Origin IGS: gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaaacaccccaaaagttagattttttctgtctaacttttggggtgcagtacaatcttgggtatcttttttcttatatgcttgttttataactcgggtgaatttc Mask Tandem Repeat Region ================================================ gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Find is-nt database================================================ Query_seq: SMT_569:SMT_570|SMT_569:SMT_570:Mn2+ and Fe2+ transporter of the NRAMP family:hypothetical protein:->->:488614..488720 107 gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_569:SMT_570|SMT_569:SMT_570:Mn2+ and Fe2+ transporter of the NRAMP family:hypothetical protein:->->:488614..488720 107 gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_569:SMT_570|SMT_569:SMT_570:Mn2+ and Fe2+ transporter of the NRAMP family:hypothetical protein:->->:488614..488720 107 gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 17 End: 106 ................ M K Q A Y K K K D T Q D C T A P Q K L D R K N L T F G V F Y . gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_569:SMT_570|SMT_569:SMT_570:Mn2+ and Fe2+ transporter of the NRAMP family:hypothetical protein:->->:488614..488720 107 gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: smit_SMT_569_SMT_570|Mn2+ and Fe2+ transporter of the NRAMP family:hypothetical protein|POSITIVE:POSITIVE|[488614,488720]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt gaaattcacccgagttataaaacaagcatataagaaaaaagatacccaagattgtactgcaccccaaaagttagacagaaaaaatctaacttttggggtgttttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUUCACCCGAGUUAUAAAACAAGCAUAUAAGAAAAAAGAUACCCAAGAUUGUACUGCACCCCAAAAGUUAGACAGAAAAAAUCUAACUUUUGGGGUGUUUUAUU ..(((((....))))).....................................(((..(((((((((((((((((.........)))))))))))))))))..))). (-28.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAACACCCCAAAAGUUAGAUUUUUUCUGUCUAACUUUUGGGGUGCAGUACAAUCUUGGGUAUCUUUUUUCUUAUAUGCUUGUUUUAUAACUCGGGUGAAUUUC .......(((((((((((((((((.......))))))))))))))))).........(((((((............................)))))))........ (-30.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 100 51 231 182 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 388 100 61 140 101 smit:SMT_734|5end_hypothetical_protein_639967..640197_POSITIVE 379 100 56 139 98 smit:SMT_542|5end_hypothetical_protein_457940..458170_POSITIVE 299 96 57 221 185 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 262 78 42 88 48 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 244 97 51 194 150 smit:SMT_675|5end_DNA_repair_protein_582977..583207_NEGATIVE 225 66 41 37 11 smit:SMT_456|5end_pyruvate_oxidase_394236..394466_POSITIVE 216 100 52 189 143 smit:SMT_356|5end_hypothetical_protein_292394..292624_POSITIVE 216 50 1 56 7 smit:SMT_144|5end_hypothetical_protein_predicted_by_Glimmer/Critica_95553..95783_POSITIVE 199 35 7 203 177 smit:SMT_679|5end_LicC_protein_589072..589302_NEGATIVE 199 98 51 175 131 smit:SMT_413|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_356677..356907_POSITIVE 198 49 1 71 8 smit:SMT_1019|5end_K03295_cation_efflux_system_protein,_CDF_family_955672..955902_NEGATIVE 196 77 31 66 18 smit:SMT_1498|5end_transcriptional_regulator,_LytR_family_1481958..1482188_POSITIVE 193 57 13 121 79 smit:SMT_942|5end_hypothetical_protein_894067..894297_NEGATIVE 191 87 47 196 161 smit:SMT_1387|5end_hypothetical_protein_1364663..1364893_POSITIVE 190 67 41 187 156 smit:SMT_628|5end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_532831..533061_POSITIVE 188 77 46 164 127 smit:SMT_2067|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1973432..1973662_POSITIVE 187 73 42 57 23 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 186 65 23 152 113 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 186 65 23 152 113 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 510 77 35 84 39 smit:SMT_571|3end_putative_transposase,_ISSmu1_490009..490159_POSITIVE 311 79 53 87 61 smit:SMT_735|3end_putative_transposase,_ISSmu1_641395..641545_POSITIVE 304 99 56 50 4 smit:SMT_1761|3end_transcriptional_activator,_putative_1737185..1737335_POSITIVE 299 96 57 111 75 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 282 99 61 63 27 smit:SMT_1313|3end_extramembranal_protein_1278622..1278772_POSITIVE 244 97 51 151 107 smit:SMT_676|3end_DNA_helicase_II_583020..583170_NEGATIVE 214 100 85 31 16 smit:SMT_569|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_488553..488703_POSITIVE 196 77 31 58 10 smit:SMT_1497|3end_acetyltransferase,_GNAT_family_1482030..1482180_POSITIVE 194 76 40 70 24 smit:SMT_1115|3end_K02245_competence_protein_ComGC_1052473..1052623_NEGATIVE 193 57 13 52 10 smit:SMT_943|3end_hypothetical_protein_894136..894286_NEGATIVE 191 87 47 63 28 smit:SMT_1386|3end_phosphoenolpyruvate-protein_phosphotransferase_1364610..1364760_POSITIVE 187 73 42 64 30 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 180 64 50 121 106 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE 178 79 37 143 105 smit:SMT_2003|3end_serine_protease_1924693..1924843_NEGATIVE 178 97 63 65 33 smit:SMT_548|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_467039..467189_POSITIVE 176 97 66 115 86 smit:SMT_1375|3end_putative_glucose-inhibited_division_protein_1353104..1353254_NEGATIVE 176 66 26 118 53 smit:SMT_991|3end_hypothetical_protein_934033..934183_NEGATIVE 176 99 55 87 43 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 173 63 25 59 21 smit:SMT_140|3end_NUDIX_family_hydrolase_91498..91648_POSITIVE 170 79 43 138 102 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE