PWMs for TFBS:
AP2_Q3
AP2_Q6_01
CAAT_01
EBOX_Q6_01
GC_01
Your input:
Genes_Alignments: CDH1___NM_004360___UCSC_multiz_28way_5000_upstream
Stringency: 95_85

Your results:
 
Available for download (use Jalview to generate output for publishing purposes) help

CDH1___NM_004360___UCSC_multiz_28way_5000_upstream.fc
CDH1___NM_004360___UCSC_multiz_28way_5000_upstream.fasta

Preview alignment (use the checkboxes to switch the TFs)
predicted TFBS found on CDH1___NM_004360___UCSC_multiz_28way_5000_upstream

HOMO SAPIENS   cgcttcagcccaggagttcgagaccaggctgggcaatacagggagacacagcgcccccac
BOSTAU3   ............................................................
CANFAM2   ............................................................
CAVPOR2   ............................................................
DASNOV1   ............................................................
ECHTEL1   ............................................................
EQUCAB1   ............................................................
ERIEUR1   ............................................................
FELCAT3   ............................................................
LOXAFR1   ............................................................
MM8   ............................................................
MONDOM4   ............................................................
ORNANA1   ............................................................
ORYCUN1   ............................................................
OTOGAR1   ............................................................
PANTRO2   cgcttcagcccaggagttcgagaccaggctgggcaatacagggagacacagcgcccccac
RHEMAC2   cacttcagcccaggagttggagaccaggctgggcaatatagggagacacagcgcccccac
RN4   ............................................................
TUPBEL1   ............................................................
pos -600 to -541
HOMO SAPIENS   tgcccctgtccgccccgacttgtctctctacaaaaaggcaaaag-aaaaaaaaattagcc
BOSTAU3   ............................................................
CANFAM2   ............................................................
CAVPOR2   .........................................-------------------
DASNOV1   ............................................................
ECHTEL1   ............................................................
EQUCAB1   ............................................................
ERIEUR1   ............................................................
FELCAT3   ............................................................
LOXAFR1   ............................................................
MM8   ............................................................
MONDOM4   ............................................................
ORNANA1   ............................................................
ORYCUN1   ............................................................
OTOGAR1   .........................................aac-aacaacaaaatagcc
PANTRO2   tgcccctgtccgccccgactcgtctctctacaaaaagacaaaag-aaaaaaaaattagcc
RHEMAC2   tgcccctgtctgccccgactcgtctctctacaaaaagacaaaagaaaaaaaaaattagcc
RN4   ............................................................
TUPBEL1   ............................................................
pos -540 to -482
HOMO SAPIENS   tggcgtggtggtgtgcacctgtactcccagctactagagaggctggggccagaggaccgc
BOSTAU3   ............................................................
CANFAM2   ............................................................
CAVPOR2   --------tggtgcacgccagtaatcccagc-acttgggaggcagaggtaggaggat---
DASNOV1   ............................................................
ECHTEL1   ............................................................
EQUCAB1   ............................................................
ERIEUR1   ............................................................
FELCAT3   ............................................................
LOXAFR1   ............................................................
MM8   ............................................................
MONDOM4   ............................................................
ORNANA1   ............................................................
ORYCUN1   ............................................................
OTOGAR1   gggcattgtggcgggtgcctgcggtcccaggtacttgggaggctgagacaagagaatctc
PANTRO2   tggcgtggtggtgtgcacctgtactcccagctactagagaggctggggccagaggaccgc
RHEMAC2   tggtgtggtcgtgtgcacctgtactcccagctactagagaggctggggccagaggactgt
RN4   ............................................................
TUPBEL1   ............................................................
pos -481 to -422
HOMO SAPIENS   ttgagcccaggagttcgaggctgcagtgagctgtgatcgcaccactgcact-----ccag
BOSTAU3   ............................................................
CANFAM2   ............................................................
CAVPOR2   ----ggttgtgagtttgtgaccaacctgggatacaa-------agtgagctcaaggccag
DASNOV1   ............................................................
ECHTEL1   ............................................................
EQUCAB1   ............................................................
ERIEUR1   ............................................................
FELCAT3   ............................................................
LOXAFR1   ............................................................
MM8   ............................................................
MONDOM4   ............................................................
ORNANA1   ............................................................
ORYCUN1   ............................................................
OTOGAR1   atgagcccaagattttaaggttgctgtgagctgtga----gccacagcact-----ctat
PANTRO2   ttgagcccaggagttcgaggctgcagtgagctgtgatcgcaccactgcact-----ccag
RHEMAC2   ttgaggcc---agttcaaggctgcagtgagctgtgatcgcaccactacact-----ccag
RN4   ............................................................
TUPBEL1   ............................................................
pos -421 to -367
HOMO SAPIENS   cttgggtgaaagagtgagaccccatctccaa-aacgaa----------caaacaaa---a
BOSTAU3   ............................................................
CANFAM2   ............................................................
CAVPOR2   cctgaactgcatagtgagatcctgtctcaaa-acaaaacaa--------aaaca------
DASNOV1   ............................................................
ECHTEL1   ............................................................
EQUCAB1   ............................................................
ERIEUR1   ............................................................
FELCAT3   ............................................................
LOXAFR1   ............................................................
MM8   ............................................................
MONDOM4   ............................................................
ORNANA1   ............................................................
ORYCUN1   ............................................................
OTOGAR1   ccagagtggcagcttgagactctgtctcaaataataaataa--------taataaa----
PANTRO2   cttgggtgaaagagtgagaccccatctccaa-aacgaataa------acaaacaaa---a
RHEMAC2   cctgggtgaaagggtgagacctcatttccaa-aacaaacaaaaatacaaaaacaaaaaca
RN4   ............................................................
TUPBEL1   ............................................................
pos -366 to -321
HOMO SAPIENS   aatcccaaaaaacaaaagaactcagccaagtgt-aaaagccctttctgatcccaggtctt
BOSTAU3   ......aaaagacag-a---agtagttaaaggg-taaaatcctctctggccccagatgtt
CANFAM2   ......-----------aaaactagttaaagagttaaagtcgtctccgtccgga-gtgtt
CAVPOR2   -----------------------------------agagtcctttctgacctcaaatctt
DASNOV1   ......-----------------------------aaaggcctttgggacgccaggtctt
ECHTEL1   ......---------aagaactca----------a-gggtctttcctgaccccaggccct
EQUCAB1   ......----------------------------aaaaattctttgtgcctccaggtgtt
ERIEUR1   ............................................................
FELCAT3   ......----------------------------agaagtcctttctgcccccaggtgtt
LOXAFR1   ......---------aagaaccca----------aggggtcctttctgacccatgt----
MM8   ......----------gaaacctagatgatgaa-taaagtcctttgtaactccatgtctc
MONDOM4   ............................................................
ORNANA1   ............................................................
ORYCUN1   ......---------aaaaaaacagctaaaggc-tgaagtcctttctgacctcaggttgt
OTOGAR1   ------------------------gccgagccg-taaattcttttctgatcccaggtttc
PANTRO2   aaccccaaaaaacaaaagaactcagccaagtgt-aaaagccctttctgatcccaggtctt
RHEMAC2   aaccccaaaaaacaaaagaactcagccaagtgt-aaaagccctttctgatcccaggtctt
RN4   ......-----------------------------aaagtcttttgtaactgcaagtctc
TUPBEL1   ......-------------------------------------------------gtctt
pos -320 to -262
HOMO SAPIENS   agtgagccacc----g----gcggggctgggattcgaac-ccagtggaat-cagaaccgt
BOSTAU3   agtgagccact---------gcgaggctggtattcgaac-ctagtggaat-aggaattgt
CANFAM2   cgtgagcctcc---------gggtgccggg------------------------------
CAVPOR2   agtggtccaca----g----gcggggctgggtttcgaac-ctggtggcac-tggaaccgt
DASNOV1   agcgagccacttggcg----gcggggctgggattcgaac-ccggtgacag-cggaatctt
ECHTEL1   actgagccact----g----gttaggcaaggaggtgaac-ccagtggagt-cacatttgt
EQUCAB1   agtgaaccact---------gcgaggctcggattcgacc-ctgttggaat-agtaatcgt
ERIEUR1   ............................................................
FELCAT3   agtgagccacc---------gcgcggctgggagg-gaac-ttggtggaac-agaaatcct
LOXAFR1   -cttagccgct----g----gtagggctaggatttgaac-ccagtgaaat-cggaatcat
MM8   cgtgggtcaga----gcacagctaggctaggattcgaacgaccgtggaat-aggaagctg
MONDOM4   ............................................................
ORNANA1   ............................................................
ORYCUN1   agggagccacc----a----gtggggctaggattccacc-gtggtgggtt-cggaatcct
OTOGAR1   agtgaactacc----g----ccgggcctgggattcgaac-ctagtggaat-cagaatcct
PANTRO2   agtgagccacg----g----gcggggctgggattcgaac-ccagtggaat-cagaaccgt
RHEMAC2   agtgagccacc----a----gcggtgctgggattcgaac-ccagtggaat-cagaaccgt
RN4   agtgggccaga----gcacagctaggctaggattcgagcgaccgaggaataaggaagcaa
TUPBEL1   agtgagccacc----a----gcagcactgggatttgaac-ccgatggaat-tgtaattgt
pos -261 to -212
HOMO SAPIENS   gcagg-tcccata----accca---cctag--------acc--ctag---caa-ctccag
BOSTAU3   ggagc-ccctactattgcatta---ctctg--------act-------------------
CANFAM2   ggagc-tgctgtc----cccca---cccgc--------gct-------------------
CAVPOR2   gcagg-tcccata----tagtc---tccgt--------tcc--gtat---cta-ttgcag
DASNOV1   acggcggcggaag----cccca---tcctc--------tca--ctacattaag-ccgtgg
ECHTEL1   gcaac-ccctaca----ccaca---ccctg--------acc--ctct---agg-cctctg
EQUCAB1   ggcgc-ccctaca----cctta---acctg--------act----ac---caa-cctccg
ERIEUR1   ............................................................
FELCAT3   ggagc-ccctatt----ccctc---cccgg--------actagcaat---cca-tcgctg
LOXAFR1   gcagc-cccaacg----ctcca---cctag--------gcc--ctac---aaa-cctctc
MM8   ggaag-tcttcta----aggccggccccat--------gcc----ac---caa-ctacag
MONDOM4   .........................cctag--------gtc----cc---caa-gtccgg
ORNANA1   ............................................................
ORYCUN1   gcagg-tcc---a----tagctggccctctctccgccggcc----at---cag-ctgggg
OTOGAR1   acagg-tccatta----cctca---ccttg--------acc--ctac---caa-a-acag
PANTRO2   acagg-tcccata----accca---cctag--------acc--ctag---caa-ctgcag
RHEMAC2   gcggg-tcccata----accca---cctag--------acc--ctag---caa-ctccag
RN4   ggaag-tctccta----agcccgg-cccat--------gtc----ac---caatttacag
TUPBEL1   gcaat-tcccata----accca---ctggg--------act--ccac---caa-ctattg
pos -211 to -174
HOMO SAPIENS   gc-taga---gggtcaccgcgtctatg---cgaggc---cggg-----------------
BOSTAU3   ac-tctc---aggtcacccggtctgc---ttgcggc---ttcg---gggc----------
CANFAM2   -------------------------c---tagaaac---tgcg-----------------
CAVPOR2   acctggg---ggttccgaggttccgaggcagggggc---ggagccatggg----------
DASNOV1   gg-cagcgagcggtcacccggacct----gcggggc---cggg----ggcgggggcgggg
ECHTEL1   gt-c------------tctggtctgc---gagggac---gaag----ggtggggacgtgg
EQUCAB1   gc-cagc---gggtcactgggccggc---gggaggc---aggg----ggc----------
ERIEUR1   ..........................---gcgaggc---gggg-----gc----------
FELCAT3   gc-cagc---cggtcacccggtaggc---ttgaggc---tgcg---aggc----------
LOXAFR1   ct-cagc---ttatcaccgggtcgtc---cgggggcccgcaag----ggcg---------
MM8   ac----------------------------aggggt---ggag-----------------
MONDOM4   gt-tt-----aggactccaggact------------------------------------
ORNANA1   ............................................................
ORYCUN1   gt--cgc---ggatcggcggacgcggggcccaaggc---ggggccggggc----------
OTOGAR1   ac-tagt---gggtcaatcggtctggt---agaggc------g-----------------
PANTRO2   ac-taga---gggtcaccgcatctatg---cgaggc---tggg-----------------
RHEMAC2   gc-taga---gggtcaccgggtctgcg---cgaggc---cggg-----------------
RN4   ac------------------------------gggt---ggag-----------------
TUPBEL1   ac-tagt---gggtcaccttgtcagcg---cgaggc---caggagagggc----------
pos -173 to -141
HOMO SAPIENS   ---------tgggcgggccgtc--agc--tc-cg-ccctggggagg------------gg
BOSTAU3   --gggatcgggggcggagcgtc--cgc--cc-aa-gtccgcggaggaagcggaggcc-tt
CANFAM2   --gggggcggggccgg---------gcg-cc-ga-ggcggcggg----------------
CAVPOR2   --tggg------------------------c-ag-gcccgcggtagaagctcagggccgt
DASNOV1   g-cgggccgggggctggg-----------cc-tggggccgcgccgga-------------
ECHTEL1   gtggggccaaggcttaggggtc--cgccccc-tgcccccgcggaagaagc----------
EQUCAB1   --gggatcatgggagggcggtc--cgac-cc-cg-cccgtcgag-ggagcggag------
ERIEUR1   --ggcaccagggctgtgggccc--cgcc-cctca-gcgcgcggtgaaatccgag------
FELCAT3   --ggggtcaggggcgggcctac--cgcc-cc-ca-gcccgcgggggaagccgagacc-ca
LOXAFR1   --ggggccatgggcgagccgct--cgcctct-cg-ctctgcggaggaagc----------
MM8   ---------------------------------------------gaagttgagggccct
MONDOM4   --gaagtggggggagaagttgc--tgc--ct-gg-gctggcctaggaagtc---------
ORNANA1   ............................................................
ORYCUN1   --cgggaccggggcgtggcgtc--tgc--tc-tg-ccccgcggaggaagagga-ggccgc
OTOGAR1   ---------ggggcggggcgcc----c--cc-tg-ccctgcggaggacgccgagggccgc
PANTRO2   ---------tgggcgggccgtc--agc--tc-cg-ccctggggagg------------gg
RHEMAC2   ---------ggggcgggccgtt--agc--tc-cg-tccgggggagg------------gg
RN4   ---------------------------------------------gaagttgagggcagt
TUPBEL1   --gggaccttgggcgggccgtctgcgc--cc-ag-ccctcgggagg-aagcaaggtccac
pos -140 to -108
HOMO SAPIENS   tc-cgcgctgctgattggctgtggc-c--ggcaggtgaaccctc-agccaatcagcggta
BOSTAU3   gc-ctcgccgctcattggttgcggc-c--ggcaggtgcatcctc-agccaatcc-tggtg
CANFAM2   gc-cgcgccgctcattggccgcccg-c--cgcaggtgcagccgc-agccaatcagcggcg
CAVPOR2   gc-ggcgcctctcattggctgcagc-t--cgcaggtgcgtctcc-agccaatcagcgtcg
DASNOV1   --..........................................................
ECHTEL1   ---ctcgccgctgattggttgcggc-cgggacaggtgcgtcctc-agccaatccgcggct
EQUCAB1   gc-cgcgccgctcattggctgcggc-c--ggcaggtgcatcctc--gccaatcagcggag
ERIEUR1   tc-cacaccgcttattggctgtgac-c-gggcaggtgccgccat-agccaatcagcgaat
FELCAT3   gc-cgcgccgctcattggctgcggt-c--cgcaggtgtgccctc-agccaatcagcgctg
LOXAFR1   ---cacgtcgcctataggctgcggc-cagggcaggtgcatcttc-ag-caatcagtggcg
MM8   gc-agttcc-----ttggctgccac-c--tgcaggtgcgtcccc-agccaatcagcggcg
MONDOM4   --caggctcgctcattggctcctcc-cggcgcaggtgtgcctgcgggccaatcagaggcg
ORNANA1   ............................................................
ORYCUN1   gc-cgcgccgctcattggctgctgc-c-aggcaggtgcatcctc-agccaatcagagccg
OTOGAR1   gc-cgcgccgttcattggctgcggcga--ggcaggtgcaccct--agccaatcagcgggg
PANTRO2   tc-cgcgctgctgattggctgtggc-c--ggcaggtgaaccctc-agccaatcagcggta
RHEMAC2   tc-cgcgctgctgattggctgtggc-c--ggcaggtgaaccctc-agccaatcagcggta
RN4   gc-ggctcc-----ttggttgccac-c--tgcaggtgcgtcccc-agccaatcagcggcg
TUPBEL1   ac-cgcgcctctcattggttgcggc-c--agcaggtgcatcctc-gaccaatgagctgtg
pos -107 to -53
HOMO SAPIENS   c-ggggggcggtgcctccggggctcacctggct---gcagccacgc-accccc-tctc
BOSTAU3   c-cgggggcgggaccgtcgaggctcacctggct---cccgccgcgc-cccgca-gctc
CANFAM2   c-ggggggcggggcctcgc-ggctcacctggcg---gccg-gacgc-ggcccc-gctc
CAVPOR2   t-cgggggcggtgcctgc-gagctcacctggca---gctgctatgt-taagta-gctc
DASNOV1   ..........................................................
ECHTEL1   c-tgggggcggcgccctcggggctcacctggcg---gccgctgcgc-cgcagt-cctc
EQUCAB1   c-cggg---cgggccttga-ggctcacctggca-----cgcggcgc-tgccca-gctc
ERIEUR1   cacgggggcggggcttcccggcctcacctggcggcggcggcggcgc-atcgca-gttc
FELCAT3   t-ggggggcggtgccttccaggctcacctggcg---gcagcgacgc-tgcccg-gctc
LOXAFR1   c-tgggggcggcaccctcgggactcacctggtg---gccgcagcgc-tgctct-gctc
MM8   c-cgggggcggtgcctgc-gggctcacctggcg---gccgcagcctctgcgct-gctc
MONDOM4   t-gggaggggagtctctcggagctcacctggct---gcc----cgc-tgcctg-gta-
ORNANA1   .........tgtcccacgaggggcttccgggct---tcatccccgt-tttccg-g---
ORYCUN1   c-caggggcggagccctcggggctcacctggcg---gctgcggcgc-tgcccg-gctc
OTOGAR1   c-cgggggcggggccttcgaggctcacctggca---gc--ctgggc-gctgccggctc
PANTRO2   c-ggggggcggtgcctccggggctcacctggcg---gcagccgcgc-accctc-tctc
RHEMAC2   c-ggggggcggtccctccgaggcacacctggcg---gcagcagcgc-accccagtctc
RN4   c-cgggggcggtgcctgc-gggctcacctggcg---gccgcagcctctgcttg-gctc
TUPBEL1   c-cgggggcggtgcctccgaggctcacctggag---gctgcggcgc-tgccag-gctc
pos -52 to -1