Origin IGS: taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta .........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 tacattttttcccctctccgtccatcaagtacttctcttgcaaggtttgtaaacgaaaacgagtatagcggaggatacgaaacaacgagacagtatcttcttctgtatcacatagagcaacaaccttcaatataaagttgtctgacgccttttgtatctgttcttttgtagaacaaaaagagagcattatcttaaagttttctgtttgagtaagtcttagcataatcatatcttttaagttcaacatta Mask Tandem Repeat Region ================================================ taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta Find is-nt database================================================ Query_seq: TF0922:TF0923|TF0922:TF0923:MATE efflux family protein:tetracycline resistance element mobilization regulatory protein:->->:961147..961395 249 taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0922:TF0923|TF0922:TF0923:MATE efflux family protein:tetracycline resistance element mobilization regulatory protein:->->:961147..961395 249 taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0922:TF0923|TF0922:TF0923:MATE efflux family protein:tetracycline resistance element mobilization regulatory protein:->->:961147..961395 249 taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 127 End: 222 .............................................................................................................................. M L L Y V I Q K K I L S R C F V S S A I L V F V Y K P C K R S T ........................... Protein_Len: 60 Strand: + Start: 3 End: 248 .. M L N L K D M I M L R L T Q T E N F K I M L S F C S T K E Q I Q K A S D N F I L K V V A L C D T E E D T V S L F R I L R . Protein_Len: 43 Strand: - Start: 118 End: 246 ..................................................................................................................... I S P Q Q E I H Y L L L Y Q R T T E Y G G S Y E N E N V F R A L S T S S P R L P S F M ... Protein_Len: 44 Strand: - Start: 44 End: 175 ........................................... V S F K L I I S E K Q E V F S C I C F A D S L K I N F T T A R H S V S S S V T E N N R M .......................................................................... taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta 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================================================ taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.9 Tail_Score: -3.35912 Start: 110 End: 129 Full_Region: ACAAAAGGCGTCAGA CAACTTT ATATTG AAGGTTG TTGCTCTATGTGATA .............................................................................................................CAACTTTATATTGAAGGTTG........................................................................................................................ Find igs database================================================ Query_seq: TF0922:TF0923|TF0922:TF0923:MATE efflux family protein:tetracycline resistance element mobilization regulatory protein:->->:961147..961395 249 taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta Intra-Species Hit: Count: 1 Min: 1 Max: 249 Len: 249 Subject: tfor_TF0922_TF0923|MATE efflux family protein:tetracycline resistance element mobilization regulatory protein|POSITIVE:POSITIVE|[961147,961395]|249 HSP 1 e-value: 1.0E-139 bit: 494.0 Len: 249 Query Start:1 Query End:249 Subject Strand: POSITIVE Subject Start: 1 Subject End: 249 taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta taatgttgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatactcgttttcgtttacaaaccttgcaagagaagtacttgatggacggagaggggaaaaaatgta Inter-species Hit: Count: 3 Min: 7 Max: 187 Len: 181 Subject: pint_PI0395_PI0396|Na+-driven multidrug efflux pump:possible tetracycline resistance element mobilization regulatory protein, C-terminal fragment|POSITIVE:POSITIVE|[361845,362132]|288 HSP 1 e-value: 1.0E-38 bit: 161.0 Len: 181 Query Start:7 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 ......tgaacttaaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatac.............................................................. ......tgaacataaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatac.............................................................. Subject: NC_002950_PG1444_PG1446|hypothetical protein:MATE efflux family protein|POSITIVE:NEGATIVE|[1529303,1529997]|695 HSP 1 e-value: 2.0E-37 bit: 157.0 Len: 175 Query Start:13 Query End:187 Subject Strand: NEGATIVE Subject Start: 518 Subject End: 692 ............taaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatac.............................................................. ............taaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatac.............................................................. Subject: NC_002950_PG0827_PG0829|MATE efflux family protein:hypothetical protein|POSITIVE:NEGATIVE|[885665,886359]|695 HSP 1 e-value: 2.0E-37 bit: 157.0 Len: 175 Query Start:13 Query End:187 Subject Strand: POSITIVE Subject Start: 4 Subject End: 178 ............taaaagatatgattatgctaagacttactcaaacagaaaactttaagataatgctctctttttgttctacaaaagaacagatacaaaaggcgtcagacaactttatattgaaggttgttgctctatgtgatacagaagaagatactgtctcgttgtttcgtatcctccgctatac.............................................................. ............taaaagatatgattatgctaagacttactcaaactgaagactttaagacaataatctctttatgctctacaaaaggacagatacaaaaagcgtcagacaactttattctgaagattattgccctatgtgatgcagaaagagatttagtctcattgtttcggaccctccgttatac.............................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACUUAAAAGAUAUGAUUAUGCUAAGACUUACUCAAACAGAAAACUUUAAGAUAAUGCUCUCUUUUUGUUCUACAAAAGAACAGAUACAAAAGGCGUCAGACAACUUUAUAUUGAAGGUUGUUGCUCUAUGUGAUACAGAAGAAGAUACUGUCUCGUUGUUUCGUAUCCUCCGCUAUAC ...........(((((((....((..((((....((....................(((((.....((((((((.....)))))))).......)))))..(((((((((......)))))))))..(((.((.....))..))).))....)))).))....)))))))........... (-30.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUAGCGGAGGAUACGAAACAACGAGACAGUAUCUUCUUCUGUAUCACAUAGAGCAACAACCUUCAAUAUAAAGUUGUCUGACGCCUUUUGUAUCUGUUCUUUUGUAGAACAAAAAGAGAGCAUUAUCUUAAAGUUUUCUGUUUGAGUAAGUCUUAGCAUAAUCAUAUCUUUUAAGUUCA ((((((.(((((((((..............))))))))).)))))).(((.(((((.(((((.((......)).)))))..((..(.....)..)).)))))..))).((((.((((((....(((((.((((..(((.((.....)).)))..)))).)))))....))))))..)))). (-34.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 167 123 58 20 tfor:TF0826|5end_primosomal_protein_N'_883751..883981_POSITIVE 299 168 123 188 138 tfor:TF1797|5end_SNF_family_transporter_1937136..1937366_POSITIVE 297 175 133 101 53 tfor:TF2926|5end_glycine_hydroxymethyltransferase_3128070..3128300_POSITIVE 295 174 137 107 68 tfor:TF0087|5end_ABC_transporter,_permease_component_93185..93415_POSITIVE 286 157 111 102 46 tfor:TF2594|5end_hypothetical_protein_2764176..2764406_POSITIVE 286 170 122 83 33 tfor:TF0261|5end_conserved_hypothetical_protein_291784..292014_POSITIVE 285 167 122 195 147 tfor:TF2782|5end_conserved_hypothetical_protein_2966455..2966685_POSITIVE 285 139 99 45 6 tfor:TF0158|5end_CRISPR-associated_helicase_Cas3_167438..167668_POSITIVE 282 120 73 68 28 tfor:TF0441|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_3_464614..464844_POSITIVE 281 168 133 92 57 tfor:TF0071|5end_conserved_hypothetical_protein_78008..78238_POSITIVE 280 174 132 86 35 tfor:TF1448|5end_possible_competence_protein_1531711..1531941_POSITIVE 269 170 125 189 142 tfor:TF2444|5end_regulatory_protein_RecX_2620957..2621187_POSITIVE 265 178 151 50 10 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 264 135 95 227 191 tfor:TF1598|5end_conserved_hypothetical_protein_1713358..1713588_POSITIVE 261 177 131 229 160 tfor:TF2936|5end_conserved_hypothetical_protein;_possible_ribosomal_subunit_interface_protein_3138522..3138752_POSITIVE 260 177 138 60 14 tfor:TF1465|5end_modulator_of_DNA_gyrase_1554148..1554378_POSITIVE 259 176 151 61 35 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 259 180 141 53 16 tfor:TF0605|5end_conserved_hypothetical_protein_636051..636281_POSITIVE 257 86 47 174 131 tfor:TF0758|5end_peptidyl-tRNA_hydrolase_805307..805537_POSITIVE 256 176 151 54 28 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 167 123 77 39 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 297 175 133 61 13 tfor:TF2925|3end_beta-N-acetylglucosaminidase_3128110..3128260_POSITIVE 295 174 137 96 57 tfor:TF0086|3end_ABC_transporter,_ATP-binding_protein_93254..93404_POSITIVE 286 157 111 88 32 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE 285 139 99 55 16 tfor:TF0157|3end_conserved_hypothetical_protein_167528..167678_POSITIVE 282 120 73 62 22 tfor:TF0440|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_464688..464838_POSITIVE 280 174 132 59 8 tfor:TF1447|3end_D-ribulose-phosphate-3_epimerase_1531764..1531914_POSITIVE 259 180 141 118 81 tfor:TF0604|3end_hypothetical_protein_636196..636346_POSITIVE 257 86 47 80 37 tfor:TF0757|3end_50S_ribosomal_protein_L25;_general_stress_protein_805293..805443_POSITIVE 256 170 121 112 61 tfor:TF1360|3end_conserved_hypothetical_protein_1441242..1441392_POSITIVE 256 176 151 119 93 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 254 130 83 121 75 tfor:TF1651|3end_integrase_1762602..1762752_POSITIVE 253 176 133 132 91 tfor:TF2523|3end_NAD(P)H-flavin_oxidoreductase_2702916..2703066_POSITIVE 252 179 132 132 76 tfor:TF1813|3end_peptide_methionine_sulfoxide_reductase_1955293..1955443_POSITIVE 252 177 138 98 56 tfor:TF1468|3end_beta-galactosidase_1561251..1561401_POSITIVE 250 175 136 64 30 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE 250 166 125 50 5 tfor:TF2019|3end_dipeptidyl_peptidase_VI_2176401..2176551_POSITIVE 247 177 144 31 1 tfor:TF0228|3end_probable_integral_outer_membrane_protein_254809..254959_POSITIVE 246 176 148 146 105 tfor:TF2610|3end_nitroreductase_2787241..2787391_POSITIVE 244 158 119 139 94 tfor:TF2040|3end_transcription_elongation_factor_2200280..2200430_POSITIVE