Neatbo.

DNA sequence logo

Generate a quantitative ACGT logo from an existing alignment, with explicit probability or information heights, gap handling, full column measurements and exact source bytes.

Browser-local processingInputAligned DNA / FASTAOutputComplete SVG pages, column CSV and JSONUp to 10 MiB per file · File limit: 1
  1. 1Add input
  2. 2Adjust settings
  3. 3Get your result

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Your input

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.fa · .fasta · .fas · .fna · .txt

Up to 10 MiB per file · File limit: 1

    0 characters · 0 bytes
    Options

    Complete the required options first. You can keep the defaults for the rest.

    Finite 0–100, added separately to A/C/G/T; raw counts remain unchanged.

    Preparing the tool…

    Before you start

    Generate a quantitative ACGT logo from an existing alignment, with explicit probability or information heights, gap handling, full column measurements and exact source bytes.

    How to use this tool

    1. Choose lines or FASTA, then paste the existing aligned DNA or select one original file.
    2. Choose probability or information heights, a gap rule and a pseudocount from 0 through 100.
    3. Generate the logo and check column count, effective counts and complete column measurements.
    4. Keep every SVG page, column CSV, report, normalized FASTA and original; copy the full report for review.

    Supported inputs and limits

    Paste an alignment or choose one UTF-8 file, up to 10 MiB. A selected file takes priority over pasted text; clear it to use the text. Filenames are limited to 512 UTF-8 bytes. No input content or name is uploaded.

    Choose one sequence per nonblank line or multi-record FASTA. ASCII spaces and tabs within sequences are removed and lowercase ACGT is converted to uppercase. FASTA fragments are concatenated; complete nonempty unique headers are retained, up to 256 UTF-16 units. One leading BOM, LF and CRLF are accepted; bare CR and malformed UTF-8 are refused.

    All sequences must already have the same length. Only ACGT is counted. With Ignore gaps, - and . remain at their original columns but are excluded from that column’s effective count. Reject gaps refuses them. IUPAC ambiguity, RNA, protein and alignment construction are outside this tool.

    At most 10,000 sequences, 3,000 columns and 9,999,999 sequence-by-column cells. All three limits apply together; 10,000 sequences of 1,000 columns exceed the cell limit.

    Pseudocount is a finite number from 0 through 100 added to each of A/C/G/T when computing probabilities. Raw counts stay unchanged. Information uses a fixed uniform background: R = 2 − H and height = probability × R, without small-sample correction. An all-gap column has null values and no glyph even with a positive pseudocount.

    Download report.json, columns.csv, alignment.fasta, every logo-NNN.svg page and original.input. Each SVG page covers at most 500 columns; no column or nonzero glyph is dropped. Column positions are one-based. The normalized FASTA and original bytes serve different purposes.

    Complete files plus full report text are limited to 56 MiB. Larger complete results are refused without shortening fields. Copy keeps the entire compact report; a limited screen preview does not replace the downloads.

    A single 10-second deadline covers source checks, file reading, loading, processing, result validation and the first result display. Cancel or timeout ends unfinished work without publishing a partial or late result. Keep the same source and options to retry.

    Worked example

    Example input

    ACGT
ACGT
ACGA
ACGG
    Example options
    {"inputMode":"lines","mode":"information","gapPolicy":"reject","pseudocount":0}

    Example output

    column,base,count,effective_count,gap_count,probability,entropy_bits,information_bits,height
1,A,4,4,0,1,0,2,2
1,C,0,4,0,0,0,2,0
1,G,0,4,0,0,0,2,0
1,T,0,4,0,0,0,2,0
2,A,0,4,0,0,0,2,0
2,C,4,4,0,1,0,2,2
2,G,0,4,0,0,0,2,0
2,T,0,4,0,0,0,2,0
3,A,0,4,0,0,0,2,0
3,C,0,4,0,0,0,2,0
3,G,4,4,0,1,0,2,2
3,T,0,4,0,0,0,2,0
4,A,1,4,0,0.25,1.5,0.5,0.125
4,C,0,4,0,0,1.5,0.5,0
4,G,1,4,0,0.25,1.5,0.5,0.125
4,T,2,4,0,0.5,1.5,0.5,0.25

    When something does not work

    Keep the alignment. Correct the format, header, alphabet or unequal lengths; choose Ignore gaps explicitly when needed. Reduce the analyzed alignment deliberately after a sequence, column, cell or complete-result limit, and record that change. Rerun the same source and options after cancel or timeout; clear the file selection to use pasted text.

    Frequently asked questions

    How do probability and information heights differ?

    Probability height is p and each observed column totals 1. Information height is p×(2−H) with a uniform DNA background; a uniform four-base column has total information height 0.

    Does Ignore gaps remove columns?

    No. - and . keep their original columns and are excluded only from that column’s effective count. An all-gap column remains in report/CSV with null values and no SVG glyph.

    Does a pseudocount change source counts?

    No. It adds a to each base for (count+a)/(effectiveCount+4a). Raw counts remain intact. The default is a=0 and there is no small-sample correction.

    Why can the logo differ from a textbook figure?

    Check the input counts and explicit model. The figure cited in the original question has a reported erratum; this tool does not derive data from that image or infer biological function.

    Documentation & further reading

    Build a quantitative DNA logo from an existing alignment →Choose probability or information heights for a DNA logo →

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