Origin IGS: tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaatactcaatgaaaatcaaagagcaaactaggaaactagccgcaggctgctcaaagcactgctttgaggttgtagataagactgacgaagtcagttacatatatctacggcaaggcgacgttgacgtggtttgaattagtataaaataacagtataggagaggtataga .........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 tctatacctctcctatactgttattttatactaattcaaaccacgtcaacgtcgccttgccgtagatatatgtaactgacttcgtcagtcttatctacaacctcaaagcagtgctttgagcagcctgcggctagtttcctagtttgctctttgattttcattgagtattacttgagcaactatactatttagaaacaaaagaagccatcaggttagcatttaacctaaacagctccttga Mask Tandem Repeat Region ================================================ tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaatactcaatgaaaatcaaagagcaaactaggaaactagccgcaggctgctcaaagcactgctttgaggttgtagataagactgacgaagtcagttacatatatctacggcaaggcgacgttgacgtggtttgaattagtataaaataacagtataggagaggtataga Find is-nt database================================================ Query_seq: SMT_603:SMT_604|SMT_603:SMT_604:hypothetical protein:DNA polymerase III, epsilon chain:->->:518593..518832 240 tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaatactcaatgaaaatcaaagagcaaactaggaaactagccgcaggctgctcaaagcactgctttgaggttgtagataagactgacgaagtcagttacatatatctacggcaaggcgacgttgacgtggtttgaattagtataaaataacagtataggagaggtataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_603:SMT_604|SMT_603:SMT_604:hypothetical protein:DNA polymerase III, epsilon chain:->->:518593..518832 240 tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaatactcaatgaaaatcaaagagcaaactaggaaactagccgcaggctgctcaaagcactgctttgaggttgtagataagactgacgaagtcagttacatatatctacggcaaggcgacgttgacgtggtttgaattagtataaaataacagtataggagaggtataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_603:SMT_604|SMT_603:SMT_604:hypothetical protein:DNA polymerase III, epsilon chain:->->:518593..518832 240 tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaatactcaatgaaaatcaaagagcaaactaggaaactagccgcaggctgctcaaagcactgctttgaggttgtagataagactgacgaagtcagttacatatatctacggcaaggcgacgttgacgtggtttgaattagtataaaataacagtataggagaggtataga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 6 Min: 74 Max: 206 Len: 133 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: 3.0E-11 bit: 62.8 Len: 93 Query Start:74 Query End:166 Subject Strand: null Subject Start: 24 Subject End: 54 ......................................................................... Y S M K I K E Q T R K L A A G C S K H C F E V V D K T D E V S .......................................................................... ......................................................................... 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 E T D E V S .......................................................................... HSP 2 e-value: 3.0E-11 bit: 27.3 Len: 36 Query Start:171 Query End:206 Subject Strand: null Subject Start: 56 Subject End: 67 .......................................................................................................................................................................... Y I Y G K A T L T W F E .................................. .......................................................................................................................................................................... H T Y G K A T L T W F E .................................. 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: 2.0E-10 bit: 61.6 Len: 87 Query Start:80 Query End:166 Subject Strand: null Subject Start: 1 Subject End: 29 ............................................................................... M K I K E Q T R K L A A G C S K H C F E V V D K T D E V S .......................................................................... ............................................................................... M K I K E Q T R K L A A G C S K H C F E V V D R T D E V S .......................................................................... HSP 2 e-value: 2.0E-10 bit: 25.4 Len: 36 Query Start:171 Query End:206 Subject Strand: null Subject Start: 46 Subject End: 57 .......................................................................................................................................................................... Y I Y G K A T L T W F E .................................. .......................................................................................................................................................................... H T Y G R A T M T W F E .................................. 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: 1.0E-9 bit: 61.2 Len: 87 Query Start:80 Query End:166 Subject Strand: null Subject Start: 1 Subject End: 29 ............................................................................... M K I K E Q T R K L A A G C S K H C F E V V D K T D E V S .......................................................................... ............................................................................... M K I K E Q T R K L A A G C S K H C F E V V D E T D E V S .......................................................................... HSP 2 e-value: 1.0E-9 bit: 23.5 Len: 36 Query Start:171 Query End:206 Subject Strand: null Subject Start: 31 Subject End: 42 .......................................................................................................................................................................... Y I Y G K A T L T W F E .................................. .......................................................................................................................................................................... H T Y G K V K L T W F E .................................. Subject: UniRef90_Q04I51 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-9 bit: 60.5 Len: 87 Query Start:80 Query End:166 Subject Strand: null Subject Start: 1 Subject End: 29 ............................................................................... M K I K E Q T R K L A A G C S K H C F E V V D K T D E V S .......................................................................... ............................................................................... M K I K E Q T R K L A A G C S K H C F E V M D R T D E V S .......................................................................... HSP 2 e-value: 5.0E-9 bit: 21.9 Len: 36 Query Start:171 Query End:206 Subject Strand: null Subject Start: 46 Subject End: 57 .......................................................................................................................................................................... Y I Y G K A T L T W F E .................................. .......................................................................................................................................................................... H T Y G E V K L T W F E .................................. 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: 1.0E-8 bit: 58.2 Len: 87 Query Start:80 Query End:166 Subject Strand: null Subject Start: 1 Subject End: 29 ............................................................................... M K I K E Q T R K L A A G C S K H C F E V V D K T D E V S .......................................................................... ............................................................................... M K I K E Q T R K L A A G C S K Q C F E V V D E T D E V S .......................................................................... HSP 2 e-value: 1.0E-8 bit: 22.7 Len: 36 Query Start:171 Query End:206 Subject Strand: null Subject Start: 31 Subject End: 42 .......................................................................................................................................................................... Y I Y G K A T L T W F E .................................. .......................................................................................................................................................................... H T Y G K A K L M W F E .................................. Subject: UniRef90_Q04KB8 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 9.0E-8 bit: 53.1 Len: 87 Query Start:80 Query End:166 Subject Strand: null Subject Start: 1 Subject End: 29 ............................................................................... M K I K E Q T R K L A A G C S K H C F E V V D K T D E V S .......................................................................... ............................................................................... M K I K E Q T R K L A A G Y S K H S F E V V D E T D E V S .......................................................................... HSP 2 e-value: 9.0E-8 bit: 25.0 Len: 36 Query Start:171 Query End:206 Subject Strand: null Subject Start: 31 Subject End: 42 .......................................................................................................................................................................... Y I Y G K A T L T W F E .................................. .......................................................................................................................................................................... H T Y S K A T L T W F E .................................. tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttagtataaaataacagtataggagaggtataga Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 80 End: 202 ............................................................................... M K I K E Q T R K L A A G C S K H C F E V V D K T D E V S Y I Y L R Q G D V D V V ...................................... Protein_Len: 38 Strand: - Start: 52 End: 165 ................................................... I T Y N S L Y Y E I F I L S C V L F S A A P Q E F C Q K S T T S L V S S T M ........................................................................... tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttagtataaaataacagtataggagaggtataga 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================================================ tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttagtataaaataacagtataggagaggtataga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -8.3 Tail_Score: -3.35996 Start: 120 End: 140 Full_Region: AACTAGCCGCAGGCT GCTCAAAGC ACT GCTTTGAGG TTGTAGATAAGACTG .......................................................................................................................GCTCAAAGCACTGCTTTGAGG.................................................................................................... TransTerm Strand: + Conf: 81 HP_score: -11.8 Tail_Score: -2.61383 Start: 121 End: 139 Full_Region: ACTAGCCGCAGGCTG CTCAAAGC ACT GCTTTGAG GTTGTAGATAAGACT ........................................................................................................................CTCAAAGCACTGCTTTGAG..................................................................................................... Find igs database================================================ Query_seq: SMT_603:SMT_604|SMT_603:SMT_604:hypothetical protein:DNA polymerase III, epsilon chain:->->:518593..518832 240 tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttagtataaaataacagtataggagaggtataga Intra-Species Hit: Count: 1 Min: 1 Max: 240 Len: 240 Subject: smit_SMT_603_SMT_604|hypothetical protein:DNA polymerase III, epsilon chain|POSITIVE:POSITIVE|[518593,518832]|240 HSP 1 e-value: 8.0E-34 bit: 145.0 Len: 73 Query Start:1 Query End:73 Subject Strand: POSITIVE Subject Start: 1 Subject End: 73 tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaa....................................................................................................................................................................... tcaaggagctgtttaggttaaatgctaacctgatggcttcttttgtttctaaatagtatagttgctcaagtaa....................................................................................................................................................................... HSP 2 e-value: 1.0E-10 bit: 67.9 Len: 34 Query Start:207 Query End:240 Subject Strand: POSITIVE Subject Start: 207 Subject End: 240 ..............................................................................................................................................................................................................ttagtataaaataacagtataggagaggtataga ..............................................................................................................................................................................................................ttagtataaaataacagtataggagaggtataga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAGGAGCUGUUUAGGUUAAAUGCUAACCUGAUGGCUUCUUUUGUUUCUAAAUAGUAUAGUUGCUCAAGUAAUACUCAAUGAAAAUCAAAGAGCAAACUAGGAAACUAGCCGCAGGCUGCUCAAAGCACUGCUUUGAGGUUGUAGAUAAGACUGACGAAGUCAGUUACAUAUAUCUACGGCAAGGCGACGUUGACGUGGUUUGAAUUAGUAUAAAAUAACAGUAUAGGAGAGGUAUAGA ..(((((((((((.((((((.....)))))))))))))))))...((((((...((((....))))......(((((.(((..((((((...(((...((((....)))).(((......((((((((...))))))))((((((((((.(((((((...))))))).....))))))))))...)))..)))....))))))..))))))))............))))))......... (-68.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUACCUCUCCUAUACUGUUAUUUUAUACUAAUUCAAACCACGUCAACGUCGCCUUGCCGUAGAUAUAUGUAACUGACUUCGUCAGUCUUAUCUACAACCUCAAAGCAGUGCUUUGAGCAGCCUGCGGCUAGUUUCCUAGUUUGCUCUUUGAUUUUCAUUGAGUAUUACUUGAGCAACUAUACUAUUUAGAAACAAAAGAAGCCAUCAGGUUAGCAUUUAACCUAAACAGCUCCUUGA .................(((((............(((.............(((((...((.(((((((......((((((...))))))..)))))))...((((((((...))))))))..))..)))))..(((((.((((((((((..((((.(((...))).))))...))))))....))))....)))))....)))......(((((((...))))))).)))))........ (-52.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 888 130 81 162 113 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 880 120 71 165 116 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 860 120 73 213 166 smit:SMT_1138|5end_hypothetical_protein_1079547..1079777_NEGATIVE 860 120 73 190 143 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 860 120 73 174 127 smit:SMT_130|5end_capsular_polysaccharide_biosynthesis_protein_80995..81225_POSITIVE 818 120 73 177 129 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 809 120 73 199 152 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 809 120 73 151 104 smit:SMT_483|5end_transcriptional_activator_TipA,_putative_418827..419057_POSITIVE 785 130 81 229 180 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 782 129 81 171 123 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 781 166 121 163 118 smit:SMT_677|5end_DNA_topoisomerase_I_587318..587548_NEGATIVE 757 120 73 164 117 smit:SMT_1963|5end_ribonuclease_BN,_putative_1896462..1896692_NEGATIVE 753 120 73 216 169 smit:SMT_1179|5end_aldose_1-epimerase_1137854..1138084_NEGATIVE 741 120 72 162 114 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 713 149 109 185 145 smit:SMT_775|5end_alpha-acetolactate_decarboxylase_685972..686202_NEGATIVE 710 200 151 61 12 smit:SMT_958|5end_hypothetical_protein_predicted_by_Glimmer/Critica_905052..905282_POSITIVE 710 140 91 214 165 smit:SMT_150|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_98787..99017_POSITIVE 704 140 91 179 130 smit:SMT_163|5end_cardiolipin_synthetase_107309..107539_POSITIVE 662 160 111 211 162 smit:SMT_1544|5end_mevalonate_kinase_1528884..1529114_NEGATIVE 646 118 76 231 189 smit:SMT_443|5end_hydroxyethylthiazole_kinase_382555..382785_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 913 200 151 68 21 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 860 200 151 66 17 smit:SMT_913|3end_putative_sucrose-specific_PTS_permease,_enzyme_II_863923..864073_NEGATIVE 802 200 151 62 14 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 736 197 151 64 18 smit:SMT_1471|3end_hypothetical_protein_1453442..1453592_NEGATIVE 730 189 142 48 1 smit:SMT_764|3end_alanyl-tRNA_synthetase_669495..669645_NEGATIVE 710 140 91 132 83 smit:SMT_149|3end_hypothetical_protein_predicted_by_Glimmer/Critica_98785..98935_POSITIVE 694 200 151 67 19 smit:SMT_678|3end_K04096_DNA_processing_protein_587447..587597_NEGATIVE 685 157 112 63 18 smit:SMT_1489|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1470714..1470864_POSITIVE 673 200 151 55 8 smit:SMT_1357|3end_endo-beta-N-acetylglucosaminidase_1334450..1334600_NEGATIVE 657 122 86 39 1 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 649 180 133 47 1 smit:SMT_1912|3end_D-alanyl-D-alanine_carboxypeptidase_1857807..1857957_NEGATIVE 649 180 133 47 1 smit:SMT_868|3end_D-alanyl-D-alanine_carboxypeptidase_816509..816659_NEGATIVE 613 122 87 38 1 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 613 200 151 61 11 smit:SMT_124|3end_hypothetical_protein_75590..75740_NEGATIVE 593 122 87 38 1 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 593 122 87 38 1 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 580 206 161 47 3 smit:SMT_1815|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1788899..1789049_NEGATIVE 577 122 86 39 1 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 572 158 119 42 3 smit:SMT_455|3end_cation_transport_ATPase_393993..394143_POSITIVE 565 140 91 48 1 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE