Origin IGS: aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctttatctatccaaatagcatcaaaagcaatttcaataatatttctttattataaacaaagctttcctccatataatttttaataaattatatcattagaaaaaaaagtaatgtaaaatatttttaagatatt Mask Tandem Repeat Region ================================================ aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa Find is-nt database================================================ Query_seq: FN0428:FN0429|FN0428:FN0429:hypothetical protein:hypothetical protein:->->:1070954..1071088 135 aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0428:FN0429|FN0428:FN0429:hypothetical protein:hypothetical protein:->->:1070954..1071088 135 aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0428:FN0429|FN0428:FN0429:hypothetical protein:hypothetical protein:->->:1070954..1071088 135 aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa Predict ORF larger than 30AA ================================================ aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa 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================================================ aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -4.2 Tail_Score: -2.70932 Start: 42 End: 62 Full_Region: caaagctttcctcca tataattt ttaat aaattata tcattagaaaaaaaa .........................................tataatttttaataaattata......................................................................... TransTerm Strand: - Conf: 36 HP_score: -2.4 Tail_Score: -2.90075 Start: 44 End: 60 Full_Region: aagctttcctccata taattt ttaat aaatta tatcattagaaaaaa ...........................................taatttttaataaatta........................................................................... Find igs database================================================ Query_seq: FN0428:FN0429|FN0428:FN0429:hypothetical protein:hypothetical protein:->->:1070954..1071088 135 aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: NC_003454_FN0428_FN0429|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1070954,1071088]|135 HSP 1 e-value: 9.0E-57 bit: 220.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 aatatcttaaaaatattttacattacnnnnnnnnctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa aatatcttaaaaatattttacattacttttttttctaatgatataatttattaaaaattatatggaggaaagctttgtttataataaagaaatattattgaaattgcttttgatgctatttggatagataaagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCUUAAAAAUAUUUUACAUUACUUUUUUUUCUAAUGAUAUAAUUUAUUAAAAAUUAUAUGGAGGAAAGCUUUGUUUAUAAUAAAGAAAUAUUAUUGAAAUUGCUUUUGAUGCUAUUUGGAUAGAUAAAGAA ............................((((((((....(((((((((.....))))))))))))))))).((((((((((.......(((((.(((..(((....)))..))).)))))..)))))))))).. (-18.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUAUCUAUCCAAAUAGCAUCAAAAGCAAUUUCAAUAAUAUUUCUUUAUUAUAAACAAAGCUUUCCUCCAUAUAAUUUUUAAUAAAUUAUAUCAUUAGAAAAAAAAGUAAUGUAAAAUAUUUUUAAGAUAUU .....(((((............((.(((((.......((((((......)))))).......))))).....(((((((((.....))))))))).....))...(((((((........))))))).))))).. (-12.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 71 38 230 193 NC_003454:FN1825|5end_hypothetical_protein_313994..314224_POSITIVE 196 56 12 72 31 NC_003454:FN1602|5end_Hypothetical_cytosolic_protein_111492..111722_NEGATIVE 192 66 22 136 96 NC_003454:FN1885|5end_Hemolysin_III_370684..370914_POSITIVE 192 129 83 226 177 NC_003454:FN1783|5end_Ethanolamine_utilization_protein_eutJ_264626..264856_POSITIVE 189 130 81 42 1 NC_003454:FN0567|5end_hypothetical_protein_1218389..1218619_POSITIVE 187 108 61 216 171 NC_003454:FN1045|5end_hypothetical_protein_1695987..1696217_NEGATIVE 184 117 72 220 163 NC_003454:FN0274|5end_Transposase_900485..900715_NEGATIVE 171 44 14 109 83 NC_003454:FN1362|5end_Dipeptide_transport_ATP-binding_protein_dppD_2013818..2014048_POSITIVE 171 119 72 61 13 NC_003454:FN0699|5end_Protein_translocase_subunit_secD_1357051..1357281_POSITIVE 169 125 92 33 1 NC_003454:FN0253|5end_Outer_membrane_protein_874510..874740_POSITIVE 169 89 57 144 107 NC_003454:FN0066|5end_Two_component_system_histidine_kinase_702327..702557_POSITIVE 169 125 92 33 1 NC_003454:FN2059|5end_Outer_membrane_protein_573332..573562_NEGATIVE 169 125 92 33 1 NC_003454:FN2048|5end_Outer_membrane_protein_559256..559486_NEGATIVE 168 130 83 222 164 NC_003454:FN1902|5end_Deoxycytidylate_deaminase_390551..390781_NEGATIVE 166 67 21 132 89 NC_003454:FN1476|5end_N-acetylmannosamine-6-phosphate_2-epimerase_2158672..2158902_POSITIVE 165 69 27 231 181 NC_003454:FN1393|5end_Signal_recognition_particle,_subunit_FFH/SRP54_2050844..2051074_NEGATIVE 163 59 13 224 176 NC_003454:FN1520|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_26073..26303_NEGATIVE 162 120 71 82 34 NC_003454:FN1806|5end_Integral_membrane_protein_287724..287954_POSITIVE 161 128 90 59 11 NC_003454:FN0826|5end_periplasmic_component_of_efflux_system_1486495..1486725_POSITIVE 160 110 63 63 17 NC_003454:FN1018|5end_hypothetical_protein_1672369..1672599_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 186 97 54 42 3 NC_003454:FN1000|3end_biotin_synthase_1656101..1656251_POSITIVE 186 54 22 128 98 NC_003454:FN1691|3end_Hypothetical_membrane-spanning_protein_186632..186782_NEGATIVE 184 117 72 98 41 NC_003454:FN0275|3end_Transposase_900607..900757_NEGATIVE 171 44 14 109 83 NC_003454:FN1361|3end_Dipeptide_transport_system_permease_protein_dppC_2013898..2014048_POSITIVE 168 45 7 115 74 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 168 130 83 101 43 NC_003454:FN1903|3end_Coenzyme_A_disulfide_reductase/_disulfide_bond_regulator_domain_390672..390822_NEGATIVE 166 67 21 117 74 NC_003454:FN1475|3end_N-acetylneuraminate_lyase_2158737..2158887_POSITIVE 161 45 26 148 129 NC_003454:FN0252|3end_hypothetical_protein_874521..874671_POSITIVE 161 45 26 148 129 NC_003454:FN2060|3end_hypothetical_protein_573401..573551_NEGATIVE 161 45 26 148 129 NC_003454:FN2049|3end_hypothetical_protein_559325..559475_NEGATIVE 160 126 104 141 114 NC_003454:FN0272|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_899503..899653_POSITIVE 160 37 1 54 20 NC_003454:FN1842|3end_Dihydroxyacetone_kinase_phosphotransfer_protein_331981..332131_POSITIVE 159 110 62 69 32 NC_003454:FN1422|3end_NA+/H+_antiporter_NHAC_2087005..2087155_NEGATIVE 156 106 71 119 85 NC_003454:FN1083|3end_putative_surface_protein_1728639..1728789_POSITIVE 153 39 14 107 80 NC_003454:FN2097|3end_hypothetical_protein_606449..606599_NEGATIVE 152 91 53 41 1 NC_003454:FN1464|3end_1-deoxy-D-xylulose-5-phosphate_synthase_2145954..2146104_NEGATIVE 152 49 26 59 34 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 152 110 66 91 49 NC_003454:FN1602|3end_Hypothetical_cytosolic_protein_111022..111172_NEGATIVE 151 123 105 57 37 NC_003454:FN1831|3end_Nitrogen_assimilation_regulatory_protein_320029..320179_NEGATIVE 150 37 1 103 67 NC_003454:FN1106|3end_L-serine_dehydratase_1751873..1752023_POSITIVE