Origin IGS: atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataacctccatgctttaagattttaacatctatacataaaaaccgtcaagtgttttatatttaaattctttttcagataacctctttttacttttagttatat Mask Tandem Repeat Region ================================================ atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Find is-nt database================================================ Query_seq: TDE0414:TDE0415|TDE0414:TDE0415:hypothetical protein:lipoprotein, putative:->->:467703..467806 104 atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0414:TDE0415|TDE0414:TDE0415:hypothetical protein:lipoprotein, putative:->->:467703..467806 104 atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0414:TDE0415|TDE0414:TDE0415:hypothetical protein:lipoprotein, putative:->->:467703..467806 104 atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Predict ORF larger than 30AA ================================================ atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata 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================================================ atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0414:TDE0415|TDE0414:TDE0415:hypothetical protein:lipoprotein, putative:->->:467703..467806 104 atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Intra-Species Hit: Count: 2 Min: 1 Max: 104 Len: 104 Subject: NC_002967_TDE0414_TDE0415|hypothetical protein:lipoprotein, putative|POSITIVE:POSITIVE|[467703,467806]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Subject: NC_002967_TDE0418_TDE0419|lipoprotein, putative:hypothetical protein|POSITIVE:POSITIVE|[470954,471062]|109 HSP 1 e-value: 5.0E-36 bit: 151.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 6 Subject End: 109 atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAACUAAAAGUAAAAAGAGGUUAUCUGAAAAAGAAUUUAAAUAUAAAACACUUGACGGUUUUUAUGUAUAGAUGUUAAAAUCUUAAAGCAUGGAGGUUAUA .(((((((....((...((((..((((((.....)))(((((.((((((((.(((....))))))))))).)))))..)))..))))...)).....))))))) (-12.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAACCUCCAUGCUUUAAGAUUUUAACAUCUAUACAUAAAAACCGUCAAGUGUUUUAUAUUUAAAUUCUUUUUCAGAUAACCUCUUUUUACUUUUAGUUAUAU ((((((...........((((.(((((.......((((............)))).......))))).))))....(((.....)))...........)))))). ( -6.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 100 53 130 83 NC_002967:TDE0417|5end_hypothetical_protein_469608..469838_NEGATIVE 211 90 41 151 91 NC_002967:TDE0476|5end_hypothetical_protein_532914..533144_NEGATIVE 206 98 53 192 139 NC_002967:TDE0961|5end_DnaJ_domain_protein_983519..983749_POSITIVE 205 54 12 68 26 NC_002967:TDE0380|5end_hypothetical_protein_433351..433581_POSITIVE 202 99 55 59 12 NC_002967:TDE0032|5end_histidine_kinase-related_ATPase,_putative_39977..40207_NEGATIVE 200 100 55 229 182 NC_002967:TDE1430|5end_beta-1,4-galactosyltransferase,_putative_1473430..1473660_POSITIVE 198 41 14 179 148 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 194 77 57 74 55 NC_002967:TDE1371|5end_RNB-like_family_protein_1415169..1415399_NEGATIVE 193 100 51 139 88 NC_002967:TDE2482|5end_hypothetical_protein_2505536..2505766_POSITIVE 189 36 8 36 8 NC_002967:TDE0121|5end_hypothetical_protein_138870..139100_POSITIVE 187 37 7 231 195 NC_002967:TDE1023|5end_methylaspartate_mutase_subunit_S_1055123..1055353_POSITIVE 180 97 55 64 7 NC_002967:TDE1091|5end_hypothetical_protein_1123775..1124005_NEGATIVE 177 100 59 209 174 NC_002967:TDE1767|5end_hypothetical_protein_1813567..1813797_NEGATIVE 176 98 54 195 151 NC_002967:TDE1522|5end_citrate_lyase_ligase_1567780..1568010_POSITIVE 175 99 51 120 75 NC_002967:TDE2235|5end_methylaspartate_ammonia-lyase_2274588..2274818_NEGATIVE 173 100 52 46 2 NC_002967:TDE0209|5end_arsenical_pump_membrane_protein,_putative_244195..244425_POSITIVE 170 85 50 186 153 NC_002967:TDE2364|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398949..2399179_NEGATIVE 169 85 51 195 160 NC_002967:TDE1738|5end_M23/M37_peptidase_domain_protein_1790536..1790766_POSITIVE 169 100 56 57 13 NC_002967:TDE0907|5end_hypothetical_protein_924644..924874_POSITIVE 166 63 26 47 8 NC_002967:TDE2611|5end_hypothetical_protein_2651980..2652210_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 100 54 101 55 NC_002967:TDE0814|3end_transcriptional_regulator,_putative_835709..835859_NEGATIVE 211 90 41 95 35 NC_002967:TDE0477|3end_hypothetical_protein_532970..533120_NEGATIVE 202 99 55 59 12 NC_002967:TDE0033|3end_DNA-binding_response_regulator_39977..40127_NEGATIVE 190 99 74 73 46 NC_002967:TDE1578|3end_phosphoesterase,_putative_1626109..1626259_POSITIVE 180 98 53 105 65 NC_002967:TDE2773|3end_hypothetical_protein_2825823..2825973_NEGATIVE 180 98 54 98 54 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 180 99 54 125 81 NC_002967:TDE1195|3end_prolyl_endopeptidase_1227634..1227784_NEGATIVE 179 96 58 113 63 NC_002967:TDE1050|3end_hypothetical_protein_1078150..1078300_POSITIVE 177 100 59 107 72 NC_002967:TDE1768|3end_hypothetical_protein_1813669..1813819_NEGATIVE 175 99 51 123 46 NC_002967:TDE2521|3end_hypothetical_protein_2547955..2548105_NEGATIVE 175 99 51 48 3 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 173 97 55 53 7 NC_002967:TDE1791|3end_hypothetical_protein_1828308..1828458_NEGATIVE 169 100 56 52 8 NC_002967:TDE0906|3end_ABC_transporter,_ATP-binding_protein_924719..924869_POSITIVE 168 78 48 74 41 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 166 99 57 58 20 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 162 59 11 76 23 NC_002967:TDE0964|3end_hypothetical_protein_990578..990728_POSITIVE 162 93 57 81 52 NC_002967:TDE0649|3end_hypothetical_protein_684034..684184_NEGATIVE 156 97 54 53 4 NC_002967:TDE2138|3end_ankyrin_repeat_protein_2172094..2172244_POSITIVE 154 66 25 49 1 NC_002967:TDE2514|3end_serine/threonine_protein_phosphatase_family_protein_2539855..2540005_NEGATIVE 152 96 58 125 83 NC_002967:TDE1583|3end_hypothetical_protein_1632007..1632157_POSITIVE