Origin IGS: gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca .........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 tgagaaaatgaagaaacgtggagaaattcaacgatgaacgaaatgtccaaaacgtgtccaaaaaaacatcttataatgggtgttttgagacctttttattgaataattgtctgatataaaggcgtttggaaatgttcaaaacgtgtccaaaagatacaataaataaactgcacgggtggcgggctaaatgaagaataaaagatataatc Mask Tandem Repeat Region ================================================ gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca Find is-nt database================================================ Query_seq: TF1937:TF1938|TF1937:TF1938:conserved hypothetical protein:hypothetical protein:->->:2085648..2085856 209 gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1937:TF1938|TF1937:TF1938:conserved hypothetical protein:hypothetical protein:->->:2085648..2085856 209 gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1937:TF1938|TF1937:TF1938:conserved hypothetical protein:hypothetical protein:->->:2085648..2085856 209 gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 7 End: 111 ...... M F Y S S F S P P P V Q F I Y C I F W T R F E H F Q T P L Y Q T I I Q .................................................................................................. Protein_Len: 45 Strand: + Start: 2 End: 136 . M I S F I L H L A R H P C S L F I V S F G H V L N I S K R L Y I R Q L F N K K V S K H P L ......................................................................... Protein_Len: 33 Strand: - Start: 94 End: 192 ............................................................................................. I L C N N L L F T E F C G N Y S T K K S V N Q V N R E D N F K E M ................. gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca 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================================================ gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.1 Tail_Score: -2.83346 Start: 161 End: 175 Full_Region: TTTTTGGACACGTTT TGGAC ATTTC GTTCA TCGTTGAATTTCTCC ................................................................................................................................................................TGGACATTTCGTTCA.................................. Find igs database================================================ Query_seq: TF1937:TF1938|TF1937:TF1938:conserved hypothetical protein:hypothetical protein:->->:2085648..2085856 209 gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: tfor_TF1937_TF1938|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2085648,2085856]|209 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgnnnnnnnggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca gattatatcttttattcttcatttagcccgccacccgtgcagtttatttattgtatcttttggacacgttttgaacatttccaaacgcctttatatcagacaattattcaataaaaaggtctcaaaacacccattataagatgtttttttggacacgttttggacatttcgttcatcgttgaatttctccacgtttcttcattttctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAUAUCUUUUAUUCUUCAUUUAGCCCGCCACCCGUGCAGUUUAUUUAUUGUAUCUUUUGGACACGUUUUGAACAUUUCCAAACGCCUUUAUAUCAGACAAUUAUUCAAUAAAAAGGUCUCAAAACACCCAUUAUAAGAUGUUUUUUUGGACACGUUUUGGACAUUUCGUUCAUCGUUGAAUUUCUCCACGUUUCUUCAUUUUCUCA ((..(((((((.((...............((((...(((((((......)))))))....))).)..(((((((............((((((.(((..((......))..))).)))))).)))))))......)).)))))))..))..(((.((((...(((......(((((....)))))...))))))).)))........... (-28.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAAAAUGAAGAAACGUGGAGAAAUUCAACGAUGAACGAAAUGUCCAAAACGUGUCCAAAAAAACAUCUUAUAAUGGGUGUUUUGAGACCUUUUUAUUGAAUAAUUGUCUGAUAUAAAGGCGUUUGGAAAUGUUCAAAACGUGUCCAAAAGAUACAAUAAAUAAACUGCACGGGUGGCGGGCUAAAUGAAGAAUAAAAGAUAUAAUC ................((((((....))).)))...........((((.(..(((((.....(((((((((......)))))))))........(((((((.......((((.......)))).((((((.((((.....)))).)))))).....)))))))......)))))..)...))))......................... (-40.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 53 19 224 189 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 313 200 155 163 118 tfor:TF3093|5end_30S_ribosomal_protein_S2_3325244..3325474_POSITIVE 294 198 156 111 62 tfor:TF0467|5end_acetyltransferase-related_protein_485936..486166_POSITIVE 292 68 28 61 13 tfor:TF2511|5end_RNA_binding_protein_2689910..2690140_POSITIVE 279 65 26 228 178 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 277 189 142 179 126 tfor:TF2952|5end_transposase_3159572..3159802_POSITIVE 274 44 1 84 29 tfor:TF3152|5end_hypothetical_protein_3386690..3386920_POSITIVE 273 184 148 219 182 tfor:TF2846|5end_cobyric_acid_synthase_3034896..3035126_POSITIVE 273 184 148 67 30 tfor:TF2847|5end_hypothetical_protein_3034744..3034974_POSITIVE 273 200 151 158 111 tfor:TF1001|5end_penicillin-binding_protein_1A_1054097..1054327_POSITIVE 271 66 26 45 4 tfor:TF1600|5end_uroporphyrinogen-III_synthase_1713964..1714194_POSITIVE 271 70 21 140 83 tfor:TF0809|5end_cation_efflux_protein_865358..865588_POSITIVE 271 197 151 199 151 tfor:TF0304|5end_peptidyl-prolyl_cis-trans_isomerase_329567..329797_POSITIVE 270 116 77 162 120 tfor:TF0012|5end_conserved_hypothetical_protein_5512..5742_POSITIVE 267 200 151 46 1 tfor:TF1873|5end_possible_hemolysin_secretion_protein_2026745..2026975_POSITIVE 267 200 151 46 1 tfor:TF1131|5end_membrane-fusion_protein;_possible_hemolysin_secretion_protein_1207611..1207841_POSITIVE 265 68 26 194 142 tfor:TF2314|5end_conserved_hypothetical_protein_2473530..2473760_POSITIVE 264 68 25 203 149 tfor:TF2687|5end_iron-regulated_ABC-type_transporter_membrane_component_2863509..2863739_POSITIVE 263 40 13 164 130 tfor:TF2466|5end_pyruvate_kinase_2644385..2644615_POSITIVE 263 175 140 228 196 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 190 141 151 102 tfor:TF1839|3end_conserved_hypothetical_protein_1989699..1989849_POSITIVE 323 53 19 128 93 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 296 62 25 107 59 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 294 198 156 67 18 tfor:TF0466|3end_amidophosphoribosyltransferase_485972..486122_POSITIVE 279 65 26 60 10 tfor:TF0880|3end_conserved_hypothetical_protein_934371..934521_POSITIVE 278 68 26 75 27 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 277 189 142 149 96 tfor:TF2951|3end_O-succinylbenzoic_acid--CoA_ligase_3159622..3159772_POSITIVE 274 42 15 137 106 tfor:TF0207|3end_conserved_hypothetical_protein_233505..233655_POSITIVE 273 200 151 150 103 tfor:TF1000|3end_sec-independent_protein_translocase_1054169..1054319_POSITIVE 271 66 26 55 14 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 271 70 21 123 66 tfor:TF0808|3end_cation_efflux_system_protein_865421..865571_POSITIVE 267 68 28 139 96 tfor:TF0001|3end_hypothetical_protein_158..308_POSITIVE 263 40 13 142 108 tfor:TF2465|3end_O-methyltransferase_2644443..2644593_POSITIVE 263 200 162 116 68 tfor:TF1697|3end_mobilizable_transposon,_excision_protein_1819293..1819443_POSITIVE 262 79 35 149 99 tfor:TF3150|3end_conserved_hypothetical_protein_3386245..3386395_POSITIVE 261 69 33 69 29 tfor:TF2499|3end_possible_thioesterase_family_protein_2674477..2674627_POSITIVE 260 189 141 110 46 tfor:TF0835|3end_conserved_hypothetical_protein_889366..889516_POSITIVE 257 200 156 129 83 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 252 66 26 69 30 tfor:TF2428|3end_conserved_hypothetical_protein_2610525..2610675_POSITIVE 252 66 26 59 20 tfor:TF2426|3end_conserved_hypothetical_protein;_possible_TonB_receptor_2605931..2606081_POSITIVE