Origin IGS: cggatgctcccccattttctgaagaatacttttcatgtctcctgtgaaaattwaactgataatatataaacagaatacaactacaaaaagataaaagggtaaaaagatactcaggataattcccaataaaatcagctctttactagacaaccctttcagcttttcaataaagcctattgatttcaaaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatggttgataaaatagggtttttattttagaaaacgtttcctttgttttcaaattgctaaaaaagtggtacaataaagggtagcttactattatctgaatcaactgatttggagagaaaggattcattttgaaatcaataggctttattgaaaagctgaaagggttgtctagtaaagagctgattttattgggaattatcctgagtatctttttacccttttatctttttgtagttgtattctgtttatatattatcagttwaattttcacaggagacatgaaaagtattcttcagaaaatgggggagcatccg Mask Tandem Repeat Region ================================================ cggatgctcccccattttctgaagaatacttttcatgtctcctgtgaaaattwaactgataatatataaacagaatacaactacaaaaagataaaagggtaaaaagatactcaggataattcccaataaaatcagctctttactagacaaccctttcagcttttcaataaagcctattgatttcaaaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata Find is-nt database================================================ Query_seq: SMT_1025:SMT_1026|SMT_1025:SMT_1026:hypothetical protein:sucrose phosphorylase:<-<-:960648..960962 315 cggatgctcccccattttctgaagaatacttttcatgtctcctgtgaaaattwaactgataatatataaacagaatacaactacaaaaagataaaagggtaaaaagatactcaggataattcccaataaaatcagctctttactagacaaccctttcagcttttcaataaagcctattgatttcaaaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1025:SMT_1026|SMT_1025:SMT_1026:hypothetical protein:sucrose phosphorylase:<-<-:960648..960962 315 cggatgctcccccattttctgaagaatacttttcatgtctcctgtgaaaattwaactgataatatataaacagaatacaactacaaaaagataaaagggtaaaaagatactcaggataattcccaataaaatcagctctttactagacaaccctttcagcttttcaataaagcctattgatttcaaaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1025:SMT_1026|SMT_1025:SMT_1026:hypothetical protein:sucrose phosphorylase:<-<-:960648..960962 315 cggatgctcccccattttctgaagaatacttttcatgtctcctgtgaaaattwaactgataatatataaacagaatacaactacaaaaagataaaagggtaaaaagatactcaggataattcccaataaaatcagctctttactagacaaccctttcagcttttcaataaagcctattgatttcaaaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 1 Max: 186 Len: 186 Subject: UniRef90_Q04IR7 Cluster: Membrane protein, putative; n=4; Streptococcus pneumoniae|Rep: Membrane protein, putative - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 2.0E-12 bit: 73.6 Len: 186 Query Start:1 Query End:186 Subject Strand: null Subject Start: 1 Subject End: 62 L K S I G F X X X X X X X X X X X X X X X X X X X X I F L P F Y L F V V V F C L Y I I S X I F T G D M K S I L Q K M G E H P ................................................................................................................................. M K S I G F I E K L K G L S S K E L I L L G I I L S I F L P F Y L F V V V L C L Y I I S L I F T G D M K S I L Q K M G E H P ................................................................................................................................. nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 107 End: 313 .......................................................................................................... M L R I I P N K I S S L L D N P F S F S I K P I D F K M N P F S P N Q L I Q I I V S Y P L L Y H F F S N L K T K E T F S .. Protein_Len: 42 Strand: - Start: 2 End: 127 . S A G G N E S S Y K E H R R H F N X Q Y Y I F L I C S C F S L L T F L Y E P Y N G M ............................................................................................................................................................................................ Protein_Len: 60 Strand: - Start: 1 End: 189 G M K Q L I S K M D G T F I X S I I Y L C F V V V F L Y F P L F I S L I I G L L I L E K S S L G K L K E I F G I S K L M .............................................................................................................................. nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata 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: 87 Start: 261 End: 290 ....................................................................................................................................................................................................................................................................TTTGAAAACAAAGGAAACGTTTTCTAAAAT......................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 240 End: 269 ...............................................................................................................................................................................................................................................GTTTTCAAATTGCTAAAAAAGTGGTACAAT.............................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 281 End: 310 ........................................................................................................................................................................................................................................................................................GTTGATAAAATAGGGTTTTTATTTTAGAAA..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -3.8 Tail_Score: -3.57792 Start: 164 End: 180 Full_Region: AACCCTTTCAGCTTT TCAATA AAGCC TATTGA TTTCAAAATGAATCC ...................................................................................................................................................................TCAATAAAGCCTATTGA....................................................................................................................................... Find igs database================================================ Query_seq: SMT_1025:SMT_1026|SMT_1025:SMT_1026:hypothetical protein:sucrose phosphorylase:<-<-:960648..960962 315 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata Intra-Species Hit: Count: 1 Min: 187 Max: 315 Len: 129 Subject: smit_SMT_1025_SMT_1026|hypothetical protein:sucrose phosphorylase|NEGATIVE:NEGATIVE|[960648,960962]|315 HSP 1 e-value: 4.0E-67 bit: 256.0 Len: 129 Query Start:187 Query End:315 Subject Strand: POSITIVE Subject Start: 187 Subject End: 315 ..........................................................................................................................................................................................aatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata ..........................................................................................................................................................................................aatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata Inter-species Hit: Count: 3 Min: 187 Max: 315 Len: 129 Subject: NC_003028_SP_1893_SP_1894|hypothetical protein:sucrose phosphorylase|NEGATIVE:NEGATIVE|[1799460,1799596]|137 HSP 1 e-value: 3.0E-55 bit: 216.0 Len: 129 Query Start:187 Query End:315 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ..........................................................................................................................................................................................aatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata ..........................................................................................................................................................................................aatgaatcctttctctccaaatcagctgattcagataatagtaagctatcctatattgtaccacttttttagcaatttgaaaacaaaggaaacgttttccaaaataaaaaccctattttatccaccata Subject: NC_008533_SPD_1672_SPD_1673|hypothetical protein:sucrose phosphorylase|NEGATIVE:NEGATIVE|[1688385,1688521]|137 HSP 1 e-value: 8.0E-53 bit: 208.0 Len: 129 Query Start:187 Query End:315 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ..........................................................................................................................................................................................aatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata ..........................................................................................................................................................................................aatgaatcctttctctccaaatctgctgattcagataatagtaagctatcctatattgtaccacttttttagcaatttgaaaacaaaggaaacgttttccaaaataaaaaccctattttatccaccata Subject: NC_003098_spr1708_spr1709|hypothetical protein:Dextransucrase (sucrose 6-glucosyltransferase)|NEGATIVE:NEGATIVE|[1680854, 1680990]|137 HSP 1 e-value: 8.0E-53 bit: 208.0 Len: 129 Query Start:187 Query End:315 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ..........................................................................................................................................................................................aatgaatcctttctctccaaatcagttgattcagataatagtaagctaccctttattgtaccacttttttagcaatttgaaaacaaaggaaacgttttctaaaataaaaaccctattttatcaaccata ..........................................................................................................................................................................................aatgaatcctttctctccaaatctgctgattcagataatagtaagctatcctatattgtaccacttttttagcaatttgaaaacaaaggaaacgttttccaaaataaaaaccctattttatccaccata Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAAUCCUUUCUCUCCAAAUCAGUUGAUUCAGAUAAUAGUAAGCUACCCUUUAUUGUACCACUUUUUUAGCAAUUUGAAAACAAAGGAAACGUUUUCUAAAAUAAAAACCCUAUUUUAUCAACCAUA ........................((((((..(((((((((((((......))))))))......((((((.......((((((...(....))))))).....))))))...))))).)))))).... (-14.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGGUUGAUAAAAUAGGGUUUUUAUUUUAGAAAACGUUUCCUUUGUUUUCAAAUUGCUAAAAAAGUGGUACAAUAAAGGGUAGCUUACUAUUAUCUGAAUCAACUGAUUUGGAGAGAAAGGAUUCAUU ....(((..((((((((.....))))))))...)))...((((((.((((((((((........((((((.((((((.((........)).)))).)).))).))))))))))))).))))))...... (-24.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 65 21 140 98 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 253 98 57 165 125 smit:SMT_180|5end_50S_ribosomal_protein_L14_119678..119908_POSITIVE 237 100 56 207 166 smit:SMT_1105|5end_K03217_preprotein_translocase_YidC_subunit_1047632..1047862_NEGATIVE 233 90 41 153 93 smit:SMT_1069|5end_acetyl_xylan_esterase,_putative_1009330..1009560_POSITIVE 230 92 51 148 111 smit:SMT_1702|5end_penicillin-binding_protein_2B_1684592..1684822_POSITIVE 229 67 28 170 132 smit:SMT_1309|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1274082..1274312_POSITIVE 229 50 4 218 183 smit:SMT_895|5end_cysteinyl-tRNA_synthetase_843037..843267_NEGATIVE 217 50 4 219 172 smit:SMT_1953|5end_hypothetical_protein_1886897..1887127_POSITIVE 217 51 11 94 52 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 214 52 11 138 91 smit:SMT_1199|5end_lactococcin_A_ABC_transporter_permease_protein_1161063..1161293_NEGATIVE 213 47 1 81 29 smit:SMT_421|5end_K02003_363031..363261_POSITIVE 211 63 21 225 177 smit:SMT_1637|5end_hypothetical_protein_1623091..1623321_POSITIVE 211 35 6 120 90 smit:SMT_395|5end_hypothetical_protein_324459..324689_POSITIVE 209 63 21 52 8 smit:SMT_246|5end_alcohol_dehydrogenase_183004..183234_NEGATIVE 204 50 4 153 101 smit:SMT_876|5end_hypothetical_protein_predicted_by_Glimmer/Critica_823502..823732_NEGATIVE 204 48 2 123 90 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 203 73 33 152 107 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 203 65 24 170 130 smit:SMT_437|5end_transcriptional_regulator,_TetR_family_378402..378632_POSITIVE 202 48 1 56 5 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 201 32 1 113 85 smit:SMT_1056|5end_K07738_ATP-cone_domain_protein_994842..995072_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 98 57 139 99 smit:SMT_179|3end_ribosomal_protein_S17_119732..119882_POSITIVE 229 50 4 136 101 smit:SMT_896|3end_hypothetical_protein_843119..843269_NEGATIVE 214 52 11 125 78 smit:SMT_1200|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1161076..1161226_NEGATIVE 211 35 6 130 100 smit:SMT_394|3end_K07729_putative_transcriptional_regulator_324549..324699_POSITIVE 210 59 24 138 110 smit:SMT_110|3end_alpha-L-fucosidase_59207..59357_POSITIVE 204 50 4 97 45 smit:SMT_877|3end_hypothetical_protein_823558..823708_NEGATIVE 204 48 2 130 97 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 203 58 12 151 106 smit:SMT_544|3end_aminoglycoside_6-adenylyltransferase_461190..461340_POSITIVE 202 43 7 151 107 smit:SMT_1773|3end_hypothetical_protein_1749905..1750055_POSITIVE 201 50 2 67 17 smit:SMT_1741|3end_surface_protein_PspA_precursor_1722303..1722453_NEGATIVE 199 90 47 63 15 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 198 59 17 57 2 smit:SMT_2067|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974216..1974366_POSITIVE 196 48 5 133 93 smit:SMT_2047|3end_choline_binding_protein_F_1957597..1957747_NEGATIVE 196 59 15 110 63 smit:SMT_828|3end_surface_protein_Rib_751186..751336_NEGATIVE 195 45 12 43 1 smit:SMT_1951|3end_ABC_transporter,_ATP-binding_protein_1885141..1885291_NEGATIVE 194 50 17 111 75 smit:SMT_1754|3end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1732363..1732513_NEGATIVE 194 50 9 147 110 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 189 51 13 139 102 smit:SMT_1617|3end_K02015_iron_complex_transport_system_permease_protein_1603544..1603694_NEGATIVE 188 90 45 74 38 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 187 58 11 89 56 smit:SMT_1936|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1874189..1874339_POSITIVE