data/macsyfinder-1.0.5/CITATION.yml:3: informations ==> information
data/macsyfinder-1.0.5/COPYRIGHT:58: Thess ==> This, these
data/macsyfinder-1.0.5/bin/macsyfinder:279: conficts ==> conflicts
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:3432: thiE ==> the, this
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:3478: thiD ==> this
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:4857: DAA ==> DATA
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:5205: repsonse ==> response
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:5431: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:6007: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:6418: ND ==> AND, 2ND
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:10256: formate ==> format
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:11012: LIEK ==> LIKE
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:12832: formate ==> format
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:13523: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:15350: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:16187: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:17189: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:18147: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru.001.c01.11.prt:20957: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:3432: thiE ==> the, this
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:3478: thiD ==> this
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:4857: DAA ==> DATA
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:5205: repsonse ==> response
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:5431: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:6007: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:6418: ND ==> AND, 2ND
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:10256: formate ==> format
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:11012: LIEK ==> LIKE
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:12832: formate ==> format
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:13523: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:15350: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:16187: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:17189: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:18147: Ser ==> Set
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:20957: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:28655: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:33027: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:33032: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:33038: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:34059: fliE ==> file
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:34059: FliE ==> file
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:53092: fpr ==> for, far, fps
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:53409: folX ==> folks
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:57825: thiD ==> this
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:57832: thiE ==> the, this
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:60613: HAA ==> HAS
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:64623: formate ==> format
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:64631: formate ==> format
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:64637: formate ==> format
data/macsyfinder-1.0.5/data/base/prru_psae.001.c01.fasta:64645: formate ==> format
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:3224: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:7596: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:7601: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:7607: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:8628: fliE ==> file
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:8628: FliE ==> file
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:27661: fpr ==> for, far, fps
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:27978: folX ==> folks
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:32394: thiD ==> this
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:32401: thiE ==> the, this
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:35182: HAA ==> HAS
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:39192: formate ==> format
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:39200: formate ==> format
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:39206: formate ==> format
data/macsyfinder-1.0.5/data/base/psae.001.c01.13.prt:39214: formate ==> format
data/macsyfinder-1.0.5/data/profiles/cas10_TypeIIIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas10_TypeIIIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas10d_TypeID.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeI-II-III.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeIC.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeID.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeIE.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeIF.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeII.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas1_TypeU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas2_TypeI-II-III.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas2_TypeIE.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas3-cas2_TypeIF.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas3_TypeI.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas3_TypeID.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas3_TypeIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas3a_TypeI.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas4_TypeI-II.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas4_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas4_TypeU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas5_TypeI.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas5_TypeIE.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas5a2_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas5a_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas5b2_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas5b_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas5c2_TypeIC.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas5c_TypeIC.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas6_TypeI-III.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas6_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas6_TypeIE.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas6_TypeIF.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas7_TypeI.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas7_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas7_TypeIE.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas7b2_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas7b3_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas7b_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas7c2_TypeIC.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas7c_TypeIC.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8a1a2_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8a1a3_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8a1b2_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8a1b3_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8a1b_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8a2a2_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8a2a_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8b_TypeIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8c2_TypeIC.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas8c_TypeIC.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas9_TypeII.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cas9_TypeIIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/casRa_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cmr1_TypeIIIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cmr3_TypeIIIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cmr4_TypeIIIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cmr5_TypeIIIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cmr6_TypeIIIB.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cpf1_TypeU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csa5_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csaX_TypeIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csb1_TypeIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csb2_TypeIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csb3_TypeIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csc1_TypeID.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csc2_TypeID.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cse1_TypeIE.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/cse2_TypeIE.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csf1_TypeU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csf2_TypeU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csf3_TypeU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csf4_TypeU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csm2_TypeIIIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csm3_TypeIIIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csm4_TypeIIIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csm5_TypeIIIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csm6_TypeIIIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csn2_TypeIIA.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csx10_TypeIIIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csx16_TypeIIIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csx17_TypeIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csx1u2_TypeIIIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csx1u_TypeIIIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csx3_TypeIIIU.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csy1_TypeIF.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csy2_TypeIF.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/profiles/csy3_TypeIF.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:1334: gud ==> good
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:1550: yaeR ==> year
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:2786: regualtor ==> regulator
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:2954: auxillary ==> auxiliary
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:2958: auxillary ==> auxiliary
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:2972: auxillary ==> auxiliary
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:3703: allS ==> all, falls
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:4037: borD ==> board, bored, border
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:4055: appY ==> apply
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:6010: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:6028: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:6666: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:6672: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:6689: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:8232: thiK ==> thick, think
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:10318: regualtor ==> regulator
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:10837: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:10844: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:11700: supressor ==> suppressor
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:13210: fucntion ==> function
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:14101: fliE ==> file
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:15300: thiD ==> this
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:16931: folX ==> folks
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:18300: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:18315: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:18346: hda ==> had
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:19841: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:19885: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:19892: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:20340: queE ==> queue
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:21655: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:22927: garD ==> guard
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:23325: partioning ==> partitioning, portioning
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:23617: nanE ==> name
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:24668: ND ==> AND, 2ND
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:27003: sytem ==> system
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:27014: wtih ==> with
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:28321: Ser ==> Set
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:28585: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:28593: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:28599: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:28606: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:28808: fpr ==> for, far, fps
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:29027: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:29027: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:29044: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:29338: thiE ==> the, this
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:30072: alsE ==> also, else, false
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:30741: TE ==> THE, BE, WE
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:31695: fimE ==> fixme, time
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:32171: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:35560: formate ==> format
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:37543: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:42525: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:42530: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:44898: Holliday ==> Holiday
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:46551: fliE ==> file
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:54835: dotA ==> data
data/macsyfinder-1.0.5/data/sequence_data/datatest_gembase.fasta:54835: DotA ==> data
data/macsyfinder-1.0.5/doc/functioning.rst:60: wether ==> weather, whether
data/macsyfinder-1.0.5/doc/gene.rst:19: instanciated ==> instantiated
data/macsyfinder-1.0.5/doc/gene.rst:46: instanciate ==> instantiate
data/macsyfinder-1.0.5/doc/implementation.rst:76: correponding ==> corresponding
data/macsyfinder-1.0.5/doc/implementation.rst:81: instanciated ==> instantiated
data/macsyfinder-1.0.5/doc/quickstart.rst:87: commmand-line ==> command-line
data/macsyfinder-1.0.5/doc/system.rst:32: instanciate ==> instantiate
data/macsyfinder-1.0.5/doc/system_parser.rst:15: instanciates ==> instantiates
data/macsyfinder-1.0.5/doc/images/fig_capture.svg:71: WHE ==> WHEN, WE
data/macsyfinder-1.0.5/doc/images/fig_capture.svg:71: ND ==> AND, 2ND
data/macsyfinder-1.0.5/etc/macsyfinder.conf:32: bellow ==> below
data/macsyfinder-1.0.5/etc/macsyfinder.conf:39: bellow ==> below
data/macsyfinder-1.0.5/etc/macsyfinder.conf:46: bellow ==> below
data/macsyfinder-1.0.5/macsypy/config.py:608: meaningfull ==> meaningful
data/macsyfinder-1.0.5/macsypy/database.py:99: asynchron ==> asynchronous
data/macsyfinder-1.0.5/macsypy/database.py:256: instanciated ==> instantiated
data/macsyfinder-1.0.5/macsypy/database.py:380: informations ==> information
data/macsyfinder-1.0.5/macsypy/gene.py:29: instanciated ==> instantiated
data/macsyfinder-1.0.5/macsypy/gene.py:173: whithout ==> without
data/macsyfinder-1.0.5/macsypy/gene.py:432: instanciated ==> instantiated
data/macsyfinder-1.0.5/macsypy/registries.py:63: defitions ==> definitions
data/macsyfinder-1.0.5/macsypy/report.py:359: instanciated ==> instantiated
data/macsyfinder-1.0.5/macsypy/search_systems.py:370: wether ==> weather, whether
data/macsyfinder-1.0.5/macsypy/search_systems.py:493: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:496: uncomplete ==> incomplete
data/macsyfinder-1.0.5/macsypy/search_systems.py:602: occurences ==> occurrences
data/macsyfinder-1.0.5/macsypy/search_systems.py:679: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:722: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:870: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:871: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:926: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:927: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:987: wether ==> weather, whether
data/macsyfinder-1.0.5/macsypy/search_systems.py:1021: uncomplete ==> incomplete
data/macsyfinder-1.0.5/macsypy/search_systems.py:1057: uncomplete ==> incomplete
data/macsyfinder-1.0.5/macsypy/search_systems.py:1357: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:1628: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:1766: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:1773: occurence ==> occurrence
data/macsyfinder-1.0.5/macsypy/search_systems.py:1778: uncomplete ==> incomplete
data/macsyfinder-1.0.5/macsypy/search_systems.py:1796: Arbitratily ==> Arbitrarily
data/macsyfinder-1.0.5/macsypy/search_systems.py:2168: ther ==> there, their, the, other
data/macsyfinder-1.0.5/macsypy/search_systems.py:2251: wether ==> weather, whether
data/macsyfinder-1.0.5/macsypy/system.py:22: instanciated ==> instantiated
data/macsyfinder-1.0.5/tests/data/DEF/bad_max_nb_genes.xml:10: fliE ==> file
data/macsyfinder-1.0.5/tests/data/DEF/bad_min_genes_required.xml:6: fliE ==> file
data/macsyfinder-1.0.5/tests/data/DEF/bad_min_mandatory_genes_required.xml:10: fliE ==> file
data/macsyfinder-1.0.5/tests/data/DEF/bad_min_mandatory_genes_required_2.xml:10: fliE ==> file
data/macsyfinder-1.0.5/tests/data/DEF/fail_invalid_presence.xml:6: fliE ==> file
data/macsyfinder-1.0.5/tests/data/DEF/fail_wo_presence.xml:5: fliE ==> file
data/macsyfinder-1.0.5/tests/data/DEF/system_1.xml:10: fliE ==> file
data/macsyfinder-1.0.5/tests/data/data_set_1/basic_run_results/macsyfinder.out:16: uncomplete ==> incomplete
data/macsyfinder-1.0.5/tests/data/data_set_1/basic_run_results/macsyfinder.out:24: uncomplete ==> incomplete
data/macsyfinder-1.0.5/tests/data/data_set_1/basic_run_results/macsyfinder.out:32: uncomplete ==> incomplete
data/macsyfinder-1.0.5/tests/data/data_set_1/basic_run_results/macsyfinder.out:52: uncomplete ==> incomplete
data/macsyfinder-1.0.5/tests/data/data_set_1/basic_run_results/macsyfinder.out:60: uncomplete ==> incomplete
data/macsyfinder-1.0.5/tests/data/data_set_1/basic_run_results/macsyfinder.out:80: uncomplete ==> incomplete
data/macsyfinder-1.0.5/tests/data/data_set_1/basic_run_results/macsyfinder.out:88: uncomplete ==> incomplete
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_flgB.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_flgC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_fliE.hmm:2: fliE ==> file
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_fliE.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_sctJ_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_sctN_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_sctQ_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_sctR_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_sctS_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_sctT_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_sctU_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Flg_sctV_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspD.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspE.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspF.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspH.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspI.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspJ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspK.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspL.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspM.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspN.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T2SS_gspO.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctJ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctN.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctQ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctR.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctS.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctT.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctU.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T3SS_sctV.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilAE.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilB.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilD.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilI_pilV.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilM.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilN.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilO.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilP.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilQ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4P_pilT_pilU.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traB.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traE.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traF.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traH.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traK.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traL.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traN.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traU.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traV.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_traW.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_F_trbC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_G_tfc7.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traE.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traI.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traK.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traL.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traM.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traN.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traO.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traP.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traQ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traR.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traT.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traU.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traW.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_traY.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_trbA.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_I_trbB.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBB.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBF.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBH.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBP1.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBP2.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBP3.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBQ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBT.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_MOBV.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_T_virB1.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_t4cp1.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_t4cp2.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_tcpA.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T4SS_virb4.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_gldJ_TIGR03524.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_gldK_TIGR03525.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_gldL_TIGR03513.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_gldM_TIGR03517.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_gldN_TIGR03523.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_porQ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_porU.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_porV.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_sprA-2_PF12118.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_sprA-3_TIGR04189.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_sprA_PF14349.hmm:6: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_sprE.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/T9SS_sprT.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_flp.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_rcpA.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_tadA.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_tadB.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_tadC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_tadE.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_tadF.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_tadV.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/data_set_1/profiles/Tad_tadZ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/hmm/gspE.search_hmm.out:112: nd ==> and, 2nd
data/macsyfinder-1.0.5/tests/data/hmm/tadA.search_hmm.out:290: te ==> the, be, we
data/macsyfinder-1.0.5/tests/data/profiles/abc.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/flgB.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/flgC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/fliE.hmm:2: fliE ==> file
data/macsyfinder-1.0.5/tests/data/profiles/fliE.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/gspD.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/sctC.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/sctJ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/sctJ_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/sctN.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/sctN_FLG.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/tadZ.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/toto.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/data/profiles/totote.hmm:4: ALPH ==> ALPHA
data/macsyfinder-1.0.5/tests/unit/test_SystemParser.py:107: fliE ==> file