Multiple sequence alignment - TraesCS2D01G196200

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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 TraesCS2D01G196200 chr2D 100.000 2987 0 0 1 2987 142669209 142666223 0.000000e+00 5517
1 TraesCS2D01G196200 chr2A 94.091 2471 97 20 358 2804 158451792 158454237 0.000000e+00 3709
2 TraesCS2D01G196200 chr2A 92.000 175 6 5 1 168 158451621 158451794 3.850000e-59 239
3 TraesCS2D01G196200 chr2B 96.095 2100 47 14 364 2450 200574433 200572356 0.000000e+00 3391
4 TraesCS2D01G196200 chr2B 87.287 527 40 19 2472 2987 200572367 200571857 7.180000e-161 577
5 TraesCS2D01G196200 chr2B 95.484 155 5 1 1 155 200574597 200574445 2.300000e-61 246
6 TraesCS2D01G196200 chr5D 96.648 179 5 1 166 343 332408846 332408668 2.250000e-76 296
7 TraesCS2D01G196200 chr5D 96.591 176 5 1 169 343 310755327 310755152 1.050000e-74 291
8 TraesCS2D01G196200 chr7D 97.126 174 3 2 172 343 593180984 593180811 2.910000e-75 292
9 TraesCS2D01G196200 chr7D 96.591 176 5 1 169 343 118926302 118926127 1.050000e-74 291
10 TraesCS2D01G196200 chr5B 96.610 177 4 2 169 343 422567459 422567635 2.910000e-75 292
11 TraesCS2D01G196200 chr3A 96.610 177 4 2 169 343 188622156 188622332 2.910000e-75 292
12 TraesCS2D01G196200 chr6D 96.591 176 5 1 169 343 90264696 90264521 1.050000e-74 291
13 TraesCS2D01G196200 chr6D 96.591 176 5 1 169 343 244681809 244681634 1.050000e-74 291
14 TraesCS2D01G196200 chr3D 96.591 176 5 1 169 343 77584708 77584883 1.050000e-74 291


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 TraesCS2D01G196200 chr2D 142666223 142669209 2986 True 5517.000000 5517 100.000000 1 2987 1 chr2D.!!$R1 2986
1 TraesCS2D01G196200 chr2A 158451621 158454237 2616 False 1974.000000 3709 93.045500 1 2804 2 chr2A.!!$F1 2803
2 TraesCS2D01G196200 chr2B 200571857 200574597 2740 True 1404.666667 3391 92.955333 1 2987 3 chr2B.!!$R1 2986

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
306 318 0.698238 AGCCAACCAATCACTAGCCA 59.302 50.000 0.0 0.0 0.0 4.75 F
307 319 1.075374 AGCCAACCAATCACTAGCCAA 59.925 47.619 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1706 0.179073 CGCCCACCATCTCCTTGTAG 60.179 60.000 0.0 0.0 0.00 2.74 R
2253 2281 4.873827 TCATTATCAAACGGGAGTACAAGC 59.126 41.667 0.0 0.0 46.69 4.01 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
108 115 8.432805 CCTAATACCCCTATGCATTTATAGAGG 58.567 40.741 3.54 3.96 35.36 3.69
179 191 6.136071 GCATAAGCACGTAGAACATAATTGG 58.864 40.000 0.00 0.00 41.58 3.16
180 192 6.238374 GCATAAGCACGTAGAACATAATTGGT 60.238 38.462 0.00 0.00 41.58 3.67
181 193 7.678690 GCATAAGCACGTAGAACATAATTGGTT 60.679 37.037 0.00 0.00 41.58 3.67
182 194 6.569179 AAGCACGTAGAACATAATTGGTTT 57.431 33.333 0.00 0.00 0.00 3.27
183 195 5.938322 AGCACGTAGAACATAATTGGTTTG 58.062 37.500 0.00 0.00 0.00 2.93
184 196 5.703592 AGCACGTAGAACATAATTGGTTTGA 59.296 36.000 0.00 0.00 0.00 2.69
185 197 6.374333 AGCACGTAGAACATAATTGGTTTGAT 59.626 34.615 0.00 0.00 0.00 2.57
186 198 6.468956 GCACGTAGAACATAATTGGTTTGATG 59.531 38.462 0.00 0.00 0.00 3.07
187 199 6.468956 CACGTAGAACATAATTGGTTTGATGC 59.531 38.462 0.00 0.00 0.00 3.91
188 200 5.971202 CGTAGAACATAATTGGTTTGATGCC 59.029 40.000 0.00 0.00 0.00 4.40
189 201 5.999205 AGAACATAATTGGTTTGATGCCA 57.001 34.783 0.00 0.00 0.00 4.92
196 208 2.721274 TGGTTTGATGCCAACAATCG 57.279 45.000 0.00 0.00 32.29 3.34
197 209 1.271934 TGGTTTGATGCCAACAATCGG 59.728 47.619 0.00 0.00 32.29 4.18
204 216 4.500396 CCAACAATCGGCATTGCC 57.500 55.556 18.10 18.10 43.03 4.52
242 254 7.396190 CCAACATTTGGCAAAATCAAAATTG 57.604 32.000 17.70 10.29 45.17 2.32
252 264 6.868430 GCAAAATCAAAATTGCCAAATGTTG 58.132 32.000 0.00 0.00 44.72 3.33
264 276 4.961435 CCAAATGTTGGCAACTTTTTGT 57.039 36.364 32.56 19.32 45.17 2.83
265 277 4.660105 CCAAATGTTGGCAACTTTTTGTG 58.340 39.130 32.56 25.34 45.17 3.33
266 278 4.394300 CCAAATGTTGGCAACTTTTTGTGA 59.606 37.500 32.56 16.94 45.17 3.58
267 279 5.447548 CCAAATGTTGGCAACTTTTTGTGAG 60.448 40.000 32.56 24.17 45.17 3.51
268 280 3.244033 TGTTGGCAACTTTTTGTGAGG 57.756 42.857 28.71 0.00 34.90 3.86
269 281 2.564947 TGTTGGCAACTTTTTGTGAGGT 59.435 40.909 28.71 0.00 34.90 3.85
270 282 3.007398 TGTTGGCAACTTTTTGTGAGGTT 59.993 39.130 28.71 0.00 34.90 3.50
271 283 3.244033 TGGCAACTTTTTGTGAGGTTG 57.756 42.857 0.00 0.00 41.07 3.77
272 284 2.828520 TGGCAACTTTTTGTGAGGTTGA 59.171 40.909 8.55 0.00 40.74 3.18
273 285 3.119173 TGGCAACTTTTTGTGAGGTTGAG 60.119 43.478 8.55 0.00 40.74 3.02
274 286 3.130340 GGCAACTTTTTGTGAGGTTGAGA 59.870 43.478 8.55 0.00 40.74 3.27
275 287 4.381505 GGCAACTTTTTGTGAGGTTGAGAA 60.382 41.667 8.55 0.00 40.74 2.87
276 288 5.167845 GCAACTTTTTGTGAGGTTGAGAAA 58.832 37.500 8.55 0.00 40.74 2.52
277 289 5.637387 GCAACTTTTTGTGAGGTTGAGAAAA 59.363 36.000 8.55 0.00 40.74 2.29
278 290 6.147000 GCAACTTTTTGTGAGGTTGAGAAAAA 59.853 34.615 8.55 0.00 40.74 1.94
304 316 3.808728 TGATAGCCAACCAATCACTAGC 58.191 45.455 0.00 0.00 0.00 3.42
305 317 2.710096 TAGCCAACCAATCACTAGCC 57.290 50.000 0.00 0.00 0.00 3.93
306 318 0.698238 AGCCAACCAATCACTAGCCA 59.302 50.000 0.00 0.00 0.00 4.75
307 319 1.075374 AGCCAACCAATCACTAGCCAA 59.925 47.619 0.00 0.00 0.00 4.52
308 320 1.202348 GCCAACCAATCACTAGCCAAC 59.798 52.381 0.00 0.00 0.00 3.77
309 321 2.513753 CCAACCAATCACTAGCCAACA 58.486 47.619 0.00 0.00 0.00 3.33
310 322 3.091545 CCAACCAATCACTAGCCAACAT 58.908 45.455 0.00 0.00 0.00 2.71
311 323 3.511146 CCAACCAATCACTAGCCAACATT 59.489 43.478 0.00 0.00 0.00 2.71
312 324 4.021192 CCAACCAATCACTAGCCAACATTT 60.021 41.667 0.00 0.00 0.00 2.32
313 325 4.789012 ACCAATCACTAGCCAACATTTG 57.211 40.909 0.00 0.00 0.00 2.32
337 349 6.529463 GCATTTGCCAAATATTGACATACC 57.471 37.500 1.66 0.00 34.31 2.73
338 350 6.047870 GCATTTGCCAAATATTGACATACCA 58.952 36.000 1.66 0.00 34.31 3.25
339 351 6.538021 GCATTTGCCAAATATTGACATACCAA 59.462 34.615 1.66 0.00 34.31 3.67
340 352 7.465781 GCATTTGCCAAATATTGACATACCAAC 60.466 37.037 1.66 0.00 34.31 3.77
341 353 6.849085 TTGCCAAATATTGACATACCAACT 57.151 33.333 0.00 0.00 0.00 3.16
342 354 6.849085 TGCCAAATATTGACATACCAACTT 57.151 33.333 0.00 0.00 0.00 2.66
343 355 6.862209 TGCCAAATATTGACATACCAACTTC 58.138 36.000 0.00 0.00 0.00 3.01
344 356 6.435591 TGCCAAATATTGACATACCAACTTCA 59.564 34.615 0.00 0.00 0.00 3.02
345 357 7.039434 TGCCAAATATTGACATACCAACTTCAA 60.039 33.333 0.00 0.00 32.71 2.69
346 358 7.981225 GCCAAATATTGACATACCAACTTCAAT 59.019 33.333 0.00 0.00 40.80 2.57
347 359 9.520204 CCAAATATTGACATACCAACTTCAATC 57.480 33.333 0.00 0.00 39.06 2.67
353 365 8.492673 TTGACATACCAACTTCAATCATACTC 57.507 34.615 0.00 0.00 0.00 2.59
354 366 6.756542 TGACATACCAACTTCAATCATACTCG 59.243 38.462 0.00 0.00 0.00 4.18
355 367 6.640518 ACATACCAACTTCAATCATACTCGT 58.359 36.000 0.00 0.00 0.00 4.18
356 368 7.778083 ACATACCAACTTCAATCATACTCGTA 58.222 34.615 0.00 0.00 0.00 3.43
447 459 3.306917 TCCTTAGCACGAAACATCGAA 57.693 42.857 5.11 0.00 36.85 3.71
484 496 1.734388 AAACGTGAAGGGCCTTGTGC 61.734 55.000 26.47 10.26 40.16 4.57
1611 1637 3.462678 GAGGAGGTGGAGGCGGAC 61.463 72.222 0.00 0.00 0.00 4.79
2211 2238 5.250200 AGGGAAAAATATGACGTGTGCTTA 58.750 37.500 0.00 0.00 0.00 3.09
2264 2292 0.610687 AGTGAGCTGCTTGTACTCCC 59.389 55.000 2.53 0.00 0.00 4.30
2320 2348 1.407437 GGACAGGGCAGGATGTACAAG 60.407 57.143 0.00 0.00 39.31 3.16
2324 2352 0.543749 GGGCAGGATGTACAAGAGCT 59.456 55.000 0.00 0.00 39.31 4.09
2325 2353 1.762957 GGGCAGGATGTACAAGAGCTA 59.237 52.381 0.00 0.00 39.31 3.32
2326 2354 2.224161 GGGCAGGATGTACAAGAGCTAG 60.224 54.545 0.00 0.00 39.31 3.42
2327 2355 2.432510 GGCAGGATGTACAAGAGCTAGT 59.567 50.000 0.00 0.00 39.31 2.57
2419 2479 4.026356 AGAAATTCTGTGTGAAGGGGAG 57.974 45.455 0.00 0.00 38.18 4.30
2438 2498 4.017126 GGAGTTTTACAGGCAAGGCTAAT 58.983 43.478 0.00 0.00 0.00 1.73
2439 2499 5.190677 GGAGTTTTACAGGCAAGGCTAATA 58.809 41.667 0.00 0.00 0.00 0.98
2440 2500 5.650703 GGAGTTTTACAGGCAAGGCTAATAA 59.349 40.000 0.00 0.00 0.00 1.40
2441 2501 6.404403 GGAGTTTTACAGGCAAGGCTAATAAC 60.404 42.308 0.00 0.60 0.00 1.89
2442 2502 6.007703 AGTTTTACAGGCAAGGCTAATAACA 58.992 36.000 0.00 0.00 0.00 2.41
2443 2503 6.492087 AGTTTTACAGGCAAGGCTAATAACAA 59.508 34.615 0.00 0.00 0.00 2.83
2444 2504 6.509418 TTTACAGGCAAGGCTAATAACAAG 57.491 37.500 0.00 0.00 0.00 3.16
2445 2505 2.755103 ACAGGCAAGGCTAATAACAAGC 59.245 45.455 0.00 0.00 39.33 4.01
2446 2506 2.754552 CAGGCAAGGCTAATAACAAGCA 59.245 45.455 0.00 0.00 41.93 3.91
2447 2507 3.382546 CAGGCAAGGCTAATAACAAGCAT 59.617 43.478 0.00 0.00 41.93 3.79
2448 2508 4.026052 AGGCAAGGCTAATAACAAGCATT 58.974 39.130 0.00 0.00 44.13 3.56
2449 2509 4.467438 AGGCAAGGCTAATAACAAGCATTT 59.533 37.500 0.00 0.00 40.79 2.32
2450 2510 5.656416 AGGCAAGGCTAATAACAAGCATTTA 59.344 36.000 0.00 0.00 40.79 1.40
2494 2554 9.683069 AGTTAACAAACATTTTGATGAGATGAC 57.317 29.630 8.61 0.00 0.00 3.06
2582 2642 4.449743 GCACGACAGGTATTGAACAAAGTA 59.550 41.667 0.00 0.00 0.00 2.24
2609 2669 1.374758 ACGAGCGGCAGAGGAAAAG 60.375 57.895 1.45 0.00 0.00 2.27
2632 2692 8.877808 AAGAACATCTTTTGAAAAATCTCCAC 57.122 30.769 0.00 0.00 31.57 4.02
2654 2714 4.216257 ACACAACATACAAATCCACAGCTC 59.784 41.667 0.00 0.00 0.00 4.09
2792 2853 9.001542 TGTTGTAAATACACACCTATACAAACC 57.998 33.333 0.00 0.00 35.68 3.27
2804 2865 5.204833 CCTATACAAACCGATCGCAAAATG 58.795 41.667 10.32 6.35 0.00 2.32
2812 2873 3.376859 ACCGATCGCAAAATGATGCTTAA 59.623 39.130 10.32 0.00 44.21 1.85
2818 2879 9.328721 CGATCGCAAAATGATGCTTAATTATAA 57.671 29.630 0.26 0.00 44.21 0.98
2851 2920 5.235616 TGTGTTAGTTCCATGAAAAGACGAC 59.764 40.000 0.00 0.00 0.00 4.34
2852 2921 5.235616 GTGTTAGTTCCATGAAAAGACGACA 59.764 40.000 0.00 0.00 0.00 4.35
2862 2931 6.585702 CCATGAAAAGACGACATATTTTTGCA 59.414 34.615 0.00 0.00 0.00 4.08
2871 2940 7.754924 AGACGACATATTTTTGCAATTTCGAAT 59.245 29.630 11.32 5.53 0.00 3.34
2882 2951 4.520874 TGCAATTTCGAATCAGGGTAAACA 59.479 37.500 0.00 0.00 0.00 2.83
2886 2955 6.642707 ATTTCGAATCAGGGTAAACAAACA 57.357 33.333 0.00 0.00 0.00 2.83
2888 2957 5.427036 TCGAATCAGGGTAAACAAACAAC 57.573 39.130 0.00 0.00 0.00 3.32
2896 2965 7.493367 TCAGGGTAAACAAACAACAATTAAGG 58.507 34.615 0.00 0.00 0.00 2.69
2897 2966 7.124448 TCAGGGTAAACAAACAACAATTAAGGT 59.876 33.333 0.00 0.00 0.00 3.50
2898 2967 7.766738 CAGGGTAAACAAACAACAATTAAGGTT 59.233 33.333 0.00 0.00 0.00 3.50
2899 2968 7.982919 AGGGTAAACAAACAACAATTAAGGTTC 59.017 33.333 0.00 0.00 0.00 3.62
2900 2969 7.764901 GGGTAAACAAACAACAATTAAGGTTCA 59.235 33.333 0.00 0.00 0.00 3.18
2901 2970 8.813282 GGTAAACAAACAACAATTAAGGTTCAG 58.187 33.333 0.00 0.00 0.00 3.02
2902 2971 9.575783 GTAAACAAACAACAATTAAGGTTCAGA 57.424 29.630 0.00 0.00 0.00 3.27
2903 2972 8.474006 AAACAAACAACAATTAAGGTTCAGAC 57.526 30.769 0.00 0.00 0.00 3.51
2912 2981 4.404691 GGTTCAGACCCAGCCAAG 57.595 61.111 0.00 0.00 40.25 3.61
2913 2982 1.973812 GGTTCAGACCCAGCCAAGC 60.974 63.158 0.00 0.00 40.25 4.01
2914 2983 1.073897 GTTCAGACCCAGCCAAGCT 59.926 57.895 0.00 0.00 40.77 3.74
2916 2985 2.045536 CAGACCCAGCCAAGCTCC 60.046 66.667 0.00 0.00 36.40 4.70
2920 2989 2.441532 CCCAGCCAAGCTCCATGG 60.442 66.667 4.97 4.97 36.40 3.66
2921 2990 2.679092 CCAGCCAAGCTCCATGGA 59.321 61.111 15.27 15.27 40.56 3.41
2922 2991 1.000521 CCAGCCAAGCTCCATGGAA 60.001 57.895 17.00 0.00 40.56 3.53
2924 2993 1.481871 CAGCCAAGCTCCATGGAAAT 58.518 50.000 17.00 4.03 40.56 2.17
2926 2995 1.188863 GCCAAGCTCCATGGAAATGT 58.811 50.000 17.00 0.00 40.56 2.71
2928 2997 1.134907 CCAAGCTCCATGGAAATGTGC 60.135 52.381 17.00 15.10 40.56 4.57
2930 2999 1.471119 AGCTCCATGGAAATGTGCAG 58.529 50.000 21.21 7.25 0.00 4.41
2931 3000 1.005097 AGCTCCATGGAAATGTGCAGA 59.995 47.619 21.21 0.00 0.00 4.26
2932 3001 2.029623 GCTCCATGGAAATGTGCAGAT 58.970 47.619 17.00 0.00 0.00 2.90
2933 3002 2.429610 GCTCCATGGAAATGTGCAGATT 59.570 45.455 17.00 2.67 0.00 2.40
2934 3003 3.490419 GCTCCATGGAAATGTGCAGATTC 60.490 47.826 17.00 3.64 0.00 2.52
2935 3004 3.952323 CTCCATGGAAATGTGCAGATTCT 59.048 43.478 17.00 0.49 0.00 2.40
2936 3005 5.114764 TCCATGGAAATGTGCAGATTCTA 57.885 39.130 13.46 2.23 0.00 2.10
2937 3006 5.128205 TCCATGGAAATGTGCAGATTCTAG 58.872 41.667 13.46 0.00 0.00 2.43
2938 3007 4.277672 CCATGGAAATGTGCAGATTCTAGG 59.722 45.833 5.56 3.65 0.00 3.02
2944 3013 2.910199 TGTGCAGATTCTAGGACATGC 58.090 47.619 2.83 2.83 30.92 4.06
2957 3026 7.496529 TCTAGGACATGCAAATATTTAGTGC 57.503 36.000 0.00 1.95 38.78 4.40
2968 3037 6.751888 GCAAATATTTAGTGCAGGGTTGTAAG 59.248 38.462 0.00 0.00 38.19 2.34
2982 3051 8.560374 GCAGGGTTGTAAGTTCATATATTCTTC 58.440 37.037 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 176 5.971202 GGCATCAAACCAATTATGTTCTACG 59.029 40.000 0.00 0.00 0.00 3.51
165 177 6.862209 TGGCATCAAACCAATTATGTTCTAC 58.138 36.000 0.00 0.00 33.12 2.59
166 178 7.473735 TTGGCATCAAACCAATTATGTTCTA 57.526 32.000 0.00 0.00 42.23 2.10
167 179 5.999205 TGGCATCAAACCAATTATGTTCT 57.001 34.783 0.00 0.00 33.12 3.01
176 188 2.288702 CCGATTGTTGGCATCAAACCAA 60.289 45.455 14.40 0.00 44.86 3.67
177 189 1.271934 CCGATTGTTGGCATCAAACCA 59.728 47.619 14.40 0.00 34.28 3.67
178 190 1.994916 CCGATTGTTGGCATCAAACC 58.005 50.000 14.40 8.91 34.28 3.27
187 199 4.500396 GGCAATGCCGATTGTTGG 57.500 55.556 9.14 0.00 41.09 3.77
204 216 5.392165 CCAAATGTTGGCTTGCCAAATATTG 60.392 40.000 26.12 25.13 45.17 1.90
205 217 4.701171 CCAAATGTTGGCTTGCCAAATATT 59.299 37.500 26.12 23.52 45.17 1.28
206 218 4.263435 CCAAATGTTGGCTTGCCAAATAT 58.737 39.130 26.12 19.92 45.17 1.28
207 219 3.672808 CCAAATGTTGGCTTGCCAAATA 58.327 40.909 26.12 18.73 45.17 1.40
208 220 2.506444 CCAAATGTTGGCTTGCCAAAT 58.494 42.857 26.12 18.32 45.17 2.32
209 221 1.964552 CCAAATGTTGGCTTGCCAAA 58.035 45.000 26.12 17.09 45.17 3.28
210 222 3.702147 CCAAATGTTGGCTTGCCAA 57.298 47.368 21.59 21.59 45.17 4.52
219 231 6.868430 GCAATTTTGATTTTGCCAAATGTTG 58.132 32.000 0.00 4.26 41.82 3.33
228 240 6.074249 CCAACATTTGGCAATTTTGATTTTGC 60.074 34.615 0.00 0.00 45.17 3.68
229 241 7.396190 CCAACATTTGGCAATTTTGATTTTG 57.604 32.000 0.00 0.93 45.17 2.44
244 256 5.447548 CCTCACAAAAAGTTGCCAACATTTG 60.448 40.000 24.88 24.88 41.84 2.32
245 257 4.635324 CCTCACAAAAAGTTGCCAACATTT 59.365 37.500 10.69 7.67 38.39 2.32
246 258 4.190772 CCTCACAAAAAGTTGCCAACATT 58.809 39.130 10.69 0.60 38.39 2.71
247 259 3.197549 ACCTCACAAAAAGTTGCCAACAT 59.802 39.130 10.69 0.00 38.39 2.71
248 260 2.564947 ACCTCACAAAAAGTTGCCAACA 59.435 40.909 10.69 0.00 38.39 3.33
249 261 3.245518 ACCTCACAAAAAGTTGCCAAC 57.754 42.857 0.00 0.00 38.39 3.77
250 262 3.259374 TCAACCTCACAAAAAGTTGCCAA 59.741 39.130 0.00 0.00 39.51 4.52
251 263 2.828520 TCAACCTCACAAAAAGTTGCCA 59.171 40.909 0.00 0.00 39.51 4.92
252 264 3.130340 TCTCAACCTCACAAAAAGTTGCC 59.870 43.478 0.00 0.00 39.51 4.52
253 265 4.370364 TCTCAACCTCACAAAAAGTTGC 57.630 40.909 0.00 0.00 39.51 4.17
254 266 7.650834 TTTTTCTCAACCTCACAAAAAGTTG 57.349 32.000 0.00 0.00 40.72 3.16
282 294 4.199310 GCTAGTGATTGGTTGGCTATCAA 58.801 43.478 0.00 0.00 30.72 2.57
283 295 3.433598 GGCTAGTGATTGGTTGGCTATCA 60.434 47.826 0.00 0.00 0.00 2.15
284 296 3.142174 GGCTAGTGATTGGTTGGCTATC 58.858 50.000 0.00 0.00 0.00 2.08
285 297 2.509548 TGGCTAGTGATTGGTTGGCTAT 59.490 45.455 0.00 0.00 0.00 2.97
286 298 1.912731 TGGCTAGTGATTGGTTGGCTA 59.087 47.619 0.00 0.00 0.00 3.93
287 299 0.698238 TGGCTAGTGATTGGTTGGCT 59.302 50.000 0.00 0.00 0.00 4.75
288 300 1.202348 GTTGGCTAGTGATTGGTTGGC 59.798 52.381 0.00 0.00 0.00 4.52
289 301 2.513753 TGTTGGCTAGTGATTGGTTGG 58.486 47.619 0.00 0.00 0.00 3.77
290 302 4.789012 AATGTTGGCTAGTGATTGGTTG 57.211 40.909 0.00 0.00 0.00 3.77
291 303 4.021192 CCAAATGTTGGCTAGTGATTGGTT 60.021 41.667 0.00 0.00 45.17 3.67
292 304 3.511146 CCAAATGTTGGCTAGTGATTGGT 59.489 43.478 0.00 0.00 45.17 3.67
293 305 4.114058 CCAAATGTTGGCTAGTGATTGG 57.886 45.455 0.00 0.00 45.17 3.16
320 332 6.862209 TGAAGTTGGTATGTCAATATTTGGC 58.138 36.000 0.00 0.00 35.37 4.52
321 333 9.520204 GATTGAAGTTGGTATGTCAATATTTGG 57.480 33.333 0.00 0.00 40.03 3.28
327 339 9.113838 GAGTATGATTGAAGTTGGTATGTCAAT 57.886 33.333 0.00 0.00 42.05 2.57
328 340 7.277760 CGAGTATGATTGAAGTTGGTATGTCAA 59.722 37.037 0.00 0.00 34.68 3.18
329 341 6.756542 CGAGTATGATTGAAGTTGGTATGTCA 59.243 38.462 0.00 0.00 0.00 3.58
330 342 6.757010 ACGAGTATGATTGAAGTTGGTATGTC 59.243 38.462 0.00 0.00 0.00 3.06
331 343 6.640518 ACGAGTATGATTGAAGTTGGTATGT 58.359 36.000 0.00 0.00 0.00 2.29
332 344 7.921214 ACTACGAGTATGATTGAAGTTGGTATG 59.079 37.037 0.00 0.00 0.00 2.39
333 345 8.008513 ACTACGAGTATGATTGAAGTTGGTAT 57.991 34.615 0.00 0.00 0.00 2.73
334 346 7.400599 ACTACGAGTATGATTGAAGTTGGTA 57.599 36.000 0.00 0.00 0.00 3.25
335 347 6.282199 ACTACGAGTATGATTGAAGTTGGT 57.718 37.500 0.00 0.00 0.00 3.67
336 348 7.255569 TGTACTACGAGTATGATTGAAGTTGG 58.744 38.462 0.00 0.00 32.65 3.77
337 349 8.746751 CATGTACTACGAGTATGATTGAAGTTG 58.253 37.037 0.00 0.00 32.65 3.16
338 350 7.435488 GCATGTACTACGAGTATGATTGAAGTT 59.565 37.037 0.00 0.00 32.65 2.66
339 351 6.918569 GCATGTACTACGAGTATGATTGAAGT 59.081 38.462 0.00 0.00 32.65 3.01
340 352 6.918022 TGCATGTACTACGAGTATGATTGAAG 59.082 38.462 0.00 0.00 32.65 3.02
341 353 6.801575 TGCATGTACTACGAGTATGATTGAA 58.198 36.000 0.00 0.00 32.65 2.69
342 354 6.385649 TGCATGTACTACGAGTATGATTGA 57.614 37.500 0.00 0.00 32.65 2.57
343 355 6.642540 ACATGCATGTACTACGAGTATGATTG 59.357 38.462 30.50 0.00 39.68 2.67
344 356 6.749139 ACATGCATGTACTACGAGTATGATT 58.251 36.000 30.50 0.00 39.68 2.57
345 357 6.332735 ACATGCATGTACTACGAGTATGAT 57.667 37.500 30.50 0.00 39.68 2.45
346 358 5.767816 ACATGCATGTACTACGAGTATGA 57.232 39.130 30.50 0.00 39.68 2.15
913 930 2.106683 CGTGCCGGCTTAAGAAGGG 61.107 63.158 29.70 4.63 0.00 3.95
970 987 0.730834 CACGAGTCGAAGTCTGCTGG 60.731 60.000 21.50 0.00 0.00 4.85
1680 1706 0.179073 CGCCCACCATCTCCTTGTAG 60.179 60.000 0.00 0.00 0.00 2.74
2253 2281 4.873827 TCATTATCAAACGGGAGTACAAGC 59.126 41.667 0.00 0.00 46.69 4.01
2264 2292 5.030295 GCAATCACCAGTCATTATCAAACG 58.970 41.667 0.00 0.00 0.00 3.60
2320 2348 0.891373 TGCCAGTCTGTGACTAGCTC 59.109 55.000 16.26 1.93 44.97 4.09
2324 2352 0.605083 CTGCTGCCAGTCTGTGACTA 59.395 55.000 0.00 0.00 41.37 2.59
2325 2353 1.370437 CTGCTGCCAGTCTGTGACT 59.630 57.895 0.00 0.00 44.44 3.41
2326 2354 3.963222 CTGCTGCCAGTCTGTGAC 58.037 61.111 0.00 0.00 34.31 3.67
2419 2479 6.262193 TGTTATTAGCCTTGCCTGTAAAAC 57.738 37.500 0.00 0.00 0.00 2.43
2465 2525 8.231692 TCTCATCAAAATGTTTGTTAACTCCA 57.768 30.769 7.22 1.29 35.24 3.86
2494 2554 2.653890 CATTGCAACTGAACTTGTCGG 58.346 47.619 0.00 0.00 38.74 4.79
2537 2597 5.163269 TGCAATATGAGCTAGAACATGTCCT 60.163 40.000 0.00 0.00 0.00 3.85
2538 2598 5.049818 GTGCAATATGAGCTAGAACATGTCC 60.050 44.000 0.00 0.00 0.00 4.02
2582 2642 1.915614 CTGCCGCTCGTGCTGATTTT 61.916 55.000 7.97 0.00 36.97 1.82
2609 2669 7.706179 TGTGTGGAGATTTTTCAAAAGATGTTC 59.294 33.333 0.00 0.00 0.00 3.18
2618 2678 7.340122 TGTATGTTGTGTGGAGATTTTTCAA 57.660 32.000 0.00 0.00 0.00 2.69
2623 2683 6.493115 TGGATTTGTATGTTGTGTGGAGATTT 59.507 34.615 0.00 0.00 0.00 2.17
2632 2692 4.216042 TGAGCTGTGGATTTGTATGTTGTG 59.784 41.667 0.00 0.00 0.00 3.33
2654 2714 2.125350 GACGGAGGAAGCAGCCTG 60.125 66.667 1.70 0.00 38.73 4.85
2754 2815 9.961264 TGTGTATTTACAACATTGGATAGGTTA 57.039 29.630 0.00 0.00 38.04 2.85
2767 2828 8.170553 CGGTTTGTATAGGTGTGTATTTACAAC 58.829 37.037 0.00 0.00 38.04 3.32
2768 2829 8.093307 TCGGTTTGTATAGGTGTGTATTTACAA 58.907 33.333 0.00 0.00 38.04 2.41
2851 2920 7.278424 ACCCTGATTCGAAATTGCAAAAATATG 59.722 33.333 1.71 0.00 0.00 1.78
2852 2921 7.330262 ACCCTGATTCGAAATTGCAAAAATAT 58.670 30.769 1.71 0.00 0.00 1.28
2862 2931 7.045126 TGTTTGTTTACCCTGATTCGAAATT 57.955 32.000 0.00 0.00 0.00 1.82
2871 2940 7.124448 ACCTTAATTGTTGTTTGTTTACCCTGA 59.876 33.333 0.00 0.00 0.00 3.86
2882 2951 5.659079 TGGGTCTGAACCTTAATTGTTGTTT 59.341 36.000 13.85 0.00 45.66 2.83
2886 2955 3.826729 GCTGGGTCTGAACCTTAATTGTT 59.173 43.478 13.85 0.00 45.66 2.83
2888 2957 2.755103 GGCTGGGTCTGAACCTTAATTG 59.245 50.000 13.85 0.00 45.66 2.32
2896 2965 0.957888 GAGCTTGGCTGGGTCTGAAC 60.958 60.000 0.00 0.00 39.88 3.18
2897 2966 1.376466 GAGCTTGGCTGGGTCTGAA 59.624 57.895 0.00 0.00 39.88 3.02
2898 2967 2.596851 GGAGCTTGGCTGGGTCTGA 61.597 63.158 0.00 0.00 39.88 3.27
2899 2968 2.045536 GGAGCTTGGCTGGGTCTG 60.046 66.667 0.00 0.00 39.88 3.51
2900 2969 1.927527 ATGGAGCTTGGCTGGGTCT 60.928 57.895 0.00 0.00 39.88 3.85
2901 2970 1.751927 CATGGAGCTTGGCTGGGTC 60.752 63.158 0.00 0.00 39.88 4.46
2902 2971 2.357836 CATGGAGCTTGGCTGGGT 59.642 61.111 0.00 0.00 39.88 4.51
2903 2972 2.441532 CCATGGAGCTTGGCTGGG 60.442 66.667 5.56 0.00 39.88 4.45
2906 2975 1.272872 ACATTTCCATGGAGCTTGGCT 60.273 47.619 15.53 0.00 36.19 4.75
2907 2976 1.134907 CACATTTCCATGGAGCTTGGC 60.135 52.381 15.53 0.00 34.27 4.52
2908 2977 1.134907 GCACATTTCCATGGAGCTTGG 60.135 52.381 15.53 7.43 34.44 3.61
2909 2978 1.546923 TGCACATTTCCATGGAGCTTG 59.453 47.619 20.08 17.64 36.81 4.01
2910 2979 1.822990 CTGCACATTTCCATGGAGCTT 59.177 47.619 20.08 6.01 36.81 3.74
2911 2980 1.005097 TCTGCACATTTCCATGGAGCT 59.995 47.619 20.08 8.14 36.81 4.09
2912 2981 1.466856 TCTGCACATTTCCATGGAGC 58.533 50.000 15.53 14.89 34.52 4.70
2913 2982 3.952323 AGAATCTGCACATTTCCATGGAG 59.048 43.478 15.53 6.22 35.74 3.86
2914 2983 3.972133 AGAATCTGCACATTTCCATGGA 58.028 40.909 11.44 11.44 34.27 3.41
2916 2985 5.008415 GTCCTAGAATCTGCACATTTCCATG 59.992 44.000 0.00 0.00 36.34 3.66
2920 2989 5.505324 GCATGTCCTAGAATCTGCACATTTC 60.505 44.000 0.00 0.00 0.00 2.17
2921 2990 4.337555 GCATGTCCTAGAATCTGCACATTT 59.662 41.667 0.00 0.00 0.00 2.32
2922 2991 3.881688 GCATGTCCTAGAATCTGCACATT 59.118 43.478 0.00 0.00 0.00 2.71
2924 2993 2.236893 TGCATGTCCTAGAATCTGCACA 59.763 45.455 0.00 0.00 34.92 4.57
2926 2995 3.632643 TTGCATGTCCTAGAATCTGCA 57.367 42.857 0.00 0.00 37.80 4.41
2931 3000 8.571336 GCACTAAATATTTGCATGTCCTAGAAT 58.429 33.333 11.05 0.00 36.22 2.40
2932 3001 7.555914 TGCACTAAATATTTGCATGTCCTAGAA 59.444 33.333 11.05 0.00 41.29 2.10
2933 3002 7.053498 TGCACTAAATATTTGCATGTCCTAGA 58.947 34.615 11.05 0.00 41.29 2.43
2934 3003 7.263100 TGCACTAAATATTTGCATGTCCTAG 57.737 36.000 11.05 0.00 41.29 3.02
2935 3004 6.262944 CCTGCACTAAATATTTGCATGTCCTA 59.737 38.462 12.47 0.00 44.94 2.94
2936 3005 5.068198 CCTGCACTAAATATTTGCATGTCCT 59.932 40.000 12.47 0.00 44.94 3.85
2937 3006 5.284079 CCTGCACTAAATATTTGCATGTCC 58.716 41.667 12.47 0.00 44.94 4.02
2938 3007 5.163519 ACCCTGCACTAAATATTTGCATGTC 60.164 40.000 12.47 5.31 44.94 3.06
2944 3013 7.826690 ACTTACAACCCTGCACTAAATATTTG 58.173 34.615 11.05 3.88 0.00 2.32
2957 3026 9.613428 TGAAGAATATATGAACTTACAACCCTG 57.387 33.333 0.00 0.00 0.00 4.45
2960 3029 9.057089 CCCTGAAGAATATATGAACTTACAACC 57.943 37.037 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.