One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt -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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_vs_db/peak-motifs_motifs_vs_db_JASPAR2024_CORE_plants_non-redundant.tab

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)
; oligos_8nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; GhGAAGTGCAww ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1

MA2419.1_shift2 (UB3)
; oligos_8nt_mkv1_m2 versus MA2419.1 (UB3); m=1/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.630406; --gAAGTACAAc ; cor=; Ncor= a 0 0 3823.0 17244.0 18109.0 293.0 754.0 18975.0 322.0 16933.0 16719.0 4243.0 c 0 0 2963.0 566.0 527.0 269.0 287.0 196.0 18929.0 795.0 1201.0 11116.0 g 0 0 11905.0 1023.0 855.0 18318.0 1213.0 675.0 693.0 1162.0 629.0 3465.0 t 0 0 1439.0 1297.0 639.0 1250.0 17876.0 284.0 186.0 1240.0 1581.0 1306.0

MA2420.1_shift3 (SBP6)
; oligos_8nt_mkv1_m2 versus MA2420.1 (SBP6); m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.529629; ---AAGTACAA- ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0 0

MA2421.1_shift3 (SBP8)
; oligos_8nt_mkv1_m2 versus MA2421.1 (SBP8); m=3/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.499596; ---arGTACAa- ; cor=; Ncor= a 0 0 0 28920.0 30785.0 200.0 256.0 48160.0 275.0 46945.0 27864.0 0 c 0 0 0 3935.0 226.0 70.0 231.0 67.0 47947.0 397.0 5026.0 0 g 0 0 0 6297.0 17080.0 48049.0 509.0 52.0 79.0 519.0 5397.0 0 t 0 0 0 9248.0 309.0 81.0 47404.0 121.0 99.0 539.0 10113.0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m4_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m4_shift0 (oligos_8nt_mkv1_m4)
; oligos_8nt_mkv1_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; wAAAAGCTCCTry ; Alignment reference a 1 2 2 2 2 0 0 0 0 0 0 1 0 c 0 0 0 0 0 0 2 0 2 2 0 0 1 g 0 0 0 0 0 2 0 0 0 0 0 1 0 t 1 0 0 0 0 0 0 2 0 0 2 0 1

MA1747.2_rc_shift1 (DOF4.3_rc)
; oligos_8nt_mkv1_m4 versus MA1747.2_rc (DOF4.3_rc); m=1/7; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.61216; -wAAAGcywCTTT ; cor=; Ncor= a 0 424.0 998.0 998.0 995.0 2.0 95.0 76.0 429.0 0.0 0.0 0.0 0.0 c 0 103.0 0.0 0.0 0.0 0.0 571.0 345.0 91.0 1000.0 0.0 0.0 0.0 g 0 66.0 2.0 0.0 5.0 995.0 147.0 2.0 178.0 0.0 0.0 0.0 0.0 t 0 407.0 0.0 2.0 0.0 3.0 188.0 578.0 302.0 0.0 1000.0 1000.0 1000.0

MA2029.2_shift3 (MYB88)
; oligos_8nt_mkv1_m4 versus MA2029.2 (MYB88); m=2/7; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.508175; ---ACGCTCCTC- ; cor=; Ncor= a 0 0 0 150.0 3.0 1.0 0.0 1.0 1.0 0.0 18.0 7.0 0 c 0 0 0 15.0 159.0 1.0 167.0 1.0 165.0 152.0 6.0 138.0 0 g 0 0 0 3.0 6.0 165.0 1.0 27.0 2.0 3.0 3.0 6.0 0 t 0 0 0 0.0 0.0 1.0 0.0 139.0 0.0 13.0 141.0 17.0 0

MA0973.2_shift0 (CDF2)
; oligos_8nt_mkv1_m4 versus MA0973.2 (CDF2); m=3/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.471427; aWAAAGy------ ; cor=; Ncor= a 608.0 693.0 980.0 979.0 868.0 17.0 53.0 0 0 0 0 0 0 c 92.0 16.0 10.0 10.0 29.0 7.0 295.0 0 0 0 0 0 0 g 150.0 41.0 4.0 2.0 81.0 969.0 154.0 0 0 0 0 0 0 t 150.0 250.0 5.0 9.0 22.0 6.0 498.0 0 0 0 0 0 0

MA1815.2_rc_shift5 (GRF4_rc)
; oligos_8nt_mkv1_m4 versus MA1815.2_rc (GRF4_rc); m=4/7; ncol2=8; w=0; offset=5; strand=R; shift=5; score=0.441764; -----GCTGCTGC ; cor=; Ncor= a 0 0 0 0 0 0.0 1.0 10.0 2.0 1.0 3.0 0.0 3.0 c 0 0 0 0 0 4.0 59.0 0.0 0.0 61.0 5.0 3.0 54.0 g 0 0 0 0 0 59.0 3.0 2.0 60.0 1.0 1.0 59.0 1.0 t 0 0 0 0 0 2.0 2.0 53.0 3.0 2.0 56.0 3.0 7.0

MA1272.3_shift0 (DOF2.2)
; oligos_8nt_mkv1_m4 versus MA1272.3 (DOF2.2); m=5/7; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.435014; AAAAAG------- ; cor=; Ncor= a 1086.0 1077.0 1086.0 1084.0 1086.0 0.0 0 0 0 0 0 0 0 c 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 g 0.0 0.0 0.0 0.0 0.0 1086.0 0 0 0 0 0 0 0 t 0.0 9.0 0.0 2.0 0.0 0.0 0 0 0 0 0 0 0

MA1280.2_shift0 (DOF5.4)
; oligos_8nt_mkv1_m4 versus MA1280.2 (DOF5.4); m=6/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.430692; AAAAAGk------ ; cor=; Ncor= a 529.0 456.0 599.0 600.0 600.0 0.0 22.0 0 0 0 0 0 0 c 17.0 0.0 0.0 0.0 0.0 0.0 37.0 0 0 0 0 0 0 g 34.0 3.0 0.0 0.0 0.0 600.0 209.0 0 0 0 0 0 0 t 20.0 141.0 1.0 0.0 0.0 0.0 332.0 0 0 0 0 0 0

MA1276.2_shift0 (DOF3.5)
; oligos_8nt_mkv1_m4 versus MA1276.2 (DOF3.5); m=7/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.405671; AwAAAGk------ ; cor=; Ncor= a 467.0 348.0 599.0 599.0 599.0 0.0 2.0 0 0 0 0 0 0 c 4.0 0.0 0.0 0.0 0.0 0.0 6.0 0 0 0 0 0 0 g 103.0 0.0 0.0 0.0 0.0 599.0 219.0 0 0 0 0 0 0 t 25.0 251.0 0.0 0.0 0.0 0.0 372.0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift2 ; 18 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m4_shift2 (oligos_7nt_mkv1_m4)
; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --hdAAAAGAGsr ; Alignment reference a 0 0 1 1 4 4 4 4 0 4 0 0 2 c 0 0 1 0 0 0 0 0 0 0 0 2 0 g 0 0 0 2 0 0 0 0 4 0 4 2 2 t 0 0 2 1 0 0 0 0 0 0 0 0 0

MA1415.2_shift2 (REF6)
; oligos_7nt_mkv1_m4 versus MA1415.2 (REF6); m=1/17; ncol2=9; w=0; offset=0; strand=D; shift=2; score=0.61003; --rAAACAGAG-- ; cor=; Ncor= a 0 0 1983.0 2634.0 3458.0 3511.0 1.0 3622.0 6.0 3533.0 45.0 0 0 c 0 0 209.0 137.0 27.0 34.0 3661.0 25.0 21.0 21.0 10.0 0 0 g 0 0 1144.0 577.0 24.0 118.0 1.0 30.0 3625.0 105.0 3581.0 0 0 t 0 0 351.0 339.0 178.0 24.0 24.0 10.0 35.0 28.0 51.0 0 0

MA0974.3_shift3 (CDF3)
; oligos_7nt_mkv1_m4 versus MA0974.3 (CDF3); m=2/17; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.563952; ---AAAAAGTG-- ; cor=; Ncor= a 0 0 0 879.0 964.0 1143.0 1133.0 1125.0 1.0 29.0 86.0 0 0 c 0 0 0 63.0 24.0 2.0 4.0 3.0 0.0 44.0 7.0 0 0 g 0 0 0 79.0 29.0 7.0 11.0 19.0 1154.0 37.0 1038.0 0 0 t 0 0 0 136.0 140.0 5.0 9.0 10.0 2.0 1047.0 26.0 0 0

MA0977.1_shift3 (DOF2.5)
; oligos_7nt_mkv1_m4 versus MA0977.1 (DOF2.5); m=3/17; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.51989; ---AwAARGTg-- ; cor=; Ncor= a 0 0 0 756.0 598.0 990.0 986.0 744.0 4.0 8.0 238.0 0 0 c 0 0 0 26.0 1.0 1.0 1.0 1.0 1.0 198.0 44.0 0 0 g 0 0 0 182.0 12.0 4.0 8.0 254.0 977.0 65.0 557.0 0 0 t 0 0 0 36.0 389.0 5.0 6.0 1.0 18.0 729.0 160.0 0 0

MA0973.2_shift3 (CDF2)
; oligos_7nt_mkv1_m4 versus MA0973.2 (CDF2); m=4/17; ncol2=7; w=0; offset=1; strand=D; shift=3; score=0.505677; ---aWAAAGy--- ; cor=; Ncor= a 0 0 0 608.0 693.0 980.0 979.0 868.0 17.0 53.0 0 0 0 c 0 0 0 92.0 16.0 10.0 10.0 29.0 7.0 295.0 0 0 0 g 0 0 0 150.0 41.0 4.0 2.0 81.0 969.0 154.0 0 0 0 t 0 0 0 150.0 250.0 5.0 9.0 22.0 6.0 498.0 0 0 0

MA1272.3_shift3 (DOF2.2)
; oligos_7nt_mkv1_m4 versus MA1272.3 (DOF2.2); m=5/17; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.489605; ---AAAAAG---- ; cor=; Ncor= a 0 0 0 1086.0 1077.0 1086.0 1084.0 1086.0 0.0 0 0 0 0 c 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 g 0 0 0 0.0 0.0 0.0 0.0 0.0 1086.0 0 0 0 0 t 0 0 0 0.0 9.0 0.0 2.0 0.0 0.0 0 0 0 0

MA1280.2_shift3 (DOF5.4)
; oligos_7nt_mkv1_m4 versus MA1280.2 (DOF5.4); m=6/17; ncol2=7; w=0; offset=1; strand=D; shift=3; score=0.482869; ---AAAAAGk--- ; cor=; Ncor= a 0 0 0 529.0 456.0 599.0 600.0 600.0 0.0 22.0 0 0 0 c 0 0 0 17.0 0.0 0.0 0.0 0.0 0.0 37.0 0 0 0 g 0 0 0 34.0 3.0 0.0 0.0 0.0 600.0 209.0 0 0 0 t 0 0 0 20.0 141.0 1.0 0.0 0.0 0.0 332.0 0 0 0

MA1276.2_shift3 (DOF3.5)
; oligos_7nt_mkv1_m4 versus MA1276.2 (DOF3.5); m=7/17; ncol2=7; w=0; offset=1; strand=D; shift=3; score=0.467031; ---AwAAAGk--- ; cor=; Ncor= a 0 0 0 467.0 348.0 599.0 599.0 599.0 0.0 2.0 0 0 0 c 0 0 0 4.0 0.0 0.0 0.0 0.0 0.0 6.0 0 0 0 g 0 0 0 103.0 0.0 0.0 0.0 0.0 599.0 219.0 0 0 0 t 0 0 0 25.0 251.0 0.0 0.0 0.0 0.0 372.0 0 0 0

MA2069.1_rc_shift4 (PK10955.1_rc)
; oligos_7nt_mkv1_m4 versus MA2069.1_rc (PK10955.1_rc); m=8/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.439423; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 615.0 979.0 988.0 857.0 17.0 0 0 0 0 c 0 0 0 0 16.0 8.0 3.0 43.0 3.0 0 0 0 0 g 0 0 0 0 59.0 4.0 0.0 89.0 970.0 0 0 0 0 t 0 0 0 0 308.0 7.0 7.0 8.0 9.0 0 0 0 0

MA2084.1_rc_shift4 (PK23009.1_rc)
; oligos_7nt_mkv1_m4 versus MA2084.1_rc (PK23009.1_rc); m=9/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.436055; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 563.0 930.0 927.0 811.0 79.0 0 0 0 0 c 0 0 0 0 25.0 18.0 19.0 54.0 5.0 0 0 0 0 g 0 0 0 0 73.0 12.0 0.0 104.0 890.0 0 0 0 0 t 0 0 0 0 338.0 39.0 52.0 29.0 24.0 0 0 0 0

MA2085.1_rc_shift4 (PK23763.1_rc)
; oligos_7nt_mkv1_m4 versus MA2085.1_rc (PK23763.1_rc); m=10/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.430016; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 489.0 944.0 941.0 839.0 26.0 0 0 0 0 c 0 0 0 0 53.0 24.0 21.0 71.0 13.0 0 0 0 0 g 0 0 0 0 91.0 8.0 6.0 52.0 933.0 0 0 0 0 t 0 0 0 0 366.0 22.0 30.0 35.0 26.0 0 0 0 0

MA2356.1_rc_shift4 (PK20555.1_rc)
; oligos_7nt_mkv1_m4 versus MA2356.1_rc (PK20555.1_rc); m=11/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.429214; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 461.0 835.0 821.0 717.0 46.0 0 0 0 0 c 0 0 0 0 73.0 52.0 59.0 146.0 51.0 0 0 0 0 g 0 0 0 0 113.0 36.0 16.0 67.0 819.0 0 0 0 0 t 0 0 0 0 351.0 75.0 101.0 68.0 82.0 0 0 0 0

MA2058.1_rc_shift4 (PK03929.1_rc)
; oligos_7nt_mkv1_m4 versus MA2058.1_rc (PK03929.1_rc); m=12/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.428413; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 458.0 940.0 941.0 839.0 35.0 0 0 0 0 c 0 0 0 0 73.0 24.0 22.0 80.0 16.0 0 0 0 0 g 0 0 0 0 118.0 10.0 4.0 46.0 908.0 0 0 0 0 t 0 0 0 0 349.0 24.0 31.0 34.0 39.0 0 0 0 0

MA2383.1_rc_shift4 (e_gw1.392.16.1_rc)
; oligos_7nt_mkv1_m4 versus MA2383.1_rc (e_gw1.392.16.1_rc); m=13/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.427214; ----wAAaG---- ; cor=; Ncor= a 0 0 0 0 482.0 860.0 925.0 672.0 70.0 0 0 0 0 c 0 0 0 0 70.0 62.0 35.0 146.0 26.0 0 0 0 0 g 0 0 0 0 117.0 12.0 0.0 51.0 897.0 0 0 0 0 t 0 0 0 0 329.0 64.0 38.0 129.0 4.0 0 0 0 0

MA0989.2_shift4 (PHYPADRAFT_153324)
; oligos_7nt_mkv1_m4 versus MA0989.2 (PHYPADRAFT_153324); m=14/17; ncol2=5; w=0; offset=2; strand=D; shift=4; score=0.42712; ----wAAaG---- ; cor=; Ncor= a 0 0 0 0 482.0 861.0 926.0 672.0 71.0 0 0 0 0 c 0 0 0 0 71.0 62.0 36.0 147.0 27.0 0 0 0 0 g 0 0 0 0 118.0 13.0 0.0 52.0 898.0 0 0 0 0 t 0 0 0 0 330.0 65.0 38.0 129.0 5.0 0 0 0 0

MA2081.1_rc_shift4 (PK20317.1_rc)
; oligos_7nt_mkv1_m4 versus MA2081.1_rc (PK20317.1_rc); m=15/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.419124; ----wAAmG---- ; cor=; Ncor= a 0 0 0 0 477.0 884.0 898.0 646.0 31.0 0 0 0 0 c 0 0 0 0 81.0 60.0 55.0 330.0 37.0 0 0 0 0 g 0 0 0 0 100.0 0.0 0.0 0.0 868.0 0 0 0 0 t 0 0 0 0 340.0 53.0 45.0 22.0 62.0 0 0 0 0

MA0021.1_shift5 (Dof3)
; oligos_7nt_mkv1_m4 versus MA0021.1 (Dof3); m=16/17; ncol2=6; w=0; offset=3; strand=D; shift=5; score=0.418396; -----AAAGyv-- ; cor=; Ncor= a 0 0 0 0 0 21.0 21.0 21.0 0.0 0.0 6.0 0 0 c 0 0 0 0 0 0.0 0.0 0.0 0.0 10.0 6.0 0 0 g 0 0 0 0 0 0.0 0.0 0.0 21.0 3.0 9.0 0 0 t 0 0 0 0 0 0.0 0.0 0.0 0.0 8.0 0.0 0 0

MA1661.2_shift0 (GTL1)
; oligos_7nt_mkv1_m4 versus MA1661.2 (GTL1); m=17/17; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.418386; GGTwAAAA----- ; cor=; Ncor= a 24.0 42.0 48.0 300.0 1038.0 1033.0 996.0 954.0 0 0 0 0 0 c 7.0 5.0 3.0 17.0 5.0 13.0 11.0 18.0 0 0 0 0 0 g 1023.0 1020.0 93.0 74.0 12.0 10.0 13.0 23.0 0 0 0 0 0 t 19.0 6.0 929.0 682.0 18.0 17.0 53.0 78.0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m3_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m3_shift1 (oligos_8nt_mkv1_m3)
; oligos_8nt_mkv1_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -rvCmCTATrGhT ; Alignment reference a 0 2 1 0 2 0 0 3 0 1 0 1 0 c 0 0 1 3 1 3 0 0 0 0 0 1 0 g 0 1 1 0 0 0 0 0 0 2 3 0 0 t 0 0 0 0 0 0 3 0 3 0 0 1 3

MA1368.3_shift2 (GT-4)
; oligos_8nt_mkv1_m3 versus MA1368.3 (GT-4); m=1/4; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.603419; --TAACYATGGTT ; cor=; Ncor= a 0 0 111.0 516.0 621.0 10.0 8.0 571.0 20.0 87.0 20.0 9.0 63.0 c 0 0 55.0 20.0 6.0 612.0 181.0 24.0 26.0 1.0 5.0 5.0 36.0 g 0 0 37.0 44.0 4.0 9.0 2.0 28.0 33.0 552.0 618.0 3.0 11.0 t 0 0 443.0 66.0 15.0 15.0 455.0 23.0 567.0 6.0 3.0 629.0 536.0

MA2404.1_shift1 (OsTRBF3)
; oligos_8nt_mkv1_m3 versus MA2404.1 (OsTRBF3); m=2/4; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.439256; -wrmCCTA----- ; cor=; Ncor= a 0 415.0 534.0 416.0 25.0 41.0 10.0 831.0 0 0 0 0 0 c 0 113.0 24.0 562.0 962.0 928.0 0.0 31.0 0 0 0 0 0 g 0 59.0 369.0 6.0 1.0 26.0 0.0 82.0 0 0 0 0 0 t 0 411.0 71.0 14.0 11.0 3.0 988.0 53.0 0 0 0 0 0

MA1030.2_shift1 (P0510F09.23)
; oligos_8nt_mkv1_m3 versus MA1030.2 (P0510F09.23); m=3/4; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.439233; -wrmCCTA----- ; cor=; Ncor= a 0 416.0 535.0 416.0 26.0 41.0 10.0 832.0 0 0 0 0 0 c 0 113.0 24.0 562.0 962.0 928.0 1.0 32.0 0 0 0 0 0 g 0 60.0 369.0 7.0 1.0 27.0 0.0 83.0 0 0 0 0 0 t 0 411.0 72.0 15.0 11.0 4.0 989.0 54.0 0 0 0 0 0

MA2032.2_shift0 (TRB1)
; oligos_8nt_mkv1_m3 versus MA2032.2 (TRB1); m=4/4; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.434271; aAACCCTAr---- ; cor=; Ncor= a 2956.0 4615.0 4355.0 138.0 86.0 71.0 108.0 4824.0 2829.0 0 0 0 0 c 451.0 128.0 40.0 4706.0 4755.0 4767.0 44.0 34.0 372.0 0 0 0 0 g 682.0 96.0 443.0 35.0 36.0 55.0 57.0 44.0 1303.0 0 0 0 0 t 854.0 104.0 105.0 64.0 66.0 50.0 4734.0 41.0 439.0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)
; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; GhGAAGTGCAw ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 c 0 1 0 0 0 0 0 0 3 0 0 g 3 0 3 0 0 3 0 3 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1

MA2419.1_shift2 (UB3)
; oligos_7nt_mkv1_m3 versus MA2419.1 (UB3); m=1/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.60174; --gAAGTACAA ; cor=; Ncor= a 0 0 3823.0 17244.0 18109.0 293.0 754.0 18975.0 322.0 16933.0 16719.0 c 0 0 2963.0 566.0 527.0 269.0 287.0 196.0 18929.0 795.0 1201.0 g 0 0 11905.0 1023.0 855.0 18318.0 1213.0 675.0 693.0 1162.0 629.0 t 0 0 1439.0 1297.0 639.0 1250.0 17876.0 284.0 186.0 1240.0 1581.0

MA2420.1_shift3 (SBP6)
; oligos_7nt_mkv1_m3 versus MA2420.1 (SBP6); m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.577777; ---AAGTACAA ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0

MA2421.1_shift3 (SBP8)
; oligos_7nt_mkv1_m3 versus MA2421.1 (SBP8); m=3/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.545014; ---arGTACAa ; cor=; Ncor= a 0 0 0 28920.0 30785.0 200.0 256.0 48160.0 275.0 46945.0 27864.0 c 0 0 0 3935.0 226.0 70.0 231.0 67.0 47947.0 397.0 5026.0 g 0 0 0 6297.0 17080.0 48049.0 509.0 52.0 79.0 519.0 5397.0 t 0 0 0 9248.0 309.0 81.0 47404.0 121.0 99.0 539.0 10113.0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift2 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --swAGTGmArw ; Alignment reference a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2

MA2420.1_shift3 (SBP6)
; oligos_6nt_mkv1_m1 versus MA2420.1 (SBP6); m=1/6; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.567971; ---AAGTACAA- ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0 0

MA1381.2_rc_shift2 (AT3G46070_rc)
; oligos_6nt_mkv1_m1 versus MA1381.2_rc (AT3G46070_rc); m=2/6; ncol2=7; w=0; offset=0; strand=R; shift=2; score=0.553548; --agAGTGA--- ; cor=; Ncor= a 0 0 106.0 35.0 202.0 0.0 2.0 0.0 193.0 0 0 0 c 0 0 10.0 22.0 0.0 0.0 0.0 0.0 0.0 0 0 0 g 0 0 44.0 131.0 0.0 200.0 0.0 202.0 0.0 0 0 0 t 0 0 42.0 14.0 0.0 2.0 200.0 0.0 9.0 0 0 0

MA1372.2_rc_shift4 (ZAT10_rc)
; oligos_6nt_mkv1_m1 versus MA1372.2_rc (ZAT10_rc); m=3/6; ncol2=10; w=0; offset=2; strand=R; shift=4; score=0.481435; ----ASTGddas ; cor=; Ncor= a 0 0 0 0 557.0 0.0 0.0 114.0 285.0 159.0 366.0 84.0 c 0 0 0 0 0.0 156.0 0.0 0.0 1.0 128.0 0.0 157.0 g 0 0 0 0 13.0 444.0 0.0 486.0 153.0 155.0 102.0 325.0 t 0 0 0 0 30.0 0.0 600.0 0.0 161.0 158.0 132.0 34.0

MA2372.1_rc_shift0 (AZF1_rc)
; oligos_6nt_mkv1_m1 versus MA2372.1_rc (AZF1_rc); m=4/6; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.456797; wGwsAGTGw--- ; cor=; Ncor= a 350.0 142.0 412.0 104.0 998.0 0.0 0.0 11.0 468.0 0 0 0 c 21.0 33.0 65.0 270.0 0.0 119.0 0.0 0.0 0.0 0 0 0 g 130.0 703.0 83.0 377.0 1.0 880.0 0.0 988.0 109.0 0 0 0 t 496.0 120.0 437.0 248.0 0.0 0.0 1000.0 0.0 422.0 0 0 0

MA1736.2_rc_shift4 (AT5G04390_rc)
; oligos_6nt_mkv1_m1 versus MA1736.2_rc (AT5G04390_rc); m=5/6; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.453164; ----AGTGw--- ; cor=; Ncor= a 0 0 0 0 1000.0 0.0 0.0 15.0 559.0 0 0 0 c 0 0 0 0 0.0 37.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0.0 963.0 0.0 985.0 170.0 0 0 0 t 0 0 0 0 0.0 0.0 1000.0 0.0 270.0 0 0 0

MA0974.3_shift0 (CDF3)
; oligos_6nt_mkv1_m1 versus MA0974.3 (CDF3); m=6/6; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.40469; AAAAAGTG---- ; cor=; Ncor= a 879.0 964.0 1143.0 1133.0 1125.0 1.0 29.0 86.0 0 0 0 0 c 63.0 24.0 2.0 4.0 3.0 0.0 44.0 7.0 0 0 0 0 g 79.0 29.0 7.0 11.0 19.0 1154.0 37.0 1038.0 0 0 0 0 t 136.0 140.0 5.0 9.0 10.0 2.0 1047.0 26.0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2)
; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; bhATGGCYCww ; Alignment reference a 1 2 8 0 0 0 1 0 0 3 2 c 2 2 0 0 1 0 7 2 7 1 1 g 3 1 0 0 7 7 0 0 1 1 0 t 2 3 0 8 0 1 0 6 0 3 5

MA1794.2_shift3 (NLP7)
; oligos_7nt_mkv1_m2 versus MA1794.2 (NLP7); m=1/2; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.540025; ---TGrCyyTT ; cor=; Ncor= a 0 0 0 10.0 66.0 329.0 0.0 0.0 18.0 10.0 39.0 c 0 0 0 182.0 0.0 175.0 1000.0 444.0 390.0 81.0 15.0 g 0 0 0 2.0 934.0 339.0 0.0 40.0 22.0 0.0 0.0 t 0 0 0 807.0 0.0 156.0 0.0 516.0 570.0 909.0 946.0

MA1414.2_rc_shift3 (E2FA_rc)
; oligos_7nt_mkv1_m2 versus MA1414.2_rc (E2FA_rc); m=2/2; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.427624; ---TGGCGC-- ; cor=; Ncor= a 0 0 0 52.0 73.0 11.0 19.0 33.0 11.0 0 0 c 0 0 0 21.0 1.0 18.0 1391.0 22.0 1355.0 0 0 g 0 0 0 10.0 1376.0 1415.0 6.0 1375.0 62.0 0 0 t 0 0 0 1368.0 1.0 7.0 35.0 21.0 23.0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m1_shift0 (oligos_8nt_mkv1_m1)
; oligos_8nt_mkv1_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; ybCTGTGGAAkh ; Alignment reference a 0 0 0 0 0 0 0 0 3 3 0 1 c 2 1 3 0 0 0 0 0 0 0 0 1 g 0 1 0 0 3 0 3 3 0 0 1 0 t 1 1 0 3 0 3 0 0 0 0 2 1

MA2021.2_rc_shift1 (LBD13_rc)
; oligos_8nt_mkv1_m1 versus MA2021.2_rc (LBD13_rc); m=1/1; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.476709; -aCGGTGGa--- ; cor=; Ncor= a 0 628.0 18.0 8.0 9.0 72.0 17.0 39.0 635.0 0 0 0 c 0 143.0 980.0 16.0 8.0 168.0 4.0 20.0 145.0 0 0 0 g 0 227.0 11.0 1021.0 1031.0 6.0 1018.0 979.0 44.0 0 0 0 t 0 57.0 46.0 10.0 7.0 809.0 16.0 17.0 231.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)				; oligos_8nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; GhGAAGTGCAww ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1
MA2419.1_shift2 (UB3)				; oligos_8nt_mkv1_m2 versus MA2419.1 (UB3); m=1/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.630406; --gAAGTACAAc ; cor=; Ncor= a 0 0 3823.0 17244.0 18109.0 293.0 754.0 18975.0 322.0 16933.0 16719.0 4243.0 c 0 0 2963.0 566.0 527.0 269.0 287.0 196.0 18929.0 795.0 1201.0 11116.0 g 0 0 11905.0 1023.0 855.0 18318.0 1213.0 675.0 693.0 1162.0 629.0 3465.0 t 0 0 1439.0 1297.0 639.0 1250.0 17876.0 284.0 186.0 1240.0 1581.0 1306.0
MA2420.1_shift3 (SBP6)				; oligos_8nt_mkv1_m2 versus MA2420.1 (SBP6); m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.529629; ---AAGTACAA- ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0 0
MA2421.1_shift3 (SBP8)				; oligos_8nt_mkv1_m2 versus MA2421.1 (SBP8); m=3/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.499596; ---arGTACAa- ; cor=; Ncor= a 0 0 0 28920.0 30785.0 200.0 256.0 48160.0 275.0 46945.0 27864.0 0 c 0 0 0 3935.0 226.0 70.0 231.0 67.0 47947.0 397.0 5026.0 0 g 0 0 0 6297.0 17080.0 48049.0 509.0 52.0 79.0 519.0 5397.0 0 t 0 0 0 9248.0 309.0 81.0 47404.0 121.0 99.0 539.0 10113.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv1_m4_shift0 (oligos_8nt_mkv1_m4)				; oligos_8nt_mkv1_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; wAAAAGCTCCTry ; Alignment reference a 1 2 2 2 2 0 0 0 0 0 0 1 0 c 0 0 0 0 0 0 2 0 2 2 0 0 1 g 0 0 0 0 0 2 0 0 0 0 0 1 0 t 1 0 0 0 0 0 0 2 0 0 2 0 1
MA1747.2_rc_shift1 (DOF4.3_rc)				; oligos_8nt_mkv1_m4 versus MA1747.2_rc (DOF4.3_rc); m=1/7; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.61216; -wAAAGcywCTTT ; cor=; Ncor= a 0 424.0 998.0 998.0 995.0 2.0 95.0 76.0 429.0 0.0 0.0 0.0 0.0 c 0 103.0 0.0 0.0 0.0 0.0 571.0 345.0 91.0 1000.0 0.0 0.0 0.0 g 0 66.0 2.0 0.0 5.0 995.0 147.0 2.0 178.0 0.0 0.0 0.0 0.0 t 0 407.0 0.0 2.0 0.0 3.0 188.0 578.0 302.0 0.0 1000.0 1000.0 1000.0
MA2029.2_shift3 (MYB88)				; oligos_8nt_mkv1_m4 versus MA2029.2 (MYB88); m=2/7; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.508175; ---ACGCTCCTC- ; cor=; Ncor= a 0 0 0 150.0 3.0 1.0 0.0 1.0 1.0 0.0 18.0 7.0 0 c 0 0 0 15.0 159.0 1.0 167.0 1.0 165.0 152.0 6.0 138.0 0 g 0 0 0 3.0 6.0 165.0 1.0 27.0 2.0 3.0 3.0 6.0 0 t 0 0 0 0.0 0.0 1.0 0.0 139.0 0.0 13.0 141.0 17.0 0
MA0973.2_shift0 (CDF2)				; oligos_8nt_mkv1_m4 versus MA0973.2 (CDF2); m=3/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.471427; aWAAAGy------ ; cor=; Ncor= a 608.0 693.0 980.0 979.0 868.0 17.0 53.0 0 0 0 0 0 0 c 92.0 16.0 10.0 10.0 29.0 7.0 295.0 0 0 0 0 0 0 g 150.0 41.0 4.0 2.0 81.0 969.0 154.0 0 0 0 0 0 0 t 150.0 250.0 5.0 9.0 22.0 6.0 498.0 0 0 0 0 0 0
MA1815.2_rc_shift5 (GRF4_rc)				; oligos_8nt_mkv1_m4 versus MA1815.2_rc (GRF4_rc); m=4/7; ncol2=8; w=0; offset=5; strand=R; shift=5; score=0.441764; -----GCTGCTGC ; cor=; Ncor= a 0 0 0 0 0 0.0 1.0 10.0 2.0 1.0 3.0 0.0 3.0 c 0 0 0 0 0 4.0 59.0 0.0 0.0 61.0 5.0 3.0 54.0 g 0 0 0 0 0 59.0 3.0 2.0 60.0 1.0 1.0 59.0 1.0 t 0 0 0 0 0 2.0 2.0 53.0 3.0 2.0 56.0 3.0 7.0
MA1272.3_shift0 (DOF2.2)				; oligos_8nt_mkv1_m4 versus MA1272.3 (DOF2.2); m=5/7; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.435014; AAAAAG------- ; cor=; Ncor= a 1086.0 1077.0 1086.0 1084.0 1086.0 0.0 0 0 0 0 0 0 0 c 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 0 0 g 0.0 0.0 0.0 0.0 0.0 1086.0 0 0 0 0 0 0 0 t 0.0 9.0 0.0 2.0 0.0 0.0 0 0 0 0 0 0 0
MA1280.2_shift0 (DOF5.4)				; oligos_8nt_mkv1_m4 versus MA1280.2 (DOF5.4); m=6/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.430692; AAAAAGk------ ; cor=; Ncor= a 529.0 456.0 599.0 600.0 600.0 0.0 22.0 0 0 0 0 0 0 c 17.0 0.0 0.0 0.0 0.0 0.0 37.0 0 0 0 0 0 0 g 34.0 3.0 0.0 0.0 0.0 600.0 209.0 0 0 0 0 0 0 t 20.0 141.0 1.0 0.0 0.0 0.0 332.0 0 0 0 0 0 0
MA1276.2_shift0 (DOF3.5)				; oligos_8nt_mkv1_m4 versus MA1276.2 (DOF3.5); m=7/7; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.405671; AwAAAGk------ ; cor=; Ncor= a 467.0 348.0 599.0 599.0 599.0 0.0 2.0 0 0 0 0 0 0 c 4.0 0.0 0.0 0.0 0.0 0.0 6.0 0 0 0 0 0 0 g 103.0 0.0 0.0 0.0 0.0 599.0 219.0 0 0 0 0 0 0 t 25.0 251.0 0.0 0.0 0.0 0.0 372.0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m4_shift2 (oligos_7nt_mkv1_m4)				; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --hdAAAAGAGsr ; Alignment reference a 0 0 1 1 4 4 4 4 0 4 0 0 2 c 0 0 1 0 0 0 0 0 0 0 0 2 0 g 0 0 0 2 0 0 0 0 4 0 4 2 2 t 0 0 2 1 0 0 0 0 0 0 0 0 0
MA1415.2_shift2 (REF6)				; oligos_7nt_mkv1_m4 versus MA1415.2 (REF6); m=1/17; ncol2=9; w=0; offset=0; strand=D; shift=2; score=0.61003; --rAAACAGAG-- ; cor=; Ncor= a 0 0 1983.0 2634.0 3458.0 3511.0 1.0 3622.0 6.0 3533.0 45.0 0 0 c 0 0 209.0 137.0 27.0 34.0 3661.0 25.0 21.0 21.0 10.0 0 0 g 0 0 1144.0 577.0 24.0 118.0 1.0 30.0 3625.0 105.0 3581.0 0 0 t 0 0 351.0 339.0 178.0 24.0 24.0 10.0 35.0 28.0 51.0 0 0
MA0974.3_shift3 (CDF3)				; oligos_7nt_mkv1_m4 versus MA0974.3 (CDF3); m=2/17; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.563952; ---AAAAAGTG-- ; cor=; Ncor= a 0 0 0 879.0 964.0 1143.0 1133.0 1125.0 1.0 29.0 86.0 0 0 c 0 0 0 63.0 24.0 2.0 4.0 3.0 0.0 44.0 7.0 0 0 g 0 0 0 79.0 29.0 7.0 11.0 19.0 1154.0 37.0 1038.0 0 0 t 0 0 0 136.0 140.0 5.0 9.0 10.0 2.0 1047.0 26.0 0 0
MA0977.1_shift3 (DOF2.5)				; oligos_7nt_mkv1_m4 versus MA0977.1 (DOF2.5); m=3/17; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.51989; ---AwAARGTg-- ; cor=; Ncor= a 0 0 0 756.0 598.0 990.0 986.0 744.0 4.0 8.0 238.0 0 0 c 0 0 0 26.0 1.0 1.0 1.0 1.0 1.0 198.0 44.0 0 0 g 0 0 0 182.0 12.0 4.0 8.0 254.0 977.0 65.0 557.0 0 0 t 0 0 0 36.0 389.0 5.0 6.0 1.0 18.0 729.0 160.0 0 0
MA0973.2_shift3 (CDF2)				; oligos_7nt_mkv1_m4 versus MA0973.2 (CDF2); m=4/17; ncol2=7; w=0; offset=1; strand=D; shift=3; score=0.505677; ---aWAAAGy--- ; cor=; Ncor= a 0 0 0 608.0 693.0 980.0 979.0 868.0 17.0 53.0 0 0 0 c 0 0 0 92.0 16.0 10.0 10.0 29.0 7.0 295.0 0 0 0 g 0 0 0 150.0 41.0 4.0 2.0 81.0 969.0 154.0 0 0 0 t 0 0 0 150.0 250.0 5.0 9.0 22.0 6.0 498.0 0 0 0
MA1272.3_shift3 (DOF2.2)				; oligos_7nt_mkv1_m4 versus MA1272.3 (DOF2.2); m=5/17; ncol2=6; w=0; offset=1; strand=D; shift=3; score=0.489605; ---AAAAAG---- ; cor=; Ncor= a 0 0 0 1086.0 1077.0 1086.0 1084.0 1086.0 0.0 0 0 0 0 c 0 0 0 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 g 0 0 0 0.0 0.0 0.0 0.0 0.0 1086.0 0 0 0 0 t 0 0 0 0.0 9.0 0.0 2.0 0.0 0.0 0 0 0 0
MA1280.2_shift3 (DOF5.4)				; oligos_7nt_mkv1_m4 versus MA1280.2 (DOF5.4); m=6/17; ncol2=7; w=0; offset=1; strand=D; shift=3; score=0.482869; ---AAAAAGk--- ; cor=; Ncor= a 0 0 0 529.0 456.0 599.0 600.0 600.0 0.0 22.0 0 0 0 c 0 0 0 17.0 0.0 0.0 0.0 0.0 0.0 37.0 0 0 0 g 0 0 0 34.0 3.0 0.0 0.0 0.0 600.0 209.0 0 0 0 t 0 0 0 20.0 141.0 1.0 0.0 0.0 0.0 332.0 0 0 0
MA1276.2_shift3 (DOF3.5)				; oligos_7nt_mkv1_m4 versus MA1276.2 (DOF3.5); m=7/17; ncol2=7; w=0; offset=1; strand=D; shift=3; score=0.467031; ---AwAAAGk--- ; cor=; Ncor= a 0 0 0 467.0 348.0 599.0 599.0 599.0 0.0 2.0 0 0 0 c 0 0 0 4.0 0.0 0.0 0.0 0.0 0.0 6.0 0 0 0 g 0 0 0 103.0 0.0 0.0 0.0 0.0 599.0 219.0 0 0 0 t 0 0 0 25.0 251.0 0.0 0.0 0.0 0.0 372.0 0 0 0
MA2069.1_rc_shift4 (PK10955.1_rc)				; oligos_7nt_mkv1_m4 versus MA2069.1_rc (PK10955.1_rc); m=8/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.439423; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 615.0 979.0 988.0 857.0 17.0 0 0 0 0 c 0 0 0 0 16.0 8.0 3.0 43.0 3.0 0 0 0 0 g 0 0 0 0 59.0 4.0 0.0 89.0 970.0 0 0 0 0 t 0 0 0 0 308.0 7.0 7.0 8.0 9.0 0 0 0 0
MA2084.1_rc_shift4 (PK23009.1_rc)				; oligos_7nt_mkv1_m4 versus MA2084.1_rc (PK23009.1_rc); m=9/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.436055; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 563.0 930.0 927.0 811.0 79.0 0 0 0 0 c 0 0 0 0 25.0 18.0 19.0 54.0 5.0 0 0 0 0 g 0 0 0 0 73.0 12.0 0.0 104.0 890.0 0 0 0 0 t 0 0 0 0 338.0 39.0 52.0 29.0 24.0 0 0 0 0
MA2085.1_rc_shift4 (PK23763.1_rc)				; oligos_7nt_mkv1_m4 versus MA2085.1_rc (PK23763.1_rc); m=10/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.430016; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 489.0 944.0 941.0 839.0 26.0 0 0 0 0 c 0 0 0 0 53.0 24.0 21.0 71.0 13.0 0 0 0 0 g 0 0 0 0 91.0 8.0 6.0 52.0 933.0 0 0 0 0 t 0 0 0 0 366.0 22.0 30.0 35.0 26.0 0 0 0 0
MA2356.1_rc_shift4 (PK20555.1_rc)				; oligos_7nt_mkv1_m4 versus MA2356.1_rc (PK20555.1_rc); m=11/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.429214; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 461.0 835.0 821.0 717.0 46.0 0 0 0 0 c 0 0 0 0 73.0 52.0 59.0 146.0 51.0 0 0 0 0 g 0 0 0 0 113.0 36.0 16.0 67.0 819.0 0 0 0 0 t 0 0 0 0 351.0 75.0 101.0 68.0 82.0 0 0 0 0
MA2058.1_rc_shift4 (PK03929.1_rc)				; oligos_7nt_mkv1_m4 versus MA2058.1_rc (PK03929.1_rc); m=12/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.428413; ----wAAAG---- ; cor=; Ncor= a 0 0 0 0 458.0 940.0 941.0 839.0 35.0 0 0 0 0 c 0 0 0 0 73.0 24.0 22.0 80.0 16.0 0 0 0 0 g 0 0 0 0 118.0 10.0 4.0 46.0 908.0 0 0 0 0 t 0 0 0 0 349.0 24.0 31.0 34.0 39.0 0 0 0 0
MA2383.1_rc_shift4 (e_gw1.392.16.1_rc)				; oligos_7nt_mkv1_m4 versus MA2383.1_rc (e_gw1.392.16.1_rc); m=13/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.427214; ----wAAaG---- ; cor=; Ncor= a 0 0 0 0 482.0 860.0 925.0 672.0 70.0 0 0 0 0 c 0 0 0 0 70.0 62.0 35.0 146.0 26.0 0 0 0 0 g 0 0 0 0 117.0 12.0 0.0 51.0 897.0 0 0 0 0 t 0 0 0 0 329.0 64.0 38.0 129.0 4.0 0 0 0 0
MA0989.2_shift4 (PHYPADRAFT_153324)				; oligos_7nt_mkv1_m4 versus MA0989.2 (PHYPADRAFT_153324); m=14/17; ncol2=5; w=0; offset=2; strand=D; shift=4; score=0.42712; ----wAAaG---- ; cor=; Ncor= a 0 0 0 0 482.0 861.0 926.0 672.0 71.0 0 0 0 0 c 0 0 0 0 71.0 62.0 36.0 147.0 27.0 0 0 0 0 g 0 0 0 0 118.0 13.0 0.0 52.0 898.0 0 0 0 0 t 0 0 0 0 330.0 65.0 38.0 129.0 5.0 0 0 0 0
MA2081.1_rc_shift4 (PK20317.1_rc)				; oligos_7nt_mkv1_m4 versus MA2081.1_rc (PK20317.1_rc); m=15/17; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.419124; ----wAAmG---- ; cor=; Ncor= a 0 0 0 0 477.0 884.0 898.0 646.0 31.0 0 0 0 0 c 0 0 0 0 81.0 60.0 55.0 330.0 37.0 0 0 0 0 g 0 0 0 0 100.0 0.0 0.0 0.0 868.0 0 0 0 0 t 0 0 0 0 340.0 53.0 45.0 22.0 62.0 0 0 0 0
MA0021.1_shift5 (Dof3)				; oligos_7nt_mkv1_m4 versus MA0021.1 (Dof3); m=16/17; ncol2=6; w=0; offset=3; strand=D; shift=5; score=0.418396; -----AAAGyv-- ; cor=; Ncor= a 0 0 0 0 0 21.0 21.0 21.0 0.0 0.0 6.0 0 0 c 0 0 0 0 0 0.0 0.0 0.0 0.0 10.0 6.0 0 0 g 0 0 0 0 0 0.0 0.0 0.0 21.0 3.0 9.0 0 0 t 0 0 0 0 0 0.0 0.0 0.0 0.0 8.0 0.0 0 0
MA1661.2_shift0 (GTL1)				; oligos_7nt_mkv1_m4 versus MA1661.2 (GTL1); m=17/17; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.418386; GGTwAAAA----- ; cor=; Ncor= a 24.0 42.0 48.0 300.0 1038.0 1033.0 996.0 954.0 0 0 0 0 0 c 7.0 5.0 3.0 17.0 5.0 13.0 11.0 18.0 0 0 0 0 0 g 1023.0 1020.0 93.0 74.0 12.0 10.0 13.0 23.0 0 0 0 0 0 t 19.0 6.0 929.0 682.0 18.0 17.0 53.0 78.0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv1_m3_shift1 (oligos_8nt_mkv1_m3)				; oligos_8nt_mkv1_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -rvCmCTATrGhT ; Alignment reference a 0 2 1 0 2 0 0 3 0 1 0 1 0 c 0 0 1 3 1 3 0 0 0 0 0 1 0 g 0 1 1 0 0 0 0 0 0 2 3 0 0 t 0 0 0 0 0 0 3 0 3 0 0 1 3
MA1368.3_shift2 (GT-4)				; oligos_8nt_mkv1_m3 versus MA1368.3 (GT-4); m=1/4; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.603419; --TAACYATGGTT ; cor=; Ncor= a 0 0 111.0 516.0 621.0 10.0 8.0 571.0 20.0 87.0 20.0 9.0 63.0 c 0 0 55.0 20.0 6.0 612.0 181.0 24.0 26.0 1.0 5.0 5.0 36.0 g 0 0 37.0 44.0 4.0 9.0 2.0 28.0 33.0 552.0 618.0 3.0 11.0 t 0 0 443.0 66.0 15.0 15.0 455.0 23.0 567.0 6.0 3.0 629.0 536.0
MA2404.1_shift1 (OsTRBF3)				; oligos_8nt_mkv1_m3 versus MA2404.1 (OsTRBF3); m=2/4; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.439256; -wrmCCTA----- ; cor=; Ncor= a 0 415.0 534.0 416.0 25.0 41.0 10.0 831.0 0 0 0 0 0 c 0 113.0 24.0 562.0 962.0 928.0 0.0 31.0 0 0 0 0 0 g 0 59.0 369.0 6.0 1.0 26.0 0.0 82.0 0 0 0 0 0 t 0 411.0 71.0 14.0 11.0 3.0 988.0 53.0 0 0 0 0 0
MA1030.2_shift1 (P0510F09.23)				; oligos_8nt_mkv1_m3 versus MA1030.2 (P0510F09.23); m=3/4; ncol2=7; w=0; offset=0; strand=D; shift=1; score=0.439233; -wrmCCTA----- ; cor=; Ncor= a 0 416.0 535.0 416.0 26.0 41.0 10.0 832.0 0 0 0 0 0 c 0 113.0 24.0 562.0 962.0 928.0 1.0 32.0 0 0 0 0 0 g 0 60.0 369.0 7.0 1.0 27.0 0.0 83.0 0 0 0 0 0 t 0 411.0 72.0 15.0 11.0 4.0 989.0 54.0 0 0 0 0 0
MA2032.2_shift0 (TRB1)				; oligos_8nt_mkv1_m3 versus MA2032.2 (TRB1); m=4/4; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score=0.434271; aAACCCTAr---- ; cor=; Ncor= a 2956.0 4615.0 4355.0 138.0 86.0 71.0 108.0 4824.0 2829.0 0 0 0 0 c 451.0 128.0 40.0 4706.0 4755.0 4767.0 44.0 34.0 372.0 0 0 0 0 g 682.0 96.0 443.0 35.0 36.0 55.0 57.0 44.0 1303.0 0 0 0 0 t 854.0 104.0 105.0 64.0 66.0 50.0 4734.0 41.0 439.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3)				; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; GhGAAGTGCAw ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 c 0 1 0 0 0 0 0 0 3 0 0 g 3 0 3 0 0 3 0 3 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1
MA2419.1_shift2 (UB3)				; oligos_7nt_mkv1_m3 versus MA2419.1 (UB3); m=1/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.60174; --gAAGTACAA ; cor=; Ncor= a 0 0 3823.0 17244.0 18109.0 293.0 754.0 18975.0 322.0 16933.0 16719.0 c 0 0 2963.0 566.0 527.0 269.0 287.0 196.0 18929.0 795.0 1201.0 g 0 0 11905.0 1023.0 855.0 18318.0 1213.0 675.0 693.0 1162.0 629.0 t 0 0 1439.0 1297.0 639.0 1250.0 17876.0 284.0 186.0 1240.0 1581.0
MA2420.1_shift3 (SBP6)				; oligos_7nt_mkv1_m3 versus MA2420.1 (SBP6); m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.577777; ---AAGTACAA ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0
MA2421.1_shift3 (SBP8)				; oligos_7nt_mkv1_m3 versus MA2421.1 (SBP8); m=3/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.545014; ---arGTACAa ; cor=; Ncor= a 0 0 0 28920.0 30785.0 200.0 256.0 48160.0 275.0 46945.0 27864.0 c 0 0 0 3935.0 226.0 70.0 231.0 67.0 47947.0 397.0 5026.0 g 0 0 0 6297.0 17080.0 48049.0 509.0 52.0 79.0 519.0 5397.0 t 0 0 0 9248.0 309.0 81.0 47404.0 121.0 99.0 539.0 10113.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1)				; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --swAGTGmArw ; Alignment reference a 0 0 1 3 6 0 0 0 2 6 3 3 c 0 0 2 0 0 0 0 0 4 0 0 1 g 0 0 3 1 0 6 0 6 0 0 2 0 t 0 0 0 2 0 0 6 0 0 0 1 2
MA2420.1_shift3 (SBP6)				; oligos_6nt_mkv1_m1 versus MA2420.1 (SBP6); m=1/6; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.567971; ---AAGTACAA- ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0 0
MA1381.2_rc_shift2 (AT3G46070_rc)				; oligos_6nt_mkv1_m1 versus MA1381.2_rc (AT3G46070_rc); m=2/6; ncol2=7; w=0; offset=0; strand=R; shift=2; score=0.553548; --agAGTGA--- ; cor=; Ncor= a 0 0 106.0 35.0 202.0 0.0 2.0 0.0 193.0 0 0 0 c 0 0 10.0 22.0 0.0 0.0 0.0 0.0 0.0 0 0 0 g 0 0 44.0 131.0 0.0 200.0 0.0 202.0 0.0 0 0 0 t 0 0 42.0 14.0 0.0 2.0 200.0 0.0 9.0 0 0 0
MA1372.2_rc_shift4 (ZAT10_rc)				; oligos_6nt_mkv1_m1 versus MA1372.2_rc (ZAT10_rc); m=3/6; ncol2=10; w=0; offset=2; strand=R; shift=4; score=0.481435; ----ASTGddas ; cor=; Ncor= a 0 0 0 0 557.0 0.0 0.0 114.0 285.0 159.0 366.0 84.0 c 0 0 0 0 0.0 156.0 0.0 0.0 1.0 128.0 0.0 157.0 g 0 0 0 0 13.0 444.0 0.0 486.0 153.0 155.0 102.0 325.0 t 0 0 0 0 30.0 0.0 600.0 0.0 161.0 158.0 132.0 34.0
MA2372.1_rc_shift0 (AZF1_rc)				; oligos_6nt_mkv1_m1 versus MA2372.1_rc (AZF1_rc); m=4/6; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.456797; wGwsAGTGw--- ; cor=; Ncor= a 350.0 142.0 412.0 104.0 998.0 0.0 0.0 11.0 468.0 0 0 0 c 21.0 33.0 65.0 270.0 0.0 119.0 0.0 0.0 0.0 0 0 0 g 130.0 703.0 83.0 377.0 1.0 880.0 0.0 988.0 109.0 0 0 0 t 496.0 120.0 437.0 248.0 0.0 0.0 1000.0 0.0 422.0 0 0 0
MA1736.2_rc_shift4 (AT5G04390_rc)				; oligos_6nt_mkv1_m1 versus MA1736.2_rc (AT5G04390_rc); m=5/6; ncol2=5; w=0; offset=2; strand=R; shift=4; score=0.453164; ----AGTGw--- ; cor=; Ncor= a 0 0 0 0 1000.0 0.0 0.0 15.0 559.0 0 0 0 c 0 0 0 0 0.0 37.0 0.0 0.0 0.0 0 0 0 g 0 0 0 0 0.0 963.0 0.0 985.0 170.0 0 0 0 t 0 0 0 0 0.0 0.0 1000.0 0.0 270.0 0 0 0
MA0974.3_shift0 (CDF3)				; oligos_6nt_mkv1_m1 versus MA0974.3 (CDF3); m=6/6; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.40469; AAAAAGTG---- ; cor=; Ncor= a 879.0 964.0 1143.0 1133.0 1125.0 1.0 29.0 86.0 0 0 0 0 c 63.0 24.0 2.0 4.0 3.0 0.0 44.0 7.0 0 0 0 0 g 79.0 29.0 7.0 11.0 19.0 1154.0 37.0 1038.0 0 0 0 0 t 136.0 140.0 5.0 9.0 10.0 2.0 1047.0 26.0 0 0 0 0