Origin IGS: agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatttactcctatgaaattgctgtaattcttgtaaaaccaacagctagtttaatgaatgttgcttgtttttgatgttttagaaagtgtttttctaaagatgagcttctcatctcttaccatagttcctaatct Mask Tandem Repeat Region ================================================ agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc Find is-nt database================================================ Query_seq: SSA_0085:SSA_0086|SSA_0085:SSA_0086:V-type sodium ATPase, subunit I, putative:V-type sodium ATPase, subunit K, putative:->->:87846..87978 133 agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0085:SSA_0086|SSA_0085:SSA_0086:V-type sodium ATPase, subunit I, putative:V-type sodium ATPase, subunit K, putative:->->:87846..87978 133 agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0085:SSA_0086|SSA_0085:SSA_0086:V-type sodium ATPase, subunit I, putative:V-type sodium ATPase, subunit K, putative:->->:87846..87978 133 agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 23 End: 121 ...................... M R S S S L E K H F L K H Q K Q A T F I K L A V G F T R I T A I S ............ agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc 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================================================ agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -8.6 Tail_Score: -3.08015 Start: 22 End: 36 Full_Region: aagtgtttttctaaa gatgag ctt ctcatc tcttaccatagttcc .....................gatgagcttctcatc................................................................................................. Find igs database================================================ Query_seq: SSA_0085:SSA_0086|SSA_0085:SSA_0086:V-type sodium ATPase, subunit I, putative:V-type sodium ATPase, subunit K, putative:->->:87846..87978 133 agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: NC_009009_SSA_0085_SSA_0086|V-type sodium ATPase, subunit I, putative:V-type sodium ATPase, subunit K, putative|POSITIVE:POSITIVE|[87846,87978]|133 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc agattaggaactatggtaagagatgagaagctcatctttagaaaaacactttctaaaacatcaaaaacaagcaacattcattaaactagctgttggttttacaagaattacagcaatttcataggagtaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUAGGAACUAUGGUAAGAGAUGAGAAGCUCAUCUUUAGAAAAACACUUUCUAAAACAUCAAAAACAAGCAACAUUCAUUAAACUAGCUGUUGGUUUUACAAGAAUUACAGCAAUUUCAUAGGAGUAAAUC .((((.....((((((...((((((((...))))))))((((((.....)))))).................................(((((.(((((.....))))))))))....)))))).....)))) (-24.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUACUCCUAUGAAAUUGCUGUAAUUCUUGUAAAACCAACAGCUAGUUUAAUGAAUGUUGCUUGUUUUUGAUGUUUUAGAAAGUGUUUUUCUAAAGAUGAGCUUCUCAUCUCUUACCAUAGUUCCUAAUCU ((((.....(((((.....(((((................))))).........(((((..(((..((........(((((((((...)))))))))))..)))....))).))....))))).....)))). (-20.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 125 83 223 178 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 244 44 1 231 183 NC_009009:SSA_1960|5end_hypothetical_protein_1958466..1958696_NEGATIVE 234 55 14 65 16 NC_009009:SSA_0774|5end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_754571..754801_POSITIVE 229 41 2 170 131 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 220 105 68 55 18 NC_009009:SSA_1909|5end_Transcriptional_attenuator_LytR,_putative_1902142..1902372_NEGATIVE 213 128 89 71 41 NC_009009:SSA_1622|5end_50S_ribosomal_protein_L1,_putative_1625441..1625671_NEGATIVE 213 54 13 67 30 NC_009009:SSA_1597|5end_hypothetical_protein_1604235..1604465_NEGATIVE 212 129 82 161 112 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 212 115 71 90 49 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 208 130 87 57 16 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 206 128 84 224 183 NC_009009:SSA_0944|5end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_951741..951971_POSITIVE 205 34 6 62 39 NC_009009:SSA_2336|5end_Transcriptional_regulator,_PadR_family,_putative_2338367..2338597_POSITIVE 205 107 71 219 179 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 203 115 86 222 193 NC_009009:SSA_2127|5end_hypothetical_protein_2130850..2131080_NEGATIVE 203 47 1 227 185 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 202 54 12 204 163 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 202 33 4 144 120 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 200 98 58 176 129 NC_009009:SSA_2143|5end_Conserved_uncharacterized_protein_2144225..2144455_NEGATIVE 200 37 3 140 110 NC_009009:SSA_1616|5end_PhoH-like_protein,_putative_1620258..1620488_NEGATIVE 200 130 86 187 144 NC_009009:SSA_1061|5end_50S_ribosomal_protein_L21,_putative_1077592..1077822_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 100 60 58 19 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 229 41 2 128 89 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 220 105 68 46 9 NC_009009:SSA_1910|3end_hypothetical_protein_1902151..1902301_NEGATIVE 219 126 86 88 40 NC_009009:SSA_0626|3end_hypothetical_protein_617212..617362_POSITIVE 202 118 80 146 103 NC_009009:SSA_1091|3end_Thymidylate_synthase,_putative_1109554..1109704_POSITIVE 200 98 58 86 39 NC_009009:SSA_2144|3end_Glutamyl-tRNA_synthetase,_putative_2144315..2144465_NEGATIVE 199 33 1 68 41 NC_009009:SSA_2235|3end_Conserved_uncharacterized_protein_2234971..2235121_NEGATIVE 199 119 73 147 97 NC_009009:SSA_0857|3end_hypothetical_protein_845482..845632_POSITIVE 196 103 64 151 115 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE 196 39 1 75 28 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 195 35 1 72 25 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 193 103 67 50 13 NC_009009:SSA_1648|3end_hypothetical_protein_1647166..1647316_NEGATIVE 192 35 1 41 2 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 190 129 86 59 21 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 190 45 2 86 31 NC_009009:SSA_0887|3end_hypothetical_protein_881165..881315_NEGATIVE 190 38 6 131 100 NC_009009:SSA_0321|3end_Methylase,_putative_314693..314843_POSITIVE 188 39 15 52 26 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 188 122 90 77 47 NC_009009:SSA_0775|3end_1,4-alpha-glucan_branching_enzyme,_putative_758371..758521_POSITIVE 188 127 88 86 42 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 187 130 84 71 25 NC_009009:SSA_1068|3end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1088367..1088517_POSITIVE