Origin IGS: gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagacgaactcagttgcagtcaactgggtttctttgcttattttagaaaaaatggatagaaaggtatagggctagtagtgtttaccatggagctcttggtatc Mask Tandem Repeat Region ================================================ gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt Find is-nt database================================================ Query_seq: SMT_991:SMT_992|SMT_991:SMT_992:hypothetical protein:hypothetical protein:<-<-:934516..934618 103 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_991:SMT_992|SMT_991:SMT_992:hypothetical protein:hypothetical protein:<-<-:934516..934618 103 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_991:SMT_992|SMT_991:SMT_992:hypothetical protein:hypothetical protein:<-<-:934516..934618 103 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt Predict ORF larger than 30AA ================================================ gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt 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================================================ gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_991:SMT_992|SMT_991:SMT_992:hypothetical protein:hypothetical protein:<-<-:934516..934618 103 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: smit_SMT_991_SMT_992|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[934516,934618]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt Inter-species Hit: Count: 3 Min: 1 Max: 103 Len: 103 Subject: NC_008533_SPD_1553_SPD_1554|hypothetical protein:iojap-related protein|NEGATIVE:NEGATIVE|[1576585,1576686]|102 HSP 1 e-value: 5.0E-33 bit: 141.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt gatactaagagctccatggtaaacaccactagccctttacctttctatcaatttt-tctaaaataagcaaagaaacccagttgactacaactgagttcatctt Subject: NC_003098_spr1588_spr1589|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1569054,1569155]|102 HSP 1 e-value: 5.0E-33 bit: 141.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt gatactaagagctccatggtaaacaccactagccctttacctttctatcaatttt-tctaaaataagcaaagaaacccagttgactacaactgagttcatctt Subject: NC_003028_SP_1743_SP_1744|hypothetical protein:iojap-related protein|NEGATIVE:NEGATIVE|[1647649,1647750]|102 HSP 1 e-value: 5.0E-33 bit: 141.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 gataccaagagctccatggtaaacactactagccctatacctttctatccattttttctaaaataagcaaagaaacccagttgactgcaactgagttcgtctt gatactaagagctccatggtaaacaccactagccctttacctttctatcaatttt-tctaaaataagcaaagaaacccagttgactacaactgagttcatctt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUACCAAGAGCUCCAUGGUAAACACUACUAGCCCUAUACCUUUCUAUCCAUUUUUUCUAAAAUAAGCAAAGAAACCCAGUUGACUGCAACUGAGUUCGUCUU ........((((((..(((((.....)))))....................((((((((......)).))))))....(((((....)))))))))))..... (-13.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGACGAACUCAGUUGCAGUCAACUGGGUUUCUUUGCUUAUUUUAGAAAAAAUGGAUAGAAAGGUAUAGGGCUAGUAGUGUUUACCAUGGAGCUCUUGGUAUC .....(((((((((((....))))))))))).((((..((((((....))))))..))))..(((((((((((....(((.....)))..))))))..))))) (-23.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 926 50 1 141 92 smit:SMT_991|5end_hypothetical_protein_934425..934655_NEGATIVE 299 59 13 165 120 smit:SMT_1820|5end_cation_transporter_CorA_family_1793600..1793830_POSITIVE 260 50 5 205 156 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 252 51 11 69 25 smit:SMT_1127|5end_transcriptional_regulator,_MarR_family_1061556..1061786_NEGATIVE 248 59 11 125 70 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 245 47 2 133 90 smit:SMT_384|5end_hypothetical_protein_319406..319636_POSITIVE 239 50 7 108 66 smit:SMT_2027|5end_competence-specific_global_transcription_modulator_1943204..1943434_NEGATIVE 237 68 21 161 110 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 236 44 1 161 125 smit:SMT_2071|5end_phosphoenolpyruvate_carboxylase_1975887..1976117_NEGATIVE 233 98 66 219 183 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 233 99 51 163 114 smit:SMT_1508|5end_hypothetical_protein_1491568..1491798_NEGATIVE 233 97 51 138 91 smit:SMT_1130|5end_MATE_efflux_family_protein_1065210..1065440_NEGATIVE 231 80 31 222 176 smit:SMT_1756|5end_hypothetical_protein_1734170..1734400_NEGATIVE 228 37 4 53 20 smit:SMT_1029|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_965632..965862_NEGATIVE 228 58 12 187 146 smit:SMT_233|5end_hypothetical_protein_172656..172886_POSITIVE 225 47 6 122 79 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 224 36 5 211 164 smit:SMT_1088|5end_hypothetical_protein_1024346..1024576_NEGATIVE 224 50 4 177 114 smit:SMT_680|5end_choline_transport_protein_589962..590192_NEGATIVE 223 98 75 69 44 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 222 50 8 52 9 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 33 1 151 107 smit:SMT_1025|3end_hypothetical_protein_959550..959700_NEGATIVE 256 100 51 46 2 smit:SMT_1021|3end_K05846_osmoprotectant_transport_system_permease_protein_956479..956629_NEGATIVE 248 59 11 128 73 smit:SMT_1283|3end_K02240_competence_protein_ComFA_1247045..1247195_POSITIVE 245 47 2 54 11 smit:SMT_383|3end_cysteinyl-tRNA_synthetase_319407..319557_POSITIVE 237 68 21 130 79 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 236 44 1 68 32 smit:SMT_2072|3end_exonuclease_RexA_1975980..1976130_NEGATIVE 233 97 51 77 30 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 225 47 6 107 64 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 224 59 23 40 2 smit:SMT_1819|3end_K03442_small_conductance_mechanosensitive_ion_channel,_MscS_family_1793555..1793705_POSITIVE 223 98 75 82 57 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 222 56 13 86 47 smit:SMT_1378|3end_DNA_polymerase_III,_delta'_subunit_1355913..1356063_NEGATIVE 222 42 5 137 100 smit:SMT_859|3end_K02086_DNA_replication_protein_803381..803531_NEGATIVE 221 97 57 92 47 smit:SMT_1600|3end_malolactic_enzyme_1591646..1591796_POSITIVE 218 75 35 72 28 smit:SMT_292|3end_dTDP-glucose_4,6-dehydratase_235933..236083_POSITIVE 216 48 2 56 7 smit:SMT_1683|3end_phenylalanyl-tRNA_synthetase_beta_chain_1666344..1666494_NEGATIVE 214 50 8 142 97 smit:SMT_1315|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1280952..1281102_POSITIVE 212 42 6 128 76 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 210 42 4 54 16 smit:SMT_1827|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1797722..1797872_POSITIVE 210 41 4 50 19 smit:SMT_1089|3end_hypothetical_protein_1024343..1024493_NEGATIVE 210 90 41 82 23 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE