#INCLUSive GFF File
#
#The results in this file are NOT complete as long as there is no END-sign at the bottom of this file.
#The first section of this file allows you to evaluate (#DatasetDimension:) the amount of noise in your input, (#List of merged non-spurious instances:) variability of the instances width in your input, (#MotifClusterRun:) post-processing of the extracted clusters.
#The section #PrintClusters describes the ensemble motif(s) extracted by the FuzzyClustering application.
#Please read more on FuzzyClustering Guidelines webpage to optimally interpretate below results.

#DatasetDimension LOADED : nbr instances = 60, nbr sequences = 5, nbr motifs = 100
#DatasetDimension FILTERED (parameter -p) : nbr instances = 16, nbr sequences = 5, nbr motifs = 96
#::Noisy motifs(4):[box_2_1_GArATGmwwrmkAnmAnwG, box_19_1_GmrATGAnnrmkAynAnTG, box_38_1_wTGnwCnsAnyAwTTATnr, box_64_1_kwwTrnwmmGnwkAyTTAT]
#List of merged non-spurious instances :
emrK_26_43_+_ATAGTTTCAAGTTGGCAC(12):[emrK_27_45_+_TAGTTTCAAGTTGGCACTA(7,1),emrK_21_39_+_GATTTATAGTTTCAAGTTG(4,1),emrK_33_51_+_CAAGTTGGCACTATAAGTC(1,1)]
emrK_59_77_+_TAATCCTACAGGCGTAAGA(29):[emrK_59_77_+_TAATCCTACAGGCGTAAGA(28,1),emrK_57_75_+_ACTAATCCTACAGGCGTAA(1,1)]
emrK_217_235_+_TCATAAATTTCATCTATGA(17):[emrK_217_235_+_TCATAAATTTCATCTATGA(12,1),emrK_218_236_+_CATAAATTTCATCTATGAG(1,1),emrK_220_238_+_TAAATTTCATCTATGAGAA(1,1),emrK_222_240_+_AATTTCATCTATGAGAAAT(1,1),emrK_213_231_+_CAATTCATAAATTTCATCT(1,1),emrK_216_234_+_TTCATAAATTTCATCTATG(1,1)]
evgA_6_24_+_AATTCTTACGCCTGTAGGA(28):[evgA_6_24_+_AATTCTTACGCCTGTAGGA(28,1)]
evgA_37_55_+_CTTATAGTGCCAACTTGGA(11):[evgA_35_53_+_GACTTATAGTGCCAACTTG(3,1),evgA_41_59_+_TAGTGCCAACTTGAAACTA(6,1),evgA_29_47_+_TAAGAAGACTTATAGTGCC(1,1),evgA_31_49_+_AGAAGACTTATAGTGCCAA(1,1)]
evgA_50_68_+_CTTGAAACTATAAATCATC(20):[evgA_50_68_+_CTTGAAACTATAAATCATC(7,1),evgA_48_66_+_AACTTGAAACTATAAATCA(3,1),evgA_52_70_+_TGAAACTATAAATCATCGG(1,1),evgA_54_72_+_AAACTATAAATCATCGGTA(2,1),evgA_47_65_+_CAACTTGAAACTATAAATC(4,1),evgA_55_73_+_AACTATAAATCATCGGTAC(2,1),evgA_53_71_+_GAAACTATAAATCATCGGT(1,1)]
evgA_64_82_+_TCATCGGTACAATCCCTGA(20):[evgA_64_82_+_TCATCGGTACAATCCCTGA(15,1),evgA_61_79_+_AAATCATCGGTACAATCCC(3,1),evgA_59_77_+_ATAAATCATCGGTACAATC(1,1),evgA_72_90_+_ACAATCCCTGATTTTATTG(1,1)]
evgA_78_95_+_CCTGATTTTATTGTTGAC(10):[evgA_81_99_+_GATTTTATTGTTGACATTT(3,1),evgA_74_92_+_AATCCCTGATTTTATTGTT(6,1),evgA_88_106_+_TTGTTGACATTTCATTTAT(1,1)]
yegR_68_86_+_CTTCAATATAATATATTAA(26):[yegR_67_85_+_TCTTCAATATAATATATTA(16,1),yegR_68_86_+_CTTCAATATAATATATTAA(1,1),yegR_72_90_+_AATATAATATATTAAAGCC(1,1),yegR_71_89_+_CAATATAATATATTAAAGC(6,1),yegR_65_83_+_CATCTTCAATATAATATAT(1,1),yegR_66_84_+_ATCTTCAATATAATATATT(1,1)]
yegR_126_144_+_AATTCCTACTTATGTAGGA(28):[yegR_126_144_+_AATTCCTACTTATGTAGGA(28,1)]
yegR_277_295_+_TAATTAGTATTTTTATTAT(10):[yegR_278_296_+_AATTAGTATTTTTATTATG(4,1),yegR_283_301_+_GTATTTTTATTATGTCTGG(1,1),yegR_280_298_+_TTAGTATTTTTATTATGTC(1,1),yegR_270_288_+_ATATCATTAATTAGTATTT(1,1),yegR_274_292_+_CATTAATTAGTATTTTTAT(1,1),yegR_276_294_+_TTAATTAGTATTTTTATTA(2,1)]
yfdX_34_52_+_CATCGATATAATAAATGAA(35):[yfdX_33_51_+_ACATCGATATAATAAATGA(17,1),yfdX_34_52_+_CATCGATATAATAAATGAC(4,1),yfdX_38_56_+_GATATAATAAATGACATCT(3,1),yfdX_37_55_+_CGATATAATAAATGACATC(6,1),yfdX_28_46_+_TATTTACATCGATATAATA(3,1),yfdX_31_49_+_TTACATCGATATAATAAAT(1,1),yfdX_32_50_+_TACATCGATATAATAAATG(1,1)]
yfdX_97_115_+_TATTCCTACAATTGTAAGA(27):[yfdX_97_115_+_TATTCCTACAATTGTAAGA(24,1),yfdX_101_119_+_CCTACAATTGTAAGACTAA(1,1),yfdX_95_113_+_CATATTCCTACAATTGTAA(1,1),yfdX_88_106_+_CAGGAAGCATATTCCTACA(1,1)]
yneN_96_114_+_AACTACATACTATAAGATA(13):[yneN_98_116_+_CTACATACTATAAGATATA(6,1),yneN_96_114_+_AACTACATACTATAAGATA(1,1),yneN_94_112_+_TAAACTACATACTATAAGA(3,1),yneN_93_111_+_TTAAACTACATACTATAAG(1,1),yneN_95_113_+_AAACTACATACTATAAGAT(2,1)]
yneN_121_139_+_TCTGCCTACAGCTGTAAGA(30):[yneN_121_139_+_TCTGCCTACAGCTGTAAGA(28,1),yneN_115_133_+_TAAACTTCTGCCTACAGCT(1,1),yneN_119_137_+_CTTCTGCCTACAGCTGTAA(1,1)]
yneN_211_229_+_TAACGATTTTTAACGTTTA(13):[yneN_209_227_+_ATTAACGATTTTTAACGTT(6,1),yneN_215_233_+_GATTTTTAACGTTATCCGC(3,1),yneN_210_228_+_TTAACGATTTTTAACGTTA(2,1),yneN_212_230_+_AACGATTTTTAACGTTATC(1,1),yneN_207_225_+_TGATTAACGATTTTTAACG(1,1)]

#MotifClusterRun::Extraction(): 11 clusters extracted by edgeclust.m 
# 8 clusters rejected for low (<= 3) number of sequences (threshold derived from parameter -i)
# 0 clusters rejected for low (<= 20) number of corresponding motifs in input file (threshold derived from parameter -j)
# 0 clusters rejected for low (<= 0.5) Consensus score (threshold set by parameter -c)

#PrintClusters:: 3 ensemble motifs :

#id: box_1_CS[19,wATTCCTACnnnTGTArGA,1.42]_%InstanceCut=0.89_%MotifCut=0.6_nbrSeq=5_nbrInst=5_nbrMotifs=29
#CS-distribution : [1.42]
#instance memberships: ( N(i)=5, Occ(i)=28)
emrK_59_77_+_TAATCCTACAGGCGTAAGA_(shift=0,occ=29)	0.46
evgA_6_24_+_AATTCTTACGCCTGTAGGA_(shift=0,occ=28)	0.45
yegR_126_144_+_AATTCCTACTTATGTAGGA_(shift=0,occ=28)	0.45
yfdX_97_115_+_TATTCCTACAATTGTAAGA_(shift=0,occ=27)	0.412
yneN_121_139_+_TCTGCCTACAGCTGTAAGA_(shift=0,occ=30)	0.463
#motif memberships: ( N(m)=28)
box_3_1_wATTCCTACnnnTGTArGA	0.192
box_5_1_wATTCCTACnnnTGTArGA	0.192
box_7_1_wATTCCTACnnnTGTArGA	0.192
box_8_1_wATTCCTACnnnTGTArGA	0.192
box_10_1_wATTCCTACnnnTGTArGA	0.192
box_14_1_wATTCCTACnnnTGTArGA	0.192
box_15_1_wATTCCTACnnnTGTArGA	0.192
box_16_1_wATTCCTACnnnTGTArGA	0.192
box_17_1_wATTCCTACnnnTGTArGA	0.192
box_20_1_wATnCCTACnnnTGTArGA	0.157
box_22_1_wATTCCTACnnnTGTArGA	0.192
box_31_1_wATTCCTACnnnTGTArGA	0.192
box_33_1_wATTCCTACnnnTGTArGA	0.192
box_43_1_wATnCCTACnnnTGTArGA	0.157
box_46_1_wATTCCTACnnnTGTArGA	0.192
box_51_1_wATTCCTACnnnTGTArGA	0.192
box_59_1_wATTCCTACnnnTGTArGA	0.192
box_62_1_wATTCCTACnnnTGTArGA	0.192
box_68_1_wATTCCTACnnnTGTArGA	0.192
box_70_1_wATTCCTACnnnTGTArGA	0.192
box_73_1_wATnCCTACnnnTGTArGA	0.157
box_75_1_wATTCCTACnnnTGTArGA	0.192
box_78_1_wATTCCTACnnnTGTArGA	0.192
box_80_1_wATTCCTACnnnTGTArGA	0.192
box_89_1_myTmnTsCTAyAnnwGTAA	0.115
box_93_1_wATTCCTACnnnTGTArGA	0.192
box_95_1_wATTCCTACnnnTGTArGA	0.192
box_96_1_wATTCCTACnnnTGTArGA	0.192
box_99_1_wATnCCTACnnnTGTArGA	0.157

#id: box_2_CS[19,CATCrATATAATAwATGAw,1.19]_%InstanceCut=0.35_%MotifCut=0.42_nbrSeq=5_nbrInst=6_nbrMotifs=32
#CS-distribution : (1.15,1.18)[1.19](1.17,1.14)
#instance memberships: ( N(i)=4, Occ(i)=24)
emrK_217_235_+_TCATAAATTTCATCTATGA_(shift=-1,occ=17)	0.336
evgA_50_68_+_CTTGAAACTATAAATCATC_(shift=1,occ=20)	0.233
evgA_64_82_+_TCATCGGTACAATCCCTGA_(shift=-1,occ=20)	0.351
yegR_68_86_+_CTTCAATATAATATATTAA_(shift=0,occ=26)	0.523
yfdX_34_52_+_CATCGATATAATAAATGAA_(shift=0,occ=35)	0.617
yneN_96_114_+_AACTACATACTATAAGATA_(shift=1,occ=13)	0.213
#motif memberships: ( N(m)=24)
box_1_1_wCwTCkwTnnAATmnnTnA	0.165
box_4_1_wCATCrrTAnAATmymTnA	0.202
box_6_1_wCwTCnnwAnAATmmnTsA	0.165
box_11_1_wmmTmrATAywATAwATkA	0.213
box_18_1_CAnnrAwATAATnwATnAn	0.163
box_21_1_TCwTCrrTnTnATmnATkA	0.202
box_23_1_TCATCrrTAyAATmnATGA	0.202
box_25_1_CwTsrmAnTATwArwywTm	0.118
box_26_1_ACAknGnnAnwmwAAATmA	0.0941
box_28_1_AwTAwAwTAAAnkAmAnyC	0.126
box_34_1_nknnAwAAnAwAwknmnkC	0.152
box_35_1_TCATCrATATAATmnATGA	0.226
box_40_1_nATwTnATynwTGAswwnT	0.11
box_47_1_TCATCrATATAATmnATGA	0.226
box_48_1_wCATCrrTAnAATmymTnA	0.202
box_49_1_TCATmrATAnAATmwmTnA	0.202
box_55_1_TCATCrATwTnATmynTkA	0.209
box_56_1_mAnmnAsATnCTAwAwnAy	0.118
box_63_1_CTwsnwACTATAArwywTm	0.118
box_65_1_TmAwCrAyATAmTAwmwGA	0.189
box_66_1_CnmnnTrAwAnAnkAnAkC	0.152
box_67_1_wCATCrrTAnAATmymTnA	0.202
box_69_1_TnAwCrATATwnTAmmTkA	0.172
box_77_1_CnwnnwAnTATAAnwnwnm	0.109
box_79_1_TCwTCrrTnTnATmnATkA	0.202
box_82_1_TCATCrrTAyAATmnATGA	0.202
box_84_1_CnwkAnAmTATAwnwnATC	0.176
box_85_1_CnwkAnAmTATAwnwnATC	0.176
box_87_1_CAymkwkAAAnTmAAAwwn	0.152
box_88_1_CwwnAwAmTAwAwrAnATn	0.176
box_90_1_wAwwTwnAAnTnnnyAsTA	0.0995
box_100_1_wwCATmwATrwAATmwATn	0.163

#id: box_3_CS[21,rATnwmTAkTTTyAAnkTkkm,1.08]_%InstanceCut=0.58_%MotifCut=0.27_nbrSeq=4_nbrInst=5_nbrMotifs=23
#CS-distribution : (0.975,1.01,1.04)[1.08](1.06,1.05,1.04)
#instance memberships: ( N(i)=4, Occ(i)=11)
emrK_26_43_+_ATAGTTTCAAGTTGGCAC_(shift=5,occ=12)	0.466
evgA_37_55_+_CTTATAGTGCCAACTTGGA_(shift=2,occ=11)	0.475
evgA_78_95_+_CCTGATTTTATTGTTGAC_(shift=4,occ=10)	0.309
yegR_277_295_+_TAATTAGTATTTTTATTAT_(shift=-1,occ=10)	0.395
yneN_211_229_+_TAACGATTTTTAACGTTTA_(shift=2,occ=13)	0.534
#motif memberships: ( N(m)=12)
box_9_1_GATTTnTArTknCAwsyTs	0.288
box_13_1_GAnTTwTnrTknyAwsyks	0.365
box_27_1_AnTmAskrwTTnyAyCGwT	0.164
box_29_1_rAAknAyCnkTnCwnTyns	0.0987
box_30_1_TAnwknnAAnTwsnmAnTA	0.183
box_36_1_AnTmAskrwTTnyAyCGwT	0.164
box_37_1_AATnAskrwTTnTAnyGwT	0.241
box_39_1_AATnAskrwTTnTAnyGwT	0.241
box_41_1_yAGTnnyAwCnTsrAwmTA	0.183
box_44_1_TnArAmkwyTTATTATnnn	0.181
box_45_1_TAnTknCAwCnnsnnAmTA	0.205
box_54_1_AATnAskrwTTnTAnyGwT	0.241
box_55_1_TCATCrATwTnATmynTkA	0.104
box_60_1_CAnsTnsnmmCnATAArwy	0.113
box_69_1_TnAwCrATATwnTAmmTkA	0.104
box_71_1_mrAwkAyTTmTnnTknyAw	0.17
box_74_1_AATnAskrwTTnTAnyGwT	0.241
box_76_1_TAnTknCAwCnnsnnAmTA	0.205
box_86_1_AmCkATnAwTyAnsknwwC	0.115
box_91_1_TAnwknnAAnTwsnmAnTA	0.183
box_92_1_TArwkynnACwTsrnnnTA	0.183
box_94_1_sAnTwwTAryknyAAnyks	0.288
box_98_1_wnnnTAAGnnTwyTTAnnr	0.181

#END - Application ends.