Shift Detector

This program checks for the possibility that a tracefile results from sequencing of two similar sequences, which one of them having a deletion of 1 to 25 bases. Such deletion would produce a superimposed tracefile following the site of deletion
Example Data Set

INPUT

Submit a file for base-calling and shift detection (ABI format)


Expect
0.000010.00010.001

Analysis from base to base

uploaded_file -> example8.abi
action -> detect
Expect -> 0.0001
base -> 1
to_base -> 500

RESULTS

Shift of 1 nucleotides was detected (Expect 1.53e-05)
Shift starts at analyzed base 163 : probability score 3.91e-03
The predicted sequence of the molecule following the shift is:
GGCTkGGGNNCNGNCCNGGkGNCNGkKTNGGGNCssCCCNGAAGCYYCCTGGGACTKTCs
CTGGCmmAGCCsGrGGsCYTGAAGGkGGCAAmmCGGCYCAGGkGCCAGCmCsCCCAGCAT
NMCCmCSSsSGGrGGGTCCAGkGGTCmNkKKNMArr

Checks for 2 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 3 nucleotide shift : No shift found (Expect 3.91e-03)

Checks for 4 nucleotide shift : No shift found (Expect 1.00e+00)

Checks for 5 nucleotide shift : No shift found (Expect 2.44e-04)

Checks for 6 nucleotide shift : No shift found (Expect 3.91e-03)

Checks for 7 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 8 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 9 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 10 nucleotide shift : No shift found (Expect 1.00e+00)

Checks for 11 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 12 nucleotide shift : No shift found (Expect 1.00e+00)

Checks for 13 nucleotide shift : No shift found (Expect 3.91e-03)

Checks for 14 nucleotide shift : No shift found (Expect 3.91e-03)

Checks for 15 nucleotide shift : No shift found (Expect 3.91e-03)

Checks for 16 nucleotide shift : No shift found (Expect 1.00e+00)

Checks for 17 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 18 nucleotide shift : No shift found (Expect 3.91e-03)

Checks for 19 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 20 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 21 nucleotide shift : No shift found (Expect 6.25e-02)

Checks for 22 nucleotide shift : No shift found (Expect 2.44e-04)

Checks for 23 nucleotide shift : No shift found (Expect 1.00e+00)

Checks for 24 nucleotide shift : No shift found (Expect 1.00e+00)

Checks for 25 nucleotide shift : No shift found (Expect 1.00e+00)

EXP format for shift 1
/cowry_data/WEB.DIR/26185
View trace with ChromatogramApplet by Eugen Buehler
Eyal Seroussi Ph. D.

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