Origin IGS: tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atattaaaatcccctaagagtgaggggatttttttacttaaagattataacaaaataataaagactactcaatatcttttatggtataatgtaatgtaaaatataaagattagaatagaggaaaaa Mask Tandem Repeat Region ================================================ tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat Find is-nt database================================================ Query_seq: FN1609:FN1610|FN1609:FN1610:hypothetical protein:33 kDa chaperonin:<-<-:119704..119829 126 tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1609:FN1610|FN1609:FN1610:hypothetical protein:33 kDa chaperonin:<-<-:119704..119829 126 tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1609:FN1610|FN1609:FN1610:hypothetical protein:33 kDa chaperonin:<-<-:119704..119829 126 tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 31 End: 126 .............................. M V N Y W L L Y Q T T K I I K N Y D K L L F I G E S K P S K L M tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat 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: 87 Start: 54 End: 83 .....................................................ATTGAGTAGTCTTTATTATTTTGTTATAAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1609:FN1610|FN1609:FN1610:hypothetical protein:33 kDa chaperonin:<-<-:119704..119829 126 tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_003454_FN1609_FN1610|hypothetical protein:33 kDa chaperonin|NEGATIVE:NEGATIVE|[119704,119829]|126 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtnnnnnnntcccctcactcttaggggattttaatat tttttcctctattctaatctttatattttacattacattataccataaaagatattgagtagtctttattattttgttataatctttaagtaaaaaaatcccctcactcttaggggattttaatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCCUCUAUUCUAAUCUUUAUAUUUUACAUUACAUUAUACCAUAAAAGAUAUUGAGUAGUCUUUAUUAUUUUGUUAUAAUCUUUAAGUAAAAAAAUCCCCUCACUCUUAGGGGAUUUUAAUAU ........((((((..((((((.........................))))))...))))))................................((((((((((.......))))))))))..... (-19.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUAAAAUCCCCUAAGAGUGAGGGGAUUUUUUUACUUAAAGAUUAUAACAAAAUAAUAAAGACUACUCAAUAUCUUUUAUGGUAUAAUGUAAUGUAAAAUAUAAAGAUUAGAAUAGAGGAAAAA .((..((((((((((.......))))))))))..)).......(((((......))))).....(((.((...(((((((((..((((......))))..))).))))))..)).)))........ (-22.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 735 120 71 211 162 NC_003454:FN1609|5end_hypothetical_protein_119613..119843_NEGATIVE 231 118 98 82 63 NC_003454:FN0864|5end_hypothetical_protein_1522900..1523130_NEGATIVE 221 45 4 143 94 NC_003454:FN1562|5end_3-deoxy-7-phosphoheptulonate_synthase_84764..84994_NEGATIVE 216 48 1 151 94 NC_003454:FN0224|5end_excinuclease_ABC_subunit_B_849602..849832_POSITIVE 212 83 43 123 88 NC_003454:FN0808|5end_Phosphoglycerate_mutase_1467955..1468185_POSITIVE 209 57 17 110 68 NC_003454:FN0626|5end_Hypothetical_cytosolic_protein_1286092..1286322_NEGATIVE 209 47 2 134 91 NC_003454:FN0240|5end_Thymidylate_synthase_863894..864124_POSITIVE 209 39 5 135 97 NC_003454:FN0084|5end_Acetaldehyde_dehydrogenase_[acetylating]_721572..721802_POSITIVE 203 41 8 79 45 NC_003454:FN1026|5end_tRNA_pseudouridine_synthase_A_1680823..1681053_NEGATIVE 201 119 74 45 1 NC_003454:FN1355|5end_Integral_membrane_protein_2007575..2007805_NEGATIVE 199 37 2 130 97 NC_003454:FN1171|5end_Acetate_kinase_1833561..1833791_NEGATIVE 194 115 75 53 20 NC_003454:FN1483|5end_adenine_phosphoribosyltransferase_2166523..2166753_NEGATIVE 193 46 5 145 96 NC_003454:FN0116|5end_Chaperone_protein_dnaK_748253..748483_POSITIVE 186 119 71 182 134 NC_003454:FN1853|5end_methylaspartate_mutase_subunit_S_342117..342347_POSITIVE 185 117 72 211 170 NC_003454:FN1398|5end_Amino_acid_carrier_protein_alsT_2052808..2053038_POSITIVE 184 48 3 141 97 NC_003454:FN0052|5end_Arsenate_reductase_688849..689079_POSITIVE 182 99 55 115 63 NC_003454:FN0610|5end_hypothetical_protein_1264815..1265045_POSITIVE 178 81 44 131 94 NC_003454:FN1657|5end_SSU_ribosomal_protein_S6P_153122..153352_NEGATIVE 172 88 47 117 62 NC_003454:FN0266|5end_membrane_protein_related_to_metalloendopeptidase_892320..892550_POSITIVE 172 60 12 142 86 NC_003454:FN1975|5end_ATP-dependent_RNA_helicase_475599..475829_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 45 4 130 81 NC_003454:FN1563|3end_hypothetical_protein_84777..84927_NEGATIVE 216 48 1 125 68 NC_003454:FN0223|3end_COME_operon_protein_3_849656..849806_POSITIVE 209 57 17 47 5 NC_003454:FN0627|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1286155..1286305_NEGATIVE 209 47 2 83 40 NC_003454:FN0239|3end_hypothetical_protein_863923..864073_POSITIVE 203 41 8 79 45 NC_003454:FN1027|3end_Rod_shape-determining_protein_rodA_1680823..1680973_NEGATIVE 199 37 2 79 46 NC_003454:FN1172|3end_Phosphate_acetyltransferase_1833612..1833762_NEGATIVE 194 115 75 38 5 NC_003454:FN1484|3end_Tetratricopeptide_repeat_family_protein_2166538..2166688_NEGATIVE 193 46 5 114 65 NC_003454:FN0114|3end_GrpE_protein_748302..748452_POSITIVE 186 119 71 61 13 NC_003454:FN1852|3end_hypothetical_protein_342076..342226_POSITIVE 178 81 44 65 28 NC_003454:FN1658|3end_prolyl-tRNA_synthetase_153188..153338_NEGATIVE 177 48 31 67 50 NC_003454:FN0059|3end_NifU_protein_695619..695769_POSITIVE 172 88 47 127 72 NC_003454:FN0265|3end_Cell_division_protein_ftsX_892410..892560_POSITIVE 167 44 3 59 13 NC_003454:FN1765|3end_pyruvate_kinase_258023..258173_NEGATIVE 166 106 72 148 112 NC_003454:FN1397|3end_glutaminase_2052830..2052980_POSITIVE 166 92 58 119 82 NC_003454:FN2110|3end_Hypothetical_exported_24-amino_acid_repeat_protein_621908..622058_NEGATIVE 165 60 13 77 33 NC_003454:FN0969|3end_hypothetical_protein_1621806..1621956_NEGATIVE 164 29 1 110 79 NC_003454:FN2127|3end_hypothetical_protein_638226..638376_NEGATIVE 164 110 63 64 12 NC_003454:FN1850|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_340214..340364_POSITIVE 163 117 73 120 61 NC_003454:FN1452|3end_Cell_division_protein_ftsA_2132733..2132883_NEGATIVE 163 116 76 83 39 NC_003454:FN1587|3end_Acetyltransferase_99334..99484_POSITIVE