I have a text file with something like this in it:
>ENSG00321 Gene_ch19 . . . .
AATAGCGGTTAACATATTAATTAAACTAATGTATAGATATTATCCGCTTCCAGATTTATTATTTTGTAAA
ATAGGCACAGTTCTTATCTGGTGTCACTTTATGCTTTTTTAATAGACGCCCAGCTCTACTCATGGCCAAG
.
.
>ENSG00531 Gene_ch5 . . . .
AAAGAAGCGTAGGCCCGCCATGCAGCGTAAAAAGGATAATGCGGAGCAGCGGTCCCCAAAGACTGATTTA
TCAAAACTGTTTTCGCAGCAATTAACACACCCACCGACCAGTAACACCGCTGCAAGCAAGGCCACGGGCA
.
.
I have some headers like (ENSG00321) too.
I want to search in text files with header and then get characters(AGCT, characters line start from below of the header line) from 5 to 100 of that header and copy to a new text file.
How can I programming this? In MATLAB or PERL or C++.

You just want to copy lines 5-100 out of one file and into another file? You could use c++ for that - look into fstream and cin.getline()

not always from 5th character. it can be different. i want find Header and then read characters from special character like 5th or 41th or etc and then read special number of characters start from 5th(ex, 100 or 102 or etc) and then copy and write them to another file. I have the address of headers and start character, and number of characters for each headers that must be read and copy from start character.
like this:
5th char "start to read 112 character after 5th character" so, end of string that will be copy must be 117th character.
Also there are a lot of headers and their characters in text file. i have the address of headers and their characters, that should be copy.