Multiple sequence alignment - TraesCS5B01G224400

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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 TraesCS5B01G224400 chr5B 100.000 2855 0 0 1 2855 399813791 399810937 0.000000e+00 5273.0
1 TraesCS5B01G224400 chr5A 93.619 2053 91 21 415 2451 441705375 441703347 0.000000e+00 3029.0
2 TraesCS5B01G224400 chr5A 93.976 83 5 0 2773 2855 441703115 441703033 2.990000e-25 126.0
3 TraesCS5B01G224400 chr5D 96.986 1526 38 5 850 2370 340760261 340758739 0.000000e+00 2556.0
4 TraesCS5B01G224400 chr5D 96.356 494 9 3 2370 2855 340758647 340758155 0.000000e+00 804.0
5 TraesCS5B01G224400 chr5D 91.146 384 19 9 416 791 340760975 340760599 9.130000e-140 507.0
6 TraesCS5B01G224400 chr5D 83.929 392 52 10 24 411 340761396 340761012 5.810000e-97 364.0
7 TraesCS5B01G224400 chr5D 89.796 98 8 2 2139 2236 310705361 310705266 1.070000e-24 124.0
8 TraesCS5B01G224400 chr2B 91.429 105 8 1 2137 2240 478114813 478114709 2.970000e-30 143.0
9 TraesCS5B01G224400 chr2B 88.542 96 11 0 2142 2237 650285641 650285736 1.800000e-22 117.0
10 TraesCS5B01G224400 chr2B 96.154 52 1 1 2591 2641 166044576 166044525 1.820000e-12 84.2
11 TraesCS5B01G224400 chrUn 91.919 99 7 1 2138 2236 101630787 101630884 1.380000e-28 137.0
12 TraesCS5B01G224400 chr4D 91.837 98 6 2 2150 2247 252173790 252173695 4.960000e-28 135.0
13 TraesCS5B01G224400 chr2A 90.909 99 6 3 2147 2242 729165687 729165589 2.310000e-26 130.0
14 TraesCS5B01G224400 chr2A 88.571 105 11 1 2137 2240 542455959 542455855 2.990000e-25 126.0
15 TraesCS5B01G224400 chr2A 90.566 53 2 3 2591 2641 694455392 694455341 1.840000e-07 67.6
16 TraesCS5B01G224400 chr2D 88.571 105 11 1 2137 2240 404087634 404087530 2.990000e-25 126.0
17 TraesCS5B01G224400 chr2D 97.872 47 0 1 2596 2641 529010332 529010286 2.360000e-11 80.5
18 TraesCS5B01G224400 chr6A 88.571 105 9 2 2145 2249 584511357 584511458 1.070000e-24 124.0
19 TraesCS5B01G224400 chr6A 94.340 53 2 1 2590 2641 51882721 51882669 2.360000e-11 80.5
20 TraesCS5B01G224400 chr6B 86.441 118 8 6 2152 2265 695054256 695054143 3.860000e-24 122.0
21 TraesCS5B01G224400 chr6B 95.556 45 1 1 2595 2638 135505680 135505636 1.420000e-08 71.3
22 TraesCS5B01G224400 chr3B 89.000 100 10 1 2142 2240 113917160 113917061 3.860000e-24 122.0
23 TraesCS5B01G224400 chr3B 88.119 101 10 2 2137 2237 154213762 154213860 5.000000e-23 119.0
24 TraesCS5B01G224400 chr3A 91.935 62 1 4 2582 2641 231001820 231001879 1.820000e-12 84.2
25 TraesCS5B01G224400 chr6D 94.340 53 2 1 2590 2641 41237300 41237248 2.360000e-11 80.5
26 TraesCS5B01G224400 chr7A 91.228 57 2 3 2584 2639 309401313 309401367 1.100000e-09 75.0


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 TraesCS5B01G224400 chr5B 399810937 399813791 2854 True 5273.00 5273 100.00000 1 2855 1 chr5B.!!$R1 2854
1 TraesCS5B01G224400 chr5A 441703033 441705375 2342 True 1577.50 3029 93.79750 415 2855 2 chr5A.!!$R1 2440
2 TraesCS5B01G224400 chr5D 340758155 340761396 3241 True 1057.75 2556 92.10425 24 2855 4 chr5D.!!$R2 2831

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
367 368 0.03759 TTTTCACCACGCCTGCCTAT 59.962 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2658 0.962356 AATTGGAGTCCTTGGCTGCG 60.962 55.0 11.33 0.0 0.0 5.18 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 3.519774 GGTTTTGACACCGACAACG 57.480 52.632 0.00 0.00 39.43 4.10
21 22 1.008329 GGTTTTGACACCGACAACGA 58.992 50.000 0.00 0.00 42.66 3.85
22 23 1.600485 GGTTTTGACACCGACAACGAT 59.400 47.619 0.00 0.00 42.66 3.73
23 24 2.801679 GGTTTTGACACCGACAACGATA 59.198 45.455 0.00 0.00 42.66 2.92
24 25 3.120786 GGTTTTGACACCGACAACGATAG 60.121 47.826 0.00 0.00 42.66 2.08
25 26 3.646611 TTTGACACCGACAACGATAGA 57.353 42.857 0.00 0.00 42.66 1.98
26 27 2.913777 TGACACCGACAACGATAGAG 57.086 50.000 0.00 0.00 42.66 2.43
34 35 4.278669 ACCGACAACGATAGAGCAATATCT 59.721 41.667 0.00 0.00 42.66 1.98
51 52 9.135189 AGCAATATCTGTATTTGGAGCAAAATA 57.865 29.630 0.00 0.00 36.90 1.40
52 53 9.918630 GCAATATCTGTATTTGGAGCAAAATAT 57.081 29.630 0.00 0.00 36.90 1.28
58 59 8.243426 TCTGTATTTGGAGCAAAATATTGTGAC 58.757 33.333 9.96 2.72 36.90 3.67
68 69 5.515184 CAAAATATTGTGACGTGTGAACCA 58.485 37.500 0.00 0.00 0.00 3.67
71 72 0.107897 TTGTGACGTGTGAACCAGCT 60.108 50.000 0.00 0.00 0.00 4.24
104 105 7.830201 ACGTTGGTTTAATATCCTGGTTCAATA 59.170 33.333 0.00 0.00 0.00 1.90
138 139 8.097038 TCTTGCTCTTACTTTCATGATAGTTGT 58.903 33.333 21.58 7.70 0.00 3.32
142 143 8.887717 GCTCTTACTTTCATGATAGTTGTTGAT 58.112 33.333 21.58 0.62 0.00 2.57
151 152 6.319405 TCATGATAGTTGTTGATTGACATGGG 59.681 38.462 0.00 0.00 35.06 4.00
177 178 7.374975 ACTAAATTAACATGGCCTAGAGCTA 57.625 36.000 3.32 0.00 43.05 3.32
178 179 7.802117 ACTAAATTAACATGGCCTAGAGCTAA 58.198 34.615 3.32 0.00 43.05 3.09
182 183 9.640952 AAATTAACATGGCCTAGAGCTAATTTA 57.359 29.630 3.32 4.93 43.05 1.40
183 184 9.813826 AATTAACATGGCCTAGAGCTAATTTAT 57.186 29.630 3.32 0.00 43.05 1.40
185 186 9.640952 TTAACATGGCCTAGAGCTAATTTATTT 57.359 29.630 3.32 0.00 43.05 1.40
193 194 8.125448 GCCTAGAGCTAATTTATTTTGTGTCTG 58.875 37.037 0.00 0.00 38.99 3.51
194 195 8.616076 CCTAGAGCTAATTTATTTTGTGTCTGG 58.384 37.037 0.00 0.00 0.00 3.86
195 196 6.856895 AGAGCTAATTTATTTTGTGTCTGGC 58.143 36.000 0.00 0.00 0.00 4.85
223 224 5.999205 TCCATTTTTGCTACCATGACATT 57.001 34.783 0.00 0.00 0.00 2.71
265 266 5.011943 ACATGTTTCATTGCCTTGGTTGTAT 59.988 36.000 0.00 0.00 0.00 2.29
268 269 6.352516 TGTTTCATTGCCTTGGTTGTATTTT 58.647 32.000 0.00 0.00 0.00 1.82
270 271 7.011857 TGTTTCATTGCCTTGGTTGTATTTTTC 59.988 33.333 0.00 0.00 0.00 2.29
271 272 6.418057 TCATTGCCTTGGTTGTATTTTTCT 57.582 33.333 0.00 0.00 0.00 2.52
281 282 2.409012 TGTATTTTTCTGCAGCGACGA 58.591 42.857 9.47 0.00 0.00 4.20
284 285 0.796312 TTTTTCTGCAGCGACGATCC 59.204 50.000 9.47 0.00 0.00 3.36
292 293 1.526384 GCAGCGACGATCCGTTTTTAC 60.526 52.381 0.00 0.00 41.37 2.01
293 294 1.990563 CAGCGACGATCCGTTTTTACT 59.009 47.619 0.00 0.00 41.37 2.24
294 295 2.410730 CAGCGACGATCCGTTTTTACTT 59.589 45.455 0.00 0.00 41.37 2.24
295 296 2.665052 AGCGACGATCCGTTTTTACTTC 59.335 45.455 0.00 0.00 41.37 3.01
298 299 3.181537 CGACGATCCGTTTTTACTTCCAC 60.182 47.826 0.00 0.00 41.37 4.02
299 300 2.733026 ACGATCCGTTTTTACTTCCACG 59.267 45.455 0.00 0.00 36.35 4.94
305 306 2.417586 CGTTTTTACTTCCACGGGATCC 59.582 50.000 1.92 1.92 0.00 3.36
306 307 3.682696 GTTTTTACTTCCACGGGATCCT 58.317 45.455 12.58 0.00 0.00 3.24
307 308 4.077108 GTTTTTACTTCCACGGGATCCTT 58.923 43.478 12.58 0.00 0.00 3.36
310 311 2.491675 ACTTCCACGGGATCCTTTTC 57.508 50.000 12.58 0.00 0.00 2.29
315 316 2.092323 CCACGGGATCCTTTTCTTTCC 58.908 52.381 12.58 0.00 0.00 3.13
323 324 5.080337 GGATCCTTTTCTTTCCCAAGAGTT 58.920 41.667 3.84 0.00 40.28 3.01
324 325 5.540337 GGATCCTTTTCTTTCCCAAGAGTTT 59.460 40.000 3.84 0.00 40.28 2.66
326 327 5.269189 TCCTTTTCTTTCCCAAGAGTTTGT 58.731 37.500 0.00 0.00 40.28 2.83
331 332 6.597832 TTCTTTCCCAAGAGTTTGTTTTCA 57.402 33.333 0.00 0.00 40.28 2.69
336 337 3.809279 CCCAAGAGTTTGTTTTCATTGCC 59.191 43.478 0.00 0.00 32.21 4.52
339 340 5.049954 CCAAGAGTTTGTTTTCATTGCCATG 60.050 40.000 0.00 0.00 32.21 3.66
346 347 5.480642 TGTTTTCATTGCCATGGTGTATT 57.519 34.783 14.67 0.00 0.00 1.89
347 348 5.862845 TGTTTTCATTGCCATGGTGTATTT 58.137 33.333 14.67 0.00 0.00 1.40
367 368 0.037590 TTTTCACCACGCCTGCCTAT 59.962 50.000 0.00 0.00 0.00 2.57
373 374 2.097466 CACCACGCCTGCCTATTTTTAG 59.903 50.000 0.00 0.00 0.00 1.85
374 375 2.290705 ACCACGCCTGCCTATTTTTAGT 60.291 45.455 0.00 0.00 0.00 2.24
401 403 6.456447 TTCACGTCAACCTATTTTTACTCG 57.544 37.500 0.00 0.00 0.00 4.18
407 409 6.237755 CGTCAACCTATTTTTACTCGGATGTC 60.238 42.308 0.00 0.00 0.00 3.06
411 413 7.553881 ACCTATTTTTACTCGGATGTCAATG 57.446 36.000 0.00 0.00 0.00 2.82
412 414 6.038271 ACCTATTTTTACTCGGATGTCAATGC 59.962 38.462 0.00 0.00 0.00 3.56
415 417 4.880886 TTTACTCGGATGTCAATGCATG 57.119 40.909 0.00 0.00 0.00 4.06
416 418 2.696989 ACTCGGATGTCAATGCATGA 57.303 45.000 0.00 0.00 35.05 3.07
417 419 2.989909 ACTCGGATGTCAATGCATGAA 58.010 42.857 0.00 0.00 40.50 2.57
418 420 2.941064 ACTCGGATGTCAATGCATGAAG 59.059 45.455 0.00 0.00 40.50 3.02
419 421 3.200483 CTCGGATGTCAATGCATGAAGA 58.800 45.455 0.00 0.00 40.50 2.87
420 422 3.608796 TCGGATGTCAATGCATGAAGAA 58.391 40.909 0.00 0.00 40.50 2.52
426 461 6.869913 GGATGTCAATGCATGAAGAAAAGAAA 59.130 34.615 0.00 0.00 40.50 2.52
436 471 7.439056 TGCATGAAGAAAAGAAAAAGCTAAAGG 59.561 33.333 0.00 0.00 0.00 3.11
442 477 7.555965 AGAAAAGAAAAAGCTAAAGGAAAGCA 58.444 30.769 0.00 0.00 42.62 3.91
451 486 6.993786 AGCTAAAGGAAAGCATAGAGAAAC 57.006 37.500 0.00 0.00 42.62 2.78
463 498 4.152402 GCATAGAGAAACGAAGACTTGCAA 59.848 41.667 0.00 0.00 0.00 4.08
465 500 4.999751 AGAGAAACGAAGACTTGCAATC 57.000 40.909 0.00 0.00 0.00 2.67
487 522 3.031013 ACCAACCCCAAGTCAAAGAAAG 58.969 45.455 0.00 0.00 0.00 2.62
499 534 5.880901 AGTCAAAGAAAGCCCTCTTCATTA 58.119 37.500 0.00 0.00 34.49 1.90
518 561 7.678194 TCATTAGAAGAAGCAAAACAAAACG 57.322 32.000 0.00 0.00 0.00 3.60
562 608 2.452600 TGTTTTCCTTGCTGGTTCCT 57.547 45.000 0.00 0.00 37.07 3.36
563 609 2.745968 TGTTTTCCTTGCTGGTTCCTT 58.254 42.857 0.00 0.00 37.07 3.36
564 610 2.693074 TGTTTTCCTTGCTGGTTCCTTC 59.307 45.455 0.00 0.00 37.07 3.46
565 611 1.995376 TTTCCTTGCTGGTTCCTTCC 58.005 50.000 0.00 0.00 37.07 3.46
577 623 1.084018 TTCCTTCCAATCCAGCCCTT 58.916 50.000 0.00 0.00 0.00 3.95
788 843 1.398234 CCCTCCCCTCTTCTTCCCT 59.602 63.158 0.00 0.00 0.00 4.20
839 894 1.628727 CCTCCCCTGGATCTCCTCA 59.371 63.158 0.00 0.00 36.82 3.86
841 896 1.643310 CTCCCCTGGATCTCCTCATC 58.357 60.000 0.00 0.00 36.82 2.92
842 897 0.192064 TCCCCTGGATCTCCTCATCC 59.808 60.000 0.00 0.00 42.68 3.51
843 898 0.839853 CCCCTGGATCTCCTCATCCC 60.840 65.000 0.00 0.00 41.78 3.85
844 899 1.190833 CCCTGGATCTCCTCATCCCG 61.191 65.000 0.00 0.00 41.78 5.14
845 900 1.670590 CTGGATCTCCTCATCCCGC 59.329 63.158 0.00 0.00 41.78 6.13
971 1306 0.689412 CAGGAAGGAGAGGGGAGGAC 60.689 65.000 0.00 0.00 0.00 3.85
1755 2091 2.154854 TCAACAAGCTCAAGGAGTCG 57.845 50.000 0.00 0.00 31.39 4.18
1993 2329 5.948992 ACTCCTCAATGAGTTTGTTTAGC 57.051 39.130 9.63 0.00 42.92 3.09
2043 2379 1.154150 GCGTGCTGAAGTTGATGGC 60.154 57.895 0.00 0.00 0.00 4.40
2122 2462 4.150098 CGTCCTGTAGAGTTAAACACTTGC 59.850 45.833 0.00 0.00 35.01 4.01
2354 2694 7.690256 ACTCCAATTCTATCACTAGTTGGTTT 58.310 34.615 0.00 0.00 34.75 3.27
2497 2929 2.822707 AAGCAGAGATGGCCAAAGAT 57.177 45.000 10.96 0.00 0.00 2.40
2550 2982 2.092968 GTGTCATGGACCAGGATAAGCA 60.093 50.000 12.76 2.48 0.00 3.91
2770 3236 8.448816 TCCCTAGACATGATTCTGAGTCTATTA 58.551 37.037 0.00 0.00 41.28 0.98
2814 3280 4.704965 TCAGAGGATGATTTCAGATGCTG 58.295 43.478 0.00 0.00 31.12 4.41
2852 3318 1.004745 GTCACACCCATCAACCCATCT 59.995 52.381 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.008329 TCGTTGTCGGTGTCAAAACC 58.992 50.000 0.00 0.00 37.69 3.27
3 4 3.737266 TCTATCGTTGTCGGTGTCAAAAC 59.263 43.478 0.00 0.00 37.69 2.43
4 5 3.979948 TCTATCGTTGTCGGTGTCAAAA 58.020 40.909 0.00 0.00 37.69 2.44
5 6 3.571571 CTCTATCGTTGTCGGTGTCAAA 58.428 45.455 0.00 0.00 37.69 2.69
6 7 2.670229 GCTCTATCGTTGTCGGTGTCAA 60.670 50.000 0.00 0.00 37.69 3.18
7 8 1.135489 GCTCTATCGTTGTCGGTGTCA 60.135 52.381 0.00 0.00 37.69 3.58
8 9 1.135489 TGCTCTATCGTTGTCGGTGTC 60.135 52.381 0.00 0.00 37.69 3.67
9 10 0.885879 TGCTCTATCGTTGTCGGTGT 59.114 50.000 0.00 0.00 37.69 4.16
10 11 1.990799 TTGCTCTATCGTTGTCGGTG 58.009 50.000 0.00 0.00 37.69 4.94
11 12 2.961526 ATTGCTCTATCGTTGTCGGT 57.038 45.000 0.00 0.00 37.69 4.69
12 13 4.618912 CAGATATTGCTCTATCGTTGTCGG 59.381 45.833 0.00 0.00 37.69 4.79
13 14 5.215903 ACAGATATTGCTCTATCGTTGTCG 58.784 41.667 0.00 0.00 34.05 4.35
14 15 8.749841 AATACAGATATTGCTCTATCGTTGTC 57.250 34.615 5.09 0.00 34.05 3.18
15 16 8.982685 CAAATACAGATATTGCTCTATCGTTGT 58.017 33.333 0.00 0.00 34.05 3.32
16 17 8.438513 CCAAATACAGATATTGCTCTATCGTTG 58.561 37.037 0.00 0.00 34.05 4.10
17 18 8.367911 TCCAAATACAGATATTGCTCTATCGTT 58.632 33.333 0.00 0.00 34.05 3.85
18 19 7.896811 TCCAAATACAGATATTGCTCTATCGT 58.103 34.615 0.00 0.00 34.05 3.73
19 20 7.009999 GCTCCAAATACAGATATTGCTCTATCG 59.990 40.741 0.00 0.00 34.05 2.92
20 21 7.821359 TGCTCCAAATACAGATATTGCTCTATC 59.179 37.037 0.00 0.00 31.07 2.08
21 22 7.683578 TGCTCCAAATACAGATATTGCTCTAT 58.316 34.615 0.00 0.00 31.07 1.98
22 23 7.066307 TGCTCCAAATACAGATATTGCTCTA 57.934 36.000 0.00 0.00 31.07 2.43
23 24 5.933617 TGCTCCAAATACAGATATTGCTCT 58.066 37.500 0.00 0.00 31.07 4.09
24 25 6.624352 TTGCTCCAAATACAGATATTGCTC 57.376 37.500 0.00 0.00 31.07 4.26
25 26 7.408756 TTTTGCTCCAAATACAGATATTGCT 57.591 32.000 0.00 0.00 33.19 3.91
26 27 9.918630 ATATTTTGCTCCAAATACAGATATTGC 57.081 29.630 0.00 0.00 33.19 3.56
34 35 7.026562 CGTCACAATATTTTGCTCCAAATACA 58.973 34.615 0.00 0.00 36.22 2.29
51 52 0.944386 GCTGGTTCACACGTCACAAT 59.056 50.000 0.00 0.00 0.00 2.71
52 53 0.107897 AGCTGGTTCACACGTCACAA 60.108 50.000 0.00 0.00 0.00 3.33
54 55 1.222115 GGAGCTGGTTCACACGTCAC 61.222 60.000 0.00 0.00 0.00 3.67
58 59 0.588252 CAAAGGAGCTGGTTCACACG 59.412 55.000 0.00 0.00 0.00 4.49
68 69 2.052782 AAACCAACGTCAAAGGAGCT 57.947 45.000 0.00 0.00 0.00 4.09
71 72 6.373216 CAGGATATTAAACCAACGTCAAAGGA 59.627 38.462 0.00 0.00 0.00 3.36
109 110 9.979578 ACTATCATGAAAGTAAGAGCAAGATAG 57.020 33.333 0.00 0.00 41.31 2.08
123 124 9.285770 CATGTCAATCAACAACTATCATGAAAG 57.714 33.333 0.00 0.00 34.14 2.62
138 139 9.083422 TGTTAATTTAGTTCCCATGTCAATCAA 57.917 29.630 0.00 0.00 0.00 2.57
142 143 7.578571 GCCATGTTAATTTAGTTCCCATGTCAA 60.579 37.037 0.00 0.00 31.26 3.18
144 145 6.273071 GCCATGTTAATTTAGTTCCCATGTC 58.727 40.000 0.00 0.00 31.26 3.06
151 152 6.768381 AGCTCTAGGCCATGTTAATTTAGTTC 59.232 38.462 5.01 0.00 43.05 3.01
177 178 3.584834 GCCGCCAGACACAAAATAAATT 58.415 40.909 0.00 0.00 0.00 1.82
178 179 2.415357 CGCCGCCAGACACAAAATAAAT 60.415 45.455 0.00 0.00 0.00 1.40
182 183 1.452145 AACGCCGCCAGACACAAAAT 61.452 50.000 0.00 0.00 0.00 1.82
183 184 2.054140 GAACGCCGCCAGACACAAAA 62.054 55.000 0.00 0.00 0.00 2.44
185 186 2.970324 GAACGCCGCCAGACACAA 60.970 61.111 0.00 0.00 0.00 3.33
193 194 2.379634 GCAAAAATGGAACGCCGCC 61.380 57.895 0.00 0.00 36.79 6.13
194 195 0.109504 TAGCAAAAATGGAACGCCGC 60.110 50.000 0.00 0.00 36.79 6.53
195 196 1.613270 GTAGCAAAAATGGAACGCCG 58.387 50.000 0.00 0.00 36.79 6.46
238 239 4.128643 ACCAAGGCAATGAAACATGTTTG 58.871 39.130 27.85 15.31 32.11 2.93
249 250 5.106987 GCAGAAAAATACAACCAAGGCAATG 60.107 40.000 0.00 0.00 0.00 2.82
256 257 3.316588 TCGCTGCAGAAAAATACAACCAA 59.683 39.130 20.43 0.00 0.00 3.67
265 266 0.796312 GGATCGTCGCTGCAGAAAAA 59.204 50.000 20.43 0.00 0.00 1.94
268 269 2.202610 CGGATCGTCGCTGCAGAA 60.203 61.111 20.43 0.54 0.00 3.02
270 271 1.626654 AAAACGGATCGTCGCTGCAG 61.627 55.000 10.11 10.11 39.99 4.41
271 272 1.225376 AAAAACGGATCGTCGCTGCA 61.225 50.000 0.00 0.00 39.99 4.41
284 285 2.417586 GGATCCCGTGGAAGTAAAAACG 59.582 50.000 0.00 0.00 34.34 3.60
292 293 2.789409 AGAAAAGGATCCCGTGGAAG 57.211 50.000 8.55 0.00 34.34 3.46
293 294 3.418047 GAAAGAAAAGGATCCCGTGGAA 58.582 45.455 8.55 0.00 34.34 3.53
294 295 2.290705 GGAAAGAAAAGGATCCCGTGGA 60.291 50.000 8.55 0.00 35.55 4.02
295 296 2.092323 GGAAAGAAAAGGATCCCGTGG 58.908 52.381 8.55 0.00 0.00 4.94
305 306 7.602265 TGAAAACAAACTCTTGGGAAAGAAAAG 59.398 33.333 0.00 0.00 36.82 2.27
306 307 7.445945 TGAAAACAAACTCTTGGGAAAGAAAA 58.554 30.769 0.00 0.00 36.82 2.29
307 308 6.998802 TGAAAACAAACTCTTGGGAAAGAAA 58.001 32.000 0.00 0.00 36.82 2.52
310 311 6.238184 GCAATGAAAACAAACTCTTGGGAAAG 60.238 38.462 0.00 0.00 36.82 2.62
315 316 4.440880 TGGCAATGAAAACAAACTCTTGG 58.559 39.130 0.00 0.00 36.82 3.61
323 324 3.834489 ACACCATGGCAATGAAAACAA 57.166 38.095 13.04 0.00 35.67 2.83
324 325 5.480642 AATACACCATGGCAATGAAAACA 57.519 34.783 13.04 0.00 35.67 2.83
347 348 0.179015 TAGGCAGGCGTGGTGAAAAA 60.179 50.000 8.72 0.00 0.00 1.94
356 357 5.462530 AAAAACTAAAAATAGGCAGGCGT 57.537 34.783 0.00 0.00 0.00 5.68
380 382 4.925054 TCCGAGTAAAAATAGGTTGACGTG 59.075 41.667 0.00 0.00 0.00 4.49
382 384 5.579511 ACATCCGAGTAAAAATAGGTTGACG 59.420 40.000 0.00 0.00 0.00 4.35
385 387 6.978343 TGACATCCGAGTAAAAATAGGTTG 57.022 37.500 0.00 0.00 0.00 3.77
389 391 7.015226 TGCATTGACATCCGAGTAAAAATAG 57.985 36.000 0.00 0.00 0.00 1.73
401 403 5.957798 TCTTTTCTTCATGCATTGACATCC 58.042 37.500 0.00 0.00 32.84 3.51
407 409 7.186021 AGCTTTTTCTTTTCTTCATGCATTG 57.814 32.000 0.00 0.00 0.00 2.82
411 413 7.653311 TCCTTTAGCTTTTTCTTTTCTTCATGC 59.347 33.333 0.00 0.00 0.00 4.06
412 414 9.533253 TTCCTTTAGCTTTTTCTTTTCTTCATG 57.467 29.630 0.00 0.00 0.00 3.07
415 417 8.543774 GCTTTCCTTTAGCTTTTTCTTTTCTTC 58.456 33.333 0.00 0.00 35.74 2.87
416 418 8.040727 TGCTTTCCTTTAGCTTTTTCTTTTCTT 58.959 29.630 0.00 0.00 39.38 2.52
417 419 7.555965 TGCTTTCCTTTAGCTTTTTCTTTTCT 58.444 30.769 0.00 0.00 39.38 2.52
418 420 7.770801 TGCTTTCCTTTAGCTTTTTCTTTTC 57.229 32.000 0.00 0.00 39.38 2.29
419 421 9.481340 CTATGCTTTCCTTTAGCTTTTTCTTTT 57.519 29.630 0.00 0.00 39.38 2.27
420 422 8.860088 TCTATGCTTTCCTTTAGCTTTTTCTTT 58.140 29.630 0.00 0.00 39.38 2.52
426 461 7.361286 CGTTTCTCTATGCTTTCCTTTAGCTTT 60.361 37.037 0.00 0.00 39.38 3.51
436 471 6.529696 CAAGTCTTCGTTTCTCTATGCTTTC 58.470 40.000 0.00 0.00 0.00 2.62
442 477 6.091441 GTGATTGCAAGTCTTCGTTTCTCTAT 59.909 38.462 4.94 0.00 0.00 1.98
451 486 2.350772 GGTTGGTGATTGCAAGTCTTCG 60.351 50.000 4.94 0.00 0.00 3.79
463 498 2.176798 TCTTTGACTTGGGGTTGGTGAT 59.823 45.455 0.00 0.00 0.00 3.06
465 500 2.065899 TCTTTGACTTGGGGTTGGTG 57.934 50.000 0.00 0.00 0.00 4.17
499 534 7.117667 ACAATTTCGTTTTGTTTTGCTTCTTCT 59.882 29.630 0.00 0.00 33.64 2.85
518 561 3.989817 GGCAAGTGTGGATGAACAATTTC 59.010 43.478 0.00 0.00 36.29 2.17
562 608 1.284785 CAGGTAAGGGCTGGATTGGAA 59.715 52.381 0.00 0.00 0.00 3.53
563 609 0.918983 CAGGTAAGGGCTGGATTGGA 59.081 55.000 0.00 0.00 0.00 3.53
564 610 0.918983 TCAGGTAAGGGCTGGATTGG 59.081 55.000 0.00 0.00 0.00 3.16
565 611 1.743772 CGTCAGGTAAGGGCTGGATTG 60.744 57.143 0.00 0.00 0.00 2.67
599 645 0.472044 GGGGCCAATTTTTGTGTGGT 59.528 50.000 4.39 0.00 34.71 4.16
788 843 1.524961 CGTGGGATTGGGGATTCGA 59.475 57.895 0.00 0.00 0.00 3.71
946 1281 1.519719 CCTCTCCTTCCTGGAAGCG 59.480 63.158 27.45 20.56 45.63 4.68
971 1306 1.332997 GGGCATCAAAGATTCGAGCTG 59.667 52.381 0.00 0.00 0.00 4.24
1755 2091 3.114065 CTCAGTTAATCCGCCGAAGTAC 58.886 50.000 0.00 0.00 0.00 2.73
1993 2329 5.510671 ACAACAAAAACGCAGTCATCTAAG 58.489 37.500 0.00 0.00 45.00 2.18
2043 2379 6.927936 CAGTATCTAGAGGGTGTTTCATCATG 59.072 42.308 0.00 0.00 0.00 3.07
2290 2630 4.429522 ATGCGCCTGCCCATGACA 62.430 61.111 4.18 0.00 41.78 3.58
2318 2658 0.962356 AATTGGAGTCCTTGGCTGCG 60.962 55.000 11.33 0.00 0.00 5.18
2376 2808 1.212688 TGGTATGGAAGCATGGACCTG 59.787 52.381 0.00 0.00 0.00 4.00
2550 2982 8.962884 TGACAATATATATGAACAACAGCTGT 57.037 30.769 15.25 15.25 41.27 4.40
2760 3226 7.265647 GCAGACTACTGACATAATAGACTCA 57.734 40.000 0.00 0.00 46.03 3.41
2814 3280 0.324830 ACCAGACTACCAGAGAGGGC 60.325 60.000 0.00 0.00 43.89 5.19


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

AutoCloner maintained by Alex Coulton.