Multiple sequence alignment - TraesCS1D01G224000

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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 TraesCS1D01G224000 chr1D 100.000 3079 0 0 1 3079 311751609 311748531 0.000000e+00 5686.0
1 TraesCS1D01G224000 chr1A 94.249 2869 113 23 1 2837 391942766 391939918 0.000000e+00 4337.0
2 TraesCS1D01G224000 chr1A 93.631 157 10 0 2923 3079 391939883 391939727 5.130000e-58 235.0
3 TraesCS1D01G224000 chr1B 93.568 2270 93 28 115 2364 422348004 422345768 0.000000e+00 3334.0
4 TraesCS1D01G224000 chr1B 80.531 113 20 2 2839 2950 667495970 667496081 5.470000e-13 86.1
5 TraesCS1D01G224000 chr4B 82.249 169 30 0 1405 1573 11905169 11905337 2.470000e-31 147.0
6 TraesCS1D01G224000 chr3D 84.932 146 20 2 1179 1323 453629849 453629993 2.470000e-31 147.0
7 TraesCS1D01G224000 chr3B 84.932 146 20 2 1179 1323 596048080 596048224 2.470000e-31 147.0
8 TraesCS1D01G224000 chr3A 84.932 146 20 2 1179 1323 595644600 595644744 2.470000e-31 147.0
9 TraesCS1D01G224000 chr3A 80.000 125 25 0 1408 1532 533131044 533130920 3.270000e-15 93.5
10 TraesCS1D01G224000 chr4D 80.473 169 33 0 1405 1573 6643363 6643531 2.490000e-26 130.0
11 TraesCS1D01G224000 chr4D 94.737 38 2 0 2589 2626 2035661 2035698 3.320000e-05 60.2
12 TraesCS1D01G224000 chr7A 79.290 169 35 0 1405 1573 33148743 33148911 5.390000e-23 119.0
13 TraesCS1D01G224000 chr4A 79.762 168 30 3 1408 1573 596771009 596770844 5.390000e-23 119.0
14 TraesCS1D01G224000 chr6A 78.814 118 20 5 2840 2953 519601473 519601589 1.180000e-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 TraesCS1D01G224000 chr1D 311748531 311751609 3078 True 5686 5686 100.000 1 3079 1 chr1D.!!$R1 3078
1 TraesCS1D01G224000 chr1A 391939727 391942766 3039 True 2286 4337 93.940 1 3079 2 chr1A.!!$R1 3078
2 TraesCS1D01G224000 chr1B 422345768 422348004 2236 True 3334 3334 93.568 115 2364 1 chr1B.!!$R1 2249

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
317 328 0.17576 TCCGGAAGATTCTTGCCTCG 59.824 55.0 0.0 6.68 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2283 0.873054 TCGTCTCTTCGTGACACCTC 59.127 55.0 0.0 0.0 34.37 3.85 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
30 31 5.461407 AGATCGATGATCACAAGAAATGACG 59.539 40.000 0.54 0.00 41.12 4.35
31 32 4.743493 TCGATGATCACAAGAAATGACGA 58.257 39.130 0.00 0.00 0.00 4.20
89 92 4.568152 AAGCAGCGTTTTAACATGAAGT 57.432 36.364 0.00 0.00 0.00 3.01
98 101 4.695217 TTTAACATGAAGTTGCCGGATC 57.305 40.909 5.05 0.00 41.50 3.36
99 102 1.463674 AACATGAAGTTGCCGGATCC 58.536 50.000 5.05 0.00 39.49 3.36
100 103 0.620556 ACATGAAGTTGCCGGATCCT 59.379 50.000 5.05 0.00 0.00 3.24
193 198 1.545428 CCTTGCTGGGCTGTACAAAGA 60.545 52.381 0.00 0.00 0.00 2.52
196 201 0.320421 GCTGGGCTGTACAAAGACGA 60.320 55.000 0.00 0.00 0.00 4.20
200 205 2.829720 TGGGCTGTACAAAGACGAGTAT 59.170 45.455 0.00 0.00 0.00 2.12
254 265 6.605594 GGGTAGTTAAATGTCATGGATTGGAA 59.394 38.462 0.00 0.00 0.00 3.53
317 328 0.175760 TCCGGAAGATTCTTGCCTCG 59.824 55.000 0.00 6.68 0.00 4.63
409 420 3.577805 TCAGGTCCACGATCTCATCTA 57.422 47.619 0.00 0.00 0.00 1.98
460 471 7.088905 CCTGGTCGACAGTAAACATATATACC 58.911 42.308 18.91 0.00 46.06 2.73
538 553 7.180051 TGGTTCATTTTAGGCCTTATCAATGTT 59.820 33.333 12.58 0.00 0.00 2.71
539 554 7.706607 GGTTCATTTTAGGCCTTATCAATGTTC 59.293 37.037 12.58 11.08 0.00 3.18
561 576 9.773328 TGTTCTACACGTTACTTACATGTATAC 57.227 33.333 6.36 0.00 35.15 1.47
635 650 4.817464 GCACGTAAATATGGTAATCACCCA 59.183 41.667 0.00 0.00 45.11 4.51
667 682 7.451501 TGACATTCTGACAGAATTAATTGCA 57.548 32.000 24.97 14.90 41.90 4.08
675 690 6.164876 TGACAGAATTAATTGCATGGTTTGG 58.835 36.000 5.17 0.00 0.00 3.28
801 816 8.879342 AATTATGTCTGTGCTGTCTAGATTAC 57.121 34.615 0.00 0.00 0.00 1.89
914 940 2.893215 TTACCCTTGTCTCTCTCGGA 57.107 50.000 0.00 0.00 0.00 4.55
1017 1046 2.013563 GCCATCGATCTCCTTGTTGCA 61.014 52.381 0.00 0.00 0.00 4.08
1021 1050 2.964740 TCGATCTCCTTGTTGCAGAAG 58.035 47.619 1.42 1.42 0.00 2.85
1159 1192 3.252484 GCACATACGACGGTCGCC 61.252 66.667 28.67 8.06 45.12 5.54
1234 1267 1.699656 CCAAGGACTGCATCTTCGCG 61.700 60.000 0.00 0.00 33.35 5.87
1343 1378 3.806521 ACGTACATACTCCTACGTAGCTG 59.193 47.826 17.41 13.26 45.40 4.24
2021 2064 4.618912 CAGAATTAGTACGAGATCCATGCG 59.381 45.833 0.00 0.00 0.00 4.73
2057 2105 7.391148 TGTCATGTTCTTATCTAAAAAGGCC 57.609 36.000 0.00 0.00 0.00 5.19
2131 2180 2.170397 TCTGACACCACAACACACATCT 59.830 45.455 0.00 0.00 0.00 2.90
2215 2264 0.317160 ACGACCGCTTGAAGATGTCA 59.683 50.000 12.75 0.00 0.00 3.58
2226 2275 6.572519 GCTTGAAGATGTCAGAGTTCTCTAT 58.427 40.000 0.00 0.00 37.61 1.98
2234 2283 4.393371 TGTCAGAGTTCTCTATCGTGACAG 59.607 45.833 13.79 0.00 38.26 3.51
2295 2344 0.108615 ACTCCAAGACATCGCCTTCG 60.109 55.000 0.00 0.00 0.00 3.79
2300 2349 2.348666 CCAAGACATCGCCTTCGTAAAG 59.651 50.000 0.00 0.00 36.96 1.85
2334 2383 1.034838 GCACCACCATTGCCCGATTA 61.035 55.000 0.00 0.00 33.58 1.75
2365 2414 5.777850 TTAAGGTTTTTACCCAGAGCAAC 57.222 39.130 0.00 0.00 0.00 4.17
2414 2463 1.792949 CCTTCACAAAGAGAACGACGG 59.207 52.381 0.00 0.00 34.14 4.79
2419 2468 0.443869 CAAAGAGAACGACGGCCATG 59.556 55.000 2.24 0.00 0.00 3.66
2421 2470 3.195698 GAGAACGACGGCCATGGC 61.196 66.667 29.47 29.47 41.06 4.40
2487 2536 3.041940 ACGCACTTTTCGCCTCCG 61.042 61.111 0.00 0.00 0.00 4.63
2494 2543 0.737715 CTTTTCGCCTCCGAGACCAG 60.738 60.000 0.00 0.00 45.35 4.00
2584 2633 1.957177 GAGCGTCACTCATAGGGATCA 59.043 52.381 0.00 0.00 45.49 2.92
2600 2649 2.158755 GGATCATTACTCCCACCACCAG 60.159 54.545 0.00 0.00 0.00 4.00
2655 2704 2.430921 CCACCAGACGTCGCTGAC 60.431 66.667 10.46 0.00 38.14 3.51
2706 2755 0.752054 TCAAAGCAAACCCTTGGCAG 59.248 50.000 0.00 0.00 32.76 4.85
2715 2764 2.044551 CCTTGGCAGGAAGGAGGC 60.045 66.667 0.00 0.00 44.87 4.70
2720 2769 4.847444 GCAGGAAGGAGGCCGAGC 62.847 72.222 0.00 0.00 0.00 5.03
2792 2841 2.752030 CTCTCTGTGGGAGGGTTATCA 58.248 52.381 0.00 0.00 42.10 2.15
2837 2886 4.497173 GGGATCGGTACTCTTACTTCGAAC 60.497 50.000 0.00 0.00 29.38 3.95
2838 2887 4.335037 GGATCGGTACTCTTACTTCGAACT 59.665 45.833 0.00 0.00 29.38 3.01
2839 2888 5.525378 GGATCGGTACTCTTACTTCGAACTA 59.475 44.000 0.00 0.00 29.38 2.24
2842 2891 4.495514 CGGTACTCTTACTTCGAACTAGCC 60.496 50.000 0.00 0.00 0.00 3.93
2843 2892 4.639755 GGTACTCTTACTTCGAACTAGCCT 59.360 45.833 0.00 0.00 0.00 4.58
2844 2893 5.125257 GGTACTCTTACTTCGAACTAGCCTT 59.875 44.000 0.00 0.00 0.00 4.35
2845 2894 5.725325 ACTCTTACTTCGAACTAGCCTTT 57.275 39.130 0.00 0.00 0.00 3.11
2846 2895 6.099159 ACTCTTACTTCGAACTAGCCTTTT 57.901 37.500 0.00 0.00 0.00 2.27
2848 2897 5.159209 TCTTACTTCGAACTAGCCTTTTCG 58.841 41.667 6.83 6.83 44.79 3.46
2855 2904 5.437383 CGAACTAGCCTTTTCGAAGTAAG 57.563 43.478 7.27 0.00 46.01 2.34
2856 2905 5.159209 CGAACTAGCCTTTTCGAAGTAAGA 58.841 41.667 10.51 0.00 46.01 2.10
2857 2906 5.286558 CGAACTAGCCTTTTCGAAGTAAGAG 59.713 44.000 10.51 3.94 46.01 2.85
2858 2907 5.725325 ACTAGCCTTTTCGAAGTAAGAGT 57.275 39.130 10.51 4.47 0.00 3.24
2859 2908 6.830873 ACTAGCCTTTTCGAAGTAAGAGTA 57.169 37.500 10.51 2.36 0.00 2.59
2860 2909 6.619744 ACTAGCCTTTTCGAAGTAAGAGTAC 58.380 40.000 10.51 0.00 0.00 2.73
2862 2911 3.611549 GCCTTTTCGAAGTAAGAGTACCG 59.388 47.826 10.51 0.00 0.00 4.02
2863 2912 4.616835 GCCTTTTCGAAGTAAGAGTACCGA 60.617 45.833 10.51 0.00 0.00 4.69
2864 2913 5.648572 CCTTTTCGAAGTAAGAGTACCGAT 58.351 41.667 10.51 0.00 0.00 4.18
2866 2915 4.889832 TTCGAAGTAAGAGTACCGATCC 57.110 45.455 0.00 0.00 0.00 3.36
2867 2916 3.209410 TCGAAGTAAGAGTACCGATCCC 58.791 50.000 0.00 0.00 0.00 3.85
2868 2917 2.947652 CGAAGTAAGAGTACCGATCCCA 59.052 50.000 0.00 0.00 0.00 4.37
2869 2918 3.243002 CGAAGTAAGAGTACCGATCCCAC 60.243 52.174 0.00 0.00 0.00 4.61
2870 2919 3.377253 AGTAAGAGTACCGATCCCACA 57.623 47.619 0.00 0.00 0.00 4.17
2871 2920 3.288964 AGTAAGAGTACCGATCCCACAG 58.711 50.000 0.00 0.00 0.00 3.66
2872 2921 2.526888 AAGAGTACCGATCCCACAGA 57.473 50.000 0.00 0.00 0.00 3.41
2873 2922 2.060050 AGAGTACCGATCCCACAGAG 57.940 55.000 0.00 0.00 0.00 3.35
2874 2923 1.564818 AGAGTACCGATCCCACAGAGA 59.435 52.381 0.00 0.00 0.00 3.10
2875 2924 1.950909 GAGTACCGATCCCACAGAGAG 59.049 57.143 0.00 0.00 0.00 3.20
2876 2925 0.386113 GTACCGATCCCACAGAGAGC 59.614 60.000 0.00 0.00 0.00 4.09
2877 2926 0.033503 TACCGATCCCACAGAGAGCA 60.034 55.000 0.00 0.00 0.00 4.26
2878 2927 1.142748 CCGATCCCACAGAGAGCAC 59.857 63.158 0.00 0.00 0.00 4.40
2879 2928 1.607801 CCGATCCCACAGAGAGCACA 61.608 60.000 0.00 0.00 0.00 4.57
2880 2929 0.463204 CGATCCCACAGAGAGCACAT 59.537 55.000 0.00 0.00 0.00 3.21
2881 2930 1.805495 CGATCCCACAGAGAGCACATG 60.805 57.143 0.00 0.00 0.00 3.21
2882 2931 1.483827 GATCCCACAGAGAGCACATGA 59.516 52.381 0.00 0.00 0.00 3.07
2883 2932 1.351076 TCCCACAGAGAGCACATGAA 58.649 50.000 0.00 0.00 0.00 2.57
2884 2933 1.911357 TCCCACAGAGAGCACATGAAT 59.089 47.619 0.00 0.00 0.00 2.57
2885 2934 2.306805 TCCCACAGAGAGCACATGAATT 59.693 45.455 0.00 0.00 0.00 2.17
2886 2935 3.519107 TCCCACAGAGAGCACATGAATTA 59.481 43.478 0.00 0.00 0.00 1.40
2887 2936 3.875727 CCCACAGAGAGCACATGAATTAG 59.124 47.826 0.00 0.00 0.00 1.73
2888 2937 4.511527 CCACAGAGAGCACATGAATTAGT 58.488 43.478 0.00 0.00 0.00 2.24
2889 2938 4.569966 CCACAGAGAGCACATGAATTAGTC 59.430 45.833 0.00 0.00 0.00 2.59
2890 2939 5.417811 CACAGAGAGCACATGAATTAGTCT 58.582 41.667 0.00 0.00 0.00 3.24
2891 2940 5.873712 CACAGAGAGCACATGAATTAGTCTT 59.126 40.000 0.00 0.00 0.00 3.01
2892 2941 6.370994 CACAGAGAGCACATGAATTAGTCTTT 59.629 38.462 0.00 0.00 0.00 2.52
2893 2942 7.547019 CACAGAGAGCACATGAATTAGTCTTTA 59.453 37.037 0.00 0.00 0.00 1.85
2894 2943 8.263640 ACAGAGAGCACATGAATTAGTCTTTAT 58.736 33.333 0.00 0.00 0.00 1.40
2895 2944 8.763356 CAGAGAGCACATGAATTAGTCTTTATC 58.237 37.037 0.00 0.00 0.00 1.75
2896 2945 8.703743 AGAGAGCACATGAATTAGTCTTTATCT 58.296 33.333 0.00 0.00 0.00 1.98
2897 2946 8.885494 AGAGCACATGAATTAGTCTTTATCTC 57.115 34.615 0.00 0.00 0.00 2.75
2898 2947 8.703743 AGAGCACATGAATTAGTCTTTATCTCT 58.296 33.333 0.00 0.00 0.00 3.10
2899 2948 9.323985 GAGCACATGAATTAGTCTTTATCTCTT 57.676 33.333 0.00 0.00 0.00 2.85
2900 2949 9.107177 AGCACATGAATTAGTCTTTATCTCTTG 57.893 33.333 0.00 0.00 0.00 3.02
2901 2950 8.887717 GCACATGAATTAGTCTTTATCTCTTGT 58.112 33.333 0.00 0.00 0.00 3.16
3034 3083 0.027979 ATAAAGTAGCGCGCGACGTA 59.972 50.000 37.18 28.26 46.11 3.57
3042 3091 1.481260 CGCGCGACGTATGTAATGG 59.519 57.895 28.94 0.00 36.87 3.16
3055 3104 7.211573 ACGTATGTAATGGTTATTGGAATCGA 58.788 34.615 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.635982 CGATCCACTCGTACGTATGTATC 58.364 47.826 16.05 14.25 42.56 2.24
31 32 4.658713 CGATCCACTCGTACGTATGTAT 57.341 45.455 16.05 7.19 42.56 2.29
98 101 1.827969 CTAGTCCTGACCAGTTGGAGG 59.172 57.143 4.92 2.38 38.94 4.30
99 102 2.808919 TCTAGTCCTGACCAGTTGGAG 58.191 52.381 4.92 0.00 38.94 3.86
100 103 2.992847 TCTAGTCCTGACCAGTTGGA 57.007 50.000 4.92 0.00 38.94 3.53
239 250 3.359033 CTGTGGTTCCAATCCATGACAT 58.641 45.455 0.00 0.00 37.30 3.06
254 265 2.957402 TTTCCTTCATCTGCTGTGGT 57.043 45.000 0.00 0.00 0.00 4.16
317 328 1.599797 AACGGTGCACCTAGTTGCC 60.600 57.895 32.28 4.89 42.25 4.52
428 439 1.183549 ACTGTCGACCAGGGATACAC 58.816 55.000 14.12 0.00 46.06 2.90
460 471 5.154215 GGCAACTACGAGTACTAGTACTG 57.846 47.826 34.67 26.84 45.63 2.74
561 576 6.699204 GTGCTGTAGGCTGTATATATAGCATG 59.301 42.308 26.71 13.42 42.86 4.06
635 650 2.998670 CTGTCAGAATGTCATGTCGCTT 59.001 45.455 0.00 0.00 32.84 4.68
667 682 0.831711 GCCAGGACAACCCAAACCAT 60.832 55.000 0.00 0.00 37.41 3.55
675 690 2.239907 AGGAATCTTAGCCAGGACAACC 59.760 50.000 0.00 0.00 0.00 3.77
801 816 6.556974 AGTAAAGGGTAAGGGTAGCTTAAG 57.443 41.667 0.00 0.00 0.00 1.85
914 940 1.883275 CTGTTGAGAGAGACTCCACGT 59.117 52.381 0.00 0.00 42.08 4.49
1126 1159 1.078214 TGCCTGCAGTGTATCAGCC 60.078 57.895 13.81 0.00 0.00 4.85
1343 1378 4.855388 GCGTCATTGCATGAAATATCATCC 59.145 41.667 0.00 0.00 44.53 3.51
1373 1408 1.867233 CATATGTTAGCGTCTGGGTGC 59.133 52.381 0.00 0.00 0.00 5.01
1377 1412 3.677121 GCATCTCATATGTTAGCGTCTGG 59.323 47.826 1.90 0.00 0.00 3.86
1608 1643 4.436998 CTGCGTCGTCCTGGGACC 62.437 72.222 13.41 1.24 41.76 4.46
1816 1851 2.562635 TGACTAGCTAGCTACGTCCAG 58.437 52.381 30.47 21.99 31.71 3.86
1870 1906 2.863132 AAACCCCTACACGTGCATAA 57.137 45.000 17.22 0.00 0.00 1.90
1927 1966 4.831107 AGAGAGAGAGGAGTTCAAAATGC 58.169 43.478 0.00 0.00 0.00 3.56
2021 2064 9.713740 GATAAGAACATGACAATGATCAGAAAC 57.286 33.333 0.00 0.00 37.90 2.78
2057 2105 7.639113 TGCTTTATCTATAAAACAAGGGTGG 57.361 36.000 0.00 0.00 32.39 4.61
2131 2180 2.290832 TGCATTGTTGTATCCTGCCTCA 60.291 45.455 0.00 0.00 31.89 3.86
2215 2264 4.196193 CCTCTGTCACGATAGAGAACTCT 58.804 47.826 19.09 9.33 45.87 3.24
2234 2283 0.873054 TCGTCTCTTCGTGACACCTC 59.127 55.000 0.00 0.00 34.37 3.85
2267 2316 3.744660 GATGTCTTGGAGTCCACAGTTT 58.255 45.455 12.69 0.00 30.78 2.66
2295 2344 1.880027 CTCCAGTGTTGTGCCCTTTAC 59.120 52.381 0.00 0.00 0.00 2.01
2300 2349 2.203337 TGCTCCAGTGTTGTGCCC 60.203 61.111 0.00 0.00 0.00 5.36
2303 2352 1.447317 GGTGGTGCTCCAGTGTTGTG 61.447 60.000 7.99 0.00 45.24 3.33
2365 2414 0.106419 AGCTACTCTCCTCCTTCGGG 60.106 60.000 0.00 0.00 0.00 5.14
2384 2433 0.882484 TTTGTGAAGGCATCGTCGCA 60.882 50.000 1.52 0.00 39.42 5.10
2385 2434 0.179215 CTTTGTGAAGGCATCGTCGC 60.179 55.000 0.00 0.00 33.55 5.19
2441 2490 1.547472 AATCCTTGCTTGGCTTGGGC 61.547 55.000 0.00 0.00 37.82 5.36
2442 2491 1.478105 GTAATCCTTGCTTGGCTTGGG 59.522 52.381 0.00 0.00 0.00 4.12
2443 2492 1.478105 GGTAATCCTTGCTTGGCTTGG 59.522 52.381 0.00 0.00 0.00 3.61
2444 2493 1.478105 GGGTAATCCTTGCTTGGCTTG 59.522 52.381 0.00 0.00 0.00 4.01
2445 2494 1.359130 AGGGTAATCCTTGCTTGGCTT 59.641 47.619 0.00 0.00 45.47 4.35
2446 2495 1.002857 AGGGTAATCCTTGCTTGGCT 58.997 50.000 0.00 0.00 45.47 4.75
2456 2505 1.377987 TGCGTGCCAAGGGTAATCC 60.378 57.895 0.00 0.00 0.00 3.01
2487 2536 0.935898 CTGCGATCAATGCTGGTCTC 59.064 55.000 0.00 0.00 29.64 3.36
2494 2543 2.095567 ACTGTTGTTCTGCGATCAATGC 60.096 45.455 0.00 0.00 0.00 3.56
2568 2617 6.031751 GGAGTAATGATCCCTATGAGTGAC 57.968 45.833 0.00 0.00 0.00 3.67
2655 2704 3.154710 GGGGGCTTATATCCTTTTTCGG 58.845 50.000 0.00 0.00 0.00 4.30
2678 2727 1.970640 GGTTTGCTTTGAGGGTGGAAT 59.029 47.619 0.00 0.00 0.00 3.01
2731 2780 1.600638 GACAACCCTCCCCTAACCG 59.399 63.158 0.00 0.00 0.00 4.44
2734 2783 0.178926 TGTCGACAACCCTCCCCTAA 60.179 55.000 17.62 0.00 0.00 2.69
2776 2825 4.837093 TTAGTTGATAACCCTCCCACAG 57.163 45.455 0.00 0.00 0.00 3.66
2782 2831 6.543831 AGCACATGAATTAGTTGATAACCCTC 59.456 38.462 0.00 0.00 0.00 4.30
2792 2841 3.935203 CACGGAGAGCACATGAATTAGTT 59.065 43.478 0.00 0.00 0.00 2.24
2821 2870 5.816449 AGGCTAGTTCGAAGTAAGAGTAC 57.184 43.478 13.50 3.01 0.00 2.73
2837 2886 6.035217 GGTACTCTTACTTCGAAAAGGCTAG 58.965 44.000 9.19 3.45 36.78 3.42
2838 2887 5.392380 CGGTACTCTTACTTCGAAAAGGCTA 60.392 44.000 9.19 0.00 36.78 3.93
2839 2888 4.617762 CGGTACTCTTACTTCGAAAAGGCT 60.618 45.833 9.19 0.00 36.78 4.58
2842 2891 5.742926 GGATCGGTACTCTTACTTCGAAAAG 59.257 44.000 0.00 0.89 38.54 2.27
2843 2892 5.393461 GGGATCGGTACTCTTACTTCGAAAA 60.393 44.000 0.00 0.00 29.38 2.29
2844 2893 4.096984 GGGATCGGTACTCTTACTTCGAAA 59.903 45.833 0.00 0.00 29.38 3.46
2845 2894 3.629398 GGGATCGGTACTCTTACTTCGAA 59.371 47.826 0.00 0.00 29.38 3.71
2846 2895 3.209410 GGGATCGGTACTCTTACTTCGA 58.791 50.000 0.00 0.00 0.00 3.71
2848 2897 3.698040 TGTGGGATCGGTACTCTTACTTC 59.302 47.826 0.00 0.00 0.00 3.01
2851 2900 3.285484 TCTGTGGGATCGGTACTCTTAC 58.715 50.000 0.00 0.00 0.00 2.34
2853 2902 2.025226 TCTCTGTGGGATCGGTACTCTT 60.025 50.000 0.00 0.00 0.00 2.85
2854 2903 1.564818 TCTCTGTGGGATCGGTACTCT 59.435 52.381 0.00 0.00 0.00 3.24
2855 2904 1.950909 CTCTCTGTGGGATCGGTACTC 59.049 57.143 0.00 0.00 0.00 2.59
2856 2905 2.024825 GCTCTCTGTGGGATCGGTACT 61.025 57.143 0.00 0.00 0.00 2.73
2857 2906 0.386113 GCTCTCTGTGGGATCGGTAC 59.614 60.000 0.00 0.00 0.00 3.34
2858 2907 0.033503 TGCTCTCTGTGGGATCGGTA 60.034 55.000 0.00 0.00 0.00 4.02
2859 2908 1.305297 TGCTCTCTGTGGGATCGGT 60.305 57.895 0.00 0.00 0.00 4.69
2860 2909 1.142748 GTGCTCTCTGTGGGATCGG 59.857 63.158 0.00 0.00 0.00 4.18
2862 2911 1.483827 TCATGTGCTCTCTGTGGGATC 59.516 52.381 0.00 0.00 0.00 3.36
2863 2912 1.576577 TCATGTGCTCTCTGTGGGAT 58.423 50.000 0.00 0.00 0.00 3.85
2864 2913 1.351076 TTCATGTGCTCTCTGTGGGA 58.649 50.000 0.00 0.00 0.00 4.37
2866 2915 4.511527 ACTAATTCATGTGCTCTCTGTGG 58.488 43.478 0.00 0.00 0.00 4.17
2867 2916 5.417811 AGACTAATTCATGTGCTCTCTGTG 58.582 41.667 0.00 0.00 0.00 3.66
2868 2917 5.674052 AGACTAATTCATGTGCTCTCTGT 57.326 39.130 0.00 0.00 0.00 3.41
2869 2918 6.981762 AAAGACTAATTCATGTGCTCTCTG 57.018 37.500 0.00 0.00 0.00 3.35
2870 2919 8.703743 AGATAAAGACTAATTCATGTGCTCTCT 58.296 33.333 0.00 0.00 0.00 3.10
2871 2920 8.885494 AGATAAAGACTAATTCATGTGCTCTC 57.115 34.615 0.00 0.00 0.00 3.20
2872 2921 8.703743 AGAGATAAAGACTAATTCATGTGCTCT 58.296 33.333 0.00 0.00 0.00 4.09
2873 2922 8.885494 AGAGATAAAGACTAATTCATGTGCTC 57.115 34.615 0.00 0.00 0.00 4.26
2874 2923 9.107177 CAAGAGATAAAGACTAATTCATGTGCT 57.893 33.333 0.00 0.00 0.00 4.40
2875 2924 8.887717 ACAAGAGATAAAGACTAATTCATGTGC 58.112 33.333 0.00 0.00 0.00 4.57
2896 2945 9.109393 GGCACTATAATTCAAATCACTACAAGA 57.891 33.333 0.00 0.00 0.00 3.02
2897 2946 9.113838 AGGCACTATAATTCAAATCACTACAAG 57.886 33.333 0.00 0.00 36.02 3.16
2898 2947 8.892723 CAGGCACTATAATTCAAATCACTACAA 58.107 33.333 0.00 0.00 36.02 2.41
2899 2948 7.012327 GCAGGCACTATAATTCAAATCACTACA 59.988 37.037 0.00 0.00 36.02 2.74
2900 2949 7.012327 TGCAGGCACTATAATTCAAATCACTAC 59.988 37.037 0.00 0.00 36.02 2.73
2901 2950 7.053498 TGCAGGCACTATAATTCAAATCACTA 58.947 34.615 0.00 0.00 36.02 2.74
2902 2951 5.887598 TGCAGGCACTATAATTCAAATCACT 59.112 36.000 0.00 0.00 36.02 3.41
2903 2952 6.135290 TGCAGGCACTATAATTCAAATCAC 57.865 37.500 0.00 0.00 36.02 3.06
2904 2953 6.377996 ACTTGCAGGCACTATAATTCAAATCA 59.622 34.615 0.00 0.00 36.02 2.57
2905 2954 6.799512 ACTTGCAGGCACTATAATTCAAATC 58.200 36.000 0.00 0.00 36.02 2.17
2906 2955 6.780457 ACTTGCAGGCACTATAATTCAAAT 57.220 33.333 0.00 0.00 36.02 2.32
2907 2956 6.588719 AACTTGCAGGCACTATAATTCAAA 57.411 33.333 0.00 0.00 36.02 2.69
2908 2957 6.884295 ACTAACTTGCAGGCACTATAATTCAA 59.116 34.615 0.00 0.00 36.02 2.69
2909 2958 6.414732 ACTAACTTGCAGGCACTATAATTCA 58.585 36.000 0.00 0.00 36.02 2.57
2910 2959 6.927294 ACTAACTTGCAGGCACTATAATTC 57.073 37.500 0.00 0.00 36.02 2.17
2911 2960 6.659242 ACAACTAACTTGCAGGCACTATAATT 59.341 34.615 0.00 0.00 31.26 1.40
2912 2961 6.094048 CACAACTAACTTGCAGGCACTATAAT 59.906 38.462 0.00 0.00 31.26 1.28
2913 2962 5.411361 CACAACTAACTTGCAGGCACTATAA 59.589 40.000 0.00 0.00 31.26 0.98
2914 2963 4.935205 CACAACTAACTTGCAGGCACTATA 59.065 41.667 0.00 0.00 31.26 1.31
2915 2964 3.753272 CACAACTAACTTGCAGGCACTAT 59.247 43.478 0.00 0.00 31.26 2.12
2916 2965 3.138304 CACAACTAACTTGCAGGCACTA 58.862 45.455 0.00 0.00 31.26 2.74
2917 2966 1.949525 CACAACTAACTTGCAGGCACT 59.050 47.619 0.00 0.00 33.38 4.40
2918 2967 1.946768 TCACAACTAACTTGCAGGCAC 59.053 47.619 0.00 0.00 32.41 5.01
2919 2968 2.340210 TCACAACTAACTTGCAGGCA 57.660 45.000 0.00 0.00 32.41 4.75
2920 2969 2.162408 GGATCACAACTAACTTGCAGGC 59.838 50.000 0.00 0.00 32.41 4.85
2921 2970 3.411446 TGGATCACAACTAACTTGCAGG 58.589 45.455 0.00 0.00 32.41 4.85
2969 3018 1.745232 TCGCACCAATCACCCAATAC 58.255 50.000 0.00 0.00 0.00 1.89
2974 3023 0.039527 GTTGTTCGCACCAATCACCC 60.040 55.000 0.00 0.00 0.00 4.61
2975 3024 0.665835 TGTTGTTCGCACCAATCACC 59.334 50.000 0.00 0.00 0.00 4.02
3027 3076 4.746115 TCCAATAACCATTACATACGTCGC 59.254 41.667 0.00 0.00 0.00 5.19
3042 3091 9.530129 CGCTTTATTTCTATCGATTCCAATAAC 57.470 33.333 1.71 0.00 0.00 1.89
3055 3104 4.165372 TCCCTGGGAACGCTTTATTTCTAT 59.835 41.667 14.48 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.