Multiple sequence alignment - TraesCS3A01G209600

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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 TraesCS3A01G209600 chr3A 100.000 3224 0 0 1 3224 374317152 374320375 0.000000e+00 5954.0
1 TraesCS3A01G209600 chr3A 91.871 652 51 2 1 651 570747149 570746499 0.000000e+00 909.0
2 TraesCS3A01G209600 chr3A 91.564 652 53 2 1 651 53892704 53892054 0.000000e+00 898.0
3 TraesCS3A01G209600 chr3A 88.372 172 16 1 2865 3036 610288708 610288541 1.520000e-48 204.0
4 TraesCS3A01G209600 chr3D 96.818 2231 51 9 651 2866 285729119 285731344 0.000000e+00 3709.0
5 TraesCS3A01G209600 chr3D 91.053 190 7 2 3035 3224 285731343 285731522 6.910000e-62 248.0
6 TraesCS3A01G209600 chr3D 90.798 163 12 3 2887 3048 102776600 102776440 7.010000e-52 215.0
7 TraesCS3A01G209600 chr3D 91.558 154 13 0 2887 3040 376343422 376343575 2.520000e-51 213.0
8 TraesCS3A01G209600 chr3B 95.666 2238 58 15 654 2866 377913676 377911453 0.000000e+00 3559.0
9 TraesCS3A01G209600 chr3B 91.265 664 53 3 1 661 114013688 114014349 0.000000e+00 900.0
10 TraesCS3A01G209600 chr3B 95.722 187 7 1 3038 3224 377911451 377911266 1.880000e-77 300.0
11 TraesCS3A01G209600 chr5A 92.166 651 51 0 1 651 91550695 91550045 0.000000e+00 920.0
12 TraesCS3A01G209600 chr2A 91.493 670 51 4 2 669 734075604 734074939 0.000000e+00 917.0
13 TraesCS3A01G209600 chr2A 88.701 177 15 2 2861 3036 305076535 305076363 9.060000e-51 211.0
14 TraesCS3A01G209600 chr5B 91.577 653 53 1 1 651 655134706 655135358 0.000000e+00 900.0
15 TraesCS3A01G209600 chr5B 97.297 74 2 0 1986 2059 184778080 184778007 3.380000e-25 126.0
16 TraesCS3A01G209600 chr1A 91.564 652 54 1 1 651 189707433 189706782 0.000000e+00 898.0
17 TraesCS3A01G209600 chr1A 89.017 173 15 1 2864 3036 253523145 253523313 9.060000e-51 211.0
18 TraesCS3A01G209600 chr1B 91.450 655 52 2 1 651 640489409 640488755 0.000000e+00 896.0
19 TraesCS3A01G209600 chr1B 91.437 654 52 3 1 651 377261251 377260599 0.000000e+00 894.0
20 TraesCS3A01G209600 chr6D 90.055 181 11 1 2860 3040 460272704 460272531 9.000000e-56 228.0
21 TraesCS3A01G209600 chr5D 93.243 148 10 0 2891 3038 52112145 52111998 5.420000e-53 219.0
22 TraesCS3A01G209600 chr4D 92.667 150 11 0 2887 3036 77835619 77835470 1.950000e-52 217.0
23 TraesCS3A01G209600 chr7A 88.372 172 16 1 2865 3036 424150056 424150223 1.520000e-48 204.0
24 TraesCS3A01G209600 chr7D 86.667 180 17 1 2857 3036 257041525 257041697 3.280000e-45 193.0
25 TraesCS3A01G209600 chr7D 100.000 29 0 0 2858 2886 16399024 16399052 2.000000e-03 54.7
26 TraesCS3A01G209600 chr6A 95.946 74 3 0 1986 2059 66383015 66383088 1.570000e-23 121.0
27 TraesCS3A01G209600 chr6A 94.595 74 4 0 1986 2059 330038521 330038594 7.310000e-22 115.0
28 TraesCS3A01G209600 chr4A 95.946 74 3 0 1986 2059 362070976 362071049 1.570000e-23 121.0
29 TraesCS3A01G209600 chr4A 95.946 74 3 0 1986 2059 521816963 521817036 1.570000e-23 121.0


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 TraesCS3A01G209600 chr3A 374317152 374320375 3223 False 5954.0 5954 100.0000 1 3224 1 chr3A.!!$F1 3223
1 TraesCS3A01G209600 chr3A 570746499 570747149 650 True 909.0 909 91.8710 1 651 1 chr3A.!!$R2 650
2 TraesCS3A01G209600 chr3A 53892054 53892704 650 True 898.0 898 91.5640 1 651 1 chr3A.!!$R1 650
3 TraesCS3A01G209600 chr3D 285729119 285731522 2403 False 1978.5 3709 93.9355 651 3224 2 chr3D.!!$F2 2573
4 TraesCS3A01G209600 chr3B 377911266 377913676 2410 True 1929.5 3559 95.6940 654 3224 2 chr3B.!!$R1 2570
5 TraesCS3A01G209600 chr3B 114013688 114014349 661 False 900.0 900 91.2650 1 661 1 chr3B.!!$F1 660
6 TraesCS3A01G209600 chr5A 91550045 91550695 650 True 920.0 920 92.1660 1 651 1 chr5A.!!$R1 650
7 TraesCS3A01G209600 chr2A 734074939 734075604 665 True 917.0 917 91.4930 2 669 1 chr2A.!!$R2 667
8 TraesCS3A01G209600 chr5B 655134706 655135358 652 False 900.0 900 91.5770 1 651 1 chr5B.!!$F1 650
9 TraesCS3A01G209600 chr1A 189706782 189707433 651 True 898.0 898 91.5640 1 651 1 chr1A.!!$R1 650
10 TraesCS3A01G209600 chr1B 640488755 640489409 654 True 896.0 896 91.4500 1 651 1 chr1B.!!$R2 650
11 TraesCS3A01G209600 chr1B 377260599 377261251 652 True 894.0 894 91.4370 1 651 1 chr1B.!!$R1 650

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
975 993 1.80591 GTAACCGACCTCCCTCGTC 59.194 63.158 0.0 0.0 31.35 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2588 2626 0.178068 CCTGCAATGCCTACTACCGT 59.822 55.0 1.53 0.0 0.0 4.83 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
100 101 4.031878 GCTTCTAGACATTACGACACTTGC 59.968 45.833 0.00 0.00 0.00 4.01
180 185 6.647229 TGATTCTATGCAGTCAAGACATCTT 58.353 36.000 2.72 0.00 36.45 2.40
246 251 6.315714 CCATAGAGGTCTCTTCCCACTATTA 58.684 44.000 5.77 0.00 40.93 0.98
252 259 6.449956 AGGTCTCTTCCCACTATTATGGTTA 58.550 40.000 0.00 0.00 38.16 2.85
321 328 3.409026 ACACTTCCTTAGCTTGTCCTG 57.591 47.619 0.00 0.00 0.00 3.86
324 331 2.027653 ACTTCCTTAGCTTGTCCTGAGC 60.028 50.000 0.00 0.00 40.43 4.26
364 371 7.112009 GTGATTATACTTGCATAAATGTGTGCG 59.888 37.037 0.00 0.00 44.36 5.34
367 374 4.340894 ACTTGCATAAATGTGTGCGTAG 57.659 40.909 0.00 3.01 44.36 3.51
465 472 8.954350 CAGGAGACATGTTGATTAAAGAGAAAT 58.046 33.333 0.00 0.00 0.00 2.17
628 635 7.547722 ACATGTATTAGTTCAAATAGACGTGCA 59.452 33.333 0.00 0.00 0.00 4.57
630 637 8.126871 TGTATTAGTTCAAATAGACGTGCATC 57.873 34.615 0.00 0.00 0.00 3.91
670 677 8.803201 ACTAGTGCTTTAAAAAGAAAATCTGC 57.197 30.769 6.64 0.00 38.28 4.26
674 681 4.686091 GCTTTAAAAAGAAAATCTGCCGCT 59.314 37.500 6.64 0.00 38.28 5.52
834 841 2.032634 GGCAAACGCACCATCTCGA 61.033 57.895 0.00 0.00 0.00 4.04
937 952 2.291540 ACACAAGGGGAGAGAGAGAGAG 60.292 54.545 0.00 0.00 0.00 3.20
973 991 2.796651 CGTAACCGACCTCCCTCG 59.203 66.667 0.00 0.00 35.63 4.63
974 992 2.042831 CGTAACCGACCTCCCTCGT 61.043 63.158 0.00 0.00 35.63 4.18
975 993 1.805910 GTAACCGACCTCCCTCGTC 59.194 63.158 0.00 0.00 31.35 4.20
1062 1097 1.079127 CAACATCCTCCTCCGCGTT 60.079 57.895 4.92 0.00 0.00 4.84
1453 1488 1.075536 GGAATGTCCCCTTGGTCTTGT 59.924 52.381 0.00 0.00 0.00 3.16
1608 1643 0.528466 CCGATGACGTGTGGATGAGG 60.528 60.000 0.00 0.00 37.88 3.86
1730 1765 1.473965 CCAGTATGTCATGAGGCGCTT 60.474 52.381 7.64 0.00 0.00 4.68
1870 1905 0.391263 CAACCAAGGGACGACTAGGC 60.391 60.000 0.00 0.00 0.00 3.93
1890 1925 0.971386 TCCGGGTCTTCAAGTACCAC 59.029 55.000 0.00 0.00 37.51 4.16
2465 2503 5.682212 GCCACTTTCAATTCAGTTCAGGTTT 60.682 40.000 0.00 0.00 0.00 3.27
2469 2507 8.352201 CACTTTCAATTCAGTTCAGGTTTGATA 58.648 33.333 0.00 0.00 32.27 2.15
2588 2626 2.815211 GATGCCGCTGTCTCGCAA 60.815 61.111 0.00 0.00 0.00 4.85
2612 2650 2.119801 AGTAGGCATTGCAGGTTCTG 57.880 50.000 11.39 0.00 34.12 3.02
2635 2673 4.441792 GTTGTTGCAACTGGAAATTCCTT 58.558 39.130 28.61 0.00 37.46 3.36
2649 2687 7.661040 TGGAAATTCCTTTTCAGTTTCTGATC 58.339 34.615 13.78 0.00 44.67 2.92
2700 2739 2.290641 TGGGTGCTCGTGGATATTGTTT 60.291 45.455 0.00 0.00 0.00 2.83
2756 2798 1.679139 TAGTGCTTTGCTGTGCAGTT 58.321 45.000 10.03 1.21 42.15 3.16
2757 2799 0.819582 AGTGCTTTGCTGTGCAGTTT 59.180 45.000 0.00 0.00 40.61 2.66
2758 2800 2.023673 AGTGCTTTGCTGTGCAGTTTA 58.976 42.857 0.00 0.00 40.61 2.01
2846 2889 2.023673 TCCACAAGCTCTTTGGTGTTG 58.976 47.619 7.81 0.00 41.25 3.33
2866 2909 4.764679 TGTTGTCAGACATGCCATTTAC 57.235 40.909 3.45 0.00 0.00 2.01
2867 2910 4.397420 TGTTGTCAGACATGCCATTTACT 58.603 39.130 3.45 0.00 0.00 2.24
2868 2911 4.455533 TGTTGTCAGACATGCCATTTACTC 59.544 41.667 3.45 0.00 0.00 2.59
2869 2912 3.609853 TGTCAGACATGCCATTTACTCC 58.390 45.455 0.00 0.00 0.00 3.85
2870 2913 2.945668 GTCAGACATGCCATTTACTCCC 59.054 50.000 0.00 0.00 0.00 4.30
2871 2914 2.846206 TCAGACATGCCATTTACTCCCT 59.154 45.455 0.00 0.00 0.00 4.20
2872 2915 3.118261 TCAGACATGCCATTTACTCCCTC 60.118 47.826 0.00 0.00 0.00 4.30
2873 2916 2.173569 AGACATGCCATTTACTCCCTCC 59.826 50.000 0.00 0.00 0.00 4.30
2874 2917 1.134098 ACATGCCATTTACTCCCTCCG 60.134 52.381 0.00 0.00 0.00 4.63
2875 2918 1.134098 CATGCCATTTACTCCCTCCGT 60.134 52.381 0.00 0.00 0.00 4.69
2876 2919 0.988832 TGCCATTTACTCCCTCCGTT 59.011 50.000 0.00 0.00 0.00 4.44
2877 2920 1.065709 TGCCATTTACTCCCTCCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
2878 2921 1.746171 GCCATTTACTCCCTCCGTTCC 60.746 57.143 0.00 0.00 0.00 3.62
2879 2922 1.838077 CCATTTACTCCCTCCGTTCCT 59.162 52.381 0.00 0.00 0.00 3.36
2880 2923 3.036091 CCATTTACTCCCTCCGTTCCTA 58.964 50.000 0.00 0.00 0.00 2.94
2881 2924 3.453353 CCATTTACTCCCTCCGTTCCTAA 59.547 47.826 0.00 0.00 0.00 2.69
2882 2925 4.080751 CCATTTACTCCCTCCGTTCCTAAA 60.081 45.833 0.00 0.00 0.00 1.85
2883 2926 5.397559 CCATTTACTCCCTCCGTTCCTAAAT 60.398 44.000 0.00 0.00 0.00 1.40
2884 2927 6.183361 CCATTTACTCCCTCCGTTCCTAAATA 60.183 42.308 0.00 0.00 0.00 1.40
2885 2928 5.859205 TTACTCCCTCCGTTCCTAAATAC 57.141 43.478 0.00 0.00 0.00 1.89
2886 2929 2.692041 ACTCCCTCCGTTCCTAAATACG 59.308 50.000 0.00 0.00 37.50 3.06
2910 2953 9.939802 ACGGAGTATAAGTCTTTTTAGACATTT 57.060 29.630 7.92 0.00 41.94 2.32
2942 2985 9.588096 AGACTACAACATATGGATGTATGTAGA 57.412 33.333 26.03 8.59 45.93 2.59
2943 2986 9.627395 GACTACAACATATGGATGTATGTAGAC 57.373 37.037 26.03 21.22 45.93 2.59
2944 2987 9.143155 ACTACAACATATGGATGTATGTAGACA 57.857 33.333 26.03 7.65 45.93 3.41
2974 3017 6.777526 AGAGTATAGATTCGCTCATTTTGC 57.222 37.500 0.00 0.00 0.00 3.68
2975 3018 6.520272 AGAGTATAGATTCGCTCATTTTGCT 58.480 36.000 0.00 0.00 0.00 3.91
2976 3019 6.644592 AGAGTATAGATTCGCTCATTTTGCTC 59.355 38.462 0.00 0.00 0.00 4.26
2977 3020 5.698545 AGTATAGATTCGCTCATTTTGCTCC 59.301 40.000 0.00 0.00 0.00 4.70
2978 3021 1.667724 AGATTCGCTCATTTTGCTCCG 59.332 47.619 0.00 0.00 0.00 4.63
2979 3022 1.398390 GATTCGCTCATTTTGCTCCGT 59.602 47.619 0.00 0.00 0.00 4.69
2980 3023 2.087501 TTCGCTCATTTTGCTCCGTA 57.912 45.000 0.00 0.00 0.00 4.02
2981 3024 2.309528 TCGCTCATTTTGCTCCGTAT 57.690 45.000 0.00 0.00 0.00 3.06
2982 3025 1.933181 TCGCTCATTTTGCTCCGTATG 59.067 47.619 0.00 0.00 0.00 2.39
2983 3026 1.665679 CGCTCATTTTGCTCCGTATGT 59.334 47.619 0.00 0.00 0.00 2.29
2984 3027 2.863740 CGCTCATTTTGCTCCGTATGTA 59.136 45.455 0.00 0.00 0.00 2.29
2985 3028 3.060272 CGCTCATTTTGCTCCGTATGTAG 60.060 47.826 0.00 0.00 0.00 2.74
2986 3029 3.871594 GCTCATTTTGCTCCGTATGTAGT 59.128 43.478 0.00 0.00 0.00 2.73
2987 3030 4.025647 GCTCATTTTGCTCCGTATGTAGTC 60.026 45.833 0.00 0.00 0.00 2.59
2988 3031 4.109766 TCATTTTGCTCCGTATGTAGTCG 58.890 43.478 0.00 0.00 0.00 4.18
2989 3032 3.581024 TTTTGCTCCGTATGTAGTCGT 57.419 42.857 0.00 0.00 0.00 4.34
2990 3033 3.581024 TTTGCTCCGTATGTAGTCGTT 57.419 42.857 0.00 0.00 0.00 3.85
2991 3034 3.581024 TTGCTCCGTATGTAGTCGTTT 57.419 42.857 0.00 0.00 0.00 3.60
2992 3035 2.871133 TGCTCCGTATGTAGTCGTTTG 58.129 47.619 0.00 0.00 0.00 2.93
2993 3036 2.229543 TGCTCCGTATGTAGTCGTTTGT 59.770 45.455 0.00 0.00 0.00 2.83
2994 3037 3.248266 GCTCCGTATGTAGTCGTTTGTT 58.752 45.455 0.00 0.00 0.00 2.83
2995 3038 3.060363 GCTCCGTATGTAGTCGTTTGTTG 59.940 47.826 0.00 0.00 0.00 3.33
2996 3039 4.478699 CTCCGTATGTAGTCGTTTGTTGA 58.521 43.478 0.00 0.00 0.00 3.18
2997 3040 4.869215 TCCGTATGTAGTCGTTTGTTGAA 58.131 39.130 0.00 0.00 0.00 2.69
2998 3041 5.288015 TCCGTATGTAGTCGTTTGTTGAAA 58.712 37.500 0.00 0.00 0.00 2.69
2999 3042 5.927689 TCCGTATGTAGTCGTTTGTTGAAAT 59.072 36.000 0.00 0.00 0.00 2.17
3000 3043 6.089820 TCCGTATGTAGTCGTTTGTTGAAATC 59.910 38.462 0.00 0.00 0.00 2.17
3001 3044 6.090358 CCGTATGTAGTCGTTTGTTGAAATCT 59.910 38.462 0.00 0.00 0.00 2.40
3002 3045 7.164858 CGTATGTAGTCGTTTGTTGAAATCTC 58.835 38.462 0.00 0.00 0.00 2.75
3003 3046 7.061905 CGTATGTAGTCGTTTGTTGAAATCTCT 59.938 37.037 0.00 0.00 0.00 3.10
3004 3047 9.350357 GTATGTAGTCGTTTGTTGAAATCTCTA 57.650 33.333 0.00 0.00 0.00 2.43
3005 3048 7.869016 TGTAGTCGTTTGTTGAAATCTCTAG 57.131 36.000 0.00 0.00 0.00 2.43
3006 3049 7.654568 TGTAGTCGTTTGTTGAAATCTCTAGA 58.345 34.615 0.00 0.00 0.00 2.43
3007 3050 8.139350 TGTAGTCGTTTGTTGAAATCTCTAGAA 58.861 33.333 0.00 0.00 0.00 2.10
3008 3051 8.975439 GTAGTCGTTTGTTGAAATCTCTAGAAA 58.025 33.333 0.00 0.00 0.00 2.52
3009 3052 8.077836 AGTCGTTTGTTGAAATCTCTAGAAAG 57.922 34.615 0.00 0.00 0.00 2.62
3010 3053 7.926555 AGTCGTTTGTTGAAATCTCTAGAAAGA 59.073 33.333 0.00 0.00 0.00 2.52
3011 3054 8.004905 GTCGTTTGTTGAAATCTCTAGAAAGAC 58.995 37.037 0.00 0.00 0.00 3.01
3012 3055 7.926555 TCGTTTGTTGAAATCTCTAGAAAGACT 59.073 33.333 0.00 0.00 0.00 3.24
3013 3056 8.552034 CGTTTGTTGAAATCTCTAGAAAGACTT 58.448 33.333 0.00 0.00 0.00 3.01
3024 3067 9.716556 ATCTCTAGAAAGACTTACATTTAGGGA 57.283 33.333 0.00 0.00 0.00 4.20
3025 3068 8.968969 TCTCTAGAAAGACTTACATTTAGGGAC 58.031 37.037 0.00 0.00 0.00 4.46
3026 3069 7.769220 TCTAGAAAGACTTACATTTAGGGACG 58.231 38.462 0.00 0.00 0.00 4.79
3027 3070 5.731591 AGAAAGACTTACATTTAGGGACGG 58.268 41.667 0.00 0.00 0.00 4.79
3028 3071 5.482878 AGAAAGACTTACATTTAGGGACGGA 59.517 40.000 0.00 0.00 0.00 4.69
3029 3072 5.340439 AAGACTTACATTTAGGGACGGAG 57.660 43.478 0.00 0.00 0.00 4.63
3030 3073 3.705072 AGACTTACATTTAGGGACGGAGG 59.295 47.826 0.00 0.00 0.00 4.30
3031 3074 3.703052 GACTTACATTTAGGGACGGAGGA 59.297 47.826 0.00 0.00 0.00 3.71
3032 3075 4.098894 ACTTACATTTAGGGACGGAGGAA 58.901 43.478 0.00 0.00 0.00 3.36
3033 3076 4.161754 ACTTACATTTAGGGACGGAGGAAG 59.838 45.833 0.00 0.00 0.00 3.46
3034 3077 2.547990 ACATTTAGGGACGGAGGAAGT 58.452 47.619 0.00 0.00 0.00 3.01
3035 3078 3.716431 ACATTTAGGGACGGAGGAAGTA 58.284 45.455 0.00 0.00 0.00 2.24
3036 3079 3.705072 ACATTTAGGGACGGAGGAAGTAG 59.295 47.826 0.00 0.00 0.00 2.57
3078 3121 3.957497 TGAATACACAAAAGCCTTGGTGT 59.043 39.130 12.77 12.77 45.57 4.16
3108 3151 6.763715 TTGCATTGATAGGTAGGGAGTATT 57.236 37.500 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 4.687948 CCATCTGATTCTACTATTGCACCG 59.312 45.833 0.00 0.00 0.00 4.94
146 151 4.634883 ACTGCATAGAATCAGCTGTGAAAG 59.365 41.667 14.67 7.34 38.69 2.62
180 185 6.155221 AGCCATTGTCAGATAGAGAAGTGTAA 59.845 38.462 0.00 0.00 32.48 2.41
288 295 1.268539 GGAAGTGTTTCAGTGCCAACG 60.269 52.381 0.00 0.00 32.77 4.10
321 328 3.811722 TCACACATGAAAATGTCGCTC 57.188 42.857 0.00 0.00 31.37 5.03
324 331 9.213819 CAAGTATAATCACACATGAAAATGTCG 57.786 33.333 0.00 0.00 38.69 4.35
364 371 7.678837 AGAAGATTCATCATGATTCTCCCTAC 58.321 38.462 11.62 3.74 36.44 3.18
367 374 8.915057 TTTAGAAGATTCATCATGATTCTCCC 57.085 34.615 11.62 7.75 36.44 4.30
414 421 1.687563 AAAGACCACCCACTTTTCCG 58.312 50.000 0.00 0.00 33.36 4.30
483 490 6.986817 CACAATCTCTTATTCCCAACTCGTAT 59.013 38.462 0.00 0.00 0.00 3.06
606 613 7.274367 CGATGCACGTCTATTTGAACTAATAC 58.726 38.462 0.00 0.00 37.22 1.89
628 635 3.438087 ACTAGTAAGTGTGCACGTACGAT 59.562 43.478 24.41 3.10 46.18 3.73
630 637 2.906776 CACTAGTAAGTGTGCACGTACG 59.093 50.000 15.01 15.01 46.76 3.67
666 673 1.580942 GCAAAATGTCAGCGGCAGA 59.419 52.632 1.45 0.00 0.00 4.26
667 674 1.444895 GGCAAAATGTCAGCGGCAG 60.445 57.895 1.45 0.00 0.00 4.85
668 675 2.650196 GGCAAAATGTCAGCGGCA 59.350 55.556 1.45 0.00 0.00 5.69
669 676 2.470801 TTCGGCAAAATGTCAGCGGC 62.471 55.000 0.00 0.00 0.00 6.53
670 677 0.729140 GTTCGGCAAAATGTCAGCGG 60.729 55.000 0.00 0.00 0.00 5.52
674 681 1.169661 AGGCGTTCGGCAAAATGTCA 61.170 50.000 19.67 0.00 46.16 3.58
815 822 2.480555 GAGATGGTGCGTTTGCCG 59.519 61.111 0.00 0.00 41.78 5.69
891 898 1.779683 CGCCGAGAAAGGTTTCGTC 59.220 57.895 0.00 0.00 41.92 4.20
1062 1097 4.733725 AAGGGGAGGTAGGCGGCA 62.734 66.667 13.08 0.00 0.00 5.69
1730 1765 2.810887 GCAGCATGTCGCAGTCGA 60.811 61.111 0.00 0.00 46.13 4.20
1870 1905 1.067071 GTGGTACTTGAAGACCCGGAG 60.067 57.143 0.73 0.00 34.58 4.63
2390 2425 0.252375 TCCCCTACCACCACTACCAC 60.252 60.000 0.00 0.00 0.00 4.16
2401 2436 3.586174 GTGGTAAATATCCCTCCCCTACC 59.414 52.174 0.00 0.00 0.00 3.18
2430 2468 8.893219 TGAATTGAAAGTGGCTAGAGTATATG 57.107 34.615 0.00 0.00 0.00 1.78
2465 2503 5.591472 GCATTGGAGCCTTATATGCATATCA 59.409 40.000 22.33 11.26 40.86 2.15
2469 2507 3.770046 TGCATTGGAGCCTTATATGCAT 58.230 40.909 3.79 3.79 44.59 3.96
2503 2541 8.525290 ACAAGAAGCCAAATATAGCAAGTAAT 57.475 30.769 0.00 0.00 0.00 1.89
2558 2596 1.605500 CGGCATCACATTTGTGTTCG 58.394 50.000 10.30 6.88 45.76 3.95
2588 2626 0.178068 CCTGCAATGCCTACTACCGT 59.822 55.000 1.53 0.00 0.00 4.83
2590 2628 2.092914 AGAACCTGCAATGCCTACTACC 60.093 50.000 1.53 0.00 0.00 3.18
2612 2650 3.130633 GGAATTTCCAGTTGCAACAACC 58.869 45.455 30.11 16.09 36.28 3.77
2635 2673 4.512944 GCACAGAGTGATCAGAAACTGAAA 59.487 41.667 18.57 0.00 37.76 2.69
2700 2739 1.043816 GGCAGGCAGTATGAGAGCTA 58.956 55.000 0.00 0.00 39.69 3.32
2756 2798 5.184864 CCATTTCTGGTACCAGCAACATTAA 59.815 40.000 33.39 19.28 43.31 1.40
2757 2799 4.704540 CCATTTCTGGTACCAGCAACATTA 59.295 41.667 33.39 14.49 43.31 1.90
2758 2800 3.511146 CCATTTCTGGTACCAGCAACATT 59.489 43.478 33.39 14.21 43.31 2.71
2802 2845 6.548441 ACACAAATTGCATGGAGATTTTTG 57.452 33.333 13.81 13.81 30.69 2.44
2846 2889 4.142600 GGAGTAAATGGCATGTCTGACAAC 60.143 45.833 15.31 9.89 45.65 3.32
2866 2909 3.366440 CGTATTTAGGAACGGAGGGAG 57.634 52.381 0.00 0.00 35.51 4.30
2873 2916 7.869800 AGACTTATACTCCGTATTTAGGAACG 58.130 38.462 0.00 0.00 37.32 3.95
2884 2927 9.939802 AAATGTCTAAAAAGACTTATACTCCGT 57.060 29.630 7.04 0.00 39.41 4.69
2916 2959 9.588096 TCTACATACATCCATATGTTGTAGTCT 57.412 33.333 22.56 7.77 44.07 3.24
2917 2960 9.627395 GTCTACATACATCCATATGTTGTAGTC 57.373 37.037 22.56 18.41 44.07 2.59
2918 2961 9.143155 TGTCTACATACATCCATATGTTGTAGT 57.857 33.333 22.56 15.48 44.07 2.73
2948 2991 8.765219 GCAAAATGAGCGAATCTATACTCTAAA 58.235 33.333 0.00 0.00 0.00 1.85
2949 2992 8.144478 AGCAAAATGAGCGAATCTATACTCTAA 58.856 33.333 0.00 0.00 37.01 2.10
2950 2993 7.661968 AGCAAAATGAGCGAATCTATACTCTA 58.338 34.615 0.00 0.00 37.01 2.43
2951 2994 6.520272 AGCAAAATGAGCGAATCTATACTCT 58.480 36.000 0.00 0.00 37.01 3.24
2952 2995 6.128688 GGAGCAAAATGAGCGAATCTATACTC 60.129 42.308 0.00 0.00 37.01 2.59
2953 2996 5.698545 GGAGCAAAATGAGCGAATCTATACT 59.301 40.000 0.00 0.00 37.01 2.12
2954 2997 5.388890 CGGAGCAAAATGAGCGAATCTATAC 60.389 44.000 0.00 0.00 37.01 1.47
2955 2998 4.686091 CGGAGCAAAATGAGCGAATCTATA 59.314 41.667 0.00 0.00 37.01 1.31
2956 2999 3.496130 CGGAGCAAAATGAGCGAATCTAT 59.504 43.478 0.00 0.00 37.01 1.98
2957 3000 2.866156 CGGAGCAAAATGAGCGAATCTA 59.134 45.455 0.00 0.00 37.01 1.98
2958 3001 1.667724 CGGAGCAAAATGAGCGAATCT 59.332 47.619 0.00 0.00 37.01 2.40
2959 3002 1.398390 ACGGAGCAAAATGAGCGAATC 59.602 47.619 0.00 0.00 37.01 2.52
2960 3003 1.453155 ACGGAGCAAAATGAGCGAAT 58.547 45.000 0.00 0.00 37.01 3.34
2961 3004 2.087501 TACGGAGCAAAATGAGCGAA 57.912 45.000 0.00 0.00 37.01 4.70
2962 3005 1.933181 CATACGGAGCAAAATGAGCGA 59.067 47.619 0.00 0.00 37.01 4.93
2963 3006 1.665679 ACATACGGAGCAAAATGAGCG 59.334 47.619 0.00 0.00 37.01 5.03
2964 3007 3.871594 ACTACATACGGAGCAAAATGAGC 59.128 43.478 0.00 0.00 0.00 4.26
2965 3008 4.207224 CGACTACATACGGAGCAAAATGAG 59.793 45.833 0.00 0.00 0.00 2.90
2966 3009 4.109766 CGACTACATACGGAGCAAAATGA 58.890 43.478 0.00 0.00 0.00 2.57
2967 3010 3.863424 ACGACTACATACGGAGCAAAATG 59.137 43.478 0.00 0.00 0.00 2.32
2968 3011 4.119442 ACGACTACATACGGAGCAAAAT 57.881 40.909 0.00 0.00 0.00 1.82
2969 3012 3.581024 ACGACTACATACGGAGCAAAA 57.419 42.857 0.00 0.00 0.00 2.44
2970 3013 3.581024 AACGACTACATACGGAGCAAA 57.419 42.857 0.00 0.00 0.00 3.68
2971 3014 3.247442 CAAACGACTACATACGGAGCAA 58.753 45.455 0.00 0.00 0.00 3.91
2972 3015 2.229543 ACAAACGACTACATACGGAGCA 59.770 45.455 0.00 0.00 0.00 4.26
2973 3016 2.872370 ACAAACGACTACATACGGAGC 58.128 47.619 0.00 0.00 0.00 4.70
2974 3017 4.478699 TCAACAAACGACTACATACGGAG 58.521 43.478 0.00 0.00 0.00 4.63
2975 3018 4.502171 TCAACAAACGACTACATACGGA 57.498 40.909 0.00 0.00 0.00 4.69
2976 3019 5.579384 TTTCAACAAACGACTACATACGG 57.421 39.130 0.00 0.00 0.00 4.02
2977 3020 7.045725 AGATTTCAACAAACGACTACATACG 57.954 36.000 0.00 0.00 0.00 3.06
2978 3021 8.240883 AGAGATTTCAACAAACGACTACATAC 57.759 34.615 0.00 0.00 0.00 2.39
2979 3022 9.569167 CTAGAGATTTCAACAAACGACTACATA 57.431 33.333 0.00 0.00 0.00 2.29
2980 3023 8.304596 TCTAGAGATTTCAACAAACGACTACAT 58.695 33.333 0.00 0.00 0.00 2.29
2981 3024 7.654568 TCTAGAGATTTCAACAAACGACTACA 58.345 34.615 0.00 0.00 0.00 2.74
2982 3025 8.516811 TTCTAGAGATTTCAACAAACGACTAC 57.483 34.615 0.00 0.00 0.00 2.73
2983 3026 9.193133 CTTTCTAGAGATTTCAACAAACGACTA 57.807 33.333 0.00 0.00 0.00 2.59
2984 3027 7.926555 TCTTTCTAGAGATTTCAACAAACGACT 59.073 33.333 0.00 0.00 0.00 4.18
2985 3028 8.004905 GTCTTTCTAGAGATTTCAACAAACGAC 58.995 37.037 0.00 0.00 0.00 4.34
2986 3029 7.926555 AGTCTTTCTAGAGATTTCAACAAACGA 59.073 33.333 0.00 0.00 0.00 3.85
2987 3030 8.077836 AGTCTTTCTAGAGATTTCAACAAACG 57.922 34.615 0.00 0.00 0.00 3.60
2998 3041 9.716556 TCCCTAAATGTAAGTCTTTCTAGAGAT 57.283 33.333 0.00 0.00 0.00 2.75
2999 3042 8.968969 GTCCCTAAATGTAAGTCTTTCTAGAGA 58.031 37.037 0.00 0.00 0.00 3.10
3000 3043 7.916450 CGTCCCTAAATGTAAGTCTTTCTAGAG 59.084 40.741 0.00 0.00 0.00 2.43
3001 3044 7.147949 CCGTCCCTAAATGTAAGTCTTTCTAGA 60.148 40.741 0.00 0.00 0.00 2.43
3002 3045 6.979238 CCGTCCCTAAATGTAAGTCTTTCTAG 59.021 42.308 0.00 0.00 0.00 2.43
3003 3046 6.664816 TCCGTCCCTAAATGTAAGTCTTTCTA 59.335 38.462 0.00 0.00 0.00 2.10
3004 3047 5.482878 TCCGTCCCTAAATGTAAGTCTTTCT 59.517 40.000 0.00 0.00 0.00 2.52
3005 3048 5.727434 TCCGTCCCTAAATGTAAGTCTTTC 58.273 41.667 0.00 0.00 0.00 2.62
3006 3049 5.338137 CCTCCGTCCCTAAATGTAAGTCTTT 60.338 44.000 0.00 0.00 0.00 2.52
3007 3050 4.161754 CCTCCGTCCCTAAATGTAAGTCTT 59.838 45.833 0.00 0.00 0.00 3.01
3008 3051 3.705072 CCTCCGTCCCTAAATGTAAGTCT 59.295 47.826 0.00 0.00 0.00 3.24
3009 3052 3.703052 TCCTCCGTCCCTAAATGTAAGTC 59.297 47.826 0.00 0.00 0.00 3.01
3010 3053 3.716431 TCCTCCGTCCCTAAATGTAAGT 58.284 45.455 0.00 0.00 0.00 2.24
3011 3054 4.161754 ACTTCCTCCGTCCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
3012 3055 4.098894 ACTTCCTCCGTCCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
3013 3056 3.716431 ACTTCCTCCGTCCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
3014 3057 2.547990 ACTTCCTCCGTCCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
3015 3058 3.705072 ACTACTTCCTCCGTCCCTAAATG 59.295 47.826 0.00 0.00 0.00 2.32
3016 3059 3.991683 ACTACTTCCTCCGTCCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3017 3060 3.463048 ACTACTTCCTCCGTCCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3018 3061 3.463048 AACTACTTCCTCCGTCCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
3019 3062 3.245371 TGAAACTACTTCCTCCGTCCCTA 60.245 47.826 0.00 0.00 32.53 3.53
3020 3063 2.177734 GAAACTACTTCCTCCGTCCCT 58.822 52.381 0.00 0.00 0.00 4.20
3021 3064 1.897802 TGAAACTACTTCCTCCGTCCC 59.102 52.381 0.00 0.00 32.53 4.46
3022 3065 3.447944 AGATGAAACTACTTCCTCCGTCC 59.552 47.826 0.00 0.00 31.02 4.79
3023 3066 4.722361 AGATGAAACTACTTCCTCCGTC 57.278 45.455 0.00 0.00 31.02 4.79
3024 3067 6.793505 ATAAGATGAAACTACTTCCTCCGT 57.206 37.500 0.00 0.00 31.02 4.69
3025 3068 8.494016 AAAATAAGATGAAACTACTTCCTCCG 57.506 34.615 0.00 0.00 31.02 4.63
3052 3095 5.047802 ACCAAGGCTTTTGTGTATTCATGAG 60.048 40.000 0.00 0.00 0.00 2.90
3078 3121 6.272090 TCCCTACCTATCAATGCAATGATACA 59.728 38.462 18.52 3.98 40.44 2.29


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

AutoCloner maintained by Alex Coulton.