCTAGTTTAC 59.811 47.826 0.00 0.00 0.00 2.01
167 168 3.181449 TGCTTTGTCTGGTGGCTAGTTTA 60.181 43.478 0.00 0.00 0.00 2.01
168 169 2.230660 GCTTTGTCTGGTGGCTAGTTT 58.769 47.619 0.00 0.00 0.00 2.66
169 170 1.142870 TGCTTTGTCTGGTGGCTAGTT 59.857 47.619 0.00 0.00 0.00 2.24
170 171 0.764890 TGCTTTGTCTGGTGGCTAGT 59.235 50.000 0.00 0.00 0.00 2.57
171 172 1.160137 GTGCTTTGTCTGGTGGCTAG 58.840 55.000 0.00 0.00 0.00 3.42
172 173 0.764890 AGTGCTTTGTCTGGTGGCTA 59.235 50.000 0.00 0.00 0.00 3.93
173 174 0.106519 AAGTGCTTTGTCTGGTGGCT 60.107 50.000 0.00 0.00 0.00 4.75
174 175 0.312102 GAAGTGCTTTGTCTGGTGGC 59.688 55.000 0.00 0.00 0.00 5.01
175 176 1.972872 AGAAGTGCTTTGTCTGGTGG 58.027 50.000 0.00 0.00 0.00 4.61
176 177 5.122396 GGTATTAGAAGTGCTTTGTCTGGTG 59.878 44.000 0.00 0.00 0.00 4.17
177 178 5.246307 GGTATTAGAAGTGCTTTGTCTGGT 58.754 41.667 0.00 0.00 0.00 4.00
178 179 4.330074 CGGTATTAGAAGTGCTTTGTCTGG 59.670 45.833 0.00 0.00 0.00 3.86
179 180 4.201724 GCGGTATTAGAAGTGCTTTGTCTG 60.202 45.833 0.00 0.00 0.00 3.51
180 181 3.933332 GCGGTATTAGAAGTGCTTTGTCT 59.067 43.478 0.00 0.00 0.00 3.41
181 182 3.682858 TGCGGTATTAGAAGTGCTTTGTC 59.317 43.478 0.00 0.00 0.00 3.18
182 183 3.670625 TGCGGTATTAGAAGTGCTTTGT 58.329 40.909 0.00 0.00 0.00 2.83
183 184 4.083537 TGTTGCGGTATTAGAAGTGCTTTG 60.084 41.667 0.00 0.00 0.00 2.77
184 185 4.069304 TGTTGCGGTATTAGAAGTGCTTT 58.931 39.130 0.00 0.00 0.00 3.51
185 186 3.435671 GTGTTGCGGTATTAGAAGTGCTT 59.564 43.478 0.00 0.00 0.00 3.91
186 187 3.000727 GTGTTGCGGTATTAGAAGTGCT 58.999 45.455 0.00 0.00 0.00 4.40
187 188 2.739913 TGTGTTGCGGTATTAGAAGTGC 59.260 45.455 0.00 0.00 0.00 4.40
188 189 3.743911 TGTGTGTTGCGGTATTAGAAGTG 59.256 43.478 0.00 0.00 0.00 3.16
189 190 3.997762 TGTGTGTTGCGGTATTAGAAGT 58.002 40.909 0.00 0.00 0.00 3.01
190 191 5.144359 GTTTGTGTGTTGCGGTATTAGAAG 58.856 41.667 0.00 0.00 0.00 2.85
191 192 4.575236 TGTTTGTGTGTTGCGGTATTAGAA 59.425 37.500 0.00 0.00 0.00 2.10
192 193 4.127907 TGTTTGTGTGTTGCGGTATTAGA 58.872 39.130 0.00 0.00 0.00 2.10
193 194 4.475763 TGTTTGTGTGTTGCGGTATTAG 57.524 40.909 0.00 0.00 0.00 1.73
194 195 5.701750 ACTATGTTTGTGTGTTGCGGTATTA 59.298 36.000 0.00 0.00 0.00 0.98
195 196 4.517453 ACTATGTTTGTGTGTTGCGGTATT 59.483 37.500 0.00 0.00 0.00 1.89
196 197 4.069304 ACTATGTTTGTGTGTTGCGGTAT 58.931 39.130 0.00 0.00 0.00 2.73
197 198 3.468770 ACTATGTTTGTGTGTTGCGGTA 58.531 40.909 0.00 0.00 0.00 4.02
198 199 2.294074 ACTATGTTTGTGTGTTGCGGT 58.706 42.857 0.00 0.00 0.00 5.68
199 200 3.248841 TGTACTATGTTTGTGTGTTGCGG 59.751 43.478 0.00 0.00 0.00 5.69
200 201 4.460471 TGTACTATGTTTGTGTGTTGCG 57.540 40.909 0.00 0.00 0.00 4.85
201 202 6.893759 TGTATGTACTATGTTTGTGTGTTGC 58.106 36.000 0.00 0.00 0.00 4.17
210 211 9.903682 GGTCGTGTATATGTATGTACTATGTTT 57.096 33.333 0.00 0.00 0.00 2.83
211 212 8.517878 GGGTCGTGTATATGTATGTACTATGTT 58.482 37.037 0.00 0.00 0.00 2.71
212 213 7.886970 AGGGTCGTGTATATGTATGTACTATGT 59.113 37.037 0.00 0.00 0.00 2.29
213 214 8.277490 AGGGTCGTGTATATGTATGTACTATG 57.723 38.462 0.00 0.00 0.00 2.23
214 215 8.874744 AAGGGTCGTGTATATGTATGTACTAT 57.125 34.615 0.00 0.00 0.00 2.12
225 226 7.466320 GCGTTCAAAATTAAGGGTCGTGTATAT 60.466 37.037 0.00 0.00 0.00 0.86
236 237 4.545610 TGCTTCAGCGTTCAAAATTAAGG 58.454 39.130 0.00 0.00 45.83 2.69
240 241 3.981211 ACATGCTTCAGCGTTCAAAATT 58.019 36.364 0.00 0.00 45.83 1.82
286 287 1.880941 ATCTGTCCAGGTTAGGTCCC 58.119 55.000 0.00 0.00 0.00 4.46
320 321 4.436317 CGAGTTTCACTTGTTCCACGAAAA 60.436 41.667 0.00 0.00 0.00 2.29
331 332 4.083802 GGAGATTTGGACGAGTTTCACTTG 60.084 45.833 0.00 0.00 35.70 3.16
386 388 5.107913 CGTACAACATGGCATTTGAGTTTTG 60.108 40.000 21.19 7.96 0.00 2.44
387 389 4.981674 CGTACAACATGGCATTTGAGTTTT 59.018 37.500 21.19 9.65 0.00 2.43
388 390 4.037446 ACGTACAACATGGCATTTGAGTTT 59.963 37.500 21.19 8.11 0.00 2.66
389 391 3.568007 ACGTACAACATGGCATTTGAGTT 59.432 39.130 21.19 10.91 0.00 3.01
390 392 3.146066 ACGTACAACATGGCATTTGAGT 58.854 40.909 21.19 16.04 0.00 3.41
391 393 3.829886 ACGTACAACATGGCATTTGAG 57.170 42.857 21.19 15.64 0.00 3.02
392 394 4.065789 TGTACGTACAACATGGCATTTGA 58.934 39.130 25.54 0.00 32.40 2.69
442 594 7.917505 GTGTCCAAATCCAATTCTTGTATGATC 59.082 37.037 0.00 0.00 0.00 2.92
460 618 7.883391 TTTTCAGTTATTAGGTGTGTCCAAA 57.117 32.000 0.00 0.00 39.02 3.28
488 649 4.038080 CGGCGGCCCTGTTTTGAC 62.038 66.667 14.55 0.00 0.00 3.18
606 875 3.384668 CTGCGACAATGGGATACTACAG 58.615 50.000 0.00 0.00 0.00 2.74
607 876 2.483013 GCTGCGACAATGGGATACTACA 60.483 50.000 0.00 0.00 0.00 2.74
608 877 2.135933 GCTGCGACAATGGGATACTAC 58.864 52.381 0.00 0.00 0.00 2.73
639 909 3.670091 CGTGGACTAGGAAGAAGACGAAC 60.670 52.174 0.00 0.00 0.00 3.95
724 1428 1.535444 TGGACTGTGACCGGGATGT 60.535 57.895 6.32 0.00 0.00 3.06
841 1568 2.101249 GAGAGAAGAGCTGGATGGAGTG 59.899 54.545 0.00 0.00 0.00 3.51
884 1628 3.638160 AGCAGCTGAATTTTCTTTGTGGA 59.362 39.130 20.43 0.00 0.00 4.02
890 1634 6.467677 TCTACTGTAGCAGCTGAATTTTCTT 58.532 36.000 20.43 0.00 34.37 2.52
898 1642 2.875317 CGATCTCTACTGTAGCAGCTGA 59.125 50.000 20.43 0.00 34.37 4.26
913 1657 0.596082 GACTAGAGGCTGGCGATCTC 59.404 60.000 0.00 0.00 0.00 2.75
919 1663 1.042559 AGCAGAGACTAGAGGCTGGC 61.043 60.000 0.00 0.00 32.76 4.85
989 1753 1.322538 GGCCGCCATTGGTTTGATCT 61.323 55.000 3.91 0.00 0.00 2.75
1050 2092 4.760047 CCCCAGTTGAGCGGGTCG 62.760 72.222 2.41 0.00 41.30 4.79
3228 4298 4.000988 GCATCAACGTTTTAGAAGAGGGA 58.999 43.478 0.00 0.00 0.00 4.20
3329 4399 1.133025 CCCTTTCGCTTACATTGGCAG 59.867 52.381 0.00 0.00 0.00 4.85
3396 4466 8.117813 TGTATGACATACAGTAAGTCTGAACA 57.882 34.615 21.76 13.03 46.27 3.18
3498 4569 3.346315 TGATAATCACAACCTGGTGCTG 58.654 45.455 0.00 0.00 38.66 4.41
3516 4587 3.806521 GCTCGAGAATGTGCTTGTATGAT 59.193 43.478 18.75 0.00 0.00 2.45
3687 4758 9.587772 GCTTATACTTGTACATTCTTCTTCTGA 57.412 33.333 0.00 0.00 0.00 3.27
3714 4786 0.391130 GCATACACTGAAGCGGGTGA 60.391 55.000 0.00 0.00 37.22 4.02
3932 5004 1.407656 TTCAGGTGTCCCTCGTGCTT 61.408 55.000 0.00 0.00 39.89 3.91


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

AutoCloner maintained by Alex Coulton.