Clover: Cis-eLement OVERrepresentation Compiled on Feb 22 2004 Sequence file: seq (7 sequences, 11205 bp, 50.3% C+G) Motif file: jaspar2 (108 motifs) *** Over- and Under-represented Motifs: Motif Raw score P-value from randomizing backseq MA0014 Bsap PAIRED 1.1 0.007 MA0095 Yin-Yang ZN-FINGER, C2H2 0.568 0.001 MA0012 Broad-complex_3 ZN-FINGER, C2H2 0.292 1 MA0003 AP2alpha AP2 0.214 1 MA0091 Tal1beta-E47S bHLH -0.0676 0.005 MA0035 GATA-1 ZN-FINGER, GATA -0.0993 0 MA0011 Broad-complex_2 ZN-FINGER, C2H2 -0.645 1 MA0036 GATA-2 ZN-FINGER, GATA -0.819 0.004 MA0037 GATA-3 ZN-FINGER, GATA -0.821 0 MA0058 Max bHLH-ZIP -0.94 0.001 MA0082 SQUA MADS -1.02 0.996 MA0085 SU_h IPT/TIG domain -1.09 0 MA0094 Ubx HOMEO -1.32 0.993 MA0015 CF2-II ZN-FINGER, C2H2 -1.36 0.006 MA0075 S8 HOMEO -1.52 1 MA0059 Myc-Max bHLH-ZIP -1.77 0.001 MA0074 RXR-VDR NUCLEAR RECEPTOR -2.06 0 MA0108 TBP TATA-BOX -2.12 0.002 MA0050 Irf-1 TRP-CLUSTER -2.79 1 MA0009 Brachyury T-BOX -2.94 0 MA0025 E4BP4 bZIP -4.17 0.999 MA0083 SRF MADS -5.01 0 *** Motif Instances with Score >= 6: Motif Location Strand Sequence Score >NM_022427|gpr88|1600bp MA0012 Broad-complex_3 ZN-FINGER, C2H2 96 - 106 - actttagttta 7.44 MA0082 SQUA MADS 215 - 228 + acataaaaagccag 7.85 MA0075 S8 HOMEO 527 - 531 - taatt 6.28 MA0095 Yin-Yang ZN-FINGER, C2H2 594 - 599 + accatc 6.4 MA0095 Yin-Yang ZN-FINGER, C2H2 605 - 610 + accatc 6.4 MA0091 Tal1beta-E47S bHLH 671 - 682 + ccgacagctggt 8.06 MA0091 Tal1beta-E47S bHLH 673 - 684 - gacagctggtgg 8.37 MA0085 SU_h IPT/TIG domain 884 - 899 - actatggtactcacac 6.86 MA0075 S8 HOMEO 964 - 968 + aatta 6.25 MA0075 S8 HOMEO 1003 - 1007 - taatt 6.28 MA0075 S8 HOMEO 1004 - 1008 + aatta 6.25 MA0075 S8 HOMEO 1097 - 1101 - taatt 6.28 MA0015 CF2-II ZN-FINGER, C2H2 1122 - 1131 + gtatatttat 6.11 MA0085 SU_h IPT/TIG domain 1132 - 1147 + ctctgagaaaagaagt 6.33 MA0082 SQUA MADS 1328 - 1341 + ctgaaaaaggtatt 6.32 MA0075 S8 HOMEO 1372 - 1376 - taatt 6.28 MA0085 SU_h IPT/TIG domain 1439 - 1454 - agtgggtttgccacat 7.47 >NM_078477|KLF16|1600bp MA0014 Bsap PAIRED 43 - 62 + agagcactggaacctgacca 7.12 MA0009 Brachyury T-BOX 96 - 106 - atgacacccag 6.42 MA0012 Broad-complex_3 ZN-FINGER, C2H2 146 - 156 + taaacatgatg 8.72 MA0011 Broad-complex_2 ZN-FINGER, C2H2 272 - 279 + tcctactt 6.53 MA0095 Yin-Yang ZN-FINGER, C2H2 318 - 323 + accatc 6.83 MA0009 Brachyury T-BOX 326 - 336 - ttcacaacttg 7.69 MA0094 Ubx HOMEO 341 - 344 - atta 6.54 MA0094 Ubx HOMEO 369 - 372 - atta 6.54 MA0050 Irf-1 TRP-CLUSTER 492 - 503 - ctgttcactttt 6.1 MA0085 SU_h IPT/TIG domain 495 - 510 - ttcacttttgccatac 6.36 MA0074 RXR-VDR NUCLEAR RECEPTOR 557 - 571 - cgaactctacaaact 9.44 MA0074 RXR-VDR NUCLEAR RECEPTOR 566 - 580 - caaactcgatcagct 6.7 MA0082 SQUA MADS 642 - 655 + ccaagaatggcatt 7.23 MA0059 Myc-Max bHLH-ZIP 730 - 740 + gcgcacgtggc 6.81 MA0058 Max bHLH-ZIP 732 - 741 - gcacgtggcc 7.07 MA0058 Max bHLH-ZIP 779 - 788 + ggccacgtgc 7.07 >NW_000028|A2AR|m1A|1600bp MA0095 Yin-Yang ZN-FINGER, C2H2 156 - 161 + gccatc 6.41 MA0014 Bsap PAIRED 177 - 196 - tgtttatgctccactgtgtt 8.42 MA0003 AP2alpha AP2 310 - 318 + gccctaagg 6.38 MA0091 Tal1beta-E47S bHLH 479 - 490 - gccagatggacc 6.42 MA0091 Tal1beta-E47S bHLH 588 - 599 - aacagctcgttg 6.85 MA0075 S8 HOMEO 691 - 695 - taatt 7.05 MA0009 Brachyury T-BOX 748 - 758 + gtaggtgacaa 6.54 MA0075 S8 HOMEO 971 - 975 + aatta 7.1 MA0085 SU_h IPT/TIG domain 1067 - 1082 + tcgtgggatcctttgg 6.36 MA0014 Bsap PAIRED 1179 - 1198 + ggggccctgctgcggagaga 7.6 >NM_008313|htr4|1600bp MA0095 Yin-Yang ZN-FINGER, C2H2 72 - 77 + gccatc 6.5 MA0108 TBP TATA-BOX 246 - 261 + aatactatataaatta 7.7 MA0075 S8 HOMEO 257 - 261 + aatta 6.31 MA0082 SQUA MADS 326 - 339 + acaaatttaataat 6.23 MA0075 S8 HOMEO 336 - 340 - taatt 6.25 MA0075 S8 HOMEO 337 - 341 + aatta 6.31 MA0075 S8 HOMEO 351 - 355 - taatt 6.25 MA0050 Irf-1 TRP-CLUSTER 363 - 374 - gctttcactgtg 7.35 MA0095 Yin-Yang ZN-FINGER, C2H2 400 - 405 + gccatc 6.5 MA0037 GATA-3 ZN-FINGER, GATA 430 - 435 + agatag 6.06 MA0012 Broad-complex_3 ZN-FINGER, C2H2 690 - 700 + aaaactaagca 6.32 MA0091 Tal1beta-E47S bHLH 1106 - 1117 - agcagatggagt 6.71 MA0058 Max bHLH-ZIP 1253 - 1262 + agtcacgtgg 8.58 MA0059 Myc-Max bHLH-ZIP 1253 - 1263 + agtcacgtggt 8.56 MA0059 Myc-Max bHLH-ZIP 1254 - 1264 - gtcacgtggtc 8.62 MA0058 Max bHLH-ZIP 1255 - 1264 - tcacgtggtc 9.98 MA0091 Tal1beta-E47S bHLH 1270 - 1281 - cacaggtggtca 6.02 MA0037 GATA-3 ZN-FINGER, GATA 1306 - 1311 + agatag 6.06 MA0095 Yin-Yang ZN-FINGER, C2H2 1312 - 1317 - gatggc 6.47 MA0050 Irf-1 TRP-CLUSTER 1364 - 1375 + acaactgaaagc 6.59 MA0003 AP2alpha AP2 1497 - 1505 + gcccagagg 6.3 MA0003 AP2alpha AP2 1513 - 1521 - gcccctggc 6.93 MA0003 AP2alpha AP2 1513 - 1521 + gcccctggc 6.77 >NM_011268|rgs9|1600bp MA0050 Irf-1 TRP-CLUSTER 35 - 46 - attttcgatttt 6.02 MA0025 E4BP4 bZIP 234 - 244 - agctcacataa 6.06 MA0083 SRF MADS 235 - 246 + gctcacataagg 6.12 MA0003 AP2alpha AP2 366 - 374 + gcccagggg 7.03 MA0085 SU_h IPT/TIG domain 368 - 383 + ccaggggaaacgagca 6.41 MA0011 Broad-complex_2 ZN-FINGER, C2H2 504 - 511 - aaatagtg 6.02 MA0015 CF2-II ZN-FINGER, C2H2 610 - 619 - gtatatctat 6.59 MA0015 CF2-II ZN-FINGER, C2H2 610 - 619 + gtatatctat 6.75 MA0059 Myc-Max bHLH-ZIP 756 - 766 + gagcaggtggc 7.55 MA0014 Bsap PAIRED 763 - 782 - tggccactctggaggcatct 7 MA0012 Broad-complex_3 ZN-FINGER, C2H2 846 - 856 + caaacaaatac 6.26 MA0075 S8 HOMEO 867 - 871 + aatta 6.44 MA0075 S8 HOMEO 883 - 887 - taatt 6.23 MA0003 AP2alpha AP2 889 - 897 + gcctaaggg 6.11 MA0011 Broad-complex_2 ZN-FINGER, C2H2 962 - 969 + tactagtt 6 MA0075 S8 HOMEO 987 - 991 + aatta 6.44 MA0091 Tal1beta-E47S bHLH 999 - 1010 + tctacatctggt 7.51 MA0091 Tal1beta-E47S bHLH 1001 - 1012 - tacatctggtat 6.14 MA0082 SQUA MADS 1128 - 1141 + tcttataaagaaat 6.92 MA0085 SU_h IPT/TIG domain 1197 - 1212 - agctcctttcccactg 8.59 MA0108 TBP TATA-BOX 1226 - 1241 + ttctgtatataaagag 8.74 MA0015 CF2-II ZN-FINGER, C2H2 1230 - 1239 + gtatataaag 6.22 MA0003 AP2alpha AP2 1259 - 1267 - ccttggggc 6.91 MA0003 AP2alpha AP2 1329 - 1337 + gccggacgc 6.43 MA0003 AP2alpha AP2 1383 - 1391 - gcgcgcggc 6.6 MA0014 Bsap PAIRED 1442 - 1461 + ggtgcgagggagagtcgagg 6.06 MA0014 Bsap PAIRED 1450 - 1469 + ggagagtcgaggggtggagg 6.37 MA0014 Bsap PAIRED 1454 - 1473 + agtcgaggggtggagggcgg 6.01 MA0003 AP2alpha AP2 1482 - 1490 + gccctgcgc 6.59 >NM_013643|ptpn5|1600bp MA0091 Tal1beta-E47S bHLH 59 - 70 - gccatatggctt 6.13 MA0014 Bsap PAIRED 66 - 85 + ggctttctggagcggagaga 8.07 MA0095 Yin-Yang ZN-FINGER, C2H2 120 - 125 + gccatc 6.11 MA0095 Yin-Yang ZN-FINGER, C2H2 247 - 252 + gccatc 6.11 MA0082 SQUA MADS 296 - 309 - atttctttctttct 6.23 MA0014 Bsap PAIRED 300 - 319 - ctttctttcttccttttttt 6.76 MA0011 Broad-complex_2 ZN-FINGER, C2H2 452 - 459 + ttcttttt 6.09 MA0014 Bsap PAIRED 651 - 670 - ctgtcccgctgcataagtca 7.28 MA0082 SQUA MADS 725 - 738 + acagaaaaagaagg 6.88 MA0091 Tal1beta-E47S bHLH 894 - 905 + catccatctgtc 7.03 MA0003 AP2alpha AP2 1171 - 1179 + gccctaggc 6.29 MA0014 Bsap PAIRED 1356 - 1375 + ggagcacgcaaggagagcgg 6.5 MA0085 SU_h IPT/TIG domain 1569 - 1584 + gtgtgagaagccggga 6.49 >NT_039474|ARPP-19|ProSeq_37|contig|1600bp MA0085 SU_h IPT/TIG domain 3 - 18 - tgacatgttcacacag 6.59 MA0108 TBP TATA-BOX 30 - 45 - caggatatatattgtg 6.09 MA0009 Brachyury T-BOX 153 - 163 + acaggtgtgaa 7.73 MA0108 TBP TATA-BOX 367 - 382 + aaaaatatatatacac 6.58 MA0108 TBP TATA-BOX 369 - 384 - aaatatatatacacac 6.29 MA0015 CF2-II ZN-FINGER, C2H2 371 - 380 - atatatatac 8.35 MA0015 CF2-II ZN-FINGER, C2H2 371 - 380 + atatatatac 8.07 MA0015 CF2-II ZN-FINGER, C2H2 373 - 382 - atatatacac 6.23 MA0015 CF2-II ZN-FINGER, C2H2 373 - 382 + atatatacac 6.8 MA0015 CF2-II ZN-FINGER, C2H2 389 - 398 - atacatatat 7.76 MA0015 CF2-II ZN-FINGER, C2H2 391 - 400 - acatatatat 6.92 MA0015 CF2-II ZN-FINGER, C2H2 393 - 402 - atatatatat 7.17 MA0015 CF2-II ZN-FINGER, C2H2 393 - 402 + atatatatat 7.17 MA0015 CF2-II ZN-FINGER, C2H2 395 - 404 + atatatataa 6.35 MA0108 TBP TATA-BOX 461 - 476 + cttgctatataagaac 7.12 MA0091 Tal1beta-E47S bHLH 605 - 616 + tggccagctggc 8.42 MA0091 Tal1beta-E47S bHLH 607 - 618 - gccagctggcca 8.61 MA0003 AP2alpha AP2 608 - 616 - ccagctggc 6.03 MA0095 Yin-Yang ZN-FINGER, C2H2 615 - 620 + gccatc 7.57 MA0035 GATA-1 ZN-FINGER, GATA 616 - 621 - ccatcc 6.84 MA0015 CF2-II ZN-FINGER, C2H2 708 - 717 - gaatatatac 6.42 MA0003 AP2alpha AP2 765 - 773 - accagcggc 6.4 MA0003 AP2alpha AP2 810 - 818 + gcccccaag 6.9 MA0014 Bsap PAIRED 995 - 1014 - tcttcctgcctcagattcct 8.46 MA0082 SQUA MADS 1196 - 1209 + ttaaataaggaaat 6.19 MA0082 SQUA MADS 1252 - 1265 + ctaaatatagacaa 7.4 MA0037 GATA-3 ZN-FINGER, GATA 1354 - 1359 - ctatct 6.33 MA0058 Max bHLH-ZIP 1416 - 1425 + tatcacatgg 6.2 Background sequence files: backseq (10 sequences, 24015 bp, 48.8% C+G) Randomizations: 1000 P-value threshold: 0.01 Motif score threshold: 6 Randomize nucleotides OFF Randomize dinucleotides OFF Randomize motifs OFF Lowercase filtering OFF Pseudocount: 0.375 Random seed: 1