file format of output from Match program of Transfac

Example:

Inspecting sequence ID ENSMUST00000070533

V$SP1_01 | 1470 (-) | 0.962 | 0.949 | tccCAGCCcc
V$SP1_01 | 2262 (+) | 1.000 | 0.967 | ggGGCGGgct

The position of first hit, 1470, is in term of the original sequence, instead of reverse complement sequence, and tccCAGCCcc is a segment of original sequence. And, in term of the original sequence, the end position of binding sequence is 1479.

1470 1479
| |
tccCAGCCcc

A good paper about evolution of transcriptional regulation

PMID: 12777501 . This paper also listed the following interested points:
1. Transcription Is "Off" by Default
2. Activator and Repressor Modules Are Often Additive in Effect

How does gene expression clustering work? - Nature Biotechnology

How does gene expression clustering work? - Nature Biotechnology: "Patrik D'haeseleer"