Origin IGS: tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcaataacgttcatcccatttgcccgcactacacttgatcagattgacgagtgacgtgggagatgaaaatcgattgaaccacttacaaggagaaagataaa Mask Tandem Repeat Region ================================================ tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga Find is-nt database================================================ Query_seq: SSA_1622:SSA_1623|SSA_1622:SSA_1623:50S ribosomal protein L1, putative:50S ribosomal protein L11, putative:<-<-:1625532..1625632 101 tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1622:SSA_1623|SSA_1622:SSA_1623:50S ribosomal protein L1, putative:50S ribosomal protein L11, putative:<-<-:1625532..1625632 101 tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1622:SSA_1623|SSA_1622:SSA_1623:50S ribosomal protein L1, putative:50S ribosomal protein L11, putative:<-<-:1625532..1625632 101 tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga Predict ORF larger than 30AA ================================================ tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga 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================================================ tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1622:SSA_1623|SSA_1622:SSA_1623:50S ribosomal protein L1, putative:50S ribosomal protein L11, putative:<-<-:1625532..1625632 101 tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_009009_SSA_1622_SSA_1623|50S ribosomal protein L1, putative:50S ribosomal protein L11, putative|NEGATIVE:NEGATIVE|[1625532,1625632]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga tttatctttctccttgtaagtggttcaatcgattttcatctcccacgtcactcgtcaatctgatcaagtgtagtgcgggcaaatgggatgaacgttattga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUCUUUCUCCUUGUAAGUGGUUCAAUCGAUUUUCAUCUCCCACGUCACUCGUCAAUCUGAUCAAGUGUAGUGCGGGCAAAUGGGAUGAACGUUAUUGA ...........((........)).(((((.(((.((((((((((((..((((.(((.....)))..))))..))).)).......))))))).)))))))) (-19.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAUAACGUUCAUCCCAUUUGCCCGCACUACACUUGAUCAGAUUGACGAGUGACGUGGGAGAUGAAAAUCGAUUGAACCACUUACAAGGAGAAAGAUAAA (((((....((((((.......(((((....((((((.((.....))))))))..))))).)))))).....))))).((........))........... (-23.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1011 90 41 181 132 NC_009009:SSA_1622|5end_50S_ribosomal_protein_L1,_putative_1625441..1625671_NEGATIVE 335 79 33 85 18 NC_009009:SSA_1165|5end_Transcriptional_regulator,_GntR_family,_putative_1191087..1191317_POSITIVE 324 88 43 56 6 NC_009009:SSA_1304|5end_hypothetical_protein_1323449..1323679_NEGATIVE 320 80 31 210 144 NC_009009:SSA_0808|5end_hypothetical_protein_790771..791001_POSITIVE 318 80 35 173 133 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 315 90 46 61 12 NC_009009:SSA_1803|5end_GTP-binding_protein,_putative_1787909..1788139_NEGATIVE 307 79 31 213 162 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 307 90 48 151 95 NC_009009:SSA_1197|5end_DNA_alkylation_repair_enzyme,_putative_1222699..1222929_NEGATIVE 304 80 33 159 103 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 299 65 28 128 80 NC_009009:SSA_1302|5end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1322484..1322714_NEGATIVE 297 95 53 207 157 NC_009009:SSA_2110|5end_30S_ribosomal_protein_S7,_putative_2115579..2115809_NEGATIVE 297 92 54 225 179 NC_009009:SSA_1907|5end_hypothetical_protein_1900446..1900676_POSITIVE 287 70 21 231 181 NC_009009:SSA_0738|5end_Ornithine_carbamoyltransferase,_catabolic,_putative_719904..720134_POSITIVE 285 87 41 66 9 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 284 80 31 136 81 NC_009009:SSA_1323|5end_hypothetical_protein_1340450..1340680_NEGATIVE 284 80 32 189 142 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 283 78 33 221 185 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 282 58 11 218 163 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 279 78 31 204 147 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 278 82 44 184 135 NC_009009:SSA_1794|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1777049..1777279_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 90 48 147 91 NC_009009:SSA_1198|3end_ATPase_(PilT_family),_putative_1222703..1222853_NEGATIVE 299 65 28 138 90 NC_009009:SSA_1303|3end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322474..1322624_NEGATIVE 287 90 50 42 1 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 285 87 41 145 88 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 280 90 41 145 85 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 275 78 37 138 100 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 274 80 31 143 86 NC_009009:SSA_1863|3end_NH(3)-dependent_NAD(+)_synthetase,_putative_1858589..1858739_NEGATIVE 267 40 7 129 97 NC_009009:SSA_1559|3end_Conserved_uncharacterized_protein_1560862..1561012_NEGATIVE 264 87 43 45 1 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 260 66 28 136 97 NC_009009:SSA_1564|3end_Histidine_kinase,_putative_1567266..1567416_NEGATIVE 260 81 47 42 15 NC_009009:SSA_0472|3end_Precorrin-3B_C17-methyltransferase,_putative_475585..475735_POSITIVE 259 66 21 148 96 NC_009009:SSA_1732|3end_Uracil_phosphoribosyltransferase,_putative_1716916..1717066_NEGATIVE 259 80 43 76 43 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 258 45 5 132 95 NC_009009:SSA_1020|3end_hypothetical_protein_1036104..1036254_POSITIVE 256 79 39 148 110 NC_009009:SSA_0563|3end_Universal_stress_protein_family,_putative_554947..555097_NEGATIVE 256 55 12 68 21 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 251 67 28 137 90 NC_009009:SSA_0776|3end_Glucose-1-phosphate_adenylyltransferase,_putative_759520..759670_POSITIVE 251 89 41 87 19 NC_009009:SSA_0588|3end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_580707..580857_POSITIVE 251 88 42 89 53 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 250 76 41 150 106 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE