Results for the job "1KmWIy Fri Jun 25 21:17:12 2004":

Parameters:
  PWM threshold: 80 %
  Homology threshold: 50 %
  Flank length: 15 bp


Plain files:
  Raw TFBSs data
  List of CONREAL aligned TFBSs
  CONREAL alignment

Graphical representation of aligned TFBSs.

Bars represent number of aligned hits found within 20 bp window calculated in coordinates of the longer sequence.
Each black line represents an aligned TFBS.

CONREAL:



CONREAL alignment:

Aligned TFBSs are shown in uppercase.
No attempts were made to align regions not covered by TFBSs (lowercase).

                  10        20        30        40        50        60
Mouse_Vps3tgtctccacgtgttcctggccggcctctacgcctctattttctccctctccccctctctc
                 |      |        |||       |  ||  | |      |        ||
Human_VPS33Accaaagtatcaaaacgcatatatcctactaatattaatagtttattgagcaattaagttc
                  10        20        30        40        50        60

                  70                                                  
Mouse_Vps3tttcccttcc--------------------------------------------------
              |   |                                                   
Human_VPS33Acaggcacccagttaagcctctcacgtggactgcacgatgaaattcataccctcattgatc
                  70        80        90       100       110       120

                                                                      
Mouse_Vps3------------------------------------------------------------
                                                                      
Human_VPS33Actcactacaactcagaggtaacatggaattttactgaggcaaatggtgggacctggattc
                 130       140       150       160       170       180

                                                                      
Mouse_Vps3------------------------------------------------------------
                                                                      
Human_VPS33Acagaagcaatactatttgtgtgaaatgtcatgtcactgtaaaagtctgttagggattacc
                 190       200       210       220       230       240

                                                  80        90       1
Mouse_Vps3--------------------------------CCTTTCCCTCctctccCCTCCCCacctc
                                             |||||||       |||| ||||  
Human_VPS33AcaaaaaaaaaaaaaaaaaaaaaagtccactcaAGATTCCCTCg-----ACTCCTCaccat
                 250       260       270       280            290     

          00       110       120       130       140       150       1
Mouse_Vps3cttcctcaactcccctccccatctccccatgccctaaataaactctattccatactatat
           ||  |  |                                                   
Human_VPS33Aattgatacat--------------------------------------------------
            300                                                       

          60       170       180       190       200       210       2
Mouse_Vps3ccgtcatatggctgttacctcatggggaagggatgtctcagcataagctcgcagaggcac
                                                                      
Human_VPS33A------------------------------------------------------------
                                                                      

          20       230       240       250       260       270       2
Mouse_Vps3caccttccacctcaccatacctcactctatcaagcatatccctggcttccttttcttgtt
                                                                      
Human_VPS33A------------------------------------------------------------
                                                                      

          80       290       300       310       320       330       3
Mouse_Vps3ttataaaacacaacaccctggaaccggagttacagatggtcacgagctatactgtggatc
                                                                      
Human_VPS33A------------------------------------------------------------
                                                                      

          40       350       360       370       380       390       4
Mouse_Vps3ctgggaacctggtctatgggagagcagcaggtgctcttaactggtgaaccatctctccag
                                                                      
Human_VPS33A------------------------------------------------------------
                                                                      

          00       410       420       430       440       450       4
Mouse_Vps3tccatttattgtttgtttatgtggagacaggtctcactgtgtagccctggttgtcctgga
                                                                      
Human_VPS33A------------------------------------------------------------
                                                                      

          60       470       480       490       500       510       5
Mouse_Vps3gctcgctatgtttaccaggctggccttgaacttggagagataaGCTTGCTctgcgattga
                                                       | |||| |  ||| |
Human_VPS33A-------------------------------------------TTTAGCTcagaaattaa
                                                       310       320  

          20       530       540       550       560       570       5
Mouse_Vps3accacttactgggtgtagtaaggtgcattttgtagtttggcctcgatcgccattttacac
          | ||          ||   ||| |        |      ||    ||      |||   |
Human_VPS33Aaacagccttgattagtgcaaagctaagaaacttctgactgctataatttaagatttgagc
               330       340       350       360       370       380  

          80       590       600       610       620       630       6
Mouse_Vps3cagtattctagctgtgaagacacaaggatggtgcttttaaacgcgacaaataacatctaa
                                                                      
Human_VPS33Aagtg--------------------------------------------------------
                                                                      

          40       650       660       670       680       690        
Mouse_Vps3attccatccttaagacctgggGATGGTGGCTCacgtcttTAATCCCAgcacttag-GAGG
                               | ||| ||| | |  || |  | |||||   |   | ||
Human_VPS33A---------------------GGTGGCGGCGCgcacctgTGGTTCCAgctactctgGCGG
                                390       400       410       420     

          700       710       720       730       740       750       
Mouse_Vps3CAGAGGCAGGcggatttctgagttcgaggccagcctgttctacagagtgagttccaggac
          | ||||  ||  |||  ||     |  ||       |              |        
Human_VPS33ACTGAGGTGGGaagatcacttgagcccgggaggtggaggctacagtgagctatgatcacgt
            430       440       450       460       470       480     

          760                  770       780       790       800      
Mouse_Vps3agcca-----------GGGCTACAcagagaaACCCTGTCTCGAAAACAAACAAACAaagt
            |             |||| |||  | || || ||||||| |||| ||| ||       
Human_VPS33AcactgcactccagcctGGGCGACAgggcgagACACTGTCTCAAAAAAAAAAAAGTTt---
            490       500       510       520       530       540     

           810       820       830       840       850       860      
Mouse_Vps3caATTTTCACtgctcaccattcttaggcatggtagggaaatactttagaaaggggcgggg
             |||||    |  |   |            |        |      |     || |  
Human_VPS33A--TTTTTCCTatccaagtttagccttaagatatcatcttgcagcaagtacctttgctgca
                 550       560       570       580       590       600

           870       880       890       900       910       920      
Mouse_Vps3aggggactcctcctcgcatgcgcactaggaccttgaaggagcatcactgtcagcaggact
          |    |      |     |    |     |      ||         | |         |
Human_VPS33Aaataaaaattcgcgatttttaaaagggacaagagagagtcaatgtctttttttttttttt
                 610       620       630       640       650       660

           930       940       950                                    
Mouse_Vps3ccgcctttcgcgttcaatgtgcctcagcga------------------------------
            |          |      ||       |                              
Human_VPS33Attgagacgaagtctgcccaggctggtctcaaactcccggcctgaagcgatcactcctacc
                 670       680       690       700       710       720

                                                                      
Mouse_Vps3------------------------------------------------------------
                                                                      
Human_VPS33Atcggcctcttaaagtgttgggattacaggcgtaagccaccgcgcccggtctactccagat
                 730       740       750       760       770       780

                                                                      
Mouse_Vps3------------------------------------------------------------
                                                                      
Human_VPS33Actttaaaatcgcttttcagcgcccgacgactcctggagtgaccagactctgaaacgcgct
                 790       800       810       820       830       840

                                                                      
Mouse_Vps3------------------------------------------------------------
                                                                      
Human_VPS33Actgggtcttggcgagaatctgaataaccaccggggtagaagaaagaggcggacactaggg
                 850       860       870       880       890       900

                                                                      
Mouse_Vps3------------------------------------------------------------
                                                                      
Human_VPS33Accagactaggtagaacccgaacccagcagattccggtttccgggttggcgtgcgctgccg
                 910       920       930       940       950       960

           960       970       980       990      1000      1010      
Mouse_Vps3CTCGGATCACGTGAACGTCCCGTCACGTGACGCAGGcggcgtctggggaaatgcgggtgc
            | | ||||||| ||||   ||||||||||   | | | |           |     | 
Human_VPS33ATACCGGTCACGTGGACGTTTGGTCACGTGACTGCGTccgtggtcctcccgtaggaaccgg
                 970       980       990      1000      1010      1020

          1020      
Mouse_Vps3ccgggcaag-
          | |       
Human_VPS33Acggact---C

CONREAL aligned hits:

Matrix Identity Seq1 from Seq1 to Seq2 from Seq2 to Strand Score1 Score2 Rel.Score1 Rel.Score2 Factor
M00750* 0.51 71 77 273 279 2 6.190 4.689 0.86 0.80 Pro only
M00492* 0.50 71 78 273 280 1 8.804 5.654 0.93 0.81 Pro only
M00500* 0.50 71 78 273 280 1 8.135 5.465 0.95 0.86 Pro only
M00499* 0.50 71 78 273 280 1 5.979 4.179 0.90 0.82 Pro only
M00493* 0.50 71 78 273 280 1 6.015 6.089 0.88 0.88 Pro only
M00496* 0.50 71 78 273 280 1 7.450 5.136 0.95 0.85 Pro only
M00497* 0.50 71 78 273 280 1 6.314 7.282 0.92 0.96 Pro only
M00704* 0.53 72 77 274 279 2 5.117 5.117 0.82 0.82 Pro only
M00739* 0.53 73 80 275 282 1 7.833 6.543 0.87 0.83 Pro only
M00736* 0.53 73 80 275 282 1 7.685 5.887 0.87 0.81 Pro only
M00695* 0.51 87 93 284 290 2 8.909 4.962 0.97 0.81 Pro only
M00624* 0.54 502 508 306 312 2 5.824 7.068 0.87 0.92 Pro only
M00469* 0.51 660 668 387 395 2 4.320 5.522 0.80 0.84 Pro only
M00428* 0.58 663 670 390 397 1 4.061 3.934 0.81 0.81 Pro only
M00493* 0.50 678 685 405 412 1 4.763 5.580 0.82 0.86 Pro only
M00494* 0.50 678 685 405 412 1 4.575 6.721 0.81 0.90 Pro only
M00695* 0.57 694 700 422 428 1 5.779 6.047 0.84 0.85 Pro only
M00695* 0.57 697 703 425 431 1 5.338 6.414 0.82 0.87 Pro only
M00706* 0.51 699 707 427 435 1 8.928 7.094 0.90 0.83 Pro only
M00695* 0.51 700 706 428 434 1 5.779 6.198 0.84 0.86 Pro only
M00428* 0.66 763 770 502 509 2 3.835 6.967 0.80 0.93 Pro only
M00792* 0.72 778 786 517 525 2 6.258 6.258 0.87 0.87 Pro only
M00419 0.67 778 789 517 528 2 5.690 4.742 0.83 0.80 MEIS1
M00456* 0.57 785 798 524 537 1 7.888 7.330 0.83 0.81 Pro only
M00473* 0.57 787 796 526 535 1 11.424 6.738 0.96 0.84 Pro only
M00160 0.60 788 799 527 538 1 9.931 6.806 0.89 0.80 SRY
M00724* 0.59 788 798 527 537 2 12.189 6.936 0.96 0.83 Pro only
M00791* 0.58 788 800 527 539 1 11.635 7.550 0.93 0.83 Pro only
M00456* 0.55 789 802 528 541 1 7.476 7.965 0.82 0.83 Pro only
M00148 0.59 790 796 529 535 1 9.061 5.137 1.00 0.84 SRY
M00130 0.57 790 801 529 540 2 14.316 8.053 0.98 0.84 FOXD3
M00473* 0.57 791 800 530 539 1 9.283 6.537 0.90 0.83 Pro only
M00472* 0.54 792 802 531 541 1 9.116 6.861 0.88 0.82 Pro only
M00734* 0.56 793 801 532 540 1 5.541 6.081 0.80 0.82 Pro only
M00750* 0.51 809 815 543 549 2 5.599 6.134 0.84 0.86 Pro only
M00500* 0.50 809 816 543 550 1 5.173 6.746 0.85 0.90 Pro only
M00496* 0.50 809 816 543 550 1 5.091 5.901 0.85 0.88 Pro only
M00494* 0.50 809 816 543 550 1 4.949 7.613 0.82 0.94 Pro only
M00539* 0.56 957 976 961 980 1 13.190 9.495 0.88 0.81 Pro only
M00539* 0.56 957 976 961 980 2 13.190 9.495 0.88 0.81 Pro only
M00615* 0.56 957 976 961 980 1 10.836 10.784 0.86 0.85 Pro only
M00615* 0.56 957 976 961 980 2 10.836 10.784 0.86 0.85 Pro only
M00113 0.60 959 970 963 974 1 8.034 7.057 0.84 0.81 CREB
M00236 0.59 959 974 963 978 1 11.946 8.573 0.89 0.83 Arnt
M00236 0.59 959 974 963 978 2 8.515 8.242 0.83 0.82 Arnt
M00119 0.61 960 973 964 977 1 10.743 9.566 0.87 0.84 Max
M00119 0.61 960 973 964 977 2 10.743 9.566 0.87 0.84 Max
M00121 0.61 960 973 964 977 1 12.888 11.904 0.93 0.91 USF
M00121 0.61 960 973 964 977 2 12.888 11.904 0.93 0.91 USF
M00122 0.61 960 973 964 977 1 8.584 7.517 0.88 0.85 USF
M00122 0.61 960 973 964 977 2 8.584 7.517 0.88 0.85 USF
M00123 0.64 961 972 965 976 2 7.635 9.246 0.82 0.86 c-Myc/Max
M00055 0.64 961 972 965 976 1 8.708 8.435 0.86 0.85 N-Myc
M00055 0.64 961 972 965 976 2 8.185 10.774 0.84 0.91 N-Myc
M00796* 0.64 961 972 965 976 2 7.597 11.752 0.82 0.93 Pro only
M00220 0.63 961 971 965 975 1 14.096 8.917 0.95 0.82 SREBP-1
M00220 0.66 962 972 966 976 2 12.608 9.085 0.91 0.83 SREBP-1
M00187 0.65 962 971 966 975 1 6.536 9.214 0.81 0.90 USF
M00187 0.65 962 971 966 975 2 8.695 9.223 0.88 0.90 USF
M00240 0.65 963 969 967 973 1 6.785 6.785 0.85 0.85 Nkx2-5
M00799* 0.65 963 969 967 973 2 7.811 7.811 0.89 0.89 Pro only
M00799* 0.68 964 970 968 974 1 7.811 10.927 0.89 1.00 Pro only
M00726* 0.67 964 969 968 973 1 8.133 8.133 1.00 1.00 Pro only
M00726* 0.67 964 969 968 973 2 8.133 8.133 1.00 1.00 Pro only
M00514* 0.62 972 983 976 987 2 7.289 7.008 0.82 0.81 Pro only
M00694* 0.65 973 982 977 986 1 8.999 8.713 0.85 0.84 Pro only
M00539* 0.52 973 992 977 996 1 13.310 14.048 0.88 0.90 Pro only
M00539* 0.52 973 992 977 996 2 13.310 14.048 0.88 0.90 Pro only
M00615* 0.52 973 992 977 996 1 10.444 9.505 0.85 0.82 Pro only
M00615* 0.52 973 992 977 996 2 10.444 9.505 0.85 0.82 Pro only
M00285 0.58 975 987 979 991 2 6.296 5.786 0.83 0.82 TCF11
M00236 0.54 975 990 979 994 2 9.342 9.331 0.84 0.84 Arnt
M00119 0.57 976 989 980 993 1 8.857 11.854 0.83 0.89 Max
M00119 0.57 976 989 980 993 2 8.857 11.854 0.83 0.89 Max
M00121 0.57 976 989 980 993 1 12.173 12.706 0.91 0.92 USF
M00121 0.57 976 989 980 993 2 12.173 12.706 0.91 0.92 USF
M00122 0.57 976 989 980 993 1 9.057 11.597 0.89 0.95 USF
M00122 0.57 976 989 980 993 2 9.057 11.597 0.89 0.95 USF
M00801* 0.67 977 982 981 986 1 9.115 5.903 1.00 0.87 Pro only
M00220 0.59 977 987 981 991 1 14.028 14.150 0.95 0.95 SREBP-1
M00055 0.57 977 988 981 992 1 9.311 8.028 0.87 0.84 N-Myc
M00055 0.57 977 988 981 992 2 9.311 8.758 0.87 0.86 N-Myc
M00796* 0.57 977 988 981 992 1 9.764 11.259 0.87 0.91 Pro only
M00796* 0.57 977 988 981 992 2 9.764 11.566 0.87 0.92 Pro only
M00694* 0.60 978 987 982 991 1 8.713 8.713 0.84 0.84 Pro only
M00694* 0.60 978 987 982 991 2 8.713 8.713 0.84 0.84 Pro only
M00322* 0.60 978 987 982 991 1 7.898 7.898 0.86 0.86 Pro only
M00322* 0.60 978 987 982 991 2 7.898 7.898 0.86 0.86 Pro only
M00187 0.60 978 987 982 991 1 11.795 11.795 0.98 0.98 USF
M00187 0.60 978 987 982 991 2 11.795 11.795 0.98 0.98 USF
M00220 0.59 978 988 982 992 2 14.028 12.945 0.95 0.92 SREBP-1
M00285 0.56 978 990 982 994 1 5.624 6.017 0.81 0.82 TCF11
M00240 0.62 979 985 983 989 1 6.785 6.785 0.85 0.85 Nkx2-5
M00799* 0.62 979 985 983 989 2 7.811 7.811 0.89 0.89 Pro only
M00041 0.61 979 986 983 990 1 6.527 6.527 0.81 0.81 CRE-BP1/c-Jun
M00041 0.61 979 986 983 990 2 6.527 6.527 0.81 0.81 CRE-BP1/c-Jun
M00726* 0.61 980 985 984 989 1 8.133 8.133 1.00 1.00 Pro only
M00726* 0.61 980 985 984 989 2 8.133 8.133 1.00 1.00 Pro only
M00240 0.59 980 986 984 990 2 6.785 6.785 0.85 0.85 Nkx2-5
M00799* 0.59 980 986 984 990 1 7.811 7.811 0.89 0.89 Pro only
M00801* 0.53 983 988 987 992 2 9.115 5.568 1.00 0.85 Pro only