Multiple sequence alignment - TraesCS5A01G124200

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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 TraesCS5A01G124200 chr5A 100.000 3329 0 0 1 3329 271497589 271494261 0.000000e+00 6148.0
1 TraesCS5A01G124200 chr5B 95.059 2732 119 13 88 2808 223649174 223646448 0.000000e+00 4283.0
2 TraesCS5A01G124200 chr5B 91.395 337 22 4 2995 3329 223557664 223557333 3.920000e-124 455.0
3 TraesCS5A01G124200 chr5B 86.471 170 19 4 2833 3001 223646477 223646311 2.040000e-42 183.0
4 TraesCS5A01G124200 chr5D 97.236 1845 48 3 977 2820 210057882 210056040 0.000000e+00 3121.0
5 TraesCS5A01G124200 chr5D 96.317 896 27 5 67 959 210058869 210057977 0.000000e+00 1467.0
6 TraesCS5A01G124200 chr5D 93.849 504 25 6 2827 3329 210056073 210055575 0.000000e+00 754.0
7 TraesCS5A01G124200 chr1B 76.866 1085 231 15 992 2066 679749273 679748199 2.210000e-166 595.0
8 TraesCS5A01G124200 chr1A 78.475 892 182 7 992 1875 586954097 586953208 2.880000e-160 575.0
9 TraesCS5A01G124200 chr1A 88.350 103 11 1 3008 3109 73316557 73316455 4.510000e-24 122.0
10 TraesCS5A01G124200 chr1D 82.372 624 108 2 1253 1875 487953006 487952384 2.920000e-150 542.0
11 TraesCS5A01G124200 chr7D 84.848 99 7 6 1087 1183 616280089 616280181 3.540000e-15 93.5


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 TraesCS5A01G124200 chr5A 271494261 271497589 3328 True 6148.000000 6148 100.000000 1 3329 1 chr5A.!!$R1 3328
1 TraesCS5A01G124200 chr5B 223646311 223649174 2863 True 2233.000000 4283 90.765000 88 3001 2 chr5B.!!$R2 2913
2 TraesCS5A01G124200 chr5D 210055575 210058869 3294 True 1780.666667 3121 95.800667 67 3329 3 chr5D.!!$R1 3262
3 TraesCS5A01G124200 chr1B 679748199 679749273 1074 True 595.000000 595 76.866000 992 2066 1 chr1B.!!$R1 1074
4 TraesCS5A01G124200 chr1A 586953208 586954097 889 True 575.000000 575 78.475000 992 1875 1 chr1A.!!$R2 883
5 TraesCS5A01G124200 chr1D 487952384 487953006 622 True 542.000000 542 82.372000 1253 1875 1 chr1D.!!$R1 622

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
443 454 0.180406 AGCACCCTTCGGCGATTATT 59.820 50.000 11.76 0.0 34.54 1.40 F
444 455 1.414919 AGCACCCTTCGGCGATTATTA 59.585 47.619 11.76 0.0 34.54 0.98 F
1315 1419 1.567357 TACCACTGATAGCCACAGCA 58.433 50.000 0.00 0.0 43.56 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1419 0.038890 GAGCCCTTCTTTCCCTTGCT 59.961 55.0 0.00 0.0 0.0 3.91 R
1759 1863 1.159713 TGCAGTGAACGCTGAAGTGG 61.160 55.0 17.75 0.0 38.7 4.00 R
2833 2938 0.047176 AGAGGAGAGGGAGAGGGAGA 59.953 60.0 0.00 0.0 0.0 3.71 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
25 26 8.693120 AGATACGGAATAGAAGACAGATTACA 57.307 34.615 0.00 0.00 0.00 2.41
26 27 9.132923 AGATACGGAATAGAAGACAGATTACAA 57.867 33.333 0.00 0.00 0.00 2.41
27 28 9.745880 GATACGGAATAGAAGACAGATTACAAA 57.254 33.333 0.00 0.00 0.00 2.83
29 30 8.425577 ACGGAATAGAAGACAGATTACAAATG 57.574 34.615 0.00 0.00 0.00 2.32
30 31 7.495934 ACGGAATAGAAGACAGATTACAAATGG 59.504 37.037 0.00 0.00 0.00 3.16
31 32 7.495934 CGGAATAGAAGACAGATTACAAATGGT 59.504 37.037 0.00 0.00 0.00 3.55
32 33 9.832445 GGAATAGAAGACAGATTACAAATGGTA 57.168 33.333 0.00 0.00 0.00 3.25
85 86 6.597562 TCTAACAATAACAACACCACTTCCT 58.402 36.000 0.00 0.00 0.00 3.36
138 143 7.205297 AGAAATGGAATGTTGTTGACAGAAAG 58.795 34.615 0.00 0.00 42.62 2.62
368 376 4.142049 CCTTCACTAGCCTTCTCTTCGATT 60.142 45.833 0.00 0.00 0.00 3.34
372 380 4.564769 CACTAGCCTTCTCTTCGATTTGAC 59.435 45.833 0.00 0.00 0.00 3.18
384 392 8.417106 TCTCTTCGATTTGACTATTCTATTGCT 58.583 33.333 0.00 0.00 0.00 3.91
421 429 2.038952 CTGACCCCATTCAGTTGACAGA 59.961 50.000 0.00 0.00 38.61 3.41
442 453 0.249911 GAGCACCCTTCGGCGATTAT 60.250 55.000 11.76 0.00 34.54 1.28
443 454 0.180406 AGCACCCTTCGGCGATTATT 59.820 50.000 11.76 0.00 34.54 1.40
444 455 1.414919 AGCACCCTTCGGCGATTATTA 59.585 47.619 11.76 0.00 34.54 0.98
445 456 2.158871 AGCACCCTTCGGCGATTATTAA 60.159 45.455 11.76 0.00 34.54 1.40
446 457 2.812011 GCACCCTTCGGCGATTATTAAT 59.188 45.455 11.76 0.00 0.00 1.40
514 525 3.214328 GAAACCTGAATCCCACGCATAT 58.786 45.455 0.00 0.00 0.00 1.78
612 623 4.944962 TTGATGCCGTTCAACTGATTAG 57.055 40.909 0.00 0.00 30.82 1.73
653 665 2.479275 GGTCGTTTAGGCAGTTTCACTC 59.521 50.000 0.00 0.00 0.00 3.51
664 676 3.061429 GCAGTTTCACTCAAGTATCGAGC 59.939 47.826 0.00 0.00 33.58 5.03
758 772 8.826710 TCACTGCTTGCACATTAATAGTTATAC 58.173 33.333 0.00 0.00 0.00 1.47
843 857 3.530265 ACGGGCAGATTTGTATCGTTA 57.470 42.857 0.00 0.00 35.85 3.18
861 875 7.730364 ATCGTTAAGAAGTTCTCAAATGTGT 57.270 32.000 5.70 1.75 0.00 3.72
875 889 8.492673 TCTCAAATGTGTAATCAGTATTGACC 57.507 34.615 0.00 0.00 35.83 4.02
947 961 7.334421 TGAAGAAGTAGTGCCAAATTCTACATC 59.666 37.037 0.00 0.00 37.20 3.06
1202 1302 5.182001 ACTTGTCGGAATTTCAATTCAGAGG 59.818 40.000 13.39 10.06 45.59 3.69
1315 1419 1.567357 TACCACTGATAGCCACAGCA 58.433 50.000 0.00 0.00 43.56 4.41
1359 1463 2.456119 GCAGCGGATGAAGTGGACG 61.456 63.158 0.00 0.00 0.00 4.79
1613 1717 2.976271 CAACTTGCAAGGTTGTGGC 58.024 52.632 29.18 0.00 39.14 5.01
1627 1731 4.819783 TGGCGAATCCAGCACTTT 57.180 50.000 0.00 0.00 40.72 2.66
1759 1863 5.007136 CGGATTAGTTTGCCTGAAGATCTTC 59.993 44.000 25.68 25.68 39.91 2.87
2006 2110 0.034756 AGTGCACACGAATGTAGCCA 59.965 50.000 21.04 0.00 36.72 4.75
2087 2191 1.610522 CTTGGCTTTGACACAGAAGGG 59.389 52.381 0.00 0.00 0.00 3.95
2315 2419 4.889409 TGAACTCAAGCTGAAAGGAAATGT 59.111 37.500 0.00 0.00 0.00 2.71
2318 2422 4.889409 ACTCAAGCTGAAAGGAAATGTCAA 59.111 37.500 0.00 0.00 0.00 3.18
2343 2447 7.848223 TCATTCATGACATATATTTAGGCGG 57.152 36.000 0.00 0.00 0.00 6.13
2352 2456 7.387673 TGACATATATTTAGGCGGTCAAGATTG 59.612 37.037 0.00 0.00 31.55 2.67
2457 2561 9.273016 GCAAGTCTGGTATTTATATGCTTCTAA 57.727 33.333 0.00 0.00 0.00 2.10
2471 2575 3.142174 GCTTCTAAGTGGTGTTTGCTCT 58.858 45.455 0.00 0.00 0.00 4.09
2485 2590 5.412594 GTGTTTGCTCTGGATGATCACTTTA 59.587 40.000 0.00 0.00 0.00 1.85
2586 2691 6.098552 GGGAGCCTTCTAGTTCTAACTAATGT 59.901 42.308 4.27 0.00 40.70 2.71
2633 2738 7.930217 TGCATCATTAGTATTTAGCAAGGTTC 58.070 34.615 0.00 0.00 0.00 3.62
2648 2753 4.519350 GCAAGGTTCTTTTAAGTGCTAGGT 59.481 41.667 0.00 0.00 0.00 3.08
2652 2757 4.154375 GGTTCTTTTAAGTGCTAGGTGCTC 59.846 45.833 0.00 0.00 43.37 4.26
2732 2837 2.448926 ACGGACATCGACATGAACAA 57.551 45.000 0.00 0.00 42.43 2.83
2785 2890 3.123620 GCCACCTTGCTCTCTGCG 61.124 66.667 0.00 0.00 46.63 5.18
2799 2904 0.541392 TCTGCGCTCTCTCTCTCTCT 59.459 55.000 9.73 0.00 0.00 3.10
2801 2906 0.541392 TGCGCTCTCTCTCTCTCTCT 59.459 55.000 9.73 0.00 0.00 3.10
2803 2908 1.202580 GCGCTCTCTCTCTCTCTCTCT 60.203 57.143 0.00 0.00 0.00 3.10
2804 2909 2.748605 CGCTCTCTCTCTCTCTCTCTC 58.251 57.143 0.00 0.00 0.00 3.20
2805 2910 2.363680 CGCTCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
2806 2911 3.551863 CGCTCTCTCTCTCTCTCTCTCTC 60.552 56.522 0.00 0.00 0.00 3.20
2807 2912 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
2808 2913 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
2809 2914 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2814 2919 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2818 2923 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2819 2924 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2821 2926 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2822 2927 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2823 2928 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2824 2929 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2825 2930 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
2826 2931 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
2827 2932 3.051803 TCTCTCTCTCTCTCTCTCTCCCT 60.052 52.174 0.00 0.00 0.00 4.20
2828 2933 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
2829 2934 3.051803 TCTCTCTCTCTCTCTCTCCCTCT 60.052 52.174 0.00 0.00 0.00 3.69
2830 2935 3.309296 TCTCTCTCTCTCTCTCCCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
2831 2936 2.370189 CTCTCTCTCTCTCTCCCTCTCC 59.630 59.091 0.00 0.00 0.00 3.71
2832 2937 1.421646 CTCTCTCTCTCTCCCTCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
2833 2938 1.010793 TCTCTCTCTCTCCCTCTCCCT 59.989 57.143 0.00 0.00 0.00 4.20
2834 2939 1.421646 CTCTCTCTCTCCCTCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
2835 2940 1.010793 TCTCTCTCTCCCTCTCCCTCT 59.989 57.143 0.00 0.00 0.00 3.69
2836 2941 1.421646 CTCTCTCTCCCTCTCCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
2837 2942 0.478507 CTCTCTCCCTCTCCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
2838 2943 0.996762 TCTCTCCCTCTCCCTCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
2839 2944 0.998945 CTCTCCCTCTCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
2840 2945 0.996762 TCTCCCTCTCCCTCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
2841 2946 0.998945 CTCCCTCTCCCTCTCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
2842 2947 0.996762 TCCCTCTCCCTCTCCCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
2843 2948 1.541672 CCTCTCCCTCTCCCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
2844 2949 1.541672 CTCTCCCTCTCCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
2845 2950 0.998945 CTCTCCCTCTCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
2846 2951 0.996762 TCTCCCTCTCCCTCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
2847 2952 0.998945 CTCCCTCTCCCTCTCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
2848 2953 0.996762 TCCCTCTCCCTCTCCCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
2849 2954 1.541672 CCTCTCCCTCTCCCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
2850 2955 0.998945 CCTCTCCCTCTCCCTCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
2851 2956 0.478507 CTCTCCCTCTCCCTCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
2852 2957 0.047176 TCTCCCTCTCCCTCTCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
2853 2958 0.478507 CTCCCTCTCCCTCTCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
2854 2959 0.996762 TCCCTCTCCCTCTCCTCTCC 60.997 65.000 0.00 0.00 0.00 3.71
2855 2960 1.541672 CCTCTCCCTCTCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
2856 2961 0.998945 CCTCTCCCTCTCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
2857 2962 0.478507 CTCTCCCTCTCCTCTCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
2858 2963 0.047176 TCTCCCTCTCCTCTCCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
2859 2964 0.478507 CTCCCTCTCCTCTCCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
2860 2965 0.047176 TCCCTCTCCTCTCCCTCTCT 59.953 60.000 0.00 0.00 0.00 3.10
2861 2966 0.478507 CCCTCTCCTCTCCCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
2862 2967 1.522900 CCTCTCCTCTCCCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
2863 2968 1.421646 CCTCTCCTCTCCCTCTCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
2864 2969 2.412591 CTCTCCTCTCCCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
2865 2970 2.370189 CTCTCCTCTCCCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
2866 2971 1.070758 CTCCTCTCCCTCTCTCTCTCG 59.929 61.905 0.00 0.00 0.00 4.04
2956 3061 1.890625 TAGCCGCCGCTTAGTTTCCA 61.891 55.000 4.51 0.00 45.55 3.53
2986 3091 2.579657 CCGCACCCCTGAGTGTACA 61.580 63.158 0.00 0.00 40.04 2.90
3052 3158 3.189287 CAGTGCTAATCCAAAAGCGAAGT 59.811 43.478 0.00 0.00 41.77 3.01
3053 3159 3.189287 AGTGCTAATCCAAAAGCGAAGTG 59.811 43.478 0.00 0.00 41.77 3.16
3063 3169 0.905337 AAGCGAAGTGGTAGGCCTCT 60.905 55.000 9.68 0.00 40.05 3.69
3216 3322 3.052455 TGAGCGATTTGTTCAGCCTTA 57.948 42.857 0.00 0.00 32.32 2.69
3255 3361 8.885494 TTGGCAATAAAATTATAGTTGCATCC 57.115 30.769 15.20 4.18 45.07 3.51
3295 3401 2.771372 AGGCTTGCCTTTCCTTGAAAAA 59.229 40.909 8.56 0.00 30.84 1.94
3315 3421 2.849880 AACATGGCATATTCGTGTGC 57.150 45.000 0.00 0.00 40.55 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.693120 TGTAATCTGTCTTCTATTCCGTATCT 57.307 34.615 0.00 0.00 0.00 1.98
1 2 9.745880 TTTGTAATCTGTCTTCTATTCCGTATC 57.254 33.333 0.00 0.00 0.00 2.24
3 4 9.529325 CATTTGTAATCTGTCTTCTATTCCGTA 57.471 33.333 0.00 0.00 0.00 4.02
4 5 7.495934 CCATTTGTAATCTGTCTTCTATTCCGT 59.504 37.037 0.00 0.00 0.00 4.69
5 6 7.495934 ACCATTTGTAATCTGTCTTCTATTCCG 59.504 37.037 0.00 0.00 0.00 4.30
6 7 8.738645 ACCATTTGTAATCTGTCTTCTATTCC 57.261 34.615 0.00 0.00 0.00 3.01
53 54 9.031537 TGGTGTTGTTATTGTTAGAGAGAGATA 57.968 33.333 0.00 0.00 0.00 1.98
54 55 7.819900 GTGGTGTTGTTATTGTTAGAGAGAGAT 59.180 37.037 0.00 0.00 0.00 2.75
55 56 7.015292 AGTGGTGTTGTTATTGTTAGAGAGAGA 59.985 37.037 0.00 0.00 0.00 3.10
56 57 7.155328 AGTGGTGTTGTTATTGTTAGAGAGAG 58.845 38.462 0.00 0.00 0.00 3.20
57 58 7.062749 AGTGGTGTTGTTATTGTTAGAGAGA 57.937 36.000 0.00 0.00 0.00 3.10
58 59 7.095187 GGAAGTGGTGTTGTTATTGTTAGAGAG 60.095 40.741 0.00 0.00 0.00 3.20
59 60 6.708949 GGAAGTGGTGTTGTTATTGTTAGAGA 59.291 38.462 0.00 0.00 0.00 3.10
60 61 6.710744 AGGAAGTGGTGTTGTTATTGTTAGAG 59.289 38.462 0.00 0.00 0.00 2.43
61 62 6.597562 AGGAAGTGGTGTTGTTATTGTTAGA 58.402 36.000 0.00 0.00 0.00 2.10
62 63 6.877611 AGGAAGTGGTGTTGTTATTGTTAG 57.122 37.500 0.00 0.00 0.00 2.34
63 64 7.648039 AAAGGAAGTGGTGTTGTTATTGTTA 57.352 32.000 0.00 0.00 0.00 2.41
64 65 6.538945 AAAGGAAGTGGTGTTGTTATTGTT 57.461 33.333 0.00 0.00 0.00 2.83
65 66 6.040054 GGTAAAGGAAGTGGTGTTGTTATTGT 59.960 38.462 0.00 0.00 0.00 2.71
108 113 7.202526 TGTCAACAACATTCCATTTCTTTCTC 58.797 34.615 0.00 0.00 31.20 2.87
138 143 2.202892 GGCGATGGGGAAGACGAC 60.203 66.667 0.00 0.00 0.00 4.34
368 376 5.357742 TCTGGCAGCAATAGAATAGTCAA 57.642 39.130 10.34 0.00 0.00 3.18
372 380 6.935771 AGAAAGATCTGGCAGCAATAGAATAG 59.064 38.462 10.34 0.00 33.59 1.73
384 392 1.556911 GTCAGGGAGAAAGATCTGGCA 59.443 52.381 0.00 0.00 35.54 4.92
444 455 9.071276 ACAAGTCACTATCTGAACAAATTCATT 57.929 29.630 0.00 0.00 43.92 2.57
445 456 8.627208 ACAAGTCACTATCTGAACAAATTCAT 57.373 30.769 0.00 0.00 43.92 2.57
446 457 8.450578 AACAAGTCACTATCTGAACAAATTCA 57.549 30.769 0.00 0.00 42.73 2.57
514 525 4.882842 TGTGCATCAGACCTAAGTTACA 57.117 40.909 0.00 0.00 0.00 2.41
612 623 5.503031 CGACCAGCAACATGATGTAAAGATC 60.503 44.000 0.00 0.00 30.62 2.75
664 676 2.486203 AGTCTCTTACGTCAGAGCACAG 59.514 50.000 19.78 0.00 40.33 3.66
675 687 4.621460 TCGAAAAGATTGCAGTCTCTTACG 59.379 41.667 12.63 14.65 35.14 3.18
758 772 2.761208 ACTGAGACCGTCCTAGATTTGG 59.239 50.000 6.63 0.00 0.00 3.28
843 857 8.682936 ACTGATTACACATTTGAGAACTTCTT 57.317 30.769 0.00 0.00 0.00 2.52
875 889 7.763172 AGTAATTCAGAAGAACTATTGAGCG 57.237 36.000 0.00 0.00 36.39 5.03
971 1068 6.712547 CCCAAAGGATCATTCCACTACTAATC 59.287 42.308 0.00 0.00 45.30 1.75
972 1069 6.389869 TCCCAAAGGATCATTCCACTACTAAT 59.610 38.462 0.00 0.00 45.30 1.73
1202 1302 2.087646 GGTGATCAGCCTTCCTTTGTC 58.912 52.381 14.08 0.00 0.00 3.18
1315 1419 0.038890 GAGCCCTTCTTTCCCTTGCT 59.961 55.000 0.00 0.00 0.00 3.91
1461 1565 1.494960 TTGCCTTCCACTTGCCTTTT 58.505 45.000 0.00 0.00 0.00 2.27
1494 1598 3.612247 ATTGCAACCTCGCTCGCCT 62.612 57.895 0.00 0.00 0.00 5.52
1627 1731 4.529769 AGAGAGATTATCCATGCGATCCAA 59.470 41.667 0.59 0.00 31.92 3.53
1759 1863 1.159713 TGCAGTGAACGCTGAAGTGG 61.160 55.000 17.75 0.00 38.70 4.00
2006 2110 1.345422 TGCCATGGGGATTAGACCTCT 60.345 52.381 15.13 0.00 35.59 3.69
2109 2213 6.034898 CGATTTTCAAGCACTGTTTTTCAAGT 59.965 34.615 0.00 0.00 0.00 3.16
2318 2422 8.049117 ACCGCCTAAATATATGTCATGAATGAT 58.951 33.333 0.00 0.00 39.30 2.45
2332 2436 3.821033 GCCAATCTTGACCGCCTAAATAT 59.179 43.478 0.00 0.00 0.00 1.28
2343 2447 3.629398 CCATCTTACAGGCCAATCTTGAC 59.371 47.826 5.01 0.00 0.00 3.18
2352 2456 4.101119 TCTTAGCTTACCATCTTACAGGCC 59.899 45.833 0.00 0.00 0.00 5.19
2457 2561 1.421268 TCATCCAGAGCAAACACCACT 59.579 47.619 0.00 0.00 0.00 4.00
2586 2691 6.105333 GCAACCAATTTACATTCCTAATGCA 58.895 36.000 0.00 0.00 42.69 3.96
2620 2725 7.290110 AGCACTTAAAAGAACCTTGCTAAAT 57.710 32.000 3.68 0.00 37.08 1.40
2697 2802 4.300669 TGTCCGTACAAAATGCTCAAGCA 61.301 43.478 7.22 7.22 43.80 3.91
2706 2811 4.500127 TCATGTCGATGTCCGTACAAAAT 58.500 39.130 0.00 0.00 39.58 1.82
2732 2837 3.833559 ATTTGATTTCTGGGTGTCCCT 57.166 42.857 6.38 0.00 45.70 4.20
2751 2856 4.777366 AGGTGGCCTTACATGCTTTAAAAT 59.223 37.500 3.32 0.00 0.00 1.82
2771 2876 2.224495 GAGAGCGCAGAGAGCAAGGT 62.224 60.000 11.47 0.00 46.13 3.50
2785 2890 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
2799 2904 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2801 2906 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2803 2908 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
2804 2909 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
2805 2910 3.051803 AGGGAGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2806 2911 3.312890 AGGGAGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2807 2912 3.051803 AGAGGGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
2808 2913 3.312890 AGAGGGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
2809 2914 3.309296 GAGAGGGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
2814 2919 1.421646 GAGGGAGAGGGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
2818 2923 0.478507 GGAGAGGGAGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
2819 2924 0.996762 GGGAGAGGGAGAGGGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
2821 2926 0.996762 GAGGGAGAGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
2822 2927 0.998945 AGAGGGAGAGGGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
2823 2928 0.996762 GAGAGGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
2824 2929 1.541672 GAGAGGGAGAGGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
2825 2930 1.541672 GGAGAGGGAGAGGGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
2826 2931 0.998945 AGGGAGAGGGAGAGGGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
2827 2932 0.996762 GAGGGAGAGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
2828 2933 0.998945 AGAGGGAGAGGGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
2829 2934 0.996762 GAGAGGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
2830 2935 1.541672 GAGAGGGAGAGGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
2831 2936 0.998945 AGGAGAGGGAGAGGGAGAGG 60.999 65.000 0.00 0.00 0.00 3.69
2832 2937 0.478507 GAGGAGAGGGAGAGGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
2833 2938 0.047176 AGAGGAGAGGGAGAGGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
2834 2939 0.478507 GAGAGGAGAGGGAGAGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
2835 2940 0.996762 GGAGAGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
2836 2941 1.541672 GGAGAGGAGAGGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
2837 2942 0.998945 AGGGAGAGGAGAGGGAGAGG 60.999 65.000 0.00 0.00 0.00 3.69
2838 2943 0.478507 GAGGGAGAGGAGAGGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
2839 2944 0.047176 AGAGGGAGAGGAGAGGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
2840 2945 0.478507 GAGAGGGAGAGGAGAGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
2841 2946 0.047176 AGAGAGGGAGAGGAGAGGGA 59.953 60.000 0.00 0.00 0.00 4.20
2842 2947 0.478507 GAGAGAGGGAGAGGAGAGGG 59.521 65.000 0.00 0.00 0.00 4.30
2843 2948 1.421646 GAGAGAGAGGGAGAGGAGAGG 59.578 61.905 0.00 0.00 0.00 3.69
2844 2949 2.370189 GAGAGAGAGAGGGAGAGGAGAG 59.630 59.091 0.00 0.00 0.00 3.20
2845 2950 2.408565 GAGAGAGAGAGGGAGAGGAGA 58.591 57.143 0.00 0.00 0.00 3.71
2846 2951 1.070758 CGAGAGAGAGAGGGAGAGGAG 59.929 61.905 0.00 0.00 0.00 3.69
2847 2952 1.128200 CGAGAGAGAGAGGGAGAGGA 58.872 60.000 0.00 0.00 0.00 3.71
2848 2953 0.535102 GCGAGAGAGAGAGGGAGAGG 60.535 65.000 0.00 0.00 0.00 3.69
2849 2954 0.535102 GGCGAGAGAGAGAGGGAGAG 60.535 65.000 0.00 0.00 0.00 3.20
2850 2955 0.986019 AGGCGAGAGAGAGAGGGAGA 60.986 60.000 0.00 0.00 0.00 3.71
2851 2956 0.762418 TAGGCGAGAGAGAGAGGGAG 59.238 60.000 0.00 0.00 0.00 4.30
2852 2957 0.762418 CTAGGCGAGAGAGAGAGGGA 59.238 60.000 0.00 0.00 0.00 4.20
2853 2958 0.889186 GCTAGGCGAGAGAGAGAGGG 60.889 65.000 0.00 0.00 0.00 4.30
2854 2959 0.889186 GGCTAGGCGAGAGAGAGAGG 60.889 65.000 0.00 0.00 0.00 3.69
2855 2960 1.227999 CGGCTAGGCGAGAGAGAGAG 61.228 65.000 32.94 0.00 0.00 3.20
2856 2961 1.227704 CGGCTAGGCGAGAGAGAGA 60.228 63.158 32.94 0.00 0.00 3.10
2857 2962 0.816018 TTCGGCTAGGCGAGAGAGAG 60.816 60.000 35.34 9.17 0.00 3.20
2858 2963 1.096386 GTTCGGCTAGGCGAGAGAGA 61.096 60.000 35.34 21.53 0.00 3.10
2859 2964 1.357334 GTTCGGCTAGGCGAGAGAG 59.643 63.158 35.34 10.62 0.00 3.20
2860 2965 0.752009 ATGTTCGGCTAGGCGAGAGA 60.752 55.000 35.34 25.42 0.00 3.10
2861 2966 0.318275 GATGTTCGGCTAGGCGAGAG 60.318 60.000 35.34 11.71 0.00 3.20
2862 2967 1.734137 GATGTTCGGCTAGGCGAGA 59.266 57.895 35.34 27.28 0.00 4.04
2863 2968 1.300233 GGATGTTCGGCTAGGCGAG 60.300 63.158 35.34 12.81 0.00 5.03
2864 2969 2.792947 GGGATGTTCGGCTAGGCGA 61.793 63.158 34.54 34.54 0.00 5.54
2865 2970 2.280186 GGGATGTTCGGCTAGGCG 60.280 66.667 31.00 31.00 0.00 5.52
2866 2971 0.107165 AAAGGGATGTTCGGCTAGGC 60.107 55.000 6.15 6.15 0.00 3.93
3033 3138 2.487762 CCACTTCGCTTTTGGATTAGCA 59.512 45.455 0.00 0.00 37.23 3.49
3039 3144 1.880646 GCCTACCACTTCGCTTTTGGA 60.881 52.381 0.00 0.00 34.24 3.53
3047 3153 1.153549 GCAGAGGCCTACCACTTCG 60.154 63.158 4.42 0.00 34.18 3.79
3052 3158 2.362369 GCTGAGCAGAGGCCTACCA 61.362 63.158 4.42 0.00 42.56 3.25
3053 3159 2.503546 GCTGAGCAGAGGCCTACC 59.496 66.667 4.42 0.00 42.56 3.18
3081 3187 0.529992 AATTGAGCGTACGCCTAGGC 60.530 55.000 34.88 24.75 43.17 3.93
3104 3210 8.500773 GCATTAGTACAGTTGCTAAAAACAGTA 58.499 33.333 0.00 0.00 34.08 2.74
3255 3361 0.963856 TCCTGGCTGCTGCATCTTTG 60.964 55.000 17.89 0.00 41.91 2.77
3295 3401 2.754552 AGCACACGAATATGCCATGTTT 59.245 40.909 0.00 0.00 43.12 2.83


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

AutoCloner maintained by Alex Coulton.