Origin IGS: agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt .........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 aatgtctcctgtaaaaatattatagtttacgatgaacagcctaacacttttgcagccttgtgtaaagtggggaaaaatttccacaccgtcctttgacacaaagtatctaaagtgcttgacaatccgtttttgtttgtatatatttttttatcaaataagtgacggcaccgtcatattgacaaaaccgttaagattgtataacatatagtatgtttactatggctaattttttaggataaaataattaaatggaggattctct Mask Tandem Repeat Region ================================================ agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt Find is-nt database================================================ Query_seq: TDE0924:TDE0925|TDE0924:TDE0925:ABC transporter, ATP-binding/permease protein:peptidase T:<-->:947725..947986 262 agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0924:TDE0925|TDE0924:TDE0925:ABC transporter, ATP-binding/permease protein:peptidase T:<-->:947725..947986 262 agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0924:TDE0925|TDE0924:TDE0925:ABC transporter, ATP-binding/permease protein:peptidase T:<-->:947725..947986 262 agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 120 End: 233 ....................................................................................................................... M Y T N K N G L S S T L D T L C Q R T V W K F F P T L H K A A K V L G C S S ............................. Protein_Len: 47 Strand: + Start: 122 End: 262 ......................................................................................................................... M Y K Q K R I V K H F R Y F V S K D G V E I F P H F T Q G C K S V R L F I V N Y N I F T G D I Protein_Len: 58 Strand: - Start: 58 End: 231 ......................................................... I N Y L R L P K T L I V T G D S I Q Y F F I Y L C F R I T L C K L Y K T D F S P T S I K G W K V C P Q L L T L S N M ............................... agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt 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: 87 Start: 59 End: 88 ..........................................................ATTGACAAAACCGTTAAGATTGTATAACAT.............................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 87 Start: 119 End: 148 ......................................................................................................................CTTGACAATCCGTTTTTGTTTGTATATATT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0924:TDE0925|TDE0924:TDE0925:ABC transporter, ATP-binding/permease protein:peptidase T:<-->:947725..947986 262 agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: NC_002967_TDE0924_TDE0925|ABC transporter, ATP-binding/permease protein:peptidase T|NEGATIVE:POSITIVE|[947725,947986]|262 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 262 Query Start:1 Query End:262 Subject Strand: POSITIVE Subject Start: 1 Subject End: 262 agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgatnnnnnnntatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt agagaatcctccatttaattattttatcctaaaaaattagccatagtaaacatactatatgttatacaatcttaacggttttgtcaatatgacggtgccgtcacttatttgataaaaaaatatatacaaacaaaaacggattgtcaagcactttagatactttgtgtcaaaggacggtgtggaaatttttccccactttacacaaggctgcaaaagtgttaggctgttcatcgtaaactataatatttttacaggagacatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGAAUCCUCCAUUUAAUUAUUUUAUCCUAAAAAAUUAGCCAUAGUAAACAUACUAUAUGUUAUACAAUCUUAACGGUUUUGUCAAUAUGACGGUGCCGUCACUUAUUUGAUAAAAAAAUAUAUACAAACAAAAACGGAUUGUCAAGCACUUUAGAUACUUUGUGUCAAAGGACGGUGUGGAAAUUUUUCCCCACUUUACACAAGGCUGCAAAAGUGUUAGGCUGUUCAUCGUAAACUAUAAUAUUUUUACAGGAGACAUU ........((((..((((((.(((......))).)))))).....(((((.(((.((((.(((.(((...........(((((((((..(((((....))))).....)))))))))....................((((.(((.((((((((.(...((((((((.((((...((...((((....)))))).))))))))))))...).)))))))).))).))))...)))))))))).))).))))).))))..... (-59.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUCUCCUGUAAAAAUAUUAUAGUUUACGAUGAACAGCCUAACACUUUUGCAGCCUUGUGUAAAGUGGGGAAAAAUUUCCACACCGUCCUUUGACACAAAGUAUCUAAAGUGCUUGACAAUCCGUUUUUGUUUGUAUAUAUUUUUUUAUCAAAUAAGUGACGGCACCGUCAUAUUGACAAAACCGUUAAGAUUGUAUAACAUAUAGUAUGUUUACUAUGGCUAAUUUUUUAGGAUAAAAUAAUUAAAUGGAGGAUUCUCU ....(((((.(((((.(((((((((((((((((...........((((((....((.(((((((((((((((((....))))...)))..)))).)))))).))....))))))((((((...(((((((((((((.(((........))))))))))).)))))....(((.....)))......)))))))))))).))).)))))))).))))).....((((....))))................)))))....... (-57.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 826 100 51 191 142 NC_002967:TDE0924|5end_ABC_transporter,_ATP-binding/permease_protein_947634..947864_NEGATIVE 295 228 191 135 91 NC_002967:TDE1260|5end_cholinephosphate_cytidylyltransferase/choline_kinase_1294028..1294258_POSITIVE 273 184 141 100 57 NC_002967:TDE0760|5end_hypothetical_protein_799436..799666_POSITIVE 269 202 164 222 180 NC_002967:TDE0562|5end_hypothetical_protein_594899..595129_POSITIVE 264 210 166 206 169 NC_002967:TDE1320|5end_ComEC/Rec2-related_protein_1357764..1357994_POSITIVE 263 106 65 195 156 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 263 180 137 84 34 NC_002967:TDE1961|5end_PIN_domain_protein_1974975..1975205_NEGATIVE 260 230 185 150 90 NC_002967:TDE1021|5end_lipoprotein,_putative_1053564..1053794_NEGATIVE 256 210 161 69 3 NC_002967:TDE0514|5end_hypothetical_protein_562743..562973_NEGATIVE 255 193 151 210 165 NC_002967:TDE0915|5end_hypothetical_protein_933320..933550_NEGATIVE 254 181 150 160 128 NC_002967:TDE2208|5end_conserved_hypothetical_protein_TIGR00486_2246733..2246963_POSITIVE 253 114 77 198 162 NC_002967:TDE2625|5end_ABC_transporter,_ATP-binding/permease_protein_2666664..2666894_NEGATIVE 252 231 191 152 118 NC_002967:TDE0986|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1013061..1013291_POSITIVE 246 250 204 207 157 NC_002967:TDE1179|5end_iron_compound_ABC_transporter,_permease_protein_1208906..1209136_NEGATIVE 244 178 137 215 179 NC_002967:TDE0325|5end_hypothetical_protein_358051..358281_POSITIVE 243 216 172 157 117 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 240 235 193 130 80 NC_002967:TDE1073|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1103515..1103745_POSITIVE 240 220 171 210 166 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 239 210 161 218 169 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 239 239 202 44 3 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 98 51 139 89 NC_002967:TDE1620|3end_hypothetical_protein_1666959..1667109_NEGATIVE 276 110 67 52 9 NC_002967:TDE1062|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1090387..1090537_POSITIVE 269 95 56 73 27 NC_002967:TDE0570|3end_hypothetical_protein_600956..601106_POSITIVE 263 180 137 106 56 NC_002967:TDE1962|3end_hypothetical_protein_1974953..1975103_NEGATIVE 255 110 67 96 60 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 252 234 191 137 87 NC_002967:TDE2180|3end_tRNA_modification_GTPase_2210590..2210740_NEGATIVE 252 231 191 65 31 NC_002967:TDE0985|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_1013054..1013204_POSITIVE 244 104 68 128 94 NC_002967:TDE1631|3end_citrate_lyase,_alpha_subunit_1680060..1680210_NEGATIVE 243 226 189 49 17 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 239 210 161 106 57 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 239 239 202 60 19 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 236 234 192 81 34 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 236 190 156 64 35 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 236 110 68 113 77 NC_002967:TDE0292|3end_hypothetical_protein_321175..321325_NEGATIVE 234 240 199 62 5 NC_002967:TDE0105|3end_MTA/SAH_nucleosidase_124732..124882_NEGATIVE 232 211 172 107 51 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 231 233 193 96 67 NC_002967:TDE1978|3end_hypothetical_protein_1991501..1991651_NEGATIVE 229 209 172 88 54 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 227 233 202 139 102 NC_002967:TDE1236|3end_triosephosphate_isomerase_1270318..1270468_POSITIVE 226 250 203 88 37 NC_002967:TDE1036|3end_hypothetical_protein_1064553..1064703_POSITIVE