Origin IGS: cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagacagccttctgccatcacaggataatcgtatcaaaatctcaaaacaaacatagcttcctaaaaacaagcgatttaaaccaacagacatccacatctgtttttttactatttttgcatcggg Mask Tandem Repeat Region ================================================ cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta Find is-nt database================================================ Query_seq: TF2928:TF2929|TF2928:TF2929:predicted DNA repair protein:conserved hypothetical protein:->->:3131500..3131623 124 cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2928:TF2929|TF2928:TF2929:predicted DNA repair protein:conserved hypothetical protein:->->:3131500..3131623 124 cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2928:TF2929|TF2928:TF2929:predicted DNA repair protein:conserved hypothetical protein:->->:3131500..3131623 124 cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 13 End: 123 ............ M V K K Q M W M S V G L N R L F L G S Y V C F E I L I R L S C D G R R L S . Protein_Len: 33 Strand: - Start: 2 End: 100 . R H L F L L F V S T S T Q Q N L D S T K L F S H K N Q S K S V I M ........................ cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta 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================================================ cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2928:TF2929|TF2928:TF2929:predicted DNA repair protein:conserved hypothetical protein:->->:3131500..3131623 124 cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: tfor_TF2928_TF2929|predicted DNA repair protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3131500,3131623]|124 HSP 1 e-value: 5.0E-52 bit: 204.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 cccgatgcaaaaatagtnnnnnnncagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta cccgatgcaaaaatagtaaaaaaacagatgtggatgtctgttggtttaaatcgcttgtttttaggaagctatgtttgttttgagattttgatacgattatcctgtgatggcagaaggctgtcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGAUGCAAAAAUAGUAAAAAAACAGAUGUGGAUGUCUGUUGGUUUAAAUCGCUUGUUUUUAGGAAGCUAUGUUUGUUUUGAGAUUUUGAUACGAUUAUCCUGUGAUGGCAGAAGGCUGUCUA ..(((.(((((.((((((((..(((((((......)))))))..)))......((((....))))..))))).))))).))).......((((....))))....((((((.....)))))).. (-23.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACAGCCUUCUGCCAUCACAGGAUAAUCGUAUCAAAAUCUCAAAACAAACAUAGCUUCCUAAAAACAAGCGAUUUAAACCAACAGACAUCCACAUCUGUUUUUUUACUAUUUUUGCAUCGGG .........(((((......)))))...(((...(((((................((((.........))))....((((..((((((........))))))..))))....)))))...))). (-13.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 120 73 57 10 tfor:TF0317|5end_conserved_hypothetical_protein_341586..341816_POSITIVE 312 69 29 43 8 tfor:TF0602|5end_aminotripeptidase;_peptidase_T_632169..632399_POSITIVE 306 119 72 175 140 tfor:TF2829|5end_conserved_hypothetical_protein_3019562..3019792_POSITIVE 303 120 82 141 95 tfor:TF0561|5end_DNA_binding_protein;_possible__HU_protein_593548..593778_POSITIVE 300 109 62 149 102 tfor:TF0382|5end_transcription_termination_factor_403175..403405_POSITIVE 291 119 92 204 168 tfor:TF2219|5end_two-component_system_sensor_histidine_2390844..2391074_POSITIVE 287 69 24 179 138 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 282 77 31 143 91 tfor:TF2450|5end_outer_membrane_protein_2626471..2626701_POSITIVE 272 119 71 148 92 tfor:TF0326|5end_hypothetical_protein_353854..354084_POSITIVE 270 120 71 221 170 tfor:TF2460|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2636757..2636987_POSITIVE 269 69 25 213 166 tfor:TF1138|5end_ribosomal_large_subunit_pseudouridine_synthase_B_1213863..1214093_POSITIVE 266 118 79 54 19 tfor:TF2388|5end_outer_membrane_protein,_TonB_dependent_receptor_2556000..2556230_POSITIVE 262 120 82 138 103 tfor:TF0013|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_6414..6644_POSITIVE 258 77 32 58 2 tfor:TF0186|5end_ribonucleotide_reductase,_alpha_subunit_199198..199428_POSITIVE 257 110 61 56 9 tfor:TF1649|5end_hypothetical_protein_1759638..1759868_POSITIVE 254 80 33 139 97 tfor:TF0227|5end_transcriptional_regulator,_Crp/Fnr_family_252820..253050_POSITIVE 251 68 21 150 97 tfor:TF0695|5end_possible_phosphatidylglycerophosphate_synthase_739021..739251_POSITIVE 251 66 21 169 120 tfor:TF0649|5end_protein_serine/threonine_phosphatase_690594..690824_POSITIVE 249 120 76 197 143 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 248 74 32 115 75 tfor:TF2846|5end_cobyric_acid_synthase_3034896..3035126_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 69 29 37 2 tfor:TF0601|3end_aminomethyltransferase_(glycine_cleavage_system_T_protein)_632243..632393_POSITIVE 303 120 82 145 99 tfor:TF0560|3end_DNA-binding_protein_593632..593782_POSITIVE 282 77 31 133 81 tfor:TF2449|3end_undecaprenyl_diphosphate_synthase_2626541..2626691_POSITIVE 251 68 21 150 97 tfor:TF0694|3end_possible_hemolysin,_acyltransferase_family_739101..739251_POSITIVE 251 66 21 146 97 tfor:TF0648|3end_possible_FHA_domain_protein_690651..690801_POSITIVE 250 120 75 150 105 tfor:TF1604|3end_possible_anti-sigma_factor_1718916..1719066_POSITIVE 249 120 76 146 92 tfor:TF2878|3end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3068283..3068433_POSITIVE 248 74 32 124 84 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 245 120 94 37 6 tfor:TF2353|3end_conserved_hypothetical_protein_2518608..2518758_POSITIVE 244 69 24 109 53 tfor:TF2735|3end_hypothetical_protein_2917928..2918078_POSITIVE 244 110 61 72 29 tfor:TF2439|3end_conserved_hypothetical_protein_2616930..2617080_POSITIVE 243 80 34 151 102 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 242 118 72 55 13 tfor:TF0549|3end_universal_stress_protein,_UspA_582658..582808_POSITIVE 238 115 82 99 54 tfor:TF1163|3end_two-component_system_response_regulator_1243771..1243921_POSITIVE 238 85 41 71 16 tfor:TF0299|3end_hypothetical_protein_325365..325515_POSITIVE 237 58 21 43 3 tfor:TF2123|3end_conserved_hypothetical_protein;_TPR-repeat_protein_2300344..2300494_POSITIVE 237 69 27 127 81 tfor:TF1795|3end_conserved_hypothetical_protein_1936476..1936626_POSITIVE 237 120 71 136 85 tfor:TF0134|3end_transposase_element_146044..146194_POSITIVE 236 78 31 75 22 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 236 40 6 41 4 tfor:TF2134|3end_conserved_hypothetical_protein_2310187..2310337_POSITIVE