Multiple sequence alignment - TraesCS2A01G118100

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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 TraesCS2A01G118100 chr2A 100.000 2888 0 0 1 2888 68811442 68814329 0.000000e+00 5334
1 TraesCS2A01G118100 chr2A 82.606 1972 287 34 2 1948 68503883 68505823 0.000000e+00 1690
2 TraesCS2A01G118100 chr2A 91.667 96 6 2 2783 2876 716179064 716179159 6.490000e-27 132
3 TraesCS2A01G118100 chr2D 92.475 2804 163 26 2 2786 65719000 65716226 0.000000e+00 3965
4 TraesCS2A01G118100 chr2D 82.971 1979 283 32 2 1955 66462784 66460835 0.000000e+00 1738
5 TraesCS2A01G118100 chr2B 91.438 2441 153 27 2 2411 105372543 105374958 0.000000e+00 3299
6 TraesCS2A01G118100 chr2B 82.716 2025 279 40 2 2004 104894305 104896280 0.000000e+00 1735
7 TraesCS2A01G118100 chr2B 88.920 352 39 0 2431 2782 105379004 105379355 4.420000e-118 435
8 TraesCS2A01G118100 chr2B 93.407 91 6 0 2777 2867 785893174 785893264 5.020000e-28 135
9 TraesCS2A01G118100 chrUn 94.505 91 4 1 2777 2867 320348002 320348091 3.880000e-29 139
10 TraesCS2A01G118100 chr5A 94.505 91 4 1 2783 2873 45001837 45001926 3.880000e-29 139
11 TraesCS2A01G118100 chr5A 87.719 114 11 3 2759 2871 7109616 7109727 2.340000e-26 130
12 TraesCS2A01G118100 chr3D 91.262 103 7 2 2774 2875 32010715 32010614 3.880000e-29 139
13 TraesCS2A01G118100 chr3B 94.253 87 5 0 2783 2869 52751929 52751843 1.810000e-27 134
14 TraesCS2A01G118100 chr6A 93.258 89 6 0 2783 2871 600459474 600459386 6.490000e-27 132
15 TraesCS2A01G118100 chr1A 92.473 93 5 2 2775 2867 90157097 90157187 6.490000e-27 132


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 TraesCS2A01G118100 chr2A 68811442 68814329 2887 False 5334 5334 100.000 1 2888 1 chr2A.!!$F2 2887
1 TraesCS2A01G118100 chr2A 68503883 68505823 1940 False 1690 1690 82.606 2 1948 1 chr2A.!!$F1 1946
2 TraesCS2A01G118100 chr2D 65716226 65719000 2774 True 3965 3965 92.475 2 2786 1 chr2D.!!$R1 2784
3 TraesCS2A01G118100 chr2D 66460835 66462784 1949 True 1738 1738 82.971 2 1955 1 chr2D.!!$R2 1953
4 TraesCS2A01G118100 chr2B 105372543 105374958 2415 False 3299 3299 91.438 2 2411 1 chr2B.!!$F2 2409
5 TraesCS2A01G118100 chr2B 104894305 104896280 1975 False 1735 1735 82.716 2 2004 1 chr2B.!!$F1 2002

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
241 243 0.390472 CTTGAACTCGTCTCTGGGGC 60.390 60.0 0.0 0.0 0.0 5.80 F
1719 1734 0.249398 ACGATGTTTTCTCCTCCCCG 59.751 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1875 2.048877 CGGTGCGGGTAGTCGTTT 60.049 61.111 0.00 0.0 0.00 3.60 R
2605 2652 0.760572 AATGGTTTTGGCTTGCAGCT 59.239 45.000 7.85 0.0 41.99 4.24 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
28 29 1.136305 GGCGTGGAGTTATGAGTAGCA 59.864 52.381 0.00 0.00 0.00 3.49
48 49 8.960591 AGTAGCACAAAATGACAGCTATATTTT 58.039 29.630 8.22 8.22 39.65 1.82
74 75 2.779755 ACGAATTGATGTAGCCACCA 57.220 45.000 0.00 0.00 0.00 4.17
98 99 4.441356 CGACCAAAATCCCCAACAATATGG 60.441 45.833 0.00 0.00 40.35 2.74
109 110 4.338118 CCCAACAATATGGACAAATAGCGT 59.662 41.667 0.00 0.00 43.54 5.07
113 114 5.376625 ACAATATGGACAAATAGCGTGGAT 58.623 37.500 0.00 0.00 0.00 3.41
120 122 2.979678 ACAAATAGCGTGGATAGGGGAT 59.020 45.455 0.00 0.00 0.00 3.85
131 133 5.825679 CGTGGATAGGGGATGACAAATAAAA 59.174 40.000 0.00 0.00 0.00 1.52
193 195 3.329520 TGCACCCAGACTACCAAGTTTAT 59.670 43.478 0.00 0.00 35.56 1.40
200 202 6.038271 CCCAGACTACCAAGTTTATGCAATAC 59.962 42.308 0.00 0.00 35.56 1.89
231 233 3.061006 GCATTTTGCAACACTTGAACTCG 60.061 43.478 0.00 0.00 44.26 4.18
241 243 0.390472 CTTGAACTCGTCTCTGGGGC 60.390 60.000 0.00 0.00 0.00 5.80
288 292 9.934521 ACCTAGCCCAAAGGTGTTATTTATGGG 62.935 44.444 3.56 3.56 45.78 4.00
289 293 3.133901 GCCCAAAGGTGTTATTTATGGGG 59.866 47.826 9.77 0.00 44.95 4.96
296 301 6.645884 AGGTGTTATTTATGGGGTTAGACA 57.354 37.500 0.00 0.00 0.00 3.41
402 407 7.105588 TGCACAACTCATCTTATCACATTAGT 58.894 34.615 0.00 0.00 0.00 2.24
425 430 1.069358 CGGACAAATAGCTCCTCCCTC 59.931 57.143 0.00 0.00 0.00 4.30
475 480 3.933861 AAACCCTCACACAAAGTCTCT 57.066 42.857 0.00 0.00 0.00 3.10
640 646 2.808761 TAGCACCGCACCCCCTAGAA 62.809 60.000 0.00 0.00 0.00 2.10
642 648 2.203877 ACCGCACCCCCTAGAACA 60.204 61.111 0.00 0.00 0.00 3.18
661 667 5.836898 AGAACAATATATACCCACAGTCGGA 59.163 40.000 0.00 0.00 0.00 4.55
664 670 7.406031 ACAATATATACCCACAGTCGGATAG 57.594 40.000 0.00 0.00 0.00 2.08
696 702 2.890808 TCTCTCCATACATCGCAACC 57.109 50.000 0.00 0.00 0.00 3.77
755 763 1.822990 CATTCATTCACAGCCTTGGCT 59.177 47.619 8.56 8.56 0.00 4.75
835 845 1.633432 ACAACCATGGCCTAGCTACAA 59.367 47.619 13.04 0.00 0.00 2.41
849 859 6.090129 CCTAGCTACAAATAATCTCGAGAGC 58.910 44.000 21.52 14.53 0.00 4.09
854 864 7.010923 AGCTACAAATAATCTCGAGAGCTTTTG 59.989 37.037 27.73 27.73 34.15 2.44
880 890 4.569228 CCAAATCATCCCCCATATCCTCAG 60.569 50.000 0.00 0.00 0.00 3.35
890 902 5.537674 CCCCCATATCCTCAGAAAAATTCAG 59.462 44.000 0.00 0.00 0.00 3.02
911 924 3.388350 AGAACCATGGCCTAGCTACTAAC 59.612 47.826 13.04 0.00 0.00 2.34
920 933 4.527038 GGCCTAGCTACTAACATGTCCATA 59.473 45.833 0.00 0.00 0.00 2.74
967 982 4.518970 TGTTAATCTGTTGGAGAGTTTGCC 59.481 41.667 0.00 0.00 32.80 4.52
1065 1080 1.137086 GTCACATACCAGCTGACCGAT 59.863 52.381 17.39 0.00 0.00 4.18
1197 1212 4.408821 GACTGGACGGCATGCCCA 62.409 66.667 30.79 21.08 0.00 5.36
1399 1414 3.825160 GAGTTGTGGCTGCACCCGA 62.825 63.158 0.50 0.00 37.83 5.14
1719 1734 0.249398 ACGATGTTTTCTCCTCCCCG 59.751 55.000 0.00 0.00 0.00 5.73
1721 1736 0.909623 GATGTTTTCTCCTCCCCGGA 59.090 55.000 0.73 0.00 40.30 5.14
1762 1783 2.282674 CTGCTGCCACCACCATGT 60.283 61.111 0.00 0.00 0.00 3.21
1842 1875 2.025155 GATGACGAAGACTCCCTGCTA 58.975 52.381 0.00 0.00 0.00 3.49
1866 1899 0.683504 ACTACCCGCACCGAGATCTT 60.684 55.000 0.00 0.00 0.00 2.40
1904 1937 2.419324 GCTAGGTATCCGAGGTATGACG 59.581 54.545 0.00 0.00 0.00 4.35
1924 1957 5.009710 TGACGATGAATTAATCTCTAGCCGT 59.990 40.000 1.21 0.00 0.00 5.68
1956 1989 1.410882 GATCCTGGAGCTAGTGTCACC 59.589 57.143 4.35 0.00 0.00 4.02
2048 2086 6.801539 ACATATTTATAGGTTGCATGTCGG 57.198 37.500 0.00 0.00 0.00 4.79
2049 2087 6.296026 ACATATTTATAGGTTGCATGTCGGT 58.704 36.000 0.00 0.00 0.00 4.69
2055 2094 0.393808 GGTTGCATGTCGGTATGGGT 60.394 55.000 0.00 0.00 0.00 4.51
2079 2118 2.118732 TGGCGGTGGTCAGTCCTA 59.881 61.111 0.00 0.00 37.07 2.94
2082 2121 0.035739 GGCGGTGGTCAGTCCTAAAA 59.964 55.000 0.00 0.00 37.07 1.52
2105 2144 7.618964 AAAACGTGTCTATATGTGTATAGCG 57.381 36.000 0.00 0.00 39.65 4.26
2255 2300 8.263940 TCCTTAAGCGCATATATATGGTTTTC 57.736 34.615 21.50 6.14 34.32 2.29
2385 2431 2.095919 CCGCTTTGTTTGGTAGTGCTAC 60.096 50.000 0.95 0.95 35.40 3.58
2386 2432 2.411031 CGCTTTGTTTGGTAGTGCTACG 60.411 50.000 3.61 0.00 36.94 3.51
2389 2435 3.688694 TTGTTTGGTAGTGCTACGGAT 57.311 42.857 3.61 0.00 36.94 4.18
2454 2501 2.871096 TAGGAAAAAGGCCGACATGT 57.129 45.000 0.00 0.00 0.00 3.21
2466 2513 2.864343 GCCGACATGTCATAGTAACCAC 59.136 50.000 24.93 0.00 0.00 4.16
2494 2541 7.761038 AAATAAAGACGAAAGAGGTTGGATT 57.239 32.000 0.00 0.00 0.00 3.01
2498 2545 4.461198 AGACGAAAGAGGTTGGATTTGTT 58.539 39.130 0.00 0.00 0.00 2.83
2503 2550 5.458779 CGAAAGAGGTTGGATTTGTTTGTTC 59.541 40.000 0.00 0.00 0.00 3.18
2504 2551 4.568152 AGAGGTTGGATTTGTTTGTTCG 57.432 40.909 0.00 0.00 0.00 3.95
2507 2554 3.120041 GGTTGGATTTGTTTGTTCGTGG 58.880 45.455 0.00 0.00 0.00 4.94
2520 2567 3.937814 TGTTCGTGGAAATACAGCTCAT 58.062 40.909 0.00 0.00 0.00 2.90
2550 2597 9.515020 TCATTTTCTATGCGGTGAAATAAATTC 57.485 29.630 0.00 0.00 38.60 2.17
2575 2622 3.243737 CGACCCGGTCTGATAAATCATCA 60.244 47.826 15.70 0.00 41.52 3.07
2605 2652 9.762381 ATAAATAGGAAACCTTGGTTTCATGTA 57.238 29.630 32.96 24.26 43.12 2.29
2631 2678 5.241662 TGCAAGCCAAAACCATTAAATACC 58.758 37.500 0.00 0.00 0.00 2.73
2634 2681 5.414789 AGCCAAAACCATTAAATACCACC 57.585 39.130 0.00 0.00 0.00 4.61
2658 2705 2.818274 GTGGAAACGCCTAGGCCG 60.818 66.667 28.09 23.32 37.98 6.13
2698 2745 3.074412 TCGAGGCCAAACAAAATCTCTC 58.926 45.455 5.01 0.00 0.00 3.20
2711 2758 5.104193 ACAAAATCTCTCTCATGCCATACCT 60.104 40.000 0.00 0.00 0.00 3.08
2713 2760 6.753913 AAATCTCTCTCATGCCATACCTAA 57.246 37.500 0.00 0.00 0.00 2.69
2717 2764 1.139989 CTCATGCCATACCTAACGCG 58.860 55.000 3.53 3.53 0.00 6.01
2718 2765 0.747852 TCATGCCATACCTAACGCGA 59.252 50.000 15.93 0.00 0.00 5.87
2731 2778 6.920569 ACCTAACGCGATAGATGAAAATTT 57.079 33.333 23.26 0.00 39.76 1.82
2734 2781 7.493320 ACCTAACGCGATAGATGAAAATTTGTA 59.507 33.333 23.26 0.00 39.76 2.41
2766 2813 4.345257 TGCCTATAGAAACCATGTCTCTCC 59.655 45.833 0.00 0.00 0.00 3.71
2786 2833 7.663905 TCTCTCCAGATGCTAAATCTAGTACTC 59.336 40.741 0.00 0.00 0.00 2.59
2787 2834 6.717540 TCTCCAGATGCTAAATCTAGTACTCC 59.282 42.308 0.00 0.00 0.00 3.85
2788 2835 5.775701 TCCAGATGCTAAATCTAGTACTCCC 59.224 44.000 0.00 0.00 0.00 4.30
2789 2836 5.777732 CCAGATGCTAAATCTAGTACTCCCT 59.222 44.000 0.00 0.00 0.00 4.20
2790 2837 6.071616 CCAGATGCTAAATCTAGTACTCCCTC 60.072 46.154 0.00 0.00 0.00 4.30
2791 2838 6.014012 AGATGCTAAATCTAGTACTCCCTCC 58.986 44.000 0.00 0.00 0.00 4.30
2792 2839 4.142790 TGCTAAATCTAGTACTCCCTCCG 58.857 47.826 0.00 0.00 0.00 4.63
2793 2840 4.143543 GCTAAATCTAGTACTCCCTCCGT 58.856 47.826 0.00 0.00 0.00 4.69
2794 2841 4.216042 GCTAAATCTAGTACTCCCTCCGTC 59.784 50.000 0.00 0.00 0.00 4.79
2795 2842 4.523168 AAATCTAGTACTCCCTCCGTCT 57.477 45.455 0.00 0.00 0.00 4.18
2796 2843 3.775261 ATCTAGTACTCCCTCCGTCTC 57.225 52.381 0.00 0.00 0.00 3.36
2797 2844 2.475155 TCTAGTACTCCCTCCGTCTCA 58.525 52.381 0.00 0.00 0.00 3.27
2798 2845 2.842496 TCTAGTACTCCCTCCGTCTCAA 59.158 50.000 0.00 0.00 0.00 3.02
2799 2846 2.599408 AGTACTCCCTCCGTCTCAAA 57.401 50.000 0.00 0.00 0.00 2.69
2800 2847 2.885616 AGTACTCCCTCCGTCTCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
2801 2848 3.442076 AGTACTCCCTCCGTCTCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
2802 2849 4.607239 AGTACTCCCTCCGTCTCAAAATA 58.393 43.478 0.00 0.00 0.00 1.40
2803 2850 5.209659 AGTACTCCCTCCGTCTCAAAATAT 58.790 41.667 0.00 0.00 0.00 1.28
2804 2851 6.371278 AGTACTCCCTCCGTCTCAAAATATA 58.629 40.000 0.00 0.00 0.00 0.86
2805 2852 6.837568 AGTACTCCCTCCGTCTCAAAATATAA 59.162 38.462 0.00 0.00 0.00 0.98
2806 2853 6.163135 ACTCCCTCCGTCTCAAAATATAAG 57.837 41.667 0.00 0.00 0.00 1.73
2807 2854 5.897824 ACTCCCTCCGTCTCAAAATATAAGA 59.102 40.000 0.00 0.00 0.00 2.10
2808 2855 6.383147 ACTCCCTCCGTCTCAAAATATAAGAA 59.617 38.462 0.00 0.00 0.00 2.52
2809 2856 6.579865 TCCCTCCGTCTCAAAATATAAGAAC 58.420 40.000 0.00 0.00 0.00 3.01
2810 2857 5.462398 CCCTCCGTCTCAAAATATAAGAACG 59.538 44.000 0.00 0.00 0.00 3.95
2811 2858 6.040878 CCTCCGTCTCAAAATATAAGAACGT 58.959 40.000 0.00 0.00 0.00 3.99
2812 2859 6.534079 CCTCCGTCTCAAAATATAAGAACGTT 59.466 38.462 0.00 0.00 0.00 3.99
2813 2860 7.064253 CCTCCGTCTCAAAATATAAGAACGTTT 59.936 37.037 0.46 0.00 0.00 3.60
2814 2861 8.314143 TCCGTCTCAAAATATAAGAACGTTTT 57.686 30.769 0.46 0.00 0.00 2.43
2815 2862 8.776470 TCCGTCTCAAAATATAAGAACGTTTTT 58.224 29.630 9.22 9.22 0.00 1.94
2843 2890 6.756221 ACTATCCTAGTGTCAAAAACGTTCT 58.244 36.000 0.00 0.00 37.69 3.01
2844 2891 7.215085 ACTATCCTAGTGTCAAAAACGTTCTT 58.785 34.615 0.00 0.00 37.69 2.52
2845 2892 8.362639 ACTATCCTAGTGTCAAAAACGTTCTTA 58.637 33.333 0.00 0.00 37.69 2.10
2846 2893 9.367444 CTATCCTAGTGTCAAAAACGTTCTTAT 57.633 33.333 0.00 0.00 0.00 1.73
2848 2895 9.886132 ATCCTAGTGTCAAAAACGTTCTTATAT 57.114 29.630 0.00 0.00 0.00 0.86
2849 2896 9.715121 TCCTAGTGTCAAAAACGTTCTTATATT 57.285 29.630 0.00 0.00 0.00 1.28
2850 2897 9.968743 CCTAGTGTCAAAAACGTTCTTATATTC 57.031 33.333 0.00 0.00 0.00 1.75
2853 2900 9.268268 AGTGTCAAAAACGTTCTTATATTCTGA 57.732 29.630 0.00 0.00 0.00 3.27
2854 2901 9.530129 GTGTCAAAAACGTTCTTATATTCTGAG 57.470 33.333 0.00 0.00 0.00 3.35
2855 2902 9.483916 TGTCAAAAACGTTCTTATATTCTGAGA 57.516 29.630 0.00 0.00 0.00 3.27
2856 2903 9.742552 GTCAAAAACGTTCTTATATTCTGAGAC 57.257 33.333 0.00 0.00 0.00 3.36
2857 2904 9.483916 TCAAAAACGTTCTTATATTCTGAGACA 57.516 29.630 0.00 0.00 0.00 3.41
2858 2905 9.746711 CAAAAACGTTCTTATATTCTGAGACAG 57.253 33.333 0.00 0.00 0.00 3.51
2859 2906 9.706691 AAAAACGTTCTTATATTCTGAGACAGA 57.293 29.630 0.00 0.00 38.87 3.41
2860 2907 8.918961 AAACGTTCTTATATTCTGAGACAGAG 57.081 34.615 0.00 0.00 41.75 3.35
2861 2908 7.033530 ACGTTCTTATATTCTGAGACAGAGG 57.966 40.000 0.00 0.00 41.75 3.69
2862 2909 6.829298 ACGTTCTTATATTCTGAGACAGAGGA 59.171 38.462 0.00 0.00 41.75 3.71
2863 2910 7.339721 ACGTTCTTATATTCTGAGACAGAGGAA 59.660 37.037 0.00 0.00 41.75 3.36
2864 2911 7.860373 CGTTCTTATATTCTGAGACAGAGGAAG 59.140 40.741 0.00 0.00 41.75 3.46
2865 2912 8.691797 GTTCTTATATTCTGAGACAGAGGAAGT 58.308 37.037 0.00 0.00 41.75 3.01
2866 2913 9.922477 TTCTTATATTCTGAGACAGAGGAAGTA 57.078 33.333 0.00 0.00 41.75 2.24
2867 2914 9.344772 TCTTATATTCTGAGACAGAGGAAGTAC 57.655 37.037 0.00 0.00 41.75 2.73
2868 2915 9.349713 CTTATATTCTGAGACAGAGGAAGTACT 57.650 37.037 0.00 0.00 41.75 2.73
2871 2918 9.875708 ATATTCTGAGACAGAGGAAGTACTATT 57.124 33.333 0.00 0.00 41.75 1.73
2872 2919 7.397892 TTCTGAGACAGAGGAAGTACTATTG 57.602 40.000 0.00 0.00 41.75 1.90
2873 2920 6.722328 TCTGAGACAGAGGAAGTACTATTGA 58.278 40.000 0.00 0.00 35.39 2.57
2874 2921 7.175797 TCTGAGACAGAGGAAGTACTATTGAA 58.824 38.462 0.00 0.00 35.39 2.69
2875 2922 7.836685 TCTGAGACAGAGGAAGTACTATTGAAT 59.163 37.037 0.00 0.00 35.39 2.57
2876 2923 8.367660 TGAGACAGAGGAAGTACTATTGAATT 57.632 34.615 0.00 0.00 0.00 2.17
2877 2924 8.816894 TGAGACAGAGGAAGTACTATTGAATTT 58.183 33.333 0.00 0.00 0.00 1.82
2878 2925 9.308318 GAGACAGAGGAAGTACTATTGAATTTC 57.692 37.037 0.00 0.00 0.00 2.17
2879 2926 9.041354 AGACAGAGGAAGTACTATTGAATTTCT 57.959 33.333 0.00 0.00 0.00 2.52
2880 2927 9.660180 GACAGAGGAAGTACTATTGAATTTCTT 57.340 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.646267 ACTCATAACTCCACGCCTAAAATAA 58.354 36.000 0.00 0.00 0.00 1.40
48 49 6.375377 GTGGCTACATCAATTCGTAAACAAA 58.625 36.000 0.00 0.00 0.00 2.83
69 70 1.248101 GGGGATTTTGGTCGTGGTGG 61.248 60.000 0.00 0.00 0.00 4.61
74 75 2.074729 TTGTTGGGGATTTTGGTCGT 57.925 45.000 0.00 0.00 0.00 4.34
98 99 2.367567 TCCCCTATCCACGCTATTTGTC 59.632 50.000 0.00 0.00 0.00 3.18
109 110 8.064389 TGAATTTTATTTGTCATCCCCTATCCA 58.936 33.333 0.00 0.00 0.00 3.41
131 133 5.039645 TCCTCTCCTCCTGGTTAATTGAAT 58.960 41.667 0.00 0.00 34.23 2.57
178 180 5.293569 GCGTATTGCATAAACTTGGTAGTCT 59.706 40.000 0.00 0.00 45.45 3.24
227 229 4.680537 ACGGCCCCAGAGACGAGT 62.681 66.667 0.00 0.00 0.00 4.18
231 233 3.775654 CCTCACGGCCCCAGAGAC 61.776 72.222 13.68 0.00 0.00 3.36
241 243 1.616865 TCAACAGTAACTCCCTCACGG 59.383 52.381 0.00 0.00 0.00 4.94
288 292 3.118542 ACACGAGTCGTTTTGTCTAACC 58.881 45.455 17.16 0.00 38.32 2.85
289 293 4.380974 CCTACACGAGTCGTTTTGTCTAAC 59.619 45.833 17.16 0.00 38.32 2.34
296 301 1.494824 GTGCCTACACGAGTCGTTTT 58.505 50.000 17.16 8.66 38.32 2.43
324 329 4.292178 GCCATCTCGAGCGAGGGG 62.292 72.222 18.57 19.33 42.20 4.79
348 353 4.724293 TGGGTGTTCATGTATCCCTTGATA 59.276 41.667 13.58 0.00 38.95 2.15
350 355 2.916269 TGGGTGTTCATGTATCCCTTGA 59.084 45.455 13.58 0.00 38.95 3.02
402 407 2.897969 GGGAGGAGCTATTTGTCCGATA 59.102 50.000 0.00 0.00 37.97 2.92
425 430 2.333926 TCTATCTTGTTTCGTGGTGCG 58.666 47.619 0.00 0.00 43.01 5.34
445 450 8.557450 ACTTTGTGTGAGGGTTTAGGATATTAT 58.443 33.333 0.00 0.00 0.00 1.28
446 451 7.924541 ACTTTGTGTGAGGGTTTAGGATATTA 58.075 34.615 0.00 0.00 0.00 0.98
447 452 6.790319 ACTTTGTGTGAGGGTTTAGGATATT 58.210 36.000 0.00 0.00 0.00 1.28
456 461 3.933861 AAGAGACTTTGTGTGAGGGTT 57.066 42.857 0.00 0.00 0.00 4.11
475 480 0.783850 CCCTTCCTCCCCTTGGAAAA 59.216 55.000 0.00 0.00 42.29 2.29
591 597 1.138069 TGAGTCGGCTGTTTTGTCTCA 59.862 47.619 0.00 0.00 0.00 3.27
640 646 7.122353 GTCTATCCGACTGTGGGTATATATTGT 59.878 40.741 8.75 0.00 39.61 2.71
642 648 6.318144 CGTCTATCCGACTGTGGGTATATATT 59.682 42.308 8.75 0.00 40.59 1.28
661 667 3.505680 GGAGAGATGTGATCTGCGTCTAT 59.494 47.826 10.95 8.90 40.38 1.98
664 670 1.406898 TGGAGAGATGTGATCTGCGTC 59.593 52.381 0.00 0.00 40.38 5.19
777 786 7.313731 AGGATGGGATGGTTTAGACTAAGATA 58.686 38.462 0.00 0.00 0.00 1.98
835 845 5.119694 GGACCAAAAGCTCTCGAGATTATT 58.880 41.667 17.03 8.27 35.80 1.40
849 859 2.501316 GGGGGATGATTTGGACCAAAAG 59.499 50.000 23.11 0.00 36.90 2.27
854 864 3.564352 GGATATGGGGGATGATTTGGACC 60.564 52.174 0.00 0.00 0.00 4.46
880 890 4.541973 AGGCCATGGTTCTGAATTTTTC 57.458 40.909 14.67 0.00 0.00 2.29
890 902 3.134081 TGTTAGTAGCTAGGCCATGGTTC 59.866 47.826 14.67 6.36 0.00 3.62
987 1002 2.367202 TTCCATGGCCGTCCTCCTC 61.367 63.158 6.96 0.00 0.00 3.71
1842 1875 2.048877 CGGTGCGGGTAGTCGTTT 60.049 61.111 0.00 0.00 0.00 3.60
1866 1899 4.283467 ACCTAGCGCATAAAGTCCATGATA 59.717 41.667 11.47 0.00 0.00 2.15
1904 1937 4.859798 CGGACGGCTAGAGATTAATTCATC 59.140 45.833 0.00 0.00 0.00 2.92
1984 2017 4.111016 CACAGCAGGCACGCATGG 62.111 66.667 5.77 0.00 0.00 3.66
2022 2055 8.227791 CCGACATGCAACCTATAAATATGTAAC 58.772 37.037 0.00 0.00 0.00 2.50
2082 2121 6.732154 ACGCTATACACATATAGACACGTTT 58.268 36.000 5.68 0.00 42.06 3.60
2089 2128 6.008331 ACCAGGAACGCTATACACATATAGA 58.992 40.000 0.00 0.00 42.06 1.98
2105 2144 5.873164 ACGACACTTATTTATGACCAGGAAC 59.127 40.000 0.00 0.00 0.00 3.62
2194 2235 7.513371 TTTACCCGACTGATAAAACAACAAT 57.487 32.000 0.00 0.00 0.00 2.71
2255 2300 4.013267 ACCAAGGAGACATTGAGTTCAG 57.987 45.455 0.00 0.00 0.00 3.02
2362 2408 1.335496 GCACTACCAAACAAAGCGGAA 59.665 47.619 0.00 0.00 0.00 4.30
2385 2431 8.820933 CAAACATATACATGCTCCTTATATCCG 58.179 37.037 0.00 0.00 35.39 4.18
2386 2432 9.890629 TCAAACATATACATGCTCCTTATATCC 57.109 33.333 0.00 0.00 35.39 2.59
2389 2435 9.710900 CACTCAAACATATACATGCTCCTTATA 57.289 33.333 0.00 0.00 35.39 0.98
2426 2472 6.764560 TGTCGGCCTTTTTCCTATAGAAATAC 59.235 38.462 0.00 0.00 43.93 1.89
2439 2486 3.686016 ACTATGACATGTCGGCCTTTTT 58.314 40.909 20.54 1.40 0.00 1.94
2466 2513 8.726988 TCCAACCTCTTTCGTCTTTATTTATTG 58.273 33.333 0.00 0.00 0.00 1.90
2484 2531 4.041723 CACGAACAAACAAATCCAACCTC 58.958 43.478 0.00 0.00 0.00 3.85
2494 2541 4.336993 AGCTGTATTTCCACGAACAAACAA 59.663 37.500 0.00 0.00 0.00 2.83
2498 2545 3.734463 TGAGCTGTATTTCCACGAACAA 58.266 40.909 0.00 0.00 0.00 2.83
2520 2567 4.400529 TCACCGCATAGAAAATGAGCTA 57.599 40.909 0.00 0.00 0.00 3.32
2550 2597 4.806869 TGATTTATCAGACCGGGTCGGAG 61.807 52.174 28.98 19.51 39.74 4.63
2556 2603 4.960938 TCTTGATGATTTATCAGACCGGG 58.039 43.478 6.32 0.00 46.01 5.73
2605 2652 0.760572 AATGGTTTTGGCTTGCAGCT 59.239 45.000 7.85 0.00 41.99 4.24
2631 2678 3.817960 CGTTTCCACGTTTGAGGTG 57.182 52.632 0.00 0.00 41.84 4.00
2658 2705 7.011857 GGCCTCGATTATTCATATGGAAATCTC 59.988 40.741 16.55 6.72 39.39 2.75
2698 2745 1.139989 CGCGTTAGGTATGGCATGAG 58.860 55.000 10.98 0.00 0.00 2.90
2766 2813 6.071616 GGAGGGAGTACTAGATTTAGCATCTG 60.072 46.154 0.00 0.00 0.00 2.90
2786 2833 5.462398 CGTTCTTATATTTTGAGACGGAGGG 59.538 44.000 0.00 0.00 0.00 4.30
2787 2834 6.040878 ACGTTCTTATATTTTGAGACGGAGG 58.959 40.000 0.00 0.00 0.00 4.30
2788 2835 7.521509 AACGTTCTTATATTTTGAGACGGAG 57.478 36.000 0.00 0.00 0.00 4.63
2789 2836 7.894376 AAACGTTCTTATATTTTGAGACGGA 57.106 32.000 0.00 0.00 0.00 4.69
2790 2837 8.944212 AAAAACGTTCTTATATTTTGAGACGG 57.056 30.769 0.00 0.00 0.00 4.79
2820 2867 7.653767 AAGAACGTTTTTGACACTAGGATAG 57.346 36.000 0.46 0.00 46.50 2.08
2822 2869 9.886132 ATATAAGAACGTTTTTGACACTAGGAT 57.114 29.630 13.87 0.00 0.00 3.24
2823 2870 9.715121 AATATAAGAACGTTTTTGACACTAGGA 57.285 29.630 13.87 0.00 0.00 2.94
2824 2871 9.968743 GAATATAAGAACGTTTTTGACACTAGG 57.031 33.333 13.87 0.00 0.00 3.02
2827 2874 9.268268 TCAGAATATAAGAACGTTTTTGACACT 57.732 29.630 13.87 4.79 0.00 3.55
2828 2875 9.530129 CTCAGAATATAAGAACGTTTTTGACAC 57.470 33.333 13.87 2.84 0.00 3.67
2829 2876 9.483916 TCTCAGAATATAAGAACGTTTTTGACA 57.516 29.630 13.87 0.01 0.00 3.58
2830 2877 9.742552 GTCTCAGAATATAAGAACGTTTTTGAC 57.257 33.333 13.87 5.89 0.00 3.18
2831 2878 9.483916 TGTCTCAGAATATAAGAACGTTTTTGA 57.516 29.630 13.87 2.81 0.00 2.69
2832 2879 9.746711 CTGTCTCAGAATATAAGAACGTTTTTG 57.253 33.333 13.87 0.00 32.44 2.44
2833 2880 9.706691 TCTGTCTCAGAATATAAGAACGTTTTT 57.293 29.630 9.22 9.22 37.57 1.94
2834 2881 9.360093 CTCTGTCTCAGAATATAAGAACGTTTT 57.640 33.333 0.46 0.00 40.18 2.43
2835 2882 7.976734 CCTCTGTCTCAGAATATAAGAACGTTT 59.023 37.037 0.46 0.00 40.18 3.60
2836 2883 7.339721 TCCTCTGTCTCAGAATATAAGAACGTT 59.660 37.037 0.00 0.00 40.18 3.99
2837 2884 6.829298 TCCTCTGTCTCAGAATATAAGAACGT 59.171 38.462 1.22 0.00 40.18 3.99
2838 2885 7.265647 TCCTCTGTCTCAGAATATAAGAACG 57.734 40.000 1.22 0.00 40.18 3.95
2839 2886 8.691797 ACTTCCTCTGTCTCAGAATATAAGAAC 58.308 37.037 1.22 0.00 40.18 3.01
2840 2887 8.830915 ACTTCCTCTGTCTCAGAATATAAGAA 57.169 34.615 1.22 0.00 40.18 2.52
2841 2888 9.344772 GTACTTCCTCTGTCTCAGAATATAAGA 57.655 37.037 1.22 0.00 40.18 2.10
2842 2889 9.349713 AGTACTTCCTCTGTCTCAGAATATAAG 57.650 37.037 0.00 5.25 40.18 1.73
2845 2892 9.875708 AATAGTACTTCCTCTGTCTCAGAATAT 57.124 33.333 0.00 0.00 40.18 1.28
2846 2893 9.126151 CAATAGTACTTCCTCTGTCTCAGAATA 57.874 37.037 0.00 0.00 40.18 1.75
2847 2894 7.836685 TCAATAGTACTTCCTCTGTCTCAGAAT 59.163 37.037 0.00 0.00 40.18 2.40
2848 2895 7.175797 TCAATAGTACTTCCTCTGTCTCAGAA 58.824 38.462 0.00 0.00 40.18 3.02
2849 2896 6.722328 TCAATAGTACTTCCTCTGTCTCAGA 58.278 40.000 0.00 0.00 38.25 3.27
2850 2897 7.397892 TTCAATAGTACTTCCTCTGTCTCAG 57.602 40.000 0.00 0.00 0.00 3.35
2851 2898 7.962995 ATTCAATAGTACTTCCTCTGTCTCA 57.037 36.000 0.00 0.00 0.00 3.27
2852 2899 9.308318 GAAATTCAATAGTACTTCCTCTGTCTC 57.692 37.037 0.00 0.00 0.00 3.36
2853 2900 9.041354 AGAAATTCAATAGTACTTCCTCTGTCT 57.959 33.333 0.00 0.00 0.00 3.41
2854 2901 9.660180 AAGAAATTCAATAGTACTTCCTCTGTC 57.340 33.333 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.