Origin IGS: agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt .........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 acattaactcctccctataatatatggaattcgaattatataataaagtaaatatattatcaataatagacttttgattttacatgatttttataagacttaattaaaattggttttgaatttatatagcataaatattttttttgtgctaaaataagagtttaggaattagggtatcaaact Mask Tandem Repeat Region ================================================ agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt Find is-nt database================================================ Query_seq: TDE2782:TDE2783|TDE2782:TDE2783:ABC transporter, ATP-binding/permease protein:methyl-accepting chemotaxis protein:<-->:2834367..2834549 183 agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2782:TDE2783|TDE2782:TDE2783:ABC transporter, ATP-binding/permease protein:methyl-accepting chemotaxis protein:<-->:2834367..2834549 183 agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2782:TDE2783|TDE2782:TDE2783:ABC transporter, ATP-binding/permease protein:methyl-accepting chemotaxis protein:<-->:2834367..2834549 183 agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 29 End: 121 ............................ M L A Q K K Y L C Y I N S K P I L I K S Y K N H V K S K V Y Y .............................................................. agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt 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: 90 Start: 120 End: 149 .......................................................................................................................ATTGATAATATATTTACTTTATTATATAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2782:TDE2783|TDE2782:TDE2783:ABC transporter, ATP-binding/permease protein:methyl-accepting chemotaxis protein:<-->:2834367..2834549 183 agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtctattattgataatatatttactttattatataattcgaattccatatattatagggaggagttaatgt Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE2782_TDE2783|ABC transporter, ATP-binding/permease protein:methyl-accepting chemotaxis protein|NEGATIVE:POSITIVE|[2834367,2834549]|183 HSP 1 e-value: 1.0E-44 bit: 180.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 agtttgataccctaattcctaaactcttattttagcacnnnnnnnntatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtc.................................................................... agtttgataccctaattcctaaactcttattttagcacaaaaaaaatatttatgctatataaattcaaaaccaattttaattaagtcttataaaaatcatgtaaaatcaaaagtc.................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUGAUACCCUAAUUCCUAAACUCUUAUUUUAGCACAAAAAAAAUAUUUAUGCUAUAUAAAUUCAAAACCAAUUUUAAUUAAGUCUUAUAAAAAUCAUGUAAAAUCAAAAGUC ..((((((..................((((..(((((.(((.......))).))))).)))).........................(((((.......))))).)))))).... ( -7.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUUUUGAUUUUACAUGAUUUUUAUAAGACUUAAUUAAAAUUGGUUUUGAAUUUAUAUAGCAUAAAUAUUUUUUUUGUGCUAAAAUAAGAGUUUAGGAAUUAGGGUAUCAAACU ....((((((....(.(((((((((...(((((..((((((....)))))).......(((((((((.......)))))))))......)))))))))))))).)..)))))).. (-20.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 691 50 1 141 92 NC_002967:TDE2782|5end_ABC_transporter,_ATP-binding/permease_protein_2834276..2834506_NEGATIVE 223 35 4 69 36 NC_002967:TDE1748|5end_GTP-binding_protein,_GTP1/Obg_family_1803080..1803310_NEGATIVE 212 39 10 115 86 NC_002967:TDE0631|5end_sigma_factor_regulatory_protein,_putative_665295..665525_POSITIVE 194 42 1 189 152 NC_002967:TDE2051|5end_hypothetical_protein_2080298..2080528_NEGATIVE 188 37 1 115 82 NC_002967:TDE0842|5end_cytoplasmic_filament_protein_A_861715..861945_POSITIVE 178 48 8 76 17 NC_002967:TDE1569|5end_hypothetical_protein_1619785..1620015_POSITIVE 170 74 54 61 42 NC_002967:TDE0106|5end_hypothetical_protein_126546..126776_NEGATIVE 165 105 84 220 200 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 165 43 7 159 115 NC_002967:TDE1843|5end_hypothetical_protein_1873005..1873235_NEGATIVE 163 30 4 116 91 NC_002967:TDE1954|5end_prevent-host-death_family_protein_1969786..1970016_POSITIVE 162 37 3 156 124 NC_002967:TDE2544|5end_hypothetical_protein_2571036..2571266_NEGATIVE 160 58 15 78 39 NC_002967:TDE1690|5end_hypothetical_protein_1747200..1747430_NEGATIVE 159 62 21 209 166 NC_002967:TDE1893|5end_GTP-binding_protein_LepA_1914017..1914247_NEGATIVE 159 34 6 95 55 NC_002967:TDE0029|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_37722..37952_NEGATIVE 156 98 55 98 55 NC_002967:TDE2427|5end_preprotein_translocase,_SecE_subunit_2455982..2456212_NEGATIVE 152 37 9 122 95 NC_002967:TDE1475|5end_flagellar_filament_core_protein_1522191..1522421_NEGATIVE 150 35 2 209 182 NC_002967:TDE1732|5end_hypothetical_protein_1787030..1787260_POSITIVE 150 110 62 57 17 NC_002967:TDE0034|5end_hypothetical_protein_41450..41680_NEGATIVE 149 37 10 192 160 NC_002967:TDE0423|5end_hypothetical_protein_476601..476831_POSITIVE 148 90 64 104 73 NC_002967:TDE1697|5end_phosphoglycerate_mutase_1756259..1756489_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 212 39 10 111 82 NC_002967:TDE0630|3end_sigma_factor_regulatory_protein,_putative_665371..665521_POSITIVE 204 36 1 125 86 NC_002967:TDE1291|3end_HD_domain_protein_1328638..1328788_NEGATIVE 198 35 3 100 65 NC_002967:TDE0254|3end_hypothetical_protein_289312..289462_POSITIVE 183 42 4 96 61 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 165 105 84 107 87 NC_002967:TDE2739|3end_hypothetical_protein_2795169..2795319_POSITIVE 149 37 10 121 89 NC_002967:TDE0422|3end_bacteriocin-type_signal_domain_protein_476610..476760_POSITIVE 147 25 1 150 126 NC_002967:TDE1660|3end_leucine_Rich_Repeat_domain_protein_1710710..1710860_NEGATIVE 147 37 5 107 77 NC_002967:TDE0914|3end_hypothetical_protein_933070..933220_NEGATIVE 146 26 10 76 55 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 144 37 16 115 97 NC_002967:TDE1393|3end_hypothetical_protein_1433167..1433317_POSITIVE 143 90 67 27 1 NC_002967:TDE1698|3end_serine/threonine_protein_phosphatase_family_protein_1756336..1756486_NEGATIVE 142 37 4 118 79 NC_002967:TDE2556|3end_hypothetical_protein_2582316..2582466_NEGATIVE 142 60 22 125 89 NC_002967:TDE2141|3end_hypothetical_protein_2175583..2175733_NEGATIVE 142 39 1 36 2 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 142 97 53 128 84 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 142 29 3 93 63 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 141 36 1 101 72 NC_002967:TDE2683|3end_sigma_factor_WhiG_2723367..2723517_NEGATIVE 141 108 84 151 124 NC_002967:TDE0658|3end_ABC_transporter,_permease_protein_695679..695829_POSITIVE 141 109 71 131 89 NC_002967:TDE0652|3end_hypothetical_protein_688991..689141_POSITIVE 141 110 84 146 120 NC_002967:TDE0540|3end_hypothetical_protein_582347..582497_POSITIVE