Origin IGS: gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcaactgtcggaattcctttgctttcaagaaacaacttcaatcaagccttttggcttgattttttgcataagtccctttacttttgactttattcatggtacaatagcccttgtgtgaaatagcagcaggaaagc Mask Tandem Repeat Region ================================================ gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct Find is-nt database================================================ Query_seq: SSA_2350:SSA_2351|SSA_2350:SSA_2351:30S ribosomal protein S4, putative:ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component, putative:<-<-:2352739..2352874 136 gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2350:SSA_2351|SSA_2350:SSA_2351:30S ribosomal protein S4, putative:ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component, putative:<-<-:2352739..2352874 136 gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2350:SSA_2351|SSA_2350:SSA_2351:30S ribosomal protein S4, putative:ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component, putative:<-<-:2352739..2352874 136 gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 21 End: 131 .................... V L A I T G H I F D F T F P S I C F I L G F P K I S T T E Q F C L F E S M ..... gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct 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: 86 Start: 31 End: 60 ..............................CTTTACTTTTGACTTTATTCATGGTACAAT............................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.9 Tail_Score: -5.09895 Start: 77 End: 94 Full_Region: aagaaacaacttcaa tcaagcc tttt ggcttga ttttttgcataagtc ............................................................................tcaagccttttggcttga.......................................... Find igs database================================================ Query_seq: SSA_2350:SSA_2351|SSA_2350:SSA_2351:30S ribosomal protein S4, putative:ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component, putative:<-<-:2352739..2352874 136 gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_009009_SSA_2350_SSA_2351|30S ribosomal protein S4, putative:ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component, putative|NEGATIVE:NEGATIVE|[2352739,2352874]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct gctttcctgctgctatttcacacaagggctattgtaccatgaataaagtcaaaagtaaagggacttatgcaaaaaatcaagccaaaaggcttgattgaagttgtttcttgaaagcaaaggaattccgacagttgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUCCUGCUGCUAUUUCACACAAGGGCUAUUGUACCAUGAAUAAAGUCAAAAGUAAAGGGACUUAUGCAAAAAAUCAAGCCAAAAGGCUUGAUUGAAGUUGUUUCUUGAAAGCAAAGGAAUUCCGACAGUUGCU ((((((..(..((.(((((...((.((((....)).)).))....(((((...........)))))........(((((((((....)))))))))))))).))..)..))))))...((....)).......... (-32.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAACUGUCGGAAUUCCUUUGCUUUCAAGAAACAACUUCAAUCAAGCCUUUUGGCUUGAUUUUUUGCAUAAGUCCCUUUACUUUUGACUUUAUUCAUGGUACAAUAGCCCUUGUGUGAAAUAGCAGCAGGAAAGC ..............((((((((((................(((((((((....)))))))))(((..((((((..(...((((..(((......))).)))).....)..))))))..))).))))).)))))... (-33.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 896 50 1 141 92 NC_009009:SSA_2350|5end_30S_ribosomal_protein_S4,_putative_2352648..2352878_NEGATIVE 274 128 81 62 21 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 266 66 28 178 132 NC_009009:SSA_0592|5end_hypothetical_protein_583626..583856_POSITIVE 265 44 7 183 143 NC_009009:SSA_1048|5end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1062947..1063177_POSITIVE 265 117 71 171 129 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 262 68 25 184 142 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 258 42 3 167 129 NC_009009:SSA_0270|5end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_262873..263103_POSITIVE 253 29 1 134 100 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 251 120 75 94 55 NC_009009:SSA_1204|5end_Phosphoglucomutase_1227787..1228017_POSITIVE 251 115 72 226 182 NC_009009:SSA_0962|5end_Lactoylglutathione_lyase,_putative_970965..971195_POSITIVE 250 41 1 58 11 NC_009009:SSA_1587|5end_hypothetical_protein_1589086..1589316_NEGATIVE 249 107 62 203 162 NC_009009:SSA_0972|5end_hypothetical_protein_979973..980203_POSITIVE 246 129 82 198 147 NC_009009:SSA_1711|5end_Endonuclease_III,_putative_1699636..1699866_NEGATIVE 245 90 41 89 37 NC_009009:SSA_1709|5end_hypothetical_protein_1698414..1698644_NEGATIVE 245 90 41 184 132 NC_009009:SSA_1708|5end_hypothetical_protein_1698319..1698549_NEGATIVE 245 50 1 132 59 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 244 38 5 50 8 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 241 40 1 140 98 NC_009009:SSA_2229|5end_hypothetical_protein_2228994..2229224_NEGATIVE 240 127 88 50 14 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 236 130 87 59 14 NC_009009:SSA_2126|5end_hypothetical_protein_2130755..2130985_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 119 71 88 41 NC_009009:SSA_0572|3end_Dehydrogenase,_putative_568552..568702_POSITIVE 253 29 1 133 99 NC_009009:SSA_0270|3end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_264314..264464_POSITIVE 251 115 72 112 68 NC_009009:SSA_0961|3end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_970931..971081_POSITIVE 250 120 71 118 59 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 246 129 82 103 52 NC_009009:SSA_1712|3end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1699731..1699881_NEGATIVE 245 50 1 132 59 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 241 129 81 67 7 NC_009009:SSA_0368|3end_hypothetical_protein_359722..359872_POSITIVE 240 127 88 96 60 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 236 130 87 62 17 NC_009009:SSA_2127|3end_hypothetical_protein_2130752..2130902_NEGATIVE 232 108 70 67 28 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 231 30 2 133 103 NC_009009:SSA_1583|3end_6-O-methylguanine-DNA_methyltransferase,_putative_1585523..1585673_NEGATIVE 228 29 1 39 4 NC_009009:SSA_1811|3end_6-phosphogluconate_dehydrogenase,_putative_1795406..1795556_NEGATIVE 228 44 1 106 62 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 228 128 81 138 104 NC_009009:SSA_0822|3end_Large_conductance_mechano-sensitive_ion_channel,_putative_801589..801739_NEGATIVE 227 47 5 144 104 NC_009009:SSA_1236|3end_Mutator_protein,_putative_1261240..1261390_NEGATIVE 226 111 81 94 68 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 226 27 4 67 45 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 225 126 85 52 15 NC_009009:SSA_1555|3end_Glucose-6-phosphate_1-dehydrogenase,_putative_1558482..1558632_POSITIVE 225 93 58 65 31 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 224 50 2 59 11 NC_009009:SSA_1957|3end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1953504..1953654_NEGATIVE