Origin IGS: ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaattaaatatcagctgatagaaagaaaatggagtttagcgactccattttttattatataaaagtaattgtttttacattaaagaagtgttaaaatatctccattaaaatttaaagtattaagggggaaaa Mask Tandem Repeat Region ================================================ ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta Find is-nt database================================================ Query_seq: FN0037:FN0038|FN0037:FN0038:hypothetical protein:hypothetical protein:<-<-:678152..678286 135 ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0037:FN0038|FN0037:FN0038:hypothetical protein:hypothetical protein:<-<-:678152..678286 135 ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0037:FN0038|FN0037:FN0038:hypothetical protein:hypothetical protein:<-<-:678152..678286 135 ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta Predict ORF larger than 30AA ================================================ ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta 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: 82 Start: 36 End: 65 ...................................ATTGTTTTTACATTAAAGAAGTGTTAAAAT...................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 65 HP_score: -5.7 Tail_Score: -4.053 Start: 81 End: 108 Full_Region: TACTTTTATATAATA AAAAATGGAGT CGCTAA ACTCCATTTTC TTTCTATCAGCTGAT ................................................................................AAAAATGGAGTCGCTAAACTCCATTTTC........................... TransTerm Strand: + Conf: 77 HP_score: -5.6 Tail_Score: -5.05113 Start: 86 End: 103 Full_Region: TTATATAATAAAAAA TGGAGT CGCTAA ACTCCA TTTTCTTTCTATCAG .....................................................................................TGGAGTCGCTAAACTCCA................................ Find igs database================================================ Query_seq: FN0037:FN0038|FN0037:FN0038:hypothetical protein:hypothetical protein:<-<-:678152..678286 135 ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: NC_003454_FN0037_FN0038|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[678152,678286]|135 HSP 1 e-value: 4.0E-71 bit: 268.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta ttttcccccttaatactttaaattttaatggagatattttaacacttctttaatgtaaaaacaattacttttatataataaaaaatggagtcgctaaactccattttctttctatcagctgatatttaattttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCCCCUUAAUACUUUAAAUUUUAAUGGAGAUAUUUUAACACUUCUUUAAUGUAAAAACAAUUACUUUUAUAUAAUAAAAAAUGGAGUCGCUAAACUCCAUUUUCUUUCUAUCAGCUGAUAUUUAAUUUUUA .................((((((.((((((((((..................((((((((........)))))))).....((((((((((......)))))))))).)))))))....))).))))))...... (-19.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUUAAAUAUCAGCUGAUAGAAAGAAAAUGGAGUUUAGCGACUCCAUUUUUUAUUAUAUAAAAGUAAUUGUUUUUACAUUAAAGAAGUGUUAAAAUAUCUCCAUUAAAAUUUAAAGUAUUAAGGGGGAAAA ................(((.(((...(((((((((((((....)))))))))))))....)))...)))...((((((.(((((.....))))).))))))(((((.((((.((.....)).)))).)))))... (-26.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 769 130 81 221 172 NC_003454:FN0037|5end_hypothetical_protein_678061..678291_NEGATIVE 344 120 77 216 168 NC_003454:FN0065|5end_Transcription_accessory_protein_(S1_RNA_binding_domain)_699933..700163_POSITIVE 278 127 82 84 36 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 246 122 88 188 154 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 238 129 86 78 36 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 216 128 81 113 68 NC_003454:FN0710|5end_hypothetical_protein_1368875..1369105_POSITIVE 212 122 85 143 106 NC_003454:FN1737|5end_V-type_ATP_synthase_subunit_F_236356..236586_NEGATIVE 205 41 4 125 96 NC_003454:FN1250|5end_Guanine-hypoxanthine_permease_1907832..1908062_NEGATIVE 201 104 82 173 146 NC_003454:FN1164|5end_Glucokinase_1821754..1821984_POSITIVE 199 125 86 40 4 NC_003454:FN1594|5end_Nitrogen_fixation_protein_RNFG_104893..105123_NEGATIVE 198 50 5 142 101 NC_003454:FN0279|5end_Lipoprotein_906479..906709_NEGATIVE 196 120 94 122 93 NC_003454:FN0084|5end_Acetaldehyde_dehydrogenase_[acetylating]_721572..721802_POSITIVE 195 47 1 135 92 NC_003454:FN0092|5end_NADPH-dependent_butanol_dehydrogenase_727908..728138_POSITIVE 194 124 100 39 12 NC_003454:FN0594|5end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1248785..1249015_POSITIVE 194 92 54 113 77 NC_003454:FN0569|5end_Hypothetical_membrane-spanning_protein_1220732..1220962_NEGATIVE 193 128 82 84 45 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 186 129 86 203 153 NC_003454:FN1744|5end_Transporter_242920..243150_NEGATIVE 184 124 86 202 148 NC_003454:FN1627|5end_SSU_ribosomal_protein_S5P_133556..133786_NEGATIVE 183 120 88 111 79 NC_003454:FN2021|5end_ABC1_family_protein_525079..525309_NEGATIVE 182 47 2 143 97 NC_003454:FN2071|5end_hypothetical_protein_582375..582605_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 120 77 125 77 NC_003454:FN0064|3end_Hypothetical_cytosolic_protein_699922..700072_POSITIVE 274 120 83 96 47 NC_003454:FN0564|3end_hypothetical_protein_1216466..1216616_NEGATIVE 243 107 74 82 50 NC_003454:FN1900|3end_pfoS/R_389316..389466_POSITIVE 227 51 17 146 110 NC_003454:FN0337|3end_hypothetical_protein_971136..971286_NEGATIVE 216 128 81 46 1 NC_003454:FN0709|3end_Virulence_factor_mviN_1368888..1369038_POSITIVE 213 107 81 47 21 NC_003454:FN1901|3end_Transcription_regulator,_CRP_family_389364..389514_NEGATIVE 202 130 91 126 86 NC_003454:FN1713|3end_tRNA_(Uracil-5-)_-methyltransferase_208968..209118_POSITIVE 201 22 2 95 73 NC_003454:FN1342|3end_Holo-[acyl-carrier_protein]_synthase_1996091..1996241_NEGATIVE 201 104 82 149 122 NC_003454:FN1163|3end_Thioredoxin_reductase_1821810..1821960_POSITIVE 199 125 86 50 14 NC_003454:FN1595|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_B_104883..105033_NEGATIVE 195 47 1 115 72 NC_003454:FN0091|3end_Phosphoserine_phosphatase_727968..728118_POSITIVE 189 49 5 151 111 NC_003454:FN0280|3end_hypothetical_protein_906469..906619_NEGATIVE 183 120 88 118 86 NC_003454:FN2022|3end_transcription_elongation_factor_NusA_525072..525222_NEGATIVE 181 130 100 72 40 NC_003454:FN0426|3end_Orotidine_5'-phosphate_decarboxylase_1069513..1069663_POSITIVE 181 50 1 107 58 NC_003454:FN2062|3end_hypothetical_protein_574107..574257_NEGATIVE 181 50 1 107 58 NC_003454:FN2051|3end_hypothetical_protein_560031..560181_NEGATIVE 181 111 75 86 43 NC_003454:FN1516|3end_hypothetical_protein_20664..20814_NEGATIVE 180 69 28 59 10 NC_003454:FN0516|3end_Acriflavin_resistance_protein_E_1167003..1167153_NEGATIVE 177 120 98 151 124 NC_003454:FN1872|3end_hypothetical_protein_362789..362939_NEGATIVE 176 121 84 57 23 NC_003454:FN1103|3end_Excinuclease_ABC_subunit_A_1749521..1749671_POSITIVE