Origin IGS: gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt .........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 acattttagtcctttgccgtataaaatcaacaataaagtatactaaaattttaagaattatgcaataagacgaatttcttgcggttaaattaatcatcgatcaaataaaccgcagtaaacgccaagcgaaaagattattaagaaaaaccgcaggtttgtcttaatgacaatccatacctctaacttaggggagatttttaagagggggggctaaaaaatgttccccctcttaaatggcgttttgaaaagatgaggggttataggggagaagaaaaacttttgctccatcaaaagtttgtcctctccc Mask Tandem Repeat Region ================================================ gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt Find is-nt database================================================ Query_seq: TDE0724:TDE0725|TDE0724:TDE0725:hypothetical protein:exopolysaccharide biosynthesis protein:->->:763298..763604 307 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0724:TDE0725|TDE0724:TDE0725:hypothetical protein:exopolysaccharide biosynthesis protein:->->:763298..763604 307 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0724:TDE0725|TDE0724:TDE0725:hypothetical protein:exopolysaccharide biosynthesis protein:->->:763298..763604 307 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 113 End: 211 ................................................................................................................ M S P K L E V W I V I K T N L R F F L I I F S L G V Y C G L F D R ................................................................................................ Protein_Len: 32 Strand: + Start: 211 End: 306 .................................................................................................................................................................................................................. M I N L T A R N S S Y C I I L K I L V Y F I V D F I R Q R T K M . gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt 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: 83 Start: 242 End: 271 .................................................................................................................................................................................................................................................ATTGCATAATTCTTAAAATTTTAGTATACT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 57 HP_score: -3.4 Tail_Score: -4.08767 Start: 69 End: 116 Full_Region: cctctaacttagggg agatttttaagagggggggc taaaaaat gttccccctcttaaatggcg ttttgaaaagatgag ....................................................................agatttttaagagggggggctaaaaaatgttccccctcttaaatggcg............................................................................................................................................................................................... TransTerm Strand: + Conf: 72 HP_score: -7.9 Tail_Score: -3.7398 Start: 141 End: 173 Full_Region: TAGAGGTATGGATTG TCATTAAGACAAACC TGC GGTTTTTCTTAATAA TCTTTTCGCTTGGCG ............................................................................................................................................TCATTAAGACAAACCTGCGGTTTTTCTTAATAA...................................................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -9.6 Tail_Score: -2.96152 Start: 144 End: 170 Full_Region: AGGTATGGATTGTCA TTAAGACAAACC TGC GGTTTTTCTTAA TAATCTTTTCGCTTG ...............................................................................................................................................TTAAGACAAACCTGCGGTTTTTCTTAA......................................................................................................................................... Find igs database================================================ Query_seq: TDE0724:TDE0725|TDE0724:TDE0725:hypothetical protein:exopolysaccharide biosynthesis protein:->->:763298..763604 307 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt Intra-Species Hit: Count: 5 Min: 1 Max: 307 Len: 307 Subject: NC_002967_TDE0724_TDE0725|hypothetical protein:exopolysaccharide biosynthesis protein|POSITIVE:POSITIVE|[763298,763604]|307 HSP 1 e-value: 1.0E-161 bit: 567.0 Len: 307 Query Start:1 Query End:307 Subject Strand: POSITIVE Subject Start: 1 Subject End: 307 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagnnnnnnntcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtatactttattgttgattttatacggcaaaggactaaaatgt Subject: NC_002967_TDE0723_TDE0724|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[761722,761992]|271 HSP 1 e-value: 2.0E-99 bit: 363.0 Len: 248 Query Start:21 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 247 ....................tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagnnnnnnntcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtat....................................... ....................tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagtta-aggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtat....................................... Subject: NC_002967_TDE0722_TDE0723|lipoprotein, putative:hypothetical protein|POSITIVE:POSITIVE|[759925,760443]|519 HSP 1 e-value: 4.0E-76 bit: 285.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagnnnnnnntcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtt..................................................................................................................... gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaaga-ggggaacattttttag-ctcccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctttgcgtt..................................................................................................................... Subject: NC_002967_TDE0715_TDE0716|hypothetical protein:CAAX amino terminal protease family protein|POSITIVE:POSITIVE|[750611,750967]|357 HSP 1 e-value: 6.0E-66 bit: 252.0 Len: 173 Query Start:8 Query End:180 Subject Strand: POSITIVE Subject Start: 8 Subject End: 178 .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagnnnnnnntcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttc............................................................................................................................... .......gacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaaga-ggggaacattttttag-ctcccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttc............................................................................................................................... Subject: NC_002967_TDE0969_TDE0970|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[994636,994908]|273 HSP 1 e-value: 2.0E-41 bit: 170.0 Len: 86 Query Start:1 Query End:86 Subject Strand: POSITIVE Subject Start: 1 Subject End: 86 gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggga............................................................................................................................................................................................................................. gggagaggacaaacttttgatggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggga............................................................................................................................................................................................................................. HSP 2 e-value: 4.0E-33 bit: 143.0 Len: 76 Query Start:105 Query End:180 Subject Strand: POSITIVE Subject Start: 187 Subject End: 262 ........................................................................................................tcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttc............................................................................................................................... ........................................................................................................tcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttc............................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAGAGGACAAACUUUUGAUGGAGCAAAAGUUUUUCUUCUCCCCUAUAACCCCUCAUCUUUUCAAAACGCCAUUUAAGAGGGGGAACAUUUUUUAGCCCCCCCUCUUAAAAAUCUCCCCUAAGUUAGAGGUAUGGAUUGUCAUUAAGACAAACCUGCGGUUUUUCUUAAUAAUCUUUUCGCUUGGCGUUUACUGCGGUUUAUUUGAUCGAUGAUUAAUUUAACCGCAAGAAAUUCGUCUUAUUGCAUAAUUCUUAAAAUUUUAGUAUACUUUAUUGUUGAUUUUAUACGGCAAAGGACUAAAAUGU (((((((((.(((((((((......))))))))).)))))))))................((((.((((((((.(((((((((((..(........)..)))))))))))..(((((..........)))))..(((((((...(((((.(((((...))))).)))))))))))).......))))))))..(((((((...((((((...))))))...))))))).))))...(((((.((((........(((((((.(((((.....)))))..)))))))....)))))))))........ (-94.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUUUAGUCCUUUGCCGUAUAAAAUCAACAAUAAAGUAUACUAAAAUUUUAAGAAUUAUGCAAUAAGACGAAUUUCUUGCGGUUAAAUUAAUCAUCGAUCAAAUAAACCGCAGUAAACGCCAAGCGAAAAGAUUAUUAAGAAAAACCGCAGGUUUGUCUUAAUGACAAUCCAUACCUCUAACUUAGGGGAGAUUUUUAAGAGGGGGGGCUAAAAAAUGUUCCCCCUCUUAAAUGGCGUUUUGAAAAGAUGAGGGGUUAUAGGGGAGAAGAAAAACUUUUGCUCCAUCAAAAGUUUGUCCUCUCCC ......((..((((((((((..((((((.....((((((........)))))).......((((.(((((((((...(((((((((...(((((.(((..........((....))...(((...)))....))).)))))....)))))))))))))))))).)).)).......((((((...)))))).))))))(((((((((((((........))))))))))))).)))))..(((....))).)))))..))...((((((.((.(((((((((......))))))))).)).)))))) (-92.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 71 34 213 170 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 393 79 34 226 179 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 384 46 1 60 15 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 384 46 1 182 137 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 381 83 41 200 160 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 367 73 31 180 137 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 358 84 41 208 169 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 351 220 174 196 149 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 345 86 41 118 76 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 337 84 41 102 62 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 337 120 74 138 108 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 329 199 154 149 99 NC_002967:TDE0916|5end_ABC_transporter,_ATP-binding/permease_protein_933359..933589_POSITIVE 326 49 1 170 126 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 313 200 154 148 99 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 310 216 179 220 179 NC_002967:TDE0785|5end_ribosomal_protein_L30_814417..814647_POSITIVE 304 227 181 142 100 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 299 217 171 231 178 NC_002967:TDE1664|5end_hypothetical_protein_1717862..1718092_POSITIVE 298 60 14 196 140 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 297 199 155 154 121 NC_002967:TDE2488|5end_modification_methylase,_HemK_family_2511384..2511614_NEGATIVE 297 197 154 45 6 NC_002967:TDE0593|5end_internalin-related_protein_633936..634166_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 471 47 1 93 47 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 471 47 1 93 47 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 471 47 1 93 47 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 468 46 1 51 7 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 449 47 1 113 67 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE 402 47 1 93 47 NC_002967:TDE0715|3end_hypothetical_protein_750550..750700_POSITIVE 387 220 180 106 64 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 383 45 1 83 43 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 369 45 1 82 41 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 359 50 1 143 95 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 354 227 182 47 7 NC_002967:TDE2707|3end_hypothetical_protein_2754929..2755079_POSITIVE 341 100 51 131 73 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 337 120 74 51 21 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 322 208 164 59 12 NC_002967:TDE2159|3end_hypothetical_protein_2193874..2194024_POSITIVE 321 200 157 53 7 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 318 84 41 68 29 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 315 64 24 108 69 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 297 199 155 147 114 NC_002967:TDE2489|3end_peptide_chain_release_factor_1_2511391..2511541_NEGATIVE 295 212 172 112 68 NC_002967:TDE1883|3end_hypothetical_protein_1904910..1905060_NEGATIVE 295 47 1 84 40 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE