Origin IGS: gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca .........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 tgtatcctatataccgcgtgacgtaacgaatacattttttattctttcttatcgctttgattgtcgcaaaacgatgtagccctcccccatcgtctttgcgtgtttgcttttatccctgtactaaagaatgtataatataattccccgcgccgaagccatacgacaccccgcttgggttttagcaattaaaatcatacctttgcaccgcgaacaaaaaacagaacataaagcgc Mask Tandem Repeat Region ================================================ gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca Find is-nt database================================================ Query_seq: TF2583:TF2584|TF2583:TF2584:possible ABC transporter, permease component:hypothetical protein:->->:2751087..2751319 233 gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2583:TF2584|TF2583:TF2584:possible ABC transporter, permease component:hypothetical protein:->->:2751087..2751319 233 gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2583:TF2584|TF2583:TF2584:possible ABC transporter, permease component:hypothetical protein:->->:2751087..2751319 233 gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 49 End: 192 ................................................ M L K P K R G V V W L R R G E L Y Y T F F S T G I K A N T Q R R W G R A T S F C D N Q S D K K E ......................................... Protein_Len: 36 Strand: - Start: 97 End: 204 ................................................................................................ I I C E K T C P Y F C V R L S S P P P S C R K A V I L A I L F F L F H M ............................. Protein_Len: 35 Strand: - Start: 2 End: 106 . A K H E T K Q E R H L P I I K I A L V W A P H R I A E A R P I I N Y M ............................................................................................................................... gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca 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================================================ gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 59 HP_score: -5.5 Tail_Score: -3.7278 Start: 134 End: 169 Full_Region: tatcgctttgattgt cgcaaaacgatgtag ccctc ccccatcgtctttgcg tgtttgcttttatcc .....................................................................................................................................cgcaaaacgatgtagccctcccccatcgtctttgcg................................................................ TransTerm Strand: + Conf: 58 HP_score: -3.2 Tail_Score: -4.08767 Start: 142 End: 162 Full_Region: GCAAACACGCAAAGA CGATGGGG GAGGG CTACATCG TTTTGCGACAATCAA .............................................................................................................................................CGATGGGGGAGGGCTACATCG....................................................................... Find igs database================================================ Query_seq: TF2583:TF2584|TF2583:TF2584:possible ABC transporter, permease component:hypothetical protein:->->:2751087..2751319 233 gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: tfor_TF2583_TF2584|possible ABC transporter, permease component:hypothetical protein|POSITIVE:POSITIVE|[2751087,2751319]|233 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca gcgctttatgttctgttttttgttcgcggtgcaaaggtatgattttaattgctaaaacccaagcggggtgtcgtatggcttcggcgcggggaattatattatacattctttagtacagggataaaagcaaacacgcaaagacgatgggggagggctacatcgttttgcgacaatcaaagcgataagaaagaataaaaaatgtattcgttacgtcacgcggtatataggataca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGCUUUAUGUUCUGUUUUUUGUUCGCGGUGCAAAGGUAUGAUUUUAAUUGCUAAAACCCAAGCGGGGUGUCGUAUGGCUUCGGCGCGGGGAAUUAUAUUAUACAUUCUUUAGUACAGGGAUAAAAGCAAACACGCAAAGACGAUGGGGGAGGGCUACAUCGUUUUGCGACAAUCAAAGCGAUAAGAAAGAAUAAAAAAUGUAUUCGUUACGUCACGCGGUAUAUAGGAUACA .((((((..(((.(((((((...((.(.(((((((((((((((..(((((.((....(((....)))((((((........)))))).)).))))).)))))))...)))).)))).).)).)))))))))).(((((.(((((((..(.....)..))))))))))))......))))))..................(((((((..(((........)))....))))))) (-64.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUCCUAUAUACCGCGUGACGUAACGAAUACAUUUUUUAUUCUUUCUUAUCGCUUUGAUUGUCGCAAAACGAUGUAGCCCUCCCCCAUCGUCUUUGCGUGUUUGCUUUUAUCCCUGUACUAAAGAAUGUAUAAUAUAAUUCCCCGCGCCGAAGCCAUACGACACCCCGCUUGGGUUUUAGCAAUUAAAAUCAUACCUUUGCACCGCGAACAAAAAACAGAACAUAAAGCGC (((((...........(((......))).)))))..................(((((((.....((((((((((((..(.....)..)))))).))))))(((((((.........(((((........)))))..............((..(((((...((......))....)))))..)).......................)))))))............))))))). (-43.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 398 97 63 78 28 tfor:TF3070|5end_conserved_hypothetical_protein_3294380..3294610_POSITIVE 393 91 51 79 37 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 388 93 51 60 12 tfor:TF0361|5end_hypothetical_protein_379458..379688_POSITIVE 384 90 57 231 187 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 380 93 58 57 20 tfor:TF1464|5end_conserved_hypothetical_protein_1553467..1553697_POSITIVE 379 91 58 188 152 tfor:TF1942|5end_conserved_hypothetical_protein_2090129..2090359_POSITIVE 378 89 50 194 151 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 376 92 51 229 183 tfor:TF2016|5end_hypothetical_protein_2172948..2173178_POSITIVE 375 90 63 59 28 tfor:TF3014|5end_oxidoreductase,_short-chain_dehydrogenase/reductase_family_3237623..3237853_POSITIVE 375 95 51 219 162 tfor:TF1570|5end_ATP_synthase_subunit_A_1678325..1678555_POSITIVE 375 89 61 212 179 tfor:TF0709|5end_preprotein_translocase,_subunit_SecA_753826..754056_POSITIVE 367 98 54 93 37 tfor:TF2529|5end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_2710670..2710900_POSITIVE 365 91 51 203 146 tfor:TF1551|5end_hypothetical_protein_1656864..1657094_POSITIVE 363 93 57 97 57 tfor:TF2296|5end_hypothetical_protein_2448892..2449122_POSITIVE 363 90 43 217 159 tfor:TF2037|5end_conserved_hypothetical_protein;_possible_anaerobic_ribonucleoside-triphosphate_reductase_2196754..2196984_POSITIVE 361 88 49 76 37 tfor:TF1795|5end_conserved_hypothetical_protein_1935746..1935976_POSITIVE 356 88 62 220 196 tfor:TF0201|5end_permease,_major_facilitator_superfamily_226041..226271_POSITIVE 355 87 59 195 161 tfor:TF0595|5end_hypothetical_protein_627820..628050_POSITIVE 350 91 51 153 97 tfor:TF1554|5end_UDP-glucose_dehydrogenase_1659623..1659853_POSITIVE 350 69 23 199 145 tfor:TF1249|5end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1331017..1331247_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 175 131 56 5 tfor:TF1327|3end_L-fucose_permease_1407195..1407345_POSITIVE 388 93 51 60 12 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 388 50 1 79 27 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE 375 106 62 145 100 tfor:TF2914|3end_hypothetical_protein_3109643..3109793_POSITIVE 375 89 61 142 109 tfor:TF0708|3end_possible_alkaline_phosphatase_753836..753986_POSITIVE 367 98 54 92 36 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 361 88 49 66 27 tfor:TF1794|3end_possible_glucose-1-phosphatase_1935816..1935966_POSITIVE 350 91 51 131 75 tfor:TF1553|3end_copper_homeostasis_protein_1659681..1659831_POSITIVE 344 80 34 98 57 tfor:TF0340|3end_hypothetical_protein_364257..364407_POSITIVE 342 105 63 59 9 tfor:TF1268|3end_conserved_hypothetical_protein_1354635..1354785_POSITIVE 341 187 141 130 70 tfor:TF2040|3end_transcription_elongation_factor_2200280..2200430_POSITIVE 339 91 51 61 25 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 338 94 59 45 9 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 336 89 49 106 45 tfor:TF2609|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_2786264..2786414_POSITIVE 331 90 59 55 26 tfor:TF1468|3end_beta-galactosidase_1561251..1561401_POSITIVE 328 91 58 50 18 tfor:TF0995|3end_conserved_hypothetical_protein_1050962..1051112_POSITIVE 327 92 68 123 97 tfor:TF1011|3end_cell_division_protein;_rod_shape-determining_protein_1068169..1068319_POSITIVE 327 68 21 104 64 tfor:TF0946|3end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_990698..990848_POSITIVE 326 91 51 127 79 tfor:TF2003|3end_dihydrofolate_reductase_2156427..2156577_POSITIVE 325 91 63 82 55 tfor:TF1612|3end_conserved_hypothetical_protein_1729866..1730016_POSITIVE