Origin IGS: agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agggacctcttttcttataagtagattatatcaaatttttaaggaaaatttgaatgactccattaggatttttaatctttttttgatataattaaaagtaagaaaaccaatctgaatcctaaaatagaaagattgatact Mask Tandem Repeat Region ================================================ agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Find is-nt database================================================ Query_seq: SMT_1874:SMT_1875|SMT_1874:SMT_1875:hypothetical protein:hypothetical protein:<-->:1832965..1833104 140 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1874:SMT_1875|SMT_1874:SMT_1875:hypothetical protein:hypothetical protein:<-->:1832965..1833104 140 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1874:SMT_1875|SMT_1874:SMT_1875:hypothetical protein:hypothetical protein:<-->:1832965..1833104 140 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Predict ORF larger than 30AA ================================================ agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct 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================================================ agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -4.0 Tail_Score: -5.59357 Start: 64 End: 74 Full_Region: gaatgactccattag gatt ttt aatc tttttttgatataat ...............................................................gatttttaatc.................................................................. TransTerm Strand: + Conf: 61 HP_score: -6.5 Tail_Score: -2.89981 Start: 88 End: 110 Full_Region: TCCTAATGGAGTCAT TCAAATTTT CCTTA AAAATTTGA TATAATCTACTTATA .......................................................................................TCAAATTTTCCTTAAAAATTTGA.............................. Find igs database================================================ Query_seq: SMT_1874:SMT_1875|SMT_1874:SMT_1875:hypothetical protein:hypothetical protein:<-->:1832965..1833104 140 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Intra-Species Hit: Count: 2 Min: 1 Max: 140 Len: 140 Subject: smit_SMT_1883_SMT_1884|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1838964,1839103]|140 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcnnnnnnngattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Subject: smit_SMT_1874_SMT_1875|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1832965,1833104]|140 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcnnnnnnngattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcaaaaaaagattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggtccct Inter-species Hit: Count: 3 Min: 1 Max: 136 Len: 136 Subject: NC_008533_SPD_0995_SPD_0996|hypothetical protein:DegV family protein|NEGATIVE:POSITIVE|[1005112,1005252]|141 HSP 1 e-value: 1.0E-40 bit: 167.0 Len: 136 Query Start:1 Query End:136 Subject Strand: NEGATIVE Subject Start: 6 Subject End: 141 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcnnnnnnn-gattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggt.... agtatcaatctttctattttaggattcagattggtttccttacttttaattatatcaaaaaaaagattaaaaatcctaatggagtcaatcaaattttccgt-aaaatttgatataatcaacttataagaaaagaggt.... Subject: NC_003098_spr1018_spr1019|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[997581,997721]|141 HSP 1 e-value: 1.0E-40 bit: 167.0 Len: 136 Query Start:1 Query End:136 Subject Strand: NEGATIVE Subject Start: 6 Subject End: 141 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcnnnnnnn-gattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggt.... agtatcaatctttctattttaggattcagattggtttccttacttttaattatatcaaaaaaaagattaaaaatcctaatggagtcaatcaaattttccgt-aaaatttgatataatcaacttataagaaaagaggt.... Subject: NC_003028_SP_1111_SP_1112|hypothetical protein:degV family protein|NEGATIVE:POSITIVE|[1041013,1041153]|141 HSP 1 e-value: 3.0E-38 bit: 159.0 Len: 136 Query Start:1 Query End:136 Subject Strand: NEGATIVE Subject Start: 6 Subject End: 141 agtatcaatctttctattttaggattcagattggttttcttacttttaattatatcnnnnnnn-gattaaaaatcctaatggagtcattcaaattttccttaaaaatttgatataatctacttataagaaaagaggt.... agtatcaatctttctattttaggattcagattggtttccttacttctaattatatcaaaaaaaagattaaaaatcctaatggagtcaatcaaattttccgt-aaaatttgatataatcaacttataagaaaagaggt.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUCAAUCUUUCUAUUUUAGGAUUCAGAUUGGUUUUCUUACUUUUAAUUAUAUCAAAAAAAGAUUAAAAAUCCUAAUGGAGUCAUUCAAAUUUUCCUUAAAAAUUUGAUAUAAUCUACUUAUAAGAAAAGAGGU ...((((((((.(((......)))...)))))))).......(((((..(((((........((((((....(((....))).....(((((((((.....)))))))))..))))))...)))))...))))).. (-21.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUCUUUUCUUAUAAGUAGAUUAUAUCAAAUUUUUAAGGAAAAUUUGAAUGACUCCAUUAGGAUUUUUAAUCUUUUUUUGAUAUAAUUAAAAGUAAGAAAACCAAUCUGAAUCCUAAAAUAGAAAGAUUGAUACU .....(((((((((...(.((((((((((((........(((((((..((((....))))..)))))))........)))))))))))).)..))))))))).((((((...((........)).))))))..... (-28.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 695 50 1 141 92 smit:SMT_1883|5end_hypothetical_protein_1838873..1839103_NEGATIVE 695 50 1 141 92 smit:SMT_1874|5end_hypothetical_protein_1832874..1833104_NEGATIVE 226 47 9 209 174 smit:SMT_232|5end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_168246..168476_POSITIVE 219 50 11 114 76 smit:SMT_922|5end_RNA-binding_protein_876566..876796_NEGATIVE 213 86 41 174 131 smit:SMT_553|5end_hypothetical_protein_471128..471358_POSITIVE 212 100 51 202 164 smit:SMT_336|5end_hypothetical_protein_275222..275452_POSITIVE 210 58 11 63 12 smit:SMT_115|5end_hypothetical_protein_65521..65751_POSITIVE 205 43 9 220 187 smit:SMT_771|5end_spermidine/putrescine_transport_system_permease_protein_PotB_682183..682413_NEGATIVE 198 115 72 117 69 smit:SMT_139|5end_hypothetical_protein_90523..90753_POSITIVE 196 44 1 143 93 smit:SMT_377|5end_hypothetical_protein_314191..314421_POSITIVE 193 36 1 128 77 smit:SMT_514|5end_tRNA_(guanine-N(1)-)-methyltransferase_441377..441607_POSITIVE 193 57 12 210 156 smit:SMT_143|5end_hypothetical_protein_95323..95553_NEGATIVE 187 39 6 128 89 smit:SMT_1130|5end_MATE_efflux_family_protein_1065210..1065440_NEGATIVE 185 38 6 127 98 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 184 61 24 111 62 smit:SMT_701|5end_hypothetical_protein_611855..612085_NEGATIVE 180 50 5 167 126 smit:SMT_1022|5end_glycine_betaine_transport_ATP-binding_protein_958720..958950_NEGATIVE 178 48 18 110 82 smit:SMT_1055|5end_transcriptional_regulator,_GntR_family_994752..994982_NEGATIVE 176 60 12 144 91 smit:SMT_1501|5end_recombination_protein_1484401..1484631_POSITIVE 175 47 2 222 164 smit:SMT_1603|5end_K05832_putative_ABC_transport_system_permease_protein_1593374..1593604_POSITIVE 174 43 6 84 43 smit:SMT_1627|5end_hypothetical_protein_1616415..1616645_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 97 59 74 35 smit:SMT_1016|3end_alcohol_dehydrogenase,_zinc-containing_953057..953207_NEGATIVE 226 47 9 105 70 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 219 50 11 121 83 smit:SMT_923|3end_methionyl-tRNA_formyltransferase_876559..876709_NEGATIVE 213 86 41 146 103 smit:SMT_552|3end_DNA_polymerase_III,_gamma_and_tau_subunits_471180..471330_POSITIVE 212 100 51 79 41 smit:SMT_335|3end_glutamine_synthetase_275179..275329_POSITIVE 211 83 53 55 27 smit:SMT_1122|3end_queuine_tRNA-ribosyltransferase_1058081..1058231_NEGATIVE 211 97 58 56 22 smit:SMT_1015|3end_galactose_operon_repressor_953019..953169_POSITIVE 201 45 6 52 7 smit:SMT_1466|3end_endopeptidase_O_1447905..1448055_POSITIVE 201 48 9 137 101 smit:SMT_506|3end_K07729_putative_transcriptional_regulator_437411..437561_NEGATIVE 201 48 9 137 101 smit:SMT_503|3end_K07729_putative_transcriptional_regulator_435980..436130_NEGATIVE 196 44 1 72 22 smit:SMT_376|3end_DNA_(cytosine-5-)-methyltransferase_314200..314350_POSITIVE 194 47 21 108 81 smit:SMT_296|3end_hypothetical_protein_predicted_by_Glimmer/Critica_238328..238478_POSITIVE 194 47 21 108 81 smit:SMT_293|3end_dTDP-4-dehydrorhamnose_reductase_236862..237012_POSITIVE 193 36 1 138 87 smit:SMT_513|3end_16S_rRNA_processing_protein_RimM_441467..441617_POSITIVE 190 48 16 59 27 smit:SMT_1313|3end_extramembranal_protein_1278622..1278772_POSITIVE 187 39 6 67 28 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 187 110 74 57 17 smit:SMT_120|3end_hypothetical_protein_72943..73093_POSITIVE 185 38 6 143 114 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 177 42 5 142 111 smit:SMT_1023|3end_hypothetical_protein_958735..958885_NEGATIVE 176 60 12 89 36 smit:SMT_1500|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1484426..1484576_POSITIVE