Origin IGS: taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agttattaggagttatttttgtttaatagaaaggaatgactttgttccagcggttgacatctgattctcaaagaacataggtgcatatagaaaaacaactaactaataatcagcaatgtgtcgaaattaatatttcagtacagatgaaaatattccattgttttttaggaatttatccattgcaacaaagtcattaaaagtta Mask Tandem Repeat Region ================================================ taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact Find is-nt database================================================ Query_seq: TF2141:TF2142|TF2141:TF2142:conserved hypothetical protein:hypothetical protein:->->:2318353..2318555 203 taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2141:TF2142|TF2141:TF2142:conserved hypothetical protein:hypothetical protein:->->:2318353..2318555 203 taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2141:TF2142|TF2141:TF2142:conserved hypothetical protein:hypothetical protein:->->:2318353..2318555 203 taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 106 End: 195 ......................................................................................................... M F F Y M H L C S L R I R C Q P L E Q S H S F L L N K N N S ........ Protein_Len: 38 Strand: - Start: 10 End: 123 ......... H S Q Q L P Y I G L F C H F I K M Q V S I N I E V C Q Q N N T L Q K E I H M ................................................................................ taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact 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================================================ taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2141:TF2142|TF2141:TF2142:conserved hypothetical protein:hypothetical protein:->->:2318353..2318555 203 taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: tfor_TF2141_TF2142|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2318353,2318555]|203 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact taacttttaatgactttgttgcaatggataaattcctaaaaaacaatggaatattttcatctgtactgaaatattaatttcgacacattgctgattattagttagttgtttttctatatgcacctatgttctttgagaatcagatgtcaaccgctggaacaaagtcattcctttctattaaacaaaaataactcctaataact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUUUAAUGACUUUGUUGCAAUGGAUAAAUUCCUAAAAAACAAUGGAAUAUUUUCAUCUGUACUGAAAUAUUAAUUUCGACACAUUGCUGAUUAUUAGUUAGUUGUUUUUCUAUAUGCACCUAUGUUCUUUGAGAAUCAGAUGUCAACCGCUGGAACAAAGUCAUUCCUUUCUAUUAAACAAAAAUAACUCCUAAUAACU ........((((((((((((.((.(((....(((((...........))))).....((((((...((((((....))))))..(((..((((((.....)))))))))(((((.....(((....))).....))))).))))))....))).)).)))))))))))).................................. (-38.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUAUUAGGAGUUAUUUUUGUUUAAUAGAAAGGAAUGACUUUGUUCCAGCGGUUGACAUCUGAUUCUCAAAGAACAUAGGUGCAUAUAGAAAAACAACUAACUAAUAAUCAGCAAUGUGUCGAAAUUAAUAUUUCAGUACAGAUGAAAAUAUUCCAUUGUUUUUUAGGAAUUUAUCCAUUGCAACAAAGUCAUUAAAAGUUA ..((((((((((......)).)))))))).....((((((((((((...(((((.((.....(((((..((((((((..((......(((........)))........(((....((((..(((((....)))))..))))..))).......))..))))))))..)))))..)).)))))))))))))))))........ (-39.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 480 166 121 130 85 tfor:TF3128|5end_hypothetical_protein_3362253..3362483_POSITIVE 371 45 10 220 185 tfor:TF3129|5end_DNA_methylase_3362477..3362707_POSITIVE 292 168 132 92 56 tfor:TF2508|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_clpX_2686315..2686545_POSITIVE 285 157 120 217 181 tfor:TF0550|5end_stationary-phase-upregulated_protein,_UstA_582584..582814_POSITIVE 272 176 131 84 38 tfor:TF2134|5end_conserved_hypothetical_protein_2308689..2308919_POSITIVE 272 159 119 131 79 tfor:TF0312|5end_outer_membrane_protein_336473..336703_POSITIVE 269 176 133 84 21 tfor:TF2020|5end_muconate_cycloisomerase_2176321..2176551_POSITIVE 265 170 121 157 106 tfor:TF2502|5end_conserved_hypothetical_protein_2678103..2678333_POSITIVE 264 178 132 59 11 tfor:TF0617|5end_alpha-1,2-mannosidase_650862..651092_POSITIVE 258 170 123 86 38 tfor:TF2596|5end_conserved_hypothetical_protein;_possible_lipoprotein_2766667..2766897_POSITIVE 251 168 123 43 10 tfor:TF2842|5end_methyltransferase_3032094..3032324_POSITIVE 251 154 117 178 137 tfor:TF2341|5end_hypothetical_protein_2505735..2505965_POSITIVE 250 160 116 229 192 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 249 171 134 125 78 tfor:TF2282|5end_hypothetical_protein_2439401..2439631_POSITIVE 248 157 111 204 150 tfor:TF2701|5end_conserved_hypothetical_protein_2874174..2874404_POSITIVE 246 155 120 50 18 tfor:TF2727|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2903273..2903503_POSITIVE 246 157 111 173 126 tfor:TF0713|5end_polypeptide_deformylase;_formylmethionine_deformylase;_763440..763670_POSITIVE 244 34 3 34 4 tfor:TF2954|5end_outer_membrane_protein,_TonB_dependent_receptor_3161238..3161468_POSITIVE 244 169 122 209 160 tfor:TF0181|5end_ATP-dependent_DNA_helicase_192408..192638_POSITIVE 240 157 112 147 87 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 35 10 144 119 tfor:TF3128|3end_hypothetical_protein_3362491..3362641_POSITIVE 335 166 138 31 3 tfor:TF3127|3end_acetyltransferase,_possible_GNAT_family_3362234..3362384_POSITIVE 292 168 132 62 26 tfor:TF2507|3end_ATP-dependent_DNA_helicase_2686365..2686515_POSITIVE 272 176 131 84 38 tfor:TF2132|3end_TIM-barrel_protein,_NifR3_family_2308769..2308919_POSITIVE 269 176 133 84 21 tfor:TF2019|3end_dipeptidyl_peptidase_VI_2176401..2176551_POSITIVE 258 170 123 56 8 tfor:TF2595|3end_conserved_hypothetical_protein_2766717..2766867_POSITIVE 251 154 117 146 105 tfor:TF2339|3end_hypothetical_protein_2505783..2505933_POSITIVE 251 154 117 146 105 tfor:TF1259|3end_hypothetical_protein_1345204..1345354_POSITIVE 249 171 134 118 71 tfor:TF2280|3end_hypothetical_protein_2439474..2439624_POSITIVE 248 157 111 84 30 tfor:TF2700|3end_possible_nifS-like_aminotransferase_2874134..2874284_POSITIVE 237 157 124 67 37 tfor:TF0852|3end_transcriptional_regulator,_TetR_family_903943..904093_POSITIVE 234 170 135 68 27 tfor:TF1143|3end_ABC_transporter,_ATP-binding/permease_component_1223601..1223751_POSITIVE 233 179 140 106 61 tfor:TF0603|3end_glycosyltransferase_634838..634988_POSITIVE 232 176 132 136 87 tfor:TF1807|3end_thioesterase_family_protein_1949425..1949575_POSITIVE 231 162 127 148 111 tfor:TF2966|3end_hypothetical_protein_3177672..3177822_POSITIVE 229 160 112 119 70 tfor:TF2021|3end_hypothetical_protein_2178588..2178738_POSITIVE 227 128 87 121 66 tfor:TF2964|3end_type_I_restriction_enzyme_3176273..3176423_POSITIVE 227 144 101 119 76 tfor:TF2397|3end_magnesium_and_cobalt_transport_protein_2569569..2569719_POSITIVE 227 86 48 149 111 tfor:TF2314|3end_conserved_hypothetical_protein_2474044..2474194_POSITIVE 227 158 114 145 86 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE