Origin IGS: aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga .........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 tcctttccattatttgaaaaaagggggagcgagacagaatccagaaaatcaaagattttcggctcgctgtcccacccccgcgacgatggctaggcttgaaatatgcttttaacaagctttttcaaaccagacagcaactgcattttgcaatgctgaaccatccatttccctaggccaagaggcatctcccaaattcctcttagaccagtatgcttgaatcatccactgtggcttggccttacctatcagcagtctcccatctgctgacagcgcaaggacttgacccaactagaagtgattgttcaagctt Mask Tandem Repeat Region ================================================ aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga Find is-nt database================================================ Query_seq: SSA_0057:SSA_0060|SSA_0057:SSA_0060:Phosphotransferase system sugar-specific EII component, putative:Tagatose-6-phosphate ketose/aldose isomerase, putative:->->:61307..61616 310 aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0057:SSA_0060|SSA_0057:SSA_0060:Phosphotransferase system sugar-specific EII component, putative:Tagatose-6-phosphate ketose/aldose isomerase, putative:->->:61307..61616 310 aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0057:SSA_0060|SSA_0057:SSA_0060:Phosphotransferase system sugar-specific EII component, putative:Tagatose-6-phosphate ketose/aldose isomerase, putative:->->:61307..61616 310 aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga Predict ORF larger than 30AA ================================================ Protein_Len: 59 Strand: + Start: 23 End: 199 ...................... M G Q V L A L S A D G R L L I G K A K P Q W M I Q A Y W S K R N L G D A S W P R E M D G S A L Q N A V A V W F E K A C ............................................................................................................... Protein_Len: 34 Strand: + Start: 117 End: 218 .................................................................................................................... M W E M P L G L G K W M V Q H C K M Q L L S G L K K L V K S I F Q A ............................................................................................ Protein_Len: 38 Strand: + Start: 196 End: 309 ................................................................................................................................................................................................... M L K A Y F K P S H R R G G G T A S R K S L I F W I L S R S P F F Q I M E R . Protein_Len: 32 Strand: - Start: 202 End: 297 ......................................................................................................................................................................................................... F C I E L R A M T A P T P C R A S F R Q N E P N Q R A G G K K M ............. Protein_Len: 44 Strand: - Start: 141 End: 272 ............................................................................................................................................ P F P H N L M A F H L Q Q R T Q F L K N F A Y K L G L W R R P P P V A L R F D K I K Q M ...................................... Protein_Len: 35 Strand: - Start: 47 End: 151 .............................................. C I P S Q Q Y T L G L W L P H N L C V P R L P I Q S I G R P R P F H M ............................................................................................................................................................... Protein_Len: 33 Strand: - Start: 3 End: 101 .. S S C D S R T P D L G Q A T L L H S V A S L Y P W A V T S S E L M ................................................................................................................................................................................................................. aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga 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================================================ aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.9 Tail_Score: -5.06451 Start: 230 End: 288 Full_Region: AGCCTAGCCATCGTC GCGGGGGTGGGACAGCGAGCCGAAAATC TTT GATTTTCTGGATTCTGTCTCGCTCCCCC TTTTTTCAAATAATG .....................................................................................................................................................................................................................................GCGGGGGTGGGACAGCGAGCCGAAAATCTTTGATTTTCTGGATTCTGTCTCGCTCCCCC...................... TransTerm Strand: + Conf: 81 HP_score: -13.1 Tail_Score: -2.77166 Start: 232 End: 286 Full_Region: CCTAGCCATCGTCGC GGGGGTGGGACAGCGAGCCGAAAATC TTT GATTTTCTGGATTCTGTCTCGCTCCC CCTTTTTTCAAATAA .......................................................................................................................................................................................................................................GGGGGTGGGACAGCGAGCCGAAAATCTTTGATTTTCTGGATTCTGTCTCGCTCCC........................ Find igs database================================================ Query_seq: SSA_0057:SSA_0060|SSA_0057:SSA_0060:Phosphotransferase system sugar-specific EII component, putative:Tagatose-6-phosphate ketose/aldose isomerase, putative:->->:61307..61616 310 aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga Intra-Species Hit: Count: 1 Min: 1 Max: 310 Len: 310 Subject: NC_009009_SSA_0057_SSA_0060|Phosphotransferase system sugar-specific EII component, putative:Tagatose-6-phosphate ketose/aldose isomerase, putative|POSITIVE:POSITIVE|[61307,61616]|310 HSP 1 e-value: 1.0E-175 bit: 615.0 Len: 310 Query Start:1 Query End:310 Subject Strand: POSITIVE Subject Start: 1 Subject End: 310 aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga aagcttgaacaatcacttctagttgggtcaagtccttgcgctgtcagcagatgggagactgctgataggtaaggccaagccacagtggatgattcaagcatactggtctaagaggaatttgggagatgcctcttggcctagggaaatggatggttcagcattgcaaaatgcagttgctgtctggtttgaaaaagcttgttaaaagcatatttcaagcctagccatcgtcgcgggggtgggacagcgagccgaaaatctttgattttctggattctgtctcgctcccccttttttcaaataatggaaagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCUUGAACAAUCACUUCUAGUUGGGUCAAGUCCUUGCGCUGUCAGCAGAUGGGAGACUGCUGAUAGGUAAGGCCAAGCCACAGUGGAUGAUUCAAGCAUACUGGUCUAAGAGGAAUUUGGGAGAUGCCUCUUGGCCUAGGGAAAUGGAUGGUUCAGCAUUGCAAAAUGCAGUUGCUGUCUGGUUUGAAAAAGCUUGUUAAAAGCAUAUUUCAAGCCUAGCCAUCGUCGCGGGGGUGGGACAGCGAGCCGAAAAUCUUUGAUUUUCUGGAUUCUGUCUCGCUCCCCCUUUUUUCAAAUAAUGGAAAGGA ..((((((...((((..((((.((((((...(.((((((.((((((((((........)))))))))))))))))...))).)))))))))))))))))...((((.((((((((.(((.....))).)))))))).)))).......((((((((((((((((.....)))).)))))...(((((((((..((((.....))))...))))))))).))))))).....(((((((((((((....(((((((((...))))))).))...)))))))))))))(((((((.........))))))). (-126.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUUCCAUUAUUUGAAAAAAGGGGGAGCGAGACAGAAUCCAGAAAAUCAAAGAUUUUCGGCUCGCUGUCCCACCCCCGCGACGAUGGCUAGGCUUGAAAUAUGCUUUUAACAAGCUUUUUCAAACCAGACAGCAACUGCAUUUUGCAAUGCUGAACCAUCCAUUUCCCUAGGCCAAGAGGCAUCUCCCAAAUUCCUCUUAGACCAGUAUGCUUGAAUCAUCCACUGUGGCUUGGCCUUACCUAUCAGCAGUCUCCCAUCUGCUGACAGCGCAAGGACUUGACCCAACUAGAAGUGAUUGUUCAAGCUU ...............((((...(((((.(.(.(((((...((.(((((((...)))))))))....))))))).))))).....(((((...((.((((((...((((.....))))..)))))).))...(((((..(((.....))).)))))..)))))..))))....(((.((((((.((.......)).)))))).).)).....(((((((.((..((((.(((.((((((((.(((.(((((((........))))))).)).).)))).......)))))))..))))..))))))))).. (-97.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 448 82 41 61 22 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 426 80 33 171 107 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 403 69 21 186 136 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 386 269 225 85 26 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 383 70 22 88 19 NC_009009:SSA_1418|5end_Conserved_uncharacterized_protein_1428927..1429157_NEGATIVE 382 290 242 211 154 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 381 250 204 201 156 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 378 258 217 216 154 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 369 68 26 137 98 NC_009009:SSA_1397|5end_hypothetical_protein_1410589..1410819_POSITIVE 358 48 2 177 127 NC_009009:SSA_0055|5end_PTS_system,_IIC_component,_putative_59034..59264_POSITIVE 357 80 38 228 189 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 357 70 22 87 23 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 353 258 211 142 101 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 351 288 241 198 157 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 349 99 51 206 152 NC_009009:SSA_1364|5end_hypothetical_protein_1381297..1381527_NEGATIVE 349 80 31 68 14 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 349 250 206 40 2 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 348 80 34 180 129 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 348 290 242 206 155 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 345 82 41 151 112 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 448 82 41 57 18 NC_009009:SSA_1728|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713424..1713574_NEGATIVE 393 280 231 57 7 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 392 80 34 69 17 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 386 269 225 101 42 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 368 260 217 66 24 NC_009009:SSA_2007|3end_Chaperone_protein_dnaK/HSP70,_putative_2007443..2007593_NEGATIVE 358 48 2 151 101 NC_009009:SSA_0054|3end_Phosphotransferase_system_sugar-specific_EIIB_component,_putative_59088..59238_POSITIVE 357 249 201 74 22 NC_009009:SSA_0288|3end_hypothetical_protein_280740..280890_NEGATIVE 353 258 211 67 26 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 351 288 241 100 59 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 349 99 51 151 97 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 349 270 222 60 12 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 349 250 206 40 2 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 348 290 242 84 33 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 347 88 41 77 23 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 343 80 33 58 5 NC_009009:SSA_0759|3end_Acetylglutamate_kinase,_putative_742658..742808_POSITIVE 342 63 21 84 30 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 339 279 235 145 84 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 332 290 243 147 106 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 325 89 41 128 65 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 319 80 38 139 100 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE