Multiple sequence alignment - TraesCS3D01G416800

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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 TraesCS3D01G416800 chr3D 100.000 3250 0 0 1 3250 528131000 528134249 0.000000e+00 6002
1 TraesCS3D01G416800 chr3B 90.686 2201 89 42 137 2306 698231139 698233254 0.000000e+00 2822
2 TraesCS3D01G416800 chr3B 85.169 236 23 5 3015 3250 698234547 698234770 7.010000e-57 231
3 TraesCS3D01G416800 chr3A 91.105 1720 79 24 1576 3250 662562868 662564558 0.000000e+00 2261
4 TraesCS3D01G416800 chr3A 90.926 1080 63 18 634 1701 662561973 662563029 0.000000e+00 1419
5 TraesCS3D01G416800 chr3A 95.760 283 7 3 367 644 662561671 662561953 4.940000e-123 451
6 TraesCS3D01G416800 chr3A 91.304 161 13 1 1 160 662561426 662561586 5.460000e-53 219


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 TraesCS3D01G416800 chr3D 528131000 528134249 3249 False 6002.0 6002 100.00000 1 3250 1 chr3D.!!$F1 3249
1 TraesCS3D01G416800 chr3B 698231139 698234770 3631 False 1526.5 2822 87.92750 137 3250 2 chr3B.!!$F1 3113
2 TraesCS3D01G416800 chr3A 662561426 662564558 3132 False 1087.5 2261 92.27375 1 3250 4 chr3A.!!$F1 3249

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
211 213 0.039437 GACCGAACGTGCAAGAGAGA 60.039 55.0 6.65 0.00 0.00 3.10 F
213 215 0.241213 CCGAACGTGCAAGAGAGAGA 59.759 55.0 6.65 0.00 0.00 3.10 F
2053 2107 0.658829 GGATGCTGACGACGATCGAG 60.659 60.0 24.34 17.22 43.74 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2186 0.035317 TGCGCAGAACTGAAGGACAT 59.965 50.000 5.66 0.0 0.0 3.06 R
2116 2187 0.601046 CTGCGCAGAACTGAAGGACA 60.601 55.000 33.66 0.0 0.0 4.02 R
3031 4050 2.554032 GCAGGCATACAGTGTTCTTGTT 59.446 45.455 0.00 0.0 0.0 2.83 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
60 61 2.721167 CGTTCCATCCCTGGCGAGA 61.721 63.158 0.00 0.00 42.80 4.04
65 66 1.670590 CATCCCTGGCGAGATCCTC 59.329 63.158 0.00 0.00 0.00 3.71
100 101 4.517703 CGTCGTCTCCGTCTCCGC 62.518 72.222 0.00 0.00 35.01 5.54
105 106 3.134792 TCTCCGTCTCCGCTGAGC 61.135 66.667 0.00 0.00 38.58 4.26
114 115 0.458197 CTCCGCTGAGCTCTTGACTG 60.458 60.000 16.19 0.00 0.00 3.51
115 116 2.099431 CCGCTGAGCTCTTGACTGC 61.099 63.158 16.19 8.49 0.00 4.40
116 117 1.079956 CGCTGAGCTCTTGACTGCT 60.080 57.895 16.19 0.00 42.82 4.24
130 132 1.996191 GACTGCTTCATCAAGGACGTC 59.004 52.381 7.13 7.13 0.00 4.34
206 208 0.511221 AAATCGACCGAACGTGCAAG 59.489 50.000 0.00 0.00 34.70 4.01
208 210 0.732880 ATCGACCGAACGTGCAAGAG 60.733 55.000 6.65 0.00 34.70 2.85
210 212 1.337817 CGACCGAACGTGCAAGAGAG 61.338 60.000 6.65 0.00 0.00 3.20
211 213 0.039437 GACCGAACGTGCAAGAGAGA 60.039 55.000 6.65 0.00 0.00 3.10
213 215 0.241213 CCGAACGTGCAAGAGAGAGA 59.759 55.000 6.65 0.00 0.00 3.10
214 216 1.612156 CGAACGTGCAAGAGAGAGAG 58.388 55.000 6.65 0.00 0.00 3.20
216 218 2.727607 CGAACGTGCAAGAGAGAGAGAG 60.728 54.545 6.65 0.00 0.00 3.20
217 219 2.192664 ACGTGCAAGAGAGAGAGAGA 57.807 50.000 6.65 0.00 0.00 3.10
218 220 2.083774 ACGTGCAAGAGAGAGAGAGAG 58.916 52.381 6.65 0.00 0.00 3.20
219 221 2.290008 ACGTGCAAGAGAGAGAGAGAGA 60.290 50.000 6.65 0.00 0.00 3.10
221 223 3.609853 GTGCAAGAGAGAGAGAGAGAGA 58.390 50.000 0.00 0.00 0.00 3.10
222 224 3.624861 GTGCAAGAGAGAGAGAGAGAGAG 59.375 52.174 0.00 0.00 0.00 3.20
223 225 3.519107 TGCAAGAGAGAGAGAGAGAGAGA 59.481 47.826 0.00 0.00 0.00 3.10
225 227 4.141846 GCAAGAGAGAGAGAGAGAGAGAGA 60.142 50.000 0.00 0.00 0.00 3.10
227 229 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
229 231 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
230 232 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
231 233 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
236 238 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
238 240 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
240 242 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
253 255 6.317312 AGAGAGAGAGAGATGGCTGATTAAT 58.683 40.000 0.00 0.00 0.00 1.40
260 262 6.047511 AGAGATGGCTGATTAATAGCGAAT 57.952 37.500 9.40 6.93 42.03 3.34
285 287 7.209471 ACGCTTGGATAAACTTGTCAAATAA 57.791 32.000 0.00 0.00 0.00 1.40
313 315 8.991243 TTTGATGAATCTAAAGCTCAATTTGG 57.009 30.769 0.00 0.00 0.00 3.28
314 316 7.943079 TGATGAATCTAAAGCTCAATTTGGA 57.057 32.000 0.00 0.00 34.66 3.53
315 317 8.352137 TGATGAATCTAAAGCTCAATTTGGAA 57.648 30.769 0.00 0.00 33.99 3.53
316 318 8.464404 TGATGAATCTAAAGCTCAATTTGGAAG 58.536 33.333 0.00 0.00 33.99 3.46
318 320 7.820648 TGAATCTAAAGCTCAATTTGGAAGAC 58.179 34.615 0.00 0.00 33.99 3.01
319 321 7.667219 TGAATCTAAAGCTCAATTTGGAAGACT 59.333 33.333 0.00 0.00 33.99 3.24
322 324 9.692325 ATCTAAAGCTCAATTTGGAAGACTTAT 57.308 29.630 0.00 0.00 33.99 1.73
326 328 9.466497 AAAGCTCAATTTGGAAGACTTATATCA 57.534 29.630 0.00 0.00 0.00 2.15
327 329 9.638176 AAGCTCAATTTGGAAGACTTATATCAT 57.362 29.630 0.00 0.00 0.00 2.45
328 330 9.064706 AGCTCAATTTGGAAGACTTATATCATG 57.935 33.333 0.00 0.00 0.00 3.07
329 331 9.060347 GCTCAATTTGGAAGACTTATATCATGA 57.940 33.333 0.00 0.00 0.00 3.07
331 333 9.565090 TCAATTTGGAAGACTTATATCATGAGG 57.435 33.333 0.09 0.00 0.00 3.86
332 334 8.790718 CAATTTGGAAGACTTATATCATGAGGG 58.209 37.037 0.09 0.00 0.00 4.30
333 335 7.690454 TTTGGAAGACTTATATCATGAGGGA 57.310 36.000 0.09 0.00 0.00 4.20
334 336 7.878621 TTGGAAGACTTATATCATGAGGGAT 57.121 36.000 0.09 0.00 0.00 3.85
335 337 7.878621 TGGAAGACTTATATCATGAGGGATT 57.121 36.000 0.09 0.00 0.00 3.01
336 338 8.280258 TGGAAGACTTATATCATGAGGGATTT 57.720 34.615 0.09 0.00 0.00 2.17
337 339 8.378565 TGGAAGACTTATATCATGAGGGATTTC 58.621 37.037 0.09 0.00 0.00 2.17
338 340 7.826744 GGAAGACTTATATCATGAGGGATTTCC 59.173 40.741 0.09 3.80 0.00 3.13
376 378 4.388577 AGTTGACCCCATTTTTCTAGCT 57.611 40.909 0.00 0.00 0.00 3.32
673 710 1.762522 ATCTATCGCCCTGCCCACTG 61.763 60.000 0.00 0.00 0.00 3.66
685 722 4.020307 CCCTGCCCACTGTGAATTAAAAAT 60.020 41.667 9.86 0.00 0.00 1.82
689 726 7.278424 CCTGCCCACTGTGAATTAAAAATAATG 59.722 37.037 9.86 0.00 0.00 1.90
748 785 5.186198 GGTTCCTACATGTATGCAAGTCTT 58.814 41.667 5.91 0.00 0.00 3.01
900 937 6.428159 TGAGGAAGTAATCAAAAGAGCACTTC 59.572 38.462 0.00 10.90 40.58 3.01
1025 1062 0.964358 GAGAAGTGCAAGGCCAGCAT 60.964 55.000 23.30 10.60 44.79 3.79
1249 1289 1.425267 TTGTGTGTGTTGCTCGACCG 61.425 55.000 0.00 0.00 0.00 4.79
1366 1411 2.509336 GGCGATGTCGTGGTGGAG 60.509 66.667 4.20 0.00 42.22 3.86
1410 1455 3.071206 GCCAGGACTCGAGCTCCA 61.071 66.667 25.85 0.00 0.00 3.86
1469 1514 3.449042 CGCAAGAAGTCCGACGAC 58.551 61.111 0.00 0.00 43.02 4.34
1694 1745 1.629043 ACAGCAACTCTTCCTACGGA 58.371 50.000 0.00 0.00 0.00 4.69
1724 1778 2.224209 CGGTGGGTACAACAACTCTTCT 60.224 50.000 0.00 0.00 32.39 2.85
1883 1937 4.070552 GGCGACCAGAAGAGGCGT 62.071 66.667 0.00 0.00 33.01 5.68
1884 1938 2.811317 GCGACCAGAAGAGGCGTG 60.811 66.667 0.00 0.00 33.01 5.34
1955 2009 1.876714 CGGCCATTTCGTCGATCGT 60.877 57.895 15.94 0.00 40.80 3.73
2029 2083 2.614446 GCGCTGGCCATGCAGATAG 61.614 63.158 21.64 9.16 0.00 2.08
2053 2107 0.658829 GGATGCTGACGACGATCGAG 60.659 60.000 24.34 17.22 43.74 4.04
2078 2147 4.999950 ACTACACTACTACTACGTGCTGTT 59.000 41.667 0.00 0.00 32.07 3.16
2115 2186 4.102524 AGTTTCCAAGTGTACCAGTGATGA 59.897 41.667 0.00 0.00 0.00 2.92
2116 2187 4.908601 TTCCAAGTGTACCAGTGATGAT 57.091 40.909 0.00 0.00 0.00 2.45
2117 2188 4.206477 TCCAAGTGTACCAGTGATGATG 57.794 45.455 0.00 0.00 0.00 3.07
2118 2189 3.582647 TCCAAGTGTACCAGTGATGATGT 59.417 43.478 0.00 0.00 0.00 3.06
2119 2190 3.935203 CCAAGTGTACCAGTGATGATGTC 59.065 47.826 0.00 0.00 0.00 3.06
2143 2214 0.250038 AGTTCTGCGCAGTGATGTGT 60.250 50.000 34.70 12.46 0.00 3.72
2144 2215 0.110509 GTTCTGCGCAGTGATGTGTG 60.111 55.000 34.70 9.30 0.00 3.82
2288 2359 6.947644 TCTTGTAATTGCATGCAGATACAT 57.052 33.333 31.31 18.32 32.74 2.29
2365 2436 9.905713 ATGGCAATCAAAAAGTCTATCTAAGTA 57.094 29.630 0.00 0.00 0.00 2.24
2367 2438 9.384764 GGCAATCAAAAAGTCTATCTAAGTACT 57.615 33.333 0.00 0.00 0.00 2.73
2452 2539 7.882791 TCAGATGTAGAAGCACCAAAATTTCTA 59.117 33.333 0.00 0.00 32.54 2.10
2462 2549 5.985530 GCACCAAAATTTCTATATTGGGCTC 59.014 40.000 8.75 0.00 45.22 4.70
2502 2589 9.337091 CTTTTCATTTCATTCCATTCAATTTGC 57.663 29.630 0.00 0.00 0.00 3.68
2506 2593 5.866335 TTCATTCCATTCAATTTGCTTGC 57.134 34.783 0.00 0.00 34.66 4.01
2510 2597 2.234414 TCCATTCAATTTGCTTGCCTCC 59.766 45.455 0.00 0.00 34.66 4.30
2514 2601 1.203038 TCAATTTGCTTGCCTCCTCCA 60.203 47.619 0.00 0.00 34.66 3.86
2539 2626 5.533903 GGGGCTTATGATGAGCATATATTGG 59.466 44.000 11.43 0.00 41.89 3.16
2711 2803 7.762615 CACATGTCCTTCGTAAAAATCCTACTA 59.237 37.037 0.00 0.00 0.00 1.82
2808 2904 6.171921 GGAGGTCTCTTTTCTACCTTTAACC 58.828 44.000 0.00 0.00 43.69 2.85
2933 3029 7.766219 AATATACACGGTGTTTAGACATGTC 57.234 36.000 20.15 18.47 38.23 3.06
2944 3040 4.790765 TTAGACATGTCACAGTCCTCAG 57.209 45.455 27.02 0.00 35.38 3.35
3005 3101 9.767684 TCATAGTAAATGCAATACAAAGAAACG 57.232 29.630 13.57 0.00 0.00 3.60
3006 3102 9.767684 CATAGTAAATGCAATACAAAGAAACGA 57.232 29.630 13.57 0.00 0.00 3.85
3040 4059 9.658799 TTTTAATTTCACCAATCAACAAGAACA 57.341 25.926 0.00 0.00 0.00 3.18
3071 4090 7.109501 TGCCTGCATAGATAGTCAAAGTTTAA 58.890 34.615 0.00 0.00 0.00 1.52
3201 4221 7.175641 CCAAAGATCCACAGAAAAATAGTCAGT 59.824 37.037 0.00 0.00 0.00 3.41
3202 4222 7.678947 AAGATCCACAGAAAAATAGTCAGTG 57.321 36.000 0.00 0.00 33.58 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.162690 AGGGATGGAACGGCTCGC 62.163 66.667 0.00 0.00 0.00 5.03
46 47 1.825281 GAGGATCTCGCCAGGGATGG 61.825 65.000 0.00 0.00 37.79 3.51
48 49 1.905843 CGAGGATCTCGCCAGGGAT 60.906 63.158 4.36 0.00 46.75 3.85
69 70 2.805546 GACGCGACTATGAGGGCA 59.194 61.111 15.93 0.00 0.00 5.36
100 101 2.452295 TGAAGCAGTCAAGAGCTCAG 57.548 50.000 17.77 8.24 40.90 3.35
114 115 1.014044 TGCGACGTCCTTGATGAAGC 61.014 55.000 10.58 4.64 0.00 3.86
115 116 0.994995 CTGCGACGTCCTTGATGAAG 59.005 55.000 10.58 0.00 0.00 3.02
116 117 1.014044 GCTGCGACGTCCTTGATGAA 61.014 55.000 10.58 0.00 0.00 2.57
206 208 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
208 210 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
210 212 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
211 213 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
213 215 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
214 216 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
216 218 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
217 219 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
218 220 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
219 221 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
221 223 4.592351 CCATCTCTCTCTCTCTCTCTCTCT 59.408 50.000 0.00 0.00 0.00 3.10
222 224 4.802248 GCCATCTCTCTCTCTCTCTCTCTC 60.802 54.167 0.00 0.00 0.00 3.20
223 225 3.072184 GCCATCTCTCTCTCTCTCTCTCT 59.928 52.174 0.00 0.00 0.00 3.10
225 227 3.051581 AGCCATCTCTCTCTCTCTCTCT 58.948 50.000 0.00 0.00 0.00 3.10
227 229 2.779430 TCAGCCATCTCTCTCTCTCTCT 59.221 50.000 0.00 0.00 0.00 3.10
229 231 3.889859 ATCAGCCATCTCTCTCTCTCT 57.110 47.619 0.00 0.00 0.00 3.10
230 232 6.594788 ATTAATCAGCCATCTCTCTCTCTC 57.405 41.667 0.00 0.00 0.00 3.20
231 233 6.153340 GCTATTAATCAGCCATCTCTCTCTCT 59.847 42.308 0.00 0.00 32.68 3.10
236 238 5.065704 TCGCTATTAATCAGCCATCTCTC 57.934 43.478 0.00 0.00 35.53 3.20
238 240 6.020281 CGTATTCGCTATTAATCAGCCATCTC 60.020 42.308 0.00 0.00 35.53 2.75
240 242 6.025707 CGTATTCGCTATTAATCAGCCATC 57.974 41.667 0.00 0.00 35.53 3.51
260 262 6.811253 ATTTGACAAGTTTATCCAAGCGTA 57.189 33.333 0.00 0.00 0.00 4.42
308 310 8.280258 TCCCTCATGATATAAGTCTTCCAAAT 57.720 34.615 0.00 0.00 0.00 2.32
312 314 7.826744 GGAAATCCCTCATGATATAAGTCTTCC 59.173 40.741 0.00 0.00 0.00 3.46
313 315 8.601546 AGGAAATCCCTCATGATATAAGTCTTC 58.398 37.037 0.00 0.00 43.31 2.87
314 316 8.517323 AGGAAATCCCTCATGATATAAGTCTT 57.483 34.615 0.00 0.00 43.31 3.01
330 332 5.440610 ACTCACATTACATGAGGAAATCCC 58.559 41.667 0.00 0.00 46.60 3.85
331 333 7.770897 ACTTACTCACATTACATGAGGAAATCC 59.229 37.037 0.00 0.00 44.60 3.01
332 334 8.723942 ACTTACTCACATTACATGAGGAAATC 57.276 34.615 0.00 0.00 44.60 2.17
333 335 8.950210 CAACTTACTCACATTACATGAGGAAAT 58.050 33.333 0.00 0.00 44.60 2.17
334 336 8.154203 TCAACTTACTCACATTACATGAGGAAA 58.846 33.333 0.00 0.76 44.60 3.13
335 337 7.602644 GTCAACTTACTCACATTACATGAGGAA 59.397 37.037 0.00 3.50 46.60 3.36
336 338 7.097192 GTCAACTTACTCACATTACATGAGGA 58.903 38.462 0.00 0.00 46.60 3.71
337 339 6.313905 GGTCAACTTACTCACATTACATGAGG 59.686 42.308 0.00 0.00 46.60 3.86
339 341 6.170506 GGGTCAACTTACTCACATTACATGA 58.829 40.000 0.00 0.00 0.00 3.07
340 342 5.354234 GGGGTCAACTTACTCACATTACATG 59.646 44.000 0.00 0.00 0.00 3.21
376 378 3.940221 GAGTACCTCTTTCGTGCTCTCTA 59.060 47.826 0.00 0.00 39.18 2.43
489 492 1.048724 TAGCCTCGCCATTACCTGCT 61.049 55.000 0.00 0.00 0.00 4.24
502 505 4.534103 ACTCATCCTTATCCCATTAGCCTC 59.466 45.833 0.00 0.00 0.00 4.70
569 576 5.932619 ATCACTATGTGGTAAGTACTGCA 57.067 39.130 0.00 0.00 33.87 4.41
689 726 9.076596 GCTTCAAATGTTGTAGTTAATTCATCC 57.923 33.333 0.00 0.00 31.53 3.51
709 746 3.071479 GGAACCATACACGAAGCTTCAA 58.929 45.455 25.47 8.57 0.00 2.69
748 785 3.769844 CCAAGTGGAAGGAGCTACTTAGA 59.230 47.826 12.33 0.00 37.47 2.10
780 817 7.198390 GCAGCTAAATTAAAGAGCATCATCAA 58.802 34.615 8.72 0.00 38.73 2.57
900 937 5.460646 AGGTCATCGTTTGTGCAATAAAAG 58.539 37.500 0.00 0.00 0.00 2.27
1025 1062 5.428253 GAGCATACCAGACAATAAAGTGGA 58.572 41.667 0.00 0.00 33.95 4.02
1150 1188 5.629079 AATTACTGAAGCTAACCAACTGC 57.371 39.130 0.00 0.00 0.00 4.40
1193 1231 8.474710 TCAGTTAAGAAAACTCTACTGGTACT 57.525 34.615 0.00 0.00 35.06 2.73
1194 1232 9.708092 AATCAGTTAAGAAAACTCTACTGGTAC 57.292 33.333 0.00 0.00 35.06 3.34
1196 1234 9.274206 GAAATCAGTTAAGAAAACTCTACTGGT 57.726 33.333 0.00 0.00 35.06 4.00
1217 1255 6.454186 GCAACACACACAAAACTTCTGAAATC 60.454 38.462 0.00 0.00 0.00 2.17
1249 1289 1.822250 GCATCGATCGGACGGAAAGC 61.822 60.000 16.41 0.00 0.00 3.51
1366 1411 2.281484 TGAAGTGCGGCTTGGACC 60.281 61.111 0.00 0.00 40.31 4.46
1469 1514 2.821688 GCGGTACTCCTCCTCGTCG 61.822 68.421 0.00 0.00 0.00 5.12
1709 1760 4.053295 TGCCGTAAGAAGAGTTGTTGTAC 58.947 43.478 0.00 0.00 43.02 2.90
1724 1778 3.347405 CCGTTGCCGTTGCCGTAA 61.347 61.111 0.00 0.00 36.33 3.18
2042 2096 2.886081 AGTGTAGTACTCGATCGTCGT 58.114 47.619 15.94 15.33 41.35 4.34
2053 2107 5.578727 ACAGCACGTAGTAGTAGTGTAGTAC 59.421 44.000 0.00 0.00 41.61 2.73
2115 2186 0.035317 TGCGCAGAACTGAAGGACAT 59.965 50.000 5.66 0.00 0.00 3.06
2116 2187 0.601046 CTGCGCAGAACTGAAGGACA 60.601 55.000 33.66 0.00 0.00 4.02
2117 2188 0.601311 ACTGCGCAGAACTGAAGGAC 60.601 55.000 42.03 0.00 0.00 3.85
2118 2189 0.601046 CACTGCGCAGAACTGAAGGA 60.601 55.000 42.03 0.00 0.00 3.36
2119 2190 0.601046 TCACTGCGCAGAACTGAAGG 60.601 55.000 42.03 19.30 0.00 3.46
2143 2214 0.961753 TGCAACACAAACCACACACA 59.038 45.000 0.00 0.00 0.00 3.72
2144 2215 2.192624 GATGCAACACAAACCACACAC 58.807 47.619 0.00 0.00 0.00 3.82
2288 2359 6.412362 ACAACAAAACCATAAGTTGCCATA 57.588 33.333 0.00 0.00 43.74 2.74
2302 2373 6.016276 AGAGGACCACATCATTACAACAAAAC 60.016 38.462 0.00 0.00 0.00 2.43
2307 2378 6.575162 AAAAGAGGACCACATCATTACAAC 57.425 37.500 0.00 0.00 0.00 3.32
2367 2438 9.157104 TGCTTTTCGACTTAATATGTCAATACA 57.843 29.630 7.02 0.00 40.69 2.29
2368 2439 9.982291 TTGCTTTTCGACTTAATATGTCAATAC 57.018 29.630 7.02 0.00 34.37 1.89
2370 2441 9.906660 TTTTGCTTTTCGACTTAATATGTCAAT 57.093 25.926 7.02 0.00 34.37 2.57
2371 2442 9.906660 ATTTTGCTTTTCGACTTAATATGTCAA 57.093 25.926 7.02 0.00 34.37 3.18
2372 2443 9.906660 AATTTTGCTTTTCGACTTAATATGTCA 57.093 25.926 7.02 0.00 34.37 3.58
2420 2491 6.048732 TGGTGCTTCTACATCTGACAAATA 57.951 37.500 0.00 0.00 0.00 1.40
2452 2539 4.870021 AACAAGGAAGAGAGCCCAATAT 57.130 40.909 0.00 0.00 0.00 1.28
2462 2549 7.491682 TGAAATGAAAAGGAAACAAGGAAGAG 58.508 34.615 0.00 0.00 0.00 2.85
2502 2589 4.120755 GCCCCTGGAGGAGGCAAG 62.121 72.222 16.26 0.00 45.24 4.01
2506 2593 0.400525 TCATAAGCCCCTGGAGGAGG 60.401 60.000 0.00 0.00 42.38 4.30
2510 2597 1.271271 GCTCATCATAAGCCCCTGGAG 60.271 57.143 0.00 0.00 33.53 3.86
2514 2601 6.363065 CAATATATGCTCATCATAAGCCCCT 58.637 40.000 0.00 0.00 40.73 4.79
2587 2674 8.228035 TGAAATTAGGTGGGTTATAAATTCCG 57.772 34.615 0.00 0.00 0.00 4.30
2711 2803 2.665185 GCAGCGGTTGGTTCTCGT 60.665 61.111 0.00 0.00 0.00 4.18
2829 2925 4.475345 AGTTTTGGGCTATTGTGGTTGTA 58.525 39.130 0.00 0.00 0.00 2.41
2864 2960 6.263168 CGGGGAGTCTTTTGCTAATATTGATT 59.737 38.462 0.00 0.00 0.00 2.57
2933 3029 5.105187 TCAGAATTACATCCTGAGGACTGTG 60.105 44.000 19.88 11.58 32.98 3.66
2944 3040 8.623903 TGTAAAGCAATCATCAGAATTACATCC 58.376 33.333 0.00 0.00 29.79 3.51
2988 3084 8.730680 AGTATCTTTCGTTTCTTTGTATTGCAT 58.269 29.630 0.00 0.00 0.00 3.96
3031 4050 2.554032 GCAGGCATACAGTGTTCTTGTT 59.446 45.455 0.00 0.00 0.00 2.83
3040 4059 4.835056 TGACTATCTATGCAGGCATACAGT 59.165 41.667 9.79 12.26 37.82 3.55
3158 4178 9.793259 GGATCTTTGGTAAATGAGGAATATGTA 57.207 33.333 0.00 0.00 0.00 2.29
3160 4180 8.571336 GTGGATCTTTGGTAAATGAGGAATATG 58.429 37.037 0.00 0.00 0.00 1.78
3166 4186 5.500234 TCTGTGGATCTTTGGTAAATGAGG 58.500 41.667 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.