Origin IGS: aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcctattgacagaaaaaataaataatgttatcctttgcaaacttagctatggctaacatctttcttttataagaaatatggttaaaacttttgttttggaggttttt Mask Tandem Repeat Region ================================================ aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa Find is-nt database================================================ Query_seq: TDE1180:TDE1181|TDE1180:TDE1181:iron compound ABC transporter, periplasmic iron compound-binding protein:methyltransferase domain protein:<-->:1209924..1210031 108 aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1180:TDE1181|TDE1180:TDE1181:iron compound ABC transporter, periplasmic iron compound-binding protein:methyltransferase domain protein:<-->:1209924..1210031 108 aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1180:TDE1181|TDE1180:TDE1181:iron compound ABC transporter, periplasmic iron compound-binding protein:methyltransferase domain protein:<-->:1209924..1210031 108 aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa Predict ORF larger than 30AA ================================================ aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa 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: 87 Start: 74 End: 103 .........................................................................ATTGACAGAAAAAATAAATAATGTTATCCT..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1180:TDE1181|TDE1180:TDE1181:iron compound ABC transporter, periplasmic iron compound-binding protein:methyltransferase domain protein:<-->:1209924..1210031 108 aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_002967_TDE1180_TDE1181|iron compound ABC transporter, periplasmic iron compound-binding protein:methyltransferase domain protein|NEGATIVE:POSITIVE|[1209924,1210031]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa aaaaacctccaaaacaaaagttttaaccatatttcttataaaagaaagatgttagccatagctaagtttgcaaaggataacattatttattttttctgtcaataggaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCUCCAAAACAAAAGUUUUAACCAUAUUUCUUAUAAAAGAAAGAUGUUAGCCAUAGCUAAGUUUGCAAAGGAUAACAUUAUUUAUUUUUUCUGUCAAUAGGAA ..........(((((....)))))........(((((((...((((((((((((.((...((.......))...)).)))))))........)))))....))))))) (-15.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUAUUGACAGAAAAAAUAAAUAAUGUUAUCCUUUGCAAACUUAGCUAUGGCUAACAUCUUUCUUUUAUAAGAAAUAUGGUUAAAACUUUUGUUUUGGAGGUUUUU ((((....(((((((..........((((((.((...((.......))...)).)))))).((((((....))))))............)))))))..))))...... (-19.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 753 100 51 191 142 NC_002967:TDE1180|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein_1209833..1210063_NEGATIVE 223 76 44 215 187 NC_002967:TDE2528|5end_hypothetical_protein_2556912..2557142_NEGATIVE 216 97 57 171 136 NC_002967:TDE0146|5end_amidohydrolase_family_protein_168637..168867_NEGATIVE 208 77 46 146 113 NC_002967:TDE2315|5end_conserved_hypothetical_protein_TIGR00044_2352272..2352502_POSITIVE 200 72 47 47 21 NC_002967:TDE2668|5end_serine_hydroxymethyltransferase_2706066..2706296_NEGATIVE 199 90 55 97 62 NC_002967:TDE2249|5end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_2288556..2288786_NEGATIVE 193 66 21 133 86 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 193 66 21 133 86 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 192 74 35 72 38 NC_002967:TDE0622|5end_radical_SAM_domain_protein_655718..655948_NEGATIVE 191 77 43 121 92 NC_002967:TDE2551|5end_hypothetical_protein_2577282..2577512_NEGATIVE 188 60 17 92 44 NC_002967:TDE2325|5end_hypothetical_protein_2359952..2360182_POSITIVE 186 66 26 169 126 NC_002967:TDE1069|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1097699..1097929_NEGATIVE 185 28 5 102 79 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 183 94 57 177 134 NC_002967:TDE0947|5end_translation_elongation_factor_G,_putative_970792..971022_NEGATIVE 183 61 25 131 85 NC_002967:TDE0377|5end_hypothetical_protein_431977..432207_NEGATIVE 181 79 45 100 67 NC_002967:TDE1740|5end_hypothetical_protein_1792785..1793015_NEGATIVE 180 100 51 184 133 NC_002967:TDE1319|5end_hypothetical_protein_1356598..1356828_POSITIVE 180 100 51 174 131 NC_002967:TDE0474|5end_hypothetical_protein_530740..530970_POSITIVE 180 87 48 206 167 NC_002967:TDE0137|5end_carbohydrate_kinase,_FGGY_family_156640..156870_POSITIVE 178 33 2 121 94 NC_002967:TDE1852|5end_ABC_transporter,_ATP-binding_protein_1881866..1882096_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 223 76 44 149 121 NC_002967:TDE2529|3end_hypothetical_protein_2556978..2557128_NEGATIVE 191 77 43 33 4 NC_002967:TDE2552|3end_ABC_transporter,_ATP-binding/permease_protein_2577370..2577520_NEGATIVE 187 69 26 70 33 NC_002967:TDE2541|3end_hypothetical_protein_2569189..2569339_POSITIVE 187 77 44 43 10 NC_002967:TDE0967|3end_hypothetical_protein_992529..992679_POSITIVE 186 79 35 58 9 NC_002967:TDE0228|3end_hypothetical_protein_259611..259761_NEGATIVE 177 70 28 118 72 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 176 84 43 50 12 NC_002967:TDE1132|3end_chorismate_synthase_1164580..1164730_POSITIVE 176 57 19 60 15 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 175 97 51 79 43 NC_002967:TDE2064|3end_ferrous_iron_transport_protein_A_2091268..2091418_NEGATIVE 174 92 55 115 76 NC_002967:TDE1682|3end_V-type_ATP_synthase_subunit_B_1733548..1733698_NEGATIVE 173 81 43 117 84 NC_002967:TDE0093|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_112308..112458_POSITIVE 171 98 57 110 61 NC_002967:TDE1920|3end_lipoprotein,_putative_1939918..1940068_NEGATIVE 171 90 55 150 110 NC_002967:TDE1752|3end_ISTde2,_transposase_1804322..1804472_NEGATIVE 171 76 45 85 46 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 171 90 55 150 110 NC_002967:TDE1022|3end_ISTde2,_transposase_1053912..1054062_NEGATIVE 171 90 55 150 110 NC_002967:TDE0140|3end_ISTde2,_transposase_163887..164037_POSITIVE 169 88 41 101 46 NC_002967:TDE2570|3end_ribonuclease_HI_2597937..2598087_POSITIVE 168 78 52 91 61 NC_002967:TDE2682|3end_hypothetical_protein_2721388..2721538_NEGATIVE 168 88 43 68 23 NC_002967:TDE2578|3end_hypothetical_protein_2602900..2603050_NEGATIVE 168 100 51 79 32 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE