Multiple sequence alignment - TraesCS3D01G053400

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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 TraesCS3D01G053400 chr3D 100.000 3421 0 0 1 3421 21902938 21906358 0.000000e+00 6318.0
1 TraesCS3D01G053400 chr3D 96.591 528 12 5 2900 3421 544383664 544383137 0.000000e+00 870.0
2 TraesCS3D01G053400 chr3D 95.192 104 5 0 2813 2916 589901974 589902077 7.590000e-37 165.0
3 TraesCS3D01G053400 chr5D 98.080 2813 41 9 1 2810 6202964 6200162 0.000000e+00 4883.0
4 TraesCS3D01G053400 chr5D 98.752 1523 16 3 1 1521 240136018 240137539 0.000000e+00 2704.0
5 TraesCS3D01G053400 chr5D 97.931 1160 24 0 1651 2810 329162138 329163297 0.000000e+00 2010.0
6 TraesCS3D01G053400 chr5D 97.674 516 8 3 2910 3421 353752026 353752541 0.000000e+00 883.0
7 TraesCS3D01G053400 chr5D 97.481 516 9 3 2910 3421 373735160 373735675 0.000000e+00 878.0
8 TraesCS3D01G053400 chr5D 94.393 107 5 1 2813 2919 546643832 546643727 2.730000e-36 163.0
9 TraesCS3D01G053400 chr1D 97.903 2813 42 8 1 2810 254496320 254499118 0.000000e+00 4852.0
10 TraesCS3D01G053400 chr1D 94.962 1866 82 9 948 2810 244484785 244482929 0.000000e+00 2915.0
11 TraesCS3D01G053400 chr1D 97.417 1587 18 6 1 1567 19956329 19957912 0.000000e+00 2682.0
12 TraesCS3D01G053400 chr1D 97.481 516 9 3 2910 3421 201507037 201506522 0.000000e+00 878.0
13 TraesCS3D01G053400 chr1D 96.591 528 12 5 2900 3421 338329251 338328724 0.000000e+00 870.0
14 TraesCS3D01G053400 chr1D 95.192 104 5 0 2813 2916 453108698 453108595 7.590000e-37 165.0
15 TraesCS3D01G053400 chr6B 97.263 2813 69 7 1 2810 22424257 22427064 0.000000e+00 4761.0
16 TraesCS3D01G053400 chr3B 97.049 2813 49 8 1 2810 201511440 201514221 0.000000e+00 4704.0
17 TraesCS3D01G053400 chr4D 96.588 2814 82 11 1 2810 19914810 19917613 0.000000e+00 4652.0
18 TraesCS3D01G053400 chr4D 97.481 516 8 4 2910 3421 429082690 429083204 0.000000e+00 876.0
19 TraesCS3D01G053400 chr4D 95.192 104 5 0 2813 2916 241459323 241459220 7.590000e-37 165.0
20 TraesCS3D01G053400 chr4D 90.244 123 11 1 2813 2935 411028117 411028238 3.530000e-35 159.0
21 TraesCS3D01G053400 chr1A 97.980 2030 31 7 65 2090 112777658 112775635 0.000000e+00 3513.0
22 TraesCS3D01G053400 chr1A 96.312 1600 46 4 1216 2810 168451039 168449448 0.000000e+00 2615.0
23 TraesCS3D01G053400 chr7A 94.430 2262 117 6 551 2810 352195159 352192905 0.000000e+00 3470.0
24 TraesCS3D01G053400 chr7D 98.824 850 8 2 54 902 484627211 484628059 0.000000e+00 1513.0
25 TraesCS3D01G053400 chr7D 97.481 516 9 3 2910 3421 411441502 411442017 0.000000e+00 878.0
26 TraesCS3D01G053400 chr7D 94.393 107 5 1 2813 2919 287109661 287109766 2.730000e-36 163.0
27 TraesCS3D01G053400 chr2D 97.674 516 8 3 2910 3421 599094675 599094160 0.000000e+00 883.0
28 TraesCS3D01G053400 chr2D 98.058 103 2 0 2813 2915 201043972 201043870 2.710000e-41 180.0
29 TraesCS3D01G053400 chr2D 93.578 109 7 0 2813 2921 363369211 363369103 2.730000e-36 163.0
30 TraesCS3D01G053400 chr6D 97.481 516 9 3 2910 3421 217275211 217274696 0.000000e+00 878.0
31 TraesCS3D01G053400 chr6D 95.238 105 5 0 2813 2917 342996280 342996384 2.110000e-37 167.0
32 TraesCS3D01G053400 chr2B 95.385 65 3 0 1 65 474897287 474897223 1.680000e-18 104.0
33 TraesCS3D01G053400 chr2A 100.000 31 0 0 1 31 689960398 689960428 1.330000e-04 58.4


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 TraesCS3D01G053400 chr3D 21902938 21906358 3420 False 6318 6318 100.000 1 3421 1 chr3D.!!$F1 3420
1 TraesCS3D01G053400 chr3D 544383137 544383664 527 True 870 870 96.591 2900 3421 1 chr3D.!!$R1 521
2 TraesCS3D01G053400 chr5D 6200162 6202964 2802 True 4883 4883 98.080 1 2810 1 chr5D.!!$R1 2809
3 TraesCS3D01G053400 chr5D 240136018 240137539 1521 False 2704 2704 98.752 1 1521 1 chr5D.!!$F1 1520
4 TraesCS3D01G053400 chr5D 329162138 329163297 1159 False 2010 2010 97.931 1651 2810 1 chr5D.!!$F2 1159
5 TraesCS3D01G053400 chr5D 353752026 353752541 515 False 883 883 97.674 2910 3421 1 chr5D.!!$F3 511
6 TraesCS3D01G053400 chr5D 373735160 373735675 515 False 878 878 97.481 2910 3421 1 chr5D.!!$F4 511
7 TraesCS3D01G053400 chr1D 254496320 254499118 2798 False 4852 4852 97.903 1 2810 1 chr1D.!!$F2 2809
8 TraesCS3D01G053400 chr1D 244482929 244484785 1856 True 2915 2915 94.962 948 2810 1 chr1D.!!$R2 1862
9 TraesCS3D01G053400 chr1D 19956329 19957912 1583 False 2682 2682 97.417 1 1567 1 chr1D.!!$F1 1566
10 TraesCS3D01G053400 chr1D 201506522 201507037 515 True 878 878 97.481 2910 3421 1 chr1D.!!$R1 511
11 TraesCS3D01G053400 chr1D 338328724 338329251 527 True 870 870 96.591 2900 3421 1 chr1D.!!$R3 521
12 TraesCS3D01G053400 chr6B 22424257 22427064 2807 False 4761 4761 97.263 1 2810 1 chr6B.!!$F1 2809
13 TraesCS3D01G053400 chr3B 201511440 201514221 2781 False 4704 4704 97.049 1 2810 1 chr3B.!!$F1 2809
14 TraesCS3D01G053400 chr4D 19914810 19917613 2803 False 4652 4652 96.588 1 2810 1 chr4D.!!$F1 2809
15 TraesCS3D01G053400 chr4D 429082690 429083204 514 False 876 876 97.481 2910 3421 1 chr4D.!!$F3 511
16 TraesCS3D01G053400 chr1A 112775635 112777658 2023 True 3513 3513 97.980 65 2090 1 chr1A.!!$R1 2025
17 TraesCS3D01G053400 chr1A 168449448 168451039 1591 True 2615 2615 96.312 1216 2810 1 chr1A.!!$R2 1594
18 TraesCS3D01G053400 chr7A 352192905 352195159 2254 True 3470 3470 94.430 551 2810 1 chr7A.!!$R1 2259
19 TraesCS3D01G053400 chr7D 484627211 484628059 848 False 1513 1513 98.824 54 902 1 chr7D.!!$F3 848
20 TraesCS3D01G053400 chr7D 411441502 411442017 515 False 878 878 97.481 2910 3421 1 chr7D.!!$F2 511
21 TraesCS3D01G053400 chr2D 599094160 599094675 515 True 883 883 97.674 2910 3421 1 chr2D.!!$R3 511
22 TraesCS3D01G053400 chr6D 217274696 217275211 515 True 878 878 97.481 2910 3421 1 chr6D.!!$R1 511

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
801 825 3.772025 CTGACACAGAATCCCCTAGAAGT 59.228 47.826 0.00 0.0 32.44 3.01 F
1721 1752 2.223758 GCCTACTCGTTATCAGTGGGAC 60.224 54.545 7.66 0.0 43.58 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 1980 0.584396 CGGCGTACAAAAAGCTCACA 59.416 50.0 0.00 0.0 32.56 3.58 R
2818 2878 0.107831 TGATACTAATGGCGCACCCC 59.892 55.0 10.83 0.0 33.59 4.95 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
177 198 7.104043 TCAAAAATAGCCATTCCTGAGATTG 57.896 36.000 0.00 0.00 0.00 2.67
256 278 4.526262 ACTCAGATATACCATGAGACCTGC 59.474 45.833 14.45 0.00 42.48 4.85
590 614 9.401058 AGGAATGTAAGACAGATTGAATAAAGG 57.599 33.333 0.00 0.00 0.00 3.11
707 731 9.244292 TGGCACTTATCGAGTATAGAATAGATT 57.756 33.333 0.00 0.00 36.65 2.40
801 825 3.772025 CTGACACAGAATCCCCTAGAAGT 59.228 47.826 0.00 0.00 32.44 3.01
1335 1360 4.671831 TCATTTATTTCTTGCAGGGGTGA 58.328 39.130 0.00 0.00 0.00 4.02
1382 1407 2.371179 TGTAACGGGTTTGTATGGTCCA 59.629 45.455 0.00 0.00 0.00 4.02
1525 1555 4.594062 TGCGGGTACATTGGGTATATTAGT 59.406 41.667 0.00 0.00 33.76 2.24
1597 1627 7.504238 AGGATTACGTATGGGCAATATTGAAAA 59.496 33.333 19.73 3.41 0.00 2.29
1721 1752 2.223758 GCCTACTCGTTATCAGTGGGAC 60.224 54.545 7.66 0.00 43.58 4.46
2198 2256 3.775661 ATTTTTGAATTAGACCGGGCG 57.224 42.857 6.32 0.00 0.00 6.13
2286 2344 5.111293 CCTTTGCTTTGCTCTTCTTTTTCA 58.889 37.500 0.00 0.00 0.00 2.69
2810 2870 1.520600 GGGTTGCCCAAACGTGGTAG 61.521 60.000 0.00 0.00 44.65 3.18
2811 2871 0.535553 GGTTGCCCAAACGTGGTAGA 60.536 55.000 0.00 0.00 44.30 2.59
2812 2872 0.872388 GTTGCCCAAACGTGGTAGAG 59.128 55.000 0.00 0.00 44.30 2.43
2813 2873 0.887387 TTGCCCAAACGTGGTAGAGC 60.887 55.000 0.00 0.00 44.30 4.09
2814 2874 1.302192 GCCCAAACGTGGTAGAGCA 60.302 57.895 0.00 0.00 44.30 4.26
2815 2875 1.574702 GCCCAAACGTGGTAGAGCAC 61.575 60.000 1.71 1.71 44.30 4.40
2831 2891 3.334891 ACCAGGGGTGCGCCATTA 61.335 61.111 19.98 0.00 32.98 1.90
2832 2892 2.516930 CCAGGGGTGCGCCATTAG 60.517 66.667 19.98 4.45 36.17 1.73
2833 2893 2.272146 CAGGGGTGCGCCATTAGT 59.728 61.111 19.98 0.00 36.17 2.24
2834 2894 1.524961 CAGGGGTGCGCCATTAGTA 59.475 57.895 19.98 0.00 36.17 1.82
2835 2895 0.108585 CAGGGGTGCGCCATTAGTAT 59.891 55.000 19.98 0.00 36.17 2.12
2836 2896 0.396811 AGGGGTGCGCCATTAGTATC 59.603 55.000 19.98 0.00 36.17 2.24
2837 2897 0.107831 GGGGTGCGCCATTAGTATCA 59.892 55.000 19.98 0.00 36.17 2.15
2838 2898 1.476110 GGGGTGCGCCATTAGTATCAA 60.476 52.381 19.98 0.00 36.17 2.57
2839 2899 2.504367 GGGTGCGCCATTAGTATCAAT 58.496 47.619 19.98 0.00 36.17 2.57
2840 2900 2.884639 GGGTGCGCCATTAGTATCAATT 59.115 45.455 19.98 0.00 36.17 2.32
2841 2901 4.069304 GGGTGCGCCATTAGTATCAATTA 58.931 43.478 19.98 0.00 36.17 1.40
2842 2902 4.083484 GGGTGCGCCATTAGTATCAATTAC 60.083 45.833 19.98 0.00 36.17 1.89
2843 2903 4.755123 GGTGCGCCATTAGTATCAATTACT 59.245 41.667 12.58 0.00 38.53 2.24
2844 2904 5.929992 GGTGCGCCATTAGTATCAATTACTA 59.070 40.000 12.58 0.00 37.25 1.82
2845 2905 6.090898 GGTGCGCCATTAGTATCAATTACTAG 59.909 42.308 12.58 0.00 38.35 2.57
2846 2906 6.645415 GTGCGCCATTAGTATCAATTACTAGT 59.355 38.462 4.18 0.00 42.83 2.57
2847 2907 6.645003 TGCGCCATTAGTATCAATTACTAGTG 59.355 38.462 4.18 7.81 44.61 2.74
2851 2911 7.050281 CATTAGTATCAATTACTAGTGGCGC 57.950 40.000 5.39 0.00 42.82 6.53
2852 2912 4.665833 AGTATCAATTACTAGTGGCGCA 57.334 40.909 10.83 0.00 39.44 6.09
2853 2913 4.369182 AGTATCAATTACTAGTGGCGCAC 58.631 43.478 10.83 5.73 39.44 5.34
2854 2914 2.018542 TCAATTACTAGTGGCGCACC 57.981 50.000 10.83 0.00 34.49 5.01
2855 2915 1.276705 TCAATTACTAGTGGCGCACCA 59.723 47.619 10.83 0.00 46.51 4.17
2856 2916 8.836760 AGTATCAATTACTAGTGGCGCACCAG 62.837 46.154 10.83 6.80 42.49 4.00
2868 2928 4.301505 CACCAGTAGTGCGCCATT 57.698 55.556 4.18 0.00 40.28 3.16
2869 2929 3.451793 CACCAGTAGTGCGCCATTA 57.548 52.632 4.18 0.00 40.28 1.90
2870 2930 1.290203 CACCAGTAGTGCGCCATTAG 58.710 55.000 4.18 0.00 40.28 1.73
2871 2931 0.902531 ACCAGTAGTGCGCCATTAGT 59.097 50.000 4.18 0.00 0.00 2.24
2872 2932 2.104967 ACCAGTAGTGCGCCATTAGTA 58.895 47.619 4.18 0.00 0.00 1.82
2873 2933 2.100916 ACCAGTAGTGCGCCATTAGTAG 59.899 50.000 4.18 0.00 0.00 2.57
2874 2934 2.545952 CCAGTAGTGCGCCATTAGTAGG 60.546 54.545 4.18 0.00 0.00 3.18
2885 2945 4.701956 CCATTAGTAGGCAAAACTGGTG 57.298 45.455 0.00 0.00 0.00 4.17
2886 2946 3.119495 CCATTAGTAGGCAAAACTGGTGC 60.119 47.826 0.00 0.00 41.45 5.01
2887 2947 1.803334 TAGTAGGCAAAACTGGTGCG 58.197 50.000 0.00 0.00 43.18 5.34
2888 2948 1.081442 GTAGGCAAAACTGGTGCGC 60.081 57.895 0.00 0.00 43.18 6.09
2889 2949 2.265182 TAGGCAAAACTGGTGCGCC 61.265 57.895 10.11 10.11 43.18 6.53
2890 2950 2.967507 TAGGCAAAACTGGTGCGCCA 62.968 55.000 19.93 19.93 45.47 5.69
2891 2951 2.658268 GCAAAACTGGTGCGCCAC 60.658 61.111 16.89 0.00 40.46 5.01
2892 2952 3.119193 CAAAACTGGTGCGCCACT 58.881 55.556 16.89 3.24 40.46 4.00
2893 2953 1.791103 GCAAAACTGGTGCGCCACTA 61.791 55.000 16.89 0.00 40.46 2.74
2894 2954 0.238289 CAAAACTGGTGCGCCACTAG 59.762 55.000 16.89 17.26 46.13 2.57
2897 2957 4.814900 CTGGTGCGCCACTAGTAG 57.185 61.111 16.89 0.00 40.46 2.57
2898 2958 1.141881 CTGGTGCGCCACTAGTAGG 59.858 63.158 16.89 0.00 40.46 3.18
2907 2967 3.351794 GCCACTAGTAGGCCTTTTTCT 57.648 47.619 12.58 7.63 46.50 2.52
2908 2968 4.482952 GCCACTAGTAGGCCTTTTTCTA 57.517 45.455 12.58 8.42 46.50 2.10
2909 2969 4.443621 GCCACTAGTAGGCCTTTTTCTAG 58.556 47.826 12.58 19.03 46.50 2.43
2910 2970 4.081031 GCCACTAGTAGGCCTTTTTCTAGT 60.081 45.833 12.58 19.64 46.50 2.57
2911 2971 5.128335 GCCACTAGTAGGCCTTTTTCTAGTA 59.872 44.000 25.02 10.68 46.50 1.82
2912 2972 6.683360 GCCACTAGTAGGCCTTTTTCTAGTAG 60.683 46.154 25.02 21.59 46.50 2.57
2913 2973 6.380560 CCACTAGTAGGCCTTTTTCTAGTAGT 59.619 42.308 25.02 19.20 45.88 2.73
2914 2974 7.407393 ACTAGTAGGCCTTTTTCTAGTAGTG 57.593 40.000 24.63 10.59 44.52 2.74
2920 2980 5.071923 AGGCCTTTTTCTAGTAGTGACTTGT 59.928 40.000 0.00 0.00 37.10 3.16
3248 3308 9.306777 AGAGTTGCATAATCTCATAGTCATAGA 57.693 33.333 0.00 0.00 0.00 1.98
3276 3336 8.454106 ACATGTATAAGTCATGAAGAAAGCAAC 58.546 33.333 11.92 0.00 43.47 4.17
3294 3354 4.084013 AGCAACAGCAACATACTAAACGAC 60.084 41.667 0.00 0.00 0.00 4.34
3297 3357 2.991190 CAGCAACATACTAAACGACCGT 59.009 45.455 0.00 0.00 0.00 4.83
3346 3409 9.716531 GTCAATCACATCATTCTCCTAATGATA 57.283 33.333 11.71 0.02 43.38 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
256 278 5.369187 GTTGCGAGATCACGAATCATATTG 58.631 41.667 17.02 0.00 36.79 1.90
590 614 5.343249 CATTCGAATCACCCATTCCTTTTC 58.657 41.667 7.92 0.00 38.17 2.29
707 731 7.933577 TCTGTTCATAAGAAGAAAGAGAAGCAA 59.066 33.333 0.00 0.00 33.63 3.91
801 825 9.696572 GACTATCCATATCCTATGTACCTAACA 57.303 37.037 0.00 0.00 43.86 2.41
859 883 6.322491 CCCTTTAGCAAAGAAAAATAGACGG 58.678 40.000 9.37 0.00 41.02 4.79
860 884 6.072119 ACCCCTTTAGCAAAGAAAAATAGACG 60.072 38.462 9.37 0.00 41.02 4.18
1335 1360 2.043604 GCCCCAAAGCCAAAGCAAGT 62.044 55.000 0.00 0.00 43.56 3.16
1434 1459 4.720902 TGCACCCCACGCTGGATG 62.721 66.667 5.71 5.20 40.96 3.51
1525 1555 4.141482 GGACACTAAGATGGAATAAGCCCA 60.141 45.833 0.00 0.00 38.19 5.36
1597 1627 5.736492 GCAGCGATACTACTGGAAAGTACAT 60.736 44.000 0.00 0.00 32.47 2.29
1721 1752 3.634397 TCTTGCTGAAAGTATCCCTGG 57.366 47.619 0.00 0.00 37.18 4.45
1947 1980 0.584396 CGGCGTACAAAAAGCTCACA 59.416 50.000 0.00 0.00 32.56 3.58
2198 2256 7.096477 CGAAAAACACCATCAGATTTCAAAGTC 60.096 37.037 0.00 0.00 0.00 3.01
2286 2344 1.885157 CGCCATGCCAAATGTGTCT 59.115 52.632 0.00 0.00 0.00 3.41
2814 2874 3.334891 TAATGGCGCACCCCTGGT 61.335 61.111 10.83 0.00 35.62 4.00
2815 2875 1.978455 TACTAATGGCGCACCCCTGG 61.978 60.000 10.83 0.00 33.59 4.45
2816 2876 0.108585 ATACTAATGGCGCACCCCTG 59.891 55.000 10.83 0.00 33.59 4.45
2817 2877 0.396811 GATACTAATGGCGCACCCCT 59.603 55.000 10.83 0.00 33.59 4.79
2818 2878 0.107831 TGATACTAATGGCGCACCCC 59.892 55.000 10.83 0.00 33.59 4.95
2819 2879 1.961793 TTGATACTAATGGCGCACCC 58.038 50.000 10.83 0.00 33.59 4.61
2820 2880 4.755123 AGTAATTGATACTAATGGCGCACC 59.245 41.667 10.83 0.00 43.16 5.01
2821 2881 5.924475 AGTAATTGATACTAATGGCGCAC 57.076 39.130 10.83 0.00 43.16 5.34
2822 2882 6.645003 CACTAGTAATTGATACTAATGGCGCA 59.355 38.462 10.83 0.00 44.50 6.09
2823 2883 7.050281 CACTAGTAATTGATACTAATGGCGC 57.950 40.000 0.00 0.00 44.50 6.53
2827 2887 6.645003 TGCGCCACTAGTAATTGATACTAATG 59.355 38.462 4.18 0.00 44.50 1.90
2828 2888 6.645415 GTGCGCCACTAGTAATTGATACTAAT 59.355 38.462 4.18 0.00 44.50 1.73
2829 2889 5.981315 GTGCGCCACTAGTAATTGATACTAA 59.019 40.000 4.18 0.00 44.50 2.24
2830 2890 5.508489 GGTGCGCCACTAGTAATTGATACTA 60.508 44.000 12.58 0.00 37.52 1.82
2831 2891 4.369182 GTGCGCCACTAGTAATTGATACT 58.631 43.478 4.18 0.00 46.62 2.12
2832 2892 3.493503 GGTGCGCCACTAGTAATTGATAC 59.506 47.826 12.58 0.00 34.40 2.24
2833 2893 3.133183 TGGTGCGCCACTAGTAATTGATA 59.867 43.478 16.89 0.00 40.46 2.15
2834 2894 2.093181 TGGTGCGCCACTAGTAATTGAT 60.093 45.455 16.89 0.00 40.46 2.57
2835 2895 1.276705 TGGTGCGCCACTAGTAATTGA 59.723 47.619 16.89 0.00 40.46 2.57
2836 2896 1.665679 CTGGTGCGCCACTAGTAATTG 59.334 52.381 16.89 0.00 40.46 2.32
2837 2897 2.024176 CTGGTGCGCCACTAGTAATT 57.976 50.000 16.89 0.00 40.46 1.40
2838 2898 3.760693 CTGGTGCGCCACTAGTAAT 57.239 52.632 16.89 0.00 40.46 1.89
2842 2902 0.458543 CACTACTGGTGCGCCACTAG 60.459 60.000 23.61 23.61 46.13 2.57
2843 2903 1.589630 CACTACTGGTGCGCCACTA 59.410 57.895 16.89 10.21 40.46 2.74
2844 2904 2.343758 CACTACTGGTGCGCCACT 59.656 61.111 16.89 9.49 40.46 4.00
2852 2912 0.902531 ACTAATGGCGCACTACTGGT 59.097 50.000 10.83 0.00 0.00 4.00
2853 2913 2.545952 CCTACTAATGGCGCACTACTGG 60.546 54.545 10.83 0.00 0.00 4.00
2854 2914 2.743938 CCTACTAATGGCGCACTACTG 58.256 52.381 10.83 0.00 0.00 2.74
2855 2915 1.068741 GCCTACTAATGGCGCACTACT 59.931 52.381 10.83 0.00 41.03 2.57
2856 2916 1.499049 GCCTACTAATGGCGCACTAC 58.501 55.000 10.83 0.00 41.03 2.73
2857 2917 3.980583 GCCTACTAATGGCGCACTA 57.019 52.632 10.83 0.00 41.03 2.74
2858 2918 4.857251 GCCTACTAATGGCGCACT 57.143 55.556 10.83 0.00 41.03 4.40
2864 2924 3.119495 GCACCAGTTTTGCCTACTAATGG 60.119 47.826 0.00 0.00 33.58 3.16
2865 2925 3.426159 CGCACCAGTTTTGCCTACTAATG 60.426 47.826 0.00 0.00 36.57 1.90
2866 2926 2.747446 CGCACCAGTTTTGCCTACTAAT 59.253 45.455 0.00 0.00 36.57 1.73
2867 2927 2.147958 CGCACCAGTTTTGCCTACTAA 58.852 47.619 0.00 0.00 36.57 2.24
2868 2928 1.803334 CGCACCAGTTTTGCCTACTA 58.197 50.000 0.00 0.00 36.57 1.82
2869 2929 1.515521 GCGCACCAGTTTTGCCTACT 61.516 55.000 0.30 0.00 36.57 2.57
2870 2930 1.081442 GCGCACCAGTTTTGCCTAC 60.081 57.895 0.30 0.00 36.57 3.18
2871 2931 2.265182 GGCGCACCAGTTTTGCCTA 61.265 57.895 10.83 0.00 42.44 3.93
2872 2932 3.605664 GGCGCACCAGTTTTGCCT 61.606 61.111 10.83 0.00 42.44 4.75
2873 2933 3.910490 TGGCGCACCAGTTTTGCC 61.910 61.111 10.83 0.00 42.67 4.52
2881 2941 3.014085 GCCTACTAGTGGCGCACCA 62.014 63.158 10.83 0.00 46.51 4.17
2882 2942 2.202892 GCCTACTAGTGGCGCACC 60.203 66.667 10.83 0.00 41.03 5.01
2888 2948 5.678955 ACTAGAAAAAGGCCTACTAGTGG 57.321 43.478 26.34 1.52 41.05 4.00
2889 2949 7.122353 TCACTACTAGAAAAAGGCCTACTAGTG 59.878 40.741 30.37 25.00 42.07 2.74
2890 2950 7.122501 GTCACTACTAGAAAAAGGCCTACTAGT 59.877 40.741 28.09 28.09 43.62 2.57
2891 2951 7.339976 AGTCACTACTAGAAAAAGGCCTACTAG 59.660 40.741 22.89 22.89 37.25 2.57
2892 2952 7.180663 AGTCACTACTAGAAAAAGGCCTACTA 58.819 38.462 5.16 7.18 32.84 1.82
2893 2953 6.017830 AGTCACTACTAGAAAAAGGCCTACT 58.982 40.000 5.16 6.30 32.84 2.57
2894 2954 6.283544 AGTCACTACTAGAAAAAGGCCTAC 57.716 41.667 5.16 0.00 32.84 3.18
2895 2955 6.269307 ACAAGTCACTACTAGAAAAAGGCCTA 59.731 38.462 5.16 0.00 33.75 3.93
2896 2956 5.071923 ACAAGTCACTACTAGAAAAAGGCCT 59.928 40.000 0.00 0.00 33.75 5.19
2897 2957 5.306394 ACAAGTCACTACTAGAAAAAGGCC 58.694 41.667 0.00 0.00 33.75 5.19
2898 2958 5.408909 GGACAAGTCACTACTAGAAAAAGGC 59.591 44.000 0.00 0.00 33.75 4.35
2899 2959 5.634020 CGGACAAGTCACTACTAGAAAAAGG 59.366 44.000 0.00 0.00 33.75 3.11
2900 2960 6.444633 TCGGACAAGTCACTACTAGAAAAAG 58.555 40.000 0.00 0.00 33.75 2.27
2901 2961 6.263842 TCTCGGACAAGTCACTACTAGAAAAA 59.736 38.462 0.00 0.00 33.75 1.94
2902 2962 5.766670 TCTCGGACAAGTCACTACTAGAAAA 59.233 40.000 0.00 0.00 33.75 2.29
2903 2963 5.311265 TCTCGGACAAGTCACTACTAGAAA 58.689 41.667 0.00 0.00 33.75 2.52
2904 2964 4.903054 TCTCGGACAAGTCACTACTAGAA 58.097 43.478 0.00 0.00 33.75 2.10
2905 2965 4.548451 TCTCGGACAAGTCACTACTAGA 57.452 45.455 0.00 0.00 33.75 2.43
2906 2966 5.502706 CGAATCTCGGACAAGTCACTACTAG 60.503 48.000 2.29 0.00 36.00 2.57
2907 2967 4.331992 CGAATCTCGGACAAGTCACTACTA 59.668 45.833 2.29 0.00 36.00 1.82
2908 2968 3.127203 CGAATCTCGGACAAGTCACTACT 59.873 47.826 2.29 0.00 36.00 2.57
2909 2969 3.126514 TCGAATCTCGGACAAGTCACTAC 59.873 47.826 2.29 0.00 40.88 2.73
2910 2970 3.340928 TCGAATCTCGGACAAGTCACTA 58.659 45.455 2.29 0.00 40.88 2.74
2911 2971 2.160205 TCGAATCTCGGACAAGTCACT 58.840 47.619 2.29 0.00 40.88 3.41
2912 2972 2.631418 TCGAATCTCGGACAAGTCAC 57.369 50.000 2.29 0.00 40.88 3.67
2913 2973 2.223272 CGATCGAATCTCGGACAAGTCA 60.223 50.000 10.26 0.00 40.88 3.41
2914 2974 2.223294 ACGATCGAATCTCGGACAAGTC 60.223 50.000 24.34 0.00 40.88 3.01
2920 2980 0.812811 ACCGACGATCGAATCTCGGA 60.813 55.000 36.54 0.36 44.97 4.55
3222 3282 9.306777 TCTATGACTATGAGATTATGCAACTCT 57.693 33.333 0.00 0.00 0.00 3.24
3248 3308 9.013229 TGCTTTCTTCATGACTTATACATGTTT 57.987 29.630 2.30 0.00 43.56 2.83
3276 3336 2.991190 ACGGTCGTTTAGTATGTTGCTG 59.009 45.455 0.00 0.00 0.00 4.41
3297 3357 2.568062 TGACCCATTCCGTTAGCTTACA 59.432 45.455 3.47 0.00 0.00 2.41
3346 3409 6.603201 AGTTGTCATTTGATTAACGGGATCAT 59.397 34.615 0.00 0.00 33.82 2.45


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

AutoCloner maintained by Alex Coulton.