Origin IGS: aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagtacatctccccatattgtaaataagttttttaaattctgaaaaatctcctgctcatctatgcgctatttttataccatactgtgaagcatttttttcatattccgtaccaggatgaggacataaaatgtatgtagacttccttaaaaacacacagttgcatcaggaaacggttaaaaagcctcaaatttatcagtttattatgtaaaaaactgataaggctcctctattttaaaaaacacaaagcaaatttaagtcaattttttagaggagcccattacaagaatcactcactatgcaaatgctgagagtgtaccagttcccctatgttcctgagtttttatcccagcataaccactgatttgtaaaaacttccacttcaggggtaatccattctgtcataatttaaattccatt Mask Tandem Repeat Region ================================================ aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg Find is-nt database================================================ Query_seq: TDE1076:TDE1077|TDE1076:TDE1077:oligopeptide/dipeptide ABC transporter, ATP-binding protein:hypothetical protein:->->:1108117..1108534 418 aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1076:TDE1077|TDE1076:TDE1077:oligopeptide/dipeptide ABC transporter, ATP-binding protein:hypothetical protein:->->:1108117..1108534 418 aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1076:TDE1077|TDE1076:TDE1077:oligopeptide/dipeptide ABC transporter, ATP-binding protein:hypothetical protein:->->:1108117..1108534 418 aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 201 End: 317 ........................................................................................................................................................................................................ M S F L H N K L I N L R L F N R F L M Q L C V F K E V Y I H F M S S S W Y G I ..................................................................................................... Protein_Len: 32 Strand: + Start: 265 End: 360 ........................................................................................................................................................................................................................................................................ M F L R K S T Y I L C P H P G T E Y E K N A S Q Y G I K I A H R .......................................................... Protein_Len: 31 Strand: - Start: 303 End: 395 .............................................................................................................................................................................................................................................................................................................. G P V S Y S F F A E C Y P I F I A C L H A P S K E S N L F S M ....................... Protein_Len: 33 Strand: - Start: 284 End: 382 ........................................................................................................................................................................................................................................................................................... M C K I D E D Q Y P I H F F H K V T H Y L F L A Y I L L L N K L M .................................... Protein_Len: 48 Strand: - Start: 113 End: 256 ................................................................................................................ C K C L S H N K Y H A G R F F Q S L N A K H K K F Y L L R I L K K C L L S I F K L S K L R K R M .................................................................................................................................................................. aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg 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================================================ aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1076:TDE1077|TDE1076:TDE1077:oligopeptide/dipeptide ABC transporter, ATP-binding protein:hypothetical protein:->->:1108117..1108534 418 aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg Intra-Species Hit: Count: 1 Min: 1 Max: 418 Len: 418 Subject: NC_002967_TDE1076_TDE1077|oligopeptide/dipeptide ABC transporter, ATP-binding protein:hypothetical protein|POSITIVE:POSITIVE|[1108117,1108534]|418 HSP 1 e-value: 0.0 bit: 787.0 Len: 418 Query Start:1 Query End:418 Subject Strand: POSITIVE Subject Start: 1 Subject End: 418 aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgnnnnnnntgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg aatggaatttaaattatgacagaatggattacccctgaagtggaagtttttacaaatcagtggttatgctgggataaaaactcaggaacataggggaactggtacactctcagcatttgcatagtgagtgattcttgtaatgggctcctctaaaaaattgacttaaatttgctttgtgttttttaaaatagaggagccttatcagttttttacataataaactgataaatttgaggctttttaaccgtttcctgatgcaactgtgtgtttttaaggaagtctacatacattttatgtcctcatcctggtacggaatatgaaaaaaatgcttcacagtatggtataaaaatagcgcatagatgagcaggagatttttcagaatttaaaaaacttatttacaatatggggagatgtactg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGAAUUUAAAUUAUGACAGAAUGGAUUACCCCUGAAGUGGAAGUUUUUACAAAUCAGUGGUUAUGCUGGGAUAAAAACUCAGGAACAUAGGGGAACUGGUACACUCUCAGCAUUUGCAUAGUGAGUGAUUCUUGUAAUGGGCUCCUCUAAAAAAUUGACUUAAAUUUGCUUUGUGUUUUUUAAAAUAGAGGAGCCUUAUCAGUUUUUUACAUAAUAAACUGAUAAAUUUGAGGCUUUUUAACCGUUUCCUGAUGCAACUGUGUGUUUUUAAGGAAGUCUACAUACAUUUUAUGUCCUCAUCCUGGUACGGAAUAUGAAAAAAAUGCUUCACAGUAUGGUAUAAAAAUAGCGCAUAGAUGAGCAGGAGAUUUUUCAGAAUUUAAAAAACUUAUUUACAAUAUGGGGAGAUGUACUG ...............................((((((..((.((.(((((((....(((((......)))))..)))))))))....)).))))))....(((((((((((.((....))...((((((((..........(((((((((((...((..(((.((((.....)))).)))..))....)))))))))))(((((((((..........)))))))))..(((((((........)).(((((((...((.(((((((((....((((.(...(((((.....)))))...).)))).((((.((((((.......))).)))...))))...........))))))))).))..)))))))....)))))...........))))))))......))))).)))))). (-102.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUACAUCUCCCCAUAUUGUAAAUAAGUUUUUUAAAUUCUGAAAAAUCUCCUGCUCAUCUAUGCGCUAUUUUUAUACCAUACUGUGAAGCAUUUUUUUCAUAUUCCGUACCAGGAUGAGGACAUAAAAUGUAUGUAGACUUCCUUAAAAACACACAGUUGCAUCAGGAAACGGUUAAAAAGCCUCAAAUUUAUCAGUUUAUUAUGUAAAAAACUGAUAAGGCUCCUCUAUUUUAAAAAACACAAAGCAAAUUUAAGUCAAUUUUUUAGAGGAGCCCAUUACAAGAAUCACUCACUAUGCAAAUGCUGAGAGUGUACCAGUUCCCCUAUGUUCCUGAGUUUUUAUCCCAGCAUAACCACUGAUUUGUAAAAACUUCCACUUCAGGGGUAAUCCAUUCUGUCAUAAUUUAAAUUCCAUU ..(((((((((..(((.(((((.....(((((((((.((((((..........((........)).............((.((((((..(((((((..((....(((......)))....))...)))))))....((.....))........))))))))..)))))).....))))))))).((....((((((((((.((....)).))))))))))((((((((((.........((..(((.....)))..))........))))))))))........))...........))))))))..)))).)))))..((((((((..((....((((((((((..(((........)))....))))))))))..))...))))).)))........................... (-82.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 270 233 79 39 NC_002967:TDE2327|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2364627..2364857_NEGATIVE 298 150 106 52 3 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 289 276 233 159 121 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 281 133 91 69 28 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 280 104 70 213 176 NC_002967:TDE2471|5end_hypothetical_protein_2494946..2495176_NEGATIVE 265 129 85 56 12 NC_002967:TDE2060|5end_hypothetical_protein_2086521..2086751_POSITIVE 263 165 133 193 152 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 263 340 296 204 156 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 261 178 132 185 133 NC_002967:TDE1831|5end_hypothetical_protein_1865032..1865262_NEGATIVE 261 178 132 185 133 NC_002967:TDE1797|5end_hypothetical_protein_1836272..1836502_NEGATIVE 261 283 245 48 10 NC_002967:TDE1659|5end_alanyl-tRNA_synthetase_1710633..1710863_NEGATIVE 260 271 231 227 179 NC_002967:TDE2423|5end_ribosomal_protein_L10_2454034..2454264_NEGATIVE 260 124 84 183 149 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 259 158 113 112 69 NC_002967:TDE2129|5end_hypothetical_protein_2161463..2161693_POSITIVE 259 283 242 45 4 NC_002967:TDE0699|5end_hypothetical_protein_735252..735482_NEGATIVE 257 150 104 55 12 NC_002967:TDE1136|5end_M23/M37_peptidase_domain_protein_1166049..1166279_NEGATIVE 256 96 51 161 118 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 254 149 110 173 134 NC_002967:TDE1593|5end_Fe-hydrogenase_1642999..1643229_NEGATIVE 254 123 85 183 136 NC_002967:TDE1391|5end_NQR2/RnfD/RnfE_family_protein_1430975..1431205_POSITIVE 252 147 112 180 142 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 210 167 78 32 NC_002967:TDE1091|3end_hypothetical_protein_1123017..1123167_NEGATIVE 289 276 233 66 28 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 281 133 91 68 27 NC_002967:TDE0284|3end_hypothetical_protein_312826..312976_NEGATIVE 279 118 85 136 104 NC_002967:TDE0325|3end_hypothetical_protein_358733..358883_POSITIVE 263 165 133 69 28 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 261 73 32 52 11 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 259 158 113 127 84 NC_002967:TDE2128|3end_hypothetical_protein_2161558..2161708_POSITIVE 256 139 91 95 43 NC_002967:TDE2337|3end_aminopeptidase_2374604..2374754_POSITIVE 255 130 84 135 79 NC_002967:TDE2136|3end_hypothetical_protein_2165390..2165540_NEGATIVE 255 137 91 58 11 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 254 184 142 99 58 NC_002967:TDE1296|3end_ribosomal_subunit_interface_protein,_putative_1333464..1333614_NEGATIVE 253 179 131 74 29 NC_002967:TDE2741|3end_hypothetical_protein_2796722..2796872_POSITIVE 248 319 288 53 15 NC_002967:TDE2303|3end_hypothetical_protein_2343527..2343677_POSITIVE 247 83 44 48 15 NC_002967:TDE2404|3end_RNA_polymerase_sigma-54_factor,_putative_2429313..2429463_NEGATIVE 247 151 111 64 31 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 245 314 271 62 24 NC_002967:TDE0894|3end_hypothetical_protein_911239..911389_POSITIVE 244 70 24 54 1 NC_002967:TDE1150|3end_hypothetical_protein_1187401..1187551_NEGATIVE 244 70 25 135 87 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 243 280 232 81 35 NC_002967:TDE1575|3end_lipoyl_synthase_1622855..1623005_POSITIVE 243 268 230 63 18 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE