Origin IGS: tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctctaaatagaaaataaaaaacgaatacctgctaatcaaaataagttgagggtattcgtttttttatgctgatttcaaagaaagacagaaacagcaacatgttttgtaagata Mask Tandem Repeat Region ================================================ tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct Find is-nt database================================================ Query_seq: SSA_0381:SSA_0382|SSA_0381:SSA_0382:hypothetical protein:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:-><-:373575..373689 115 tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0381:SSA_0382|SSA_0381:SSA_0382:hypothetical protein:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:-><-:373575..373689 115 tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0381:SSA_0382|SSA_0381:SSA_0382:hypothetical protein:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:-><-:373575..373689 115 tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct Predict ORF larger than 30AA ================================================ tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct 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================================================ tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0381:SSA_0382|SSA_0381:SSA_0382:hypothetical protein:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative:-><-:373575..373689 115 tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_009009_SSA_0381_SSA_0382|hypothetical protein:Transcriptional regulator, AraC family (arabinose-binding/dimerisation), putative|POSITIVE:NEGATIVE|[373575,373689]|115 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcatnnnnnnncgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct tatcttacaaaacatgttgctgtttctgtctttctttgaaatcagcataaaaaaacgaataccctcaacttattttgattagcaggtattcgttttttattttctatttagagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUUACAAAACAUGUUGCUGUUUCUGUCUUUCUUUGAAAUCAGCAUAAAAAAACGAAUACCCUCAACUUAUUUUGAUUAGCAGGUAUUCGUUUUUUAUUUUCUAUUUAGAGCU ..(((............(((((((((...........)))).)))))..((((((((((((((.((((......))))......))))))))))))))...........)))... (-23.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUCUAAAUAGAAAAUAAAAAACGAAUACCUGCUAAUCAAAAUAAGUUGAGGGUAUUCGUUUUUUUAUGCUGAUUUCAAAGAAAGACAGAAACAGCAACAUGUUUUGUAAGAUA ...(((..((((((...(((((((((((((((..((((........)))).)))))))))))))))..(((((.((((...........))))))))).....)))))).))).. (-27.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 108 62 139 96 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 270 68 26 181 134 NC_009009:SSA_1735|5end_UreX,_putative_1721072..1721302_NEGATIVE 269 105 62 226 182 NC_009009:SSA_0695|5end_hypothetical_protein_678449..678679_POSITIVE 249 104 66 223 184 NC_009009:SSA_0876|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870233..870463_POSITIVE 240 59 17 193 145 NC_009009:SSA_2272|5end_hypothetical_protein_2272876..2273106_NEGATIVE 238 109 63 142 101 NC_009009:SSA_1049|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064085..1064315_POSITIVE 237 47 19 71 39 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 231 104 63 102 59 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 228 47 12 214 174 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 228 47 1 141 91 NC_009009:SSA_0916|5end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase,_putative_928085..928315_POSITIVE 228 47 13 127 89 NC_009009:SSA_0503|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_502231..502461_POSITIVE 225 70 27 154 119 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 222 46 1 158 104 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 209 107 61 219 170 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 209 46 10 62 28 NC_009009:SSA_0663|5end_Acetyltransferase,_putative_648352..648582_POSITIVE 209 98 69 55 25 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 207 58 13 97 53 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 206 58 15 116 83 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 205 59 22 42 1 NC_009009:SSA_0595|5end_hypothetical_protein_586490..586720_POSITIVE 204 66 22 102 71 NC_009009:SSA_1671|5end_hypothetical_protein_1669304..1669534_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 105 62 118 74 NC_009009:SSA_0694|3end_Mutator_protein,_putative_678421..678571_POSITIVE 267 76 32 89 44 NC_009009:SSA_2014|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014019..2014169_NEGATIVE 249 104 66 150 111 NC_009009:SSA_0875|3end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_870240..870390_POSITIVE 231 104 63 83 40 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 228 108 63 41 1 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 228 47 13 139 101 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 225 70 27 127 92 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 223 106 61 140 85 NC_009009:SSA_1990|3end_Zn-porter_lipoprotein,_putative_1985402..1985552_NEGATIVE 222 46 1 114 60 NC_009009:SSA_0487|3end_Delta-aminolevulinic_acid_dehydratase,_putative_488400..488550_POSITIVE 214 105 77 91 65 NC_009009:SSA_0259|3end_Thiol_peroxidase,_putative_253013..253163_NEGATIVE 213 50 2 124 67 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 209 98 69 51 21 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 207 58 13 140 96 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 206 58 15 37 4 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 206 87 41 76 40 NC_009009:SSA_0904|3end_CshA-like_fibrillar_surface_protein_A_902958..903108_POSITIVE 204 104 61 126 76 NC_009009:SSA_1834|3end_30S_ribosomal_interface_protein_S30EA,_putative_1829652..1829802_NEGATIVE 199 46 1 150 106 NC_009009:SSA_1331|3end_Conserved_uncharacterized_protein_1346473..1346623_NEGATIVE 199 46 13 99 65 NC_009009:SSA_0650|3end_GTP-binding_protein_TypA/BipA,_putative_634604..634754_POSITIVE 198 47 19 50 28 NC_009009:SSA_2127|3end_hypothetical_protein_2130752..2130902_NEGATIVE 198 48 13 117 70 NC_009009:SSA_1895|3end_Ribosome-binding_factor_A,_putative_1890815..1890965_NEGATIVE