Multiple sequence alignment - TraesCS4D01G085400

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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 TraesCS4D01G085400 chr4D 100.000 3188 0 0 1 3188 60132190 60135377 0.000000e+00 5888.0
1 TraesCS4D01G085400 chr4B 96.879 2884 67 7 1 2863 89302111 89304992 0.000000e+00 4806.0
2 TraesCS4D01G085400 chr4B 95.556 180 8 0 3006 3185 89304975 89305154 4.020000e-74 289.0
3 TraesCS4D01G085400 chr4B 90.517 116 10 1 2892 3007 510355435 510355549 5.510000e-33 152.0
4 TraesCS4D01G085400 chr4B 96.875 32 1 0 2471 2502 161553249 161553218 2.000000e-03 54.7
5 TraesCS4D01G085400 chr4B 96.875 32 1 0 2472 2503 656162614 656162645 2.000000e-03 54.7
6 TraesCS4D01G085400 chr4A 97.745 2395 41 7 1 2383 536199636 536197243 0.000000e+00 4111.0
7 TraesCS4D01G085400 chr3B 94.444 108 5 1 2896 3003 723457795 723457689 7.070000e-37 165.0
8 TraesCS4D01G085400 chr3B 90.435 115 11 0 2895 3009 729051765 729051879 5.510000e-33 152.0
9 TraesCS4D01G085400 chr6A 92.174 115 9 0 2895 3009 571932555 571932441 2.540000e-36 163.0
10 TraesCS4D01G085400 chr1B 92.857 112 7 1 2895 3006 595074513 595074623 9.150000e-36 161.0
11 TraesCS4D01G085400 chr7B 92.035 113 9 0 2895 3007 615783156 615783044 3.290000e-35 159.0
12 TraesCS4D01G085400 chr7B 91.071 112 7 2 2895 3006 145972249 145972357 7.120000e-32 148.0
13 TraesCS4D01G085400 chr5B 90.351 114 11 0 2895 3008 87712276 87712389 1.980000e-32 150.0
14 TraesCS4D01G085400 chr5B 96.875 32 1 0 2473 2504 564992408 564992377 2.000000e-03 54.7
15 TraesCS4D01G085400 chr3D 91.071 112 8 2 2895 3006 32590223 32590332 1.980000e-32 150.0
16 TraesCS4D01G085400 chr7D 97.059 34 1 0 2472 2505 103820625 103820592 1.240000e-04 58.4
17 TraesCS4D01G085400 chr5D 100.000 31 0 0 2472 2502 421173809 421173839 1.240000e-04 58.4
18 TraesCS4D01G085400 chr6D 100.000 30 0 0 2473 2502 342467204 342467233 4.440000e-04 56.5
19 TraesCS4D01G085400 chr6D 100.000 29 0 0 2471 2499 95294899 95294927 2.000000e-03 54.7
20 TraesCS4D01G085400 chr5A 96.875 32 1 0 2473 2504 326659580 326659549 2.000000e-03 54.7


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 TraesCS4D01G085400 chr4D 60132190 60135377 3187 False 5888.0 5888 100.0000 1 3188 1 chr4D.!!$F1 3187
1 TraesCS4D01G085400 chr4B 89302111 89305154 3043 False 2547.5 4806 96.2175 1 3185 2 chr4B.!!$F3 3184
2 TraesCS4D01G085400 chr4A 536197243 536199636 2393 True 4111.0 4111 97.7450 1 2383 1 chr4A.!!$R1 2382

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
776 794 0.254747 TTCCCCAAGTCATAAGGCCG 59.745 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 2414 0.034896 GAGACCGCAACAAAGGAGGA 59.965 55.0 0.0 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
163 164 7.834068 TCTCTCTATTGAAAACATCTTTCGG 57.166 36.000 0.00 0.00 0.00 4.30
278 279 8.012957 ACATCAACACCACCATTAAACTAAAA 57.987 30.769 0.00 0.00 0.00 1.52
286 287 6.780522 ACCACCATTAAACTAAAACCATGACT 59.219 34.615 0.00 0.00 0.00 3.41
446 447 1.559682 TGCTTCTCCTGGGAATGTACC 59.440 52.381 0.00 0.00 0.00 3.34
776 794 0.254747 TTCCCCAAGTCATAAGGCCG 59.745 55.000 0.00 0.00 0.00 6.13
2035 2056 0.631753 AGAGGATGGTCGGAAGGAGA 59.368 55.000 0.00 0.00 0.00 3.71
2308 2335 5.415701 TGCAAGGTTAATCATTCTGAAGGAC 59.584 40.000 6.93 0.00 0.00 3.85
2387 2414 5.993748 TGTTTCCTTTTGTTCTTTGGTCT 57.006 34.783 0.00 0.00 0.00 3.85
2412 2439 3.382227 TCCTTTGTTGCGGTCTCGATATA 59.618 43.478 0.00 0.00 39.00 0.86
2420 2447 2.223294 GCGGTCTCGATATATCCTTCCG 60.223 54.545 19.61 19.61 39.00 4.30
2460 2487 5.534207 TCTTTGCCATCATGTTTGAACTT 57.466 34.783 0.00 0.00 34.96 2.66
2462 2489 5.302568 TCTTTGCCATCATGTTTGAACTTCT 59.697 36.000 0.00 0.00 34.96 2.85
2543 2570 6.774673 TGTAACTTGGATGGATAGTGTTTCA 58.225 36.000 0.00 0.00 0.00 2.69
2547 2574 3.205338 TGGATGGATAGTGTTTCATGCG 58.795 45.455 0.00 0.00 31.92 4.73
2574 2601 3.993234 GCGATGCTCATGGCGACG 61.993 66.667 14.82 14.82 45.43 5.12
2614 2641 3.622826 AGCGTGGTACTTGCCGGT 61.623 61.111 1.90 0.00 0.00 5.28
2643 2670 2.754658 CGGGGGTGCTCGTCTACT 60.755 66.667 0.00 0.00 0.00 2.57
2685 2712 1.142748 GACCATGTGCTCTCCCTCG 59.857 63.158 0.00 0.00 0.00 4.63
2713 2740 2.173669 GCGGATGTGTGGTGGATCG 61.174 63.158 0.00 0.00 0.00 3.69
2821 2848 0.949105 CCTACGGCACAACACACCTC 60.949 60.000 0.00 0.00 0.00 3.85
2822 2849 1.282248 CTACGGCACAACACACCTCG 61.282 60.000 0.00 0.00 0.00 4.63
2827 2854 2.029073 ACAACACACCTCGAGCGG 59.971 61.111 6.99 3.25 0.00 5.52
2829 2856 3.923864 AACACACCTCGAGCGGCA 61.924 61.111 6.99 0.00 0.00 5.69
2843 2870 4.571250 GGCACGAATGACAGACGA 57.429 55.556 10.26 0.00 32.03 4.20
2863 2890 3.740115 GAGGTGAGAGTGGTTTAAAGCA 58.260 45.455 15.83 15.83 0.00 3.91
2864 2891 4.327680 GAGGTGAGAGTGGTTTAAAGCAT 58.672 43.478 21.88 11.65 38.81 3.79
2865 2892 4.729868 AGGTGAGAGTGGTTTAAAGCATT 58.270 39.130 21.88 18.11 38.81 3.56
2866 2893 5.140454 AGGTGAGAGTGGTTTAAAGCATTT 58.860 37.500 21.88 13.84 43.42 2.32
2867 2894 5.598417 AGGTGAGAGTGGTTTAAAGCATTTT 59.402 36.000 21.88 13.66 40.09 1.82
2868 2895 6.098266 AGGTGAGAGTGGTTTAAAGCATTTTT 59.902 34.615 21.88 10.97 40.09 1.94
2887 2914 3.918258 TTTTTCGATCCGCTGTTATCG 57.082 42.857 0.00 0.00 44.88 2.92
2889 2916 0.596600 TTCGATCCGCTGTTATCGGC 60.597 55.000 5.04 0.00 46.05 5.54
2890 2917 1.299850 CGATCCGCTGTTATCGGCA 60.300 57.895 5.49 0.00 46.05 5.69
2891 2918 0.667487 CGATCCGCTGTTATCGGCAT 60.667 55.000 5.49 0.00 46.05 4.40
2892 2919 1.512926 GATCCGCTGTTATCGGCATT 58.487 50.000 5.49 0.00 46.05 3.56
2893 2920 1.873591 GATCCGCTGTTATCGGCATTT 59.126 47.619 5.49 0.00 46.05 2.32
2894 2921 1.745232 TCCGCTGTTATCGGCATTTT 58.255 45.000 5.49 0.00 46.05 1.82
2895 2922 2.088423 TCCGCTGTTATCGGCATTTTT 58.912 42.857 5.49 0.00 46.05 1.94
2917 2944 7.552458 TTTTTCTCTTTCATTTCTTTTGGGC 57.448 32.000 0.00 0.00 0.00 5.36
2918 2945 4.503741 TCTCTTTCATTTCTTTTGGGCG 57.496 40.909 0.00 0.00 0.00 6.13
2919 2946 3.888930 TCTCTTTCATTTCTTTTGGGCGT 59.111 39.130 0.00 0.00 0.00 5.68
2920 2947 3.976169 TCTTTCATTTCTTTTGGGCGTG 58.024 40.909 0.00 0.00 0.00 5.34
2921 2948 3.634448 TCTTTCATTTCTTTTGGGCGTGA 59.366 39.130 0.00 0.00 0.00 4.35
2922 2949 3.363341 TTCATTTCTTTTGGGCGTGAC 57.637 42.857 0.00 0.00 0.00 3.67
2923 2950 2.582052 TCATTTCTTTTGGGCGTGACT 58.418 42.857 0.00 0.00 0.00 3.41
2924 2951 2.293122 TCATTTCTTTTGGGCGTGACTG 59.707 45.455 0.00 0.00 0.00 3.51
2925 2952 1.757682 TTTCTTTTGGGCGTGACTGT 58.242 45.000 0.00 0.00 0.00 3.55
2926 2953 1.021202 TTCTTTTGGGCGTGACTGTG 58.979 50.000 0.00 0.00 0.00 3.66
2927 2954 0.107410 TCTTTTGGGCGTGACTGTGT 60.107 50.000 0.00 0.00 0.00 3.72
2928 2955 0.738389 CTTTTGGGCGTGACTGTGTT 59.262 50.000 0.00 0.00 0.00 3.32
2929 2956 0.453793 TTTTGGGCGTGACTGTGTTG 59.546 50.000 0.00 0.00 0.00 3.33
2930 2957 1.999071 TTTGGGCGTGACTGTGTTGC 61.999 55.000 0.00 0.00 0.00 4.17
2931 2958 2.591715 GGGCGTGACTGTGTTGCT 60.592 61.111 0.00 0.00 0.00 3.91
2932 2959 2.186826 GGGCGTGACTGTGTTGCTT 61.187 57.895 0.00 0.00 0.00 3.91
2933 2960 1.724582 GGGCGTGACTGTGTTGCTTT 61.725 55.000 0.00 0.00 0.00 3.51
2934 2961 0.317020 GGCGTGACTGTGTTGCTTTC 60.317 55.000 0.00 0.00 0.00 2.62
2935 2962 0.376852 GCGTGACTGTGTTGCTTTCA 59.623 50.000 0.00 0.00 0.00 2.69
2936 2963 1.856014 GCGTGACTGTGTTGCTTTCAC 60.856 52.381 0.00 0.00 34.48 3.18
2937 2964 1.268032 CGTGACTGTGTTGCTTTCACC 60.268 52.381 0.00 0.00 34.33 4.02
2938 2965 1.065551 GTGACTGTGTTGCTTTCACCC 59.934 52.381 0.00 0.00 35.25 4.61
2939 2966 0.668535 GACTGTGTTGCTTTCACCCC 59.331 55.000 0.00 0.00 35.25 4.95
2940 2967 0.033601 ACTGTGTTGCTTTCACCCCA 60.034 50.000 0.00 0.00 35.25 4.96
2941 2968 1.110442 CTGTGTTGCTTTCACCCCAA 58.890 50.000 0.00 0.00 35.25 4.12
2942 2969 0.820871 TGTGTTGCTTTCACCCCAAC 59.179 50.000 0.00 0.00 39.32 3.77
2943 2970 0.820871 GTGTTGCTTTCACCCCAACA 59.179 50.000 1.70 1.70 44.46 3.33
2944 2971 0.820871 TGTTGCTTTCACCCCAACAC 59.179 50.000 1.70 0.00 42.56 3.32
2945 2972 1.111277 GTTGCTTTCACCCCAACACT 58.889 50.000 0.00 0.00 38.85 3.55
2946 2973 1.480545 GTTGCTTTCACCCCAACACTT 59.519 47.619 0.00 0.00 38.85 3.16
2947 2974 2.691011 GTTGCTTTCACCCCAACACTTA 59.309 45.455 0.00 0.00 38.85 2.24
2948 2975 3.237268 TGCTTTCACCCCAACACTTAT 57.763 42.857 0.00 0.00 0.00 1.73
2949 2976 3.153919 TGCTTTCACCCCAACACTTATC 58.846 45.455 0.00 0.00 0.00 1.75
2950 2977 2.161609 GCTTTCACCCCAACACTTATCG 59.838 50.000 0.00 0.00 0.00 2.92
2951 2978 3.408634 CTTTCACCCCAACACTTATCGT 58.591 45.455 0.00 0.00 0.00 3.73
2952 2979 3.495434 TTCACCCCAACACTTATCGTT 57.505 42.857 0.00 0.00 0.00 3.85
2953 2980 2.773487 TCACCCCAACACTTATCGTTG 58.227 47.619 0.00 0.00 42.73 4.10
2961 2988 5.018695 CAACACTTATCGTTGGTTGTCTC 57.981 43.478 0.00 0.00 40.05 3.36
2962 2989 3.314553 ACACTTATCGTTGGTTGTCTCG 58.685 45.455 0.00 0.00 0.00 4.04
2963 2990 2.666508 CACTTATCGTTGGTTGTCTCGG 59.333 50.000 0.00 0.00 0.00 4.63
2964 2991 2.559668 ACTTATCGTTGGTTGTCTCGGA 59.440 45.455 0.00 0.00 0.00 4.55
2965 2992 3.194968 ACTTATCGTTGGTTGTCTCGGAT 59.805 43.478 0.00 0.00 0.00 4.18
2966 2993 2.010145 ATCGTTGGTTGTCTCGGATG 57.990 50.000 0.00 0.00 0.00 3.51
2967 2994 0.037697 TCGTTGGTTGTCTCGGATGG 60.038 55.000 0.00 0.00 0.00 3.51
2968 2995 0.320421 CGTTGGTTGTCTCGGATGGT 60.320 55.000 0.00 0.00 0.00 3.55
2969 2996 1.876416 CGTTGGTTGTCTCGGATGGTT 60.876 52.381 0.00 0.00 0.00 3.67
2970 2997 1.535462 GTTGGTTGTCTCGGATGGTTG 59.465 52.381 0.00 0.00 0.00 3.77
2971 2998 0.605319 TGGTTGTCTCGGATGGTTGC 60.605 55.000 0.00 0.00 0.00 4.17
2972 2999 0.321653 GGTTGTCTCGGATGGTTGCT 60.322 55.000 0.00 0.00 0.00 3.91
2973 3000 1.523758 GTTGTCTCGGATGGTTGCTT 58.476 50.000 0.00 0.00 0.00 3.91
2974 3001 1.880027 GTTGTCTCGGATGGTTGCTTT 59.120 47.619 0.00 0.00 0.00 3.51
2975 3002 1.522668 TGTCTCGGATGGTTGCTTTG 58.477 50.000 0.00 0.00 0.00 2.77
2976 3003 1.202758 TGTCTCGGATGGTTGCTTTGT 60.203 47.619 0.00 0.00 0.00 2.83
2977 3004 2.037902 TGTCTCGGATGGTTGCTTTGTA 59.962 45.455 0.00 0.00 0.00 2.41
2978 3005 3.071479 GTCTCGGATGGTTGCTTTGTAA 58.929 45.455 0.00 0.00 0.00 2.41
2979 3006 3.689649 GTCTCGGATGGTTGCTTTGTAAT 59.310 43.478 0.00 0.00 0.00 1.89
2980 3007 4.873827 GTCTCGGATGGTTGCTTTGTAATA 59.126 41.667 0.00 0.00 0.00 0.98
2981 3008 5.527582 GTCTCGGATGGTTGCTTTGTAATAT 59.472 40.000 0.00 0.00 0.00 1.28
2982 3009 6.704493 GTCTCGGATGGTTGCTTTGTAATATA 59.296 38.462 0.00 0.00 0.00 0.86
2983 3010 7.225931 GTCTCGGATGGTTGCTTTGTAATATAA 59.774 37.037 0.00 0.00 0.00 0.98
2984 3011 7.771361 TCTCGGATGGTTGCTTTGTAATATAAA 59.229 33.333 0.00 0.00 0.00 1.40
2985 3012 7.925993 TCGGATGGTTGCTTTGTAATATAAAG 58.074 34.615 5.31 5.31 38.00 1.85
3012 3039 3.748083 GGAAACCCCTTTTCGTTAGAGT 58.252 45.455 0.00 0.00 44.20 3.24
3013 3040 3.501062 GGAAACCCCTTTTCGTTAGAGTG 59.499 47.826 0.00 0.00 44.20 3.51
3014 3041 2.853235 ACCCCTTTTCGTTAGAGTGG 57.147 50.000 0.00 0.00 0.00 4.00
3015 3042 2.052468 ACCCCTTTTCGTTAGAGTGGT 58.948 47.619 0.00 0.00 0.00 4.16
3016 3043 2.440627 ACCCCTTTTCGTTAGAGTGGTT 59.559 45.455 0.00 0.00 0.00 3.67
3017 3044 3.117776 ACCCCTTTTCGTTAGAGTGGTTT 60.118 43.478 0.00 0.00 0.00 3.27
3018 3045 4.102996 ACCCCTTTTCGTTAGAGTGGTTTA 59.897 41.667 0.00 0.00 0.00 2.01
3019 3046 5.065235 CCCCTTTTCGTTAGAGTGGTTTAA 58.935 41.667 0.00 0.00 0.00 1.52
3020 3047 5.532032 CCCCTTTTCGTTAGAGTGGTTTAAA 59.468 40.000 0.00 0.00 0.00 1.52
3021 3048 6.293790 CCCCTTTTCGTTAGAGTGGTTTAAAG 60.294 42.308 0.00 0.00 0.00 1.85
3022 3049 6.140786 CCTTTTCGTTAGAGTGGTTTAAAGC 58.859 40.000 10.47 10.47 0.00 3.51
3103 3130 1.024271 GCACAGAGAGCCACAAACAA 58.976 50.000 0.00 0.00 0.00 2.83
3105 3132 1.334869 CACAGAGAGCCACAAACAACC 59.665 52.381 0.00 0.00 0.00 3.77
3134 3161 0.824109 GTCGGTGATGGTGGAGATCA 59.176 55.000 0.00 0.00 0.00 2.92
3163 3190 1.918957 AGGATGAGGGAGTTTGAAGGG 59.081 52.381 0.00 0.00 0.00 3.95
3167 3194 0.038310 GAGGGAGTTTGAAGGGTGGG 59.962 60.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 6.997239 AAGTGTTAGGTTCGATAATTTCCC 57.003 37.500 0.00 0.00 0.00 3.97
278 279 1.555075 ACAACGCCTCATAGTCATGGT 59.445 47.619 0.00 0.00 32.61 3.55
286 287 1.407712 GGGGCTTTACAACGCCTCATA 60.408 52.381 9.09 0.00 46.21 2.15
446 447 1.802365 GCACGGTTAACCCACACTTAG 59.198 52.381 19.09 4.79 0.00 2.18
1065 1086 0.609131 CCGTGGAAGCCTTGTTGGAT 60.609 55.000 0.00 0.00 38.35 3.41
1570 1591 2.040544 CGTGATCTTGTGGTGGGGC 61.041 63.158 0.00 0.00 0.00 5.80
2190 2211 7.034967 ACTCCTACATACTAATAGCTAGGCT 57.965 40.000 0.00 0.00 43.41 4.58
2200 2221 8.946085 CATTGCAAAAGAACTCCTACATACTAA 58.054 33.333 1.71 0.00 0.00 2.24
2308 2335 1.081892 CAGCTGAATGAAGACACGGG 58.918 55.000 8.42 0.00 0.00 5.28
2387 2414 0.034896 GAGACCGCAACAAAGGAGGA 59.965 55.000 0.00 0.00 0.00 3.71
2420 2447 1.602377 AGAACACAAAACACGCTAGGC 59.398 47.619 0.00 0.00 0.00 3.93
2460 2487 7.993758 CGGAGGGAGTATATATGATCACTTAGA 59.006 40.741 0.00 0.00 0.00 2.10
2462 2489 7.640313 ACGGAGGGAGTATATATGATCACTTA 58.360 38.462 0.00 0.00 0.00 2.24
2558 2585 3.993234 GCGTCGCCATGAGCATCG 61.993 66.667 5.75 5.14 44.04 3.84
2581 2608 2.738521 CTGACCACCGCGAGTTGG 60.739 66.667 8.23 13.94 0.00 3.77
2589 2616 2.430382 AAGTACCACGCTGACCACCG 62.430 60.000 0.00 0.00 0.00 4.94
2665 2692 2.592308 GGGAGAGCACATGGTCCC 59.408 66.667 7.44 8.36 43.11 4.46
2685 2712 2.158959 CACATCCGCCTTCGTCGAC 61.159 63.158 5.18 5.18 0.00 4.20
2732 2759 1.860078 GCACGGAACAACTTCCTCG 59.140 57.895 0.00 0.00 43.73 4.63
2774 2801 1.560923 CCTCTCCAAGTATCGCAACG 58.439 55.000 0.00 0.00 0.00 4.10
2821 2848 2.792290 CTGTCATTCGTGCCGCTCG 61.792 63.158 8.51 8.51 0.00 5.03
2822 2849 1.446099 TCTGTCATTCGTGCCGCTC 60.446 57.895 0.00 0.00 0.00 5.03
2827 2854 0.388649 ACCTCGTCTGTCATTCGTGC 60.389 55.000 0.00 0.00 0.00 5.34
2829 2856 1.200252 CTCACCTCGTCTGTCATTCGT 59.800 52.381 0.00 0.00 0.00 3.85
2840 2867 3.802675 GCTTTAAACCACTCTCACCTCGT 60.803 47.826 0.00 0.00 0.00 4.18
2843 2870 3.857157 TGCTTTAAACCACTCTCACCT 57.143 42.857 0.00 0.00 0.00 4.00
2867 2894 3.918258 CGATAACAGCGGATCGAAAAA 57.082 42.857 2.46 0.00 46.19 1.94
2893 2920 6.257630 CGCCCAAAAGAAATGAAAGAGAAAAA 59.742 34.615 0.00 0.00 0.00 1.94
2894 2921 5.752955 CGCCCAAAAGAAATGAAAGAGAAAA 59.247 36.000 0.00 0.00 0.00 2.29
2895 2922 5.163457 ACGCCCAAAAGAAATGAAAGAGAAA 60.163 36.000 0.00 0.00 0.00 2.52
2896 2923 4.340950 ACGCCCAAAAGAAATGAAAGAGAA 59.659 37.500 0.00 0.00 0.00 2.87
2897 2924 3.888930 ACGCCCAAAAGAAATGAAAGAGA 59.111 39.130 0.00 0.00 0.00 3.10
2898 2925 3.983344 CACGCCCAAAAGAAATGAAAGAG 59.017 43.478 0.00 0.00 0.00 2.85
2899 2926 3.634448 TCACGCCCAAAAGAAATGAAAGA 59.366 39.130 0.00 0.00 0.00 2.52
2900 2927 3.735746 GTCACGCCCAAAAGAAATGAAAG 59.264 43.478 0.00 0.00 0.00 2.62
2901 2928 3.383185 AGTCACGCCCAAAAGAAATGAAA 59.617 39.130 0.00 0.00 0.00 2.69
2902 2929 2.955660 AGTCACGCCCAAAAGAAATGAA 59.044 40.909 0.00 0.00 0.00 2.57
2903 2930 2.293122 CAGTCACGCCCAAAAGAAATGA 59.707 45.455 0.00 0.00 0.00 2.57
2904 2931 2.034558 ACAGTCACGCCCAAAAGAAATG 59.965 45.455 0.00 0.00 0.00 2.32
2905 2932 2.034558 CACAGTCACGCCCAAAAGAAAT 59.965 45.455 0.00 0.00 0.00 2.17
2906 2933 1.403679 CACAGTCACGCCCAAAAGAAA 59.596 47.619 0.00 0.00 0.00 2.52
2907 2934 1.021202 CACAGTCACGCCCAAAAGAA 58.979 50.000 0.00 0.00 0.00 2.52
2908 2935 0.107410 ACACAGTCACGCCCAAAAGA 60.107 50.000 0.00 0.00 0.00 2.52
2909 2936 0.738389 AACACAGTCACGCCCAAAAG 59.262 50.000 0.00 0.00 0.00 2.27
2910 2937 0.453793 CAACACAGTCACGCCCAAAA 59.546 50.000 0.00 0.00 0.00 2.44
2911 2938 1.999071 GCAACACAGTCACGCCCAAA 61.999 55.000 0.00 0.00 0.00 3.28
2912 2939 2.477176 GCAACACAGTCACGCCCAA 61.477 57.895 0.00 0.00 0.00 4.12
2913 2940 2.884997 AAGCAACACAGTCACGCCCA 62.885 55.000 0.00 0.00 0.00 5.36
2914 2941 1.724582 AAAGCAACACAGTCACGCCC 61.725 55.000 0.00 0.00 0.00 6.13
2915 2942 0.317020 GAAAGCAACACAGTCACGCC 60.317 55.000 0.00 0.00 0.00 5.68
2916 2943 0.376852 TGAAAGCAACACAGTCACGC 59.623 50.000 0.00 0.00 0.00 5.34
2917 2944 1.268032 GGTGAAAGCAACACAGTCACG 60.268 52.381 0.00 0.00 39.58 4.35
2918 2945 1.065551 GGGTGAAAGCAACACAGTCAC 59.934 52.381 0.00 0.00 39.65 3.67
2919 2946 1.388547 GGGTGAAAGCAACACAGTCA 58.611 50.000 0.00 0.00 39.65 3.41
2920 2947 0.668535 GGGGTGAAAGCAACACAGTC 59.331 55.000 0.00 0.00 34.41 3.51
2921 2948 0.033601 TGGGGTGAAAGCAACACAGT 60.034 50.000 0.00 0.00 41.06 3.55
2922 2949 2.805897 TGGGGTGAAAGCAACACAG 58.194 52.632 0.00 0.00 41.06 3.66
2923 2950 0.820871 GTTGGGGTGAAAGCAACACA 59.179 50.000 0.00 0.00 45.15 3.72
2924 2951 0.820871 TGTTGGGGTGAAAGCAACAC 59.179 50.000 0.00 0.00 35.01 3.32
2925 2952 0.820871 GTGTTGGGGTGAAAGCAACA 59.179 50.000 0.00 0.00 34.77 3.33
2926 2953 1.111277 AGTGTTGGGGTGAAAGCAAC 58.889 50.000 0.00 0.00 34.77 4.17
2927 2954 1.859302 AAGTGTTGGGGTGAAAGCAA 58.141 45.000 0.00 0.00 34.77 3.91
2928 2955 2.738587 TAAGTGTTGGGGTGAAAGCA 57.261 45.000 0.00 0.00 34.77 3.91
2929 2956 2.161609 CGATAAGTGTTGGGGTGAAAGC 59.838 50.000 0.00 0.00 0.00 3.51
2930 2957 3.408634 ACGATAAGTGTTGGGGTGAAAG 58.591 45.455 0.00 0.00 0.00 2.62
2931 2958 3.495434 ACGATAAGTGTTGGGGTGAAA 57.505 42.857 0.00 0.00 0.00 2.69
2932 2959 3.142951 CAACGATAAGTGTTGGGGTGAA 58.857 45.455 0.00 0.00 42.27 3.18
2933 2960 2.773487 CAACGATAAGTGTTGGGGTGA 58.227 47.619 0.00 0.00 42.27 4.02
2939 2966 4.376008 CGAGACAACCAACGATAAGTGTTG 60.376 45.833 0.00 0.00 44.86 3.33
2940 2967 3.739300 CGAGACAACCAACGATAAGTGTT 59.261 43.478 0.00 0.00 0.00 3.32
2941 2968 3.314553 CGAGACAACCAACGATAAGTGT 58.685 45.455 0.00 0.00 0.00 3.55
2942 2969 2.666508 CCGAGACAACCAACGATAAGTG 59.333 50.000 0.00 0.00 0.00 3.16
2943 2970 2.559668 TCCGAGACAACCAACGATAAGT 59.440 45.455 0.00 0.00 0.00 2.24
2944 2971 3.226346 TCCGAGACAACCAACGATAAG 57.774 47.619 0.00 0.00 0.00 1.73
2945 2972 3.517602 CATCCGAGACAACCAACGATAA 58.482 45.455 0.00 0.00 0.00 1.75
2946 2973 2.159156 CCATCCGAGACAACCAACGATA 60.159 50.000 0.00 0.00 0.00 2.92
2947 2974 1.405526 CCATCCGAGACAACCAACGAT 60.406 52.381 0.00 0.00 0.00 3.73
2948 2975 0.037697 CCATCCGAGACAACCAACGA 60.038 55.000 0.00 0.00 0.00 3.85
2949 2976 0.320421 ACCATCCGAGACAACCAACG 60.320 55.000 0.00 0.00 0.00 4.10
2950 2977 1.535462 CAACCATCCGAGACAACCAAC 59.465 52.381 0.00 0.00 0.00 3.77
2951 2978 1.890876 CAACCATCCGAGACAACCAA 58.109 50.000 0.00 0.00 0.00 3.67
2952 2979 0.605319 GCAACCATCCGAGACAACCA 60.605 55.000 0.00 0.00 0.00 3.67
2953 2980 0.321653 AGCAACCATCCGAGACAACC 60.322 55.000 0.00 0.00 0.00 3.77
2954 2981 1.523758 AAGCAACCATCCGAGACAAC 58.476 50.000 0.00 0.00 0.00 3.32
2955 2982 1.879380 CAAAGCAACCATCCGAGACAA 59.121 47.619 0.00 0.00 0.00 3.18
2956 2983 1.202758 ACAAAGCAACCATCCGAGACA 60.203 47.619 0.00 0.00 0.00 3.41
2957 2984 1.523758 ACAAAGCAACCATCCGAGAC 58.476 50.000 0.00 0.00 0.00 3.36
2958 2985 3.410631 TTACAAAGCAACCATCCGAGA 57.589 42.857 0.00 0.00 0.00 4.04
2959 2986 7.490962 TTATATTACAAAGCAACCATCCGAG 57.509 36.000 0.00 0.00 0.00 4.63
2960 2987 7.867305 TTTATATTACAAAGCAACCATCCGA 57.133 32.000 0.00 0.00 0.00 4.55
2991 3018 3.501062 CACTCTAACGAAAAGGGGTTTCC 59.499 47.826 0.00 0.00 42.39 3.13
2992 3019 3.501062 CCACTCTAACGAAAAGGGGTTTC 59.499 47.826 0.00 0.00 42.01 2.78
2993 3020 3.117776 ACCACTCTAACGAAAAGGGGTTT 60.118 43.478 0.00 0.00 44.48 3.27
2994 3021 2.440627 ACCACTCTAACGAAAAGGGGTT 59.559 45.455 0.00 0.00 44.48 4.11
2995 3022 2.052468 ACCACTCTAACGAAAAGGGGT 58.948 47.619 0.00 0.00 42.05 4.95
2996 3023 2.853235 ACCACTCTAACGAAAAGGGG 57.147 50.000 0.00 0.00 39.62 4.79
2997 3024 6.622833 TTTAAACCACTCTAACGAAAAGGG 57.377 37.500 0.00 0.00 0.00 3.95
2998 3025 6.140786 GCTTTAAACCACTCTAACGAAAAGG 58.859 40.000 0.00 0.00 0.00 3.11
2999 3026 6.140786 GGCTTTAAACCACTCTAACGAAAAG 58.859 40.000 0.00 0.00 0.00 2.27
3000 3027 5.589452 TGGCTTTAAACCACTCTAACGAAAA 59.411 36.000 5.67 0.00 30.29 2.29
3001 3028 5.124645 TGGCTTTAAACCACTCTAACGAAA 58.875 37.500 5.67 0.00 30.29 3.46
3002 3029 4.706035 TGGCTTTAAACCACTCTAACGAA 58.294 39.130 5.67 0.00 30.29 3.85
3003 3030 4.339872 TGGCTTTAAACCACTCTAACGA 57.660 40.909 5.67 0.00 30.29 3.85
3004 3031 4.693566 TGATGGCTTTAAACCACTCTAACG 59.306 41.667 10.47 0.00 40.82 3.18
3005 3032 5.123979 CCTGATGGCTTTAAACCACTCTAAC 59.876 44.000 10.47 2.63 40.82 2.34
3006 3033 5.253330 CCTGATGGCTTTAAACCACTCTAA 58.747 41.667 10.47 0.00 40.82 2.10
3007 3034 4.324254 CCCTGATGGCTTTAAACCACTCTA 60.324 45.833 10.47 0.66 40.82 2.43
3008 3035 3.562176 CCCTGATGGCTTTAAACCACTCT 60.562 47.826 10.47 0.00 40.82 3.24
3009 3036 2.755103 CCCTGATGGCTTTAAACCACTC 59.245 50.000 10.47 9.92 40.82 3.51
3010 3037 2.557452 CCCCTGATGGCTTTAAACCACT 60.557 50.000 10.47 3.11 40.82 4.00
3011 3038 1.824852 CCCCTGATGGCTTTAAACCAC 59.175 52.381 10.47 6.90 40.82 4.16
3012 3039 1.431243 ACCCCTGATGGCTTTAAACCA 59.569 47.619 10.61 10.61 42.61 3.67
3013 3040 2.231716 ACCCCTGATGGCTTTAAACC 57.768 50.000 0.00 0.00 0.00 3.27
3014 3041 2.233676 CCAACCCCTGATGGCTTTAAAC 59.766 50.000 0.00 0.00 0.00 2.01
3015 3042 2.158234 ACCAACCCCTGATGGCTTTAAA 60.158 45.455 0.00 0.00 40.51 1.52
3016 3043 1.431243 ACCAACCCCTGATGGCTTTAA 59.569 47.619 0.00 0.00 40.51 1.52
3017 3044 1.080638 ACCAACCCCTGATGGCTTTA 58.919 50.000 0.00 0.00 40.51 1.85
3018 3045 0.542702 CACCAACCCCTGATGGCTTT 60.543 55.000 0.00 0.00 40.51 3.51
3019 3046 1.077265 CACCAACCCCTGATGGCTT 59.923 57.895 0.00 0.00 40.51 4.35
3020 3047 2.765969 CACCAACCCCTGATGGCT 59.234 61.111 0.00 0.00 40.51 4.75
3021 3048 2.362889 CCACCAACCCCTGATGGC 60.363 66.667 0.00 0.00 40.51 4.40
3022 3049 1.304282 CTCCACCAACCCCTGATGG 59.696 63.158 0.00 0.00 42.60 3.51
3120 3147 2.677902 GCTTTCGTGATCTCCACCATCA 60.678 50.000 0.00 0.00 42.76 3.07
3134 3161 0.970937 TCCCTCATCCTCGCTTTCGT 60.971 55.000 0.00 0.00 36.96 3.85
3137 3164 1.280457 AACTCCCTCATCCTCGCTTT 58.720 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.