Origin IGS: tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaatttctatctatgaagatgggttctcagttagggtggggtggttaggctgccccaccttcctattattatctattgtgagattgagcgggggctaaaattctggaaaggattgaggatgccccttgtatcta Mask Tandem Repeat Region ================================================ tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc Find is-nt database================================================ Query_seq: SSA_2091:SSA_2092|SSA_2091:SSA_2092:Phosphotransferase system sugar-specific EII component, putative:Phosphotransferase system sugar-specific EII component, putative:<-<-:2095653..2095786 134 tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2091:SSA_2092|SSA_2091:SSA_2092:Phosphotransferase system sugar-specific EII component, putative:Phosphotransferase system sugar-specific EII component, putative:<-<-:2095653..2095786 134 tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2091:SSA_2092|SSA_2091:SSA_2092:Phosphotransferase system sugar-specific EII component, putative:Phosphotransferase system sugar-specific EII component, putative:<-<-:2095653..2095786 134 tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 40 End: 132 ....................................... G G S L R V I S L L L F T P C G L W G V R V S F G D E Y I S M .. Protein_Len: 31 Strand: - Start: 2 End: 94 . S V L P M R L G K W F K L G R E I E C Y I I I P L H P L R V M ........................................ tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc 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================================================ tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2091:SSA_2092|SSA_2091:SSA_2092:Phosphotransferase system sugar-specific EII component, putative:Phosphotransferase system sugar-specific EII component, putative:<-<-:2095653..2095786 134 tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_009009_SSA_2091_SSA_2092|Phosphotransferase system sugar-specific EII component, putative:Phosphotransferase system sugar-specific EII component, putative|NEGATIVE:NEGATIVE|[2095653,2095786]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc tagatacaaggggcatcctcaatcctttccagaattttagcccccgctcaatctcacaatagataataataggaaggtggggcagcctaaccaccccaccctaactgagaacccatcttcatagatagaaattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUACAAGGGGCAUCCUCAAUCCUUUCCAGAAUUUUAGCCCCCGCUCAAUCUCACAAUAGAUAAUAAUAGGAAGGUGGGGCAGCCUAACCACCCCACCCUAACUGAGAACCCAUCUUCAUAGAUAGAAAUUC .........(((.....((((.....((((........(((....)))..((((......)))).......))))(((((((...........))))))).....))))..))).................... (-26.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUUUCUAUCUAUGAAGAUGGGUUCUCAGUUAGGGUGGGGUGGUUAGGCUGCCCCACCUUCCUAUUAUUAUCUAUUGUGAGAUUGAGCGGGGGCUAAAAUUCUGGAAAGGAUUGAGGAUGCCCCUUGUAUCUA .((((((.((..((((.((((((.........(((((((((..(.....)..))))))))))))))).))))..))...))))))..((((((((...((((((....))))))......))))).)))..... (-47.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1078 120 71 211 162 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 330 113 71 184 138 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 315 117 78 67 30 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 311 83 44 76 27 NC_009009:SSA_1342|5end_Carbamoyl-phosphate_synthase_small_chain,_putative_1361017..1361247_NEGATIVE 310 115 72 67 9 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 299 120 71 213 166 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 299 122 83 229 182 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 298 117 72 71 15 NC_009009:SSA_1562|5end_hypothetical_protein_1566364..1566594_NEGATIVE 294 80 44 57 10 NC_009009:SSA_1522|5end_Cell_division_protein_FtsW,_putative_1531962..1532192_NEGATIVE 293 103 63 84 23 NC_009009:SSA_0298|5end_Malate_permease,_putative_291336..291566_POSITIVE 292 120 72 64 11 NC_009009:SSA_1196|5end_Acetyltransferase,_GNAT_family,_putative_1222052..1222282_NEGATIVE 290 118 76 71 19 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 285 117 74 136 82 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 284 115 71 185 138 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 283 88 42 178 130 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 274 119 75 94 39 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 274 33 9 87 56 NC_009009:SSA_0499|5end_ABC-type_dipeptide_transport_system,_periplasmic_component,_putative_498915..499145_POSITIVE 273 59 11 105 55 NC_009009:SSA_1671|5end_hypothetical_protein_1669304..1669534_POSITIVE 273 113 71 66 9 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 273 110 62 200 127 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 113 71 119 73 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 311 83 44 51 2 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 304 118 75 142 74 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 293 103 63 79 18 NC_009009:SSA_0297|3end_Malolactic_enzyme,_putative_291411..291561_POSITIVE 292 120 72 67 14 NC_009009:SSA_1197|3end_DNA_alkylation_repair_enzyme,_putative_1222049..1222199_NEGATIVE 290 118 76 74 22 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 285 117 74 136 82 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 284 115 71 120 73 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 281 113 71 48 1 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 274 119 75 91 36 NC_009009:SSA_1073|3end_Gamma-glutamyl_phosphate_reductase,_putative_1092228..1092378_POSITIVE 268 118 71 130 79 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 264 56 19 93 49 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 262 116 72 75 11 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE 260 44 7 44 6 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE 260 129 81 113 74 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 259 106 73 89 54 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 259 107 61 73 13 NC_009009:SSA_0460|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_463146..463296_POSITIVE 258 58 12 60 5 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 257 49 10 141 112 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 256 56 12 134 85 NC_009009:SSA_2302|3end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2303304..2303454_NEGATIVE