Origin IGS: gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataacctccataccttaagattttaacatctatatatagaagttgtcaagtgttttatatttaaattctttttcagataacctctttttacttttagttatattcatc Mask Tandem Repeat Region ================================================ gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Find is-nt database================================================ Query_seq: TDE0418:TDE0419|TDE0418:TDE0419:lipoprotein, putative:hypothetical protein:->->:470954..471062 109 gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0418:TDE0419|TDE0418:TDE0419:lipoprotein, putative:hypothetical protein:->->:470954..471062 109 gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0418:TDE0419|TDE0418:TDE0419:lipoprotein, putative:hypothetical protein:->->:470954..471062 109 gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Predict ORF larger than 30AA ================================================ gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata 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================================================ gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0418:TDE0419|TDE0418:TDE0419:lipoprotein, putative:hypothetical protein:->->:470954..471062 109 gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Intra-Species Hit: Count: 2 Min: 1 Max: 109 Len: 109 Subject: NC_002967_TDE0418_TDE0419|lipoprotein, putative:hypothetical protein|POSITIVE:POSITIVE|[470954,471062]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata gatgaatataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata Subject: NC_002967_TDE0414_TDE0415|hypothetical protein:lipoprotein, putative|POSITIVE:POSITIVE|[467703,467806]|104 HSP 1 e-value: 5.0E-36 bit: 151.0 Len: 104 Query Start:6 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 .....atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacaacttctatatatagatgttaaaatcttaaggtatggaggttata .....atataactaaaagtaaaaagaggttatctgaaaaagaatttaaatataaaacacttgacggtttttatgtatagatgttaaaatcttaaagcatggaggttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAAUAUAACUAAAAGUAAAAAGAGGUUAUCUGAAAAAGAAUUUAAAUAUAAAACACUUGACAACUUCUAUAUAUAGAUGUUAAAAUCUUAAGGUAUGGAGGUUAUA .......((((((.............))))))................................(((((((((((..((((......))))....)))))))))))... (-15.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAACCUCCAUACCUUAAGAUUUUAACAUCUAUAUAUAGAAGUUGUCAAGUGUUUUAUAUUUAAAUUCUUUUUCAGAUAACCUCUUUUUACUUUUAGUUAUAUUCAUC ((((((............((((......))))......(((.(((((((((.((((.......)))).))).....)))))).)))...........))))))...... (-10.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 100 52 125 77 NC_002967:TDE0417|5end_hypothetical_protein_469608..469838_NEGATIVE 208 41 4 36 3 NC_002967:TDE0121|5end_hypothetical_protein_138870..139100_POSITIVE 205 59 17 68 26 NC_002967:TDE0380|5end_hypothetical_protein_433351..433581_POSITIVE 201 99 58 221 182 NC_002967:TDE1854|5end_nucleotidyltransferase_family_protein_1882715..1882945_NEGATIVE 198 46 19 179 148 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 187 42 12 231 195 NC_002967:TDE1023|5end_methylaspartate_mutase_subunit_S_1055123..1055353_POSITIVE 172 97 51 156 107 NC_002967:TDE0457|5end_hypothetical_protein_513525..513755_POSITIVE 169 46 1 191 152 NC_002967:TDE2254|5end_hypothetical_protein_2291642..2291872_NEGATIVE 164 96 60 220 187 NC_002967:TDE0795|5end_hypothetical_protein_819974..820204_NEGATIVE 163 79 32 220 174 NC_002967:TDE2546|5end_hypothetical_protein_2572761..2572991_NEGATIVE 162 100 60 226 187 NC_002967:TDE1337|5end_hypothetical_protein_1374806..1375036_NEGATIVE 156 78 39 75 31 NC_002967:TDE2361|5end_high-affinity_branched_chain_amino_acid_ABC_transporter,_amino_acid-binding_protein_2396966..2397196_NEGATIVE 156 70 26 150 98 NC_002967:TDE0232|5end_appr-1-p_processing_enzyme_domain_protein_265214..265444_POSITIVE 154 98 57 130 81 NC_002967:TDE1073|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1103515..1103745_POSITIVE 153 70 26 161 110 NC_002967:TDE1234|5end_hypothetical_protein_1269316..1269546_NEGATIVE 152 71 32 59 12 NC_002967:TDE0744|5end_thioredoxin_779844..780074_POSITIVE 149 97 58 138 93 NC_002967:TDE1040|5end_ribosomal_protein_S15_1067939..1068169_POSITIVE 147 43 12 54 25 NC_002967:TDE0757|5end_iron_compound_ABC_transporter,_permease_protein,_putative_797926..798156_NEGATIVE 147 86 60 141 115 NC_002967:TDE0423|5end_hypothetical_protein_476601..476831_POSITIVE 145 100 55 112 64 NC_002967:TDE1654|5end_ATP-dependent_helicase_HrpA,_putative_1702219..1702449_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 70 21 82 28 NC_002967:TDE0964|3end_hypothetical_protein_990578..990728_POSITIVE 156 78 39 78 34 NC_002967:TDE2362|3end_hypothetical_protein_2396963..2397113_NEGATIVE 149 97 58 134 89 NC_002967:TDE1039|3end_riboflavin_biosynthesis_protein,_putative_1068015..1068165_POSITIVE 147 43 12 52 23 NC_002967:TDE0758|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_797928..798078_NEGATIVE 147 86 60 70 44 NC_002967:TDE0422|3end_bacteriocin-type_signal_domain_protein_476610..476760_POSITIVE 147 86 60 31 5 NC_002967:TDE0418|3end_lipoprotein,_putative_470893..471043_POSITIVE 145 96 59 72 33 NC_002967:TDE1251|3end_batB_protein,_putative_1286496..1286646_POSITIVE 145 99 51 116 56 NC_002967:TDE0048|3end_hypothetical_protein_57187..57337_NEGATIVE 141 86 43 78 33 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 140 47 21 70 40 NC_002967:TDE2249|3end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_2287498..2287648_NEGATIVE 139 37 12 71 48 NC_002967:TDE0878|3end_hypothetical_protein_899929..900079_POSITIVE 137 41 7 81 49 NC_002967:TDE2777|3end_hypothetical_protein_2829351..2829501_POSITIVE 137 36 12 130 99 NC_002967:TDE1678|3end_ribosomal_protein_S6_1730202..1730352_NEGATIVE 136 65 28 125 88 NC_002967:TDE1289|3end_hypothetical_protein_1327510..1327660_POSITIVE 136 92 67 99 74 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE 135 99 67 50 19 NC_002967:TDE1791|3end_hypothetical_protein_1828308..1828458_NEGATIVE 135 97 67 90 57 NC_002967:TDE0003|3end_hypothetical_protein_4282..4432_POSITIVE 134 47 8 62 24 NC_002967:TDE1945|3end_hypothetical_protein_1961119..1961269_NEGATIVE 134 51 27 89 65 NC_002967:TDE0633|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_668658..668808_POSITIVE 133 90 56 66 37 NC_002967:TDE2058|3end_hypothetical_protein_2085354..2085504_NEGATIVE