Origin IGS: gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt .........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 accatgctcctttctaacgacaaaagcctttcaaaaagcgagaaaatgcaaaatcaaaactcaatactggtacaaactagcttttctccaagacttttaaagataaacttcattcgcaaaacggactctggtattagtataacatttttggaagaaaaagacgaaaaaacctgtatccatgaagatacttttcgattgaaagcttcatcaatacagattctaagaatatatttgaatttcataaaaagacaatgaataaacttctaagaaagccaaactcatctgagcacttc Mask Tandem Repeat Region ================================================ gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt Find is-nt database================================================ Query_seq: SSA_0596:SSA_0597|SSA_0596:SSA_0597:hypothetical protein:hypothetical protein:->->:587413..587705 293 gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0596:SSA_0597|SSA_0596:SSA_0597:hypothetical protein:hypothetical protein:->->:587413..587705 293 gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0596:SSA_0597|SSA_0596:SSA_0597:hypothetical protein:hypothetical protein:->->:587413..587705 293 gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 65 End: 157 ................................................................ M F L E S V L M K L S I E K Y L H G Y R F F R L F L P K M L Y ........................................................................................................................................ Protein_Len: 60 Strand: + Start: 37 End: 237 .................................... M H C L F M K F K Y I L R I C I D E A F N R K V S S W I Q V F S S F S S K N V I L I P E S V L R M K F I F K S L G E K L ........................................................ Protein_Len: 60 Strand: - Start: 42 End: 290 ......................................... E H I C T K E D K E E L F T I S I G S D T K R I F N I K L L R P S F S T Q V L I S N Q N Q M K E S K S L S K D N S L L M ... Protein_Len: 33 Strand: - Start: 1 End: 99 F H E S S N P K R L L K N M T K K H F E F I N K S D T N I F S E M .................................................................................................................................................................................................. gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt 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================================================ gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0596:SSA_0597|SSA_0596:SSA_0597:hypothetical protein:hypothetical protein:->->:587413..587705 293 gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt Intra-Species Hit: Count: 1 Min: 1 Max: 293 Len: 293 Subject: NC_009009_SSA_0596_SSA_0597|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[587413,587705]|293 HSP 1 e-value: 1.0E-165 bit: 581.0 Len: 293 Query Start:1 Query End:293 Subject Strand: POSITIVE Subject Start: 1 Subject End: 293 gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt gaagtgctcagatgagtttggctttcttagaagtttattcattgtctttttatgaaattcaaatatattcttagaatctgtattgatgaagctttcaatcgaaaagtatcttcatggatacaggttttttcgtctttttcttccaaaaatgttatactaataccagagtccgttttgcgaatgaagtttatctttaaaagtcttggagaaaagctagtttgtaccagtattgagttttgattttgcattttctcgctttttgaaaggcttttgtcgttagaaaggagcatggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUGCUCAGAUGAGUUUGGCUUUCUUAGAAGUUUAUUCAUUGUCUUUUUAUGAAAUUCAAAUAUAUUCUUAGAAUCUGUAUUGAUGAAGCUUUCAAUCGAAAAGUAUCUUCAUGGAUACAGGUUUUUUCGUCUUUUUCUUCCAAAAAUGUUAUACUAAUACCAGAGUCCGUUUUGCGAAUGAAGUUUAUCUUUAAAAGUCUUGGAGAAAAGCUAGUUUGUACCAGUAUUGAGUUUUGAUUUUGCAUUUUCUCGCUUUUUGAAAGGCUUUUGUCGUUAGAAAGGAGCAUGGU ((((.....(((((((((((..((((.((((((..((.....))..)))))).))))..)))))........((((((((((((.((((((.((((....)))).....)))))).)))))))))))).))))))....))))..................((((...(((.((((((((..(((((((.((...((((((....(((((((((.((((...(((......).))...))))..)).))))))))))))).)).)))))))..))).))))).)))...)))) (-69.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAUGCUCCUUUCUAACGACAAAAGCCUUUCAAAAAGCGAGAAAAUGCAAAAUCAAAACUCAAUACUGGUACAAACUAGCUUUUCUCCAAGACUUUUAAAGAUAAACUUCAUUCGCAAAACGGACUCUGGUAUUAGUAUAACAUUUUUGGAAGAAAAAGACGAAAAAACCUGUAUCCAUGAAGAUACUUUUCGAUUGAAAGCUUCAUCAAUACAGAUUCUAAGAAUAUAUUUGAAUUUCAUAAAAAGACAAUGAAUAAACUUCUAAGAAAGCCAAACUCAUCUGAGCACUUC ....(((((...((....))...................(((.....((..............((((((((((............................((......)).((((.....)))).....))))))))))....((((((((((................((((((..((((((...(((((.....)))))))))))..)))))).....................(((((.........)))))....)))))))))).))....)))....))))).... (-46.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 267 223 95 48 NC_009009:SSA_0917|5end_Cobalamin-independent_methionine_synthase_II,_putative_930250..930480_NEGATIVE 304 289 251 51 7 NC_009009:SSA_2117|5end_DNA_recombination_protein_RmuC,_putative_2119812..2120042_NEGATIVE 300 289 245 144 97 NC_009009:SSA_0961|5end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_969913..970143_POSITIVE 297 288 241 110 54 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 293 258 212 100 58 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 293 289 247 135 97 NC_009009:SSA_0056|5end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_59926..60156_POSITIVE 286 135 95 110 63 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 286 141 108 100 62 NC_009009:SSA_0602|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_589918..590148_POSITIVE 280 277 231 133 78 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 279 129 81 138 91 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 279 145 112 103 75 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 276 129 87 143 102 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 272 180 135 123 76 NC_009009:SSA_1820|5end_hypothetical_protein_1809822..1810052_NEGATIVE 272 46 10 70 34 NC_009009:SSA_1763|5end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750077..1750307_POSITIVE 271 289 245 190 146 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 268 263 230 111 74 NC_009009:SSA_1710|5end_Transcriptional_regulator,_XRE_family,_putative_1698338..1698568_POSITIVE 264 48 3 120 65 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 264 150 115 228 194 NC_009009:SSA_1238|5end_hypothetical_protein_1263154..1263384_NEGATIVE 263 280 231 60 6 NC_009009:SSA_0664|5end_Conserved_uncharacterized_protein_649086..649316_NEGATIVE 263 280 240 122 90 NC_009009:SSA_0256|5end_Metalloregulator_ScaR_(Fe/Mn-dependent_transcriptional_repressor),_putative_248699..248929_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 289 251 49 5 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 300 289 245 128 81 NC_009009:SSA_0960|3end_Sensor_protein_ciaH,_putative_969977..970127_POSITIVE 293 258 212 110 68 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 293 289 247 148 110 NC_009009:SSA_0055|3end_PTS_system,_IIC_component,_putative_60019..60169_POSITIVE 286 141 108 90 52 NC_009009:SSA_0601|3end_Phosphorylase,_Pnp/Udp_family,_putative_589988..590138_POSITIVE 280 277 231 131 76 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 279 129 81 92 45 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 279 145 112 51 23 NC_009009:SSA_0307|3end_Glutamine_synthetase_type_1,_putative_304413..304563_POSITIVE 259 206 162 62 14 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 256 47 3 137 89 NC_009009:SSA_1829|3end_RNA_methyltransferase,_putative_1818959..1819109_NEGATIVE 256 270 223 119 70 NC_009009:SSA_1206|3end_A/G-specific_adenine_glycosylase,_putative_1230071..1230221_NEGATIVE 254 178 131 135 81 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 252 142 105 113 78 NC_009009:SSA_1850|3end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1845710..1845860_NEGATIVE 251 143 101 89 45 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE 250 180 131 66 5 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 249 55 16 113 78 NC_009009:SSA_2138|3end_RNA-binding_protein,_Jag_family,_putative_2138462..2138612_NEGATIVE 249 289 241 146 89 NC_009009:SSA_1358|3end_hypothetical_protein_1373104..1373254_NEGATIVE 248 145 109 130 98 NC_009009:SSA_1012|3end_Phosphoenolpyruvate_synthase,_putative_1017314..1017464_POSITIVE 247 145 124 122 101 NC_009009:SSA_1400|3end_Pyridoxal_kinase,_putative_1412206..1412356_NEGATIVE 247 259 212 87 35 NC_009009:SSA_0181|3end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_186292..186442_POSITIVE