Origin IGS: ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttagtcctccaaaatcttaatattaatttaattataacatattctttataaaaaaagtaaaataaaaatccctcttttttaaagggattcttatttaggaaatcagtatcttaaagaa Mask Tandem Repeat Region ================================================ ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat Find is-nt database================================================ Query_seq: FN1852:FN1853|FN1852:FN1853:hypothetical protein:methylaspartate mutase subunit S:->->:342137..342256 120 ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1852:FN1853|FN1852:FN1853:hypothetical protein:methylaspartate mutase subunit S:->->:342137..342256 120 ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1852:FN1853|FN1852:FN1853:hypothetical protein:methylaspartate mutase subunit S:->->:342137..342256 120 ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat Predict ORF larger than 30AA ================================================ ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat 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================================================ ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 66 HP_score: -2.6 Tail_Score: -5.60993 Start: 21 End: 62 Full_Region: TAAGATACTGATTTC CTAAATAAGAATCCCTTT AAAAA AGAGGGATTTTTATTTTAC TTTTTTTATAAAGAA ....................CTAAATAAGAATCCCTTTAAAAAAGAGGGATTTTTATTTTAC.......................................................... TransTerm Strand: + Conf: 64 HP_score: -6.1 Tail_Score: -3.95873 Start: 22 End: 61 Full_Region: AAGATACTGATTTCC TAAATAAGAATCCCTTT AAAAA AGAGGGATTTTTATTTTA CTTTTTTTATAAAGA .....................TAAATAAGAATCCCTTTAAAAAAGAGGGATTTTTATTTTA........................................................... TransTerm Strand: - Conf: 49 HP_score: -4.1 Tail_Score: -3.55761 Start: 26 End: 56 Full_Region: ataaaaaaagtaaaa taaaaatccctct ttttt aaagggattctta tttaggaaatcagta .........................taaaaatccctcttttttaaagggattctta................................................................ Find igs database================================================ Query_seq: FN1852:FN1853|FN1852:FN1853:hypothetical protein:methylaspartate mutase subunit S:->->:342137..342256 120 ttctttaagatactgatttcctaaataagaatccctttaaaaaagagggatttttattttactttttttataaagaatatgttataattaaattaatattaagattttggaggactaaat Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_003454_FN1852_FN1853|hypothetical protein:methylaspartate mutase subunit S|POSITIVE:POSITIVE|[342137,342256]|120 HSP 1 e-value: 5.0E-21 bit: 101.0 Len: 51 Query Start:70 Query End:120 Subject Strand: POSITIVE Subject Start: 70 Subject End: 120 .....................................................................ataaagaatatgttataattaaattaatattaagattttggaggactaaat .....................................................................ataaagaatatgttataattaaattaatattaagattttggaggactaaat HSP 2 e-value: 2.0E-20 bit: 99.6 Len: 50 Query Start:1 Query End:50 Subject Strand: POSITIVE Subject Start: 1 Subject End: 50 ttctttaagatactgatttcctaaataagaatccctttaaaaaagaggga...................................................................... ttctttaagatactgatttcctaaataagaatccctttaaaaaagaggga...................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUAAGAUACUGAUUUCCUAAAUAAGAAUCCCUUUAAAAAAGAGGGAUUUUUAUUUUACUUUUUUUAUAAAGAAUAUGUUAUAAUUAAAUUAAUAUUAAGAUUUUGGAGGACUAAAU (((((((((((..((((.....((((((((((((((((.....))))))))))))))))...(((..((((((........))))))..))).....))))..)))))))))))...... (-26.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAGUCCUCCAAAAUCUUAAUAUUAAUUUAAUUAUAACAUAUUCUUUAUAAAAAAAGUAAAAUAAAAAUCCCUCUUUUUUAAAGGGAUUCUUAUUUAGGAAAUCAGUAUCUUAAAGAA .........(((.....................((((((........))))))........((((((.