Origin IGS: tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagacagataaatataaagaatactgtgtcacggaaagacagggtatgaatatctttttccgtgacacagtacttatacttaagtaagtgttcaatttatacctgta Mask Tandem Repeat Region ================================================ tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta Find is-nt database================================================ Query_seq: TF2115:TF2116|TF2115:TF2116:conserved hypothetical protein; possible carboxylesterase:conserved hypothetical protein; possible hemagglutinin/hemolysin:->->:2285832..2285938 107 tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2115:TF2116|TF2115:TF2116:conserved hypothetical protein; possible carboxylesterase:conserved hypothetical protein; possible hemagglutinin/hemolysin:->->:2285832..2285938 107 tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2115:TF2116|TF2115:TF2116:conserved hypothetical protein; possible carboxylesterase:conserved hypothetical protein; possible hemagglutinin/hemolysin:->->:2285832..2285938 107 tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 13 End: 105 ............ M N T Y L S I S T V S R K K I F I P C L S V T Q Y S L Y L S V .. Protein_Len: 32 Strand: + Start: 12 End: 107 ........... M E H L L K Y K Y C V T E K D I H T L S F R D T V F F I F I C L tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta 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================================================ tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -6.1 Tail_Score: -4.44187 Start: 33 End: 89 Full_Region: CACTTACTTAAGTAT AAGTACTGTGTCACGGAAAAAGA TATTCATACCC TGTCTTTCCGTGACACAGTATTC TTTATATTTATCTGT ................................AAGTACTGTGTCACGGAAAAAGATATTCATACCCTGTCTTTCCGTGACACAGTATTC.................. TransTerm Strand: + Conf: 86 HP_score: -10.0 Tail_Score: -4.30253 Start: 36 End: 86 Full_Region: TTACTTAAGTATAAG TACTGTGTCACGGAAAAAGA TATTCATACCC TGTCTTTCCGTGACACAGTA TTCTTTATATTTATC ...................................TACTGTGTCACGGAAAAAGATATTCATACCCTGTCTTTCCGTGACACAGTA..................... TransTerm Strand: - Conf: 85 HP_score: -12.8 Tail_Score: -2.7127 Start: 36 End: 86 Full_Region: gataaatataaagaa tactgtgtcacggaaagacagggt atg aatatctttttccgtgacacagta cttatacttaagtaa ...................................tactgtgtcacggaaagacagggtatgaatatctttttccgtgacacagta..................... TransTerm Strand: - Conf: 79 HP_score: -11.0 Tail_Score: -2.89714 Start: 38 End: 84 Full_Region: taaatataaagaata ctgtgtcacggaaagacagggt atg aatatctttttccgtgacacag tacttatacttaagt .....................................ctgtgtcacggaaagacagggtatgaatatctttttccgtgacacag....................... Find igs database================================================ Query_seq: TF2115:TF2116|TF2115:TF2116:conserved hypothetical protein; possible carboxylesterase:conserved hypothetical protein; possible hemagglutinin/hemolysin:->->:2285832..2285938 107 tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: tfor_TF2115_TF2116|conserved hypothetical protein; possible carboxylesterase:conserved hypothetical protein; possible hemagglutinin/hemolysin|POSITIVE:POSITIVE|[2285832, 2285938]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta tacaggtataaattgaacacttacttaagtataagtactgtgtcacggaaaaagatattcataccctgtctttccgtgacacagtattctttatatttatctgtcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAGGUAUAAAUUGAACACUUACUUAAGUAUAAGUACUGUGUCACGGAAAAAGAUAUUCAUACCCUGUCUUUCCGUGACACAGUAUUCUUUAUAUUUAUCUGUCUA .(((((((..........((((....))))...(((((((((((((((((..(((((.........)))))))))))))))))))))).........)))))))... (-35.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACAGAUAAAUAUAAAGAAUACUGUGUCACGGAAAGACAGGGUAUGAAUAUCUUUUUCCGUGACACAGUACUUAUACUUAAGUAAGUGUUCAAUUUAUACCUGUA ...((((((((((........(((((((((((((((((...(((((....))))))))))))))))))))))...((((((....))))))...))))))..)))). (-35.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 90 46 208 163 tfor:TF1988|5end_hypothetical_protein_2137237..2137467_POSITIVE 266 80 37 96 47 tfor:TF3018|5end_polyphosphate_kinase_3240122..3240352_POSITIVE 264 77 31 224 171 tfor:TF0286|5end_hypothetical_protein_315543..315773_POSITIVE 264 78 39 185 133 tfor:TF0193|5end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_207955..208185_POSITIVE 260 86 42 120 66 tfor:TF1047|5end_tRNA_pseudouridylate_synthetase_A_(pseudouridylate_synthase_I)_1108483..1108713_POSITIVE 250 80 34 195 146 tfor:TF1233|5end_dihydrodipicolinate_synthase_1317885..1318115_POSITIVE 249 77 34 137 93 tfor:TF2526|5end_outer_membrane_protein,_TonB_dependent_receptor_2705547..2705777_POSITIVE 249 78 38 176 140 tfor:TF0436|5end_conserved_hyothetical_protein_459207..459437_POSITIVE 248 100 52 74 24 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 247 91 54 124 83 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 244 97 66 207 180 tfor:TF2639|5end_hypothetical_protein_2809020..2809250_POSITIVE 244 79 35 118 56 tfor:TF0321|5end_glycosyltransferase_347438..347668_POSITIVE 243 95 54 130 93 tfor:TF1435|5end_acetate_coenzyme_A_transferase_1519574..1519804_POSITIVE 241 77 40 108 72 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 241 78 35 198 156 tfor:TF0960|5end_beta-galactosidase_1008618..1008848_POSITIVE 235 84 41 70 22 tfor:TF1441|5end_conserved_hypothetical_protein_1525567..1525797_POSITIVE 235 80 31 218 166 tfor:TF0859|5end_conserved_hypothetical_protein_911753..911983_POSITIVE 234 79 37 204 162 tfor:TF2920|5end_conserved_hypothetical_protein_3115903..3116133_POSITIVE 234 78 38 63 21 tfor:TF0668|5end_inorganic_pyrophosphatase_712493..712723_POSITIVE 230 80 34 230 179 tfor:TF0825|5end_hypothetical_protein_883597..883827_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 423 88 41 57 10 tfor:TF2115|3end_conserved_hypothetical_protein;_possible_carboxylesterase_2285771..2285921_POSITIVE 294 77 35 63 10 tfor:TF0323|3end_NAD-dependent_epimerase/dehydratase_family_protein_351053..351203_POSITIVE 264 77 31 135 82 tfor:TF0285|3end_conserved_hypothetical_protein_315534..315684_POSITIVE 264 78 39 134 82 tfor:TF0192|3end_hypothetical_protein_207984..208134_POSITIVE 249 77 34 122 78 tfor:TF2525|3end_conserved_hypothetical_protein_2705612..2705762_POSITIVE 247 91 54 146 105 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 244 79 35 118 56 tfor:TF0320|3end_dihydroorotase_347518..347668_POSITIVE 243 95 54 71 34 tfor:TF1434|3end_transketolase_1519595..1519745_POSITIVE 235 84 41 82 34 tfor:TF1440|3end_hypothetical_protein_1525659..1525809_POSITIVE 234 76 39 141 98 tfor:TF2996|3end_hypothetical_protein_3211121..3211271_POSITIVE 232 75 31 110 58 tfor:TF2158|3end_conserved_hypothetical_protein_2334584..2334734_POSITIVE 225 87 66 119 101 tfor:TF2570|3end_50S_ribosomal_protein_L18_2742619..2742769_POSITIVE 224 73 31 53 10 tfor:TF0086|3end_ABC_transporter,_ATP-binding_protein_93254..93404_POSITIVE 223 87 41 132 92 tfor:TF0975|3end_hypothetical_protein_1024361..1024511_POSITIVE 222 92 51 62 12 tfor:TF2511|3end_RNA_binding_protein_2690232..2690382_POSITIVE 215 80 38 78 25 tfor:TF0717|3end_signal_recognition_particle_769059..769209_POSITIVE 214 80 33 139 91 tfor:TF2564|3end_50S_ribosomal_protein_L14_2740046..2740196_POSITIVE 214 79 31 85 29 tfor:TF2495|3end_succinate-semialdehyde_dehydrogenase_(NADP+)_2670891..2671041_POSITIVE 213 76 41 117 92 tfor:TF0643|3end_probable_tRNA_methyltransferase_685690..685840_POSITIVE 211 78 34 80 40 tfor:TF1296|3end_possible_DNA-binding_protein,_histone-like_family_1378982..1379132_POSITIVE