List of Reads Having the Most Matches in Searches of the Transcripts Database
| Gene ID | Gene description | No. of hits |
| gi‖285928‖dbj‖D14718‖HUMHMG1 | Human chromosomal protein HMG1 related gene | 32 |
| gi‖531475‖emb‖X80910‖HSPPP1CB | PPP1CB gene; protein phosphatase 1. | 34 |
| gi‖32326‖emb‖X12597‖HSHMG1 | Human mRNA for high mobility group-1 protein (HMG-1) | 35 |
| gi‖968887‖dbj‖D63874‖HUMFM1 | Homo sapiens high-mobility group (nonhistone chromosomal) protein 1(HMG1). | 36 |
| gi‖4519269‖dbj‖AB011414‖AB011414 | Human zinc finger protein ZNF136 | 36 |
| gi‖430993‖gb‖U02478‖HSU02478 | trithorax (Drosophila) homolog | 36 |
| gi‖337494‖gb‖M36072‖HUMRPL7A | Human ribosomal protein L7a (surf 3) large subunit mRNA | 37 |
| gi‖2792017‖emb‖Y10530‖HSHTPCR2 | H. sapiensgene encoding putative olfactory receptor | 39 |
| gi‖498735‖emb‖X78932‖HSHZF9 | Human repressor transcriptional factor (ZNF85) mRNA | 39 |
| gi‖2565195‖gb‖AF000381‖HSAF000381 | Human 18S rRNA gene | 39 |
| gi‖1017721‖gb‖U35376‖HSU35376 | Human repressor transcriptional factor (ZNF85) mRNA | 42 |
| gi‖1262328‖dbj‖D42073‖HUMRCN | Human mRNA for reticulocalbin, calcium binding domain | 43 |
| gi‖487784‖gb‖U09367‖HSU09367 | Human zinc finger protein ZNF136 | 55 |
| gi‖337377‖gb‖K03432‖HUMRGEA | Human 18S rRNA gene | 71 |
| gi‖1497857‖gb‖U34995‖HSU34995 | glyceraldehyde-3-phosphate dehydrogenase (GAPD) | 82 |
| gi‖35052‖emb‖X53778‖HSNGMRNA | H. sapienshng mRNA for uracil DNA glycosylase, GAPD | 84 |
[i] These reads all contain domains that are shared by large gene families. No known repetitive elements have been observed.