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