Origin IGS: gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga .........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 tctagtaaaagttctgacctttattttaccataaatccagctcaatgaatgtttcaaaactgatagaaaatctgaaaatatggacgagttaagaggaagtctgtcaaaccgctgaacagaaaagacttactagctaggcttctaacaatccttgtccttcctctctggaaaagcaaagaacctgagaataatctcagattcctttaagc Mask Tandem Repeat Region ================================================ gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga Find is-nt database================================================ Query_seq: SSA_0688:SSA_0689|SSA_0688:SSA_0689:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:Penicillin-binding protein 2B, putative:->->:672193..672401 209 gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0688:SSA_0689|SSA_0688:SSA_0689:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:Penicillin-binding protein 2B, putative:->->:672193..672401 209 gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0688:SSA_0689|SSA_0688:SSA_0689:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:Penicillin-binding protein 2B, putative:->->:672193..672401 209 gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 13 End: 153 ............ M R L F S G S L L F Q R G R T R I V R S L A S K S F L F S G L T D F L L T R P Y F Q I F Y Q F ........................................................ Protein_Len: 32 Strand: - Start: 6 End: 98 ..... * L F R L N N E P E K S K W L P L V L I T L L R A L L D K R N M ............................................................................................................... gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga 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================================================ gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0688:SSA_0689|SSA_0688:SSA_0689:2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:Penicillin-binding protein 2B, putative:->->:672193..672401 209 gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_009009_SSA_0688_SSA_0689|2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, putative:Penicillin-binding protein 2B, putative|POSITIVE:POSITIVE|[672193,672401]|209 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga gcttaaaggaatctgagattattctcaggttctttgcttttccagagaggaaggacaaggattgttagaagcctagctagtaagtcttttctgttcagcggtttgacagacttcctcttaactcgtccatattttcagattttctatcagttttgaaacattcattgagctggatttatggtaaaataaaggtcagaacttttactaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUAAAGGAAUCUGAGAUUAUUCUCAGGUUCUUUGCUUUUCCAGAGAGGAAGGACAAGGAUUGUUAGAAGCCUAGCUAGUAAGUCUUUUCUGUUCAGCGGUUUGACAGACUUCCUCUUAACUCGUCCAUAUUUUCAGAUUUUCUAUCAGUUUUGAAACAUUCAUUGAGCUGGAUUUAUGGUAAAAUAAAGGUCAGAACUUUUACUAGA ((...(((((((((((((....))))))))))))))).......(((((((((...((((((((((((....))))).....)))))))(((((.(((....))))))))))))))))).......(((((..(((((........((((...(((.....))))))).)))))..))))).....(((((((....)))))))..... (-55.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAGUAAAAGUUCUGACCUUUAUUUUACCAUAAAUCCAGCUCAAUGAAUGUUUCAAAACUGAUAGAAAAUCUGAAAAUAUGGACGAGUUAAGAGGAAGUCUGUCAAACCGCUGAACAGAAAAGACUUACUAGCUAGGCUUCUAACAAUCCUUGUCCUUCCUCUCUGGAAAAGCAAAGAACCUGAGAAUAAUCUCAGAUUCCUUUAAGC .(((((((...(((((...(((((......)))))..((((....(((.....)))....(((((((...(((..................))).....)))))))....))))..))))).....)))))))....((((..........((((..((((.....))))..)))).(((.((((((....)))))).)))....)))) (-41.27) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 140 92 66 18 NC_009009:SSA_2008|5end_Molecular_chaperone_GrpE_(HSP-70_cofactor),_putative_2010062..2010292_NEGATIVE 344 130 84 225 166 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 336 96 52 68 18 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 318 105 61 207 159 NC_009009:SSA_0527|5end_Propanediol_utilization_protein_PduL_524625..524855_POSITIVE 317 119 71 86 36 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 314 102 63 223 175 NC_009009:SSA_0370|5end_Acetyltransferase,_GNAT_family,_putative_360382..360612_NEGATIVE 309 90 43 76 26 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 307 110 64 201 145 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 306 76 36 67 13 NC_009009:SSA_0388|5end_Mismatch_repair_ATPase_(MutS_family),_putative_382474..382704_POSITIVE 304 103 64 56 12 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 302 135 97 217 174 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 296 96 53 162 114 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 296 111 72 206 172 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 294 135 91 105 55 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 293 78 32 149 100 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 290 87 41 47 2 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 289 83 42 69 28 NC_009009:SSA_0733|5end_hypothetical_protein_716069..716299_POSITIVE 288 119 72 59 13 NC_009009:SSA_0746|5end_Glucosamine-6-phosphate_deaminase,_putative_727078..727308_POSITIVE 287 114 71 111 62 NC_009009:SSA_2036|5end_Conserved_hypothetical_cytosolic_protein_2040799..2041029_NEGATIVE 287 136 91 216 171 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 50 1 103 54 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 310 49 2 71 17 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 309 50 5 86 36 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 304 103 64 52 8 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 296 96 53 150 102 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 294 77 32 139 101 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE 293 78 32 143 94 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 290 87 41 57 12 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 290 106 66 72 24 NC_009009:SSA_0907|3end_Fibronectin-binding_protein_A,_putative_917568..917718_NEGATIVE 288 116 71 97 51 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 287 114 71 114 65 NC_009009:SSA_2037|3end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2040796..2040946_NEGATIVE 281 70 28 59 11 NC_009009:SSA_1610|3end_hypothetical_protein_1614004..1614154_NEGATIVE 280 136 94 144 101 NC_009009:SSA_0855|3end_O-acetylhomoserine_sulfhydrylase,_putative_843192..843342_POSITIVE 280 34 6 98 67 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 279 116 71 98 39 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 279 67 23 142 89 NC_009009:SSA_1769|3end_hypothetical_protein_1756939..1757089_NEGATIVE 278 117 75 49 3 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 278 104 74 149 116 NC_009009:SSA_0865|3end_hypothetical_protein_856850..857000_POSITIVE 277 138 92 104 58 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 277 99 54 151 109 NC_009009:SSA_0049|3end_Dihydroxyacetone_kinase_(Dak1),_putative_54681..54831_POSITIVE