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Sequences are sets of DNA residues comprising a chromosome. Sequences can be fully or partially loaded from local files, QuickLoad sites, or DAS servers. It is recommended to load sequence data only for small regions of the genome at a time. IGB allows you to examine sequence data in a separate window called the Sequence Viewer. Read Working With with Sequence Data
Alignments or Reads represent how sequences obtained from an experiment (such as reads from an RNA-Seq experiment) align onto the reference genomic sequence. At low zoom they look like annotations, but with marks representing mismatches between the read and the reference genome whenever these data are available. At higher zoom they show the sequence of the aligned read, and sometimes indicate scores and the degree of agreement with the reference sequence. These are typically loaded from BAM (binary alignment) files. Read Viewing short read alignments