(((((((.........))))))).)))))).))).................. (-14.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 67 27 226 185 NC_003454:FN1609|5end_hypothetical_protein_119613..119843_NEGATIVE 197 65 32 49 11 NC_003454:FN2004|5end_Cobalt_transport_ATP-binding_protein_cbiO_504303..504533_POSITIVE 196 50 1 123 79 NC_003454:FN1349|5end_ABC_transporter_permease_protein_2002355..2002585_NEGATIVE 192 90 44 66 17 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 187 55 14 153 100 NC_003454:FN0908|5end_Tpl_protein_1566935..1567165_NEGATIVE 186 73 32 62 15 NC_003454:FN1340|5end_Glutamyl-tRNA_synthetase_1994903..1995133_NEGATIVE 185 108 61 151 103 NC_003454:FN0622|5end_N-glycosylase/DNA_lyase_1281278..1281508_POSITIVE 179 52 19 45 11 NC_003454:FN1355|5end_Integral_membrane_protein_2007575..2007805_NEGATIVE 179 69 28 106 62 NC_003454:FN0216|5end_3-oxoacyl-[acyl-carrier_protein]_reductase_840864..841094_NEGATIVE 169 80 34 210 162 NC_003454:FN0789|5end_Transporter_1445278..1445508_NEGATIVE 167 51 13 125 93 NC_003454:FN0802|5end_Amino_acid_transport_system_permease_protein_1462136..1462366_NEGATIVE 165 47 4 74 32 NC_003454:FN1173|5end_hypothetical_protein_1835261..1835491_POSITIVE 162 49 17 145 110 NC_003454:FN2038|5end_LSU_ribosomal_protein_L10P_547696..547926_NEGATIVE 161 60 17 147 102 NC_003454:FN1485|5end_Transporter_2168022..2168252_NEGATIVE 160 39 14 68 42 NC_003454:FN1381|5end_hypothetical_protein_2032434..2032664_NEGATIVE 160 100 51 138 84 NC_003454:FN1188|5end_hypothetical_protein_1850780..1851010_POSITIVE 158 63 28 74 42 NC_003454:FN1039|5end_Branched-chain_amino_acid_transport_protein_azlC_1690997..1691227_POSITIVE 156 114 72 153 112 NC_003454:FN1328|5end_Exodeoxyribonuclease_VII_small_subunit_1983129..1983359_NEGATIVE 156 76 46 219 187 NC_003454:FN0968|5end_hypothetical_protein_1621809..1622039_NEGATIVE 156 76 46 223 191 NC_003454:FN0967|5end_CbiD_protein_1621050..1621280_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 59 23 68 32 NC_003454:FN1852|3end_hypothetical_protein_342076..342226_POSITIVE 243 67 27 99 58 NC_003454:FN1610|3end_33_kDa_chaperonin_119740..119890_NEGATIVE 197 65 32 39 1 NC_003454:FN2003|3end_bioY_protein_504373..504523_POSITIVE 196 50 1 119 75 NC_003454:FN1350|3end_Integral_membrane_protein_2002359..2002509_NEGATIVE 196 116 99 108 91 NC_003454:FN0555|3end_Transcriptional_regulator,_MerR_family_1208332..1208482_POSITIVE 194 50 4 80 32 NC_003454:FN1442|3end_Transposase_2110155..2110305_NEGATIVE 187 55 14 132 79 NC_003454:FN0909|3end_DNA_repair_protein_radC_1566956..1567106_NEGATIVE 178 75 42 43 14 NC_003454:FN1647|3end_hypothetical_protein_142482..142632_POSITIVE 165 50 7 40 7 NC_003454:FN1422|3end_NA+/H+_antiporter_NHAC_2087005..2087155_NEGATIVE 161 60 17 150 105 NC_003454:FN1486|3end_Integral_membrane_protein_with_CBS_domains_2168019..2168169_NEGATIVE 158 63 28 63 31 NC_003454:FN1038|3end_Transporter_1691066..1691216_POSITIVE 158 83 49 122 81 NC_003454:FN2044|3end_LSU_ribosomal_protein_L33P_549957..550107_NEGATIVE 158 36 1 151 118 NC_003454:FN1792|3end_hypothetical_protein_272899..273049_NEGATIVE 156 109 62 71 27 NC_003454:FN0577|3end_hypothetical_protein_1228042..1228192_POSITIVE 155 49 1 135 84 NC_003454:FN1073|3end_hypothetical_protein_1720989..1721139_POSITIVE 154 110 61 139 84 NC_003454:FN0560|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1214219..1214369_POSITIVE 151 98 65 40 9 NC_003454:FN1344|3end_hypothetical_protein_1998034..1998184_POSITIVE 149 69 34 121 86 NC_003454:FN1215|3end_Hypothetical_cytosolic_protein_1875460..1875610_NEGATIVE 149 38 6 27 4 NC_003454:FN0854|3end_Glucose-1-phosphate_adenylyltransferase_1512324..1512474_NEGATIVE 149 74 35 135 105 NC_003454:FN0118|3end_Chaperone_protein_dnaJ_752156..752306_POSITIVE