aligncopypair: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/aligncopypair - from package: emboss

You may install the required package with command apt-get install {package}

Error in other languages:
aligncopypair: bevel nie gevind nie
aligncopypair: comandă negăsită
aligncopypair: comando não encontrado
aligncopypair: commande introuvable
aligncopypair: command not found
aligncopypair: käsku ei ole
aligncopypair: không tìm thấy lệnh
aligncopypair: komanda nerasta
aligncopypair: Kommando nicht gefunden.
aligncopypair: kommandot finns inte
aligncopypair: komut yok
aligncopypair: nie znaleziono polecenia
aligncopypair: níor aimsíodh an t-ordú
aligncopypair: no se encontró la orden
aligncopypair: no s'ha trobat l'ordre
aligncopypair: opdracht niet gevonden
aligncopypair: parancs nem található
aligncopypair: perintah tidak ditemukan
aligncopypair: príkaz nenájdený
aligncopypair: příkaz nenalezen
aligncopypair: команда не найдена
aligncopypair: командата не е открита
aligncopypair: 命令找不到
aligncopypair: コマンドが見つかりません