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.2025-04-28.203737_2025-04-28.203737_n2namY/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.2025-04-28.203737_2025-04-28.203737_n2namY/results/discovered_vs_db/peak-motifs_motifs_vs_db_DMMPMM_drosophila.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift1 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -haTCGATAGyw ; Alignment reference a 0 25 45 5 2 0 85 4 74 3 11 31 c 0 24 11 5 84 1 2 2 0 12 27 15 g 0 14 16 4 1 86 0 3 8 69 12 14 t 0 25 16 74 1 1 1 79 6 4 38 28

Dref_shift0 (Dref)
; positions_6nt_m1 versus Dref; m=1/1; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.685196; aTAwCGATAr-- ; cor=; Ncor= a 6.66667 1.11111 7.77778 3.33333 0 1.11111 10 0 7.77778 3.33333 0 0 c 1.11111 0 1.11111 0 10 0 0 0 1.11111 0 0 0 g 0 1.11111 0 0 0 8.88889 0 0 1.11111 6.66667 0 0 t 2.22222 7.77778 1.11111 6.66667 0 0 0 10 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; twaATAAATAww ; Alignment reference a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12

br-Z4_rc_shift4 (br-Z4_rc)
; oligos_7nt_mkv2_m3 versus br-Z4_rc; m=1/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.526082; ----TAAhYAdT ; cor=; Ncor= a 0 0 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 0 t 0 0 0 0 7 1 0 3 6 0 3 7

zen_shift2 (zen)
; oligos_7nt_mkv2_m3 versus zen; m=2/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.473161; --AATwAA---- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 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 t 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0

gt_shift0 (gt)
; oligos_7nt_mkv2_m3 versus gt; m=3/6; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.445613; GTmAwAW----- ; cor=; Ncor= a 0 1 5 8 3 8 6 0 0 0 0 0 c 1 1 3 0 0 0 0 0 0 0 0 0 g 7 0 0 0 0 0 0 0 0 0 0 0 t 0 6 0 0 5 0 2 0 0 0 0 0

Antp_shift2 (Antp)
; oligos_7nt_mkv2_m3 versus Antp; m=4/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.432536; --mATAAw---- ; cor=; Ncor= a 0 0 10.5 18 0 16.5 18 7.5 0 0 0 0 c 0 0 4.5 0 0 0 0 0 0 0 0 0 g 0 0 3 0 0 1.5 0 0 0 0 0 0 t 0 0 0 0 18 0 0 10.5 0 0 0 0

br-Z2_rc_shift4 (br-Z2_rc)
; oligos_7nt_mkv2_m3 versus br-Z2_rc; m=5/6; ncol2=7; w=0; offset=4; strand=R; shift=4; score=0.414599; ----twaaTAG- ; cor=; Ncor= a 0 0 0 0 5 9 12 11 0 21 1 0 c 0 0 0 0 4 1 3 3 0 0 0 0 g 0 0 0 0 0 3 1 3 0 0 20 0 t 0 0 0 0 12 8 5 4 21 0 0 0

abd-A_shift3 (abd-A)
; oligos_7nt_mkv2_m3 versus abd-A; m=6/6; ncol2=6; w=0; offset=3; strand=D; shift=3; score=0.407691; ---aTAAWT--- ; cor=; Ncor= a 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -rwAAAATAww ; Alignment reference a 0 12 13 35 35 35 35 0 35 10 10 c 0 5 6 0 0 0 0 0 0 8 8 g 0 10 6 0 0 0 0 0 0 4 7 t 0 8 10 0 0 0 0 35 0 13 10

hb_shift0 (hb)
; oligos_6nt_mkv2_m3 versus hb; m=1/6; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.520993; 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_m3 versus Antp; m=2/6; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.487699; -----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_m3 versus ap; m=3/6; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.462393; -----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_m3 versus zen; m=4/6; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.451626; -----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_m3 versus br-Z3_rc; m=5/6; ncol2=11; w=0; offset=2; strand=R; shift=3; score=0.447748; ---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

gt_shift0 (gt)
; oligos_6nt_mkv2_m3 versus gt; m=6/6; ncol2=7; w=-1; offset=-1; strand=D; shift=0; score=0.403305; 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: dyads_m3_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift1 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wrwAAAATAww ; Alignment reference a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11

hb_shift0 (hb)
; dyads_m3 versus hb; m=1/6; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.489914; 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

Antp_shift6 (Antp)
; dyads_m3 versus Antp; m=2/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.448324; ------mATAAw ; cor=; Ncor= a 0 0 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 0 0 18 0 0 10.5

pan_shift1 (pan)
; dyads_m3 versus pan; m=3/6; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.421604; -WtCAAA----- ; cor=; Ncor= a 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 0 0 0 c 0 0 4.16 20.8 0 1.04 0 0 0 0 0 0 g 0 0 0 1.04 0 0 0 0 0 0 0 0 t 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0 0 0 0

ap_shift6 (ap)
; dyads_m3 versus ap; m=4/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.417999; ------AAThAt ; cor=; Ncor= a 0 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 0 12 4 0 8

br-Z3_rc_shift4 (br-Z3_rc)
; dyads_m3 versus br-Z3_rc; m=5/6; ncol2=11; w=0; offset=3; strand=R; shift=4; score=0.412983; ----AwAMTAdW ; cor=; Ncor= a 0 0 0 0 14 8 13 4 1 13 5 4 c 0 0 0 0 0 0 1 11 1 1 0 0 g 0 0 0 0 1 0 2 0 1 0 6 0 t 0 0 0 0 1 8 0 1 13 2 5 12

zen_shift6 (zen)
; dyads_m3 versus zen; m=6/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.411051; ------AATwAA ; cor=; Ncor= a 0 0 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 c 0 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 0 t 0 0 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=16; shift=0; ncol=16; wwTAAwrhwymAAAaw ; Alignment reference a 11 9 0 23 23 9 9 6 9 4 8 22 23 23 11 9 c 3 5 0 0 0 1 1 8 2 7 6 0 0 0 3 5 g 2 2 0 0 0 4 8 3 5 5 5 0 0 0 4 2 t 7 7 23 0 0 9 5 6 7 7 4 1 0 0 5 7

hb_shift7 (hb)
; dyads_m9 versus hb; m=1/2; ncol2=9; w=0; offset=7; strand=D; shift=7; score=0.47691; -------mayAAAAAa ; cor=; Ncor= a 0 0 0 0 0 0 0 30.2913 47.4563 1.00971 96.932 101.981 104 97.9417 102.99 68.6602 c 0 0 0 0 0 0 0 49.4757 16.1553 29.2816 1.00971 1.00971 0 1.00971 1.00971 8.07767 g 0 0 0 0 0 0 0 21.2039 17.165 11.1068 4.03883 0 0 4.03883 0 12.1165 t 0 0 0 0 0 0 0 3.02913 23.2233 62.6019 2.01942 1.00971 0 1.00971 0 15.1456

cad_rc_shift5 (cad_rc)
; dyads_m9 versus cad_rc; m=2/2; ncol2=9; w=0; offset=5; strand=R; shift=5; score=0.411694; -----WrtYrwAAA-- ; cor=; Ncor= a 0 0 0 0 0 9 8 1 0 7 4 12 11 11 0 0 c 0 0 0 0 0 0 1 3 9 1 2 0 2 0 0 0 g 0 0 0 0 0 0 4 3 0 5 1 1 0 0 0 0 t 0 0 0 0 0 4 0 6 4 0 6 0 0 2 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=21; shift=0; ncol=21; swwmyaTCGATAsTATCGAth ; Alignment reference a 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 c 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 g 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 t 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6

Dref_shift3 (Dref)
; oligos_6nt_mkv2_m2 versus Dref; m=1/1; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.420742; ---aTAwCGATAr-------- ; cor=; Ncor= a 0 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 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 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 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_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; twaATAAATAww ; Alignment reference a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12
br-Z4_rc_shift4 (br-Z4_rc)				; oligos_7nt_mkv2_m3 versus br-Z4_rc; m=1/6; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.526082; ----TAAhYAdT ; cor=; Ncor= a 0 0 0 0 1 7 8 2 0 8 3 1 c 0 0 0 0 0 0 0 3 2 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 0 t 0 0 0 0 7 1 0 3 6 0 3 7
zen_shift2 (zen)				; oligos_7nt_mkv2_m3 versus zen; m=2/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.473161; --AATwAA---- ; cor=; Ncor= a 0 0 11.9167 11.9167 0 8.66667 13 13 0 0 0 0 c 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 t 0 0 0.541667 1.08333 11.9167 4.33333 0 0 0 0 0 0
gt_shift0 (gt)				; oligos_7nt_mkv2_m3 versus gt; m=3/6; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.445613; GTmAwAW----- ; cor=; Ncor= a 0 1 5 8 3 8 6 0 0 0 0 0 c 1 1 3 0 0 0 0 0 0 0 0 0 g 7 0 0 0 0 0 0 0 0 0 0 0 t 0 6 0 0 5 0 2 0 0 0 0 0
Antp_shift2 (Antp)				; oligos_7nt_mkv2_m3 versus Antp; m=4/6; ncol2=6; w=0; offset=2; strand=D; shift=2; score=0.432536; --mATAAw---- ; cor=; Ncor= a 0 0 10.5 18 0 16.5 18 7.5 0 0 0 0 c 0 0 4.5 0 0 0 0 0 0 0 0 0 g 0 0 3 0 0 1.5 0 0 0 0 0 0 t 0 0 0 0 18 0 0 10.5 0 0 0 0
br-Z2_rc_shift4 (br-Z2_rc)				; oligos_7nt_mkv2_m3 versus br-Z2_rc; m=5/6; ncol2=7; w=0; offset=4; strand=R; shift=4; score=0.414599; ----twaaTAG- ; cor=; Ncor= a 0 0 0 0 5 9 12 11 0 21 1 0 c 0 0 0 0 4 1 3 3 0 0 0 0 g 0 0 0 0 0 3 1 3 0 0 20 0 t 0 0 0 0 12 8 5 4 21 0 0 0
abd-A_shift3 (abd-A)				; oligos_7nt_mkv2_m3 versus abd-A; m=6/6; ncol2=6; w=0; offset=3; strand=D; shift=3; score=0.407691; ---aTAAWT--- ; cor=; Ncor= a 0 0 0 27.439 0 40.6098 40.6098 14.2683 0 0 0 0 c 0 0 0 5.4878 3.29268 1.09756 0 0 3.29268 0 0 0 g 0 0 0 4.39024 1.09756 3.29268 0 0 6.58537 0 0 0 t 0 0 0 7.68293 40.6098 0 4.39024 30.7317 35.122 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -rwAAAATAww ; Alignment reference a 0 12 13 35 35 35 35 0 35 10 10 c 0 5 6 0 0 0 0 0 0 8 8 g 0 10 6 0 0 0 0 0 0 4 7 t 0 8 10 0 0 0 0 35 0 13 10
hb_shift0 (hb)				; oligos_6nt_mkv2_m3 versus hb; m=1/6; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.520993; 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_m3 versus Antp; m=2/6; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.487699; -----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_m3 versus ap; m=3/6; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.462393; -----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_m3 versus zen; m=4/6; ncol2=6; w=0; offset=4; strand=D; shift=5; score=0.451626; -----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_m3 versus br-Z3_rc; m=5/6; ncol2=11; w=0; offset=2; strand=R; shift=3; score=0.447748; ---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
gt_shift0 (gt)				; oligos_6nt_mkv2_m3 versus gt; m=6/6; ncol2=7; w=-1; offset=-1; strand=D; shift=0; score=0.403305; 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift1 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wrwAAAATAww ; Alignment reference a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11
hb_shift0 (hb)				; dyads_m3 versus hb; m=1/6; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.489914; 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
Antp_shift6 (Antp)				; dyads_m3 versus Antp; m=2/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.448324; ------mATAAw ; cor=; Ncor= a 0 0 0 0 0 0 10.5 18 0 16.5 18 7.5 c 0 0 0 0 0 0 4.5 0 0 0 0 0 g 0 0 0 0 0 0 3 0 0 1.5 0 0 t 0 0 0 0 0 0 0 0 18 0 0 10.5
pan_shift1 (pan)				; dyads_m3 versus pan; m=3/6; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.421604; -WtCAAA----- ; cor=; Ncor= a 0 18.72 5.2 3.12 20.8 23.92 23.92 0 0 0 0 0 c 0 0 4.16 20.8 0 1.04 0 0 0 0 0 0 g 0 0 0 1.04 0 0 0 0 0 0 0 0 t 0 7.28 16.64 1.04 5.2 1.04 2.08 0 0 0 0 0
ap_shift6 (ap)				; dyads_m3 versus ap; m=4/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.417999; ------AAThAt ; cor=; Ncor= a 0 0 0 0 0 0 14 14 0 5 13 2 c 0 0 0 0 0 0 0 0 1 4 0 1 g 0 0 0 0 0 0 0 0 1 1 1 3 t 0 0 0 0 0 0 0 0 12 4 0 8
br-Z3_rc_shift4 (br-Z3_rc)				; dyads_m3 versus br-Z3_rc; m=5/6; ncol2=11; w=0; offset=3; strand=R; shift=4; score=0.412983; ----AwAMTAdW ; cor=; Ncor= a 0 0 0 0 14 8 13 4 1 13 5 4 c 0 0 0 0 0 0 1 11 1 1 0 0 g 0 0 0 0 1 0 2 0 1 0 6 0 t 0 0 0 0 1 8 0 1 13 2 5 12
zen_shift6 (zen)				; dyads_m3 versus zen; m=6/6; ncol2=6; w=0; offset=5; strand=D; shift=6; score=0.411051; ------AATwAA ; cor=; Ncor= a 0 0 0 0 0 0 11.9167 11.9167 0 8.66667 13 13 c 0 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 0 t 0 0 0 0 0 0 0.541667 1.08333 11.9167 4.33333 0 0