Origin IGS: agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttatttatcccccatcggcaaaagtttaacataatttattttattttacaatgggagctgttgagaagtgtacaagggtgtacgttgctcaagtattttgcagttaaacaaaaaaactgcattcccttacaaaaagactgaaggtgtgttataatacaatcgatgaaggagcagct Mask Tandem Repeat Region ================================================ agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag Find is-nt database================================================ Query_seq: TDE2678:TDE2679|TDE2678:TDE2679:alpha-amylase family protein:hypothetical protein:<-->:2719481..2719657 177 agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2678:TDE2679|TDE2678:TDE2679:alpha-amylase family protein:hypothetical protein:<-->:2719481..2719657 177 agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2678:TDE2679|TDE2678:TDE2679:alpha-amylase family protein:hypothetical protein:<-->:2719481..2719657 177 agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 13 End: 138 ............ M D C I I T H L Q S F C K G M Q F F C L T A K Y L S N V H P C T L L N S S H C K I K ....................................... Protein_Len: 44 Strand: - Start: 39 End: 170 ...................................... D K Q L P I C N K Q K V A F Y K L L T C G Q V S R L L E W Q L I F Y I I N F K Q R H P M ....... agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag 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: 84 Start: 22 End: 51 .....................CTTACAAAAAGACTGAAGGTGTGTTATAAT.............................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 125 End: 154 ............................................................................................................................ATTGTAAAATAAAATAAATTATGTTAAACT....................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2678:TDE2679|TDE2678:TDE2679:alpha-amylase family protein:hypothetical protein:<-->:2719481..2719657 177 agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_002967_TDE2678_TDE2679|alpha-amylase family protein:hypothetical protein|NEGATIVE:POSITIVE|[2719481,2719657]|177 HSP 1 e-value: 2.0E-83 bit: 309.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagnnnnnnngtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag agctgctccttcatcgattgtattataacacaccttcagtctttttgtaagggaatgcagtttttttgtttaactgcaaaatacttgagcaacgtacacccttgtacacttctcaacagctcccattgtaaaataaaataaattatgttaaacttttgccgatgggggataaataag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGCUCCUUCAUCGAUUGUAUUAUAACACACCUUCAGUCUUUUUGUAAGGGAAUGCAGUUUUUUUGUUUAACUGCAAAAUACUUGAGCAACGUACACCCUUGUACACUUCUCAACAGCUCCCAUUGUAAAAUAAAAUAAAUUAUGUUAAACUUUUGCCGAUGGGGGAUAAAUAAG ......((((((((((.........(((((............((((((((((((.(((((((.........)))))))......(((((....(((((....)))))....)))))....)))).))))))))............))))).........))))))))))........ (-39.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUUUAUCCCCCAUCGGCAAAAGUUUAACAUAAUUUAUUUUAUUUUACAAUGGGAGCUGUUGAGAAGUGUACAAGGGUGUACGUUGCUCAAGUAUUUUGCAGUUAAACAAAAAAACUGCAUUCCCUUACAAAAAGACUGAAGGUGUGUUAUAAUACAAUCGAUGAAGGAGCAGCU ........(((..((((((........(((((((.((((.(((.((((.....((((....(((((...((((((....))))))...)))))......(((((((.........))))))).))))....))))))).))))..)))))))........))))))..)))...... (-40.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 926 130 81 221 172 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 350 80 31 167 120 NC_002967:TDE0975|5end_hypothetical_protein_998921..999151_POSITIVE 305 48 1 79 30 NC_002967:TDE1763|5end_hypothetical_protein_1811205..1811435_NEGATIVE 295 56 11 147 102 NC_002967:TDE0948|5end_hypothetical_protein_971837..972067_NEGATIVE 291 80 34 218 156 NC_002967:TDE1985|5end_hypothetical_protein_2000329..2000559_NEGATIVE 278 133 109 29 4 NC_002967:TDE1613|5end_hypothetical_protein_1661625..1661855_POSITIVE 275 78 31 81 42 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 275 78 31 157 118 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 272 50 2 115 53 NC_002967:TDE1151|5end_hypothetical_protein_1188534..1188764_NEGATIVE 271 128 91 43 2 NC_002967:TDE1139|5end_hypothetical_protein_1168615..1168845_NEGATIVE 260 118 74 111 60 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 260 39 2 48 11 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 260 55 13 80 44 NC_002967:TDE0689|5end_5-methylthioribose_kinase_725690..725920_POSITIVE 256 78 32 199 146 NC_002967:TDE2115|5end_HAMP_domain_protein_2144760..2144990_NEGATIVE 256 100 51 173 123 NC_002967:TDE1075|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1105962..1106192_POSITIVE 254 42 1 172 131 NC_002967:TDE0390|5end_hypothetical_protein_441246..441476_POSITIVE 251 79 31 224 171 NC_002967:TDE1278|5end_conserved_hypothetical_protein_TIGR01440_1312788..1313018_NEGATIVE 251 126 89 91 55 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 245 58 23 213 181 NC_002967:TDE2166|5end_hydrogenase_nickel_insertion_protein_HypA_2198084..2198314_NEGATIVE 245 101 73 203 172 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 50 1 143 95 NC_002967:TDE1905|3end_hypothetical_protein_1923722..1923872_NEGATIVE 340 80 34 41 2 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 305 48 1 57 8 NC_002967:TDE1764|3end_hypothetical_protein_1811227..1811377_NEGATIVE 272 50 2 122 60 NC_002967:TDE1152|3end_head-to-tail_joining_protein,_putative_1188527..1188677_NEGATIVE 260 118 74 118 67 NC_002967:TDE1864|3end_crossover_junction_endodeoxyribonuclease_RuvC_1888572..1888722_NEGATIVE 260 55 13 67 31 NC_002967:TDE0688|3end_hypothetical_protein_725757..725907_POSITIVE 248 70 34 147 105 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 248 110 64 145 85 NC_002967:TDE0350|3end_MATE_efflux_family_protein_395019..395169_POSITIVE 247 80 32 135 93 NC_002967:TDE1074|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1106029..1106179_POSITIVE 245 101 73 110 79 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 241 90 43 91 39 NC_002967:TDE2049|3end_bacterial_extracellular_solute-binding_proteins,_family_5_2079537..2079687_POSITIVE 233 63 31 126 88 NC_002967:TDE0771|3end_ribosomal_protein_S19_809153..809303_POSITIVE 230 130 84 121 81 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 229 101 73 110 79 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 227 79 41 58 14 NC_002967:TDE2691|3end_hypothetical_protein_2729346..2729496_POSITIVE 226 101 73 86 55 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 225 65 30 137 93 NC_002967:TDE1959|3end_hypothetical_protein_1973805..1973955_NEGATIVE 224 107 61 143 81 NC_002967:TDE1085|3end_UDP-N-acetylmuramate--L-alanine_ligase_1117850..1118000_POSITIVE 222 130 83 55 3 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 221 68 30 137 93 NC_002967:TDE1711|3end_RelA/SpoT_domain_protein_1765552..1765702_NEGATIVE