How to search cis-regulatory elemens using promoter multifasta from non-model plant?

Question

[rimgubaev]

I need to find cis-regulatory elements in multifasta file with promoters of Nicotiana tabacum. I've tried PlantPAN and PlantTFDB but these programs output quite useless information on TF families that binds to a certain region. Nice one is PLACE database however its outdated and lacks the multiple query (in case of Nicotiana tabacum it is c.a. 50K promoters)

[ATpoint]

quite useless information on TF families that binds to a certain region

Motif presence is the only information that a fasta file can give you. What exactly do you expect and what kind of information are you actually looking for (yes, CRMs, but do you have an idea how to identify them beyond motif presence or motif overrepresentation?)

[rimgubaev]

I am interested in regulatory elements that may affect gene expression under certain condition. For example the presence of several ABREs (Abscisic acid responsive elements) within promoter region indicate that this gene is likely to be up-regulated under unfavorable conditions or ABA treatment. In contrast, PlantPAN and PlantTFDB gives us information like that: 5 C2H2 and 3 bZIP familiy transcription factors bind to this region. This is meanless since there are thousands of bZIPs as well as C2H2s in the cell and all of them may regulate genes related to a wide range of processes (flowering, pathogen attack, germination etc.).