<?php
 
$str= "spawn needle /var/www/html/trabalho/arquivo/emboss/needle/alvos.txt /var/www/html/trabalho/arquivo/emboss/needle/modelos.txt Needleman-Wunsch global alignment of two sequences Warning: Unknown swissprot line type ' ' Warning: Unknown swissprot line type ' ' Warning: Unknown swissprot line type ' ' Warning: Unknown swissprot line type ' ' Warning: Unknown swissprot line type ' ' Warning: Unknown swissprot line type ' ' Warning: Unknown swissprot line type ' ' Warning: Unknown swissprot line type ' ' Gap opening penalty [10.0]: 10.0 Gap extension penalty [0.5]: 0.5 Output alignment [hba_human.needle]:";
 
 
$posInicio  = strripos($str, "[");
 
$posFim  = strripos($str, "]");
 
$quant= ($posFim-$posInicio-1);
 
 
echo substr($str, $posInicio+1, $quant);

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