This is part of the output of the command
qod --verbose \
--ref-seq genomes/Escherichia_coli/AP009048_GR.fsa.gz \
alignments/Escherichia_coli/AP009048_GR_CP00024*.mat.gz
where the files are those in the sample directory provided with the qod package:
******************************************************************************* * * * The QOD project aims to compare multiple genomes. * * qod version 1.0.2 * * * * Copyright © 2009-2012 -- LIRMM/CNRS * * (Laboratoire d'Informatique, de Robotique et de * * Microélectronique de Montpellier / * * Centre National de la Recherche Scientifique). * * * * Auteurs/Authors: The QOD Project <qod-project@lirmm.fr> * * Alban MANCHERON <alban.mancheron@lirmm.fr> * * Eric RIVALS <eric.rivals@lirmm.fr> * * Raluca URICARU <raluca.uricaru@lirmm.fr> * * * * Utilisez l'option '--full-version' pour de plus amples details. * * Run with the '--full-version' option for more details. * * * ******************************************************************************* Length of the central genome sequence [from file 'genomes/Escherichia_coli/AP009048_ GR.fsa.gz']: 4646332. Local similarities files: * alignments/Escherichia_coli/AP009048_GR_CP000243_GR_10.mat.gz * alignments/Escherichia_coli/AP009048_GR_CP000247_GR_10.mat.gz Segmentation: [1 ; 15390] [16691 ; 16835] [16728 ; 17166] [17142 ; 58179] [59255 ; 59670] ⋮ [4633324 ; 4633534] [4633350 ; 4633538] [4633358 ; 4633553] [4633374 ; 4633569] [4633407 ; 4633570] [4633418 ; 4633581] [4633511 ; 4646332] * Filtering with [1 ; 15390] (1 available multiple alignment) 0: [1 ; 15390] [1 ; 15442] (14958/15442) 1: [1 ; 15390] [1 ; 15455] (14916/15455) * Filtering with [16691 ; 16835] (1 available multiple alignment) 0: [16691 ; 16844] [1530398 ; 1530554] (96/157) 1: [16691 ; 16835] [1432551 ; 1432698] (91/148) * Filtering with [16728 ; 17166] (1 available multiple alignment) 0: [16728 ; 17177] [15431 ; 15881] (427/451) 1: [16728 ; 17166] [15444 ; 15882] (411/439) * Filtering with [17142 ; 58179] (1 available multiple alignment) 0: [17142 ; 58179] [19774 ; 61377] (38524/41604) 1: [17142 ; 58179] [19790 ; 60284] (38496/41038) * Filtering with [59255 ; 59670] (1 available multiple alignment) 0: [59255 ; 59670] [1121975 ; 1122368] (315/416) 1: [59255 ; 59670] [333904 ; 334297] (313/416) ⋮ * Filtering with [4633324 ; 4633534] (1 available multiple alignment) 0: [4633324 ; 4633534] [2453176 ; 2453384] (144/211) 1: [4633324 ; 4633534] [2353921 ; 2354129] (144/211) * Filtering with [4633350 ; 4633538] (1 available multiple alignment) 0: [4633350 ; 4633538] [9867 ; 10049] (106/189) 1: [4633350 ; 4633538] [9880 ; 10062] (106/189) * Filtering with [4633358 ; 4633553] (1 available multiple alignment) 0: [4633358 ; 4633553] [5038186 ; 5038367] (136/196) 1: [4633358 ; 4633553] [4912408 ; 4912589] (136/196) * Filtering with [4633374 ; 4633569] (1 available multiple alignment) 0: [4633374 ; 4633569] [394212 ; 394390] (143/196) 1: [4633374 ; 4633569] [447444 ; 447622] (143/196) * Filtering with [4633407 ; 4633570] (1 available multiple alignment) 0: [4633407 ; 4633570] [2255869 ; 2256022] (106/164) 1: [4633407 ; 4633570] [2156169 ; 2156322] (106/164) * Filtering with [4633418 ; 4633581] (1 available multiple alignment) 0: [4633418 ; 4633581] [423165 ; 423330] (99/166) 1: [4633418 ; 4633581] [476399 ; 476564] (99/166) * Filtering with [4633511 ; 4646332] (1 available multiple alignment) 0: [4633511 ; 4646332] [5052983 ; 5065741] (12483/12822) 1: [4633511 ; 4646332] [4926162 ; 4938920] (12487/12822) Partition: P#1 => [1 ; 15390]: 1 covering interval and 1 available multiple alignment. P#2 => [15391 ; 16690]: 0 covering interval and 0 available multiple alignment. P#3 => [16691 ; 16727]: 1 covering interval and 1 available multiple alignment. P#4 => [16728 ; 16835]: 2 covering intervals and 4 available multiple alignments. P#5 => [16836 ; 17141]: 1 covering interval and 1 available multiple alignment. P#6 => [17142 ; 17166]: 2 covering intervals and 4 available multiple alignments. P#7 => [17167 ; 58179]: 1 covering interval and 1 available multiple alignment. P#8 => [58180 ; 59254]: 0 covering interval and 0 available multiple alignment. P#9 => [59255 ; 59670]: 1 covering interval and 1 available multiple alignment. ⋮ P#1910 => [4633407 ; 4633417]: 5 covering intervals and 30 available multiple alignments. P#1911 => [4633418 ; 4633510]: 6 covering intervals and 42 available multiple alignments. P#1912 => [4633511 ; 4633534]: 7 covering intervals and 49 available multiple alignments. P#1913 => [4633535 ; 4633538]: 6 covering intervals and 36 available multiple alignments. P#1914 => [4633539 ; 4633553]: 5 covering intervals and 25 available multiple alignments. P#1915 => [4633554 ; 4633569]: 4 covering intervals and 16 available multiple alignments. P#1916 => [4633570 ; 4633570]: 3 covering intervals and 9 available multiple alignments. P#1917 => [4633571 ; 4633581]: 2 covering intervals and 4 available multiple alignments. P#1918 => [4633582 ; 4646332]: 1 covering interval and 1 available multiple alignment. That's All, Folks!!!