One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; waCTATCGATAstw ; Alignment reference a 37 37 3 12 83 2 3 1 85 2 73 8 21 32 c 14 14 67 10 3 2 90 0 2 5 2 47 16 16 g 14 22 17 3 5 2 0 91 4 0 12 31 17 13 t 28 20 6 68 2 87 0 1 2 86 6 7 39 32

Dref_rc_shift2 (Dref_rc)
; positions_6nt_m2 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.634776; --yTATCGwTAt-- ; cor=; Ncor= a 0 0 0 0 10 0 0 0 6.66667 1.11111 7.77778 2.22222 0 0 c 0 0 6.66667 1.11111 0 0 8.88889 0 0 0 1.11111 0 0 0 g 0 0 0 1.11111 0 0 0 10 0 1.11111 0 1.11111 0 0 t 0 0 3.33333 7.77778 0 10 1.11111 0 3.33333 7.77778 1.11111 6.66667 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; wacTATCGATAgyw ; Alignment reference a 34 40 7 11 88 2 0 0 92 2 69 8 19 34 c 13 14 65 15 3 1 97 0 2 4 2 17 25 16 g 17 24 17 2 4 2 0 97 1 3 15 65 14 13 t 33 19 8 69 2 92 0 0 2 88 11 7 39 34

Dref_shift2 (Dref)
; positions_6nt_m1 versus Dref; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.632364; --aTAwCGATAr-- ; cor=; Ncor= a 0 0 6.66667 1.11111 7.77778 3.33333 0 1.11111 10 0 7.77778 3.33333 0 0 c 0 0 1.11111 0 1.11111 0 10 0 0 0 1.11111 0 0 0 g 0 0 0 1.11111 0 0 0 8.88889 0 0 1.11111 6.66667 0 0 t 0 0 2.22222 7.77778 1.11111 6.66667 0 0 0 10 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; awacTATCGATrgt ; Alignment reference a 42 38 68 15 4 103 0 0 0 93 6 37 19 25 c 22 15 11 69 9 3 0 109 0 6 8 5 25 24 g 19 16 18 21 1 2 4 0 110 7 4 56 42 18 t 27 41 13 5 96 2 106 1 0 4 92 12 24 43

Dref_rc_shift3 (Dref_rc)
; positions_7nt_m2 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.629324; ---yTATCGwTAt- ; cor=; Ncor= a 0 0 0 0 0 10 0 0 0 6.66667 1.11111 7.77778 2.22222 0 c 0 0 0 6.66667 1.11111 0 0 8.88889 0 0 0 1.11111 0 0 g 0 0 0 0 1.11111 0 0 0 10 0 1.11111 0 1.11111 0 t 0 0 0 3.33333 7.77778 0 10 1.11111 0 3.33333 7.77778 1.11111 6.66667 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift2 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift2 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --hrATAAATAwh ; Alignment reference a 0 0 19 19 52 1 51 44 48 0 53 17 17 c 0 0 14 8 2 1 2 2 1 2 1 10 14 g 0 0 6 16 1 4 0 4 6 0 1 9 8 t 0 0 16 12 0 49 2 5 0 53 0 19 16

br-Z4_rc_shift5 (br-Z4_rc)
; oligos_7nt_mkv2_m5 versus br-Z4_rc; m=1/9; ncol2=8; w=0; offset=3; strand=R; shift=5; score=0.589885; -----TAAhYAdT ; cor=; Ncor= a 0 0 0 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2 0 t 0 0 0 0 0 7 1 0 3 6 0 3 7

zen_shift3 (zen)
; oligos_7nt_mkv2_m5 versus zen; m=2/9; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.488425; ---AATwAA---- ; cor=; Ncor= a 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0 0 0 0.541667 0 1.08333 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0

Antp_shift3 (Antp)
; oligos_7nt_mkv2_m5 versus Antp; m=3/9; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.477163; ---mATAAw---- ; cor=; Ncor= a 0 0 0 10.5 18 0 16.5 18 7.5 0 0 0 0 c 0 0 0 4.5 0 0 0 0 0 0 0 0 0 g 0 0 0 3 0 0 1.5 0 0 0 0 0 0 t 0 0 0 0 0 18 0 0 10.5 0 0 0 0

br-Z2_rc_shift5 (br-Z2_rc)
; oligos_7nt_mkv2_m5 versus br-Z2_rc; m=4/9; ncol2=7; w=0; offset=3; strand=R; shift=5; score=0.466547; -----twaaTAG- ; cor=; Ncor= a 0 0 0 0 0 5 9 12 11 0 21 1 0 c 0 0 0 0 0 4 1 3 3 0 0 0 0 g 0 0 0 0 0 0 3 1 3 0 0 20 0 t 0 0 0 0 0 12 8 5 4 21 0 0 0

abd-A_shift4 (abd-A)
; oligos_7nt_mkv2_m5 versus abd-A; m=5/9; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.456306; ----aTAAWT--- ; cor=; Ncor= a 0 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0

gt_shift1 (gt)
; oligos_7nt_mkv2_m5 versus gt; m=6/9; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.422784; -GTmAwAW----- ; cor=; Ncor= a 0 0 1 5 8 3 8 6 0 0 0 0 0 c 0 1 1 3 0 0 0 0 0 0 0 0 0 g 0 7 0 0 0 0 0 0 0 0 0 0 0 t 0 0 6 0 0 5 0 2 0 0 0 0 0

ap_shift7 (ap)
; oligos_7nt_mkv2_m5 versus ap; m=7/9; ncol2=6; w=0; offset=5; strand=D; shift=7; score=0.407629; -------AAThAt ; cor=; Ncor= a 0 0 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 0 0 12 4 0 8

vvl_rc_shift5 (vvl_rc)
; oligos_7nt_mkv2_m5 versus vvl_rc; m=8/9; ncol2=6; w=0; offset=3; strand=R; shift=5; score=0.40578; -----TgmwTA-- ; cor=; Ncor= a 0 0 0 0 0 0 2.36364 8.27273 5.90909 0 13 0 0 c 0 0 0 0 0 0 1.18182 4.72727 0 0 0 0 0 g 0 0 0 0 0 0 8.27273 0 0 1.18182 0 0 0 t 0 0 0 0 0 13 1.18182 0 7.09091 11.8182 0 0 0

cad_rc_shift0 (cad_rc)
; oligos_7nt_mkv2_m5 versus cad_rc; m=9/9; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.403226; WrtYrwAAA---- ; cor=; Ncor= a 9 8 1 0 7 4 12 11 11 0 0 0 0 c 0 1 3 9 1 2 0 2 0 0 0 0 0 g 0 4 3 0 5 1 1 0 0 0 0 0 0 t 4 0 6 4 0 6 0 0 2 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; awacTATCGATAgtwt ; Alignment reference a 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15 c 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21 g 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17 t 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35

Dref_rc_shift3 (Dref_rc)
; positions_7nt_m1 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.554241; ---yTATCGwTAt--- ; cor=; Ncor= a 0 0 0 0 0 10 0 0 0 6.66667 1.11111 7.77778 2.22222 0 0 0 c 0 0 0 6.66667 1.11111 0 0 8.88889 0 0 0 1.11111 0 0 0 0 g 0 0 0 0 1.11111 0 0 0 10 0 1.11111 0 1.11111 0 0 0 t 0 0 0 3.33333 7.77778 0 10 1.11111 0 3.33333 7.77778 1.11111 6.66667 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; wdwAAAATAtwd ; Alignment reference a 27 21 23 63 66 63 67 0 66 16 21 17 c 15 12 11 1 0 0 0 0 0 12 15 7 g 2 17 6 2 0 0 0 1 1 5 13 20 t 23 17 27 1 1 4 0 66 0 34 18 23

hb_shift0 (hb)
; dyads_m4 versus hb; m=1/2; ncol2=9; w=0; offset=0; strand=D; shift=0; score=0.526125; mayAAAAAa--- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0 0

br-Z3_rc_shift3 (br-Z3_rc)
; dyads_m4 versus br-Z3_rc; m=2/2; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.459766; ---AwAMTAdWd ; cor=; Ncor= a 0 0 0 14 8 13 4 1 13 5 4 5 c 0 0 0 0 0 1 11 1 1 0 0 0 g 0 0 0 1 0 2 0 1 0 6 0 4 t 0 0 0 1 8 0 1 13 2 5 12 7

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -rwAAAATAwh ; Alignment reference a 0 19 24 59 59 59 59 0 59 18 17 c 0 11 11 0 0 0 0 0 0 11 15 g 0 15 7 0 0 0 0 0 0 5 11 t 0 14 17 0 0 0 0 59 0 25 16

hb_shift0 (hb)
; oligos_6nt_mkv2_m5 versus hb; m=1/7; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.51966; mayAAAAAa-- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0

Antp_shift5 (Antp)
; oligos_6nt_mkv2_m5 versus Antp; m=2/7; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.487548; -----mATAAw ; cor=; Ncor= a 0 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 0 18 0 0 10.5

ap_shift5 (ap)
; oligos_6nt_mkv2_m5 versus ap; m=3/7; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.46152; -----AAThAt ; cor=; Ncor= a 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 12 4 0 8

zen_shift5 (zen)
; oligos_6nt_mkv2_m5 versus zen; m=4/7; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.453341; -----AATwAA ; cor=; Ncor= a 0 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 c 0 0 0 0 0 0.541667 0 1.08333 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0

br-Z3_rc_shift3 (br-Z3_rc)
; oligos_6nt_mkv2_m5 versus br-Z3_rc; m=5/7; ncol2=11; w=0; offset=2; strand=R; shift=3; score=0.446447; ---AwAMTAdW ; cor=; Ncor= a 0 0 0 14 8 13 4 1 13 5 4 c 0 0 0 0 0 1 11 1 1 0 0 g 0 0 0 1 0 2 0 1 0 6 0 t 0 0 0 1 8 0 1 13 2 5 12

abd-A_rc_shift4 (abd-A_rc)
; oligos_6nt_mkv2_m5 versus abd-A_rc; m=6/7; ncol2=6; w=0; offset=3; strand=R; shift=4; score=0.42065; ----AWTTAt- ; cor=; Ncor= a 0 0 0 0 35.122 30.7317 4.39024 0 40.6098 7.68293 0 c 0 0 0 0 6.58537 0 0 3.29268 1.09756 4.39024 0 g 0 0 0 0 3.29268 0 0 1.09756 3.29268 5.4878 0 t 0 0 0 0 0 14.2683 40.6098 40.6098 0 27.439 0

gt_shift0 (gt)
; oligos_6nt_mkv2_m5 versus gt; m=7/7; ncol2=7; w=-1; offset=-1; strand=D; shift=0; score=0.409815; GTmAwAW---- ; cor=; Ncor= a 0 1 5 8 3 8 6 0 0 0 0 c 1 1 3 0 0 0 0 0 0 0 0 g 7 0 0 0 0 0 0 0 0 0 0 t 0 6 0 0 5 0 2 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; hdmyatCGATAsTATCGayr ; Alignment reference a 22 19 19 14 32 6 0 2 62 0 61 1 1 59 2 2 3 35 14 22 c 18 10 24 22 10 11 63 0 0 1 0 25 3 2 3 59 1 13 16 9 g 6 18 10 9 12 7 0 60 1 3 1 35 0 1 1 0 59 10 12 18 t 18 17 11 19 10 40 1 2 1 60 2 3 60 2 58 3 1 6 22 15

Dref_shift2 (Dref)
; oligos_6nt_mkv2_m2 versus Dref; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.436093; --aTAwCGATAr-------- ; cor=; Ncor= a 0 0 6.66667 1.11111 7.77778 3.33333 0 1.11111 10 0 7.77778 3.33333 0 0 0 0 0 0 0 0 c 0 0 1.11111 0 1.11111 0 10 0 0 0 1.11111 0 0 0 0 0 0 0 0 0 g 0 0 0 1.11111 0 0 0 8.88889 0 0 1.11111 6.66667 0 0 0 0 0 0 0 0 t 0 0 2.22222 7.77778 1.11111 6.66667 0 0 0 10 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift2 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --hrATAAATAwh ; Alignment reference a 0 0 19 19 52 1 51 44 48 0 53 17 17 c 0 0 14 8 2 1 2 2 1 2 1 10 14 g 0 0 6 16 1 4 0 4 6 0 1 9 8 t 0 0 16 12 0 49 2 5 0 53 0 19 16
br-Z4_rc_shift5 (br-Z4_rc)				; oligos_7nt_mkv2_m5 versus br-Z4_rc; m=1/9; ncol2=8; w=0; offset=3; strand=R; shift=5; score=0.589885; -----TAAhYAdT ; cor=; Ncor= a 0 0 0 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2 0 t 0 0 0 0 0 7 1 0 3 6 0 3 7
zen_shift3 (zen)				; oligos_7nt_mkv2_m5 versus zen; m=2/9; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.488425; ---AATwAA---- ; cor=; Ncor= a 0 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 0 0 0 0.541667 0 1.08333 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0
Antp_shift3 (Antp)				; oligos_7nt_mkv2_m5 versus Antp; m=3/9; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.477163; ---mATAAw---- ; cor=; Ncor= a 0 0 0 10.5 18 0 16.5 18 7.5 0 0 0 0 c 0 0 0 4.5 0 0 0 0 0 0 0 0 0 g 0 0 0 3 0 0 1.5 0 0 0 0 0 0 t 0 0 0 0 0 18 0 0 10.5 0 0 0 0
br-Z2_rc_shift5 (br-Z2_rc)				; oligos_7nt_mkv2_m5 versus br-Z2_rc; m=4/9; ncol2=7; w=0; offset=3; strand=R; shift=5; score=0.466547; -----twaaTAG- ; cor=; Ncor= a 0 0 0 0 0 5 9 12 11 0 21 1 0 c 0 0 0 0 0 4 1 3 3 0 0 0 0 g 0 0 0 0 0 0 3 1 3 0 0 20 0 t 0 0 0 0 0 12 8 5 4 21 0 0 0
abd-A_shift4 (abd-A)				; oligos_7nt_mkv2_m5 versus abd-A; m=5/9; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.456306; ----aTAAWT--- ; cor=; Ncor= a 0 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0
gt_shift1 (gt)				; oligos_7nt_mkv2_m5 versus gt; m=6/9; ncol2=7; w=-1; offset=-1; strand=D; shift=1; score=0.422784; -GTmAwAW----- ; cor=; Ncor= a 0 0 1 5 8 3 8 6 0 0 0 0 0 c 0 1 1 3 0 0 0 0 0 0 0 0 0 g 0 7 0 0 0 0 0 0 0 0 0 0 0 t 0 0 6 0 0 5 0 2 0 0 0 0 0
ap_shift7 (ap)				; oligos_7nt_mkv2_m5 versus ap; m=7/9; ncol2=6; w=0; offset=5; strand=D; shift=7; score=0.407629; -------AAThAt ; cor=; Ncor= a 0 0 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 0 0 12 4 0 8
vvl_rc_shift5 (vvl_rc)				; oligos_7nt_mkv2_m5 versus vvl_rc; m=8/9; ncol2=6; w=0; offset=3; strand=R; shift=5; score=0.40578; -----TgmwTA-- ; cor=; Ncor= a 0 0 0 0 0 0 2.36364 8.27273 5.90909 0 13 0 0 c 0 0 0 0 0 0 1.18182 4.72727 0 0 0 0 0 g 0 0 0 0 0 0 8.27273 0 0 1.18182 0 0 0 t 0 0 0 0 0 13 1.18182 0 7.09091 11.8182 0 0 0
cad_rc_shift0 (cad_rc)				; oligos_7nt_mkv2_m5 versus cad_rc; m=9/9; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.403226; WrtYrwAAA---- ; cor=; Ncor= a 9 8 1 0 7 4 12 11 11 0 0 0 0 c 0 1 3 9 1 2 0 2 0 0 0 0 0 g 0 4 3 0 5 1 1 0 0 0 0 0 0 t 4 0 6 4 0 6 0 0 2 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -rwAAAATAwh ; Alignment reference a 0 19 24 59 59 59 59 0 59 18 17 c 0 11 11 0 0 0 0 0 0 11 15 g 0 15 7 0 0 0 0 0 0 5 11 t 0 14 17 0 0 0 0 59 0 25 16
hb_shift0 (hb)				; oligos_6nt_mkv2_m5 versus hb; m=1/7; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.51966; mayAAAAAa-- ; cor=; Ncor= a 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 0 0 c 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 0 0 g 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 0 0 t 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456 0 0
Antp_shift5 (Antp)				; oligos_6nt_mkv2_m5 versus Antp; m=2/7; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.487548; -----mATAAw ; cor=; Ncor= a 0 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 0 18 0 0 10.5
ap_shift5 (ap)				; oligos_6nt_mkv2_m5 versus ap; m=3/7; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.46152; -----AAThAt ; cor=; Ncor= a 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 12 4 0 8
zen_shift5 (zen)				; oligos_6nt_mkv2_m5 versus zen; m=4/7; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.453341; -----AATwAA ; cor=; Ncor= a 0 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 c 0 0 0 0 0 0.541667 0 1.08333 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0
br-Z3_rc_shift3 (br-Z3_rc)				; oligos_6nt_mkv2_m5 versus br-Z3_rc; m=5/7; ncol2=11; w=0; offset=2; strand=R; shift=3; score=0.446447; ---AwAMTAdW ; cor=; Ncor= a 0 0 0 14 8 13 4 1 13 5 4 c 0 0 0 0 0 1 11 1 1 0 0 g 0 0 0 1 0 2 0 1 0 6 0 t 0 0 0 1 8 0 1 13 2 5 12
abd-A_rc_shift4 (abd-A_rc)				; oligos_6nt_mkv2_m5 versus abd-A_rc; m=6/7; ncol2=6; w=0; offset=3; strand=R; shift=4; score=0.42065; ----AWTTAt- ; cor=; Ncor= a 0 0 0 0 35.122 30.7317 4.39024 0 40.6098 7.68293 0 c 0 0 0 0 6.58537 0 0 3.29268 1.09756 4.39024 0 g 0 0 0 0 3.29268 0 0 1.09756 3.29268 5.4878 0 t 0 0 0 0 0 14.2683 40.6098 40.6098 0 27.439 0
gt_shift0 (gt)				; oligos_6nt_mkv2_m5 versus gt; m=7/7; ncol2=7; w=-1; offset=-1; strand=D; shift=0; score=0.409815; GTmAwAW---- ; cor=; Ncor= a 0 1 5 8 3 8 6 0 0 0 0 c 1 1 3 0 0 0 0 0 0 0 0 g 7 0 0 0 0 0 0 0 0 0 0 t 0 6 0 0 5 0 2 0 0 0 0