Origin IGS: tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca .........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 tgattttttacactcactgtgtgtattgctatcacatattcacaaaccaaatcacgtaaaacacatatttcatgactcctttatattgattctttattctgcaatatttcggccaattacatatctgtcaatatggtaattttgacgttttcaagattaccgttgaccggatgaatcaaacatctccacgagaaatgtcggtcagcgatccacctccaataagatttcccta Mask Tandem Repeat Region ================================================ tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca Find is-nt database================================================ Query_seq: TF0120:TF0121|TF0120:TF0121:hexouronate transporter:hypothetical protein:->->:132872..133103 232 tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0120:TF0121|TF0120:TF0121:hexouronate transporter:hypothetical protein:->->:132872..133103 232 tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0120:TF0121|TF0120:TF0121:hexouronate transporter:hypothetical protein:->->:132872..133103 232 tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 24 End: 113 ....................... M A D R H F S W R C L I H P V N G N L E N V K I T I L T D M ....................................................................................................................... Protein_Len: 30 Strand: + Start: 109 End: 198 ............................................................................................................ M C N W P K Y C R I K N Q Y K G V M K Y V F Y V I W F V N M .................................. Protein_Len: 40 Strand: - Start: 97 End: 216 ................................................................................................ W I S L Y T I P R F I A S Y L I L I F S D H F I H K V H N P K H I H S L L V C M ................ Protein_Len: 45 Strand: - Start: 3 End: 137 .. P F R I P P P D S V S M E R P S T Q N M R D V T I K F V D F N G Y Q C I H L Q G F Y Q L M ............................................................................................... tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca 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: 101 End: 130 ....................................................................................................ATTGACAGATATGTAATTGGCCGAAATATT...................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: + Score: 81 Start: 117 End: 133 ....................................................................................................................TTGGCCGAAATATTGCA................................................................................................... tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -3.2 Tail_Score: -3.0395 Start: 71 End: 99 Full_Region: GATTCATCCGGTCAA CGGTAATCTTGA AAACG TCAAAATTACCA TATTGACAGATATGT ......................................................................CGGTAATCTTGAAAACGTCAAAATTACCA..................................................................................................................................... Find igs database================================================ Query_seq: TF0120:TF0121|TF0120:TF0121:hexouronate transporter:hypothetical protein:->->:132872..133103 232 tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: tfor_TF0120_TF0121|hexouronate transporter:hypothetical protein|POSITIVE:POSITIVE|[132872,133103]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca tagggaaatcttattggaggtggatcgctgaccgacatttctcgtggagatgtttgattcatccggtcaacggtaatcttgaaaacgtcaaaattaccatattgacagatatgtaattggccgaaatattgcagaataaagaatcaatataaaggagtcatgaaatatgtgttttacgtgatttggtttgtgaatatgtgatagcaatacacacagtgagtgtaaaaaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGAAAUCUUAUUGGAGGUGGAUCGCUGACCGACAUUUCUCGUGGAGAUGUUUGAUUCAUCCGGUCAACGGUAAUCUUGAAAACGUCAAAAUUACCAUAUUGACAGAUAUGUAAUUGGCCGAAAUAUUGCAGAAUAAAGAAUCAAUAUAAAGGAGUCAUGAAAUAUGUGUUUUACGUGAUUUGGUUUGUGAAUAUGUGAUAGCAAUACACACAGUGAGUGUAAAAAAUCA .........(((((((...(((..((((.((((.(((((((.....)))))))(((((((...(((((((.((((((.((((.....)))).))))))......(((....)))..)))))))...((((....))))..))))))).......(((((((((((.......))).)))))))))))).))))...(((....)))...))).)))))))............ (-56.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUUUACACUCACUGUGUGUAUUGCUAUCACAUAUUCACAAACCAAAUCACGUAAAACACAUAUUUCAUGACUCCUUUAUAUUGAUUCUUUAUUCUGCAAUAUUUCGGCCAAUUACAUAUCUGUCAAUAUGGUAAUUUUGACGUUUUCAAGAUUACCGUUGACCGGAUGAAUCAAACAUCUCCACGAGAAAUGUCGGUCAGCGAUCCACCUCCAAUAAGAUUUCCCUA .((..(((((.......(((((((.((((..........................)))).)))))))..((.(((((........(((((((........((.........)).........((((((((((..(((((((((((.....)))))))))))))))).))))))))))))...((((...))))......)))))..))...........)))))..)).... (-42.87) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 69 21 160 106 tfor:TF1609|5end_hypothetical_protein_1728340..1728570_POSITIVE 361 60 13 120 56 tfor:TF0704|5end_TPR-repeat-containing_protein_747888..748118_POSITIVE 336 50 2 74 13 tfor:TF1620|5end_TPR_domain_protein_1734454..1734684_POSITIVE 335 52 14 74 22 tfor:TF1800|5end_conserved_hypothetical_protein_1941214..1941444_POSITIVE 334 49 3 70 18 tfor:TF0374|5end_glycerophosphoryl_diester_phosphodiesterase_392527..392757_POSITIVE 324 59 17 68 17 tfor:TF2589|5end_translation_elongation_factor_G_protein_2753434..2753664_POSITIVE 318 49 2 187 131 tfor:TF2911|5end_hypothetical_protein_3105871..3106101_POSITIVE 313 50 3 184 131 tfor:TF2791|5end_GTP-binding_protein_TypA_2975298..2975528_POSITIVE 311 70 25 212 174 tfor:TF0982|5end_conserved_hypothetical_protein_1038633..1038863_POSITIVE 309 68 21 144 106 tfor:TF2438|5end_hypothetical_protein_2615781..2616011_POSITIVE 303 65 23 45 1 tfor:TF2916|5end_conserved_hypothetical_protein_3111559..3111789_POSITIVE 302 51 11 66 30 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 301 60 15 57 7 tfor:TF2027|5end_conserved_hypothetical_protein_2183863..2184093_POSITIVE 300 57 16 71 13 tfor:TF2243|5end_possible_mobilization_protein_2417384..2417614_POSITIVE 299 47 3 93 43 tfor:TF2350|5end_hypothetical_protein_2515063..2515293_POSITIVE 299 86 43 153 115 tfor:TF0473|5end_cation_or_acridine_efflux_membrane-fusion_protein_491047..491277_POSITIVE 298 57 19 209 167 tfor:TF0248|5end_hypothetical_protein_278249..278479_POSITIVE 295 57 14 138 74 tfor:TF2395|5end_conserved_hypothetical_protein_2566532..2566762_POSITIVE 295 69 21 230 196 tfor:TF2145|5end_conserved_hypothetical_protein;_possible_rhodanese-domain_protein_2319764..2319994_POSITIVE 293 50 2 167 121 tfor:TF2052|5end_acetyl_transferase_2216507..2216737_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 60 13 107 43 tfor:TF0703|3end_conserved_hypothetical_protein_747955..748105_POSITIVE 345 52 17 99 60 tfor:TF2696|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2871611..2871761_POSITIVE 336 50 2 68 7 tfor:TF1619|3end_riboflavin_synthase,_beta_subunit_1734528..1734678_POSITIVE 335 52 14 74 22 tfor:TF1799|3end_quinolinate_synthetase_1941294..1941444_POSITIVE 334 49 3 59 7 tfor:TF0373|3end_conserved_hypothetical_protein,_yngK-related_392596..392746_POSITIVE 307 68 21 140 92 tfor:TF0602|3end_aminotripeptidase;_peptidase_T_633472..633622_POSITIVE 299 86 43 83 45 tfor:TF0472|3end_multidrug_resistance_protein,_AcrB/AcrD/AcrF_family_(cation_efflux_pump)_491057..491207_POSITIVE 295 57 14 116 52 tfor:TF2394|3end_integrase/recombinase_XerD_2566590..2566740_POSITIVE 295 69 21 90 56 tfor:TF2143|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2319704..2319854_POSITIVE 293 49 2 81 26 tfor:TF2179|3end_integral_membrane_protein,_MarC_family_2352369..2352519_POSITIVE 292 74 32 146 111 tfor:TF2381|3end_muramidase/hemagglutinin_2546811..2546961_POSITIVE 292 44 2 111 70 tfor:TF0890|3end_transfer_region-related_protein,_TraQ_940555..940705_POSITIVE 291 50 6 61 16 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 289 50 1 122 50 tfor:TF0813|3end_glycosyl_hydrolase,_secreted_872181..872331_POSITIVE 288 67 27 88 32 tfor:TF2799|3end_RNA_polymerase_ECF-type_sigma_factor_2985052..2985202_POSITIVE 287 69 26 90 56 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 287 57 15 144 92 tfor:TF0071|3end_conserved_hypothetical_protein_80871..81021_POSITIVE 286 52 11 98 58 tfor:TF1553|3end_copper_homeostasis_protein_1659681..1659831_POSITIVE 284 49 2 69 5 tfor:TF1577|3end_hypothetical_protein_1686234..1686384_POSITIVE 283 70 23 143 93 tfor:TF1944|3end_conserved_hypothetical_protein_2093309..2093459_POSITIVE