Origin IGS: aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccactttctaagtttttattattatagttttttaaacacaatagttaagtaacacttaacataatttattttaccattcattaccaaaattgtcaacttt Mask Tandem Repeat Region ================================================ aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga Find is-nt database================================================ Query_seq: FN1083:FN1084|FN1083:FN1084:putative surface protein:hypothetical protein:->->:1728700..1728800 101 aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1083:FN1084|FN1083:FN1084:putative surface protein:hypothetical protein:->->:1728700..1728800 101 aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1083:FN1084|FN1083:FN1084:putative surface protein:hypothetical protein:->->:1728700..1728800 101 aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga Predict ORF larger than 30AA ================================================ aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga 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: 94 Start: 4 End: 33 ...GTTGACAATTTTGGTAATGAATGGTAAAAT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1083:FN1084|FN1083:FN1084:putative surface protein:hypothetical protein:->->:1728700..1728800 101 aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_003454_FN1083_FN1084|putative surface protein:hypothetical protein|POSITIVE:POSITIVE|[1728700,1728800]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga aaagttgacaattttggtaatgaatggtaaaataaattatgttaagtgttacttaactattgtgtttaaaaaactataataataaaaacttagaaagtgga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUGACAAUUUUGGUAAUGAAUGGUAAAAUAAAUUAUGUUAAGUGUUACUUAACUAUUGUGUUUAAAAAACUAUAAUAAUAAAAACUUAGAAAGUGGA .(((((..((....)).......(((((....(((((...((((((.....))))))......)))))....))))).........))))).......... ( -9.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCACUUUCUAAGUUUUUAUUAUUAUAGUUUUUUAAACACAAUAGUUAAGUAACACUUAACAUAAUUUAUUUUACCAUUCAUUACCAAAAUUGUCAACUUU ..........(((((............(((.....)))......((((((.....))))))..................................))))). ( -6.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 59 30 150 121 NC_003454:FN0512|5end_Flavoprotein_1162597..1162827_NEGATIVE 179 67 23 155 114 NC_003454:FN1841|5end_Dihydroxyacetone_kinase_330879..331109_POSITIVE 160 68 38 188 147 NC_003454:FN2121|5end_Hypothetical_exported_24-amino_acid_repeat_protein_629728..629958_NEGATIVE 154 65 39 81 54 NC_003454:FN1452|5end_Cell_division_protein_ftsA_2134076..2134306_NEGATIVE 154 75 40 147 107 NC_003454:FN1728|5end_Pyrrolidone-carboxylate_peptidase_228366..228596_NEGATIVE 153 65 25 204 157 NC_003454:FN1479|5end_hypothetical_protein_2161269..2161499_NEGATIVE 150 49 13 77 39 NC_003454:FN0355|5end_S-adenosylmethionine_synthetase_987227..987457_NEGATIVE 148 52 14 85 52 NC_003454:FN0554|5end_D-serine_permease_1207443..1207673_NEGATIVE 146 100 54 79 40 NC_003454:FN1549|5end_Stomatin_like_protein_63889..64119_POSITIVE 141 29 3 224 197 NC_003454:FN0110|5end_seryl-tRNA_synthetase_746067..746297_NEGATIVE 141 42 2 84 49 NC_003454:FN0052|5end_Arsenate_reductase_688849..689079_POSITIVE 139 69 28 200 158 NC_003454:FN0249|5end_hypothetical_protein_872823..873053_POSITIVE 138 45 1 207 157 NC_003454:FN2003|5end_bioY_protein_503745..503975_POSITIVE 135 66 35 32 4 NC_003454:FN0022|5end_hypothetical_protein_660790..661020_POSITIVE 134 79 47 77 43 NC_003454:FN1490|5end_4-hydroxybenzoate_octaprenyltransferase_2172283..2172513_NEGATIVE 134 50 5 73 28 NC_003454:FN0195|5end_Dipeptide_transport_ATP-binding_protein_dppD_820558..820788_POSITIVE 133 45 17 33 3 NC_003454:FN0570|5end_hypothetical_protein_1220912..1221142_POSITIVE 130 63 25 84 49 NC_003454:FN0979|5end_hypothetical_protein_1632096..1632326_POSITIVE 130 90 45 166 111 NC_003454:FN2107|5end_galactokinase_618150..618380_POSITIVE 128 99 51 78 30 NC_003454:FN0814|5end_Propionate_CoA-transferase_1472717..1472947_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 179 67 23 109 68 NC_003454:FN1840|3end_Dihydroxyacetone_kinase_330913..331063_POSITIVE 161 24 3 77 57 NC_003454:FN0598|3end_Phospholipid-lipopolysaccharide_ABC_transporter_1253712..1253862_POSITIVE 160 68 38 118 77 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 154 65 39 84 57 NC_003454:FN1453|3end_hypothetical_protein_2134073..2134223_NEGATIVE 152 60 12 65 7 NC_003454:FN1525|3end_Dipeptide_transport_ATP-binding_protein_dppF_31631..31781_POSITIVE 146 100 54 60 21 NC_003454:FN1548|3end_hypothetical_protein_63950..64100_POSITIVE 141 29 3 136 109 NC_003454:FN0111|3end_hypothetical_protein_746155..746305_NEGATIVE 137 36 11 64 39 NC_003454:FN1044|3end_hypothetical_protein_1694453..1694603_NEGATIVE 134 79 47 58 24 NC_003454:FN1491|3end_PTS_system,_IIA_component_2172302..2172452_NEGATIVE 130 51 17 149 117 NC_003454:FN0747|3end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1405739..1405889_NEGATIVE 129 98 58 68 22 NC_003454:FN1313|3end_Oligopeptide-binding_protein_oppA_1968557..1968707_POSITIVE 129 85 50 49 8 NC_003454:FN1668|3end_Cholinephosphate_cytidylyltransferase_164691..164841_NEGATIVE 127 48 3 42 1 NC_003454:FN1382|3end_ATPase_2034437..2034587_POSITIVE 127 48 1 85 37 NC_003454:FN1064|3end_hypothetical_protein_1711369..1711519_POSITIVE 123 68 40 76 47 NC_003454:FN0945|3end_Ser/Thr_and_Tyr_protein_phosphatase_(dual_specificity)_1599025..1599175_NEGATIVE 123 50 1 142 93 NC_003454:FN1740|3end_ATP_synthase_subunit_K_237918..238068_NEGATIVE 120 100 56 53 5 NC_003454:FN1140|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_1790473..1790623_POSITIVE 120 72 33 104 60 NC_003454:FN1682|3end_Heteropolysaccharide_repeat_unit_export_protein_177063..177213_NEGATIVE 119 78 46 111 88 NC_003454:FN1321|3end_Acetoacetate_metabolism_regulatory_protein_atoC_1975981..1976131_NEGATIVE 118 50 2 136 88 NC_003454:FN0538|3end_Protein_translocase_subunit_secG_1192151..1192301_POSITIVE