Origin IGS: tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgatgaaactgtcgtttaattggtttcatttgatactcttatttccctgcttttactttttttattggatagataatgctgatagaaacagtaagtttttccccattatctactatttctactggatttatatttcccttttagctctgtttagcttggatatgacaattttttcattcttatttttcccttttgttctaaattatgtatcagatgctagtacttggggtgtttggttgcttttgatagtcttatctctaggcagtgactggttagactatatctttttcaaaaacatgttttgcttgagacgggaactaggacaatctaaaggcgaaaggcattgatttatatggtttttattgataggaggtagctt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagctacctcctatcaataaaaaccatataaatcaatgcctttcgcctttagattgtcctagttcccgtctcaagcaaaacatgtttttgaaaaagatatagtctaaccagtcactgcctagagataagactatcaaaagcaaccaaacaccccaagtactagcatctgatacataatttagaacaaaagggaaaaataagaatgaaaaaattgtcatatccaagctaaacagagctaaaagggaaatataaatccagtagaaatagtagataatggggaaaaacttactgtttctatcagcattatctatccaataaaaaaagtaaaagcagggaaataagagtatcaaatgaaaccaattaaacgacagtttcatcatcgacacctcctctttaaaattgttttctttagtttcattctattaaatgttcttaccaatataaa Mask Tandem Repeat Region ================================================ tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgatgaaactgtcgtttaattggtttcatttgatactcttatttccctgcttttactttttttattggatagataatgctgatagaaacagtaagtttttccccattatctactatttctactggatttatatttcccttttagctctgtttagcttggatatgacaattttttcattcttatttttcccttttgttctaaattatgtatcagatgctagtacttggggtgtttggttgcttttgatagtcttatctctaggcagtgactggttagactatatctttttcaaaaacatgttttgcttgagacgggaactaggacaatctaaaggcgaaaggcattgatttatatggtttttattgataggaggtagctt Find is-nt database================================================ Query_seq: SMT_1061:SMT_1062|SMT_1061:SMT_1062:hypothetical protein:hypothetical protein:->->:999976..1000420 445 tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgatgaaactgtcgtttaattggtttcatttgatactcttatttccctgcttttactttttttattggatagataatgctgatagaaacagtaagtttttccccattatctactatttctactggatttatatttcccttttagctctgtttagcttggatatgacaattttttcattcttatttttcccttttgttctaaattatgtatcagatgctagtacttggggtgtttggttgcttttgatagtcttatctctaggcagtgactggttagactatatctttttcaaaaacatgttttgcttgagacgggaactaggacaatctaaaggcgaaaggcattgatttatatggtttttattgataggaggtagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1061:SMT_1062|SMT_1061:SMT_1062:hypothetical protein:hypothetical protein:->->:999976..1000420 445 tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgatgaaactgtcgtttaattggtttcatttgatactcttatttccctgcttttactttttttattggatagataatgctgatagaaacagtaagtttttccccattatctactatttctactggatttatatttcccttttagctctgtttagcttggatatgacaattttttcattcttatttttcccttttgttctaaattatgtatcagatgctagtacttggggtgtttggttgcttttgatagtcttatctctaggcagtgactggttagactatatctttttcaaaaacatgttttgcttgagacgggaactaggacaatctaaaggcgaaaggcattgatttatatggtttttattgataggaggtagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1061:SMT_1062|SMT_1061:SMT_1062:hypothetical protein:hypothetical protein:->->:999976..1000420 445 tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgatgaaactgtcgtttaattggtttcatttgatactcttatttccctgcttttactttttttattggatagataatgctgatagaaacagtaagtttttccccattatctactatttctactggatttatatttcccttttagctctgtttagcttggatatgacaattttttcattcttatttttcccttttgttctaaattatgtatcagatgctagtacttggggtgtttggttgcttttgatagtcttatctctaggcagtgactggttagactatatctttttcaaaaacatgttttgcttgagacgggaactaggacaatctaaaggcgaaaggcattgatttatatggtttttattgataggaggtagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 2 Min: 69 Max: 410 Len: 342 Subject: UniRef90_Q97PD1 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 2.0E-26 bit: 120.0 Len: 321 Query Start:90 Query End:410 Subject Strand: null Subject Start: 6 Subject End: 112 ......................................................................................... F H L I L L F P C F Y F F Y W I D N A D R N S K X X X X X X X X X X X X X S L L A L F S L D M T I F S F L F F P F V L N Y V S D A S T W G V W L L L I V L S L G S D W L D Y I F F K N M F C L R R E L G Q S K G E R H ................................... ......................................................................................... F K M I I L L P C F Y F F S W I D K D N R E S K F F P I F Y Y F Y W I Y I T L Y A L F S L A W T V F S V L F F N I V L R N L T D I K L W G I W L L L L L I A F A S D W L A Y V F F K K M L D L R R E L G K S K G G R H ................................... Subject: UniRef90_Q97PD0 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 4.0E-21 bit: 102.0 Len: 342 Query Start:69 Query End:410 Subject Strand: null Subject Start: 1 Subject End: 114 .................................................................... M K L S F N W F H L I L L F P C F Y F F Y W I D N A D R N S K X X X X X X X X X X X X X S L L A L F S L D M T I F S F L F F P F V L N Y V S D A S T W G V W L L L I V L S L G S D W L D Y I F F K N M F C L R R E L G Q S K G E R H ................................... .................................................................... M S V M E H L F K F L L L A P Y F Y F D N W I E K A N R N S K F F P I F Y Y F Y W F Y I P F Y S L F S L A W T V V S V L F F N T V L R N V T D I K L W G I W F L F I L L A I G M N W L T Y S C F K E M F R L R Q E L G K S K G G R H ................................... tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgatttatatggtttttattgataggaggtagctt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 60 End: 410 ........................................................... M S M M K L S F N W F H L I L L F P C F Y F F Y W I D N A D R N S K F F P I I Y Y F Y W I Y I S L L A L F S L D M T I F ................................... Protein_Len: 30 Strand: - Start: 108 End: 197 ........................................................................................................... K G A K V K K I P Y I I S I S V T L K E G N D V I E V P N M ........................................................................................................................................................................................................................................................ Protein_Len: 31 Strand: - Start: 3 End: 95 .. I N T L V N L L I F S F F V I K F L L H R H H F Q R K I P K M .............................................................................................................................................................................................................................................................................................................................................................. tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgatttatatggtttttattgataggaggtagctt 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================================================ tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgatttatatggtttttattgataggaggtagctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1061:SMT_1062|SMT_1061:SMT_1062:hypothetical protein:hypothetical protein:->->:999976..1000420 445 tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgatgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgatttatatggtttttattgataggaggtagctt Intra-Species Hit: Count: 1 Min: 1 Max: 445 Len: 445 Subject: smit_SMT_1061_SMT_1062|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[999976,1000420]|445 HSP 1 e-value: 6.0E-30 bit: 133.0 Len: 67 Query Start:1 Query End:67 Subject Strand: POSITIVE Subject Start: 1 Subject End: 67 tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgat.......................................................................................................................................................................................................................................................................................................................................................................................... tttatattggtaagaacatttaatagaatgaaactaaagaaaacaattttaaagaggaggtgtcgat.......................................................................................................................................................................................................................................................................................................................................................................................... HSP 2 e-value: 7.0E-11 bit: 69.9 Len: 35 Query Start:411 Query End:445 Subject Strand: POSITIVE Subject Start: 411 Subject End: 445 ..........................................................................................................................................................................................................................................................................................................................................................................................................................tgatttatatggtttttattgataggaggtagctt ..........................................................................................................................................................................................................................................................................................................................................................................................................................tgatttatatggtttttattgataggaggtagctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAUUGGUAAGAACAUUUAAUAGAAUGAAACUAAAGAAAACAAUUUUAAAGAGGAGGUGUCGAUGAUGAAACUGUCGUUUAAUUGGUUUCAUUUGAUACUCUUAUUUCCCUGCUUUUACUUUUUUUAUUGGAUAGAUAAUGCUGAUAGAAACAGUAAGUUUUUCCCCAUUAUCUACUAUUUCUACUGGAUUUAUAUUUCCCUUUUAGCUCUGUUUAGCUUGGAUAUGACAAUUUUUUCAUUCUUAUUUUUCCCUUUUGUUCUAAAUUAUGUAUCAGAUGCUAGUACUUGGGGUGUUUGGUUGCUUUUGAUAGUCUUAUCUCUAGGCAGUGACUGGUUAGACUAUAUCUUUUUCAAAAACAUGUUUUGCUUGAGACGGGAACUAGGACAAUCUAAAGGCGAAAGGCAUUGAUUUAUAUGGUUUUUAUUGAUAGGAGGUAGCUU ....(((..((((((((.......(((((((((.....................(((((.((((((..(((((((((.........))))))))))))))))))))...(((..(((...((.........(((.(((((((((..((..(((((.....)))))))..))))))))))))........(((........)))...........))..)))..)))...........)))))))))..((((((((((((((((((.((((.((((((((((((.........))))))))).)))...))))..(((..((((.((((((.(((((........................)).)))))))))))))..)))..)))))))....))))).))))))..............))))))))..)))........... (-94.96) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCUACCUCCUAUCAAUAAAAACCAUAUAAAUCAAUGCCUUUCGCCUUUAGAUUGUCCUAGUUCCCGUCUCAAGCAAAACAUGUUUUUGAAAAAGAUAUAGUCUAACCAGUCACUGCCUAGAGAUAAGACUAUCAAAAGCAACCAAACACCCCAAGUACUAGCAUCUGAUACAUAAUUUAGAACAAAAGGGAAAAAUAAGAAUGAAAAAAUUGUCAUAUCCAAGCUAAACAGAGCUAAAAGGGAAAUAUAAAUCCAGUAGAAAUAGUAGAUAAUGGGGAAAAACUUACUGUUUCUAUCAGCAUUAUCUAUCCAAUAAAAAAAGUAAAAGCAGGGAAAUAAGAGUAUCAAAUGAAACCAAUUAAACGACAGUUUCAUCAUCGACACCUCCUCUUUAAAAUUGUUUUCUUUAGUUUCAUUCUAUUAAAUGUUCUUACCAAUAUAAA ...............................((((((((.....((.((.((((.(.........).)))).))))......(((((((((........((((((.....(((.((....)).))).)))))))))))))))....................)))).)))).........(((((.(((((((.......((.(((..((((((((...(((..(((........(((....(((........)))..))).....((((((((((..((.((((.....))))...))..)))))))))).................)))..))).....(.((.((....)).)))........))))))))..)))))......))).))))............((((((........)))))).)))))............ (-65.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 228 181 85 33 smit:SMT_1673|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1659831..1660061_POSITIVE 372 340 291 104 49 smit:SMT_791|5end_thiamine_biosynthesis_protein_ThiI_702377..702607_NEGATIVE 308 329 282 45 1 smit:SMT_916|5end_3-hydroxy-3-methylglutaryl-CoA_reductase_870004..870234_NEGATIVE 305 339 294 76 22 smit:SMT_603|5end_hypothetical_protein_517961..518191_POSITIVE 303 416 371 62 10 smit:SMT_1257|5end_acetolactate_synthase_small_subunit_1223173..1223403_NEGATIVE 297 330 282 77 30 smit:SMT_1500|5end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483384..1483614_POSITIVE 291 336 296 52 12 smit:SMT_837|5end_cation_transport_ATPase_782667..782897_NEGATIVE 291 414 378 206 160 smit:SMT_125|5end_hypothetical_protein_77664..77894_NEGATIVE 289 337 291 166 118 smit:SMT_693|5end_hypothetical_protein_603819..604049_POSITIVE 286 339 291 80 22 smit:SMT_2070|5end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1974729..1974959_POSITIVE 286 337 291 66 22 smit:SMT_1824|5end_hypothetical_protein_1796126..1796356_POSITIVE 284 435 393 70 30 smit:SMT_1112|5end_K02248_competence_protein_ComGF_1051848..1052078_NEGATIVE 283 405 362 53 11 smit:SMT_1668|5end_K+_transport_system,_NAD-binding_component_1658288..1658518_NEGATIVE 281 337 291 69 10 smit:SMT_1638|5end_UTP-glucose-1-phosphate_uridylyltransferase_1624781..1625011_NEGATIVE 278 343 302 218 164 smit:SMT_2018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1936760..1936990_POSITIVE 278 343 302 218 164 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 276 340 292 77 17 smit:SMT_1932|5end_K02008_cobalt_transport_system_permease_protein_1872001..1872231_NEGATIVE 276 338 291 230 189 smit:SMT_1458|5end_K02040_phosphate_transport_system_substrate-binding_protein_1440277..1440507_POSITIVE 276 338 291 204 159 smit:SMT_1147|5end_hypothetical_protein_1092144..1092374_NEGATIVE 275 346 307 206 166 smit:SMT_785|5end_hypothetical_protein_697242..697472_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 329 282 45 1 smit:SMT_917|3end_hydroxymethylglutaryl-CoA_synthase_870004..870154_NEGATIVE 303 416 371 69 17 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 296 330 294 38 9 smit:SMT_1499|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483425..1483575_POSITIVE 286 339 291 114 56 smit:SMT_2069|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1974843..1974993_POSITIVE 284 435 393 107 67 smit:SMT_1113|3end_hypothetical_protein_1051811..1051961_NEGATIVE 283 338 291 138 92 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE 280 319 273 47 7 smit:SMT_2123|3end_hypothetical_protein_2008541..2008691_POSITIVE 276 340 292 92 32 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 272 409 369 39 1 smit:SMT_203|3end_putative_ABC_transporter_BitD_133821..133971_NEGATIVE 269 160 111 143 94 smit:SMT_1673|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1660042..1660192_POSITIVE 264 312 279 147 112 smit:SMT_362|3end_K02519_translation_initiation_factor_IF-2_297950..298100_POSITIVE 254 190 143 106 50 smit:SMT_1290|3end_autolysin_1253753..1253903_POSITIVE 253 307 271 61 22 smit:SMT_1529|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1512776..1512926_NEGATIVE 253 338 292 80 17 smit:SMT_995|3end_K07574_putative_RNA-binding_protein_containing_KH_domain_936157..936307_NEGATIVE 253 324 294 102 64 smit:SMT_446|3end_ABC-type_cobalt_transport_system,_ATPase_component_386335..386485_POSITIVE 252 339 291 122 82 smit:SMT_1174|3end_acylneuraminate_cytidylyltransferase_1125617..1125767_NEGATIVE 252 340 301 49 3 smit:SMT_876|3end_hypothetical_protein_predicted_by_Glimmer/Critica_823371..823521_NEGATIVE 251 247 203 146 107 smit:SMT_1938|3end_zinc_metalloprotease_ZmpB,_putative_1876230..1876380_POSITIVE 251 339 295 103 57 smit:SMT_1918|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1861816..1861966_NEGATIVE 251 307 261 136 73 smit:SMT_183|3end_30S_ribosomal_protein_S14_121279..121429_POSITIVE