Origin IGS: agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcagattgtttttttggtgaataatattctgagatgtaattattgacattacattaggatgtgctatactaatagatgtaacaaaaacaattacaatataaaattaactatcggaggataagact Mask Tandem Repeat Region ================================================ agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc Find is-nt database================================================ Query_seq: SSA_1585:SSA_1586|SSA_1585:SSA_1586:hypothetical protein:hypothetical protein:<-<-:1587695..1587819 125 agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1585:SSA_1586|SSA_1585:SSA_1586:hypothetical protein:hypothetical protein:<-<-:1587695..1587819 125 agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1585:SSA_1586|SSA_1585:SSA_1586:hypothetical protein:hypothetical protein:<-<-:1587695..1587819 125 agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 29 End: 124 ............................ M V I V F V T S I S I A H P N V M S I I T S Q N I I H Q K N N L . agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc 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================================================ agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1585:SSA_1586|SSA_1585:SSA_1586:hypothetical protein:hypothetical protein:<-<-:1587695..1587819 125 agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcaccaaaaaaacaatctgc Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_009009_SSA_1585_SSA_1586|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1587695,1587819]|125 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcacc............... agtcttatcctccgatagttaattttatattgtaattgtttttgttacatctattagtatagcacatcctaatgtaatgtcaataattacatctcagaatattattcacc............... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUUAUCCUCCGAUAGUUAAUUUUAUAUUGUAAUUGUUUUUGUUACAUCUAUUAGUAUAGCACAUCCUAAUGUAAUGUCAAUAAUUACAUCUCAGAAUAUUAUUCACC .............((((((..(((((....((((((((((..((((((((((((....)))).........))))))))..))))))))))....))))))))))).... (-15.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGAAUAAUAUUCUGAGAUGUAAUUAUUGACAUUACAUUAGGAUGUGCUAUACUAAUAGAUGUAACAAAAACAAUUACAAUAUAAAAUUAACUAUCGGAGGAUAAGACU ((((....(((((((..((((((((.......)))))))))))))))....))))......(((((.........))))).............((((....))))..... (-13.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 771 110 61 201 152 NC_009009:SSA_1585|5end_hypothetical_protein_1587604..1587834_NEGATIVE 225 18 2 34 18 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 217 65 30 167 128 NC_009009:SSA_1809|5end_PTS_system_glucose-specific_EIIC_BA_component_(EIICBA-Glc)_(EII-_Glc/EIII-Glc),_putative_1794419..1794649_NEGATIVE 216 52 25 163 136 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 211 49 3 144 93 NC_009009:SSA_1964|5end_conserved_uncharacterized_protein_1961211..1961441_NEGATIVE 206 53 11 184 137 NC_009009:SSA_0295|5end_Transcriptional_regulator,_LysR_family,_putative_288901..289131_NEGATIVE 200 99 54 227 182 NC_009009:SSA_1774|5end_RRNA_methylase,_putative_1761043..1761273_NEGATIVE 199 50 2 142 83 NC_009009:SSA_0984|5end_SlyA-like_protein,_putative_987054..987284_POSITIVE 199 70 38 223 181 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 199 79 39 211 164 NC_009009:SSA_0264|5end_PEP_phosphonomutase-like_protein,_putative_258400..258630_POSITIVE 196 72 39 98 61 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 193 50 8 220 166 NC_009009:SSA_1751|5end_Dextran_glucosidase,_alpha_amylase_family,_putative_1739801..1740031_NEGATIVE 192 77 39 127 81 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 190 97 54 48 6 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 188 58 14 79 35 NC_009009:SSA_0262|5end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_256204..256434_NEGATIVE 187 81 47 109 75 NC_009009:SSA_1941|5end_hypothetical_protein_1927452..1927682_NEGATIVE 186 75 31 109 71 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 183 49 1 141 82 NC_009009:SSA_0696|5end_hypothetical_protein_679154..679384_POSITIVE 183 48 1 126 90 NC_009009:SSA_0455|5end_Sucrose-6-phosphate_hydrolase,_putative_458450..458680_NEGATIVE 182 46 6 136 97 NC_009009:SSA_0524|5end_Microcompartment_protein,_putative_523150..523380_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 216 52 25 118 91 NC_009009:SSA_2054|3end_hypothetical_protein_2057792..2057942_NEGATIVE 206 53 11 72 25 NC_009009:SSA_0296|3end_Transcriptional_regulator,_XRE_family,_putative_289013..289163_NEGATIVE 201 38 1 70 22 NC_009009:SSA_1224|3end_hypothetical_protein_1247251..1247401_NEGATIVE 196 72 39 94 57 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 191 66 34 69 40 NC_009009:SSA_2184|3end_hypothetical_protein_2183284..2183434_NEGATIVE 188 53 13 113 71 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 186 75 31 109 71 NC_009009:SSA_0784|3end_Proton-translocating_ATPase,_F0_sector,_subunit_b,_putative_768124..768274_POSITIVE 183 49 1 122 63 NC_009009:SSA_0695|3end_hypothetical_protein_679215..679365_POSITIVE 182 46 6 101 62 NC_009009:SSA_0523|3end_Aldehyde_dehydrogenase,_putative_523195..523345_POSITIVE 181 39 8 114 83 NC_009009:SSA_1492|3end_hypothetical_protein_1497659..1497809_NEGATIVE 180 94 61 74 41 NC_009009:SSA_0758|3end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_741909..742059_POSITIVE 178 47 4 136 103 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 177 104 61 118 76 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 175 99 54 58 15 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 174 70 39 56 26 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 170 70 32 83 49 NC_009009:SSA_2019|3end_hypothetical_protein_2018812..2018962_NEGATIVE 167 20 2 147 128 NC_009009:SSA_1260|3end_Phosphopentomutase,_putative_1285752..1285902_NEGATIVE 167 97 55 105 68 NC_009009:SSA_0940|3end_NOL1/NOP2/sun_family_protein,_putative_949010..949160_POSITIVE 166 45 9 113 79 NC_009009:SSA_2079|3end_Acetyltransferase,_putative_2084599..2084749_POSITIVE 166 88 41 71 31 NC_009009:SSA_1266|3end_crcB-like_protein_1,_putative_1290650..1290800_NEGATIVE