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CompBioBench item

align-one-sequence-to-reference-q1

Question

Where does CACACACAGGAGAT align to in the given GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna? Report as 0-based coordinates in contig:start-end format (no commas).

Inferred answer
NT_033779.5:4280595-4280609Uniquely inferred from submitted scores.
Domain
Genomics
Question style
Routine Analysis

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.

Galaxy

12/12 terminal item results

UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

CorrectUDT-only
AnswerNT_033779.5:4280595-4280609
Workflow
Exact FASTA match CACACACAGGAGAT
Total tokens
245.8K
Output
2.4K
Galaxy historyAgent trace
Codex GPT-5.5

Replicate 2

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
Bg Find SubsequencesEmboss: Fuzznuc37
Total tokens
1.0M
Output
4.9K
Galaxy historyAgent trace
Codex GPT-5.5

Replicate 3

CorrectUDT + standard tools
AnswerNT_033779.5:4280595-4280609
Workflow
Bg Find SubsequencesNcbi Blastn WrapperExact short sequence scan CACACACAGGAGATExact short sequence scan CACACACAGGAGAT v2
Total tokens
789.2K
Output
7.7K
Galaxy historyAgent trace

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
Fasta Regex FinderNcbi Blastn WrapperBowtie2Bg Find SubsequencesCreateinterval2 more tools
Galaxy historyAgent trace
Codex GPT-5.6 Sol

Replicate 2

CorrectUDT-only
AnswerNT_033779.5:4280595-4280609
Workflow
Exact motif coordinate search CACACACAGGAGAT
Total tokens
261.6K
Output
2.8K
Galaxy historyAgent trace
Codex GPT-5.6 Sol

Replicate 3

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
Fasta Regex Finder
Total tokens
736.9K
Output
3.2K
Galaxy historyAgent trace

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
Bg Find SubsequencesNcbi Blastn Wrapper
Total tokens
1.2M
Output
15.9K
Galaxy historyAgent trace
Codex + DeepSeek-v4-pro-0813

Replicate 2

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
No Galaxy tool job recorded
Total tokens
1.3M
Output
13.7K
Galaxy historyAgent trace
Codex + DeepSeek-v4-pro-0813

Replicate 3

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
Bwa MemBam To SamNcbi MakeblastdbNcbi Blastn Wrapper
Total tokens
3.7M
Output
30.5K
Galaxy historyAgent trace

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
Bg Find SubsequencesFasta Regex FinderNcbi Blastn WrapperFilter TabularBedtools Getfastabed
Total tokens
4.0M
Output
18.4K
Galaxy historyAgent trace
Codex GPT-5.6 Luna

Replicate 2

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
Fasta Regex Finder
Total tokens
292.9K
Output
5.4K
Galaxy historyAgent trace
Codex GPT-5.6 Luna

Replicate 3

CorrectStandard tools only
AnswerNT_033779.5:4280595-4280609
Workflow
Fasta Regex Finder
Total tokens
131.2K
Output
2.3K
Galaxy historyAgent trace

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codePython
Agent trace
Codex GPT-5.5

Replicate 2

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codePython
Agent trace
Codex GPT-5.5

Replicate 3

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codePython
Agent trace

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codePython
Agent trace
Codex GPT-5.6 Sol

Replicate 2

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codeSamtools
Agent trace
Codex GPT-5.6 Sol

Replicate 3

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local code
Agent trace

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codePythonBLASTNBowtie2BWA-MEM1 more tools
Total tokens
605.2K
Output
10.6K
Agent trace
Codex + DeepSeek-v4-pro-0813

Replicate 2

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codePython
Total tokens
107.7K
Output
2.6K
Agent trace
Codex + DeepSeek-v4-pro-0813

Replicate 3

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codePython
Total tokens
152.8K
Output
5.4K
Agent trace

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local code
Agent trace
Codex GPT-5.6 Luna

Replicate 2

Incorrect
AnswerNT_033779.5:4280595-4280608
Workflow
Local code
Agent trace
Codex GPT-5.6 Luna

Replicate 3

Incorrect
AnswerNT_033779.5:4280595-4280608
Workflow
Local code
Agent trace

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Correct
AnswerNT_033779.5:4280595-4280609
Workflow
Local codePython
Total tokens
45.0K
Output
406
Agent trace