Can you provide the exact command you are using? Your reads do have truseq adapters in them so the inserts may be smaller than you expected.
Code:
@M02344:9008:000000000-AJ1PF:1:1110:28244:16073 1:N:0:TGACCAAT+ATAGAGGC TCTGCCGTCATCGACTTCGAAGGTTCGAATCCTTCCCCTCTAACCACGGCCGAAATTCAATACCCGGATCAAGCTCAATTCGGGTCGAGGTCGGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGA[COLOR="Red"]GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATGTCGTATGCCGTCTTCTGCTTG[/COLOR]AAAAAAAATAAGTGGTGCGAAGAGAGCCTGTGGCCAACCTCATATGCGTGGAGATGTCTCG
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