Origin IGS: actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcattcatactcttcgaaaatctcttcaaaccacgtcagcttccatctgcaacctcaaaacagtgttttgagcaacctgcgactagcttcctagtttgctctttgcttttcattgagtatcaaaatatcaaggaggggat .........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 atcccctccttgatattttgatactcaatgaaaagcaaagagcaaactaggaagctagtcgcaggttgctcaaaacactgttttgaggttgcagatggaagctgacgtggtttgaagagattttcgaagagtatgaatgctaaaaacaggtaattaatactagtataacgcaggtattcggtagaaggcaagtatttataatcatttttctgagtaaaaacaaaagagactgacaaaaccagtctccttctagt Mask Tandem Repeat Region ================================================ actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcattcatactcttcgaaaatctcttcaaaccacgtcagcttccatctgcaacctcaaaacagtgttttgagcaacctgcgactagcttcctagtttgctctttgcttttcattgagtatcaaaatatcaaggaggggat Find is-nt database================================================ Query_seq: SMT_162:SMT_163|SMT_162:SMT_163:hypothetical protein:cardiolipin synthetase:->->:107195..107448 254 actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcattcatactcttcgaaaatctcttcaaaccacgtcagcttccatctgcaacctcaaaacagtgttttgagcaacctgcgactagcttcctagtttgctctttgcttttcattgagtatcaaaatatcaaggaggggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_162:SMT_163|SMT_162:SMT_163:hypothetical protein:cardiolipin synthetase:->->:107195..107448 254 actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcattcatactcttcgaaaatctcttcaaaccacgtcagcttccatctgcaacctcaaaacagtgttttgagcaacctgcgactagcttcctagtttgctctttgcttttcattgagtatcaaaatatcaaggaggggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_162:SMT_163|SMT_162:SMT_163:hypothetical protein:cardiolipin synthetase:->->:107195..107448 254 actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcattcatactcttcgaaaatctcttcaaaccacgtcagcttccatctgcaacctcaaaacagtgttttgagcaacctgcgactagcttcctagtttgctctttgcttttcattgagtatcaaaatatcaaggaggggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 5 Min: 118 Max: 248 Len: 131 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: 120 Query Start:121 Query End:240 Subject Strand: null Subject Start: 7 Subject End: 46 ........................................................................................................................ I L F E N L F K P R Q L P S A T S K Q C F E Q P A T S F L V C S L L F I E Y Q N .............. ........................................................................................................................ 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 K N .............. 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: 8.0E-8 bit: 50.8 Len: 90 Query Start:159 Query End:248 Subject Strand: null Subject Start: 19 Subject End: 48 .............................................................................................................................................................. S L I F * Y S M K S K E Q T R K L V A G C S K H C F E V A D ...... .............................................................................................................................................................. S K I F L 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: 8.0E-8 bit: 27.3 Len: 33 Query Start:121 Query End:153 Subject Strand: null Subject Start: 63 Subject End: 73 ........................................................................................................................ L T W F E E I F E E Y ..................................................................................................... ........................................................................................................................ L T W F E E I F E K Y ..................................................................................................... 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-7 bit: 46.2 Len: 69 Query Start:159 Query End:227 Subject Strand: null Subject Start: 1 Subject End: 23 .............................................................................................................................................................. M K S K E Q T R K L V A G C S K H 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: 1.0E-7 bit: 31.2 Len: 39 Query Start:118 Query End:156 Subject Strand: null Subject Start: 37 Subject End: 49 ..................................................................................................................... K L T W F E E I F E E Y E .................................................................................................. ..................................................................................................................... K L T W F E E I F E E Y K .................................................................................................. 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: 9.0E-7 bit: 46.2 Len: 69 Query Start:159 Query End:227 Subject Strand: null Subject Start: 1 Subject End: 23 .............................................................................................................................................................. M K S K E Q T R K L V A G C S K H 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: 9.0E-7 bit: 28.5 Len: 42 Query Start:121 Query End:162 Subject Strand: null Subject Start: 50 Subject End: 63 ........................................................................................................................ R W K L T W F E E I F E E Y ............................................................................................ ........................................................................................................................ R A T M T W F E E I F E 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: 5.0E-6 bit: 43.1 Len: 69 Query Start:159 Query End:227 Subject Strand: null Subject Start: 1 Subject End: 23 .............................................................................................................................................................. M K S K E Q T R K L V A G C S K H 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: 5.0E-6 bit: 28.9 Len: 39 Query Start:118 Query End:156 Subject Strand: null Subject Start: 37 Subject End: 49 ..................................................................................................................... K L T W F E E I F E E Y E .................................................................................................. ..................................................................................................................... K L M W F E E I F E E Y K .................................................................................................. actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 13 End: 252 ............ M V L S V S F V F T Q K N D Y K Y L P S T E Y L R Y T S I N Y L F L A F I L F E N L F K P R Q L P S A T S K Q C F E Q P .. actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggat 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================================================ actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 62 HP_score: -3.7 Tail_Score: -4.27062 Start: 184 End: 215 Full_Region: TCAAAACAGTGTTTT GAGCAACCTGCGA CTAGCT TCCTAGTTTGCTC TTTGCTTTTCATTGA .......................................................................................................................................................................................GAGCAACCTGCGACTAGCTTCCTAGTTTGCTC....................................... Find igs database================================================ Query_seq: SMT_162:SMT_163|SMT_162:SMT_163:hypothetical protein:cardiolipin synthetase:->->:107195..107448 254 actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggat Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: smit_SMT_162_SMT_163|hypothetical protein:cardiolipin synthetase|POSITIVE:POSITIVE|[107195,107448]|254 HSP 1 e-value: 5.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagca......................................................................................................................................... actagaaggagactggttttgtcagtctcttttgtttttactcagaaaaatgattataaatacttgccttctaccgaatacctgcgttatactagtattaattacctgtttttagca......................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAGAAGGAGACUGGUUUUGUCAGUCUCUUUUGUUUUUACUCAGAAAAAUGAUUAUAAAUACUUGCCUUCUACCGAAUACCUGCGUUAUACUAGUAUUAAUUACCUGUUUUUAGCA ..((((((((((((((.....))))))))...(((((.((.(((......))).)).))))).....))))))............((((.((..(((.....)))..))...)))). (-22.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUAAAAACAGGUAAUUAAUACUAGUAUAACGCAGGUAUUCGGUAGAAGGCAAGUAUUUAUAAUCAUUUUUCUGAGUAAAAACAAAAGAGACUGACAAAACCAGUCUCCUUCUAGU (((.....((.((((.....)))).)).....))).........((((((....((.(((((..(((......)))))))).))....(((((((.......))))))))))))).. (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 35 2 141 106 smit:SMT_1590|5end_DNA-entry_nuclease_1578565..1578795_POSITIVE 293 48 1 165 108 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 284 47 1 196 140 smit:SMT_1922|5end_exonuclease_RexA_1865998..1866228_NEGATIVE 274 47 1 197 140 smit:SMT_1484|5end_exonuclease_RexA_1464936..1465166_NEGATIVE 270 42 4 186 145 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 264 42 4 162 117 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 260 93 51 78 25 smit:SMT_1613|5end_ribosomal_large_subunit_pseudouridine_synthase_B_1600608..1600838_POSITIVE 243 110 65 138 96 smit:SMT_1299|5end_MutT/NUDIX_family_protein_1261719..1261949_POSITIVE 243 36 7 86 59 smit:SMT_893|5end_leucine_rich_protein_841311..841541_NEGATIVE 242 69 25 66 24 smit:SMT_813|5end_acetyltransferase,_GNAT_family_722322..722552_NEGATIVE 241 44 9 74 43 smit:SMT_1373|5end_K02838_ribosome_recycling_factor_1352274..1352504_NEGATIVE 239 83 52 209 175 smit:SMT_1788|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1765029..1765259_NEGATIVE 238 42 7 37 5 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 238 42 7 137 105 smit:SMT_1666|5end_hypothetical_protein_1657467..1657697_NEGATIVE 236 46 4 56 12 smit:SMT_1123|5end_hypothetical_protein_1059292..1059522_POSITIVE 236 42 2 217 179 smit:SMT_232|5end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_168246..168476_POSITIVE 228 84 63 208 180 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 227 107 62 148 95 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 225 109 63 55 1 smit:SMT_767|5end_hypothetical_protein_676454..676684_NEGATIVE 225 110 69 83 40 smit:SMT_659|5end_hypothetical_protein_570545..570775_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 35 2 102 67 smit:SMT_1589|3end_hypothetical_protein_1578606..1578756_POSITIVE 271 40 5 88 57 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 270 42 4 100 59 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 264 42 4 91 46 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 260 93 51 91 38 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 253 39 4 89 56 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 252 109 61 58 2 smit:SMT_768|3end_hypothetical_protein_676451..676601_NEGATIVE 244 36 7 92 65 smit:SMT_640|3end_PTS_system,_lactose-specific_IIBC_component_545099..545249_NEGATIVE 243 110 65 136 94 smit:SMT_1298|3end_K03811_nicotinamide_mononucleotide_transporter_1261797..1261947_POSITIVE 243 36 7 82 55 smit:SMT_894|3end_hypothetical_protein_841315..841465_NEGATIVE 242 69 25 56 14 smit:SMT_814|3end_UDP-N-acetyl_muramate-alanine_ligase_722332..722482_NEGATIVE 241 44 9 65 34 smit:SMT_1374|3end_uridylate_kinase_1352283..1352433_NEGATIVE 236 42 2 113 75 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 227 107 62 117 64 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 225 110 69 90 47 smit:SMT_660|3end_two-component_sensor_histidine_kinase_570538..570688_NEGATIVE 224 96 63 151 123 smit:SMT_1084|3end_hypothetical_protein_1021326..1021476_NEGATIVE 220 34 7 43 10 smit:SMT_632|3end_hypothetical_protein_537274..537424_NEGATIVE 218 39 3 91 46 smit:SMT_1534|3end_signal_peptidase_I_1517912..1518062_POSITIVE 215 44 2 127 74 smit:SMT_1291|3end_hypothetical_protein_1254296..1254446_POSITIVE 214 106 62 85 52 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE