position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.012409_2025-05-16.012409_IdvjkC/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title Main -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.012409_2025-05-16.012409_IdvjkC/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab Citation: van Helden, et al. (2000). Nucleic Acids Res 28, 1000-1010. Sequence file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.012409_2025-05-16.012409_IdvjkC/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.012409_2025-05-16.012409_IdvjkC/results/composition/peak-motifs_ctrl_profiles-1str-ovlp_2nt_ci20.tab Oligo length 2 Occurrences counted on a single strands Conditions of applicability checked. Background model estimation: homogeneous repartition Sequence statistics: Nb of sequences 79 Sum of sequence lengths 25775 Min sequence length 0 Max sequence length 1000 Average sequence length 326 Possible positions 25696 Sequences: # length ID 1 1000 ChrE_C_glabrata_CBS138_bPeak_1 2 1000 ChrE_C_glabrata_CBS138_bPeak_2 3 351 ChrE_C_glabrata_CBS138_bPeak_3 4 201 ChrE_C_glabrata_CBS138_bPeak_4 5 301 ChrE_C_glabrata_CBS138_bPeak_5 6 151 ChrE_C_glabrata_CBS138_bPeak_6 7 651 ChrG_C_glabrata_CBS138_bPeak_1 8 201 ChrG_C_glabrata_CBS138_bPeak_2 9 551 ChrG_C_glabrata_CBS138_bPeak_3 10 301 ChrG_C_glabrata_CBS138_bPeak_4 11 401 ChrG_C_glabrata_CBS138_bPeak_5 12 151 ChrG_C_glabrata_CBS138_bPeak_6 13 1000 ChrD_C_glabrata_CBS138_bPeak_1 14 401 ChrD_C_glabrata_CBS138_bPeak_2 15 501 ChrD_C_glabrata_CBS138_bPeak_3 16 301 ChrD_C_glabrata_CBS138_bPeak_4 17 251 ChrD_C_glabrata_CBS138_bPeak_5 18 201 ChrD_C_glabrata_CBS138_bPeak_6 19 651 ChrC_C_glabrata_CBS138_bPeak_1 20 201 ChrC_C_glabrata_CBS138_bPeak_2 21 951 ChrI_C_glabrata_CBS138_bPeak_1 22 801 ChrI_C_glabrata_CBS138_bPeak_2 23 451 ChrI_C_glabrata_CBS138_bPeak_3 24 601 ChrI_C_glabrata_CBS138_bPeak_4 25 501 ChrI_C_glabrata_CBS138_bPeak_5 26 201 ChrI_C_glabrata_CBS138_bPeak_6 27 351 ChrI_C_glabrata_CBS138_bPeak_7 28 401 ChrI_C_glabrata_CBS138_bPeak_8 29 151 ChrI_C_glabrata_CBS138_bPeak_9 30 251 ChrI_C_glabrata_CBS138_bPeak_10 31 751 ChrF_C_glabrata_CBS138_bPeak_1 32 351 ChrF_C_glabrata_CBS138_bPeak_2 33 251 ChrF_C_glabrata_CBS138_bPeak_3 34 251 ChrF_C_glabrata_CBS138_bPeak_4 35 151 ChrF_C_glabrata_CBS138_bPeak_5 36 351 ChrF_C_glabrata_CBS138_bPeak_6 37 1000 ChrK_C_glabrata_CBS138_bPeak_1 38 201 ChrK_C_glabrata_CBS138_bPeak_2 39 201 ChrK_C_glabrata_CBS138_bPeak_3 40 451 ChrK_C_glabrata_CBS138_bPeak_4 41 251 ChrK_C_glabrata_CBS138_bPeak_5 42 201 ChrK_C_glabrata_CBS138_bPeak_6 43 251 ChrK_C_glabrata_CBS138_bPeak_7 44 301 ChrK_C_glabrata_CBS138_bPeak_8 45 201 ChrK_C_glabrata_CBS138_bPeak_9 46 151 ChrK_C_glabrata_CBS138_bPeak_10 47 151 ChrK_C_glabrata_CBS138_bPeak_11 48 201 ChrK_C_glabrata_CBS138_bPeak_12 49 151 ChrK_C_glabrata_CBS138_bPeak_13 50 151 ChrK_C_glabrata_CBS138_bPeak_14 51 201 ChrK_C_glabrata_CBS138_bPeak_15 52 151 ChrK_C_glabrata_CBS138_bPeak_16 53 151 ChrK_C_glabrata_CBS138_bPeak_17 54 151 ChrK_C_glabrata_CBS138_bPeak_18 55 151 ChrK_C_glabrata_CBS138_bPeak_19 56 201 ChrK_C_glabrata_CBS138_bPeak_20 57 201 ChrK_C_glabrata_CBS138_bPeak_21 58 151 ChrK_C_glabrata_CBS138_bPeak_22 59 151 ChrK_C_glabrata_CBS138_bPeak_23 60 451 ChrH_C_glabrata_CBS138_bPeak_1 61 251 ChrH_C_glabrata_CBS138_bPeak_2 62 251 ChrH_C_glabrata_CBS138_bPeak_3 63 601 ChrJ_C_glabrata_CBS138_bPeak_1 64 201 ChrJ_C_glabrata_CBS138_bPeak_2 65 201 ChrJ_C_glabrata_CBS138_bPeak_3 66 351 ChrL_C_glabrata_CBS138_bPeak_1 67 251 ChrL_C_glabrata_CBS138_bPeak_2 68 201 ChrL_C_glabrata_CBS138_bPeak_3 69 201 ChrL_C_glabrata_CBS138_bPeak_4 70 251 ChrL_C_glabrata_CBS138_bPeak_5 71 151 ChrL_C_glabrata_CBS138_bPeak_6 72 151 ChrB_C_glabrata_CBS138_bPeak_1 73 151 ChrB_C_glabrata_CBS138_bPeak_2 74 251 ChrB_C_glabrata_CBS138_bPeak_3 75 201 ChrB_C_glabrata_CBS138_bPeak_4 76 151 mito_C_glabrata_CBS138_bPeaks_1 77 151 ChrA_C_glabrata_CBS138_bPeak_1 78 151 ChrA_C_glabrata_CBS138_bPeak_2 79 301 ChrM_C_glabrata_CBS138_bPeaks_1 Oligonucleotide statistics: Total occurrences 25405 Position interval parameters: Position interval 20 Number of windows 50 Total positions 25696 Degrees of freedom 49 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -25 [-499,-480] -489.5 4 80 2 -24 [-479,-460] -469.5 5 96 3 -23 [-459,-440] -449.5 5 100 4 -22 [-439,-420] -429.5 5 100 5 -21 [-419,-400] -409.5 6 101 6 -20 [-399,-380] -389.5 6 120 7 -19 [-379,-360] -369.5 7 136 8 -18 [-359,-340] -349.5 7 140 9 -17 [-339,-320] -329.5 9 152 10 -16 [-319,-300] -309.5 11 182 11 -15 [-299,-280] -289.5 11 220 12 -14 [-279,-260] -269.5 12 236 13 -13 [-259,-240] -249.5 14 262 14 -12 [-239,-220] -229.5 17 298 15 -11 [-219,-200] -209.5 20 343 16 -10 [-199,-180] -189.5 20 400 17 -9 [-179,-160] -169.5 25 480 18 -8 [-159,-140] -149.5 30 555 19 -7 [-139,-120] -129.5 41 666 20 -6 [-119,-100] -109.5 59 838 21 -5 [-99,-80] -89.5 59 1180 22 -4 [-79,-60] -69.5 79 1500 23 -3 [-59,-40] -49.5 79 1580 24 -2 [-39,-20] -29.5 79 1580 25 -1 [-19,0] -9.5 79 1580 26 0 [1,20] 10.5 79 1580 27 1 [21,40] 30.5 79 1580 28 2 [41,60] 50.5 79 1580 29 3 [61,80] 70.5 79 1460 30 4 [81,100] 90.5 59 1162 31 5 [101,120] 110.5 41 820 32 6 [121,140] 130.5 41 644 33 7 [141,160] 150.5 30 545 34 8 [161,180] 170.5 25 470 35 9 [181,200] 190.5 20 397 36 10 [201,220] 210.5 17 340 37 11 [221,240] 230.5 17 292 38 12 [241,260] 250.5 14 258 39 13 [261,280] 270.5 12 234 40 14 [281,300] 290.5 11 218 41 15 [301,320] 310.5 9 180 42 16 [321,340] 330.5 9 148 43 17 [341,360] 350.5 7 140 44 18 [361,380] 370.5 7 134 45 19 [381,400] 390.5 6 119 46 20 [401,420] 410.5 5 100 47 21 [421,440] 430.5 5 100 48 22 [441,460] 450.5 5 100 49 23 [461,480] 470.5 5 94 50 24 [481,500] 490.5 4 76 Column headers 1 seq pattern sequence 2 id pattern identifier 3 occ pattern occurrences 4 chi2 observed chi-square 5 df degrees of freedom 6 Pval P-value (probability for one word to be a false positive) 7 Eval E-value; expected number of false positives (Eval = Pval * nb_tests) 8 sig Significance (sig = -log10(Eval)) 9 rank rank of the pattern according to sorting criterion 10 -489.5 occurrences in window 1 [-499,-480] 11 -469.5 occurrences in window 2 [-479,-460] 12 -449.5 occurrences in window 3 [-459,-440] 13 -429.5 occurrences in window 4 [-439,-420] 14 -409.5 occurrences in window 5 [-419,-400] 15 -389.5 occurrences in window 6 [-399,-380] 16 -369.5 occurrences in window 7 [-379,-360] 17 -349.5 occurrences in window 8 [-359,-340] 18 -329.5 occurrences in window 9 [-339,-320] 19 -309.5 occurrences in window 10 [-319,-300] 20 -289.5 occurrences in window 11 [-299,-280] 21 -269.5 occurrences in window 12 [-279,-260] 22 -249.5 occurrences in window 13 [-259,-240] 23 -229.5 occurrences in window 14 [-239,-220] 24 -209.5 occurrences in window 15 [-219,-200] 25 -189.5 occurrences in window 16 [-199,-180] 26 -169.5 occurrences in window 17 [-179,-160] 27 -149.5 occurrences in window 18 [-159,-140] 28 -129.5 occurrences in window 19 [-139,-120] 29 -109.5 occurrences in window 20 [-119,-100] 30 -89.5 occurrences in window 21 [-99,-80] 31 -69.5 occurrences in window 22 [-79,-60] 32 -49.5 occurrences in window 23 [-59,-40] 33 -29.5 occurrences in window 24 [-39,-20] 34 -9.5 occurrences in window 25 [-19,0] 35 10.5 occurrences in window 26 [1,20] 36 30.5 occurrences in window 27 [21,40] 37 50.5 occurrences in window 28 [41,60] 38 70.5 occurrences in window 29 [61,80] 39 90.5 occurrences in window 30 [81,100] 40 110.5 occurrences in window 31 [101,120] 41 130.5 occurrences in window 32 [121,140] 42 150.5 occurrences in window 33 [141,160] 43 170.5 occurrences in window 34 [161,180] 44 190.5 occurrences in window 35 [181,200] 45 210.5 occurrences in window 36 [201,220] 46 230.5 occurrences in window 37 [221,240] 47 250.5 occurrences in window 38 [241,260] 48 270.5 occurrences in window 39 [261,280] 49 290.5 occurrences in window 40 [281,300] 50 310.5 occurrences in window 41 [301,320] 51 330.5 occurrences in window 42 [321,340] 52 350.5 occurrences in window 43 [341,360] 53 370.5 occurrences in window 44 [361,380] 54 390.5 occurrences in window 45 [381,400] 55 410.5 occurrences in window 46 [401,420] 56 430.5 occurrences in window 47 [421,440] 57 450.5 occurrences in window 48 [441,460] 58 470.5 occurrences in window 49 [461,480] 59 490.5 occurrences in window 50 [481,500]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -489.5 | -469.5 | -449.5 | -429.5 | -409.5 | -389.5 | -369.5 | -349.5 | -329.5 | -309.5 | -289.5 | -269.5 | -249.5 | -229.5 | -209.5 | -189.5 | -169.5 | -149.5 | -129.5 | -109.5 | -89.5 | -69.5 | -49.5 | -29.5 | -9.5 | 10.5 | 30.5 | 50.5 | 70.5 | 90.5 | 110.5 | 130.5 | 150.5 | 170.5 | 190.5 | 210.5 | 230.5 | 250.5 | 270.5 | 290.5 | 310.5 | 330.5 | 350.5 | 370.5 | 390.5 | 410.5 | 430.5 | 450.5 | 470.5 | 490.5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tt | tt | 2697 | 68.6 | 49 | 3.4e-02 | 0.54 | 0.27 | 1 | 5 | 3 | 9 | 6 | 4 | 12 | 14 | 17 | 12 | 11 | 23 | 17 | 22 | 17 | 39 | 43 | 46 | 57 | 62 | 106 | 118 | 158 | 195 | 173 | 178 | 195 | 157 | 157 | 174 | 120 | 88 | 63 | 48 | 56 | 37 | 34 | 35 | 26 | 24 | 19 | 19 | 11 | 9 | 11 | 14 | 16 | 12 | 16 | 7 | 2 |
| cc | cc | 940 | 66.2 | 49 | 5.1e-02 | 0.82 | 0.09 | 2 | 4 | 4 | 3 | 6 | 2 | 10 | 2 | 7 | 3 | 11 | 8 | 6 | 10 | 22 | 9 | 11 | 26 | 19 | 34 | 32 | 38 | 68 | 69 | 70 | 70 | 56 | 50 | 49 | 44 | 27 | 24 | 21 | 14 | 17 | 16 | 7 | 5 | 14 | 4 | 4 | 2 | 5 | 5 | 4 | 2 | 5 | 4 | 5 | 4 | 8 |
| aa | aa | 2745 | 60.2 | 49 | 1.3e-01 | 2.1 | -0.32 | 3 | 13 | 8 | 10 | 15 | 13 | 14 | 12 | 14 | 19 | 26 | 23 | 43 | 32 | 31 | 32 | 37 | 58 | 67 | 70 | 66 | 131 | 145 | 162 | 164 | 177 | 177 | 160 | 177 | 154 | 112 | 98 | 62 | 62 | 34 | 47 | 38 | 26 | 28 | 38 | 27 | 17 | 15 | 13 | 13 | 9 | 11 | 8 | 9 | 16 | 12 |
| gg | gg | 939 | 57.4 | 49 | 1.9e-01 | 3.1 | -0.49 | 4 | 1 | 3 | 4 | 1 | 5 | 1 | 7 | 0 | 6 | 9 | 13 | 8 | 10 | 17 | 20 | 17 | 26 | 21 | 32 | 28 | 30 | 58 | 45 | 63 | 71 | 39 | 65 | 45 | 50 | 41 | 30 | 20 | 19 | 20 | 19 | 9 | 4 | 8 | 9 | 11 | 7 | 2 | 8 | 5 | 8 | 5 | 6 | 7 | 4 | 2 |
| tg | tg | 1654 | 53.1 | 49 | 3.2e-01 | 5.1 | -0.71 | 5 | 6 | 9 | 9 | 9 | 9 | 4 | 5 | 13 | 9 | 9 | 18 | 13 | 16 | 16 | 19 | 23 | 27 | 36 | 43 | 73 | 90 | 74 | 94 | 97 | 95 | 84 | 96 | 99 | 108 | 84 | 50 | 46 | 28 | 32 | 27 | 21 | 17 | 23 | 13 | 17 | 12 | 11 | 12 | 15 | 13 | 5 | 8 | 5 | 8 | 4 |
| ta | ta | 2079 | 47.2 | 49 | 5.4e-01 | 8.7 | -0.94 | 6 | 8 | 8 | 7 | 10 | 5 | 12 | 11 | 9 | 13 | 14 | 13 | 23 | 20 | 19 | 25 | 31 | 32 | 39 | 43 | 63 | 93 | 118 | 117 | 131 | 133 | 145 | 147 | 132 | 116 | 97 | 64 | 52 | 46 | 38 | 33 | 45 | 32 | 22 | 23 | 14 | 17 | 15 | 6 | 8 | 4 | 8 | 5 | 5 | 3 | 5 |
| ga | ga | 1436 | 47.0 | 49 | 5.5e-01 | 8.9 | -0.95 | 7 | 2 | 5 | 7 | 6 | 6 | 6 | 13 | 9 | 8 | 14 | 11 | 17 | 15 | 17 | 14 | 24 | 38 | 30 | 38 | 51 | 56 | 84 | 74 | 80 | 77 | 81 | 99 | 82 | 89 | 63 | 40 | 39 | 29 | 31 | 30 | 20 | 11 | 8 | 11 | 15 | 11 | 8 | 13 | 9 | 12 | 5 | 9 | 10 | 5 | 4 |
| ct | ct | 1480 | 46.4 | 49 | 5.8e-01 | 9.3 | -0.97 | 8 | 6 | 4 | 5 | 6 | 9 | 5 | 9 | 9 | 4 | 7 | 17 | 8 | 12 | 16 | 25 | 24 | 25 | 25 | 35 | 51 | 65 | 83 | 90 | 103 | 96 | 97 | 92 | 101 | 85 | 72 | 46 | 33 | 27 | 20 | 14 | 18 | 23 | 23 | 10 | 12 | 5 | 7 | 8 | 9 | 8 | 13 | 5 | 5 | 7 | 1 |
| ag | ag | 1542 | 41.6 | 49 | 7.6e-01 | 12 | -1.09 | 9 | 2 | 7 | 5 | 4 | 8 | 3 | 14 | 6 | 11 | 13 | 10 | 20 | 17 | 19 | 13 | 34 | 36 | 36 | 44 | 41 | 67 | 86 | 94 | 98 | 88 | 97 | 105 | 91 | 79 | 64 | 47 | 40 | 34 | 31 | 31 | 20 | 13 | 10 | 11 | 19 | 14 | 11 | 9 | 7 | 9 | 4 | 6 | 8 | 3 | 3 |
| at | at | 2352 | 40.9 | 49 | 7.9e-01 | 13 | -1.10 | 10 | 10 | 5 | 12 | 10 | 7 | 16 | 10 | 14 | 17 | 15 | 16 | 18 | 24 | 27 | 29 | 27 | 37 | 51 | 56 | 86 | 107 | 137 | 128 | 130 | 153 | 154 | 166 | 145 | 144 | 110 | 65 | 62 | 54 | 41 | 41 | 42 | 29 | 22 | 24 | 13 | 21 | 12 | 10 | 14 | 8 | 5 | 8 | 6 | 5 | 9 |
| ca | ca | 1715 | 37.7 | 49 | 8.8e-01 | 14 | -1.15 | 11 | 6 | 8 | 7 | 3 | 7 | 9 | 9 | 8 | 12 | 13 | 15 | 7 | 17 | 28 | 26 | 28 | 32 | 49 | 56 | 47 | 83 | 109 | 112 | 98 | 105 | 111 | 93 | 112 | 81 | 72 | 54 | 44 | 39 | 30 | 21 | 17 | 20 | 17 | 14 | 14 | 17 | 13 | 10 | 8 | 7 | 3 | 7 | 4 | 6 | 7 |
| tc | tc | 1527 | 37.1 | 49 | 8.9e-01 | 14 | -1.16 | 12 | 4 | 3 | 5 | 4 | 9 | 9 | 8 | 10 | 9 | 6 | 12 | 8 | 16 | 18 | 25 | 28 | 25 | 30 | 46 | 45 | 78 | 105 | 94 | 94 | 105 | 101 | 91 | 101 | 87 | 70 | 45 | 31 | 32 | 22 | 13 | 14 | 23 | 12 | 14 | 10 | 6 | 5 | 10 | 8 | 5 | 7 | 6 | 6 | 6 | 6 |
| gc | gc | 942 | 36.7 | 49 | 9.0e-01 | 14 | -1.16 | 13 | 4 | 7 | 6 | 4 | 6 | 0 | 5 | 5 | 7 | 9 | 11 | 10 | 14 | 17 | 13 | 15 | 18 | 17 | 23 | 35 | 46 | 42 | 64 | 65 | 44 | 51 | 52 | 66 | 42 | 46 | 29 | 22 | 25 | 13 | 14 | 11 | 8 | 15 | 4 | 14 | 8 | 6 | 4 | 5 | 4 | 4 | 3 | 2 | 4 | 3 |
| gt | gt | 1422 | 29.9 | 49 | 9.9e-01 | 16 | -1.20 | 14 | 4 | 9 | 5 | 6 | 6 | 6 | 5 | 10 | 8 | 9 | 9 | 17 | 18 | 8 | 18 | 28 | 19 | 33 | 39 | 54 | 76 | 75 | 92 | 91 | 86 | 76 | 83 | 81 | 85 | 62 | 48 | 33 | 27 | 28 | 23 | 18 | 20 | 12 | 15 | 12 | 11 | 11 | 8 | 10 | 8 | 2 | 4 | 5 | 5 | 4 |
| ac | ac | 1332 | 25.7 | 49 | 1.0e+00 | 16 | -1.20 | 15 | 5 | 8 | 3 | 6 | 3 | 10 | 7 | 5 | 8 | 11 | 14 | 11 | 7 | 18 | 25 | 18 | 26 | 35 | 35 | 37 | 56 | 78 | 86 | 80 | 74 | 87 | 76 | 82 | 70 | 62 | 40 | 33 | 27 | 24 | 16 | 20 | 18 | 15 | 13 | 11 | 10 | 13 | 10 | 6 | 6 | 6 | 6 | 4 | 8 | 3 |
| cg | cg | 603 | 25.7 | 49 | 1.0e+00 | 16 | -1.20 | 16 | 0 | 5 | 3 | 4 | 2 | 3 | 5 | 4 | 6 | 5 | 7 | 10 | 12 | 8 | 11 | 12 | 9 | 10 | 10 | 22 | 26 | 41 | 41 | 35 | 28 | 29 | 32 | 40 | 32 | 27 | 17 | 14 | 14 | 13 | 8 | 6 | 8 | 3 | 7 | 6 | 3 | 3 | 5 | 2 | 2 | 1 | 3 | 3 | 3 | 3 |
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