Origin IGS: ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa .........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 ttagttggtaaaaaacagcataatgctgggttttaacactcttaacgacaggcgctcaccagattttctgacaagctcgccagagttaaagtgaggtcgtcagattttctgataaggtgtttttgggcaaattctgtttggcagaaaatctggcgagtattttttgagtaaaagacgaacgtttgtttttctggcaagtagtttttaagcaaaaaactttttctgaaaatcagaaacggtaaaaagggaattaaagttaaaataaataaaaaatttaggagattataaaa Mask Tandem Repeat Region ================================================ ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa Find is-nt database================================================ Query_seq: SSA_1230:SSA_1231|SSA_1230:SSA_1231:Conserved uncharacterized protein:hypothetical protein:<-<-:1253449..1253738 290 ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1230:SSA_1231|SSA_1230:SSA_1231:Conserved uncharacterized protein:hypothetical protein:<-<-:1253449..1253738 290 ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1230:SSA_1231|SSA_1230:SSA_1231:Conserved uncharacterized protein:hypothetical protein:<-<-:1253449..1253738 290 ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 28 End: 246 ........................... M L T L I P F L P F L I F R K S F L L K N Y L P E K Q T F V F Y S K N T R Q I F C Q T E F A Q K H L I R K S D D L T L T ............................................ ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa 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================================================ ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -3.4 Tail_Score: -5.26875 Start: 52 End: 74 Full_Region: TTAATTCCCTTTTTA CCGTTTCTGA TTT TCAGAAAAAG TTTTTTGCTTAAAAA ...................................................CCGTTTCTGATTTTCAGAAAAAG........................................................................................................................................................................................................................ TransTerm Strand: - Conf: 70 HP_score: -3.8 Tail_Score: -4.84359 Start: 74 End: 90 Full_Region: tttttctggcaagta gttttt aagca aaaaac tttttctgaaaatca .........................................................................gtttttaagcaaaaaac........................................................................................................................................................................................................ TransTerm Strand: - Conf: 59 HP_score: -2.0 Tail_Score: -4.46926 Start: 187 End: 224 Full_Region: gcgctcaccagattt tctgacaagctcgc cagagttaaa gtgaggtcgtcaga ttttctgataaggtg ..........................................................................................................................................................................................tctgacaagctcgccagagttaaagtgaggtcgtcaga.................................................................. Find igs database================================================ Query_seq: SSA_1230:SSA_1231|SSA_1230:SSA_1231:Conserved uncharacterized protein:hypothetical protein:<-<-:1253449..1253738 290 ttttataatctcctaaattttttatttattttaactttaattccctttttaccgtttctgattttcagaaaaagttttttgcttaaaaactacttgccagaaaaacaaacgttcgtcttttactcaaaaaatactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa Intra-Species Hit: Count: 1 Min: 132 Max: 290 Len: 159 Subject: NC_009009_SSA_1230_SSA_1231|Conserved uncharacterized protein:hypothetical protein|NEGATIVE:NEGATIVE|[1253449,1253738]|290 HSP 1 e-value: 5.0E-85 bit: 315.0 Len: 159 Query Start:132 Query End:290 Subject Strand: POSITIVE Subject Start: 132 Subject End: 290 ...................................................................................................................................tactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa ...................................................................................................................................tactcgccagattttctgccaaacagaatttgcccaaaaacaccttatcagaaaatctgacgacctcactttaactctggcgagcttgtcagaaaatctggtgagcgcctgtcgttaagagtgttaaaacccagcattatgctgttttttaccaactaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUCGCCAGAUUUUCUGCCAAACAGAAUUUGCCCAAAAACACCUUAUCAGAAAAUCUGACGACCUCACUUUAACUCUGGCGAGCUUGUCAGAAAAUCUGGUGAGCGCCUGUCGUUAAGAGUGUUAAAACCCAGCAUUAUGCUGUUUUUUACCAACUAA ..((((((((((((((((.....)))))...........................((((((((.(((.((........)).))).)))))))).)))))))))))..............(((..(((((..((((.....))))..)))))...))).. (-44.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUUGGUAAAAAACAGCAUAAUGCUGGGUUUUAACACUCUUAACGACAGGCGCUCACCAGAUUUUCUGACAAGCUCGCCAGAGUUAAAGUGAGGUCGUCAGAUUUUCUGAUAAGGUGUUUUUGGGCAAAUUCUGUUUGGCAGAAAAUCUGGCGAGUA ...((((.(((((..((((.....))))..)))))..........))))....((((.((((((((((((.((((..((((.((.((......)).)).((((.....))))...))))..))))..(((((...))))).)))))))))))).)))). (-49.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 137 91 54 11 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 351 118 75 76 32 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 341 45 3 210 169 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 332 113 75 159 126 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 328 150 102 87 21 NC_009009:SSA_0304|5end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301143..301373_POSITIVE 323 120 78 66 10 NC_009009:SSA_0291|5end_Oxidoreductase,_putative_285362..285592_POSITIVE 320 116 73 171 130 NC_009009:SSA_1521|5end_Phosphoenolpyruvate_carboxylase,_putative_1530683..1530913_NEGATIVE 318 138 91 70 23 NC_009009:SSA_0021|5end_hypothetical_protein_26842..27072_POSITIVE 317 120 77 56 7 NC_009009:SSA_1182|5end_Gid-like_protein,_putative_1210866..1211096_NEGATIVE 316 113 73 49 8 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 312 120 78 197 157 NC_009009:SSA_1483|5end_Sphingosine_kinase_(diacylglycerol_kinase),_putative_1490220..1490450_NEGATIVE 306 109 61 59 7 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 304 116 72 172 123 NC_009009:SSA_1062|5end_50S_ribosomal_protein_L27,_putative_1078284..1078514_POSITIVE 303 116 75 193 136 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 300 89 41 231 167 NC_009009:SSA_0151|5end_hypothetical_protein_145354..145584_POSITIVE 298 150 101 71 20 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 297 109 63 152 101 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 296 50 2 205 158 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 296 116 75 53 10 NC_009009:SSA_1026|5end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1042794..1043024_POSITIVE 295 44 3 156 116 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 137 91 69 26 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 351 118 75 83 39 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 335 114 84 111 86 NC_009009:SSA_1302|3end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1321762..1321912_NEGATIVE 320 116 73 124 83 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 317 109 61 145 92 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 297 90 41 79 14 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 287 116 79 78 44 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 287 120 76 67 3 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 286 120 74 58 13 NC_009009:SSA_0775|3end_1,4-alpha-glucan_branching_enzyme,_putative_758371..758521_POSITIVE 285 109 66 51 3 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 284 118 73 143 107 NC_009009:SSA_1347|3end_PhnA_protein,_putative_1364791..1364941_NEGATIVE 281 109 75 80 45 NC_009009:SSA_0207|3end_hypothetical_protein_204944..205094_POSITIVE 278 150 101 78 19 NC_009009:SSA_2392|3end_50S_ribosomal_protein_L36,_putative_120394..120544_POSITIVE 277 36 2 81 38 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 273 129 81 81 35 NC_009009:SSA_2243|3end_Conserved_uncharacterized_protein_2238769..2238919_NEGATIVE 272 117 79 44 7 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 272 108 63 131 93 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 272 58 13 116 69 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 270 100 58 151 111 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 269 114 73 114 75 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE