Origin IGS: tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat .........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 attaatcgactcctttctgtttgattgttgatactgcttgcaaaattattatttttatcattaaattcgacttttttcaaaaaaaaataaagaaatatgccttttttgattaagttggtatttttttagtctgttatggctttggcttttatcaatcgattcgtgtctttatatcacttttaaagtggttttagaataaattgtagtaatttttgtgtgaattagaggtgggaaaactgttttttatatacgaacggataaaaattgaggtcagaatatccgataaggatttagccctgcttcaaatggaacgtttatgtattataaggtgttttgaataaagacaaggtatgaagtaaaataaacaagagggtgaacttcaatcgattaccctcttgtccatattctttttataaatgtaagaaaatcta Mask Tandem Repeat Region ================================================ tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat Find is-nt database================================================ Query_seq: TF1219:TF1220|TF1219:TF1220:conserved hypothetical protein:conserved hypothetical protein:->->:1305867..1306297 431 tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1219:TF1220|TF1219:TF1220:conserved hypothetical protein:conserved hypothetical protein:->->:1305867..1306297 431 tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1219:TF1220|TF1219:TF1220:conserved hypothetical protein:conserved hypothetical protein:->->:1305867..1306297 431 tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 276 End: 368 ................................................................................................................................................................................................................................................................................... M D K S Q S H N R L K K Y Q L N Q K R H I S L F F F E K S R I ............................................................... Protein_Len: 36 Strand: + Start: 322 End: 429 ................................................................................................................................................................................................................................................................................................................................. M K K G I F L Y F F L K K V E F N D K N N N F A S S I N N Q T E R S R L .. Protein_Len: 30 Strand: - Start: 322 End: 411 ................................................................................................................................................................................................................................................................................................................................. D F F A Y K K I K K Q F F D F K I I F I I I K C A T D V I M .................... Protein_Len: 42 Strand: - Start: 94 End: 219 ............................................................................................. E F C R I I C L R E M Q L L A L D K D S I R V E I K I R E Y I F F L K G V E L E C M .................................................................................................................................................................................................................... tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat 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: 84 Start: 70 End: 99 .....................................................................TTTGAATAAAGACAAGGTATGAAGTAAAAT............................................................................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 351 End: 380 ..............................................................................................................................................................................................................................................................................................................................................................TTTGAAAAAAGTCGAATTTAATGATAAAAA................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 210 End: 239 .................................................................................................................................................................................................................ATTCACACAAAAATTACTACAATTTATTCT................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 53 HP_score: -3.3 Tail_Score: -3.86816 Start: 30 End: 70 Full_Region: aggtatgaagtaaaa taaacaagagggtgaac ttcaatc gattaccctcttgtcca tattctttttataaa .............................taaacaagagggtgaacttcaatcgattaccctcttgtcca......................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 77 HP_score: -6.3 Tail_Score: -4.78981 Start: 34 End: 66 Full_Region: TAAAAAGAATATGGA CAAGAGGGTAATC GATTGAA GTTCACCCTCTTG TTTATTTTACTTCAT .................................CAAGAGGGTAATCGATTGAAGTTCACCCTCTTG............................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 53 HP_score: -4.4 Tail_Score: -3.45634 Start: 37 End: 63 Full_Region: aagtaaaataaacaa gagggtgaac ttcaatc gattaccctc ttgtccatattcttt ....................................gagggtgaacttcaatcgattaccctc................................................................................................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TF1219:TF1220|TF1219:TF1220:conserved hypothetical protein:conserved hypothetical protein:->->:1305867..1306297 431 tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat Intra-Species Hit: Count: 1 Min: 1 Max: 431 Len: 431 Subject: tfor_TF1219_TF1220|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1305867,1306297]|431 HSP 1 e-value: 0.0 bit: 759.0 Len: 431 Query Start:1 Query End:431 Subject Strand: POSITIVE Subject Start: 1 Subject End: 431 tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactnnnnnnntaccaacttaatcaaaaaaggcatatttctttannnnnnnnngaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat tagattttcttacatttataaaaagaatatggacaagagggtaatcgattgaagttcaccctcttgtttattttacttcataccttgtctttattcaaaacaccttataatacataaacgttccatttgaagcagggctaaatccttatcggatattctgacctcaatttttatccgttcgtatataaaaaacagttttcccacctctaattcacacaaaaattactacaatttattctaaaaccactttaaaagtgatataaagacacgaatcgattgataaaagccaaagccataacagactaaaaaaataccaacttaatcaaaaaaggcatatttctttatttttttttgaaaaaagtcgaatttaatgataaaaataataattttgcaagcagtatcaacaatcaaacagaaaggagtcgattaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUUUUCUUACAUUUAUAAAAAGAAUAUGGACAAGAGGGUAAUCGAUUGAAGUUCACCCUCUUGUUUAUUUUACUUCAUACCUUGUCUUUAUUCAAAACACCUUAUAAUACAUAAACGUUCCAUUUGAAGCAGGGCUAAAUCCUUAUCGGAUAUUCUGACCUCAAUUUUUAUCCGUUCGUAUAUAAAAAACAGUUUUCCCACCUCUAAUUCACACAAAAAUUACUACAAUUUAUUCUAAAACCACUUUAAAAGUGAUAUAAAGACACGAAUCGAUUGAUAAAAGCCAAAGCCAUAACAGACUAAAAAAAUACCAACUUAAUCAAAAAAGGCAUAUUUCUUUAUUUUUUUUUGAAAAAAGUCGAAUUUAAUGAUAAAAAUAAUAAUUUUGCAAGCAGUAUCAACAAUCAAACAGAAAGGAGUCGAUUAAU ......(((((...........))))).(((((((((((((((((........))).))))))))))))))...(((((...(((((.(((((.....(((...((((.....))))..))).....))))))))))....((((.....)))).(((((......(((((((((.(((..(((((.................................(((((.....)))))..........((((.....)))))))))..))).....((((((.......((....)).............................((((((((((.(((......)))))))))))))....)))))).......))))))))).......(((....)))..............))))).)))))........ (-62.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAUCGACUCCUUUCUGUUUGAUUGUUGAUACUGCUUGCAAAAUUAUUAUUUUUAUCAUUAAAUUCGACUUUUUUCAAAAAAAAAUAAAGAAAUAUGCCUUUUUUGAUUAAGUUGGUAUUUUUUUAGUCUGUUAUGGCUUUGGCUUUUAUCAAUCGAUUCGUGUCUUUAUAUCACUUUUAAAGUGGUUUUAGAAUAAAUUGUAGUAAUUUUUGUGUGAAUUAGAGGUGGGAAAACUGUUUUUUAUAUACGAACGGAUAAAAAUUGAGGUCAGAAUAUCCGAUAAGGAUUUAGCCCUGCUUCAAAUGGAACGUUUAUGUAUUAUAAGGUGUUUUGAAUAAAGACAAGGUAUGAAGUAAAAUAAACAAGAGGGUGAACUUCAAUCGAUUACCCUCUUGUCCAUAUUCUUUUUAUAAAUGUAAGAAAAUCUA ....((((((.....((.....))..))))))....((((((........(((((((((.......(((((((...((((((((..(((......)))...))))))))..))))))).............((((.((((((..(.(((((((...(((((..(.(((....((((((.....))))))...))))..)))))........((((((((....(((((..(.....)..)))))..))))))))..))))))).)..)))))).))))...)))))))))...............(((((...(((((...(((((...((((((.....))))))...))))).))))).....(((((((((((.(.......).))))))))))))))))..............))))))........ (-90.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 159 119 66 13 tfor:TF1783|5end_conserved_hypothetical_protein_1923408..1923638_POSITIVE 314 69 21 147 95 tfor:TF2000|5end_conserved_hypothetical_protein_2153931..2154161_POSITIVE 277 155 118 157 122 tfor:TF2289|5end_secretion_protein,_possible_HlyD_family_2442725..2442955_POSITIVE 275 180 135 198 147 tfor:TF0506|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_helicase_531031..531261_POSITIVE 274 66 23 83 18 tfor:TF2409|5end_hypothetical_protein_2582972..2583202_POSITIVE 274 178 132 81 29 tfor:TF0146|5end_glutamine-dependent_NAD(+)_synthetase_154855..155085_POSITIVE 273 165 126 61 26 tfor:TF0973|5end_conserved_hypothetical_protein_1023263..1023493_POSITIVE 272 68 27 107 72 tfor:TF3155|5end_glycosyltransferase,_group_2_family_protein_3390417..3390647_POSITIVE 269 427 391 76 39 tfor:TF0279|5end_conserved_hypothetical_protein_307142..307372_POSITIVE 268 163 123 89 58 tfor:TF2340|5end_hypothetical_protein_2500665..2500895_POSITIVE 267 162 121 231 180 tfor:TF3126|5end_glycosyltransferase,_group_2_family_3360439..3360669_POSITIVE 267 152 119 174 144 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 264 160 113 63 14 tfor:TF2215|5end_conserved_hypothetical_protein_2387501..2387731_POSITIVE 263 138 101 198 159 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 262 277 231 67 22 tfor:TF2658|5end_transposase_2831155..2831385_POSITIVE 262 277 231 67 22 tfor:TF2541|5end_transposase_2723914..2724144_POSITIVE 262 160 116 166 130 tfor:TF0886|5end_conjugative_transposon_protein_fragment_937914..938144_POSITIVE 261 168 121 168 121 tfor:TF1317|5end_hypothetical_protein_1391378..1391608_POSITIVE 259 160 119 203 169 tfor:TF1808|5end_DNA_processing_protein_subunit_A_1949356..1949586_POSITIVE 253 160 114 182 139 tfor:TF2661|5end_hypothetical_protein_2833509..2833739_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 70 29 61 20 tfor:TF1219|3end_conserved_hypothetical_protein_1305806..1305956_POSITIVE 314 69 21 70 18 tfor:TF1999|3end_ArgK_protein_with_ATPase_and_kinase_domains_2153934..2154084_POSITIVE 273 168 122 105 42 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 272 68 27 99 64 tfor:TF3154|3end_conserved_hypothetical_protein_3390489..3390639_POSITIVE 269 427 391 48 11 tfor:TF0278|3end_conserved_hypothetical_protein_307194..307344_POSITIVE 263 160 118 46 1 tfor:TF2214|3end_peptidyl-prolyl_cis-trans_isomerase_2387564..2387714_POSITIVE 259 160 119 151 115 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 259 90 44 88 44 tfor:TF0100|3end_conserved_hypothetical_protein_111703..111853_POSITIVE 253 160 114 133 90 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 251 188 143 75 24 tfor:TF1115|3end_lantibiotic_biosynthesis_protein_1186544..1186694_POSITIVE 251 164 123 41 1 tfor:TF0382|3end_transcription_termination_factor_405228..405378_POSITIVE 250 182 143 74 33 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 250 164 129 81 44 tfor:TF1585|3end_hypothetical_protein_1690610..1690760_POSITIVE 250 164 129 74 37 tfor:TF1584|3end_hypothetical_protein_1690603..1690753_POSITIVE 249 65 26 107 60 tfor:TF1667|3end_biotin_acetyl-CoA_carboxylase_ligase/biotin_operon_repressor_bifunctional_protein_1780311..1780461_POSITIVE 247 180 131 123 62 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 246 181 142 125 96 tfor:TF0977|3end_possible_outer_membrane_protein_1029436..1029586_POSITIVE 246 154 115 60 19 tfor:TF0054|3end_possible_flavodoxin_58460..58610_POSITIVE 244 65 28 119 69 tfor:TF1445|3end_RNA_polymerase_sigma_factor_1530718..1530868_POSITIVE 242 67 30 58 18 tfor:TF2804|3end_conserved_hypothetical_protein_2994449..2994599_POSITIVE