Origin IGS: aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaataaaagaattattataagaaaaattataatgattctttttttattgcaatattttttattatatgatagtatattaaaaaattagtgttttattttaaaataaaaaatataaaaaaaaaacacttttcagactttagcttttataaataattttttagagaaaatatatgattaaaaattttaggaggtggactt Mask Tandem Repeat Region ================================================ aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt Find is-nt database================================================ Query_seq: FN0881:FN0882|FN0881:FN0882:ABC transporter integral membrane protein:Hemin transport system ATP-binding protein hmuV:<-<-:1542838..1543036 199 aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0881:FN0882|FN0881:FN0882:ABC transporter integral membrane protein:Hemin transport system ATP-binding protein hmuV:<-<-:1542838..1543036 199 aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0881:FN0882|FN0881:FN0882:ABC transporter integral membrane protein:Hemin transport system ATP-binding protein hmuV:<-<-:1542838..1543036 199 aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt Predict ORF larger than 30AA ================================================ aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt 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: 83 Start: 124 End: 153 ...........................................................................................................................ATTGCAATATTTTTTATTATATGATAGTAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0881:FN0882|FN0881:FN0882:ABC transporter integral membrane protein:Hemin transport system ATP-binding protein hmuV:<-<-:1542838..1543036 199 aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtgttttttttttatattttttattttaaaataaaacactaattttttaatatactatcatataataaaaaatattgcaataaaaaaagaatcattataatttttcttataataattcttttatttt Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: NC_003454_FN0881_FN0882|ABC transporter integral membrane protein:Hemin transport system ATP-binding protein hmuV|NEGATIVE:NEGATIVE|[1542838,1543036]|199 HSP 1 e-value: 4.0E-35 bit: 149.0 Len: 75 Query Start:1 Query End:75 Subject Strand: POSITIVE Subject Start: 1 Subject End: 75 aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtg............................................................................................................................ aagtccacctcctaaaatttttaatcatatattttctctaaaaaattatttataaaagctaaagtctgaaaagtg............................................................................................................................ HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 39 Query Start:161 Query End:199 Subject Strand: POSITIVE Subject Start: 161 Subject End: 199 ................................................................................................................................................................gaatcattataatttttcttataataattcttttatttt ................................................................................................................................................................gaatcattataatttttcttataataattcttttatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUCCACCUCCUAAAAUUUUUAAUCAUAUAUUUUCUCUAAAAAAUUAUUUAUAAAAGCUAAAGUCUGAAAAGUGUUUUUUUUUUAUAUUUUUUAUUUUAAAAUAAAACACUAAUUUUUUAAUAUACUAUCAUAUAAUAAAAAAUAUUGCAAUAAAAAAAGAAUCAUUAUAAUUUUUCUUAUAAUAAUUCUUUUAUUUU .........................................................((............((((((((.((((.(((.....)))...)))).)))))))).((((((((.((((......)))).))))))))...))......((((((((.(((((((......))))))).))))))))..... (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAAAAGAAUUAUUAUAAGAAAAAUUAUAAUGAUUCUUUUUUUAUUGCAAUAUUUUUUAUUAUAUGAUAGUAUAUUAAAAAAUUAGUGUUUUAUUUUAAAAUAAAAAAUAUAAAAAAAAAACACUUUUCAGACUUUAGCUUUUAUAAAUAAUUUUUUAGAGAAAAUAUAUGAUUAAAAAUUUUAGGAGGUGGACUU ..((.((((((((((((((((......)))))))))))))))).))......((((((((((((.((.(((((.(((((((....))))))).))))).)).))))))))))))..........((((((..(((.(((.....(((((....((((((....)))))).)))))....))).)))..))))))..... (-35.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 646 50 1 141 92 NC_003454:FN0881|5end_ABC_transporter_integral_membrane_protein_1542747..1542977_NEGATIVE 238 50 4 109 59 NC_003454:FN1685|5end_dTDP-4-dehydrorhamnose_reductase_181013..181243_NEGATIVE 220 41 2 139 92 NC_003454:FN0417|5end_Type_III_restriction-modification_system_restriction_subunit_1055887..1056117_POSITIVE 217 100 59 86 34 NC_003454:FN1476|5end_N-acetylmannosamine-6-phosphate_2-epimerase_2158672..2158902_POSITIVE 212 88 45 43 6 NC_003454:FN1240|5end_Lipopolysaccharide_core_biosynthesis_protein_rfaY_1897779..1898009_NEGATIVE 207 94 58 155 120 NC_003454:FN0850|5end_Hypothetical_cytosolic_protein_1508913..1509143_POSITIVE 203 41 1 102 56 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 199 40 5 133 98 NC_003454:FN1585|5end_hypothetical_protein_97394..97624_NEGATIVE 198 179 132 165 117 NC_003454:FN1668|5end_Cholinephosphate_cytidylyltransferase_165563..165793_NEGATIVE 191 28 5 116 88 NC_003454:FN1379|5end_Citrate_lyase_beta_chain_2026355..2026585_POSITIVE 190 91 57 147 116 NC_003454:FN1422|5end_NA+/H+_antiporter_NHAC_2088426..2088656_NEGATIVE 186 27 3 117 86 NC_003454:FN1989|5end_Sodium-dependent_tyrosine_transporter_492431..492661_POSITIVE 185 98 61 162 125 NC_003454:FN1394|5end_Signal_recognition_particle_associated_protein_2051166..2051396_NEGATIVE 183 170 121 222 173 NC_003454:FN1926|5end_Nitrogen_regulatory_IIA_protein_425287..425517_NEGATIVE 182 94 57 86 44 NC_003454:FN1865|5end_hypothetical_protein_357105..357335_NEGATIVE 181 35 8 209 186 NC_003454:FN1270|5end_Hypothetical_cytosolic_protein_1926592..1926822_NEGATIVE 180 97 60 105 61 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 179 125 81 145 100 NC_003454:FN2126|5end_DNA_gyrase_subunit_B_638225..638455_NEGATIVE 178 43 1 128 73 NC_003454:FN0542|5end_Beta_1,4_glucosyltransferase_1195223..1195453_POSITIVE 177 55 16 48 8 NC_003454:FN1731|5end_Anthranilate_synthase_component_II_231037..231267_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 50 4 95 45 NC_003454:FN1686|3end_Spore_coat_polysaccharide_biosynthesis_protein_spsF_181027..181177_NEGATIVE 220 41 2 129 82 NC_003454:FN0416|3end_Type_III_restriction-modification_system_methylation_subunit_1055957..1056107_POSITIVE 217 100 59 71 19 NC_003454:FN1475|3end_N-acetylneuraminate_lyase_2158737..2158887_POSITIVE 212 88 45 41 4 NC_003454:FN1241|3end_Hypohetical_Teichoic_Acid_Biosynthesis_Protein_1897781..1897931_NEGATIVE 199 40 5 112 77 NC_003454:FN1586|3end_O-succinylbenzoate-CoA_synthase_97415..97565_NEGATIVE 193 44 8 39 2 NC_003454:FN1002|3end_Adenosylmethionine-8-amino-7-oxononanoate_aminotransferase_1658176..1658326_POSITIVE 191 28 5 107 79 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 185 98 61 97 60 NC_003454:FN1395|3end_hypothetical_protein_2051231..2051381_NEGATIVE 183 170 121 94 45 NC_003454:FN1927|3end_DEGV_protein_425415..425565_NEGATIVE 181 35 8 56 33 NC_003454:FN1271|3end_Protease_IV_1926745..1926895_NEGATIVE 179 91 58 151 119 NC_003454:FN0849|3end_8-amino-7-oxononanoate_synthase_1508992..1509142_POSITIVE 179 125 81 144 99 NC_003454:FN2127|3end_hypothetical_protein_638226..638376_NEGATIVE 178 43 1 122 67 NC_003454:FN0541|3end_Hypothetical_cytosolic_protein_1195297..1195447_POSITIVE 175 38 6 77 37 NC_003454:FN1914|3end_Anti-sigma_F_factor_antagonist_411643..411793_NEGATIVE 174 39 2 109 82 NC_003454:FN1491|3end_PTS_system,_IIA_component_2172302..2172452_NEGATIVE 174 17 2 41 25 NC_003454:FN1239|3end_hypothetical_protein_1896403..1896553_NEGATIVE 174 65 25 120 78 NC_003454:FN0629|3end_PTS_system,_IID_component_1288267..1288417_NEGATIVE 172 39 2 88 46 NC_003454:FN0754|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1413183..1413333_NEGATIVE 169 41 5 45 14 NC_003454:FN1404|3end_Imidazolonepropionase_2064366..2064516_POSITIVE 167 42 8 118 82 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE