Final answer:
The numbers differing in sequence alignment between cDNA Query and TSA Subject Contig indicate a reversed sequence orientation. This reversed orientation is a common situation in genetic analysis and does not indicate a mismatch or technical error but rather antiparallel alignment of the sequences.
Step-by-step explanation:
The observation of sequence numbers for the cDNA Query increasing while those of the TSA Subject Contig decreasing typically signifies a reversed orientation in the alignment. This is an indication that the sequences are antiparallel to each other, that is, they are aligned in opposite directions. This situation can arise in sequence alignment processes and is an important aspect to recognize for correct interpretation of genetic information. In the context of molecular biology, understanding the orientation of DNA or RNA sequences is critical when analyzing gene expression or when engaging in gene cloning and other genetic manipulation techniques.
When an mRNA is shorter than the DNA sequence, it is often because the mRNA represents an expressed sequence tag (EST), which is a portion of the transcribed sequence identified with cDNA. Due to processes such as splicing, the mRNA reflects the mature transcript that is translated into proteins, excluding intronic (non-coding) regions that are present in the genomic DNA. Therefore, ESTs are used to identify gene transcripts and are valuable in gene discovery and in understanding gene expression patterns.