Origin IGS: cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg .........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 caaaactttttagaggtatttatgaagaagaacagaatttttttaagttttttgattttaattttgtttacggtatttttaagcgttacctgcaaacaaaatgtaggtttgggcggaactatcgatattgaacgcccggagggagaaattacttatcctgatgcaggagaaactcctattaggggtagttttgtg Mask Tandem Repeat Region ================================================ cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg Find is-nt database================================================ Query_seq: TDE2708:TDE2709|TDE2708:TDE2709:hypothetical protein:BNR domain protein:<-<-:2761589..2761783 195 cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2708:TDE2709|TDE2708:TDE2709:hypothetical protein:BNR domain protein:<-<-:2761589..2761783 195 cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2708:TDE2709|TDE2708:TDE2709:hypothetical protein:BNR domain protein:<-<-:2761589..2761783 195 cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 47 End: 193 .............................................. M S P S G R S I S I V P P K P T F C L Q V T L K N T V N K I K I K K L K K I L F F F I N T S K K F .. Protein_Len: 37 Strand: - Start: 68 End: 178 ................................................................... Y R Y N R G F R C K T Q L Y R K F I G Y V F N F D F F K F F N Q E E E Y M ................. Protein_Len: 58 Strand: - Start: 1 End: 174 V F S G R I P T E G A D P Y T I E G E P R E I D I T G G L G V N Q K C T V S L F V T F L I L I L F S L F I R N K K M ..................... cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg 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================================================ cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2708:TDE2709|TDE2708:TDE2709:hypothetical protein:BNR domain protein:<-<-:2761589..2761783 195 cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgcttaaaaataccgtaaacaaaattaaaatcaaaaaacttaaaaaaattctgttcttcttcataaatacctctaaaaagttttg Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: NC_002967_TDE2708_TDE2709|hypothetical protein:BNR domain protein|NEGATIVE:NEGATIVE|[2761589,2761783]|195 HSP 1 e-value: 2.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgct................................................................................. cacaaaactacccctaataggagtttctcctgcatcaggataagtaatttctccctccgggcgttcaatatcgatagttccgcccaaacctacattttgtttgcaggtaacgct................................................................................. HSP 2 e-value: 2.0E-12 bit: 73.8 Len: 37 Query Start:159 Query End:195 Subject Strand: POSITIVE Subject Start: 159 Subject End: 195 ..............................................................................................................................................................ttctgttcttcttcataaatacctctaaaaagttttg ..............................................................................................................................................................ttctgttcttcttcataaatacctctaaaaagttttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACAAAACUACCCCUAAUAGGAGUUUCUCCUGCAUCAGGAUAAGUAAUUUCUCCCUCCGGGCGUUCAAUAUCGAUAGUUCCGCCCAAACCUACAUUUUGUUUGCAGGUAACGCUUAAAAAUACCGUAAACAAAAUUAAAAUCAAAAAACUUAAAAAAAUUCUGUUCUUCUUCAUAAAUACCUCUAAAAAGUUUUG ..(((((((...(((..((((((...))))))....))).(((((.............(((((.................)))))........(((((((((((.((((...........)))))))))))))))............)))))....................................))))))) (-36.53) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAACUUUUUAGAGGUAUUUAUGAAGAAGAACAGAAUUUUUUUAAGUUUUUUGAUUUUAAUUUUGUUUACGGUAUUUUUAAGCGUUACCUGCAAACAAAAUGUAGGUUUGGGCGGAACUAUCGAUAUUGAACGCCCGGAGGGAGAAAUUACUUAUCCUGAUGCAGGAGAAACUCCUAUUAGGGGUAGUUUUGUG .....((((((.(.((..((((.......((((((((((.....(((((....))))).)))))))))).(((((.(((...((.(.(((((((.......)))))))..).)).))).)))))....))))..))))))))).(((((((((...((((((..(((((...))))))))))))))))))))... (-46.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 986 100 51 191 142 NC_002967:TDE2708|5end_hypothetical_protein_2761498..2761728_NEGATIVE 350 95 51 124 76 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 333 96 51 150 102 NC_002967:TDE1292|5end_TldD/PmbA_family_protein_1330621..1330851_NEGATIVE 329 67 21 143 93 NC_002967:TDE0916|5end_ABC_transporter,_ATP-binding/permease_protein_933359..933589_POSITIVE 323 97 52 102 39 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 313 85 57 65 27 NC_002967:TDE2395|5end_Jag_protein,_putative_2423454..2423684_NEGATIVE 311 60 11 184 135 NC_002967:TDE1086|5end_conserved_hypothetical_protein_TIGR00255_1117786..1118016_POSITIVE 298 92 54 147 98 NC_002967:TDE1084|5end_folylpolyglutamate_synthetase,_putative_1116286..1116516_NEGATIVE 293 115 71 225 164 NC_002967:TDE2342|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2380383..2380613_NEGATIVE 291 66 28 194 145 NC_002967:TDE2405|5end_hypothetical_protein_2432050..2432280_NEGATIVE 291 91 57 152 112 NC_002967:TDE2227|5end_hypothetical_protein_2266395..2266625_POSITIVE 290 97 51 142 95 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 285 40 4 50 13 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 281 60 11 103 50 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 279 88 42 106 65 NC_002967:TDE2199|5end_racemase,_Asp/Glu/Hydantoin_family_2237150..2237380_NEGATIVE 279 67 27 173 138 NC_002967:TDE1313|5end_signal_peptidase_I_1350650..1350880_POSITIVE 278 90 44 222 168 NC_002967:TDE1287|5end_transcription-repair_coupling_factor_1322738..1322968_POSITIVE 277 125 81 145 102 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 276 60 11 172 121 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 274 79 31 128 70 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 95 51 119 71 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 333 96 51 150 102 NC_002967:TDE1293|3end_TldD/PmbA_family_protein_1330621..1330771_NEGATIVE 323 97 52 88 25 NC_002967:TDE1144|3end_hypothetical_protein_1181848..1181998_NEGATIVE 297 85 44 48 4 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 295 108 61 68 14 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 291 91 57 89 49 NC_002967:TDE2226|3end_ABC_transporter,_substrate-binding_protein,_putative_2266412..2266562_POSITIVE 276 60 11 85 34 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 272 83 44 135 103 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 264 90 46 120 71 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 262 90 47 62 16 NC_002967:TDE0099|3end_adenine-specific_DNA_modification_methyltransferase_117014..117164_POSITIVE 257 66 21 128 65 NC_002967:TDE0512|3end_hypothetical_protein_561284..561434_NEGATIVE 254 64 22 141 93 NC_002967:TDE2003|3end_internalin-related_protein_2023631..2023781_POSITIVE 253 83 44 82 37 NC_002967:TDE1894|3end_ferredoxin_1915041..1915191_POSITIVE 253 115 77 84 39 NC_002967:TDE1427|3end_glycosyl_transferase,_group_1_family_protein_1471190..1471340_POSITIVE 248 63 29 116 71 NC_002967:TDE2009|3end_hypothetical_protein_2031247..2031397_POSITIVE 247 99 54 52 10 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 247 63 27 45 15 NC_002967:TDE1543|3end_conserved_hypothetical_protein_TIGR00247_1587170..1587320_POSITIVE 245 66 21 107 70 NC_002967:TDE1645|3end_polypeptide_deformylase_1695543..1695693_NEGATIVE 244 85 47 91 38 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 243 92 58 54 18 NC_002967:TDE2040|3end_lipoprotein_releasing_system,_ATP-binding_protein_2069541..2069691_NEGATIVE