Origin IGS: taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actcttttggttttaatcgtgatacattctattggtcacttcaatataggcatattcacttctttgaaagaatctgccttttatcggatattggtacagctatggggttacttccgcataggcacgacctcctgcctatgtattccggcagaggttctcattttcgtttatcaggacaatcgttcgattgcatccacttttgtacatttatacgttcgaggatctcgttcatcgagagtggatattatcgaagatatataccctcgcagacacattcgacaatgcaaaaatatggctttatggtactgttgtcagtagctttttgctaactgcgtacttgtggcttcgatttgcgtatttgtgaccctgtgaaaggtaagtggttta Mask Tandem Repeat Region ================================================ taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt Find is-nt database================================================ Query_seq: TF0925:TF0926|TF0925:TF0926:hypothetical protein:conserved hypothetical protein; possible TraB protein:->->:962188..962574 387 taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0925:TF0926|TF0925:TF0926:hypothetical protein:conserved hypothetical protein; possible TraB protein:->->:962188..962574 387 taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0925:TF0926|TF0925:TF0926:hypothetical protein:conserved hypothetical protein; possible TraB protein:->->:962188..962574 387 taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 95 End: 214 .............................................................................................. M F L H C R M C L R G Y I S S I I S T L D E R D P R T Y K C T K V D A I E R L S ............................................................................................................................................................................. Protein_Len: 31 Strand: + Start: 237 End: 329 ............................................................................................................................................................................................................................................ M P E Y I G R R S C L C G S N P I A V P I S D K R Q I L S K K .......................................................... Protein_Len: 60 Strand: - Start: 73 End: 381 ........................................................................ S R N D Q Y V F I L V E A P I C L C S T T G I R F Y G W L Q V L I R Y F A S E K L S T F I G I N F H G I S H I V I L V M ...... Protein_Len: 60 Strand: - Start: 62 End: 334 ............................................................. I F S I R S R I F T C F H I C D F S Q G S L R F H S G R G S Y M P L L D H R H P L L G M A T G I D S L L C I R E F F H M ..................................................... Protein_Len: 60 Strand: - Start: 27 End: 218 .......................... R L W L Y A T L L F S S V V T G Y L W I K A N D F T D A L T Y I K S L I W E R H V L D E F T Y I Y L L P H L R V I T R M ......................................................................................................................................................................... taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt 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: 81 Start: 296 End: 325 .......................................................................................................................................................................................................................................................................................................TTTGAAAGAATCTGCCTTTTATCGGATATT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -9.6 Tail_Score: -3.01791 Start: 248 End: 271 Full_Region: atggggttacttccg cataggcacg acct cctgcctatg tattccggcagaggt .......................................................................................................................................................................................................................................................cataggcacgacctcctgcctatg.................................................................................................................... Find igs database================================================ Query_seq: TF0925:TF0926|TF0925:TF0926:hypothetical protein:conserved hypothetical protein; possible TraB protein:->->:962188..962574 387 taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt Intra-Species Hit: Count: 1 Min: 1 Max: 387 Len: 387 Subject: tfor_TF0925_TF0926|hypothetical protein:conserved hypothetical protein; possible TraB protein|POSITIVE:POSITIVE|[962188,962574]|387 HSP 1 e-value: 0.0 bit: 767.0 Len: 387 Query Start:1 Query End:387 Subject Strand: POSITIVE Subject Start: 1 Subject End: 387 taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt taaaccacttacctttcacagggtcacaaatacgcaaatcgaagccacaagtacgcagttagcaaaaagctactgacaacagtaccataaagccatatttttgcattgtcgaatgtgtctgcgagggtatatatcttcgataatatccactctcgatgaacgagatcctcgaacgtataaatgtacaaaagtggatgcaatcgaacgattgtcctgataaacgaaaatgagaacctctgccggaatacataggcaggaggtcgtgcctatgcggaagtaaccccatagctgtaccaatatccgataaaaggcagattctttcaaagaagtgaatatgcctatattgaagtgaccaatagaatgtatcacgattaaaaccaaaagagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACCACUUACCUUUCACAGGGUCACAAAUACGCAAAUCGAAGCCACAAGUACGCAGUUAGCAAAAAGCUACUGACAACAGUACCAUAAAGCCAUAUUUUUGCAUUGUCGAAUGUGUCUGCGAGGGUAUAUAUCUUCGAUAAUAUCCACUCUCGAUGAACGAGAUCCUCGAACGUAUAAAUGUACAAAAGUGGAUGCAAUCGAACGAUUGUCCUGAUAAACGAAAAUGAGAACCUCUGCCGGAAUACAUAGGCAGGAGGUCGUGCCUAUGCGGAAGUAACCCCAUAGCUGUACCAAUAUCCGAUAAAAGGCAGAUUCUUUCAAAGAAGUGAAUAUGCCUAUAUUGAAGUGACCAAUAGAAUGUAUCACGAUUAAAACCAAAAGAGU .........(((..(((....((((((......(((((.....((.....((((.((((.(((.....)))))))......))))......))......))))).((((((.((((.((((((.((((((..(((((((((..((((((((.((((.((......)).))))..((((....))))...))))))))..)))))).))).......................(((((((((..........)))).))))).)))))).)))))).....................)))).)))))).(((((.((((((((...)))).)))).)))))........))))))....))).)))...................... (-94.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUUUUGGUUUUAAUCGUGAUACAUUCUAUUGGUCACUUCAAUAUAGGCAUAUUCACUUCUUUGAAAGAAUCUGCCUUUUAUCGGAUAUUGGUACAGCUAUGGGGUUACUUCCGCAUAGGCACGACCUCCUGCCUAUGUAUUCCGGCAGAGGUUCUCAUUUUCGUUUAUCAGGACAAUCGUUCGAUUGCAUCCACUUUUGUACAUUUAUACGUUCGAGGAUCUCGUUCAUCGAGAGUGGAUAUUAUCGAAGAUAUAUACCCUCGCAGACACAUUCGACAAUGCAAAAAUAUGGCUUUAUGGUACUGUUGUCAGUAGCUUUUUGCUAACUGCGUACUUGUGGCUUCGAUUUGCGUAUUUGUGACCCUGUGAAAGGUAAGUGGUUUA .((((.((((........(((((.((......)))))))....(((((((((.......(((..((((((.......))))))..)))....(((...((((((.((......)).)))).))...)))...)))))))))...)))).))))(((((.((........)).))))).(((.((((((...(((((((((((...........(..((((...))))..)..)))))))))))...)))))))))...((((.((((((.((((.......(((((((.....((((....(((((....(.(((((((.....))).))))))))))...))))....)))))))...))))...))))))..))))......... (-100.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 443 273 231 50 15 tfor:TF0298|5end_dipeptidase_323127..323357_POSITIVE 393 280 234 72 27 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 389 279 239 171 121 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 389 279 239 131 81 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 384 277 234 231 177 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 383 274 231 67 18 tfor:TF2895|5end_hypothetical_protein_3083936..3084166_POSITIVE 381 275 231 78 34 tfor:TF3155|5end_glycosyltransferase,_group_2_family_protein_3390417..3390647_POSITIVE 380 280 234 226 184 tfor:TF2699|5end_hypothetical_protein_2872490..2872720_POSITIVE 380 280 234 211 169 tfor:TF2698|5end_hypothetical_protein_2872475..2872705_POSITIVE 379 61 23 224 186 tfor:TF0022|5end_two-component_system_sensor_histidine_kinase_17295..17525_POSITIVE 376 78 38 222 183 tfor:TF1291|5end_response_regulator_(fimR__protein)_1371959..1372189_POSITIVE 372 290 241 108 54 tfor:TF2351|5end_acetate_kinase_2515480..2515710_POSITIVE 372 277 234 221 174 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 370 269 221 156 101 tfor:TF0390|5end_conserved_hypothetical_protein_409263..409493_POSITIVE 367 274 231 90 52 tfor:TF0013|5end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_6414..6644_POSITIVE 366 278 233 139 69 tfor:TF3067|5end_conserved_hypothetical_protein_3292432..3292662_POSITIVE 361 277 235 54 3 tfor:TF0252|5end_hypothetical_protein_283530..283760_POSITIVE 354 274 235 70 21 tfor:TF1902|5end_two-component_system_sensor_histidine_kinase_2057521..2057751_POSITIVE 353 276 234 214 163 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 352 277 234 44 4 tfor:TF2154|5end_conserved_hypothetical_protein_2329153..2329383_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 402 58 15 150 101 tfor:TF3127|3end_acetyltransferase,_possible_GNAT_family_3362234..3362384_POSITIVE 381 275 231 70 26 tfor:TF3154|3end_conserved_hypothetical_protein_3390489..3390639_POSITIVE 380 272 239 149 109 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 370 269 221 149 94 tfor:TF0389|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_409336..409486_POSITIVE 354 274 235 96 47 tfor:TF1903|3end_hypothetical_protein_2057627..2057777_POSITIVE 347 276 234 118 59 tfor:TF1841|3end_hypothetical_protein_1992267..1992417_POSITIVE 342 280 232 71 14 tfor:TF0093|3end_outer_membrane_protein,_TonB_dependent_receptor_103618..103768_POSITIVE 336 275 237 91 44 tfor:TF1852|3end_prtQ_protein_2006546..2006696_POSITIVE 333 288 241 63 19 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 329 277 235 50 5 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 328 295 251 83 32 tfor:TF2456|3end_ABC_transporter,_ATP-binding_protein_2633208..2633358_POSITIVE 326 277 235 62 27 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 323 277 237 74 37 tfor:TF0855|3end_membrane_protein,_possible_exporter_908199..908349_POSITIVE 318 264 223 66 15 tfor:TF0657|3end_conserved_hypothetical_protein_703881..704031_POSITIVE 317 275 238 144 104 tfor:TF1448|3end_possible_competence_protein_1533050..1533200_POSITIVE 317 237 193 75 24 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 313 290 254 128 68 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 312 268 226 59 1 tfor:TF2154|3end_conserved_hypothetical_protein_2329529..2329679_POSITIVE 311 296 252 151 107 tfor:TF0596|3end_conserved_hypothetical_protein_628652..628802_POSITIVE 309 276 237 46 3 tfor:TF2897|3end_iron(III)_ABC_transporter,_permease_component_3087096..3087246_POSITIVE