Origin IGS: tatatccccgccaccctttttcattttatactcttcgaaaacctcttcaaaccacgtcagcttccatctgcaacctcaaaacactgttttgagcaacctgcggctagcttcctagtttgctctttgattttcattgagtattagcgattgttactgtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa .........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 ttgtatctttctaaaaggtgttttctatatgagtattattatatagagaaatgtgctttatttcaagtctaggagaaaaattgcttgttgtaaggatattacttacagtaacaatcgctaatactcaatgaaaatcaaagagcaaactaggaagctagccgcaggttgctcaaaacagtgttttgaggttgcagatggaagctgacgtggtttgaagaggttttcgaagagtataaaatgaaaaagggtggcggggatata Mask Tandem Repeat Region ================================================ tatatccccgccaccctttttcattttatactcttcgaaaacctcttcaaaccacgtcagcttccatctgcaacctcaaaacactgttttgagcaacctgcggctagcttcctagtttgctctttgattttcattgagtattagcgattgttactgtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa Find is-nt database================================================ Query_seq: SMT_1144:SMT_1145|SMT_1144:SMT_1145:K02026 multiple sugar transport system permease protein:maltodextrose utilization protein MalA:->->:1089205..1089465 261 tatatccccgccaccctttttcattttatactcttcgaaaacctcttcaaaccacgtcagcttccatctgcaacctcaaaacactgttttgagcaacctgcggctagcttcctagtttgctctttgattttcattgagtattagcgattgttactgtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1144:SMT_1145|SMT_1144:SMT_1145:K02026 multiple sugar transport system permease protein:maltodextrose utilization protein MalA:->->:1089205..1089465 261 tatatccccgccaccctttttcattttatactcttcgaaaacctcttcaaaccacgtcagcttccatctgcaacctcaaaacactgttttgagcaacctgcggctagcttcctagtttgctctttgattttcattgagtattagcgattgttactgtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1144:SMT_1145|SMT_1144:SMT_1145:K02026 multiple sugar transport system permease protein:maltodextrose utilization protein MalA:->->:1089205..1089465 261 tatatccccgccaccctttttcattttatactcttcgaaaacctcttcaaaccacgtcagcttccatctgcaacctcaaaacactgttttgagcaacctgcggctagcttcctagtttgctctttgattttcattgagtattagcgattgttactgtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 6 Min: 1 Max: 141 Len: 141 Subject: UniRef90_O05164 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 5.0E-14 bit: 79.0 Len: 126 Query Start:16 Query End:141 Subject Strand: null Subject Start: 3 Subject End: 44 ............... L F H F I L F E N L F K P R Q L P S A T S K H C F E Q P A A S F L V C S L I F I E Y ........................................................................................................................ ............... L Y D L I L F E N L F K P R Q L P S T T S K Q C F E Q P A A S F L V C S L I F I E Y ........................................................................................................................ Subject: UniRef90_Q04M07 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 6.0E-9 bit: 48.9 Len: 69 Query Start:66 Query End:134 Subject Strand: null Subject Start: 1 Subject End: 23 ................................................................. M K I K E Q T R K L A A G C S K Q C F E V A D ............................................................................................................................... ................................................................. M K I K E Q T R K L A A G C S K Q C F E V V D ............................................................................................................................... HSP 2 e-value: 6.0E-9 bit: 33.1 Len: 63 Query Start:1 Query End:63 Subject Strand: null Subject Start: 37 Subject End: 57 K L T W F E E V F E E Y K M K K G G G D I ...................................................................................................................................................................................................... K L M W F E E I F E E Y K M M G K A G Q L ...................................................................................................................................................................................................... Subject: UniRef90_Q04IR5 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 4.0E-8 bit: 47.0 Len: 69 Query Start:66 Query End:134 Subject Strand: null Subject Start: 1 Subject End: 23 ................................................................. M K I K E Q T R K L A A G C S K Q C F E V A D ............................................................................................................................... ................................................................. M K I K E Q T R K L A A G C S K H C F E V V D ............................................................................................................................... HSP 2 e-value: 4.0E-8 bit: 32.3 Len: 39 Query Start:25 Query End:63 Subject Strand: null Subject Start: 37 Subject End: 49 ........................ K L T W F E E V F E E Y K ...................................................................................................................................................................................................... ........................ K L T W F E E I F E E Y K ...................................................................................................................................................................................................... Subject: UniRef90_Q04I61 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 5.0E-7 bit: 48.5 Len: 75 Query Start:66 Query End:140 Subject Strand: null Subject Start: 24 Subject End: 48 ................................................................. Y S M K I K E Q T R K L A A G C S K Q C F E V A D ......................................................................................................................... ................................................................. Y S M K I K V Q T R K L A A G C S K H C F E V V D ......................................................................................................................... HSP 2 e-value: 5.0E-7 bit: 26.9 Len: 33 Query Start:28 Query End:60 Subject Strand: null Subject Start: 63 Subject End: 73 ........................... L T W F E E V F E E Y ......................................................................................................................................................................................................... ........................... L T W F E E I F E K Y ......................................................................................................................................................................................................... Subject: UniRef90_Q04LB4 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 7.0E-7 bit: 47.0 Len: 69 Query Start:66 Query End:134 Subject Strand: null Subject Start: 1 Subject End: 23 ................................................................. M K I K E Q T R K L A A G C S K Q C F E V A D ............................................................................................................................... ................................................................. M K I K E Q T R K L A A G C S K H C F E V V D ............................................................................................................................... HSP 2 e-value: 7.0E-7 bit: 28.1 Len: 42 Query Start:28 Query End:69 Subject Strand: null Subject Start: 50 Subject End: 63 ........................... R W K L T W F E E V F E E Y ................................................................................................................................................................................................ ........................... R A T M T W F E E I F E E Y ................................................................................................................................................................................................ Subject: UniRef90_Q04L28 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 9.0E-6 bit: 48.5 Len: 69 Query Start:66 Query End:134 Subject Strand: null Subject Start: 1 Subject End: 23 ................................................................. M K I K E Q T R K L A A G C S K Q C F E V A D ............................................................................................................................... ................................................................. M K I K E Q T R K L A A G C S K H C F E V A D ............................................................................................................................... HSP 2 e-value: 9.0E-6 bit: 22.7 Len: 36 Query Start:25 Query End:60 Subject Strand: null Subject Start: 53 Subject End: 64 ........................ L T W F E E V F E E Y K ......................................................................................................................................................................................................... ........................ L T R I E E I F E E Y K ......................................................................................................................................................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 2 End: 112 . M S P P P F F I L Y S S K T S S N H V S F H L Q P Q N T V L S N L R L A S ..................................................................................................................................................... Protein_Len: 46 Strand: + Start: 4 End: 141 ... M P A T L F H F I L F E N L F K P R Q L P S A T S K H C F E Q P A A S F L V C S L I F I E Y ........................................................................................................................ Protein_Len: 34 Strand: + Start: 147 End: 248 .................................................................................................................................................. M V T V S N I L T T S N F S P R L E I K H I S L Y N N T H I E N T F ............. nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa 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: 90 Start: 195 End: 224 ..................................................................................................................................................................................................CTTGAAATAAAGCACATTTCTCTATATAAT..................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1144:SMT_1145|SMT_1144:SMT_1145:K02026 multiple sugar transport system permease protein:maltodextrose utilization protein MalA:->->:1089205..1089465 261 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtaagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa Intra-Species Hit: Count: 1 Min: 157 Max: 261 Len: 105 Subject: smit_SMT_1144_SMT_1145|K02026 multiple sugar transport system permease protein:maltodextrose utilization protein MalA|POSITIVE:POSITIVE|[1089205,1089465]|261 HSP 1 e-value: 7.0E-53 bit: 208.0 Len: 105 Query Start:157 Query End:261 Subject Strand: POSITIVE Subject Start: 157 Subject End: 261 ............................................................................................................................................................taagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa ............................................................................................................................................................taagtaatatccttacaacaagcaatttttctcctagacttgaaataaagcacatttctctatataataatactcatatagaaaacaccttttagaaagatacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUAAUAUCCUUACAACAAGCAAUUUUUCUCCUAGACUUGAAAUAAAGCACAUUUCUCUAUAUAAUAAUACUCAUAUAGAAAACACCUUUUAGAAAGAUACAA ...((((.....))))........((((((((...((....(((((.......)))))(((((((..........)))))))......))...)))))))).... (-10.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUAUCUUUCUAAAAGGUGUUUUCUAUAUGAGUAUUAUUAUAUAGAGAAAUGUGCUUUAUUUCAAGUCUAGGAGAAAAAUUGCUUGUUGUAAGGAUAUUACUUA ...((((((.....)))))).(((((((((((......)))))))))))(((((.((((((..(((((..............)))))..)))))))))))..... (-20.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 61 23 100 59 smit:SMT_1345|5end_K06198_competence_protein_CoiA_1323770..1324000_NEGATIVE 230 42 1 132 91 smit:SMT_205|5end_K02012_iron(III)_transport_system_substrate-binding_protein_137174..137404_NEGATIVE 228 51 15 185 148 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 218 78 36 92 36 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 206 43 9 131 99 smit:SMT_550|5end_K02945_small_subunit_ribosomal_protein_S1_467660..467890_POSITIVE 205 54 11 59 26 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 202 55 11 60 13 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 195 79 31 186 134 smit:SMT_1202|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1164097..1164327_NEGATIVE 192 60 21 71 29 smit:SMT_2166|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2039569..2039799_POSITIVE 192 39 6 112 75 smit:SMT_1791|5end_hypothetical_protein_1765907..1766137_POSITIVE 189 36 3 104 66 smit:SMT_79|5end_ABC_transporter,_ATP-binding_protein_6687..6917_POSITIVE 188 64 30 150 111 smit:SMT_1675|5end_adenylosuccinate_synthetase_1661147..1661377_NEGATIVE 182 77 32 113 69 smit:SMT_1903|5end_hypothetical_protein_1852411..1852641_POSITIVE 182 60 18 103 69 smit:SMT_1537|5end_hypothetical_protein_1522668..1522898_NEGATIVE 181 43 4 170 130 smit:SMT_1586|5end_K07177_PDZ_domain-containing_protein_1575714..1575944_POSITIVE 179 44 4 84 43 smit:SMT_574|5end_PTS_system,_fructose_specific_IIABC_components_491884..492114_POSITIVE 177 60 11 49 3 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 176 60 20 129 86 smit:SMT_1130|5end_MATE_efflux_family_protein_1065210..1065440_NEGATIVE 176 67 24 176 114 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 176 67 24 176 114 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 76 34 70 32 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE 218 78 36 95 39 smit:SMT_1283|3end_K02240_competence_protein_ComFA_1247045..1247195_POSITIVE 195 79 31 62 10 smit:SMT_1203|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1164221..1164371_NEGATIVE 192 60 21 52 10 smit:SMT_2165|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2039630..2039780_POSITIVE 192 39 6 40 3 smit:SMT_1790|3end_hypothetical_protein_1765915..1766065_POSITIVE 190 35 9 30 1 smit:SMT_1346|3end_tellurite_resistance_protein_TehB_1323843..1323993_NEGATIVE 189 59 25 72 39 smit:SMT_120|3end_hypothetical_protein_72943..73093_POSITIVE 183 60 11 122 73 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE 182 60 18 102 68 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 179 44 4 87 46 smit:SMT_573|3end_1-phosphofructokinase_491967..492117_POSITIVE 176 60 20 68 25 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 175 60 11 138 83 smit:SMT_903|3end_hypothetical_protein_851945..852095_NEGATIVE 174 60 29 137 113 smit:SMT_567|3end_conserved_hypothetical_protein_485752..485902_POSITIVE 173 55 20 46 8 smit:SMT_1798|3end_exonuclease_RexA_1772818..1772968_NEGATIVE 172 74 38 41 1 smit:SMT_901|3end_hypothetical_protein_851141..851291_NEGATIVE 171 94 54 125 84 smit:SMT_860|3end_homoserine_O-succinyltransferase_804067..804217_NEGATIVE 170 66 32 123 99 smit:SMT_409|3end_pneumococcal_surface_protein,_putative_354406..354556_POSITIVE 169 76 51 103 76 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 169 67 38 62 28 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 169 67 38 62 28 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE