Origin IGS: cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggattctcctttatttatttttagtattagaaggataatagtaataatagagtctgtgaaatctgtggaaaacagactttaaacaagtcatatcaagtttttgggcttgtttaaaaaatgtggataaaaaagataataaagtaaaagttatccacaag Mask Tandem Repeat Region ================================================ cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc Find is-nt database================================================ Query_seq: SMT_89:SMT_90|SMT_89:SMT_90:chromosomal replication initiator protein:DNA polymerase III beta subunit:->->:21359..21516 158 cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_89:SMT_90|SMT_89:SMT_90:chromosomal replication initiator protein:DNA polymerase III beta subunit:->->:21359..21516 158 cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_89:SMT_90|SMT_89:SMT_90:chromosomal replication initiator protein:DNA polymerase III beta subunit:->->:21359..21516 158 cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 2 End: 145 . M W I T F T L L S F L S T F F K Q A Q K L D M T C L K S V F H R F H R L Y Y Y Y Y P S N T K N K ............. Protein_Len: 32 Strand: - Start: 1 End: 96 K H I V K V K N D K K D V N K L C A W F S S I V Q K F D T K W M .............................................................. cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc 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: 98 End: 127 .................................................................................................TTTCACAGACTCTATTATTACTATTATCCT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_89:SMT_90|SMT_89:SMT_90:chromosomal replication initiator protein:DNA polymerase III beta subunit:->->:21359..21516 158 cttgtggataacttttactttattatcttttttatccacattttttaaacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc Intra-Species Hit: Count: 1 Min: 48 Max: 158 Len: 111 Subject: smit_SMT_89_SMT_90|chromosomal replication initiator protein:DNA polymerase III beta subunit|POSITIVE:POSITIVE|[21359,21516]|158 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 111 Query Start:48 Query End:158 Subject Strand: POSITIVE Subject Start: 48 Subject End: 158 ...............................................aacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc ...............................................aacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc Inter-species Hit: Count: 3 Min: 48 Max: 158 Len: 111 Subject: NC_003028_SP_0001_SP_0002|chromosomal replication initiation protein:DNA polymerase III subunit beta|POSITIVE:POSITIVE|[1559,1716]|158 HSP 1 e-value: 4.0E-47 bit: 188.0 Len: 111 Query Start:48 Query End:158 Subject Strand: POSITIVE Subject Start: 48 Subject End: 158 ...............................................aacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc ...............................................aacaagctaaaaaacttgatatgacttgtttaaaggctgttttccacagatttcacagactctattattactattatctttctaatactaaaaataaataaaggagaatcc Subject: NC_008533_SPD_0001_SPD_0002|chromosomal replication initiator protein DnaA:DNA polymerase III, beta subunit|POSITIVE:POSITIVE|[1363,1520]|158 HSP 1 e-value: 9.0E-45 bit: 180.0 Len: 111 Query Start:48 Query End:158 Subject Strand: POSITIVE Subject Start: 48 Subject End: 158 ...............................................aacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc ...............................................aacaagctaaaaaacttgataggacttgtttaaaggctgttttccacagatttcacagactctattattactattatctttctaatactaaaaataaataaaggagaatcc Subject: NC_003098_spr0001_spr0002|chromosomal replication initiation protein:DNA polymerase III subunit beta|POSITIVE:POSITIVE|[1363,1520]|158 HSP 1 e-value: 9.0E-45 bit: 180.0 Len: 111 Query Start:48 Query End:158 Subject Strand: POSITIVE Subject Start: 48 Subject End: 158 ...............................................aacaagcccaaaaacttgatatgacttgtttaaagtctgttttccacagatttcacagactctattattactattatccttctaatactaaaaataaataaaggagaatcc ...............................................aacaagctaaaaaacttgataggacttgtttaaaggctgttttccacagatttcacagactctattattactattatctttctaatactaaaaataaataaaggagaatcc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAGCCCAAAAACUUGAUAUGACUUGUUUAAAGUCUGUUUUCCACAGAUUUCACAGACUCUAUUAUUACUAUUAUCCUUCUAAUACUAAAAAUAAAUAAAGGAGAAUCC ..