Origin IGS: atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaatgaataggggtgcttatctcacaagctggaagctctgaacggtacgcaaaagattaaaataaccattgatgctaacagcgggaacattttgaacgaaagaattaaataatatcgttggtatatggtttggaattgctttgttaggcacggacgaaagttcgtgtctttttccttgtagatttagagctaaacctgttcaaaatatgatatactggaacaagactgtcttagcgaaacattgccttttcaaagtgtttagaggaagggtgaactgagaagttaaaaggactattcatcaaagtctcacattagttatttttgttgtaaaatattttaaatagtaaatgatgttttaaaaaagttattgatacagatatggtatttctagcttattgaagaaagagaagctagcgactgtctgttagagcagatctatcaaaataaataacaaatgctatcttactaatgctgattagtttaaaaaatatgattgggagaatat Mask Tandem Repeat Region ================================================ atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt Find is-nt database================================================ Query_seq: SSA_2178:SSA_2179|SSA_2178:SSA_2179:hypothetical protein:Conserved uncharacterized protein:<-<-:2177686..2178193 508 atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2178:SSA_2179|SSA_2178:SSA_2179:hypothetical protein:Conserved uncharacterized protein:<-<-:2177686..2178193 508 atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2178:SSA_2179|SSA_2178:SSA_2179:hypothetical protein:Conserved uncharacterized protein:<-<-:2177686..2178193 508 atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M L P I I F F K L I S I S K I A F V I Y F D R S A L T D S R ................................................................................................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 31 Strand: + Start: 211 End: 303 .................................................................................................................................................................................................................. M V L L T S Q F T L P L N T L K R Q C F A K T V L F Q Y I I F ............................................................................................................................................................................................................. Protein_Len: 53 Strand: + Start: 323 End: 481 .................................................................................................................................................................................................................................................................................................................................. M Y K E K D T N F R P C L T K Q F Q T I Y Q R Y Y L I L S F K M F P L L A S M V I L I F C V P F R A S S L ........................... Protein_Len: 44 Strand: + Start: 355 End: 486 .................................................................................................................................................................................................................................................................................................................................................................. M P N K A I P N H I P T I L F N S F V Q N V P A V S I N G Y F N L L R T V Q S F Q L V R ...................... Protein_Len: 54 Strand: - Start: 231 End: 392 ...................................................................................................................................................................................................................................... N V R G R F V K F L C H K A L V T K N W Y I M N Q V P K A R F R C P F L C S S E D T G L L A I G F W I G V M .................................................................................................................... atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt 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: 81 Start: 295 End: 324 ......................................................................................................................................................................................................................................................................................................ATTTAGAGCTAAACCTGTTCAAAATATGAT........................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -8.7 Tail_Score: -4.93968 Start: 338 End: 359 Full_Region: ggaattgctttgtta ggcacggac gaaa gttcgtgtc tttttccttgtagat .................................................................................................................................................................................................................................................................................................................................................ggcacggacgaaagttcgtgtc..................................................................................................................................................... Find igs database================================================ Query_seq: SSA_2178:SSA_2179|SSA_2178:SSA_2179:hypothetical protein:Conserved uncharacterized protein:<-<-:2177686..2178193 508 atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt Intra-Species Hit: Count: 1 Min: 1 Max: 508 Len: 508 Subject: NC_009009_SSA_2178_SSA_2179|hypothetical protein:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2177686,2178193]|508 HSP 1 e-value: 0.0 bit: 1007.0 Len: 508 Query Start:1 Query End:508 Subject Strand: POSITIVE Subject Start: 1 Subject End: 508 atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt atattctcccaatcatattttttaaactaatcagcattagtaagatagcatttgttatttattttgatagatctgctctaacagacagtcgctagcttctctttcttcaataagctagaaataccatatctgtatcaataacttttttaaaacatcatttactatttaaaatattttacaacaaaaataactaatgtgagactttgatgaatagtccttttaacttctcagttcacccttcctctaaacactttgaaaaggcaatgtttcgctaagacagtcttgttccagtatatcatattttgaacaggtttagctctaaatctacaaggaaaaagacacgaactttcgtccgtgcctaacaaagcaattccaaaccatataccaacgatattatttaattctttcgttcaaaatgttcccgctgttagcatcaatggttattttaatcttttgcgtaccgttcagagcttccagcttgtgagataagcacccctattcatttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUCUCCCAAUCAUAUUUUUUAAACUAAUCAGCAUUAGUAAGAUAGCAUUUGUUAUUUAUUUUGAUAGAUCUGCUCUAACAGACAGUCGCUAGCUUCUCUUUCUUCAAUAAGCUAGAAAUACCAUAUCUGUAUCAAUAACUUUUUUAAAACAUCAUUUACUAUUUAAAAUAUUUUACAACAAAAAUAACUAAUGUGAGACUUUGAUGAAUAGUCCUUUUAACUUCUCAGUUCACCCUUCCUCUAAACACUUUGAAAAGGCAAUGUUUCGCUAAGACAGUCUUGUUCCAGUAUAUCAUAUUUUGAACAGGUUUAGCUCUAAAUCUACAAGGAAAAAGACACGAACUUUCGUCCGUGCCUAACAAAGCAAUUCCAAACCAUAUACCAACGAUAUUAUUUAAUUCUUUCGUUCAAAAUGUUCCCGCUGUUAGCAUCAAUGGUUAUUUUAAUCUUUUGCGUACCGUUCAGAGCUUCCAGCUUGUGAGAUAAGCACCCCUAUUCAUUUAUU ....((((.................((((((....))))))......(((((.(((((((...((((((..((((......))))..((..(((((((.............)))))))..))..........))))))......(((((((.............))))))).............))))))).)))))))))....(((((((((...........(((((................((((.(((((....((..((((..((...(((.(((((.((((......(((.....)))..(((((((....)))))))....)))).)))))..((....)))))...))..))))..))...................((((...............))))))))).))))...((((..(((.((((((((..................))))))..)))))..))))...))))).........))))))))).... (-85.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAAUGAAUAGGGGUGCUUAUCUCACAAGCUGGAAGCUCUGAACGGUACGCAAAAGAUUAAAAUAACCAUUGAUGCUAACAGCGGGAACAUUUUGAACGAAAGAAUUAAAUAAUAUCGUUGGUAUAUGGUUUGGAAUUGCUUUGUUAGGCACGGACGAAAGUUCGUGUCUUUUUCCUUGUAGAUUUAGAGCUAAACCUGUUCAAAAUAUGAUAUACUGGAACAAGACUGUCUUAGCGAAACAUUGCCUUUUCAAAGUGUUUAGAGGAAGGGUGAACUGAGAAGUUAAAAGGACUAUUCAUCAAAGUCUCACAUUAGUUAUUUUUGUUGUAAAAUAUUUUAAAUAGUAAAUGAUGUUUUAAAAAAGUUAUUGAUACAGAUAUGGUAUUUCUAGCUUAUUGAAGAAAGAGAAGCUAGCGACUGUCUGUUAGAGCAGAUCUAUCAAAAUAAAUAACAAAUGCUAUCUUACUAAUGCUGAUUAGUUUAAAAAAUAUGAUUGGGAGAAUAU ......((((((((..(((((((((.(((((...(((((((..(((.(((..(...(((((((........))))).))..((((((......(((((.(....)..))))).....)))))))..))).)))..))...)))))...((((((((((....)))))))))).....)))))))))...)))).)..)))))))).....(((((..(((.((((.(((.((((((((......(..(((((((............)))))))..)..((((.((((.....)))).))))......((((.((((..((((((.((((....))))....))))))..))))...((((((..((((((..(((((.......)))))..)))))).))))))...)))).))))).))).)))))))....)))...)))))............................(.(..((((............))))..).)...... (-117.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 896 120 71 211 162 NC_009009:SSA_2178|5end_hypothetical_protein_2177595..2177825_NEGATIVE 358 497 456 39 1 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 347 374 340 165 134 NC_009009:SSA_1156|5end_hypothetical_protein_1184562..1184792_POSITIVE 334 480 431 171 122 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 327 126 82 123 79 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 323 107 63 179 111 NC_009009:SSA_0482|5end_ATP:cobalamin_adenosyl_transferase,_putative_483458..483688_POSITIVE 323 108 61 137 93 NC_009009:SSA_0311|5end_hypothetical_protein_305877..306107_POSITIVE 320 490 449 202 154 NC_009009:SSA_2370|5end_Zn-dependemt_peptidase_(insulinase),_M16_family,_putative_2372422..2372652_NEGATIVE 320 499 458 195 156 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 315 497 451 62 8 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 311 436 402 57 29 NC_009009:SSA_1218|5end_DNA_repair_protein_radC,_putative_1240459..1240689_NEGATIVE 310 126 82 183 131 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 310 103 62 72 30 NC_009009:SSA_1664|5end_Phosphatidylethanolamine_N-methyltransferase,_putative_1665189..1665419_NEGATIVE 309 118 83 184 144 NC_009009:SSA_0154|5end_hypothetical_protein_149836..150066_POSITIVE 301 498 451 219 161 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 297 107 61 181 122 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 297 109 74 90 52 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 296 465 421 200 150 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 295 109 66 195 145 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 294 389 341 210 168 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 126 82 136 92 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 319 477 431 150 105 NC_009009:SSA_1438|3end_Acetyltransferase,_putative_1443142..1443292_NEGATIVE 315 497 451 56 2 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 314 497 469 28 2 NC_009009:SSA_1469|3end_Shikimate_dehydrogenase,_putative_1475463..1475613_NEGATIVE 309 359 311 151 94 NC_009009:SSA_1155|3end_Serine_hydroxymethyltransferase,_putative_1184640..1184790_POSITIVE 305 254 212 137 92 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 297 109 74 118 80 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 292 100 51 145 100 NC_009009:SSA_0310|3end_hypothetical_protein_305973..306123_POSITIVE 290 478 431 139 94 NC_009009:SSA_1526|3end_hypothetical_protein_1534674..1534824_POSITIVE 287 108 61 107 65 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 286 289 241 55 2 NC_009009:SSA_1086|3end_TRNA_nucleotidyltransferase,_putative_1104607..1104757_POSITIVE 282 117 71 138 90 NC_009009:SSA_1406|3end_Histone_acetyltransferase_HPA2,_putative_1419455..1419605_NEGATIVE 281 491 451 46 1 NC_009009:SSA_0055|3end_PTS_system,_IIC_component,_putative_60019..60169_POSITIVE 279 470 427 140 94 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 276 492 462 151 117 NC_009009:SSA_2191|3end_Conserved_uncharacterized_protein_2193082..2193232_POSITIVE 275 98 61 141 97 NC_009009:SSA_2240|3end_Holliday_junction_resolvase,_putative_2237258..2237408_NEGATIVE 275 95 60 49 13 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE 275 95 51 150 103 NC_009009:SSA_0481|3end_Cobyric_acid_synthase,_putative_483541..483691_POSITIVE 274 495 459 145 92 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 272 497 456 49 5 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE