Multiple sequence alignment - TraesCS5B01G271600

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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 TraesCS5B01G271600 chr5B 100.000 2939 0 0 1 2939 457128830 457125892 0.000000e+00 5428
1 TraesCS5B01G271600 chr5A 91.689 2960 179 25 1 2909 481897383 481894440 0.000000e+00 4041
2 TraesCS5B01G271600 chr5D 94.870 1930 85 12 993 2916 381028997 381027076 0.000000e+00 3003
3 TraesCS5B01G271600 chr5D 89.351 385 16 8 554 927 381029396 381029026 7.420000e-126 460
4 TraesCS5B01G271600 chr5D 85.520 221 8 10 1 199 381029914 381029696 2.970000e-50 209


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 TraesCS5B01G271600 chr5B 457125892 457128830 2938 True 5428 5428 100.000000 1 2939 1 chr5B.!!$R1 2938
1 TraesCS5B01G271600 chr5A 481894440 481897383 2943 True 4041 4041 91.689000 1 2909 1 chr5A.!!$R1 2908
2 TraesCS5B01G271600 chr5D 381027076 381029914 2838 True 1224 3003 89.913667 1 2916 3 chr5D.!!$R1 2915

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
948 1041 0.596577 TGCGCGTAAGAAGAGACACT 59.403 50.0 8.43 0.0 43.02 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 2548 0.036388 TCGATTCCCTGCCAAGTCAC 60.036 55.0 0.0 0.0 0.0 3.67 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
54 55 7.307930 CGATTGTATTGTGCATATTTCTGCCTA 60.308 37.037 0.00 0.00 41.58 3.93
74 75 5.520649 GCCTACTCTCAGTTTAATACAGCAC 59.479 44.000 0.00 0.00 0.00 4.40
76 77 3.927142 ACTCTCAGTTTAATACAGCACGC 59.073 43.478 0.00 0.00 0.00 5.34
176 197 6.762333 AGCCTTTTGAATATGCTGAAAACTT 58.238 32.000 0.00 0.00 0.00 2.66
179 200 6.128472 CCTTTTGAATATGCTGAAAACTTGCC 60.128 38.462 0.00 0.00 0.00 4.52
205 226 0.796927 GTTGTCGCTACCTTCCTTGC 59.203 55.000 0.00 0.00 0.00 4.01
224 245 3.620488 TGCTCCATGTAAACATCCTTCC 58.380 45.455 0.00 0.00 33.61 3.46
225 246 2.952310 GCTCCATGTAAACATCCTTCCC 59.048 50.000 0.00 0.00 33.61 3.97
238 259 1.318158 CCTTCCCAACTGCTCATGGC 61.318 60.000 0.00 0.00 42.22 4.40
245 266 2.165030 CCAACTGCTCATGGCCTTTTAG 59.835 50.000 3.32 0.00 40.92 1.85
252 273 4.080356 TGCTCATGGCCTTTTAGACACTAT 60.080 41.667 3.32 0.00 40.92 2.12
256 277 2.835764 TGGCCTTTTAGACACTATCGGT 59.164 45.455 3.32 0.00 0.00 4.69
258 279 4.259356 GGCCTTTTAGACACTATCGGTTT 58.741 43.478 0.00 0.00 0.00 3.27
259 280 5.046448 TGGCCTTTTAGACACTATCGGTTTA 60.046 40.000 3.32 0.00 0.00 2.01
275 296 2.349155 GGTTTAACGAGGTTCTGTTGCG 60.349 50.000 0.00 0.00 0.00 4.85
279 300 1.658994 ACGAGGTTCTGTTGCGAAAA 58.341 45.000 0.00 0.00 0.00 2.29
311 332 1.662629 GGCGATCATTGTCTCAGTGTG 59.337 52.381 0.00 0.00 0.00 3.82
316 337 4.033702 CGATCATTGTCTCAGTGTGGAATG 59.966 45.833 0.00 9.70 0.00 2.67
326 347 5.101648 TCAGTGTGGAATGCTATGATGAA 57.898 39.130 0.00 0.00 0.00 2.57
336 357 5.881777 ATGCTATGATGAACTGATGATGC 57.118 39.130 0.00 0.00 0.00 3.91
344 365 3.086282 TGAACTGATGATGCTGCACAAT 58.914 40.909 3.57 0.79 0.00 2.71
353 374 1.514003 TGCTGCACAATTTTGCCATG 58.486 45.000 13.77 5.71 42.25 3.66
360 381 3.676873 GCACAATTTTGCCATGGACCTAG 60.677 47.826 18.40 0.48 36.42 3.02
371 392 1.246056 TGGACCTAGTTGACCGTCCG 61.246 60.000 8.50 0.00 46.47 4.79
444 465 1.621814 CGGGAGTTCTACAACCTGGAA 59.378 52.381 0.00 0.00 32.22 3.53
503 524 0.610687 GAGACCCAGCTGCAGTAACT 59.389 55.000 16.64 0.34 0.00 2.24
541 567 2.434359 GGAGCCAAACGAGGACGG 60.434 66.667 0.00 0.00 44.46 4.79
593 665 2.740055 GTCGCACAGCTGGACAGG 60.740 66.667 19.93 2.99 0.00 4.00
594 666 2.917227 TCGCACAGCTGGACAGGA 60.917 61.111 19.93 4.92 0.00 3.86
595 667 2.740055 CGCACAGCTGGACAGGAC 60.740 66.667 19.93 0.00 0.00 3.85
596 668 2.427320 GCACAGCTGGACAGGACA 59.573 61.111 19.93 0.00 0.00 4.02
597 669 1.670406 GCACAGCTGGACAGGACAG 60.670 63.158 19.93 0.00 38.95 3.51
629 701 2.497675 TGACCACTCTCCTGAAGTATGC 59.502 50.000 0.00 0.00 0.00 3.14
699 771 7.109501 ACCATGTGTATCATTGTAGCAACTAA 58.890 34.615 0.00 0.00 34.09 2.24
704 783 5.584649 TGTATCATTGTAGCAACTAAGCACC 59.415 40.000 0.00 0.00 36.85 5.01
789 869 5.689383 TCACAGTGCTGGAAATTTTCTAC 57.311 39.130 8.93 4.35 34.19 2.59
790 870 5.376625 TCACAGTGCTGGAAATTTTCTACT 58.623 37.500 8.93 6.21 34.19 2.57
791 871 6.530120 TCACAGTGCTGGAAATTTTCTACTA 58.470 36.000 8.93 0.00 34.19 1.82
792 872 6.426937 TCACAGTGCTGGAAATTTTCTACTAC 59.573 38.462 8.93 3.46 34.19 2.73
793 873 6.428159 CACAGTGCTGGAAATTTTCTACTACT 59.572 38.462 8.93 5.40 34.19 2.57
794 874 6.428159 ACAGTGCTGGAAATTTTCTACTACTG 59.572 38.462 20.71 20.71 36.11 2.74
843 927 6.775594 ACCAGCCTACAATATTTTTCTTCC 57.224 37.500 0.00 0.00 0.00 3.46
875 966 1.204941 ACTATTCTGACGGTCAGTGGC 59.795 52.381 31.09 0.00 44.58 5.01
904 996 5.698545 ACTGTTATTCTGAACTCTGAACTGC 59.301 40.000 0.00 0.00 36.79 4.40
932 1025 2.111756 GCAAAAGACAGTTGAAGTGCG 58.888 47.619 0.00 0.00 0.00 5.34
944 1037 1.268625 TGAAGTGCGCGTAAGAAGAGA 59.731 47.619 8.43 0.00 43.02 3.10
948 1041 0.596577 TGCGCGTAAGAAGAGACACT 59.403 50.000 8.43 0.00 43.02 3.55
1291 1384 2.328589 CCCTCCTCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
1347 1440 2.591429 TTCACTGTGGCGGCACTG 60.591 61.111 36.19 36.19 0.00 3.66
1609 1702 2.337170 CGTACACCACGTGCTGGA 59.663 61.111 15.02 3.53 43.95 3.86
2066 2171 7.720442 TGTCACCTAGATATCTTCAGAATGTG 58.280 38.462 11.25 6.10 37.40 3.21
2318 2423 2.440409 TGGCTCATCAAAAGGCTTCTC 58.560 47.619 0.00 0.00 39.86 2.87
2387 2493 4.337555 CCTTTGTAGCATTCCTCTTGATGG 59.662 45.833 0.00 0.00 0.00 3.51
2391 2497 2.584236 AGCATTCCTCTTGATGGCATC 58.416 47.619 20.52 20.52 0.00 3.91
2401 2508 6.070596 TCCTCTTGATGGCATCATTATCGTAT 60.071 38.462 29.22 0.00 39.39 3.06
2423 2530 7.743400 CGTATATATCTGCAAGCAAATGAACTG 59.257 37.037 0.00 0.00 0.00 3.16
2424 2531 7.812690 ATATATCTGCAAGCAAATGAACTGA 57.187 32.000 0.00 0.00 0.00 3.41
2425 2532 4.859304 ATCTGCAAGCAAATGAACTGAA 57.141 36.364 0.00 0.00 0.00 3.02
2426 2533 4.859304 TCTGCAAGCAAATGAACTGAAT 57.141 36.364 0.00 0.00 0.00 2.57
2430 2537 6.539464 TCTGCAAGCAAATGAACTGAATTTTT 59.461 30.769 0.00 0.00 0.00 1.94
2431 2538 6.487960 TGCAAGCAAATGAACTGAATTTTTG 58.512 32.000 0.00 0.00 0.00 2.44
2432 2539 6.093771 TGCAAGCAAATGAACTGAATTTTTGT 59.906 30.769 0.00 0.00 31.56 2.83
2433 2540 6.412653 GCAAGCAAATGAACTGAATTTTTGTG 59.587 34.615 0.00 0.00 31.56 3.33
2434 2541 6.607735 AGCAAATGAACTGAATTTTTGTGG 57.392 33.333 0.00 0.00 31.56 4.17
2435 2542 6.347696 AGCAAATGAACTGAATTTTTGTGGA 58.652 32.000 0.00 0.00 31.56 4.02
2437 2544 7.499895 AGCAAATGAACTGAATTTTTGTGGATT 59.500 29.630 0.00 0.00 31.56 3.01
2439 2546 9.654417 CAAATGAACTGAATTTTTGTGGATTTC 57.346 29.630 0.00 0.00 0.00 2.17
2441 2548 8.597662 ATGAACTGAATTTTTGTGGATTTCTG 57.402 30.769 0.00 0.00 0.00 3.02
2444 2551 7.111247 ACTGAATTTTTGTGGATTTCTGTGA 57.889 32.000 0.00 0.00 0.00 3.58
2445 2552 6.980397 ACTGAATTTTTGTGGATTTCTGTGAC 59.020 34.615 0.00 0.00 0.00 3.67
2460 2569 0.036388 GTGACTTGGCAGGGAATCGA 60.036 55.000 0.44 0.00 0.00 3.59
2487 2596 2.065899 TGGGACACCTTTGGAAACTG 57.934 50.000 0.00 0.00 37.76 3.16
2550 2659 0.693049 TGGAGGAAGGGAGCTTTGAC 59.307 55.000 0.00 0.00 0.00 3.18
2574 2683 1.303561 TGTGATGGCTTGTGAGGGC 60.304 57.895 0.00 0.00 0.00 5.19
2586 2695 0.741221 GTGAGGGCGTCTTCCACATC 60.741 60.000 8.82 0.00 0.00 3.06
2592 2701 1.920051 CGTCTTCCACATCGCATCG 59.080 57.895 0.00 0.00 0.00 3.84
2610 2719 1.153147 GCCTGTCCTCGGGAAATCC 60.153 63.158 0.00 0.00 42.46 3.01
2627 2736 0.400213 TCCGACTCCAATTGCAAGGT 59.600 50.000 4.94 0.00 0.00 3.50
2656 2765 3.257933 GCTTCAAGCACCCGACTG 58.742 61.111 3.89 0.00 41.89 3.51
2673 2782 5.874810 CCCGACTGTATTATCATTACCATGG 59.125 44.000 11.19 11.19 0.00 3.66
2679 2788 7.175467 ACTGTATTATCATTACCATGGCATGTG 59.825 37.037 24.80 18.13 0.00 3.21
2776 2885 2.476997 GTGCAAGAAGAGTCCGTTTCTC 59.523 50.000 0.00 0.00 32.71 2.87
2780 2889 4.035208 GCAAGAAGAGTCCGTTTCTCAAAA 59.965 41.667 0.00 0.00 32.71 2.44
2830 2939 2.500504 GGTGAGGATTAGGGACGAAACT 59.499 50.000 0.00 0.00 0.00 2.66
2920 3029 3.552604 ATGCGGAACATTGTAACACAC 57.447 42.857 0.00 0.00 34.40 3.82
2921 3030 1.261885 TGCGGAACATTGTAACACACG 59.738 47.619 0.00 0.00 0.00 4.49
2922 3031 1.262151 GCGGAACATTGTAACACACGT 59.738 47.619 0.00 0.00 0.00 4.49
2923 3032 2.286536 GCGGAACATTGTAACACACGTT 60.287 45.455 0.00 0.00 39.24 3.99
2924 3033 3.284914 CGGAACATTGTAACACACGTTG 58.715 45.455 0.00 0.00 36.52 4.10
2925 3034 3.242478 CGGAACATTGTAACACACGTTGT 60.242 43.478 0.00 0.00 41.74 3.32
2926 3035 4.025896 CGGAACATTGTAACACACGTTGTA 60.026 41.667 4.24 0.00 37.51 2.41
2927 3036 5.502058 CGGAACATTGTAACACACGTTGTAA 60.502 40.000 4.24 0.00 37.51 2.41
2928 3037 6.256686 GGAACATTGTAACACACGTTGTAAA 58.743 36.000 4.24 1.81 37.51 2.01
2929 3038 6.195060 GGAACATTGTAACACACGTTGTAAAC 59.805 38.462 4.24 6.58 45.31 2.01
2930 3039 6.425577 ACATTGTAACACACGTTGTAAACT 57.574 33.333 4.24 0.00 46.99 2.66
2931 3040 6.252281 ACATTGTAACACACGTTGTAAACTG 58.748 36.000 4.24 4.88 46.99 3.16
2932 3041 5.859521 TTGTAACACACGTTGTAAACTGT 57.140 34.783 4.24 0.00 46.99 3.55
2933 3042 6.957984 TTGTAACACACGTTGTAAACTGTA 57.042 33.333 4.24 0.00 46.99 2.74
2934 3043 6.329838 TGTAACACACGTTGTAAACTGTAC 57.670 37.500 4.24 0.00 46.99 2.90
2935 3044 6.098679 TGTAACACACGTTGTAAACTGTACT 58.901 36.000 4.24 0.00 46.99 2.73
2936 3045 5.707411 AACACACGTTGTAAACTGTACTC 57.293 39.130 4.24 0.00 46.99 2.59
2937 3046 4.114794 ACACACGTTGTAAACTGTACTCC 58.885 43.478 0.00 0.00 46.99 3.85
2938 3047 4.114073 CACACGTTGTAAACTGTACTCCA 58.886 43.478 0.00 0.00 46.99 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.927142 GCGTGCTGTATTAAACTGAGAGT 59.073 43.478 0.00 0.00 0.00 3.24
74 75 0.305922 GGCTACTTGCATTGCTAGCG 59.694 55.000 18.13 11.48 45.15 4.26
76 77 2.636830 ACTGGCTACTTGCATTGCTAG 58.363 47.619 16.88 16.88 45.15 3.42
194 215 4.042311 TGTTTACATGGAGCAAGGAAGGTA 59.958 41.667 0.00 0.00 0.00 3.08
205 226 4.235079 TGGGAAGGATGTTTACATGGAG 57.765 45.455 0.00 0.00 36.57 3.86
224 245 0.971386 AAAAGGCCATGAGCAGTTGG 59.029 50.000 5.01 0.00 46.50 3.77
225 246 3.084039 TCTAAAAGGCCATGAGCAGTTG 58.916 45.455 5.01 0.00 46.50 3.16
238 259 6.808212 TCGTTAAACCGATAGTGTCTAAAAGG 59.192 38.462 0.00 0.00 30.63 3.11
245 266 4.102035 ACCTCGTTAAACCGATAGTGTC 57.898 45.455 0.00 0.00 36.08 3.67
252 273 3.125316 CAACAGAACCTCGTTAAACCGA 58.875 45.455 0.00 0.00 35.22 4.69
256 277 2.823984 TCGCAACAGAACCTCGTTAAA 58.176 42.857 0.00 0.00 0.00 1.52
258 279 2.512485 TTCGCAACAGAACCTCGTTA 57.488 45.000 0.00 0.00 0.00 3.18
259 280 1.658994 TTTCGCAACAGAACCTCGTT 58.341 45.000 0.00 0.00 0.00 3.85
275 296 3.775065 GCCAGGCGAGTTTCTTTTC 57.225 52.632 0.00 0.00 0.00 2.29
292 313 1.662629 CCACACTGAGACAATGATCGC 59.337 52.381 0.00 0.00 0.00 4.58
299 320 2.936919 AGCATTCCACACTGAGACAA 57.063 45.000 0.00 0.00 0.00 3.18
311 332 6.623114 GCATCATCAGTTCATCATAGCATTCC 60.623 42.308 0.00 0.00 0.00 3.01
316 337 4.378563 GCAGCATCATCAGTTCATCATAGC 60.379 45.833 0.00 0.00 0.00 2.97
326 347 4.242475 CAAAATTGTGCAGCATCATCAGT 58.758 39.130 0.00 0.00 0.00 3.41
336 357 2.070783 GTCCATGGCAAAATTGTGCAG 58.929 47.619 21.93 10.82 46.81 4.41
344 365 3.153919 GTCAACTAGGTCCATGGCAAAA 58.846 45.455 6.96 0.00 0.00 2.44
353 374 1.509923 CGGACGGTCAACTAGGTCC 59.490 63.158 10.76 0.00 44.31 4.46
360 381 3.712881 GTGCAGCGGACGGTCAAC 61.713 66.667 10.76 0.89 0.00 3.18
429 450 5.216614 AGAACTCTTCCAGGTTGTAGAAC 57.783 43.478 0.00 0.00 0.00 3.01
444 465 1.080025 GGCGTTGCCGTAGAACTCT 60.080 57.895 0.00 0.00 39.62 3.24
503 524 0.464036 ATGCCAAGATTCGAGCGGTA 59.536 50.000 0.00 0.00 0.00 4.02
541 567 0.951040 CCTGCGGGTCTTTGAGTGAC 60.951 60.000 2.29 0.00 0.00 3.67
560 632 4.023107 TGTGCGACCAAGCTATCTATCTAC 60.023 45.833 0.00 0.00 38.13 2.59
593 665 1.741770 GTCACCCGGCATCACTGTC 60.742 63.158 0.00 0.00 0.00 3.51
594 666 2.347490 GTCACCCGGCATCACTGT 59.653 61.111 0.00 0.00 0.00 3.55
595 667 2.436646 GGTCACCCGGCATCACTG 60.437 66.667 0.00 0.00 0.00 3.66
596 668 2.927856 TGGTCACCCGGCATCACT 60.928 61.111 0.00 0.00 0.00 3.41
597 669 2.746277 GTGGTCACCCGGCATCAC 60.746 66.667 0.00 0.00 0.00 3.06
612 684 3.510388 TTCGCATACTTCAGGAGAGTG 57.490 47.619 0.00 0.00 0.00 3.51
629 701 1.583451 CATGACGGCGCCAATTTCG 60.583 57.895 28.98 13.91 0.00 3.46
642 714 7.086376 ACAGATTACAAGAATGTTTGCATGAC 58.914 34.615 0.00 0.00 41.05 3.06
699 771 5.528043 TGTTAACATTGTTCAATGGTGCT 57.472 34.783 21.59 10.10 34.56 4.40
704 783 6.364165 CCTCTTGCTGTTAACATTGTTCAATG 59.636 38.462 19.75 19.75 36.29 2.82
789 869 4.999950 AGCAGACAAGATCAAAACCAGTAG 59.000 41.667 0.00 0.00 0.00 2.57
790 870 4.756642 CAGCAGACAAGATCAAAACCAGTA 59.243 41.667 0.00 0.00 0.00 2.74
791 871 3.567164 CAGCAGACAAGATCAAAACCAGT 59.433 43.478 0.00 0.00 0.00 4.00
792 872 3.817084 TCAGCAGACAAGATCAAAACCAG 59.183 43.478 0.00 0.00 0.00 4.00
793 873 3.565482 GTCAGCAGACAAGATCAAAACCA 59.435 43.478 4.10 0.00 44.34 3.67
794 874 4.152607 GTCAGCAGACAAGATCAAAACC 57.847 45.455 4.10 0.00 44.34 3.27
830 914 7.504924 TCAGACAACGTGGAAGAAAAATATT 57.495 32.000 0.00 0.00 0.00 1.28
831 915 7.228706 AGTTCAGACAACGTGGAAGAAAAATAT 59.771 33.333 0.00 0.00 0.00 1.28
843 927 4.088638 CGTCAGAATAGTTCAGACAACGTG 59.911 45.833 13.28 0.00 43.80 4.49
904 996 6.480320 ACTTCAACTGTCTTTTGCTAGTAGTG 59.520 38.462 0.00 0.00 0.00 2.74
932 1025 2.488545 TCTCCAGTGTCTCTTCTTACGC 59.511 50.000 0.00 0.00 0.00 4.42
944 1037 5.136068 TCTGAAGGATATCTCTCCAGTGT 57.864 43.478 2.05 0.00 37.81 3.55
948 1041 6.618501 TCTGAATCTGAAGGATATCTCTCCA 58.381 40.000 2.05 0.00 37.81 3.86
1180 1273 2.122813 CAGGAGGTAGGGGCGGAT 60.123 66.667 0.00 0.00 0.00 4.18
1291 1384 2.285743 GGAGAGGGGAAGCTGGGT 60.286 66.667 0.00 0.00 0.00 4.51
1317 1410 4.162690 GTGAAGGGGAGCGCGGAT 62.163 66.667 8.83 0.00 0.00 4.18
1354 1447 4.436998 GTCCAGGAGGTCGGCGTG 62.437 72.222 6.85 0.00 35.89 5.34
1377 1470 2.125350 CAGAGCCTGGCGAGGAAC 60.125 66.667 20.35 10.98 42.93 3.62
1665 1758 0.172578 CCGAGCTGGTGAACACGATA 59.827 55.000 0.00 0.00 0.00 2.92
1946 2051 8.922676 GTGACTCGAAGAAAGAATGTTTACATA 58.077 33.333 0.00 0.00 32.60 2.29
1955 2060 7.872993 TGATAACTTGTGACTCGAAGAAAGAAT 59.127 33.333 0.00 0.00 34.09 2.40
2066 2171 5.449177 GGTTGGTAGAATGCAGATTTACAGC 60.449 44.000 0.00 0.00 0.00 4.40
2312 2417 3.717400 TGATATCCACACTCGAGAAGC 57.283 47.619 21.68 0.00 0.00 3.86
2318 2423 5.405797 CCTATCACATGATATCCACACTCG 58.594 45.833 0.00 0.00 36.53 4.18
2387 2493 8.219769 GCTTGCAGATATATACGATAATGATGC 58.780 37.037 0.00 0.00 0.00 3.91
2401 2508 7.628769 TTCAGTTCATTTGCTTGCAGATATA 57.371 32.000 0.00 0.00 0.00 0.86
2423 2530 7.042523 CCAAGTCACAGAAATCCACAAAAATTC 60.043 37.037 0.00 0.00 0.00 2.17
2424 2531 6.762661 CCAAGTCACAGAAATCCACAAAAATT 59.237 34.615 0.00 0.00 0.00 1.82
2425 2532 6.282930 CCAAGTCACAGAAATCCACAAAAAT 58.717 36.000 0.00 0.00 0.00 1.82
2426 2533 5.659463 CCAAGTCACAGAAATCCACAAAAA 58.341 37.500 0.00 0.00 0.00 1.94
2430 2537 2.229792 GCCAAGTCACAGAAATCCACA 58.770 47.619 0.00 0.00 0.00 4.17
2431 2538 2.227388 CTGCCAAGTCACAGAAATCCAC 59.773 50.000 0.00 0.00 35.90 4.02
2432 2539 2.507484 CTGCCAAGTCACAGAAATCCA 58.493 47.619 0.00 0.00 35.90 3.41
2433 2540 1.815003 CCTGCCAAGTCACAGAAATCC 59.185 52.381 0.00 0.00 35.90 3.01
2434 2541 1.815003 CCCTGCCAAGTCACAGAAATC 59.185 52.381 0.00 0.00 35.90 2.17
2435 2542 1.425066 TCCCTGCCAAGTCACAGAAAT 59.575 47.619 0.00 0.00 35.90 2.17
2437 2544 0.843309 TTCCCTGCCAAGTCACAGAA 59.157 50.000 0.00 0.00 35.90 3.02
2439 2546 1.457346 GATTCCCTGCCAAGTCACAG 58.543 55.000 0.00 0.00 0.00 3.66
2441 2548 0.036388 TCGATTCCCTGCCAAGTCAC 60.036 55.000 0.00 0.00 0.00 3.67
2444 2551 2.286365 TTTTCGATTCCCTGCCAAGT 57.714 45.000 0.00 0.00 0.00 3.16
2469 2578 0.673985 GCAGTTTCCAAAGGTGTCCC 59.326 55.000 0.00 0.00 0.00 4.46
2487 2596 1.941999 GCCTCTCATTTGCACCAGGC 61.942 60.000 0.00 0.00 45.13 4.85
2550 2659 0.098200 CACAAGCCATCACAGCATCG 59.902 55.000 0.00 0.00 0.00 3.84
2574 2683 1.920051 CGATGCGATGTGGAAGACG 59.080 57.895 0.00 0.00 0.00 4.18
2592 2701 1.153147 GGATTTCCCGAGGACAGGC 60.153 63.158 0.00 0.00 0.00 4.85
2610 2719 3.680642 CATACCTTGCAATTGGAGTCG 57.319 47.619 11.47 0.00 0.00 4.18
2627 2736 2.883574 GCTTGAAGCAAATGCAGCATA 58.116 42.857 13.09 0.00 45.16 3.14
2650 2759 5.351465 GCCATGGTAATGATAATACAGTCGG 59.649 44.000 14.67 0.00 35.67 4.79
2654 2763 7.532571 CACATGCCATGGTAATGATAATACAG 58.467 38.462 26.85 6.44 35.67 2.74
2655 2764 6.072008 GCACATGCCATGGTAATGATAATACA 60.072 38.462 26.85 9.09 35.67 2.29
2656 2765 6.324819 GCACATGCCATGGTAATGATAATAC 58.675 40.000 26.85 11.55 35.67 1.89
2673 2782 4.216902 TGAATAGCATATTCAGGCACATGC 59.783 41.667 7.89 0.00 43.24 4.06
2679 2788 5.159209 GCAACATGAATAGCATATTCAGGC 58.841 41.667 18.83 14.02 41.76 4.85
2776 2885 5.067674 TGAAGATGTGAGAACAACCCTTTTG 59.932 40.000 0.00 0.00 0.00 2.44
2780 2889 4.583871 GATGAAGATGTGAGAACAACCCT 58.416 43.478 0.00 0.00 0.00 4.34
2830 2939 0.181114 ACAACAGTTCTGGCTGCTGA 59.819 50.000 0.00 0.00 39.96 4.26
2902 3011 1.262151 ACGTGTGTTACAATGTTCCGC 59.738 47.619 0.00 0.00 0.00 5.54
2916 3025 4.114073 TGGAGTACAGTTTACAACGTGTG 58.886 43.478 0.00 0.00 36.23 3.82
2917 3026 4.389890 TGGAGTACAGTTTACAACGTGT 57.610 40.909 0.00 0.00 36.23 4.49


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

AutoCloner maintained by Alex Coulton.