At the top of the results, in the light orange box, are the names of the sequences which were compared. Just below is a description of the orientations of each sequence that produced the best match. Both sequences should be in the plus orientation; if they are not, then reverse complement the genomic sequence using a program such as EMBOSS's REVSEQ ( 9 ) or go back to the UCSC Genome Browser and retrieve the sequence again in the appropriate orientation.
As was depicted in the UCSC Genome Browser, there are 7 exons in this transcript. The Genomic Coordinates column shows where each of those exons maps on the genomic fragment that you submitted. This is the information necessary for annotation.
| Genomic: lcl|mouse_IL1a_IL1b |
| mRNA: lcl|X01450 |
| Alignment is on plus strand of genomic
sequence and on plus strand of
mRNA sequence mRNA coverage: 100% Overall percent identity: 99.1% |
| 113076 |  |  |
| |
| |
| |
| |
| |
|
123438 |
| EXON | Genomic coordinates | mRNA coordinates | length | identity | mismatches | gaps | Donor site | Acc. site |
| Exon 1 | 113076 - 113127 | 1-52 | 52 | 100.0% | 0 | 0 | d | |
| Exon 2 | 113939 - 113993 | 53-107 | 55 | 100.0% | 0 | 0 | d | a |
| Exon 3 | 115117 - 115165 | 108-156 | 49 | 100.0% | 0 | 0 | d | a |
| Exon 4 | 116356 - 116584 | 157-385 | 229 | 100.0% | 0 | 0 | d | a |
| Exon 5 | 118202 - 118375 | 386-559 | 174 | 100.0% | 0 | 0 | d | a |
| Exon 6 | 120051 - 120175 | 560-684 | 125 | 100.0% | 0 | 0 | d | a |
| Exon 7 | 122149 - 123438 | 685-1974 | 1290 | 98.6% | 18 | 2 | a |
