Multiple sequence alignment - TraesCS1A01G134000

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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 TraesCS1A01G134000 chr1A 100.000 2519 0 0 1 2519 193516450 193518968 0.000000e+00 4652.0
1 TraesCS1A01G134000 chr1D 94.925 1675 53 11 263 1908 135725631 135727302 0.000000e+00 2593.0
2 TraesCS1A01G134000 chr1D 91.228 285 21 2 2238 2519 308869954 308870237 3.930000e-103 385.0
3 TraesCS1A01G134000 chr1D 90.377 239 14 6 1 232 135663893 135664129 3.150000e-79 305.0
4 TraesCS1A01G134000 chr1D 82.682 358 29 10 1906 2241 308869572 308869918 1.140000e-73 287.0
5 TraesCS1A01G134000 chr1D 81.061 132 15 7 2085 2216 404757212 404757333 2.060000e-16 97.1
6 TraesCS1A01G134000 chr1B 95.752 1483 53 4 431 1905 215535240 215536720 0.000000e+00 2381.0
7 TraesCS1A01G134000 chr1B 91.697 277 18 3 2246 2519 596878746 596879020 1.830000e-101 379.0
8 TraesCS1A01G134000 chr1B 81.402 371 27 13 1908 2239 596878333 596878700 5.340000e-67 265.0
9 TraesCS1A01G134000 chr2A 91.958 286 19 2 2238 2519 374126975 374126690 5.050000e-107 398.0
10 TraesCS1A01G134000 chr2A 82.353 374 26 14 1906 2241 374127382 374127011 3.170000e-74 289.0
11 TraesCS1A01G134000 chr7A 92.058 277 19 1 2246 2519 673783795 673783519 1.090000e-103 387.0
12 TraesCS1A01G134000 chr7A 81.818 374 26 19 1906 2241 673784208 673783839 2.470000e-70 276.0
13 TraesCS1A01G134000 chr5A 90.614 277 23 1 2246 2519 81353177 81352901 5.120000e-97 364.0
14 TraesCS1A01G134000 chr5A 81.867 375 26 14 1906 2241 81353592 81353221 6.860000e-71 278.0
15 TraesCS1A01G134000 chr3B 86.555 119 15 1 1962 2079 5368798 5368680 2.030000e-26 130.0
16 TraesCS1A01G134000 chr3B 79.545 88 15 3 1985 2069 789443879 789443792 2.710000e-05 60.2
17 TraesCS1A01G134000 chr3B 94.595 37 1 1 1982 2017 778353418 778353454 3.500000e-04 56.5
18 TraesCS1A01G134000 chr5B 79.121 91 16 3 1982 2069 20982999 20983089 2.710000e-05 60.2
19 TraesCS1A01G134000 chr7D 97.059 34 0 1 1985 2017 569309897 569309864 3.500000e-04 56.5
20 TraesCS1A01G134000 chr4B 94.595 37 1 1 1982 2017 381138146 381138182 3.500000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G134000 chr1A 193516450 193518968 2518 False 4652.0 4652 100.0000 1 2519 1 chr1A.!!$F1 2518
1 TraesCS1A01G134000 chr1D 135725631 135727302 1671 False 2593.0 2593 94.9250 263 1908 1 chr1D.!!$F2 1645
2 TraesCS1A01G134000 chr1D 308869572 308870237 665 False 336.0 385 86.9550 1906 2519 2 chr1D.!!$F4 613
3 TraesCS1A01G134000 chr1B 215535240 215536720 1480 False 2381.0 2381 95.7520 431 1905 1 chr1B.!!$F1 1474
4 TraesCS1A01G134000 chr1B 596878333 596879020 687 False 322.0 379 86.5495 1908 2519 2 chr1B.!!$F2 611
5 TraesCS1A01G134000 chr2A 374126690 374127382 692 True 343.5 398 87.1555 1906 2519 2 chr2A.!!$R1 613
6 TraesCS1A01G134000 chr7A 673783519 673784208 689 True 331.5 387 86.9380 1906 2519 2 chr7A.!!$R1 613
7 TraesCS1A01G134000 chr5A 81352901 81353592 691 True 321.0 364 86.2405 1906 2519 2 chr5A.!!$R1 613

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
153 154 0.178953 ACATGCCTCCCTTGCAACTT 60.179 50.0 0.0 0.0 42.92 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2044 0.25361 TTTTGACGTGTGGGACCAGT 59.746 50.0 0.0 0.0 0.0 4.0 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
65 66 8.063200 AGACCTTGTACCTTAATTTAATTGGC 57.937 34.615 0.00 0.00 0.00 4.52
66 67 7.672239 AGACCTTGTACCTTAATTTAATTGGCA 59.328 33.333 0.00 0.00 0.00 4.92
67 68 7.836842 ACCTTGTACCTTAATTTAATTGGCAG 58.163 34.615 0.00 0.00 0.00 4.85
68 69 6.756542 CCTTGTACCTTAATTTAATTGGCAGC 59.243 38.462 0.00 0.00 0.00 5.25
69 70 7.363793 CCTTGTACCTTAATTTAATTGGCAGCT 60.364 37.037 0.00 0.00 0.00 4.24
70 71 8.582657 TTGTACCTTAATTTAATTGGCAGCTA 57.417 30.769 0.00 0.00 0.00 3.32
71 72 8.220755 TGTACCTTAATTTAATTGGCAGCTAG 57.779 34.615 0.00 0.00 0.00 3.42
72 73 8.050325 TGTACCTTAATTTAATTGGCAGCTAGA 58.950 33.333 0.00 0.00 0.00 2.43
73 74 7.954666 ACCTTAATTTAATTGGCAGCTAGAA 57.045 32.000 0.00 0.00 0.00 2.10
74 75 8.539117 ACCTTAATTTAATTGGCAGCTAGAAT 57.461 30.769 0.00 0.00 0.00 2.40
75 76 8.981659 ACCTTAATTTAATTGGCAGCTAGAATT 58.018 29.630 0.00 0.00 0.00 2.17
76 77 9.468532 CCTTAATTTAATTGGCAGCTAGAATTC 57.531 33.333 0.00 0.00 0.00 2.17
80 81 9.895138 AATTTAATTGGCAGCTAGAATTCATTT 57.105 25.926 8.44 0.00 0.00 2.32
81 82 9.895138 ATTTAATTGGCAGCTAGAATTCATTTT 57.105 25.926 8.44 0.00 0.00 1.82
82 83 8.931385 TTAATTGGCAGCTAGAATTCATTTTC 57.069 30.769 8.44 0.00 0.00 2.29
83 84 5.981088 TTGGCAGCTAGAATTCATTTTCA 57.019 34.783 8.44 0.00 0.00 2.69
84 85 5.981088 TGGCAGCTAGAATTCATTTTCAA 57.019 34.783 8.44 0.00 0.00 2.69
85 86 6.534475 TGGCAGCTAGAATTCATTTTCAAT 57.466 33.333 8.44 0.00 0.00 2.57
86 87 7.643569 TGGCAGCTAGAATTCATTTTCAATA 57.356 32.000 8.44 0.00 0.00 1.90
87 88 8.241497 TGGCAGCTAGAATTCATTTTCAATAT 57.759 30.769 8.44 0.00 0.00 1.28
88 89 8.139350 TGGCAGCTAGAATTCATTTTCAATATG 58.861 33.333 8.44 0.00 0.00 1.78
89 90 8.139989 GGCAGCTAGAATTCATTTTCAATATGT 58.860 33.333 8.44 0.00 0.00 2.29
138 139 7.832503 TGTGAATCACAGTCATTACTACATG 57.167 36.000 12.63 0.00 39.62 3.21
139 140 6.313658 TGTGAATCACAGTCATTACTACATGC 59.686 38.462 12.63 0.00 39.62 4.06
140 141 5.817296 TGAATCACAGTCATTACTACATGCC 59.183 40.000 0.00 0.00 33.48 4.40
141 142 5.620738 ATCACAGTCATTACTACATGCCT 57.379 39.130 0.00 0.00 33.48 4.75
142 143 5.011090 TCACAGTCATTACTACATGCCTC 57.989 43.478 0.00 0.00 33.48 4.70
143 144 4.122776 CACAGTCATTACTACATGCCTCC 58.877 47.826 0.00 0.00 33.48 4.30
144 145 3.134804 ACAGTCATTACTACATGCCTCCC 59.865 47.826 0.00 0.00 33.48 4.30
145 146 3.389329 CAGTCATTACTACATGCCTCCCT 59.611 47.826 0.00 0.00 33.48 4.20
146 147 4.040755 AGTCATTACTACATGCCTCCCTT 58.959 43.478 0.00 0.00 32.84 3.95
147 148 4.130118 GTCATTACTACATGCCTCCCTTG 58.870 47.826 0.00 0.00 0.00 3.61
148 149 2.710096 TTACTACATGCCTCCCTTGC 57.290 50.000 0.00 0.00 0.00 4.01
149 150 1.578897 TACTACATGCCTCCCTTGCA 58.421 50.000 0.00 0.00 43.97 4.08
150 151 0.698238 ACTACATGCCTCCCTTGCAA 59.302 50.000 0.00 0.00 42.92 4.08
151 152 1.098050 CTACATGCCTCCCTTGCAAC 58.902 55.000 0.00 0.00 42.92 4.17
152 153 0.698238 TACATGCCTCCCTTGCAACT 59.302 50.000 0.00 0.00 42.92 3.16
153 154 0.178953 ACATGCCTCCCTTGCAACTT 60.179 50.000 0.00 0.00 42.92 2.66
154 155 0.971386 CATGCCTCCCTTGCAACTTT 59.029 50.000 0.00 0.00 42.92 2.66
155 156 1.067354 CATGCCTCCCTTGCAACTTTC 60.067 52.381 0.00 0.00 42.92 2.62
156 157 0.185901 TGCCTCCCTTGCAACTTTCT 59.814 50.000 0.00 0.00 35.40 2.52
157 158 1.423541 TGCCTCCCTTGCAACTTTCTA 59.576 47.619 0.00 0.00 35.40 2.10
158 159 2.158534 TGCCTCCCTTGCAACTTTCTAA 60.159 45.455 0.00 0.00 35.40 2.10
159 160 3.092301 GCCTCCCTTGCAACTTTCTAAT 58.908 45.455 0.00 0.00 0.00 1.73
160 161 4.263727 TGCCTCCCTTGCAACTTTCTAATA 60.264 41.667 0.00 0.00 35.40 0.98
161 162 4.705023 GCCTCCCTTGCAACTTTCTAATAA 59.295 41.667 0.00 0.00 0.00 1.40
162 163 5.185056 GCCTCCCTTGCAACTTTCTAATAAA 59.815 40.000 0.00 0.00 0.00 1.40
163 164 6.295067 GCCTCCCTTGCAACTTTCTAATAAAA 60.295 38.462 0.00 0.00 0.00 1.52
164 165 7.666623 CCTCCCTTGCAACTTTCTAATAAAAA 58.333 34.615 0.00 0.00 0.00 1.94
165 166 7.814587 CCTCCCTTGCAACTTTCTAATAAAAAG 59.185 37.037 0.00 0.00 39.20 2.27
166 167 8.472007 TCCCTTGCAACTTTCTAATAAAAAGA 57.528 30.769 0.00 0.00 37.22 2.52
167 168 9.088987 TCCCTTGCAACTTTCTAATAAAAAGAT 57.911 29.630 0.00 0.00 37.22 2.40
190 191 9.384764 AGATAAAAGGAAGAAGAAGGTTATTCG 57.615 33.333 0.00 0.00 33.84 3.34
191 192 9.379791 GATAAAAGGAAGAAGAAGGTTATTCGA 57.620 33.333 0.00 0.00 33.84 3.71
192 193 9.734984 ATAAAAGGAAGAAGAAGGTTATTCGAA 57.265 29.630 0.00 0.00 33.84 3.71
193 194 8.459911 AAAAGGAAGAAGAAGGTTATTCGAAA 57.540 30.769 0.00 0.00 33.84 3.46
194 195 7.436430 AAGGAAGAAGAAGGTTATTCGAAAC 57.564 36.000 0.00 0.00 33.84 2.78
195 196 6.770542 AGGAAGAAGAAGGTTATTCGAAACT 58.229 36.000 0.00 0.00 33.84 2.66
196 197 7.225011 AGGAAGAAGAAGGTTATTCGAAACTT 58.775 34.615 0.00 4.72 33.84 2.66
197 198 7.720074 AGGAAGAAGAAGGTTATTCGAAACTTT 59.280 33.333 0.00 0.00 33.84 2.66
198 199 8.016229 GGAAGAAGAAGGTTATTCGAAACTTTC 58.984 37.037 13.92 13.92 42.59 2.62
207 208 9.406828 AGGTTATTCGAAACTTTCTTTTTATGC 57.593 29.630 0.00 0.00 0.00 3.14
208 209 8.363029 GGTTATTCGAAACTTTCTTTTTATGCG 58.637 33.333 0.00 0.00 0.00 4.73
209 210 9.109533 GTTATTCGAAACTTTCTTTTTATGCGA 57.890 29.630 0.00 0.00 0.00 5.10
210 211 6.963017 TTCGAAACTTTCTTTTTATGCGAC 57.037 33.333 0.00 0.00 0.00 5.19
211 212 6.295039 TCGAAACTTTCTTTTTATGCGACT 57.705 33.333 0.12 0.00 0.00 4.18
212 213 6.721321 TCGAAACTTTCTTTTTATGCGACTT 58.279 32.000 0.12 0.00 0.00 3.01
213 214 7.190871 TCGAAACTTTCTTTTTATGCGACTTT 58.809 30.769 0.12 0.00 0.00 2.66
214 215 8.336806 TCGAAACTTTCTTTTTATGCGACTTTA 58.663 29.630 0.12 0.00 0.00 1.85
215 216 8.407458 CGAAACTTTCTTTTTATGCGACTTTAC 58.593 33.333 0.12 0.00 0.00 2.01
216 217 9.447040 GAAACTTTCTTTTTATGCGACTTTACT 57.553 29.630 0.00 0.00 0.00 2.24
217 218 9.447040 AAACTTTCTTTTTATGCGACTTTACTC 57.553 29.630 0.00 0.00 0.00 2.59
218 219 8.379457 ACTTTCTTTTTATGCGACTTTACTCT 57.621 30.769 0.00 0.00 0.00 3.24
219 220 9.485206 ACTTTCTTTTTATGCGACTTTACTCTA 57.515 29.630 0.00 0.00 0.00 2.43
223 224 8.715088 TCTTTTTATGCGACTTTACTCTAAACC 58.285 33.333 0.00 0.00 0.00 3.27
224 225 6.636666 TTTATGCGACTTTACTCTAAACCG 57.363 37.500 0.00 0.00 0.00 4.44
225 226 3.648339 TGCGACTTTACTCTAAACCGT 57.352 42.857 0.00 0.00 0.00 4.83
226 227 3.981211 TGCGACTTTACTCTAAACCGTT 58.019 40.909 0.00 0.00 0.00 4.44
227 228 3.737266 TGCGACTTTACTCTAAACCGTTG 59.263 43.478 0.00 0.00 0.00 4.10
228 229 3.737774 GCGACTTTACTCTAAACCGTTGT 59.262 43.478 0.00 0.00 0.00 3.32
229 230 4.917415 GCGACTTTACTCTAAACCGTTGTA 59.083 41.667 0.00 0.00 0.00 2.41
230 231 5.574443 GCGACTTTACTCTAAACCGTTGTAT 59.426 40.000 0.00 0.00 0.00 2.29
231 232 6.747280 GCGACTTTACTCTAAACCGTTGTATA 59.253 38.462 0.00 0.00 0.00 1.47
232 233 7.433425 GCGACTTTACTCTAAACCGTTGTATAT 59.567 37.037 0.00 0.00 0.00 0.86
233 234 9.935682 CGACTTTACTCTAAACCGTTGTATATA 57.064 33.333 0.00 0.00 0.00 0.86
273 274 9.204570 CTAACAAGAAGAAGAAGGTTATTCGAA 57.795 33.333 0.00 0.00 33.84 3.71
275 276 8.622948 ACAAGAAGAAGAAGGTTATTCGAAAT 57.377 30.769 0.00 0.00 33.84 2.17
276 277 9.067986 ACAAGAAGAAGAAGGTTATTCGAAATT 57.932 29.630 0.00 0.00 33.84 1.82
280 281 7.158099 AGAAGAAGGTTATTCGAAATTTGGG 57.842 36.000 0.00 0.00 33.84 4.12
305 306 2.082231 CACCATCCTCACTTTGCTGAG 58.918 52.381 0.00 0.00 37.94 3.35
311 312 0.873054 CTCACTTTGCTGAGCCTGTG 59.127 55.000 0.23 8.52 31.57 3.66
538 539 3.294214 TCGTACTCCTATTTCCCCTCAC 58.706 50.000 0.00 0.00 0.00 3.51
539 540 3.028850 CGTACTCCTATTTCCCCTCACA 58.971 50.000 0.00 0.00 0.00 3.58
543 544 2.101582 CTCCTATTTCCCCTCACAGTCG 59.898 54.545 0.00 0.00 0.00 4.18
595 596 3.775654 GGCCCTCACTCACTCCCG 61.776 72.222 0.00 0.00 0.00 5.14
603 604 4.180946 CTCACTCCCGGACGCTCG 62.181 72.222 0.73 0.00 0.00 5.03
658 659 2.434359 AGTCGCTAGCAAACGCCC 60.434 61.111 16.45 0.00 0.00 6.13
781 782 1.289109 CTGGCACCCGTCGTTGTTAG 61.289 60.000 0.00 0.00 0.00 2.34
815 816 3.406361 GGCCGATATGCGCAGACG 61.406 66.667 18.32 19.90 44.07 4.18
1245 1248 3.041940 CACGAGTTCGCCGCCTTT 61.042 61.111 0.73 0.00 44.43 3.11
1437 1440 0.595825 CTGACTGCTCGCGCATGATA 60.596 55.000 8.75 0.00 46.74 2.15
1521 1524 0.756070 GCGGAGGTAGGAGCTAGGTT 60.756 60.000 0.00 0.00 0.00 3.50
1538 1541 3.352990 TTGGTAAGGGCCGGCCATC 62.353 63.158 44.46 29.41 37.98 3.51
1550 1553 0.244450 CGGCCATCAGCAAACAATGT 59.756 50.000 2.24 0.00 46.50 2.71
1583 1586 2.572290 CCTCGTTGAGGGTTTTGTTCT 58.428 47.619 4.89 0.00 45.43 3.01
1655 1658 2.404215 CTCCCCGTAATGCGAATACTG 58.596 52.381 0.00 0.00 44.77 2.74
1743 1758 7.007723 TGATGGGTGTACTAAGAAATTTGGTT 58.992 34.615 0.00 0.00 0.00 3.67
1850 1887 1.905637 AGGTTGTGAAAATCGGGTCC 58.094 50.000 0.00 0.00 0.00 4.46
1852 1889 0.109919 GTTGTGAAAATCGGGTCCGC 60.110 55.000 4.27 0.00 39.59 5.54
1868 1905 2.946947 CGCAAGTTCTTGGGGATGT 58.053 52.632 17.81 0.00 0.00 3.06
1869 1906 0.804989 CGCAAGTTCTTGGGGATGTC 59.195 55.000 17.81 0.00 0.00 3.06
1884 1921 5.306937 TGGGGATGTCGTTGAATCTGTATAT 59.693 40.000 0.00 0.00 0.00 0.86
1970 2025 5.637006 TTTATTTTGAATCTGGTCCCACG 57.363 39.130 0.00 0.00 0.00 4.94
1989 2044 4.869861 CCACGTGTCATGTTGATCTCATAA 59.130 41.667 15.65 0.00 0.00 1.90
2003 2058 1.275291 CTCATAACTGGTCCCACACGT 59.725 52.381 0.00 0.00 0.00 4.49
2010 2065 1.953686 CTGGTCCCACACGTCAAAAAT 59.046 47.619 0.00 0.00 0.00 1.82
2034 2089 4.677584 TCAAAACTTGTCACCCATTTTCG 58.322 39.130 0.00 0.00 0.00 3.46
2047 2102 1.602377 CATTTTCGTAAGCGGATCCCC 59.398 52.381 6.06 0.00 38.89 4.81
2048 2103 0.906775 TTTTCGTAAGCGGATCCCCT 59.093 50.000 6.06 0.00 38.89 4.79
2049 2104 0.177141 TTTCGTAAGCGGATCCCCTG 59.823 55.000 6.06 0.00 38.89 4.45
2050 2105 1.682451 TTCGTAAGCGGATCCCCTGG 61.682 60.000 6.06 0.00 38.89 4.45
2051 2106 2.432300 CGTAAGCGGATCCCCTGGT 61.432 63.158 6.06 0.00 0.00 4.00
2052 2107 1.446366 GTAAGCGGATCCCCTGGTC 59.554 63.158 6.06 0.00 0.00 4.02
2069 2124 3.828451 CTGGTCAGGTTTCCATTTCACAT 59.172 43.478 0.00 0.00 33.01 3.21
2078 2159 8.036575 CAGGTTTCCATTTCACATGTATCAAAT 58.963 33.333 0.00 0.90 0.00 2.32
2113 2194 5.052040 GCACATGAAATTCGTCGAAAACAAA 60.052 36.000 12.40 0.00 0.00 2.83
2114 2195 6.345723 GCACATGAAATTCGTCGAAAACAAAT 60.346 34.615 12.40 0.21 0.00 2.32
2197 2278 5.814764 ATGCTACTCTTTCTTGAGCAATG 57.185 39.130 0.00 0.00 45.58 2.82
2221 2302 2.955660 TCATGGTTTCACACTTCCAACC 59.044 45.455 0.00 0.00 39.41 3.77
2242 2362 4.166919 ACCTCCTTTTATGCCTGAAGCTAT 59.833 41.667 0.00 0.00 44.23 2.97
2244 2364 6.126478 ACCTCCTTTTATGCCTGAAGCTATAA 60.126 38.462 0.00 0.00 44.23 0.98
2348 2471 2.859165 TGGAACAAAGGTGCTCCTAG 57.141 50.000 7.96 6.70 44.35 3.02
2384 2507 4.839668 ATGAGCATAAGAGTCTACGGTC 57.160 45.455 0.00 0.93 0.00 4.79
2403 2527 9.543783 CTACGGTCCTATTTTTCTAAGCTAAAT 57.456 33.333 0.00 0.00 0.00 1.40
2416 2540 4.650972 AAGCTAAATACACCAAGTCCCA 57.349 40.909 0.00 0.00 0.00 4.37
2435 2559 4.279671 TCCCAGCGTTTTGAAACAATATGT 59.720 37.500 7.32 0.00 38.81 2.29
2491 2615 2.031683 GGGCCTGAATTCAAATACGTCG 59.968 50.000 9.88 0.00 0.00 5.12
2500 2624 9.914923 CTGAATTCAAATACGTCGAATAAATGA 57.085 29.630 9.88 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 8.528643 GCCAATTAAATTAAGGTACAAGGTCTT 58.471 33.333 0.00 0.00 0.00 3.01
40 41 7.672239 TGCCAATTAAATTAAGGTACAAGGTCT 59.328 33.333 0.00 0.00 0.00 3.85
41 42 7.832769 TGCCAATTAAATTAAGGTACAAGGTC 58.167 34.615 0.00 0.00 0.00 3.85
42 43 7.578763 GCTGCCAATTAAATTAAGGTACAAGGT 60.579 37.037 0.00 0.00 0.00 3.50
43 44 6.756542 GCTGCCAATTAAATTAAGGTACAAGG 59.243 38.462 0.00 0.00 0.00 3.61
44 45 7.547227 AGCTGCCAATTAAATTAAGGTACAAG 58.453 34.615 0.00 0.00 0.00 3.16
45 46 7.475137 AGCTGCCAATTAAATTAAGGTACAA 57.525 32.000 0.00 0.00 0.00 2.41
46 47 8.050325 TCTAGCTGCCAATTAAATTAAGGTACA 58.950 33.333 0.00 0.00 0.00 2.90
47 48 8.446599 TCTAGCTGCCAATTAAATTAAGGTAC 57.553 34.615 0.00 0.00 0.00 3.34
48 49 9.640952 ATTCTAGCTGCCAATTAAATTAAGGTA 57.359 29.630 0.00 0.00 0.00 3.08
49 50 7.954666 TTCTAGCTGCCAATTAAATTAAGGT 57.045 32.000 0.00 0.00 0.00 3.50
50 51 9.468532 GAATTCTAGCTGCCAATTAAATTAAGG 57.531 33.333 0.00 0.00 0.00 2.69
54 55 9.895138 AAATGAATTCTAGCTGCCAATTAAATT 57.105 25.926 7.05 0.14 0.00 1.82
55 56 9.895138 AAAATGAATTCTAGCTGCCAATTAAAT 57.105 25.926 7.05 0.00 0.00 1.40
56 57 9.369904 GAAAATGAATTCTAGCTGCCAATTAAA 57.630 29.630 7.05 0.00 0.00 1.52
57 58 8.530311 TGAAAATGAATTCTAGCTGCCAATTAA 58.470 29.630 7.05 0.00 0.00 1.40
58 59 8.065473 TGAAAATGAATTCTAGCTGCCAATTA 57.935 30.769 7.05 0.00 0.00 1.40
59 60 6.938507 TGAAAATGAATTCTAGCTGCCAATT 58.061 32.000 7.05 0.00 0.00 2.32
60 61 6.534475 TGAAAATGAATTCTAGCTGCCAAT 57.466 33.333 7.05 0.00 0.00 3.16
61 62 5.981088 TGAAAATGAATTCTAGCTGCCAA 57.019 34.783 7.05 0.00 0.00 4.52
62 63 5.981088 TTGAAAATGAATTCTAGCTGCCA 57.019 34.783 7.05 0.00 0.00 4.92
63 64 8.139989 ACATATTGAAAATGAATTCTAGCTGCC 58.860 33.333 7.05 0.00 0.00 4.85
99 100 9.797556 CTGTGATTCACATATCATTTCATTGTT 57.202 29.630 19.29 0.00 43.71 2.83
100 101 8.963725 ACTGTGATTCACATATCATTTCATTGT 58.036 29.630 19.29 6.78 43.71 2.71
101 102 9.447040 GACTGTGATTCACATATCATTTCATTG 57.553 33.333 19.29 6.19 43.71 2.82
102 103 9.181061 TGACTGTGATTCACATATCATTTCATT 57.819 29.630 19.29 0.00 43.71 2.57
103 104 8.741603 TGACTGTGATTCACATATCATTTCAT 57.258 30.769 19.29 0.00 43.71 2.57
104 105 8.741603 ATGACTGTGATTCACATATCATTTCA 57.258 30.769 26.13 17.48 42.30 2.69
109 110 9.750125 GTAGTAATGACTGTGATTCACATATCA 57.250 33.333 24.73 24.73 43.71 2.15
110 111 9.750125 TGTAGTAATGACTGTGATTCACATATC 57.250 33.333 19.29 18.50 43.71 1.63
112 113 9.533253 CATGTAGTAATGACTGTGATTCACATA 57.467 33.333 19.29 9.86 43.71 2.29
113 114 7.011763 GCATGTAGTAATGACTGTGATTCACAT 59.988 37.037 19.29 10.08 43.71 3.21
114 115 6.313658 GCATGTAGTAATGACTGTGATTCACA 59.686 38.462 18.08 18.08 42.45 3.58
115 116 6.238211 GGCATGTAGTAATGACTGTGATTCAC 60.238 42.308 9.93 9.93 36.28 3.18
116 117 5.817296 GGCATGTAGTAATGACTGTGATTCA 59.183 40.000 0.00 0.00 36.28 2.57
117 118 6.051717 AGGCATGTAGTAATGACTGTGATTC 58.948 40.000 0.00 0.00 44.54 2.52
118 119 5.994250 AGGCATGTAGTAATGACTGTGATT 58.006 37.500 0.00 0.00 44.54 2.57
119 120 5.453903 GGAGGCATGTAGTAATGACTGTGAT 60.454 44.000 0.00 0.00 46.27 3.06
120 121 4.141937 GGAGGCATGTAGTAATGACTGTGA 60.142 45.833 0.00 0.00 46.27 3.58
121 122 4.122776 GGAGGCATGTAGTAATGACTGTG 58.877 47.826 0.00 0.00 46.27 3.66
122 123 3.134804 GGGAGGCATGTAGTAATGACTGT 59.865 47.826 0.00 0.00 46.27 3.55
123 124 3.389329 AGGGAGGCATGTAGTAATGACTG 59.611 47.826 0.00 0.00 46.27 3.51
125 126 4.130118 CAAGGGAGGCATGTAGTAATGAC 58.870 47.826 0.00 0.00 35.64 3.06
126 127 3.433598 GCAAGGGAGGCATGTAGTAATGA 60.434 47.826 0.00 0.00 0.00 2.57
127 128 2.880890 GCAAGGGAGGCATGTAGTAATG 59.119 50.000 0.00 0.00 0.00 1.90
128 129 2.509548 TGCAAGGGAGGCATGTAGTAAT 59.490 45.455 0.00 0.00 36.11 1.89
129 130 1.912731 TGCAAGGGAGGCATGTAGTAA 59.087 47.619 0.00 0.00 36.11 2.24
130 131 1.578897 TGCAAGGGAGGCATGTAGTA 58.421 50.000 0.00 0.00 36.11 1.82
131 132 0.698238 TTGCAAGGGAGGCATGTAGT 59.302 50.000 0.00 0.00 41.58 2.73
132 133 1.098050 GTTGCAAGGGAGGCATGTAG 58.902 55.000 0.00 0.00 41.58 2.74
133 134 0.698238 AGTTGCAAGGGAGGCATGTA 59.302 50.000 0.00 0.00 41.58 2.29
134 135 0.178953 AAGTTGCAAGGGAGGCATGT 60.179 50.000 0.00 0.00 41.58 3.21
135 136 0.971386 AAAGTTGCAAGGGAGGCATG 59.029 50.000 0.00 0.00 41.58 4.06
136 137 1.203100 AGAAAGTTGCAAGGGAGGCAT 60.203 47.619 0.00 0.00 41.58 4.40
137 138 0.185901 AGAAAGTTGCAAGGGAGGCA 59.814 50.000 0.00 0.00 40.00 4.75
138 139 2.200373 TAGAAAGTTGCAAGGGAGGC 57.800 50.000 0.00 0.00 0.00 4.70
139 140 6.834168 TTTATTAGAAAGTTGCAAGGGAGG 57.166 37.500 0.00 0.00 0.00 4.30
140 141 8.576442 TCTTTTTATTAGAAAGTTGCAAGGGAG 58.424 33.333 0.00 0.00 35.95 4.30
141 142 8.472007 TCTTTTTATTAGAAAGTTGCAAGGGA 57.528 30.769 0.00 0.00 35.95 4.20
164 165 9.384764 CGAATAACCTTCTTCTTCCTTTTATCT 57.615 33.333 0.00 0.00 0.00 1.98
165 166 9.379791 TCGAATAACCTTCTTCTTCCTTTTATC 57.620 33.333 0.00 0.00 0.00 1.75
166 167 9.734984 TTCGAATAACCTTCTTCTTCCTTTTAT 57.265 29.630 0.00 0.00 0.00 1.40
167 168 9.563748 TTTCGAATAACCTTCTTCTTCCTTTTA 57.436 29.630 0.00 0.00 0.00 1.52
168 169 8.350722 GTTTCGAATAACCTTCTTCTTCCTTTT 58.649 33.333 0.00 0.00 0.00 2.27
169 170 7.720074 AGTTTCGAATAACCTTCTTCTTCCTTT 59.280 33.333 0.00 0.00 0.00 3.11
170 171 7.225011 AGTTTCGAATAACCTTCTTCTTCCTT 58.775 34.615 0.00 0.00 0.00 3.36
171 172 6.770542 AGTTTCGAATAACCTTCTTCTTCCT 58.229 36.000 0.00 0.00 0.00 3.36
172 173 7.436430 AAGTTTCGAATAACCTTCTTCTTCC 57.564 36.000 0.00 0.00 0.00 3.46
173 174 8.775527 AGAAAGTTTCGAATAACCTTCTTCTTC 58.224 33.333 9.91 0.67 36.06 2.87
174 175 8.678593 AGAAAGTTTCGAATAACCTTCTTCTT 57.321 30.769 9.91 0.00 36.06 2.52
175 176 8.678593 AAGAAAGTTTCGAATAACCTTCTTCT 57.321 30.769 15.89 8.52 41.49 2.85
176 177 9.731819 AAAAGAAAGTTTCGAATAACCTTCTTC 57.268 29.630 19.51 8.99 43.11 2.87
181 182 9.406828 GCATAAAAAGAAAGTTTCGAATAACCT 57.593 29.630 9.91 0.00 34.02 3.50
182 183 8.363029 CGCATAAAAAGAAAGTTTCGAATAACC 58.637 33.333 9.91 0.00 34.02 2.85
183 184 9.109533 TCGCATAAAAAGAAAGTTTCGAATAAC 57.890 29.630 9.91 0.00 34.02 1.89
184 185 9.109533 GTCGCATAAAAAGAAAGTTTCGAATAA 57.890 29.630 9.91 0.00 34.02 1.40
185 186 8.500773 AGTCGCATAAAAAGAAAGTTTCGAATA 58.499 29.630 9.91 3.53 34.02 1.75
186 187 7.360361 AGTCGCATAAAAAGAAAGTTTCGAAT 58.640 30.769 9.91 0.00 34.02 3.34
187 188 6.721321 AGTCGCATAAAAAGAAAGTTTCGAA 58.279 32.000 9.91 0.00 34.02 3.71
188 189 6.295039 AGTCGCATAAAAAGAAAGTTTCGA 57.705 33.333 9.91 0.00 34.02 3.71
189 190 6.969669 AAGTCGCATAAAAAGAAAGTTTCG 57.030 33.333 9.91 0.00 34.02 3.46
190 191 9.447040 AGTAAAGTCGCATAAAAAGAAAGTTTC 57.553 29.630 7.57 7.57 0.00 2.78
191 192 9.447040 GAGTAAAGTCGCATAAAAAGAAAGTTT 57.553 29.630 0.00 0.00 0.00 2.66
192 193 8.837389 AGAGTAAAGTCGCATAAAAAGAAAGTT 58.163 29.630 0.00 0.00 0.00 2.66
193 194 8.379457 AGAGTAAAGTCGCATAAAAAGAAAGT 57.621 30.769 0.00 0.00 0.00 2.66
197 198 8.715088 GGTTTAGAGTAAAGTCGCATAAAAAGA 58.285 33.333 0.00 0.00 0.00 2.52
198 199 7.686938 CGGTTTAGAGTAAAGTCGCATAAAAAG 59.313 37.037 0.00 0.00 0.00 2.27
199 200 7.171337 ACGGTTTAGAGTAAAGTCGCATAAAAA 59.829 33.333 0.00 0.00 32.43 1.94
200 201 6.646240 ACGGTTTAGAGTAAAGTCGCATAAAA 59.354 34.615 0.00 0.00 32.43 1.52
201 202 6.158598 ACGGTTTAGAGTAAAGTCGCATAAA 58.841 36.000 0.00 0.00 32.43 1.40
202 203 5.713025 ACGGTTTAGAGTAAAGTCGCATAA 58.287 37.500 0.00 0.00 32.43 1.90
203 204 5.314923 ACGGTTTAGAGTAAAGTCGCATA 57.685 39.130 0.00 0.00 32.43 3.14
204 205 4.184079 ACGGTTTAGAGTAAAGTCGCAT 57.816 40.909 0.00 0.00 32.43 4.73
205 206 3.648339 ACGGTTTAGAGTAAAGTCGCA 57.352 42.857 0.00 0.00 32.43 5.10
206 207 3.737774 ACAACGGTTTAGAGTAAAGTCGC 59.262 43.478 0.00 0.00 32.43 5.19
207 208 8.847444 ATATACAACGGTTTAGAGTAAAGTCG 57.153 34.615 0.00 0.00 34.14 4.18
238 239 9.549078 CCTTCTTCTTCTTGTTAGAAAGTTACT 57.451 33.333 0.00 0.00 39.80 2.24
239 240 9.327628 ACCTTCTTCTTCTTGTTAGAAAGTTAC 57.672 33.333 0.00 0.00 39.80 2.50
240 241 9.901172 AACCTTCTTCTTCTTGTTAGAAAGTTA 57.099 29.630 0.00 0.00 39.80 2.24
241 242 8.809468 AACCTTCTTCTTCTTGTTAGAAAGTT 57.191 30.769 0.00 0.00 39.80 2.66
245 246 9.204570 CGAATAACCTTCTTCTTCTTGTTAGAA 57.795 33.333 0.00 0.00 38.06 2.10
246 247 8.582437 TCGAATAACCTTCTTCTTCTTGTTAGA 58.418 33.333 0.00 0.00 0.00 2.10
247 248 8.758633 TCGAATAACCTTCTTCTTCTTGTTAG 57.241 34.615 0.00 0.00 0.00 2.34
248 249 9.550406 TTTCGAATAACCTTCTTCTTCTTGTTA 57.450 29.630 0.00 0.00 0.00 2.41
249 250 8.446599 TTTCGAATAACCTTCTTCTTCTTGTT 57.553 30.769 0.00 0.00 0.00 2.83
250 251 8.622948 ATTTCGAATAACCTTCTTCTTCTTGT 57.377 30.769 0.00 0.00 0.00 3.16
251 252 9.899226 AAATTTCGAATAACCTTCTTCTTCTTG 57.101 29.630 0.00 0.00 0.00 3.02
252 253 9.899226 CAAATTTCGAATAACCTTCTTCTTCTT 57.101 29.630 0.00 0.00 0.00 2.52
253 254 8.515414 CCAAATTTCGAATAACCTTCTTCTTCT 58.485 33.333 0.00 0.00 0.00 2.85
254 255 7.755373 CCCAAATTTCGAATAACCTTCTTCTTC 59.245 37.037 0.00 0.00 0.00 2.87
255 256 7.450323 TCCCAAATTTCGAATAACCTTCTTCTT 59.550 33.333 0.00 0.00 0.00 2.52
256 257 6.946009 TCCCAAATTTCGAATAACCTTCTTCT 59.054 34.615 0.00 0.00 0.00 2.85
257 258 7.027760 GTCCCAAATTTCGAATAACCTTCTTC 58.972 38.462 0.00 0.00 0.00 2.87
258 259 6.349033 CGTCCCAAATTTCGAATAACCTTCTT 60.349 38.462 0.00 0.00 0.00 2.52
259 260 5.123344 CGTCCCAAATTTCGAATAACCTTCT 59.877 40.000 0.00 0.00 0.00 2.85
260 261 5.329493 CGTCCCAAATTTCGAATAACCTTC 58.671 41.667 0.00 0.00 0.00 3.46
261 262 4.380128 GCGTCCCAAATTTCGAATAACCTT 60.380 41.667 0.00 0.00 0.00 3.50
270 271 1.211709 GGTGGCGTCCCAAATTTCG 59.788 57.895 0.00 0.00 44.33 3.46
273 274 0.970427 GGATGGTGGCGTCCCAAATT 60.970 55.000 1.25 0.00 44.33 1.82
275 276 2.034999 GGATGGTGGCGTCCCAAA 59.965 61.111 1.25 0.00 44.33 3.28
276 277 2.933287 AGGATGGTGGCGTCCCAA 60.933 61.111 1.25 0.00 44.33 4.12
280 281 0.321653 AAAGTGAGGATGGTGGCGTC 60.322 55.000 0.00 0.00 0.00 5.19
305 306 1.202405 CGCCATAATTTTCCCACAGGC 60.202 52.381 0.00 0.00 37.54 4.85
311 312 1.037493 GGGGTCGCCATAATTTTCCC 58.963 55.000 0.00 0.00 0.00 3.97
397 398 0.974010 ACCGCGTAGGGATTTCCTCA 60.974 55.000 4.92 0.00 44.06 3.86
543 544 1.083401 CGCTGTCGAGTTGTGCAAC 60.083 57.895 6.94 6.94 41.45 4.17
643 644 3.950794 CTGGGGCGTTTGCTAGCGA 62.951 63.158 10.77 5.12 42.25 4.93
763 764 1.301087 CTAACAACGACGGGTGCCA 60.301 57.895 0.00 0.00 0.00 4.92
781 782 1.173913 GCCCACATGTAAACTGGGTC 58.826 55.000 17.24 8.11 45.90 4.46
1311 1314 1.153469 GAAGGCCTCCTTGAGCTCG 60.153 63.158 5.23 0.00 44.82 5.03
1521 1524 3.804329 GATGGCCGGCCCTTACCA 61.804 66.667 41.75 23.71 36.43 3.25
1606 1609 7.978099 AGCCTTTCACTTTGGGATTAATTAT 57.022 32.000 0.00 0.00 0.00 1.28
1616 1619 2.489722 GAGCCTAAGCCTTTCACTTTGG 59.510 50.000 0.00 0.00 41.28 3.28
1655 1658 1.600957 CACTTCACCCGCATCATCATC 59.399 52.381 0.00 0.00 0.00 2.92
1743 1758 7.002250 TCTAATTCATTGCAAACAATCCCAA 57.998 32.000 1.71 0.00 44.83 4.12
1831 1868 1.880646 CGGACCCGATTTTCACAACCT 60.881 52.381 1.54 0.00 42.83 3.50
1850 1887 0.804989 GACATCCCCAAGAACTTGCG 59.195 55.000 8.81 1.17 39.16 4.85
1852 1889 2.185004 ACGACATCCCCAAGAACTTG 57.815 50.000 7.49 7.49 40.13 3.16
1866 1903 8.716646 ACAAATGATATACAGATTCAACGACA 57.283 30.769 0.00 0.00 0.00 4.35
1868 1905 9.161629 ACAACAAATGATATACAGATTCAACGA 57.838 29.630 0.00 0.00 0.00 3.85
1884 1921 8.226819 TGTGGTAATTTGAGTACAACAAATGA 57.773 30.769 22.33 16.33 43.94 2.57
1959 1996 1.118965 ACATGACACGTGGGACCAGA 61.119 55.000 21.57 0.00 0.00 3.86
1970 2025 5.877012 ACCAGTTATGAGATCAACATGACAC 59.123 40.000 20.68 12.74 36.93 3.67
1989 2044 0.253610 TTTTGACGTGTGGGACCAGT 59.746 50.000 0.00 0.00 0.00 4.00
2003 2058 6.936900 TGGGTGACAAGTTTTGAAATTTTTGA 59.063 30.769 5.31 0.00 0.00 2.69
2010 2065 5.578727 CGAAAATGGGTGACAAGTTTTGAAA 59.421 36.000 0.00 0.00 0.00 2.69
2034 2089 1.335132 TGACCAGGGGATCCGCTTAC 61.335 60.000 27.76 20.27 37.10 2.34
2047 2102 3.221771 TGTGAAATGGAAACCTGACCAG 58.778 45.455 0.00 0.00 39.62 4.00
2048 2103 3.304911 TGTGAAATGGAAACCTGACCA 57.695 42.857 0.00 0.00 40.57 4.02
2049 2104 3.573967 ACATGTGAAATGGAAACCTGACC 59.426 43.478 0.00 0.00 0.00 4.02
2050 2105 4.853924 ACATGTGAAATGGAAACCTGAC 57.146 40.909 0.00 0.00 0.00 3.51
2051 2106 6.244654 TGATACATGTGAAATGGAAACCTGA 58.755 36.000 9.11 0.00 0.00 3.86
2052 2107 6.513806 TGATACATGTGAAATGGAAACCTG 57.486 37.500 9.11 0.00 0.00 4.00
2069 2124 5.422012 TGTGCTCTCTGGTCTATTTGATACA 59.578 40.000 0.00 0.00 0.00 2.29
2078 2159 5.423015 GAATTTCATGTGCTCTCTGGTCTA 58.577 41.667 0.00 0.00 0.00 2.59
2182 2263 4.082408 CCATGAAGCATTGCTCAAGAAAGA 60.082 41.667 12.39 0.00 38.25 2.52
2197 2278 2.622942 TGGAAGTGTGAAACCATGAAGC 59.377 45.455 0.00 0.00 34.36 3.86
2221 2302 7.992754 ATTATAGCTTCAGGCATAAAAGGAG 57.007 36.000 0.00 0.00 44.79 3.69
2244 2364 8.082242 GTGCCTTGTTTTTATCAGTTCTTGTAT 58.918 33.333 0.00 0.00 0.00 2.29
2347 2470 2.163010 GCTCATTGCAATGTGCTACACT 59.837 45.455 39.45 7.53 46.66 3.55
2348 2471 2.523015 GCTCATTGCAATGTGCTACAC 58.477 47.619 39.45 22.25 46.66 2.90
2379 2502 9.322773 GTATTTAGCTTAGAAAAATAGGACCGT 57.677 33.333 0.00 0.00 0.00 4.83
2403 2527 0.470766 AAACGCTGGGACTTGGTGTA 59.529 50.000 0.00 0.00 0.00 2.90
2416 2540 8.268850 AGATAGACATATTGTTTCAAAACGCT 57.731 30.769 1.52 0.00 41.74 5.07


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

AutoCloner maintained by Alex Coulton.