Origin IGS: taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaatcgttttttttcaagatcgaggaaaaaaggtgtcgaaacttgattgaatgacagaatgtgggaaaaatgatataatgggatggacgaaaaattgacaagttagaatttagaggtaaatatatta Mask Tandem Repeat Region ================================================ taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat Find is-nt database================================================ Query_seq: TDE1306:TDE1307|TDE1306:TDE1307:hypothetical protein:hypothetical protein:<-->:1340965..1341093 129 taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1306:TDE1307|TDE1306:TDE1307:hypothetical protein:hypothetical protein:<-->:1340965..1341093 129 taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1306:TDE1307|TDE1306:TDE1307:hypothetical protein:hypothetical protein:<-->:1340965..1341093 129 taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 19 End: 111 .................. M L T C Q F F V H P I I S F F P H S V I Q S S F D T F F P R S .................. Protein_Len: 42 Strand: + Start: 3 End: 125 .. M Y L P L N S N L S I F R P S H Y I I F P T F C H S I K F R H L F S S I L K K N D * .... taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat 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: 84 Start: 49 End: 78 ................................................AATGACAGAATGTGGGAAAAATGATATAAT................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 5 End: 34 ....ATTGACAAGTTAGAATTTAGAGGTAAATAT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1306:TDE1307|TDE1306:TDE1307:hypothetical protein:hypothetical protein:<-->:1340965..1341093 129 taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttgaaaaaaaacgattaat Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_002967_TDE1306_TDE1307|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1340965,1341093]|129 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttg................ taatatatttacctctaaattctaacttgtcaatttttcgtccatcccattatatcatttttcccacattctgtcattcaatcaagtttcgacaccttttttcctcgatcttg................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUAUUUACCUCUAAAUUCUAACUUGUCAAUUUUUCGUCCAUCCCAUUAUAUCAUUUUUCCCACAUUCUGUCAUUCAAUCAAGUUUCGACACCUUUUUUCCUCGAUCUUG ..................................................................................((((..((((............)))).)))) ( -3.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGAUCGAGGAAAAAAGGUGUCGAAACUUGAUUGAAUGACAGAAUGUGGGAAAAAUGAUAUAAUGGGAUGGACGAAAAAUUGACAAGUUAGAAUUUAGAGGUAAAUAUAUUA .....((((.(........).))))((((((.....((..((..((((.(......).))))..))..))...(((....))).))))))....................... ( -8.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 859 110 61 201 152 NC_002967:TDE1306|5end_hypothetical_protein_1340874..1341104_NEGATIVE 322 100 53 202 145 NC_002967:TDE0865|5end_hypothetical_protein_887127..887357_POSITIVE 279 78 36 200 159 NC_002967:TDE0722|5end_lipoprotein,_putative_758519..758749_POSITIVE 274 80 32 123 68 NC_002967:TDE0536|5end_hypothetical_protein_578864..579094_NEGATIVE 269 94 56 47 14 NC_002967:TDE1667|5end_translation_initiation_factor_IF-2B_subunit_alpha_1721051..1721281_NEGATIVE 266 74 39 117 85 NC_002967:TDE0389|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_440008..440238_POSITIVE 256 107 61 127 66 NC_002967:TDE0596|5end_hypothetical_protein_636010..636240_NEGATIVE 245 65 33 115 83 NC_002967:TDE2048|5end_hypothetical_protein_2076411..2076641_POSITIVE 229 63 25 107 67 NC_002967:TDE1812|5end_hypothetical_protein_1847855..1848085_NEGATIVE 229 63 25 107 67 NC_002967:TDE1789|5end_hypothetical_protein_1827613..1827843_NEGATIVE 229 79 35 177 129 NC_002967:TDE1004|5end_flagellar_filament_core_protein_1030136..1030366_NEGATIVE 227 78 32 219 167 NC_002967:TDE1286|5end_TPR_domain_protein_1322057..1322287_POSITIVE 224 92 57 105 69 NC_002967:TDE0489|5end_hypothetical_protein_546055..546285_NEGATIVE 222 78 37 183 133 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 219 78 31 136 76 NC_002967:TDE2090|5end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2118636..2118866_NEGATIVE 219 79 35 141 85 NC_002967:TDE1165|5end_hypothetical_protein_1198390..1198620_NEGATIVE 214 64 32 101 68 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 213 77 40 66 20 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 209 67 25 100 56 NC_002967:TDE2726|5end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2784169..2784399_NEGATIVE 209 76 34 194 155 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 87 53 143 115 NC_002967:TDE0864|3end_phosphohexose_mutase_family_protein_887177..887327_POSITIVE 266 74 39 79 47 NC_002967:TDE0388|3end_hypothetical_protein_440050..440200_POSITIVE 256 107 61 118 57 NC_002967:TDE0597|3end_hypothetical_protein_636019..636169_NEGATIVE 250 110 61 119 72 NC_002967:TDE2655|3end_hypothetical_protein_2692963..2693113_NEGATIVE 249 45 7 89 47 NC_002967:TDE0343|3end_hydrolase,_alpha/beta_fold_family_384247..384397_NEGATIVE 245 107 63 96 54 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 230 79 33 57 1 NC_002967:TDE0501|3end_hypothetical_protein_554185..554335_NEGATIVE 229 63 25 99 59 NC_002967:TDE1813|3end_hypothetical_protein_1847863..1848013_NEGATIVE 229 63 25 99 59 NC_002967:TDE1790|3end_hypothetical_protein_1827621..1827771_NEGATIVE 219 79 35 137 81 NC_002967:TDE1166|3end_hypothetical_protein_1198394..1198544_NEGATIVE 212 90 41 138 82 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 209 55 11 51 6 NC_002967:TDE2442|3end_surface_protein,_putative_2472471..2472621_NEGATIVE 209 76 34 62 23 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 209 106 65 116 81 NC_002967:TDE0461|3end_hypothetical_protein_516125..516275_POSITIVE 208 68 34 111 71 NC_002967:TDE1898|3end_translocase_1918122..1918272_NEGATIVE 207 105 73 148 117 NC_002967:TDE2165|3end_hydrogenase_accessory_protein_HypB_2197053..2197203_NEGATIVE 206 80 32 151 101 NC_002967:TDE1285|3end_flagellar_motor_switch_protein_FliG_,_putative_1322071..1322221_POSITIVE 204 72 37 119 81 NC_002967:TDE2096|3end_hypothetical_protein_2124491..2124641_POSITIVE 203 109 69 117 76 NC_002967:TDE0667|3end_FeS_assembly_protein_SufB_705836..705986_POSITIVE 202 76 36 44 7 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE