Origin IGS: tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata .........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 tatgcacctcctatgattttttggggtttccccggattttgtgaagactcgcctagcatcgtgggacgaaccacttctatctcacagagtgagcaacgatgatcgtgcggttgcacaggaatgtgcatagtcaactctataagtatagcacttctaccgctctttagcaagctttttcatctcatgaaaacggattttcaaggattatctttaaattttatcta Mask Tandem Repeat Region ================================================ tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata Find is-nt database================================================ Query_seq: SSA_1060:SSA_1061|SSA_1060:SSA_1061:hypothetical protein:50S ribosomal protein L21, putative:->->:1077508..1077731 224 tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1060:SSA_1061|SSA_1060:SSA_1061:hypothetical protein:50S ribosomal protein L21, putative:->->:1077508..1077731 224 tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1060:SSA_1061|SSA_1060:SSA_1061:hypothetical protein:50S ribosomal protein L21, putative:->->:1077508..1077731 224 tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 55 End: 222 ...................................................... M L K S G R S A I L I E L T M H I P V Q P H D H R C S L C E I E V V R P T M L G E S S Q N P G K P Q K I I G G A .. Protein_Len: 34 Strand: - Start: 3 End: 104 .. I F N L S L G Q F D T K M L H F L K S F L P L L A I S I S N V I C M ........................................................................................................................ tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata 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: 82 Start: 54 End: 83 .....................................................CTTGCTAAAGAGCGGTAGAAGTGCTATACT............................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1060:SSA_1061|SSA_1060:SSA_1061:hypothetical protein:50S ribosomal protein L21, putative:->->:1077508..1077731 224 tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata Intra-Species Hit: Count: 1 Min: 1 Max: 224 Len: 224 Subject: NC_009009_SSA_1060_SSA_1061|hypothetical protein:50S ribosomal protein L21, putative|POSITIVE:POSITIVE|[1077508,1077731]|224 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 224 Query Start:1 Query End:224 Subject Strand: POSITIVE Subject Start: 1 Subject End: 224 tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata tagataaaatttaaagataatccttgaaaatccgttttcatgagatgaaaaagcttgctaaagagcggtagaagtgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgctcactctgtgagatagaagtggttcgtcccacgatgctaggcgagtcttcacaaaatccggggaaaccccaaaaaatcataggaggtgcata Inter-species Hit: Count: 3 Min: 75 Max: 224 Len: 150 Subject: NC_003028_SP_1104_SP_1105|hypothetical protein:50S ribosomal protein L21|POSITIVE:POSITIVE|[1037035,1037215]|181 HSP 1 e-value: 6.0E-22 bit: 105.0 Len: 76 Query Start:149 Query End:224 Subject Strand: POSITIVE Subject Start: 105 Subject End: 181 ....................................................................................................................................................aagtggttcgtcccacgatgctaggcgagtcttcac-aaaatccggggaaaccccaaaaaatcataggaggtgcata ....................................................................................................................................................aagtggttcgtcccacgatgctaggcgagtcttcacaaaaaatcggggaaacccataaaaatcataggaggtgcata HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 59 Query Start:75 Query End:133 Subject Strand: POSITIVE Subject Start: 31 Subject End: 89 ..........................................................................tgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgct........................................................................................... ..........................................................................tgctatacttgaagagttgactatgcacgatcctgtgcaaccgcacgaacatcgttgct........................................................................................... Subject: NC_008533_SPD_0988_SPD_0989|integral membrane protein:ribosomal protein L21|POSITIVE:POSITIVE|[1001135,1001315]|181 HSP 1 e-value: 2.0E-19 bit: 97.6 Len: 76 Query Start:149 Query End:224 Subject Strand: POSITIVE Subject Start: 105 Subject End: 181 ....................................................................................................................................................aagtggttcgtcccacgatgctaggcgagtcttcac-aaaatccggggaaaccccaaaaaatcataggaggtgcata ....................................................................................................................................................aagtggttcgtcccacgatgctaggcgagtcttcacaaaaaatcggggaaatccataaaaatcataggaggtgcata HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 59 Query Start:75 Query End:133 Subject Strand: POSITIVE Subject Start: 31 Subject End: 89 ..........................................................................tgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgct........................................................................................... ..........................................................................tgctatacttgaagagttgactatgcacgatcctgtgcaaccgcacgaacatcgttgct........................................................................................... Subject: NC_003098_spr1011_spr1012|hypothetical protein:50S ribosomal protein L21|POSITIVE:POSITIVE|[993604,993784]|181 HSP 1 e-value: 2.0E-19 bit: 97.6 Len: 76 Query Start:149 Query End:224 Subject Strand: POSITIVE Subject Start: 105 Subject End: 181 ....................................................................................................................................................aagtggttcgtcccacgatgctaggcgagtcttcac-aaaatccggggaaaccccaaaaaatcataggaggtgcata ....................................................................................................................................................aagtggttcgtcccacgatgctaggcgagtcttcacaaaaaatcggggaaatccataaaaatcataggaggtgcata HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 59 Query Start:75 Query End:133 Subject Strand: POSITIVE Subject Start: 31 Subject End: 89 ..........................................................................tgctatacttatagagttgactatgcacattcctgtgcaaccgcacgatcatcgttgct........................................................................................... ..........................................................................tgctatacttgaagagttgactatgcacgatcctgtgcaaccgcacgaacatcgttgct........................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUAUACUUAUAGAGUUGACUAUGCACAUUCCUGUGCAACCGCACGAUCAUCGUUGCUCACUCUGUGAGAUAGAAGUGGUUCGUCCCACGAUGCUAGGCGAGUCUUCACAAAAUCCGGGGAAACCCCAAAAAAUCAUAGGAGGUGCAUA ..((((.((((((((((......((((((....))))))...(((((.....)).)))..))))))))))))))..((((......))))........(((..((((..........(((....)))...........))))..)))... (-44.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGCACCUCCUAUGAUUUUUUGGGGUUUCCCCGGAUUUUGUGAAGACUCGCCUAGCAUCGUGGGACGAACCACUUCUAUCUCACAGAGUGAGCAACGAUGAUCGUGCGGUUGCACAGGAAUGUGCAUAGUCAACUCUAUAAGUAUAGCA (((((((.(((........(((((((...)))))))...((((..(((.((((...((((((((......))........(((((...)))))..))))))...).)))))).)))))))..)))))))..................... (-41.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 130 81 63 10 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 352 89 41 228 160 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 343 78 31 84 36 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 338 80 31 185 119 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 335 110 63 183 141 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 324 60 11 216 168 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 317 128 83 45 5 NC_009009:SSA_1859|5end_Penicillin-binding_protein-like_factor_A/_recombinase,_putative_1853704..1853934_POSITIVE 315 110 67 148 101 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 313 89 41 43 4 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 312 120 71 217 175 NC_009009:SSA_0738|5end_Ornithine_carbamoyltransferase,_catabolic,_putative_719904..720134_POSITIVE 310 67 23 194 150 NC_009009:SSA_2255|5end_Transcriptional_regulator,_XRE_family,_putative_2250144..2250374_POSITIVE 307 90 41 184 134 NC_009009:SSA_1563|5end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1567256..1567486_NEGATIVE 305 109 62 218 159 NC_009009:SSA_0808|5end_hypothetical_protein_790771..791001_POSITIVE 303 117 71 60 20 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 302 90 41 99 46 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 300 69 23 69 20 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 299 100 57 218 175 NC_009009:SSA_0357|5end_Thioredoxin,_putative_350763..350993_POSITIVE 298 47 2 66 21 NC_009009:SSA_0283|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274559..274789_POSITIVE 296 110 64 183 128 NC_009009:SSA_0533|5end_Glycerol_dehydratase_large_subunit_pduC,_putative_528970..529200_POSITIVE 295 100 52 209 138 NC_009009:SSA_0571|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_565381..565611_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 130 81 55 2 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 343 78 31 75 27 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 303 117 71 100 60 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 302 90 41 102 49 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 300 69 23 96 47 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 299 100 57 132 89 NC_009009:SSA_0356|3end_Dipeptidase,_putative_350757..350907_POSITIVE 289 105 62 100 46 NC_009009:SSA_0022|3end_Surface_protein_cell_wall_anchor,_sortase_B_family,_putative_28428..28578_POSITIVE 286 119 81 68 18 NC_009009:SSA_2245|3end_RecA_protein,_putative_2239961..2240111_NEGATIVE 286 100 53 103 58 NC_009009:SSA_0335|3end_Phosphomevalonate_kinase,_putative_329891..330041_POSITIVE 285 108 62 104 43 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 282 100 56 150 97 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 282 75 33 64 20 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 279 117 77 97 54 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 278 108 61 151 97 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 275 100 58 137 84 NC_009009:SSA_0532|3end_Propanediol_utilization_protein_PduB,_putative_529028..529178_POSITIVE 274 130 86 53 4 NC_009009:SSA_0353|3end_Conserved_uncharacterized_protein_346310..346460_POSITIVE 274 100 54 143 86 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 273 140 94 49 4 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 272 71 32 48 1 NC_009009:SSA_0225|3end_10_kDa_chaperonin_219003..219153_POSITIVE 272 83 53 69 39 NC_009009:SSA_0171|3end_Cro-like_transcriptional_repressor,_XRE_family,_putative_168765..168915_NEGATIVE