Origin IGS: caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc .........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 ggcttcctccttttgctatgtaaaacaaactttacttttcaaatatagtatagctacctttacatcttttgtcaagaagaaagcggcaaaaaaagaggctgggacaaaagtcctagcctctcaattgtctttggattgtcgagcaagacgcagtggttgagtgggctctactacgctgatttcatcagcttttacagccctactcaactgtgcggaggtgggacgacgaaatcgaattctaacgaattaccgatttctgtcccactctcttttatcatctttattgatttcctttg Mask Tandem Repeat Region ================================================ caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc Find is-nt database================================================ Query_seq: SSA_0205:SSA_2393|SSA_0205:SSA_2393:NisK (sensor-receptor histidine kinase domain), putative:Transcriptional regulator, XRE family, putative:->->:203900..204195 296 caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0205:SSA_2393|SSA_0205:SSA_2393:NisK (sensor-receptor histidine kinase domain), putative:Transcriptional regulator, XRE family, putative:->->:203900..204195 296 caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0205:SSA_2393|SSA_0205:SSA_2393:NisK (sensor-receptor histidine kinase domain), putative:Transcriptional regulator, XRE family, putative:->->:203900..204195 296 caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 60 End: 173 ........................................................... M R F R R P T S A Q L S R A V K A D E I S V V E P T Q P L R L A R Q S K D N ........................................................................................................................... Protein_Len: 36 Strand: - Start: 140 End: 247 ........................................................................................................................................... G S R R A R C D L S L Q S A L V K T G A E K K A A K K K V F S T F T A M ................................................. Protein_Len: 60 Strand: - Start: 3 End: 233 .. N S N S K T T G G G C L Q T P S Y F S I F D A Y Y L G S L W Q T K S S L G F V I S L S P S K D W G R K K G S E E Q C F M ............................................................... Protein_Len: 45 Strand: - Start: 2 End: 136 . F S I L L S S L L S H S L F R Y N T L I R N R R G V E A C N L L A T F A S S I L T T S G M ................................................................................................................................................................ caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc 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: 87 Start: 221 End: 250 ............................................................................................................................................................................................................................CTTGACAAAAGATGTAAAGGTAGCTATACT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -8.6 Tail_Score: -4.08945 Start: 108 End: 122 Full_Region: agtgggctctactac gctgat ttc atcagc ttttacagccctact ...........................................................................................................gctgatttcatcagc.............................................................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -13.3 Tail_Score: -5.4477 Start: 177 End: 202 Full_Region: TCCAAAGACAATTGA GAGGCTAGGAC TTTT GTCCCAGCCTC TTTTTTTGCCGCTTT ................................................................................................................................................................................GAGGCTAGGACTTTTGTCCCAGCCTC.............................................................................................. TransTerm Strand: - Conf: 100 HP_score: -15.5 Tail_Score: -2.68952 Start: 177 End: 202 Full_Region: aaagcggcaaaaaaa gaggctgggac aaaa gtcctagcctc tcaattgtctttgga ................................................................................................................................................................................gaggctgggacaaaagtcctagcctc.............................................................................................. Find igs database================================================ Query_seq: SSA_0205:SSA_2393|SSA_0205:SSA_2393:NisK (sensor-receptor histidine kinase domain), putative:Transcriptional regulator, XRE family, putative:->->:203900..204195 296 caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc Intra-Species Hit: Count: 2 Min: 1 Max: 296 Len: 296 Subject: NC_009009_SSA_0205_SSA_2393|NisK (sensor-receptor histidine kinase domain), putative:Transcriptional regulator, XRE family, putative|POSITIVE:POSITIVE|[203900,204195]|296 HSP 1 e-value: 1.0E-154 bit: 545.0 Len: 296 Query Start:1 Query End:296 Subject Strand: POSITIVE Subject Start: 1 Subject End: 296 caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctcnnnnnnngccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc caaaggaaatcaataaagatgataaaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccagcctctttttttgccgctttcttcttgacaaaagatgtaaaggtagctatactatatttgaaaagtaaagtttgttttacatagcaaaaggaggaagcc Subject: NC_009009_SSA_1008_SSA_1009|Galactokinase, putative:Galactose-1-phosphate-uridylyltransferase, putative|POSITIVE:POSITIVE|[1011175,1011393]|219 HSP 1 e-value: 3.0E-89 bit: 329.0 Len: 174 Query Start:25 Query End:198 Subject Strand: NEGATIVE Subject Start: 23 Subject End: 196 ........................aaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccag.................................................................................................. ........................aaagagagtgggacagaaatcggtaattcgttagaattcgatttcgtcgtcccacctccgcacagttgattagggctgtaaaagctgatgaaatcagcgtaatagagcccactcaaccactgcgtcttgctcgacaatccaaagacaattgagaggctaggacttttgtcccag.................................................................................................. Inter-species Hit: Count: 1 Min: 30 Max: 142 Len: 113 Subject: NC_004116_SAG0025_SAG0026|phosphoribosylformylglycinamidine synthase, putative:amidophosphoribosyltransferase|POSITIVE:POSITIV E|[40309,40719]|411 HSP 1 e-value: 3.0E-15 bit: 83.8 Len: 113 Query Start:30 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 .............................gagtgggacagaaatcggtaattcgttag-aattcgatttcgtcgtcccacctccgcacagttgagtagggctgtaaaagctgatgaaatcagcgtagtagagcccactcaacc.......................................................................................................................................................... .............................gagtgggacaaaaatcggtaattccaaaggaattcgattttgtcgtccc-cctccgcacagttgagtggggctgtaagagttgat-ttatcagcgaattagagcccactcaacc.......................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUGGGACAGAAAUCGGUAAUUCGUUAGAAUUCGAUUUCGUCGUCCCACCUCCGCACAGUUGAGUAGGGCUGUAAAAGCUGAUGAAAUCAGCGUAGUAGAGCCCACUCAACC (((((((((.((((((((..((((....))))))))))))...)))))).)))......(((((((.(((((.((...((((((...))))))....)).)))))))))))). (-52.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUGAGUGGGCUCUACUACGCUGAUUUCAUCAGCUUUUACAGCCCUACUCAACUGUGCGGAGGUGGGACGACGAAAUCGAAUUCUAACGAAUUACCGAUUUCUGUCCCACUC (((((((((((((.((..(.((((((...)))))))..)).))))).)))))))).......(((((((((..((((((((((((....)))))..)))))))))))))))). (-51.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 950 60 11 179 130 NC_009009:SSA_1009|5end_Galactose-1-phosphate-uridylyltransferase,_putative_1011254..1011484_POSITIVE 368 50 1 175 132 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 361 80 36 135 83 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 349 56 16 172 126 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 348 84 42 59 18 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 330 105 63 61 21 NC_009009:SSA_2165|5end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2161734..2161964_POSITIVE 326 50 1 168 122 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 324 106 65 176 124 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 324 74 32 205 163 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 317 80 32 141 74 NC_009009:SSA_0537|5end_Propanediol_utilization:dioldehydratase_reactivation,_putative_531957..532187_POSITIVE 317 74 32 214 159 NC_009009:SSA_0354|5end_Uncharacterized_membrane_protein_346241..346471_POSITIVE 313 60 16 182 130 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 313 74 35 191 147 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 311 81 51 62 25 NC_009009:SSA_1729|5end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1715699..1715929_NEGATIVE 311 79 35 75 42 NC_009009:SSA_0549|5end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_543556..543786_POSITIVE 311 99 51 231 184 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 310 86 45 129 92 NC_009009:SSA_0246|5end_Conserved_uncharacterized_protein_239703..239933_POSITIVE 306 70 22 183 135 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 305 70 25 120 74 NC_009009:SSA_1554|5end_hypothetical_protein_1555949..1556179_POSITIVE 304 97 51 54 7 NC_009009:SSA_1041|5end_Sugar_ABC_transporter,_permease_protein,_putative_1056398..1056628_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 50 1 59 9 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 368 50 1 149 106 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 361 80 36 145 93 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 348 84 42 53 12 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 305 70 25 123 77 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE 304 67 32 123 90 NC_009009:SSA_1402|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1414481..1414631_NEGATIVE 304 97 51 52 5 NC_009009:SSA_1040|3end_Sugar_ABC_transporter,_permease_protein,_putative_1056476..1056626_POSITIVE 304 82 43 128 74 NC_009009:SSA_0049|3end_Dihydroxyacetone_kinase_(Dak1),_putative_54681..54831_POSITIVE 300 93 51 87 46 NC_009009:SSA_2197|3end_hypothetical_protein_2197314..2197464_NEGATIVE 298 82 41 113 68 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 294 107 68 70 16 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 291 74 47 35 4 NC_009009:SSA_2027|3end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2033109..2033259_NEGATIVE 288 86 42 89 40 NC_009009:SSA_1482|3end_Pullulanase,_putative_1486949..1487099_NEGATIVE 288 110 62 123 80 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 286 77 31 140 93 NC_009009:SSA_0949|3end_hypothetical_protein_956395..956545_POSITIVE 282 110 63 149 99 NC_009009:SSA_0843|3end_hypothetical_protein_828478..828628_POSITIVE 279 60 14 137 93 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 277 70 42 121 80 NC_009009:SSA_2304|3end_Conserved_uncharacterized_protein_2305185..2305335_NEGATIVE 277 72 40 44 9 NC_009009:SSA_2208|3end_Preprotein_translocase_secE_component,_putative_2207734..2207884_NEGATIVE 277 55 25 116 82 NC_009009:SSA_1303|3end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322474..1322624_NEGATIVE