grep (bash) multi-line pattern

Question

In bash (4.3.46(1)) I have some multi-line so called fasta records where each record is initiated by on line with >name and the following lines DNA sequence ([AGCTNacgtn]),

Answer 1

The best tool for working with multi-line records is awk.

In your case:

awk 'BEGIN{RS=">"} NR==2 {print RS$0}' input.txt

input.txt

>chr1
AGCTACTTTT
AGGGNGGTNN
>chr2
TTGNACACCC
TGGGGGAGTA
>chr3
TGACGTGGGT
TCGGGTTTTT

Explanation:

BEGIN{RS=">"} Initially set record separator to ">"

NR==2 filter for record #2 only

{print RS$0} print record #2 with the missing record separator back