Origin IGS: aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagttggaaaacagcaatttgacaaacatacgtttatatgtaaaaatgaaagtaagcataagagcttgcttttctttttttatgtcgaaagtatggtataatggtgagataaatgtaaggtggtaatt Mask Tandem Repeat Region ================================================ aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Find is-nt database================================================ Query_seq: SSA_1802:SSA_1803|SSA_1802:SSA_1803:Snf2 family protein, putative:GTP-binding protein, putative:<-<-:1786561..1786688 128 aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1802:SSA_1803|SSA_1802:SSA_1803:Snf2 family protein, putative:GTP-binding protein, putative:<-<-:1786561..1786688 128 aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1802:SSA_1803|SSA_1802:SSA_1803:Snf2 family protein, putative:GTP-binding protein, putative:<-<-:1786561..1786688 128 aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 19 End: 126 .................. M S P L Y H T F D I K K E K Q A L M L T F I F T Y K R M F V K L L F S N .. Protein_Len: 41 Strand: - Start: 6 End: 125 ..... * W R V N I E G N Y W V K S M F F S F C A R I S V K M K V Y L R I N T L N S N E M ... aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 82 End: 111 .................................................................................TTTGACAAACATACGTTTATATGTAAAAAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -2.4 Tail_Score: -5.71712 Start: 55 End: 81 Full_Region: tttatatgtaaaaat gaaagtaagc ataaga gcttgcttttc tttttttatgtcgaa ......................................................gaaagtaagcataagagcttgcttttc............................................... TransTerm Strand: - Conf: 79 HP_score: -3.4 Tail_Score: -5.61277 Start: 60 End: 77 Full_Region: tatgtaaaaatgaaa gtaagc ataaga gcttgc ttttctttttttatg ...........................................................gtaagcataagagcttgc................................................... Find igs database================================================ Query_seq: SSA_1802:SSA_1803|SSA_1802:SSA_1803:Snf2 family protein, putative:GTP-binding protein, putative:<-<-:1786561..1786688 128 aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_009009_SSA_1802_SSA_1803|Snf2 family protein, putative:GTP-binding protein, putative|NEGATIVE:NEGATIVE|[1786561,1786688]|128 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 aattaccaccttacatttatctcaccattataccatactttcgacatnnnnnnngaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc aattaccaccttacatttatctcaccattataccatactttcgacataaaaaaagaaaagcaagctcttatgcttactttcatttttacatataaacgtatgtttgtcaaattgctgttttccaactc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUACCACCUUACAUUUAUCUCACCAUUAUACCAUACUUUCGACAUAAAAAAAGAAAAGCAAGCUCUUAUGCUUACUUUCAUUUUUACAUAUAAACGUAUGUUUGUCAAAUUGCUGUUUUCCAACUC ..........................................((((...(((((..((((.((((......)))).))))..)))))((((((....)))))).)))).................... (-14.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUUGGAAAACAGCAAUUUGACAAACAUACGUUUAUAUGUAAAAAUGAAAGUAAGCAUAAGAGCUUGCUUUUCUUUUUUUAUGUCGAAAGUAUGGUAUAAUGGUGAGAUAAAUGUAAGGUGGUAAUU ..((((.....)))).((((.((...(((((.((((((((.(((((.((((((((((......)))))))))).))))).))))).))).)))))........)).)))).................. (-27.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 781 70 21 161 112 NC_009009:SSA_1802|5end_Snf2_family_protein,_putative_1786470..1786700_NEGATIVE 252 44 1 199 147 NC_009009:SSA_1495|5end_S-adenosylmethionine_synthetase,_putative_1502209..1502439_NEGATIVE 245 46 7 136 95 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 232 100 59 49 5 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 223 80 33 138 88 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 219 88 47 230 187 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 218 47 5 114 57 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 211 74 33 133 88 NC_009009:SSA_2190|5end_33_kDa_chaperonin,_putative_2191166..2191396_POSITIVE 211 78 34 63 13 NC_009009:SSA_0858|5end_DTDP-L-rhamnose_synthase,_putative_845512..845742_POSITIVE 210 75 31 177 125 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 208 50 3 120 70 NC_009009:SSA_1197|5end_DNA_alkylation_repair_enzyme,_putative_1222699..1222929_NEGATIVE 207 108 65 154 113 NC_009009:SSA_2266|5end_4-alpha-glucanotransferase,_putative_2265741..2265971_NEGATIVE 205 74 38 52 1 NC_009009:SSA_0938|5end_hypothetical_protein_946587..946817_POSITIVE 205 84 60 23 1 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 204 39 9 143 109 NC_009009:SSA_0686|5end_Fe2+/Zn2+_uptake_regulation_protein,_putative_669556..669786_POSITIVE 201 67 24 155 110 NC_009009:SSA_1523|5end_Glutathione_peroxidase,_putative_1532067..1532297_POSITIVE 201 119 73 155 107 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 201 99 59 196 149 NC_009009:SSA_0740|5end_C4-dicarboxylate_anaerobic_carrier,_possible_arginine_transporter,_putative_722240..722470_POSITIVE 200 80 31 191 133 NC_009009:SSA_1165|5end_Transcriptional_regulator,_GntR_family,_putative_1191087..1191317_POSITIVE 198 86 43 182 128 NC_009009:SSA_2143|5end_Conserved_uncharacterized_protein_2144225..2144455_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 45 9 53 9 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 223 80 33 101 51 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 222 79 32 86 38 NC_009009:SSA_1030|3end_Transcriptional_regulator,_TetR_family,_putative_1047749..1047899_POSITIVE 221 110 62 101 41 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 219 88 47 93 50 NC_009009:SSA_1998|3end_Trigger_factor,_putative_1995048..1995198_NEGATIVE 218 47 5 101 44 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 210 75 31 72 20 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 209 81 41 53 13 NC_009009:SSA_0281|3end_hypothetical_protein_273963..274113_POSITIVE 208 50 3 116 66 NC_009009:SSA_1198|3end_ATPase_(PilT_family),_putative_1222703..1222853_NEGATIVE 202 65 21 71 18 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 202 75 31 59 8 NC_009009:SSA_0207|3end_hypothetical_protein_204944..205094_POSITIVE 201 119 73 99 51 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 201 74 44 49 6 NC_009009:SSA_0937|3end_Arsenate_reductase,_glutaredoxin_family,_putative_946664..946814_POSITIVE 198 86 43 92 38 NC_009009:SSA_2144|3end_Glutamyl-tRNA_synthetase,_putative_2144315..2144465_NEGATIVE 198 80 35 92 42 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 194 88 45 80 31 NC_009009:SSA_0973|3end_hypothetical_protein_980687..980837_POSITIVE 190 78 37 95 47 NC_009009:SSA_0829|3end_Platelet-binding_glycoprotein_812165..812315_POSITIVE 188 76 31 57 12 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 187 86 46 78 36 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 185 81 53 101 71 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE