Origin IGS: atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc .........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 gggtttacaaacattgcttttcactatgctgtttaatatgttcatagcggttttatgttatatttttatggtatataatgtactttattatcggaattccggaatgaaatcgtcatagttatcctcgtaattatcgaatcatttataacctactgctagaaaaacaccattaaaaatgatacaatcctcaatacaaaataactttgagaaaaaaat Mask Tandem Repeat Region ================================================ atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc Find is-nt database================================================ Query_seq: TDE0493:TDE0494|TDE0493:TDE0494:hypothetical protein:hypothetical protein:<-<-:549433..549648 216 atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0493:TDE0494|TDE0493:TDE0494:hypothetical protein:hypothetical protein:<-<-:549433..549648 216 atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0493:TDE0494|TDE0493:TDE0494:hypothetical protein:hypothetical protein:<-<-:549433..549648 216 atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 102 End: 203 ..................................................................................................... S S K M G S N R Y Y L V N Y V M F I Y C L V A I F M N F L M T F L M ............. atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc 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================================================ atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0493:TDE0494|TDE0493:TDE0494:hypothetical protein:hypothetical protein:<-<-:549433..549648 216 atttttttctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc Intra-Species Hit: Count: 1 Min: 9 Max: 216 Len: 208 Subject: NC_002967_TDE0493_TDE0494|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[549433,549648]|216 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 208 Query Start:9 Query End:216 Subject Strand: POSITIVE Subject Start: 9 Subject End: 216 ........ctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc ........ctcaaagttattttgtattgaggattgtatcatttttaatggtgtttttctagcagtaggttataaatgattcgataattacgaggataactatgacgatttcattccggaattccgataataaagtacattatataccataaaaatataacataaaaccgctatgaacatattaaacagcatagtgaaaagcaatgtttgtaaaccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAAAGUUAUUUUGUAUUGAGGAUUGUAUCAUUUUUAAUGGUGUUUUUCUAGCAGUAGGUUAUAAAUGAUUCGAUAAUUACGAGGAUAACUAUGACGAUUUCAUUCCGGAAUUCCGAUAAUAAAGUACAUUAUAUACCAUAAAAAUAUAACAUAAAACCGCUAUGAACAUAUUAAACAGCAUAGUGAAAAGCAAUGUUUGUAAACCC .(((.((((((((((((......((((.(((((((.(((((.((((.....)))).)..)))).))))))).))))...))))).))))))).)))...........(((....))).............................((((((((.....(((((((..............))))))).......))).)))))..... (-32.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUUUACAAACAUUGCUUUUCACUAUGCUGUUUAAUAUGUUCAUAGCGGUUUUAUGUUAUAUUUUUAUGGUAUAUAAUGUACUUUAUUAUCGGAAUUCCGGAAUGAAAUCGUCAUAGUUAUCCUCGUAAUUAUCGAAUCAUUUAUAACCUACUGCUAGAAAAACACCAUUAAAAAUGAUACAAUCCUCAAUACAAAAUAACUUUGAG ((((((..(((((..((..........)))))))......(((.(((((((.....((((((.....(((((...........((((((.((((....)))))))))).(((..((((((((....)))))))))))))))).))))))..)))))))))))))).))..................(((((............))))) (-33.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 836 120 71 219 170 NC_002967:TDE0493|5end_hypothetical_protein_549342..549572_NEGATIVE 330 50 6 199 156 NC_002967:TDE0499|5end_hypothetical_protein_553497..553727_NEGATIVE 308 64 24 175 138 NC_002967:TDE0521|5end_carboxylesterase_family_protein_568252..568482_NEGATIVE 253 89 44 44 1 NC_002967:TDE0909|5end_type_II_DNA_modification_methyltransferase_M.TdeIII_927166..927396_POSITIVE 252 77 41 207 171 NC_002967:TDE0050|5end_RNA_methyltransferase,_TrmH_family_60071..60301_NEGATIVE 251 57 11 80 37 NC_002967:TDE2733|5end_hypothetical_protein_2788573..2788803_POSITIVE 242 50 14 140 102 NC_002967:TDE1545|5end_phosphoribosyl_transferase_domain_protein_1588330..1588560_POSITIVE 238 128 84 56 11 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 237 130 81 219 164 NC_002967:TDE0910|5end_hypothetical_protein_928774..929004_POSITIVE 231 99 53 229 180 NC_002967:TDE1899|5end_hypothetical_protein_1921088..1921318_NEGATIVE 224 59 12 162 115 NC_002967:TDE0668|5end_FeS_assembly_protein_SufD_705759..705989_POSITIVE 223 146 104 96 48 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 220 55 20 90 53 NC_002967:TDE2357|5end_iron_compound_ABC_transporter,_permease_protein_2392038..2392268_POSITIVE 219 182 141 77 41 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 218 140 93 90 43 NC_002967:TDE2456|5end_hypothetical_protein_2484573..2484803_NEGATIVE 218 57 14 152 113 NC_002967:TDE0829|5end_putative_aminopeptidase_2_851477..851707_NEGATIVE 218 117 71 184 126 NC_002967:TDE0088|5end_Trk_system_potassium_uptake_protein_TrkH_105347..105577_POSITIVE 216 128 81 218 172 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 213 50 1 79 33 NC_002967:TDE0512|5end_hypothetical_protein_561442..561672_NEGATIVE 209 146 106 134 93 NC_002967:TDE1685|5end_GGDEF_domain_protein_1740315..1740545_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 50 6 132 89 NC_002967:TDE0500|3end_hypothetical_protein_553564..553714_NEGATIVE 251 57 11 47 4 NC_002967:TDE2732|3end_hypothetical_protein_2788620..2788770_POSITIVE 242 50 14 76 38 NC_002967:TDE1544|3end_mannosyltransferase,_putative_1588346..1588496_POSITIVE 240 120 78 151 113 NC_002967:TDE2035|3end_glucose-1-phosphate_adenylyltransferase_2064155..2064305_POSITIVE 238 128 84 63 18 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 229 86 41 102 58 NC_002967:TDE2778|3end_PspC_domain_protein_2829371..2829521_NEGATIVE 223 146 104 72 24 NC_002967:TDE1095|3end_alanine_racemase_1131045..1131195_POSITIVE 220 55 20 70 33 NC_002967:TDE2356|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2392098..2392248_POSITIVE 220 86 41 90 46 NC_002967:TDE1931|3end_cytidine_deaminase_1949020..1949170_POSITIVE 208 114 76 61 21 NC_002967:TDE2180|3end_tRNA_modification_GTPase_2210590..2210740_NEGATIVE 207 140 101 96 51 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 200 52 11 76 38 NC_002967:TDE1107|3end_transcription_elongation_factor_NusA_1140890..1141040_NEGATIVE 197 59 19 42 1 NC_002967:TDE1885|3end_hypothetical_protein_1907146..1907296_POSITIVE 197 117 76 134 88 NC_002967:TDE1054|3end_methyl-accepting_chemotaxis_protein_1082998..1083148_POSITIVE 197 146 101 65 17 NC_002967:TDE0171|3end_nuclease_SbcCD,_C_subunit,_putative_203137..203287_POSITIVE 196 113 82 43 3 NC_002967:TDE0753|3end_hypothetical_protein_793918..794068_POSITIVE 195 60 11 130 82 NC_002967:TDE2088|3end_C4_zinc_finger_domain_protein,_DksA/TraR_family_2116183..2116333_POSITIVE 194 90 45 118 74 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 194 55 32 90 62 NC_002967:TDE1833|3end_hypothetical_protein_1866277..1866427_NEGATIVE 194 55 32 90 62 NC_002967:TDE1777|3end_hypothetical_protein_1819956..1820106_NEGATIVE