Origin IGS: agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc .........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 ggcagactcctttactcgaatacacctatctaccatccagtatagcacaaagctggacgcggaaacaaaaatagagagcaaataatcaataatcagccctctaattttgctattatgatatatcgccttcaaaggagatgacaagggattcataagaaaaatcaagctccaagacccacttgccatctgccttgacaaatttcaactgataatctcgttctggtttggaagcaaggcacagtcagccaaattcatctccttcataagttaatactatgacttttgtactttaccatacttagctgcactggtaaatatagtttgagacttctcatcacagaaaaacctgtagctccaactacaggtcaagtatct Mask Tandem Repeat Region ================================================ agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc Find is-nt database================================================ Query_seq: SSA_0586:SSA_0587|SSA_0586:SSA_0587:Conserved uncharacterized protein:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:->->:578304..578678 375 agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0586:SSA_0587|SSA_0586:SSA_0587:Conserved uncharacterized protein:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:->->:578304..578678 375 agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0586:SSA_0587|SSA_0586:SSA_0587:Conserved uncharacterized protein:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:->->:578304..578678 375 agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 7 End: 99 ...... M T C S W S Y R F F C D E K S Q T I F T S A A K Y G K V Q K S .................................................................................................................................................................................................................................................................................... Protein_Len: 42 Strand: + Start: 135 End: 260 ...................................................................................................................................... M C L A S K P E R D Y Q L K F V K A D G K W V L E L D F S Y E S L V I S F E G D I S ................................................................................................................... Protein_Len: 60 Strand: + Start: 178 End: 375 ................................................................................................................................................................................. M S R Q M A S G S W S L I F L M N P L S S P L K A I Y H N S K I R G L I I D Y L L S I F V S A S S F V L Y W M V D R C I Protein_Len: 49 Strand: - Start: 108 End: 254 ........................................................................................................... S I F S I F K A S Q A K S G F W F S I I L Q F K D L C I A L P D Q L K I K R I F G K D D G K F A M ......................................................................................................................... Protein_Len: 31 Strand: - Start: 1 End: 93 S V Q G T T P A V P K E T I L L R L S Y K G T C S L I T F Y M .......................................................................................................................................................................................................................................................................................... agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc 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================================================ agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -3.0 Tail_Score: -5.27938 Start: 273 End: 304 Full_Region: TCATAATAGCAAAAT TAGAGGGCTGATTA TTGA TTATTTGCTCTCTA TTTTTGTTTCCGCGT ................................................................................................................................................................................................................................................................................TAGAGGGCTGATTATTGATTATTTGCTCTCTA....................................................................... Find igs database================================================ Query_seq: SSA_0586:SSA_0587|SSA_0586:SSA_0587:Conserved uncharacterized protein:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:->->:578304..578678 375 agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc Intra-Species Hit: Count: 1 Min: 1 Max: 375 Len: 375 Subject: NC_009009_SSA_0586_SSA_0587|Conserved uncharacterized protein:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative|POSITIVE:POSITIVE|[578304,578678]|375 HSP 1 e-value: 0.0 bit: 743.0 Len: 375 Query Start:1 Query End:375 Subject Strand: POSITIVE Subject Start: 1 Subject End: 375 agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc agatacttgacctgtagttggagctacaggtttttctgtgatgagaagtctcaaactatatttaccagtgcagctaagtatggtaaagtacaaaagtcatagtattaacttatgaaggagatgaatttggctgactgtgccttgcttccaaaccagaacgagattatcagttgaaatttgtcaaggcagatggcaagtgggtcttggagcttgatttttcttatgaatcccttgtcatctcctttgaaggcgatatatcataatagcaaaattagagggctgattattgattatttgctctctatttttgtttccgcgtccagctttgtgctatactggatggtagataggtgtattcgagtaaaggagtctgcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUACUUGACCUGUAGUUGGAGCUACAGGUUUUUCUGUGAUGAGAAGUCUCAAACUAUAUUUACCAGUGCAGCUAAGUAUGGUAAAGUACAAAAGUCAUAGUAUUAACUUAUGAAGGAGAUGAAUUUGGCUGACUGUGCCUUGCUUCCAAACCAGAACGAGAUUAUCAGUUGAAAUUUGUCAAGGCAGAUGGCAAGUGGGUCUUGGAGCUUGAUUUUUCUUAUGAAUCCCUUGUCAUCUCCUUUGAAGGCGAUAUAUCAUAAUAGCAAAAUUAGAGGGCUGAUUAUUGAUUAUUUGCUCUCUAUUUUUGUUUCCGCGUCCAGCUUUGUGCUAUACUGGAUGGUAGAUAGGUGUAUUCGAGUAAAGGAGUCUGCC ........((((((((((....))))))))))...((((((((((....)))........(((((((.(((......))))))))))........))))))).................((..((((..(((((..((..((((.(((.......)))))))))..)))))..).)))..))..((((((.((((((.(((((..((((........))))...).))))))))))..((((((((....(((((((((.....(((((((.((((((((.(((........))).)))))))).)))))))....(((((((..(......)..))))))).......)))))).)))..)))))))))))))) (-113.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCAGACUCCUUUACUCGAAUACACCUAUCUACCAUCCAGUAUAGCACAAAGCUGGACGCGGAAACAAAAAUAGAGAGCAAAUAAUCAAUAAUCAGCCCUCUAAUUUUGCUAUUAUGAUAUAUCGCCUUCAAAGGAGAUGACAAGGGAUUCAUAAGAAAAAUCAAGCUCCAAGACCCACUUGCCAUCUGCCUUGACAAAUUUCAACUGAUAAUCUCGUUCUGGUUUGGAAGCAAGGCACAGUCAGCCAAAUUCAUCUCCUUCAUAAGUUAAUACUAUGACUUUUGUACUUUACCAUACUUAGCUGCACUGGUAAAUAUAGUUUGAGACUUCUCAUCACAGAAAAACCUGUAGCUCCAACUACAGGUCAAGUAUCU ..............(((((((.....(((.(((((((((((..........)))))).((((...(((((.(((((.((................)).))))).)))))....((((..............((((((((((....((......................((((.....)))).....(((((((.((((((..(((.((.....)))))..))))))....))))))).......))....))))))))))((.((((((......)))))).))........)))).....))))..))))).)))..)))))))..((((......))))..((((((((......))))))))......... (-81.89) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 240 191 191 139 NC_009009:SSA_2029|5end_Transposase_and_inactivated_derivatives,_putative_2036028..2036258_NEGATIVE 328 159 117 202 156 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 319 209 163 76 21 NC_009009:SSA_0684|5end_Fibril-like_structure_subunit_FibA,_putative_664992..665222_POSITIVE 315 148 112 145 118 NC_009009:SSA_2202|5end_Elongation_factor_Ts,_putative_2203350..2203580_NEGATIVE 313 169 129 83 33 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 311 345 314 50 19 NC_009009:SSA_1232|5end_Topoisomerase_IV_subunit_B,_putative_1256755..1256985_NEGATIVE 310 230 181 57 12 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 306 208 165 48 10 NC_009009:SSA_1633|5end_FimA_fimbrial_subunit-like_protein,_putative_1635545..1635775_NEGATIVE 303 269 224 125 84 NC_009009:SSA_1845|5end_Serine/threonine_protein_kinase,_putative_1840181..1840411_NEGATIVE 302 338 296 155 116 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 301 361 330 36 2 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 300 209 161 219 159 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 299 347 302 221 165 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 297 229 181 71 19 NC_009009:SSA_1337|5end_hypothetical_protein_1351091..1351321_NEGATIVE 296 167 125 63 15 NC_009009:SSA_1576|5end_Catabolite_control_protein_A,_putative_1580181..1580411_NEGATIVE 295 340 295 59 20 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 294 169 122 127 69 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 293 238 191 91 45 NC_009009:SSA_0868|5end_hypothetical_protein_861535..861765_NEGATIVE 291 337 293 61 14 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 291 229 182 151 105 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 159 117 146 100 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 315 148 112 72 45 NC_009009:SSA_2203|3end_30S_ribosomal_protein_S2,_putative_2203423..2203573_NEGATIVE 313 169 129 62 12 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 310 230 181 60 15 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 303 269 224 128 87 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 301 361 330 36 2 NC_009009:SSA_1694|3end_PTS_system,_lactose-specific_IIA_component,_putative_1686811..1686961_NEGATIVE 294 169 122 93 35 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 294 329 282 122 77 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 289 174 141 126 95 NC_009009:SSA_0526|3end_hypothetical_protein_524681..524831_POSITIVE 288 308 265 115 53 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 288 340 291 145 95 NC_009009:SSA_0164|3end_hypothetical_protein_163997..164147_POSITIVE 287 239 193 132 80 NC_009009:SSA_0962|3end_Lactoylglutathione_lyase,_putative_971431..971581_POSITIVE 283 332 297 143 113 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 282 169 122 145 103 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE 281 359 315 52 4 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 279 254 216 45 2 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 279 176 138 43 1 NC_009009:SSA_1619|3end_Ribosome_recycling_factor,_putative_1621679..1621829_NEGATIVE 279 355 311 74 23 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 276 338 294 151 90 NC_009009:SSA_1338|3end_hypothetical_protein_1351200..1351350_NEGATIVE 276 319 274 87 21 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE