Origin IGS: ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagtgtctccaaaattattctgtgataagtatagcataatttatagagaaagtccgagtctataggaaaaatcactggtcttgtgttataataaatagaataccctaaaagg Mask Tandem Repeat Region ================================================ ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt Find is-nt database================================================ Query_seq: SSA_1318:SSA_1319|SSA_1318:SSA_1319:GTP-binding protein lepA, putative:hypothetical protein:<-->:1335912..1336024 113 ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1318:SSA_1319|SSA_1318:SSA_1319:GTP-binding protein lepA, putative:hypothetical protein:<-->:1335912..1336024 113 ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1318:SSA_1319|SSA_1318:SSA_1319:GTP-binding protein lepA, putative:hypothetical protein:<-->:1335912..1336024 113 ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 17 End: 112 ................ M Y Y N T R P V I F P I D S D F L Y K L C Y T Y H R I I L E T L . ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt 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================================================ ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1318:SSA_1319|SSA_1318:SSA_1319:GTP-binding protein lepA, putative:hypothetical protein:<-->:1335912..1336024 113 ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_1318_SSA_1319|GTP-binding protein lepA, putative:hypothetical protein|NEGATIVE:POSITIVE|[1335912,1336024]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt ccttttagggtattctatttattataacacaagaccagtgatttttcctatagactcggactttctctataaattatgctatacttatcacagaataattttggagacacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUUAGGGUAUUCUAUUUAUUAUAACACAAGACCAGUGAUUUUUCCUAUAGACUCGGACUUUCUCUAUAAAUUAUGCUAUACUUAUCACAGAAUAAUUUUGGAGACACUUU .......(((...(((((.........(((.......))).........))))))))......((((((.(((((((.((...........)).)))))))))))))...... (-13.67) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUGUCUCCAAAAUUAUUCUGUGAUAAGUAUAGCAUAAUUUAUAGAGAAAGUCCGAGUCUAUAGGAAAAAUCACUGGUCUUGUGUUAUAAUAAAUAGAAUACCCUAAAAGG ................((((((((......((((((((((....(((.((...(((.........)))....)).)))...))))))))))....)))))))).......... (-20.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 819 80 31 171 122 NC_009009:SSA_1318|5end_GTP-binding_protein_lepA,_putative_1335821..1336051_NEGATIVE 296 50 2 155 107 NC_009009:SSA_1494|5end_Conserved_uncharacterized_protein_1500773..1501003_NEGATIVE 270 93 55 112 62 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 256 78 44 140 109 NC_009009:SSA_1431|5end_hypothetical_protein_1438730..1438960_NEGATIVE 250 70 31 204 152 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 246 69 21 178 131 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 230 95 51 163 117 NC_009009:SSA_2214|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215835..2216065_NEGATIVE 230 59 13 63 16 NC_009009:SSA_2094|5end_Conserved_uncharacterized_protein_2098247..2098477_NEGATIVE 219 42 9 151 114 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 217 68 27 84 45 NC_009009:SSA_0244|5end_hypothetical_protein_238698..238928_POSITIVE 216 65 31 58 21 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 215 67 38 182 156 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 213 79 35 110 69 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 211 61 30 78 43 NC_009009:SSA_0734|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_716895..717125_POSITIVE 210 37 1 135 99 NC_009009:SSA_1718|5end_Site-specific_DNA-methyltransferase,_putative_1705811..1706041_NEGATIVE 208 90 42 211 162 NC_009009:SSA_0247|5end_hypothetical_protein_240032..240262_POSITIVE 207 66 33 222 179 NC_009009:SSA_1478|5end_Transposase_ORF1,_putative_1482889..1483119_POSITIVE 207 67 37 115 77 NC_009009:SSA_1323|5end_hypothetical_protein_1340450..1340680_NEGATIVE 207 79 31 41 5 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 206 89 42 92 41 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 93 55 140 90 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 250 70 31 119 67 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 246 69 21 72 25 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 233 60 15 139 91 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 233 68 31 73 31 NC_009009:SSA_0145|3end_Transcriptional_regulator,_TetR_family,_putative_138778..138928_NEGATIVE 228 76 31 71 12 NC_009009:SSA_0302|3end_Phosphoglycerate_kinase,_putative_296166..296316_POSITIVE 224 73 40 120 87 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 219 42 9 89 52 NC_009009:SSA_1406|3end_Histone_acetyltransferase_HPA2,_putative_1419455..1419605_NEGATIVE 213 79 35 76 35 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 211 61 30 40 5 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 210 80 35 62 6 NC_009009:SSA_0729|3end_hypothetical_protein_714677..714827_POSITIVE 207 67 37 137 99 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 207 79 31 44 8 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 206 89 42 120 69 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 203 45 6 92 44 NC_009009:SSA_0133|3end_50S_ribosomal_protein_L17,_putative_122562..122712_POSITIVE 202 69 23 122 72 NC_009009:SSA_2099|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103621..2103771_NEGATIVE 202 79 36 140 102 NC_009009:SSA_1623|3end_50S_ribosomal_protein_L11,_putative_1625543..1625693_NEGATIVE 202 68 31 79 42 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 201 49 5 49 10 NC_009009:SSA_1904|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1898233..1898383_NEGATIVE 201 66 28 76 41 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE