LOG FILE for sequence file=SCN4ADIVa.fasta GENECONV version 1.81 Command line: GENECONV SCN4ADIVa.fasta SCN4ADIV_2.cfg /g1 Contents of parameter configuration file: SCN4ADIV_2.cfg: -Startseed=123 -group Ambystoma SCN4A_Ambystoma_mexicanum SCN4A_alternative_Amybstoma_mexicanum -group Pleurodeles SCN4A_Pleurodeles_waltl SCN4A_alternative_Pleurodeles_waltl -group Plethodon SCN4A_Plethodon_cinereus SCN4A_alternative_Plethodon_cinereus -group Notophthalmus SCN4A_Notophthalmus_viridescens SCN4A_alternative_Notophthalmus_viridescens -group Tgranulosa SCN4A_Taricha_granulosa SCN4A_alternative_Taricha_granulosa -group Ttorosa SCN4A_Taricha_torosa SCN4A_alternative_Taricha_torosa -group Bolitoglossa SCN4A_Bolitoglossa_vallecula_GHME01165342.1 SCN4A_alternative_Bolitoglossa_vallecula_GHME01165341.1 -group Salamandra SCN4A_Salamandra_salamandra SCN4A_alternative_Salamandra_salamandra -group Tylototriton SCN4A_Tylototriton_wenxianensis_GESS01000732.1_GESS01024789.1 SCN4A_alternative_Tylototriton_wenxianensis_GESS01029581.1 FASTA format sequence file `SCN4ADIVa.fasta' Read `SCN4A_Ambystoma_mexicanum': length=1084 Read `SCN4A_Salamandra_salamandra': length=1084 Read `SCN4A_Pleurodeles_waltl': length=1084 Read `SCN4A_Tylototriton_wenxianensis_GESS01000732.1_GESS01024789.1': length=1084 Read `SCN4A_Notophthalmus_viridescens': length=1084 Read `SCN4A_Taricha_granulosa': length=1084 Read `SCN4A_Taricha_torosa': length=1084 Read `SCN4A_Bolitoglossa_vallecula_GHME01165342.1': length=1084 Read `SCN4A_Plethodon_cinereus': length=1084 Read `SCN4A_Cryptobranchus_alleganiensis': length=1084 Read `SCN4A_alternative_Bolitoglossa_vallecula_GHME01165341.1': length=1084 Read `SCN4A_alternative_Plethodon_cinereus': length=1084 Read `SCN4A_alternative_Amybstoma_mexicanum': length=1084 Read `SCN4A_alternative_Salamandra_salamandra': length=1084 Read `SCN4A_alternative_Pleurodeles_waltl': length=1084 Read `SCN4A_alternative_Tylototriton_wenxianensis_GESS01029581.1': length=1084 Read `SCN4A_alternative_Notophthalmus_viridescens': length=1084 Read `SCN4A_alternative_Taricha_granulosa': length=1084 Read `SCN4A_alternative_Taricha_torosa': length=1084 1084 bases read. 19 sequences 1084 bases. SKIPPING SEQUENCE: SCN4A_Cryptobranchus_alleganiensis Options and features: Using 18 DNA sequences, 1084 aligned bases, 381 polymorphisms, FASTA format, gscale=1 for mismatches, 9 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, no maxKAPairPval limits, no maxKAGlobPval limits, simPvals based on 10,000 permutations, global P-values based on BLAST-like global scores, fragment limits: minlength=1, minnpolys=2, minscore=2, no pairwise fragment lists, at most one overlapping fragment, starting seed=123, contiguous sites with indels are one polymorphism, 6 indel blocks with up to 259 sites each, no match (replacement) char in source file. Groups: Ambystoma (2): SCN4A_Ambystoma_mexicanum SCN4A_alternative_Amybstoma_mexicanum Pleurodeles (2): SCN4A_Pleurodeles_waltl SCN4A_alternative_Pleurodeles_waltl Plethodon (2): SCN4A_Plethodon_cinereus SCN4A_alternative_Plethodon_cinereus Notophthalmus (2): SCN4A_Notophthalmus_viridescens SCN4A_alternative_Notophthalmus_viridescens Tgranulosa (2): SCN4A_Taricha_granulosa SCN4A_alternative_Taricha_granulosa Ttorosa (2): SCN4A_Taricha_torosa SCN4A_alternative_Taricha_torosa Bolitoglossa (2): SCN4A_Bolitoglossa_vallecula_GHME01165342.1 SCN4A_alternative_Bolitoglossa_vallecula_GHME01165341.1 Salamandra (2): SCN4A_Salamandra_salamandra SCN4A_alternative_Salamandra_salamandra Tylototriton (2): SCN4A_Tylototriton_wenxianensis_GESS01000732.1_GESS01024789.1 SCN4A_alternative_Tylototriton_wenxianensis_GESS01029581.1 Sequences not in group list: SCN4A_Cryptobranchus_alleganiensis Looking at within-group fragments only (9 groups) Mismatch penalty: 1 * npolys / num_ppen where `num_ppen' is the number of ``potential penalties'': sequence differences for inner fragments, local monomorphisms for outer fragments. Nucleotide codes in data: T(5511) C(3610) A(5494) G(4030) Other(867) CG/TCAG ratio: 40.98% Non-nucleotide characters in data: -(2DH)(n=867) 286 sites with missing data or unrecognized characters. (These characters are treated as indels for the purpose of creating indel blocks.) No sites with all gap or unrecognized characters. 375 polymorphic and 423 monomorphic sites with no indels. No single polymorphic sites with indels. 6 indel blocks with more than one site (each block is treated as a single polymorphism). 381 polymorphisms to be permuted. No match (replacement) char in file Elapsed time for building arrays: 0.00 secs. Elapsed time for simulations: 0.67 secs. Per iteration: 0.000067 secs. Written to SCN4ADIVa.frags: 2 I and 1 O significant global fragments. No pairwise fragments. OUTPUT FILES WRITTEN: `SCN4ADIVa.frags' LOG FILE: `SCN4ADIVa.sum' The starting random number seed is 123. Simulated P-values are based on 10,000 permutations. Maximum BLAST-like scores (18 sequences, 9 groups): Inner Max Sim S.D.s above S.D. of frags Score P-value sim. mean sims SCORE 5.795 0.0107 3.22 1.1630 OuterSeq frags 5.970 0.0075 3.36 1.1823 Total memory allocated: 484,121 bytes. No reallocations. Maximum input sequence-file line width: 1084 bytes.