((((........))))......(((.((((.(((((((..((....))....))))))).((((.(((.(((((......))))).))).))))..)))).)))..... (-15.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUUCUCCUUUAUUUAUUUUUAGUAUUAGAAGGAUAAUAGUAAUAAUAGAGUCUGUGAAAUCUGUGGAAAACAGACUUUAAACAAGUCAUAUCAAGUUUUUGGGCUUGUU ..(((.((((((...(((.....)))...)))))).)))........((((((((((....((....))..)))))))))).(((((((..............))))))). (-23.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 65 21 221 182 smit:SMT_630|5end_phosphoserine_phosphatase_535459..535689_POSITIVE 239 66 23 107 65 smit:SMT_1636|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1622568..1622798_POSITIVE 237 62 21 109 61 smit:SMT_777|5end_hypothetical_protein_686770..687000_NEGATIVE 235 65 21 170 131 smit:SMT_629|5end_glycogen_synthase_533967..534197_POSITIVE 232 46 7 140 99 smit:SMT_83|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_15295..15525_NEGATIVE 228 79 31 74 32 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 228 79 31 74 32 smit:SMT_1205|5end_response_regulator_1165700..1165930_NEGATIVE 227 63 22 138 100 smit:SMT_438|5end_hypothetical_protein_predicted_by_Glimmer/Critica_379136..379366_POSITIVE 226 72 37 225 185 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 226 78 32 176 128 smit:SMT_149|5end_hypothetical_protein_predicted_by_Glimmer/Critica_98592..98822_POSITIVE 221 50 3 129 83 smit:SMT_282|5end_hypothetical_protein_224866..225096_POSITIVE 220 54 14 200 151 smit:SMT_1112|5end_K02248_competence_protein_ComGF_1051848..1052078_NEGATIVE 215 70 32 42 1 smit:SMT_1849|5end_hypothetical_protein_1813074..1813304_POSITIVE 214 50 4 71 21 smit:SMT_1158|5end_DNA_gyrase_subunit_B_1103957..1104187_NEGATIVE 213 45 2 61 12 smit:SMT_1525|5end_pneumococcal_histidine_triad_protein_A_precursor_1509259..1509489_NEGATIVE 209 70 21 109 65 smit:SMT_275|5end_transcriptional_activator-exopolysaccharide_biosynthesis_217369..217599_POSITIVE 206 50 5 134 61 smit:SMT_2053|5end_hypothetical_membrane_associated_protein_1964422..1964652_NEGATIVE 205 79 31 119 74 smit:SMT_1838|5end_response_regulator_1805400..1805630_NEGATIVE 205 45 3 49 8 smit:SMT_122|5end_hypothetical_protein_74456..74686_POSITIVE 203 90 49 57 19 smit:SMT_976|5end_hypothetical_protein_925183..925413_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 66 23 95 53 smit:SMT_1635|3end_putative_N-acetyldiaminopimelate_deacetylase_1622636..1622786_POSITIVE 232 45 5 151 108 smit:SMT_424|3end_transcriptional_regulatory_protein_368108..368258_POSITIVE 232 46 7 143 102 smit:SMT_84|3end_predicted_signal_transduction_protein_with_a_C-terminal_ATPase_domain_15292..15442_NEGATIVE 228 79 31 77 35 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 227 110 68 60 21 smit:SMT_981|3end_hypothetical_protein_929202..929352_POSITIVE 226 72 37 139 99 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 226 78 32 105 57 smit:SMT_148|3end_glycoprotein_endopeptidase_98601..98751_POSITIVE 214 50 4 56 6 smit:SMT_1159|3end_hypothetical_protein_1103972..1104122_NEGATIVE 205 79 31 107 62 smit:SMT_1839|3end_6-phosphogluconate_dehydrogenase,_decarboxylating_1805412..1805562_NEGATIVE 205 83 50 110 80 smit:SMT_1777|3end_hypothetical_protein_1753378..1753528_POSITIVE 202 62 33 125 88 smit:SMT_1061|3end_hypothetical_protein_999915..1000065_POSITIVE 200 48 3 72 27 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 200 76 36 86 37 smit:SMT_1500|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1484426..1484576_POSITIVE 200 59 22 102 64 smit:SMT_1293|3end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1256063..1256213_POSITIVE 191 110 71 65 16 smit:SMT_1268|3end_acetoin_reductase_1232655..1232805_NEGATIVE 189 80 34 76 16 smit:SMT_967|3end_K01992_ABC-2_type_transport_system_permease_protein_912215..912365_NEGATIVE 185 54 15 55 11 smit:SMT_1287|3end_50S_ribosomal_protein_L9_1250890..1251040_POSITIVE 185 48 6 82 41 smit:SMT_818|3end_cystathionine_gamma-synthase_728707..728857_NEGATIVE 184 79 40 64 28 smit:SMT_845|3end_hypothetical_protein_791089..791239_NEGATIVE 184 58 18 56 1 smit:SMT_617|3end_hypothetical_protein_526761..526911_POSITIVE