Origin IGS: ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataataaaaaataagatagtaggataatgggagctggagcttttattttatgcaccagctcctttataatacaataaataaaaataagtgagttacattccagtaatgaactatttttgtatttgaataagggggaaattataa Mask Tandem Repeat Region ================================================ ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat Find is-nt database================================================ Query_seq: FN1898:FN1899|FN1898:FN1899:Sugar transport ATP-binding protein:Hypothetical lipoprotein:<-<-:386660..386803 144 ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1898:FN1899|FN1898:FN1899:Sugar transport ATP-binding protein:Hypothetical lipoprotein:<-<-:386660..386803 144 ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1898:FN1899|FN1898:FN1899:Sugar transport ATP-binding protein:Hypothetical lipoprotein:<-<-:386660..386803 144 ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 3 End: 143 .. M I S P L F K Y K N S S L L E C N S L I F I Y C I I K E L V H K I K A P A P I I L L S Y F L L . ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat 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: 75 End: 104 ..........................................................................TTTTATTTTATGCACCAGCTCCTTTATAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 44 HP_score: -2.1 Tail_Score: -3.46965 Start: 81 End: 117 Full_Region: ATTTATTGTATTATA AAGGAGCTGGTGCAT AAAATAA AAGCTCCAGCTCCCA TTATCCTACTATCTT ................................................................................AAGGAGCTGGTGCATAAAATAAAAGCTCCAGCTCCCA........................... TransTerm Strand: + Conf: 55 HP_score: -5.6 Tail_Score: -2.67456 Start: 82 End: 116 Full_Region: TTTATTGTATTATAA AGGAGCTGGTGCAT AAAATAA AAGCTCCAGCTCCC ATTATCCTACTATCT .................................................................................AGGAGCTGGTGCATAAAATAAAAGCTCCAGCTCCC............................ TransTerm Strand: - Conf: 84 HP_score: -9.1 Tail_Score: -3.9712 Start: 83 End: 115 Full_Region: gatagtaggataatg ggagctggagctt ttatttt atgcaccagctcc tttataatacaataa ..................................................................................ggagctggagcttttattttatgcaccagctcc............................. Find igs database================================================ Query_seq: FN1898:FN1899|FN1898:FN1899:Sugar transport ATP-binding protein:Hypothetical lipoprotein:<-<-:386660..386803 144 ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: NC_003454_FN1898_FN1899|Sugar transport ATP-binding protein:Hypothetical lipoprotein|NEGATIVE:NEGATIVE|[386660,386803]|144 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat ttataatttcccccttattcaaatacaaaaatagttcattactggaatgtaactcacttatttttatttattgtattataaaggagctggtgcataaaataaaagctccagctcccattatcctactatcttattttttattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAAUUUCCCCCUUAUUCAAAUACAAAAAUAGUUCAUUACUGGAAUGUAACUCACUUAUUUUUAUUUAUUGUAUUAUAAAGGAGCUGGUGCAUAAAAUAAAAGCUCCAGCUCCCAUUAUCCUACUAUCUUAUUUUUUAUUAU ..........................(((((((((...((((......))))...)).))))))).......(((..((((.((((((((.((...........)).))))))))..))))..))).................. (-24.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAAAAAAUAAGAUAGUAGGAUAAUGGGAGCUGGAGCUUUUAUUUUAUGCACCAGCUCCUUUAUAAUACAAUAAAUAAAAAUAAGUGAGUUACAUUCCAGUAAUGAACUAUUUUUGUAUUUGAAUAAGGGGGAAAUUAUAA (((((.............(((..((((.(((((((((.((...........)).)))))))))))))..))).....(((((((((.((..(((((......)))))..))))))))))).................))))).. (-35.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 912 130 81 221 172 NC_003454:FN1898|5end_Sugar_transport_ATP-binding_protein_386569..386799_NEGATIVE 281 65 42 139 116 NC_003454:FN1460|5end_Hypothetical_cytosolic_protein_2141429..2141659_POSITIVE 262 64 43 228 207 NC_003454:FN1615|5end_Integral_membrane_protein_125125..125355_POSITIVE 255 66 42 161 137 NC_003454:FN1440|5end_1-phosphofructokinase_2107238..2107468_POSITIVE 252 129 83 194 146 NC_003454:FN0769|5end_Hemin_transport_system_permease_protein_hmuU_1425704..1425934_POSITIVE 234 79 43 205 171 NC_003454:FN0367|5end_Integral_membrane_protein_996901..997131_NEGATIVE 232 117 85 63 32 NC_003454:FN1620|5end_30S_ribosomal_protein_S2_127896..128126_POSITIVE 232 125 105 230 204 NC_003454:FN1584|5end_Beta-lactamase_96158..96388_NEGATIVE 231 140 100 112 76 NC_003454:FN1369|5end_Zinc_finger_protein_2019006..2019236_NEGATIVE 228 115 87 34 1 NC_003454:FN1621|5end_elongation_factor_Ts_128673..128903_POSITIVE 224 128 81 60 16 NC_003454:FN1192|5end_hypothetical_protein_1854679..1854909_POSITIVE 221 125 82 195 150 NC_003454:FN1941|5end_ClpB_protein_441279..441509_POSITIVE 213 133 99 214 176 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 210 48 10 144 111 NC_003454:FN0679|5end_GTPase_1334596..1334826_POSITIVE 209 122 105 32 15 NC_003454:FN0347|5end_phosphatidylserine_decarboxylase_980156..980386_NEGATIVE 209 140 99 130 72 NC_003454:FN0176|5end_Cell_division_inhibitor_MinD_801157..801387_POSITIVE 209 115 86 133 111 NC_003454:FN1805|5end_hypothetical_protein_286453..286683_POSITIVE 207 130 87 222 177 NC_003454:FN1104|5end_Holliday_junction_DNA_helicase_ruvA_1749453..1749683_POSITIVE 204 127 83 83 34 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 204 120 79 80 26 NC_003454:FN2072|5end_Guanine-hypoxanthine_permease_582506..582736_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 65 27 36 1 NC_003454:FN1427|3end_Phenazine_biosynthesis_protein_phzF_2096763..2096913_POSITIVE 259 115 79 84 44 NC_003454:FN0736|3end_Methyltransferase_1394658..1394808_NEGATIVE 255 66 42 88 64 NC_003454:FN1439|3end_Transcriptional_regulator,_DeoR_family_2107245..2107395_POSITIVE 254 75 42 83 53 NC_003454:FN0713|3end_Chromate_transport_protein_1371943..1372093_POSITIVE 237 128 104 139 115 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 235 69 33 42 3 NC_003454:FN1825|3end_hypothetical_protein_314511..314661_POSITIVE 234 79 43 68 34 NC_003454:FN0368|3end_adenylosuccinate_lyase_997038..997188_NEGATIVE 231 140 100 128 92 NC_003454:FN1370|3end_Endonuclease_2018990..2019140_NEGATIVE 215 114 75 80 39 NC_003454:FN1005|3end_hypothetical_protein_1660975..1661125_POSITIVE 213 113 80 62 36 NC_003454:FN1114|3end_hypothetical_protein_1758686..1758836_POSITIVE 213 122 81 72 19 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 210 118 74 101 59 NC_003454:FN0879|3end_ABC_transporter_integral_membrane_protein_1540161..1540311_NEGATIVE 210 48 10 119 86 NC_003454:FN0678|3end_Ser/Thr_protein_kinase_1334651..1334801_POSITIVE 209 140 99 128 70 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 209 115 86 65 43 NC_003454:FN1804|3end_Aminoacyl-histidine_dipeptidase_286465..286615_POSITIVE 208 139 102 131 95 NC_003454:FN0359|3end_ATP_synthase_gamma_chain,_sodium_ion_specific_989995..990145_NEGATIVE 203 132 106 139 113 NC_003454:FN0121|3end_hypothetical_protein_752908..753058_NEGATIVE 203 128 82 75 25 NC_003454:FN1533|3end_Electron_transfer_flavoprotein_alpha-subunit_45350..45500_NEGATIVE 201 132 106 57 22 NC_003454:FN0795|3end_CBS_domain_containing_protein_1453076..1453226_POSITIVE 197 88 46 74 22 NC_003454:FN0490|3end_Integral_membrane_protein_1135452..1135602_NEGATIVE