Origin IGS: agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattcttgtaaagcctattttataatttgacataaatctgaaaacagtgtataatttattaaatttgttagattaattgtctataagaaacttaattcttaattttttggcaattaacatacaaaaaaggagtttct Mask Tandem Repeat Region ================================================ agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Find is-nt database================================================ Query_seq: TDE1950:TDE1951|TDE1950:TDE1951:membrane lipoprotein TmpC, putative:ribonuclease Z:<-<-:1967355..1967492 138 agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1950:TDE1951|TDE1950:TDE1951:membrane lipoprotein TmpC, putative:ribonuclease Z:<-<-:1967355..1967492 138 agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1950:TDE1951|TDE1950:TDE1951:membrane lipoprotein TmpC, putative:ribonuclease Z:<-<-:1967355..1967492 138 agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Predict ORF larger than 30AA ================================================ agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 93 Start: 83 End: 112 ..................................................................................TTTGACATAAATCTGAAAACAGTGTATAAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.8 Tail_Score: -3.62577 Start: 37 End: 54 Full_Region: tagattaattgtcta taagaa acttaa ttctta attttttggcaatta ....................................taagaaacttaattctta.................................................................................... Find igs database================================================ Query_seq: TDE1950:TDE1951|TDE1950:TDE1951:membrane lipoprotein TmpC, putative:ribonuclease Z:<-<-:1967355..1967492 138 agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_002967_TDE1950_TDE1951|membrane lipoprotein TmpC, putative:ribonuclease Z|NEGATIVE:NEGATIVE|[1967355,1967492]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt agaaactccttttttgtatgttaattgccaaaaaattaagaattaagtttcttatagacaattaatctaacaaatttaataaattatacactgttttcagatttatgtcaaattataaaataggctttacaagaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAACUCCUUUUUUGUAUGUUAAUUGCCAAAAAAUUAAGAAUUAAGUUUCUUAUAGACAAUUAAUCUAACAAAUUUAAUAAAUUAUACACUGUUUUCAGAUUUAUGUCAAAUUAUAAAAUAGGCUUUACAAGAAUUU ..........((((((((........(((.......((((((......))))))..((((...(((((((((...................))))...)))))..)))).............)))..))))))))... (-18.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUCUUGUAAAGCCUAUUUUAUAAUUUGACAUAAAUCUGAAAACAGUGUAUAAUUUAUUAAAUUUGUUAGAUUAAUUGUCUAUAAGAAACUUAAUUCUUAAUUUUUUGGCAAUUAACAUACAAAAAAGGAGUUUCU ......((((((((....))))))))...((((..(((((((.......(((.....)))........)))))))...))))....((((((((.........(((((((............))))))).)))))))) (-19.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 666 130 81 221 172 NC_002967:TDE1950|5end_membrane_lipoprotein_TmpC,_putative_1967264..1967494_NEGATIVE 220 50 8 82 43 NC_002967:TDE1192|5end_hypothetical_protein_1219332..1219562_POSITIVE 186 50 10 114 71 NC_002967:TDE0997|5end_glutamate_dehydrogenase_1025283..1025513_NEGATIVE 176 41 5 47 3 NC_002967:TDE0263|5end_spermidine_N1-acetyltransferase,_putative_296942..297172_NEGATIVE 175 31 8 213 190 NC_002967:TDE1282|5end_hypothetical_protein_1316801..1317031_POSITIVE 174 29 1 124 94 NC_002967:TDE1712|5end_flagellar_filament_outer_layer_protein_1767915..1768145_NEGATIVE 171 45 5 51 21 NC_002967:TDE1555|5end_hypothetical_protein_1598018..1598248_POSITIVE 169 49 7 57 18 NC_002967:TDE2337|5end_aminopeptidase_2373295..2373525_POSITIVE 168 99 51 227 176 NC_002967:TDE0439|5end_hypothetical_protein_495823..496053_NEGATIVE 167 49 6 141 103 NC_002967:TDE0695|5end_hypothetical_protein_731922..732152_POSITIVE 163 99 51 65 24 NC_002967:TDE1528|5end_hypothetical_protein_1571725..1571955_POSITIVE 161 129 91 69 36 NC_002967:TDE1763|5end_hypothetical_protein_1811205..1811435_NEGATIVE 158 30 7 102 78 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 155 28 1 123 94 NC_002967:TDE1526|5end_hypothetical_protein_1570565..1570795_POSITIVE 154 129 89 205 170 NC_002967:TDE0189|5end_hypothetical_protein_226460..226690_NEGATIVE 153 42 6 71 31 NC_002967:TDE2524|5end_ABC_transporter,_ATP-binding_protein_2550456..2550686_POSITIVE 153 68 27 50 22 NC_002967:TDE2323|5end_mechanosensitive_ion_channel_family_protein_2359084..2359314_NEGATIVE 151 125 87 190 143 NC_002967:TDE2165|5end_hydrogenase_accessory_protein_HypB_2197715..2197945_NEGATIVE 151 29 8 47 27 NC_002967:TDE0318|5end_hypothetical_protein_351082..351312_POSITIVE 150 109 65 201 159 NC_002967:TDE1965|5end_sodium/hydrogen_exchanger_family_protein_1980151..1980381_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 171 45 5 54 24 NC_002967:TDE1554|3end_hypothetical_protein_1598101..1598251_POSITIVE 167 49 6 141 103 NC_002967:TDE0694|3end_ABC_transporter,_ATP-binding_protein_732002..732152_POSITIVE 163 99 51 55 14 NC_002967:TDE1527|3end_hypothetical_protein_1571795..1571945_POSITIVE 161 129 91 47 14 NC_002967:TDE1764|3end_hypothetical_protein_1811227..1811377_NEGATIVE 155 29 3 29 1 NC_002967:TDE1713|3end_hypothetical_protein_1768010..1768160_NEGATIVE 155 28 1 132 103 NC_002967:TDE1525|3end_hypothetical_protein_1570654..1570804_POSITIVE 153 42 6 50 10 NC_002967:TDE2523|3end_hypothetical_protein_2550515..2550665_POSITIVE 149 125 90 67 27 NC_002967:TDE0231|3end_DNA_polymerase_III,_beta_subunit_263890..264040_NEGATIVE 148 34 1 99 63 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 148 35 4 65 23 NC_002967:TDE0178|3end_methyl-accepting_chemotaxis_protein_210538..210688_NEGATIVE 145 70 35 37 2 NC_002967:TDE2390|3end_hypothetical_protein_2419515..2419665_NEGATIVE 144 48 4 128 72 NC_002967:TDE2391|3end_peptidyl-prolyl_cis-trans_isomerase_2420582..2420732_NEGATIVE 142 50 6 83 41 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 142 55 14 84 38 NC_002967:TDE0800|3end_acetyltransferase,_GNAT_family_823454..823604_NEGATIVE 140 129 90 38 3 NC_002967:TDE1421|3end_hypothetical_protein_1465810..1465960_POSITIVE 140 92 57 99 67 NC_002967:TDE0618|3end_hypothetical_protein_650242..650392_NEGATIVE 140 29 1 111 82 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 139 43 3 60 13 NC_002967:TDE2612|3end_hypothetical_protein_2655459..2655609_POSITIVE 139 128 93 57 21 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 139 37 1 67 31 NC_002967:TDE1583|3end_hypothetical_protein_1632007..1632157_POSITIVE