127	All long introns	Every intron in these hits is of length 250000-400000bp, we require at least one intron to be shorter than 250000bp
67	No overlap	No coordinate overlap with any Ensembl transcript
63	Was not best match	Did not top best transcript match score (0.98)
7	No Master	The dependent xref was not matched due to there being no master xref
129	Low coverage	Coverage of the best alignment is less than 90% - see query_score for coverage
2	Marker does not align	Unable to align to the genome
1	Marker matches multiple times	Marker aligns to the genome > 3 times
136	See kill-list database	This sequence has been excluded from the analysis - see the kill-list database for further details
125	Failed to match at thresholds	Unable to match at the thresholds of 55% for the query or 55% for the target
44	Was not best match	Did not top best transcript match score (0.79)
55	Was not best match	Did not top best transcript match score (0.90)
128	GSS sequence	This cDNA has been excluded from the analysis because it is in the GSS (Genome Survey Sequence) division of GenBank
134	Parent xref failed to match	Unable to match as parent xref was not mapped
57	Was not best match	Did not top best transcript match score (0.92)
40	Was not best match	Did not top best transcript match score (0.75)
61	Was not best match	Did not top best transcript match score (0.96)
135	Processed pseudogene	Rejected as a processed pseudogene because there are multiple-exon hits with the same coverage which have been rejected for other reasons
59	Was not best match	Did not top best transcript match score (0.94)
49	Was not best match	Did not top best transcript match score (0.84)
131	Low percent_id with long intron	Hits containing introns longer than 250000bp are rejected if percentage identity is less than 98% - see query_score for percent_id
130	Low coverage with long intron	Hits containing introns longer than 250000bp are rejected if coverage is less than 98% - see query_score for coverage
53	Was not best match	Did not top best transcript match score (0.88)
48	Was not best match	Did not top best transcript match score (0.83)
42	Was not best match	Did not top best transcript match score (0.77)
46	Was not best match	Did not top best transcript match score (0.81)
133	No output from Exonerate	Exonerate returned no hits using standard parameters plus options --maxintron 400000 and --softmasktarget FALSE
96	Failed to match at thresholds	Unable to match at the thresholds of 100% for the query or 100% for the target
65	Was not best match	Did not top best transcript match score (1.00)
126	>10% N-strings	More than 10% of the sequence consists of strings of Ns. Sequences are not rejected for this reason but this may explain a low coverage hit
6	Failed to match at thresholds	Unable to match at the thresholds of 90% for the query or 90% for the target
50	Was not best match	Did not top best transcript match score (0.85)
64	Was not best match	Did not top best transcript match score (0.99)
3	Failed to find Stable ID	Stable ID that this xref was linked to no longer exists
138	Marker matches multiple times	Marker aligns to the genome > 5 times
51	Was not best match	Did not top best transcript match score (0.86)
41	Was not best match	Did not top best transcript match score (0.76)
58	Was not best match	Did not top best transcript match score (0.93)
47	Was not best match	Did not top best transcript match score (0.82)
137	Failed to match at thresholds	Unable to match at the thresholds of 99% for the query or 99% for the target
8	Master failed	The dependent xref was not matched due to the master xref not being mapped
52	Was not best match	Did not top best transcript match score (0.87)
4	No mapping done	No mapping done for this type of xref
60	Was not best match	Did not top best transcript match score (0.95)
56	Was not best match	Did not top best transcript match score (0.91)
132	Low percent_id	Percentage identity of the best alignment is less than 97% - see query_score for percent_id
66	Did not meet threshold	Match score for transcript lower than threshold (0.75)
45	Was not best match	Did not top best transcript match score (0.80)
43	Was not best match	Did not top best transcript match score (0.78)
62	Was not best match	Did not top best transcript match score (0.97)
5	Failed to match	Unable to match to any ensembl entity at all
54	Was not best match	Did not top best transcript match score (0.89)