Origin IGS: cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaataaaacgaggtcgggaatttttcctaacctcgttttaaatttacgatttaaattgacatatatttacaattcaaaaggctataaaagctgttataacaacaattcgatataattcgtttacactataagcgatattttgtaaatgaaatttacaaaaacgtaaatctcatgtaatg Mask Tandem Repeat Region ================================================ cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt Find is-nt database================================================ Query_seq: SSA_2373:SSA_2374|SSA_2373:SSA_2374:DNA replication and repair protein recF, putative:Inosine-5'-monophosphate dehydrogenase, putative:-><-:2375443..2375623 181 cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2373:SSA_2374|SSA_2373:SSA_2374:DNA replication and repair protein recF, putative:Inosine-5'-monophosphate dehydrogenase, putative:-><-:2375443..2375623 181 cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2373:SSA_2374|SSA_2373:SSA_2374:DNA replication and repair protein recF, putative:Inosine-5'-monophosphate dehydrogenase, putative:-><-:2375443..2375623 181 cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 68 End: 160 ................................................................... I S N N N Y C S K Y G K S N Y I Y T L K F R L N L V L N P F M ..................... cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt 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================================================ cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2373:SSA_2374|SSA_2373:SSA_2374:DNA replication and repair protein recF, putative:Inosine-5'-monophosphate dehydrogenase, putative:-><-:2375443..2375623 181 cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_009009_SSA_2373_SSA_2374|DNA replication and repair protein recF, putative:Inosine-5'-monophosphate dehydrogenase, putative|POSITIVE:NEGATIVE|[2375443,2375623]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt cattacatgagatttacgtttttgtaaatttcatttacaaaatatcgcttatagtgtaaacgaattatatcgaattgttgttataacagcttttatagccttttgaattgtaaatatatgtcaatttaaatcgtaaatttaaaacgaggttaggaaaaattcccgacctcgttttattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUACAUGAGAUUUACGUUUUUGUAAAUUUCAUUUACAAAAUAUCGCUUAUAGUGUAAACGAAUUAUAUCGAAUUGUUGUUAUAACAGCUUUUAUAGCCUUUUGAAUUGUAAAUAUAUGUCAAUUUAAAUCGUAAAUUUAAAACGAGGUUAGGAAAAAUUCCCGACCUCGUUUUAUUUUU ......((((((((((((....))))))))))))..........(((..((((((........)))))).)))...(((((....))))).......((..(((((((((...........)))))))))..)).....(((((((((((..(((.....)))..)))))))))))..... (-44.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUAAAACGAGGUCGGGAAUUUUUCCUAACCUCGUUUUAAAUUUACGAUUUAAAUUGACAUAUAUUUACAAUUCAAAAGGCUAUAAAAGCUGUUAUAACAACAAUUCGAUAUAAUUCGUUUACACUAUAAGCGAUAUUUUGUAAAUGAAAUUUACAAAAACGUAAAUCUCAUGUAAUG .....(((((((((((..(((.....)))..)))))))))))...(((((................((((((((.......((((.....))))........................(((((((.....)))))))....))))))))((.((((((......)))))).)).))))).. (-40.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 180 137 187 142 NC_009009:SSA_0325|5end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_317603..317833_POSITIVE 254 180 142 149 111 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 247 110 79 217 182 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 243 106 61 215 158 NC_009009:SSA_0027|5end_Acyl_carrier_protein,_putative_31474..31704_POSITIVE 226 175 141 200 165 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 224 175 138 144 103 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 221 106 61 225 169 NC_009009:SSA_1602|5end_Exoribonuclease,_VacB/Rnb_family,_putative_1609370..1609600_NEGATIVE 219 166 146 70 48 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 216 100 51 226 163 NC_009009:SSA_0599|5end_hypothetical_protein_588667..588897_POSITIVE 215 174 148 29 2 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 215 104 64 48 5 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 214 122 85 39 7 NC_009009:SSA_2195|5end_ATPase/kinase,_putative_2196743..2196973_NEGATIVE 214 179 133 180 132 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 213 108 83 212 187 NC_009009:SSA_1472|5end_hypothetical_protein_1478655..1478885_NEGATIVE 209 115 76 166 132 NC_009009:SSA_1834|5end_30S_ribosomal_interface_protein_S30EA,_putative_1830194..1830424_NEGATIVE 208 175 145 70 40 NC_009009:SSA_0921|5end_Zn-dependeant_threonine_dehydrogenase,_putative_931047..931277_POSITIVE 203 168 143 150 122 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 201 103 67 191 155 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 200 95 51 222 179 NC_009009:SSA_1802|5end_Snf2_family_protein,_putative_1786470..1786700_NEGATIVE 200 173 138 49 11 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 177 140 69 29 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE 286 180 137 97 52 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 254 180 142 70 32 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 230 112 87 130 106 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 227 177 140 78 38 NC_009009:SSA_1161|3end_hypothetical_protein_1188443..1188593_POSITIVE 226 175 141 87 52 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 225 176 143 93 56 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 224 175 138 45 4 NC_009009:SSA_1786|3end_Conserved_uncharacterized_protein_1769996..1770146_NEGATIVE 222 173 131 77 25 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 218 113 86 46 22 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 214 179 133 80 32 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 213 108 83 138 113 NC_009009:SSA_1473|3end_hypothetical_protein_1478729..1478879_NEGATIVE 212 174 140 86 57 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 209 115 76 84 50 NC_009009:SSA_1835|3end_Late_competence_protein,_putative_1830276..1830426_NEGATIVE 208 104 69 106 69 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE 204 180 141 97 62 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 202 110 61 128 85 NC_009009:SSA_1372|3end_hypothetical_protein_1388946..1389096_NEGATIVE 200 95 51 93 50 NC_009009:SSA_1803|3end_GTP-binding_protein,_putative_1786599..1786749_NEGATIVE 200 104 76 140 108 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 199 122 88 120 85 NC_009009:SSA_1992|3end_Fructose-bisphosphate_aldolase,_putative_1989091..1989241_NEGATIVE