Sapio Sciences
Elain Multisequence Alignment  |  Experiment #9053098

Multisequence Alignment Report

Automated analysis via Elain AI Co-Scientist  ·  Global pairwise alignment (Needleman–Wunsch)

Experiment
Claude MSA Test  (ID 9053098)
Notebook
TW-1  ·  twalker
Sequences Aligned
3 DNA sequences
Method
Global alignment  ·  match +2  ·  mismatch −1  ·  gap −5/−0.5
Registry IDs
Plas00001170  ·  Plas00001171  ·  Plas00001172
Report Date
March 26, 2026

Sequence Summary

# Accession Description Type Length (bp) Registry ID
1 MH011443.1 Homo sapiens TP53 gene, exon 5 and partial cds DNA 123 Plas00001170
2 MF098562.1 Homo sapiens BRCA2 gene, partial cds (isolate B47) DNA 287 Plas00001171
3 PV942393.1 Eupentacta fraudatrix VEGFA mRNA, complete cds DNA 1,276 Plas00001172
Note on sequence diversity: These three sequences represent distinct genes from different genomic and taxonomic contexts — a human tumor suppressor (TP53), a human DNA repair gene (BRCA2), and a sea cucumber angiogenesis-related mRNA (VEGFA homolog). Low pairwise identities are expected across this set.

Alignment Statistics

3
Sequences
1,276 bp
Longest sequence
123 bp
Shortest sequence
26.8%
Best pairwise identity
8.0%
Lowest pairwise identity
Global
Alignment mode

Pairwise Identity Matrix

Sequence MH011443.1 TP53 MF098562.1 BRCA2 PV942393.1 VEGFA
MH011443.1 TP53 100% 26.83% 7.99%
MF098562.1 BRCA2 26.83% 100% 17.32%
PV942393.1 VEGFA 7.99% 17.32% 100%

Identity calculated as: (matching positions) / (aligned length excluding double-gap columns) × 100

Pairwise Alignment Details

MH011443.1 TP53  ×  MF098562.1 BRCA2

26.83% identity
26.83%
% Identity
77
Matched bases
287
Aligned length
164
Total gap chars
-37.0
Alignment score
MH011443.1        --------------------------TGGGTT-------GATTCCACACCCCCGCC---- 1-60
                                            ||| ||       | ||| | |    | ||    
MF098562.1        ATTTTACAACATAACCAAAATATGTCTGGATTGGAGAAAGTTTCTAAAATATCACCTTGT

MH011443.1        ----------CGGCACCCGC--------GTCCGCGCCGT---GGCCATCT--ACAAG-CA 61-120
                             || | |  |        ||    |  ||   ||  | ||  | ||| ||
MF098562.1        GATGTTAGTTTGGAAACTTCAGATATATGTAAATGTAGTATAGGGAAGCTTCATAAGTCA

MH011443.1        GTCACAGC-------ACATGACGGAGGTT-----------GTG----------------- 121-180
                  ||| || |       || ||  |||  ||           |||                 
MF098562.1        GTCTCATCTGCAAATACTTGTGGGATTTTTAGCACAGCAAGTGGAAAATCTGTCCAGGTA

MH011443.1        --AGGCGCT-------------------------------------------GCCCCCAC 181-240
                    ||  |||                                           |  || | 
MF098562.1        TCAGATGCTTCATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAACATAGTACCAAG

MH011443.1        CATG----------AGCGCTGCTCAGA--TAGCG-----------AT 241-287
                  || |          ||   || | | |  || ||           | 
MF098562.1        CAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACAA

MH011443.1 TP53  ×  PV942393.1 VEGFA

7.99% identity
7.99%
% Identity
102
Matched bases
1276
Aligned length
1153
Total gap chars
-470.0
Alignment score
MH011443.1        ------------------------------------------------------------ 1-60
                                                                              
PV942393.1        CCAGACTAGACGACTGCTCCGCTTCTCTTCGGAATGAAACAGTGATGAGTGAGTGAGCCG

MH011443.1        ------------------------------------------------------------ 61-120
                                                                              
PV942393.1        TAGATTAGTGTGTATATCTCGAGGCCTTCATATATAATACGGTCGGTTACACCGTTTACA

MH011443.1        ------------------------------------------------------------ 121-180
                                                                              
PV942393.1        GCCTCTCCGAATTTGACTATTTTTGTTCAGCGTGGTCTCTGGGGCTGTATATATATTAAT

MH011443.1        ------------------------------------------------------------ 181-240
                                                                              
PV942393.1        GATACAGCATGGCAATGGGCAAATAAATAGTCATCTCGAATTTACACAGTACAGCTGACT

MH011443.1        ------------------------------------------------------------ 241-300
                                                                              
PV942393.1        ACACTCGACTTCGACGTCGCTCGCTAATTGGGAAGACTATCGAAAAGCCTGGCAGCAGAC

... alignment truncated at 300 bp for display (full length: 1276 bp) ...

MF098562.1 BRCA2  ×  PV942393.1 VEGFA

17.32% identity
17.32%
% Identity
221
Matched bases
1276
Aligned length
989
Total gap chars
-276.0
Alignment score
MF098562.1        ------------------------------------------------------------ 1-60
                                                                              
PV942393.1        CCAGACTAGACGACTGCTCCGCTTCTCTTCGGAATGAAACAGTGATGAGTGAGTGAGCCG

MF098562.1        ------------------------------------------------------------ 61-120
                                                                              
PV942393.1        TAGATTAGTGTGTATATCTCGAGGCCTTCATATATAATACGGTCGGTTACACCGTTTACA

MF098562.1        ------------------ATTT-------------------------------------- 121-180
                                    ||||                                      
PV942393.1        GCCTCTCCGAATTTGACTATTTTTGTTCAGCGTGGTCTCTGGGGCTGTATATATATTAAT

MF098562.1        --TACAACAT-------------------------------------------------- 181-240
                    |||| |||                                                  
PV942393.1        GATACAGCATGGCAATGGGCAAATAAATAGTCATCTCGAATTTACACAGTACAGCTGACT

MF098562.1        ------------------------------------------------------------ 241-300
                                                                              
PV942393.1        ACACTCGACTTCGACGTCGCTCGCTAATTGGGAAGACTATCGAAAAGCCTGGCAGCAGAC

... alignment truncated at 300 bp for display (full length: 1276 bp) ...

Biological Interpretation

The multisequence alignment of these three sequences reveals very low overall nucleotide identity across all pairwise comparisons, consistent with the distinct evolutionary origins and biological functions of the genes involved.


TP53 vs BRCA2 (26.83%): Both genes are human tumor suppressors, but they operate through fundamentally different mechanisms — TP53 as a transcription factor and DNA damage sensor, BRCA2 in homologous recombination repair. The limited nucleotide similarity at this partial exon/cds region reflects their divergent protein domains and evolutionary histories, even though both play critical roles in genome stability.


TP53 vs VEGFA (8.00%): The extremely low identity between the human TP53 exon 5 fragment and the Eupentacta fraudatrix VEGFA mRNA is expected — these are unrelated genes from divergent taxa (mammals vs. echinoderms), with no known functional relationship at the nucleotide level.


BRCA2 vs VEGFA (17.32%): Similarly, the partial BRCA2 coding sequence shares minimal nucleotide identity with the sea cucumber VEGFA mRNA. The slightly higher value compared to TP53 vs VEGFA likely reflects stochastic local similarities or the longer BRCA2 fragment providing more opportunity for coincidental matches.


Summary: All three sequences are effectively unrelated at the nucleotide level. No conserved regulatory elements, shared coding domains, or meaningful homology is indicated. This alignment serves to confirm sequence individuality and establish baseline divergence metrics for these registry entries (Plas00001170–1172) within Experiment 9053098.