Origin IGS: tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat .........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 attaattgcctcatttctttattttcaagcaaaacaaaagcccacacacagaaaaaatctgtgtgagggcgtataatcgcggtgccacctcaattatggagcaaagtatagactgcctccatatctctgtcttgtctaacaacaagttgcactgtaaggtgtgctcaccgaatttttattgcttcaaattcattttttacatcagcccacttcataatcccccactacctgtttccaccaaccacaggctccctgaaagtagaaaaattattacttttctgatgatttattttattataggcctttccctttttcttgtcaagaaaaaatttaattttttcttctaaacccgaactttttcttca Mask Tandem Repeat Region ================================================ tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat Find is-nt database================================================ Query_seq: SSA_0629:SSA_0631|SSA_0629:SSA_0631:hypothetical protein:Tryptophan synthase beta chain, putative:->->:619647..620011 365 tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0629:SSA_0631|SSA_0629:SSA_0631:hypothetical protein:Tryptophan synthase beta chain, putative:->->:619647..620011 365 tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0629:SSA_0631|SSA_0629:SSA_0631:hypothetical protein:Tryptophan synthase beta chain, putative:->->:619647..620011 365 tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 31 End: 138 .............................. M K F F L D K K K G K A Y N K I N H Q K S N N F S T F R E P V V G G N R ................................................................................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 221 End: 352 ............................................................................................................................................................................................................................ M L L D K T E I W R Q S I L C S I I E V A P R L Y A L T Q I F S V C G L L F C L K I K K ............. Protein_Len: 53 Strand: - Start: 87 End: 245 ...................................................................................... F L L L K E V K L S G T T P P F L Y H P I I F H A S T F F S N S A I F I R H A C R V T C S T T L C S L S M ........................................................................................................................ Protein_Len: 60 Strand: - Start: 22 End: 360 ..................... F C Y F N P S C V K C H L K N N S L V S I H L C D I S Q E M I S T A G R N Y A R V C I K E T H P S K N Q K F I F F H P M ..... tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat 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: 89 Start: 43 End: 72 ..........................................CTTGACAAGAAAAAGGGAAAGGCCTATAAT..................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.5 Tail_Score: -5.18643 Start: 296 End: 326 Full_Region: GCACCGCGATTATAC GCCCTCACACAGA TTTTT TCTGTGTGTGGGC TTTTGTTTTGCTTGA .......................................................................................................................................................................................................................................................................................................GCCCTCACACAGATTTTTTCTGTGTGTGGGC....................................... Find igs database================================================ Query_seq: SSA_0629:SSA_0631|SSA_0629:SSA_0631:hypothetical protein:Tryptophan synthase beta chain, putative:->->:619647..620011 365 tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat Intra-Species Hit: Count: 2 Min: 1 Max: 365 Len: 365 Subject: NC_009009_SSA_0629_SSA_0631|hypothetical protein:Tryptophan synthase beta chain, putative|POSITIVE:POSITIVE|[619647,620011]|365 HSP 1 e-value: 0.0 bit: 724.0 Len: 365 Query Start:1 Query End:365 Subject Strand: POSITIVE Subject Start: 1 Subject End: 365 tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat tgaagaaaaagttcgggtttagaagaaaaaattaaattttttcttgacaagaaaaagggaaaggcctataataaaataaatcatcagaaaagtaataatttttctactttcagggagcctgtggttggtggaaacaggtagtgggggattatgaagtgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatggaggcagtctatactttgctccataattgaggtggcaccgcgattatacgccctcacacagattttttctgtgtgtgggcttttgttttgcttgaaaataaagaaatgaggcaattaat Subject: NC_009009_SSA_0907_SSA_0908|Fibronectin-binding protein A, putative:ABC-type uncharacterized transport system, periplasmic component, putative|NEGATIVE:POSITIVE|[919308,919839]|532 HSP 1 e-value: 4.0E-18 bit: 93.7 Len: 91 Query Start:157 Query End:247 Subject Strand: POSITIVE Subject Start: 262 Subject End: 352 ............................................................................................................................................................tgggctgatgtaaaaaatgaatttgaagcaataaaaattcggtgagcacaccttacagtgcaacttgttgttagacaagacagagatatgg...................................................................................................................... ............................................................................................................................................................tgggctaatggataaaatgaatttgaaacaataagaattcggtgggcacaccttacagtgcagcttgtttgatgacaagacagagatatgg...................................................................................................................... HSP 2 e-value: 6.0E-11 bit: 69.9 Len: 43 Query Start:266 Query End:308 Subject Strand: POSITIVE Subject Start: 369 Subject End: 410 .........................................................................................................................................................................................................................................................................tccataattgaggtggcaccgcgattatacgccctcacacaga......................................................... .........................................................................................................................................................................................................................................................................tccataattgaggtggcaccgcgatt-tacgccctcacacaga......................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAGAAAAAGUUCGGGUUUAGAAGAAAAAAUUAAAUUUUUUCUUGACAAGAAAAAGGGAAAGGCCUAUAAUAAAAUAAAUCAUCAGAAAAGUAAUAAUUUUUCUACUUUCAGGGAGCCUGUGGUUGGUGGAAACAGGUAGUGGGGGAUUAUGAAGUGGGCUGAUGUAAAAAAUGAAUUUGAAGCAAUAAAAAUUCGGUGAGCACACCUUACAGUGCAACUUGUUGUUAGACAAGACAGAGAUAUGGAGGCAGUCUAUACUUUGCUCCAUAAUUGAGGUGGCACCGCGAUUAUACGCCCUCACACAGAUUUUUUCUGUGUGUGGGCUUUUGUUUUGCUUGAAAAUAAAGAAAUGAGGCAAUUAAU ...........(((..(((.((((((((........)))))))).)))..)))..........((((..............((((((.......(((((.(..(((((........((((((...........)))))))))))..))))))........))))))...........(((.((((((....(((((((((....(((((((........((((((....)))))).......(((((((.(((........))))))))))..))))))).))))).))))....((((.((((((((.....)))))))).)))).......)))))).)))...........))))....... (-103.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAUUGCCUCAUUUCUUUAUUUUCAAGCAAAACAAAAGCCCACACACAGAAAAAAUCUGUGUGAGGGCGUAUAAUCGCGGUGCCACCUCAAUUAUGGAGCAAAGUAUAGACUGCCUCCAUAUCUCUGUCUUGUCUAACAACAAGUUGCACUGUAAGGUGUGCUCACCGAAUUUUUAUUGCUUCAAAUUCAUUUUUUACAUCAGCCCACUUCAUAAUCCCCCACUACCUGUUUCCACCAACCACAGGCUCCCUGAAAGUAGAAAAAUUAUUACUUUUCUGAUGAUUUAUUUUAUUAUAGGCCUUUCCCUUUUUCUUGUCAAGAAAAAAUUUAAUUUUUUCUUCUAAACCCGAACUUUUUCUUCA .......((((...........(((.((((((.......((((.((((((((.....)))))))).))))........(((((((.........(((((((...(((....)))..))))))).......(((((......)))))..)))))))..((((....)))).........)))))).)))...........((((((......................(((((...........)))))......((((((((........))))))))))))))..............))))..................((((((((((...))))))))))...................... (-79.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 299 251 203 151 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 351 242 201 51 10 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 334 159 111 152 89 NC_009009:SSA_1227|5end_Aminoglycoside_adenylyltransferase,_putative_1252297..1252527_NEGATIVE 323 300 260 229 195 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 318 160 112 54 7 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 315 178 137 77 40 NC_009009:SSA_1386|5end_NADPH-dependent_FMN_reductase,_putative_1402800..1403030_POSITIVE 314 146 102 177 108 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 312 326 298 226 200 NC_009009:SSA_0908|5end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_919700..919930_POSITIVE 310 150 104 186 137 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 307 149 111 117 81 NC_009009:SSA_2210|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2210475..2210705_POSITIVE 305 159 112 145 96 NC_009009:SSA_2162|5end_hypothetical_protein_2160592..2160822_POSITIVE 302 329 284 60 19 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 302 300 252 211 160 NC_009009:SSA_0863|5end_Cof_family_protein,_putative_855015..855245_NEGATIVE 301 147 101 145 94 NC_009009:SSA_0549|5end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_543556..543786_POSITIVE 298 308 262 85 38 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 296 316 276 172 136 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 295 167 126 190 138 NC_009009:SSA_1763|5end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750077..1750307_POSITIVE 295 150 112 53 6 NC_009009:SSA_0454|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_457015..457245_NEGATIVE 292 158 112 227 182 NC_009009:SSA_2046|5end_Uridine_phosphorylase,_putative_2049721..2049951_NEGATIVE 288 298 254 67 15 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 159 111 135 72 NC_009009:SSA_1229|3end_hypothetical_protein_1252314..1252464_NEGATIVE 318 160 112 57 10 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 311 268 221 74 29 NC_009009:SSA_1687|3end_NADH-binding_ferric-oxidoreductase,_putative_1681823..1681973_POSITIVE 303 146 102 147 89 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 298 158 111 52 3 NC_009009:SSA_1777|3end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1764427..1764577_NEGATIVE 296 166 121 54 10 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE 295 150 112 72 25 NC_009009:SSA_0455|3end_Sucrose-6-phosphate_hydrolase,_putative_456996..457146_NEGATIVE 287 138 100 72 21 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 285 160 120 149 111 NC_009009:SSA_2292|3end_DNA_segregation_ATPase_FtsK/SpoIIIE-like_protein,_putative_2295353..2295503_POSITIVE 284 289 245 142 87 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 281 249 201 69 15 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 279 165 121 146 98 NC_009009:SSA_0049|3end_Dihydroxyacetone_kinase_(Dak1),_putative_54681..54831_POSITIVE 276 140 91 58 2 NC_009009:SSA_1381|3end_hypothetical_protein_1399146..1399296_NEGATIVE 272 326 281 64 23 NC_009009:SSA_1417|3end_SAM-dependent_methyltransferase,_putative_1427304..1427454_NEGATIVE 269 329 281 120 59 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 269 300 255 72 17 NC_009009:SSA_1547|3end_HPr_kinase/phosphorylase,_putative_1550045..1550195_NEGATIVE 269 169 121 87 18 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 269 301 264 129 101 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 268 129 83 151 103 NC_009009:SSA_1511|3end_Glycosyltransferase,_putative_1515450..1515600_NEGATIVE 266 143 101 78 25 NC_009009:SSA_1080|3end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1098361..1098511_POSITIVE