Origin IGS: agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtacgatttatttaaagtaataacgaaaaccgaaagaacttagtatggatttcttccttatgttttcataattcaaatttattcgatagatttgtatctttaaaatataaatacagacctgact Mask Tandem Repeat Region ================================================ agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg Find is-nt database================================================ Query_seq: TF3025:TF3026|TF3025:TF3026:hypothetical protein:conserved hypothetical protein:->->:3249152..3249276 125 agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3025:TF3026|TF3025:TF3026:hypothetical protein:conserved hypothetical protein:->->:3249152..3249276 125 agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3025:TF3026|TF3025:TF3026:hypothetical protein:conserved hypothetical protein:->->:3249152..3249276 125 agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 13 End: 114 ............ M Y I L K I Q I Y R I N L N Y E N I R K K S I L S S F G F R Y Y F K ........... agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg 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================================================ agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3025:TF3026|TF3025:TF3026:hypothetical protein:conserved hypothetical protein:->->:3249152..3249276 125 agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: tfor_TF3025_TF3026|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3249152,3249276]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg agtcaggtctgtatttatattttaaagatacaaatctatcgaataaatttgaattatgaaaacataaggaagaaatccatactaagttctttcggttttcgttattactttaaataaatcgtacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCAGGUCUGUAUUUAUAUUUUAAAGAUACAAAUCUAUCGAAUAAAUUUGAAUUAUGAAAACAUAAGGAAGAAAUCCAUACUAAGUUCUUUCGGUUUUCGUUAUUACUUUAAAUAAAUCGUACG ....((((.(((((((.........))))))).))))..(((....(((((((..((((((((....(((((((............))))))).))))))))......)))))))...))).... (-20.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUACGAUUUAUUUAAAGUAAUAACGAAAACCGAAAGAACUUAGUAUGGAUUUCUUCCUUAUGUUUUCAUAAUUCAAAUUUAUUCGAUAGAUUUGUAUCUUUAAAAUAUAAAUACAGACCUGACU .((...((((((((((((.......(((((((....)......(((.(((.....))).)))))))))......(((((((((...)))))))))...))))))...))))))....))...... (-16.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 102 62 211 163 tfor:TF1881|5end_hypothetical_protein_2033412..2033642_POSITIVE 232 116 72 203 153 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 224 102 63 139 87 tfor:TF2187|5end_conserved_hypothetical_protein_2361693..2361923_POSITIVE 222 43 1 183 140 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 217 102 66 123 74 tfor:TF2257|5end_transfer_region-related_protein,_TraJ_2428541..2428771_POSITIVE 212 105 63 137 89 tfor:TF1446|5end_hypothetical_protein_1530649..1530879_POSITIVE 202 46 1 82 45 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 201 109 61 68 18 tfor:TF2564|5end_50S_ribosomal_protein_L14_2739604..2739834_POSITIVE 197 103 68 224 192 tfor:TF2710|5end_ABC_transporter,_ATP-binding_protein/permease_component_2882352..2882582_POSITIVE 193 109 68 215 182 tfor:TF2891|5end_lipoprotein_3078762..3078992_POSITIVE 192 45 1 58 16 tfor:TF0174|5end_hypothetical_protein_185362..185592_POSITIVE 191 110 61 98 60 tfor:TF2299|5end_hypothetical_protein_2449994..2450224_POSITIVE 190 107 61 77 27 tfor:TF2694|5end_hypothetical_protein_2870403..2870633_POSITIVE 189 103 62 55 6 tfor:TF3045|5end_two-component_system_response_regulator_3273807..3274037_POSITIVE 189 95 51 215 170 tfor:TF2806|5end_conserved_hypothetical_protein_2994475..2994705_POSITIVE 188 32 2 154 121 tfor:TF2866|5end_conserved_hypothetical_protein_3058640..3058870_POSITIVE 188 114 82 127 91 tfor:TF0591|5end_RNA_polymerase,_ECF-type_sigma_factor_624578..624808_POSITIVE 186 101 68 224 187 tfor:TF2927|5end_superoxide_dismutase,_Fe-Mn_3129902..3130132_POSITIVE 186 108 76 177 138 tfor:TF1334|5end_hypothetical_protein_1415996..1416226_POSITIVE 180 101 69 185 143 tfor:TF2458|5end_ribosome-binding_factor_A_2635233..2635463_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 102 62 124 76 tfor:TF1880|3end_transposase_2033405..2033555_POSITIVE 217 102 66 116 67 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 212 105 63 126 78 tfor:TF1445|3end_RNA_polymerase_sigma_factor_1530718..1530868_POSITIVE 208 105 77 126 98 tfor:TF2139|3end_hypothetical_protein_2316178..2316328_POSITIVE 206 103 66 55 20 tfor:TF2385|3end_conserved_hypothetical_protein;_possible_MazG_family_protein_2551544..2551694_POSITIVE 202 46 1 82 45 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 202 19 1 145 127 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 201 109 61 63 13 tfor:TF2563|3end_30S_ribosomal_protein_S17_2739679..2739829_POSITIVE 193 109 68 61 28 tfor:TF2889|3end_50S_ribosomal_protein_L27_3078688..3078838_POSITIVE 192 95 51 131 86 tfor:TF2597|3end_outer_membrane_receptor_protein;_possible_TonB_dependent_receptor_2770851..2771001_POSITIVE 190 107 61 131 81 tfor:TF2695|3end_prephenate_dehydratase_2870537..2870687_POSITIVE 189 95 51 109 64 tfor:TF2804|3end_conserved_hypothetical_protein_2994449..2994599_POSITIVE 189 72 40 112 76 tfor:TF1315|3end_purine_nucleoside_phosphorylase_1391125..1391275_POSITIVE 188 32 2 146 113 tfor:TF2865|3end_conserved_hypothetical_protein;_possible_Rhs_family_protein_3058712..3058862_POSITIVE 188 114 82 72 36 tfor:TF0589|3end_anti-sigma_factor_624603..624753_POSITIVE 186 108 76 115 76 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 184 95 54 140 93 tfor:TF0919|3end_conserved_hypothetical_protein_957773..957923_POSITIVE 181 45 4 39 1 tfor:TF0173|3end_hypothetical_protein_185423..185573_POSITIVE 180 102 76 143 116 tfor:TF1753|3end_topoisomerase_IV_subunit_A_1890993..1891143_POSITIVE 179 97 68 71 45 tfor:TF1331|3end_outer_membrane_protein_1410934..1411084_POSITIVE