Multiple sequence alignment - TraesCS4B01G280000

Loading Multiple Alignment...

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 TraesCS4B01G280000 chr4B 100.000 4460 0 0 1 4460 562879284 562883743 0.000000e+00 8237.0
1 TraesCS4B01G280000 chr4D 96.412 4181 116 15 293 4460 450137097 450141256 0.000000e+00 6859.0
2 TraesCS4B01G280000 chr4D 91.787 207 8 1 16 213 450136715 450136921 3.400000e-71 279.0
3 TraesCS4B01G280000 chr4D 88.344 163 16 2 293 455 450136714 450136873 4.550000e-45 193.0
4 TraesCS4B01G280000 chr4D 89.855 138 11 2 16 150 450137098 450137235 1.650000e-39 174.0
5 TraesCS4B01G280000 chr4A 95.475 3072 110 17 1412 4460 16512042 16508977 0.000000e+00 4876.0
6 TraesCS4B01G280000 chr4A 95.485 753 24 3 708 1460 16512772 16512030 0.000000e+00 1194.0
7 TraesCS4B01G280000 chr4A 91.844 282 14 3 293 574 16513163 16512891 7.000000e-103 385.0
8 TraesCS4B01G280000 chr4A 91.705 217 9 1 19 226 16513539 16513323 4.360000e-75 292.0
9 TraesCS4B01G280000 chr4A 88.344 163 16 2 293 455 16513543 16513384 4.550000e-45 193.0
10 TraesCS4B01G280000 chr4A 94.805 77 3 1 570 646 16512847 16512772 7.840000e-23 119.0
11 TraesCS4B01G280000 chr3D 88.401 3164 283 40 572 3680 495323867 495320733 0.000000e+00 3733.0
12 TraesCS4B01G280000 chr3D 90.196 51 5 0 1352 1402 495322897 495322847 2.880000e-07 67.6
13 TraesCS4B01G280000 chr3B 88.509 2489 191 38 1231 3686 654358193 654355767 0.000000e+00 2924.0
14 TraesCS4B01G280000 chr3B 84.933 750 85 21 572 1303 654358926 654358187 0.000000e+00 734.0
15 TraesCS4B01G280000 chr3B 88.235 51 6 0 1352 1402 654357937 654357887 1.340000e-05 62.1
16 TraesCS4B01G280000 chr3A 90.346 1792 133 17 1257 3035 634726060 634724296 0.000000e+00 2314.0
17 TraesCS4B01G280000 chr3A 83.832 668 69 17 3033 3680 634712540 634711892 2.300000e-167 599.0
18 TraesCS4B01G280000 chr3A 86.275 51 7 0 1352 1402 634725803 634725753 6.230000e-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 TraesCS4B01G280000 chr4B 562879284 562883743 4459 False 8237.000000 8237 100.000000 1 4460 1 chr4B.!!$F1 4459
1 TraesCS4B01G280000 chr4D 450136714 450141256 4542 False 2443.666667 6859 92.181000 16 4460 3 chr4D.!!$F2 4444
2 TraesCS4B01G280000 chr4A 16508977 16513543 4566 True 1176.500000 4876 92.943000 19 4460 6 chr4A.!!$R1 4441
3 TraesCS4B01G280000 chr3D 495320733 495323867 3134 True 1900.300000 3733 89.298500 572 3680 2 chr3D.!!$R1 3108
4 TraesCS4B01G280000 chr3B 654355767 654358926 3159 True 1240.033333 2924 87.225667 572 3686 3 chr3B.!!$R1 3114
5 TraesCS4B01G280000 chr3A 634724296 634726060 1764 True 1185.250000 2314 88.310500 1257 3035 2 chr3A.!!$R2 1778
6 TraesCS4B01G280000 chr3A 634711892 634712540 648 True 599.000000 599 83.832000 3033 3680 1 chr3A.!!$R1 647

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
277 294 0.321021 TGGAACACCATGCAATTGGC 59.679 50.0 7.72 0.15 40.68 4.52 F
627 791 1.533625 TTTTGGACGGGCAATCTCAG 58.466 50.0 0.00 0.00 0.00 3.35 F
1926 2254 1.103398 ACACAAGCCTGTTGCACCTC 61.103 55.0 0.00 0.00 44.83 3.85 F
2133 2461 1.186267 AGGTTCCAGGTGTCGAGGTC 61.186 60.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1187 1365 0.322098 CGGAACACCACCAGGCATTA 60.322 55.0 0.00 0.00 39.06 1.90 R
2478 2806 0.710588 TCTCCACCCAGGCTTCTCTA 59.289 55.0 0.00 0.00 37.29 2.43 R
3237 3566 0.957395 AGCTGTGGTTCATGAAGCGG 60.957 55.0 27.39 21.01 41.36 5.52 R
4032 4395 0.319900 CAGCAGTTACTGTGCCGAGT 60.320 55.0 14.23 0.00 42.24 4.18 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
20 21 2.656947 TCAAACTTTGAGGGGTCCTG 57.343 50.000 0.00 0.00 34.08 3.86
21 22 1.850345 TCAAACTTTGAGGGGTCCTGT 59.150 47.619 0.00 0.00 34.08 4.00
22 23 2.158667 TCAAACTTTGAGGGGTCCTGTC 60.159 50.000 0.00 0.00 34.08 3.51
26 27 1.477685 TTTGAGGGGTCCTGTCGTCC 61.478 60.000 0.00 0.00 31.76 4.79
63 64 6.095440 ACAGCAAACAACAAGTCTATCAGTTT 59.905 34.615 0.00 0.00 0.00 2.66
130 131 4.887748 TCCTTGAAGTTGTCTTAGCTCAG 58.112 43.478 0.00 0.00 33.64 3.35
226 243 7.849322 ACCATTTTTAATTGTCAGTAGGGTT 57.151 32.000 0.00 0.00 0.00 4.11
227 244 7.666623 ACCATTTTTAATTGTCAGTAGGGTTG 58.333 34.615 0.00 0.00 0.00 3.77
228 245 7.507616 ACCATTTTTAATTGTCAGTAGGGTTGA 59.492 33.333 0.00 0.00 0.00 3.18
229 246 8.364142 CCATTTTTAATTGTCAGTAGGGTTGAA 58.636 33.333 0.00 0.00 0.00 2.69
230 247 9.191995 CATTTTTAATTGTCAGTAGGGTTGAAC 57.808 33.333 0.00 0.00 0.00 3.18
232 249 9.629878 TTTTTAATTGTCAGTAGGGTTGAACTA 57.370 29.630 0.00 0.00 0.00 2.24
235 252 9.802039 TTAATTGTCAGTAGGGTTGAACTATTT 57.198 29.630 0.00 0.00 0.00 1.40
236 253 7.687941 ATTGTCAGTAGGGTTGAACTATTTG 57.312 36.000 0.00 0.00 0.00 2.32
239 256 7.458397 TGTCAGTAGGGTTGAACTATTTGATT 58.542 34.615 0.00 0.00 0.00 2.57
240 257 7.606456 TGTCAGTAGGGTTGAACTATTTGATTC 59.394 37.037 0.00 0.00 0.00 2.52
241 258 7.065923 GTCAGTAGGGTTGAACTATTTGATTCC 59.934 40.741 0.00 0.00 0.00 3.01
242 259 6.884295 CAGTAGGGTTGAACTATTTGATTCCA 59.116 38.462 0.00 0.00 0.00 3.53
243 260 7.066284 CAGTAGGGTTGAACTATTTGATTCCAG 59.934 40.741 0.00 0.00 0.00 3.86
244 261 5.892348 AGGGTTGAACTATTTGATTCCAGT 58.108 37.500 0.00 0.00 0.00 4.00
247 264 6.389906 GGTTGAACTATTTGATTCCAGTTGG 58.610 40.000 0.00 0.00 31.57 3.77
248 265 5.643379 TGAACTATTTGATTCCAGTTGGC 57.357 39.130 0.00 0.00 31.57 4.52
249 266 5.076182 TGAACTATTTGATTCCAGTTGGCA 58.924 37.500 0.00 0.00 31.57 4.92
252 269 7.395772 TGAACTATTTGATTCCAGTTGGCATAA 59.604 33.333 0.00 0.00 31.57 1.90
253 270 7.716799 ACTATTTGATTCCAGTTGGCATAAA 57.283 32.000 0.00 0.00 34.44 1.40
255 272 8.761689 ACTATTTGATTCCAGTTGGCATAAAAT 58.238 29.630 9.94 9.94 36.36 1.82
256 273 9.603921 CTATTTGATTCCAGTTGGCATAAAATT 57.396 29.630 10.22 0.00 34.85 1.82
257 274 7.903995 TTTGATTCCAGTTGGCATAAAATTC 57.096 32.000 0.00 0.00 34.44 2.17
258 275 6.855763 TGATTCCAGTTGGCATAAAATTCT 57.144 33.333 0.00 0.00 34.44 2.40
259 276 6.632909 TGATTCCAGTTGGCATAAAATTCTG 58.367 36.000 0.00 0.00 34.44 3.02
260 277 5.404466 TTCCAGTTGGCATAAAATTCTGG 57.596 39.130 0.00 0.00 41.30 3.86
261 278 4.671831 TCCAGTTGGCATAAAATTCTGGA 58.328 39.130 6.87 6.87 44.73 3.86
262 279 5.083122 TCCAGTTGGCATAAAATTCTGGAA 58.917 37.500 8.29 0.00 44.22 3.53
263 280 5.047377 TCCAGTTGGCATAAAATTCTGGAAC 60.047 40.000 8.29 0.00 44.22 3.62
264 281 5.279406 CCAGTTGGCATAAAATTCTGGAACA 60.279 40.000 0.00 0.00 42.16 3.18
265 282 5.634859 CAGTTGGCATAAAATTCTGGAACAC 59.365 40.000 0.00 0.00 0.00 3.32
266 283 4.799564 TGGCATAAAATTCTGGAACACC 57.200 40.909 0.00 0.00 0.00 4.16
267 284 4.155709 TGGCATAAAATTCTGGAACACCA 58.844 39.130 0.00 0.00 0.00 4.17
268 285 4.776837 TGGCATAAAATTCTGGAACACCAT 59.223 37.500 0.00 0.00 32.90 3.55
269 286 5.111293 GGCATAAAATTCTGGAACACCATG 58.889 41.667 0.00 0.00 32.90 3.66
271 288 5.722263 CATAAAATTCTGGAACACCATGCA 58.278 37.500 0.00 0.00 32.90 3.96
272 289 4.686191 AAAATTCTGGAACACCATGCAA 57.314 36.364 0.00 0.00 32.90 4.08
277 294 0.321021 TGGAACACCATGCAATTGGC 59.679 50.000 7.72 0.15 40.68 4.52
313 427 8.073768 CCAAAAGTTCTGTTGTCGTACATATTT 58.926 33.333 0.00 0.00 0.00 1.40
407 521 2.106511 TGCTCCTTGAAGTTGGCTTAGT 59.893 45.455 0.00 0.00 34.61 2.24
615 779 6.691388 GTCGAATACTAATGCCATTTTTGGAC 59.309 38.462 0.00 0.00 0.00 4.02
627 791 1.533625 TTTTGGACGGGCAATCTCAG 58.466 50.000 0.00 0.00 0.00 3.35
685 849 3.059166 GGCACAGTTACCAAGCAAAATG 58.941 45.455 0.00 0.00 0.00 2.32
772 946 7.838771 TCAGTGAACTGTAATCTGATGAATG 57.161 36.000 10.14 0.00 44.12 2.67
881 1058 1.701847 ACACTCAAGGCACTGAAGGAT 59.298 47.619 0.00 0.00 40.86 3.24
1227 1405 3.436704 CGCCAATGTTAACATCACTGTCT 59.563 43.478 21.02 1.22 35.10 3.41
1419 1672 5.778241 TCAAGATACCACTACTGTTCCTTCA 59.222 40.000 0.00 0.00 0.00 3.02
1453 1733 1.977685 CCGGTTCCTACGGTTCCTT 59.022 57.895 0.00 0.00 46.03 3.36
1462 1778 2.094130 CCTACGGTTCCTTCAGTTCCTC 60.094 54.545 0.00 0.00 0.00 3.71
1466 1782 1.611936 GGTTCCTTCAGTTCCTCCAGC 60.612 57.143 0.00 0.00 0.00 4.85
1516 1832 1.342074 TGTTCTCCAGACACCTCCTG 58.658 55.000 0.00 0.00 0.00 3.86
1548 1864 2.376518 ACAGGAATCTGGCAAGAGGAAA 59.623 45.455 0.00 0.00 44.99 3.13
1926 2254 1.103398 ACACAAGCCTGTTGCACCTC 61.103 55.000 0.00 0.00 44.83 3.85
2133 2461 1.186267 AGGTTCCAGGTGTCGAGGTC 61.186 60.000 0.00 0.00 0.00 3.85
2478 2806 7.702785 ACATATATGATGGCCTTTACCAGATT 58.297 34.615 19.63 0.00 44.71 2.40
2886 3215 4.054780 TGTTAGTCGGATGCCTATGTTC 57.945 45.455 0.00 0.00 0.00 3.18
3153 3482 5.815581 TGGAACTATGCACCAGAATTACTT 58.184 37.500 4.22 0.00 0.00 2.24
3417 3764 1.675116 GGGTGTCGGAGGACTAAAAGC 60.675 57.143 0.00 0.00 43.79 3.51
3435 3782 1.276421 AGCTGCTTATGTTGGTCTCGT 59.724 47.619 0.00 0.00 0.00 4.18
3498 3845 4.142160 GGGATAATTTGCCAGTTGAAGGTC 60.142 45.833 0.00 0.00 35.48 3.85
3546 3894 6.585695 TCTGTACATTACTTCTCCGAAAGT 57.414 37.500 0.00 3.81 42.10 2.66
3599 3951 4.715534 TTGGAGTTTGAAGGGTGTGATA 57.284 40.909 0.00 0.00 0.00 2.15
3630 3982 7.933396 TGAGATGTTGGTAGATGCAAATATTG 58.067 34.615 0.00 0.00 0.00 1.90
3704 4056 2.831685 TAACGGGGCATATGCAGTAG 57.168 50.000 28.07 17.62 44.36 2.57
3705 4057 0.535102 AACGGGGCATATGCAGTAGC 60.535 55.000 28.07 10.89 44.36 3.58
3759 4111 0.886563 AGCAAGAAAGATGTGCCAGC 59.113 50.000 0.00 0.00 39.13 4.85
3760 4112 0.599558 GCAAGAAAGATGTGCCAGCA 59.400 50.000 0.00 0.00 31.94 4.41
3766 4118 0.463295 AAGATGTGCCAGCAGGATCG 60.463 55.000 0.00 0.00 36.89 3.69
3777 4129 0.935898 GCAGGATCGCTTCATGTCAG 59.064 55.000 0.00 0.00 38.40 3.51
3788 4140 4.054671 GCTTCATGTCAGGATAGCAGTAC 58.945 47.826 13.28 0.00 0.00 2.73
3818 4170 6.492254 GTCGGTCAGAAATTGTTTAAACACT 58.508 36.000 20.43 12.78 38.92 3.55
3839 4191 5.615289 ACTGCAGTGAGAAAATACTGAACT 58.385 37.500 20.97 0.00 45.46 3.01
3847 4199 9.482627 AGTGAGAAAATACTGAACTTGTAGAAG 57.517 33.333 0.00 0.00 35.07 2.85
3851 4203 9.699703 AGAAAATACTGAACTTGTAGAAGACTC 57.300 33.333 6.63 3.43 32.98 3.36
3860 4212 9.298250 TGAACTTGTAGAAGACTCTATACACTT 57.702 33.333 6.63 0.00 36.54 3.16
3886 4238 0.469917 ACCAATCTCCATGCCTACCG 59.530 55.000 0.00 0.00 0.00 4.02
3888 4240 1.541233 CCAATCTCCATGCCTACCGAC 60.541 57.143 0.00 0.00 0.00 4.79
3890 4242 1.043816 ATCTCCATGCCTACCGACAG 58.956 55.000 0.00 0.00 0.00 3.51
3937 4289 3.197766 TCGAGCACTGTTTTGGATATCCT 59.802 43.478 22.35 0.00 36.82 3.24
4004 4367 4.288105 TCTCCCTCTCTTGATTTGAGCTTT 59.712 41.667 0.00 0.00 0.00 3.51
4036 4399 9.162793 GTTATGATGAAATTTGCATAAGACTCG 57.837 33.333 13.68 0.00 34.84 4.18
4037 4400 6.122850 TGATGAAATTTGCATAAGACTCGG 57.877 37.500 0.00 0.00 0.00 4.63
4043 4406 0.608130 TGCATAAGACTCGGCACAGT 59.392 50.000 0.00 0.00 0.00 3.55
4097 4460 5.220416 CCTGTAGAAGCTGTTAATTGTACGC 60.220 44.000 0.00 0.00 30.08 4.42
4201 4566 0.538287 ACTGGAAGAACTTGCTGCCC 60.538 55.000 11.33 0.00 37.43 5.36
4207 4572 1.589414 AGAACTTGCTGCCCCTCTAT 58.411 50.000 0.00 0.00 0.00 1.98
4266 4631 6.715347 AGATGTTGTAATAAAAGGCCATCC 57.285 37.500 5.01 0.00 0.00 3.51
4312 4677 1.076632 TTGTGTGCTCCGGGGTTTT 60.077 52.632 1.62 0.00 0.00 2.43
4315 4680 1.320507 GTGTGCTCCGGGGTTTTAAA 58.679 50.000 1.62 0.00 0.00 1.52
4383 4748 2.033662 GCCGCAGTGAATCTATCGTTTC 60.034 50.000 0.00 0.00 0.00 2.78
4384 4749 3.448686 CCGCAGTGAATCTATCGTTTCT 58.551 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.850345 ACAGGACCCCTCAAAGTTTGA 59.150 47.619 17.16 17.16 38.17 2.69
2 3 2.230660 GACAGGACCCCTCAAAGTTTG 58.769 52.381 9.44 9.44 0.00 2.93
3 4 1.202770 CGACAGGACCCCTCAAAGTTT 60.203 52.381 0.00 0.00 0.00 2.66
4 5 0.396811 CGACAGGACCCCTCAAAGTT 59.603 55.000 0.00 0.00 0.00 2.66
5 6 0.763223 ACGACAGGACCCCTCAAAGT 60.763 55.000 0.00 0.00 0.00 2.66
6 7 0.037232 GACGACAGGACCCCTCAAAG 60.037 60.000 0.00 0.00 0.00 2.77
8 9 1.911766 GGACGACAGGACCCCTCAA 60.912 63.158 0.00 0.00 0.00 3.02
9 10 1.503401 TAGGACGACAGGACCCCTCA 61.503 60.000 0.00 0.00 0.00 3.86
10 11 1.036481 GTAGGACGACAGGACCCCTC 61.036 65.000 0.00 0.00 0.00 4.30
11 12 1.000107 GTAGGACGACAGGACCCCT 60.000 63.158 0.00 0.00 0.00 4.79
12 13 0.686769 ATGTAGGACGACAGGACCCC 60.687 60.000 0.00 0.00 31.51 4.95
13 14 2.062971 TATGTAGGACGACAGGACCC 57.937 55.000 0.00 0.00 31.51 4.46
14 15 3.635373 TGAATATGTAGGACGACAGGACC 59.365 47.826 0.00 0.00 31.51 4.46
15 16 4.913335 TGAATATGTAGGACGACAGGAC 57.087 45.455 0.00 0.00 31.51 3.85
16 17 5.186215 TGTTTGAATATGTAGGACGACAGGA 59.814 40.000 0.00 0.00 31.51 3.86
17 18 5.416083 TGTTTGAATATGTAGGACGACAGG 58.584 41.667 0.00 0.00 31.51 4.00
18 19 5.005779 GCTGTTTGAATATGTAGGACGACAG 59.994 44.000 0.00 0.00 35.22 3.51
19 20 4.868171 GCTGTTTGAATATGTAGGACGACA 59.132 41.667 0.00 0.00 0.00 4.35
20 21 4.868171 TGCTGTTTGAATATGTAGGACGAC 59.132 41.667 0.00 0.00 0.00 4.34
21 22 5.079689 TGCTGTTTGAATATGTAGGACGA 57.920 39.130 0.00 0.00 0.00 4.20
22 23 5.794687 TTGCTGTTTGAATATGTAGGACG 57.205 39.130 0.00 0.00 0.00 4.79
26 27 8.572828 TTGTTGTTTGCTGTTTGAATATGTAG 57.427 30.769 0.00 0.00 0.00 2.74
63 64 8.693625 GTTAAGCAGAAAGGACCTATTAGTAGA 58.306 37.037 0.00 0.00 0.00 2.59
81 82 2.222596 GCACGACGAATGAGTTAAGCAG 60.223 50.000 0.00 0.00 0.00 4.24
130 131 4.459337 ACAGTTTTAGGCTACAAATGGCTC 59.541 41.667 20.75 0.00 40.79 4.70
226 243 5.076182 TGCCAACTGGAATCAAATAGTTCA 58.924 37.500 0.00 0.00 37.39 3.18
227 244 5.643379 TGCCAACTGGAATCAAATAGTTC 57.357 39.130 0.00 0.00 37.39 3.01
228 245 7.716799 TTATGCCAACTGGAATCAAATAGTT 57.283 32.000 0.00 0.00 34.53 2.24
229 246 7.716799 TTTATGCCAACTGGAATCAAATAGT 57.283 32.000 0.00 0.00 34.53 2.12
230 247 9.603921 AATTTTATGCCAACTGGAATCAAATAG 57.396 29.630 8.64 0.00 36.49 1.73
232 249 8.323567 AGAATTTTATGCCAACTGGAATCAAAT 58.676 29.630 0.00 1.62 38.21 2.32
235 252 6.351202 CCAGAATTTTATGCCAACTGGAATCA 60.351 38.462 0.00 0.00 43.91 2.57
236 253 6.044682 CCAGAATTTTATGCCAACTGGAATC 58.955 40.000 0.00 0.00 43.91 2.52
239 256 4.671831 TCCAGAATTTTATGCCAACTGGA 58.328 39.130 0.00 0.00 46.29 3.86
240 257 5.170748 GTTCCAGAATTTTATGCCAACTGG 58.829 41.667 0.00 0.00 42.97 4.00
241 258 5.634859 GTGTTCCAGAATTTTATGCCAACTG 59.365 40.000 0.00 0.00 0.00 3.16
242 259 5.279456 GGTGTTCCAGAATTTTATGCCAACT 60.279 40.000 0.00 0.00 0.00 3.16
243 260 4.929211 GGTGTTCCAGAATTTTATGCCAAC 59.071 41.667 0.00 0.00 0.00 3.77
244 261 4.590647 TGGTGTTCCAGAATTTTATGCCAA 59.409 37.500 0.00 0.00 39.03 4.52
259 276 3.142124 GCCAATTGCATGGTGTTCC 57.858 52.632 8.13 0.00 42.75 3.62
269 286 7.369607 ACTTTTGGAAATTTTATGCCAATTGC 58.630 30.769 9.24 0.00 39.87 3.56
271 288 9.353431 AGAACTTTTGGAAATTTTATGCCAATT 57.647 25.926 9.24 2.84 39.87 2.32
272 289 8.785946 CAGAACTTTTGGAAATTTTATGCCAAT 58.214 29.630 9.24 0.00 39.87 3.16
278 295 9.030301 CGACAACAGAACTTTTGGAAATTTTAT 57.970 29.630 5.84 0.00 0.00 1.40
279 296 8.030106 ACGACAACAGAACTTTTGGAAATTTTA 58.970 29.630 5.84 0.00 0.00 1.52
280 297 6.871492 ACGACAACAGAACTTTTGGAAATTTT 59.129 30.769 5.84 0.00 0.00 1.82
281 298 6.394809 ACGACAACAGAACTTTTGGAAATTT 58.605 32.000 0.00 0.00 0.00 1.82
282 299 5.961272 ACGACAACAGAACTTTTGGAAATT 58.039 33.333 5.84 0.00 0.00 1.82
284 301 5.411977 TGTACGACAACAGAACTTTTGGAAA 59.588 36.000 5.84 0.00 0.00 3.13
287 304 4.868450 TGTACGACAACAGAACTTTTGG 57.132 40.909 5.84 0.00 0.00 3.28
313 427 9.593134 AAATAGATGTTTGTTGTTTGCTGTTTA 57.407 25.926 0.00 0.00 0.00 2.01
407 521 4.568072 TTAGGCTACAAATGGCTCAGAA 57.432 40.909 0.00 0.00 40.79 3.02
615 779 5.811399 TTTTGTAATACTGAGATTGCCCG 57.189 39.130 0.00 0.00 0.00 6.13
848 1023 6.150140 GTGCCTTGAGTGTAGAATTCAGAAAT 59.850 38.462 8.44 0.00 0.00 2.17
929 1106 5.353394 TCCTTTGTGTCTTTGTCTACAGT 57.647 39.130 0.00 0.00 0.00 3.55
1187 1365 0.322098 CGGAACACCACCAGGCATTA 60.322 55.000 0.00 0.00 39.06 1.90
1395 1648 5.778241 TGAAGGAACAGTAGTGGTATCTTGA 59.222 40.000 8.02 0.00 0.00 3.02
1453 1733 1.270907 GAAGGAGCTGGAGGAACTGA 58.729 55.000 0.00 0.00 41.55 3.41
1466 1782 1.481772 CTTCTGGAGGAGCTGAAGGAG 59.518 57.143 0.00 0.00 34.12 3.69
1516 1832 1.639298 GATTCCTGTGTGACGGCTGC 61.639 60.000 0.00 0.00 0.00 5.25
2133 2461 4.174411 TCTGAAGTAGAACATGTCACCG 57.826 45.455 0.00 0.00 30.84 4.94
2478 2806 0.710588 TCTCCACCCAGGCTTCTCTA 59.289 55.000 0.00 0.00 37.29 2.43
2886 3215 3.310501 TGCATGAATCATTGCACTCGTAG 59.689 43.478 13.52 0.00 31.84 3.51
3153 3482 4.602340 GTCAGAAAGACTAGGTTCACCA 57.398 45.455 0.00 0.00 44.09 4.17
3177 3506 5.163591 TGGCAACTGCTTAGATGATTCATTG 60.164 40.000 0.00 0.00 41.70 2.82
3180 3509 3.954200 TGGCAACTGCTTAGATGATTCA 58.046 40.909 1.06 0.00 41.70 2.57
3237 3566 0.957395 AGCTGTGGTTCATGAAGCGG 60.957 55.000 27.39 21.01 41.36 5.52
3288 3617 2.705658 TCCCTCATCACCATGGTCATAC 59.294 50.000 16.53 0.00 0.00 2.39
3417 3764 4.327357 CACTTACGAGACCAACATAAGCAG 59.673 45.833 0.00 0.00 0.00 4.24
3435 3782 1.203001 CCAAAGGAACCCCTGCACTTA 60.203 52.381 0.00 0.00 43.48 2.24
3537 3885 8.970691 AAATGAAAATATGACAACTTTCGGAG 57.029 30.769 0.00 0.00 31.74 4.63
3574 3926 3.758554 CACACCCTTCAAACTCCAATAGG 59.241 47.826 0.00 0.00 0.00 2.57
3599 3951 6.182627 TGCATCTACCAACATCTCAGAAAAT 58.817 36.000 0.00 0.00 0.00 1.82
3630 3982 3.362110 GCAAACGAGCAATACTCTATCGC 60.362 47.826 0.00 0.00 43.85 4.58
3759 4111 1.137675 TCCTGACATGAAGCGATCCTG 59.862 52.381 0.00 0.00 0.00 3.86
3760 4112 1.489481 TCCTGACATGAAGCGATCCT 58.511 50.000 0.00 0.00 0.00 3.24
3766 4118 3.191078 ACTGCTATCCTGACATGAAGC 57.809 47.619 0.00 7.47 0.00 3.86
3777 4129 1.784525 GACGCATGGTACTGCTATCC 58.215 55.000 5.66 0.00 40.06 2.59
3788 4140 1.086696 AATTTCTGACCGACGCATGG 58.913 50.000 0.00 0.00 0.00 3.66
3818 4170 5.822519 ACAAGTTCAGTATTTTCTCACTGCA 59.177 36.000 0.00 0.00 41.58 4.41
3839 4191 7.039293 TGCCAAAGTGTATAGAGTCTTCTACAA 60.039 37.037 13.78 0.00 38.69 2.41
3847 4199 3.933332 GGTGTGCCAAAGTGTATAGAGTC 59.067 47.826 0.00 0.00 34.09 3.36
3886 4238 4.061596 GTGAGCTATTTATCCTGGCTGTC 58.938 47.826 0.00 0.00 33.13 3.51
3888 4240 3.072184 AGGTGAGCTATTTATCCTGGCTG 59.928 47.826 0.00 0.00 33.13 4.85
3890 4242 3.181450 ACAGGTGAGCTATTTATCCTGGC 60.181 47.826 16.70 0.00 44.39 4.85
3937 4289 7.978414 CCACATGTGGCATAAAACAACATTATA 59.022 33.333 31.13 0.00 44.73 0.98
4032 4395 0.319900 CAGCAGTTACTGTGCCGAGT 60.320 55.000 14.23 0.00 42.24 4.18
4036 4399 2.031682 CAGTTTCAGCAGTTACTGTGCC 60.032 50.000 14.23 0.00 42.24 5.01
4037 4400 2.614057 ACAGTTTCAGCAGTTACTGTGC 59.386 45.455 14.23 1.11 46.76 4.57
4043 4406 4.157656 AGCAACAAACAGTTTCAGCAGTTA 59.842 37.500 13.48 0.00 38.74 2.24
4097 4460 2.798499 GGTCATCAGAATACGACCCACG 60.798 54.545 0.00 0.00 41.77 4.94
4150 4513 0.541392 ACCTCACTCATAATGCCGCA 59.459 50.000 0.00 0.00 0.00 5.69
4152 4515 2.315925 ACACCTCACTCATAATGCCG 57.684 50.000 0.00 0.00 0.00 5.69
4201 4566 2.851195 CATTCAAACCCCGGATAGAGG 58.149 52.381 0.73 0.00 0.00 3.69
4207 4572 3.059386 GCGCATTCAAACCCCGGA 61.059 61.111 0.73 0.00 0.00 5.14
4216 4581 0.037419 TGTACTCTGCTGCGCATTCA 60.037 50.000 12.24 11.62 38.13 2.57
4227 4592 6.692486 ACAACATCTAGTCCTTTGTACTCTG 58.308 40.000 0.00 0.00 0.00 3.35
4258 4623 4.141088 ACATCATAGAAACATGGATGGCCT 60.141 41.667 3.32 0.00 34.31 5.19
4266 4631 7.755591 ACAGCTAACAACATCATAGAAACATG 58.244 34.615 0.00 0.00 0.00 3.21
4312 4677 8.024145 ACATAAAATTCCACTGGTTGGTTTTA 57.976 30.769 0.00 4.22 46.97 1.52
4315 4680 7.790782 ATACATAAAATTCCACTGGTTGGTT 57.209 32.000 0.00 0.00 46.97 3.67
4412 4778 1.191489 TCTCCACGGCAATCACAGGA 61.191 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.